Query 042344
Match_columns 302
No_of_seqs 194 out of 350
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 05:20:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042344.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042344hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2578 Transcription factor E 100.0 2.5E-46 5.5E-51 353.7 7.7 256 36-296 118-387 (388)
2 KOG2577 Transcription factor E 100.0 6.9E-32 1.5E-36 259.0 10.0 111 69-200 63-173 (354)
3 PF02319 E2F_TDP: E2F/DP famil 99.9 5.3E-23 1.1E-27 157.1 5.0 71 74-154 1-71 (71)
4 KOG2578 Transcription factor E 99.7 2.1E-18 4.4E-23 164.6 6.2 77 69-160 16-92 (388)
5 KOG2829 E2F-like protein [Tran 99.5 3.4E-14 7.3E-19 134.8 9.2 166 53-246 20-198 (326)
6 PF01978 TrmB: Sugar-specific 88.6 1.1 2.4E-05 33.0 5.0 45 84-140 11-55 (68)
7 PF08279 HTH_11: HTH domain; 81.7 4.4 9.5E-05 28.4 5.1 46 84-140 3-49 (55)
8 cd08768 Cdc6_C Winged-helix do 79.5 5.5 0.00012 30.2 5.4 45 96-140 21-65 (87)
9 cd00092 HTH_CRP helix_turn_hel 79.0 8.1 0.00018 27.4 5.8 49 82-140 5-58 (67)
10 PF09339 HTH_IclR: IclR helix- 76.4 5.2 0.00011 28.3 4.1 45 85-140 7-51 (52)
11 smart00420 HTH_DEOR helix_turn 73.5 9.7 0.00021 25.4 4.8 44 85-140 4-47 (53)
12 smart00346 HTH_ICLR helix_turn 71.6 9.7 0.00021 28.8 4.8 46 84-140 8-53 (91)
13 PF12802 MarR_2: MarR family; 68.5 14 0.00031 25.9 4.9 45 86-140 10-54 (62)
14 PF10587 EF-1_beta_acid: Eukar 68.1 1.9 4E-05 28.8 0.2 11 34-44 2-12 (28)
15 PF09079 Cdc6_C: CDC6, C termi 67.2 6.2 0.00013 30.3 3.0 23 119-141 37-59 (85)
16 COG1378 Predicted transcriptio 64.3 30 0.00065 32.5 7.5 35 96-140 29-63 (247)
17 PF02082 Rrf2: Transcriptional 63.5 21 0.00046 27.4 5.3 49 82-140 9-58 (83)
18 PF13412 HTH_24: Winged helix- 62.9 22 0.00047 24.4 4.8 43 84-138 6-48 (48)
19 PF13463 HTH_27: Winged helix 61.2 29 0.00062 24.8 5.4 38 94-141 15-52 (68)
20 cd00090 HTH_ARSR Arsenical Res 61.0 25 0.00055 24.2 5.0 44 84-140 10-53 (78)
21 smart00418 HTH_ARSR helix_turn 60.5 17 0.00037 24.5 3.9 35 96-140 9-43 (66)
22 COG3355 Predicted transcriptio 60.3 21 0.00046 31.0 5.2 49 95-154 40-88 (126)
23 TIGR02944 suf_reg_Xantho FeS a 59.7 21 0.00045 29.3 5.0 46 85-140 13-58 (130)
24 PF04182 B-block_TFIIIC: B-blo 59.4 18 0.00039 27.7 4.3 48 85-142 6-53 (75)
25 smart00550 Zalpha Z-DNA-bindin 58.4 30 0.00064 26.1 5.2 48 83-140 8-55 (68)
26 PF03376 Adeno_E3B: Adenovirus 56.7 5.8 0.00013 31.2 1.1 15 265-279 51-65 (67)
27 PF09012 FeoC: FeoC like trans 49.2 34 0.00074 25.5 4.2 37 95-141 12-48 (69)
28 smart00419 HTH_CRP helix_turn_ 47.6 37 0.00079 22.4 3.8 34 97-140 8-41 (48)
29 PF08220 HTH_DeoR: DeoR-like h 45.8 52 0.0011 23.9 4.7 45 85-141 4-48 (57)
30 PF01047 MarR: MarR family; I 45.8 24 0.00052 24.8 2.8 36 96-141 16-51 (59)
31 TIGR02716 C20_methyl_CrtF C-20 45.5 20 0.00042 33.5 3.0 35 96-140 22-56 (306)
32 PF01475 FUR: Ferric uptake re 44.9 30 0.00066 27.9 3.6 53 85-143 12-64 (120)
33 smart00347 HTH_MARR helix_turn 44.3 80 0.0017 23.4 5.6 44 85-140 14-57 (101)
34 PF13730 HTH_36: Helix-turn-he 43.0 30 0.00066 24.1 3.0 30 98-137 26-55 (55)
35 PF03374 ANT: Phage antirepres 41.4 40 0.00087 26.9 3.8 41 86-140 14-54 (111)
36 PF08784 RPA_C: Replication pr 39.2 59 0.0013 25.7 4.4 50 78-137 44-95 (102)
37 TIGR00738 rrf2_super rrf2 fami 39.1 72 0.0016 25.9 5.0 36 95-140 23-58 (132)
38 PF01022 HTH_5: Bacterial regu 38.7 60 0.0013 22.4 3.9 41 86-139 7-47 (47)
39 PF08595 RXT2_N: RXT2-like, N- 37.3 25 0.00055 31.1 2.2 45 65-109 104-148 (149)
40 smart00344 HTH_ASNC helix_turn 37.3 63 0.0014 25.3 4.3 47 82-140 4-50 (108)
41 TIGR01610 phage_O_Nterm phage 35.6 1E+02 0.0022 24.5 5.3 36 95-140 45-80 (95)
42 PF12840 HTH_20: Helix-turn-he 32.5 1.2E+02 0.0025 21.9 4.7 45 84-140 13-57 (61)
43 PF00392 GntR: Bacterial regul 31.6 1.8E+02 0.0039 21.0 5.7 47 84-140 7-57 (64)
44 PF03444 HrcA_DNA-bdg: Winged 30.3 1.4E+02 0.003 24.1 5.1 45 86-141 13-57 (78)
45 smart00345 HTH_GNTR helix_turn 29.8 1.8E+02 0.0039 19.6 5.2 37 94-140 16-53 (60)
46 cd07153 Fur_like Ferric uptake 29.6 1.3E+02 0.0028 23.8 4.9 51 86-142 6-56 (116)
47 PF03836 RasGAP_C: RasGAP C-te 28.5 17 0.00038 31.1 -0.3 21 120-140 5-25 (142)
48 TIGR02337 HpaR homoprotocatech 28.2 57 0.0012 26.1 2.7 37 95-141 40-76 (118)
49 PRK09834 DNA-binding transcrip 28.1 1.1E+02 0.0025 28.1 5.0 44 86-140 16-59 (263)
50 PF01726 LexA_DNA_bind: LexA D 28.0 87 0.0019 23.7 3.5 45 86-140 14-59 (65)
51 PRK13509 transcriptional repre 26.7 1.1E+02 0.0024 28.3 4.7 44 86-141 10-53 (251)
52 TIGR02702 SufR_cyano iron-sulf 26.3 2E+02 0.0044 25.5 6.1 58 84-153 4-62 (203)
53 PRK06266 transcription initiat 26.1 1.7E+02 0.0036 26.3 5.6 58 84-153 25-84 (178)
54 PF08020 DUF1706: Protein of u 25.8 1E+02 0.0022 27.6 4.1 62 73-157 79-140 (166)
55 PRK09462 fur ferric uptake reg 25.7 1.5E+02 0.0033 25.0 5.0 52 86-142 22-73 (148)
56 PRK10163 DNA-binding transcrip 25.2 1.9E+02 0.0042 26.8 6.0 45 85-140 29-73 (271)
57 TIGR01764 excise DNA binding d 25.1 78 0.0017 20.7 2.5 22 98-129 2-23 (49)
58 PF14830 Haemocyan_bet_s: Haem 24.6 27 0.00058 29.5 0.2 13 125-137 58-70 (103)
59 COG1510 Predicted transcriptio 23.8 79 0.0017 29.1 3.0 46 95-150 39-84 (177)
60 PF09940 DUF2172: Domain of un 23.4 87 0.0019 32.0 3.5 35 94-138 352-386 (386)
61 COG1474 CDC6 Cdc6-related prot 23.4 62 0.0013 32.0 2.5 21 120-140 314-334 (366)
62 PF01920 Prefoldin_2: Prefoldi 23.0 2.2E+02 0.0048 22.0 5.1 73 120-198 24-96 (106)
63 cd07377 WHTH_GntR Winged helix 21.7 2.3E+02 0.0049 19.5 4.5 34 97-140 25-58 (66)
64 TIGR02431 pcaR_pcaU beta-ketoa 21.7 1.7E+02 0.0036 26.6 4.7 45 85-140 13-57 (248)
65 PRK10857 DNA-binding transcrip 20.9 2.1E+02 0.0045 25.2 5.1 37 94-140 22-58 (164)
No 1
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=100.00 E-value=2.5e-46 Score=353.67 Aligned_cols=256 Identities=36% Similarity=0.508 Sum_probs=203.0
Q ss_pred CCCCCCCccCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCHHHHHHHHHHHHhhCCCc-eecHHHHHHHHhcCc
Q 042344 36 SDDEDDDEDDDSSSNPNPGSQSDSLNPRS---AHKSSKNDSRREKSLGLLTQNFVRLFVCSNVD-MITLDEVAKLLLGDA 111 (302)
Q Consensus 36 sd~~~~~~~~d~~~~~~~~sq~~~~~p~s---~~~~~k~~~RkdKSLglLTqkFV~L~l~sp~g-vIdLneAA~~L~g~~ 111 (302)
.++|+|+|+ .+.|.+.++.+.+.|++ ...+++.+.|+++||++|||+||+||+++++. .|+|+.||+.|+++.
T Consensus 118 ~s~e~~~ee---~~~s~tstptd~s~~g~l~e~S~~~k~DnrkekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds 194 (388)
T KOG2578|consen 118 VSFEEESEE---RGVSCTSTPTDQSTDGLLEERSRSSKRDNRKEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDS 194 (388)
T ss_pred ccccccccc---cCCccccCCCCCCCCCcchhcCCCCcccchhhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCC
Confidence 455555555 56788888888888887 45567889999999999999999999999987 999999999999999
Q ss_pred CCccccccchhhhhhHHHHHhhhhhheecccCCCCCCcEEeecccccccc-----cccccCcchHHHhhhHHHHHHHHHH
Q 042344 112 HNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKPAFRWLGVNRLEIG-----LADSLNLDESRKRTFGTDVTNISFK 186 (302)
Q Consensus 112 ~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn~iqWiG~~~~~n~-----~~~a~~~~~s~kr~l~~El~nL~~~ 186 (302)
+++..|++++||||||||||.+||||||+|+..++||+|+|+|..++..+ +...+..+.++.++|++||+|+.++
T Consensus 195 ~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkPafrwlG~~~~~t~sf~~gs~sL~~~n~~K~rafgteItnvnak 274 (388)
T KOG2578|consen 195 EDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKPAFRWLGSKPIQTGSFFQGSRSLSEQNLPKPRAFGTEITNVNAK 274 (388)
T ss_pred CCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccchhheeCCCccccccccccchhHhhcCCCCcccCCccccchhhh
Confidence 99999999999999999999999999999999999999999999874332 3445556888889999999999999
Q ss_pred HHhHHHHhhh-hcchhhhhhhhhccCCceeeecCCCcccccCCCCCCccccCCCc-cCCcccc---CCcCCcccccchhh
Q 042344 187 RKRMDTSING-DISQSIKMEKQMKVDDLVRVVDGSNSENYVNQGPRSYQFGPFAP-ESVPEVN---TSKNNVKGAHDWES 261 (302)
Q Consensus 187 E~~LD~~I~~-~~~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gpf~p-~~~~~~~---~~~~~~~~~~dwe~ 261 (302)
+++--+.-.. ...-.++|.+|....... +.--++-..+++..++|+||||+| ++++... +...+.++..++|+
T Consensus 275 r~kSs~s~~en~~~~~~~~~k~~~e~~~y--e~~~~l~~~~~p~~~~~~~gp~~P~igt~~t~~~~~~~~~srr~f~ie~ 352 (388)
T KOG2578|consen 275 RNKSSCSSMENFMFAEVVTKKHAAEKMRY--EAFAQLSSRLKPLPMAYLFGPFLPEIGTSQTNKQFNFPATSRRLFNIEA 352 (388)
T ss_pred hccCcchhhhhHHHHHhhhhhccchhhhh--hhhhhhhhccCCcccccccCCCCCCCCCcchhhccCCCCCccccccchh
Confidence 9986443222 222223333332222111 000112345788888999999999 6655444 44668999999999
Q ss_pred hhhccCcccccHHHHHHHHHHHHHHHHHHHHHhcc
Q 042344 262 LTSKYCPQYHNQALRDLFSHYMEAWQSWYTEVAGK 296 (302)
Q Consensus 262 la~~~~pqy~nqal~~lf~hy~eawkswy~e~~~~ 296 (302)
|++.|+|+|||.++..+|.||.+++.+-..+++|.
T Consensus 353 l~sdyqPsy~n~e~~~~~~~~~~~f~v~k~~~~r~ 387 (388)
T KOG2578|consen 353 LTSDYQPSYCNSESKKFKQGTNSTFQVVKKGETRP 387 (388)
T ss_pred cccccCccccChhhhhhhcccceeeeeeccccCCC
Confidence 99999999999999999999999998887777664
No 2
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=99.97 E-value=6.9e-32 Score=259.02 Aligned_cols=111 Identities=31% Similarity=0.499 Sum_probs=101.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccCCCCCC
Q 042344 69 SKNDSRREKSLGLLTQNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKP 148 (302)
Q Consensus 69 ~k~~~RkdKSLglLTqkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn 148 (302)
....+|+++|||+||+|||.|++.+|+|+++|+.||++| .|+|||||||||||||||||||+ +||
T Consensus 63 ~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L----------~VqKRRIYDITNVLEGI~LIeKk-----sKN 127 (354)
T KOG2577|consen 63 PSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVL----------NVQKRRIYDITNVLEGIGLIEKK-----SKN 127 (354)
T ss_pred CCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHh----------ccccceeeehhhhhhcccceeec-----ccc
Confidence 446689999999999999999999999999999999999 89999999999999999999999 899
Q ss_pred cEEeecccccccccccccCcchHHHhhhHHHHHHHHHHHHhHHHHhhhhcch
Q 042344 149 AFRWLGVNRLEIGLADSLNLDESRKRTFGTDVTNISFKRKRMDTSINGDISQ 200 (302)
Q Consensus 149 ~iqWiG~~~~~n~~~~a~~~~~s~kr~l~~El~nL~~~E~~LD~~I~~~~~q 200 (302)
+|||+|.+.... .+ ...+.+.|++|++.|+++|+.||++|+.|+.+
T Consensus 128 ~IqW~G~~~~~~---~~---~~e~~~~l~~e~~~L~~~E~~LD~~i~~~q~~ 173 (354)
T KOG2577|consen 128 NIQWIGGDFNST---GG---VPERLNGLEAEVEDLSQEEDDLDQLIRDCQQN 173 (354)
T ss_pred ceeeecCCCccc---cc---cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999986321 12 34677889999999999999999999999976
No 3
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=99.87 E-value=5.3e-23 Score=157.08 Aligned_cols=71 Identities=49% Similarity=0.838 Sum_probs=63.5
Q ss_pred CCCCCHHHHHHHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccCCCCCCcEEee
Q 042344 74 RREKSLGLLTQNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKPAFRWL 153 (302)
Q Consensus 74 RkdKSLglLTqkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn~iqWi 153 (302)
|+++||+.||++||++|...+.+.+++++||+.|+.+ ..++++||||||+|||+|||||+|. +|+.|+|+
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~-----~~k~~~RRlYDI~NVLealgli~K~-----~k~~~~W~ 70 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISE-----NVKTQRRRLYDIINVLEALGLIEKQ-----SKNSYKWI 70 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHH-----CCHHHCHHHHHHHHHHHHCTSEEEE-----ETTEEEE-
T ss_pred CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHccc-----ccccccchhhHHHHHHHHhCceeec-----CCCceEec
Confidence 7899999999999999999888999999999999543 2356999999999999999999998 79999999
Q ss_pred c
Q 042344 154 G 154 (302)
Q Consensus 154 G 154 (302)
|
T Consensus 71 G 71 (71)
T PF02319_consen 71 G 71 (71)
T ss_dssp -
T ss_pred C
Confidence 8
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.74 E-value=2.1e-18 Score=164.56 Aligned_cols=77 Identities=40% Similarity=0.672 Sum_probs=71.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccCCCCCC
Q 042344 69 SKNDSRREKSLGLLTQNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKP 148 (302)
Q Consensus 69 ~k~~~RkdKSLglLTqkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn 148 (302)
....+|++||||+||++|+.|+.......+-|++||..| +|.+||||||+||||+||++.|. .||
T Consensus 16 lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~Kl----------gVErRRIYDiVNvlEsig~var~-----~Kn 80 (388)
T KOG2578|consen 16 LQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKL----------GVERRRIYDIVNVLESIGAVARR-----GKN 80 (388)
T ss_pred chhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhc----------CchHHHHHHHHHHHHHHHHHHhc-----ccC
Confidence 356789999999999999999999888999999999999 89999999999999999999998 899
Q ss_pred cEEeeccccccc
Q 042344 149 AFRWLGVNRLEI 160 (302)
Q Consensus 149 ~iqWiG~~~~~n 160 (302)
.|.|+|...++.
T Consensus 81 qYsWkGf~aiPr 92 (388)
T KOG2578|consen 81 QYSWKGFGAIPR 92 (388)
T ss_pred cccccchhhhhH
Confidence 999999987653
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=99.52 E-value=3.4e-14 Score=134.83 Aligned_cols=166 Identities=20% Similarity=0.247 Sum_probs=122.7
Q ss_pred CCCCCCCCC-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhhCCCceecHHHHHHHHhcCcCC------------cccccc
Q 042344 53 PGSQSDSLN-PRSAHKSSKNDSRREKSLGLLTQNFVRLFVCSNVDMITLDEVAKLLLGDAHN------------TSVMRT 119 (302)
Q Consensus 53 ~~sq~~~~~-p~s~~~~~k~~~RkdKSLglLTqkFV~L~l~sp~gvIdLneAA~~L~g~~~~------------~s~~kv 119 (302)
.+.+++.+. +|+++. .+......+.|.+++.+.++-+.. .|.++.+++|+.|+.+... ...+++
T Consensus 20 ~~~~~s~~~~~~~a~~-~~ks~k~g~gLRhfs~kVCeKve~--Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KN 96 (326)
T KOG2829|consen 20 LGNQPSDSGSSWSAGR-KRKSDKAGGGLRHFSMKVCEKVER--KGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKN 96 (326)
T ss_pred ccCCcCCCCCcccccc-CCCCCCCCcchhhhhHHHHHHHHh--cCCccHHHHHHHHHHHHhccccccccCccccccchHH
Confidence 444444433 565554 334445678899999999998887 5799999999999755321 236899
Q ss_pred chhhhhhHHHHHhhhhhheecccCCCCCCcEEeecccccccccccccCcchHHHhhhHHHHHHHHHHHHhHHHHhhhhcc
Q 042344 120 KVRRLYDIANVLSSMNLIEKTHTADTRKPAFRWLGVNRLEIGLADSLNLDESRKRTFGTDVTNISFKRKRMDTSINGDIS 199 (302)
Q Consensus 120 kkRRLYDItNVLEgIgLIEK~~~~~~sKn~iqWiG~~~~~n~~~~a~~~~~s~kr~l~~El~nL~~~E~~LD~~I~~~~~ 199 (302)
.+||+||..|||++|+||.|. |..|+|+|.+... .+|+++|+.++.++-++|+.++.
T Consensus 97 IRRRVYDALNVlmAmnIIsKd------KKEIrW~GLP~~s-----------------s~dv~~le~Er~k~~erI~kK~a 153 (326)
T KOG2829|consen 97 IRRRVYDALNVLMAMNIISKD------KKEIRWIGLPATS-----------------SQDVSELEEERKKRMERIKKKAA 153 (326)
T ss_pred HHHHHHHHHHHHHHHHHHhcc------cceeeeeccCccc-----------------hHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999997 8899999998511 17899999999999999999988
Q ss_pred hhhhhhhhhccCCceeeecCCCcccccCCCCCCccccCCCccCCccc
Q 042344 200 QSIKMEKQMKVDDLVRVVDGSNSENYVNQGPRSYQFGPFAPESVPEV 246 (302)
Q Consensus 200 q~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gpf~p~~~~~~ 246 (302)
+...|..|...=-+|+.-++.+..++-.+.. + .+=||-=....+.
T Consensus 154 ~lqEl~~q~~~fknLV~RN~~~e~~~~~P~~-~-i~LPFiiinT~k~ 198 (326)
T KOG2829|consen 154 QLQELIEQVSAFKNLVQRNRHAESQGQPPSE-N-IHLPFIIINTSKK 198 (326)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhccCCCCc-c-cccceEEEecCCC
Confidence 8777777665555666555555555222222 3 6678866555444
No 6
>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=88.62 E-value=1.1 Score=32.99 Aligned_cols=45 Identities=18% Similarity=0.204 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.+.+..|+. .+..+..+.|+.+ +..+..+|++.+-|+..|||++.
T Consensus 11 ~~vy~~Ll~--~~~~t~~eIa~~l----------~i~~~~v~~~L~~L~~~GlV~~~ 55 (68)
T PF01978_consen 11 AKVYLALLK--NGPATAEEIAEEL----------GISRSTVYRALKSLEEKGLVERE 55 (68)
T ss_dssp HHHHHHHHH--HCHEEHHHHHHHH----------TSSHHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHH--cCCCCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEEE
Confidence 344444443 3679999999999 78999999999999999999998
No 7
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=81.65 E-value=4.4 Score=28.44 Aligned_cols=46 Identities=24% Similarity=0.251 Sum_probs=35.9
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhh-hheec
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMN-LIEKT 140 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIg-LIEK~ 140 (302)
.+.+.+|...... ++..+.|+.| ++.+|-||--.+.|+..| .|+..
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l----------~vS~rTi~~~i~~L~~~~~~I~~~ 49 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEEL----------GVSRRTIRRDIKELREWGIPIESK 49 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHC----------TS-HHHHHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHh----------CCCHHHHHHHHHHHHHCCCeEEee
Confidence 3567777666544 9999999999 799999999999999998 44433
No 8
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=79.51 E-value=5.5 Score=30.20 Aligned_cols=45 Identities=22% Similarity=0.237 Sum_probs=29.0
Q ss_pred ceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 96 DMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 96 gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..+++.++-+....-+..........||++||.|-|+.+|||+-.
T Consensus 21 ~~~~~~~vy~~Y~~~c~~~~~~~l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 21 EEATTGEVYEVYEELCEEIGVDPLTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CCccHHHHHHHHHHHHHHcCCCCCcHHHHHHHHHHHHHcCCeEEE
Confidence 446666666555221111111134569999999999999999865
No 9
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=79.02 E-value=8.1 Score=27.42 Aligned_cols=49 Identities=18% Similarity=0.127 Sum_probs=39.0
Q ss_pred HHHHHHHHHhhC-----CCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 82 LTQNFVRLFVCS-----NVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 82 LTqkFV~L~l~s-----p~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
++.-|+.|.... ....++..++|+.+ ++.+.-++.+.+.|+.-|+|++.
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~----------g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYL----------GLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCEEec
Confidence 444555555442 24679999999999 78889999999999999999987
No 10
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=76.44 E-value=5.2 Score=28.26 Aligned_cols=45 Identities=18% Similarity=0.251 Sum_probs=36.1
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..+++|...+ +.+++.+.|+.+ +..+=-+|-|.+.|+..|+|+|.
T Consensus 7 ~iL~~l~~~~-~~~t~~eia~~~----------gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 7 RILEALAESG-GPLTLSEIARAL----------GLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHCHHCTB-SCEEHHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHcCC-CCCCHHHHHHHH----------CcCHHHHHHHHHHHHHCcCeecC
Confidence 3455566654 457999999999 67888999999999999999875
No 11
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=73.52 E-value=9.7 Score=25.39 Aligned_cols=44 Identities=18% Similarity=0.296 Sum_probs=36.6
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.++..+... +.++..+.++.| ++.++.+|.+..-|+..|+|++.
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l----------~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELL----------GVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCEEEe
Confidence 345555554 458999999999 78899999999999999999987
No 12
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=71.55 E-value=9.7 Score=28.76 Aligned_cols=46 Identities=20% Similarity=0.230 Sum_probs=38.1
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
...+++|...+ +.+++.+.|+.+ +..+..+|-+.+.|+..|+|++.
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l----------~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERL----------GLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHh----------CCCHHHHHHHHHHHHHCCCeeec
Confidence 34556665543 479999999999 78889999999999999999986
No 13
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=68.46 E-value=14 Score=25.94 Aligned_cols=45 Identities=18% Similarity=0.192 Sum_probs=36.5
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.+..+...+...++..+.|+.| ...+=.+--+++-|+.-|||+|.
T Consensus 10 vL~~l~~~~~~~~t~~~la~~l----------~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 10 VLMALARHPGEELTQSELAERL----------GISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHSTTSGEEHHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHCCCCCcCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEEe
Confidence 4445556665569999999999 67778888999999999999998
No 14
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=68.06 E-value=1.9 Score=28.76 Aligned_cols=11 Identities=64% Similarity=1.265 Sum_probs=8.3
Q ss_pred cCCCCCCCCcc
Q 042344 34 WGSDDEDDDED 44 (302)
Q Consensus 34 ~~sd~~~~~~~ 44 (302)
+|||||+||++
T Consensus 2 FGSddEeed~e 12 (28)
T PF10587_consen 2 FGSDDEEEDEE 12 (28)
T ss_pred CCCccccccHH
Confidence 58999976664
No 15
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=67.15 E-value=6.2 Score=30.32 Aligned_cols=23 Identities=30% Similarity=0.395 Sum_probs=19.2
Q ss_pred cchhhhhhHHHHHhhhhhheecc
Q 042344 119 TKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 119 vkkRRLYDItNVLEgIgLIEK~~ 141 (302)
...||+||+.+-|+.+|||+-..
T Consensus 37 ls~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 37 LSYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp --HHHHHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHHHHHhCCCeEEEe
Confidence 45699999999999999998763
No 16
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=64.26 E-value=30 Score=32.52 Aligned_cols=35 Identities=20% Similarity=0.289 Sum_probs=29.2
Q ss_pred ceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 96 DMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 96 gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
|..+-.++|+.. ++..=|+|||.+.|++-|+|+..
T Consensus 29 g~~tA~eis~~s----------gvP~~kvY~vl~sLe~kG~v~~~ 63 (247)
T COG1378 29 GEATAKEISEAS----------GVPRPKVYDVLRSLEKKGLVEVI 63 (247)
T ss_pred CCccHHHHHHHc----------CCCchhHHHHHHHHHHCCCEEee
Confidence 346666666666 78888999999999999999987
No 17
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=63.50 E-value=21 Score=27.36 Aligned_cols=49 Identities=18% Similarity=0.174 Sum_probs=37.7
Q ss_pred HHHHHHHHHhhCCC-ceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 82 LTQNFVRLFVCSNV-DMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 82 LTqkFV~L~l~sp~-gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
++-+++..+-..++ ..++..+.|+.+ ++..+.|..|.+-|..-|||+..
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~----------~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERL----------GISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHH----------CcCHHHHHHHHHHHhhCCeeEec
Confidence 34445555554444 459999999999 89999999999999999999876
No 18
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=62.86 E-value=22 Score=24.38 Aligned_cols=43 Identities=21% Similarity=0.199 Sum_probs=34.9
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhhe
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIE 138 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIE 138 (302)
.+.+.++...| .++..+.|+.+ +.....++.+.+-|+.-|+|+
T Consensus 6 ~~Il~~l~~~~--~~t~~ela~~~----------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENP--RITQKELAEKL----------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCT--TS-HHHHHHHH----------TS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcC--CCCHHHHHHHh----------CCCHHHHHHHHHHHHHCcCcC
Confidence 45677777754 59999999999 788899999999999999985
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=61.20 E-value=29 Score=24.77 Aligned_cols=38 Identities=21% Similarity=0.226 Sum_probs=31.2
Q ss_pred CCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 94 NVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 94 p~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
..+.+++.+.|+.+ ...+--+..+++-|...|||+|..
T Consensus 15 ~~~~~t~~~l~~~~----------~~~~~~vs~~i~~L~~~glv~~~~ 52 (68)
T PF13463_consen 15 SDGPMTQSDLAERL----------GISKSTVSRIIKKLEEKGLVEKER 52 (68)
T ss_dssp -TS-BEHHHHHHHT----------T--HHHHHHHHHHHHHTTSEEEEE
T ss_pred cCCCcCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEecC
Confidence 57889999999999 678889999999999999999983
No 20
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=60.95 E-value=25 Score=24.20 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=35.3
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..++..+...+ ++..++++.+ ++....++-+.+.|+..|+|.+.
T Consensus 10 ~~il~~l~~~~---~~~~ei~~~~----------~i~~~~i~~~l~~L~~~g~i~~~ 53 (78)
T cd00090 10 LRILRLLLEGP---LTVSELAERL----------GLSQSTVSRHLKKLEEAGLVESR 53 (78)
T ss_pred HHHHHHHHHCC---cCHHHHHHHH----------CcCHhHHHHHHHHHHHCCCeEEE
Confidence 34455555543 9999999999 67778899999999999999987
No 21
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=60.50 E-value=17 Score=24.50 Aligned_cols=35 Identities=17% Similarity=0.202 Sum_probs=31.5
Q ss_pred ceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 96 DMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 96 gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
+.+++.+++..| ++.+..++.+.+.|..-|+|++.
T Consensus 9 ~~~~~~~i~~~l----------~is~~~v~~~l~~L~~~g~i~~~ 43 (66)
T smart00418 9 GELCVCELAEIL----------GLSQSTVSHHLKKLREAGLVESR 43 (66)
T ss_pred CCccHHHHHHHH----------CCCHHHHHHHHHHHHHCCCeeee
Confidence 468999999999 67888999999999999999876
No 22
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.26 E-value=21 Score=30.97 Aligned_cols=49 Identities=20% Similarity=0.308 Sum_probs=38.3
Q ss_pred CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccCCCCCCcEEeec
Q 042344 95 VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKPAFRWLG 154 (302)
Q Consensus 95 ~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn~iqWiG 154 (302)
.+.++.++.|+.| ...+=.+|-..|=|...|||+|...+. .+..|+++.
T Consensus 40 ~~~~tvdelae~l----------nr~rStv~rsl~~L~~~GlV~Rek~~~-~~Ggy~yiY 88 (126)
T COG3355 40 NGPLTVDELAEIL----------NRSRSTVYRSLQNLLEAGLVEREKVNL-KGGGYYYLY 88 (126)
T ss_pred cCCcCHHHHHHHH----------CccHHHHHHHHHHHHHcCCeeeeeecc-CCCceeEEE
Confidence 4679999999999 667788999999999999999985542 334444444
No 23
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=59.74 E-value=21 Score=29.33 Aligned_cols=46 Identities=11% Similarity=0.105 Sum_probs=38.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
+.+.+|-..+++.++..+.|+.| ++....++.|...|+.-|||+..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l----------~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQT----------GLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHH----------CcCHHHHHHHHHHHHHCCcEEec
Confidence 34445545556789999999999 78999999999999999999765
No 24
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=59.43 E-value=18 Score=27.69 Aligned_cols=48 Identities=23% Similarity=0.252 Sum_probs=37.1
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheeccc
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHT 142 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~ 142 (302)
.+++.+-.+...-+.-.+.+..+ +...|-++=+.++|+..|||.|...
T Consensus 6 ~~Le~I~rsR~~Gi~q~~L~~~~----------~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 6 CLLERIARSRYNGITQSDLSKLL----------GIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHHHHhcCCCCEehhHHHHHh----------CCCchHHHHHHHHHHHCCCEEEEEe
Confidence 45666666655555666777777 6788999999999999999999854
No 25
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.36 E-value=30 Score=26.06 Aligned_cols=48 Identities=15% Similarity=0.113 Sum_probs=39.5
Q ss_pred HHHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 83 TQNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 83 TqkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
-.+.+.+|...+...+++.+.|+.| ++.++-+.-+..-|+.-|+|++.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~l----------gl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNL----------GLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCEEec
Confidence 3567788887753359999999999 67777888888899999999987
No 26
>PF03376 Adeno_E3B: Adenovirus E3B protein; InterPro: IPR005041 Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) []. One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface []. Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID []. This entry represents the E3B region 10.4K protein, also known as the RID alpha subunit.; GO: 0016020 membrane
Probab=56.70 E-value=5.8 Score=31.20 Aligned_cols=15 Identities=40% Similarity=0.713 Sum_probs=12.4
Q ss_pred ccCcccccHHHHHHH
Q 042344 265 KYCPQYHNQALRDLF 279 (302)
Q Consensus 265 ~~~pqy~nqal~~lf 279 (302)
.+-||||||.+-.|.
T Consensus 51 RHhPqYrn~~iA~LL 65 (67)
T PF03376_consen 51 RHHPQYRNQQIAALL 65 (67)
T ss_pred HcCchhcCHHHHHHh
Confidence 357999999998874
No 27
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=49.16 E-value=34 Score=25.51 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=31.5
Q ss_pred CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 95 VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 95 ~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
.+.+++.+.|..| ++...-|=.+..+|+..|.|+|..
T Consensus 12 ~~~~S~~eLa~~~----------~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 12 RGRVSLAELAREF----------GISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp S-SEEHHHHHHHT----------T--HHHHHHHHHHHHCCTSCEEEE
T ss_pred cCCcCHHHHHHHH----------CcCHHHHHHHHHHHHHCCcEEEec
Confidence 4789999999999 788899999999999999999983
No 28
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=47.58 E-value=37 Score=22.42 Aligned_cols=34 Identities=24% Similarity=0.257 Sum_probs=30.2
Q ss_pred eecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 97 MITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 97 vIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.++..+.|+.+ ++.+..++.+.+.|+.-|+|++.
T Consensus 8 ~~s~~~la~~l----------~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELL----------GLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCEEEe
Confidence 36788899998 78889999999999999999876
No 29
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=45.81 E-value=52 Score=23.89 Aligned_cols=45 Identities=20% Similarity=0.257 Sum_probs=32.3
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
..++++.. .+.+++.++|+.| ++...-|.==.|.|+.-|+|.|.+
T Consensus 4 ~Il~~l~~--~~~~s~~ela~~~----------~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 4 QILELLKE--KGKVSVKELAEEF----------GVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHH--cCCEEHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEEEc
Confidence 45566666 4689999999999 333333333367899999999984
No 30
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=45.75 E-value=24 Score=24.76 Aligned_cols=36 Identities=28% Similarity=0.267 Sum_probs=31.4
Q ss_pred ceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 96 DMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 96 gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
+.+++.+.|+.+ ++.+-.+-.+++-|+.-|+|+|..
T Consensus 16 ~~~~~~~la~~~----------~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 16 GGITQSELAEKL----------GISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp SSEEHHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred CCCCHHHHHHHH----------CCChhHHHHHHHHHHHCCCEEecc
Confidence 349999999999 788889999999999999999983
No 31
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=45.52 E-value=20 Score=33.48 Aligned_cols=35 Identities=20% Similarity=0.120 Sum_probs=32.3
Q ss_pred ceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 96 DMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 96 gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
+..++.+.|..+ ++..|+++-+...|.++||+++.
T Consensus 22 gp~t~~eLA~~~----------~~~~~~~~~lL~~L~~lgll~~~ 56 (306)
T TIGR02716 22 GPKDLATLAADT----------GSVPPRLEMLLETLRQMRVINLE 56 (306)
T ss_pred CCCCHHHHHHHc----------CCChHHHHHHHHHHHhCCCeEec
Confidence 578999999999 78899999999999999999986
No 32
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=44.92 E-value=30 Score=27.91 Aligned_cols=53 Identities=21% Similarity=0.264 Sum_probs=38.8
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccC
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTA 143 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~ 143 (302)
..+++|...+. .++.++..+.|...+ ..+-.=-||-..+.|+..|||.|....
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~~~~-----~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLRKKG-----PRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHHHTT-----TT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhhhcc-----CCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 46777888765 899999999994211 123333599999999999999998543
No 33
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=44.33 E-value=80 Score=23.40 Aligned_cols=44 Identities=18% Similarity=0.254 Sum_probs=35.2
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..+.++... +.++..++|..+ ...+..|+-+.+-|+..|+|++.
T Consensus 14 ~il~~l~~~--~~~~~~~la~~~----------~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 14 LVLRILYEE--GPLSVSELAKRL----------GVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHc--CCcCHHHHHHHH----------CCCchhHHHHHHHHHHCCCeEec
Confidence 344455443 358999999998 67778899999999999999987
No 34
>PF13730 HTH_36: Helix-turn-helix domain
Probab=42.96 E-value=30 Score=24.10 Aligned_cols=30 Identities=23% Similarity=0.195 Sum_probs=27.0
Q ss_pred ecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhh
Q 042344 98 ITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLI 137 (302)
Q Consensus 98 IdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLI 137 (302)
.+....|+.+ +..+|.++-..+.|+..|+|
T Consensus 26 pS~~~la~~~----------g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDL----------GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHH----------CcCHHHHHHHHHHHHHCcCC
Confidence 3788999998 78899999999999999987
No 35
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=41.41 E-value=40 Score=26.88 Aligned_cols=41 Identities=29% Similarity=0.375 Sum_probs=34.5
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
|.+-|..+ ++.+++.++|+.| +...++|++ .|...|+|-|.
T Consensus 14 ~~d~~~~~-~~~~ti~~~AK~L----------~i~~~~l~~---~Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVDS-DGLYTIREAAKLL----------GIGRNKLFQ---WLREKGWLYRR 54 (111)
T ss_pred HHHHHHcC-CCCccHHHHHHHh----------CCCHHHHHH---HHHhCCceEEC
Confidence 66777776 4899999999999 788899987 58889999883
No 36
>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=39.20 E-value=59 Score=25.75 Aligned_cols=50 Identities=18% Similarity=0.228 Sum_probs=38.5
Q ss_pred CHHHHHHHHHHHHhhCC--CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhh
Q 042344 78 SLGLLTQNFVRLFVCSN--VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLI 137 (302)
Q Consensus 78 SLglLTqkFV~L~l~sp--~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLI 137 (302)
+|.-+.++.+.+|...+ ..=|.+++.++.| +.-...|..++.-|..-|+|
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l----------~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL----------GMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS----------TS-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh----------CcCHHHHHHHHHHHHhCCeE
Confidence 78899999999998821 2449999999999 45668888999999988887
No 37
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=39.10 E-value=72 Score=25.86 Aligned_cols=36 Identities=19% Similarity=0.212 Sum_probs=32.7
Q ss_pred CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 95 VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 95 ~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.+.++..+.|+.+ ++.++.+++|...|..-|||...
T Consensus 23 ~~~~s~~eia~~~----------~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 23 EGPVSVKEIAERQ----------GISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCcCcHHHHHHHH----------CcCHHHHHHHHHHHHHCCcEEec
Confidence 3489999999999 88999999999999999999764
No 38
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=38.69 E-value=60 Score=22.43 Aligned_cols=41 Identities=22% Similarity=0.266 Sum_probs=32.0
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhhee
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEK 139 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK 139 (302)
.+.++.. +..+..+.|+.| +..+--++==.++|+..|||+|
T Consensus 7 Il~~L~~---~~~~~~el~~~l----------~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE---GPLTVSELAEEL----------GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT---SSEEHHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh---CCCchhhHHHhc----------cccchHHHHHHHHHHHCcCeeC
Confidence 4445554 569999999999 6777778888999999999986
No 39
>PF08595 RXT2_N: RXT2-like, N-terminal; InterPro: IPR013904 The entry represents the N-terminal region of RXT2-like proteins. In Saccharomyces cerevisiae (Baker's yeast), RXT2 has been demonstrated to be involved in conjugation with cellular fusion (mating) and invasive growth []. A high throughput localisation study has localised RXT2 to the nucleus [].
Probab=37.27 E-value=25 Score=31.13 Aligned_cols=45 Identities=16% Similarity=0.302 Sum_probs=32.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhhCCCceecHHHHHHHHhc
Q 042344 65 AHKSSKNDSRREKSLGLLTQNFVRLFVCSNVDMITLDEVAKLLLG 109 (302)
Q Consensus 65 ~~~~~k~~~RkdKSLglLTqkFV~L~l~sp~gvIdLneAA~~L~g 109 (302)
+.-|.-+..=+.+.|..|+..-+.++.....-++.+......|+|
T Consensus 104 ~tHPaiS~~f~Sk~L~~La~q~i~~iekEq~~l~~~~kLl~vllG 148 (149)
T PF08595_consen 104 PTHPAISRTFKSKALSKLALQLIEMIEKEQNSLWRLKKLLEVLLG 148 (149)
T ss_pred cCCcccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 444455556688999999999999998865556666666666655
No 40
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=37.26 E-value=63 Score=25.29 Aligned_cols=47 Identities=15% Similarity=0.160 Sum_probs=39.5
Q ss_pred HHHHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 82 LTQNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 82 LTqkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
+=++.+.+|... +.++..+.|+.+ ++...-++...+-|+.-|+|.+.
T Consensus 4 ~D~~il~~L~~~--~~~~~~~la~~l----------~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKD--ARISLAELAKKV----------GLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCeece
Confidence 346788888875 479999999999 67788888899999999999865
No 41
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=35.58 E-value=1e+02 Score=24.51 Aligned_cols=36 Identities=19% Similarity=0.201 Sum_probs=31.4
Q ss_pred CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 95 VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 95 ~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
...++-.+.|..+ ++.+--+-.+.+.|+..|+|++.
T Consensus 45 ~~~is~~eLa~~~----------g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRVTATVIAELT----------GLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCccCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCeeee
Confidence 4578888999888 67888899999999999999987
No 42
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=32.48 E-value=1.2e+02 Score=21.90 Aligned_cols=45 Identities=22% Similarity=0.214 Sum_probs=35.4
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.+.+.+|.. .+..+..+.|+.| +...=.+|-=.++|+..|||+..
T Consensus 13 ~~Il~~L~~--~~~~t~~ela~~l----------~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 13 LRILRLLAS--NGPMTVSELAEEL----------GISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHHHHHH--CSTBEHHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHhc--CCCCCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCeEEe
Confidence 445666633 3579999999999 56677789999999999999886
No 43
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=31.55 E-value=1.8e+02 Score=21.01 Aligned_cols=47 Identities=15% Similarity=0.183 Sum_probs=34.4
Q ss_pred HHHHHHHhh---CCCcee-cHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 84 QNFVRLFVC---SNVDMI-TLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 84 qkFV~L~l~---sp~gvI-dLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
......+.. .++..+ +..+.|+.+ ++.+.-+....+.|+..|+|++.
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~----------~vsr~tvr~al~~L~~~g~i~~~ 57 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERY----------GVSRTTVREALRRLEAEGLIERR 57 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHH----------TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHh----------ccCCcHHHHHHHHHHHCCcEEEE
Confidence 334444444 345677 999999999 78888888889999999999987
No 44
>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=30.27 E-value=1.4e+02 Score=24.10 Aligned_cols=45 Identities=16% Similarity=0.238 Sum_probs=30.8
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
.|+++... ...|.-.+.|+.| ....=-|-.+.-.|+.+|||++++
T Consensus 13 lV~~Y~~~-~~PVgSk~ia~~l----------~~s~aTIRN~M~~Le~lGlve~~p 57 (78)
T PF03444_consen 13 LVELYIET-GEPVGSKTIAEEL----------GRSPATIRNEMADLEELGLVESQP 57 (78)
T ss_pred HHHHHHhc-CCCcCHHHHHHHH----------CCChHHHHHHHHHHHHCCCccCCC
Confidence 45555555 4678888888887 222334556677899999999864
No 45
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=29.75 E-value=1.8e+02 Score=19.61 Aligned_cols=37 Identities=16% Similarity=0.195 Sum_probs=30.8
Q ss_pred CCcee-cHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 94 NVDMI-TLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 94 p~gvI-dLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
+...+ +..+.|+.+ ++.+=-+....+-|+.-|+|++.
T Consensus 16 ~~~~l~s~~~la~~~----------~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 16 PGDKLPSERELAAQL----------GVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CCCcCcCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCEEEe
Confidence 34456 899999999 67777888889999999999877
No 46
>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=29.57 E-value=1.3e+02 Score=23.84 Aligned_cols=51 Identities=14% Similarity=0.241 Sum_probs=38.0
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheeccc
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHT 142 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~ 142 (302)
.+++|... .+.++.+++.+.|..... ...+=-+|-+.+.|+..|||.|...
T Consensus 6 Il~~l~~~-~~~~sa~ei~~~l~~~~~-----~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 6 ILEVLLES-DGHLTAEEIYERLRKKGP-----SISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHhC-CCCCCHHHHHHHHHhcCC-----CCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 45666665 478999999999843211 2445679999999999999999853
No 47
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=28.49 E-value=17 Score=31.06 Aligned_cols=21 Identities=10% Similarity=0.349 Sum_probs=0.0
Q ss_pred chhhhhhHHHHHhhhhhheec
Q 042344 120 KVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 120 kkRRLYDItNVLEgIgLIEK~ 140 (302)
.++++-+-...||.+|+|.+.
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~ 25 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS 25 (142)
T ss_dssp ---------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc
Confidence 457788888999999999765
No 48
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=28.15 E-value=57 Score=26.15 Aligned_cols=37 Identities=14% Similarity=0.098 Sum_probs=31.2
Q ss_pred CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 95 VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 95 ~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
.+.++..+.|+.+ .+.+--+.=+.+-|+.-|||++..
T Consensus 40 ~~~~t~~ela~~~----------~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 40 QGSMEFTQLANQA----------CILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred cCCcCHHHHHHHh----------CCCchhHHHHHHHHHHCCCEEecc
Confidence 3568889999998 566678899999999999999983
No 49
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=28.06 E-value=1.1e+02 Score=28.11 Aligned_cols=44 Identities=11% Similarity=0.132 Sum_probs=36.2
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
.+++|...+ +.+++.+.|+.| +..+=-+|-+.+-|+..|+|++.
T Consensus 16 iL~~l~~~~-~~ls~~eia~~l----------gl~kstv~RlL~tL~~~g~v~~~ 59 (263)
T PRK09834 16 VLRALNRLD-GGATVGLLAELT----------GLHRTTVRRLLETLQEEGYVRRS 59 (263)
T ss_pred HHHHHHhcC-CCCCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEEe
Confidence 445554443 459999999999 67888999999999999999987
No 50
>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=27.97 E-value=87 Score=23.73 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=33.3
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccc-hhhhhhHHHHHhhhhhheec
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTK-VRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvk-kRRLYDItNVLEgIgLIEK~ 140 (302)
||.-+.......-++.|.|+.| +.+ ..-++.....|+.-|+|++.
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~----------g~~S~~tv~~~L~~Le~kG~I~r~ 59 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEAL----------GLKSTSTVQRHLKALERKGYIRRD 59 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHH----------TSSSHHHHHHHHHHHHHTTSEEEG
T ss_pred HHHHHHHHcCCCCCHHHHHHHh----------CCCChHHHHHHHHHHHHCcCccCC
Confidence 4444444444567999999999 555 78899999999999999998
No 51
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=26.75 E-value=1.1e+02 Score=28.33 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=32.3
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecc
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTH 141 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~ 141 (302)
-+++|.. .+.+++.+.|+.| ++...-++--.+.|+..|+|.|.+
T Consensus 10 Il~~l~~--~~~~~~~ela~~l----------~vS~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 10 LLELLAQ--LGFVTVEKVIERL----------GISPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHH--cCCcCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEEec
Confidence 4455554 4789999999999 444444444477799999999984
No 52
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=26.33 E-value=2e+02 Score=25.50 Aligned_cols=58 Identities=14% Similarity=0.213 Sum_probs=39.0
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheeccc-CCCCCCcEEee
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHT-ADTRKPAFRWL 153 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~-~~~sKn~iqWi 153 (302)
.+.+.++... +.++..+.|+.| ++..=-+.-....|+.-|||++... ...+++.+.|.
T Consensus 4 ~~IL~~L~~~--~~~t~~eLA~~l----------gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~ 62 (203)
T TIGR02702 4 EDILSYLLKQ--GQATAAALAEAL----------AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQ 62 (203)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEE
Confidence 3456666654 459999999999 3444445555678999999998732 22356666663
No 53
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=26.09 E-value=1.7e+02 Score=26.32 Aligned_cols=58 Identities=16% Similarity=0.252 Sum_probs=40.2
Q ss_pred HHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhhe--ecccCCCCCCcEEee
Q 042344 84 QNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIE--KTHTADTRKPAFRWL 153 (302)
Q Consensus 84 qkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIE--K~~~~~~sKn~iqWi 153 (302)
..++.+|.. .+.++-++.|..| +.+..-+=-|.+-|..-|||. +.....++.+.|-|.
T Consensus 25 ~~Vl~~L~~--~g~~tdeeLA~~L----------gi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~ 84 (178)
T PRK06266 25 FEVLKALIK--KGEVTDEEIAEQT----------GIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWK 84 (178)
T ss_pred hHHHHHHHH--cCCcCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEE
Confidence 445565555 3579999999999 455555555688899999999 332223466888887
No 54
>PF08020 DUF1706: Protein of unknown function (DUF1706) ; InterPro: IPR012550 This family contains many hypothetical proteins from bacteria and yeast.
Probab=25.80 E-value=1e+02 Score=27.61 Aligned_cols=62 Identities=26% Similarity=0.451 Sum_probs=49.5
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccCCCCCCcEEe
Q 042344 73 SRREKSLGLLTQNFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKPAFRW 152 (302)
Q Consensus 73 ~RkdKSLglLTqkFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn~iqW 152 (302)
.-+=+-||.|.+.|.+-... ++|.++-..| .....+|.+.+.-|.-=-|.+| +.|.|
T Consensus 79 gykWn~lg~Ln~~f~~~y~~-----~sl~e~~~~l----------~~s~~~v~~lI~~~sdeeLf~~--------~~~~W 135 (166)
T PF08020_consen 79 GYKWNQLGELNQSFYEKYQD-----TSLEELKALL----------KESHQKVIALIESFSDEELFEK--------GQFKW 135 (166)
T ss_pred CCChhhhhHHHHHHHHHHcC-----CCHHHHHHHH----------HHHHHHHHHHHHhCcchhhccc--------cccCC
Confidence 35677899999999886654 7899999999 5667888888888877777754 58889
Q ss_pred ecccc
Q 042344 153 LGVNR 157 (302)
Q Consensus 153 iG~~~ 157 (302)
.|.-+
T Consensus 136 ~~~~t 140 (166)
T PF08020_consen 136 TGKWT 140 (166)
T ss_pred cCCCc
Confidence 87665
No 55
>PRK09462 fur ferric uptake regulator; Provisional
Probab=25.71 E-value=1.5e+02 Score=25.00 Aligned_cols=52 Identities=8% Similarity=0.254 Sum_probs=38.6
Q ss_pred HHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheeccc
Q 042344 86 FVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHT 142 (302)
Q Consensus 86 FV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~ 142 (302)
.+++|...+.+.++.+++.+.|..... .+..=-+|-+.+.|+..|||.|...
T Consensus 22 Il~~l~~~~~~h~sa~eI~~~l~~~~~-----~i~~aTVYR~L~~L~e~Gli~~~~~ 73 (148)
T PRK09462 22 ILEVLQEPDNHHVSAEDLYKRLIDMGE-----EIGLATVYRVLNQFDDAGIVTRHNF 73 (148)
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHhhCC-----CCCHHHHHHHHHHHHHCCCEEEEEc
Confidence 566666655568999999999843221 2344568999999999999999853
No 56
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=25.15 E-value=1.9e+02 Score=26.84 Aligned_cols=45 Identities=9% Similarity=0.221 Sum_probs=37.1
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..+++|-..+ ..+++.+.|+.| +..|=.+|.+.+-|+..|++++.
T Consensus 29 ~IL~~~~~~~-~~~tl~eIa~~l----------glpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 29 AILQYLEKSG-GSSSVSDISLNL----------DLPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred HHHHHHHhCC-CCcCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEEc
Confidence 3456665543 469999999999 67788999999999999999886
No 57
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=25.12 E-value=78 Score=20.66 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=18.5
Q ss_pred ecHHHHHHHHhcCcCCccccccchhhhhhHHH
Q 042344 98 ITLDEVAKLLLGDAHNTSVMRTKVRRLYDIAN 129 (302)
Q Consensus 98 IdLneAA~~L~g~~~~~s~~kvkkRRLYDItN 129 (302)
+++.+||+.| ++.++.||-.++
T Consensus 2 lt~~e~a~~l----------gis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYL----------GVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHH----------CCCHHHHHHHHH
Confidence 5789999999 788899998764
No 58
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=24.61 E-value=27 Score=29.48 Aligned_cols=13 Identities=38% Similarity=0.733 Sum_probs=9.7
Q ss_pred hhHHHHHhhhhhh
Q 042344 125 YDIANVLSSMNLI 137 (302)
Q Consensus 125 YDItNVLEgIgLI 137 (302)
||||.+|..+||=
T Consensus 58 ydIT~~l~~l~l~ 70 (103)
T PF14830_consen 58 YDITDALKKLGLH 70 (103)
T ss_dssp EE-HHHHHHCT--
T ss_pred hhHHHHHHHcCCC
Confidence 8999999999996
No 59
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=23.80 E-value=79 Score=29.13 Aligned_cols=46 Identities=28% Similarity=0.298 Sum_probs=34.2
Q ss_pred CceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheecccCCCCCCcE
Q 042344 95 VDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKTHTADTRKPAF 150 (302)
Q Consensus 95 ~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~~~~~~sKn~i 150 (302)
...++|++.++.| +..+=++-=..-+|++.||++|++...-+|..|
T Consensus 39 ~~Pmtl~Ei~E~l----------g~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F 84 (177)
T COG1510 39 RKPLTLDEIAEAL----------GMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYF 84 (177)
T ss_pred CCCccHHHHHHHH----------CCCcchHHHHHHHHHhcchHHhhhccCcchhhh
Confidence 3679999999999 455556666677899999999996553344443
No 60
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=23.41 E-value=87 Score=31.98 Aligned_cols=35 Identities=20% Similarity=0.185 Sum_probs=29.3
Q ss_pred CCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhhe
Q 042344 94 NVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIE 138 (302)
Q Consensus 94 p~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIE 138 (302)
.+|.-+|-+.|+++ +..-++|+|+++.|...|||+
T Consensus 352 ~DG~~slldIA~~~----------~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 352 SDGKNSLLDIAERI----------GLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -EEEEEHHHHHHHH----------T--HHHHHHHHHHHHHTT-EE
T ss_pred ccCCCcHHHHHHHH----------CcCHHHHHHHHHHHHHcCCCC
Confidence 37999999999999 788999999999999999985
No 61
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=23.37 E-value=62 Score=32.05 Aligned_cols=21 Identities=24% Similarity=0.477 Sum_probs=18.9
Q ss_pred chhhhhhHHHHHhhhhhheec
Q 042344 120 KVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 120 kkRRLYDItNVLEgIgLIEK~ 140 (302)
..||+|||.|-|+.+|+|+-.
T Consensus 314 ~~~~~~~ii~~L~~lgiv~~~ 334 (366)
T COG1474 314 SQRRFSDIISELEGLGIVSAS 334 (366)
T ss_pred hHHHHHHHHHHHHhcCeEEee
Confidence 779999999999999999743
No 62
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=23.03 E-value=2.2e+02 Score=22.00 Aligned_cols=73 Identities=10% Similarity=0.205 Sum_probs=38.4
Q ss_pred chhhhhhHHHHHhhhhhheecccCCCCCCcEEeecccccccccccccCcchHHHhhhHHHHHHHHHHHHhHHHHhhhhc
Q 042344 120 KVRRLYDIANVLSSMNLIEKTHTADTRKPAFRWLGVNRLEIGLADSLNLDESRKRTFGTDVTNISFKRKRMDTSINGDI 198 (302)
Q Consensus 120 kkRRLYDItNVLEgIgLIEK~~~~~~sKn~iqWiG~~~~~n~~~~a~~~~~s~kr~l~~El~nL~~~E~~LD~~I~~~~ 198 (302)
..+.+-.+.-|++-|..+.-. .+.|+=+|.--+......+.+....++..+..+|..|+.....+...++...
T Consensus 24 l~~~~~~~~~~~~eL~~l~~~------~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~ 96 (106)
T PF01920_consen 24 LERQLRELELTLEELEKLDDD------RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELK 96 (106)
T ss_dssp HHHHHHHHHHHHHHHHTSSTT-------EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCc------chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455566667777666433 3345545554333322222222445566666666666666666666555543
No 63
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=21.68 E-value=2.3e+02 Score=19.49 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=28.9
Q ss_pred eecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 97 MITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 97 vIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
+.+..+.|+.+ ++.+=.+....+-|+.-|+|++.
T Consensus 25 ~~~~~~la~~~----------~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 25 LPSERELAEEL----------GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CCCHHHHHHHH----------CCCHHHHHHHHHHHHHCCCEEec
Confidence 34599999998 67777888999999999999876
No 64
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=21.65 E-value=1.7e+02 Score=26.60 Aligned_cols=45 Identities=13% Similarity=0.122 Sum_probs=36.8
Q ss_pred HHHHHHhhCCCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 85 NFVRLFVCSNVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 85 kFV~L~l~sp~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..+++|-.. ...+++.|.|+.| +..|=.+|-|.+-|+..|++++.
T Consensus 13 ~IL~~l~~~-~~~~~l~eia~~l----------glpksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 13 AVIEAFGAE-RPRLTLTDVAEAT----------GLTRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHHhcC-CCCCCHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEeC
Confidence 345555544 3679999999999 67788999999999999999875
No 65
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=20.91 E-value=2.1e+02 Score=25.25 Aligned_cols=37 Identities=11% Similarity=0.176 Sum_probs=32.6
Q ss_pred CCceecHHHHHHHHhcCcCCccccccchhhhhhHHHHHhhhhhheec
Q 042344 94 NVDMITLDEVAKLLLGDAHNTSVMRTKVRRLYDIANVLSSMNLIEKT 140 (302)
Q Consensus 94 p~gvIdLneAA~~L~g~~~~~s~~kvkkRRLYDItNVLEgIgLIEK~ 140 (302)
..+.+++.+.|+.+ .+..+-|..|.+-|.--|||+-.
T Consensus 22 ~~~~vs~~eIA~~~----------~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 22 EAGPVPLADISERQ----------GISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCcCcHHHHHHHH----------CcCHHHHHHHHHHHHHCCCEEeC
Confidence 34689999999999 78889999999999999999854
Done!