Psyllid ID: psy13676

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200
Protein Sequence
MGHVSLTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANLRNGDGTSRKKKKKKKKKKKKKKKKKKKKKKKKKRLYIFKKHT
Secondary Structure (PSIPRED)
ccccccHHHHHccccccccccccHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEEEcccEEEEEcccHHHHHHHHHHHcccccccccccccccccccHHHHHHHHHHHHHHHHcccEEEEEccccccccccccHHHHHHHHHHHHHHHHHHHHHHHHccccEEEEcccc
Secondary Structure Prediction (SSPRO)
ccHHHHHHHHHHHccccccccccHHHHHHHcccccccccEEEEEEEEEcccccccccHHHHEEEEccccccccEEEEEccEEEEEEccccEEEEEcccccHHHcHHHHHHcEEEcccccEEcccccccHHHHHHHHHHHHHHHHcccEEEEHHHHHHHcccccccHHHHHHccccccHHHHHHHHHHHHccEEEEEEccc
Coil and Loop (DISEMBL)
MGHVSLTISQLINiipitqsspdaslleefrippditamFTLSGFIssaihghgrstadrqfyfvnsrpcepskvsgqaEGFIIVKydsdlfiidqhatdekynfetlqkttviksqklvvpqnlhltkinqcilkdnlpvfyknGFEFRITMMFANlrngdgtsrkkKKKKKKKKKKKKKKKKKKKKKKKRLYIFKKHT
Flexible Loop (DISEMBL)
MGHVSLTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLtkinqcilkdnLPVFYKNGFEFRITMMFanlrngdgtsrkkkkkkkkkkkkkkkkkkkkkkkkkrlyifkkht
Low Complexity Region (SEG)
MGHVSLTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANLRNGDGTSRkkkkkkkkkkkkkkkkkkkkkkkkkRLYIFKKHT
Disordered region (IsUnstruct)
*****LTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANL******************************************
Disordered Region (DISOPRED)
*********************************************************************CEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANLRN********************************LYIFKK**
Disordered Region (DISEMBL)
MGHVSLTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANLRNG*******************************LYIFKKHT
Disordered Region (DISPRO)
**HVSLTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANLRNGDGTSRKKKKKKKKKKKKKKKKKKKKKKKKKRLYIFKK**
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooHHHHHHHHHHHHHHHHHiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MGHVSLTISQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITMMFANLRNGDGTSxxxxxxxxxxxxxxxxxxxxxxxxxxxxYIFKKHT
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	200	2.2.26 [Sep-21-2011]
P54278	862	Mismatch repair endonucle	yes	N/A	0.345	0.080	0.591	9e-21
P54279	859	Mismatch repair endonucle	yes	N/A	0.355	0.082	0.563	5e-20
P14242	873	DNA mismatch repair prote	yes	N/A	0.39	0.089	0.602	1e-19
P54280	794	DNA mismatch repair prote	yes	N/A	0.4	0.100	0.432	1e-12
Q54QA0	1022	Mismatch repair endonucle	yes	N/A	0.355	0.069	0.540	4e-12
A5GEV5	602	DNA mismatch repair prote	yes	N/A	0.635	0.210	0.257	2e-05
B1H0C7	595	DNA mismatch repair prote	yes	N/A	0.435	0.146	0.343	3e-05
A3CWX7	585	DNA mismatch repair prote	yes	N/A	0.355	0.121	0.333	0.0002
C5CF28	602	DNA mismatch repair prote	yes	N/A	0.465	0.154	0.319	0.0002
Q895H3	620	DNA mismatch repair prote	yes	N/A	0.39	0.125	0.378	0.0003

>sp|P54278|PMS2_HUMAN Mismatch repair endonuclease PMS2 OS=Homo sapiens GN=PMS2 PE=1 SV=2

 Score =  100 bits (248), Expect = 9e-21,   Method: Compositional matrix adjust.
 Identities = 42/71 (59%), Positives = 57/71 (80%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII K + D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+ PQ L+LT +N+ +L +NL 
Sbjct: 685 GFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNEAVLIENLE 744

Query: 141 VFYKNGFEFRI 151
           +F KNGF+F I
Sbjct: 745 IFRKNGFDFVI 755

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with MLH1 to form MutL alpha. DNA repair is initiated by MutS alpha (MSH2-MSH6) or MutS beta (MSH2-MSH6) binding to a dsDNA mismatch, then MutL alpha is recruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of RFC and PCNA is sufficient to activate endonuclease activity of PMS2. It introduces single-strand breaks near the mismatch and thus generates new entry points for the exonuclease EXO1 to degrade the strand containing the mismatch. DNA methylation would prevent cleavage and therefore assure that only the newly mutated DNA strand is going to be corrected. MulL alpha (MLH1-PMS2) interacts physically with the clamp loader subunits of DNA polymerase III, suggesting that it may play a role to recruit the DNA polymerase III to the site of the MMR. Also implicated in DNA damage signaling, a process which induces cell cycle arrest and can lead to apoptosis in case of major DNA damages.
Homo sapiens (taxid: 9606)
EC: 3EC: .EC: 1EC: .EC: -EC: .EC: -

>sp|P54279|PMS2_MOUSE Mismatch repair endonuclease PMS2 OS=Mus musculus GN=Pms2 PE=1 SV=1

 Score = 97.8 bits (242), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 40/71 (56%), Positives = 56/71 (78%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFI+ K   DLF++DQHA DEKYNFE LQ+ TV+++Q+L+ PQ L+LT +N+ +L +NL 
Sbjct: 682 GFIVTKLKEDLFLVDQHAADEKYNFEMLQQHTVLQAQRLITPQTLNLTAVNEAVLIENLE 741

Query: 141 VFYKNGFEFRI 151
           +F KNGF+F I
Sbjct: 742 IFRKNGFDFVI 752

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with Mlh1 to form MutL alpha. DNA repair is initiated by MutS alpha (Msh2-Msh6) or MutS beta (Msh2-Msh6) binding to a dsDNA mismatch, then MutL alpha is recruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of RFC and PCNA is sufficient to activate endonuclease activity of pms2. It introduces single-strand breaks near the mismatch and thus generates new entry points for the exonuclease EXO1 to degrade the strand containing the mismatch. DNA methylation would prevent cleavage and therefore assure that only the newly mutated DNA strand is going to be corrected. MulL alpha (Mlh1-PMS2) interacts physically with the clamp loader subunits of DNA polymerase III, suggesting that it may play a role to recruit the DNA polymerase III to the site of the MMR. Also implicated in DNA damage signaling, a process which induces cell cycle arrest and can lead to apoptosis in case of major DNA damages.

Mus musculus (taxid: 10090)

>sp|P14242|PMS1_YEAST DNA mismatch repair protein PMS1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PMS1 PE=1 SV=3

 Score = 96.3 bits (238), Expect = 1e-19,   Method: Compositional matrix adjust.
 Identities = 50/83 (60%), Positives = 64/83 (77%), Gaps = 5/83 (6%)

Query: 74  KVSGQAE-GFIIV--KYDS--DLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLT 128
           +V GQ   GFIIV  K D+  DLFI+DQHA+DEKYNFETLQ  TV KSQKL++PQ + L+
Sbjct: 675 EVVGQFNLGFIIVTRKVDNKYDLFIVDQHASDEKYNFETLQAVTVFKSQKLIIPQPVELS 734

Query: 129 KINQCILKDNLPVFYKNGFEFRI 151
            I++ ++ DNLPVF KNGF+ +I
Sbjct: 735 VIDELVVLDNLPVFEKNGFKLKI 757

Required for DNA mismatch repair (MMR), correcting base-base mismatches and insertion-deletion loops (IDLs) resulting from DNA replication, DNA damage or from recombination events between non-identical sequences during meiosis. Component of the MutLalpha heterodimer that forms a ternary complex with the MutS heterodimers, which initially recognize the DNA mismatches. This complex is thought to be responsible for directing the downsteam MMR events, including strand discrimination, excision, and resynthesis. Plays a major role in maintaining the genetic stability of simple sequence repeats and in the repair of heteroduplex sites present in meiotic recombination intermediates.

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

>sp|P54280|PMS1_SCHPO DNA mismatch repair protein pms1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=pms1 PE=3 SV=1

 Score = 72.8 bits (177), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 35/81 (43%), Positives = 53/81 (65%), Gaps = 1/81 (1%)

Query: 74  KVSGQ-AEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
           +V GQ   GFI+V + ++LFIIDQHA+DEK+N+E L+   VI SQ LV+P+ L L    +
Sbjct: 612 RVVGQFNRGFIVVVHGNNLFIIDQHASDEKFNYEHLKSNLVINSQDLVLPKRLDLAATEE 671

Query: 133 CILKDNLPVFYKNGFEFRITM 153
            +L D++ +  + GF   I +
Sbjct: 672 TVLIDHIDLIRRKGFGVAIDL 692

This protein is involved in the repair of mismatches in DNA.

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

>sp|Q54QA0|PMS1_DICDI Mismatch repair endonuclease pms1 OS=Dictyostelium discoideum GN=pms1 PE=3 SV=1

 Score = 71.2 bits (173), Expect = 4e-12,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 50/74 (67%), Gaps = 3/74 (4%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKT--TVIKSQKLVVPQNL-HLTKINQCILKD 137
           GFII K  +DLFIIDQHA DEKYNFE L K+  + I SQ L+ P  L  LT   + I+ +
Sbjct: 823 GFIIAKLGNDLFIIDQHAADEKYNFEILSKSVESSINSQPLLKPDTLSDLTSEEELIIIE 882

Query: 138 NLPVFYKNGFEFRI 151
           N+ +F KNGF+F I
Sbjct: 883 NVDLFKKNGFKFII 896

Component of the post-replicative DNA mismatch repair system (MMR). Heterodimerizes with mlh1 to form MutL alpha. DNA repair is initiated by MutS alpha (msh2-msh6) or MutS beta (msh2-msh3) binding to a dsDNA mismatch, then MutL alpha is recruited to the heteroduplex. Assembly of the MutL-MutS-heteroduplex ternary complex in presence of rfc and pcna is sufficient to activate endonuclease activity of pms1. It introduces single-strand breaks near the mismatch and thus generates new entry points for the exonuclease exo1 to degrade the strand containing the mismatch.

Dictyostelium discoideum (taxid: 44689)

>sp|A5GEV5|MUTL_GEOUR DNA mismatch repair protein MutL OS=Geobacter uraniireducens (strain Rf4) GN=mutL PE=3 SV=1

 Score = 49.3 bits (116), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 36/140 (25%), Positives = 64/140 (45%), Gaps = 13/140 (9%)

Query: 17  ITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTA----DRQFYFVNSRPCEP 72
           + + SP+  L + F +PP  T      G +S  +      TA    + + Y+     C  
Sbjct: 362 LARYSPEKHLQQSFTVPPAATFQ-RQQGAVSLPVAAREDDTASDKTESKGYY-----CSL 415

Query: 73  SKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQ---KTTVIKSQKLVVPQNLHLTK 129
           S +      +I+ +  +DL IIDQHA  E+  FE L+       ++SQ+L+ P+ + L+ 
Sbjct: 416 SVIGQFNAAYILCQDGTDLVIIDQHAAHERVAFEKLKAQFAAAQVESQRLLFPETIELSF 475

Query: 130 INQCILKDNLPVFYKNGFEF 149
                L+++L    + GF  
Sbjct: 476 KEGATLREHLAELGRLGFSL 495

This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex.

Geobacter uraniireducens (strain Rf4) (taxid: 351605)

>sp|B1H0C7|MUTL_UNCTG DNA mismatch repair protein MutL OS=Uncultured termite group 1 bacterium phylotype Rs-D17 GN=mutL PE=3 SV=1

 Score = 48.5 bits (114), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 34/99 (34%), Positives = 51/99 (51%), Gaps = 12/99 (12%)

Query: 74  KVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFE---TLQKTTVIKSQKLVVPQNLHLTK 129
           KV GQ  + +II     DL+I DQHA  E+  +E   +  K+  IK Q++++P+N  L+ 
Sbjct: 410 KVIGQVFDTYIIASNKGDLYIFDQHAAAERVRYEFYLSQMKSQTIKIQQMLMPENFDLSP 469

Query: 130 INQCILKDNLPVFYKNGF--------EFRITMMFANLRN 160
               +LK N+ +F + G          FRIT   A L N
Sbjct: 470 SISELLKANINIFNELGISIEEFGQNSFRITAYPALLGN 508

This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex.

Uncultured termite group 1 bacterium phylotype Rs-D17 (taxid: 471821)

>sp|A3CWX7|MUTL_METMJ DNA mismatch repair protein MutL OS=Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1) GN=mutL PE=3 SV=1

 Score = 45.4 bits (106), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 4/75 (5%)

Query: 77  GQAEGFIIVKYDSD--LFIIDQHATDEK--YNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
           GQ     IV   +D  L+++DQHA  E+  Y+  T Q+     SQ+L+ P  L L     
Sbjct: 402 GQVAATYIVAEGADGTLYLVDQHAAHERVLYDQVTEQRDKAAGSQELITPVVLSLPPKES 461

Query: 133 CILKDNLPVFYKNGF 147
             L+D +P+    GF
Sbjct: 462 AALRDAIPLLADEGF 476

This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex.

Methanoculleus marisnigri (strain ATCC 35101 / DSM 1498 / JR1) (taxid: 368407)

>sp|C5CF28|MUTL_KOSOT DNA mismatch repair protein MutL OS=Kosmotoga olearia (strain TBF 19.5.1) GN=mutL PE=3 SV=1

 Score = 45.4 bits (106), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 30/94 (31%), Positives = 47/94 (50%), Gaps = 1/94 (1%)

Query: 57  TADRQFYFVNSRPC-EPSKVSGQAEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIK 115
           TA R+F    ++   EP       E +I+ +    L I+DQHA  E+  +E L+K   I+
Sbjct: 405 TASRRFEKTEAKETGEPRLFGVFGERYILAETKDGLLIVDQHAAHERLIYEKLKKAAKIQ 464

Query: 116 SQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEF 149
           SQKL+ P  L L    + +L++      K GF+ 
Sbjct: 465 SQKLLSPIRLTLEDSRKSLLREKKNDVEKLGFQI 498

This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex.

Kosmotoga olearia (strain TBF 19.5.1) (taxid: 521045)

>sp|Q895H3|MUTL_CLOTE DNA mismatch repair protein MutL OS=Clostridium tetani (strain Massachusetts / E88) GN=mutL PE=3 SV=1

 Score = 45.1 bits (105), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 31/82 (37%), Positives = 44/82 (53%), Gaps = 4/82 (4%)

Query: 74  KVSGQAEG-FIIVKYDSDLFIIDQHATDEKYNFETLQ---KTTVIKSQKLVVPQNLHLTK 129
           K+ GQ +  +I+ +   +L+IIDQHA  EK  FET +   K   +KSQ L+ P  L L  
Sbjct: 433 KIIGQFDNTYILAESVKNLYIIDQHAAHEKILFETYRDKIKKDEVKSQLLLQPIVLELDS 492

Query: 130 INQCILKDNLPVFYKNGFEFRI 151
            +     DN  +FYK GF   +
Sbjct: 493 EDFSYYVDNKELFYKTGFNIEV 514

This protein is involved in the repair of mismatches in DNA. It is required for dam-dependent methyl-directed DNA mismatch repair. May act as a "molecular matchmaker", a protein that promotes the formation of a stable complex between two or more DNA-binding proteins in an ATP-dependent manner without itself being part of a final effector complex.

Clostridium tetani (strain Massachusetts / E88) (taxid: 212717)

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	200
157124912	874	DNA mismatch repair protein pms2 [Aedes	0.355	0.081	0.676	2e-21
157136917	926	DNA mismatch repair protein pms2 [Aedes	0.355	0.076	0.676	2e-21
195120550	489	GI20105 [Drosophila mojavensis] gi|19390	0.355	0.145	0.647	3e-21
301604746	848	PREDICTED: mismatch repair endonuclease	0.335	0.079	0.666	3e-21
195455398	875	GK23208 [Drosophila willistoni] gi|19417	0.355	0.081	0.676	3e-21
170063399	860	DNA mismatch repair protein pms1 [Culex	0.355	0.082	0.647	4e-21
357606259	820	putative DNA mismatch repair protein pms	0.39	0.095	0.670	5e-21
449283315	893	Mismatch repair endonuclease PMS2, parti	0.345	0.077	0.661	7e-21
328708648	591	PREDICTED: mismatch repair endonuclease	0.35	0.118	0.685	7e-21
158286232	882	AGAP007126-PA [Anopheles gambiae str. PE	0.355	0.080	0.647	8e-21

>gi|157124912|ref|XP_001660584.1| DNA mismatch repair protein pms2 [Aedes aegypti] gi|108873824|gb|EAT38049.1| AAEL010033-PA [Aedes aegypti]

 Score =  108 bits (269), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/71 (67%), Positives = 58/71 (81%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII + + DLFIIDQHATDEKYNFE LQ+TTV+++QKLVVPQ L LT +N+ IL DNL 
Sbjct: 688 GFIIARLEQDLFIIDQHATDEKYNFEDLQRTTVLQNQKLVVPQQLELTAVNEMILMDNLE 747

Query: 141 VFYKNGFEFRI 151
           +F  NGF+F I
Sbjct: 748 IFEMNGFKFEI 758

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157136917|ref|XP_001663861.1| DNA mismatch repair protein pms2 [Aedes aegypti] gi|108869823|gb|EAT34048.1| AAEL013690-PA [Aedes aegypti]

 Score =  107 bits (268), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 48/71 (67%), Positives = 58/71 (81%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII + + DLFIIDQHATDEKYNFE LQ+TTV+++QKLVVPQ L LT +N+ IL DNL 
Sbjct: 740 GFIIARLEQDLFIIDQHATDEKYNFEDLQRTTVLQNQKLVVPQQLELTAVNEMILMDNLE 799

Query: 141 VFYKNGFEFRI 151
           +F  NGF+F I
Sbjct: 800 IFEMNGFKFEI 810

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195120550|ref|XP_002004787.1| GI20105 [Drosophila mojavensis] gi|193909855|gb|EDW08722.1| GI20105 [Drosophila mojavensis]

 Score =  107 bits (267), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 46/71 (64%), Positives = 57/71 (80%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFIIVK + DLFI+DQHA DEKYNFE LQ+ T ++ Q+L VPQ L LT +N+ IL+D+LP
Sbjct: 328 GFIIVKLEDDLFIVDQHAADEKYNFEMLQRNTQLEHQRLTVPQTLELTAVNEMILQDHLP 387

Query: 141 VFYKNGFEFRI 151
           VF KNGF+F I
Sbjct: 388 VFEKNGFKFEI 398

Source: Drosophila mojavensis

Species: Drosophila mojavensis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|301604746|ref|XP_002932025.1| PREDICTED: mismatch repair endonuclease PMS2-like [Xenopus (Silurana) tropicalis]

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 46/69 (66%), Positives = 57/69 (82%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII K DSDLF+IDQHATDEKYNFE LQ+ TV++ Q+L+ PQ LHLT +N+ +L DNL 
Sbjct: 671 GFIITKLDSDLFMIDQHATDEKYNFEMLQQETVLQGQRLIAPQKLHLTAVNETVLIDNLD 730

Query: 141 VFYKNGFEF 149
           +F KNGF+F
Sbjct: 731 IFKKNGFDF 739

Source: Xenopus (Silurana) tropicalis

Species: Xenopus (Silurana) tropicalis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|195455398|ref|XP_002074706.1| GK23208 [Drosophila willistoni] gi|194170791|gb|EDW85692.1| GK23208 [Drosophila willistoni]

 Score =  107 bits (266), Expect = 3e-21,   Method: Compositional matrix adjust.
 Identities = 48/71 (67%), Positives = 58/71 (81%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFIIVK + DLFI+DQHA DEKYNFETLQK T ++ Q+L VPQ L LT IN+ +L D+LP
Sbjct: 686 GFIIVKLEDDLFIVDQHAADEKYNFETLQKCTQLEYQRLAVPQPLELTAINEMVLMDHLP 745

Query: 141 VFYKNGFEFRI 151
           VF KNGF+F+I
Sbjct: 746 VFEKNGFKFQI 756

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170063399|ref|XP_001867088.1| DNA mismatch repair protein pms1 [Culex quinquefasciatus] gi|167881032|gb|EDS44415.1| DNA mismatch repair protein pms1 [Culex quinquefasciatus]

 Score =  107 bits (266), Expect = 4e-21,   Method: Compositional matrix adjust.
 Identities = 46/71 (64%), Positives = 58/71 (81%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII + D+DLFIIDQHATDEKYNFE LQ+ TV+++QKLVVPQ L LT +N+ IL D+L 
Sbjct: 667 GFIIARLDADLFIIDQHATDEKYNFEDLQRNTVLQNQKLVVPQPLELTAVNEMILMDSLE 726

Query: 141 VFYKNGFEFRI 151
           +F  NGF+F +
Sbjct: 727 IFEMNGFQFEV 737

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357606259|gb|EHJ64985.1| putative DNA mismatch repair protein pms2 [Danaus plexippus]

 Score =  106 bits (265), Expect = 5e-21,   Method: Compositional matrix adjust.
 Identities = 53/79 (67%), Positives = 60/79 (75%), Gaps = 1/79 (1%)

Query: 74  KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
           K+ GQ   GFII + D DLFIIDQHATDE YNFETLQKTT + SQKLV+PQ L LT +N+
Sbjct: 634 KIIGQFNLGFIITRLDDDLFIIDQHATDEIYNFETLQKTTELTSQKLVIPQQLELTGVNE 693

Query: 133 CILKDNLPVFYKNGFEFRI 151
            IL DNL +F KNGF F I
Sbjct: 694 QILMDNLDIFKKNGFTFAI 712

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|449283315|gb|EMC89990.1| Mismatch repair endonuclease PMS2, partial [Columba livia]

 Score =  106 bits (264), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 47/71 (66%), Positives = 59/71 (83%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII K +SDLFIIDQHATDEKYNFE LQ+ TV++ QKL+ PQNL+LT +N+ +L +NL 
Sbjct: 716 GFIIAKLNSDLFIIDQHATDEKYNFEMLQQHTVLQGQKLIAPQNLNLTAVNETVLIENLE 775

Query: 141 VFYKNGFEFRI 151
           +F KNGF+F I
Sbjct: 776 IFRKNGFDFVI 786

Source: Columba livia

Species: Columba livia

Genus: Columba

Family: Columbidae

Order: Columbiformes

Class: Aves

Phylum: Chordata

Superkingdom: Eukaryota

>gi|328708648|ref|XP_003243755.1| PREDICTED: mismatch repair endonuclease PMS2-like [Acyrthosiphon pisum]

 Score =  105 bits (263), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 48/70 (68%), Positives = 57/70 (81%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFII K D+DLFI+DQHATDEKYNFETLQ TT I SQKLVVPQ L LT +N+ +L +N+ 
Sbjct: 412 GFIITKLDADLFIVDQHATDEKYNFETLQNTTKITSQKLVVPQQLELTAVNEIVLMENIN 471

Query: 141 VFYKNGFEFR 150
           VF  NGF+F+
Sbjct: 472 VFQMNGFDFQ 481

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158286232|ref|XP_308635.4| AGAP007126-PA [Anopheles gambiae str. PEST] gi|157020370|gb|EAA04111.4| AGAP007126-PA [Anopheles gambiae str. PEST]

 Score =  105 bits (263), Expect = 8e-21,   Method: Compositional matrix adjust.
 Identities = 46/71 (64%), Positives = 58/71 (81%)

Query: 81  GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLP 140
           GFIIV+   DLFI+DQHATDEKYNFE LQ+TTV+++Q+LVVPQ L LT +N+ +L DNL 
Sbjct: 687 GFIIVRLGDDLFIVDQHATDEKYNFEDLQRTTVLQNQRLVVPQPLELTAVNEMVLIDNLD 746

Query: 141 VFYKNGFEFRI 151
           VF  NGF+F +
Sbjct: 747 VFEMNGFKFEV 757

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	200
UNIPROTKB|F1NQJ2	878	Gga.22468 "Uncharacterized pro	0.39	0.088	0.620	3.7e-35
ZFIN|ZDB-GENE-030131-686	851	pms2 "PMS2 postmeiotic segrega	0.39	0.091	0.620	5.3e-35
UNIPROTKB|F1RFM9	852	PMS2 "Uncharacterized protein"	0.39	0.091	0.569	5e-34
UNIPROTKB|F1PNW0	866	PMS2 "Uncharacterized protein"	0.39	0.090	0.569	5.4e-34
UNIPROTKB|F1PNU2	897	PMS2 "Uncharacterized protein"	0.39	0.086	0.569	6e-34
UNIPROTKB|C9J167	756	PMS2 "Mismatch repair endonucl	0.39	0.103	0.556	9e-34
UNIPROTKB|I3L0B5	815	PMS2 "Mismatch repair endonucl	0.39	0.095	0.556	1.2e-33
UNIPROTKB|P54278	862	PMS2 "Mismatch repair endonucl	0.39	0.090	0.556	1.4e-33
FB|FBgn0011660	899	Pms2 "Pms2" [Drosophila melano	0.39	0.086	0.594	5.6e-32
UNIPROTKB|F1NQJ3	858	Gga.22468 "Uncharacterized pro	0.31	0.072	0.661	7e-32

UNIPROTKB|F1NQJ2 Gga.22468 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 254 (94.5 bits), Expect = 3.7e-35, Sum P(2) = 3.7e-35
 Identities = 49/79 (62%), Positives = 63/79 (79%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K +SDLFIIDQHATDEKYNFE LQ+ TV++ QKL+ PQNL+LT +N+
Sbjct:   693 EIIGQFNLGFIIAKLNSDLFIIDQHATDEKYNFEMLQQHTVLQGQKLIAPQNLNLTAVNE 752

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +NL +F KNGF+F I
Sbjct:   753 TVLIENLEIFRKNGFDFVI 771

GO:0005524 "ATP binding" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

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

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

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

GO:0032389 "MutLalpha complex" evidence=IEA

GO:0032407 "MutSalpha complex binding" evidence=IEA

ZFIN|ZDB-GENE-030131-686 pms2 "PMS2 postmeiotic segregation increased 2 (S. cerevisiae)" [Danio rerio (taxid:7955)]

 Score = 254 (94.5 bits), Expect = 5.3e-35, Sum P(2) = 5.3e-35
 Identities = 49/79 (62%), Positives = 62/79 (78%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K  SDLFIIDQHATDEKYNFE LQ+ TV+K Q+L+VPQ+LHL  I++
Sbjct:   666 EIIGQFNLGFIITKIKSDLFIIDQHATDEKYNFEMLQQNTVLKGQRLIVPQSLHLPAISE 725

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +NL +F KNGF+F I
Sbjct:   726 TVLMENLEIFRKNGFDFLI 744

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

UNIPROTKB|F1RFM9 PMS2 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 244 (91.0 bits), Expect = 5.0e-34, Sum P(2) = 5.0e-34
 Identities = 45/79 (56%), Positives = 63/79 (79%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K ++D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+VPQ L+LT +N+
Sbjct:   667 EIIGQFNLGFIITKLNADIFIVDQHATDEKYNFEMLQQHTVLQGQRLIVPQTLNLTAVNE 726

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +NL +F KNGF+F I
Sbjct:   727 AVLIENLDIFRKNGFDFVI 745

GO:0032407 "MutSalpha complex binding" evidence=IEA

GO:0032389 "MutLalpha complex" evidence=IEA

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

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

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

GO:0006298 "mismatch repair" evidence=IEA

GO:0003697 "single-stranded DNA binding" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1PNW0 PMS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 239 (89.2 bits), Expect = 5.4e-34, Sum P(2) = 5.4e-34
 Identities = 45/79 (56%), Positives = 61/79 (77%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K  +D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+ PQ L+LT +N+
Sbjct:   681 EIIGQFNLGFIITKLKADIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNE 740

Query:   133 CILKDNLPVFYKNGFEFRI 151
              IL +NL +F KNGF+F I
Sbjct:   741 AILIENLEIFRKNGFDFVI 759

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|F1PNU2 PMS2 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 239 (89.2 bits), Expect = 6.0e-34, Sum P(2) = 6.0e-34
 Identities = 45/79 (56%), Positives = 61/79 (77%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K  +D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+ PQ L+LT +N+
Sbjct:   712 EIIGQFNLGFIITKLKADIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNE 771

Query:   133 CILKDNLPVFYKNGFEFRI 151
              IL +NL +F KNGF+F I
Sbjct:   772 AILIENLEIFRKNGFDFVI 790

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0005524 "ATP binding" evidence=IEA

UNIPROTKB|C9J167 PMS2 "Mismatch repair endonuclease PMS2" [Homo sapiens (taxid:9606)]

 Score = 239 (89.2 bits), Expect = 9.0e-34, Sum P(2) = 9.0e-34
 Identities = 44/79 (55%), Positives = 61/79 (77%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K + D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+ PQ L+LT +N+
Sbjct:   571 EIIGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNE 630

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +NL +F KNGF+F I
Sbjct:   631 AVLIENLEIFRKNGFDFVI 649

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

UNIPROTKB|I3L0B5 PMS2 "Mismatch repair endonuclease PMS2" [Homo sapiens (taxid:9606)]

 Score = 239 (89.2 bits), Expect = 1.2e-33, Sum P(2) = 1.2e-33
 Identities = 44/79 (55%), Positives = 61/79 (77%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K + D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+ PQ L+LT +N+
Sbjct:   630 EIIGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNE 689

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +NL +F KNGF+F I
Sbjct:   690 AVLIENLEIFRKNGFDFVI 708

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

UNIPROTKB|P54278 PMS2 "Mismatch repair endonuclease PMS2" [Homo sapiens (taxid:9606)]

 Score = 239 (89.2 bits), Expect = 1.4e-33, Sum P(2) = 1.4e-33
 Identities = 44/79 (55%), Positives = 61/79 (77%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFII K + D+FI+DQHATDEKYNFE LQ+ TV++ Q+L+ PQ L+LT +N+
Sbjct:   677 EIIGQFNLGFIITKLNEDIFIVDQHATDEKYNFEMLQQHTVLQGQRLIAPQTLNLTAVNE 736

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +NL +F KNGF+F I
Sbjct:   737 AVLIENLEIFRKNGFDFVI 755

GO:0005524 "ATP binding" evidence=IEA

GO:0004519 "endonuclease activity" evidence=IEA

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

GO:0042493 "response to drug" evidence=IEA

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

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

GO:0016887 "ATPase activity" evidence=IBA

GO:0032300 "mismatch repair complex" evidence=IBA

GO:0032389 "MutLalpha complex" evidence=IBA

GO:0005515 "protein binding" evidence=IPI

GO:0032407 "MutSalpha complex binding" evidence=IDA

GO:0003677 "DNA binding" evidence=IDA

GO:0005634 "nucleus" evidence=IC

GO:0006298 "mismatch repair" evidence=IDA

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

GO:0003697 "single-stranded DNA binding" evidence=IDA

GO:0006200 "ATP catabolic process" evidence=IBA

FB|FBgn0011660 Pms2 "Pms2" [Drosophila melanogaster (taxid:7227)]

 Score = 252 (93.8 bits), Expect = 5.6e-32, Sum P(2) = 5.6e-32
 Identities = 47/79 (59%), Positives = 63/79 (79%)

Query:    74 KVSGQAE-GFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQ 132
             ++ GQ   GFIIVK + DLFI+DQHATDEKYNFETLQ+TT ++ Q+L VPQNL LT +N+
Sbjct:   702 EIIGQFNLGFIIVKLEDDLFIVDQHATDEKYNFETLQRTTQLEYQRLAVPQNLELTAVNE 761

Query:   133 CILKDNLPVFYKNGFEFRI 151
              +L +++ VF KNGF+F +
Sbjct:   762 MVLLNHIDVFEKNGFKFEV 780

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

GO:0005524 "ATP binding" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

GO:0005875 "microtubule associated complex" evidence=IDA

GO:0032389 "MutLalpha complex" evidence=IBA

GO:0032300 "mismatch repair complex" evidence=IBA

GO:0003697 "single-stranded DNA binding" evidence=IBA

GO:0016887 "ATPase activity" evidence=IBA

GO:0032407 "MutSalpha complex binding" evidence=IBA

GO:0007131 "reciprocal meiotic recombination" evidence=IBA

UNIPROTKB|F1NQJ3 Gga.22468 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 223 (83.6 bits), Expect = 7.0e-32, Sum P(2) = 7.0e-32
 Identities = 41/62 (66%), Positives = 52/62 (83%)

Query:    90 DLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEF 149
             DLFIIDQHATDEKYNFE LQ+ TV++ QKL+ PQNL+LT +N+ +L +NL +F KNGF+F
Sbjct:   692 DLFIIDQHATDEKYNFEMLQQHTVLQGQKLIAPQNLNLTAVNETVLIENLEIFRKNGFDF 751

Query:   150 RI 151
              I
Sbjct:   752 VI 753

GO:0005524 "ATP binding" evidence=IEA

GO:0006298 "mismatch repair" evidence=IEA

GO:0030983 "mismatched DNA binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	200
smart00853	140	smart00853, MutL_C, MutL C terminal dimerisation d	5e-18
pfam08676	144	pfam08676, MutL_C, MutL C terminal dimerisation do	3e-14
cd03484	142	cd03484, MutL_Trans_hPMS_2_like, MutL_Trans_hPMS2_	5e-14
COG0323	638	COG0323, MutL, DNA mismatch repair enzyme (predict	1e-13
PRK00095	617	PRK00095, mutL, DNA mismatch repair protein; Revie	8e-07
cd00782	122	cd00782, MutL_Trans, MutL_Trans: transducer domain	1e-06
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-06
pfam08496	154	pfam08496, Peptidase_S49_N, Peptidase family S49 N	1e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	2e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	4e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	5e-05
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	5e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	7e-05
pfam10278	178	pfam10278, Med19, Mediator of RNA pol II transcrip	7e-05
PRK11778	330	PRK11778, PRK11778, putative inner membrane peptid	8e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	9e-05
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	1e-04
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-04
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-04
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	1e-04
pfam10278	178	pfam10278, Med19, Mediator of RNA pol II transcrip	2e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	3e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	4e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	5e-04
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.001
PRK11192	434	PRK11192, PRK11192, ATP-dependent RNA helicase Srm	0.001
PRK14552	414	PRK14552, PRK14552, C/D box methylation guide ribo	0.001
TIGR00585	312	TIGR00585, mutl, DNA mismatch repair protein MutL	0.001
PTZ00074	135	PTZ00074, PTZ00074, 60S ribosomal protein L34; Pro	0.001
PTZ00074	135	PTZ00074, PTZ00074, 60S ribosomal protein L34; Pro	0.002
pfam07771	120	pfam07771, TSGP1, Tick salivary peptide group 1	0.002
pfam01119	119	pfam01119, DNA_mis_repair, DNA mismatch repair pro	0.002
PTZ00074	135	PTZ00074, PTZ00074, 60S ribosomal protein L34; Pro	0.003
cd00329	107	cd00329, TopoII_MutL_Trans, MutL_Trans: transducer	0.003
pfam06658	142	pfam06658, DUF1168, Protein of unknown function (D	0.004

>gnl|CDD|214857 smart00853, MutL_C, MutL C terminal dimerisation domain

 Score = 76.2 bits (188), Expect = 5e-18
 Identities = 25/77 (32%), Positives = 45/77 (58%), Gaps = 2/77 (2%)

Query: 77  GQ-AEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTV-IKSQKLVVPQNLHLTKINQCI 134
           GQ A  +I+ + +  L+++DQHA  E+  +E L K    ++SQ L++P  L L+     +
Sbjct: 3   GQVAGTYILAEREDGLYLLDQHAAHERILYEQLLKQAGGLESQPLLIPVRLELSPQEAAL 62

Query: 135 LKDNLPVFYKNGFEFRI 151
           L+++L +  + GFE  I
Sbjct: 63  LEEHLELLRQLGFELEI 79

MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation. Length = 140

>gnl|CDD|219965 pfam08676, MutL_C, MutL C terminal dimerisation domain

 Score = 66.1 bits (162), Expect = 3e-14
 Identities = 21/76 (27%), Positives = 41/76 (53%), Gaps = 3/76 (3%)

Query: 77  GQ-AEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTT--VIKSQKLVVPQNLHLTKINQC 133
           GQ    +I+ + +  L+++DQHA  E+  +E L+       +SQ L++P  L L+     
Sbjct: 7   GQVHGTYILAENEDGLYLVDQHAAHERILYEKLKSKLKEGGQSQPLLIPLTLELSPEEAA 66

Query: 134 ILKDNLPVFYKNGFEF 149
           +L+++  +  + GFE 
Sbjct: 67  LLEEHKELLARLGFEL 82

MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation. Length = 144

>gnl|CDD|239566 cd03484, MutL_Trans_hPMS_2_like, MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2)

 Score = 65.8 bits (161), Expect = 5e-14
 Identities = 23/70 (32%), Positives = 36/70 (51%), Gaps = 1/70 (1%)

Query: 8  ISQLINIIPITQSSPDASLLEEFRIPPD-ITAMFTLSGFISSAIHGHGRSTADRQFYFVN 66
             +  +IPI          EE     D   +   ++G+IS   HG GRS++DRQF+++N
Sbjct: 12 GKVIKGLIPINLELDVNPTKEELDSDEDLADSEVKITGYISKPSHGCGRSSSDRQFFYIN 71

Query: 67 SRPCEPSKVS 76
           RP +  KV+
Sbjct: 72 GRPVDLKKVA 81

hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome. Length = 142

>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]

 Score = 68.1 bits (167), Expect = 1e-13
 Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 74  KVSGQ-AEGFIIVKYDSDLFIIDQHATDEKYNFETLQKT--TVIKSQKLVVPQNLHLTKI 130
           +  GQ    +I+ +++  L ++DQHA  E+  +E L+     V + Q L++P  L L+  
Sbjct: 453 EAIGQVHGTYILAEHEDGLVLVDQHAAHERILYEKLKNELGNVGELQPLLIPIRLELSPE 512

Query: 131 NQCILKDNLPVFYKNGFEF 149
              +L+++     K GFE 
Sbjct: 513 EADVLEEHKEELEKLGFEI 531

Length = 638

>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed

 Score = 48.3 bits (116), Expect = 8e-07
 Identities = 21/77 (27%), Positives = 41/77 (53%), Gaps = 4/77 (5%)

Query: 77  GQAEG-FIIVKYDSDLFIIDQHATDEKYNFETLQ---KTTVIKSQKLVVPQNLHLTKINQ 132
           GQ  G +I+ + +  L+++DQHA  E+  +E L+       + SQ L++P  L L++   
Sbjct: 435 GQLHGTYILAENEDGLYLVDQHAAHERLLYEQLKDKLAEVGLASQPLLIPLVLELSEDEA 494

Query: 133 CILKDNLPVFYKNGFEF 149
             L+++  +  + G E 
Sbjct: 495 DRLEEHKELLARLGLEL 511

Length = 617

>gnl|CDD|238405 cd00782, MutL_Trans, MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family

 Score = 45.6 bits (109), Expect = 1e-06
 Identities = 18/37 (48%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 40 FTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVS 76
          F +SG+IS      GRS+ DRQF FVN RP     +S
Sbjct: 27 FRISGYISKP--DFGRSSKDRQFLFVNGRPVRDKLLS 61

This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome. Mutation in hMLH1 accounts for a large fraction of HNPCC families. There is no convincing evidence to support hPMS1 having a role in HNPCC predisposition. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Length = 122

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 46.5 bits (111), Expect = 3e-06
 Identities = 12/27 (44%), Positives = 18/27 (66%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           R +KK+K+K+K K KK+ +  K   KR
Sbjct: 399 RAEKKEKEKEKPKVKKRHRDTKNIGKR 425

Length = 434

>gnl|CDD|219868 pfam08496, Peptidase_S49_N, Peptidase family S49 N-terminal

 Score = 43.3 bits (103), Expect = 1e-05
 Identities = 16/34 (47%), Positives = 23/34 (67%), Gaps = 2/34 (5%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKRLYI--FK 197
            K +KK +K K K +KKK KK++ K RL++  FK
Sbjct: 72  EKAEKKAEKAKAKAEKKKAKKEEPKPRLFVLDFK 105

This domain is found to the N-terminus of bacterial signal peptidases of the S49 family (pfam01343). Length = 154

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 44.2 bits (105), Expect = 1e-05
 Identities = 16/27 (59%), Positives = 25/27 (92%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           +K+++KK +K+KKKKK+KKK KK+KK+
Sbjct: 385 KKREEKKPQKRKKKKKRKKKGKKRKKK 411

Length = 414

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 44.2 bits (105), Expect = 2e-05
 Identities = 13/31 (41%), Positives = 20/31 (64%)

Query: 162 DGTSRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           +  + K  KK   K+ +KK+K+K+K K KKR
Sbjct: 385 EKKTGKPSKKVLAKRAEKKEKEKEKPKVKKR 415

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 44.2 bits (105), Expect = 2e-05
 Identities = 11/27 (40%), Positives = 18/27 (66%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
            +KK+K+K+K K KK+ +  K   K+R
Sbjct: 400 AEKKEKEKEKPKVKKRHRDTKNIGKRR 426

Length = 434

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 43.0 bits (102), Expect = 4e-05
 Identities = 16/27 (59%), Positives = 25/27 (92%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           +KK+++KK +K+KKKKK+KKK KK+K+
Sbjct: 384 KKKREEKKPQKRKKKKKRKKKGKKRKK 410

Length = 414

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 43.0 bits (102), Expect = 5e-05
 Identities = 13/34 (38%), Positives = 22/34 (64%)

Query: 165 SRKKKKKKKKKKKKKKKKKKKKKKKKKRLYIFKK 198
           S+K   K+ +KK+K+K+K K KK+ +    I K+
Sbjct: 392 SKKVLAKRAEKKEKEKEKPKVKKRHRDTKNIGKR 425

Length = 434

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 18/27 (66%), Positives = 24/27 (88%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           R++KK +K+KKKKK+KKK KK+KKK R
Sbjct: 387 REEKKPQKRKKKKKRKKKGKKRKKKGR 413

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 42.6 bits (101), Expect = 5e-05
 Identities = 16/27 (59%), Positives = 24/27 (88%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           ++++KK +K+KKKKK+KKK KK+KKK 
Sbjct: 386 KREEKKPQKRKKKKKRKKKGKKRKKKG 412

Length = 414

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 42.2 bits (100), Expect = 7e-05
 Identities = 10/26 (38%), Positives = 18/26 (69%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKK 191
           +K+K+K+K K KK+ +  K   K++K
Sbjct: 402 KKEKEKEKPKVKKRHRDTKNIGKRRK 427

Length = 434

>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19

 Score = 41.4 bits (97), Expect = 7e-05
 Identities = 19/31 (61%), Positives = 24/31 (77%)

Query: 162 DGTSRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
            G  +K KKKK +  K++KKKKK+KKKKKKR
Sbjct: 138 KGHEKKHKKKKHEDDKERKKKKKEKKKKKKR 168

Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. Length = 178

>gnl|CDD|236978 PRK11778, PRK11778, putative inner membrane peptidase; Provisional

 Score = 42.1 bits (100), Expect = 8e-05
 Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKKRLYI--FK 197
            K   K +KKK+K++ K  K K K RL++  FK
Sbjct: 66  LKAWHKAQKKKEKQEAKAAKAKSKPRLFVLDFK 98

Length = 330

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 41.9 bits (99), Expect = 9e-05
 Identities = 10/26 (38%), Positives = 18/26 (69%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKKR 192
           KK+K+K+K K KK+ +  K   K+++
Sbjct: 402 KKEKEKEKPKVKKRHRDTKNIGKRRK 427

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 12/28 (42%), Positives = 18/28 (64%)

Query: 165 SRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           S KK  K  KK   K+ +KK+K+K+K +
Sbjct: 384 SEKKTGKPSKKVLAKRAEKKEKEKEKPK 411

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 12/29 (41%), Positives = 19/29 (65%)

Query: 163 GTSRKKKKKKKKKKKKKKKKKKKKKKKKK 191
           G   KK   K+ +KK+K+K+K K KK+ +
Sbjct: 389 GKPSKKVLAKRAEKKEKEKEKPKVKKRHR 417

Length = 434

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 17/26 (65%), Positives = 22/26 (84%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKK 191
            KK +K+KKKKK+KKK KK+KKK +K
Sbjct: 389 EKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 41.9 bits (99), Expect = 1e-04
 Identities = 16/26 (61%), Positives = 23/26 (88%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKKR 192
           +KK +K+KKKKK+KKK KK+KKK ++
Sbjct: 389 EKKPQKRKKKKKRKKKGKKRKKKGRK 414

Length = 414

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 41.5 bits (98), Expect = 1e-04
 Identities = 17/26 (65%), Positives = 23/26 (88%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKKR 192
            KKK+++KK +K+KKKKK+KKK KKR
Sbjct: 383 PKKKREEKKPQKRKKKKKRKKKGKKR 408

Length = 414

>gnl|CDD|150884 pfam10278, Med19, Mediator of RNA pol II transcription subunit 19

 Score = 39.8 bits (93), Expect = 2e-04
 Identities = 18/32 (56%), Positives = 23/32 (71%)

Query: 161 GDGTSRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           G     KK KKKK +  K++KKKKK+KKKKK+
Sbjct: 136 GLKGHEKKHKKKKHEDDKERKKKKKEKKKKKK 167

Med19 represents a family of conserved proteins which are members of the multi-protein co-activator Mediator complex. Mediator is required for activation of RNA polymerase II transcription by DNA binding transactivators. Length = 178

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 40.7 bits (96), Expect = 3e-04
 Identities = 12/29 (41%), Positives = 19/29 (65%)

Query: 164 TSRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           T +  KK   K+ +KK+K+K+K K KK+ 
Sbjct: 388 TGKPSKKVLAKRAEKKEKEKEKPKVKKRH 416

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 40.7 bits (96), Expect = 3e-04
 Identities = 9/26 (34%), Positives = 17/26 (65%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKK 191
           ++K+K+K K KK+ +  K   K++K 
Sbjct: 403 KEKEKEKPKVKKRHRDTKNIGKRRKP 428

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 39.9 bits (94), Expect = 4e-04
 Identities = 10/33 (30%), Positives = 20/33 (60%)

Query: 160 NGDGTSRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
            G  + +   K+ +KK+K+K+K K KK+ +  +
Sbjct: 388 TGKPSKKVLAKRAEKKEKEKEKPKVKKRHRDTK 420

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 39.9 bits (94), Expect = 5e-04
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKK 191
           K+K+K K KK+ +  K   K++K  
Sbjct: 405 KEKEKPKVKKRHRDTKNIGKRRKPS 429

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 12/33 (36%), Positives = 21/33 (63%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKKRLYIFKKH 199
            +KK  K  KK   K+ +KK+K+K++  + K+H
Sbjct: 384 SEKKTGKPSKKVLAKRAEKKEKEKEKPKVKKRH 416

Length = 434

>gnl|CDD|236877 PRK11192, PRK11192, ATP-dependent RNA helicase SrmB; Provisional

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 8/27 (29%), Positives = 15/27 (55%)

Query: 166 RKKKKKKKKKKKKKKKKKKKKKKKKKR 192
           ++K+K K KK+ +  K   K++K    
Sbjct: 405 KEKEKPKVKKRHRDTKNIGKRRKPSGT 431

Length = 434

>gnl|CDD|237753 PRK14552, PRK14552, C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional

 Score = 38.8 bits (91), Expect = 0.001
 Identities = 15/26 (57%), Positives = 22/26 (84%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKKR 192
           K  KKK+++KK +K+KKKKK+KKK +
Sbjct: 381 KPPKKKREEKKPQKRKKKKKRKKKGK 406

Length = 414

>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL

 Score = 38.0 bits (89), Expect = 0.001
 Identities = 13/37 (35%), Positives = 16/37 (43%), Gaps = 1/37 (2%)

Query: 40  FTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVS 76
             L GFIS       R +   QF F+N RP E   + 
Sbjct: 235 LQLEGFISQPNVTRSRRSGW-QFLFINGRPVELKLLL 270

All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University) [DNA metabolism, DNA replication, recombination, and repair]. Length = 312

>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional

 Score = 37.0 bits (86), Expect = 0.001
 Identities = 18/28 (64%), Positives = 22/28 (78%)

Query: 165 SRKKKKKKKKKKKKKKKKKKKKKKKKKR 192
            + K+KK+KKKKKKKKKKK  KK  KK+
Sbjct: 107 EKAKQKKQKKKKKKKKKKKTSKKAAKKK 134

Length = 135

>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional

 Score = 37.0 bits (86), Expect = 0.002
 Identities = 19/28 (67%), Positives = 23/28 (82%)

Query: 164 TSRKKKKKKKKKKKKKKKKKKKKKKKKK 191
            +++KK+KKKKKKKKKKK  KK  KKKK
Sbjct: 108 KAKQKKQKKKKKKKKKKKTSKKAAKKKK 135

Length = 135

>gnl|CDD|219564 pfam07771, TSGP1, Tick salivary peptide group 1

 Score = 36.4 bits (84), Expect = 0.002
 Identities = 16/32 (50%), Positives = 17/32 (53%)

Query: 160 NGDGTSRKKKKKKKKKKKKKKKKKKKKKKKKK 191
             D      +K KKKKKK KK KK KK  KK 
Sbjct: 89  PDDHPPEPTEKPKKKKKKSKKTKKPKKSSKKD 120

This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis. Also present are peptides from a related tick species, Ixodes ricinus. They are characterized by a putative signal peptide indicative of secretion and conserved cysteine residues. Length = 120

>gnl|CDD|201604 pfam01119, DNA_mis_repair, DNA mismatch repair protein, C-terminal domain

 Score = 36.3 bits (85), Expect = 0.002
 Identities = 15/30 (50%), Positives = 16/30 (53%), Gaps = 2/30 (6%)

Query: 40 FTLSGFISSAIHGHGRSTADRQFYFVNSRP 69
            LSGFIS       RS  D Q+ FVN RP
Sbjct: 23 LRLSGFISKP--ELSRSNRDYQYLFVNGRP 50

This family represents the C-terminal domain of the mutL/hexB/PMS1 family. This domain has a ribosomal S5 domain 2-like fold. Length = 119

>gnl|CDD|185429 PTZ00074, PTZ00074, 60S ribosomal protein L34; Provisional

 Score = 35.8 bits (83), Expect = 0.003
 Identities = 18/25 (72%), Positives = 21/25 (84%)

Query: 167 KKKKKKKKKKKKKKKKKKKKKKKKK 191
           K+K K+KK+KKKKKKKKKKK  KK 
Sbjct: 106 KEKAKQKKQKKKKKKKKKKKTSKKA 130

Length = 135

>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins

 Score = 35.7 bits (83), Expect = 0.003
 Identities = 16/35 (45%), Positives = 18/35 (51%), Gaps = 2/35 (5%)

Query: 40 FTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSK 74
          F + G IS      GRS+ DRQF FVN RP     
Sbjct: 27 FRVEGAISYP--DSGRSSKDRQFSFVNGRPVREGG 59

This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch repair (MMR). Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families. Length = 107

>gnl|CDD|219124 pfam06658, DUF1168, Protein of unknown function (DUF1168)

 Score = 36.2 bits (84), Expect = 0.004
 Identities = 17/27 (62%), Positives = 22/27 (81%)

Query: 165 SRKKKKKKKKKKKKKKKKKKKKKKKKK 191
           + KK+ K++KKK+KKKKKKK KK  KK
Sbjct: 83  TAKKRAKRQKKKQKKKKKKKAKKGNKK 109

This family consists of several hypothetical eukaryotic proteins of unknown function. Length = 142

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	200
PF08676	144	MutL_C: MutL C terminal dimerisation domain; Inter	99.82
smart00853	136	MutL_C MutL C terminal dimerisation domain. MutL a	99.8
PRK00095	617	mutL DNA mismatch repair protein; Reviewed	99.71
COG0323	638	MutL DNA mismatch repair enzyme (predicted ATPase)	99.71
KOG1978|consensus	672		99.35
cd03485	132	MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: tran	98.72
cd03484	142	MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: tran	98.62
cd03482	123	MutL_Trans_MutL MutL_Trans_MutL: transducer domain	98.58
cd03483	127	MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain	98.53
PF01119	119	DNA_mis_repair: DNA mismatch repair protein, C-ter	98.46
cd03486	141	MutL_Trans_MLH3 MutL_Trans_MLH3: transducer domain	98.41
cd00782	122	MutL_Trans MutL_Trans: transducer domain, having a	98.39
KOG1977|consensus	1142		97.99
KOG1978|consensus	672		97.81
TIGR00585	312	mutl DNA mismatch repair protein MutL. All protein	97.35
PRK00095	617	mutL DNA mismatch repair protein; Reviewed	97.29
cd00329	107	TopoII_MutL_Trans MutL_Trans: transducer domain, h	96.72
KOG1979|consensus	694		80.4

>PF08676 MutL_C: MutL C terminal dimerisation domain; InterPro: IPR014790 MutL and MutS are key components of the DNA repair machinery that corrects replication errors []

Probab=99.82  E-value=2.3e-20  Score=147.45  Aligned_cols=84  Identities=32%  Similarity=0.429  Sum_probs=73.2

Q ss_pred             Ccccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhhcc--ccccccccCceeecCHHHHHHHHhhHHHHHhCCCee
Q psy13676         73 SKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTV--IKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEF  149 (200)
Q Consensus        73 ~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~~~--~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~lGf~i  149 (200)
                      .+++||+ ++||+++.+++|++||||||||||+||+|+++..  ..+|+|++|+.+++++.+.+.+.++.+.|++|||++
T Consensus         3 ~~vlgq~~~~yil~~~~~~L~liDqHAAhERi~~E~l~~~~~~~~~~q~Ll~P~~~~ls~~e~~~l~~~~~~L~~~Gf~~   82 (144)
T PF08676_consen    3 LKVLGQLDNKYILAESEDGLYLIDQHAAHERILYEKLLKQLEEGEQSQPLLFPIELELSPQEAELLEENKEELEKLGFEI   82 (144)
T ss_dssp             -EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHCS-EEEEEEEEEEE--HHHHHHHHHHHHHHHHTT-EE
T ss_pred             eeeHhHhCCEEEEEEeCCCEEEEEHHHHHHHHHHHHHHHhhccCCCceecCCCccCCCCHHHHHHHHHHHHHHHhCCeEE
Confidence            4789999 9999999999999999999999999999999832  289999999999999999999999999999999999


Q ss_pred             EEcCCcc
Q psy13676        150 RITMMFA  156 (200)
Q Consensus       150 e~~g~~~  156 (200)
                      +.++++.
T Consensus        83 ~~~~~~~   89 (144)
T PF08676_consen   83 EEFGENS   89 (144)
T ss_dssp             EEESTTE
T ss_pred             EEecCCE
Confidence            9766664

MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signalling complex for repair. The N-terminal region of MutL contains the ATPase domain and the C-terminal is involved in dimerisation []. ; GO: 0005524 ATP binding, 0006298 mismatch repair; PDB: 3NCV_B 1X9Z_B 3GAB_C 3KDK_A 3KDG_A.

>smart00853 MutL_C MutL C terminal dimerisation domain

Probab=99.80  E-value=2.2e-19  Score=140.00  Aligned_cols=84  Identities=30%  Similarity=0.506  Sum_probs=77.0

Q ss_pred             Ccccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhh--c-cc-cccccccCceeecCHHHHHHHHhhHHHHHhCCC
Q psy13676         73 SKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT--T-VI-KSQKLVVPQNLHLTKINQCILKDNLPVFYKNGF  147 (200)
Q Consensus        73 ~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~--~-~~-~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~lGf  147 (200)
                      .+++||+ ++||+++.+++|++|||||||||++||++++.  . .. .+|++++|+.+++++.+.+.+.++.+.|++|||
T Consensus         2 ~~~l~qv~~~yil~~~~~~l~liDqhaA~ERi~~e~l~~~~~~~~~~~~Q~Ll~P~~i~l~~~e~~~l~~~~~~l~~~Gf   81 (136)
T smart00853        2 GRVLGQVHGTYILAESEDGLVLIDQHAAHERILYEQLKAKLQAGLLEKSQPLLIPVILELSPEEAALLEEHQELLARLGF   81 (136)
T ss_pred             ccEEEEEcCEEEEEEcCCCEEEEEhHHHHHHHHHHHHHHHHhcCCCccccccCCCEEEEcCHHHHHHHHHHHHHHHHcCe
Confidence            4678899 99999999999999999999999999999986  2 33 479999999999999999999999999999999


Q ss_pred             eeEEcCCcc
Q psy13676        148 EFRITMMFA  156 (200)
Q Consensus       148 ~ie~~g~~~  156 (200)
                      +++++|+.+
T Consensus        82 ~~~~~~~~~   90 (136)
T smart00853       82 ELEIFGGQS   90 (136)
T ss_pred             EEEccCCCE
Confidence            999988774

MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.

>PRK00095 mutL DNA mismatch repair protein; Reviewed

Probab=99.71  E-value=3e-17  Score=157.84  Aligned_cols=86  Identities=23%  Similarity=0.358  Sum_probs=79.6

Q ss_pred             Ccccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhh-c--cccccccccCceeecCHHHHHHHHhhHHHHHhCCCe
Q psy13676         73 SKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT-T--VIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFE  148 (200)
Q Consensus        73 ~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~-~--~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~lGf~  148 (200)
                      .+++||+ ++|||++.+++|++||||||||||+||+|++. .  ...+|.|++|+.++|++.|.+.++++.+.|++|||+
T Consensus       431 ~~vigQv~~~YIl~e~~~~L~iIDQHAAhERI~yE~l~~~~~~~~~~~Q~LL~P~~l~Ls~~e~~~l~~~~~~L~~lGf~  510 (617)
T PRK00095        431 GYALGQLHGTYILAENEDGLYLVDQHAAHERLLYEQLKDKLAEVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLE  510 (617)
T ss_pred             ceEeEEEcCEEEEEEeCCcEEEEEHHHHHHHHHHHHHHHHhccCCCcccccccCeEEeeCHHHHHHHHHHHHHHHhCCcE
Confidence            4689999 99999999999999999999999999999997 2  477899999999999999999999999999999999


Q ss_pred             eEEcCCccee
Q psy13676        149 FRITMMFANL  158 (200)
Q Consensus       149 ie~~g~~~~~  158 (200)
                      ++.+|+++..
T Consensus       511 ~e~fg~~si~  520 (617)
T PRK00095        511 LEPFGPNSFA  520 (617)
T ss_pred             EEEcCCCEEE
Confidence            9998877633

>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]

Probab=99.71  E-value=5e-17  Score=156.96  Aligned_cols=80  Identities=26%  Similarity=0.390  Sum_probs=73.5

Q ss_pred             ccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhhccc--cccccccCceeecCHHHHHHHHhhHHHHHhCCCeeEEcC
Q psy13676         77 GQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVI--KSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFRITM  153 (200)
Q Consensus        77 gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~~~~--~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~lGf~ie~~g  153 (200)
                      +|+ ++|||++.+++|++|||||||||++||.|+.....  ..|+|++|..+++++.|...+.++.+.|+++||+++.++
T Consensus       456 ~q~~~~yil~e~~~~L~lvDqhaa~Eri~ye~l~~~~~~~~~~Q~LliP~~~~l~~~e~~~~~~~~~~l~~~G~~i~~~g  535 (638)
T COG0323         456 GQVHGTYILAEHEDGLVLVDQHAAHERILYEKLKNELGNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIESFG  535 (638)
T ss_pred             EEecceEEEEEeCCCEEEEEhHHhHHHHHHHHHHHHhcccccccccccCeeeecCHHHHHHHHHHHHHHHhcCEEEEEcC
Confidence            444 78999999999999999999999999999998322  799999999999999999999999999999999999888


Q ss_pred             Ccc
Q psy13676        154 MFA  156 (200)
Q Consensus       154 ~~~  156 (200)
                      +..
T Consensus       536 ~~~  538 (638)
T COG0323         536 ENS  538 (638)
T ss_pred             Cce
Confidence            875

>KOG1978|consensus

Probab=99.35  E-value=7.4e-13  Score=127.09  Aligned_cols=95  Identities=51%  Similarity=0.752  Sum_probs=89.0

Q ss_pred             ecCCCCCCCcccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhhccccccccccCceeecCHHHHHHHHhhHHHHH
Q psy13676         65 VNSRPCEPSKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPVFY  143 (200)
Q Consensus        65 INkrp~~~~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~~~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~  143 (200)
                      +++..+.-+.++||| .+||++.++.+|+++||||+||..+||.|.+...+..|+|+.|+.+++++.+...+.++++.|+
T Consensus       481 v~k~df~~meiigqfNlgFIi~~l~~dlfIvdqha~dEk~Nfe~l~~~~~L~~Q~l~~P~~l~ls~~nE~vl~d~l~~f~  560 (672)
T KOG1978|consen  481 VAKADFSRMEIIGQFNLGFIIVKLEKDLFIVDQHASDEKRNFERLQSTTVLKAQPLICPQALDLSAINEMVLLDNLPLFE  560 (672)
T ss_pred             ccccchhhcceeeeccccceeeeccCceEEeccchhhhhhhHHHHHHhcccccccccCccccccCcccceeehhhhHHHH
Confidence            678888877899999 9999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             hCCCeeEEcCCcceec
Q psy13676        144 KNGFEFRITMMFANLR  159 (200)
Q Consensus       144 ~lGf~ie~~g~~~~~~  159 (200)
                      ++||.+++..+.....
T Consensus       561 knGF~~~~~~n~~~~~  576 (672)
T KOG1978|consen  561 KNGFKVKIDENAPDGK  576 (672)
T ss_pred             hcCceEeecCCCcccc
Confidence            9999999887766443

>cd03485 MutL_Trans_hPMS_1_like MutL_Trans_hPMS1_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM1 (hPSM1) and yeast MLH2

Probab=98.72  E-value=7.5e-09  Score=81.45  Aligned_cols=96  Identities=13%  Similarity=0.195  Sum_probs=66.1

Q ss_pred             ccccccCCCccccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCC-Ccccccc-------------
Q psy13676         14 IIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEP-SKVSGQA-------------   79 (200)
Q Consensus        14 ~l~~~~~~~~~~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~-~Kv~gq~-------------   79 (200)
                      +..+++... ...|.+++... .+..++|+|+||.|.++.+|++.|+||+|||+||+.. ..+.+.+             
T Consensus         6 i~~v~G~~~-~~~li~i~~~~-~~~~~~i~G~is~p~~~~~~~~~~~q~~fVN~R~v~~~~~l~k~i~~~y~~~~~~~~~   83 (132)
T cd03485           6 LARVLGTAV-AANMVPVQSTD-EDPQISLEGFLPKPGSDVSKTKSDGKFISVNSRPVSLGKDIGKLLRQYYSSAYRKSSL   83 (132)
T ss_pred             HHHHhCHHH-HhccEEEeccC-CCCcEEEEEEECCCCcCCCcccCCcEEEEECCeecccchHHHHHHHHHHHHHhccccc
Confidence            333444433 33455555431 1256999999999988899999999999999999998 5554443             


Q ss_pred             --ceEEEEEeCCceeeeechh---------hhHHHHHHHHhhh
Q psy13676         80 --EGFIIVKYDSDLFIIDQHA---------TDEKYNFETLQKT  111 (200)
Q Consensus        80 --~~yIla~~~~~L~lIDqHA---------AhERIlyE~L~~~  111 (200)
                        .+++++.+.-+.-.+|.|.         .+|+.+++.+...
T Consensus        84 ~~~P~~~L~i~~~~~~vDVNVhP~K~eV~f~~e~~v~~~i~~~  126 (132)
T cd03485          84 RRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVLQAVENL  126 (132)
T ss_pred             cCCCEEEEEEEcCCCceeeccCCccCEEEEcChHHHHHHHHHH
Confidence              2456667666666788877         5677777766553

hPSM1 and yMLH2 are members of the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. PMS1 forms a heterodimer with MLH1. The MLH1-PMS1 complex functions in meiosis. Loss of yMLH2 results in a small but significant decrease in spore viability and a significant increase in gene conversion frequencies. A role for hMLH1-hPMS1 in DNA mismatch repair has not been established. Mutation in hMLH1 accounts for a large fraction of Lynch syndrome (HNPCC) families, however there is no convincing evidence to support hPMS1 having a role in HNPCC predisposition.

>cd03484 MutL_Trans_hPMS_2_like MutL_Trans_hPMS2_like: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to human PSM2 (hPSM2)

Probab=98.62  E-value=9.4e-08  Score=76.37  Aligned_cols=74  Identities=32%  Similarity=0.577  Sum_probs=56.5

Q ss_pred             cceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc-----------ceEEEEEeCCceeeeechh--------
Q psy13676         38 AMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA-----------EGFIIVKYDSDLFIIDQHA--------   98 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~-----------~~yIla~~~~~L~lIDqHA--------   98 (200)
                      ..++++|+||.|..+++|++.++||+|||+||+....+...+           .+++++.+.-..-.+|.|.        
T Consensus        43 ~~~~i~G~is~p~~~~~r~~~~~q~~fVN~R~V~~~~l~~aI~~~y~~~~~~~~P~~vL~i~vp~~~vDvNVhP~K~eV~  122 (142)
T cd03484          43 SEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKKVAKLINEVYKSFNSRQYPFFILNISLPTSLYDVNVTPDKRTVL  122 (142)
T ss_pred             CcEEEEEEECCCcccCCCCCCCcEEEEECCeecCCHHHHHHHHHHHHHhcCcCCcEEEEEEEeCCcceeeeeCCccCEEE
Confidence            569999999999778999999999999999999986655554           2455556555555677755        


Q ss_pred             -hhHHHHHHHHhhh
Q psy13676         99 -TDEKYNFETLQKT  111 (200)
Q Consensus        99 -AhERIlyE~L~~~  111 (200)
                       ++|+..++.+.+.
T Consensus       123 f~~e~~i~~~i~~~  136 (142)
T cd03484         123 LHDEDRLIDTLKTS  136 (142)
T ss_pred             EcChHHHHHHHHHH
Confidence             6677777766553

hPSM2 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to yeast PMS1. The yeast MLH1-PMS1 and the human MLH1-PMS2 heterodimers play a role in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Cells lacking hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hPMS2 causes predisposition to HPNCC and Turcot syndrome.

>cd03482 MutL_Trans_MutL MutL_Trans_MutL: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to Escherichia coli MutL

Probab=98.58  E-value=3.9e-08  Score=76.73  Aligned_cols=71  Identities=23%  Similarity=0.337  Sum_probs=55.9

Q ss_pred             cceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------------ceEEEEEeCCceeeeechh-------
Q psy13676         38 AMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------------EGFIIVKYDSDLFIIDQHA-------   98 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------------~~yIla~~~~~L~lIDqHA-------   98 (200)
                      ..++|+|+||.|.  .+|++.|+||+|||+||+..+.+...+            .++.++.+.-+.-.+|.|.       
T Consensus        25 ~~~~i~G~is~p~--~~r~~~~~q~ifVN~R~V~~~~l~~ai~~~y~~~~~~~~~P~~vL~l~ipp~~vDvNVhP~K~eV  102 (123)
T cd03482          25 GGLRLSGWIALPT--FARSQADIQYFYVNGRMVRDKLISHAVRQAYSDVLHGGRHPAYVLYLELDPAQVDVNVHPAKHEV  102 (123)
T ss_pred             CCEEEEEEEeCch--hccCCCCcEEEEEcCcEECChHHHHHHHHHHHHhccCCCCcEEEEEEEcChHheeeccCCCccEE
Confidence            6699999999997  569999999999999999987666554            2566677777777788877       


Q ss_pred             --hhHHHHHHHHhh
Q psy13676         99 --TDEKYNFETLQK  110 (200)
Q Consensus        99 --AhERIlyE~L~~  110 (200)
                        ++|+..++.+.+
T Consensus       103 ~f~~e~~i~~~i~~  116 (123)
T cd03482         103 RFRDSRLVHDFIYH  116 (123)
T ss_pred             EECCHHHHHHHHHH
Confidence              567777776654

EcMutL belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from the ATP-binding site to the DNA breakage/reunion regions of the enzymes. It has been suggested that during initiation of DNA mismatch repair in E. coli, the mismatch recognition protein MutS recruits MutL in the presence of ATP. The MutS(ATP)-MutL ternary complex formed, then recruits the latent endonuclease MutH. Prokaryotic MutS and MutL are homodimers.

>cd03483 MutL_Trans_MLH1 MutL_Trans_MLH1: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH1 (MutL homologue 1)

Probab=98.53  E-value=5.3e-08  Score=76.37  Aligned_cols=71  Identities=23%  Similarity=0.235  Sum_probs=55.3

Q ss_pred             cceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------------ceEEEEEeCCceeeeechh-------
Q psy13676         38 AMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------------EGFIIVKYDSDLFIIDQHA-------   98 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------------~~yIla~~~~~L~lIDqHA-------   98 (200)
                      ..++|+||+|.|..+   +.+|+||+||||||+..+.+...+            .+++++.+.-+.-.||.|.       
T Consensus        30 ~~~~i~G~is~p~~~---~~~~~q~~fVNgR~V~~~~l~~aI~~~Y~~~l~~~~~P~~~L~i~i~p~~vDVNVHP~K~eV  106 (127)
T cd03483          30 LGFKVKGLISNANYS---KKKIIFILFINNRLVECSALRRAIENVYANYLPKGAHPFVYLSLEIPPENVDVNVHPTKREV  106 (127)
T ss_pred             CcEEEEEEEcCchhc---CCCceEEEEEcCCEecCHHHHHHHHHHHHHhCcCCCccEEEEEEEeChHHeeeccCCCccEE
Confidence            469999999999866   557999999999999988766554            2566667666667778877       


Q ss_pred             --hhHHHHHHHHhhh
Q psy13676         99 --TDEKYNFETLQKT  111 (200)
Q Consensus        99 --AhERIlyE~L~~~  111 (200)
                        ++|+..++.+.+.
T Consensus       107 ~f~~e~~i~~~i~~~  121 (127)
T cd03483         107 HFLNEEEIIERIQKL  121 (127)
T ss_pred             EecCHHHHHHHHHHH
Confidence              6788887777653

This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking hMLH1 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot syndrome (HNPCC variant). Mutation in hMLH1 accounts for a large fraction of HNPCC families.

>PF01119 DNA_mis_repair: DNA mismatch repair protein, C-terminal domain; InterPro: IPR013507 This entry represents the C-terminal domain of DNA mismatch repair proteins, such as MutL

Probab=98.46  E-value=3.8e-08  Score=75.97  Aligned_cols=81  Identities=28%  Similarity=0.373  Sum_probs=54.4

Q ss_pred             ccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------------ceEEEEEeCCcee
Q psy13676         25 SLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------------EGFIIVKYDSDLF   92 (200)
Q Consensus        25 ~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------------~~yIla~~~~~L~   92 (200)
                      +.|.+++..   +..++++||||.|.  .+|+++|+||+|||+||++.+.+...+            .+++++.+.-..-
T Consensus        11 ~~l~~i~~~---~~~~~i~G~is~p~--~~~~~~~~q~ifVN~R~V~~~~l~~~I~~~y~~~~~~~~~P~~vL~i~~p~~   85 (119)
T PF01119_consen   11 SNLIEIDSE---DEDFSIEGYISKPD--VSRSSRDRQFIFVNGRPVENKALSKAINEAYRERLPKGRYPIFVLFIEIPPS   85 (119)
T ss_dssp             CCEEEEEEE---ECCEEEEEEEE-SS--CSBSSCTCEEEEETTEEE--HHHHHHHHHHHHCTTCTTSB-EEEEEEE-SGG
T ss_pred             hccEEEecc---CCCEEEEEEEECch--hccCCCCcEEEEeCCCeEeChHHHHHHHHHHhhcccCCCCceEEEEEEcchH
Confidence            334555532   36699999999996  789999999999999999988666443            3566667666666


Q ss_pred             eeechh---------hhHHHHHHHHhh
Q psy13676         93 IIDQHA---------TDEKYNFETLQK  110 (200)
Q Consensus        93 lIDqHA---------AhERIlyE~L~~  110 (200)
                      .+|.|.         .+|...++.+.+
T Consensus        86 ~vDVNvhP~K~eV~f~~e~~i~~~i~~  112 (119)
T PF01119_consen   86 EVDVNVHPAKREVRFRDEDEILNLIEE  112 (119)
T ss_dssp             GEEETSSTTTT-EEETTHHHHHHHHHH
T ss_pred             HccccccccceEEEecCHHHHHHHHHH
Confidence            778777         455555555443

This domain functions in promoting dimerisation []. The dimeric MutL protein has a key function in communicating mismatch recognition by MutS to downstream repair processes. Mismatch repair contributes to the overall fidelity of DNA replication by targeting mispaired bases that arise through replication errors during homologous recombination and as a result of DNA damage. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex [].; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1B62_A 1NHJ_A 1BKN_B 1NHH_A 1B63_A 1NHI_A 3NA3_A 1EA6_A 1H7U_A 1H7S_B ....

>cd03486 MutL_Trans_MLH3 MutL_Trans_MLH3: transducer domain, having a ribosomal S5 domain 2-like fold, found in proteins similar to yeast and human MLH3 (MutL homologue 3)

Probab=98.41  E-value=1.8e-07  Score=74.49  Aligned_cols=59  Identities=22%  Similarity=0.215  Sum_probs=42.2

Q ss_pred             ccccccCCCccccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc
Q psy13676         14 IIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA   79 (200)
Q Consensus        14 ~l~~~~~~~~~~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~   79 (200)
                      .+.-+++....+.|.+++..   ...++|+|+||.|.    |++.|+||+|||+||+....+...+
T Consensus         5 ~i~~i~G~~~~~~l~~v~~~---~~~~~v~G~is~p~----~~sk~~q~ifVN~R~v~~~~l~~aI   63 (141)
T cd03486           5 VFKQIYGLVLAQKLKEVSAK---FQEYEVSGYISSEG----HYSKSFQFIYVNGRLYLKTRFHKLI   63 (141)
T ss_pred             HHHHHhChhhhccEEEeecc---cCcEEEEEEEcCCC----CCCCceEEEEECCEEechHHHHHHH
Confidence            33344444444456666654   36799999999986    7899999999999999876554443

MLH3 belongs to the DNA mismatch repair (MutL/MLH1/PMS2) family. This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. MLH1 forms heterodimers with MLH3. The MLH1-MLH3 complex plays a role in meiosis. A role for hMLH1-hMLH3 in DNA mismatch repair (MMR) has not been established. It has been suggested that hMLH3 may be a low risk gene for colorectal cancer; however there is little evidence to support it having a role in classical HNPCC.

>cd00782 MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of DNA mismatch repair (MutL/MLH1/PMS2) family

Probab=98.39  E-value=1.9e-07  Score=71.68  Aligned_cols=80  Identities=30%  Similarity=0.470  Sum_probs=55.8

Q ss_pred             cccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------------ceEEEEEeCCceee
Q psy13676         26 LLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------------EGFIIVKYDSDLFI   93 (200)
Q Consensus        26 ~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------------~~yIla~~~~~L~l   93 (200)
                      .|.+++..   ...++++|++|.|..  +|++.|+||+|||+||+..+.+.+.+            .+++++.+.-..-.
T Consensus        16 ~l~~i~~~---~~~~~i~G~is~~~~--~~~~~~~q~~fVN~R~v~~~~l~~ai~~~y~~~~~~~~~P~~~L~i~~~~~~   90 (122)
T cd00782          16 NLIEVELE---SGDFRISGYISKPDF--GRSSKDRQFLFVNGRPVRDKLLSKAINEAYRSYLPKGRYPVFVLNLELPPEL   90 (122)
T ss_pred             cceEEecc---CCCEEEEEEEECchh--hcCCCccEEEEECCeEecCHHHHHHHHHHHHHhCcCCCCcEEEEEEEeChhh
Confidence            35555543   367999999999984  89999999999999999977666554            23455555555455


Q ss_pred             eechh---------hhHHHHHHHHhh
Q psy13676         94 IDQHA---------TDEKYNFETLQK  110 (200)
Q Consensus        94 IDqHA---------AhERIlyE~L~~  110 (200)
                      +|.|.         .+|+.+++.+.+
T Consensus        91 ~DvNvhP~K~eV~f~~~~~i~~~i~~  116 (122)
T cd00782          91 VDVNVHPTKREVRFSDEEEVLELIRE  116 (122)
T ss_pred             eeeeeCCCCCEEEecCHHHHHHHHHH
Confidence            66665         456666555543

This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. Included in this group are proteins similar to human MLH1, hPMS2, hPMS1, hMLH3 and E. coli MutL, MLH1 forms heterodimers with PMS2, PMS1 and MLH3. These three complexes have distinct functions in meiosis. hMLH1-hPMS2 also participates in the repair of all DNA mismatch repair (MMR) substrates. Roles for hMLH1-hPMS1 or hMLH1-hMLH3 in MMR have not been established. Cells lacking either hMLH1 or hPMS2 have a strong mutator phenotype and display microsatellite instability (MSI). Mutation in hMLH1 causes predisposition to HNPCC, Muir-Torre syndrome and Turcot synd

>KOG1977|consensus

Probab=97.99  E-value=6.3e-06  Score=80.77  Aligned_cols=93  Identities=19%  Similarity=0.185  Sum_probs=81.2

Q ss_pred             eeecCCCCCCCcccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhhccccccccccCceeecCHHHHHHHHhhHHH
Q psy13676         63 YFVNSRPCEPSKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILKDNLPV  141 (200)
Q Consensus        63 ~~INkrp~~~~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~~~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~  141 (200)
                      +-+|+.+++.++|+.|+ +.||-+-+-......||||++||+..|.+... .+.+..|++|+.+.+.|....+|..+.+.
T Consensus       903 ~~~nk~~i~~~qvlqqvDkkyi~~v~~~~~~~~~qha~dek~~~q~~~~k-~l~~s~li~~l~~kvlpm~~~ll~~Y~~~  981 (1142)
T KOG1977|consen  903 YRFNKGMIHSMQVLQQVDKKYIACVMSTKTEENGQHASDEKQQAQGSGRK-KLLSSTLIPPLEIKVLPMQRRLLWCYHKN  981 (1142)
T ss_pred             hhhcccchhhHHHHHhhchhheeeeeeccccccccchhHHHHHhhhhccc-cccccccccceeEEechhhHHHHHHHHHH
Confidence            34699999999999999 99999999999999999999999998887665 35556689999999999999999999999


Q ss_pred             HHhCCCeeEEcCCcc
Q psy13676        142 FYKNGFEFRITMMFA  156 (200)
Q Consensus       142 L~~lGf~ie~~g~~~  156 (200)
                      ++.|||++.+...+.
T Consensus       982 ~~d~gw~~~~~~~~~  996 (1142)
T KOG1977|consen  982 LEDLGWEFVFPDTSD  996 (1142)
T ss_pred             hhhhceEEecccccc
Confidence            999999987665544

>KOG1978|consensus

Probab=97.81  E-value=9.3e-06  Score=78.85  Aligned_cols=65  Identities=35%  Similarity=0.576  Sum_probs=52.2

Q ss_pred             EEeccccCCCCCCCcceeeeecCCCCCCCcccccc---------ceEEEEEeCCceeeeechh---------hhHHHHHH
Q psy13676         45 FISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA---------EGFIIVKYDSDLFIIDQHA---------TDEKYNFE  106 (200)
Q Consensus        45 ~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~---------~~yIla~~~~~L~lIDqHA---------AhERIlyE  106 (200)
                      +||.+.||+||++.||||+|||+|||++++|+..+         ..|+.+..+  --.+|.|+         ++||.+..
T Consensus       230 ~is~~~~g~~r~s~drqf~fIn~Rpv~~~~i~~~inevy~~~~~~q~l~i~V~--~~~iDvNvtPDK~~vll~~e~~vl~  307 (672)
T KOG1978|consen  230 FISSCHHGCGRSSEDRQFIFINRRPVFPSDICRVINEVYKLYNERQYLFLDVP--EGCIDVNVTPDKRQVLLSNERSVLF  307 (672)
T ss_pred             ccccccccccccCccceeeeecCccCCHHHHHHHHHHHhhhhccccceeeecc--ccceeeeeCCCcceeeccchHHHHH
Confidence            38999999999999999999999999999999876         345333332  23466666         78999999


Q ss_pred             HHhhh
Q psy13676        107 TLQKT  111 (200)
Q Consensus       107 ~L~~~  111 (200)
                      .|++.
T Consensus       308 ~l~~~  312 (672)
T KOG1978|consen  308 SLRNS  312 (672)
T ss_pred             HHHHH
Confidence            99886

>TIGR00585 mutl DNA mismatch repair protein MutL

Probab=97.35  E-value=9.9e-05  Score=65.65  Aligned_cols=82  Identities=22%  Similarity=0.211  Sum_probs=52.2

Q ss_pred             cccccCCCccccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------------ceE
Q psy13676         15 IPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------------EGF   82 (200)
Q Consensus        15 l~~~~~~~~~~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------------~~y   82 (200)
                      +..+++....+.|.++...  ....+.++||||.|..+.++.+.| ||+|||+||+..+.+.+.+            .++
T Consensus       212 i~~v~G~~~~~~l~~~~~~--~~~~~~v~G~is~p~~~~~~~~~~-q~ifvNgR~v~~~~l~k~I~~~y~~~~~~~~~P~  288 (312)
T TIGR00585       212 IRSVFGTAVLSKLFPLLEW--EDGDLQLEGFISEPNVTRSRRSGW-QFLFINGRPVELKLLLKAIREVYHEYLPKGQYPV  288 (312)
T ss_pred             HHHHhChHhHhhceeeecc--cCCCEEEEEEEcCcccccCCCCcc-eEEEECCcEecchHHHHHHHHHHHHhccCCCCcE
Confidence            4444444333344444421  236799999999999765554444 9999999999988776665            145


Q ss_pred             EEEEeCCceeeeechhh
Q psy13676         83 IIVKYDSDLFIIDQHAT   99 (200)
Q Consensus        83 Ila~~~~~L~lIDqHAA   99 (200)
                      +++.+.-..-.+|.+.+
T Consensus       289 ~vL~i~~p~~~iDvNv~  305 (312)
T TIGR00585       289 FVLNLEIDPELVDVNVH  305 (312)
T ss_pred             EEEEEEEChHHcccCCC
Confidence            55555555555666554

All proteins in this family for which the functions are known are involved in the process of generalized mismatch repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).

>PRK00095 mutL DNA mismatch repair protein; Reviewed

Probab=97.29  E-value=0.00017  Score=70.15  Aligned_cols=97  Identities=18%  Similarity=0.217  Sum_probs=66.6

Q ss_pred             hhhhccccccCCCccccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc----------
Q psy13676         10 QLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA----------   79 (200)
Q Consensus        10 ~l~~~l~~~~~~~~~~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~----------   79 (200)
                      ++.+.+..+++......+..++..   ...+.|+||||.|.  .+|++.++||+|||+|++....+...+          
T Consensus       203 ~~~~~i~~i~g~~~~~~l~~~~~~---~~~~~i~g~is~p~--~~~~~~~~~~~fvN~R~v~~~~l~~ai~~~y~~~~~~  277 (617)
T PRK00095        203 QLLQRLAAILGREFAENALPIDAE---HGDLRLSGYVGLPT--LSRANRDYQYLFVNGRYVRDKLLNHAIRQAYHDLLPR  277 (617)
T ss_pred             CHHHHHHHHhCHHhHhheEEEecc---CCCEEEEEEEeCcc--cccCCCcceEEEECCcEecCHHHHHHHHHHHHHhccC
Confidence            344444444433323334444433   25689999999984  678999999999999999876655444          


Q ss_pred             --ceEEEEEeCCceeeeechh---------hhHHHHHHHHhhh
Q psy13676         80 --EGFIIVKYDSDLFIIDQHA---------TDEKYNFETLQKT  111 (200)
Q Consensus        80 --~~yIla~~~~~L~lIDqHA---------AhERIlyE~L~~~  111 (200)
                        .+++++.+..+.-.+|.|.         .+|+.+++.+...
T Consensus       278 ~~~P~~~l~i~~~~~~~DvNvhP~K~ev~f~~e~~i~~~i~~~  320 (617)
T PRK00095        278 GRYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLVHDLIVQA  320 (617)
T ss_pred             CCCcEEEEEEEeChHhcccccCCCcCEEEeCCHHHHHHHHHHH
Confidence              1455666666666788887         7888888887775

>cd00329 TopoII_MutL_Trans MutL_Trans: transducer domain, having a ribosomal S5 domain 2-like fold, conserved in the C-terminal domain of type II DNA topoisomerases (Topo II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins

Probab=96.72  E-value=0.0011  Score=48.44  Aligned_cols=37  Identities=43%  Similarity=0.585  Sum_probs=31.4

Q ss_pred             cceEEEEEEeccccCCCCCCCcceeeeecCCCCC-CCccc
Q psy13676         38 AMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCE-PSKVS   76 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~-~~Kv~   76 (200)
                      ..+.++|+++.+..+  |+..++||+|+|+|++. ...+.
T Consensus        25 ~~~~v~g~l~~~~~~--~~~~~~~~~fvN~r~v~~~~~~~   62 (107)
T cd00329          25 DGFRVEGAISYPDSG--RSSKDRQFSFVNGRPVREGGTHV   62 (107)
T ss_pred             CCEEEEEEEeCCccC--cccCCcEEEEEcCeEEcCCHHHH
Confidence            568999999999865  88899999999999998 54443

This transducer domain is homologous to the second domain of the DNA gyrase B subunit, which is known to be important in nucleotide hydrolysis and the transduction of structural signals from ATP-binding site to the DNA breakage/reunion regions of the enzymes. The GyrB dimerizes in response to ATP binding, and is homologous to the N-terminal half of eukaryotic Topo II and the ATPase fragment of MutL. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. Included in this group are proteins similar to human MLH1 and PMS2. MLH1 forms a heterodimer with PMS2 which functions in meiosis and in DNA mismatch

>KOG1979|consensus

Probab=80.40  E-value=0.75  Score=45.07  Aligned_cols=87  Identities=23%  Similarity=0.242  Sum_probs=59.0

Q ss_pred             hhhhhccccccCCCccccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCccc-------ccc--
Q psy13676          9 SQLINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVS-------GQA--   79 (200)
Q Consensus         9 ~~l~~~l~~~~~~~~~~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~-------gq~--   79 (200)
                      .-..++=.+++.....+.+.+++-..+..-.+..+||||.+..-   +......+|||+|.++...+-       +.+  
T Consensus       211 s~~D~ir~i~g~~Va~~ll~els~~~~~~l~f~~~g~Isn~n~~---akk~i~vlFIN~RLVes~~Lr~ale~VYa~yLp  287 (694)
T KOG1979|consen  211 SREDNIRNIYGVSVAKNLLNELSKCDSKLLKFSAEGYISNANYS---AKKSILVLFINGRLVESDELRHALEEVYAAYLP  287 (694)
T ss_pred             ccccchhhhhhhHHHHHHHHHhhhccCceeEEeccceEechhhh---hhhheEEEEEcCcEeehHHHHHHHHHHHHHhcC
Confidence            33445555666666666555665434445677789999998755   555666899999999865322       222  


Q ss_pred             ---ceEEEEEeCCceeeeechh
Q psy13676         80 ---EGFIIVKYDSDLFIIDQHA   98 (200)
Q Consensus        80 ---~~yIla~~~~~L~lIDqHA   98 (200)
                         .+|+-+.++.+.--||.|+
T Consensus       288 k~~~pFvYLsL~i~p~~vDVNV  309 (694)
T KOG1979|consen  288 KGHHPFVYLSLNIDPENVDVNV  309 (694)
T ss_pred             CCCCceEEEEEecCHHHccccc
Confidence               5788888888888888887

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	200
4fmn_B	240	Structure Of The C-terminal Domain Of The Saccharom		4e-20
4e4w_B	239	Structure Of The C-terminal Domain Of The Saccharom		4e-20
1ea6_A	364	N-Terminal 40kda Fragment Of Nhpms2 Complexed With		9e-13
1h7u_A	365	Hpms2-atpgs Length = 365		9e-13
1h7s_A	365	N-Terminal 40kda Fragment Of Human Pms2 Length = 36		1e-12

>pdb|4FMN|B Chain B, Structure Of The C-terminal Domain Of The Saccharomyces Cerevisiae Mutl Alpha (mlh1/pms1) Heterodimer Bound To A Fragment Of Ntg2 Length = 240

Iteration: 1
 Score = 94.4 bits (233), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 47/75 (62%), Positives = 60/75 (80%), Gaps = 4/75 (5%)
Query: 81  GFIIV--KYDS--DLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILK 136
           GFIIV  K D+  DLFI+DQHA+DEKYNFETLQ  TV KSQKL++PQ + L+ I++ ++ 
Sbjct: 50  GFIIVTRKVDNKYDLFIVDQHASDEKYNFETLQAVTVFKSQKLIIPQPVELSVIDELVVL 109
Query: 137 DNLPVFYKNGFEFRI 151
           DNLPVF KNGF+ +I
Sbjct: 110 DNLPVFEKNGFKLKI 124

>pdb|4E4W|B Chain B, Structure Of The C-terminal Domain Of The Saccharomyces Cerevisiae Mutl Alpha (mlh1/pms1) Heterodimer Length = 239

Iteration: 1
 Score = 94.4 bits (233), Expect = 4e-20,   Method: Compositional matrix adjust.
 Identities = 47/75 (62%), Positives = 60/75 (80%), Gaps = 4/75 (5%)
Query: 81  GFIIV--KYDS--DLFIIDQHATDEKYNFETLQKTTVIKSQKLVVPQNLHLTKINQCILK 136
           GFIIV  K D+  DLFI+DQHA+DEKYNFETLQ  TV KSQKL++PQ + L+ I++ ++ 
Sbjct: 49  GFIIVTRKVDNKYDLFIVDQHASDEKYNFETLQAVTVFKSQKLIIPQPVELSVIDELVVL 108
Query: 137 DNLPVFYKNGFEFRI 151
           DNLPVF KNGF+ +I
Sbjct: 109 DNLPVFEKNGFKLKI 123

>pdb|1EA6|A Chain A, N-Terminal 40kda Fragment Of Nhpms2 Complexed With Adp Length = 364

Iteration: 1
 Score = 69.7 bits (169), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 45/68 (66%), Gaps = 2/68 (2%)
Query: 10  QLINIIPITQSSPDASLLEEFRIPPD--ITAMFTLSGFISSAIHGHGRSTADRQFYFVNS 67
           QL ++IP  Q  P  S+ EE+ +     +  +F +SGFIS   HG GRS+ DRQF+F+N 
Sbjct: 235 QLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINR 294
Query: 68  RPCEPSKV 75
           RPC+P+KV
Sbjct: 295 RPCDPAKV 302

>pdb|1H7U|A Chain A, Hpms2-atpgs Length = 365

Iteration: 1
 Score = 69.7 bits (169), Expect = 9e-13,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 45/68 (66%), Gaps = 2/68 (2%)
Query: 10  QLINIIPITQSSPDASLLEEFRIPPD--ITAMFTLSGFISSAIHGHGRSTADRQFYFVNS 67
           QL ++IP  Q  P  S+ EE+ +     +  +F +SGFIS   HG GRS+ DRQF+F+N 
Sbjct: 235 QLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINR 294
Query: 68  RPCEPSKV 75
           RPC+P+KV
Sbjct: 295 RPCDPAKV 302

>pdb|1H7S|A Chain A, N-Terminal 40kda Fragment Of Human Pms2 Length = 365

Iteration: 1
 Score = 69.7 bits (169), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/68 (47%), Positives = 45/68 (66%), Gaps = 2/68 (2%)
Query: 10  QLINIIPITQSSPDASLLEEFRIPPD--ITAMFTLSGFISSAIHGHGRSTADRQFYFVNS 67
           QL ++IP  Q  P  S+ EE+ +     +  +F +SGFIS   HG GRS+ DRQF+F+N 
Sbjct: 235 QLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINR 294
Query: 68  RPCEPSKV 75
           RPC+P+KV
Sbjct: 295 RPCDPAKV 302

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	200
3kdg_A	197	DNA mismatch repair protein MUTL; endonuclease, DN	4e-13
3ncv_A	220	DNA mismatch repair protein MUTL; endonuclease, di	5e-13
1h7s_A	365	PMS1 protein homolog 2; DNA repair, GHL ATPase, mi	4e-12
1x9z_A	188	DNA mismatch repair protein MUTL; alpha-beta fold,	2e-11
3h4l_A	367	DNA mismatch repair protein PMS1; ATP binding, DNA	5e-10

>3kdg_A DNA mismatch repair protein MUTL; endonuclease, DNA damage, DNA repair, hydrolase; HET: DNA; 2.00A {Bacillus subtilis} PDB: 3gab_A* 3kdk_A* Length = 197

 Score = 64.1 bits (157), Expect = 4e-13
 Identities = 16/71 (22%), Positives = 34/71 (47%), Gaps = 3/71 (4%)

Query: 82  FIIVKYDSDLFIIDQHATDEKYNFETLQK---TTVIKSQKLVVPQNLHLTKINQCILKDN 138
           +I+ + ++ L+IIDQHA  E+  +E  ++       + Q+++VP   H +     I++ +
Sbjct: 19  YILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTFHYSTNEALIIEQH 78

Query: 139 LPVFYKNGFEF 149
                  G   
Sbjct: 79  KQELESVGVFL 89

>3ncv_A DNA mismatch repair protein MUTL; endonuclease, dimer, hydrolase; HET: DNA; 2.40A {Neisseria gonorrhoeae} Length = 220

 Score = 64.2 bits (157), Expect = 5e-13
 Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 5/78 (6%)

Query: 77  GQAEG-FIIVKYDSDLFIIDQHATDEKYNFETL----QKTTVIKSQKLVVPQNLHLTKIN 131
            Q  G +I+ + +  L +ID HA  E+ N+E +    Q+   ++SQ L++P     +   
Sbjct: 34  AQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAASHEE 93

Query: 132 QCILKDNLPVFYKNGFEF 149
              L D+       G E 
Sbjct: 94  CAALADHAETLAGFGLEL 111

>1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair, HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2 PDB: 1h7u_A* 1ea6_A* Length = 365

 Score = 63.0 bits (154), Expect = 4e-12
 Identities = 30/66 (45%), Positives = 43/66 (65%), Gaps = 2/66 (3%)

Query: 13  NIIPITQSSPDASLLEEFRIPPD--ITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPC 70
           ++IP  Q  P  S+ EE+ +     +  +F +SGFIS   HG GRS+ DRQF+F+N RPC
Sbjct: 238 SLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPC 297

Query: 71  EPSKVS 76
           +P+KV 
Sbjct: 298 DPAKVC 303

>1x9z_A DNA mismatch repair protein MUTL; alpha-beta fold, dimer, replication, signaling protein; HET: DNA MSE; 2.10A {Escherichia coli} SCOP: d.292.1.1 Length = 188

 Score = 58.9 bits (143), Expect = 2e-11
 Identities = 10/80 (12%), Positives = 30/80 (37%), Gaps = 2/80 (2%)

Query: 74  KVSGQ-AEGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTV-IKSQKLVVPQNLHLTKIN 131
           +V         +++ D ++ ++     +       L      + +Q L++P  L ++   
Sbjct: 10  RVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEE 69

Query: 132 QCILKDNLPVFYKNGFEFRI 151
           +  L+       + G +F+ 
Sbjct: 70  KSALEKAQSALAELGIDFQS 89

>3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA damage, nucleus, phosphop DNA binding protein, protein binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae} Length = 367

 Score = 56.8 bits (138), Expect = 5e-10
 Identities = 19/74 (25%), Positives = 32/74 (43%), Gaps = 4/74 (5%)

Query: 7   TISQLINIIPITQSSPDASLLEEFRIPP----DITAMFTLSGFISSAIHGHGRSTADRQF 62
            +  L  +  +   +P  + +           D+     + G+IS    G GR++ DRQF
Sbjct: 225 GMRGLEEVDLVLDLNPFKNRMLGKYTDDPDFLDLDYKIRVKGYISQNSFGCGRNSKDRQF 284

Query: 63  YFVNSRPCEPSKVS 76
            +VN RP E S + 
Sbjct: 285 IYVNKRPVEYSTLL 298

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	200
3kdg_A	197	DNA mismatch repair protein MUTL; endonuclease, DN	99.84
3ncv_A	220	DNA mismatch repair protein MUTL; endonuclease, di	99.83
1x9z_A	188	DNA mismatch repair protein MUTL; alpha-beta fold,	99.78
3h4l_A	367	DNA mismatch repair protein PMS1; ATP binding, DNA	98.81
1h7s_A	365	PMS1 protein homolog 2; DNA repair, GHL ATPase, mi	98.49
3na3_A	348	DNA mismatch repair protein MLH1; MUTL protein hom	97.77
1b63_A	333	MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A	97.58

>3kdg_A DNA mismatch repair protein MUTL; endonuclease, DNA damage, DNA repair, hydrolase; HET: DNA; 2.00A {Bacillus subtilis} PDB: 3gab_A* 3kdk_A*

Probab=99.84  E-value=2.8e-21  Score=160.36  Aligned_cols=87  Identities=21%  Similarity=0.321  Sum_probs=81.2

Q ss_pred             CCCCcccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhh---ccccccccccCceeecCHHHHHHHHhhHHHHHhC
Q psy13676         70 CEPSKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT---TVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKN  145 (200)
Q Consensus        70 ~~~~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~---~~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~l  145 (200)
                      +...+++||+ ++|||++.+++|++||||||||||+||+|++.   ....+|+|++|+.+++++.|.+.+.++.+.|++|
T Consensus         6 ~~~~~~igQ~~~~yIl~~~~~~L~lIDQHAAhERi~yE~l~~~~~~~~~~sQ~LL~P~~l~ls~~e~~~l~~~~~~l~~~   85 (197)
T 3kdg_A            6 VPIMYPIGQMHGTYILAQNENGLYIIDQHAAQERIKYEYFREKVGEVEPEVQEMIVPLTFHYSTNEALIIEQHKQELESV   85 (197)
T ss_dssp             CCCCEEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHCSSCCEEEEEEEEEEECCTTHHHHHHHTHHHHHHT
T ss_pred             CCCCeEEEEEcCEEEEEEeCCCEEEEEHHHHHHHHHHHHHHHHHccCCCCccccCCCEEEecCHHHHHHHHHHHHHHHhC
Confidence            4557899999 99999999999999999999999999999987   4578999999999999999999999999999999


Q ss_pred             CCeeEEcCCcc
Q psy13676        146 GFEFRITMMFA  156 (200)
Q Consensus       146 Gf~ie~~g~~~  156 (200)
                      ||+++.+|+++
T Consensus        86 Gf~~e~~g~~~   96 (197)
T 3kdg_A           86 GVFLESFGSNS   96 (197)
T ss_dssp             TCCCEECSTTE
T ss_pred             CCEEEECCCCE
Confidence            99999988765

>3ncv_A DNA mismatch repair protein MUTL; endonuclease, dimer, hydrolase; HET: DNA; 2.40A {Neisseria gonorrhoeae}

Probab=99.83  E-value=1.1e-20  Score=159.80  Aligned_cols=86  Identities=21%  Similarity=0.301  Sum_probs=79.9

Q ss_pred             CCCcccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhh----ccccccccccCceeecCHHHHHHHHhhHHHHHhC
Q psy13676         71 EPSKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT----TVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKN  145 (200)
Q Consensus        71 ~~~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~----~~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~l  145 (200)
                      ...+++||+ ++|||++.+++|++||||||||||+||+|+++    ....+|+|++|+.+++++.|.+++.++.+.|++|
T Consensus        28 p~g~vigQv~~~YIL~e~~~gL~lIDQHAAhERi~yE~l~~~~~~~~~~~sQ~LL~P~~l~Ls~~e~~~l~~~~~~L~~l  107 (220)
T 3ncv_A           28 PLGFAIAQLLGIYILAQAEDSLLLIDMHAAAERVNYEKMKRQRQENGNLQSQHLLIPVTFAASHEECAALADHAETLAGF  107 (220)
T ss_dssp             TTCEEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHSSCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHT
T ss_pred             CCceeeeeEcCEEEEEEeCCCEEEEEHHHHHHHHHHHHHHHHHhccCCccceeeCCCeEEEcCHHHHHHHHHHHHHHHhC
Confidence            346899999 99999999999999999999999999999985    3478999999999999999999999999999999


Q ss_pred             CCeeEEcCCcc
Q psy13676        146 GFEFRITMMFA  156 (200)
Q Consensus       146 Gf~ie~~g~~~  156 (200)
                      ||+++.+|++.
T Consensus       108 Gf~ie~fg~~~  118 (220)
T 3ncv_A          108 GLELSDMGGNT  118 (220)
T ss_dssp             TCEEECCSTTE
T ss_pred             CCEEEECCCCE
Confidence            99999987765

>1x9z_A DNA mismatch repair protein MUTL; alpha-beta fold, dimer, replication, signaling protein; HET: DNA MSE; 2.10A {Escherichia coli} SCOP: d.292.1.1

Probab=99.78  E-value=2.8e-19  Score=147.03  Aligned_cols=85  Identities=12%  Similarity=0.226  Sum_probs=79.0

Q ss_pred             CCCcccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhh--ccccccccccCceeecCHHHHHHHHhhHHHHHhCCC
Q psy13676         71 EPSKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT--TVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGF  147 (200)
Q Consensus        71 ~~~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~--~~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~lGf  147 (200)
                      ...+++||+ ++|||++.+++|++|||||| |||+||++++.  ....+|+|++|+.+++++.|.+.+.++.+.|+++||
T Consensus         7 ~~~~vlgQ~~~~yIl~~~~~~L~lIDQHAA-ERi~yE~l~~~~~~~~~~Q~LL~P~~l~ls~~e~~~l~~~~~~l~~~Gf   85 (188)
T 1x9z_A            7 SFGRVLTIVHSDCALLERDGNISLLSLPVA-ERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGI   85 (188)
T ss_dssp             CCCEEEEEETTTEEEEEETTEEEEEEHHHH-HHHHHHHHHSBTTBCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCceeeeeecCEEEEEEeCCCEEEEeHHHH-HHHHHHHHHHhcCCCCCcccCCCCEEEEeCHHHHHHHHHHHHHHHhCCc
Confidence            445788999 99999999999999999999 99999999986  457899999999999999999999999999999999


Q ss_pred             eeEEcCCcc
Q psy13676        148 EFRITMMFA  156 (200)
Q Consensus       148 ~ie~~g~~~  156 (200)
                      +++.+|++.
T Consensus        86 ~~e~~g~~~   94 (188)
T 1x9z_A           86 DFQSDAQHV   94 (188)
T ss_dssp             EEEECSSEE
T ss_pred             EEEEcCCcE
Confidence            999998873

>3h4l_A DNA mismatch repair protein PMS1; ATP binding, DNA repair, DNA damage, nucleus, phosphop DNA binding protein, protein binding; HET: DNA ANP; 2.50A {Saccharomyces cerevisiae}

Probab=98.81  E-value=1.2e-09  Score=98.55  Aligned_cols=86  Identities=27%  Similarity=0.449  Sum_probs=69.9

Q ss_pred             CcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc-----------ceEEEEEeCCceeeeechh-------
Q psy13676         37 TAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA-----------EGFIIVKYDSDLFIIDQHA-------   98 (200)
Q Consensus        37 ~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~-----------~~yIla~~~~~L~lIDqHA-------   98 (200)
                      ...++|+||||.|.++++|+++|+||+|||+|||..+.+.+.+           .+++++.+.-+.-.+|.|.       
T Consensus       259 ~~~~~i~G~is~p~~~~~r~~~~~q~~fVNgR~v~~~~l~~ai~~~y~~~~~~~~P~~~L~l~~~p~~vDVNVhP~K~eV  338 (367)
T 3h4l_A          259 DYKIRVKGYISQNSFGCGRNSKDRQFIYVNKRPVEYSTLLKCCNEVYKTFNNVQFPAVFLNLELPMSLIDVNVTPDKRVI  338 (367)
T ss_dssp             CCEEEEEEEEECCSTTCSBSSSSSEEEEETTEEECCHHHHHHHHHHHHTTCSSCBCCEEEEEECCGGGEECCCSSSTTCC
T ss_pred             CCcEEEEEEEeCCcccccCCCCCcEEEEECCCEecCHHHHHHHHHHHHhcCCCCCcEEEEEEEcChHHcceeECCCCCEE
Confidence            3678999999999999999999999999999999988776654           3667888888888899887       


Q ss_pred             --hhHHHHHHHHhhh--ccccccccccC
Q psy13676         99 --TDEKYNFETLQKT--TVIKSQKLVVP  122 (200)
Q Consensus        99 --AhERIlyE~L~~~--~~~~sQ~Ll~P  122 (200)
                        .+|+.+++.+...  ..+..+...+|
T Consensus       339 ~f~~e~~i~~~i~~~l~~~~~~~~~~~~  366 (367)
T 3h4l_A          339 LLHNERAVIDIFKTTLSDYYNRQELALP  366 (367)
T ss_dssp             EETTHHHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             EEcCHHHHHHHHHHHHHHHHhhcCCCCC
Confidence              7899999988876  34444444444

>1h7s_A PMS1 protein homolog 2; DNA repair, GHL ATPase, mismatch repair, HNPCC; 1.95A {Homo sapiens} SCOP: d.14.1.3 d.122.1.2 PDB: 1h7u_A* 1ea6_A*

Probab=98.49  E-value=9.7e-08  Score=85.73  Aligned_cols=74  Identities=39%  Similarity=0.751  Sum_probs=60.4

Q ss_pred             cceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc-----------ceEEEEEeCCceeeeechh--------
Q psy13676         38 AMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA-----------EGFIIVKYDSDLFIIDQHA--------   98 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~-----------~~yIla~~~~~L~lIDqHA--------   98 (200)
                      ..++|+||||.|.+++||+++|+||+|||+||+..+.+.+.+           .+++++.+.-+.-.+|.|.        
T Consensus       265 ~~~~v~G~i~~p~~~~~r~~~~~q~~fvNgR~v~~~~l~~ai~~~y~~~~~~~~P~~~L~l~~~p~~vDvNVhP~K~eV~  344 (365)
T 1h7s_A          265 NLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQIL  344 (365)
T ss_dssp             CCCEEEEEEECCSTTTSBSSSTTEEEEETTEEECCHHHHHHHHHHHHTTCTTCBCCEEEEEECCGGGEEEC------CEE
T ss_pred             ccEEEEEEEeCcccccccCCCcceEEEECCeEecCHHHHHHHHHHHHhhCccCCcEEEEEEEeChHHcceEECCCcCEEE
Confidence            568999999999999999999999999999999988765444           3667788888878889888        


Q ss_pred             -hhHHHHHHHHhhh
Q psy13676         99 -TDEKYNFETLQKT  111 (200)
Q Consensus        99 -AhERIlyE~L~~~  111 (200)
                       .+|+.+++.+...
T Consensus       345 f~~e~~i~~~i~~~  358 (365)
T 1h7s_A          345 LQEEKLLLAVLKTS  358 (365)
T ss_dssp             ETTHHHHHHHHHHH
T ss_pred             EcCHHHHHHHHHHH
Confidence             6677777766553

>3na3_A DNA mismatch repair protein MLH1; MUTL protein homolog 1, DNA damag repair, structural genomics consortium, SGC, protein bindin; HET: DNA ATP; 2.50A {Homo sapiens}

Probab=97.77  E-value=4.4e-06  Score=74.77  Aligned_cols=96  Identities=19%  Similarity=0.210  Sum_probs=53.0

Q ss_pred             hhhccccccCCCccccccccCCCCCCCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc-----------
Q psy13676         11 LINIIPITQSSPDASLLEEFRIPPDITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA-----------   79 (200)
Q Consensus        11 l~~~l~~~~~~~~~~~L~~~~~~~~~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~-----------   79 (200)
                      +.+.+..+++..-...|.+++... ....+.|+||||.|...   +..++||+|||+|++..+.+.+.+           
T Consensus       213 ~~~~i~~i~G~~~~~~l~~v~~~~-~~~~~~i~G~is~p~~~---~~~~~q~~fVNgR~v~~~~l~~ai~~~y~~~l~~~  288 (348)
T 3na3_A          213 TVDNIRSIFGNAVSRELIEIGCED-KTLAFKMNGYISNANYS---VKKCIFLLFINHRLVESTSLRKAIETVYAAYLPKN  288 (348)
T ss_dssp             HHHHHHHHHCHHHHTTEEEEEEEE-GGGTEEEEEEEECSSCC---BSSCEEEEEETTEECCCTTHHHHHHHHHHTTSCTT
T ss_pred             HHHHHHHHhChHhHhhcEEEEeec-CCccEEEEEEEeCCccC---CCcccEEEEECCeEecCHHHHHHHHHHHHHhCcCC
Confidence            344444444433333344444431 11358999999999855   234689999999999988776554           


Q ss_pred             -ceEEEEEeCCceeeeechh---------hhHHHHHHHHhh
Q psy13676         80 -EGFIIVKYDSDLFIIDQHA---------TDEKYNFETLQK  110 (200)
Q Consensus        80 -~~yIla~~~~~L~lIDqHA---------AhERIlyE~L~~  110 (200)
                       .|++++.+.-+.-.+|.|.         .+|+.+++.+..
T Consensus       289 ~~P~~~L~l~~~p~~vDVNvhP~K~eV~f~~e~~i~~~i~~  329 (348)
T 3na3_A          289 THPFLYLSLEISPQNVDVNVHPTKHEVHFLHEESILERVQQ  329 (348)
T ss_dssp             CBCEEEEEEECC----------------------CTHHHHH
T ss_pred             CceEEEEEEEeChhheeeeeCCCcCEEEEcCHHHHHHHHHH
Confidence             2678888888888899988         445555554444

>1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia coli K12} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A* 1bkn_A 1nhj_A* 1b62_A*

Probab=97.58  E-value=1.4e-05  Score=70.57  Aligned_cols=72  Identities=15%  Similarity=0.283  Sum_probs=55.6

Q ss_pred             cceEEEEEEeccccCCCCCC-CcceeeeecCCCCCCCcccccc------------ceEEEEEeCCceeeeechh------
Q psy13676         38 AMFTLSGFISSAIHGHGRST-ADRQFYFVNSRPCEPSKVSGQA------------EGFIIVKYDSDLFIIDQHA------   98 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~-~Drq~~~INkrp~~~~Kv~gq~------------~~yIla~~~~~L~lIDqHA------   98 (200)
                      ..++|+|+|+.|..  +|+. .++||+|+|+|++..+.+.+.+            .+++++.+.-+.-.+|.|+      
T Consensus       234 ~~~~v~G~i~~p~~--~~~~~~~~~~~fvNgR~V~~~~l~~ai~~~y~~~l~~~~~P~~~l~l~~~p~~vDvNvhP~K~e  311 (333)
T 1b63_A          234 GDLTLRGWVADPNH--TTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHE  311 (333)
T ss_dssp             TTEEEEEEEECGGG--CCTTGGGCEEEEETTEECCCHHHHHHHHHHHHHHSSSCCCCCEEEEEECCGGGEECTTSTTCCC
T ss_pred             CCEEEEEEEEcCcc--ccCCCCCcEEEEECCEEecCHHHHHHHHHHHHhhccCCCCcEEEEEEEeCchhccceECCCcCE
Confidence            56899999999984  5777 8999999999999987665443            2456777777777888887      


Q ss_pred             ---hhHHHHHHHHhhh
Q psy13676         99 ---TDEKYNFETLQKT  111 (200)
Q Consensus        99 ---AhERIlyE~L~~~  111 (200)
                         .+|+.+++.+...
T Consensus       312 v~f~~~~~v~~~i~~~  327 (333)
T 1b63_A          312 VRFHQSRLVHDFIYQG  327 (333)
T ss_dssp             CEETTHHHHHHHHHHH
T ss_pred             EEeCCHHHHHHHHHHH
Confidence               6677777766543

---

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	200
d1x9za_	182	d.292.1.1 (A:) DNA mismatch repair protein MutL {E	2e-13
d1h7sa1	134	d.14.1.3 (A:232-365) DNA mismatch repair protein P	1e-10
d1b63a1	115	d.14.1.3 (A:217-331) DNA mismatch repair protein M	2e-04

>d1x9za_ d.292.1.1 (A:) DNA mismatch repair protein MutL {Escherichia coli [TaxId: 562]} Length = 182

class: Alpha and beta proteins (a+b)
fold: DNA mismatch repair protein MutL
superfamily: DNA mismatch repair protein MutL
family: DNA mismatch repair protein MutL
domain: DNA mismatch repair protein MutL
species: Escherichia coli [TaxId: 562]

 Score = 63.7 bits (155), Expect = 2e-13
 Identities = 11/88 (12%), Positives = 32/88 (36%), Gaps = 2/88 (2%)

Query: 74  KVSGQ-AEGFIIVKYDSDLFIIDQHATDEKYNFETL-QKTTVIKSQKLVVPQNLHLTKIN 131
           +V         +++ D ++ ++     +       L      + +Q L++P  L ++   
Sbjct: 5   RVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEE 64

Query: 132 QCILKDNLPVFYKNGFEFRITMMFANLR 159
           +  L+       + G +F+       +R
Sbjct: 65  KSALEKAQSALAELGIDFQSDAQHVTIR 92

>d1h7sa1 d.14.1.3 (A:232-365) DNA mismatch repair protein PMS2 {Human (Homo sapiens) [TaxId: 9606]} Length = 134

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: DNA gyrase/MutL, second domain
domain: DNA mismatch repair protein PMS2
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 55.0 bits (132), Expect = 1e-10
 Identities = 32/69 (46%), Positives = 45/69 (65%), Gaps = 2/69 (2%)

Query: 10 QLINIIPITQSSPDASLLEEFRIPP--DITAMFTLSGFISSAIHGHGRSTADRQFYFVNS 67
          QL ++IP  Q  P  S+ EE+ +     +  +F +SGFIS   HG GRS+ DRQF+F+N 
Sbjct: 4  QLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINR 63

Query: 68 RPCEPSKVS 76
          RPC+P+KV 
Sbjct: 64 RPCDPAKVC 72

>d1b63a1 d.14.1.3 (A:217-331) DNA mismatch repair protein MutL {Escherichia coli [TaxId: 562]} Length = 115

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: DNA gyrase/MutL, second domain
domain: DNA mismatch repair protein MutL
species: Escherichia coli [TaxId: 562]

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 9/45 (20%), Positives = 18/45 (40%), Gaps = 1/45 (2%)

Query: 40 FTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQAEGFII 84
           TL G+++   H    + A+ Q+ +VN R      ++        
Sbjct: 18 LTLRGWVADPNH-TTPALAEIQYCYVNGRMMRDRLINHAIRQACE 61

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	200
d1x9za_	182	DNA mismatch repair protein MutL {Escherichia coli	99.77
d1h7sa1	134	DNA mismatch repair protein PMS2 {Human (Homo sapi	99.41
d1b63a1	115	DNA mismatch repair protein MutL {Escherichia coli	98.61

>d1x9za_ d.292.1.1 (A:) DNA mismatch repair protein MutL {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: DNA mismatch repair protein MutL
superfamily: DNA mismatch repair protein MutL
family: DNA mismatch repair protein MutL
domain: DNA mismatch repair protein MutL
species: Escherichia coli [TaxId: 562]

Probab=99.77  E-value=2.2e-19  Score=144.84  Aligned_cols=87  Identities=13%  Similarity=0.250  Sum_probs=80.7

Q ss_pred             Ccccccc-ceEEEEEeCCceeeeechhhhHHHHHHHHhhh-ccccccccccCceeecCHHHHHHHHhhHHHHHhCCCeeE
Q psy13676         73 SKVSGQA-EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT-TVIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFR  150 (200)
Q Consensus        73 ~Kv~gq~-~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~-~~~~sQ~Ll~P~~l~Ls~~e~~ll~e~~~~L~~lGf~ie  150 (200)
                      .+|+|++ ++||+++.+++|++|||||||||+.||+|... ....+|+|++|+.+++++.+...+.++.+.|+++||+++
T Consensus         4 grvl~~v~~~Yil~e~~~gl~lidqhaA~eri~~e~l~~~~~~i~sQ~LL~P~~l~ls~~e~~~l~~~~~~L~~~Gf~~e   83 (182)
T d1x9za_           4 GRVLTIVHSDCALLERDGNISLLSLPVAERWLRQAQLTPGEAPVCAQPLLIPLRLKVSAEEKSALEKAQSALAELGIDFQ   83 (182)
T ss_dssp             CEEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHSBTTBCCCEEEEEEEEEEECCHHHHHHHHHHHHHHHHTTCEEE
T ss_pred             hhhhhhhcCEEEEEEeCCceEEEeHHHHHHHHHHHHHHhccCCCCccccCCCeeecCCHHHHHHHHHHHHHHHHcCCEEE
Confidence            3789999 99999999999999999999999999999876 678899999999999999999999999999999999999


Q ss_pred             EcCCcceec
Q psy13676        151 ITMMFANLR  159 (200)
Q Consensus       151 ~~g~~~~~~  159 (200)
                      +++++..++
T Consensus        84 ~~g~~i~v~   92 (182)
T d1x9za_          84 SDAQHVTIR   92 (182)
T ss_dssp             ECSSEEEEE
T ss_pred             ccccceeee
Confidence            998765443

>d1h7sa1 d.14.1.3 (A:232-365) DNA mismatch repair protein PMS2 {Human (Homo sapiens) [TaxId: 9606]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: DNA gyrase/MutL, second domain
domain: DNA mismatch repair protein PMS2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.41  E-value=5.9e-14  Score=108.71  Aligned_cols=104  Identities=37%  Similarity=0.679  Sum_probs=83.6

Q ss_pred             hhhhhhccccccCCCccccccccCCCCC--CCcceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------
Q psy13676          8 ISQLINIIPITQSSPDASLLEEFRIPPD--ITAMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------   79 (200)
Q Consensus         8 ~~~l~~~l~~~~~~~~~~~L~~~~~~~~--~~~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------   79 (200)
                      ++++++++|+.+.+|....++.+++..+  ....++|+||||.|.+++||++.|+||+|||+||+..+.+...+      
T Consensus         2 ~~~~~~l~p~~~~~p~~~i~~~~g~~~~~~~~~~~~i~G~is~p~~~~~R~~~~~q~~fVN~R~V~~~~l~~ai~~~y~~   81 (134)
T d1h7sa1           2 QKQLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHM   81 (134)
T ss_dssp             HHHHHTEEECCCCCCCHHHHHHHTCCTTTTTSCCCEEEEEEECCSTTTSBSSSTTEEEEETTEEECCHHHHHHHHHHHHT
T ss_pred             cchhhhccccccCCCchhHHHHhCcccccccCCceEEEEEEcCCCccCCccCCCcEEEEEcCCcccCHHHHHHHHHHHHH
Confidence            5799999999999999999888877533  34668999999999999999999999999999999987666544      


Q ss_pred             -----ceEEEEEeCCceeeeechh---------hhHHHHHHHHhhh
Q psy13676         80 -----EGFIIVKYDSDLFIIDQHA---------TDEKYNFETLQKT  111 (200)
Q Consensus        80 -----~~yIla~~~~~L~lIDqHA---------AhERIlyE~L~~~  111 (200)
                           .+++++.+....-.||.|+         .+|..+++.+.+.
T Consensus        82 ~~~~~~P~~~L~i~ip~~~vDVNVhP~K~eV~f~~e~~i~~~i~~~  127 (134)
T d1h7sa1          82 YNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTS  127 (134)
T ss_dssp             TCTTCBCCEEEEEECCGGGEEEC------CEEETTHHHHHHHHHHH
T ss_pred             cCCCCCCEEEEEEEecCceEEecCCCcccEEEEcCHHHHHHHHHHH
Confidence                 2567777776667788887         6677777766554

>d1b63a1 d.14.1.3 (A:217-331) DNA mismatch repair protein MutL {Escherichia coli [TaxId: 562]}

class: Alpha and beta proteins (a+b)
fold: Ribosomal protein S5 domain 2-like
superfamily: Ribosomal protein S5 domain 2-like
family: DNA gyrase/MutL, second domain
domain: DNA mismatch repair protein MutL
species: Escherichia coli [TaxId: 562]

Probab=98.61  E-value=1.3e-08  Score=76.02  Aligned_cols=73  Identities=15%  Similarity=0.269  Sum_probs=58.0

Q ss_pred             cceEEEEEEeccccCCCCCCCcceeeeecCCCCCCCcccccc------------ceEEEEEeCCceeeeechh-------
Q psy13676         38 AMFTLSGFISSAIHGHGRSTADRQFYFVNSRPCEPSKVSGQA------------EGFIIVKYDSDLFIIDQHA-------   98 (200)
Q Consensus        38 ~~~~v~G~is~~~~g~gRs~~Drq~~~INkrp~~~~Kv~gq~------------~~yIla~~~~~L~lIDqHA-------   98 (200)
                      ..++|+||||.|.. .+++++|+||+||||||+..+.+...+            .+++++.+.-+.-.+|.|.       
T Consensus        16 ~~~~i~G~is~P~~-~~~~~~~~q~~fVN~R~V~~~~l~~ai~~~y~~~l~~~~~P~~~L~l~i~p~~vDVNVhP~K~eV   94 (115)
T d1b63a1          16 GDLTLRGWVADPNH-TTPALAEIQYCYVNGRMMRDRLINHAIRQACEDKLGADQQPAFVLYLEIDPHQVDVNVHPAKHEV   94 (115)
T ss_dssp             TTEEEEEEEECGGG-CCTTGGGCEEEEETTEECCCHHHHHHHHHHHHHHSSSCCCCCEEEEEECCGGGEECTTSTTCCCC
T ss_pred             CCEEEEEEEeCchh-hccCCCCcEEEEEcCCeEchHHHHHHHHHHHHHhccCCCCceEEEEEEEcccEEEEEeCCCccEE
Confidence            67999999999986 367788999999999999987766554            2567777777777788887       


Q ss_pred             --hhHHHHHHHHhhh
Q psy13676         99 --TDEKYNFETLQKT  111 (200)
Q Consensus        99 --AhERIlyE~L~~~  111 (200)
                        .+|+..++.+...
T Consensus        95 ~f~~e~~i~~~i~~~  109 (115)
T d1b63a1          95 RFHQSRLVHDFIYQG  109 (115)
T ss_dssp             EETTHHHHHHHHHHH
T ss_pred             EEcCHHHHHHHHHHH
Confidence              6788888777653