Query T0586 3NEU, Listeria innocua Clip11262, 125 residues
Match_columns 125
No_of_seqs 117 out of 8289
Neff 8.0
Searched_HMMs 11830
Date Sun Jun 13 15:31:51 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0586.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0586.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00392 GntR: Bacterial regul 99.7 6.6E-17 5.6E-21 129.3 8.2 64 14-77 1-64 (64)
2 PF01726 LexA_DNA_bind: LexA D 97.6 3.5E-05 2.9E-09 52.3 5.4 58 12-74 5-63 (65)
3 PF08279 HTH_11: HTH domain; 97.0 0.00013 1.1E-08 48.5 2.7 43 33-76 12-55 (55)
4 PF08220 HTH_DeoR: DeoR-like h 97.0 0.00045 3.8E-08 44.9 5.0 44 34-78 12-55 (57)
5 PF01325 Fe_dep_repress: Iron 97.0 0.00048 4E-08 44.8 5.0 42 33-75 19-60 (60)
6 PF02082 Rrf2: Transcriptional 96.7 0.0019 1.6E-07 40.8 6.4 58 22-80 11-70 (83)
7 PF05732 RepL: Firmicute plasm 96.6 0.0024 2E-07 40.2 6.5 48 32-80 70-117 (165)
8 PF03444 DUF293: Domain of unk 96.4 0.0011 9E-08 42.5 3.8 57 21-78 8-65 (78)
9 PF04703 FaeA: FaeA-like prote 96.4 0.0022 1.9E-07 40.4 5.3 50 16-74 3-53 (62)
10 PF01978 TrmB: Sugar-specific 96.2 0.002 1.7E-07 40.6 3.9 38 39-76 24-61 (68)
11 PF04492 Phage_rep_O: Bacterio 95.6 0.011 8.9E-07 35.9 5.6 45 28-73 46-90 (100)
12 PF08784 RPA_C: Replication pr 95.4 0.0083 7E-07 36.6 4.7 54 11-70 45-98 (102)
13 PF01710 Transposase_14: Trans 95.1 0.028 2.4E-06 33.1 6.6 89 21-119 6-94 (119)
14 PF03428 RP-C: Replication pro 94.7 0.05 4.3E-06 31.5 6.9 55 17-71 47-105 (177)
15 PF08222 HTH_CodY: CodY helix- 94.4 0.01 8.8E-07 36.0 2.9 44 39-82 6-51 (61)
16 PF01047 MarR: MarR family; I 94.4 0.018 1.5E-06 34.4 4.0 36 38-73 18-53 (59)
17 PF09339 HTH_IclR: IclR helix- 94.1 0.024 2E-06 33.6 4.2 37 34-71 16-52 (52)
18 PF00325 Crp: Bacterial regula 93.6 0.028 2.3E-06 33.2 3.8 29 39-67 4-32 (32)
19 PF03965 Pencillinase_R: Penic 93.6 0.12 9.7E-06 29.1 6.9 92 24-117 6-110 (115)
20 PF01022 HTH_5: Bacterial regu 93.0 0.047 4E-06 31.6 4.2 32 37-69 16-47 (47)
21 PF07848 PaaX: PaaX-like prote 92.7 0.064 5.4E-06 30.8 4.5 44 36-79 22-68 (70)
22 PF06163 DUF977: Bacterial pro 92.0 0.071 6E-06 30.5 4.1 46 34-80 24-69 (127)
23 PF03297 Ribosomal_S25: S25 ri 91.7 0.065 5.5E-06 30.7 3.6 50 16-71 44-93 (105)
24 PF09397 Ftsk_gamma: Ftsk gamm 90.4 0.31 2.6E-05 26.2 6.0 58 9-76 2-59 (65)
25 PF12298 Bot1p: Eukaryotic mit 89.8 0.32 2.7E-05 26.2 5.6 55 4-65 7-61 (172)
26 PF05043 Mga: Mga helix-turn-h 89.2 0.68 5.8E-05 24.0 7.8 52 33-87 27-82 (87)
27 PF04967 HTH_10: HTH DNA bindi 88.4 0.56 4.8E-05 24.6 6.1 44 19-63 6-49 (53)
28 PF01090 Ribosomal_S19e: Ribos 87.4 0.45 3.8E-05 25.2 5.1 63 15-84 51-127 (139)
29 PF07900 DUF1670: Protein of u 87.4 0.36 3E-05 25.9 4.6 55 18-73 87-142 (220)
30 PF01638 HxlR: HxlR-like helix 85.8 0.57 4.8E-05 24.5 4.9 48 39-86 20-74 (90)
31 PF09012 FeoC: FeoC like trans 85.4 0.26 2.2E-05 26.7 3.1 37 36-73 14-50 (69)
32 PF02002 TFIIE_alpha: TFIIE al 84.8 0.29 2.4E-05 26.5 3.0 35 36-71 27-61 (105)
33 PF05225 HTH_psq: helix-turn-h 84.6 0.23 1.9E-05 27.1 2.5 29 31-61 12-40 (45)
34 PF00356 LacI: Bacterial regul 84.4 0.32 2.7E-05 26.2 3.1 22 39-60 1-22 (46)
35 PF02796 HTH_7: Helix-turn-hel 83.7 0.27 2.3E-05 26.7 2.5 32 20-59 12-43 (45)
36 PF05584 Sulfolobus_pRN: Sulfo 82.7 0.73 6.2E-05 23.8 4.4 33 39-71 20-52 (72)
37 PF09681 Phage_rep_org_N: N-te 82.0 1.5 0.00013 21.7 9.3 64 18-81 27-97 (121)
38 PF00292 PAX: 'Paired box' dom 78.6 1.7 0.00014 21.4 5.1 62 7-76 11-72 (125)
39 PF04079 DUF387: Putative tran 77.7 2.1 0.00018 20.8 7.5 82 31-114 8-103 (159)
40 PF10007 DUF2250: Uncharacteri 77.7 1.2 0.0001 22.3 4.2 34 40-73 24-57 (92)
41 PF01418 HTH_6: Helix-turn-hel 77.5 0.7 5.9E-05 23.9 2.9 57 10-72 13-69 (107)
42 PF06970 RepA_N: Replication i 76.9 1.9 0.00016 21.1 5.0 49 13-61 25-76 (76)
43 PF04218 CENP-B_N: CENP-B N-te 76.3 0.27 2.3E-05 26.7 0.5 21 39-59 24-44 (53)
44 PF09862 DUF2089: Protein of u 75.9 1.2 9.7E-05 22.5 3.7 61 39-117 51-112 (113)
45 PF08221 HTH_9: RNA polymerase 74.9 1.4 0.00012 22.0 3.9 52 16-69 8-59 (62)
46 PF10668 Phage_terminase: Phag 73.9 0.91 7.7E-05 23.2 2.7 36 12-56 6-41 (60)
47 PF08461 HTH_12: Ribonuclease 73.5 1.5 0.00013 21.7 3.8 47 33-80 10-61 (66)
48 PF01475 FUR: Ferric uptake re 73.4 0.74 6.3E-05 23.8 2.2 36 38-73 24-64 (120)
49 PF04433 SWIRM: SWIRM domain; 70.2 1.8 0.00015 21.3 3.5 51 17-68 32-83 (84)
50 PF08765 Mor: Mor transcriptio 68.9 2.3 0.0002 20.5 3.9 50 13-66 52-101 (108)
51 PF09170 DUF1879: Domain of un 68.7 1.9 0.00016 21.1 3.3 82 14-95 52-151 (174)
52 PF08280 HTH_Mga: M protein tr 68.2 2.1 0.00018 20.8 3.5 30 34-64 17-46 (59)
53 PF04157 EAP30: EAP30/Vps36 fa 68.2 2.3 0.0002 20.5 3.8 71 10-81 87-168 (223)
54 PF07453 NUMOD1: NUMOD1 domain 67.8 1.2 0.0001 22.4 2.2 23 36-58 15-37 (37)
55 PF00126 HTH_1: Bacterial regu 66.9 2.1 0.00017 20.9 3.3 40 38-78 14-56 (60)
56 PF03551 PadR: Transcriptional 66.8 2.3 0.00019 20.6 3.5 50 21-73 10-63 (86)
57 PF12116 SpoIIID: Stage III sp 66.6 0.95 8E-05 23.1 1.5 28 34-62 17-45 (82)
58 PF04297 UPF0122: Putative hel 64.4 2.4 0.00021 20.4 3.3 28 34-62 31-58 (101)
59 PF07638 Sigma70_ECF: ECF sigm 62.9 3.3 0.00028 19.5 3.7 14 104-117 148-161 (185)
60 PF07023 DUF1315: Protein of u 62.4 3.7 0.00031 19.2 3.9 55 16-79 10-68 (93)
61 PF01371 Trp_repressor: Trp re 62.3 3.2 0.00027 19.6 3.6 25 39-63 51-75 (87)
62 PF06056 Terminase_5: Putative 59.0 3.5 0.00029 19.4 3.2 31 39-69 15-45 (58)
63 PF03374 ANT: Phage antirepres 57.5 4.7 0.0004 18.5 3.7 37 36-76 23-59 (111)
64 PF01498 Transposase_5: Transp 57.5 3.3 0.00028 19.5 2.9 36 39-77 15-55 (72)
65 PF00376 MerR: MerR family reg 57.3 1.9 0.00016 21.1 1.7 25 39-67 1-25 (38)
66 PF12471 GTP_CH_N: GTP cyclohy 56.3 5.1 0.00043 18.3 3.7 40 20-59 135-192 (194)
67 PF08281 Sigma70_r4_2: Sigma-7 55.7 2.9 0.00025 19.9 2.4 25 37-62 27-51 (54)
68 PF11740 KfrA_N: Plasmid repli 55.6 5.8 0.00049 17.9 6.1 46 15-66 3-49 (120)
69 PF06413 Neugrin: Neugrin; In 54.9 3.7 0.00031 19.2 2.8 21 39-59 31-51 (225)
70 PF09079 Cdc6_C: CDC6, C termi 54.9 5.9 0.0005 17.8 3.9 42 30-71 15-59 (85)
71 PF02295 z-alpha: Adenosine de 54.7 6 0.00051 17.8 3.9 40 34-74 18-57 (66)
72 PF05930 Phage_AlpA: Prophage 54.3 2.2 0.00018 20.7 1.6 24 36-59 2-25 (51)
73 PF02001 DUF134: Protein of un 53.6 4.8 0.00041 18.4 3.2 30 31-61 52-81 (106)
74 PF07471 Phage_Nu1: Phage DNA 51.2 2.4 0.0002 20.5 1.3 34 39-76 4-38 (164)
75 PF06971 Put_DNA-bind_N: Putat 50.8 4.3 0.00036 18.8 2.6 39 13-59 12-50 (50)
76 PF09182 PuR_N: Bacterial puri 50.0 7.1 0.0006 17.3 4.3 42 32-74 16-63 (70)
77 PF04539 Sigma70_r3: Sigma-70 47.6 5.7 0.00048 17.9 2.9 28 35-62 18-45 (78)
78 PF04182 B-block_TFIIIC: B-blo 47.1 7.9 0.00067 17.0 3.5 48 21-72 6-53 (75)
79 PF03811 Ins_element1: Inserti 47.1 6.1 0.00052 17.7 2.9 34 18-59 52-85 (88)
80 PF10264 Stork_head: Winged he 44.3 8.7 0.00074 16.7 3.5 29 50-79 50-78 (80)
81 PF00196 GerE: Bacterial regul 43.9 8.8 0.00074 16.7 3.6 25 39-63 20-44 (58)
82 PF09756 DDRGK: DDRGK domain; 43.6 7.3 0.00062 17.2 2.9 58 18-81 100-160 (188)
83 PF06504 RepC: Replication pro 43.5 8.9 0.00076 16.7 5.0 67 7-73 81-153 (281)
84 PF05402 PqqD: Coenzyme PQQ sy 42.7 9.2 0.00078 16.6 3.5 29 40-68 49-81 (81)
85 PF07022 Phage_CI_repr: Bacter 42.6 3.6 0.00031 19.3 1.2 22 38-59 13-35 (66)
86 PF07377 DUF1493: Protein of u 42.0 9.4 0.0008 16.5 5.2 53 13-65 3-55 (111)
87 PF03962 Mnd1: Mnd1 family; I 41.9 9.5 0.0008 16.5 5.0 33 44-77 22-54 (188)
88 PF08535 KorB: KorB domain; I 40.9 3 0.00025 19.8 0.6 37 39-75 5-41 (93)
89 PF03180 Lipoprotein_9: NLPA l 40.9 8 0.00068 17.0 2.8 30 50-79 105-134 (237)
90 PF07750 GcrA: GcrA cell cycle 40.7 7.3 0.00062 17.2 2.5 29 36-65 18-47 (162)
91 PF00165 HTH_AraC: Bacterial r 38.7 11 0.00089 16.2 3.7 28 34-62 6-33 (42)
92 PF01381 HTH_3: Helix-turn-hel 38.2 8.1 0.00069 16.9 2.4 21 39-59 11-31 (55)
93 PF10557 Cullin_Nedd8: Cullin 37.9 7.6 0.00064 17.1 2.2 30 43-72 36-65 (68)
94 PF02954 HTH_8: Bacterial regu 37.8 9.8 0.00083 16.4 2.8 22 39-60 20-41 (42)
95 PF05848 CtsR: Firmicute trans 37.5 11 0.00092 16.1 3.0 63 14-78 4-69 (152)
96 PF12481 DUF3700: Aluminium in 37.0 6.6 0.00056 17.5 1.8 55 4-65 57-119 (124)
97 PF07374 DUF1492: Protein of u 36.4 11 0.00097 16.0 3.0 25 36-61 71-99 (100)
98 PF05158 RNA_pol_Rpc34: RNA po 34.5 12 0.001 15.8 8.2 31 40-70 104-134 (325)
99 PF06322 Phage_NinH: Phage Nin 34.5 8.6 0.00073 16.8 2.1 27 39-65 18-44 (64)
100 PF10141 ssDNA-exonuc_C: Singl 33.6 13 0.0011 15.7 9.1 68 11-81 93-160 (195)
101 PF04545 Sigma70_r4: Sigma-70, 33.5 2.5 0.00021 20.3 -0.8 27 34-61 18-44 (50)
102 PF04936 DUF658: Protein of un 33.3 9.5 0.0008 16.5 2.1 30 39-72 16-45 (186)
103 PF07278 DUF1441: Protein of u 31.1 14 0.0011 15.5 2.6 26 36-62 1-26 (152)
104 PF09048 Cro: Cro; InterPro: 29.5 15 0.0013 15.2 2.6 23 39-61 14-36 (59)
105 PF09107 SelB-wing_3: Elongati 28.9 15 0.0013 15.2 2.8 39 33-72 7-45 (50)
106 PF05331 DUF742: Protein of un 28.2 11 0.0009 16.2 1.7 39 36-75 55-93 (114)
107 PF10543 ORF6N: ORF6N domain 28.2 16 0.0013 15.1 2.6 41 34-79 9-50 (88)
108 PF06353 DUF1062: Protein of u 27.7 16 0.0013 15.0 3.9 38 30-73 98-135 (142)
109 PF04337 DUF480: Protein of un 27.7 8.9 0.00075 16.7 1.2 34 47-81 44-77 (148)
110 PF00440 TetR_N: Bacterial reg 27.5 16 0.0014 15.0 2.6 24 35-59 15-38 (47)
111 PF01527 Transposase_8: Transp 27.3 6.9 0.00059 17.4 0.6 24 39-62 25-48 (76)
112 PF04645 DUF603: Protein of un 27.2 16 0.0014 15.0 2.7 32 31-64 15-46 (181)
113 PF04760 IF2_N: Translation in 26.9 15 0.0013 15.2 2.3 36 35-73 2-37 (54)
114 PF01399 PCI: PCI domain; Int 26.6 2.9 0.00024 19.9 -1.5 64 13-77 37-102 (105)
115 PF12324 HTH_15: Helix-turn-he 23.9 16 0.0013 15.0 1.9 32 31-63 33-64 (77)
116 PF00538 Linker_histone: linke 23.3 19 0.0016 14.5 5.3 60 13-75 3-69 (77)
117 PF05491 RuvB_C: Holliday junc 23.3 19 0.0016 14.5 3.0 45 34-80 23-68 (76)
118 PF07514 TraI_2: Putative heli 23.2 19 0.0016 14.5 3.3 59 9-67 239-299 (327)
119 PF06530 Phage_antitermQ: Phag 23.2 19 0.0016 14.5 3.2 21 39-59 80-100 (125)
120 PF09904 DUF2131: Uncharacteri 21.3 21 0.0018 14.2 3.4 39 42-80 3-47 (67)
121 PF10771 DUF2582: Protein of u 20.8 21 0.0018 14.2 4.7 45 31-76 17-61 (65)
No 1
>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 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2ra5_A 3by6_D 2ek5_C 2du9_A 1v4r_A 3bwg_A 3eet_B 1h9t_B 1hw2_B 1hw1_B ....
Probab=99.67 E-value=6.6e-17 Score=129.32 Aligned_cols=64 Identities=36% Similarity=0.711 Sum_probs=63.2
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEE
Q ss_conf 8999999999997649899888178878999985898789999999998879167317833686
Q T0586 14 IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 77 (125)
Q Consensus 14 ly~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V 77 (125)
+|+||+++|++.|.+|.|+||++|||+++||++|||||+|||+||..|+.+|+|++.+|+|+||
T Consensus 1 l~~~v~~~i~~~I~~g~l~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~~~G~~V 64 (64)
T PF00392_consen 1 LYEQVYEYIRRDILSGELKPGDRLPSERELAERFGVSRTTVREALKRLEEEGLIERRPGRGTFV 64 (64)
T ss_dssp HHHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHT--HHHHHHHHHHHHHTTSEEEETT---EE
T ss_pred CHHHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEC
T ss_conf 9899999999999849999999936899999886879899999999999889589976963679
No 2
>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: 0008992 repressor LexA activity, 0006508 proteolysis; PDB: 1lea_A 1jhh_A 1jhf_A 1leb_A.
Probab=97.63 E-value=3.5e-05 Score=52.26 Aligned_cols=58 Identities=29% Similarity=0.563 Sum_probs=52.5
Q ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCEEEECCCCE
Q ss_conf 988999999999997649899888178878999985898-789999999998879167317833
Q T0586 12 KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVN-PNTVSRAYQELERAGYIYAKRGMG 74 (125)
Q Consensus 12 ~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VS-r~TVr~Al~~L~~~G~i~~~~g~G 74 (125)
+|...+|.++|.+.|....++ ||.+++|+.||++ ++||..-++.|+..|||.+.+|+.
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~-----Pt~rEI~~~~gl~S~~tV~~~L~~Le~kG~I~r~~~~~ 63 (65)
T PF01726_consen 5 TPRQQEVLDFIKDYIREHGYP-----PTVREIAEALGLKSPSTVHKHLKALEKKGYITRDPGKA 63 (65)
T ss_dssp -HHHHHHHHHHHHHHHH-----------HHHHHHH----SHHHHHHHHHHHHH---EE------
T ss_pred CHHHHHHHHHHHHHHHHCCCC-----CCHHHHHHHCCCCCCHHHHHHHHHHHHCCCEECCCCCC
T ss_conf 999999999999999983889-----88999998819998099999999999982951689999
No 3
>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: 1j5y_A 2ewn_B 1hxd_B 1bia_A 1bib_A 2dbb_B 1i1g_B 2cg4_B.
Probab=97.03 E-value=0.00013 Score=48.48 Aligned_cols=43 Identities=30% Similarity=0.473 Sum_probs=38.4
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC-EEEECCCCEEE
Q ss_conf 888178878999985898789999999998879-16731783368
Q T0586 33 GEDKLPSVREMGVKLAVNPNTVSRAYQELERAG-YIYAKRGMGSF 76 (125)
Q Consensus 33 ~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G-~i~~~~g~G~~ 76 (125)
.+..+ |..+||+.+|||+.||++.++.|.+.| .|...+|+|++
T Consensus 12 ~~~~i-t~~eLA~~l~vS~~Ti~~~i~~L~~~g~~I~s~~~~Gy~ 55 (55)
T PF08279_consen 12 NDGPI-TAKELAEELGVSRRTIRRDIKELEEEGIPIESKPGRGYR 55 (55)
T ss_dssp CCTTS--HHHHHHHCTS-HHHHHHHHHHHHH--EB-BB-TTT---
T ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf 59998-899999996979999999999999869969860789989
No 4
>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 Escherichia coli 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 oligomerization 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 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=96.97 E-value=0.00045 Score=44.94 Aligned_cols=44 Identities=30% Similarity=0.433 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEEC
Q ss_conf 881788789999858987899999999988791673178336862
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT 78 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~ 78 (125)
..++ |..+||+.||||..|||+-+..|+++|+|.+.+|.-..+.
T Consensus 12 ~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~Gg~~~~~ 55 (57)
T PF08220_consen 12 HGKV-SVKELAEEFGVSEMTIRRDLNELEEQGLIRRVHGGAVLNS 55 (57)
T ss_pred CCCE-EHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEECC
T ss_conf 6989-7999999989498899998999998898899619799468
No 5
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group . In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N-terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation .; GO: 0003700 transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2h09_A 1ddn_A 1bi3_B 1g3t_A 1f5t_C 2qqb_A 2qq9_A 1bi0_A 1bi2_B 1c0w_C ....
Probab=96.96 E-value=0.00048 Score=44.77 Aligned_cols=42 Identities=26% Similarity=0.390 Sum_probs=37.9
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf 8881788789999858987899999999988791673178336
Q T0586 33 GEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS 75 (125)
Q Consensus 33 ~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~ 75 (125)
.|... +..++|+.+|||+.||.++++.|.++|||...+.+|.
T Consensus 19 ~~~~v-~~~~IA~~L~vs~~TVs~ml~kL~~~Glv~~~~y~gv 60 (60)
T PF01325_consen 19 EGGPV-STSDIAERLGVSPPTVSEMLKKLEEEGLVEYEKYGGV 60 (60)
T ss_dssp H-S---BHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTSBE
T ss_pred CCCCC-CHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCC
T ss_conf 69972-1999999978990789999999998899885146989
No 6
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio 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 strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 1xd7_A 1ylf_A.
Probab=96.69 E-value=0.0019 Score=40.82 Aligned_cols=58 Identities=21% Similarity=0.463 Sum_probs=44.2
Q ss_pred HHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC-EEE-ECCC
Q ss_conf 9999764989988817887899998589878999999999887916731783-368-6288
Q T0586 22 MKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM-GSF-VTSD 80 (125)
Q Consensus 22 l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~-G~~-V~~~ 80 (125)
++..+.-..-+.+..+ |..++|+.+|+|+.++++.++.|...|+|.+.+|. |-| .+.+
T Consensus 11 i~~L~~La~~~~~~~~-t~~~IA~~~~i~~~~v~kil~~L~~~Glv~s~~G~~GG~~L~~~ 70 (83)
T PF02082_consen 11 IRILIYLARQPDGKPV-TSKEIAERLGISPSYVRKILQKLRKAGLVKSVRGRGGGYRLARD 70 (83)
T ss_dssp HHHHHHHHCSTTCC----HHHHHHHHTS-HHHHHHHHHHHHHTTSEE---------EESS-
T ss_pred HHHHHHHHHCCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEECCC
T ss_conf 9999999809999849-89999988890999999999999888987623678778202289
No 7
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This family consists of Firmicute RepL proteins which are involved in plasmid replication.; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=96.61 E-value=0.0024 Score=40.19 Aligned_cols=48 Identities=25% Similarity=0.424 Sum_probs=40.3
Q ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf 9888178878999985898789999999998879167317833686288
Q T0586 32 KGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD 80 (125)
Q Consensus 32 ~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~ 80 (125)
-.+.-+.|.+++|+.+|+|+.||.++++.|++.|+|...+ .|+|.-.+
T Consensus 70 ~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK~L~ek~iI~k~~-~G~Y~iNP 117 (165)
T PF05732_consen 70 SDNAVVATQKEIAEELGISKPTVSRTIKELEEKGIIKKIK-NGTYFINP 117 (165)
T ss_pred CCCEEEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEC-CCEEEECH
T ss_conf 7983987899999997988889999999998799789823-98799883
No 8
>PF03444 DUF293: Domain of unknown function; InterPro: IPR005104 This domain is always found N-terminal to a pair of cystathionine-beta-synthase (CBS) domains IPR000644 from INTERPRO. This region may be distantly related to the HrcA proteins of prokaryotes.
Probab=96.43 E-value=0.0011 Score=42.48 Aligned_cols=57 Identities=12% Similarity=0.195 Sum_probs=44.4
Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC-CEEEEC
Q ss_conf 9999976498998881788789999858987899999999988791673178-336862
Q T0586 21 WMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG-MGSFVT 78 (125)
Q Consensus 21 ~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g-~G~~V~ 78 (125)
.|...|+.-....|+.+- -+.+|+.+++|..|||.-+..|++.|+|+..|+ +|=+|-
T Consensus 8 ~IL~~lv~~Y~~~~~PVg-Sk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ph~s~GriP 65 (78)
T PF03444_consen 8 EILKALVELYIETGEPVG-SKTIAEELDRSPATIRNEMADLEELGLVESQPHPSAGRIP 65 (78)
T ss_pred HHHHHHHHHHHHCCCCCC-HHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf 999999999997399776-6999998688908899999999987983367999988783
No 9
>PF04703 FaeA: FaeA-like protein; InterPro: IPR006793 This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase , .; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription, 0009289 fimbrium; PDB: 2htj_A 2jt1_A.
Probab=96.41 E-value=0.0022 Score=40.41 Aligned_cols=50 Identities=24% Similarity=0.354 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC-CCE
Q ss_conf 99999999997649899888178878999985898789999999998879167317-833
Q T0586 16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR-GMG 74 (125)
Q Consensus 16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~-g~G 74 (125)
++|.++|... +... +.+++|+.+|+|+.++|.-+..|+.+|.|...| ++|
T Consensus 3 e~Il~~i~~~--------~~p~-~t~eiA~~~gls~~qaR~~L~~L~~eG~Vk~~~~rrG 53 (62)
T PF04703_consen 3 EKILEYIKRQ--------NGPC-STREIAEALGLSIYQARYYLQKLEKEGKVKRSPVRRG 53 (62)
T ss_dssp HCHHHHHHHH-----------B--HHHHHHHHTS-HHHHHHHHHHHHH---EEEE-----
T ss_pred HHHHHHHHHC--------CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCC
T ss_conf 8899999962--------7998-8999999969889999999999988797785205788
No 10
>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 1sfx_A.
Probab=96.16 E-value=0.002 Score=40.65 Aligned_cols=38 Identities=26% Similarity=0.404 Sum_probs=35.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf 87899998589878999999999887916731783368
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF 76 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~ 76 (125)
+..+||+.+|+|++||.++++.|++.|+|+...++...
T Consensus 24 t~~eia~~~~i~~~~v~~~l~~L~~~GlV~~~~~~~~~ 61 (68)
T PF01978_consen 24 TASEIAEKLGISRSTVYRILKRLEEKGLVEREKGKPKK 61 (68)
T ss_dssp EHHHHHHHHT--HHHHHHHHHHHHH---EEEEE----E
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEE
T ss_conf 99999999890999999999999988998997685069
No 11
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This set of protein sequences, defined by an N-terminal domain, represent phage lambda replication protein O and other homologous phage and prophage proteins. ; GO: 0006260 DNA replication
Probab=95.58 E-value=0.011 Score=35.92 Aligned_cols=45 Identities=27% Similarity=0.265 Sum_probs=39.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 4989988817887899998589878999999999887916731783
Q T0586 28 TGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 28 ~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
.|.=++++++ |-.++++..|+|+.+|.+|++.|...|+|.+..+.
T Consensus 46 yG~nK~~d~I-s~sq~~e~tg~~~~~V~~al~~Li~~~vi~~~G~~ 90 (100)
T PF04492_consen 46 YGWNKKMDRI-SNSQIAEMTGISRDHVSRALKELIRMNVIIIEGRQ 90 (100)
T ss_pred CCCCCCCHHE-EHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCE
T ss_conf 3889840040-09999988698989999999999975887644937
No 12
>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_A 2pqa_C 2pi2_C 1l1o_B 1z1d_A 2z6k_B 1dpu_A.
Probab=95.44 E-value=0.0083 Score=36.60 Aligned_cols=54 Identities=28% Similarity=0.501 Sum_probs=43.8
Q ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC
Q ss_conf 898899999999999764989988817887899998589878999999999887916731
Q T0586 11 DKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK 70 (125)
Q Consensus 11 ~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~ 70 (125)
..|+.++|++.|+. +..- .+=+ ++.+|++.++++...|++|+..|.++|+|++-
T Consensus 45 ~~~~~~~Vl~~i~~---~~~~--~eGv-~v~~i~~~l~~~~~~v~~a~~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQQRVLNFIKQ---SPQS--EEGV-HVDEIAQKLGMPENEVRKAIDELSDEGLIYST 98 (102)
T ss_dssp --HHHHHHHHHHHC--------------BHHHHHHHSTS-HHHHHHHHHHHHH---EEES
T ss_pred CCHHHHHHHHHHHH---CCCC--CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCEEECC
T ss_conf 88899999999984---4688--7871-89999999693999999999999859847266
No 13
>PF01710 Transposase_14: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily . More information about these proteins can be found at Protein of the Month: Transposase .
Probab=95.12 E-value=0.028 Score=33.12 Aligned_cols=89 Identities=21% Similarity=0.225 Sum_probs=52.3
Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999764989988817887899998589878999999999887916731783368628807899999999999999999
Q T0586 21 WMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFL 100 (125)
Q Consensus 21 ~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~~~~~~~~~~~~~~~~~~~~ 100 (125)
+|+..|+. .+..|. |.++.|..||||++||.+-++ -...|.+...++.+..+ +...+......--...+ .
T Consensus 6 DlR~kvi~-~~~~G~---S~~eaA~~F~VS~~Tv~rW~k-~~~~G~~~~~~r~~~Ki--d~e~l~~~v~~~~d~tl---~ 75 (119)
T PF01710_consen 6 DLRQKVIA-YVEQGM---SIREAAKRFGVSRSTVYRWLK-RRETGDLKPKPRGRKKI--DAEELKELVEENPDITL---K 75 (119)
T ss_pred HHHHHHHH-HHHCCC---CHHHHHHHHCCCHHHHHHHHH-HHHCCCCCCCCCCCCCC--CHHHHHHHHHHCCCCCH---H
T ss_conf 99999999-999599---999999996955999999998-64113446788765402--59999999998889769---9
Q ss_pred HHHHHCCCCHHHHHHHHHH
Q ss_conf 9999819999899999999
Q T0586 101 EEAKSIGLDDQTAIELLIK 119 (125)
Q Consensus 101 ~~~~~~~~~~~~~~~l~~~ 119 (125)
+.+..+|++...+..++.+
T Consensus 76 Ela~~~~vs~~ti~r~Lkr 94 (119)
T PF01710_consen 76 ELAEKLGVSKSTISRALKR 94 (119)
T ss_pred HHHHHCCCCHHHHHHHHHH
T ss_conf 9999929989999999998
No 14
>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=94.66 E-value=0.05 Score=31.45 Aligned_cols=55 Identities=22% Similarity=0.414 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHCCCCCCCCC---CCCHHHHHHHH-CCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf 99999999976498998881---78878999985-898789999999998879167317
Q T0586 17 QISDWMKKQMITGEWKGEDK---LPSVREMGVKL-AVNPNTVSRAYQELERAGYIYAKR 71 (125)
Q Consensus 17 qI~~~l~~~I~~G~l~~G~~---LPser~La~~~-~VSr~TVr~Al~~L~~~G~i~~~~ 71 (125)
.+-+.|...--...|.+|.. .||-.+||... |+|.+|+|+.+..|.+-|+|..+.
T Consensus 47 ~vL~aLlsf~~~~d~~~~~~~iVfpSN~~La~r~~G~s~~tlrRhla~LveaGLI~r~D 105 (177)
T PF03428_consen 47 AVLDALLSFTPEDDWSGGRRPIVFPSNAQLAERLHGMSERTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred HHHHHHHHHCCCCCCCCCCCCEEECCHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf 99999997688634578887255208999999985999899999999999889846412
No 15
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions . The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk .; PDB: 2b0l_C.
Probab=94.43 E-value=0.01 Score=35.96 Aligned_cols=44 Identities=16% Similarity=0.343 Sum_probs=38.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC--CEEEECCCHH
Q ss_conf 8789999858987899999999988791673178--3368628807
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG--MGSFVTSDKA 82 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g--~G~~V~~~~~ 82 (125)
.-.++|++.|++++++-+|++.|+.-|+|+.+.- +|||+.--..
T Consensus 6 taS~IAd~vGiTrSvivnaLRKlESAGVIe~rslgmkGtyikvln~ 51 (61)
T PF08222_consen 6 TASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLND 51 (61)
T ss_dssp -HHHHHCC----HHHHHHHHHHHHH---EEEE-------EEEE--T
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCEEEEECCH
T ss_conf 0888888848839999999998886385311346776047531038
No 16
>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 dimerization. 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 dimerization, as most marR-like transcription regulators form dimers , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3bj6_A 2fbi_A 3e6m_E 3cjn_A 3cdh_A 2fxa_B 2fa5_B 1lnw_B 3ech_A 1jgs_A ....
Probab=94.36 E-value=0.018 Score=34.41 Aligned_cols=36 Identities=28% Similarity=0.393 Sum_probs=33.0
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 887899998589878999999999887916731783
Q T0586 38 PSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 38 Pser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
.+..+||+.++++++|+.+.++.|++.|||++.+..
T Consensus 18 ~t~~~la~~l~~~~~~vs~~i~~L~~~glI~r~~~~ 53 (59)
T PF01047_consen 18 MTQSELAERLGISKSTVSRIIKRLEKKGLIEREPDP 53 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 899999999886873899999999988987872899
No 17
>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: 2ia2_C 2g7u_D 2o0y_D 1mkm_B.
Probab=94.08 E-value=0.024 Score=33.56 Aligned_cols=37 Identities=30% Similarity=0.442 Sum_probs=33.1
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf 88178878999985898789999999998879167317
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR 71 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~ 71 (125)
+..+ +..++|+.+|++++|+.+-+..|++.|||+..|
T Consensus 16 ~~~~-t~~eia~~~gl~~st~~r~l~~L~~~g~v~~d~ 52 (52)
T PF09339_consen 16 PRPL-TLSEIARALGLPKSTVHRLLQTLEEAGFVERDP 52 (52)
T ss_dssp BSSE-EHHHHHHHTT--HHHHHHHHHHHHHT--EEE--
T ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
T ss_conf 9998-999999998919999999999999991942092
No 18
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA , . Within this family, the HTH motif is situated towards the C-terminus. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2gzw_A 1o3q_A 1lb2_A 1i6x_A 1ruo_B 1hw5_B 1zrf_A 1i5z_B 1j59_B 1o3s_A ....
Probab=93.63 E-value=0.028 Score=33.16 Aligned_cols=29 Identities=31% Similarity=0.440 Sum_probs=27.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEE
Q ss_conf 87899998589878999999999887916
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYI 67 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i 67 (125)
+-.+||+..|.+|.||.+.++.|.++|+|
T Consensus 4 t~~elA~~~G~tretvsR~l~~l~~~GlI 32 (32)
T PF00325_consen 4 THQELADLLGTTRETVSRILSRLRKEGLI 32 (32)
T ss_dssp -HHHHHHHCTC-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCC
T ss_conf 99999988698699999999999996799
No 19
>PF03965 Pencillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis . BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth . MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected . At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0016481 negative regulation of transcription; PDB: 1sd4_B 1xsd_A 1sd7_A 1sd6_A 2d45_A 1okr_A 1sax_A 1p6r_A 2p7c_B 2k4b_A ....
Probab=93.56 E-value=0.12 Score=29.09 Aligned_cols=92 Identities=20% Similarity=0.233 Sum_probs=52.8
Q ss_pred HHHHCCCCCCCCCCCCHHHHHHHHCCC----HHHHHHHHHHHHHCCEEEECCCCEEEEC----CCHHHHHHHHHHHHH--
Q ss_conf 997649899888178878999985898----7899999999988791673178336862----880789999999999--
Q T0586 24 KQMITGEWKGEDKLPSVREMGVKLAVN----PNTVSRAYQELERAGYIYAKRGMGSFVT----SDKALFDQLKKELAD-- 93 (125)
Q Consensus 24 ~~I~~G~l~~G~~LPser~La~~~~VS----r~TVr~Al~~L~~~G~i~~~~g~G~~V~----~~~~~~~~~~~~~~~-- 93 (125)
..|+.-.|..|. + +.+++.+.++-. ++||+-.+.+|.+.|+|.+....+.|+- ............+..
T Consensus 6 ~~IM~~lW~~~~-~-t~~ei~~~l~~~~~~~~sTV~t~L~rL~eKg~l~~~~~gr~~~Y~~~i~~~e~~~~~~~~~l~~~ 83 (115)
T PF03965_consen 6 LEIMEILWEHGP-I-TVREIVEELKEDRDWSYSTVQTLLNRLVEKGLLTREKIGRAYIYSPLISREEYLRQELKQLLDRF 83 (115)
T ss_dssp HHHHHHHHCHSS-E-EHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCC-C-CHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEECCCCEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf 999999995799-7-79999999861316418789999999998898577713884588747889999999999999998
Q ss_pred --HHHHHHHHHH-HHCCCCHHHHHHHH
Q ss_conf --9999999999-98199998999999
Q T0586 94 --AITERFLEEA-KSIGLDDQTAIELL 117 (125)
Q Consensus 94 --~~~~~~~~~~-~~~~~~~~~~~~l~ 117 (125)
.....++... ....++++++.+|-
T Consensus 84 ~~gs~~~ll~~l~~~~~ls~~el~~L~ 110 (115)
T PF03965_consen 84 FDGSLSALLAALLDEEELSPEELEELR 110 (115)
T ss_dssp S---HHHHHHHHHHCT-S-HHHHHHHH
T ss_pred HCCCHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf 688999999999856799999999999
No 20
>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 recognized by multimeric arsR-type metalloregulators. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1uly_A 2cwe_A 1ku9_A 3gw2_A 2p4w_B 3f6v_A 3f6o_B 2oqg_D 2ia0_B 2zny_C ....
Probab=92.96 E-value=0.047 Score=31.63 Aligned_cols=32 Identities=41% Similarity=0.592 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
Q ss_conf 788789999858987899999999988791673
Q T0586 37 LPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 69 (125)
Q Consensus 37 LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~ 69 (125)
+ +..++++.+|+|++||.+-++.|++.|+|..
T Consensus 16 ~-~~~eia~~l~~s~~tvs~HL~~L~~~glV~~ 47 (47)
T PF01022_consen 16 L-SVSEIAEELGISQSTVSRHLKKLEEAGLVKK 47 (47)
T ss_dssp E-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred C-CHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 6-7999883612356589999999999808419
No 21
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid . The gene product has been shown to bind to the promoter sites and repress their transcription .
Probab=92.68 E-value=0.064 Score=30.77 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC---EEEECC
Q ss_conf 17887899998589878999999999887916731783---368628
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM---GSFVTS 79 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~---G~~V~~ 79 (125)
.+.+.-.+++.||||...||-|+.+|..+||++..+.- ++..++
T Consensus 22 ~~~~Li~l~~~~Gi~e~avR~Al~RL~~~G~l~~~r~GR~s~Y~Lt~ 68 (70)
T PF07848_consen 22 WVGSLIRLLEAFGISERAVRTALSRLVKEGWLESERRGRRSYYRLTE 68 (70)
T ss_pred EHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEEECC
T ss_conf 19999999998299905899999999873866757607832477488
No 22
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=92.04 E-value=0.071 Score=30.48 Aligned_cols=46 Identities=20% Similarity=0.384 Sum_probs=39.5
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf 88178878999985898789999999998879167317833686288
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD 80 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~ 80 (125)
.-++ +.++|...+|+||+|+++-+..|.+.|-|+..-..|.|=.+.
T Consensus 24 ~GRi-Ti~ql~~~TG~sR~T~k~~lr~Lv~~G~v~~~G~~GiFpseq 69 (127)
T PF06163_consen 24 HGRI-TIRQLVKMTGASRNTAKKYLRELVESGDVYRHGRCGIFPSEQ 69 (127)
T ss_pred HCHH-HHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCHH
T ss_conf 1630-299999997867999999999999738831168767584199
No 23
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S25 ribosomal protein is a component of the 40S ribosomal subunit.
Probab=91.70 E-value=0.065 Score=30.71 Aligned_cols=50 Identities=24% Similarity=0.285 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf 99999999997649899888178878999985898789999999998879167317
Q T0586 16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR 71 (125)
Q Consensus 16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~ 71 (125)
...++.|...|- ..++-+...||+.|+|+-+.+|+||+.|+.+|+|...-
T Consensus 44 k~t~dki~kEV~------k~K~ITps~l~erlkI~~SlAr~~Lr~L~~~G~Ik~V~ 93 (105)
T PF03297_consen 44 KETYDKILKEVP------KYKLITPSVLSERLKINGSLARKALRELEEKGLIKPVS 93 (105)
T ss_pred HHHHHHHHHHHH------HCCEECHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 999999999840------06330399987777424899999999999789989984
No 24
>PF09397 Ftsk_gamma: Ftsk gamma domain; PDB: 2ve8_D 2ve9_C 2j5o_A 2j5p_A.
Probab=90.37 E-value=0.31 Score=26.25 Aligned_cols=58 Identities=17% Similarity=0.374 Sum_probs=49.4
Q ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf 88898899999999999764989988817887899998589878999999999887916731783368
Q T0586 9 HADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF 76 (125)
Q Consensus 9 ~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~ 76 (125)
+..-|+|.++.+.+.. +.-.|..-|-..|+|..+-+.+-+..|+.+|+|.-..|+|..
T Consensus 2 ~~~D~ly~~a~~~V~~----------~~~~S~S~lQR~lrIGYnrAariid~LE~~GiVs~~~~~~~R 59 (65)
T PF09397_consen 2 DEEDPLYDEAVEFVIE----------EGKASISLLQRRLRIGYNRAARIIDQLEEEGIVSPANGSKPR 59 (65)
T ss_dssp -TTSTTHHHHHHHHHH----------CTCESHHHHHHHHT---HHHHHHHHHHHH---BE-------E
T ss_pred CCCCHHHHHHHHHHHH----------HCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 5210899999999998----------087579999999714799999999999988777887799898
No 25
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein
Probab=89.76 E-value=0.32 Score=26.20 Aligned_cols=55 Identities=20% Similarity=0.294 Sum_probs=45.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 77776888988999999999997649899888178878999985898789999999998879
Q T0586 4 MNPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAG 65 (125)
Q Consensus 4 M~~~~~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G 65 (125)
+|..|.+..+|.+.+.+.|-+.+..+.. |.+++|..|||+...|.-.++.-+-++
T Consensus 7 ~Np~f~~~~~lse~lr~~I~~~v~~~~~-------sv~~vS~kygi~~~RV~AIvrL~eiEk 61 (172)
T PF12298_consen 7 LNPHFRSNPVLSEELRQEIYEDVMEKGK-------SVREVSVKYGIKMQRVEAIVRLKEIEK 61 (172)
T ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHCCC-------CHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 9987678776799999999999982896-------899999996977899999999999999
No 26
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions . The family also contains VirR like proteins which match only at the C terminus of the alignment.
Probab=89.22 E-value=0.68 Score=24.02 Aligned_cols=52 Identities=13% Similarity=0.289 Sum_probs=40.1
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHH----HHCCEEEECCCCEEEECCCHHHHHHH
Q ss_conf 88817887899998589878999999999----88791673178336862880789999
Q T0586 33 GEDKLPSVREMGVKLAVNPNTVSRAYQEL----ERAGYIYAKRGMGSFVTSDKALFDQL 87 (125)
Q Consensus 33 ~G~~LPser~La~~~~VSr~TVr~Al~~L----~~~G~i~~~~g~G~~V~~~~~~~~~~ 87 (125)
..+.+ +..+||+.+.||++|+.+-++.+ ..-|+-- ++.|..+..++..+...
T Consensus 27 ~~~~~-~~~~la~~l~vS~sTi~~~lk~i~~~L~~~~l~l--~~~~~~i~G~E~~iR~~ 82 (87)
T PF05043_consen 27 NNEYV-SIEDLAEELYVSRSTIYRDLKKINQILKKYGLKL--KKKGLRIEGSEKNIRYF 82 (87)
T ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCEEE--CCCCEEEEECHHHHHHH
T ss_conf 48996-8999999979899999999999999999959076--38994798079999999
No 27
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium halobium and described as a putative bacterio-opsin activator.
Probab=88.37 E-value=0.56 Score=24.55 Aligned_cols=44 Identities=16% Similarity=0.324 Sum_probs=35.8
Q ss_pred HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 999999976498998881788789999858987899999999988
Q T0586 19 SDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELER 63 (125)
Q Consensus 19 ~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~ 63 (125)
.+.|......|.|..--.. +..+||+++|||++|+.+-++.-+.
T Consensus 6 ~e~L~~A~~~GYfd~PR~~-tl~elA~~lgis~~T~~~~LRrae~ 49 (53)
T PF04967_consen 6 REVLRTAYEMGYFDWPRRI-TLEELAEELGISKSTFSEHLRRAER 49 (53)
T ss_pred HHHHHHHHHCCCCCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 9999999986887798758-8999998949999999999999999
No 28
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2v7f_A.
Probab=87.44 E-value=0.45 Score=25.23 Aligned_cols=63 Identities=19% Similarity=0.266 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf 9999999999976498998881788789999858--------------98789999999998879167317833686288
Q T0586 15 YSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA--------------VNPNTVSRAYQELERAGYIYAKRGMGSFVTSD 80 (125)
Q Consensus 15 y~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~--------------VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~ 80 (125)
|.+.+.-++.-=+.| .+ ++..|+..|| -|.+-+|.+++.|+..|+|+..++.|-.+++.
T Consensus 51 Y~RaASilRklY~~g------~v-Gv~~lr~~YGg~k~rG~rP~h~~~asg~iiR~~lQqLE~~glvek~~~~GR~lT~~ 123 (139)
T PF01090_consen 51 YIRAASILRKLYIRG------PV-GVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPK 123 (139)
T ss_dssp HHHHHHHHHHHHH-------------HHHHHH----------TTS-------HHHHHHHHHHH---EE-------EE---
T ss_pred HHHHHHHHHHHHHCC------CC-CHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCEECHH
T ss_conf 999999999998249------97-57899999787778999998646776189999999998689867769999788984
Q ss_pred HHHH
Q ss_conf 0789
Q T0586 81 KALF 84 (125)
Q Consensus 81 ~~~~ 84 (125)
-...
T Consensus 124 G~~~ 127 (139)
T PF01090_consen 124 GRSD 127 (139)
T ss_dssp --HH
T ss_pred HHHH
T ss_conf 7999
No 29
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=87.43 E-value=0.36 Score=25.88 Aligned_cols=55 Identities=22% Similarity=0.413 Sum_probs=43.8
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CEEEECCCC
Q ss_conf 99999999764989988817887899998589878999999999887-916731783
Q T0586 18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERA-GYIYAKRGM 73 (125)
Q Consensus 18 I~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~-G~i~~~~g~ 73 (125)
+.......|..-.|.-|--| +..+||..|++|+.||++-++.++.+ |.+.-.+|.
T Consensus 87 l~~~~ivRl~~EA~dQgalL-T~~Dla~LL~~S~~TI~~~vk~ye~~~g~vvPtRG~ 142 (220)
T PF07900_consen 87 LRKHRIVRLFNEAYDQGALL-TQEDLAILLGVSPKTISRDVKEYEEEHGEVVPTRGT 142 (220)
T ss_pred HHHHHHHHHHHHHHHCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 99999999999998647857-599999998889888999999999961965235762
No 30
>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: 1z7u_A 2f2e_B 3df8_A 2hzt_C 2fsw_A 1yyv_B.
Probab=85.78 E-value=0.57 Score=24.54 Aligned_cols=48 Identities=19% Similarity=0.243 Sum_probs=36.3
Q ss_pred CHHHHHHHH-CCCHHHHHHHHHHHHHCCEEEECCC------CEEEECCCHHHHHH
Q ss_conf 878999985-8987899999999988791673178------33686288078999
Q T0586 39 SVREMGVKL-AVNPNTVSRAYQELERAGYIYAKRG------MGSFVTSDKALFDQ 86 (125)
Q Consensus 39 ser~La~~~-~VSr~TVr~Al~~L~~~G~i~~~~g------~G~~V~~~~~~~~~ 86 (125)
.-.+|.+.+ |||..+..+.++.|++.|+|.+... ..|.+++....+..
T Consensus 20 rf~el~~~l~gis~~~Ls~rL~~Le~~glv~r~~~~~~p~~v~Y~LT~~G~~l~~ 74 (90)
T PF01638_consen 20 RFNELQRSLPGISPKVLSQRLKELEENGLVERRVYPEVPPRVEYSLTEKGKDLLP 74 (90)
T ss_dssp EHHHHHHH-TTS-HHHHHHHHHHHHH---EEEEEE-SSS-EEEEEE-----CCHH
T ss_pred CHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEECCCCHHHHHH
T ss_conf 8999997740557778999999999778814654489998654756816999999
No 31
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This set of hypothetical proteins is found in prokaryotes. ; PDB: 2k02_A 1xn7_A.
Probab=85.40 E-value=0.26 Score=26.74 Aligned_cols=37 Identities=22% Similarity=0.405 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 17887899998589878999999999887916731783
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
.. |..+||.+|++|+.+|+.-+..|...|.|....-.
T Consensus 14 ~~-s~~eLa~~f~~s~~~v~aMLe~l~~kG~i~k~~~~ 50 (69)
T PF09012_consen 14 RV-SLSELARHFGISPDAVEAMLEQLIRKGKIEKVEDS 50 (69)
T ss_dssp -E-EHHHHHHHTT--HHHHHHHHHHHHC---EEEEEEE
T ss_pred CC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 81-89999999790999999999999988916873169
No 32
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR002853 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha P29083 from SWISSPROT and TFIIE-beta P29084 from SWISSPROT and joins the preinitiation complex after RNA polymerase II and TFIIF . This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also .; GO: 0003702 RNA polymerase II transcription factor activity, 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1q1h_A 1vd4_A.
Probab=84.85 E-value=0.29 Score=26.51 Aligned_cols=35 Identities=11% Similarity=0.251 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf 178878999985898789999999998879167317
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR 71 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~ 71 (125)
.+ ++.+||+.+|++..++|+.+..|.++|+|..+.
T Consensus 27 ~l-~ee~La~~l~i~~k~lR~~L~~L~e~~lv~~~~ 61 (105)
T PF02002_consen 27 EL-TEEDLAELLGIKSKELRKILYKLYEDKLVKYRR 61 (105)
T ss_dssp -B--HHHHHHTT-S-HHHHHHHHHHHHH----EEEE
T ss_pred CC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf 90-899999890999899999999999889837898
No 33
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster . In pipsqueak this domain binds to GAGA sequence . The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex .; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2cob_A.
Probab=84.64 E-value=0.23 Score=27.13 Aligned_cols=29 Identities=28% Similarity=0.308 Sum_probs=23.4
Q ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9988817887899998589878999999999
Q T0586 31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQEL 61 (125)
Q Consensus 31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L 61 (125)
+..|. + |.++.|..|||+++|++..++.-
T Consensus 12 v~~g~-~-Si~~aA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 12 VKNGK-L-SIRKAARKYGVPRSTLRRRLKGK 40 (45)
T ss_dssp HH-------HHHHHHH----HHHHHHHHHH-
T ss_pred HHCCC-C-CHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 99099-5-79999999893989999999278
No 34
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR , . Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1l1m_B 2bjc_A 1lcc_A 1osl_A 2pe5_A 1lcd_A 1efa_A 1cjg_B 1lqc_A 1jwl_A ....
Probab=84.43 E-value=0.32 Score=26.19 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=19.5
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8789999858987899999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQE 60 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~ 60 (125)
+.+++|+..|||.+||.++|..
T Consensus 1 Ti~diA~~agvS~~TVSr~Ln~ 22 (46)
T PF00356_consen 1 TIKDIAKAAGVSVATVSRVLNG 22 (46)
T ss_dssp SHHHHHHHTTSSHHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHCC
T ss_conf 9999998989499999999758
No 35
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known . The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second , called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1jko_C 1jkp_C 1jj8_C 1hcr_A 1jkq_C 1jj6_C 1ijw_C 1jkr_C 1zr4_B 2gm4_A ....
Probab=83.70 E-value=0.27 Score=26.66 Aligned_cols=32 Identities=22% Similarity=0.400 Sum_probs=23.6
Q ss_pred HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 9999997649899888178878999985898789999999
Q T0586 20 DWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 20 ~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~ 59 (125)
+.+.....+| . |..++|+.|||||+||-+.+.
T Consensus 12 ~~i~~l~~~G-------~-s~~~IAk~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 12 EEIRELYAQG-------M-SISEIAKRFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH------------HHHHHHHCTS-HHHHHHHHC
T ss_pred HHHHHHHHCC-------C-CHHHHHHHHCCCHHHHHHHHH
T ss_conf 9999999979-------9-999999998919999999974
No 36
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=82.69 E-value=0.73 Score=23.82 Aligned_cols=33 Identities=24% Similarity=0.388 Sum_probs=31.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf 878999985898789999999998879167317
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKR 71 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~ 71 (125)
|..+|.+..|++++++--.+..|.++|+|++.=
T Consensus 20 tLeeL~e~Tgi~k~~llV~LsrL~k~GiI~RkW 52 (72)
T PF05584_consen 20 TLEELEEKTGIKKNELLVYLSRLAKEGIIYRKW 52 (72)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf 699999996898779999999998789266431
No 37
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N)
Probab=81.98 E-value=1.5 Score=21.69 Aligned_cols=64 Identities=19% Similarity=0.308 Sum_probs=48.1
Q ss_pred HHHHHHHHHHCCCCCCC------CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCH
Q ss_conf 99999999764989988------8178-8789999858987899999999988791673178336862880
Q T0586 18 ISDWMKKQMITGEWKGE------DKLP-SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK 81 (125)
Q Consensus 18 I~~~l~~~I~~G~l~~G------~~LP-ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~ 81 (125)
++-+++-...+|.+..+ ..+| +...||..|+.+-.||+-|+..|.+.|+|+.--+.-.++..-.
T Consensus 27 ~~I~lkLll~sgk~~~~G~L~~~~~ipyt~E~LA~~~~~~~~~V~~aL~~f~~~gmIe~~e~~~i~i~n~~ 97 (121)
T PF09681_consen 27 TIIWLKLLLLSGKLNNEGKLYLSGNIPYTAEMLATIFDRPVETVRLALQVFQKLGMIEIDENGVIYITNWE 97 (121)
T ss_pred HHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEECHH
T ss_conf 99999999984344788189976888986999999978878899999999987897899329908974588
No 38
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see ) , . Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0007275 multicellular organismal development, 0005634 nucleus; PDB: 6pax_A 1pdn_C 1k78_E 1mdm_A 2k27_A.
Probab=78.60 E-value=1.7 Score=21.44 Aligned_cols=62 Identities=18% Similarity=0.249 Sum_probs=47.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf 7688898899999999999764989988817887899998589878999999999887916731783368
Q T0586 7 TFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF 76 (125)
Q Consensus 7 ~~~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~ 76 (125)
-|.+.+||-..+...|.+.-..| + +-.++|.+|+||..+|.+-+.+..+-|-|.-.+.-|..
T Consensus 11 ~f~nGRPlp~~~R~rIv~l~~~G-------~-r~~~Isr~l~VS~gcVsKIl~Ry~eTGsI~Pg~iGGsk 72 (125)
T PF00292_consen 11 VFVNGRPLPNELRQRIVELAHEG-------V-RPCDISRQLRVSHGCVSKILKRYRETGSIRPGPIGGSK 72 (125)
T ss_dssp -------S-HHHHHHHHHHHH------------HHHHHHHHT-----HHHHHHHTTT----S--------
T ss_pred CEECCCCCCHHHHHHHHHHHHCC-------C-CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 00278528899999999997625-------8-77489987651476999999999986176765557999
No 39
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation , . The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli , where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes . ; PDB: 1t6s_A 2z99_A.
Probab=77.72 E-value=2.1 Score=20.81 Aligned_cols=82 Identities=16% Similarity=0.191 Sum_probs=50.1
Q ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC------CEEEECCCCEEEECCCHHHH---HH-----HHHHHHHHHH
Q ss_conf 9988817887899998589878999999999887------91673178336862880789---99-----9999999999
Q T0586 31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERA------GYIYAKRGMGSFVTSDKALF---DQ-----LKKELADAIT 96 (125)
Q Consensus 31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~------G~i~~~~g~G~~V~~~~~~~---~~-----~~~~~~~~~~ 96 (125)
|-.|+.+ |..+|++.++ +...|++++..|..+ |+-...-+.|+.....+... .. ....+-...+
T Consensus 8 F~s~~pv-s~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~g~y~l~tk~e~~~~v~~~~~~~~~~~LS~aal 85 (159)
T PF04079_consen 8 FASGEPV-SIKELAEILG-SEEEVREALEELQEEYEERDRGLELVEVAGGYRLQTKPEYAEYVRRLFGKPKPRKLSQAAL 85 (159)
T ss_dssp HH-SS----HHHHHHHCT--HHHHHHHHHHHHHHHHH----EEEE------EEEE-GGGHHHHHHHHC-HHHHHHHHHHH
T ss_pred HHCCCCC-CHHHHHHHHC-CHHHHHHHHHHHHHHHCCCCCCEEEEEECCEEEEEEHHHHHHHHHHHHCCCCCCCCCHHHH
T ss_conf 6608988-9999999859-9999999999999986308997799999999999886999999999865556688899999
Q ss_pred HHHHHHHHHCCCCHHHHH
Q ss_conf 999999998199998999
Q T0586 97 ERFLEEAKSIGLDDQTAI 114 (125)
Q Consensus 97 ~~~~~~~~~~~~~~~~~~ 114 (125)
+.+..-+....++..++.
T Consensus 86 EtLAiIAY~QPiTr~eIe 103 (159)
T PF04079_consen 86 ETLAIIAYKQPITRAEIE 103 (159)
T ss_dssp HHHHHHHHH-SEEHHHHH
T ss_pred HHHHHHHHCCCCCHHHHH
T ss_conf 999999974983899999
No 40
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250)
Probab=77.65 E-value=1.2 Score=22.32 Aligned_cols=34 Identities=18% Similarity=0.322 Sum_probs=30.8
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 7899998589878999999999887916731783
Q T0586 40 VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 40 er~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
-.-+|..++++..-|+.++..|++.|+|+...|+
T Consensus 24 ak~ia~~l~~~l~eV~~~l~~Le~~GLlErv~g~ 57 (92)
T PF10007_consen 24 AKMIARRLGIPLEEVRERLKKLEEMGLLERVEGS 57 (92)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCH
T ss_conf 9999999689999999999999988784321133
No 41
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif . Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2o3f_C.
Probab=77.54 E-value=0.7 Score=23.93 Aligned_cols=57 Identities=23% Similarity=0.298 Sum_probs=43.3
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf 889889999999999976498998881788789999858987899999999988791673178
Q T0586 10 ADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG 72 (125)
Q Consensus 10 ~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g 72 (125)
+=+|--.+|+++|.+.... + ..+ |..+||+..|||.+||-+-.+.|.-.||-+-+..
T Consensus 13 ~lt~~e~~Ia~yil~~~~~--~---~~~-si~~lA~~~~vS~atv~Rf~kkLGf~gf~efk~~ 69 (107)
T PF01418_consen 13 SLTPSEKKIADYILNNPDK--I---ANM-SISELAKAAGVSPATVVRFCKKLGFSGFSEFKVD 69 (107)
T ss_dssp GS-HHHHHHHHHHHH-HHH--H---TT---HHHHHHHTT--HHHHHHHHHH------HHHHHH
T ss_pred HCCHHHHHHHHHHHHCHHH--H---HHC-CHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHH
T ss_conf 1799999999999929999--9---775-4999999979898899999999289999999999
No 42
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids . Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=76.86 E-value=1.9 Score=21.09 Aligned_cols=49 Identities=20% Similarity=0.211 Sum_probs=39.6
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCC---CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 88999999999997649899888---17887899998589878999999999
Q T0586 13 PIYSQISDWMKKQMITGEWKGED---KLPSVREMGVKLAVNPNTVSRAYQEL 61 (125)
Q Consensus 13 Ply~qI~~~l~~~I~~G~l~~G~---~LPser~La~~~~VSr~TVr~Al~~L 61 (125)
-+|.-+.+.+.-.+.+|.....- -+-|..+|++.+|+|+.||.++.+.|
T Consensus 25 ilY~lL~dR~~lS~kN~wiD~~g~vY~ift~~el~~~L~~s~~~v~k~~kEL 76 (76)
T PF06970_consen 25 ILYSLLLDRMELSIKNGWIDEDGNVYIIFTNEELMEILNCSKKKVIKIKKEL 76 (76)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 9999999999876635678799998999659999999887888999999619
No 43
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure .; GO: 0003677 DNA binding, 0000775 chromosome, pericentric region; PDB: 2elh_A 1hlv_A 1bw6_A.
Probab=76.28 E-value=0.27 Score=26.66 Aligned_cols=21 Identities=29% Similarity=0.491 Sum_probs=19.1
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 878999985898789999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~ 59 (125)
|.+++|..|||+++||+..++
T Consensus 24 s~~~iAr~fgi~~sTi~~i~k 44 (53)
T PF04218_consen 24 SQREIAREFGISRSTISRILK 44 (53)
T ss_dssp -HHHHHHHHT--CCHHHHHCC
T ss_pred CHHHHHHHCCCCHHHHHHHHH
T ss_conf 899999891998889999998
No 44
>PF09862 DUF2089: Protein of unknown function(DUF2089)
Probab=75.87 E-value=1.2 Score=22.52 Aligned_cols=61 Identities=18% Similarity=0.278 Sum_probs=37.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH-CCEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 8789999858987899999999988-791673178336862880789999999999999999999998199998999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELER-AGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKSIGLDDQTAIELL 117 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~-~G~i~~~~g~G~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~ 117 (125)
|.+++++.||||..|||.=+..+.+ -|+.. ........ .....+..+..-.++.+++++++
T Consensus 51 nlKe~ak~lgiSYpTvR~rLd~ii~~lg~~~----------~~~~~~~~--------~~~~IL~~L~~GeIs~eeA~~~L 112 (113)
T PF09862_consen 51 NLKEVAKELGISYPTVRNRLDRIIEKLGYEE----------EEEEEEND--------ERKEILDKLEKGEISVEEAIKLL 112 (113)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC----------CCCCCCCH--------HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 8999999978882899999999999817987----------76654444--------69999999990997999999984
No 45
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa . This region is probably a DNA-binding helix-turn-helix.
Probab=74.95 E-value=1.4 Score=21.95 Aligned_cols=52 Identities=13% Similarity=0.167 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
Q ss_conf 999999999976498998881788789999858987899999999988791673
Q T0586 16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA 69 (125)
Q Consensus 16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~ 69 (125)
++.+..+...|.+--+..| ++ +.+++...-+.|+..|+.++..|.+.|++.-
T Consensus 8 ~~~FGe~~~~V~~~L~~~g-~l-tl~~i~~~t~l~~~~Vk~~L~~Liqh~~V~y 59 (62)
T PF08221_consen 8 EDHFGEIAAKVFECLLSRG-RL-TLREIVRRTKLSPSQVKKALAVLIQHNCVQY 59 (62)
T ss_pred HHHHCHHHHHHHHHHHHCC-CC-CHHHHHHHCCCCHHHHHHHHHHHHHCCCCHH
T ss_conf 9880748999999999758-94-9999997839999999999999998086122
No 46
>PF10668 Phage_terminase: Phage terminase small subunit
Probab=73.88 E-value=0.91 Score=23.19 Aligned_cols=36 Identities=19% Similarity=0.392 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf 988999999999997649899888178878999985898789999
Q T0586 12 KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSR 56 (125)
Q Consensus 12 ~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~ 56 (125)
.|-.++.++...+ .|..++ .+++|++||||.+||+.
T Consensus 6 sp~RdkA~e~y~~--------~~g~~~-~k~IAe~lgvs~~tIr~ 41 (60)
T PF10668_consen 6 SPNRDKAFEIYKE--------SNGKIK-LKDIAEKLGVSESTIRK 41 (60)
T ss_pred CCCHHHHHHHHHH--------CCCCCC-HHHHHHHHCCCHHHHHH
T ss_conf 9588999999998--------189841-99999997979999873
No 47
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=73.47 E-value=1.5 Score=21.75 Aligned_cols=47 Identities=19% Similarity=0.365 Sum_probs=34.8
Q ss_pred CCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf 888178878999985-----898789999999998879167317833686288
Q T0586 33 GEDKLPSVREMGVKL-----AVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD 80 (125)
Q Consensus 33 ~G~~LPser~La~~~-----~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~ 80 (125)
.+..+ |-.+||+.+ .+|..+||.-++.|+.+|++..+.+.|+.+++.
T Consensus 10 ~~~P~-~~~~l~~~L~~~g~~~s~~avRrrLr~me~dG~t~~~~~~G~~ite~ 61 (66)
T PF08461_consen 10 SGKPI-GRKELAEELKLRGEELSEEAVRRRLRAMERDGFTRRQGYAGRSITEK 61 (66)
T ss_pred CCCCC-CHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH
T ss_conf 49998-99999999984066757999999999999878812057777606886
No 48
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator or FUR family includes metal ion uptake regulator proteins, which bind to the operator DNA and control the transcription of metal ion-responsive genes. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2w57_A 2fu4_A 1mzb_A 2o03_A 3f8n_A 2rgv_A 2fe3_A 3eyy_A.
Probab=73.37 E-value=0.74 Score=23.77 Aligned_cols=36 Identities=28% Similarity=0.173 Sum_probs=29.9
Q ss_pred CCHHHHHHH-----HCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 887899998-----589878999999999887916731783
Q T0586 38 PSVREMGVK-----LAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 38 Pser~La~~-----~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
||..++.+. .+||++||=+++..|++.|+|......
T Consensus 24 ~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 24 LSAEEIYDRLREKGPSISLATVYRTLDLLEEAGLIHRIELG 64 (120)
T ss_dssp EEHHHHHHHHHHT-TT--HHHHHHHHHHHHH---EEEEE--
T ss_pred CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCEEEEEECC
T ss_conf 99999999988618999862499999999868909999918
No 49
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; PDB: 2v1d_A 2com_A 2z3y_A 2iw5_A 2hko_A 2uxx_A 2dw4_A 2uxn_A 2ejr_A 2z5u_A ....
Probab=70.23 E-value=1.8 Score=21.29 Aligned_cols=51 Identities=22% Similarity=0.296 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHCC-CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEE
Q ss_conf 9999999997649-899888178878999985898789999999998879167
Q T0586 17 QISDWMKKQMITG-EWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIY 68 (125)
Q Consensus 17 qI~~~l~~~I~~G-~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~ 68 (125)
+.|-.+++.|+.- ...|+..| +..+....+.+-.+-+++++.-|+..|||.
T Consensus 32 ~~Yl~iRn~il~~w~~~~~~~l-t~~~~~~~~~~d~~~~~ri~~FL~~~G~IN 83 (84)
T PF04433_consen 32 EPYLNIRNHILNEWRKNPNKYL-TKTDARRLIKIDVNKVRRIYDFLERWGYIN 83 (84)
T ss_dssp HHHHHHHHHHHHHHHHHTTS----HHHHHHHCTSSHHHHHHHHHHHHHTT--S
T ss_pred HHHHHHHHHHHHHHHHCCCCCE-EHHHHHHHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 8999999999999998799836-299999885237999999999999859768
No 50
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C terminal contains a helix-turn-helix motif which binds DNA. ; PDB: 1rr7_A.
Probab=68.89 E-value=2.3 Score=20.53 Aligned_cols=50 Identities=16% Similarity=0.225 Sum_probs=31.7
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCE
Q ss_conf 889999999999976498998881788789999858987899999999988791
Q T0586 13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGY 66 (125)
Q Consensus 13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~ 66 (125)
|.-..+...+++.=+...|. |. +.++||..||+|..+|++.++.....-.
T Consensus 52 P~~~~~~~~~Rn~~I~~~f~-G~---n~~eLArkY~lS~r~I~~Ii~~~~~~~~ 101 (108)
T PF08765_consen 52 PKCDSALRALRNREIRREFN-GM---NVRELARKYGLSERWIYRIIKRQRKEER 101 (108)
T ss_dssp ----HHHHHHHHHHHHHH---------HHHHHHH----HHHHHHHHHHHHH---
T ss_pred CCCCHHHHHHHHHHHHHHHC-CC---CHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 59607889999999999838-99---7999998979669999999999888899
No 51
>PF09170 DUF1879: Domain of unknown function (DUF1879); InterPro: IPR015253 This domain is found in a set of hypothetical eukaryotic proteins, as well as in oligonucleotide/oligosaccharide-binding fold-containing protein-1. ; PDB: 1wj5_A.
Probab=68.67 E-value=1.9 Score=21.15 Aligned_cols=82 Identities=11% Similarity=0.230 Sum_probs=46.9
Q ss_pred HHHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHHHH--------CC--CHHHHH----HHHHHHHHCCEEEECCCC---EE
Q ss_conf 899999999999764989988-8178878999985--------89--878999----999999887916731783---36
Q T0586 14 IYSQISDWMKKQMITGEWKGE-DKLPSVREMGVKL--------AV--NPNTVS----RAYQELERAGYIYAKRGM---GS 75 (125)
Q Consensus 14 ly~qI~~~l~~~I~~G~l~~G-~~LPser~La~~~--------~V--Sr~TVr----~Al~~L~~~G~i~~~~g~---G~ 75 (125)
+.+.|.+.|.+.=+...++.. +-++|.-.+|..= .. +-..|+ +|++.|+++|+|+.+.+. =+
T Consensus 52 LsekikeFL~e~~V~~Fyq~ele~v~sL~~~a~~pv~~s~q~~~~~sts~qi~slfkeAl~lL~~~G~Vfqk~~~~D~vY 131 (174)
T PF09170_consen 52 LSEKIKEFLMENKVQNFYQKELESVESLISVASRPVSCSDQESKSSSTSKQIRSLFKEALKLLQDEGLVFQKDQNQDEVY 131 (174)
T ss_dssp HHHHHHHHHHHHT-S-B-HHHHHT-HHHHHHHSS-------S---------HHHHHHHHHHHHHH---EE-S-------B
T ss_pred HHHHHHHHHHHCCHHHEHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCCEE
T ss_conf 99999999865533103088887688899763586533345778862799999999999999987795786279976517
Q ss_pred EECCCHHHHHHHHHHHHHHH
Q ss_conf 86288078999999999999
Q T0586 76 FVTSDKALFDQLKKELADAI 95 (125)
Q Consensus 76 ~V~~~~~~~~~~~~~~~~~~ 95 (125)
+|+..+..+......+..+.
T Consensus 132 ~Vt~~DKdLh~~il~II~ed 151 (174)
T PF09170_consen 132 YVTDQDKDLHKAILNIIQED 151 (174)
T ss_dssp EE-SSS--------------
T ss_pred EEECCCHHHHHHHHHHHHHH
T ss_conf 87436366899999999998
No 52
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions .
Probab=68.23 E-value=2.1 Score=20.80 Aligned_cols=30 Identities=20% Similarity=0.401 Sum_probs=25.9
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 8817887899998589878999999999887
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELERA 64 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~ 64 (125)
...+ +..++|+.+|+|+-||+.-+..|.+.
T Consensus 17 ~~~~-t~~ela~~l~~S~~ti~~~I~~l~~~ 46 (59)
T PF08280_consen 17 NGWI-TLKELAKKLGLSERTIRNDINELNEE 46 (59)
T ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 7979-79999999798899999999999998
No 53
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 3cuq_A 2zme_A 1w7p_D 1u5t_B.
Probab=68.20 E-value=2.3 Score=20.52 Aligned_cols=71 Identities=18% Similarity=0.282 Sum_probs=51.9
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCE--EEECCCCE-EEEC
Q ss_conf 88988999999999997649899888178878999985--------8987899999999988791--67317833-6862
Q T0586 10 ADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKL--------AVNPNTVSRAYQELERAGY--IYAKRGMG-SFVT 78 (125)
Q Consensus 10 ~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~--------~VSr~TVr~Al~~L~~~G~--i~~~~g~G-~~V~ 78 (125)
+..-.|.+++.+|.+....-.=..|--+ +..+|-..| -||+..+.+|...|...|. -..+-++| .+|.
T Consensus 87 ~~~~f~~ELa~qI~e~c~~~~~~nGGii-~L~dl~~~~nr~r~g~~lISp~Di~~A~~~l~~Lg~~~~l~~~~sg~~~v~ 165 (223)
T PF04157_consen 87 GGGDFYYELAVQIVEVCLSTRKKNGGII-SLSDLYCLYNRARGGTELISPEDILKACKKLEKLGLGFKLRKIGSGVKVVQ 165 (223)
T ss_dssp CCCHHHHHHHHHHHHHHHHHCTTSSSEE-EHHHHHHHHHHCC----T--HHHHHHHHHHHCCCT-TEEEEEETTTEEEEE
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHCCCEE-EHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCEEEEE
T ss_conf 5006999999999999999997588856-799999999986267787599999999999998499859999668606986
Q ss_pred CCH
Q ss_conf 880
Q T0586 79 SDK 81 (125)
Q Consensus 79 ~~~ 81 (125)
..+
T Consensus 166 s~~ 168 (223)
T PF04157_consen 166 SVP 168 (223)
T ss_dssp CST
T ss_pred CCC
T ss_conf 077
No 54
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases .
Probab=67.79 E-value=1.2 Score=22.44 Aligned_cols=23 Identities=26% Similarity=0.426 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf 17887899998589878999999
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAY 58 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al 58 (125)
..||.++.|+.+|+|+.||++.+
T Consensus 15 ~f~Si~eAa~~l~~~~~tI~~~l 37 (37)
T PF07453_consen 15 SFSSIREAARALNISHSTISKYL 37 (37)
T ss_pred EECCHHHHHHHHCCCHHHHHHHC
T ss_conf 97489999998099877898759
No 55
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI , , , , . The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ixc_B 1iz1_Q 2esn_D 1o7l_B 1b9n_A 1b9m_B 3fzv_B.
Probab=66.89 E-value=2.1 Score=20.87 Aligned_cols=40 Identities=25% Similarity=0.296 Sum_probs=29.7
Q ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC---CEEEECCCCEEEEC
Q ss_conf 887899998589878999999999887---91673178336862
Q T0586 38 PSVREMGVKLAVNPNTVSRAYQELERA---GYIYAKRGMGSFVT 78 (125)
Q Consensus 38 Pser~La~~~~VSr~TVr~Al~~L~~~---G~i~~~~g~G~~V~ 78 (125)
.|...=|+.+|+|+++|.++++.|++. -++.+ .++|...+
T Consensus 14 gs~~~AA~~l~~s~~~vs~~i~~LE~~lg~~Lf~r-~~~~~~lT 56 (60)
T PF00126_consen 14 GSFSRAAEQLGISQSAVSRRIKRLEEELGVPLFDR-TGRGLRLT 56 (60)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEE-----EEE-
T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHHHHHCCEEEEE-CCCCEEEC
T ss_conf 99999998708995389999999999829968998-89975489
No 56
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response .; PDB: 3f8b_A 3f8f_B 3f8c_A 1xma_B 3hhh_B 3elk_B 1yg2_A 2dql_A 2e1n_B 2zfw_D ....
Probab=66.77 E-value=2.3 Score=20.56 Aligned_cols=50 Identities=18% Similarity=0.256 Sum_probs=32.9
Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHH----HCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 99999764989988817887899998----589878999999999887916731783
Q T0586 21 WMKKQMITGEWKGEDKLPSVREMGVK----LAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 21 ~l~~~I~~G~l~~G~~LPser~La~~----~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
.|...+..+.. .|-.| .+.|.+. +.+|.++|-.+++.|+++|+|+.....
T Consensus 10 ~IL~~L~~~~~-~gyei--~~~l~~~~~~~~~~s~g~iY~~L~~Le~~Gli~~~~~~ 63 (86)
T PF03551_consen 10 AILGLLSEGPM-HGYEI--KKELEERYGGFWKVSPGSIYPALKRLEEEGLIESRWED 63 (86)
T ss_dssp HHHHHHHHS-B-E--HH--HHHHHHHSTTTEE--HHHHHHHHHHHHHTTSEEEEEEE
T ss_pred HHHHHHHHCCC-CHHHH--HHHHHHHHCCCEECCCCHHHHHHHHHHHCCCEEEEEEE
T ss_conf 99999702899-59999--99999984887242654899999999978986987653
No 57
>PF12116 SpoIIID: Stage III sporulation protein D
Probab=66.62 E-value=0.95 Score=23.08 Aligned_cols=28 Identities=29% Similarity=0.401 Sum_probs=22.3
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH-HHH
Q ss_conf 88178878999985898789999999-998
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQ-ELE 62 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~-~L~ 62 (125)
..+- ++|+.|+.||||.+||.+-+. +|.
T Consensus 17 ~~~a-TVR~tAk~FGVSKSTVHkDvTeRL~ 45 (82)
T PF12116_consen 17 ENKA-TVRQTAKVFGVSKSTVHKDVTERLP 45 (82)
T ss_pred HCCH-HHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 7451-6999999978529999899999997
No 58
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway .; PDB: 1s7o_B 1xsv_A.
Probab=64.42 E-value=2.4 Score=20.39 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=23.3
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 88178878999985898789999999998
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELE 62 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~ 62 (125)
.+-+ |..++|+.+||||..|...+++-.
T Consensus 31 ~eDl-SlsEIAe~~~iSRqaVyD~ikr~~ 58 (101)
T PF04297_consen 31 NEDL-SLSEIAEELGISRQAVYDNIKRAE 58 (101)
T ss_dssp TS----HHHHHHHCT--HHHHHHHHHHHH
T ss_pred HCCC-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 8799-899999896988999999999999
No 59
>PF07638 Sigma70_ECF: ECF sigma factor; InterPro: IPR011517 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent
Probab=62.90 E-value=3.3 Score=19.49 Aligned_cols=14 Identities=29% Similarity=0.114 Sum_probs=6.9
Q ss_pred HHCCCCHHHHHHHH
Q ss_conf 98199998999999
Q T0586 104 KSIGLDDQTAIELL 117 (125)
Q Consensus 104 ~~~~~~~~~~~~l~ 117 (125)
...|++.+|+.+.+
T Consensus 148 ~f~Glt~~EiA~~L 161 (185)
T PF07638_consen 148 YFGGLTVEEIAEAL 161 (185)
T ss_pred HHCCCCHHHHHHHH
T ss_conf 98799999999896
No 60
>PF07023 DUF1315: Protein of unknown function (DUF1315); InterPro: IPR009749 This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=62.42 E-value=3.7 Score=19.22 Aligned_cols=55 Identities=11% Similarity=0.189 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC----EEEECC
Q ss_conf 9999999999764989988817887899998589878999999999887916731783----368628
Q T0586 16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM----GSFVTS 79 (125)
Q Consensus 16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~----G~~V~~ 79 (125)
-.||+.|+..+..|.||-|.+| |..+-. +--+|+-.-+....+...+.. |..+..
T Consensus 10 PevY~rL~~AVElGKWpDG~~L-T~eQre--------~~lQaVm~yq~~~n~~~e~~ti~~~G~I~~~ 68 (93)
T PF07023_consen 10 PEVYERLKQAVELGKWPDGRAL-TPEQRE--------SCLQAVMLYQARHNLPEEHRTIGAGGYIDMK 68 (93)
T ss_pred HHHHHHHHHHHHHCCCCCCCCC-CHHHHH--------HHHHHHHHHHHHCCCCHHHEECCCCCEECCC
T ss_conf 9999999999992879898988-999999--------9999999999870898888013679766402
No 61
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1trr_K 1tro_E 1p6z_R 1jhg_A 1co0_A 1rcs_B 3wrp_A 1zt9_B 1wrp_R 1wrt_S ....
Probab=62.33 E-value=3.2 Score=19.58 Aligned_cols=25 Identities=28% Similarity=0.290 Sum_probs=22.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 8789999858987899999999988
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELER 63 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~ 63 (125)
|.|++++.+|+|..||.+.=+.|..
T Consensus 51 syreI~~~tG~S~aTIsR~sr~Lk~ 75 (87)
T PF01371_consen 51 SYREIAEETGASIATISRVSRCLKY 75 (87)
T ss_dssp SHHHHHHH----HHHHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 8999999978778899999999880
No 62
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after . Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=58.99 E-value=3.5 Score=19.38 Aligned_cols=31 Identities=19% Similarity=0.205 Sum_probs=25.8
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
Q ss_conf 8789999858987899999999988791673
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYIYA 69 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~ 69 (125)
+..++|+.+|||+.||..=...-..+|+.-.
T Consensus 15 ~~~eIA~~Lgv~~~TV~~W~~r~~w~~~~~~ 45 (58)
T PF06056_consen 15 TPKEIAEELGVSRRTVYSWKKRYGWDGLLPL 45 (58)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHCCCCCCCH
T ss_conf 9999999988688899999997561666742
No 63
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 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=57.50 E-value=4.7 Score=18.52 Aligned_cols=37 Identities=27% Similarity=0.523 Sum_probs=28.4
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf 17887899998589878999999999887916731783368
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF 76 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~ 76 (125)
-..+.++.|+.+|+++. +-+..|.+.||++.+ ++|..
T Consensus 23 ~~~~i~~~AK~lgi~~~---~l~~~Lr~~~il~~~-~~~~~ 59 (111)
T PF03374_consen 23 GSMTIREAAKILGIGPN---KLFKWLREKGILYRR-GSGRN 59 (111)
T ss_pred CCEEHHHHHHHHCCCHH---HHHHHHHHCCCEEEC-CCCCC
T ss_conf 95779999999399999---999999986977856-89976
No 64
>PF01498 Transposase_5: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in . Tc3 is a member of the Tc1/mariner family of transposable elements. More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration, 0005634 nucleus; PDB: 3f2k_B 1u78_A.
Probab=57.49 E-value=3.3 Score=19.54 Aligned_cols=36 Identities=28% Similarity=0.440 Sum_probs=26.8
Q ss_pred CHHHHHHHH-----CCCHHHHHHHHHHHHHCCEEEECCCCEEEE
Q ss_conf 878999985-----898789999999998879167317833686
Q T0586 39 SVREMGVKL-----AVNPNTVSRAYQELERAGYIYAKRGMGSFV 77 (125)
Q Consensus 39 ser~La~~~-----~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V 77 (125)
|.++|+..+ +||.+||+++|. ..||-...+..-.++
T Consensus 15 T~~~l~~~l~~~~~~vS~~Tv~R~L~---~~G~~~~~~~~kP~L 55 (72)
T PF01498_consen 15 TLRELARELQEEGISVSKSTVRRRLK---EMGYRKRKARKKPLL 55 (72)
T ss_dssp -HHHHHHHT---T--S-HHHHHHHHH---H--------------
T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHH---HCCCEEECCCCCCCC
T ss_conf 49999999986589979999999999---868920277889999
No 65
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA , , , , , . Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1r8d_B 1jbg_A 3hh0_C 3d6z_A 3d71_A 3d6y_A 1r8e_A 1exi_A 1exj_A 1q06_A ....
Probab=57.34 E-value=1.9 Score=21.13 Aligned_cols=25 Identities=28% Similarity=0.426 Sum_probs=21.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEE
Q ss_conf 87899998589878999999999887916
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYI 67 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i 67 (125)
|..++|+.+|||..|+| ..+.+|+|
T Consensus 1 ti~e~a~~~gvs~~tlR----~ye~~gll 25 (38)
T PF00376_consen 1 TIGEVAKLLGVSVRTLR----YYEREGLL 25 (38)
T ss_dssp EHHHHHHHCT--HHHHH----HHHHTTSS
T ss_pred CHHHHHHHHCCCHHHHH----HHHHCCCC
T ss_conf 98999999896999999----99987898
No 66
>PF12471 GTP_CH_N: GTP cyclohydrolase N terminal
Probab=56.33 E-value=5.1 Score=18.26 Aligned_cols=40 Identities=13% Similarity=0.254 Sum_probs=30.7
Q ss_pred HHHHHHHHCCCCCCCCCCCC------------------HHHHHHHHCCCHHHHHHHHH
Q ss_conf 99999976498998881788------------------78999985898789999999
Q T0586 20 DWMKKQMITGEWKGEDKLPS------------------VREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 20 ~~l~~~I~~G~l~~G~~LPs------------------er~La~~~~VSr~TVr~Al~ 59 (125)
-.|.+.|..|.|++.-++-- .-..|+.|||+-++.|++|-
T Consensus 135 pEi~eav~~GrL~~DG~i~~~~~G~~~VtK~AvePVWYLPGVA~RFGi~E~~LRR~LF 192 (194)
T PF12471_consen 135 PEIREAVAKGRLKPDGKIVLNSNGDVRVTKAAVEPVWYLPGVAERFGISEGELRRALF 192 (194)
T ss_pred HHHHHHHHCCCCCCCCEEEECCCCCEEEEEEEECCCCCCHHHHHHCCCCHHHHHHHHH
T ss_conf 8899999849978887177158986889987623321361159780997999988872
No 67
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2h27_D 1or7_A 2o8x_B.
Probab=55.67 E-value=2.9 Score=19.88 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=21.4
Q ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 78878999985898789999999998
Q T0586 37 LPSVREMGVKLAVNPNTVSRAYQELE 62 (125)
Q Consensus 37 LPser~La~~~~VSr~TVr~Al~~L~ 62 (125)
+ |..++|+.+|+|.+||+..+.+-.
T Consensus 27 ~-s~~eIA~~l~is~~tv~~~l~ra~ 51 (54)
T PF08281_consen 27 L-SYKEIAEILGISESTVKSRLSRAR 51 (54)
T ss_dssp ---HHHHHHHCTS----HHHHHHHHH
T ss_pred C-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 5-899999998919999999999999
No 68
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term
Probab=55.62 E-value=5.8 Score=17.89 Aligned_cols=46 Identities=17% Similarity=0.302 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCE
Q ss_conf 9999999999976498998881788789999858-987899999999988791
Q T0586 15 YSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA-VNPNTVSRAYQELERAGY 66 (125)
Q Consensus 15 y~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~-VSr~TVr~Al~~L~~~G~ 66 (125)
|++|+..-...+..|. -||...+-..+| .|.+||.+.++....+--
T Consensus 3 ~e~V~~Aa~~L~~~G~------~PTv~~VR~~lG~GS~~ti~~~lk~w~~~~~ 49 (120)
T PF11740_consen 3 YEDVAAAADALLAAGK------RPTVDAVRERLGTGSMSTISKHLKEWREEQR 49 (120)
T ss_pred HHHHHHHHHHHHHCCC------CCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf 9999999999987489------9989999999879588999999999998753
No 69
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation .
Probab=54.90 E-value=3.7 Score=19.19 Aligned_cols=21 Identities=14% Similarity=0.431 Sum_probs=18.9
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 878999985898789999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~ 59 (125)
+...||+.|+||+-.||+.|+
T Consensus 31 t~~~LAe~F~vSpeaIrRILK 51 (225)
T PF06413_consen 31 TTERLAESFKVSPEAIRRILK 51 (225)
T ss_pred CHHHHHHHCCCCHHHHHHHHH
T ss_conf 799998767999999999997
No 70
>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_B 2v1u_A 1w5t_C 1w5s_A 1fnn_A.
Probab=54.89 E-value=5.9 Score=17.84 Aligned_cols=42 Identities=26% Similarity=0.295 Sum_probs=32.6
Q ss_pred CCCCCCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCEEEECC
Q ss_conf 89988817887899998589---8789999999998879167317
Q T0586 30 EWKGEDKLPSVREMGVKLAV---NPNTVSRAYQELERAGYIYAKR 71 (125)
Q Consensus 30 ~l~~G~~LPser~La~~~~V---Sr~TVr~Al~~L~~~G~i~~~~ 71 (125)
....|+-...-..+|+.+|+ |.+.+..-++.|+..|+|.++.
T Consensus 15 ~~~~~~vy~~Y~~lc~~~~~~pls~~r~~~~l~~L~~~gli~~~~ 59 (85)
T PF09079_consen 15 EVTTGEVYEQYEELCEKIGVDPLSQRRFSDILSELEMLGLIESER 59 (85)
T ss_dssp SEE-HHHHHHHHHHHHHCTS----HHHHHHHHHHHHH---EEEEE
T ss_pred CCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf 630899999999999984899998999999999998578703433
No 71
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase () converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1sfu_A 1xmk_A 3eyi_A 1qbj_A 3f23_B 3f21_B 3f22_B 2acj_D 2gxb_B 1qgp_A ....
Probab=54.67 E-value=6 Score=17.79 Aligned_cols=40 Identities=20% Similarity=0.292 Sum_probs=31.5
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCE
Q ss_conf 88178878999985898789999999998879167317833
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMG 74 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G 74 (125)
++.. ..-.++..+++-..+|.++|-.|+.+|.|...++..
T Consensus 18 ~~~a-~~i~~~~~l~~~k~~vNr~LY~L~k~g~v~~~~~~P 57 (66)
T PF02295_consen 18 KSTA-TAIAKALGLSVPKKEVNRQLYRLEKSGKVCKSPGNP 57 (66)
T ss_dssp -EEC-CHHHHHHHCTS-HHHHHHHHHHHHHTTSEEEECSSS
T ss_pred CHHH-HHHHHHHCCCHHHHHHHHHHHHHHHCCCEECCCCCC
T ss_conf 7189-999998361252889999999999779665279979
No 72
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This family consists of several short bacterial and phage proteins, which are related to the Escherichia coli protein AlpA. AlpA suppresses two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light . Several of the sequences in this family are thought to be DNA-binding proteins.; PDB: 1z4h_A.
Probab=54.27 E-value=2.2 Score=20.73 Aligned_cols=24 Identities=25% Similarity=0.379 Sum_probs=19.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 178878999985898789999999
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~ 59 (125)
++-+..++++.+|+|++|+.+=.+
T Consensus 2 r~l~~~ev~~~lgvs~~t~y~~~~ 25 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTLYRLIK 25 (51)
T ss_dssp -EE-HHHHHHH-----HHHHHHHH
T ss_pred CEECHHHHHHHHCCCHHHHHHHHH
T ss_conf 512499999998949999999977
No 73
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=53.65 E-value=4.8 Score=18.45 Aligned_cols=30 Identities=17% Similarity=0.209 Sum_probs=23.3
Q ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 9988817887899998589878999999999
Q T0586 31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQEL 61 (125)
Q Consensus 31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L 61 (125)
|.-.+.| +..+-|..+||||.|+.+.|..=
T Consensus 52 L~D~egl-~QeeAA~~MgVSR~Tf~ril~~A 81 (106)
T PF02001_consen 52 LVDYEGL-TQEEAAEQMGVSRQTFQRILKSA 81 (106)
T ss_pred HHHHHCC-CHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 9888179-89999998497799999999999
No 74
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA .; PDB: 1j9i_B.
Probab=51.15 E-value=2.4 Score=20.47 Aligned_cols=34 Identities=21% Similarity=0.312 Sum_probs=25.2
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEE-EECCCCEEE
Q ss_conf 87899998589878999999999887916-731783368
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYI-YAKRGMGSF 76 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i-~~~~g~G~~ 76 (125)
+-.+||+.||||..||.+-. .+|+- ...-|+|..
T Consensus 4 nk~~lA~~~gVS~~ti~~W~----~~G~Pv~~~gg~G~~ 38 (164)
T PF07471_consen 4 NKKQLAEILGVSERTITKWQ----RQGMPVVRRGGRGRE 38 (164)
T ss_dssp EHHHHHHH----HHHHHHHT----T--------------
T ss_pred CHHHHHHHHCCCHHHHHHHH----HCCCCEEECCCCCCC
T ss_conf 89999999798999999999----879974445889851
No 75
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria . They modulate transcription in response to changes in cellular NADH/NAD^(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0016564 transcription repressor activity, 0006980 redox signal response, 0016481 negative regulation of transcription, 0005737 cytoplasm; PDB: 1xcb_F 2dt5_A 2vt3_A 2vt2_B.
Probab=50.80 E-value=4.3 Score=18.78 Aligned_cols=39 Identities=21% Similarity=0.496 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 88999999999997649899888178878999985898789999999
Q T0586 13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~ 59 (125)
|+|-+.-..+. ..|. +.+ |-.+||+.+||+.++||+=++
T Consensus 12 p~Y~r~L~~l~---~~g~----~~i-SS~eLa~~~gi~~~qVRKDlS 50 (50)
T PF06971_consen 12 PLYLRYLKQLQ---EEGV----ERI-SSKELAEALGITPSQVRKDLS 50 (50)
T ss_dssp HHHHHHHHHHH---H--------B---TTTHHHCCSS-HHHHHHHHH
T ss_pred HHHHHHHHHHH---HCCC----EEE-CHHHHHHHHCCCHHHHHCCCC
T ss_conf 99999999999---8599----458-799999997979999612257
No 76
>PF09182 PuR_N: Bacterial purine repressor, N-terminal; InterPro: IPR015265 The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA . ; PDB: 1p4a_B 1o57_D.
Probab=50.03 E-value=7.1 Score=17.31 Aligned_cols=42 Identities=10% Similarity=0.153 Sum_probs=34.2
Q ss_pred CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH------HCCEEEECCCCE
Q ss_conf 9888178878999985898789999999998------879167317833
Q T0586 32 KGEDKLPSVREMGVKLAVNPNTVSRAYQELE------RAGYIYAKRGMG 74 (125)
Q Consensus 32 ~~G~~LPser~La~~~~VSr~TVr~Al~~L~------~~G~i~~~~g~G 74 (125)
.|+..+ |...+|+.|+++.+||.+-+..+. ..|.|++.+|..
T Consensus 16 ~P~~li-~L~~F~e~~~~AKSsISEDl~iik~~~~~~~~G~leTi~GAa 63 (70)
T PF09182_consen 16 NPNKLI-SLTFFAERFGSAKSSISEDLVIIKETFEKEGLGRLETIPGAA 63 (70)
T ss_dssp STT-----HHHHHHHHT--HHHHHHHHHHHHHHHHH-----EE------
T ss_pred CCCCEE-CHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf 997547-599999986331021476799999999875986399856877
No 77
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 1tty_A 1rp3_G 1sc5_A 1l0o_C 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F ....
Probab=47.59 E-value=5.7 Score=17.95 Aligned_cols=28 Identities=14% Similarity=0.296 Sum_probs=24.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 8178878999985898789999999998
Q T0586 35 DKLPSVREMGVKLAVNPNTVSRAYQELE 62 (125)
Q Consensus 35 ~~LPser~La~~~~VSr~TVr~Al~~L~ 62 (125)
-+-|+..++|+.+|+|..-|++++..-.
T Consensus 18 gR~Pt~eEIA~~lgis~~~v~~~~~~~~ 45 (78)
T PF04539_consen 18 GREPTEEEIAEELGISEEEVRELLEASR 45 (78)
T ss_dssp ----BHHHHHHH----HHHHHHHHHHHS
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf 8898999999997888999999999746
No 78
>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 .
Probab=47.08 E-value=7.9 Score=17.03 Aligned_cols=48 Identities=13% Similarity=0.206 Sum_probs=38.6
Q ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf 9999976498998881788789999858987899999999988791673178
Q T0586 21 WMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG 72 (125)
Q Consensus 21 ~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g 72 (125)
.+-+.|....+. |. ...+|++.+|+....+-.-.+.|.+.|+|+..+-
T Consensus 6 ~lLe~Ia~~r~~-Gi---~q~dL~k~~~~D~r~~~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 6 CLLERIARSRYN-GI---TQSDLWKLFGQDPRSVFYRVKKLEDKGLIVKQQI 53 (75)
T ss_pred HHHHHHHHHCCC-CC---CHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf 999999967768-82---0537799858992256899999977899788883
No 79
>PF03811 Ins_element1: Insertion element protein; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. This protein is absolutely required for transposition of insertion element 1.; GO: 0006313 transposition, DNA-mediated
Probab=47.08 E-value=6.1 Score=17.75 Aligned_cols=34 Identities=26% Similarity=0.446 Sum_probs=25.0
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 999999997649899888178878999985898789999999
Q T0586 18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 18 I~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~ 59 (125)
+...+.+...+| + |.|..|..+|||.+||-+-++
T Consensus 52 ~k~~i~~l~~~G-------~-siR~iArvl~Is~~Tv~r~lK 85 (88)
T PF03811_consen 52 VKQKILELMVEG-------M-SIRDIARVLGISINTVLRWLK 85 (88)
T ss_pred HHHHHHHHHHCC-------C-CHHHHHHHHCCCHHHHHHHHH
T ss_conf 999999998768-------5-199999986878999999986
No 80
>PF10264 Stork_head: Winged helix Storkhead-box1 domain
Probab=44.32 E-value=8.7 Score=16.75 Aligned_cols=29 Identities=21% Similarity=0.398 Sum_probs=24.4
Q ss_pred CHHHHHHHHHHHHHCCEEEECCCCEEEECC
Q ss_conf 878999999999887916731783368628
Q T0586 50 NPNTVSRAYQELERAGYIYAKRGMGSFVTS 79 (125)
Q Consensus 50 Sr~TVr~Al~~L~~~G~i~~~~g~G~~V~~ 79 (125)
|...++.++..|..++-|+.. |.|+|+.-
T Consensus 50 s~e~~~~tL~~L~~e~kIY~t-~~GYfivt 78 (80)
T PF10264_consen 50 STEVLYNTLGTLIKERKIYHT-GEGYFIVT 78 (80)
T ss_pred CHHHHHHHHHHHHHCCCEEEC-CCCEEEEC
T ss_conf 689999999999971632547-99668607
No 81
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers , , . LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase , . Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria : V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE . B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT . E. coli malT (activates maltose operon; MalT binds ATP and maltotriose) ; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1fse_B 2jpc_A 1x3u_A 1yio_A 1zn2_A 1p4w_A 3clo_B 1l3l_C 1h0m_B 2q0o_A ....
Probab=43.94 E-value=8.8 Score=16.71 Aligned_cols=25 Identities=20% Similarity=0.368 Sum_probs=21.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 8789999858987899999999988
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELER 63 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~ 63 (125)
+..++|..+|+|..||+.-...+..
T Consensus 20 ~~~eIA~~l~is~~TV~~~~~~i~~ 44 (58)
T PF00196_consen 20 SNKEIAERLGISEKTVKSHRRRIMK 44 (58)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 8378998835452479999999999
No 82
>PF09756 DDRGK: DDRGK domain; PDB: 1wi9_A.
Probab=43.65 E-value=7.3 Score=17.25 Aligned_cols=58 Identities=17% Similarity=0.295 Sum_probs=41.0
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC---CCCEEEECCCH
Q ss_conf 99999999764989988817887899998589878999999999887916731---78336862880
Q T0586 18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK---RGMGSFVTSDK 81 (125)
Q Consensus 18 I~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~---~g~G~~V~~~~ 81 (125)
+-....+.|... ++-...+||..||++..-+..-++.|+..|.|.-. +|+-.||++..
T Consensus 100 lL~~Fi~~Ik~~------k~v~l~~la~~f~l~t~~~i~ri~~L~~~~~i~Gv~DdrGk~iyis~~E 160 (188)
T PF09756_consen 100 LLQDFINYIKKK------KVVNLEDLAAEFGLKTQDVINRIQELEEQGRITGVIDDRGKFIYISQEE 160 (188)
T ss_dssp -HHHHHHHHHH-------SEE-HHHHHHH----HHHHHHHHHHHHH-------B-----EE------
T ss_pred HHHHHHHHHHHC------CEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCEEEECHHH
T ss_conf 999999999986------8310999998909987999999999998798446885998868855999
No 83
>PF06504 RepC: Replication protein C (RepC); InterPro: IPR010522 This family consists of several bacterial replication protein C (RepC) sequences.
Probab=43.53 E-value=8.9 Score=16.67 Aligned_cols=67 Identities=15% Similarity=0.099 Sum_probs=51.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC------CCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 768889889999999999976498998881788789999858------9878999999999887916731783
Q T0586 7 TFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA------VNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 7 ~~~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~------VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
.-+...+.++|+.-.|.-+..+-.-.+=-.--|.++|+.++| .....|++.+.+|..-.+++.+.++
T Consensus 81 ~~~p~~e~g~qLRl~Le~k~ea~~~~~~~vktS~r~La~~~Gy~~d~g~~~~~IresL~RL~~Vsv~~~~~~~ 153 (281)
T PF06504_consen 81 PPEPKTEIGQQLRLFLEPKWEAVEDDAMVVKTSYRSLASELGYADDGGKNFRRIRESLERLWNVSVIVQRGGK 153 (281)
T ss_pred CCCCCCCHHHHHHHHHCCCCCCCCCCCEEEHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC
T ss_conf 8888883257788651446333546542541529999998286677882089999999986286899974753
No 84
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; GO: 0018189 pyrroloquinoline quinone biosynthetic process
Probab=42.74 E-value=9.2 Score=16.59 Aligned_cols=29 Identities=24% Similarity=0.447 Sum_probs=19.9
Q ss_pred HHHHHHHHCCCHHHHH----HHHHHHHHCCEEE
Q ss_conf 7899998589878999----9999998879167
Q T0586 40 VREMGVKLAVNPNTVS----RAYQELERAGYIY 68 (125)
Q Consensus 40 er~La~~~~VSr~TVr----~Al~~L~~~G~i~ 68 (125)
...|+++|++++.++. .-+..|.+.|+|+
T Consensus 49 v~~L~~~Y~~~~e~~~~dv~~fL~~L~~~~lIE 81 (81)
T PF05402_consen 49 VAELAEEYDVDPEEIEQDVLAFLEQLREKGLIE 81 (81)
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 999998819978999999999999999874939
No 85
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic .; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 2fjr_A 3bd1_B.
Probab=42.60 E-value=3.6 Score=19.25 Aligned_cols=22 Identities=27% Similarity=0.332 Sum_probs=17.7
Q ss_pred CCHHHHHHHHCCCHHHHH-HHHH
Q ss_conf 887899998589878999-9999
Q T0586 38 PSVREMGVKLAVNPNTVS-RAYQ 59 (125)
Q Consensus 38 Pser~La~~~~VSr~TVr-~Al~ 59 (125)
-+..+||+.+|||++|+. ...+
T Consensus 13 ~~~~elA~~LgIs~stvs~~~~~ 35 (66)
T PF07022_consen 13 KTDKELAEKLGISQSTVSHTWKK 35 (66)
T ss_dssp -SCHHHHCCTT--HHHHH-HHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 96999999919988885567641
No 86
>PF07377 DUF1493: Protein of unknown function (DUF1493); InterPro: IPR010862 This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.
Probab=41.96 E-value=9.4 Score=16.51 Aligned_cols=53 Identities=11% Similarity=0.214 Sum_probs=47.4
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 88999999999997649899888178878999985898789999999998879
Q T0586 13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAG 65 (125)
Q Consensus 13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G 65 (125)
-+.+||.+.+++.+-.+.+..+..|.....|...|+++..-+.+.+....+.=
T Consensus 3 ~i~~~i~~fvr~e~g~~l~~~~~~lt~~TdL~~DL~~~gdDa~e~m~~f~~~F 55 (111)
T PF07377_consen 3 DIWKEILEFVREEIGTPLFKKKIELTPDTDLNEDLGLDGDDAEEFMEKFFERF 55 (111)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHC
T ss_conf 59999999999870744357777068877478752997689999999999981
No 87
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair .
Probab=41.90 E-value=9.5 Score=16.51 Aligned_cols=33 Identities=21% Similarity=0.254 Sum_probs=27.1
Q ss_pred HHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEE
Q ss_conf 9985898789999999998879167317833686
Q T0586 44 GVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV 77 (125)
Q Consensus 44 a~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V 77 (125)
.+.-||+..+|.+.++.|.++|+|.... .|+-.
T Consensus 22 pK~~gI~~m~VKdvlQ~LvDDglV~~EK-iGssn 54 (188)
T PF03962_consen 22 PKVKGINSMSVKDVLQSLVDDGLVEVEK-IGSSN 54 (188)
T ss_pred CCCCCCCHHHHHHHHHHHHCCCCCHHHH-CCCEE
T ss_conf 6324976402999999986367621021-07755
No 88
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon . This domain includes the DNA-binding HTH motif . ; PDB: 1r71_B.
Probab=40.89 E-value=3 Score=19.79 Aligned_cols=37 Identities=16% Similarity=0.141 Sum_probs=27.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf 8789999858987899999999988791673178336
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS 75 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~ 75 (125)
|..++|+.+|-|+++|...+..|.--..|...-..|.
T Consensus 5 tq~eIA~~lGks~s~Vs~~L~Ll~lp~~v~~~v~~G~ 41 (93)
T PF08535_consen 5 TQEEIAKRLGKSRSWVSNHLRLLDLPEDVKEAVEEGR 41 (93)
T ss_dssp ----HHHH----HHHHHHHHGGGS--HHHHHHHH---
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 9999999988799999999998669999999999599
No 89
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins. ; PDB: 1p99_A 1xs5_A.
Probab=40.87 E-value=8 Score=16.97 Aligned_cols=30 Identities=37% Similarity=0.443 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHHCCEEEECCCCEEEECC
Q ss_conf 878999999999887916731783368628
Q T0586 50 NPNTVSRAYQELERAGYIYAKRGMGSFVTS 79 (125)
Q Consensus 50 Sr~TVr~Al~~L~~~G~i~~~~g~G~~V~~ 79 (125)
.++---+||..|++.|+|..+++.|...+.
T Consensus 105 DpsN~~RAL~lLq~~GLIkLk~~~~~~~t~ 134 (237)
T PF03180_consen 105 DPSNQGRALLLLQEAGLIKLKDGNGLTATV 134 (237)
T ss_dssp SHHHHHHHHHHHHH----EE-TT------G
T ss_pred CCCCHHHHHHHHHHCCCEEECCCCCCCCCH
T ss_conf 976586999999848957986899976784
No 90
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis . During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes . More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery .
Probab=40.74 E-value=7.3 Score=17.25 Aligned_cols=29 Identities=28% Similarity=0.360 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHC-CCHHHHHHHHHHHHHCC
Q ss_conf 1788789999858-98789999999998879
Q T0586 36 KLPSVREMGVKLA-VNPNTVSRAYQELERAG 65 (125)
Q Consensus 36 ~LPser~La~~~~-VSr~TVr~Al~~L~~~G 65 (125)
-| |-+++|++|| |||+.|.-=+++|.-.+
T Consensus 18 Gl-SasqIA~~LGgvsRNAViGK~hRLgL~~ 47 (162)
T PF07750_consen 18 GL-SASQIAKQLGGVSRNAVIGKVHRLGLSG 47 (162)
T ss_pred CC-CHHHHHHHHCCCCHHHHHHHHHHCCCCC
T ss_conf 88-8999999975520666777776436666
No 91
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; InterPro: IPR000005 Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' (HTH) motif. One major subfamily of these proteins , is related to the arabinose operon regulatory protein AraC , . Except for celD , all of these proteins seem to be positive transcriptional factors. Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C-terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerization . The known structure of MarA (P27246 from SWISSPROT) shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27 angstroms, which causes the cognate DNA to bend.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1xs9_A 1bl0_A 1d5y_A 1wpk_A 2k9s_A 1zgw_A 1u8b_A.
Probab=38.70 E-value=11 Score=16.19 Aligned_cols=28 Identities=18% Similarity=0.401 Sum_probs=23.7
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 88178878999985898789999999998
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELE 62 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~ 62 (125)
.+.+ ++.++|..+|+|++...+.++..-
T Consensus 6 ~~~~-~i~~iA~~~g~s~~~~~r~Fk~~~ 33 (42)
T PF00165_consen 6 SEPI-SIEDIAEELGYSPSYFSRLFKKEF 33 (42)
T ss_dssp CSS---HHHHHHHTTSSHHHHHHHHHHHC
T ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 8989-799999997989999999999999
No 92
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2ef8_B 3f6w_A 3eus_A 1x57_A 1utx_A 2gzu_A 1rio_A 1lli_A 1lmb_3 3bdn_B ....
Probab=38.19 E-value=8.1 Score=16.93 Aligned_cols=21 Identities=29% Similarity=0.428 Sum_probs=17.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 878999985898789999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~ 59 (125)
|..++|+.+|||++||.+-.+
T Consensus 11 s~~~la~~~gis~~~i~~~e~ 31 (55)
T PF01381_consen 11 SQEELARRLGISRSTISRIEN 31 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHCCCCHHHHHHHHC
T ss_conf 999998864987878889976
No 93
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; PDB: 3dpl_C 3dqv_C 1iuy_A 2do7_A 2hye_C 1ldk_B 1u6g_A 1ldj_A.
Probab=37.87 E-value=7.6 Score=17.15 Aligned_cols=30 Identities=10% Similarity=0.187 Sum_probs=25.5
Q ss_pred HHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf 999858987899999999988791673178
Q T0586 43 MGVKLAVNPNTVSRAYQELERAGYIYAKRG 72 (125)
Q Consensus 43 La~~~~VSr~TVr~Al~~L~~~G~i~~~~g 72 (125)
+...|.++...+.+++..|...|||.+..+
T Consensus 36 l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~ 65 (68)
T PF10557_consen 36 LKKRFPPTVSDIKKRIEYLIEKEYIERDEN 65 (68)
T ss_dssp TTTSS---HHHHHHHHHHHHHTTSEEEESS
T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 746479999999999999998548871889
No 94
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences ,. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli . Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor . The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution ,. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as 'feelers' suitable for DNA or protein (invertase) recognition . Other proteins belonging to this subfamily include: Escherichia coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ojl_E 1fip_A 1etw_B 4fis_B 1fia_A 1etq_D 3fis_A 1f36_A 1ety_B 1etx_A ....
Probab=37.85 E-value=9.8 Score=16.40 Aligned_cols=22 Identities=14% Similarity=0.283 Sum_probs=17.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 8789999858987899999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQE 60 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~ 60 (125)
+..+-|+.+||||+|+.+=++.
T Consensus 20 n~~~aA~~Lgi~r~tL~~klkk 41 (42)
T PF02954_consen 20 NISKAARLLGISRSTLYRKLKK 41 (42)
T ss_dssp -HHHHHHH----HHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
T ss_conf 8999999979899999999984
No 95
>PF05848 CtsR: Firmicute transcriptional repressor of class III stress genes (CtsR); InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon .
Probab=37.55 E-value=11 Score=16.11 Aligned_cols=63 Identities=17% Similarity=0.311 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH--HHHCC-EEEECCCCEEEEC
Q ss_conf 89999999999976498998881788789999858987899999999--98879-1673178336862
Q T0586 14 IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQE--LERAG-YIYAKRGMGSFVT 78 (125)
Q Consensus 14 ly~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~--L~~~G-~i~~~~g~G~~V~ 78 (125)
+...|..+|+..+.... .|.-----.+||++|++.|+-+.-+++- =.+.| +|++++|-|=|+.
T Consensus 4 iSDiIE~ylK~~L~~s~--~~~iEIkR~eLA~~F~CvPSQINYVi~TRFT~e~GY~VESkRGGGGYIR 69 (152)
T PF05848_consen 4 ISDIIEQYLKQLLEESE--EGQIEIKRNELADRFDCVPSQINYVISTRFTPERGYLVESKRGGGGYIR 69 (152)
T ss_pred HHHHHHHHHHHHHHHCC--CCEEEEEHHHHHHHHCCCHHHCCEEEECCCCCCCCEEEEEECCCCCEEE
T ss_conf 78999999999997387--8728654888888718674661045542523778728986338986799
No 96
>PF12481 DUF3700: Aluminium induced protein
Probab=37.01 E-value=6.6 Score=17.54 Aligned_cols=55 Identities=16% Similarity=0.359 Sum_probs=30.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHH---HCCCCCCCCCCCCHHHHHHHHCCCHHH-----HHHHHHHHHHCC
Q ss_conf 77776888988999999999997---649899888178878999985898789-----999999998879
Q T0586 4 MNPTFHADKPIYSQISDWMKKQM---ITGEWKGEDKLPSVREMGVKLAVNPNT-----VSRAYQELERAG 65 (125)
Q Consensus 4 M~~~~~~~~Ply~qI~~~l~~~I---~~G~l~~G~~LPser~La~~~~VSr~T-----Vr~Al~~L~~~G 65 (125)
|....+...|+..+.+.-+ +.| ..|. |-..-.|-++||.|++| |-|||+-|.+.|
T Consensus 57 lAys~~~~~~l~pR~F~~~-DdIfClF~G~------L~NL~~L~qqYGLsK~~nEa~lVIEAYrtLRDRg 119 (124)
T PF12481_consen 57 LAYSHHNQSPLRPRLFCVV-DDIFCLFQGS------LDNLCSLRQQYGLSKSANEAMLVIEAYRTLRDRG 119 (124)
T ss_pred EEEECCCCCCCCCCEEEEE-CCEEEEEECH------HHHHHHHHHHHCCCCCCCEEEEEHHHHHHHHHCC
T ss_conf 8986488888765314641-5678998521------4438889998485667644756088887765159
No 97
>PF07374 DUF1492: Protein of unknown function (DUF1492); InterPro: IPR010861 This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown.
Probab=36.43 E-value=11 Score=15.96 Aligned_cols=25 Identities=36% Similarity=0.441 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHCCCHHHH----HHHHHHH
Q ss_conf 1788789999858987899----9999999
Q T0586 36 KLPSVREMGVKLAVNPNTV----SRAYQEL 61 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TV----r~Al~~L 61 (125)
++ +..+.|+.+|+|++|+ ++|+..|
T Consensus 71 ~~-~~~~I~~~L~iS~~tyYr~~~kAl~~L 99 (100)
T PF07374_consen 71 KL-SWDEICEELNISRSTYYRKKRKALKEL 99 (100)
T ss_pred CC-CHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf 59-899999998788999999999999841
No 98
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus; PDB: 2dk5_A 2yu3_A 2dk8_A.
Probab=34.52 E-value=12 Score=15.76 Aligned_cols=31 Identities=19% Similarity=0.321 Sum_probs=17.1
Q ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC
Q ss_conf 7899998589878999999999887916731
Q T0586 40 VREMGVKLAVNPNTVSRAYQELERAGYIYAK 70 (125)
Q Consensus 40 er~La~~~~VSr~TVr~Al~~L~~~G~i~~~ 70 (125)
.++|....|+..+.|.++++.|+..++|...
T Consensus 104 tk~ik~~tnL~~~~v~k~LK~Le~k~lIKsV 134 (325)
T PF05158_consen 104 TKDIKKKTNLHQNQVNKCLKSLESKKLIKSV 134 (325)
T ss_dssp HHHHHHHCT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf 9999987499899999999999857986753
No 99
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=34.50 E-value=8.6 Score=16.77 Aligned_cols=27 Identities=19% Similarity=0.123 Sum_probs=21.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf 878999985898789999999998879
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAG 65 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G 65 (125)
...+.|..++++|.|||+-..-.+.+.
T Consensus 18 N~teVaR~L~c~R~TVrkY~~D~~g~~ 44 (64)
T PF06322_consen 18 NQTEVARMLNCYRATVRKYARDKEGKK 44 (64)
T ss_pred CHHHHHHHHCCHHHHHHHHHCCCCCCE
T ss_conf 689887885101887997722556624
No 100
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain
Probab=33.59 E-value=13 Score=15.66 Aligned_cols=68 Identities=16% Similarity=0.150 Sum_probs=52.6
Q ss_pred CCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCH
Q ss_conf 89889999999999976498998881788789999858987899999999988791673178336862880
Q T0586 11 DKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK 81 (125)
Q Consensus 11 ~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~ 81 (125)
..|--++-+...+.-.....+.-...+ .+||..+|+++.++.--++...+-|+|....|.=+.+....
T Consensus 93 g~PtRe~F~~lYk~i~~~~~~~l~~~~---~~La~~l~~~~~~l~FMi~VF~EL~FVtiedG~i~~~~~~~ 160 (195)
T PF10141_consen 93 GMPTREQFAKLYKFIYQHPEFDLRKKL---MQLAKYLGWSKETLIFMIQVFFELGFVTIEDGVITVNKNPE 160 (195)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCHHHHH---HHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEECCCCC
T ss_conf 599899999999999967999878899---99988859799999999999987390797788886258856
No 101
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , . Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif . Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2p7v_B 1tlh_B 1tty_A 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F 2a69_F ....
Probab=33.52 E-value=2.5 Score=20.26 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=21.2
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 8817887899998589878999999999
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQEL 61 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L 61 (125)
.+.+ |..++|+.+|+|+.||+.-++.-
T Consensus 18 ~~~~-t~~eIa~~lg~s~~~V~~~~~ra 44 (50)
T PF04545_consen 18 FEGL-TLEEIAERLGISESTVRQRLKRA 44 (50)
T ss_dssp TST--CTCCCHHHHHHHHHHHHHHHHHH
T ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 4999-99999989797999998999999
No 102
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=33.30 E-value=9.5 Score=16.49 Aligned_cols=30 Identities=20% Similarity=0.169 Sum_probs=18.0
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf 8789999858987899999999988791673178
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG 72 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g 72 (125)
+..++|+.|+||+++|- .+...|.+-.+.+
T Consensus 16 t~~e~~~~~~vS~~sv~----~WvKNG~~p~~a~ 45 (186)
T PF04936_consen 16 TIDEIADYFDVSRASVS----LWVKNGKDPKKAN 45 (186)
T ss_pred CHHHHHHHHCCCHHHHH----HHHHCCCCCCCCC
T ss_conf 38999998756899999----9998388872334
No 103
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=31.12 E-value=14 Score=15.47 Aligned_cols=26 Identities=15% Similarity=0.351 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 178878999985898789999999998
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQELE 62 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~~L~ 62 (125)
++ |+.+||+.||..|.||.+=++-+.
T Consensus 1 ~~-nI~qla~~~glhRqTV~~Rl~~~~ 26 (152)
T PF07278_consen 1 KL-NINQLAELFGLHRQTVAKRLKGAN 26 (152)
T ss_pred CC-CHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf 98-799999998421999999970799
No 104
>PF09048 Cro: Cro; InterPro: IPR000655 Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change . Most Cro proteins, such as P22 Cro and phage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement . This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1cop_D 2a63_A 2ovg_A 1d1m_A 6cro_A 5cro_B 1orc_A 2ecs_B 1d1l_A 3orc_A ....
Probab=29.47 E-value=15 Score=15.22 Aligned_cols=23 Identities=17% Similarity=0.200 Sum_probs=19.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 87899998589878999999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQEL 61 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L 61 (125)
.....|+.|||+.+-|.+|++.=
T Consensus 14 GQak~A~~lGV~qsAISKairag 36 (59)
T PF09048_consen 14 GQAKAAKALGVTQSAISKAIRAG 36 (59)
T ss_dssp -HHHHHHH----HHHHHHHHH--
T ss_pred HHHHHHHHCCCCHHHHHHHHHHC
T ss_conf 67999998297689999999828
No 105
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing . Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity . ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2pjp_A 2uwm_B 2ply_A 1wsu_D 1lva_A.
Probab=28.86 E-value=15 Score=15.15 Aligned_cols=39 Identities=13% Similarity=0.166 Sum_probs=34.3
Q ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf 8881788789999858987899999999988791673178
Q T0586 33 GEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG 72 (125)
Q Consensus 33 ~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g 72 (125)
.+..+ +..++-+.+|.||-.+-.-+..|...|++.+..+
T Consensus 7 ~~~~i-~va~~rd~~g~sRK~ai~lLE~~D~~~~T~R~gd 45 (50)
T PF09107_consen 7 KNGEI-TVAEFRDALGLSRKYAIPLLEYFDREGITRRVGD 45 (50)
T ss_dssp T---B-EHHHHHHH----HHHHHHHHHHHHHTTSEEE---
T ss_pred CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEECC
T ss_conf 48957-2999999978539999999998750298786399
No 106
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=28.25 E-value=11 Score=16.15 Aligned_cols=39 Identities=26% Similarity=0.301 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf 1788789999858987899999999988791673178336
Q T0586 36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS 75 (125)
Q Consensus 36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~ 75 (125)
.+ |+.|+|..+++-.++||==+.-|.+.|+|..+.-...
T Consensus 55 p~-SVAEiAA~L~LPlgVvrVLl~DL~~~G~v~v~~p~~~ 93 (114)
T PF05331_consen 55 PL-SVAEIAAHLRLPLGVVRVLLSDLLDAGLVRVRAPVPS 93 (114)
T ss_pred CC-CHHHHHHHCCCCCCEEEEEHHHHHHCCCEEEECCCCC
T ss_conf 63-0999998619983011005776976897786079876
No 107
>PF10543 ORF6N: ORF6N domain
Probab=28.20 E-value=16 Score=15.08 Aligned_cols=41 Identities=7% Similarity=0.170 Sum_probs=30.8
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC-CCEEEECC
Q ss_conf 88178878999985898789999999998879167317-83368628
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR-GMGSFVTS 79 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~-g~G~~V~~ 79 (125)
|.+.-+..+||+.||+-..+++++++.=.+ +-+ |..+|.-.
T Consensus 9 g~~Vmt~~~lA~lyg~~~~~i~~~~~rN~~-----rF~eg~~~f~L~ 50 (88)
T PF10543_consen 9 GQRVMTDEDLAELYGVETKRINQNFKRNRD-----RFPEGDDYFQLT 50 (88)
T ss_pred CEEEEEHHHHHHHHCCCHHHHHHHHHHHHH-----HCCCCCEEEEEC
T ss_conf 978987999999959686799999997486-----378887599972
No 108
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=27.73 E-value=16 Score=15.02 Aligned_cols=38 Identities=21% Similarity=0.249 Sum_probs=28.2
Q ss_pred CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 89988817887899998589878999999999887916731783
Q T0586 30 EWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 30 ~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
.++..-++ .+-|++.+|+||+-+ +.|.+.|.|...+++
T Consensus 98 ~~~~~vRl--~~lLa~~L~LSrs~l----~~L~~~G~I~~~~~~ 135 (142)
T PF06353_consen 98 PFPFPVRL--DRLLAEELGLSRSRL----QRLIEQGKIRSDPGK 135 (142)
T ss_pred CCCCCCCH--HHHHHHHHCCCHHHH----HHHHHCCCEEECCCC
T ss_conf 78777529--999998838479999----999988977825740
No 109
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3bz6_A.
Probab=27.69 E-value=8.9 Score=16.69 Aligned_cols=34 Identities=26% Similarity=0.469 Sum_probs=28.5
Q ss_pred HCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCH
Q ss_conf 58987899999999988791673178336862880
Q T0586 47 LAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK 81 (125)
Q Consensus 47 ~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~ 81 (125)
+++|-+.|..|+..|...|++.. .+.|..|..-.
T Consensus 44 m~lse~eV~~ald~L~~~~Lv~~-~~~gsRv~ky~ 77 (148)
T PF04337_consen 44 MNLSESEVQQALDELRKKGLVRE-SGFGSRVPKYE 77 (148)
T ss_dssp ----------HHHHH-----EEE--E------EEE
T ss_pred CCCCHHHHHHHHHHHHHCCCEEE-CCCCCCHHHHH
T ss_conf 26789999999999997847001-26775148999
No 110
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD , , . Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution . TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1zk8_A 2oi8_A 2g7l_A 2opt_B 3b6a_F 3b6c_B 2hxo_A 2hxi_B 1z0x_B 1bjy_A ....
Probab=27.46 E-value=16 Score=14.99 Aligned_cols=24 Identities=13% Similarity=0.480 Sum_probs=19.5
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 8178878999985898789999999
Q T0586 35 DKLPSVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 35 ~~LPser~La~~~~VSr~TVr~Al~ 59 (125)
+.+ |.+++|+..|||++++-.-+.
T Consensus 15 ~~~-t~~~ia~~agvs~~~iy~~F~ 38 (47)
T PF00440_consen 15 EAV-TIRDIAERAGVSRGSIYRHFP 38 (47)
T ss_dssp TTS-SHHHHHHHHTSBHHHHHHHSS
T ss_pred CCC-CHHHHHHHHCCCCCCHHHHCC
T ss_conf 218-799999876479350256569
No 111
>PF01527 Transposase_8: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 . More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2rn7_A 2jn6_A.
Probab=27.33 E-value=6.9 Score=17.39 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=22.3
Q ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf 878999985898789999999998
Q T0586 39 SVREMGVKLAVNPNTVSRAYQELE 62 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~~L~ 62 (125)
|..++|..||||++|+..=.+...
T Consensus 25 s~~~va~~~gI~~~tl~~W~~~~~ 48 (76)
T PF01527_consen 25 SVSEVAREYGISPSTLYRWVRQYR 48 (76)
T ss_dssp HHHHHCCC----HHHHHHHHHHHH
T ss_pred CHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 799999970533026669999986
No 112
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=27.16 E-value=16 Score=14.96 Aligned_cols=32 Identities=25% Similarity=0.289 Sum_probs=24.6
Q ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf 9988817887899998589878999999999887
Q T0586 31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERA 64 (125)
Q Consensus 31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~ 64 (125)
|+.|. | +-.++|+.+||||.-|-++=+.-+.-
T Consensus 15 F~eG~-L-~D~eIA~~LGVsr~nV~kmR~Kwes~ 46 (181)
T PF04645_consen 15 FKEGS-L-NDAEIAQELGVSRVNVWKMRQKWESS 46 (181)
T ss_pred HHCCC-C-CHHHHHHHHCCHHHHHHHHHHHHHHC
T ss_conf 95388-7-57999999782199999999998813
No 113
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms . Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1nd9_A.
Probab=26.87 E-value=15 Score=15.19 Aligned_cols=36 Identities=17% Similarity=0.320 Sum_probs=23.2
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf 817887899998589878999999999887916731783
Q T0586 35 DKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM 73 (125)
Q Consensus 35 ~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~ 73 (125)
+++ ++.+||+.+|++...+-+.+. .+.|+-...+++
T Consensus 2 ~~~-rV~elAk~l~~~~~~ii~~L~--~~~Gi~~~~~~~ 37 (54)
T PF04760_consen 2 EKI-RVYELAKELGVSSKEIIKKLF--KELGIMVKSHNS 37 (54)
T ss_dssp -EE--TTHHHHHHSSSHHHHHHHH---HH------SSSS
T ss_pred CCE-EHHHHHHHHCCCHHHHHHHHH--HHCCCCCCCCCC
T ss_conf 953-699999998929999999999--968955466357
No 114
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) . Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 ; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 , ; Arabidopsis COP9 and FUS6/COP11 ; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; PDB: 1ufm_A 3chm_A.
Probab=26.60 E-value=2.9 Score=19.92 Aligned_cols=64 Identities=20% Similarity=0.278 Sum_probs=47.0
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC--CCCEEEE
Q ss_conf 8899999999999764989988817887899998589878999999999887916731--7833686
Q T0586 13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK--RGMGSFV 77 (125)
Q Consensus 13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~--~g~G~~V 77 (125)
++.+++...+....+..-+++.+.+ +...+|+.++++...|-..+..+...|.|..+ +..|+.+
T Consensus 37 ~~~~~l~~~i~~~~l~~~~~~y~~i-~~~~ia~~l~~~~~~vE~~l~~lI~~g~i~~~ID~~~~~v~ 102 (105)
T PF01399_consen 37 QYVEQLKQKIRRRLLRQLSKPYSSI-SISEIAKALQISEEEVEKILINLISSGRIKAKIDQVNGVVV 102 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHC-SEE-ECCCHHHHCTS-CHHHHHHHHCCCC---EE-EEETTTTEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEE
T ss_conf 9999999999999999999983778-89999875099878999999999986997999978999897
No 115
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; PDB: 3f2f_A 3f0p_B 3f0o_B 3f2g_A 3fn8_A 3f2h_B 1s6l_A.
Probab=23.91 E-value=16 Score=15.03 Aligned_cols=32 Identities=9% Similarity=0.112 Sum_probs=27.3
Q ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf 998881788789999858987899999999988
Q T0586 31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELER 63 (125)
Q Consensus 31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~ 63 (125)
|.-|... |+.+||...|.+...|+.++..+.+
T Consensus 33 LA~G~PV-t~~~LA~atG~~ve~V~~~L~~~p~ 64 (77)
T PF12324_consen 33 LADGRPV-TVETLAAATGWPVEEVRAALAQMPD 64 (77)
T ss_dssp HT----B--HHHH-------HHHHHHHHHH-TT
T ss_pred HHCCCCC-CHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 9768982-6999999979899999999985768
No 116
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known , . The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 1ust_A 1uhm_A 1uss_A 1yqa_A 1ghc_A 1hst_A.
Probab=23.31 E-value=19 Score=14.50 Aligned_cols=60 Identities=15% Similarity=0.322 Sum_probs=41.1
Q ss_pred CHHHHHHHHHHHHHHCCCCCCCCCCCCHH-HHHHHHC--CCH----HHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf 88999999999997649899888178878-9999858--987----899999999988791673178336
Q T0586 13 PIYSQISDWMKKQMITGEWKGEDKLPSVR-EMGVKLA--VNP----NTVSRAYQELERAGYIYAKRGMGS 75 (125)
Q Consensus 13 Ply~qI~~~l~~~I~~G~l~~G~~LPser-~La~~~~--VSr----~TVr~Al~~L~~~G~i~~~~g~G~ 75 (125)
|-|.+ -|.+.|..-.=+.|.-+++.. -+.+.|+ +.. .-++.|++.+.+.|.+....|.|.
T Consensus 3 P~y~~---MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~q~kG~G~ 69 (77)
T PF00538_consen 3 PPYSE---MILEAITALKERKGSSRQAIKKYIESNYPVDLPPSNFKSLLKKALKKLVEKGKLVQVKGTGA 69 (77)
T ss_dssp --HHH---HHHHHHHTTTTT---THHHHHHHHHHHSTTSSSHTTHHHHHHHHHHHHHH---EEE------
T ss_pred CCHHH---HHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf 98899---99999997588799799999999998657788768899999999999986895787403688
No 117
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein . This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1in7_A 1in5_A 1j7k_A 1in8_A 1in6_A 1in4_A 1ixr_C 1ixs_B 1hqc_A.
Probab=23.28 E-value=19 Score=14.49 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=37.3
Q ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHH-HHHHCCEEEECCCCEEEECCC
Q ss_conf 88178878999985898789999999-998879167317833686288
Q T0586 34 EDKLPSVREMGVKLAVNPNTVSRAYQ-ELERAGYIYAKRGMGSFVTSD 80 (125)
Q Consensus 34 G~~LPser~La~~~~VSr~TVr~Al~-~L~~~G~i~~~~g~G~~V~~~ 80 (125)
|-.. +...||..+|..+.|+-..|. .|-+.|+|.+.| +|-.++..
T Consensus 23 ggPV-Gl~tlA~~l~e~~~TiEdv~EPyLiq~g~i~RTp-RGR~~T~~ 68 (76)
T PF05491_consen 23 GGPV-GLDTLAAALGEERDTIEDVIEPYLIQIGFIERTP-RGRVATPK 68 (76)
T ss_dssp -------HHHHHHTTS-HHHHHHCTHHHHHH---EE-------EE-HH
T ss_pred CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHH
T ss_conf 9871-0999999987986089998518999960686388-55887899
No 118
>PF07514 TraI_2: Putative helicase; InterPro: IPR011119 The members of this family are restricted to the proteobacteria. Some members have been annotated as helicase, conjugative relaxase or nickase. The majority contain an HD domain, which is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in the nucleic acid metabolism, signal transduction and possibly other functions in bacteria.
Probab=23.25 E-value=19 Score=14.49 Aligned_cols=59 Identities=12% Similarity=0.097 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHH-HCCCCCCCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCEE
Q ss_conf 888988999999999997-64989988817-887899998589878999999999887916
Q T0586 9 HADKPIYSQISDWMKKQM-ITGEWKGEDKL-PSVREMGVKLAVNPNTVSRAYQELERAGYI 67 (125)
Q Consensus 9 ~~~~Ply~qI~~~l~~~I-~~G~l~~G~~L-Pser~La~~~~VSr~TVr~Al~~L~~~G~i 67 (125)
....|+.+++.+.|+..| ..+.|++.+.= +.=-.=-..|=||++++.+....|..+|+-
T Consensus 239 ~~~~~l~~~l~~alR~ll~~~~~~~~n~~~~~~w~~~d~l~lv~k~~~d~ir~~l~~~g~~ 299 (327)
T PF07514_consen 239 APGVPLERYLLDALRRLLSEEGKWNINEPGSDGWLTQDGLWLVWKTAADDIRAHLLSQGID 299 (327)
T ss_pred CCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCEEEEEEHHHHHHHHHHHHHCCCC
T ss_conf 8898689999999999985168668899998844736826998302699999999972998
No 119
>PF06530 Phage_antitermQ: Phage antitermination protein Q; InterPro: IPR010534 This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream .; GO: 0003677 DNA binding, 0030401 transcription antiterminator activity, 0045449 regulation of transcription
Probab=23.20 E-value=19 Score=14.48 Aligned_cols=21 Identities=24% Similarity=0.343 Sum_probs=13.7
Q ss_pred CHHHHHHHHCCCHHHHHHHHH
Q ss_conf 878999985898789999999
Q T0586 39 SVREMGVKLAVNPNTVSRAYQ 59 (125)
Q Consensus 39 ser~La~~~~VSr~TVr~Al~ 59 (125)
|.+.+|..+++|..+||+=++
T Consensus 80 s~r~IAr~~~~s~~~ir~~l~ 100 (125)
T PF06530_consen 80 SKRAIARKLKCSEGKIRKMLQ 100 (125)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
T ss_conf 899999996888889999999
No 120
>PF09904 DUF2131: Uncharacterized protein conserved in bacteria (DUF2131)
Probab=21.34 E-value=21 Score=14.24 Aligned_cols=39 Identities=13% Similarity=0.140 Sum_probs=32.5
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHCCEEEE------CCCCEEEECCC
Q ss_conf 9999858987899999999988791673------17833686288
Q T0586 42 EMGVKLAVNPNTVSRAYQELERAGYIYA------KRGMGSFVTSD 80 (125)
Q Consensus 42 ~La~~~~VSr~TVr~Al~~L~~~G~i~~------~~g~G~~V~~~ 80 (125)
.|.+.-|.-|-|++.+++.|.+-|+.-. +.+.|+|.-.+
T Consensus 3 ~l~~~TGmPRRT~QDti~AL~dlgI~~~FvQ~G~Rn~~G~Y~i~~ 47 (67)
T PF09904_consen 3 SLMELTGMPRRTAQDTIAALPDLGIECEFVQDGERNNAGYYRIRD 47 (67)
T ss_pred HHHHHHCCCHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCEEEEE
T ss_conf 177652886747999998601488189997546316787488742
No 121
>PF10771 DUF2582: Protein of unknown function (DUF2582)
Probab=20.84 E-value=21 Score=14.17 Aligned_cols=45 Identities=16% Similarity=0.150 Sum_probs=38.2
Q ss_pred CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf 9988817887899998589878999999999887916731783368
Q T0586 31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF 76 (125)
Q Consensus 31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~ 76 (125)
|.....+ |..+|++..|.+..-+--|+--|..|+=|......|..
T Consensus 17 L~e~~~~-s~~~Lkk~~~l~~~~~~~AiGWLarE~KI~~~~~~~~~ 61 (65)
T PF10771_consen 17 LNENGEW-SYKELKKATGLSDKELALAIGWLARENKIEFEEKNGEL 61 (65)
T ss_pred HCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEECCCEE
T ss_conf 7338878-89999988498989999988888516716787308878
Done!