Query 015409
Match_columns 407
No_of_seqs 130 out of 215
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:02:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015409.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015409hhsearch_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 2E-132 4E-137 1017.8 43.5 392 10-405 1-403 (448)
2 KOG3471 RNA polymerase II tran 100.0 3E-131 7E-136 982.5 34.2 399 3-406 7-419 (465)
3 PF03849 Tfb2: Transcription f 100.0 2E-116 4E-121 890.2 38.5 350 13-364 1-366 (366)
4 COG5144 TFB2 RNA polymerase II 100.0 1E-114 2E-119 841.9 25.6 390 7-405 6-401 (447)
5 PF13625 Helicase_C_3: Helicas 99.6 2.8E-14 6E-19 125.0 11.7 94 297-398 2-97 (129)
6 TIGR00603 rad25 DNA repair hel 97.2 0.0019 4.1E-08 71.7 10.2 88 294-394 22-110 (732)
7 PF08671 SinI: Anti-repressor 91.3 0.19 4.2E-06 33.8 2.4 22 340-361 8-29 (30)
8 TIGR01615 A_thal_3542 uncharac 77.2 1.3 2.8E-05 39.7 1.4 65 293-375 47-112 (131)
9 KOG1123 RNA polymerase II tran 64.4 13 0.00028 40.5 5.6 89 293-393 81-169 (776)
10 PRK05718 keto-hydroxyglutarate 56.7 94 0.002 29.8 9.6 126 245-397 1-138 (212)
11 PF08356 EF_assoc_2: EF hand a 56.0 17 0.00037 30.4 3.9 27 184-210 26-57 (89)
12 PRK14529 adenylate kinase; Pro 54.2 24 0.00052 34.0 5.2 67 324-405 22-88 (223)
13 COG1420 HrcA Transcriptional r 51.7 12 0.00027 38.5 2.9 61 203-279 12-72 (346)
14 PF04720 DUF506: Protein of un 46.3 9.7 0.00021 36.9 1.1 66 292-375 135-201 (218)
15 PF03428 RP-C: Replication pro 46.2 69 0.0015 30.0 6.7 69 203-273 25-112 (177)
16 smart00418 HTH_ARSR helix_turn 45.5 1.1E+02 0.0023 21.6 6.6 54 48-103 2-56 (66)
17 TIGR03853 matur_matur probable 45.2 29 0.00063 28.4 3.5 27 336-362 18-58 (77)
18 PF00406 ADK: Adenylate kinase 43.9 10 0.00023 33.2 0.9 67 325-405 19-85 (151)
19 PRK10141 DNA-binding transcrip 41.3 1.9E+02 0.0041 25.2 8.3 70 33-103 6-76 (117)
20 COG1497 Predicted transcriptio 38.8 11 0.00025 37.1 0.3 39 162-200 40-78 (260)
21 PRK03911 heat-inducible transc 37.5 29 0.00063 34.5 2.9 47 232-280 24-70 (260)
22 PF01706 FliG_C: FliG C-termin 37.0 1.5E+02 0.0032 25.0 6.9 60 6-65 28-89 (110)
23 PF10678 DUF2492: Protein of u 36.1 49 0.0011 27.1 3.5 27 336-362 20-60 (78)
24 PF01081 Aldolase: KDPG and KH 35.9 71 0.0015 30.4 5.2 89 294-398 32-132 (196)
25 PF03444 HrcA_DNA-bdg: Winged 35.1 40 0.00087 27.6 2.9 33 246-279 37-69 (78)
26 PF13463 HTH_27: Winged helix 35.0 1.6E+02 0.0034 21.8 6.1 58 44-102 4-66 (68)
27 PRK13824 replication initiatio 34.2 1.3E+02 0.0028 31.7 7.3 69 202-273 36-124 (404)
28 PLN02459 probable adenylate ki 33.3 79 0.0017 31.4 5.2 69 325-405 52-120 (261)
29 TIGR02425 decarb_PcaC 4-carbox 31.8 53 0.0012 28.8 3.4 25 338-362 76-100 (123)
30 PRK06015 keto-hydroxyglutarate 31.3 2.1E+02 0.0045 27.4 7.5 90 294-399 28-129 (201)
31 PRK00135 scpB segregation and 26.9 1.3E+02 0.0029 28.3 5.3 55 48-106 95-154 (188)
32 PF03918 CcmH: Cytochrome C bi 26.3 58 0.0012 29.6 2.7 28 338-365 63-90 (148)
33 PF13833 EF-hand_8: EF-hand do 25.7 74 0.0016 22.7 2.7 20 334-353 3-26 (54)
34 cd07153 Fur_like Ferric uptake 24.7 2.1E+02 0.0046 23.7 5.8 57 45-101 3-66 (116)
35 smart00195 DSPc Dual specifici 24.2 1.8E+02 0.0038 24.8 5.3 52 329-386 80-137 (138)
36 TIGR03147 cyt_nit_nrfF cytochr 22.8 1.5E+02 0.0033 26.4 4.6 29 338-366 63-91 (126)
37 PF12637 TSCPD: TSCPD domain; 22.2 1.5E+02 0.0034 24.6 4.3 54 315-384 37-90 (95)
38 PF08784 RPA_C: Replication pr 21.5 1.1E+02 0.0023 25.4 3.2 51 196-263 45-96 (102)
39 PF01638 HxlR: HxlR-like helix 21.1 3.4E+02 0.0073 21.9 6.1 56 48-104 10-69 (90)
40 PRK10144 formate-dependent nit 20.9 1.8E+02 0.0038 26.0 4.6 29 338-366 63-91 (126)
41 COG4902 Uncharacterized protei 20.6 1.5E+02 0.0032 27.4 4.1 75 38-118 58-134 (189)
42 PLN02674 adenylate kinase 20.4 1.1E+02 0.0023 30.1 3.5 67 325-405 54-120 (244)
43 PF05184 SapB_1: Saposin-like 20.1 97 0.0021 20.8 2.3 21 340-360 13-33 (39)
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=1.6e-132 Score=1017.76 Aligned_cols=392 Identities=34% Similarity=0.616 Sum_probs=363.7
Q ss_pred hHHHHHhhCCHHHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceee
Q 015409 10 NFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFS 89 (407)
Q Consensus 10 ~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~ 89 (407)
+++|||++||+.++++||++||||+||||+||||||+|||||||+++|+|.++++.|+++++++++++|+++|++||||+
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 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ec-CCCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCCCC-CCCChHHHHHHHhhhHHHHHHHHhCCCCCCCCCCCchH
Q 015409 90 EE-KKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITA-RLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSS 167 (407)
Q Consensus 90 ~~-~~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~~~-~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s~~ 167 (407)
+. .+|.+.|.||++||+|||.||+|||.+++++++...++ +.+++++||+||++|||+|||||||++.. ..++++
T Consensus 81 ~~~~~~~~~~~Ln~~F~~~lr~aL~g~~~~~s~~v~~~~~d~~~~~~~~Ld~yA~~~WE~IL~fmVgs~~~---~~~s~~ 157 (448)
T TIGR00625 81 TQLLPGLQGIILNPIFRQNLRIALTGGGKANSFGVSQLGPDKHAVDVDSLDKYAEERWETILHFMVGTPSA---KVPSED 157 (448)
T ss_pred ecCCCCceeEEECHHHHHHHHHHhcCCCCCCCCCCcccCCCCCCCCHHHHHHHHHHHHHHHHHHHcCCCCc---CCCchH
Confidence 73 34557899999999999999999999999988876555 48999999999999999999999997653 347889
Q ss_pred HHHHHHhcCcccc-C-CCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCC
Q 015409 168 MMKVFQRGLLSRR-D-KEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTL 245 (407)
Q Consensus 168 ~~~lL~~~ll~~~-~-~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~l 245 (407)
++++|++|+|+++ + ++.+.||++||||||+|+|+|+|+||++||+++|++|+|.+|+|+|||+||++++|++|++++|
T Consensus 158 v~~lL~~~~Lm~~~~~~~~~~IT~~GFqFLLqd~n~QvW~lll~YL~~~e~~g~d~vevLsFLf~Ls~l~lG~~Y~~~~L 237 (448)
T TIGR00625 158 VLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAESRGMDLVEVLHFLFMLGFLTLGKAYSVDGL 237 (448)
T ss_pred HHHHHHhCCCCcccCCCCCccCchhhHHHHcCChhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhccccCCccCCCCC
Confidence 9999988666655 3 3347999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccc----c--ccccceEEEeeCceEEEecCCHhHHHHHH
Q 015409 246 SEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS----S--ARKEGFIVVETNFRMYAYSTSKLHCEILR 319 (407)
Q Consensus 246 t~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~----~--~~~~g~IIVETNFrvYAYT~S~lqiaiL~ 319 (407)
|++|++||+||+|+||||++ +.++++||||+||++||+++... + +.++|+|||||||||||||+||||++||+
T Consensus 238 t~tq~~~L~dL~dlGLVy~~-~~~~~~fYPTrLAt~Lts~~~~l~~~~~~~~~~~g~iivEtNfrvYaYt~s~l~~~il~ 316 (448)
T TIGR00625 238 SDTQLIMLQDLREYGLVFQR-KRKSRRFYPTRLAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIA 316 (448)
T ss_pred CHHHHHHHHHHHHcCeEEEe-cCCCCcccchHHHHHHhcCccccccccccccCCCceEEEEecceEEEecCCHHHHHHHH
Confidence 99999999999999999855 45677899999999999874421 1 25679999999999999999999999999
Q ss_pred HHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccc-cCCCCCChhHHHHHHHHHHhcCceeeeCeee
Q 015409 320 LFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVA-DRMPSVPENVCDQIRLWESDLNRVEMTPAHY 398 (407)
Q Consensus 320 lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~-~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~L 398 (407)
+||++.|||||||||+||||||++|+++||||||||+||++||||+|+ ++.|+|||||+|||||||.||||+++++|||
T Consensus 317 lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GITa~qIi~fl~~~ahp~~~~~~~~~lP~tv~dQi~lWe~e~~R~~~~~~~l 396 (448)
T TIGR00625 317 LFSELLARFPNMVVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDRLRFTEGVL 396 (448)
T ss_pred HHHHHHhcCCceEEEEecHHHHHHHHHcCCCHHHHHHHHHhcCChhhhccCCCCCChHHHHHHHHHHHHhcceEeeccee
Confidence 999999999999999999999999999999999999999999999998 5889999999999999999999999999999
Q ss_pred ecCCCCC
Q 015409 399 YDEFPSR 405 (407)
Q Consensus 399 y~~F~s~ 405 (407)
|+||+|.
T Consensus 397 ~~~f~s~ 403 (448)
T TIGR00625 397 YNDFLTQ 403 (448)
T ss_pred eeecCCH
Confidence 9999985
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=3e-131 Score=982.47 Aligned_cols=399 Identities=38% Similarity=0.644 Sum_probs=365.3
Q ss_pred chhhhhhhHHHHHhhCCH--HHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHH
Q 015409 3 LVKIIAKNFMDMVASLTA--RDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAID 80 (407)
Q Consensus 3 ~~~~~~~~~~~yL~~Lp~--~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~ 80 (407)
+.--.++++.+||+.||. .+++|||++|++|+||||+|||+||+|||+|||.++|||.++++.|++.++++++++|++
T Consensus 7 ~~~~~~~~~c~~leeLp~~~~~l~RLY~~Pa~ClAIfR~LPpLAkqfVm~MLf~~~pVP~a~~~~Wv~~~~tk~q~eaik 86 (465)
T KOG3471|consen 7 QGWPYAKNICDYLEELPRIPHSLDRLYGKPAICLAIFRELPPLAKQFVMQMLFKDQPVPLADVDLWVKVEETKEQEEAIK 86 (465)
T ss_pred ccCcccchHHHHHHHhhccchHHHHHhCCchHHHHHHHhCcHHHHHHHHHHHhcCCCccHHHHHHHhhhhhHHHHHHHHH
Confidence 333478899999999999 589999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhccceeeecC-CCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCC-CCCCCChHHHHHHHhhhHHHHHHHHhCCCCC
Q 015409 81 RLVQLRLFSEEK-KKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGI-TARLPTLEDLEAYAIGQWECFLLQLISSTQA 158 (407)
Q Consensus 81 ~L~~L~I~~~~~-~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~-~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~ 158 (407)
.|.+||||.+.. .| +.+.|||+||+|+|.||+|||..++++.+.-. ..+.+++++||+||.+|||||||||||++.+
T Consensus 87 ~L~~L~I~~~~~~~g-~~i~Lnp~fr~s~~~al~gg~~~~s~~s~~l~~~~~~r~v~~ld~ya~~rwe~ILh~mvgt~~a 165 (465)
T KOG3471|consen 87 LLKRLRIFHKQGTPG-QAINLNPTFRRSLRDALTGGGKQNSFGSLVLGEDKHNRDVDFLDKYASERWECILHFMVGTPEA 165 (465)
T ss_pred HHhheeeEeecCCCC-ceEEeCHHHHHHHHHHHhcCCCcccCCCcccCCCcCcccchhhHHHHHHHHHHHHHHHhCCccc
Confidence 999999999732 23 67999999999999999999999887543322 2258999999999999999999999998743
Q ss_pred CCCCCCchHHHHHHHhcCccccCCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCc
Q 015409 159 ERPTNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGE 238 (407)
Q Consensus 159 ~~~~~~s~~~~~lL~~~ll~~~~~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~ 238 (407)
..+|.++.++|..|++++++.....||++||||||+|+++|+|+++++||++.|++|||.+|+|+|||+||++++|+
T Consensus 166 ---~~~se~v~~ll~~a~lm~~~~~~~~IT~~GFQFLL~~~~aQlW~~~LqyLk~~~~~~~dlvevL~~LfqL~~~~~G~ 242 (465)
T KOG3471|consen 166 ---KAVSEGVLNLLKHAGLMSRDENQIEITNAGFQFLLLDINAQLWTLVLQYLKLFESSGMDLVEVLEFLFQLSALALGR 242 (465)
T ss_pred ---cccChhHHHHHHhcCccCCCCCCceEeecchhhhhcCcHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHhcc
Confidence 46889999999766666665667899999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccc--------cccccceEEEeeCceEEEecC
Q 015409 239 AYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS--------SARKEGFIVVETNFRMYAYST 310 (407)
Q Consensus 239 ~Y~~~~lt~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~--------~~~~~g~IIVETNFrvYAYT~ 310 (407)
+|+++++|++|+.||+||||+|||| |++.|+.+||||+||++++++.... .+.+.|||||||||||||||+
T Consensus 243 ~Ysvd~~~~~~~~~lq~Lre~Glvf-Qrk~k~~rfyptrla~~~ss~~~~~~~~~~~~~~edd~G~iIVETN~riYAYT~ 321 (465)
T KOG3471|consen 243 AYSVDALTETQRILLQHLRELGLVF-QRKIKILRFYPTRLAIGLSSDQLGAASLVHQNRNEDDVGFIIVETNYRIYAYTN 321 (465)
T ss_pred cceeehhhHHHHHHHHHHHHhhHHH-HhhhhhheecchhhhhccchhhhhhhhhhhcccccccCceEEEEeccEEEEecC
Confidence 9999999999999999999999996 7778999999999999998863321 123459999999999999999
Q ss_pred CHhHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCC--CCCChhHHHHHHHHHHhc
Q 015409 311 SKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM--PSVPENVCDQIRLWESDL 388 (407)
Q Consensus 311 S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~--p~lP~tV~dQIrLWe~Er 388 (407)
||||+||++|||++.|||||||||+|||||||+|+++||||+|||+||++||||||+... |++||||+|||||||.||
T Consensus 322 S~lQiAvi~LF~~l~~rf~nlvvG~iTreSVr~Al~~GITa~QII~fLet~ahpqm~~~~~~~~LPpTv~dQIrLWEler 401 (465)
T KOG3471|consen 322 SPLQIAVIALFTELTYRFPNLVVGVITRESVRRALDNGITAEQIIHFLETHAHPQMRMLSPVPCLPPTVVDQIRLWELER 401 (465)
T ss_pred CHHHHHHHHHHHHHHhhccccceeeeeHHHHHHHHhcCCcHHHHHHHHHhccCchhhhcCCCCCCCchHHhHHHHHHHhh
Confidence 999999999999999999999999999999999999999999999999999999998755 899999999999999999
Q ss_pred CceeeeCeeeecCCCCCC
Q 015409 389 NRVEMTPAHYYDEFPSRV 406 (407)
Q Consensus 389 ~R~~~~~g~Ly~~F~s~~ 406 (407)
||+.++|||||++|+|.+
T Consensus 402 nR~~~~~g~LYs~Fls~~ 419 (465)
T KOG3471|consen 402 NRLRMTEGYLYSDFLSLS 419 (465)
T ss_pred cceecccchhHHhhhhhh
Confidence 999999999999999853
No 3
>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=1.7e-116 Score=890.17 Aligned_cols=350 Identities=43% Similarity=0.747 Sum_probs=324.8
Q ss_pred HHHhhCCHHHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeeec-
Q 015409 13 DMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEE- 91 (407)
Q Consensus 13 ~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~- 91 (407)
|||++||++++++||++||||+||||+||++||||||||||+++|||++++++||++++++++++|+++|.+||||++.
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 6999999999999999999999999999999999999999999999999999999999999999999999999999873
Q ss_pred -CCCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCCC-CCCCChHHHHHHHhhhHHHHHHHHhCCCCCCCCCCCchHHH
Q 015409 92 -KKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGIT-ARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSSSMM 169 (407)
Q Consensus 92 -~~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~~-~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s~~~~ 169 (407)
+++.+.|.|||+||+|||.||+|||..+++++++... .+.+++++||+||++|||+|||||||++...... +|++++
T Consensus 81 ~~~~~~~~~Ln~~F~~~Lr~aL~ggg~~~~~~~~~~~~~~~~~~~~~Ld~yA~~rWE~IL~~mVgs~~~~~~~-~s~~v~ 159 (366)
T PF03849_consen 81 SPGGKQQYQLNPIFRKNLRNALTGGGKPWSFGVPSEEPDKKAPDVEFLDEYARERWESILHYMVGSSSSSNSS-PSQDVK 159 (366)
T ss_pred CCCCceeEEeCHHHHHHHHHHHhCCCCCcccCcccccccCCCCCHHHHHHHHHHHHHHHHHHHhcCcccccCC-CCHHHH
Confidence 3344789999999999999999999999998887765 4689999999999999999999999998764333 789999
Q ss_pred HHHHhcCcccc--CCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCCCH
Q 015409 170 KVFQRGLLSRR--DKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSE 247 (407)
Q Consensus 170 ~lL~~~ll~~~--~~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~lt~ 247 (407)
++|+.++|++. .+++..||++||||||+|+|+|+|+||++||+.+|++|+|.+|+|+|||+||++++|++|++++||+
T Consensus 160 ~lL~~sgLm~~~~~~~~~~IT~~GFqFLL~d~~~QlW~lll~yL~~~e~~~~~~~~~l~flf~L~~~~~g~~Y~~~~ls~ 239 (366)
T PF03849_consen 160 QLLKRSGLMKRSESGGSLKITSKGFQFLLQDTNAQLWTLLLQYLKMAEARGMDLVEVLSFLFQLSFLELGKAYSTEGLSE 239 (366)
T ss_pred HHHHHcCCCcCcCCCCCCcEehhheeeecCChHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhcccccCCcCcCCCCCH
Confidence 99977555554 4567899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccc-----------cccccceEEEeeCceEEEecCCHhHHH
Q 015409 248 IQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDS-----------SARKEGFIVVETNFRMYAYSTSKLHCE 316 (407)
Q Consensus 248 ~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~-----------~~~~~g~IIVETNFrvYAYT~S~lqia 316 (407)
+|++||+||+|+||||.++ +++++|||||||++|+++++.. ...++|||||||||||||||+||||+|
T Consensus 240 ~q~~~L~~l~~~GLvy~~~-~~~~~fypT~La~~l~~~~~~~~~~~~~~~~~~~~~~~g~iivETNfrvYAYT~s~l~ia 318 (366)
T PF03849_consen 240 TQKNMLQDLRELGLVYQRK-RKSRRFYPTRLATNLTSGSSALRSASSALDSSSSSNKEGFIIVETNFRVYAYTNSPLQIA 318 (366)
T ss_pred HHHHHHHHHHHCCeEEEec-CCCCeEechHHHHHHhcCCCcccccccccccccccccCceEEEEecceEEEecCCHHHHH
Confidence 9999999999999998554 5788899999999999976521 235789999999999999999999999
Q ss_pred HHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCcc
Q 015409 317 ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHP 364 (407)
Q Consensus 317 iL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp 364 (407)
||++||++.|||||||||+|||||||+|+++||||||||+||++||||
T Consensus 319 iL~lF~~~~~r~pnlvvg~iTr~Sv~~A~~~GIta~qIi~fL~~~aHp 366 (366)
T PF03849_consen 319 ILSLFCELKYRFPNLVVGQITRESVRRALKNGITADQIISFLRSHAHP 366 (366)
T ss_pred HHHHHHHHHhcCCCeEEEEEcHHHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 999999999999999999999999999999999999999999999998
No 4
>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=1.1e-114 Score=841.86 Aligned_cols=390 Identities=31% Similarity=0.541 Sum_probs=362.1
Q ss_pred hhhhHHHHHhhCCHHHHHHHhcCchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccc
Q 015409 7 IAKNFMDMVASLTARDLDRLYENPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLR 86 (407)
Q Consensus 7 ~~~~~~~yL~~Lp~~~~~~LY~~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~ 86 (407)
.+.++.+|||.||.....|||+.|++|+|+||.||++|++|||.|||.+.+||..+.+.|++.+.+-...+++..+.++|
T Consensus 6 ~k~si~~ylE~lP~~~~~rLY~~Pa~cla~~rvlp~la~~fvm~mlfn~~~v~lld~d~wik~~~Ki~~~~~v~~~k~~h 85 (447)
T COG5144 6 YKISIIEYLEMLPRHSKTRLYGAPAFCLAFLRVLPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKKGNH 85 (447)
T ss_pred ccccHHHHHHHhhhhhhhhhhcCcHHHHHHHHhccHHHHHHHHHHHcCCCCcchhhHHHHHhhhhHHHHHHHHhhhccce
Confidence 45789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeeecCCCceeEEeCHHHHHHHHHHHHcCCCCCCCCCCCCCCCCCCChHHHHHHHhhhHHHHHHHHhCCCCCCCCCCCch
Q 015409 87 LFSEEKKKETTYRLNSTFQSNLRKHLIYGGALPREPMPSGITARLPTLEDLEAYAIGQWECFLLQLISSTQAERPTNFSS 166 (407)
Q Consensus 87 I~~~~~~~~~~~~Ln~~F~~~lr~aL~ggg~~~~~~~~~~~~~~~~~~~~Ld~ya~~~WE~IL~~mV~~~~~~~~~~~s~ 166 (407)
|...+ | ..+++||.||.+|+.|||||+..+++++ -+..+.+++++||+||.++||+|||||||...+. -++.
T Consensus 86 i~~~~--g-~~i~ln~~fk~sl~~altgg~~~nsfgv--~i~E~lvsvd~ld~ys~~kwEtILhfmVgtpeak---ip~e 157 (447)
T COG5144 86 IYLDE--G-LMIRLNPEFKISLMDALTGGTMENSFGV--CIGEKLVSVDMLDSYSSRKWETILHFMVGTPEAK---IPAE 157 (447)
T ss_pred EEecC--C-ceEEeChHHHHHHHHHhhccccccccce--eeccceeeeehhhhhhhhhHHHHHHHHhCCcccc---Ccch
Confidence 99863 3 6899999999999999999999887776 2233578999999999999999999999987652 3577
Q ss_pred HHHHHHHhcCccccCCCCCccchhhhhhhccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCCC
Q 015409 167 SMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLS 246 (407)
Q Consensus 167 ~~~~lL~~~ll~~~~~~~~~IT~~GFqFLL~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~lt 246 (407)
.|+++|+.|+++.++....+||++|||||||+.|+|+|+++++||++.|...||++++|+||||||.+++|++|+++.||
T Consensus 158 gVl~lLk~ggLm~~~~ne~kITn~GFqFLLq~in~QlWtLlL~yLK~~e~s~md~v~VLhflFmLgal~vG~aY~id~ls 237 (447)
T COG5144 158 GVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVLHFLFMLGALAVGTAYKIDALS 237 (447)
T ss_pred hHHHHHHhcccccCCcccceeehhHHHHHHHHHHHHHHHHHHHHHHHhccccccHHHHHHHHHHhcchhhcceeeecccc
Confidence 89999988777777667889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccc----cc--cccccceEEEeeCceEEEecCCHhHHHHHHH
Q 015409 247 EIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLT----DS--SARKEGFIVVETNFRMYAYSTSKLHCEILRL 320 (407)
Q Consensus 247 ~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~----~~--~~~~~g~IIVETNFrvYAYT~S~lqiaiL~l 320 (407)
++|+-||+|+|++|||+ +++-.++.||||+||+.+++.-. .. .+.+.|||||||||||||||+||||+|+++|
T Consensus 238 dtqqiml~D~R~yglv~-q~~i~~~~fYpt~LA~glt~d~~~~~s~qnr~edd~gfiIVETN~kiYaYtnSplqiavi~L 316 (447)
T COG5144 238 DTQQIMLMDRRLYGLVE-QLGILRKIFYPTGLAIGLTFDQLFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHL 316 (447)
T ss_pred hHHHHHHHHHHHhhHHH-HhccchhhccccccchhhhhHHHHHhhhhccccccCceEEEEecceEEEecCChHHHHHHHH
Confidence 99999999999999996 66666788999999999988521 11 2256799999999999999999999999999
Q ss_pred HHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeec
Q 015409 321 FSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYD 400 (407)
Q Consensus 321 F~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~ 400 (407)
||++..||||||+|+|||||||+|+.+||||+|||.||++||||||+++.+.+||||+|||+|||.|+||+...||+||+
T Consensus 317 F~nl~arf~Nlv~GiITreSirrAl~nGIta~QII~yLethahpqmr~~l~llPPtivdQI~lWele~nRi~~~pG~Lys 396 (447)
T COG5144 317 FCNLTARFPNLVKGIITRESIRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYS 396 (447)
T ss_pred hhhhhcccchhhhhhccHHHHHHHHhcCccHHHHHHHHHhccChhhhhcCCCCChhhhhheeeeeeccCcEEeecchHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCC
Q 015409 401 EFPSR 405 (407)
Q Consensus 401 ~F~s~ 405 (407)
||.+.
T Consensus 397 dFlt~ 401 (447)
T COG5144 397 DFLTL 401 (447)
T ss_pred hhhch
Confidence 99874
No 5
>PF13625 Helicase_C_3: Helicase conserved C-terminal domain
Probab=99.56 E-value=2.8e-14 Score=124.95 Aligned_cols=94 Identities=27% Similarity=0.444 Sum_probs=85.1
Q ss_pred EEEeeCceEEEecCCH-hH-HHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCC
Q 015409 297 IVVETNFRMYAYSTSK-LH-CEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVP 374 (407)
Q Consensus 297 IIVETNFrvYAYT~S~-lq-iaiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP 374 (407)
+||++||.|.+++.+| .. ...|..||++ .+..+|.+++||+.|+.+|++.|+|+++|++||+.|+. ..||
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-KSPDTMHVYRLTPASLWRAASAGLTAEEIIEFLERYSK-------NPLP 73 (129)
T ss_pred EEECCCCEEEEeCCCCCHHHHHHHHHHhcc-cccCceEEEEECHHHHHHHHHcCCCHHHHHHHHHHHcC-------CCCC
Confidence 7999999999977666 34 4599999999 56799999999999999999999999999999999995 5789
Q ss_pred hhHHHHHHHHHHhcCceeeeCeee
Q 015409 375 ENVCDQIRLWESDLNRVEMTPAHY 398 (407)
Q Consensus 375 ~tV~dQIrLWe~Er~R~~~~~g~L 398 (407)
+||..+|+-|+...+|+++.++..
T Consensus 74 ~~v~~~i~~w~~~~g~v~l~~~~~ 97 (129)
T PF13625_consen 74 QNVEQSIEDWARRYGRVRLYKGAY 97 (129)
T ss_pred HHHHHHHHHHHHhcCCEEEecCeE
Confidence 999999999999999999998433
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=97.17 E-value=0.0019 Score=71.73 Aligned_cols=88 Identities=23% Similarity=0.385 Sum_probs=75.7
Q ss_pred cceEEEeeCceEEEecCCHhHH-HHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCC
Q 015409 294 EGFIVVETNFRMYAYSTSKLHC-EILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPS 372 (407)
Q Consensus 294 ~g~IIVETNFrvYAYT~S~lqi-aiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~ 372 (407)
+|.|++||--.+| =|. .-|..|+|+.+|--+|..++||-=|+-.|...|+++++||++|...+. ..
T Consensus 22 d~~i~lE~~~p~~------~~a~~fl~~~aEp~~rp~~iHeY~lT~~sl~~A~s~g~~~~~ii~~L~~~sk-------~~ 88 (732)
T TIGR00603 22 DGHIFLESFSPLY------KQAQDFLVAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLETEDIIEVLGRLSK-------TP 88 (732)
T ss_pred CCeEEEEeCCccH------HHHHHHHHHhcccccChhheEEEeccHHHHHHHHHcCCCHHHHHHHHHHHhC-------CC
Confidence 5667777643322 122 289999999999999999999999999999999999999999999985 57
Q ss_pred CChhHHHHHHHHHHhcCceeee
Q 015409 373 VPENVCDQIRLWESDLNRVEMT 394 (407)
Q Consensus 373 lP~tV~dQIrLWe~Er~R~~~~ 394 (407)
||++|.+.|+.+-.-.+++++.
T Consensus 89 ~p~~i~~~i~~~~~~ygk~klv 110 (732)
T TIGR00603 89 IPKGIIEFIRLCTQSYGKVKLV 110 (732)
T ss_pred CCHHHHHHHHHHHHhcCcEEEE
Confidence 9999999999999999999883
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=91.25 E-value=0.19 Score=33.80 Aligned_cols=22 Identities=36% Similarity=0.525 Sum_probs=17.7
Q ss_pred HHHHHHHcCCCHHHHHHHHhhc
Q 015409 340 SLYNAFENGITAEQIISFLQQN 361 (407)
Q Consensus 340 Svr~Al~~GITA~QII~fL~~h 361 (407)
=|+.|...|||.+||-.||+.+
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
>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=77.18 E-value=1.3 Score=39.66 Aligned_cols=65 Identities=17% Similarity=0.383 Sum_probs=51.3
Q ss_pred ccceEEEeeCceEEEecCCHhHHH-HHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCC
Q 015409 293 KEGFIVVETNFRMYAYSTSKLHCE-ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMP 371 (407)
Q Consensus 293 ~~g~IIVETNFrvYAYT~S~lqia-iL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p 371 (407)
++..+|||.||| +.+.|| ==.-+..+...+|.+.||...| -.||++.+-..|.-.|+++.-
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 456899999999 777766 3445778888899999998765 278999999888888887766
Q ss_pred CCCh
Q 015409 372 SVPE 375 (407)
Q Consensus 372 ~lP~ 375 (407)
-+||
T Consensus 109 hlPP 112 (131)
T TIGR01615 109 PLPP 112 (131)
T ss_pred CCCC
Confidence 6676
No 9
>KOG1123 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, 3'-5' helicase subunit SSL2 [Transcription; Replication, recombination and repair]
Probab=64.41 E-value=13 Score=40.53 Aligned_cols=89 Identities=24% Similarity=0.359 Sum_probs=70.3
Q ss_pred ccceEEEeeCceEEEecCCHhHHHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCC
Q 015409 293 KEGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPS 372 (407)
Q Consensus 293 ~~g~IIVETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~ 372 (407)
-+|.||+||==-+|-+- ...|--.+|..+|=-.+.=+.||-=|+-.|..-|.+-+.||++|..-+. ..
T Consensus 81 ~dG~IfLEsFsp~ykqA-----~DFLiaIaEPvcRP~~iHEy~lTaySLYAAVSVGL~T~dIie~L~rlSK-------t~ 148 (776)
T KOG1123|consen 81 PDGHIFLETFSPLYKQA-----QDFLIAIAEPVCRPEHIHEYKLTAYSLYAAVSVGLQTEDIIEVLDRLSK-------TP 148 (776)
T ss_pred CCCeEEeeecCHHHHhH-----hhhhhhhccccCChhhhhhhcchhhhhhhhhccccchHHHHHHHHHhcc-------CC
Confidence 36999999843333221 2255556788888888999999999999999999999999999998875 67
Q ss_pred CChhHHHHHHHHHHhcCceee
Q 015409 373 VPENVCDQIRLWESDLNRVEM 393 (407)
Q Consensus 373 lP~tV~dQIrLWe~Er~R~~~ 393 (407)
||+.|++=|++--.--+.++.
T Consensus 149 lp~~ii~FI~~cT~sYGKVKL 169 (776)
T KOG1123|consen 149 LPESIIEFIRACTVSYGKVKL 169 (776)
T ss_pred CCHHHHHHHHHHhhccccEEE
Confidence 999999999987766555543
No 10
>PRK05718 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=56.69 E-value=94 Score=29.78 Aligned_cols=126 Identities=21% Similarity=0.263 Sum_probs=82.6
Q ss_pred CCHHHHHHHHHHhhcCceeeecCCCccccccchhhhhhccccccccccccceEEEeeCceEEEecCCHhHHHHHHHHHhh
Q 015409 245 LSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLATNLSMSLTDSSARKEGFIVVETNFRMYAYSTSKLHCEILRLFSKV 324 (407)
Q Consensus 245 lt~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~~L~~~~~~~~~~~~g~IIVETNFrvYAYT~S~lqiaiL~lF~~l 324 (407)
+++++..+++.|.+.|+|-.-+..+.... -+++-.+ .+.|.=++|--++ +|-- +..+.++
T Consensus 1 ~~~~~~~~~~~l~~~~~iaV~r~~~~~~a--~~i~~al---------~~~Gi~~iEitl~------~~~~---~~~I~~l 60 (212)
T PRK05718 1 MKNWKTSIEEILRAGPVVPVIVINKLEDA--VPLAKAL---------VAGGLPVLEVTLR------TPAA---LEAIRLI 60 (212)
T ss_pred CchhHHHHHHHHHHCCEEEEEEcCCHHHH--HHHHHHH---------HHcCCCEEEEecC------CccH---HHHHHHH
Confidence 36788889999999999976554321111 1122112 1235667776643 4433 3444555
Q ss_pred hhcCCceEEEE---eCHHHHHHHHHcCC-------CHHHHHHHHhhcCccccccCCCCCCh--hHHHHHHHHHHhcCcee
Q 015409 325 EYQLPNLIVGA---ITKESLYNAFENGI-------TAEQIISFLQQNAHPRVADRMPSVPE--NVCDQIRLWESDLNRVE 392 (407)
Q Consensus 325 ~~r~Pnlvvg~---iTReSvr~Al~~GI-------TA~QII~fL~~hAHp~m~~~~p~lP~--tV~dQIrLWe~Er~R~~ 392 (407)
..+||++.||. +|.+.++.|++.|- ..+.+|++-..+-. +.+|- |..+=...|+.--+-++
T Consensus 61 ~~~~p~~~IGAGTVl~~~~a~~a~~aGA~FivsP~~~~~vi~~a~~~~i-------~~iPG~~TptEi~~a~~~Ga~~vK 133 (212)
T PRK05718 61 AKEVPEALIGAGTVLNPEQLAQAIEAGAQFIVSPGLTPPLLKAAQEGPI-------PLIPGVSTPSELMLGMELGLRTFK 133 (212)
T ss_pred HHHCCCCEEEEeeccCHHHHHHHHHcCCCEEECCCCCHHHHHHHHHcCC-------CEeCCCCCHHHHHHHHHCCCCEEE
Confidence 66799999995 99999999999983 45689998887655 45553 33553448888888888
Q ss_pred eeCee
Q 015409 393 MTPAH 397 (407)
Q Consensus 393 ~~~g~ 397 (407)
+.|+-
T Consensus 134 lFPa~ 138 (212)
T PRK05718 134 FFPAE 138 (212)
T ss_pred Eccch
Confidence 87753
No 11
>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=55.99 E-value=17 Score=30.43 Aligned_cols=27 Identities=26% Similarity=0.585 Sum_probs=22.9
Q ss_pred CCccchhhhhhh-----ccChhhHHHHHHHHH
Q 015409 184 APRLTESGFQFL-----LMDTNAQLWYIVREY 210 (407)
Q Consensus 184 ~~~IT~~GFqFL-----L~d~~~Q~W~lll~y 210 (407)
...||.+||-|| -+.+++-.|++|+.+
T Consensus 26 ~~GiT~~GFl~L~~lfierGR~ETtW~vLR~F 57 (89)
T PF08356_consen 26 DNGITLDGFLFLNKLFIERGRHETTWTVLRKF 57 (89)
T ss_pred CCccchhhHHHHHHHHHHhCcchHHHHHHHHc
Confidence 347999999855 889999999999973
No 12
>PRK14529 adenylate kinase; Provisional
Probab=54.20 E-value=24 Score=34.03 Aligned_cols=67 Identities=18% Similarity=0.292 Sum_probs=49.3
Q ss_pred hhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeecCCC
Q 015409 324 VEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFP 403 (407)
Q Consensus 324 l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~F~ 403 (407)
-.+.++.+.+|.+.|+.+.. ..-.+++|=.|+.+ ...+|..++-++-.+.....- ..|++++.||
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 34678999999999998753 22234566666643 357899999998888876543 7899999998
Q ss_pred CC
Q 015409 404 SR 405 (407)
Q Consensus 404 s~ 405 (407)
..
T Consensus 87 Rt 88 (223)
T PRK14529 87 RN 88 (223)
T ss_pred CC
Confidence 63
No 13
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=51.67 E-value=12 Score=38.52 Aligned_cols=61 Identities=25% Similarity=0.433 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhh
Q 015409 203 LWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLA 279 (407)
Q Consensus 203 ~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La 279 (407)
++.++-.|++..| + .|+-.+-+.|..+--+.|-++.+.+|.++|+++ +...+++|- ||.++
T Consensus 12 L~aIV~~Yi~t~e-----P---------VGSk~L~e~~~l~~SsATIRN~Ma~LE~~GlI~-k~HtSsGRv-PT~~G 72 (346)
T COG1420 12 LRAIVEDYLATGE-----P---------VGSKTLSEKYNLDLSSATIRNEMADLEKLGLIE-KPHTSSGRV-PTDKG 72 (346)
T ss_pred HHHHHHHHHhcCC-----c---------cchHHHHHHhCCCCCchhHHHHHHHHHHCCCcc-CccccCCcC-CcHhH
Confidence 3666777888775 1 233444455655555789999999999999997 555566665 77655
No 14
>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=46.29 E-value=9.7 Score=36.86 Aligned_cols=66 Identities=23% Similarity=0.386 Sum_probs=50.7
Q ss_pred cccceEEEeeCceEEEecCCHhHHH-HHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCC
Q 015409 292 RKEGFIVVETNFRMYAYSTSKLHCE-ILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRM 370 (407)
Q Consensus 292 ~~~g~IIVETNFrvYAYT~S~lqia-iL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~ 370 (407)
.+.-.+|||+||| +.+.|| -=.-|..+...+|...||...| + .||++.+-.-+.-.|+++.
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 3556899999999 666666 4456777888899999997543 3 6888888888887787776
Q ss_pred CCCCh
Q 015409 371 PSVPE 375 (407)
Q Consensus 371 p~lP~ 375 (407)
--+||
T Consensus 197 ~~lPP 201 (218)
T PF04720_consen 197 MHLPP 201 (218)
T ss_pred CCCCC
Confidence 66776
No 15
>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=46.23 E-value=69 Score=29.99 Aligned_cols=69 Identities=17% Similarity=0.364 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHcCCChHH--HHHHHHhhcccccCc----------------cccCCCCCHHH-HHHHHHHhhcCcee
Q 015409 203 LWYIVREYISNSQERGINQAD--LISFLLELSFHVAGE----------------AYNLNTLSEIQ-KSMIKDFADLGLVK 263 (407)
Q Consensus 203 ~W~lll~yl~~~e~~~~~~~~--~l~fLf~Ls~~~~G~----------------~Y~~~~lt~~q-~~~L~~L~d~GLvy 263 (407)
=|.++..--+.....|++..+ +|..|+.. ..... ...+.++++.+ +..|..|.|.|||.
T Consensus 25 k~~ll~~l~~a~~~lgl~~~~l~vL~aLls~--~~~~d~~~~~~piVfpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~ 102 (177)
T PF03428_consen 25 KWQLLRALKEARPALGLSDRALAVLDALLSF--TPPDDWEPGRRPIVFPSNAQLAERLNGMSERTLRRHLARLVEAGLIV 102 (177)
T ss_pred HHHHHHHHHHHHHhcCCChhHHHHHHHHHHh--CCcccccCCCCceeecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCee
Confidence 377766644455555776543 45544443 32222 11223566655 78899999999997
Q ss_pred eecCCCcccc
Q 015409 264 LQQGRKENWF 273 (407)
Q Consensus 264 ~~~~~~~~~f 273 (407)
.+...+.++|
T Consensus 103 rrDS~NgkRy 112 (177)
T PF03428_consen 103 RRDSPNGKRY 112 (177)
T ss_pred eccCCCCCcc
Confidence 6554455666
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=45.52 E-value=1.1e+02 Score=21.65 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=40.0
Q ss_pred HHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeeecC-CCceeEEeCHH
Q 015409 48 VMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEK-KKETTYRLNST 103 (407)
Q Consensus 48 vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~~-~~~~~~~Ln~~ 103 (407)
|+..++ ..+++..++..... -++....++++.|.+.+++.... ++...|.+++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~-is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~ 56 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG-LSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDE 56 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC-CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchH
Confidence 455666 78888888888764 45667889999999999997633 44457888884
No 17
>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=45.16 E-value=29 Score=28.38 Aligned_cols=27 Identities=41% Similarity=0.694 Sum_probs=22.7
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHhhcC
Q 015409 336 ITKESLYNAFE--------------NGITAEQIISFLQQNA 362 (407)
Q Consensus 336 iTReSvr~Al~--------------~GITA~QII~fL~~hA 362 (407)
+||+|++.|+. .|.||+++|+||...-
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 58888888874 6999999999999764
No 18
>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=43.87 E-value=10 Score=33.18 Aligned_cols=67 Identities=19% Similarity=0.338 Sum_probs=46.6
Q ss_pred hhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeecCCCC
Q 015409 325 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 404 (407)
Q Consensus 325 ~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~F~s 404 (407)
.|.++.+.+|.+=|+.+++ ..-.+++|-++|.+. -.||+.++-++-.++.+.. ....|++.+.||.
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 4567777777776666633 223357788887643 4789999999988888866 6679999999986
Q ss_pred C
Q 015409 405 R 405 (407)
Q Consensus 405 ~ 405 (407)
.
T Consensus 85 t 85 (151)
T PF00406_consen 85 T 85 (151)
T ss_dssp S
T ss_pred c
Confidence 4
No 19
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=41.29 E-value=1.9e+02 Score=25.19 Aligned_cols=70 Identities=14% Similarity=0.108 Sum_probs=53.1
Q ss_pred HHHHHhcCChhHHHHHHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeeecC-CCceeEEeCHH
Q 015409 33 CEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSEEK-KKETTYRLNST 103 (407)
Q Consensus 33 claifR~Lp~lak~~vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~~~-~~~~~~~Ln~~ 103 (407)
...+|+.|.+-.+.=|+++|...++.+..++..=+ .-++......++.|++-.++...+ +....|.+|+.
T Consensus 6 ~~~~fkaLadptRl~IL~~L~~~~~~~v~ela~~l-~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~ 76 (117)
T PRK10141 6 PLQLFKILSDETRLGIVLLLRESGELCVCDLCTAL-DQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPH 76 (117)
T ss_pred HHHHHHHhCCHHHHHHHHHHHHcCCcCHHHHHHHH-CcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECch
Confidence 35788888888888888888766788888776532 345666778899999999998744 44567899985
No 20
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=38.83 E-value=11 Score=37.09 Aligned_cols=39 Identities=18% Similarity=0.401 Sum_probs=28.7
Q ss_pred CCCchHHHHHHHhcCccccCCCCCccchhhhhhhccChh
Q 015409 162 TNFSSSMMKVFQRGLLSRRDKEAPRLTESGFQFLLMDTN 200 (407)
Q Consensus 162 ~~~s~~~~~lL~~~ll~~~~~~~~~IT~~GFqFLL~d~~ 200 (407)
+++|.-+++|-..|+..+.+.....||.+||+||+....
T Consensus 40 QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~ 78 (260)
T COG1497 40 QAVSEHIKELVKEGLIEKEGRGEYEITKKGAEWLLEQLS 78 (260)
T ss_pred HHHHHHHHHHHhccceeecCCeeEEEehhHHHHHHHHHH
Confidence 346777778777888877533356999999999985443
No 21
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=37.45 E-value=29 Score=34.47 Aligned_cols=47 Identities=21% Similarity=0.198 Sum_probs=35.7
Q ss_pred cccccCccccCCCCCHHHHHHHHHHhhcCceeeecCCCccccccchhhh
Q 015409 232 SFHVAGEAYNLNTLSEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLAT 280 (407)
Q Consensus 232 s~~~~G~~Y~~~~lt~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La~ 280 (407)
|+.++.+.|..+--+.|-++.+.+|.+.|++. +...++++- ||..+-
T Consensus 24 GSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~-qpHtSsGRI-PT~~gy 70 (260)
T PRK03911 24 GSNELKSLMNLKISAATIRNYFKKLSDEGLLT-QLHISGGRI-PTIKAM 70 (260)
T ss_pred CHHHHHHHcCCCCCcHHHHHHHHHHHHCcCcc-CCcCCCCcC-CCHHHH
Confidence 44555667777767789999999999999996 555666766 887663
No 22
>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=37.04 E-value=1.5e+02 Score=25.02 Aligned_cols=60 Identities=15% Similarity=0.215 Sum_probs=42.0
Q ss_pred hhhhhHHHHHhhCCHHHHHHHhc--CchhHHHHHhcCChhHHHHHHHHhcCCCCCChHHHHh
Q 015409 6 IIAKNFMDMVASLTARDLDRLYE--NPFICEAILRSLPPLAKKYVMQMFYIDGAIPAKMMEE 65 (407)
Q Consensus 6 ~~~~~~~~yL~~Lp~~~~~~LY~--~p~tclaifR~Lp~lak~~vmrlL~~~~~v~~~~l~~ 65 (407)
+-..++...|...|..++-.... ++..+..||+.+|+-++..+..-+=.-+|++.++++.
T Consensus 28 l~~~~l~~ll~~v~~~~la~ALkga~~e~~~~il~nms~r~a~~l~~e~~~~g~v~~~di~~ 89 (110)
T PF01706_consen 28 LDDRDLQKLLREVDPDDLALALKGASEELREKILSNMSKRAAEMLREEMEALGPVRLSDIEE 89 (110)
T ss_dssp S-HHHHHHHHTTS-HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHHHH-S--HHHHHH
T ss_pred CCHHHHHHHHHHCCHhHHHHHHccCCHHHHHHHHHHcCHHHHHHHHHHHHhcCCCCHHHHHH
Confidence 34556667777777777776665 5788999999999999999988776668999998874
No 23
>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=36.09 E-value=49 Score=27.12 Aligned_cols=27 Identities=37% Similarity=0.642 Sum_probs=22.7
Q ss_pred eCHHHHHHHHH--------------cCCCHHHHHHHHhhcC
Q 015409 336 ITKESLYNAFE--------------NGITAEQIISFLQQNA 362 (407)
Q Consensus 336 iTReSvr~Al~--------------~GITA~QII~fL~~hA 362 (407)
+||+++.+|+. .|.||+++|.||...-
T Consensus 20 ~t~~~L~~ai~~~FG~~arFhTCSae~m~a~eLv~FL~~rg 60 (78)
T PF10678_consen 20 YTKEELKAAIIEKFGEDARFHTCSAEGMTADELVDFLEERG 60 (78)
T ss_pred cCHHHHHHHHHHHhCCCceEEecCCCCCCHHHHHHHHHHcC
Confidence 58888888875 6999999999998764
No 24
>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=35.89 E-value=71 Score=30.36 Aligned_cols=89 Identities=21% Similarity=0.376 Sum_probs=57.7
Q ss_pred cceEEEeeCceEEEecCCHhHHHHHHHHHhhhhcCCceEEEE---eCHHHHHHHHHcCC-------CHHHHHHHHhhcCc
Q 015409 294 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGA---ITKESLYNAFENGI-------TAEQIISFLQQNAH 363 (407)
Q Consensus 294 ~g~IIVETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~---iTReSvr~Al~~GI-------TA~QII~fL~~hAH 363 (407)
.|.=++|--|| +|--. ....++..++|+|.||. +|.|.+++|++.|- .-++++.+-+.|-.
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 46667888777 33222 33345566789999996 99999999999994 46889999888877
Q ss_pred cccccCCCCCC--hhHHHHHHHHHHhcCceeeeCeee
Q 015409 364 PRVADRMPSVP--ENVCDQIRLWESDLNRVEMTPAHY 398 (407)
Q Consensus 364 p~m~~~~p~lP--~tV~dQIrLWe~Er~R~~~~~g~L 398 (407)
| .+| -|..+=..-|+.--+-+|+.|+-.
T Consensus 103 ~-------~iPG~~TptEi~~A~~~G~~~vK~FPA~~ 132 (196)
T PF01081_consen 103 P-------YIPGVMTPTEIMQALEAGADIVKLFPAGA 132 (196)
T ss_dssp E-------EEEEESSHHHHHHHHHTT-SEEEETTTTT
T ss_pred c-------ccCCcCCHHHHHHHHHCCCCEEEEecchh
Confidence 5 344 244555556777677777766543
No 25
>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=35.06 E-value=40 Score=27.64 Aligned_cols=33 Identities=30% Similarity=0.402 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHhhcCceeeecCCCccccccchhh
Q 015409 246 SEIQKSMIKDFADLGLVKLQQGRKENWFIPTKLA 279 (407)
Q Consensus 246 t~~q~~~L~~L~d~GLvy~~~~~~~~~f~pT~La 279 (407)
+.|-++.+++|.++|||.-+.+.+.+ +.||.-|
T Consensus 37 ~aTIRN~M~~Le~lGlve~~p~~s~G-riPT~~a 69 (78)
T PF03444_consen 37 PATIRNEMADLEELGLVESQPHPSGG-RIPTDKA 69 (78)
T ss_pred hHHHHHHHHHHHHCCCccCCCCCCCC-CCcCHHH
Confidence 57899999999999999633333344 4588765
No 26
>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=34.97 E-value=1.6e+02 Score=21.82 Aligned_cols=58 Identities=19% Similarity=0.267 Sum_probs=38.4
Q ss_pred HHHHHHHHhc-CCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeee--c-C-CCceeEEeCH
Q 015409 44 AKKYVMQMFY-IDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--E-K-KKETTYRLNS 102 (407)
Q Consensus 44 ak~~vmrlL~-~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~--~-~-~~~~~~~Ln~ 102 (407)
.+..||+.+. .+.+.+.+++.....- .+.....+++.|....++.. + . +....|.|+|
T Consensus 4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~-~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~ 66 (68)
T PF13463_consen 4 PQWQVLRALAHSDGPMTQSDLAERLGI-SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTP 66 (68)
T ss_dssp HHHHHHHHHT--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-H
T ss_pred HHHHHHHHHHccCCCcCHHHHHHHHCc-CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCC
Confidence 3456788888 6788888999886553 34456689999999999975 2 1 2235677776
No 27
>PRK13824 replication initiation protein RepC; Provisional
Probab=34.21 E-value=1.3e+02 Score=31.72 Aligned_cols=69 Identities=13% Similarity=0.332 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHHcCCChHH--HHHHHHhhcccccCcccc-----------------CCCCCHHH-HHHHHHHhhcCc
Q 015409 202 QLWYIVREYISNSQERGINQAD--LISFLLELSFHVAGEAYN-----------------LNTLSEIQ-KSMIKDFADLGL 261 (407)
Q Consensus 202 Q~W~lll~yl~~~e~~~~~~~~--~l~fLf~Ls~~~~G~~Y~-----------------~~~lt~~q-~~~L~~L~d~GL 261 (407)
.=|.++..--+.....|++..+ +|..|+ +| .+.++++ +.++++++ +..|..|.|.||
T Consensus 36 ~Kw~l~r~l~~a~~~lGl~~~~l~vL~aLl--sf-~p~~~~~~~~~~IVfpSN~~La~r~~Gms~~tlrRhla~LveaGL 112 (404)
T PRK13824 36 DKWKLFRDLCEARALLGVSDRALAVLNALL--SF-YPETELSEEAGLVVFPSNAQLSLRAHGMAGATLRRHLAALVEAGL 112 (404)
T ss_pred CHHHHHHHHHHHHHhcCCChhHHHHHHHHH--hh-CCcccccCCCCceechhHHHHHHHHcCCCHHHHHHHHHHHHHCCC
Confidence 4488888866666667887754 444433 33 3434332 22466655 788999999999
Q ss_pred eeeecCCCcccc
Q 015409 262 VKLQQGRKENWF 273 (407)
Q Consensus 262 vy~~~~~~~~~f 273 (407)
|..+...+.++|
T Consensus 113 I~rrDSpNGKRy 124 (404)
T PRK13824 113 IIRRDSPNGKRY 124 (404)
T ss_pred eEeecCCCCccc
Confidence 976544445565
No 28
>PLN02459 probable adenylate kinase
Probab=33.26 E-value=79 Score=31.42 Aligned_cols=69 Identities=17% Similarity=0.257 Sum_probs=48.7
Q ss_pred hhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeecCCCC
Q 015409 325 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 404 (407)
Q Consensus 325 ~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~F~s 404 (407)
.+.++.+.+|.|=|+.|..--..| .+|-+|+.+ ...||+.++.++-..+.....-.-..|++++.||-
T Consensus 52 ~~~~~~is~gdllR~ei~~~t~lg---~~i~~~~~~---------G~lVPdeiv~~ll~~~l~~~~~~~~~g~iLDGFPR 119 (261)
T PLN02459 52 LLGVPHIATGDLVREEIKSSGPLG---AQLKEIVNQ---------GKLVPDEIIFSLLSKRLEAGEEEGESGFILDGFPR 119 (261)
T ss_pred HhCCcEEeCcHHHHHHHhccchhH---HHHHHHHHc---------CCccCHHHHHHHHHHHHhcccccCCceEEEeCCCC
Confidence 567999999999888876533333 455556553 35799999998887766543223468999999985
Q ss_pred C
Q 015409 405 R 405 (407)
Q Consensus 405 ~ 405 (407)
.
T Consensus 120 t 120 (261)
T PLN02459 120 T 120 (261)
T ss_pred C
Confidence 3
No 29
>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=31.76 E-value=53 Score=28.75 Aligned_cols=25 Identities=20% Similarity=0.250 Sum_probs=20.8
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcC
Q 015409 338 KESLYNAFENGITAEQIISFLQQNA 362 (407)
Q Consensus 338 ReSvr~Al~~GITA~QII~fL~~hA 362 (407)
+.-++.|+++|+|.+||..-|..-+
T Consensus 76 ~~h~~~Al~~G~T~~ei~Evl~q~~ 100 (123)
T TIGR02425 76 AMHVRATANTGVTEDDIKEVLLHVA 100 (123)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 4567899999999999999877554
No 30
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=31.33 E-value=2.1e+02 Score=27.36 Aligned_cols=90 Identities=20% Similarity=0.345 Sum_probs=65.3
Q ss_pred cceEEEeeCceEEEecCCHhHHHHHHHHHhhhhcCCceEEEE---eCHHHHHHHHHcCC-------CHHHHHHHHhhcCc
Q 015409 294 EGFIVVETNFRMYAYSTSKLHCEILRLFSKVEYQLPNLIVGA---ITKESLYNAFENGI-------TAEQIISFLQQNAH 363 (407)
Q Consensus 294 ~g~IIVETNFrvYAYT~S~lqiaiL~lF~~l~~r~Pnlvvg~---iTReSvr~Al~~GI-------TA~QII~fL~~hAH 363 (407)
.|.=+||-.|+ +|-- +..+.++..++|++.||. +|.|.+++|.+.|- .-+.++++-+.+-.
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 46667787775 3333 334455667789999996 99999999999994 46889999887776
Q ss_pred cccccCCCCCC--hhHHHHHHHHHHhcCceeeeCeeee
Q 015409 364 PRVADRMPSVP--ENVCDQIRLWESDLNRVEMTPAHYY 399 (407)
Q Consensus 364 p~m~~~~p~lP--~tV~dQIrLWe~Er~R~~~~~g~Ly 399 (407)
| .+| -|..+=..-|+.=-+-+|+.|+-.+
T Consensus 99 ~-------~iPG~~TptEi~~A~~~Ga~~vK~FPa~~~ 129 (201)
T PRK06015 99 P-------LLPGAATPSEVMALREEGYTVLKFFPAEQA 129 (201)
T ss_pred C-------EeCCCCCHHHHHHHHHCCCCEEEECCchhh
Confidence 4 444 2556667788888888888886444
No 31
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=26.86 E-value=1.3e+02 Score=28.34 Aligned_cols=55 Identities=16% Similarity=0.182 Sum_probs=41.9
Q ss_pred HHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeee-----cCCCceeEEeCHHHHH
Q 015409 48 VMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSE-----EKKKETTYRLNSTFQS 106 (407)
Q Consensus 48 vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~-----~~~~~~~~~Ln~~F~~ 106 (407)
++..++..+|++.++++..-..++ ...++.|...+++.. ..+....|.+++.|..
T Consensus 95 tLaiIay~qPiTr~eI~~irGv~~----~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~~ 154 (188)
T PRK00135 95 VLAIIAYKQPITRIEIDEIRGVNS----DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFLD 154 (188)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCH----HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHHH
Confidence 567777789999999998654433 778999999999975 1234557889999966
No 32
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=26.32 E-value=58 Score=29.61 Aligned_cols=28 Identities=14% Similarity=0.325 Sum_probs=22.1
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCccc
Q 015409 338 KESLYNAFENGITAEQIISFLQQNAHPR 365 (407)
Q Consensus 338 ReSvr~Al~~GITA~QII~fL~~hAHp~ 365 (407)
|+-|++-+..|-|.+||++|+.++-=+.
T Consensus 63 R~~I~~~l~~G~s~~eI~~~~v~rYG~~ 90 (148)
T PF03918_consen 63 RREIREMLAEGKSDEEIIDYFVERYGEF 90 (148)
T ss_dssp HHHHHHHHHHT--HHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCcc
Confidence 6788999999999999999999874443
No 33
>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=25.70 E-value=74 Score=22.72 Aligned_cols=20 Identities=35% Similarity=0.689 Sum_probs=16.1
Q ss_pred EEeCHHHHHHHHHc-C---CCHHH
Q 015409 334 GAITKESLYNAFEN-G---ITAEQ 353 (407)
Q Consensus 334 g~iTReSvr~Al~~-G---ITA~Q 353 (407)
|.||++.++.|+.. | +|.++
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 55655
No 34
>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=24.72 E-value=2.1e+02 Score=23.67 Aligned_cols=57 Identities=18% Similarity=0.274 Sum_probs=42.0
Q ss_pred HHHHHHHhcC-CCCCChHHHHhhcCCc----chhHHHHHHHHHhccceeee--cCCCceeEEeC
Q 015409 45 KKYVMQMFYI-DGAIPAKMMEEWVLPD----GFTKHRVAIDRLVQLRLFSE--EKKKETTYRLN 101 (407)
Q Consensus 45 k~~vmrlL~~-~~~v~~~~l~~W~~~~----~~~~~~~al~~L~~L~I~~~--~~~~~~~~~Ln 101 (407)
|.-|+..|+. +.+++..++...++.. +....-+.|+.|.+.+++.. ..++...|.++
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 5688999998888643 45666788999999999986 22344566665
No 35
>smart00195 DSPc Dual specificity phosphatase, catalytic domain.
Probab=24.24 E-value=1.8e+02 Score=24.78 Aligned_cols=52 Identities=10% Similarity=0.155 Sum_probs=36.4
Q ss_pred CceEEEE--eCHHHHHHHH----HcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHH
Q 015409 329 PNLIVGA--ITKESLYNAF----ENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWES 386 (407)
Q Consensus 329 Pnlvvg~--iTReSvr~Al----~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~ 386 (407)
|-+|-+. ++|...--|. ..|+++++.+.|+++ ++|.+. .-+...+|++.||.
T Consensus 80 ~VlVHC~~G~~RS~~v~~~yl~~~~~~~~~~A~~~v~~-~R~~~~-----p~~~~~~qL~~~e~ 137 (138)
T smart00195 80 KVLVHCQAGVSRSATLIIAYLMKYRNLSLNDAYDFVKD-RRPIIS-----PNFGFLRQLIEYER 137 (138)
T ss_pred eEEEECCCCCchHHHHHHHHHHHHhCCCHHHHHHHHHH-HCCccC-----CCHhHHHHHHHHhh
Confidence 3444444 6788764443 579999999999975 445432 23589999999995
No 36
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=22.77 E-value=1.5e+02 Score=26.42 Aligned_cols=29 Identities=24% Similarity=0.453 Sum_probs=24.6
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCcccc
Q 015409 338 KESLYNAFENGITAEQIISFLQQNAHPRV 366 (407)
Q Consensus 338 ReSvr~Al~~GITA~QII~fL~~hAHp~m 366 (407)
|+-|++-++.|-|-+||++|+...-=..+
T Consensus 63 R~~Vr~~i~~G~Sd~eI~~~~v~RYG~~V 91 (126)
T TIGR03147 63 RHEVYSMVNEGKSNQQIIDFMTARFGDFV 91 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeE
Confidence 67899999999999999999998754433
No 37
>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=22.17 E-value=1.5e+02 Score=24.61 Aligned_cols=54 Identities=19% Similarity=0.087 Sum_probs=35.5
Q ss_pred HHHHHHHHhhhhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHH
Q 015409 315 CEILRLFSKVEYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLW 384 (407)
Q Consensus 315 iaiL~lF~~l~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLW 384 (407)
-+.+.-++++.+ -||++|++++.||+=|+.-.-+.-....+.....+.|||-.+
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 557777777776 799999999999999986644322111113334567776543
No 38
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=21.50 E-value=1.1e+02 Score=25.35 Aligned_cols=51 Identities=14% Similarity=0.302 Sum_probs=31.6
Q ss_pred ccChhhHHHHHHHHHHHHHHHcCCChHHHHHHHHhhcccccCccccCCCCCHHH-HHHHHHHhhcCcee
Q 015409 196 LMDTNAQLWYIVREYISNSQERGINQADLISFLLELSFHVAGEAYNLNTLSEIQ-KSMIKDFADLGLVK 263 (407)
Q Consensus 196 L~d~~~Q~W~lll~yl~~~e~~~~~~~~~l~fLf~Ls~~~~G~~Y~~~~lt~~q-~~~L~~L~d~GLvy 263 (407)
+.+...+|+.++.. ....+.|+...++..-| .+++.+ +..+++|.+.|.||
T Consensus 45 ~~~~~~~Vl~~i~~--~~~~~~Gv~v~~I~~~l---------------~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQ--QPNSEEGVHVDEIAQQL---------------GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC------TTTEEHHHHHHHS---------------TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHh--cCCCCCcccHHHHHHHh---------------CcCHHHHHHHHHHHHhCCeEe
Confidence 45556666666666 22224588777777633 234544 78899999999998
No 39
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=21.09 E-value=3.4e+02 Score=21.87 Aligned_cols=56 Identities=9% Similarity=0.106 Sum_probs=41.7
Q ss_pred HHHHhcCCCCCChHHHHhhcCCcchhHHHHHHHHHhccceeee--cC--CCceeEEeCHHH
Q 015409 48 VMQMFYIDGAIPAKMMEEWVLPDGFTKHRVAIDRLVQLRLFSE--EK--KKETTYRLNSTF 104 (407)
Q Consensus 48 vmrlL~~~~~v~~~~l~~W~~~~~~~~~~~al~~L~~L~I~~~--~~--~~~~~~~Ln~~F 104 (407)
|++-|.. +|..-+++...+..-+.+...+.++.|.+..++.. .+ .....|.|++.=
T Consensus 10 IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G 69 (90)
T PF01638_consen 10 ILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKG 69 (90)
T ss_dssp HHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHH
T ss_pred HHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCH
Confidence 5555555 78888999999988889999999999999999975 12 223579898753
No 40
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=20.88 E-value=1.8e+02 Score=26.02 Aligned_cols=29 Identities=17% Similarity=0.376 Sum_probs=24.5
Q ss_pred HHHHHHHHHcCCCHHHHHHHHhhcCcccc
Q 015409 338 KESLYNAFENGITAEQIISFLQQNAHPRV 366 (407)
Q Consensus 338 ReSvr~Al~~GITA~QII~fL~~hAHp~m 366 (407)
|+-|++-+..|-|-+||++|+...-=..+
T Consensus 63 R~~Vr~~i~~G~sd~eI~~~~v~RYG~~V 91 (126)
T PRK10144 63 RHQVYSMVAEGKSEVEIIGWMTERYGDFV 91 (126)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcCCeE
Confidence 67899999999999999999998754433
No 41
>COG4902 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.57 E-value=1.5e+02 Score=27.43 Aligned_cols=75 Identities=16% Similarity=0.158 Sum_probs=45.2
Q ss_pred hcCChhHHHHHHHHhcCCCCCCh-HHHHhhcCCcchhHHHHHHH-HHhccceeeecCCCceeEEeCHHHHHHHHHHHHcC
Q 015409 38 RSLPPLAKKYVMQMFYIDGAIPA-KMMEEWVLPDGFTKHRVAID-RLVQLRLFSEEKKKETTYRLNSTFQSNLRKHLIYG 115 (407)
Q Consensus 38 R~Lp~lak~~vmrlL~~~~~v~~-~~l~~W~~~~~~~~~~~al~-~L~~L~I~~~~~~~~~~~~Ln~~F~~~lr~aL~gg 115 (407)
|.=-.|||- |.--||.+-.+|. ..+. .+.+.|-+|++ .|.+..|-.+.....-+.-=||.|++-+...+.-|
T Consensus 58 rEEEKLARD-VYL~LYnkw~l~IF~nIA-----~SEQ~HmDAVk~LlekYnv~dP~~~~siGvF~NpelqeLYn~Lve~G 131 (189)
T COG4902 58 REEEKLARD-VYLYLYNKWNLPIFRNIA-----ASEQEHMDAVKSLLEKYNVQDPASTTSIGVFTNPELQELYNQLVEQG 131 (189)
T ss_pred HHHHHHHhh-HHhhhhhccCcHHHHHHH-----HhHHHHHHHHHHHHHHcCCCCCCccCcceeecCHHHHHHHHHHHHcc
Confidence 544555655 4444555544443 2221 34556666766 66777776663333345668999999888888766
Q ss_pred CCC
Q 015409 116 GAL 118 (407)
Q Consensus 116 g~~ 118 (407)
..+
T Consensus 132 s~S 134 (189)
T COG4902 132 SVS 134 (189)
T ss_pred chh
Confidence 553
No 42
>PLN02674 adenylate kinase
Probab=20.44 E-value=1.1e+02 Score=30.06 Aligned_cols=67 Identities=16% Similarity=0.155 Sum_probs=46.9
Q ss_pred hhcCCceEEEEeCHHHHHHHHHcCCCHHHHHHHHhhcCccccccCCCCCChhHHHHHHHHHHhcCceeeeCeeeecCCCC
Q 015409 325 EYQLPNLIVGAITKESLYNAFENGITAEQIISFLQQNAHPRVADRMPSVPENVCDQIRLWESDLNRVEMTPAHYYDEFPS 404 (407)
Q Consensus 325 ~~r~Pnlvvg~iTReSvr~Al~~GITA~QII~fL~~hAHp~m~~~~p~lP~tV~dQIrLWe~Er~R~~~~~g~Ly~~F~s 404 (407)
+|.++.+.+|.+=|+.|+..=..| .+|-+++.+ ...+|+.++.++-.++.... ....|++++.||-
T Consensus 54 ~~~~~his~GdllR~~i~~~s~~g---~~i~~~~~~---------G~lvpd~iv~~lv~~~l~~~--~~~~g~ilDGfPR 119 (244)
T PLN02674 54 EYCLCHLATGDMLRAAVAAKTPLG---IKAKEAMDK---------GELVSDDLVVGIIDEAMKKP--SCQKGFILDGFPR 119 (244)
T ss_pred HcCCcEEchhHHHHHHHhccChhh---HHHHHHHHc---------CCccCHHHHHHHHHHHHhCc--CcCCcEEEeCCCC
Confidence 567899999998888776444444 344444432 35799999998887776543 3458999999985
Q ss_pred C
Q 015409 405 R 405 (407)
Q Consensus 405 ~ 405 (407)
.
T Consensus 120 t 120 (244)
T PLN02674 120 T 120 (244)
T ss_pred C
Confidence 3
No 43
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=20.10 E-value=97 Score=20.84 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=18.4
Q ss_pred HHHHHHHcCCCHHHHHHHHhh
Q 015409 340 SLYNAFENGITAEQIISFLQQ 360 (407)
Q Consensus 340 Svr~Al~~GITA~QII~fL~~ 360 (407)
-++..+.++.|-++|+++|..
T Consensus 13 ~i~~~l~~~~t~~~I~~~l~~ 33 (39)
T PF05184_consen 13 EIEKLLKNNKTEEEIKKALEK 33 (39)
T ss_dssp HHHHHHHSTCHHHHHHHHHHH
T ss_pred HHHHHHHcCccHHHHHHHHHH
Confidence 467889999999999999985
Done!