Psyllid ID: psy13254

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130--
Protein Sequence
NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR
Secondary Structure (PSIPRED)
ccccccccccccHHHHHHHHHHccccEEEEEEcccHHHHHHHHHcccccccccEEEEcEEEEEccccccccccccccccccccEEEEEEEcccEEEEEEEEcccccEEEEEEcccHHHHHHHHHHccccccc
Secondary Structure Prediction (SSPRO)
cccccccccHHHHHHHHHHHHHcccEEEEEEEcccHHHHHHHHHcccccccccEEEEEEEEEEccccEEccccccccccccccEEEEEEccccEEEEEEEEEccEEEEEEEEcccHHHHHHHHHHHcccccc
Coil and Loop (DISEMBL)
neyahsgfpeisygKFAQTLVEKGYKVARVEQTESAEQMDirtkrdkvpqkqrVVRREICKITCrgaqtfsimdvdanyvdnkfllgvtkegdrlgvcfidttigefhvgefeddkqFSRLSTlmshyppcr
Flexible Loop (DISEMBL)
neyahsgfpeisygkfAQTLVEKGYKVARveqtesaeqmdirtkrdkvpqkqrvvrreickitcrgaqtfsimdvdanyVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKqfsrlstlmshyppcr
Low Complexity Region (SEG)
NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR
Disordered region (IsUnstruct)
*********EISYGKFAQTLVEKGYKVA************************RVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFED******************
Disordered Region (DISOPRED)
NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTES******************VVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPC*
Disordered Region (DISEMBL)
NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQ*********************VVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR
Disordered Region (DISPRO)
*EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYP***
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR
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	132	2.2.26 [Sep-21-2011]
P54276	1358	DNA mismatch repair prote	yes	N/A	0.969	0.094	0.477	2e-33
P52701	1360	DNA mismatch repair prote	yes	N/A	0.969	0.094	0.485	4e-33
Q9VUM0	1190	Probable DNA mismatch rep	yes	N/A	0.977	0.108	0.563	1e-32
O04716	1324	DNA mismatch repair prote	yes	N/A	0.924	0.092	0.347	1e-15
O74502	1254	DNA mismatch repair prote	yes	N/A	0.931	0.098	0.330	3e-13
Q55GU9	1260	DNA mismatch repair prote	yes	N/A	0.909	0.095	0.304	5e-10
Q03834	1242	DNA mismatch repair prote	yes	N/A	0.901	0.095	0.309	3e-09
Q5M1Z0	852	DNA mismatch repair prote	yes	N/A	0.742	0.115	0.307	5e-08
Q03MY4	852	DNA mismatch repair prote	yes	N/A	0.742	0.115	0.307	5e-08
Q5M6I1	852	DNA mismatch repair prote	yes	N/A	0.742	0.115	0.307	5e-08

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

 Score =  140 bits (354), Expect = 2e-33,   Method: Compositional matrix adjust.
 Identities = 65/136 (47%), Positives = 99/136 (72%), Gaps = 8/136 (5%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
           +AHSGFPEI++G+F+ +LV+KGYKVARVEQTE+ E M+ R ++   V +  RVVRREIC+
Sbjct: 455 WAHSGFPEIAFGRFSDSLVQKGYKVARVEQTETPEMMEARCRKMAHVSKFDRVVRREICR 514

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDR-------LGVCFIDTTIGEFHVGEFED 114
           I  +G QT+S++D D +   +++LL + ++ +         GVCF+DT++G+F +G+F D
Sbjct: 515 IITKGTQTYSVLDGDPSENYSRYLLSLKEKEEETSGHTRVYGVCFVDTSLGKFFIGQFSD 574

Query: 115 DKQFSRLSTLMSHYPP 130
           D+  SR  TL++HYPP
Sbjct: 575 DRHCSRFRTLVAHYPP 590

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

 Score =  139 bits (351), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 66/136 (48%), Positives = 99/136 (72%), Gaps = 8/136 (5%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
           +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++   + +  RVVRREIC+
Sbjct: 456 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 515

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGDR------LGVCFIDTTIGEFHVGEFED 114
           I  +G QT+S+++ D +   +K+LL +  KE D        GVCF+DT++G+F +G+F D
Sbjct: 516 IITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSD 575

Query: 115 DKQFSRLSTLMSHYPP 130
           D+  SR  TL++HYPP
Sbjct: 576 DRHCSRFRTLVAHYPP 591

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

 Score =  138 bits (347), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 75/133 (56%), Positives = 93/133 (69%), Gaps = 4/133 (3%)

Query: 2   EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICK 61
           E+AHSGFPEIS+ K +  LV++G+KVARVEQTE+ + M  R KR K  +  +VV REIC+
Sbjct: 310 EFAHSGFPEISFDKMSTILVDRGFKVARVEQTETPDMMTERCKRIKATKFDKVVAREICQ 369

Query: 62  ITCRGAQTF-SIMDVDANYVDNKFLLGVTK-EG--DRLGVCFIDTTIGEFHVGEFEDDKQ 117
           IT RG Q F S   +  N+  N  L  V K EG   R GVCFIDT+IG+FH+GEFEDDK 
Sbjct: 370 ITNRGTQVFGSQCKIGPNHQPNYMLAIVEKDEGTCSRYGVCFIDTSIGDFHLGEFEDDKN 429

Query: 118 FSRLSTLMSHYPP 130
            SRL TL+SH+ P
Sbjct: 430 CSRLLTLVSHHMP 442

Involved in post-replicative DNA-mismatch repair.

Drosophila melanogaster (taxid: 7227)

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

 Score = 81.3 bits (199), Expect = 1e-15,   Method: Compositional matrix adjust.
 Identities = 49/141 (34%), Positives = 77/141 (54%), Gaps = 19/141 (13%)

Query: 2   EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICK 61
           E  H GFPE ++    + LV KGY+V  VEQTE+ +Q++ R  R +   K +VV+RE+C 
Sbjct: 428 EQPHCGFPEKNFSVNIEKLVRKGYRVLVVEQTETPDQLEQR--RKETGSKDKVVKREVCA 485

Query: 62  ITCRGAQT---FSIMDVDANYVDNKFLLGVTKEGDRL---------GVCFIDTTIGEFHV 109
           +  +G  T     + + DA+Y     L+ +T+ G+ L         GVC +D    +  +
Sbjct: 486 VVTKGTLTDGEMLLTNPDASY-----LMALTEGGESLTNPTAEHNFGVCLVDVATQKIIL 540

Query: 110 GEFEDDKQFSRLSTLMSHYPP 130
           G+F+DD+  S LS L+S   P
Sbjct: 541 GQFKDDQDCSALSCLLSEMRP 561

Involved in post-replicative DNA-mismatch repair.

Arabidopsis thaliana (taxid: 3702)

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

 Score = 73.6 bits (179), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 42/127 (33%), Positives = 69/127 (54%), Gaps = 4/127 (3%)

Query: 7   GFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRG 66
           G PE S+  +A   + KGY++ARV+Q E+A   +I+  R +  ++++VV+R + ++   G
Sbjct: 429 GIPEASFDYWASQFIAKGYRIARVDQLETALGKEIK-DRQRTQKEEKVVQRGLTQVLTSG 487

Query: 67  AQTFSIM---DVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLST 123
                 M   D+    +  K  L    E    G+CFIDT+ G FH+ EF DD   ++L T
Sbjct: 488 TLVDEAMLTSDLSTYCMAIKESLQSDNEEPSFGICFIDTSTGGFHMCEFTDDIHRTKLDT 547

Query: 124 LMSHYPP 130
           L++   P
Sbjct: 548 LLTQVRP 554

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|Q55GU9|MSH6_DICDI DNA mismatch repair protein Msh6 OS=Dictyostelium discoideum GN=msh6 PE=3 SV=1

 Score = 62.8 bits (151), Expect = 5e-10,   Method: Compositional matrix adjust.
 Identities = 39/128 (30%), Positives = 68/128 (53%), Gaps = 8/128 (6%)

Query: 7   GFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIR-TKRDKVPQKQRVVRREICKITCR 65
           G PE+S+  +A  L+  G+KVA+V+Q E++  M  R  ++    +K  +++RE+  I   
Sbjct: 415 GVPEMSFNHWASKLIHLGHKVAKVDQMETSIGMAKRQNEKGGRNKKDSIIQRELTSILTA 474

Query: 66  GAQTFSIMDVDANYVDNKFLLGVTKEGD---RLGVCFIDTTIGEFHVGEFEDDKQFSRLS 122
           G      M  D     + +L+ + KE +   + GVCF+D +IGEF++   +DD    +  
Sbjct: 475 GTLLDEQMITDQT---STYLMAI-KENEYDKQYGVCFVDVSIGEFYLCTIQDDDNRMQFE 530

Query: 123 TLMSHYPP 130
           TL+    P
Sbjct: 531 TLLLQMMP 538

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 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.

Dictyostelium discoideum (taxid: 44689)

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

 Score = 60.8 bits (146), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 44/142 (30%), Positives = 68/142 (47%), Gaps = 23/142 (16%)

Query: 6   SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
           +G PE+S+  +A   ++ GYKVA+V+Q ES    ++R         + +V+RE+  I   
Sbjct: 367 AGIPEMSFEYWAAQFIQMGYKVAKVDQRESMLAKEMREG------SKGIVKRELQCILTS 420

Query: 66  GAQT-------------FSIMDVDANYVDNKFLLGVT---KEGDRL-GVCFIDTTIGEFH 108
           G  T              +I +   N+ +   L   T   K   ++ G  FIDT  GE  
Sbjct: 421 GTLTDGDMLHSDLATFCLAIREEPGNFYNETQLDSSTIVQKLNTKIFGAAFIDTATGELQ 480

Query: 109 VGEFEDDKQFSRLSTLMSHYPP 130
           + EFEDD + ++L TLMS   P
Sbjct: 481 MLEFEDDSECTKLDTLMSQVRP 502

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|Q5M1Z0|MUTS_STRT1 DNA mismatch repair protein MutS OS=Streptococcus thermophilus (strain CNRZ 1066) GN=mutS PE=3 SV=1

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 52/114 (45%), Gaps = 16/114 (14%)

Query: 1   NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
           N    +G P  S   +   LVE GYKVA  EQ E  +Q               VV+RE+ 
Sbjct: 60  NPIPMAGVPYHSAQAYIDVLVEMGYKVAIAEQMEDPKQ------------AVGVVKREVV 107

Query: 61  KITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFED 114
           ++   G    +++D       N FL+ + K G R G+ ++D + GEF   E +D
Sbjct: 108 QVITPG----TVVDSSKPDSANNFLVAIDKVGSRFGLSYMDVSTGEFFATELDD 157

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.

Streptococcus thermophilus (strain CNRZ 1066) (taxid: 299768)

>sp|Q03MY4|MUTS_STRTD DNA mismatch repair protein MutS OS=Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9) GN=mutS PE=3 SV=1

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 52/114 (45%), Gaps = 16/114 (14%)

Query: 1   NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
           N    +G P  S   +   LVE GYKVA  EQ E  +Q               VV+RE+ 
Sbjct: 60  NPIPMAGVPYHSAQAYIDVLVEMGYKVAIAEQMEDPKQ------------AVGVVKREVV 107

Query: 61  KITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFED 114
           ++   G    +++D       N FL+ + K G R G+ ++D + GEF   E +D
Sbjct: 108 QVITPG----TVVDSSKPDSANNFLVAIDKVGSRFGLSYMDVSTGEFFATELDD 157

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.

Streptococcus thermophilus (strain ATCC BAA-491 / LMD-9) (taxid: 322159)

>sp|Q5M6I1|MUTS_STRT2 DNA mismatch repair protein MutS OS=Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) GN=mutS PE=3 SV=1

 Score = 56.6 bits (135), Expect = 5e-08,   Method: Compositional matrix adjust.
 Identities = 35/114 (30%), Positives = 52/114 (45%), Gaps = 16/114 (14%)

Query: 1   NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
           N    +G P  S   +   LVE GYKVA  EQ E  +Q               VV+RE+ 
Sbjct: 60  NPIPMAGVPYHSAQAYIDVLVEMGYKVAIAEQMEDPKQ------------AVGVVKREVV 107

Query: 61  KITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFED 114
           ++   G    +++D       N FL+ + K G R G+ ++D + GEF   E +D
Sbjct: 108 QVITPG----TVVDSSKPDSANNFLVAIDKVGSRFGLSYMDVSTGEFFATELDD 157

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.

Streptococcus thermophilus (strain ATCC BAA-250 / LMG 18311) (taxid: 264199)

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	132
383847693	1125	PREDICTED: probable DNA mismatch repair	0.977	0.114	0.507	1e-33
170285324	978	LOC100145639 protein [Xenopus (Silurana)	0.984	0.132	0.5	3e-33
15625580	1369	mismatch repair protein Msh6 [Danio reri	0.984	0.094	0.489	3e-33
301611818	1338	PREDICTED: DNA mismatch repair protein M	0.984	0.097	0.5	4e-33
242011381	1265	conserved hypothetical protein [Pediculu	0.992	0.103	0.510	4e-33
33504503	1369	DNA mismatch repair protein Msh6 [Danio	0.984	0.094	0.489	4e-33
449496462	1359	PREDICTED: DNA mismatch repair protein M	0.969	0.094	0.522	5e-33
336109982	283	mutS protein 6 [Sphenodon punctatus]	0.984	0.459	0.485	5e-33
348507016	1381	PREDICTED: DNA mismatch repair protein M	0.969	0.092	0.510	7e-33
322778889	838	hypothetical protein SINV_13902 [Solenop	0.977	0.153	0.485	1e-32

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

 Score =  147 bits (371), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 69/136 (50%), Positives = 100/136 (73%), Gaps = 7/136 (5%)

Query: 2   EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREIC 60
           E+AHSGFPEI YG+F+ +L+EKGYKVARVEQTE+ E M  R  +   P K  +VV+REIC
Sbjct: 265 EFAHSGFPEIGYGRFSASLIEKGYKVARVEQTENPEMMAQRCSKMHRPTKFDKVVKREIC 324

Query: 61  KITCRGAQTFSIMDVDANYVDNKFLLGVTKE------GDRLGVCFIDTTIGEFHVGEFED 114
           +I+ RG + ++ +DV+A+  ++ +LL + ++          GVCF+DTTIG+F++G+FED
Sbjct: 325 QISTRGTRAYTALDVEASTPNSNYLLSLIEKCQSGSNTSHYGVCFLDTTIGDFYLGQFED 384

Query: 115 DKQFSRLSTLMSHYPP 130
           D+  SRL TL++HYPP
Sbjct: 385 DRCSSRLLTLLAHYPP 400

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170285324|gb|AAI61405.1| LOC100145639 protein [Xenopus (Silurana) tropicalis]

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 69/138 (50%), Positives = 99/138 (71%), Gaps = 8/138 (5%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPEI++G+F+  LV+KGYKVARVEQTE+ E M++R K    P K  RVVRREIC+
Sbjct: 435 WAHSGFPEIAFGRFSDVLVQKGYKVARVEQTETPEMMEVRCKSMSHPSKFDRVVRREICR 494

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDR-------LGVCFIDTTIGEFHVGEFED 114
           I  +G QT+S++D + +   +K+LL   ++ D         GV F+DT++G+FHVG+FED
Sbjct: 495 IITKGTQTYSVLDGNPSESHSKYLLCFKEKMDDSSGQRRIYGVSFVDTSVGKFHVGQFED 554

Query: 115 DKQFSRLSTLMSHYPPCR 132
           D+  SR  TL++H+PP +
Sbjct: 555 DRHCSRFRTLVAHFPPIQ 572

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|15625580|gb|AAL04170.1|AF412834_1 mismatch repair protein Msh6 [Danio rerio]

 Score =  146 bits (368), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 68/139 (48%), Positives = 97/139 (69%), Gaps = 9/139 (6%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPEI +G+F+  LV+KGYKVARVEQTE+ + M+ R K+   P K  +VV+RE+C+
Sbjct: 455 WAHSGFPEIGFGRFSDVLVQKGYKVARVEQTETPDMMEARCKKLARPTKFDKVVKREVCR 514

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGV--------TKEGDRLGVCFIDTTIGEFHVGEFE 113
           I  RG QT+S++D   +   +K+LL +        T  G   GVCFIDT++G FH+G+F+
Sbjct: 515 IITRGTQTYSVLDGAPSETQSKYLLSIKEKSEEDSTGHGHIYGVCFIDTSVGRFHIGQFQ 574

Query: 114 DDKQFSRLSTLMSHYPPCR 132
           DD+  SRL TL++HY P +
Sbjct: 575 DDRHCSRLRTLVAHYSPAQ 593

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|301611818|ref|XP_002935421.1| PREDICTED: DNA mismatch repair protein Msh6 [Xenopus (Silurana) tropicalis]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 69/138 (50%), Positives = 99/138 (71%), Gaps = 8/138 (5%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPEI++G+F+  LV+KGYKVARVEQTE+ E M++R K    P K  RVVRREIC+
Sbjct: 435 WAHSGFPEIAFGRFSDVLVQKGYKVARVEQTETPEMMEVRCKSMSHPSKFDRVVRREICR 494

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDR-------LGVCFIDTTIGEFHVGEFED 114
           I  +G QT+S++D + +   +K+LL   ++ D         GV F+DT++G+FHVG+FED
Sbjct: 495 IITKGTQTYSVLDGNPSESHSKYLLCFKEKMDDSSGQRRIYGVSFVDTSVGKFHVGQFED 554

Query: 115 DKQFSRLSTLMSHYPPCR 132
           D+  SR  TL++H+PP +
Sbjct: 555 DRHCSRFRTLVAHFPPIQ 572

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|242011381|ref|XP_002426429.1| conserved hypothetical protein [Pediculus humanus corporis] gi|212510534|gb|EEB13691.1| conserved hypothetical protein [Pediculus humanus corporis]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 70/137 (51%), Positives = 96/137 (70%), Gaps = 6/137 (4%)

Query: 2   EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTK-RDKVPQKQRVVRREIC 60
           ++AHSGFPEISYG+F+  LV+KGYKVARVEQTE+ E M  R K + KV +  +VV REIC
Sbjct: 382 DFAHSGFPEISYGRFSTILVQKGYKVARVEQTETPEMMTERCKHQSKVTKFDKVVNREIC 441

Query: 61  KITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDR-----LGVCFIDTTIGEFHVGEFEDD 115
           ++T +G Q FS +D +A   +  +L  + ++ D       GVCFIDT+IG FH+G+F DD
Sbjct: 442 QVTTKGTQIFSFIDGEAKEYETNYLFALAEKTDNSGNIAFGVCFIDTSIGTFHLGQFNDD 501

Query: 116 KQFSRLSTLMSHYPPCR 132
           K  SRL  ++SH+PP +
Sbjct: 502 KFLSRLRIVLSHHPPVQ 518

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|33504503|ref|NP_878280.1| DNA mismatch repair protein Msh6 [Danio rerio] gi|27882481|gb|AAH44350.1| MutS homolog 6 (E. coli) [Danio rerio]

 Score =  145 bits (367), Expect = 4e-33,   Method: Compositional matrix adjust.
 Identities = 68/139 (48%), Positives = 96/139 (69%), Gaps = 9/139 (6%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPEI +G+F+  LV+KGYKVARVEQTE+   M+ R K+   P K  +VV+RE+C+
Sbjct: 455 WAHSGFPEIGFGRFSDVLVQKGYKVARVEQTETPNMMEARCKKLARPTKFDKVVKREVCR 514

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGV--------TKEGDRLGVCFIDTTIGEFHVGEFE 113
           I  RG QT+S++D   +   +K+LL +        T  G   GVCFIDT++G FH+G+F+
Sbjct: 515 IITRGTQTYSVLDGAPSETQSKYLLSIKEKSEEDSTGHGHIYGVCFIDTSVGRFHIGQFQ 574

Query: 114 DDKQFSRLSTLMSHYPPCR 132
           DD+  SRL TL++HY P +
Sbjct: 575 DDRHCSRLRTLVAHYSPAQ 593

Source: Danio rerio

Species: Danio rerio

Genus: Danio

Family: Cyprinidae

Order: Cypriniformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|449496462|ref|XP_002196049.2| PREDICTED: DNA mismatch repair protein Msh6 [Taeniopygia guttata]

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 70/134 (52%), Positives = 95/134 (70%), Gaps = 6/134 (4%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPE ++G+F+  LV+KGYKVARVEQTE+ E M+ R K      K  +VVRREIC+
Sbjct: 457 WAHSGFPETAFGRFSDVLVQKGYKVARVEQTETPEMMEARCKSKGQSTKFDKVVRREICR 516

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDRL-----GVCFIDTTIGEFHVGEFEDDK 116
           I  +G QT+S+MD D +   +KFLL V ++ D       GVCF+DT++G+FHVG+F DD+
Sbjct: 517 IITKGTQTYSVMDCDPSENHSKFLLSVKEKEDSAGTRVYGVCFVDTSMGKFHVGQFPDDR 576

Query: 117 QFSRLSTLMSHYPP 130
             SR  TL++HY P
Sbjct: 577 HCSRFRTLVAHYTP 590

Source: Taeniopygia guttata

Species: Taeniopygia guttata

Genus: Taeniopygia

Family: Estrildidae

Order: Passeriformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|336109982|gb|AEI16759.1| mutS protein 6 [Sphenodon punctatus]

 Score =  145 bits (366), Expect = 5e-33,   Method: Compositional matrix adjust.
 Identities = 67/138 (48%), Positives = 98/138 (71%), Gaps = 8/138 (5%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPEI++G+F+  LV+KG+KV RVEQTE+ E M+ R K    P K  RVVRRE+C+
Sbjct: 42  WAHSGFPEIAFGRFSDVLVQKGHKVVRVEQTETPEMMEARCKSTNHPTKYDRVVRREVCR 101

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDR-------LGVCFIDTTIGEFHVGEFED 114
           I  +G QT+S++D D +   NK+LL + ++ +         GVCF+DT++G+F+VG+F D
Sbjct: 102 IITKGTQTYSVLDGDPSETHNKYLLCIKEKAEDCAGHQRIYGVCFVDTSVGKFYVGQFTD 161

Query: 115 DKQFSRLSTLMSHYPPCR 132
           D+  SR  TL++HYPP +
Sbjct: 162 DRHSSRFRTLVAHYPPVQ 179

Source: Sphenodon punctatus

Species: Sphenodon punctatus

Genus: Sphenodon

Family: Sphenodontidae

Order: Sphenodontia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|348507016|ref|XP_003441053.1| PREDICTED: DNA mismatch repair protein Msh6 [Oreochromis niloticus]

 Score =  145 bits (365), Expect = 7e-33,   Method: Compositional matrix adjust.
 Identities = 70/137 (51%), Positives = 95/137 (69%), Gaps = 9/137 (6%)

Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
           +AHSGFPEI +G+F+  LV+KGYKVARVEQTE+ E M+ R K    P K  RVVRRE+C+
Sbjct: 469 WAHSGFPEIGFGRFSDVLVQKGYKVARVEQTETPEMMEARCKTMLKPTKFDRVVRREVCR 528

Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVTKEGDR--------LGVCFIDTTIGEFHVGEFE 113
           I  RG QT+S++D   +   +KFLL + ++ +          GVCF+DT++G FHVG+F 
Sbjct: 529 IITRGTQTYSVLDGAPSESQSKFLLSLKEKAEEEGSGRCRTYGVCFVDTSVGCFHVGQFS 588

Query: 114 DDKQFSRLSTLMSHYPP 130
           DD+  SRL TL++HY P
Sbjct: 589 DDRHCSRLRTLIAHYAP 605

Source: Oreochromis niloticus

Species: Oreochromis niloticus

Genus: Oreochromis

Family: Cichlidae

Order: Perciformes

Class: Actinopterygii

Phylum: Chordata

Superkingdom: Eukaryota

>gi|322778889|gb|EFZ09305.1| hypothetical protein SINV_13902 [Solenopsis invicta]

 Score =  144 bits (362), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 66/136 (48%), Positives = 100/136 (73%), Gaps = 7/136 (5%)

Query: 2   EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREIC 60
           E+AHSGFPEI YG+++ +L+E+GYKVAR+EQTE+ E M  R  +   P K  +VV+REIC
Sbjct: 236 EFAHSGFPEIGYGRYSASLIERGYKVARIEQTENPEMMATRCSKMSRPTKFDKVVKREIC 295

Query: 61  KITCRGAQTFSIMDVDANYVDNKFLLGVTKEGD------RLGVCFIDTTIGEFHVGEFED 114
           +++ RG + ++ +DV+A+  ++ +LL + ++ D        GVCFIDTTIGEF++G+F D
Sbjct: 296 QVSTRGTRVYTPLDVEASTPNSNYLLSLVEKCDVGSTASSYGVCFIDTTIGEFYLGQFVD 355

Query: 115 DKQFSRLSTLMSHYPP 130
           D+  SRL TL++H+PP
Sbjct: 356 DRCNSRLLTLLAHHPP 371

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

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	132
ZFIN|ZDB-GENE-020905-3	1369	msh6 "mutS homolog 6 (E. coli)	0.984	0.094	0.489	2.3e-31
UNIPROTKB|E1BYJ2	1341	MSH6 "Uncharacterized protein"	0.969	0.095	0.529	9.6e-31
UNIPROTKB|E1BWV7	1357	MSH6 "Uncharacterized protein"	0.969	0.094	0.529	9.7e-31
RGD|2322311	1361	Msh6 "mutS homolog 6 (E. coli)	0.969	0.094	0.507	1.3e-30
FB|FBgn0036486	1190	Msh6 "Msh6" [Drosophila melano	0.977	0.108	0.563	1.6e-30
UNIPROTKB|I3LUG7	1011	LOC100624532 "Uncharacterized	0.969	0.126	0.485	2.6e-30
UNIPROTKB|F5H2F9	1058	MSH6 "DNA mismatch repair prot	0.969	0.120	0.485	3.6e-30
UNIPROTKB|I3LHZ9	1334	LOC100739477 "Uncharacterized	0.969	0.095	0.485	4.1e-30
MGI|MGI:1343961	1358	Msh6 "mutS homolog 6 (E. coli)	0.969	0.094	0.5	4.3e-30
UNIPROTKB|B4DF41	1230	MSH6 "DNA mismatch repair prot	0.969	0.104	0.485	4.7e-30

ZFIN|ZDB-GENE-020905-3 msh6 "mutS homolog 6 (E. coli)" [Danio rerio (taxid:7955)]

 Score = 358 (131.1 bits), Expect = 2.3e-31, P = 2.3e-31
 Identities = 68/139 (48%), Positives = 97/139 (69%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
             +AHSGFPEI +G+F+  LV+KGYKVARVEQTE+ + M+ R K+   P K  +VV+RE+C+
Sbjct:   455 WAHSGFPEIGFGRFSDVLVQKGYKVARVEQTETPDMMEARCKKLARPTKFDKVVKREVCR 514

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGV--------TKEGDRLGVCFIDTTIGEFHVGEFE 113
             I  RG QT+S++D   +   +K+LL +        T  G   GVCFIDT++G FH+G+F+
Sbjct:   515 IITRGTQTYSVLDGAPSETQSKYLLSIKEKSEEDSTGHGHIYGVCFIDTSVGRFHIGQFQ 574

Query:   114 DDKQFSRLSTLMSHYPPCR 132
             DD+  SRL TL++HY P +
Sbjct:   575 DDRHCSRLRTLVAHYSPAQ 593

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

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

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

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

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

GO:0000228 "nuclear chromosome" evidence=IBA

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

GO:0009411 "response to UV" evidence=IBA

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

GO:0000710 "meiotic mismatch repair" evidence=IBA

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

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

GO:0032301 "MutSalpha complex" evidence=IBA

GO:0003684 "damaged DNA binding" evidence=IBA

GO:0006200 "ATP catabolic process" evidence=IBA

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

GO:0045190 "isotype switching" evidence=IBA

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

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

GO:0003677 "DNA binding" evidence=IEA

UNIPROTKB|E1BYJ2 MSH6 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 352 (129.0 bits), Expect = 9.6e-31, P = 9.6e-31
 Identities = 71/134 (52%), Positives = 96/134 (71%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
             +AHSGFPE ++G+F+  LV+KGYK+ARVEQTE+ E M+ R K      K  +VVRREIC+
Sbjct:   439 WAHSGFPETAFGRFSAILVQKGYKIARVEQTETPEMMEARCKATAHTTKFDKVVRREICR 498

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KE---GDRL-GVCFIDTTIGEFHVGEFEDDK 116
             I  +G QT+SI+D D     NK+LL V  KE   G R+ GVCF+DT++G+F+VG+F DD+
Sbjct:   499 IITKGTQTYSIIDCDPTENHNKYLLCVKEKEDSSGQRVYGVCFVDTSVGKFYVGQFSDDR 558

Query:   117 QFSRLSTLMSHYPP 130
               SR  TL++HY P
Sbjct:   559 HCSRFRTLVAHYTP 572

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 = 352 (129.0 bits), Expect = 9.7e-31, P = 9.7e-31
 Identities = 71/134 (52%), Positives = 96/134 (71%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQK-QRVVRREICK 61
             +AHSGFPE ++G+F+  LV+KGYK+ARVEQTE+ E M+ R K      K  +VVRREIC+
Sbjct:   455 WAHSGFPETAFGRFSAILVQKGYKIARVEQTETPEMMEARCKATAHTTKFDKVVRREICR 514

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KE---GDRL-GVCFIDTTIGEFHVGEFEDDK 116
             I  +G QT+SI+D D     NK+LL V  KE   G R+ GVCF+DT++G+F+VG+F DD+
Sbjct:   515 IITKGTQTYSIIDCDPTENHNKYLLCVKEKEDSSGQRVYGVCFVDTSVGKFYVGQFSDDR 574

Query:   117 QFSRLSTLMSHYPP 130
               SR  TL++HY P
Sbjct:   575 HCSRFRTLVAHYTP 588

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

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

 Score = 351 (128.6 bits), Expect = 1.3e-30, P = 1.3e-30
 Identities = 69/136 (50%), Positives = 100/136 (73%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
             +AHSGFPEI++G+F+ +LV+KGYKVARVEQTE+ E M+ R ++   V +  RVVRREIC+
Sbjct:   458 WAHSGFPEIAFGRFSDSLVQKGYKVARVEQTETPEMMEARCRKMAHVSKFDRVVRREICR 517

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGDR------LGVCFIDTTIGEFHVGEFED 114
             I  +G QT+S++D D +   +++LL +  KE D        GVCF+DT++G+F +G+F D
Sbjct:   518 IITKGTQTYSVLDGDPSENYSRYLLSLKEKEEDSSGHMRAYGVCFVDTSLGKFFLGQFSD 577

Query:   115 DKQFSRLSTLMSHYPP 130
             D+  SRL TL++HYPP
Sbjct:   578 DRHCSRLRTLVAHYPP 593

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

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

 Score = 349 (127.9 bits), Expect = 1.6e-30, P = 1.6e-30
 Identities = 75/133 (56%), Positives = 93/133 (69%)

Query:     2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICK 61
             E+AHSGFPEIS+ K +  LV++G+KVARVEQTE+ + M  R KR K  +  +VV REIC+
Sbjct:   310 EFAHSGFPEISFDKMSTILVDRGFKVARVEQTETPDMMTERCKRIKATKFDKVVAREICQ 369

Query:    62 ITCRGAQTF-SIMDVDANYVDNKFLLGVTK-EG--DRLGVCFIDTTIGEFHVGEFEDDKQ 117
             IT RG Q F S   +  N+  N  L  V K EG   R GVCFIDT+IG+FH+GEFEDDK 
Sbjct:   370 ITNRGTQVFGSQCKIGPNHQPNYMLAIVEKDEGTCSRYGVCFIDTSIGDFHLGEFEDDKN 429

Query:   118 FSRLSTLMSHYPP 130
              SRL TL+SH+ P
Sbjct:   430 CSRLLTLVSHHMP 442

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

UNIPROTKB|I3LUG7 LOC100624532 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 346 (126.9 bits), Expect = 2.6e-30, P = 2.6e-30
 Identities = 66/136 (48%), Positives = 101/136 (74%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
             +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++   + +  RVVRREIC+
Sbjct:   306 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 365

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGD-----RL-GVCFIDTTIGEFHVGEFED 114
             +  +G QT+S+++ D +   +K+LL +  KE D     R+ GVCF+DT++G+F +G+F D
Sbjct:   366 VITKGTQTYSVLEGDPSENYSKYLLSLKEKEDDSSGHTRVYGVCFVDTSLGKFFIGQFSD 425

Query:   115 DKQFSRLSTLMSHYPP 130
             D+  SR  TL++HYPP
Sbjct:   426 DRHCSRFRTLVAHYPP 441

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F5H2F9 MSH6 "DNA mismatch repair protein Msh6" [Homo sapiens (taxid:9606)]

 Score = 345 (126.5 bits), Expect = 3.6e-30, P = 3.6e-30
 Identities = 66/136 (48%), Positives = 99/136 (72%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
             +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++   + +  RVVRREIC+
Sbjct:   154 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 213

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGDR------LGVCFIDTTIGEFHVGEFED 114
             I  +G QT+S+++ D +   +K+LL +  KE D        GVCF+DT++G+F +G+F D
Sbjct:   214 IITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSD 273

Query:   115 DKQFSRLSTLMSHYPP 130
             D+  SR  TL++HYPP
Sbjct:   274 DRHCSRFRTLVAHYPP 289

GO:0005524 "ATP binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0003684 "damaged DNA 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:0032137 "guanine/thymine mispair binding" evidence=IEA

GO:0032301 "MutSalpha complex" evidence=IEA

GO:0045190 "isotype switching" evidence=IEA

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

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

 Score = 346 (126.9 bits), Expect = 4.1e-30, P = 4.1e-30
 Identities = 66/136 (48%), Positives = 101/136 (74%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
             +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++   + +  RVVRREIC+
Sbjct:   431 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 490

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGD-----RL-GVCFIDTTIGEFHVGEFED 114
             +  +G QT+S+++ D +   +K+LL +  KE D     R+ GVCF+DT++G+F +G+F D
Sbjct:   491 VITKGTQTYSVLEGDPSENYSKYLLSLKEKEDDSSGHTRVYGVCFVDTSLGKFFIGQFSD 550

Query:   115 DKQFSRLSTLMSHYPP 130
             D+  SR  TL++HYPP
Sbjct:   551 DRHCSRFRTLVAHYPP 566

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 346 (126.9 bits), Expect = 4.3e-30, P = 4.3e-30
 Identities = 68/136 (50%), Positives = 101/136 (74%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
             +AHSGFPEI++G+F+ +LV+KGYKVARVEQTE+ E M+ R ++   V +  RVVRREIC+
Sbjct:   455 WAHSGFPEIAFGRFSDSLVQKGYKVARVEQTETPEMMEARCRKMAHVSKFDRVVRREICR 514

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGD-----RL-GVCFIDTTIGEFHVGEFED 114
             I  +G QT+S++D D +   +++LL +  KE +     R+ GVCF+DT++G+F +G+F D
Sbjct:   515 IITKGTQTYSVLDGDPSENYSRYLLSLKEKEEETSGHTRVYGVCFVDTSLGKFFIGQFSD 574

Query:   115 DKQFSRLSTLMSHYPP 130
             D+  SR  TL++HYPP
Sbjct:   575 DRHCSRFRTLVAHYPP 590

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

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

 Score = 345 (126.5 bits), Expect = 4.7e-30, P = 4.7e-30
 Identities = 66/136 (48%), Positives = 99/136 (72%)

Query:     3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
             +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++   + +  RVVRREIC+
Sbjct:   326 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 385

Query:    62 ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGDR------LGVCFIDTTIGEFHVGEFED 114
             I  +G QT+S+++ D +   +K+LL +  KE D        GVCF+DT++G+F +G+F D
Sbjct:   386 IITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSD 445

Query:   115 DKQFSRLSTLMSHYPP 130
             D+  SR  TL++HYPP
Sbjct:   446 DRHCSRFRTLVAHYPP 461

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q9VUM0	MSH6_DROME	No assigned EC number	0.5639	0.9772	0.1084	yes	N/A

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	132
COG0249	843	COG0249, MutS, Mismatch repair ATPase (MutS family	6e-14
pfam01624	113	pfam01624, MutS_I, MutS domain I	6e-11
PRK05399	854	PRK05399, PRK05399, DNA mismatch repair protein Mu	1e-08
TIGR01070	840	TIGR01070, mutS1, DNA mismatch repair protein MutS	3e-07
pfam05188	133	pfam05188, MutS_II, MutS domain II	5e-07

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

 Score = 66.9 bits (164), Expect = 6e-14
 Identities = 35/121 (28%), Positives = 53/121 (43%), Gaps = 18/121 (14%)

Query: 6   SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
           +G P  +   +   L+E GYKVA  EQ E   +     +R         V R +   T  
Sbjct: 60  AGVPYHALDYYLAKLIELGYKVAICEQLEDPAEAKGVVERK--------VVRVVTPGT-- 109

Query: 66  GAQTFSIMDVDA-NYVDNKFLLGVTKEGD-RLGVCFIDTTIGEFHVGEFEDDKQFSRLST 123
                 + D    +  +N +L  +  + D ++G+ FID + GEF V EFE +K  S L  
Sbjct: 110 ------LTDEALLSDRENNYLAALAIDRDGKVGLAFIDLSTGEFFVSEFEREKLLSELKR 163

Query: 124 L 124
           L
Sbjct: 164 L 164

Length = 843

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

 Score = 55.3 bits (134), Expect = 6e-11
 Identities = 21/69 (30%), Positives = 32/69 (46%), Gaps = 12/69 (17%)

Query: 1   NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
                +G PE ++  + + LV KGYKVA  EQTE               + + VV+RE+ 
Sbjct: 54  KRIPMAGVPEHAFETYLRRLVNKGYKVAICEQTEDPA------------EAKGVVKREVV 101

Query: 61  KITCRGAQT 69
           ++   G  T
Sbjct: 102 RVITPGTLT 110

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|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional

 Score = 51.6 bits (125), Expect = 1e-08
 Identities = 29/105 (27%), Positives = 47/105 (44%), Gaps = 29/105 (27%)

Query: 19  TLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKI----TCRGAQTFSIMD 74
            LV+KGYKVA  EQ E         K          V+RE+ +I    T        + D
Sbjct: 80  KLVKKGYKVAICEQVEDPAT----AKG--------PVKREVVRIVTPGT--------VTD 119

Query: 75  ---VDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDK 116
              +D     N +L  + ++G   G+ ++D + GEF V E ++++
Sbjct: 120 EALLDEK--QNNYLAAIAQDGGGYGLAYLDLSTGEFRVTELDEEE 162

Length = 854

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

 Score = 47.8 bits (114), Expect = 3e-07
 Identities = 26/111 (23%), Positives = 45/111 (40%), Gaps = 19/111 (17%)

Query: 6   SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
           +G P  +   + + LV++G  VA  EQ E  +              +  V RE+ ++   
Sbjct: 60  AGIPYHAVEAYLEKLVKQGESVAICEQIEDPK------------TAKGPVEREVVQLITP 107

Query: 66  G--AQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFED 114
           G  +    + +   N      L  + +E +  G+  +D T GEF V E  D
Sbjct: 108 GTVSDEALLPERQDN-----LLAAIAQESNGFGLATLDLTTGEFKVTELAD 153

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

>gnl|CDD|218486 pfam05188, MutS_II, MutS domain II

 Score = 45.4 bits (108), Expect = 5e-07
 Identities = 17/42 (40%), Positives = 23/42 (54%), Gaps = 3/42 (7%)

Query: 90  KEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPC 131
            +G+R G+ F+D + GEF V EFED   F  L   +S   P 
Sbjct: 9   GDGNRYGLAFLDLSTGEFGVSEFED---FEELLAELSRLSPK 47

This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam00488, pfam01624, 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. This domain corresponds to domain II in Thermus aquaticus MutS as characterized in, and has similarity resembles RNAse-H-like domains (see pfam00075). Length = 133

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	132
TIGR01070	840	mutS1 DNA mismatch repair protein MutS.	100.0
PRK05399	854	DNA mismatch repair protein MutS; Provisional	100.0
COG0249	843	MutS Mismatch repair ATPase (MutS family) [DNA rep	99.97
KOG0217|consensus	1125		99.96
KOG0218|consensus	1070		99.84
PF01624	113	MutS_I: MutS domain I C-terminus.; InterPro: IPR00	99.82
PF05188	137	MutS_II: MutS domain II; InterPro: IPR007860 Misma	99.21
KOG0219|consensus	902		86.29
KOG0220|consensus	867		82.11

>TIGR01070 mutS1 DNA mismatch repair protein MutS

Probab=100.00  E-value=2.7e-35  Score=260.96  Aligned_cols=113  Identities=24%  Similarity=0.398  Sum_probs=101.3

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD   81 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~   81 (132)
                      ++||||||+|+++.|++|||++|||||||||+|+|+.+            .++|+|+|++||||||++++.+   +++.+
T Consensus        56 ~~pm~GvP~ha~~~yl~kLv~~G~kVai~eQ~e~~~~~------------kg~v~Rev~ri~TpGT~~~~~~---l~~~~  120 (840)
T TIGR01070        56 PIPMAGIPYHAVEAYLEKLVKQGESVAICEQIEDPKTA------------KGPVEREVVQLITPGTVSDEAL---LPERQ  120 (840)
T ss_pred             CCCcccCCHHHHHHHHHHHHHCCCEEEEEEecCCchhc------------CCceeeEEEEEECCCccccccc---ccCCC
Confidence            58999999999999999999999999999999998753            2799999999999999998643   67889


Q ss_pred             cceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         82 NKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        82 ~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      +|||+||......||+||+|+|||+|++++|.|+   +.|.++|.+++|+|
T Consensus       121 ~nyl~ai~~~~~~~gla~~D~sTG~~~~~~~~d~---~~l~~~l~~~~P~E  168 (840)
T TIGR01070       121 DNLLAAIAQESNGFGLATLDLTTGEFKVTELADK---ETLYAELQRLNPAE  168 (840)
T ss_pred             CceEEEEEeCCCeEEEEEEEccccEEEEEEecCH---HHHHHHHhccCCeE
Confidence            9999999743446999999999999999999875   36999999999986

>PRK05399 DNA mismatch repair protein MutS; Provisional

Probab=100.00  E-value=5.4e-34  Score=253.20  Aligned_cols=112  Identities=28%  Similarity=0.481  Sum_probs=101.3

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD   81 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~   81 (132)
                      ++||||||+|+++.|+++||++|||||||||+|+|+.+            .++|+|+|++||||||++++.+   +++..
T Consensus        63 ~~pm~GvP~h~~~~yl~kLv~~GyKVaI~EQ~e~~~~~------------k~~v~R~v~~i~TpGT~~~~~~---l~~~~  127 (854)
T PRK05399         63 PIPMAGVPYHAAEGYLAKLVKKGYKVAICEQVEDPATA------------KGPVKREVVRIVTPGTVTDEAL---LDEKQ  127 (854)
T ss_pred             CCCEecCcHHHHHHHHHHHHHCCCEEEEEEecCChhhc------------CCccceEEEEEECCCeeecccc---cCCCC
Confidence            57999999999999999999999999999999999754            1799999999999999998644   67889


Q ss_pred             cceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         82 NKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        82 ~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      ++||+||......||+||+|+|||+|++++|.    +++|+++|.+++|++
T Consensus       128 ~~yl~ai~~~~~~~Gia~~D~stg~~~~~~~~----~~~L~~~l~~~~P~E  174 (854)
T PRK05399        128 NNYLAAIAQDGGGYGLAYLDLSTGEFRVTELD----EEELLAELARLNPAE  174 (854)
T ss_pred             CcEEEEEEECCCeEEEEEEECCCCeEEEEEEc----HHHHHHHHHhcCCcE
Confidence            99999998655679999999999999999993    468999999999985

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

Probab=99.97  E-value=1e-30  Score=231.41  Aligned_cols=112  Identities=29%  Similarity=0.505  Sum_probs=101.5

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD   81 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~   81 (132)
                      ++||||||+|+++.|+.+||++|||||||||+|+|+.+            .++|+|+|+||+||||++|+.+   +.+..
T Consensus        56 ~~pm~gvP~h~~~~yl~~li~~g~kVAiceQ~e~~~~~------------k~~v~R~v~rv~TpGt~~d~~~---l~~~~  120 (843)
T COG0249          56 NIPMAGVPYHALDYYLAKLIELGYKVAICEQLEDPAEA------------KGVVERKVVRVVTPGTLTDEAL---LSDRE  120 (843)
T ss_pred             CCcCCCCccccHHHHHHHHHhCCCeEEEEEcccChhhh------------cCcceeEEEEEECCCeeecccc---ccccc
Confidence            37999999999999999999999999999999999875            2699999999999999999755   56779


Q ss_pred             cceEEEEEecCC-EEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         82 NKFLLGVTKEGD-RLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        82 ~~yllai~~~~~-~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      +|||+||..... .||+||+|+|||+|++.+|.    +.+|.+.|.|++|++
T Consensus       121 ~n~l~a~~~~~~~~~gla~~dlstGef~~~~~~----~~~l~~~l~r~~p~E  168 (843)
T COG0249         121 NNYLAALAIDRDGKVGLAFIDLSTGEFFVSEFE----REKLLSELKRLQPKE  168 (843)
T ss_pred             cceEEEEEecCCCEEEEEEEEcccCeEEEEEee----HHHHHHHHHhCCCcE
Confidence            999999985444 79999999999999999999    358999999999985

>KOG0217|consensus

Probab=99.96  E-value=6.9e-31  Score=231.20  Aligned_cols=126  Identities=43%  Similarity=0.738  Sum_probs=114.4

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCCC
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYVD   81 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~~   81 (132)
                      ++||+|||+++++.|+.+|+++|||||+|||+|++..+..|.++.+  +++++|+|||++|+|.||++|+.+   +.+..
T Consensus       297 N~~~~GfPE~sf~~~a~q~iq~GYkvarVEQtEt~l~~e~r~~~~~--~kdkvvrRev~~ilt~GT~td~~l---~~~~~  371 (1125)
T KOG0217|consen  297 NMPHSGFPEGSFDYWADQFIQKGYKVARVEQTETPLGKEIRERKTG--KKDKVVRREVCRILTNGTLTDIAL---LTSDL  371 (1125)
T ss_pred             ccccCCCCccchhhHHHHHHhccceeeeeccccChHHhhhhhcccc--cchhhHHHHHHHHhcCCcchhHHH---hccHH
Confidence            6899999999999999999999999999999999999999988776  457999999999999999998644   45566


Q ss_pred             cceEEEEEec-------CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         82 NKFLLGVTKE-------GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        82 ~~yllai~~~-------~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      +.|||||.+.       ...+|+|++|.+||+|++++|+||..++.|.|+|++++|+|
T Consensus       372 akylmai~e~~~~~~~~~~s~gvc~iDtstge~~~~eF~DDr~~s~L~tlLs~~rp~E  429 (1125)
T KOG0217|consen  372 AKYLMAIKESEESYSTGEVSFGVCFIDTSTGEINIGEFCDDRHCSKLDTLLSQVRPVE  429 (1125)
T ss_pred             HHHHHHHhhcCCCCCcCceeeeEEEEEcccceEEEEEeecchhhhHHHHHHHcccHHH
Confidence            8899999753       14799999999999999999999999999999999999975

>KOG0218|consensus

Probab=99.84  E-value=1.5e-21  Score=168.64  Aligned_cols=125  Identities=23%  Similarity=0.307  Sum_probs=107.0

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeecccc--c--ccc
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIM--D--VDA   77 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~--~--~~l   77 (132)
                      +|+.|.||.++++.|++|||.+|||||||+|+||++.+     +.+.+ +.+++.|.++++||+||+.++..  .  ...
T Consensus       212 nFmtaS~P~~Rl~vHleRLv~~g~KVaVVkQtETAAiK-----s~gas-RsslF~RklsavyTKaTl~eds~~~~r~e~~  285 (1070)
T KOG0218|consen  212 NFMTASFPDVRLNVHLERLVHHGLKVAVVKQTETAAIK-----SHGAS-RSSLFERKLSAVYTKATLGEDSTFVLRGERI  285 (1070)
T ss_pred             ceeeccCCcchhhHHHHHHHhcCceEEEEeehhhHHHH-----hcCCc-ccchHHHHHHHHhhhhhhccccccccchhhh
Confidence            58889999999999999999999999999999999875     33333 35899999999999999997642  0  012


Q ss_pred             CCCCcceEEEEEec---------CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         78 NYVDNKFLLGVTKE---------GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        78 ~~~~~~yllai~~~---------~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      -...++||+|+...         ...+|+.-+.+|||++-+++|.|+..|++|++.|.+++|.+
T Consensus       286 ~~~~ssfllcv~dn~~ksk~ksg~v~vgligVqlstGevVydeFqdnf~rseLqtrisslqP~E  349 (1070)
T KOG0218|consen  286 LGDTSSFLLCVRDNVHKSKEKSGVVKVGLIGVQLSTGEVVYDEFQDNFARSELQTRISSLQPIE  349 (1070)
T ss_pred             cCCcceEEEEEehhhhhhhhhcCceEEEEEEEecCCCcEehHhhhhhHHHHHHHHHHhccCcce
Confidence            34578999999751         25899999999999999999999999999999999999975

>PF01624 MutS_I: MutS domain I C-terminus

Probab=99.82  E-value=2.6e-20  Score=129.63  Aligned_cols=57  Identities=30%  Similarity=0.533  Sum_probs=47.2

Q ss_pred             eeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeecc
Q psy13254          3 YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFS   71 (132)
Q Consensus         3 ~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~   71 (132)
                      +||||||.++++.|+++|+++||+|+||||.|++...            .++++|+|++|+||||++|+
T Consensus        56 ~~~~gfp~~~l~~~l~~Ll~~G~~V~i~~q~~~~~~~------------~~~~~R~v~~i~TpGt~~~~  112 (113)
T PF01624_consen   56 VPMAGFPKSQLDKYLKKLLEAGYRVAIYEQVETPSET------------KGLIEREVTRIYTPGTLIDD  112 (113)
T ss_dssp             EEEEEEEGGGHHHHHHHHHHTT-EEEEEEE-S-HHHH------------SSS--EEEEEEEBTTS-TST
T ss_pred             ccEecccHHHHHHHHHHHHHcCCEEEEEEecCCcccc------------CCCccEEEEEEECcCeecCc
Confidence            7999999999999999999999999999999998764            26899999999999999874

; 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 ....

>PF05188 MutS_II: MutS domain II; InterPro: IPR007860 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome

Probab=99.21  E-value=3.1e-11  Score=84.59  Aligned_cols=47  Identities=34%  Similarity=0.693  Sum_probs=42.2

Q ss_pred             ceEEEEEe--cCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         83 KFLLGVTK--EGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        83 ~yllai~~--~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      |||+||..  ....+|+||+|+|||+|++++|.|   +++|.+.|.+++|+|
T Consensus         1 Nyl~aI~~~~~~~~~gla~~D~sTGe~~~~~~~d---~~~L~~~L~~~~P~E   49 (137)
T PF05188_consen    1 NYLAAIYEKNDEDSYGLAYIDLSTGEFYVTEFED---YSELKSELARLSPRE   49 (137)
T ss_dssp             -EEEEEEEETCSSEEEEEEEETTTTEEEEEEEEC---HHHHHHHHHHH-ESE
T ss_pred             CEEEEEEEecCCCEEEEEEEECCCCEEEEEEeCC---HHHHHHHHHhcCCeE
Confidence            79999998  667899999999999999999998   689999999999986

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 connector domain (domain 2) found in proteins of the MutS family. The structure of the MutS connector domain consists of a parallel beta-sheet surrounded by four alpha helices, which is similar to the structure of the Holliday junction resolvase ruvC.; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2O8F_A 3THW_A 3THX_A 2O8C_A 3THY_A 2O8E_A 2O8B_A 3THZ_A 2O8D_A 2WTU_A ....

>KOG0219|consensus

Probab=86.29  E-value=1.9  Score=39.47  Aligned_cols=105  Identities=21%  Similarity=0.259  Sum_probs=69.7

Q ss_pred             eeecCcCHHHHHHHHH-HcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccC--CCCc
Q psy13254          6 SGFPEISYGKFAQTLV-EKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDAN--YVDN   82 (132)
Q Consensus         6 aGfP~~~l~~y~~kLv-~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~--~~~~   82 (132)
                      +.+--..++..++.|+ ..+|+|-+.+=-|.               ..++++|     =+||-+.+-  ++.+.  .+.+
T Consensus        77 v~ls~~~~e~~vr~~l~~~~~~Ve~y~~~~~---------------~w~l~~~-----~sPGN~~~f--edll~~~~~v~  134 (902)
T KOG0219|consen   77 VSLSKGNFEKVVRELLLVLRYRVEVYSSNQG---------------DWKLTKR-----GSPGNLVQF--EDLLFSNNDVP  134 (902)
T ss_pred             EEecHHHHHHHHHHHHHHhccceEEeecCcc---------------ceeEEec-----CCCCcHHHH--HHHHcccccch
Confidence            3444456777777766 47999987762211               1234444     479987642  22121  1111


Q ss_pred             ---ceEEEEEe---cCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         83 ---KFLLGVTK---EGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        83 ---~yllai~~---~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                         -|+...+.   +..++|+|++|.+--.+++.+|.|+..++.|+..|.++.|.+
T Consensus       135 is~~~~~v~~~~~~~~~~vgv~~~d~~~~k~~~~ef~Dn~~~snle~~l~~lg~kE  190 (902)
T KOG0219|consen  135 ISIISLIVKHPGVDGQRRVGVAFVDTINVKIGLSEFVDDDSFSNLEALLIQLGPKE  190 (902)
T ss_pred             hhhhheeEEeeccCCCceeEEEEechhheeeehhhhcCcHHHHHHHHHHHhcCCeE
Confidence               13333332   246899999999999999999999999999999999999974

>KOG0220|consensus

Probab=82.11  E-value=2.1  Score=38.80  Aligned_cols=78  Identities=14%  Similarity=0.153  Sum_probs=50.9

Q ss_pred             CeEEeeeeEEEccceeeccccccccCCCCcceEEEEEec----CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccC
Q psy13254         53 RVVRREICKITCRGAQTFSIMDVDANYVDNKFLLGVTKE----GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHY  128 (132)
Q Consensus        53 ~~v~Rev~~I~TpGT~~~~~~~~~l~~~~~~yllai~~~----~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~  128 (132)
                      +..+|...+--+|.-.........+.+....-++|+.+.    ...+|+|.+|+-++|+++++|-|+..+.++.+-|.-+
T Consensus        74 ~~~qrs~~~~~a~sl~~sssn~s~~~~~~~~v~~~v~e~r~~~~~~Ig~~~~~~~~~q~~l~~f~dst~y~~v~~~l~i~  153 (867)
T KOG0220|consen   74 GNPQRSGYKSWAPSLGYSSSNSSAISAHSPSVIVAVVEGRGLARGEIGMASIDLKNPQIILSQFADSTTYAKVITKLKIL  153 (867)
T ss_pred             cccchhhhhhccchhhccccchhhhccCCCceEEEEEecCCcccceeEEEEecCCCCceehhhhhccchhHHHHhHhhcc
Confidence            456666665544433221111111233334456666653    3589999999999999999999998888888777666


Q ss_pred             CC
Q psy13254        129 PP  130 (132)
Q Consensus       129 ~P  130 (132)
                      .|
T Consensus       154 s~  155 (867)
T KOG0220|consen  154 SP  155 (867)
T ss_pred             Ch
Confidence            65

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	132
2o8b_B	1022	Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T M		4e-34
1nne_A	765	Crystal Structure Of The Muts-adpbef3-dna Complex L		6e-05
1ewq_A	765	Crystal Structure Taq Muts Complexed With A Heterod		6e-05
1fw6_A	768	Crystal Structure Of A Taq Muts-Dna-Adp Ternary Com		7e-05

>pdb|2O8B|B Chain B, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR Length = 1022

Iteration: 1
 Score =  139 bits (351), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 66/136 (48%), Positives = 99/136 (72%), Gaps = 8/136 (5%)
Query: 3   YAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKR-DKVPQKQRVVRREICK 61
           +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++   + +  RVVRREIC+
Sbjct: 118 WAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICR 177
Query: 62  ITCRGAQTFSIMDVDANYVDNKFLLGVT-KEGDR------LGVCFIDTTIGEFHVGEFED 114
           I  +G QT+S+++ D +   +K+LL +  KE D        GVCF+DT++G+F +G+F D
Sbjct: 178 IITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSD 237
Query: 115 DKQFSRLSTLMSHYPP 130
           D+  SR  TL++HYPP
Sbjct: 238 DRHCSRFRTLVAHYPP 253

>pdb|1NNE|A Chain A, Crystal Structure Of The Muts-adpbef3-dna Complex Length = 765

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 19/103 (18%)
Query: 6   SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
           +G P  ++  +A+ L++ G+++A  +Q E AE            + + +VRRE+ ++   
Sbjct: 71  AGIPLRAFEAYAERLLKMGFRLAVADQVEPAE------------EAEGLVRREVTQLLTP 118
Query: 66  GA-QTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEF 107
           G     S++  +ANY      L     GD  G+ F+D + GEF
Sbjct: 119 GTLLQESLLPREANY------LAAIATGDGWGLAFLDVSTGEF 155

>pdb|1EWQ|A Chain A, Crystal Structure Taq Muts Complexed With A Heteroduplex Dna At 2.2 A Resolution Length = 765

Iteration: 1
 Score = 42.7 bits (99), Expect = 6e-05,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 19/103 (18%)
Query: 6   SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
           +G P  ++  +A+ L++ G+++A  +Q E AE            + + +VRRE+ ++   
Sbjct: 71  AGIPLRAFEAYAERLLKXGFRLAVADQVEPAE------------EAEGLVRREVTQLLTP 118
Query: 66  GA-QTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEF 107
           G     S++  +ANY      L     GD  G+ F+D + GEF
Sbjct: 119 GTLLQESLLPREANY------LAAIATGDGWGLAFLDVSTGEF 155

>pdb|1FW6|A Chain A, Crystal Structure Of A Taq Muts-Dna-Adp Ternary Complex Length = 768

Iteration: 1
 Score = 42.4 bits (98), Expect = 7e-05,   Method: Composition-based stats.
 Identities = 28/103 (27%), Positives = 51/103 (49%), Gaps = 19/103 (18%)
Query: 6   SGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
           +G P  ++  +A+ L++ G+++A  +Q E AE            + + +VRRE+ ++   
Sbjct: 71  AGIPLRAFEAYAERLLKXGFRLAVADQVEPAE------------EAEGLVRREVTQLLTP 118
Query: 66  GA-QTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEF 107
           G     S++  +ANY      L     GD  G+ F+D + GEF
Sbjct: 119 GTLLQESLLPREANY------LAAIATGDGWGLAFLDVSTGEF 155

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	132
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	8e-34
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	3e-15
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	6e-10
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	5e-09
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	1e-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 =  122 bits (309), Expect = 8e-34
 Identities = 63/138 (45%), Positives = 92/138 (66%), Gaps = 8/138 (5%)

Query: 2   EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQ-RVVRREIC 60
            +AHSGFPEI++G+++ +LV+KGYKVARVEQTE+ E M+ R ++     K  RVVRREIC
Sbjct: 117 NWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREIC 176

Query: 61  KITCRGAQTFSIMDVD--ANY-----VDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFE 113
           +I  +G QT+S+++ D   NY        +     +      GVCF+DT++G+F +G+F 
Sbjct: 177 RIITKGTQTYSVLEGDPSENYSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFS 236

Query: 114 DDKQFSRLSTLMSHYPPC 131
           DD+  SR  TL++HYPP 
Sbjct: 237 DDRHCSRFRTLVAHYPPV 254

>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 = 3e-15
 Identities = 29/134 (21%), Positives = 43/134 (32%), Gaps = 28/134 (20%)

Query: 20  LVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKI----------------T 63
           LV KGYKV  V+QTE+A    I   R  +        R++  +                 
Sbjct: 81  LVAKGYKVGVVKQTETAALKAIGDNRSSL------FSRKLTALYTKSTLIGEDVNPLIKL 134

Query: 64  CRGAQTFSIMDVDAN------YVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQ 117
                   IM   +         + + +    K    +G+  +    GE     F+D   
Sbjct: 135 DDAVNVDEIMTDTSTSYLLCISENKENVRDKKKGNIFIGIVGVQPATGEVVFDSFQDSAS 194

Query: 118 FSRLSTLMSHYPPC 131
            S L T MS   P 
Sbjct: 195 RSELETRMSSLQPV 208

>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 = 54.6 bits (132), Expect = 6e-10
 Identities = 19/131 (14%), Positives = 45/131 (34%), Gaps = 20/131 (15%)

Query: 7   GFPEISYGKF-AQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR 65
              ++++  F    L+ + Y+V   +                  +  +     +      
Sbjct: 79  VLSKMNFESFVKDLLLVRQYRVEVYKNRAG-------------NKASKENDWYLAYKASP 125

Query: 66  G--AQTFSIMDVDANYVDN----KFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFS 119
           G  +Q   I+  + +   +       +       ++GV ++D+   +  + EF D+ QFS
Sbjct: 126 GNLSQFEDILFGNNDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFS 185

Query: 120 RLSTLMSHYPP 130
            L  L+    P
Sbjct: 186 NLEALLIQIGP 196

>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 = 52.1 bits (126), Expect = 5e-09
 Identities = 20/103 (19%), Positives = 35/103 (33%), Gaps = 21/103 (20%)

Query: 18  QTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDA 77
             LV +G  VA  EQ          +K          V R++ +I   G  +      D 
Sbjct: 81  AKLVNQGESVAICEQIGDPAT----SKG--------PVERKVVRIVTPGTIS------DE 122

Query: 78  NYVDNK---FLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQ 117
             +  +    L  + ++    G   +D + G F + E  D + 
Sbjct: 123 ALLQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEPADRET 165

>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 = 48.2 bits (116), Expect = 1e-07
 Identities = 22/100 (22%), Positives = 42/100 (42%), Gaps = 17/100 (17%)

Query: 18  QTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDA 77
           + L++ G+++A  +Q E AE+     +         +VRRE+ ++   G      +    
Sbjct: 83  ERLLKMGFRLAVADQVEPAEE----AE--------GLVRREVTQLLTPGTLLQESLLPRE 130

Query: 78  NYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQ 117
               N +L  +   GD  G+ F+D + GEF     +    
Sbjct: 131 A---N-YLAAIA-TGDGWGLAFLDVSTGEFKGTVLKSKSA 165

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	132
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	100.0
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	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
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	99.89

>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=1.4e-37  Score=276.36  Aligned_cols=126  Identities=22%  Similarity=0.316  Sum_probs=107.9

Q ss_pred             CCeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccc------
Q psy13254          1 NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMD------   74 (132)
Q Consensus         1 ~~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~------   74 (132)
                      +++||||||+|+++.|++|||++|||||||||+|+|+.++.+.      +++++|+|+||+||||||++|+.++      
T Consensus        62 ~~~pmaGvP~ha~~~yl~rLv~~G~kVai~eQ~E~p~~k~~~~------~k~~~v~R~v~rvvTpGT~~d~~~~~~~~~~  135 (918)
T 3thx_B           62 HNFMTASIPTHRLFVHVRRLVAKGYKVGVVKQTETAALKAIGD------NRSSLFSRKLTALYTKSTLIGEDVNPLIKLD  135 (918)
T ss_dssp             TTEEEEEEEGGGHHHHHHHHHHHTCCEEEEEECSCHHHHTTST------TCSSCCCEEEEEEECTTCCCSTTTCCEEEC-
T ss_pred             CCeeEEeccHhHHHHHHHHHHHcCCcEEEEeccCChhhhhccc------ccCCceeeeEEEEECCCcccccccccccccc
Confidence            4689999999999999999999999999999999998753221      1247999999999999999987541      


Q ss_pred             ------cccCCCCcceEEEEEecC----------CEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         75 ------VDANYVDNKFLLGVTKEG----------DRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        75 ------~~l~~~~~~yllai~~~~----------~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                            +.+++..+|||+||+...          ..||+||+|+|||+|.+++|.|+..+++|.++|.+++|+|
T Consensus       136 ~~~~~~~~l~~~~~nyL~ai~~~~~~~~~~~~~~~~~Gla~~D~sTGef~~~~f~d~~~~~~L~~~L~~~~P~E  209 (918)
T 3thx_B          136 DAVNVDEIMTDTSTSYLLCISENKENVRDKKKGNIFIGIVGVQPATGEVVFDSFQDSASRSELETRMSSLQPVE  209 (918)
T ss_dssp             -CEEECCCSCTTSCCCEEEEEEEC---------CEEEEEEEEETTTTEEEEEEEEECTTCHHHHHHHHHHCCSE
T ss_pred             cccccccccCCCCCcEEEEEEecccccccccccCceEEEEEEEccCCeEEEEEecCchhHHHHHHHHHhcCCeE
Confidence                  125678899999998531          1599999999999999999998877889999999999985

>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=2.4e-37  Score=277.29  Aligned_cols=131  Identities=49%  Similarity=0.970  Sum_probs=114.7

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCC-CCCCCCeEEeeeeEEEccceeeccccccccCCC
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDK-VPQKQRVVRREICKITCRGAQTFSIMDVDANYV   80 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~-~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~   80 (132)
                      ++||||||+|+++.|+++||++|||||||||+|+|+.++.|.|+.+ ++|++++|+|+||+||||||++|+.+++.++..
T Consensus       117 ~~pmaGvP~ha~~~yl~~Lv~~GykVai~eQ~e~p~~~~~r~~~~~~~~k~~~~v~Rev~rvvTpGT~~d~~~~~~l~~~  196 (1022)
T 2o8b_B          117 NWAHSGFPEIAFGRYSDSLVQKGYKVARVEQTETPEMMEARCRKMAHISKYDRVVRREICRIITKGTQTYSVLEGDPSEN  196 (1022)
T ss_dssp             SSCEEEEEGGGHHHHHHHHHHTTCCEEEEEECSCHHHHHHHHHTCSSCCSGGGSCCEEEEEEECTTSCCCCTTSCCCSCS
T ss_pred             CCCCCCCchhHHHHHHHHHHHCCCeEEEEeCCCCchhhhhhhhhcccccccCCceeeeEEEEECCCeeecccccccccCC
Confidence            4899999999999999999999999999999999998877777543 233458999999999999999987654456788


Q ss_pred             CcceEEEEEec-----C--CEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         81 DNKFLLGVTKE-----G--DRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        81 ~~~yllai~~~-----~--~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      .+|||+||+..     +  ..||+||+|+|||+|++++|.|+..+++|.++|.+++|+|
T Consensus       197 ~~n~l~ai~~~~~~~~~~~~~~Gla~~D~sTGe~~~~e~~d~~~~~~L~~~L~~~~P~E  255 (1022)
T 2o8b_B          197 YSKYLLSLKEKEEDSSGHTRAYGVCFVDTSLGKFFIGQFSDDRHCSRFRTLVAHYPPVQ  255 (1022)
T ss_dssp             SCCEEEEEEEEECSCC-CCEEEEEEEECTTTCCEEEEEEEECSSCHHHHHHHHHSCEEE
T ss_pred             CCcEEEEEEEccccccCCCcEEEEEEEECCCCEEEEEEecCchHHHHHHHHHHhcCCcE
Confidence            99999999852     1  2799999999999999999998877889999999999985

>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=9.7e-36  Score=261.65  Aligned_cols=114  Identities=18%  Similarity=0.311  Sum_probs=104.2

Q ss_pred             CCeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCC
Q psy13254          1 NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYV   80 (132)
Q Consensus         1 ~~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~   80 (132)
                      +++||||||+|+++.|+++||++|||||||||+|+|+..          |  ++|+|+|++|+||||++|+.+   ++..
T Consensus        64 ~~~pm~GvP~~~~~~yl~~Lv~~G~kVai~eQ~e~~~~~----------k--~~v~R~v~~v~TpGT~~~~~~---l~~~  128 (800)
T 1wb9_A           64 EPIPMAGIPYHAVENYLAKLVNQGESVAICEQIGDPATS----------K--GPVERKVVRIVTPGTISDEAL---LQER  128 (800)
T ss_dssp             CCEEEEEEEGGGHHHHHHHHHHTTCCEEEEEECSCGGGC----------S--SSCCEEEEEEECTTTCCCGGG---SCTT
T ss_pred             CcCCccCCCHHHHHHHHHHHHHCCCeEEEEEccCCcccc----------C--CcceEEEEEEecCCccccccc---ccCC
Confidence            369999999999999999999999999999999999753          1  799999999999999998644   6788


Q ss_pred             CcceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         81 DNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        81 ~~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      .+|||+||+.....||+||+|+|||+|++.+|.|   +++|.++|.+++|++
T Consensus       129 ~~n~l~ai~~~~~~~Gla~~D~stg~~~~~~~~d---~~~l~~~l~~~~P~E  177 (800)
T 1wb9_A          129 QDNLLAAIWQDSKGFGYATLDISSGRFRLSEPAD---RETMAAELQRTNPAE  177 (800)
T ss_dssp             SCCCEEEEEECSSCEEEEEECTTTCCEEEECCCS---HHHHHHHHHHHCCSE
T ss_pred             CCcEEEEEEEcCCEEEEEEEECCCCEEEEEEecC---HHHHHHHHHhcCCeE
Confidence            9999999987666899999999999999999987   579999999999985

>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=1.9e-35  Score=258.87  Aligned_cols=112  Identities=24%  Similarity=0.445  Sum_probs=101.9

Q ss_pred             CCeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeeccccccccCCC
Q psy13254          1 NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDANYV   80 (132)
Q Consensus         1 ~~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l~~~   80 (132)
                      +++||||||+|+++.|+++||++|||||||||+|+|+..          |  ++|+|+|++|+||||++|+.+   + ..
T Consensus        66 ~~~pm~GvP~~~~~~y~~~Lv~~G~kVai~eQ~e~~~~~----------k--g~v~R~v~~v~TpGT~~~~~~---l-~~  129 (765)
T 1ewq_A           66 FTTPMAGIPLRAFEAYAERLLKMGFRLAVADQVEPAEEA----------E--GLVRREVTQLLTPGTLLQESL---L-PR  129 (765)
T ss_dssp             CEEEEEEEEGGGHHHHHHHHHHTTCCEEEEEECSCGGGC----------S--SSCCEEEEEEECGGGCCCGGG---S-CS
T ss_pred             CCCceecCcHHHHHHHHHHHHHCCCEEEEEecCCCcccc----------c--CceeEEEEEEEcCceecchhh---c-CC
Confidence            368999999999999999999999999999999999764          1  799999999999999998643   6 78


Q ss_pred             CcceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         81 DNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        81 ~~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      .+|||+||+ .+..||+||+|+|||+|++.+|.|+   ++|.++|.+++|++
T Consensus       130 ~~n~l~ai~-~~~~~Gla~~D~stg~~~~~~~~d~---~~l~~~l~~~~P~E  177 (765)
T 1ewq_A          130 EANYLAAIA-TGDGWGLAFLDVSTGEFKGTVLKSK---SALYDELFRHRPAE  177 (765)
T ss_dssp             SCCCEEEEE-ESSSEEEEEEETTTTEEEEEEESSH---HHHHHHHHHHCCSE
T ss_pred             CCcEEEEEE-eCCEEEEEEEECCCCEEEEEEecCH---HHHHHHHHhcCCeE
Confidence            999999998 4557999999999999999999976   69999999999985

>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=99.89  E-value=1e-23  Score=187.85  Aligned_cols=116  Identities=16%  Similarity=0.280  Sum_probs=94.6

Q ss_pred             CeeeeeecCcCHHHHHHH-HHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccceeecccccccc---
Q psy13254          2 EYAHSGFPEISYGKFAQT-LVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGAQTFSIMDVDA---   77 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~k-Lv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT~~~~~~~~~l---   77 (132)
                      ++|++++|.+.++.|+++ |+.+||||+||||.++++.             .+.++|+|++++||||+++-  ++.+   
T Consensus        74 ~~~~v~i~~~~~~~~l~~~Ll~~g~rVei~~q~~~~~~-------------~~~~~r~l~~~~TPGnl~~~--ed~L~~~  138 (934)
T 3thx_A           74 NLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKA-------------SKENDWYLAYKASPGNLSQF--EDILFGN  138 (934)
T ss_dssp             CEEEEEEEHHHHHHHHHHHHHTTCCEEEEEEECC-----------------CCCCCEEEEEEEBTTBCTTC--HHHHC--
T ss_pred             CCCeeeeCHHHHHHHHHHHHHHcCCEEEEEecCCcccc-------------cCccceEEEEEECCCcHHHH--HHHhhcc
Confidence            589999999999999998 9999999999999776532             25689999999999999962  1112   


Q ss_pred             -CCCCcceEEEEEec----CCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         78 -NYVDNKFLLGVTKE----GDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        78 -~~~~~~yllai~~~----~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                       +-..++||+||...    ...||+||+|+|||+|.+.+|.|+..++.|.++|.+++|+|
T Consensus       139 ~d~~~~~~l~AIk~~~~~~~~~~Gla~~D~stge~~~~~~~d~~~~~~l~~~l~~~~P~E  198 (934)
T 3thx_A          139 NDMSASIGVVGVKMSAVDGQRQVGVGYVDSIQRKLGLCEFPDNDQFSNLEALLIQIGPKE  198 (934)
T ss_dssp             ------CCEEEEEECCSSSSCEEEEEEEETTTTEEEEEEEECCTTCHHHHHHHHHHCCSE
T ss_pred             ccccccceEEEEEEeecCCCcEEEEEEEECCCCeEEEEecCCchHHHHHHHHHHhCCCeE
Confidence             22347899999862    35899999999999999999999887889999999999985

---

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	132
d1wb9a4	115	d.75.2.1 (A:2-116) DNA repair protein MutS, domain	6e-05
d1ewqa4	120	d.75.2.1 (A:1-120) DNA repair protein MutS, domain	0.001
d1wb9a3	153	c.55.6.1 (A:117-269) DNA repair protein MutS, doma	0.003
d1ewqa3	146	c.55.6.1 (A:121-266) DNA repair protein MutS, doma	0.004

>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 = 37.6 bits (87), Expect = 6e-05
 Identities = 12/62 (19%), Positives = 20/62 (32%), Gaps = 12/62 (19%)

Query: 1   NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
                +G P  +   +   LV +G  VA  EQ                   +  V R++ 
Sbjct: 63  EPIPMAGIPYHAVENYLAKLVNQGESVAICEQIGDPA------------TSKGPVERKVV 110

Query: 61  KI 62
           +I
Sbjct: 111 RI 112

>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 = 34.2 bits (78), Expect = 0.001
 Identities = 14/62 (22%), Positives = 31/62 (50%), Gaps = 12/62 (19%)

Query: 1   NEYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREIC 60
                +G P  ++  +A+ L++ G+++A  +Q E AE            + + +VRRE+ 
Sbjct: 66  FTTPMAGIPLRAFEAYAERLLKMGFRLAVADQVEPAE------------EAEGLVRREVT 113

Query: 61  KI 62
           ++
Sbjct: 114 QL 115

>d1wb9a3 c.55.6.1 (A:117-269) DNA repair protein MutS, domain II {Escherichia coli [TaxId: 562]} Length = 153

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: DNA repair protein MutS, domain II
family: DNA repair protein MutS, domain II
domain: DNA repair protein MutS, domain II
species: Escherichia coli [TaxId: 562]

 Score = 33.6 bits (76), Expect = 0.003
 Identities = 7/37 (18%), Positives = 15/37 (40%)

Query: 82  NKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQF 118
           +  L  + ++    G   +D + G F + E  D +  
Sbjct: 14  DNLLAAIWQDSKGFGYATLDISSGRFRLSEPADRETM 50

>d1ewqa3 c.55.6.1 (A:121-266) DNA repair protein MutS, domain II {Thermus aquaticus [TaxId: 271]} Length = 146

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: DNA repair protein MutS, domain II
family: DNA repair protein MutS, domain II
domain: DNA repair protein MutS, domain II
species: Thermus aquaticus [TaxId: 271]

 Score = 33.1 bits (75), Expect = 0.004
 Identities = 9/38 (23%), Positives = 16/38 (42%), Gaps = 1/38 (2%)

Query: 81  DNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQF 118
           +  +L  +   GD  G+ F+D + GEF     +     
Sbjct: 10  EANYLAAIA-TGDGWGLAFLDVSTGEFKGTVLKSKSAL 46

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	132
d1ewqa4	120	DNA repair protein MutS, domain I {Thermus aquatic	99.85
d1wb9a4	115	DNA repair protein MutS, domain I {Escherichia col	99.84
d1wb9a3	153	DNA repair protein MutS, domain II {Escherichia co	99.53
d1ewqa3	146	DNA repair protein MutS, domain II {Thermus aquati	99.22

>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=99.85  E-value=2.2e-22  Score=139.31  Aligned_cols=54  Identities=28%  Similarity=0.563  Sum_probs=49.7

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEccce
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCRGA   67 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~TpGT   67 (132)
                      +.||||||+++++.|+++|+++||+||||||+|++...            .++++|+|++||||||
T Consensus        67 ~~~maGfP~~~l~~yl~~L~~~GytV~v~eQ~e~~~~~------------~~~~~R~vt~I~SPGT  120 (120)
T d1ewqa4          67 TTPMAGIPLRAFEAYAERLLKMGFRLAVADQVEPAEEA------------EGLVRREVTQLLTPGT  120 (120)
T ss_dssp             EEEEEEEEGGGHHHHHHHHHHTTCCEEEEEECSCGGGC------------SSSCCEEEEEEECGGG
T ss_pred             CCccccCCHhHHHHHHHHHHHCCceEEEEEEccccccc------------CCCceEeEEEEECCCC
Confidence            57999999999999999999999999999999987543            2689999999999998

>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=99.84  E-value=1.3e-21  Score=134.51  Aligned_cols=52  Identities=23%  Similarity=0.330  Sum_probs=47.9

Q ss_pred             CeeeeeecCcCHHHHHHHHHHcCCeEEEEeeccChhhhhhhhccCCCCCCCCeEEeeeeEEEcc
Q psy13254          2 EYAHSGFPEISYGKFAQTLVEKGYKVARVEQTESAEQMDIRTKRDKVPQKQRVVRREICKITCR   65 (132)
Q Consensus         2 ~~~maGfP~~~l~~y~~kLv~~G~kVaiveQ~e~~~~~~~r~k~~~~~~~~~~v~Rev~~I~Tp   65 (132)
                      ++||||||+|+++.|+++|+++|||||||||+|++...            .++++|+|++||||
T Consensus        64 ~v~m~GfP~~~l~~yl~~Lv~~G~kVai~eQ~~~~~~~------------~~~~~R~VtrIiTP  115 (115)
T d1wb9a4          64 PIPMAGIPYHAVENYLAKLVNQGESVAICEQIGDPATS------------KGPVERKVVRIVTP  115 (115)
T ss_dssp             CEEEEEEEGGGHHHHHHHHHHTTCCEEEEEECSCGGGC------------SSSCCEEEEEEECT
T ss_pred             ceEEEecCHHHHHHHHHHHHHCCceEEEEEeccCcccc------------CCcceEeEEEEECc
Confidence            58999999999999999999999999999999987543            37899999999998

>d1wb9a3 c.55.6.1 (A:117-269) DNA repair protein MutS, domain II {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: DNA repair protein MutS, domain II
family: DNA repair protein MutS, domain II
domain: DNA repair protein MutS, domain II
species: Escherichia coli [TaxId: 562]

Probab=99.53  E-value=3.2e-15  Score=105.65  Aligned_cols=61  Identities=15%  Similarity=0.311  Sum_probs=54.8

Q ss_pred             ceeeccccccccCCCCcceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         66 GAQTFSIMDVDANYVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        66 GT~~~~~~~~~l~~~~~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      ||++|+.+   +++..||||+||+..+..||+||+|+|||+|++.++.+.   +.|.++|.|++|+|
T Consensus         1 GT~~d~~~---L~~~~nnyL~ai~~~~~~~gla~~DiSTG~f~~~~~~~~---~~l~~~l~r~~P~E   61 (153)
T d1wb9a3           1 GTISDEAL---LQERQDNLLAAIWQDSKGFGYATLDISSGRFRLSEPADR---ETMAAELQRTNPAE   61 (153)
T ss_dssp             TTCCCGGG---SCTTSCCCEEEEEECSSCEEEEEECTTTCCEEEECCCSH---HHHHHHHHHHCCSE
T ss_pred             Cccccccc---cCCCCccEEEEEEECCCeEEEEEEEccccEEEEEEcCCH---HHHHHHHHhcCCcc
Confidence            89998644   799999999999987778999999999999999988765   58999999999986

>d1ewqa3 c.55.6.1 (A:121-266) DNA repair protein MutS, domain II {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: Ribonuclease H-like motif
superfamily: DNA repair protein MutS, domain II
family: DNA repair protein MutS, domain II
domain: DNA repair protein MutS, domain II
species: Thermus aquaticus [TaxId: 271]

Probab=99.22  E-value=9e-12  Score=86.85  Aligned_cols=50  Identities=20%  Similarity=0.367  Sum_probs=44.6

Q ss_pred             CCCcceEEEEEecCCEEEEEEEECCcceEEEEEEeChhhHHHHHHhhccCCCCC
Q psy13254         79 YVDNKFLLGVTKEGDRLGVCFIDTTIGEFHVGEFEDDKQFSRLSTLMSHYPPCR  132 (132)
Q Consensus        79 ~~~~~yllai~~~~~~~Gi~~~D~sTg~~~~~~~~d~~~~~~L~t~l~~~~P~~  132 (132)
                      +.+||||+||+..+ .||+||+|+|||+|++.++.+.   ++|.+.|.|++|+|
T Consensus         8 ~~~nNyLaai~~~~-~~giA~~DiSTGef~~~~~~~~---~~l~~~l~r~~P~E   57 (146)
T d1ewqa3           8 PREANYLAAIATGD-GWGLAFLDVSTGEFKGTVLKSK---SALYDELFRHRPAE   57 (146)
T ss_dssp             CSSCCCEEEEEESS-SEEEEEEETTTTEEEEEEESSH---HHHHHHHHHHCCSE
T ss_pred             cCcCcEEEEEEECC-CeEEEEEEccCCeEEEEEecch---hhHHHHHHcCCCcE
Confidence            57899999998755 5999999999999999999875   48999999999986