Query 015440
Match_columns 406
No_of_seqs 137 out of 213
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:20:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015440.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015440hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00625 tfb2 Transcription f 100.0 4E-132 9E-137 1015.4 44.2 387 10-406 1-448 (448)
2 KOG3471 RNA polymerase II tran 100.0 7E-132 2E-136 989.8 34.1 396 1-406 5-463 (465)
3 COG5144 TFB2 RNA polymerase II 100.0 1E-112 2E-117 831.2 25.7 382 8-405 7-445 (447)
4 PF03849 Tfb2: Transcription f 100.0 8E-102 2E-106 782.3 33.9 300 13-320 1-366 (366)
5 PF13625 Helicase_C_3: Helicas 99.6 1.1E-14 2.3E-19 127.4 12.1 116 253-376 2-119 (129)
6 TIGR00603 rad25 DNA repair hel 97.0 0.0052 1.1E-07 68.4 12.1 105 250-369 22-131 (732)
7 PF08671 SinI: Anti-repressor 90.7 0.24 5.3E-06 33.6 2.5 22 296-317 8-29 (30)
8 PRK05718 keto-hydroxyglutarate 86.3 18 0.00038 34.8 13.0 162 201-403 1-175 (212)
9 PRK06015 keto-hydroxyglutarate 77.5 17 0.00037 34.8 9.2 126 249-403 27-164 (201)
10 KOG1123 RNA polymerase II tran 65.2 11 0.00025 41.1 5.4 89 249-349 81-169 (776)
11 PRK07114 keto-hydroxyglutarate 64.6 95 0.0021 30.2 11.2 156 207-403 7-180 (222)
12 TIGR01182 eda Entner-Doudoroff 63.5 65 0.0014 30.9 9.8 125 250-403 32-168 (204)
13 TIGR01615 A_thal_3542 uncharac 62.9 3.6 7.9E-05 37.0 1.1 65 249-331 47-112 (131)
14 smart00418 HTH_ARSR helix_turn 56.2 61 0.0013 22.9 6.6 54 48-103 2-56 (66)
15 PF01081 Aldolase: KDPG and KH 54.9 30 0.00064 33.0 5.8 125 250-403 32-168 (196)
16 PRK10141 DNA-binding transcrip 54.0 90 0.002 27.3 8.3 70 33-103 6-76 (117)
17 PF01978 TrmB: Sugar-specific 53.4 17 0.00037 27.9 3.3 33 200-233 33-66 (68)
18 PRK14529 adenylate kinase; Pro 51.0 51 0.0011 31.9 6.9 78 281-373 23-101 (223)
19 PF13463 HTH_27: Winged helix 49.8 77 0.0017 23.6 6.4 58 45-103 5-67 (68)
20 PF00406 ADK: Adenylate kinase 45.0 43 0.00093 29.2 5.0 74 281-369 19-94 (151)
21 PF03444 HrcA_DNA-bdg: Winged 44.6 18 0.00039 29.9 2.2 35 202-237 37-71 (78)
22 PRK00135 scpB segregation and 42.7 53 0.0011 31.1 5.4 57 48-108 95-156 (188)
23 PRK06552 keto-hydroxyglutarate 41.7 2.5E+02 0.0054 26.9 10.0 117 207-351 5-137 (213)
24 COG1313 PflX Uncharacterized F 40.1 36 0.00078 34.9 4.0 52 307-376 273-329 (335)
25 COG1420 HrcA Transcriptional r 40.0 22 0.00048 36.8 2.6 45 192-238 31-75 (346)
26 PRK03911 heat-inducible transc 38.6 26 0.00057 34.9 2.8 45 192-238 28-72 (260)
27 TIGR03853 matur_matur probable 38.0 44 0.00095 27.6 3.5 26 292-317 18-57 (77)
28 PF01706 FliG_C: FliG C-termin 35.5 1.5E+02 0.0033 25.0 6.7 73 7-84 29-103 (110)
29 PF01316 Arg_repressor: Argini 35.4 47 0.001 26.6 3.3 28 202-229 35-62 (70)
30 PRK00441 argR arginine repress 33.5 1.1E+02 0.0023 28.0 5.7 28 202-229 34-61 (149)
31 cd07153 Fur_like Ferric uptake 31.4 1.5E+02 0.0032 24.7 5.9 57 45-101 3-66 (116)
32 PF02244 Propep_M14: Carboxype 29.9 2E+02 0.0044 22.1 6.1 46 359-404 6-55 (74)
33 TIGR02425 decarb_PcaC 4-carbox 29.8 61 0.0013 28.5 3.4 25 294-318 76-100 (123)
34 smart00195 DSPc Dual specifici 29.7 1.2E+02 0.0026 25.9 5.2 45 292-342 89-137 (138)
35 PF10678 DUF2492: Protein of u 29.4 74 0.0016 26.3 3.6 26 292-317 20-59 (78)
36 COG1412 Uncharacterized protei 28.4 1.2E+02 0.0025 27.5 5.0 18 249-266 9-26 (136)
37 smart00550 Zalpha Z-DNA-bindin 27.6 2E+02 0.0043 22.4 5.7 60 42-102 5-66 (68)
38 PF01216 Calsequestrin: Calseq 26.5 1.4E+02 0.0031 31.3 5.8 86 305-403 234-322 (383)
39 KOG4175 Tryptophan synthase al 26.4 2.4E+02 0.0051 27.8 6.9 77 295-378 67-151 (268)
40 PF04720 DUF506: Protein of un 25.9 31 0.00068 33.5 1.0 109 202-331 87-201 (218)
41 PF01638 HxlR: HxlR-like helix 24.7 2.1E+02 0.0046 23.1 5.6 55 48-103 10-68 (90)
42 PF12840 HTH_20: Helix-turn-he 24.0 1.2E+02 0.0027 22.6 3.8 55 36-91 3-57 (61)
43 COG1438 ArgR Arginine represso 23.5 52 0.0011 30.3 1.9 28 202-229 36-63 (150)
44 PF00085 Thioredoxin: Thioredo 23.4 1.8E+02 0.004 22.6 4.9 37 261-297 22-60 (103)
45 COG1378 Predicted transcriptio 23.2 1.1E+02 0.0024 30.0 4.3 129 166-308 3-163 (247)
46 PF03918 CcmH: Cytochrome C bi 23.1 74 0.0016 29.0 2.8 30 294-323 63-92 (148)
47 PF09713 A_thal_3526: Plant pr 23.1 1.2E+02 0.0025 23.5 3.4 24 295-318 3-26 (54)
48 TIGR03147 cyt_nit_nrfF cytochr 23.0 1.5E+02 0.0033 26.6 4.6 34 294-327 63-96 (126)
49 PRK12928 lipoyl synthase; Prov 22.8 7.8E+02 0.017 24.6 10.7 34 183-218 72-105 (290)
50 PF02082 Rrf2: Transcriptional 22.3 3.5E+02 0.0075 21.5 6.3 59 44-103 10-70 (83)
51 PF03428 RP-C: Replication pro 21.2 97 0.0021 29.1 3.2 31 199-229 81-113 (177)
52 PF09079 Cdc6_C: CDC6, C termi 21.1 1.2E+02 0.0026 24.2 3.3 31 192-222 28-59 (85)
53 PRK10144 formate-dependent nit 21.0 1.8E+02 0.0038 26.2 4.6 34 294-327 63-96 (126)
54 COG0563 Adk Adenylate kinase a 20.6 65 0.0014 29.9 1.9 79 282-375 24-104 (178)
55 PF12637 TSCPD: TSCPD domain; 20.4 1.7E+02 0.0038 24.4 4.3 53 271-339 37-89 (95)
56 PF03965 Penicillinase_R: Peni 20.2 1.2E+02 0.0025 25.8 3.3 30 203-232 36-65 (115)
No 1
>TIGR00625 tfb2 Transcription factor tfb2. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=4.1e-132 Score=1015.43 Aligned_cols=387 Identities=31% Similarity=0.576 Sum_probs=366.2
Q ss_pred hHHHHHhhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceee
Q 015440 10 NFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFS 89 (406)
Q Consensus 10 ~~~~yL~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~ 89 (406)
+++|||++||+.++++||++||||+||||+||||||+|||||||+++|||.++++.|+++++++++++|+++|++||||+
T Consensus 1 ~~~~yL~~Lp~~~~~~LY~~PatclAIfR~Lp~lAK~~vmrlL~~~~pv~~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~ 80 (448)
T TIGR00625 1 SLQEFLEGLPPGVLDRLYGHPATCLAVFRELPSLAKNWVMRMLFNEQPVPLADVDLWVKKEFKKAQEESTGLLSGLHIWH 80 (448)
T ss_pred ChHHHHHhCCHHHHHHHhCCcHHHHHHHHcCcHHHHHHHHHHHcCCCCCCHHHHHHHhCccchHHHHHHHHHHHhCEeEE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred ec-CCCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCcCCCCCCC
Q 015440 90 EE-KKKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTN 163 (406)
Q Consensus 90 ~~-~~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mVgs~~~~~~~~ 163 (406)
+. .+|.+.|.||++||+|||.||+||| ++|++.++++ .+++++||+||++|||+|||||||++.. ..
T Consensus 81 ~~~~~~~~~~~Ln~~F~~~lr~aL~g~~~~~s~~v~~~~~d~~----~~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~ 153 (448)
T TIGR00625 81 TQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGPDKH----AVDVDSLDKYAEERWETILHFMVGTPSA---KV 153 (448)
T ss_pred ecCCCCceeEEECHHHHHHHHHHhcCCCCCCCCCCcccCCCCC----CCCHHHHHHHHHHHHHHHHHHHcCCCCc---CC
Confidence 73 3355789999999999999999998 4667777765 8999999999999999999999998753 57
Q ss_pred CChhHHHHHHhcCCccc-c-----------------------------------------------hhhhccchhhhhcc
Q 015440 164 FSSSMMKVFQRGLLIQS-I-----------------------------------------------LRSLKFLCQGILEA 195 (406)
Q Consensus 164 ~s~~v~~lL~~~gLm~~-~-----------------------------------------------lf~Ls~l~~~lG~~ 195 (406)
+|++|+++|+++|||++ + ||+|||++ +|++
T Consensus 154 ~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~--lG~~ 231 (448)
T TIGR00625 154 PSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLT--LGKA 231 (448)
T ss_pred CchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccc--cCCc
Confidence 99999999999999976 1 59999999 9999
Q ss_pred ccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCCc----cc--ccccceEEEeeCceEEeecCChh
Q 015440 196 YNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD----SS--ARKEGFVVVETNFRMYAYSTSKL 269 (406)
Q Consensus 196 Ys~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~~----~~--~~~~g~iivETNfrvYAYt~s~l 269 (406)
|++++||++|++||+||+|+||||++++++++|| |||||++||++.++ ++ +.++|||||||||||||||+|||
T Consensus 232 Y~~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l 310 (448)
T TIGR00625 232 YSVDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPL 310 (448)
T ss_pred cCCCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHH
Confidence 9999999999999999999999999999999999 99999999887542 11 25679999999999999999999
Q ss_pred HHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCcccc-ccCCCCChhHHHHHHHHHHhcCcee
Q 015440 270 HCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRIPSVPENVCDQIRLWESDLNRVE 348 (406)
Q Consensus 270 ~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~-~~~p~iP~tV~dQIrlWe~E~~R~~ 348 (406)
|++||++||++.||||||+||+|||+||++|+++||||||||+||++||||+|+ ++.|+|||||+|||||||.||||++
T Consensus 311 ~~~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~ 390 (448)
T TIGR00625 311 QIALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLR 390 (448)
T ss_pred HHHHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceE
Confidence 999999999999999999999999999999999999999999999999999998 4789999999999999999999999
Q ss_pred eccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 015440 349 MTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406 (406)
Q Consensus 349 ~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~~ 406 (406)
+++|+||++|+|+++|+++++||+++|+|+|+|+.||+|||+.+||++||+|||++|+
T Consensus 391 ~~~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~ 448 (448)
T TIGR00625 391 FTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448 (448)
T ss_pred eecceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence 9999999999999999999999999999999999999999999999999999999986
No 2
>KOG3471 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription; Replication, recombination and repair]
Probab=100.00 E-value=7e-132 Score=989.84 Aligned_cols=396 Identities=36% Similarity=0.615 Sum_probs=372.4
Q ss_pred CCchhcchhhHHHHHhhcCH--HHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHH
Q 015440 1 MPQVKIIAKNFMDMVASLTA--RDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVA 78 (406)
Q Consensus 1 m~~~~~~~~~~~~yL~~Lp~--~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~a 78 (406)
||+....++++.+||+.||. .+++|||++|++|+||||+|||+||+|||+|||.++|||.+++++|++.++.+++++|
T Consensus 5 ~~~~~~~~~~~c~~leeLp~~~~~l~RLY~~Pa~ClAIfR~LPpLAkqfVm~MLf~~~pVP~a~~~~Wv~~~~tk~q~ea 84 (465)
T KOG3471|consen 5 PSQGWPYAKNICDYLEELPRIPHSLDRLYGKPAICLAIFRELPPLAKQFVMQMLFKDQPVPLADVDLWVKVEETKEQEEA 84 (465)
T ss_pred ccccCcccchHHHHHHHhhccchHHHHHhCCchHHHHHHHhCcHHHHHHHHHHHhcCCCccHHHHHHHhhhhhHHHHHHH
Confidence 45556688999999999999 5899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCceeeecCCCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHh
Q 015440 79 IDRLVQLRLFSEEKKKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLI 153 (406)
Q Consensus 79 l~~L~~L~I~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mV 153 (406)
++.|.+||||+.....++.+.|||+||+|+|.||+||| ++++.++|++ .+++++||+||.+||||||||||
T Consensus 85 ik~L~~L~I~~~~~~~g~~i~Lnp~fr~s~~~al~gg~~~~s~~s~~l~~~~~----~r~v~~ld~ya~~rwe~ILh~mv 160 (465)
T KOG3471|consen 85 IKLLKRLRIFHKQGTPGQAINLNPTFRRSLRDALTGGGKQNSFGSLVLGEDKH----NRDVDFLDKYASERWECILHFMV 160 (465)
T ss_pred HHHHhheeeEeecCCCCceEEeCHHHHHHHHHHHhcCCCcccCCCcccCCCcC----cccchhhHHHHHHHHHHHHHHHh
Confidence 99999999998853222778999999999999999999 4666777877 89999999999999999999999
Q ss_pred CCcCCCCCCCCChhHHHHHHhcCCcccc----------------------------------------------hhhhcc
Q 015440 154 SSAQAERPTNFSSSMMKVFQRGLLIQSI----------------------------------------------LRSLKF 187 (406)
Q Consensus 154 gs~~~~~~~~~s~~v~~lL~~~gLm~~~----------------------------------------------lf~Ls~ 187 (406)
|++.. ..+|++|.+||+++|||+++ |||||+
T Consensus 161 gt~~a---~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~~~~~dlvevL~~LfqL~~ 237 (465)
T KOG3471|consen 161 GTPEA---KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFESSGMDLVEVLEFLFQLSA 237 (465)
T ss_pred CCccc---cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 99755 78999999999999999976 599999
Q ss_pred chhhhhccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCCc--------ccccccceEEEeeCc
Q 015440 188 LCQGILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD--------SSARKEGFVVVETNF 259 (406)
Q Consensus 188 l~~~lG~~Ys~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~~--------~~~~~~g~iivETNf 259 (406)
++ +|++|++++||++|+.||+||||+|||||+|.+..+|| ||+||+++|++..+ ..+++.|||||||||
T Consensus 238 ~~--~G~~Ysvd~~~~~~~~~lq~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~ 314 (465)
T KOG3471|consen 238 LA--LGRAYSVDALTETQRILLQHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNY 314 (465)
T ss_pred HH--hcccceeehhhHHHHHHHHHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEecc
Confidence 99 99999999999999999999999999999999999999 99999999886442 122455999999999
Q ss_pred eEEeecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC--CCCChhHHHHH
Q 015440 260 RMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI--PSVPENVCDQI 337 (406)
Q Consensus 260 rvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~--p~iP~tV~dQI 337 (406)
||||||+||||+|+++|||++.|||||||||+|||||||+|+++||||+|||+||++||||||+... |.+||||+|||
T Consensus 315 riYAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQI 394 (465)
T KOG3471|consen 315 RIYAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQI 394 (465)
T ss_pred EEEEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHH
Confidence 9999999999999999999999999999999999999999999999999999999999999998776 88999999999
Q ss_pred HHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 015440 338 RLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQNK 406 (406)
Q Consensus 338 rlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~~ 406 (406)
||||.||||+.+++|+||++|.|..||+.+++||+++|+|+|+|+.||+|||+.+||++|++||||++|
T Consensus 395 rLWElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k 463 (465)
T KOG3471|consen 395 RLWELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK 463 (465)
T ss_pred HHHHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence 999999999999999999999999999999999999999999999999999999999999999999764
No 3
>COG5144 TFB2 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB2 [Transcription / DNA replication, recombination, and repair]
Probab=100.00 E-value=1e-112 Score=831.24 Aligned_cols=382 Identities=29% Similarity=0.505 Sum_probs=360.4
Q ss_pred hhhHHHHHhhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCce
Q 015440 8 AKNFMDMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRL 87 (406)
Q Consensus 8 ~~~~~~yL~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I 87 (406)
..++.+||+.||.....|||+.|++|+|+||.||++|++|||.|||.+.|||..+.+.|++.+.+-.+.+++..+.++||
T Consensus 7 k~si~~ylE~lP~~~~~rLY~~Pa~cla~~rvlp~la~~fvm~mlfn~~~v~lld~d~wik~~~Ki~~~~~v~~~k~~hi 86 (447)
T COG5144 7 KISIIEYLEMLPRHSKTRLYGAPAFCLAFLRVLPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKKGNHI 86 (447)
T ss_pred cccHHHHHHHhhhhhhhhhhcCcHHHHHHHHhccHHHHHHHHHHHcCCCCcchhhHHHHHhhhhHHHHHHHHhhhccceE
Confidence 45788999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCcCCCCCC
Q 015440 88 FSEEKKKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPT 162 (406)
Q Consensus 88 ~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mVgs~~~~~~~ 162 (406)
.... ...+.|||+||.+|++|||||+ |+ |..+ + .++++.||.||.++||+|||||||+... .
T Consensus 87 ~~~~---g~~i~ln~~fk~sl~~altgg~~~nsfgv-~i~E--~----lvsvd~ld~ys~~kwEtILhfmVgtpea---k 153 (447)
T COG5144 87 YLDE---GLMIRLNPEFKISLMDALTGGTMENSFGV-CIGE--K----LVSVDMLDSYSSRKWETILHFMVGTPEA---K 153 (447)
T ss_pred EecC---CceEEeChHHHHHHHHHhhccccccccce-eecc--c----eeeeehhhhhhhhhHHHHHHHHhCCccc---c
Confidence 9764 2678999999999999999998 34 3332 2 6899999999999999999999998775 6
Q ss_pred CCChhHHHHHHhcCCcccc----------------------------------------------hhhhccchhhhhccc
Q 015440 163 NFSSSMMKVFQRGLLIQSI----------------------------------------------LRSLKFLCQGILEAY 196 (406)
Q Consensus 163 ~~s~~v~~lL~~~gLm~~~----------------------------------------------lf~Ls~l~~~lG~~Y 196 (406)
-|+.+|+++|+++|||.++ +||||.++ +|++|
T Consensus 154 ip~egVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s~md~v~VLhflFmLgal~--vG~aY 231 (447)
T COG5144 154 IPAEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALA--VGTAY 231 (447)
T ss_pred CcchhHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHhcchh--hccee
Confidence 7899999999999999976 59999999 99999
Q ss_pred cCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCC----c--ccccccceEEEeeCceEEeecCChhH
Q 015440 197 NLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLT----D--SSARKEGFVVVETNFRMYAYSTSKLH 270 (406)
Q Consensus 197 s~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~----~--~~~~~~g~iivETNfrvYAYt~s~l~ 270 (406)
+++.||+||+.||+|+|++||||+++-.+.+|| ||+||+.||++.. . ...++.||||||||||||||||||||
T Consensus 232 ~id~lsdtqqiml~D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplq 310 (447)
T COG5144 232 KIDALSDTQQIMLMDRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQ 310 (447)
T ss_pred eecccchHHHHHHHHHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHH
Confidence 999999999999999999999999988888999 9999999987533 1 22356799999999999999999999
Q ss_pred HHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCChhHHHHHHHHHHhcCceeec
Q 015440 271 CEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMT 350 (406)
Q Consensus 271 iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrlWe~E~~R~~~~ 350 (406)
+|++.|||++..||||||+|+|||||||+|+.+||||+|||.||++||||||+++.|.+||||+|||+|||.|+||+.+.
T Consensus 311 iavi~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~ 390 (447)
T COG5144 311 IAVIHLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMV 390 (447)
T ss_pred HHHHHHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhcc
Q 015440 351 PAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRGQN 405 (406)
Q Consensus 351 ~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~~~ 405 (406)
+|+||+||.+..+|+.+.+||++.|||+|+|+.||||||+.+||.+|++|.||+-
T Consensus 391 pG~LysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 391 PGYLYSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred cchHHhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 9999999999999999999999999999999999999999999999999999964
No 4
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=100.00 E-value=7.6e-102 Score=782.27 Aligned_cols=300 Identities=41% Similarity=0.744 Sum_probs=279.9
Q ss_pred HHHhhcCHHHHHHhhCChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecC
Q 015440 13 DMVASLTARDLNKLYENPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEK 92 (406)
Q Consensus 13 ~yL~~Lp~~~~~~LY~~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~ 92 (406)
|||++||++++++||++||||+||||+||++||+|||||||+++|||++++++||++++++++++|+++|.+||||++.+
T Consensus 1 eYL~~Lp~~~l~~LY~~P~tclAIfR~LP~LAK~~VmrLL~~~~pv~~~~l~~Wv~~~~~~~~~~al~~L~~L~Ii~~~~ 80 (366)
T PF03849_consen 1 EYLESLPPATLDRLYQSPATCLAIFRSLPPLAKQYVMRLLFVEQPVPQADLESWVKPESKKEHDEALKRLRSLHIIQESE 80 (366)
T ss_pred ChhHHCCHHHHHHHHcCcHHHHHHHHhccHHHHHHHHHHHhcCCCcCHHHHHHHhCccchHHHHHHHHHHhhCeeEeecc
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999998743
Q ss_pred --CCceeEEeCHHHHHHHHHHHhcCC-----CCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCcCCCCCCCCC
Q 015440 93 --KKETTYRLNSTFQSNLQKHLINGG-----ALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSAQAERPTNFS 165 (406)
Q Consensus 93 --~~~~~~~Ln~~F~~~lr~aL~ggg-----~~~~~~~~~~~~~~~~~~~~Ld~ya~~kWE~IL~~mVgs~~~~~~~~~s 165 (406)
++.+.|.|||+||+|||.||+||| ++|++.++++ .+++++||+||++|||+|||||||++.... ..||
T Consensus 81 ~~~~~~~~~Ln~~F~~~Lr~aL~ggg~~~~~~~~~~~~~~~----~~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~-~~~s 155 (366)
T PF03849_consen 81 SPGGKQQYQLNPIFRKNLRNALTGGGKPWSFGVPSEEPDKK----APDVEFLDEYARERWESILHYMVGSSSSSN-SSPS 155 (366)
T ss_pred CCCCceeEEeCHHHHHHHHHHHhCCCCCcccCcccccccCC----CCCHHHHHHHHHHHHHHHHHHHhcCccccc-CCCC
Confidence 334889999999999999999999 4556655555 899999999999999999999999987521 2299
Q ss_pred hhHHHHHHhcCCcccc------------------------------------------------hhhhccchhhhhcccc
Q 015440 166 SSMMKVFQRGLLIQSI------------------------------------------------LRSLKFLCQGILEAYN 197 (406)
Q Consensus 166 ~~v~~lL~~~gLm~~~------------------------------------------------lf~Ls~l~~~lG~~Ys 197 (406)
++|+++|+++|||+.+ ||+||+++ +|++|+
T Consensus 156 ~~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~l~flf~L~~~~--~g~~Y~ 233 (366)
T PF03849_consen 156 QDVKQLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAEARGMDLVEVLSFLFQLSFLE--LGKAYS 233 (366)
T ss_pred HHHHHHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccc--cCCcCc
Confidence 9999999999999982 59999999 999999
Q ss_pred CCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhhccCCCc-----------ccccccceEEEeeCceEEeecC
Q 015440 198 LNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNLSMSLTD-----------SSARKEGFVVVETNFRMYAYST 266 (406)
Q Consensus 198 ~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~Lt~~~~~-----------~~~~~~g~iivETNfrvYAYt~ 266 (406)
+++||++|++||+||+|+||||++++++++|| |||||++|+++.+. ....++|||||||||||||||+
T Consensus 234 ~~~ls~~q~~~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~ 312 (366)
T PF03849_consen 234 TEGLSETQKNMLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTN 312 (366)
T ss_pred CCCCCHHHHHHHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecC
Confidence 99999999999999999999999999999999 99999999887662 1246789999999999999999
Q ss_pred ChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCc
Q 015440 267 SKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 320 (406)
Q Consensus 267 s~l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp 320 (406)
||||||||++||++.|||||||||+||||||++|+++||||||||+||++||||
T Consensus 313 s~l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 313 SPLQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred CHHHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 999999999999999999999999999999999999999999999999999998
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=99.59 E-value=1.1e-14 Score=127.45 Aligned_cols=116 Identities=22% Similarity=0.350 Sum_probs=103.4
Q ss_pred EEEeeCceEEeecCCh--hHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCC
Q 015440 253 VVVETNFRMYAYSTSK--LHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVP 330 (406)
Q Consensus 253 iivETNfrvYAYt~s~--l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP 330 (406)
+||++||.|.+.+.+| -..+.|..|+++ .+..+|.+++||+.|+.+|++.|+|+++|+.||+.|+.. .||
T Consensus 2 liVqpd~~I~v~~~~~~~~~~~~L~~fae~-~s~~~~~~yrlT~~Sl~~A~~~G~~~e~i~~~L~~~S~~-------~lP 73 (129)
T PF13625_consen 2 LIVQPDFEILVEPGHPSPADAWFLARFAEL-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSKN-------PLP 73 (129)
T ss_pred EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcCC-------CCC
Confidence 7999999999977665 345999999999 667999999999999999999999999999999999944 699
Q ss_pred hhHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCe
Q 015440 331 ENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 376 (406)
Q Consensus 331 ~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~ 376 (406)
+||..+|+-|+...+|+++.++.+|-.+.+.+..+.+.+..+-.++
T Consensus 74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~ 119 (129)
T PF13625_consen 74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKL 119 (129)
T ss_pred HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhh
Confidence 9999999999999999999996666699999999988877665443
No 6
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.04 E-value=0.0052 Score=68.40 Aligned_cols=105 Identities=23% Similarity=0.398 Sum_probs=84.1
Q ss_pred cceEEEeeCceEEeecCChh--HH-HHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccC
Q 015440 250 EGFVVVETNFRMYAYSTSKL--HC-EILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRI 326 (406)
Q Consensus 250 ~g~iivETNfrvYAYt~s~l--~i-aiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~ 326 (406)
+|.|++||- +|+ |. ..|.-|+|+..|--+|..++||-=|+-.|...|+++++||++|...+-.
T Consensus 22 d~~i~lE~~--------~p~~~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk~------ 87 (732)
T TIGR00603 22 DGHIFLESF--------SPLYKQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSKT------ 87 (732)
T ss_pred CCeEEEEeC--------CccHHHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhCC------
Confidence 466666663 443 33 7899999999999999999999999999999999999999999999843
Q ss_pred CCCChhHHHHHHHHHHhcCceeec--cceeecCCCCHHHHHHHHH
Q 015440 327 PSVPENVCDQIRLWESDLNRVEMT--PAHYYEEFPSRDVFEAACD 369 (406)
Q Consensus 327 p~iP~tV~dQIrlWe~E~~R~~~~--~g~L~~~f~s~~~f~~~~~ 369 (406)
.||++|.+.|+.+-.-.+++++. ++--|-+-.+.+..+.+.+
T Consensus 88 -~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~ 131 (732)
T TIGR00603 88 -PIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLK 131 (732)
T ss_pred -CCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHh
Confidence 79999999999999999999883 2211334455555555553
No 7
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=90.70 E-value=0.24 Score=33.63 Aligned_cols=22 Identities=36% Similarity=0.525 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCHHHHHHHHhhc
Q 015440 296 SLYNAFENGITAEQIISFLQQN 317 (406)
Q Consensus 296 Sv~~A~~~GITA~QIi~fL~~h 317 (406)
=|++|...|||.+||..||+.+
T Consensus 8 Li~eA~~~Gls~eeir~FL~~~ 29 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHhC
Confidence 3689999999999999999864
No 8
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=86.31 E-value=18 Score=34.79 Aligned_cols=162 Identities=18% Similarity=0.214 Sum_probs=104.5
Q ss_pred CCHHHHHHHHHhhhcCeeeEeeCC-CcceecchhhhhhhccCCCcccccccceEEEeeCceEEeecCChhHHHHHHHHHh
Q 015440 201 LSEIQRSMIKDFADLGLVKLQQGR-KESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSK 279 (406)
Q Consensus 201 Lt~tq~~~L~~L~~lGLVy~~~~~-~~~fy~pT~La~~Lt~~~~~~~~~~~g~iivETNfrvYAYt~s~l~iaiL~lF~~ 279 (406)
+++++..+++.|.+-|+|-.-+.. ..... +++-.| .+.|.=++|--++ +|- =+..+.+
T Consensus 1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a~---~i~~al---------~~~Gi~~iEitl~------~~~---~~~~I~~ 59 (212)
T PRK05718 1 MKNWKTSIEEILRAGPVVPVIVINKLEDAV---PLAKAL---------VAGGLPVLEVTLR------TPA---ALEAIRL 59 (212)
T ss_pred CchhHHHHHHHHHHCCEEEEEEcCCHHHHH---HHHHHH---------HHcCCCEEEEecC------Ccc---HHHHHHH
Confidence 468888999999999999665432 22211 222222 2236667776643 343 3344455
Q ss_pred hHhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCccccccCCCCCh--hHHHHHHHHHHhcCce
Q 015440 280 IEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRIPSVPE--NVCDQIRLWESDLNRV 347 (406)
Q Consensus 280 l~~r~pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~hahp~m~~~~p~iP~--tV~dQIrlWe~E~~R~ 347 (406)
+..+||++.|| ++|.+.++.|++.|- ..+.+|++-..+-.| .+|- |..+=...|+.--+-+
T Consensus 60 l~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i~-------~iPG~~TptEi~~a~~~Ga~~v 132 (212)
T PRK05718 60 IAKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPIP-------LIPGVSTPSELMLGMELGLRTF 132 (212)
T ss_pred HHHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EeCCCCCHHHHHHHHHCCCCEE
Confidence 66679999999 899999999999984 455899988876544 6665 4466444888888888
Q ss_pred eeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 015440 348 EMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHMREFLRG 403 (406)
Q Consensus 348 ~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v~~f~k~ 403 (406)
++.|+-.+- =.+|-+.+...+ +.-+.+.+..=.-+++++|++.
T Consensus 133 KlFPa~~~g----------g~~~lk~l~~p~---p~~~~~ptGGV~~~ni~~~l~a 175 (212)
T PRK05718 133 KFFPAEASG----------GVKMLKALAGPF---PDVRFCPTGGISPANYRDYLAL 175 (212)
T ss_pred EEccchhcc----------CHHHHHHHhccC---CCCeEEEeCCCCHHHHHHHHhC
Confidence 886533220 145556655444 3455555444445789999874
No 9
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=77.54 E-value=17 Score=34.78 Aligned_cols=126 Identities=16% Similarity=0.260 Sum_probs=86.2
Q ss_pred ccceEEEeeCceEEeecCChhHHHHHHHHHhhHhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcC
Q 015440 249 KEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNA 318 (406)
Q Consensus 249 ~~g~iivETNfrvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~ha 318 (406)
+.|+=++|-.|+ +|-- +..+.++..++|++.|| ++|.|.+++|.+.|- .-+.++.+-+.+-
T Consensus 27 ~gGi~~iEit~~------tp~a---~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~ 97 (201)
T PRK06015 27 AGGLPAIEITLR------TPAA---LDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSD 97 (201)
T ss_pred HCCCCEEEEeCC------CccH---HHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcC
Confidence 346777887775 3332 33445566778999999 899999999999995 4678899888776
Q ss_pred CccccccCCCCCh--hHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHH
Q 015440 319 HPRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMH 396 (406)
Q Consensus 319 hp~m~~~~p~iP~--tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~ 396 (406)
.| .+|= |..+=..-|+.--+-+++.++-.+- . .+|.+.+...+ +.-+++-+..=.-++
T Consensus 98 i~-------~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n 157 (201)
T PRK06015 98 VP-------LLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKN 157 (201)
T ss_pred CC-------EeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHH
Confidence 55 6664 7788888999999999998864441 0 24555554444 334444433333477
Q ss_pred HHHHHhh
Q 015440 397 MREFLRG 403 (406)
Q Consensus 397 v~~f~k~ 403 (406)
+.+|++.
T Consensus 158 ~~~~l~a 164 (201)
T PRK06015 158 ARDYLSL 164 (201)
T ss_pred HHHHHhC
Confidence 8888764
No 10
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=65.22 E-value=11 Score=41.12 Aligned_cols=89 Identities=22% Similarity=0.353 Sum_probs=69.8
Q ss_pred ccceEEEeeCceEEeecCChhHHHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCC
Q 015440 249 KEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPS 328 (406)
Q Consensus 249 ~~g~iivETNfrvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~ 328 (406)
-+|.||+||==-+|-+- ...|--.+|..+|=-.+.-+.||-=|+..|..-|.+-+.||++|..-+-. .
T Consensus 81 ~dG~IfLEsFsp~ykqA-----~DFLiaIaEPvcRP~~iHEy~lTaySLYAAVSVGL~T~dIie~L~rlSKt-------~ 148 (776)
T KOG1123|consen 81 PDGHIFLETFSPLYKQA-----QDFLIAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLQTEDIIEVLDRLSKT-------P 148 (776)
T ss_pred CCCeEEeeecCHHHHhH-----hhhhhhhccccCChhhhhhhcchhhhhhhhhccccchHHHHHHHHHhccC-------C
Confidence 36899999742222211 14555568888888889999999999999999999999999999977643 7
Q ss_pred CChhHHHHHHHHHHhcCceee
Q 015440 329 VPENVCDQIRLWESDLNRVEM 349 (406)
Q Consensus 329 iP~tV~dQIrlWe~E~~R~~~ 349 (406)
||+.|++=|++--..-+.++.
T Consensus 149 lp~~ii~FI~~cT~sYGKVKL 169 (776)
T KOG1123|consen 149 LPESIIEFIRACTVSYGKVKL 169 (776)
T ss_pred CCHHHHHHHHHHhhccccEEE
Confidence 999999999988777666554
No 11
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=64.56 E-value=95 Score=30.15 Aligned_cols=156 Identities=14% Similarity=0.164 Sum_probs=100.0
Q ss_pred HHHHHhhhcCeeeEeeCC-CcceecchhhhhhhccCCCcccccccceEEEeeCceEEeecCChhHHHHHHHHH-hhHhcC
Q 015440 207 SMIKDFADLGLVKLQQGR-KESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFS-KIEYQL 284 (406)
Q Consensus 207 ~~L~~L~~lGLVy~~~~~-~~~fy~pT~La~~Lt~~~~~~~~~~~g~iivETNfrvYAYt~s~l~iaiL~lF~-~l~~r~ 284 (406)
.+++.|.+.|+|-.-+.. ...-. +++-.| .+.|.=++|-=|| +|--...+.... +...++
T Consensus 7 ~~~~~l~~~~vi~Vvr~~~~~~a~---~~~~al---------~~gGi~~iEiT~~------tp~a~~~i~~l~~~~~~~~ 68 (222)
T PRK07114 7 AVLTAMKATGMVPVFYHADVEVAK---KVIKAC---------YDGGARVFEFTNR------GDFAHEVFAELVKYAAKEL 68 (222)
T ss_pred HHHHHHHhCCEEEEEEcCCHHHHH---HHHHHH---------HHCCCCEEEEeCC------CCcHHHHHHHHHHHHHhhC
Confidence 567888888988665432 11111 122222 2346667776664 333333333332 444679
Q ss_pred CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCccccccCCCCCh--hHHHHHHHHHHhcCceeeccc
Q 015440 285 PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPA 352 (406)
Q Consensus 285 pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~hahp~m~~~~p~iP~--tV~dQIrlWe~E~~R~~~~~g 352 (406)
|++.|| ++|.+.++.|.+.|- .-..++++.+.+-.| .+|= |..+=..-|+.=-+-+++.++
T Consensus 69 p~~~vGaGTVl~~e~a~~a~~aGA~FiVsP~~~~~v~~~~~~~~i~-------~iPG~~TpsEi~~A~~~Ga~~vKlFPA 141 (222)
T PRK07114 69 PGMILGVGSIVDAATAALYIQLGANFIVTPLFNPDIAKVCNRRKVP-------YSPGCGSLSEIGYAEELGCEIVKLFPG 141 (222)
T ss_pred CCeEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EeCCCCCHHHHHHHHHCCCCEEEECcc
Confidence 999999 899999999999995 457889998887665 6664 777888899999999999986
Q ss_pred eeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEecccc----HHHHHHHhh
Q 015440 353 HYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIH----MHMREFLRG 403 (406)
Q Consensus 353 ~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h----~~v~~f~k~ 403 (406)
-.+. .+|-+.+...+ +.-++ +...|- +++.+|++.
T Consensus 142 ~~~G-----------~~~ikal~~p~---p~i~~--~ptGGV~~~~~n~~~yl~a 180 (222)
T PRK07114 142 SVYG-----------PGFVKAIKGPM---PWTKI--MPTGGVEPTEENLKKWFGA 180 (222)
T ss_pred cccC-----------HHHHHHHhccC---CCCeE--EeCCCCCcchhcHHHHHhC
Confidence 5431 45566655544 33333 333333 578888763
No 12
>TIGR01182 eda Entner-Doudoroff aldolase. 2-deydro-3-deoxyphosphogluconate aldolase (EC 4.1.2.14) is an enzyme of the Entner-Doudoroff pathway. This aldolase has another function, 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.3.16) shown experimentally in Escherichia coli and Pseudomonas putida
Probab=63.52 E-value=65 Score=30.89 Aligned_cols=125 Identities=15% Similarity=0.298 Sum_probs=84.8
Q ss_pred cceEEEeeCceEEeecCChhHHHHHHHHHhhHhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 015440 250 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 319 (406)
Q Consensus 250 ~g~iivETNfrvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~hah 319 (406)
.|.=++|--|+ +|--... +.++..++|++.|| ++|.+.+++|.+.|- .-..++.+.+.+--
T Consensus 32 ~Gi~~iEit~~------t~~a~~~---i~~l~~~~~~~~vGAGTVl~~~~a~~a~~aGA~FivsP~~~~~v~~~~~~~~i 102 (204)
T TIGR01182 32 GGLRVLEVTLR------TPVALDA---IRLLRKEVPDALIGAGTVLNPEQLRQAVDAGAQFIVSPGLTPELAKHAQDHGI 102 (204)
T ss_pred cCCCEEEEeCC------CccHHHH---HHHHHHHCCCCEEEEEeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 46667776663 4544443 44455578999999 899999999999994 34677777776643
Q ss_pred ccccccCCCCCh--hHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHH
Q 015440 320 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 397 (406)
Q Consensus 320 p~m~~~~p~iP~--tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v 397 (406)
|.+|= |..+=..-|+.--+-+++.++-.+-. .+|-+.+...+ +.-+++.+..=.-+++
T Consensus 103 -------~~iPG~~TptEi~~A~~~Ga~~vKlFPA~~~GG----------~~yikal~~pl---p~i~~~ptGGV~~~N~ 162 (204)
T TIGR01182 103 -------PIIPGVATPSEIMLALELGITALKLFPAEVSGG----------VKMLKALAGPF---PQVRFCPTGGINLANV 162 (204)
T ss_pred -------cEECCCCCHHHHHHHHHCCCCEEEECCchhcCC----------HHHHHHHhccC---CCCcEEecCCCCHHHH
Confidence 46664 77778889999899999988654410 35666666554 3444444434444789
Q ss_pred HHHHhh
Q 015440 398 REFLRG 403 (406)
Q Consensus 398 ~~f~k~ 403 (406)
.+|++.
T Consensus 163 ~~~l~a 168 (204)
T TIGR01182 163 RDYLAA 168 (204)
T ss_pred HHHHhC
Confidence 999874
No 13
>TIGR01615 A_thal_3542 uncharacterized plant-specific domain TIGR01615. of a number of uncharacterized plant proteins. The domain is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=62.89 E-value=3.6 Score=36.97 Aligned_cols=65 Identities=18% Similarity=0.385 Sum_probs=48.5
Q ss_pred ccceEEEeeCceEEeecCChhHHH-HHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCC
Q 015440 249 KEGFVVVETNFRMYAYSTSKLHCE-ILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIP 327 (406)
Q Consensus 249 ~~g~iivETNfrvYAYt~s~l~ia-iL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p 327 (406)
....+|||.||| +.+.|| ==.-+.++...+|.+.||...| -.||+..+-..|--.|++++-
T Consensus 47 ~~~R~iVd~dFr------~~FeiARpt~~Y~~ll~~LP~vFVG~~~r------------L~~iV~~mc~Aak~Slk~~gm 108 (131)
T TIGR01615 47 QEMRVIIDLDFR------SEFEIARPTEEYKRLLESLPEVFVGTTER------------LRQLVRLMCDAAKKSLKKKGM 108 (131)
T ss_pred CcceEEEeccch------hhceecCCCHHHHHHHHhCCcceECCHHH------------HHHHHHHHHHHHHHHHHHcCC
Confidence 345899999998 555552 1223567777899999996544 368999999888888888877
Q ss_pred CCCh
Q 015440 328 SVPE 331 (406)
Q Consensus 328 ~iP~ 331 (406)
-+||
T Consensus 109 hlPP 112 (131)
T TIGR01615 109 PLPP 112 (131)
T ss_pred CCCC
Confidence 7887
No 14
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=56.21 E-value=61 Score=22.95 Aligned_cols=54 Identities=15% Similarity=0.238 Sum_probs=41.4
Q ss_pred HHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecC-CCceeEEeCHH
Q 015440 48 VFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEK-KKETTYRLNST 103 (406)
Q Consensus 48 VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~-~~~~~~~Ln~~ 103 (406)
|+..++ ..+++..++..... -+......+++.|.+.+++.... ++...|.+++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~-is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~ 56 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG-LSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDE 56 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC-CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchH
Confidence 455666 78899999999886 44678899999999999997643 34466888883
No 15
>PF01081 Aldolase: KDPG and KHG aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related []. They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3VCR_A 1FQ0_A 1EUN_A 1EUA_B 1FWR_A 2C0A_B 1WBH_A 1WAU_A 2YW3_B 2YW4_A ....
Probab=54.91 E-value=30 Score=32.98 Aligned_cols=125 Identities=18% Similarity=0.312 Sum_probs=80.3
Q ss_pred cceEEEeeCceEEeecCChhHHHHHHHHHhhHhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCC
Q 015440 250 EGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 319 (406)
Q Consensus 250 ~g~iivETNfrvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~hah 319 (406)
.|.=++|--|| +|--. ....++..++|+|.|| ++|.|.+++|.+.|- .-++++.+-+.+-.
T Consensus 32 gGi~~iEiT~~------t~~a~---~~I~~l~~~~p~~~vGAGTV~~~e~a~~a~~aGA~FivSP~~~~~v~~~~~~~~i 102 (196)
T PF01081_consen 32 GGIRAIEITLR------TPNAL---EAIEALRKEFPDLLVGAGTVLTAEQAEAAIAAGAQFIVSPGFDPEVIEYAREYGI 102 (196)
T ss_dssp TT--EEEEETT------STTHH---HHHHHHHHHHTTSEEEEES--SHHHHHHHHHHT-SEEEESS--HHHHHHHHHHTS
T ss_pred CCCCEEEEecC------CccHH---HHHHHHHHHCCCCeeEEEeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 47778888877 33222 3344556678999999 899999999999994 46789999888876
Q ss_pred ccccccCCCCCh--hHHHHHHHHHHhcCceeeccceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHH
Q 015440 320 PRVADRIPSVPE--NVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSGLLWEDSKKMRLVVNAEIHMHM 397 (406)
Q Consensus 320 p~m~~~~p~iP~--tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~llW~~~~kr~~~V~~~~h~~v 397 (406)
| .+|= |..+=...|+.-.+-+++.++-.+- =.+|.+++...+ +.-+.+.+..=.-+++
T Consensus 103 ~-------~iPG~~TptEi~~A~~~G~~~vK~FPA~~~G----------G~~~ik~l~~p~---p~~~~~ptGGV~~~N~ 162 (196)
T PF01081_consen 103 P-------YIPGVMTPTEIMQALEAGADIVKLFPAGALG----------GPSYIKALRGPF---PDLPFMPTGGVNPDNL 162 (196)
T ss_dssp E-------EEEEESSHHHHHHHHHTT-SEEEETTTTTTT----------HHHHHHHHHTTT---TT-EEEEBSS--TTTH
T ss_pred c-------ccCCcCCHHHHHHHHHCCCCEEEEecchhcC----------cHHHHHHHhccC---CCCeEEEcCCCCHHHH
Confidence 6 6773 7777788899999999999976651 134555544332 3334444334445678
Q ss_pred HHHHhh
Q 015440 398 REFLRG 403 (406)
Q Consensus 398 ~~f~k~ 403 (406)
++|++.
T Consensus 163 ~~~l~a 168 (196)
T PF01081_consen 163 AEYLKA 168 (196)
T ss_dssp HHHHTS
T ss_pred HHHHhC
Confidence 888874
No 16
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=53.97 E-value=90 Score=27.33 Aligned_cols=70 Identities=16% Similarity=0.123 Sum_probs=54.4
Q ss_pred HHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecCC-CceeEEeCHH
Q 015440 33 CEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKK-KETTYRLNST 103 (406)
Q Consensus 33 claIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~~-~~~~~~Ln~~ 103 (406)
...+|+.|-+=.+.-|+.+|...++.+..++..=+. -++......++.|++-+++...+. ....|.+|+.
T Consensus 6 ~~~~fkaLadptRl~IL~~L~~~~~~~v~ela~~l~-lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~ 76 (117)
T PRK10141 6 PLQLFKILSDETRLGIVLLLRESGELCVCDLCTALD-QSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPH 76 (117)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCcCHHHHHHHHC-cCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECch
Confidence 357888888888888888887667888888876553 347778889999999999987543 4467889975
No 17
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=53.40 E-value=17 Score=27.88 Aligned_cols=33 Identities=21% Similarity=0.373 Sum_probs=24.6
Q ss_pred CCCHHH-HHHHHHhhhcCeeeEeeCCCcceecchh
Q 015440 200 TLSEIQ-RSMIKDFADLGLVKLQQGRKESWFIPTK 233 (406)
Q Consensus 200 ~Lt~tq-~~~L~~L~~lGLVy~~~~~~~~fy~pT~ 233 (406)
+++.++ ...|+.|.+.|||....++...|+ |++
T Consensus 33 ~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~-a~~ 66 (68)
T PF01978_consen 33 GISRSTVYRALKSLEEKGLVEREEGRPKVYR-AVP 66 (68)
T ss_dssp TSSHHHHHHHHHHHHHTTSEEEEEECCEEEE-EE-
T ss_pred CcCHHHHHHHHHHHHHCCCEEEEcCceEEEE-EeC
Confidence 345444 779999999999999887766666 543
No 18
>PRK14529 adenylate kinase; Provisional
Probab=51.05 E-value=51 Score=31.88 Aligned_cols=78 Identities=15% Similarity=0.227 Sum_probs=53.7
Q ss_pred HhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCChhHHHHHHHHHHhcCceeeccceeecCCCC
Q 015440 281 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPS 360 (406)
Q Consensus 281 ~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s 360 (406)
.+.++.+.+|.+.|+.+.. ..-.+++|-.|+.. ...+|..++-++-.+.....- ..|++++.|+-
T Consensus 23 ~~~~~~is~gdllr~~i~~---~t~lg~~i~~~i~~---------G~lvpdei~~~lv~~~l~~~~---~~g~iLDGfPR 87 (223)
T PRK14529 23 KYDLAHIESGAIFREHIGG---GTELGKKAKEYIDR---------GDLVPDDITIPMILETLKQDG---KNGWLLDGFPR 87 (223)
T ss_pred HHCCCCcccchhhhhhccC---CChHHHHHHHHHhc---------cCcchHHHHHHHHHHHHhccC---CCcEEEeCCCC
Confidence 4568999999999997743 22234556666653 348999999998888876543 77999999997
Q ss_pred H-HHHHHHHHHHHH
Q 015440 361 R-DVFEAACDYARD 373 (406)
Q Consensus 361 ~-~~f~~~~~ya~~ 373 (406)
. +..+.+-+...+
T Consensus 88 t~~Qa~~l~~~l~~ 101 (223)
T PRK14529 88 NKVQAEKLWEALQK 101 (223)
T ss_pred CHHHHHHHHHHHHh
Confidence 5 344444444333
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=49.76 E-value=77 Score=23.63 Aligned_cols=58 Identities=22% Similarity=0.300 Sum_probs=40.1
Q ss_pred HHHHHHHhc-CCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeec---C-CCceeEEeCHH
Q 015440 45 KKYVFQMLY-IDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEE---K-KKETTYRLNST 103 (406)
Q Consensus 45 k~~VmrlL~-~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~---~-~~~~~~~Ln~~ 103 (406)
+..||..+. .+.+.+.++|.....-+ +.....+|+.|...++++.. . +....|.|+|.
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLGIS-KSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 556788888 77899999999988765 55666999999999999652 1 23356778763
No 20
>PF00406 ADK: Adenylate kinase; InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction AMP + MgATP = ADP + MgADP an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells [], this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate []. ADK has also been identified in different bacterial species and in yeast []. Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase-containing compound kinase activity, 0006139 nucleobase-containing compound metabolic process; PDB: 1ZD8_A 3TLX_D 1TEV_A 1ZAK_B 3CM0_A 3ADK_A 1ZIP_A 1ZIO_A 1ZIN_A 3NDP_A ....
Probab=44.99 E-value=43 Score=29.24 Aligned_cols=74 Identities=19% Similarity=0.316 Sum_probs=49.1
Q ss_pred HhcCCceEEEEeCHHHHHHHHHcC-CCHHHHHHHHhhcCCccccccCCCCChhHHHHHHHHHHhcCceeeccceeecCCC
Q 015440 281 EYQLPNLIVGAITKESLYNAFENG-ITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFP 359 (406)
Q Consensus 281 ~~r~pnmvvg~iTreSv~~A~~~G-ITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrlWe~E~~R~~~~~g~L~~~f~ 359 (406)
.|.++.+.+|.+=|+.+ +.+ -.+++|-++|.+. ..||+.++-++-.++.+.. ....|++.+.|+
T Consensus 19 ~~~~~~is~~~llr~~~----~~~s~~g~~i~~~l~~g---------~~vp~~~v~~ll~~~l~~~--~~~~g~ildGfP 83 (151)
T PF00406_consen 19 RYGLVHISVGDLLREEI----KSDSELGKQIQEYLDNG---------ELVPDELVIELLKERLEQP--PCNRGFILDGFP 83 (151)
T ss_dssp HHTSEEEEHHHHHHHHH----HTTSHHHHHHHHHHHTT---------SS--HHHHHHHHHHHHHSG--GTTTEEEEESB-
T ss_pred hcCcceechHHHHHHHH----hhhhHHHHHHHHHHHhh---------ccchHHHHHHHHHHHHhhh--cccceeeeeecc
Confidence 35677777776655555 333 2357777787754 3799999999988888876 567899999999
Q ss_pred CH-HHHHHHHH
Q 015440 360 SR-DVFEAACD 369 (406)
Q Consensus 360 s~-~~f~~~~~ 369 (406)
.. +.++.+.+
T Consensus 84 rt~~Qa~~l~~ 94 (151)
T PF00406_consen 84 RTLEQAEALEE 94 (151)
T ss_dssp SSHHHHHHHHH
T ss_pred ccHHHHHHHHH
Confidence 85 44455444
No 21
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=44.60 E-value=18 Score=29.86 Aligned_cols=35 Identities=29% Similarity=0.370 Sum_probs=26.2
Q ss_pred CHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhh
Q 015440 202 SEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATN 237 (406)
Q Consensus 202 t~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~ 237 (406)
+-|-|+.+++|.++|||....+.+.-+- ||.-|..
T Consensus 37 ~aTIRN~M~~Le~lGlve~~p~~s~Gri-PT~~aYr 71 (78)
T PF03444_consen 37 PATIRNEMADLEELGLVESQPHPSGGRI-PTDKAYR 71 (78)
T ss_pred hHHHHHHHHHHHHCCCccCCCCCCCCCC-cCHHHHH
Confidence 6899999999999999975433334444 9987754
No 22
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=42.66 E-value=53 Score=31.11 Aligned_cols=57 Identities=16% Similarity=0.201 Sum_probs=45.1
Q ss_pred HHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeee-----cCCCceeEEeCHHHHHHH
Q 015440 48 VFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSE-----EKKKETTYRLNSTFQSNL 108 (406)
Q Consensus 48 VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~-----~~~~~~~~~Ln~~F~~~l 108 (406)
++..+...+||+.++++..-..++ ...++.|...++|.+ ..|....|.+++.|..-|
T Consensus 95 tLaiIay~qPiTr~eI~~irGv~~----~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~~~f 156 (188)
T PRK00135 95 VLAIIAYKQPITRIEIDEIRGVNS----DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFLDYF 156 (188)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCH----HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHHHHc
Confidence 577777899999999999766553 788999999999975 233456788999998744
No 23
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=41.71 E-value=2.5e+02 Score=26.90 Aligned_cols=117 Identities=16% Similarity=0.314 Sum_probs=76.4
Q ss_pred HHHHHhhhcCeeeEeeCC-CcceecchhhhhhhccCCCcccccccceEEEeeCceEEeecCChhHHHHHHHHHhhHhcC-
Q 015440 207 SMIKDFADLGLVKLQQGR-KESWFIPTKLATNLSMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQL- 284 (406)
Q Consensus 207 ~~L~~L~~lGLVy~~~~~-~~~fy~pT~La~~Lt~~~~~~~~~~~g~iivETNfrvYAYt~s~l~iaiL~lF~~l~~r~- 284 (406)
.+++.|.+.|+|-.-+.. ..... +++-.| .+.|.=++|-=|| +|--. ..+.++..++
T Consensus 5 ~~~~~l~~~~vi~vir~~~~~~a~---~~~~al---------~~~Gi~~iEit~~------~~~a~---~~i~~l~~~~~ 63 (213)
T PRK06552 5 EILTKLKANGVVAVVRGESKEEAL---KISLAV---------IKGGIKAIEVTYT------NPFAS---EVIKELVELYK 63 (213)
T ss_pred HHHHHHHHCCEEEEEECCCHHHHH---HHHHHH---------HHCCCCEEEEECC------CccHH---HHHHHHHHHcC
Confidence 357888888988665432 11111 222222 2347777887665 34333 3444555567
Q ss_pred --CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHhhcCCccccccCCCCCh--hHHHHHHHHHHhcCceeec
Q 015440 285 --PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRIPSVPE--NVCDQIRLWESDLNRVEMT 350 (406)
Q Consensus 285 --pnmvvg---~iTreSv~~A~~~GI-------TA~QIi~fL~~hahp~m~~~~p~iP~--tV~dQIrlWe~E~~R~~~~ 350 (406)
|++.|| ++|.+.+++|.+.|- .-+.++.+-+.+-.| .+|= |..+=.+.|+.--+-+++.
T Consensus 64 ~~p~~~vGaGTV~~~~~~~~a~~aGA~FivsP~~~~~v~~~~~~~~i~-------~iPG~~T~~E~~~A~~~Gad~vklF 136 (213)
T PRK06552 64 DDPEVLIGAGTVLDAVTARLAILAGAQFIVSPSFNRETAKICNLYQIP-------YLPGCMTVTEIVTALEAGSEIVKLF 136 (213)
T ss_pred CCCCeEEeeeeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EECCcCCHHHHHHHHHcCCCEEEEC
Confidence 579999 899999999999994 456788887766655 6664 5556667888888888875
Q ss_pred c
Q 015440 351 P 351 (406)
Q Consensus 351 ~ 351 (406)
+
T Consensus 137 P 137 (213)
T PRK06552 137 P 137 (213)
T ss_pred C
Confidence 5
No 24
>COG1313 PflX Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]
Probab=40.07 E-value=36 Score=34.86 Aligned_cols=52 Identities=23% Similarity=0.309 Sum_probs=40.9
Q ss_pred HHHHHHHHhhcCCccccccCCCCChhHHHHH----HHHHH-hcCceeeccceeecCCCCHHHHHHHHHHHHHcCe
Q 015440 307 AEQIISFLQQNAHPRVADRIPSVPENVCDQI----RLWES-DLNRVEMTPAHYYEEFPSRDVFEAACDYARDRSG 376 (406)
Q Consensus 307 A~QIi~fL~~hahp~m~~~~p~iP~tV~dQI----rlWe~-E~~R~~~~~g~L~~~f~s~~~f~~~~~ya~~~g~ 376 (406)
..-|++|+..|.- .-++-||++|- +-||. |-+ +..+.++|+++.+||+..|.
T Consensus 273 TkpI~~wiae~~g-------~~~~vNiM~QY~P~ykA~eypeI~-----------R~lt~eE~e~a~~~a~~~gl 329 (335)
T COG1313 273 TKPILRWIAENLG-------NDVRVNIMFQYRPEYKAEEYPEIN-----------RRLTREEYEKALEYAEKLGL 329 (335)
T ss_pred cHHHHHHHHHhCC-------CCeeEEehhhccchhhhhhchhhc-----------ccCCHHHHHHHHHHHHHcCC
Confidence 3568999988862 15778999994 57776 544 67889999999999999985
No 25
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=39.99 E-value=22 Score=36.79 Aligned_cols=45 Identities=27% Similarity=0.423 Sum_probs=33.5
Q ss_pred hhccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhh
Q 015440 192 ILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNL 238 (406)
Q Consensus 192 lG~~Ys~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~L 238 (406)
+-+-|..+--+-|-|+.+.+|.++|++++.--.++| +||.++...
T Consensus 31 L~e~~~l~~SsATIRN~Ma~LE~~GlI~k~HtSsGR--vPT~~Gyr~ 75 (346)
T COG1420 31 LSEKYNLDLSSATIRNEMADLEKLGLIEKPHTSSGR--VPTDKGYRY 75 (346)
T ss_pred HHHHhCCCCCchhHHHHHHHHHHCCCccCccccCCc--CCcHhHHHH
Confidence 444555444478999999999999999998655555 388887643
No 26
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=38.56 E-value=26 Score=34.94 Aligned_cols=45 Identities=24% Similarity=0.241 Sum_probs=35.4
Q ss_pred hhccccCCCCCHHHHHHHHHhhhcCeeeEeeCCCcceecchhhhhhh
Q 015440 192 ILEAYNLNTLSEIQRSMIKDFADLGLVKLQQGRKESWFIPTKLATNL 238 (406)
Q Consensus 192 lG~~Ys~~~Lt~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~L 238 (406)
+.+.|.++--+-|-|+.+.+|.+.|++.++-..++| +||..+...
T Consensus 28 L~~~~~l~~SsATIRn~m~~LE~~G~L~qpHtSsGR--IPT~~gyr~ 72 (260)
T PRK03911 28 LKSLMNLKISAATIRNYFKKLSDEGLLTQLHISGGR--IPTIKAMKN 72 (260)
T ss_pred HHHHcCCCCCcHHHHHHHHHHHHCcCccCCcCCCCc--CCCHHHHHH
Confidence 556666665588999999999999999998655555 499888643
No 27
>TIGR03853 matur_matur probable metal-binding protein. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulfatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulfur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulfatase/maturase systems.
Probab=38.00 E-value=44 Score=27.58 Aligned_cols=26 Identities=42% Similarity=0.714 Sum_probs=21.5
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHhhc
Q 015440 292 ITKESLYNAFE--------------NGITAEQIISFLQQN 317 (406)
Q Consensus 292 iTreSv~~A~~--------------~GITA~QIi~fL~~h 317 (406)
+||+|++.|+. .|.||+++|+||...
T Consensus 18 ~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~k 57 (77)
T TIGR03853 18 YTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLKK 57 (77)
T ss_pred cCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHHC
Confidence 47777777774 699999999999865
No 28
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=35.55 E-value=1.5e+02 Score=25.04 Aligned_cols=73 Identities=15% Similarity=0.193 Sum_probs=48.3
Q ss_pred chhhHHHHHhhcCHHHHHHhhC--ChhhHHHHHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHc
Q 015440 7 IAKNFMDMVASLTARDLNKLYE--NPFICEAILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQ 84 (406)
Q Consensus 7 ~~~~~~~yL~~Lp~~~~~~LY~--~p~tclaIfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~ 84 (406)
-..++...|...|..++-.... ++..+..||+.+|+-+...+-.-+=.-+||+.++++. .++..-+.++.|.+
T Consensus 29 ~~~~l~~ll~~v~~~~la~ALkga~~e~~~~il~nms~r~a~~l~~e~~~~g~v~~~di~~-----Aq~~iv~~~r~l~~ 103 (110)
T PF01706_consen 29 DDRDLQKLLREVDPDDLALALKGASEELREKILSNMSKRAAEMLREEMEALGPVRLSDIEE-----AQREIVEIVRRLEE 103 (110)
T ss_dssp -HHHHHHHHTTS-HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHHHH-S--HHHHHH-----HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHCCHhHHHHHHccCCHHHHHHHHHHcCHHHHHHHHHHHHhcCCCCHHHHHH-----HHHHHHHHHHHHHH
Confidence 4455666677777777766665 6889999999999999999988877678999998876 24555555555543
No 29
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=35.38 E-value=47 Score=26.65 Aligned_cols=28 Identities=25% Similarity=0.487 Sum_probs=22.1
Q ss_pred CHHHHHHHHHhhhcCeeeEeeCCCccee
Q 015440 202 SEIQRSMIKDFADLGLVKLQQGRKESWF 229 (406)
Q Consensus 202 t~tq~~~L~~L~~lGLVy~~~~~~~~fy 229 (406)
+-||-++=+||+++|+|..+..++...|
T Consensus 35 ~vTQaTiSRDLkeL~~vKv~~~~g~~~Y 62 (70)
T PF01316_consen 35 EVTQATISRDLKELGAVKVPDGNGKYRY 62 (70)
T ss_dssp T--HHHHHHHHHHHT-EEEECTTSSEEE
T ss_pred CcchhHHHHHHHHcCcEEeeCCCCCEEE
Confidence 5789999999999999999977777777
No 30
>PRK00441 argR arginine repressor; Provisional
Probab=33.54 E-value=1.1e+02 Score=27.96 Aligned_cols=28 Identities=18% Similarity=0.306 Sum_probs=23.7
Q ss_pred CHHHHHHHHHhhhcCeeeEeeCCCccee
Q 015440 202 SEIQRSMIKDFADLGLVKLQQGRKESWF 229 (406)
Q Consensus 202 t~tq~~~L~~L~~lGLVy~~~~~~~~fy 229 (406)
.-+|-++=+||+++|+|..+..++...|
T Consensus 34 ~vSqaTisRDl~~L~lvKv~~~~G~~~Y 61 (149)
T PRK00441 34 DVTQATVSRDIKELKLIKVLSNDGKYKY 61 (149)
T ss_pred CcCHHHHHHHHHHcCcEEeECCCCCEEE
Confidence 5678888899999999999877777677
No 31
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=31.38 E-value=1.5e+02 Score=24.73 Aligned_cols=57 Identities=19% Similarity=0.266 Sum_probs=43.7
Q ss_pred HHHHHHHhcC-CCCCChhHHHhhcCC----cchhHHHHHHHHHHcCceeeec--CCCceeEEeC
Q 015440 45 KKYVFQMLYI-DGAIPAKTMEEWVLP----DGFTKHKVAIDRLVQLRLFSEE--KKKETTYRLN 101 (406)
Q Consensus 45 k~~VmrlL~~-~~~vp~~~l~~Wv~~----~~~~~~~~al~~L~~L~I~~~~--~~~~~~~~Ln 101 (406)
|..|+..|.. +.+++..++..+++. -+....-++|+.|.+.+++..- .++...|.++
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 5668888875 678999999999864 3577788999999999999862 2344667665
No 32
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=29.91 E-value=2e+02 Score=22.08 Aligned_cols=46 Identities=13% Similarity=0.294 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHHcCeEeeecCC----CceEEEeccccHHHHHHHhhc
Q 015440 359 PSRDVFEAACDYARDRSGLLWEDSK----KMRLVVNAEIHMHMREFLRGQ 404 (406)
Q Consensus 359 ~s~~~f~~~~~ya~~~g~llW~~~~----kr~~~V~~~~h~~v~~f~k~~ 404 (406)
.+.+..+.+.+.....++-.|..+. .-.+.|+++....+.+++++.
T Consensus 6 ~t~~q~~~L~~L~~~~~~dfW~~~~~~~~~~dv~V~p~~~~~f~~~L~~~ 55 (74)
T PF02244_consen 6 KTEEQLELLQELEQSNELDFWKEPSSVGRPVDVMVPPEKLEEFEELLKEH 55 (74)
T ss_dssp SSHHHHHHHHHHHHHSTEEEEESSSSTTSEEEEEEEGGGHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHhcccceeeecCCCCCCCeEEEEECHHHHHHHHHHHHHC
Confidence 4577888899999999999998887 246789999999999999864
No 33
>TIGR02425 decarb_PcaC 4-carboxymuconolactone decarboxylase. Members of this family are 4-carboxymuconolactone decarboxylase, which catalyzes the third step in the catabolism of protocatechuate (and therefore the fourth step in the catabolism of para-hydroxybenzoate, of 3-hydroxybenzoate, of vanillate, etc.). Most members of this family are encoded within protocatechuate catabolism operons. This protein is sometimes found as a fusion protein with other enzymes of the pathway, as in Rhodococcus opacus, Streptomyces avermitilis, and Caulobacter crescentus.
Probab=29.81 E-value=61 Score=28.50 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=20.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcC
Q 015440 294 KESLYNAFENGITAEQIISFLQQNA 318 (406)
Q Consensus 294 reSv~~A~~~GITA~QIi~fL~~ha 318 (406)
+.-++.|+++|+|.+||..-|..-+
T Consensus 76 ~~h~~~Al~~G~T~~ei~Evl~q~~ 100 (123)
T TIGR02425 76 AMHVRATANTGVTEDDIKEVLLHVA 100 (123)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 3467899999999999999877554
No 34
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=29.72 E-value=1.2e+02 Score=25.87 Aligned_cols=45 Identities=11% Similarity=0.186 Sum_probs=32.7
Q ss_pred eCHHHHHHHH----HcCCCHHHHHHHHhhcCCccccccCCCCChhHHHHHHHHHH
Q 015440 292 ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWES 342 (406)
Q Consensus 292 iTreSv~~A~----~~GITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrlWe~ 342 (406)
++|...--|. ..|+++++.+.|+++ ++|.+ ...+...+|++.||.
T Consensus 89 ~~RS~~v~~~yl~~~~~~~~~~A~~~v~~-~R~~~-----~p~~~~~~qL~~~e~ 137 (138)
T smart00195 89 VSRSATLIIAYLMKYRNLSLNDAYDFVKD-RRPII-----SPNFGFLRQLIEYER 137 (138)
T ss_pred CchHHHHHHHHHHHHhCCCHHHHHHHHHH-HCCcc-----CCCHhHHHHHHHHhh
Confidence 5677754333 579999999999975 44543 223589999999985
No 35
>PF10678 DUF2492: Protein of unknown function (DUF2492); InterPro: IPR019620 This entry describes a family of small cytosolic proteins, about 80 amino acids in length, in which the eight invariant residues include three His residues and two Cys residues. Two pairs of these invariant residues occur in motifs HxH (where x is A or G) and CxH, both of which suggest metal-binding activity. This protein family was identified by searching with a phylogenetic profile based on an anaerobic sulphatase-maturase enzyme, which contains multiple 4Fe-4S clusters. The linkages by phylogenetic profiling and by iron-sulphur cluster-related motifs together suggest this protein may be an accessory protein to certain maturases in sulphatase/maturase systems.
Probab=29.43 E-value=74 Score=26.30 Aligned_cols=26 Identities=38% Similarity=0.661 Sum_probs=21.5
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHhhc
Q 015440 292 ITKESLYNAFE--------------NGITAEQIISFLQQN 317 (406)
Q Consensus 292 iTreSv~~A~~--------------~GITA~QIi~fL~~h 317 (406)
+|++++..|+. .|.||+++|.||...
T Consensus 20 ~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~FL~~r 59 (78)
T PF10678_consen 20 YTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDFLEER 59 (78)
T ss_pred cCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHHHHHc
Confidence 57888877774 699999999999865
No 36
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=28.40 E-value=1.2e+02 Score=27.53 Aligned_cols=18 Identities=44% Similarity=0.652 Sum_probs=14.3
Q ss_pred ccceEEEeeCceEEeecC
Q 015440 249 KEGFVVVETNFRMYAYST 266 (406)
Q Consensus 249 ~~g~iivETNfrvYAYt~ 266 (406)
..-+|+|+|||=+|.|..
T Consensus 9 ~~~~VlvDTNfl~~~~q~ 26 (136)
T COG1412 9 KPYQVLVDTNFLLYPYQF 26 (136)
T ss_pred CceEEEecchHHHHHHHc
Confidence 345699999998888765
No 37
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=27.61 E-value=2e+02 Score=22.35 Aligned_cols=60 Identities=8% Similarity=0.045 Sum_probs=44.0
Q ss_pred hhHHHHHHHHhcCCCC--CChhHHHhhcCCcchhHHHHHHHHHHcCceeeecCCCceeEEeCH
Q 015440 42 PLAKKYVFQMLYIDGA--IPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNS 102 (406)
Q Consensus 42 ~lak~~VmrlL~~~~~--vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~~~~~~~~Ln~ 102 (406)
.-.+.-|+.+|--.++ ++..+|..=+.-+ +.....+|..|.+-+.+....+.+..|.|..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~-~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLP-KKEVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 3345667777776656 9999998877665 4578899999999999976443446777653
No 38
>PF01216 Calsequestrin: Calsequestrin; InterPro: IPR001393 Calsequestrin is the principal calcium-binding protein present in the sarcoplasmic reticulum of cardiac and skeletal muscle []. It is a highly acidic protein that is able to bind over 40 calcium ions and acts as an internal calcium store in muscle. Sequence analysis has suggested that calcium is not bound in distinct pockets via EF-hand motifs, but rather via presentation of a charged protein surface. Two forms of calsequestrin have been identified. The cardiac form is present in cardiac and slow skeletal muscle and the fast skeletal form is found in fast skeletal muscle. The release of calsequestrin-bound calcium (through a a calcium release channel) triggers muscle contraction. The active protein is not highly structured, more than 50% of it adopting a random coil conformation []. When calcium binds there is a structural change whereby the alpha-helical content of the protein increases from 3 to 11% []. Both forms of calsequestrin are phosphorylated by casein kinase II, but the cardiac form is phosphorylated more rapidly and to a higher degree [].; GO: 0005509 calcium ion binding; PDB: 1SJI_B 2VAF_A 3UOM_C 1A8Y_A 3TRQ_A 3TRP_A 3US3_A.
Probab=26.48 E-value=1.4e+02 Score=31.31 Aligned_cols=86 Identities=17% Similarity=0.390 Sum_probs=52.9
Q ss_pred CCHHHHHHHHhhcCCccccccCCCCChhHHHHHHHHHHhcCceeeccceeecCCCCH---HHHHHHHHHHHHcCeEeeec
Q 015440 305 ITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSR---DVFEAACDYARDRSGLLWED 381 (406)
Q Consensus 305 ITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~---~~f~~~~~ya~~~g~llW~~ 381 (406)
.|-+.|..|++.|-.|.|+|-. |. |=...||.+.+-+.+ +-|.+=.+. +-++.+.+.|+++- .+
T Consensus 234 ~~e~e~~~fi~~h~rptlrkl~---~~---~m~e~Wedd~~g~hI---vaFaee~dpdG~efleilk~va~~nt----~n 300 (383)
T PF01216_consen 234 YTEEELVEFIEEHKRPTLRKLR---PE---DMFETWEDDIDGIHI---VAFAEEEDPDGFEFLEILKQVARDNT----DN 300 (383)
T ss_dssp --HHHHHHHHHHT-S-SEEE-----GG---GHHHHHHSSSSSEEE---EEE--TTSHHHHHHHHHHHHHHHHCT----T-
T ss_pred CCHHHHHHHHHHhchhHhhhCC---hh---hhhhhhcccCCCceE---EEEecCCCCchHHHHHHHHHHHHhcC----cC
Confidence 3667999999999999999843 33 346789987553322 223333332 55688889999876 45
Q ss_pred CCCceEEEeccccHHHHHHHhh
Q 015440 382 SKKMRLVVNAEIHMHMREFLRG 403 (406)
Q Consensus 382 ~~kr~~~V~~~~h~~v~~f~k~ 403 (406)
+.--.+-|.++.-.-+..||.+
T Consensus 301 p~LsivwIDPD~fPllv~yWE~ 322 (383)
T PF01216_consen 301 PDLSIVWIDPDDFPLLVPYWEK 322 (383)
T ss_dssp TT--EEEE-GGG-HHHHHHHHH
T ss_pred CceeEEEECCCCCchhHHHHHh
Confidence 5556667788888899999876
No 39
>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=26.44 E-value=2.4e+02 Score=27.81 Aligned_cols=77 Identities=21% Similarity=0.235 Sum_probs=49.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHhhcCCcc--------ccccCCCCChhHHHHHHHHHHhcCceeeccceeecCCCCHHHHHH
Q 015440 295 ESLYNAFENGITAEQIISFLQQNAHPR--------VADRIPSVPENVCDQIRLWESDLNRVEMTPAHYYEEFPSRDVFEA 366 (406)
Q Consensus 295 eSv~~A~~~GITA~QIi~fL~~hahp~--------m~~~~p~iP~tV~dQIrlWe~E~~R~~~~~g~L~~~f~s~~~f~~ 366 (406)
.+-+.|+.+|+|-.+||+-++. |.|+ |.=..|++---+..-|.-=. + .=.+|++.-|.+ .++.+.
T Consensus 67 ~~n~~aL~ng~tl~~i~emvk~-ar~~gvt~PIiLmgYYNPIl~yG~e~~iq~ak-~----aGanGfiivDlP-pEEa~~ 139 (268)
T KOG4175|consen 67 AANRRALLNGTTLNSIIEMVKE-ARPQGVTCPIILMGYYNPILRYGVENYIQVAK-N----AGANGFIIVDLP-PEEAET 139 (268)
T ss_pred hhHHHHHHcCCcHHHHHHHHHH-hcccCcccceeeeecccHHHhhhHHHHHHHHH-h----cCCCceEeccCC-hHHHHH
Confidence 3557899999999999999874 4454 21223444333333333111 1 124677776655 688999
Q ss_pred HHHHHHHcCeEe
Q 015440 367 ACDYARDRSGLL 378 (406)
Q Consensus 367 ~~~ya~~~g~ll 378 (406)
++++|++.|+-+
T Consensus 140 ~Rne~~k~gisl 151 (268)
T KOG4175|consen 140 LRNEARKHGISL 151 (268)
T ss_pred HHHHHHhcCceE
Confidence 999999999743
No 40
>PF04720 DUF506: Protein of unknown function (DUF506) ; InterPro: IPR006502 This family of uncharacterised plant proteins are defined by a region found toward the C terminus. This region is strongly conserved (greater than 30 % sequence identity between most pairs of members) but flanked by highly divergent regions including stretches of low-complexity sequence.
Probab=25.88 E-value=31 Score=33.52 Aligned_cols=109 Identities=22% Similarity=0.354 Sum_probs=64.2
Q ss_pred CHHHHHHHHHhhhcCee-eEeeCC---Ccceecchhhhhhh-ccCCCcccccccceEEEeeCceEEeecCChhHHH-HHH
Q 015440 202 SEIQRSMIKDFADLGLV-KLQQGR---KESWFIPTKLATNL-SMSLTDSSARKEGFVVVETNFRMYAYSTSKLHCE-ILR 275 (406)
Q Consensus 202 t~tq~~~L~~L~~lGLV-y~~~~~---~~~fy~pT~La~~L-t~~~~~~~~~~~g~iivETNfrvYAYt~s~l~ia-iL~ 275 (406)
+-..+.+...|+..|.- -..|.+ +.. + |. .--.. .--..+........+|||+||| +.+.|| -=.
T Consensus 87 ~~~rr~v~~~Lr~~GydAaiCkS~W~~s~~-~-p~-g~yeyIdV~~~~~~~~~~~r~IVd~~fr------~~FeiArpt~ 157 (218)
T PF04720_consen 87 SCLRRSVMSRLRALGYDAAICKSRWESSGG-I-PA-GEYEYIDVIVSGSSSGKSERYIVDPDFR------SQFEIARPTP 157 (218)
T ss_pred HHHHHHHHHHHHhCCCCEEEEEecCCCCCC-C-CC-cceeEEEEEECCCCCCcceeEEEecchH------hCeeecCCCH
Confidence 44568899999999975 233322 111 1 10 00000 0000001123456799999998 444331 123
Q ss_pred HHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCCh
Q 015440 276 LFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPE 331 (406)
Q Consensus 276 lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP~ 331 (406)
-+..+...+|...||... -+ .||++.+-.-+.-.|+++.--|||
T Consensus 158 ~Y~~ll~~lP~vfVG~~~--~L----------~~iV~~~c~a~k~s~k~~g~~lPP 201 (218)
T PF04720_consen 158 EYAALLAALPEVFVGTPE--RL----------KQIVRLMCDAAKRSFKERGMHLPP 201 (218)
T ss_pred HHHHHHHhCCCceEcCHH--HH----------HHHHHHHHHHHHHHHHHCCCCCCC
Confidence 456677789999999443 33 478888888887778887777888
No 41
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=24.70 E-value=2.1e+02 Score=23.14 Aligned_cols=55 Identities=11% Similarity=0.189 Sum_probs=41.9
Q ss_pred HHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeec--CC--CceeEEeCHH
Q 015440 48 VFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEE--KK--KETTYRLNST 103 (406)
Q Consensus 48 VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~--~~--~~~~~~Ln~~ 103 (406)
|++-|+. +|..-+++...+..-+.+...+.++.|.+.+++... +. ....|.|++.
T Consensus 10 IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~ 68 (90)
T PF01638_consen 10 ILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEK 68 (90)
T ss_dssp HHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HH
T ss_pred HHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcC
Confidence 5555555 788889999999888899999999999999999752 21 2367999885
No 42
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=23.98 E-value=1.2e+02 Score=22.65 Aligned_cols=55 Identities=15% Similarity=0.238 Sum_probs=40.7
Q ss_pred HHhcCChhHHHHHHHHhcCCCCCChhHHHhhcCCcchhHHHHHHHHHHcCceeeec
Q 015440 36 ILRSLPPLAKKYVFQMLYIDGAIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEE 91 (406)
Q Consensus 36 IfR~LP~lak~~VmrlL~~~~~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~ 91 (406)
||+.|-.=.+.=|+++|..+.|.+..++..=+.-+ .......++.|.+.+++...
T Consensus 3 i~~aL~~p~R~~Il~~L~~~~~~t~~ela~~l~~~-~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 3 IFKALSDPTRLRILRLLASNGPMTVSELAEELGIS-QSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHHTSHHHHHHHHHHHHCSTBEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHhCCHHHHHHHHHHhcCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeEEe
Confidence 45555555566677777778899999998877543 55677889999999999764
No 43
>COG1438 ArgR Arginine repressor [Transcription]
Probab=23.50 E-value=52 Score=30.29 Aligned_cols=28 Identities=25% Similarity=0.469 Sum_probs=24.3
Q ss_pred CHHHHHHHHHhhhcCeeeEeeCCCccee
Q 015440 202 SEIQRSMIKDFADLGLVKLQQGRKESWF 229 (406)
Q Consensus 202 t~tq~~~L~~L~~lGLVy~~~~~~~~fy 229 (406)
.=||-++=+||+++|+|..+..++.++|
T Consensus 36 ~vTQaTvSRDlkelglvKv~~~~g~~~Y 63 (150)
T COG1438 36 EVTQATVSRDLKELGLVKVRNEKGTYVY 63 (150)
T ss_pred eEehHHHHHHHHHcCCEEecCCCCcEEE
Confidence 4578889999999999999987777778
No 44
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=23.43 E-value=1.8e+02 Score=22.59 Aligned_cols=37 Identities=14% Similarity=0.272 Sum_probs=26.7
Q ss_pred EEeecCChhHH-HHHHHHHhhHhcCC-ceEEEEeCHHHH
Q 015440 261 MYAYSTSKLHC-EILRLFSKIEYQLP-NLIVGAITKESL 297 (406)
Q Consensus 261 vYAYt~s~l~i-aiL~lF~~l~~r~p-nmvvg~iTreSv 297 (406)
||-|++.--++ ++...|.++...++ ++..+.+.-+.-
T Consensus 22 v~f~~~~C~~C~~~~~~~~~~~~~~~~~v~~~~vd~~~~ 60 (103)
T PF00085_consen 22 VYFYAPWCPPCKAFKPILEKLAKEYKDNVKFAKVDCDEN 60 (103)
T ss_dssp EEEESTTSHHHHHHHHHHHHHHHHTTTTSEEEEEETTTS
T ss_pred EEEeCCCCCccccccceecccccccccccccchhhhhcc
Confidence 34566666666 67778888888888 888888776543
No 45
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=23.18 E-value=1.1e+02 Score=29.99 Aligned_cols=129 Identities=16% Similarity=0.197 Sum_probs=84.7
Q ss_pred hhHHHHHHhcCCcccc------hhhhccchhhhhccccCCCCCHHH-HHHHHHhhhcCeeeEeeCCCcceecchhhhhhh
Q 015440 166 SSMMKVFQRGLLIQSI------LRSLKFLCQGILEAYNLNTLSEIQ-RSMIKDFADLGLVKLQQGRKESWFIPTKLATNL 238 (406)
Q Consensus 166 ~~v~~lL~~~gLm~~~------lf~Ls~l~~~lG~~Ys~~~Lt~tq-~~~L~~L~~lGLVy~~~~~~~~fy~pT~La~~L 238 (406)
..+.+.|+.-||.+.+ |.++|-++ ........+.+-++ =++|+.|.+-|+|....+++.+|. +.+...-+
T Consensus 3 ~~~~~~L~~lGlt~yEa~vY~aLl~~g~~t--A~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~-av~p~~~i 79 (247)
T COG1378 3 EELEENLQKLGLTEYEAKVYLALLCLGEAT--AKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYR-AVPPEELI 79 (247)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHhCCcc--HHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEE-eCCHHHHH
Confidence 4678889999998866 67888888 66677777777665 579999999999999888888887 65555422
Q ss_pred cc-------CCC---------cc--cccccceEEEeeCceEEeecCChhHHHHHHHHHhhHhcCCceEEEEeC-------
Q 015440 239 SM-------SLT---------DS--SARKEGFVVVETNFRMYAYSTSKLHCEILRLFSKIEYQLPNLIVGAIT------- 293 (406)
Q Consensus 239 t~-------~~~---------~~--~~~~~g~iivETNfrvYAYt~s~l~iaiL~lF~~l~~r~pnmvvg~iT------- 293 (406)
.- ... .. ......++. +..+ .-.+.+.+.++....-+.++..++
T Consensus 80 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---------~i~g--~~~i~~~~~e~i~~a~~ei~~~~~~e~~~~l 148 (247)
T COG1378 80 ERIKEELQELLRELESELEELERELARRESPYLW---------LIKG--SEEIIEKIKEVINEAEKEIIIVLPYEIFKEL 148 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhccccccCccee---------ccCC--HHHHHHHHHHHHHhhhcEEEEEeCHHHHHHh
Confidence 10 000 00 011111111 1111 236778888888888888888888
Q ss_pred HHHHHHHHHcCCCHH
Q 015440 294 KESLYNAFENGITAE 308 (406)
Q Consensus 294 reSv~~A~~~GITA~ 308 (406)
++.+..|++.|++-.
T Consensus 149 ~~~l~~~~~rgv~v~ 163 (247)
T COG1378 149 KEPLIRALKRGVRVL 163 (247)
T ss_pred HHHHHHHHHccCeEE
Confidence 455666677776543
No 46
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=23.11 E-value=74 Score=29.02 Aligned_cols=30 Identities=17% Similarity=0.328 Sum_probs=23.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCcccc
Q 015440 294 KESLYNAFENGITAEQIISFLQQNAHPRVA 323 (406)
Q Consensus 294 reSv~~A~~~GITA~QIi~fL~~hahp~m~ 323 (406)
|+-|++-+..|-|.+||++|+.++-=+...
T Consensus 63 R~~I~~~l~~G~s~~eI~~~~v~rYG~~Vl 92 (148)
T PF03918_consen 63 RREIREMLAEGKSDEEIIDYFVERYGEFVL 92 (148)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHHHHTTT-E
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCccee
Confidence 778999999999999999999987655544
No 47
>PF09713 A_thal_3526: Plant protein 1589 of unknown function (A_thal_3526); InterPro: IPR006476 This plant-specific family of proteins are defined by an uncharacterised region 57 residues in length. It is found toward the N terminus of most proteins that contain it. Examples include at least several proteins from Arabidopsis thaliana (Mouse-ear cress) and Oryza sativa (Rice). The function of the proteins are unknown.
Probab=23.11 E-value=1.2e+02 Score=23.48 Aligned_cols=24 Identities=17% Similarity=0.225 Sum_probs=21.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHhhcC
Q 015440 295 ESLYNAFENGITAEQIISFLQQNA 318 (406)
Q Consensus 295 eSv~~A~~~GITA~QIi~fL~~ha 318 (406)
.-|.+.+....|-++++..|..||
T Consensus 3 ~lIErCl~~yMsk~E~v~~L~~~a 26 (54)
T PF09713_consen 3 NLIERCLQLYMSKEECVRALQKQA 26 (54)
T ss_pred hHHHHHHHHcCCHHHHHHHHHHHc
Confidence 346789999999999999999997
No 48
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=22.98 E-value=1.5e+02 Score=26.57 Aligned_cols=34 Identities=24% Similarity=0.399 Sum_probs=27.0
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCccccccCC
Q 015440 294 KESLYNAFENGITAEQIISFLQQNAHPRVADRIP 327 (406)
Q Consensus 294 reSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p 327 (406)
|+-|++-+..|-|-+||++|+...-=....-++|
T Consensus 63 R~~Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~Pp 96 (126)
T TIGR03147 63 RHEVYSMVNEGKSNQQIIDFMTARFGDFVLYNPP 96 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCC
Confidence 7789999999999999999999876554443333
No 49
>PRK12928 lipoyl synthase; Provisional
Probab=22.81 E-value=7.8e+02 Score=24.64 Aligned_cols=34 Identities=21% Similarity=0.203 Sum_probs=20.0
Q ss_pred hhhccchhhhhccccCCCCCHHHHHHHHHhhhcCee
Q 015440 183 RSLKFLCQGILEAYNLNTLSEIQRSMIKDFADLGLV 218 (406)
Q Consensus 183 f~Ls~l~~~lG~~Ys~~~Lt~tq~~~L~~L~~lGLV 218 (406)
..++||....|+.|+.+ .+.-.+..+.+.+.|+=
T Consensus 72 ~~C~FCa~~~g~~~~~~--~eei~~~a~~~~~~G~k 105 (290)
T PRK12928 72 RRCAFCQVDKGRPMPLD--PDEPERVAEAVAALGLR 105 (290)
T ss_pred CcCCCCCccCCCCCCCC--HHHHHHHHHHHHHCCCC
Confidence 45666653345655542 23446677788888863
No 50
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=22.33 E-value=3.5e+02 Score=21.49 Aligned_cols=59 Identities=14% Similarity=0.195 Sum_probs=40.2
Q ss_pred HHHHHHHHhcCCC--CCChhHHHhhcCCcchhHHHHHHHHHHcCceeeecCCCceeEEeCHH
Q 015440 44 AKKYVFQMLYIDG--AIPAKTMEEWVLPDGFTKHKVAIDRLVQLRLFSEEKKKETTYRLNST 103 (406)
Q Consensus 44 ak~~VmrlL~~~~--~vp~~~l~~Wv~~~~~~~~~~al~~L~~L~I~~~~~~~~~~~~Ln~~ 103 (406)
|-++++.|-..+. |++..++.....-+ .......++.|.+-+++...+|...+|.|+..
T Consensus 10 Al~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~ 70 (83)
T PF02082_consen 10 ALRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQKLKKAGLIESSRGRGGGYRLARP 70 (83)
T ss_dssp HHHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-
T ss_pred HHHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHHHHhhCCeeEecCCCCCceeecCC
Confidence 3344444443332 58899999877744 77788899999999999876655577877654
No 51
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=21.20 E-value=97 Score=29.14 Aligned_cols=31 Identities=19% Similarity=0.328 Sum_probs=23.2
Q ss_pred CCCCHHH-HHHHHHhhhcCeeeEee-CCCccee
Q 015440 199 NTLSEIQ-RSMIKDFADLGLVKLQQ-GRKESWF 229 (406)
Q Consensus 199 ~~Lt~tq-~~~L~~L~~lGLVy~~~-~~~~~fy 229 (406)
.++|+++ +..|..|.|.|||..+. .+.++|-
T Consensus 81 ~G~s~~tlrR~l~~LveaGLI~rrDS~NgkRy~ 113 (177)
T PF03428_consen 81 NGMSERTLRRHLARLVEAGLIVRRDSPNGKRYA 113 (177)
T ss_pred cCCCHHHHHHHHHHHHHCCCeeeccCCCCCccC
Confidence 4666666 77999999999998764 4555554
No 52
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=21.08 E-value=1.2e+02 Score=24.25 Aligned_cols=31 Identities=19% Similarity=0.408 Sum_probs=22.8
Q ss_pred hhccccCCCCCHHH-HHHHHHhhhcCeeeEee
Q 015440 192 ILEAYNLNTLSEIQ-RSMIKDFADLGLVKLQQ 222 (406)
Q Consensus 192 lG~~Ys~~~Lt~tq-~~~L~~L~~lGLVy~~~ 222 (406)
+.+.+..+.+|.++ .++|.+|..+|+|-..+
T Consensus 28 lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 28 LCESLGVDPLSYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 55677888899888 77999999999998776
No 53
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=20.98 E-value=1.8e+02 Score=26.16 Aligned_cols=34 Identities=18% Similarity=0.340 Sum_probs=26.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCCccccccCC
Q 015440 294 KESLYNAFENGITAEQIISFLQQNAHPRVADRIP 327 (406)
Q Consensus 294 reSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p 327 (406)
|.-|++-+..|-|-+||++|+...-=....-++|
T Consensus 63 R~~Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp 96 (126)
T PRK10144 63 RHQVYSMVAEGKSEVEIIGWMTERYGDFVRYNPP 96 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeEEecCC
Confidence 7789999999999999999999876544443333
No 54
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=20.61 E-value=65 Score=29.90 Aligned_cols=79 Identities=15% Similarity=0.271 Sum_probs=53.9
Q ss_pred hcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCChhHHHHHH-HHHHhcCceeeccceeecCCCC
Q 015440 282 YQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIR-LWESDLNRVEMTPAHYYEEFPS 360 (406)
Q Consensus 282 ~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIr-lWe~E~~R~~~~~g~L~~~f~s 360 (406)
+.+|++..|-+=|+.+.++-..|..+.+ |+... -.+|..++.++- -|=.+.+ ...|++|..|+-
T Consensus 24 ~~i~hlstgd~~r~~~~~~t~lg~~~k~---~i~~g---------~lv~d~i~~~~v~~rl~~~d---~~~~~I~dg~PR 88 (178)
T COG0563 24 LGLPHLDTGDILRAAIAERTELGEEIKK---YIDKG---------ELVPDEIVNGLVKERLDEAD---CKAGFILDGFPR 88 (178)
T ss_pred hCCcEEcHhHHhHhhhccCChHHHHHHH---HHHcC---------CccchHHHHHHHHHHHHhhc---ccCeEEEeCCCC
Confidence 6789999998888887777666665555 54433 289999986644 4443331 112899999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 015440 361 R-DVFEAACDYARDRS 375 (406)
Q Consensus 361 ~-~~f~~~~~ya~~~g 375 (406)
. ..++.+.++-.+.|
T Consensus 89 ~~~qa~~l~r~l~~~g 104 (178)
T COG0563 89 TLCQARALKRLLKELG 104 (178)
T ss_pred cHHHHHHHHHHHHHcC
Confidence 6 66677777766655
No 55
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=20.41 E-value=1.7e+02 Score=24.39 Aligned_cols=53 Identities=19% Similarity=0.111 Sum_probs=34.4
Q ss_pred HHHHHHHHhhHhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCCccccccCCCCChhHHHHHHH
Q 015440 271 CEILRLFSKIEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRIPSVPENVCDQIRL 339 (406)
Q Consensus 271 iaiL~lF~~l~~r~pnmvvg~iTreSv~~A~~~GITA~QIi~fL~~hahp~m~~~~p~iP~tV~dQIrl 339 (406)
-+.+.-++++.. -||++|++++.||+=|+.---+.-....+.....+.|||-.
T Consensus 37 ~~~~~ai~rliS----------------~~Lr~G~~~~~ii~~L~gi~~~~~~~~~~~~~~S~~D~Ia~ 89 (95)
T PF12637_consen 37 SGNLEAIARLIS----------------LALRSGVPPEEIIDQLRGIRCGPSGTVGGSRVTSCPDAIAK 89 (95)
T ss_pred hHHHHHHHHHHH----------------HHHHcCCCHHHHHHHhcCCCCCCCCccCCCccCcHHHHHHH
Confidence 466667777766 79999999999999998654332111112333357777653
No 56
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=20.16 E-value=1.2e+02 Score=25.79 Aligned_cols=30 Identities=7% Similarity=0.265 Sum_probs=22.7
Q ss_pred HHHHHHHHHhhhcCeeeEeeCCCcceecch
Q 015440 203 EIQRSMIKDFADLGLVKLQQGRKESWFIPT 232 (406)
Q Consensus 203 ~tq~~~L~~L~~lGLVy~~~~~~~~fy~pT 232 (406)
.|-+.+|..|.+-|+|...+....++|.|+
T Consensus 36 sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~ 65 (115)
T PF03965_consen 36 STVQTLLNRLVEKGFLTREKIGRAYVYSPL 65 (115)
T ss_dssp HHHHHHHHHHHHTTSEEEEEETTCEEEEES
T ss_pred hHHHHHHHHHHhCCceeEeecCCceEEEeC
Confidence 667899999999999988865445555343
Done!