Query psy13670
Match_columns 380
No_of_seqs 252 out of 1503
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 17:25:54 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13670.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13670hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00095 mutL DNA mismatch rep 100.0 1.3E-49 2.8E-54 417.2 29.0 325 2-380 265-597 (617)
2 COG0323 MutL DNA mismatch repa 100.0 2.4E-48 5.2E-53 406.4 31.2 170 207-380 447-618 (638)
3 KOG1978|consensus 100.0 1.5E-37 3.4E-42 315.0 24.2 192 188-380 465-658 (672)
4 PF08676 MutL_C: MutL C termin 100.0 2.4E-34 5.3E-39 249.1 13.5 141 211-357 2-144 (144)
5 smart00853 MutL_C MutL C termi 99.9 1.9E-26 4E-31 197.6 15.8 131 212-346 2-136 (136)
6 KOG1977|consensus 99.8 1.3E-20 2.8E-25 190.9 11.3 176 203-380 904-1093(1142)
7 cd03483 MutL_Trans_MLH1 MutL_T 99.8 7.1E-19 1.5E-23 149.1 6.9 61 2-62 66-127 (127)
8 cd03482 MutL_Trans_MutL MutL_T 99.7 1.7E-17 3.6E-22 140.0 7.0 61 2-62 62-123 (123)
9 cd03485 MutL_Trans_hPMS_1_like 99.7 4.6E-17 1E-21 139.0 7.4 61 2-62 68-132 (132)
10 PF01119 DNA_mis_repair: DNA m 99.7 7.4E-17 1.6E-21 135.3 6.7 61 2-62 58-119 (119)
11 cd03484 MutL_Trans_hPMS_2_like 99.6 2.9E-16 6.2E-21 135.7 7.6 62 1-62 81-142 (142)
12 cd00782 MutL_Trans MutL_Trans: 99.6 1.5E-15 3.2E-20 127.8 7.4 60 2-61 62-122 (122)
13 cd03486 MutL_Trans_MLH3 MutL_T 99.6 1.3E-15 2.8E-20 131.5 7.0 61 2-62 61-141 (141)
14 KOG1979|consensus 99.5 1.4E-13 3E-18 138.2 16.4 64 2-65 276-340 (694)
15 cd00329 TopoII_MutL_Trans MutL 98.7 7.8E-09 1.7E-13 83.8 3.4 41 2-42 63-107 (107)
16 PRK14867 DNA topoisomerase VI 87.1 0.51 1.1E-05 50.5 3.3 28 2-29 280-308 (659)
17 KOG1977|consensus 81.1 1.1 2.4E-05 47.7 2.6 50 14-63 261-310 (1142)
18 COG1654 BirA Biotin operon rep 47.9 28 0.0006 26.9 3.6 34 273-308 34-67 (79)
19 PF03484 B5: tRNA synthetase B 43.8 1.3E+02 0.0028 22.2 6.7 29 276-307 22-50 (70)
20 PF05848 CtsR: Firmicute trans 37.5 80 0.0017 27.5 5.3 47 260-307 30-76 (152)
21 PF06569 DUF1128: Protein of u 35.9 36 0.00078 25.7 2.5 22 352-373 49-70 (71)
22 PF11272 DUF3072: Protein of u 35.4 1.1E+02 0.0024 22.1 4.7 36 336-371 18-53 (57)
23 PF13224 DUF4032: Domain of un 31.8 3.7E+02 0.0079 23.8 9.8 36 267-302 13-52 (165)
24 KOG0030|consensus 31.1 97 0.0021 26.7 4.6 45 316-368 86-132 (152)
25 PF14122 YokU: YokU-like prote 26.0 16 0.00035 28.6 -0.8 28 224-251 51-78 (87)
26 PF03997 VPS28: VPS28 protein; 24.2 2.4E+02 0.0053 25.4 6.3 33 336-371 146-178 (188)
27 PF02742 Fe_dep_repr_C: Iron d 22.8 83 0.0018 23.3 2.6 33 345-380 32-64 (71)
28 PF03460 NIR_SIR_ferr: Nitrite 21.2 3.2E+02 0.007 19.6 5.8 48 266-325 20-67 (69)
29 COG4840 Uncharacterized protei 20.8 83 0.0018 23.4 2.1 23 351-373 48-70 (71)
No 1
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=100.00 E-value=1.3e-49 Score=417.20 Aligned_cols=325 Identities=19% Similarity=0.278 Sum_probs=210.5
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhccCcccCCCcccccccCCC
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYAIGFTVDGNNMNQSMEQDP 80 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~~~~~~~~~~~~~~~~~~~ 80 (380)
++|+++|+++++ ++||+|||+|++||+.|||||||+|++|+|.+|+.|+++|..+|+.+|.. .. . . +... .
T Consensus 265 ~ai~~~y~~~~~~~~~P~~~l~i~~~~~~~DvNvhP~K~ev~f~~e~~i~~~i~~~i~~~l~~---~~-~-~-~~~~--~ 336 (617)
T PRK00095 265 HAIRQAYHDLLPRGRYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLVHDLIVQAIQEALAQ---SG-L-I-PAAA--G 336 (617)
T ss_pred HHHHHHHHHhccCCCCcEEEEEEEeChHhcccccCCCcCEEEeCCHHHHHHHHHHHHHHHHhc---cC-C-C-cccc--c
Confidence 689999999998 99999999999999999999999999999999999999999999999975 11 1 0 0000 0
Q ss_pred CCccchhhhccCCCccccccCCCCCCCCCCCccccccccCCCCCcCCCCCCCcceecCCCCCcccccCCCCCcccchhhh
Q psy13670 81 SSDVDMEKIQRSNSEEVEHETIPVPSEDNSNFSHEANLQQSPETVEPDTPDETIEVIDDMPRLQGSYRQSTPVTLSLDII 160 (380)
Q Consensus 81 ~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 160 (380)
......+ ..+.+..... ..+.+. . . . ....+...........+....
T Consensus 337 ---~~~~~~~--------~~~~~~~~~~-~~~~~~------~-------~---~-~~~~~~~~~~~~~~~~~~~~~---- 383 (617)
T PRK00095 337 ---ANQVLEP--------AEPEPLPLQQ-TPLYAS------G-------S---S-PPASSPSSAPPEQSEESQEES---- 383 (617)
T ss_pred ---ccccccc--------cccccccccc-cccCcc------c-------c---c-ccccccccccccccccccccc----
Confidence 0000000 0000000000 000000 0 0 0 000000000000000000000
Q ss_pred Hhhhhhhhhhhhh---cccchhhhhhhhcccCCCcchhhH-HHhhhhccccccccceEEEEEeCcEEEEEeCCeEEEEeh
Q psy13670 161 QDQLKARYARRTV---QAQDRCVENRFHANIDPSKNKEAE-SELNRVIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQ 236 (380)
Q Consensus 161 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~ae-~~~~~~~~~~~~~~~~~igQ~~~~yIl~~~~~~L~lIDQ 236 (380)
. ....... .+.. ..+... ...+....... ...........++.+++|||++++|||++.+++||||||
T Consensus 384 ----~-~~~~~~~~~~~~~~-~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~vigQv~~~YIl~e~~~~L~iIDQ 455 (617)
T PRK00095 384 ----S-AEKNPLQPNASQSE-AAAAAS--AEAAAAAPAAAPEPAEAAEEADSFPLGYALGQLHGTYILAENEDGLYLVDQ 455 (617)
T ss_pred ----c-cccccccccccccc-cccccc--cccccccccccccccccccccccCcCceEeEEEcCEEEEEEeCCcEEEEEH
Confidence 0 0000000 0000 000000 00000000000 000001112344567899999999999999999999999
Q ss_pred hHHHHHHHHHHHHhhc---CCCccccccceeeecCHHHHHHHHHhHHHHHhCCeEEEEecCCCCeEEEEecCCCCCccCC
Q psy13670 237 HATDEKYNFETLQKTT---LIKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLG 313 (380)
Q Consensus 237 HAAhERilyE~l~~~~---~~~sQ~LL~P~~l~l~~~e~~~l~~~~~~L~~lGf~~~~~~~g~~~~~I~~vP~~l~~~~~ 313 (380)
|||||||+||+|+++. ...+|+||+|+.++|++.+..+++++.+.|++|||+++ .+|++++.|++||.++.....
T Consensus 456 HAAhERI~yE~l~~~~~~~~~~~Q~LL~P~~l~Ls~~e~~~l~~~~~~L~~lGf~~e--~fg~~si~I~~vP~~l~~~~~ 533 (617)
T PRK00095 456 HAAHERLLYEQLKDKLAEVGLASQPLLIPLVLELSEDEADRLEEHKELLARLGLELE--PFGPNSFAVREVPALLGQQEL 533 (617)
T ss_pred HHHHHHHHHHHHHHHhccCCCcccccccCeEEeeCHHHHHHHHHHHHHHHhCCcEEE--EcCCCEEEEEecChhhcccCH
Confidence 9999999999999863 46789999999999999999999999999999999998 568899999999998764433
Q ss_pred hhhHHHHHHHHhhcCCCCCCChHHHHHHHHHHHhhhhhhcCCCCCHHHHHHHHHHHhccCCCCCCCC
Q psy13670 314 REDIEELLFMLQHTNSTEHCRPSRIRAMFASRACRKSVMIGRALSVGEMTGLVRNMGRIDQPWVSMG 380 (380)
Q Consensus 314 ~~~l~~ll~~l~~~~~~~~~~~~~~~~~la~~ACr~Aik~g~~Ls~~E~~~Ll~~L~~c~~P~~CPH 380 (380)
...+.+++..|.+.. .. ....+.++++++|||+|||+|+.|+.+||++||++|++|++||+|||
T Consensus 534 ~~~l~ell~~l~~~~-~~--~~~~~~~~las~ACr~AIk~g~~Ls~~E~~~Ll~~L~~~~~P~~CPH 597 (617)
T PRK00095 534 EELIRDLLDELAEEG-DS--DTLKERELLATMACHGAIRAGRRLTLEEMNALLRQLEATENPGTCPH 597 (617)
T ss_pred HHHHHHHHHHHHhcC-Cc--chHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHHHHHhcccccCCCC
Confidence 555666666665432 11 12223378999999999999999999999999999999999999999
No 2
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.4e-48 Score=406.44 Aligned_cols=170 Identities=28% Similarity=0.401 Sum_probs=150.6
Q ss_pred cccccceEEEEEeCcEEEEEeCCeEEEEehhHHHHHHHHHHHHhhcCC--CccccccceeeecCHHHHHHHHHhHHHHHh
Q psy13670 207 SMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTLI--KSQKLVVPQNLHLTKINQCILKDNLPVFYK 284 (380)
Q Consensus 207 ~~~~~~~~igQ~~~~yIl~~~~~~L~lIDQHAAhERilyE~l~~~~~~--~sQ~LL~P~~l~l~~~e~~~l~~~~~~L~~ 284 (380)
..++.++++||++++|||++.+++||||||||||||++||+|+..... ..|+||+|+.++|++.|...+.++.+.|.+
T Consensus 447 ~~~~~~~~i~q~~~~yil~e~~~~L~lvDqhaa~Eri~ye~l~~~~~~~~~~Q~LliP~~~~l~~~e~~~~~~~~~~l~~ 526 (638)
T COG0323 447 DVFPLGEAIGQVHGTYILAEHEDGLVLVDQHAAHERILYEKLKNELGNVGELQPLLIPIRLELSPEEADVLEEHKEELEK 526 (638)
T ss_pred cccccceEEEEecceEEEEEeCCCEEEEEhHHhHHHHHHHHHHHHhcccccccccccCeeeecCHHHHHHHHHHHHHHHh
Confidence 567889999999999999999999999999999999999999987433 699999999999999999999999999999
Q ss_pred CCeEEEEecCCCCeEEEEecCCCCCccCChhhHHHHHHHHhhcCCCCCCChHHHHHHHHHHHhhhhhhcCCCCCHHHHHH
Q psy13670 285 NGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEHCRPSRIRAMFASRACRKSVMIGRALSVGEMTG 364 (380)
Q Consensus 285 lGf~~~~~~~g~~~~~I~~vP~~l~~~~~~~~l~~ll~~l~~~~~~~~~~~~~~~~~la~~ACr~Aik~g~~Ls~~E~~~ 364 (380)
+||+++ .+|++.+.|++||.++........+.+++..+.+ . .........++++++||||+|||+|+.|+.++|..
T Consensus 527 ~G~~i~--~~g~~~~~v~~vP~~l~~~~~~~~i~~l~~~~~~-~-~~~~~~~~~~~~~a~~aC~~svk~~~~l~~~~m~~ 602 (638)
T COG0323 527 LGFEIE--SFGENSVAVRSVPAMLGKAEVQELIRELLDDLLE-G-KLKDLKELLEELAATMACRSAVKAGRELSAEEMNA 602 (638)
T ss_pred cCEEEE--EcCCceEEEEecChhhcccchHHHHHHHHHHhhc-c-cccchhHHHHHHHHHHHHHHhhhcCCcCCHHHHHH
Confidence 999998 4688999999999998765556666777777765 3 22222345678999999999999999999999999
Q ss_pred HHHHHhccCCCCCCCC
Q psy13670 365 LVRNMGRIDQPWVSMG 380 (380)
Q Consensus 365 Ll~~L~~c~~P~~CPH 380 (380)
|+++|..|++||+|||
T Consensus 603 Ll~~~~~~~~~~~cpH 618 (638)
T COG0323 603 LLRDLEACPNPWTCPH 618 (638)
T ss_pred HHHHHHhCCCccCCCC
Confidence 9999999999999999
No 3
>KOG1978|consensus
Probab=100.00 E-value=1.5e-37 Score=314.99 Aligned_cols=192 Identities=50% Similarity=0.828 Sum_probs=173.6
Q ss_pred cCCCcchhhHHHhhhhccccccccceEEEEEeCcEEEEEeCCeEEEEehhHHHHHHHHHHHHhhcCCCccccccceeeec
Q psy13670 188 IDPSKNKEAESELNRVIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTLIKSQKLVVPQNLHL 267 (380)
Q Consensus 188 ~~~~~~~~ae~~~~~~~~~~~~~~~~~igQ~~~~yIl~~~~~~L~lIDQHAAhERilyE~l~~~~~~~sQ~LL~P~~l~l 267 (380)
+.+..+..++.+......+.+|..+++|||++.+||++..+.+|+||||||++|..+||+|++...+.+|+|..|..++|
T Consensus 465 ~~~~~N~~~e~~~s~~v~k~df~~meiigqfNlgFIi~~l~~dlfIvdqha~dEk~Nfe~l~~~~~L~~Q~l~~P~~l~l 544 (672)
T KOG1978|consen 465 INPGHNDSVELEESREVAKADFSRMEIIGQFNLGFIIVKLEKDLFIVDQHASDEKRNFERLQSTTVLKAQPLICPQALDL 544 (672)
T ss_pred cCcccchhhhchhhhcccccchhhcceeeeccccceeeeccCceEEeccchhhhhhhHHHHHHhcccccccccCcccccc
Confidence 34444544555555567788999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHhHHHHHhCCeEEEEecCC--CCeEEEEecCCCCCccCChhhHHHHHHHHhhcCCCCCCChHHHHHHHHHH
Q psy13670 268 TKINQCILKDNLPVFYKNGFEFSFDSSD--DGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEHCRPSRIRAMFASR 345 (380)
Q Consensus 268 ~~~e~~~l~~~~~~L~~lGf~~~~~~~g--~~~~~I~~vP~~l~~~~~~~~l~~ll~~l~~~~~~~~~~~~~~~~~la~~ 345 (380)
++.+...+.++++.|++.||.+++.+.. +..+++.++|....+.++..++.++|..|.+.. +....|..++.++|+.
T Consensus 545 s~~nE~vl~d~l~~f~knGF~~~~~~n~~~~~~~~l~~~p~skn~~fg~~dl~Eli~~l~~~~-~~~~rp~~vr~m~as~ 623 (672)
T KOG1978|consen 545 SAINEMVLLDNLPLFEKNGFKVKIDENAPDGKRVRLLSVPVSKNQTFGVSDLKELISVLKNFP-EETYRPSKVRSMIASK 623 (672)
T ss_pred CcccceeehhhhHHHHhcCceEeecCCCcccceeeecccccccccccCHHHHHHHHHHHhhCC-CcEeehHHHHHHHHHH
Confidence 9999999999999999999999975322 267889999999999999999999999999887 4447789999999999
Q ss_pred HhhhhhhcCCCCCHHHHHHHHHHHhccCCCCCCCC
Q psy13670 346 ACRKSVMIGRALSVGEMTGLVRNMGRIDQPWVSMG 380 (380)
Q Consensus 346 ACr~Aik~g~~Ls~~E~~~Ll~~L~~c~~P~~CPH 380 (380)
|||.++|.|+.|+..+|..++..|...+.||.|||
T Consensus 624 AcR~Svmig~~L~~~dm~~iv~~L~~l~~pwnCpH 658 (672)
T KOG1978|consen 624 ACRSSVMIGDPLSKDDMTRIVRSLAELEHPWNCPH 658 (672)
T ss_pred HhhhhhhcccccCHHHHHHHHHHHHHhcCCCCCCC
Confidence 99999999999999999999999999999999999
No 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 []. 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=100.00 E-value=2.4e-34 Score=249.06 Aligned_cols=141 Identities=30% Similarity=0.464 Sum_probs=113.7
Q ss_pred cceEEEEEeCcEEEEEeCCeEEEEehhHHHHHHHHHHHHhhcC--CCccccccceeeecCHHHHHHHHHhHHHHHhCCeE
Q psy13670 211 KMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTL--IKSQKLVVPQNLHLTKINQCILKDNLPVFYKNGFE 288 (380)
Q Consensus 211 ~~~~igQ~~~~yIl~~~~~~L~lIDQHAAhERilyE~l~~~~~--~~sQ~LL~P~~l~l~~~e~~~l~~~~~~L~~lGf~ 288 (380)
.+++|||++++|||++.+++||+||||||||||+||+|+++.. ..+|+|++|+.+++++.+...+.++.+.|++|||+
T Consensus 2 ~~~vlgq~~~~yil~~~~~~L~liDqHAAhERi~~E~l~~~~~~~~~~q~Ll~P~~~~ls~~e~~~l~~~~~~L~~~Gf~ 81 (144)
T PF08676_consen 2 LLKVLGQLDNKYILAESEDGLYLIDQHAAHERILYEKLLKQLEEGEQSQPLLFPIELELSPQEAELLEENKEELEKLGFE 81 (144)
T ss_dssp T-EEEEEETTTEEEEEETTEEEEEEHHHHHHHHHHHHHHHHCCHCS-EEEEEEEEEEE--HHHHHHHHHHHHHHHHTT-E
T ss_pred ceeeHhHhCCEEEEEEeCCCEEEEEHHHHHHHHHHHHHHHhhccCCCceecCCCccCCCCHHHHHHHHHHHHHHHhCCeE
Confidence 4799999999999999999999999999999999999998732 38999999999999999999999999999999999
Q ss_pred EEEecCCCCeEEEEecCCCCCccCChhhHHHHHHHHhhcCCCCCCChHHHHHHHHHHHhhhhhhcCCCC
Q psy13670 289 FSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEHCRPSRIRAMFASRACRKSVMIGRAL 357 (380)
Q Consensus 289 ~~~~~~g~~~~~I~~vP~~l~~~~~~~~l~~ll~~l~~~~~~~~~~~~~~~~~la~~ACr~Aik~g~~L 357 (380)
++. +|++++.|++||.++........+.+++..+.+.. . . +..+.++++++|||+|||+||+|
T Consensus 82 ~~~--~~~~~~~v~~vP~~l~~~~~~~~l~~ll~~l~~~~-~--~-~~~~~~~~~~~AC~~Aik~g~~L 144 (144)
T PF08676_consen 82 IEE--FGENSIIVRSVPAILREQDLEELLRELLEELQEKE-E--S-PEIIEELLASMACRSAIKAGDKL 144 (144)
T ss_dssp EEE--ESTTEEEEEEEECCCTTSSHHHHHHHHHHHHCTCS-S----CCCHHHHHHHHHTTSSSSSS---
T ss_pred EEE--ecCCEEEEEEeCcccccccHHHHHHHHHHHHHhCC-C--c-HHHHHHHHHHHHHHHhhcCCCCC
Confidence 984 67899999999999874433444555555555433 1 1 45678899999999999999986
No 5
>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=99.94 E-value=1.9e-26 Score=197.55 Aligned_cols=131 Identities=30% Similarity=0.442 Sum_probs=105.7
Q ss_pred ceEEEEEeCcEEEEEeCCeEEEEehhHHHHHHHHHHHHhhc---CC-CccccccceeeecCHHHHHHHHHhHHHHHhCCe
Q psy13670 212 MKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTT---LI-KSQKLVVPQNLHLTKINQCILKDNLPVFYKNGF 287 (380)
Q Consensus 212 ~~~igQ~~~~yIl~~~~~~L~lIDQHAAhERilyE~l~~~~---~~-~sQ~LL~P~~l~l~~~e~~~l~~~~~~L~~lGf 287 (380)
++++||++++||+++.+++|++||||||||||+||++++.. .. .+|+||+|+.+++++.+...+.++.+.|++|||
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 47899999999999999999999999999999999999752 23 479999999999999999999999999999999
Q ss_pred EEEEecCCCCeEEEEecCCCCCccCChhhHHHHHHHHhhcCCCCCCChHHHHHHHHHHH
Q psy13670 288 EFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQHTNSTEHCRPSRIRAMFASRA 346 (380)
Q Consensus 288 ~~~~~~~g~~~~~I~~vP~~l~~~~~~~~l~~ll~~l~~~~~~~~~~~~~~~~~la~~A 346 (380)
+++ .+|++++.|+++|.++........+.+++..+.+.. ....+...+++++++|
T Consensus 82 ~~~--~~~~~~~~i~~vP~~l~~~~~~~~l~~ll~~l~~~~--~~~~~~~~~~~la~~A 136 (136)
T smart00853 82 ELE--IFGGQSVILRSVPALLRQQNLQELIPELLDLLAEGG--STSLPQLVEALLASLA 136 (136)
T ss_pred EEE--ccCCCEEEEEeECccccCcCHHHHHHHHHHHHHhCC--CccHHHHHHHHHHhhC
Confidence 998 467899999999998764434455566666555422 2223444555666654
No 6
>KOG1977|consensus
Probab=99.83 E-value=1.3e-20 Score=190.86 Aligned_cols=176 Identities=22% Similarity=0.349 Sum_probs=145.7
Q ss_pred hccccccccceEEEEEeCcEEEEEeCCeEEEEehhHHHHHHHHHHHHhhcCCCccccccceeeecCHHHHHHHHHhHHHH
Q psy13670 203 VIKKSMFEKMKIVGQFNLGFIIVKYDSDLFIIDQHATDEKYNFETLQKTTLIKSQKLVVPQNLHLTKINQCILKDNLPVF 282 (380)
Q Consensus 203 ~~~~~~~~~~~~igQ~~~~yIl~~~~~~L~lIDQHAAhERilyE~l~~~~~~~sQ~LL~P~~l~l~~~e~~~l~~~~~~L 282 (380)
.+++.++..++++-|++++||-+-.-+..-++||||++||+..|.+..+ .+.+-.|++|++|.+.|.+..+|..|.+.+
T Consensus 904 ~~nk~~i~~~qvlqqvDkkyi~~v~~~~~~~~~qha~dek~~~q~~~~k-~l~~s~li~~l~~kvlpm~~~ll~~Y~~~~ 982 (1142)
T KOG1977|consen 904 RFNKGMIHSMQVLQQVDKKYIACVMSTKTEENGQHASDEKQQAQGSGRK-KLLSSTLIPPLEIKVLPMQRRLLWCYHKNL 982 (1142)
T ss_pred hhcccchhhHHHHHhhchhheeeeeeccccccccchhHHHHHhhhhccc-cccccccccceeEEechhhHHHHHHHHHHh
Confidence 4566777889999999999999999999999999999999999987654 355678999999999999999999999999
Q ss_pred HhCCeEEEEecCCCCeEEEEecCCCCCcc-----------CChhhHHHHHH---HHhhcCCCCCCChHHHHHHHHHHHhh
Q psy13670 283 YKNGFEFSFDSSDDGNVLLTSLPMSKNTT-----------LGREDIEELLF---MLQHTNSTEHCRPSRIRAMFASRACR 348 (380)
Q Consensus 283 ~~lGf~~~~~~~g~~~~~I~~vP~~l~~~-----------~~~~~l~~ll~---~l~~~~~~~~~~~~~~~~~la~~ACr 348 (380)
+.||+++.+-..|...+.+..+|..+.+. .......++|+ +|++.. |....|..+.++|++.|||
T Consensus 983 ~d~gw~~~~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~e~i~~~~el~~t~-gsstlP~tv~kVLnSkACr 1061 (1142)
T KOG1977|consen 983 EDLGWEFVFPDTSDSLVLVGKVPLCFVEREANELRRGRSTVTKSIVEEFIREQLELLQTT-GSSTLPLTVQKVLNSKACR 1061 (1142)
T ss_pred hhhceEEecccccccceeccccceecccccchhhccccccccchhHHHHHHHHHHHhccC-CCCccCHHHHHHHhhhhhh
Confidence 99999998654555667777777665432 11223345554 344433 5566788899999999999
Q ss_pred hhhhcCCCCCHHHHHHHHHHHhccCCCCCCCC
Q psy13670 349 KSVMIGRALSVGEMTGLVRNMGRIDQPWVSMG 380 (380)
Q Consensus 349 ~Aik~g~~Ls~~E~~~Ll~~L~~c~~P~~CPH 380 (380)
+|||+||.|+..|+-.||+.|.+|..||+|+|
T Consensus 1062 gAImFgD~L~~qEc~~lI~~Ls~c~lpFqCAH 1093 (1142)
T KOG1977|consen 1062 GAIMFGDGLSLQECCRLIEALSSCQLPFQCAH 1093 (1142)
T ss_pred hceeeCCccCHHHHHHHHHHHHhcCCchhhcc
Confidence 99999999999999999999999999999999
No 7
>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=99.76 E-value=7.1e-19 Score=149.13 Aligned_cols=61 Identities=26% Similarity=0.566 Sum_probs=59.1
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhc
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYA 62 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~ 62 (380)
|+|++||+++++ ++||++||+|+|||+.|||||||+|+||+|++|+.|+++|+++|+++|.
T Consensus 66 ~aI~~~Y~~~l~~~~~P~~~L~i~i~p~~vDVNVHP~K~eV~f~~e~~i~~~i~~~v~~~L~ 127 (127)
T cd03483 66 RAIENVYANYLPKGAHPFVYLSLEIPPENVDVNVHPTKREVHFLNEEEIIERIQKLVEDKLS 127 (127)
T ss_pred HHHHHHHHHhCcCCCccEEEEEEEeChHHeeeccCCCccEEEecCHHHHHHHHHHHHHHHhC
Confidence 789999999998 9999999999999999999999999999999999999999999999874
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=99.71 E-value=1.7e-17 Score=139.98 Aligned_cols=61 Identities=23% Similarity=0.390 Sum_probs=58.9
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhc
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYA 62 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~ 62 (380)
++|++||+++++ ++||+|||+|+|||+.|||||||+|+||+|.+++.|+++|.++|+++|.
T Consensus 62 ~ai~~~y~~~~~~~~~P~~vL~l~ipp~~vDvNVhP~K~eV~f~~e~~i~~~i~~~i~~~L~ 123 (123)
T cd03482 62 HAVRQAYSDVLHGGRHPAYVLYLELDPAQVDVNVHPAKHEVRFRDSRLVHDFIYHAVKKALA 123 (123)
T ss_pred HHHHHHHHHhccCCCCcEEEEEEEcChHheeeccCCCccEEEECCHHHHHHHHHHHHHHHhC
Confidence 689999999998 9999999999999999999999999999999999999999999999874
No 9
>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=99.69 E-value=4.6e-17 Score=138.99 Aligned_cols=61 Identities=30% Similarity=0.557 Sum_probs=58.5
Q ss_pred cHHHHHHHhhC---C-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhc
Q psy13670 2 KLVNEVYHQFN---N-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYA 62 (380)
Q Consensus 2 ~~v~~~y~~~~---~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~ 62 (380)
|+|++||++++ + ++||+++|+|++||+.|||||||+|+||+|.+|+.|+++|+.+|+..|.
T Consensus 68 k~i~~~y~~~~~~~~~~~~P~~~L~i~~~~~~vDVNVhP~K~eV~f~~e~~v~~~i~~~v~~~~~ 132 (132)
T cd03485 68 KLLRQYYSSAYRKSSLRRYPVFFLNILCPPGLVDVNIEPDKDDVLLQNKEAVLQAVENLLESLYG 132 (132)
T ss_pred HHHHHHHHHHhccccccCCCEEEEEEEcCCCceeeccCCccCEEEEcChHHHHHHHHHHHHHHcC
Confidence 78999999999 7 9999999999999999999999999999999999999999999998763
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=99.67 E-value=7.4e-17 Score=135.26 Aligned_cols=61 Identities=33% Similarity=0.553 Sum_probs=55.2
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhc
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYA 62 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~ 62 (380)
|+|+++|++.++ ++||+|||+|++||+.|||||||+|+||+|.+|+.|+++|+++|+++|.
T Consensus 58 ~~I~~~y~~~~~~~~~P~~vL~i~~p~~~vDVNvhP~K~eV~f~~e~~i~~~i~~~i~~~L~ 119 (119)
T PF01119_consen 58 KAINEAYRERLPKGRYPIFVLFIEIPPSEVDVNVHPAKREVRFRDEDEILNLIEEAIREALS 119 (119)
T ss_dssp HHHHHHHHCTTCTTSB-EEEEEEE-SGGGEEETSSTTTT-EEETTHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHhhcccCCCCceEEEEEEcchHHccccccccceEEEecCHHHHHHHHHHHHHHHhC
Confidence 789999998887 9999999999999999999999999999999999999999999999884
No 11
>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=99.65 E-value=2.9e-16 Score=135.68 Aligned_cols=62 Identities=47% Similarity=0.839 Sum_probs=59.5
Q ss_pred CcHHHHHHHhhCCCCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhc
Q psy13670 1 MKLVNEVYHQFNNHQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYA 62 (380)
Q Consensus 1 ~~~v~~~y~~~~~~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~ 62 (380)
.|+|++||++++.++||+|||+|+|||+.|||||||+|+||+|++++.|+++|+++|+++|.
T Consensus 81 ~~aI~~~y~~~~~~~~P~~vL~i~vp~~~vDvNVhP~K~eV~f~~e~~i~~~i~~~v~~~~~ 142 (142)
T cd03484 81 AKLINEVYKSFNSRQYPFFILNISLPTSLYDVNVTPDKRTVLLHDEDRLIDTLKTSLSELFE 142 (142)
T ss_pred HHHHHHHHHHhcCcCCcEEEEEEEeCCcceeeeeCCccCEEEEcChHHHHHHHHHHHHHHhC
Confidence 37899999999999999999999999999999999999999999999999999999999873
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=99.60 E-value=1.5e-15 Score=127.77 Aligned_cols=60 Identities=32% Similarity=0.617 Sum_probs=57.9
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhh
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSY 61 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l 61 (380)
|+|+++|+++++ ++||+|+|+|++||+.|||||||+|++|+|.+++.|+++|+.+++++|
T Consensus 62 ~ai~~~y~~~~~~~~~P~~~L~i~~~~~~~DvNvhP~K~eV~f~~~~~i~~~i~~~v~~~l 122 (122)
T cd00782 62 KAINEAYRSYLPKGRYPVFVLNLELPPELVDVNVHPTKREVRFSDEEEVLELIREALRSAL 122 (122)
T ss_pred HHHHHHHHHhCcCCCCcEEEEEEEeChhheeeeeCCCCCEEEecCHHHHHHHHHHHHHHhC
Confidence 789999999998 999999999999999999999999999999999999999999998875
No 13
>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=99.60 E-value=1.3e-15 Score=131.47 Aligned_cols=61 Identities=25% Similarity=0.403 Sum_probs=57.5
Q ss_pred cHHHHHHHh--------hC-----------C-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhh
Q psy13670 2 KLVNEVYHQ--------FN-----------N-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSY 61 (380)
Q Consensus 2 ~~v~~~y~~--------~~-----------~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l 61 (380)
|+|+++|+. .+ + ++||+|||+|+|||+.|||||||+|+||+|.+++.|+++|+.+|+++|
T Consensus 61 ~aI~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~vL~i~~p~~~vDvNvhP~K~eV~f~~~~~i~~~i~~~i~~~L 140 (141)
T cd03486 61 KLINKLFRKTSAVAKNKSSPQSKSSRRGKRSQESYPVFVLNITCPASEYDLSQEPSKTIIEFKDWKTLLPLILEVVKSFL 140 (141)
T ss_pred HHHHHHHhhccccccccccccccccccccCCccCCCEEEEEEecCchHheeeeCCceeEEEecChHHHHHHHHHHHHHHh
Confidence 789999999 44 6 899999999999999999999999999999999999999999999987
Q ss_pred c
Q psy13670 62 A 62 (380)
Q Consensus 62 ~ 62 (380)
.
T Consensus 141 ~ 141 (141)
T cd03486 141 K 141 (141)
T ss_pred C
Confidence 3
No 14
>KOG1979|consensus
Probab=99.54 E-value=1.4e-13 Score=138.18 Aligned_cols=64 Identities=23% Similarity=0.452 Sum_probs=60.8
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhccCc
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYAIGF 65 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~~~~ 65 (380)
|+|.++|..++| +.+||++|.|+|||+.|||||||+|+||.|.++++|.+-|++.|...|...+
T Consensus 276 ~ale~VYa~yLpk~~~pFvYLsL~i~p~~vDVNVHPTK~eV~FL~qEeIie~I~~~ie~~L~~~d 340 (694)
T KOG1979|consen 276 HALEEVYAAYLPKGHHPFVYLSLNIDPENVDVNVHPTKREVHFLNQEEIIERICQQIEERLSALD 340 (694)
T ss_pred HHHHHHHHHhcCCCCCceEEEEEecCHHHcccccCCCcceeEeecHHHHHHHHHHHHHHHHhccC
Confidence 689999999999 9999999999999999999999999999999999999999999999997633
No 15
>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=98.72 E-value=7.8e-09 Score=83.82 Aligned_cols=41 Identities=34% Similarity=0.616 Sum_probs=38.8
Q ss_pred cHHHHHHHhhC---C-CCCceEEEEEEeCCCcceeeecCCCcEEE
Q psy13670 2 KLVNEVYHQFN---N-HQYPFIILNIEMSRDSVDVNVTPDKRQIF 42 (380)
Q Consensus 2 ~~v~~~y~~~~---~-~~~P~~~l~l~~~p~~iDvNvhP~K~ev~ 42 (380)
++|.++|++++ + +++|+++|++++|++.+||||||+|++|+
T Consensus 63 ~~i~~~~~~~~~~~~~~~~p~~vl~i~~~~~~~d~nv~p~K~~v~ 107 (107)
T cd00329 63 KAVREAYTRALNGDDVRRYPVAVLSLKIPPSLVDVNVHPTKEEVR 107 (107)
T ss_pred HHHHHHHHHHhcccCCCCCCEEEEEEEeChHHeeeCCCCCccccC
Confidence 68999999997 6 99999999999999999999999999984
No 16
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=87.12 E-value=0.51 Score=50.45 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=26.1
Q ss_pred cHHHHHHHhhCC-CCCceEEEEEEeCCCc
Q psy13670 2 KLVNEVYHQFNN-HQYPFIILNIEMSRDS 29 (380)
Q Consensus 2 ~~v~~~y~~~~~-~~~P~~~l~l~~~p~~ 29 (380)
++|.++|+.+++ ++||+|||+|++||-.
T Consensus 280 ~ai~~ay~~~l~~~~~P~~~L~l~i~~~~ 308 (659)
T PRK14867 280 DLLLENYRDSVFWDTVVSCYLNFDFTKYF 308 (659)
T ss_pred HHHHHHHhhcccCCCcceEEEEEEeCccc
Confidence 689999999999 9999999999999965
No 17
>KOG1977|consensus
Probab=81.14 E-value=1.1 Score=47.72 Aligned_cols=50 Identities=18% Similarity=0.139 Sum_probs=47.1
Q ss_pred CCCceEEEEEEeCCCcceeeecCCCcEEEeCChHHHHHHHHHHHHHhhcc
Q psy13670 14 HQYPFIILNIEMSRDSVDVNVTPDKRQIFMDHEKLLLATVKVHITDSYAI 63 (380)
Q Consensus 14 ~~~P~~~l~l~~~p~~iDvNvhP~K~ev~f~~~~~i~~~i~~~~~~~l~~ 63 (380)
.-.|-|||++.+|--.+||-..|+|+-|.|.++..++.+|.+.++..|.+
T Consensus 261 ~~~P~yvi~v~cp~~ly~vs~epakt~ieF~~w~~~l~~I~~~~~~~~kk 310 (1142)
T KOG1977|consen 261 ICKPKYVINVQCPFCLYDVSMEPAKTLIEFQNWDTLLFCIQEGVKMFLKK 310 (1142)
T ss_pred eccCcceeecccchhhhhhhcCcccchhhhhcchhhHhHHHHhhhhhhhc
Confidence 35799999999999999999999999999999999999999999998865
No 18
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=47.91 E-value=28 Score=26.91 Aligned_cols=34 Identities=15% Similarity=0.176 Sum_probs=26.5
Q ss_pred HHHHHhHHHHHhCCeEEEEecCCCCeEEEEecCCCC
Q psy13670 273 CILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSK 308 (380)
Q Consensus 273 ~~l~~~~~~L~~lGf~~~~~~~g~~~~~I~~vP~~l 308 (380)
..+..+.+.|+++|++|+.. .+..+.+-..|..+
T Consensus 34 taVwK~Iq~Lr~~G~~I~s~--~~kGY~L~~~~~ll 67 (79)
T COG1654 34 TAVWKHIQQLREEGVDIESV--RGKGYLLPQLPDLL 67 (79)
T ss_pred HHHHHHHHHHHHhCCceEec--CCCceeccCccccC
Confidence 45778889999999999853 34578888888764
No 19
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=43.77 E-value=1.3e+02 Score=22.23 Aligned_cols=29 Identities=14% Similarity=0.321 Sum_probs=19.1
Q ss_pred HHhHHHHHhCCeEEEEecCCCCeEEEEecCCC
Q psy13670 276 KDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMS 307 (380)
Q Consensus 276 ~~~~~~L~~lGf~~~~~~~g~~~~~I~~vP~~ 307 (380)
.+..+.|+++||.++.. +++.+.| .+|.+
T Consensus 22 ~~i~~~L~~lg~~~~~~--~~~~~~v-~vP~~ 50 (70)
T PF03484_consen 22 EEIIKILKRLGFKVEKI--DGDTLEV-TVPSY 50 (70)
T ss_dssp HHHHHHHHHTT-EEEE---CTTEEEE-EEETT
T ss_pred HHHHHHHHHCCCEEEEC--CCCEEEE-EcCCC
Confidence 35678899999999842 3456644 56876
No 20
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of Listeria monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon [].; PDB: 3H0D_A.
Probab=37.47 E-value=80 Score=27.55 Aligned_cols=47 Identities=6% Similarity=0.136 Sum_probs=29.5
Q ss_pred ccceeeecCHHHHHHHHHhHHHHHhCCeEEEEecCCCCeEEEEecCCC
Q psy13670 260 VVPQNLHLTKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMS 307 (380)
Q Consensus 260 L~P~~l~l~~~e~~~l~~~~~~L~~lGf~~~~~~~g~~~~~I~~vP~~ 307 (380)
-..-.|+..|++..-+..-.=. ..-||-+|...-|++.+.|..|+..
T Consensus 30 eLA~~F~CvPSQINYVl~TRFT-~e~GY~VESrRGGGGyIRI~rv~~~ 76 (152)
T PF05848_consen 30 ELAERFNCVPSQINYVLSTRFT-PERGYIVESRRGGGGYIRIVRVPLD 76 (152)
T ss_dssp HHHHHTTS-THHHHHHHHHHSS-CCCTEEEEEE-STT-EEEEEEEEES
T ss_pred HHHHHhCCchhhhheeeecccc-CCCCeEEEeccCCCceEEEEEEccC
Confidence 3445566667776654443321 2579999976667789999999964
No 21
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=35.91 E-value=36 Score=25.72 Aligned_cols=22 Identities=23% Similarity=0.471 Sum_probs=18.6
Q ss_pred hcCCCCCHHHHHHHHHHHhccC
Q psy13670 352 MIGRALSVGEMTGLVRNMGRID 373 (380)
Q Consensus 352 k~g~~Ls~~E~~~Ll~~L~~c~ 373 (380)
+.-+.+|..||++++.+|++..
T Consensus 49 ~~K~~fS~sEm~aI~~ELG~LR 70 (71)
T PF06569_consen 49 MSKDSFSPSEMQAIAEELGQLR 70 (71)
T ss_pred HhccCCCHHHHHHHHHHHHhhc
Confidence 4457899999999999998764
No 22
>PF11272 DUF3072: Protein of unknown function (DUF3072); InterPro: IPR021425 This bacterial family of proteins has no known function.
Probab=35.36 E-value=1.1e+02 Score=22.11 Aligned_cols=36 Identities=6% Similarity=0.027 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhhhhhhcCCCCCHHHHHHHHHHHhc
Q psy13670 336 SRIRAMFASRACRKSVMIGRALSVGEMTGLVRNMGR 371 (380)
Q Consensus 336 ~~~~~~la~~ACr~Aik~g~~Ls~~E~~~Ll~~L~~ 371 (380)
......|.++|-.+--.+-+.|+..|+..+|+.|.+
T Consensus 18 ~aQ~syL~tL~e~Age~~~~~LtkaeAs~rId~L~~ 53 (57)
T PF11272_consen 18 GAQASYLKTLSEEAGEPFPDDLTKAEASERIDELQA 53 (57)
T ss_pred HHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHHHH
Confidence 344557777766666677788999999999999965
No 23
>PF13224 DUF4032: Domain of unknown function (DUF4032)
Probab=31.80 E-value=3.7e+02 Score=23.83 Aligned_cols=36 Identities=8% Similarity=0.188 Sum_probs=25.8
Q ss_pred cCHHHHHHHHHhHHHHHhCCeEEEEe----cCCCCeEEEE
Q psy13670 267 LTKINQCILKDNLPVFYKNGFEFSFD----SSDDGNVLLT 302 (380)
Q Consensus 267 l~~~e~~~l~~~~~~L~~lGf~~~~~----~~g~~~~~I~ 302 (380)
+++.|.-.+++....|+.|||++..- ..++.++.|+
T Consensus 13 ~~~~e~~ri~~ri~rLN~LGFdV~El~~~~~~~g~~~~i~ 52 (165)
T PF13224_consen 13 FSPDERWRIEERIRRLNELGFDVGELEITTDDDGTRLRIQ 52 (165)
T ss_pred CCchHHHHHHHHHHHHHhcCCceeeeEeEEcCCCCEEEEE
Confidence 45677788999999999999998731 1234555555
No 24
>KOG0030|consensus
Probab=31.13 E-value=97 Score=26.75 Aligned_cols=45 Identities=16% Similarity=0.237 Sum_probs=32.0
Q ss_pred hHHHHHHHHhhcCC-CC-CCChHHHHHHHHHHHhhhhhhcCCCCCHHHHHHHHHH
Q psy13670 316 DIEELLFMLQHTNS-TE-HCRPSRIRAMFASRACRKSVMIGRALSVGEMTGLVRN 368 (380)
Q Consensus 316 ~l~~ll~~l~~~~~-~~-~~~~~~~~~~la~~ACr~Aik~g~~Ls~~E~~~Ll~~ 368 (380)
..+++++.|..... +. ......++++|.++ |++|+.+|...|+..
T Consensus 86 t~edfvegLrvFDkeg~G~i~~aeLRhvLttl--------Gekl~eeEVe~Llag 132 (152)
T KOG0030|consen 86 TYEDFVEGLRVFDKEGNGTIMGAELRHVLTTL--------GEKLTEEEVEELLAG 132 (152)
T ss_pred cHHHHHHHHHhhcccCCcceeHHHHHHHHHHH--------HhhccHHHHHHHHcc
Confidence 45667776664331 22 33356788899888 999999999999864
No 25
>PF14122 YokU: YokU-like protein
Probab=25.98 E-value=16 Score=28.56 Aligned_cols=28 Identities=25% Similarity=0.487 Sum_probs=24.0
Q ss_pred EEEeCCeEEEEehhHHHHHHHHHHHHhh
Q psy13670 224 IVKYDSDLFIIDQHATDEKYNFETLQKT 251 (380)
Q Consensus 224 l~~~~~~L~lIDQHAAhERilyE~l~~~ 251 (380)
+-+.++.|+|||....-+-|.|++|++.
T Consensus 51 i~EIEdql~Lidtk~l~~sity~~LM~~ 78 (87)
T PF14122_consen 51 IKEIEDQLFLIDTKKLPNSITYEELMNQ 78 (87)
T ss_pred HHHHhhheEEEecccCCccccHHHHhhc
Confidence 3445689999999999999999999974
No 26
>PF03997 VPS28: VPS28 protein; InterPro: IPR007143 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ].; PDB: 2J9W_B 2J9U_C 2G3K_A 2F66_E 2F6M_D 2J9V_A 2CAZ_E 2P22_B.
Probab=24.24 E-value=2.4e+02 Score=25.44 Aligned_cols=33 Identities=12% Similarity=0.147 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhhhhhhcCCCCCHHHHHHHHHHHhc
Q psy13670 336 SRIRAMFASRACRKSVMIGRALSVGEMTGLVRNMGR 371 (380)
Q Consensus 336 ~~~~~~la~~ACr~Aik~g~~Ls~~E~~~Ll~~L~~ 371 (380)
.++.+|+..+ ...+++|.|+.+|+++|+-+|..
T Consensus 146 ~kl~~Wl~~L---n~m~asdeL~e~q~rqllfDle~ 178 (188)
T PF03997_consen 146 SKLVEWLIKL---NGMKASDELSEEQARQLLFDLES 178 (188)
T ss_dssp HHHHHHHHHH---HTS-TT-B--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHH---hCCCcccccCHHHHHHHHHHHHH
Confidence 3455565555 56677999999999999999864
No 27
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=22.75 E-value=83 Score=23.30 Aligned_cols=33 Identities=15% Similarity=0.122 Sum_probs=24.0
Q ss_pred HHhhhhhhcCCCCCHHHHHHHHHHHhccCCCCCCCC
Q psy13670 345 RACRKSVMIGRALSVGEMTGLVRNMGRIDQPWVSMG 380 (380)
Q Consensus 345 ~ACr~Aik~g~~Ls~~E~~~Ll~~L~~c~~P~~CPH 380 (380)
.|++-|-+.-..||.+-...|..-| .+|-.|||
T Consensus 32 ~a~~~A~~iEH~is~e~~~~l~~~l---~~~~~~P~ 64 (71)
T PF02742_consen 32 EAEEEACRIEHVISPETIERLCKFL---GFPETCPH 64 (71)
T ss_dssp HHHHHHHHHGCCS-HHHHHHHHHHT---TCTSBETT
T ss_pred HHHHHHHHHHccCCHHHHHHHHHHh---cCCCcCcC
Confidence 4455555566889999999988776 57888998
No 28
>PF03460 NIR_SIR_ferr: Nitrite/Sulfite reductase ferredoxin-like half domain; InterPro: IPR005117 Sulphite reductases (SiRs) and related nitrite reductases (NiRs) catalyse the six-electron reduction reactions of sulphite to sulphide, and nitrite to ammonia, respectively. The Escherichia coli SiR enzyme is a complex composed of two proteins, a flavoprotein alpha-component (SiR-FP) and a hemoprotein beta-component (SiR-HP), and has an alpha(8)beta(4) quaternary structure []. SiR-FP contains both FAD and FMN, while SiR-HP contains a Fe(4)S(4) cluster coupled to a sirohaem through a cysteine bridge. Electrons are transferred from NADPH to FAD, and on to FMN in SiR-FP, from which they are transferred to the metal centre of SiR-HP, where they reduce the siroheme-bound sulphite. SiR-HP has a two-fold symmetry, which generates a distinctive three-domain alpha/beta fold that controls assembly and reactivity []. This entry describes the ferrodoxin-like (alpha/beta sandwich) domain, which consists of a duplication containing two subdomains of this fold.; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 3B0H_A 4GEP_A 2GEP_A 2AOP_A 5AOP_A 6GEP_A 4AOP_A 1AOP_A 3AOP_A 8GEP_A ....
Probab=21.23 E-value=3.2e+02 Score=19.59 Aligned_cols=48 Identities=13% Similarity=0.233 Sum_probs=28.4
Q ss_pred ecCHHHHHHHHHhHHHHHhCCeEEEEecCCCCeEEEEecCCCCCccCChhhHHHHHHHHh
Q psy13670 266 HLTKINQCILKDNLPVFYKNGFEFSFDSSDDGNVLLTSLPMSKNTTLGREDIEELLFMLQ 325 (380)
Q Consensus 266 ~l~~~e~~~l~~~~~~L~~lGf~~~~~~~g~~~~~I~~vP~~l~~~~~~~~l~~ll~~l~ 325 (380)
.+++.+...+.+..+.+..--+.+. +.+.+.|..|| .+++.++...|.
T Consensus 20 ~i~~~~l~~la~ia~~yg~~~irlT----~~Q~l~l~~v~--------~~~~~~i~~~L~ 67 (69)
T PF03460_consen 20 RISAEQLRALAEIAEKYGDGEIRLT----TRQNLQLRGVP--------EENLPAIFEELK 67 (69)
T ss_dssp EEEHHHHHHHHHHHHHHSTSEEEEE----TTSCEEEEEEE--------GGGHHHHHHHHH
T ss_pred EECHHHHHHHHHHHHHhCCCeEEEC----CCCeEEEeCCC--------HHHHHHHHHHHH
Confidence 3456665555555544333223333 34779999999 456777776664
No 29
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.78 E-value=83 Score=23.41 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=19.1
Q ss_pred hhcCCCCCHHHHHHHHHHHhccC
Q psy13670 351 VMIGRALSVGEMTGLVRNMGRID 373 (380)
Q Consensus 351 ik~g~~Ls~~E~~~Ll~~L~~c~ 373 (380)
||.-..+|+.||+++-.+|.+..
T Consensus 48 vkkkenfSpsEmqaiA~eL~rlR 70 (71)
T COG4840 48 VKKKENFSPSEMQAIADELGRLR 70 (71)
T ss_pred HHHhccCCHHHHHHHHHHHHHhh
Confidence 45567899999999999998764
Done!