Query 013058
Match_columns 450
No_of_seqs 136 out of 210
Neff 5.4
Searched_HMMs 46136
Date Thu Mar 28 23:58:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013058.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013058hhsearch_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 3E-147 7E-152 1140.4 50.0 433 10-450 1-448 (448)
2 KOG3471 RNA polymerase II tran 100.0 1E-147 2E-152 1113.8 39.7 442 1-450 5-463 (465)
3 COG5144 TFB2 RNA polymerase II 100.0 3E-127 7E-132 940.0 30.7 430 8-449 7-445 (447)
4 PF03849 Tfb2: Transcription f 100.0 6E-116 1E-120 898.3 38.3 346 13-364 1-366 (366)
5 PF13625 Helicase_C_3: Helicas 99.6 5.9E-15 1.3E-19 131.0 12.2 117 297-421 2-120 (129)
6 TIGR00603 rad25 DNA repair hel 97.1 0.0046 1E-07 69.7 12.2 106 294-414 22-132 (732)
7 PF08671 SinI: Anti-repressor 90.7 0.24 5.3E-06 33.8 2.5 22 340-361 8-29 (30)
8 PRK05718 keto-hydroxyglutarate 81.5 38 0.00082 33.0 13.2 162 245-447 1-175 (212)
9 PRK06015 keto-hydroxyglutarate 76.9 17 0.00037 35.2 9.1 125 294-447 28-164 (201)
10 TIGR01615 A_thal_3542 uncharac 66.3 3.4 7.3E-05 37.5 1.6 65 293-375 47-112 (131)
11 KOG1123 RNA polymerase II tran 65.4 12 0.00025 41.4 5.6 89 293-393 81-169 (776)
12 TIGR01182 eda Entner-Doudoroff 63.1 62 0.0014 31.4 9.7 125 294-447 32-168 (204)
13 PF08356 EF_assoc_2: EF hand a 60.8 12 0.00026 31.8 3.8 26 185-210 27-57 (89)
14 PRK07114 keto-hydroxyglutarate 60.2 1.2E+02 0.0026 29.8 11.3 156 251-447 7-180 (222)
15 PRK10141 DNA-binding transcrip 57.8 79 0.0017 28.0 8.6 70 33-103 6-76 (117)
16 PF01081 Aldolase: KDPG and KH 55.6 26 0.00057 33.8 5.7 125 294-447 32-168 (196)
17 PRK14529 adenylate kinase; Pro 53.6 67 0.0015 31.5 8.3 81 324-419 22-103 (223)
18 PF14947 HTH_45: Winged helix- 51.8 7.3 0.00016 31.6 1.1 30 167-196 38-67 (77)
19 smart00418 HTH_ARSR helix_turn 50.9 83 0.0018 22.6 6.7 54 48-103 2-56 (66)
20 PF00406 ADK: Adenylate kinase 46.2 33 0.00072 30.5 4.5 81 325-419 19-100 (151)
21 PF13463 HTH_27: Winged helix 45.7 93 0.002 23.5 6.4 57 45-102 5-66 (68)
22 COG1420 HrcA Transcriptional r 43.7 18 0.00039 37.9 2.7 62 203-280 12-73 (346)
23 PF03428 RP-C: Replication pro 43.0 90 0.002 29.7 7.1 73 201-273 23-113 (177)
24 TIGR03853 matur_matur probable 42.7 33 0.00073 28.5 3.5 27 336-362 18-58 (77)
25 COG3432 Predicted transcriptio 40.9 20 0.00043 30.9 2.1 31 165-195 48-82 (95)
26 PF01978 TrmB: Sugar-specific 40.7 20 0.00043 27.8 1.9 33 244-277 33-66 (68)
27 PRK06552 keto-hydroxyglutarate 40.7 2.5E+02 0.0053 27.3 9.9 116 252-395 6-137 (213)
28 PF10711 DUF2513: Hypothetical 40.4 23 0.0005 30.3 2.4 42 169-210 41-92 (102)
29 PF06969 HemN_C: HemN C-termin 39.5 16 0.00034 28.1 1.2 27 166-192 39-65 (66)
30 PF09639 YjcQ: YjcQ protein; 37.0 20 0.00043 30.0 1.5 45 143-197 25-69 (88)
31 PRK00135 scpB segregation and 36.8 70 0.0015 30.6 5.3 57 48-108 95-156 (188)
32 PRK13824 replication initiatio 36.2 1.4E+02 0.0031 32.0 8.0 70 202-272 36-124 (404)
33 PF02244 Propep_M14: Carboxype 36.0 1.2E+02 0.0026 23.6 5.9 46 403-448 6-55 (74)
34 PF03444 HrcA_DNA-bdg: Winged 35.8 37 0.00081 28.2 2.9 34 246-280 37-70 (78)
35 PF01706 FliG_C: FliG C-termin 34.4 1.4E+02 0.003 25.7 6.3 73 7-84 29-103 (110)
36 PF10678 DUF2492: Protein of u 33.5 57 0.0012 27.2 3.6 28 335-362 19-60 (78)
37 TIGR02010 IscR iron-sulfur clu 32.5 43 0.00094 29.7 3.0 53 224-277 10-69 (135)
38 cd07153 Fur_like Ferric uptake 31.0 1.4E+02 0.003 25.2 5.8 57 45-101 3-66 (116)
39 TIGR02425 decarb_PcaC 4-carbox 30.9 56 0.0012 29.1 3.4 25 338-362 76-100 (123)
40 COG1313 PflX Uncharacterized F 30.5 63 0.0014 33.5 4.0 51 352-420 274-329 (335)
41 PF01726 LexA_DNA_bind: LexA D 30.2 55 0.0012 25.9 2.9 57 196-268 4-62 (65)
42 KOG4175 Tryptophan synthase al 29.4 1.9E+02 0.0041 28.6 6.9 77 339-422 67-151 (268)
43 PRK09333 30S ribosomal protein 28.7 45 0.00097 31.1 2.5 34 163-196 96-129 (150)
44 PF04720 DUF506: Protein of un 28.4 28 0.00062 34.2 1.2 66 292-375 135-201 (218)
45 smart00195 DSPc Dual specifici 27.2 1.4E+02 0.0029 25.9 5.2 52 329-386 80-137 (138)
46 PRK03911 heat-inducible transc 26.6 42 0.00092 33.8 2.0 61 204-280 10-70 (260)
47 smart00550 Zalpha Z-DNA-bindin 26.4 2.2E+02 0.0048 22.4 5.8 59 42-101 5-65 (68)
48 PF12840 HTH_20: Helix-turn-he 25.8 1.1E+02 0.0023 23.3 3.8 55 36-91 3-57 (61)
49 COG2238 RPS19A Ribosomal prote 25.4 47 0.001 30.7 1.9 34 162-195 95-128 (147)
50 PF09713 A_thal_3526: Plant pr 24.7 1E+02 0.0022 23.9 3.4 31 340-379 4-34 (54)
51 PF14338 Mrr_N: Mrr N-terminal 24.4 65 0.0014 26.7 2.5 31 168-198 60-91 (92)
52 COG1497 Predicted transcriptio 24.1 35 0.00075 34.3 0.9 38 162-200 40-78 (260)
53 PF03918 CcmH: Cytochrome C bi 23.9 69 0.0015 29.5 2.8 30 338-367 63-92 (148)
54 PF01316 Arg_repressor: Argini 23.3 94 0.002 25.2 3.1 28 246-273 35-62 (70)
55 TIGR03147 cyt_nit_nrfF cytochr 22.2 1.5E+02 0.0033 26.8 4.6 34 338-371 63-96 (126)
56 PLN02459 probable adenylate ki 21.7 1.7E+02 0.0037 29.5 5.3 69 325-405 52-120 (261)
57 PF13833 EF-hand_8: EF-hand do 21.6 1E+02 0.0022 22.4 2.8 20 334-353 3-26 (54)
58 smart00529 HTH_DTXR Helix-turn 21.3 3.8E+02 0.0082 21.6 6.6 62 166-232 17-80 (96)
59 PF00085 Thioredoxin: Thioredo 20.8 2.1E+02 0.0046 22.6 4.9 37 305-341 22-60 (103)
60 PRK12928 lipoyl synthase; Prov 20.8 8.9E+02 0.019 24.5 10.7 21 339-359 175-195 (290)
61 PF12637 TSCPD: TSCPD domain; 20.6 1.6E+02 0.0035 24.9 4.2 54 315-384 37-90 (95)
62 PF07801 DUF1647: Protein of u 20.5 4.4E+02 0.0095 24.3 7.2 104 235-380 24-131 (142)
63 PRK10144 formate-dependent nit 20.5 1.8E+02 0.0038 26.4 4.6 34 338-371 63-96 (126)
64 PRK13808 adenylate kinase; Pro 20.0 2.5E+02 0.0054 29.4 6.2 77 325-416 23-101 (333)
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=3.4e-147 Score=1140.35 Aligned_cols=433 Identities=33% Similarity=0.611 Sum_probs=411.6
Q ss_pred hHHHHHhcCCHHHHHHhhcChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceee
Q 013058 10 NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFS 89 (450)
Q Consensus 10 ~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~ 89 (450)
+++|||++||+.++++||++||||+||||+||||||+|||||||+++|||.++++.|+++++++++++|+++|.+||||+
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 57899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ec-CCCceeEEeCHHHHHHHHHHHhcCCC-----CCCCCCCCCCCCCCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCC
Q 013058 90 EE-KKKETTYRLNSTFQSNLRKHLIYGGA-----LPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTN 163 (450)
Q Consensus 90 ~~-~~~~~~~~Ln~~F~~~lr~aL~ggg~-----~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~ 163 (450)
+. .+|.+.|.|||+||+|||.||+|||+ +|+..++++ .+++++||+||++|||+|||||||++.. ..
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 33557899999999999999999997 677777776 8999999999999999999999998754 57
Q ss_pred CChhHHHHHHhCCCccCC--CCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCcccc
Q 013058 164 FSSSMMKVFQRGLLSRRD--KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYN 241 (450)
Q Consensus 164 ~s~~v~~lL~~~gL~~~~--~~~~~IT~~GfqFLL~d~~~Q~W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y~ 241 (450)
+|++|+++|+++|||+.+ ++.+.||++||||||+|+|+|+|+||++||+++|++|+|++|+|+|||+||++++|++|+
T Consensus 154 ~s~~v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~lG~~Y~ 233 (448)
T TIGR00625 154 PSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLTLGKAYS 233 (448)
T ss_pred CchHHHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCccC
Confidence 899999999999999973 335899999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhhhhcccCCC----cc--ccccceEEEeeCceEEeecCChhHH
Q 013058 242 LNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD----SS--ARKEGFIVVETNFRMYAYSTSKLHC 315 (450)
Q Consensus 242 ~~~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~~L~~~~~~----~~--~~~~g~IIvETNFrvYAYT~S~lqi 315 (450)
+++||++|++||+||+|+||||++++++++|| |||||++|+++.++ ++ +.++|||||||||||||||+|||||
T Consensus 234 ~~~Lt~tq~~~L~dL~dlGLVy~~~~~~~~fY-PTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~ 312 (448)
T TIGR00625 234 VDGLSDTQLIMLQDLREYGLVFQRKRKSRRFY-PTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQI 312 (448)
T ss_pred CCCCCHHHHHHHHHHHHcCeEEEecCCCCccc-chHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHH
Confidence 99999999999999999999999999999999 99999999886542 11 2567999999999999999999999
Q ss_pred HHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCcccc-ccCCCCChhHHHHHHHHHHhcCceeee
Q 013058 316 EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRMPSVPENVCDQIRLWESDLNRVEMT 394 (450)
Q Consensus 316 aiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~-~~~~~lP~tV~dQIrLWe~Er~R~~~~ 394 (450)
+||++||++.|||||||||+||||||++|+++||||||||+||++||||+|+ ++.|+|||||+|||||||.||||++++
T Consensus 313 ~il~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~ 392 (448)
T TIGR00625 313 ALIALFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFT 392 (448)
T ss_pred HHHHHHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEee
Confidence 9999999999999999999999999999999999999999999999999998 478999999999999999999999999
Q ss_pred cceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 013058 395 PAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 450 (450)
Q Consensus 395 ~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~vr~f~k~~~~ 450 (450)
+||||++|+|++||+++++||+++|||+|+|+.||+|||+.+||++||+|||++|+
T Consensus 393 ~~~l~~~f~s~~~y~~~~~ya~~~~~l~w~~~~kr~~~V~~~gh~~v~~f~k~~~~ 448 (448)
T TIGR00625 393 EGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFWKRQKH 448 (448)
T ss_pred cceeeeecCCHHHHHHHHHHHHHcCEEEEecCCceEEEEeccchHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999999999999999999999986
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=1e-147 Score=1113.84 Aligned_cols=442 Identities=37% Similarity=0.640 Sum_probs=418.5
Q ss_pred CCchhcchhhHHHHHhcCCH--HHHHHhhcChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHH
Q 013058 1 MPLVKIIAKNFMDMVASLTA--RDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVA 78 (450)
Q Consensus 1 m~~~~~~~~~~~~yL~~Lp~--~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~a 78 (450)
||+....++++.+||+.||. .+++|||++|++|+||||+|||+||+|||+|||.++|||.++++.|++.++.+++++|
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 35555688999999999999 5899999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCceeeecCCCceeEEeCHHHHHHHHHHHhcCCC-----CCCCCCCCCCCCCCCChhHHHHHHhhhHHHHHHHHh
Q 013058 79 IDRLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYGGA-----LPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLI 153 (450)
Q Consensus 79 l~~L~~L~I~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg~-----~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV 153 (450)
+++|.+||||+......+.+.|||+||+|+|.||+|||+ +++..+|++ .+++++||+||.+||||||||||
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 999999999998422227789999999999999999998 556778887 89999999999999999999999
Q ss_pred CCCCCCCCCCCChhHHHHHHhCCCccCCCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChhHHHHHHHHhcc
Q 013058 154 SSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSF 233 (450)
Q Consensus 154 ~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yL~~~e~~g~~~~e~L~flf~L~~ 233 (450)
|++.. ..+|+++.++|+++|||+++...++||++||||||+|+++|+|+++++||++.|.+|||++|+|+|||+||+
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 99765 899999999999999999988899999999999999999999999999999999999999999999999999
Q ss_pred cccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhhhhcccCCC--------ccccccceEEEeeCceE
Q 013058 234 HVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD--------SSARKEGFIVVETNFRM 305 (450)
Q Consensus 234 ~~~G~~Y~~~~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~~L~~~~~~--------~~~~~~g~IIvETNFrv 305 (450)
+++|++|+++++|++|+.||+||||+|||||+|.+..+|| ||+||++++++-.+ ..+++.|||||||||||
T Consensus 238 ~~~G~~Ysvd~~~~~~~~~lq~Lre~GlvfQrk~k~~rfy-ptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~ri 316 (465)
T KOG3471|consen 238 LALGRAYSVDALTETQRILLQHLRELGLVFQRKIKILRFY-PTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRI 316 (465)
T ss_pred HHhcccceeehhhHHHHHHHHHHHHhhHHHHhhhhhheec-chhhhhccchhhhhhhhhhhcccccccCceEEEEeccEE
Confidence 9999999999999999999999999999999999999999 99999999885432 12245699999999999
Q ss_pred EeecCChhHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccC--CCCChhHHHHHHH
Q 013058 306 YAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM--PSVPENVCDQIRL 383 (450)
Q Consensus 306 YAYT~S~lqiaiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~--~~lP~tV~dQIrL 383 (450)
||||+||||+|||+|||++.|||||||||+|||||||+|+++||||+|||+||++||||||+... |++||||+|||||
T Consensus 317 YAYT~S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrL 396 (465)
T KOG3471|consen 317 YAYTNSPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRL 396 (465)
T ss_pred EEecCCHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999998776 8999999999999
Q ss_pred HHHhcCceeeecceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhccC
Q 013058 384 WESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQNK 450 (450)
Q Consensus 384 We~Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~vr~f~k~~~~ 450 (450)
||.||||+.++||+||++|.|..||+.+++||+++|+|+|+|+.||+|||+.+||++|++||||++|
T Consensus 397 WElernR~~~~~g~LYs~Fls~~df~~l~eya~~~~vLvw~d~~kr~~vV~~~Ghs~Vk~f~Kr~~k 463 (465)
T KOG3471|consen 397 WELERNRLRMTEGYLYSDFLSLSDFQLLLEYAREIGVLVWSDSDKRMFVVTKEGHSLVKRFWKRKSK 463 (465)
T ss_pred HHHhhcceecccchhHHhhhhhhhHHHHHHHHHHcCeEEEecCcceEEEEecCccHHHHHHHHHhhc
Confidence 9999999999999999999999999999999999999999999999999999999999999999765
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=3.4e-127 Score=940.02 Aligned_cols=430 Identities=30% Similarity=0.525 Sum_probs=407.2
Q ss_pred hhhHHHHHhcCCHHHHHHhhcChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCce
Q 013058 8 AKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRL 87 (450)
Q Consensus 8 ~~~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I 87 (450)
..++.+||+.||.....|||+.|++|+|+||.||++|++|||.|||.+.+||..+.+.|++..++-...+++..+.++||
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 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCceeEEeCHHHHHHHHHHHhcCCC---CCCCCCCCCCCCCCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCCC
Q 013058 88 FSEEKKKETTYRLNSTFQSNLRKHLIYGGA---LPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNF 164 (450)
Q Consensus 88 ~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg~---~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~ 164 (450)
.... ...+.|||+||.+|+.|||||+. .... .+.+ .+++++||.||.++||+|||||||+..+ .-|
T Consensus 87 ~~~~---g~~i~ln~~fk~sl~~altgg~~~nsfgv~-i~E~----lvsvd~ld~ys~~kwEtILhfmVgtpea---kip 155 (447)
T COG5144 87 YLDE---GLMIRLNPEFKISLMDALTGGTMENSFGVC-IGEK----LVSVDMLDSYSSRKWETILHFMVGTPEA---KIP 155 (447)
T ss_pred EecC---CceEEeChHHHHHHHHHhhcccccccccee-eccc----eeeeehhhhhhhhhHHHHHHHHhCCccc---cCc
Confidence 9763 37789999999999999999986 2221 2333 6899999999999999999999998876 778
Q ss_pred ChhHHHHHHhCCCccCCCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCccccCCC
Q 013058 165 SSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNT 244 (450)
Q Consensus 165 s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y~~~~ 244 (450)
+++|+++|+++|||.++...++||++|||||||+.|+|+|+++++||++.|...||++++|+||||||.+++|++|+++.
T Consensus 156 ~egVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s~md~v~VLhflFmLgal~vG~aY~id~ 235 (447)
T COG5144 156 AEGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDA 235 (447)
T ss_pred chhHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHhcchhhcceeeecc
Confidence 99999999999999998889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCHHHHHHHHHHhhcCceeeecCCCcccccchhhhhhhcccCC----C--ccccccceEEEeeCceEEeecCChhHHHHH
Q 013058 245 LSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLT----D--SSARKEGFIVVETNFRMYAYSTSKLHCEIL 318 (450)
Q Consensus 245 lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~~L~~~~~----~--~~~~~~g~IIvETNFrvYAYT~S~lqiaiL 318 (450)
||++|+.||+|+|++|||+++.-.+.+|| ||+||++|+++-- . ...++.|||||||||||||||+||||+|++
T Consensus 236 lsdtqqiml~D~R~yglv~q~~i~~~~fY-pt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi 314 (447)
T COG5144 236 LSDTQQIMLMDRRLYGLVEQLGILRKIFY-PTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVI 314 (447)
T ss_pred cchHHHHHHHHHHHhhHHHHhccchhhcc-ccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHH
Confidence 99999999999999999999998889999 9999999987422 1 223567999999999999999999999999
Q ss_pred HHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeeccee
Q 013058 319 RLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHY 398 (450)
Q Consensus 319 ~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~L 398 (450)
+|||++..||||||+|+|||||||+|+.+||||+|||.||++||||||+++.|.+||||+|||+|||.|+||+.+.||+|
T Consensus 315 ~LF~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~L 394 (447)
T COG5144 315 HLFCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYL 394 (447)
T ss_pred HHhhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhhcc
Q 013058 399 YDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRGQN 449 (450)
Q Consensus 399 y~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~vr~f~k~~~ 449 (450)
|+||.+..+|+.+.+||++.|||+|++..||||||+.+||.+|++|.||+-
T Consensus 395 ysdFlt~s~y~~~~eya~~~gvLvw~d~~Krmffi~~eG~s~v~~f~Kr~l 445 (447)
T COG5144 395 YSDFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEFVKRIL 445 (447)
T ss_pred HhhhhchhhHHHHHHHHHhcCeEEeecccceEEEEEccCcHHHHHHHHHHh
Confidence 999999999999999999999999999999999999999999999999974
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=5.6e-116 Score=898.33 Aligned_cols=346 Identities=43% Similarity=0.769 Sum_probs=325.9
Q ss_pred HHHhcCCHHHHHHhhcChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeeec-
Q 013058 13 DMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEE- 91 (450)
Q Consensus 13 ~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~- 91 (450)
|||++||++++++||++||||+||||+||++||+|||||||+++|||++++++||++++++++++|+++|.+||||++.
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 6999999999999999999999999999999999999999999999999999999999999999999999999999874
Q ss_pred -CCCceeEEeCHHHHHHHHHHHhcCCC-----CCCCCCCCCCCCCCCChhHHHHHHhhhHHHHHHHHhCCCCCCCCCCCC
Q 013058 92 -KKKETTYRLNSTFQSNLRKHLIYGGA-----LPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFS 165 (450)
Q Consensus 92 -~~~~~~~~Ln~~F~~~lr~aL~ggg~-----~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s 165 (450)
+++.+.|.|||+||+|||.||+|||+ +|+..++++ .+++++||+||++|||+|||||||++.... ..||
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 33348899999999999999999998 556666555 899999999999999999999999987521 2299
Q ss_pred hhHHHHHHhCCCccC--CCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCccccCC
Q 013058 166 SSMMKVFQRGLLSRR--DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLN 243 (450)
Q Consensus 166 ~~v~~lL~~~gL~~~--~~~~~~IT~~GfqFLL~d~~~Q~W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y~~~ 243 (450)
++|+++|+++|||+. ++++..||++||||||+|+++|+|+||++||+++|++|+|.+|+|+|||+||++++|++|+++
T Consensus 156 ~~v~~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~l~flf~L~~~~~g~~Y~~~ 235 (366)
T PF03849_consen 156 QDVKQLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAEARGMDLVEVLSFLFQLSFLELGKAYSTE 235 (366)
T ss_pred HHHHHHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccccCCcCcCC
Confidence 999999999999998 567899999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhhhhcccCCC-----------ccccccceEEEeeCceEEeecCCh
Q 013058 244 TLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTD-----------SSARKEGFIVVETNFRMYAYSTSK 312 (450)
Q Consensus 244 ~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~~L~~~~~~-----------~~~~~~g~IIvETNFrvYAYT~S~ 312 (450)
+||++|++||+||+|+||||++++++++|| |||||++|+++.+. ....++|||||||||||||||+||
T Consensus 236 ~ls~~q~~~L~~l~~~GLvy~~~~~~~~fy-pT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~ 314 (366)
T PF03849_consen 236 GLSETQKNMLQDLRELGLVYQRKRKSRRFY-PTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSP 314 (366)
T ss_pred CCCHHHHHHHHHHHHCCeEEEecCCCCeEe-chHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCH
Confidence 999999999999999999999999999999 99999999887652 134678999999999999999999
Q ss_pred hHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCc
Q 013058 313 LHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 364 (450)
Q Consensus 313 lqiaiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp 364 (450)
||||||++||++.|||||||||+||||||++|+++||||||||+||++||||
T Consensus 315 l~iaiL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 315 LQIAILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred HHHHHHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 9999999999999999999999999999999999999999999999999999
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=99.61 E-value=5.9e-15 Score=131.01 Aligned_cols=117 Identities=22% Similarity=0.352 Sum_probs=104.7
Q ss_pred EEEeeCceEEeecCCh--hHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCC
Q 013058 297 IVVETNFRMYAYSTSK--LHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVP 374 (450)
Q Consensus 297 IIvETNFrvYAYT~S~--lqiaiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP 374 (450)
+||++||.|.+++.+| -..+.|..|+++ .+..+|.+++||+.|+.+|++.|+|+++|+.||+.|+.. .||
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 7999999999977666 345999999999 567999999999999999999999999999999999954 699
Q ss_pred hhHHHHHHHHHHhcCceeeecceeecCCCCHHHHHHHHHHHHHcCeE
Q 013058 375 ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGL 421 (450)
Q Consensus 375 ~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~l 421 (450)
+||..+|+-|+...+|+++.++.+|-.+.+.+..+.+.+..+-.++.
T Consensus 74 ~~v~~~i~~w~~~~g~v~l~~~~~~l~~~d~~~l~~l~~~~~~~~~~ 120 (129)
T PF13625_consen 74 QNVEQSIEDWARRYGRVRLYKGAYLLECDDPELLDELLADPELAKLI 120 (129)
T ss_pred HHHHHHHHHHHHhcCCEEEecCeEEEEECCHHHHHHHHhChhhhhhh
Confidence 99999999999999999999966666999999999988877665543
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=97.08 E-value=0.0046 Score=69.71 Aligned_cols=106 Identities=24% Similarity=0.388 Sum_probs=84.8
Q ss_pred cceEEEeeCceEEeecCChh--HH-HHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccC
Q 013058 294 EGFIVVETNFRMYAYSTSKL--HC-EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM 370 (450)
Q Consensus 294 ~g~IIvETNFrvYAYT~S~l--qi-aiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~ 370 (450)
+|.|++||- +|+ |. .-|.-|+|+.+|--+|..++||-=|+-+|...|+++++||++|..++-.
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 7899999999999999999999999999999999999999999999844
Q ss_pred CCCChhHHHHHHHHHHhcCceeee--cceeecCCCCHHHHHHHHHH
Q 013058 371 PSVPENVCDQIRLWESDLNRVEMT--PAHYYDEFPSRDVFEAACDY 414 (450)
Q Consensus 371 ~~lP~tV~dQIrLWe~Er~R~~~~--~g~Ly~~f~s~~~f~~v~~y 414 (450)
.||++|.+.|+.+-.-.+++++. ++--|-+-.+.+..+.+.+.
T Consensus 88 -~~p~~i~~~i~~~~~~ygk~klv~~~~~~~~es~~~~~l~~l~~~ 132 (732)
T TIGR00603 88 -PIPKGIIEFIRLCTQSYGKVKLVLKHNRYFVESPHPEVLQRLLKD 132 (732)
T ss_pred -CCCHHHHHHHHHHHHhcCcEEEEEcCCceEEecCCHHHHHHHHhc
Confidence 79999999999999999999883 22113344555555655543
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=90.69 E-value=0.24 Score=33.80 Aligned_cols=22 Identities=36% Similarity=0.525 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHhc
Q 013058 340 SLYNAFENGITAEQIISFLQQN 361 (450)
Q Consensus 340 Sv~~Al~~GITA~QII~fL~~h 361 (450)
=|+.|...|||.+||..||+.+
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 3789999999999999999864
No 8
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=81.50 E-value=38 Score=32.96 Aligned_cols=162 Identities=18% Similarity=0.229 Sum_probs=101.9
Q ss_pred CCHHHHHHHHHHhhcCceeeecCC-CcccccchhhhhhhcccCCCccccccceEEEeeCceEEeecCChhHHHHHHHHHh
Q 013058 245 LSEIQKSMIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSK 323 (450)
Q Consensus 245 lt~~q~~~L~~L~~~GLv~~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~ 323 (450)
+++++..+++.|.+.|+|-.-... ..... +++-.| .+.|.=++|--++ +|- =+..+.+
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 467888899999999999665432 11111 111122 2235667776543 343 2344455
Q ss_pred hhhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCce
Q 013058 324 VEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRV 391 (450)
Q Consensus 324 l~~r~PNlvvg---~iTReSv~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~lP~--tV~dQIrLWe~Er~R~ 391 (450)
+..+||++.|| ++|.+.++.|++.|- ..+.+|.+-..+-.| .+|- |..+=...|+.--+-+
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 56679999999 899999999999983 456899988876555 6765 4466444888888888
Q ss_pred eeecceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHHHHHHhh
Q 013058 392 EMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHMREFLRG 447 (450)
Q Consensus 392 ~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~vr~f~k~ 447 (450)
++.|+-.+- =.+|-+.+...+ +.-+.+.+.-=.-+++++|++.
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 885532220 145666655444 3344444322223789999874
No 9
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=76.88 E-value=17 Score=35.19 Aligned_cols=125 Identities=17% Similarity=0.260 Sum_probs=85.4
Q ss_pred cceEEEeeCceEEeecCChhHHHHHHHHHhhhhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCC
Q 013058 294 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 363 (450)
Q Consensus 294 ~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~PNlvvg---~iTReSv~~Al~~GI-------TA~QII~fL~~hAH 363 (450)
.|+=++|-.|+ +|-- +..+.++..++|++.|| ++|.|.+++|.+.|- .-+.++.+-+.+-.
T Consensus 28 gGi~~iEit~~------tp~a---~~~I~~l~~~~~~~~vGAGTVl~~e~a~~ai~aGA~FivSP~~~~~vi~~a~~~~i 98 (201)
T PRK06015 28 GGLPAIEITLR------TPAA---LDAIRAVAAEVEEAIVGAGTILNAKQFEDAAKAGSRFIVSPGTTQELLAAANDSDV 98 (201)
T ss_pred CCCCEEEEeCC------CccH---HHHHHHHHHHCCCCEEeeEeCcCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC
Confidence 46667777665 3332 23445566778999999 899999999999994 46789999888776
Q ss_pred ccccccCCCCCh--hHHHHHHHHHHhcCceeeecceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHH
Q 013058 364 PRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHM 441 (450)
Q Consensus 364 p~m~~~~~~lP~--tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~v 441 (450)
| .+|= |..+=..-|+.=-+-+++.++-.+- . .+|.+.+...+ +.-+.|-+.-=.-+++
T Consensus 99 ~-------~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~G---G-------~~yikal~~pl---p~~~l~ptGGV~~~n~ 158 (201)
T PRK06015 99 P-------LLPGAATPSEVMALREEGYTVLKFFPAEQAG---G-------AAFLKALSSPL---AGTFFCPTGGISLKNA 158 (201)
T ss_pred C-------EeCCCCCHHHHHHHHHCCCCEEEECCchhhC---C-------HHHHHHHHhhC---CCCcEEecCCCCHHHH
Confidence 6 6664 7788888999999999998864431 0 34556655444 3333343222222778
Q ss_pred HHHHhh
Q 013058 442 REFLRG 447 (450)
Q Consensus 442 r~f~k~ 447 (450)
.+|++.
T Consensus 159 ~~~l~a 164 (201)
T PRK06015 159 RDYLSL 164 (201)
T ss_pred HHHHhC
Confidence 888874
No 10
>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=66.25 E-value=3.4 Score=37.53 Aligned_cols=65 Identities=17% Similarity=0.383 Sum_probs=49.7
Q ss_pred ccceEEEeeCceEEeecCChhHHH-HHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCC
Q 013058 293 KEGFIVVETNFRMYAYSTSKLHCE-ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMP 371 (450)
Q Consensus 293 ~~g~IIvETNFrvYAYT~S~lqia-iL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~ 371 (450)
....+|||.||| +.+.|| ==.-+..+...+|.+.||...| -.||+..+-..|--.|++++-
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 456899999998 555541 1223567777899999996654 368999999999888998887
Q ss_pred CCCh
Q 013058 372 SVPE 375 (450)
Q Consensus 372 ~lP~ 375 (450)
-+||
T Consensus 109 hlPP 112 (131)
T TIGR01615 109 PLPP 112 (131)
T ss_pred CCCC
Confidence 7888
No 11
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=65.41 E-value=12 Score=41.39 Aligned_cols=89 Identities=24% Similarity=0.359 Sum_probs=69.6
Q ss_pred ccceEEEeeCceEEeecCChhHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCC
Q 013058 293 KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPS 372 (450)
Q Consensus 293 ~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~ 372 (450)
-+|.|++||==-+|-+- ...|=-.+|..+|=-.+.-+.||-=|+..|..-|.+-+.||+||..-+.. .
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 46899999843333221 13444457888888889999999999999999999999999999987644 7
Q ss_pred CChhHHHHHHHHHHhcCceee
Q 013058 373 VPENVCDQIRLWESDLNRVEM 393 (450)
Q Consensus 373 lP~tV~dQIrLWe~Er~R~~~ 393 (450)
||+.|++=|++--.--+.++.
T Consensus 149 lp~~ii~FI~~cT~sYGKVKL 169 (776)
T KOG1123|consen 149 LPESIIEFIRACTVSYGKVKL 169 (776)
T ss_pred CCHHHHHHHHHHhhccccEEE
Confidence 999999999988776666554
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=63.09 E-value=62 Score=31.39 Aligned_cols=125 Identities=16% Similarity=0.313 Sum_probs=83.3
Q ss_pred cceEEEeeCceEEeecCChhHHHHHHHHHhhhhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCC
Q 013058 294 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 363 (450)
Q Consensus 294 ~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~PNlvvg---~iTReSv~~Al~~GI-------TA~QII~fL~~hAH 363 (450)
.|.=++|--|+ +|--... +.++..++|++.|| ++|.|.+++|.+.|- .-..++.+.+.+--
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 35556666663 4444443 44445578999999 899999999999994 34677777776654
Q ss_pred ccccccCCCCCh--hHHHHHHHHHHhcCceeeecceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHH
Q 013058 364 PRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHM 441 (450)
Q Consensus 364 p~m~~~~~~lP~--tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~v 441 (450)
| .+|= |..+=..-|+.--+-+++.|+-.+-. .+|-+.+...+ +.-+.+.+.-=.-+++
T Consensus 103 ~-------~iPG~~TptEi~~A~~~Ga~~vKlFPA~~~GG----------~~yikal~~pl---p~i~~~ptGGV~~~N~ 162 (204)
T TIGR01182 103 P-------IIPGVATPSEIMLALELGITALKLFPAEVSGG----------VKMLKALAGPF---PQVRFCPTGGINLANV 162 (204)
T ss_pred c-------EECCCCCHHHHHHHHHCCCCEEEECCchhcCC----------HHHHHHHhccC---CCCcEEecCCCCHHHH
Confidence 4 6663 77778889998899999988654410 35667766554 3344443222223789
Q ss_pred HHHHhh
Q 013058 442 REFLRG 447 (450)
Q Consensus 442 r~f~k~ 447 (450)
.+|++.
T Consensus 163 ~~~l~a 168 (204)
T TIGR01182 163 RDYLAA 168 (204)
T ss_pred HHHHhC
Confidence 999874
No 13
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=60.84 E-value=12 Score=31.80 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=22.8
Q ss_pred Cccchhhhhhh-----ccChhhHHHHHHHHH
Q 013058 185 PRLTESGFQFL-----LMDTNAQLWYIVREY 210 (450)
Q Consensus 185 ~~IT~~GfqFL-----L~d~~~Q~W~lll~y 210 (450)
-.||.+||-|| -..+++-.|++|+.+
T Consensus 27 ~GiT~~GFl~L~~lfierGR~ETtW~vLR~F 57 (89)
T PF08356_consen 27 NGITLDGFLFLNKLFIERGRHETTWTVLRKF 57 (89)
T ss_pred CccchhhHHHHHHHHHHhCcchHHHHHHHHc
Confidence 36999999866 889999999999987
No 14
>PRK07114 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=60.24 E-value=1.2e+02 Score=29.77 Aligned_cols=156 Identities=15% Similarity=0.197 Sum_probs=99.3
Q ss_pred HHHHHHhhcCceeeecCC-CcccccchhhhhhhcccCCCccccccceEEEeeCceEEeecCChhHHHHHHHH-HhhhhcC
Q 013058 251 SMIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLF-SKVEYQL 328 (450)
Q Consensus 251 ~~L~~L~~~GLv~~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF-~~l~~r~ 328 (450)
.+++.|.+.|+|-.-... ...-. +++-.| -+.|.=++|-=|| +|--...+... .+...++
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 467888888888654322 11111 111122 2235566776554 33333333333 2444579
Q ss_pred CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCceeeecc
Q 013058 329 PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRVEMTPA 396 (450)
Q Consensus 329 PNlvvg---~iTReSv~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~lP~--tV~dQIrLWe~Er~R~~~~~g 396 (450)
|++.|| ++|.|.++.|.+.|- .-..++.+.+.+-.| .+|= |..+=..-|+.=.+-+++.|+
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 457899998888766 6664 777888899999999999986
Q ss_pred eeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEecccc----HHHHHHHhh
Q 013058 397 HYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIH----MHMREFLRG 447 (450)
Q Consensus 397 ~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~----~~vr~f~k~ 447 (450)
-.+ . .+|-+.+...+ +.-+ |+...|- +++.+|++.
T Consensus 142 ~~~----------G-~~~ikal~~p~---p~i~--~~ptGGV~~~~~n~~~yl~a 180 (222)
T PRK07114 142 SVY----------G-PGFVKAIKGPM---PWTK--IMPTGGVEPTEENLKKWFGA 180 (222)
T ss_pred ccc----------C-HHHHHHHhccC---CCCe--EEeCCCCCcchhcHHHHHhC
Confidence 543 1 45666665544 3332 3334443 578888873
No 15
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=57.76 E-value=79 Score=28.03 Aligned_cols=70 Identities=14% Similarity=0.093 Sum_probs=54.9
Q ss_pred HHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeeecC-CCceeEEeCHH
Q 013058 33 CEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEK-KKETTYRLNST 103 (450)
Q Consensus 33 claifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~~-~~~~~~~Ln~~ 103 (450)
...+|+.|.+-.+.-|+.+|...++.+..++..=+. -++......++.|++-+++...+ |....|.+|+.
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 357899999989988999888767888788866543 34677889999999999998743 34467889975
No 16
>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=55.58 E-value=26 Score=33.77 Aligned_cols=125 Identities=19% Similarity=0.352 Sum_probs=79.6
Q ss_pred cceEEEeeCceEEeecCChhHHHHHHHHHhhhhcCCceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCC
Q 013058 294 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAH 363 (450)
Q Consensus 294 ~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~PNlvvg---~iTReSv~~Al~~GI-------TA~QII~fL~~hAH 363 (450)
.|.=++|--|| |...+ ....++..++|+|.|| ++|.|.+++|++.|- .-++++.+-+.|-.
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 46677887776 23333 2334556678999999 899999999999994 46789999998887
Q ss_pred ccccccCCCCC--hhHHHHHHHHHHhcCceeeecceeecCCCCHHHHHHHHHHHHHcCeEeeecCCCceEEEeccccHHH
Q 013058 364 PRVADRMPSVP--ENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSGLLWEDPKKMRLVVKAEIHMHM 441 (450)
Q Consensus 364 p~m~~~~~~lP--~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~llw~~~~kr~~~V~~~~~~~v 441 (450)
| .+| -|..+=..-|+.-.+-+++.|+-.+- =.+|.+++...+ +.-+.+.+.-=.-+++
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 7 677 37777788899999999999976651 134556554332 2222332222223779
Q ss_pred HHHHhh
Q 013058 442 REFLRG 447 (450)
Q Consensus 442 r~f~k~ 447 (450)
++|++.
T Consensus 163 ~~~l~a 168 (196)
T PF01081_consen 163 AEYLKA 168 (196)
T ss_dssp HHHHTS
T ss_pred HHHHhC
Confidence 999874
No 17
>PRK14529 adenylate kinase; Provisional
Probab=53.59 E-value=67 Score=31.46 Aligned_cols=81 Identities=16% Similarity=0.233 Sum_probs=57.1
Q ss_pred hhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeecceeecCCC
Q 013058 324 VEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFP 403 (450)
Q Consensus 324 l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~ 403 (450)
-.+.++.+.+|.+.|+.+.. ..-.+++|=.|+.. ...+|..++-++-.+.....- ..|++++.|+
T Consensus 22 ~~~~~~~is~gdllr~~i~~---~t~lg~~i~~~i~~---------G~lvpdei~~~lv~~~l~~~~---~~g~iLDGfP 86 (223)
T PRK14529 22 KKYDLAHIESGAIFREHIGG---GTELGKKAKEYIDR---------GDLVPDDITIPMILETLKQDG---KNGWLLDGFP 86 (223)
T ss_pred HHHCCCCcccchhhhhhccC---CChHHHHHHHHHhc---------cCcchHHHHHHHHHHHHhccC---CCcEEEeCCC
Confidence 34568999999999998753 22234566666654 348999999999888876543 7899999999
Q ss_pred CH-HHHHHHHHHHHHcC
Q 013058 404 SR-DVFEAACDYARDQS 419 (450)
Q Consensus 404 s~-~~f~~v~~ya~~~g 419 (450)
-. +..+.+-+..++.|
T Consensus 87 Rt~~Qa~~l~~~l~~~~ 103 (223)
T PRK14529 87 RNKVQAEKLWEALQKEG 103 (223)
T ss_pred CCHHHHHHHHHHHHhcC
Confidence 85 44455555544444
No 18
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=51.81 E-value=7.3 Score=31.57 Aligned_cols=30 Identities=30% Similarity=0.390 Sum_probs=24.5
Q ss_pred hHHHHHHhCCCccCCCCCCccchhhhhhhc
Q 013058 167 SMMKVFQRGLLSRRDKEAPRLTESGFQFLL 196 (450)
Q Consensus 167 ~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL 196 (450)
..++-|...||++.+++...||++|-+||-
T Consensus 38 ~yL~~L~~~gLI~~~~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 38 KYLKELEEKGLIKKKDGKYRLTEKGKEFLE 67 (77)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHH
T ss_pred HHHHHHHHCcCeeCCCCEEEECccHHHHHH
Confidence 346788999999887788999999999874
No 19
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=50.87 E-value=83 Score=22.61 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=41.0
Q ss_pred HHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeeecC-CCceeEEeCHH
Q 013058 48 VMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEK-KKETTYRLNST 103 (450)
Q Consensus 48 vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~~-~~~~~~~Ln~~ 103 (450)
|+..++ ..+++..++...+. -+......+++.|.+.+++.... ++...|.+++.
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 455566 77888889888876 34678899999999999998643 34466888883
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=46.23 E-value=33 Score=30.46 Aligned_cols=81 Identities=19% Similarity=0.308 Sum_probs=51.9
Q ss_pred hhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeecceeecCCCC
Q 013058 325 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 404 (450)
Q Consensus 325 ~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s 404 (450)
.|.++.+.+|-+=|+.+++ ..-.+++|-++|... ..||+.++-++-.++.+.. ....|++.+.|+.
T Consensus 19 ~~~~~~is~~~llr~~~~~---~s~~g~~i~~~l~~g---------~~vp~~~v~~ll~~~l~~~--~~~~g~ildGfPr 84 (151)
T PF00406_consen 19 RYGLVHISVGDLLREEIKS---DSELGKQIQEYLDNG---------ELVPDELVIELLKERLEQP--PCNRGFILDGFPR 84 (151)
T ss_dssp HHTSEEEEHHHHHHHHHHT---TSHHHHHHHHHHHTT---------SS--HHHHHHHHHHHHHSG--GTTTEEEEESB-S
T ss_pred hcCcceechHHHHHHHHhh---hhHHHHHHHHHHHhh---------ccchHHHHHHHHHHHHhhh--cccceeeeeeccc
Confidence 3567777777665655532 223357788887754 3899999999988888876 6678999999998
Q ss_pred H-HHHHHHHHHHHHcC
Q 013058 405 R-DVFEAACDYARDQS 419 (450)
Q Consensus 405 ~-~~f~~v~~ya~~~g 419 (450)
. +.++.+.+.....+
T Consensus 85 t~~Qa~~l~~~~~~~~ 100 (151)
T PF00406_consen 85 TLEQAEALEEILEEEG 100 (151)
T ss_dssp SHHHHHHHHHHHHHTT
T ss_pred cHHHHHHHHHHHhhcc
Confidence 5 44555544333333
No 21
>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=45.74 E-value=93 Score=23.50 Aligned_cols=57 Identities=21% Similarity=0.275 Sum_probs=39.4
Q ss_pred HHHHHHHhc-CCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeeec----CCCceeEEeCH
Q 013058 45 KKYVMQMFY-IDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEE----KKKETTYRLNS 102 (450)
Q Consensus 45 k~~vmrlL~-~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~----~~~~~~~~Ln~ 102 (450)
+..||+.+. .+.+.+.+++.....-+ +.....+++.|...++++.. .+....|.|+|
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~ 66 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLGIS-KSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTP 66 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-H
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCC
Confidence 456777787 67788889999877755 56677999999999999652 12336677876
No 22
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=43.71 E-value=18 Score=37.87 Aligned_cols=62 Identities=24% Similarity=0.423 Sum_probs=43.1
Q ss_pred HHHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhh
Q 013058 203 LWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 280 (450)
Q Consensus 203 ~W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y~~~~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~ 280 (450)
++.++-.||++.| | .|+.++-+-|..+--+.|-|+.+++|.+.|++++.--.++| +||.++.
T Consensus 12 L~aIV~~Yi~t~e-----P---------VGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~k~HtSsGR--vPT~~Gy 73 (346)
T COG1420 12 LRAIVEDYLATGE-----P---------VGSKTLSEKYNLDLSSATIRNEMADLEKLGLIEKPHTSSGR--VPTDKGY 73 (346)
T ss_pred HHHHHHHHHhcCC-----c---------cchHHHHHHhCCCCCchhHHHHHHHHHHCCCccCccccCCc--CCcHhHH
Confidence 4778888877643 2 23333445565555588999999999999999998544555 4666654
No 23
>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=43.01 E-value=90 Score=29.70 Aligned_cols=73 Identities=16% Similarity=0.352 Sum_probs=43.5
Q ss_pred hHHHHHHHHHHHHHHHcCCChhH--HHHHHHHhccc---ccCc---ccc--------CCCCCHHH-HHHHHHHhhcCcee
Q 013058 201 AQLWYIVREYISNSQERGINQAD--LISFLLELSFH---VAGE---AYN--------LNTLSEIQ-KSMIKDFADLGLVK 263 (450)
Q Consensus 201 ~Q~W~lll~yL~~~e~~g~~~~e--~L~flf~L~~~---~~G~---~Y~--------~~~lt~~q-~~~L~~L~~~GLv~ 263 (450)
..=|.++...-+.....|++..+ +|..|+...-. +.|. -|+ ++++|++. +..|..|.|.|||.
T Consensus 23 ~~k~~ll~~l~~a~~~lgl~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~ 102 (177)
T PF03428_consen 23 VTKWQLLRALKEARPALGLSDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIV 102 (177)
T ss_pred CCHHHHHHHHHHHHHhcCCChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCee
Confidence 34577777665555556776544 45555544421 1111 122 23677666 67999999999997
Q ss_pred ee-cCCCcccc
Q 013058 264 LQ-QGRKENWF 273 (450)
Q Consensus 264 ~~-~~~~~~fy 273 (450)
.+ +.++++|-
T Consensus 103 rrDS~NgkRy~ 113 (177)
T PF03428_consen 103 RRDSPNGKRYA 113 (177)
T ss_pred eccCCCCCccC
Confidence 76 45556655
No 24
>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=42.65 E-value=33 Score=28.48 Aligned_cols=27 Identities=41% Similarity=0.694 Sum_probs=22.3
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHHhcC
Q 013058 336 ITKESLYNAFE--------------NGITAEQIISFLQQNA 362 (450)
Q Consensus 336 iTReSv~~Al~--------------~GITA~QII~fL~~hA 362 (450)
+||+|.+.|+. .|.||+++|+||...-
T Consensus 18 ~t~~~L~~~i~~~FG~~arFhTCSa~~m~a~~Li~FL~~kg 58 (77)
T TIGR03853 18 YTRESLKAAIEQKFGEDARFHTCSAEGMTADELLQFLLKKG 58 (77)
T ss_pred cCHHHHHHHHHHHhCCCceEeecccccCCHHHHHHHHHHCC
Confidence 57888887774 6999999999998763
No 25
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=40.91 E-value=20 Score=30.90 Aligned_cols=31 Identities=23% Similarity=0.325 Sum_probs=24.1
Q ss_pred ChhHHHHHHhCCCccCCCC----CCccchhhhhhh
Q 013058 165 SSSMMKVFQRGLLSRRDKE----APRLTESGFQFL 195 (450)
Q Consensus 165 s~~v~~lL~~~gL~~~~~~----~~~IT~~GfqFL 195 (450)
-+..++-|...|++....+ ...||++|..||
T Consensus 48 ~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fl 82 (95)
T COG3432 48 AQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFL 82 (95)
T ss_pred HHHHHHHHHhCCCEEeccCCccceEEEChhHHHHH
Confidence 3677889999997765432 489999999993
No 26
>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=40.71 E-value=20 Score=27.84 Aligned_cols=33 Identities=21% Similarity=0.358 Sum_probs=23.4
Q ss_pred CCCHHH-HHHHHHHhhcCceeeecCCCcccccchh
Q 013058 244 TLSEIQ-KSMIKDFADLGLVKLQQGRKENWFIPTK 277 (450)
Q Consensus 244 ~lt~~q-~~~L~~L~~~GLv~~~~~~~~~fy~pT~ 277 (450)
+++.+. ...|+.|.+.|+|....++...|. +.+
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 344444 669999999999998887656665 543
No 27
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=40.68 E-value=2.5e+02 Score=27.31 Aligned_cols=116 Identities=16% Similarity=0.314 Sum_probs=75.2
Q ss_pred HHHHHhhcCceeeecCC-CcccccchhhhhhhcccCCCccccccceEEEeeCceEEeecCChhHHHHHHHHHhhhhcC--
Q 013058 252 MIKDFADLGLVKLQQGR-KENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQL-- 328 (450)
Q Consensus 252 ~L~~L~~~GLv~~~~~~-~~~fy~pT~La~~L~~~~~~~~~~~~g~IIvETNFrvYAYT~S~lqiaiL~lF~~l~~r~-- 328 (450)
+++.|.+.|++-.-+.. ..... +++-.| .+.|.=++|-=|| +|--. ..+.++..++
T Consensus 6 ~~~~l~~~~vi~vir~~~~~~a~---~~~~al---------~~~Gi~~iEit~~------~~~a~---~~i~~l~~~~~~ 64 (213)
T PRK06552 6 ILTKLKANGVVAVVRGESKEEAL---KISLAV---------IKGGIKAIEVTYT------NPFAS---EVIKELVELYKD 64 (213)
T ss_pred HHHHHHHCCEEEEEECCCHHHHH---HHHHHH---------HHCCCCEEEEECC------CccHH---HHHHHHHHHcCC
Confidence 67888888888665432 11111 122222 2346667776665 34333 3444555567
Q ss_pred -CceEEE---EeCHHHHHHHHHcCC-------CHHHHHHHHHhcCCccccccCCCCCh--hHHHHHHHHHHhcCceeeec
Q 013058 329 -PNLIVG---AITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRVEMTP 395 (450)
Q Consensus 329 -PNlvvg---~iTReSv~~Al~~GI-------TA~QII~fL~~hAHp~m~~~~~~lP~--tV~dQIrLWe~Er~R~~~~~ 395 (450)
|++.|| ++|.+.+++|.+.|- .-+.++.+-+.+-.| .+|= |..+=.+.|+.--+-+++.+
T Consensus 65 ~p~~~vGaGTV~~~~~~~~a~~aGA~FivsP~~~~~v~~~~~~~~i~-------~iPG~~T~~E~~~A~~~Gad~vklFP 137 (213)
T PRK06552 65 DPEVLIGAGTVLDAVTARLAILAGAQFIVSPSFNRETAKICNLYQIP-------YLPGCMTVTEIVTALEAGSEIVKLFP 137 (213)
T ss_pred CCCeEEeeeeCCCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCCC-------EECCcCCHHHHHHHHHcCCCEEEECC
Confidence 579999 899999999999994 457788887777665 6664 55555668888888888755
No 28
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=40.41 E-value=23 Score=30.27 Aligned_cols=42 Identities=24% Similarity=0.342 Sum_probs=32.0
Q ss_pred HHHHHhCCCccCCCC----------CCccchhhhhhhccChhhHHHHHHHHH
Q 013058 169 MKVFQRGLLSRRDKE----------APRLTESGFQFLLMDTNAQLWYIVREY 210 (450)
Q Consensus 169 ~~lL~~~gL~~~~~~----------~~~IT~~GfqFLL~d~~~Q~W~lll~y 210 (450)
+.+|..+||+..... ...||.+|.+||-.=++.-+|.=...-
T Consensus 41 l~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~IRd~~vW~k~K~~ 92 (102)
T PF10711_consen 41 LKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAIRDDTVWNKTKDK 92 (102)
T ss_pred HHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHhcCchHHHHHHHH
Confidence 456777788774321 248999999999999999999877644
No 29
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=39.50 E-value=16 Score=28.12 Aligned_cols=27 Identities=30% Similarity=0.240 Sum_probs=21.4
Q ss_pred hhHHHHHHhCCCccCCCCCCccchhhh
Q 013058 166 SSMMKVFQRGLLSRRDKEAPRLTESGF 192 (450)
Q Consensus 166 ~~v~~lL~~~gL~~~~~~~~~IT~~Gf 192 (450)
...++-|...||+..+++.+.+|++|+
T Consensus 39 ~~~l~~l~~~Gll~~~~~~l~lT~~G~ 65 (66)
T PF06969_consen 39 QKELEELQEDGLLEIDGGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHTTSEEE-SSEEEE-TTTG
T ss_pred HHHHHHHHHCCCEEEeCCEEEECcccC
Confidence 456778888999999999999999996
No 30
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=36.99 E-value=20 Score=29.98 Aligned_cols=45 Identities=18% Similarity=0.200 Sum_probs=22.5
Q ss_pred hhHHHHHHHHhCCCCCCCCCCCChhHHHHHHhCCCccCCCCCCccchhhhhhhcc
Q 013058 143 GQWECFLLQLISSTQAERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLM 197 (450)
Q Consensus 143 ~~WE~IL~~mV~~~~~~~~~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL~ 197 (450)
..|..|++.|+..+--.+ -..... +.+. ....+.||.+|.+||-.
T Consensus 25 ~~~~~il~~L~d~GyI~G-~~~~~~--------~~~~-~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKG-VSVVRY--------SPYV-ALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HHHHHHHHHHHHHTSEE---EESSS--------SEE---SS--EE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCccc-eEEEec--------ccee-ecCCceEcHHHHHHHHH
Confidence 678888888875443211 001011 1111 23467899999999853
No 31
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=36.84 E-value=70 Score=30.64 Aligned_cols=57 Identities=16% Similarity=0.179 Sum_probs=44.9
Q ss_pred HHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeee-----cCCCceeEEeCHHHHHHH
Q 013058 48 VMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSE-----EKKKETTYRLNSTFQSNL 108 (450)
Q Consensus 48 vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~-----~~~~~~~~~Ln~~F~~~l 108 (450)
++..++..+|++.++++..-..++ ...++.|...+++.+ ..+....|.+++.|..-|
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 567777789999999998765543 788999999999975 233457788999998854
No 32
>PRK13824 replication initiation protein RepC; Provisional
Probab=36.21 E-value=1.4e+02 Score=31.97 Aligned_cols=70 Identities=13% Similarity=0.261 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCccc---------cC--------CCCCHHH-HHHHHHHhhcCcee
Q 013058 202 QLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAY---------NL--------NTLSEIQ-KSMIKDFADLGLVK 263 (450)
Q Consensus 202 Q~W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y---------~~--------~~lt~~q-~~~L~~L~~~GLv~ 263 (450)
.=|.++..--+.....|++..++--.--.|+| .+..++ +. .++++++ +..|..|.|.|||-
T Consensus 36 ~Kw~l~r~l~~a~~~lGl~~~~l~vL~aLlsf-~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~LveaGLI~ 114 (404)
T PRK13824 36 DKWKLFRDLCEARALLGVSDRALAVLNALLSF-YPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGLII 114 (404)
T ss_pred CHHHHHHHHHHHHHhcCCChhHHHHHHHHHhh-CCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHCCCeE
Confidence 56998888877777778876544332233333 333332 22 2577666 67999999999996
Q ss_pred ee-cCCCccc
Q 013058 264 LQ-QGRKENW 272 (450)
Q Consensus 264 ~~-~~~~~~f 272 (450)
.+ +.+++||
T Consensus 115 rrDSpNGKRy 124 (404)
T PRK13824 115 RRDSPNGKRY 124 (404)
T ss_pred eecCCCCccc
Confidence 66 4555665
No 33
>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=36.05 E-value=1.2e+02 Score=23.65 Aligned_cols=46 Identities=15% Similarity=0.351 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHHcCeEeeecCC----CceEEEeccccHHHHHHHhhc
Q 013058 403 PSRDVFEAACDYARDQSGLLWEDPK----KMRLVVKAEIHMHMREFLRGQ 448 (450)
Q Consensus 403 ~s~~~f~~v~~ya~~~g~llw~~~~----kr~~~V~~~~~~~vr~f~k~~ 448 (450)
.+.+..+.+.+.....++-.|..+. .-.+.|+++..+.+.+++++.
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 3567888899999999999998887 247899999999999999864
No 34
>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=35.80 E-value=37 Score=28.24 Aligned_cols=34 Identities=26% Similarity=0.358 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHhhcCceeeecCCCcccccchhhhh
Q 013058 246 SEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 280 (450)
Q Consensus 246 t~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~ 280 (450)
+.|-++.+++|.++|||....+.+.-+. ||.-|-
T Consensus 37 ~aTIRN~M~~Le~lGlve~~p~~s~Gri-PT~~aY 70 (78)
T PF03444_consen 37 PATIRNEMADLEELGLVESQPHPSGGRI-PTDKAY 70 (78)
T ss_pred hHHHHHHHHHHHHCCCccCCCCCCCCCC-cCHHHH
Confidence 5789999999999999975433344445 887654
No 35
>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=34.38 E-value=1.4e+02 Score=25.67 Aligned_cols=73 Identities=15% Similarity=0.179 Sum_probs=48.7
Q ss_pred chhhHHHHHhcCCHHHHHHhhc--ChhhHHHHHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhc
Q 013058 7 IAKNFMDMVASLTARDLDRLYE--NPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQ 84 (450)
Q Consensus 7 ~~~~~~~yL~~Lp~~~~~~LY~--~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~ 84 (450)
-...+-..|...|..++..... ++..+-.||+.||+-++..+-.-+=.-+|++.++++. .+++.-..++.|.+
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 4455667777777777776665 5788999999999999999988887778999998865 24455555555543
No 36
>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=33.51 E-value=57 Score=27.17 Aligned_cols=28 Identities=36% Similarity=0.623 Sum_probs=22.7
Q ss_pred EeCHHHHHHHHH--------------cCCCHHHHHHHHHhcC
Q 013058 335 AITKESLYNAFE--------------NGITAEQIISFLQQNA 362 (450)
Q Consensus 335 ~iTReSv~~Al~--------------~GITA~QII~fL~~hA 362 (450)
-+||+|+.+|+. .|.||+++|.||...-
T Consensus 19 ~~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~FL~~rg 60 (78)
T PF10678_consen 19 PYTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDFLEERG 60 (78)
T ss_pred CcCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHHHHHcC
Confidence 358888887774 6999999999998653
No 37
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=32.50 E-value=43 Score=29.75 Aligned_cols=53 Identities=19% Similarity=0.323 Sum_probs=34.5
Q ss_pred HHHHHHHhcccccCccccCCCCCHH-------HHHHHHHHhhcCceeeecCCCcccccchh
Q 013058 224 LISFLLELSFHVAGEAYNLNTLSEI-------QKSMIKDFADLGLVKLQQGRKENWFIPTK 277 (450)
Q Consensus 224 ~L~flf~L~~~~~G~~Y~~~~lt~~-------q~~~L~~L~~~GLv~~~~~~~~~fy~pT~ 277 (450)
.+..+..|....-+...+.+.+++. -..+|+.|++-|||...++..+.|. |++
T Consensus 10 Al~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~-l~~ 69 (135)
T TIGR02010 10 AVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQ-LGR 69 (135)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEe-ccC
Confidence 3555666665444445555543322 2669999999999987666666777 666
No 38
>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=30.98 E-value=1.4e+02 Score=25.22 Aligned_cols=57 Identities=18% Similarity=0.250 Sum_probs=43.4
Q ss_pred HHHHHHHhcC-CCCCChHHHHhhcCC----cchhHHHHHHHHHhcCceeeec--CCCceeEEeC
Q 013058 45 KKYVMQMFYI-DGAIPAKMMEEWVLP----DGFTKHRVAIDRLVQLRLFSEE--KKKETTYRLN 101 (450)
Q Consensus 45 k~~vmrlL~~-~~~v~~~~l~~W~~~----~~~~~~~~al~~L~~L~I~~~~--~~~~~~~~Ln 101 (450)
|..|+..|.. +.+++..++...++. -+....-.+|+.|.+.+++..- .++...|.++
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 5678888876 568899999988864 3567788999999999999862 3344667665
No 39
>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=30.87 E-value=56 Score=29.06 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=20.9
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcC
Q 013058 338 KESLYNAFENGITAEQIISFLQQNA 362 (450)
Q Consensus 338 ReSv~~Al~~GITA~QII~fL~~hA 362 (450)
+.-++.|+++|+|.+||..-|.+-+
T Consensus 76 ~~h~~~Al~~G~T~~ei~Evl~q~~ 100 (123)
T TIGR02425 76 AMHVRATANTGVTEDDIKEVLLHVA 100 (123)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4567899999999999999877544
No 40
>COG1313 PflX Uncharacterized Fe-S protein PflX, homolog of pyruvate formate lyase activating proteins [General function prediction only]
Probab=30.55 E-value=63 Score=33.49 Aligned_cols=51 Identities=24% Similarity=0.315 Sum_probs=40.7
Q ss_pred HHHHHHHHhcCCccccccCCCCChhHHHHH----HHHHH-hcCceeeecceeecCCCCHHHHHHHHHHHHHcCe
Q 013058 352 EQIISFLQQNAHPRVADRMPSVPENVCDQI----RLWES-DLNRVEMTPAHYYDEFPSRDVFEAACDYARDQSG 420 (450)
Q Consensus 352 ~QII~fL~~hAHp~m~~~~~~lP~tV~dQI----rLWe~-Er~R~~~~~g~Ly~~f~s~~~f~~v~~ya~~~g~ 420 (450)
.-|++|+..|.-- -++-||.+|- +-||. |-+ +..+.++|+.+.+||+..|.
T Consensus 274 kpI~~wiae~~g~-------~~~vNiM~QY~P~ykA~eypeI~-----------R~lt~eE~e~a~~~a~~~gl 329 (335)
T COG1313 274 KPILRWIAENLGN-------DVRVNIMFQYRPEYKAEEYPEIN-----------RRLTREEYEKALEYAEKLGL 329 (335)
T ss_pred HHHHHHHHHhCCC-------CeeEEehhhccchhhhhhchhhc-----------ccCCHHHHHHHHHHHHHcCC
Confidence 5699999988621 5778899995 47776 555 67889999999999999885
No 41
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=30.21 E-value=55 Score=25.91 Aligned_cols=57 Identities=19% Similarity=0.432 Sum_probs=35.0
Q ss_pred ccChhhHHHHHHHHHHHHHHHcCCCh--hHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCC
Q 013058 196 LMDTNAQLWYIVREYISNSQERGINQ--ADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGR 268 (450)
Q Consensus 196 L~d~~~Q~W~lll~yL~~~e~~g~~~--~e~L~flf~L~~~~~G~~Y~~~~lt~~q~~~L~~L~~~GLv~~~~~~ 268 (450)
|-+++.++..++..| .++.|..+ .|+-. .+.+.. +.+-...|..|.+-|+|-...+.
T Consensus 4 LT~rQ~~vL~~I~~~---~~~~G~~Pt~rEIa~------------~~g~~S-~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 4 LTERQKEVLEFIREY---IEENGYPPTVREIAE------------ALGLKS-TSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp --HHHHHHHHHHHHH---HHHHSS---HHHHHH------------HHTSSS-HHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CCHHHHHHHHHHHHH---HHHcCCCCCHHHHHH------------HhCCCC-hHHHHHHHHHHHHCcCccCCCCC
Confidence 446778888888888 44566543 33322 222221 45667799999999999766543
No 42
>KOG4175 consensus Tryptophan synthase alpha chain [Amino acid transport and metabolism]
Probab=29.39 E-value=1.9e+02 Score=28.63 Aligned_cols=77 Identities=21% Similarity=0.226 Sum_probs=51.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHhcCCcc--------ccccCCCCChhHHHHHHHHHHhcCceeeecceeecCCCCHHHHHH
Q 013058 339 ESLYNAFENGITAEQIISFLQQNAHPR--------VADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPSRDVFEA 410 (450)
Q Consensus 339 eSv~~Al~~GITA~QII~fL~~hAHp~--------m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s~~~f~~ 410 (450)
.+-+.|+.+|+|-.+||+-++. |.|+ |.=.+|++---+..-|.-= .+- =.+|++.-|.+ .++.+.
T Consensus 67 ~~n~~aL~ng~tl~~i~emvk~-ar~~gvt~PIiLmgYYNPIl~yG~e~~iq~a-k~a----GanGfiivDlP-pEEa~~ 139 (268)
T KOG4175|consen 67 AANRRALLNGTTLNSIIEMVKE-ARPQGVTCPIILMGYYNPILRYGVENYIQVA-KNA----GANGFIIVDLP-PEEAET 139 (268)
T ss_pred hhHHHHHHcCCcHHHHHHHHHH-hcccCcccceeeeecccHHHhhhHHHHHHHH-Hhc----CCCceEeccCC-hHHHHH
Confidence 3568999999999999999874 4454 2223455444444433321 111 24677776655 688999
Q ss_pred HHHHHHHcCeEe
Q 013058 411 ACDYARDQSGLL 422 (450)
Q Consensus 411 v~~ya~~~g~ll 422 (450)
++++|++.|+-+
T Consensus 140 ~Rne~~k~gisl 151 (268)
T KOG4175|consen 140 LRNEARKHGISL 151 (268)
T ss_pred HHHHHHhcCceE
Confidence 999999999744
No 43
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=28.74 E-value=45 Score=31.06 Aligned_cols=34 Identities=15% Similarity=0.260 Sum_probs=27.3
Q ss_pred CCChhHHHHHHhCCCccCCCCCCccchhhhhhhc
Q 013058 163 NFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLL 196 (450)
Q Consensus 163 ~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFLL 196 (450)
.+-..+++-|...||++.+.++..||++|=+||=
T Consensus 96 ~iiR~~LqqLE~~glVek~~~GR~lT~~G~~~LD 129 (150)
T PRK09333 96 SIIRKILQQLEKAGLVEKTKKGRVITPKGRSLLD 129 (150)
T ss_pred HHHHHHHHHHHHCCCeeeCCCCCEeCHHHHHHHH
Confidence 3445678888999999977677789999988863
No 44
>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=28.42 E-value=28 Score=34.20 Aligned_cols=66 Identities=23% Similarity=0.386 Sum_probs=48.2
Q ss_pred cccceEEEeeCceEEeecCChhHHH-HHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccC
Q 013058 292 RKEGFIVVETNFRMYAYSTSKLHCE-ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM 370 (450)
Q Consensus 292 ~~~g~IIvETNFrvYAYT~S~lqia-iL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~ 370 (450)
...-.+|||+||| +.+.|| -=.-|..+...+|...||...| + .||++.+-.-+.-.|++++
T Consensus 135 ~~~~r~IVd~~fr------~~FeiArpt~~Y~~ll~~lP~vfVG~~~~--L----------~~iV~~~c~a~k~s~k~~g 196 (218)
T PF04720_consen 135 GKSERYIVDPDFR------SQFEIARPTPEYAALLAALPEVFVGTPER--L----------KQIVRLMCDAAKRSFKERG 196 (218)
T ss_pred CcceeEEEecchH------hCeeecCCCHHHHHHHHhCCCceEcCHHH--H----------HHHHHHHHHHHHHHHHHCC
Confidence 3566799999998 333331 1234566777899999995433 2 5789999888888888888
Q ss_pred CCCCh
Q 013058 371 PSVPE 375 (450)
Q Consensus 371 ~~lP~ 375 (450)
--|||
T Consensus 197 ~~lPP 201 (218)
T PF04720_consen 197 MHLPP 201 (218)
T ss_pred CCCCC
Confidence 88888
No 45
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=27.22 E-value=1.4e+02 Score=25.93 Aligned_cols=52 Identities=12% Similarity=0.162 Sum_probs=36.0
Q ss_pred CceEEEE--eCHHHHHHHH----HcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHH
Q 013058 329 PNLIVGA--ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWES 386 (450)
Q Consensus 329 PNlvvg~--iTReSv~~Al----~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~dQIrLWe~ 386 (450)
|-+|-+. ++|...--|. ..|+++++.+.|+++ ++|.+ ...+...+|++.||.
T Consensus 80 ~VlVHC~~G~~RS~~v~~~yl~~~~~~~~~~A~~~v~~-~R~~~-----~p~~~~~~qL~~~e~ 137 (138)
T smart00195 80 KVLVHCQAGVSRSATLIIAYLMKYRNLSLNDAYDFVKD-RRPII-----SPNFGFLRQLIEYER 137 (138)
T ss_pred eEEEECCCCCchHHHHHHHHHHHHhCCCHHHHHHHHHH-HCCcc-----CCCHhHHHHHHHHhh
Confidence 3444443 5677754333 579999999999975 44543 223589999999995
No 46
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=26.56 E-value=42 Score=33.83 Aligned_cols=61 Identities=20% Similarity=0.256 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHcCCChhHHHHHHHHhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhh
Q 013058 204 WYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 280 (450)
Q Consensus 204 W~lll~yL~~~e~~g~~~~e~L~flf~L~~~~~G~~Y~~~~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~ 280 (450)
..++-.|+++.+ + .|+.++.+.|..+--+.|-|+.+.+|.+.|++.++-..++| +||..+.
T Consensus 10 ~~iV~~Yi~t~~-----P---------VGSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~qpHtSsGR--IPT~~gy 70 (260)
T PRK03911 10 DSIIQTYLQDNE-----P---------IGSNELKSLMNLKISAATIRNYFKKLSDEGLLTQLHISGGR--IPTIKAM 70 (260)
T ss_pred HHHHHHHhccCC-----c---------cCHHHHHHHcCCCCCcHHHHHHHHHHHHCcCccCCcCCCCc--CCCHHHH
Confidence 456667766532 1 24445556677776689999999999999999988655555 4776655
No 47
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=26.36 E-value=2.2e+02 Score=22.38 Aligned_cols=59 Identities=7% Similarity=0.027 Sum_probs=43.6
Q ss_pred hhHHHHHHHHhcCCCC--CChHHHHhhcCCcchhHHHHHHHHHhcCceeeecCCCceeEEeC
Q 013058 42 PLAKKYVMQMFYIDGA--IPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEKKKETTYRLN 101 (450)
Q Consensus 42 ~lak~~vmrlL~~~~~--v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~~~~~~~~~Ln 101 (450)
.-.+.-|+.+|--.++ ++..++..=+.-+ ++.....|..|.+-+.+....+.+..|.+.
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~-~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~ 65 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLP-KKEVNRVLYSLEKKGKVCKQGGTPPLWKLT 65 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEecCCCCCceEee
Confidence 3345667777777656 9999998766655 568899999999999997644344677765
No 48
>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=25.78 E-value=1.1e+02 Score=23.25 Aligned_cols=55 Identities=13% Similarity=0.217 Sum_probs=42.3
Q ss_pred HHhhCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhcCceeeec
Q 013058 36 ILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEE 91 (450)
Q Consensus 36 ifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~ 91 (450)
||+.|-+-.+.-|+++|..+.|.+..++..=+.-. .......++.|.+.+++...
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 56666666677788888778899989888766533 56678889999999999764
No 49
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=25.44 E-value=47 Score=30.69 Aligned_cols=34 Identities=15% Similarity=0.255 Sum_probs=28.3
Q ss_pred CCCChhHHHHHHhCCCccCCCCCCccchhhhhhh
Q 013058 162 TNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFL 195 (450)
Q Consensus 162 ~~~s~~v~~lL~~~gL~~~~~~~~~IT~~GfqFL 195 (450)
..+...+++=|..+|++++..++..||++|-.||
T Consensus 95 gsI~RkilqqLE~~G~V~k~~~GR~ltp~Grsll 128 (147)
T COG2238 95 GSIIRKVLQQLEKAGLVEKTPKGRVLTPKGRSLL 128 (147)
T ss_pred chHHHHHHHHHHHCCceeecCCCceeCccchhHH
Confidence 4566778888999999998766778999998876
No 50
>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=24.68 E-value=1e+02 Score=23.92 Aligned_cols=31 Identities=13% Similarity=0.175 Sum_probs=25.3
Q ss_pred HHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHH
Q 013058 340 SLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCD 379 (450)
Q Consensus 340 Sv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~d 379 (450)
-|.+.+....|-++++..|..|| .|+|.|+.
T Consensus 4 lIErCl~~yMsk~E~v~~L~~~a---------~I~P~~T~ 34 (54)
T PF09713_consen 4 LIERCLQLYMSKEECVRALQKQA---------NIEPVFTS 34 (54)
T ss_pred HHHHHHHHcCCHHHHHHHHHHHc---------CCChHHHH
Confidence 46788999999999999999997 56665543
No 51
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=24.40 E-value=65 Score=26.72 Aligned_cols=31 Identities=23% Similarity=0.207 Sum_probs=24.8
Q ss_pred HHHHHHhCCCccCC-CCCCccchhhhhhhccC
Q 013058 168 MMKVFQRGLLSRRD-KEAPRLTESGFQFLLMD 198 (450)
Q Consensus 168 v~~lL~~~gL~~~~-~~~~~IT~~GfqFLL~d 198 (450)
.+.-|..+|++++. .+...||++|-++|-..
T Consensus 60 a~~~L~~aGli~~~~rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 60 ARSYLKKAGLIERPKRGIWRITEKGRKALAEH 91 (92)
T ss_pred HHHHHHHCCCccCCCCCceEECHhHHHHHhhC
Confidence 35678999999974 45789999999998653
No 52
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=24.13 E-value=35 Score=34.28 Aligned_cols=38 Identities=16% Similarity=0.251 Sum_probs=26.5
Q ss_pred CCCChhHHHHHHhCCCccCCC-CCCccchhhhhhhccChh
Q 013058 162 TNFSSSMMKVFQRGLLSRRDK-EAPRLTESGFQFLLMDTN 200 (450)
Q Consensus 162 ~~~s~~v~~lL~~~gL~~~~~-~~~~IT~~GfqFLL~d~~ 200 (450)
+.+|.-+++ |...||++..+ +..+||.+||+||+....
T Consensus 40 QaVsehiK~-Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~ 78 (260)
T COG1497 40 QAVSEHIKE-LVKEGLIEKEGRGEYEITKKGAEWLLEQLS 78 (260)
T ss_pred HHHHHHHHH-HHhccceeecCCeeEEEehhHHHHHHHHHH
Confidence 445555544 46778888654 367899999999985443
No 53
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=23.86 E-value=69 Score=29.53 Aligned_cols=30 Identities=17% Similarity=0.328 Sum_probs=23.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCcccc
Q 013058 338 KESLYNAFENGITAEQIISFLQQNAHPRVA 367 (450)
Q Consensus 338 ReSv~~Al~~GITA~QII~fL~~hAHp~m~ 367 (450)
|+-|++-+..|-|.+||++|+.++-=+...
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 54
>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=23.35 E-value=94 Score=25.17 Aligned_cols=28 Identities=25% Similarity=0.495 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHhhcCceeeecCCCcccc
Q 013058 246 SEIQKSMIKDFADLGLVKLQQGRKENWF 273 (450)
Q Consensus 246 t~~q~~~L~~L~~~GLv~~~~~~~~~fy 273 (450)
.-+|-++=+||+++|+|..+..++...|
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 4678899999999999999977666666
No 55
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=22.24 E-value=1.5e+02 Score=26.78 Aligned_cols=34 Identities=24% Similarity=0.401 Sum_probs=26.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCccccccCC
Q 013058 338 KESLYNAFENGITAEQIISFLQQNAHPRVADRMP 371 (450)
Q Consensus 338 ReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~ 371 (450)
|.-|++-+..|-|-+||++|+...-=....-++|
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 7789999999999999999999776544443333
No 56
>PLN02459 probable adenylate kinase
Probab=21.71 E-value=1.7e+02 Score=29.52 Aligned_cols=69 Identities=17% Similarity=0.276 Sum_probs=46.5
Q ss_pred hhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeecceeecCCCC
Q 013058 325 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 404 (450)
Q Consensus 325 ~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~s 404 (450)
.+.++.+.+|.|=|+.|..--..| .+|-.|+.+- ..||..++-++-..++....-.-..|++++.|+-
T Consensus 52 ~~~~~~is~gdllR~ei~~~t~lg---~~i~~~~~~G---------~lVPdeiv~~ll~~~l~~~~~~~~~g~iLDGFPR 119 (261)
T PLN02459 52 LLGVPHIATGDLVREEIKSSGPLG---AQLKEIVNQG---------KLVPDEIIFSLLSKRLEAGEEEGESGFILDGFPR 119 (261)
T ss_pred HhCCcEEeCcHHHHHHHhccchhH---HHHHHHHHcC---------CccCHHHHHHHHHHHHhcccccCCceEEEeCCCC
Confidence 467899999988888775433322 4555555443 4789988888777666543223467899999987
Q ss_pred H
Q 013058 405 R 405 (450)
Q Consensus 405 ~ 405 (450)
.
T Consensus 120 t 120 (261)
T PLN02459 120 T 120 (261)
T ss_pred C
Confidence 5
No 57
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=21.61 E-value=1e+02 Score=22.36 Aligned_cols=20 Identities=35% Similarity=0.689 Sum_probs=15.8
Q ss_pred EEeCHHHHHHHHHc-C---CCHHH
Q 013058 334 GAITKESLYNAFEN-G---ITAEQ 353 (450)
Q Consensus 334 g~iTReSv~~Al~~-G---ITA~Q 353 (450)
|.||++.++.|+.. | +|.++
T Consensus 3 G~i~~~~~~~~l~~~g~~~~s~~e 26 (54)
T PF13833_consen 3 GKITREEFRRALSKLGIKDLSEEE 26 (54)
T ss_dssp SEEEHHHHHHHHHHTTSSSSCHHH
T ss_pred CEECHHHHHHHHHHhCCCCCCHHH
Confidence 78999999999965 5 55555
No 58
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=21.34 E-value=3.8e+02 Score=21.61 Aligned_cols=62 Identities=18% Similarity=0.160 Sum_probs=39.4
Q ss_pred hhHHHHHHhCCCccCCC-CCCccchhhhhhhccChhhHHHHHHHHHHHHHH-HcCCChhHHHHHHHHhc
Q 013058 166 SSMMKVFQRGLLSRRDK-EAPRLTESGFQFLLMDTNAQLWYIVREYISNSQ-ERGINQADLISFLLELS 232 (450)
Q Consensus 166 ~~v~~lL~~~gL~~~~~-~~~~IT~~GfqFLL~d~~~Q~W~lll~yL~~~e-~~g~~~~e~L~flf~L~ 232 (450)
...++-|...||+.+.. ....+|++|-+.. .++......+-..+. ..|.+..++-.++..|.
T Consensus 17 s~~l~~L~~~glI~r~~~~~~~lT~~g~~~~-----~~~~~~~~~~~~~l~~~~~~~~~e~~~l~~~l~ 80 (96)
T smart00529 17 TQMLKKLEKDGLVEYEPYRGITLTEKGRRLA-----RRLLRKHRLLERFLVDVLGVDEEEVHEEAERLE 80 (96)
T ss_pred HHHHHHHHHCCCEEEcCCCceEechhHHHHH-----HHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 45567788899999755 4789999998864 222232222222222 24788888877776665
No 59
>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=20.84 E-value=2.1e+02 Score=22.62 Aligned_cols=37 Identities=14% Similarity=0.263 Sum_probs=26.2
Q ss_pred EEeecCChhHH-HHHHHHHhhhhcCC-ceEEEEeCHHHH
Q 013058 305 MYAYSTSKLHC-EILRLFSKVEYQLP-NLIVGAITKESL 341 (450)
Q Consensus 305 vYAYT~S~lqi-aiL~lF~~l~~r~P-Nlvvg~iTReSv 341 (450)
||-|++.--++ ++...|.++...++ ++.++.+.-+.-
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 888887766543
No 60
>PRK12928 lipoyl synthase; Provisional
Probab=20.75 E-value=8.9e+02 Score=24.55 Aligned_cols=21 Identities=19% Similarity=0.314 Sum_probs=13.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHH
Q 013058 339 ESLYNAFENGITAEQIISFLQ 359 (450)
Q Consensus 339 eSv~~Al~~GITA~QII~fL~ 359 (450)
+.|...+..|.|.++.+..++
T Consensus 175 ~~vl~~m~r~~t~e~~le~l~ 195 (290)
T PRK12928 175 PRLQKAVRRGADYQRSLDLLA 195 (290)
T ss_pred HHHHHHhCCCCCHHHHHHHHH
Confidence 666666666666666665554
No 61
>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=20.59 E-value=1.6e+02 Score=24.86 Aligned_cols=54 Identities=19% Similarity=0.087 Sum_probs=35.3
Q ss_pred HHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHHhcCCccccccCCCCChhHHHHHHHH
Q 013058 315 CEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLW 384 (450)
Q Consensus 315 iaiL~lF~~l~~r~PNlvvg~iTReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~~lP~tV~dQIrLW 384 (450)
-+.+.-++++.+ -||++|++++.||.=|+.---+.-....+....++.|||-.+
T Consensus 37 ~~~~~ai~rliS----------------~~Lr~G~~~~~ii~~L~gi~~~~~~~~~~~~~~S~~D~Ia~~ 90 (95)
T PF12637_consen 37 SGNLEAIARLIS----------------LALRSGVPPEEIIDQLRGIRCGPSGTVGGSRVTSCPDAIAKA 90 (95)
T ss_pred hHHHHHHHHHHH----------------HHHHcCCCHHHHHHHhcCCCCCCCCccCCCccCcHHHHHHHH
Confidence 466667777766 899999999999999986543322111123344577777543
No 62
>PF07801 DUF1647: Protein of unknown function (DUF1647); InterPro: IPR012444 This entry consists of hypothetical proteins of unknown function.
Probab=20.50 E-value=4.4e+02 Score=24.33 Aligned_cols=104 Identities=19% Similarity=0.325 Sum_probs=62.9
Q ss_pred ccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCcccccchhhhhhhcccCCCccccccceEEEeeCceEEeecCChhH
Q 013058 235 VAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLH 314 (450)
Q Consensus 235 ~~G~~Y~~~~lt~~q~~~L~~L~~~GLv~~~~~~~~~fy~pT~La~~L~~~~~~~~~~~~g~IIvETNFrvYAYT~S~lq 314 (450)
..|+.|+.+ .|..|.+++|+-.. +.|+ +.++....++. .-+-.++++.--
T Consensus 24 ~iGkkF~C~--------~l~~Le~l~l~~~~----~~~v-----------~l~~~~~n~~~-------vvfVSa~S~~h~ 73 (142)
T PF07801_consen 24 SIGKKFDCS--------LLETLEDLKLLDNP----GPFV-----------DLSSSSKNSSD-------VVFVSATSDNHF 73 (142)
T ss_pred ccCceecch--------HHHHHhhhhhccCC----Ccce-----------ecccccccCCc-------cEEEEEecchHH
Confidence 467777777 79999999999443 3455 11111112222 223344444444
Q ss_pred HHHHHHHHhhhhcCCc--eEEEEeCHHHHHHHHHcCCCHHHHHHHHHhc-CCcccccc-CCCCChhHHHH
Q 013058 315 CEILRLFSKVEYQLPN--LIVGAITKESLYNAFENGITAEQIISFLQQN-AHPRVADR-MPSVPENVCDQ 380 (450)
Q Consensus 315 iaiL~lF~~l~~r~PN--lvvg~iTReSv~~Al~~GITA~QII~fL~~h-AHp~m~~~-~~~lP~tV~dQ 380 (450)
-..+.++..+..-+|| ++++- -|++..||-.. .++ ..=++++- ...-|+-|.+.
T Consensus 74 ~~~~~~i~si~~~~P~~k~ilY~-----------LgL~~~~i~~L-~~~~~n~evr~Fn~s~YP~yV~n~ 131 (142)
T PF07801_consen 74 NESMKSISSIRKFYPNHKIILYD-----------LGLSEEQIKKL-KKNFCNVEVRKFNFSKYPKYVNNW 131 (142)
T ss_pred HHHHHHHHHHHHHCCCCcEEEEe-----------CCCCHHHHHHH-HhcCCceEEEECCCccCcHHHHHH
Confidence 4788889999988999 77774 48999987654 332 22233332 36677777664
No 63
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=20.47 E-value=1.8e+02 Score=26.40 Aligned_cols=34 Identities=18% Similarity=0.341 Sum_probs=26.7
Q ss_pred HHHHHHHHHcCCCHHHHHHHHHhcCCccccccCC
Q 013058 338 KESLYNAFENGITAEQIISFLQQNAHPRVADRMP 371 (450)
Q Consensus 338 ReSv~~Al~~GITA~QII~fL~~hAHp~m~~~~~ 371 (450)
|.-|++-+..|-|-+||++|+...-=....-++|
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 7789999999999999999999876444443333
No 64
>PRK13808 adenylate kinase; Provisional
Probab=20.02 E-value=2.5e+02 Score=29.37 Aligned_cols=77 Identities=17% Similarity=0.190 Sum_probs=47.9
Q ss_pred hhcCCceEEEEeCHHHHHHHHHcCCCHHHH-HHHHHhcCCccccccCCCCChhHHHHHHHHHHhcCceeeecceeecCCC
Q 013058 325 EYQLPNLIVGAITKESLYNAFENGITAEQI-ISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFP 403 (450)
Q Consensus 325 ~~r~PNlvvg~iTReSv~~Al~~GITA~QI-I~fL~~hAHp~m~~~~~~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~f~ 403 (450)
.|.++.+.+|-|=|+-| ..|...... -.++. .+..+|..++.+|-.++++... ...|++++.|+
T Consensus 23 ~ygl~~is~gdlLR~~i----~~~s~~g~~~~~~~~---------~G~lVPdeiv~~li~e~l~~~~--~~~G~ILDGFP 87 (333)
T PRK13808 23 QYGIVQLSTGDMLRAAV----AAGTPVGLKAKDIMA---------SGGLVPDEVVVGIISDRIEQPD--AANGFILDGFP 87 (333)
T ss_pred HhCCceecccHHHHHHh----hcCChhhHHHHHHHH---------cCCCCCHHHHHHHHHHHHhccc--ccCCEEEeCCC
Confidence 45678888886655544 444433332 22322 2457999999999888876543 46799999999
Q ss_pred CH-HHHHHHHHHHH
Q 013058 404 SR-DVFEAACDYAR 416 (450)
Q Consensus 404 s~-~~f~~v~~ya~ 416 (450)
.. ++.+.+-....
T Consensus 88 Rt~~QA~~L~~ll~ 101 (333)
T PRK13808 88 RTVPQAEALDALLK 101 (333)
T ss_pred CCHHHHHHHHHHHH
Confidence 75 44444433333
Done!