Psyllid ID: psy13263

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240-------250-------260-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-------440-------450-------460-------470-------480-------490-------500-------510-------520-------530-------540-------550-------560-------570-------
Protein Sequence
MYLDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWWPSPSNDPCSASPPCEETMPPVA
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccHHHHHcccHHHHHHHHHHHHcccEEEEEEccccHHHHHHHHHHHHHHHHHHHHccccccccccHHHccccccccccccccccHHHHHHHHHHcccccccccccEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHccccccccccccccccEEEEcccccHHccHHHHHHHHHHHHHHHHHccccccccccHHHHHHHHHHHHHHHHccccEEEcccccHHHHHHcccccEEEEEEEEEEEcccccccEEEEEEEcccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccccccHHHHHHHHHHHcccccccccHHHHHHHHHHHcccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHHcccccccccccccccHHcccccccccccccccccccHHccccccccccccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccHHHHccccccHHHccccccccccccccccccHHHHHHHcHHHHHHHcHHHccHHHHHHHHcHHHHHHHHHHHHHHHHHHcHHHHHHHHHHHHHHcccHHHHHHHHHHcccccEEEEEEEEcccccccccccEEEEEccccccHHHHHHHHHHHHHHHHHHcccccHHccEEcEcHEEEEcccHHHHHHccccccEEEHHHHHHHHHHHcccccEEEEEccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccHHHccccEEEEEEEEEcccccccccEEEEEEEccccccccHHHHHHHHccccHHHHHHHHHHHHHHHHccccccccccccHcHccccccccccHHHHHHHHcccccccHHHHHHHcccccHccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
myldskespekkgdsesstpasskgkktskspakseddspvtkrprrksaKRVKSAiqsdsepddmlqdngsedeyvppkaevesesehssgeeeleesvedptpssseaevtpmkngnkrglssksgqptkkpkltapstpstpsfpvsdtsettpstsgaqdwshnhyqflhpdhildadrrspkhpdynpktlyvppeflkkqtpcmgqwwtiksqnfdcVLFFKVGKFYELFHMDAVIGADELACSYmkesgctgesTLLTQLCnyesqtpsgcfpdmSELLKYFENAfdhkeassagniipkagvdkeYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKknvenyvtpecrgtgtndgcVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKlvpgicpksfgfnvaelagipedvvkFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQTkkdledlpggvagagtewwpspsndpcsasppceetmppva
Flexible Loop (DISEMBL)
myldskespekkgdsesstpasskgkktskspakseddspvtkrprrksakrvksaiqsdsepddmlqdngsEDEYVPPKAevesesehssgeeeleesvedptpssseaevtpmkngnkrglssksgqptkkpkltapstpstpsfpvsdtSETTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHkeassagniipkagvdKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKyaskaksnhqrvatkkknvenyvtpecrgtgtndgCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESVksfesqtkkdledlpGGVAGAGTEWWPSPSNDPCsasppceetmppva
Low Complexity Region (SEG)
MYLDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAevesesehssgeeeleesveDPTPSSSEAEVTPMKNGNKRGLSSKSGQptkkpkltapstpstpsfpvsdtsETTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWWPSPSNDPCSASPPCEETMPPVA
Disordered region (IsUnstruct)
***********************************************************************************************************************************************************************NHYQFLHPDHIL**************KTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHK****AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLE**********************VENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKS****************************************************************
Disordered Region (DISOPRED)
************************************************************************************************************************************************************************HYQFLHPDHIL********HPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLC*********CFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAF*****************************ELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWW**********SPP****MP***
Disordered Region (DISEMBL)
******************************************************************************************************************************************************************QDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKY*************KKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWWP*********************
Disordered Region (DISPRO)
******************************************************************************************************************MKNGNKRGLSSKSGQPTKKPKLTAPSTPST**FP***T**TTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR**********************VEELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWWPSPS***C**S***********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
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TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MYLDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPxxxxxxxxxxxxxxxxxxxxxxxxxxxxQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWWPSPSNDPCSASPPCEETMPPVA
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	577	2.2.26 [Sep-21-2011]
P54276	1358	DNA mismatch repair prote	yes	N/A	0.367	0.156	0.369	2e-32
Q9VUM0	1190	Probable DNA mismatch rep	yes	N/A	0.422	0.205	0.351	3e-31
P52701	1360	DNA mismatch repair prote	yes	N/A	0.363	0.154	0.377	4e-31
O04716	1324	DNA mismatch repair prote	yes	N/A	0.155	0.067	0.516	1e-20
Q9SMV7	1109	DNA mismatch repair prote	no	N/A	0.124	0.064	0.487	7e-17
B9LB04	966	DNA mismatch repair prote	yes	N/A	0.173	0.103	0.416	1e-14
A9WFZ9	966	DNA mismatch repair prote	yes	N/A	0.173	0.103	0.416	1e-14
O74502	1254	DNA mismatch repair prote	yes	N/A	0.176	0.081	0.415	2e-14
Q03834	1242	DNA mismatch repair prote	yes	N/A	0.305	0.141	0.319	2e-14
O65607	1081	DNA mismatch repair prote	no	N/A	0.194	0.103	0.384	4e-14

>sp|P54276|MSH6_MOUSE DNA mismatch repair protein Msh6 OS=Mus musculus GN=Msh6 PE=1 SV=3

 Score =  140 bits (354), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 36  EDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSG--- 92
           E+  P  + PRR S +  K  + SDSE D      GS+ E+ P   +  S  + SSG   
Sbjct: 229 EEAQPSVQGPRRSSRQVKKRRVISDSESDI----GGSDVEFKPDTKQEGSSDDASSGVGD 284

Query: 93  -EEELEESVEDPTPSSSEAEVTPMKNGNKR-GLSSKSGQPTKKPKLTAPSTPSTPSFPVS 150
            + E   +     P    A V   + G +R  L  ++G   +   + + +  +  +F   
Sbjct: 285 SDSEDLGTFGKGAPKRKRAMVA--QGGLRRKSLKKETGSAKRATPILSETKSTLSAFSAP 342

Query: 151 DTSETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFL 203
             SE+    SG  +       W H   ++L P+   D  RR P HP++NP TLYVP EFL
Sbjct: 343 QNSESQTHVSGGGNDSSGPTVWYHETLEWLKPEKRRDEHRRRPDHPEFNPTTLYVPEEFL 402

Query: 204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
              TP M +WW +KSQNFD V+F+KVGKFYEL+HMDAVIG  EL   +MK
Sbjct: 403 NSCTPGMRKWWQLKSQNFDLVIFYKVGKFYELYHMDAVIGVSELGLIFMK 452

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. ATP binding and hydrolysis play a pivotal role in mismatch repair functions. The ATPase activity associated with MutS alpha regulates binding similar to a molecular switch: mismatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts MutS alpha into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. This transition is crucial for mismatch repair. MutS alpha may also play a role in DNA homologous recombination repair.
Mus musculus (taxid: 10090)

>sp|Q9VUM0|MSH6_DROME Probable DNA mismatch repair protein Msh6 OS=Drosophila melanogaster GN=Msh6 PE=1 SV=2

 Score =  137 bits (344), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 97/276 (35%), Positives = 136/276 (49%), Gaps = 32/276 (11%)

Query: 4   DSKESPEKKGDSESSTPASSKGKKTSKSPAKSE-----DDSPVTKRPRRKSAKRVKSAIQ 58
           D   S  +K + ++  P    GKK +  PA        DD P + + +RK   R+    +
Sbjct: 39  DPDASKSEKENLQNQQPKVKDGKKEASKPAAKRKLPISDDEPASGQRKRK---RIVQP-E 94

Query: 59  SDSEPDDMLQDNGSEDE-------YVPPKAEVESESEHSSGEE----ELEESVEDPTPSS 107
           SDSEP+  ++   SED+       Y P + E   +S  S  EE    E + SV+ PTP  
Sbjct: 95  SDSEPE--MEVTKSEDDFSDCASDYEPDENEASDDSVSSGAEEVSPSENDMSVDSPTPKK 152

Query: 108 SEAEVTPMKNGNKRGLSSKSGQ----------PTKKPKLTAPSTPSTPSFPVSDTSETTP 157
           S  +   + N N    SSK  +           T + KL    + +       D    T 
Sbjct: 153 SRKKSKILNNNNNNEPSSKKVKLESTIQLAEGATFQEKLKNLQSNAKQDASYDDIVTNTS 212

Query: 158 STSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIK 217
           +      W H   +FL PD I D + R P HPDY+  TL+VP +FL   +P + QWW +K
Sbjct: 213 NLDEPVVWPHQKLEFLQPDKIKDKEGRRPDHPDYDKSTLHVPEKFLNGLSPGVRQWWVLK 272

Query: 218 SQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
           S N+DCVLFFKVGKFYEL+HMDA +G +EL  +YM+
Sbjct: 273 SDNYDCVLFFKVGKFYELYHMDADVGVNELGFTYMR 308

Involved in post-replicative DNA-mismatch repair.

Drosophila melanogaster (taxid: 7227)

>sp|P52701|MSH6_HUMAN DNA mismatch repair protein Msh6 OS=Homo sapiens GN=MSH6 PE=1 SV=2

 Score =  136 bits (343), Expect = 4e-31,   Method: Compositional matrix adjust.
 Identities = 85/225 (37%), Positives = 117/225 (52%), Gaps = 15/225 (6%)

Query: 40  PVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELE-E 98
           P T+  RR S +  K  + SDSE D      GS+ E+ P   E  S  E SSG  + E E
Sbjct: 233 PKTQGSRRSSRQIKKRRVISDSESDI----GGSDVEFKPDTKEEGSSDEISSGVGDSESE 288

Query: 99  SVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPS---TPSFPVSDTSET 155
            +  P   + + +     NG+ +  SS+   P+   + T+ S+ +     +F     SE+
Sbjct: 289 GLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSATKQATSISSETKNTLRAFSAPQNSES 348

Query: 156 TPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTP 208
               SG  D       W H   ++L  +   D  RR P HPD++  TLYVP +FL   TP
Sbjct: 349 QAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTP 408

Query: 209 CMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
            M +WW IKSQNFD V+ +KVGKFYEL+HMDA+IG  EL   +MK
Sbjct: 409 GMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMK 453

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs, and recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. After mismatch binding, forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. ATP binding and hydrolysis play a pivotal role in mismatch repair functions. The ATPase activity associated with MutS alpha regulates binding similar to a molecular switch: mismatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts MutS alpha into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. This transition is crucial for mismatch repair. MutS alpha may also play a role in DNA homologous recombination repair.

Homo sapiens (taxid: 9606)

>sp|O04716|MSH6_ARATH DNA mismatch repair protein MSH6 OS=Arabidopsis thaliana GN=MSH6 PE=1 SV=2

 Score =  102 bits (253), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 48/93 (51%), Positives = 63/93 (67%), Gaps = 3/93 (3%)

Query: 161 GAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQN 220
           GA+D     ++FL  D   DA RR P   +Y+P+TLY+PP+F+KK T    QWW  K+++
Sbjct: 337 GARD--SEKFRFLGVDR-RDAKRRRPTDENYDPRTLYLPPDFVKKLTGGQRQWWEFKAKH 393

Query: 221 FDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
            D V+FFK+GKFYELF MDA +GA EL   YMK
Sbjct: 394 MDKVVFFKMGKFYELFEMDAHVGAKELDIQYMK 426

Involved in post-replicative DNA-mismatch repair.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9SMV7|MSH7_ARATH DNA mismatch repair protein MSH7 OS=Arabidopsis thaliana GN=MSH7 PE=1 SV=1

 Score = 89.4 bits (220), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 38/78 (48%), Positives = 54/78 (69%)

Query: 170 YQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKV 229
           +++L    I DA+RR P  P Y+ KTL++PP+  KK +    Q+W++KS+  D VLFFKV
Sbjct: 231 FEWLESSRIRDANRRRPDDPLYDRKTLHIPPDVFKKMSASQKQYWSVKSEYMDIVLFFKV 290

Query: 230 GKFYELFHMDAVIGADEL 247
           GKFYEL+ +DA +G  EL
Sbjct: 291 GKFYELYELDAELGHKEL 308

Involved in post-replicative DNA-mismatch repair.

Arabidopsis thaliana (taxid: 3702)

>sp|B9LB04|MUTS_CHLSY DNA mismatch repair protein MutS OS=Chloroflexus aurantiacus (strain ATCC 29364 / DSM 637 / Y-400-fl) GN=mutS PE=3 SV=1

 Score = 82.4 bits (202), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 65/108 (60%), Gaps = 8/108 (7%)

Query: 390 RGTGTNDGCVIARVTLEKFL---QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKR 446
           RGT T DG  IAR  +E      ++GC T+FATHYH +    RE P V   +M+ +E   
Sbjct: 792 RGTSTYDGMAIARAVVEYIHDHPRLGCRTLFATHYHELIALERELPRVRNYHMAAVE--- 848

Query: 447 NDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
            DG   +VFL++L PG   +S+G +VAELAGIP +V++  + +   +E
Sbjct: 849 RDG--RVVFLHELRPGGADRSYGIHVAELAGIPPEVIRRASALLADLE 894

This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.

Chloroflexus aurantiacus (strain ATCC 29364 / DSM 637 / Y-400-fl) (taxid: 480224)

>sp|A9WFZ9|MUTS_CHLAA DNA mismatch repair protein MutS OS=Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) GN=mutS PE=3 SV=1

 Score = 82.4 bits (202), Expect = 1e-14,   Method: Compositional matrix adjust.
 Identities = 45/108 (41%), Positives = 65/108 (60%), Gaps = 8/108 (7%)

Query: 390 RGTGTNDGCVIARVTLEKFL---QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKR 446
           RGT T DG  IAR  +E      ++GC T+FATHYH +    RE P V   +M+ +E   
Sbjct: 792 RGTSTYDGMAIARAVVEYIHDHPRLGCRTLFATHYHELIALERELPRVRNYHMAAVE--- 848

Query: 447 NDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
            DG   +VFL++L PG   +S+G +VAELAGIP +V++  + +   +E
Sbjct: 849 RDG--RVVFLHELRPGGADRSYGIHVAELAGIPPEVIRRASALLADLE 894

This protein is involved in the repair of mismatches in DNA. It is possible that it carries out the mismatch recognition step. This protein has a weak ATPase activity.

Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (taxid: 324602)

>sp|O74502|MSH6_SCHPO DNA mismatch repair protein msh6 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=msh6 PE=1 SV=1

 Score = 81.6 bits (200), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 57/106 (53%), Gaps = 4/106 (3%)

Query: 390  RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
            RGT T DG  IA   L   +  IGCL  F+THY S+         V    M+   D++  
Sbjct: 1107 RGTSTYDGHAIAYAVLHHLVSNIGCLGFFSTHYQSLCVDFMHHRQVRLMQMAAAVDEK-- 1164

Query: 449  GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
             I  + FLYKL  GICPKS+G NVA +AG+PE V+      A ++E
Sbjct: 1165 -IRRVTFLYKLEDGICPKSYGMNVASMAGLPEKVIDAAEEKASELE 1209

Involved in post-replicative DNA-mismatch repair. Has a role towards base-base mispairs and insertion-deletion loops.

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

>sp|Q03834|MSH6_YEAST DNA mismatch repair protein MSH6 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MSH6 PE=1 SV=1

 Score = 81.3 bits (199), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 68/213 (31%), Positives = 98/213 (46%), Gaps = 37/213 (17%)

Query: 49  SAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEE----ELEESVEDPT 104
           +AKR K  +  DSE D        EDEY+P K + + + + +  +E    EL E   D  
Sbjct: 155 TAKRKKGKV-VDSESD--------EDEYLPDKNDGDEDDDIADDKEDIKGELAEDSGDDD 205

Query: 105 PSSSEAEVT--------------PMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVS 150
              S AE T              P      R  S K  +P + P  +   + S PS    
Sbjct: 206 DLISLAETTSKKKFSYNTSHSSSPFTRNISRDNSKKKSRPNQAPSRSYNPSHSQPS---- 261

Query: 151 DTSETTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCM 210
                T  +S     +   YQ+L  +   DA RR    P+Y+P+TLY+P     K TP  
Sbjct: 262 ----ATSKSSKFNKQNEERYQWLVDER--DAQRRPKSDPEYDPRTLYIPSSAWNKFTPFE 315

Query: 211 GQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIG 243
            Q+W IKS+ +DC++FFK GKF+EL+  DA++ 
Sbjct: 316 KQYWEIKSKMWDCIVFFKKGKFFELYEKDALLA 348

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MSH2 to form MutS alpha, which binds to DNA mismatches thereby initiating DNA repair. MSH6 provides substrate-binding and substrate-specificity to the complex. When bound, MutS alpha bends the DNA helix and shields approximately 20 base pairs. Acts mainly to repair base-base and single insertion-deletion mismatches that occur during replication, but can also repair longer insertion-deletion loops (IDLs), although with decreasing efficiency as the size of the extrahelical loop increases. After mismatch binding, forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. ATP binding and hydrolysis by the MutS alpha complex is crucial for MMR. Both subunits bind ATP, but with differing affinities, and their ATPase kinetics are also very different. MSH6 binds and hydrolyzes ATP rapidly, whereas MSH2 catalyzes ATP at a substantially slower rate. Binding to a mismatched base pair suppresses MSH6-catalyzed ATP hydrolysis, but not the activity of MSH2. ATP binding to both subunits is necessary to trigger a change in MutS alpha interaction with mismatched DNA, converting MutS alpha into a sliding clamp capable of hydrolysis-independent movement along DNA, and also facilitates formation of ternary complexes containing MutS and MutL proteins and the mismatch. May also be involved in resolution of recombination intermediates.

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

>sp|O65607|MSH3_ARATH DNA mismatch repair protein MSH3 OS=Arabidopsis thaliana GN=MSH3 PE=1 SV=2

 Score = 80.1 bits (196), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 45/117 (38%), Positives = 69/117 (58%), Gaps = 5/117 (4%)

Query: 390  RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEP-NVAFEYMSYIEDKRN 447
            RGT T+DG  IA  TL+  L +  CL +F THY  +A      P +V   ++SY+  +++
Sbjct: 900  RGTSTHDGVAIAYATLQHLLAEKRCLVLFVTHYPEIAEISNGFPGSVGTYHVSYLTLQKD 959

Query: 448  DGI---DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQ 501
             G    D + +LYKLV G+C +SFGF VA+LA IP   ++   ++A ++EA    R+
Sbjct: 960  KGSYDHDDVTYLYKLVRGLCSRSFGFKVAQLAQIPPSCIRRAISMAAKLEAEVRARE 1016

Not known. Probable DNA-repair 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	577
156549300	1151	PREDICTED: probable DNA mismatch repair	0.303	0.152	0.412	2e-32
355704543	1278	mutS-like protein 6 [Mustela putorius fu	0.379	0.171	0.377	9e-32
395829624	1228	PREDICTED: DNA mismatch repair protein M	0.363	0.171	0.406	3e-31
395829620	1358	PREDICTED: DNA mismatch repair protein M	0.363	0.154	0.406	5e-31
350419676	1129	PREDICTED: probable DNA mismatch repair	0.285	0.146	0.406	5e-31
383847693	1125	PREDICTED: probable DNA mismatch repair	0.374	0.192	0.359	5e-31
6754744	1358	DNA mismatch repair protein Msh6 [Mus mu	0.367	0.156	0.369	1e-30
26353224	1358	unnamed protein product [Mus musculus]	0.367	0.156	0.369	1e-30
148706690	1379	mCG15886 [Mus musculus]	0.367	0.153	0.369	2e-30
301753267	1362	PREDICTED: DNA mismatch repair protein M	0.363	0.154	0.377	4e-30

>gi|156549300|ref|XP_001600292.1| PREDICTED: probable DNA mismatch repair protein Msh6 [Nasonia vitripennis]

 Score =  147 bits (371), Expect = 2e-32,   Method: Compositional matrix adjust.
 Identities = 80/194 (41%), Positives = 109/194 (56%), Gaps = 19/194 (9%)

Query: 63  PDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESV---EDPTPSSSEAEVTPMKNGN 119
           P+D  +D+G  DEY P         E +  EE+L+ SV    +P  +S + + TP K   
Sbjct: 100 PEDNSEDSG--DEYKP--------DESAESEEDLDLSVVSESEPNTASEDEDETPKKKQK 149

Query: 120 KRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHIL 179
              + + S +     K  A     T         + T   S  QDW H  Y+FL  D I 
Sbjct: 150 MSNIKTPSRRGGGAKKSIAKKDSGTGQ------EQPTGKASDTQDWPHLKYEFLQKDKIR 203

Query: 180 DADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMD 239
           D  +R    PDY+P+T+YVPP+FL KQTP M QWW +KS ++DCVLFFKVGKFYEL+HMD
Sbjct: 204 DNKKRRSTDPDYDPRTVYVPPDFLDKQTPAMRQWWVLKSDHYDCVLFFKVGKFYELYHMD 263

Query: 240 AVIGADELACSYMK 253
           AV G +EL+ ++M+
Sbjct: 264 AVTGVNELSLTFMR 277

Source: Nasonia vitripennis

Species: Nasonia vitripennis

Genus: Nasonia

Family: Pteromalidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|355704543|gb|AES02262.1| mutS-like protein 6 [Mustela putorius furo]

 Score =  144 bits (364), Expect = 9e-32,   Method: Compositional matrix adjust.
 Identities = 92/244 (37%), Positives = 124/244 (50%), Gaps = 25/244 (10%)

Query: 31  SPAKSEDDS----------PVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPK 80
           S  KSEDD           P  +  RR S +  K  + SDSE D      GS+ E+ P  
Sbjct: 133 SSGKSEDDDHEIESEEEVRPKVQGSRRSSRQIKKRRVISDSESDI----GGSDVEFKPDG 188

Query: 81  AEVESESEHSSGEEELE-ESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAP 139
            E  S  E SSG  + + E ++ P   +S+ +     NG+ +  SS+   P    + T  
Sbjct: 189 KEEGSSDEISSGVGDSDSEGLDSPVKVASKRKKMVTGNGSLKRKSSRKEMPLATKRSTGI 248

Query: 140 ST---PSTPSFPVSDTSETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHP 189
           S+    +  +F     SE+    SG  D       W H   ++L  D   D  RR P HP
Sbjct: 249 SSETKSALNAFSAPQNSESQAHVSGGCDDNSRPTIWYHETLEWLKEDKRRDLQRRRPDHP 308

Query: 190 DYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELAC 249
           D++  TLYVP +FL   TP M +WW IKSQNFD V+F+KVGKFYEL+HMDA+IG +EL  
Sbjct: 309 DFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVIFYKVGKFYELYHMDALIGVNELGL 368

Query: 250 SYMK 253
            +MK
Sbjct: 369 VFMK 372

Source: Mustela putorius furo

Species: Mustela putorius

Genus: Mustela

Family: Mustelidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395829624|ref|XP_003787949.1| PREDICTED: DNA mismatch repair protein Msh6-like isoform 3 [Otolemur garnettii]

 Score =  142 bits (359), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 91/224 (40%), Positives = 119/224 (53%), Gaps = 14/224 (6%)

Query: 40  PVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELE-E 98
           P T+  RR S +  K  + SDSE D      GS+ E+ P   E  S  E SSG  + E E
Sbjct: 103 PKTQGSRRSSRQIKKLRVISDSESDI----GGSDVEFKPDAKEEGSSDEISSGVGDSESE 158

Query: 99  SVEDPTPSSSEAEVTPMKNG-NKRGLSSKSGQPTKKPKLTAPSTPSTPS-FPVSDTSETT 156
            ++ P   + + +     NG +KR  S K    TK+    +  T ST S F     SE+ 
Sbjct: 159 GLDSPVKVARKRKRMITGNGSHKRKGSRKEMPSTKRATGISSETKSTLSAFSAPQNSESQ 218

Query: 157 PSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPC 209
              SG  D       W H   ++L  +   D  RR P HPD++  TLYVP +FL   TP 
Sbjct: 219 AHVSGGGDDSSRPTIWYHETLEWLKKEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPG 278

Query: 210 MGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
           M +WW IKSQNFD V+F+KVGKFYEL+HMDA+IG +EL   +MK
Sbjct: 279 MRKWWQIKSQNFDLVIFYKVGKFYELYHMDALIGVNELGLVFMK 322

Source: Otolemur garnettii

Species: Otolemur garnettii

Genus: Otolemur

Family: Galagidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|395829620|ref|XP_003787947.1| PREDICTED: DNA mismatch repair protein Msh6-like isoform 1 [Otolemur garnettii]

 Score =  142 bits (358), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 91/224 (40%), Positives = 119/224 (53%), Gaps = 14/224 (6%)

Query: 40  PVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELE-E 98
           P T+  RR S +  K  + SDSE D      GS+ E+ P   E  S  E SSG  + E E
Sbjct: 233 PKTQGSRRSSRQIKKLRVISDSESDI----GGSDVEFKPDAKEEGSSDEISSGVGDSESE 288

Query: 99  SVEDPTPSSSEAEVTPMKNG-NKRGLSSKSGQPTKKPKLTAPSTPSTPS-FPVSDTSETT 156
            ++ P   + + +     NG +KR  S K    TK+    +  T ST S F     SE+ 
Sbjct: 289 GLDSPVKVARKRKRMITGNGSHKRKGSRKEMPSTKRATGISSETKSTLSAFSAPQNSESQ 348

Query: 157 PSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPC 209
              SG  D       W H   ++L  +   D  RR P HPD++  TLYVP +FL   TP 
Sbjct: 349 AHVSGGGDDSSRPTIWYHETLEWLKKEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPG 408

Query: 210 MGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
           M +WW IKSQNFD V+F+KVGKFYEL+HMDA+IG +EL   +MK
Sbjct: 409 MRKWWQIKSQNFDLVIFYKVGKFYELYHMDALIGVNELGLVFMK 452

Source: Otolemur garnettii

Species: Otolemur garnettii

Genus: Otolemur

Family: Galagidae

Order: Primates

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|350419676|ref|XP_003492265.1| PREDICTED: probable DNA mismatch repair protein Msh6-like [Bombus impatiens]

 Score =  142 bits (358), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 78/192 (40%), Positives = 109/192 (56%), Gaps = 27/192 (14%)

Query: 62  EPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKR 121
           +P+D  +D+ S  E V      +SE   +S EE  E+ ++       + E++ MKN    
Sbjct: 104 DPEDESEDSDSVSEGVS-----KSEPPTASEEESPEKKIKLAKAPRRKPEISTMKN---- 154

Query: 122 GLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHILDA 181
              +K  +   KP+                 ++T  S S  + W H  Y FL P+ I D 
Sbjct: 155 ---TKDAKKESKPQ---------------QQNQTKGSDSVTESWPHLKYDFLQPNKIRDI 196

Query: 182 DRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAV 241
            R+ P  PDY+PKTLYVPP+FL +QTP M QWW +KS++FDCVLFFKVGKFYEL+HMDAV
Sbjct: 197 RRKPPSDPDYDPKTLYVPPDFLNQQTPAMRQWWELKSKHFDCVLFFKVGKFYELYHMDAV 256

Query: 242 IGADELACSYMK 253
           I  +E+  +YM+
Sbjct: 257 ISVNEINLTYMR 268

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383847693|ref|XP_003699487.1| PREDICTED: probable DNA mismatch repair protein Msh6-like [Megachile rotundata]

 Score =  142 bits (358), Expect = 5e-31,   Method: Compositional matrix adjust.
 Identities = 91/253 (35%), Positives = 133/253 (52%), Gaps = 37/253 (14%)

Query: 18  STPASSKGKKT-SKSPAKSEDDSPVTKRPR----------------RKSAKRVKSAIQSD 60
           STP SSK +K  +K+P+K +++  V  R R                R   +R+   I  D
Sbjct: 31  STPKSSKEQKNKAKTPSKGKENKNVEDRKRVYKEDDENEEEENEPVRPKKRRL---IIPD 87

Query: 61  SEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNK 120
            +  D   D G  DE+ P     ES+S      E   E+V +      + +V+    G +
Sbjct: 88  VDSGD---DTG--DEFKPENESEESDSGSEGVTESEPETVSEEESPEKKRKVSNNSRGRQ 142

Query: 121 RGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHILD 180
              + K+G+  KK               +S  ++T  S +  + W H  Y FL P+ I D
Sbjct: 143 GARTKKNGKEDKKES------------KLSQQNQTQSSNNVVESWPHLKYDFLQPNKIRD 190

Query: 181 ADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDA 240
            +R+    PDY+PKT+YVP +FL +QTP M QWW +KS+++DCVLFFKVGKFYEL+HMDA
Sbjct: 191 INRKPLSDPDYDPKTVYVPQDFLNQQTPAMRQWWELKSKHYDCVLFFKVGKFYELYHMDA 250

Query: 241 VIGADELACSYMK 253
           V+G +EL  +YM+
Sbjct: 251 VVGVNELNLTYMR 263

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|6754744|ref|NP_034960.1| DNA mismatch repair protein Msh6 [Mus musculus] gi|341940990|sp|P54276.3|MSH6_MOUSE RecName: Full=DNA mismatch repair protein Msh6; AltName: Full=G/T mismatch-binding protein; Short=GTBP; Short=GTMBP; AltName: Full=MutS-alpha 160 kDa subunit; AltName: Full=p160 gi|2665637|gb|AAB88445.1| mismatch repair protein MSH6 [Mus musculus] gi|30109297|gb|AAH51160.1| MutS homolog 6 (E. coli) [Mus musculus] gi|30185718|gb|AAH51634.1| MutS homolog 6 (E. coli) [Mus musculus]

 Score =  140 bits (354), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 36  EDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSG--- 92
           E+  P  + PRR S +  K  + SDSE D      GS+ E+ P   +  S  + SSG   
Sbjct: 229 EEAQPSVQGPRRSSRQVKKRRVISDSESDI----GGSDVEFKPDTKQEGSSDDASSGVGD 284

Query: 93  -EEELEESVEDPTPSSSEAEVTPMKNGNKR-GLSSKSGQPTKKPKLTAPSTPSTPSFPVS 150
            + E   +     P    A V   + G +R  L  ++G   +   + + +  +  +F   
Sbjct: 285 SDSEDLGTFGKGAPKRKRAMVA--QGGLRRKSLKKETGSAKRATPILSETKSTLSAFSAP 342

Query: 151 DTSETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFL 203
             SE+    SG  +       W H   ++L P+   D  RR P HP++NP TLYVP EFL
Sbjct: 343 QNSESQTHVSGGGNDSSGPTVWYHETLEWLKPEKRRDEHRRRPDHPEFNPTTLYVPEEFL 402

Query: 204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
              TP M +WW +KSQNFD V+F+KVGKFYEL+HMDAVIG  EL   +MK
Sbjct: 403 NSCTPGMRKWWQLKSQNFDLVIFYKVGKFYELYHMDAVIGVSELGLIFMK 452

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|26353224|dbj|BAC40242.1| unnamed protein product [Mus musculus]

 Score =  140 bits (354), Expect = 1e-30,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 36  EDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSG--- 92
           E+  P  + PRR S +  K  + SDSE D      GS+ E+ P   +  S  + SSG   
Sbjct: 229 EEAQPSVQGPRRSSRQVKKRRVISDSESDI----GGSDVEFKPDTKQEGSSDDASSGVGD 284

Query: 93  -EEELEESVEDPTPSSSEAEVTPMKNGNKR-GLSSKSGQPTKKPKLTAPSTPSTPSFPVS 150
            + E   +     P    A V   + G +R  L  ++G   +   + + +  +  +F   
Sbjct: 285 SDSEDLGTFGKGAPKRKRAMVA--QGGLRRKSLKKETGSAKRATPILSETKSTLSAFSAP 342

Query: 151 DTSETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFL 203
             SE+    SG  +       W H   ++L P+   D  RR P HP++NP TLYVP EFL
Sbjct: 343 QNSESQTHVSGGGNDSSGPTVWYHETLEWLKPEKRRDEHRRRPDHPEFNPTTLYVPEEFL 402

Query: 204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
              TP M +WW +KSQNFD V+F+KVGKFYEL+HMDAVIG  EL   +MK
Sbjct: 403 NSCTPGMRKWWQLKSQNFDLVIFYKVGKFYELYHMDAVIGVSELGLIFMK 452

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|148706690|gb|EDL38637.1| mCG15886 [Mus musculus]

 Score =  140 bits (354), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 85/230 (36%), Positives = 118/230 (51%), Gaps = 18/230 (7%)

Query: 36  EDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSG--- 92
           E+  P  + PRR S +  K  + SDSE D      GS+ E+ P   +  S  + SSG   
Sbjct: 250 EEAQPSVQGPRRSSRQVKKRRVISDSESDI----GGSDVEFKPDTKQEGSSDDASSGVGD 305

Query: 93  -EEELEESVEDPTPSSSEAEVTPMKNGNKR-GLSSKSGQPTKKPKLTAPSTPSTPSFPVS 150
            + E   +     P    A V   + G +R  L  ++G   +   + + +  +  +F   
Sbjct: 306 SDSEDLGTFGKGAPKRKRAMVA--QGGLRRKSLKKETGSAKRATPILSETKSTLSAFSAP 363

Query: 151 DTSETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFL 203
             SE+    SG  +       W H   ++L P+   D  RR P HP++NP TLYVP EFL
Sbjct: 364 QNSESQTHVSGGGNDSSGPTVWYHETLEWLKPEKRRDEHRRRPDHPEFNPTTLYVPEEFL 423

Query: 204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
              TP M +WW +KSQNFD V+F+KVGKFYEL+HMDAVIG  EL   +MK
Sbjct: 424 NSCTPGMRKWWQLKSQNFDLVIFYKVGKFYELYHMDAVIGVSELGLIFMK 473

Source: Mus musculus

Species: Mus musculus

Genus: Mus

Family: Muridae

Order: Rodentia

Class: Mammalia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|301753267|ref|XP_002912469.1| PREDICTED: DNA mismatch repair protein Msh6-like [Ailuropoda melanoleuca] gi|281352643|gb|EFB28227.1| hypothetical protein PANDA_000220 [Ailuropoda melanoleuca]

 Score =  139 bits (350), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 85/225 (37%), Positives = 118/225 (52%), Gaps = 15/225 (6%)

Query: 40  PVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELE-E 98
           P  +  RR S +  K  + SDSE D      GS+ E+ P   E  S  E SSG  + + E
Sbjct: 234 PKVQGSRRSSRQIKKRRVISDSESDI----GGSDVEFKPDAKEEGSSDELSSGVGDSDSE 289

Query: 99  SVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPST---PSTPSFPVSDTSET 155
            +E P   +S+ +     NG+ +  SS+   P    + T  S+    +  +F     SE+
Sbjct: 290 GLESPVKVASKRKKMVTGNGSLKRKSSRKEMPLATKRSTGISSETKSALNAFSAPQNSES 349

Query: 156 TPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTP 208
               SG  D       W H   ++L  +   D  RR P HPD++  TLYVP +FL   TP
Sbjct: 350 QAHISGGCDDSSRPTVWYHETLEWLKEEKRRDLHRRRPDHPDFDASTLYVPEDFLNSCTP 409

Query: 209 CMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
            M +WW IKSQNFD V+F+KVGKFYEL+HMDA+IG ++L   +MK
Sbjct: 410 GMRKWWQIKSQNFDLVIFYKVGKFYELYHMDALIGVNKLGLVFMK 454

Source: Ailuropoda melanoleuca

Species: Ailuropoda melanoleuca

Genus: Ailuropoda

Family: Ursidae

Order: Carnivora

Class: Mammalia

Phylum: Chordata

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	577
FB|FBgn0036486	1190	Msh6 "Msh6" [Drosophila melano	0.422	0.205	0.308	8.1e-64
MGI|MGI:1343961	1358	Msh6 "mutS homolog 6 (E. coli)	0.421	0.178	0.323	1.9e-60
RGD|2322311	1361	Msh6 "mutS homolog 6 (E. coli)	0.426	0.180	0.316	9.8e-60
UNIPROTKB|E1B9Q4	1360	MSH6 "Uncharacterized protein"	0.422	0.179	0.319	4.4e-59
UNIPROTKB|J9P5H1	1279	MSH6 "Uncharacterized protein"	0.426	0.192	0.298	4.9e-59
UNIPROTKB|P52701	1360	MSH6 "DNA mismatch repair prot	0.424	0.180	0.312	7.4e-59
UNIPROTKB|I3LHZ9	1334	LOC100739477 "Uncharacterized	0.403	0.174	0.324	8.6e-58
UNIPROTKB|F1PM27	1263	MSH6 "Uncharacterized protein"	0.426	0.194	0.298	1.7e-57
UNIPROTKB|B4DF41	1230	MSH6 "DNA mismatch repair prot	0.405	0.190	0.316	3.8e-57
UNIPROTKB|E1BWV7	1357	MSH6 "Uncharacterized protein"	0.422	0.179	0.319	1e-56

FB|FBgn0036486 Msh6 "Msh6" [Drosophila melanogaster (taxid:7227)]

 Score = 318 (117.0 bits), Expect = 8.1e-64, Sum P(4) = 8.1e-64
 Identities = 82/266 (30%), Positives = 118/266 (44%)

Query:     3 LDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
             L +++   K G  E+S PA+ +     K P    DD P + + +RK   + +S  + + E
Sbjct:    50 LQNQQPKVKDGKKEASKPAAKR-----KLPIS--DDEPASGQRKRKRIVQPESDSEPEME 102

Query:    63 ---PDDMLQDNGSEDEYVPPKAXXXXXXXXXXXXXXXXXXXX--DPTPSSSEAEVTPMKN 117
                 +D   D  S+ E    +A                       PTP  S  +   + N
Sbjct:   103 VTKSEDDFSDCASDYEPDENEASDDSVSSGAEEVSPSENDMSVDSPTPKKSRKKSKILNN 162

Query:   118 GNKRGLSSKSGQXXXXXXXXXXXXXX-------XXXXXXXXXXETTPSTSGAQD---WSH 167
              N    SSK  +                               +   +TS   +   W H
Sbjct:   163 NNNNEPSSKKVKLESTIQLAEGATFQEKLKNLQSNAKQDASYDDIVTNTSNLDEPVVWPH 222

Query:   168 NHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFF 227
                +FL PD I D + R P HPDY+  TL+VP +FL   +P + QWW +KS N+DCVLFF
Sbjct:   223 QKLEFLQPDKIKDKEGRRPDHPDYDKSTLHVPEKFLNGLSPGVRQWWVLKSDNYDCVLFF 282

Query:   228 KVGKFYELFHMDAVIGADELACSYMK 253
             KVGKFYEL+HMDA +G +EL  +YM+
Sbjct:   283 KVGKFYELYHMDADVGVNELGFTYMR 308

GO:0006281 "DNA repair" evidence=ISS

GO:0006301 "postreplication repair" evidence=NAS

GO:0005524 "ATP binding" evidence=IEA

GO:0000710 "meiotic mismatch repair" evidence=IMP

GO:0032138 "single base insertion or deletion binding" evidence=IBA

GO:0045910 "negative regulation of DNA recombination" evidence=IBA

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

GO:0032301 "MutSalpha complex" evidence=IBA

GO:0000228 "nuclear chromosome" evidence=IBA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IBA

GO:0032137 "guanine/thymine mispair binding" evidence=IBA

GO:0009411 "response to UV" evidence=IBA

GO:0000400 "four-way junction DNA binding" evidence=IBA

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

GO:0003684 "damaged DNA binding" evidence=IBA

GO:0043570 "maintenance of DNA repeat elements" evidence=IBA

MGI|MGI:1343961 Msh6 "mutS homolog 6 (E. coli)" [Mus musculus (taxid:10090)]

 Score = 325 (119.5 bits), Expect = 1.9e-60, Sum P(3) = 1.9e-60
 Identities = 85/263 (32%), Positives = 119/263 (45%)

Query:     4 DSKESPEKKGDSE-SSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
             D    PE++ ++E      S K ++ + + ++ E+  P  + PRR S +  K  + SDSE
Sbjct:   197 DEPSEPEEEEETEVHEAYLSDKSEEDNYNESE-EEAQPSVQGPRRSSRQVKKRRVISDSE 255

Query:    63 PDDMLQDNGSEDEYVPPK----AXXXXXXXXXXXXXXXXXXXXDPTPSSSEAEVTPMKNG 118
              D      GS+ E+ P      +                       P    A V   + G
Sbjct:   256 SDI----GGSDVEFKPDTKQEGSSDDASSGVGDSDSEDLGTFGKGAPKRKRAMVA--QGG 309

Query:   119 NKR-GLSSKSGQXXXXXXXXXXXXXXXXXXXXXXXXET-TPSTSGAQD------WSHNHY 170
              +R  L  ++G                         E+ T  + G  D      W H   
Sbjct:   310 LRRKSLKKETGSAKRATPILSETKSTLSAFSAPQNSESQTHVSGGGNDSSGPTVWYHETL 369

Query:   171 QFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVG 230
             ++L P+   D  RR P HP++NP TLYVP EFL   TP M +WW +KSQNFD V+F+KVG
Sbjct:   370 EWLKPEKRRDEHRRRPDHPEFNPTTLYVPEEFLNSCTPGMRKWWQLKSQNFDLVIFYKVG 429

Query:   231 KFYELFHMDAVIGADELACSYMK 253
             KFYEL+HMDAVIG  EL   +MK
Sbjct:   430 KFYELYHMDAVIGVSELGLIFMK 452

GO:0000166 "nucleotide binding" evidence=IEA

GO:0000400 "four-way junction DNA binding" evidence=IBA

GO:0000710 "meiotic mismatch repair" evidence=IBA

GO:0000790 "nuclear chromatin" evidence=IDA

GO:0003677 "DNA binding" evidence=IGI;IMP

GO:0003682 "chromatin binding" evidence=IDA

GO:0003684 "damaged DNA binding" evidence=IGI;IMP

GO:0005524 "ATP binding" evidence=IEA

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006281 "DNA repair" evidence=ISO

GO:0006298 "mismatch repair" evidence=ISO;IGI;IMP

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

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

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

GO:0008340 "determination of adult lifespan" evidence=IMP

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IMP

GO:0009411 "response to UV" evidence=IMP

GO:0016446 "somatic hypermutation of immunoglobulin genes" evidence=IMP

GO:0016447 "somatic recombination of immunoglobulin gene segments" evidence=IMP

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0032137 "guanine/thymine mispair binding" evidence=IDA

GO:0032138 "single base insertion or deletion binding" evidence=IBA

GO:0032301 "MutSalpha complex" evidence=ISO;IDA

GO:0043570 "maintenance of DNA repeat elements" evidence=IBA

GO:0045190 "isotype switching" evidence=IMP

GO:0045910 "negative regulation of DNA recombination" evidence=ISO;IMP

GO:0051096 "positive regulation of helicase activity" evidence=ISO

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=IMP

RGD|2322311 Msh6 "mutS homolog 6 (E. coli)" [Rattus norvegicus (taxid:10116)]

 Score = 321 (118.1 bits), Expect = 9.8e-60, Sum P(3) = 9.8e-60
 Identities = 84/265 (31%), Positives = 116/265 (43%)

Query:     4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDS-----PVTKRPRRKSAKRVKSAIQ 58
             D    PE++ + E           + KS  +++D+S     P  + PRR S +  K  + 
Sbjct:   195 DEPSEPEEEEEEEEEETQVHGAYLSDKSEEENQDESEEETQPNAQGPRRSSRQVKKRRVI 254

Query:    59 SDSEPDDMLQDNGSEDEYVPP-KAXXXXXXXXXXXXXXXXXXXXDPTPSSSEAEVTPMKN 117
             SDSE D      GS+ E+ P  K                          + + + T   +
Sbjct:   255 SDSESDI----GGSDVEFKPDSKQEGSSDEVSSGVGDSDSEGLGSFGKGAPKRKRTVAAH 310

Query:   118 GN--KRGLSSKSGQXXXXXXXXXXXXXXXXXXXXXXXXET-TPSTSGAQD------WSHN 168
             G   ++ L  ++G                         E+ T    G  D      W H 
Sbjct:   311 GGLKRKSLKKETGSAKQATRILSETKSTLSAFCAPQNSESQTHVCGGGNDSSGPTIWYHE 370

Query:   169 HYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFK 228
               ++L P+   D +RR P HPDYN  TLYVP +FL   TP M +WW  KSQNFD V+F+K
Sbjct:   371 TLEWLKPEKRRDENRRRPDHPDYNSSTLYVPEDFLNSCTPGMRRWWQFKSQNFDLVIFYK 430

Query:   229 VGKFYELFHMDAVIGADELACSYMK 253
             VGKFYEL+HMDAVIG  EL   +MK
Sbjct:   431 VGKFYELYHMDAVIGVSELGLIFMK 455

GO:0000790 "nuclear chromatin" evidence=ISO

GO:0003677 "DNA binding" evidence=ISO

GO:0003682 "chromatin binding" evidence=ISO

GO:0003684 "damaged DNA binding" evidence=ISO

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

GO:0006200 "ATP catabolic process" evidence=ISO

GO:0006281 "DNA repair" evidence=ISO

GO:0006298 "mismatch repair" evidence=IEA;ISO

GO:0008340 "determination of adult lifespan" evidence=ISO

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=ISO

GO:0009411 "response to UV" evidence=ISO

GO:0016446 "somatic hypermutation of immunoglobulin genes" evidence=ISO

GO:0016447 "somatic recombination of immunoglobulin gene segments" evidence=ISO

GO:0030983 "mismatched DNA binding" evidence=IEA;ISO

GO:0032137 "guanine/thymine mispair binding" evidence=ISO

GO:0032301 "MutSalpha complex" evidence=ISO

GO:0045190 "isotype switching" evidence=ISO

GO:0045910 "negative regulation of DNA recombination" evidence=ISO

GO:0051096 "positive regulation of helicase activity" evidence=ISO

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=ISO

GO:0042803 "protein homodimerization activity" evidence=ISO

GO:0043570 "maintenance of DNA repeat elements" evidence=ISO

GO:0000287 "magnesium ion binding" evidence=ISO

GO:0000400 "four-way junction DNA binding" evidence=ISO

GO:0003690 "double-stranded DNA binding" evidence=ISO

GO:0016887 "ATPase activity" evidence=ISO

GO:0032142 "single guanine insertion binding" evidence=ISO

GO:0032143 "single thymine insertion binding" evidence=ISO

GO:0032357 "oxidized purine DNA binding" evidence=ISO

GO:0032405 "MutLalpha complex binding" evidence=ISO

GO:0043531 "ADP binding" evidence=ISO

UNIPROTKB|E1B9Q4 MSH6 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 309 (113.8 bits), Expect = 4.4e-59, Sum P(3) = 4.4e-59
 Identities = 84/263 (31%), Positives = 114/263 (43%)

Query:     4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDD-SPVTKRPRRKSAKRVKSAIQSDSE 62
             D    PE++ ++E     +S  K   ++  +SE++  P  +  RR S +  K  + SDSE
Sbjct:   196 DEPSEPEEEEETEVGATYTSD-KSEEENDIESEEEVRPKVQGSRRSSRQIKKRRVISDSE 254

Query:    63 PDDMLQDNGSEDEYVPPKAXXXXXXXXXXXXXXXXXXXXDPTPSSSEAEVTPMKNGN--- 119
              D      GS+ E+ P                       D TP     +   M  GN   
Sbjct:   255 SDV----GGSDVEFKPDTKEEASSDEISSGVGDSDSEGLD-TPVKVAPKRKRMVTGNGSL 309

Query:   120 KRGLSSKSGQXXXXXXXXXXXXXXXXXXXXXXXXETTPST--SGAQD-------WSHNHY 170
             KR  S K                            + P    SG  D       W H   
Sbjct:   310 KRKSSRKEMPSATKRATGISSETKNTLSAFSVPQNSEPQAHISGGCDDSNRPTVWYHETL 369

Query:   171 QFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVG 230
             ++L  +   D  RR P HPD++  TLYVP +FL   TP M +WW IKSQNFD V+F+KVG
Sbjct:   370 EWLKEEKRRDVHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVIFYKVG 429

Query:   231 KFYELFHMDAVIGADELACSYMK 253
             KFYE++HMDA+IG  EL   +MK
Sbjct:   430 KFYEMYHMDALIGVSELGLVFMK 452

GO:0051096 "positive regulation of helicase activity" evidence=IEA

GO:0045910 "negative regulation of DNA recombination" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

GO:0032357 "oxidized purine DNA binding" evidence=IEA

GO:0032301 "MutSalpha complex" evidence=IEA

GO:0032143 "single thymine insertion binding" evidence=IEA

GO:0032142 "single guanine insertion binding" evidence=IEA

GO:0032137 "guanine/thymine mispair binding" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0016446 "somatic hypermutation of immunoglobulin genes" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IEA

GO:0008340 "determination of adult lifespan" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0000400 "four-way junction DNA binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|J9P5H1 MSH6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 305 (112.4 bits), Expect = 4.9e-59, Sum P(3) = 4.9e-59
 Identities = 78/261 (29%), Positives = 112/261 (42%)

Query:     4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEP 63
             D    PE++ + E     SS+  +        E+  P  +  RR S +  K  + SDSE 
Sbjct:   115 DEPSEPEEEEEMEVGATHSSEKSEEDNEIESEEEVRPKVQGSRRSSRQIKKRRVISDSES 174

Query:    64 DDMLQDNGSEDEYVPPKAXXXXXXXXXXXXXXXXXXXXD-PTPSSSEAEVTPMKNGNKRG 122
             D      GS+ E+ P                       D P   +S+ +     NG+ + 
Sbjct:   175 DI----GGSDVEFKPDAKEEGSSDEISSGVGDSDSEGLDSPVKVASKRKKMVTGNGSLKR 230

Query:   123 LSSKSGQXXXXXXXXXXXXXXXXXXXXXXXXETTPSTS----GAQD------WSHNHYQF 172
              SS+                           + + S +    G  D      W H   ++
Sbjct:   231 KSSRKEMPPATKRSTGISSETKSALNAYSAPQNSESQAHIGGGCDDSSRPTIWYHETLEW 290

Query:   173 LHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKF 232
             L  +   D  RR P HPD++  TLYVP +FL   TP M +WW IKSQNFD ++F+KVGKF
Sbjct:   291 LKEEKRRDLHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLIIFYKVGKF 350

Query:   233 YELFHMDAVIGADELACSYMK 253
             YEL+HMDA+ G +EL   +MK
Sbjct:   351 YELYHMDALTGVNELGLVFMK 371

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|P52701 MSH6 "DNA mismatch repair protein Msh6" [Homo sapiens (taxid:9606)]

 Score = 301 (111.0 bits), Expect = 7.4e-59, Sum P(3) = 7.4e-59
 Identities = 82/262 (31%), Positives = 116/262 (44%)

Query:     4 DSKESPEKKGDSE-SSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
             D    PE++ + E  +T  + K ++ ++  ++ E+  P T+  RR S +  K  + SDSE
Sbjct:   197 DEPSEPEEEEEMEVGTTYVTDKSEEDNEIESE-EEVQPKTQGSRRSSRQIKKRRVISDSE 255

Query:    63 PDDMLQDNGSEDEYVPP-KAXXXXXXXXXXXXXXXXXXXXDPTPSSSEAEVTPMKNGN-K 120
              D      GS+ E+ P  K                      P   + + +     NG+ K
Sbjct:   256 SDI----GGSDVEFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLK 311

Query:   121 RGLSSKSGQXXXXXXXXXXXXXXXXXXXXXX--XXETTPSTSGAQD-------WSHNHYQ 171
             R  S K                             E+    SG  D       W H   +
Sbjct:   312 RKSSRKETPSATKQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLE 371

Query:   172 FLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGK 231
             +L  +   D  RR P HPD++  TLYVP +FL   TP M +WW IKSQNFD V+ +KVGK
Sbjct:   372 WLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGK 431

Query:   232 FYELFHMDAVIGADELACSYMK 253
             FYEL+HMDA+IG  EL   +MK
Sbjct:   432 FYELYHMDALIGVSELGLVFMK 453

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000228 "nuclear chromosome" evidence=IBA

GO:0000710 "meiotic mismatch repair" evidence=ISS;IBA

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

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

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=ISS;IBA

GO:0009411 "response to UV" evidence=ISS;IBA

GO:0016446 "somatic hypermutation of immunoglobulin genes" evidence=ISS;IBA

GO:0045190 "isotype switching" evidence=ISS;IBA

GO:0005515 "protein binding" evidence=IPI

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0032405 "MutLalpha complex binding" evidence=IDA

GO:0000400 "four-way junction DNA binding" evidence=IDA

GO:0006298 "mismatch repair" evidence=IDA;IMP

GO:0032301 "MutSalpha complex" evidence=IDA

GO:0030983 "mismatched DNA binding" evidence=IDA

GO:0032137 "guanine/thymine mispair binding" evidence=IDA

GO:0032142 "single guanine insertion binding" evidence=IDA

GO:0032143 "single thymine insertion binding" evidence=IDA

GO:0032357 "oxidized purine DNA binding" evidence=IDA

GO:0016887 "ATPase activity" evidence=IDA

GO:0000287 "magnesium ion binding" evidence=IDA

GO:0005524 "ATP binding" evidence=IDA

GO:0043531 "ADP binding" evidence=IDA

GO:0003690 "double-stranded DNA binding" evidence=IDA

GO:0097193 "intrinsic apoptotic signaling pathway" evidence=ISS

GO:0008340 "determination of adult lifespan" evidence=ISS

GO:0016447 "somatic recombination of immunoglobulin gene segments" evidence=ISS

GO:0006281 "DNA repair" evidence=IDA

GO:0043570 "maintenance of DNA repeat elements" evidence=IMP

GO:0045910 "negative regulation of DNA recombination" evidence=IDA

GO:0051096 "positive regulation of helicase activity" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IDA

UNIPROTKB|I3LHZ9 LOC100739477 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 298 (110.0 bits), Expect = 8.6e-58, Sum P(3) = 8.6e-58
 Identities = 81/250 (32%), Positives = 108/250 (43%)

Query:    16 ESSTPASSKGKKTSKSPAKSEDD-SPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSED 74
             E S P   + K   ++  +SE++  P  +  RR S    K  + SDSE D      GS+ 
Sbjct:   184 EPSEPEEEE-KSEEENEMESEEEVQPKVQGSRRSSRHIKKRRVISDSESDV----GGSDV 238

Query:    75 EYVPPKAXXXXXXXXXXXXXXXXXXXXD-PTPSSSEAEVTPMKNGN-KRGLSSKSGQXXX 132
             E+ P                       D P   + + +     NG+ KR  S K      
Sbjct:   239 EFKPDTKEEGSSDEMSSGVGDSDSEGLDSPVKIAPKRKRMVTGNGSLKRKSSRKEMPSAT 298

Query:   133 XXXXXXXXXXXXXXXXXXXXXETTPST--SGAQD-------WSHNHYQFLHPDHILDADR 183
                                   + P    SG  D       W H   ++L  +   D  R
Sbjct:   299 KRAIGISSETRSTLSAFSAPQNSEPQAHISGGCDDSNRPTVWYHETLEWLKEERRRDVHR 358

Query:   184 RSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIG 243
             R P HPD++  TLYVP +FL   TP M +WW IKSQNFD V+F+KVGKFYEL+HMDA+IG
Sbjct:   359 RRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVIFYKVGKFYELYHMDALIG 418

Query:   244 ADELACSYMK 253
               EL   +MK
Sbjct:   419 VSELGLVFMK 428

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1PM27 MSH6 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 305 (112.4 bits), Expect = 1.7e-57, Sum P(3) = 1.7e-57
 Identities = 78/261 (29%), Positives = 112/261 (42%)

Query:     4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEP 63
             D    PE++ + E     SS+  +        E+  P  +  RR S +  K  + SDSE 
Sbjct:   125 DEPSEPEEEEEMEVGATHSSEKSEEDNEIESEEEVRPKVQGSRRSSRQIKKRRVISDSES 184

Query:    64 DDMLQDNGSEDEYVPPKAXXXXXXXXXXXXXXXXXXXXD-PTPSSSEAEVTPMKNGNKRG 122
             D      GS+ E+ P                       D P   +S+ +     NG+ + 
Sbjct:   185 DI----GGSDVEFKPDAKEEGSSDEISSGVGDSDSEGLDSPVKVASKRKKMVTGNGSLKR 240

Query:   123 LSSKSGQXXXXXXXXXXXXXXXXXXXXXXXXETTPSTS----GAQD------WSHNHYQF 172
              SS+                           + + S +    G  D      W H   ++
Sbjct:   241 KSSRKEMPPATKRSTGISSETKSALNAYSAPQNSESQAHIGGGCDDSSRPTIWYHETLEW 300

Query:   173 LHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKF 232
             L  +   D  RR P HPD++  TLYVP +FL   TP M +WW IKSQNFD ++F+KVGKF
Sbjct:   301 LKEEKRRDLHRRRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLIIFYKVGKF 360

Query:   233 YELFHMDAVIGADELACSYMK 253
             YEL+HMDA+ G +EL   +MK
Sbjct:   361 YELYHMDALTGVNELGLVFMK 381

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|B4DF41 MSH6 "DNA mismatch repair protein Msh6" [Homo sapiens (taxid:9606)]

 Score = 289 (106.8 bits), Expect = 3.8e-57, Sum P(4) = 3.8e-57
 Identities = 79/250 (31%), Positives = 110/250 (44%)

Query:    15 SESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSED 74
             S  +T  + K ++ ++  ++ E+  P T+  RR S +  K  + SDSE D      GS+ 
Sbjct:    79 SVGTTYVTDKSEEDNEIESE-EEVQPKTQGSRRSSRQIKKRRVISDSESDI----GGSDV 133

Query:    75 EYVPP-KAXXXXXXXXXXXXXXXXXXXXDPTPSSSEAEVTPMKNGN-KRGLSSKSGQXXX 132
             E+ P  K                      P   + + +     NG+ KR  S K      
Sbjct:   134 EFKPDTKEEGSSDEISSGVGDSESEGLNSPVKVARKRKRMVTGNGSLKRKSSRKETPSAT 193

Query:   133 XXXXXXXXXXXXXXXXXXX--XXETTPSTSGAQD-------WSHNHYQFLHPDHILDADR 183
                                    E+    SG  D       W H   ++L  +   D  R
Sbjct:   194 KQATSISSETKNTLRAFSAPQNSESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHR 253

Query:   184 RSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIG 243
             R P HPD++  TLYVP +FL   TP M +WW IKSQNFD V+ +KVGKFYEL+HMDA+IG
Sbjct:   254 RRPDHPDFDASTLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIG 313

Query:   244 ADELACSYMK 253
               EL   +MK
Sbjct:   314 VSELGLVFMK 323

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

UNIPROTKB|E1BWV7 MSH6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 290 (107.1 bits), Expect = 1.0e-56, Sum P(3) = 1.0e-56
 Identities = 86/269 (31%), Positives = 114/269 (42%)

Query:     5 SKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKR-PRRKSAKRVKSAIQSDSEP 63
             S+ S  ++ + E     S      S   + SE+D    KR P R SA + K     DS+ 
Sbjct:   193 SEPSDTEEAEEEEMEQMSGSASGDSDD-SNSEEDVKGNKRVPNRGSAIKAKRRRVLDSDS 251

Query:    64 DDMLQDNGSEDEYVPPKAXXXXXXXXXXXXXXXXXXXXDPTPSSSEAEV-TPMKNGNKRG 122
             D   +D GS+ E+ P                           S  E+ +  P K   KRG
Sbjct:   252 D---RD-GSDVEFKPDVKEASSEEASSGVDENEATDVETDEESIEESPIKVPSKR--KRG 305

Query:   123 LSSKSGQXXXXXXXXXXXXXXXXXXXXXXXXETT----PS------------TSGAQDWS 166
               SK  +                        + T    P             T+G   W 
Sbjct:   306 NVSKPSKRSSLENEHSEAPKRAAPVSLEAKSKLTLFAAPENFESQANACSGGTNGFAAWE 365

Query:   167 HNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLF 226
             H   ++L      DA RR   HPDY+P TLYVP ++L K TP M +WW +KSQNFD V+ 
Sbjct:   366 HEKLEWLQEGKKKDAHRRRQNHPDYDPCTLYVPEDYLNKCTPGMRRWWQLKSQNFDAVIC 425

Query:   227 FKVGKFYELFHMDAVIGADELACSYMKES 255
             +KVGKFYEL+HMDAV G +EL   +MK S
Sbjct:   426 YKVGKFYELYHMDAVTGVNELGLIFMKGS 454

GO:0005524 "ATP binding" evidence=IEA

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0000400 "four-way junction DNA binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0008340 "determination of adult lifespan" evidence=IEA

GO:0008630 "intrinsic apoptotic signaling pathway in response to DNA damage" evidence=IEA

GO:0009411 "response to UV" evidence=IEA

GO:0016446 "somatic hypermutation of immunoglobulin genes" evidence=IEA

GO:0016887 "ATPase activity" evidence=IEA

GO:0032137 "guanine/thymine mispair binding" evidence=IEA

GO:0032142 "single guanine insertion binding" evidence=IEA

GO:0032143 "single thymine insertion binding" evidence=IEA

GO:0032301 "MutSalpha complex" evidence=IEA

GO:0032357 "oxidized purine DNA binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

GO:0045910 "negative regulation of DNA recombination" evidence=IEA

GO:0051096 "positive regulation of helicase activity" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	577
cd03286	218	cd03286, ABC_MSH6_euk, ATP-binding cassette domain	2e-30
smart00534	185	smart00534, MUTSac, ATPase domain of DNA mismatch	4e-29
pfam00488	235	pfam00488, MutS_V, MutS domain V	1e-24
COG0249	843	COG0249, MutS, Mismatch repair ATPase (MutS family	4e-24
cd03287	222	cd03287, ABC_MSH3_euk, ATP-binding cassette domain	2e-23
cd03243	202	cd03243, ABC_MutS_homologs, ATP-binding cassette d	2e-21
cd03284	216	cd03284, ABC_MutS1, ATP-binding cassette domain of	8e-20
PRK05399	854	PRK05399, PRK05399, DNA mismatch repair protein Mu	5e-19
cd03285	222	cd03285, ABC_MSH2_euk, ATP-binding cassette domain	3e-17
pfam01624	113	pfam01624, MutS_I, MutS domain I	1e-16
TIGR01070	840	TIGR01070, mutS1, DNA mismatch repair protein MutS	5e-14
PRK05399	854	PRK05399, PRK05399, DNA mismatch repair protein Mu	1e-11
COG0249	843	COG0249, MutS, Mismatch repair ATPase (MutS family	2e-11
cd03281	213	cd03281, ABC_MSH5_euk, ATP-binding cassette domain	2e-11
pfam05190	92	pfam05190, MutS_IV, MutS family domain IV	1e-08
TIGR01070	840	TIGR01070, mutS1, DNA mismatch repair protein MutS	2e-07
pfam05192	290	pfam05192, MutS_III, MutS domain III	3e-07
smart00533	308	smart00533, MUTSd, DNA-binding domain of DNA misma	5e-07
cd03283	199	cd03283, ABC_MutS-like, ATP-binding cassette domai	6e-07
COG0249	843	COG0249, MutS, Mismatch repair ATPase (MutS family	3e-05
cd03282	204	cd03282, ABC_MSH4_euk, ATP-binding cassette domain	9e-05
COG1193	753	COG1193, COG1193, Mismatch repair ATPase (MutS fam	1e-04
TIGR01069	771	TIGR01069, mutS2, MutS2 family protein	3e-04
cd03280	200	cd03280, ABC_MutS2, ATP-binding cassette domain of	0.002

>gnl|CDD|213253 cd03286, ABC_MSH6_euk, ATP-binding cassette domain of eukaryotic MutS6 homolog

 Score =  118 bits (297), Expect = 2e-30
 Identities = 46/97 (47%), Positives = 60/97 (61%), Gaps = 2/97 (2%)

Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T+DG  IA   LE  ++ + CLT+F+THYHS+     E   V   +M+      +D
Sbjct: 120 RGTSTHDGYAIAHAVLEYLVKKVKCLTLFSTHYHSLCDEFHEHGGVRLGHMACAVKNESD 179

Query: 449 G-IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK 484
             I  I FLYKLV GICPKS+G  VA +AGIP+ VV+
Sbjct: 180 PTIRDITFLYKLVAGICPKSYGLYVALMAGIPDGVVE 216

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 218

>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS family

 Score =  113 bits (285), Expect = 4e-29
 Identities = 43/97 (44%), Positives = 59/97 (60%), Gaps = 6/97 (6%)

Query: 389 CRGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRN 447
            RGT T DG  IA   LE  L +IG  T+FATHYH + +     P V   +MS +E+   
Sbjct: 88  GRGTSTYDGLAIAAAILEYLLEKIGARTLFATHYHELTKLADNHPGVRNLHMSALEET-- 145

Query: 448 DGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK 484
              + I FLYKL PG+  KS+G  VA+LAG+P++V++
Sbjct: 146 ---ENITFLYKLKPGVAGKSYGIEVAKLAGLPKEVIE 179

Length = 185

>gnl|CDD|215944 pfam00488, MutS_V, MutS domain V

 Score =  102 bits (256), Expect = 1e-24
 Identities = 45/108 (41%), Positives = 60/108 (55%), Gaps = 6/108 (5%)

Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  IA    E   + I   T+FATHYH + +   + P V   +M+ +E     
Sbjct: 133 RGTSTYDGLAIAWAVAEHLAEKIRARTLFATHYHELTKLAEKLPAVKNVHMAAVET---- 188

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR 496
               IVFLYK+ PG   KS+G +VAELAG+PE VV+    V  ++E R
Sbjct: 189 -NGDIVFLYKVKPGAADKSYGIHVAELAGLPESVVERAREVLAELEDR 235

This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS as characterized in, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters. Length = 235

>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

 Score =  106 bits (268), Expect = 4e-24
 Identities = 54/145 (37%), Positives = 80/145 (55%), Gaps = 12/145 (8%)

Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  IA   LE   + IGC T+FATHYH +     + P V   +MS +E+    
Sbjct: 697 RGTSTYDGLAIAWAVLEYLHEKIGCRTLFATHYHELTELEEKLPQVKNYHMSAVEEG--- 753

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARH-----NLRQLF 503
               I FLYK+ PGI  KS+G +VA+LAG+PE+V++    +  ++E         L Q  
Sbjct: 754 --GDITFLYKVKPGIADKSYGIHVAKLAGLPEEVIERAREILAELEKESRSSNLELNQKD 811

Query: 504 IHKFASLVKSGEKVDVEEL-QKALE 527
           +  F  ++K+ + +D +EL  +AL 
Sbjct: 812 LSLFPKVLKALKSLDPDELTPRALN 836

Length = 843

>gnl|CDD|213254 cd03287, ABC_MSH3_euk, ATP-binding cassette domain of eukaryotic MutS3 homolog

 Score = 98.7 bits (246), Expect = 2e-23
 Identities = 43/99 (43%), Positives = 61/99 (61%), Gaps = 5/99 (5%)

Query: 390 RGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLRE-EPNVAFEYMSYIEDKRN 447
           RGT T+DG  IA  TL   L+   CL +F THY S+   LR  E ++   +MSY+E +++
Sbjct: 121 RGTSTHDGIAIAYATLHYLLEEKKCLVLFVTHYPSLGEILRRFEGSIRNYHMSYLESQKD 180

Query: 448 DGI---DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
                  +I FLYKLV G+  +SFG NVA LAG+P+ ++
Sbjct: 181 FETSDSQSITFLYKLVRGLASRSFGLNVARLAGLPKSII 219

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 222

>gnl|CDD|213210 cd03243, ABC_MutS_homologs, ATP-binding cassette domain of MutS homologs

 Score = 92.3 bits (230), Expect = 2e-21
 Identities = 38/108 (35%), Positives = 53/108 (49%), Gaps = 13/108 (12%)

Query: 379 KNVENYVTPE--------CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLRE 430
           K + +  TP          RGT T +G  IA   LE  L+ GC T+FATH+H +A    +
Sbjct: 100 KEILSLATPRSLVLIDELGRGTSTAEGLAIAYAVLEHLLEKGCRTLFATHFHELADLPEQ 159

Query: 431 EPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
            P V   +M  +          + F YKL+ GIC  S+   +AELAG+
Sbjct: 160 VPGVKNLHMEELITT-----GGLTFTYKLIDGICDPSYALQIAELAGL 202

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, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 202

>gnl|CDD|213251 cd03284, ABC_MutS1, ATP-binding cassette domain of MutS1 homolog

 Score = 87.7 bits (218), Expect = 8e-20
 Identities = 38/96 (39%), Positives = 54/96 (56%), Gaps = 6/96 (6%)

Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  IA   +E    +IG  T+FATHYH +     + P V   +++  E     
Sbjct: 120 RGTSTYDGLSIAWAIVEYLHEKIGAKTLFATHYHELTELEGKLPRVKNFHVAVKEKG--- 176

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK 484
               +VFL+K+V G   KS+G  VA LAG+PE+V++
Sbjct: 177 --GGVVFLHKIVEGAADKSYGIEVARLAGLPEEVIE 210

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 216

>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional

 Score = 90.9 bits (227), Expect = 5e-19
 Identities = 56/159 (35%), Positives = 77/159 (48%), Gaps = 29/159 (18%)

Query: 390 RGTGTNDGCVIARVTLEKFL--QIGCLTVFATHYH---SVARRLREEPNVAFEYMSYIED 444
           RGT T DG  IA    E +L  +IG  T+FATHYH    +  +L   P V   +++  E 
Sbjct: 697 RGTSTYDGLSIAWAVAE-YLHDKIGAKTLFATHYHELTELEEKL---PGVKNVHVAVKEH 752

Query: 445 KRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFI 504
                   IVFL+K+VPG   KS+G +VA+LAG+P  V+K          AR  L QL  
Sbjct: 753 G-----GDIVFLHKVVPGAADKSYGIHVAKLAGLPASVIK---------RAREILAQL-- 796

Query: 505 HKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDL 543
               S  +  +    EE Q +L +    ES   + L+ L
Sbjct: 797 ---ESASEKAKAASAEEDQLSLFAEPE-ESPLLEALKAL 831

Length = 854

>gnl|CDD|213252 cd03285, ABC_MSH2_euk, ATP-binding cassette domain of eukaryotic MutS2 homolog

 Score = 80.5 bits (199), Expect = 3e-17
 Identities = 40/106 (37%), Positives = 58/106 (54%), Gaps = 4/106 (3%)

Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    QI C  +FATH+H +     E PNV   +++ + D   D
Sbjct: 120 RGTSTYDGFGLAWAIAEYIATQIKCFCLFATHFHELTALADEVPNVKNLHVTALTD---D 176

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
              T+  LYK+  G C +SFG +VAELA  P++V++     A ++E
Sbjct: 177 ASRTLTMLYKVEKGACDQSFGIHVAELANFPKEVIEMAKQKALELE 222

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 222

>gnl|CDD|216613 pfam01624, MutS_I, MutS domain I

 Score = 75.7 bits (187), Expect = 1e-16
 Identities = 26/56 (46%), Positives = 33/56 (58%)

Query: 207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGEST 262
           TP M Q+  +KS+  D VLFF+VG FYELF  DA I A EL  +     G +G+  
Sbjct: 1   TPMMRQYLELKSKYPDAVLFFRVGDFYELFGEDAEIAARELGITLTVRGGGSGKRI 56

This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam05192 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with globular domain I, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in. Length = 113

>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS

 Score = 74.8 bits (184), Expect = 5e-14
 Identities = 38/112 (33%), Positives = 58/112 (51%), Gaps = 6/112 (5%)

Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E   + I   T+FATHY  +       P +   +++ +E     
Sbjct: 682 RGTSTYDGLALAWAIAEYLHEHIRAKTLFATHYFELTALEESLPGLKNVHVAALEHN--- 738

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLR 500
              TIVFL++++PG   KS+G  VA LAG+P++V+     +  Q+EAR    
Sbjct: 739 --GTIVFLHQVLPGPASKSYGLAVAALAGLPKEVIARARQILTQLEARSTES 788

[DNA metabolism, DNA replication, recombination, and repair]. Length = 840

>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional

 Score = 67.4 bits (166), Expect = 1e-11
 Identities = 21/45 (46%), Positives = 28/45 (62%)

Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
           + K TP M Q+  IK+Q  D +LFF++G FYELF  DA   +  L
Sbjct: 5   MSKLTPMMQQYLEIKAQYPDALLFFRMGDFYELFFEDAKKASRLL 49

Length = 854

>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

 Score = 66.5 bits (163), Expect = 2e-11
 Identities = 23/45 (51%), Positives = 28/45 (62%)

Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
             K TP M Q+  IK+Q  D +LFF++G FYELF  DA I A  L
Sbjct: 3   KAKLTPMMQQYLEIKAQYPDTLLFFRMGDFYELFFEDAKIAARLL 47

Length = 843

>gnl|CDD|213248 cd03281, ABC_MSH5_euk, ATP-binding cassette domain of eukaryotic MutS5 homolog

 Score = 63.9 bits (156), Expect = 2e-11
 Identities = 32/95 (33%), Positives = 48/95 (50%), Gaps = 6/95 (6%)

Query: 390 RGTGTNDGCVIARVTLEKFLQIG--C-LTVFATHYHSVARR--LREEPNVAFEYMS-YIE 443
           +GT T DG  +   T+E  L+ G  C   + +TH+H +  R  L E   + F  M   + 
Sbjct: 119 KGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRSLLPERLKIKFLTMEVLLN 178

Query: 444 DKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
                  + I +LY+LVPG+   SF  + A+LAGI
Sbjct: 179 PTSTSPNEDITYLYRLVPGLADTSFAIHCAKLAGI 213

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 213

>gnl|CDD|218487 pfam05190, MutS_IV, MutS family domain IV

 Score = 52.2 bits (126), Expect = 1e-08
 Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 8/83 (9%)

Query: 309 GVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCT---VIYSEAQKKQKKYVLEVPSKYAS 365
           G D+E DE+ D ++ +E E+   L  +    G     V Y+    K   Y +EV    A 
Sbjct: 1   GFDEELDELRDLLEELESELDELLAKERERLGIKSLKVGYN----KVFGYYIEVTRSEAK 56

Query: 366 KAKSNHQRVATKKKNVENYVTPE 388
           K   ++ R  T  KN   + TPE
Sbjct: 57  KVPKDYIRRQT-LKNGVRFTTPE 78

This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam00488. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds in part with globular domain IV, which is involved in DNA binding, in Thermus aquaticus MutS as characterized in. Length = 92

>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS

 Score = 53.6 bits (129), Expect = 2e-07
 Identities = 21/56 (37%), Positives = 30/56 (53%)

Query: 207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGEST 262
           TP M Q+  +K+++ D +LFF++G FYELF+ DA   A  L  S         E  
Sbjct: 2   TPMMQQYLKLKAEHPDALLFFRMGDFYELFYEDAKKAAQLLDISLTSRGQSADEPI 57

[DNA metabolism, DNA replication, recombination, and repair]. Length = 840

>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III

 Score = 52.0 bits (125), Expect = 3e-07
 Identities = 27/111 (24%), Positives = 46/111 (41%), Gaps = 2/111 (1%)

Query: 281 DMSELLKYFENAFD-HKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHF 339
            + ELL+  E A D     S     + K G D E DE+   +  + +++   L  +    
Sbjct: 127 PLPELLELLERAIDEDPPLSLRDGGVIKDGYDPELDELRALLDELREKLAELLERERERT 186

Query: 340 GCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECR 390
           G   +     +    YV+EV +  A K   ++ R  +  KN   + TPE +
Sbjct: 187 GIKSLKVGYNRVFGYYVIEVKASKADKVPGDYIRR-STTKNAVRFTTPELK 236

This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam05188, pfam01624 and pfam05190. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterized in. Length = 290

>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS family

 Score = 51.5 bits (124), Expect = 5e-07
 Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 10/108 (9%)

Query: 284 ELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-- 341
           ELL    N  D  E +  G +I K G D E DE+ ++++ +E+E++  L+ +    G   
Sbjct: 122 ELLLELLNDDDPLEVND-GGLI-KDGFDPELDELREKLEELEEELEELLKKEREELGIDS 179

Query: 342 -TVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPE 388
             + Y+    K   Y +EV    A K   +  R ++  KN E + TPE
Sbjct: 180 LKLGYN----KVHGYYIEVTKSEAKKVPKDFIRRSS-LKNTERFTTPE 222

Length = 308

>gnl|CDD|213250 cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like homolog

 Score = 50.0 bits (120), Expect = 6e-07
 Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 7/91 (7%)

Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMS-YIEDKRN 447
            +GT + +    +   L+       + + +TH   +A  L  +  V   +    I+D   
Sbjct: 115 FKGTNSRERQAASAAVLKFLKNKNTIGIISTHDLELADLLDLDSAVRNYHFREDIDD--- 171

Query: 448 DGIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
              + ++F YKL PG+ P      + +  GI
Sbjct: 172 ---NKLIFDYKLKPGVSPTRNALRLMKKIGI 199

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 199

>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

 Score = 46.5 bits (111), Expect = 3e-05
 Identities = 27/110 (24%), Positives = 44/110 (40%), Gaps = 2/110 (1%)

Query: 279 FPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAH 338
              ++ELL+  E A +     +  + I K G + E DE+ D + + ++ I      +   
Sbjct: 398 LDYLAELLELLETAINEDPPLAVRDGIIKEGYNIELDELRDLLNNAKEWIAKLELEERER 457

Query: 339 FGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPE 388
            G          K   Y +EV    A     ++ R  T  KN E + TPE
Sbjct: 458 TGIK-SLKIKYNKVYGYYIEVTKSNAKLVPDDYIRRQT-LKNAERFTTPE 505

Length = 843

>gnl|CDD|213249 cd03282, ABC_MSH4_euk, ATP-binding cassette domain of eukaryotic MutS4 homolog

 Score = 43.5 bits (103), Expect = 9e-05
 Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           RGT + DG  I+   LE  ++      FATH+  +A  L  +  V   +M       N  
Sbjct: 119 RGTSSADGFAISLAILECLIKKESTVFFATHFRDIAAILGNKSCVVHLHMKAQSINSNG- 177

Query: 450 IDTIVFLYKLVPG 462
              I   YKLV G
Sbjct: 178 ---IEMAYKLVLG 187

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 clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 204

>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

 Score = 45.0 bits (107), Expect = 1e-04
 Identities = 38/158 (24%), Positives = 67/158 (42%), Gaps = 14/158 (8%)

Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
             GT  ++G  +A   LE  L+     V  THY  +     E   V    M +       
Sbjct: 405 GSGTDPDEGAALAIAILEDLLEKPAKIVATTHYRELKALAAEREGVENASMEFDA----- 459

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFA 508
             +T+   Y+L+ G+  +S  F++A   G+PE +++   T   +      L +  I K  
Sbjct: 460 --ETLRPTYRLLEGVPGRSNAFDIALRLGLPEPIIEEAKT---EFGEEKELLEELIEKLE 514

Query: 509 SLVKSGEKVDVEELQKALESVKSFE---SQTKKDLEDL 543
            + K   + ++EE++K L+ V+      S  K  L +L
Sbjct: 515 EVRKE-LEEELEEVEKLLDEVELLTGANSGGKTSLLEL 551

Length = 753

>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein

 Score = 43.3 bits (102), Expect = 3e-04
 Identities = 38/155 (24%), Positives = 70/155 (45%), Gaps = 11/155 (7%)

Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
             GT  ++G  +A   LE  L+     +  THY  +  +     N   E  S + D    
Sbjct: 412 GAGTDPDEGSALAISILEYLLKQNAQVLITTHYKEL--KALMYNNEGVENASVLFD---- 465

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFA 508
             +T+   YKL+ GI  +S+ F +A+  GIP  +++   T             + I K +
Sbjct: 466 -EETLSPTYKLLKGIPGESYAFEIAQRYGIPHFIIEQAKT---FYGEFKEEINVLIEKLS 521

Query: 509 SLVKSGEKVDVEELQKALESVKSFESQTKKDLEDL 543
           +L K  E+   E L+K L+  +  + + ++++E+L
Sbjct: 522 ALEKELEQ-KNEHLEKLLKEQEKLKKELEQEMEEL 555

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function [DNA metabolism, Other]. Length = 771

>gnl|CDD|213247 cd03280, ABC_MutS2, ATP-binding cassette domain of MutS2

 Score = 39.5 bits (93), Expect = 0.002
 Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 7/90 (7%)

Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
             GT   +G  +A   LE+ L+ G L +  THY  +     +   V    M +       
Sbjct: 118 GSGTDPVEGAALAIAILEELLERGALVIATTHYGELKAYAYKREGVENASMEF------- 170

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
             +T+   Y+L+ G+  +S    +A   G+
Sbjct: 171 DPETLKPTYRLLIGVPGRSNALEIARRLGL 200

MutS2 homologs in bacteria and eukaryotes. 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, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 200

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	577
KOG0217|consensus	1125		100.0
COG0249	843	MutS Mismatch repair ATPase (MutS family) [DNA rep	100.0
TIGR01070	840	mutS1 DNA mismatch repair protein MutS.	100.0
KOG0218|consensus	1070		100.0
PRK05399	854	DNA mismatch repair protein MutS; Provisional	100.0
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	100.0
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	100.0
KOG0220|consensus	867		100.0
KOG0219|consensus	902		100.0
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	100.0
PRK00409	782	recombination and DNA strand exchange inhibitor pr	100.0
KOG0221|consensus	849		100.0
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	100.0
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	100.0
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	100.0
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	100.0
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	100.0
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	100.0
COG1193	753	Mismatch repair ATPase (MutS family) [DNA replicat	99.97
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	99.96
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	99.95
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	99.95
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	99.68
TIGR01070	840	mutS1 DNA mismatch repair protein MutS.	98.69
PRK05399	854	DNA mismatch repair protein MutS; Provisional	98.59
PF01624	113	MutS_I: MutS domain I C-terminus.; InterPro: IPR00	98.52
COG0249	843	MutS Mismatch repair ATPase (MutS family) [DNA rep	98.43
KOG0219|consensus	902		98.06
KOG0217|consensus	1125		97.74
cd00267	157	ABC_ATPase ABC (ATP-binding cassette) transporter	96.53
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	96.46
cd03214	180	ABC_Iron-Siderophores_B12_Hemin ABC transporters,	96.01
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	95.99
cd03238	176	ABC_UvrA The excision repair protein UvrA; Nucleot	95.99
COG4586	325	ABC-type uncharacterized transport system, ATPase	95.67
COG1121	254	ZnuC ABC-type Mn/Zn transport systems, ATPase comp	95.66
cd03246	173	ABCC_Protease_Secretion This family represents the	95.54
cd03217	200	ABC_FeS_Assembly ABC-type transport system involve	95.42
cd03216	163	ABC_Carb_Monos_I This family represents the domain	95.42
cd03228	171	ABCC_MRP_Like The MRP (Mutidrug Resistance Protein	95.39
cd03247	178	ABCC_cytochrome_bd The CYD subfamily implicated in	95.38
cd03223	166	ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cass	95.32
KOG0220|consensus	867		95.22
cd03221	144	ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is	95.22
KOG0218|consensus	1070		95.16
cd03230	173	ABC_DR_subfamily_A This family of ATP-binding prot	95.1
cd03229	178	ABC_Class3 This class is comprised of all BPD (Bin	94.98
COG0396	251	sufC Cysteine desulfurase activator ATPase [Posttr	94.96
cd03250	204	ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.	94.88
COG2884	223	FtsE Predicted ATPase involved in cell division [C	94.52
cd03268	208	ABC_BcrA_bacitracin_resist The BcrA subfamily repr	94.45
PRK10584	228	putative ABC transporter ATP-binding protein YbbA;	94.38
PRK13543	214	cytochrome c biogenesis protein CcmA; Provisional	94.33
cd03258	233	ABC_MetN_methionine_transporter MetN (also known a	94.33
cd03269	210	ABC_putative_ATPase This subfamily is involved in	94.32
COG4152	300	ABC-type uncharacterized transport system, ATPase	94.28
COG1131	293	CcmA ABC-type multidrug transport system, ATPase c	94.26
cd03215	182	ABC_Carb_Monos_II This family represents domain II	94.26
cd03226	205	ABC_cobalt_CbiO_domain2 Domain II of the ABC compo	94.18
cd03213	194	ABCG_EPDR ABCG transporters are involved in eye pi	94.11
cd03293	220	ABC_NrtD_SsuB_transporters NrtD and SsuB are the A	94.0
cd03239	178	ABC_SMC_head The structural maintenance of chromos	93.98
cd03262	213	ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-	93.87
PRK00409	782	recombination and DNA strand exchange inhibitor pr	93.85
cd03232	192	ABC_PDR_domain2 The pleiotropic drug resistance-li	93.81
cd03265	220	ABC_DrrA DrrA is the ATP-binding protein component	93.53
COG3910	233	Predicted ATPase [General function prediction only	93.33
cd03256	241	ABC_PhnC_transporter ABC-type phosphate/phosphonat	93.29
cd03261	235	ABC_Org_Solvent_Resistant ABC (ATP-binding cassett	93.24
PRK11124	242	artP arginine transporter ATP-binding subunit; Pro	93.18
PRK10247	225	putative ABC transporter ATP-binding protein YbbL;	93.12
PRK11300	255	livG leucine/isoleucine/valine transporter ATP-bin	93.04
TIGR01188	302	drrA daunorubicin resistance ABC transporter ATP-b	92.93
cd03296	239	ABC_CysA_sulfate_importer Part of the ABC transpor	92.87
PRK09536	402	btuD corrinoid ABC transporter ATPase; Reviewed	92.87
cd03219	236	ABC_Mj1267_LivG_branched The Mj1267/LivG ABC trans	92.75
TIGR03864	236	PQQ_ABC_ATP ABC transporter, ATP-binding subunit,	92.75
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	92.75
TIGR03740	223	galliderm_ABC gallidermin-class lantibiotic protec	92.61
cd03266	218	ABC_NatA_sodium_exporter NatA is the ATPase compon	92.58
PRK13539	207	cytochrome c biogenesis protein CcmA; Provisional	92.56
PRK13540	200	cytochrome c biogenesis protein CcmA; Provisional	92.55
COG4555	245	NatA ABC-type Na+ transport system, ATPase compone	92.52
PRK13632	271	cbiO cobalt transporter ATP-binding subunit; Provi	92.5
PRK11629	233	lolD lipoprotein transporter ATP-binding subunit;	92.47
COG4133	209	CcmA ABC-type transport system involved in cytochr	92.44
cd03278	197	ABC_SMC_barmotin Barmotin is a tight junction-asso	92.41
cd03301	213	ABC_MalK_N The N-terminal ATPase domain of the mal	92.29
PRK09493	240	glnQ glutamine ABC transporter ATP-binding protein	92.21
PRK10619	257	histidine/lysine/arginine/ornithine transporter su	92.18
PRK14250	241	phosphate ABC transporter ATP-binding protein; Pro	92.13
PRK13541	195	cytochrome c biogenesis protein CcmA; Provisional	92.12
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	92.12
PRK10575	265	iron-hydroxamate transporter ATP-binding subunit;	92.03
cd03276	198	ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC protein	92.0
cd03295	242	ABC_OpuCA_Osmoprotection OpuCA is a the ATP bindin	91.85
COG1120	258	FepC ABC-type cobalamin/Fe3+-siderophores transpor	91.8
cd03218	232	ABC_YhbG The ABC transporters belonging to the Yhb	91.78
PRK13536	340	nodulation factor exporter subunit NodI; Provision	91.74
COG1119	257	ModF ABC-type molybdenum transport system, ATPase	91.68
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	91.56
TIGR01288	303	nodI ATP-binding ABC transporter family nodulation	91.42
PRK13635	279	cbiO cobalt transporter ATP-binding subunit; Provi	91.35
PRK13637	287	cbiO cobalt transporter ATP-binding subunit; Provi	91.11
cd03234	226	ABCG_White The White subfamily represents ABC tran	91.05
PRK10908	222	cell division protein FtsE; Provisional	90.99
PRK13537	306	nodulation ABC transporter NodI; Provisional	90.92
PRK13548	258	hmuV hemin importer ATP-binding subunit; Provision	90.88
TIGR03265	353	PhnT2 putative 2-aminoethylphosphonate ABC transpo	90.65
KOG0062|consensus	582		90.37
PRK11144	352	modC molybdate transporter ATP-binding protein; Pr	90.33
PRK13634	290	cbiO cobalt transporter ATP-binding subunit; Provi	90.06
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	90.06
PRK13545	549	tagH teichoic acids export protein ATP-binding sub	89.88
cd03274	212	ABC_SMC4_euk Eukaryotic SMC4 proteins; SMC protein	89.86
TIGR03522	301	GldA_ABC_ATP gliding motility-associated ABC trans	89.7
TIGR01186	363	proV glycine betaine/L-proline transport ATP bindi	89.66
COG4619	223	ABC-type uncharacterized transport system, ATPase	89.6
PRK10070	400	glycine betaine transporter ATP-binding subunit; P	89.56
PRK13639	275	cbiO cobalt transporter ATP-binding subunit; Provi	89.47
TIGR02203	571	MsbA_lipidA lipid A export permease/ATP-binding pr	89.24
TIGR02142	354	modC_ABC molybdenum ABC transporter, ATP-binding p	89.17
PRK11176	582	lipid transporter ATP-binding/permease protein; Pr	89.15
cd01120	165	RecA-like_NTPases RecA-like NTPases. This family i	88.9
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	88.74
TIGR03796	710	NHPM_micro_ABC1 NHPM bacteriocin system ABC transp	88.65
cd03264	211	ABC_drug_resistance_like ABC-type multidrug transp	87.81
cd03233	202	ABC_PDR_domain1 The pleiotropic drug resistance (P	87.57
PRK15064	530	ABC transporter ATP-binding protein; Provisional	87.28
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	87.25
COG1134	249	TagH ABC-type polysaccharide/polyol phosphate tran	87.1
PRK09183	259	transposase/IS protein; Provisional	86.93
TIGR02858	270	spore_III_AA stage III sporulation protein AA. Mem	86.84
COG0488	530	Uup ATPase components of ABC transporters with dup	86.62
PLN03073	718	ABC transporter F family; Provisional	86.46
COG1129	500	MglA ABC-type sugar transport system, ATPase compo	86.23
COG0488	530	Uup ATPase components of ABC transporters with dup	86.22
KOG0059|consensus	885		85.68
PRK10636	638	putative ABC transporter ATP-binding protein; Prov	85.64
PRK13657	588	cyclic beta-1,2-glucan ABC transporter; Provisiona	85.62
TIGR02204	576	MsbA_rel ABC transporter, permease/ATP-binding pro	85.57
TIGR01271	1490	CFTR_protein cystic fibrosis transmembrane conduct	85.17
COG1122	235	CbiO ABC-type cobalt transport system, ATPase comp	85.09
PRK15439	510	autoinducer 2 ABC transporter ATP-binding protein	84.84
PRK10790	592	putative multidrug transporter membrane\ATP-bindin	84.59
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	84.31
COG1125	309	OpuBA ABC-type proline/glycine betaine transport s	84.31
PRK11147	635	ABC transporter ATPase component; Reviewed	84.27
COG1193	753	Mismatch repair ATPase (MutS family) [DNA replicat	84.2
PRK10938	490	putative molybdenum transport ATP-binding protein	83.81
COG4618	580	ArpD ABC-type protease/lipase transport system, AT	83.77
KOG0221|consensus	849		83.71
cd03277	213	ABC_SMC5_euk Eukaryotic SMC5 proteins; SMC protein	83.51
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	83.23
cd00009	151	AAA The AAA+ (ATPases Associated with a wide varie	83.01
PRK08181	269	transposase; Validated	82.91
PRK08116	268	hypothetical protein; Validated	82.83
TIGR03797	686	NHPM_micro_ABC2 NHPM bacteriocin system ABC transp	82.32
COG1117	253	PstB ABC-type phosphate transport system, ATPase c	82.3
TIGR02881	261	spore_V_K stage V sporulation protein K. Members o	81.68
cd03237	246	ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 o	81.32
TIGR01193	708	bacteriocin_ABC ABC-type bacteriocin transporter.	81.2
TIGR01846	694	type_I_sec_HlyB type I secretion system ABC transp	81.13
TIGR03608	206	L_ocin_972_ABC putative bacteriocin export ABC tra	80.9
COG2401	593	ABC-type ATPase fused to a predicted acetyltransfe	80.87
TIGR03375	694	type_I_sec_LssB type I secretion system ATPase, Ls	80.59
cd03298	211	ABC_ThiQ_thiamine_transporter ABC-type thiamine tr	80.26

>KOG0217|consensus

Probab=100.00  E-value=2.1e-58  Score=517.32  Aligned_cols=239  Identities=24%  Similarity=0.346  Sum_probs=207.8

Q ss_pred             cCcccccCcccccc---ccccccccc---ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeee
Q psy13263        274 TPSGCFPDMSELLK---YFENAFDHK---EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYS  346 (577)
Q Consensus       274 i~~GrhPlLe~~l~---~~~n~F~~~---~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~  346 (577)
                      +..++||.+.....   |++|+...+   +++..++||||||||+..+++++..+ ||||+||+|||..+++.. |+||+
T Consensus       869 ~~~~~Hpcfsl~s~~~~fipN~v~~g~~~e~~~~llTGpNmgGKSTllRq~c~~v-ilaq~G~~VPa~~~~~tpidrI~t  947 (1125)
T KOG0217|consen  869 VKGLRHPCFSLPSTGTSFIPNDVELGGAEENREGLLTGPNMGGKSTLLRQACIAV-ILAQIGCDVPAEVMELTPIDRIFT  947 (1125)
T ss_pred             EecccCceeecCcCCCccccchhhccccccceeeeeccCCcCCchHHHHHHHHHH-HHHHhCCCccHHHhcccchHHHhh
Confidence            35677998766443   788877666   33334489999999999999999998 999999999999999999 99999


Q ss_pred             cccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEec
Q psy13263        347 EAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFAT  419 (577)
Q Consensus       347 ~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaT  419 (577)
                      ++|+      ++|||++|+.+...|+.+++.+|||++||        |||||+|.||.|||.|||+||... +|+++|+|
T Consensus       948 RlGA~D~im~g~STF~vELsET~~IL~~aT~~SLvi~DE--------LGRGtst~DG~aIA~aVLe~l~~~i~c~~fFST 1019 (1125)
T KOG0217|consen  948 RLGANDDIMSGESTFFVELSETKKILKHATRHSLVIVDE--------LGRGTSTFDGTAIAEAVLEHLSEGIQCLGFFST 1019 (1125)
T ss_pred             hcccccchhcCCceEEEeccchHHHHhhcCccceeeehh--------hcCcccccCCcchHHHHHHHHHhcccccCCccc
Confidence            9997      55999999999999999999999999999        999999999999999999999996 99999999


Q ss_pred             chHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhh--
Q psy13263        420 HYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARH--  497 (577)
Q Consensus       420 Hy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~--  497 (577)
                      |||.|+....++|+|++.||.+...+.    ..++|+|||.+|+|+.|||+++|+++|||..||++|...+.+++...  
T Consensus      1020 HYhsl~~~~~~~p~Vrl~~Ma~~vd~e----~~vtFLYkl~~G~cpkSyG~~vArmaglp~~vi~~a~~~a~E~e~~~~~ 1095 (1125)
T KOG0217|consen 1020 HYHSLCVDFMHHPQVRLLHMACVVDEE----IDVTFLYKLEEGICPKSYGFNVARMAGLPDQVIDRAEIKAHELEKSSAN 1095 (1125)
T ss_pred             cccchhHhhhcCccccchhheeeecCC----ccEEEeehhccCCCCcchhHHHHHhcCCcHHHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999997542    36999999999999999999999999999999999999999999887  


Q ss_pred             hHHHHHHHHHHHHHhccCCCCHHHHHHHHH
Q psy13263        498 NLRQLFIHKFASLVKSGEKVDVEELQKALE  527 (577)
Q Consensus       498 ~~~~~~~~L~~~~~~~~~~ld~~~l~~l~~  527 (577)
                      ....+++++...+  ...+++..++..+++
T Consensus      1096 ~~d~~~r~~~~~~--~~s~~s~~~l~sil~ 1123 (1125)
T KOG0217|consen 1096 AADGKIREVVECA--LDSSLSISELHSILD 1123 (1125)
T ss_pred             hhhHHHHhhhhhh--hccccCHHHHHHHHh
Confidence            3444555554333  455666766655554

>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

Probab=100.00  E-value=5.5e-55  Score=500.16  Aligned_cols=247  Identities=26%  Similarity=0.393  Sum_probs=220.8

Q ss_pred             cCCcchhhhhhhhhhccCcccccCcccccc--cccccccccc-cccccccCCCCCCCchhHHHHHHHHHHHHHhcccccc
Q psy13263        258 TGESTLLTQLCNYESQTPSGCFPDMSELLK--YFENAFDHKE-ASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRT  334 (577)
Q Consensus       258 ~GKStlLk~i~~~~i~i~~GrhPlLe~~l~--~~~n~F~~~~-a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA  334 (577)
                      ..++++....+   +.|.+||||+++..+.  |++|+++.+. .+..+||||||||||+|+||+|+|+ ||||+||||||
T Consensus       567 y~rP~~~~~~~---l~i~~gRHPvvE~~~~~~fVpNd~~L~~~~~i~lITGPNM~GKSTylRQvali~-imAQiGsfVPA  642 (843)
T COG0249         567 YVRPEFVDSND---LEIKEGRHPVVEAVLDNGFVPNDIDLSGNRRIILITGPNMGGKSTYLRQVALIV-ILAQIGSFVPA  642 (843)
T ss_pred             CCCceecCCCC---EEEEecCcchhhhhccCCcccCceeeCCCceEEEEECCCCCccHHHHHHHHHHH-HHHHcCCCeeH
Confidence            44555555544   8899999999999887  8999998887 4456799999999999999999999 99999999999


Q ss_pred             ccceecc-ceeeecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHH
Q psy13263        335 QCAHFGC-TVIYSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEK  407 (577)
Q Consensus       335 ~~a~l~~-d~if~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~  407 (577)
                      .+|++|+ |+||+++|.      |+||||.||.+++.|+++++.+|||||||        +||||||+||+||||||+||
T Consensus       643 ~~A~i~ivD~IfTRiGa~DDL~~G~STFMvEM~Eta~IL~~AT~~SLvilDE--------iGRGTsT~DGlaIA~Av~ey  714 (843)
T COG0249         643 EKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDE--------IGRGTSTYDGLAIAWAVLEY  714 (843)
T ss_pred             HHccccccceeeecccccchhhccccHHHHHHHHHHHHHHhCCCCcEEEEec--------ccCCCCcchhHHHHHHHHHH
Confidence            9999999 999999987      56999999999999999999999999999        99999999999999999999


Q ss_pred             HHhc-CCeEEEecchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHH
Q psy13263        408 FLQI-GCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFG  486 (577)
Q Consensus       408 L~~~-~~~~lfaTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA  486 (577)
                      |+++ +|++|||||||||+++....++|.|+||...+.+     +.++|+|+|++|+|.+||||+||+++|+|.+||+||
T Consensus       715 L~~~~~~~tLFATHy~ELt~l~~~~~~v~N~h~~~~e~~-----~~i~Fl~kv~~G~a~~SyGi~VAklaGlP~~Vi~rA  789 (843)
T COG0249         715 LHEKIGCRTLFATHYHELTELEEKLPQVKNYHMSAVEEG-----GDITFLYKVKPGIADKSYGIHVAKLAGLPEEVIERA  789 (843)
T ss_pred             HHhccCceEEEeccHHHHHHhhhcccccceeEEEEEEcC-----CceEEEEEeccCCCCccHHHHHHHHhCCCHHHHHHH
Confidence            9997 9999999999999999999999999999988754     469999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhh-------H--HHHHHHHHHHHHhccCCCCHHHHHHH
Q psy13263        487 TTVAFQMEARHN-------L--RQLFIHKFASLVKSGEKVDVEELQKA  525 (577)
Q Consensus       487 ~ei~~~le~~~~-------~--~~~~~~L~~~~~~~~~~ld~~~l~~l  525 (577)
                      ++++.++++...       .  ...+.    .+.+.+..+|++.++|.
T Consensus       790 ~~il~~le~~~~~~~~~~~~~~~~~~~----~i~~~~~~~~~~~~tp~  833 (843)
T COG0249         790 REILAELEKESRSSNLELNQKDLSLFP----KVLKALKSLDPDELTPR  833 (843)
T ss_pred             HHHHHHHhhcccCcccchhhhhHhHHH----HHHHHHHhCChhhcCHH
Confidence            999999998652       1  22222    34456777888888875

>TIGR01070 mutS1 DNA mismatch repair protein MutS

Probab=100.00  E-value=2.2e-50  Score=464.82  Aligned_cols=213  Identities=23%  Similarity=0.357  Sum_probs=199.0

Q ss_pred             hhhccCcccccCccccc--cccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceee
Q psy13263        270 YESQTPSGCFPDMSELL--KYFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIY  345 (577)
Q Consensus       270 ~~i~i~~GrhPlLe~~l--~~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if  345 (577)
                      ..+.+.+||||+++..+  .|++|++..+.. +..+||||||||||+|+|++++|+ +|||+|+||||.+|++++ |+||
T Consensus       561 ~~i~i~~~RHP~le~~~~~~~VpNdi~l~~~~~~~iITGPNmgGKSt~lrqvali~-imAq~G~~VPA~~a~i~~~D~If  639 (840)
T TIGR01070       561 PQLRIREGRHPVVEQVLRTPFVPNDLEMAHNRRMLLITGPNMGGKSTYMRQTALIA-LLAQIGSFVPAESAELPLFDRIF  639 (840)
T ss_pred             CcEEEEeeECHHHHhccCCCeEeeeeecCCCccEEEEECCCCCCchHHHHHHHHHH-HHHhcCCCccchheEeccccEEE
Confidence            35889999999998644  489999988754 456799999999999999999999 999999999999999999 9999


Q ss_pred             ecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEe
Q psy13263        346 SEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFA  418 (577)
Q Consensus       346 ~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfa  418 (577)
                      +++|.      ++|||+.||.+++.|+.+++.+|||||||        |||||++.||.||||||++||.+ .+|++|||
T Consensus       640 trig~~d~i~~g~STF~~Em~e~a~IL~~at~~sLvllDE--------~GrGT~~~dg~aia~ai~e~l~~~~~~~~~~~  711 (840)
T TIGR01070       640 TRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLFDE--------IGRGTSTYDGLALAWAIAEYLHEHIRAKTLFA  711 (840)
T ss_pred             EecCcccchhcCcchHHHHHHHHHHHHhhCCCCEEEEEcc--------CCCCCChhHHHHHHHHHHHHHHhcCCCEEEEE
Confidence            99997      45999999999999999999999999999        99999999999999999999999 59999999


Q ss_pred             cchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Q psy13263        419 THYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR  496 (577)
Q Consensus       419 THy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~  496 (577)
                      ||||+|+.+...+++|.|+||.+.+.+     ++++|+|||.+|+|++||||+||+++|||++||+||++++.+++..
T Consensus       712 TH~~eL~~l~~~~~~v~n~~~~~~~~~-----~~l~flYkl~~G~~~~Sygi~VA~laGlP~~VI~rA~~il~~le~~  784 (840)
T TIGR01070       712 THYFELTALEESLPGLKNVHVAALEHN-----GTIVFLHQVLPGPASKSYGLAVAALAGLPKEVIARARQILTQLEAR  784 (840)
T ss_pred             cCchHHHHHhhhCCCeEEEEEEEEEEC-----CcEEEEEEECCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHhc
Confidence            999999999999999999999998643     5899999999999999999999999999999999999999999964

>KOG0218|consensus

Probab=100.00  E-value=8.2e-51  Score=442.22  Aligned_cols=252  Identities=23%  Similarity=0.357  Sum_probs=217.5

Q ss_pred             hhhhhhhhhhhhhccccC----ccCCcchhhhhhhhhhccCcccccCcccccc--ccccccccc--ccccccccCCCCCC
Q psy13263        239 DAVIGADELACSYMKESG----CTGESTLLTQLCNYESQTPSGCFPDMSELLK--YFENAFDHK--EASSAGNIIPKAGV  310 (577)
Q Consensus       239 DA~i~a~eLdl~~mkGsn----~~GKStlLk~i~~~~i~i~~GrhPlLe~~l~--~~~n~F~~~--~a~~~~I~gPN~gG  310 (577)
                      .+...-..++|.+.-...    ...++++...+  -.|.|++||||+++.++.  |+||+.+..  ..+-.+||||||||
T Consensus       765 kat~~LatlDCi~SlA~~s~n~nYvRPtfvd~~--~eI~ikngRhPvIe~Ll~d~fVPNdi~ls~egerc~IITGPNMGG  842 (1070)
T KOG0218|consen  765 KATLNLATLDCILSLAATSCNVNYVRPTFVDGQ--QEIIIKNGRHPVIESLLVDYFVPNDIMLSPEGERCNIITGPNMGG  842 (1070)
T ss_pred             HHHHHHHHHHHHHHHHHHhccCCccCcccccch--hhhhhhcCCCchHHHHhhhccCCCcceecCCCceEEEEeCCCCCC
Confidence            344444557777543221    23355555543  358899999999997664  789987655  34557899999999


Q ss_pred             CchhHHHHHHHHHHHHHhccccccccceecc-ceeeecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcc
Q psy13263        311 DKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVEN  383 (577)
Q Consensus       311 Ksvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n  383 (577)
                      |+.|.||+++|. ||||+|+||||..|++++ |.||++||.      |.|||+.||.+++.|+.+++.+|||||||    
T Consensus       843 KSsyIrQvALit-IMAQiGsfVPAeea~l~IfdgvltRmGAsDnI~~grSTFm~Emldt~eil~kat~~SlvilDE----  917 (1070)
T KOG0218|consen  843 KSSYIRQVALIT-IMAQIGSFVPAEEARLSIFDGVLTRMGASDNIINGRSTFMVEMLDTLEILKKATKRSLVILDE----  917 (1070)
T ss_pred             chHHHHHHHHHH-HHHHhcCccchHHhhhhHHhhHHHhhccccccccchhHHHHHHHHHHHHHHhcccchhhhhHh----
Confidence            999999999999 999999999999999999 999999997      45999999999999999999999999999    


Q ss_pred             cccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHhhcCC-CcccccceeeeecC--CCCcceEEEEEee
Q psy13263        384 YVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLREEP-NVAFEYMSYIEDKR--NDGIDTIVFLYKL  459 (577)
Q Consensus       384 ~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~~~~~-~V~n~hm~~~~~~~--~~~~~~l~flYkL  459 (577)
                          |||||+|.||+|||+|+++||.+. +|.+||+|||..|+++...+| .|.||||.+.+..+  ..+.+.++|+|||
T Consensus       918 ----lGRGTsThDGiAIsYAtL~yf~~~~k~l~LFvTHfP~l~eie~~f~gqv~nyHmgyl~sedk~~~d~dsVtfLYkl  993 (1070)
T KOG0218|consen  918 ----LGRGTSTHDGIAISYATLKYFSELSKCLILFVTHFPMLGEIESGFPGQVRNYHMGYLESEDKTGEDWDSVTFLYKL  993 (1070)
T ss_pred             ----hcCCCccccchhHHHHHHHHHHHhhceeEEeeecCcchhhhhcCCCccccceeeeeeeeccccCCCchhhhhHHHH
Confidence                999999999999999999999998 999999999999999999887 58999999997432  3467889999999


Q ss_pred             cCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhHHH
Q psy13263        460 VPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQ  501 (577)
Q Consensus       460 ~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~~~~~  501 (577)
                      ++|+|.+|||++||++|++|.+||.||-.++++++......+
T Consensus       994 vrGlasrSyGlnVAklA~ip~sii~rA~siSeeleke~rn~r 1035 (1070)
T KOG0218|consen  994 VRGLASRSYGLNVAKLARIPKSIINRAFSISEELEKESRNER 1035 (1070)
T ss_pred             hhhhhhccccccHHHHhCCCHHHHHHHHHHHHHHHHHHhhHH
Confidence            999999999999999999999999999999999998776433

>PRK05399 DNA mismatch repair protein MutS; Provisional

Probab=100.00  E-value=7.1e-49  Score=453.76  Aligned_cols=213  Identities=26%  Similarity=0.363  Sum_probs=198.6

Q ss_pred             hhhccCcccccCccccc---cccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-cee
Q psy13263        270 YESQTPSGCFPDMSELL---KYFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVI  344 (577)
Q Consensus       270 ~~i~i~~GrhPlLe~~l---~~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~i  344 (577)
                      ..+.+.+||||+++..+   .|++|++..+.. +..+||||||||||+|++++++|+ +|||+|+||||.+|++++ |.|
T Consensus       575 ~~l~i~~~rHP~le~~~~~~~~vpnd~~l~~~~~~~iiTGpN~~GKSt~lr~v~l~~-ilAq~G~~VPa~~a~i~~~d~I  653 (854)
T PRK05399        575 PGIDIEEGRHPVVEQVLGGEPFVPNDCDLDEERRLLLITGPNMAGKSTYMRQVALIV-LLAQIGSFVPAESARIGIVDRI  653 (854)
T ss_pred             CCEEEEeccCcEEecccCCCceEecceeeCCCCcEEEEECCCCCCcHHHHHHHHHHH-HHHhcCCceeccceEecccCee
Confidence            35889999999998752   489999888743 456899999999999999999999 999999999999999999 999


Q ss_pred             eecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEE
Q psy13263        345 YSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVF  417 (577)
Q Consensus       345 f~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lf  417 (577)
                      |+++|.      ++|||+.||.+++.|+.+++.++||||||        +||||++.||.||||||++||.+. +|++||
T Consensus       654 ~triga~d~i~~g~STF~~E~~~~~~il~~at~~sLvllDE--------~GrGTs~~dg~aia~aile~l~~~~~~~~l~  725 (854)
T PRK05399        654 FTRIGASDDLASGRSTFMVEMTETANILNNATERSLVLLDE--------IGRGTSTYDGLSIAWAVAEYLHDKIGAKTLF  725 (854)
T ss_pred             eeccCcccccccCcccHHHHHHHHHHHHHhCCCCcEEEEec--------CCCCCCcchhHHHHHHHHHHHHhcCCceEEE
Confidence            999997      45999999999999999999999999999        999999999999999999999998 699999


Q ss_pred             ecchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Q psy13263        418 ATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR  496 (577)
Q Consensus       418 aTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~  496 (577)
                      +||||+|+.+...+++|.|+||.+.+.     +++++|+|||.+|+|++||||+||+++|||++||+||++++.++++.
T Consensus       726 aTH~~el~~l~~~~~~v~n~~m~~~~~-----~~~l~flYkl~~G~~~~SyGi~VA~laGlP~~VI~rA~~i~~~le~~  799 (854)
T PRK05399        726 ATHYHELTELEEKLPGVKNVHVAVKEH-----GGDIVFLHKVVPGAADKSYGIHVAKLAGLPASVIKRAREILAQLESA  799 (854)
T ss_pred             EechHHHHHHhhhcCCeEEEEEEEEEe-----CCeEEEEEEeCcCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHhhc
Confidence            999999999999999999999999864     36899999999999999999999999999999999999999999953

>PF00488 MutS_V: MutS domain V C-terminus

Probab=100.00  E-value=1.3e-48  Score=391.32  Aligned_cols=211  Identities=25%  Similarity=0.414  Sum_probs=182.5

Q ss_pred             hhccCcccccCccccc---ccccccccccccc--cccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-cee
Q psy13263        271 ESQTPSGCFPDMSELL---KYFENAFDHKEAS--SAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVI  344 (577)
Q Consensus       271 ~i~i~~GrhPlLe~~l---~~~~n~F~~~~a~--~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~i  344 (577)
                      .+.+++||||+++..+   ++++|++......  ..+||||||||||+|+|++++++ +|||+|+||||.++++++ |.|
T Consensus        11 ~l~i~~~~HPll~~~~~~~~~v~ndi~~~~~~~~~~iiTGpN~sGKSt~lk~i~~~~-ilaq~G~~VPA~~~~i~~~d~I   89 (235)
T PF00488_consen   11 SLKIKEGRHPLLEEKLENKKFVPNDIELSNNKSRIIIITGPNMSGKSTFLKQIGLIV-ILAQIGCFVPAESAEIPIFDRI   89 (235)
T ss_dssp             EEEEEEE--TTHHHHTTTSSC--EEEEESSSSSSEEEEESSTTSSHHHHHHHHHHHH-HHHTTT--BSSSEEEEE--SEE
T ss_pred             CEEEEeccCCEEeccccCCceecceeecCCCceeEEEEeCCCccchhhHHHHHHHHh-hhhhcCceeeecccccccccEE
Confidence            5788999999999875   4899999888654  57899999999999999999999 999999999999999999 999


Q ss_pred             eecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEE
Q psy13263        345 YSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVF  417 (577)
Q Consensus       345 f~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lf  417 (577)
                      |+++|.      +.|+|+.||.+++.++..++.+|||||||        |||||++.||.||++|++++|.++ +|++||
T Consensus        90 ~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~sLvliDE--------~g~gT~~~eg~ai~~aile~l~~~~~~~~i~  161 (235)
T PF00488_consen   90 FTRIGDDDSIESGLSTFMAEMKRLSSILRNATEKSLVLIDE--------LGRGTNPEEGIAIAIAILEYLLEKSGCFVII  161 (235)
T ss_dssp             EEEES---SSTTSSSHHHHHHHHHHHHHHH--TTEEEEEES--------TTTTSSHHHHHHHHHHHHHHHHHTTT-EEEE
T ss_pred             EeecccccccccccccHHHhHHHHHhhhhhcccceeeeccc--------ccCCCChhHHHHHHHHHHHHHHHhccccEEE
Confidence            999876      34999999999999999999999999999        999999999999999999999995 999999


Q ss_pred             ecchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy13263        418 ATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEA  495 (577)
Q Consensus       418 aTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~  495 (577)
                      ||||++|.++...+++|.++||++...+     ++++|+|+|.+|++..|||+++|+++|+|++||+||++++++|++
T Consensus       162 ~TH~~~l~~~~~~~~~v~~~~~~~~~~~-----~~~~f~Ykl~~G~~~~S~ai~iA~~~g~p~~II~rA~~i~~~l~~  234 (235)
T PF00488_consen  162 ATHFHELAELLERNPNVQNYHMEVEEDN-----DSLTFTYKLKEGICSSSYAIEIAKLAGLPEEIIERAKEILKQLEE  234 (235)
T ss_dssp             EES-GGGGGHHHHSTTEEEEEEEEEEET-----TEEEEEEEEEES--SSTCHHHHHHHTT--HHHHHHHHHHHHHHHT
T ss_pred             EeccchhHHHhhhCccccccceeeeeec-----cccceeEEEeECCCCCcHHHHHHHHhCcCHHHHHHHHHHHHHHhc
Confidence            9999999999998999999999999653     699999999999999999999999999999999999999999985

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=100.00  E-value=6.6e-43  Score=346.81  Aligned_cols=204  Identities=26%  Similarity=0.393  Sum_probs=185.6

Q ss_pred             cCcccccCccccc--ccccccccccc--cccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecc
Q psy13263        274 TPSGCFPDMSELL--KYFENAFDHKE--ASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEA  348 (577)
Q Consensus       274 i~~GrhPlLe~~l--~~~~n~F~~~~--a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~i  348 (577)
                      +.+||||+++...  ++++|++....  .+..+++|||++||++|++++++++ +|+|+|+||||.++++++ |.||+++
T Consensus         2 ~~~~rHPll~~~~~~~~v~ndi~l~~~~~~~~~itG~n~~gKs~~l~~i~~~~-~la~~G~~vpa~~~~i~~~~~i~~~~   80 (218)
T cd03286           2 FEELRHPCLNASTASSFVPNDVDLGATSPRILVLTGPNMGGKSTLLRTVCLAV-IMAQMGMDVPAKSMRLSLVDRIFTRI   80 (218)
T ss_pred             cccccCCEEecccCCCeEEeeeEEeecCCcEEEEECCCCCchHHHHHHHHHHH-HHHHcCCccCccccEeccccEEEEec
Confidence            5789999997543  48888877654  4567899999999999999999999 999999999999999999 9999998


Q ss_pred             cc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecch
Q psy13263        349 QK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHY  421 (577)
Q Consensus       349 G~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy  421 (577)
                      |.      ++|+|+.||.+++.|+..++.++||||||        +||||++.||.+|+++|+++|.+. +|.+||+|||
T Consensus        81 ~~~d~~~~~~StF~~e~~~~~~il~~~~~~sLvLlDE--------~~~Gt~~~dg~~la~ail~~L~~~~~~~~i~~TH~  152 (218)
T cd03286          81 GARDDIMKGESTFMVELSETANILRHATPDSLVILDE--------LGRGTSTHDGYAIAHAVLEYLVKKVKCLTLFSTHY  152 (218)
T ss_pred             CcccccccCcchHHHHHHHHHHHHHhCCCCeEEEEec--------ccCCCCchHHHHHHHHHHHHHHHhcCCcEEEEecc
Confidence            76      44999999999999999999999999999        999999999999999999999998 9999999999


Q ss_pred             HHHHHHhhcCCCcccccceeeeecC-CCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHH
Q psy13263        422 HSVARRLREEPNVAFEYMSYIEDKR-NDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFG  486 (577)
Q Consensus       422 ~eL~~l~~~~~~V~n~hm~~~~~~~-~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA  486 (577)
                      ++|...+..+++|.++||++...+. +...++++|+|||.+|+++.|||+++|+++|+|++||+||
T Consensus       153 ~el~~~~~~~~~v~~~~m~~~~~~~~~~~~~~~~~~Ykl~~G~~~~s~al~~A~~~g~p~~vi~rA  218 (218)
T cd03286         153 HSLCDEFHEHGGVRLGHMACAVKNESDPTIRDITFLYKLVAGICPKSYGLYVALMAGIPDGVVERA  218 (218)
T ss_pred             HHHHHHhhcCcceEEEEEEEEEeccccCCCCceEEEEEECcCCCCCcHHHHHHHHhCcCHHHHhcC
Confidence            9999999888999999999986431 2234789999999999999999999999999999999997

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

>KOG0220|consensus

Probab=100.00  E-value=5.9e-43  Score=382.06  Aligned_cols=253  Identities=21%  Similarity=0.265  Sum_probs=212.0

Q ss_pred             hccCcccccCcccccc--ccccccccccccc-ccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeec
Q psy13263        272 SQTPSGCFPDMSELLK--YFENAFDHKEASS-AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSE  347 (577)
Q Consensus       272 i~i~~GrhPlLe~~l~--~~~n~F~~~~a~~-~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~  347 (577)
                      +.|.+||||+|+....  ++.|+.....+++ .+||||||+||++|+||+++++ |||||||||||.+|.|++ ++||+|
T Consensus       592 laI~qGRHPILe~i~~ek~i~N~t~~t~~s~f~IITGPNMsGKSTYLKQvAl~~-IMAQIGc~IPA~YaS~pIf~RIFtR  670 (867)
T KOG0220|consen  592 LAIKQGRHPILEKISAEKPIANNTYVTEGSNFLIITGPNMSGKSTYLKQVALCQ-IMAQIGSYVPAEYASFRVFKRIFTR  670 (867)
T ss_pred             eeeccCCCchhhhhcccCcccCcceeecccceEEEECCCCCcchHHHHHHHHHH-HHHHhccCcchhhccchHHHHHHHH
Confidence            7889999999998664  5667666666555 4577999999999999999999 999999999999999999 999999


Q ss_pred             ccccc------hhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecch
Q psy13263        348 AQKKQ------KKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHY  421 (577)
Q Consensus       348 iG~~q------StF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy  421 (577)
                      ||..+      |+|+.||++++.|+.+++.+|||+|||        ||||||+.||+||+|||||||+..+++|+|||||
T Consensus       671 mg~nDele~NsS~F~sEMke~A~Ilq~a~~~SLiVlDE--------LgR~TSteeGiaityAvCE~lL~LkayTflATHF  742 (867)
T KOG0220|consen  671 MGTNDELERNSSTFMSEMKEAAYILQNANKNSLIVLDE--------LGRGTSTEEGIAITYAVCEYLLSLKAYTFLATHF  742 (867)
T ss_pred             hcCchhhhhchhHHHHHHHHHHHHHHhCCcCcEEEEhh--------hccCCccccchhhHHHHHHHHHHhhHhHHHHHHH
Confidence            99733      999999999999999999999999999        9999999999999999999999999999999999


Q ss_pred             HHHHHHhhcCCCcccccceeeeecCCCCcceEE-EEEeecCCCC-CCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhh-
Q psy13263        422 HSVARRLREEPNVAFEYMSYIEDKRNDGIDTIV-FLYKLVPGIC-PKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN-  498 (577)
Q Consensus       422 ~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~-flYkL~~G~~-~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~~-  498 (577)
                      .+|+.++.-+|+|.|+||.+...+     ++.. ..|||..|.. +.-||+.+|++.-+|.+|++.|+.+.-++..... 
T Consensus       743 ldIa~lan~~paVdnlHF~~q~~e-----Nssk~~k~kLsrg~~~~~~yG~~~vE~s~iPd~i~e~a~~~~t~i~A~v~~  817 (867)
T KOG0220|consen  743 LDIAAIANYYPAVDNLHFLVQTDE-----NSSKNKKYKLSRGLTEEKNYGLKAAEVSSLPDSIVEDAKEITTQITAQILQ  817 (867)
T ss_pred             HHHHHHhhcCccccceeeeeeecc-----cchhhhhhhhhhhhhhcccccceEEEEecCCHHHHHhhhHHHHHHHHHHHh
Confidence            999999999999999999998643     2333 3699999997 5799999999999999999999999988876543 


Q ss_pred             --------HHH-HHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHhhc
Q psy13263        499 --------LRQ-LFIHKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLE  541 (577)
Q Consensus       499 --------~~~-~~~~L~~~~~~~~~~ld~~~l~~l~~~L~~~~~~~~~~l~  541 (577)
                              .++ ....+..-+.+--.+.++   ..++.+|+.+++.|++++.
T Consensus       818 ~~rd~~~~~rq~~Vy~~a~~~~~t~gn~~e---~~~~~klk~l~k~~ve~~~  866 (867)
T KOG0220|consen  818 NQRDTPEMERQRAVYHLATRLVQTAGNSDE---DSLRIKLKNLKKKYKEDFP  866 (867)
T ss_pred             hccCchHHHHHHHHHHHHHHHHHhhCCCCc---HHHHHHHHHHHHHHHhhcc
Confidence                    111 111122211111122233   3368899999999998864

>KOG0219|consensus

Probab=100.00  E-value=1.4e-42  Score=383.74  Aligned_cols=214  Identities=22%  Similarity=0.351  Sum_probs=199.4

Q ss_pred             hhccCcccccCcccc--ccccccccccc--ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceee
Q psy13263        271 ESQTPSGCFPDMSEL--LKYFENAFDHK--EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIY  345 (577)
Q Consensus       271 ~i~i~~GrhPlLe~~--l~~~~n~F~~~--~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if  345 (577)
                      .+.+.++|||+++..  +.|++|+.+..  +.+..+|||||||||++|.++++.|. +|||||||||+..|.+++ |.||
T Consensus       614 rl~l~~~rHp~lE~Qd~~~fIpNdv~le~~~~~~~IiTGpNMGGKSTyir~~Gvi~-lmAQIGcfVPce~A~i~IvD~Il  692 (902)
T KOG0219|consen  614 RLELKQSRHPVLEGQDEIPFIPNDVVLEKGKCRMLIITGPNMGGKSTYIRQVGVIV-LMAQIGCFVPCESATISIVDGIL  692 (902)
T ss_pred             HHHHHhcccchhhccccCCCCCCccccccCCceEEEEeCCCcCccchhhhhhhHHH-HHHHhCCceehhhcCCchhhHHH
Confidence            567788999999864  45899976666  66778899999999999999999999 999999999999999999 9999


Q ss_pred             ecccccc------hhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEe
Q psy13263        346 SEAQKKQ------KKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFA  418 (577)
Q Consensus       346 ~~iG~~q------StF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfa  418 (577)
                      +++|.++      ||||.||-+++.|++.++.+|||+|||        +||||+++||++|||||.||++.+ +|++|||
T Consensus       693 ~RVGA~D~q~kG~STFM~Emleta~Ilr~at~~SliiiDE--------LGRGTSt~DGfgiAwai~ehi~~ki~cf~lfA  764 (902)
T KOG0219|consen  693 TRVGAGDSQLKGISTFMAEMLETASILRRATKNSLIIIDE--------LGRGTSTYDGFGIAWAIAEHIATKIGCFCLFA  764 (902)
T ss_pred             hhhccchhhhcchHHHHHHHHHHHHHHHhcCCCcEEEEec--------cCCCceeccCccHHHHHHHHHHHHHhHhHHHH
Confidence            9988643      999999999999999999999999999        999999999999999999999998 8999999


Q ss_pred             cchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhh
Q psy13263        419 THYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN  498 (577)
Q Consensus       419 THy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~~  498 (577)
                      ||||||+.+...++.|+|.||.+...+     +.++.+|++.+|+|+.||||+||+++|||+.||+.|++++.++++...
T Consensus       765 THfhElt~lae~~~~vKn~h~~a~i~~-----~~~~llY~V~~Gv~d~SFGi~VA~~a~fp~~vie~A~~~~~ele~~~~  839 (902)
T KOG0219|consen  765 THFHELTKLAEQLPTVKNLHVTAQIEN-----DDITLLYKVFEGVCDQSFGIHVAELVGFPEHVIEMAKQKAEELEDELV  839 (902)
T ss_pred             hHHHHHHhhhhhhhhhhhheeeeEecC-----cchhhHHHHhcccccCcchhhHHHHcCCChHHHHHHHHHHHHHHHHHh
Confidence            999999999999999999999999754     689999999999999999999999999999999999999999987654

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=100.00  E-value=3.8e-41  Score=335.08  Aligned_cols=206  Identities=27%  Similarity=0.427  Sum_probs=184.9

Q ss_pred             hccCcccccCccccc--cccccccccc--ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeee
Q psy13263        272 SQTPSGCFPDMSELL--KYFENAFDHK--EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYS  346 (577)
Q Consensus       272 i~i~~GrhPlLe~~l--~~~~n~F~~~--~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~  346 (577)
                      |.+++||||+++...  .+++|++...  ..+..+|+|||++||++|+++++.+. +++|+|+||||..++++. |.||+
T Consensus         1 ~~i~~~rHPlle~~~~~~~v~n~i~~~~~~g~~~~itG~N~~GKStll~~i~~~~-~la~~G~~v~a~~~~~~~~~~i~~   79 (222)
T cd03287           1 ILIKEGRHPMIESLLDKSFVPNDIHLSAEGGYCQIITGPNMGGKSSYIRQVALIT-IMAQIGSFVPASSATLSIFDSVLT   79 (222)
T ss_pred             CeeecccCCEEeccCCCCEEEEeEEEEecCCcEEEEECCCCCCHHHHHHHHHHHH-HHHhCCCEEEcCceEEeccceEEE
Confidence            357899999998755  4788877665  34567899999999999999999998 999999999999999999 99999


Q ss_pred             cccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEec
Q psy13263        347 EAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFAT  419 (577)
Q Consensus       347 ~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaT  419 (577)
                      ++|.      ++|+|+.||.+++.++..++.++||||||        +|+||++.||.+|+++++++|.+. +|.+|++|
T Consensus        80 ~~~~~d~~~~~~StF~~e~~~~~~il~~~~~~sLvllDE--------~~~gT~~~d~~~i~~~il~~l~~~~~~~~i~~T  151 (222)
T cd03287          80 RMGASDSIQHGMSTFMVELSETSHILSNCTSRSLVILDE--------LGRGTSTHDGIAIAYATLHYLLEEKKCLVLFVT  151 (222)
T ss_pred             EecCccccccccchHHHHHHHHHHHHHhCCCCeEEEEcc--------CCCCCChhhHHHHHHHHHHHHHhccCCeEEEEc
Confidence            9986      34899999999999999999999999999        999999999999999999999998 89999999


Q ss_pred             chHHHHHHhhcC-CCcccccceeeeecC---CCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHH
Q psy13263        420 HYHSVARRLREE-PNVAFEYMSYIEDKR---NDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFG  486 (577)
Q Consensus       420 Hy~eL~~l~~~~-~~V~n~hm~~~~~~~---~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA  486 (577)
                      ||++|.+++..+ ++|.|+||.+.....   ....++++|+|||.+|+++.|||++||+++|||++||+||
T Consensus       152 H~~~l~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~l~~~Ykl~~G~~~~s~a~~~a~~~g~p~~vi~rA  222 (222)
T cd03287         152 HYPSLGEILRRFEGSIRNYHMSYLESQKDFETSDSQSITFLYKLVRGLASRSFGLNVARLAGLPKSIISRA  222 (222)
T ss_pred             ccHHHHHHHHhcccCeEEEEEEEEEeccccccccCCcEEEEEEECcCCCCCcHHHHHHHHhCcCHHHHhcC
Confidence            999999988764 469999999885421   1245789999999999999999999999999999999997

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

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=100.00  E-value=7.3e-40  Score=375.61  Aligned_cols=279  Identities=14%  Similarity=0.137  Sum_probs=220.5

Q ss_pred             CCCccccCcccccccCcchhhHHHHHhhCcC--chhhhHh----hhhHHHhhhhhhhhhhhhhhhhccccC----ccCCc
Q psy13263        192 NPKTLYVPPEFLKKQTPCMGQWWTIKSQNFD--CVLFFKV----GKFYELFHMDAVIGADELACSYMKESG----CTGES  261 (577)
Q Consensus       192 d~sTl~Ipp~~l~~~TPl~rQ~~~lKa~~~D--~vLLfrv----G~FYElf~~DA~i~a~eLdl~~mkGsn----~~GKS  261 (577)
                      -++|+||.|..   +..+..++.++..+...  .-++.++    ....+.+ ..+......+|+.+.....    ....+
T Consensus       218 sg~t~y~ep~~---~~~ln~~l~~l~~~~~~~~~~il~~l~~~i~~~~~~l-~~~~~~l~~lD~l~a~a~~a~~~~~~~P  293 (782)
T PRK00409        218 SGATLYIEPQS---VVELNNEIRELRNKEEQEIERILKELSAKVAKNLDFL-KFLNKIFDELDFIFARARYAKALKATFP  293 (782)
T ss_pred             CCCEEEEEcHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCCccc
Confidence            35789998875   34445555555544333  1222222    2222222 1222222345555443322    12333


Q ss_pred             chhhhhhhhhhccCcccccCcccccccccccccccccc-cccccCCCCCCCchhHHHHHHHHHHHHHhcccccccc-cee
Q psy13263        262 TLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEAS-SAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQC-AHF  339 (577)
Q Consensus       262 tlLk~i~~~~i~i~~GrhPlLe~~l~~~~n~F~~~~a~-~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~-a~l  339 (577)
                      .+.   ....+.+.+||||++.. -.+++|++..+... ..+||||||||||+|+|++++++ +|+|+|+||||.. +.+
T Consensus       294 ~~~---~~~~i~l~~~rHPll~~-~~~Vpndi~l~~~~~~~iITGpN~gGKTt~lktigl~~-~maq~G~~vpa~~~~~i  368 (782)
T PRK00409        294 LFN---DEGKIDLRQARHPLLDG-EKVVPKDISLGFDKTVLVITGPNTGGKTVTLKTLGLAA-LMAKSGLPIPANEPSEI  368 (782)
T ss_pred             eEc---CCCcEEEcCcCCceecc-CceECceeEECCCceEEEEECCCCCCcHHHHHHHHHHH-HHHHhCCCcccCCCccc
Confidence            333   23358889999999864 34889999887543 46789999999999999999999 9999999999986 899


Q ss_pred             cc-ceeeecccccc------hhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcC
Q psy13263        340 GC-TVIYSEAQKKQ------KKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIG  412 (577)
Q Consensus       340 ~~-d~if~~iG~~q------StF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~  412 (577)
                      ++ |.||+++|+.|      |+|+.+|.++..++..++.++||||||        +|+||++.+|.+|+.+++++|.+.+
T Consensus       369 ~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~Il~~~~~~sLvLlDE--------~~~GtDp~eg~ala~aile~l~~~~  440 (782)
T PRK00409        369 PVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKADKNSLVLFDE--------LGAGTDPDEGAALAISILEYLRKRG  440 (782)
T ss_pred             cccceEEEecCCccchhhchhHHHHHHHHHHHHHHhCCcCcEEEecC--------CCCCCCHHHHHHHHHHHHHHHHHCC
Confidence            99 99999999754      899999999999998889999999999        9999999999999999999999999


Q ss_pred             CeEEEecchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy13263        413 CLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQ  492 (577)
Q Consensus       413 ~~~lfaTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~  492 (577)
                      |.+||+|||++|+.++...++|.|++|.++.       +++.|+|+|..|+++.||||+||+++|||++||++|++++..
T Consensus       441 ~~vIitTH~~el~~~~~~~~~v~~~~~~~d~-------~~l~~~Ykl~~G~~g~S~a~~iA~~~Glp~~ii~~A~~~~~~  513 (782)
T PRK00409        441 AKIIATTHYKELKALMYNREGVENASVEFDE-------ETLRPTYRLLIGIPGKSNAFEIAKRLGLPENIIEEAKKLIGE  513 (782)
T ss_pred             CEEEEECChHHHHHHHhcCCCeEEEEEEEec-------CcCcEEEEEeeCCCCCcHHHHHHHHhCcCHHHHHHHHHHHhh
Confidence            9999999999999999989999999998864       479999999999999999999999999999999999999876


Q ss_pred             HH
Q psy13263        493 ME  494 (577)
Q Consensus       493 le  494 (577)
                      -.
T Consensus       514 ~~  515 (782)
T PRK00409        514 DK  515 (782)
T ss_pred             hh
Confidence            43

>KOG0221|consensus

Probab=100.00  E-value=1.8e-40  Score=357.45  Aligned_cols=230  Identities=19%  Similarity=0.300  Sum_probs=204.9

Q ss_pred             CcchhhhhhhhhhccCcccccCcccccc-ccccccccc--ccccccccCCCCCCCchhHHHHHHHHHHHHHhcccccccc
Q psy13263        260 ESTLLTQLCNYESQTPSGCFPDMSELLK-YFENAFDHK--EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQC  336 (577)
Q Consensus       260 KStlLk~i~~~~i~i~~GrhPlLe~~l~-~~~n~F~~~--~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~  336 (577)
                      .+.+..+.+.  +.|++||||+++..++ |++|+...+  +.|..+|||||++||++|+|++++|+ +++|||+||||..
T Consensus       560 ~P~lv~e~~i--l~I~ngrh~l~e~~~dtfvPNst~iggdkgri~vITGpNasGKSiYlkqvgliv-fLahIGsFVPAe~  636 (849)
T KOG0221|consen  560 RPRLVPEVLI--LRIQNGRHPLMELCADTFVPNSTEIGGDKGRIKVITGPNASGKSIYLKQVGLIV-FLAHIGSFVPAEE  636 (849)
T ss_pred             CCccccHHHH--HHHHcCChhHHHHHHHhcCCCceeecCCCceEEEEeCCCCCCceEEEeechhhh-HHHhhccccchhh
Confidence            4445555443  6789999999998876 899977655  66777899999999999999999999 9999999999999


Q ss_pred             ceecc-ceeeecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHH
Q psy13263        337 AHFGC-TVIYSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFL  409 (577)
Q Consensus       337 a~l~~-d~if~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~  409 (577)
                      |++|+ |+||++|+.      +||||+.++.+++..+++|+.+|||||||        +|+||++.||.+|..+|+.|++
T Consensus       637 A~IGivDrI~tri~s~esv~~gqSTFmiD~~Qva~aLr~AT~~SLvlIDE--------fGKGT~tedGlsLlasvm~~w~  708 (849)
T KOG0221|consen  637 AEIGIVDRIFTRIHSCESVSLGQSTFMIDLNQVAKALRNATAQSLVLIDE--------FGKGTNTEDGLSLLASVMRHWL  708 (849)
T ss_pred             hhcchHHHHHHHhhhhhhhhhhhhHHHHhHHHHHHHHHHhhcCcEEEEhh--------ccCCccccccHHHHHHHHHHHH
Confidence            99999 999999875      78999999999999999999999999999        9999999999999999999999


Q ss_pred             hc---CCeEEEecchHHHHHH--hhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHH
Q psy13263        410 QI---GCLTVFATHYHSVARR--LREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK  484 (577)
Q Consensus       410 ~~---~~~~lfaTHy~eL~~l--~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~  484 (577)
                      ++   .++++++||||+|...  +...+-+++|.|.+...    +.+.|+|+||+.+|.+..|||+++|+.+|+|++||.
T Consensus       709 ~rg~~~PrifvcThfheL~ne~~L~~n~i~qfltm~vlr~----~ge~I~flyrv~~gl~k~sfal~~ak~~glp~~vV~  784 (849)
T KOG0221|consen  709 ARGPTCPRIFVCTHFHELVNEQLLPQNPIVQFLTMEVLRE----DGEDIVFLYRVCEGLAKASFALHTAKQAGLPDKVVA  784 (849)
T ss_pred             hcCCCCCeEEEeccHHHhhhhccCCcchhhhhhhHHHHHh----ccCCeEEEEEeccchhhhcccchhHhhcCCCHHHHH
Confidence            98   3599999999999985  45566788999988853    247899999999999999999999999999999999


Q ss_pred             HHHHHHHHHHHhhhHHHHHH
Q psy13263        485 FGTTVAFQMEARHNLRQLFI  504 (577)
Q Consensus       485 rA~ei~~~le~~~~~~~~~~  504 (577)
                      ||++++..++.+....+...
T Consensus       785 Ra~~v~~ai~sg~~vk~~k~  804 (849)
T KOG0221|consen  785 RAKEVSDAIRSGKPVKPVKD  804 (849)
T ss_pred             HHHHHHHHHHcCCCchhhhh
Confidence            99999999999987654443

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=100.00  E-value=7.5e-39  Score=318.11  Aligned_cols=208  Identities=23%  Similarity=0.342  Sum_probs=186.8

Q ss_pred             cCcccccCcccc--ccccccccccc--ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecc
Q psy13263        274 TPSGCFPDMSEL--LKYFENAFDHK--EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEA  348 (577)
Q Consensus       274 i~~GrhPlLe~~--l~~~~n~F~~~--~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~i  348 (577)
                      +.+||||+++..  -++++|++...  ..+..+++|||+|||++|+++++++. +|+|+|+||||..+.+++ +.+|.++
T Consensus         2 ~~~~~hpll~~~~~~~~v~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~-~la~~g~~vpa~~~~~~~~~~il~~~   80 (222)
T cd03285           2 LKEARHPCVEAQDDVAFIPNDVTLTRGKSRFLIITGPNMGGKSTYIRQIGVIV-LMAQIGCFVPCDSADIPIVDCILARV   80 (222)
T ss_pred             ccccCCCEEeccCCCCeEEeeEEEeecCCeEEEEECCCCCChHHHHHHHHHHH-HHHHhCCCcCcccEEEeccceeEeee
Confidence            578999999862  23778877665  34556899999999999999999998 999999999999999999 9999987


Q ss_pred             cc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecch
Q psy13263        349 QK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHY  421 (577)
Q Consensus       349 G~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy  421 (577)
                      |.      +.|+|+.||.+++.++..++.++||||||        +||||++.||.+++++++++|.+. ++.+||+||+
T Consensus        81 ~l~d~~~~~lS~~~~e~~~~a~il~~~~~~sLvLLDE--------p~~gT~~lD~~~~~~~il~~l~~~~~~~vlisTH~  152 (222)
T cd03285          81 GASDSQLKGVSTFMAEMLETAAILKSATENSLIIIDE--------LGRGTSTYDGFGLAWAIAEYIATQIKCFCLFATHF  152 (222)
T ss_pred             ccccchhcCcChHHHHHHHHHHHHHhCCCCeEEEEec--------CcCCCChHHHHHHHHHHHHHHHhcCCCeEEEEech
Confidence            75      34999999999999988788999999999        999999999999999999999875 8999999999


Q ss_pred             HHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHH
Q psy13263        422 HSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQM  493 (577)
Q Consensus       422 ~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~l  493 (577)
                      ++|.++....+.+.++||.+....   ..+++.|+|||.+|+++.|||+++|+++|||++||+||+++++++
T Consensus       153 ~el~~~~~~~~~i~~g~~~~~~~~---~~~~~~~~Y~l~~G~~~~s~a~~~a~~~g~p~~vi~~A~~~~~~~  221 (222)
T cd03285         153 HELTALADEVPNVKNLHVTALTDD---ASRTLTMLYKVEKGACDQSFGIHVAELANFPKEVIEMAKQKALEL  221 (222)
T ss_pred             HHHHHHhhcCCCeEEEEEEEEEeC---CCCcEeEEEEEeeCCCCCcHHHHHHHHhCcCHHHHHHHHHHHHhc
Confidence            999999988889999999877532   246899999999999999999999999999999999999999876

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

>TIGR01069 mutS2 MutS2 family protein

Probab=100.00  E-value=3.6e-38  Score=361.04  Aligned_cols=285  Identities=15%  Similarity=0.148  Sum_probs=224.4

Q ss_pred             CCCccccCcccccccCcchhhHHHHHhhCcC--chhhhH----hhhhHHHhhhhhhhhhhhhhhhhccccCc-cCCcchh
Q psy13263        192 NPKTLYVPPEFLKKQTPCMGQWWTIKSQNFD--CVLFFK----VGKFYELFHMDAVIGADELACSYMKESGC-TGESTLL  264 (577)
Q Consensus       192 d~sTl~Ipp~~l~~~TPl~rQ~~~lKa~~~D--~vLLfr----vG~FYElf~~DA~i~a~eLdl~~mkGsn~-~GKStlL  264 (577)
                      -++|+||.|..   ++.+..++.++..+...  ..|+.+    +......+..... ....+|+.+.+.... ..+.+++
T Consensus       213 sg~t~~~ep~~---~~~ln~~l~~l~~~~~~e~~~il~~L~~~i~~~~~~l~~~~~-~l~~lD~l~a~a~~a~~~~~~~P  288 (771)
T TIGR01069       213 SGETFYIEPQA---IVKLNNKLAQLKNEEECEIEKILRTLSEKVQEYLLELKFLFK-EFDFLDSLQARARYAKAVKGEFP  288 (771)
T ss_pred             CCCEEEEEcHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHCCCeec
Confidence            46899999875   45556666666655333  122222    2333332222222 223456655443321 1112223


Q ss_pred             hhhhhhhhccCcccccCccccccccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhcccccccc-ceecc-
Q psy13263        265 TQLCNYESQTPSGCFPDMSELLKYFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQC-AHFGC-  341 (577)
Q Consensus       265 k~i~~~~i~i~~GrhPlLe~~l~~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~-a~l~~-  341 (577)
                      .......+.+.+++||++.. -.+++|+|..... +..+|+|||+||||+|+++++.+. +|+|.|+|||+.. +.+++ 
T Consensus       289 ~~~~~~~i~l~~~rhPll~~-~~~vp~di~l~~~~~~liItGpNg~GKSTlLK~i~~~~-l~aq~G~~Vpa~~~~~~~~~  366 (771)
T TIGR01069       289 MPSFTGKIILENARHPLLKE-PKVVPFTLNLKFEKRVLAITGPNTGGKTVTLKTLGLLA-LMFQSGIPIPANEHSEIPYF  366 (771)
T ss_pred             eecCCCCEEEccccCceecC-CceEeceeEeCCCceEEEEECCCCCCchHHHHHHHHHH-HHHHhCCCccCCccccccch
Confidence            22222368889999999863 2478899988765 567899999999999999999998 9999999999986 78998 


Q ss_pred             ceeeecccccc------hhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeE
Q psy13263        342 TVIYSEAQKKQ------KKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLT  415 (577)
Q Consensus       342 d~if~~iG~~q------StF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~  415 (577)
                      |.+|+++|..+      |+|+.+|.++..++..++.++||||||        +|+||++.+|.+|+++++++|.+++|.+
T Consensus       367 d~i~~~i~~~~si~~~LStfS~~m~~~~~il~~~~~~sLvLlDE--------~g~GtD~~eg~ala~aiLe~l~~~g~~v  438 (771)
T TIGR01069       367 EEIFADIGDEQSIEQNLSTFSGHMKNISAILSKTTENSLVLFDE--------LGAGTDPDEGSALAISILEYLLKQNAQV  438 (771)
T ss_pred             hheeeecChHhHHhhhhhHHHHHHHHHHHHHHhcCCCcEEEecC--------CCCCCCHHHHHHHHHHHHHHHHhcCCEE
Confidence            99999988743      999999999999998889999999999        9999999999999999999999999999


Q ss_pred             EEecchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy13263        416 VFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEA  495 (577)
Q Consensus       416 lfaTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~  495 (577)
                      ||+|||++|..+....++|.|++|.++.       +++.|+|+|.+|+++.||||+||+++|||++||++|++++.....
T Consensus       439 iitTH~~eL~~~~~~~~~v~~~~~~~d~-------~~l~p~Ykl~~G~~g~S~a~~iA~~~Glp~~ii~~A~~~~~~~~~  511 (771)
T TIGR01069       439 LITTHYKELKALMYNNEGVENASVLFDE-------ETLSPTYKLLKGIPGESYAFEIAQRYGIPHFIIEQAKTFYGEFKE  511 (771)
T ss_pred             EEECChHHHHHHhcCCCCeEEeEEEEcC-------CCCceEEEECCCCCCCcHHHHHHHHhCcCHHHHHHHHHHHHhhHH
Confidence            9999999999998889999999999875       379999999999999999999999999999999999999987654


Q ss_pred             hh
Q psy13263        496 RH  497 (577)
Q Consensus       496 ~~  497 (577)
                      ..
T Consensus       512 ~~  513 (771)
T TIGR01069       512 EI  513 (771)
T ss_pred             HH
Confidence            43

Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=100.00  E-value=8.7e-37  Score=302.03  Aligned_cols=203  Identities=24%  Similarity=0.347  Sum_probs=185.4

Q ss_pred             cCcccccCccccc---cccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecc
Q psy13263        274 TPSGCFPDMSELL---KYFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEA  348 (577)
Q Consensus       274 i~~GrhPlLe~~l---~~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~i  348 (577)
                      |.+||||+++..+   .+++|+++.... +..+++|||++|||+|+++++.+. +++|+|+++||..+.++. +.+|+++
T Consensus         2 i~~~~hp~~~~~~~~~~~v~n~~~l~~~~~~~~l~Gpn~sGKstllr~i~~~~-~l~~~g~~vp~~~~~i~~~~~i~~~~   80 (216)
T cd03284           2 IEGGRHPVVEQVLDNEPFVPNDTELDPERQILLITGPNMAGKSTYLRQVALIA-LLAQIGSFVPASKAEIGVVDRIFTRI   80 (216)
T ss_pred             cccccCCEEeeccCCCceEeeeEEecCCceEEEEECCCCCChHHHHHHHHHHH-HHhccCCeeccccceecceeeEeccC
Confidence            5789999998764   378888876643 456799999999999999999988 999999999999999999 9999987


Q ss_pred             cc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecch
Q psy13263        349 QK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHY  421 (577)
Q Consensus       349 G~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy  421 (577)
                      +.      ++|+|+.||.++..++..++.++||||||        +|+||++.||.+++++++++|.+. ++.+|++||+
T Consensus        81 ~~~~~ls~g~s~f~~e~~~l~~~l~~~~~~~llllDE--------p~~gt~~lD~~~~~~~il~~l~~~~~~~vi~~TH~  152 (216)
T cd03284          81 GASDDLAGGRSTFMVEMVETANILNNATERSLVLLDE--------IGRGTSTYDGLSIAWAIVEYLHEKIGAKTLFATHY  152 (216)
T ss_pred             CchhhhccCcchHHHHHHHHHHHHHhCCCCeEEEEec--------CCCCCChHHHHHHHHHHHHHHHhccCCcEEEEeCc
Confidence            64      56999999999999998899999999999        999999999999999999999998 9999999999


Q ss_pred             HHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHH
Q psy13263        422 HSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVA  490 (577)
Q Consensus       422 ~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~  490 (577)
                      ++|.++....+.+.++||.+...     .++++|+|+|.+|.++.|||+.+|+++|+|++||+||++++
T Consensus       153 ~~l~~l~~~~~~v~~~~~~~~~~-----~~~l~~~ykl~~G~~~~s~a~~~a~~~g~~~~ii~rA~~~~  216 (216)
T cd03284         153 HELTELEGKLPRVKNFHVAVKEK-----GGGVVFLHKIVEGAADKSYGIEVARLAGLPEEVIERAREIL  216 (216)
T ss_pred             HHHHHHhhcCCCeEEEEEEEEee-----CCeEEEEEEECcCCCCCcHHHHHHHHhCcCHHHHHHHHHhC
Confidence            99999998889999999988754     36899999999999999999999999999999999999873

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=100.00  E-value=5.2e-36  Score=295.92  Aligned_cols=196  Identities=21%  Similarity=0.333  Sum_probs=175.5

Q ss_pred             cCcccccCccccc-cccccccccccc--ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeeccc
Q psy13263        274 TPSGCFPDMSELL-KYFENAFDHKEA--SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQ  349 (577)
Q Consensus       274 i~~GrhPlLe~~l-~~~~n~F~~~~a--~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG  349 (577)
                      +++||||+++... .+++|+|..+..  +..+|+|||++|||+|+++++.+. +|+|+|+|+||..++++. |++|++++
T Consensus         2 i~~~rHPll~~~~~~~vpnd~~l~~~~~~~~~itGpNg~GKStlLk~i~~~~-~la~~G~~v~a~~~~~~~~d~i~~~l~   80 (213)
T cd03281           2 IQGGRHPLLELFVDSFVPNDTEIGGGGPSIMVITGPNSSGKSVYLKQVALIV-FLAHIGSFVPADSATIGLVDKIFTRMS   80 (213)
T ss_pred             cccccCCEEeccCCceEcceEEecCCCceEEEEECCCCCChHHHHHHHHHHH-HHHhCCCeeEcCCcEEeeeeeeeeeeC
Confidence            5789999998633 489999988765  667899999999999999999998 899999999999999999 99999887


Q ss_pred             cc------chhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc---CCeEEEecc
Q psy13263        350 KK------QKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI---GCLTVFATH  420 (577)
Q Consensus       350 ~~------qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~---~~~~lfaTH  420 (577)
                      ..      .|+|+.||.++..++..++.++||||||        +|+||++.+|.+++++++++|.+.   ++.+||+||
T Consensus        81 ~~~si~~~~S~f~~el~~l~~~l~~~~~~slvllDE--------~~~gtd~~~~~~~~~ail~~l~~~~~~~~~vli~TH  152 (213)
T cd03281          81 SRESVSSGQSAFMIDLYQVSKALRLATRRSLVLIDE--------FGKGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTH  152 (213)
T ss_pred             CccChhhccchHHHHHHHHHHHHHhCCCCcEEEecc--------ccCCCCHHHHHHHHHHHHHHHHhcCCCCcEEEEEcC
Confidence            63      4899999999999999999999999999        999999999999999999999875   358999999


Q ss_pred             hHHHHHHhh--cCCCcccccceeeeecC-CCCcceEEEEEeecCCCCCCcHHHHHHHHcCC
Q psy13263        421 YHSVARRLR--EEPNVAFEYMSYIEDKR-NDGIDTIVFLYKLVPGICPKSFGFNVAELAGI  478 (577)
Q Consensus       421 y~eL~~l~~--~~~~V~n~hm~~~~~~~-~~~~~~l~flYkL~~G~~~~SyGi~vArlaGl  478 (577)
                      |+++...+.  ..+.+.++||++..+.. .+..++++|+|||.+|+++.|||++||+++|+
T Consensus       153 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~l~~G~~~~s~a~~~a~~~g~  213 (213)
T cd03281         153 FHELFNRSLLPERLKIKFLTMEVLLNPTSTSPNEDITYLYRLVPGLADTSFAIHCAKLAGI  213 (213)
T ss_pred             hHHHHHhhhhccCCceEEEEEEEEEcCCccCCCCcEEEEEEEeeCCCCCCHHHHHHHHcCC
Confidence            999999876  57899999999976421 12357999999999999999999999999996

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

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=100.00  E-value=1.1e-34  Score=285.15  Aligned_cols=191  Identities=17%  Similarity=0.192  Sum_probs=172.5

Q ss_pred             cCcccccCcccccc-cccccccccc--cccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeeccc
Q psy13263        274 TPSGCFPDMSELLK-YFENAFDHKE--ASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQ  349 (577)
Q Consensus       274 i~~GrhPlLe~~l~-~~~n~F~~~~--a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG  349 (577)
                      |++||||+++...+ ++.|+++...  .+..+++|||++|||+|+++++.++ +|+|+|+||||..+++++ +.||+.++
T Consensus         2 i~~~~hpll~~~~~~~v~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~-~la~~G~~vpa~~~~l~~~d~I~~~~~   80 (204)
T cd03282           2 IRDSRHPILDRDKKNFIPNDIYLTRGSSRFHIITGPNMSGKSTYLKQIALLA-IMAQIGCFVPAEYATLPIFNRLLSRLS   80 (204)
T ss_pred             cccccCCeEeccCCcEEEeeeEEeeCCCcEEEEECCCCCCHHHHHHHHHHHH-HHHHcCCCcchhhcCccChhheeEecC
Confidence            57899999986443 7777666554  3557899999999999999999999 999999999999999999 99999877


Q ss_pred             cc------chhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHH
Q psy13263        350 KK------QKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHS  423 (577)
Q Consensus       350 ~~------qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~e  423 (577)
                      ..      .|+|+.||.++..++..++.++||||||        +|+||++.||.+++++++++|.+.++.+|++||+++
T Consensus        81 ~~d~~~~~~S~fs~e~~~~~~il~~~~~~~lvllDE--------~~~gt~~~~~~~l~~~il~~l~~~~~~~i~~TH~~~  152 (204)
T cd03282          81 NDDSMERNLSTFASEMSETAYILDYADGDSLVLIDE--------LGRGTSSADGFAISLAILECLIKKESTVFFATHFRD  152 (204)
T ss_pred             CccccchhhhHHHHHHHHHHHHHHhcCCCcEEEecc--------ccCCCCHHHHHHHHHHHHHHHHhcCCEEEEECChHH
Confidence            53      3899999999999998899999999999        999999999999999999999999999999999999


Q ss_pred             HHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCC-CcHHHHHHHHcC
Q psy13263        424 VARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICP-KSFGFNVAELAG  477 (577)
Q Consensus       424 L~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~-~SyGi~vArlaG  477 (577)
                      +.+++...++|.++||.+....    ++++.|+|||.+|+|. .||||+|||++.
T Consensus       153 l~~~~~~~~~v~~~~~~~~~~~----~~~~~~~ykl~~G~~~~~~~g~~~a~~~~  203 (204)
T cd03282         153 IAAILGNKSCVVHLHMKAQSIN----SNGIEMAYKLVLGLYRIVDDGIRFVRVLA  203 (204)
T ss_pred             HHHHhhcCCCeEEEEEEEEEcC----CCceeeEEEEeeCCCCCCccHHHHHHHhh
Confidence            9999988899999999988642    2688999999999999 999999999864

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

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=100.00  E-value=9.9e-34  Score=272.98  Aligned_cols=175  Identities=30%  Similarity=0.470  Sum_probs=163.6

Q ss_pred             cccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecccc------cchhhhhchhhhHHhhhcCCCceE
Q psy13263        302 GNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQK------KQKKYVLEVPSKYASKAKSNHQRV  374 (577)
Q Consensus       302 ~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG~------~qStF~~Em~e~~~il~~a~~~sL  374 (577)
                      ++||||+||||+|+|+++++. +|+|+|+||||..+.++. |.+|..++.      +.|+|+.||.+++.++..++.++|
T Consensus         3 ~ltG~N~~GKst~l~~i~~~~-~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~l   81 (185)
T smart00534        3 IITGPNMGGKSTYLRQVGLIV-IMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSL   81 (185)
T ss_pred             EEECCCCCcHHHHHHHHHHHH-HHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeE
Confidence            589999999999999999998 999999999999999999 999988764      349999999999999988899999


Q ss_pred             EeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHhhcCCCcccccceeeeecCCCCcceE
Q psy13263        375 ATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTI  453 (577)
Q Consensus       375 VLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l  453 (577)
                      +|+||        +++||++.+|.+++++++++|.++ ++.+|++||+++|.++....++|.++||.+...+     +.+
T Consensus        82 lllDE--------p~~g~d~~~~~~~~~~~l~~l~~~~~~~iii~TH~~~l~~~~~~~~~v~~~~~~~~~~~-----~~~  148 (185)
T smart00534       82 VLLDE--------LGRGTSTYDGVAIAAAVLEYLLEKIGALTLFATHYHELTKLADEHPGVRNLHMSADEET-----ENL  148 (185)
T ss_pred             EEEec--------CCCCCCHHHHHHHHHHHHHHHHhcCCCeEEEEecHHHHHHHhhcCccceEEEEEEEEec-----Cce
Confidence            99999        999999999999999999999985 8999999999999999888889999999988642     579


Q ss_pred             EEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHH
Q psy13263        454 VFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVA  490 (577)
Q Consensus       454 ~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~  490 (577)
                      .|+|+|.+|++..|||+++|+++|+|++||+||++++
T Consensus       149 ~~~Y~l~~G~~~~s~a~~~a~~~g~~~~i~~~a~~~~  185 (185)
T smart00534      149 TFLYKLTPGVAGKSYGIEVAKLAGLPKEVIERAKEIL  185 (185)
T ss_pred             eEEEEEeECCCCCcHHHHHHHHhCCCHHHHHHHHHhC
Confidence            9999999999999999999999999999999999873

>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

Probab=99.97  E-value=2e-31  Score=302.66  Aligned_cols=202  Identities=17%  Similarity=0.195  Sum_probs=184.6

Q ss_pred             hhhccCcccccCccccccccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccc-eecc-ceeee
Q psy13263        270 YESQTPSGCFPDMSELLKYFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCA-HFGC-TVIYS  346 (577)
Q Consensus       270 ~~i~i~~GrhPlLe~~l~~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a-~l~~-d~if~  346 (577)
                      ..+.+..++||++...   +++.+..+.. +...|||||+||||+.+++++++. +|+|+|.++||... ++++ +.||+
T Consensus       291 ~~l~l~~~~HPll~~~---v~~~i~~~~e~~~l~ITGpN~GGKtvtLKTlgl~~-lm~q~gl~i~a~~gsei~~F~~i~a  366 (753)
T COG1193         291 GVLELLDARHPLLKED---VPNDLELGEELDRLIITGPNTGGKTVTLKTLGLLR-LMAQSGLPIPALEGSELPVFVKIFA  366 (753)
T ss_pred             ceEEeccccCccCccc---cccccccccccceeeEecCCCCcceehHHHHHHHH-HHHHcCCCeeccCCCcchhHHHhhh
Confidence            3578899999999875   5566655544 446789999999999999999999 99999999999875 9999 99999


Q ss_pred             cccccc------hhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecc
Q psy13263        347 EAQKKQ------KKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATH  420 (577)
Q Consensus       347 ~iG~~q------StF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTH  420 (577)
                      +||+.|      |||..+|..+..|+..++  +||++||        ||.||+|.+|.|+|.+|+++|.+++|.++.+||
T Consensus       367 DIGDeQsIeqsLSTFSshm~~i~~il~~~d--sLvl~DE--------lg~GTdp~EgaaLai~ile~l~~~~~~~~~tTH  436 (753)
T COG1193         367 DIGDEQSIEQSLSTFSSHMTNIVEILEKAD--SLVLFDE--------LGSGTDPDEGAALAIAILEDLLEKPAKIVATTH  436 (753)
T ss_pred             ccCcHHHHHHHHhhhHHHHHHHHHHHhhcc--hhHHHHH--------hhcCCCcchhHHHHHHHHHHHHhcccceehHhh
Confidence            999966      999999999999985455  9999999        999999999999999999999999999999999


Q ss_pred             hHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHH
Q psy13263        421 YHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQ  492 (577)
Q Consensus       421 y~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~  492 (577)
                      |.+|..+...+++|.|..|+++.       +++.++|+|..|+.+.||||.+|..+|||..||++|+.....
T Consensus       437 ~~elk~~~~~~~~v~nas~~fd~-------etL~ptY~l~~G~~g~S~Af~ia~rlGl~~~iie~a~~~~g~  501 (753)
T COG1193         437 YRELKALAAEREGVENASMEFDA-------ETLRPTYRLLEGVPGRSNAFDIALRLGLPEPIIEEAKTEFGE  501 (753)
T ss_pred             HHHHHHHHhcchhhhchhhhhhH-------HHhhHHHHHhcCCcccchHHHHHHHcCCCHHHHHHHHHhcCc
Confidence            99999999999999999999986       489999999999999999999999999999999999988844

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=99.96  E-value=1.1e-28  Score=241.39  Aligned_cols=190  Identities=14%  Similarity=0.124  Sum_probs=170.2

Q ss_pred             cCcccccCcccccccccccccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccc---
Q psy13263        274 TPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQK---  350 (577)
Q Consensus       274 i~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~---  350 (577)
                      ++++|||+++. -+++.|+++....+..+++|||++|||+|+++++.+. ++++.|++|||..+.+..+.+|..+..   
T Consensus         2 ~~~~~hp~~~~-~~~v~n~i~l~~g~~~~ltGpNg~GKSTllr~i~~~~-~l~~~G~~v~a~~~~~q~~~l~~~~~~~d~   79 (199)
T cd03283           2 AKNLGHPLIGR-EKRVANDIDMEKKNGILITGSNMSGKSTFLRTIGVNV-ILAQAGAPVCASSFELPPVKIFTSIRVSDD   79 (199)
T ss_pred             CcccCCCeecC-CCeecceEEEcCCcEEEEECCCCCChHHHHHHHHHHH-HHHHcCCEEecCccCcccceEEEeccchhc
Confidence            57899999983 3578898888777777899999999999999999988 899999999998887777778876543   


Q ss_pred             ---cchhhhhchhhhHHhhhcCC--CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHH
Q psy13263        351 ---KQKKYVLEVPSKYASKAKSN--HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVA  425 (577)
Q Consensus       351 ---~qStF~~Em~e~~~il~~a~--~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~  425 (577)
                         +.|+|..|+.++..++...+  ...|+|+||        .++||++.++..+.+++++.|.+.++.+|++||++++.
T Consensus        80 l~~~~s~~~~e~~~~~~iL~~~~~~~p~llllDE--------p~~glD~~~~~~l~~~ll~~l~~~~~tiiivTH~~~~~  151 (199)
T cd03283          80 LRDGISYFYAELRRLKEIVEKAKKGEPVLFLLDE--------IFKGTNSRERQAASAAVLKFLKNKNTIGIISTHDLELA  151 (199)
T ss_pred             cccccChHHHHHHHHHHHHHhccCCCCeEEEEec--------ccCCCCHHHHHHHHHHHHHHHHHCCCEEEEEcCcHHHH
Confidence               33889999988888888888  899999999        99999999999999999999988789999999999999


Q ss_pred             HHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCC
Q psy13263        426 RRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI  478 (577)
Q Consensus       426 ~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGl  478 (577)
                      ..+...++|.++||.+....     ++++|+|||.+|+|..|||+++|+++|+
T Consensus       152 ~~~~~~~~v~~~~~~~~~~~-----~~~~~~y~~~~G~~~~s~~~~~a~~~g~  199 (199)
T cd03283         152 DLLDLDSAVRNYHFREDIDD-----NKLIFDYKLKPGVSPTRNALRLMKKIGI  199 (199)
T ss_pred             HhhhcCCCeEEEEEEEEEEC-----CeeeEEEEeCCCCCCCcHHHHHHHHcCC
Confidence            99988899999999998752     6999999999999999999999999996

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

>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch

Probab=99.95  E-value=5.5e-28  Score=235.44  Aligned_cols=191  Identities=24%  Similarity=0.366  Sum_probs=173.6

Q ss_pred             cCcccccCcccc---cccccccccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeeccc
Q psy13263        274 TPSGCFPDMSEL---LKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQ  349 (577)
Q Consensus       274 i~~GrhPlLe~~---l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG  349 (577)
                      +++++||+++..   -++++|+|........+++|||++|||+++++++.+. +++|.|+|+|+..+.++. +.+|..++
T Consensus         2 ~~~~~~p~l~~~~~~~~~~~~~~~l~~~~~~~l~G~Ng~GKStll~~i~~~~-~~~~~g~~~~~~~~~i~~~dqi~~~~~   80 (202)
T cd03243           2 IKGGRHPVLLALTKGETFVPNDINLGSGRLLLITGPNMGGKSTYLRSIGLAV-LLAQIGCFVPAESASIPLVDRIFTRIG   80 (202)
T ss_pred             cccccCCEEeccccCCceEeeeEEEcCCeEEEEECCCCCccHHHHHHHHHHH-HHHHcCCCccccccccCCcCEEEEEec
Confidence            578999999863   4489999988877778899999999999999999887 899999999999999999 99998776


Q ss_pred             c------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHH
Q psy13263        350 K------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHS  423 (577)
Q Consensus       350 ~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~e  423 (577)
                      .      +.|+|..|+.++..++.......++|+||        .+.||++.++..+.+++++.+.+.++.+|++||+++
T Consensus        81 ~~d~i~~~~s~~~~e~~~l~~i~~~~~~~~llllDE--------p~~gld~~~~~~l~~~ll~~l~~~~~~vi~~tH~~~  152 (202)
T cd03243          81 AEDSISDGRSTFMAELLELKEILSLATPRSLVLIDE--------LGRGTSTAEGLAIAYAVLEHLLEKGCRTLFATHFHE  152 (202)
T ss_pred             CcccccCCceeHHHHHHHHHHHHHhccCCeEEEEec--------CCCCCCHHHHHHHHHHHHHHHHhcCCeEEEECChHH
Confidence            4      33999999999999998889999999999        999999999999999999999988999999999999


Q ss_pred             HHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCC
Q psy13263        424 VARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI  478 (577)
Q Consensus       424 L~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGl  478 (577)
                      +...+...+.+.++||.+...     .+++.|+|||.+|.+.+|||+.+|++.|+
T Consensus       153 ~~~~~~~~~~l~~~~~~~~~~-----~~~~~~~ykl~~g~~~~~~a~~~~~~~g~  202 (202)
T cd03243         153 LADLPEQVPGVKNLHMEELIT-----TGGLTFTYKLIDGICDPSYALQIAELAGL  202 (202)
T ss_pred             HHHHhhcCCCeEEEEEEEEec-----CCeeeEEEEEeECCCCCcHHHHHHHHcCC
Confidence            999988778899999988754     25799999999999999999999999986

Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=99.95  E-value=4.5e-28  Score=235.96  Aligned_cols=190  Identities=15%  Similarity=0.161  Sum_probs=167.1

Q ss_pred             ccCcccccCccccc-cccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhcccccccc-ceecc-ceeeecc
Q psy13263        273 QTPSGCFPDMSELL-KYFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQC-AHFGC-TVIYSEA  348 (577)
Q Consensus       273 ~i~~GrhPlLe~~l-~~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~-a~l~~-d~if~~i  348 (577)
                      .|++||||+++... ++++|+|..... +..+++|||++|||+|+++++.+. +++|+|+|||+.. ..++. +.+|..+
T Consensus         1 ~~~~~~hp~~~~~~~~~~~~~~~i~~~~~~~~ltG~Ng~GKStll~~i~~~~-~~~~~G~~vp~~~~~~~~~~~~~~~~l   79 (200)
T cd03280           1 RLREARHPLLPLQGEKVVPLDIQLGENKRVLVITGPNAGGKTVTLKTLGLLT-LMAQSGLPIPAAEGSSLPVFENIFADI   79 (200)
T ss_pred             CCcccCCCEEeccCCceEcceEEECCCceEEEEECCCCCChHHHHHHHHHHH-HHHHcCCCccccccccCcCccEEEEec
Confidence            36889999998643 378999998876 458899999999999999999877 9999999999975 67887 9999887


Q ss_pred             cc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchH
Q psy13263        349 QK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYH  422 (577)
Q Consensus       349 G~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~  422 (577)
                      |.      +.|+|+.+|.+...+........++|+||        .++||++.++..++.++++.|.+.++.+|++||++
T Consensus        80 g~~~~l~~~~s~fs~g~~~~~~i~~~~~~p~llllDE--------p~~glD~~~~~~i~~~~l~~l~~~~~~vi~~tH~~  151 (200)
T cd03280          80 GDEQSIEQSLSTFSSHMKNIARILQHADPDSLVLLDE--------LGSGTDPVEGAALAIAILEELLERGALVIATTHYG  151 (200)
T ss_pred             CchhhhhcCcchHHHHHHHHHHHHHhCCCCcEEEEcC--------CCCCCCHHHHHHHHHHHHHHHHhcCCEEEEECCHH
Confidence            74      34999999999888877778889999999        99999999999999999999988899999999999


Q ss_pred             HHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCC
Q psy13263        423 SVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI  478 (577)
Q Consensus       423 eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGl  478 (577)
                      ++..+......+.+.+|.++.       +.+.|+|+|++|+++.|||+++|+++||
T Consensus       152 ~l~~~~d~~~~l~~g~l~~~~-------~~~~~~ykl~~G~~~~s~a~~~a~~~g~  200 (200)
T cd03280         152 ELKAYAYKREGVENASMEFDP-------ETLKPTYRLLIGVPGRSNALEIARRLGL  200 (200)
T ss_pred             HHHHHHhcCCCeEEEEEEEec-------CcccEEEEEeECCCCCcHHHHHHHHcCC
Confidence            999888776677777776552       4789999999999999999999999996

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

>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport

Probab=99.68  E-value=8.8e-17  Score=151.94  Aligned_cols=143  Identities=16%  Similarity=0.147  Sum_probs=120.6

Q ss_pred             cCcccccCcccccccccccccccccccccccCCCCCCCchhHHHHHHHHHHHHH----------hccccccccceeccce
Q psy13263        274 TPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKE----------IQTYLRTQCAHFGCTV  343 (577)
Q Consensus       274 i~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaq----------ig~~VpA~~a~l~~d~  343 (577)
                      +..++||.+     +.+|++.....+..+|+|||++|||+|+++++.+. .+++          .|+++|+..+.+    
T Consensus         2 i~~~~~~~~-----~~~~~i~~~~~~~~~i~G~NgsGKS~~l~~i~~~~-~~~~~~~~~~~~~~~g~~~~~~~~~~----   71 (162)
T cd03227           2 IVLGRFPSY-----FVPNDVTFGEGSLTIITGPNGSGKSTILDAIGLAL-GGAQSATRRRSGVKAGCIVAAVSAEL----   71 (162)
T ss_pred             ceeCCCCEE-----EeccEEecCCCCEEEEECCCCCCHHHHHHHHHHHH-HhcchhhhccCcccCCCcceeeEEEE----
Confidence            456789877     45666665555677899999999999999999998 8999          999999988777    


Q ss_pred             eeecccccchhhhhchhhhHHhhhcCC--CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecch
Q psy13263        344 IYSEAQKKQKKYVLEVPSKYASKAKSN--HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHY  421 (577)
Q Consensus       344 if~~iG~~qStF~~Em~e~~~il~~a~--~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy  421 (577)
                      +|+.++-  |..+.++..++.++....  ...|+|+||        +++||++.++.+++.++.+++.+ ++.+|++||+
T Consensus        72 i~~~~~l--S~G~~~~~~la~~L~~~~~~~~~llllDE--------p~~gld~~~~~~l~~~l~~~~~~-~~~vii~TH~  140 (162)
T cd03227          72 IFTRLQL--SGGEKELSALALILALASLKPRPLYILDE--------IDRGLDPRDGQALAEAILEHLVK-GAQVIVITHL  140 (162)
T ss_pred             ehheeec--cccHHHHHHHHHHHHhcCCCCCCEEEEeC--------CCCCCCHHHHHHHHHHHHHHHhc-CCEEEEEcCC
Confidence            7777776  889999999988887655  789999999        99999999999999999999887 8999999999


Q ss_pred             HHHHHHhhcCCCcccccceee
Q psy13263        422 HSVARRLREEPNVAFEYMSYI  442 (577)
Q Consensus       422 ~eL~~l~~~~~~V~n~hm~~~  442 (577)
                      +++...+.     +.+||...
T Consensus       141 ~~~~~~~d-----~~~~l~~~  156 (162)
T cd03227         141 PELAELAD-----KLIHIKKV  156 (162)
T ss_pred             HHHHHhhh-----hEEEEEEE
Confidence            99988653     34566543

These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.

>TIGR01070 mutS1 DNA mismatch repair protein MutS

Probab=98.69  E-value=2.4e-09  Score=125.36  Aligned_cols=51  Identities=39%  Similarity=0.610  Sum_probs=48.3

Q ss_pred             cCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccccC
Q psy13263        206 QTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESG  256 (577)
Q Consensus       206 ~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGsn  256 (577)
                      +||||+|||++|++|||++||||+|+|||+|++||.+++++|+++++++.+
T Consensus         1 ~TPm~~Qy~~iK~~~~D~iLffr~GdFYElf~eDA~~~a~~L~i~lt~r~~   51 (840)
T TIGR01070         1 LTPMMQQYLKLKAEHPDALLFFRMGDFYELFYEDAKKAAQLLDISLTSRGQ   51 (840)
T ss_pred             CCHHHHHHHHHHHhCCCEEEEEEcCCEEEEehhhHHHHHHHhCeEEeecCC
Confidence            589999999999999999999999999999999999999999999987544

>PRK05399 DNA mismatch repair protein MutS; Provisional

Probab=98.59  E-value=7.1e-09  Score=121.74  Aligned_cols=54  Identities=41%  Similarity=0.605  Sum_probs=50.1

Q ss_pred             cccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccccCc
Q psy13263        204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGC  257 (577)
Q Consensus       204 ~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGsn~  257 (577)
                      .++||||+|||++|++|||+++|||+|+|||+|++||++++..|+++++++.+.
T Consensus         6 ~~~TP~~~Qy~~iK~~~~D~ilffr~GdFYElf~eDA~~~s~~L~i~lt~r~~~   59 (854)
T PRK05399          6 SKLTPMMQQYLEIKAQYPDALLFFRMGDFYELFFEDAKKASRLLDITLTKRGKS   59 (854)
T ss_pred             CCCCHHHHHHHHHHhhCCCEEEEEEcCCEEEEeHhhHHHHHHHhCeEEeeccCC
Confidence            468999999999999999999999999999999999999999999999875433

>PF01624 MutS_I: MutS domain I C-terminus

Probab=98.52  E-value=6.8e-09  Score=93.26  Aligned_cols=54  Identities=33%  Similarity=0.575  Sum_probs=48.3

Q ss_pred             CcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccccCccCC
Q psy13263        207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE  260 (577)
Q Consensus       207 TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGsn~~GK  260 (577)
                      ||+++|||++|++|||+|+||++|+||++|.+||+.++..+++.+++.....++
T Consensus         1 Tp~~~~y~~lk~k~~d~i~lf~~G~fYe~y~~DA~~~a~~l~~~~~~~~~~~~~   54 (113)
T PF01624_consen    1 TPFEQQYWELKEKYPDTIVLFQVGDFYEAYGEDAEFVAEILGLKLSKRKTGGGK   54 (113)
T ss_dssp             -HHHHHHHHHHCTSTTSEEEEEETTEEEEECHHHHHHHHHHTSSSEEEECSSSE
T ss_pred             ChHHHHHHHHHhhCCCeEEEEEcCCEEEEEccCHHHHHHhccceeeeccccccc
Confidence            799999999999999999999999999999999999999999999876544443

; InterPro: IPR007695 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the N-terminal domain of proteins in the MutS family of DNA mismatch repair proteins, as well as closely related proteins. The N-terminal domain of MutS is responsible for mismatch recognition and forms a 6-stranded mixed beta-sheet surrounded by three alpha-helices, which is similar to the structure of tRNA endonuclease. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 3THY_B 3THZ_B 3THW_B 3THX_B 2WTU_A 1OH7_A ....

>COG0249 MutS Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

Probab=98.43  E-value=7e-08  Score=112.82  Aligned_cols=54  Identities=44%  Similarity=0.637  Sum_probs=51.0

Q ss_pred             ccccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccccC
Q psy13263        203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESG  256 (577)
Q Consensus       203 l~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGsn  256 (577)
                      ..++||+|+|||++|++|+|+++|||+|+|||+|++||..+++.|++++.++.+
T Consensus         3 ~~~~tP~m~qy~~ik~~~~d~llffr~GdfYelf~~DA~~~s~~l~itlT~r~~   56 (843)
T COG0249           3 KAKLTPMMQQYLEIKAQYPDTLLFFRMGDFYELFFEDAKIAARLLDITLTKRGN   56 (843)
T ss_pred             cccCCcHHHHHHHHHHhCCccEEEEecccchhhhHHHHHHHHHhhCceeecCCC
Confidence            357899999999999999999999999999999999999999999999988765

>KOG0219|consensus

Probab=98.06  E-value=5.3e-07  Score=102.62  Aligned_cols=199  Identities=8%  Similarity=-0.028  Sum_probs=142.2

Q ss_pred             HHhhhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccccCcccccccccccccccccccccccCCCCCCCch
Q psy13263        234 ELFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKE  313 (577)
Q Consensus       234 Elf~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsv  313 (577)
                      .++++|...-....++.+++|+||+||||++|+++..+++++.|+|-.++..-                        .++
T Consensus       632 ~fIpNdv~le~~~~~~~IiTGpNMGGKSTyir~~Gvi~lmAQIGcfVPce~A~------------------------i~I  687 (902)
T KOG0219|consen  632 PFIPNDVVLEKGKCRMLIITGPNMGGKSTYIRQVGVIVLMAQIGCFVPCESAT------------------------ISI  687 (902)
T ss_pred             CCCCCccccccCCceEEEEeCCCcCccchhhhhhhHHHHHHHhCCceehhhcC------------------------Cch
Confidence            34556666665567888999999999999999999999999999874433210                        112


Q ss_pred             hHHHHHHHHHHHHHhccccccccceecc-ceeeec-------ccccchhhhhchhhhHHhhhcCCCceEEeecccCcccc
Q psy13263        314 YDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSE-------AQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYV  385 (577)
Q Consensus       314 y~k~valI~~imaqig~~VpA~~a~l~~-d~if~~-------iG~~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v  385 (577)
                      -+.++++.+                  . |..+.+       |+.  ++|+.++.....++.-..-......++      
T Consensus       688 vD~Il~RVG------------------A~D~q~kG~STFM~Emle--ta~Ilr~at~~SliiiDELGRGTSt~D------  741 (902)
T KOG0219|consen  688 VDGILTRVG------------------AGDSQLKGISTFMAEMLE--TASILRRATKNSLIIIDELGRGTSTYD------  741 (902)
T ss_pred             hhHHHhhhc------------------cchhhhcchHHHHHHHHH--HHHHHHhcCCCcEEEEeccCCCceecc------
Confidence            222222211                  1 111111       233  677777776666555566677888899      


Q ss_pred             cccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHhhcCCCccc--ccceeeeecCCCCcceEEEEEeecCC
Q psy13263        386 TPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLREEPNVAF--EYMSYIEDKRNDGIDTIVFLYKLVPG  462 (577)
Q Consensus       386 ~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~~~~~~V~n--~hm~~~~~~~~~~~~~l~flYkL~~G  462 (577)
                        .|+++.+.++.-++|+.+.+|... .|...+.||++.-...+.....|.+  .+|-             .-.|.-+.|
T Consensus       742 --GfgiAwai~ehi~~ki~cf~lfATHfhElt~lae~~~~vKn~h~~a~i~~~~~~ll-------------Y~V~~Gv~d  806 (902)
T KOG0219|consen  742 --GFGIAWAIAEHIATKIGCFCLFATHFHELTKLAEQLPTVKNLHVTAQIENDDITLL-------------YKVFEGVCD  806 (902)
T ss_pred             --CccHHHHHHHHHHHHHhHhHHHHhHHHHHHhhhhhhhhhhhheeeeEecCcchhhH-------------HHHhccccc
Confidence              999999999999999999998876 8999999999999987655444443  2222             224556678


Q ss_pred             CCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhh
Q psy13263        463 ICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARH  497 (577)
Q Consensus       463 ~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~  497 (577)
                      .+-..++.++|...-.+-++.+++.+-++.+....
T Consensus       807 ~SFGi~VA~~a~fp~~vie~A~~~~~ele~~~~~~  841 (902)
T KOG0219|consen  807 QSFGIHVAELVGFPEHVIEMAKQKAEELEDELVIK  841 (902)
T ss_pred             CcchhhHHHHcCCChHHHHHHHHHHHHHHHHHhhh
Confidence            88899999999999999999888887777766553

>KOG0217|consensus

Probab=97.74  E-value=7.7e-07  Score=103.21  Aligned_cols=211  Identities=31%  Similarity=0.470  Sum_probs=144.5

Q ss_pred             CCCCCCCCCCccchhhhhhcccccCCCcchhhhcCCCCCCCCCCCcccccccccCCCcccccc-ccCCCCCCCCccccCC
Q psy13263         36 EDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEE-SVEDPTPSSSEAEVTP  114 (577)
Q Consensus        36 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~p  114 (577)
                      |...+.+..-++++++..++...+|||+|    .++.+.+|+|+ ..+++.|+..+|.++... +.++.+|. .....++
T Consensus        68 e~~~~d~~~~~~~~~~~~k~~~~sDsd~d----~g~k~~~~~~~-~d~~~~D~~~~d~~~~~~ee~~~~~~~-~~~~~~~  141 (1125)
T KOG0217|consen   68 EAVGDDADIVVESSSEKPKSGLDSDSDED----FGGKEVEEKED-SDEELDDETASDYEVVISEESEGGEPV-CRVSDTD  141 (1125)
T ss_pred             hhcCCCccceeeecccCCccccCCCcccc----cCccccccccc-ccccccccccCCcceeccccccCCCcc-cccCCCc
Confidence            33444455667788889999999999999    88999999999 667777777777665322 11222221 1111122


Q ss_pred             cccCCccCCCC--------CCCCCCCCCccCCCCCCCCCC---CCcCCCCCCCCC-------CCCCCccccccccccCCC
Q psy13263        115 MKNGNKRGLSS--------KSGQPTKKPKLTAPSTPSTPS---FPVSDTSETTPS-------TSGAQDWSHNHYQFLHPD  176 (577)
Q Consensus       115 ~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~-------~~~~~~~~~~~~~fl~p~  176 (577)
                      ......+.++.        ..+.+   .......-++|+.   ..++.....+.+       .+....|.|+.+.||.++
T Consensus       142 ~r~~~a~~v~k~~~kk~~~~~~~~---~~~~~~~~~~p~~~~~~~a~r~~~~~~~i~~~~~~~~~~~a~~~E~~r~l~~e  218 (1125)
T KOG0217|consen  142 SRSRKAESVSKGKSKKSPSDSGAV---SMGHDLDFNDPMPLREGQASRSASGYCGISNGETELSRMEAFDHEKERYLKLE  218 (1125)
T ss_pred             ccchhcccccccccCCCCCCcccc---ccccccccCCCCccccCccccccccccccccccccccchhhhcccchhhccHH
Confidence            21111111111        00010   0000111111111   111111111111       123667889999999999


Q ss_pred             CccccCCCCCCCCCCCCCccccCcccccccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhcccc
Q psy13263        177 HILDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKES  255 (577)
Q Consensus       177 ~i~D~~~r~p~~p~Yd~sTl~Ipp~~l~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGs  255 (577)
                      .+||+++||++||+|||+||||||+++.++||.++|||++|++|+|+||||++|+|||+|.+||.+++..++|.||+|.
T Consensus       219 ~~RD~~rrr~~dp~yDp~TLyiP~s~~~kftpg~kqwWeiKs~~fD~ivfFk~GKFyELye~DA~vg~~~~dl~f~~vN  297 (1125)
T KOG0217|consen  219 DVRDALRRRRGDPEYDPRTLYIPPSFWKKFTPGEKQWWEIKSDNFDTIVFFKKGKFYELYEMDALVGARLFDLKFMDVN  297 (1125)
T ss_pred             HhhhhhcCCCCCCCCCccceecCHHHHhcCCchhhhhhhhhhhcccEEEEEecchHHHHHhhhhhhhhhhcceeecccc
Confidence            9999999999999999999999999999999999999999999999999999999999999999999999999999964

>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=96.53  E-value=0.0075  Score=56.32  Aligned_cols=116  Identities=8%  Similarity=-0.023  Sum_probs=69.3

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeee----------cccc--cchhhhhch
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYS----------EAQK--KQKKYVLEV  359 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~----------~iG~--~qStF~~Em  359 (577)
                      +|........+|+|||.+|||.++++++-+.          +...-++.++....          .++-  ..|  ..|.
T Consensus        19 ~~~i~~g~~~~i~G~nGsGKStll~~l~g~~----------~~~~G~i~~~~~~~~~~~~~~~~~~i~~~~qlS--~G~~   86 (157)
T cd00267          19 SLTLKAGEIVALVGPNGSGKSTLLRAIAGLL----------KPTSGEILIDGKDIAKLPLEELRRRIGYVPQLS--GGQR   86 (157)
T ss_pred             EEEEcCCCEEEEECCCCCCHHHHHHHHhCCC----------CCCccEEEECCEEcccCCHHHHHhceEEEeeCC--HHHH
Confidence            4454555567899999999999998875432          22222232211000          0000  012  1233


Q ss_pred             hhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh
Q psy13263        360 PSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL  428 (577)
Q Consensus       360 ~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~  428 (577)
                      ..+...+..+....++++||        .-.|.+......+...+.+ +...++.+|++||..+.....
T Consensus        87 ~r~~l~~~l~~~~~i~ilDE--------p~~~lD~~~~~~l~~~l~~-~~~~~~tii~~sh~~~~~~~~  146 (157)
T cd00267          87 QRVALARALLLNPDLLLLDE--------PTSGLDPASRERLLELLRE-LAEEGRTVIIVTHDPELAELA  146 (157)
T ss_pred             HHHHHHHHHhcCCCEEEEeC--------CCcCCCHHHHHHHHHHHHH-HHHCCCEEEEEeCCHHHHHHh
Confidence            33333344455678999999        8888888666555555544 444468899999999887754

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.

>PF00488 MutS_V: MutS domain V C-terminus

Probab=96.46  E-value=0.0012  Score=66.85  Aligned_cols=87  Identities=18%  Similarity=0.219  Sum_probs=55.9

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhH
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYD  315 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~  315 (577)
                      ++|........++.+++|+|++|||++||+++..+++++.|.+ |--...+..++.-|.+-..     .---..|.+.|.
T Consensus        33 ~ndi~~~~~~~~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~~~i~~~d~I~t~~~~-----~d~~~~~~S~F~  107 (235)
T PF00488_consen   33 PNDIELSNNKSRIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAESAEIPIFDRIFTRIGD-----DDSIESGLSTFM  107 (235)
T ss_dssp             -EEEEESSSSSSEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSEEEEE--SEEEEEES--------SSTTSSSHHH
T ss_pred             cceeecCCCceeEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecccccccccEEEeeccc-----ccccccccccHH
Confidence            4666665544468899999999999999999999999999987 5444344444433331110     011245688998


Q ss_pred             HHHHHHHHHHHHh
Q psy13263        316 EVMDEIKSIEKEI  328 (577)
Q Consensus       316 k~valI~~imaqi  328 (577)
                      .-+..+..++.+.
T Consensus       108 ~E~~~~~~il~~~  120 (235)
T PF00488_consen  108 AEMKRLSSILRNA  120 (235)
T ss_dssp             HHHHHHHHHHHH-
T ss_pred             HhHHHHHhhhhhc
Confidence            8888887666554

; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....

>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=96.01  E-value=0.0099  Score=57.04  Aligned_cols=52  Identities=12%  Similarity=0.050  Sum_probs=36.0

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +.......++|+||        --.|-++..-. ....++..+.+. ++.+|++||..+...
T Consensus       110 ral~~~p~llllDE--------P~~~LD~~~~~-~~~~~l~~~~~~~~~tiii~sh~~~~~~  162 (180)
T cd03214         110 RALAQEPPILLLDE--------PTSHLDIAHQI-ELLELLRRLARERGKTVVMVLHDLNLAA  162 (180)
T ss_pred             HHHhcCCCEEEEeC--------CccCCCHHHHH-HHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            34455778999999        77777664443 344455555555 789999999988653

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.

>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=95.99  E-value=0.019  Score=55.79  Aligned_cols=114  Identities=10%  Similarity=-0.068  Sum_probs=63.1

Q ss_pred             ccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-c--eeeecccccchhhhhchhhhHHhhhcC
Q psy13263        293 FDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-T--VIYSEAQKKQKKYVLEVPSKYASKAKS  369 (577)
Q Consensus       293 F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d--~if~~iG~~qStF~~Em~e~~~il~~a  369 (577)
                      |........+++|||.+|||+++++++-+.          +...-++.+ .  .-|..-....|.-+.  .++...+...
T Consensus        20 ~~i~~Ge~~~l~G~nGsGKSTLl~~l~Gl~----------~p~~G~i~~~g~~i~~~~q~~~LSgGq~--qrv~laral~   87 (177)
T cd03222          20 GVVKEGEVIGIVGPNGTGKTTAVKILAGQL----------IPNGDNDEWDGITPVYKPQYIDLSGGEL--QRVAIAAALL   87 (177)
T ss_pred             cEECCCCEEEEECCCCChHHHHHHHHHcCC----------CCCCcEEEECCEEEEEEcccCCCCHHHH--HHHHHHHHHh
Confidence            333344456799999999999998765332          222333333 1  111100000122222  2222233445


Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARR  427 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l  427 (577)
                      ....++|+||        --.|-++..-..+...+. .+.++ +..+|++||..+....
T Consensus        88 ~~p~lllLDE--------Pts~LD~~~~~~l~~~l~-~~~~~~~~tiiivsH~~~~~~~  137 (177)
T cd03222          88 RNATFYLFDE--------PSAYLDIEQRLNAARAIR-RLSEEGKKTALVVEHDLAVLDY  137 (177)
T ss_pred             cCCCEEEEEC--------CcccCCHHHHHHHHHHHH-HHHHcCCCEEEEEECCHHHHHH
Confidence            5668999999        666666555444444443 44444 4789999999877663

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.

>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion

Probab=95.99  E-value=0.012  Score=57.28  Aligned_cols=47  Identities=13%  Similarity=0.174  Sum_probs=33.9

Q ss_pred             ceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        372 QRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       372 ~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ..++|+||        --.|-++..-..+...+ ..+.+.+..+|++||..+....
T Consensus       108 p~llLlDE--------Pt~~LD~~~~~~l~~~l-~~~~~~g~tvIivSH~~~~~~~  154 (176)
T cd03238         108 GTLFILDE--------PSTGLHQQDINQLLEVI-KGLIDLGNTVILIEHNLDVLSS  154 (176)
T ss_pred             CCEEEEeC--------CcccCCHHHHHHHHHHH-HHHHhCCCEEEEEeCCHHHHHh
Confidence            68999999        77777776655554444 3444457899999999987543

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.

>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=95.67  E-value=0.026  Score=58.90  Aligned_cols=129  Identities=9%  Similarity=0.047  Sum_probs=71.9

Q ss_pred             ccccccccccccccCCCCCCCchhHHHHHHHHHHHH----Hhcccccccc-----ce----ecc-ceeee----------
Q psy13263        291 NAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEK----EIQTYLRTQC-----AH----FGC-TVIYS----------  346 (577)
Q Consensus       291 n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~ima----qig~~VpA~~-----a~----l~~-d~if~----------  346 (577)
                      -+|+.......|.+|||..|||+.+|.+.=|- +-.    .++.++|-.+     ++    +|- -...|          
T Consensus        43 isf~IP~G~ivgflGaNGAGKSTtLKmLTGll-~p~~G~v~V~G~~Pf~~~~~~~~~~~~v~gqk~ql~Wdlp~~ds~~v  121 (325)
T COG4586          43 ISFEIPKGEIVGFLGANGAGKSTTLKMLTGLL-LPTSGKVRVNGKDPFRRREEYLRSIGLVMGQKLQLWWDLPALDSLEV  121 (325)
T ss_pred             eeeecCCCcEEEEEcCCCCcchhhHHHHhCcc-ccCCCeEEecCcCcchhHHHHHHHHHHHhhhhheeeeechhhhhHHH
Confidence            37888888888999999999999999874221 000    1112222220     00    111 12222          


Q ss_pred             -----cccccchhhhhchhhhHHhhhcC-------------------------CCceEEeecccCcccccccccCCCCcc
Q psy13263        347 -----EAQKKQKKYVLEVPSKYASKAKS-------------------------NHQRVATKKKNVENYVTPECRGTGTND  396 (577)
Q Consensus       347 -----~iG~~qStF~~Em~e~~~il~~a-------------------------~~~sLVLlDEtg~n~v~~LGRGTst~D  396 (577)
                           ++++  +.|..-|..+..++..-                         ...-+++|||        -==|=+..-
T Consensus       122 ~~~Iy~Ipd--~~F~~r~~~l~eiLdl~~~lk~~vr~LSlGqRmraeLaaaLLh~p~VLfLDE--------pTvgLDV~a  191 (325)
T COG4586         122 LKLIYEIPD--DEFAERLDFLTEILDLEGFLKWPVRKLSLGQRMRAELAAALLHPPKVLFLDE--------PTVGLDVNA  191 (325)
T ss_pred             HHHHHhCCH--HHHHHHHHHHHHHhcchhhhhhhhhhccchHHHHHHHHHHhcCCCcEEEecC--------CccCcchhH
Confidence                 3344  55554333333322111                         1456788999        444444444


Q ss_pred             hhhHHHHHHHHHHhcCCeEEEecch-HHHHHHhhc
Q psy13263        397 GCVIARVTLEKFLQIGCLTVFATHY-HSVARRLRE  430 (577)
Q Consensus       397 G~ALA~AIlE~L~~~~~~~lfaTHy-~eL~~l~~~  430 (577)
                      -.+|--.+-+|-..++|.++.|||| -.|+.++.+
T Consensus       192 q~~ir~Flke~n~~~~aTVllTTH~~~di~~lc~r  226 (325)
T COG4586         192 QANIREFLKEYNEERQATVLLTTHIFDDIATLCDR  226 (325)
T ss_pred             HHHHHHHHHHHHHhhCceEEEEecchhhHHHhhhh
Confidence            4455555555555569999999999 456666654

>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]

Probab=95.66  E-value=0.015  Score=59.92  Aligned_cols=61  Identities=13%  Similarity=0.070  Sum_probs=46.4

Q ss_pred             hchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       357 ~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.++..-.+..+...-|+||||        -.-|-++. +....+.++..|.+.+|.+|++||+.+...
T Consensus       143 GQ~QRV~lARAL~~~p~lllLDE--------P~~gvD~~-~~~~i~~lL~~l~~eg~tIl~vtHDL~~v~  203 (254)
T COG1121         143 GQKQRVLLARALAQNPDLLLLDE--------PFTGVDVA-GQKEIYDLLKELRQEGKTVLMVTHDLGLVM  203 (254)
T ss_pred             HHHHHHHHHHHhccCCCEEEecC--------CcccCCHH-HHHHHHHHHHHHHHCCCEEEEEeCCcHHhH
Confidence            34555555566678888999999        66666653 566777888999888999999999976655

>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=95.54  E-value=0.043  Score=52.30  Aligned_cols=123  Identities=9%  Similarity=0.073  Sum_probs=64.5

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccc-----------cceecc---c-eeeecc-ccc-chh
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQ-----------CAHFGC---T-VIYSEA-QKK-QKK  354 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~-----------~a~l~~---d-~if~~i-G~~-qSt  354 (577)
                      +|........+|+|||.+|||+++++++-+.  ...-|...-..           +..++.   + .+|... ... .|.
T Consensus        22 ~~~i~~Ge~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~lLS~   99 (173)
T cd03246          22 SFSIEPGESLAIIGPSGSGKSTLARLILGLL--RPTSGRVRLDGADISQWDPNELGDHVGYLPQDDELFSGSIAENILSG   99 (173)
T ss_pred             EEEECCCCEEEEECCCCCCHHHHHHHHHhcc--CCCCCeEEECCEEcccCCHHHHHhheEEECCCCccccCcHHHHCcCH
Confidence            3444455567899999999999999886542  11112110000           001111   0 000000 000 010


Q ss_pred             hhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        355 YVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       355 F~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                        .|..++.-.+.......++|+||        --.|-++..-..+.. ++..+.+.+..+|++||..+....
T Consensus       100 --G~~qrv~la~al~~~p~~lllDE--------Pt~~LD~~~~~~l~~-~l~~~~~~~~tii~~sh~~~~~~~  161 (173)
T cd03246         100 --GQRQRLGLARALYGNPRILVLDE--------PNSHLDVEGERALNQ-AIAALKAAGATRIVIAHRPETLAS  161 (173)
T ss_pred             --HHHHHHHHHHHHhcCCCEEEEEC--------CccccCHHHHHHHHH-HHHHHHhCCCEEEEEeCCHHHHHh
Confidence              12223333344566778999999        666666554444433 444555557889999999876653

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

>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component

Probab=95.42  E-value=0.023  Score=55.53  Aligned_cols=52  Identities=13%  Similarity=0.129  Sum_probs=35.0

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +..+....++|+||        --.|-++..-. ..+.++..+.+.++.+|++||..++..
T Consensus       117 ral~~~p~illlDE--------Pt~~LD~~~~~-~l~~~L~~~~~~~~tiii~sh~~~~~~  168 (200)
T cd03217         117 QLLLLEPDLAILDE--------PDSGLDIDALR-LVAEVINKLREEGKSVLIITHYQRLLD  168 (200)
T ss_pred             HHHhcCCCEEEEeC--------CCccCCHHHHH-HHHHHHHHHHHCCCEEEEEecCHHHHH
Confidence            34455678999999        55555554333 334455555555789999999998776

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.

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

Probab=95.42  E-value=0.044  Score=51.97  Aligned_cols=114  Identities=6%  Similarity=-0.004  Sum_probs=64.0

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceee-e----------cccc-c-chhhhhc
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIY-S----------EAQK-K-QKKYVLE  358 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if-~----------~iG~-~-qStF~~E  358 (577)
                      +|........+++|||.+|||+++++++-+.          +...-++-++..- .          .+|- . .|.  .+
T Consensus        20 ~~~i~~Ge~~~l~G~nGsGKSTLl~~i~G~~----------~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~--G~   87 (163)
T cd03216          20 SLSVRRGEVHALLGENGAGKSTLMKILSGLY----------KPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSV--GE   87 (163)
T ss_pred             EEEEeCCCEEEEECCCCCCHHHHHHHHhCCC----------CCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCH--HH
Confidence            3444455566799999999999999876432          2222222221000 0          0110 0 011  12


Q ss_pred             hhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        359 VPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       359 m~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ..++.-.+.......++|+||        --.|-++.--..+. .++..+.+.+..+|++||..+...
T Consensus        88 ~qrl~laral~~~p~illlDE--------P~~~LD~~~~~~l~-~~l~~~~~~~~tiii~sh~~~~~~  146 (163)
T cd03216          88 RQMVEIARALARNARLLILDE--------PTAALTPAEVERLF-KVIRRLRAQGVAVIFISHRLDEVF  146 (163)
T ss_pred             HHHHHHHHHHhcCCCEEEEEC--------CCcCCCHHHHHHHH-HHHHHHHHCCCEEEEEeCCHHHHH
Confidence            233333344556778999999        66676655444343 344445555788999999987543

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.

>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export

Probab=95.39  E-value=0.04  Score=52.39  Aligned_cols=122  Identities=8%  Similarity=0.068  Sum_probs=62.8

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccc-----------cceecc---c-eeeecc-ccc-chh
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQ-----------CAHFGC---T-VIYSEA-QKK-QKK  354 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~-----------~a~l~~---d-~if~~i-G~~-qSt  354 (577)
                      +|........+++|||.+|||+++++++-+.  ...-|...-..           +..++.   + .+|... .+. .|.
T Consensus        22 ~~~i~~G~~~~l~G~nGsGKstLl~~i~G~~--~~~~G~i~~~g~~~~~~~~~~~~~~i~~~~~~~~~~~~t~~e~lLS~   99 (171)
T cd03228          22 SLTIKPGEKVAIVGPSGSGKSTLLKLLLRLY--DPTSGEILIDGVDLRDLDLESLRKNIAYVPQDPFLFSGTIRENILSG   99 (171)
T ss_pred             EEEEcCCCEEEEECCCCCCHHHHHHHHHcCC--CCCCCEEEECCEEhhhcCHHHHHhhEEEEcCCchhccchHHHHhhCH
Confidence            3444455567899999999999999886542  11112110000           001111   0 000000 000 011


Q ss_pred             hhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        355 YVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       355 F~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                        .|..++.-.........++|+||        --.|-++..-.. .+.++..+.+ ++.+|++||..+....
T Consensus       100 --G~~~rl~la~al~~~p~llllDE--------P~~gLD~~~~~~-l~~~l~~~~~-~~tii~~sh~~~~~~~  160 (171)
T cd03228         100 --GQRQRIAIARALLRDPPILILDE--------ATSALDPETEAL-ILEALRALAK-GKTVIVIAHRLSTIRD  160 (171)
T ss_pred             --HHHHHHHHHHHHhcCCCEEEEEC--------CCcCCCHHHHHH-HHHHHHHhcC-CCEEEEEecCHHHHHh
Confidence              12222222334455678999999        666666644333 3333444433 6788999999987754

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.

>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis

Probab=95.38  E-value=0.044  Score=52.39  Aligned_cols=122  Identities=5%  Similarity=-0.027  Sum_probs=63.8

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccc---------c-ccceecc---c-eeeec-----ccccc
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLR---------T-QCAHFGC---T-VIYSE-----AQKKQ  352 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~Vp---------A-~~a~l~~---d-~if~~-----iG~~q  352 (577)
                      +|........+++|||.+|||+++++++-+.  ...-|...-         . .+..++.   + .+|..     +....
T Consensus        22 ~~~i~~Ge~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~tv~~~i~~~L   99 (178)
T cd03247          22 SLELKQGEKIALLGRSGSGKSTLLQLLTGDL--KPQQGEITLDGVPVSDLEKALSSLISVLNQRPYLFDTTLRNNLGRRF   99 (178)
T ss_pred             EEEEcCCCEEEEECCCCCCHHHHHHHHhccC--CCCCCEEEECCEEHHHHHHHHHhhEEEEccCCeeecccHHHhhcccC
Confidence            4555555567899999999999999886542  111121100         0 0011111   0 01100     00001


Q ss_pred             hhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        353 KKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       353 StF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      |.  .|...+.-.+.......++|+||        --.|-++..-..+ +.++..+. +++.+|++||+.++...
T Consensus       100 S~--G~~qrv~laral~~~p~~lllDE--------P~~~LD~~~~~~l-~~~l~~~~-~~~tii~~sh~~~~~~~  162 (178)
T cd03247         100 SG--GERQRLALARILLQDAPIVLLDE--------PTVGLDPITERQL-LSLIFEVL-KDKTLIWITHHLTGIEH  162 (178)
T ss_pred             CH--HHHHHHHHHHHHhcCCCEEEEEC--------CcccCCHHHHHHH-HHHHHHHc-CCCEEEEEecCHHHHHh
Confidence            11  12223333344556778999999        6666665443333 33334443 37789999999987653

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.

>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=95.32  E-value=0.019  Score=54.63  Aligned_cols=120  Identities=7%  Similarity=-0.072  Sum_probs=62.0

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhcc----------ccccccce--ecc-ceeeecccccchhhhhc
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQT----------YLRTQCAH--FGC-TVIYSEAQKKQKKYVLE  358 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~----------~VpA~~a~--l~~-d~if~~iG~~qStF~~E  358 (577)
                      +|+.......+++|||.+|||+++++++-+.  ..+-|.          ||+....-  ..+ +.+........|.-  +
T Consensus        21 ~l~i~~Ge~~~i~G~nGsGKSTLl~~l~G~~--~~~~G~i~~~~~~~i~~~~q~~~~~~~tv~~nl~~~~~~~LS~G--~   96 (166)
T cd03223          21 SFEIKPGDRLLITGPSGTGKSSLFRALAGLW--PWGSGRIGMPEGEDLLFLPQRPYLPLGTLREQLIYPWDDVLSGG--E   96 (166)
T ss_pred             eEEECCCCEEEEECCCCCCHHHHHHHHhcCC--CCCCceEEECCCceEEEECCCCccccccHHHHhhccCCCCCCHH--H
Confidence            3444455566899999999999999886542  112221          22222110  011 11110001111221  2


Q ss_pred             hhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        359 VPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       359 m~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      -.++.-.+.......++|+||        --.|-++..-.    .+.+.|.+.+..+|++||+.++..+
T Consensus        97 ~~rv~laral~~~p~~lllDE--------Pt~~LD~~~~~----~l~~~l~~~~~tiiivsh~~~~~~~  153 (166)
T cd03223          97 QQRLAFARLLLHKPKFVFLDE--------ATSALDEESED----RLYQLLKELGITVISVGHRPSLWKF  153 (166)
T ss_pred             HHHHHHHHHHHcCCCEEEEEC--------CccccCHHHHH----HHHHHHHHhCCEEEEEeCChhHHhh
Confidence            222222334456778999999        55555544333    2333343336789999999876543

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

>KOG0220|consensus

Probab=95.22  E-value=0.0073  Score=69.08  Aligned_cols=32  Identities=19%  Similarity=0.280  Sum_probs=29.7

Q ss_pred             hhhhccccCccCCcchhhhhhhhhhccCcccc
Q psy13263        248 ACSYMKESGCTGESTLLTQLCNYESQTPSGCF  279 (577)
Q Consensus       248 dl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh  279 (577)
                      ++.+++|+||+||||+|||++..+||+|.|++
T Consensus       622 ~f~IITGPNMsGKSTYLKQvAl~~IMAQIGc~  653 (867)
T KOG0220|consen  622 NFLIITGPNMSGKSTYLKQVALCQIMAQIGSY  653 (867)
T ss_pred             ceEEEECCCCCcchHHHHHHHHHHHHHHhccC
Confidence            56678999999999999999999999999986

>cd03221 ABCF_EF-3 ABCF_EF-3 Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth

Probab=95.22  E-value=0.046  Score=50.87  Aligned_cols=110  Identities=4%  Similarity=-0.117  Sum_probs=60.9

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccc--cchhhhhchhhhHHhhhcC
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQK--KQKKYVLEVPSKYASKAKS  369 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~--~qStF~~Em~e~~~il~~a  369 (577)
                      +|........+|+|||.+|||+++++++-+.          +...-++-++.. ..++-  ..|.-+  ..++.-.+...
T Consensus        20 ~~~~~~Ge~~~i~G~nGsGKStLl~~l~G~~----------~~~~G~i~~~~~-~~i~~~~~lS~G~--~~rv~laral~   86 (144)
T cd03221          20 SLTINPGDRIGLVGRNGAGKSTLLKLIAGEL----------EPDEGIVTWGST-VKIGYFEQLSGGE--KMRLALAKLLL   86 (144)
T ss_pred             EEEECCCCEEEEECCCCCCHHHHHHHHcCCC----------CCCceEEEECCe-EEEEEEccCCHHH--HHHHHHHHHHh
Confidence            4444455566799999999999998764331          223333333100 00110  012222  22333333445


Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ....++|+||        --.|-++..-..    +.+.|.+.++.+|++||..+...
T Consensus        87 ~~p~illlDE--------P~~~LD~~~~~~----l~~~l~~~~~til~~th~~~~~~  131 (144)
T cd03221          87 ENPNLLLLDE--------PTNHLDLESIEA----LEEALKEYPGTVILVSHDRYFLD  131 (144)
T ss_pred             cCCCEEEEeC--------CccCCCHHHHHH----HHHHHHHcCCEEEEEECCHHHHH
Confidence            5678999999        666665543332    23333333678999999987664

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.

>KOG0218|consensus

Probab=95.16  E-value=0.0073  Score=69.07  Aligned_cols=86  Identities=16%  Similarity=0.215  Sum_probs=62.4

Q ss_pred             HhhhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCch
Q psy13263        235 LFHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKE  313 (577)
Q Consensus       235 lf~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsv  313 (577)
                      +.++|..+...--.|.+++|+||+|||.+.||+++..||+|.|.| |.-+..+..|++-|.+-.|...++     -|.++
T Consensus       818 fVPNdi~ls~egerc~IITGPNMGGKSsyIrQvALitIMAQiGsfVPAeea~l~IfdgvltRmGAsDnI~-----~grST  892 (1070)
T KOG0218|consen  818 FVPNDIMLSPEGERCNIITGPNMGGKSSYIRQVALITIMAQIGSFVPAEEARLSIFDGVLTRMGASDNII-----NGRST  892 (1070)
T ss_pred             cCCCcceecCCCceEEEEeCCCCCCchHHHHHHHHHHHHHHhcCccchHHhhhhHHhhHHHhhccccccc-----cchhH
Confidence            356777776666678899999999999999999999999999998 655556666777776544433332     24677


Q ss_pred             hHHHHHHHHHHH
Q psy13263        314 YDEVMDEIKSIE  325 (577)
Q Consensus       314 y~k~valI~~im  325 (577)
                      |+--+-.+.+|+
T Consensus       893 Fm~Emldt~eil  904 (1070)
T KOG0218|consen  893 FMVEMLDTLEIL  904 (1070)
T ss_pred             HHHHHHHHHHHH
Confidence            877665554443

>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity

Probab=95.10  E-value=0.037  Score=52.76  Aligned_cols=122  Identities=8%  Similarity=0.047  Sum_probs=62.9

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccc----------cccceecc---c-eeeecc--ccc--ch
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLR----------TQCAHFGC---T-VIYSEA--QKK--QK  353 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~Vp----------A~~a~l~~---d-~if~~i--G~~--qS  353 (577)
                      +|........+|+|||.+|||+++++++-+.  ...-|...-          ..+..++.   + .+|...  ...  .|
T Consensus        20 ~~~i~~Ge~~~i~G~nGsGKStLl~~l~G~~--~~~~G~i~~~g~~~~~~~~~~~~~i~~~~q~~~~~~~~tv~~~~~LS   97 (173)
T cd03230          20 SLTVEKGEIYGLLGPNGAGKTTLIKIILGLL--KPDSGEIKVLGKDIKKEPEEVKRRIGYLPEEPSLYENLTVRENLKLS   97 (173)
T ss_pred             EEEEcCCcEEEEECCCCCCHHHHHHHHhCCC--CCCCeEEEECCEEcccchHhhhccEEEEecCCccccCCcHHHHhhcC
Confidence            4444455567799999999999999886432  111111100          00011111   0 001000  000  01


Q ss_pred             hhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        354 KYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       354 tF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .  .|.+++.-.+..+....++|+||        --.|-++.....+. .+++.+.+++..+|++||+.++..
T Consensus        98 ~--G~~qrv~laral~~~p~illlDE--------Pt~~LD~~~~~~l~-~~l~~~~~~g~tiii~th~~~~~~  159 (173)
T cd03230          98 G--GMKQRLALAQALLHDPELLILDE--------PTSGLDPESRREFW-ELLRELKKEGKTILLSSHILEEAE  159 (173)
T ss_pred             H--HHHHHHHHHHHHHcCCCEEEEeC--------CccCCCHHHHHHHH-HHHHHHHHCCCEEEEECCCHHHHH
Confidence            1  12223333344556778999999        55565554443333 334445544778999999987665

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.

>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=94.98  E-value=0.052  Score=51.94  Aligned_cols=56  Identities=16%  Similarity=0.049  Sum_probs=37.9

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +.-.+......-++++||        --.|-++.- ......++..+.+. +..+|++||..++..
T Consensus       109 ~~la~al~~~p~llilDE--------P~~~LD~~~-~~~l~~~l~~~~~~~~~tiii~sH~~~~~~  165 (178)
T cd03229         109 VALARALAMDPDVLLLDE--------PTSALDPIT-RREVRALLKSLQAQLGITVVLVTHDLDEAA  165 (178)
T ss_pred             HHHHHHHHCCCCEEEEeC--------CcccCCHHH-HHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            333445566778999999        566655543 34445556666665 688999999987765

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.

>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]

Probab=94.96  E-value=0.036  Score=56.50  Aligned_cols=50  Identities=16%  Similarity=0.234  Sum_probs=40.9

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      ...|++|||        .=.|-+. |++.+-.-.++.|...+.-+|+.|||.+|.++..
T Consensus       162 ePkl~ILDE--------~DSGLDI-dalk~V~~~i~~lr~~~~~~liITHy~rll~~i~  211 (251)
T COG0396         162 EPKLAILDE--------PDSGLDI-DALKIVAEGINALREEGRGVLIITHYQRLLDYIK  211 (251)
T ss_pred             CCCEEEecC--------CCcCccH-HHHHHHHHHHHHHhcCCCeEEEEecHHHHHhhcC
Confidence            568999999        6666654 5667777778888888999999999999998765

>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C

Probab=94.88  E-value=0.033  Score=54.29  Aligned_cols=51  Identities=10%  Similarity=0.027  Sum_probs=34.3

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      +....++|+||        -..|-++..-..+...++..+.+.+..+|++||..++...
T Consensus       143 ~~~p~llllDE--------P~~~LD~~~~~~l~~~ll~~~~~~~~tvi~~sh~~~~~~~  193 (204)
T cd03250         143 YSDADIYLLDD--------PLSAVDAHVGRHIFENCILGLLLNNKTRILVTHQLQLLPH  193 (204)
T ss_pred             hcCCCEEEEeC--------ccccCCHHHHHHHHHHHHHHhccCCCEEEEEeCCHHHHhh
Confidence            34678999999        6666666444444444444444446899999999887764

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.

>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]

Probab=94.52  E-value=0.078  Score=52.93  Aligned_cols=60  Identities=23%  Similarity=0.273  Sum_probs=40.6

Q ss_pred             chhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh---cCCeEEEecchHHHHHHhh
Q psy13263        358 EVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ---IGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       358 Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~---~~~~~lfaTHy~eL~~l~~  429 (577)
                      |-.+.+..++..+...|+|-||           =|.-.| -.+||-|+.-|.+   .|..+|+|||+.+|.+-..
T Consensus       142 EQQRvaIARAiV~~P~vLlADE-----------PTGNLD-p~~s~~im~lfeeinr~GtTVl~ATHd~~lv~~~~  204 (223)
T COG2884         142 EQQRVAIARAIVNQPAVLLADE-----------PTGNLD-PDLSWEIMRLFEEINRLGTTVLMATHDLELVNRMR  204 (223)
T ss_pred             HHHHHHHHHHHccCCCeEeecC-----------CCCCCC-hHHHHHHHHHHHHHhhcCcEEEEEeccHHHHHhcc
Confidence            3344444445556678888999           233333 2678888765544   4899999999999988654

>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance

Probab=94.45  E-value=0.22  Score=48.53  Aligned_cols=54  Identities=11%  Similarity=0.103  Sum_probs=36.1

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ++..+....++|+||        --.|-++..-..+ +.++..+.+.+..+|++||..+....
T Consensus       138 a~al~~~p~llllDE--------Pt~~LD~~~~~~l-~~~l~~~~~~~~tii~~tH~~~~~~~  191 (208)
T cd03268         138 ALALLGNPDLLILDE--------PTNGLDPDGIKEL-RELILSLRDQGITVLISSHLLSEIQK  191 (208)
T ss_pred             HHHHhcCCCEEEECC--------CcccCCHHHHHHH-HHHHHHHHHCCCEEEEEcCCHHHHHH
Confidence            344556678999999        6666655443333 34555555557889999999887653

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.

>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional

Probab=94.38  E-value=0.21  Score=49.44  Aligned_cols=59  Identities=15%  Similarity=0.073  Sum_probs=38.3

Q ss_pred             hhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHH
Q psy13263        360 PSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARR  427 (577)
Q Consensus       360 ~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l  427 (577)
                      ..+.-.+......-|+|+||        --.|-++.... ..+.++..+.+. +..+|++||+.+....
T Consensus       153 qrl~la~al~~~p~llllDE--------Pt~~LD~~~~~-~l~~~l~~~~~~~~~tii~~sH~~~~~~~  212 (228)
T PRK10584        153 QRVALARAFNGRPDVLFADE--------PTGNLDRQTGD-KIADLLFSLNREHGTTLILVTHDLQLAAR  212 (228)
T ss_pred             HHHHHHHHHhcCCCEEEEeC--------CCCCCCHHHHH-HHHHHHHHHHHhcCCEEEEEecCHHHHHh
Confidence            33333344456678999999        66676664433 344445555544 7899999999886543

>PRK13543 cytochrome c biogenesis protein CcmA; Provisional

Probab=94.33  E-value=0.099  Score=51.53  Aligned_cols=53  Identities=9%  Similarity=-0.004  Sum_probs=36.1

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.......++|+||        --.|-++... ...+.++..+.+.+..+||+||..+...
T Consensus       149 aral~~~p~llllDE--------Pt~~LD~~~~-~~l~~~l~~~~~~~~tiii~sH~~~~~~  201 (214)
T PRK13543        149 ARLWLSPAPLWLLDE--------PYANLDLEGI-TLVNRMISAHLRGGGAALVTTHGAYAAP  201 (214)
T ss_pred             HHHHhcCCCEEEEeC--------CcccCCHHHH-HHHHHHHHHHHhCCCEEEEEecChhhhh
Confidence            344555668999999        5566655533 3444455555566789999999987664

>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=94.33  E-value=0.079  Score=52.61  Aligned_cols=57  Identities=18%  Similarity=0.130  Sum_probs=38.0

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .+.-.+.......|+|+||        --.|-++.--..+ +.++..+.+. +..+|++||..+...
T Consensus       148 rv~la~al~~~p~lllLDE--------P~~~LD~~~~~~l-~~~l~~~~~~~~~tvii~sH~~~~~~  205 (233)
T cd03258         148 RVGIARALANNPKVLLCDE--------ATSALDPETTQSI-LALLRDINRELGLTIVLITHEMEVVK  205 (233)
T ss_pred             HHHHHHHHhcCCCEEEecC--------CCCcCCHHHHHHH-HHHHHHHHHHcCCEEEEEeCCHHHHH
Confidence            3333344556678999999        7777766544433 3444455554 789999999987654

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.

>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity

Probab=94.32  E-value=0.079  Score=51.76  Aligned_cols=53  Identities=9%  Similarity=0.126  Sum_probs=35.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.......++|+||        --.|-++.--..+. .+++.+.+.++.+|++||+.++..
T Consensus       140 a~al~~~p~~lllDE--------P~~~LD~~~~~~~~-~~l~~~~~~~~tii~~sH~~~~~~  192 (210)
T cd03269         140 IAAVIHDPELLILDE--------PFSGLDPVNVELLK-DVIRELARAGKTVILSTHQMELVE  192 (210)
T ss_pred             HHHHhcCCCEEEEeC--------CCcCCCHHHHHHHH-HHHHHHHHCCCEEEEECCCHHHHH
Confidence            344455668999999        66666665433333 344455555789999999987654

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.

>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=94.28  E-value=0.072  Score=55.05  Aligned_cols=47  Identities=11%  Similarity=0.181  Sum_probs=38.2

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ..-|++|||        -..|=+|.---+|=-+|.+ |.+.|+.+||+||-++=.+
T Consensus       148 ePeLlILDE--------PFSGLDPVN~elLk~~I~~-lk~~GatIifSsH~Me~vE  194 (300)
T COG4152         148 EPELLILDE--------PFSGLDPVNVELLKDAIFE-LKEEGATIIFSSHRMEHVE  194 (300)
T ss_pred             CCCEEEecC--------CccCCChhhHHHHHHHHHH-HHhcCCEEEEecchHHHHH
Confidence            668999999        8999999987777766664 5666999999999976544

>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]

Probab=94.26  E-value=0.096  Score=54.80  Aligned_cols=67  Identities=12%  Similarity=0.099  Sum_probs=44.7

Q ss_pred             hhhhhchhhhHH-hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcC-CeEEEecchHHHHHHh
Q psy13263        353 KKYVLEVPSKYA-SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIG-CLTVFATHYHSVARRL  428 (577)
Q Consensus       353 StF~~Em~e~~~-il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~-~~~lfaTHy~eL~~l~  428 (577)
                      ++|..-|++-.. .........|++|||        --.|=++. +....+.++..|.+.+ ..+|++||+.+-....
T Consensus       135 ~~lS~G~kqrl~ia~aL~~~P~lliLDE--------Pt~GLDp~-~~~~~~~~l~~l~~~g~~tvlissH~l~e~~~~  203 (293)
T COG1131         135 RTLSGGMKQRLSIALALLHDPELLILDE--------PTSGLDPE-SRREIWELLRELAKEGGVTILLSTHILEEAEEL  203 (293)
T ss_pred             hhcCHHHHHHHHHHHHHhcCCCEEEECC--------CCcCCCHH-HHHHHHHHHHHHHhCCCcEEEEeCCcHHHHHHh
Confidence            446655555332 344556669999999        55555553 3445566677777765 8999999998776654

>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos)

Probab=94.26  E-value=0.072  Score=51.18  Aligned_cols=52  Identities=13%  Similarity=0.134  Sum_probs=35.0

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.......++|+||        --.|-++..-..+.. ++..+.+.+..+|++||+.+...
T Consensus       117 ~al~~~p~llllDE--------P~~~LD~~~~~~l~~-~l~~~~~~~~tiii~sh~~~~~~  168 (182)
T cd03215         117 RWLARDPRVLILDE--------PTRGVDVGAKAEIYR-LIRELADAGKAVLLISSELDELL  168 (182)
T ss_pred             HHHccCCCEEEECC--------CCcCCCHHHHHHHHH-HHHHHHHCCCEEEEEeCCHHHHH
Confidence            34455778999999        667776655444443 44455555788999999975443

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.

>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota

Probab=94.18  E-value=0.23  Score=48.44  Aligned_cols=52  Identities=10%  Similarity=0.020  Sum_probs=35.9

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.......++|+||        --.|-++..-..+ +.++..+.+.+..+|++||+.+...
T Consensus       139 ral~~~p~llllDE--------Pt~~LD~~~~~~l-~~~l~~~~~~~~tii~~sH~~~~~~  190 (205)
T cd03226         139 AALLSGKDLLIFDE--------PTSGLDYKNMERV-GELIRELAAQGKAVIVITHDYEFLA  190 (205)
T ss_pred             HHHHhCCCEEEEeC--------CCccCCHHHHHHH-HHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            33455668999999        6667766544333 4555556555788999999987654

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.

>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR)

Probab=94.11  E-value=0.2  Score=48.74  Aligned_cols=55  Identities=9%  Similarity=0.089  Sum_probs=36.1

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHH--HHHHhh
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHS--VARRLR  429 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~e--L~~l~~  429 (577)
                      +..+....++|+||        --.|-++..-. ....++..+.+++..+|++||..+  +..+..
T Consensus       124 ral~~~p~illlDE--------P~~~LD~~~~~-~l~~~l~~~~~~~~tiii~sh~~~~~~~~~~d  180 (194)
T cd03213         124 LELVSNPSLLFLDE--------PTSGLDSSSAL-QVMSLLRRLADTGRTIICSIHQPSSEIFELFD  180 (194)
T ss_pred             HHHHcCCCEEEEeC--------CCcCCCHHHHH-HHHHHHHHHHhCCCEEEEEecCchHHHHHhcC
Confidence            33455667999999        77777765443 344455556555788999999974  444443

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.

>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=94.00  E-value=0.09  Score=51.83  Aligned_cols=57  Identities=12%  Similarity=0.018  Sum_probs=35.7

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~  426 (577)
                      ++...+.......++|+||        --.|-++.--..+.. ++..+.+ .+..+|++||+.+...
T Consensus       139 rl~la~al~~~p~lllLDE--------Pt~~LD~~~~~~~~~-~l~~~~~~~~~tiii~sH~~~~~~  196 (220)
T cd03293         139 RVALARALAVDPDVLLLDE--------PFSALDALTREQLQE-ELLDIWRETGKTVLLVTHDIDEAV  196 (220)
T ss_pred             HHHHHHHHHcCCCEEEECC--------CCCCCCHHHHHHHHH-HHHHHHHHcCCEEEEEecCHHHHH
Confidence            3333344455678999999        666666554443333 3344443 3788999999987543

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.

>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms

Probab=93.98  E-value=0.16  Score=49.32  Aligned_cols=50  Identities=2%  Similarity=-0.059  Sum_probs=35.9

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL  428 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~  428 (577)
                      ....++++||        .-.|-++..-..+.. ++..+...++.+|++||..++...+
T Consensus       115 ~~p~llilDE--------p~~~LD~~~~~~i~~-~L~~~~~~g~tiIiiSH~~~~~~~a  164 (178)
T cd03239         115 KPSPFYVLDE--------IDAALDPTNRRRVSD-MIKEMAKHTSQFIVITLKKEMFENA  164 (178)
T ss_pred             CCCCEEEEEC--------CCCCCCHHHHHHHHH-HHHHHHhCCCEEEEEECCHHHHhhC
Confidence            4558899999        777777776655554 3444555468999999999877643

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.

>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively

Probab=93.87  E-value=0.32  Score=47.41  Aligned_cols=53  Identities=15%  Similarity=0.093  Sum_probs=34.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.......|+|+||        --.|-++.. ....+.++..+.+.+..+|++||..+...
T Consensus       147 a~al~~~p~llllDE--------P~~~LD~~~-~~~l~~~l~~~~~~~~tvi~~sh~~~~~~  199 (213)
T cd03262         147 ARALAMNPKVMLFDE--------PTSALDPEL-VGEVLDVMKDLAEEGMTMVVVTHEMGFAR  199 (213)
T ss_pred             HHHHhcCCCEEEEeC--------CccCCCHHH-HHHHHHHHHHHHHcCCEEEEEeCCHHHHH
Confidence            344455668999999        555555433 33444455555555778999999987654

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

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=93.85  E-value=0.052  Score=64.15  Aligned_cols=57  Identities=18%  Similarity=0.204  Sum_probs=41.5

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcc-ccccccccccc
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMS-ELLKYFENAFD  294 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe-~~l~~~~n~F~  294 (577)
                      ++|..+.. ...+.+++|+|++||||+||+++..+++++.|+| |.-+ ..+.+|.+-|.
T Consensus       318 pndi~l~~-~~~~~iITGpN~gGKTt~lktigl~~~maq~G~~vpa~~~~~i~~~~~i~~  376 (782)
T PRK00409        318 PKDISLGF-DKTVLVITGPNTGGKTVTLKTLGLAALMAKSGLPIPANEPSEIPVFKEIFA  376 (782)
T ss_pred             CceeEECC-CceEEEEECCCCCCcHHHHHHHHHHHHHHHhCCCcccCCCccccccceEEE
Confidence            34444433 2356789999999999999999999999999987 5443 34556655554

>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters

Probab=93.81  E-value=0.1  Score=50.58  Aligned_cols=49  Identities=12%  Similarity=0.070  Sum_probs=34.3

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHS  423 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~e  423 (577)
                      ........++|+||        -..|-++..-. ..+.++..+.+.++.+|++||+.+
T Consensus       121 ~al~~~p~vlllDE--------P~~~LD~~~~~-~l~~~l~~~~~~~~tiiivtH~~~  169 (192)
T cd03232         121 VELAAKPSILFLDE--------PTSGLDSQAAY-NIVRFLKKLADSGQAILCTIHQPS  169 (192)
T ss_pred             HHHhcCCcEEEEeC--------CCcCCCHHHHH-HHHHHHHHHHHcCCEEEEEEcCCh
Confidence            34455678999999        67776655443 444455566666789999999976

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.

>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=93.53  E-value=0.13  Score=50.64  Aligned_cols=58  Identities=16%  Similarity=0.155  Sum_probs=37.6

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l  427 (577)
                      ++.-.+.......|+|+||        --.|-++.--. ..+.++..+.+. +..+|++||..+....
T Consensus       139 r~~la~al~~~p~llllDE--------Pt~~LD~~~~~-~l~~~l~~~~~~~~~tvi~~tH~~~~~~~  197 (220)
T cd03265         139 RLEIARSLVHRPEVLFLDE--------PTIGLDPQTRA-HVWEYIEKLKEEFGMTILLTTHYMEEAEQ  197 (220)
T ss_pred             HHHHHHHHhcCCCEEEEcC--------CccCCCHHHHH-HHHHHHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            3333344556678999999        66666664433 333445555554 7889999999876553

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.

>COG3910 Predicted ATPase [General function prediction only]

Probab=93.33  E-value=0.14  Score=51.20  Aligned_cols=52  Identities=13%  Similarity=0.111  Sum_probs=40.6

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+..+.+.+.+|||        --.|-|+.--++|. |++..|.+.|+.+|++||-.=|..
T Consensus       141 ~~rf~~~GiYiLDE--------PEa~LSp~RQlell-a~l~~la~sGaQ~IiATHSPiLlA  192 (233)
T COG3910         141 HNRFNGQGIYILDE--------PEAALSPSRQLELL-AILRDLADSGAQIIIATHSPILLA  192 (233)
T ss_pred             HHHhccCceEEecC--------ccccCCHHHHHHHH-HHHHHHHhcCCeEEEEecChhhee
Confidence            34566789999999        66666766666654 788899999999999999985543

>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system

Probab=93.29  E-value=0.43  Score=47.43  Aligned_cols=53  Identities=11%  Similarity=0.133  Sum_probs=36.0

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .+..+....++|+||        --.|-++.-- ...+.++..+.+. +..+|++||..+...
T Consensus       156 a~al~~~p~llllDE--------Pt~~LD~~~~-~~l~~~l~~~~~~~~~tii~~tH~~~~~~  209 (241)
T cd03256         156 ARALMQQPKLILADE--------PVASLDPASS-RQVMDLLKRINREEGITVIVSLHQVDLAR  209 (241)
T ss_pred             HHHHhcCCCEEEEeC--------ccccCCHHHH-HHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            344456678999999        6666665433 3344555566554 788999999987765

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.

>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=93.24  E-value=0.49  Score=47.10  Aligned_cols=57  Identities=11%  Similarity=0.046  Sum_probs=37.4

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      ++...+.......++|+||        --.|-++.- ....+.++..+.+. +..+|++||..+...
T Consensus       144 rv~ia~al~~~p~llllDE--------Pt~~LD~~~-~~~l~~~l~~~~~~~~~tvi~vsH~~~~~~  201 (235)
T cd03261         144 RVALARALALDPELLLYDE--------PTAGLDPIA-SGVIDDLIRSLKKELGLTSIMVTHDLDTAF  201 (235)
T ss_pred             HHHHHHHHhcCCCEEEecC--------CcccCCHHH-HHHHHHHHHHHHHhcCcEEEEEecCHHHHH
Confidence            3333444556778999999        666666543 33334455556554 789999999987654

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.

>PRK11124 artP arginine transporter ATP-binding subunit; Provisional

Probab=93.18  E-value=0.14  Score=51.10  Aligned_cols=53  Identities=17%  Similarity=0.123  Sum_probs=34.8

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.......|+|+||        --.|-++.- ......+++.+.+.+..+|++||+.+...
T Consensus       153 aral~~~p~llilDE--------Pt~~LD~~~-~~~l~~~l~~~~~~~~tii~~sh~~~~~~  205 (242)
T PRK11124        153 ARALMMEPQVLLFDE--------PTAALDPEI-TAQIVSIIRELAETGITQVIVTHEVEVAR  205 (242)
T ss_pred             HHHHhcCCCEEEEcC--------CCCcCCHHH-HHHHHHHHHHHHHcCCEEEEEeCCHHHHH
Confidence            344455668999999        656665533 33333445555555788999999987764

>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional

Probab=93.12  E-value=0.44  Score=47.30  Aligned_cols=58  Identities=5%  Similarity=0.024  Sum_probs=37.3

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~l  427 (577)
                      ++.-.+.......++|+||        --.|-++..- .....++..+.+ .+..+|++||..+....
T Consensus       145 rv~laral~~~p~llllDE--------Pt~~LD~~~~-~~l~~~l~~~~~~~~~tvii~sh~~~~~~~  203 (225)
T PRK10247        145 RISLIRNLQFMPKVLLLDE--------ITSALDESNK-HNVNEIIHRYVREQNIAVLWVTHDKDEINH  203 (225)
T ss_pred             HHHHHHHHhcCCCEEEEeC--------CcccCCHHHH-HHHHHHHHHHHHhcCCEEEEEECChHHHHh
Confidence            3333344556778999999        6666665443 333344445544 37899999999887653

>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional

Probab=93.04  E-value=0.51  Score=47.49  Aligned_cols=53  Identities=4%  Similarity=0.053  Sum_probs=36.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .........|+|+||        --.|-++.--. ..+.++..+.+. ++.+|++||+.+...
T Consensus       165 a~al~~~p~llllDE--------Pt~~LD~~~~~-~l~~~L~~~~~~~~~tii~~sH~~~~~~  218 (255)
T PRK11300        165 ARCMVTQPEILMLDE--------PAAGLNPKETK-ELDELIAELRNEHNVTVLLIEHDMKLVM  218 (255)
T ss_pred             HHHHhcCCCEEEEcC--------CccCCCHHHHH-HHHHHHHHHHhhcCCEEEEEeCCHHHHH
Confidence            344556778999999        65665555433 334555566665 789999999987764

>TIGR01188 drrA daunorubicin resistance ABC transporter ATP-binding subunit

Probab=92.93  E-value=0.22  Score=51.94  Aligned_cols=52  Identities=13%  Similarity=0.118  Sum_probs=35.9

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +......-|+|+||        --.|=++.-. ...+.++..+.+.+..+|++||+.+...
T Consensus       137 ~al~~~p~lllLDE--------Pt~gLD~~~~-~~l~~~l~~~~~~g~tvi~~sH~~~~~~  188 (302)
T TIGR01188       137 ASLIHQPDVLFLDE--------PTTGLDPRTR-RAIWDYIRALKEEGVTILLTTHYMEEAD  188 (302)
T ss_pred             HHHhcCCCEEEEeC--------CCcCCCHHHH-HHHHHHHHHHHhCCCEEEEECCCHHHHH
Confidence            34455678999999        6666665443 3444555666655889999999987655

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.

>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import

Probab=92.87  E-value=0.2  Score=50.15  Aligned_cols=56  Identities=18%  Similarity=0.065  Sum_probs=36.6

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +.-++.......++|+||        --.|-++.-- ...+.++..+.+. +..+|++||+.+...
T Consensus       145 l~la~al~~~p~llllDE--------P~~~LD~~~~-~~l~~~l~~~~~~~~~tvii~sH~~~~~~  201 (239)
T cd03296         145 VALARALAVEPKVLLLDE--------PFGALDAKVR-KELRRWLRRLHDELHVTTVFVTHDQEEAL  201 (239)
T ss_pred             HHHHHHHhcCCCEEEEcC--------CcccCCHHHH-HHHHHHHHHHHHHcCCEEEEEeCCHHHHH
Confidence            333344455668999999        6666666443 3344455566554 788999999987543

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.

>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed

Probab=92.87  E-value=0.15  Score=55.82  Aligned_cols=48  Identities=15%  Similarity=0.070  Sum_probs=32.2

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ....++||||        --.|=++.--. -...++..|.+.+..+|++||+.++..
T Consensus       156 ~~P~iLLLDE--------PtsgLD~~~~~-~l~~lL~~l~~~g~TIIivsHdl~~~~  203 (402)
T PRK09536        156 QATPVLLLDE--------PTASLDINHQV-RTLELVRRLVDDGKTAVAAIHDLDLAA  203 (402)
T ss_pred             cCCCEEEEEC--------CcccCCHHHHH-HHHHHHHHHHhcCCEEEEEECCHHHHH
Confidence            3678999999        44444443222 233555666655778999999988875

>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=92.75  E-value=0.23  Score=49.37  Aligned_cols=54  Identities=9%  Similarity=0.136  Sum_probs=35.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      .+.......++|+||        --.|-++.- ....+.++..+.+.+..+|++||..+....
T Consensus       155 a~al~~~p~llllDE--------Pt~~LD~~~-~~~l~~~l~~~~~~~~tii~vsH~~~~~~~  208 (236)
T cd03219         155 ARALATDPKLLLLDE--------PAAGLNPEE-TEELAELIRELRERGITVLLVEHDMDVVMS  208 (236)
T ss_pred             HHHHhcCCCEEEEcC--------CcccCCHHH-HHHHHHHHHHHHHCCCEEEEEecCHHHHHH
Confidence            344455678999999        555555433 333444555555557889999999887643

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).

>TIGR03864 PQQ_ABC_ATP ABC transporter, ATP-binding subunit, PQQ-dependent alcohol dehydrogenase system

Probab=92.75  E-value=0.24  Score=49.46  Aligned_cols=58  Identities=12%  Similarity=0.110  Sum_probs=39.1

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~l  427 (577)
                      ++.-.+.......++|+||        --.|-++.--..+.. ++..+.+ .+..+|++||..+....
T Consensus       140 rl~laral~~~p~llllDE--------P~~~LD~~~~~~l~~-~l~~~~~~~~~tiii~sH~~~~~~~  198 (236)
T TIGR03864       140 RVEIARALLHRPALLLLDE--------PTVGLDPASRAAIVA-HVRALCRDQGLSVLWATHLVDEIEA  198 (236)
T ss_pred             HHHHHHHHhcCCCEEEEcC--------CccCCCHHHHHHHHH-HHHHHHHhCCCEEEEEecChhhHhh
Confidence            3333444566778999999        667766665555544 3444554 47889999999987653

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.

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=92.75  E-value=0.085  Score=51.11  Aligned_cols=44  Identities=27%  Similarity=0.341  Sum_probs=33.1

Q ss_pred             hhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccc
Q psy13263        250 SYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAF  293 (577)
Q Consensus       250 ~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F  293 (577)
                      .+++|+|++||||++|+++..+++++.|++ |.-...+.++...|
T Consensus         2 ~~ltG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il   46 (185)
T smart00534        2 VIITGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIF   46 (185)
T ss_pred             EEEECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEE
Confidence            457999999999999999999999999987 33333344444433

>TIGR03740 galliderm_ABC gallidermin-class lantibiotic protection ABC transporter, ATP-binding subunit

Probab=92.61  E-value=0.24  Score=48.86  Aligned_cols=53  Identities=17%  Similarity=0.201  Sum_probs=35.8

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.......++|+||        --.|-++.--..+ +.++..+.+.+..+|++||+.+...
T Consensus       136 aral~~~p~llllDE--------P~~~LD~~~~~~l-~~~L~~~~~~~~tiii~sH~~~~~~  188 (223)
T TIGR03740       136 AIALLNHPKLLILDE--------PTNGLDPIGIQEL-RELIRSFPEQGITVILSSHILSEVQ  188 (223)
T ss_pred             HHHHhcCCCEEEECC--------CccCCCHHHHHHH-HHHHHHHHHCCCEEEEEcCCHHHHH
Confidence            344556778999999        6666665544433 4444455555778999999988664

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.

>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=92.58  E-value=0.17  Score=49.67  Aligned_cols=53  Identities=15%  Similarity=0.160  Sum_probs=35.3

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+......-++|+||        --.|-++..-. ..+.++..+.+.++.+|++||..+...
T Consensus       148 aral~~~p~illlDE--------Pt~~LD~~~~~-~l~~~l~~~~~~~~tii~~tH~~~~~~  200 (218)
T cd03266         148 ARALVHDPPVLLLDE--------PTTGLDVMATR-ALREFIRQLRALGKCILFSTHIMQEVE  200 (218)
T ss_pred             HHHHhcCCCEEEEcC--------CCcCCCHHHHH-HHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            344456668999999        66666654433 334445555555789999999987654

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.

>PRK13539 cytochrome c biogenesis protein CcmA; Provisional

Probab=92.56  E-value=0.16  Score=49.71  Aligned_cols=58  Identities=9%  Similarity=0.018  Sum_probs=38.3

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ++.-++......-|+|+||        --.|-++..-..| +.++..+.+.+..+|++||..+....
T Consensus       135 rl~la~al~~~p~llllDE--------Pt~~LD~~~~~~l-~~~l~~~~~~~~tiii~sH~~~~~~~  192 (207)
T PRK13539        135 RVALARLLVSNRPIWILDE--------PTAALDAAAVALF-AELIRAHLAQGGIVIAATHIPLGLPG  192 (207)
T ss_pred             HHHHHHHHhcCCCEEEEeC--------CcccCCHHHHHHH-HHHHHHHHHCCCEEEEEeCCchhhcc
Confidence            3333344555678999999        6666666555444 34445555558899999999876653

>PRK13540 cytochrome c biogenesis protein CcmA; Provisional

Probab=92.55  E-value=0.47  Score=46.18  Aligned_cols=60  Identities=5%  Similarity=-0.077  Sum_probs=37.6

Q ss_pred             hhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh
Q psy13263        360 PSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL  428 (577)
Q Consensus       360 ~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~  428 (577)
                      .++.-.+......-++|+||        --.|-+...-..+...+ ..+.+.++.+|++||..++.+.+
T Consensus       134 ~rv~laral~~~p~~lilDE--------P~~~LD~~~~~~l~~~l-~~~~~~~~tiii~sh~~~~~~~~  193 (200)
T PRK13540        134 RQVALLRLWMSKAKLWLLDE--------PLVALDELSLLTIITKI-QEHRAKGGAVLLTSHQDLPLNKA  193 (200)
T ss_pred             HHHHHHHHHhcCCCEEEEeC--------CCcccCHHHHHHHHHHH-HHHHHcCCEEEEEeCCchhcccc
Confidence            34443444556778999999        66665544433333333 33444578999999998877643

>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]

Probab=92.52  E-value=0.12  Score=52.24  Aligned_cols=31  Identities=10%  Similarity=0.169  Sum_probs=26.6

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIK  322 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~  322 (577)
                      +|...+....|+.|||..|||+.++.++-+-
T Consensus        22 SF~ae~Gei~GlLG~NGAGKTT~LRmiatlL   52 (245)
T COG4555          22 SFEAEEGEITGLLGENGAGKTTLLRMIATLL   52 (245)
T ss_pred             eEEeccceEEEEEcCCCCCchhHHHHHHHhc
Confidence            6777777788999999999999999998654

>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=92.50  E-value=0.46  Score=48.65  Aligned_cols=57  Identities=5%  Similarity=-0.115  Sum_probs=37.0

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .+.-.+.......|+|+||        -..|-++.. ....+.++..+.+. +..+|++||..+...
T Consensus       150 rl~laral~~~p~lllLDE--------P~~gLD~~~-~~~l~~~l~~~~~~~~~tiii~sH~~~~~~  207 (271)
T PRK13632        150 RVAIASVLALNPEIIIFDE--------STSMLDPKG-KREIKKIMVDLRKTRKKTLISITHDMDEAI  207 (271)
T ss_pred             HHHHHHHHHcCCCEEEEeC--------CcccCCHHH-HHHHHHHHHHHHHhcCcEEEEEEechhHHh
Confidence            3333444566778999999        666666633 33344455555554 478999999987664

>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional

Probab=92.47  E-value=0.23  Score=49.44  Aligned_cols=54  Identities=17%  Similarity=0.169  Sum_probs=36.1

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARR  427 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~l  427 (577)
                      .+.......++|+||        --.|-++.-- ...+.++..+.+ .+..+|++||+.+....
T Consensus       157 a~al~~~p~lllLDE--------Pt~~LD~~~~-~~l~~~l~~~~~~~g~tvii~sH~~~~~~~  211 (233)
T PRK11629        157 ARALVNNPRLVLADE--------PTGNLDARNA-DSIFQLLGELNRLQGTAFLVVTHDLQLAKR  211 (233)
T ss_pred             HHHHhcCCCEEEEeC--------CCCCCCHHHH-HHHHHHHHHHHHhCCCEEEEEeCCHHHHHh
Confidence            344456778999999        6666665433 334445555554 37899999999887653

>COG4133 CcmA ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones]

Probab=92.44  E-value=0.29  Score=48.80  Aligned_cols=155  Identities=9%  Similarity=0.043  Sum_probs=76.6

Q ss_pred             hhhhccccCccCCcchhhhhhhhhhccCcccccCccccccccccccccc-ccccccccCCCCCCCchhHHHHHHHHHHHH
Q psy13263        248 ACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHK-EASSAGNIIPKAGVDKEYDEVMDEIKSIEK  326 (577)
Q Consensus       248 dl~~mkGsn~~GKStlLk~i~~~~i~i~~GrhPlLe~~l~~~~n~F~~~-~a~~~~I~gPN~gGKsvy~k~valI~~ima  326 (577)
                      .+++++|+|-.|||++||.++.  ++-..+.+-.+...  .+  .-... -.+....+|=+.|.|+..- ....+. +-.
T Consensus        29 e~~~i~G~NG~GKTtLLRilaG--Ll~p~~G~v~~~~~--~i--~~~~~~~~~~l~yLGH~~giK~eLT-a~ENL~-F~~  100 (209)
T COG4133          29 EALQITGPNGAGKTTLLRILAG--LLRPDAGEVYWQGE--PI--QNVRESYHQALLYLGHQPGIKTELT-ALENLH-FWQ  100 (209)
T ss_pred             CEEEEECCCCCcHHHHHHHHHc--ccCCCCCeEEecCC--CC--ccchhhHHHHHHHhhccccccchhh-HHHHHH-HHH
Confidence            4677899999999999999864  22222222111100  00  00111 1133446677777776532 222233 333


Q ss_pred             Hhccc-----cccccceecc-ceeeecccccchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhH
Q psy13263        327 EIQTY-----LRTQCAHFGC-TVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVI  400 (577)
Q Consensus       327 qig~~-----VpA~~a~l~~-d~if~~iG~~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~AL  400 (577)
                      .+...     +++.-+.+++ +..-.-.+. .|.=+.  ++++..+--.+...|-|+||        -..+-+ .+|.++
T Consensus       101 ~~~~~~~~~~i~~Al~~vgL~g~~dlp~~~-LSAGQq--RRvAlArL~ls~~pLWiLDE--------P~taLD-k~g~a~  168 (209)
T COG4133         101 RFHGSGNAATIWEALAQVGLAGLEDLPVGQ-LSAGQQ--RRVALARLWLSPAPLWILDE--------PFTALD-KEGVAL  168 (209)
T ss_pred             HHhCCCchhhHHHHHHHcCcccccccchhh-cchhHH--HHHHHHHHHcCCCCceeecC--------cccccC-HHHHHH
Confidence            33322     2222233444 221111111 021111  12222233467789999999        333332 246666


Q ss_pred             HHHHHHHHHhcCCeEEEecchH
Q psy13263        401 ARVTLEKFLQIGCLTVFATHYH  422 (577)
Q Consensus       401 A~AIlE~L~~~~~~~lfaTHy~  422 (577)
                      ..+++..=+.++-.||+|||..
T Consensus       169 l~~l~~~H~~~GGiVllttHq~  190 (209)
T COG4133         169 LTALMAAHAAQGGIVLLTTHQP  190 (209)
T ss_pred             HHHHHHHHhcCCCEEEEecCCc
Confidence            6666655555588999999975

>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function

Probab=92.41  E-value=0.47  Score=46.61  Aligned_cols=48  Identities=13%  Similarity=0.069  Sum_probs=32.0

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ....++|+||        --.|-++..-..+.. +++.+.+ ++.+|++||..++.+.
T Consensus       134 ~~~~illlDE--------P~~~LD~~~~~~l~~-~l~~~~~-~~tiIiitH~~~~~~~  181 (197)
T cd03278         134 RPSPFCVLDE--------VDAALDDANVERFAR-LLKEFSK-ETQFIVITHRKGTMEA  181 (197)
T ss_pred             CCCCEEEEeC--------CcccCCHHHHHHHHH-HHHHhcc-CCEEEEEECCHHHHhh
Confidence            3447999999        766766665444443 3344433 6779999999987553

Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w

>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK

Probab=92.29  E-value=0.19  Score=49.08  Aligned_cols=52  Identities=19%  Similarity=0.195  Sum_probs=34.0

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +......-++|+||        --.|-++..-.. .+.++..+.+. ++.+|++||..+...
T Consensus       143 ral~~~p~llllDE--------Pt~~LD~~~~~~-l~~~l~~~~~~~~~tvi~~sH~~~~~~  195 (213)
T cd03301         143 RAIVREPKVFLMDE--------PLSNLDAKLRVQ-MRAELKRLQQRLGTTTIYVTHDQVEAM  195 (213)
T ss_pred             HHHhcCCCEEEEcC--------CcccCCHHHHHH-HHHHHHHHHHHcCCEEEEEeCCHHHHH
Confidence            34455668999999        556655544333 33445555554 789999999986554

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.

>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed

Probab=92.21  E-value=0.22  Score=49.78  Aligned_cols=52  Identities=12%  Similarity=0.122  Sum_probs=35.4

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.......++|+||        --.|-++.--..+.. ++..+.+.+..+|++||+.+...
T Consensus       149 ~al~~~p~llllDE--------P~~~LD~~~~~~l~~-~l~~~~~~~~tiii~sH~~~~~~  200 (240)
T PRK09493        149 RALAVKPKLMLFDE--------PTSALDPELRHEVLK-VMQDLAEEGMTMVIVTHEIGFAE  200 (240)
T ss_pred             HHHhcCCCEEEEcC--------CcccCCHHHHHHHHH-HHHHHHHcCCEEEEEeCCHHHHH
Confidence            33455668999999        666666654444433 45555555778999999988765

>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional

Probab=92.18  E-value=0.23  Score=50.34  Aligned_cols=53  Identities=15%  Similarity=0.084  Sum_probs=34.1

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      +.......++|+||        --.|-++..-..|. .++..|.+.++.+|++||+.+....
T Consensus       165 ral~~~p~llllDE--------Pt~~LD~~~~~~l~-~~l~~l~~~g~tiiivsH~~~~~~~  217 (257)
T PRK10619        165 RALAMEPEVLLFDE--------PTSALDPELVGEVL-RIMQQLAEEGKTMVVVTHEMGFARH  217 (257)
T ss_pred             HHHhcCCCEEEEeC--------CcccCCHHHHHHHH-HHHHHHHhcCCEEEEEeCCHHHHHH
Confidence            34455667999999        55555544333333 3444555558899999999877653

>PRK14250 phosphate ABC transporter ATP-binding protein; Provisional

Probab=92.13  E-value=0.66  Score=46.57  Aligned_cols=52  Identities=13%  Similarity=0.136  Sum_probs=35.3

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +.......++|+||        --.|-++.. ......++..+.+. +..+|++||+.+...
T Consensus       144 ~al~~~p~llllDE--------Pt~~LD~~~-~~~l~~~l~~~~~~~g~tii~~sH~~~~~~  196 (241)
T PRK14250        144 RTLANNPEVLLLDE--------PTSALDPTS-TEIIEELIVKLKNKMNLTVIWITHNMEQAK  196 (241)
T ss_pred             HHHhcCCCEEEEeC--------CcccCCHHH-HHHHHHHHHHHHHhCCCEEEEEeccHHHHH
Confidence            33455668999999        666666543 33444555566654 789999999988654

>PRK13541 cytochrome c biogenesis protein CcmA; Provisional

Probab=92.12  E-value=0.2  Score=48.64  Aligned_cols=58  Identities=5%  Similarity=0.003  Sum_probs=37.2

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      .+.-.+.......++|+||        --.|-++.-- ...+.++..+.+.+..+|++||..+....
T Consensus       131 rl~la~al~~~p~~lllDE--------P~~~LD~~~~-~~l~~~l~~~~~~~~tiii~sh~~~~i~~  188 (195)
T PRK13541        131 IVAIARLIACQSDLWLLDE--------VETNLSKENR-DLLNNLIVMKANSGGIVLLSSHLESSIKS  188 (195)
T ss_pred             HHHHHHHHhcCCCEEEEeC--------CcccCCHHHH-HHHHHHHHHHHhCCCEEEEEeCCccccch
Confidence            3333444556778999999        6666665543 33334444444557899999999876554

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=92.12  E-value=0.079  Score=52.80  Aligned_cols=86  Identities=14%  Similarity=0.181  Sum_probs=52.3

Q ss_pred             hhhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchh
Q psy13263        236 FHMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEY  314 (577)
Q Consensus       236 f~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy  314 (577)
                      .++|..+....-.+.+++|+|++||||+||+++...++++.|.+ |.-...+.+++..|..-....     .-..+.+.|
T Consensus        18 vpnd~~l~~~~~~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~~~~-----si~~~~S~f   92 (213)
T cd03281          18 VPNDTEIGGGGPSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMSSRE-----SVSSGQSAF   92 (213)
T ss_pred             EcceEEecCCCceEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeCCcc-----ChhhccchH
Confidence            45677766543366778999999999999999987777888875 333333445544433211110     011234677


Q ss_pred             HHHHHHHHHHHH
Q psy13263        315 DEVMDEIKSIEK  326 (577)
Q Consensus       315 ~k~valI~~ima  326 (577)
                      ..-+..+..+++
T Consensus        93 ~~el~~l~~~l~  104 (213)
T cd03281          93 MIDLYQVSKALR  104 (213)
T ss_pred             HHHHHHHHHHHH
Confidence            777766663333

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

>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional

Probab=92.03  E-value=0.79  Score=46.74  Aligned_cols=57  Identities=9%  Similarity=0.042  Sum_probs=36.4

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      ++.-.+.......++|+||        --.|-++..-. ..+.++..+.+. ++.+|++||..+...
T Consensus       155 rv~laral~~~p~lllLDE--------Pt~~LD~~~~~-~~~~~l~~l~~~~~~tiii~sH~~~~i~  212 (265)
T PRK10575        155 RAWIAMLVAQDSRCLLLDE--------PTSALDIAHQV-DVLALVHRLSQERGLTVIAVLHDINMAA  212 (265)
T ss_pred             HHHHHHHHhcCCCEEEEcC--------CcccCCHHHHH-HHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            3333344556778999999        55555544332 234455556554 789999999987654

>cd03276 ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=92.00  E-value=0.35  Score=47.55  Aligned_cols=50  Identities=2%  Similarity=-0.193  Sum_probs=35.7

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHH
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVAR  426 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~  426 (577)
                      .....++|+||        .-.|.+......+...+.+.....  ++.+|++||..+...
T Consensus       129 ~~~p~illlDE--------P~~glD~~~~~~~~~~l~~~~~~~~~~~~iii~th~~~~i~  180 (198)
T cd03276         129 VMESPFRCLDE--------FDVFMDMVNRKISTDLLVKEAKKQPGRQFIFITPQDISGLA  180 (198)
T ss_pred             ccCCCEEEecC--------cccccCHHHHHHHHHHHHHHHhcCCCcEEEEEECCcccccc
Confidence            46678999999        888888777666666555544431  357899999987554

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for

>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=91.85  E-value=0.32  Score=48.73  Aligned_cols=53  Identities=15%  Similarity=0.061  Sum_probs=35.1

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .+.......|+|+||        --.|-++.. ......++..+.+. ++.+|++||..+...
T Consensus       147 aral~~~p~llllDE--------Pt~~LD~~~-~~~l~~~L~~~~~~~g~tvii~sH~~~~~~  200 (242)
T cd03295         147 ARALAADPPLLLMDE--------PFGALDPIT-RDQLQEEFKRLQQELGKTIVFVTHDIDEAF  200 (242)
T ss_pred             HHHHhcCCCEEEecC--------CcccCCHHH-HHHHHHHHHHHHHHcCCEEEEEecCHHHHH
Confidence            344455678999999        555555533 33444555566554 788999999987543

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.

>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]

Probab=91.80  E-value=0.27  Score=50.98  Aligned_cols=122  Identities=16%  Similarity=0.167  Sum_probs=70.4

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHHHH-------------------HHHHhcccccccc-ceecc---ceeeecc
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEIKS-------------------IEKEIQTYLRTQC-AHFGC---TVIYSEA  348 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~-------------------imaqig~~VpA~~-a~l~~---d~if~~i  348 (577)
                      +|...+....+|+|||.+|||+.+|.++.+..                   -.|+.=.|||... .-+++   |.|.  +
T Consensus        22 s~~i~~G~i~~iiGpNG~GKSTLLk~l~g~l~p~~G~V~l~g~~i~~~~~kelAk~ia~vpQ~~~~~~~~tV~d~V~--~   99 (258)
T COG1120          22 SFSIPKGEITGILGPNGSGKSTLLKCLAGLLKPKSGEVLLDGKDIASLSPKELAKKLAYVPQSPSAPFGLTVYELVL--L   99 (258)
T ss_pred             eEEecCCcEEEEECCCCCCHHHHHHHHhccCCCCCCEEEECCCchhhcCHHHHhhhEEEeccCCCCCCCcEEeehHh--h
Confidence            44445555677999999999999999865321                   1344445787763 33333   3332  3


Q ss_pred             cc--cchhhh---------------------------hch-----hhhHHhhhcCCCceEEeecccCcccccccccCCCC
Q psy13263        349 QK--KQKKYV---------------------------LEV-----PSKYASKAKSNHQRVATKKKNVENYVTPECRGTGT  394 (577)
Q Consensus       349 G~--~qStF~---------------------------~Em-----~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst  394 (577)
                      |+  .++.|.                           .|+     ......+..+...-++|+||           =|+.
T Consensus       100 GR~p~~~~~~~~~~~D~~~v~~aL~~~~~~~la~r~~~~LSGGerQrv~iArALaQ~~~iLLLDE-----------PTs~  168 (258)
T COG1120         100 GRYPHLGLFGRPSKEDEEIVEEALELLGLEHLADRPVDELSGGERQRVLIARALAQETPILLLDE-----------PTSH  168 (258)
T ss_pred             cCCcccccccCCCHhHHHHHHHHHHHhCcHHHhcCcccccChhHHHHHHHHHHHhcCCCEEEeCC-----------Cccc
Confidence            32  122232                           011     11111223344678899999           3544


Q ss_pred             cchhhHHHH-----HHHHHHhc-CCeEEEecchHHHHHHhh
Q psy13263        395 NDGCVIARV-----TLEKFLQI-GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       395 ~DG~ALA~A-----IlE~L~~~-~~~~lfaTHy~eL~~l~~  429 (577)
                      -|   |...     ++..|.+. +..+|+++|+..++....
T Consensus       169 LD---i~~Q~evl~ll~~l~~~~~~tvv~vlHDlN~A~rya  206 (258)
T COG1120         169 LD---IAHQIEVLELLRDLNREKGLTVVMVLHDLNLAARYA  206 (258)
T ss_pred             cC---HHHHHHHHHHHHHHHHhcCCEEEEEecCHHHHHHhC
Confidence            44   4433     34556644 788999999999887543

>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=91.78  E-value=0.47  Score=46.97  Aligned_cols=56  Identities=7%  Similarity=-0.017  Sum_probs=36.7

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.-.+......-++|+||        --.|-++.-- ...+.++..+.+.+..+|++||..+...
T Consensus       142 l~la~al~~~p~llllDE--------Pt~~LD~~~~-~~~~~~l~~~~~~~~tii~~sH~~~~~~  197 (232)
T cd03218         142 VEIARALATNPKFLLLDE--------PFAGVDPIAV-QDIQKIIKILKDRGIGVLITDHNVRETL  197 (232)
T ss_pred             HHHHHHHhcCCCEEEecC--------CcccCCHHHH-HHHHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            333444556778999999        6666666443 3344455566655778999999986443

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.

>PRK13536 nodulation factor exporter subunit NodI; Provisional

Probab=91.74  E-value=0.34  Score=51.81  Aligned_cols=52  Identities=19%  Similarity=0.251  Sum_probs=36.4

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ........|+|+||        --.|-++.-...+ +.++..|.+.+..+|++||+.+...
T Consensus       185 ~aL~~~P~lLiLDE--------Pt~gLD~~~r~~l-~~~l~~l~~~g~tilisSH~l~e~~  236 (340)
T PRK13536        185 RALINDPQLLILDE--------PTTGLDPHARHLI-WERLRSLLARGKTILLTTHFMEEAE  236 (340)
T ss_pred             HHHhcCCCEEEEEC--------CCCCCCHHHHHHH-HHHHHHHHhCCCEEEEECCCHHHHH
Confidence            44456678999999        6667766544433 4444555555889999999988764

>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]

Probab=91.68  E-value=0.56  Score=48.43  Aligned_cols=44  Identities=14%  Similarity=0.018  Sum_probs=28.3

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhH--HHHHHHHHHhc--CCeEEEecchHH
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVI--ARVTLEKFLQI--GCLTVFATHYHS  423 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~AL--A~AIlE~L~~~--~~~~lfaTHy~e  423 (577)
                      -...-|+||||           .|+--|..+-  +...++.++..  ...+||+|||.|
T Consensus       187 v~~P~LLiLDE-----------P~~GLDl~~re~ll~~l~~~~~~~~~~~ll~VtHh~e  234 (257)
T COG1119         187 VKDPELLILDE-----------PAQGLDLIAREQLLNRLEELAASPGAPALLFVTHHAE  234 (257)
T ss_pred             hcCCCEEEecC-----------ccccCChHHHHHHHHHHHHHhcCCCCceEEEEEcchh
Confidence            34668999999           3444444333  34445555555  568999999974

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=91.56  E-value=0.095  Score=52.74  Aligned_cols=87  Identities=20%  Similarity=0.191  Sum_probs=56.6

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhH
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYD  315 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~  315 (577)
                      ++|.......-.+.+++|+|++||++++++++..+++++.|.+ |--...+.++..-|.+-....     --..|.+.|.
T Consensus        20 ~ndi~l~~~~~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~~d-----~~~~~~StF~   94 (218)
T cd03286          20 PNDVDLGATSPRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGARD-----DIMKGESTFM   94 (218)
T ss_pred             EeeeEEeecCCcEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCccc-----ccccCcchHH
Confidence            4555554433457789999999999999999999999999986 443334444444443211111     1135578888


Q ss_pred             HHHHHHHHHHHHh
Q psy13263        316 EVMDEIKSIEKEI  328 (577)
Q Consensus       316 k~valI~~imaqi  328 (577)
                      .-+..+..++...
T Consensus        95 ~e~~~~~~il~~~  107 (218)
T cd03286          95 VELSETANILRHA  107 (218)
T ss_pred             HHHHHHHHHHHhC
Confidence            7777776566554

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

>TIGR01288 nodI ATP-binding ABC transporter family nodulation protein NodI

Probab=91.42  E-value=0.42  Score=49.91  Aligned_cols=53  Identities=17%  Similarity=0.229  Sum_probs=35.3

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+......-|+|+||        --.|=++.--. ..+.++..+.+.+..+|++||+.+...
T Consensus       147 a~al~~~p~lllLDE--------Pt~gLD~~~~~-~l~~~l~~~~~~g~til~~sH~~~~~~  199 (303)
T TIGR01288       147 ARALINDPQLLILDE--------PTTGLDPHARH-LIWERLRSLLARGKTILLTTHFMEEAE  199 (303)
T ss_pred             HHHHhcCCCEEEEeC--------CCcCCCHHHHH-HHHHHHHHHHhCCCEEEEECCCHHHHH
Confidence            344456778999999        55555554333 334455555555789999999988665

This model does not recognize the highly divergent NodI from Azorhizobium caulinodans.

>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=91.35  E-value=0.73  Score=47.58  Aligned_cols=53  Identities=9%  Similarity=-0.024  Sum_probs=37.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .........|+|+||        --.|-++.... ..+.++..+.+. ++.+|++||+.+...
T Consensus       152 aral~~~p~lllLDE--------Pt~gLD~~~~~-~l~~~l~~l~~~~~~tilivsH~~~~~~  205 (279)
T PRK13635        152 AGVLALQPDIIILDE--------ATSMLDPRGRR-EVLETVRQLKEQKGITVLSITHDLDEAA  205 (279)
T ss_pred             HHHHHcCCCEEEEeC--------CcccCCHHHHH-HHHHHHHHHHHcCCCEEEEEecCHHHHH
Confidence            344556778999999        77777766443 334455566655 789999999998765

>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=91.11  E-value=1.1  Score=46.58  Aligned_cols=53  Identities=4%  Similarity=0.009  Sum_probs=36.9

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      ....+....++|+||        --.|-++.- ..-.+.++..|.+. +..+|++||+.+...
T Consensus       156 AraL~~~P~llllDE--------Pt~gLD~~~-~~~l~~~l~~l~~~~g~tvi~vtHd~~~~~  209 (287)
T PRK13637        156 AGVVAMEPKILILDE--------PTAGLDPKG-RDEILNKIKELHKEYNMTIILVSHSMEDVA  209 (287)
T ss_pred             HHHHHcCCCEEEEEC--------CccCCCHHH-HHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            344456778999999        666766643 34445556666654 788999999987654

>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors

Probab=91.05  E-value=0.59  Score=46.32  Aligned_cols=59  Identities=10%  Similarity=0.081  Sum_probs=38.6

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchH--HHHHHhh
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYH--SVARRLR  429 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~--eL~~l~~  429 (577)
                      +..++.......++|+||        --.|-++..-..+. .++..+.+.+..+|++||..  ++.+++.
T Consensus       152 l~laral~~~p~illlDE--------P~~gLD~~~~~~~~-~~l~~~~~~~~tiii~sh~~~~~~~~~~d  212 (226)
T cd03234         152 VSIAVQLLWDPKVLILDE--------PTSGLDSFTALNLV-STLSQLARRNRIVILTIHQPRSDLFRLFD  212 (226)
T ss_pred             HHHHHHHHhCCCEEEEeC--------CCcCCCHHHHHHHH-HHHHHHHHCCCEEEEEecCCCHHHHHhCC
Confidence            333344455678999999        77777765544443 34444555578999999996  5666554

The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan. The pigment precursors are encoded by the white, brown, and scarlet genes, respectively. Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan. However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes. Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in

>PRK10908 cell division protein FtsE; Provisional

Probab=90.99  E-value=0.34  Score=47.80  Aligned_cols=53  Identities=21%  Similarity=0.194  Sum_probs=33.9

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      +......-|+|+||        --.|-++..-..+. .++..+.+.+..+|++||+.+....
T Consensus       150 ral~~~p~llllDE--------Pt~~LD~~~~~~l~-~~l~~~~~~~~tiii~sH~~~~~~~  202 (222)
T PRK10908        150 RAVVNKPAVLLADE--------PTGNLDDALSEGIL-RLFEEFNRVGVTVLMATHDIGLISR  202 (222)
T ss_pred             HHHHcCCCEEEEeC--------CCCcCCHHHHHHHH-HHHHHHHHCCCEEEEEeCCHHHHHH
Confidence            34445667999999        55555544333333 4444555557889999999876653

>PRK13537 nodulation ABC transporter NodI; Provisional

Probab=90.92  E-value=0.49  Score=49.63  Aligned_cols=53  Identities=21%  Similarity=0.251  Sum_probs=37.5

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      .......-|+++||        --.|-++.--.. .+.++..|.+.+..+|++||+.+....
T Consensus       151 ~aL~~~P~lllLDE--------Pt~gLD~~~~~~-l~~~l~~l~~~g~till~sH~l~e~~~  203 (306)
T PRK13537        151 RALVNDPDVLVLDE--------PTTGLDPQARHL-MWERLRSLLARGKTILLTTHFMEEAER  203 (306)
T ss_pred             HHHhCCCCEEEEeC--------CCcCCCHHHHHH-HHHHHHHHHhCCCEEEEECCCHHHHHH
Confidence            44456778999999        667777664444 444555666568899999999886643

>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional

Probab=90.88  E-value=0.44  Score=48.43  Aligned_cols=48  Identities=8%  Similarity=0.016  Sum_probs=32.3

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHH-hcCCeEEEecchHHHHH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVAR  426 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~-~~~~~~lfaTHy~eL~~  426 (577)
                      ....++|+||        --.|-++.--..+. .++..+. +.+..+|++||..+...
T Consensus       157 ~~p~lllLDE--------Pt~~LD~~~~~~l~-~~l~~~~~~~~~tiii~sH~~~~~~  205 (258)
T PRK13548        157 GPPRWLLLDE--------PTSALDLAHQHHVL-RLARQLAHERGLAVIVVLHDLNLAA  205 (258)
T ss_pred             CCCCEEEEeC--------CcccCCHHHHHHHH-HHHHHHHHhcCCEEEEEECCHHHHH
Confidence            3568999999        66666655444333 3344455 45778999999987665

>TIGR03265 PhnT2 putative 2-aminoethylphosphonate ABC transporter, ATP-binding protein

Probab=90.65  E-value=0.84  Score=49.07  Aligned_cols=49  Identities=10%  Similarity=0.051  Sum_probs=32.3

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +....++|+||        --.|-+..--..+...+ ..+.+. +..+|++||+.+.+.
T Consensus       150 ~~~P~llLLDE--------P~s~LD~~~r~~l~~~L-~~l~~~~~~tvi~vTHd~~ea~  199 (353)
T TIGR03265       150 ATSPGLLLLDE--------PLSALDARVREHLRTEI-RQLQRRLGVTTIMVTHDQEEAL  199 (353)
T ss_pred             hcCCCEEEEcC--------CcccCCHHHHHHHHHHH-HHHHHhcCCEEEEEcCCHHHHH
Confidence            34678999999        55565555444444333 344443 889999999987654

This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.

>KOG0062|consensus

Probab=90.37  E-value=0.34  Score=54.46  Aligned_cols=117  Identities=9%  Similarity=-0.005  Sum_probs=72.0

Q ss_pred             ccccccccCCCCCCCchhHHHHHH----HHHHHHHh-ccccccccceecc-----ceeeec----cc-ccc---------
Q psy13263        297 EASSAGNIIPKAGVDKEYDEVMDE----IKSIEKEI-QTYLRTQCAHFGC-----TVIYSE----AQ-KKQ---------  352 (577)
Q Consensus       297 ~a~~~~I~gPN~gGKsvy~k~val----I~~imaqi-g~~VpA~~a~l~~-----d~if~~----iG-~~q---------  352 (577)
                      ..++-|+.|+|.-|||++++.++.    +-.+.+++ |+|+++...-+-.     |.++-.    .+ ..+         
T Consensus       105 ~GrRYGLvGrNG~GKsTLLRaia~~~v~~f~veqE~~g~~t~~~~~~l~~D~~~~dfl~~e~~l~~~~~l~ei~~~~L~g  184 (582)
T KOG0062|consen  105 RGRRYGLVGRNGIGKSTLLRAIANGQVSGFHVEQEVRGDDTEALQSVLESDTERLDFLAEEKELLAGLTLEEIYDKILAG  184 (582)
T ss_pred             cccccceeCCCCCcHHHHHHHHHhcCcCccCchhheeccchHHHhhhhhccHHHHHHHHhhhhhhccchHHHHHHHHHHh
Confidence            456778999999999999999976    11134444 6666664433322     112111    11 000         


Q ss_pred             hhhhhchhhhHH-----------hh--hcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEec
Q psy13263        353 KKYVLEVPSKYA-----------SK--AKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFAT  419 (577)
Q Consensus       353 StF~~Em~e~~~-----------il--~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaT  419 (577)
                      =-|..||.....           .|  +.-...-|.||||           =||--|=.||+| +-+||...+..+|+++
T Consensus       185 lGFt~emq~~pt~slSGGWrMrlaLARAlf~~pDlLLLDE-----------PTNhLDv~av~W-Le~yL~t~~~T~liVS  252 (582)
T KOG0062|consen  185 LGFTPEMQLQPTKSLSGGWRMRLALARALFAKPDLLLLDE-----------PTNHLDVVAVAW-LENYLQTWKITSLIVS  252 (582)
T ss_pred             CCCCHHHHhccccccCcchhhHHHHHHHHhcCCCEEeecC-----------CcccchhHHHHH-HHHHHhhCCceEEEEe
Confidence            124455543211           11  1112456899999           699999999998 4568888788999999


Q ss_pred             chHHHH
Q psy13263        420 HYHSVA  425 (577)
Q Consensus       420 Hy~eL~  425 (577)
                      |+....
T Consensus       253 HDr~FL  258 (582)
T KOG0062|consen  253 HDRNFL  258 (582)
T ss_pred             ccHHHH
Confidence            986543

>PRK11144 modC molybdate transporter ATP-binding protein; Provisional

Probab=90.33  E-value=1.2  Score=47.64  Aligned_cols=57  Identities=7%  Similarity=-0.031  Sum_probs=35.2

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +++-.+..+....++|+||        --.|-++.-...+ +.++..+.+. +..+|++||+.+...
T Consensus       136 RvalaraL~~~p~llLLDE--------Pts~LD~~~~~~l-~~~L~~l~~~~g~tii~vTHd~~~~~  193 (352)
T PRK11144        136 RVAIGRALLTAPELLLMDE--------PLASLDLPRKREL-LPYLERLAREINIPILYVSHSLDEIL  193 (352)
T ss_pred             HHHHHHHHHcCCCEEEEcC--------CcccCCHHHHHHH-HHHHHHHHHhcCCeEEEEecCHHHHH
Confidence            3333344556678999999        5555554433333 3344455554 788999999987543

>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=90.06  E-value=0.67  Score=48.10  Aligned_cols=52  Identities=17%  Similarity=0.061  Sum_probs=35.2

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      ...+....++|+||        --.|-++.. ......++..|.+. +..+|++||+.+...
T Consensus       158 raL~~~P~llllDE--------Pt~~LD~~~-~~~l~~~L~~l~~~~g~tviiitHd~~~~~  210 (290)
T PRK13634        158 GVLAMEPEVLVLDE--------PTAGLDPKG-RKEMMEMFYKLHKEKGLTTVLVTHSMEDAA  210 (290)
T ss_pred             HHHHcCCCEEEEEC--------CcccCCHHH-HHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            34455678999999        556665543 33334455666554 789999999988654

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=90.06  E-value=0.13  Score=51.73  Aligned_cols=85  Identities=16%  Similarity=0.119  Sum_probs=52.8

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhH
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYD  315 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~  315 (577)
                      ++|.......-.+..++|+|++|||+++++++..+++++.|++ |.-...+..+..-|..-.     ..---..+.+.|.
T Consensus        20 ~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~~la~~g~~vpa~~~~~~~~~~il~~~~-----l~d~~~~~lS~~~   94 (222)
T cd03285          20 PNDVTLTRGKSRFLIITGPNMGGKSTYIRQIGVIVLMAQIGCFVPCDSADIPIVDCILARVG-----ASDSQLKGVSTFM   94 (222)
T ss_pred             EeeEEEeecCCeEEEEECCCCCChHHHHHHHHHHHHHHHhCCCcCcccEEEeccceeEeeec-----cccchhcCcChHH
Confidence            3455554444567889999999999999999999999999964 443333333333232111     1101134567787


Q ss_pred             HHHHHHHHHHH
Q psy13263        316 EVMDEIKSIEK  326 (577)
Q Consensus       316 k~valI~~ima  326 (577)
                      +.+-.+..++.
T Consensus        95 ~e~~~~a~il~  105 (222)
T cd03285          95 AEMLETAAILK  105 (222)
T ss_pred             HHHHHHHHHHH
Confidence            77766664443

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

>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional

Probab=89.88  E-value=0.96  Score=51.56  Aligned_cols=48  Identities=10%  Similarity=0.028  Sum_probs=31.9

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ....++|+||        --.|-++.--..+. .++..+.+.++.+|++||+.+...
T Consensus       160 ~~P~LLLLDE--------PTsgLD~~sr~~Ll-elL~el~~~G~TIIIVSHdl~~i~  207 (549)
T PRK13545        160 INPDILVIDE--------ALSVGDQTFTKKCL-DKMNEFKEQGKTIFFISHSLSQVK  207 (549)
T ss_pred             hCCCEEEEEC--------CcccCCHHHHHHHH-HHHHHHHhCCCEEEEEECCHHHHH
Confidence            3668999999        55555544333333 344445555889999999987654

>cd03274 ABC_SMC4_euk Eukaryotic SMC4 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=89.86  E-value=1.6  Score=43.50  Aligned_cols=49  Identities=0%  Similarity=-0.111  Sum_probs=33.7

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      ...++++||        --.|-++.....+ +.++..+. .+..+|++||..++.+++.
T Consensus       149 ~p~ililDE--------Pt~gLD~~~~~~l-~~~l~~~~-~~~~~iivs~~~~~~~~~d  197 (212)
T cd03274         149 PTPLYVMDE--------IDAALDFRNVSIV-ANYIKERT-KNAQFIVISLRNNMFELAD  197 (212)
T ss_pred             CCCEEEEcC--------CCcCCCHHHHHHH-HHHHHHHc-CCCEEEEEECcHHHHHhCC
Confidence            347999999        7788877665433 34444443 3678899999988776554

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (fo

>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA

Probab=89.70  E-value=0.66  Score=48.43  Aligned_cols=54  Identities=15%  Similarity=0.113  Sum_probs=35.1

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH-Hhh
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR-RLR  429 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~-l~~  429 (577)
                      ........|+|+||        --.|-++.-- ...+.++..+.+ +..+|++||+.+... ++.
T Consensus       146 ~al~~~p~lliLDE--------Pt~gLD~~~~-~~l~~~l~~~~~-~~tiii~sH~l~~~~~~~d  200 (301)
T TIGR03522       146 QALIHDPKVLILDE--------PTTGLDPNQL-VEIRNVIKNIGK-DKTIILSTHIMQEVEAICD  200 (301)
T ss_pred             HHHhcCCCEEEEcC--------CcccCCHHHH-HHHHHHHHHhcC-CCEEEEEcCCHHHHHHhCC
Confidence            44456778999999        5555555432 334445555544 678999999987554 444

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.

>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit

Probab=89.66  E-value=0.75  Score=49.80  Aligned_cols=55  Identities=11%  Similarity=-0.046  Sum_probs=36.6

Q ss_pred             HhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        364 ASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       364 ~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      -.+..+....++|+||        -..|-++.-...|...+.+.-...+..+||+||+.+.+.
T Consensus       140 lARAL~~~p~iLLlDE--------P~saLD~~~r~~l~~~l~~l~~~~~~Tii~vTHd~~ea~  194 (363)
T TIGR01186       140 LARALAAEPDILLMDE--------AFSALDPLIRDSMQDELKKLQATLQKTIVFITHDLDEAI  194 (363)
T ss_pred             HHHHHhcCCCEEEEeC--------CcccCCHHHHHHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            3445566778999999        667777665555544444332233778999999987653

This model describes the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporter is the obligatory coupling of ATP hydrolysis to substrate translocation. The minimal configuration of bacterial ABC transport system: an ATPase or ATP binding subunit; An integral membrane protein; a hydrophilic polypetpide, which likely functions as substrate binding protein. Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits these transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L.lact

>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]

Probab=89.60  E-value=0.61  Score=46.11  Aligned_cols=63  Identities=6%  Similarity=-0.012  Sum_probs=41.0

Q ss_pred             hhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHH-HHHhhc
Q psy13263        360 PSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSV-ARRLRE  430 (577)
Q Consensus       360 ~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL-~~l~~~  430 (577)
                      ..++-++......-+.||||        +-..-++...-+|-.-|.+|+...+.-++..||...= .+.+..
T Consensus       140 QriAliR~Lq~~P~ILLLDE--------~TsALD~~nkr~ie~mi~~~v~~q~vAv~WiTHd~dqa~rha~k  203 (223)
T COG4619         140 QRIALIRNLQFMPKILLLDE--------ITSALDESNKRNIEEMIHRYVREQNVAVLWITHDKDQAIRHADK  203 (223)
T ss_pred             HHHHHHHHhhcCCceEEecC--------chhhcChhhHHHHHHHHHHHhhhhceEEEEEecChHHHhhhhhe
Confidence            34444555566677889999        5444445555566655666666778889999999754 444443

>PRK10070 glycine betaine transporter ATP-binding subunit; Provisional

Probab=89.56  E-value=1.6  Score=47.95  Aligned_cols=53  Identities=13%  Similarity=0.011  Sum_probs=35.0

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~  426 (577)
                      .+..+....++|+||        -..|-++.-...|. .++..+.+ .+..+||+||+.+...
T Consensus       176 ArAL~~~P~iLLLDE--------Pts~LD~~~r~~l~-~~L~~l~~~~g~TIIivTHd~~~~~  229 (400)
T PRK10070        176 ARALAINPDILLMDE--------AFSALDPLIRTEMQ-DELVKLQAKHQRTIVFISHDLDEAM  229 (400)
T ss_pred             HHHHhcCCCEEEEEC--------CCccCCHHHHHHHH-HHHHHHHHHCCCeEEEEECCHHHHH
Confidence            344556778999999        66666665443333 33444444 3788999999987654

>PRK13639 cbiO cobalt transporter ATP-binding subunit; Provisional

Probab=89.47  E-value=0.53  Score=48.37  Aligned_cols=53  Identities=9%  Similarity=0.120  Sum_probs=37.4

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .+.......|+|+||        --.|-++.....|...+. .+.+.+..+|++||+.+...
T Consensus       149 aral~~~p~llllDE--------Pt~gLD~~~~~~l~~~l~-~l~~~~~til~vtH~~~~~~  201 (275)
T PRK13639        149 AGILAMKPEIIVLDE--------PTSGLDPMGASQIMKLLY-DLNKEGITIIISTHDVDLVP  201 (275)
T ss_pred             HHHHhcCCCEEEEeC--------CCcCCCHHHHHHHHHHHH-HHHHCCCEEEEEecCHHHHH
Confidence            344456778999999        777777766555554444 44444788999999988655

>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA

Probab=89.24  E-value=1.2  Score=50.14  Aligned_cols=61  Identities=11%  Similarity=0.043  Sum_probs=41.5

Q ss_pred             hchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHhh
Q psy13263        357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       357 ~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~~  429 (577)
                      .|-++++-.+.......++|+||           .|+.-|...-. .+.+.|.+.  ++.+|++||...+...+.
T Consensus       473 GqrQRiaLARall~~~~illLDE-----------pts~LD~~~~~-~i~~~L~~~~~~~tiIiitH~~~~~~~~D  535 (571)
T TIGR02203       473 GQRQRLAIARALLKDAPILILDE-----------ATSALDNESER-LVQAALERLMQGRTTLVIAHRLSTIEKAD  535 (571)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeC-----------ccccCCHHHHH-HHHHHHHHHhCCCEEEEEehhhHHHHhCC
Confidence            44455544445566779999999           67777764333 455556554  689999999997766544

This family consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes.

>TIGR02142 modC_ABC molybdenum ABC transporter, ATP-binding protein

Probab=89.17  E-value=0.66  Score=49.72  Aligned_cols=53  Identities=13%  Similarity=0.085  Sum_probs=34.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      .+..+....++|+||        --.|=++.--..+ +.++..+.+. +..+|++||+.+...
T Consensus       143 AraL~~~p~lllLDE--------Pts~LD~~~~~~l-~~~L~~l~~~~g~tiiivtH~~~~~~  196 (354)
T TIGR02142       143 GRALLSSPRLLLMDE--------PLAALDDPRKYEI-LPYLERLHAEFGIPILYVSHSLQEVL  196 (354)
T ss_pred             HHHHHcCCCEEEEcC--------CCcCCCHHHHHHH-HHHHHHHHHhcCCEEEEEecCHHHHH
Confidence            344455668999999        5555555433333 3444555554 788999999987654

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.

>PRK11176 lipid transporter ATP-binding/permease protein; Provisional

Probab=89.15  E-value=1.2  Score=50.43  Aligned_cols=48  Identities=8%  Similarity=0.027  Sum_probs=35.4

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHhh
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~~  429 (577)
                      ....++|+||           .|+.-|-.+-. .+.+.|.+.  ++.+|++||..++.+.+.
T Consensus       497 ~~~~ililDE-----------ptsaLD~~t~~-~i~~~l~~~~~~~tvI~VtHr~~~~~~~D  546 (582)
T PRK11176        497 RDSPILILDE-----------ATSALDTESER-AIQAALDELQKNRTSLVIAHRLSTIEKAD  546 (582)
T ss_pred             hCCCEEEEEC-----------ccccCCHHHHH-HHHHHHHHHhCCCEEEEEecchHHHHhCC
Confidence            3668899999           78888875544 366666554  689999999997766544

>cd01120 RecA-like_NTPases RecA-like NTPases

Probab=88.90  E-value=1.1  Score=40.41  Aligned_cols=21  Identities=5%  Similarity=-0.220  Sum_probs=17.2

Q ss_pred             cccCCCCCCCchhHHHHHHHH
Q psy13263        302 GNIIPKAGVDKEYDEVMDEIK  322 (577)
Q Consensus       302 ~I~gPN~gGKsvy~k~valI~  322 (577)
                      +|+||+..|||.+...++.-.
T Consensus         3 ~i~G~~G~GKT~l~~~i~~~~   23 (165)
T cd01120           3 LVFGPTGSGKTTLALQLALNI   23 (165)
T ss_pred             eEeCCCCCCHHHHHHHHHHHH
Confidence            578999999999998886543

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.

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=88.74  E-value=0.23  Score=50.10  Aligned_cols=98  Identities=16%  Similarity=0.182  Sum_probs=60.5

Q ss_pred             hhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhHH
Q psy13263        238 MDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDE  316 (577)
Q Consensus       238 ~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k  316 (577)
                      +|.......-.+..++|+|+.|||+++++++..+++++.|.+ |--...+.+++.-|.+-.+..     --..|.+.|..
T Consensus        22 n~i~~~~~~g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~~~d-----~~~~~~StF~~   96 (222)
T cd03287          22 NDIHLSAEGGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASD-----SIQHGMSTFMV   96 (222)
T ss_pred             EeEEEEecCCcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEecCcc-----ccccccchHHH
Confidence            344433333346678999999999999999999999999986 333333445544443211111     11346788888


Q ss_pred             HHHHHHHHHHHhccccccccceecc-ceeee
Q psy13263        317 VMDEIKSIEKEIQTYLRTQCAHFGC-TVIYS  346 (577)
Q Consensus       317 ~valI~~imaqig~~VpA~~a~l~~-d~if~  346 (577)
                      -+..+..++.+..      ...|-+ |.++.
T Consensus        97 e~~~~~~il~~~~------~~sLvllDE~~~  121 (222)
T cd03287          97 ELSETSHILSNCT------SRSLVILDELGR  121 (222)
T ss_pred             HHHHHHHHHHhCC------CCeEEEEccCCC
Confidence            8877776655533      334444 66543

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

>TIGR03796 NHPM_micro_ABC1 NHPM bacteriocin system ABC transporter, peptidase/ATP-binding protein

Probab=88.65  E-value=1.5  Score=51.04  Aligned_cols=48  Identities=15%  Similarity=0.234  Sum_probs=36.5

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      ....++|+||           .|+.-|-. -...|.+.|.+.++.+|++||-.++...+.
T Consensus       632 ~~p~iliLDE-----------ptS~LD~~-te~~i~~~l~~~~~T~IiitHrl~~i~~~D  679 (710)
T TIGR03796       632 RNPSILILDE-----------ATSALDPE-TEKIIDDNLRRRGCTCIIVAHRLSTIRDCD  679 (710)
T ss_pred             hCCCEEEEEC-----------ccccCCHH-HHHHHHHHHHhcCCEEEEEecCHHHHHhCC
Confidence            3668899999           67777763 355677777777899999999998776544

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.

>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component

Probab=87.81  E-value=0.82  Score=44.65  Aligned_cols=55  Identities=11%  Similarity=0.088  Sum_probs=34.6

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.-.+..+...-++|+||        --.|-++..-. ....+++.+.+ +..+|++||..++..
T Consensus       139 v~la~al~~~p~llllDE--------Pt~~LD~~~~~-~l~~~l~~~~~-~~tii~vsH~~~~~~  193 (211)
T cd03264         139 VGIAQALVGDPSILIVDE--------PTAGLDPEERI-RFRNLLSELGE-DRIVILSTHIVEDVE  193 (211)
T ss_pred             HHHHHHHhcCCCEEEEcC--------CcccCCHHHHH-HHHHHHHHHhC-CCEEEEEcCCHHHHH
Confidence            333445566778999999        55555543332 22344455544 578899999988764

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.

>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters

Probab=87.57  E-value=1.8  Score=42.45  Aligned_cols=61  Identities=8%  Similarity=0.039  Sum_probs=33.4

Q ss_pred             hhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEec-chH-HHHHHhh
Q psy13263        360 PSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFAT-HYH-SVARRLR  429 (577)
Q Consensus       360 ~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaT-Hy~-eL~~l~~  429 (577)
                      .++.-.+.......++|+||        --.|-++.-.. ..+.+++.+.+. +..+|++| |.. ++.++..
T Consensus       125 qrl~laral~~~p~llllDE--------Pt~~LD~~~~~-~~~~~l~~~~~~~~~t~ii~~~h~~~~~~~~~d  188 (202)
T cd03233         125 KRVSIAEALVSRASVLCWDN--------STRGLDSSTAL-EILKCIRTMADVLKTTTFVSLYQASDEIYDLFD  188 (202)
T ss_pred             HHHHHHHHHhhCCCEEEEcC--------CCccCCHHHHH-HHHHHHHHHHHhCCCEEEEEEcCCHHHHHHhCC
Confidence            33333344455667999999        66666654443 334455555554 55555554 543 4445443

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.

>PRK15064 ABC transporter ATP-binding protein; Provisional

Probab=87.28  E-value=2.5  Score=47.59  Aligned_cols=29  Identities=3%  Similarity=-0.184  Sum_probs=23.0

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDE  320 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~val  320 (577)
                      +|........+|+|||.+|||+++++++-
T Consensus       339 s~~i~~Ge~~~l~G~NGsGKSTLl~~i~G  367 (530)
T PRK15064        339 NLLLEAGERLAIIGENGVGKTTLLRTLVG  367 (530)
T ss_pred             EEEECCCCEEEEECCCCCCHHHHHHHHhC
Confidence            45555556678999999999999998864

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=87.25  E-value=0.36  Score=48.20  Aligned_cols=84  Identities=19%  Similarity=0.207  Sum_probs=49.8

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhH
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYD  315 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~  315 (577)
                      ++|....... .+..++|+|.+||||+++.++..+++.+.|.+ |--...+.++..-|.+-     ....--.+|.+.|.
T Consensus        21 ~n~~~l~~~~-~~~~l~Gpn~sGKstllr~i~~~~~l~~~g~~vp~~~~~i~~~~~i~~~~-----~~~~~ls~g~s~f~   94 (216)
T cd03284          21 PNDTELDPER-QILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRI-----GASDDLAGGRSTFM   94 (216)
T ss_pred             eeeEEecCCc-eEEEEECCCCCChHHHHHHHHHHHHHhccCCeeccccceecceeeEeccC-----CchhhhccCcchHH
Confidence            4555544433 67789999999999999999988888888876 33333344443333211     01111134556665


Q ss_pred             HHHHHHHHHHH
Q psy13263        316 EVMDEIKSIEK  326 (577)
Q Consensus       316 k~valI~~ima  326 (577)
                      .-+..|..+++
T Consensus        95 ~e~~~l~~~l~  105 (216)
T cd03284          95 VEMVETANILN  105 (216)
T ss_pred             HHHHHHHHHHH
Confidence            54444443443

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam

>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]

Probab=87.10  E-value=1.6  Score=45.11  Aligned_cols=29  Identities=10%  Similarity=0.116  Sum_probs=24.8

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDE  320 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~val  320 (577)
                      +|...+.-..||+|+|.+|||+.+++++-
T Consensus        47 sf~i~~Ge~vGiiG~NGaGKSTLlkliaG   75 (249)
T COG1134          47 SFEIYKGERVGIIGHNGAGKSTLLKLIAG   75 (249)
T ss_pred             eEEEeCCCEEEEECCCCCcHHHHHHHHhC
Confidence            67777777889999999999999998754

>PRK09183 transposase/IS protein; Provisional

Probab=86.93  E-value=1.8  Score=44.54  Aligned_cols=95  Identities=7%  Similarity=0.026  Sum_probs=57.1

Q ss_pred             cccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccccchhhhhchhh------hHHhhhc-CCCc
Q psy13263        300 SAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPS------KYASKAK-SNHQ  372 (577)
Q Consensus       300 ~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e------~~~il~~-a~~~  372 (577)
                      ..+++||+..|||.....++... .  +-|.-           ..|+....    +..++..      ...++.. ....
T Consensus       104 ~v~l~Gp~GtGKThLa~al~~~a-~--~~G~~-----------v~~~~~~~----l~~~l~~a~~~~~~~~~~~~~~~~~  165 (259)
T PRK09183        104 NIVLLGPSGVGKTHLAIALGYEA-V--RAGIK-----------VRFTTAAD----LLLQLSTAQRQGRYKTTLQRGVMAP  165 (259)
T ss_pred             eEEEEeCCCCCHHHHHHHHHHHH-H--HcCCe-----------EEEEeHHH----HHHHHHHHHHCCcHHHHHHHHhcCC
Confidence            45688999999999998886543 1  22211           12222111    1111111      1111211 2344


Q ss_pred             eEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecch
Q psy13263        373 RVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHY  421 (577)
Q Consensus       373 sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy  421 (577)
                      .|++|||        +|-..-..++..+..-++....++++ +||||++
T Consensus       166 dlLiiDd--------lg~~~~~~~~~~~lf~li~~r~~~~s-~iiTsn~  205 (259)
T PRK09183        166 RLLIIDE--------IGYLPFSQEEANLFFQVIAKRYEKGS-MILTSNL  205 (259)
T ss_pred             CEEEEcc--------cccCCCChHHHHHHHHHHHHHHhcCc-EEEecCC
Confidence            6999999        99877777777778888887776654 7888887

>TIGR02858 spore_III_AA stage III sporulation protein AA

Probab=86.84  E-value=1.8  Score=45.06  Aligned_cols=45  Identities=18%  Similarity=0.104  Sum_probs=32.5

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      +...-++|+||        .|+.       ....++++.+. .+..+|++||...+.++..
T Consensus       192 ~~~P~villDE--------~~~~-------e~~~~l~~~~~-~G~~vI~ttH~~~~~~~~~  236 (270)
T TIGR02858       192 SMSPDVIVVDE--------IGRE-------EDVEALLEALH-AGVSIIATAHGRDVEDLYK  236 (270)
T ss_pred             hCCCCEEEEeC--------CCcH-------HHHHHHHHHHh-CCCEEEEEechhHHHHHHh
Confidence            34668999999        7642       34566776664 5889999999987766543

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.

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=86.62  E-value=1.1  Score=50.96  Aligned_cols=44  Identities=9%  Similarity=-0.050  Sum_probs=35.0

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ..-|.||||           =||--|--+|+| +-+||.+....+||+||+....+
T Consensus       171 ~pDlLLLDE-----------PTNHLD~~~i~W-Le~~L~~~~gtviiVSHDR~FLd  214 (530)
T COG0488         171 EPDLLLLDE-----------PTNHLDLESIEW-LEDYLKRYPGTVIVVSHDRYFLD  214 (530)
T ss_pred             CCCEEEEcC-----------CCcccCHHHHHH-HHHHHHhCCCcEEEEeCCHHHHH
Confidence            556899999           699999999988 34556565558999999987766

>PLN03073 ABC transporter F family; Provisional

Probab=86.46  E-value=2.6  Score=49.69  Aligned_cols=47  Identities=4%  Similarity=0.024  Sum_probs=31.8

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ....-++|+||           =|+..|-.+. ..+++.|.+.+..+|++||+.++...
T Consensus       643 ~~~p~lLLLDE-----------PT~~LD~~s~-~~l~~~L~~~~gtvIivSHd~~~i~~  689 (718)
T PLN03073        643 FKKPHILLLDE-----------PSNHLDLDAV-EALIQGLVLFQGGVLMVSHDEHLISG  689 (718)
T ss_pred             hcCCCEEEEcC-----------CCCCCCHHHH-HHHHHHHHHcCCEEEEEECCHHHHHH
Confidence            34678999999           3555554443 34666666544589999999887664

>COG1129 MglA ABC-type sugar transport system, ATPase component [Carbohydrate transport and metabolism]

Probab=86.23  E-value=3.5  Score=46.65  Aligned_cols=62  Identities=10%  Similarity=0.008  Sum_probs=40.1

Q ss_pred             hhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcc--hhhHHHHHHHHHHhcCCeEEEecch-HHHHHHhhc
Q psy13263        356 VLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTND--GCVIARVTLEKFLQIGCLTVFATHY-HSVARRLRE  430 (577)
Q Consensus       356 ~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~D--G~ALA~AIlE~L~~~~~~~lfaTHy-~eL~~l~~~  430 (577)
                      +..|-+++..+..  .--|+++||           =|+.-.  =......+++.|..+|.-+||.||. +|+.+++..
T Consensus       150 qrQ~VeIArAl~~--~arllIlDE-----------PTaaLt~~E~~~Lf~~ir~Lk~~Gv~ii~ISHrl~Ei~~i~Dr  214 (500)
T COG1129         150 QRQMVEIARALSF--DARVLILDE-----------PTAALTVKETERLFDLIRRLKAQGVAIIYISHRLDEVFEIADR  214 (500)
T ss_pred             HHHHHHHHHHHhc--CCCEEEEcC-----------CcccCCHHHHHHHHHHHHHHHhCCCEEEEEcCcHHHHHHhcCE
Confidence            4556666655443  223999999           233322  2344556778888889999999998 566666543

>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]

Probab=86.22  E-value=1.4  Score=50.27  Aligned_cols=46  Identities=13%  Similarity=0.077  Sum_probs=34.5

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL  428 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~  428 (577)
                      ..-|.||||           =||--|=.++- |+.+.|.+-.-.+||+||+..+.+-.
T Consensus       457 ~pNvLiLDE-----------PTNhLDi~s~~-aLe~aL~~f~Gtvl~VSHDr~Fl~~v  502 (530)
T COG0488         457 PPNLLLLDE-----------PTNHLDIESLE-ALEEALLDFEGTVLLVSHDRYFLDRV  502 (530)
T ss_pred             CCCEEEEcC-----------CCccCCHHHHH-HHHHHHHhCCCeEEEEeCCHHHHHhh
Confidence            556888999           58888865543 55566666678899999999888743

>KOG0059|consensus

Probab=85.68  E-value=2.6  Score=50.77  Aligned_cols=80  Identities=10%  Similarity=0.054  Sum_probs=53.4

Q ss_pred             hhhhhchhhh-HHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh-hc
Q psy13263        353 KKYVLEVPSK-YASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL-RE  430 (577)
Q Consensus       353 StF~~Em~e~-~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~-~~  430 (577)
                      .+|..-+++. ...+......++|+|||        ---|-+| .+-=..|.++..+.+.+--+|+|||+.|-++.+ .+
T Consensus       697 ~~ySgG~kRkLs~aialig~p~vi~LDE--------PstGmDP-~arr~lW~ii~~~~k~g~aiiLTSHsMeE~EaLCtR  767 (885)
T KOG0059|consen  697 RTYSGGNKRRLSFAIALIGDPSVILLDE--------PSTGLDP-KARRHLWDIIARLRKNGKAIILTSHSMEEAEALCTR  767 (885)
T ss_pred             hhCCCcchhhHHHHHHHhcCCCEEEecC--------CCCCCCH-HHHHHHHHHHHHHHhcCCEEEEEcCCHHHHHHHhhh
Confidence            3455444542 22334455679999999        7888888 555678888888888743999999999998854 33


Q ss_pred             CCCccccccee
Q psy13263        431 EPNVAFEYMSY  441 (577)
Q Consensus       431 ~~~V~n~hm~~  441 (577)
                      ..-..+.++.+
T Consensus       768 ~aImv~G~l~c  778 (885)
T KOG0059|consen  768 TAIMVIGQLRC  778 (885)
T ss_pred             hheeecCeeEE
Confidence            33333444444

>PRK10636 putative ABC transporter ATP-binding protein; Provisional

Probab=85.64  E-value=2  Score=49.72  Aligned_cols=29  Identities=7%  Similarity=0.029  Sum_probs=23.1

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDE  320 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~val  320 (577)
                      +|........+|+|||.+|||+++++++-
T Consensus       332 sl~i~~Ge~~~l~G~NGsGKSTLlk~l~G  360 (638)
T PRK10636        332 KLNLVPGSRIGLLGRNGAGKSTLIKLLAG  360 (638)
T ss_pred             eEEECCCCEEEEECCCCCCHHHHHHHHhC
Confidence            45555566778999999999999998864

>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional

Probab=85.62  E-value=2.1  Score=48.73  Aligned_cols=61  Identities=11%  Similarity=0.040  Sum_probs=39.2

Q ss_pred             hchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHhh
Q psy13263        357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       357 ~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~~  429 (577)
                      .|.+++.-.+.......++|+||        --.+-++.-..    .+.+.|.+.  ++.+|++||..++.+.+.
T Consensus       475 Gq~QRialARall~~~~iliLDE--------pts~LD~~t~~----~i~~~l~~~~~~~tvIiitHr~~~~~~~D  537 (588)
T PRK13657        475 GERQRLAIARALLKDPPILILDE--------ATSALDVETEA----KVKAALDELMKGRTTFIIAHRLSTVRNAD  537 (588)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeC--------CccCCCHHHHH----HHHHHHHHHhcCCEEEEEEecHHHHHhCC
Confidence            45566655555667888999999        44444443333    344444433  689999999998766543

>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein

Probab=85.57  E-value=2.7  Score=47.40  Aligned_cols=61  Identities=10%  Similarity=0.057  Sum_probs=40.3

Q ss_pred             hchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHhh
Q psy13263        357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       357 ~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~~  429 (577)
                      .|..++.-.+.......++|+||           .|+..|-.. ...+.+.|.+.  ++.+|++||..++.....
T Consensus       480 Gq~Qrl~laRal~~~~~ililDE-----------pts~lD~~~-~~~i~~~l~~~~~~~t~IiitH~~~~~~~~d  542 (576)
T TIGR02204       480 GQRQRIAIARAILKDAPILLLDE-----------ATSALDAES-EQLVQQALETLMKGRTTLIIAHRLATVLKAD  542 (576)
T ss_pred             HHHHHHHHHHHHHhCCCeEEEeC-----------cccccCHHH-HHHHHHHHHHHhCCCEEEEEecchHHHHhCC
Confidence            35555544444455678999999           566666553 34455666553  689999999997765443

This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins.

>TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR)

Probab=85.17  E-value=1.9  Score=54.70  Aligned_cols=54  Identities=9%  Similarity=0.003  Sum_probs=40.1

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      .+.......++|+||        .-.|-++.-+..|...++..+.+ +..+|++||..+....
T Consensus       560 ARAl~~~~~illLDe--------p~saLD~~~~~~i~~~~l~~~~~-~~tvilvtH~~~~~~~  613 (1490)
T TIGR01271       560 ARAVYKDADLYLLDS--------PFTHLDVVTEKEIFESCLCKLMS-NKTRILVTSKLEHLKK  613 (1490)
T ss_pred             HHHHHcCCCEEEEeC--------CcccCCHHHHHHHHHHHHHHHhc-CCeEEEEeCChHHHHh
Confidence            334445668999999        88888888777777665555543 7889999999887664

The model describes the cystis fibrosis transmembrane conductor regulator (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.

>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=85.09  E-value=2.9  Score=42.71  Aligned_cols=60  Identities=12%  Similarity=-0.027  Sum_probs=38.0

Q ss_pred             chhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchh--hHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        358 EVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGC--VIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       358 Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~--ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      |.++.+..-..+-..-++|+||           =|+--|..  .-...++..|... +-.+|++||+++.....
T Consensus       143 qkqRvaIA~vLa~~P~iliLDE-----------Pta~LD~~~~~~l~~~l~~L~~~~~~tii~~tHd~~~~~~~  205 (235)
T COG1122         143 QKQRVAIAGVLAMGPEILLLDE-----------PTAGLDPKGRRELLELLKKLKEEGGKTIIIVTHDLELVLEY  205 (235)
T ss_pred             ceeeHHhhHHHHcCCCEEEEcC-----------CCCCCCHHHHHHHHHHHHHHHhcCCCeEEEEeCcHHHHHhh
Confidence            4444333223345567899999           34444443  3445556777766 67899999999877653

>PRK15439 autoinducer 2 ABC transporter ATP-binding protein LsrA; Provisional

Probab=84.84  E-value=4  Score=45.81  Aligned_cols=52  Identities=13%  Similarity=0.123  Sum_probs=34.2

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.......++|+||        --.|=++.--.. .+.++..+.+.+..+|++||+.+...
T Consensus       153 ~aL~~~p~lllLDE--------Pt~~LD~~~~~~-l~~~l~~~~~~g~tiiivtHd~~~~~  204 (510)
T PRK15439        153 RGLMRDSRILILDE--------PTASLTPAETER-LFSRIRELLAQGVGIVFISHKLPEIR  204 (510)
T ss_pred             HHHHcCCCEEEEEC--------CCCCCCHHHHHH-HHHHHHHHHHCCCEEEEEeCCHHHHH
Confidence            34456678999999        555555443333 33445556555789999999987654

>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional

Probab=84.59  E-value=3.4  Score=46.96  Aligned_cols=60  Identities=8%  Similarity=0.000  Sum_probs=40.9

Q ss_pred             hchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHh
Q psy13263        357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRL  428 (577)
Q Consensus       357 ~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~  428 (577)
                      .|.+++.-.+.......++|+||           .|+.-|-.. ...|.+.|.+.  ++.+|++||..++...+
T Consensus       480 GqrQRialARaLl~~~~illlDE-----------pts~LD~~t-~~~i~~~l~~~~~~~tvIivtHr~~~l~~~  541 (592)
T PRK10790        480 GQKQLLALARVLVQTPQILILDE-----------ATANIDSGT-EQAIQQALAAVREHTTLVVIAHRLSTIVEA  541 (592)
T ss_pred             HHHHHHHHHHHHHhCCCEEEEeC-----------CcccCCHHH-HHHHHHHHHHHhCCCEEEEEecchHHHHhC
Confidence            35555544444556678999999           677777543 45666666654  68999999998765543

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=84.31  E-value=0.83  Score=45.05  Aligned_cols=40  Identities=18%  Similarity=0.140  Sum_probs=31.1

Q ss_pred             hhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc
Q psy13263        238 MDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF  279 (577)
Q Consensus       238 ~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh  279 (577)
                      +|..+...  .+..++|+|++||||++|+++..+++.+.|++
T Consensus        18 n~i~l~~g--~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~   57 (199)
T cd03283          18 NDIDMEKK--NGILITGSNMSGKSTFLRTIGVNVILAQAGAP   57 (199)
T ss_pred             ceEEEcCC--cEEEEECCCCCChHHHHHHHHHHHHHHHcCCE
Confidence            44444432  57788999999999999999987777777864

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

>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]

Probab=84.31  E-value=2.4  Score=44.36  Aligned_cols=56  Identities=13%  Similarity=0.034  Sum_probs=33.3

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +-.+++.+-..-++|+||        -..--+|.-...|=--+ ..|.+. +..++|.||+.+-+-
T Consensus       144 VGv~RALAadP~ilLMDE--------PFgALDpI~R~~lQ~e~-~~lq~~l~kTivfVTHDidEA~  200 (309)
T COG1125         144 VGVARALAADPPILLMDE--------PFGALDPITRKQLQEEI-KELQKELGKTIVFVTHDIDEAL  200 (309)
T ss_pred             HHHHHHHhcCCCeEeecC--------CccccChhhHHHHHHHH-HHHHHHhCCEEEEEecCHHHHH
Confidence            333455566677999999        33344444443332222 234444 889999999976543

>PRK11147 ABC transporter ATPase component; Reviewed

Probab=84.27  E-value=3.7  Score=47.42  Aligned_cols=49  Identities=8%  Similarity=-0.014  Sum_probs=32.3

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +......-|+|+||           =|+..|-.+. ..+.+.|.+.+..+|++||+.++..
T Consensus       453 ~al~~~p~lLlLDE-----------Pt~~LD~~~~-~~l~~~l~~~~~tvi~vSHd~~~~~  501 (635)
T PRK11147        453 RLFLKPSNLLILDE-----------PTNDLDVETL-ELLEELLDSYQGTVLLVSHDRQFVD  501 (635)
T ss_pred             HHHhcCCCEEEEcC-----------CCCCCCHHHH-HHHHHHHHhCCCeEEEEECCHHHHH
Confidence            33445668999999           4555555442 3445555444668999999987665

>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]

Probab=84.20  E-value=0.31  Score=57.43  Aligned_cols=69  Identities=22%  Similarity=0.220  Sum_probs=48.9

Q ss_pred             hhhhhhccccCccCCcchhhhhhhhhhccCcccccCcccccccccccccccccccccccCCCCCC--CchhHHHHHHHHH
Q psy13263        246 ELACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGV--DKEYDEVMDEIKS  323 (577)
Q Consensus       246 eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gG--Ksvy~k~valI~~  323 (577)
                      .++...++|+|++||++.|++++..+++.+.|.+                         +|...|  -.+|.++++.|+ 
T Consensus       316 e~~~l~ITGpN~GGKtvtLKTlgl~~lm~q~gl~-------------------------i~a~~gsei~~F~~i~aDIG-  369 (753)
T COG1193         316 ELDRLIITGPNTGGKTVTLKTLGLLRLMAQSGLP-------------------------IPALEGSELPVFVKIFADIG-  369 (753)
T ss_pred             ccceeeEecCCCCcceehHHHHHHHHHHHHcCCC-------------------------eeccCCCcchhHHHhhhccC-
Confidence            3566778999999999999999999999998865                         222222  356777777776 


Q ss_pred             HHHHhccccccccceec
Q psy13263        324 IEKEIQTYLRTQCAHFG  340 (577)
Q Consensus       324 imaqig~~VpA~~a~l~  340 (577)
                      .++.|+.-+....+++.
T Consensus       370 DeQsIeqsLSTFSshm~  386 (753)
T COG1193         370 DEQSIEQSLSTFSSHMT  386 (753)
T ss_pred             cHHHHHHHHhhhHHHHH
Confidence            45666655555555544

>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional

Probab=83.81  E-value=4.7  Score=44.77  Aligned_cols=52  Identities=12%  Similarity=0.027  Sum_probs=33.1

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      .......-++|+||        --.|=++... ...+.++..+.+.+..+|++||+.+...
T Consensus       148 ~al~~~p~lllLDE--------Pt~~LD~~~~-~~l~~~l~~~~~~g~tvii~tH~~~~~~  199 (490)
T PRK10938        148 QALMSEPDLLILDE--------PFDGLDVASR-QQLAELLASLHQSGITLVLVLNRFDEIP  199 (490)
T ss_pred             HHHHcCCCEEEEcC--------CcccCCHHHH-HHHHHHHHHHHhcCCeEEEEeCCHHHHH
Confidence            34455668999999        4444444332 3333445555555788999999987653

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

Probab=83.77  E-value=3  Score=47.21  Aligned_cols=49  Identities=14%  Similarity=0.094  Sum_probs=33.0

Q ss_pred             CceEEeecccCcccccccccCCCCcchh-hHHHHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGC-VIARVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~-ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      ..-||+|||  ||      ..=+ .+|- ||+.|| ..+-.+++.++++||-..+.....
T Consensus       490 ~P~lvVLDE--PN------sNLD-~~GE~AL~~Ai-~~~k~rG~~vvviaHRPs~L~~~D  539 (580)
T COG4618         490 DPFLVVLDE--PN------SNLD-SEGEAALAAAI-LAAKARGGTVVVIAHRPSALASVD  539 (580)
T ss_pred             CCcEEEecC--CC------CCcc-hhHHHHHHHHH-HHHHHcCCEEEEEecCHHHHhhcc
Confidence            567999999  43      1111 2343 455444 466677999999999998877554

>KOG0221|consensus

Probab=83.71  E-value=0.34  Score=55.24  Aligned_cols=43  Identities=21%  Similarity=0.217  Sum_probs=37.1

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF  279 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh  279 (577)
                      +++..++...-.+.+++|+|..|||++++++++.+++++.|+|
T Consensus       589 PNst~iggdkgri~vITGpNasGKSiYlkqvglivfLahIGsF  631 (849)
T KOG0221|consen  589 PNSTEIGGDKGRIKVITGPNASGKSIYLKQVGLIVFLAHIGSF  631 (849)
T ss_pred             CCceeecCCCceEEEEeCCCCCCceEEEeechhhhHHHhhccc
Confidence            4566666556678999999999999999999999999999987

>cd03277 ABC_SMC5_euk Eukaryotic SMC5 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains

Probab=83.51  E-value=2.4  Score=42.25  Aligned_cols=44  Identities=9%  Similarity=-0.007  Sum_probs=30.5

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-C-CeEEEecchH
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-G-CLTVFATHYH  422 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~-~~~lfaTHy~  422 (577)
                      ...-++|+||        .-.|.++.....+...+.+ +.+. + +.+|++||+.
T Consensus       147 ~~p~llllDE--------P~~~LD~~~~~~i~~~l~~-~~~~~g~~~viiith~~  192 (213)
T cd03277         147 TRCPFRVVDE--------INQGMDPTNERKVFDMLVE-TACKEGTSQYFLITPKL  192 (213)
T ss_pred             cCCCEEEEec--------ccccCCHHHHHHHHHHHHH-HhhcCCCceEEEEchhh
Confidence            4557899999        8888888776665544444 4444 4 4578888875

Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=83.23  E-value=0.28  Score=48.73  Aligned_cols=54  Identities=22%  Similarity=0.337  Sum_probs=39.5

Q ss_pred             hhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccc
Q psy13263        238 MDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFEN  291 (577)
Q Consensus       238 ~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n  291 (577)
                      +|.......-.+.+++|+|++|||++++.++..+++.+.|++ |.....+..+.+
T Consensus        20 ~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~   74 (204)
T cd03282          20 NDIYLTRGSSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNR   74 (204)
T ss_pred             eeeEEeeCCCcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhh
Confidence            344443333356788999999999999999999999999987 655555544433

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

>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=83.01  E-value=2.2  Score=37.07  Aligned_cols=22  Identities=5%  Similarity=-0.129  Sum_probs=17.5

Q ss_pred             cccccCCCCCCCchhHHHHHHH
Q psy13263        300 SAGNIIPKAGVDKEYDEVMDEI  321 (577)
Q Consensus       300 ~~~I~gPN~gGKsvy~k~valI  321 (577)
                      ..+|+||...|||...+.+..-
T Consensus        21 ~v~i~G~~G~GKT~l~~~i~~~   42 (151)
T cd00009          21 NLLLYGPPGTGKTTLARAIANE   42 (151)
T ss_pred             eEEEECCCCCCHHHHHHHHHHH
Confidence            3568899999999988877653

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.

>PRK08181 transposase; Validated

Probab=82.91  E-value=3  Score=43.43  Aligned_cols=97  Identities=7%  Similarity=-0.030  Sum_probs=60.0

Q ss_pred             ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccccchhhhhchhhh------HHhhhcCCCc
Q psy13263        299 SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSK------YASKAKSNHQ  372 (577)
Q Consensus       299 ~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e~------~~il~~a~~~  372 (577)
                      ...+++||...|||.....++.-.  .. -|.           ..+|+.+..    +..++...      ...+..-..-
T Consensus       107 ~nlll~Gp~GtGKTHLa~Aia~~a--~~-~g~-----------~v~f~~~~~----L~~~l~~a~~~~~~~~~l~~l~~~  168 (269)
T PRK08181        107 ANLLLFGPPGGGKSHLAAAIGLAL--IE-NGW-----------RVLFTRTTD----LVQKLQVARRELQLESAIAKLDKF  168 (269)
T ss_pred             ceEEEEecCCCcHHHHHHHHHHHH--HH-cCC-----------ceeeeeHHH----HHHHHHHHHhCCcHHHHHHHHhcC
Confidence            345678999999999998887533  11 131           123433222    22222111      1112222234


Q ss_pred             eEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchH
Q psy13263        373 RVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYH  422 (577)
Q Consensus       373 sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~  422 (577)
                      .|++|||        ||.-.....+..+...|+.+...+ ..+||||.+.
T Consensus       169 dLLIIDD--------lg~~~~~~~~~~~Lf~lin~R~~~-~s~IiTSN~~  209 (269)
T PRK08181        169 DLLILDD--------LAYVTKDQAETSVLFELISARYER-RSILITANQP  209 (269)
T ss_pred             CEEEEec--------cccccCCHHHHHHHHHHHHHHHhC-CCEEEEcCCC
Confidence            6999999        998888777777888888877765 5788999883

>PRK08116 hypothetical protein; Validated

Probab=82.83  E-value=3.8  Score=42.45  Aligned_cols=96  Identities=7%  Similarity=-0.076  Sum_probs=58.6

Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccccchhhhhchhhh---------HHhhhcCCC
Q psy13263        301 AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSK---------YASKAKSNH  371 (577)
Q Consensus       301 ~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e~---------~~il~~a~~  371 (577)
                      .++.||...|||.....++.-  ++.+ |..           .+|+....    |..++...         ..++.....
T Consensus       117 l~l~G~~GtGKThLa~aia~~--l~~~-~~~-----------v~~~~~~~----ll~~i~~~~~~~~~~~~~~~~~~l~~  178 (268)
T PRK08116        117 LLLWGSVGTGKTYLAACIANE--LIEK-GVP-----------VIFVNFPQ----LLNRIKSTYKSSGKEDENEIIRSLVN  178 (268)
T ss_pred             EEEECCCCCCHHHHHHHHHHH--HHHc-CCe-----------EEEEEHHH----HHHHHHHHHhccccccHHHHHHHhcC
Confidence            457799999999998876542  2222 311           23333222    22222211         011222223


Q ss_pred             ceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchH
Q psy13263        372 QRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYH  422 (577)
Q Consensus       372 ~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~  422 (577)
                      -.|++||+        ||.--.+.-.......|+......+..+||||.+.
T Consensus       179 ~dlLviDD--------lg~e~~t~~~~~~l~~iin~r~~~~~~~IiTsN~~  221 (268)
T PRK08116        179 ADLLILDD--------LGAERDTEWAREKVYNIIDSRYRKGLPTIVTTNLS  221 (268)
T ss_pred             CCEEEEec--------ccCCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCC
Confidence            35899999        98766666677777888888877778899999874

>TIGR03797 NHPM_micro_ABC2 NHPM bacteriocin system ABC transporter, ATP-binding protein

Probab=82.32  E-value=5.6  Score=46.23  Aligned_cols=61  Identities=13%  Similarity=0.094  Sum_probs=41.5

Q ss_pred             hchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       357 ~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      .|-++++-.+.......++++||           .|+.-|...- ..|.+.|.+.++.+|++||..+....+.
T Consensus       592 GQrQRialARAll~~p~iLiLDE-----------pTS~LD~~te-~~i~~~L~~~~~T~IiItHr~~~i~~~D  652 (686)
T TIGR03797       592 GQRQRLLIARALVRKPRILLFDE-----------ATSALDNRTQ-AIVSESLERLKVTRIVIAHRLSTIRNAD  652 (686)
T ss_pred             HHHHHHHHHHHHhcCCCEEEEeC-----------CccCCCHHHH-HHHHHHHHHhCCeEEEEecChHHHHcCC
Confidence            34444444444556778999999           6777776443 3566777666789999999987765443

Members of this protein family are ABC transporter ATP-binding subunits, part of a three-gene putative bacteriocin transport operon. The other subunits include another ATP-binding subunit (TIGR03796), which has an N-terminal propeptide cleavage domain, and an HlyD homolog (TIGR03794). In a number of genomes, a conserved propeptide sequence with a classic Gly-Gly motif

>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]

Probab=82.30  E-value=1.5  Score=44.74  Aligned_cols=175  Identities=19%  Similarity=0.197  Sum_probs=86.0

Q ss_pred             hhhhccccCccCCcchhhhhhhhhhccCcccccCcccccccc-ccc----cccccccc-cccc--CCCCCCCchhHHHHH
Q psy13263        248 ACSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYF-ENA----FDHKEASS-AGNI--IPKAGVDKEYDEVMD  319 (577)
Q Consensus       248 dl~~mkGsn~~GKStlLk~i~~~~i~i~~GrhPlLe~~l~~~-~n~----F~~~~a~~-~~I~--gPN~gGKsvy~k~va  319 (577)
                      .++-+=|+...|||||||.+....-++.+.|+   +..+.+. .|-    ++..+-|+ .|..  -||.--+|+|+.+.-
T Consensus        34 ~VTAlIGPSGcGKST~LR~lNRmndl~~~~r~---~G~v~~~g~ni~~~~~d~~~lRr~vGMVFQkPnPFp~SIydNVay  110 (253)
T COG1117          34 KVTALIGPSGCGKSTLLRCLNRMNDLIPGARV---EGEVLLDGKNIYDPKVDVVELRRRVGMVFQKPNPFPMSIYDNVAY  110 (253)
T ss_pred             ceEEEECCCCcCHHHHHHHHHhhcccCcCceE---EEEEEECCeeccCCCCCHHHHHHHheeeccCCCCCCchHHHHHHH
Confidence            34445588889999999988764444433332   1111111 122    22223333 2322  388777888887653


Q ss_pred             HHH--HHH-HHhccccccccceecc-ceeeecccccchhhh---hchhhhHHhhhcCCCceEEeecccCcccccccccCC
Q psy13263        320 EIK--SIE-KEIQTYLRTQCAHFGC-TVIYSEAQKKQKKYV---LEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGT  392 (577)
Q Consensus       320 lI~--~im-aqig~~VpA~~a~l~~-d~if~~iG~~qStF~---~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGT  392 (577)
                      -+.  .+. +.+...|-..-..-.+ |.+--+..+  |.+.   ..-.++-..+..|-...++|+||           =|
T Consensus       111 G~r~~g~~~~~ldeiVe~sLk~AaLWdEVKDrL~~--sa~~LSGGQQQRLcIARalAv~PeVlLmDE-----------Pt  177 (253)
T COG1117         111 GLRLHGIKDKELDEIVESSLKKAALWDEVKDRLHK--SALGLSGGQQQRLCIARALAVKPEVLLMDE-----------PT  177 (253)
T ss_pred             hHHhhccchHHHHHHHHHHHHHhHhHHHhHHHhhC--CccCCChhHHHHHHHHHHHhcCCcEEEecC-----------cc
Confidence            221  000 1111111000000111 111111111  2221   11122222344566778899999           46


Q ss_pred             CCcchhhHHHHHHHHHHhc---CCeEEEecchHHHHHHhhcCCCcccccceee
Q psy13263        393 GTNDGCVIARVTLEKFLQI---GCLTVFATHYHSVARRLREEPNVAFEYMSYI  442 (577)
Q Consensus       393 st~DG~ALA~AIlE~L~~~---~~~~lfaTHy~eL~~l~~~~~~V~n~hm~~~  442 (577)
                      |..|  -|+.+-+|.|+..   +-.++++||.+.=+.-...  ...++++...
T Consensus       178 SALD--PIsT~kIEeLi~eLk~~yTIviVTHnmqQAaRvSD--~taFf~~G~L  226 (253)
T COG1117         178 SALD--PISTLKIEELITELKKKYTIVIVTHNMQQAARVSD--YTAFFYLGEL  226 (253)
T ss_pred             cccC--chhHHHHHHHHHHHHhccEEEEEeCCHHHHHHHhH--hhhhhcccEE
Confidence            6666  3566778888765   6788999999865553332  3445666544

>TIGR02881 spore_V_K stage V sporulation protein K

Probab=81.68  E-value=4.3  Score=41.40  Aligned_cols=117  Identities=9%  Similarity=0.030  Sum_probs=57.1

Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecccccchhhhhchh-hhHHhhhcCCCceEEeec
Q psy13263        301 AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQKKQKKYVLEVP-SKYASKAKSNHQRVATKK  378 (577)
Q Consensus       301 ~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG~~qStF~~Em~-e~~~il~~a~~~sLVLlD  378 (577)
                      .+++||...|||..-+.++..-   ..++.........+.+ +.+        +.|..+.. .+..++..+ ..++++||
T Consensus        45 vll~GppGtGKTtlA~~ia~~l---~~~~~~~~~~~v~~~~~~l~--------~~~~g~~~~~~~~~~~~a-~~~VL~ID  112 (261)
T TIGR02881        45 MIFKGNPGTGKTTVARILGKLF---KEMNVLSKGHLIEVERADLV--------GEYIGHTAQKTREVIKKA-LGGVLFID  112 (261)
T ss_pred             EEEEcCCCCCHHHHHHHHHHHH---HhcCcccCCceEEecHHHhh--------hhhccchHHHHHHHHHhc-cCCEEEEe
Confidence            4578999999999999998753   3333211111111111 111        11221211 122233333 24789999


Q ss_pred             ccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHhhcCCCc
Q psy13263        379 KNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRLREEPNV  434 (577)
Q Consensus       379 Etg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~~~~~~V  434 (577)
                      |     ++-|.+|....-|......++..+-..  .+.+++++...++..+....|.+
T Consensus       113 E-----~~~L~~~~~~~~~~~~i~~Ll~~~e~~~~~~~vila~~~~~~~~~~~~~p~L  165 (261)
T TIGR02881       113 E-----AYSLARGGEKDFGKEAIDTLVKGMEDNRNEFVLILAGYSDEMDYFLSLNPGL  165 (261)
T ss_pred             c-----hhhhccCCccchHHHHHHHHHHHHhccCCCEEEEecCCcchhHHHHhcChHH
Confidence            9     222445544333433344455555443  33556677666665544433433

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.

>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor

Probab=81.32  E-value=3.1  Score=42.28  Aligned_cols=60  Identities=7%  Similarity=0.021  Sum_probs=40.3

Q ss_pred             hhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHHH
Q psy13263        359 VPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARR  427 (577)
Q Consensus       359 m~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~l  427 (577)
                      ..+++..+..+....++|+||        --.|-++.....+... +..+.+ .+..+|++||..++...
T Consensus       121 ~qrv~iaraL~~~p~llllDE--------Pt~~LD~~~~~~l~~~-l~~~~~~~~~tiiivsHd~~~~~~  181 (246)
T cd03237         121 LQRVAIAACLSKDADIYLLDE--------PSAYLDVEQRLMASKV-IRRFAENNEKTAFVVEHDIIMIDY  181 (246)
T ss_pred             HHHHHHHHHHhcCCCEEEEeC--------CcccCCHHHHHHHHHH-HHHHHHhcCCEEEEEeCCHHHHHH
Confidence            334444445566778999999        6666666655555444 444444 47899999999887764

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.

>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter

Probab=81.20  E-value=5.1  Score=46.69  Aligned_cols=47  Identities=19%  Similarity=0.282  Sum_probs=33.6

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHhh
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~~  429 (577)
                      ...++|+||           .|+.-|... ...|.+.|.+. ++.+|++||..++...+.
T Consensus       629 ~p~iliLDE-----------~Ts~LD~~t-e~~i~~~L~~~~~~T~IiitHr~~~~~~~D  676 (708)
T TIGR01193       629 DSKVLILDE-----------STSNLDTIT-EKKIVNNLLNLQDKTIIFVAHRLSVAKQSD  676 (708)
T ss_pred             CCCEEEEeC-----------ccccCCHHH-HHHHHHHHHHhcCCEEEEEecchHHHHcCC
Confidence            568899999           677777643 44555666553 688999999998766543

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.

>TIGR01846 type_I_sec_HlyB type I secretion system ABC transporter, HlyB family

Probab=81.13  E-value=5.1  Score=46.64  Aligned_cols=47  Identities=17%  Similarity=0.196  Sum_probs=31.7

Q ss_pred             CCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHh
Q psy13263        370 NHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRL  428 (577)
Q Consensus       370 ~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~  428 (577)
                      ....++|+||           .|+.-|... ...+.+.|.+.  ++.+|++||..+....+
T Consensus       610 ~~~~ililDE-----------pts~LD~~~-~~~i~~~l~~~~~~~t~i~itH~~~~~~~~  658 (694)
T TIGR01846       610 GNPRILIFDE-----------ATSALDYES-EALIMRNMREICRGRTVIIIAHRLSTVRAC  658 (694)
T ss_pred             hCCCEEEEEC-----------CCcCCCHHH-HHHHHHHHHHHhCCCEEEEEeCChHHHHhC
Confidence            3667889999           566666543 33444555443  78999999998776543

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion.

>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group

Probab=80.90  E-value=3.5  Score=39.96  Aligned_cols=58  Identities=12%  Similarity=0.034  Sum_probs=37.8

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ++.-.+.......++|+||        --.|-++..-. ..+.++..+.+.+..+|++||+.++..+
T Consensus       142 r~~laral~~~p~llllDE--------Pt~~LD~~~~~-~l~~~l~~~~~~~~tii~~sh~~~~~~~  199 (206)
T TIGR03608       142 RVALARAILKDPPLILADE--------PTGSLDPKNRD-EVLDLLLELNDEGKTIIIVTHDPEVAKQ  199 (206)
T ss_pred             HHHHHHHHHcCCCEEEEeC--------CcCCCCHHHHH-HHHHHHHHHHhcCCEEEEEeCCHHHHhh
Confidence            3333344556778999999        66666654433 3334445555557889999999987654

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.

>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]

Probab=80.87  E-value=2.5  Score=46.98  Aligned_cols=166  Identities=14%  Similarity=0.102  Sum_probs=82.7

Q ss_pred             hhhhhhhccccCccCCcchhhhhhhhhhcc-CcccccCcccccccccccccccccccccccCCCCCCCchhHHHHHHHHH
Q psy13263        245 DELACSYMKESGCTGESTLLTQLCNYESQT-PSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKS  323 (577)
Q Consensus       245 ~eLdl~~mkGsn~~GKStlLk~i~~~~i~i-~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~  323 (577)
                      ..-++.++.|....||+|+++.+....... ..+.-|.-.. +....|+.   .+..-+..-|.-++.++.........+
T Consensus       407 kpGdvvaVvGqSGaGKttllRmi~G~~~~~~ee~y~p~sg~-v~vp~nt~---~a~iPge~Ep~f~~~tilehl~s~tGD  482 (593)
T COG2401         407 KPGDVVAVVGQSGAGKTTLLRMILGAQKGRGEEKYRPDSGK-VEVPKNTV---SALIPGEYEPEFGEVTILEHLRSKTGD  482 (593)
T ss_pred             cCCCeEEEEecCCCCcchHHHHHHHHhhcccccccCCCCCc-eeccccch---hhccCcccccccCchhHHHHHhhccCc
Confidence            334566778888899999999876533211 1111232111 11111111   111122333665555544443332222


Q ss_pred             HHHHhccccccccceecc-ceeeeccc-ccchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHH
Q psy13263        324 IEKEIQTYLRTQCAHFGC-TVIYSEAQ-KKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIA  401 (577)
Q Consensus       324 imaqig~~VpA~~a~l~~-d~if~~iG-~~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA  401 (577)
                      +-+.++.     -.+.|+ |.++.+-- ...|+=+.|=..++..  .+....|.++||        |+.--++.-..-+|
T Consensus       483 ~~~AveI-----LnraGlsDAvlyRr~f~ELStGQKeR~KLAkl--laerpn~~~iDE--------F~AhLD~~TA~rVA  547 (593)
T COG2401         483 LNAAVEI-----LNRAGLSDAVLYRRKFSELSTGQKERAKLAKL--LAERPNVLLIDE--------FAAHLDELTAVRVA  547 (593)
T ss_pred             hhHHHHH-----HHhhccchhhhhhccHhhcCcchHHHHHHHHH--HhcCCCcEEhhh--------hhhhcCHHHHHHHH
Confidence            1111110     012233 33332211 1113333333333332  245557889999        88777776666666


Q ss_pred             HHHHHHHHhcCCeEEEecchHHHHHHhh
Q psy13263        402 RVTLEKFLQIGCLTVFATHYHSVARRLR  429 (577)
Q Consensus       402 ~AIlE~L~~~~~~~lfaTHy~eL~~l~~  429 (577)
                      ..|-+---+.+...+++||..++.+-+.
T Consensus       548 rkiselaRe~giTlivvThrpEv~~AL~  575 (593)
T COG2401         548 RKISELAREAGITLIVVTHRPEVGNALR  575 (593)
T ss_pred             HHHHHHHHHhCCeEEEEecCHHHHhccC
Confidence            6555433334899999999999998664

>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family

Probab=80.59  E-value=6  Score=46.02  Aligned_cols=49  Identities=14%  Similarity=0.087  Sum_probs=31.7

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHHhh
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARRLR  429 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l~~  429 (577)
                      .....++|+||           .|+.-|-. -...|.+.|.+.  ++.+|++||..+....+.
T Consensus       617 l~~p~iliLDE-----------~Ts~LD~~-te~~i~~~l~~~~~~~T~iiItHrl~~~~~~D  667 (694)
T TIGR03375       617 LRDPPILLLDE-----------PTSAMDNR-SEERFKDRLKRWLAGKTLVLVTHRTSLLDLVD  667 (694)
T ss_pred             hcCCCEEEEeC-----------CCCCCCHH-HHHHHHHHHHHHhCCCEEEEEecCHHHHHhCC
Confidence            34668899999           56666542 223344444443  689999999998765443

Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.

>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=80.26  E-value=3.6  Score=40.10  Aligned_cols=53  Identities=8%  Similarity=0.012  Sum_probs=35.3

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVAR  426 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~  426 (577)
                      .+.......++|+||        --.|-++..-..+...+ ..+.+ .++.+|++||+.+...
T Consensus       140 a~al~~~p~llllDE--------P~~~LD~~~~~~l~~~l-~~~~~~~~~tii~~sH~~~~~~  193 (211)
T cd03298         140 ARVLVRDKPVLLLDE--------PFAALDPALRAEMLDLV-LDLHAETKMTVLMVTHQPEDAK  193 (211)
T ss_pred             HHHHhcCCCEEEEcC--------CcccCCHHHHHHHHHHH-HHHHHhcCCEEEEEecCHHHHH
Confidence            344456778999999        66666655544443333 34444 3789999999988664

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.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	577
2o8b_B	1022	Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T M		4e-25
2o8b_B	1022	Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T M		9e-18
3thw_B	918	Human Mutsbeta Complexed With An Idl Of 4 Bases (Lo		1e-11
3k0s_A	799	Crystal Structure Of E.Coli Dna Mismatch Repair Pro		2e-09
1wbd_A	800	Crystal Structure Of E. Coli Dna Mismatch Repair En		3e-09
1oh5_A	800	The Crystal Structure Of E. Coli Muts Binding To Dn		3e-09
1wbb_A	800	Crystal Structure Of E. Coli Dna Mismatch Repair En		3e-09
1wb9_A	800	Crystal Structure Of E. Coli Dna Mismatch Repair En		3e-09
1e3m_A	800	The Crystal Structure Of E. Coli Muts Binding To Dn		5e-09
1ng9_A	800	E.Coli Muts R697a: An Atpase-Asymmetry Mutant Lengt		1e-08
2o8e_A	934	Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR,		5e-07
2o8b_A	934	Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T M		5e-07
1nne_A	765	Crystal Structure Of The Muts-adpbef3-dna Complex L		7e-07
1fw6_A	768	Crystal Structure Of A Taq Muts-Dna-Adp Ternary Com		7e-06
1ewr_A	649	Crystal Structure Of Taq Muts Length = 649		7e-06
1ewq_A	765	Crystal Structure Taq Muts Complexed With A Heterod		7e-06

>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR Length = 1022

Iteration: 1
 Score =  112 bits (281), Expect = 4e-25,   Method: Compositional matrix adjust.
 Identities = 52/107 (48%), Positives = 65/107 (60%), Gaps = 7/107 (6%)
Query: 154 ETTPSTSGAQD-------WSHNHYQFLHPDHILDADRRSPKHPDYNPKTLYVPPEFLKKQ 206
           E+    SG  D       W H   ++L  +   D  RR P HPD++  TLYVP +FL   
Sbjct: 9   ESQAHVSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDASTLYVPEDFLNSC 68
Query: 207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
           TP M +WW IKSQNFD V+ +KVGKFYEL+HMDA+IG  EL   +MK
Sbjct: 69  TPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMK 115

>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR Length = 1022

Iteration: 1
 Score = 88.6 bits (218), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 53/146 (36%), Positives = 79/146 (54%), Gaps = 5/146 (3%)
Query: 390  RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMS-YIEDKRN 447
            RGT T DG  IA   +++  + I C T+F+THYHS+     +   V   +M+  +E++  
Sbjct: 879  RGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECE 938
Query: 448  D-GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHK 506
            D   +TI FLYK + G CPKS+GFN A LA +PE+V++ G   A + E  +   +LF  +
Sbjct: 939  DPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLF--R 996
Query: 507  FASLVKSGEKVDVEELQKALESVKSF 532
               L      VD E + K L  +K  
Sbjct: 997  EVCLASERSTVDAEAVHKLLTLIKEL 1022

>pdb|3THW|B Chain B, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4) And Adp Length = 918

Iteration: 1
 Score = 68.2 bits (165), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 51/158 (32%), Positives = 81/158 (51%), Gaps = 14/158 (8%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEY-MSYI----E 443
           RGT T+DG  IA  TLE F++ +  LT+F THY  V    +   +    Y M ++    E
Sbjct: 763 RGTSTHDGIAIAYATLEYFIRDVKSLTLFVTHYPPVCELEKNYSHQVGNYHMGFLVSEDE 822
Query: 444 DKRNDGI-----DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN 498
            K + G      D + FLY++  GI  +S+G NVA+LA +P +++K     + ++E   N
Sbjct: 823 SKLDPGAAEQVPDFVTFLYQITRGIAARSYGLNVAKLADVPGEILKKAAHKSKELEGLIN 882
Query: 499 LRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQT 536
            ++  +  FA L       + ++LQK  E     E+QT
Sbjct: 883 TKRKRLKYFAKLWTMH---NAQDLQKWTEEFNMEETQT 917

>pdb|3K0S|A Chain A, Crystal Structure Of E.Coli Dna Mismatch Repair Protein Muts, D693n Mutant, In Complex With Gt Mismatched Dna Length = 799

Iteration: 1
 Score = 60.5 bits (145), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E     
Sbjct: 696 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 752
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
             DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 753 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 795

>pdb|1WBD|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme Muts, E38q Mutant, In Complex With A G.T Mismatch Length = 800

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E     
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
             DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>pdb|1OH5|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With A C:a Mismatch Length = 800

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E     
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
             DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>pdb|1WBB|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme Muts, E38a Mutant, In Complex With A G.T Mismatch Length = 800

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E     
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
             DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>pdb|1WB9|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme Muts, E38t Mutant, In Complex With A G.T Mismatch Length = 800

Iteration: 1
 Score = 60.5 bits (145), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 58/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E     
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
             DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 754 --DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>pdb|1E3M|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With A G:t Mismatch Length = 800

Iteration: 1
 Score = 59.7 bits (143), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 40/114 (35%), Positives = 57/114 (50%), Gaps = 15/114 (13%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E     
Sbjct: 697 RGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKXEGVANVHLDALEHG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
             DTI F + +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 754 --DTIAFXHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>pdb|1NG9|A Chain A, E.Coli Muts R697a: An Atpase-Asymmetry Mutant Length = 800

Iteration: 1
 Score = 58.2 bits (139), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 39/113 (34%), Positives = 57/113 (50%), Gaps = 15/113 (13%)
Query: 391 GTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           GT T DG  +A    E    +I  LT+FATHY  + +   +   VA  ++  +E      
Sbjct: 698 GTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEHG---- 753
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
            DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 754 -DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH ADP BOUND TO Msh2 Only Length = 934

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 390 RGTGTNDGCVIARVTLEKF-LQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +IG   +FATH+H +     + P V     + +      
Sbjct: 752 RGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTV-----NNLHVTALT 806
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
             +T+  LY++  G+C +SFG +VAELA  P+ V++     A ++E
Sbjct: 807 TEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELE 852

>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR Length = 934

Iteration: 1
 Score = 52.8 bits (125), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 34/106 (32%), Positives = 54/106 (50%), Gaps = 6/106 (5%)
Query: 390 RGTGTNDGCVIARVTLEKF-LQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
           RGT T DG  +A    E    +IG   +FATH+H +     + P V     + +      
Sbjct: 752 RGTSTYDGFGLAWAISEYIATKIGAFCMFATHFHELTALANQIPTV-----NNLHVTALT 806
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
             +T+  LY++  G+C +SFG +VAELA  P+ V++     A ++E
Sbjct: 807 TEETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELE 852

>pdb|1NNE|A Chain A, Crystal Structure Of The Muts-adpbef3-dna Complex Length = 765

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-07,   Method: Compositional matrix adjust.
 Identities = 31/107 (28%), Positives = 50/107 (46%), Gaps = 7/107 (6%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           RGT + DG  IA    E   +    T+FATHY  +         +    +  +     + 
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 718
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR 496
              +VF ++++PG   KS+G  VA +AG+P++VV     +   M AR
Sbjct: 719 AGGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVARARALLQAMAAR 765

>pdb|1FW6|A Chain A, Crystal Structure Of A Taq Muts-Dna-Adp Ternary Complex Length = 768

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           RGT + DG  IA    E   +    T+FATHY  +         +    +  +     + 
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 718
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
              +VF ++++PG   KS+G  VA  AG+P++VV
Sbjct: 719 AGGLVFYHQVLPGPASKSYGVEVAAXAGLPKEVV 752

>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts Length = 649

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           RGT + DG  IA    E   +    T+FATHY  +         +    +  +     + 
Sbjct: 550 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 602
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
              +VF ++++PG   KS+G  VA  AG+P++VV
Sbjct: 603 AGGLVFYHQVLPGPASKSYGVEVAAXAGLPKEVV 636

>pdb|1EWQ|A Chain A, Crystal Structure Taq Muts Complexed With A Heteroduplex Dna At 2.2 A Resolution Length = 765

Iteration: 1
 Score = 48.9 bits (115), Expect = 7e-06,   Method: Compositional matrix adjust.
 Identities = 28/94 (29%), Positives = 45/94 (47%), Gaps = 7/94 (7%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           RGT + DG  IA    E   +    T+FATHY  +         +    +  +     + 
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELT-------ALGLPRLKNLHVAAREE 718
Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
              +VF ++++PG   KS+G  VA  AG+P++VV
Sbjct: 719 AGGLVFYHQVLPGPASKSYGVEVAAXAGLPKEVV 752

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	577
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	4e-42
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	4e-31
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	1e-20
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	6e-26
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	2e-12
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	9e-05
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	1e-22
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	3e-08
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	1e-18
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	2e-10
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	3e-18
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	6e-11
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	2e-07

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B* Length = 1022

 Score =  161 bits (409), Expect = 4e-42
 Identities = 51/119 (42%), Positives = 66/119 (55%), Gaps = 5/119 (4%)

Query: 135 KLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPK 194
                ++ S         S     +S    W H   ++L  +   D  RR P HPD++  
Sbjct: 2   GSAPQNSESQAH-----VSGGGDDSSRPTVWYHETLEWLKEEKRRDEHRRRPDHPDFDAS 56

Query: 195 TLYVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMK 253
           TLYVP +FL   TP M +WW IKSQNFD V+ +KVGKFYEL+HMDA+IG  EL   +MK
Sbjct: 57  TLYVPEDFLNSCTPGMRKWWQIKSQNFDLVICYKVGKFYELYHMDALIGVSELGLVFMK 115

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B* Length = 1022

 Score =  128 bits (323), Expect = 4e-31
 Identities = 51/145 (35%), Positives = 76/145 (52%), Gaps = 5/145 (3%)

Query: 390  RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRN- 447
            RGT T DG  IA   +++  + I C T+F+THYHS+     +   V   +M+ + +    
Sbjct: 879  RGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECE 938

Query: 448  -DGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHK 506
                +TI FLYK + G CPKS+GFN A LA +PE+V++ G   A + E  +   +LF  +
Sbjct: 939  DPSQETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLF--R 996

Query: 507  FASLVKSGEKVDVEELQKALESVKS 531
               L      VD E + K L  +K 
Sbjct: 997  EVCLASERSTVDAEAVHKLLTLIKE 1021

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B* Length = 1022

 Score = 95.5 bits (238), Expect = 1e-20
 Identities = 41/144 (28%), Positives = 70/144 (48%), Gaps = 9/144 (6%)

Query: 249 CSYMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKA 308
              M+E     +S +L Q+ + +++ P G FPD++  L  ++ AFDH++A   G I PKA
Sbjct: 534 IGIMEEVADGFKSKILKQVISLQTKNPEGRFPDLTVELNRWDTAFDHEKARKTGLITPKA 593

Query: 309 GVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCT---VIYSEAQKKQKKYVLEVP-SKYA 364
           G D +YD+ + +I+  E+ +  YL  Q    GC             + +Y LE+P +   
Sbjct: 594 GFDSDYDQALADIRENEQSLLEYLEKQRNRIGCRTIVYWGI----GRNRYQLEIPENFTT 649

Query: 365 SKAKSNHQRVATKKKNVENYVTPE 388
                 ++  +T KK  + Y T  
Sbjct: 650 RNLPEEYELKST-KKGCKRYWTKT 672

>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* Length = 918

 Score =  111 bits (281), Expect = 6e-26
 Identities = 48/158 (30%), Positives = 79/158 (50%), Gaps = 14/158 (8%)

Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEP----NVAFEYMSYIED 444
           RGT T+DG  IA  TLE F++ +  LT+F THY  V    +       N    ++   ++
Sbjct: 763 RGTSTHDGIAIAYATLEYFIRDVKSLTLFVTHYPPVCELEKNYSHQVGNYHMGFLVSEDE 822

Query: 445 KRNDGI------DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHN 498
            + D        D + FLY++  GI  +S+G NVA+LA +P +++K     + ++E   N
Sbjct: 823 SKLDPGAAEQVPDFVTFLYQITRGIAARSYGLNVAKLADVPGEILKKAAHKSKELEGLIN 882

Query: 499 LRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQT 536
            ++  +  FA   K     + ++LQK  E     E+QT
Sbjct: 883 TKRKRLKYFA---KLWTMHNAQDLQKWTEEFNMEETQT 917

>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* Length = 918

 Score = 69.6 bits (171), Expect = 2e-12
 Identities = 17/44 (38%), Positives = 21/44 (47%)

Query: 204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
              TP   Q+  +K Q+ D VL  + G  Y  F  DA I A EL
Sbjct: 11  SIYTPLELQYIEMKQQHKDAVLCVECGYKYRFFGEDAEIAAREL 54

>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* Length = 918

 Score = 44.5 bits (106), Expect = 9e-05
 Identities = 22/152 (14%), Positives = 52/152 (34%), Gaps = 38/152 (25%)

Query: 252 MKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSA--GNIIPKAG 309
           +       +S LL  +            P++   ++++    + + A       +  K  
Sbjct: 440 IPAVNSHIQSDLLRTVIL--------EIPELLSPVEHYLKILNEQAAKVGDKTELF-KDL 490

Query: 310 VDKEYDEV-MDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQK--KQKK----------YV 356
            D    +   DEI+ +  EI+ +L+             E +K  K             ++
Sbjct: 491 SDFPLIKKRKDEIQGVIDEIRMHLQ-------------EIRKILKNPSAQYVTVSGQEFM 537

Query: 357 LEVPSKYASKAKSNHQRVATKKKNVENYVTPE 388
           +E+ +   S   ++  +V + K  V  + +P 
Sbjct: 538 IEIKNSAVSCIPTDWVKVGSTK-AVSRFHSPF 568

>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* Length = 934

 Score =  102 bits (255), Expect = 1e-22
 Identities = 38/147 (25%), Positives = 74/147 (50%), Gaps = 14/147 (9%)

Query: 390 RGTGTNDGCVIARVTLEKFL--QIGCLTVFATHYH---SVARRLREEPNVAFEYMSYIED 444
           RGT T DG  +A    E ++  +IG   +FATH+H   ++A ++   P V   +++ +  
Sbjct: 752 RGTSTYDGFGLAWAISE-YIATKIGAFCMFATHFHELTALANQI---PTVNNLHVTALTT 807

Query: 445 KRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFI 504
           +     +T+  LY++  G+C +SFG +VAELA  P+ V++     A ++E    + +   
Sbjct: 808 E-----ETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQYIGESQG 862

Query: 505 HKFASLVKSGEKVDVEELQKALESVKS 531
           +           ++ E+ +K ++   S
Sbjct: 863 YDIMEPAAKKCYLEREQGEKIIQEFLS 889

>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* Length = 934

 Score = 55.4 bits (134), Expect = 3e-08
 Identities = 13/63 (20%), Positives = 22/63 (34%), Gaps = 2/63 (3%)

Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL--ACSYMKESGCTGE 260
              +   +  +  +  +    V  F  G FY     DA++ A E+      +K  G  G 
Sbjct: 13  SAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGA 72

Query: 261 STL 263
             L
Sbjct: 73  KNL 75

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A* Length = 765

 Score = 89.1 bits (222), Expect = 1e-18
 Identities = 34/113 (30%), Positives = 55/113 (48%), Gaps = 16/113 (14%)

Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
           RGT + DG  IA    E   +    T+FATHY  +   L   P +   +++  E+     
Sbjct: 666 RGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTA-L-GLPRLKNLHVAAREEA---- 719

Query: 450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
              +VF ++++PG   KS+G  VA +AG+P++VV           AR  L+ +
Sbjct: 720 -GGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVA---------RARALLQAM 762

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A* Length = 765

 Score = 62.9 bits (154), Expect = 2e-10
 Identities = 16/44 (36%), Positives = 22/44 (50%)

Query: 204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
               P + Q+  ++ Q  D +L F+VG FYE F  DA   A  L
Sbjct: 11  GPLPPLLQQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARAL 54

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A* Length = 800

 Score = 87.5 bits (218), Expect = 3e-18
 Identities = 41/118 (34%), Positives = 59/118 (50%), Gaps = 23/118 (19%)

Query: 390 RGTGTNDGCVIARVTLEKFL--QIGCLTVFATHYH---SVARRLREEPNVAFEYMSYIED 444
           RGT T DG  +A    E  L  +I  LT+FATHY     +  ++    NV   ++  +E 
Sbjct: 697 RGTSTYDGLSLAWACAE-NLANKIKALTLFATHYFELTQLPEKMEGVANV---HLDALEH 752

Query: 445 KRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQL 502
                 DTI F++ +  G   KS+G  VA LAG+P++V+K          AR  LR+L
Sbjct: 753 G-----DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIK---------RARQKLREL 796

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A* Length = 800

 Score = 64.4 bits (158), Expect = 6e-11
 Identities = 16/45 (35%), Positives = 27/45 (60%)

Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
               TP M Q+  +K+Q+ + +LF+++G FY LF+ DA   +  L
Sbjct: 7   FDAHTPMMQQYLRLKAQHPEILLFYRMGDFYTLFYDDAKRASQLL 51

>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 = 56.4 bits (135), Expect = 2e-08
 Identities = 61/426 (14%), Positives = 118/426 (27%), Gaps = 132/426 (30%)

Query: 150 SDTSETTP-STSGAQDWSHNHYQFLHPDH-----ILDADRRSPKHP---DYNPKTL---- 196
           SD S          Q             +     +L  + ++ K     + + K L    
Sbjct: 217 SDHSSNIKLRIHSIQAELRRL--LKSKPYENCLLVLL-NVQNAKAWNAFNLSCKILLTTR 273

Query: 197 ------YVPPEFLKKQTPCMGQWWTIKSQNFDCVLFFKV--GKFYEL---------FHMD 239
                 ++        +           +     L  K    +  +L           + 
Sbjct: 274 FKQVTDFLSAATTTHISLDHHSMTLTPDEVKS--LLLKYLDCRPQDLPREVLTTNPRRL- 330

Query: 240 AVIGA---DELACS-YMKESGCTGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDH 295
           ++I     D LA     K   C   +T++ +        P+       E  K F+     
Sbjct: 331 SIIAESIRDGLATWDNWKHVNCDKLTTII-ESS-LNVLEPA-------EYRKMFDRLS-- 379

Query: 296 KEASSAGNIIPK-----AGV------DKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVI 344
                   + P        +      D    +VM  +  + K                  
Sbjct: 380 --------VFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK------------------ 413

Query: 345 YSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVT 404
           YS  +K+ K+  + +PS Y           A  +  V++Y  P+      +D  +   + 
Sbjct: 414 YSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTF---DSDDLIPPYLD 470

Query: 405 LEKFLQIGCLTVFATHYHSVARRLREE----PNVAFEYMSYIEDK-RNDGI--------- 450
              +  IG        +H       E       V  ++  ++E K R+D           
Sbjct: 471 QYFYSHIG--------HHLKNIEHPERMTLFRMVFLDF-RFLEQKIRHDSTAWNASGSIL 521

Query: 451 DTIVFL--YKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFA 508
           +T+  L  YK  P IC      N  +   +   ++ F      ++E       L   K+ 
Sbjct: 522 NTLQQLKFYK--PYICD-----NDPKYERLVNAILDF----LPKIEE-----NLICSKYT 565

Query: 509 SLVKSG 514
            L++  
Sbjct: 566 DLLRIA 571

>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 = 53.3 bits (127), Expect = 2e-07
 Identities = 54/437 (12%), Positives = 106/437 (24%), Gaps = 167/437 (38%)

Query: 170 YQFLHPDHILDADRRSPKHPDYNPKTLYV---------PPEFLKKQTPCMGQWWTIKSQN 220
           Y+FL     +   +   + P      +Y+            F K     +  +  ++   
Sbjct: 91  YKFL-----MSPIKTEQRQPS-MMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQ-- 142

Query: 221 FDCVLFFKVGKFYELFHMDAVI--GADELACSYMKESGCTGESTLLTQLCN---YESQTP 275
                        EL     V+  G        +   G  G++ +   +C     + +  
Sbjct: 143 ----------ALLELRPAKNVLIDG--------VL--GS-GKTWVALDVCLSYKVQCKMD 181

Query: 276 SGCF---------PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIE- 325
              F         P+   +L+  +                   +D  +    D   +I+ 
Sbjct: 182 FKIFWLNLKNCNSPE--TVLEMLQKLLYQ--------------IDPNWTSRSDHSSNIKL 225

Query: 326 --KEIQTYLRTQCAHFGCTVIYSEAQKKQKKY-----VLEVPSKYASKAKSNHQRVATKK 378
               IQ  LR                 K K Y     VL                     
Sbjct: 226 RIHSIQAELRR---LL-----------KSKPYENCLLVLL-------------------- 251

Query: 379 KNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEY 438
            NV+N    +                   F  + C  +  T +  V   L      A   
Sbjct: 252 -NVQN---AK---------------AWNAF-NLSCKILLTTRFKQVTDFL-----SAATT 286

Query: 439 MSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK--------FGTTVA 490
                D  +            V  +  K       +L   P +V+            ++ 
Sbjct: 287 THISLDHHSMT-----LTPDEVKSLLLKYLDCRPQDL---PREVLTTNPRRLSIIAESIR 338

Query: 491 FQMEAR-HNLRQLFIHKFASLVKSG-EKVDVEELQKALESVKSFESQTK---KDLEDLPG 545
               A   N + +   K  ++++S    ++  E +K  + +  F          L  +  
Sbjct: 339 -DGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLI-- 395

Query: 546 GVAGAGTEWWPSPSNDP 562
                   W+    +D 
Sbjct: 396 --------WFDVIKSDV 404

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	577
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	100.0
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	100.0
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	100.0
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	100.0
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	100.0
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	98.68
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	98.62
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	98.62
3ec2_A	180	DNA replication protein DNAC; helicase loader, rep	96.39
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	95.92
4gp7_A	171	Metallophosphoesterase; polynucleotide kinase phos	94.9
1ye8_A	178	Protein THEP1, hypothetical UPF0334 kinase-like pr	94.8
4g1u_C	266	Hemin import ATP-binding protein HMUV; membrane tr	94.19
2ehv_A	251	Hypothetical protein PH0186; KAIC, RECA ATPase, un	93.8
1vpl_A	256	ABC transporter, ATP-binding protein; TM0544, stru	92.92
3fvq_A	359	Fe(3+) IONS import ATP-binding protein FBPC; nucle	92.78
2onk_A	240	Molybdate/tungstate ABC transporter, ATP-binding p	92.75
2kjq_A	149	DNAA-related protein; solution structure, NESG, st	92.71
3tui_C	366	Methionine import ATP-binding protein METN; ABC-tr	92.57
1sgw_A	214	Putative ABC transporter; structural genomics, P p	92.48
1mv5_A	243	LMRA, multidrug resistance ABC transporter ATP-bin	92.28
1z47_A	355	CYSA, putative ABC-transporter ATP-binding protein	91.85
3rlf_A	381	Maltose/maltodextrin import ATP-binding protein M;	91.55
2yyz_A	359	Sugar ABC transporter, ATP-binding protein; sugar	91.43
2yz2_A	266	Putative ABC transporter ATP-binding protein TM_0;	91.24
1v43_A	372	Sugar-binding transport ATP-binding protein; ATPas	91.18
2w0m_A	235	SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus	90.69
3gfo_A	275	Cobalt import ATP-binding protein CBIO 1; structur	90.16
4a74_A	231	DNA repair and recombination protein RADA; hydrola	89.45
2cbz_A	237	Multidrug resistance-associated protein 1; ABC pro	87.85
2it1_A	362	362AA long hypothetical maltose/maltodextrin trans	87.71
3ux8_A	670	Excinuclease ABC, A subunit; UVRA, nucleotide exci	87.65
2iw3_A	986	Elongation factor 3A; acetylation, ATP-binding, pr	87.63
1g29_1	372	MALK, maltose transport protein MALK; ATPase, acti	87.51
3bk7_A	607	ABC transporter ATP-binding protein; ABC ATPase, i	87.26
2pjz_A	263	Hypothetical protein ST1066; ATP binding protein,	87.07
3bos_A	242	Putative DNA replication factor; P-loop containing	85.86
1nlf_A	279	Regulatory protein REPA; replicative DNA helicase	84.69
2z4s_A	440	Chromosomal replication initiator protein DNAA; AA	84.33
3nh6_A	306	ATP-binding cassette SUB-family B member 6, mitoc;	83.95
3qf4_B	598	Uncharacterized ABC transporter ATP-binding prote	82.95
2pcj_A	224	ABC transporter, lipoprotein-releasing system ATP-	82.42
3tif_A	235	Uncharacterized ABC transporter ATP-binding prote;	82.4
2cvh_A	220	DNA repair and recombination protein RADB; filamen	82.13
2w58_A	202	DNAI, primosome component (helicase loader); ATP-b	81.43
1jbk_A	195	CLPB protein; beta barrel, chaperone; 1.80A {Esche	80.01

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B*

Probab=100.00  E-value=2.9e-49  Score=463.07  Aligned_cols=221  Identities=24%  Similarity=0.412  Sum_probs=172.8

Q ss_pred             cccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecccc------cchhhhhchhhhHHhhhcCCCc
Q psy13263        300 SAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQK------KQKKYVLEVPSKYASKAKSNHQ  372 (577)
Q Consensus       300 ~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG~------~qStF~~Em~e~~~il~~a~~~  372 (577)
                      ..+|+|||++|||+|+++++++. +|+|+|+|||+..+.+++ |.||+++|.      +.|+|+.||.+++.++..++.+
T Consensus       791 i~~ItGpNgsGKSTlLr~iGl~~-~~aqiG~~Vpq~~~~l~v~d~I~~rig~~d~~~~~~stf~~em~~~a~al~la~~~  869 (1022)
T 2o8b_B          791 CVLVTGPNMGGKSTLMRQAGLLA-VMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAH  869 (1022)
T ss_dssp             EEEEECCTTSSHHHHHHHHHHHH-HHHTTTCCEESSEEEECCCSBEEEECC---------CHHHHHHHHHHHHHHHCCTT
T ss_pred             EEEEECCCCCChHHHHHHHHHHH-HHhheeEEeccCcCCCCHHHHHHHHcCCHHHHhhchhhhHHHHHHHHHHHHhCCCC
Confidence            34588999999999999999998 999999999999999999 999999885      3489999999999999999999


Q ss_pred             eEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHhhcCCCcccccceeeeecC--CCC
Q psy13263        373 RVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKR--NDG  449 (577)
Q Consensus       373 sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~~~~~~V~n~hm~~~~~~~--~~~  449 (577)
                      +||||||        +|+||++.||.+++++++++|.+. +|.+||+|||++++..+..+..|.++||.+.....  +..
T Consensus       870 sLlLLDE--------p~~Gtd~~dg~~~~~~il~~L~~~~g~~vl~~TH~~el~~~~~d~~~v~~g~~~~~~~~~~~~~~  941 (1022)
T 2o8b_B          870 SLVLVDE--------LGRGTATFDGTAIANAVVKELAETIKCRTLFSTHYHSLVEDYSQNVAVRLGHMACMVENECEDPS  941 (1022)
T ss_dssp             CEEEEEC--------TTTTSCHHHHHHHHHHHHHHHHHTSCCEEEEECCCHHHHHHTSSCSSEEEEEEEEC---------
T ss_pred             cEEEEEC--------CCCCCChHHHHHHHHHHHHHHHhcCCCEEEEEeCCHHHHHHhCCcceeecCeEEEEEecCcccCC
Confidence            9999999        999999999999999999999987 99999999999999998888889999998654211  112


Q ss_pred             cceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHhccCCCCHHHHHHHHHHH
Q psy13263        450 IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASLVKSGEKVDVEELQKALESV  529 (577)
Q Consensus       450 ~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~~~~~~~~~L~~~~~~~~~~ld~~~l~~l~~~L  529 (577)
                      .+.++|+|+|.+|+|++||||+||+++|||++||+||++++.+|+.....++++.+|.+.+  ....++.+.+..++..|
T Consensus       942 ~~~l~~ly~l~~G~~~~Sygi~vA~l~Glp~~vi~rA~~~~~~le~~~~~~~~~~~l~~~~--~~~~~~~~~~~~~~~~~ 1019 (1022)
T 2o8b_B          942 QETITFLYKFIKGACPKSYGFNAARLANLPEEVIQKGHRKAREFEKMNQSLRLFREVCLAS--ERSTVDAEAVHKLLTLI 1019 (1022)
T ss_dssp             ----CEEEEEESSCCCCCHHHHHHHHTTCCHHHHHHHHHHHHHTTSSTTSTTTSCC------------------------
T ss_pred             CCceEEEeeecCCCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--cccccCHHHHHHHHHHH
Confidence            4679999999999999999999999999999999999999999998887777776666544  34566677777676666


Q ss_pred             HH
Q psy13263        530 KS  531 (577)
Q Consensus       530 ~~  531 (577)
                      +.
T Consensus      1020 ~~ 1021 (1022)
T 2o8b_B         1020 KE 1021 (1022)
T ss_dssp             --
T ss_pred             hh
Confidence            43

>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=100.00  E-value=4.7e-37  Score=356.05  Aligned_cols=245  Identities=26%  Similarity=0.375  Sum_probs=203.9

Q ss_pred             hhccCcccccCccccc----cccccccccc--ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ce
Q psy13263        271 ESQTPSGCFPDMSELL----KYFENAFDHK--EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TV  343 (577)
Q Consensus       271 ~i~i~~GrhPlLe~~l----~~~~n~F~~~--~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~  343 (577)
                      .+.+.+||||+++..+    .+++|++...  .....+|+|||++|||+|+++++.|. +|+|+|+|||+..+.+++ +.
T Consensus       640 ~i~i~~~rHP~le~~~~~~~~~V~ndvsl~~~~g~i~~ItGPNGaGKSTlLr~i~~i~-~~aq~g~~vpa~~~~i~~~d~  718 (918)
T 3thx_B          640 KIVIKNGRHPVIDVLLGEQDQYVPNNTDLSEDSERVMIITGPNMGGKSSYIKQVALIT-IMAQIGSYVPAEEATIGIVDG  718 (918)
T ss_dssp             EEEEEEECCHHHHHHTCSCSSSCCEEEEECTTSCCEEEEESCCCHHHHHHHHHHHHHH-HHHHHTCCBSSSEEEEECCSE
T ss_pred             cEEEEeccchhhhhhhccCCceecccccccCCCCeEEEEECCCCCchHHHHHHHHHHH-HHhhcCccccchhhhhhHHHH
Confidence            5888999999987543    4778876654  44567899999999999999999999 999999999999999999 99


Q ss_pred             eeecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEE
Q psy13263        344 IYSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTV  416 (577)
Q Consensus       344 if~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~l  416 (577)
                      +|.++|.      +.|+|+.+|.++..++..++..+||||||        +|+||++.+|.+|+++++++|.+. ++.+|
T Consensus       719 i~~~ig~~d~l~~~~stfs~em~~~~~il~~a~~p~LlLLDE--------P~~GlD~~~~~~i~~~il~~L~~~~g~tvl  790 (918)
T 3thx_B          719 IFTRMGAADNIYKGRSTFMEELTDTAEIIRKATSQSLVILDE--------LGRGTSTHDGIAIAYATLEYFIRDVKSLTL  790 (918)
T ss_dssp             EEEEC----------CCHHHHHHHHHHHHHHCCTTCEEEEES--------TTTTSCHHHHHHHHHHHHHHHHHTTCCEEE
T ss_pred             HHHhCChHHHHHHhHHHhhHHHHHHHHHHHhccCCCEEEEeC--------CCCCCCHHHHHHHHHHHHHHHHHhcCCeEE
Confidence            9998875      34999999999999998899999999999        999999999999999999999874 99999


Q ss_pred             EecchHHHHHHhhcCCC-cccccceeeeecCC---------CCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHH
Q psy13263        417 FATHYHSVARRLREEPN-VAFEYMSYIEDKRN---------DGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFG  486 (577)
Q Consensus       417 faTHy~eL~~l~~~~~~-V~n~hm~~~~~~~~---------~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA  486 (577)
                      |+|||++|++++..+++ |.|+||.+...+.+         ...++++|+|||.+|+|++||||+||+++|||++||+||
T Consensus       791 ~vTH~~el~~l~~~~~~~v~n~~~~~~~~~~~~~~~~~~~~~~~~~l~flykl~~G~~~~S~gi~vA~~aGlp~~vi~rA  870 (918)
T 3thx_B          791 FVTHYPPVCELEKNYSHQVGNYHMGFLVSEDESKLDPGAAEQVPDFVTFLYQITRGIAARSYGLNVAKLADVPGEILKKA  870 (918)
T ss_dssp             EECSCGGGGGHHHHTTTTEEEEEEEEECC-----------------CCEEEEEEESCCCTTTTHHHHTTTTCCHHHHHHH
T ss_pred             EEeCcHHHHHHHhhcccceEEEEEEEEEcccccccccccccCCCCceeEeeeeccCCCCCcHHHHHHHHhCcCHHHHHHH
Confidence            99999999999988885 99999999743210         013579999999999999999999999999999999999


Q ss_pred             HHHHHHHHHhhhHH----HHHHHHHHHHHhccCCCCHHHHHHHHHHHHH
Q psy13263        487 TTVAFQMEARHNLR----QLFIHKFASLVKSGEKVDVEELQKALESVKS  531 (577)
Q Consensus       487 ~ei~~~le~~~~~~----~~~~~L~~~~~~~~~~ld~~~l~~l~~~L~~  531 (577)
                      ++++.+||+....+    +.+++|+.       ..+..+++.|++.++.
T Consensus       871 ~~~~~~LE~~~~~~~k~~~~~~~~~~-------~~~~~~~~~~~~~~~~  912 (918)
T 3thx_B          871 AHKSKELEGLINTKRKRLKYFAKLWT-------MHNAQDLQKWTEEFNM  912 (918)
T ss_dssp             HHHHHHHHHHHHHHHHHHHHHHHHHT-------CCSHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHc-------CCCHHHHHHHHHHHHh
Confidence            99999999887643    34444442       2345677777665543

>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=100.00  E-value=2.5e-36  Score=350.74  Aligned_cols=255  Identities=17%  Similarity=0.243  Sum_probs=214.5

Q ss_pred             hhhccCcccccCccccc--cccccccccc--ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-cee
Q psy13263        270 YESQTPSGCFPDMSELL--KYFENAFDHK--EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVI  344 (577)
Q Consensus       270 ~~i~i~~GrhPlLe~~l--~~~~n~F~~~--~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~i  344 (577)
                      ..+.+.+||||+++...  .+++|++...  .....+|+|||++|||+|+++++++. +|+|+|+|||+..+.+++ +.+
T Consensus       630 ~~i~i~~~rHP~le~~~~~~~v~ndisl~~~~g~i~~ItGpNGsGKSTlLr~ial~~-~~aq~G~~vpa~~~~~~~~d~i  708 (934)
T 3thx_A          630 GRIILKASRHACVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGGKSTYIRQTGVIV-LMAQIGCFVPCESAEVSIVDCI  708 (934)
T ss_dssp             CEEEEEEECCTTTTTC--CCCCCEEEEEETTTBCEEEEECCTTSSHHHHHHHHHHHH-HHHHHTCCBSEEEEEEECCSEE
T ss_pred             cceEeecCccchhhhcCCceeecccceeecCCCeEEEEECCCCCCHHHHHHHHHHHH-HHHhcCCccccccccchHHHHH
Confidence            35888999999998652  4778876555  34567899999999999999999999 999999999999999999 999


Q ss_pred             eecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEE
Q psy13263        345 YSEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVF  417 (577)
Q Consensus       345 f~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lf  417 (577)
                      |.++|.      +.|+|+.+|.+++.++..++.++||||||        +|+||++.+|.+|+++++++|.+. +|.+||
T Consensus       709 ~~~ig~~d~l~~~lStf~~e~~~~a~il~~a~~~sLlLLDE--------p~~GlD~~~~~~i~~~il~~l~~~~g~~vl~  780 (934)
T 3thx_A          709 LARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDE--------LGRGTSTYDGFGLAWAISEYIATKIGAFCMF  780 (934)
T ss_dssp             EEECC---------CHHHHHHHHHHHHHHHCCTTCEEEEES--------CSCSSCHHHHHHHHHHHHHHHHHTTCCEEEE
T ss_pred             HHhcCchhhHHHhHhhhHHHHHHHHHHHHhccCCcEEEEeC--------CCCCCCHHHHHHHHHHHHHHHHhcCCCEEEE
Confidence            999885      34999999999999998899999999999        999999999999999999999985 999999


Q ss_pred             ecchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHhh
Q psy13263        418 ATHYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARH  497 (577)
Q Consensus       418 aTHy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~~  497 (577)
                      +|||++|..++...+.|.|+||.+....     +.++|+|+|.+|.++.||||+||+++|||++||+||++++.+|++..
T Consensus       781 aTH~~el~~lad~~~~v~ng~v~~~~~~-----~~l~~~y~l~~G~~~~S~gi~vA~~~glp~~vi~~A~~~~~~le~~~  855 (934)
T 3thx_A          781 ATHFHELTALANQIPTVNNLHVTALTTE-----ETLTMLYQVKKGVCDQSFGIHVAELANFPKHVIECAKQKALELEEFQ  855 (934)
T ss_dssp             EESCGGGGGGGGTCTTEEEEEEEEEEET-----TEEEEEEEEEESCCCCCCHHHHHHHTTCCHHHHHHHHHHHHHTTTTT
T ss_pred             EcCcHHHHHHhcccceeEeeEEEEEecC-----CcEEEEEEEeeCCCCCchHHHHHHHcCCCHHHHHHHHHHHHHHHhcc
Confidence            9999999999999999999999987653     58999999999999999999999999999999999999999998764


Q ss_pred             hHH-------------------HHHHHHHHHHHhccCCCCHHHHHH--HHHHHHHHHHHHHH
Q psy13263        498 NLR-------------------QLFIHKFASLVKSGEKVDVEELQK--ALESVKSFESQTKK  538 (577)
Q Consensus       498 ~~~-------------------~~~~~L~~~~~~~~~~ld~~~l~~--l~~~L~~~~~~~~~  538 (577)
                      ...                   ..-..+.+.+++++..+|.++++|  .++.|.+++++...
T Consensus       856 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~tp~eal~~l~~l~~~~~~  917 (934)
T 3thx_A          856 YIGESQGYDIMEPAAKKCYLEREQGEKIIQEFLSKVKQMPFTEMSEENITIKLKQLKAEVIA  917 (934)
T ss_dssp             C---------------CCSHHHHHHHHHHHHHHHHHHTCCGGGCCHHHHHHHHHHHHHHHHH
T ss_pred             cccccccccccccccccccccccccchHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHHh
Confidence            210                   011123334556667777777555  45666666665443

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=100.00  E-value=5e-35  Score=335.54  Aligned_cols=213  Identities=23%  Similarity=0.327  Sum_probs=189.6

Q ss_pred             hhhccCcccccCccccc--cccccccccc-ccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceee
Q psy13263        270 YESQTPSGCFPDMSELL--KYFENAFDHK-EASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIY  345 (577)
Q Consensus       270 ~~i~i~~GrhPlLe~~l--~~~~n~F~~~-~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if  345 (577)
                      ..+.+.+||||+++..+  .++.|++... .....+|+|||++|||+|+++++.+. +|+|+|+|||+..+.+++ +.+|
T Consensus       576 ~~i~i~~~rHP~le~~~~~~~vlndisl~~~g~i~~ItGpNGsGKSTlLr~iagl~-~~~q~G~~vpa~~~~i~~~~~i~  654 (800)
T 1wb9_A          576 PGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIA-LMAYIGSYVPAQKVEIGPIDRIF  654 (800)
T ss_dssp             SCEEEEEECCTTHHHHCSSCCCCEEEEECSSSCEEEEECCTTSSHHHHHHHHHHHH-HHHTTTCCBSSSEEEECCCCEEE
T ss_pred             CCEEEEeccccEEEccCCCceeeecccccCCCcEEEEECCCCCChHHHHHHHHHHH-HHHhcCcccchhcccceeHHHHH
Confidence            35889999999998643  3667766554 34457799999999999999999998 999999999999999999 9999


Q ss_pred             ecccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEe
Q psy13263        346 SEAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFA  418 (577)
Q Consensus       346 ~~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfa  418 (577)
                      .++|.      +.|+|+.||.++..++..++..+|+|+||        +|+||++.||.+++++++++|.+. ++.+||+
T Consensus       655 ~~~~~~d~l~~~~stf~~e~~~~~~il~~a~~psLlLLDE--------p~~Gtd~~d~~~i~~~ll~~l~~~~g~~vl~~  726 (800)
T 1wb9_A          655 TRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDE--------IGRGTSTYDGLSLAWACAENLANKIKALTLFA  726 (800)
T ss_dssp             EEEC-----------CHHHHHHHHHHHHHCCTTEEEEEES--------CCCCSSSSHHHHHHHHHHHHHHHTTCCEEEEE
T ss_pred             hhCCHHHHHHhhhhhhhHHHHHHHHHHHhccCCCEEEEEC--------CCCCCChhHHHHHHHHHHHHHHhccCCeEEEE
Confidence            98875      34899999999999998999999999999        999999999999999999999985 9999999


Q ss_pred             cchHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Q psy13263        419 THYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR  496 (577)
Q Consensus       419 THy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~~  496 (577)
                      |||+++..++...++|.|+||.+.+..     +.++|+|+|.+|++++||||+||+++|||++||+||++++.++++.
T Consensus       727 TH~~el~~l~d~~~~v~n~~~~~~~~~-----~~l~~~ykl~~G~~~~S~gi~vA~~~GlP~~vi~rA~~~l~~le~~  799 (800)
T 1wb9_A          727 THYFELTQLPEKMEGVANVHLDALEHG-----DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELESI  799 (800)
T ss_dssp             CSCGGGGGHHHHSTTEEEEEEEEEEET-----TEEEEEEEEEESCCSSCCHHHHHHHTTCCHHHHHHHHHHHHHHHTC
T ss_pred             eCCHHHHHHhhhhhceEEEEEEEEEcC-----CcEEEEEEEEECCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHhhc
Confidence            999999999888999999999998753     5899999999999999999999999999999999999999999853

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=100.00  E-value=8.3e-34  Score=324.03  Aligned_cols=209  Identities=21%  Similarity=0.294  Sum_probs=188.7

Q ss_pred             hhhccCcccccCcccccccccccccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecc
Q psy13263        270 YESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEA  348 (577)
Q Consensus       270 ~~i~i~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~i  348 (577)
                      ..+.+.+||||+++..-.++.|++... ....+|+|||++|||+|+++++.+. +|+|+|++||+..+.+++ +.+|.++
T Consensus       549 ~~i~i~~~rHP~le~~~~~vl~disl~-g~i~~I~GpNGsGKSTlLr~iagl~-~~~~~G~~vpa~~~~i~~v~~i~~~~  626 (765)
T 1ewq_A          549 DRLQIRAGRHPVVERRTEFVPNDLEMA-HELVLITGPNMAGKSTFLRQTALIA-LLAQVGSFVPAEEAHLPLFDGIYTRI  626 (765)
T ss_dssp             SSEEEEEECCTTGGGTSCCCCEEEEES-SCEEEEESCSSSSHHHHHHHHHHHH-HHHTTTCCBSSSEEEECCCSEEEEEC
T ss_pred             CcEEEEEeECceEccCCceEeeeccCC-CcEEEEECCCCCChHHHHHHHHhhh-hhcccCceeehhccceeeHHHhhccC
Confidence            458899999999874123667766665 5667899999999999999999998 899999999999999999 9999987


Q ss_pred             cc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchH
Q psy13263        349 QK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYH  422 (577)
Q Consensus       349 G~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~  422 (577)
                      |.      ++|+|+.||.+++.++..++..+|+|+||        +||||++.||.+++++|+++|.+.++.+||+|||+
T Consensus       627 ~~~d~l~~g~S~~~~e~~~la~il~~a~~p~LlLLDE--------pgrGTs~lD~~~~~~~i~~~L~~~g~~vl~~TH~~  698 (765)
T 1ewq_A          627 GASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDE--------VGRGTSSLDGVAIATAVAEALHERRAYTLFATHYF  698 (765)
T ss_dssp             CC------CCSHHHHHHHHHHHHHHHCCTTEEEEEES--------TTTTSCHHHHHHHHHHHHHHHHHHTCEEEEECCCH
T ss_pred             CHHHHHHhcccHHHHHHHHHHHHHHhccCCCEEEEEC--------CCCCCCCcCHHHHHHHHHHHHHhCCCEEEEEeCCH
Confidence            64      45999999999999998899999999999        99999999999999999999998899999999999


Q ss_pred             HHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy13263        423 SVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEA  495 (577)
Q Consensus       423 eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~  495 (577)
                      ++..+.  .++|.|+||.+.+.     .+.++|+|+|.+|.+++||||+||+++|||++||+||++++.+|++
T Consensus       699 ~l~~~~--~~~v~n~~~~~~~~-----~~~l~f~ykl~~G~~~~Sygi~vA~~aGlP~~VI~rA~~~l~~le~  764 (765)
T 1ewq_A          699 ELTALG--LPRLKNLHVAAREE-----AGGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVARARALLQAMAA  764 (765)
T ss_dssp             HHHTCC--CTTEEEEEEEEECC-----SSSCEEEEEEEESCCSSCCHHHHHHHTTCCHHHHHHHHHHHHHHTT
T ss_pred             HHHHhh--hhcceEEEEEEEEc-----CCeEEEEEEEEECCCCCchHHHHHHHcCCCHHHHHHHHHHHHHHhc
Confidence            999877  78999999999864     3579999999999999999999999999999999999999999874

>1ewq_A DNA mismatch repair protein MUTS; multiple domains of protein, mostly mixed alpha-beta structures, one domain is entirely helical; HET: DNA; 2.20A {Thermus aquaticus} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1nne_A* 1fw6_A* 1ewr_A*

Probab=98.68  E-value=1.2e-09  Score=125.29  Aligned_cols=50  Identities=32%  Similarity=0.458  Sum_probs=48.6

Q ss_pred             ccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccc
Q psy13263        205 KQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKE  254 (577)
Q Consensus       205 ~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkG  254 (577)
                      ++||||+|||++|++|||++||||+|+|||+|++||++++++|+|+++++
T Consensus        12 ~~tp~~~qy~~iK~~~~d~~l~~r~GdFYE~f~~DA~~~~~~L~i~lt~r   61 (765)
T 1ewq_A           12 PLPPLLQQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHK   61 (765)
T ss_dssp             CCCHHHHHHHHHHHHCTTSEEEEEETTEEEEEHHHHHHHHHHHTCCCEEE
T ss_pred             CCChHHHHHHHHHHHCCCEEEEEecCceeEEcHHHHHHHHHHhCcEEecc
Confidence            58999999999999999999999999999999999999999999999987

>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=98.62  E-value=2.2e-09  Score=125.06  Aligned_cols=51  Identities=33%  Similarity=0.347  Sum_probs=47.4

Q ss_pred             cccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccc
Q psy13263        204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKE  254 (577)
Q Consensus       204 ~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkG  254 (577)
                      .++||||+|||++|++|||++||||+|+|||+|++||++++++|+|++..+
T Consensus        11 ~~~TPmm~Qy~~iK~~~~D~lLffr~GdFYElF~eDA~~as~~L~i~lt~~   61 (918)
T 3thx_B           11 SIYTPLELQYIEMKQQHKDAVLCVECGYKYRFFGEDAEIAARELNIYCHLD   61 (918)
T ss_dssp             TTSCHHHHHHHHHHTTTTTSEEEEECSSEEEEEHHHHHHHHHHHTCCCEEE
T ss_pred             CCCCHHHHHHHHHHHHCCCeEEEEEcCCEeeeeHhhHHHHHHHhCceeecC
Confidence            358999999999999999999999999999999999999999999986544

>1wb9_A DNA mismatch repair protein MUTS; DNA-binding, ATP-binding, DNA binding, DNA repair, mismatch recognition; HET: DNA ADP; 2.10A {Escherichia coli} SCOP: a.113.1.1 c.37.1.12 c.55.6.1 d.75.2.1 PDB: 1wbb_A* 1e3m_A* 1oh5_A* 1oh6_A* 1oh7_A* 1oh8_A* 1w7a_A* 2wtu_A* 1wbd_A* 1ng9_A* 3k0s_A*

Probab=98.62  E-value=3.1e-09  Score=122.39  Aligned_cols=52  Identities=35%  Similarity=0.572  Sum_probs=49.3

Q ss_pred             cccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhcccc
Q psy13263        204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKES  255 (577)
Q Consensus       204 ~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGs  255 (577)
                      .++||||+|||++|++|||+++|||+|+|||+|++||++++++|+++++++.
T Consensus         8 ~~~tp~~~qy~~ik~~~~d~~lffr~GdFYE~f~~DA~~~a~~l~i~lt~r~   59 (800)
T 1wb9_A            8 DAHTPMMQQYLRLKAQHPEILLFYRMGDFYTLFYDDAKRASQLLDISLTKRG   59 (800)
T ss_dssp             GGSCHHHHHHHHHHHHSTTSEEEEEETTEEEEEHHHHHHHHHHHTCCCEEEC
T ss_pred             cCCCHHHHHHHHHHHhCCCEEEEEEcCCEEEEehhhHHHHHHHhCcEEeccc
Confidence            4679999999999999999999999999999999999999999999998764

>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=96.39  E-value=0.0055  Score=56.38  Aligned_cols=105  Identities=6%  Similarity=-0.077  Sum_probs=59.5

Q ss_pred             ccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccccchhhhhchhhhH------Hhh
Q psy13263        293 FDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKY------ASK  366 (577)
Q Consensus       293 F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e~~------~il  366 (577)
                      |........+++|||..|||...+.++...  ..+-|..           .+|.....    +..++....      ..+
T Consensus        33 ~~~~~g~~~~l~G~~G~GKTtL~~~i~~~~--~~~~g~~-----------~~~~~~~~----~~~~~~~~~~~~~~~~~~   95 (180)
T 3ec2_A           33 FNPEEGKGLTFVGSPGVGKTHLAVATLKAI--YEKKGIR-----------GYFFDTKD----LIFRLKHLMDEGKDTKFL   95 (180)
T ss_dssp             CCGGGCCEEEECCSSSSSHHHHHHHHHHHH--HHHSCCC-----------CCEEEHHH----HHHHHHHHHHHTCCSHHH
T ss_pred             ccccCCCEEEEECCCCCCHHHHHHHHHHHH--HHHcCCe-----------EEEEEHHH----HHHHHHHHhcCchHHHHH
Confidence            333334456788999999999999887643  2222311           12221111    111111000      111


Q ss_pred             hcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchH
Q psy13263        367 AKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYH  422 (577)
Q Consensus       367 ~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~  422 (577)
                      .......|++|||        ++..-.......+...+++.+...+..+|++||+.
T Consensus        96 ~~~~~~~llilDE--------~~~~~~~~~~~~~l~~ll~~~~~~~~~ii~tsn~~  143 (180)
T 3ec2_A           96 KTVLNSPVLVLDD--------LGSERLSDWQRELISYIITYRYNNLKSTIITTNYS  143 (180)
T ss_dssp             HHHHTCSEEEEET--------CSSSCCCHHHHHHHHHHHHHHHHTTCEEEEECCCC
T ss_pred             HHhcCCCEEEEeC--------CCCCcCCHHHHHHHHHHHHHHHHcCCCEEEEcCCC
Confidence            1112347899999        88533333445566777778777789999999985

>3thx_A DNA mismatch repair protein MSH2; ABC family ATPase, mismatch recognition, mismatched unpaired DNA binding protein-DNA complex; HET: DNA ADP; 2.70A {Homo sapiens} PDB: 2o8c_A* 2o8d_A* 2o8f_A* 3thw_A* 2o8b_A* 3thy_A* 3thz_A* 2o8e_A*

Probab=95.92  E-value=0.00029  Score=82.51  Aligned_cols=48  Identities=19%  Similarity=0.255  Sum_probs=44.0

Q ss_pred             cccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhh
Q psy13263        204 KKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSY  251 (577)
Q Consensus       204 ~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~  251 (577)
                      .+.+|+++||+++|++|+|+|+||++|+||++|.+||+.++..+.++.
T Consensus        14 ~~~~~f~~~y~~Lk~k~~dtv~~F~~GdfYe~~~~DA~~vA~~l~~t~   61 (934)
T 3thx_A           14 AAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQ   61 (934)
T ss_dssp             HHHHHHHHHHHTSCCCCTTEEEEEECSSEEEEETHHHHHHHHHTTSSS
T ss_pred             ccccHHHHHHHhccccCCCeEEEEEcCCeeeeehhhHHHHHHHHhhhh
Confidence            457899999999999999999999999999999999999998887654

>4gp7_A Metallophosphoesterase; polynucleotide kinase phosphatase, RNA repair, transferase; HET: ATP CIT; 2.00A {Clostridium thermocellum} PDB: 4gp6_A*

Probab=94.90  E-value=0.039  Score=50.83  Aligned_cols=21  Identities=14%  Similarity=-0.018  Sum_probs=17.0

Q ss_pred             ccccccccCCCCCCCchhHHH
Q psy13263        297 EASSAGNIIPKAGVDKEYDEV  317 (577)
Q Consensus       297 ~a~~~~I~gPN~gGKsvy~k~  317 (577)
                      .....+++|||.+|||++.+.
T Consensus         8 ~gei~~l~G~nGsGKSTl~~~   28 (171)
T 4gp7_A            8 ELSLVVLIGSSGSGKSTFAKK   28 (171)
T ss_dssp             SSEEEEEECCTTSCHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHH
Confidence            334457899999999999994

>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=94.80  E-value=0.043  Score=51.44  Aligned_cols=59  Identities=8%  Similarity=0.072  Sum_probs=33.9

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecc---hHHHHHHhhcCCCcccc
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATH---YHSVARRLREEPNVAFE  437 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTH---y~eL~~l~~~~~~V~n~  437 (577)
                      .....|++|||        +| -|+-.|- ....++.+.|.+.++.+|++||   .+.+..-....++++.+
T Consensus        97 ~~~p~llilDE--------ig-p~~~ld~-~~~~~l~~~l~~~~~~~i~~~H~~h~~~~~~~i~~r~~~~i~  158 (178)
T 1ye8_A           97 KDRRKVIIIDE--------IG-KMELFSK-KFRDLVRQIMHDPNVNVVATIPIRDVHPLVKEIRRLPGAVLI  158 (178)
T ss_dssp             HCTTCEEEECC--------CS-TTGGGCH-HHHHHHHHHHTCTTSEEEEECCSSCCSHHHHHHHTCTTCEEE
T ss_pred             ccCCCEEEEeC--------CC-CcccCCH-HHHHHHHHHHhcCCCeEEEEEccCCCchHHHHHHhcCCcEEE
Confidence            45567999999        88 3443332 2334455555444666888886   55666554444444333

>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=94.19  E-value=0.094  Score=52.43  Aligned_cols=48  Identities=8%  Similarity=-0.097  Sum_probs=31.9

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHH
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARR  427 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l  427 (577)
                      ...|+|+||        --.|=++.....+ ..++..|.+. ++.+|++||+.++...
T Consensus       165 ~p~lLllDE--------Pts~LD~~~~~~i-~~~l~~l~~~~~~tvi~vtHdl~~~~~  213 (266)
T 4g1u_C          165 TPRWLFLDE--------PTSALDLYHQQHT-LRLLRQLTRQEPLAVCCVLHDLNLAAL  213 (266)
T ss_dssp             CCEEEEECC--------CCSSCCHHHHHHH-HHHHHHHHHHSSEEEEEECSCHHHHHH
T ss_pred             CCCEEEEeC--------ccccCCHHHHHHH-HHHHHHHHHcCCCEEEEEEcCHHHHHH
Confidence            568999999        5455554433333 3455556555 5689999999887653

>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=92.92  E-value=0.11  Score=51.64  Aligned_cols=56  Identities=16%  Similarity=0.131  Sum_probs=36.6

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +.-.+..+....|+|+||        --.|=++.--..+ +.++..+.+.+..+|++||+.+...
T Consensus       155 v~lAraL~~~p~lllLDE--------Pts~LD~~~~~~l-~~~l~~l~~~g~tiiivtHd~~~~~  210 (256)
T 1vpl_A          155 LLIARALMVNPRLAILDE--------PTSGLDVLNAREV-RKILKQASQEGLTILVSSHNMLEVE  210 (256)
T ss_dssp             HHHHHHHTTCCSEEEEES--------TTTTCCHHHHHHH-HHHHHHHHHTTCEEEEEECCHHHHT
T ss_pred             HHHHHHHHcCCCEEEEeC--------CccccCHHHHHHH-HHHHHHHHhCCCEEEEEcCCHHHHH
Confidence            333445566778999999        5555555433333 3445555555889999999987654

>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=92.78  E-value=0.28  Score=51.53  Aligned_cols=59  Identities=12%  Similarity=0.045  Sum_probs=36.2

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      +++-.+..+....|+|+||        --.|=++.-...+..-+.+.+.+.+..+|++||+.+.+..
T Consensus       146 RValArAL~~~P~lLLLDE--------Pts~LD~~~r~~l~~~l~~~~~~~g~tvi~vTHd~~ea~~  204 (359)
T 3fvq_A          146 RAALARALAPDPELILLDE--------PFSALDEQLRRQIREDMIAALRANGKSAVFVSHDREEALQ  204 (359)
T ss_dssp             HHHHHHHHTTCCSEEEEES--------TTTTSCHHHHHHHHHHHHHHHHHTTCEEEEECCCHHHHHH
T ss_pred             HHHHHHHHHcCCCEEEEeC--------CcccCCHHHHHHHHHHHHHHHHhCCCEEEEEeCCHHHHHH
Confidence            3444445567778999999        4444444433333333333333448999999999876653

>2onk_A Molybdate/tungstate ABC transporter, ATP-binding protein; membrane protein; 3.10A {Archaeoglobus fulgidus} SCOP: c.37.1.12

Probab=92.75  E-value=0.36  Score=47.39  Aligned_cols=57  Identities=11%  Similarity=-0.052  Sum_probs=36.3

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +++-.+..+....++|+||        --.|=++.-. ...+.++..+.+. +..+|++||+.+...
T Consensus       134 Rv~lAral~~~p~lllLDE--------Pts~LD~~~~-~~~~~~l~~l~~~~g~tvi~vtHd~~~~~  191 (240)
T 2onk_A          134 RVALARALVIQPRLLLLDE--------PLSAVDLKTK-GVLMEELRFVQREFDVPILHVTHDLIEAA  191 (240)
T ss_dssp             HHHHHHHHTTCCSSBEEES--------TTSSCCHHHH-HHHHHHHHHHHHHHTCCEEEEESCHHHHH
T ss_pred             HHHHHHHHHcCCCEEEEeC--------CcccCCHHHH-HHHHHHHHHHHHhcCCEEEEEeCCHHHHH
Confidence            3333445566778999999        5555554333 3334455556544 889999999987554

>2kjq_A DNAA-related protein; solution structure, NESG, structural genomics, PSI-2, protei structure initiative; NMR {Neisseria meningitidis serogroup B}

Probab=92.71  E-value=0.18  Score=45.75  Aligned_cols=85  Identities=8%  Similarity=-0.027  Sum_probs=51.4

Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccccchhhhhchhhhHHhhhcCCCceEEeeccc
Q psy13263        301 AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKN  380 (577)
Q Consensus       301 ~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e~~~il~~a~~~sLVLlDEt  380 (577)
                      .+++||+..|||...+.++...  . .-|           ...+|.....    +..+     ..+   ....|++||| 
T Consensus        39 ~~l~G~~G~GKTtL~~~i~~~~--~-~~g-----------~~~~~~~~~~----~~~~-----~~~---~~~~lLilDE-   91 (149)
T 2kjq_A           39 IYVWGEEGAGKSHLLQAWVAQA--L-EAG-----------KNAAYIDAAS----MPLT-----DAA---FEAEYLAVDQ-   91 (149)
T ss_dssp             EEEESSSTTTTCHHHHHHHHHH--H-TTT-----------CCEEEEETTT----SCCC-----GGG---GGCSEEEEES-
T ss_pred             EEEECCCCCCHHHHHHHHHHHH--H-hcC-----------CcEEEEcHHH----hhHH-----HHH---hCCCEEEEeC-
Confidence            4688999999999999887643  1 112           1233332221    1111     111   1246889999 


Q ss_pred             CcccccccccCCCCcchhhHHHHHHHHHHhcCCe-EEEecch
Q psy13263        381 VENYVTPECRGTGTNDGCVIARVTLEKFLQIGCL-TVFATHY  421 (577)
Q Consensus       381 g~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~-~lfaTHy  421 (577)
                             ++......  ....+.+++.+.+.+.. +|+|||.
T Consensus        92 -------~~~~~~~~--~~~l~~li~~~~~~g~~~iiits~~  124 (149)
T 2kjq_A           92 -------VEKLGNEE--QALLFSIFNRFRNSGKGFLLLGSEY  124 (149)
T ss_dssp             -------TTCCCSHH--HHHHHHHHHHHHHHTCCEEEEEESS
T ss_pred             -------ccccChHH--HHHHHHHHHHHHHcCCcEEEEECCC
Confidence                   87743322  55566777777777665 8999996

>3tui_C Methionine import ATP-binding protein METN; ABC-transporter, type I ABC type importer, methionine uptake transporter, membrane protein; HET: ADP; 2.90A {Escherichia coli} PDB: 3tuj_C 3tuz_C* 3dhw_C

Probab=92.57  E-value=0.35  Score=50.96  Aligned_cols=53  Identities=15%  Similarity=0.138  Sum_probs=34.0

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARR  427 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l  427 (577)
                      +..+....|+|+||        --.|=++..... ...++..|.+. +..+|++||+.++...
T Consensus       176 rAL~~~P~lLLlDE--------PTs~LD~~~~~~-i~~lL~~l~~~~g~Tii~vTHdl~~~~~  229 (366)
T 3tui_C          176 RALASNPKVLLCDQ--------ATSALDPATTRS-ILELLKDINRRLGLTILLITHEMDVVKR  229 (366)
T ss_dssp             HHTTTCCSEEEEES--------TTTTSCHHHHHH-HHHHHHHHHHHSCCEEEEEESCHHHHHH
T ss_pred             HHHhcCCCEEEEEC--------CCccCCHHHHHH-HHHHHHHHHHhCCCEEEEEecCHHHHHH
Confidence            33455778999999        433433333222 23445556554 8999999999887654

>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=92.48  E-value=0.13  Score=49.78  Aligned_cols=56  Identities=2%  Similarity=-0.008  Sum_probs=37.4

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVA  425 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~  425 (577)
                      ++...+.......++|+||        --.|=++.-...+.. ++..+.+.+..+|++||+.+..
T Consensus       141 rv~laraL~~~p~lllLDE--------Pts~LD~~~~~~l~~-~l~~~~~~g~tiiivtHd~~~~  196 (214)
T 1sgw_A          141 RVQLASTLLVNAEIYVLDD--------PVVAIDEDSKHKVLK-SILEILKEKGIVIISSREELSY  196 (214)
T ss_dssp             HHHHHHHTTSCCSEEEEES--------TTTTSCTTTHHHHHH-HHHHHHHHHSEEEEEESSCCTT
T ss_pred             HHHHHHHHHhCCCEEEEEC--------CCcCCCHHHHHHHHH-HHHHHHhCCCEEEEEeCCHHHH
Confidence            3333455567778999999        777777655444443 4445554578899999997543

>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=92.28  E-value=0.51  Score=46.13  Aligned_cols=52  Identities=12%  Similarity=0.197  Sum_probs=36.1

Q ss_pred             hhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        366 KAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       366 l~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      +.......|+|+||        --.|=++..-..|... +..+. .+..+|++||..++...
T Consensus       152 ral~~~p~lllLDE--------Pts~LD~~~~~~i~~~-l~~~~-~~~tvi~vtH~~~~~~~  203 (243)
T 1mv5_A          152 RAFLRNPKILMLDE--------ATASLDSESESMVQKA-LDSLM-KGRTTLVIAHRLSTIVD  203 (243)
T ss_dssp             HHHHHCCSEEEEEC--------CSCSSCSSSCCHHHHH-HHHHH-TTSEEEEECCSHHHHHH
T ss_pred             HHHhcCCCEEEEEC--------CcccCCHHHHHHHHHH-HHHhc-CCCEEEEEeCChHHHHh
Confidence            33344567999999        7777777665555544 44455 48899999999876653

>1z47_A CYSA, putative ABC-transporter ATP-binding protein; alpha/beta motif, beta sandwich, ligand binding protein; 1.90A {Alicyclobacillus acidocaldarius}

Probab=91.85  E-value=0.44  Score=49.85  Aligned_cols=30  Identities=13%  Similarity=0.245  Sum_probs=22.3

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEI  321 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI  321 (577)
                      +|........+++|||.+|||+.+++++-+
T Consensus        35 sl~i~~Ge~~~llGpnGsGKSTLLr~iaGl   64 (355)
T 1z47_A           35 SFQIREGEMVGLLGPSGSGKTTILRLIAGL   64 (355)
T ss_dssp             EEEEETTCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCEEEEECCCCCcHHHHHHHHhCC
Confidence            344444445678999999999999988643

>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=91.55  E-value=0.34  Score=51.30  Aligned_cols=30  Identities=10%  Similarity=0.049  Sum_probs=22.2

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEI  321 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI  321 (577)
                      +|........+++|||.+|||+.+++++-+
T Consensus        23 sl~i~~Ge~~~llGpsGsGKSTLLr~iaGl   52 (381)
T 3rlf_A           23 NLDIHEGEFVVFVGPSGCGKSTLLRMIAGL   52 (381)
T ss_dssp             EEEECTTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCEEEEEcCCCchHHHHHHHHHcC
Confidence            344444445679999999999999988643

>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=91.43  E-value=0.53  Score=49.30  Aligned_cols=30  Identities=13%  Similarity=0.119  Sum_probs=22.3

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEI  321 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI  321 (577)
                      +|........+++|||.+|||+.+++++-+
T Consensus        23 sl~i~~Ge~~~llGpnGsGKSTLLr~iaGl   52 (359)
T 2yyz_A           23 SFEVKDGEFVALLGPSGCGKTTTLLMLAGI   52 (359)
T ss_dssp             EEEECTTCEEEEECSTTSSHHHHHHHHHTS
T ss_pred             EEEEcCCCEEEEEcCCCchHHHHHHHHHCC
Confidence            344444445678999999999999988643

>2yz2_A Putative ABC transporter ATP-binding protein TM_0; cobalt transport, TM02 hydrolase, inner membrane, membrane, nucleotide-binding; 2.30A {Thermotoga maritima}

Probab=91.24  E-value=0.42  Score=47.49  Aligned_cols=57  Identities=9%  Similarity=0.042  Sum_probs=36.2

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +++-.+..+....|+|+||        --.|=++.-- ...+.++..+.+.+..+|++||+.+...
T Consensus       146 Rv~lAraL~~~p~lllLDE--------Pts~LD~~~~-~~l~~~l~~l~~~g~tii~vtHd~~~~~  202 (266)
T 2yz2_A          146 RVAIASVIVHEPDILILDE--------PLVGLDREGK-TDLLRIVEKWKTLGKTVILISHDIETVI  202 (266)
T ss_dssp             HHHHHHHHTTCCSEEEEES--------TTTTCCHHHH-HHHHHHHHHHHHTTCEEEEECSCCTTTG
T ss_pred             HHHHHHHHHcCCCEEEEcC--------ccccCCHHHH-HHHHHHHHHHHHcCCEEEEEeCCHHHHH
Confidence            3333445567778999999        5555555333 3333445555545789999999976543

>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=91.18  E-value=0.53  Score=49.50  Aligned_cols=30  Identities=7%  Similarity=-0.022  Sum_probs=22.7

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDEI  321 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~valI  321 (577)
                      +|........+++|||.+|||+.+++++-+
T Consensus        31 sl~i~~Ge~~~llGpnGsGKSTLLr~iaGl   60 (372)
T 1v43_A           31 NLTIKDGEFLVLLGPSGCGKTTTLRMIAGL   60 (372)
T ss_dssp             EEEECTTCEEEEECCTTSSHHHHHHHHHTS
T ss_pred             EEEECCCCEEEEECCCCChHHHHHHHHHcC
Confidence            444444555679999999999999988643

>2w0m_A SSO2452; RECA, SSPF, unknown FUN; 2.0A {Sulfolobus solfataricus P2}

Probab=90.69  E-value=0.19  Score=46.92  Aligned_cols=23  Identities=0%  Similarity=-0.328  Sum_probs=18.8

Q ss_pred             cccccCCCCCCCchhHHHHHHHH
Q psy13263        300 SAGNIIPKAGVDKEYDEVMDEIK  322 (577)
Q Consensus       300 ~~~I~gPN~gGKsvy~k~valI~  322 (577)
                      ..+++|||.+|||++.++++...
T Consensus        25 ~~~i~G~~GsGKTtl~~~l~~~~   47 (235)
T 2w0m_A           25 FIALTGEPGTGKTIFSLHFIAKG   47 (235)
T ss_dssp             EEEEECSTTSSHHHHHHHHHHHH
T ss_pred             EEEEEcCCCCCHHHHHHHHHHHH
Confidence            34688999999999999987543

>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=90.16  E-value=0.49  Score=47.53  Aligned_cols=57  Identities=12%  Similarity=0.053  Sum_probs=36.5

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHH-hcCCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~-~~~~~~lfaTHy~eL~~  426 (577)
                      +++..+..+....|+|+||        --.|=++.... ..+.++..|. +.+..+|++||+.++..
T Consensus       151 Rv~iAraL~~~P~lLlLDE--------Pts~LD~~~~~-~i~~~l~~l~~~~g~tvi~vtHdl~~~~  208 (275)
T 3gfo_A          151 RVAIAGVLVMEPKVLILDE--------PTAGLDPMGVS-EIMKLLVEMQKELGITIIIATHDIDIVP  208 (275)
T ss_dssp             HHHHHHHHTTCCSEEEEEC--------TTTTCCHHHHH-HHHHHHHHHHHHHCCEEEEEESCCSSGG
T ss_pred             HHHHHHHHHcCCCEEEEEC--------ccccCCHHHHH-HHHHHHHHHHhhCCCEEEEEecCHHHHH
Confidence            3333444566778999999        44444444333 3345566666 44889999999986554

>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=89.45  E-value=0.34  Score=45.28  Aligned_cols=22  Identities=0%  Similarity=-0.124  Sum_probs=18.2

Q ss_pred             cccccCCCCCCCchhHHHHHHH
Q psy13263        300 SAGNIIPKAGVDKEYDEVMDEI  321 (577)
Q Consensus       300 ~~~I~gPN~gGKsvy~k~valI  321 (577)
                      ..+|+|||.+|||++.++++-.
T Consensus        27 ~~~l~G~nGsGKSTll~~l~g~   48 (231)
T 4a74_A           27 ITEVFGEFGSGKTQLAHTLAVM   48 (231)
T ss_dssp             EEEEEESTTSSHHHHHHHHHHH
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
Confidence            3468899999999999988653

>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=87.85  E-value=0.089  Score=51.53  Aligned_cols=21  Identities=24%  Similarity=0.189  Sum_probs=17.4

Q ss_pred             hhhccccCccCCcchhhhhhh
Q psy13263        249 CSYMKESGCTGESTLLTQLCN  269 (577)
Q Consensus       249 l~~mkGsn~~GKStlLk~i~~  269 (577)
                      ++.+-|+|..||||+++.++.
T Consensus        33 ~~~i~G~nGsGKSTLl~~l~G   53 (237)
T 2cbz_A           33 LVAVVGQVGCGKSSLLSALLA   53 (237)
T ss_dssp             EEEEECSTTSSHHHHHHHHTT
T ss_pred             EEEEECCCCCCHHHHHHHHhc
Confidence            455679999999999998864

>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding protein; structural genomics, NPPSFA; 1.94A {Pyrococcus horikoshii}

Probab=87.71  E-value=0.59  Score=48.96  Aligned_cols=57  Identities=18%  Similarity=0.135  Sum_probs=35.1

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      +++-.+..+....|+|+||        --.|=++.-...+ +..+..|.+. +..+|++||+.+.+.
T Consensus       141 RvalArAL~~~P~lLLLDE--------P~s~LD~~~r~~l-~~~l~~l~~~~g~tvi~vTHd~~~a~  198 (362)
T 2it1_A          141 RVAIARALVKEPEVLLLDE--------PLSNLDALLRLEV-RAELKRLQKELGITTVYVTHDQAEAL  198 (362)
T ss_dssp             HHHHHHHHTTCCSEEEEES--------GGGGSCHHHHHHH-HHHHHHHHHHHTCEEEEEESCHHHHH
T ss_pred             HHHHHHHHHcCCCEEEEEC--------ccccCCHHHHHHH-HHHHHHHHHhCCCEEEEECCCHHHHH
Confidence            3333445567778999999        4444444333222 2334445444 889999999977654

>3ux8_A Excinuclease ABC, A subunit; UVRA, nucleotide excision repair, DNA repair, ABC ATPase, DN binding protein; HET: ADP; 2.10A {Geobacillus}

Probab=87.65  E-value=0.71  Score=51.68  Aligned_cols=47  Identities=13%  Similarity=0.154  Sum_probs=32.2

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      ...|+|+||        --.|=++.....|. .++..|.+.+..+|++||+.++..
T Consensus       564 ~p~llllDE--------Pt~~LD~~~~~~i~-~~l~~l~~~g~tvi~vtHd~~~~~  610 (670)
T 3ux8_A          564 GRTLYILDE--------PTTGLHVDDIARLL-DVLHRLVDNGDTVLVIEHNLDVIK  610 (670)
T ss_dssp             SCEEEEEES--------TTTTCCHHHHHHHH-HHHHHHHHTTCEEEEECCCHHHHT
T ss_pred             CCcEEEEeC--------CCCCCCHHHHHHHH-HHHHHHHHCCCEEEEEeCCHHHHH
Confidence            346999999        55555554444433 445556666889999999998754

>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=87.63  E-value=1.1  Score=53.00  Aligned_cols=28  Identities=14%  Similarity=0.062  Sum_probs=23.4

Q ss_pred             cccccccccccccCCCCCCCchhHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMD  319 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~va  319 (577)
                      +|........+|+|||.+|||+++++++
T Consensus       455 sl~I~~Ge~v~LiGpNGsGKSTLLk~La  482 (986)
T 2iw3_A          455 QLRLKRARRYGICGPNGCGKSTLMRAIA  482 (986)
T ss_dssp             EEEEETTCEEEEECSTTSSHHHHHHHHH
T ss_pred             eEEEcCCCEEEEECCCCCCHHHHHHHHh
Confidence            5555566677899999999999999986

>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=87.51  E-value=0.52  Score=49.53  Aligned_cols=56  Identities=18%  Similarity=0.165  Sum_probs=33.9

Q ss_pred             hHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHH
Q psy13263        362 KYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVAR  426 (577)
Q Consensus       362 ~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~  426 (577)
                      ++-.+..+....|+|+||        --.|=++.-...+ +..+..|.+. +..+|++||+.+.+.
T Consensus       148 valArAL~~~P~lLLLDE--------P~s~LD~~~r~~l-~~~l~~l~~~~g~tvi~vTHd~~~a~  204 (372)
T 1g29_1          148 VALGRAIVRKPQVFLMDE--------PLSNLDAKLRVRM-RAELKKLQRQLGVTTIYVTHDQVEAM  204 (372)
T ss_dssp             HHHHHHHHTCCSEEEEEC--------TTTTSCHHHHHHH-HHHHHHHHHHHTCEEEEEESCHHHHH
T ss_pred             HHHHHHHhcCCCEEEECC--------CCccCCHHHHHHH-HHHHHHHHHhcCCEEEEECCCHHHHH
Confidence            333344456678999999        4444443322222 2334445444 889999999977654

>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=87.26  E-value=2.1  Score=47.78  Aligned_cols=62  Identities=3%  Similarity=-0.011  Sum_probs=38.4

Q ss_pred             chhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh-cCCeEEEecchHHHHHHh
Q psy13263        358 EVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRL  428 (577)
Q Consensus       358 Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~-~~~~~lfaTHy~eL~~l~  428 (577)
                      |-.++...+..+...-|+|+||        --.|=++.--..|. .++..|.+ .+..+|++||+.++....
T Consensus       476 e~QRv~iAraL~~~p~lLlLDE--------Pt~~LD~~~~~~l~-~~l~~l~~~~g~tvi~vsHd~~~~~~~  538 (607)
T 3bk7_A          476 ELQRVAIAATLLRDADIYLLDE--------PSAYLDVEQRLAVS-RAIRHLMEKNEKTALVVEHDVLMIDYV  538 (607)
T ss_dssp             HHHHHHHHHHHTSCCSEEEEEC--------TTTTCCHHHHHHHH-HHHHHHHHHTTCEEEEECSCHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCEEEEeC--------CccCCCHHHHHHHH-HHHHHHHHhCCCEEEEEeCCHHHHHHh
Confidence            3334443444566778999999        55555544333333 34455553 488999999998877643

>2pjz_A Hypothetical protein ST1066; ATP binding protein, structural genomics, NPPSFA; 1.90A {Sulfolobus tokodaii}

Probab=87.07  E-value=1.8  Score=43.07  Aligned_cols=49  Identities=14%  Similarity=0.079  Sum_probs=30.5

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHH
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVA  425 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~  425 (577)
                      .+..+....|+|+||           =|+.-|-. ....+++.|.+....+|++||+.+..
T Consensus       140 AraL~~~p~lllLDE-----------Pts~LD~~-~~~~l~~~L~~~~~tviivtHd~~~~  188 (263)
T 2pjz_A          140 SLALASQPEIVGLDE-----------PFENVDAA-RRHVISRYIKEYGKEGILVTHELDML  188 (263)
T ss_dssp             HHHHHTCCSEEEEEC-----------TTTTCCHH-HHHHHHHHHHHSCSEEEEEESCGGGG
T ss_pred             HHHHHhCCCEEEEEC-----------CccccCHH-HHHHHHHHHHHhcCcEEEEEcCHHHH
Confidence            344456678999999           34444432 23345555555422899999997654

>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=85.86  E-value=1.9  Score=40.04  Aligned_cols=92  Identities=3%  Similarity=-0.229  Sum_probs=52.9

Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccccchhhhhchhhhHHhhhcCCCceEEeeccc
Q psy13263        301 AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKN  380 (577)
Q Consensus       301 ~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e~~~il~~a~~~sLVLlDEt  380 (577)
                      .+++||...|||.+.+.++.-.  ... +.           ..+|.....    +...+.+.   +.......+++||| 
T Consensus        55 ~ll~G~~G~GKT~la~~l~~~~--~~~-~~-----------~~~~~~~~~----~~~~~~~~---~~~~~~~~vliiDe-  112 (242)
T 3bos_A           55 IYLWGPVKSGRTHLIHAACARA--NEL-ER-----------RSFYIPLGI----HASISTAL---LEGLEQFDLICIDD-  112 (242)
T ss_dssp             EEEECSTTSSHHHHHHHHHHHH--HHT-TC-----------CEEEEEGGG----GGGSCGGG---GTTGGGSSEEEEET-
T ss_pred             EEEECCCCCCHHHHHHHHHHHH--HHc-CC-----------eEEEEEHHH----HHHHHHHH---HHhccCCCEEEEec-
Confidence            4588999999999998876532  111 11           122332222    22222221   11223457999999 


Q ss_pred             CcccccccccCCCCcchhhHHHHHHHHHHhcCCe-EEEecch
Q psy13263        381 VENYVTPECRGTGTNDGCVIARVTLEKFLQIGCL-TVFATHY  421 (577)
Q Consensus       381 g~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~-~lfaTHy  421 (577)
                             +..-............+++.+...+.. +|++|+.
T Consensus       113 -------~~~~~~~~~~~~~l~~~l~~~~~~~~~~ii~~~~~  147 (242)
T 3bos_A          113 -------VDAVAGHPLWEEAIFDLYNRVAEQKRGSLIVSASA  147 (242)
T ss_dssp             -------GGGGTTCHHHHHHHHHHHHHHHHHCSCEEEEEESS
T ss_pred             -------cccccCCHHHHHHHHHHHHHHHHcCCCeEEEEcCC
Confidence                   877655544455555666666666544 8888875

>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=84.69  E-value=0.72  Score=45.36  Aligned_cols=47  Identities=21%  Similarity=0.173  Sum_probs=28.2

Q ss_pred             CceEEeecccCccccccccc--CCCCcc--hhhHHHHHHHHHHh-cCCeEEEecchHHHH
Q psy13263        371 HQRVATKKKNVENYVTPECR--GTGTND--GCVIARVTLEKFLQ-IGCLTVFATHYHSVA  425 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGR--GTst~D--G~ALA~AIlE~L~~-~~~~~lfaTHy~eL~  425 (577)
                      .-.||+|||        +..  |-+..+  .+.-....+..|++ .+|.+||+||.....
T Consensus       133 ~~~livlDe--------~~~~~~~d~~~~~~~~~~~~~L~~l~~~~g~tvi~i~H~~~~~  184 (279)
T 1nlf_A          133 GRRLMVLDT--------LRRFHIEEENASGPMAQVIGRMEAIAADTGCSIVFLHHASKGA  184 (279)
T ss_dssp             TCSEEEEEC--------GGGGCCSCTTCHHHHHHHHHHHHHHHHHHCCEEEEEEEC----
T ss_pred             CCCEEEECC--------HHHhcCCCcCchHHHHHHHHHHHHHHHHcCCEEEEEecCCCcc
Confidence            357999999        766  443322  12344455566654 499999999998765

>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=84.33  E-value=1.3  Score=47.08  Aligned_cols=97  Identities=8%  Similarity=-0.042  Sum_probs=56.4

Q ss_pred             cccccCCCCCCCchhHHHHHHHHHHHHHh-ccccccccceeccceeeecccccchhhhhchhhh------HHhhhcCC-C
Q psy13263        300 SAGNIIPKAGVDKEYDEVMDEIKSIEKEI-QTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSK------YASKAKSN-H  371 (577)
Q Consensus       300 ~~~I~gPN~gGKsvy~k~valI~~imaqi-g~~VpA~~a~l~~d~if~~iG~~qStF~~Em~e~------~~il~~a~-~  371 (577)
                      ..++.||+..|||...+.++...  ..+. +           ...+|....    .|..++...      ........ .
T Consensus       132 ~lll~Gp~G~GKTtLa~aia~~l--~~~~~~-----------~~v~~v~~~----~~~~~~~~~~~~~~~~~~~~~~~~~  194 (440)
T 2z4s_A          132 PLFIYGGVGLGKTHLLQSIGNYV--VQNEPD-----------LRVMYITSE----KFLNDLVDSMKEGKLNEFREKYRKK  194 (440)
T ss_dssp             CEEEECSSSSSHHHHHHHHHHHH--HHHCCS-----------SCEEEEEHH----HHHHHHHHHHHTTCHHHHHHHHTTT
T ss_pred             eEEEECCCCCCHHHHHHHHHHHH--HHhCCC-----------CeEEEeeHH----HHHHHHHHHHHcccHHHHHHHhcCC
Confidence            34578999999999999887532  1210 1           122332222    222222111      01111112 4


Q ss_pred             ceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecch
Q psy13263        372 QRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHY  421 (577)
Q Consensus       372 ~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy  421 (577)
                      ..+++|||        +.+-............+++.+...++.+|++||.
T Consensus       195 ~~vL~IDE--------i~~l~~~~~~q~~l~~~l~~l~~~~~~iIitt~~  236 (440)
T 2z4s_A          195 VDILLIDD--------VQFLIGKTGVQTELFHTFNELHDSGKQIVICSDR  236 (440)
T ss_dssp             CSEEEEEC--------GGGGSSCHHHHHHHHHHHHHHHTTTCEEEEEESS
T ss_pred             CCEEEEeC--------cccccCChHHHHHHHHHHHHHHHCCCeEEEEECC
Confidence            67999999        8776654344445556677777778899999996

>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=83.95  E-value=1  Score=46.10  Aligned_cols=29  Identities=7%  Similarity=0.041  Sum_probs=22.4

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDE  320 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~val  320 (577)
                      +|........+|+|||.+|||+.++++.-
T Consensus        74 sl~i~~Ge~vaivG~sGsGKSTLl~ll~g  102 (306)
T 3nh6_A           74 SFTVMPGQTLALVGPSGAGKSTILRLLFR  102 (306)
T ss_dssp             EEEECTTCEEEEESSSCHHHHHHHHHHTT
T ss_pred             eEEEcCCCEEEEECCCCchHHHHHHHHHc
Confidence            45555555678999999999999998743

>3qf4_B Uncharacterized ABC transporter ATP-binding prote TM_0288; multidrug transporter, transport protein; HET: ANP; 2.90A {Thermotoga maritima}

Probab=82.95  E-value=1.3  Score=49.12  Aligned_cols=27  Identities=11%  Similarity=0.121  Sum_probs=21.1

Q ss_pred             ccccccccccccCCCCCCCchhHHHHH
Q psy13263        293 FDHKEASSAGNIIPKAGVDKEYDEVMD  319 (577)
Q Consensus       293 F~~~~a~~~~I~gPN~gGKsvy~k~va  319 (577)
                      |........+|+|||.+|||+.++.+.
T Consensus       376 l~i~~G~~~~ivG~sGsGKSTll~~l~  402 (598)
T 3qf4_B          376 FHIKPGQKVALVGPTGSGKTTIVNLLM  402 (598)
T ss_dssp             EECCTTCEEEEECCTTSSTTHHHHHHT
T ss_pred             EEEcCCCEEEEECCCCCcHHHHHHHHh
Confidence            444455567799999999999998874

>2pcj_A ABC transporter, lipoprotein-releasing system ATP-binding protein; structural genomics; 1.70A {Aquifex aeolicus} PDB: 2pcl_A

Probab=82.42  E-value=1.7  Score=41.94  Aligned_cols=57  Identities=14%  Similarity=0.056  Sum_probs=36.2

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      +++-.+.......|+|+||        --.|=++.-- ...+.++..|.+.+..+|++||+.++..
T Consensus       148 rv~laral~~~p~lllLDE--------Pt~~LD~~~~-~~~~~~l~~l~~~g~tvi~vtHd~~~~~  204 (224)
T 2pcj_A          148 RVAIARALANEPILLFADE--------PTGNLDSANT-KRVMDIFLKINEGGTSIVMVTHERELAE  204 (224)
T ss_dssp             HHHHHHHTTTCCSEEEEES--------TTTTCCHHHH-HHHHHHHHHHHHTTCEEEEECSCHHHHT
T ss_pred             HHHHHHHHHcCCCEEEEeC--------CCCCCCHHHH-HHHHHHHHHHHHCCCEEEEEcCCHHHHH
Confidence            3333445566778999999        5555554332 2333445555555889999999987653

>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=82.40  E-value=1.3  Score=42.99  Aligned_cols=58  Identities=22%  Similarity=0.182  Sum_probs=37.2

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHH
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARR  427 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l  427 (577)
                      +++-.+..+....++|+||        --.|=++.....+ +.++..|.+. +..+|++||+.++..+
T Consensus       153 Rv~iAral~~~p~llllDE--------Pts~LD~~~~~~i-~~~l~~l~~~~g~tvi~vtHd~~~~~~  211 (235)
T 3tif_A          153 RVAIARALANNPPIILADQ--------PTWALDSKTGEKI-MQLLKKLNEEDGKTVVVVTHDINVARF  211 (235)
T ss_dssp             HHHHHHHHTTCCSEEEEES--------TTTTSCHHHHHHH-HHHHHHHHHHHCCEEEEECSCHHHHTT
T ss_pred             HHHHHHHHHcCCCEEEEeC--------CcccCCHHHHHHH-HHHHHHHHHHcCCEEEEEcCCHHHHHh
Confidence            3333444566778999999        5455554443333 3445556554 8999999999986543

>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=82.13  E-value=2.2  Score=39.44  Aligned_cols=20  Identities=10%  Similarity=-0.167  Sum_probs=17.3

Q ss_pred             ccccCCCCCCCchhHHHHHH
Q psy13263        301 AGNIIPKAGVDKEYDEVMDE  320 (577)
Q Consensus       301 ~~I~gPN~gGKsvy~k~val  320 (577)
                      .+++||+.+|||.+..+++.
T Consensus        23 ~~i~G~~GsGKTtl~~~l~~   42 (220)
T 2cvh_A           23 TQVYGPYASGKTTLALQTGL   42 (220)
T ss_dssp             EEEECSTTSSHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHH
Confidence            45889999999999998875

>2w58_A DNAI, primosome component (helicase loader); ATP-binding, nucleotide-binding, hydrolase; HET: ADP; 2.50A {Geobacillus kaustophilus HTA426}

Probab=81.43  E-value=1.3  Score=40.76  Aligned_cols=47  Identities=11%  Similarity=-0.026  Sum_probs=29.2

Q ss_pred             eEEeecccCcccccccccCCCCcchh-hHHHHHHHHHHhcCCeEEEecch--HHHHHH
Q psy13263        373 RVATKKKNVENYVTPECRGTGTNDGC-VIARVTLEKFLQIGCLTVFATHY--HSVARR  427 (577)
Q Consensus       373 sLVLlDEtg~n~v~~LGRGTst~DG~-ALA~AIlE~L~~~~~~~lfaTHy--~eL~~l  427 (577)
                      .+++|||        +|.-....... .+...+++.....+..+|+||++  .+|...
T Consensus       117 ~~lilDe--------i~~~~~~~~~~~~ll~~~l~~~~~~~~~~i~tsn~~~~~l~~~  166 (202)
T 2w58_A          117 PVLMLDD--------LGAEAMSSWVRDDVFGPILQYRMFENLPTFFTSNFDMQQLAHH  166 (202)
T ss_dssp             SEEEEEE--------ECCC---CCGGGTTHHHHHHHHHHTTCCEEEEESSCHHHHHHH
T ss_pred             CEEEEcC--------CCCCcCCHHHHHHHHHHHHHHHHhCCCCEEEEcCCCHHHHHHH
Confidence            4899999        87643333223 36666777766667788888886  344443

>1jbk_A CLPB protein; beta barrel, chaperone; 1.80A {Escherichia coli} SCOP: c.37.1.20

Probab=80.01  E-value=1.8  Score=38.28  Aligned_cols=112  Identities=11%  Similarity=-0.050  Sum_probs=54.7

Q ss_pred             ccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceeccceeeecccc------cchhhhhchhhhHHhhhcCCCceE
Q psy13263        301 AGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQK------KQKKYVLEVPSKYASKAKSNHQRV  374 (577)
Q Consensus       301 ~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~d~if~~iG~------~qStF~~Em~e~~~il~~a~~~sL  374 (577)
                      .+++||...|||...+.++.-.  . .  ..++....  +...++...+.      ....+...+.+....+.......+
T Consensus        46 ~ll~G~~G~GKT~l~~~~~~~~--~-~--~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v  118 (195)
T 1jbk_A           46 PVLIGEPGVGKTAIVEGLAQRI--I-N--GEVPEGLK--GRRVLALDMGALVAGAKYRGEFEERLKGVLNDLAKQEGNVI  118 (195)
T ss_dssp             EEEECCTTSCHHHHHHHHHHHH--H-H--TCSCGGGT--TCEEEEECHHHHHTTTCSHHHHHHHHHHHHHHHHHSTTTEE
T ss_pred             eEEECCCCCCHHHHHHHHHHHH--H-h--CCCchhhc--CCcEEEeeHHHHhccCCccccHHHHHHHHHHHHhhcCCCeE
Confidence            4578999999999998776432  1 1  11111100  01122222211      001111222233222334566789


Q ss_pred             EeecccCcccccccccCCC---CcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        375 ATKKKNVENYVTPECRGTG---TNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       375 VLlDEtg~n~v~~LGRGTs---t~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      ++|||        +.+=+.   ......+. ..+..+... +..+|++|....+....
T Consensus       119 l~iDe--------~~~l~~~~~~~~~~~~~-~~l~~~~~~~~~~~i~~~~~~~~~~~~  167 (195)
T 1jbk_A          119 LFIDE--------LHTMVGAGKADGAMDAG-NMLKPALARGELHCVGATTLDEYRQYI  167 (195)
T ss_dssp             EEEET--------GGGGTT------CCCCH-HHHHHHHHTTSCCEEEEECHHHHHHHT
T ss_pred             EEEeC--------HHHHhccCcccchHHHH-HHHHHhhccCCeEEEEeCCHHHHHHHH
Confidence            99999        544321   11112223 334444444 78889999888766544

---

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	577
d1wb9a2	234	c.37.1.12 (A:567-800) DNA repair protein MutS, the	4e-16
d1wb9a4	115	d.75.2.1 (A:2-116) DNA repair protein MutS, domain	7e-15
d1ewqa2	224	c.37.1.12 (A:542-765) DNA repair protein MutS, the	3e-14
d1ewqa4	120	d.75.2.1 (A:1-120) DNA repair protein MutS, domain	9e-13
d1ewqa1	275	a.113.1.1 (A:267-541) DNA repair protein MutS, dom	2e-05

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]} Length = 234

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]

 Score = 75.6 bits (185), Expect = 4e-16
 Identities = 35/109 (32%), Positives = 54/109 (49%), Gaps = 6/109 (5%)

Query: 388 ECRGTGTNDGCVIARVTLEKFLQIG-CLTVFATHYHSVARRLREEPNVAFEYMSYIEDKR 446
             RGT T DG  +A    E        LT+FATHY  + +   +   VA  ++  +E   
Sbjct: 129 IGRGTSTYDGLSLAWACAENLANKIKALTLFATHYFELTQLPEKMEGVANVHLDALEH-- 186

Query: 447 NDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEA 495
               DTI F++ +  G   KS+G  VA LAG+P++V+K       ++E+
Sbjct: 187 ---GDTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELES 232

>d1wb9a4 d.75.2.1 (A:2-116) DNA repair protein MutS, domain I {Escherichia coli [TaxId: 562]} Length = 115

class: Alpha and beta proteins (a+b)
fold: MutS N-terminal domain-like
superfamily: DNA repair protein MutS, domain I
family: DNA repair protein MutS, domain I
domain: DNA repair protein MutS, domain I
species: Escherichia coli [TaxId: 562]

 Score = 68.8 bits (168), Expect = 7e-15
 Identities = 20/58 (34%), Positives = 31/58 (53%)

Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGE 260
               TP M Q+  +K+Q+ + +LF+++G FY LF+ DA   +  L  S  K     GE
Sbjct: 6   FDAHTPMMQQYLRLKAQHPEILLFYRMGDFYTLFYDDAKRASQLLDISLTKRGASAGE 63

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]} Length = 224

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]

 Score = 70.2 bits (171), Expect = 3e-14
 Identities = 33/108 (30%), Positives = 53/108 (49%), Gaps = 7/108 (6%)

Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
            RGT + DG  IA    E   +    T+FATHY  +       P +   +++  E+    
Sbjct: 124 GRGTSSLDGVAIATAVAEALHERRAYTLFATHYFELTAL--GLPRLKNLHVAAREE---- 177

Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR 496
               +VF ++++PG   KS+G  VA +AG+P++VV     +   M AR
Sbjct: 178 -AGGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVARARALLQAMAAR 224

>d1ewqa4 d.75.2.1 (A:1-120) DNA repair protein MutS, domain I {Thermus aquaticus [TaxId: 271]} Length = 120

class: Alpha and beta proteins (a+b)
fold: MutS N-terminal domain-like
superfamily: DNA repair protein MutS, domain I
family: DNA repair protein MutS, domain I
domain: DNA repair protein MutS, domain I
species: Thermus aquaticus [TaxId: 271]

 Score = 63.1 bits (153), Expect = 9e-13
 Identities = 16/52 (30%), Positives = 24/52 (46%)

Query: 205 KQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESG 256
              P + Q+  ++ Q  D +L F+VG FYE F  DA   A  L      ++ 
Sbjct: 12  PLPPLLQQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTS 63

>d1ewqa1 a.113.1.1 (A:267-541) DNA repair protein MutS, domain III {Thermus aquaticus [TaxId: 271]} Length = 275

class: All alpha proteins
fold: DNA repair protein MutS, domain III
superfamily: DNA repair protein MutS, domain III
family: DNA repair protein MutS, domain III
domain: DNA repair protein MutS, domain III
species: Thermus aquaticus [TaxId: 271]

 Score = 44.5 bits (104), Expect = 2e-05
 Identities = 23/117 (19%), Positives = 38/117 (32%), Gaps = 5/117 (4%)

Query: 276 SGCFPDMSELLKYFENAFDHKEASSA--GNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLR 333
               PD+S L +  E A           G +I + G D + D +    +           
Sbjct: 103 EVGLPDLSPLKEELEAALVEDPPLKVSEGGLI-REGYDPDLDALRAAHREGVAYFLELEE 161

Query: 334 TQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECR 390
            +    G   +          Y LEV   Y  +    ++ V T  K+ + Y  PE +
Sbjct: 162 RERERTGIPTLKVGYNAVFGYY-LEVTRPYYERVPKEYRPVQT-LKDRQRYTLPEMK 216

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	577
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	100.0
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	100.0
d1wb9a4	115	DNA repair protein MutS, domain I {Escherichia col	99.15
d1ewqa4	120	DNA repair protein MutS, domain I {Thermus aquatic	98.78
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	96.5
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	96.05
d1v43a3	239	Hypothetical protein PH0022, N-terminal domain {Py	95.24
d1l2ta_	230	MJ0796 {Archaeon Methanococcus jannaschii [TaxId:	94.99
d1ye8a1	178	Hypothetical kinase-like protein Aq_1292 {Aquifex	94.96
d1g2912	240	Maltose transport protein MalK, N-terminal domain	94.93
d3dhwc1	240	Methionine import ATP-binding protein MetN {Escher	94.84
d1vpla_	238	Putative ABC transporter TM0544 {Thermotoga mariti	94.84
d1ji0a_	240	Branched chain aminoacid ABC transporter {Thermoto	94.72
d1l7vc_	231	ABC transporter involved in vitamin B12 uptake, Bt	94.12
d2awna2	232	Maltose transport protein MalK, N-terminal domain	94.07
d1mv5a_	242	Multidrug resistance ABC transporter LmrA, C-termi	93.45
d2pmka1	241	Haemolysin B ATP-binding protein {Escherichia coli	93.33
d1sgwa_	200	Putative ABC transporter PF0895 {Pyrococcus furios	93.0
d2onka1	240	Molybdate/tungstate import ATP-binding protein Wtp	92.91
d1jj7a_	251	Peptide transporter Tap1, C-terminal ABC domain {H	92.12
d2hyda1	255	Putative multidrug export ATP-binding/permease pro	90.98
d3b60a1	253	Multidrug resistance ABC transporter MsbA, C-termi	90.47
d1r0wa_	281	Cystic fibrosis transmembrane conductance regulato	88.55

>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=100.00  E-value=1.6e-49  Score=393.74  Aligned_cols=211  Identities=23%  Similarity=0.338  Sum_probs=192.3

Q ss_pred             hhccCcccccCcccccc--ccccccccccc-ccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeee
Q psy13263        271 ESQTPSGCFPDMSELLK--YFENAFDHKEA-SSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYS  346 (577)
Q Consensus       271 ~i~i~~GrhPlLe~~l~--~~~n~F~~~~a-~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~  346 (577)
                      .+.+.+||||+++..+.  +++|++..+.. +..+||||||||||+|+|++++++ +|||+|+||||..+.+++ |+||+
T Consensus        11 ~l~i~~~rHPlle~~~~~~~VpNdi~l~~~~~~~iiTGpN~~GKSt~lk~i~l~~-~laq~G~~VpA~~a~~~~~d~I~~   89 (234)
T d1wb9a2          11 GIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIA-LMAYIGSYVPAQKVEIGPIDRIFT   89 (234)
T ss_dssp             CEEEEEECCTTHHHHCSSCCCCEEEEECSSSCEEEEECCTTSSHHHHHHHHHHHH-HHHTTTCCBSSSEEEECCCCEEEE
T ss_pred             cEEEEEeECCEEEcccCCCccceeEEECCCceEEEEeccCchhhHHHHHHHHHHH-HHHHcCCeEecCceecccchhhee
Confidence            47789999999986543  89999987643 456899999999999999999999 999999999999999999 99999


Q ss_pred             cccc------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEec
Q psy13263        347 EAQK------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFAT  419 (577)
Q Consensus       347 ~iG~------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaT  419 (577)
                      ++|.      ++|+|+.||.+++.|+.+++.+|||||||        |||||++.||.+|++|++++|..+ +|++||||
T Consensus        90 ~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~sLvliDE--------~~~gT~~~eg~~l~~a~l~~l~~~~~~~~i~tT  161 (234)
T d1wb9a2          90 RVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDE--------IGRGTSTYDGLSLAWACAENLANKIKALTLFAT  161 (234)
T ss_dssp             EEC-----------CHHHHHHHHHHHHHCCTTEEEEEES--------CCCCSSSSHHHHHHHHHHHHHHHTTCCEEEEEC
T ss_pred             EEccCcccccchhHHHHHHHHHHHHHHhcccccEEeecc--------cccCCChhhhhHHHHHhhhhhhccccceEEEec
Confidence            8876      45999999999999999999999999999        999999999999999999999877 78999999


Q ss_pred             chHHHHHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy13263        420 HYHSVARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEA  495 (577)
Q Consensus       420 Hy~eL~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~  495 (577)
                      ||++|..+....++|.++||.+...+     ++++|+|||.+|+++.|||++||+++|||++||+||++++++||+
T Consensus       162 H~~~l~~~~~~~~~v~~~~~~~~~~~-----~~i~f~YkL~~G~~~~s~ai~iA~~~Glp~~ii~~A~~i~~~lE~  232 (234)
T d1wb9a2         162 HYFELTQLPEKMEGVANVHLDALEHG-----DTIAFMHSVQDGAASKSYGLAVAALAGVPKEVIKRARQKLRELES  232 (234)
T ss_dssp             SCGGGGGHHHHSTTEEEEEEEEEEET-----TEEEEEEEEEESCCSSCCHHHHHHHTTCCHHHHHHHHHHHHHHHT
T ss_pred             chHHHhhhhhcccceEEEEEEEeecc-----CcceEEEEecCCCCCCcHHHHHHHHhCcCHHHHHHHHHHHHHHhc
Confidence            99999999999999999999988753     689999999999999999999999999999999999999999875

>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=100.00  E-value=2e-49  Score=390.79  Aligned_cols=207  Identities=21%  Similarity=0.303  Sum_probs=191.4

Q ss_pred             hccCcccccCcccccccccccccccccccccccCCCCCCCchhHHHHHHHHHHHHHhccccccccceecc-ceeeecccc
Q psy13263        272 SQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEAQK  350 (577)
Q Consensus       272 i~i~~GrhPlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~k~valI~~imaqig~~VpA~~a~l~~-d~if~~iG~  350 (577)
                      +.+.++|||+++....+++|++..+. +..+||||||||||+|+|++++++ +|||+|+||||..+++++ |.||+++|.
T Consensus        10 ~~i~~~rHPlle~~~~~VpNdi~~~~-~~~iiTGpN~~GKSt~lk~i~l~~-ilAq~G~~vpA~~~~i~~~d~I~~~~~~   87 (224)
T d1ewqa2          10 LQIRAGRHPVVERRTEFVPNDLEMAH-ELVLITGPNMAGKSTFLRQTALIA-LLAQVGSFVPAEEAHLPLFDGIYTRIGA   87 (224)
T ss_dssp             EEEEEECCTTGGGTSCCCCEEEEESS-CEEEEESCSSSSHHHHHHHHHHHH-HHHTTTCCBSSSEEEECCCSEEEEECCC
T ss_pred             EEEEeCcCCEEcCCCCeecceEEeCC-cEEEEECCCccccchhhhhhHHHH-HHHhccceeecCceEEeecceEEEEECC
Confidence            66789999999876678999998764 356899999999999999999999 999999999999999999 999999886


Q ss_pred             ------cchhhhhchhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHH
Q psy13263        351 ------KQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSV  424 (577)
Q Consensus       351 ------~qStF~~Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL  424 (577)
                            ++|+|+.||.++..|+.+++.+|||||||        |||||++.||.|||+|++|+|.+.+|+++|+|||++|
T Consensus        88 ~d~~~~~~StF~~el~~~~~il~~~~~~sLvliDE--------~~~gT~~~eg~ala~aile~L~~~~~~~i~tTH~~eL  159 (224)
T d1ewqa2          88 SDDLAGGKSTFMVEMEEVALILKEATENSLVLLDE--------VGRGTSSLDGVAIATAVAEALHERRAYTLFATHYFEL  159 (224)
T ss_dssp             ------CCSHHHHHHHHHHHHHHHCCTTEEEEEES--------TTTTSCHHHHHHHHHHHHHHHHHHTCEEEEECCCHHH
T ss_pred             CccccCCccHHHHhHHHHHHHhccCCCCcEEeecc--------cccCcchhhhcchHHHHHHHHhhcCcceEEeeechhh
Confidence                  44999999999999999999999999999        9999999999999999999999999999999999999


Q ss_pred             HHHhhcCCCcccccceeeeecCCCCcceEEEEEeecCCCCCCcHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Q psy13263        425 ARRLREEPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEA  495 (577)
Q Consensus       425 ~~l~~~~~~V~n~hm~~~~~~~~~~~~~l~flYkL~~G~~~~SyGi~vArlaGlP~~VI~rA~ei~~~le~  495 (577)
                      ..+.  .+.+.++||.+...     .+.++|+|||.+|+++.|||++||+++|||++||+||+++++.|+.
T Consensus       160 ~~l~--~~~~~~~~~~~~~~-----~~~~~f~Ykl~~G~~~~s~ai~iA~~~Glp~~II~rA~~i~~~l~~  223 (224)
T d1ewqa2         160 TALG--LPRLKNLHVAAREE-----AGGLVFYHQVLPGPASKSYGVEVAAMAGLPKEVVARARALLQAMAA  223 (224)
T ss_dssp             HTCC--CTTEEEEEEEEECC-----SSSCEEEEEEEESCCSSCCHHHHHHHTTCCHHHHHHHHHHHHHHTT
T ss_pred             hhhh--hcccceEEEEEEEe-----CCCeEEEEEEeeCCCCccHHHHHHHHhCcCHHHHHHHHHHHHHHhC
Confidence            8864  46789999998754     3689999999999999999999999999999999999999998864

>d1wb9a4 d.75.2.1 (A:2-116) DNA repair protein MutS, domain I {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: MutS N-terminal domain-like
superfamily: DNA repair protein MutS, domain I
family: DNA repair protein MutS, domain I
domain: DNA repair protein MutS, domain I
species: Escherichia coli [TaxId: 562]

Probab=99.15  E-value=1.2e-12  Score=115.20  Aligned_cols=57  Identities=33%  Similarity=0.579  Sum_probs=51.6

Q ss_pred             ccccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccccCccC
Q psy13263        203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTG  259 (577)
Q Consensus       203 l~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGsn~~G  259 (577)
                      +.++||+|+|||++|++|||+|||||+|+|||+|.+||++++..|||.++++....+
T Consensus         6 ~~~~TP~~~Qy~eiK~~~pd~ill~rvG~FYE~y~~DA~~~~~~L~i~lt~~~~~~~   62 (115)
T d1wb9a4           6 FDAHTPMMQQYLRLKAQHPEILLFYRMGDFYTLFYDDAKRASQLLDISLTKRGASAG   62 (115)
T ss_dssp             GGGSCHHHHHHHHHHHHSTTSEEEEEETTEEEEEHHHHHHHHHHHTCCCEEECCSSS
T ss_pred             cccCCHHHHHHHHHHHHCCCeEEEEEeCcchhhhhhhHHHHHhhheeEEeccCCCCC
Confidence            467899999999999999999999999999999999999999999999986544333

>d1ewqa4 d.75.2.1 (A:1-120) DNA repair protein MutS, domain I {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a+b)
fold: MutS N-terminal domain-like
superfamily: DNA repair protein MutS, domain I
family: DNA repair protein MutS, domain I
domain: DNA repair protein MutS, domain I
species: Thermus aquaticus [TaxId: 271]

Probab=98.78  E-value=1.8e-10  Score=101.63  Aligned_cols=56  Identities=29%  Similarity=0.353  Sum_probs=51.1

Q ss_pred             cccccCcchhhHHHHHhhCcCchhhhHhhhhHHHhhhhhhhhhhhhhhhhccccCc
Q psy13263        202 FLKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGC  257 (577)
Q Consensus       202 ~l~~~TPl~rQ~~~lKa~~~D~vLLfrvG~FYElf~~DA~i~a~eLdl~~mkGsn~  257 (577)
                      ...++|||++|||++|++|+|+|||+|+|+|||+|..||+.++..++|.++++.+.
T Consensus         9 ~~~~ltPm~~qY~~~K~~~~d~Ivl~qvG~FYE~Y~~Da~~~~~~l~i~l~~~~~~   64 (120)
T d1ewqa4           9 GPGPLPPLLQQYVELRDQYPDYLLLFQVGDFYECFGEDAERLARALGLVLTHKTSK   64 (120)
T ss_dssp             CCSCCCHHHHHHHHHHHHCTTSEEEEEETTEEEEEHHHHHHHHHHHTCCCEEEECS
T ss_pred             CCCCCCHHHHHHHHHHHHCCCeEEEEEeCCEEEEccchHHHHHHHhCceEeecccC
Confidence            34579999999999999999999999999999999999999999999999876543

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=96.50  E-value=0.0006  Score=64.84  Aligned_cols=98  Identities=19%  Similarity=0.181  Sum_probs=62.1

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhH
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYD  315 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~  315 (577)
                      ++|.....   ++.+++|+|++||||+||+++.++++++.|++ |--...+.++..-|.+-..     .---..|.+.|.
T Consensus        28 pNdi~~~~---~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~d~I~~~~~~-----~d~~~~~~StF~   99 (224)
T d1ewqa2          28 PNDLEMAH---ELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGA-----SDDLAGGKSTFM   99 (224)
T ss_dssp             CEEEEESS---CEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCSEEEEECCC-----------CCSHHH
T ss_pred             cceEEeCC---cEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeecceEEEEECC-----CccccCCccHHH
Confidence            45555443   36789999999999999999999999999987 4433344445444332110     011245689998


Q ss_pred             HHHHHHHHHHHHhccccccccceecc-ceeeecc
Q psy13263        316 EVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEA  348 (577)
Q Consensus       316 k~valI~~imaqig~~VpA~~a~l~~-d~if~~i  348 (577)
                      .-+..+..++.+.+      ...|=+ |-++.++
T Consensus       100 ~el~~~~~il~~~~------~~sLvliDE~~~gT  127 (224)
T d1ewqa2         100 VEMEEVALILKEAT------ENSLVLLDEVGRGT  127 (224)
T ss_dssp             HHHHHHHHHHHHCC------TTEEEEEESTTTTS
T ss_pred             HhHHHHHHHhccCC------CCcEEeecccccCc
Confidence            88888877776643      233433 6665443

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=96.05  E-value=0.0011  Score=63.29  Aligned_cols=100  Identities=13%  Similarity=0.040  Sum_probs=59.5

Q ss_pred             hhhhhhhhhhhhhhhccccCccCCcchhhhhhhhhhccCcccc-cCcccccccccccccccccccccccCCCCCCCchhH
Q psy13263        237 HMDAVIGADELACSYMKESGCTGESTLLTQLCNYESQTPSGCF-PDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYD  315 (577)
Q Consensus       237 ~~DA~i~a~eLdl~~mkGsn~~GKStlLk~i~~~~i~i~~Grh-PlLe~~l~~~~n~F~~~~a~~~~I~gPN~gGKsvy~  315 (577)
                      ++|..+... ..+.+++|+|++|||++||+++.++++++.|.+ |.-...+..+..-|.+-...     ---..|.+.|.
T Consensus        32 pNdi~l~~~-~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~~~~~d~I~~~~~~~-----d~~~~~~S~F~  105 (234)
T d1wb9a2          32 ANPLNLSPQ-RRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAA-----DDLASGRSTFM  105 (234)
T ss_dssp             CEEEEECSS-SCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC----------------CH
T ss_pred             ceeEEECCC-ceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCceecccchhheeEEccC-----cccccchhHHH
Confidence            456554432 367889999999999999999999999999987 44443444444333211100     00134578888


Q ss_pred             HHHHHHHHHHHHhccccccccceecc-ceeeecc
Q psy13263        316 EVMDEIKSIEKEIQTYLRTQCAHFGC-TVIYSEA  348 (577)
Q Consensus       316 k~valI~~imaqig~~VpA~~a~l~~-d~if~~i  348 (577)
                      .-+..+..++....      ...|=+ |-++.++
T Consensus       106 ~E~~~~~~il~~~~------~~sLvliDE~~~gT  133 (234)
T d1wb9a2         106 VEMTETANILHNAT------EYSLVLMDEIGRGT  133 (234)
T ss_dssp             HHHHHHHHHHHHCC------TTEEEEEESCCCCS
T ss_pred             HHHHHHHHHHHhcc------cccEEeecccccCC
Confidence            88887776666543      233444 7776543

>d1v43a3 c.37.1.12 (A:7-245) Hypothetical protein PH0022, N-terminal domain {Pyrococcus horikoshii [TaxId: 53953]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Hypothetical protein PH0022, N-terminal domain
species: Pyrococcus horikoshii [TaxId: 53953]

Probab=95.24  E-value=0.025  Score=54.02  Aligned_cols=53  Identities=17%  Similarity=0.120  Sum_probs=35.3

Q ss_pred             hcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        367 AKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       367 ~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      ..+....++|+||        --.|=++.-.. --+.++..|.+. +..+|++||+.+.+..+
T Consensus       150 aL~~~P~iLllDE--------Pts~LD~~~~~-~i~~ll~~l~~~~g~tii~vTHd~~~a~~~  203 (239)
T d1v43a3         150 AIVVEPDVLLMDE--------PLSNLDAKLRV-AMRAEIKKLQQKLKVTTIYVTHDQVEAMTM  203 (239)
T ss_dssp             HHTTCCSEEEEES--------TTTTSCHHHHH-HHHHHHHHHHHHHTCEEEEEESCHHHHHHH
T ss_pred             hhccCCCceeecC--------CcccCCHHHHH-HHHHHHHHHHHhcCCeEEEEeCCHHHHHHh
Confidence            3445788999999        43444433332 334555666555 99999999999887654

>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=94.99  E-value=0.026  Score=53.47  Aligned_cols=53  Identities=26%  Similarity=0.200  Sum_probs=35.3

Q ss_pred             hhhcCCCceEEeecccCcccccccccCCCCcch--hhHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        365 SKAKSNHQRVATKKKNVENYVTPECRGTGTNDG--CVIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       365 il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG--~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      .+..+...-|+|+||        -   |+.-|-  ....+.++..|.+. +..+|++||+.++++++
T Consensus       157 AraL~~~P~lLllDE--------P---Ts~LD~~~~~~i~~~l~~l~~~~g~tii~vTHd~~~a~~~  212 (230)
T d1l2ta_         157 ARALANNPPIILADQ--------P---TGALDSKTGEKIMQLLKKLNEEDGKTVVVVTHDINVARFG  212 (230)
T ss_dssp             HHHHTTCCSEEEEES--------T---TTTSCHHHHHHHHHHHHHHHHTTCCEEEEECSCHHHHTTS
T ss_pred             HhhhhcCCCEEEecC--------C---ccccCHHHHHHHHHHHHHHHHhhCCEEEEECCCHHHHHhC
Confidence            344556778999999        3   444442  23344555566554 89999999999877544

>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=94.96  E-value=0.018  Score=49.92  Aligned_cols=50  Identities=8%  Similarity=-0.086  Sum_probs=34.7

Q ss_pred             cCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        368 KSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       368 ~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      ......++++||        .|  ....++.....++.+.|...++.+|+++|...+..+
T Consensus        96 ~~~~~~vlllDE--------~~--~~~~~~~~~~~~l~~~l~~~~~~il~~~h~~~~~~~  145 (178)
T d1ye8a1          96 KKDRRKVIIIDE--------IG--KMELFSKKFRDLVRQIMHDPNVNVVATIPIRDVHPL  145 (178)
T ss_dssp             HHCTTCEEEECC--------CS--TTGGGCHHHHHHHHHHHTCTTSEEEEECCSSCCSHH
T ss_pred             HhcCCCceeecC--------CC--ccchhhHHHHHHHHHHhccCCCEEEEEEccHHHHHh
Confidence            345678999999        74  444456666667777766668889999998544333

>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=94.93  E-value=0.028  Score=53.62  Aligned_cols=52  Identities=15%  Similarity=0.158  Sum_probs=34.4

Q ss_pred             cCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        368 KSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       368 ~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      .+....++|+||        --.|=++.-...|. .++..|.+. +..+||+||+.+.+.-.
T Consensus       154 L~~~P~iLllDE--------Pt~~LD~~~~~~i~-~~l~~l~~~~g~tvi~vTHd~~~~~~~  206 (240)
T d1g2912         154 IVRKPQVFLMDE--------PLSNLDAKLRVRMR-AELKKLQRQLGVTTIYVTHDQVEAMTM  206 (240)
T ss_dssp             HHTCCSEEEEEC--------TTTTSCHHHHHHHH-HHHHHHHHHHTCEEEEEESCHHHHHHH
T ss_pred             HhcCCCEEEecC--------CCcccCHHHHHHHH-HHHHHHHhccCCEEEEEcCCHHHHHHh
Confidence            344778999999        55555554443333 344444444 99999999999877644

>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=94.84  E-value=0.025  Score=54.04  Aligned_cols=51  Identities=14%  Similarity=0.135  Sum_probs=34.3

Q ss_pred             CCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        369 SNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       369 a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      +...-|+|+||        --.|=++.-.. .-+.++..|.+. +..+|++||+.+++...
T Consensus       156 ~~~P~lLllDE--------Pt~~LD~~~~~-~i~~~l~~l~~~~g~tvi~vTHdl~~~~~~  207 (240)
T d3dhwc1         156 ASNPKVLLCDE--------ATSALDPATTR-SILELLKDINRRLGLTILLITHEMDVVKRI  207 (240)
T ss_dssp             HTCCSEEEEES--------GGGSSCHHHHH-HHHHHHHHHHHHHCCEEEEEBSCHHHHHHH
T ss_pred             ccCCCeEEecc--------ccccCCHHHhh-HHHHHHHHHHhccCCEEEEEcCCHHHHHHh
Confidence            34678999999        44455544332 334445555555 99999999999887754

>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=94.84  E-value=0.037  Score=52.48  Aligned_cols=53  Identities=19%  Similarity=0.137  Sum_probs=40.3

Q ss_pred             hcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh
Q psy13263        367 AKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL  428 (577)
Q Consensus       367 ~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~  428 (577)
                      ..+...-++|+||        --.|=++..-..| +.++..+.+.+..+|++||+.+....+
T Consensus       147 al~~~p~illLDE--------Pt~gLD~~~~~~i-~~~i~~~~~~g~tii~~tH~l~~~~~~  199 (238)
T d1vpla_         147 ALMVNPRLAILDE--------PTSGLDVLNAREV-RKILKQASQEGLTILVSSHNMLEVEFL  199 (238)
T ss_dssp             HHTTCCSEEEEES--------TTTTCCHHHHHHH-HHHHHHHHHTTCEEEEEECCHHHHTTT
T ss_pred             HHhcCCCEEEecC--------CCCCCCHHHHHHH-HHHHHHHHhcCCEEEEEeCCHHHHHHh
Confidence            3445678999999        8888888654444 777777777788999999998776643

>d1ji0a_ c.37.1.12 (A:) Branched chain aminoacid ABC transporter {Thermotoga maritima, TM1139 [TaxId: 2336]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: Branched chain aminoacid ABC transporter
species: Thermotoga maritima, TM1139 [TaxId: 2336]

Probab=94.72  E-value=0.027  Score=53.49  Aligned_cols=51  Identities=10%  Similarity=0.026  Sum_probs=38.2

Q ss_pred             cCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHH
Q psy13263        368 KSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARR  427 (577)
Q Consensus       368 ~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l  427 (577)
                      .+....|+|+||        --.|=++.....|.. +++.|.+.+..+|++||+.+...-
T Consensus       154 L~~~P~lLllDE--------Pt~gLD~~~~~~i~~-~i~~l~~~g~til~~tH~l~~~~~  204 (240)
T d1ji0a_         154 LMSRPKLLMMDE--------PSLGLAPILVSEVFE-VIQKINQEGTTILLVEQNALGALK  204 (240)
T ss_dssp             HTTCCSEEEEEC--------TTTTCCHHHHHHHHH-HHHHHHHTTCCEEEEESCHHHHHH
T ss_pred             HHhCCCEeeecC--------CCcCCCHHHHHHHHH-HHHHHHhCCCEEEEEeCCHHHHHH
Confidence            445778999999        777777776655554 556677779999999999766543

>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=94.12  E-value=0.077  Score=49.79  Aligned_cols=45  Identities=11%  Similarity=0.055  Sum_probs=33.8

Q ss_pred             eEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHH
Q psy13263        373 RVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVAR  426 (577)
Q Consensus       373 sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~  426 (577)
                      -|+|+||        --.|=++..- ..-+.++..|.+.+..+|++||+.+...
T Consensus       152 ~llllDE--------Pt~gLD~~~~-~~i~~~i~~l~~~g~tii~vtHdl~~~~  196 (231)
T d1l7vc_         152 QLLLLDE--------PMNSLDVAQQ-SALDKILSALCQQGLAIVMSSHDLNHTL  196 (231)
T ss_dssp             CEEEESS--------CSTTCCHHHH-HHHHHHHHHHHHTTCEEEECCCCHHHHH
T ss_pred             CEEEEcC--------CCCCCCHHHH-HHHHHHHHHHHhCCCEEEEEeCCHHHHH
Confidence            6999999        7777775443 4446677777777999999999976544

>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=94.07  E-value=0.044  Score=51.93  Aligned_cols=29  Identities=10%  Similarity=0.019  Sum_probs=22.6

Q ss_pred             cccccccccccccCCCCCCCchhHHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMDE  320 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~val  320 (577)
                      +|+..+....+++|||.+|||+.++.++-
T Consensus        20 sl~i~~Gei~~liGpsGsGKSTLl~~i~G   48 (232)
T d2awna2          20 NLDIHEGEFVVFVGPSGCGKSTLLRMIAG   48 (232)
T ss_dssp             EEEECTTCEEEEECCTTSSHHHHHHHHHT
T ss_pred             EEEEcCCCEEEEECCCCChHHHHHHHHhc
Confidence            45555555678999999999999998743

>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=93.45  E-value=0.048  Score=51.75  Aligned_cols=48  Identities=10%  Similarity=0.167  Sum_probs=30.7

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhcCCeEEEecchHHHHHHh
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRL  428 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~~~~~lfaTHy~eL~~l~  428 (577)
                      ...++|+||        --.+-++.-- ...+..++.|. +++.+|++||..++...+
T Consensus       157 ~p~ililDE--------pts~LD~~~~-~~i~~~l~~l~-~~~Tvi~itH~l~~~~~~  204 (242)
T d1mv5a_         157 NPKILMLDE--------ATASLDSESE-SMVQKALDSLM-KGRTTLVIAHRLSTIVDA  204 (242)
T ss_dssp             CCSEEEEEC--------CSCSSCSSSC-CHHHHHHHHHH-TTSEEEEECCSHHHHHHC
T ss_pred             CCCEEEecC--------CccccCHHHH-HHHHHHHHHHc-CCCEEEEEECCHHHHHhC
Confidence            567999999        4444443322 23334444554 388999999999877653

>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=93.33  E-value=0.062  Score=51.00  Aligned_cols=49  Identities=18%  Similarity=0.215  Sum_probs=32.0

Q ss_pred             hcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHH
Q psy13263        367 AKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARR  427 (577)
Q Consensus       367 ~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l  427 (577)
                      .......++|+||           -|+.-|... ...|++.|.+.  +..+|++||..++...
T Consensus       153 al~~~p~ililDE-----------pts~LD~~~-~~~i~~~l~~l~~~~Tvi~itH~l~~~~~  203 (241)
T d2pmka1         153 ALVNNPKILIFDE-----------ATSALDYES-EHVIMRNMHKICKGRTVIIIAHRLSTVKN  203 (241)
T ss_dssp             HHTTCCSEEEECC-----------CCSCCCHHH-HHHHHHHHHHHHTTSEEEEECSSGGGGTT
T ss_pred             hhhcccchhhhhC-----------CccccCHHH-HHHHHHHHHHHhCCCEEEEEECCHHHHHh
Confidence            3445678999999           466666532 33444444432  7899999999876543

>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=93.00  E-value=0.072  Score=48.89  Aligned_cols=28  Identities=4%  Similarity=-0.053  Sum_probs=22.2

Q ss_pred             cccccccccccccCCCCCCCchhHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMD  319 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~va  319 (577)
                      +|........+++|||.+|||+++++++
T Consensus        21 s~~i~~Gei~~l~G~NGsGKSTLl~~i~   48 (200)
T d1sgwa_          21 TMTIEKGNVVNFHGPNGIGKTTLLKTIS   48 (200)
T ss_dssp             EEEEETTCCEEEECCTTSSHHHHHHHHT
T ss_pred             EEEEcCCCEEEEECCCCChHHHHHHHHh
Confidence            4555555567899999999999999874

>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=92.91  E-value=0.17  Score=48.08  Aligned_cols=59  Identities=14%  Similarity=-0.028  Sum_probs=36.8

Q ss_pred             hhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc-CCeEEEecchHHHHHHh
Q psy13263        361 SKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       361 e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~-~~~~lfaTHy~eL~~l~  428 (577)
                      +++..+.......++|+||        --.|=++.-... -+.++..|.+. +..+|++||+.+.+...
T Consensus       134 RvaiAral~~~P~illlDE--------Pts~LD~~~~~~-i~~~i~~l~~~~g~tvi~vtHd~~~~~~~  193 (240)
T d2onka1         134 RVALARALVIQPRLLLLDE--------PLSAVDLKTKGV-LMEELRFVQREFDVPILHVTHDLIEAAML  193 (240)
T ss_dssp             HHHHHHHHTTCCSSBEEES--------TTSSCCHHHHHH-HHHHHHHHHHHHTCCEEEEESCHHHHHHH
T ss_pred             HHHHHHHHhccCCceEecC--------ccccCCHHHHHH-HHHHHHHHHHhcCCeEEEEeCCHHHHHHh
Confidence            3333455567778999999        444444443322 33344445444 89999999997766543

>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=92.12  E-value=0.072  Score=50.74  Aligned_cols=50  Identities=12%  Similarity=-0.012  Sum_probs=33.6

Q ss_pred             hcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHh---c-CCeEEEecchHHHHHHh
Q psy13263        367 AKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQ---I-GCLTVFATHYHSVARRL  428 (577)
Q Consensus       367 ~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~---~-~~~~lfaTHy~eL~~l~  428 (577)
                      .......++|+||           -|+.-|-. -...|.+.|.+   . +..+|++||..++...+
T Consensus       165 al~~~p~ililDE-----------pTs~LD~~-~~~~i~~~l~~l~~~~~~Tvi~itH~l~~~~~a  218 (251)
T d1jj7a_         165 ALIRKPCVLILDD-----------ATSALDAN-SQLQVEQLLYESPERYSRSVLLITQHLSLVEQA  218 (251)
T ss_dssp             HHTTCCSEEEEES-----------TTTTCCHH-HHHHHHHHHHTCGGGGGCEEEEECSCHHHHHTC
T ss_pred             ccccCCcEEEecC-----------cCcccChh-hHHHHHHHHHHHhhhcCCEEEEEeCCHHHHHhC
Confidence            3445678999999           57777743 23344555533   2 67899999998876643

>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=90.98  E-value=0.063  Score=51.40  Aligned_cols=45  Identities=13%  Similarity=0.063  Sum_probs=31.8

Q ss_pred             CceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc--CCeEEEecchHHHHHH
Q psy13263        371 HQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI--GCLTVFATHYHSVARR  427 (577)
Q Consensus       371 ~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~--~~~~lfaTHy~eL~~l  427 (577)
                      ...++|+||           -|+.-|-.. ...|.+.|...  +..+|++||..++...
T Consensus       172 ~p~ililDE-----------pts~LD~~t-~~~i~~~l~~l~~~~TvI~itH~~~~~~~  218 (255)
T d2hyda1         172 NPPILILDE-----------ATSALDLES-ESIIQEALDVLSKDRTTLIVAHRLSTITH  218 (255)
T ss_dssp             CCSEEEEES-----------TTTTCCHHH-HHHHHHHHHHHTTTSEEEEECSSGGGTTT
T ss_pred             CCCEEEEeC-----------ccccCCHHH-HHHHHHHHHHHhcCCEEEEEeCCHHHHHh
Confidence            567899999           677777653 55666666443  6788999999875543

>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=90.47  E-value=0.084  Score=50.34  Aligned_cols=28  Identities=0%  Similarity=-0.015  Sum_probs=22.0

Q ss_pred             cccccccccccccCCCCCCCchhHHHHH
Q psy13263        292 AFDHKEASSAGNIIPKAGVDKEYDEVMD  319 (577)
Q Consensus       292 ~F~~~~a~~~~I~gPN~gGKsvy~k~va  319 (577)
                      +|........+|+||+.+|||+..+.+.
T Consensus        35 sl~i~~Ge~iaivG~sGsGKSTLl~ll~   62 (253)
T d3b60a1          35 NLKIPAGKTVALVGRSGSGKSTIASLIT   62 (253)
T ss_dssp             EEEECTTCEEEEEECTTSSHHHHHHHHT
T ss_pred             EEEEcCCCEEEEECCCCChHHHHHHHHh
Confidence            4555555667899999999999988773

>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=88.55  E-value=0.074  Score=51.48  Aligned_cols=59  Identities=10%  Similarity=-0.010  Sum_probs=34.6

Q ss_pred             chhhhHHhhhcCCCceEEeecccCcccccccccCCCCcchhhHHHHHHHHHHhc---CCeEEEecchHHHHHHh
Q psy13263        358 EVPSKYASKAKSNHQRVATKKKNVENYVTPECRGTGTNDGCVIARVTLEKFLQI---GCLTVFATHYHSVARRL  428 (577)
Q Consensus       358 Em~e~~~il~~a~~~sLVLlDEtg~n~v~~LGRGTst~DG~ALA~AIlE~L~~~---~~~~lfaTHy~eL~~l~  428 (577)
                      +..+++-.+.......++|+||           -|+..|-.. ...|++.++..   +..+|++||..+....+
T Consensus       163 qkQRv~lARaL~~~p~illLDE-----------Pts~LD~~~-~~~i~~~~~~~~~~~~tvi~itH~~~~l~~a  224 (281)
T d1r0wa_         163 QRARISLARAVYKDADLYLLDS-----------PFGYLDVFT-EEQVFESCVCKLMANKTRILVTSKMEHLRKA  224 (281)
T ss_dssp             HHHHHHHHHHHHSCCSEEEEES-----------CCCSSCHHH-HHHHHHHCCCCCTTTSEEEEECSCHHHHHTC
T ss_pred             HHHHHHHHHHHHhCccchhhcC-----------ccccCCHHH-HHHHHHHHHHHhhCCCEEEEEechHHHHHhC
Confidence            3334433344455667999999           455555221 23344443332   67899999998766543