Query T0617 3NRV, Acinetobacter sp. ADP1, 148 residues
Match_columns 148
No_of_seqs 131 out of 6702
Neff 8.8
Searched_HMMs 11830
Date Mon Jul 5 09:09:33 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0617.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0617.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01047 MarR: MarR family; I 99.1 4.4E-11 3.7E-15 90.9 4.4 59 38-96 1-59 (59)
2 PF03965 Pencillinase_R: Penic 98.4 3.8E-07 3.2E-11 64.7 8.3 100 38-140 1-115 (115)
3 PF01978 TrmB: Sugar-specific 98.1 1.4E-06 1.2E-10 61.0 4.3 57 34-90 2-58 (68)
4 PF01638 HxlR: HxlR-like helix 98.0 1.7E-06 1.4E-10 60.4 3.4 76 44-121 9-85 (90)
5 PF01726 LexA_DNA_bind: LexA D 97.4 4.9E-05 4.1E-09 50.6 4.2 54 37-90 3-62 (65)
6 PF01325 Fe_dep_repress: Iron 97.4 5.8E-05 4.9E-09 50.2 4.2 40 51-90 19-58 (60)
7 PF03551 PadR: Transcriptional 97.3 5.1E-05 4.3E-09 50.5 2.8 70 40-110 6-85 (86)
8 PF09339 HTH_IclR: IclR helix- 97.1 0.00011 9.7E-09 48.2 2.8 47 42-88 5-52 (52)
9 PF01022 HTH_5: Bacterial regu 97.1 0.00022 1.8E-08 46.3 4.2 46 40-86 2-47 (47)
10 PF03428 RP-C: Replication pro 97.1 0.01 8.7E-07 35.2 12.6 64 33-96 36-113 (177)
11 PF04182 B-block_TFIIIC: B-blo 96.9 0.00035 3E-08 44.9 4.1 52 39-90 1-54 (75)
12 PF03444 DUF293: Domain of unk 96.6 0.0035 3E-07 38.3 7.1 68 38-109 2-74 (78)
13 PF02082 Rrf2: Transcriptional 96.3 0.0018 1.5E-07 40.3 4.4 51 42-92 10-63 (83)
14 PF10007 DUF2250: Uncharacteri 96.3 0.0034 2.9E-07 38.4 5.6 74 37-110 4-91 (92)
15 PF08220 HTH_DeoR: DeoR-like h 96.1 0.0024 2E-07 39.4 4.1 48 42-89 2-49 (57)
16 PF04703 FaeA: FaeA-like prote 95.7 0.0034 2.9E-07 38.4 3.5 46 44-89 4-50 (62)
17 PF01418 HTH_6: Helix-turn-hel 95.4 0.009 7.6E-07 35.6 4.8 56 36-91 12-71 (107)
18 PF00126 HTH_1: Bacterial regu 95.4 0.012 1E-06 34.8 5.3 59 41-105 2-60 (60)
19 PF09012 FeoC: FeoC like trans 95.4 0.0026 2.2E-07 39.2 1.8 50 44-93 4-53 (69)
20 PF09202 Rio2_N: Rio2, N-termi 95.4 0.012 1E-06 34.7 5.3 68 38-109 4-75 (82)
21 PF08279 HTH_11: HTH domain; 95.3 0.01 8.4E-07 35.3 4.8 41 42-82 2-43 (55)
22 PF05732 RepL: Firmicute plasm 95.1 0.0083 7E-07 35.8 3.8 60 38-103 53-118 (165)
23 PF04967 HTH_10: HTH DNA bindi 94.8 0.024 2E-06 32.8 5.5 44 38-81 1-50 (53)
24 PF00325 Crp: Bacterial regula 94.3 0.0076 6.4E-07 36.1 2.0 31 54-84 2-32 (32)
25 PF07037 DUF1323: Putative tra 94.3 0.097 8.2E-06 28.7 7.6 83 55-140 1-107 (122)
26 PF07381 DUF1495: Winged helix 94.1 0.056 4.7E-06 30.3 6.1 68 40-110 9-89 (90)
27 PF08784 RPA_C: Replication pr 94.0 0.03 2.5E-06 32.1 4.5 54 37-90 44-101 (102)
28 PF01090 Ribosomal_S19e: Ribos 94.0 0.049 4.1E-06 30.7 5.6 65 45-115 57-135 (139)
29 PF02002 TFIIE_alpha: TFIIE al 93.8 0.015 1.2E-06 34.2 2.6 59 38-96 11-69 (105)
30 PF05158 RNA_pol_Rpc34: RNA po 93.7 0.015 1.3E-06 34.0 2.7 64 37-100 82-147 (325)
31 PF08461 HTH_12: Ribonuclease 93.7 0.039 3.3E-06 31.3 4.7 58 44-107 2-65 (66)
32 PF09114 MotA_activ: Transcrip 93.6 0.05 4.3E-06 30.6 5.1 73 38-117 14-88 (96)
33 PF07848 PaaX: PaaX-like prote 93.5 0.012 1E-06 34.8 1.8 53 49-104 14-70 (70)
34 PF04079 DUF387: Putative tran 93.4 0.015 1.3E-06 34.0 2.2 69 37-108 79-148 (159)
35 PF05584 Sulfolobus_pRN: Sulfo 93.4 0.038 3.2E-06 31.4 4.2 53 44-97 9-61 (72)
36 PF04492 Phage_rep_O: Bacterio 93.1 0.08 6.7E-06 29.3 5.5 53 36-88 28-88 (100)
37 PF06163 DUF977: Bacterial pro 92.9 0.11 9E-06 28.4 5.9 84 43-134 15-98 (127)
38 PF04297 UPF0122: Putative hel 92.8 0.075 6.4E-06 29.4 5.0 43 38-81 18-60 (101)
39 PF00196 GerE: Bacterial regul 92.4 0.088 7.4E-06 29.0 4.9 43 37-81 3-45 (58)
40 PF00392 GntR: Bacterial regul 92.3 0.033 2.8E-06 31.8 2.6 37 54-90 23-60 (64)
41 PF01475 FUR: Ferric uptake re 90.7 0.057 4.8E-06 30.2 2.5 55 38-92 6-66 (120)
42 PF02001 DUF134: Protein of un 90.2 0.19 1.6E-05 26.7 4.8 49 36-85 40-91 (106)
43 PF05043 Mga: Mga helix-turn-h 89.3 0.29 2.5E-05 25.5 5.2 41 40-80 16-56 (87)
44 PF01710 Transposase_14: Trans 89.1 0.15 1.3E-05 27.4 3.6 32 53-85 17-48 (119)
45 PF02796 HTH_7: Helix-turn-hel 88.4 0.12 1E-05 28.1 2.7 39 37-76 5-43 (45)
46 PF05491 RuvB_C: Holliday junc 87.7 0.21 1.8E-05 26.5 3.6 67 35-108 3-73 (76)
47 PF11313 DUF3116: Protein of u 86.9 0.83 7E-05 22.5 6.3 60 51-113 17-83 (85)
48 PF08222 HTH_CodY: CodY helix- 86.8 0.076 6.5E-06 29.4 0.9 39 52-90 2-40 (61)
49 PF07750 GcrA: GcrA cell cycle 86.3 0.38 3.2E-05 24.7 4.3 47 39-89 4-51 (162)
50 PF09756 DDRGK: DDRGK domain; 86.3 0.26 2.2E-05 25.8 3.4 68 43-113 102-169 (188)
51 PF08281 Sigma70_r4_2: Sigma-7 86.0 0.47 3.9E-05 24.1 4.6 43 37-80 10-52 (54)
52 PF00292 PAX: 'Paired box' dom 86.0 0.37 3.1E-05 24.8 4.1 72 37-112 17-88 (125)
53 PF07106 TBPIP: Tat binding pr 86.0 0.92 7.7E-05 22.2 7.2 55 42-99 3-60 (169)
54 PF02295 z-alpha: Adenosine de 85.5 0.16 1.3E-05 27.3 1.9 49 41-89 5-55 (66)
55 PF07900 DUF1670: Protein of u 85.3 0.99 8.4E-05 22.0 9.1 52 34-85 80-137 (220)
56 PF04218 CENP-B_N: CENP-B N-te 85.1 0.22 1.8E-05 26.4 2.5 41 37-78 6-46 (53)
57 PF03297 Ribosomal_S25: S25 ri 84.6 0.36 3.1E-05 24.9 3.5 50 38-87 42-92 (105)
58 PF08280 HTH_Mga: M protein tr 83.7 0.87 7.4E-05 22.3 5.1 42 40-81 5-46 (59)
59 PF04545 Sigma70_r4: Sigma-70, 83.1 0.2 1.7E-05 26.6 1.7 43 37-80 4-46 (50)
60 PF00888 Cullin: Cullin family 83.0 0.14 1.2E-05 27.5 0.9 53 38-90 519-571 (589)
61 PF01131 Topoisom_bac: DNA top 82.1 0.31 2.6E-05 25.3 2.3 51 56-112 317-371 (404)
62 PF11994 DUF3489: Protein of u 81.9 0.98 8.3E-05 22.0 4.8 61 39-100 9-71 (72)
63 PF09821 ABC_transp: ABC nitra 81.9 0.9 7.6E-05 22.2 4.6 58 59-123 2-59 (120)
64 PF04157 EAP30: EAP30/Vps36 fa 81.7 0.63 5.3E-05 23.3 3.8 40 65-105 132-171 (223)
65 PF09397 Ftsk_gamma: Ftsk gamm 81.6 0.71 6E-05 22.9 4.0 53 44-97 10-62 (65)
66 PF00356 LacI: Bacterial regul 81.1 0.34 2.9E-05 25.0 2.3 22 56-77 1-22 (46)
67 PF08221 HTH_9: RNA polymerase 80.5 0.95 8.1E-05 22.1 4.4 48 39-86 12-59 (62)
68 PF04552 Sigma54_DBD: Sigma-54 80.4 0.14 1.2E-05 27.7 0.0 28 50-77 45-72 (160)
69 PF10711 DUF2513: Hypothetical 80.3 0.62 5.3E-05 23.3 3.4 69 45-113 10-82 (102)
70 PF05331 DUF742: Protein of un 80.2 0.69 5.8E-05 23.0 3.6 55 36-92 39-93 (114)
71 PF06969 HemN_C: HemN C-termin 79.6 0.82 7E-05 22.5 3.8 61 38-105 53-117 (118)
72 PF01371 Trp_repressor: Trp re 76.8 0.55 4.6E-05 23.7 2.2 42 38-79 27-74 (87)
73 PF08535 KorB: KorB domain; I 75.8 1.1 9E-05 21.8 3.4 80 53-140 2-88 (93)
74 PF03374 ANT: Phage antirepres 75.6 2.1 0.00018 19.8 5.5 65 46-113 16-106 (111)
75 PF07638 Sigma70_ECF: ECF sigm 75.0 2.1 0.00018 19.7 6.1 23 116-138 142-164 (185)
76 PF09862 DUF2089: Protein of u 74.6 1.7 0.00014 20.4 4.3 45 37-83 33-79 (113)
77 PF01381 HTH_3: Helix-turn-hel 74.4 0.73 6.2E-05 22.8 2.3 30 48-77 3-32 (55)
78 PF09382 RQC: RQC domain; PDB: 74.1 0.76 6.4E-05 22.7 2.4 45 64-110 52-96 (106)
79 PF02387 IncFII_repA: IncFII R 72.5 2 0.00017 19.9 4.2 55 54-108 95-163 (281)
80 PF10668 Phage_terminase: Phag 70.7 1.2 0.0001 21.4 2.7 28 47-74 15-42 (60)
81 PF04458 DUF505: Protein of un 67.8 3.1 0.00026 18.7 5.7 75 35-111 282-370 (591)
82 PF06056 Terminase_5: Putative 65.0 1.7 0.00014 20.5 2.5 33 53-85 12-44 (58)
83 PF06413 Neugrin: Neugrin; In 64.8 3.5 0.0003 18.3 4.3 40 38-77 11-52 (225)
84 PF01498 Transposase_5: Transp 63.3 2 0.00017 19.9 2.7 55 44-107 3-62 (72)
85 PF08721 TnsA_C: TnsA endonucl 63.0 3.5 0.0003 18.3 3.9 42 44-85 31-76 (79)
86 PF11972 HTH_13: HTH DNA bindi 62.6 3.8 0.00032 18.1 3.9 36 45-80 4-39 (54)
87 PF02954 HTH_8: Bacterial regu 61.6 4 0.00034 17.9 4.3 34 44-78 9-42 (42)
88 PF07506 RepB: RepB plasmid pa 60.5 4.2 0.00036 17.8 4.6 40 37-76 4-43 (185)
89 PF06224 DUF1006: Protein of u 59.4 4.4 0.00037 17.7 4.6 60 42-103 121-186 (371)
90 PF09107 SelB-wing_3: Elongati 58.9 3 0.00025 18.8 2.9 44 46-89 2-45 (50)
91 PF10654 DUF2481: Protein of u 57.5 2.8 0.00024 19.0 2.6 37 37-77 67-103 (126)
92 PF07278 DUF1441: Protein of u 56.7 4.9 0.00041 17.4 8.3 81 55-135 2-99 (152)
93 PF09048 Cro: Cro; InterPro: 54.8 3 0.00026 18.7 2.4 27 48-77 9-35 (59)
94 PF01316 Arg_repressor: Argini 53.4 5 0.00042 17.3 3.3 46 41-90 6-56 (70)
95 PF04337 DUF480: Protein of un 53.1 3.8 0.00032 18.1 2.6 46 63-110 43-96 (148)
96 PF03501 S10_plectin: Plectin/ 52.7 4.2 0.00035 17.8 2.8 46 64-112 33-78 (95)
97 PF00165 HTH_AraC: Bacterial r 52.2 4.1 0.00034 17.9 2.7 27 52-78 6-32 (42)
98 PF00440 TetR_N: Bacterial reg 51.4 5.5 0.00046 17.0 3.2 31 46-76 6-38 (47)
99 PF11855 DUF3375: Protein of u 49.8 6.2 0.00053 16.6 6.5 47 67-114 64-112 (478)
100 PF00376 MerR: MerR family reg 47.5 3.6 0.00031 18.2 1.8 33 56-92 1-34 (38)
101 PF08100 Dimerisation: Dimeris 46.9 5.5 0.00047 17.0 2.7 38 42-79 8-47 (51)
102 PF02650 HTH_WhiA: Sporulation 46.8 6.9 0.00058 16.3 9.3 43 38-80 143-187 (190)
103 PF05269 Phage_CII: Bacterioph 46.3 5.9 0.00049 16.8 2.7 31 42-75 14-44 (91)
104 PF07022 Phage_CI_repr: Bacter 46.1 3.2 0.00027 18.6 1.4 33 45-77 2-36 (66)
105 PF06242 DUF1013: Protein of u 45.4 7.2 0.00061 16.2 3.1 33 44-76 73-105 (140)
106 PF01527 Transposase_8: Transp 43.0 2.1 0.00018 19.8 0.1 32 48-79 17-48 (76)
107 PF03811 Ins_element1: Inserti 43.0 5.9 0.0005 16.8 2.4 25 53-77 62-86 (88)
108 PF10557 Cullin_Nedd8: Cullin 42.7 2.4 0.0002 19.4 0.3 29 63-91 39-67 (68)
109 PF09669 Phage_pRha: Phage reg 41.4 8.3 0.0007 15.8 4.0 56 55-110 2-67 (92)
110 PF10771 DUF2582: Protein of u 40.5 8.6 0.00073 15.7 3.8 50 38-87 6-55 (65)
111 PF09079 Cdc6_C: CDC6, C termi 39.7 7.1 0.0006 16.3 2.3 49 59-107 27-81 (85)
112 PF12324 HTH_15: Helix-turn-he 39.4 5.1 0.00043 17.2 1.5 38 43-80 27-64 (77)
113 PF09940 DUF2172: Domain of un 38.9 9.1 0.00077 15.6 4.6 43 43-85 343-386 (386)
114 PF12116 SpoIIID: Stage III sp 38.0 8.8 0.00074 15.6 2.6 32 47-79 13-45 (82)
115 PF03962 Mnd1: Mnd1 family; I 36.2 10 0.00084 15.3 8.1 62 46-108 2-68 (188)
116 PF05930 Phage_AlpA: Prophage 35.7 6.4 0.00054 16.6 1.6 22 55-76 4-25 (51)
117 PF05225 HTH_psq: helix-turn-h 35.2 10 0.00088 15.2 3.2 32 46-78 9-40 (45)
118 PF07574 SMC_Nse1: Nse1 non-SM 34.8 6.7 0.00057 16.4 1.6 43 57-105 155-197 (200)
119 PF10141 ssDNA-exonuc_C: Singl 34.2 11 0.00091 15.1 5.2 55 32-87 90-149 (195)
120 PF09681 Phage_rep_org_N: N-te 33.9 11 0.00092 15.0 2.7 35 52-86 51-85 (121)
121 PF03333 PapB: Adhesin biosynt 33.7 11 0.00092 15.0 5.0 48 37-84 22-83 (91)
122 PF08299 Bac_DnaA_C: domain; 32.7 6.9 0.00058 16.4 1.3 40 38-77 29-69 (70)
123 PF06970 RepA_N: Replication i 31.3 8.5 0.00072 15.7 1.6 24 55-78 53-76 (76)
124 PF04645 DUF603: Protein of un 30.8 12 0.001 14.7 3.7 35 49-83 14-48 (181)
125 PF08765 Mor: Mor transcriptio 30.1 12 0.0011 14.6 4.1 38 50-87 68-105 (108)
126 PF09639 YjcQ: YjcQ protein; P 29.6 12 0.00098 14.8 2.1 45 69-113 25-72 (88)
127 PF07471 Phage_Nu1: Phage DNA 28.9 5 0.00042 17.3 0.1 23 55-77 3-25 (164)
128 PF08278 DnaG_DnaB_bind: DNA p 28.3 13 0.0011 14.4 5.8 85 47-138 41-127 (127)
129 PF09106 SelB-wing_2: Elongati 27.9 14 0.0011 14.4 2.4 38 52-89 15-55 (59)
130 PF06971 Put_DNA-bind_N: Putat 27.9 7.8 0.00066 16.0 1.0 32 42-73 14-47 (50)
131 PF02319 E2F_TDP: E2F/DP famil 26.8 14 0.0012 14.4 2.0 37 52-88 23-66 (74)
132 PF09170 DUF1879: Domain of un 26.4 14 0.0012 14.2 3.0 42 73-117 109-150 (174)
133 PF07789 DUF1627: Protein of u 26.4 13 0.0011 14.5 1.9 41 49-89 1-41 (155)
134 PF03849 Tfb2: Transcription f 26.2 15 0.0012 14.2 6.9 68 40-109 31-99 (366)
135 PF04433 SWIRM: SWIRM domain; 25.8 15 0.0012 14.1 5.2 56 30-85 20-83 (84)
136 PF03882 KicB: KicB killing fa 24.5 14 0.0012 14.3 1.7 42 69-110 72-113 (440)
137 PF02540 NAD_synthase: NAD syn 23.7 16 0.0014 13.9 5.2 12 57-68 159-170 (242)
138 PF11662 DUF3263: Protein of u 22.7 17 0.0014 13.7 4.9 47 37-83 2-51 (77)
139 PF07453 NUMOD1: NUMOD1 domain 22.3 15 0.0013 14.1 1.5 20 55-74 17-36 (37)
140 PF04936 DUF658: Protein of un 21.8 18 0.0015 13.6 2.1 20 55-74 15-34 (186)
No 1
>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=99.06 E-value=4.4e-11 Score=90.95 Aligned_cols=59 Identities=31% Similarity=0.554 Sum_probs=57.4
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEE
Q ss_conf 99989999999970889998899998658901145899999984132125674322300
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTY 96 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~ 96 (148)
||..||.+|..|+..|++++++||+.++++++++|+++++|+++|||++.++|.|+|.+
T Consensus 1 lt~~q~~iL~~l~~~~~~t~~~la~~l~~~~~~vs~~i~~L~~~glI~r~~~~~D~R~v 59 (59)
T PF01047_consen 1 LTPSQFRILRILYENPGMTQSELAERLGISKSTVSRIIKRLEKKGLIEREPDPEDRRSV 59 (59)
T ss_dssp STHHHHHHHHHHHHSSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETTCE
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf 98999999999998799899999999886873899999999988987872899898939
No 2
>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=98.45 E-value=3.8e-07 Score=64.70 Aligned_cols=100 Identities=20% Similarity=0.226 Sum_probs=77.5
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCC----CCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHH-
Q ss_conf 999899999999708899988999986589----011458999999841321256743223000001788899999999-
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILGLD----KAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVAS- 112 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~i~----~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~- 112 (148)
||..++.||.+||.+|++|+++|.+.+.-+ ++||...+++|+++|||++... +|...+..+-.-.++.....
T Consensus 1 Ls~~E~~IM~~lW~~~~~t~~ei~~~l~~~~~~~~sTV~t~L~rL~eKg~l~~~~~---gr~~~Y~~~i~~~e~~~~~~~ 77 (115)
T PF03965_consen 1 LSDLELEIMEILWEHGPITVREIVEELKEDRDWSYSTVQTLLNRLVEKGLLTREKI---GRAYIYSPLISREEYLRQELK 77 (115)
T ss_dssp --HHHHHHHHHHHCHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE---TTCEEEEESSSHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEC---CCCEEEEECCCHHHHHHHHHH
T ss_conf 98899999999995799779999999861316418789999999998898577713---884588747889999999999
Q ss_pred HH--------HHHHHHHHHHC--CCHHHHHHHHHHHHH
Q ss_conf 99--------99999999857--999899999999999
Q T0617 113 DF--------AIEREKQLLEE--FEEAEKDQLFILLKK 140 (148)
Q Consensus 113 ~~--------~~~~~~~~~~~--l~~ee~~~l~~~L~~ 140 (148)
.. .......+++. ++++|++.+.+++++
T Consensus 78 ~~l~~~~~gs~~~ll~~l~~~~~ls~~el~~L~~~i~e 115 (115)
T PF03965_consen 78 QLLDRFFDGSLSALLAALLDEEELSPEELEELRKLIDE 115 (115)
T ss_dssp HHHHHHS---HHHHHHHHHHCT-S-HHHHHHHHHHHH-
T ss_pred HHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHC
T ss_conf 99999868899999999985679999999999999709
No 3
>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=98.07 E-value=1.4e-06 Score=61.00 Aligned_cols=57 Identities=28% Similarity=0.448 Sum_probs=53.7
Q ss_pred HHCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 872899989999999970889998899998658901145899999984132125674
Q T0617 34 QKFGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 34 ~~~glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
+.+||+..++.++..|..+|+.|+.+|++.++++++++++.+++|+++|+|++....
T Consensus 2 ~~~GLs~~e~~v~~~L~~~~~~t~~eia~~~~i~~~~v~~~l~~L~~~GlV~~~~~~ 58 (68)
T PF01978_consen 2 QKLGLSEYEAKVYLALLENGGATASEIAEKLGISRSTVYRILKRLEEKGLVEREKGK 58 (68)
T ss_dssp HHCT--HHHHHHHHHHHHTS-EEHHHHHHHHT--HHHHHHHHHHHHH---EEEEE--
T ss_pred CCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 758939999999999995799599999999890999999999999988998997685
No 4
>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=97.98 E-value=1.7e-06 Score=60.36 Aligned_cols=76 Identities=24% Similarity=0.317 Sum_probs=64.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHH-CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999708899988999986-589011458999999841321256743223000001788899999999999999999
Q T0617 44 RIISVLSSASDCSVQKISDIL-GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQ 121 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l-~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~~~~~~~ 121 (148)
.||..|.. |+...++|.+.+ ++++..+|..++.|++.|+|+|...+.....+.+.||++|+++.+-+.+. ..|-++
T Consensus 9 ~Il~~L~~-g~~rf~el~~~l~gis~~~Ls~rL~~Le~~glv~r~~~~~~p~~v~Y~LT~~G~~l~~~l~~l-~~W~~~ 85 (90)
T PF01638_consen 9 LILRELFD-GPKRFNELQRSLPGISPKVLSQRLKELEENGLVERRVYPEVPPRVEYSLTEKGKDLLPILEAL-IEWGEK 85 (90)
T ss_dssp HHHHHHCT-S-EEHHHHHHH-TTS-HHHHHHHHHHHHH---EEEEEE-SSS-EEEEEE-----CCHHHHHHH-HHHHHH
T ss_pred HHHHHHHC-CCCCHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEECCCCHHHHHHHHHHH-HHHHHH
T ss_conf 99999972-998899999774055777899999999977881465448999865475681699999999999-999999
No 5
>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=97.44 E-value=4.9e-05 Score=50.65 Aligned_cols=54 Identities=22% Similarity=0.393 Sum_probs=47.1
Q ss_pred CCCHHHHHHHHHHHH----CC-CCCHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 899989999999970----88-99988999986589-01145899999984132125674
Q T0617 37 GIGMTEWRIISVLSS----AS-DCSVQKISDILGLD-KAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 37 glt~~q~~iL~~l~~----~~-~~t~~eLa~~l~i~-~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
+||..|-.||.+|.. +| +.|+.||++.+|+. +++|...++.|+++|||++.+..
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEI~~~~gl~S~~tV~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 3 PLTPRQQEVLDFIKDYIREHGYPPTVREIAEALGLKSPSTVHKHLKALEKKGYITRDPGK 62 (65)
T ss_dssp ---HHHHHHHHHHHHHHHH------HHHHHHH----SHHHHHHHHHHHHH---EE-----
T ss_pred CCCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCEECCCCC
T ss_conf 679999999999999999838898899999881999809999999999998295168999
No 6
>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=97.41 E-value=5.8e-05 Score=50.15 Aligned_cols=40 Identities=30% Similarity=0.421 Sum_probs=36.8
Q ss_pred HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 0889998899998658901145899999984132125674
Q T0617 51 SASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 51 ~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
..++.+.++||+.+++++++||.++++|.+.|||...+..
T Consensus 19 ~~~~v~~~~IA~~L~vs~~TVs~ml~kL~~~Glv~~~~y~ 58 (60)
T PF01325_consen 19 EGGPVSTSDIAERLGVSPPTVSEMLKKLEEEGLVEYEKYG 58 (60)
T ss_dssp H-S--BHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTS
T ss_pred CCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCC
T ss_conf 6997219999999789907899999999988998851469
No 7
>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=97.30 E-value=5.1e-05 Score=50.52 Aligned_cols=70 Identities=23% Similarity=0.255 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHH--------CCCCCHHHHHHHHHHHHHHHHCCCCC--CCCCEECCCCCHHHHHHHH
Q ss_conf 9899999999708899988999986--------58901145899999984132125674--3223000001788899999
Q T0617 40 MTEWRIISVLSSASDCSVQKISDIL--------GLDKAAVSRTVKKLEEKKYIEVNGHS--EDKRTYAINLTEMGQELYE 109 (148)
Q Consensus 40 ~~q~~iL~~l~~~~~~t~~eLa~~l--------~i~~~~vs~~i~~L~~~gli~r~~~~--~D~R~~~l~LT~~G~~~~~ 109 (148)
..++.||..|.. ++.+.-+|.+.+ .++.+++-..+++|+++|||+..... ..++.+.+.||++|++.+.
T Consensus 6 ~~~~~IL~~L~~-~~~~gyei~~~l~~~~~~~~~~s~g~iY~~L~~Le~~Gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 84 (86)
T PF03551_consen 6 LLRLAILGLLSE-GPMHGYEIKKELEERYGGFWKVSPGSIYPALKRLEEEGLIESRWEDSGGGPPRKYYTITEEGREELE 84 (86)
T ss_dssp HHHHHHHHHHHH-S-BE--HHHHHHHHHSTTTEE--HHHHHHHHHHHHHTTSEEEEEEEC-SSSEEEEEEESCCSSHHHH
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHHHHHCCCEECCCCHHHHHHHHHHHCCCEEEEEEECCCCCCCEEEEECHHHHHHHC
T ss_conf 099999999702-8995999999999984887242654899999999978986987653578988779998978899860
Q ss_pred H
Q ss_conf 9
Q T0617 110 V 110 (148)
Q Consensus 110 ~ 110 (148)
+
T Consensus 85 ~ 85 (86)
T PF03551_consen 85 E 85 (86)
T ss_dssp H
T ss_pred C
T ss_conf 2
No 8
>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=97.09 E-value=0.00011 Score=48.19 Aligned_cols=47 Identities=30% Similarity=0.507 Sum_probs=41.3
Q ss_pred HHHHHHHHHHCCC-CCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf 9999999970889-9988999986589011458999999841321256
Q T0617 42 EWRIISVLSSASD-CSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNG 88 (148)
Q Consensus 42 q~~iL~~l~~~~~-~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~ 88 (148)
-+.||..+..+++ ++.+|||+.++++++++.+.++.|++.|||++.+
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~st~~r~l~~L~~~g~v~~d~ 52 (52)
T PF09339_consen 5 ALQILEALARAPRPLTLSEIARALGLPKSTVHRLLQTLEEAGFVERDP 52 (52)
T ss_dssp HHHHHHTHCTTBSSEEHHHHHHHTT--HHHHHHHHHHHHHT--EEE--
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
T ss_conf 999999998789998999999998919999999999999991942092
No 9
>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=97.08 E-value=0.00022 Score=46.35 Aligned_cols=46 Identities=37% Similarity=0.548 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 98999999997088999889999865890114589999998413212
Q T0617 40 MTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEV 86 (148)
Q Consensus 40 ~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r 86 (148)
+....+|..|.. ++++++||++.++++++++++.++.|++.|+|++
T Consensus 2 ~~R~~Il~~L~~-~~~~~~eia~~l~~s~~tvs~HL~~L~~~glV~~ 47 (47)
T PF01022_consen 2 PTRLKILKLLSE-GPLSVSEIAEELGISQSTVSRHLKKLEEAGLVKK 47 (47)
T ss_dssp HHHHHHHHHHHH-SCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf 889999999986-8967999883612356589999999999808419
No 10
>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=97.06 E-value=0.01 Score=35.19 Aligned_cols=64 Identities=19% Similarity=0.286 Sum_probs=53.6
Q ss_pred HHHCCCCHHHHHHHHHHHH-CC---------C---CCHHHHHHHH-CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEE
Q ss_conf 9872899989999999970-88---------9---9988999986-58901145899999984132125674322300
Q T0617 33 TQKFGIGMTEWRIISVLSS-AS---------D---CSVQKISDIL-GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTY 96 (148)
Q Consensus 33 ~~~~glt~~q~~iL~~l~~-~~---------~---~t~~eLa~~l-~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~ 96 (148)
...+||+...+.+|..+-. .| + .+..+|+.++ |++.+++.+.+..|++.|+|.+..+|+-+|..
T Consensus 36 ~~~lGl~~~~l~vL~aLlsf~~~~d~~~~~~~iVfpSN~~La~r~~G~s~~tlrRhla~LveaGLI~r~DS~NGKRy~ 113 (177)
T PF03428_consen 36 RPALGLSDRALAVLDALLSFTPEDDWSGGRRPIVFPSNAQLAERLHGMSERTLRRHLARLVEAGLIVRRDSPNGKRYA 113 (177)
T ss_pred HHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCEEECCHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEECCCCCCEEE
T ss_conf 997599876999999999768863457888725520899999998599989999999999988984641289874000
No 11
>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=96.92 E-value=0.00035 Score=44.93 Aligned_cols=52 Identities=19% Similarity=0.232 Sum_probs=47.5
Q ss_pred CHHHHHHHHHHHH--CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 9989999999970--889998899998658901145899999984132125674
Q T0617 39 GMTEWRIISVLSS--ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 39 t~~q~~iL~~l~~--~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
|+.+|.+|..|+. ..|.++.+|+..+++++.++...++.|++.|||++.+-+
T Consensus 1 ~~~~~~lLe~Ia~~r~~Gi~q~dL~k~~~~D~r~~~~~~k~L~~~gLI~k~~~~ 54 (75)
T PF04182_consen 1 TPLQYCLLERIARSRYNGITQSDLWKLFGQDPRSVFYRVKKLEDKGLIVKQQII 54 (75)
T ss_pred CCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEEEE
T ss_conf 907899999999677688205377998589922568999999778997888830
No 12
>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=96.57 E-value=0.0035 Score=38.29 Aligned_cols=68 Identities=19% Similarity=0.264 Sum_probs=56.7
Q ss_pred CCHHHHHHHHHHH-----HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHH
Q ss_conf 9998999999997-----08899988999986589011458999999841321256743223000001788899999
Q T0617 38 IGMTEWRIISVLS-----SASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE 109 (148)
Q Consensus 38 lt~~q~~iL~~l~-----~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~ 109 (148)
||..|-.||..|- ...|+..++||+.++++++||-.....|++.|||+..+.+.-+| ..|.+|-+++.
T Consensus 2 Lt~rq~~IL~~lv~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ph~s~Gr----iPT~kgYr~l~ 74 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEELDRSPATIRNEMADLEELGLVESQPHPSAGR----IPTDKGYRALN 74 (78)
T ss_pred CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCC----CCCHHHHHHHC
T ss_conf 78899999999999999739977669999986889088999999999879833679999887----83899999871
No 13
>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=96.33 E-value=0.0018 Score=40.29 Aligned_cols=51 Identities=20% Similarity=0.335 Sum_probs=42.6
Q ss_pred HHHHHHHHHHCCC---CCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 9999999970889---99889999865890114589999998413212567432
Q T0617 42 EWRIISVLSSASD---CSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSED 92 (148)
Q Consensus 42 q~~iL~~l~~~~~---~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D 92 (148)
-..+|.+|..+++ ++.++||+.++++++.+.++++.|.+.|+|+..+.+..
T Consensus 10 ai~~L~~La~~~~~~~~t~~~IA~~~~i~~~~v~kil~~L~~~Glv~s~~G~~G 63 (83)
T PF02082_consen 10 AIRILIYLARQPDGKPVTSKEIAERLGISPSYVRKILQKLRKAGLVKSVRGRGG 63 (83)
T ss_dssp HHHHHHHHHCSTTCC---HHHHHHHHTS-HHHHHHHHHHHHHTTSEE-------
T ss_pred HHHHHHHHHHCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCC
T ss_conf 999999998099998498999998889099999999999988898762367877
No 14
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250)
Probab=96.28 E-value=0.0034 Score=38.37 Aligned_cols=74 Identities=26% Similarity=0.199 Sum_probs=61.4
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCC--------------CEECCCCCH
Q ss_conf 899989999999970889998899998658901145899999984132125674322--------------300000178
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDK--------------RTYAINLTE 102 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~--------------R~~~l~LT~ 102 (148)
-.++..+.||..+...||-.+.-+|..++++..-|...++.|++.|||++...+.-+ --..+.||.
T Consensus 4 ~~~~~~l~IL~hl~~~~~Dyak~ia~~l~~~l~eV~~~l~~Le~~GLlErv~g~~iK~~~~k~K~~~e~h~hHtYY~Ltr 83 (92)
T PF10007_consen 4 IEDPLDLKILKHLKKAGPDYAKMIARRLGIPLEEVRERLKKLEEMGLLERVEGSTIKRTEAKFKPKKEVHKHHTYYRLTR 83 (92)
T ss_pred CCCHHHHHHHHHHHHHCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCHHHHHHHHHHCHHHHHHCCCCCEEECH
T ss_conf 22777899999999968860999999968999999999999998878432113378677764020066636864202064
Q ss_pred HHHHHHHH
Q ss_conf 88999999
Q T0617 103 MGQELYEV 110 (148)
Q Consensus 103 ~G~~~~~~ 110 (148)
+|..++.+
T Consensus 84 ~G~~~lR~ 91 (92)
T PF10007_consen 84 EGELLLRE 91 (92)
T ss_pred HHHHHHHC
T ss_conf 58999851
No 15
>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=96.09 E-value=0.0024 Score=39.40 Aligned_cols=48 Identities=21% Similarity=0.406 Sum_probs=43.3
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 999999997088999889999865890114589999998413212567
Q T0617 42 EWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 42 q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
+-.++..|..+|.++..+|++.+++|..|+-|-++.|++.|+|.|...
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 2 QQQILELLKQHGKVSVKELAEEFGVSEMTIRRDLNELEEQGLIRRVHG 49 (57)
T ss_pred HHHHHHHHHHCCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 899999999969897999999989498899998999998898899619
No 16
>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=95.70 E-value=0.0034 Score=38.38 Aligned_cols=46 Identities=22% Similarity=0.391 Sum_probs=41.4
Q ss_pred HHHHHHHH-CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999970-88999889999865890114589999998413212567
Q T0617 44 RIISVLSS-ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 44 ~iL~~l~~-~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
.||.+|.. ++|++..|||+.++++..++-..+..|++.|.|++.+-
T Consensus 4 ~Il~~i~~~~~p~~t~eiA~~~gls~~qaR~~L~~L~~eG~Vk~~~~ 50 (62)
T PF04703_consen 4 KILEYIKRQNGPCSTREIAEALGLSIYQARYYLQKLEKEGKVKRSPV 50 (62)
T ss_dssp CHHHHHHHH---B-HHHHHHHHTS-HHHHHHHHHHHHH---EEEE--
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 89999996279988999999969889999999999988797785205
No 17
>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=95.43 E-value=0.009 Score=35.56 Aligned_cols=56 Identities=20% Similarity=0.227 Sum_probs=48.7
Q ss_pred CCCCHHHHHHHHHHHHCC----CCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 289998999999997088----99988999986589011458999999841321256743
Q T0617 36 FGIGMTEWRIISVLSSAS----DCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSE 91 (148)
Q Consensus 36 ~glt~~q~~iL~~l~~~~----~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~ 91 (148)
..+|+.+..|..+|-.++ .++..+||+..++++++|+|.+++|.-.||-+-+..-.
T Consensus 12 ~~lt~~e~~Ia~yil~~~~~~~~~si~~lA~~~~vS~atv~Rf~kkLGf~gf~efk~~l~ 71 (107)
T PF01418_consen 12 DSLTPSEKKIADYILNNPDKIANMSISELAKAAGVSPATVVRFCKKLGFSGFSEFKVDLA 71 (107)
T ss_dssp GGS-HHHHHHHHHHHH-HHHHTT--HHHHHHHTT--HHHHHHHHHH------HHHHHHH-
T ss_pred HHCCHHHHHHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 417999999999999299999775499999997989889999999928999999999999
No 18
>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=95.36 E-value=0.012 Score=34.75 Aligned_cols=59 Identities=31% Similarity=0.497 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHH
Q ss_conf 89999999970889998899998658901145899999984132125674322300000178889
Q T0617 41 TEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQ 105 (148)
Q Consensus 41 ~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~ 105 (148)
.++.++..+.++| +.+.-|+.++++++++|+.|++||+.==+. --++....+.+|+.|+
T Consensus 2 ~~l~~f~~l~~~g--s~~~AA~~l~~s~~~vs~~i~~LE~~lg~~----Lf~r~~~~~~lT~~G~ 60 (60)
T PF00126_consen 2 RQLRVFVALAETG--SFSRAAEQLGISQSAVSRRIKRLEEELGVP----LFDRTGRGLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHHHS---HHHHHHHHTS-HHHHHHHHHHHHHHHTS-----SEEE----EEE-HHHH
T ss_pred HHHHHHHHHHHHC--CHHHHHHHCCCCCCHHHHHHHHHHHHHCCE----EEEECCCCEEECCCCC
T ss_conf 6799999999979--999999870899538999999999982996----8998899754893039
No 19
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This set of hypothetical proteins is found in prokaryotes. ; PDB: 2k02_A 1xn7_A.
Probab=95.36 E-value=0.0026 Score=39.21 Aligned_cols=50 Identities=22% Similarity=0.225 Sum_probs=44.6
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 99999970889998899998658901145899999984132125674322
Q T0617 44 RIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDK 93 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~ 93 (148)
.+.-+|..++..+.++||..+++++++|-.++..|+++|.|++...+...
T Consensus 4 ~i~~~l~~~g~~s~~eLa~~f~~s~~~v~aMLe~l~~kG~i~k~~~~~~~ 53 (69)
T PF09012_consen 4 QIRDYLALRGRVSLSELARHFGISPDAVEAMLEQLIRKGKIEKVEDSSCC 53 (69)
T ss_dssp HHHHHHHH---EEHHHHHHHTT--HHHHHHHHHHHHC---EEEEEEE---
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCCC
T ss_conf 99999999398189999999790999999999999988916873169999
No 20
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains . ; PDB: 1tqm_A 1zar_A 1tqi_A 1zao_A 1tqp_A.
Probab=95.35 E-value=0.012 Score=34.74 Aligned_cols=68 Identities=21% Similarity=0.331 Sum_probs=59.2
Q ss_pred CCHHHHHHHHHHHH----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHH
Q ss_conf 99989999999970----8899988999986589011458999999841321256743223000001788899999
Q T0617 38 IGMTEWRIISVLSS----ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE 109 (148)
Q Consensus 38 lt~~q~~iL~~l~~----~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~ 109 (148)
|+..+|+||..|.. ++-.+...|.+..++..+.+...+++|.+.++|.+...+-|+ +.||-.|-++++
T Consensus 4 L~~~d~RvL~avE~gmrnhE~VP~~lI~~~s~l~~~~~~~~L~~L~k~kLv~~~~~~Y~G----YrLT~~GyD~LA 75 (82)
T PF09202_consen 4 LSKEDFRVLRAVEMGMRNHEWVPVELIESISGLREEEVSKRLSRLLKLKLVSRRNKKYDG----YRLTFLGYDYLA 75 (82)
T ss_dssp ---HHHHHHHHHHTTTTT-SS--HHHHHHHHT---HHHHHHHHHHHHTTSEE---SS--------EE-----HHHH
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCC----EEEEECCHHHHH
T ss_conf 679999999999972457870899999999785887899999999867793366999762----587535516999
No 21
>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=95.34 E-value=0.01 Score=35.27 Aligned_cols=41 Identities=22% Similarity=0.494 Sum_probs=36.2
Q ss_pred HHHHHHHHH-HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 999999997-08899988999986589011458999999841
Q T0617 42 EWRIISVLS-SASDCSVQKISDILGLDKAAVSRTVKKLEEKK 82 (148)
Q Consensus 42 q~~iL~~l~-~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~g 82 (148)
+..+|..|. ..+++|..+||+.+++|+.||.+-++.|.+.|
T Consensus 2 ~~~Il~~L~~~~~~it~~eLA~~l~vS~~Ti~~~i~~L~~~g 43 (55)
T PF08279_consen 2 QQQILELLLKNDGPITAKELAEELGVSRRTIRRDIKELEEEG 43 (55)
T ss_dssp HHHHHHHHHHCCTTS-HHHHHHHCTS-HHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf 899999999859998899999996979999999999999869
No 22
>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=95.08 E-value=0.0083 Score=35.80 Aligned_cols=60 Identities=28% Similarity=0.409 Sum_probs=46.0
Q ss_pred CCHHHHHHHHHHHHC-C-----CCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHH
Q ss_conf 999899999999708-8-----99988999986589011458999999841321256743223000001788
Q T0617 38 IGMTEWRIISVLSSA-S-----DCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEM 103 (148)
Q Consensus 38 lt~~q~~iL~~l~~~-~-----~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~ 103 (148)
++..++.||.+|..+ . -+++++||+.++++++|+++.++.|+++|+|.+... -.+.+-|.
T Consensus 53 ~g~k~~~Vl~~ll~~~d~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK~L~ek~iI~k~~~------G~Y~iNP~ 118 (165)
T PF05732_consen 53 LGNKKFRVLMFLLENMDSDNAVVATQKEIAEELGISKPTVSRTIKELEEKGIIKKIKN------GTYFINPD 118 (165)
T ss_pred HCCCHHHHHHHHHHHCCCCCEEEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECC------CEEEECHH
T ss_conf 3414799999999843779839878999999979888899999999987997898239------87998838
No 23
>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=94.84 E-value=0.024 Score=32.79 Aligned_cols=44 Identities=14% Similarity=0.339 Sum_probs=37.6
Q ss_pred CCHHHHHHHHHHHHCC------CCCHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 9998999999997088------9998899998658901145899999984
Q T0617 38 IGMTEWRIISVLSSAS------DCSVQKISDILGLDKAAVSRTVKKLEEK 81 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~------~~t~~eLa~~l~i~~~~vs~~i~~L~~~ 81 (148)
||..|..+|..-.+.| +++..+||+.+|+++++++..+.+-+++
T Consensus 1 LT~~q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~~T~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREVLRTAYEMGYFDWPRRITLEELAEELGISKSTFSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 98899999999998688779875889999989499999999999999998
No 24
>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=94.33 E-value=0.0076 Score=36.05 Aligned_cols=31 Identities=29% Similarity=0.530 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf 9998899998658901145899999984132
Q T0617 54 DCSVQKISDILGLDKAAVSRTVKKLEEKKYI 84 (148)
Q Consensus 54 ~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli 84 (148)
++|..|||+.+|.++.+|||.+++|.+.|+|
T Consensus 2 ~lt~~elA~~~G~tretvsR~l~~l~~~GlI 32 (32)
T PF00325_consen 2 PLTHQELADLLGTTRETVSRILSRLRKEGLI 32 (32)
T ss_dssp E--HHHHHHHCTC-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCC
T ss_conf 9799999988698699999999999996799
No 25
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=94.27 E-value=0.097 Score=28.69 Aligned_cols=83 Identities=20% Similarity=0.323 Sum_probs=60.6
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHC-CCCCCCCCEECCCCCHHHHHHHHHHHHH-------------------
Q ss_conf 99889999865890114589999998413212-5674322300000178889999999999-------------------
Q T0617 55 CSVQKISDILGLDKAAVSRTVKKLEEKKYIEV-NGHSEDKRTYAINLTEMGQELYEVASDF------------------- 114 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r-~~~~~D~R~~~l~LT~~G~~~~~~~~~~------------------- 114 (148)
+|+.|||+.+|+++++|++.|. +.||-+- .+.-..+|...|++.+.=++++..+.+.
T Consensus 1 MT~eELA~~tG~arQTINrWvR---k~gW~T~~~pGVkGGkARLIhId~~Vrefi~~~~a~r~~~~~~~~~E~~a~y~~~ 77 (122)
T PF07037_consen 1 MTPEELAELTGYARQTINRWVR---KEGWKTEPKPGVKGGKARLIHIDEQVREFIRNAPAFRNRPTLYRAEEPPAEYTVT 77 (122)
T ss_pred CCHHHHHHHHCHHHHHHHHHHH---HCCCCCCCCCCCCCCEEEEEEECHHHHHHHHCCHHHHCCHHHHHCCCCCHHCCCC
T ss_conf 9878999974505999999999---7286237788875760257766489999998057752330455324550101688
Q ss_pred ----HHHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf ----99999999857999899999999999
Q T0617 115 ----AIEREKQLLEEFEEAEKDQLFILLKK 140 (148)
Q Consensus 115 ----~~~~~~~~~~~l~~ee~~~l~~~L~~ 140 (148)
.....-.....|++.|+..|..+|.+
T Consensus 78 ~~~~l~~qii~~~~~Mtp~EQ~~l~~lL~R 107 (122)
T PF07037_consen 78 NDSPLERQIITLLEEMTPSEQEQLASLLLR 107 (122)
T ss_pred CCCHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 765299999999998699999999999998
No 26
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=94.09 E-value=0.056 Score=30.30 Aligned_cols=68 Identities=18% Similarity=0.199 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHC-C-CCCHHHHHHHHCCCCCHHHHHHH----------HHHHHHHH-HCCCCCCCCCEECCCCCHHHHH
Q ss_conf 9899999999708-8-99988999986589011458999----------99984132-1256743223000001788899
Q T0617 40 MTEWRIISVLSSA-S-DCSVQKISDILGLDKAAVSRTVK----------KLEEKKYI-EVNGHSEDKRTYAINLTEMGQE 106 (148)
Q Consensus 40 ~~q~~iL~~l~~~-~-~~t~~eLa~~l~i~~~~vs~~i~----------~L~~~gli-~r~~~~~D~R~~~l~LT~~G~~ 106 (148)
....-||.+|+.. | +..+.+|++..+.+++++...+. .|+..||| .+... +..+.+.+||+|+.
T Consensus 9 ~~R~kVL~~L~~~~~~~~~~~eis~~v~~~~sNv~GaL~G~g~rY~~e~SLv~lGLV~~~~~~---~g~k~y~lT~~G~~ 85 (90)
T PF07381_consen 9 KVRRKVLEYLYSIYPEPTYLSEISRRVRSDPSNVRGALEGMGKRYNGESSLVGLGLVSEEESK---RGFKYYRLTPYGKR 85 (90)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHCCCEEEEECC---CCCCEEEECHHHHH
T ss_conf 999999999996088768999999997459077889996036664416768864774576214---76017874666678
Q ss_pred HHHH
Q ss_conf 9999
Q T0617 107 LYEV 110 (148)
Q Consensus 107 ~~~~ 110 (148)
+.+.
T Consensus 86 i~~~ 89 (90)
T PF07381_consen 86 IVEY 89 (90)
T ss_pred HHHH
T ss_conf 8860
No 27
>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=93.98 E-value=0.03 Score=32.07 Aligned_cols=54 Identities=17% Similarity=0.362 Sum_probs=48.9
Q ss_pred CCCHHHHHHHHHHHH----CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 899989999999970----889998899998658901145899999984132125674
Q T0617 37 GIGMTEWRIISVLSS----ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 37 glt~~q~~iL~~l~~----~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
+++..+-.||.+|.. ..|+++.+|+..++++...|...++.|...|+|-...|.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~eGv~v~~i~~~l~~~~~~v~~a~~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 44 GLSPLQQRVLNFIKQSPQSEEGVHVDEIAQKLGMPENEVRKAIDELSDEGLIYSTIDD 101 (102)
T ss_dssp ---HHHHHHHHHHHC--------BHHHHHHHSTS-HHHHHHHHHHHHH---EEESSST
T ss_pred CCCHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEECCCCC
T ss_conf 8888999999999844688787189999999693999999999999859847266689
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=93.96 E-value=0.049 Score=30.66 Aligned_cols=65 Identities=18% Similarity=0.291 Sum_probs=43.0
Q ss_pred HHHHHHHCCCCCHHHHHHHHC--------------CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHH
Q ss_conf 999997088999889999865--------------890114589999998413212567432230000017888999999
Q T0617 45 IISVLSSASDCSVQKISDILG--------------LDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEV 110 (148)
Q Consensus 45 iL~~l~~~~~~t~~eLa~~l~--------------i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~ 110 (148)
+|..|+-.||+.+..|...-| -+.+-+-.+++.||+.|||++.+ ..+| .||++|+..+++
T Consensus 57 ilRklY~~g~vGv~~lr~~YGg~k~rG~rP~h~~~asg~iiR~~lQqLE~~glvek~~--~~GR----~lT~~G~~~LD~ 130 (139)
T PF01090_consen 57 ILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP--KGGR----RLTPKGRSDLDR 130 (139)
T ss_dssp HHHHHHH------HHHHHH----------TTS-------HHHHHHHHHHH---EE-------------EE-----HHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECC--CCCC----EECHHHHHHHHH
T ss_conf 9999982499757899999787778999998646776189999999998689867769--9997----889847999999
Q ss_pred HHHHH
Q ss_conf 99999
Q T0617 111 ASDFA 115 (148)
Q Consensus 111 ~~~~~ 115 (148)
+....
T Consensus 131 iA~~i 135 (139)
T PF01090_consen 131 IAGQI 135 (139)
T ss_dssp HHHHH
T ss_pred HHHHH
T ss_conf 99999
No 29
>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=93.77 E-value=0.015 Score=34.17 Aligned_cols=59 Identities=20% Similarity=0.406 Sum_probs=49.8
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEE
Q ss_conf 99989999999970889998899998658901145899999984132125674322300
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTY 96 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~ 96 (148)
.+.....|+..|..+|.++-.+||..++++...+.+++..|...|+|......++.|..
T Consensus 11 yg~~~~~Vl~~L~~~~~l~ee~La~~l~i~~k~lR~~L~~L~e~~lv~~~~~~e~~~~~ 69 (105)
T PF02002_consen 11 YGDEAVRVLDALLRHGELTEEDLAELLGIKSKELRKILYKLYEDKLVKYRRVKEDERGW 69 (105)
T ss_dssp ---TTHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHH----EEEEE-------
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCE
T ss_conf 39669999999998699089999989099989999999999988983789887079875
No 30
>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=93.73 E-value=0.015 Score=33.99 Aligned_cols=64 Identities=20% Similarity=0.235 Sum_probs=53.9
Q ss_pred CCCHHHHHHHHHHHHCC--CCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCC
Q ss_conf 89998999999997088--99988999986589011458999999841321256743223000001
Q T0617 37 GIGMTEWRIISVLSSAS--DCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINL 100 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~--~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~L 100 (148)
+|+..+..|...|...| |+-.++|....++..+.+.+.++.|+.++||....+-..+..+.+.|
T Consensus 82 ~l~~~e~lVY~~I~~sG~~GIWtk~ik~~tnL~~~~v~k~LK~Le~k~lIKsVksV~~~~rKiYmL 147 (325)
T PF05158_consen 82 SLSDEERLVYSLIESSGNEGIWTKDIKKKTNLHQNQVNKCLKSLESKKLIKSVKSVKNPNRKIYML 147 (325)
T ss_dssp ---CCHHHHHHHHHH------BHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEE
T ss_pred CCCHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEE
T ss_conf 798788999999998075782799999874998999999999998579867532567887589998
No 31
>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=93.69 E-value=0.039 Score=31.29 Aligned_cols=58 Identities=21% Similarity=0.354 Sum_probs=44.2
Q ss_pred HHHHHHHHC-CCCCHHHHHHHHCCCC-----CHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHH
Q ss_conf 999999708-8999889999865890-----114589999998413212567432230000017888999
Q T0617 44 RIISVLSSA-SDCSVQKISDILGLDK-----AAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQEL 107 (148)
Q Consensus 44 ~iL~~l~~~-~~~t~~eLa~~l~i~~-----~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~ 107 (148)
.||.+|.++ .|++..+|++.+.... .++-+-++.|+++||+.+.... --.||++|.+.
T Consensus 2 ~IL~~L~e~~~P~~~~~l~~~L~~~g~~~s~~avRrrLr~me~dG~t~~~~~~------G~~ite~Gl~~ 65 (66)
T PF08461_consen 2 FILRILRESGKPIGRKELAEELKLRGEELSEEAVRRRLRAMERDGFTRRQGYA------GRSITEKGLDE 65 (66)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCC------CCCCCHHHHHH
T ss_conf 78999998499989999999998406675799999999999987881205777------76068866854
No 32
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds . MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 .; GO: 0005515 protein binding, 0045941 positive regulation of transcription; PDB: 1bja_A 1i1s_A.
Probab=93.63 E-value=0.05 Score=30.59 Aligned_cols=73 Identities=15% Similarity=0.237 Sum_probs=63.1
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHH--CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHH
Q ss_conf 999899999999708899988999986--589011458999999841321256743223000001788899999999999
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDIL--GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFA 115 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l--~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~ 115 (148)
|+...-.++..+..+.=+|..++++.+ .++++.|..-+.-|.++|||++.- |+ +-.|..|..++.++...+
T Consensus 14 lne~ta~i~i~iaKk~FiTa~ev~eav~~e~n~~~V~SNIGVliKKgliEKSG---DG----~v~T~~~~~ii~~AA~l~ 86 (96)
T PF09114_consen 14 LNEKTASIFIQIAKKNFITAAEVREAVHTEMNKNVVNSNIGVLIKKGLIEKSG---DG----LVTTGEADDIIQEAAELW 86 (96)
T ss_dssp S-HHHHHHHHHHHHSTT--HHHHHH-T-TT---HHHHHH---TTT---EE-------------EE---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCC---CC----EEEECCHHHHHHHHHHHH
T ss_conf 51325689999997501329999999879887787732433320121342168---82----586062889999999998
Q ss_pred HH
Q ss_conf 99
Q T0617 116 IE 117 (148)
Q Consensus 116 ~~ 117 (148)
.+
T Consensus 87 ~~ 88 (96)
T PF09114_consen 87 AQ 88 (96)
T ss_dssp HH
T ss_pred HH
T ss_conf 74
No 33
>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=93.52 E-value=0.012 Score=34.77 Aligned_cols=53 Identities=21% Similarity=0.316 Sum_probs=42.6
Q ss_pred HHHCC-CCC---HHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHH
Q ss_conf 97088-999---889999865890114589999998413212567432230000017888
Q T0617 49 LSSAS-DCS---VQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMG 104 (148)
Q Consensus 49 l~~~~-~~t---~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G 104 (148)
+..+| .+. ..++.+.+|++.+++-..+.+|.++|+++.... +|...+.||++|
T Consensus 14 ~~~~g~~i~~~~Li~l~~~~Gi~e~avR~Al~RL~~~G~l~~~r~---GR~s~Y~Lt~~g 70 (70)
T PF07848_consen 14 LRPRGGWIWVGSLIRLLEAFGISERAVRTALSRLVKEGWLESERR---GRRSYYRLTERG 70 (70)
T ss_pred HHCCCCCEEHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEEEEE---CCCCEEEECCCC
T ss_conf 624798061999999999829990589999999987386675760---783247748899
No 34
>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=93.39 E-value=0.015 Score=34.00 Aligned_cols=69 Identities=14% Similarity=0.241 Sum_probs=59.3
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC-CCCCCEECCCCCHHHHHHH
Q ss_conf 89998999999997088999889999865890114589999998413212567-4322300000178889999
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH-SEDKRTYAINLTEMGQELY 108 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~-~~D~R~~~l~LT~~G~~~~ 108 (148)
.||.+...+|.+|+-++|+|..+|.+.-|++ ...+|+.|.++|||+.... +..+|-..+..|++-.+.+
T Consensus 79 ~LS~aalEtLAiIAY~QPiTr~eIe~IRGv~---s~~~l~~L~e~gLI~~~gr~~~~Grp~lY~tT~~Fl~~F 148 (159)
T PF04079_consen 79 KLSQAALETLAIIAYKQPITRAEIEEIRGVN---SDGILRTLLERGLIREVGRKDTPGRPILYGTTDKFLEYF 148 (159)
T ss_dssp HHHHHHHHHHHHHHHH-SEEHHHHHHH--------HCHHHHHHH---EEE----S------EEEE-HHHHHHT
T ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHCCCC---HHHHHHHHHHCCCEEECCCCCCCCCCEEEHHHHHHHHHH
T ss_conf 8899999999999974983899999975987---699999999888968838379999752110079999981
No 35
>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=93.36 E-value=0.038 Score=31.40 Aligned_cols=53 Identities=19% Similarity=0.306 Sum_probs=44.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEC
Q ss_conf 999999708899988999986589011458999999841321256743223000
Q T0617 44 RIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYA 97 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~ 97 (148)
.+|..++.. .+|.-+|.+..+++++++.-.+.+|.+.|.|.|....-+++...
T Consensus 9 ~Il~~ls~~-c~tLeeL~e~Tgi~k~~llV~LsrL~k~GiI~RkW~~~~gkK~R 61 (72)
T PF05584_consen 9 LILIVLSKN-CCTLEELEEKTGIKKNELLVYLSRLAKEGIIYRKWRRFGGKKYR 61 (72)
T ss_pred HHHHHHHHC-CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEEEECCEEEE
T ss_conf 999999754-35699999996898779999999998789266431883683789
No 36
>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=93.11 E-value=0.08 Score=29.25 Aligned_cols=53 Identities=19% Similarity=0.342 Sum_probs=45.2
Q ss_pred CCCCHHHHHHHHHHHHC------C--CCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf 28999899999999708------8--99988999986589011458999999841321256
Q T0617 36 FGIGMTEWRIISVLSSA------S--DCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNG 88 (148)
Q Consensus 36 ~glt~~q~~iL~~l~~~------~--~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~ 88 (148)
.+|+..|+.++..+... + -++.+++++..++++.+|++.++.|++.|+|.+..
T Consensus 28 ~~ls~r~~~v~lav~RkTyG~nK~~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vi~~~G 88 (100)
T PF04492_consen 28 ADLSGRQLKVLLAVIRKTYGWNKKMDRISNSQIAEMTGISRDHVSRALKELIRMNVIIIEG 88 (100)
T ss_pred CCCCHHHHHHHHHHHHHHCCCCCCCHHEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
T ss_conf 8643789999999999833889840040099999886989899999999999758876449
No 37
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=92.90 E-value=0.11 Score=28.41 Aligned_cols=84 Identities=13% Similarity=0.238 Sum_probs=62.9
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999997088999889999865890114589999998413212567432230000017888999999999999999999
Q T0617 43 WRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQL 122 (148)
Q Consensus 43 ~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~~~~~~~~ 122 (148)
..|+.++..+|-+|.+|+....|+++.++.+.+..|++.|-|.+.-.. -|+.++.....|....... ....+
T Consensus 15 ~rIVElVR~~GRiTi~ql~~~TG~sR~T~k~~lr~Lv~~G~v~~~G~~------GiFpseqA~~dw~~~~~~~--~d~~l 86 (127)
T PF06163_consen 15 ARIVELVREHGRITIRQLVKMTGASRNTAKKYLRELVESGDVYRHGRC------GIFPSEQARIDWDKARKKL--VDPDL 86 (127)
T ss_pred HHHHHHHHHHCHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCC------CCCCCHHHHHHHHHHHHHC--CCCHH
T ss_conf 999999998163029999999786799999999999973883116876------7584199999999868860--26103
Q ss_pred HHCCCHHHHHHH
Q ss_conf 857999899999
Q T0617 123 LEEFEEAEKDQL 134 (148)
Q Consensus 123 ~~~l~~ee~~~l 134 (148)
+-.+++-|+...
T Consensus 87 i~~lpdgeirry 98 (127)
T PF06163_consen 87 IWKLPDGEIRRY 98 (127)
T ss_pred HHCCCCCCHHCC
T ss_conf 421886401001
No 38
>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=92.83 E-value=0.075 Score=29.42 Aligned_cols=43 Identities=23% Similarity=0.393 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 99989999999970889998899998658901145899999984
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK 81 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~ 81 (148)
||..|..++..- -...++.+|||+.+++|+++|...+++.++.
T Consensus 18 LT~kQ~~~l~ly-y~eDlSlsEIAe~~~iSRqaVyD~ikr~~~~ 60 (101)
T PF04297_consen 18 LTEKQKEYLELY-YNEDLSLSEIAEELGISRQAVYDNIKRAEKK 60 (101)
T ss_dssp S-HHHHHHHHHH-CTS---HHHHHHHCT--HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH-HHCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 759999999999-8879989999989698899999999999999
No 39
>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=92.41 E-value=0.088 Score=28.97 Aligned_cols=43 Identities=19% Similarity=0.376 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 899989999999970889998899998658901145899999984
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK 81 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~ 81 (148)
.||+.|+.+|..+. .|.+.++||..++++..+|...+.++-++
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l~is~~TV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTPREREVLRLLA--QGLSNKEIAERLGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHC--TT--HHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH--HCCCCHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 13899999999999--73983789988354524799999999998
No 40
>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=92.28 E-value=0.033 Score=31.81 Aligned_cols=37 Identities=24% Similarity=0.416 Sum_probs=33.5
Q ss_pred CC-CHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99-98899998658901145899999984132125674
Q T0617 54 DC-SVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 54 ~~-t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
.+ +..+||+.+++++++|.+.+..|+..|+|++.+..
T Consensus 23 ~lPs~~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 23 RLPSERELAERFGVSRTTVREALKRLEEEGLIERRPGR 60 (64)
T ss_dssp B---HHHHHHHHT--HHHHHHHHHHHHHTTSEEEETT-
T ss_pred EECCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf 93689999988687989999999999988958997696
No 41
>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=90.74 E-value=0.057 Score=30.21 Aligned_cols=55 Identities=27% Similarity=0.301 Sum_probs=46.1
Q ss_pred CCHHHHHHHHHHHHC-CCCCHHHHHHHH-----CCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 999899999999708-899988999986-----5890114589999998413212567432
Q T0617 38 IGMTEWRIISVLSSA-SDCSVQKISDIL-----GLDKAAVSRTVKKLEEKKYIEVNGHSED 92 (148)
Q Consensus 38 lt~~q~~iL~~l~~~-~~~t~~eLa~~l-----~i~~~~vs~~i~~L~~~gli~r~~~~~D 92 (148)
+|+....||..|... ++++..+|.+.+ .++.+||-|.++.|++.|+|.+...++.
T Consensus 6 ~T~qR~~Il~~l~~~~~~~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Gli~~~~~~~~ 66 (120)
T PF01475_consen 6 LTPQRRAILEVLEESKEHLSAEEIYDRLREKGPSISLATVYRTLDLLEEAGLIHRIELGDG 66 (120)
T ss_dssp HHHHHHHHHHHHHHGGSSEEHHHHHHHHHHT-TT--HHHHHHHHHHHHH---EEEEE----
T ss_pred CCHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCEEEEEECCCC
T ss_conf 7999999999998279999999999998861899986249999999986890999991898
No 42
>PF02001 DUF134: Protein of unknown function DUF134; InterPro: IPR002852 The bacterial and archaeal proteins in this family have no known function.
Probab=90.18 E-value=0.19 Score=26.68 Aligned_cols=49 Identities=12% Similarity=0.268 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHH---HHHHHHH
Q ss_conf 2899989999999970889998899998658901145899999---9841321
Q T0617 36 FGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKL---EEKKYIE 85 (148)
Q Consensus 36 ~glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L---~~~gli~ 85 (148)
..|+..++.+|..+. ..++++.+-|..|+||++|+.++++.- +++-||.
T Consensus 40 v~L~~dElEAiRL~D-~egl~QeeAA~~MgVSR~Tf~ril~~AR~KvA~aLv~ 91 (106)
T PF02001_consen 40 VVLTVDELEAIRLVD-YEGLTQEEAAEQMGVSRQTFQRILKSARRKVADALVE 91 (106)
T ss_pred EEEEHHHHHHHHHHH-HHCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHC
T ss_conf 773289999999988-8179899999984977999999999999999999987
No 43
>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=89.29 E-value=0.29 Score=25.49 Aligned_cols=41 Identities=15% Similarity=0.370 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 98999999997088999889999865890114589999998
Q T0617 40 MTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEE 80 (148)
Q Consensus 40 ~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~ 80 (148)
...+.++..+-.+++.+..++|+.+.+|++|+.+.++.+.+
T Consensus 16 s~~~~ll~~l~~~~~~~~~~la~~l~vS~sTi~~~lk~i~~ 56 (87)
T PF05043_consen 16 SRSYILLKLLLNNEYVSIEDLAEELYVSRSTIYRDLKKINQ 56 (87)
T ss_pred HHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 39999999998489968999999979899999999999999
No 44
>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=89.06 E-value=0.15 Score=27.38 Aligned_cols=32 Identities=19% Similarity=0.322 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 899988999986589011458999999841321
Q T0617 53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIE 85 (148)
Q Consensus 53 ~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~ 85 (148)
+|.+..++|..++|+++++.+.++ -.+.|.+.
T Consensus 17 ~G~S~~eaA~~F~VS~~Tv~rW~k-~~~~G~~~ 48 (119)
T PF01710_consen 17 QGMSIREAAKRFGVSRSTVYRWLK-RRETGDLK 48 (119)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH-HHHCCCCC
T ss_conf 599999999996955999999998-64113446
No 45
>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=88.42 E-value=0.12 Score=28.12 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHH
Q ss_conf 8999899999999708899988999986589011458999
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVK 76 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~ 76 (148)
.++..++..+..+...| .++++||+.++++++|+-|.++
T Consensus 5 ~~~~~~~~~i~~l~~~G-~s~~~IAk~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 5 KLTDEQIEEIRELYAQG-MSISEIAKRFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSHCCHHHHHHHHH-----HHHHHHHCTS-HHHHHHHHC
T ss_pred CCCHHHHHHHHHHHHCC-CCHHHHHHHHCCCHHHHHHHHH
T ss_conf 89999999999999979-9999999998919999999974
No 46
>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=87.75 E-value=0.21 Score=26.49 Aligned_cols=67 Identities=16% Similarity=0.291 Sum_probs=53.8
Q ss_pred HCCCCHHHHHHHHHHHH---CCCCCHHHHHHHHCCCCCHHHHHHHH-HHHHHHHHCCCCCCCCCEECCCCCHHHHHHH
Q ss_conf 72899989999999970---88999889999865890114589999-9984132125674322300000178889999
Q T0617 35 KFGIGMTEWRIISVLSS---ASDCSVQKISDILGLDKAAVSRTVKK-LEEKKYIEVNGHSEDKRTYAINLTEMGQELY 108 (148)
Q Consensus 35 ~~glt~~q~~iL~~l~~---~~~~t~~eLa~~l~i~~~~vs~~i~~-L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~ 108 (148)
++||...+..+|..|.+ .||.-...||..++.++.|+--.+.. |.+.|||.|.+. +| .+|++|.+.+
T Consensus 3 ~~GLd~~D~~~L~~l~~~f~ggPVGl~tlA~~l~e~~~TiEdv~EPyLiq~g~i~RTpR---GR----~~T~~a~~hL 73 (76)
T PF05491_consen 3 ELGLDEMDRRYLKTLIENFGGGPVGLDTLAAALGEERDTIEDVIEPYLIQIGFIERTPR---GR----VATPKAYEHL 73 (76)
T ss_dssp ----BHHHHHHHHHHHHHH-------HHHHHHTTS-HHHHHHCTHHHHHH---EE-------------EE-HHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCC---HH----HHHHHHHHHH
T ss_conf 55688999999999998718987109999999879860899985189999606863885---58----8789999985
No 47
>PF11313 DUF3116: Protein of unknown function (DUF3116)
Probab=86.87 E-value=0.83 Score=22.48 Aligned_cols=60 Identities=20% Similarity=0.197 Sum_probs=39.9
Q ss_pred HCCCCCHHHHHHHH-------CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHH
Q ss_conf 08899988999986-------5890114589999998413212567432230000017888999999999
Q T0617 51 SASDCSVQKISDIL-------GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASD 113 (148)
Q Consensus 51 ~~~~~t~~eLa~~l-------~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~ 113 (148)
..+..++..+.-.+ ..++.-+-..+==||..|||.|..+.. .+.+++|++|..+++++..
T Consensus 17 ~~~n~~i~~l~~e~~~~~~~~~~TKNELL~~~YWLE~~GYI~R~~~~~---~krY~~T~kG~~ll~~l~~ 83 (85)
T PF11313_consen 17 KNPNTTINILSFEFIDFPGARDFTKNELLYTVYWLEYNGYIKRINSNA---EKRYSITEKGHLLLAELEN 83 (85)
T ss_pred CCCCCCHHHHHHHHHCCHHHHHCCHHHHHHHHHHHHHCCEEEEECCCC---CEEEEECCCHHHHHHHHHH
T ss_conf 287753899999986250143301999999999999768334303688---4368861006899999874
No 48
>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=86.79 E-value=0.076 Score=29.38 Aligned_cols=39 Identities=23% Similarity=0.410 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 889998899998658901145899999984132125674
Q T0617 52 ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 52 ~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
.|-++.++||+..|+++|.+-+.+++|+..|.|+.+...
T Consensus 2 eG~ltaS~IAd~vGiTrSvivnaLRKlESAGVIe~rslg 40 (61)
T PF08222_consen 2 EGRLTASKIADRVGITRSVIVNALRKLESAGVIESRSLG 40 (61)
T ss_dssp -----HHHHHCC----HHHHHHHHHHHHH---EEEE---
T ss_pred CCEEHHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCC
T ss_conf 744208888888488399999999988863853113467
No 49
>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=86.34 E-value=0.38 Score=24.73 Aligned_cols=47 Identities=19% Similarity=0.169 Sum_probs=36.6
Q ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 998999999997088999889999865-890114589999998413212567
Q T0617 39 GMTEWRIISVLSSASDCSVQKISDILG-LDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 39 t~~q~~iL~~l~~~~~~t~~eLa~~l~-i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
|......|.-|+..| +|.++||+.|| +++.+|...+.+| ||--+...
T Consensus 4 Tderve~Lk~lw~eG-lSasqIA~~LGgvsRNAViGK~hRL---gL~~r~~~ 51 (162)
T PF07750_consen 4 TDERVERLKKLWAEG-LSASQIAKQLGGVSRNAVIGKVHRL---GLSGRASP 51 (162)
T ss_pred CHHHHHHHHHHHHCC-CCHHHHHHHHCCCCHHHHHHHHHHC---CCCCCCCC
T ss_conf 789999999999858-8899999997552066677777643---66666777
No 50
>PF09756 DDRGK: DDRGK domain; PDB: 1wi9_A.
Probab=86.29 E-value=0.26 Score=25.83 Aligned_cols=68 Identities=16% Similarity=0.157 Sum_probs=56.7
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHH
Q ss_conf 99999997088999889999865890114589999998413212567432230000017888999999999
Q T0617 43 WRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASD 113 (148)
Q Consensus 43 ~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~ 113 (148)
...+.+|-.+.-++..+||..++++.+.+..-|+.|+..|.|.-..|. |+++|++|+.-...++....
T Consensus 102 ~~Fi~~Ik~~k~v~l~~la~~f~l~t~~~i~ri~~L~~~~~i~Gv~Dd---rGk~iyis~~E~~~va~~i~ 169 (188)
T PF09756_consen 102 QDFINYIKKKKVVNLEDLAAEFGLKTQDVINRIQELEEQGRITGVIDD---RGKFIYISQEELEAVAKFIK 169 (188)
T ss_dssp HHHHHHHHH-SEE-HHHHHHH----HHHHHHHHHHHHH-------B--------EE---------------
T ss_pred HHHHHHHHHCCEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECC---CCCEEEECHHHHHHHHHHHH
T ss_conf 999999998683109999989099879999999999987984468859---98868855999999999999
No 51
>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=86.05 E-value=0.47 Score=24.14 Aligned_cols=43 Identities=19% Similarity=0.314 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 89998999999997088999889999865890114589999998
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEE 80 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~ 80 (148)
.|+..+-. +..+..-.|.|..|||+.+|++.++|...+.+--+
T Consensus 10 ~L~~~~r~-i~~l~~~~g~s~~eIA~~l~is~~tv~~~l~ra~~ 52 (54)
T PF08281_consen 10 KLPERQRE-IFLLRYFEGLSYKEIAEILGISESTVKSRLSRARK 52 (54)
T ss_dssp CS-HHHHH-HHHHHHT----HHHHHHHCTS----HHHHHHHHHH
T ss_pred CCCHHHHH-HHHHHHHHCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 78999999-99999996958999999989199999999999997
No 52
>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=86.01 E-value=0.37 Score=24.84 Aligned_cols=72 Identities=19% Similarity=0.071 Sum_probs=50.3
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHH
Q ss_conf 8999899999999708899988999986589011458999999841321256743223000001788899999999
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVAS 112 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~ 112 (148)
.|+...-.-+..++. .|+++.+||+.++++.+.|++++++-.+.|-|.-.+-...+ -+ -.||.=...+++..
T Consensus 17 Plp~~~R~rIv~l~~-~G~r~~~Isr~l~VS~gcVsKIl~Ry~eTGsI~Pg~iGGsk-Pr--v~tp~v~~~I~~~k 88 (125)
T PF00292_consen 17 PLPNELRQRIVELAH-EGVRPCDISRQLRVSHGCVSKILKRYRETGSIRPGPIGGSK-PR--VATPEVVEKIEEYK 88 (125)
T ss_dssp -S-HHHHHHHHHHHH-----HHHHHHHHT-----HHHHHHHTTT----S----------S--SS-HCHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHH-CCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCC-CC--CCCHHHHHHHHHHH
T ss_conf 288999999999976-25877489987651476999999999986176765557999-98--88789999999998
No 53
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation .
Probab=86.00 E-value=0.92 Score=22.19 Aligned_cols=55 Identities=22% Similarity=0.216 Sum_probs=42.5
Q ss_pred HHHHHHHHH-HCCCCCHHHHHHHH--CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCC
Q ss_conf 999999997-08899988999986--58901145899999984132125674322300000
Q T0617 42 EWRIISVLS-SASDCSVQKISDIL--GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAIN 99 (148)
Q Consensus 42 q~~iL~~l~-~~~~~t~~eLa~~l--~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~ 99 (148)
+-.|+.++. .+-|.++.+++..| +++++.+.+.++.|...|.|..... |..+.++
T Consensus 3 ~~~i~~y~~~qnRPys~~~v~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~---GKqkVY~ 60 (169)
T PF07106_consen 3 EEAILEYMKEQNRPYSAQDVFDNLHNKIKKTAVQKALDQLVEEGKIICKEY---GKQKVYF 60 (169)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEEC---CCEEEEE
T ss_conf 889999999808998599999998630348999999999998697357643---7768985
No 54
>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=85.48 E-value=0.16 Score=27.31 Aligned_cols=49 Identities=18% Similarity=0.184 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHCCCCC--HHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 8999999997088999--889999865890114589999998413212567
Q T0617 41 TEWRIISVLSSASDCS--VQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 41 ~q~~iL~~l~~~~~~t--~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
.+-.||.+|...|+.+ ..+++..+++.++.|.+.+-+|++.|.|.+...
T Consensus 5 ~e~kIl~~L~~~g~~~a~~i~~~~~l~~~k~~vNr~LY~L~k~g~v~~~~~ 55 (66)
T PF02295_consen 5 LEEKILDFLKNSGKSTATAIAKALGLSVPKKEVNRQLYRLEKSGKVCKSPG 55 (66)
T ss_dssp HHHHHHHHHHHT--EECCHHHHHHHCTS-HHHHHHHHHHHHHTTSEEEECS
T ss_pred HHHHHHHHHHHCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCEECCCC
T ss_conf 899999999977971899999983612528899999999997796652799
No 55
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=85.27 E-value=0.99 Score=21.96 Aligned_cols=52 Identities=21% Similarity=0.262 Sum_probs=36.7
Q ss_pred HHCCCCHHHHHHHHHH----HHCCC-CCHHHHHHHHCCCCCHHHHHHHHHHHH-HHHH
Q ss_conf 8728999899999999----70889-998899998658901145899999984-1321
Q T0617 34 QKFGIGMTEWRIISVL----SSASD-CSVQKISDILGLDKAAVSRTVKKLEEK-KYIE 85 (148)
Q Consensus 34 ~~~glt~~q~~iL~~l----~~~~~-~t~~eLa~~l~i~~~~vs~~i~~L~~~-gli~ 85 (148)
++++++.-.-..+..+ +++|+ +|+.|||..+++|++++++-++..++. |-+.
T Consensus 80 ~k~~~~~l~~~~ivRl~~EA~dQgalLT~~Dla~LL~~S~~TI~~~vk~ye~~~g~vv 137 (220)
T PF07900_consen 80 KKYKKRELRKHRIVRLFNEAYDQGALLTQEDLAILLGVSPKTISRDVKEYEEEHGEVV 137 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 6751899999999999999986478575999999988898889999999999619652
No 56
>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=85.12 E-value=0.22 Score=26.35 Aligned_cols=41 Identities=20% Similarity=0.264 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 899989999999970889998899998658901145899999
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKL 78 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L 78 (148)
.||..|=.-+.-..+.|+ ++.+||..+|++++|+++++++=
T Consensus 6 ~LTl~eK~~ii~~~e~g~-s~~~iAr~fgi~~sTi~~i~k~k 46 (53)
T PF04218_consen 6 SLTLEEKIEIIKRYEEGK-SQREIAREFGISRSTISRILKNK 46 (53)
T ss_dssp S--HHHHHHHHHHHHC-T--HHHHHHHHT--CCHHHHHCCTH
T ss_pred CCCHHHHHHHHHHHHCCC-CHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 089999999999998499-89999989199888999999839
No 57
>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=84.61 E-value=0.36 Score=24.87 Aligned_cols=50 Identities=16% Similarity=0.248 Sum_probs=39.3
Q ss_pred CCHHHHH-HHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 9998999-9999970889998899998658901145899999984132125
Q T0617 38 IGMTEWR-IISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN 87 (148)
Q Consensus 38 lt~~q~~-iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~ 87 (148)
+....|. ++..+-..-=+|++.|++++.|+-|.+-+.+..|+++|+|...
T Consensus 42 ~dk~t~dki~kEV~k~K~ITps~l~erlkI~~SlAr~~Lr~L~~~G~Ik~V 92 (105)
T PF03297_consen 42 FDKETYDKILKEVPKYKLITPSVLSERLKINGSLARKALRELEEKGLIKPV 92 (105)
T ss_pred ECHHHHHHHHHHHHHCCEECHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf 669999999998400633039998777742489999999999978998998
No 58
>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=83.70 E-value=0.87 Score=22.34 Aligned_cols=42 Identities=14% Similarity=0.383 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 989999999970889998899998658901145899999984
Q T0617 40 MTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEK 81 (148)
Q Consensus 40 ~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~ 81 (148)
..+..+|..|...+.++..+||+.++++.-++..-+..|...
T Consensus 5 ~r~~~Ll~~L~~~~~~t~~ela~~l~~S~~ti~~~I~~l~~~ 46 (59)
T PF08280_consen 5 KRQLKLLELLLKNGWITLKELAKKLGLSERTIRNDINELNEE 46 (59)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 999999999997797979999999798899999999999998
No 59
>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=83.15 E-value=0.2 Score=26.57 Aligned_cols=43 Identities=19% Similarity=0.307 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 89998999999997088999889999865890114589999998
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEE 80 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~ 80 (148)
.|+..+-.++.... .++.|..|||+.+|++.++|++..++-.+
T Consensus 4 ~L~~~er~ii~~~~-~~~~t~~eIa~~lg~s~~~V~~~~~ral~ 46 (50)
T PF04545_consen 4 QLPEREREIIRLRY-FEGLTLEEIAERLGISESTVRQRLKRALR 46 (50)
T ss_dssp TS-HHHHHHHHHHH-TST-CTCCCHHHHHHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHH-CCCCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 19999999999998-49999999998979799999899999999
No 60
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) , play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins , , . This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2hye_C 3dpl_C 3dqv_C 1ldk_B 1u6g_A 1ldj_A.
Probab=83.05 E-value=0.14 Score=27.52 Aligned_cols=53 Identities=15% Similarity=0.299 Sum_probs=43.0
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 99989999999970889998899998658901145899999984132125674
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
++.-|..+|....+.+++|..+|++.+|++...+.+.++.|...|++.....|
T Consensus 519 ~s~~q~~iLllFn~~~~~t~~~i~~~t~~~~~~l~~~L~~l~~~~~~~~~~~~ 571 (589)
T PF00888_consen 519 VSTLQAAILLLFNDQEELTVEEISERTGISEDELKRQLQSLIKAKLLILLKSP 571 (589)
T ss_dssp E-HHHHHHHHCCCTTSEEEHHHHHHHC---HHHHHHHHHHHHCTTTESCCETT
T ss_pred EEHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCC
T ss_conf 62999999999567788579999988791999999999999838831331587
No 61
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove , . This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome; PDB: 2gai_B 2gaj_A 1cy8_A 1cy7_A 1cy1_A 1cy9_B 1cy4_A 1cyy_B 1mw9_X 1cy0_A ....
Probab=82.07 E-value=0.31 Score=25.30 Aligned_cols=51 Identities=20% Similarity=0.363 Sum_probs=39.0
Q ss_pred CHHHHHHHH---CC-CCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHH
Q ss_conf 988999986---58-9011458999999841321256743223000001788899999999
Q T0617 56 SVQKISDIL---GL-DKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVAS 112 (148)
Q Consensus 56 t~~eLa~~l---~i-~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~ 112 (148)
|.+.|-..| |+ +++|-+.+|..|.++|||++. ..+.+..|+.|+.+++.+.
T Consensus 317 Te~tLl~~Me~~GIGTpATra~iI~~L~~r~Yi~~~------k~k~l~pT~~G~~li~~l~ 371 (404)
T PF01131_consen 317 TEATLLKAMEKAGIGTPATRASIIETLKKRGYIERE------KGKKLIPTPLGRALIEALP 371 (404)
T ss_dssp EHHHHHHHHHH-----TTTHHHHHHHHHHTTSEEE-------ETTEEEEB----HHHHHHH
T ss_pred CHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHC------CCCEEEEHHHHHHHHHHHH
T ss_conf 999999999857999877489999998654351113------5774756388999999997
No 62
>PF11994 DUF3489: Protein of unknown function (DUF3489)
Probab=81.95 E-value=0.98 Score=22.00 Aligned_cols=61 Identities=11% Similarity=0.193 Sum_probs=45.2
Q ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHH--HHHHHHHCCCCCCCCCEECCCC
Q ss_conf 9989999999970889998899998658901145899999--9841321256743223000001
Q T0617 39 GMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKL--EEKKYIEVNGHSEDKRTYAINL 100 (148)
Q Consensus 39 t~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L--~~~gli~r~~~~~D~R~~~l~L 100 (148)
+..|..++..|...+|.|+.+|++.+|.-+.++-..+..+ -+.||-.....++ ++...+.+
T Consensus 9 ~sKqa~~i~mL~~p~Gati~~i~~atGWq~HTvRgalaG~~kKKlgl~i~sek~~-g~~r~YrI 71 (72)
T PF11994_consen 9 GSKQAQVIAMLRRPEGATIAEISEATGWQAHTVRGALAGALKKKLGLTITSEKVD-GGGRRYRI 71 (72)
T ss_pred CCHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCEEEEECCC-CCCEEEEE
T ss_conf 6579999999708789989999985386043799999888898609777763168-97026863
No 63
>PF09821 ABC_transp: ABC nitrate/sulfonate/bicarbonate family transporter, ATPase subunit
Probab=81.88 E-value=0.9 Score=22.24 Aligned_cols=58 Identities=28% Similarity=0.283 Sum_probs=46.0
Q ss_pred HHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99998658901145899999984132125674322300000178889999999999999999998
Q T0617 59 KISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIEREKQLL 123 (148)
Q Consensus 59 eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~~~~~~~~~ 123 (148)
+||+.++++-.-...++..++-.|+++... + -+.||+.|++++..-....++...+.+
T Consensus 2 ~La~~l~~~iDdL~pi~eaa~lLgf~~~~~--G-----Di~LT~~G~~f~~~~i~~RK~lf~~~L 59 (120)
T PF09821_consen 2 QLADELQLEIDDLFPIVEAAELLGFAEVEG--G-----DIILTPAGRRFAEADIDERKELFREQL 59 (120)
T ss_pred CHHHHHCCCHHHHHHHHHHHHHCCCEEECC--C-----CEEECHHHHHHHHCCHHHHHHHHHHHH
T ss_conf 557772986678999999999769746569--9-----867788289999789799999999999
No 64
>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=81.67 E-value=0.63 Score=23.28 Aligned_cols=40 Identities=10% Similarity=-0.013 Sum_probs=20.5
Q ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHH
Q ss_conf 58901145899999984132125674322300000178889
Q T0617 65 GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQ 105 (148)
Q Consensus 65 ~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~ 105 (148)
-+++..+-+.++.|...|+=-+...- ++....+.-.|.+.
T Consensus 132 lISp~Di~~A~~~l~~Lg~~~~l~~~-~sg~~~v~s~~~~e 171 (223)
T PF04157_consen 132 LISPEDILKACKKLEKLGLGFKLRKI-GSGVKVVQSVPSSE 171 (223)
T ss_dssp T--HHHHHHHHHHHCCCT-TEEEEEE-TTTEEEEECST-CH
T ss_pred CCCHHHHHHHHHHHHHCCCCEEEEEE-CCCEEEEECCCCHH
T ss_conf 75999999999999984998599996-68606986077202
No 65
>PF09397 Ftsk_gamma: Ftsk gamma domain; PDB: 2ve8_D 2ve9_C 2j5o_A 2j5p_A.
Probab=81.63 E-value=0.71 Score=22.93 Aligned_cols=53 Identities=13% Similarity=0.237 Sum_probs=42.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEC
Q ss_conf 999999708899988999986589011458999999841321256743223000
Q T0617 44 RIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYA 97 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~ 97 (148)
.+..++...+..+++-|-+++.+--..++++++.|++.|.|... +....|.+.
T Consensus 10 ~a~~~V~~~~~~S~S~lQR~lrIGYnrAariid~LE~~GiVs~~-~~~~~ReVL 62 (65)
T PF09397_consen 10 EAVEFVIEEGKASISLLQRRLRIGYNRAARIIDQLEEEGIVSPA-NGSKPREVL 62 (65)
T ss_dssp HHHHHHHHCTCESHHHHHHHHT---HHHHHHHHHHHH---BE--------EEB-
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCC-CCCCCCEEC
T ss_conf 99999998087579999999714799999999999988777887-799898541
No 66
>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=81.11 E-value=0.34 Score=25.03 Aligned_cols=22 Identities=27% Similarity=0.489 Sum_probs=19.9
Q ss_pred CHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 9889999865890114589999
Q T0617 56 SVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 56 t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
|.+|||+..|++.+|||+.++.
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 67
>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=80.54 E-value=0.95 Score=22.07 Aligned_cols=48 Identities=15% Similarity=0.226 Sum_probs=41.8
Q ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 998999999997088999889999865890114589999998413212
Q T0617 39 GMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEV 86 (148)
Q Consensus 39 t~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r 86 (148)
...--.|...|-..|..|.++|....+++++.+-..+-.|.+.|+|.-
T Consensus 12 Ge~~~~V~~~L~~~g~ltl~~i~~~t~l~~~~Vk~~L~~Liqh~~V~y 59 (62)
T PF08221_consen 12 GEIAAKVFECLLSRGRLTLREIVRRTKLSPSQVKKALAVLIQHNCVQY 59 (62)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHCCCCHHHHHHHHHHHHHCCCCHH
T ss_conf 748999999999758949999997839999999999999998086122
No 68
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins .; PDB: 2o9l_A 2ahq_A 2o8k_A.
Probab=80.37 E-value=0.14 Score=27.70 Aligned_cols=28 Identities=25% Similarity=0.483 Sum_probs=24.1
Q ss_pred HHCCCCCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 7088999889999865890114589999
Q T0617 50 SSASDCSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 50 ~~~~~~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
..--|++.+++|+.+|+..|||||.|+.
T Consensus 45 ~~l~Pltl~~vA~~lglheSTVSRav~~ 72 (160)
T PF04552_consen 45 KALKPLTLKDVAEELGLHESTVSRAVSN 72 (160)
T ss_dssp ----------------------------
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHCC
T ss_conf 3576854999999839883057798748
No 69
>PF10711 DUF2513: Hypothetical protein (DUF2513)
Probab=80.33 E-value=0.62 Score=23.30 Aligned_cols=69 Identities=19% Similarity=0.191 Sum_probs=48.5
Q ss_pred HHHHHHHCCCCCHH-HHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCE---ECCCCCHHHHHHHHHHHH
Q ss_conf 99999708899988-9999865890114589999998413212567432230---000017888999999999
Q T0617 45 IISVLSSASDCSVQ-KISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRT---YAINLTEMGQELYEVASD 113 (148)
Q Consensus 45 iL~~l~~~~~~t~~-eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~---~~l~LT~~G~~~~~~~~~ 113 (148)
+|..+-..+..... .....-+.+.-.+...++.|.+.|||+......+... ....||-+|.++++.++.
T Consensus 10 iLl~iE~~~~~~~~~~~~~~~~~s~e~i~YH~~lL~eAgli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~iRd 82 (102)
T PF10711_consen 10 ILLAIEENEKPYHSIDELEIDGYSEEEIIYHLKLLIEAGLIEAEGSGYMDGPISFVIKRLTWSGHDFLDAIRD 82 (102)
T ss_pred HHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCHHHCCCCHHHHHHHHCC
T ss_conf 9999982777665434211147889999999999988878020066557775521010046016689987035
No 70
>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=80.20 E-value=0.69 Score=23.01 Aligned_cols=55 Identities=22% Similarity=0.233 Sum_probs=45.0
Q ss_pred CCCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 289998999999997088999889999865890114589999998413212567432
Q T0617 36 FGIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSED 92 (148)
Q Consensus 36 ~glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D 92 (148)
.++++.+-.|+ .++.. +.++.|||..+++.-+.+.-++..|...|+|........
T Consensus 39 ~~l~pE~~~Il-~lC~~-p~SVAEiAA~L~LPlgVvrVLl~DL~~~G~v~v~~p~~~ 93 (114)
T PF05331_consen 39 PGLGPEHRAIL-RLCRR-PLSVAEIAAHLRLPLGVVRVLLSDLLDAGLVRVRAPVPS 93 (114)
T ss_pred CCCCHHHHHHH-HHHCC-CCCHHHHHHHCCCCCCEEEEEHHHHHHCCCEEEECCCCC
T ss_conf 88898999999-99868-630999998619983011005776976897786079876
No 71
>PF06969 HemN_C: HemN C-terminal region; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX , one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin biosynthetic process, 0005737 cytoplasm; PDB: 1olt_A.
Probab=79.59 E-value=0.82 Score=22.50 Aligned_cols=61 Identities=20% Similarity=0.301 Sum_probs=45.4
Q ss_pred CCHHH---HHHHHHHHHCCCCCHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHH
Q ss_conf 99989---99999997088999889999865890114-5899999984132125674322300000178889
Q T0617 38 IGMTE---WRIISVLSSASDCSVQKISDILGLDKAAV-SRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQ 105 (148)
Q Consensus 38 lt~~q---~~iL~~l~~~~~~t~~eLa~~l~i~~~~v-s~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~ 105 (148)
++..+ ..++.-|....++....+....+.+.... ...++.+++.|+++... ..+.+|++|+
T Consensus 53 ls~~e~~~~~l~~~Lr~~~gld~~~~~~~~g~~~~~~~~~~l~~l~~~gll~~~~-------~~l~lT~~G~ 117 (118)
T PF06969_consen 53 LSPEERLREFLMLGLRLREGLDLAEFEQRFGVDFEEEYQPELARLEEEGLLEIDG-------DRLRLTPKGR 117 (118)
T ss_dssp --HHHHHHHHHHHHHHHHSB--HHHHHHHTT--HHHHTHHHHHHHHH---EE-------------EE-----
T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEEEC-------CEEEECCCCC
T ss_conf 9986999999999987155959899999979689999999999999779899979-------9999893308
No 72
>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=76.80 E-value=0.55 Score=23.69 Aligned_cols=42 Identities=19% Similarity=0.207 Sum_probs=30.9
Q ss_pred CCHHHHHHHH---HHH---HCCCCCHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 9998999999---997---08899988999986589011458999999
Q T0617 38 IGMTEWRIIS---VLS---SASDCSVQKISDILGLDKAAVSRTVKKLE 79 (148)
Q Consensus 38 lt~~q~~iL~---~l~---~~~~~t~~eLa~~l~i~~~~vs~~i~~L~ 79 (148)
+|+.+...|. .|. -.++.|+.+|++.+|++..|+||.=+-|.
T Consensus 27 ~T~~E~~al~~R~~Va~~lL~~~~syreI~~~tG~S~aTIsR~sr~Lk 74 (87)
T PF01371_consen 27 CTPDEREALAQRLQVAKELLRGGKSYREIAEETGASIATISRVSRCLK 74 (87)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHTTHSHHHHHHH----HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf 999999999999999999988799899999997877889999999988
No 73
>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=75.76 E-value=1.1 Score=21.77 Aligned_cols=80 Identities=18% Similarity=0.204 Sum_probs=43.7
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHH--HHHHHHHHHHHHHHH-----HHC
Q ss_conf 8999889999865890114589999998413212567432230000017888999--999999999999999-----857
Q T0617 53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQEL--YEVASDFAIEREKQL-----LEE 125 (148)
Q Consensus 53 ~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~--~~~~~~~~~~~~~~~-----~~~ 125 (148)
.|+|+.+||+.+|.+++.|++.+.-|.--..|..-.+. ++ ++ .+..+ +.............+ -.+
T Consensus 2 ~G~tq~eIA~~lGks~s~Vs~~L~Ll~lp~~v~~~v~~--G~-----is-~~~a~~~L~~~~~~~~~~v~~~v~~~~~~~ 73 (93)
T PF08535_consen 2 FGLTQEEIAKRLGKSRSWVSNHLRLLDLPEDVKEAVEE--GR-----IS-DGRALYELRKLAKKHPQKVEAVVKKAAEEG 73 (93)
T ss_dssp -------HHHH----HHHHHHHHGGGS--HHHHHHHH--------------HHHHHHHHHHHHH-HHHHHHHH-HSTTS-
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHC--CC-----CC-HHHHHHHHHHHHHHCHHHHHHHHHHHHHCC
T ss_conf 89999999999887999999999986699999999995--99-----76-599999989889878999999998862230
Q ss_pred CCHHHHHHHHHHHHH
Q ss_conf 999899999999999
Q T0617 126 FEEAEKDQLFILLKK 140 (148)
Q Consensus 126 l~~ee~~~l~~~L~~ 140 (148)
++..+...+.+-+..
T Consensus 74 lt~~~v~~l~~~lk~ 88 (93)
T PF08535_consen 74 LTRREVEALVKELKE 88 (93)
T ss_dssp -----HHHHHHHHH-
T ss_pred CHHHHHHHHHHHHHH
T ss_conf 219999999999987
No 74
>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=75.59 E-value=2.1 Score=19.82 Aligned_cols=65 Identities=22% Similarity=0.226 Sum_probs=42.3
Q ss_pred HHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC--------------------CCC---CC---CCEECCC
Q ss_conf 999970889998899998658901145899999984132125--------------------674---32---2300000
Q T0617 46 ISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN--------------------GHS---ED---KRTYAIN 99 (148)
Q Consensus 46 L~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~--------------------~~~---~D---~R~~~l~ 99 (148)
=.++...+.++.+++|+.+++.+. ++.+-|.++|++.+. ... .| .-.....
T Consensus 16 d~~~~~~~~~~i~~~AK~lgi~~~---~l~~~Lr~~~il~~~~~~~~~pyq~~~~~G~~~~~~~~~~~~~g~~~~~~~~~ 92 (111)
T PF03374_consen 16 DRFLNSDGSMTIREAAKILGIGPN---KLFKWLREKGILYRRGSGRNLPYQRYIDKGYFEVKTTVYTHSDGNEHIKPQTR 92 (111)
T ss_pred HHHHCCCCCEEHHHHHHHHCCCHH---HHHHHHHHCCCEEECCCCCCCCCHHHHHCCCEEEEEEEEECCCCCEEEEEEEE
T ss_conf 999568995779999999399999---99999998697785689976604689949988998677873899778888889
Q ss_pred CCHHHHHHHHHHHH
Q ss_conf 17888999999999
Q T0617 100 LTEMGQELYEVASD 113 (148)
Q Consensus 100 LT~~G~~~~~~~~~ 113 (148)
+|++|...+.+...
T Consensus 93 vT~kG~~~i~~~l~ 106 (111)
T PF03374_consen 93 VTPKGQEWIAEKLK 106 (111)
T ss_pred EEHHHHHHHHHHHH
T ss_conf 90157999999998
No 75
>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=75.04 E-value=2.1 Score=19.72 Aligned_cols=23 Identities=9% Similarity=-0.041 Sum_probs=15.8
Q ss_pred HHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf 99999998579998999999999
Q T0617 116 IEREKQLLEEFEEAEKDQLFILL 138 (148)
Q Consensus 116 ~~~~~~~~~~l~~ee~~~l~~~L 138 (148)
..++-..|+|++.+|+.....+-
T Consensus 142 ~~velr~f~Glt~~EiA~~LgiS 164 (185)
T PF07638_consen 142 RVVELRYFGGLTVEEIAEALGIS 164 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 99999998799999999896969
No 76
>PF09862 DUF2089: Protein of unknown function(DUF2089)
Probab=74.56 E-value=1.7 Score=20.39 Aligned_cols=45 Identities=16% Similarity=0.357 Sum_probs=35.7
Q ss_pred CCCHHHHHHHH-HHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH-HHH
Q ss_conf 89998999999-997088999889999865890114589999998-413
Q T0617 37 GIGMTEWRIIS-VLSSASDCSVQKISDILGLDKAAVSRTVKKLEE-KKY 83 (148)
Q Consensus 37 glt~~q~~iL~-~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~-~gl 83 (148)
.|+..++..+. +|...| +.+++++.++++-+||-.-++++.+ -|+
T Consensus 33 ~L~~E~l~Fi~~Fl~~~G--nlKe~ak~lgiSYpTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 33 RLSPEDLEFIKLFLKCRG--NLKEVAKELGISYPTVRNRLDRIIEKLGY 79 (113)
T ss_pred CCCHHHHHHHHHHHHHCC--CHHHHHHHHCCCHHHHHHHHHHHHHHHCC
T ss_conf 499999999999999189--89999999788828999999999998179
No 77
>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=74.38 E-value=0.73 Score=22.84 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=24.1
Q ss_pred HHHHCCCCCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 997088999889999865890114589999
Q T0617 48 VLSSASDCSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 48 ~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
.+...-++|+.++|+.+++++++++++.+.
T Consensus 3 ~~r~~~gls~~~la~~~gis~~~i~~~e~g 32 (55)
T PF01381_consen 3 KLREERGLSQEELARRLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHTT--HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHCCCCHHHHHHHCCCCHHHHHHHHCC
T ss_conf 989786999999988649878788899769
No 78
>PF09382 RQC: RQC domain; PDB: 1oyy_A 1oyw_A 2axl_A 2v1x_B.
Probab=74.12 E-value=0.76 Score=22.72 Aligned_cols=45 Identities=16% Similarity=0.203 Sum_probs=36.2
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHH
Q ss_conf 65890114589999998413212567432230000017888999999
Q T0617 64 LGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEV 110 (148)
Q Consensus 64 l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~ 110 (148)
-++++.-+.++++.|...||+....+. .....+.+|++|++++..
T Consensus 52 k~~~~~~~~~li~~Li~~g~L~~~~~~--~~~~~l~l~~~~~~~l~g 96 (106)
T PF09382_consen 52 KDLSKSEWERLIRQLIAEGYLKESNEH--FTYPYLKLGPKAKEVLKG 96 (106)
T ss_dssp -SS-HHHHHHHHHHHHHTTSEEEECCT--CCTCEEEE-GGGHHHHCC
T ss_pred CCCCHHHHHHHHHHHHHCCCEEECCCC--CCCCEEEECHHHHHHHCC
T ss_conf 769999999999999987995732775--542279999769999779
No 79
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions .; GO: 0006276 plasmid maintenance
Probab=72.52 E-value=2 Score=19.89 Aligned_cols=55 Identities=24% Similarity=0.208 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHCCCC---------CHHHHHH-HHHHHHHHHH--CCCCCCCCCE--ECCCCCHHHHHHH
Q ss_conf 999889999865890---------1145899-9999841321--2567432230--0000178889999
Q T0617 54 DCSVQKISDILGLDK---------AAVSRTV-KKLEEKKYIE--VNGHSEDKRT--YAINLTEMGQELY 108 (148)
Q Consensus 54 ~~t~~eLa~~l~i~~---------~~vs~~i-~~L~~~gli~--r~~~~~D~R~--~~l~LT~~G~~~~ 108 (148)
++++.+||+..|++. +-+||.+ ..|+..|+|+ +..|+.+++. +.|.|||.+..++
T Consensus 95 ~~sie~LA~ecGLst~s~~Gn~sItRasR~i~e~le~~Gli~~~~~~D~~~~~~~Pk~I~lT~~FF~l~ 163 (281)
T PF02387_consen 95 QASIEQLADECGLSTKSKAGNKSITRASRLITEFLEPMGLITCEKEWDPYNGNYIPKHIWLTPLFFMLL 163 (281)
T ss_pred HCCHHHHHHHHCCCCCCCCCCEEHHHHHHHHHHHHHHCCCEEEEEEECHHHCCCCCEEEEECHHHHHHH
T ss_conf 204999999809875288999607899999999998647844332353322363680799878999983
No 80
>PF10668 Phage_terminase: Phage terminase small subunit
Probab=70.72 E-value=1.2 Score=21.41 Aligned_cols=28 Identities=14% Similarity=0.292 Sum_probs=23.6
Q ss_pred HHHHHCCCCCHHHHHHHHCCCCCHHHHH
Q ss_conf 9997088999889999865890114589
Q T0617 47 SVLSSASDCSVQKISDILGLDKAAVSRT 74 (148)
Q Consensus 47 ~~l~~~~~~t~~eLa~~l~i~~~~vs~~ 74 (148)
.++...|.++..+||+.++++.++|+.-
T Consensus 15 ~y~~~~g~~~~k~IAe~lgvs~~tIr~W 42 (60)
T PF10668_consen 15 IYKESNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHCCCCCCHHHHHHHHCCCHHHHHHH
T ss_conf 9998189841999999979799998734
No 81
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=67.78 E-value=3.1 Score=18.66 Aligned_cols=75 Identities=17% Similarity=0.212 Sum_probs=44.4
Q ss_pred HCCCCHHHHHHHHHHHH-------CCC--CCHHHHHH----HHCCCCC-HHHHHHHHHHHHHHHHCCCCCCCCCEECCCC
Q ss_conf 72899989999999970-------889--99889999----8658901-1458999999841321256743223000001
Q T0617 35 KFGIGMTEWRIISVLSS-------ASD--CSVQKISD----ILGLDKA-AVSRTVKKLEEKKYIEVNGHSEDKRTYAINL 100 (148)
Q Consensus 35 ~~glt~~q~~iL~~l~~-------~~~--~t~~eLa~----~l~i~~~-~vs~~i~~L~~~gli~r~~~~~D~R~~~l~L 100 (148)
.|+|+..+..+|..|.+ +|+ .|..+|.+ ..+-+-. .+...+..|+..|||++..+.. + .-.+.+
T Consensus 282 ~f~le~~e~~vLk~Id~iwkK~~~NPe~~PT~~eI~~~l~~ew~~~~~d~l~~~Ly~LEaf~LI~~~~~~~-G-K~vY~l 359 (591)
T PF04458_consen 282 SFALEVDEEEVLKAIDHIWKKYEENPEIIPTFKEIKRELIEEWFEKNFDDLGEALYSLEAFGLIESEVHEK-G-KAVYWL 359 (591)
T ss_pred CEECCHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHC-C-CEEEEE
T ss_conf 63136889999999999974145897658888999999999987602058999999877754688888753-8-547986
Q ss_pred CHHHHHHHHHH
Q ss_conf 78889999999
Q T0617 101 TEMGQELYEVA 111 (148)
Q Consensus 101 T~~G~~~~~~~ 111 (148)
|+-|+++++..
T Consensus 360 Te~G~kvled~ 370 (591)
T PF04458_consen 360 TEYGEKVLEDQ 370 (591)
T ss_pred HHHHHHHHHHH
T ss_conf 17569998754
No 82
>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=65.02 E-value=1.7 Score=20.48 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 899988999986589011458999999841321
Q T0617 53 SDCSVQKISDILGLDKAAVSRTVKKLEEKKYIE 85 (148)
Q Consensus 53 ~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~ 85 (148)
.|.++.+||+.++++++||..-+++-...|+.-
T Consensus 12 ~G~~~~eIA~~Lgv~~~TV~~W~~r~~w~~~~~ 44 (58)
T PF06056_consen 12 QGYTPKEIAEELGVSRRTVYSWKKRYGWDGLLP 44 (58)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCC
T ss_conf 689999999998868889999999756166674
No 83
>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=64.79 E-value=3.5 Score=18.29 Aligned_cols=40 Identities=13% Similarity=0.320 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHC-CC-CCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 999899999999708-89-99889999865890114589999
Q T0617 38 IGMTEWRIISVLSSA-SD-CSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 38 lt~~q~~iL~~l~~~-~~-~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
||+.+..-+..|... |. .|...||+.+.+++-+|.|+++.
T Consensus 11 Ls~~~~e~IR~Lh~~~Pe~~t~~~LAe~F~vSpeaIrRILKS 52 (225)
T PF06413_consen 11 LSREAMEQIRLLHQQDPEEWTTERLAESFKVSPEAIRRILKS 52 (225)
T ss_pred CCHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHC
T ss_conf 899999999999885923047999987679999999999973
No 84
>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=63.35 E-value=2 Score=19.87 Aligned_cols=55 Identities=20% Similarity=0.367 Sum_probs=37.1
Q ss_pred HHHHHHHHCCCCCHHHHHHHH-----CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHH
Q ss_conf 999999708899988999986-----5890114589999998413212567432230000017888999
Q T0617 44 RIISVLSSASDCSVQKISDIL-----GLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQEL 107 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l-----~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~ 107 (148)
.|+..+..+|..|..+|+..+ .++++||.+.++.. ||-.+.+. .+. .||++-++.
T Consensus 3 ~I~~~i~~~p~~T~~~l~~~l~~~~~~vS~~Tv~R~L~~~---G~~~~~~~-----~kP-~Ls~~~~~~ 62 (72)
T PF01498_consen 3 RIIRIIRRNPRITLRELARELQEEGISVSKSTVRRRLKEM---GYRKRKAR-----KKP-LLSEKHKKA 62 (72)
T ss_dssp HHHH-HHHH----HHHHHHHT---T--S-HHHHHHHHHH------------------------HHHHHH
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHC---CCEEECCC-----CCC-CCCHHHHHH
T ss_conf 8999998788624999999998658997999999999986---89202778-----899-999999999
No 85
>PF08721 TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5, end of the transposon is carried out by TnsA, and breakage and joining at the 3, end is carried out by TnsB. The C terminal domain of TnsA binds DNA. ; PDB: 1f1z_B 1t0f_A.
Probab=62.95 E-value=3.5 Score=18.30 Aligned_cols=42 Identities=17% Similarity=0.226 Sum_probs=38.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHH----CCCCCHHHHHHHHHHHHHHHH
Q ss_conf 999999708899988999986----589011458999999841321
Q T0617 44 RIISVLSSASDCSVQKISDIL----GLDKAAVSRTVKKLEEKKYIE 85 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l----~i~~~~vs~~i~~L~~~gli~ 85 (148)
.++..+.+.|+.|+.++...+ +++++..-..+..|.+.+.|.
T Consensus 31 ~i~~~l~~~~~~ti~~l~~~~d~~~~l~~g~~l~~l~~LIA~k~i~ 76 (79)
T PF08721_consen 31 LILEYLRENGTTTIRQLLAELDDDYNLEPGTSLPLLRHLIATKQIY 76 (79)
T ss_dssp HHHHHHHH----BHHHHHHHHHHHCT-----HHHHHHHHHH---EE
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCHHC
T ss_conf 9999999869988999999998752888677199999998457200
No 86
>PF11972 HTH_13: HTH DNA binding domain
Probab=62.58 E-value=3.8 Score=18.11 Aligned_cols=36 Identities=31% Similarity=0.355 Sum_probs=29.6
Q ss_pred HHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 999997088999889999865890114589999998
Q T0617 45 IISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEE 80 (148)
Q Consensus 45 iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~ 80 (148)
++..+...|=.|..-+++.+++|++++.+++..|.-
T Consensus 4 Lidll~~~PlVSa~mia~~l~vt~~~A~rlv~~lgl 39 (54)
T PF11972_consen 4 LIDLLLSRPLVSAPMIAKELGVTRQAAQRLVAELGL 39 (54)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCC
T ss_conf 999999474242999999978789999999998275
No 87
>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=61.61 E-value=4 Score=17.91 Aligned_cols=34 Identities=24% Similarity=0.437 Sum_probs=26.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 99999970889998899998658901145899999
Q T0617 44 RIISVLSSASDCSVQKISDILGLDKAAVSRTVKKL 78 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L 78 (148)
.+...+..+++ ++++.|+.+|++++++.+-+++.
T Consensus 9 ~i~~aL~~~~g-n~~~aA~~Lgi~r~tL~~klkk~ 42 (42)
T PF02954_consen 9 LIEEALERHGG-NISKAARLLGISRSTLYRKLKKY 42 (42)
T ss_dssp HHHHHHHHTTT--HHHHHHH----HHHHHHHHHH-
T ss_pred HHHHHHHHHCC-CHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 99999998299-89999999798999999999849
No 88
>PF07506 RepB: RepB plasmid partitioning protein; InterPro: IPR011111 This family includes proteins with sequence similarity to the RepB partitioning protein of the large Ti (tumour-inducing) plasmids of Agrobacterium tumefaciens , .
Probab=60.47 E-value=4.2 Score=17.78 Aligned_cols=40 Identities=23% Similarity=0.314 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHH
Q ss_conf 8999899999999708899988999986589011458999
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVK 76 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~ 76 (148)
+|++-|-..+..=-...|.+...|+..++++++.+|+++.
T Consensus 4 ~Ls~IE~~~~a~~l~~~G~~~~~I~~aL~~~~~~ls~~~~ 43 (185)
T PF07506_consen 4 DLSFIERARFARRLEERGFSREEIAAALGVDKSTLSRMLS 43 (185)
T ss_pred CCCHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 4769999999999998699989999997899999999898
No 89
>PF06224 DUF1006: Protein of unknown function (DUF1006); InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=59.37 E-value=4.4 Score=17.66 Aligned_cols=60 Identities=10% Similarity=-0.001 Sum_probs=44.5
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHC------CCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHH
Q ss_conf 999999997088999889999865------89011458999999841321256743223000001788
Q T0617 42 EWRIISVLSSASDCSVQKISDILG------LDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEM 103 (148)
Q Consensus 42 q~~iL~~l~~~~~~t~~eLa~~l~------i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~ 103 (148)
--.|+..|..+|+++.+||...-. .+.+.....+..|--.|.|...+.. +..+.+.||+.
T Consensus 121 ~~~Vl~~i~~~Gpl~~~dl~~~~~~~~g~wW~~~~~k~aLe~L~~~G~l~v~~R~--g~~r~YdL~er 186 (371)
T PF06224_consen 121 LDAVLARIRARGPLTARDLEHEEPRGSGGWWNWSPSKRALEYLFWAGELCVAPRR--GFERVYDLTER 186 (371)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHCCEEEEECCC--CCEEEEECCCC
T ss_conf 9999999996699678886420267778877676489999999968879981567--97578736010
No 90
>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=58.90 E-value=3 Score=18.78 Aligned_cols=44 Identities=16% Similarity=0.270 Sum_probs=39.0
Q ss_pred HHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99997088999889999865890114589999998413212567
Q T0617 46 ISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 46 L~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
..++..++++++++.-+.+|+++-.+-.++..|-+.|+..|..+
T Consensus 2 ~~~~~~~~~i~va~~rd~~g~sRK~ai~lLE~~D~~~~T~R~gd 45 (50)
T PF09107_consen 2 RELLKKNGEITVAEFRDALGLSRKYAIPLLEYFDREGITRRVGD 45 (50)
T ss_dssp HHHHHT---BEHHHHHHH----HHHHHHHHHHHHHTTSEEE---
T ss_pred HHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEECC
T ss_conf 57882489572999999978539999999998750298786399
No 91
>PF10654 DUF2481: Protein of unknown function (DUF2481)
Probab=57.49 E-value=2.8 Score=18.95 Aligned_cols=37 Identities=16% Similarity=0.265 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 89998999999997088999889999865890114589999
Q T0617 37 GIGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 37 glt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
.++..||.-| .+.|+|..+||+.+++++++|...+++
T Consensus 67 ei~i~Ef~~l----R~AGvt~~~IAd~F~Isks~v~Nf~qr 103 (126)
T PF10654_consen 67 EITIREFAEL----RHAGVTWYAIADHFNISKSTVFNFTQR 103 (126)
T ss_pred CCCHHHHHHH----HHCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf 1219999999----964887899999828739999999998
No 92
>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=56.67 E-value=4.9 Score=17.36 Aligned_cols=81 Identities=11% Similarity=0.232 Sum_probs=38.1
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHH-HHH----------------HHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 9988999986589011458999999-841----------------32125674322300000178889999999999999
Q T0617 55 CSVQKISDILGLDKAAVSRTVKKLE-EKK----------------YIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIE 117 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~i~~L~-~~g----------------li~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~~~ 117 (148)
+++++||+.+|+.++||+.-++.+. .-| ++.......+.-.-.-.+||+-++-|.+.......
T Consensus 2 ~nI~qla~~~glhRqTV~~Rl~~~~pa~g~~~~~~lY~l~dv~~~l~~~~~~~~~~~~~p~~m~P~dRKaw~qSE~eRlk 81 (152)
T PF07278_consen 2 LNINQLAELFGLHRQTVAKRLKGANPAAGSNSGLKLYRLRDVLPALFAAPMSADDEEMDPRDMTPKDRKAWYQSENERLK 81 (152)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf 87999999984219999999707998878777986104999999994798864423248101587999999996788999
Q ss_pred HHHHHHHCCCHHHHHHHH
Q ss_conf 999998579998999999
Q T0617 118 REKQLLEEFEEAEKDQLF 135 (148)
Q Consensus 118 ~~~~~~~~l~~ee~~~l~ 135 (148)
++.+.-+-+..+|+..-.
T Consensus 82 ~E~et~qLipa~eV~~~~ 99 (152)
T PF07278_consen 82 FEKETGQLIPASEVRREY 99 (152)
T ss_pred HHHHHHHHCCHHHHHHHH
T ss_conf 999871115199999999
No 93
>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=54.79 E-value=3 Score=18.73 Aligned_cols=27 Identities=19% Similarity=0.416 Sum_probs=21.6
Q ss_pred HHHHCCCCCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 997088999889999865890114589999
Q T0617 48 VLSSASDCSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 48 ~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
++.++| |+.+|+.+|+.++++|+.+..
T Consensus 9 Y~~~~G---Qak~A~~lGV~qsAISKaira 35 (59)
T PF09048_consen 9 YVEEHG---QAKAAKALGVTQSAISKAIRA 35 (59)
T ss_dssp HHHH-----HHHHHHH----HHHHHHHHH-
T ss_pred HHHHHH---HHHHHHHCCCCHHHHHHHHHH
T ss_conf 999976---799999829768999999982
No 94
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR001669 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein . Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1b4a_C 1f9n_A 2p5l_H 2p5k_A 3fhz_C 3ere_D 1aoy_A.
Probab=53.36 E-value=5 Score=17.28 Aligned_cols=46 Identities=13% Similarity=0.232 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHH-----CCCCCHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 899999999708899988999986-----58901145899999984132125674
Q T0617 41 TEWRIISVLSSASDCSVQKISDIL-----GLDKAAVSRTVKKLEEKKYIEVNGHS 90 (148)
Q Consensus 41 ~q~~iL~~l~~~~~~t~~eLa~~l-----~i~~~~vs~~i~~L~~~gli~r~~~~ 90 (148)
.+-.+...|..++-.++.||.+.+ .++.+|+||-++. .|.+. .++.
T Consensus 6 R~~~I~~lI~~~~I~tQ~eL~~~L~~~Gi~vTQaTiSRDl~e---L~~vK-v~~~ 56 (70)
T PF01316_consen 6 RQELIKELIKEEEISTQEELVELLEERGIEVTQATISRDLKE---LGAVK-VRNG 56 (70)
T ss_dssp HHHHHHHHHHCS---SHHHHHHHHHH------HHHHHHHHHH---CT-EE-EE-T
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHH---CCCEE-EECC
T ss_conf 999999999868988999999999985987038889999998---49888-3179
No 95
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3bz6_A.
Probab=53.14 E-value=3.8 Score=18.09 Aligned_cols=46 Identities=15% Similarity=0.271 Sum_probs=27.0
Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEEC--------CCCCHHHHHHHHH
Q ss_conf 86589011458999999841321256743223000--------0017888999999
Q T0617 63 ILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYA--------INLTEMGQELYEV 110 (148)
Q Consensus 63 ~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~--------l~LT~~G~~~~~~ 110 (148)
.|.++-+.|...++.|.++|+|.. +....|... +.+++...+++..
T Consensus 43 Vm~lse~eV~~ald~L~~~~Lv~~--~~~gsRv~ky~H~~~~~l~l~~~~~All~~ 96 (148)
T PF04337_consen 43 VMNLSESEVQQALDELRKKGLVRE--SGFGSRVPKYEHRFCNTLQLSPQELALLCL 96 (148)
T ss_dssp -----------HHHHH-----EEE---E------EEEE-S-------HHHHHH---
T ss_pred CCCCCHHHHHHHHHHHHHCCCEEE--CCCCCCHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf 626789999999999997847001--267751489999887761898789999999
No 96
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.
Probab=52.67 E-value=4.2 Score=17.80 Aligned_cols=46 Identities=22% Similarity=0.257 Sum_probs=37.1
Q ss_pred HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHH
Q ss_conf 6589011458999999841321256743223000001788899999999
Q T0617 64 LGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVAS 112 (148)
Q Consensus 64 l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~ 112 (148)
+++.-=.|...++.|..+|||..+-+ =|-....||+.|.+.+.+..
T Consensus 33 ~~vpNL~Vik~mqSL~Srg~Vkeqfa---WrhyYw~LT~eGieyLR~yL 78 (95)
T PF03501_consen 33 LDVPNLHVIKAMQSLKSRGYVKEQFA---WRHYYWYLTNEGIEYLREYL 78 (95)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHEEE---EEEEEEEECHHHHHHHHHHH
T ss_conf 68873189999874410434530663---36789998738799999872
No 97
>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=52.20 E-value=4.1 Score=17.88 Aligned_cols=27 Identities=30% Similarity=0.383 Sum_probs=22.1
Q ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 889998899998658901145899999
Q T0617 52 ASDCSVQKISDILGLDKAAVSRTVKKL 78 (148)
Q Consensus 52 ~~~~t~~eLa~~l~i~~~~vs~~i~~L 78 (148)
..+.++.+||..+|++++..++..++-
T Consensus 6 ~~~~~i~~iA~~~g~s~~~~~r~Fk~~ 32 (42)
T PF00165_consen 6 SEPISIEDIAEELGYSPSYFSRLFKKE 32 (42)
T ss_dssp CSS--HHHHHHHTTSSHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 898979999999798999999999999
No 98
>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=51.45 E-value=5.5 Score=17.02 Aligned_cols=31 Identities=13% Similarity=0.409 Sum_probs=23.5
Q ss_pred HHHHHHCC--CCCHHHHHHHHCCCCCHHHHHHH
Q ss_conf 99997088--99988999986589011458999
Q T0617 46 ISVLSSAS--DCSVQKISDILGLDKAAVSRTVK 76 (148)
Q Consensus 46 L~~l~~~~--~~t~~eLa~~l~i~~~~vs~~i~ 76 (148)
+..+.++| +.|+.+||+..|++++++.+.-.
T Consensus 6 ~~l~~~~G~~~~t~~~ia~~agvs~~~iy~~F~ 38 (47)
T PF00440_consen 6 IELFAERGYEAVTIRDIAERAGVSRGSIYRHFP 38 (47)
T ss_dssp HHHHHHS-GTTSSHHHHHHHHTSBHHHHHHHSS
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCCCCHHHHCC
T ss_conf 999998592218799999876479350256569
No 99
>PF11855 DUF3375: Protein of unknown function (DUF3375)
Probab=49.76 E-value=6.2 Score=16.64 Aligned_cols=47 Identities=4% Similarity=0.038 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHH--HHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHH
Q ss_conf 901145899999984--132125674322300000178889999999999
Q T0617 67 DKAAVSRTVKKLEEK--KYIEVNGHSEDKRTYAINLTEMGQELYEVASDF 114 (148)
Q Consensus 67 ~~~~vs~~i~~L~~~--gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~ 114 (148)
.+.+....++...+. ||+.+..++.+ ...++.||+.....+.-+...
T Consensus 64 ~p~~a~~yl~~W~~~~~gwL~r~~~~~~-~e~~y~LT~~a~~Al~~v~~L 112 (478)
T PF11855_consen 64 LPQSARAYLNDWVAQDKGWLRRRYPPGS-DEEVYELTPAAEKALDFVDRL 112 (478)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHCCCCCC-CCEEEECCHHHHHHHHHHHHH
T ss_conf 6602999999999987678885177889-971686088999999999983
No 100
>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=47.54 E-value=3.6 Score=18.19 Aligned_cols=33 Identities=9% Similarity=0.312 Sum_probs=23.8
Q ss_pred CHHHHHHHHCCCCCHHHHHHHHHHHHHHHH-CCCCCCC
Q ss_conf 988999986589011458999999841321-2567432
Q T0617 56 SVQKISDILGLDKAAVSRTVKKLEEKKYIE-VNGHSED 92 (148)
Q Consensus 56 t~~eLa~~l~i~~~~vs~~i~~L~~~gli~-r~~~~~D 92 (148)
|++|+|+.+|++.++ |...++.|+|. ...++..
T Consensus 1 ti~e~a~~~gvs~~t----lR~ye~~gll~~~~r~~~g 34 (38)
T PF00376_consen 1 TIGEVAKLLGVSVRT----LRYYEREGLLPPPRRTENG 34 (38)
T ss_dssp EHHHHHHHCT--HHH----HHHHHHTTSSTTSEETTT-
T ss_pred CHHHHHHHHCCCHHH----HHHHHHCCCCCCCCCCCCC
T ss_conf 989999998969999----9999987898998569998
No 101
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins .; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1zg3_A 1zgj_A 1zga_A 1zhf_A 1kyz_E 1kyw_A 1fp1_D 1fpq_A 1fpx_A 1fp2_A ....
Probab=46.92 E-value=5.5 Score=16.99 Aligned_cols=38 Identities=13% Similarity=0.208 Sum_probs=25.8
Q ss_pred HHHHHHHHHHCC--CCCHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 999999997088--99988999986589011458999999
Q T0617 42 EWRIISVLSSAS--DCSVQKISDILGLDKAAVSRTVKKLE 79 (148)
Q Consensus 42 q~~iL~~l~~~~--~~t~~eLa~~l~i~~~~vs~~i~~L~ 79 (148)
|..+.-.|..+| ++|.+||+..+...++.....+.|+-
T Consensus 8 eLgI~diI~~~g~~~ls~~ela~~l~~~~p~~~~~L~Rim 47 (51)
T PF08100_consen 8 ELGIPDIIHNAGGGPLSLSELAAALPTINPSAPPMLDRIM 47 (51)
T ss_dssp HTTHHHHHHH-S---EEHHHHHHHCTG--GGGHHHHHHHH
T ss_pred HCCCHHHHHHCCCCCCCHHHHHHHCCCCCCCHHHHHHHHH
T ss_conf 8384999988489887999999865767830267998799
No 102
>PF02650 HTH_WhiA: Sporulation Regulator WhiA C terminal domain; InterPro: IPR003802 This entry describes proteins of unknown function.
Probab=46.79 E-value=6.9 Score=16.34 Aligned_cols=43 Identities=21% Similarity=0.379 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHH--CCCCCHHHHHHHHHHH
Q ss_conf 999899999999708899988999986--5890114589999998
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDIL--GLDKAAVSRTVKKLEE 80 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l--~i~~~~vs~~i~~L~~ 80 (148)
++.....+...=-++|..+..||++.+ .+|+|.|..-++++.+
T Consensus 143 lp~~l~~~a~lRl~~Pd~SL~ELge~l~~~isKSgvnhrlrKl~~ 187 (190)
T PF02650_consen 143 LPEKLREIAKLRLENPDASLKELGELLEPPISKSGVNHRLRKLEK 187 (190)
T ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf 999999999999869403699999870799889999999999999
No 103
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 This family consists of several phage CII regulatory proteins. CII plays a key role in the lysis-lysogeny decision in bacteriophage lambda and related phages .; GO: 0003677 DNA binding, 0030528 transcription regulator activity, 0045449 regulation of transcription; PDB: 1xwr_B 1zs4_B 1zpq_D.
Probab=46.33 E-value=5.9 Score=16.82 Aligned_cols=31 Identities=29% Similarity=0.483 Sum_probs=23.8
Q ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHH
Q ss_conf 9999999970889998899998658901145899
Q T0617 42 EWRIISVLSSASDCSVQKISDILGLDKAAVSRTV 75 (148)
Q Consensus 42 q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i 75 (148)
+-.+|..|.. ++++.+|+.+|++.|++||.-
T Consensus 14 es~iL~rlA~---vgQ~~vA~~~Gv~eS~ISR~k 44 (91)
T PF05269_consen 14 ESEILNRLAS---VGQKKVAKAMGVDESTISRWK 44 (91)
T ss_dssp HHHHHHHHHH------HHHHHH----TTTHHHHH
T ss_pred HHHHHHHHHH---HHHHHHHHHHCCCHHHHHHCC
T ss_conf 9999999999---710999999499698875014
No 104
>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=46.08 E-value=3.2 Score=18.55 Aligned_cols=33 Identities=21% Similarity=0.307 Sum_probs=22.4
Q ss_pred HHHHHHH-CCCCCHHHHHHHHCCCCCHHH-HHHHH
Q ss_conf 9999970-889998899998658901145-89999
Q T0617 45 IISVLSS-ASDCSVQKISDILGLDKAAVS-RTVKK 77 (148)
Q Consensus 45 iL~~l~~-~~~~t~~eLa~~l~i~~~~vs-~~i~~ 77 (148)
++..|.+ .|-.+.++||+.+|++++++| ...++
T Consensus 2 ~i~Rl~~~~g~~~~~elA~~LgIs~stvs~~~~~r 36 (66)
T PF07022_consen 2 VIERLKEAYGIKTDKELAEKLGISQSTVSHTWKKR 36 (66)
T ss_dssp HHHHHHHH----SCHHHHCCTT--HHHHH-HHHH-
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHC
T ss_conf 89999999689969999999199888855676416
No 105
>PF06242 DUF1013: Protein of unknown function (DUF1013); InterPro: IPR010421 This is a family of uncharacterised proteins found in Proteobacteria.
Probab=45.44 E-value=7.2 Score=16.22 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=28.2
Q ss_pred HHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHH
Q ss_conf 999999708899988999986589011458999
Q T0617 44 RIISVLSSASDCSVQKISDILGLDKAAVSRTVK 76 (148)
Q Consensus 44 ~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~ 76 (148)
.++..|..+|.++-.+|++.+|.+++|+..+=+
T Consensus 73 aI~wl~r~hPel~D~qI~kLiGTTk~TI~~IRd 105 (140)
T PF06242_consen 73 AIAWLLRNHPELSDAQIAKLIGTTKPTIEAIRD 105 (140)
T ss_pred HHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHC
T ss_conf 677998609842377878874576889999861
No 106
>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=43.04 E-value=2.1 Score=19.79 Aligned_cols=32 Identities=16% Similarity=0.217 Sum_probs=27.9
Q ss_pred HHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf 99708899988999986589011458999999
Q T0617 48 VLSSASDCSVQKISDILGLDKAAVSRTVKKLE 79 (148)
Q Consensus 48 ~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~ 79 (148)
.....++.+++++|..+||+++++.+.++...
T Consensus 17 ~~~~~~g~s~~~va~~~gI~~~tl~~W~~~~~ 48 (76)
T PF01527_consen 17 EEALEEGRSVSEVAREYGISPSTLYRWVRQYR 48 (76)
T ss_dssp HHHCHH-HHHHHHCCC----HHHHHHHHHHHH
T ss_pred HHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 99998799799999970533026669999986
No 107
>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=42.96 E-value=5.9 Score=16.78 Aligned_cols=25 Identities=28% Similarity=0.468 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 8999889999865890114589999
Q T0617 53 SDCSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 53 ~~~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
.|.+..++|+.++++..||.+.|+.
T Consensus 62 ~G~siR~iArvl~Is~~Tv~r~lK~ 86 (88)
T PF03811_consen 62 EGMSIRDIARVLGISINTVLRWLKN 86 (88)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 6851999999868789999999862
No 108
>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=42.71 E-value=2.4 Score=19.39 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=23.3
Q ss_pred HHCCCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 86589011458999999841321256743
Q T0617 63 ILGLDKAAVSRTVKKLEEKKYIEVNGHSE 91 (148)
Q Consensus 63 ~l~i~~~~vs~~i~~L~~~gli~r~~~~~ 91 (148)
.+..+.+.+-+.+..|..+|||+|..+..
T Consensus 39 ~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~ 67 (68)
T PF10557_consen 39 RFPPTVSDIKKRIEYLIEKEYIERDENDP 67 (68)
T ss_dssp SS---HHHHHHHHHHHHHTTSEEEESSET
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 47999999999999999854887188999
No 109
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha)
Probab=41.44 E-value=8.3 Score=15.81 Aligned_cols=56 Identities=20% Similarity=0.281 Sum_probs=40.9
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHHHHH-----HHHHC----C-CCCCCCCEECCCCCHHHHHHHHH
Q ss_conf 998899998658901145899999984-----13212----5-67432230000017888999999
Q T0617 55 CSVQKISDILGLDKAAVSRTVKKLEEK-----KYIEV----N-GHSEDKRTYAINLTEMGQELYEV 110 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~i~~L~~~-----gli~r----~-~~~~D~R~~~l~LT~~G~~~~~~ 110 (148)
++..+||+.++..+..|-+.|.++..+ |.+.- . .+...+....+.||..|-.++.-
T Consensus 2 ~tS~~IAe~~~k~H~~Vlr~Ir~~~~~~~~~f~~~~f~~~~~y~~~~g~~~~~Y~L~k~~~~llv~ 67 (92)
T PF09669_consen 2 TTSREIAELFGKRHKNVLRDIRKLIEDCSEEFGSLNFFIESSYKDGNGRSYPCYLLTKDGFMLLVM 67 (92)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCHHHHHH
T ss_conf 778999999881689999999999987424305545665443227899575699986460788786
No 110
>PF10771 DUF2582: Protein of unknown function (DUF2582)
Probab=40.47 E-value=8.6 Score=15.71 Aligned_cols=50 Identities=20% Similarity=0.318 Sum_probs=38.8
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 99989999999970889998899998658901145899999984132125
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN 87 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~ 87 (148)
+....-.|-..|...++++.++|++..+++..-+...+.=|.+.+=|...
T Consensus 6 IG~nAG~Iw~~L~e~~~~s~~~Lkk~~~l~~~~~~~AiGWLarE~KI~~~ 55 (65)
T PF10771_consen 6 IGENAGKIWHLLNENGEWSYKELKKATGLSDKELALAIGWLARENKIEFE 55 (65)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEE
T ss_conf 88989999999733887889999988498989999988888516716787
No 111
>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=39.68 E-value=7.1 Score=16.27 Aligned_cols=49 Identities=20% Similarity=0.293 Sum_probs=30.8
Q ss_pred HHHHHHCC---CCCHHHHHHHHHHHHHHHHCCCC---CCCCCEECCCCCHHHHHH
Q ss_conf 99998658---90114589999998413212567---432230000017888999
Q T0617 59 KISDILGL---DKAAVSRTVKKLEEKKYIEVNGH---SEDKRTYAINLTEMGQEL 107 (148)
Q Consensus 59 eLa~~l~i---~~~~vs~~i~~L~~~gli~r~~~---~~D~R~~~l~LT~~G~~~ 107 (148)
+|++..++ +...++.+++.|+..|+|..... ...+|...+.|...-..+
T Consensus 27 ~lc~~~~~~pls~~r~~~~l~~L~~~gli~~~~~~~G~~~G~~~~~~L~~~~~~v 81 (85)
T PF09079_consen 27 ELCEKIGVDPLSQRRFSDILSELEMLGLIESERKSRGRGRGRTREISLNVDPEDV 81 (85)
T ss_dssp HHHHHCTS----HHHHHHHHHHHHH---EEEEEE--------EEEEEEESSSHHH
T ss_pred HHHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEECCCHHHH
T ss_conf 9999848999989999999999985787034332688888815899856999999
No 112
>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=39.36 E-value=5.1 Score=17.23 Aligned_cols=38 Identities=11% Similarity=0.288 Sum_probs=31.0
Q ss_pred HHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf 99999997088999889999865890114589999998
Q T0617 43 WRIISVLSSASDCSVQKISDILGLDKAAVSRTVKKLEE 80 (148)
Q Consensus 43 ~~iL~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~ 80 (148)
-.+|..|....|.|..+||..+|.+...|...+..+..
T Consensus 27 r~llr~LA~G~PVt~~~LA~atG~~ve~V~~~L~~~p~ 64 (77)
T PF12324_consen 27 RPLLRLLADGRPVTVETLAAATGWPVEEVRAALAQMPD 64 (77)
T ss_dssp HHHHHHHT----B-HHHH-------HHHHHHHHHH-TT
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf 99999997689826999999979899999999985768
No 113
>PF09940 DUF2172: Domain of unknown function (DUF2172)
Probab=38.95 E-value=9.1 Score=15.56 Aligned_cols=43 Identities=21% Similarity=0.294 Sum_probs=35.2
Q ss_pred HHHHHHHHH-CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 999999970-8899988999986589011458999999841321
Q T0617 43 WRIISVLSS-ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIE 85 (148)
Q Consensus 43 ~~iL~~l~~-~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~ 85 (148)
-.+|.+|.- .|..+.-|||+.++++...+...+++|.+.|+|+
T Consensus 343 ~~~l~~L~~~DG~~slldiAe~~~~~~~~~~~~~~~l~~~gLl~ 386 (386)
T PF09940_consen 343 MIMLWVLNYSDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHCCCCC
T ss_conf 99999998614751599999883999899999999997646559
No 114
>PF12116 SpoIIID: Stage III sporulation protein D
Probab=38.05 E-value=8.8 Score=15.64 Aligned_cols=32 Identities=19% Similarity=0.482 Sum_probs=23.4
Q ss_pred HHHHHCCCCCHHHHHHHHCCCCCHHHHHH-HHHH
Q ss_conf 99970889998899998658901145899-9999
Q T0617 47 SVLSSASDCSVQKISDILGLDKAAVSRTV-KKLE 79 (148)
Q Consensus 47 ~~l~~~~~~t~~eLa~~l~i~~~~vs~~i-~~L~ 79 (148)
.+|-++ ..|+.+.|..+|+|+|||.+=+ .+|.
T Consensus 13 ~yIi~~-~aTVR~tAk~FGVSKSTVHkDvTeRL~ 45 (82)
T PF12116_consen 13 NYIIEN-KATVRQTAKVFGVSKSTVHKDVTERLP 45 (82)
T ss_pred HHHHHC-CHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 999974-516999999978529999899999997
No 115
>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=36.17 E-value=10 Score=15.27 Aligned_cols=62 Identities=10% Similarity=0.224 Sum_probs=38.8
Q ss_pred HHHHHHCC-CCCHHHHHHH----HCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHH
Q ss_conf 99997088-9998899998----658901145899999984132125674322300000178889999
Q T0617 46 ISVLSSAS-DCSVQKISDI----LGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELY 108 (148)
Q Consensus 46 L~~l~~~~-~~t~~eLa~~----l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~ 108 (148)
|.++...+ .-+.+||-.. -||++.+|--+|+.|+..|+|....-.. .-..--+.+.++...-
T Consensus 2 l~~f~~s~~~y~LKeLEKl~pK~~gI~~m~VKdvlQ~LvDDglV~~EKiGs-sn~YWsFps~~~~~~~ 68 (188)
T PF03962_consen 2 LEIFHESKTFYTLKELEKLAPKVKGINSMSVKDVLQSLVDDGLVEVEKIGS-SNYYWSFPSQAKKKRQ 68 (188)
T ss_pred HHHHHHCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHCCC-EEEEEECCHHHHHHHH
T ss_conf 588964688341999998746324976402999999986367621021077-5578658699999999
No 116
>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=35.69 E-value=6.4 Score=16.57 Aligned_cols=22 Identities=18% Similarity=0.617 Sum_probs=19.0
Q ss_pred CCHHHHHHHHCCCCCHHHHHHH
Q ss_conf 9988999986589011458999
Q T0617 55 CSVQKISDILGLDKAAVSRTVK 76 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~i~ 76 (148)
++..|+++.++++++++-+.++
T Consensus 4 l~~~ev~~~lgvs~~t~y~~~~ 25 (51)
T PF05930_consen 4 LRIKEVAELLGVSRSTLYRLIK 25 (51)
T ss_dssp E-HHHHHHH-----HHHHHHHH
T ss_pred ECHHHHHHHHCCCHHHHHHHHH
T ss_conf 2499999998949999999977
No 117
>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=35.16 E-value=10 Score=15.17 Aligned_cols=32 Identities=19% Similarity=0.347 Sum_probs=24.0
Q ss_pred HHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 999970889998899998658901145899999
Q T0617 46 ISVLSSASDCSVQKISDILGLDKAAVSRTVKKL 78 (148)
Q Consensus 46 L~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L 78 (148)
+..+. .|.+++...|...||+++|+.+-++.-
T Consensus 9 i~~v~-~g~~Si~~aA~~ygVp~sTL~~r~~g~ 40 (45)
T PF05225_consen 9 IEAVK-NGKLSIRKAARKYGVPRSTLRRRLKGK 40 (45)
T ss_dssp HHHHH------HHHHHHH----HHHHHHHHHH-
T ss_pred HHHHH-CCCCCHHHHHHHHCCCHHHHHHHHCCC
T ss_conf 99999-099579999999893989999999278
No 118
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism , . It is conserved in eukaryotes from yeast to human.
Probab=34.80 E-value=6.7 Score=16.41 Aligned_cols=43 Identities=14% Similarity=0.220 Sum_probs=27.8
Q ss_pred HHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHH
Q ss_conf 8899998658901145899999984132125674322300000178889
Q T0617 57 VQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQ 105 (148)
Q Consensus 57 ~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~ 105 (148)
....+..-+++++-+-.++++|++.||+.+.++ + .+.|+|.+.
T Consensus 155 ~~~~~~~~~ls~~eaE~lL~~Lv~~gWl~~s~~---g---~~~L~pR~l 197 (200)
T PF07574_consen 155 SGQLAAFQNLSKSEAEELLDRLVEDGWLERSRD---G---RYSLGPRAL 197 (200)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHCCCCEECCC---C---EEEECHHHH
T ss_conf 332211366778899999999997788067579---8---388762776
No 119
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain
Probab=34.17 E-value=11 Score=15.07 Aligned_cols=55 Identities=9% Similarity=0.261 Sum_probs=43.6
Q ss_pred HHHHCCCCHHHHHHH-HHHHHCCCCC----HHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 998728999899999-9997088999----8899998658901145899999984132125
Q T0617 32 YTQKFGIGMTEWRII-SVLSSASDCS----VQKISDILGLDKAAVSRTVKKLEEKKYIEVN 87 (148)
Q Consensus 32 ~~~~~glt~~q~~iL-~~l~~~~~~t----~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~ 87 (148)
+...++ |..+|.-+ .+|..+|+.. ..+||..+++++.++.-+++--.+.|+|+..
T Consensus 90 y~~g~P-tRe~F~~lYk~i~~~~~~~l~~~~~~La~~l~~~~~~l~FMi~VF~EL~FVtie 149 (195)
T PF10141_consen 90 YLEGMP-TREQFAKLYKFIYQHPEFDLRKKLMQLAKYLGWSKETLIFMIQVFFELGFVTIE 149 (195)
T ss_pred HHCCCC-CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf 341599-899999999999967999878899999888597999999999999873907977
No 120
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N)
Probab=33.86 E-value=11 Score=15.03 Aligned_cols=35 Identities=11% Similarity=0.192 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHC
Q ss_conf 88999889999865890114589999998413212
Q T0617 52 ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEV 86 (148)
Q Consensus 52 ~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r 86 (148)
+-|-+...||..++.+-.+|-..++-+++.|+|+.
T Consensus 51 ~ipyt~E~LA~~~~~~~~~V~~aL~~f~~~gmIe~ 85 (121)
T PF09681_consen 51 NIPYTAEMLATIFDRPVETVRLALQVFQKLGMIEI 85 (121)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
T ss_conf 88986999999978878899999999987897899
No 121
>PF03333 PapB: Adhesin biosynthesis transcription regulatory protein; InterPro: IPR004356 P pili, or fimbriae, are ~68A in diameter and 1 micron in length, the bulk of which is a fibre composed of the main structural protein PapA . At its tip, the pilus is terminated by a fibrillum consisting of repeating units of the PapE protein. This, in turn, is topped by the adhesins, PapF and PapG, both of which are needed for receptor binding. The tip fibrillum is anchored to the main PapA fibre by the PapK pilus-adaptor protein. PapH, an outer membrane protein, then anchors the entire rod in the bacterial envelope . A cytoplasmic chaperone (PapD) assists in assembling the monomers of the macromolecule in the membrane. All of the functional pap genes are arranged in a cluster (operon) on the Escherichia coli genome. It is believed that selective pressure exerted by the host's urinal and intestinal tract isoreceptors forced the spread of this operon to other strains via lateral transfer . PapB, encoded within the cluster, acts as a transcriptional regulator of the functional pap genes and is located in the bacterial cytoplasm . Its mechanism involves differential binding to separate sites in the cluster, suggesting that this protein is both an activator and repressor of pilus-adhesion transcription. The protein shares similarity with other E. coli fimbrial- adhesion transcription regulators, such as AfaA, DaaA and FanB. ; GO: 0006355 regulation of transcription, DNA-dependent
Probab=33.70 E-value=11 Score=15.02 Aligned_cols=48 Identities=13% Similarity=0.248 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHH--------------CCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf 899989999999970--------------889998899998658901145899999984132
Q T0617 37 GIGMTEWRIISVLSS--------------ASDCSVQKISDILGLDKAAVSRTVKKLEEKKYI 84 (148)
Q Consensus 37 glt~~q~~iL~~l~~--------------~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli 84 (148)
.++..||.+|.-|.. -.|.+-++.++.-+++.|..|+.+++|..-.-.
T Consensus 22 ~vsee~f~LLl~is~I~S~kvI~AL~dyLV~G~~rkeac~r~~V~~~yfs~aL~rL~~v~~~ 83 (91)
T PF03333_consen 22 KVSEEHFWLLLEISPIRSEKVIAALRDYLVEGYSRKEACERHGVNQSYFSRALNRLNRVSQT 83 (91)
T ss_pred CCCHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCHHHHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 66799999999964668599999999999758749999998098789999999999999999
No 122
>PF08299 Bac_DnaA_C: domain; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins , , that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) .; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA replication initiation, 0006275 regulation of DNA replication; PDB: 1j1v_A 2hcb_C 1l8q_A.
Probab=32.68 E-value=6.9 Score=16.35 Aligned_cols=40 Identities=20% Similarity=0.288 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHCCCCCHHHHHHHHC-CCCCHHHHHHHH
Q ss_conf 9998999999997088999889999865-890114589999
Q T0617 38 IGMTEWRIISVLSSASDCSVQKISDILG-LDKAAVSRTVKK 77 (148)
Q Consensus 38 lt~~q~~iL~~l~~~~~~t~~eLa~~l~-i~~~~vs~~i~~ 77 (148)
+..+...++....+..+.+..+|+..+| -++++|...+++
T Consensus 29 i~~aR~iamyL~r~~~~~sl~~Ig~~fg~RdHsTV~~a~~k 69 (70)
T PF08299_consen 29 IVQARQIAMYLARELTGLSLSEIGKIFGGRDHSTVIHAIRK 69 (70)
T ss_dssp CHHHHHHHHHHHHHCS---CCCHHTTSS-S-CHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 21499999999999858989999989189977899999851
No 123
>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=31.31 E-value=8.5 Score=15.73 Aligned_cols=24 Identities=25% Similarity=0.358 Sum_probs=21.2
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf 998899998658901145899999
Q T0617 55 CSVQKISDILGLDKAAVSRTVKKL 78 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~i~~L 78 (148)
-|..||++.++.++++|+++.+.|
T Consensus 53 ft~~el~~~L~~s~~~v~k~~kEL 76 (76)
T PF06970_consen 53 FTNEELMEILNCSKKKVIKIKKEL 76 (76)
T ss_pred EEHHHHHHHHCCCHHHHHHHHHCC
T ss_conf 659999999887888999999619
No 124
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=30.79 E-value=12 Score=14.70 Aligned_cols=35 Identities=17% Similarity=0.201 Sum_probs=28.3
Q ss_pred HHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 97088999889999865890114589999998413
Q T0617 49 LSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKY 83 (148)
Q Consensus 49 l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gl 83 (148)
....|.++-.|||..+|++++.|.++=++-+..+=
T Consensus 14 yF~eG~L~D~eIA~~LGVsr~nV~kmR~Kwes~~~ 48 (181)
T PF04645_consen 14 YFKEGSLNDAEIAQELGVSRVNVWKMRQKWESSED 48 (181)
T ss_pred HHHCCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCC
T ss_conf 99538875799999978219999999999881377
No 125
>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=30.12 E-value=12 Score=14.63 Aligned_cols=38 Identities=13% Similarity=0.244 Sum_probs=30.8
Q ss_pred HHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf 70889998899998658901145899999984132125
Q T0617 50 SSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVN 87 (148)
Q Consensus 50 ~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~ 87 (148)
.+..|.+..+||...++|..+|-++|++..+...=.++
T Consensus 68 ~~f~G~n~~eLArkY~lS~r~I~~Ii~~~~~~~~~~~Q 105 (108)
T PF08765_consen 68 REFNGMNVRELARKYGLSERWIYRIIKRQRKEERARRQ 105 (108)
T ss_dssp HH-----HHHHHHH----HHHHHHHHHHHHH-------
T ss_pred HHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf 98389979999989796699999999998888998536
No 126
>PF09639 YjcQ: YjcQ protein; PDB: 2hgc_A.
Probab=29.57 E-value=12 Score=14.83 Aligned_cols=45 Identities=18% Similarity=0.089 Sum_probs=30.8
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCC---EECCCCCHHHHHHHHHHHH
Q ss_conf 11458999999841321256743223---0000017888999999999
Q T0617 69 AAVSRTVKKLEEKKYIEVNGHSEDKR---TYAINLTEMGQELYEVASD 113 (148)
Q Consensus 69 ~~vs~~i~~L~~~gli~r~~~~~D~R---~~~l~LT~~G~~~~~~~~~ 113 (148)
.-.++++..|.+.|||.-..-..... .....+|..|.+++.+-..
T Consensus 25 ~~~~~~l~~L~d~G~I~Gv~~~~~~~~~~~~~~~iT~~Gi~YLeENs~ 72 (88)
T PF09639_consen 25 DYWSDILEMLVDEGYIKGVSFTRTDPIVAITDPYITLDGIQYLEENSM 72 (88)
T ss_dssp HHHHHHHHHHHH---EE--EESSSSEE------EE-----HHHHH---
T ss_pred HHHHHHHHHHHHCCCEECEEEEECCEEEECCCCEECHHHHHHHHHHHH
T ss_conf 999999999997898502377526226851686430788999998558
No 127
>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=28.94 E-value=5 Score=17.29 Aligned_cols=23 Identities=13% Similarity=0.485 Sum_probs=17.9
Q ss_pred CCHHHHHHHHCCCCCHHHHHHHH
Q ss_conf 99889999865890114589999
Q T0617 55 CSVQKISDILGLDKAAVSRTVKK 77 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~i~~ 77 (148)
++.++||+.+|+|.+|++..++.
T Consensus 3 vnk~~lA~~~gVS~~ti~~W~~~ 25 (164)
T PF07471_consen 3 VNKKQLAEILGVSERTITKWQRQ 25 (164)
T ss_dssp EEHHHHHHH----HHHHHHHTT-
T ss_pred CCHHHHHHHHCCCHHHHHHHHHC
T ss_conf 68999999979899999999987
No 128
>PF08278 DnaG_DnaB_bind: DNA primase DnaG DnaB-binding ; InterPro: IPR013173 Eubacterial DnaG primases interact with several factors to form the replisome. One of these factors is DnaB, a helicase. This domain has been demonstrated to be responsible for the interaction between DnaG and DnaB . This domain has a multi-helical structure that forms an orthogonal bundle .; PDB: 2haj_A.
Probab=28.29 E-value=13 Score=14.43 Aligned_cols=85 Identities=12% Similarity=0.109 Sum_probs=43.6
Q ss_pred HHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHH-HHHHHHHHH-H
Q ss_conf 99970889998899998658901145899999984132125674322300000178889999999999-999999998-5
Q T0617 47 SVLSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDF-AIEREKQLL-E 124 (148)
Q Consensus 47 ~~l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~-~~~~~~~~~-~ 124 (148)
..+...|.++...+.+++. .+.-...+..|........ .... ...+..+.=..+....... ......... .
T Consensus 41 ~~~~~~p~~~~~~lle~~r--~~~~~~~l~~La~~e~~~~-~~~~----~~~~f~d~l~rL~~~~~~~~i~~L~~k~~~~ 113 (127)
T PF08278_consen 41 ELCGGRPNINTGQLLEHWR--DTPYGELLAQLATWEHLIK-DEED----IEQEFQDALARLQEQLLERRIEELKSKLQRG 113 (127)
T ss_dssp HHHHH--------HHHHT-----TTHHHHHHHHS-TTT----SHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHS--
T ss_pred HHHCCCCCCCHHHHHHHHH--CCCHHHHHHHHHHCCCCCC-CCHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 9980689988999999996--8870899999983851025-6223----8999999999999999999999999878447
Q ss_pred CCCHHHHHHHHHHH
Q ss_conf 79998999999999
Q T0617 125 EFEEAEKDQLFILL 138 (148)
Q Consensus 125 ~l~~ee~~~l~~~L 138 (148)
+++++|...+..++
T Consensus 114 ~l~~~Ek~el~~Ll 127 (127)
T PF08278_consen 114 GLTDEEKQELRELL 127 (127)
T ss_dssp ---HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHC
T ss_conf 97999999999869
No 129
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix Elongation factor SelB, winged helix ; InterPro: IPR015190 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 2". 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: 2ply_A 1lva_A 2v9v_A 2uwm_B.
Probab=27.94 E-value=14 Score=14.39 Aligned_cols=38 Identities=11% Similarity=0.171 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHH---CCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 8899988999986---5890114589999998413212567
Q T0617 52 ASDCSVQKISDIL---GLDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 52 ~~~~t~~eLa~~l---~i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
.+|++-.+|...+ +++......+++.|+++|.|....+
T Consensus 15 ~~G~~keeLrsr~~~~~l~~~~f~~lL~~l~~~g~l~~~g~ 55 (59)
T PF09106_consen 15 RPGMPKEELRSRLAKPRLPPKLFDALLEALVAEGLLKQEGD 55 (59)
T ss_dssp ----BHHHHHHHCST-TS-HCCHHHHHHHHHH---EEEESS
T ss_pred CCCCCHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf 52839999997720035998999999999997898143799
No 130
>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=27.88 E-value=7.8 Score=15.99 Aligned_cols=32 Identities=19% Similarity=0.363 Sum_probs=23.0
Q ss_pred HHHHHHHHHHCC--CCCHHHHHHHHCCCCCHHHH
Q ss_conf 999999997088--99988999986589011458
Q T0617 42 EWRIISVLSSAS--DCSVQKISDILGLDKAAVSR 73 (148)
Q Consensus 42 q~~iL~~l~~~~--~~t~~eLa~~l~i~~~~vs~ 73 (148)
-+++|..+...| -++..+||+.+|++++.|-+
T Consensus 14 Y~r~L~~l~~~g~~~iSS~eLa~~~gi~~~qVRK 47 (50)
T PF06971_consen 14 YLRYLKQLQEEGVERISSKELAEALGITPSQVRK 47 (50)
T ss_dssp HHHHHHHHHH----B--TTTHHHCCSS-HHHHHH
T ss_pred HHHHHHHHHHCCCEEECHHHHHHHHCCCHHHHHC
T ss_conf 9999999998599458799999997979999612
No 131
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners .; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1cf7_A.
Probab=26.77 E-value=14 Score=14.35 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHH-----CC--CCCHHHHHHHHHHHHHHHHCCC
Q ss_conf 8899988999986-----58--9011458999999841321256
Q T0617 52 ASDCSVQKISDIL-----GL--DKAAVSRTVKKLEEKKYIEVNG 88 (148)
Q Consensus 52 ~~~~t~~eLa~~l-----~i--~~~~vs~~i~~L~~~gli~r~~ 88 (148)
.+.++..++|..+ ++ .+-.+--+++-|+.-|+|++..
T Consensus 23 ~~~~~l~~va~~L~~~~~~~k~~~RRlYDi~NVL~a~gli~K~~ 66 (74)
T PF02319_consen 23 KGIVTLNEVADKLISEEDNVKTQRRRLYDITNVLEAIGLIEKKS 66 (74)
T ss_dssp ---EEHHHHHHHCHHHT-CCHHHCHHHHHHHHHHHHTTSEEEEE
T ss_pred CCEEEHHHHHHHHHHCCCHHCCCHHHHHHHHHHHHHHCCEEECC
T ss_conf 67362999999997500001000335988999998845041368
No 132
>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=26.37 E-value=14 Score=14.20 Aligned_cols=42 Identities=14% Similarity=0.266 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 899999984132125674322300000178889999999999999
Q T0617 73 RTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEVASDFAIE 117 (148)
Q Consensus 73 ~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~~~~~~~~ 117 (148)
..|+-|+++|+|-.+.+..|. .+++|++-+++...+..+..+
T Consensus 109 eAl~lL~~~G~Vfqk~~~~D~---vY~Vt~~DKdLh~~il~II~e 150 (174)
T PF09170_consen 109 EALKLLQDEGLVFQKDQNQDE---VYYVTDQDKDLHKAILNIIQE 150 (174)
T ss_dssp HHHHHHHH---EE-S----------BEE-SSS-------------
T ss_pred HHHHHHHHCCEEEECCCCCCC---EEEEECCCHHHHHHHHHHHHH
T ss_conf 999999877957862799765---178743636689999999999
No 133
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=26.36 E-value=13 Score=14.46 Aligned_cols=41 Identities=10% Similarity=0.142 Sum_probs=32.9
Q ss_pred HHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf 97088999889999865890114589999998413212567
Q T0617 49 LSSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIEVNGH 89 (148)
Q Consensus 49 l~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~r~~~ 89 (148)
|..+|+.|..|||..+|++.--+...+.--..+|-+.|..-
T Consensus 1 i~q~g~qt~dela~~fg~tsr~~~stla~~~s~grl~rvnq 41 (155)
T PF07789_consen 1 IEQHGPQTADELALMFGITSRKVASTLAMAISKGRLIRVNQ 41 (155)
T ss_pred CCCCCCCCHHHHHHHHCCHHHHHHHHHHHHHHCCEEEEECC
T ss_conf 98667322999999866007878778999862571799748
No 134
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0003702 RNA polymerase II transcription factor activity, 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=26.19 E-value=15 Score=14.18 Aligned_cols=68 Identities=10% Similarity=0.096 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCC-CCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHH
Q ss_conf 9899999999708899988999986589-011458999999841321256743223000001788899999
Q T0617 40 MTEWRIISVLSSASDCSVQKISDILGLD-KAAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYE 109 (148)
Q Consensus 40 ~~q~~iL~~l~~~~~~t~~eLa~~l~i~-~~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~ 109 (148)
..+..|+..|...+|.+.+++.....-+ +......+++|.+...+.......+. ..+.|++.-+.-+.
T Consensus 31 LAK~~ImrLLf~~~pv~~~~l~~Wv~~~~~~~~~~al~~L~~L~Ii~~~~~~~~~--~~~~Ln~~Fr~sLr 99 (366)
T PF03849_consen 31 LAKQYIMRLLFIDQPVPASDLELWVKPESKKEHDEALKRLRSLHIIQETESKGGN--QQYRLNPTFRKSLR 99 (366)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCHHHHHHHHHHHHHHHHCCCEEECCCCCCC--EEEEECHHHHHHHH
T ss_conf 9999999997079998999999884720058999999999867612212568874--06897779999999
No 135
>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=25.84 E-value=15 Score=14.14 Aligned_cols=56 Identities=18% Similarity=0.215 Sum_probs=39.8
Q ss_pred HHHHHHCCC-CHHHHHHHH--HH-----HHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 999987289-998999999--99-----708899988999986589011458999999841321
Q T0617 30 TAYTQKFGI-GMTEWRIIS--VL-----SSASDCSVQKISDILGLDKAAVSRTVKKLEEKKYIE 85 (148)
Q Consensus 30 ~~~~~~~gl-t~~q~~iL~--~l-----~~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gli~ 85 (148)
+.+..++.+ ++..|..+. .| ...+.++.++....+..+...+.++.+-|+..|||-
T Consensus 20 ~~~~~e~~~~~p~~Yl~iRn~il~~w~~~~~~~lt~~~~~~~~~~d~~~~~ri~~FL~~~G~IN 83 (84)
T PF04433_consen 20 KQLCPEFFLKTPEPYLNIRNHILNEWRKNPNKYLTKTDARRLIKIDVNKVRRIYDFLERWGYIN 83 (84)
T ss_dssp HHHCHHCT-CHHHHHHHHHHHHHHHHHHHTTS---HHHHHHHCTSSHHHHHHHHHHHHHTT--S
T ss_pred HHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEHHHHHHHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf 9980887644848999999999999998799836299999885237999999999999859768
No 136
>PF03882 KicB: KicB killing factor; InterPro: IPR005582 This family contains MukF, which are proteins involved in the segregation and condensation of prokaryotic chromosomes. MukE (IPR007385 from INTERPRO) along with MukF interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli . The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC . ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; PDB: 3euh_B 1t98_A 3euj_B 3euk_E.
Probab=24.49 E-value=14 Score=14.33 Aligned_cols=42 Identities=7% Similarity=0.100 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCHHHHHHHHH
Q ss_conf 114589999998413212567432230000017888999999
Q T0617 69 AAVSRTVKKLEEKKYIEVNGHSEDKRTYAINLTEMGQELYEV 110 (148)
Q Consensus 69 ~~vs~~i~~L~~~gli~r~~~~~D~R~~~l~LT~~G~~~~~~ 110 (148)
..++..|++|++.+++.|-.+..--+.-.+.|||-|..+.+-
T Consensus 72 ~RANNAIndlv~QrlL~Rf~se~~~g~~iYRLT~L~igi~dy 113 (440)
T PF03882_consen 72 VRANNAINDLVRQRLLNRFTSEFAEGAAIYRLTPLAIGISDY 113 (440)
T ss_dssp -HHHHHHHHHHHTTSEEEEE-TT----EEEEE-------HHH
T ss_pred HHHHHHHHHHHHHHHHHHCCCHHHCCCCEEEECHHHCCCHHH
T ss_conf 888889999999989986210010343325403653020698
No 137
>PF02540 NAD_synthase: NAD synthase; InterPro: IPR003694 NAD+ synthase (6.3.5.1 from EC) catalyzes the last step in the biosynthesis of nicotinamide adenine dinucleotide and is induced by stress factors such as heat shock and glucose limitation. The three-dimensional structure of NH3-dependent NAD+ synthetase from Bacillus subtilis, in its free form and in complex with ATP shows that the enzyme consists of a tight homodimer with alpha/beta subunit topology .; GO: 0003952 NAD+ synthase (glutamine-hydrolyzing) activity, 0005524 ATP binding, 0009435 NAD biosynthetic process; PDB: 1xng_B 1xnh_A 2dpl_B 2z0c_B 2vxo_A 1gpm_C 2e18_A 3hmq_A 1wxe_A 1wxi_A ....
Probab=23.75 E-value=16 Score=13.88 Aligned_cols=12 Identities=25% Similarity=0.636 Sum_probs=7.1
Q ss_pred HHHHHHHHCCCC
Q ss_conf 889999865890
Q T0617 57 VQKISDILGLDK 68 (148)
Q Consensus 57 ~~eLa~~l~i~~ 68 (148)
+.+||+.+++..
T Consensus 159 V~~La~~l~ip~ 170 (242)
T PF02540_consen 159 VRELARYLGIPE 170 (242)
T ss_dssp HHHHHHHTT--H
T ss_pred HHHHHHHHCCHH
T ss_conf 999999978669
No 138
>PF11662 DUF3263: Protein of unknown function (DUF3263)
Probab=22.67 E-value=17 Score=13.75 Aligned_cols=47 Identities=13% Similarity=0.203 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHH---HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf 89998999999997---088999889999865890114589999998413
Q T0617 37 GIGMTEWRIISVLS---SASDCSVQKISDILGLDKAAVSRTVKKLEEKKY 83 (148)
Q Consensus 37 glt~~q~~iL~~l~---~~~~~t~~eLa~~l~i~~~~vs~~i~~L~~~gl 83 (148)
+||..+..+|-+-. ..+|-.-..|-+.+|+++..--..++.|.+..-
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIr~~fGlSptrYyQ~Ln~LiD~p~ 51 (77)
T PF11662_consen 2 GLSDRDRAILAFERQWWRYGGAKEEAIREEFGLSPTRYYQRLNALIDTPA 51 (77)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHCCHH
T ss_conf 89989999999998715368995899999979889999999999967867
No 139
>PF07453 NUMOD1: NUMOD1 domain; InterPro: IPR010896 This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases .
Probab=22.32 E-value=15 Score=14.13 Aligned_cols=20 Identities=15% Similarity=0.391 Sum_probs=16.9
Q ss_pred CCHHHHHHHHCCCCCHHHHH
Q ss_conf 99889999865890114589
Q T0617 55 CSVQKISDILGLDKAAVSRT 74 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~ 74 (148)
.+.+|.|+.++++++++++-
T Consensus 17 ~Si~eAa~~l~~~~~tI~~~ 36 (37)
T PF07453_consen 17 SSIREAARALNISHSTISKY 36 (37)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 48999999809987789875
No 140
>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=21.84 E-value=18 Score=13.64 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=11.1
Q ss_pred CCHHHHHHHHCCCCCHHHHH
Q ss_conf 99889999865890114589
Q T0617 55 CSVQKISDILGLDKAAVSRT 74 (148)
Q Consensus 55 ~t~~eLa~~l~i~~~~vs~~ 74 (148)
-|..|||+.+++|+.+|+-.
T Consensus 15 gt~~e~~~~~~vS~~sv~~W 34 (186)
T PF04936_consen 15 GTIDEIADYFDVSRASVSLW 34 (186)
T ss_pred CCHHHHHHHHCCCHHHHHHH
T ss_conf 63899999875689999999
Done!