Query psy13676
Match_columns 200
No_of_seqs 205 out of 1119
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 17:34:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13676.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13676hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08676 MutL_C: MutL C termin 99.8 2.3E-20 4.9E-25 147.5 7.9 84 73-156 3-89 (144)
2 smart00853 MutL_C MutL C termi 99.8 2.2E-19 4.8E-24 140.0 9.3 84 73-156 2-90 (136)
3 PRK00095 mutL DNA mismatch rep 99.7 3E-17 6.6E-22 157.8 9.7 86 73-158 431-520 (617)
4 COG0323 MutL DNA mismatch repa 99.7 5E-17 1.1E-21 157.0 11.2 80 77-156 456-538 (638)
5 KOG1978|consensus 99.3 7.4E-13 1.6E-17 127.1 5.3 95 65-159 481-576 (672)
6 cd03485 MutL_Trans_hPMS_1_like 98.7 7.5E-09 1.6E-13 81.5 3.2 96 14-111 6-126 (132)
7 cd03484 MutL_Trans_hPMS_2_like 98.6 9.4E-08 2E-12 76.4 6.8 74 38-111 43-136 (142)
8 cd03482 MutL_Trans_MutL MutL_T 98.6 3.9E-08 8.4E-13 76.7 3.4 71 38-110 25-116 (123)
9 cd03483 MutL_Trans_MLH1 MutL_T 98.5 5.3E-08 1.2E-12 76.4 3.0 71 38-111 30-121 (127)
10 PF01119 DNA_mis_repair: DNA m 98.5 3.8E-08 8.3E-13 76.0 0.6 81 25-110 11-112 (119)
11 cd03486 MutL_Trans_MLH3 MutL_T 98.4 1.8E-07 4E-12 74.5 3.3 59 14-79 5-63 (141)
12 cd00782 MutL_Trans MutL_Trans: 98.4 1.9E-07 4.2E-12 71.7 2.9 80 26-110 16-116 (122)
13 KOG1977|consensus 98.0 6.3E-06 1.4E-10 80.8 4.5 93 63-156 903-996 (1142)
14 KOG1978|consensus 97.8 9.3E-06 2E-10 78.8 2.4 65 45-111 230-312 (672)
15 TIGR00585 mutl DNA mismatch re 97.3 9.9E-05 2.1E-09 65.6 2.2 82 15-99 212-305 (312)
16 PRK00095 mutL DNA mismatch rep 97.3 0.00017 3.6E-09 70.2 3.2 97 10-111 203-320 (617)
17 cd00329 TopoII_MutL_Trans MutL 96.7 0.0011 2.3E-08 48.4 2.4 37 38-76 25-62 (107)
18 KOG1979|consensus 80.4 0.75 1.6E-05 45.1 1.0 87 9-98 211-309 (694)
19 PF08496 Peptidase_S49_N: Pept 48.6 13 0.00028 30.4 2.1 8 189-196 96-103 (155)
20 PF07505 Gp37_Gp68: Phage prot 41.6 15 0.00033 32.5 1.5 70 55-126 107-182 (261)
21 PF08208 RNA_polI_A34: DNA-dir 37.7 11 0.00024 31.3 0.0 6 27-32 21-26 (198)
22 PF07771 TSGP1: Tick salivary 35.1 3.9 8.4E-05 32.2 -2.9 13 61-73 53-65 (120)
23 PF14122 YokU: YokU-like prote 33.3 13 0.00028 27.8 -0.2 29 83-111 50-78 (87)
24 KOG2812|consensus 30.6 36 0.00078 31.8 2.1 13 97-109 143-155 (426)
25 KOG2422|consensus 29.2 14 0.00031 36.5 -0.7 18 157-174 80-97 (665)
26 PF15002 ERK-JNK_inhib: ERK an 27.8 58 0.0012 28.0 2.8 14 180-193 189-202 (207)
27 KOG3794|consensus 24.6 52 0.0011 31.1 2.1 13 11-23 64-76 (453)
28 TIGR00869 sec62 protein transl 22.3 57 0.0012 28.5 1.8 6 142-147 190-195 (232)
29 KOG3794|consensus 20.2 70 0.0015 30.3 2.0 8 53-60 133-140 (453)
No 1
>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 []. 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.
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
No 2
>smart00853 MutL_C MutL C terminal dimerisation domain. 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.
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
No 3
>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
No 4
>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
No 5
>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
No 6
>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. 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.
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
No 7
>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). 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.
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
No 8
>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. 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.
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
No 9
>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). 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.
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
No 10
>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. 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 ....
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
No 11
>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). 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.
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
No 12
>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. 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
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
No 13
>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
No 14
>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
No 15
>TIGR00585 mutl DNA mismatch repair protein MutL. 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).
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
No 16
>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
No 17
>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. 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
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
No 18
>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
No 19
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=48.59 E-value=13 Score=30.37 Aligned_cols=8 Identities=38% Similarity=0.870 Sum_probs=5.8
Q ss_pred hhhhhccc
Q psy13676 189 KKKRLYIF 196 (200)
Q Consensus 189 ~~~~~~~~ 196 (200)
.++|+|+.
T Consensus 96 ~~~r~~Vl 103 (155)
T PF08496_consen 96 PKPRLFVL 103 (155)
T ss_pred CCCeEEEE
Confidence 37888874
No 20
>PF07505 Gp37_Gp68: Phage protein Gp37/Gp68; InterPro: IPR011101 This entry is represented by Burkholderia phage phiE125, Gp37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=41.55 E-value=15 Score=32.50 Aligned_cols=70 Identities=20% Similarity=0.272 Sum_probs=44.8
Q ss_pred CCCCcceeeeecCCCCCCCcccccc--ceEEEEEeCCceeeeechhhhHHHHHHHHhhh----ccccccccccCceee
Q psy13676 55 RSTADRQFYFVNSRPCEPSKVSGQA--EGFIIVKYDSDLFIIDQHATDEKYNFETLQKT----TVIKSQKLVVPQNLH 126 (200)
Q Consensus 55 Rs~~Drq~~~INkrp~~~~Kv~gq~--~~yIla~~~~~L~lIDqHAAhERIlyE~L~~~----~~~~sQ~Ll~P~~l~ 126 (200)
+.+++..|.++++||-...+++..- ...+.-+.-.+.-+-||..|++||-. |++- .++...|||-|+.+.
T Consensus 107 ~~~p~h~f~~LTKRp~R~~~~l~~~~~~~~~~~NvwlGvTvenQ~~ad~Rip~--L~~~pa~~rflS~EPLLg~i~l~ 182 (261)
T PF07505_consen 107 RARPQHTFQFLTKRPERMREYLPSDWGDGDWPPNVWLGVTVENQKRADERIPI--LLETPAKVRFLSCEPLLGPIDLS 182 (261)
T ss_pred HhCCCeEEEEeeCCHHHHHHhccccccccCCCCceEEEEEEEchHHHHHhHHH--HHhCCccEEEEEeccccCCcCcc
Confidence 6677788888888887665554432 11111222224467899999999864 4442 456678888888765
No 21
>PF08208 RNA_polI_A34: DNA-directed RNA polymerase I subunit RPA34.5; InterPro: IPR013240 This is a family of proteins conserved from yeasts to human. Subunit A34.5 of RNA polymerase I is a non-essential subunit which is thought to help Pol I overcome topological constraints imposed on ribosomal DNA during the process of transcription [].; PDB: 3NFG_N.
Probab=37.65 E-value=11 Score=31.35 Aligned_cols=6 Identities=33% Similarity=0.528 Sum_probs=1.3
Q ss_pred ccccCC
Q psy13676 27 LEEFRI 32 (200)
Q Consensus 27 L~~~~~ 32 (200)
|..+.+
T Consensus 21 l~~l~i 26 (198)
T PF08208_consen 21 LKGLPI 26 (198)
T ss_dssp -SEE--
T ss_pred hCCcee
Confidence 444444
No 22
>PF07771 TSGP1: Tick salivary peptide group 1; InterPro: IPR011694 This entry contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis (Black-legged tick) []. Also present are peptides from a related tick species, Ixodes ricinus (Sheep tick). They are characterised by a putative signal peptide, indicative of secretion, and conserved cysteine residues.
Probab=35.11 E-value=3.9 Score=32.18 Aligned_cols=13 Identities=15% Similarity=0.396 Sum_probs=9.3
Q ss_pred eeeeecCCCCCCC
Q psy13676 61 QFYFVNSRPCEPS 73 (200)
Q Consensus 61 q~~~INkrp~~~~ 73 (200)
.+||.||.+|.+.
T Consensus 53 ~g~~~dGt~C~y~ 65 (120)
T PF07771_consen 53 YGFYGDGTPCFYN 65 (120)
T ss_pred EEEecCCCccccC
Confidence 5667788888754
No 23
>PF14122 YokU: YokU-like protein
Probab=33.28 E-value=13 Score=27.77 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=25.4
Q ss_pred EEEEeCCceeeeechhhhHHHHHHHHhhh
Q psy13676 83 IIVKYDSDLFIIDQHATDEKYNFETLQKT 111 (200)
Q Consensus 83 Ila~~~~~L~lIDqHAAhERIlyE~L~~~ 111 (200)
++-++++.|++||.....+-|.|++|++.
T Consensus 50 vi~EIEdql~Lidtk~l~~sity~~LM~~ 78 (87)
T PF14122_consen 50 VIKEIEDQLFLIDTKKLPNSITYEELMNQ 78 (87)
T ss_pred HHHHHhhheEEEecccCCccccHHHHhhc
Confidence 44567899999999999999999999875
No 24
>KOG2812|consensus
Probab=30.61 E-value=36 Score=31.80 Aligned_cols=13 Identities=8% Similarity=0.181 Sum_probs=6.4
Q ss_pred hhhhHHHHHHHHh
Q psy13676 97 HATDEKYNFETLQ 109 (200)
Q Consensus 97 HAAhERIlyE~L~ 109 (200)
..-.+|++.-.+-
T Consensus 143 rRr~qr~rige~g 155 (426)
T KOG2812|consen 143 RRRSQRVRIGELG 155 (426)
T ss_pred HHHHHHhhhhhcc
Confidence 3455555554443
No 25
>KOG2422|consensus
Probab=29.19 E-value=14 Score=36.46 Aligned_cols=18 Identities=44% Similarity=0.545 Sum_probs=7.5
Q ss_pred eecCCCCchhhHHHHHHH
Q psy13676 157 NLRNGDGTSRKKKKKKKK 174 (200)
Q Consensus 157 ~~~~~~~~~~~~~~~~~~ 174 (200)
++-.....+++|+|||+|
T Consensus 80 ~~~~~~~~sk~k~KKK~k 97 (665)
T KOG2422|consen 80 RITLASKSSKNKKKKKKK 97 (665)
T ss_pred cccccchhhccccchhhh
Confidence 333334444444444433
No 26
>PF15002 ERK-JNK_inhib: ERK and JNK pathways, inhibitor
Probab=27.83 E-value=58 Score=27.95 Aligned_cols=14 Identities=79% Similarity=0.802 Sum_probs=6.1
Q ss_pred HHHHHHHHhhhhhh
Q psy13676 180 KKKKKKKKKKKKRL 193 (200)
Q Consensus 180 ~~~~~~~~~~~~~~ 193 (200)
||+++|+.+|+.||
T Consensus 189 kKk~kkk~kKgPrl 202 (207)
T PF15002_consen 189 KKKKKKKIKKGPRL 202 (207)
T ss_pred HHHHHHHhccCCCc
Confidence 33333334455554
No 27
>KOG3794|consensus
Probab=24.63 E-value=52 Score=31.11 Aligned_cols=13 Identities=15% Similarity=0.235 Sum_probs=7.6
Q ss_pred hhhccccccCCCc
Q psy13676 11 LINIIPITQSSPD 23 (200)
Q Consensus 11 l~~~l~~~~~~~~ 23 (200)
+.+.|+|.+.+|-
T Consensus 64 ~K~~~sFMY~~PP 76 (453)
T KOG3794|consen 64 VKNGLSFMYEAPP 76 (453)
T ss_pred hhcccceeecCCC
Confidence 3456666666553
No 28
>TIGR00869 sec62 protein translocation protein, Sec62 family. protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins has been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.
Probab=22.34 E-value=57 Score=28.52 Aligned_cols=6 Identities=50% Similarity=0.927 Sum_probs=2.9
Q ss_pred HHhCCC
Q psy13676 142 FYKNGF 147 (200)
Q Consensus 142 L~~lGf 147 (200)
|+.+||
T Consensus 190 feD~Gf 195 (232)
T TIGR00869 190 FADVGF 195 (232)
T ss_pred hcccCc
Confidence 444554
No 29
>KOG3794|consensus
Probab=20.19 E-value=70 Score=30.30 Aligned_cols=8 Identities=38% Similarity=0.630 Sum_probs=4.4
Q ss_pred CCCCCCcc
Q psy13676 53 HGRSTADR 60 (200)
Q Consensus 53 ~gRs~~Dr 60 (200)
+|..+.|+
T Consensus 133 wGH~n~Dr 140 (453)
T KOG3794|consen 133 WGHINTDR 140 (453)
T ss_pred cccccCCc
Confidence 45555555
Done!