Query psy8492
Match_columns 489
No_of_seqs 350 out of 1540
Neff 4.8
Searched_HMMs 46136
Date Fri Aug 16 20:15:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8492.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8492hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0323 MutL DNA mismatch repa 100.0 9.1E-48 2E-52 421.2 24.3 266 160-430 167-625 (638)
2 PRK00095 mutL DNA mismatch rep 100.0 2.3E-46 5E-51 409.2 23.9 274 160-439 165-612 (617)
3 PF08676 MutL_C: MutL C termin 99.9 8.3E-27 1.8E-31 209.8 11.9 98 277-376 3-103 (144)
4 smart00853 MutL_C MutL C termi 99.9 1.8E-23 3.9E-28 185.6 13.1 98 277-376 2-104 (136)
5 KOG1978|consensus 99.8 1.3E-20 2.8E-25 204.4 12.5 266 157-434 162-669 (672)
6 KOG1977|consensus 99.7 3.2E-18 6.9E-23 185.6 2.1 179 276-458 912-1128(1142)
7 KOG3806|consensus 99.5 2E-15 4.3E-20 142.0 1.8 69 411-480 98-168 (177)
8 TIGR00585 mutl DNA mismatch re 99.4 3.9E-13 8.4E-18 136.4 10.7 107 158-264 164-278 (312)
9 cd03482 MutL_Trans_MutL MutL_T 99.3 2.4E-12 5.3E-17 114.8 7.1 64 201-264 2-69 (123)
10 cd03483 MutL_Trans_MLH1 MutL_T 99.3 2.6E-12 5.6E-17 115.2 7.0 66 199-264 1-73 (127)
11 smart00413 ETS erythroblast tr 99.3 1E-12 2.2E-17 111.4 2.3 56 410-465 30-87 (87)
12 PF01119 DNA_mis_repair: DNA m 99.2 7.2E-12 1.6E-16 110.6 5.7 61 204-264 1-65 (119)
13 cd03485 MutL_Trans_hPMS_1_like 99.2 2.3E-11 5.1E-16 109.4 7.1 66 199-264 1-75 (132)
14 cd03486 MutL_Trans_MLH3 MutL_T 99.2 5.2E-11 1.1E-15 108.5 6.5 67 199-265 1-69 (141)
15 cd03484 MutL_Trans_hPMS_2_like 99.1 1.3E-10 2.7E-15 106.3 7.3 66 199-264 1-89 (142)
16 cd00782 MutL_Trans MutL_Trans: 99.1 1.4E-10 3.1E-15 101.8 6.4 64 201-264 2-69 (122)
17 PF00178 Ets: Ets-domain; Int 98.8 5.3E-10 1.2E-14 94.7 -0.1 54 410-463 30-85 (85)
18 cd00329 TopoII_MutL_Trans MutL 98.8 1.6E-08 3.4E-13 84.9 6.4 64 201-264 2-70 (107)
19 PRK14867 DNA topoisomerase VI 98.6 1.4E-07 3E-12 105.0 8.3 91 161-263 186-286 (659)
20 KOG3804|consensus 98.5 5.2E-08 1.1E-12 102.6 2.1 64 408-471 321-386 (390)
21 KOG1979|consensus 98.3 7.4E-07 1.6E-11 97.0 5.5 103 160-262 171-281 (694)
22 KOG3805|consensus 97.9 3E-06 6.4E-11 86.4 1.6 55 408-462 300-357 (361)
23 PRK05218 heat shock protein 90 97.3 0.00043 9.3E-09 77.3 7.5 90 161-254 187-299 (613)
24 PRK14868 DNA topoisomerase VI 96.6 0.00055 1.2E-08 77.7 0.4 74 162-238 195-274 (795)
25 smart00433 TOP2c Topoisomerase 85.0 4.5 9.8E-05 45.6 9.5 99 159-262 148-255 (594)
26 KOG1977|consensus 67.4 9.1 0.0002 44.3 5.4 83 160-262 168-254 (1142)
27 PRK05559 DNA topoisomerase IV 58.9 26 0.00057 39.9 7.3 98 161-263 186-291 (631)
28 KOG3804|consensus 42.9 10 0.00022 41.0 0.7 44 418-461 209-256 (390)
29 PRK04184 DNA topoisomerase VI 42.2 24 0.00051 39.7 3.5 27 162-188 189-216 (535)
30 PRK00036 primosomal replicatio 41.1 30 0.00065 31.0 3.3 77 176-255 23-106 (107)
31 TIGR01052 top6b DNA topoisomer 39.0 28 0.00062 38.6 3.4 26 162-187 180-205 (488)
32 PF14424 Toxin-deaminase: The 31.6 84 0.0018 29.0 4.7 52 105-186 79-132 (133)
33 PRK01178 rps24e 30S ribosomal 29.9 71 0.0015 28.2 3.8 51 174-230 14-69 (99)
34 COG1654 BirA Biotin operon rep 28.8 64 0.0014 27.4 3.2 36 338-374 34-69 (79)
35 KOG1979|consensus 25.0 1.3E+02 0.0028 34.6 5.5 93 276-374 472-590 (694)
36 PF02742 Fe_dep_repr_C: Iron d 24.9 44 0.00096 27.0 1.5 32 393-426 37-69 (71)
37 TIGR01059 gyrB DNA gyrase, B s 24.8 59 0.0013 37.2 3.1 100 161-263 177-285 (654)
38 PF07908 D-aminoacyl_C: D-amin 24.1 53 0.0012 25.0 1.7 13 239-251 19-31 (48)
39 TIGR01055 parE_Gneg DNA topois 23.8 63 0.0014 36.9 3.0 25 161-185 179-203 (625)
No 1
>COG0323 MutL DNA mismatch repair enzyme (predicted ATPase) [DNA replication, recombination, and repair]
Probab=100.00 E-value=9.1e-48 Score=421.21 Aligned_cols=266 Identities=22% Similarity=0.253 Sum_probs=224.3
Q ss_pred hHHHHHHHHHHHhhhcCCCceEEEEeCCc---ccchhhhhhccHHHHHHHHccHHHhcccCcc--ccCCeEEEEEEeCCC
Q psy8492 160 NERKYCEDNIKVDNNLERKTKYCLEANEQ---KPEEAEEIAIEQLEVAKDIYAMKMVENFPEH--KREDYEVDGYISREP 234 (489)
Q Consensus 160 ~E~~h~~d~vkRlALa~p~v~F~L~~ngr---~l~~~~~~s~~l~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~P~ 234 (489)
-|++||.++|+|+||+||+|+|+|+|||| .+..+ ..+++..+||++|||..|+++++++ +.++++|+||+|.|+
T Consensus 167 ~E~~~i~~vv~r~ALahp~I~F~l~~~gk~~~~~~~~-~~~~~~~~ri~~i~G~~~~~~~l~i~~~~~~~~l~G~v~~P~ 245 (638)
T COG0323 167 TEFGHITELINRYALAHPDISFSLSHNGKLRIELLKL-PGTGDLEERIAAVYGTEFLKNALPIENEHEDLRLSGYVSLPE 245 (638)
T ss_pred HHHHHHHHHHHHHHhcCCCeEEEEEECCceeeEEEec-CCCCcHHHHHHHHhCHHHHHhhcccccCCCceEEEEEecccc
Confidence 49999999999999999999999999999 44422 3345777899999999999999999 778999999999999
Q ss_pred CCCC--cceEEeeccccccchhHHHHHHHhh----------------------------ccc------------------
Q psy8492 235 ISQP--QYQNIYINKRLVTNTILHDTINKLL----------------------------VKS------------------ 266 (489)
Q Consensus 235 ~sR~--~~Qy~FVNGR~VRdk~L~~AIr~AL----------------------------~~~------------------ 266 (489)
++|+ ++||+|||||+|+|+.|.+||++|| |++
T Consensus 246 ~~r~~~~~q~~fVNgR~V~~~~l~~Ai~~aY~~~L~~~r~P~~vL~l~l~p~~vDVNVHP~K~EVrf~~~~~i~~~I~~~ 325 (638)
T COG0323 246 FTRASRDYQYLFVNGRPVRDKLLNHALREAYADYLPRGRYPVFVLFLELDPELVDVNVHPAKKEVRFSDERLVHDLIYEA 325 (638)
T ss_pred cccCCccceEEEECCCEeccHHHHHHHHHHHHhhccCCCCcEEEEEEeeChhhcccccCCCcceEEecCHHHHHHHHHHH
Confidence 9999 9999999999999999999999992 000
Q ss_pred ----c------c-----cc--------------------------------------c------ccc-------------
Q psy8492 267 ----F------Y-----LN--------------------------------------I------TKE------------- 274 (489)
Q Consensus 267 ----~------~-----~~--------------------------------------~------~~~------------- 274 (489)
+ . .. . ...
T Consensus 326 I~~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 405 (638)
T COG0323 326 IKEALAQQGLIPPASVEAPKSASQPLPAFQEPSPLPESRIQKSKVAKSGSSKSDAPSIAEPASGASPSPASPSIRPLSKN 405 (638)
T ss_pred HHHHHHhcccCCcccccccccccccccccccCcccccccccccccccccCCcccccccccccccCCcccccccccccccc
Confidence 0 0 00 0 000
Q ss_pred --------------------------------------------ccceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHH
Q psy8492 275 --------------------------------------------SNKLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIR 310 (489)
Q Consensus 275 --------------------------------------------~~~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIl 310 (489)
+.++++||++++|||++.++|| |||||||||||++
T Consensus 406 ~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~i~q~~~~yil~e~~~~L-~lvDqhaa~Eri~ 484 (638)
T COG0323 406 ILPESSPGSLKNEDRSYDDLLEEPAESEDKQEEAEQKAISEDVFPLGEAIGQVHGTYILAEHEDGL-VLVDQHAAHERIL 484 (638)
T ss_pred ccccccccccchhcccccccccccchhcccccccccccccccccccceEEEEecceEEEEEeCCCE-EEEEhHHhHHHHH
Confidence 0235699999999999999997 9999999999999
Q ss_pred HHHHHhhcCc--cCC-CCCceEeecCHHHHHHHHHHHHHHhhcCeEEEEeCCCcEEEEeecCcchhhccchhh-----hh
Q psy8492 311 VEKLFSYGAF--LSH-PITPCVLNLTPQEINTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCLFVKVHKEE-----DR 382 (489)
Q Consensus 311 yErL~~~~~i--~sQ-LLiPl~l~Ls~~E~~~Lee~~e~L~~lGfeie~fG~~~ti~VrsVPalL~~~~~~~~-----~~ 382 (489)
||+|+..++. ..| ||+|+.++|++.|+..++++.+.|.++||+++.|| +++++|++||++|........ ..
T Consensus 485 ye~l~~~~~~~~~~Q~LliP~~~~l~~~e~~~~~~~~~~l~~~G~~i~~~g-~~~~~v~~vP~~l~~~~~~~~i~~l~~~ 563 (638)
T COG0323 485 YEKLKNELGNVGELQPLLIPIRLELSPEEADVLEEHKEELEKLGFEIESFG-ENSVAVRSVPAMLGKAEVQELIRELLDD 563 (638)
T ss_pred HHHHHHHhcccccccccccCeeeecCHHHHHHHHHHHHHHHhcCEEEEEcC-CceEEEEecChhhcccchHHHHHHHHHH
Confidence 9999998733 467 99999999999999999999999999999999999 789999999999987543221 11
Q ss_pred hh-----------hh---ccCccchhhhcCcCChhhhcC--CccCCCCCCcccCCCCCCCCCCC
Q psy8492 383 IR-----------EN---QTSREPTSTVYDKVCLGRESN--PQSSACKHVFPRKHHVLRSPMYP 430 (489)
Q Consensus 383 lr-----------~~---~~~r~~AIK~gD~LS~~E~e~--~qL~~ce~PftCPHGrpRp~m~P 430 (489)
+. .. .++|..|||+|+.|+.++|.. ++|..|++|++|||| ||++..
T Consensus 564 ~~~~~~~~~~~~~~~~~a~~aC~~svk~~~~l~~~~m~~Ll~~~~~~~~~~~cpHG--Rp~~~~ 625 (638)
T COG0323 564 LLEGKLKDLKELLEELAATMACRSAVKAGRELSAEEMNALLRDLEACPNPWTCPHG--RPTYIV 625 (638)
T ss_pred hhcccccchhHHHHHHHHHHHHHHhhhcCCcCCHHHHHHHHHHHHhCCCccCCCCC--CCceEe
Confidence 11 10 234555999999999999999 999999999999999 888764
No 2
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=100.00 E-value=2.3e-46 Score=409.22 Aligned_cols=274 Identities=22% Similarity=0.256 Sum_probs=225.9
Q ss_pred hHHHHHHHHHHHhhhcCCCceEEEEeCCcccchhhhhhccHHHHHHHHccHHHhcccCcc--ccCCeEEEEEEeCCCCCC
Q psy8492 160 NERKYCEDNIKVDNNLERKTKYCLEANEQKPEEAEEIAIEQLEVAKDIYAMKMVENFPEH--KREDYEVDGYISREPISQ 237 (489)
Q Consensus 160 ~E~~h~~d~vkRlALa~p~v~F~L~~ngr~l~~~~~~s~~l~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~P~~sR 237 (489)
.|+.+|.+.|+++|+++|+|.|+|.++|+.+... .+++++.+||..+||.++..+++++ +.++++|+||++.|.++|
T Consensus 165 ~e~~~i~~~v~~~Al~~p~i~f~l~~~~~~~~~~-~~~~~~~~~i~~i~g~~~~~~l~~~~~~~~~~~i~g~is~p~~~~ 243 (617)
T PRK00095 165 TELGHIDDVVNRLALAHPDVAFTLTHNGKLVLQT-RGAGQLLQRLAAILGREFAENALPIDAEHGDLRLSGYVGLPTLSR 243 (617)
T ss_pred HHHHHHHHHHHHHhhcCCCcEEEEEECCEEEEEe-CCCCCHHHHHHHHhCHHhHhheEEEeccCCCEEEEEEEeCccccc
Confidence 6899999999999999999999999999844322 2235899999999999999999999 667899999999999988
Q ss_pred C--cceEEeeccccccchhHHHHHHHhh---------c-------------------c----------------------
Q psy8492 238 P--QYQNIYINKRLVTNTILHDTINKLL---------V-------------------K---------------------- 265 (489)
Q Consensus 238 ~--~~Qy~FVNGR~VRdk~L~~AIr~AL---------~-------------------~---------------------- 265 (489)
+ ..||+|||||+|+++.|.+||.+|| | +
T Consensus 244 ~~~~~~~~fvN~R~v~~~~l~~ai~~~y~~~~~~~~~P~~~l~i~~~~~~~DvNvhP~K~ev~f~~e~~i~~~i~~~i~~ 323 (617)
T PRK00095 244 ANRDYQYLFVNGRYVRDKLLNHAIRQAYHDLLPRGRYPAFVLFLELDPHQVDVNVHPAKHEVRFRDERLVHDLIVQAIQE 323 (617)
T ss_pred CCCcceEEEECCcEecCHHHHHHHHHHHHHhccCCCCcEEEEEEEeChHhcccccCCCcCEEEeCCHHHHHHHHHHHHHH
Confidence 8 8999999999999999999999993 0 0
Q ss_pred cc------c-------------c-----c--------------cc--------------------------c--------
Q psy8492 266 SF------Y-------------L-----N--------------IT--------------------------K-------- 273 (489)
Q Consensus 266 ~~------~-------------~-----~--------------~~--------------------------~-------- 273 (489)
.+ . . . .. .
T Consensus 324 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 403 (617)
T PRK00095 324 ALAQSGLIPAAAGANQVLEPAEPEPLPLQQTPLYASGSSPPASSPSSAPPEQSEESQEESSAEKNPLQPNASQSEAAAAA 403 (617)
T ss_pred HHhccCCCcccccccccccccccccccccccccCcccccccccccccccccccccccccccccccccccccccccccccc
Confidence 00 0 0 0 00 0
Q ss_pred -------------c-----------ccceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHHHHHHHhhc---CccCC-CC
Q psy8492 274 -------------E-----------SNKLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYG---AFLSH-PI 325 (489)
Q Consensus 274 -------------~-----------~~~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIlyErL~~~~---~i~sQ-LL 325 (489)
. ..++++||++++||||+.++|| ||||||||||||+||+|++.+ ++.+| ||
T Consensus 404 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vigQv~~~YIl~e~~~~L-~iIDQHAAhERI~yE~l~~~~~~~~~~~Q~LL 482 (617)
T PRK00095 404 SAEAAAAAPAAAPEPAEAAEEADSFPLGYALGQLHGTYILAENEDGL-YLVDQHAAHERLLYEQLKDKLAEVGLASQPLL 482 (617)
T ss_pred ccccccccccccccccccccccccCcCceEeEEEcCEEEEEEeCCcE-EEEEHHHHHHHHHHHHHHHHhccCCCcccccc
Confidence 0 0135799999999999999997 999999999999999999976 35567 99
Q ss_pred CceEeecCHHHHHHHHHHHHHHhhcCeEEEEeCCCcEEEEeecCcchhhccchhh-----hhh-----------hh--hc
Q psy8492 326 TPCVLNLTPQEINTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCLFVKVHKEE-----DRI-----------RE--NQ 387 (489)
Q Consensus 326 iPl~l~Ls~~E~~~Lee~~e~L~~lGfeie~fG~~~ti~VrsVPalL~~~~~~~~-----~~l-----------r~--~~ 387 (489)
+|+.++|++.|.+.++++.+.|.+|||+++.|| +++++|++||++|........ ..+ +. ..
T Consensus 483 ~P~~l~Ls~~e~~~l~~~~~~L~~lGf~~e~fg-~~si~I~~vP~~l~~~~~~~~l~ell~~l~~~~~~~~~~~~~~las 561 (617)
T PRK00095 483 IPLVLELSEDEADRLEEHKELLARLGLELEPFG-PNSFAVREVPALLGQQELEELIRDLLDELAEEGDSDTLKERELLAT 561 (617)
T ss_pred cCeEEeeCHHHHHHHHHHHHHHHhCCcEEEEcC-CCEEEEEecChhhcccCHHHHHHHHHHHHHhcCCcchHHHHHHHHH
Confidence 999999999999999999999999999999999 699999999998875432111 001 10 12
Q ss_pred cCccchhhhcCcCChhhhcC--CccCCCCCCcccCCCCCCCCCCCcCChhhhhh
Q psy8492 388 TSREPTSTVYDKVCLGRESN--PQSSACKHVFPRKHHVLRSPMYPNVCLSKFTR 439 (489)
Q Consensus 388 ~~r~~AIK~gD~LS~~E~e~--~qL~~ce~PftCPHGrpRp~m~P~mnyeKLsR 439 (489)
++|+.|||+||.|+.+||+. ++|+.|++||+|||| ||++. .+....|.+
T Consensus 562 ~ACr~AIk~g~~Ls~~E~~~Ll~~L~~~~~P~~CPHG--RPt~i-~l~~~elek 612 (617)
T PRK00095 562 MACHGAIRAGRRLTLEEMNALLRQLEATENPGTCPHG--RPTYI-ELSLSDLEK 612 (617)
T ss_pred HHHHHhhhccCCCCHHHHHHHHHHHHhcccccCCCCC--CeeEE-ECCHHHHHH
Confidence 34555999999999999999 999999999999999 88876 455555554
No 3
>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=99.94 E-value=8.3e-27 Score=209.81 Aligned_cols=98 Identities=34% Similarity=0.384 Sum_probs=87.4
Q ss_pred ceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHHHHHHHhhc--CccCC-CCCceEeecCHHHHHHHHHHHHHHhhcCeE
Q psy8492 277 KLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYG--AFLSH-PITPCVLNLTPQEINTLSNRQTCLQYYGLE 353 (489)
Q Consensus 277 ~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIlyErL~~~~--~i~sQ-LLiPl~l~Ls~~E~~~Lee~~e~L~~lGfe 353 (489)
+++|||++++|||++.+++| |+||||||||||+||+|++.+ +..+| ||+|+.+++++.+.+.++++.+.|++|||+
T Consensus 3 ~~vlgq~~~~yil~~~~~~L-~liDqHAAhERi~~E~l~~~~~~~~~~q~Ll~P~~~~ls~~e~~~l~~~~~~L~~~Gf~ 81 (144)
T PF08676_consen 3 LKVLGQLDNKYILAESEDGL-YLIDQHAAHERILYEKLLKQLEEGEQSQPLLFPIELELSPQEAELLEENKEELEKLGFE 81 (144)
T ss_dssp -EEEEEETTTEEEEEETTEE-EEEEHHHHHHHHHHHHHHHHCCHCS-EEEEEEEEEEE--HHHHHHHHHHHHHHHHTT-E
T ss_pred eeeHhHhCCEEEEEEeCCCE-EEEEHHHHHHHHHHHHHHHhhccCCCceecCCCccCCCCHHHHHHHHHHHHHHHhCCeE
Confidence 58999999999999999997 999999999999999999987 23666 999999999999999999999999999999
Q ss_pred EEEeCCCcEEEEeecCcchhhcc
Q psy8492 354 FEFKNTGKCVKVTHVPKCLFVKV 376 (489)
Q Consensus 354 ie~fG~~~ti~VrsVPalL~~~~ 376 (489)
++.+| ++++.|++||.++....
T Consensus 82 ~~~~~-~~~~~v~~vP~~l~~~~ 103 (144)
T PF08676_consen 82 IEEFG-ENSIIVRSVPAILREQD 103 (144)
T ss_dssp EEEES-TTEEEEEEEECCCTTSS
T ss_pred EEEec-CCEEEEEEeCccccccc
Confidence 99999 79999999999998754
No 4
>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=99.90 E-value=1.8e-23 Score=185.65 Aligned_cols=98 Identities=34% Similarity=0.436 Sum_probs=89.5
Q ss_pred ceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHHHHHHHhhc---Cc-cCC-CCCceEeecCHHHHHHHHHHHHHHhhcC
Q psy8492 277 KLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYG---AF-LSH-PITPCVLNLTPQEINTLSNRQTCLQYYG 351 (489)
Q Consensus 277 ~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIlyErL~~~~---~i-~sQ-LLiPl~l~Ls~~E~~~Lee~~e~L~~lG 351 (489)
++++||++++||+++.++|| +|||||||||||+||+|++.+ .. .+| ||+|+.+++++.+.+.+.++.+.|++||
T Consensus 2 ~~~l~qv~~~yil~~~~~~l-~liDqhaA~ERi~~e~l~~~~~~~~~~~~Q~Ll~P~~i~l~~~e~~~l~~~~~~l~~~G 80 (136)
T smart00853 2 GRVLGQVHGTYILAESEDGL-VLIDQHAAHERILYEQLKAKLQAGLLEKSQPLLIPVILELSPEEAALLEEHQELLARLG 80 (136)
T ss_pred ccEEEEEcCEEEEEEcCCCE-EEEEhHHHHHHHHHHHHHHHHhcCCCccccccCCCEEEEcCHHHHHHHHHHHHHHHHcC
Confidence 46899999999999999997 999999999999999999875 33 356 9999999999999999999999999999
Q ss_pred eEEEEeCCCcEEEEeecCcchhhcc
Q psy8492 352 LEFEFKNTGKCVKVTHVPKCLFVKV 376 (489)
Q Consensus 352 feie~fG~~~ti~VrsVPalL~~~~ 376 (489)
|+++.+| ++++.|+++|.++.+..
T Consensus 81 f~~~~~~-~~~~~i~~vP~~l~~~~ 104 (136)
T smart00853 81 FELEIFG-GQSVILRSVPALLRQQN 104 (136)
T ss_pred eEEEccC-CCEEEEEeECccccCcC
Confidence 9999999 68999999999886644
No 5
>KOG1978|consensus
Probab=99.83 E-value=1.3e-20 Score=204.44 Aligned_cols=266 Identities=19% Similarity=0.193 Sum_probs=205.8
Q ss_pred hhhhHHHHHHHHHHHhhhcCCCceEEEEeCC----cccchhhhhhccHHHHHHHHccHHHhcccCccccCCeEEEEEEeC
Q psy8492 157 TLNNERKYCEDNIKVDNNLERKTKYCLEANE----QKPEEAEEIAIEQLEVAKDIYAMKMVENFPEHKREDYEVDGYISR 232 (489)
Q Consensus 157 ~~~~E~~h~~d~vkRlALa~p~v~F~L~~ng----r~l~~~~~~s~~l~eRIa~IlG~~fa~~li~Ie~~~l~I~G~Is~ 232 (489)
.+--||+.|..++.-+|+.+++|.|..++.- +.+.-.+...++.++-|.++||...+..+.++. + ++.
T Consensus 162 ~~Kref~k~i~li~~y~li~~~ir~~~~n~t~~~~k~iil~t~~~~~~k~~i~svfg~~~~~~l~p~~-~-------is~ 233 (672)
T KOG1978|consen 162 NIKRKFVKLISLIQAYALISTAIKFLVSNSTLAGKKNIILKTGGYGSDKINISSNFGSVEEENLEPLI-F-------ISS 233 (672)
T ss_pred chhhhhhhHHhhHHHHHhhcccceeeeeeccccCCceeEEecCCcchHHHHHHhhhhhhhhhcccccc-c-------ccc
Confidence 4567999999999999999999999988642 222223344568999999999999999999873 1 555
Q ss_pred CCC--CCC--cceEEeeccccccchhHHHHHHHhh-----------------------c---------------------
Q psy8492 233 EPI--SQP--QYQNIYINKRLVTNTILHDTINKLL-----------------------V--------------------- 264 (489)
Q Consensus 233 P~~--sR~--~~Qy~FVNGR~VRdk~L~~AIr~AL-----------------------~--------------------- 264 (489)
+.+ .|+ +.||+|||+|||-.+.+..+|++-+ |
T Consensus 234 ~~~g~~r~s~drqf~fIn~Rpv~~~~i~~~inevy~~~~~~q~l~i~V~~~~iDvNvtPDK~~vll~~e~~vl~~l~~~l 313 (672)
T KOG1978|consen 234 CHHGCGRSSEDRQFIFINRRPVFPSDICRVINEVYKLYNERQYLFLDVPEGCIDVNVTPDKRQVLLSNERSVLFSLRNSL 313 (672)
T ss_pred ccccccccCccceeeeecCccCCHHHHHHHHHHHhhhhccccceeeeccccceeeeeCCCcceeeccchHHHHHHHHHHH
Confidence 442 233 8999999999999999999988761 0
Q ss_pred --------------------c----------------------------------c----------------------cc
Q psy8492 265 --------------------K----------------------------------S----------------------FY 268 (489)
Q Consensus 265 --------------------~----------------------------------~----------------------~~ 268 (489)
+ + ..
T Consensus 314 ~~~~~s~~~~~~~~~s~~p~k~~~s~~~~s~~~~~~~~~~~~~~~~~~~~i~~~~P~~~~~~~~~~~~~~~~pd~~~~~~ 393 (672)
T KOG1978|consen 314 VDFYNSNCDLNFSDVSMLPVQNPSSLTERSDPIENKLVSRTDSMIGIKTNISEDHPNEESNFLTPEFLKITTPDKEKECS 393 (672)
T ss_pred HHHHhhccccccccccccCccCCCccccccccchhhhcccchhhhccccccccCCCcccccccCcccccccCCccccccc
Confidence 0 0 00
Q ss_pred ----cc--------------------ccc-----------------------------------------c---------
Q psy8492 269 ----LN--------------------ITK-----------------------------------------E--------- 274 (489)
Q Consensus 269 ----~~--------------------~~~-----------------------------------------~--------- 274 (489)
.. +.. .
T Consensus 394 s~~d~~~~~~~~~~~~~~~~~~~~~~~ed~~~~~t~s~~~~se~~~~se~~~~~~~~~~~~~~~~~~~~~~~~~~~N~~~ 473 (672)
T KOG1978|consen 394 SKKDLTAIPLEKNPSLKKPDLEDTENLEDETNVETPSSSPLSEDKSLSEQEKLKIEVYSKIKFARKASETKINPGHNDSV 473 (672)
T ss_pred CCCCccccccccCccccccchhhhhhccccccccCCCcccchhhccccccchhhhccccchhhhcccchhhcCcccchhh
Confidence 00 000 0
Q ss_pred -------------ccceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHHHHHHHhhcCccCC-CCCceEeecCHHHHHHH
Q psy8492 275 -------------SNKLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAFLSH-PITPCVLNLTPQEINTL 340 (489)
Q Consensus 275 -------------~~~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIlyErL~~~~~i~sQ-LLiPl~l~Ls~~E~~~L 340 (489)
..+.+|||++..||++..+..| +||||||++|..+||+|++..-+.+| |+.|..+++++.+-..+
T Consensus 474 e~~~s~~v~k~df~~meiigqfNlgFIi~~l~~dl-fIvdqha~dEk~Nfe~l~~~~~L~~Q~l~~P~~l~ls~~nE~vl 552 (672)
T KOG1978|consen 474 ELEESREVAKADFSRMEIIGQFNLGFIIVKLEKDL-FIVDQHASDEKRNFERLQSTTVLKAQPLICPQALDLSAINEMVL 552 (672)
T ss_pred hchhhhcccccchhhcceeeeccccceeeeccCce-EEeccchhhhhhhHHHHHHhcccccccccCccccccCcccceee
Confidence 0258999999999999988886 99999999999999999998778888 99999999999999999
Q ss_pred HHHHHHHhhcCeEEEEeCC---CcEEEEeecCcchhhcc-chhhhh----h-------------hh---hccCccchhhh
Q psy8492 341 SNRQTCLQYYGLEFEFKNT---GKCVKVTHVPKCLFVKV-HKEEDR----I-------------RE---NQTSREPTSTV 396 (489)
Q Consensus 341 ee~~e~L~~lGfeie~fG~---~~ti~VrsVPalL~~~~-~~~~~~----l-------------r~---~~~~r~~AIK~ 396 (489)
.++.+.|++.||.++...+ +..+.+.++|...-... ..++.. + +. ..+||. ++|-
T Consensus 553 ~d~l~~f~knGF~~~~~~n~~~~~~~~l~~~p~skn~~fg~~dl~Eli~~l~~~~~~~~rp~~vr~m~as~AcR~-Svmi 631 (672)
T KOG1978|consen 553 LDNLPLFEKNGFKVKIDENAPDGKRVRLLSVPVSKNQTFGVSDLKELISVLKNFPEETYRPSKVRSMIASKACRS-SVMI 631 (672)
T ss_pred hhhhHHHHhcCceEeecCCCcccceeeecccccccccccCHHHHHHHHHHHhhCCCcEeehHHHHHHHHHHHhhh-hhhc
Confidence 9999999999999998642 35678999997643221 111111 1 10 124665 9999
Q ss_pred cCcCChhhhcC--CccCCCCCCcccCCCCCCCCCCCcCCh
Q psy8492 397 YDKVCLGRESN--PQSSACKHVFPRKHHVLRSPMYPNVCL 434 (489)
Q Consensus 397 gD~LS~~E~e~--~qL~~ce~PftCPHGrpRp~m~P~mny 434 (489)
|+.|+..+|.. ..|.+.+.||.|||| ||+|...+++
T Consensus 632 g~~L~~~dm~~iv~~L~~l~~pwnCpHG--RPTmrhL~~l 669 (672)
T KOG1978|consen 632 GDPLSKDDMTRIVRSLAELEHPWNCPHG--RPTMRHLCEL 669 (672)
T ss_pred ccccCHHHHHHHHHHHHHhcCCCCCCCC--chhHHHHhhc
Confidence 99999999999 889988999999999 9999766554
No 6
>KOG1977|consensus
Probab=99.70 E-value=3.2e-18 Score=185.58 Aligned_cols=179 Identities=26% Similarity=0.319 Sum_probs=140.6
Q ss_pred cceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHHHHHHHhhcCccCCCCCceEeecCHHHHHHHHHHHHHHhhcCeEEE
Q psy8492 276 NKLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYGAFLSHPITPCVLNLTPQEINTLSNRQTCLQYYGLEFE 355 (489)
Q Consensus 276 ~~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIlyErL~~~~~i~sQLLiPl~l~Ls~~E~~~Lee~~e~L~~lGfeie 355 (489)
.++++.|++++||-+-.-... -++||||++||+..|.+..+.-..+.|+.|++|.+.|.+..+|+.|.+.++.|||++.
T Consensus 912 ~~qvlqqvDkkyi~~v~~~~~-~~~~qha~dek~~~q~~~~k~l~~s~li~~l~~kvlpm~~~ll~~Y~~~~~d~gw~~~ 990 (1142)
T KOG1977|consen 912 SMQVLQQVDKKYIACVMSTKT-EENGQHASDEKQQAQGSGRKKLLSSTLIPPLEIKVLPMQRRLLWCYHKNLEDLGWEFV 990 (1142)
T ss_pred hHHHHHhhchhheeeeeeccc-cccccchhHHHHHhhhhccccccccccccceeEEechhhHHHHHHHHHHhhhhceEEe
Confidence 468999999999999888776 8899999999999998877642333488899999999999999999999999999988
Q ss_pred EeCC-CcEEEEeecCcchhhccchhh-------------hhhhh----------------------hccCccchhhhcCc
Q psy8492 356 FKNT-GKCVKVTHVPKCLFVKVHKEE-------------DRIRE----------------------NQTSREPTSTVYDK 399 (489)
Q Consensus 356 ~fG~-~~ti~VrsVPalL~~~~~~~~-------------~~lr~----------------------~~~~r~~AIK~gD~ 399 (489)
+..+ ...+.+.-+|.++.++..+.. ++++. ..+|+ +||||||.
T Consensus 991 ~~~~~~s~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~e~i~~~~el~~t~gsstlP~tv~kVLnSkACr-gAImFgD~ 1069 (1142)
T KOG1977|consen 991 FPDTSDSLVLVGKVPLCFVEREANELRRGRSTVTKSIVEEFIREQLELLQTTGSSTLPLTVQKVLNSKACR-GAIMFGDG 1069 (1142)
T ss_pred cccccccceeccccceecccccchhhccccccccchhHHHHHHHHHHHhccCCCCccCHHHHHHHhhhhhh-hceeeCCc
Confidence 7543 355778888887766543221 12211 02355 59999999
Q ss_pred CChhhhcC--CccCCCCCCcccCCCCCCCCCCCcCChhhhhhhhcccCCcccccccceEEE
Q psy8492 400 VCLGRESN--PQSSACKHVFPRKHHVLRSPMYPNVCLSKFTRRYYYDKNIIHKTAGKRYVY 458 (489)
Q Consensus 400 LS~~E~e~--~qL~~ce~PftCPHGrpRp~m~P~mnyeKLsRRyyy~k~ii~Kv~g~r~vy 458 (489)
|++.||.. ..|+.|..||+|+|| ||.|.|..++..|.+.---.-+.+.|+..+|..+
T Consensus 1070 L~~qEc~~lI~~Ls~c~lpFqCAHG--RPsmvPladlk~l~kqi~~~~~k~~~~~~~~r~~ 1128 (1142)
T KOG1977|consen 1070 LSLQECCRLIEALSSCQLPFQCAHG--RPSMVPLADLKHLEKQIKPNLTKLRKMAQAWRLF 1128 (1142)
T ss_pred cCHHHHHHHHHHHHhcCCchhhccC--CCCccchhhHHHHHHHhhhhhHHHHHHHHHHHHh
Confidence 99999999 999999999999999 9999999999999863333334455555555544
No 7
>KOG3806|consensus
Probab=99.53 E-value=2e-15 Score=142.00 Aligned_cols=69 Identities=35% Similarity=0.507 Sum_probs=60.7
Q ss_pred CCCCCCcccCCCCCCCCCCCcCChhhhhh--hhcccCCcccccccceEEEeeccChhhhhCCChhhhhhccc
Q psy8492 411 SACKHVFPRKHHVLRSPMYPNVCLSKFTR--RYYYDKNIIHKTAGKRYVYRFVCDLQTLLGYSPEELHAMVD 480 (489)
Q Consensus 411 ~~ce~PftCPHGrpRp~m~P~mnyeKLsR--Ryyy~k~ii~Kv~g~r~vy~F~~d~~~~~~~~~~~~~~~~~ 480 (489)
|...+|.-.+.-|+..+++|+|||||||| ||||++|||+||+|+||||+|+||+..+ .+.|.....+.+
T Consensus 98 Fkl~dp~eVArlWG~rK~kp~MNYdKLSRaLRyyY~kni~~Kv~Gkr~~YkF~~~~~~~-~~~~~~~~~~~~ 168 (177)
T KOG3806|consen 98 FKLVDPDEVARLWGARKNKPNMNYDKLSRALRYYYDKNILKKVPGKRFVYKFVFDPLNL-ALYPHTLKNIKG 168 (177)
T ss_pred EEecCHHHHHHHHhhhhCCCCCCHHHHHHHHHHHHhcCceeecCCceEEEEEecCHHHh-ccCccccccccc
Confidence 56677777888888999999999999999 9999999999999999999999999999 666766666544
No 8
>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=99.44 E-value=3.9e-13 Score=136.43 Aligned_cols=107 Identities=15% Similarity=0.221 Sum_probs=93.0
Q ss_pred hhhHHHHHHHHHHHhhhcCCCceEEEEeCCcccchh-hhhhccHHH-HHHHHccHHHhcccCcc---ccCCeEEEEEEeC
Q psy8492 158 LNNERKYCEDNIKVDNNLERKTKYCLEANEQKPEEA-EEIAIEQLE-VAKDIYAMKMVENFPEH---KREDYEVDGYISR 232 (489)
Q Consensus 158 ~~~E~~h~~d~vkRlALa~p~v~F~L~~ngr~l~~~-~~~s~~l~e-RIa~IlG~~fa~~li~I---e~~~l~I~G~Is~ 232 (489)
+..|++.+.+.+.++|+.+|+|+|.|.++|+..... +....++.+ ||..+||.+++.+|+++ +.++++|.||++.
T Consensus 164 ~~~~~~~i~~~l~~~al~~p~i~f~l~~~~~~~~~~~~~~~~~~~~~~i~~v~G~~~~~~l~~~~~~~~~~~~v~G~is~ 243 (312)
T TIGR00585 164 PKKEFRKILDLLNRYALIHPDVSFSLTHDGKKVLQLSTKPNQSLKERRIRSVFGTAVLSKLFPLLEWEDGDLQLEGFISE 243 (312)
T ss_pred cHHHHHHHHHHHHHHhhcCCCeEEEEEECCEEEEEEcCCCCCCHHHHHHHHHhChHhHhhceeeecccCCCEEEEEEEcC
Confidence 457899999999999999999999999999833322 222358899 79999999999999998 5678999999999
Q ss_pred CCCCCC--cc-eEEeeccccccchhHHHHHHHhhc
Q psy8492 233 EPISQP--QY-QNIYINKRLVTNTILHDTINKLLV 264 (489)
Q Consensus 233 P~~sR~--~~-Qy~FVNGR~VRdk~L~~AIr~AL~ 264 (489)
|+..++ .. ||+|||||+|.++.|.+||.+++.
T Consensus 244 p~~~~~~~~~~q~ifvNgR~v~~~~l~k~I~~~y~ 278 (312)
T TIGR00585 244 PNVTRSRRSGWQFLFINGRPVELKLLLKAIREVYH 278 (312)
T ss_pred cccccCCCCcceEEEECCcEecchHHHHHHHHHHH
Confidence 998887 46 999999999999999999999864
No 9
>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=99.33 E-value=2.4e-12 Score=114.80 Aligned_cols=64 Identities=17% Similarity=0.350 Sum_probs=59.9
Q ss_pred HHHHHHHccHHHhcccCcc--ccCCeEEEEEEeCCCCCCC--cceEEeeccccccchhHHHHHHHhhc
Q psy8492 201 LEVAKDIYAMKMVENFPEH--KREDYEVDGYISREPISQP--QYQNIYINKRLVTNTILHDTINKLLV 264 (489)
Q Consensus 201 ~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~P~~sR~--~~Qy~FVNGR~VRdk~L~~AIr~AL~ 264 (489)
.+||+++||.+++++|+++ +.++++|+||++.|+.+|+ +.||+|||||+|+++.|.+||.+|+.
T Consensus 2 ~~ri~~v~G~~~~~~li~i~~~~~~~~i~G~is~p~~~r~~~~~q~ifVN~R~V~~~~l~~ai~~~y~ 69 (123)
T cd03482 2 LQRLADILGEDFAEQALAIDEEAGGLRLSGWIALPTFARSQADIQYFYVNGRMVRDKLISHAVRQAYS 69 (123)
T ss_pred HhHHHHHhCHHHHhccceEeccCCCEEEEEEEeCchhccCCCCcEEEEEcCcEECChHHHHHHHHHHH
Confidence 4799999999999999999 6677999999999999888 89999999999999999999999964
No 10
>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=99.32 E-value=2.6e-12 Score=115.19 Aligned_cols=66 Identities=21% Similarity=0.353 Sum_probs=59.9
Q ss_pred cHHHHHHHHccHHHhcccCcc--cc----CCeEEEEEEeCCCCCCC-cceEEeeccccccchhHHHHHHHhhc
Q psy8492 199 EQLEVAKDIYAMKMVENFPEH--KR----EDYEVDGYISREPISQP-QYQNIYINKRLVTNTILHDTINKLLV 264 (489)
Q Consensus 199 ~l~eRIa~IlG~~fa~~li~I--e~----~~l~I~G~Is~P~~sR~-~~Qy~FVNGR~VRdk~L~~AIr~AL~ 264 (489)
++.+||.+|||.+++++|+++ +. ++++|+||++.|+++.. +.||+|||||||+++.|.+||.+||.
T Consensus 1 ~~~~~i~~v~G~~~~~~li~i~~~~~~~~~~~~i~G~is~p~~~~~~~~q~~fVNgR~V~~~~l~~aI~~~Y~ 73 (127)
T cd03483 1 STKDNIRSVYGAAVANELIEVEISDDDDDLGFKVKGLISNANYSKKKIIFILFINNRLVECSALRRAIENVYA 73 (127)
T ss_pred CHHHHHHHHhCHHHHhcceEEecccCCcCCcEEEEEEEcCchhcCCCceEEEEEcCCEecCHHHHHHHHHHHH
Confidence 367999999999999999999 33 57999999999999844 99999999999999999999999964
No 11
>smart00413 ETS erythroblast transformation specific domain. variation of the helix-turn-helix motif
Probab=99.29 E-value=1e-12 Score=111.35 Aligned_cols=56 Identities=34% Similarity=0.461 Sum_probs=49.3
Q ss_pred cCCCCCCcccCCCCCCCCCCCcCChhhhhh--hhcccCCcccccccceEEEeeccChh
Q psy8492 410 SSACKHVFPRKHHVLRSPMYPNVCLSKFTR--RYYYDKNIIHKTAGKRYVYRFVCDLQ 465 (489)
Q Consensus 410 L~~ce~PftCPHGrpRp~m~P~mnyeKLsR--Ryyy~k~ii~Kv~g~r~vy~F~~d~~ 465 (489)
-|...+|...+.-|+..+++|+|||+|||| ||||++|||.||.|+|++|+|+++|.
T Consensus 30 ~Fkl~~~~~vA~lWG~~Knk~~M~YeklSRaLRyyy~~~il~Kv~g~rl~Y~F~~~~~ 87 (87)
T smart00413 30 EFKLVDPEEVARLWGQRKNKPNMNYEKLSRALRYYYKKNILRKVPGKRLVYKFVKNPL 87 (87)
T ss_pred EEEecCHHHHHHHHhhhcCCCCCCHHHHHHHHHHHHhcCcEEecCCceEEEecCCCCC
Confidence 355666666777677999999999999999 99999999999999999999999873
No 12
>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=99.25 E-value=7.2e-12 Score=110.61 Aligned_cols=61 Identities=31% Similarity=0.538 Sum_probs=54.6
Q ss_pred HHHHccHHHhcccCcc--ccCCeEEEEEEeCCCCCCC--cceEEeeccccccchhHHHHHHHhhc
Q psy8492 204 AKDIYAMKMVENFPEH--KREDYEVDGYISREPISQP--QYQNIYINKRLVTNTILHDTINKLLV 264 (489)
Q Consensus 204 Ia~IlG~~fa~~li~I--e~~~l~I~G~Is~P~~sR~--~~Qy~FVNGR~VRdk~L~~AIr~AL~ 264 (489)
|++|||.+++++|+++ +.++++|+||+++|+.+|+ +.||+|||||+|+++.|.+||.+|+.
T Consensus 1 I~~i~G~~~~~~l~~i~~~~~~~~i~G~is~p~~~~~~~~~q~ifVN~R~V~~~~l~~~I~~~y~ 65 (119)
T PF01119_consen 1 IAQIFGKEFASNLIEIDSEDEDFSIEGYISKPDVSRSSRDRQFIFVNGRPVENKALSKAINEAYR 65 (119)
T ss_dssp HHHHHHHHHHCCEEEEEEEECCEEEEEEEE-SSCSBSSCTCEEEEETTEEE--HHHHHHHHHHHH
T ss_pred CeEeECHHHHhccEEEeccCCCEEEEEEEECchhccCCCCcEEEEeCCCeEeChHHHHHHHHHHh
Confidence 6789999999999999 7888999999999999988 89999999999999999999999864
No 13
>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=99.21 E-value=2.3e-11 Score=109.43 Aligned_cols=66 Identities=12% Similarity=0.233 Sum_probs=59.6
Q ss_pred cHHHHHHHHccHHHhcccCcc--cc--CCeEEEEEEeCC--CCCCC--cceEEeeccccccc-hhHHHHHHHhhc
Q psy8492 199 EQLEVAKDIYAMKMVENFPEH--KR--EDYEVDGYISRE--PISQP--QYQNIYINKRLVTN-TILHDTINKLLV 264 (489)
Q Consensus 199 ~l~eRIa~IlG~~fa~~li~I--e~--~~l~I~G~Is~P--~~sR~--~~Qy~FVNGR~VRd-k~L~~AIr~AL~ 264 (489)
++.++|++|||.+++++|+++ +. ++++|+||++.| +..|+ +.||+|||||+|++ +.|.+||.+|+.
T Consensus 1 ~l~~~i~~v~G~~~~~~li~i~~~~~~~~~~i~G~is~p~~~~~~~~~~~q~~fVN~R~v~~~~~l~k~i~~~y~ 75 (132)
T cd03485 1 DHKEALARVLGTAVAANMVPVQSTDEDPQISLEGFLPKPGSDVSKTKSDGKFISVNSRPVSLGKDIGKLLRQYYS 75 (132)
T ss_pred CHHHHHHHHhCHHHHhccEEEeccCCCCcEEEEEEECCCCcCCCcccCCcEEEEECCeecccchHHHHHHHHHHH
Confidence 467999999999999999999 44 679999999999 55775 99999999999999 999999999964
No 14
>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=99.15 E-value=5.2e-11 Score=108.51 Aligned_cols=67 Identities=42% Similarity=0.608 Sum_probs=59.8
Q ss_pred cHHHHHHHHccHHHhcccCcc--ccCCeEEEEEEeCCCCCCCcceEEeeccccccchhHHHHHHHhhcc
Q psy8492 199 EQLEVAKDIYAMKMVENFPEH--KREDYEVDGYISREPISQPQYQNIYINKRLVTNTILHDTINKLLVK 265 (489)
Q Consensus 199 ~l~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~P~~sR~~~Qy~FVNGR~VRdk~L~~AIr~AL~~ 265 (489)
++.+||.+|||.+++..|+++ +.++++|+|||+.|+.+..+.||+|||||+|+++.|.+||.+|+..
T Consensus 1 ~~~~~i~~i~G~~~~~~l~~v~~~~~~~~v~G~is~p~~~sk~~q~ifVN~R~v~~~~l~~aI~~~y~~ 69 (141)
T cd03486 1 SILSVFKQIYGLVLAQKLKEVSAKFQEYEVSGYISSEGHYSKSFQFIYVNGRLYLKTRFHKLINKLFRK 69 (141)
T ss_pred CHHHHHHHHhChhhhccEEEeecccCcEEEEEEEcCCCCCCCceEEEEECCEEechHHHHHHHHHHHhh
Confidence 357899999999999999999 7778999999999993323999999999999999999999999754
No 15
>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=99.12 E-value=1.3e-10 Score=106.31 Aligned_cols=66 Identities=20% Similarity=0.313 Sum_probs=59.6
Q ss_pred cHHHHHHHHccHHHhcccCcc--cc-----------------CCeEEEEEEeCC--CCCCC--cceEEeeccccccchhH
Q psy8492 199 EQLEVAKDIYAMKMVENFPEH--KR-----------------EDYEVDGYISRE--PISQP--QYQNIYINKRLVTNTIL 255 (489)
Q Consensus 199 ~l~eRIa~IlG~~fa~~li~I--e~-----------------~~l~I~G~Is~P--~~sR~--~~Qy~FVNGR~VRdk~L 255 (489)
++++||..|||..++++|+++ .. ++++|+||++.| +..|+ +.||+|||||+|+++.|
T Consensus 1 ~~~~~i~~v~G~~~~~~li~v~~~~~~~~~~~~~~~~~~~~~~~~~i~G~is~p~~~~~r~~~~~q~~fVN~R~V~~~~l 80 (142)
T cd03484 1 DIKDNIINVFGGKVIKGLIPINLELDVNPTKEELDSDEDLADSEVKITGYISKPSHGCGRSSSDRQFFYINGRPVDLKKV 80 (142)
T ss_pred CHHHHHHHHhCHHHHhcccceeccccccccccccccccccCCCcEEEEEEECCCcccCCCCCCCcEEEEECCeecCCHHH
Confidence 367999999999999999999 44 669999999999 77777 89999999999999999
Q ss_pred HHHHHHhhc
Q psy8492 256 HDTINKLLV 264 (489)
Q Consensus 256 ~~AIr~AL~ 264 (489)
.+||.+|+.
T Consensus 81 ~~aI~~~y~ 89 (142)
T cd03484 81 AKLINEVYK 89 (142)
T ss_pred HHHHHHHHH
Confidence 999999864
No 16
>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=99.09 E-value=1.4e-10 Score=101.82 Aligned_cols=64 Identities=23% Similarity=0.472 Sum_probs=59.3
Q ss_pred HHHHHHHccHHHhcccCcc--ccCCeEEEEEEeCCCCCCC--cceEEeeccccccchhHHHHHHHhhc
Q psy8492 201 LEVAKDIYAMKMVENFPEH--KREDYEVDGYISREPISQP--QYQNIYINKRLVTNTILHDTINKLLV 264 (489)
Q Consensus 201 ~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~P~~sR~--~~Qy~FVNGR~VRdk~L~~AIr~AL~ 264 (489)
.+++.++||.++..+++++ +.++++|+||++.|+.+|+ +.||+|||||+|.++.|.+||.+|+.
T Consensus 2 ~~~i~~v~G~~~~~~l~~i~~~~~~~~i~G~is~~~~~~~~~~~q~~fVN~R~v~~~~l~~ai~~~y~ 69 (122)
T cd00782 2 KDRIAQVYGKEVAKNLIEVELESGDFRISGYISKPDFGRSSKDRQFLFVNGRPVRDKLLSKAINEAYR 69 (122)
T ss_pred HHHHHHHcCHHHHhcceEEeccCCCEEEEEEEECchhhcCCCccEEEEECCeEecCHHHHHHHHHHHH
Confidence 4799999999999999999 6677999999999998777 89999999999999999999999864
No 17
>PF00178 Ets: Ets-domain; InterPro: IPR000418 Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription []. The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain [, , ]. This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others [, , ]. It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus. NMR-analysis of the structure of the Ets domains revealed that it contains three alpha-helixes (1-3) and four-stranded beta-sheets (1-4) arranged in the order alpha1-beta1-beta2-alpha2-alpha3-beta3-beta4 forming a winged helix-turn-helix (wHTH) topology []. The third alpha-helix is responsive to contact to the major groove of the DNA. Different members of the Ets family proteins display distinct DNA binding specificities. The Ets domains and the flanking amino acid sequences of the proteins influence the binding affinity, and the alteration of a single amino acid in the Ets domain can change its DNA binding specificities. Avian leukemia virus E26 is a replication defective retrovirus that induces a mixed erythroid/myeloid leukemia in chickens.This virus carries two distinct oncogenes: v-myb and v-ets. The ets portion of this oncogene is required for the induction of erythroblastosis. V-ets and c-ets-1, its cellular progenitor, have been shown [] to be nuclear DNA-binding proteins. Ets-1 differs slightly from v-ets at its carboxy-terminal region. In most species where it has been sequenced, c-ets-1 exists in various isoforms generated by alternative splicing and differential phosphorylation.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DUX_F 4AVP_B 1HBX_G 1BC7_C 1K6O_A 1BC8_C 1PUE_E 1FLI_A 2DAO_A 1WWX_A ....
Probab=98.83 E-value=5.3e-10 Score=94.72 Aligned_cols=54 Identities=33% Similarity=0.493 Sum_probs=46.4
Q ss_pred cCCCCCCcccCCCCCCCCCCCcCChhhhhh--hhcccCCcccccccceEEEeeccC
Q psy8492 410 SSACKHVFPRKHHVLRSPMYPNVCLSKFTR--RYYYDKNIIHKTAGKRYVYRFVCD 463 (489)
Q Consensus 410 L~~ce~PftCPHGrpRp~m~P~mnyeKLsR--Ryyy~k~ii~Kv~g~r~vy~F~~d 463 (489)
-+...+|..-+.-|+..++.|.|+|+||+| ||||++|||.||.|+|++|+|+|+
T Consensus 30 eFki~d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy~k~il~kv~g~r~~Y~F~~~ 85 (85)
T PF00178_consen 30 EFKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVKGQRLVYRFVEN 85 (85)
T ss_dssp EEEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEETTSTTEEEESS-
T ss_pred eEEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecCCcEEEEecCcC
Confidence 356667777777777899999999999999 999999999999999999999984
No 18
>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=98.76 E-value=1.6e-08 Score=84.92 Aligned_cols=64 Identities=16% Similarity=0.213 Sum_probs=58.3
Q ss_pred HHHHHHHccHHHhcccCcc--ccCCeEEEEEEeCCCCCCC--cceEEeecccccc-chhHHHHHHHhhc
Q psy8492 201 LEVAKDIYAMKMVENFPEH--KREDYEVDGYISREPISQP--QYQNIYINKRLVT-NTILHDTINKLLV 264 (489)
Q Consensus 201 ~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~P~~sR~--~~Qy~FVNGR~VR-dk~L~~AIr~AL~ 264 (489)
+++|..+||....+.++++ ..++++|+|+++.|+..|+ +.||+|||||+|. ++.+.+||.+|+.
T Consensus 2 ~~~i~~~~g~~~~~~~~~~~~~~~~~~v~g~l~~~~~~~~~~~~~~~fvN~r~v~~~~~~~~~i~~~~~ 70 (107)
T cd00329 2 KDRLAEILGDKVADKLIYVEGESDGFRVEGAISYPDSGRSSKDRQFSFVNGRPVREGGTHVKAVREAYT 70 (107)
T ss_pred HhHHHHHhCHHhHhhcEEEeccCCCEEEEEEEeCCccCcccCCcEEEEEcCeEEcCCHHHHHHHHHHHH
Confidence 5789999999999999988 5677999999999998766 8999999999999 9999999999864
No 19
>PRK14867 DNA topoisomerase VI subunit B; Provisional
Probab=98.56 E-value=1.4e-07 Score=105.02 Aligned_cols=91 Identities=13% Similarity=0.135 Sum_probs=78.3
Q ss_pred HHHHHHHHHHHhhhcCCCceEEEEeCC------cccchhhhhhccHHHHHHHHccHHHhcccCcc--ccCCeEEEEEEeC
Q psy8492 161 ERKYCEDNIKVDNNLERKTKYCLEANE------QKPEEAEEIAIEQLEVAKDIYAMKMVENFPEH--KREDYEVDGYISR 232 (489)
Q Consensus 161 E~~h~~d~vkRlALa~p~v~F~L~~ng------r~l~~~~~~s~~l~eRIa~IlG~~fa~~li~I--e~~~l~I~G~Is~ 232 (489)
|.+ |.|.|+|+||++|+++|+|.++| |.... .+ +.+.+|+..++|.+ +++|+++ +.++++|+||+ .
T Consensus 186 E~~-i~e~l~r~ALanP~i~f~l~~~~~~~~~~r~~~~-lp--~~~~e~~ph~~G~~-~~~Li~i~~~~~~~~v~gfl-~ 259 (659)
T PRK14867 186 EQG-PFEYLRRISLSTPHAKITLKDPEETVVFDRTVDE-IP--EKPEEMKPHPYGLT-TDELLYIARKTDSSKVSSML-N 259 (659)
T ss_pred hHH-HHHHHHHHHHhCCCcEEEEEeCCccccCCcceee-cC--cCHHHHhhccCccc-hhhceehhccCCceEEEEEe-c
Confidence 777 89999999999999999999994 41110 11 27789999999999 9999999 67789999998 9
Q ss_pred CCCCCC--cceEEeeccccccchhHHHHHHHhh
Q psy8492 233 EPISQP--QYQNIYINKRLVTNTILHDTINKLL 263 (489)
Q Consensus 233 P~~sR~--~~Qy~FVNGR~VRdk~L~~AIr~AL 263 (489)
|+++|. ..|+ +|+|+.|.+||.+|+
T Consensus 260 p~~sR~~~~~~~------~V~~~~l~~ai~~ay 286 (659)
T PRK14867 260 SELSRVTTKRIK------ELEEYVLRDLLLENY 286 (659)
T ss_pred chhccCCCCcEE------EEccHHHHHHHHHHH
Confidence 999999 5666 999999999999995
No 20
>KOG3804|consensus
Probab=98.47 E-value=5.2e-08 Score=102.61 Aligned_cols=64 Identities=22% Similarity=0.293 Sum_probs=57.5
Q ss_pred CccCCCCCCcccCCCCCCCCCCCcCChhhhhh--hhcccCCcccccccceEEEeeccChhhhhCCC
Q psy8492 408 PQSSACKHVFPRKHHVLRSPMYPNVCLSKFTR--RYYYDKNIIHKTAGKRYVYRFVCDLQTLLGYS 471 (489)
Q Consensus 408 ~qL~~ce~PftCPHGrpRp~m~P~mnyeKLsR--Ryyy~k~ii~Kv~g~r~vy~F~~d~~~~~~~~ 471 (489)
...|+.-++-.-++-|+-+++.++|+||||+| ||||..+||.||.|+|+||+|+..|..+.+..
T Consensus 321 ~GVFrvVds~a~arlWG~~Kn~~~MtYekmsRAlRyYYk~~IL~kv~GqrLvyqF~k~~~~~~e~~ 386 (390)
T KOG3804|consen 321 KGVFRVVDSEALARLWGMHKNNSSMTYEKMSRALRYYYKREILRKVDGQRLVYQFVKNPSGWAEIK 386 (390)
T ss_pred CCeeEEecccHHHHHhcCcCCCCCcCHHHHhHHhhhhhhcceeecCCCceeeEEeccCcccccccc
Confidence 45777788888889888999999999999999 99999999999999999999999888776543
No 21
>KOG1979|consensus
Probab=98.29 E-value=7.4e-07 Score=96.96 Aligned_cols=103 Identities=18% Similarity=0.331 Sum_probs=86.2
Q ss_pred hHHHHHHHHHHHhhhcCCCceEEEEeCCcccch-hhhhhccHHHHHHHHccHHHhcccC-cc-ccC----CeEEEEEEeC
Q psy8492 160 NERKYCEDNIKVDNNLERKTKYCLEANEQKPEE-AEEIAIEQLEVAKDIYAMKMVENFP-EH-KRE----DYEVDGYISR 232 (489)
Q Consensus 160 ~E~~h~~d~vkRlALa~p~v~F~L~~ngr~l~~-~~~~s~~l~eRIa~IlG~~fa~~li-~I-e~~----~l~I~G~Is~ 232 (489)
.|++.|.|+|-|+|.-+|+|+|.|...|-.... .+..+.+..++|..|||...+.+|+ ++ +.+ .+...|||+.
T Consensus 171 EE~~ki~dlv~ryAIHn~~VsFs~rk~Gd~~~dl~t~~~~s~~D~ir~i~g~~Va~~ll~els~~~~~~l~f~~~g~Isn 250 (694)
T KOG1979|consen 171 EEYRKIMDLVGRYAIHNPRVSFSLRKQGDTVADLRTSVSCSREDNIRNIYGVSVAKNLLNELSKCDSKLLKFSAEGYISN 250 (694)
T ss_pred HHHHHHHHHHHHHheeCCCcceEEeeccccccccccCCccccccchhhhhhhHHHHHHHHHhhhccCceeEEeccceEec
Confidence 599999999999999999999999988752221 1233457889999999999999999 77 222 3568999999
Q ss_pred CCCCCC-cceEEeeccccccchhHHHHHHHh
Q psy8492 233 EPISQP-QYQNIYINKRLVTNTILHDTINKL 262 (489)
Q Consensus 233 P~~sR~-~~Qy~FVNGR~VRdk~L~~AIr~A 262 (489)
+.++.. ..-.+|||||.|..-.|.|||..-
T Consensus 251 ~n~~akk~i~vlFIN~RLVes~~Lr~ale~V 281 (694)
T KOG1979|consen 251 ANYSAKKSILVLFINGRLVESDELRHALEEV 281 (694)
T ss_pred hhhhhhhheEEEEEcCcEeehHHHHHHHHHH
Confidence 999888 556889999999999999999876
No 22
>KOG3805|consensus
Probab=97.95 E-value=3e-06 Score=86.35 Aligned_cols=55 Identities=24% Similarity=0.213 Sum_probs=47.5
Q ss_pred CccCCCCCCcccCCCCCCCCCCCcCChhhhhh--hhcccCCccccc-ccceEEEeecc
Q psy8492 408 PQSSACKHVFPRKHHVLRSPMYPNVCLSKFTR--RYYYDKNIIHKT-AGKRYVYRFVC 462 (489)
Q Consensus 408 ~qL~~ce~PftCPHGrpRp~m~P~mnyeKLsR--Ryyy~k~ii~Kv-~g~r~vy~F~~ 462 (489)
+..|+.+.--.-+|-|+++++.|.|||+||+| |-||.||||+|+ ..+|+||+|+.
T Consensus 300 KGiFkiess~~lArlWG~RKNR~~MnYdKlsRslRqYyKkGiikK~ekkqrLvyqf~p 357 (361)
T KOG3805|consen 300 KGIFKIESSEKLARLWGIRKNRKAMNYDKLSRSLRQYYKKGIIKKPEKKQRLVYQFQP 357 (361)
T ss_pred CceEEeecHHHHHHHhhhhcccccccHHHHHHHHHHHhhcCccccchhhhheeeeecC
Confidence 34556666667888888999999999999999 999999999999 55899999975
No 23
>PRK05218 heat shock protein 90; Provisional
Probab=97.33 E-value=0.00043 Score=77.32 Aligned_cols=90 Identities=8% Similarity=-0.012 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHhh--hcCCCceE-----EEEeCCc-ccchhhhhhccHHHHHHHHccHHHhc----ccCcc---ccCCeE
Q psy8492 161 ERKYCEDNIKVDN--NLERKTKY-----CLEANEQ-KPEEAEEIAIEQLEVAKDIYAMKMVE----NFPEH---KREDYE 225 (489)
Q Consensus 161 E~~h~~d~vkRlA--La~p~v~F-----~L~~ngr-~l~~~~~~s~~l~eRIa~IlG~~fa~----~li~I---e~~~l~ 225 (489)
|..+|.++|+++| +.+| |.| .+..+++ -|... ..++.++....||+.+.. .|..+ ..+++.
T Consensus 187 e~~~i~~li~kys~~l~~P-I~~~~~~~~~in~~~~~w~~~---~~~i~~~~~~~fy~~~~~~~~~pl~~i~~~~e~~~~ 262 (613)
T PRK05218 187 DEWRIRSIIKKYSDFIPVP-IKLEKEEEETINSASALWTRS---KSEITDEEYKEFYKHLAHDFDDPLFWIHNNVEGPFE 262 (613)
T ss_pred CHHHHHHHHHHHHhcCCCC-EEEecccceeecCCccceecC---CccccHHHHHHHhhhhcccccCCcEEEEcccCCceE
Confidence 3488999999999 9998 888 4555555 33211 126778889998777644 46666 555699
Q ss_pred EEEEEeCCCCC------CC--cceEEeeccccccchh
Q psy8492 226 VDGYISREPIS------QP--QYQNIYINKRLVTNTI 254 (489)
Q Consensus 226 I~G~Is~P~~s------R~--~~Qy~FVNGR~VRdk~ 254 (489)
++|++..|..+ +. ..+++|||||+|+|+.
T Consensus 263 ~~gll~iP~~~~~~~~~~~~~~~~~lyvn~v~I~d~~ 299 (613)
T PRK05218 263 YTGLLYIPKKAPFDLFNRDRKGGLKLYVKRVFIMDDA 299 (613)
T ss_pred EEEEEEeCCCCccchhhhcccccEEEEECcEEeeCch
Confidence 99999999987 54 7899999999999986
No 24
>PRK14868 DNA topoisomerase VI subunit B; Provisional
Probab=96.63 E-value=0.00055 Score=77.70 Aligned_cols=74 Identities=15% Similarity=0.262 Sum_probs=61.9
Q ss_pred HHHHHHHHHHhhhcCCCceEEEEeCCcccchhhhhhccHHHHHHHH----ccHHHhcccCcc--ccCCeEEEEEEeCCCC
Q psy8492 162 RKYCEDNIKVDNNLERKTKYCLEANEQKPEEAEEIAIEQLEVAKDI----YAMKMVENFPEH--KREDYEVDGYISREPI 235 (489)
Q Consensus 162 ~~h~~d~vkRlALa~p~v~F~L~~ngr~l~~~~~~s~~l~eRIa~I----lG~~fa~~li~I--e~~~l~I~G~Is~P~~ 235 (489)
...|.+.|+|+||++|+++|+|.+++..+.. ..+++.+.+++..| +|.++ ..|+++ ..+.++|+||+ .|++
T Consensus 195 R~kI~eyl~r~Al~nP~a~f~l~~~~~~~~~-~r~t~~lp~~p~eIkPHP~Gve~-~~L~~m~~~t~~~~l~gFL-~~ef 271 (795)
T PRK14868 195 RQQLHDYIKHTAVVNPHARIELREPDESLKF-ERATDQLPAETEEIRPHPHGVEL-GTLLKMLEATDSYSVSGFL-QEEF 271 (795)
T ss_pred hhhHHHHHHHHHhhCCCeEEEEEECCEEEEe-cccccccccCchhccCCCCCcCH-HHHHHHHhccCCcEeHHhh-hhhh
Confidence 3459999999999999999999999553321 12234788999999 99999 889988 77889999999 9999
Q ss_pred CCC
Q psy8492 236 SQP 238 (489)
Q Consensus 236 sR~ 238 (489)
+|-
T Consensus 272 sRV 274 (795)
T PRK14868 272 TRV 274 (795)
T ss_pred ccc
Confidence 985
No 25
>smart00433 TOP2c TopoisomeraseII. Eukaryotic DNA topoisomerase II, GyrB, ParE
Probab=85.00 E-value=4.5 Score=45.59 Aligned_cols=99 Identities=8% Similarity=-0.002 Sum_probs=64.0
Q ss_pred hhHHHHHHHHHHHhhhcCCCceEEEEeCCc-c---cchhhhhhccHHHHHHHHccHHHhccc--Ccc--ccCCeEEEEEE
Q psy8492 159 NNERKYCEDNIKVDNNLERKTKYCLEANEQ-K---PEEAEEIAIEQLEVAKDIYAMKMVENF--PEH--KREDYEVDGYI 230 (489)
Q Consensus 159 ~~E~~h~~d~vkRlALa~p~v~F~L~~ngr-~---l~~~~~~s~~l~eRIa~IlG~~fa~~l--i~I--e~~~l~I~G~I 230 (489)
.-|+.+|.+.|+++|+++|+|.|.|..... . +.. . +.+.+=+..+.+..-.-.. +.+ +..++.+++.+
T Consensus 148 ~~~~~~i~~rl~~~A~l~pgl~i~l~der~~~~~~f~~--~--~Gl~~yv~~~~~~~~~~~~~~i~~~~~~~~~~veval 223 (594)
T smart00433 148 DDDFELLKRRLRELAFLNKGVKITLNDERSDEEETFLF--E--GGIKDYVELLNKNKELLSPEPTYIEGEKDNIRVEVAF 223 (594)
T ss_pred cchHHHHHHHHHHHHhcCCCcEEEEeccCCCcceEEEC--C--CCHHHHHHHHhCCCCcccCCCeEEEEEeCCcEEEEEE
Confidence 457899999999999999999999996431 1 111 1 3777777776654322111 222 44567788777
Q ss_pred eCCCCCCCcceEEeeccccccch-hHHHHHHHh
Q psy8492 231 SREPISQPQYQNIYINKRLVTNT-ILHDTINKL 262 (489)
Q Consensus 231 s~P~~sR~~~Qy~FVNGR~VRdk-~L~~AIr~A 262 (489)
.-.+- ....++.|||+.+..+. .-..++++|
T Consensus 224 ~~~~~-~~~~~~SFvN~I~T~~GGTHv~g~~~a 255 (594)
T smart00433 224 QYTDG-YSENIVSFVNNIATTEGGTHENGFKDA 255 (594)
T ss_pred EccCC-CCcEEEEEECCccCCCCCcHHHHHHHH
Confidence 66542 23679999999998743 333344444
No 26
>KOG1977|consensus
Probab=67.42 E-value=9.1 Score=44.34 Aligned_cols=83 Identities=14% Similarity=0.141 Sum_probs=52.1
Q ss_pred hHHHHHHHHHHHhhhcCCCceEEEEeCCc--ccchhhhhhccHHHHHHHHccHHHhcccCccccCCeEEEEEEeCCCCCC
Q psy8492 160 NERKYCEDNIKVDNNLERKTKYCLEANEQ--KPEEAEEIAIEQLEVAKDIYAMKMVENFPEHKREDYEVDGYISREPISQ 237 (489)
Q Consensus 160 ~E~~h~~d~vkRlALa~p~v~F~L~~ngr--~l~~~~~~s~~l~eRIa~IlG~~fa~~li~Ie~~~l~I~G~Is~P~~sR 237 (489)
-||..|...|.++||-||.|.|.+..+.. -+. ..+.|+.+.+-+-..- |+=.....+.
T Consensus 168 k~fe~Ik~~i~~i~lmHp~iSfsv~~~~s~~~~l-q~n~s~~~~eilfr~k-------------------~~e~~~s~~~ 227 (1142)
T KOG1977|consen 168 KEFEKIKQRIEAISLMHPSISFSVRNDVSGSMVL-QLNKSQKLREILFRYK-------------------EFELSSSEAH 227 (1142)
T ss_pred HHHHHHHHHHHHHHhhccceeEEEEeccCcceee-ecCccchhhhhhhhhc-------------------ccccccchhc
Confidence 46888999999999999999999998776 222 2232333333211111 1111111112
Q ss_pred -C-cceEEeeccccccchhHHHHHHHh
Q psy8492 238 -P-QYQNIYINKRLVTNTILHDTINKL 262 (489)
Q Consensus 238 -~-~~Qy~FVNGR~VRdk~L~~AIr~A 262 (489)
. ..+++|||||.|-+.-.+.-+.+-
T Consensus 228 ~N~t~g~l~v~~~~~~~~~kh~~~~q~ 254 (1142)
T KOG1977|consen 228 YNKTMGFLFVNKRLVLRTKKHKLIDQL 254 (1142)
T ss_pred cccccceeeecchhhhccchhhHHHHH
Confidence 2 679999999999776666666665
No 27
>PRK05559 DNA topoisomerase IV subunit B; Reviewed
Probab=58.94 E-value=26 Score=39.92 Aligned_cols=98 Identities=9% Similarity=-0.003 Sum_probs=61.7
Q ss_pred HHHHHHHHHHHhhhcCCCceEEEEeCC-c-ccchhhhhhccHHHHHHHHccHH-HhcccCcc--c--cCCeEEEEEEeCC
Q psy8492 161 ERKYCEDNIKVDNNLERKTKYCLEANE-Q-KPEEAEEIAIEQLEVAKDIYAMK-MVENFPEH--K--REDYEVDGYISRE 233 (489)
Q Consensus 161 E~~h~~d~vkRlALa~p~v~F~L~~ng-r-~l~~~~~~s~~l~eRIa~IlG~~-fa~~li~I--e--~~~l~I~G~Is~P 233 (489)
|+..+.+.++++|+.+|++.|.|..++ + .+. . + +++.+.|..++... ..-.-.++ + .++..++--+.--
T Consensus 186 ~~~~i~~~l~~~A~lnpgl~i~l~d~~~~~~f~-~-~--~gl~~~v~~~~~~~~~i~~~~~i~~~~~~~~~~veval~~~ 261 (631)
T PRK05559 186 SPERLKERLRSKAFLLPGLTITLNDERERQTFH-Y-E--NGLKDYLAELNEGKETLPEEFVGSFEGEAEGEAVEWALQWT 261 (631)
T ss_pred CHHHHHHHHHHHHhhCCCeEEEEEeCCceEEEE-C-C--ccHHHHHHHHhCCCCccCCCCceEEeeeeccceEEEEEEec
Confidence 577899999999999999999999987 4 222 1 1 37889999888542 11000122 2 2345554323221
Q ss_pred CCCCCcceEEeeccccccc-hhHHHHHHHhh
Q psy8492 234 PISQPQYQNIYINKRLVTN-TILHDTINKLL 263 (489)
Q Consensus 234 ~~sR~~~Qy~FVNGR~VRd-k~L~~AIr~AL 263 (489)
+ .....++-|||+-+-.+ ..-..++++||
T Consensus 262 ~-~~~~~~~SFvN~I~T~~GGTHv~g~~~al 291 (631)
T PRK05559 262 D-EGGENIESYVNLIPTPQGGTHENGFREGL 291 (631)
T ss_pred C-CCCeEEEEEECcccCCCCCCHHHHHHHHH
Confidence 1 11256888999988665 46666666664
No 28
>KOG3804|consensus
Probab=42.87 E-value=10 Score=40.99 Aligned_cols=44 Identities=18% Similarity=0.194 Sum_probs=37.1
Q ss_pred ccCCCCCCCCCCCcCChhhhhh--hhcccCCcccccc--cceEEEeec
Q psy8492 418 PRKHHVLRSPMYPNVCLSKFTR--RYYYDKNIIHKTA--GKRYVYRFV 461 (489)
Q Consensus 418 tCPHGrpRp~m~P~mnyeKLsR--Ryyy~k~ii~Kv~--g~r~vy~F~ 461 (489)
..++-|+...++|.|+|+-+.+ ||||..+|+.|+. +++-++++.
T Consensus 209 ~~s~~~~a~sn~~~m~~~~m~~a~~~~~q~~il~~~~~~~~~~~~q~~ 256 (390)
T KOG3804|consen 209 AVSKLWGAHSNKPDMNYETMGRALRYYPQRGILAKVEGVLQRSCHQNK 256 (390)
T ss_pred cccccchhhccCccccccccccccccccCCccccccchhhhhhcccCC
Confidence 3455455778999999999999 8999999999999 788887774
No 29
>PRK04184 DNA topoisomerase VI subunit B; Validated
Probab=42.25 E-value=24 Score=39.69 Aligned_cols=27 Identities=4% Similarity=0.142 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhhhcCCCceEEEEe-CCc
Q psy8492 162 RKYCEDNIKVDNNLERKTKYCLEA-NEQ 188 (489)
Q Consensus 162 ~~h~~d~vkRlALa~p~v~F~L~~-ngr 188 (489)
..+|.+.|+|+|+++|++.|+|.+ ||.
T Consensus 189 ~~~I~e~i~r~Al~nP~~~~~l~~~~g~ 216 (535)
T PRK04184 189 KQRIYEYLKRTAIVNPHARITFKDPDGE 216 (535)
T ss_pred HHHHHHHHHHHHHhCCCeEEEEEeCCCe
Confidence 799999999999999999999994 454
No 30
>PRK00036 primosomal replication protein N; Reviewed
Probab=41.10 E-value=30 Score=31.05 Aligned_cols=77 Identities=9% Similarity=0.036 Sum_probs=43.4
Q ss_pred CCCceEEEEeCCcccchhhhhhccHHHHHH-HHccHHHhcccCcc-ccCCeEEEEEEeC-CCCCCC----cceEEeeccc
Q psy8492 176 ERKTKYCLEANEQKPEEAEEIAIEQLEVAK-DIYAMKMVENFPEH-KREDYEVDGYISR-EPISQP----QYQNIYINKR 248 (489)
Q Consensus 176 ~p~v~F~L~~ngr~l~~~~~~s~~l~eRIa-~IlG~~fa~~li~I-e~~~l~I~G~Is~-P~~sR~----~~Qy~FVNGR 248 (489)
-|++.|.|.|-.......-+. ...=+|. -+.| ++++.+-.+ .+..+++.||++. ..-++. ..+.=|++|-
T Consensus 23 Ip~~~~~LeH~S~q~EAG~~R--qv~~~i~ava~G-~~a~~~~~l~~Gs~v~v~GFLa~~~~~~~~LVLHi~~Ie~i~~~ 99 (107)
T PRK00036 23 LPALELLLVHESEVVEAGHPR--RVELTISAVALG-DLALLLADTPLGTEMQVQGFLAPARKDSVKVKLHLQQARRIAGS 99 (107)
T ss_pred CceEEEEEEEeEEeEeCCCcc--eEEEEEEEEEEh-hHHHHhcccCCCCEEEEEEEEEECCCCCCcEEEEhHHeEEcccc
Confidence 488999999988633211000 0000111 1445 566666556 6677999999996 222222 3344456777
Q ss_pred cccchhH
Q psy8492 249 LVTNTIL 255 (489)
Q Consensus 249 ~VRdk~L 255 (489)
.++|+.+
T Consensus 100 ~~~~~~~ 106 (107)
T PRK00036 100 MGRDPLV 106 (107)
T ss_pred cccCccc
Confidence 7777654
No 31
>TIGR01052 top6b DNA topoisomerase VI, B subunit. This model describes DNA topoisomerase VI, an archaeal type II DNA topoisomerase (DNA gyrase).
Probab=39.04 E-value=28 Score=38.64 Aligned_cols=26 Identities=8% Similarity=0.078 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhhhcCCCceEEEEeCC
Q psy8492 162 RKYCEDNIKVDNNLERKTKYCLEANE 187 (489)
Q Consensus 162 ~~h~~d~vkRlALa~p~v~F~L~~ng 187 (489)
..+|.+.|+++|+++|++.|+|.+.+
T Consensus 180 k~~i~e~l~~~Al~nP~~~i~l~~~~ 205 (488)
T TIGR01052 180 KQGVYEYLRRTAVANPHAKIVLVDPD 205 (488)
T ss_pred HHHHHHHHHHHHhhCCCeEEEEEeCC
Confidence 37999999999999999999999874
No 32
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=31.58 E-value=84 Score=28.96 Aligned_cols=52 Identities=21% Similarity=0.191 Sum_probs=40.3
Q ss_pred HHHHHHHHHhhcccCC--ccccCCcccccCCCCCchhhhhhhcccCCCCcccchhhhhHHHHHHHHHHHhhhcCCCceEE
Q psy8492 105 KDIKKIATSFHNKRNL--QYLDERPKITHSNGKNDQNYRKQRKEQSLPTEQSNVTLNNERKYCEDNIKVDNNLERKTKYC 182 (489)
Q Consensus 105 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~E~~h~~d~vkRlALa~p~v~F~ 182 (489)
|=+.+||..+.+.... +.+++ .+.++.|.| |..+|+.+...+|+|.+.
T Consensus 79 KiL~~ia~~l~~~~~~~~G~i~l--------------------~te~~pC~S----------C~~vi~qF~~~~pni~~~ 128 (133)
T PF14424_consen 79 KILEDIAKKLGDNPDPSGGTIDL--------------------FTELPPCES----------CSNVIEQFKKDFPNIKVN 128 (133)
T ss_pred HHHHHHHHHhccccccCCceEEE--------------------EecCCcChh----------HHHHHHHHHHHCCCcEEE
Confidence 4466778877765554 33333 567788988 999999999999999999
Q ss_pred EEeC
Q psy8492 183 LEAN 186 (489)
Q Consensus 183 L~~n 186 (489)
+.|+
T Consensus 129 v~~~ 132 (133)
T PF14424_consen 129 VVYN 132 (133)
T ss_pred EecC
Confidence 9876
No 33
>PRK01178 rps24e 30S ribosomal protein S24e; Reviewed
Probab=29.91 E-value=71 Score=28.25 Aligned_cols=51 Identities=8% Similarity=-0.008 Sum_probs=35.2
Q ss_pred hcCCCceEEEEeCCcccchhhhhhccHHHHHHHHccHHHhcccCcc-----ccCCeEEEEEE
Q psy8492 174 NLERKTKYCLEANEQKPEEAEEIAIEQLEVAKDIYAMKMVENFPEH-----KREDYEVDGYI 230 (489)
Q Consensus 174 La~p~v~F~L~~ngr~l~~~~~~s~~l~eRIa~IlG~~fa~~li~I-----e~~~l~I~G~I 230 (489)
|.+-++.|.+.|.|+--+.- .++++.|++.||. ..+++-| .-|+-+-.||+
T Consensus 14 L~Rke~~~~v~h~g~~tpsr----~eirekLa~~~~~--~~~~vvv~~~~t~fG~g~s~G~a 69 (99)
T PRK01178 14 LGRREIKFEVYHEGSATPSR----KDVRKKLAAMLNA--DKELVVVRKIKTEYGMGKSKGYA 69 (99)
T ss_pred cCcEEEEEEEEeCCCCCCCH----HHHHHHHHHHHCc--CCCEEEEEccCccCCCceEEEEE
Confidence 57788999999999733321 2889999999993 3344444 45555666665
No 34
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=28.79 E-value=64 Score=27.37 Aligned_cols=36 Identities=19% Similarity=0.216 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhhcCeEEEEeCCCcEEEEeecCcchhh
Q psy8492 338 NTLSNRQTCLQYYGLEFEFKNTGKCVKVTHVPKCLFV 374 (489)
Q Consensus 338 ~~Lee~~e~L~~lGfeie~fG~~~ti~VrsVPalL~~ 374 (489)
..+..+.+.|+++|++|+... +.-+.+-..|.++..
T Consensus 34 taVwK~Iq~Lr~~G~~I~s~~-~kGY~L~~~~~ll~~ 69 (79)
T COG1654 34 TAVWKHIQQLREEGVDIESVR-GKGYLLPQLPDLLPQ 69 (79)
T ss_pred HHHHHHHHHHHHhCCceEecC-CCceeccCccccCcH
Confidence 356788999999999999987 446888888887653
No 35
>KOG1979|consensus
Probab=25.01 E-value=1.3e+02 Score=34.58 Aligned_cols=93 Identities=19% Similarity=0.265 Sum_probs=64.8
Q ss_pred cceEEEEEcCeEEEEEeCCceEEEEehhhHHHHHHHHHHHhhc-CccC-CCCCceEe------ecCHH------------
Q psy8492 276 NKLVIAQVDKKYIVVLLNKTLLVAFDQHAVDERIRVEKLFSYG-AFLS-HPITPCVL------NLTPQ------------ 335 (489)
Q Consensus 276 ~~~vIgQl~~~YILae~~dgLLvLIDQHAAHERIlyErL~~~~-~i~s-QLLiPl~l------~Ls~~------------ 335 (489)
+..++|-++..++++|.+-+| |++|---.-+-.-|..+...+ .+.. +|..|..+ .+...
T Consensus 472 n~~yVG~vd~~~alvQh~t~L-y~~d~~~ls~ElfYQi~i~dF~Nfg~~~l~~p~~l~el~~l~l~~e~~~~~~~d~~ke 550 (694)
T KOG1979|consen 472 NLSYVGVVDERTALVQHGTSL-YLCDTVSLSKELFYQILITDFGNFGKIRLSEPLPLSELLMLALESEEPGWTADDGFKE 550 (694)
T ss_pred hcceeeeechhhhhhhcCceE-EEechHHHHHHHHHHHHHHHhcccceeecCCCccHHHHHHHhccCccCCCCccchhHH
Confidence 468999999999999999997 999999988888898888776 2332 34444321 11111
Q ss_pred -----HHHHHHHHHHHH-hhcCeEEEEeCCCcEEEEeecCcchhh
Q psy8492 336 -----EINTLSNRQTCL-QYYGLEFEFKNTGKCVKVTHVPKCLFV 374 (489)
Q Consensus 336 -----E~~~Lee~~e~L-~~lGfeie~fG~~~ti~VrsVPalL~~ 374 (489)
-++.|.++.+.| .=+++++...| .+.++|.++..
T Consensus 551 ~~~~~~~e~l~~ka~ml~dYFsi~i~e~g-----~l~~lP~L~~~ 590 (694)
T KOG1979|consen 551 KIARFAAEKLLEKADMLHDYFSIEIDEEG-----LLTGLPSLLHQ 590 (694)
T ss_pred HHHHHHHHHHhhhHHHHhhheEEEEccCC-----ceecCchhhcc
Confidence 234455667777 44677777554 28999988743
No 36
>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=24.89 E-value=44 Score=26.97 Aligned_cols=32 Identities=3% Similarity=-0.206 Sum_probs=19.6
Q ss_pred hhhhcCcCChhhhcC-CccCCCCCCcccCCCCCCC
Q psy8492 393 TSTVYDKVCLGRESN-PQSSACKHVFPRKHHVLRS 426 (489)
Q Consensus 393 AIK~gD~LS~~E~e~-~qL~~ce~PftCPHGrpRp 426 (489)
|-+.-..||.+-... ..+ ..+|-.||||.|.|
T Consensus 37 A~~iEH~is~e~~~~l~~~--l~~~~~~P~~~~ip 69 (71)
T PF02742_consen 37 ACRIEHVISPETIERLCKF--LGFPETCPHGNPIP 69 (71)
T ss_dssp HHHHGCCS-HHHHHHHHHH--TTCTSBETTSCBST
T ss_pred HHHHHccCCHHHHHHHHHH--hcCCCcCcCCCCCC
Confidence 445556667666666 322 36789999995544
No 37
>TIGR01059 gyrB DNA gyrase, B subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV. Proteins scoring above the noise cutoff for this model and below the trusted cutoff for topoisomerase IV models probably should be designated GyrB.
Probab=24.83 E-value=59 Score=37.25 Aligned_cols=100 Identities=13% Similarity=0.034 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHhhhcCCCceEEEEeCC----cccchhhhhhccHHHHHHHHccHH-Hh-cccCcc--ccCCeEEEEEEeC
Q psy8492 161 ERKYCEDNIKVDNNLERKTKYCLEANE----QKPEEAEEIAIEQLEVAKDIYAMK-MV-ENFPEH--KREDYEVDGYISR 232 (489)
Q Consensus 161 E~~h~~d~vkRlALa~p~v~F~L~~ng----r~l~~~~~~s~~l~eRIa~IlG~~-fa-~~li~I--e~~~l~I~G~Is~ 232 (489)
|+.+|.+.|+++|+++|+|.|.|.+.. +......+ +.+.+=+..+-... .. ...+.+ +.+++.+.--+.-
T Consensus 177 e~~~i~~rl~~~A~l~pgl~i~l~~er~~~~~~~~f~~~--~Gl~~yv~~l~~~~~~l~~~~i~~~~~~~~~~veva~~~ 254 (654)
T TIGR01059 177 DFDILAKRLRELAFLNSGVKISLEDERDGKGKSVTFHYE--GGIKSFVKYLNRNKEPLHEEIIYIKGEKEGIEVEVALQW 254 (654)
T ss_pred CHHHHHHHHHHhhccCCCeEEEEEeecCCCCceeEEEcC--CcHHHHHHHHhcCCCcCCCCCeEEEecccCeEEEEEEEe
Confidence 688999999999999999999999752 11000111 13444333221110 00 011122 2235555543333
Q ss_pred CCCCCCcceEEeeccccc-cchhHHHHHHHhh
Q psy8492 233 EPISQPQYQNIYINKRLV-TNTILHDTINKLL 263 (489)
Q Consensus 233 P~~sR~~~Qy~FVNGR~V-Rdk~L~~AIr~AL 263 (489)
.+ .-...++-|||+=+- .-..-..+++.||
T Consensus 255 ~~-~~~~~~~SFvN~I~T~~GGTHv~g~~~al 285 (654)
T TIGR01059 255 ND-GYSENILSFVNNINTREGGTHLEGFRSAL 285 (654)
T ss_pred cC-CCceeEEEEECcccCCCCCcHHHHHHHHH
Confidence 22 111446889999764 4446666777774
No 38
>PF07908 D-aminoacyl_C: D-aminoacylase, C-terminal region; InterPro: IPR012855 D-aminoacylase (Q9AGH8 from SWISSPROT, 3.5.1.81 from EC) hydrolyses a wide variety of N-acyl derivatives of neutral D-amino acids, in a zinc-dependent manner. The enzyme is composed of a small beta-barrel domain and a larger catalytic alpha/beta-barrel that contains a short alpha/beta insert. The overall structure shares significant similarity to the alpha/beta-barrel amidohydrolase superfamily, in which the beta-strands in both barrels superimpose well []. The C-terminal region featured in this entry forms part of the beta-barrel domain, together with a short N-terminal segment. This domain does not seem to contribute to the substrate-binding site or to be involved in the catalytic process.; GO: 0008270 zinc ion binding, 0016811 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides; PDB: 3GIQ_B 3GIP_B 1V4Y_A 1M7J_A 1RK5_A 1RJP_A 1RJR_A 1RJQ_A 1RK6_A 1V51_A.
Probab=24.07 E-value=53 Score=24.98 Aligned_cols=13 Identities=15% Similarity=0.501 Sum_probs=10.8
Q ss_pred cceEEeecccccc
Q psy8492 239 QYQNIYINKRLVT 251 (489)
Q Consensus 239 ~~Qy~FVNGR~VR 251 (489)
..-|+||||+.|-
T Consensus 19 GI~~V~VNG~~vv 31 (48)
T PF07908_consen 19 GIDYVFVNGQIVV 31 (48)
T ss_dssp SEEEEEETTEEEE
T ss_pred CEEEEEECCEEEE
Confidence 5689999999863
No 39
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit, proteobacterial. This protein is active as an alpha(2)beta(2) heterotetramer.
Probab=23.81 E-value=63 Score=36.94 Aligned_cols=25 Identities=12% Similarity=0.014 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhhhcCCCceEEEEe
Q psy8492 161 ERKYCEDNIKVDNNLERKTKYCLEA 185 (489)
Q Consensus 161 E~~h~~d~vkRlALa~p~v~F~L~~ 185 (489)
|+.+|.+.++++|+++|+|.|.|..
T Consensus 179 e~~~i~~~l~~lA~lnpgi~~~l~d 203 (625)
T TIGR01055 179 SVSRLYHILRAKAVLCRGVEIEFED 203 (625)
T ss_pred CHHHHHHHHHHHHhhCCCcEEEEee
Confidence 6889999999999999999999984
Done!