Psyllid ID: psy13255

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150------
Protein Sequence
ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL
Secondary Structure (PSIPRED)
cccHHHHHHccccccccccccccHHHHHHHHHccHHHHHHHcccccccccHHHHHHccHHHHHccccccHHHHHHHHHccccHHHHHHHHHHHHHHcccccccccccccccHHHHHHcccccccccccccHHHHHHHHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHHHHHHHHHHcccccccHHHHHHHHHHHHHHHHHHHHHccccccccHHHHHccHHHHHHHHcccccccccccccccccHHHHHHHHHHHHHHHcccccHHccEcccHHHEEEEccccHHcccccccHHHHHHHHHHHHHHHccccEEEEccc
Coil and Loop (DISEMBL)
ILDSTALanlhvltnsdnttegtLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLermlpsstflsfqgcrvpadsltltpvdRIFTrmgakdnlsgaQSTYLAELTESETIMRHASKYSLALVDEL
Flexible Loop (DISEMBL)
ildstalaNLHVltnsdnttegtlIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSStflsfqgcrvpadsltlTPVDRIFTRmgakdnlsgaQSTYLAELTESETIMRHASKYSLALVDEL
Low Complexity Region (SEG)
ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL
Disordered region (IsUnstruct)
********NLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHIT***************MLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKD*******TYLA***********************
Disordered Region (DISOPRED)
ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL
Disordered Region (DISEMBL)
ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL
Disordered Region (DISPRO)
ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL
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	156	2.2.26 [Sep-21-2011]
Q55GU9	1260	DNA mismatch repair prote	yes	N/A	0.564	0.069	0.460	8e-16
P54276	1358	DNA mismatch repair prote	yes	N/A	0.371	0.042	0.559	2e-14
A6W1Q6	883	DNA mismatch repair prote	yes	N/A	0.410	0.072	0.523	4e-14
Q7NRW7	873	DNA mismatch repair prote	yes	N/A	0.397	0.071	0.507	7e-14
Q31F87	871	DNA mismatch repair prote	yes	N/A	0.403	0.072	0.5	2e-13
Q5X4B2	846	DNA mismatch repair prote	yes	N/A	0.384	0.070	0.523	2e-13
A4G717	893	DNA mismatch repair prote	yes	N/A	0.365	0.063	0.507	3e-13
Q47DJ8	860	DNA mismatch repair prote	yes	N/A	0.410	0.074	0.492	3e-13
Q8Y093	882	DNA mismatch repair prote	yes	N/A	0.403	0.071	0.476	3e-13
P52701	1360	DNA mismatch repair prote	yes	N/A	0.371	0.042	0.525	4e-13

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

 Score = 82.8 bits (203), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 41/89 (46%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
           ILD   L NL +  NS D +TEGTL + +D C T+FGKRM R  + +PL N +AI  RQ 
Sbjct: 645 ILDGQCLVNLEIFNNSTDGSTEGTLFKLMDRCTTAFGKRMFRQWICRPLANKNAIVDRQK 704

Query: 60  AISVLLDQKHITEQMRAKMKDLRDLERML 88
           AI  L D     +++ A +  L DLERM+
Sbjct: 705 AIEFLRDSPETLQKVTAILNKLPDLERMI 733

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

 Score = 78.2 bits (191), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 33/59 (55%), Positives = 45/59 (76%)

Query: 98   GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
            GC VPA+   LTPVDR+FTR+GA D +   +ST+  EL+E+ +I+RHA+ +SL LVDEL
Sbjct: 1155 GCYVPAEKCRLTPVDRVFTRLGASDRIMSGESTFFVELSETASILRHATAHSLVLVDEL 1213

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|A6W1Q6|MUTS_MARMS DNA mismatch repair protein MutS OS=Marinomonas sp. (strain MWYL1) GN=mutS PE=3 SV=1

 Score = 77.0 bits (188), Expect = 4e-14,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 51/65 (78%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
           T L+  GC VPA+S +++ VDRIFTRMG+ D+L+G +ST++ E+TE+  I+ +ASK SL 
Sbjct: 636 TLLAHTGCFVPAESASISVVDRIFTRMGSSDDLAGGRSTFMVEMTETANILNNASKNSLV 695

Query: 152 LVDEL 156
           L+DE+
Sbjct: 696 LMDEV 700

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.

Marinomonas sp. (strain MWYL1) (taxid: 400668)

>sp|Q7NRW7|MUTS_CHRVO DNA mismatch repair protein MutS OS=Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) GN=mutS PE=3 SV=1

 Score = 76.3 bits (186), Expect = 7e-14,   Method: Compositional matrix adjust.
 Identities = 33/65 (50%), Positives = 50/65 (76%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
           T L+  G  VPADS  + P+DRIFTR+GA D+L+G +ST++ E+TE+  I+ +AS++SL 
Sbjct: 652 TLLAHVGSFVPADSAVIGPIDRIFTRIGASDDLAGGRSTFMVEMTETANILNNASEHSLV 711

Query: 152 LVDEL 156
           L+DE+
Sbjct: 712 LMDEV 716

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.

Chromobacterium violaceum (strain ATCC 12472 / DSM 30191 / JCM 1249 / NBRC 12614 / NCIMB 9131 / NCTC 9757) (taxid: 243365)

>sp|Q31F87|MUTS_THICR DNA mismatch repair protein MutS OS=Thiomicrospira crunogena (strain XCL-2) GN=mutS PE=3 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 32/64 (50%), Positives = 48/64 (75%)

Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA+S TL P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ HAS  SL L
Sbjct: 635 IMAYMGSFVPAESATLGPIDRIFTRIGASDDLTSGRSTFMVEMTETANILHHASPESLIL 694

Query: 153 VDEL 156
           +DE+
Sbjct: 695 MDEV 698

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.

Thiomicrospira crunogena (strain XCL-2) (taxid: 317025)

>sp|Q5X4B2|MUTS_LEGPA DNA mismatch repair protein MutS OS=Legionella pneumophila (strain Paris) GN=mutS PE=3 SV=1

 Score = 74.7 bits (182), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 34/65 (52%), Positives = 47/65 (72%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
             LS  G  VPAD +TL P+DRIFTR+GA D+LS  +ST++ E+TE+  I+R A+  SL 
Sbjct: 627 VLLSHIGSFVPADEVTLGPLDRIFTRIGASDDLSSGRSTFMVEMTETAQILRQATSQSLV 686

Query: 152 LVDEL 156
           L+DE+
Sbjct: 687 LIDEI 691

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.

Legionella pneumophila (strain Paris) (taxid: 297246)

>sp|A4G717|MUTS_HERAR DNA mismatch repair protein MutS OS=Herminiimonas arsenicoxydans GN=mutS PE=3 SV=3

 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 33/65 (50%), Positives = 49/65 (75%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
           T L++ G  VPA S T+ P+DRIFTR+GA D+L+G +ST++ E+TES  I+  A++ SL 
Sbjct: 658 TLLAYVGSFVPATSATIGPIDRIFTRIGAADDLAGGRSTFMVEMTESAAILNGATENSLV 717

Query: 152 LVDEL 156
           L+DE+
Sbjct: 718 LMDEV 722

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.

Herminiimonas arsenicoxydans (taxid: 204773)

>sp|Q47DJ8|MUTS_DECAR DNA mismatch repair protein MutS OS=Dechloromonas aromatica (strain RCB) GN=mutS PE=3 SV=1

 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 32/65 (49%), Positives = 46/65 (70%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
             L+  GC VPAD   L P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ HA+  SL 
Sbjct: 637 ALLAHIGCYVPADRCVLGPLDRIFTRIGASDDLASGRSTFMVEMTEAAAILHHATNQSLV 696

Query: 152 LVDEL 156
           L+DE+
Sbjct: 697 LMDEI 701

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.

Dechloromonas aromatica (strain RCB) (taxid: 159087)

>sp|Q8Y093|MUTS_RALSO DNA mismatch repair protein MutS OS=Ralstonia solanacearum (strain GMI1000) GN=mutS PE=3 SV=1

 Score = 74.3 bits (181), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 31/65 (47%), Positives = 48/65 (73%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
             L++ G  VPAD+ T+ P+DRIFTR+GA D+L+G +ST++ E+TE+  I+  A+  SL 
Sbjct: 646 VLLAYVGAFVPADAATIGPIDRIFTRIGAADDLAGGRSTFMVEMTEAAAILHRATPNSLV 705

Query: 152 LVDEL 156
           L+DE+
Sbjct: 706 LMDEI 710

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.

Ralstonia solanacearum (strain GMI1000) (taxid: 267608)

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

 Score = 73.9 bits (180), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query: 98   GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
            GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct: 1157 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 1215

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)

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	156
328718270	1185	PREDICTED: DNA mismatch repair protein M	0.467	0.061	0.561	6e-15
326498831	1331	predicted protein [Hordeum vulgare subsp	0.564	0.066	0.471	2e-14
66827461	1260	hypothetical protein DDB_G0268614 [Dicty	0.564	0.069	0.460	5e-14
294940586	616	DNA mismatch repair protein MSH6-1, puta	0.455	0.115	0.507	9e-14
390334252	1462	PREDICTED: DNA mismatch repair protein M	0.378	0.040	0.593	1e-13
294892329	943	DNA mismatch repair protein mutS, putati	0.455	0.075	0.507	1e-13
346974058	1211	DNA mismatch repair protein msh6 [Vertic	0.564	0.072	0.449	1e-13
302416361	1193	DNA mismatch repair protein msh6 [Vertic	0.564	0.073	0.449	2e-13
71018553	1716	hypothetical protein UM03360.1 [Ustilago	0.570	0.051	0.449	2e-13
383936558	857	DNA mismatch repair protein MutS [Rheinh	0.397	0.072	0.507	2e-13

>gi|328718270|ref|XP_001946118.2| PREDICTED: DNA mismatch repair protein Msh6-like [Acyrthosiphon pisum]

 Score = 85.9 bits (211), Expect = 6e-15,   Method: Composition-based stats.
 Identities = 41/73 (56%), Positives = 51/73 (69%)

Query: 84   LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMR 143
            L R L   T ++  GCRVPA SL L PVDRIFTR+GA DN+   +ST+  EL E+  I+ 
Sbjct: 972  LMRQLGIITVMAHMGCRVPAKSLLLNPVDRIFTRIGANDNIIAGESTFFVELCETSAILH 1031

Query: 144  HASKYSLALVDEL 156
            HAS++SL LVDEL
Sbjct: 1032 HASRFSLVLVDEL 1044

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|326498831|dbj|BAK02401.1| predicted protein [Hordeum vulgare subsp. vulgare]

 Score = 84.0 bits (206), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 42/89 (47%), Positives = 57/89 (64%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
           ILD+ AL NL +L N+     GTL EQL+HCVT FGKR+L+  +V+PL + +AI QRQ A
Sbjct: 697 ILDAAALENLEILENATGGLSGTLYEQLNHCVTGFGKRLLKRWIVRPLYDREAILQRQGA 756

Query: 61  ISVLLDQKH-ITEQMRAKMKDLRDLERML 88
           I++     H    Q R  +  L D+ER+L
Sbjct: 757 IAIFKGVGHECAMQFRKDLCRLPDMERLL 785

Source: Hordeum vulgare subsp. vulgare

Species: Hordeum vulgare

Genus: Hordeum

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|66827461|ref|XP_647085.1| hypothetical protein DDB_G0268614 [Dictyostelium discoideum AX4] gi|74897500|sp|Q55GU9.1|MSH6_DICDI RecName: Full=DNA mismatch repair protein Msh6 gi|60475825|gb|EAL73760.1| hypothetical protein DDB_G0268614 [Dictyostelium discoideum AX4]

 Score = 82.8 bits (203), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 41/89 (46%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
           ILD   L NL +  NS D +TEGTL + +D C T+FGKRM R  + +PL N +AI  RQ 
Sbjct: 645 ILDGQCLVNLEIFNNSTDGSTEGTLFKLMDRCTTAFGKRMFRQWICRPLANKNAIVDRQK 704

Query: 60  AISVLLDQKHITEQMRAKMKDLRDLERML 88
           AI  L D     +++ A +  L DLERM+
Sbjct: 705 AIEFLRDSPETLQKVTAILNKLPDLERMI 733

Source: Dictyostelium discoideum AX4

Species: Dictyostelium discoideum

Genus: Dictyostelium

Order: Dictyosteliida

Superkingdom: Eukaryota

>gi|294940586|ref|XP_002782821.1| DNA mismatch repair protein MSH6-1, putative [Perkinsus marinus ATCC 50983] gi|239894872|gb|EER14617.1| DNA mismatch repair protein MSH6-1, putative [Perkinsus marinus ATCC 50983]

 Score = 81.6 bits (200), Expect = 9e-14,   Method: Compositional matrix adjust.
 Identities = 36/71 (50%), Positives = 55/71 (77%)

Query: 86  RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
           R+  ++  ++  GCRVPA S  LTPVDRIFTR+GA+D++   +ST+L EL E+  +++HA
Sbjct: 415 RLGATAVIIAQLGCRVPASSFKLTPVDRIFTRIGARDSILENKSTFLIELEETGAVLQHA 474

Query: 146 SKYSLALVDEL 156
           +K+SLA++DEL
Sbjct: 475 TKHSLAVIDEL 485

Source: Perkinsus marinus ATCC 50983

Species: Perkinsus marinus

Genus: Perkinsus

Family: Perkinsidae

Order: Perkinsida

Superkingdom: Eukaryota

>gi|390334252|ref|XP_797647.3| PREDICTED: DNA mismatch repair protein Msh6-like [Strongylocentrotus purpuratus]

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Composition-based stats.
 Identities = 35/59 (59%), Positives = 48/59 (81%)

Query: 98   GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
            GC VPA+   LTPVDR+FTR+GA+DN+   +ST+  EL+E+ +I++HASK+SL LVDEL
Sbjct: 1260 GCYVPAEGCRLTPVDRVFTRLGARDNILSGESTFFVELSETASILKHASKHSLVLVDEL 1318

Source: Strongylocentrotus purpuratus

Species: Strongylocentrotus purpuratus

Genus: Strongylocentrotus

Family: Strongylocentrotidae

Order: Echinoida

Class: Echinoidea

Phylum: Echinodermata

Superkingdom: Eukaryota

>gi|294892329|ref|XP_002774009.1| DNA mismatch repair protein mutS, putative [Perkinsus marinus ATCC 50983] gi|239879213|gb|EER05825.1| DNA mismatch repair protein mutS, putative [Perkinsus marinus ATCC 50983]

 Score = 81.3 bits (199), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 36/71 (50%), Positives = 55/71 (77%)

Query: 86  RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
           R+  ++  ++  GCRVPA S  LTPVDRIFTR+GA+D++   +ST+L EL E+  +++HA
Sbjct: 742 RLSATAVIIAQLGCRVPASSFKLTPVDRIFTRIGARDSILENKSTFLIELEETGAVLQHA 801

Query: 146 SKYSLALVDEL 156
           +K+SLA++DEL
Sbjct: 802 TKHSLAVIDEL 812

Source: Perkinsus marinus ATCC 50983

Species: Perkinsus marinus

Genus: Perkinsus

Family: Perkinsidae

Order: Perkinsida

Superkingdom: Eukaryota

>gi|346974058|gb|EGY17510.1| DNA mismatch repair protein msh6 [Verticillium dahliae VdLs.17]

 Score = 80.9 bits (198), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 40/89 (44%), Positives = 55/89 (61%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTNSDN-TTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
           ILD   L NL V  NS N +TEGTL   L+ CVT FGKR+ R  +  PL ++D I +R D
Sbjct: 624 ILDGQTLINLEVFANSANGSTEGTLFTLLNKCVTPFGKRLFRQWVCHPLCDIDRINERLD 683

Query: 60  AISVLLDQKHITEQMRAKMKDLRDLERML 88
           A+ +L   + + EQ  A+M  + DLER++
Sbjct: 684 AVDMLNSDRSVREQFSAQMTKMPDLERLI 712

Source: Verticillium dahliae VdLs.17

Species: Verticillium dahliae

Genus: Verticillium

Family: Plectosphaerellaceae

Order: Glomerellales

Class: Sordariomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|302416361|ref|XP_003006012.1| DNA mismatch repair protein msh6 [Verticillium albo-atrum VaMs.102] gi|261355428|gb|EEY17856.1| DNA mismatch repair protein msh6 [Verticillium albo-atrum VaMs.102]

 Score = 80.9 bits (198), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/89 (44%), Positives = 55/89 (61%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTNSDN-TTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
           ILD   L NL V  NS N +TEGTL   L+ CVT FGKR+ R  +  PL ++D I +R D
Sbjct: 606 ILDGQTLINLEVFANSANGSTEGTLFTLLNKCVTPFGKRLFRQWVCHPLCDIDRINERLD 665

Query: 60  AISVLLDQKHITEQMRAKMKDLRDLERML 88
           A+ +L   + + EQ  A+M  + DLER++
Sbjct: 666 AVDMLNSDRSVREQFSAQMTKMPDLERLI 694

Source: Verticillium albo-atrum VaMs.102

Species: Verticillium alfalfae

Genus: Verticillium

Family: Plectosphaerellaceae

Order: Glomerellales

Class: Sordariomycetes

Phylum: Ascomycota

Superkingdom: Eukaryota

>gi|71018553|ref|XP_759507.1| hypothetical protein UM03360.1 [Ustilago maydis 521] gi|46098995|gb|EAK84228.1| hypothetical protein UM03360.1 [Ustilago maydis 521]

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 40/89 (44%), Positives = 54/89 (60%)

Query: 1   ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
           +LD+ +L +L+VL N + T EGTL   L+ CVT FGKR+ +  LV PL   DAI  RQDA
Sbjct: 689 VLDAQSLTHLNVLQNDEGTDEGTLHRLLNRCVTPFGKRLFKIWLVAPLATADAINARQDA 748

Query: 61  ISVLLDQKHITEQMRAKMKDLRDLERMLP 89
           +  LL      +Q     K L D+ER++P
Sbjct: 749 VEDLLKNPCFGDQFETFGKALPDIERIVP 777

Source: Ustilago maydis 521

Species: Ustilago maydis

Genus: Ustilago

Family: Ustilaginaceae

Order: Ustilaginales

Class: Ustilaginomycetes

Phylum: Basidiomycota

Superkingdom: Eukaryota

>gi|383936558|ref|ZP_09989982.1| DNA mismatch repair protein MutS [Rheinheimera nanhaiensis E407-8] gi|383702340|dbj|GAB60073.1| DNA mismatch repair protein MutS [Rheinheimera nanhaiensis E407-8]

 Score = 80.5 bits (197), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 33/65 (50%), Positives = 51/65 (78%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
             +++ GC VPADS  + PVDRIFTR+GA D+L+  +ST++ E+TE+ TI+ HA+++SL 
Sbjct: 635 VLMAYIGCFVPADSAEIGPVDRIFTRIGASDDLASGRSTFMVEMTETATILHHATEHSLV 694

Query: 152 LVDEL 156
           L+DE+
Sbjct: 695 LMDEI 699

Source: Rheinheimera nanhaiensis E407-8

Species: Rheinheimera nanhaiensis

Genus: Rheinheimera

Family: Chromatiaceae

Order: Chromatiales

Class: Gammaproteobacteria

Phylum: Proteobacteria

Superkingdom: Bacteria

---

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	156
UNIPROTKB|E1BYJ2	1341	MSH6 "Uncharacterized protein"	0.564	0.065	0.460	2.3e-28
UNIPROTKB|E1BWV7	1357	MSH6 "Uncharacterized protein"	0.564	0.064	0.460	2.4e-28
ZFIN|ZDB-GENE-020905-3	1369	msh6 "mutS homolog 6 (E. coli)	0.378	0.043	0.559	5e-28
RGD|2322311	1361	Msh6 "mutS homolog 6 (E. coli)	0.378	0.043	0.559	1.3e-27
DICTYBASE|DDB_G0268614	1260	msh6 "mutS homolog" [Dictyoste	0.564	0.069	0.460	1.3e-27
MGI|MGI:1343961	1358	Msh6 "mutS homolog 6 (E. coli)	0.378	0.043	0.559	2.1e-27
UNIPROTKB|F5H2F9	1058	MSH6 "DNA mismatch repair prot	0.378	0.055	0.525	1.6e-26
UNIPROTKB|E1B9Q4	1360	MSH6 "Uncharacterized protein"	0.378	0.043	0.525	1.9e-26
UNIPROTKB|B4DF41	1230	MSH6 "DNA mismatch repair prot	0.378	0.047	0.525	2.4e-26
UNIPROTKB|P52701	1360	MSH6 "DNA mismatch repair prot	0.378	0.043	0.525	3e-26

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

 Score = 181 (68.8 bits), Expect = 2.3e-28, Sum P(2) = 2.3e-28
 Identities = 41/89 (46%), Positives = 53/89 (59%)

Query:     1 ILDSTALANLHVLTNSDN-TTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
             +LD   L NL VL N  N TTEGTL+E++D C T FGKR+L+  L  PL N  +I  R D
Sbjct:   715 VLDGVTLMNLEVLQNGTNGTTEGTLLERIDSCCTPFGKRLLKQWLCAPLCNPTSINDRLD 774

Query:    60 AISVLLDQKHITEQMRAKMKDLRDLERML 88
             A+  LL       ++   +K L DLER+L
Sbjct:   775 AVEDLLAVPAKLTEITEHLKKLPDLERLL 803

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 = 181 (68.8 bits), Expect = 2.4e-28, Sum P(2) = 2.4e-28
 Identities = 41/89 (46%), Positives = 53/89 (59%)

Query:     1 ILDSTALANLHVLTNSDN-TTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
             +LD   L NL VL N  N TTEGTL+E++D C T FGKR+L+  L  PL N  +I  R D
Sbjct:   731 VLDGVTLMNLEVLQNGTNGTTEGTLLERIDSCCTPFGKRLLKQWLCAPLCNPTSINDRLD 790

Query:    60 AISVLLDQKHITEQMRAKMKDLRDLERML 88
             A+  LL       ++   +K L DLER+L
Sbjct:   791 AVEDLLAVPAKLTEITEHLKKLPDLERLL 819

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

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

 Score = 183 (69.5 bits), Expect = 5.0e-28, Sum P(2) = 5.0e-28
 Identities = 33/59 (55%), Positives = 46/59 (77%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+SL LTPVDR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL L+DEL
Sbjct:  1166 GCYVPAESLRLTPVDRVFTRLGASDRIMSGESTFFVELSETASILLHATNHSLVLLDEL 1224

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

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

 Score = 181 (68.8 bits), Expect = 1.3e-27, Sum P(2) = 1.3e-27
 Identities = 33/59 (55%), Positives = 45/59 (76%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+   LTPVDR+FTR+GA D +   +ST+  EL+E+ +I+RHA+ +SL LVDEL
Sbjct:  1158 GCYVPAELCRLTPVDRVFTRLGASDRIMSGESTFFVELSETASILRHATAHSLVLVDEL 1216

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

DICTYBASE|DDB_G0268614 msh6 "mutS homolog" [Dictyostelium discoideum (taxid:44689)]

 Score = 194 (73.4 bits), Expect = 1.3e-27, Sum P(2) = 1.3e-27
 Identities = 41/89 (46%), Positives = 54/89 (60%)

Query:     1 ILDSTALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
             ILD   L NL +  NS D +TEGTL + +D C T+FGKRM R  + +PL N +AI  RQ 
Sbjct:   645 ILDGQCLVNLEIFNNSTDGSTEGTLFKLMDRCTTAFGKRMFRQWICRPLANKNAIVDRQK 704

Query:    60 AISVLLDQKHITEQMRAKMKDLRDLERML 88
             AI  L D     +++ A +  L DLERM+
Sbjct:   705 AIEFLRDSPETLQKVTAILNKLPDLERMI 733

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

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

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

GO:0032301 "MutSalpha complex" evidence=ISS;IBA

GO:0016887 "ATPase activity" evidence=ISS

GO:0006200 "ATP catabolic process" evidence=ISS

GO:0005634 "nucleus" evidence=IEA;ISS

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

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

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

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

GO:0009411 "response to UV" evidence=IBA

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

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

GO:0003684 "damaged DNA binding" evidence=IBA

GO:0000710 "meiotic mismatch repair" evidence=IBA

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

GO:0000228 "nuclear chromosome" evidence=IBA

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

GO:0006281 "DNA repair" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0000166 "nucleotide binding" evidence=IEA

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

 Score = 183 (69.5 bits), Expect = 2.1e-27, Sum P(2) = 2.1e-27
 Identities = 33/59 (55%), Positives = 45/59 (76%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+   LTPVDR+FTR+GA D +   +ST+  EL+E+ +I+RHA+ +SL LVDEL
Sbjct:  1155 GCYVPAEKCRLTPVDRVFTRLGASDRIMSGESTFFVELSETASILRHATAHSLVLVDEL 1213

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

 Score = 174 (66.3 bits), Expect = 1.6e-26, Sum P(2) = 1.6e-26
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct:   855 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 913

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

 Score = 174 (66.3 bits), Expect = 1.9e-26, Sum P(2) = 1.9e-26
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct:  1157 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILTHATAHSLVLVDEL 1215

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

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

GO:0045190 "isotype switching" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

GO:0032405 "MutLalpha complex binding" evidence=IEA

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

GO:0032301 "MutSalpha complex" evidence=IEA

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

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

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

GO:0016887 "ATPase activity" evidence=IEA

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

GO:0009411 "response to UV" evidence=IEA

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

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

GO:0006298 "mismatch repair" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000790 "nuclear chromatin" evidence=IEA

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

GO:0000287 "magnesium ion binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

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

 Score = 174 (66.3 bits), Expect = 2.4e-26, Sum P(2) = 2.4e-26
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct:  1027 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 1085

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

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

 Score = 174 (66.3 bits), Expect = 3.0e-26, Sum P(2) = 3.0e-26
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query:    98 GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
             GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct:  1157 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 1215

GO:0000790 "nuclear chromatin" evidence=IEA

GO:0003682 "chromatin binding" evidence=IEA

GO:0000228 "nuclear chromosome" evidence=IBA

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

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

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

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

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

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

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

GO:0005515 "protein binding" evidence=IPI

GO:0042803 "protein homodimerization activity" evidence=IPI

GO:0032405 "MutLalpha complex binding" evidence=IDA

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

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

GO:0032301 "MutSalpha complex" evidence=IDA

GO:0030983 "mismatched DNA binding" evidence=IDA

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

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

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

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

GO:0016887 "ATPase activity" evidence=IDA

GO:0000287 "magnesium ion binding" evidence=IDA

GO:0005524 "ATP binding" evidence=IDA

GO:0043531 "ADP binding" evidence=IDA

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

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

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

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

GO:0006281 "DNA repair" evidence=IDA

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

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

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

GO:0006200 "ATP catabolic process" evidence=IDA

---

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)
A6W1Q6	MUTS_MARMS	No assigned EC number	0.5230	0.4102	0.0724	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	156
PRK05399	854	PRK05399, PRK05399, DNA mismatch repair protein Mu	3e-21
COG0249	843	COG0249, MutS, Mismatch repair ATPase (MutS family	5e-21
pfam05192	290	pfam05192, MutS_III, MutS domain III	6e-21
cd03286	218	cd03286, ABC_MSH6_euk, ATP-binding cassette domain	8e-20
smart00534	185	smart00534, MUTSac, ATPase domain of DNA mismatch	1e-19
COG0249	843	COG0249, MutS, Mismatch repair ATPase (MutS family	9e-18
pfam00488	235	pfam00488, MutS_V, MutS domain V	1e-17
PRK05399	854	PRK05399, PRK05399, DNA mismatch repair protein Mu	2e-17
cd03284	216	cd03284, ABC_MutS1, ATP-binding cassette domain of	2e-17
smart00533	308	smart00533, MUTSd, DNA-binding domain of DNA misma	2e-16
TIGR01070	840	TIGR01070, mutS1, DNA mismatch repair protein MutS	2e-16
cd03243	202	cd03243, ABC_MutS_homologs, ATP-binding cassette d	1e-14
cd03287	222	cd03287, ABC_MSH3_euk, ATP-binding cassette domain	6e-14
cd03281	213	cd03281, ABC_MSH5_euk, ATP-binding cassette domain	3e-13
TIGR01070	840	TIGR01070, mutS1, DNA mismatch repair protein MutS	7e-13
cd03285	222	cd03285, ABC_MSH2_euk, ATP-binding cassette domain	3e-12
cd03282	204	cd03282, ABC_MSH4_euk, ATP-binding cassette domain	5e-08
cd03283	199	cd03283, ABC_MutS-like, ATP-binding cassette domai	2e-06

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

 Score = 88.6 bits (221), Expect = 3e-21
 Identities = 33/88 (37%), Positives = 51/88 (57%)

Query: 1   ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
           ILD+    NL +  N     + +L+  LD  VT+ G R+LR  L +PL + +AI+ R DA
Sbjct: 264 ILDAATRRNLELTENLRGGRKNSLLSVLDRTVTAMGGRLLRRWLHRPLRDREAIEARLDA 323

Query: 61  ISVLLDQKHITEQMRAKMKDLRDLERML 88
           +  LL+   + E +R  +K + DLER+L
Sbjct: 324 VEELLEDPLLREDLRELLKGVYDLERLL 351

Length = 854

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

 Score = 88.1 bits (219), Expect = 5e-21
 Identities = 32/89 (35%), Positives = 53/89 (59%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTN-SDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
           +LD+    NL + +N   N  +G+L   LD  VT  G R+L+  L++PL + + I++R D
Sbjct: 261 VLDAATRRNLELFSNLRGNGKKGSLFWLLDRTVTPMGSRLLKRWLLQPLLDKEEIEERLD 320

Query: 60  AISVLLDQKHITEQMRAKMKDLRDLERML 88
           A+  L D   + E++R  +K + DLER+L
Sbjct: 321 AVEELKDNPELREKLREMLKKVPDLERLL 349

Length = 843

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

 Score = 85.9 bits (213), Expect = 6e-21
 Identities = 35/85 (41%), Positives = 52/85 (61%), Gaps = 2/85 (2%)

Query: 4  STALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISV 63
          +  L NL +  N     +G+L+  LD  VT  GKR+LR  L++PLT+LD I  R DA+  
Sbjct: 1  AATLRNLELFRNLRGGKKGSLLGLLDRTVTPMGKRLLRRWLLRPLTDLDEINARLDAVEE 60

Query: 64 LLDQKHITEQMRAKMKDLRDLERML 88
          LL+   + E++R  +K + DLER+L
Sbjct: 61 LLE--DLREELREALKGIPDLERLL 83

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

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

 Score = 81.7 bits (202), Expect = 8e-20
 Identities = 30/59 (50%), Positives = 45/59 (76%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA S+ L+ VDRIFTR+GA+D++   +ST++ EL+E+  I+RHA+  SL ++DEL
Sbjct: 60  GMDVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATPDSLVILDEL 118

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 218

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

 Score = 80.3 bits (199), Expect = 1e-19
 Identities = 30/71 (42%), Positives = 46/71 (64%)

Query: 86  RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
           R +     ++  G  VPA+S  L   DRIFTR+GA D+L+   ST++ E+ E+  I+++A
Sbjct: 17  RQVALIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNA 76

Query: 146 SKYSLALVDEL 156
           +K SL L+DEL
Sbjct: 77  TKNSLVLLDEL 87

Length = 185

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

 Score = 78.9 bits (195), Expect = 9e-18
 Identities = 25/59 (42%), Positives = 42/59 (71%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA+   +  VDRIFTR+GA D+L+  +ST++ E+ E+  I+ +A++ SL ++DE+
Sbjct: 637 GSFVPAEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDEI 695

Length = 843

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

 Score = 76.5 bits (189), Expect = 1e-17
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA+S  +  VDRIFTR+GA D+L+  +ST++ E+ E+  I+ +A+  SL ++DEL
Sbjct: 73  GSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMLETANILHNATDKSLVILDEL 131

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

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

 Score = 77.4 bits (192), Expect = 2e-17
 Identities = 28/58 (48%), Positives = 43/58 (74%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDE 155
           G  VPA+S  +  VDRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++ SL L+DE
Sbjct: 637 GSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTETANILNNATERSLVLLDE 694

Length = 854

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

 Score = 75.0 bits (185), Expect = 2e-17
 Identities = 27/59 (45%), Positives = 42/59 (71%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA    +  VDRIFTR+GA D+L+G +ST++ E+ E+  I+ +A++ SL L+DE+
Sbjct: 60  GSFVPASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATERSLVLLDEI 118

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 216

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

 Score = 74.3 bits (183), Expect = 2e-16
 Identities = 27/68 (39%), Positives = 45/68 (66%)

Query: 21 EGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD 80
          +G+L E L+H  T  GKR+LR  L++PL +L  I +R DA+  L++   + +++R  +K 
Sbjct: 1  KGSLFELLNHTKTPMGKRLLRRWLLQPLLDLKEINERLDAVEELVENPELRQKLRQLLKR 60

Query: 81 LRDLERML 88
          + DLER+L
Sbjct: 61 IPDLERLL 68

Length = 308

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

 Score = 75.2 bits (185), Expect = 2e-16
 Identities = 29/65 (44%), Positives = 44/65 (67%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
             L+  G  VPA+S  L   DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++ SL 
Sbjct: 616 ALLAQIGSFVPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLV 675

Query: 152 LVDEL 156
           L DE+
Sbjct: 676 LFDEI 680

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

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

 Score = 67.7 bits (166), Expect = 1e-14
 Identities = 32/65 (49%), Positives = 47/65 (72%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
             L+  GC VPA+S ++  VDRIFTR+GA+D++S  +ST++AEL E + I+  A+  SL 
Sbjct: 53  VLLAQIGCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPRSLV 112

Query: 152 LVDEL 156
           L+DEL
Sbjct: 113 LIDEL 117

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 202

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

 Score = 66.0 bits (161), Expect = 6e-14
 Identities = 27/71 (38%), Positives = 43/71 (60%)

Query: 86  RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
           R +   T ++  G  VPA S TL+  D + TRMGA D++    ST++ EL+E+  I+ + 
Sbjct: 49  RQVALITIMAQIGSFVPASSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNC 108

Query: 146 SKYSLALVDEL 156
           +  SL ++DEL
Sbjct: 109 TSRSLVILDEL 119

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 222

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

 Score = 64.2 bits (157), Expect = 3e-13
 Identities = 27/64 (42%), Positives = 43/64 (67%)

Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
            FL+  G  VPADS T+  VD+IFTRM +++++S  QS ++ +L +    +R A++ SL 
Sbjct: 53  VFLAHIGSFVPADSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRRSLV 112

Query: 152 LVDE 155
           L+DE
Sbjct: 113 LIDE 116

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 213

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

 Score = 64.8 bits (158), Expect = 7e-13
 Identities = 29/88 (32%), Positives = 47/88 (53%)

Query: 1   ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
            LD+    NL +  N     + TL   LD   T+ G R+L+  L +PL + + ++ RQD 
Sbjct: 250 QLDAATRRNLELTENLRGGKQNTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDT 309

Query: 61  ISVLLDQKHITEQMRAKMKDLRDLERML 88
           + VLL    + E +R  +K++ DLER+ 
Sbjct: 310 VEVLLRHFFLREGLRPLLKEVGDLERLA 337

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

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

 Score = 61.2 bits (149), Expect = 3e-12
 Identities = 25/59 (42%), Positives = 38/59 (64%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VP DS  +  VD I  R+GA D+     ST++AE+ E+  I++ A++ SL ++DEL
Sbjct: 60  GCFVPCDSADIPIVDCILARVGASDSQLKGVSTFMAEMLETAAILKSATENSLIIIDEL 118

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 222

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

 Score = 49.7 bits (119), Expect = 5e-08
 Identities = 22/59 (37%), Positives = 37/59 (62%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VPA+  TL   +R+ +R+   D++    ST+ +E++E+  I+ +A   SL L+DEL
Sbjct: 59  GCFVPAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGDSLVLIDEL 117

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 204

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

 Score = 45.4 bits (108), Expect = 2e-06
 Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 3/73 (4%)

Query: 86  RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
           R +  +  L+  G  V A S  L P  +IFT +   D+L    S + AEL   + I+  A
Sbjct: 43  RTIGVNVILAQAGAPVCASSFEL-PPVKIFTSIRVSDDLRDGISYFYAELRRLKEIVEKA 101

Query: 146 SK--YSLALVDEL 156
            K    L L+DE+
Sbjct: 102 KKGEPVLFLLDEI 114

The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA structures or lesions results in ADP/ATP exchange. Length = 199

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	156
COG0249	843	MutS Mismatch repair ATPase (MutS family) [DNA rep	100.0
TIGR01070	840	mutS1 DNA mismatch repair protein MutS.	99.97
PRK05399	854	DNA mismatch repair protein MutS; Provisional	99.97
KOG0218|consensus	1070		99.97
KOG0220|consensus	867		99.95
PF00488	235	MutS_V: MutS domain V C-terminus.; InterPro: IPR00	99.95
KOG0217|consensus	1125		99.94
KOG0219|consensus	902		99.92
KOG0221|consensus	849		99.92
cd03286	218	ABC_MSH6_euk MutS6 homolog in eukaryotes. The MutS	99.9
PRK00409	782	recombination and DNA strand exchange inhibitor pr	99.9
cd03287	222	ABC_MSH3_euk MutS3 homolog in eukaryotes. The MutS	99.87
cd03281	213	ABC_MSH5_euk MutS5 homolog in eukaryotes. The MutS	99.8
cd03282	204	ABC_MSH4_euk MutS4 homolog in eukaryotes. The MutS	99.79
cd03285	222	ABC_MSH2_euk MutS2 homolog in eukaryotes. The MutS	99.77
TIGR01069	771	mutS2 MutS2 family protein. Function of MutS2 is u	99.76
cd03284	216	ABC_MutS1 MutS1 homolog in eukaryotes. The MutS pr	99.75
smart00534	185	MUTSac ATPase domain of DNA mismatch repair MUTS f	99.67
COG1193	753	Mismatch repair ATPase (MutS family) [DNA replicat	99.66
TIGR01070	840	mutS1 DNA mismatch repair protein MutS.	99.59
cd03243	202	ABC_MutS_homologs The MutS protein initiates DNA m	99.57
cd03280	200	ABC_MutS2 MutS2 homologs in bacteria and eukaryote	99.57
COG0249	843	MutS Mismatch repair ATPase (MutS family) [DNA rep	99.53
cd03283	199	ABC_MutS-like MutS-like homolog in eukaryotes. The	99.52
PF05192	204	MutS_III: MutS domain III C-terminus.; InterPro: I	99.52
KOG0218|consensus	1070		99.34
smart00533	308	MUTSd DNA-binding domain of DNA mismatch repair MU	98.95
KOG0221|consensus	849		98.88
KOG0219|consensus	902		98.37
cd03227	162	ABC_Class2 ABC-type Class 2 contains systems invol	98.29
KOG0220|consensus	867		97.96
PRK05399	854	DNA mismatch repair protein MutS; Provisional	97.03
smart00533	308	MUTSd DNA-binding domain of DNA mismatch repair MU	96.65
PRK00409	782	recombination and DNA strand exchange inhibitor pr	87.48
PF13173	128	AAA_14: AAA domain	87.05
cd03222	177	ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibi	84.01
COG1373	398	Predicted ATPase (AAA+ superfamily) [General funct	83.16
cd03216	163	ABC_Carb_Monos_I This family represents the domain	80.37

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

Probab=100.00  E-value=1.6e-36  Score=260.53  Aligned_cols=134  Identities=28%  Similarity=0.429  Sum_probs=121.1

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCHH----HHHhhHHHHHHHhhchhhHHHHHHhh-hh--hhhhhhhchhH---
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNLD----AIKQRQDAISVLLDQKHITEQMRAKM-KD--LRDLERMLPSS---   91 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~----~i~~Rhplv~~l~~~~~v~~~i~~~l-~~--~~~~~n~~gk~---   91 (156)
                      ...++.|| |+.+++..+...+|++|.++..    +.++|||+||..+++.+|||++...- ++  +.|+|||+|||   
T Consensus       546 a~aLa~lD-~l~slA~~a~~~~y~rP~~~~~~~l~i~~gRHPvvE~~~~~~fVpNd~~L~~~~~i~lITGPNM~GKSTyl  624 (843)
T COG0249         546 AKALAELD-VLSSLAEIAAEQNYVRPEFVDSNDLEIKEGRHPVVEAVLDNGFVPNDIDLSGNRRIILITGPNMGGKSTYL  624 (843)
T ss_pred             HHHHHHHH-HHHHHHHHHhhCCCCCceecCCCCEEEEecCcchhhhhccCCcccCceeeCCCceEEEEECCCCCccHHHH
Confidence            47899999 9999999999999999988644    56899999999888779999997331 11  34679999998   


Q ss_pred             ------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 ------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                            ++|||+||||||++|.++++|+||||||+.|++..|.||||+||.|+++||++||++|||||||+
T Consensus       625 RQvali~imAQiGsfVPA~~A~i~ivD~IfTRiGa~DDL~~G~STFMvEM~Eta~IL~~AT~~SLvilDEi  695 (843)
T COG0249         625 RQVALIVILAQIGSFVPAEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDEI  695 (843)
T ss_pred             HHHHHHHHHHHcCCCeeHHHccccccceeeecccccchhhccccHHHHHHHHHHHHHHhCCCCcEEEEecc
Confidence                  46899999999999999999999999999999999999999999999999999999999999996

>TIGR01070 mutS1 DNA mismatch repair protein MutS

Probab=99.97  E-value=5.7e-33  Score=239.99  Aligned_cols=134  Identities=28%  Similarity=0.423  Sum_probs=119.1

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCHH----HHHhhHHHHHHHhhchhhHHHHHHhhh---hhhhhhhhchhH---
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNLD----AIKQRQDAISVLLDQKHITEQMRAKMK---DLRDLERMLPSS---   91 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~----~i~~Rhplv~~l~~~~~v~~~i~~~l~---~~~~~~n~~gk~---   91 (156)
                      ...++.|| |+.+++..+...+|++|.++.+    +.++|||+++......+||||+...-.   -+.++|||+|||   
T Consensus       531 ~~~la~lD-~l~s~A~~a~~~~~~~P~~~~~~~i~i~~~RHP~le~~~~~~~VpNdi~l~~~~~~~iITGPNmgGKSt~l  609 (840)
T TIGR01070       531 ARALAELD-VLANLAEVAETLHYTRPRFGDDPQLRIREGRHPVVEQVLRTPFVPNDLEMAHNRRMLLITGPNMGGKSTYM  609 (840)
T ss_pred             HHHHHHHH-HHHHHHHHHHHCCCcCceecCCCcEEEEeeECHHHHhccCCCeEeeeeecCCCccEEEEECCCCCCchHHH
Confidence            47899999 9999999999999999998633    468999999876556789999974311   134679999998   


Q ss_pred             ------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 ------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                            ++|||+||||||+++.+|++|+||||||+.|++..|+|||++||.+++.|+++++++||||+||+
T Consensus       610 rqvali~imAq~G~~VPA~~a~i~~~D~Iftrig~~d~i~~g~STF~~Em~e~a~IL~~at~~sLvllDE~  680 (840)
T TIGR01070       610 RQTALIALLAQIGSFVPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANILHNATENSLVLFDEI  680 (840)
T ss_pred             HHHHHHHHHHhcCCCccchheEeccccEEEEecCcccchhcCcchHHHHHHHHHHHHhhCCCCEEEEEccC
Confidence                  47899999999999999999999999999999999999999999999999999999999999996

>PRK05399 DNA mismatch repair protein MutS; Provisional

Probab=99.97  E-value=2.2e-31  Score=230.90  Aligned_cols=65  Identities=45%  Similarity=0.724  Sum_probs=63.3

Q ss_pred             HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ++|||+||||||+++.++++|+||||||+.|++..|+|||++||.+++.|+++++++||||+||+
T Consensus       631 ~ilAq~G~~VPa~~a~i~~~d~I~triga~d~i~~g~STF~~E~~~~~~il~~at~~sLvllDE~  695 (854)
T PRK05399        631 VLLAQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTETANILNNATERSLVLLDEI  695 (854)
T ss_pred             HHHHhcCCceeccceEecccCeeeeccCcccccccCcccHHHHHHHHHHHHHhCCCCcEEEEecC
Confidence            36899999999999999999999999999999999999999999999999999999999999996

>KOG0218|consensus

Probab=99.97  E-value=6.4e-33  Score=228.94  Aligned_cols=133  Identities=28%  Similarity=0.406  Sum_probs=120.4

Q ss_pred             cHHHHhhHhhhhHHHHHHHccccCCCCCHH-----HHHhhHHHHHHHhhchhhHHHHHHhhh----hhhhhhhhchhH--
Q psy13255         23 TLIEQLDHCVTSFGKRMLRAQLVKPLTNLD-----AIKQRQDAISVLLDQKHITEQMRAKMK----DLRDLERMLPSS--   91 (156)
Q Consensus        23 sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~-----~i~~Rhplv~~l~~~~~v~~~i~~~l~----~~~~~~n~~gk~--   91 (156)
                      ..++.+| |+.++++..-..+|+||.+..+     +.++|||.+|.++.+.+|||++...-.    .+.++|||+||+  
T Consensus       768 ~~LatlD-Ci~SlA~~s~n~nYvRPtfvd~~~eI~ikngRhPvIe~Ll~d~fVPNdi~ls~egerc~IITGPNMGGKSsy  846 (1070)
T KOG0218|consen  768 LNLATLD-CILSLAATSCNVNYVRPTFVDGQQEIIIKNGRHPVIESLLVDYFVPNDIMLSPEGERCNIITGPNMGGKSSY  846 (1070)
T ss_pred             HHHHHHH-HHHHHHHHhccCCccCcccccchhhhhhhcCCCchHHHHhhhccCCCcceecCCCceEEEEeCCCCCCchHH
Confidence            5789999 9999999999999999999742     347999999998888899999853322    245789999997  


Q ss_pred             -------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 -------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 -------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                             ++|||+|+||||+++.+++||+||||||+.|++..|.|||++||.+++.|+++|+++||||+||+
T Consensus       847 IrQvALitIMAQiGsfVPAeea~l~IfdgvltRmGAsDnI~~grSTFm~Emldt~eil~kat~~SlvilDEl  918 (1070)
T KOG0218|consen  847 IRQVALITIMAQIGSFVPAEEARLSIFDGVLTRMGASDNIINGRSTFMVEMLDTLEILKKATKRSLVILDEL  918 (1070)
T ss_pred             HHHHHHHHHHHHhcCccchHHhhhhHHhhHHHhhccccccccchhHHHHHHHHHHHHHHhcccchhhhhHhh
Confidence                   58999999999999999999999999999999999999999999999999999999999999996

>KOG0220|consensus

Probab=99.95  E-value=5.7e-30  Score=211.32  Aligned_cols=133  Identities=27%  Similarity=0.370  Sum_probs=116.9

Q ss_pred             cHHHHhhHhhhhHHHHHHHccccCCCCCHH--HHHhhHHHHHHHhhchhhHHHHHHhh---hhhhhhhhhchhH------
Q psy13255         23 TLIEQLDHCVTSFGKRMLRAQLVKPLTNLD--AIKQRQDAISVLLDQKHITEQMRAKM---KDLRDLERMLPSS------   91 (156)
Q Consensus        23 sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~--~i~~Rhplv~~l~~~~~v~~~i~~~l---~~~~~~~n~~gk~------   91 (156)
                      .++..|| .+++++.......+++|.+...  +.++|||++++...+.++.|+....-   -++.++|||+||+      
T Consensus       563 e~~~~lD-~l~sfa~~~~~~~y~~P~fT~slaI~qGRHPILe~i~~ek~i~N~t~~t~~s~f~IITGPNMsGKSTYLKQv  641 (867)
T KOG0220|consen  563 EAVSMLD-MLCSFAHACTLSDYVRPEFTDSLAIKQGRHPILEKISAEKPIANNTYVTEGSNFLIITGPNMSGKSTYLKQV  641 (867)
T ss_pred             HHHHHHH-HHHHHHHhhccccccccccCCceeeccCCCchhhhhcccCcccCcceeecccceEEEECCCCCcchHHHHHH
Confidence            5778899 7888999999999999998754  56799999998777766777664210   1345779999998      


Q ss_pred             ---HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 ---TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ---~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                         ++|||+||||||.++++|+|++||+|||..|+++.+.|+|+.||++++.|++.++++|||++||+
T Consensus       642 Al~~IMAQIGc~IPA~YaS~pIf~RIFtRmg~nDele~NsS~F~sEMke~A~Ilq~a~~~SLiVlDEL  709 (867)
T KOG0220|consen  642 ALCQIMAQIGSYVPAEYASFRVFKRIFTRMGTNDELERNSSTFMSEMKEAAYILQNANKNSLIVLDEL  709 (867)
T ss_pred             HHHHHHHHhccCcchhhccchHHHHHHHHhcCchhhhhchhHHHHHHHHHHHHHHhCCcCcEEEEhhh
Confidence               47999999999999999999999999999999999999999999999999999999999999996

>PF00488 MutS_V: MutS domain V C-terminus

Probab=99.95  E-value=5.2e-30  Score=193.66  Aligned_cols=113  Identities=30%  Similarity=0.490  Sum_probs=84.8

Q ss_pred             ccCCCCCHH----HHHhhHHHHHHHh-hchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCc
Q psy13255         44 LVKPLTNLD----AIKQRQDAISVLL-DQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADS  105 (156)
Q Consensus        44 ~~~P~~~~~----~i~~Rhplv~~l~-~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~  105 (156)
                      |++|.+..+    +.++|||+++..+ .+.++||++...-..    +.++|||+||+         ++|||+|+||||++
T Consensus         1 y~~P~~~~~~~l~i~~~~HPll~~~~~~~~~v~ndi~~~~~~~~~~iiTGpN~sGKSt~lk~i~~~~ilaq~G~~VPA~~   80 (235)
T PF00488_consen    1 YCRPKISEEKSLKIKEGRHPLLEEKLENKKFVPNDIELSNNKSRIIIITGPNMSGKSTFLKQIGLIVILAQIGCFVPAES   80 (235)
T ss_dssp             EB-EEEESTTEEEEEEE--TTHHHHTTTSSC--EEEEESSSSSSEEEEESSTTSSHHHHHHHHHHHHHHHTTT--BSSSE
T ss_pred             CcccEEcCCCCEEEEeccCCEEeccccCCceecceeecCCCceeEEEEeCCCccchhhHHHHHHHHhhhhhcCceeeecc
Confidence            678877642    4579999999875 456899988633222    45679999998         47899999999999


Q ss_pred             ccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        106 LTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       106 ~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      +.++++|+||+++++.|++..|.|+|+.||.+++.|+++++++|||||||+
T Consensus        81 ~~i~~~d~I~t~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~sLvliDE~  131 (235)
T PF00488_consen   81 AEIPIFDRIFTRIGDDDSIESGLSTFMAEMKRLSSILRNATEKSLVLIDEL  131 (235)
T ss_dssp             EEEE--SEEEEEES---SSTTSSSHHHHHHHHHHHHHHH--TTEEEEEEST
T ss_pred             cccccccEEEeecccccccccccccHHHhHHHHHhhhhhcccceeeecccc
Confidence            999999999999999999999999999999999999999999999999997

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

>KOG0217|consensus

Probab=99.94  E-value=7.9e-28  Score=204.49  Aligned_cols=65  Identities=49%  Similarity=0.910  Sum_probs=63.3

Q ss_pred             HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ++|||+||+|||+.++++++|+||||+|+.|++..|.|||+.|+.+.+.|++.+|++|||++||+
T Consensus       923 vilaq~G~~VPa~~~~~tpidrI~tRlGA~D~im~g~STF~vELsET~~IL~~aT~~SLvi~DEL  987 (1125)
T KOG0217|consen  923 VILAQIGCDVPAEVMELTPIDRIFTRLGANDDIMSGESTFFVELSETKKILKHATRHSLVIVDEL  987 (1125)
T ss_pred             HHHHHhCCCccHHHhcccchHHHhhhcccccchhcCCceEEEeccchHHHHhhcCccceeeehhh
Confidence            36899999999999999999999999999999999999999999999999999999999999996

>KOG0219|consensus

Probab=99.92  E-value=4e-26  Score=190.78  Aligned_cols=135  Identities=29%  Similarity=0.415  Sum_probs=111.6

Q ss_pred             cccHHHHhhHhhhhHHHHHH--HccccCCCCC------HHHHHhhHHHHHHHhhchhhHHHHHHh-------------hh
Q psy13255         21 EGTLIEQLDHCVTSFGKRML--RAQLVKPLTN------LDAIKQRQDAISVLLDQKHITEQMRAK-------------MK   79 (156)
Q Consensus        21 ~~sl~~~LD~~~t~~g~~~l--~~~~~~P~~~------~~~i~~Rhplv~~l~~~~~v~~~i~~~-------------l~   79 (156)
                      -+.+++.|| ++.+++..+-  --.|+||.+-      ....+.|||+++.=-..+++||++...             +.
T Consensus       578 l~~vlAhLD-v~~SFa~~st~a~~pYvRP~~l~~gs~rl~l~~~rHp~lE~Qd~~~fIpNdv~le~~~~~~~IiTGpNMG  656 (902)
T KOG0219|consen  578 LNQVLAHLD-VFVSFAHAATVAPIPYVRPKLLPLGSKRLELKQSRHPVLEGQDEIPFIPNDVVLEKGKCRMLIITGPNMG  656 (902)
T ss_pred             HHHHHHHHH-hheeehhhcccCCCCccCccccccchhHHHHHhcccchhhccccCCCCCCccccccCCceEEEEeCCCcC
Confidence            347899999 8999998887  4669999553      235679999998422236889887532             23


Q ss_pred             hhhhhhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         80 DLRDLERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        80 ~~~~~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ++.+++|++|++++|||+||||||++|.++++|.|++|.|+.|+...|.||||+||.+.+.|++.++++||++|||+
T Consensus       657 GKSTyir~~Gvi~lmAQIGcfVPce~A~i~IvD~Il~RVGA~D~q~kG~STFM~Emleta~Ilr~at~~SliiiDEL  733 (902)
T KOG0219|consen  657 GKSTYIRQVGVIVLMAQIGCFVPCESATISIVDGILTRVGAGDSQLKGISTFMAEMLETASILRRATKNSLIIIDEL  733 (902)
T ss_pred             ccchhhhhhhHHHHHHHhCCceehhhcCCchhhHHHhhhccchhhhcchHHHHHHHHHHHHHHHhcCCCcEEEEecc
Confidence            34444555555679999999999999999999999999999999999999999999999999999999999999996

>KOG0221|consensus

Probab=99.92  E-value=5e-26  Score=185.80  Aligned_cols=135  Identities=24%  Similarity=0.308  Sum_probs=118.1

Q ss_pred             ccccHHHHhhHhhhhHHHHHHHccccCCCCCHH-----HHHhhHHHHHHHhhchhhHHHHHHhhh----hhhhhhhhchh
Q psy13255         20 TEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLD-----AIKQRQDAISVLLDQKHITEQMRAKMK----DLRDLERMLPS   90 (156)
Q Consensus        20 ~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~-----~i~~Rhplv~~l~~~~~v~~~i~~~l~----~~~~~~n~~gk   90 (156)
                      +.-++...|| .+.++|..+..++|.+|....+     ++++|||+++... +.++||+....=.    .+.++||.+||
T Consensus       535 ~~l~laSrld-vLls~a~~aa~~gy~~P~lv~e~~il~I~ngrh~l~e~~~-dtfvPNst~iggdkgri~vITGpNasGK  612 (849)
T KOG0221|consen  535 RVLDLASRLD-VLLSLASAAADYGYSRPRLVPEVLILRIQNGRHPLMELCA-DTFVPNSTEIGGDKGRIKVITGPNASGK  612 (849)
T ss_pred             HHHHHHHHHH-HHHHHHHHHHhcCCCCCccccHHHHHHHHcCChhHHHHHH-HhcCCCceeecCCCceEEEEeCCCCCCc
Confidence            3447888999 8899999999999999988744     5689999998654 5689998753211    23567999999


Q ss_pred             H---------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         91 S---------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        91 ~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      +         ++|||+||||||++|+++++|+|||||+.-+++..++|||+.++.+++..+++||.+|||||||+
T Consensus       613 SiYlkqvglivfLahIGsFVPAe~A~IGivDrI~tri~s~esv~~gqSTFmiD~~Qva~aLr~AT~~SLvlIDEf  687 (849)
T KOG0221|consen  613 SIYLKQVGLIVFLAHIGSFVPAEEAEIGIVDRIFTRIHSCESVSLGQSTFMIDLNQVAKALRNATAQSLVLIDEF  687 (849)
T ss_pred             eEEEeechhhhHHHhhccccchhhhhcchHHHHHHHhhhhhhhhhhhhHHHHhHHHHHHHHHHhhcCcEEEEhhc
Confidence            7         68999999999999999999999999999999999999999999999999999999999999997

>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes

Probab=99.90  E-value=1.6e-25  Score=167.29  Aligned_cols=103  Identities=32%  Similarity=0.500  Sum_probs=90.0

Q ss_pred             HHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCCc
Q psy13255         54 IKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMGA  120 (156)
Q Consensus        54 i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~  120 (156)
                      .++|||+++....++++||++....++    .-+++|++||+         ++|||+|+||||+++.++++|+||++++.
T Consensus         3 ~~~rHPll~~~~~~~~v~ndi~l~~~~~~~~~itG~n~~gKs~~l~~i~~~~~la~~G~~vpa~~~~i~~~~~i~~~~~~   82 (218)
T cd03286           3 EELRHPCLNASTASSFVPNDVDLGATSPRILVLTGPNMGGKSTLLRTVCLAVIMAQMGMDVPAKSMRLSLVDRIFTRIGA   82 (218)
T ss_pred             ccccCCEEecccCCCeEEeeeEEeecCCcEEEEECCCCCchHHHHHHHHHHHHHHHcCCccCccccEeccccEEEEecCc
Confidence            468999997655567899998643221    23458999987         57999999999999999999999999999


Q ss_pred             cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      .|++..+.|||+.||.+++.|++.+++++||||||+
T Consensus        83 ~d~~~~~~StF~~e~~~~~~il~~~~~~sLvLlDE~  118 (218)
T cd03286          83 RDDIMKGESTFMVELSETANILRHATPDSLVILDEL  118 (218)
T ss_pred             ccccccCcchHHHHHHHHHHHHHhCCCCeEEEEecc
Confidence            999999999999999999999999999999999996

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

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=99.90  E-value=8.1e-25  Score=188.47  Aligned_cols=131  Identities=20%  Similarity=0.303  Sum_probs=114.5

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhH---
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSS---   91 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~---   91 (156)
                      ...++.|| |+.++++.+...+|++|.++.    .+.++|||+++.   ..++||++...-. +  +.++|||+||+   
T Consensus       269 ~~~l~~lD-~l~a~a~~a~~~~~~~P~~~~~~~i~l~~~rHPll~~---~~~Vpndi~l~~~~~~~iITGpN~gGKTt~l  344 (782)
T PRK00409        269 NKIFDELD-FIFARARYAKALKATFPLFNDEGKIDLRQARHPLLDG---EKVVPKDISLGFDKTVLVITGPNTGGKTVTL  344 (782)
T ss_pred             HHHHHHHH-HHHHHHHHHHHCCCccceEcCCCcEEEcCcCCceecc---CceECceeEECCCceEEEEECCCCCCcHHHH
Confidence            36899999 999999999999999999963    356899999853   4578999863211 1  34679999998   


Q ss_pred             ------HHHHhhCCCCCCCc-ccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 ------TFLSFQGCRVPADS-LTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ------~~laq~g~~vpa~~-~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                            ++|||+|+||||.+ +.+|+||+||+++|+.|++..+.|+|+.+|.++..|+..+++++|||+||+
T Consensus       345 ktigl~~~maq~G~~vpa~~~~~i~~~~~i~~~ig~~~si~~~lStfS~~m~~~~~Il~~~~~~sLvLlDE~  416 (782)
T PRK00409        345 KTLGLAALMAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKADKNSLVLFDEL  416 (782)
T ss_pred             HHHHHHHHHHHhCCCcccCCCccccccceEEEecCCccchhhchhHHHHHHHHHHHHHHhCCcCcEEEecCC
Confidence                  47999999999996 799999999999999999999999999999999999999999999999996

>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes

Probab=99.87  E-value=4.5e-24  Score=159.93  Aligned_cols=104  Identities=32%  Similarity=0.466  Sum_probs=90.1

Q ss_pred             HHHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCC
Q psy13255         53 AIKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMG  119 (156)
Q Consensus        53 ~i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~  119 (156)
                      +.++|||+++.....+++++++.....+    .-+++|++||+         ++|+|+|++|||+.++++++|+||++|+
T Consensus         3 i~~~rHPlle~~~~~~~v~n~i~~~~~~g~~~~itG~N~~GKStll~~i~~~~~la~~G~~v~a~~~~~~~~~~i~~~~~   82 (222)
T cd03287           3 IKEGRHPMIESLLDKSFVPNDIHLSAEGGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPASSATLSIFDSVLTRMG   82 (222)
T ss_pred             eecccCCEEeccCCCCEEEEeEEEEecCCcEEEEECCCCCCHHHHHHHHHHHHHHHhCCCEEEcCceEEeccceEEEEec
Confidence            3579999998765556788887543221    23459999998         4689999999999999999999999999


Q ss_pred             ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        120 AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       120 ~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      +.|++..+.|+|++||.+++.|++++++++|+|+||+
T Consensus        83 ~~d~~~~~~StF~~e~~~~~~il~~~~~~sLvllDE~  119 (222)
T cd03287          83 ASDSIQHGMSTFMVELSETSHILSNCTSRSLVILDEL  119 (222)
T ss_pred             CccccccccchHHHHHHHHHHHHHhCCCCeEEEEccC
Confidence            9999999999999999999999999999999999995

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

>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes

Probab=99.80  E-value=2.8e-21  Score=144.17  Aligned_cols=103  Identities=28%  Similarity=0.412  Sum_probs=88.7

Q ss_pred             HHHhhHHHHHHHhhchhhHHHHHHhhh--h--hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCC
Q psy13255         53 AIKQRQDAISVLLDQKHITEQMRAKMK--D--LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMG  119 (156)
Q Consensus        53 ~i~~Rhplv~~l~~~~~v~~~i~~~l~--~--~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~  119 (156)
                      +.++|||+++.. .+.+|||++...-.  +  .-+++|++||++         +|+|+|++|||..+.++++|++|++++
T Consensus         2 i~~~rHPll~~~-~~~~vpnd~~l~~~~~~~~~itGpNg~GKStlLk~i~~~~~la~~G~~v~a~~~~~~~~d~i~~~l~   80 (213)
T cd03281           2 IQGGRHPLLELF-VDSFVPNDTEIGGGGPSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPADSATIGLVDKIFTRMS   80 (213)
T ss_pred             cccccCCEEecc-CCceEcceEEecCCCceEEEEECCCCCChHHHHHHHHHHHHHHhCCCeeEcCCcEEeeeeeeeeeeC
Confidence            357899999852 34689999864311  1  235699999985         368999999999999999999999999


Q ss_pred             ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        120 AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       120 ~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ..|++..+.|+|+.||.+++.++..+++++|+|+||+
T Consensus        81 ~~~si~~~~S~f~~el~~l~~~l~~~~~~slvllDE~  117 (213)
T cd03281          81 SRESVSSGQSAFMIDLYQVSKALRLATRRSLVLIDEF  117 (213)
T ss_pred             CccChhhccchHHHHHHHHHHHHHhCCCCcEEEeccc
Confidence            9999999999999999999999999999999999996

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

>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes

Probab=99.79  E-value=8.8e-21  Score=140.63  Aligned_cols=102  Identities=26%  Similarity=0.381  Sum_probs=86.8

Q ss_pred             HHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCc
Q psy13255         54 IKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGA  120 (156)
Q Consensus        54 i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~  120 (156)
                      .++|||+++. ...+++++++......    .-+++|++||++         +|+|+|++|||.++.++++|+||++++.
T Consensus         3 ~~~~hpll~~-~~~~~v~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~~la~~G~~vpa~~~~l~~~d~I~~~~~~   81 (204)
T cd03282           3 RDSRHPILDR-DKKNFIPNDIYLTRGSSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFVPAEYATLPIFNRLLSRLSN   81 (204)
T ss_pred             ccccCCeEec-cCCcEEEeeeEEeeCCCcEEEEECCCCCCHHHHHHHHHHHHHHHHcCCCcchhhcCccChhheeEecCC
Confidence            4689999875 2345778887543221    124589999974         6899999999999999999999999999


Q ss_pred             cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      .|++..+.|+|+.||++++.+++.+++++|+|+||+
T Consensus        82 ~d~~~~~~S~fs~e~~~~~~il~~~~~~~lvllDE~  117 (204)
T cd03282          82 DDSMERNLSTFASEMSETAYILDYADGDSLVLIDEL  117 (204)
T ss_pred             ccccchhhhHHHHHHHHHHHHHHhcCCCcEEEeccc
Confidence            999999999999999999999999999999999995

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

>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes

Probab=99.77  E-value=3.1e-20  Score=139.40  Aligned_cols=103  Identities=29%  Similarity=0.420  Sum_probs=88.3

Q ss_pred             HHhhHHHHHHHhhchhhHHHHHHhhhh----hhhhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCCc
Q psy13255         54 IKQRQDAISVLLDQKHITEQMRAKMKD----LRDLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMGA  120 (156)
Q Consensus        54 i~~Rhplv~~l~~~~~v~~~i~~~l~~----~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~  120 (156)
                      .++|||+++......++++++.....+    .-+++|++||+         ++|||+|+||||+++.++++|+|+++++.
T Consensus         3 ~~~~hpll~~~~~~~~v~~~~~~~~~~~~~~~l~G~n~~GKstll~~i~~~~~la~~g~~vpa~~~~~~~~~~il~~~~l   82 (222)
T cd03285           3 KEARHPCVEAQDDVAFIPNDVTLTRGKSRFLIITGPNMGGKSTYIRQIGVIVLMAQIGCFVPCDSADIPIVDCILARVGA   82 (222)
T ss_pred             cccCCCEEeccCCCCeEEeeEEEeecCCeEEEEECCCCCChHHHHHHHHHHHHHHHhCCCcCcccEEEeccceeEeeecc
Confidence            468999998654456788888643211    23458999987         46899999999999999999999999999


Q ss_pred             cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      .|++..+.|+|+.||.+++.+++.+++++|+|+||+
T Consensus        83 ~d~~~~~lS~~~~e~~~~a~il~~~~~~sLvLLDEp  118 (222)
T cd03285          83 SDSQLKGVSTFMAEMLETAAILKSATENSLIIIDEL  118 (222)
T ss_pred             ccchhcCcChHHHHHHHHHHHHHhCCCCeEEEEecC
Confidence            999999999999999999999999999999999996

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

>TIGR01069 mutS2 MutS2 family protein

Probab=99.76  E-value=1.2e-19  Score=156.39  Aligned_cols=131  Identities=16%  Similarity=0.217  Sum_probs=112.1

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhHH--
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSST--   92 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~~--   92 (156)
                      ...++.|| ++.+.+..+....++.|.+..    ...++|||+++.   ..++|+++...-. .  ..++||++||++  
T Consensus       264 ~~~l~~lD-~l~a~a~~a~~~~~~~P~~~~~~~i~l~~~rhPll~~---~~~vp~di~l~~~~~~liItGpNg~GKSTlL  339 (771)
T TIGR01069       264 FKEFDFLD-SLQARARYAKAVKGEFPMPSFTGKIILENARHPLLKE---PKVVPFTLNLKFEKRVLAITGPNTGGKTVTL  339 (771)
T ss_pred             HHHHHHHH-HHHHHHHHHHHCCCeeceecCCCCEEEccccCceecC---CceEeceeEeCCCceEEEEECCCCCCchHHH
Confidence            36899999 999999999999999998753    356899999852   3478888863211 1  235699999984  


Q ss_pred             -------HHHhhCCCCCCCc-ccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         93 -------FLSFQGCRVPADS-LTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        93 -------~laq~g~~vpa~~-~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                             +|+|+|++|||.. +.+++||++|+++++.|++.++.|+|+.||.++..|+..+++++|||+||+
T Consensus       340 K~i~~~~l~aq~G~~Vpa~~~~~~~~~d~i~~~i~~~~si~~~LStfS~~m~~~~~il~~~~~~sLvLlDE~  411 (771)
T TIGR01069       340 KTLGLLALMFQSGIPIPANEHSEIPYFEEIFADIGDEQSIEQNLSTFSGHMKNISAILSKTTENSLVLFDEL  411 (771)
T ss_pred             HHHHHHHHHHHhCCCccCCccccccchhheeeecChHhHHhhhhhHHHHHHHHHHHHHHhcCCCcEEEecCC
Confidence                   5899999999987 689999999999999999999999999999999999999999999999996

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

>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes

Probab=99.75  E-value=8e-20  Score=136.63  Aligned_cols=104  Identities=34%  Similarity=0.518  Sum_probs=89.1

Q ss_pred             HHHhhHHHHHHHhh-chhhHHHHHHhhh-h--hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCC
Q psy13255         53 AIKQRQDAISVLLD-QKHITEQMRAKMK-D--LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMG  119 (156)
Q Consensus        53 ~i~~Rhplv~~l~~-~~~v~~~i~~~l~-~--~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~  119 (156)
                      +.++|||+++...+ ..+++|++....+ +  .-+++|++||++         +|+|+|+++||.++.+++++++|++++
T Consensus         2 i~~~~hp~~~~~~~~~~~v~n~~~l~~~~~~~~l~Gpn~sGKstllr~i~~~~~l~~~g~~vp~~~~~i~~~~~i~~~~~   81 (216)
T cd03284           2 IEGGRHPVVEQVLDNEPFVPNDTELDPERQILLITGPNMAGKSTYLRQVALIALLAQIGSFVPASKAEIGVVDRIFTRIG   81 (216)
T ss_pred             cccccCCEEeeccCCCceEeeeEEecCCceEEEEECCCCCChHHHHHHHHHHHHHhccCCeeccccceecceeeEeccCC
Confidence            34689999987654 5578888863322 1  234699999984         578999999999999999999999999


Q ss_pred             ccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        120 AKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       120 ~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ..|++..|.|+|+.||.+++.++..+++++|+|+||+
T Consensus        82 ~~~~ls~g~s~f~~e~~~l~~~l~~~~~~~llllDEp  118 (216)
T cd03284          82 ASDDLAGGRSTFMVEMVETANILNNATERSLVLLDEI  118 (216)
T ss_pred             chhhhccCcchHHHHHHHHHHHHHhCCCCeEEEEecC
Confidence            9999999999999999999999999999999999995

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

>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family

Probab=99.67  E-value=8.2e-17  Score=117.63  Aligned_cols=74  Identities=41%  Similarity=0.589  Sum_probs=69.5

Q ss_pred             hhhhhchhH---------HHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEe
Q psy13255         83 DLERMLPSS---------TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALV  153 (156)
Q Consensus        83 ~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvli  153 (156)
                      +++|++||+         ++|||+|++|||+++.++++|++|++++..|++..+.|+|+.||.+++.++..+++++|+|+
T Consensus         5 tG~N~~GKst~l~~i~~~~~la~~G~~v~a~~~~~~~~d~il~~~~~~d~~~~~~s~fs~~~~~l~~~l~~~~~~~llll   84 (185)
T smart00534        5 TGPNMGGKSTYLRQVGLIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLSTFMVEMKETANILKNATENSLVLL   84 (185)
T ss_pred             ECCCCCcHHHHHHHHHHHHHHHHhCCCeeehheEecccceEEEEeCCCCchhccccHHHHHHHHHHHHHHhCCCCeEEEE
Confidence            467888887         46899999999999999999999999999999999999999999999999999999999999


Q ss_pred             ccC
Q psy13255        154 DEL  156 (156)
Q Consensus       154 DE~  156 (156)
                      ||+
T Consensus        85 DEp   87 (185)
T smart00534       85 DEL   87 (185)
T ss_pred             ecC
Confidence            995

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

Probab=99.66  E-value=3.9e-18  Score=145.65  Aligned_cols=127  Identities=20%  Similarity=0.259  Sum_probs=108.4

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCC----HHHHHhhHHHHHHHhhchhhHHHHHHhh---hhhhhhhhhchhH---
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTN----LDAIKQRQDAISVLLDQKHITEQMRAKM---KDLRDLERMLPSS---   91 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~----~~~i~~Rhplv~~l~~~~~v~~~i~~~l---~~~~~~~n~~gk~---   91 (156)
                      ...++.+| ++.+..+.+.......|.++    .+..++|||++..-     +++++....   .-+.++||++||+   
T Consensus       261 ~~~~~~lD-~i~Ak~~~~~~~~~v~P~~~~~~~l~l~~~~HPll~~~-----v~~~i~~~~e~~~l~ITGpN~GGKtvtL  334 (753)
T COG1193         261 LEIIGELD-FIEAKVRYAKALKGVKPDFSNDGVLELLDARHPLLKED-----VPNDLELGEELDRLIITGPNTGGKTVTL  334 (753)
T ss_pred             HHHhhhhH-HHHHHHHHHHhhccCCCccCCCceEEeccccCccCccc-----cccccccccccceeeEecCCCCcceehH
Confidence            36889999 89999999999889999998    34678999998742     555554321   2345789999997   


Q ss_pred             ------HHHHhhCCCCCCCcc-cccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         92 ------TFLSFQGCRVPADSL-TLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        92 ------~~laq~g~~vpa~~~-~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                            ++|+|.|.++||.+. .+++|+++|..||+.|++++++|||+.+|..+++|+..++  ||+++||+
T Consensus       335 KTlgl~~lm~q~gl~i~a~~gsei~~F~~i~aDIGDeQsIeqsLSTFSshm~~i~~il~~~d--sLvl~DEl  404 (753)
T COG1193         335 KTLGLLRLMAQSGLPIPALEGSELPVFVKIFADIGDEQSIEQSLSTFSSHMTNIVEILEKAD--SLVLFDEL  404 (753)
T ss_pred             HHHHHHHHHHHcCCCeeccCCCcchhHHHhhhccCcHHHHHHHHhhhHHHHHHHHHHHhhcc--hhHHHHHh
Confidence                  589999999999986 8999999999999999999999999999999999996666  99999996

>TIGR01070 mutS1 DNA mismatch repair protein MutS

Probab=99.59  E-value=2.8e-15  Score=130.53  Aligned_cols=91  Identities=32%  Similarity=0.511  Sum_probs=84.0

Q ss_pred             CCCHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhh
Q psy13255          1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD   80 (156)
Q Consensus         1 ~id~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~   80 (156)
                      .||.+|++||||+++..+++++||++.+|+|.|++|+|+++.|+++|+.+.+.|+.||.+|+++..+......++..+++
T Consensus       250 ~lD~~t~~~LEl~~~~~~~~~gSL~~~ld~t~T~~G~RlLr~wl~~Pl~d~~~I~~Rld~Ve~l~~~~~l~~~l~~~L~~  329 (840)
T TIGR01070       250 QLDAATRRNLELTENLRGGKQNTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDTVEVLLRHFFLREGLRPLLKE  329 (840)
T ss_pred             EeCHHHHHhccCCccCCCCCCCcHHHHHhhcCCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHhCHHHHHHHHHHhcc
Confidence            48999999999998876667899999999999999999999999999999999999999999999887788889888999


Q ss_pred             hhhhhhhchhH
Q psy13255         81 LRDLERMLPSS   91 (156)
Q Consensus        81 ~~~~~n~~gk~   91 (156)
                      ++|++++.+|.
T Consensus       330 i~Dlerll~ri  340 (840)
T TIGR01070       330 VGDLERLAARV  340 (840)
T ss_pred             CcCHHHHHHHH
Confidence            99998888764

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

Probab=99.57  E-value=3.1e-16  Score=115.95  Aligned_cols=103  Identities=37%  Similarity=0.510  Sum_probs=87.5

Q ss_pred             HHhhHHHHHHH-hhchhhHHHHHHhhhh--hhhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCcc
Q psy13255         54 IKQRQDAISVL-LDQKHITEQMRAKMKD--LRDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGAK  121 (156)
Q Consensus        54 i~~Rhplv~~l-~~~~~v~~~i~~~l~~--~~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~~  121 (156)
                      .++|||+++.. ...+++|+++...-++  .-+++|++||++         +++|.|+++|+.++.++++|++|+.++..
T Consensus         3 ~~~~~p~l~~~~~~~~~~~~~~~l~~~~~~~l~G~Ng~GKStll~~i~~~~~~~~~g~~~~~~~~~i~~~dqi~~~~~~~   82 (202)
T cd03243           3 KGGRHPVLLALTKGETFVPNDINLGSGRLLLITGPNMGGKSTYLRSIGLAVLLAQIGCFVPAESASIPLVDRIFTRIGAE   82 (202)
T ss_pred             ccccCCEEeccccCCceEeeeEEEcCCeEEEEECCCCCccHHHHHHHHHHHHHHHcCCCccccccccCCcCEEEEEecCc
Confidence            46899999865 2345789988643111  234699999984         45789999999999999999999999999


Q ss_pred             ccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        122 DNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       122 d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      +++..+.|+|..|++++..++..+.+.+++|+||.
T Consensus        83 d~i~~~~s~~~~e~~~l~~i~~~~~~~~llllDEp  117 (202)
T cd03243          83 DSISDGRSTFMAELLELKEILSLATPRSLVLIDEL  117 (202)
T ss_pred             ccccCCceeHHHHHHHHHHHHHhccCCeEEEEecC
Confidence            99999999999999999999999999999999995

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

>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes

Probab=99.57  E-value=3.8e-16  Score=115.37  Aligned_cols=102  Identities=20%  Similarity=0.327  Sum_probs=84.9

Q ss_pred             HHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhHH---------HHHhhCCCCCCCc-ccccccceeeccCCc
Q psy13255         54 IKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSST---------FLSFQGCRVPADS-LTLTPVDRIFTRMGA  120 (156)
Q Consensus        54 i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~~---------~laq~g~~vpa~~-~~l~~~d~i~~~~~~  120 (156)
                      .++|||+++.. ...++++++...-. +  .-++||++||++         +++|+|++||+.+ ..++++|++|++++.
T Consensus         3 ~~~~hp~~~~~-~~~~~~~~~~i~~~~~~~~ltG~Ng~GKStll~~i~~~~~~~~~G~~vp~~~~~~~~~~~~~~~~lg~   81 (200)
T cd03280           3 REARHPLLPLQ-GEKVVPLDIQLGENKRVLVITGPNAGGKTVTLKTLGLLTLMAQSGLPIPAAEGSSLPVFENIFADIGD   81 (200)
T ss_pred             cccCCCEEecc-CCceEcceEEECCCceEEEEECCCCCChHHHHHHHHHHHHHHHcCCCccccccccCcCccEEEEecCc
Confidence            46899999853 44577888764321 1  134699999984         4678899999986 679999999999999


Q ss_pred             cccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        121 KDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       121 ~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      .+++..+.|+|+.+|++...++..+++.+++++||.
T Consensus        82 ~~~l~~~~s~fs~g~~~~~~i~~~~~~p~llllDEp  117 (200)
T cd03280          82 EQSIEQSLSTFSSHMKNIARILQHADPDSLVLLDEL  117 (200)
T ss_pred             hhhhhcCcchHHHHHHHHHHHHHhCCCCcEEEEcCC
Confidence            999999999999999999999999999999999995

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

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

Probab=99.53  E-value=1.2e-14  Score=126.11  Aligned_cols=91  Identities=34%  Similarity=0.577  Sum_probs=84.5

Q ss_pred             CCCHHHHhhccccccCCC-CccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhh
Q psy13255          1 ILDSTALANLHVLTNSDN-TTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMK   79 (156)
Q Consensus         1 ~id~~t~~~Lei~~~~~~-~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~   79 (156)
                      .||.+|.+||||+++..+ +++|+|++.||+|.|++|+|++++|+.+|+.+.+.|+.||++|+.+..+......++..|+
T Consensus       261 ~lD~~t~~nLEl~~~~~~~~~~gSL~~~ld~t~T~mG~RlL~~wl~~PL~~~~~I~~Rld~Ve~l~~~~~l~~~L~~~L~  340 (843)
T COG0249         261 VLDAATRRNLELFSNLRGNGKKGSLFWLLDRTVTPMGSRLLKRWLLQPLLDKEEIEERLDAVEELKDNPELREKLREMLK  340 (843)
T ss_pred             EEcHHHHhcccccccCCCCCCCCcHHHHhccCCCchhHHHHHHHhhCcccCHHHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence            489999999999988654 7888999999999999999999999999999999999999999999988778888988899


Q ss_pred             hhhhhhhhchhH
Q psy13255         80 DLRDLERMLPSS   91 (156)
Q Consensus        80 ~~~~~~n~~gk~   91 (156)
                      +++|++|..++.
T Consensus       341 ~v~DleRl~~Rl  352 (843)
T COG0249         341 KVPDLERLLSRL  352 (843)
T ss_pred             cCcCHHHHHHHH
Confidence            999999998875

>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes

Probab=99.52  E-value=1.9e-15  Score=111.68  Aligned_cols=99  Identities=27%  Similarity=0.320  Sum_probs=84.4

Q ss_pred             HHhhHHHHHHHhhchhhHHHHHHhhhhh--hhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCccc
Q psy13255         54 IKQRQDAISVLLDQKHITEQMRAKMKDL--RDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGAKD  122 (156)
Q Consensus        54 i~~Rhplv~~l~~~~~v~~~i~~~l~~~--~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~~d  122 (156)
                      .++|||+++   ++++++|++...-+++  -++||++|||+         +++|.|++|||..+.++ .+.+|.++...|
T Consensus         3 ~~~~hp~~~---~~~~v~n~i~l~~g~~~~ltGpNg~GKSTllr~i~~~~~l~~~G~~v~a~~~~~q-~~~l~~~~~~~d   78 (199)
T cd03283           3 KNLGHPLIG---REKRVANDIDMEKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCASSFELP-PVKIFTSIRVSD   78 (199)
T ss_pred             cccCCCeec---CCCeecceEEEcCCcEEEEECCCCCChHHHHHHHHHHHHHHHcCCEEecCccCcc-cceEEEeccchh
Confidence            468999987   4567888886432222  34699999985         45899999999999998 799999999999


Q ss_pred             cccCCcCcHHHHHHHHHHHHHhcC--CCceEEeccC
Q psy13255        123 NLSGAQSTYLAELTESETIMRHAS--KYSLALVDEL  156 (156)
Q Consensus       123 ~l~~~~S~F~~e~~~~~~il~~~~--~~slvliDE~  156 (156)
                      ++..+.|+|..|+.++..+++.++  +.+++|+||.
T Consensus        79 ~l~~~~s~~~~e~~~~~~iL~~~~~~~p~llllDEp  114 (199)
T cd03283          79 DLRDGISYFYAELRRLKEIVEKAKKGEPVLFLLDEI  114 (199)
T ss_pred             ccccccChHHHHHHHHHHHHHhccCCCCeEEEEecc
Confidence            999999999999999999999999  8899999994

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

>PF05192 MutS_III: MutS domain III C-terminus

Probab=99.52  E-value=3.4e-14  Score=104.41  Aligned_cols=88  Identities=34%  Similarity=0.657  Sum_probs=72.1

Q ss_pred             HHHHhhccccccC-CCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhhhh
Q psy13255          4 STALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLR   82 (156)
Q Consensus         4 ~~t~~~Lei~~~~-~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~~   82 (156)
                      ++|+++|||+++. ++++.++|++.+|+|.|+.|+++++.|+.+|+.+.+.|+.||..|+++..++.+..++...+++++
T Consensus         1 ~~Tl~~L~i~~~~~~~~~~~sL~~~ln~t~T~~Gkr~L~~~l~~P~~d~~~I~~R~~~v~~~~~n~~~~~~~~~~l~~~~   80 (204)
T PF05192_consen    1 ANTLKSLEIFENSRSGKKKGSLFSLLNRTSTPMGKRLLRSWLLQPLTDIEEIEKRQDAVEEFLQNEELREELRSILKKIP   80 (204)
T ss_dssp             HHHHHHTTSSSBTTTSSSSTSHHHHH---SSHHHHHHHHHHHHS-BS-HHHHHHHHHHHHHHHHTHHHHHHHHHHHTTC-
T ss_pred             ChhHHhccCCCCCCCCCCCCcHHHHHhcCCChHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHhhhHhhhhhhhhhccc
Confidence            5899999999775 667788999999999999999999999999999999999999999999987777788887788888


Q ss_pred             hhhhhchhH
Q psy13255         83 DLERMLPSS   91 (156)
Q Consensus        83 ~~~n~~gk~   91 (156)
                      |+.+...+.
T Consensus        81 di~~~l~~l   89 (204)
T PF05192_consen   81 DIERILKRL   89 (204)
T ss_dssp             SHHHHHHHH
T ss_pred             hHHHHHHHH
Confidence            877666653

; InterPro: IPR007696 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 core domain (domain 3) found in proteins of the MutS family. The core domain of MutS adopts a multi-helical structure comprised of two subdomains, which are interrupted by the clamp domain. Two of the helices in the core domain comprise the levers that extend towards the DNA. This domain is found associated with Pfam:PF00488, Pfam:PF05188, Pfam:PF01624 and Pfam:PF05190. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in [].; 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 1FW6_A ....

>KOG0218|consensus

Probab=99.34  E-value=7.8e-13  Score=110.86  Aligned_cols=90  Identities=36%  Similarity=0.540  Sum_probs=79.0

Q ss_pred             CCHHHHhhccccccC-CCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhh---chhhHHHHHHh
Q psy13255          2 LDSTALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD---QKHITEQMRAK   77 (156)
Q Consensus         2 id~~t~~~Lei~~~~-~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~---~~~v~~~i~~~   77 (156)
                      |+++|+++|||++|+ +++.+|+||+.||++.|++|.|+++.|+.+|+.+.+.|++|.++|+++..   ++.+...+...
T Consensus       460 ls~ntLq~Leif~nqtd~~~kGSLfwvldhT~TsfG~RmLr~WvtkPLvd~~~I~eRLDAVeeitshssnS~vf~si~~~  539 (1070)
T KOG0218|consen  460 LSPNTLQSLEIFTNQTDGSEKGSLFWVLDHTRTSFGLRMLREWVTKPLVDVHQIEERLDAVEEITSHSSNSIVFESINQM  539 (1070)
T ss_pred             echhhhhceeeeeecCCCCcccceEEEeccchhHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHhcccchHHHHHHHHH
Confidence            689999999999885 66778999999999999999999999999999999999999999999833   34478888888


Q ss_pred             hhhhhhhhhhchhH
Q psy13255         78 MKDLRDLERMLPSS   91 (156)
Q Consensus        78 l~~~~~~~n~~gk~   91 (156)
                      |.+.+|+.|.+.++
T Consensus       540 l~rlpDl~rgL~rI  553 (1070)
T KOG0218|consen  540 LNRLPDLLRGLNRI  553 (1070)
T ss_pred             HHhCcHhHhhHHHH
Confidence            89999987776553

>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family

Probab=98.95  E-value=9.9e-10  Score=85.62  Aligned_cols=71  Identities=38%  Similarity=0.684  Sum_probs=62.8

Q ss_pred             cccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhhhhhhhhhchhH
Q psy13255         21 EGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSS   91 (156)
Q Consensus        21 ~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~~~~~n~~gk~   91 (156)
                      ++||++.||+|.|++|+|.++.|+++|+.+.+.|+.|+..|+++..++.+...++..+++++|++++..|.
T Consensus         1 ~~sL~~~l~~~~T~~G~r~L~~wl~~Pl~~~~~I~~R~~~v~~~~~~~~l~~~l~~~L~~~~Di~~~l~~~   71 (308)
T smart00533        1 KGSLFELLNHTKTPMGKRLLRRWLLQPLLDLKEINERLDAVEELVENPELRQKLRQLLKRIPDLERLLSRI   71 (308)
T ss_pred             CCCHHHHHccCCCcHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHhChHHHHHHHHHHccCCcHHHHHHHH
Confidence            36899999999999999999999999999999999999999999987777777777788888887666653

>KOG0221|consensus

Probab=98.88  E-value=9.9e-10  Score=91.18  Aligned_cols=141  Identities=16%  Similarity=0.284  Sum_probs=92.0

Q ss_pred             CCHHHHhhccccccCCC---C----cc-ccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhh--chhhH
Q psy13255          2 LDSTALANLHVLTNSDN---T----TE-GTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLD--QKHIT   71 (156)
Q Consensus         2 id~~t~~~Lei~~~~~~---~----~~-~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~--~~~v~   71 (156)
                      ||.+|+.+|.||++...   .    +. -|+|+.+|+|.+..|++.++.|+.+|+.+...+..|+.++..++.  |..+.
T Consensus       239 iD~nTisaL~Ifp~e~~~~~~k~~~~~g~Slf~l~n~c~s~~g~k~Lr~Wf~nPttd~~~l~sR~~~i~~fl~~qNa~~~  318 (849)
T KOG0221|consen  239 IDQNTISALQIFPSESHPSKVKSGLKEGLSLFGLLNRCHSKWGEKLLRLWFTNPTTDLGELSSRLDVIQFFLLPQNADMA  318 (849)
T ss_pred             eccchHHHHHhcccccccchhhhhhhcchhHHHHHHHHhhHHHHHHHHHHhcCCCCcHHHHHHHHHHHHHHhcchhhHHH
Confidence            79999999999987432   1    22 299999999999999999999999999999999999999998876  44577


Q ss_pred             HHHHHhhhhhhhhhhh-----chhHHHHHhhCCCCCCCcccccccceeeccCCcccccc-CCcCcHHHHHHHHHHHHHh
Q psy13255         72 EQMRAKMKDLRDLERM-----LPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLS-GAQSTYLAELTESETIMRH  144 (156)
Q Consensus        72 ~~i~~~l~~~~~~~n~-----~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~-~~~S~F~~e~~~~~~il~~  144 (156)
                      ..+...++++++.+-.     +|++ -+.+.-+++..-++.+++++ +..+....-.+. .-.+-|..++.+++++...
T Consensus       319 ~~Ls~~lgr~k~~~~~~~~~~sg~t-~l~~W~~~~stv~~~~~i~~-~~rslp~s~~~~~~~~~~~~~~l~eia~~~g~  395 (849)
T KOG0221|consen  319 QMLSRLLGRIKNVPLILKRMKSGHT-KLSDWQVLYSTVYSALGIRD-ACRSLPQSIQLFRDIAQEFSDDLHEIASLIGK  395 (849)
T ss_pred             HHHHHHHhhcccHHHHHHHHhcCCc-eechHHHHHHHHHHHHHHHH-HHHhCccchhhhhHHHHHHHHHHHHHHHHhhh
Confidence            7777667776654322     2222 11222222222233333433 211111111111 1245677888888877655

>KOG0219|consensus

Probab=98.37  E-value=5e-07  Score=77.36  Aligned_cols=89  Identities=30%  Similarity=0.558  Sum_probs=70.9

Q ss_pred             CCHHHHhhccccccCCCC--ccccHHH-HhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHH-h
Q psy13255          2 LDSTALANLHVLTNSDNT--TEGTLIE-QLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRA-K   77 (156)
Q Consensus         2 id~~t~~~Lei~~~~~~~--~~~sl~~-~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~-~   77 (156)
                      +|..|.++|++|+...+.  +..+|.. .||+|.|..|.|.+..|+.+|+.+.+.++.||++|+.+..+......++. .
T Consensus       290 ld~~av~alnlf~~~~~~~~~s~~L~~~~LN~c~t~~G~rll~~w~~qpL~~~~ri~~r~d~v~~l~~~~~~rq~L~~~l  369 (902)
T KOG0219|consen  290 LDSAAVRALNLFPLPYNNPEKSNNLALSLLNHCKTLQGERLLRQWLKQPLRDIDRINERHDLVEALVEDAEIRQKLRDDL  369 (902)
T ss_pred             HHHHHHHHHhhcCCCCCCccccchhhHHHHhhcccccchhhhhhhhhcchHHHHHHHHHhhhHHHHHhhhHHHHHHHHHH
Confidence            689999999999876443  3335666 89999999999999999999999999999999999998887655555543 3


Q ss_pred             hhhhhhhhhhchh
Q psy13255         78 MKDLRDLERMLPS   90 (156)
Q Consensus        78 l~~~~~~~n~~gk   90 (156)
                      +..++++.+..-+
T Consensus       370 L~~~pdi~rl~~~  382 (902)
T KOG0219|consen  370 LRRIPDISRLARR  382 (902)
T ss_pred             hhcChhHHHhhhh
Confidence            4566676555554

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

Probab=98.29  E-value=7.8e-07  Score=63.54  Aligned_cols=62  Identities=34%  Similarity=0.280  Sum_probs=50.8

Q ss_pred             hhhhhhchhHHH---------HHh----------hCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHH
Q psy13255         82 RDLERMLPSSTF---------LSF----------QGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIM  142 (156)
Q Consensus        82 ~~~~n~~gk~~~---------laq----------~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il  142 (156)
                      .+++|++||+++         +++          .|+++|+.++.+     +|++++        +|....++..+++++
T Consensus        26 i~G~NgsGKS~~l~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~-----i~~~~~--------lS~G~~~~~~la~~L   92 (162)
T cd03227          26 ITGPNGSGKSTILDAIGLALGGAQSATRRRSGVKAGCIVAAVSAEL-----IFTRLQ--------LSGGEKELSALALIL   92 (162)
T ss_pred             EECCCCCCHHHHHHHHHHHHHhcchhhhccCcccCCCcceeeEEEE-----ehheee--------ccccHHHHHHHHHHH
Confidence            356999999854         466          899999888766     666554        788899999999999


Q ss_pred             HhcC--CCceEEeccC
Q psy13255        143 RHAS--KYSLALVDEL  156 (156)
Q Consensus       143 ~~~~--~~slvliDE~  156 (156)
                      ..++  +.+++|+||+
T Consensus        93 ~~~~~~~~~llllDEp  108 (162)
T cd03227          93 ALASLKPRPLYILDEI  108 (162)
T ss_pred             HhcCCCCCCEEEEeCC
Confidence            9865  7899999995

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

>KOG0220|consensus

Probab=97.96  E-value=2.9e-06  Score=72.02  Aligned_cols=85  Identities=29%  Similarity=0.473  Sum_probs=73.4

Q ss_pred             CCCHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhh
Q psy13255          1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD   80 (156)
Q Consensus         1 ~id~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~   80 (156)
                      .||..+..+||++.+.+.+...++++.+|++.++.|+|.++....+|+.+...++.|..+++++..++.....++..+++
T Consensus       260 ~id~~~~~~lelV~~~~~kn~~~l~~vl~~T~t~~g~r~lRssilqpl~d~~ti~~rleaiqeL~a~~~L~~~Lr~~~k~  339 (867)
T KOG0220|consen  260 MIDSSSAQSLELVINNQYKNNHTLFGVLNYTKTPGGYRRLRSSILQPLTDIETINMRLEAIQELLADEELFFGLRSVIKR  339 (867)
T ss_pred             eeecccccceEEechhhhhcccceeeeeeeeecccchhhHHhhhcccccchhhhhHHHHHHHHHhcCchHhhhhHHHHhh
Confidence            47899999999998877766789999999999999999999999999999999999999999998887666666655665


Q ss_pred             hhhhh
Q psy13255         81 LRDLE   85 (156)
Q Consensus        81 ~~~~~   85 (156)
                      ..+..
T Consensus       340 ~~dld  344 (867)
T KOG0220|consen  340 FLDLD  344 (867)
T ss_pred             hhhHH
Confidence            55543

>PRK05399 DNA mismatch repair protein MutS; Provisional

Probab=97.03  E-value=3.2e-05  Score=68.48  Aligned_cols=101  Identities=17%  Similarity=0.179  Sum_probs=72.4

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHh-hchhhHHHHHHhhh---hhhhhhhhchhHHH
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLL-DQKHITEQMRAKMK---DLRDLERMLPSSTF   93 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~-~~~~v~~~i~~~l~---~~~~~~n~~gk~~~   93 (156)
                      ...++.|| |+.+++..+...+|++|.+..    ++.++|||+++..+ ...++|||+...-.   -+.++|||+||+++
T Consensus       545 ~~~la~lD-~l~s~A~~a~~~~~~~P~~~~~~~l~i~~~rHP~le~~~~~~~~vpnd~~l~~~~~~~iiTGpN~~GKSt~  623 (854)
T PRK05399        545 AKALAELD-VLASLAEVAEENNYVRPEFTDDPGIDIEEGRHPVVEQVLGGEPFVPNDCDLDEERRLLLITGPNMAGKSTY  623 (854)
T ss_pred             HHHHHHHH-HHHHHHHHHHHCCccccEEeCCCCEEEEeccCcEEecccCCCceEecceeeCCCCcEEEEECCCCCCcHHH
Confidence            36899999 999999999999999999863    35689999998653 35689999974311   13467999999999


Q ss_pred             HHhhCCCCCCCcccccc-cceeeccCCcccccc
Q psy13255         94 LSFQGCRVPADSLTLTP-VDRIFTRMGAKDNLS  125 (156)
Q Consensus        94 laq~g~~vpa~~~~l~~-~d~i~~~~~~~d~l~  125 (156)
                      |.|+|..|--.  +++. +..-.+.++.-|.+.
T Consensus       624 lr~v~l~~ilA--q~G~~VPa~~a~i~~~d~I~  654 (854)
T PRK05399        624 MRQVALIVLLA--QIGSFVPAESARIGIVDRIF  654 (854)
T ss_pred             HHHHHHHHHHH--hcCCceeccceEecccCeee
Confidence            99998775322  2222 222235555556553

>smart00533 MUTSd DNA-binding domain of DNA mismatch repair MUTS family

Probab=96.65  E-value=0.00038  Score=54.20  Aligned_cols=40  Identities=15%  Similarity=0.215  Sum_probs=35.3

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHH
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAIS   62 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~   62 (156)
                      ...++.|| |+.++|..+...+|++|.++.    .+.++|||+++
T Consensus       263 ~~~i~~lD-~l~s~a~~a~~~~~~~P~i~~~~~l~i~~~rHPlle  306 (308)
T smart00533      263 AEALAELD-VLLSLATLAAEGNYVRPEFVDSGELEIKNGRHPVLE  306 (308)
T ss_pred             HHHHHHHH-HHHHHHHHHHHCCCcCCeeCCCCCEEEeeCCCCccc
Confidence            37899999 999999999999999999863    36789999986

>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed

Probab=87.48  E-value=0.99  Score=40.19  Aligned_cols=41  Identities=17%  Similarity=0.331  Sum_probs=33.8

Q ss_pred             cHHHHh-hHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHh
Q psy13255         23 TLIEQL-DHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLL   65 (156)
Q Consensus        23 sl~~~L-D~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~   65 (156)
                      .+...| |.|.|++|++++..  ..|..+.+.++.|+..++++.
T Consensus        13 ~i~~~l~~~~~t~~Gk~~l~~--l~P~~~~~~i~~~l~~~~e~~   54 (782)
T PRK00409         13 KIKEQLKTFAASELGKEKVLQ--LDPETDFEEVEELLEETDEAA   54 (782)
T ss_pred             HHHHHHHhHcCCHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHH
Confidence            344444 56999999999998  589999999999999988764

>PF13173 AAA_14: AAA domain

Probab=87.05  E-value=0.36  Score=32.69  Aligned_cols=19  Identities=16%  Similarity=0.032  Sum_probs=14.8

Q ss_pred             hhhhhchhHHHHHhhCCCC
Q psy13255         83 DLERMLPSSTFLSFQGCRV  101 (156)
Q Consensus        83 ~~~n~~gk~~~laq~g~~v  101 (156)
                      .+++.+||++++.|+....
T Consensus         8 ~G~R~vGKTtll~~~~~~~   26 (128)
T PF13173_consen    8 TGPRGVGKTTLLKQLAKDL   26 (128)
T ss_pred             ECCCCCCHHHHHHHHHHHh
Confidence            4589999999998876443

>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids

Probab=84.01  E-value=4  Score=29.52  Aligned_cols=67  Identities=7%  Similarity=-0.143  Sum_probs=38.1

Q ss_pred             hhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ++|-+||++++.-+....+..+-.+.+-..-...+  .+..  .+|.=......+++.+  +.+..++++||-
T Consensus        32 G~nGsGKSTLl~~l~Gl~~p~~G~i~~~g~~i~~~--~q~~--~LSgGq~qrv~laral--~~~p~lllLDEP   98 (177)
T cd03222          32 GPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYK--PQYI--DLSGGELQRVAIAAAL--LRNATFYLFDEP   98 (177)
T ss_pred             CCCCChHHHHHHHHHcCCCCCCcEEEECCEEEEEE--cccC--CCCHHHHHHHHHHHHH--hcCCCEEEEECC
Confidence            48999999988766555555554444322111111  1111  1666555555554444  356699999993

RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.

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

Probab=83.16  E-value=1.3  Score=36.33  Aligned_cols=22  Identities=14%  Similarity=-0.005  Sum_probs=15.7

Q ss_pred             hhhhhchhHHHHHhhCCCCCCC
Q psy13255         83 DLERMLPSSTFLSFQGCRVPAD  104 (156)
Q Consensus        83 ~~~n~~gk~~~laq~g~~vpa~  104 (156)
                      .+||.+||++++.+.....+..
T Consensus        43 ~GpR~~GKTtll~~l~~~~~~~   64 (398)
T COG1373          43 LGPRQVGKTTLLKLLIKGLLEE   64 (398)
T ss_pred             ECCccccHHHHHHHHHhhCCcc
Confidence            3599999999986655554433

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

Probab=80.37  E-value=2.8  Score=29.55  Aligned_cols=71  Identities=17%  Similarity=0.004  Sum_probs=35.9

Q ss_pred             hhhhchhHHHHHhhCCCCCCCcccccccceeeccCCccccccC------CcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         84 LERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSG------AQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        84 ~~n~~gk~~~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~------~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ++|-+||++++.-+....|..+-.+-+-+.-.......+....      .+|.=.  .+++.-...-+.+..++|+||-
T Consensus        33 G~nGsGKSTLl~~i~G~~~~~~G~v~~~g~~~~~~~~~~~~~~~i~~~~qLS~G~--~qrl~laral~~~p~illlDEP  109 (163)
T cd03216          33 GENGAGKSTLMKILSGLYKPDSGEILVDGKEVSFASPRDARRAGIAMVYQLSVGE--RQMVEIARALARNARLLILDEP  109 (163)
T ss_pred             CCCCCCHHHHHHHHhCCCCCCCeEEEECCEECCcCCHHHHHhcCeEEEEecCHHH--HHHHHHHHHHhcCCCEEEEECC
Confidence            4899999999887765665555443322211111100000000      144333  3333333333567799999993

The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis. Pentoses include xylose, arabinose, and ribose. Important hexoses include glucose, galactose, and fructose. In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains. However, it is assumed that two copies of the ABC domains are present in the assembled transporter.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	156
2o8b_B	1022	Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T M		3e-14
1wb9_A	800	Crystal Structure Of E. Coli Dna Mismatch Repair En		3e-13
1ng9_A	800	E.Coli Muts R697a: An Atpase-Asymmetry Mutant Lengt		3e-13
1wbd_A	800	Crystal Structure Of E. Coli Dna Mismatch Repair En		3e-13
1wbb_A	800	Crystal Structure Of E. Coli Dna Mismatch Repair En		3e-13
1oh5_A	800	The Crystal Structure Of E. Coli Muts Binding To Dn		3e-13
3k0s_A	799	Crystal Structure Of E.Coli Dna Mismatch Repair Pro		1e-12
1e3m_A	800	The Crystal Structure Of E. Coli Muts Binding To Dn		5e-12
3thw_B	918	Human Mutsbeta Complexed With An Idl Of 4 Bases (Lo		1e-10
2o8e_A	934	Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR,		2e-08
2o8b_A	934	Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T M		2e-08
1nne_A	765	Crystal Structure Of The Muts-adpbef3-dna Complex L		7e-08
1fw6_A	768	Crystal Structure Of A Taq Muts-Dna-Adp Ternary Com		3e-07
1ewq_A	765	Crystal Structure Taq Muts Complexed With A Heterod		3e-07
1ewr_A	649	Crystal Structure Of Taq Muts Length = 649		3e-07

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

Iteration: 1
 Score = 74.3 bits (181), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 31/59 (52%), Positives = 44/59 (74%)
Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct: 819 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 877

>pdb|1WB9|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme Muts, E38t Mutant, In Complex With A G.T Mismatch Length = 800

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L
Sbjct: 632 LMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVL 691
Query: 153 VDEL 156
           +DE+
Sbjct: 692 MDEI 695

>pdb|1NG9|A Chain A, E.Coli Muts R697a: An Atpase-Asymmetry Mutant Length = 800

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L
Sbjct: 632 LMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVL 691
Query: 153 VDEL 156
           +DE+
Sbjct: 692 MDEI 695

>pdb|1WBD|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme Muts, E38q Mutant, In Complex With A G.T Mismatch Length = 800

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L
Sbjct: 632 LMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVL 691
Query: 153 VDEL 156
           +DE+
Sbjct: 692 MDEI 695

>pdb|1WBB|A Chain A, Crystal Structure Of E. Coli Dna Mismatch Repair Enzyme Muts, E38a Mutant, In Complex With A G.T Mismatch Length = 800

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L
Sbjct: 632 LMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVL 691
Query: 153 VDEL 156
           +DE+
Sbjct: 692 MDEI 695

>pdb|1OH5|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With A C:a Mismatch Length = 800

Iteration: 1
 Score = 70.5 bits (171), Expect = 3e-13,   Method: Compositional matrix adjust.
 Identities = 28/64 (43%), Positives = 48/64 (75%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L
Sbjct: 632 LMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVL 691
Query: 153 VDEL 156
           +DE+
Sbjct: 692 MDEI 695

>pdb|3K0S|A Chain A, Crystal Structure Of E.Coli Dna Mismatch Repair Protein Muts, D693n Mutant, In Complex With Gt Mismatched Dna Length = 799

Iteration: 1
 Score = 68.9 bits (167), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 27/64 (42%), Positives = 48/64 (75%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L
Sbjct: 631 LMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVL 690
Query: 153 VDEL 156
           ++E+
Sbjct: 691 MNEI 694

>pdb|1E3M|A Chain A, The Crystal Structure Of E. Coli Muts Binding To Dna With A G:t Mismatch Length = 800

Iteration: 1
 Score = 66.6 bits (161), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 28/62 (45%), Positives = 44/62 (70%)
Query: 95  SFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVD 154
           ++ G  VPA  + + P+DRIFTR+GA D+L+  +ST+  E TE+  I+ +A++YSL L D
Sbjct: 634 AYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFXVEXTETANILHNATEYSLVLXD 693
Query: 155 EL 156
           E+
Sbjct: 694 EI 695

>pdb|3THW|B Chain B, Human Mutsbeta Complexed With An Idl Of 4 Bases (Loop4) And Adp Length = 918

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 30/65 (46%), Positives = 44/65 (67%)
Query: 92  TFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA 151
           T ++  G  VPA+  T+  VD IFTRMGA DN+   +ST++ ELT++  I+R A+  SL 
Sbjct: 697 TIMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKATSQSLV 756
Query: 152 LVDEL 156
           ++DEL
Sbjct: 757 ILDEL 761

>pdb|2O8E|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO A G T MISPAIR, WITH ADP BOUND TO Msh2 Only Length = 934

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%)
Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VP +S  ++ VD I  R+GA D+     ST++AE+ E+ +I+R A+K SL ++DEL
Sbjct: 692 GCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDEL 750

>pdb|2O8B|A Chain A, Human Mutsalpha (Msh2MSH6) BOUND TO ADP AND A G T MISPAIR Length = 934

Iteration: 1
 Score = 54.7 bits (130), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%)
Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VP +S  ++ VD I  R+GA D+     ST++AE+ E+ +I+R A+K SL ++DEL
Sbjct: 692 GCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDEL 750

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

Iteration: 1
 Score = 53.1 bits (126), Expect = 7e-08,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 40/59 (67%)
Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA+   L   D I+TR+GA D+L+G +ST++ E+ E   I++ A++ SL L+DE+
Sbjct: 606 GSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEV 664

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 40/64 (62%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            L+  G  VPA+   L   D I+TR+GA D+L+G +ST+  E  E   I++ A++ SL L
Sbjct: 601 LLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFXVEXEEVALILKEATENSLVL 660
Query: 153 VDEL 156
           +DE+
Sbjct: 661 LDEV 664

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 26/64 (40%), Positives = 40/64 (62%)
Query: 93  FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLAL 152
            L+  G  VPA+   L   D I+TR+GA D+L+G +ST+  E  E   I++ A++ SL L
Sbjct: 601 LLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFXVEXEEVALILKEATENSLVL 660
Query: 153 VDEL 156
           +DE+
Sbjct: 661 LDEV 664

>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts Length = 649

Iteration: 1
 Score = 50.8 bits (120), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 25/59 (42%), Positives = 38/59 (64%)
Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA+   L   D I+TR+GA D+L+G +ST+  E  E   I++ A++ SL L+DE+
Sbjct: 490 GSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFXVEXEEVALILKEATENSLVLLDEV 548

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	156
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	7e-27
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	7e-24
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	3e-22
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	5e-21
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	2e-19
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	3e-18
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	4e-19
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	5e-18
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	6e-19
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	5e-18

>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 =  104 bits (261), Expect = 7e-27
 Identities = 38/89 (42%), Positives = 54/89 (60%), Gaps = 1/89 (1%)

Query: 1   ILDSTALANLHVLTN-SDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
           +LD+  L NL +  N ++ +TEGTL+E++D C T FGKR+L+  L  PL N  AI  R D
Sbjct: 396 VLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLD 455

Query: 60  AISVLLDQKHITEQMRAKMKDLRDLERML 88
           AI  L+       ++   +K L DLER+L
Sbjct: 456 AIEDLMVVPDKISEVVELLKKLPDLERLL 484

>2o8b_B DNA mismatch repair protein MSH6; DNA damage response, somatic hypermutat protein-DNA complex, DNA mispair, cancer; HET: DNA ADP; 2.75A {Homo sapiens} PDB: 2o8c_B* 2o8d_B* 2o8e_B* 2o8f_B* Length = 1022

 Score = 95.5 bits (238), Expect = 7e-24
 Identities = 31/59 (52%), Positives = 44/59 (74%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VPA+   LTP+DR+FTR+GA D +   +ST+  EL+E+ +I+ HA+ +SL LVDEL
Sbjct: 819 GCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLVLVDEL 877

>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 = 90.8 bits (226), Expect = 3e-22
 Identities = 44/162 (27%), Positives = 73/162 (45%), Gaps = 12/162 (7%)

Query: 1   ILDSTALANLHVLTN-SDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQD 59
            ++ T L NL +L N +D  T+G+L+  LDH  TSFG+R L+  + +PL  L  I  R D
Sbjct: 320 TINGTTLRNLEILQNQTDMKTKGSLLWVLDHTKTSFGRRKLKKWVTQPLLKLREINARLD 379

Query: 60  AISVLLDQKHIT-EQMRAKMKDLRDLERMLPSSTFLSFQGCRVPAD--SL--TLTPVDRI 114
           A+S +L  +     Q+   ++ L D+ER L     +  + C    +   +  TL  +   
Sbjct: 380 AVSEVLHSESSVFGQIENHLRKLPDIERGL---CSIYHKKCS-TQEFFLIVKTLYHLKSE 435

Query: 115 FTRMGAKDNLSGAQSTYLAELTES-ETIMRHASKYSLALVDE 155
           F  +      S  QS  L  +      ++     Y   L ++
Sbjct: 436 FQAI-IPAVNSHIQSDLLRTVILEIPELLSPVEHYLKILNEQ 476

>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 = 87.3 bits (217), Expect = 5e-21
 Identities = 29/59 (49%), Positives = 41/59 (69%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA+  T+  VD IFTRMGA DN+   +ST++ ELT++  I+R A+  SL ++DEL
Sbjct: 703 GSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKATSQSLVILDEL 761

>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 = 82.5 bits (205), Expect = 2e-19
 Identities = 24/88 (27%), Positives = 40/88 (45%), Gaps = 2/88 (2%)

Query: 1   ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
            L    L  L V        + TL   LD   T+ G+R+L++ L  PL +   ++ R D 
Sbjct: 251 RLPEATLRALEVFEPL--RGQDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEARLDR 308

Query: 61  ISVLLDQKHITEQMRAKMKDLRDLERML 88
           +   + +  + E +R  +  L DLER+ 
Sbjct: 309 VEGFVREGALREGVRRLLYRLADLERLA 336

>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 = 79.1 bits (196), Expect = 3e-18
 Identities = 25/59 (42%), Positives = 40/59 (67%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA+   L   D I+TR+GA D+L+G +ST++ E+ E   I++ A++ SL L+DE+
Sbjct: 606 GSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEV 664

>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 = 82.0 bits (203), Expect = 4e-19
 Identities = 26/59 (44%), Positives = 40/59 (67%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           GC VP +S  ++ VD I  R+GA D+     ST++AE+ E+ +I+R A+K SL ++DEL
Sbjct: 692 GCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDEL 750

>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 = 78.9 bits (195), Expect = 5e-18
 Identities = 20/91 (21%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 1   ILDSTALANLHVLTNS--DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQ 58
            LD  A+  L++   S  D T   +L   L+ C T  G+R++   + +PL + + I++R 
Sbjct: 301 KLDIAAVRALNLFQGSVEDTTGSQSLAALLNKCKTPQGQRLVNQWIKQPLMDKNRIEERL 360

Query: 59  DAISVLLDQKHITEQMRAK-MKDLRDLERML 88
           + +   ++   + + ++   ++   DL R+ 
Sbjct: 361 NLVEAFVEDAELRQTLQEDLLRRFPDLNRLA 391

>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 = 81.4 bits (202), Expect = 6e-19
 Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 3/88 (3%)

Query: 1   ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDA 60
           I+D+    NL +  N     E TL   LD  VT  G RML+  L  P+ +   + +RQ  
Sbjct: 268 IMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQT 327

Query: 61  ISVLLDQKHITEQMRAKMKDLRDLERML 88
           I  L D       ++  ++ + DLER+L
Sbjct: 328 IGALQDFT---AGLQPVLRQVGDLERIL 352

>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 = 79.1 bits (196), Expect = 5e-18
 Identities = 28/59 (47%), Positives = 45/59 (76%)

Query: 98  GCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL 156
           G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A++YSL L+DE+
Sbjct: 637 GSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEI 695

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	156
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	99.86
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	99.86
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	99.75
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	99.74
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	99.68
2o8b_B	1022	DNA mismatch repair protein MSH6; DNA damage respo	99.68
1wb9_A	800	DNA mismatch repair protein MUTS; DNA-binding, ATP	99.4
1ewq_A	765	DNA mismatch repair protein MUTS; multiple domains	99.4
3thx_B	918	DNA mismatch repair protein MSH3; ABC family ATPas	93.95
3thx_A	934	DNA mismatch repair protein MSH2; ABC family ATPas	87.38

>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=99.86  E-value=1.1e-21  Score=170.38  Aligned_cols=64  Identities=45%  Similarity=0.701  Sum_probs=51.6

Q ss_pred             HHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         93 FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        93 ~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      +|+|.|++||+..+.++.++++|++++..|++..+.|+|+.||.++..|++.+++++|+|+||.
T Consensus       698 ~~aq~g~~vpa~~~~i~~~d~i~~~ig~~d~l~~~~stfs~em~~~~~il~~a~~p~LlLLDEP  761 (918)
T 3thx_B          698 IMAQIGSYVPAEEATIGIVDGIFTRMGAADNIYKGRSTFMEELTDTAEIIRKATSQSLVILDEL  761 (918)
T ss_dssp             HHHHHTCCBSSSEEEEECCSEEEEEC----------CCHHHHHHHHHHHHHHCCTTCEEEEEST
T ss_pred             HHhhcCccccchhhhhhHHHHHHHhCChHHHHHHhHHHhhHHHHHHHHHHHhccCCCEEEEeCC
Confidence            4689999999999999999999999999999999999999999999999999999999999995

>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=99.86  E-value=7.6e-22  Score=171.73  Aligned_cols=64  Identities=41%  Similarity=0.649  Sum_probs=52.6

Q ss_pred             HHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         93 FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        93 ~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      +|+|+|++||+..+.++.+|++|++++..|++..+.|+|+.||.+++.+++.+++++|+|+||+
T Consensus       687 ~~aq~G~~vpa~~~~~~~~d~i~~~ig~~d~l~~~lStf~~e~~~~a~il~~a~~~sLlLLDEp  750 (934)
T 3thx_A          687 LMAQIGCFVPCESAEVSIVDCILARVGAGDSQLKGVSTFMAEMLETASILRSATKDSLIIIDEL  750 (934)
T ss_dssp             HHHHHTCCBSEEEEEEECCSEEEEECC---------CHHHHHHHHHHHHHHHCCTTCEEEEESC
T ss_pred             HHHhcCCccccccccchHHHHHHHhcCchhhHHHhHhhhHHHHHHHHHHHHhccCCcEEEEeCC
Confidence            4688999999999999999999999999999999999999999999999999999999999995

>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=99.75  E-value=4.6e-20  Score=158.71  Aligned_cols=134  Identities=28%  Similarity=0.509  Sum_probs=102.8

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHhhchhhHHHHHHhhhh-h--hhhhhhchhHH--
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLLDQKHITEQMRAKMKD-L--RDLERMLPSST--   92 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~~~~~v~~~i~~~l~~-~--~~~~n~~gk~~--   92 (156)
                      ...++.|| |+.+++..+...+|++|.++.    ++.++|||+++....+.++++++...-.+ +  -++||++|||+  
T Consensus       546 ~~~la~lD-~l~s~A~~a~~~~~~~P~~~~~~~i~i~~~rHP~le~~~~~~~vlndisl~~~g~i~~ItGpNGsGKSTlL  624 (800)
T 1wb9_A          546 ASALAELD-VLVNLAERAYTLNYTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYM  624 (800)
T ss_dssp             HHHHHHHH-HHHHHHHHHHHTTCBCCEECSSSCEEEEEECCTTHHHHCSSCCCCEEEEECSSSCEEEEECCTTSSHHHHH
T ss_pred             HHHHHHHH-HHHHHHHHHHhCCCcccEECCCCCEEEEeccccEEEccCCCceeeecccccCCCcEEEEECCCCCChHHHH
Confidence            36889999 999999999999999998863    35679999998655445677766432011 1  24599999985  


Q ss_pred             -------HHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         93 -------FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        93 -------~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                             +++|.|++||+..+.+++++++|++++..|++..+.|+|+.||.++..+++.+++++|+|+||+
T Consensus       625 r~iagl~~~~q~G~~vpa~~~~i~~~~~i~~~~~~~d~l~~~~stf~~e~~~~~~il~~a~~psLlLLDEp  695 (800)
T 1wb9_A          625 RQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEI  695 (800)
T ss_dssp             HHHHHHHHHHTTTCCBSSSEEEECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCTTEEEEEESC
T ss_pred             HHHHHHHHHHhcCcccchhcccceeHHHHHhhCCHHHHHHhhhhhhhHHHHHHHHHHHhccCCCEEEEECC
Confidence                   4689999999999999999999999999999999999999999999999999999999999995

>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=99.74  E-value=1.9e-20  Score=164.40  Aligned_cols=133  Identities=32%  Similarity=0.480  Sum_probs=99.6

Q ss_pred             cHHHHhhHhhhhHHHHHH--HccccCCCCC--------HHHHHhhHHHHHHHh-hchhhHHHHHHhhh---------hh-
Q psy13255         23 TLIEQLDHCVTSFGKRML--RAQLVKPLTN--------LDAIKQRQDAISVLL-DQKHITEQMRAKMK---------DL-   81 (156)
Q Consensus        23 sl~~~LD~~~t~~g~~~l--~~~~~~P~~~--------~~~i~~Rhplv~~l~-~~~~v~~~i~~~l~---------~~-   81 (156)
                      ..++.|| |+.+++..+.  ...|++|.+.        .++.++|||+++... .+.++++++.....         .+ 
T Consensus       714 ~~la~lD-~l~s~A~~a~~~~~~~~~P~~~~~~~~~~~l~i~~~rHP~l~~~~~~~~~v~ndi~l~~~~~~~~~~~g~i~  792 (1022)
T 2o8b_B          714 ECIAVLD-VLLCLANYSRGGDGPMCRPVILLPEDTPPFLELKGSRHPCITKTFFGDDFIPNDILIGCEEEEQENGKAYCV  792 (1022)
T ss_dssp             HHHHHHH-HHHHHHHHTTCSSSCEECCEECCTTTSCCCEEEEEECCCC------CCCCCCEEEEESCCCSCC---CCCEE
T ss_pred             HHHHHHH-HHHhHHHHHhhccCCccCCccccCCCCCceEEEEeccccEEEEEecCCceEeeeeeeccccccccCCCCcEE
Confidence            6789999 8999999998  6889999865        234578999987544 34567777653322         11 


Q ss_pred             -hhhhhhchhHH---------HHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceE
Q psy13255         82 -RDLERMLPSST---------FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLA  151 (156)
Q Consensus        82 -~~~~n~~gk~~---------~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slv  151 (156)
                       .++||++|||+         +|+|+|+|||+..+.++++|+||+++|..|++..+.|+|+.||.+++.++..+++++|+
T Consensus       793 ~ItGpNgsGKSTlLr~iGl~~~~aqiG~~Vpq~~~~l~v~d~I~~rig~~d~~~~~~stf~~em~~~a~al~la~~~sLl  872 (1022)
T 2o8b_B          793 LVTGPNMGGKSTLMRQAGLLAVMAQMGCYVPAEVCRLTPIDRVFTRLGASDRIMSGESTFFVELSETASILMHATAHSLV  872 (1022)
T ss_dssp             EEECCTTSSHHHHHHHHHHHHHHHTTTCCEESSEEEECCCSBEEEECC---------CHHHHHHHHHHHHHHHCCTTCEE
T ss_pred             EEECCCCCChHHHHHHHHHHHHHhheeEEeccCcCCCCHHHHHHHHcCCHHHHhhchhhhHHHHHHHHHHHHhCCCCcEE
Confidence             24699999985         46899999999999999999999999999999999999999999999999999999999


Q ss_pred             EeccC
Q psy13255        152 LVDEL  156 (156)
Q Consensus       152 liDE~  156 (156)
                      |+||+
T Consensus       873 LLDEp  877 (1022)
T 2o8b_B          873 LVDEL  877 (1022)
T ss_dssp             EEECT
T ss_pred             EEECC
Confidence            99996

>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=99.68  E-value=1.1e-18  Score=149.48  Aligned_cols=131  Identities=27%  Similarity=0.448  Sum_probs=104.7

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH--HHHHhhHHHHHHHhhchhhHHHHHHhhhhh--hhhhhhchhHH-----
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL--DAIKQRQDAISVLLDQKHITEQMRAKMKDL--RDLERMLPSST-----   92 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~--~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~--~~~~n~~gk~~-----   92 (156)
                      ...++.|| |+.+++..+....|++|.++.  ++.++|||+++.  .+.++++++... ..+  -++||++|||+     
T Consensus       521 ~~~la~LD-~l~s~a~~a~~~~~~~P~~~~~i~i~~~rHP~le~--~~~~vl~disl~-g~i~~I~GpNGsGKSTlLr~i  596 (765)
T 1ewq_A          521 ARILAELD-VYAALAEVAVRYGYVRPRFGDRLQIRAGRHPVVER--RTEFVPNDLEMA-HELVLITGPNMAGKSTFLRQT  596 (765)
T ss_dssp             HHHHHHHH-HHHHHHHHHHHHTCBCCEESSSEEEEEECCTTGGG--TSCCCCEEEEES-SCEEEEESCSSSSHHHHHHHH
T ss_pred             HHHHHHHH-HHHhhHHHHHhCCceeeccCCcEEEEEeECceEcc--CCceEeeeccCC-CcEEEEECCCCCChHHHHHHH
Confidence            36889999 999999999999999998842  245689999874  345666666432 222  24599999985     


Q ss_pred             ----HHHhhCCCCCCCcccccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255         93 ----FLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus        93 ----~laq~g~~vpa~~~~l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                          +++|.|+++|+..+.+++++++|++++..|++..+.|+|+.||.+++.+++.+++++|+|+||.
T Consensus       597 agl~~~~~~G~~vpa~~~~i~~v~~i~~~~~~~d~l~~g~S~~~~e~~~la~il~~a~~p~LlLLDEp  664 (765)
T 1ewq_A          597 ALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEV  664 (765)
T ss_dssp             HHHHHHHTTTCCBSSSEEEECCCSEEEEECCC------CCSHHHHHHHHHHHHHHHCCTTEEEEEEST
T ss_pred             HhhhhhcccCceeehhccceeeHHHhhccCCHHHHHHhcccHHHHHHHHHHHHHHhccCCCEEEEECC
Confidence                3589999999999999999999999999999999999999999999999999999999999995

>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=99.68  E-value=4.3e-17  Score=143.29  Aligned_cols=93  Identities=41%  Similarity=0.618  Sum_probs=86.0

Q ss_pred             CCCHHHHhhccccccC-CCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhh
Q psy13255          1 ILDSTALANLHVLTNS-DNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMK   79 (156)
Q Consensus         1 ~id~~t~~~Lei~~~~-~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~   79 (156)
                      +||.+|++||||+++. +++++|||++.||+|.|++|+|+|++|+++|+.+.+.|+.||++|++++.+.....+++..|+
T Consensus       396 ~LD~~T~~nLEl~~~~~~g~~~gSLl~~Ld~t~T~mG~RLLr~WL~~PL~d~~~I~~RldaVe~l~~~~~~~~~l~~~L~  475 (1022)
T 2o8b_B          396 VLDAVTLNNLEIFLNGTNGSTEGTLLERVDTCHTPFGKRLLKQWLCAPLCNHYAINDRLDAIEDLMVVPDKISEVVELLK  475 (1022)
T ss_dssp             BCCHHHHHHTTCSSCCSSSSCCCSHHHHHCCCSSHHHHHHHHHHHHSCBCCHHHHHHHHHHHHHHHTCHHHHHHHHHHHT
T ss_pred             EeCHHHHHhhcCCccCCCCCCCCcHHHHhCcCCCchhHHHHHHHHhCccCCHHHHHHHHHHHHHHHhChHHHHHHHHHHh
Confidence            4899999999999885 566789999999999999999999999999999999999999999999998888899999999


Q ss_pred             hhhhhhhhchhHHH
Q psy13255         80 DLRDLERMLPSSTF   93 (156)
Q Consensus        80 ~~~~~~n~~gk~~~   93 (156)
                      +++|++|+.+|+..
T Consensus       476 ~i~DlERll~Ri~~  489 (1022)
T 2o8b_B          476 KLPDLERLLSKIHN  489 (1022)
T ss_dssp             TCCCHHHHHHHHHH
T ss_pred             cCccHHHHHHHHHh
Confidence            99999999888754

>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=99.40  E-value=2e-13  Score=117.55  Aligned_cols=88  Identities=33%  Similarity=0.501  Sum_probs=79.6

Q ss_pred             CCCHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhh
Q psy13255          1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD   80 (156)
Q Consensus         1 ~id~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~   80 (156)
                      +||.+|+++||++++..++++|||++.+|+|.|++|+|+++.|+.+|+.+.+.|+.||..|+++..   ....++..+++
T Consensus       268 ~ld~~t~~~LEl~~~~~~~~~gSL~~ll~~t~T~~G~RlL~~wl~~Pl~d~~~I~~R~~~v~~~~~---~~~~l~~~L~~  344 (800)
T 1wb9_A          268 IMDAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQTIGALQD---FTAGLQPVLRQ  344 (800)
T ss_dssp             EECHHHHHHTTSSSCTTSCSTTSHHHHHCCCSSHHHHHHHHHHHHSCBCCHHHHHHHHHHHHHTGG---GHHHHHHHHHT
T ss_pred             EecHHHHHhccCcccCCCCccccHHHHhCCCcCHHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHH---HHHHHHHHhcC
Confidence            379999999999988766678999999999999999999999999999999999999999999876   66777777889


Q ss_pred             hhhhhhhchhH
Q psy13255         81 LRDLERMLPSS   91 (156)
Q Consensus        81 ~~~~~n~~gk~   91 (156)
                      ++|+++..+|.
T Consensus       345 ~~Dler~l~r~  355 (800)
T 1wb9_A          345 VGDLERILARL  355 (800)
T ss_dssp             TCSHHHHHHHH
T ss_pred             CccHHHHHHHH
Confidence            99998888764

>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=99.40  E-value=2.7e-13  Score=116.27  Aligned_cols=89  Identities=27%  Similarity=0.390  Sum_probs=81.0

Q ss_pred             CCCHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhh
Q psy13255          1 ILDSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD   80 (156)
Q Consensus         1 ~id~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~   80 (156)
                      .||.+|+++||++++..+  .++|++.+|+|.|++|+|++++|+.+|+.+.+.|+.||..|+++..++.....++..+++
T Consensus       251 ~lD~~t~~~LEl~~~~~~--~gsL~~~ld~t~T~~G~RlL~~wl~~Pl~d~~~I~~R~~~V~~l~~~~~~~~~l~~~L~~  328 (765)
T 1ewq_A          251 RLPEATLRALEVFEPLRG--QDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEARLDRVEGFVREGALREGVRRLLYR  328 (765)
T ss_dssp             BCCHHHHHHTTSSSCSSS--CCCHHHHHCCCSSHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHTT
T ss_pred             EecHHHHHhCcCccCCCc--cchHHHHhCCCCCHHHHHHHHHHhhCcCCCHHHHHHHHHHHHHHHhCHHHHHHHHHHHhc
Confidence            489999999999987665  689999999999999999999999999999999999999999999887778888888899


Q ss_pred             hhhhhhhchhH
Q psy13255         81 LRDLERMLPSS   91 (156)
Q Consensus        81 ~~~~~n~~gk~   91 (156)
                      ++|+++..+|.
T Consensus       329 ~~Dler~l~r~  339 (765)
T 1ewq_A          329 LADLERLATRL  339 (765)
T ss_dssp             CCCHHHHHHHH
T ss_pred             CCCHHHHHHHH
Confidence            99998887764

>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=93.95  E-value=0.0014  Score=57.46  Aligned_cols=78  Identities=15%  Similarity=0.198  Sum_probs=60.2

Q ss_pred             ccHHHHhhHhhhhHHHHHHHccccCCCCCH----HHHHhhHHHHHHHhh--chhhHHHHHHhhh-h-h--hhhhhhchhH
Q psy13255         22 GTLIEQLDHCVTSFGKRMLRAQLVKPLTNL----DAIKQRQDAISVLLD--QKHITEQMRAKMK-D-L--RDLERMLPSS   91 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~----~~i~~Rhplv~~l~~--~~~v~~~i~~~l~-~-~--~~~~n~~gk~   91 (156)
                      ...++.|| |+.++|..+...+|++|.++.    .+.++|||+++..+.  +.++++++..... + +  -++||++|||
T Consensus       609 ~~~la~lD-~l~s~A~~a~~~~~~~P~~~~~~~i~i~~~rHP~le~~~~~~~~~V~ndvsl~~~~g~i~~ItGPNGaGKS  687 (918)
T 3thx_B          609 VHHLATVD-CIFSLAKVAKQGDYCRPTVQEERKIVIKNGRHPVIDVLLGEQDQYVPNNTDLSEDSERVMIITGPNMGGKS  687 (918)
T ss_dssp             HHHHHHHH-HHHHHHHHHTSSSCBCCEEESSCEEEEEEECCHHHHHHTCSCSSSCCEEEEECTTSCCEEEEESCCCHHHH
T ss_pred             HHHHHHHH-HHHHHHHHHhcCCCcCCcccCCCcEEEEeccchhhhhhhccCCceecccccccCCCCeEEEEECCCCCchH
Confidence            36899999 999999999999999998753    346799999997664  3578887753322 1 1  3469999999


Q ss_pred             HHHHhhCCC
Q psy13255         92 TFLSFQGCR  100 (156)
Q Consensus        92 ~~laq~g~~  100 (156)
                      ++|.++|..
T Consensus       688 TlLr~i~~i  696 (918)
T 3thx_B          688 SYIKQVALI  696 (918)
T ss_dssp             HHHHHHHHH
T ss_pred             HHHHHHHHH
Confidence            999888643

>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=87.38  E-value=0.0064  Score=53.44  Aligned_cols=78  Identities=19%  Similarity=0.166  Sum_probs=56.8

Q ss_pred             ccHHHHhhHhhhhHHHHHHH--ccccCCCCCH------HHHHhhHHHHHHHhhchhhHHHHHHhhh--h--hhhhhhhch
Q psy13255         22 GTLIEQLDHCVTSFGKRMLR--AQLVKPLTNL------DAIKQRQDAISVLLDQKHITEQMRAKMK--D--LRDLERMLP   89 (156)
Q Consensus        22 ~sl~~~LD~~~t~~g~~~l~--~~~~~P~~~~------~~i~~Rhplv~~l~~~~~v~~~i~~~l~--~--~~~~~n~~g   89 (156)
                      ...++.|| |+.+++..+..  .+|++|.+..      ++.++|||+++....+.++++++.....  .  .-++||++|
T Consensus       596 ~~~la~lD-~l~s~A~~a~~~~~~~~rP~~~~~~~~~i~i~~~rHP~le~~~~~~~v~ndisl~~~~g~i~~ItGpNGsG  674 (934)
T 3thx_A          596 NDVLAQLD-AVVSFAHVSNGAPVPYVRPAILEKGQGRIILKASRHACVEVQDEIAFIPNDVYFEKDKQMFHIITGPNMGG  674 (934)
T ss_dssp             HHHHHHHH-HHHHHHHHHHTSSSCCBCCEEECTTSCEEEEEEECCTTTTTC--CCCCCEEEEEETTTBCEEEEECCTTSS
T ss_pred             HHHHHHHH-HHHHHHHHHHhccCCCcCCeeccCCCcceEeecCccchhhhcCCceeecccceeecCCCeEEEEECCCCCC
Confidence            36899999 99999999987  6799998753      2457999999854334577777753322  1  134699999


Q ss_pred             hHHHHHhhCCC
Q psy13255         90 SSTFLSFQGCR  100 (156)
Q Consensus        90 k~~~laq~g~~  100 (156)
                      ||++|.++|..
T Consensus       675 KSTlLr~ial~  685 (934)
T 3thx_A          675 KSTYIRQTGVI  685 (934)
T ss_dssp             HHHHHHHHHHH
T ss_pred             HHHHHHHHHHH
Confidence            99999888543

---

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	156
d1wb9a1	297	a.113.1.1 (A:270-566) DNA repair protein MutS, dom	1e-16
d1ewqa1	275	a.113.1.1 (A:267-541) DNA repair protein MutS, dom	6e-16
d1ewqa2	224	c.37.1.12 (A:542-765) DNA repair protein MutS, the	4e-07
d1wb9a2	234	c.37.1.12 (A:567-800) DNA repair protein MutS, the	9e-07

>d1wb9a1 a.113.1.1 (A:270-566) DNA repair protein MutS, domain III {Escherichia coli [TaxId: 562]} Length = 297

class: All alpha proteins
fold: DNA repair protein MutS, domain III
superfamily: DNA repair protein MutS, domain III
family: DNA repair protein MutS, domain III
domain: DNA repair protein MutS, domain III
species: Escherichia coli [TaxId: 562]

 Score = 72.7 bits (177), Expect = 1e-16
 Identities = 25/86 (29%), Positives = 37/86 (43%)

Query: 3  DSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAIS 62
          D+    NL +  N     E TL   LD  VT  G RML+  L  P+ +   + +RQ  I 
Sbjct: 1  DAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQTIG 60

Query: 63 VLLDQKHITEQMRAKMKDLRDLERML 88
           L D     + +  ++ DL  +   L
Sbjct: 61 ALQDFTAGLQPVLRQVGDLERILARL 86

>d1ewqa1 a.113.1.1 (A:267-541) DNA repair protein MutS, domain III {Thermus aquaticus [TaxId: 271]} Length = 275

class: All alpha proteins
fold: DNA repair protein MutS, domain III
superfamily: DNA repair protein MutS, domain III
family: DNA repair protein MutS, domain III
domain: DNA repair protein MutS, domain III
species: Thermus aquaticus [TaxId: 271]

 Score = 70.3 bits (171), Expect = 6e-16
 Identities = 20/68 (29%), Positives = 36/68 (52%)

Query: 21 EGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKD 80
          + TL   LD   T+ G+R+L++ L  PL +   ++ R D +   + +  + E +R  +  
Sbjct: 3  QDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEARLDRVEGFVREGALREGVRRLLYR 62

Query: 81 LRDLERML 88
          L DLER+ 
Sbjct: 63 LADLERLA 70

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]} Length = 224

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

 Score = 45.6 bits (107), Expect = 4e-07
 Identities = 27/72 (37%), Positives = 43/72 (59%)

Query: 85  ERMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRH 144
            R       L+  G  VPA+   L   D I+TR+GA D+L+G +ST++ E+ E   I++ 
Sbjct: 52  LRQTALIALLAQVGSFVPAEEAHLPLFDGIYTRIGASDDLAGGKSTFMVEMEEVALILKE 111

Query: 145 ASKYSLALVDEL 156
           A++ SL L+DE+
Sbjct: 112 ATENSLVLLDEV 123

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]} Length = 234

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

 Score = 44.8 bits (105), Expect = 9e-07
 Identities = 29/71 (40%), Positives = 49/71 (69%)

Query: 86  RMLPSSTFLSFQGCRVPADSLTLTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHA 145
           R       +++ G  VPA  + + P+DRIFTR+GA D+L+  +ST++ E+TE+  I+ +A
Sbjct: 59  RQTALIALMAYIGSYVPAQKVEIGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNA 118

Query: 146 SKYSLALVDEL 156
           ++YSL L+DE+
Sbjct: 119 TEYSLVLMDEI 129

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	156
d1wb9a2	234	DNA repair protein MutS, the C-terminal domain {Es	99.95
d1ewqa2	224	DNA repair protein MutS, the C-terminal domain {Th	99.94
d1wb9a1	297	DNA repair protein MutS, domain III {Escherichia c	99.7
d1ewqa1	275	DNA repair protein MutS, domain III {Thermus aquat	99.41

>d1wb9a2 c.37.1.12 (A:567-800) DNA repair protein MutS, the C-terminal domain {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Escherichia coli [TaxId: 562]

Probab=99.95  E-value=1.6e-31  Score=198.92  Aligned_cols=113  Identities=30%  Similarity=0.530  Sum_probs=88.3

Q ss_pred             ccCCCCCHH----HHHhhHHHHHHHhhchhhHHHHHHhhh-h--hhhhhhhchhH---------HHHHhhCCCCCCCccc
Q psy13255         44 LVKPLTNLD----AIKQRQDAISVLLDQKHITEQMRAKMK-D--LRDLERMLPSS---------TFLSFQGCRVPADSLT  107 (156)
Q Consensus        44 ~~~P~~~~~----~i~~Rhplv~~l~~~~~v~~~i~~~l~-~--~~~~~n~~gk~---------~~laq~g~~vpa~~~~  107 (156)
                      |++|.+..+    ..++|||+++....+++|||++...-. +  +.++|||+||+         ++|||+|+||||+++.
T Consensus         1 y~~P~~~~~~~l~i~~~rHPlle~~~~~~~VpNdi~l~~~~~~~iiTGpN~~GKSt~lk~i~l~~~laq~G~~VpA~~a~   80 (234)
T d1wb9a2           1 YTCPTFIDKPGIRITEGRHPVVEQVLNEPFIANPLNLSPQRRMLIITGPNMGGKSTYMRQTALIALMAYIGSYVPAQKVE   80 (234)
T ss_dssp             CBCCEECSSSCEEEEEECCTTHHHHCSSCCCCEEEEECSSSCEEEEECCTTSSHHHHHHHHHHHHHHHTTTCCBSSSEEE
T ss_pred             CCCCEEcCCCcEEEEEeECCEEEcccCCCccceeEEECCCceEEEEeccCchhhHHHHHHHHHHHHHHHcCCeEecCcee
Confidence            688988533    567999999987777889999853211 1  45679999998         4789999999999999


Q ss_pred             ccccceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        108 LTPVDRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       108 l~~~d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      ++++|+||+++++.|++..|+|+|++||.+++.|++.++++|||||||+
T Consensus        81 ~~~~d~I~~~~~~~d~~~~~~S~F~~E~~~~~~il~~~~~~sLvliDE~  129 (234)
T d1wb9a2          81 IGPIDRIFTRVGAADDLASGRSTFMVEMTETANILHNATEYSLVLMDEI  129 (234)
T ss_dssp             ECCCCEEEEEEC-----------CHHHHHHHHHHHHHCCTTEEEEEESC
T ss_pred             cccchhheeEEccCcccccchhHHHHHHHHHHHHHHhcccccEEeeccc
Confidence            9999999999999999999999999999999999999999999999997

>d1ewqa2 c.37.1.12 (A:542-765) DNA repair protein MutS, the C-terminal domain {Thermus aquaticus [TaxId: 271]}

class: Alpha and beta proteins (a/b)
fold: P-loop containing nucleoside triphosphate hydrolases
superfamily: P-loop containing nucleoside triphosphate hydrolases
family: ABC transporter ATPase domain-like
domain: DNA repair protein MutS, the C-terminal domain
species: Thermus aquaticus [TaxId: 271]

Probab=99.94  E-value=2.4e-30  Score=191.39  Aligned_cols=111  Identities=29%  Similarity=0.437  Sum_probs=89.4

Q ss_pred             ccCCCCCHH--HHHhhHHHHHHHhhchhhHHHHHHhhh-hhhhhhhhchhH---------HHHHhhCCCCCCCccccccc
Q psy13255         44 LVKPLTNLD--AIKQRQDAISVLLDQKHITEQMRAKMK-DLRDLERMLPSS---------TFLSFQGCRVPADSLTLTPV  111 (156)
Q Consensus        44 ~~~P~~~~~--~i~~Rhplv~~l~~~~~v~~~i~~~l~-~~~~~~n~~gk~---------~~laq~g~~vpa~~~~l~~~  111 (156)
                      |++|.+..+  +.++|||+++.  .+.+||||+...-+ -+-++|||+||+         ++|||+|+||||+++.++++
T Consensus         1 y~~P~~~~~~~i~~~rHPlle~--~~~~VpNdi~~~~~~~iiTGpN~~GKSt~lk~i~l~~ilAq~G~~vpA~~~~i~~~   78 (224)
T d1ewqa2           1 YVRPRFGDRLQIRAGRHPVVER--RTEFVPNDLEMAHELVLITGPNMAGKSTFLRQTALIALLAQVGSFVPAEEAHLPLF   78 (224)
T ss_dssp             CBCCEESSSEEEEEECCTTGGG--TSCCCCEEEEESSCEEEEESCSSSSHHHHHHHHHHHHHHHTTTCCBSSSEEEECCC
T ss_pred             CCCCccCCcEEEEeCcCCEEcC--CCCeecceEEeCCcEEEEECCCccccchhhhhhHHHHHHHhccceeecCceEEeec
Confidence            688988643  45799999863  34678888753201 235679999998         47999999999999999999


Q ss_pred             ceeeccCCccccccCCcCcHHHHHHHHHHHHHhcCCCceEEeccC
Q psy13255        112 DRIFTRMGAKDNLSGAQSTYLAELTESETIMRHASKYSLALVDEL  156 (156)
Q Consensus       112 d~i~~~~~~~d~l~~~~S~F~~e~~~~~~il~~~~~~slvliDE~  156 (156)
                      |+||+++++.|++..|+|+|+.||.+++.|+++++++|||||||+
T Consensus        79 d~I~~~~~~~d~~~~~~StF~~el~~~~~il~~~~~~sLvliDE~  123 (224)
T d1ewqa2          79 DGIYTRIGASDDLAGGKSTFMVEMEEVALILKEATENSLVLLDEV  123 (224)
T ss_dssp             SEEEEECCC------CCSHHHHHHHHHHHHHHHCCTTEEEEEEST
T ss_pred             ceEEEEECCCccccCCccHHHHhHHHHHHHhccCCCCcEEeeccc
Confidence            999999999999999999999999999999999999999999997

>d1wb9a1 a.113.1.1 (A:270-566) DNA repair protein MutS, domain III {Escherichia coli [TaxId: 562]}

class: All alpha proteins
fold: DNA repair protein MutS, domain III
superfamily: DNA repair protein MutS, domain III
family: DNA repair protein MutS, domain III
domain: DNA repair protein MutS, domain III
species: Escherichia coli [TaxId: 562]

Probab=99.70  E-value=7.4e-18  Score=127.24  Aligned_cols=86  Identities=33%  Similarity=0.487  Sum_probs=78.4

Q ss_pred             CHHHHhhccccccCCCCccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhhhh
Q psy13255          3 DSTALANLHVLTNSDNTTEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLR   82 (156)
Q Consensus         3 d~~t~~~Lei~~~~~~~~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~~   82 (156)
                      |++|++||||+++..|+++|||++.||+|.|++|+|.++.|+++|+.+.+.|+.||.+|+++..   ...+++..+++++
T Consensus         1 D~~T~~nLEl~~~~~g~~~~SL~~~ln~c~T~~GkRlLr~wLl~Pl~d~~~I~~R~d~Ve~l~~---~~~~l~~~L~~l~   77 (297)
T d1wb9a1           1 DAATRRNLEITQNLAGGAENTLASVLDCTVTPMGSRMLKRWLHMPVRDTRVLLERQQTIGALQD---FTAGLQPVLRQVG   77 (297)
T ss_dssp             CHHHHHHTTSSSCTTSCSTTSHHHHHCCCSSHHHHHHHHHHHHSCBCCHHHHHHHHHHHHHTGG---GHHHHHHHHHTTC
T ss_pred             CHhHHHHhCcCcCCCCCCCCcHHHHHcCCCCcHHHHHHHHHHhCccCCHHHHHHHHHHHHHHHH---hHHHHHHHHhccc
Confidence            8999999999998888888999999999999999999999999999999999999999999865   3567787889999


Q ss_pred             hhhhhchhH
Q psy13255         83 DLERMLPSS   91 (156)
Q Consensus        83 ~~~n~~gk~   91 (156)
                      |++++..|.
T Consensus        78 Dierl~~k~   86 (297)
T d1wb9a1          78 DLERILARL   86 (297)
T ss_dssp             SHHHHHHHH
T ss_pred             hHHHHHHHH
Confidence            998888764

>d1ewqa1 a.113.1.1 (A:267-541) DNA repair protein MutS, domain III {Thermus aquaticus [TaxId: 271]}

class: All alpha proteins
fold: DNA repair protein MutS, domain III
superfamily: DNA repair protein MutS, domain III
family: DNA repair protein MutS, domain III
domain: DNA repair protein MutS, domain III
species: Thermus aquaticus [TaxId: 271]

Probab=99.41  E-value=7.9e-14  Score=103.82  Aligned_cols=72  Identities=28%  Similarity=0.421  Sum_probs=66.5

Q ss_pred             ccccHHHHhhHhhhhHHHHHHHccccCCCCCHHHHHhhHHHHHHHhhchhhHHHHHHhhhhhhhhhhhchhH
Q psy13255         20 TEGTLIEQLDHCVTSFGKRMLRAQLVKPLTNLDAIKQRQDAISVLLDQKHITEQMRAKMKDLRDLERMLPSS   91 (156)
Q Consensus        20 ~~~sl~~~LD~~~t~~g~~~l~~~~~~P~~~~~~i~~Rhplv~~l~~~~~v~~~i~~~l~~~~~~~n~~gk~   91 (156)
                      .+|||++.||+|.|++|+|.++.|+++|+.+.+.|+.||.+|+++..++.+...++..|++++|++++..+.
T Consensus         2 ~kgSL~~~ln~t~T~~GkRlLr~wl~~Pl~d~~~I~~R~d~Ve~l~~~~~~~~~l~~~L~~i~Dler~l~~~   73 (275)
T d1ewqa1           2 GQDTLFSVLDETRTAPGRRLLQSWLRHPLLDRGPLEARLDRVEGFVREGALREGVRRLLYRLADLERLATRL   73 (275)
T ss_dssp             SCCCHHHHHCCCSSHHHHHHHHHHHHSCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTCCCHHHHHHHH
T ss_pred             CCCcHHHHHcCCCChHHHHHHHHHHhCccCCHHHHHHHHHHHHHHHhChhhHHHHHHHHhccchhHHHHHHH
Confidence            357999999999999999999999999999999999999999999988888888988899999998887764