Query psy10346
Match_columns 292
No_of_seqs 159 out of 1241
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 15:36:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10346.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10346hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02853 Probable phenylalanyl 100.0 2E-73 4.4E-78 561.4 28.3 276 2-281 1-281 (492)
2 PTZ00326 phenylalanyl-tRNA syn 100.0 7E-73 1.5E-77 559.4 28.1 279 3-282 5-290 (494)
3 KOG2784|consensus 100.0 7.7E-73 1.7E-77 533.9 18.2 272 3-282 2-273 (483)
4 PRK04172 pheS phenylalanyl-tRN 100.0 2.8E-62 6.1E-67 487.0 27.5 273 3-279 5-290 (489)
5 COG0016 PheS Phenylalanyl-tRNA 100.0 1.1E-34 2.5E-39 275.4 3.1 163 99-278 2-167 (335)
6 PLN02788 phenylalanine-tRNA sy 99.9 3.4E-23 7.3E-28 201.8 6.7 83 194-278 43-128 (402)
7 PF01409 tRNA-synt_2d: tRNA sy 99.9 1.1E-22 2.4E-27 187.3 5.5 75 205-280 1-75 (247)
8 PRK00488 pheS phenylalanyl-tRN 99.9 2.1E-22 4.5E-27 192.4 5.8 73 205-278 92-164 (339)
9 TIGR00469 pheS_mito phenylalan 99.8 1.8E-19 4E-24 177.5 5.7 82 195-278 17-107 (460)
10 TIGR00468 pheS phenylalanyl-tR 99.8 2.6E-20 5.7E-25 175.3 -2.8 97 180-277 31-127 (294)
11 KOG2783|consensus 99.0 3E-10 6.5E-15 109.6 4.2 82 195-278 48-132 (436)
12 PF14947 HTH_45: Winged helix- 97.7 0.00013 2.9E-09 55.7 6.1 62 4-70 6-67 (77)
13 TIGR02337 HpaR homoprotocatech 97.6 0.00021 4.5E-09 58.1 7.5 73 4-77 28-104 (118)
14 PF13463 HTH_27: Winged helix 97.6 0.00032 6.9E-09 51.1 6.9 61 4-65 3-68 (68)
15 PF13601 HTH_34: Winged helix 97.5 0.00024 5.3E-09 54.9 6.2 64 6-70 2-70 (80)
16 cd00496 PheRS_alpha_core Pheny 97.4 0.00023 4.9E-09 64.3 5.4 58 221-279 1-58 (218)
17 PRK11512 DNA-binding transcrip 97.4 0.00094 2E-08 56.2 8.4 89 4-94 40-134 (144)
18 smart00347 HTH_MARR helix_turn 97.4 0.00078 1.7E-08 51.7 7.2 67 4-71 10-80 (101)
19 PF01978 TrmB: Sugar-specific 97.0 0.0011 2.4E-08 48.9 4.8 58 4-62 8-65 (68)
20 COG1846 MarR Transcriptional r 97.0 0.0045 9.8E-08 48.7 8.4 87 4-91 22-112 (126)
21 TIGR01889 Staph_reg_Sar staphy 97.0 0.0034 7.4E-08 50.7 7.3 73 4-77 25-105 (109)
22 smart00550 Zalpha Z-DNA-bindin 96.9 0.0019 4.1E-08 48.3 5.3 60 3-63 5-66 (68)
23 PRK03573 transcriptional regul 96.9 0.0045 9.7E-08 51.8 7.9 89 4-94 31-125 (144)
24 PRK10870 transcriptional repre 96.9 0.0048 1E-07 54.1 8.0 89 4-94 55-150 (176)
25 PRK13777 transcriptional regul 96.8 0.0054 1.2E-07 54.7 7.6 73 4-77 45-121 (185)
26 PF03551 PadR: Transcriptional 96.8 0.005 1.1E-07 46.3 6.3 42 29-71 28-75 (75)
27 PF13412 HTH_24: Winged helix- 96.7 0.0046 1E-07 42.5 5.4 46 4-50 3-48 (48)
28 PRK03902 manganese transport t 96.7 0.0077 1.7E-07 50.7 7.6 62 7-71 11-72 (142)
29 cd00090 HTH_ARSR Arsenical Res 96.6 0.015 3.2E-07 41.6 7.8 64 3-69 6-70 (78)
30 TIGR01884 cas_HTH CRISPR locus 96.5 0.0068 1.5E-07 54.1 6.2 61 4-65 143-203 (203)
31 TIGR02702 SufR_cyano iron-sulf 96.2 0.013 2.9E-07 52.2 6.9 66 5-71 2-73 (203)
32 PRK14165 winged helix-turn-hel 96.2 0.015 3.2E-07 53.2 7.2 66 11-77 14-80 (217)
33 COG1497 Predicted transcriptio 96.1 0.018 3.9E-07 53.4 7.0 73 4-79 10-83 (260)
34 smart00418 HTH_ARSR helix_turn 96.1 0.03 6.4E-07 38.9 6.7 59 9-69 2-62 (66)
35 PF10007 DUF2250: Uncharacteri 96.0 0.029 6.3E-07 44.8 6.8 67 3-70 6-90 (92)
36 COG4754 Uncharacterized conser 95.9 0.019 4.2E-07 49.4 6.0 67 8-78 16-84 (157)
37 TIGR03433 padR_acidobact trans 95.9 0.025 5.5E-07 45.1 6.4 74 3-78 3-90 (100)
38 PRK11050 manganese transport r 95.8 0.032 7E-07 47.8 7.1 71 7-80 40-110 (152)
39 COG1321 TroR Mn-dependent tran 95.8 0.023 5E-07 49.2 6.1 59 9-70 15-73 (154)
40 PF12840 HTH_20: Helix-turn-he 95.7 0.027 5.8E-07 40.7 5.2 53 1-54 7-59 (61)
41 PF12802 MarR_2: MarR family; 95.7 0.027 5.9E-07 40.0 5.2 49 4-53 5-55 (62)
42 PF07381 DUF1495: Winged helix 95.6 0.053 1.1E-06 43.2 6.9 66 4-70 9-88 (90)
43 PF01638 HxlR: HxlR-like helix 95.6 0.06 1.3E-06 42.0 7.2 60 8-69 9-73 (90)
44 PF03501 S10_plectin: Plectin/ 95.4 0.019 4.1E-07 46.1 3.8 48 28-76 33-83 (95)
45 PRK09616 pheT phenylalanyl-tRN 95.4 0.037 8.1E-07 56.8 6.9 120 146-280 291-411 (552)
46 PTZ00034 40S ribosomal protein 95.4 0.024 5.2E-07 47.5 4.4 74 4-78 7-88 (124)
47 PF03444 HrcA_DNA-bdg: Winged 95.2 0.039 8.4E-07 42.8 4.8 70 1-71 1-75 (78)
48 smart00529 HTH_DTXR Helix-turn 95.1 0.037 8E-07 42.9 4.5 51 22-75 3-53 (96)
49 PF01047 MarR: MarR family; I 95.0 0.047 1E-06 38.6 4.4 50 4-54 3-52 (59)
50 PHA00738 putative HTH transcri 94.9 0.1 2.3E-06 42.8 6.9 71 2-81 10-81 (108)
51 COG2345 Predicted transcriptio 94.9 0.07 1.5E-06 48.9 6.5 64 4-68 11-80 (218)
52 COG1695 Predicted transcriptio 94.9 0.093 2E-06 43.7 6.7 68 4-73 9-90 (138)
53 PRK09416 lstR lineage-specific 94.6 0.12 2.6E-06 44.1 6.7 67 3-72 42-118 (135)
54 PRK09537 pylS pyrolysyl-tRNA s 94.6 0.035 7.6E-07 55.4 4.0 58 215-276 198-255 (417)
55 PF08220 HTH_DeoR: DeoR-like h 94.4 0.081 1.8E-06 38.1 4.5 45 6-51 2-46 (57)
56 COG1733 Predicted transcriptio 94.3 0.19 4.1E-06 41.8 7.2 60 8-69 27-91 (120)
57 COG4742 Predicted transcriptio 94.2 0.13 2.7E-06 48.4 6.5 78 3-85 12-89 (260)
58 PRK10141 DNA-binding transcrip 94.1 0.35 7.6E-06 40.1 8.3 65 1-66 13-78 (117)
59 COG3432 Predicted transcriptio 94.0 0.11 2.4E-06 41.8 4.8 64 5-70 19-83 (95)
60 PRK06253 O-phosphoseryl-tRNA s 93.9 0.051 1.1E-06 55.5 3.6 40 211-251 37-76 (529)
61 smart00346 HTH_ICLR helix_turn 93.9 0.25 5.5E-06 37.6 6.7 63 5-69 6-69 (91)
62 PRK05638 threonine synthase; V 93.9 0.13 2.9E-06 51.2 6.4 65 4-70 371-439 (442)
63 COG5045 Ribosomal protein S10E 93.9 0.13 2.8E-06 41.2 5.0 43 28-71 35-78 (105)
64 TIGR00470 sepS O-phosphoseryl- 93.8 0.056 1.2E-06 54.8 3.6 40 211-251 37-76 (533)
65 PF01022 HTH_5: Bacterial regu 93.7 0.15 3.4E-06 34.9 4.7 45 4-50 2-46 (47)
66 TIGR02719 repress_PhaQ poly-be 93.6 0.36 7.7E-06 41.3 7.7 74 4-79 24-109 (138)
67 PHA02943 hypothetical protein; 93.6 0.38 8.3E-06 42.0 7.8 74 6-84 13-89 (165)
68 TIGR02367 PylS pyrrolysyl-tRNA 93.6 0.11 2.3E-06 52.4 5.0 57 216-276 235-291 (453)
69 smart00344 HTH_ASNC helix_turn 93.5 0.17 3.7E-06 40.0 5.3 46 4-50 3-48 (108)
70 PF09012 FeoC: FeoC like trans 93.4 0.16 3.4E-06 37.7 4.7 46 7-53 3-48 (69)
71 PF01325 Fe_dep_repress: Iron 93.3 0.19 4.1E-06 36.7 4.8 45 8-53 12-56 (60)
72 TIGR02716 C20_methyl_CrtF C-20 93.3 0.15 3.3E-06 47.8 5.6 68 4-76 10-77 (306)
73 smart00420 HTH_DEOR helix_turn 93.2 0.32 7E-06 32.7 5.7 45 6-51 2-46 (53)
74 COG2024 Phenylalanyl-tRNA synt 93.1 0.073 1.6E-06 52.6 2.9 40 211-251 37-76 (536)
75 PF08279 HTH_11: HTH domain; 93.0 0.22 4.7E-06 34.8 4.7 45 6-52 2-47 (55)
76 PRK11169 leucine-responsive tr 92.7 0.27 5.9E-06 42.4 5.7 47 3-50 13-59 (164)
77 PF09821 AAA_assoc_C: C-termin 92.6 0.24 5.3E-06 41.2 5.1 51 23-77 2-52 (120)
78 PRK11179 DNA-binding transcrip 92.6 0.26 5.7E-06 42.0 5.5 47 4-51 9-55 (153)
79 TIGR02698 CopY_TcrY copper tra 92.5 1.5 3.2E-05 36.8 9.8 91 3-94 3-109 (130)
80 COG1522 Lrp Transcriptional re 92.3 0.31 6.8E-06 40.7 5.5 50 3-53 7-56 (154)
81 COG2512 Predicted membrane-ass 92.3 0.32 6.9E-06 45.6 6.0 59 4-63 195-255 (258)
82 PF01726 LexA_DNA_bind: LexA D 92.2 0.38 8.1E-06 35.8 5.2 50 3-53 5-60 (65)
83 COG3355 Predicted transcriptio 92.2 0.44 9.6E-06 40.2 6.1 50 4-54 27-77 (126)
84 PRK00215 LexA repressor; Valid 92.1 0.41 8.9E-06 42.4 6.3 66 1-67 1-72 (205)
85 PF02295 z-alpha: Adenosine de 92.1 0.068 1.5E-06 40.0 1.0 63 1-64 1-65 (66)
86 PF09339 HTH_IclR: IclR helix- 91.9 0.2 4.4E-06 35.0 3.3 45 6-51 5-50 (52)
87 PRK06266 transcription initiat 91.9 0.63 1.4E-05 41.2 7.2 60 5-65 23-89 (178)
88 PRK06474 hypothetical protein; 91.4 0.78 1.7E-05 40.4 7.2 67 1-68 8-82 (178)
89 COG1339 Transcriptional regula 91.1 0.47 1E-05 43.0 5.5 67 8-75 4-76 (214)
90 PF13404 HTH_AsnC-type: AsnC-t 91.0 0.56 1.2E-05 31.9 4.6 40 4-43 3-42 (42)
91 TIGR01610 phage_O_Nterm phage 90.8 0.78 1.7E-05 36.2 6.0 49 4-53 25-81 (95)
92 PF04703 FaeA: FaeA-like prote 90.6 0.3 6.5E-06 36.2 3.2 53 8-61 4-60 (62)
93 PF09202 Rio2_N: Rio2, N-termi 90.2 1.1 2.5E-05 34.8 6.3 67 3-70 5-75 (82)
94 COG2524 Predicted transcriptio 90.1 0.41 8.8E-06 45.2 4.4 75 3-78 5-84 (294)
95 KOG3344|consensus 90.1 0.16 3.4E-06 43.4 1.5 41 30-71 37-78 (150)
96 cd00092 HTH_CRP helix_turn_hel 89.7 0.79 1.7E-05 32.7 4.8 42 18-62 25-66 (67)
97 TIGR02277 PaaX_trns_reg phenyl 89.6 0.49 1.1E-05 44.7 4.6 56 22-80 24-80 (280)
98 PRK09834 DNA-binding transcrip 89.5 0.94 2E-05 41.8 6.4 62 7-70 14-76 (263)
99 PF00126 HTH_1: Bacterial regu 89.5 0.55 1.2E-05 33.7 3.8 58 6-66 3-60 (60)
100 PF03965 Penicillinase_R: Peni 89.3 1.5 3.2E-05 35.5 6.7 91 3-94 2-108 (115)
101 COG4189 Predicted transcriptio 89.2 0.66 1.4E-05 43.3 5.0 53 2-55 21-73 (308)
102 TIGR00498 lexA SOS regulatory 88.6 0.63 1.4E-05 41.0 4.3 60 3-63 5-70 (199)
103 PF08461 HTH_12: Ribonuclease 88.4 0.82 1.8E-05 34.0 4.2 59 8-69 2-66 (66)
104 COG1378 Predicted transcriptio 88.4 0.85 1.9E-05 42.4 5.2 57 5-62 17-73 (247)
105 PF02082 Rrf2: Transcriptional 88.3 0.99 2.1E-05 34.5 4.7 61 4-65 8-71 (83)
106 smart00345 HTH_GNTR helix_turn 88.1 1.5 3.3E-05 30.1 5.3 37 16-53 17-54 (60)
107 PRK15090 DNA-binding transcrip 88.0 1.1 2.4E-05 41.1 5.7 65 6-72 16-84 (257)
108 PRK13509 transcriptional repre 87.9 1.2 2.5E-05 41.2 5.7 48 3-51 4-51 (251)
109 TIGR02787 codY_Gpos GTP-sensin 87.8 1.1 2.4E-05 41.9 5.5 47 6-53 185-232 (251)
110 PF13814 Replic_Relax: Replica 87.8 1.1 2.4E-05 38.8 5.3 61 10-71 1-72 (191)
111 PF11313 DUF3116: Protein of u 87.5 1.9 4.2E-05 34.0 5.9 69 1-70 1-79 (85)
112 PF10771 DUF2582: Protein of u 87.5 1.4 3.1E-05 32.9 5.0 51 8-59 12-62 (65)
113 COG1349 GlpR Transcriptional r 87.1 0.94 2E-05 42.0 4.7 48 3-51 4-51 (253)
114 TIGR00637 ModE_repress ModE mo 87.1 1.9 4E-05 34.5 5.8 63 5-69 5-71 (99)
115 PRK09954 putative kinase; Prov 87.0 1.3 2.7E-05 42.5 5.7 45 4-49 3-47 (362)
116 PRK03601 transcriptional regul 86.9 1.6 3.5E-05 39.8 6.1 64 6-72 5-68 (275)
117 PF14338 Mrr_N: Mrr N-terminal 86.7 1.8 4E-05 33.7 5.5 32 38-72 60-91 (92)
118 PHA02701 ORF020 dsRNA-binding 86.6 1.2 2.6E-05 39.9 4.8 63 1-64 1-64 (183)
119 PRK10434 srlR DNA-bindng trans 86.6 1.2 2.6E-05 41.3 5.1 48 3-51 4-51 (256)
120 PF02002 TFIIE_alpha: TFIIE al 86.3 0.98 2.1E-05 36.0 3.8 51 5-56 14-64 (105)
121 PRK10906 DNA-binding transcrip 86.3 1.3 2.8E-05 41.0 5.1 48 3-51 4-51 (252)
122 PRK11242 DNA-binding transcrip 86.2 1.7 3.7E-05 39.5 5.8 63 6-71 5-67 (296)
123 TIGR00373 conserved hypothetic 85.9 2.1 4.6E-05 37.1 6.0 48 5-53 15-62 (158)
124 smart00419 HTH_CRP helix_turn_ 85.7 2.3 5E-05 28.1 4.9 40 19-62 9-48 (48)
125 PRK00082 hrcA heat-inducible t 85.6 1.4 2.9E-05 42.8 5.1 65 2-68 4-75 (339)
126 PF07848 PaaX: PaaX-like prote 85.6 1.7 3.7E-05 32.9 4.5 43 22-65 27-70 (70)
127 PRK09791 putative DNA-binding 85.5 0.98 2.1E-05 41.5 3.9 65 5-72 8-72 (302)
128 PF04182 B-block_TFIIIC: B-blo 85.2 2.4 5.2E-05 32.0 5.3 50 4-54 2-53 (75)
129 PF05158 RNA_pol_Rpc34: RNA po 85.2 3.6 7.8E-05 39.9 7.7 113 3-116 8-134 (327)
130 PF13730 HTH_36: Helix-turn-he 85.1 2.5 5.5E-05 29.3 5.0 45 4-49 5-55 (55)
131 PRK10094 DNA-binding transcrip 85.0 2.9 6.3E-05 38.9 6.9 66 3-71 3-68 (308)
132 PRK15421 DNA-binding transcrip 84.3 3 6.5E-05 39.1 6.7 67 1-70 1-67 (317)
133 PRK10837 putative DNA-binding 84.1 2.9 6.4E-05 37.8 6.4 66 4-72 5-70 (290)
134 TIGR02431 pcaR_pcaU beta-ketoa 83.7 2.5 5.5E-05 38.5 5.7 54 7-64 12-66 (248)
135 PF14090 HTH_39: Helix-turn-he 83.3 5.6 0.00012 29.6 6.5 45 5-52 2-46 (70)
136 cd07377 WHTH_GntR Winged helix 82.7 4.6 0.0001 28.2 5.7 39 21-62 28-66 (66)
137 PRK10163 DNA-binding transcrip 82.6 2.6 5.7E-05 39.2 5.4 57 6-64 27-84 (271)
138 PRK10632 transcriptional regul 82.4 3.3 7.2E-05 38.4 6.1 69 1-72 1-69 (309)
139 PF10771 DUF2582: Protein of u 82.0 1.1 2.4E-05 33.6 2.2 43 77-119 12-59 (65)
140 PRK11569 transcriptional repre 81.9 2.7 5.8E-05 39.1 5.2 62 7-70 31-97 (274)
141 PRK11074 putative DNA-binding 81.9 3.7 8.1E-05 37.8 6.2 66 1-69 1-66 (300)
142 PF00325 Crp: Bacterial regula 81.6 2.2 4.8E-05 27.6 3.2 29 20-49 4-32 (32)
143 TIGR02036 dsdC D-serine deamin 81.6 3.5 7.5E-05 38.2 5.9 64 6-72 12-75 (302)
144 TIGR00122 birA_repr_reg BirA b 81.2 5.5 0.00012 29.1 5.7 52 7-62 3-54 (69)
145 COG3373 Uncharacterized protei 81.0 5.4 0.00012 32.1 5.8 65 4-69 17-94 (108)
146 TIGR02424 TF_pcaQ pca operon t 81.0 3.1 6.8E-05 38.0 5.3 61 6-69 7-67 (300)
147 TIGR03339 phn_lysR aminoethylp 80.9 2.7 5.8E-05 37.6 4.8 60 8-70 3-62 (279)
148 PRK11062 nhaR transcriptional 80.9 4.9 0.00011 37.0 6.6 64 6-72 8-71 (296)
149 PF06969 HemN_C: HemN C-termin 80.8 2 4.3E-05 31.0 3.2 55 8-66 10-65 (66)
150 PF01710 HTH_Tnp_IS630: Transp 80.7 6.7 0.00015 32.1 6.7 98 1-116 1-102 (119)
151 COG1568 Predicted methyltransf 80.5 4.1 8.8E-05 39.2 5.9 58 7-70 25-82 (354)
152 PRK04424 fatty acid biosynthes 80.4 2 4.4E-05 38.0 3.7 47 3-50 6-52 (185)
153 PRK13348 chromosome replicatio 80.0 3.8 8.2E-05 37.4 5.5 63 4-70 4-66 (294)
154 PF08784 RPA_C: Replication pr 80.0 3.6 7.9E-05 32.4 4.7 47 3-50 46-96 (102)
155 PF09756 DDRGK: DDRGK domain; 79.8 2.2 4.8E-05 38.3 3.8 78 7-94 102-181 (188)
156 PRK09986 DNA-binding transcrip 79.8 3.5 7.6E-05 37.4 5.2 62 6-70 11-72 (294)
157 PRK10411 DNA-binding transcrip 79.7 4 8.7E-05 37.5 5.6 48 3-51 3-50 (240)
158 PRK09863 putative frv operon r 79.7 12 0.00026 38.6 9.5 92 1-96 1-102 (584)
159 PRK09906 DNA-binding transcrip 79.4 3.7 8E-05 37.4 5.2 62 6-70 5-66 (296)
160 PRK10341 DNA-binding transcrip 79.3 4.7 0.0001 37.4 6.0 64 5-71 10-73 (312)
161 PRK10082 cell density-dependen 79.1 4.3 9.4E-05 37.4 5.6 63 6-71 15-77 (303)
162 PRK14997 LysR family transcrip 78.8 5.6 0.00012 36.4 6.2 63 6-71 6-68 (301)
163 PF09639 YjcQ: YjcQ protein; 78.7 2 4.2E-05 33.7 2.7 74 6-83 1-81 (88)
164 COG1654 BirA Biotin operon rep 78.6 7.1 0.00015 30.3 5.8 47 14-62 15-61 (79)
165 TIGR00738 rrf2_super rrf2 fami 78.5 2.9 6.4E-05 34.1 3.9 59 7-66 11-72 (132)
166 PRK11013 DNA-binding transcrip 78.4 4.2 9E-05 37.7 5.3 64 4-70 6-69 (309)
167 PRK09802 DNA-binding transcrip 77.9 3.5 7.7E-05 38.5 4.7 46 4-50 17-62 (269)
168 COG4190 Predicted transcriptio 77.7 5.8 0.00013 34.0 5.4 49 4-53 64-112 (144)
169 COG0640 ArsR Predicted transcr 77.3 14 0.0003 27.0 7.1 61 4-65 25-86 (110)
170 PF05584 Sulfolobus_pRN: Sulfo 76.8 7.4 0.00016 29.8 5.3 46 5-52 6-51 (72)
171 PRK10086 DNA-binding transcrip 76.7 5.4 0.00012 37.1 5.6 63 6-71 18-80 (311)
172 PRK15092 DNA-binding transcrip 76.6 5.5 0.00012 37.3 5.6 64 6-72 15-78 (310)
173 TIGR03298 argP transcriptional 76.5 3.9 8.5E-05 37.3 4.5 62 6-71 5-66 (292)
174 COG1414 IclR Transcriptional r 76.5 5.2 0.00011 36.9 5.3 57 6-64 6-63 (246)
175 PRK11233 nitrogen assimilation 76.5 5.3 0.00012 36.9 5.4 66 6-74 5-70 (305)
176 TIGR03418 chol_sulf_TF putativ 76.4 3.3 7.2E-05 37.6 4.0 63 6-71 5-67 (291)
177 PLN02265 probable phenylalanyl 76.0 2.8 6.2E-05 43.7 3.8 46 216-262 392-437 (597)
178 COG0583 LysR Transcriptional r 76.0 5.5 0.00012 35.5 5.2 61 8-71 7-67 (297)
179 TIGR02944 suf_reg_Xantho FeS a 75.8 4.1 8.9E-05 33.4 4.0 47 6-53 11-59 (130)
180 CHL00180 rbcR LysR transcripti 75.7 7.2 0.00016 35.9 6.1 65 5-72 8-72 (305)
181 PF14277 DUF4364: Domain of un 75.3 3.8 8.3E-05 35.8 3.9 51 18-69 15-71 (163)
182 PRK09801 transcriptional activ 75.1 5.8 0.00013 37.0 5.3 65 6-73 10-74 (310)
183 PF13545 HTH_Crp_2: Crp-like h 75.0 6.4 0.00014 28.8 4.6 35 19-54 29-63 (76)
184 PRK15243 transcriptional regul 75.0 7.7 0.00017 36.6 6.2 66 4-72 6-71 (297)
185 PRK12679 cbl transcriptional r 74.2 7.1 0.00015 36.4 5.7 64 6-70 5-68 (316)
186 PRK12682 transcriptional regul 74.0 4.1 8.8E-05 37.7 4.0 52 20-72 18-70 (309)
187 PRK11151 DNA-binding transcrip 73.8 5.8 0.00013 36.4 4.9 63 6-71 5-67 (305)
188 TIGR00635 ruvB Holliday juncti 73.6 4.2 9E-05 37.7 3.9 63 5-71 239-305 (305)
189 TIGR02010 IscR iron-sulfur clu 73.6 7.7 0.00017 32.3 5.2 56 7-63 11-69 (135)
190 PRK11139 DNA-binding transcrip 73.5 6.8 0.00015 35.8 5.3 64 6-72 10-73 (297)
191 TIGR03338 phnR_burk phosphonat 72.9 7.3 0.00016 34.2 5.2 43 16-59 32-74 (212)
192 PRK11014 transcriptional repre 72.7 6.9 0.00015 32.7 4.7 44 18-62 25-68 (141)
193 PRK11534 DNA-binding transcrip 72.7 8.6 0.00019 34.2 5.6 43 16-59 28-70 (224)
194 PRK03635 chromosome replicatio 72.0 8.5 0.00018 35.3 5.6 61 6-70 6-66 (294)
195 PF00392 GntR: Bacterial regul 71.9 12 0.00025 27.0 5.2 36 18-54 23-59 (64)
196 PRK12683 transcriptional regul 71.4 8.4 0.00018 35.8 5.4 64 6-71 5-69 (309)
197 TIGR02681 phage_pRha phage reg 71.2 4.7 0.0001 32.9 3.2 55 19-73 14-81 (108)
198 PF04458 DUF505: Protein of un 71.0 4.1 8.8E-05 42.4 3.4 68 5-75 433-506 (591)
199 PRK10681 DNA-binding transcrip 70.0 9.8 0.00021 35.1 5.5 42 3-44 6-47 (252)
200 PRK11886 bifunctional biotin-- 69.8 12 0.00025 35.6 6.1 56 5-62 5-60 (319)
201 PF09669 Phage_pRha: Phage reg 69.5 6.9 0.00015 30.6 3.8 55 19-73 2-70 (93)
202 PF09382 RQC: RQC domain; Int 69.1 11 0.00025 29.5 5.0 43 29-72 53-97 (106)
203 TIGR00471 pheT_arch phenylalan 68.7 5 0.00011 41.4 3.6 46 216-262 357-402 (551)
204 PRK09508 leuO leucine transcri 68.4 8.7 0.00019 35.6 4.9 63 6-71 26-88 (314)
205 cd07153 Fur_like Ferric uptake 68.2 24 0.00052 27.9 6.8 56 6-62 3-66 (116)
206 PF08222 HTH_CodY: CodY helix- 66.9 25 0.00054 26.0 5.8 35 19-54 5-39 (61)
207 PRK11482 putative DNA-binding 66.8 10 0.00023 35.5 5.1 64 7-73 34-97 (317)
208 COG1959 Predicted transcriptio 66.2 9 0.0002 32.8 4.1 59 8-67 12-73 (150)
209 COG1675 TFA1 Transcription ini 65.9 14 0.00031 32.9 5.4 48 6-54 20-67 (176)
210 PRK15431 ferrous iron transpor 65.7 18 0.00038 28.2 5.2 47 1-50 1-47 (78)
211 PRK00441 argR arginine repress 65.7 19 0.0004 31.0 6.0 73 2-83 2-80 (149)
212 TIGR03697 NtcA_cyano global ni 65.6 13 0.00028 31.6 5.0 36 19-55 144-179 (193)
213 PRK10676 DNA-binding transcrip 64.9 19 0.0004 33.7 6.3 64 4-69 19-86 (263)
214 PRK12423 LexA repressor; Provi 64.9 18 0.00038 32.2 5.9 56 3-59 5-66 (202)
215 PRK08898 coproporphyrinogen II 64.5 23 0.00049 34.8 7.1 59 8-70 328-386 (394)
216 PRK05472 redox-sensing transcr 64.0 11 0.00023 33.8 4.3 44 4-48 16-61 (213)
217 PRK12680 transcriptional regul 64.0 12 0.00025 35.4 4.9 65 6-73 5-71 (327)
218 COG1725 Predicted transcriptio 63.4 32 0.0007 29.0 6.8 45 20-67 37-81 (125)
219 PRK11753 DNA-binding transcrip 63.2 15 0.00032 31.7 5.1 38 19-57 169-206 (211)
220 PF04458 DUF505: Protein of un 63.1 11 0.00024 39.4 4.7 43 29-72 326-370 (591)
221 PRK11920 rirA iron-responsive 62.9 16 0.00034 31.3 5.0 57 8-65 12-70 (153)
222 PRK11414 colanic acid/biofilm 62.9 9.3 0.0002 34.0 3.8 39 16-55 32-70 (221)
223 PRK05660 HemN family oxidoredu 62.6 24 0.00052 34.5 6.8 57 9-69 312-368 (378)
224 COG4738 Predicted transcriptio 62.4 8.7 0.00019 32.1 3.1 47 9-56 32-78 (124)
225 PRK12684 transcriptional regul 62.2 14 0.00031 34.3 5.0 63 6-70 5-68 (313)
226 PRK05799 coproporphyrinogen II 62.1 29 0.00062 33.6 7.3 60 7-70 306-366 (374)
227 PHA03103 double-strand RNA-bin 60.4 21 0.00045 32.0 5.5 54 4-58 13-66 (183)
228 PF05491 RuvB_C: Holliday junc 60.3 31 0.00067 26.7 5.7 62 4-70 8-74 (76)
229 PRK13347 coproporphyrinogen II 59.7 29 0.00064 34.7 7.1 60 6-69 369-431 (453)
230 PRK12681 cysB transcriptional 59.6 9.4 0.0002 35.9 3.3 61 7-69 6-67 (324)
231 PF08280 HTH_Mga: M protein tr 59.1 15 0.00032 26.3 3.6 40 5-44 6-45 (59)
232 COG1542 Uncharacterized conser 58.9 6 0.00013 40.4 1.9 67 4-72 284-363 (593)
233 PRK10225 DNA-binding transcrip 58.8 29 0.00062 31.6 6.3 43 16-59 30-73 (257)
234 PF05732 RepL: Firmicute plasm 58.4 22 0.00047 31.1 5.2 53 19-77 76-128 (165)
235 PRK09391 fixK transcriptional 58.1 24 0.00052 31.6 5.6 34 19-53 180-213 (230)
236 PRK10216 DNA-binding transcrip 58.1 19 0.00041 33.4 5.1 61 6-69 12-72 (319)
237 PRK08208 coproporphyrinogen II 58.1 28 0.0006 34.6 6.5 57 9-69 352-408 (430)
238 PRK10857 DNA-binding transcrip 57.7 29 0.00062 30.2 5.8 46 16-62 23-68 (164)
239 PRK10079 phosphonate metabolis 57.5 24 0.00053 31.8 5.6 55 4-59 20-75 (241)
240 PRK04984 fatty acid metabolism 57.5 26 0.00056 31.4 5.7 43 16-59 28-71 (239)
241 PRK13918 CRP/FNR family transc 57.4 19 0.00042 30.9 4.7 35 19-54 150-184 (202)
242 PF09114 MotA_activ: Transcrip 57.2 37 0.00081 27.2 5.7 59 8-70 20-80 (96)
243 PF12324 HTH_15: Helix-turn-he 57.0 23 0.0005 27.5 4.5 39 5-43 25-63 (77)
244 TIGR00331 hrcA heat shock gene 56.9 19 0.0004 35.0 4.9 64 4-69 2-72 (337)
245 PF04967 HTH_10: HTH DNA bindi 56.7 24 0.00052 25.3 4.3 42 4-45 3-50 (53)
246 PF14502 HTH_41: Helix-turn-he 56.5 22 0.00048 25.2 3.9 34 20-54 8-41 (48)
247 COG4738 Predicted transcriptio 56.1 37 0.00081 28.4 5.8 18 97-114 56-73 (124)
248 PRK08599 coproporphyrinogen II 55.9 38 0.00083 32.8 7.0 60 7-70 307-367 (377)
249 PRK11716 DNA-binding transcrip 55.7 16 0.00035 32.2 4.0 42 28-70 1-42 (269)
250 PF13518 HTH_28: Helix-turn-he 55.0 29 0.00063 23.2 4.4 38 8-48 4-41 (52)
251 PF08221 HTH_9: RNA polymerase 54.5 35 0.00075 24.9 4.9 48 5-53 14-61 (62)
252 PRK10402 DNA-binding transcrip 54.2 22 0.00049 31.5 4.7 59 4-65 150-213 (226)
253 COG0478 RIO-like serine/threon 53.8 33 0.00071 33.1 5.9 65 4-69 13-81 (304)
254 PF14394 DUF4423: Domain of un 53.7 27 0.00059 30.6 5.0 45 19-66 40-86 (171)
255 PF06971 Put_DNA-bind_N: Putat 53.5 18 0.00039 25.6 3.1 33 7-39 15-49 (50)
256 TIGR02647 DNA conserved hypoth 52.9 13 0.00027 28.9 2.4 34 32-70 33-66 (77)
257 smart00531 TFIIE Transcription 51.9 21 0.00046 30.3 4.0 43 8-51 5-47 (147)
258 TIGR02812 fadR_gamma fatty aci 51.8 25 0.00053 31.5 4.6 43 16-59 27-70 (235)
259 PRK03837 transcriptional regul 51.7 28 0.00062 31.0 5.0 43 16-59 34-77 (241)
260 PRK06582 coproporphyrinogen II 51.5 45 0.00098 32.8 6.7 59 7-70 322-382 (390)
261 PRK09990 DNA-binding transcrip 51.4 31 0.00067 31.2 5.2 43 16-59 28-71 (251)
262 PF13542 HTH_Tnp_ISL3: Helix-t 51.3 34 0.00074 23.2 4.3 38 2-41 13-50 (52)
263 PRK09249 coproporphyrinogen II 50.8 46 0.00099 33.3 6.8 60 7-70 369-432 (453)
264 PF13384 HTH_23: Homeodomain-l 50.5 18 0.00038 24.4 2.7 39 7-48 8-46 (50)
265 PRK10421 DNA-binding transcrip 50.4 34 0.00073 31.1 5.3 43 16-59 23-66 (253)
266 PRK09350 poxB regulator PoxA; 50.1 16 0.00035 34.8 3.3 35 224-260 9-43 (306)
267 PRK11161 fumarate/nitrate redu 49.8 30 0.00064 30.6 4.8 36 19-55 185-220 (235)
268 COG0072 PheT Phenylalanyl-tRNA 49.6 19 0.0004 38.1 3.9 44 219-263 349-392 (650)
269 COG1777 Predicted transcriptio 49.5 25 0.00055 32.3 4.2 45 5-51 16-60 (217)
270 PRK10736 hypothetical protein; 49.4 32 0.0007 34.1 5.3 47 6-54 310-356 (374)
271 PRK09464 pdhR transcriptional 49.4 36 0.00079 30.8 5.4 43 16-59 31-74 (254)
272 PRK11523 DNA-binding transcrip 48.9 37 0.00081 30.8 5.4 43 16-59 29-72 (253)
273 PF09681 Phage_rep_org_N: N-te 48.4 64 0.0014 26.9 6.2 43 18-63 53-95 (121)
274 PRK03341 arginine repressor; P 47.5 48 0.001 29.2 5.6 59 3-65 14-79 (168)
275 COG3888 Predicted transcriptio 47.1 54 0.0012 31.4 6.1 53 5-58 5-59 (321)
276 PF05158 RNA_pol_Rpc34: RNA po 47.0 32 0.00068 33.4 4.8 59 4-63 84-148 (327)
277 PF00196 GerE: Bacterial regul 47.0 35 0.00075 23.9 3.9 41 3-45 5-45 (58)
278 KOG3233|consensus 46.7 12 0.00027 35.6 1.8 58 3-61 83-146 (297)
279 COG4565 CitB Response regulato 46.3 57 0.0012 30.2 6.0 49 4-53 158-207 (224)
280 PRK04172 pheS phenylalanyl-tRN 45.0 55 0.0012 33.3 6.3 35 37-72 156-190 (489)
281 TIGR02404 trehalos_R_Bsub treh 45.0 45 0.00096 29.8 5.2 37 22-59 28-64 (233)
282 PF01475 FUR: Ferric uptake re 44.7 38 0.00083 27.1 4.3 59 4-63 8-74 (120)
283 KOG2165|consensus 44.6 38 0.00081 36.3 5.1 67 3-70 601-669 (765)
284 TIGR02844 spore_III_D sporulat 43.9 44 0.00096 25.9 4.3 35 4-39 6-40 (80)
285 COG0735 Fur Fe2+/Zn2+ uptake r 43.9 98 0.0021 26.2 6.8 62 3-65 20-89 (145)
286 PRK14999 histidine utilization 43.7 45 0.00097 30.1 5.0 38 21-59 39-76 (241)
287 TIGR02018 his_ut_repres histid 43.6 49 0.0011 29.6 5.2 37 22-59 29-65 (230)
288 PF10711 DUF2513: Hypothetical 43.3 57 0.0012 25.9 5.0 64 5-69 6-77 (102)
289 PF01316 Arg_repressor: Argini 43.2 69 0.0015 24.2 5.1 59 3-65 4-68 (70)
290 PF10826 DUF2551: Protein of u 42.7 76 0.0016 25.0 5.4 61 4-64 11-78 (83)
291 TIGR00538 hemN oxygen-independ 42.6 73 0.0016 31.9 6.7 63 9-75 371-437 (455)
292 PRK11402 DNA-binding transcrip 42.4 55 0.0012 29.4 5.4 37 22-59 37-73 (241)
293 TIGR02325 C_P_lyase_phnF phosp 41.7 59 0.0013 28.9 5.5 37 22-59 36-72 (238)
294 KOG3054|consensus 41.7 65 0.0014 30.5 5.7 75 8-95 204-283 (299)
295 PF06163 DUF977: Bacterial pro 41.3 63 0.0014 27.4 5.1 47 4-51 12-58 (127)
296 PRK00037 hisS histidyl-tRNA sy 41.0 15 0.00032 35.9 1.5 36 214-250 12-47 (412)
297 TIGR02698 CopY_TcrY copper tra 40.9 95 0.0021 25.8 6.2 86 75-163 6-116 (130)
298 PRK09334 30S ribosomal protein 40.7 1.1E+02 0.0024 24.2 6.0 45 6-51 29-73 (86)
299 PF07927 YcfA: YcfA-like prote 40.7 11 0.00024 26.3 0.4 41 228-269 2-44 (56)
300 PRK09764 DNA-binding transcrip 40.5 61 0.0013 29.2 5.4 41 18-59 28-69 (240)
301 PF01418 HTH_6: Helix-turn-hel 40.3 34 0.00074 25.7 3.1 40 4-43 16-59 (77)
302 PLN03238 probable histone acet 38.9 1.1E+02 0.0023 29.6 6.8 53 7-64 211-264 (290)
303 PRK00080 ruvB Holliday junctio 38.9 29 0.00064 32.8 3.1 64 4-71 259-326 (328)
304 PRK09333 30S ribosomal protein 38.2 52 0.0011 28.6 4.3 60 7-70 56-129 (150)
305 COG2186 FadR Transcriptional r 38.1 37 0.00081 31.0 3.6 37 22-59 38-74 (241)
306 TIGR01714 phage_rep_org_N phag 37.6 99 0.0021 25.8 5.7 45 8-53 33-85 (119)
307 TIGR00442 hisS histidyl-tRNA s 37.1 21 0.00044 34.8 1.8 37 214-251 8-44 (397)
308 PRK11512 DNA-binding transcrip 35.6 63 0.0014 26.7 4.3 44 73-116 40-88 (144)
309 COG1510 Predicted transcriptio 35.5 37 0.0008 30.3 2.9 36 16-52 39-74 (177)
310 PRK09462 fur ferric uptake reg 34.9 1.9E+02 0.0042 24.1 7.3 58 4-62 17-83 (148)
311 PF11994 DUF3489: Protein of u 34.8 1.9E+02 0.0042 22.1 6.4 47 4-51 10-58 (72)
312 COG2188 PhnF Transcriptional r 34.5 96 0.0021 28.1 5.7 37 22-59 35-71 (236)
313 PF03297 Ribosomal_S25: S25 ri 34.2 76 0.0017 25.9 4.4 46 5-51 46-91 (105)
314 PF13551 HTH_29: Winged helix- 33.7 82 0.0018 24.2 4.5 39 8-48 3-41 (112)
315 CHL00192 syfB phenylalanyl-tRN 33.4 52 0.0011 35.1 4.2 37 216-252 393-429 (704)
316 PRK09057 coproporphyrinogen II 33.2 99 0.0021 30.1 5.9 59 7-70 314-372 (380)
317 PF04492 Phage_rep_O: Bacterio 32.9 66 0.0014 25.9 3.8 35 18-53 54-88 (100)
318 PF02796 HTH_7: Helix-turn-hel 32.7 63 0.0014 21.7 3.2 33 6-40 11-43 (45)
319 PRK15481 transcriptional regul 32.1 74 0.0016 31.0 4.8 42 17-59 27-69 (431)
320 PRK10046 dpiA two-component re 32.0 1.2E+02 0.0027 26.5 5.8 47 6-53 164-211 (225)
321 PRK15418 transcriptional regul 31.8 59 0.0013 31.2 4.0 37 19-56 30-66 (318)
322 PF13936 HTH_38: Helix-turn-he 31.6 79 0.0017 21.2 3.5 33 7-40 10-42 (44)
323 PF05043 Mga: Mga helix-turn-h 31.0 46 0.00099 25.1 2.5 41 3-43 15-55 (87)
324 COG3327 PaaX Phenylacetic acid 30.9 62 0.0014 30.8 3.8 59 22-83 32-91 (291)
325 COG1802 GntR Transcriptional r 30.3 51 0.0011 29.4 3.1 43 16-59 37-79 (230)
326 PRK09775 putative DNA-binding 30.1 1.2E+02 0.0025 30.7 5.9 56 8-67 4-60 (442)
327 PRK08629 coproporphyrinogen II 30.0 1.7E+02 0.0037 29.3 7.0 59 6-69 347-406 (433)
328 PRK07379 coproporphyrinogen II 29.8 1.6E+02 0.0034 29.1 6.7 57 11-71 328-387 (400)
329 COG2390 DeoR Transcriptional r 29.7 1E+02 0.0022 29.9 5.2 38 18-56 26-63 (321)
330 smart00421 HTH_LUXR helix_turn 29.4 1.5E+02 0.0032 19.3 4.7 40 4-45 6-45 (58)
331 PF04079 DUF387: Putative tran 29.3 1.4E+02 0.003 26.0 5.5 108 8-116 1-127 (159)
332 PF14357 DUF4404: Domain of un 28.6 50 0.0011 25.7 2.4 21 219-239 64-85 (85)
333 PF07750 GcrA: GcrA cell cycle 28.5 70 0.0015 27.9 3.6 41 1-42 1-43 (162)
334 PF09929 DUF2161: Uncharacteri 28.0 1.5E+02 0.0031 24.9 5.1 56 7-68 62-117 (118)
335 PRK03911 heat-inducible transc 27.1 1.1E+02 0.0024 28.9 4.8 62 5-68 4-72 (260)
336 PF01710 HTH_Tnp_IS630: Transp 26.5 1.2E+02 0.0026 24.6 4.5 34 9-42 62-95 (119)
337 PF13182 DUF4007: Protein of u 26.3 1.1E+02 0.0024 28.9 4.7 59 8-69 17-76 (286)
338 TIGR03879 near_KaiC_dom probab 26.2 89 0.0019 23.9 3.3 32 18-49 32-63 (73)
339 PRK15201 fimbriae regulatory p 26.1 1.3E+02 0.0028 27.3 4.8 41 3-45 135-175 (198)
340 COG4901 Ribosomal protein S25 26.0 1.5E+02 0.0033 24.3 4.8 44 7-51 48-91 (107)
341 PRK13239 alkylmercury lyase; P 25.9 1.4E+02 0.003 27.3 5.1 39 5-43 23-61 (206)
342 PLN00104 MYST -like histone ac 25.5 1.8E+02 0.0039 29.7 6.2 52 7-63 362-414 (450)
343 PRK00135 scpB segregation and 25.4 2.2E+02 0.0049 25.4 6.3 61 4-68 90-155 (188)
344 PRK11639 zinc uptake transcrip 25.2 1.6E+02 0.0035 25.5 5.3 48 4-52 26-79 (169)
345 PRK11302 DNA-binding transcrip 25.1 95 0.0021 28.4 4.0 47 3-50 15-65 (284)
346 COG4465 CodY Pleiotropic trans 25.0 1E+02 0.0022 28.7 4.0 43 9-52 194-237 (261)
347 PLN03239 histone acetyltransfe 24.8 2.3E+02 0.0051 28.0 6.7 52 7-63 269-324 (351)
348 cd00768 class_II_aaRS-like_cor 24.8 63 0.0014 27.5 2.6 27 224-251 3-29 (211)
349 COG3398 Uncharacterized protei 24.7 1.8E+02 0.004 27.1 5.6 58 5-63 175-233 (240)
350 cd06170 LuxR_C_like C-terminal 24.6 2.1E+02 0.0045 18.7 4.8 39 4-44 3-41 (57)
351 COG2469 Uncharacterized conser 24.5 71 0.0015 30.6 3.0 63 4-70 216-278 (284)
352 PF06224 HTH_42: Winged helix 24.2 2.3E+02 0.005 26.5 6.5 63 3-65 166-230 (327)
353 TIGR00462 genX lysyl-tRNA synt 23.9 67 0.0015 30.5 2.8 27 224-251 5-31 (304)
354 TIGR00281 segregation and cond 23.5 5.3E+02 0.012 23.0 10.2 103 14-116 12-132 (186)
355 PRK00629 pheT phenylalanyl-tRN 23.4 1E+02 0.0022 33.3 4.4 35 216-250 482-516 (791)
356 smart00422 HTH_MERR helix_turn 23.4 1.1E+02 0.0024 21.6 3.3 63 20-94 2-65 (70)
357 PRK04158 transcriptional repre 23.1 58 0.0012 30.8 2.1 43 9-52 191-234 (256)
358 PRK09392 ftrB transcriptional 22.5 1.9E+02 0.0042 25.4 5.4 43 21-67 176-218 (236)
359 COG1542 Uncharacterized conser 22.3 78 0.0017 32.6 3.0 45 21-68 445-489 (593)
360 PF02387 IncFII_repA: IncFII R 22.2 2.9E+02 0.0062 26.4 6.6 61 19-82 96-174 (281)
361 TIGR02147 Fsuc_second hypothet 22.1 1.6E+02 0.0034 27.9 4.9 46 17-65 136-183 (271)
362 COG2771 CsgD DNA-binding HTH d 22.1 2.4E+02 0.0051 19.2 4.8 41 3-45 6-46 (65)
363 PF07106 TBPIP: Tat binding pr 21.8 3E+02 0.0064 23.6 6.2 60 5-65 2-65 (169)
364 PF10623 PilI: Plasmid conjuga 21.7 41 0.00089 26.3 0.7 8 260-267 1-8 (83)
365 TIGR03826 YvyF flagellar opero 21.4 1.8E+02 0.0038 24.9 4.6 36 6-41 32-69 (137)
366 COG2344 AT-rich DNA-binding pr 21.0 1.4E+02 0.0031 27.2 4.1 39 5-43 17-57 (211)
367 PRK15411 rcsA colanic acid cap 20.5 1.9E+02 0.0041 25.6 4.8 41 3-45 139-179 (207)
368 COG4344 Uncharacterized protei 20.5 2E+02 0.0043 25.4 4.7 54 23-77 36-107 (175)
369 PRK09058 coproporphyrinogen II 20.5 2.4E+02 0.0052 28.3 6.0 56 9-71 374-430 (449)
370 PF00888 Cullin: Cullin family 20.4 85 0.0018 31.7 2.9 47 3-50 519-565 (588)
371 TIGR03337 phnR transcriptional 20.3 1.7E+02 0.0037 25.8 4.5 39 20-59 27-65 (231)
372 PRK10840 transcriptional regul 20.1 1.9E+02 0.0042 24.8 4.8 41 3-45 152-192 (216)
No 1
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=100.00 E-value=2e-73 Score=561.42 Aligned_cols=276 Identities=46% Similarity=0.778 Sum_probs=254.6
Q ss_pred CcHHHHHHHHHhccCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346 2 ASDLTEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFN 80 (292)
Q Consensus 2 ~~~~e~~iL~~L~~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~ 80 (292)
+.+.|++||.+|...+. ++++++|+.+|++|++|+++++||+++ |+|++++.+.+.|+||+||++|+++||||+||++
T Consensus 1 ~~~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-g~v~~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~ 79 (492)
T PLN02853 1 AAMAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGF-RYVDAQDIKRETWVLTEEGKKYAAEGSPEVQLFA 79 (492)
T ss_pred CchHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHH
Confidence 35789999999988775 799999999999999999999999998 9999999999999999999999999999999999
Q ss_pred hcCCCC-CChHHHhhcCC--chhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCCCCCChhhHHhhhc
Q psy10346 81 NVPSEG-IGQKELLATFP--NAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKK 157 (292)
Q Consensus 81 ~l~~~~-~~~~el~~~~~--~~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~~~l~~~~~~~Lkk 157 (292)
+|++.| ++++||.+.++ .++||+|+|+|+|||+++++ |.+.+..+...|.++..|+.+..+. .++++.+++|+|
T Consensus 80 ~l~~~~~~~~~eL~~~l~~~~~~i~~g~a~k~gwi~i~~~-~~v~~~~~~~~d~~~~~L~~l~~~~--~~~~~~l~~Lkk 156 (492)
T PLN02853 80 AVPAEGSISKDELQKKLDPAVFDIGFKQAMKNKWLEMGGK-PQVSRKVQHVEDEVKELLLAIQEGK--EVDDKDIDALKK 156 (492)
T ss_pred HHhhcCCccHHHHHHhhCchhHHHHHHHHHHCCcEEECCC-CcEEeccCccchHHHHHHHHHhcCC--CCCHHHHHHHHh
Confidence 998744 89999988763 68999999999999999843 4666667777888999999998764 466678999999
Q ss_pred cc-ceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhh
Q psy10346 158 RK-LLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLD 236 (292)
Q Consensus 158 Rk-Lv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~ 236 (292)
|| ||+.++.+++.|++|+++..++++++|+||+|||+||+|+++.||+|||+++|+.++.|+.|||++++++|++||.+
T Consensus 157 Rk~Li~~~~~~~~~v~~~~~~~~~~~~~~t~LT~eml~sg~Wk~~~fk~Yn~~a~g~~~~~G~~HPl~~~~~ei~~if~~ 236 (492)
T PLN02853 157 RRKLITLETWKGYSIKKGPNYAPERKKAATDLTREMLQSGDWKDLEFKEYNFNALGAPPEGGHLHPLLKVRQQFRKIFLQ 236 (492)
T ss_pred hhcceEEEEEEEEEEEECCccccccccccccCCHHHhcCCCcccCCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHHHh
Confidence 98 99999999999999999888889999999999999999999999999999999999999999999999999999999
Q ss_pred CCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCC
Q psy10346 237 MGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTS 281 (292)
Q Consensus 237 mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~ 281 (292)
|||++|++||+|||+||||||||||||||||||||||||+.|..+
T Consensus 237 mGF~e~~~g~~ves~f~NFDaL~~PqdHPARd~qDTFyl~~~~~~ 281 (492)
T PLN02853 237 MGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLKAPATT 281 (492)
T ss_pred CCCEEecCCCCeechhhhhhhhcCCCCCCCCCccceEEEcCcccc
Confidence 999999779999999999999999999999999999999987654
No 2
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=100.00 E-value=7e-73 Score=559.40 Aligned_cols=279 Identities=47% Similarity=0.779 Sum_probs=255.2
Q ss_pred cHHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhh
Q psy10346 3 SDLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNN 81 (292)
Q Consensus 3 ~~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~ 81 (292)
+..|++||..|.+ ++..+++++|+.+|++|++|+++++||+++ |+|++++++...|+||+||++|+++||||+||+++
T Consensus 5 ~~~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~k-g~v~~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~~ 83 (494)
T PTZ00326 5 ELEENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESA-NYITTEMKKSNTWTLTEEGEDYLKNGSPEYRLWQK 83 (494)
T ss_pred hHHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHH
Confidence 6889999999987 567899999999999999999999999997 99999999999999999999999999999999999
Q ss_pred cCCCCCChHHHhhcC--CchhhHHHHHHHcCCeecccCcceeec---cCCCchHHHHHHHHHHhccC-CCCCChhhHHhh
Q psy10346 82 VPSEGIGQKELLATF--PNAKVGFSKAMAKGWISLDKATGKVLR---KVDSVTDELQAHLKLIANNE-YDKVPEANKVDY 155 (292)
Q Consensus 82 l~~~~~~~~el~~~~--~~~~ig~~~a~k~gwi~i~~~~g~v~~---~~~~~~d~~~~~L~~i~~~~-~~~l~~~~~~~L 155 (292)
|+++|.++.++.+.+ ++++||+|+|+|+|||+++++.+.+.. ..+.+.|.++.+|+.+..+. .+.++++.+++|
T Consensus 84 l~~~~~~~~~l~~~~~~~~~~i~~g~~~k~~wi~i~~~~~~i~~~~~~~~~~~d~~~~~L~~i~~~~~~~~~~~~~~~~L 163 (494)
T PTZ00326 84 LKEGGISKADDAKKLGGKVADIGLGNAMKKKWIKLNKGDKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKEL 163 (494)
T ss_pred hhhcCCCHHHHHhhhcchhHHHHHHHHHHCCcEEEcCCCceeecccccccccccHHHHHHHHHhccCccccCCHHHHHHH
Confidence 998888888877653 478999999999999999976444443 35566788999999998762 235777889999
Q ss_pred hcccceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhh
Q psy10346 156 KKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFL 235 (292)
Q Consensus 156 kkRkLv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~ 235 (292)
+|||||+.++.++|.|++|++++.++++++|+||+|||+||+|+++.||+|||+++|+.+++|+.|||++++++|++||.
T Consensus 164 kkRkLi~~~~~~~~~i~~~~~~~~~~~~~~t~LT~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~i~~if~ 243 (494)
T PTZ00326 164 KKRKLATLEKIKYFVVTKGPKFAKEIKKQITDLTQEMLLNGSWKNAEFKEYNFNALGKKIGGGNLHPLLKVRREFREILL 243 (494)
T ss_pred hcCCCeEEEEEEEEEEEECCccccccccccccCCHHHhhCCccccCCcccceecCCCCCCCCCCCChHHHHHHHHHHHHH
Confidence 99999999999999999999998889999999999999999999999999999999999999999999999999999999
Q ss_pred hCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCCC
Q psy10346 236 DMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE 282 (292)
Q Consensus 236 ~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~~ 282 (292)
+|||+||+++++|||+||||||||||||||||||||||||+.|..+.
T Consensus 244 ~mGF~e~~~~~~ves~f~NFDaL~~PqdHPARd~~DTFyl~~~~~~~ 290 (494)
T PTZ00326 244 EMGFEEMPTNRYVESSFWNFDALFQPQQHPARDAQDTFFLSKPETSK 290 (494)
T ss_pred hCCCEEecCCCCccccchhhhhhcCCCCCCCCCcCceEEEcCccccc
Confidence 99999998778999999999999999999999999999999876553
No 3
>KOG2784|consensus
Probab=100.00 E-value=7.7e-73 Score=533.86 Aligned_cols=272 Identities=57% Similarity=0.931 Sum_probs=258.9
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNV 82 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l 82 (292)
++.+.+||..|+..++.++.+++...+.+|+.++++++||++. |+|+++..+...|.||.||++++.+||||++|+.++
T Consensus 2 ~~~~~~iL~~L~~~de~~s~~l~a~~~~~h~~~v~al~SL~a~-~~i~~~~~~~~~~~LT~EG~~i~~eGS~E~~v~~~i 80 (483)
T KOG2784|consen 2 EALAEKILEKLQESDEVDSSDLAAPFNEDHQQVVGALKSLQAG-GVIEVKDVETKTYELTAEGEEIAREGSHEALVFESI 80 (483)
T ss_pred chHHHHHHHHHHhccCCChhhhcCchhhhhHHHHHHHHHHhhc-CceEEEeeeeEEEeeChhHHHHHhcCCcceeeeecc
Confidence 5788999999998888999999999999999999999999996 999999999999999999999999999999999999
Q ss_pred CCCCCChHHHhhcCCchhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCCCCCChhhHHhhhccccee
Q psy10346 83 PSEGIGQKELLATFPNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKVPEANKVDYKKRKLLQ 162 (292)
Q Consensus 83 ~~~~~~~~el~~~~~~~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~~~l~~~~~~~LkkRkLv~ 162 (292)
++.|+.++||.+.+ . .||+++|+|+|||+++++ .+.++++++.|++++.|.+|+.|.. .++++++|+|||||.
T Consensus 81 ~~~gl~~~el~~k~-~-giG~~~A~~nkWI~~d~~--~~~r~v~~itD~v~~~l~~ik~g~~---~ake~~dlkKrKLi~ 153 (483)
T KOG2784|consen 81 PEEGLAIAELMKKL-V-GIGQSKAFKNKWIRVDKS--RVVRDVDSITDEVRNQLQQIKRGSA---DAKEVEDLKKRKLIS 153 (483)
T ss_pred CccccCHHHHHhhh-h-ccchhhhhccceEEecCc--ccccchhhhhHHHHHHHHHHHcCcc---hHHHHHHHHhhhhhc
Confidence 99999999999854 3 399999999999999886 6778999999999999999998753 378899999999999
Q ss_pred eEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceec
Q psy10346 163 EVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEM 242 (292)
Q Consensus 163 ~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~ 242 (292)
+.+.+.|.+++|++|+..+.+.+||||+|||.||+|++..||+|||++.|..+.+|++|||+++++++|+||.+|||+||
T Consensus 154 ~~~~~~f~v~KGp~Fst~l~k~eTdLT~emi~~gsw~dl~FK~YNF~a~G~~p~~G~lHPLmKvR~eFRqiF~emGFsEM 233 (483)
T KOG2784|consen 154 EVKIKVFSVTKGPNFSTSLTKLETDLTSEMIASGSWKDLKFKPYNFNAEGVPPSSGHLHPLMKVREEFRQIFFEMGFSEM 233 (483)
T ss_pred cceeEEEEEecCCcccchHHHHhhhccHHHhccCchhhccCcccCcccCCCCCCCCccchHHHHHHHHHHHHHHcccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccceeccccCCCCCCCCCCCCCCceeecCCCCCC
Q psy10346 243 PTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKTSE 282 (292)
Q Consensus 243 ~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~~~ 282 (292)
+++++|||+|||||||||||+|||||.|||||+++|+.+.
T Consensus 234 ptn~yVEssFWNFDALfqPQqHpARDahDTFfl~~Pa~s~ 273 (483)
T KOG2784|consen 234 PTNNYVESSFWNFDALFQPQQHPARDAHDTFFLKDPATST 273 (483)
T ss_pred ccccchhhccccchhhcCcccCCccccccceEecChhhcc
Confidence 9999999999999999999999999999999999998764
No 4
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=100.00 E-value=2.8e-62 Score=486.98 Aligned_cols=273 Identities=31% Similarity=0.507 Sum_probs=247.5
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNV 82 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l 82 (292)
+..|..||..|...+.+++.++|+.+|+++++|++++++|+++ |||+.+......+.||++|++|+++|+||+|+++++
T Consensus 5 t~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~k-GlV~~~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l 83 (489)
T PRK04172 5 HPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEK-GLVKVEERVEEVYVLTEEGKKYAEEGLPERRLLNAL 83 (489)
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhC-CCEEEEeeeEEEEEECHHHHHHHHhcCHHHHHHHhh
Confidence 5789999999988788899999999999999999999999997 999999988899999999999999999999999999
Q ss_pred CC-CCCChHHHhhc-C--CchhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCC---CCCChhhHHhh
Q psy10346 83 PS-EGIGQKELLAT-F--PNAKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEY---DKVPEANKVDY 155 (292)
Q Consensus 83 ~~-~~~~~~el~~~-~--~~~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~---~~l~~~~~~~L 155 (292)
.+ .|++++||.+. + +..++|+++|+|+||+++++| .+.+..+...|.++..|+.+.+|.. ..++.+.+++|
T Consensus 84 ~~~~g~~~~el~~~aL~~~~~~i~~~~l~k~g~i~i~~G--~~i~~~~~~~d~~~~~L~~l~~g~~~~~~~~~~~~l~~L 161 (489)
T PRK04172 84 KDGGEVSLDELKEALLDKKEVGIALGNLARKGWAKIEKG--KVILKPDAYEDPEEKALKALAEGDKEELSEEDLKVLKEL 161 (489)
T ss_pred HhcCCcCHHHHHHhhccchhHHHHHHHHHHCCCeecCCC--ceeecCcccCcHHHHHHHHHhccCccccccCCHHHHHHH
Confidence 85 46899999886 4 478999999999999999654 6666555667888999999987652 24567789999
Q ss_pred hcccceeeEEEEEEEEe---cCcccc---ccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHH
Q psy10346 156 KKRKLLQEVTIKSFLLK---KGPEFS---TTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAE 229 (292)
Q Consensus 156 kkRkLv~~~~~~~~~v~---~g~~~~---~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~ 229 (292)
+|||||+.++++.+.++ +|.+++ ..+++++|+||+|||+||+|+++.||+||++++++.+++|..||+.+++++
T Consensus 162 kkRkL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~e~l~~g~w~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~ 241 (489)
T PRK04172 162 KKRKLVEEKERTERSVELTDAGLELLKEGIELKEEITQLTPELLKSGEWKEKEFRPYNVKAPPPKIYPGKKHPYREFIDE 241 (489)
T ss_pred HhcCCeEEEEEEEEEEEEccchhhhhhcccccccccccCCHHHhcCCCccCCCCccceeCCCCCCCCCCCCChHHHHHHH
Confidence 99999999999999975 567776 347888999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCC
Q psy10346 230 FRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK 279 (292)
Q Consensus 230 i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~ 279 (292)
|+++|.+|||+||. +|.||++|||||+||||||||||++|||||++.|.
T Consensus 242 ~~~~f~~~Gf~e~~-~p~vE~~~~nfd~lf~p~~hpaR~~~dtf~~~~~~ 290 (489)
T PRK04172 242 VRDILVEMGFEEMK-GPLVETEFWNFDALFQPQDHPAREMQDTFYLKYPG 290 (489)
T ss_pred HHHHHHHCCCEEee-CCeeeecCcccccccCCCCCCCCCccceEEECCcc
Confidence 99999999999996 89999999999999999999999999999999876
No 5
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.1e-34 Score=275.43 Aligned_cols=163 Identities=34% Similarity=0.517 Sum_probs=123.7
Q ss_pred hhhHHHHHHHcCCeecccCcceeeccCCCchHHHHHHHHHHhccCCCCC-ChhhHHhh-hccc-ceeeEEEEEEEEecCc
Q psy10346 99 AKVGFSKAMAKGWISLDKATGKVLRKVDSVTDELQAHLKLIANNEYDKV-PEANKVDY-KKRK-LLQEVTIKSFLLKKGP 175 (292)
Q Consensus 99 ~~ig~~~a~k~gwi~i~~~~g~v~~~~~~~~d~~~~~L~~i~~~~~~~l-~~~~~~~L-kkRk-Lv~~~~~~~~~v~~g~ 175 (292)
..+++++++++||..++.. .+. .+.|..+... .+ +...+..+ ++.| +...++++.+.+...
T Consensus 2 ~~~~l~~l~~~~~~~i~~~-----------~~~-~~~L~~~~~~---~lgk~g~l~~~~k~l~~~~~~eer~~~g~~in- 65 (335)
T COG0016 2 VMIALGRLAKKGIAAIELA-----------SDL-LKALEELKVK---YLGKKGVLTDLLKKLGKLSPLEERKEVGALIN- 65 (335)
T ss_pred chHHHHHHHHHHHHHHHhh-----------ccH-HHHHHHHHHH---hcCcccchHHHHHHhccCChhhhhhhhhhhHH-
Confidence 3578999999999887642 222 3445544422 11 22235544 4443 443233333322110
Q ss_pred cccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceecc
Q psy10346 176 EFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNF 255 (292)
Q Consensus 176 ~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NF 255 (292)
....++.+.++++|++++.+|.|++..+++||+++||+..++|+.|||++++++|+++|.+|||+++. ||+||++||||
T Consensus 66 ~~~~~~~~~~~~~~~~l~~~~~~~~l~~e~~dv~lp~~~~~~G~~Hpl~~~~e~i~~iF~~mGF~~~~-gp~IE~d~~NF 144 (335)
T COG0016 66 ELKKEVEDAITELTPELEAAGLWERLAFEKIDVTLPGRRIYPGSLHPLTQTIEEIEDIFLGMGFTEVE-GPEIETDFYNF 144 (335)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHhhhccCCCcCCCCccCCCCCcChHHHHHHHHHHHHHHcCceecc-CCcccccccch
Confidence 00123567789999999999999999999999999999999999999999999999999999999985 99999999999
Q ss_pred ccCCCCCCCCCCCCCCceeecCC
Q psy10346 256 DALFQPQQHPARDAHDTFFVTDP 278 (292)
Q Consensus 256 D~L~~PqdHPAR~~~DTfyl~~~ 278 (292)
||||||||||||+||||||+++.
T Consensus 145 DaLn~P~dHPARdmqDTFy~~~~ 167 (335)
T COG0016 145 DALNIPQDHPARDMQDTFYLKDD 167 (335)
T ss_pred hhhcCCCCCCcccccceEEEcCC
Confidence 99999999999999999999974
No 6
>PLN02788 phenylalanine-tRNA synthetase
Probab=99.88 E-value=3.4e-23 Score=201.77 Aligned_cols=83 Identities=22% Similarity=0.345 Sum_probs=76.3
Q ss_pred cCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhC---CceecCCCCccccceeccccCCCCCCCCCCCCC
Q psy10346 194 ASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM---GFTEMPTNNFVESSFWNFDALFQPQQHPARDAH 270 (292)
Q Consensus 194 ~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~m---GF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~ 270 (292)
....|.|. .++++++.|+.++.|+.|||++++++|+++|.+| ||++++..++||++|||||+||+|||||||++|
T Consensus 43 ~~~~~~n~--~~~i~~~~~~~l~~~~~HPl~~~~~~i~~~f~~~~~~gf~~~~~~~~iv~~~~NFD~L~~P~dHPaR~~~ 120 (402)
T PLN02788 43 EDDPTNNV--PDHIFSKIGMQLHRRPDHPLGILKNAIYDYFDENYSNKFKKFDDLSPIVSTKQNFDDVLVPPDHVSRSYN 120 (402)
T ss_pred cCCccCCC--ChhHhccCCccCCCCCCChHHHHHHHHHHHHhhcccCCcEEecCCCCccchhhhhhhhCCCCCCCccCcc
Confidence 34579987 4999999999999999999999999999999998 999986338999999999999999999999999
Q ss_pred CceeecCC
Q psy10346 271 DTFFVTDP 278 (292)
Q Consensus 271 DTfyl~~~ 278 (292)
|||||++.
T Consensus 121 DTfy~~~~ 128 (402)
T PLN02788 121 DTYYVDAQ 128 (402)
T ss_pred ceEEecCC
Confidence 99999864
No 7
>PF01409 tRNA-synt_2d: tRNA synthetases class II core domain (F); InterPro: IPR002319 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [].; GO: 0000049 tRNA binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 3TUP_A 3HFV_A 3CMQ_A 3TEG_A 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B ....
Probab=99.86 E-value=1.1e-22 Score=187.30 Aligned_cols=75 Identities=45% Similarity=0.802 Sum_probs=69.7
Q ss_pred CCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCC
Q psy10346 205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT 280 (292)
Q Consensus 205 ~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~ 280 (292)
+||+++|++..+.|+.||+++++++|+++|.+|||+++. +++|||++||||+||+|+|||||++|||||+++|..
T Consensus 1 ~~d~~~p~~~~~~G~~hp~~~~~~~i~~~~~~~Gf~e~~-~~~v~s~~~nFD~Ln~p~dHpaR~~~Dtfyi~~p~~ 75 (247)
T PF01409_consen 1 KIDVTLPGKRFTPGRLHPITKFIREIRDIFVGMGFQEVE-GPEVESEFYNFDALNIPQDHPARDMQDTFYISNPYS 75 (247)
T ss_dssp ---TTSGCTTCCCSBTSHHHHHHHHHHHHHHCTTSEEES-TTSEEEHHHHTGGGTSTTTSCGGCGTTSEBSCSSSB
T ss_pred CccccCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCeEee-CCeEEeeHHHHHhhCcCCCccccccccceeeecccc
Confidence 589999999999999999999999999999999999996 899999999999999999999999999999987765
No 8
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=99.86 E-value=2.1e-22 Score=192.41 Aligned_cols=73 Identities=36% Similarity=0.689 Sum_probs=69.4
Q ss_pred CCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCC
Q psy10346 205 PYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDP 278 (292)
Q Consensus 205 ~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~ 278 (292)
.||+++||+..+.|+.||+++++++|+++|.+|||+++. ||+||+++||||+||+|+|||||+|||||||++.
T Consensus 92 ~~d~t~p~~~~~~G~~HPl~~~~~~Ir~if~~mGF~ev~-gpeIes~~~NFdaLn~P~dHPaR~~~DTfyI~~~ 164 (339)
T PRK00488 92 TIDVTLPGRRIELGSLHPITQTIEEIEDIFVGMGFEVAE-GPEIETDYYNFEALNIPKDHPARDMQDTFYIDDG 164 (339)
T ss_pred cccccCCCCCCCCCCCCHHHHHHHHHHHHHHhCCCEEEe-CCccccHHHHHHHhCCCCCCcccccCceEEEcCC
Confidence 489999998899999999999999999999999999985 8999999999999999999999999999999754
No 9
>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase, mitochondrial. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This alignment models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species.
Probab=99.77 E-value=1.8e-19 Score=177.51 Aligned_cols=82 Identities=20% Similarity=0.259 Sum_probs=72.5
Q ss_pred CCCee-ccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhC--------CceecCCCCccccceeccccCCCCCCCC
Q psy10346 195 SGSWK-TLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDM--------GFTEMPTNNFVESSFWNFDALFQPQQHP 265 (292)
Q Consensus 195 sg~w~-~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~m--------GF~e~~~~~~Ves~f~NFD~L~~PqdHP 265 (292)
+.+|. |. -|.+++..|+.++.|..|||+.++++|+++|.+| ||+.+...++|||+++|||+|++|+|||
T Consensus 17 ~d~~~~n~--~~~i~~~~~r~~~~~~~HPl~~~~~~I~~~F~~~~~~~~~~~gf~v~~~~~Pvvt~~~NFD~Ln~P~dHP 94 (460)
T TIGR00469 17 TDGQTTNV--TDKIIKLTDANKHLKEDHPLGIIRDLIEKKFNGADNNQRGNPLFKIFDNFKPVVTTMENFDNLGFPADHP 94 (460)
T ss_pred CCcccCCC--ChHHHHhhccCccCCCCCcHHHHHHHHHHHHHhhhcccccCCCeEEeeCCCCccchhhhhhhcCCCCCCc
Confidence 34677 65 4788899999999999999999999999999999 9997652234999999999999999999
Q ss_pred CCCCCCceeecCC
Q psy10346 266 ARDAHDTFFVTDP 278 (292)
Q Consensus 266 AR~~~DTfyl~~~ 278 (292)
||++|||||+++.
T Consensus 95 aR~~~DT~Yi~~~ 107 (460)
T TIGR00469 95 GRQKSDCYYINEQ 107 (460)
T ss_pred ccCcccceEecCC
Confidence 9999999999864
No 10
>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment.
Probab=99.76 E-value=2.6e-20 Score=175.31 Aligned_cols=97 Identities=46% Similarity=0.856 Sum_probs=90.8
Q ss_pred cccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCC
Q psy10346 180 TIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALF 259 (292)
Q Consensus 180 ~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~ 259 (292)
++...++++|.+++.++.|++..+++||+.+|+.....|..||+.+++++|+++|.+|||.|+. ++.+++++||||+|+
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~tlp~~~~~~g~~~p~~~~~~~ir~~l~~~Gf~Ev~-~~~~~s~~~~fd~l~ 109 (294)
T TIGR00468 31 ELEDELTKLKPELEKAGLWSKLKFETYDVTLPGTKIYPGSLHPLTRVIDEIRDIFLGLGFTEEK-GPEVETDFWNFDALN 109 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccCcccCCCCCCCCCCcCHHHHHHHHHHHHHHHCCCEEee-CCceeccHHHHHHhC
Confidence 4567778999999999999999999999999987778899999999999999999999999985 788999999999999
Q ss_pred CCCCCCCCCCCCceeecC
Q psy10346 260 QPQQHPARDAHDTFFVTD 277 (292)
Q Consensus 260 ~PqdHPAR~~~DTfyl~~ 277 (292)
+|++||||++|||||+++
T Consensus 110 ~~~~hpar~~~d~~~l~d 127 (294)
T TIGR00468 110 IPQDHPARDMQDTFYIKD 127 (294)
T ss_pred CCCCCcchhhccceeecC
Confidence 999999999999999974
No 11
>KOG2783|consensus
Probab=98.99 E-value=3e-10 Score=109.62 Aligned_cols=82 Identities=24% Similarity=0.482 Sum_probs=73.2
Q ss_pred CCCeeccccCCCcccCCCCCCCCCCCChHHHHHHHHHHHhhhCC---ceecCCCCccccceeccccCCCCCCCCCCCCCC
Q psy10346 195 SGSWKTLNFKPYNFDAMGISLPSGHLHPLMKVRAEFRQIFLDMG---FTEMPTNNFVESSFWNFDALFQPQQHPARDAHD 271 (292)
Q Consensus 195 sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~~~~~~i~~if~~mG---F~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~D 271 (292)
...|.|.+++ .....|+.++.-..|||+.+++.|.+.|...| |+..+.-++|++...|||+|++|.|||+|...|
T Consensus 48 ~d~~~Nv~~~--i~~~~gr~lh~~~~hplg~lr~~i~~~f~~~~~~~fs~~~~~spvvt~~qnfdsl~~p~dh~sr~ksd 125 (436)
T KOG2783|consen 48 TDAWSNVTPS--ILSLLGRNLHQKESHPLGILRQRIEDYFYKTYRNLFSIFENESPVVTTYQNFDSLLFPADHVSRSKSD 125 (436)
T ss_pred CcccccCChh--hhhhcccchhhhccCchhHHHHHHHHHHHHhhcccchhccCCCceeehhhhcccccCcccccccCcCC
Confidence 5568887644 77788999999999999999999999998765 788777889999999999999999999999999
Q ss_pred ceeecCC
Q psy10346 272 TFFVTDP 278 (292)
Q Consensus 272 Tfyl~~~ 278 (292)
|||++..
T Consensus 126 tyy~n~~ 132 (436)
T KOG2783|consen 126 TYYVNHT 132 (436)
T ss_pred ceeecce
Confidence 9999974
No 12
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=97.65 E-value=0.00013 Score=55.74 Aligned_cols=62 Identities=16% Similarity=0.197 Sum_probs=48.6
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
.+-.+||..+. .+.....+++...|+++..+...+..|.++ |+| ......|.||+.|+++++
T Consensus 6 ~Ii~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~-gLI---~~~~~~Y~lTekG~~~l~ 67 (77)
T PF14947_consen 6 EIIFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEK-GLI---KKKDGKYRLTEKGKEFLE 67 (77)
T ss_dssp HHHHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHT-TSE---EEETTEEEE-HHHHHHHH
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-cCe---eCCCCEEEECccHHHHHH
Confidence 45578999997 555677899999999999999999999987 999 347889999999999885
No 13
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=97.64 E-value=0.00021 Score=58.10 Aligned_cols=73 Identities=15% Similarity=0.093 Sum_probs=62.9
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
..+..||..|..++.++..++|...|+++..|.+.+..|+.+ |+|.-.. .-...+.||++|+++++.-.|..+
T Consensus 28 ~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~-GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~ 104 (118)
T TIGR02337 28 EQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERD-GLVTRLKASNDQRRVYISLTPKGQALYASLSPQIE 104 (118)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHC-CCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHH
Confidence 567889999988888888999999999999999999999987 9999753 345689999999999987776654
No 14
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=97.57 E-value=0.00032 Score=51.07 Aligned_cols=61 Identities=23% Similarity=0.250 Sum_probs=48.0
Q ss_pred HHHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhH
Q psy10346 4 DLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEG 65 (292)
Q Consensus 4 ~~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG 65 (292)
..|..||..|. .++.....+++..++++...+.+.++.|..+ |+|+-.... ...|.||++|
T Consensus 3 ~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~-glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 3 RPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEK-GLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHT-TSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEecCCCCcCCeeEEEeCCCC
Confidence 45788999998 6777888999999999999999999999987 999665443 4789999998
No 15
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=97.54 E-value=0.00024 Score=54.85 Aligned_cols=64 Identities=20% Similarity=0.234 Sum_probs=52.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-----EEEEEeChhHHHHhh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-----HKIWELTGEGNQVKD 70 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-----~~~~~LTeEG~~yl~ 70 (292)
...||..|...+..+..++.+.+|++...+..-++.|+.. |||+++... .+.|.||+.|++.++
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~-GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~ 70 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEA-GYVEVEKEFEGRRPRTWYSLTDKGREAFE 70 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHT-TSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred HHHHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-CCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence 4578999987777888999999999999999999999987 999996553 667999999999774
No 16
>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.
Probab=97.42 E-value=0.00023 Score=64.34 Aligned_cols=58 Identities=55% Similarity=0.967 Sum_probs=51.4
Q ss_pred ChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCC
Q psy10346 221 HPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPK 279 (292)
Q Consensus 221 Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~ 279 (292)
||+.++.+.||++|.++||.|+.+-+. .+...++|.+.++.+||.|.+.+++++.+|-
T Consensus 1 ~~~~~~~~~ir~~L~~~Gf~Ev~tys~-~~~~~~~~~~~~~~~~~~~~~~~~v~l~NP~ 58 (218)
T cd00496 1 HPLNKVIEEIEDIFVSMGFTEVEGPEV-ETDFYNFDALNIPQDHPARDMQDTFYINDPA 58 (218)
T ss_pred ChHHHHHHHHHHHHHHCCCEEEeCCcc-cccchhhhhcCCCCCCcccccCceEEECCCc
Confidence 899999999999999999999976544 4665789999999999999999999999884
No 17
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.38 E-value=0.00094 Score=56.18 Aligned_cols=89 Identities=12% Similarity=0.160 Sum_probs=68.7
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHH--H
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEV--L 77 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~--r 77 (292)
..|..||..|...+.+...++|..+++++..|.+.++.|+.+ |||.-+. .-...+.||++|+..++...++. .
T Consensus 40 ~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~-GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~~ 118 (144)
T PRK11512 40 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCK-GWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQD 118 (144)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEeccCcccCCeeEeEEChhHHHHHHHHHHHHHHH
Confidence 567889999977777888999999999999999999999987 9998743 45677799999999988877664 2
Q ss_pred HHhhcCCCCCChHHHhh
Q psy10346 78 VFNNVPSEGIGQKELLA 94 (292)
Q Consensus 78 l~~~l~~~~~~~~el~~ 94 (292)
+...+- .+++-+|+..
T Consensus 119 ~~~~l~-~~ls~ee~~~ 134 (144)
T PRK11512 119 LHQELT-KNLTADEVAT 134 (144)
T ss_pred HHHHHH-ccCCHHHHHH
Confidence 333222 3555555443
No 18
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=97.37 E-value=0.00078 Score=51.68 Aligned_cols=67 Identities=19% Similarity=0.231 Sum_probs=57.9
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhc
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDN 71 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~ 71 (292)
..+..||..|...+..+..+++...++++..|.+.++.|.+. |+|..... ....|.||+.|..++..
T Consensus 10 ~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~-g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 10 PTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKK-GLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHC-CCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 567889999987777888999999999999999999999987 99987644 45789999999998754
No 19
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=97.04 E-value=0.0011 Score=48.89 Aligned_cols=58 Identities=19% Similarity=0.199 Sum_probs=51.0
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
..|.+|+..|-..+..+..++|..+|++...|-+++++|..+ |+|.........|..+
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~-GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEK-GLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT-TSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEcCceEEEEEe
Confidence 567888888877777889999999999999999999999987 9999988877777665
No 20
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=97.02 E-value=0.0045 Score=48.74 Aligned_cols=87 Identities=15% Similarity=0.087 Sum_probs=65.3
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHHHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVLVF 79 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~rl~ 79 (292)
..|..+|..|...+.....++|..++++...|.+.++.|+.+ |+|.-... -...+.||++|++.+..-.|...-+
T Consensus 22 ~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~-glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~~~~~ 100 (126)
T COG1846 22 PPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDK-GLIERLRDPEDRRAVLVRLTEKGRELLEQLLPAAQEL 100 (126)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeecCCccccceeeEEECccHHHHHHHhccHHHHH
Confidence 467888988876655432789999999999999999999987 99998554 3568899999999998888855533
Q ss_pred hhcCCCCCChHH
Q psy10346 80 NNVPSEGIGQKE 91 (292)
Q Consensus 80 ~~l~~~~~~~~e 91 (292)
...--.+.+-++
T Consensus 101 ~~~~~~~l~~~e 112 (126)
T COG1846 101 LAEILAGLSEEE 112 (126)
T ss_pred HHHhccCCCHHH
Confidence 222223444444
No 21
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=96.96 E-value=0.0034 Score=50.65 Aligned_cols=73 Identities=18% Similarity=0.110 Sum_probs=59.5
Q ss_pred HHHHHHHHHhc----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChH
Q psy10346 4 DLTEKILKYLD----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHE 75 (292)
Q Consensus 4 ~~e~~iL~~L~----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE 75 (292)
..|..||..|. .++.++..++|..++++...|.+.+..|+.+ |+|.-... -...+.||++|++.++.-.+|
T Consensus 25 ~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~k-g~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~ 103 (109)
T TIGR01889 25 LEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKK-GYLSKERSEDDERKVIISINKEQRSKIESLISE 103 (109)
T ss_pred HHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCEeccCCcccCCeEEEEECHHHHHHHHHHHHH
Confidence 45778888887 4567889999999999999999999999987 99986333 367789999999988766655
Q ss_pred HH
Q psy10346 76 VL 77 (292)
Q Consensus 76 ~r 77 (292)
..
T Consensus 104 ~~ 105 (109)
T TIGR01889 104 IE 105 (109)
T ss_pred HH
Confidence 43
No 22
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.94 E-value=0.0019 Score=48.25 Aligned_cols=60 Identities=27% Similarity=0.366 Sum_probs=51.1
Q ss_pred cHHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346 3 SDLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe 63 (292)
...+.+||..|...+. +...+||+.+|++...|-+.+..|+.. |+|.........|.++.
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~-G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK-GKVCKQGGTPPLWKLTD 66 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCceEeec
Confidence 4678899999987766 899999999999999999999999987 99987655446777764
No 23
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=96.91 E-value=0.0045 Score=51.81 Aligned_cols=89 Identities=15% Similarity=0.161 Sum_probs=66.0
Q ss_pred HHHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeChhHHHHhhcCChHHH-
Q psy10346 4 DLTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTGEGNQVKDNGSHEVL- 77 (292)
Q Consensus 4 ~~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTeEG~~yl~~GlPE~r- 77 (292)
..+..+|..|... +..+..++|..+++++..|.+.+..|+.+ |+|.-.. .-...+.||+.|++.++...+-..
T Consensus 31 ~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~-GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~ 109 (144)
T PRK03573 31 QTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEK-GLISRQTCASDRRAKRIKLTEKAEPLISEVEAVINK 109 (144)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHC-CCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHHHH
Confidence 4567788888654 44677899999999999999999999987 9999753 345788999999999987666554
Q ss_pred HHhhcCCCCCChHHHhh
Q psy10346 78 VFNNVPSEGIGQKELLA 94 (292)
Q Consensus 78 l~~~l~~~~~~~~el~~ 94 (292)
+...+ -.+++-+|+..
T Consensus 110 ~~~~~-~~~l~~ee~~~ 125 (144)
T PRK03573 110 TRAEI-LHGISAEEIEQ 125 (144)
T ss_pred HHHHH-HhCCCHHHHHH
Confidence 22222 13555555444
No 24
>PRK10870 transcriptional repressor MprA; Provisional
Probab=96.86 E-value=0.0048 Score=54.14 Aligned_cols=89 Identities=10% Similarity=0.060 Sum_probs=67.2
Q ss_pred HHHHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHhhcCChHHH
Q psy10346 4 DLTEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 4 ~~e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
..+..||..|.. ++.+...++|..+++++..|.+.+..|+.+ |+|.-... -...+.||++|+..++.-.|...
T Consensus 55 ~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~k-GlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~~~~ 133 (176)
T PRK10870 55 ETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKR-GWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQH 133 (176)
T ss_pred HHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence 457788888864 345777899999999999999999999987 99997544 34688999999999988877766
Q ss_pred -HHhhcCCCCCChHHHhh
Q psy10346 78 -VFNNVPSEGIGQKELLA 94 (292)
Q Consensus 78 -l~~~l~~~~~~~~el~~ 94 (292)
....+- .+++-+++..
T Consensus 134 ~~~~~~~-~~ls~~e~~~ 150 (176)
T PRK10870 134 NCLHQLW-SALSTTEKDQ 150 (176)
T ss_pred HHHHHHH-hcCCHHHHHH
Confidence 332221 3455555443
No 25
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=96.76 E-value=0.0054 Score=54.66 Aligned_cols=73 Identities=18% Similarity=0.045 Sum_probs=62.1
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe----eeeEEEEEeChhHHHHhhcCChHHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE----PLSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e----~~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
..|..||..|..++.++..++|+..+++...|.+.+..|+.+ |+|.-. .+-...+.||++|++.+++-.|...
T Consensus 45 ~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~k-GlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~~~ 121 (185)
T PRK13777 45 INEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEER-GYLTFSKKEDDKRNTYIELTEKGEELLLETMEEYD 121 (185)
T ss_pred HHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHC-CCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence 457789999987778889999999999999999999999987 999964 3556788999999999877666555
No 26
>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: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=96.76 E-value=0.005 Score=46.31 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHHhhc
Q psy10346 29 NEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQVKDN 71 (292)
Q Consensus 29 ~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~yl~~ 71 (292)
.+++..|-.+++.|+.. |+|+..... ++.|.||+.|++++++
T Consensus 28 ~i~~g~lY~~L~~Le~~-gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEE-GLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp ETTHHHHHHHHHHHHHT-TSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred ccChhHHHHHHHHHHhC-CCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 57899999999999987 999996665 8999999999998864
No 27
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=96.70 E-value=0.0046 Score=42.47 Aligned_cols=46 Identities=26% Similarity=0.377 Sum_probs=40.6
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
..+.+||..|.+++.++..++|+.+|++...|-+.++.|..+ |+|+
T Consensus 3 ~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~-g~I~ 48 (48)
T PF13412_consen 3 ETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEK-GLIE 48 (48)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHT-TSEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-cCcC
Confidence 568899999998888999999999999999999999999987 9985
No 28
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.67 E-value=0.0077 Score=50.70 Aligned_cols=62 Identities=21% Similarity=0.285 Sum_probs=50.4
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
..|+..+..++.....++|..+++++.+|.++++.|+.+ |+|.... ...+.||+.|+..+..
T Consensus 11 ~~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~-Gli~~~~--~~~i~LT~~G~~~a~~ 72 (142)
T PRK03902 11 EQIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKD-EYLIYEK--YRGLVLTPKGKKIGKR 72 (142)
T ss_pred HHHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHC-CCEEEec--CceEEECHHHHHHHHH
Confidence 344555566777788999999999999999999999987 9998543 3569999999987755
No 29
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=96.61 E-value=0.015 Score=41.57 Aligned_cols=64 Identities=17% Similarity=0.225 Sum_probs=52.6
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHh
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVK 69 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl 69 (292)
...+..||..+..++ +...+++..+|++...+-+++..|.+. |+|..... ....|.+|+ |+++.
T Consensus 6 ~~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~-g~i~~~~~~~~~~~~~~~-g~~~~ 70 (78)
T cd00090 6 DPTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEA-GLVESRREGRRVYYSLTD-AERLL 70 (78)
T ss_pred ChHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHC-CCeEEEEeccEEEEEeCC-chHHH
Confidence 356778898887666 788999999999999999999999987 99987543 467899998 77655
No 30
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=96.45 E-value=0.0068 Score=54.10 Aligned_cols=61 Identities=16% Similarity=0.182 Sum_probs=54.0
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG 65 (292)
..+.+||..|..++..+..++|+.+|+++..+.+.+..|+.. |+|.........|.||+.|
T Consensus 143 ~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~-GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 143 REELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKK-GLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEcCCccEEEeCCCC
Confidence 567899999987777888999999999999999999999987 9999876567789999987
No 31
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=96.25 E-value=0.013 Score=52.23 Aligned_cols=66 Identities=23% Similarity=0.248 Sum_probs=55.8
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHHhhc
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~yl~~ 71 (292)
...+||..|...+..+..++|..+|++...|.+.+..|+.. |+|.... .....|.||+.|+..+.+
T Consensus 2 tr~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~-GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 2 TKEDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETE-GLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeEEeecccCCCCCceEEEECcchhhhccc
Confidence 35789999977777889999999999999999999999987 9998652 345678999999987654
No 32
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=96.24 E-value=0.015 Score=53.22 Aligned_cols=66 Identities=12% Similarity=0.125 Sum_probs=53.1
Q ss_pred HHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcCChHHH
Q psy10346 11 KYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 11 ~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
..+.+...++..++|+.++++++++.+.++.|+.+ |+|+-+. .....+.||+.|++.++.-..++.
T Consensus 14 g~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~-GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~~ 80 (217)
T PRK14165 14 GAVNNTVKISSSEFANHTGTSSKTAARILKQLEDE-GYITRTIVPRGQLITITEKGLDVLYNEYADYS 80 (217)
T ss_pred hccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEEEcCCceEEEECHHHHHHHHHHHHHHH
Confidence 33344445788999999999999999999999987 9997643 345789999999999977666665
No 33
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=96.09 E-value=0.018 Score=53.44 Aligned_cols=73 Identities=18% Similarity=0.148 Sum_probs=63.6
Q ss_pred HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHH
Q psy10346 4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVF 79 (292)
Q Consensus 4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~ 79 (292)
....+||..|.- ++.+...++|.++|+..|+|...++.|-+. |+|+. .-...|++|++|.+.+.+-+-|.|-|
T Consensus 10 ~t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~e-G~i~~--~gR~~Y~iTkkG~e~l~~~~~dlr~f 83 (260)
T COG1497 10 LTRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKE-GLIEK--EGRGEYEITKKGAEWLLEQLSDLRRF 83 (260)
T ss_pred chHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhc-cceee--cCCeeEEEehhHHHHHHHHHHHHHHH
Confidence 566788888854 577899999999999999999999999976 99987 55668999999999999998888865
No 34
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.09 E-value=0.03 Score=38.92 Aligned_cols=59 Identities=17% Similarity=0.188 Sum_probs=48.4
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeCh-hHHHHh
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTG-EGNQVK 69 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTe-EG~~yl 69 (292)
||..|. .+..+..+++..+|++...+.+.+..|.+. |+|.... .....|.+|+ .|.+.+
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~-g~i~~~~~~~~~~~~~~~~~~~~~~ 62 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREA-GLVESRREGKRVYYSLTDEKVADLL 62 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeeeecCCEEEEEEchHHHHHHH
Confidence 566666 566788999999999999999999999987 9999765 5567789998 776654
No 35
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=95.96 E-value=0.029 Score=44.81 Aligned_cols=67 Identities=22% Similarity=0.257 Sum_probs=54.9
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee------------------eEEEEEeChh
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL------------------SHKIWELTGE 64 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~------------------~~~~~~LTeE 64 (292)
.+....||..|..-+.-.+-.+|..++++.+.|...+..|+.. |||+-..- -.+.|.||.+
T Consensus 6 ~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~-GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~ 84 (92)
T PF10007_consen 6 DPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEM-GLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTRE 84 (92)
T ss_pred ChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEecCcccchhhhhcccchhhhcCCceeeecHh
Confidence 4678899999987666556779999999999999999999997 99864322 2468999999
Q ss_pred HHHHhh
Q psy10346 65 GNQVKD 70 (292)
Q Consensus 65 G~~yl~ 70 (292)
|+.+++
T Consensus 85 G~~llR 90 (92)
T PF10007_consen 85 GELLLR 90 (92)
T ss_pred HHHHHh
Confidence 998875
No 36
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=95.93 E-value=0.019 Score=49.42 Aligned_cols=67 Identities=21% Similarity=0.142 Sum_probs=57.8
Q ss_pred HHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHH
Q psy10346 8 KILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLV 78 (292)
Q Consensus 8 ~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl 78 (292)
-+|..+.+ +|..|..-++++.+++.+.+|.++.-++.. |+|+.+.- -..||++|+.|++.+.||++-
T Consensus 16 GLL~~l~n~fnGraDl~~L~~e~~vdidDL~piv~ta~~L-glv~~e~G---DiilT~~Gk~~v~~~~~erK~ 84 (157)
T COG4754 16 GLLYVLNNIFNGRADLPYLEKEMEVDIDDLMPIVETASLL-GLVTAESG---DIILTDEGKEYVESPIRERKE 84 (157)
T ss_pred HHHHHHHHHhCCcccchhHHHHhCCChhhHHHHHHHHHhc-CceeccCC---CEEEehhhHHHHhCChHHHHH
Confidence 35566654 677899999999999999999999999998 99998764 478999999999999999983
No 37
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=95.92 E-value=0.025 Score=45.05 Aligned_cols=74 Identities=18% Similarity=0.235 Sum_probs=55.5
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHh--------cCCCHHHHHHHHHHhhccCCcEEEee------eeEEEEEeChhHHHH
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKL--------FNEDHQKVVGGMKSIETLGEYLIVEP------LSHKIWELTGEGNQV 68 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~--------~~~~~~~v~~~~~~L~s~~glv~~e~------~~~~~~~LTeEG~~y 68 (292)
..++.-||..|..+ +..-.++.+. ..+++..|-.++..|+.+ |+|+... ...+.|.||+.|+++
T Consensus 3 g~l~~~iL~~L~~~-~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~-GlI~~~~~~~~~~~~rk~y~iT~~Gr~~ 80 (100)
T TIGR03433 3 GTLDLLILKTLSLG-PLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERR-GWIAAEWGESENNRRAKFYRLTAAGRKQ 80 (100)
T ss_pred chHHHHHHHHHhcC-CCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHC-CCeEEEeeecCCCCCceEEEECHHHHHH
Confidence 35678899999744 3344555544 357889999999999987 9999842 225899999999999
Q ss_pred hhcCChHHHH
Q psy10346 69 KDNGSHEVLV 78 (292)
Q Consensus 69 l~~GlPE~rl 78 (292)
+++-.++.+-
T Consensus 81 l~~~~~~~~~ 90 (100)
T TIGR03433 81 LAAETESWAR 90 (100)
T ss_pred HHHHHHHHHH
Confidence 9877666653
No 38
>PRK11050 manganese transport regulator MntR; Provisional
Probab=95.83 E-value=0.032 Score=47.81 Aligned_cols=71 Identities=15% Similarity=0.175 Sum_probs=56.6
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFN 80 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~ 80 (292)
..|+.++..++.....++|+.+++++..|.+++..|++. |+|.... ...+.||+.|+..+....+-.+.+.
T Consensus 40 ~~I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~-GlI~r~~--~~~v~LT~~G~~l~~~~~~~~~~le 110 (152)
T PRK11050 40 ELIADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARD-GLVEMRP--YRGVFLTPEGEKLAQESRERHQIVE 110 (152)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEec--CCceEECchHHHHHHHHHHHHHHHH
Confidence 345556666677788999999999999999999999987 9987543 3468999999998877766666554
No 39
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=95.81 E-value=0.023 Score=49.22 Aligned_cols=59 Identities=24% Similarity=0.247 Sum_probs=49.3
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
|......++.+.+.++|..+++.+.+|..+++.|++. |||+.+. ..-+.||+.|++.+.
T Consensus 15 Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~-GlV~~~~--y~gi~LT~~G~~~a~ 73 (154)
T COG1321 15 IYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERL-GLVEYEP--YGGVTLTEKGREKAK 73 (154)
T ss_pred HHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHC-CCeEEec--CCCeEEChhhHHHHH
Confidence 4444556778899999999999999999999999987 9998654 456899999998764
No 40
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=95.69 E-value=0.027 Score=40.71 Aligned_cols=53 Identities=23% Similarity=0.299 Sum_probs=45.8
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
|+++...+||..|...++.+..++|+.+|++.+.+..-++.|+.. |+|+.++.
T Consensus 7 L~~p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~a-Gli~~~~~ 59 (61)
T PF12840_consen 7 LSDPTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEA-GLIEVERE 59 (61)
T ss_dssp HTSHHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEEEE
T ss_pred hCCHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEecc
Confidence 456788999999966777889999999999999999999999986 99998764
No 41
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=95.69 E-value=0.027 Score=40.04 Aligned_cols=49 Identities=18% Similarity=0.165 Sum_probs=42.2
Q ss_pred HHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 4 DLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
..+..||..|...+. +...++|..++++++.|.+.++.|+++ |||..+.
T Consensus 5 ~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~-Glv~r~~ 55 (62)
T PF12802_consen 5 PSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK-GLVERER 55 (62)
T ss_dssp HHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEEE
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeC
Confidence 568899999977666 788999999999999999999999987 9998764
No 42
>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=95.61 E-value=0.053 Score=43.17 Aligned_cols=66 Identities=24% Similarity=0.428 Sum_probs=52.8
Q ss_pred HHHHHHHHHhccC--CCCChHHHHHhcCCCHHHHHHHHH----------HhhccCCcE--EEeeeeEEEEEeChhHHHHh
Q psy10346 4 DLTEKILKYLDTN--PPVDTLDLAKLFNEDHQKVVGGMK----------SIETLGEYL--IVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 4 ~~e~~iL~~L~~~--~~~~~~ela~~~~~~~~~v~~~~~----------~L~s~~glv--~~e~~~~~~~~LTeEG~~yl 69 (292)
.+..+||..|.+. ......++|...|.+.+.|.+++. ||-.. ||| ..+..-.+.|.||++|+.++
T Consensus 9 ~~R~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~l-GLV~~~~~~~g~k~Y~lT~~G~~~~ 87 (90)
T PF07381_consen 9 KVRKKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGL-GLVEEEEEKGGFKYYRLTEKGKRIA 87 (90)
T ss_pred HHHHHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHc-CCeeEeeecCCeeEEEeChhhhhHH
Confidence 4567899999765 235678999999999999999985 67777 999 33445667999999999876
Q ss_pred h
Q psy10346 70 D 70 (292)
Q Consensus 70 ~ 70 (292)
+
T Consensus 88 ~ 88 (90)
T PF07381_consen 88 E 88 (90)
T ss_pred h
Confidence 4
No 43
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=95.58 E-value=0.06 Score=41.95 Aligned_cols=60 Identities=17% Similarity=0.204 Sum_probs=47.4
Q ss_pred HHHHHhccCCCCChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346 8 KILKYLDTNPPVDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK 69 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl 69 (292)
.||..|.. +.....++.+.+ |++...+...++.|++. |+|.-... ....|.||+.|++.+
T Consensus 9 ~IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~-GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 9 LILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEA-GLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHT-TSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHc-chhhcccccCCCCCCccCCCcCHHHHH
Confidence 57777765 566778898888 99999999999999997 99976543 357899999999865
No 44
>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.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=95.42 E-value=0.019 Score=46.10 Aligned_cols=48 Identities=23% Similarity=0.307 Sum_probs=36.0
Q ss_pred cCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc--CChHH
Q psy10346 28 FNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN--GSHEV 76 (292)
Q Consensus 28 ~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~--GlPE~ 76 (292)
++++-=.|+.+++||.|+ |+|+-.- =....|.||+||.+||++ .+|+.
T Consensus 33 l~vpNL~V~k~mqSL~Sr-gyVke~faWrh~Yw~LT~eGIeyLR~yL~LP~e 83 (95)
T PF03501_consen 33 LNVPNLHVIKAMQSLKSR-GYVKEQFAWRHYYWYLTNEGIEYLREYLHLPAE 83 (95)
T ss_dssp TSSBHHHHHHHHHHHHHC-TSEEEEECTTEEEEEE-HHHHHHHHHHC-SSTT
T ss_pred cCCCcHHHHHHHhcccch-hhhcCeecceEEEEEEcchhHHHHHHHhCCChh
Confidence 366766799999999998 9998643 356678999999999975 34443
No 45
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=95.39 E-value=0.037 Score=56.77 Aligned_cols=120 Identities=15% Similarity=0.257 Sum_probs=74.1
Q ss_pred CCChhh-HHhhhcccceeeEEEEEEEEecCccccccccccccccCcccccCCCeeccccCCCcccCCCCCCCCCCCChHH
Q psy10346 146 KVPEAN-KVDYKKRKLLQEVTIKSFLLKKGPEFSTTIQKPETELTPEMIASGSWKTLNFKPYNFDAMGISLPSGHLHPLM 224 (292)
Q Consensus 146 ~l~~~~-~~~LkkRkLv~~~~~~~~~v~~g~~~~~~~~~~~t~LT~eml~sg~w~~~~fk~y~~~~~~~~~~~g~~Hpl~ 224 (292)
.++.++ .+.|++-|+-.......+.|.. |.+-..+.- ..||-.|.+.---|.+..- ..|. ....|..||..
T Consensus 291 ~i~~~~i~~iL~~Lgf~~~~~~~~~~v~v-P~~R~DI~~-~~DliEEiaR~yGyd~i~~-----~~p~-~~~~~~~~~~~ 362 (552)
T PRK09616 291 DLSAEEIIELLERMRYDAEIGDDKVKVTV-PPYRVDILH-EVDVIEDVAIAYGYNNLEP-----ELPK-VFTIGRLHPIE 362 (552)
T ss_pred CCCHHHHHHHHHHcCCCcEecCCeEEEEe-CCCcccccc-cchHHHHHHHHhCcccCCc-----cCCC-CccCCCCChHH
Confidence 444433 4557777764322222333432 122222222 2377777765444444321 1121 33458899999
Q ss_pred HHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeecCCCC
Q psy10346 225 KVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVTDPKT 280 (292)
Q Consensus 225 ~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~~~~~ 280 (292)
++.+.+|++|.++||.|+.+.+. .+..+||+.++++.+|+ +.-|.+|-+
T Consensus 363 ~~~~~ir~~L~~~Gf~Ev~tys~-~s~~~~~~~~~~~~~~~------~i~l~NPls 411 (552)
T PRK09616 363 KLERAIRDLMVGLGFQEVMNFTL-TSEEVLFEKMNLEPEED------YVEVLNPIS 411 (552)
T ss_pred HHHHHHHHHHHhCCcceeccceE-echHHHHHHhCCCCCCC------eEEEcCCCc
Confidence 99999999999999999987665 47778899999998883 466777744
No 46
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=95.38 E-value=0.024 Score=47.50 Aligned_cols=74 Identities=18% Similarity=0.127 Sum_probs=47.4
Q ss_pred HHHHHHHHHhccCCCC----ChH-HHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc--CChH
Q psy10346 4 DLTEKILKYLDTNPPV----DTL-DLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN--GSHE 75 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~----~~~-ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~--GlPE 75 (292)
.....|...|=+.|.+ |.. .--..++++-=.|+.+++||.|+ |+|+..- =....|.||+||.+||++ ++|+
T Consensus 7 ~~r~~Iye~LfkeGVlvakKd~~~~~h~el~vpNL~Vik~mqSL~Sr-g~Vke~f~WrhyYw~LT~eGieyLR~yL~LP~ 85 (124)
T PTZ00034 7 ANRKAIYRYLFKEGVIVCKKDPKGPWHPELNVPNLHVMMLMRSLKSR-GLVKEQFAWQHYYYYLTDEGIEYLRTYLHLPP 85 (124)
T ss_pred HHHHHHHHHHhhCceEEEecCCCCCCCCccCCccHHHHHHHHccccC-CceEEEEeeEEEEEEEchHHHHHHHHHhCCCc
Confidence 3455677777544431 110 00011245555799999999998 9998744 456677999999999975 4555
Q ss_pred HHH
Q psy10346 76 VLV 78 (292)
Q Consensus 76 ~rl 78 (292)
..+
T Consensus 86 eiv 88 (124)
T PTZ00034 86 DVF 88 (124)
T ss_pred ccC
Confidence 543
No 47
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=95.22 E-value=0.039 Score=42.83 Aligned_cols=70 Identities=20% Similarity=0.232 Sum_probs=60.1
Q ss_pred CCcHHHHHHHHHhc-----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 1 MASDLTEKILKYLD-----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 1 m~~~~e~~iL~~L~-----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
|=.+.|++||.+|. .+.++.+.++|+.++++...|-..+..|++. |||+-.....--++.|+.|-+++..
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~l-Glve~~p~~s~GriPT~~aYr~~~~ 75 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEEL-GLVESQPHPSGGRIPTDKAYRALNR 75 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHC-CCccCCCCCCCCCCcCHHHHHHHcc
Confidence 44577899998884 3667899999999999999999999999998 9998777778889999999887754
No 48
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=95.07 E-value=0.037 Score=42.87 Aligned_cols=51 Identities=20% Similarity=0.212 Sum_probs=42.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChH
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHE 75 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE 75 (292)
.++|..+|+++..|.+++..|+++ |+|..... ..|.||+.|+.....=.+.
T Consensus 3 ~ela~~l~is~stvs~~l~~L~~~-glI~r~~~--~~~~lT~~g~~~~~~~~~~ 53 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLKKLEKD-GLVEYEPY--RGITLTEKGRRLARRLLRK 53 (96)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHC-CCEEEcCC--CceEechhHHHHHHHHHHH
Confidence 578999999999999999999987 99988664 3799999999986444333
No 49
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=94.97 E-value=0.047 Score=38.61 Aligned_cols=50 Identities=20% Similarity=0.147 Sum_probs=43.3
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
..|..+|..|...+.++..++|...++++..+.+.++.|+.+ |+|.-+..
T Consensus 3 ~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~-g~I~r~~~ 52 (59)
T PF01047_consen 3 PSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKK-GLIERERD 52 (59)
T ss_dssp HHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHC-CCEEeccC
Confidence 467889999988777888999999999999999999999987 99987654
No 50
>PHA00738 putative HTH transcription regulator
Probab=94.95 E-value=0.1 Score=42.82 Aligned_cols=71 Identities=17% Similarity=0.198 Sum_probs=57.9
Q ss_pred CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEE-EEEeChhHHHHhhcCChHHHHHh
Q psy10346 2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHK-IWELTGEGNQVKDNGSHEVLVFN 80 (292)
Q Consensus 2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~-~~~LTeEG~~yl~~GlPE~rl~~ 80 (292)
+++...+||..|..++.....+++..+++++.+|.+=++-|+.- |+|..+..-.. +|.|. .+.|++++++
T Consensus 10 ~dptRr~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreA-GLV~srK~Gr~vyY~Ln--------~~~~~~~l~~ 80 (108)
T PHA00738 10 AKILRRKILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQ-GYIELYKEGRTLYAKIR--------ENSKEIQILN 80 (108)
T ss_pred CCHHHHHHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHC-CceEEEEECCEEEEEEC--------CCccHHHHHh
Confidence 35778899999987766778899999999999999999999986 99999766554 45655 6677887775
Q ss_pred h
Q psy10346 81 N 81 (292)
Q Consensus 81 ~ 81 (292)
.
T Consensus 81 ~ 81 (108)
T PHA00738 81 S 81 (108)
T ss_pred h
Confidence 4
No 51
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=94.94 E-value=0.07 Score=48.90 Aligned_cols=64 Identities=25% Similarity=0.342 Sum_probs=56.5
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQV 68 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~y 68 (292)
+...+||.+|...+.....++|+.+|++..+|-+=+..|+++ |+|.++... ...|.||+.|..-
T Consensus 11 ~tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~-Glv~~~~~~~g~GRP~~~y~Lt~~g~~~ 80 (218)
T COG2345 11 STRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAE-GLVEVERQQGGRGRPAKLYRLTEKGREQ 80 (218)
T ss_pred cHHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhC-cceeeeeccCCCCCCceeeeecccchhh
Confidence 466789999998889999999999999999999999999987 999998544 3789999999873
No 52
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=94.88 E-value=0.093 Score=43.69 Aligned_cols=68 Identities=18% Similarity=0.157 Sum_probs=50.9
Q ss_pred HHHHHHHHHhccCCCCChHHHHHh----cC----CCHHHHHHHHHHhhccCCcEEEeeee------EEEEEeChhHHHHh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKL----FN----EDHQKVVGGMKSIETLGEYLIVEPLS------HKIWELTGEGNQVK 69 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~----~~----~~~~~v~~~~~~L~s~~glv~~e~~~------~~~~~LTeEG~~yl 69 (292)
.++..||..|... +..-.++.+. .+ .++..|-.++..|+.. |+|+..... ...|.||+.|++++
T Consensus 9 ~l~~~iL~~L~~~-~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~-Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l 86 (138)
T COG1695 9 SLELLILSLLSEK-PSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKE-GLIESRWEESGGGPPRKYYRLTEKGKEEL 86 (138)
T ss_pred hHHHHHHHHHhcC-CchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHC-CCeEEEecccCCCCCceEEEECHHHHHHH
Confidence 4678889988765 4333445443 22 6788999999999987 999986332 58999999999998
Q ss_pred hcCC
Q psy10346 70 DNGS 73 (292)
Q Consensus 70 ~~Gl 73 (292)
..-.
T Consensus 87 ~~~~ 90 (138)
T COG1695 87 AELR 90 (138)
T ss_pred HHHH
Confidence 6544
No 53
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=94.61 E-value=0.12 Score=44.09 Aligned_cols=67 Identities=19% Similarity=0.299 Sum_probs=49.8
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHh--------cCCCHHHHHHHHHHhhccCCcEEEee--eeEEEEEeChhHHHHhhcC
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKL--------FNEDHQKVVGGMKSIETLGEYLIVEP--LSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~--------~~~~~~~v~~~~~~L~s~~glv~~e~--~~~~~~~LTeEG~~yl~~G 72 (292)
+++...||..|... ..-.++.+. ..+++..|-.++..|+.. |+|+... ..+..|.||+.|+++++.=
T Consensus 42 ~~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~-GlI~s~~~~~~RK~Y~ITe~Gre~L~e~ 118 (135)
T PRK09416 42 EDILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQN-RFIQSSWDHEGAKYYQLTDKGNKMLRKA 118 (135)
T ss_pred ccHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHC-CCeEEeecCCCceEEEECHHHHHHHHHH
Confidence 35667789988755 333445443 235689999999999987 9999843 4578999999999988643
No 54
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=94.59 E-value=0.035 Score=55.36 Aligned_cols=58 Identities=16% Similarity=0.221 Sum_probs=45.3
Q ss_pred CCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeec
Q psy10346 215 LPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVT 276 (292)
Q Consensus 215 ~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~ 276 (292)
...|+.||+..+.+.|+++|.++||.|+.+ |.+++.. .|+.+..+.+++.++ +.|+++
T Consensus 198 ~~~g~~~~~s~Le~aIR~~f~~~GF~EV~T-PtLt~ee-~~e~~g~~~g~~i~~--~my~id 255 (417)
T PRK09537 198 YEEDREDYLGKLERDITKFFVDRGFLEIKS-PILIPAE-YIERMGIDNDTELSK--QIFRVD 255 (417)
T ss_pred hccCCCCHHHHHHHHHHHHHHHCCCEEEEC-CeeecHH-HHHHhCCCCcccchh--hheeeC
Confidence 467999999999999999999999999974 7776544 389888877766543 345554
No 55
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=94.38 E-value=0.081 Score=38.05 Aligned_cols=45 Identities=18% Similarity=0.275 Sum_probs=40.7
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
+..||..|..++.+...++|+.+|++...|-+.+..|+.. |+|.-
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~-g~i~r 46 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQ-GLIKR 46 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence 4689999998999999999999999999999999999986 88653
No 56
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=94.35 E-value=0.19 Score=41.81 Aligned_cols=60 Identities=17% Similarity=0.138 Sum_probs=49.1
Q ss_pred HHHHHhccCCCCChHHHHHhcC-CCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFN-EDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK 69 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~-~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl 69 (292)
.||..|.. +.....++-..++ +++..+.+-++.|+.. |+|.-+... +..|.||+.|+...
T Consensus 27 lIl~~L~~-g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~-Glv~R~~~~~~PprveY~LT~~G~~L~ 91 (120)
T COG1733 27 LILRDLFD-GPKRFNELRRSIGGISPKMLSRRLKELEED-GLVERVVYPEEPPRVEYRLTEKGRDLL 91 (120)
T ss_pred HHHHHHhc-CCCcHHHHHHHccccCHHHHHHHHHHHHHC-CCEEeeecCCCCceeEEEEhhhHHHHH
Confidence 36666654 5667788888876 9999999999999987 999876664 89999999998744
No 57
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=94.18 E-value=0.13 Score=48.43 Aligned_cols=78 Identities=12% Similarity=0.190 Sum_probs=66.9
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHHHhhc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLVFNNV 82 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l 82 (292)
+...++||.+|.+ ++-+.+++-..++++..+++..++.|... |+|.-+ ...|.||+.|+-.+.+-.|=...++++
T Consensus 12 SekRk~lLllL~e-gPkti~EI~~~l~vs~~ai~pqiKkL~~~-~LV~~~---~~~Y~LS~~G~iiv~km~~ll~tl~v~ 86 (260)
T COG4742 12 SEKRKDLLLLLKE-GPKTIEEIKNELNVSSSAILPQIKKLKDK-GLVVQE---GDRYSLSSLGKIIVEKMEPLLDTLEVF 86 (260)
T ss_pred cHHHHHHHHHHHh-CCCCHHHHHHHhCCCcHHHHHHHHHHhhC-CCEEec---CCEEEecchHHHHHHHHHHHHHHHHHH
Confidence 3567789999986 56688999999999999999999999986 998744 789999999999999998888888888
Q ss_pred CCC
Q psy10346 83 PSE 85 (292)
Q Consensus 83 ~~~ 85 (292)
.++
T Consensus 87 e~n 89 (260)
T COG4742 87 EEN 89 (260)
T ss_pred Hhh
Confidence 643
No 58
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=94.08 E-value=0.35 Score=40.12 Aligned_cols=65 Identities=11% Similarity=0.137 Sum_probs=53.7
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE-EEEEeChhHH
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH-KIWELTGEGN 66 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~-~~~~LTeEG~ 66 (292)
++++...+||..|...++...-++++.+|+++..|..-++-|+.. |+|+.++.-. ..|.|.+...
T Consensus 13 LadptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~A-GLV~~~r~Gr~~~Y~l~~~~~ 78 (117)
T PRK10141 13 LSDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRES-GLLLDRKQGKWVHYRLSPHIP 78 (117)
T ss_pred hCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CceEEEEEcCEEEEEECchHH
Confidence 456788899999976667788999999999999999999999986 9999866644 5678876543
No 59
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=93.97 E-value=0.11 Score=41.81 Aligned_cols=64 Identities=16% Similarity=0.197 Sum_probs=47.8
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhHHHHhh
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEGNQVKD 70 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG~~yl~ 70 (292)
+-..||++. ..+.+....+.-..|++.......+..|.++ |++...... ...|.||+.|++.++
T Consensus 19 Ii~dIL~~~-~~~~~~~Tri~y~aNlny~~~~~yi~~L~~~-Gli~~~~~~~~~~y~lT~KG~~fle 83 (95)
T COG3432 19 IIFDILKAI-SEGGIGITRIIYGANLNYKRAQKYIEMLVEK-GLIIKQDNGRRKVYELTEKGKRFLE 83 (95)
T ss_pred HHHHHHHHh-cCCCCCceeeeeecCcCHHHHHHHHHHHHhC-CCEEeccCCccceEEEChhHHHHHH
Confidence 344566663 4555555667777899999999999999987 966665444 559999999999763
No 60
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=93.93 E-value=0.051 Score=55.47 Aligned_cols=40 Identities=28% Similarity=0.490 Sum_probs=34.1
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346 211 MGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS 251 (292)
Q Consensus 211 ~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~ 251 (292)
|-..+..|+.||+...++++|+...+|||+||- +|.|..+
T Consensus 37 p~~~~~~~~~hp~~~ti~~lr~ayl~~gf~e~~-np~iv~~ 76 (529)
T PRK06253 37 PRLKPSYGKPHPVYDTIERLREAYLRMGFEEMI-NPVIVDE 76 (529)
T ss_pred CcccccCCCCCcHHHHHHHHHHHHHhcChHhhc-CceeecH
Confidence 334567899999999999999999999999995 7877654
No 61
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.91 E-value=0.25 Score=37.59 Aligned_cols=63 Identities=11% Similarity=0.128 Sum_probs=50.1
Q ss_pred HHHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 5 LTEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 5 ~e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
....||..|... +.....++|..+|++...|.+.+..|.+. |+|.-.. ....|.|+.....+.
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~-g~l~~~~-~~~~y~l~~~~~~~~ 69 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQEL-GYVEQDG-QNGRYRLGPKVLELG 69 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeeecC-CCCceeecHHHHHHH
Confidence 346788888765 67889999999999999999999999987 9997643 245688887665543
No 62
>PRK05638 threonine synthase; Validated
Probab=93.88 E-value=0.13 Score=51.19 Aligned_cols=65 Identities=20% Similarity=0.224 Sum_probs=53.8
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcC--CCHHHHHHHHHHhhccCCcEEEe--eeeEEEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFN--EDHQKVVGGMKSIETLGEYLIVE--PLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~--~~~~~v~~~~~~L~s~~glv~~e--~~~~~~~~LTeEG~~yl~ 70 (292)
.....||..|..+ +....++++.++ ++...|.+.++.|+.. |||+.. +-....|.||+.|++++.
T Consensus 371 ~~r~~IL~~L~~~-~~~~~el~~~l~~~~s~~~v~~hL~~Le~~-GLV~~~~~~g~~~~Y~Lt~~g~~~l~ 439 (442)
T PRK05638 371 GTKLEILKILSER-EMYGYEIWKALGKPLKYQAVYQHIKELEEL-GLIEEAYRKGRRVYYKLTEKGRRLLE 439 (442)
T ss_pred chHHHHHHHHhhC-CccHHHHHHHHcccCCcchHHHHHHHHHHC-CCEEEeecCCCcEEEEECcHHHHHHH
Confidence 4577899999854 567799999998 8889999999999986 999864 334678999999999875
No 63
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=93.87 E-value=0.13 Score=41.18 Aligned_cols=43 Identities=21% Similarity=0.319 Sum_probs=34.7
Q ss_pred cCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhhc
Q psy10346 28 FNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 28 ~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~~ 71 (292)
++++---|+.++++|-|+ |+|+. ..=....|.||+||.+||++
T Consensus 35 l~ipNL~vika~qsl~S~-GYvkt~~~W~~~YytLT~eGveyLRE 78 (105)
T COG5045 35 LEIPNLHVIKAMQSLISY-GYVKTIHVWRHSYYTLTPEGVEYLRE 78 (105)
T ss_pred cCCCchHHHHHHHHHhhc-ceeEEEeeeeeeEEEecHHHHHHHHH
Confidence 355555689999999997 99987 45566778999999999964
No 64
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.
Probab=93.82 E-value=0.056 Score=54.80 Aligned_cols=40 Identities=33% Similarity=0.605 Sum_probs=34.0
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346 211 MGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS 251 (292)
Q Consensus 211 ~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~ 251 (292)
|-..+..|+.||+...++++|+...+|||+||- +|.|..+
T Consensus 37 pr~~~~~gk~hpv~~ti~~lreayl~~gf~e~~-np~iv~e 76 (533)
T TIGR00470 37 PRLKFVYGKPHPLMETIERLREAYLRMGFSEMV-NPLIVDE 76 (533)
T ss_pred CcccccCCCCCcHHHHHHHHHHHHHhcChHhhc-CceeecH
Confidence 334567899999999999999999999999995 7877654
No 65
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=93.75 E-value=0.15 Score=34.94 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=39.0
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
+...+||.+|.+ ++.+..++++.+|+++..|..-++.|+.. |+|+
T Consensus 2 ~~R~~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~-glV~ 46 (47)
T PF01022_consen 2 PTRLRILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREA-GLVE 46 (47)
T ss_dssp HHHHHHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEE
T ss_pred HHHHHHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHC-cCee
Confidence 456789999986 67788999999999999999999999987 9986
No 66
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=93.61 E-value=0.36 Score=41.28 Aligned_cols=74 Identities=16% Similarity=0.156 Sum_probs=52.4
Q ss_pred HHHHHHHHHhccCCCCChHHHHHh------cCCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHHhhc
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKL------FNEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQVKDN 71 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~------~~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~yl~~ 71 (292)
.++.-||..|..+.. --.++.+. ..+++..|-.+++.|+.. |+|..... ..+.|.||+.|++++..
T Consensus 24 ~l~~~IL~~L~~~p~-hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~-GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~ 101 (138)
T TIGR02719 24 FLVPFLLLCLKDWNL-HGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKD-NLISSQWDTSAEGPAKRIYSLTDAGEQYLSM 101 (138)
T ss_pred HHHHHHHHHHccCCC-CHHHHHHHHHHcCCCCCCcChHHHHHHHHHHC-CCEEEEeeecCCCCCcEEEEECHHHHHHHHH
Confidence 456678888876442 22333332 246788999999999986 99987432 25889999999999977
Q ss_pred CChHHHHH
Q psy10346 72 GSHEVLVF 79 (292)
Q Consensus 72 GlPE~rl~ 79 (292)
-..+.+.+
T Consensus 102 ~~~~w~~~ 109 (138)
T TIGR02719 102 CANSFEHY 109 (138)
T ss_pred HHHHHHHH
Confidence 66665543
No 67
>PHA02943 hypothetical protein; Provisional
Probab=93.58 E-value=0.38 Score=41.95 Aligned_cols=74 Identities=18% Similarity=0.180 Sum_probs=54.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhhcCChHHH--HHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKDNGSHEVL--VFNNV 82 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~~GlPE~r--l~~~l 82 (292)
-.+||..| ..|..++.++|+.+|+++.++-..++-|+.. |+|.- +.-....|.|.+ ..|+ ++--+.. ++.+|
T Consensus 13 ~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErE-G~VkrV~~G~~tyw~l~~--day~-~~v~~~~Relwrlv 87 (165)
T PHA02943 13 MIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKE-GMVLKVEIGRAAIWCLDE--DAYT-NLVFEIKRELWRLV 87 (165)
T ss_pred HHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHc-CceEEEeecceEEEEECh--HHHH-HHHHHHHHHHHHHH
Confidence 35688888 6777788999999999999999999999976 88766 445578889998 4444 3333332 55555
Q ss_pred CC
Q psy10346 83 PS 84 (292)
Q Consensus 83 ~~ 84 (292)
..
T Consensus 88 ~s 89 (165)
T PHA02943 88 CN 89 (165)
T ss_pred Hh
Confidence 43
No 68
>TIGR02367 PylS pyrrolysyl-tRNA synthetase. PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase.
Probab=93.58 E-value=0.11 Score=52.37 Aligned_cols=57 Identities=16% Similarity=0.216 Sum_probs=43.4
Q ss_pred CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCCCCCCCCCCceeec
Q psy10346 216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQHPARDAHDTFFVT 276 (292)
Q Consensus 216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~PqdHPAR~~~DTfyl~ 276 (292)
..|+.||+..+.+.||++|.++||.|+. .|.+++. -.||.+..+.+++ -.++.|.++
T Consensus 235 TiG~~~~~~~Led~IRevfvg~GFqEV~-TPtLt~e-E~~E~m~~~~g~e--I~n~Iyk~e 291 (453)
T TIGR02367 235 AEDREDYLGKLERDITKFFVDRGFLEIK-SPILIPA-EYIERMGIDNDTE--LSKQIFRVD 291 (453)
T ss_pred ccCcccHHHHHHHHHHHHHHHCCCEEEE-CCeecch-HHHHhhcCccCCc--ccccceEec
Confidence 6799999999999999999999999996 4777533 3468888776644 234555543
No 69
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.50 E-value=0.17 Score=40.02 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=42.3
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
..+.+||..|..++.....++|+.+|++...|.+.+..|+.. |+|.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~-g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE-GVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCee
Confidence 468899999988888888999999999999999999999987 9987
No 70
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=93.45 E-value=0.16 Score=37.73 Aligned_cols=46 Identities=20% Similarity=0.247 Sum_probs=37.8
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
.+|+..|...+.++..+||..++++++.|...+.-|..+ |+|.-..
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~k-G~I~~~~ 48 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRK-GYIRKVD 48 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCC-TSCEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEEec
Confidence 467888988999999999999999999999999999987 9887543
No 71
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=93.34 E-value=0.19 Score=36.74 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=36.5
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
.|+..-..++.+.+.++|+.+|+++.+|..+++.|+.+ |||+.+.
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~-GlV~~~~ 56 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEK-GLVEYEP 56 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEET
T ss_pred HHHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHC-CCEEecC
Confidence 34444455667889999999999999999999999986 9998764
No 72
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=93.34 E-value=0.15 Score=47.78 Aligned_cols=68 Identities=13% Similarity=0.163 Sum_probs=57.9
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEV 76 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~ 76 (292)
+.+..|...|.+ +..+.+++|+.+|++...+-+.+..|.+. |+++.. ...|.+|+.+..++..++|.+
T Consensus 10 a~~Lglfd~L~~-gp~t~~eLA~~~~~~~~~~~~lL~~L~~l-gll~~~---~~~y~~t~~~~~~l~~~~~~~ 77 (306)
T TIGR02716 10 AIELDLFSHMAE-GPKDLATLAADTGSVPPRLEMLLETLRQM-RVINLE---DGKWSLTEFADYMFSPTPKEP 77 (306)
T ss_pred HHHcCcHHHHhc-CCCCHHHHHHHcCCChHHHHHHHHHHHhC-CCeEec---CCcEecchhHHhhccCCccch
Confidence 456677888865 56788999999999999999999999998 999864 368999999999998888753
No 73
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=93.22 E-value=0.32 Score=32.74 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=39.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
+..||..|..++..+..+++..++++...|.+.+..|..+ |+|..
T Consensus 2 ~~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~-g~i~~ 46 (53)
T smart00420 2 QQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQ-GLLTR 46 (53)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEE
Confidence 4678888877777889999999999999999999999987 89864
No 74
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=93.06 E-value=0.073 Score=52.58 Aligned_cols=40 Identities=30% Similarity=0.605 Sum_probs=33.8
Q ss_pred CCCCCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346 211 MGISLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS 251 (292)
Q Consensus 211 ~~~~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~ 251 (292)
|-.....|+.||+...++++|+...+|||+||. +|.|..+
T Consensus 37 PRl~f~~Gk~Hpl~~TIq~lReAYLr~GF~Emv-NPlivde 76 (536)
T COG2024 37 PRLKFETGKPHPLYETIQRLREAYLRMGFSEMV-NPLIVDE 76 (536)
T ss_pred CccccccCCcCcHHHHHHHHHHHHHHhhHHHhc-CccccCH
Confidence 334556799999999999999999999999996 7877654
No 75
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=93.03 E-value=0.22 Score=34.84 Aligned_cols=45 Identities=20% Similarity=0.423 Sum_probs=36.1
Q ss_pred HHHHHHHh-ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 6 TEKILKYL-DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 6 e~~iL~~L-~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
+.+||..| ..++.++..++|+.+|++...|.+.++.|++. | +.++
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~-~-~~I~ 47 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREW-G-IPIE 47 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHT-T--EEE
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-C-CeEE
Confidence 56788888 55556899999999999999999999999976 6 4443
No 76
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=92.70 E-value=0.27 Score=42.43 Aligned_cols=47 Identities=13% Similarity=0.286 Sum_probs=43.5
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
.....+||..|..++.....++|+..|++...|.+-++.|+.. |+|+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~-GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ-GFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeE
Confidence 3578999999999999999999999999999999999999987 9986
No 77
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=92.63 E-value=0.24 Score=41.22 Aligned_cols=51 Identities=20% Similarity=0.169 Sum_probs=46.0
Q ss_pred HHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHH
Q psy10346 23 DLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 23 ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
.+|..++++.+.++.++.-++-. |++++.. -.+.||+.|+++++.+..|++
T Consensus 2 ~La~~l~~eiDdL~p~~eAaelL-gf~~~~~---Gdi~LT~~G~~f~~a~~~~rK 52 (120)
T PF09821_consen 2 QLADELHLEIDDLLPIVEAAELL-GFAEVEE---GDIRLTPLGRRFAEADIDERK 52 (120)
T ss_pred chHHHhCCcHHHHHHHHHHHHHc-CCeeecC---CcEEeccchHHHHHCChHHHH
Confidence 47888999999999999999988 9999865 578999999999999999988
No 78
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=92.61 E-value=0.26 Score=41.98 Aligned_cols=47 Identities=19% Similarity=0.194 Sum_probs=43.7
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
....+||..|..++.....++|+.+|++..+|.+-++.|++. |+|..
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~-GvI~~ 55 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA-GIITG 55 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeee
Confidence 678999999998999999999999999999999999999997 99874
No 79
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=92.53 E-value=1.5 Score=36.77 Aligned_cols=91 Identities=10% Similarity=0.086 Sum_probs=60.5
Q ss_pred cHHHHHHHHHhccCCCCChHHH----HHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEE--eChhHH------HH-
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDL----AKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWE--LTGEGN------QV- 68 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~el----a~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~--LTeEG~------~y- 68 (292)
.+.|..|+..|=..+...+.++ ++..++++..|...+..|..| |+|..... ....|. .|++-- +.
T Consensus 3 t~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~K-G~v~~~k~gr~~~Y~p~vs~ee~~~~~~~~~~ 81 (130)
T TIGR02698 3 SDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDK-GCLTTEKEGRKFIYTALVSEDEAVENAAQELF 81 (130)
T ss_pred CHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHC-CceeeecCCCcEEEEecCCHHHHHHHHHHHHH
Confidence 3678889999965667777774 444588999999999999986 99986532 233555 343322 11
Q ss_pred --hhcCChHHHHHhhcCCCCCChHHHhh
Q psy10346 69 --KDNGSHEVLVFNNVPSEGIGQKELLA 94 (292)
Q Consensus 69 --l~~GlPE~rl~~~l~~~~~~~~el~~ 94 (292)
+=.|++..-|..++.+..++.+|+.+
T Consensus 82 ~~~f~gs~~~ll~~l~~~~~ls~eele~ 109 (130)
T TIGR02698 82 SRICSRKVGAVIADLIEESPLSQTDIEK 109 (130)
T ss_pred HHHHCCCHHHHHHHHHhcCCCCHHHHHH
Confidence 22467776666666655566666554
No 80
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=92.30 E-value=0.31 Score=40.70 Aligned_cols=50 Identities=18% Similarity=0.280 Sum_probs=44.9
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
.+.+.+||..|+.++.....++|+..|++..+|..-++.|+.. |+|+-..
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~-GiI~~~~ 56 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEE-GVIKGYT 56 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CceeeEE
Confidence 5788999999998888888999999999999999999999987 9887533
No 81
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=92.28 E-value=0.32 Score=45.63 Aligned_cols=59 Identities=14% Similarity=0.166 Sum_probs=48.8
Q ss_pred HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE-EeCh
Q psy10346 4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW-ELTG 63 (292)
Q Consensus 4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~-~LTe 63 (292)
+.++.||+++.. +|.+.-.|+.+++|++...|-++++.|+.+ |||+.++.-.+.+ +|.+
T Consensus 195 ~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~-GlIe~~K~G~~n~V~l~~ 255 (258)
T COG2512 195 EDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKR-GLIEKEKKGRTNIVELRD 255 (258)
T ss_pred HHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhC-CceEEEEeCCeeEEEEec
Confidence 578899999965 556888999999999999999999999976 9999977765544 4443
No 82
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=92.20 E-value=0.38 Score=35.81 Aligned_cols=50 Identities=18% Similarity=0.404 Sum_probs=39.0
Q ss_pred cHHHHHHHHHhcc----CC-CCChHHHHHhcCCC-HHHHHHHHHHhhccCCcEEEee
Q psy10346 3 SDLTEKILKYLDT----NP-PVDTLDLAKLFNED-HQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 3 ~~~e~~iL~~L~~----~~-~~~~~ela~~~~~~-~~~v~~~~~~L~s~~glv~~e~ 53 (292)
...|.+||..+.+ ++ .-+..|+|+.+|+. +..|...++.|+.+ |+|+-..
T Consensus 5 T~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~k-G~I~r~~ 60 (65)
T PF01726_consen 5 TERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERK-GYIRRDP 60 (65)
T ss_dssp -HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHT-TSEEEGC
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC-cCccCCC
Confidence 4778999998854 33 34669999999997 99999999999987 9998643
No 83
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=92.18 E-value=0.44 Score=40.20 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=41.7
Q ss_pred HHHHHHHHHhc-cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 4 DLTEKILKYLD-TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 4 ~~e~~iL~~L~-~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
..+..++.+|- .+++.+.+++|+.+|.+.+.|-++++.|... |+|.-+..
T Consensus 27 ~~Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~-GlV~Rek~ 77 (126)
T COG3355 27 ELDVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA-GLVEREKV 77 (126)
T ss_pred HHHHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc-CCeeeeee
Confidence 45566776665 6888999999999999999999999999987 99875443
No 84
>PRK00215 LexA repressor; Validated
Probab=92.09 E-value=0.41 Score=42.39 Aligned_cols=66 Identities=15% Similarity=0.271 Sum_probs=53.7
Q ss_pred CCcHHHHHHHHHhcc-----CCCCChHHHHHhcCC-CHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346 1 MASDLTEKILKYLDT-----NPPVDTLDLAKLFNE-DHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ 67 (292)
Q Consensus 1 m~~~~e~~iL~~L~~-----~~~~~~~ela~~~~~-~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~ 67 (292)
|-...|..||..|.. +......++|..+|+ ++.+|.+.+..|+.+ |+|+-.......+.|+.+|.-
T Consensus 1 ~lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~-g~i~~~~~~~r~~~l~~~~~~ 72 (205)
T PRK00215 1 MLTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERK-GFIRRDPGRSRAIEVAAPAQL 72 (205)
T ss_pred CCCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC-CCEEeCCCCcceEEecccccc
Confidence 445778999998852 334577899999999 999999999999987 999888777778888777654
No 85
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) 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: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=92.05 E-value=0.068 Score=39.97 Aligned_cols=63 Identities=24% Similarity=0.253 Sum_probs=45.5
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHh--cCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKL--FNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE 64 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~--~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE 64 (292)
|..+.+.+||.+|.+.+......+|.. ++.+...|-+.+..|+.. |.|..+...--.|.||+.
T Consensus 1 ~~~~~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~-g~v~k~~~~PP~W~l~~~ 65 (66)
T PF02295_consen 1 DMQDLEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQ-GKVCKEGGTPPKWSLTEK 65 (66)
T ss_dssp HHHHHHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEECSSSTEEEE-HC
T ss_pred CchhHHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHC-CCEeeCCCCCCceEeccC
Confidence 345788999999977554444445544 555589999999999986 999877767777887753
No 86
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=91.93 E-value=0.2 Score=35.00 Aligned_cols=45 Identities=13% Similarity=0.152 Sum_probs=36.9
Q ss_pred HHHHHHHhccCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 6 TEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 6 e~~iL~~L~~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
-.+||.+|...+. ....++|+.+|++...+.+.+..|... |+|.-
T Consensus 5 al~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~-g~v~~ 50 (52)
T PF09339_consen 5 ALRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEE-GYVER 50 (52)
T ss_dssp HHHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEE
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-cCeec
Confidence 3468888865544 578999999999999999999999987 99874
No 87
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.91 E-value=0.63 Score=41.24 Aligned_cols=60 Identities=13% Similarity=0.001 Sum_probs=48.5
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE-------EEEEeChhH
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH-------KIWELTGEG 65 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~-------~~~~LTeEG 65 (292)
....||.+|..++.++.+++|..+|+...+|-+.+..|... |||...+... ..|.||.+-
T Consensus 23 ~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~-gLv~~~r~r~~~~Gr~~y~w~l~~~~ 89 (178)
T PRK06266 23 EGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDA-RLADYKREKDEETNWYTYTWKPELEK 89 (178)
T ss_pred cHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEeeeeccCCCcEEEEEEeCHHH
Confidence 34678898888788899999999999999999999999987 9999755333 356676543
No 88
>PRK06474 hypothetical protein; Provisional
Probab=91.38 E-value=0.78 Score=40.44 Aligned_cols=67 Identities=18% Similarity=0.263 Sum_probs=54.8
Q ss_pred CCcHHHHHHHHHhccCCC-CChHHHHHhc-CCCHHHHHHHHHHhhccCCcEEEeee------eEEEEEeChhHHHH
Q psy10346 1 MASDLTEKILKYLDTNPP-VDTLDLAKLF-NEDHQKVVGGMKSIETLGEYLIVEPL------SHKIWELTGEGNQV 68 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~-~~~~ela~~~-~~~~~~v~~~~~~L~s~~glv~~e~~------~~~~~~LTeEG~~y 68 (292)
++++...+||..|...+. .+..+++..+ +++...|-+-++.|+.. |+|..... ....|.++.++-..
T Consensus 8 La~p~R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~-GLI~~~~~~~~~~~~ek~y~~~~~~~~~ 82 (178)
T PRK06474 8 LMHPVRMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDS-GILHVVKEKKVRSVSEKYYAINEEDAKI 82 (178)
T ss_pred hCCHHHHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHC-CCEEEeecccccCceeEEEEeccceeee
Confidence 357888999999976654 8889999988 78999999999999986 99997543 34789999887653
No 89
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=91.14 E-value=0.47 Score=43.03 Aligned_cols=67 Identities=19% Similarity=0.237 Sum_probs=52.1
Q ss_pred HHHHHhccCC-----CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhcCChH
Q psy10346 8 KILKYLDTNP-----PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDNGSHE 75 (292)
Q Consensus 8 ~iL~~L~~~~-----~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~GlPE 75 (292)
++|+.|..-+ .+++.++|+.++.+.+...+.+++|+.. |+|.-+. ..-+...+||.|.+.|.+=.-+
T Consensus 4 ~~lk~l~~~~a~~~~~~t~~ela~~l~~S~qta~R~l~~le~~-~~I~R~~~~~Gq~i~iTekG~~~L~~~~~d 76 (214)
T COG1339 4 RLLKKLALRGAVRGVKVTSSELAKRLGVSSQTAARKLKELEDE-GYITRTISKRGQLITITEKGIDLLYKEYED 76 (214)
T ss_pred HHHHHHHHhhhhcCccccHHHHHHHhCcCcHHHHHHHHhhccC-CcEEEEecCCCcEEEehHhHHHHHHHHHHH
Confidence 5666664322 2678999999999999999999999976 8888655 5667789999999988554333
No 90
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=90.97 E-value=0.56 Score=31.90 Aligned_cols=40 Identities=23% Similarity=0.335 Sum_probs=33.1
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIE 43 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~ 43 (292)
.+..+||..|..++.....++|+..|++...|.+-+..|+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 5678999999988888889999999999999999888774
No 91
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=90.85 E-value=0.78 Score=36.25 Aligned_cols=49 Identities=14% Similarity=0.123 Sum_probs=38.7
Q ss_pred HHHHHHHHHhc--------cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 4 DLTEKILKYLD--------TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 4 ~~e~~iL~~L~--------~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
..+.++|..|. ....++..++|+.+|++++.|.+++..|+.+ |+|..+.
T Consensus 25 ~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~-GlI~r~~ 81 (95)
T TIGR01610 25 GREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARR-RIIFRQG 81 (95)
T ss_pred HHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHC-CCeeeec
Confidence 34556666664 2344677899999999999999999999987 9998654
No 92
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=90.55 E-value=0.3 Score=36.21 Aligned_cols=53 Identities=23% Similarity=0.342 Sum_probs=40.1
Q ss_pred HHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee---eeEEEEEe
Q psy10346 8 KILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP---LSHKIWEL 61 (292)
Q Consensus 8 ~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~---~~~~~~~L 61 (292)
+||..|.. +++..+.++|+.+|+++..+-..+..|+.. |.|+..+ -....|.|
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~e-G~V~~~~~~rG~~~~W~l 60 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKE-GKVERSPVRRGKSTYWRL 60 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHC-TSEEEES-SSSSS-EEEE
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEecCCCCcceeeee
Confidence 58888876 777899999999999999999999999976 9887533 22245555
No 93
>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 []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=90.16 E-value=1.1 Score=34.84 Aligned_cols=67 Identities=15% Similarity=0.075 Sum_probs=50.3
Q ss_pred cHHHHHHHHHhccCC---C-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 3 SDLTEKILKYLDTNP---P-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~---~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
++.+.+||.+++.+- + +-.+.+++..|++++.+...+..|-.. ++|.-....-.-|.||-.|-+++.
T Consensus 5 ~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~-kLv~~~~~~Y~GYrLT~~GYD~LA 75 (82)
T PF09202_consen 5 SKEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKL-KLVSRRNKPYDGYRLTFLGYDYLA 75 (82)
T ss_dssp -HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHT-TSEEEE-SSS-EEEE-HHHHHHHH
T ss_pred CHHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhc-CCccccCCCcceEEEeecchhHHH
Confidence 467889999997532 2 455788888999999999999999876 899986666678999999999873
No 94
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=90.13 E-value=0.41 Score=45.22 Aligned_cols=75 Identities=17% Similarity=0.209 Sum_probs=67.0
Q ss_pred cHHHHHHHHHhc-----cCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHH
Q psy10346 3 SDLTEKILKYLD-----TNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 3 ~~~e~~iL~~L~-----~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
++.|+.||.+|- .++.+.++|+|..+|.++-.|-..+.||.+. |||+-..--+--|..|-.+-+.+..-.|+.-
T Consensus 5 T~~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaL-gLVegvpGPkGGY~PT~kAYe~L~iqt~~~~ 83 (294)
T COG2524 5 TSSQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLKAL-GLVEGVPGPKGGYKPTSKAYEALSIQTLETE 83 (294)
T ss_pred cHHHHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHHhc-CccccccCCCCCccccHHHHHHhccCCCCcc
Confidence 689999999994 3667899999999999999999999999999 9999999999999999999999988887655
Q ss_pred H
Q psy10346 78 V 78 (292)
Q Consensus 78 l 78 (292)
.
T Consensus 84 ~ 84 (294)
T COG2524 84 F 84 (294)
T ss_pred e
Confidence 4
No 95
>KOG3344|consensus
Probab=90.09 E-value=0.16 Score=43.44 Aligned_cols=41 Identities=24% Similarity=0.355 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeChhHHHHhhc
Q psy10346 30 EDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 30 ~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTeEG~~yl~~ 71 (292)
++--.||.+++||.|+ |||+..- =-..+|.||.||.+||++
T Consensus 37 vpNL~vikaMQSl~Sr-gYvkeqfaWrH~Yw~LTneGi~yLR~ 78 (150)
T KOG3344|consen 37 VPNLHVIKAMQSLKSR-GYVKEQFAWRHFYWYLTNEGIEYLRE 78 (150)
T ss_pred CccHHHHHHHHHHhhh-hhHHhhhhhheeeeeechhHHHHHHH
Confidence 4445689999999998 9998643 345677999999999965
No 96
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=89.68 E-value=0.79 Score=32.67 Aligned_cols=42 Identities=12% Similarity=0.234 Sum_probs=35.2
Q ss_pred CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
.+...++|+.+|+++..|.+.+..|+.. |+|.... ...|.||
T Consensus 25 ~~s~~ela~~~g~s~~tv~r~l~~L~~~-g~i~~~~--~~~~~l~ 66 (67)
T cd00092 25 PLTRQEIADYLGLTRETVSRTLKELEEE-GLISRRG--RGKYRVN 66 (67)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecC--CCeEEeC
Confidence 4677899999999999999999999987 9998765 3456665
No 97
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator 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=89.56 E-value=0.49 Score=44.67 Aligned_cols=56 Identities=11% Similarity=0.202 Sum_probs=46.1
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeChhHHHHhhcCChHHHHHh
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELTGEGNQVKDNGSHEVLVFN 80 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LTeEG~~yl~~GlPE~rl~~ 80 (292)
..+...+|++..+|..++..|.+. |+|+.+.. ....|.||+.|++.++.+ ..|++.
T Consensus 24 i~l~~~~gi~~~~vr~al~RL~~~-G~l~~~~~grr~~Y~LT~~g~~~l~~~--~~rIy~ 80 (280)
T TIGR02277 24 IEFLAGLGINERLVRTAVSRLVAQ-GWLQSERKGRRSFYSLTDKGRRRFAAA--AQRIYD 80 (280)
T ss_pred HHHHHhcCCCcchHHHHHHHHHHC-CCEEeeecCCCCEEEECHHHHHHHHHH--hhhhcC
Confidence 456777899999999999999986 99988643 358999999999999875 456665
No 98
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=89.54 E-value=0.94 Score=41.84 Aligned_cols=62 Identities=16% Similarity=0.112 Sum_probs=49.4
Q ss_pred HHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
.+||..|...+ .+...+++..+|++...+.+.+..|+.. |||.-... ...|.||..+.++..
T Consensus 14 l~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~-g~v~~~~~-~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 14 LMVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEE-GYVRRSAS-DDSFRLTLKVRQLSE 76 (263)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEecC-CCcEEEcHHHHHHHH
Confidence 45788886544 4788999999999999999999999987 99985432 346999988766543
No 99
>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 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=89.46 E-value=0.55 Score=33.69 Aligned_cols=58 Identities=16% Similarity=0.076 Sum_probs=40.7
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGN 66 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~ 66 (292)
+.+++.++...+ +...-|+.+|+++..|.+.++.|+..-|.-=++ +....+.||+.|+
T Consensus 3 ~l~~f~~v~~~g--s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~-r~~~~~~lT~~G~ 60 (60)
T PF00126_consen 3 QLRYFLAVAETG--SISAAAEELGISQSAVSRQIKQLEEELGVPLFE-RSGRGLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHHS--SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEE-ECSSSEEE-HHHH
T ss_pred HHHHHHHHHHhC--CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEE-ECCCCeeEChhhC
Confidence 345566665544 467788899999999999999999865543233 3334599999996
No 100
>PF03965 Penicillinase_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, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=89.32 E-value=1.5 Score=35.54 Aligned_cols=91 Identities=19% Similarity=0.152 Sum_probs=58.3
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhc----CCCHHHHHHHHHHhhccCCcEEEeeeeE-EEEEeChhHHHHh--------
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLF----NEDHQKVVGGMKSIETLGEYLIVEPLSH-KIWELTGEGNQVK-------- 69 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~----~~~~~~v~~~~~~L~s~~glv~~e~~~~-~~~~LTeEG~~yl-------- 69 (292)
.+.|..|+..|=+.+.+++.++.+.+ ++....|...+..|..| |+|+.+..-. ..|..+=.=++|+
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~K-g~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l 80 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEK-GFLTREKIGRAYVYSPLISREEYLAQELRQFL 80 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHT-TSEEEEEETTCEEEEESSSHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhC-CceeEeecCCceEEEeCCcHHHHHHHHHHHHH
Confidence 36788999999665667777776654 45699999999999987 9999976433 3354332222222
Q ss_pred ---hcCChHHHHHhhcCCCCCChHHHhh
Q psy10346 70 ---DNGSHEVLVFNNVPSEGIGQKELLA 94 (292)
Q Consensus 70 ---~~GlPE~rl~~~l~~~~~~~~el~~ 94 (292)
-.|++..-+..++....++.+++..
T Consensus 81 ~~~~~gs~~~l~~~l~~~~~ls~~el~~ 108 (115)
T PF03965_consen 81 DRLFDGSIPQLVAALVESEELSPEELEE 108 (115)
T ss_dssp HHHSTTHHHHHHHHHHHCT-S-HHHHHH
T ss_pred HHHhCCCHHHHHHHHHhcCCCCHHHHHH
Confidence 2567777777776655566665554
No 101
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=89.22 E-value=0.66 Score=43.34 Aligned_cols=53 Identities=19% Similarity=0.322 Sum_probs=46.5
Q ss_pred CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346 2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS 55 (292)
Q Consensus 2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~ 55 (292)
|+.+.-+||..|...+..+..++|+..|++++.+..-++.|+.- |+|.++..+
T Consensus 21 aS~vRv~Il~lL~~k~plNvneiAe~lgLpqst~s~~ik~Le~a-GlirT~t~k 73 (308)
T COG4189 21 ASKVRVAILQLLHRKGPLNVNEIAEALGLPQSTMSANIKVLEKA-GLIRTETVK 73 (308)
T ss_pred HHHHHHHHHHHHHHhCCCCHHHHHHHhCCchhhhhhhHHHHHhc-Cceeeeeec
Confidence 45677789999988888999999999999999999999999975 999987653
No 102
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=88.57 E-value=0.63 Score=41.03 Aligned_cols=60 Identities=12% Similarity=0.227 Sum_probs=48.2
Q ss_pred cHHHHHHHHHhccC----C-CCChHHHHHhcCCC-HHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346 3 SDLTEKILKYLDTN----P-PVDTLDLAKLFNED-HQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63 (292)
Q Consensus 3 ~~~e~~iL~~L~~~----~-~~~~~ela~~~~~~-~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe 63 (292)
.+.|.+||..|... + ..+..++|+.+|++ ...|.+.+..|+.+ |+|+-+........+++
T Consensus 5 t~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~-g~i~~~~~~~~~~~~~~ 70 (199)
T TIGR00498 5 TARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERK-GYIERDPGKPRAIRILD 70 (199)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHC-CCEecCCCCCCeEEeCC
Confidence 57899999999742 1 24568999999999 99999999999987 99998765555666664
No 103
>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=88.38 E-value=0.82 Score=34.00 Aligned_cols=59 Identities=19% Similarity=0.226 Sum_probs=43.3
Q ss_pred HHHHHhcc-CCCCChHHHHHhc---CCC--HHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 8 KILKYLDT-NPPVDTLDLAKLF---NED--HQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 8 ~iL~~L~~-~~~~~~~ela~~~---~~~--~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
-||..|.+ +.++....+++.+ |.+ .++|-+-++.|+.. |++. ..-..-..||+.|.+.|
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~-Glt~--~~g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERD-GLTR--KVGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHC-CCcc--ccCCcccccCHHHHhhC
Confidence 47888865 4557888887765 554 48999999999987 9766 34444568999998754
No 104
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=88.36 E-value=0.85 Score=42.39 Aligned_cols=57 Identities=14% Similarity=0.052 Sum_probs=47.8
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
-|-++..+|-..|..+..+++...|++...|-.++++|+.+ |+|.+..-.-..|+.-
T Consensus 17 yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~k-G~v~~~~g~P~~y~av 73 (247)
T COG1378 17 YEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKK-GLVEVIEGRPKKYRAV 73 (247)
T ss_pred HHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHC-CCEEeeCCCCceEEeC
Confidence 35566666666777889999999999999999999999987 9999987777777655
No 105
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=88.29 E-value=0.99 Score=34.47 Aligned_cols=61 Identities=16% Similarity=0.219 Sum_probs=45.9
Q ss_pred HHHHHHHHHhccCC---CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346 4 DLTEKILKYLDTNP---PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65 (292)
Q Consensus 4 ~~e~~iL~~L~~~~---~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG 65 (292)
+...++|..|...+ .+++.++|+.+|+++..|.+.+..|... |+|+..+-..--|.|+...
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~-Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA-GLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEETSTTSEEEESS-C
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC-CeeEecCCCCCceeecCCH
Confidence 34456677775433 2788999999999999999999999976 9999887767777776543
No 106
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=88.12 E-value=1.5 Score=30.10 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=31.2
Q ss_pred CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
+..+ +..++|+.+|++...|.+++..|++. |+|....
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~-g~i~~~~ 54 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAE-GLVQRRP 54 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEec
Confidence 4445 67899999999999999999999986 9987543
No 107
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=88.00 E-value=1.1 Score=41.12 Aligned_cols=65 Identities=20% Similarity=0.203 Sum_probs=50.4
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh----hHHHHhhcC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG----EGNQVKDNG 72 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe----EG~~yl~~G 72 (292)
-.+||..|...+.....++|+.+|++.+.+.+.+..|... |||.-. .....|.|+. -|..|....
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~-G~l~~~-~~~~~Y~lG~~~~~lg~~~~~~~ 84 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTL-GYVAQE-GESEKYSLTLKLFELGAKALQNV 84 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEc-CCCCcEEecHHHHHHHHHHHhhC
Confidence 3468888876666788999999999999999999999987 998754 3345688774 455555443
No 108
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=87.87 E-value=1.2 Score=41.24 Aligned_cols=48 Identities=8% Similarity=0.028 Sum_probs=43.2
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
+..+.+||..|..++.+...++|+.+|++...|-+.++.|++. |++.-
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~-g~i~r 51 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDES-GKLKK 51 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence 4567889999999999999999999999999999999999987 88753
No 109
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=87.84 E-value=1.1 Score=41.86 Aligned_cols=47 Identities=15% Similarity=0.210 Sum_probs=42.1
Q ss_pred HHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 6 TEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 6 e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
-++||..|+. ++.+...++|...|++...+..+++.|++. |+|+...
T Consensus 185 v~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~a-GvIe~r~ 232 (251)
T TIGR02787 185 VEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA-GVIESRS 232 (251)
T ss_pred HHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecc
Confidence 3578999987 477888999999999999999999999997 9999887
No 110
>PF13814 Replic_Relax: Replication-relaxation
Probab=87.83 E-value=1.1 Score=38.76 Aligned_cols=61 Identities=16% Similarity=0.183 Sum_probs=50.2
Q ss_pred HHHhccCCCCChHHHHHhcCCCHH---HHHHHHHHhhccCCcEEEeee--------eEEEEEeChhHHHHhhc
Q psy10346 10 LKYLDTNPPVDTLDLAKLFNEDHQ---KVVGGMKSIETLGEYLIVEPL--------SHKIWELTGEGNQVKDN 71 (292)
Q Consensus 10 L~~L~~~~~~~~~ela~~~~~~~~---~v~~~~~~L~s~~glv~~e~~--------~~~~~~LTeEG~~yl~~ 71 (292)
|..|...+.+++++++..++.+.. .+-+.++.|... |+|..... ....|.||..|.+++..
T Consensus 1 L~~L~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~-glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~ 72 (191)
T PF13814_consen 1 LRLLARHRFLTTDQIARLLFPSSKSERTARRRLKRLREL-GLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD 72 (191)
T ss_pred ChhHHHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhC-CcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence 455666777889999998887765 799999999876 99988665 55789999999999863
No 111
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=87.53 E-value=1.9 Score=34.01 Aligned_cols=69 Identities=17% Similarity=0.232 Sum_probs=44.6
Q ss_pred CCcHHHHHHHHHhcc--CCCCChHHHHHh-------cCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhh
Q psy10346 1 MASDLTEKILKYLDT--NPPVDTLDLAKL-------FNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 1 m~~~~e~~iL~~L~~--~~~~~~~ela~~-------~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~ 70 (292)
|..+.+..|+..|.. +...+..++... ......++.-.+.||+.. |+|.- .....+.|.+|+.|...++
T Consensus 1 M~~p~~~~I~~iL~~~~~~~~~i~~L~~e~~~~~~~~~~TKNelL~~vYWLE~n-gyI~R~~~~~~~rY~~T~kG~~ll~ 79 (85)
T PF11313_consen 1 MEKPSEELIYQILNFVKDPNATINHLTFEFIDFPGAYDFTKNELLYTVYWLEEN-GYIFRDNNNNEKRYSLTEKGKELLA 79 (85)
T ss_pred CCCccHHHHHHHHHHhcCccccHHHHHHHHHhccccccccHHHHHHHHHHHhhc-CeeEeecCCCcceeEEeccHHHHHH
Confidence 555555555555532 222333334332 234578999999999998 87765 5556677999999998664
No 112
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=87.53 E-value=1.4 Score=32.94 Aligned_cols=51 Identities=14% Similarity=0.158 Sum_probs=42.7
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.|..+|..++..+..++++..|++...+..++-||.- +|=|.+++.....|
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLar-E~KI~~~~~~~~~~ 62 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLAR-ENKIEFEEKNGELY 62 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHC-TTSEEEEEETTEEE
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhc-cCceeEEeeCCEEE
Confidence 5788898888889999999999999999999999975 58888877665554
No 113
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=87.12 E-value=0.94 Score=41.98 Aligned_cols=48 Identities=23% Similarity=0.356 Sum_probs=43.6
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
+.-..+||..|..++.+...+||+.+|++...|-|.+..|++. |++.-
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~-g~l~R 51 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQ-GLLLR 51 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHC-CcEEE
Confidence 4577889999999999999999999999999999999999987 87764
No 114
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=87.11 E-value=1.9 Score=34.55 Aligned_cols=63 Identities=16% Similarity=0.037 Sum_probs=46.8
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee----EEEEEeChhHHHHh
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS----HKIWELTGEGNQVK 69 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~----~~~~~LTeEG~~yl 69 (292)
.+.++|.++.+.+. ...-|+.+|+++.+|.+.++.|+..-|..=+++.. ..-++||+.|+.++
T Consensus 5 ~~l~~~~av~~~gS--is~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 5 RRVALLKAIARMGS--ISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred HHHHHHHHHHHhCC--HHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 35567777766553 45678889999999999999999764544344432 35899999999877
No 115
>PRK09954 putative kinase; Provisional
Probab=86.97 E-value=1.3 Score=42.51 Aligned_cols=45 Identities=16% Similarity=0.304 Sum_probs=41.3
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYL 49 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv 49 (292)
..+++||..|.+++.+...++|+.+|++...|-..++.|+++ |+|
T Consensus 3 ~~~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~-g~i 47 (362)
T PRK09954 3 NREKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRK-GRI 47 (362)
T ss_pred hHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCc
Confidence 467789999998888899999999999999999999999986 887
No 116
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=86.92 E-value=1.6 Score=39.79 Aligned_cols=64 Identities=11% Similarity=-0.025 Sum_probs=49.2
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
+.+++..+.+.+ +...-|+.+++.+.+|.+.++.||+.=|. ..-.+....++||+.|+.+++.-
T Consensus 5 ~l~~f~~v~~~g--s~s~AA~~L~isqpavS~~I~~LE~~lG~-~LF~R~~r~~~lT~~G~~l~~~a 68 (275)
T PRK03601 5 LLKTFLEVSRTR--HFGRAAESLYLTQSAVSFRIRQLENQLGV-NLFTRHRNNIRLTAAGERLLPYA 68 (275)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCC-ceEEECCCceEECHhHHHHHHHH
Confidence 456666666555 34667888999999999999999986454 55666678899999999976443
No 117
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=86.71 E-value=1.8 Score=33.73 Aligned_cols=32 Identities=13% Similarity=0.285 Sum_probs=23.6
Q ss_pred HHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 38 GMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 38 ~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
++..|.. .|+|+ ....-.|.||++|++++.++
T Consensus 60 a~~~L~~-aGli~--~~~rG~~~iT~~G~~~l~~~ 91 (92)
T PF14338_consen 60 ARSYLKK-AGLIE--RPKRGIWRITEKGRKALAEH 91 (92)
T ss_pred HHHHHHH-CCCcc--CCCCCceEECHhHHHHHhhC
Confidence 3455665 48984 44477999999999998764
No 118
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=86.58 E-value=1.2 Score=39.89 Aligned_cols=63 Identities=16% Similarity=0.210 Sum_probs=52.4
Q ss_pred CCcHHHHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346 1 MASDLTEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE 64 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE 64 (292)
|+-+-+.+||..|...+ .+..-++|.++|++...|-+.+..|... |.|......--.|.++-+
T Consensus 1 ~~~~~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~-~~v~~~~~~pP~W~~~~~ 64 (183)
T PHA02701 1 MSCDCASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLES-DAVSCEDGCPPLWSVECE 64 (183)
T ss_pred CcchHHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhc-CcEecCCCCCCccccccC
Confidence 77788999999998776 5788999999999999999999999976 899877666666655433
No 119
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=86.56 E-value=1.2 Score=41.28 Aligned_cols=48 Identities=19% Similarity=0.280 Sum_probs=43.1
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
+.-+.+||..|...+.+...++|+.+|++...|-+.+..|+.. |+|.-
T Consensus 4 ~eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~-g~l~r 51 (256)
T PRK10434 4 RQRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHA-GTVIR 51 (256)
T ss_pred HHHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEE
Confidence 5577889999999999999999999999999999999999986 87654
No 120
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 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 and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=86.29 E-value=0.98 Score=36.00 Aligned_cols=51 Identities=16% Similarity=0.034 Sum_probs=36.9
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH 56 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~ 56 (292)
....||..|..++.+.-+++|..+|++...|-+.+..|... |+|.+.....
T Consensus 14 ~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~-~lv~~~~~~d 64 (105)
T PF02002_consen 14 EAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYED-GLVSYRRRKD 64 (105)
T ss_dssp TTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHH-SS-EEEEE--
T ss_pred hHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCeEEEEEEc
Confidence 34578888876777888999999999999999999999987 9998875433
No 121
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.29 E-value=1.3 Score=41.02 Aligned_cols=48 Identities=13% Similarity=0.239 Sum_probs=43.1
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
...+.+||..|...+.+...++|+.++++...|.+.+..|++. |++.-
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~-g~l~r 51 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQ-NKILR 51 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEE
Confidence 4567889999998998999999999999999999999999987 88753
No 122
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=86.17 E-value=1.7 Score=39.51 Aligned_cols=63 Identities=10% Similarity=0.023 Sum_probs=48.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++.++.+.+ +...-|+.+|+++.+|.+.++.||+.-|. ..-.+....+.||++|+..++.
T Consensus 5 ~L~~f~~v~~~g--s~s~AA~~L~isqsavS~~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~~ 67 (296)
T PRK11242 5 HIRYFLAVAEHG--NFTRAAEALHVSQPTLSQQIRQLEESLGV-QLFDRSGRTVRLTDAGEVYLRY 67 (296)
T ss_pred HHHHHHHHHHhC--CHHHHHHHcCCCchHHHHHHHHHHHHhCC-eeEeEcCCceeechhHHHHHHH
Confidence 345666665554 45677888999999999999999987444 5556678889999999987743
No 123
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=85.90 E-value=2.1 Score=37.09 Aligned_cols=48 Identities=6% Similarity=-0.049 Sum_probs=41.5
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
....||.+|-.++.++.+++|..+|++...|-+.+..|... |||...+
T Consensus 15 ~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~-~Lv~~~r 62 (158)
T TIGR00373 15 EVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDA-GLADYKR 62 (158)
T ss_pred hHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCceeee
Confidence 44678888876778888999999999999999999999987 9997544
No 124
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=85.73 E-value=2.3 Score=28.12 Aligned_cols=40 Identities=15% Similarity=0.164 Sum_probs=32.5
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
....++|..+|++...+.+.+..|++. |+|.... ..|.+|
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~-g~l~~~~---~~~~i~ 48 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKE-GLISREG---GRIVIL 48 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeC---CEEEEC
Confidence 456889999999999999999999987 9997653 345544
No 125
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=85.60 E-value=1.4 Score=42.84 Aligned_cols=65 Identities=23% Similarity=0.337 Sum_probs=56.5
Q ss_pred CcHHHHHHHH-----HhccCCCCChHHHHHh--cCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346 2 ASDLTEKILK-----YLDTNPPVDTLDLAKL--FNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV 68 (292)
Q Consensus 2 ~~~~e~~iL~-----~L~~~~~~~~~ela~~--~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y 68 (292)
-+..+++||. ++..++++.+.++|+. +|++...|-+.+..|+.. |++. ......-...|+.|-+|
T Consensus 4 l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~-G~l~-~~h~sagrIPT~kGYR~ 75 (339)
T PRK00082 4 LDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEEL-GLLE-KPHTSSGRIPTDKGYRY 75 (339)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhC-CCcC-CCcCCCCCCcCHHHHHH
Confidence 3567888998 6778888999999976 899999999999999987 9988 67777778999999887
No 126
>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 []. ; PDB: 3KFW_X 3L09_B.
Probab=85.57 E-value=1.7 Score=32.86 Aligned_cols=43 Identities=19% Similarity=0.262 Sum_probs=33.5
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhH
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEG 65 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG 65 (292)
-++....|++..+|-.++..|.+. |+++.++.- ...|.||+.|
T Consensus 27 i~ll~~~Gv~e~avR~alsRl~~~-G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 27 IRLLAAFGVSESAVRTALSRLVRR-GWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp HHHHCCTT--HHHHHHHHHHHHHT-TSEEEECCCTEEEEEE-HHH
T ss_pred HHHHHHcCCChHHHHHHHHHHHHc-CceeeeecCccceEeeCCCC
Confidence 455667899999999999999986 998886655 7889999987
No 127
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=85.52 E-value=0.98 Score=41.53 Aligned_cols=65 Identities=9% Similarity=0.052 Sum_probs=48.6
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
.+.+++..+.+.+ +...-|+.+|+.+.+|.+.++.||+.-|..=.+ +....+.||++|+.+++..
T Consensus 8 ~~L~~f~~v~~~g--s~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~-R~~r~~~lT~~G~~l~~~a 72 (302)
T PRK09791 8 HQIRAFVEVARQG--SIRGASRMLNMSQPALTKSIQELEEGLAAQLFF-RRSKGVTLTDAGESFYQHA 72 (302)
T ss_pred HHHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEE-EcCCCceECccHHHHHHHH
Confidence 3444555555554 456778889999999999999999876664444 5667789999999987533
No 128
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=85.24 E-value=2.4 Score=32.03 Aligned_cols=50 Identities=18% Similarity=0.320 Sum_probs=41.7
Q ss_pred HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
+.++.+|..+...+ .+...+++..+|+|...+-..++.|+.. |||.-...
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~-gLI~k~~~ 53 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKK-GLIVKQSV 53 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHC-CCEEEEEe
Confidence 57899999996533 3566889999999999999999999987 99886555
No 129
>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, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=85.22 E-value=3.6 Score=39.87 Aligned_cols=113 Identities=21% Similarity=0.229 Sum_probs=72.4
Q ss_pred cHHHHHHHHHhccC--C-CCChHHHHHh-cCCCHHHHHHHHHHhhccCCcEEEeee-eEEEEEeC--hhHHHHhhcCChH
Q psy10346 3 SDLTEKILKYLDTN--P-PVDTLDLAKL-FNEDHQKVVGGMKSIETLGEYLIVEPL-SHKIWELT--GEGNQVKDNGSHE 75 (292)
Q Consensus 3 ~~~e~~iL~~L~~~--~-~~~~~ela~~-~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~~~~LT--eEG~~yl~~GlPE 75 (292)
..++.+||..+... + .+..++|.+. .+++.+.++.++..|.+. |++++... ....|.+- ++...+..--.-|
T Consensus 8 ~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~-~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e 86 (327)
T PF05158_consen 8 SELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSS-GLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEE 86 (327)
T ss_dssp HHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHH-TSEEEEE-SSSEEEEE--SSS-----SSSCCH
T ss_pred HHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhC-CCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHH
Confidence 36889999988654 2 3555778777 688999999999999987 88888553 44566665 5565555555566
Q ss_pred HHHHhhcCC---CCCChHHHhhcC--C--chhhHHHHHHHcCCeeccc
Q psy10346 76 VLVFNNVPS---EGIGQKELLATF--P--NAKVGFSKAMAKGWISLDK 116 (292)
Q Consensus 76 ~rl~~~l~~---~~~~~~el~~~~--~--~~~ig~~~a~k~gwi~i~~ 116 (292)
+.||.++.+ .|+-..+|+... + ...=.+..+-.++.|+--+
T Consensus 87 ~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 87 RLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEec
Confidence 668888874 468888998763 2 2333455566678887633
No 130
>PF13730 HTH_36: Helix-turn-helix domain
Probab=85.09 E-value=2.5 Score=29.30 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=33.8
Q ss_pred HHHHHHHHHhcc-----CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346 4 DLTEKILKYLDT-----NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYL 49 (292)
Q Consensus 4 ~~e~~iL~~L~~-----~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv 49 (292)
+.++.|+..|.. ++.. ..+.+|+.+|+....|.++++.|+.+ |+|
T Consensus 5 ~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~-G~I 55 (55)
T PF13730_consen 5 PTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEK-GLI 55 (55)
T ss_pred HHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-cCC
Confidence 456666666632 2222 34899999999999999999999987 875
No 131
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=84.96 E-value=2.9 Score=38.92 Aligned_cols=66 Identities=11% Similarity=0.017 Sum_probs=50.5
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
.-.+.+++..+.+.+ +....|+++|+++.+|.+.++.||+.-|. ..-.+....+.||++|+.+++.
T Consensus 3 ~~~~L~~f~~v~e~g--s~s~AA~~L~iSQpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~ 68 (308)
T PRK10094 3 DPETLRTFIAVAETG--SFSKAAERLCKTTATISYRIKLLEENTGV-ALFFRTTRSVTLTAAGEHLLSQ 68 (308)
T ss_pred CHHHHHHHHHHHHhC--CHHHHHHHhcCCHHHHHHHHHHHHHHhCC-EEEeeCCCceeECHhHHHHHHH
Confidence 334556666676554 45678889999999999999999986443 5566677789999999998743
No 132
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=84.29 E-value=3 Score=39.12 Aligned_cols=67 Identities=12% Similarity=0.057 Sum_probs=51.1
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
|-+-.+.+++.++.+.+ +...-|+++++.+.+|.+.++.||+.-|. ..-.+....+.||++|+..++
T Consensus 1 ~m~l~~L~~f~av~~~g--s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~-~LF~R~~r~v~lT~~G~~l~~ 67 (317)
T PRK15421 1 MIEVKHLKTLQALRNCG--SLAAAAATLHQTQSALSHQFSDLEQRLGF-RLFVRKSQPLRFTPQGEILLQ 67 (317)
T ss_pred CccHHHHHHHHHHHHcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-EEEEecCCCceECHhHHHHHH
Confidence 44455667777776655 45678888999999999999999987555 444456677899999998874
No 133
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=84.08 E-value=2.9 Score=37.79 Aligned_cols=66 Identities=8% Similarity=-0.020 Sum_probs=50.3
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
-.+.+++.++.+.+ +...-|+.+|+.+.+|.+.++.||+.-|. ..-.+....++||+.|+.++...
T Consensus 5 l~~L~~f~~v~e~~--s~t~AA~~L~isqpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a 70 (290)
T PRK10837 5 LRQLEVFAEVLKSG--STTQASVMLALSQSAVSAALTDLEGQLGV-QLFDRVGKRLVVNEHGRLLYPRA 70 (290)
T ss_pred HHHHHHHHHHHHcC--CHHHHHHHhCCCccHHHHHHHHHHHHhCC-ccEeecCCeEEECHhHHHHHHHH
Confidence 34556666776555 45677888999999999999999986444 44555777799999999987643
No 134
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=83.66 E-value=2.5 Score=38.46 Aligned_cols=54 Identities=13% Similarity=0.202 Sum_probs=44.3
Q ss_pred HHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346 7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE 64 (292)
Q Consensus 7 ~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE 64 (292)
..||..+.. .+.....|+|..+|++.+.+.+.+..|.+. |||.-+ ...|.|+..
T Consensus 12 l~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~-G~l~~~---~~~Y~lG~~ 66 (248)
T TIGR02431 12 LAVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVEL-GYVTSD---GRLFWLTPR 66 (248)
T ss_pred HHHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeC---CCEEEecHH
Confidence 467888864 456788999999999999999999999987 999742 357988754
No 135
>PF14090 HTH_39: Helix-turn-helix domain
Probab=83.25 E-value=5.6 Score=29.61 Aligned_cols=45 Identities=18% Similarity=0.261 Sum_probs=34.5
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
+..+||.+|..++.+++.+....+|+-+ .-.-+..|+.+ |+--..
T Consensus 2 Q~~rIL~~L~~~~~it~~ea~~~~gi~~--~~aRI~eLR~~-G~~I~t 46 (70)
T PF14090_consen 2 QCKRILAALRRGGSITTLEARRELGIMR--LAARISELRKK-GYPIVT 46 (70)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHcCCCC--HHHHHHHHHHc-CCeeeE
Confidence 5688999998899999988888888764 44667788876 874433
No 136
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=82.75 E-value=4.6 Score=28.20 Aligned_cols=39 Identities=13% Similarity=0.122 Sum_probs=31.2
Q ss_pred hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 21 TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 21 ~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
..++|..+|++...|-.++..|+.. |+|+... ...+.||
T Consensus 28 ~~~la~~~~is~~~v~~~l~~L~~~-G~i~~~~--~~~~~l~ 66 (66)
T cd07377 28 ERELAEELGVSRTTVREALRELEAE-GLVERRP--GRGTFVA 66 (66)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC-CCEEecC--CCeEEeC
Confidence 6789999999999999999999986 9987543 2344443
No 137
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=82.57 E-value=2.6 Score=39.17 Aligned_cols=57 Identities=12% Similarity=0.237 Sum_probs=45.6
Q ss_pred HHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346 6 TEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE 64 (292)
Q Consensus 6 e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE 64 (292)
-..||..|... +.+...++|+.+|++.+.+.+.+..|.+. |||.-.. ....|.|+..
T Consensus 27 ~l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~-G~l~~~~-~~~~Y~lG~~ 84 (271)
T PRK10163 27 GIAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAA-DFVYQDS-QLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEcC-CCCeEEecHH
Confidence 34688888654 45788999999999999999999999987 9996543 4567888754
No 138
>PRK10632 transcriptional regulator; Provisional
Probab=82.42 E-value=3.3 Score=38.42 Aligned_cols=69 Identities=10% Similarity=-0.029 Sum_probs=51.9
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
|-.-.+.+++..+.+.+ +...-|+.+++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.+++.-
T Consensus 1 ~~~l~~L~~F~~v~e~g--S~t~AA~~L~isQpavS~~I~~LE~~lg~-~Lf~R~~r~i~lT~~G~~l~~~a 69 (309)
T PRK10632 1 MERLKRMSVFAKVVEFG--SFTAAARQLQMSVSSISQTVSKLEDELQV-KLLNRSTRSIGLTEAGRIYYQGC 69 (309)
T ss_pred CcchHHHHHHHHHHhcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-eeecccCCCceechhHHHHHHHH
Confidence 43345566677776555 35667888999999999999999976444 55667778899999999987443
No 139
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=81.96 E-value=1.1 Score=33.55 Aligned_cols=43 Identities=12% Similarity=0.129 Sum_probs=34.3
Q ss_pred HHHhhcCCC-CCChHHHhhcC--C--chhhHHHHHHHcCCeecccCcc
Q psy10346 77 LVFNNVPSE-GIGQKELLATF--P--NAKVGFSKAMAKGWISLDKATG 119 (292)
Q Consensus 77 rl~~~l~~~-~~~~~el~~~~--~--~~~ig~~~a~k~gwi~i~~~~g 119 (292)
.|+++|.+. ..++++|.+.. + ....|+||+.|.+.|.++..++
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~~ 59 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKNG 59 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETT
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeCC
Confidence 578899875 48999998763 2 4678999999999999876655
No 140
>PRK11569 transcriptional repressor IclR; Provisional
Probab=81.91 E-value=2.7 Score=39.12 Aligned_cols=62 Identities=13% Similarity=0.201 Sum_probs=48.0
Q ss_pred HHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh----HHHHhh
Q psy10346 7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE----GNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE----G~~yl~ 70 (292)
..||..|.. ...+...++|+.+|++.+.|.+.+..|... ||+.-. .....|.|+.. |..++.
T Consensus 31 l~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~-G~l~~~-~~~~~Y~lG~~l~~Lg~~~~~ 97 (274)
T PRK11569 31 LKLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQ-GFVRQV-GELGHWAIGAHAFIVGSSFLQ 97 (274)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEc-CCCCeEecCHHHHHHHHHHHh
Confidence 457888865 445788999999999999999999999987 999743 33567887654 555543
No 141
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=81.91 E-value=3.7 Score=37.77 Aligned_cols=66 Identities=15% Similarity=0.065 Sum_probs=51.2
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
|-+-.+.+++..+.+.+ +...-|+.+++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.++
T Consensus 1 ~~~~~~L~~f~~v~e~~--s~s~AA~~L~isQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~ 66 (300)
T PRK11074 1 MWSEYSLEVVDAVARTG--SFSAAAQELHRVPSAVSYTVRQLEEWLAV-PLFERRHRDVELTPAGEWFV 66 (300)
T ss_pred CCCHHHHHHHHHHHHhC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-eeEEeCCCCceECccHHHHH
Confidence 33445667777776655 35667888999999999999999976443 55566778899999999987
No 142
>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 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=81.62 E-value=2.2 Score=27.62 Aligned_cols=29 Identities=17% Similarity=0.234 Sum_probs=24.5
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346 20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYL 49 (292)
Q Consensus 20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv 49 (292)
.-.++|.-+|+..+.|.+.++.|+.. |+|
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~~-glI 32 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLERQ-GLI 32 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHT-TSE
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHHc-CCC
Confidence 34789999999999999999999986 886
No 143
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=81.61 E-value=3.5 Score=38.15 Aligned_cols=64 Identities=14% Similarity=0.010 Sum_probs=48.0
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
+.+++.++...+ +...-|+.+|+++.+|.+.++.||+.-|. ..-.+....+.||++|+.++..-
T Consensus 12 ~L~~F~~va~~g--s~s~AA~~L~isQpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a 75 (302)
T TIGR02036 12 KMHTFEVAARHQ--SFSLAAEELSLTPSAISHRINQLEEELGI-QLFVRSHRKVELTHEGKRIYWAL 75 (302)
T ss_pred HHHHHHHHHHhC--CHHHHHHHHCCCHHHHHHHHHHHHHHhCC-ceEEECCCceeECHhHHHHHHHH
Confidence 344455554444 34567888999999999999999987444 55677788999999999987443
No 144
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=81.24 E-value=5.5 Score=29.10 Aligned_cols=52 Identities=15% Similarity=0.218 Sum_probs=40.7
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
.+||..|.+. .....++|+.+|++...|.+.+..|++. |+..... ..-|.|.
T Consensus 3 ~~il~~L~~~-~~~~~eLa~~l~vS~~tv~~~l~~L~~~-g~~i~~~--~~g~~l~ 54 (69)
T TIGR00122 3 LRLLALLADN-PFSGEKLGEALGMSRTAVNKHIQTLREW-GVDVLTV--GKGYRLP 54 (69)
T ss_pred HHHHHHHHcC-CcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeEEec--CCceEec
Confidence 5788888754 4568999999999999999999999986 8865544 4455553
No 145
>COG3373 Uncharacterized protein conserved in archaea [Function unknown]
Probab=81.01 E-value=5.4 Score=32.07 Aligned_cols=65 Identities=26% Similarity=0.355 Sum_probs=46.5
Q ss_pred HHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHH----------hhccCCcEEEe-eeeEEEEEeChhHHHHh
Q psy10346 4 DLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKS----------IETLGEYLIVE-PLSHKIWELTGEGNQVK 69 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~----------L~s~~glv~~e-~~~~~~~~LTeEG~~yl 69 (292)
.+.++||-.|-+--+ .-..|++...+-|++.|.+.+.- |-.. |+|.++ +.-.+.|.|||.|+...
T Consensus 17 eLRrkiL~yLy~iYP~~~YLSEIsR~V~SDPSNV~GcL~Glg~RYnGe~SLi~L-GLVe~~~~nGfKyykltdygkk~v 94 (108)
T COG3373 17 ELRRKILFYLYSIYPYRSYLSEISRAVKSDPSNVKGCLEGLGVRYNGEESLIGL-GLVEVEQKNGFKYYKLTEYGKKMV 94 (108)
T ss_pred HHHHHHHHHHHHHccchhHHHHHHHHHcCCchHHHHHHHhcCCcccCchhhhhc-ceeEeeecCCEEEEehhHHHHHHH
Confidence 455677777743211 23478898899999999999864 4445 778774 45678899999999865
No 146
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=80.97 E-value=3.1 Score=37.99 Aligned_cols=61 Identities=10% Similarity=0.007 Sum_probs=47.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
+.+++..+.+.+ +...-|+++|+++.+|.+.++.||+.-|. ..-.+....++||+.|+.++
T Consensus 7 ~l~~f~~v~~~g--S~s~AA~~L~isq~avS~~I~~LE~~lg~-~LF~R~~~~~~lT~~G~~l~ 67 (300)
T TIGR02424 7 HLQCFVEVARQG--SVKRAAEALHITQPAVSKTLRELEEILGT-PLFERDRRGIRLTRYGELFL 67 (300)
T ss_pred HHHHHHHHHHhC--CHHHHHHHhCCChHHHHHHHHHHHHHhCC-eEEEEcCCCccccHhHHHHH
Confidence 445566665554 35677888999999999999999987554 45556677799999999987
No 147
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=80.95 E-value=2.7 Score=37.62 Aligned_cols=60 Identities=13% Similarity=0.077 Sum_probs=45.5
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
+.+.++.+.+ +...-|+.+++++.+|.+.++.||+.-|. ..-.+....++||++|+..++
T Consensus 3 ~~f~~v~~~g--s~~~AA~~L~isqsavS~~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~ 62 (279)
T TIGR03339 3 KAFHAVARCG--SFTRAAERLGLSQPTVTDQVRKLEERYGV-ELFHRNGRRLELTDAGHRLLP 62 (279)
T ss_pred hhhHHHHhcC--CHHHHHHHhcCCchHHHHHHHHHHHHhCC-ccEEEcCCeEEEChhHHHHHH
Confidence 3455555444 34667888999999999999999986443 445557888999999998774
No 148
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=80.92 E-value=4.9 Score=36.98 Aligned_cols=64 Identities=14% Similarity=-0.003 Sum_probs=48.0
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
+.+++..+.+.+ +...-|+.+|+++.+|.+.++.||+.-|. ..-.+....+.||++|+.+++..
T Consensus 8 ~L~~F~~v~e~g--s~s~AA~~L~isqpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a 71 (296)
T PRK11062 8 HLYYFWMVCKEG--SVVGAAEALFLTPQTITGQIKALEERLQG-KLFKRKGRGLEPTELGELVFRYA 71 (296)
T ss_pred HHHHHHHHHhcC--CHHHHHHHhCCChHHHHHHHHHHHHHcCc-cceeecCCceeECHhHHHHHHHH
Confidence 445555555544 35667888999999999999999986444 45556678899999999886433
No 149
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=80.81 E-value=2 Score=31.01 Aligned_cols=55 Identities=18% Similarity=0.222 Sum_probs=38.1
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHH-HHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKV-VGGMKSIETLGEYLIVEPLSHKIWELTGEGN 66 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v-~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~ 66 (292)
.|...|.-...++..++.+.+|.+.... ...+..+.+. |+|+.+ ...++||++|.
T Consensus 10 ~i~~~LR~~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~-Gll~~~---~~~l~lT~~G~ 65 (66)
T PF06969_consen 10 YIMLGLRCNEGIDLSEFEQRFGIDFAEEFQKELEELQED-GLLEID---GGRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--THHH-HHHHHHHHHT-TSEEE----SSEEEE-TTTG
T ss_pred HHHHHHHhHCCcCHHHHHHHHCcCHHHHHHHHHHHHHHC-CCEEEe---CCEEEECcccC
Confidence 3444454455578899999999985444 7779999987 999654 47899999984
No 150
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry 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=80.68 E-value=6.7 Score=32.08 Aligned_cols=98 Identities=20% Similarity=0.204 Sum_probs=64.7
Q ss_pred CC--cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHHH
Q psy10346 1 MA--SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVLV 78 (292)
Q Consensus 1 m~--~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~rl 78 (292)
|| -++.++||.+.+.+. +..+.|..++++...|.+|++ -... |-+........ . .+...|
T Consensus 1 maYS~DlR~rVl~~~~~g~--s~~eaa~~F~VS~~Tv~~W~k-~~~~-G~~~~k~r~~~--K------------id~~~L 62 (119)
T PF01710_consen 1 MAYSLDLRQRVLAYIEKGK--SIREAAKRFGVSRNTVYRWLK-RKET-GDLEPKPRGRK--K------------IDRDEL 62 (119)
T ss_pred CCCCHHHHHHHHHHHHccc--hHHHHHHHhCcHHHHHHHHHH-hccc-ccccccccccc--c------------ccHHHH
Confidence 66 478889999998654 568899999999999999999 3333 44433222211 1 123446
Q ss_pred HhhcCCC-CCChHHHhhcCCchhhHHHHHHH-cCCeeccc
Q psy10346 79 FNNVPSE-GIGQKELLATFPNAKVGFSKAMA-KGWISLDK 116 (292)
Q Consensus 79 ~~~l~~~-~~~~~el~~~~~~~~ig~~~a~k-~gwi~i~~ 116 (292)
-..|.+. +.++.|+.+.+....-++..+++ .|+....+
T Consensus 63 ~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 63 KALVEENPDATLRELAERLGVSPSTIWRALKRLGITRKKK 102 (119)
T ss_pred HHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHcCchhccC
Confidence 6666665 48999998877654445565555 48865533
No 151
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=80.49 E-value=4.1 Score=39.24 Aligned_cols=58 Identities=17% Similarity=0.189 Sum_probs=46.9
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..||.+|-.++ +.-.++....++.-.|.+.+..|+.. |+|++++.. ..||+.|++.++
T Consensus 25 e~vl~ail~~~--d~wkIvd~s~~plp~v~~i~~~l~~e-giv~~~~g~---v~~TekG~E~~e 82 (354)
T COG1568 25 ENVLSAILATN--DFWKIVDYSDLPLPLVASILEILEDE-GIVKIEEGG---VELTEKGEELAE 82 (354)
T ss_pred HHHHHHHHcCc--chHhhhhhccCCchHHHHHHHHHHhc-CcEEEecCc---EeehhhhHHHHH
Confidence 34666664443 66778888888888999999999986 999988776 899999999886
No 152
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=80.45 E-value=2 Score=38.00 Aligned_cols=47 Identities=15% Similarity=0.169 Sum_probs=42.3
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
+.-+.+||..|..++.+...++|+.+|++.+.|-+.+..|+.. |++.
T Consensus 6 ~~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~-g~~~ 52 (185)
T PRK04424 6 KERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIP-ELRE 52 (185)
T ss_pred HHHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcc-hHHH
Confidence 4567889999999999999999999999999999999999986 8765
No 153
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=80.00 E-value=3.8 Score=37.39 Aligned_cols=63 Identities=11% Similarity=-0.012 Sum_probs=48.2
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
-.+.+++..+.+.+ +...-|+.+|+.+.+|.+.++.||+.-|.-=.++ .. .++||++|+.+++
T Consensus 4 l~~L~~f~~v~~~g--s~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R-~r-~i~lT~~G~~l~~ 66 (294)
T PRK13348 4 YKQLEALAAVVETG--SFERAARRLHVTPSAVSQRIKALEESLGQPLLVR-GR-PCRPTPAGQRLLR 66 (294)
T ss_pred HHHHHHHHHHHHcC--CHHHHHHHhCCCchHHHHHHHHHHHHhCceeeec-CC-CCccChhHHHHHH
Confidence 34556666666554 4567788899999999999999998766655555 44 7999999988763
No 154
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=79.99 E-value=3.6 Score=32.45 Aligned_cols=47 Identities=15% Similarity=0.274 Sum_probs=37.9
Q ss_pred cHHHHHHHHHhcc----CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 3 SDLTEKILKYLDT----NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 3 ~~~e~~iL~~L~~----~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
.+.+.+||.+|.. ..-+...+|++.++++...|..++..|... |+|=
T Consensus 46 ~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e-G~IY 96 (102)
T PF08784_consen 46 SPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE-GHIY 96 (102)
T ss_dssp -HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT-TSEE
T ss_pred CHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC-CeEe
Confidence 4678999999976 122567899999999999999999999986 8874
No 155
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=79.83 E-value=2.2 Score=38.29 Aligned_cols=78 Identities=21% Similarity=0.247 Sum_probs=34.4
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHHHhhcCChHHHHHhhcCCC
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSE 85 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l~~~ 85 (292)
...+.++.....+..++||..+|+..+.++.-+..|.+. |.++- -.---.++.+|++--. .|.++|...
T Consensus 102 ~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~-g~ltGv~DdrGkfIyIs~eE~~---------~va~fi~~r 171 (188)
T PF09756_consen 102 QEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAE-GRLTGVIDDRGKFIYISEEEME---------AVAKFIKQR 171 (188)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHH-SSS-EEE-TT--EEE-------------------------
T ss_pred HHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHC-CCceeeEcCCCCeEEecHHHHH---------HHHHHHHHc
Confidence 345566777777889999999999999999999999987 65543 2222344445544332 155777776
Q ss_pred C-CChHHHhh
Q psy10346 86 G-IGQKELLA 94 (292)
Q Consensus 86 ~-~~~~el~~ 94 (292)
| +|+.+|.+
T Consensus 172 GRvsi~el~~ 181 (188)
T PF09756_consen 172 GRVSISELAQ 181 (188)
T ss_dssp ----------
T ss_pred CCccHHHHHH
Confidence 7 88888876
No 156
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=79.75 E-value=3.5 Score=37.36 Aligned_cols=62 Identities=11% Similarity=-0.049 Sum_probs=47.0
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
+.+++..+.+.+ +...-|+.+++++.+|.+.++.||+.-|. +.-.+....++||+.|+.++.
T Consensus 11 ~l~~f~~v~~~g--s~t~AA~~L~itq~avS~~i~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~ 72 (294)
T PRK09986 11 LLRYFLAVAEEL--HFGRAAARLNISQPPLSIHIKELEDQLGT-PLFIRHSRSVVLTHAGKILME 72 (294)
T ss_pred HHHHHHHHHHhc--CHHHHHHHhCCCCCHHHHHHHHHHHHhCC-eeEeeCCCceeECHhHHHHHH
Confidence 445555555554 34567888999999999999999987444 555666788999999998874
No 157
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=79.72 E-value=4 Score=37.49 Aligned_cols=48 Identities=15% Similarity=0.228 Sum_probs=42.6
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
+..+.+||..|..++.+...++|+.+|++...|.+.+..|+.. |.+.-
T Consensus 3 ~~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~-~~l~r 50 (240)
T PRK10411 3 AARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQ-GKILR 50 (240)
T ss_pred hHHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEE
Confidence 4567889999998888999999999999999999999999876 77754
No 158
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=79.68 E-value=12 Score=38.59 Aligned_cols=92 Identities=13% Similarity=0.094 Sum_probs=62.2
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhh----ccCCcEEEeeeeEEEEEeC----hhHHHHhhcC
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIE----TLGEYLIVEPLSHKIWELT----GEGNQVKDNG 72 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~----s~~glv~~e~~~~~~~~LT----eEG~~yl~~G 72 (292)
|-...+.+||..|.+ +.++..++|+.+|++...|.+.++.|. .. |+..+... .-|.|. .....++..-
T Consensus 1 ~l~~R~~~iL~~L~~-~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~-~~~~i~~~--~Gy~l~~~~~~~~~~~~~~~ 76 (584)
T PRK09863 1 MLNERELKIVDLLEQ-QDRSGGELAQQLGVSRRTIVRDIAYINFTLNGK-AIGSISGS--AKYHLEILNRRSLFQLLQKS 76 (584)
T ss_pred ChHHHHHHHHHHHHc-CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhc-chhheecC--CceEEEeCCHHHHHHHHhcC
Confidence 345678899999954 567889999999999999999999664 33 45333331 256664 2233444455
Q ss_pred ChHHH--HHhhcCCCCCChHHHhhcC
Q psy10346 73 SHEVL--VFNNVPSEGIGQKELLATF 96 (292)
Q Consensus 73 lPE~r--l~~~l~~~~~~~~el~~~~ 96 (292)
.||++ ++++|...++++.+|.+.+
T Consensus 77 ~~e~~~il~~Ll~~~~~~~~~La~~l 102 (584)
T PRK09863 77 DNEDRLLLLRLLLNTFTPMAQLASAL 102 (584)
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHHh
Confidence 67776 3345555678999998763
No 159
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=79.39 E-value=3.7 Score=37.41 Aligned_cols=62 Identities=10% Similarity=0.051 Sum_probs=48.5
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
+.+++..+.+.+ +....|+.+++++.+|.+.++.||..-|. ..-.+....+.||+.|+..++
T Consensus 5 ~L~~f~~v~~~g--s~s~AA~~L~isQ~avSr~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~ 66 (296)
T PRK09906 5 HLRYFVAVAEEL--NFTKAAEKLHTAQPSLSQQIKDLENCVGV-PLLVRDKRKVALTAAGEVFLQ 66 (296)
T ss_pred HHHHHHHHHhhC--CHHHHHHHhCCCCcHHHHHHHHHHHHhCC-eeeeeCCCcceEcHhHHHHHH
Confidence 445566665554 45678888999999999999999986444 556667888999999999874
No 160
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=79.26 E-value=4.7 Score=37.39 Aligned_cols=64 Identities=13% Similarity=-0.043 Sum_probs=48.7
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
.+.+++.++.+.+ +....|+++++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.+++.
T Consensus 10 ~~L~~F~av~e~g--s~s~AA~~L~iSQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~~~ 73 (312)
T PRK10341 10 QHLVVFQEVIRSG--SIGSAAKELGLTQPAVSKIINDIEDYFGV-ELIVRKNTGVTLTPAGQVLLSR 73 (312)
T ss_pred HHHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCC-eEEEEcCCCceEChhHHHHHHH
Confidence 3455556665544 35677888999999999999999986444 4456667789999999998854
No 161
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=79.09 E-value=4.3 Score=37.39 Aligned_cols=63 Identities=10% Similarity=-0.046 Sum_probs=47.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++.++.+.+ +...-|+.+++.+.+|.+.++.||+.=|. ..-.+....+.||+.|+.+++.
T Consensus 15 ~l~~F~av~e~g--S~t~AA~~L~iSQpavS~~I~~LE~~lG~-~Lf~R~~r~~~lT~~G~~l~~~ 77 (303)
T PRK10082 15 WLYDFLTLEKCR--NFSQAAVSRNVSQPAFSRRIRALEQAIGV-ELFNRQVTPLQLSEQGKIFHSQ 77 (303)
T ss_pred HHHHHHHHHhcC--CHHHHHHHhCCChHHHHHHHHHHHHHcCC-EEEEecCCCCccCHHHHHHHHH
Confidence 344555555544 35677888999999999999999986554 4455666789999999998854
No 162
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=78.79 E-value=5.6 Score=36.41 Aligned_cols=63 Identities=8% Similarity=0.049 Sum_probs=48.2
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++.++.+.+ +...-|+.+++.+.+|.+.++.||+.-|. ..-.+....++||+.|+.++..
T Consensus 6 ~L~~f~~va~~g--s~s~AA~~L~isQpavS~~I~~LE~~lG~-~LF~R~~r~~~lT~~G~~l~~~ 68 (301)
T PRK14997 6 DFAWFVHVVEEG--GFAAAGRALDEPKSKLSRRIAQLEERLGV-RLIQRTTRQFNVTEVGQTFYEH 68 (301)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-EeeeeccCcceEcHhHHHHHHH
Confidence 455666666554 35667888999999999999999987554 4455567789999999988743
No 163
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=78.75 E-value=2 Score=33.68 Aligned_cols=74 Identities=14% Similarity=0.016 Sum_probs=39.7
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE-------EeeeeEEEEEeChhHHHHhhcCChHHHH
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI-------VEPLSHKIWELTGEGNQVKDNGSHEVLV 78 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~-------~e~~~~~~~~LTeEG~~yl~~GlPE~rl 78 (292)
.++||+.|...-.-. .+. ..++.......++..|... |||+ .-........+|.+|.+||++.|==.++
T Consensus 1 ~YkIL~~l~~~~~~~-~~~--~~~~~~~~~~~il~~L~d~-GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~ENS~mkKa 76 (88)
T PF09639_consen 1 IYKILKYLYKCMKNG-KEP--DPDITDSYWSDILRMLQDE-GYIKGVSVVRYSPYVALSDPRITLKGIEYLEENSMMKKA 76 (88)
T ss_dssp HHHHHHHHHHH-S----HH--HHTS-HHHHHHHHHHHHHH-TSEE--EESSSSEE--SS--EE-HHHHHHHHHHT-S---
T ss_pred CchHHHHHHHHHcCC-CCC--CcchhHHHHHHHHHHHHHC-CCccceEEEeccceeecCCceEcHHHHHHHHHHHHHHHH
Confidence 368888886421101 111 1244458889999999987 9996 2233456667999999999987766666
Q ss_pred HhhcC
Q psy10346 79 FNNVP 83 (292)
Q Consensus 79 ~~~l~ 83 (292)
++.++
T Consensus 77 ~k~lK 81 (88)
T PF09639_consen 77 YKFLK 81 (88)
T ss_dssp -----
T ss_pred HHHHH
Confidence 66665
No 164
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=78.59 E-value=7.1 Score=30.29 Aligned_cols=47 Identities=17% Similarity=0.062 Sum_probs=37.6
Q ss_pred ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 14 DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 14 ~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
.+.+.+.=+++|+++|++..+|-..++.|+.. |+ .++.....-|.|.
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~-G~-~I~s~~~kGY~L~ 61 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAVWKHIQQLREE-GV-DIESVRGKGYLLP 61 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHHHHHHHHHHHh-CC-ceEecCCCceecc
Confidence 34445566999999999999999999999976 76 7777777677665
No 165
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=78.51 E-value=2.9 Score=34.09 Aligned_cols=59 Identities=10% Similarity=0.025 Sum_probs=42.1
Q ss_pred HHHHHHhcc---CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346 7 EKILKYLDT---NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGN 66 (292)
Q Consensus 7 ~~iL~~L~~---~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~ 66 (292)
.++|..|.. .+.+++.++|..+|++...|.+.+..|... |+|....-..--|.|+...+
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~-gli~~~~g~~ggy~l~~~~~ 72 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRA-GLVESVRGPGGGYRLARPPE 72 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEeccCCCCCccCCCCHH
Confidence 345555532 236789999999999999999999999986 99875433333565654443
No 166
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=78.37 E-value=4.2 Score=37.68 Aligned_cols=64 Identities=13% Similarity=0.038 Sum_probs=49.0
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
-.+.+++.++.+.+ +...-|+.+++.+.+|.+.++.||+.-|. ..-.+....+.||+.|+.+++
T Consensus 6 l~~L~~f~av~~~g--S~s~AAe~L~isqsavS~~Ik~LE~~lg~-~Lf~R~~~~v~LT~~G~~l~~ 69 (309)
T PRK11013 6 LRHIEIFHAVMTAG--SLTEAARLLHTSQPTVSRELARFEKVIGL-KLFERVRGRLHPTVQGLRLFE 69 (309)
T ss_pred HHHHHHHHHHHHhC--cHHHHHHHHCCCcHHHHHHHHHHHHHhCc-eeeeecCCCcccCHHHHHHHH
Confidence 34566677776655 45677888999999999999999987555 344456667999999998875
No 167
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=77.90 E-value=3.5 Score=38.50 Aligned_cols=46 Identities=17% Similarity=0.282 Sum_probs=41.1
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
....+|+..|..++.+...++|+.+|++...|.|.+..|++. |++.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~-G~l~ 62 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQ-GIAV 62 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhC-CCeE
Confidence 346779999988888999999999999999999999999987 8876
No 168
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=77.68 E-value=5.8 Score=33.97 Aligned_cols=49 Identities=18% Similarity=0.331 Sum_probs=43.7
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
+.-.++|+.+...+..+..|+|+..|-+...|.+.+..|+.. |+|..++
T Consensus 64 p~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~-GlI~fe~ 112 (144)
T COG4190 64 PRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADL-GLIFFEE 112 (144)
T ss_pred hhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhc-CeEEEec
Confidence 455678899988888888999999999999999999999986 9999876
No 169
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=77.26 E-value=14 Score=27.01 Aligned_cols=61 Identities=15% Similarity=0.184 Sum_probs=45.6
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee-EEEEEeChhH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS-HKIWELTGEG 65 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~-~~~~~LTeEG 65 (292)
+.-.+||..|.........+++...++++..|..-+..|... |+|...... ...|.|.++.
T Consensus 25 ~~r~~il~~l~~~~~~~~~~l~~~~~~~~~~v~~hL~~L~~~-glv~~~~~~~~~~~~l~~~~ 86 (110)
T COG0640 25 PTRLEILSLLAEGGELTVGELAEALGLSQSTVSHHLKVLREA-GLVELRREGRLRLYRLADEK 86 (110)
T ss_pred HHHHHHHHHHHhcCCccHHHHHHHHCCChhHHHHHHHHHHHC-CCeEEEecccEEEEecCcHH
Confidence 445678888876545567889999999999999999999986 999984433 3445555554
No 170
>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=76.84 E-value=7.4 Score=29.82 Aligned_cols=46 Identities=13% Similarity=0.095 Sum_probs=39.2
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
+-.+||..|+.. ..+.+++.+..|++.+.+.-.+..|... |+|.-.
T Consensus 6 ~~~~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~-GiI~Rk 51 (72)
T PF05584_consen 6 VTQKILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKR-GIIERK 51 (72)
T ss_pred HHHHHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCeeee
Confidence 456788888755 7788999999999999999999999976 998754
No 171
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=76.72 E-value=5.4 Score=37.05 Aligned_cols=63 Identities=17% Similarity=0.047 Sum_probs=48.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++..+.+.+ +...-|+.+|+.+.+|.+.++.||+.-| +..-.+....++||+.|+.+++.
T Consensus 18 ~L~~f~~va~~g--s~s~AA~~L~iSQpavS~~I~~LE~~lG-~~LF~R~~r~~~LT~~G~~l~~~ 80 (311)
T PRK10086 18 KLHTFEVAARHQ--SFALAADELSLTPSAVSHRINQLEEELG-IKLFVRSHRKVELTEEGKRVFWA 80 (311)
T ss_pred HHHHHHHHHHcC--CHHHHHHHHCCCHHHHHHHHHHHHHHhC-CeeEEEcCCCcccCHhHHHHHHH
Confidence 445555555444 3466788899999999999999997533 57777788999999999998753
No 172
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=76.64 E-value=5.5 Score=37.35 Aligned_cols=64 Identities=14% Similarity=-0.017 Sum_probs=48.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
+.+++.++.+.+ +...-|+.+++++.+|.+.++.||+.-|. ..-.+....+.||+.|+.++...
T Consensus 15 ~L~~F~~v~e~g--s~s~AA~~L~iSQpavS~~I~~LE~~lG~-~LF~R~~~~~~LT~~G~~l~~~a 78 (310)
T PRK15092 15 LLRTFVAVADLN--TFAAAAAAVCRTQSAVSQQMQRLEQLVGK-ELFARHGRNKLLTEHGIQLLGYA 78 (310)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCc-ceEEECCCCceECHhHHHHHHHH
Confidence 455666665544 35667888999999999999999987444 55556777889999999987444
No 173
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=76.51 E-value=3.9 Score=37.26 Aligned_cols=62 Identities=11% Similarity=0.022 Sum_probs=46.2
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++..+.+.+ +...-|+.+++++.+|.+.++.||..=|.-=+++ . ..++||++|+.+++.
T Consensus 5 ~l~~f~~v~~~~--s~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R-~-r~~~lT~~G~~l~~~ 66 (292)
T TIGR03298 5 QLAALAAVVEEG--SFERAAAALSVTPSAVSQRIKALEERLGQPLLVR-T-QPCRATEAGQRLLRH 66 (292)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCchheec-C-CCCcCCHhHHHHHHH
Confidence 345555565544 4567788899999999999999997655444455 4 589999999998744
No 174
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=76.51 E-value=5.2 Score=36.86 Aligned_cols=57 Identities=19% Similarity=0.267 Sum_probs=45.4
Q ss_pred HHHHHHHhccCCC-CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346 6 TEKILKYLDTNPP-VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE 64 (292)
Q Consensus 6 e~~iL~~L~~~~~-~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE 64 (292)
-.+||.+|...+. ....++|+.+|++.+.+-+.+..|... |||.-... ...|.|+..
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~-G~v~~d~~-~g~Y~Lg~~ 63 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVEL-GYVEQDPE-DGRYRLGPR 63 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHC-CCEEEcCC-CCcEeehHH
Confidence 3568888876444 468999999999999999999999987 99986544 446777754
No 175
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=76.45 E-value=5.3 Score=36.89 Aligned_cols=66 Identities=8% Similarity=-0.043 Sum_probs=49.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCCh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSH 74 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlP 74 (292)
+.+++..+.+.+ +...-|+.+|+.+.+|.+.++.||+.-|. ..-.+....+.||++|+.++....+
T Consensus 5 ~L~~F~~v~~~~--S~s~AA~~L~isQ~avS~~I~~LE~~lg~-~LF~R~~r~v~lT~~G~~l~~~a~~ 70 (305)
T PRK11233 5 RLKYFVKIVDIG--SLTQAAEVLHIAQPALSQQVATLEGELNQ-QLLIRTKRGVTPTEAGKILYTHARA 70 (305)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCCCchHHHHHHHHHHHHhCC-ceEEeCCCCceECHhHHHHHHHHHH
Confidence 344555555444 45678888999999999999999987555 4444566889999999998865544
No 176
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=76.35 E-value=3.3 Score=37.62 Aligned_cols=63 Identities=14% Similarity=0.108 Sum_probs=47.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++..+.+.+ +...-|+.+++.+.+|.+.++.||+.-|. ..-.+....+.||+.|+..++.
T Consensus 5 ~L~~f~~v~~~g--s~s~AA~~L~itqpavS~~Ik~LE~~lg~-~LF~R~~r~~~lT~~G~~l~~~ 67 (291)
T TIGR03418 5 ALRVFESAARLA--SFTAAARELGSTQPAVSQQVKRLEEELGT-PLFERGHRGIELTEDGQRLFEA 67 (291)
T ss_pred HHHHHHHHHHhC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCc-HHhhcCCCceeEcHhHHHHHHH
Confidence 345555555544 45678889999999999999999987443 4455667789999999988643
No 177
>PLN02265 probable phenylalanyl-tRNA synthetase beta chain
Probab=75.99 E-value=2.8 Score=43.66 Aligned_cols=46 Identities=28% Similarity=0.268 Sum_probs=36.9
Q ss_pred CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCC
Q psy10346 216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQ 262 (292)
Q Consensus 216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~Pq 262 (292)
..|..||+.++.+.+|+.|.++||.|+-+-+.+ +.--||+.++.|.
T Consensus 392 ~~g~~~~~~~~~~~iR~~l~~~Gf~Ev~t~sl~-s~~~~~~~~~~~~ 437 (597)
T PLN02265 392 TVGKQQPLNQFSDLLRAEVAMAGFTEVLTWILC-SHKENFAMLNRED 437 (597)
T ss_pred cCCCCCHHHHHHHHHHHHHHHCCceeeeceeeC-ChHHHHHhhcCCc
Confidence 458899999999999999999999998765554 4446688776653
No 178
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=75.96 E-value=5.5 Score=35.51 Aligned_cols=61 Identities=13% Similarity=0.132 Sum_probs=43.2
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+++.++...+ +...-|+.+++.+.+|.+.++.||..-|.-=..+.... +.||++|+.++..
T Consensus 7 ~~F~~v~~~~--s~t~AA~~L~isqsavS~~I~~LE~~lg~~Lf~R~~~~-~~lT~~G~~l~~~ 67 (297)
T COG0583 7 RAFVAVAEEG--SFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTRR-VRLTEAGERLLER 67 (297)
T ss_pred HHHHHHHHcC--cHHHHHHHhCCCChHHHHHHHHHHHHhCchheeecCCc-eeeCHhHHHHHHH
Confidence 4444554433 34667888999999999999999976454333443333 9999999998743
No 179
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=75.82 E-value=4.1 Score=33.43 Aligned_cols=47 Identities=13% Similarity=0.152 Sum_probs=37.7
Q ss_pred HHHHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 6 TEKILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 6 e~~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
..++|..|.. ++.++..++|..+|++...|.+.+..|+.. |+|....
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~-Gli~~~~ 59 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLA-GIVTSKR 59 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHC-CcEEecC
Confidence 3456667743 345788999999999999999999999986 9997643
No 180
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=75.73 E-value=7.2 Score=35.94 Aligned_cols=65 Identities=20% Similarity=0.085 Sum_probs=49.4
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
.+.+++..+.+.+ +....|..+++++.+|.+.++.||..-|. ..-.+....++||+.|+..++..
T Consensus 8 ~~L~~f~~v~e~g--s~s~AA~~L~isqpavS~~i~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~~a 72 (305)
T CHL00180 8 DQLRILKAIATEG--SFKKAAESLYISQPAVSLQIKNLEKQLNI-PLFDRSKNKASLTEAGELLLRYG 72 (305)
T ss_pred HHHHHHHHHHHcC--CHHHHHHHhcCCChHHHHHHHHHHHHhCC-EEEEecCCCceECHhHHHHHHHH
Confidence 4456666666655 34667888999999999999999987555 44455677899999999987544
No 181
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=75.32 E-value=3.8 Score=35.81 Aligned_cols=51 Identities=8% Similarity=0.193 Sum_probs=38.9
Q ss_pred CCChHHHHHh---c-CCCHHHHHHHHHHhhccCCcEEEe--eeeEEEEEeChhHHHHh
Q psy10346 18 PVDTLDLAKL---F-NEDHQKVVGGMKSIETLGEYLIVE--PLSHKIWELTGEGNQVK 69 (292)
Q Consensus 18 ~~~~~ela~~---~-~~~~~~v~~~~~~L~s~~glv~~e--~~~~~~~~LTeEG~~yl 69 (292)
+++..++..- . -++-=.+..++..|.+. |+|..+ ......|.+|++|++.+
T Consensus 15 pltn~qit~~iL~~~~~nYF~lqq~l~eL~es-~~i~~~~~~~~~~~y~iTe~G~~tl 71 (163)
T PF14277_consen 15 PLTNSQITEFILENEYTNYFTLQQALSELVES-GLITLETDSDNKTRYSITEKGKETL 71 (163)
T ss_pred CCCHHHHHHHHHhcCcccHHHHHHHHHHHHHC-CCEEEeeccCCCcEEEECHhhHHHH
Confidence 4555555432 2 35677888999999987 999986 56679999999999876
No 182
>PRK09801 transcriptional activator TtdR; Provisional
Probab=75.11 E-value=5.8 Score=36.99 Aligned_cols=65 Identities=12% Similarity=0.029 Sum_probs=49.0
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGS 73 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~Gl 73 (292)
+.+++..+.+.+ +...-|+.+|+.+.+|.+.++.||+.=|. ..-.+....+.||+.|+.++....
T Consensus 10 ~L~~F~~v~~~g--s~t~AA~~L~iSQpavS~~I~~LE~~LG~-~Lf~R~~r~~~lT~~G~~l~~~a~ 74 (310)
T PRK09801 10 DLQVLVEIVHSG--SFSAAAATLGQTPAFVTKRIQILENTLAT-TLLNRSARGVALTESGQRCYEHAL 74 (310)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCcCHHHHHHHHHHHHHHhCC-EeeeecCCCCcccHhHHHHHHHHH
Confidence 445555555444 34667888999999999999999986454 555667889999999999885543
No 183
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=75.03 E-value=6.4 Score=28.76 Aligned_cols=35 Identities=11% Similarity=0.149 Sum_probs=31.3
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
++.+++|..+|+..+.|.+.++.|+.. |+|.+...
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~-g~I~~~~~ 63 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDE-GIIEVKRG 63 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHT-TSEEEETT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEcCC
Confidence 567999999999999999999999986 99997655
No 184
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=74.99 E-value=7.7 Score=36.60 Aligned_cols=66 Identities=8% Similarity=-0.129 Sum_probs=49.5
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
+.+.+.+-.+.+.+ +...-|+.+++++.+|...++.||..-|. ..-.+....+.||++|+.+++.-
T Consensus 6 ~rqL~~F~aVae~g--Sfs~AA~~L~isQpavS~~Ik~LE~eLG~-~LF~R~~r~~~LT~aG~~ll~~a 71 (297)
T PRK15243 6 NKKLKIFITLMETG--SFSIATSVLYITRTPLSRVISDLERELKQ-RLFIRKNGTLIPTEFAQTIYRKV 71 (297)
T ss_pred HHHHHHHHHHHHcC--CHHHHHHHHCcCHHHHHHHHHHHHHHhCC-ccEEeCCCCeeECHHHHHHHHHH
Confidence 34455555555544 35667888999999999999999976444 55666888999999999987443
No 185
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=74.16 E-value=7.1 Score=36.39 Aligned_cols=64 Identities=13% Similarity=0.126 Sum_probs=45.2
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
+.+++..+...+. +...-|+.+++++.+|.+.++.||+.-|.-=.++.....+.||+.|+..+.
T Consensus 5 ~l~~f~~v~~~~~-s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~l~~ 68 (316)
T PRK12679 5 QLKIIREAARQDY-NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLV 68 (316)
T ss_pred HHHHHHHHHHcCC-CHHHHHHHhcCCchHHHHHHHHHHHHhCCEEEEECCCcccccCHhHHHHHH
Confidence 4455555543321 346678889999999999999999875554445544444789999998763
No 186
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=74.03 E-value=4.1 Score=37.67 Aligned_cols=52 Identities=21% Similarity=0.072 Sum_probs=39.7
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE-EeChhHHHHhhcC
Q psy10346 20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW-ELTGEGNQVKDNG 72 (292)
Q Consensus 20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~-~LTeEG~~yl~~G 72 (292)
+...-|+.+|+++.+|.+.++.||+.-|.-= -.+....+ .||+.|+.++...
T Consensus 18 s~s~AA~~L~isq~avSr~I~~LE~~lg~~L-F~R~~~~~~~lT~~G~~l~~~~ 70 (309)
T PRK12682 18 NLTEAAKALHTSQPGVSKAIIELEEELGIEI-FIRHGKRLKGLTEPGKAVLDVI 70 (309)
T ss_pred CHHHHHHHhcCccHHHHHHHHHHHHHhCCee-EEECCCCcCccCHhHHHHHHHH
Confidence 3567888899999999999999998755533 34444454 8999999987443
No 187
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=73.83 E-value=5.8 Score=36.44 Aligned_cols=63 Identities=13% Similarity=0.068 Sum_probs=48.6
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++..+.+.+ +...-|+.+++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.+++.
T Consensus 5 ~L~~f~~v~~~g--S~s~AA~~L~itQpavS~~i~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~~~ 67 (305)
T PRK11151 5 DLEYLVALAEHR--HFRRAADSCHVSQPTLSGQIRKLEDELGV-MLLERTSRKVLFTQAGLLLVDQ 67 (305)
T ss_pred HHHHHHHHHHhC--CHHHHHHHhCCCchHHHHHHHHHHHHhCc-hheeeCCCceeECccHHHHHHH
Confidence 445666665554 45677888999999999999999976444 4456689999999999998743
No 188
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=73.57 E-value=4.2 Score=37.74 Aligned_cols=63 Identities=17% Similarity=0.132 Sum_probs=49.2
Q ss_pred HHHHHHHHhc---cCCCCChHHHHHhcCCCHHHHHHHHH-HhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 5 LTEKILKYLD---TNPPVDTLDLAKLFNEDHQKVVGGMK-SIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 5 ~e~~iL~~L~---~~~~~~~~ela~~~~~~~~~v~~~~~-~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
.+..+|.++. .++.....++|..+|.++..+.+.+. .|-.+ |+|. ....-.+.|.+|.+|+.+
T Consensus 239 ~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~-~li~---~~~~g~~~~~~~~~~~~~ 305 (305)
T TIGR00635 239 IDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQI-GFLQ---RTPRGRIATELAYEHLGL 305 (305)
T ss_pred HHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHc-CCcc---cCCchhhhhHHHHHHhCC
Confidence 4555666552 34557789999999999999999888 58776 9994 666677899999999863
No 189
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=73.57 E-value=7.7 Score=32.25 Aligned_cols=56 Identities=9% Similarity=-0.032 Sum_probs=41.9
Q ss_pred HHHHHHhcc---CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346 7 EKILKYLDT---NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63 (292)
Q Consensus 7 ~~iL~~L~~---~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe 63 (292)
.++|..|.. ++.+++.++|+..+++..-+...+..|... |+|...+-..--|.|+.
T Consensus 11 l~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~-glv~s~~G~~Ggy~l~~ 69 (135)
T TIGR02010 11 VTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA-GLVKSVRGPGGGYQLGR 69 (135)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC-CceEEEeCCCCCEeccC
Confidence 445666642 335788999999999999999999999976 99986544444555553
No 190
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=73.46 E-value=6.8 Score=35.83 Aligned_cols=64 Identities=13% Similarity=0.004 Sum_probs=48.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
+.+++..+.+.+ +...-|+.+++.+.+|.+.++.||..-|. ..-.+....+.||+.|+.++...
T Consensus 10 ~l~~f~~v~~~g--s~s~AA~~L~isq~avS~~i~~LE~~lg~-~Lf~R~~r~l~lT~~G~~l~~~~ 73 (297)
T PRK11139 10 ALRAFEAAARHL--SFTRAAEELFVTQAAVSHQIKALEDFLGL-KLFRRRNRSLLLTEEGQRYFLDI 73 (297)
T ss_pred HHHHHHHHHHhC--CHHHHHHHhCCChHHHHHHHHHHHHHhCc-hheEecCCceeECHhHHHHHHHH
Confidence 445555555444 35677888999999999999999986554 44566678899999999987554
No 191
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=72.88 E-value=7.3 Score=34.20 Aligned_cols=43 Identities=12% Similarity=0.098 Sum_probs=35.5
Q ss_pred CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+...++|+.+|++...|-.++..|++. |+|++....-..+
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~e-Glv~~~~~~G~~V 74 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEA-GLVRNEKNRGVFV 74 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHC-CCEEEecCCCeEE
Confidence 445666899999999999999999999987 9999876654443
No 192
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=72.71 E-value=6.9 Score=32.73 Aligned_cols=44 Identities=7% Similarity=0.095 Sum_probs=38.8
Q ss_pred CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
.+...++|+.+|++..-|..++..|... |+|+..+-..--|.|+
T Consensus 25 ~~s~~~ia~~~~is~~~vrk~l~~L~~~-Glv~s~~G~~GG~~l~ 68 (141)
T PRK11014 25 MTSISEVTEVYGVSRNHMVKIINQLSRA-GYVTAVRGKNGGIRLG 68 (141)
T ss_pred ccCHHHHHHHHCcCHHHHHHHHHHHHhC-CEEEEecCCCCCeeec
Confidence 4567999999999999999999999986 9999988887777776
No 193
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=72.70 E-value=8.6 Score=34.20 Aligned_cols=43 Identities=5% Similarity=-0.072 Sum_probs=35.8
Q ss_pred CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+...++|+.+|++...|-.++..|++. |+|++....-..+
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~e-Glv~~~~~~G~~V 70 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVAE-RLVTVVNQKGYRV 70 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHHC-CCEEEeCCCceEe
Confidence 445777899999999999999999999987 9999876654433
No 194
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=71.98 E-value=8.5 Score=35.26 Aligned_cols=61 Identities=11% Similarity=0.061 Sum_probs=46.1
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
+.+++..+.+.+ +...-|+.+|+.+.+|.+.++.||+.-|..=.++ . ..++||+.|+..++
T Consensus 6 ~L~~f~~v~e~g--s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R-~-~~~~lT~~G~~l~~ 66 (294)
T PRK03635 6 QLEALAAVVREG--SFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-T-QPCRPTEAGQRLLR 66 (294)
T ss_pred HHHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeec-C-CCCccCHHHHHHHH
Confidence 445555555544 3567788899999999999999998766554555 4 48999999998864
No 195
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=71.93 E-value=12 Score=26.96 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=29.7
Q ss_pred CC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 18 PV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 18 ~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
.+ +..++|+.+|++...|..++..|++. |+|.....
T Consensus 23 ~lps~~~la~~~~vsr~tvr~al~~L~~~-g~i~~~~~ 59 (64)
T PF00392_consen 23 RLPSERELAERYGVSRTTVREALRRLEAE-GLIERRPG 59 (64)
T ss_dssp BE--HHHHHHHHTS-HHHHHHHHHHHHHT-TSEEEETT
T ss_pred EeCCHHHHHHHhccCCcHHHHHHHHHHHC-CcEEEECC
Confidence 35 66899999999999999999999987 99987654
No 196
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=71.40 E-value=8.4 Score=35.84 Aligned_cols=64 Identities=16% Similarity=0.112 Sum_probs=45.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE-EeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW-ELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~-~LTeEG~~yl~~ 71 (292)
+.+++.++.+.+ -+...-|+.+|+++.+|.+.++.||+.-|.-=+.+ ....+ +||+.|+.+++.
T Consensus 5 ~L~~F~~v~~~~-~S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R-~~r~~~~lT~~G~~l~~~ 69 (309)
T PRK12683 5 QLRIIREAVRQN-FNLTEVANALYTSQSGVSKQIKDLEDELGVEIFIR-RGKRLTGLTEPGKELLQI 69 (309)
T ss_pred HHHHHHHHHHcc-CCHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEee-CCCCcCCcCHHHHHHHHH
Confidence 445555554332 03466788899999999999999998766544444 44555 899999988743
No 197
>TIGR02681 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein.
Probab=71.20 E-value=4.7 Score=32.93 Aligned_cols=55 Identities=20% Similarity=0.388 Sum_probs=38.3
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccC-----C---cEEE-----eeeeEEEEEeChhHHHHhhcCC
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLG-----E---YLIV-----EPLSHKIWELTGEGNQVKDNGS 73 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~-----g---lv~~-----e~~~~~~~~LTeEG~~yl~~Gl 73 (292)
.+|.++|+..|-.|..|++.++.|.... + +... .......|.||.+|-..|--|.
T Consensus 14 ttS~~IAe~fgK~H~~VlR~Ir~l~~~~~~~~f~~~~F~~~~y~~~~g~~~~~Y~ltkdgf~lLvmg~ 81 (108)
T TIGR02681 14 TDSLTMAQMFGKRHDNVIRDIKVLLIEANETEFGQLNFEETQYQDEQNKKQPMFNLTEDGFTIVAMGY 81 (108)
T ss_pred EeHHHHHHHHCcchHHHHHHHHHHHhhhccccccccCceeeEEEcCCCcEEEEEEEcCCceEEEEecC
Confidence 5889999999999999999999995321 1 1111 1233467888888866665553
No 198
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=71.03 E-value=4.1 Score=42.41 Aligned_cols=68 Identities=13% Similarity=0.302 Sum_probs=51.4
Q ss_pred HHHHHHHHhccCCCCChHHHHH----hcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH--hhcCChH
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAK----LFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV--KDNGSHE 75 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~----~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y--l~~GlPE 75 (292)
-|..||..+-..+.+..+++.+ ..|.+...+..++.+|+++ |+|++ -..-.++||+-|+.. +-.|-|+
T Consensus 433 ~E~~vl~kiP~~~~i~~~~~~e~~~d~~~~ee~~i~~AL~kLEAr-GfI~~--Lp~g~iilTeaG~~ik~Alsg~p~ 506 (591)
T PF04458_consen 433 YEMEVLHKIPDKGYIHREELVEFIKDHVGKEEEEIIEALEKLEAR-GFIEI--LPNGMIILTEAGELIKRALSGVPE 506 (591)
T ss_pred HHHHHHHhCCccccccHHHHHHHhhcccccchHHHHHHHHHHHhc-chHHH--cCCCcEEEehhhHHHHHHHhcCCc
Confidence 3566777776666555555544 4677888899999999998 99865 456678999999876 5578888
No 199
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=70.00 E-value=9.8 Score=35.08 Aligned_cols=42 Identities=12% Similarity=0.188 Sum_probs=38.6
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIET 44 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s 44 (292)
+..+.+|+..|..++.+...+||+.+|++...|-+.+..|+.
T Consensus 6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~ 47 (252)
T PRK10681 6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSA 47 (252)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 456788999999999999999999999999999999999984
No 200
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=69.83 E-value=12 Score=35.57 Aligned_cols=56 Identities=13% Similarity=0.109 Sum_probs=42.9
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
...+||..|..+......++|+.+|++...|.+.++.|++. |++-..... .-|.|.
T Consensus 5 r~~~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~-G~~i~~~~~-~Gy~L~ 60 (319)
T PRK11886 5 VMLQLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEW-GLDIFSVKG-KGYRLA 60 (319)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCceEEecC-CeEEec
Confidence 46789999987666778899999999999999999999986 884333222 245553
No 201
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha); InterPro: IPR019104 This entry represents a family of proteins which are encoded in temperate phages and bacterial prophage regions. They include the product of the late operon rha gene from lambdoid phage phi-80. The presence of this gene interferes with the infection of bacterial strains lacking the integration host factor that regulates the rha gene. Rha is thought to function as a phage regulatory protein.
Probab=69.46 E-value=6.9 Score=30.63 Aligned_cols=55 Identities=16% Similarity=0.241 Sum_probs=40.3
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccC-----Cc----EEE-----eeeeEEEEEeChhHHHHhhcCC
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLG-----EY----LIV-----EPLSHKIWELTGEGNQVKDNGS 73 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~-----gl----v~~-----e~~~~~~~~LTeEG~~yl~~Gl 73 (292)
.+|.++|+..|..|..|++.+..+.... |. ..+ ..+....|.||+.|--.|-.|.
T Consensus 2 ~tS~~IAe~~gk~H~~Vlr~I~~~~~~~~~~~~~~~~f~~~~~y~~~~gr~~~~y~Ltk~g~~lL~~~~ 70 (93)
T PF09669_consen 2 TTSREIAEMFGKRHKNVLRDIRKLIEKECSPEFGQLNFFIESKYKDGQGRSYPCYLLTKDGFTLLVMGY 70 (93)
T ss_pred CCHHHHHHHHCccHHHHHHHHHHHHhhhcchhhhhccCcceeeeECCCCcEeEEEEEccChhheehhhh
Confidence 4789999999999999999999998430 11 111 1224668899999987776663
No 202
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=69.09 E-value=11 Score=29.47 Aligned_cols=43 Identities=12% Similarity=0.106 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHhhccCCcEEEeee--eEEEEEeChhHHHHhhcC
Q psy10346 29 NEDHQKVVGGMKSIETLGEYLIVEPL--SHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 29 ~~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~LTeEG~~yl~~G 72 (292)
+++...+.+.+..|-.. |++..... ....+.||+.|+++++..
T Consensus 53 ~~~~~~~~~li~~Li~~-g~L~~~~~~~~~~~l~~~~~~~~~l~g~ 97 (106)
T PF09382_consen 53 DMSKDDWERLIRQLILE-GYLSEDNGGFAYPYLKLTPKGKELLNGK 97 (106)
T ss_dssp TS-HHHHHHHHHHHHHT-TSEEEEECCCCTEEEEE-GGGHHHHCTT
T ss_pred cCCHHHHHHHHHHHHHc-CCceecCCcccccEEEECHHHHHHHCCC
Confidence 46788999999999987 99988777 777999999999998654
No 203
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes.
Probab=68.69 E-value=5 Score=41.36 Aligned_cols=46 Identities=30% Similarity=0.444 Sum_probs=37.1
Q ss_pred CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCC
Q psy10346 216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQ 262 (292)
Q Consensus 216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~Pq 262 (292)
..|..+|...+.+.+|+.|.++||.|+-+-+.+ +...+|+.+.+|.
T Consensus 357 ~~~~~~~~~~~~~~ir~~L~~~Gf~E~itysf~-s~~~~~~~~~~~~ 402 (551)
T TIGR00471 357 TIGRLKPLNKVSDIIREIMVGLGFQEVIPLTLT-SEEVNFKRMRIED 402 (551)
T ss_pred ccCCcChHHHHHHHHHHHHHhCCceeeccceEc-cHHHHHHHhccCC
Confidence 447899999999999999999999999877765 5545567776654
No 204
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=68.41 E-value=8.7 Score=35.62 Aligned_cols=63 Identities=6% Similarity=-0.059 Sum_probs=47.3
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
+.+++.++.+.+. ...-|+.+++++.+|.+.++.||..-|. ..-.+....++||+.|+.++..
T Consensus 26 ~L~~f~avae~gs--~s~AA~~L~isQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~~~ 88 (314)
T PRK09508 26 LLTVFDAVMQEQN--ITRAAHNLGMSQPAVSNAVARLKVMFND-ELFVRYGRGIQPTARARQLFGP 88 (314)
T ss_pred HHHHHHHHHhcCC--HHHHHHHhCCCHHHHHHHHHHHHHhhCC-CcEEEcCCCCcCcHHHHHHHHH
Confidence 3445555554443 4567888999999999999999976444 5566667889999999998754
No 205
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=68.16 E-value=24 Score=27.92 Aligned_cols=56 Identities=14% Similarity=0.120 Sum_probs=41.9
Q ss_pred HHHHHHHhcc-CCCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEeeee--EEEEEeC
Q psy10346 6 TEKILKYLDT-NPPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVEPLS--HKIWELT 62 (292)
Q Consensus 6 e~~iL~~L~~-~~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e~~~--~~~~~LT 62 (292)
...||..|.. ....+.+++.+.+ +++...|-+.+..|.+. |+|...... ...|.++
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~-Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEA-GLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhC-CCEEEEEeCCCceEEEeC
Confidence 4678888865 4457888887765 68899999999999987 998864432 3566664
No 206
>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=66.88 E-value=25 Score=26.00 Aligned_cols=35 Identities=11% Similarity=0.192 Sum_probs=27.5
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
+....+|.+.|+..+-++.+++.|+|- |+|+....
T Consensus 5 lvas~iAd~~GiTRSvIVNALRKleSa-GvIesrSl 39 (61)
T PF08222_consen 5 LVASKIADRVGITRSVIVNALRKLESA-GVIESRSL 39 (61)
T ss_dssp E-HHHHHHHHT--HHHHHHHHHHHHHT-TSEEEEET
T ss_pred ehHHHHHHHhCccHHHHHHHHHHHHhc-Cceeeccc
Confidence 345789999999999999999999997 99986543
No 207
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=66.77 E-value=10 Score=35.46 Aligned_cols=64 Identities=9% Similarity=0.016 Sum_probs=47.0
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCC
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGS 73 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~Gl 73 (292)
.+++.++.+.+ +...-|+.+++++.+|.+.++.||..-|. ..-.+....+.||+.|+..++...
T Consensus 34 L~~f~av~e~g--s~s~AA~~L~isQpavS~~I~~LE~~lG~-~LF~R~~r~v~lT~~G~~l~~~~~ 97 (317)
T PRK11482 34 LTIFEAVYVHK--GIVNAAKILNLTPSAISQSIQKLRVIFPD-PLFIRKGQGVTPTAYATHLHEYIS 97 (317)
T ss_pred HHHHHHHHHcC--CHHHHHHHhCCChHHHHHHHHHHHHHhCC-cceEecCCCccCCHHHHHHHHHHH
Confidence 34444554444 35667888999999999999999986555 344456778999999998876543
No 208
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=66.17 E-value=9 Score=32.81 Aligned_cols=59 Identities=12% Similarity=0.092 Sum_probs=46.5
Q ss_pred HHHHHhcc---CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346 8 KILKYLDT---NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ 67 (292)
Q Consensus 8 ~iL~~L~~---~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~ 67 (292)
.+|-.|.. ++.+++.++|+..|+++.-+.+.+..|... |+|+..+=..-=|.|.....+
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka-GlV~S~rG~~GGy~Lar~~~~ 73 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA-GLVKSVRGKGGGYRLARPPEE 73 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc-CCEEeecCCCCCccCCCChHH
Confidence 45555543 225778999999999999999999999875 999998888888877755443
No 209
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.92 E-value=14 Score=32.86 Aligned_cols=48 Identities=10% Similarity=0.036 Sum_probs=40.5
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
-..|++.|...+.++.+++|..+|+....|-+++..|... |+|.....
T Consensus 20 ~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~-~li~~~k~ 67 (176)
T COG1675 20 AVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYED-GLISYRKK 67 (176)
T ss_pred hhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhC-CceEEEee
Confidence 3567777877677888999999999999999999999987 99986543
No 210
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=65.75 E-value=18 Score=28.19 Aligned_cols=47 Identities=13% Similarity=0.247 Sum_probs=38.3
Q ss_pred CCcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 1 MASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 1 m~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
|+.-.|-+ .+|..++..+..+||..++.+...|-..+..|..+ |-|.
T Consensus 1 M~~L~qlR--d~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~k-Gkve 47 (78)
T PRK15431 1 MASLIQVR--DLLALRGRMEAAQISQTLNTPQPMINAMLQQLESM-GKAV 47 (78)
T ss_pred CccHHHHH--HHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHC-CCeE
Confidence 44444444 67777888999999999999999999999999987 7655
No 211
>PRK00441 argR arginine repressor; Provisional
Probab=65.67 E-value=19 Score=31.03 Aligned_cols=73 Identities=12% Similarity=0.118 Sum_probs=54.5
Q ss_pred CcHHHHHHHHHhccCCCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEe-eeeEEEEEeChhHHHHhhcCChH
Q psy10346 2 ASDLTEKILKYLDTNPPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVE-PLSHKIWELTGEGNQVKDNGSHE 75 (292)
Q Consensus 2 ~~~~e~~iL~~L~~~~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e-~~~~~~~~LTeEG~~yl~~GlPE 75 (292)
....+..|+..|..++..+.++++..+ +++...|-|.++.| |++++. ..-...|.|..+.. . .+.
T Consensus 2 k~~R~~~I~~ll~~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~~L----~lvKv~~~~G~~~Y~l~~~~~----~-~~~ 72 (149)
T PRK00441 2 KVSRHAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIKEL----KLIKVLSNDGKYKYATISKTE----S-NLS 72 (149)
T ss_pred hHHHHHHHHHHHHHcCCCcHHHHHHHHHhcCCCcCHHHHHHHHHHc----CcEEeECCCCCEEEEeCcccc----c-chH
Confidence 345678899999888888889999986 88899999999998 588884 45567888866542 1 244
Q ss_pred HHHHhhcC
Q psy10346 76 VLVFNNVP 83 (292)
Q Consensus 76 ~rl~~~l~ 83 (292)
.++-..+.
T Consensus 73 ~~l~~~~~ 80 (149)
T PRK00441 73 DRLVNIFS 80 (149)
T ss_pred HHHHHHHH
Confidence 56666655
No 212
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=65.56 E-value=13 Score=31.60 Aligned_cols=36 Identities=3% Similarity=0.098 Sum_probs=31.8
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS 55 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~ 55 (292)
++-+++|..+|+..+.|.++++.|+.. |+|++....
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~-g~I~~~~~~ 179 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKK-KLISIHKKK 179 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHC-CCEEecCCE
Confidence 456999999999999999999999986 999987643
No 213
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=64.87 E-value=19 Score=33.67 Aligned_cols=64 Identities=19% Similarity=0.119 Sum_probs=48.1
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee----eEEEEEeChhHHHHh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL----SHKIWELTGEGNQVK 69 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~----~~~~~~LTeEG~~yl 69 (292)
..+.++|..+...+. ...-|+.+|+++.++-..++.|+..-|+-=+++. ......||++|+..+
T Consensus 19 ~~~l~~l~~v~~~gS--~s~AA~~l~~s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~~lT~~G~~l~ 86 (263)
T PRK10676 19 PRRISLLKQIALTGS--ISQGAKLAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGERLI 86 (263)
T ss_pred HHHHHHHHHHHHHCC--HHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCcEECHHHHHHH
Confidence 345677777766653 4567888999999999999999975455444444 145699999999988
No 214
>PRK12423 LexA repressor; Provisional
Probab=64.85 E-value=18 Score=32.23 Aligned_cols=56 Identities=13% Similarity=0.174 Sum_probs=43.7
Q ss_pred cHHHHHHHHHhcc----CC-CCChHHHHHhcCC-CHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 3 SDLTEKILKYLDT----NP-PVDTLDLAKLFNE-DHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 3 ~~~e~~iL~~L~~----~~-~~~~~ela~~~~~-~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+.+.+||..|.+ ++ .-+..++|+.+|+ +...|...+..|+.+ |+|+.........
T Consensus 5 t~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~-G~l~~~~~~~~~~ 66 (202)
T PRK12423 5 TPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEA-GLIEVVPNQARGI 66 (202)
T ss_pred CHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHC-CCEEecCCCccee
Confidence 5788899988864 22 2366899999995 899999999999987 9999876643333
No 215
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=64.47 E-value=23 Score=34.85 Aligned_cols=59 Identities=14% Similarity=0.024 Sum_probs=45.0
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
.++..|.-...++...+....|.+.+.+...+..|.+. |++..+ ...+.||++|..++.
T Consensus 328 ~~~l~LR~~~Gld~~~f~~~~g~~~~~~~~~l~~l~~~-gll~~~---~~~~~LT~~G~~~~d 386 (394)
T PRK08898 328 FMLNALRLTDGVPAHLFQERTGLPLAAIEPQLAAAEQR-GLLERD---HTRIRPTPLGQRFLN 386 (394)
T ss_pred HHHHHHHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEE---CCEEEEChhHhHHHH
Confidence 34455555555788888888898877788888899886 998854 357999999987653
No 216
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=63.98 E-value=11 Score=33.79 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=38.7
Q ss_pred HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCc
Q psy10346 4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEY 48 (292)
Q Consensus 4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~gl 48 (292)
...++||..|...+ .+++.++|+..|+++..|-+.+.+|+.. |.
T Consensus 16 ~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~-G~ 61 (213)
T PRK05472 16 PLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEF-GK 61 (213)
T ss_pred HHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhc-CC
Confidence 45678999998888 7899999999999999999999999865 64
No 217
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=63.97 E-value=12 Score=35.39 Aligned_cols=65 Identities=11% Similarity=0.068 Sum_probs=47.6
Q ss_pred HHHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE-EeChhHHHHhhcCC
Q psy10346 6 TEKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW-ELTGEGNQVKDNGS 73 (292)
Q Consensus 6 e~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~-~LTeEG~~yl~~Gl 73 (292)
+.+++.++.+. + +...-|+.+++++.+|.+.++.||+.-|. ..-.+....+ .||+.|+.+++...
T Consensus 5 ~L~~F~~vae~~g--S~s~AA~~L~isQpavS~~I~~LE~~lG~-~LF~R~~r~v~~LT~~G~~l~~~a~ 71 (327)
T PRK12680 5 QLRYLVAIADAEL--NITLAAARVHATQPGLSKQLKQLEDELGF-LLFVRKGRSLESVTPAGVEVIERAR 71 (327)
T ss_pred HHHHHHHHHHccC--CHHHHHHHhcCCchHHHHHHHHHHHHhCC-eEEEECCCcCCccCccHHHHHHHHH
Confidence 45566666552 3 35667888999999999999999987555 4445555667 49999999875543
No 218
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=63.39 E-value=32 Score=28.98 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=37.4
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346 20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ 67 (292)
Q Consensus 20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~ 67 (292)
+..++|..+|+++..|-++-..|+.. |+|.+.+..-+++ |+.|.+
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~e-G~i~t~rg~G~fV--~~~~~~ 81 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELERE-GIVETKRGKGTFV--TEDAKE 81 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEecCeeEEE--cCCchh
Confidence 55899999999999999999999986 9999887766554 555554
No 219
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=63.17 E-value=15 Score=31.73 Aligned_cols=38 Identities=8% Similarity=0.103 Sum_probs=32.2
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEE
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHK 57 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~ 57 (292)
++-.++|+.+|+.++.|.++++.|+.. |+|+.......
T Consensus 169 ~t~~~lA~~lG~tr~tvsR~l~~l~~~-gii~~~~~~i~ 206 (211)
T PRK11753 169 ITRQEIGRIVGCSREMVGRVLKMLEDQ-GLISAHGKTIV 206 (211)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEecCCEEE
Confidence 344899999999999999999999986 99998765543
No 220
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=63.12 E-value=11 Score=39.37 Aligned_cols=43 Identities=16% Similarity=0.279 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHhhccCCcEEEee-ee-EEEEEeChhHHHHhhcC
Q psy10346 29 NEDHQKVVGGMKSIETLGEYLIVEP-LS-HKIWELTGEGNQVKDNG 72 (292)
Q Consensus 29 ~~~~~~v~~~~~~L~s~~glv~~e~-~~-~~~~~LTeEG~~yl~~G 72 (292)
.-+.+.+-.++.+|+|. ++|+.+. .. +..|.||+.|++.+++-
T Consensus 326 ~~~~d~l~~~Ly~LEsf-~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 326 RKNFDDLRESLYSLESF-GLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred hcchhHHHHHHHHHHhh-hhHHhhhhccCceeEEechhHHHHHHhh
Confidence 44556688899999998 9998865 44 78899999999988643
No 221
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=62.94 E-value=16 Score=31.34 Aligned_cols=57 Identities=7% Similarity=0.023 Sum_probs=44.9
Q ss_pred HHHHHhcc--CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346 8 KILKYLDT--NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65 (292)
Q Consensus 8 ~iL~~L~~--~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG 65 (292)
++|-.|.. ++.+.+.++|+..|+++.-+.+.+..|... |+|+..+-..-=|.|+..-
T Consensus 12 r~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a-Glv~S~rG~~GGy~La~~p 70 (153)
T PRK11920 12 RMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEA-GLVETVRGRNGGVRLGRPA 70 (153)
T ss_pred HHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeecCCCCCeeecCCH
Confidence 45555542 334678999999999999999999999865 9999988877777776443
No 222
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=62.92 E-value=9.3 Score=33.95 Aligned_cols=39 Identities=18% Similarity=0.183 Sum_probs=33.6
Q ss_pred CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346 16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS 55 (292)
Q Consensus 16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~ 55 (292)
+..+...+||+.+|++...|-.++..|++. |+|++....
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L~~e-GLV~~~~~~ 70 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRLVSV-NALSVAPAQ 70 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHHHHC-CCEEecCCC
Confidence 445777899999999999999999999987 999986554
No 223
>PRK05660 HemN family oxidoreductase; Provisional
Probab=62.63 E-value=24 Score=34.48 Aligned_cols=57 Identities=11% Similarity=0.153 Sum_probs=43.9
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
++-.|.....++...+....|.+..+....+..|.+. |++..+ ...+.||++|.-++
T Consensus 312 ~~~~Lr~~~G~~~~~~~~~~g~~~~~~~~~l~~l~~~-gl~~~~---~~~~~lt~~G~~~~ 368 (378)
T PRK05660 312 FMNRFRLLEAAPRADFEAYTGLPESVIRPQLDEALAQ-GYLTET---ADHWQITEHGKLFL 368 (378)
T ss_pred HHHhchhccCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEe---CCEEEECcchhHHH
Confidence 4444554445788888888999887788889999987 998854 45799999998765
No 224
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=62.43 E-value=8.7 Score=32.10 Aligned_cols=47 Identities=9% Similarity=0.085 Sum_probs=38.4
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH 56 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~ 56 (292)
.|..|.+.+++.|.++....|+.+-.|.=|+++|+.. |.|+..+.++
T Consensus 32 tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~-gWV~~R~eKK 78 (124)
T COG4738 32 TLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLREN-GWVDEREEKK 78 (124)
T ss_pred HHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHc-cccchHHhcc
Confidence 4556667778888888888999999999999999987 9999765443
No 225
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=62.24 E-value=14 Score=34.28 Aligned_cols=63 Identities=14% Similarity=0.047 Sum_probs=43.9
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEE-EEeChhHHHHhh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI-WELTGEGNQVKD 70 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~-~~LTeEG~~yl~ 70 (292)
+.+++..+...+. +...-|+.+++++.+|.+.++.||+.=|.-=..+ .... +.||+.|+.+++
T Consensus 5 ~L~~f~~v~~~g~-S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~R-~~r~~~~lT~~G~~l~~ 68 (313)
T PRK12684 5 QLRFVREAVRQNF-NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTR-HGKRLRGLTEPGRIILA 68 (313)
T ss_pred HHHHHHHHHHcCC-CHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEEE-cCCcccccChhHHHHHH
Confidence 4455555554431 2456788899999999999999997655433344 4444 589999998874
No 226
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=62.13 E-value=29 Score=33.55 Aligned_cols=60 Identities=18% Similarity=0.102 Sum_probs=43.5
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHH-HHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQ-KVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~-~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..++..|.....++...+.+..|.+.. .+...+..|.+. |++..+ ...+.||++|..++.
T Consensus 306 ~~~~~~lr~~~g~~~~~~~~~~~~~~~~~~~~~l~~l~~~-gl~~~~---~~~~~lT~~G~~~~~ 366 (374)
T PRK05799 306 EFMFMGLRKIKGICIEDFKKRFGKNIYEVYGEVINKYIKL-GLLIEK---EGRIYLSERGIEVSN 366 (374)
T ss_pred HHHHHHHHhhCCcCHHHHHHHHCcCHHHHHHHHHHHHHHC-CCEEEE---CCEEEEChhHHHHHH
Confidence 345555655556788888888888754 455678888876 998864 357999999998764
No 227
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=60.41 E-value=21 Score=32.02 Aligned_cols=54 Identities=11% Similarity=0.201 Sum_probs=43.5
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI 58 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~ 58 (292)
.+-.+++..|..++.+...++|.++|++...|-+.+..|+.. |.|....-.--.
T Consensus 13 ~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~-~~v~~~~~~pp~ 66 (183)
T PHA03103 13 ELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQRE-GMVYMSDSNPPK 66 (183)
T ss_pred HHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhc-CceecCCCCCCC
Confidence 345677888887777888999999999999999999999976 888765444333
No 228
>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 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=60.25 E-value=31 Score=26.70 Aligned_cols=62 Identities=21% Similarity=0.273 Sum_probs=44.9
Q ss_pred HHHHHHHHHhcc---CCCCChHHHHHhcCCCHHHHHHHHH--HhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDT---NPPVDTLDLAKLFNEDHQKVVGGMK--SIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~---~~~~~~~ela~~~~~~~~~v~~~~~--~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
....++|+.|.. ++++-.+.+|..+|.+.+.+...+. .|+ . |+|.-..+-. ++|+.|.+|+.
T Consensus 8 ~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq-~-G~I~RT~rGR---~~T~~a~~~l~ 74 (76)
T PF05491_consen 8 ELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQ-I-GFIQRTPRGR---VATPKAYEHLG 74 (76)
T ss_dssp HHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHH-T-TSEEEETTEE---EE-HHHHHHTT
T ss_pred HHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHH-h-hhHhhCccHH---HhHHHHHHHhC
Confidence 567889999954 6778899999999999988877765 444 3 8987555444 79999999874
No 229
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=59.67 E-value=29 Score=34.69 Aligned_cols=60 Identities=17% Similarity=0.147 Sum_probs=44.1
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHH---HHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQK---VVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~---v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
...++..|.....++...+.+..|.+... +...+..|++. |+|..+ ...+.||+.|+-++
T Consensus 369 ~~~~~~~L~~~~~ld~~~~~~~~g~~~~~~~~~~~~l~~l~~~-gl~~~~---~~~~~lT~~G~~~~ 431 (453)
T PRK13347 369 RRAIIETLMCNFPVDLAAIAARHGFFARYFLDELARLEPLAAD-GLVTID---GGGIRVTPEGRPLI 431 (453)
T ss_pred HHHHHHHHHhhCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHC-CCEEEE---CCEEEECcchhHHH
Confidence 34455556555667888888889988543 35677888886 998865 34799999998876
No 230
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=59.55 E-value=9.4 Score=35.94 Aligned_cols=61 Identities=10% Similarity=0.031 Sum_probs=43.0
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE-EeChhHHHHh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW-ELTGEGNQVK 69 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~-~LTeEG~~yl 69 (292)
.+.+.++.+.+. +...-|+.+++++.+|.+.++.||+.-|. ..-.+....+ .||+.|+.++
T Consensus 6 L~~f~avae~g~-S~s~AA~~L~iSQpavS~~I~~LE~~lG~-~LF~R~~r~~~~LT~~G~~l~ 67 (324)
T PRK12681 6 LRYIVEVVNHNL-NVSATAEGLYTSQPGISKQVRMLEDELGI-QIFARSGKHLTQVTPAGEEII 67 (324)
T ss_pred HHHHHHHHHccC-CHHHHHHHhcCCcHHHHHHHHHHHHHhCC-EeEEECCCCCCccCHHHHHHH
Confidence 444454543320 34567888999999999999999986554 4444445555 7999999986
No 231
>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 [].; PDB: 2WTE_A 3SQN_A.
Probab=59.06 E-value=15 Score=26.35 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=33.9
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhc
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIET 44 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s 44 (292)
.+.+||..|-+++.+...++|..+|++...+...+..|..
T Consensus 6 rq~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 6 RQLKLLELLLKNKWITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4677899997677788899999999999999999999973
No 232
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=58.89 E-value=6 Score=40.36 Aligned_cols=67 Identities=19% Similarity=0.281 Sum_probs=45.4
Q ss_pred HHHHHHHHHhcc-------CC--CCCh--HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE--EEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDT-------NP--PVDT--LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH--KIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~-------~~--~~~~--~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~--~~~~LTeEG~~yl~ 70 (292)
..|.++|+.++. ++ ++.. ..+-...+++.- |--++++|+|. |+|+.+..+. -.|+||+.|++.++
T Consensus 284 ~dE~rlLk~IdkL~kk~e~~~~Peik~iek~~~~e~k~~Dl-vt~aL~~LEs~-glik~ev~k~g~l~yvlTe~Gekvle 361 (593)
T COG1542 284 EDEIRLLKAIDKLKKKHETNPAPEIKPIEKEIKWETKIDDL-VTAALYTLESF-GLIKREVVKNGDLTYVLTEFGEKVLE 361 (593)
T ss_pred hhHHHHHHHHHHHHhhhccCCCcccchHHHHhhHHhcccch-HHHHHHhhhhc-cchhhhhhhcCceEEEehhhhHHHHh
Confidence 456777777643 11 1111 234445666544 88999999998 9998755443 47999999999886
Q ss_pred cC
Q psy10346 71 NG 72 (292)
Q Consensus 71 ~G 72 (292)
.+
T Consensus 362 ~l 363 (593)
T COG1542 362 DL 363 (593)
T ss_pred cc
Confidence 55
No 233
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=58.77 E-value=29 Score=31.56 Aligned_cols=43 Identities=9% Similarity=0.050 Sum_probs=35.0
Q ss_pred CCCCC-hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPVD-TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~~-~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+. -.+||+.+|++...|-.++..|++. |+|++....-..+
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~e-GlV~~~~~~G~~V 73 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEIK-GLVEVRRGAGIYV 73 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEecCCEEEE
Confidence 44463 4689999999999999999999997 9999877654444
No 234
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=58.37 E-value=22 Score=31.10 Aligned_cols=53 Identities=9% Similarity=0.080 Sum_probs=39.8
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChHHH
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
.+..++|+.+|++...|.++++.|+.+ +++.-. ..-.|.+.+.= +=+|+.-.+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~-~iI~k~--~~G~Y~iNP~~---~~kG~~~~~ 128 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEK-NIIKKI--RNGAYMINPNF---FFKGDRDKR 128 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhC-CcEEEc--cCCeEEECcHH---heeCcHHHH
Confidence 355789999999999999999999987 888643 44578888752 335655443
No 235
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=58.10 E-value=24 Score=31.56 Aligned_cols=34 Identities=9% Similarity=0.144 Sum_probs=29.7
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
++-.++|..+|+.++.|.++++.|+.. |+|+...
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~-GlI~~~~ 213 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDR-GLIGLSG 213 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHC-CcEEecC
Confidence 345899999999999999999999986 9998654
No 236
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=58.09 E-value=19 Score=33.44 Aligned_cols=61 Identities=11% Similarity=-0.094 Sum_probs=46.0
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
+.+++.++.+.+ +...-|+.+++++.+|.+.++.||..-|. ..-.+......||+.|+...
T Consensus 12 ~L~~f~av~e~g--s~t~AA~~L~iSQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~ 72 (319)
T PRK10216 12 LLLCLQLLMQER--SVTKAAKRMNVTPSAVSKSLAKLRAWFDD-PLFVNTPLGLSPTPLMVSME 72 (319)
T ss_pred HHHHHHHHHHhC--CHHHHHHHhCCCHHHHHHHHHHHHHHhCC-ceEEecCCCcccCHHHHHHH
Confidence 445566665555 35667888999999999999999986444 55566677799999998653
No 237
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=58.06 E-value=28 Score=34.65 Aligned_cols=57 Identities=21% Similarity=0.199 Sum_probs=43.1
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
++..|.....++...+.+..|.+.......+..|.+. |++..+ ...+.||++|+.+.
T Consensus 352 ~~~~Lr~~~gl~~~~~~~~~g~~~~~~~~~l~~l~~~-gll~~~---~~~l~lT~~G~~~~ 408 (430)
T PRK08208 352 IIKSLLQAQGLDLADYRQRFGSDPLRDFPELELLIDR-GWLEQN---GGRLRLTEEGLALS 408 (430)
T ss_pred HHHHHHHhCCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEE---CCEEEECcchhhHH
Confidence 4444544556788888888999877677788888876 998864 45799999998764
No 238
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=57.69 E-value=29 Score=30.24 Aligned_cols=46 Identities=9% Similarity=-0.068 Sum_probs=37.5
Q ss_pred CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeC
Q psy10346 16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELT 62 (292)
Q Consensus 16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LT 62 (292)
++.+.+.++|+..|++..-+...+..|... |||...+-..--|.|.
T Consensus 23 ~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a-GLv~s~rG~~GGy~La 68 (164)
T PRK10857 23 AGPVPLADISERQGISLSYLEQLFSRLRKN-GLVSSVRGPGGGYLLG 68 (164)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeCCCCCCCeecc
Confidence 345789999999999999999999999976 9999765555555554
No 239
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=57.55 E-value=24 Score=31.80 Aligned_cols=55 Identities=5% Similarity=0.065 Sum_probs=40.2
Q ss_pred HHHHHHHHHhccCCCCCh-HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 4 DLTEKILKYLDTNPPVDT-LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~-~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+..+|...+..+..+-+ .+||+.+|++...|-+|+..|... |+|.-..-.-+++
T Consensus 20 ~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~e-Gli~r~~G~GtfV 75 (241)
T PRK10079 20 KLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEK-GWVQRRQGVGVLV 75 (241)
T ss_pred HHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCEEEE
Confidence 344445443444444544 689999999999999999999986 9999766665554
No 240
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=57.53 E-value=26 Score=31.39 Aligned_cols=43 Identities=7% Similarity=0.075 Sum_probs=35.3
Q ss_pred CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+ +-.+||+.+|++...|-.++..|++. |+|.+....-.++
T Consensus 28 G~~LPsE~eLae~~gVSRt~VReAL~~L~~e-Glv~~~~g~G~~V 71 (239)
T PRK04984 28 GSILPAERELSELIGVTRTTLREVLQRLARD-GWLTIQHGKPTKV 71 (239)
T ss_pred CCcCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeCCCeeEe
Confidence 3345 34689999999999999999999987 9999877765554
No 241
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=57.43 E-value=19 Score=30.89 Aligned_cols=35 Identities=11% Similarity=0.023 Sum_probs=30.5
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
++-+++|..+|+..+.|.+.++.|+.. |+|.....
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~-g~I~~~~~ 184 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSRE-GYIRSGYG 184 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHC-CCEEcCCC
Confidence 455899999999999999999999986 99986543
No 242
>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 [].; PDB: 1BJA_B 1I1S_A.
Probab=57.18 E-value=37 Score=27.24 Aligned_cols=59 Identities=10% Similarity=0.073 Sum_probs=40.2
Q ss_pred HHHHHhccCCCCChHHHHHhc--CCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 8 KILKYLDTNPPVDTLDLAKLF--NEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~--~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
.||-.+.+++-+++.+++... .+...+|-+-+.-|-.+ |||+-.- .-|.+|++|...+.
T Consensus 20 ~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKk-glIEKSG---DGlv~T~~g~~Ii~ 80 (96)
T PF09114_consen 20 NILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKK-GLIEKSG---DGLVITEEGMDIII 80 (96)
T ss_dssp HHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHT-TSEEEET---TEEEE-HHHHHHHH
T ss_pred HHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHc-CcccccC---CceEEechHHHHHH
Confidence 456666667777888888865 56677888877777755 9987433 33999999998763
No 243
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=57.03 E-value=23 Score=27.50 Aligned_cols=39 Identities=21% Similarity=0.310 Sum_probs=29.6
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIE 43 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~ 43 (292)
+-.-+|..|..+.++...++|...|.+.+.|..++..+-
T Consensus 25 L~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 25 LLRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 445688999999999999999999999999999888774
No 244
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=56.92 E-value=19 Score=34.97 Aligned_cols=64 Identities=23% Similarity=0.348 Sum_probs=51.7
Q ss_pred HHHHHHHH-----HhccCCCCChHHHHHh--cCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 4 DLTEKILK-----YLDTNPPVDTLDLAKL--FNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 4 ~~e~~iL~-----~L~~~~~~~~~ela~~--~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
+-++.||. ++..++++.+.++++. +|++...|-+.+..|++. |++. ......-...|+.|-+|-
T Consensus 2 ~R~~~il~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~-G~l~-~~h~sagript~kGYR~y 72 (337)
T TIGR00331 2 ERQRKILKAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDL-GFIE-KPHTSSGRIPTDKGYRYY 72 (337)
T ss_pred hHHHHHHHHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHC-CCcc-CCCCCCCcCcChhHHHHH
Confidence 34677885 6677888999999999 888999999999999987 9986 355556667888877763
No 245
>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 salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=56.67 E-value=24 Score=25.27 Aligned_cols=42 Identities=19% Similarity=0.138 Sum_probs=31.4
Q ss_pred HHHHHHHHHhccCC------CCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 4 DLTEKILKYLDTNP------PVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 4 ~~e~~iL~~L~~~~------~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
+.|.++|..--..| .++..++|+.+|++.+.+..-+..-+++
T Consensus 3 ~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 3 DRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAERK 50 (53)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 45667776554333 3678999999999999998888877654
No 246
>PF14502 HTH_41: Helix-turn-helix domain
Probab=56.49 E-value=22 Score=25.16 Aligned_cols=34 Identities=12% Similarity=0.161 Sum_probs=30.4
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
...++++++++..-.|-.+++.|++. |-|.++.+
T Consensus 8 tI~e~~~~~~vs~GtiQ~Alk~Le~~-gaI~Le~r 41 (48)
T PF14502_consen 8 TISEYSEKFGVSRGTIQNALKFLEEN-GAIKLESR 41 (48)
T ss_pred CHHHHHHHhCcchhHHHHHHHHHHHC-CcEEeeec
Confidence 45899999999999999999999987 99988764
No 247
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=56.05 E-value=37 Score=28.42 Aligned_cols=18 Identities=17% Similarity=0.577 Sum_probs=16.9
Q ss_pred CchhhHHHHHHHcCCeec
Q psy10346 97 PNAKVGFSKAMAKGWISL 114 (292)
Q Consensus 97 ~~~~ig~~~a~k~gwi~i 114 (292)
|+.+||+.+++.+|||..
T Consensus 56 PEVSiAMr~Lre~gWV~~ 73 (124)
T COG4738 56 PEVSIAMRYLRENGWVDE 73 (124)
T ss_pred chhHHHHHHHHHccccch
Confidence 789999999999999987
No 248
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=55.85 E-value=38 Score=32.77 Aligned_cols=60 Identities=13% Similarity=0.201 Sum_probs=43.4
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHH-HHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQK-VVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~-v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..++..|.....++...+....|.+..+ +...+..|.+. |++... ...+.||++|+.++.
T Consensus 307 ~~~~~~Lr~~~gl~~~~~~~~~~~~~~~~~~~~~~~l~~~-gl~~~~---~~~~~lt~~G~~~~~ 367 (377)
T PRK08599 307 EEMFLGLRKKSGVSKARFEEKFGQSFEDVFGETIQELQEQ-GLLEED---DDHVRLTKKGKFLGN 367 (377)
T ss_pred HHHHHhHHhhCCcCHHHHHHHHCcCHHHHHHHHHHHHHHC-CCEEEE---CCEEEECccHhHHHH
Confidence 3455555545567888888888888555 55678888876 998864 457999999987653
No 249
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=55.69 E-value=16 Score=32.25 Aligned_cols=42 Identities=10% Similarity=0.079 Sum_probs=33.9
Q ss_pred cCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 28 FNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 28 ~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
+++.+.+|.+.++.||..-|. ..-.+....++||+.|+.+++
T Consensus 1 L~isQpavS~~I~~LE~~lg~-~Lf~R~~r~~~lT~~G~~l~~ 42 (269)
T PRK11716 1 MHVSPSTLSRQIQRLEEELGQ-PLFVRDNRSVTLTEAGEELRP 42 (269)
T ss_pred CCcChHHHHHHHHHHHHHhCC-eeEEecCCceeECHhHHHHHH
Confidence 467889999999999987554 445557788999999998763
No 250
>PF13518 HTH_28: Helix-turn-helix domain
Probab=55.01 E-value=29 Score=23.22 Aligned_cols=38 Identities=13% Similarity=0.099 Sum_probs=29.2
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCc
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEY 48 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~gl 48 (292)
+|+....+ +. +..++|..+|+++..|-++++..+.. |+
T Consensus 4 ~iv~~~~~-g~-s~~~~a~~~gis~~tv~~w~~~y~~~-G~ 41 (52)
T PF13518_consen 4 QIVELYLE-GE-SVREIAREFGISRSTVYRWIKRYREG-GI 41 (52)
T ss_pred HHHHHHHc-CC-CHHHHHHHHCCCHhHHHHHHHHHHhc-CH
Confidence 34444443 33 77899999999999999999999875 65
No 251
>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 kDa, 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 (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. 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.; PDB: 2XV4_S 2XUB_A.
Probab=54.51 E-value=35 Score=24.86 Aligned_cols=48 Identities=6% Similarity=0.009 Sum_probs=38.2
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
+-.+|...|-..|.....++.+..++++..|-.++-.|-.. |+|....
T Consensus 14 ~~~~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh-~~v~y~~ 61 (62)
T PF08221_consen 14 IVAKVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQH-NLVQYFE 61 (62)
T ss_dssp HHHHHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHT-TSEEEEE
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHc-CCeeeec
Confidence 45577888877888888999999999999999999999987 9998653
No 252
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=54.23 E-value=22 Score=31.53 Aligned_cols=59 Identities=7% Similarity=0.008 Sum_probs=41.7
Q ss_pred HHHHHHHHHhcc---CCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346 4 DLTEKILKYLDT---NPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65 (292)
Q Consensus 4 ~~e~~iL~~L~~---~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG 65 (292)
+.+.+|...|.. .+. .+-.++|+.+|+..+.|.+.++.|+.. |+|+..... ...+..++
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~-G~I~~~~~~--i~I~d~~~ 213 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD-GYLKKSKRG--YLIKNRKQ 213 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC-CCEEeeCCE--EEEeCHHH
Confidence 445666665532 122 345899999999999999999999986 999987643 34444444
No 253
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=53.82 E-value=33 Score=33.09 Aligned_cols=65 Identities=15% Similarity=0.166 Sum_probs=54.3
Q ss_pred HHHHHHHHHhccCCC----CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 4 DLTEKILKYLDTNPP----VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~----~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
+...+||.+++.+-. +-.+.+.+...++.+++...++.|-.. ++|.-......-|.||-.|-++|
T Consensus 13 ~~D~rlLraiE~~mR~~e~VP~~~i~~~ar~~~~~~~~~L~~L~~l-~lv~r~~~~y~Gy~lT~~GyD~L 81 (304)
T COG0478 13 KEDFRLLRAIEGGMRSHEWVPLELIKKRARMDEEELLYRLKRLDKL-KLVSRRTISYEGYQLTFSGYDAL 81 (304)
T ss_pred HHHHHHHHHHHhcccccccccHHHHHHHcCCCHHHHHHHHHHHHhc-CceeccCCcceeEEEEecchhHH
Confidence 567889999975322 455788888999999999999999877 89988777888999999999987
No 254
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=53.69 E-value=27 Score=30.56 Aligned_cols=45 Identities=16% Similarity=0.087 Sum_probs=38.0
Q ss_pred CChHHHHHhc--CCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHH
Q psy10346 19 VDTLDLAKLF--NEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGN 66 (292)
Q Consensus 19 ~~~~ela~~~--~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~ 66 (292)
-+..++|+.+ +++.+.|-.++..|... |+|+-... ..|+.|+..-
T Consensus 40 ~d~~~iak~l~p~is~~ev~~sL~~L~~~-gli~k~~~--g~y~~t~~~l 86 (171)
T PF14394_consen 40 PDPEWIAKRLRPKISAEEVRDSLEFLEKL-GLIKKDGD--GKYVQTDKSL 86 (171)
T ss_pred CCHHHHHHHhcCCCCHHHHHHHHHHHHHC-CCeEECCC--CcEEEeccee
Confidence 3889999999 99999999999999987 99886544 6788887653
No 255
>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: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=53.49 E-value=18 Score=25.63 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=23.8
Q ss_pred HHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHH
Q psy10346 7 EKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGM 39 (292)
Q Consensus 7 ~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~ 39 (292)
+++|+.|...|. +.+.++|+.+|++...|-+.+
T Consensus 15 ~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 15 LRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 567888876554 789999999999998876654
No 256
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=52.94 E-value=13 Score=28.88 Aligned_cols=34 Identities=12% Similarity=0.033 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 32 HQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 32 ~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..+++.++..|-.| |+|.--.-. .||++|.+.++
T Consensus 33 ~p~~i~a~~RLheK-GLI~~pdGg----yLT~~G~~~aE 66 (77)
T TIGR02647 33 SPAAVAAAARLHEK-GLTTQPDGG----YLTSLGLEAAE 66 (77)
T ss_pred CHHHHHHHHHHHHc-CCccCCCCC----EecHHHHHHHH
Confidence 35788999999987 999854433 89999998764
No 257
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=51.88 E-value=21 Score=30.31 Aligned_cols=43 Identities=19% Similarity=0.153 Sum_probs=34.9
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
.||.+|-.++.+.-++||..+|++...|-+.+..|... +++.+
T Consensus 5 ~v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed-~~~~~ 47 (147)
T smart00531 5 LVLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDE-KLIKI 47 (147)
T ss_pred eehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhh-hcchh
Confidence 46677766677788999999999999999999999974 45443
No 258
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=51.77 E-value=25 Score=31.47 Aligned_cols=43 Identities=7% Similarity=0.075 Sum_probs=35.2
Q ss_pred CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+ +-.++|+.+|++...|-.++..|++. |+|++....-..+
T Consensus 27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~e-GlV~~~~~~G~~V 70 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLREVLQRLARD-GWLTIQHGKPTKV 70 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEEeCCCccEe
Confidence 4456 55789999999999999999999987 9999877654433
No 259
>PRK03837 transcriptional regulator NanR; Provisional
Probab=51.66 E-value=28 Score=31.02 Aligned_cols=43 Identities=7% Similarity=0.105 Sum_probs=35.0
Q ss_pred CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+ .-.++|+.+|++...|-.++..|++. |+|++....-..+
T Consensus 34 G~~Lp~E~~Lae~~gVSRt~VREAL~~L~~e-Glv~~~~~~G~~V 77 (241)
T PRK03837 34 GDQLPSERELMAFFGVGRPAVREALQALKRK-GLVQISHGERARV 77 (241)
T ss_pred CCCCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEecCCceeE
Confidence 3345 45789999999999999999999997 9999976654443
No 260
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=51.53 E-value=45 Score=32.83 Aligned_cols=59 Identities=15% Similarity=0.250 Sum_probs=43.1
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHH--HHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKV--VGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v--~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..|+..|.-...++..++.+..|.+.... ...+..|... |++.. . ..+.||++|..++.
T Consensus 322 e~i~l~LR~~~Gl~~~~~~~~~g~~~~~~~~~~~l~~l~~~-gll~~-~---~~l~lT~~G~~~~d 382 (390)
T PRK06582 322 EILMMGLRLSKGINISTLEQKLNTKLENILDMNNLKHYQAL-DLIRL-D---ENIYLTDKGLMLHS 382 (390)
T ss_pred HHHHHHHHhhCCCCHHHHHHHHCcCHHHhhhHHHHHHHHHC-CCEEE-C---CEEEECcchhHHHH
Confidence 34555565555678888888899886653 4778888876 99886 2 45999999988763
No 261
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=51.41 E-value=31 Score=31.16 Aligned_cols=43 Identities=5% Similarity=0.014 Sum_probs=35.3
Q ss_pred CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+ +-.+||+.+|++...|-.++..|++. |+|++....-.++
T Consensus 28 G~~LPsE~eLa~~~gVSRtpVREAL~~L~~e-GlV~~~~~~G~~V 71 (251)
T PRK09990 28 GQALPSERRLCEKLGFSRSALREGLTVLRGR-GIIETAQGRGSFV 71 (251)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeCCCeeEE
Confidence 3346 44699999999999999999999987 9999987654444
No 262
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=51.33 E-value=34 Score=23.16 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=30.5
Q ss_pred CcHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHH
Q psy10346 2 ASDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKS 41 (292)
Q Consensus 2 ~~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~ 41 (292)
+...+..|+..|... .+..++|..+|++...|.+.+..
T Consensus 13 T~~~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 13 TKRLEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHh
Confidence 346778888888754 46789999999999999988764
No 263
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=50.79 E-value=46 Score=33.30 Aligned_cols=60 Identities=13% Similarity=0.170 Sum_probs=43.0
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHH----HHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVV----GGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~----~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..++..|.....++...+.+..|.+..... ..+..|... |++..+ ...+.||++|..++.
T Consensus 369 ~~~~~~Lr~~~gl~~~~~~~~fg~~~~~~~~~~~~~l~~l~~~-gll~~~---~~~~~lT~~G~~~~d 432 (453)
T PRK09249 369 RDVIEQLMCNFELDFAAIEAAFGIDFAEYFAEELERLAPLEAD-GLVELD---ENGITVTPKGRLLVR 432 (453)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHC-CCEEEE---CCEEEECccchHHHH
Confidence 345555665666788888888898855433 345678876 998864 357999999998763
No 264
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=50.48 E-value=18 Score=24.41 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=22.6
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCc
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEY 48 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~gl 48 (292)
..++..+.. ..+..++|+.+|+++..|-++++...+. |+
T Consensus 8 ~~ii~l~~~--G~s~~~ia~~lgvs~~Tv~~w~kr~~~~-G~ 46 (50)
T PF13384_consen 8 AQIIRLLRE--GWSIREIAKRLGVSRSTVYRWIKRYREE-GL 46 (50)
T ss_dssp --HHHHHHH--T--HHHHHHHHTS-HHHHHHHHT--------
T ss_pred HHHHHHHHC--CCCHHHHHHHHCcCHHHHHHHHHHcccc-cc
Confidence 446666654 2467899999999999999999998764 65
No 265
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=50.42 E-value=34 Score=31.06 Aligned_cols=43 Identities=7% Similarity=0.016 Sum_probs=34.9
Q ss_pred CCCCC-hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPVD-TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~~-~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+. -.+||+.+|++...|-.++..|++. |+|++....-.++
T Consensus 23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~-GlV~~~~~~G~~V 66 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSRNSLREALAKLVSE-GVLLSRRGGGTFI 66 (253)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEeCCCeEEE
Confidence 44463 4699999999999999999999997 9999877654444
No 266
>PRK09350 poxB regulator PoxA; Provisional
Probab=50.09 E-value=16 Score=34.80 Aligned_cols=35 Identities=31% Similarity=0.339 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhhCCceecCCCCccccceeccccCCC
Q psy10346 224 MKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQ 260 (292)
Q Consensus 224 ~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~ 260 (292)
++++..||++|.+.||.|+.+ |.+ +.++++++...
T Consensus 9 ~~i~~~ir~~f~~~gf~EV~T-P~l-~~~~~~~~~~~ 43 (306)
T PRK09350 9 AKIIAEIRRFFADRGVLEVET-PIL-SQATVTDIHLV 43 (306)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-CeE-ecccCCCccCC
Confidence 578899999999999999964 655 66778887553
No 267
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=49.82 E-value=30 Score=30.59 Aligned_cols=36 Identities=8% Similarity=0.051 Sum_probs=31.6
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeee
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLS 55 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~ 55 (292)
++-.++|+-+|+..+.|.+.++.|+.. |+|......
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~-g~I~~~~~~ 220 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKS-GMLAVKGKY 220 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHC-CCEEecCCE
Confidence 455899999999999999999999986 999987753
No 268
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=49.62 E-value=19 Score=38.11 Aligned_cols=44 Identities=25% Similarity=0.300 Sum_probs=36.9
Q ss_pred CCChHHHHHHHHHHHhhhCCceecCCCCccccceeccccCCCCCC
Q psy10346 219 HLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSFWNFDALFQPQQ 263 (292)
Q Consensus 219 ~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f~NFD~L~~Pqd 263 (292)
..+++..+.+.+|+++.++||.|+-+.+.+ +..++++..+.+.+
T Consensus 349 ~~~~~~~~~r~vr~~l~~~G~~Evitysl~-s~e~~~~~~~~~~~ 392 (650)
T COG0072 349 GLTPLQKFRRKVRRALVGLGFQEVITYSLT-SPEEAKLFGLENDE 392 (650)
T ss_pred CCChHHHHHHHHHHHHHhCCcceEeeeccC-CHHHHHHhccCCCc
Confidence 389999999999999999999999876664 77788877776655
No 269
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=49.48 E-value=25 Score=32.26 Aligned_cols=45 Identities=13% Similarity=0.271 Sum_probs=38.2
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
...+||..|.... ....+++..+|+.+.+|+.-+..|+.. |+|+.
T Consensus 16 tRR~Il~lLt~~p-~yvsEiS~~lgvsqkAVl~HL~~LE~A-GlveS 60 (217)
T COG1777 16 TRRRILQLLTRRP-CYVSEISRELGVSQKAVLKHLRILERA-GLVES 60 (217)
T ss_pred HHHHHHHHHhcCc-hHHHHHHhhcCcCHHHHHHHHHHHHHc-CCchh
Confidence 4567888887554 667889999999999999999999975 99987
No 270
>PRK10736 hypothetical protein; Provisional
Probab=49.38 E-value=32 Score=34.06 Aligned_cols=47 Identities=13% Similarity=0.094 Sum_probs=39.1
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL 54 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~ 54 (292)
+..||..|.. .....++++..+|++...|...+..||-+ |+|.-..-
T Consensus 310 ~~~v~~~l~~-~~~~iD~L~~~~~l~~~~v~~~L~~LEl~-G~v~~~~g 356 (374)
T PRK10736 310 FPELLANVGD-EVTPVDVVAERAGQPVPEVVTQLLELELA-GWIAAVPG 356 (374)
T ss_pred HHHHHHhcCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHhC-CcEEEcCC
Confidence 5678888853 45678999999999999999999999986 99986544
No 271
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=49.35 E-value=36 Score=30.76 Aligned_cols=43 Identities=14% Similarity=0.177 Sum_probs=34.8
Q ss_pred CCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+ +-.+||+.+|++...|-.++..|++. |+|++....-.++
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~e-Glv~~~~~~G~~V 74 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAK-GLLLRRQGGGTFV 74 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHC-CCEEEecCceeEE
Confidence 3345 45789999999999999999999987 9999887654433
No 272
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=48.88 E-value=37 Score=30.76 Aligned_cols=43 Identities=16% Similarity=-0.017 Sum_probs=35.5
Q ss_pred CCCCCh-HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPVDT-LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~~~-~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..+.+ .+||+.+|++...|-.++..|++. |+|++....-..+
T Consensus 29 G~~LpsE~eLae~~gVSRtpVREAL~~L~~e-GlV~~~~~~G~~V 72 (253)
T PRK11523 29 GDKLPAERFIADEKNVSRTVVREAIIMLEVE-GYVEVRKGSGIHV 72 (253)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCeeEE
Confidence 445644 689999999999999999999987 9999887765544
No 273
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=48.38 E-value=64 Score=26.87 Aligned_cols=43 Identities=14% Similarity=0.140 Sum_probs=34.6
Q ss_pred CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346 18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63 (292)
Q Consensus 18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe 63 (292)
+.+.+++|..++-+.+.|..++.-|+.. |||++.+. ..+.++.
T Consensus 53 py~~e~LA~~~~~~~~~V~~AL~~f~k~-glIe~~ed--~~i~i~~ 95 (121)
T PF09681_consen 53 PYTAEMLALEFDRPVDTVRLALAVFQKL-GLIEIDED--GVIYIPN 95 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecC--CeEEeec
Confidence 4677999999999999999999999986 99998543 4444443
No 274
>PRK03341 arginine repressor; Provisional
Probab=47.55 E-value=48 Score=29.20 Aligned_cols=59 Identities=12% Similarity=0.214 Sum_probs=44.3
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEeeee-EE-EEEeChhH
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVEPLS-HK-IWELTGEG 65 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e~~~-~~-~~~LTeEG 65 (292)
...+..|+..|.+++..+-++|+..+ ++.+..|.|.++.|. ++++.... .. .|.|..+.
T Consensus 14 ~~R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiSRDl~eL~----~~Kv~~~~G~~~~Y~lp~~~ 79 (168)
T PRK03341 14 AARQARIVAILSRQSVRSQAELAALLADEGIEVTQATLSRDLDELG----AVKLRGADGGLGVYVVPEEG 79 (168)
T ss_pred HHHHHHHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHHHHHHHhc----CEeeecCCCCEEEEEecccc
Confidence 45677788888877777778998877 777899999999994 67765443 34 78886654
No 275
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=47.14 E-value=54 Score=31.41 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=42.2
Q ss_pred HHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEE
Q psy10346 5 LTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKI 58 (292)
Q Consensus 5 ~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~ 58 (292)
...+|+..|+..++ ++-.++.+..|++.+.|..++..|+.. |+|+-....-+.
T Consensus 5 ~reklir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~-giv~RrkvsGKs 59 (321)
T COG3888 5 LREKLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQ-GIVKRRKVSGKS 59 (321)
T ss_pred HHHHHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhc-CeeeeeeecCcc
Confidence 45567788876666 788899999999999999999999986 898765554333
No 276
>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, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=47.02 E-value=32 Score=33.39 Aligned_cols=59 Identities=17% Similarity=0.191 Sum_probs=41.2
Q ss_pred HHHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee----eeEEEEEeCh
Q psy10346 4 DLTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP----LSHKIWELTG 63 (292)
Q Consensus 4 ~~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~----~~~~~~~LTe 63 (292)
+.|+.|+.+++..+ .+-+.++-.+.|+.+..|.+.++.|+++ +||+.-. ..++.|.|.+
T Consensus 84 ~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k-~lIK~vksv~~~~rK~Yml~~ 148 (327)
T PF05158_consen 84 DEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESK-KLIKSVKSVKNPNRKVYMLYD 148 (327)
T ss_dssp CCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHT-TSEEEE--SS-SS--EEEESS
T ss_pred HHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhC-CCEEEecCcCCCCeEEEEEcc
Confidence 44667888886422 3667899999999999999999999997 8998643 3455776653
No 277
>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 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=47.00 E-value=35 Score=23.91 Aligned_cols=41 Identities=12% Similarity=0.170 Sum_probs=33.1
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
++.|.+||..+..+. +..++|..+|+++..|-.....+..+
T Consensus 5 T~~E~~vl~~l~~G~--~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 5 TERELEVLRLLAQGM--SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp -HHHHHHHHHHHTTS---HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHhcC--CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 467899999997653 57999999999999998888887654
No 278
>KOG3233|consensus
Probab=46.75 E-value=12 Score=35.63 Aligned_cols=58 Identities=12% Similarity=0.158 Sum_probs=43.2
Q ss_pred cHHHHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE----eeeeEEEEEe
Q psy10346 3 SDLTEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV----EPLSHKIWEL 61 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~----e~~~~~~~~L 61 (292)
++.|+.++..++..+. +-+-++-.+.|+++..|-+.+++|++| .||+. ....++.|.|
T Consensus 83 e~eEk~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsK-kLIKsVKsv~n~~~KvYmL 146 (297)
T KOG3233|consen 83 ENEEKLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESK-KLIKSVKSVKNSRKKVYML 146 (297)
T ss_pred ChHHHHHHHHHHHcCCCceeeehhhhccCCCHHHHHHHHHHHHHH-HHHHHHHhhcCCCceEEEE
Confidence 5778888888865432 566788888999999999999999998 78763 3333355544
No 279
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=46.32 E-value=57 Score=30.18 Aligned_cols=49 Identities=12% Similarity=0.057 Sum_probs=39.2
Q ss_pred HHHHHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 4 DLTEKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 4 ~~e~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
..-.+|...++. +-..+.+++|+.+|+++.++-+.+..|.+. |.+..+-
T Consensus 158 ~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~-~~l~a~i 207 (224)
T COG4565 158 LTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSN-GILEAEI 207 (224)
T ss_pred HHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhc-CeeeEEe
Confidence 345567777763 334678999999999999999999999997 8887654
No 280
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=45.02 E-value=55 Score=33.27 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=30.6
Q ss_pred HHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcC
Q psy10346 37 GGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNG 72 (292)
Q Consensus 37 ~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~G 72 (292)
..++.|..+ +||+..+.+...+.+|+.|.+++++|
T Consensus 156 ~~l~~LkkR-kL~~~~~~~~~~~~~~~~~~~~~~~~ 190 (489)
T PRK04172 156 KVLKELKKR-KLVEEKERTERSVELTDAGLELLKEG 190 (489)
T ss_pred HHHHHHHhc-CCeEEEEEEEEEEEEccchhhhhhcc
Confidence 357778765 89999999999999999999999887
No 281
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=44.95 E-value=45 Score=29.81 Aligned_cols=37 Identities=11% Similarity=0.130 Sum_probs=32.7
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+||..+|++...|-+|+..|... |+|.-..-.-+++
T Consensus 28 ~eLa~~~gVSR~TVR~Al~~L~~e-Gli~r~~G~GTfV 64 (233)
T TIGR02404 28 HELMDQYGASRETVRKALNLLTEA-GYIQKIQGKGSIV 64 (233)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeCCceEEE
Confidence 789999999999999999999987 9999777666655
No 282
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=44.70 E-value=38 Score=27.14 Aligned_cols=59 Identities=12% Similarity=0.117 Sum_probs=41.3
Q ss_pred HHHHHHHHHhccC-CCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEeee--eEEEEEeCh
Q psy10346 4 DLTEKILKYLDTN-PPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVEPL--SHKIWELTG 63 (292)
Q Consensus 4 ~~e~~iL~~L~~~-~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~LTe 63 (292)
.....||..|.+. +..+.+++...+ +++...|-+.+..|.+. |+|.--.. ....|.+..
T Consensus 8 ~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~-Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 8 PQRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEA-GLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHT-TSEEEEEETTSEEEEEESS
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHC-CeEEEEEcCCCcceEeecC
Confidence 4567799999653 356667776543 67889999999999987 99876433 356777765
No 283
>KOG2165|consensus
Probab=44.59 E-value=38 Score=36.30 Aligned_cols=67 Identities=9% Similarity=0.033 Sum_probs=52.2
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee--eEEEEEeChhHHHHhh
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL--SHKIWELTGEGNQVKD 70 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~LTeEG~~yl~ 70 (292)
++.+..|+....+.+.+..+++++..|++...+-+-+..+-++ |++.-+.. ..-.+.++|.+...-+
T Consensus 601 sp~qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~-GvL~e~~~~s~tgt~T~iEse~d~~q 669 (765)
T KOG2165|consen 601 SPEQAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQK-GVLREEPIISDTGTLTVIESEMDFDQ 669 (765)
T ss_pred CHHHHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHc-CeeecCCCCCCCceeeeccccccccc
Confidence 4667778888888888999999999999999999999999887 99876652 3455666665554433
No 284
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=43.94 E-value=44 Score=25.91 Aligned_cols=35 Identities=20% Similarity=0.234 Sum_probs=30.5
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGM 39 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~ 39 (292)
.-..+|+..|.. +.+...++|+..|++...|.+++
T Consensus 6 ~R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 6 ERVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 345679999988 88899999999999999998866
No 285
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=43.91 E-value=98 Score=26.22 Aligned_cols=62 Identities=15% Similarity=0.079 Sum_probs=44.6
Q ss_pred cHHHHHHHHHhccC-CCCChHHHHHh-----cCCCHHHHHHHHHHhhccCCcEEEeeee--EEEEEeChhH
Q psy10346 3 SDLTEKILKYLDTN-PPVDTLDLAKL-----FNEDHQKVVGGMKSIETLGEYLIVEPLS--HKIWELTGEG 65 (292)
Q Consensus 3 ~~~e~~iL~~L~~~-~~~~~~ela~~-----~~~~~~~v~~~~~~L~s~~glv~~e~~~--~~~~~LTeEG 65 (292)
......||.+|... +..+.+++-.. .+++...|-++++.|... |+|...... ...|.++.++
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~-Glv~~~~~~~~~~~y~~~~~~ 89 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEA-GLVHRLEFEGGKTRYELNSEP 89 (145)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHC-CCEEEEEeCCCEEEEecCCCC
Confidence 35677899999643 44666666433 457899999999999987 999886553 4667666554
No 286
>PRK14999 histidine utilization repressor; Provisional
Probab=43.66 E-value=45 Score=30.06 Aligned_cols=38 Identities=5% Similarity=0.076 Sum_probs=32.7
Q ss_pred hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 21 TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 21 ~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
-.+||+.+|++...|-+|+..|... |+|....-.-+++
T Consensus 39 E~eLa~~~gVSR~TVR~Al~~L~~e-Gli~r~~GkGTfV 76 (241)
T PRK14999 39 EAELVAQYGFSRMTINRALRELTDE-GWLVRLQGVGTFV 76 (241)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCcEEEE
Confidence 3789999999999999999999986 9998776666554
No 287
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=43.60 E-value=49 Score=29.56 Aligned_cols=37 Identities=8% Similarity=0.038 Sum_probs=32.7
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+||+.+|++...|-+|+..|... |+|....-.-+++
T Consensus 29 ~eLa~~~~VSR~TVR~Al~~L~~e-Gli~r~~G~GtfV 65 (230)
T TIGR02018 29 HELVAQYGCSRMTVNRALRELTDA-GLLERRQGVGTFV 65 (230)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCEEEE
Confidence 689999999999999999999986 9999877766665
No 288
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=43.25 E-value=57 Score=25.93 Aligned_cols=64 Identities=16% Similarity=0.165 Sum_probs=45.7
Q ss_pred HHHHHHHHhccCCCCC-hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE-------EEEEeChhHHHHh
Q psy10346 5 LTEKILKYLDTNPPVD-TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH-------KIWELTGEGNQVK 69 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~-~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~-------~~~~LTeEG~~yl 69 (292)
.-+.||-.+++..... .-....-.+.+.+.|.-.+..|... |+|....... ....||-+|-++|
T Consensus 6 lIR~iLl~iE~~~~~~~~~~~~~~~~y~~~~i~YHl~lL~ea-gli~~~~~~~~~~~~~~~i~~LT~~GHdFL 77 (102)
T PF10711_consen 6 LIRDILLEIEENPDPPNPIEEDEIDGYSKEEIAYHLKLLDEA-GLIEGSVSGTMNGPYSFIIKRLTWSGHDFL 77 (102)
T ss_pred HHHHHHHHHHcCCCcCcccchhcccCCCHHHHHHHHHHHHHC-CCeeeccccccCCccchhhcccChhHHHHH
Confidence 4467888887654321 1122333577889999999999986 9999876555 3469999999988
No 289
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=43.15 E-value=69 Score=24.18 Aligned_cols=59 Identities=15% Similarity=0.113 Sum_probs=36.3
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHh---cCC--CHHHHHHHHHHhhccCCcEEEe-eeeEEEEEeChhH
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKL---FNE--DHQKVVGGMKSIETLGEYLIVE-PLSHKIWELTGEG 65 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~---~~~--~~~~v~~~~~~L~s~~glv~~e-~~~~~~~~LTeEG 65 (292)
+..+..|+..|..+...+-++|... .|+ .+..|.+.++.| |++++. ......|.|-+++
T Consensus 4 ~~R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~vTQaTiSRDLkeL----~~vKv~~~~g~~~Y~l~~~~ 68 (70)
T PF01316_consen 4 SKRQELIKELISEHEISSQEELVELLEEEGIEVTQATISRDLKEL----GAVKVPDGNGKYRYVLPEET 68 (70)
T ss_dssp HHHHHHHHHHHHHS---SHHHHHHHHHHTT-T--HHHHHHHHHHH----T-EEEECTTSSEEEE-TTST
T ss_pred HHHHHHHHHHHHHCCcCCHHHHHHHHHHcCCCcchhHHHHHHHHc----CcEEeeCCCCCEEEEecCcC
Confidence 3456667777766554444666553 355 478899999988 588886 6667788887765
No 290
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=42.74 E-value=76 Score=25.00 Aligned_cols=61 Identities=16% Similarity=0.172 Sum_probs=47.7
Q ss_pred HHHHHHHHHhccCCCCChH----HHHHhcCCCHHHHHHHHHHhhccCCcEEE---eeeeEEEEEeChh
Q psy10346 4 DLTEKILKYLDTNPPVDTL----DLAKLFNEDHQKVVGGMKSIETLGEYLIV---EPLSHKIWELTGE 64 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~----ela~~~~~~~~~v~~~~~~L~s~~glv~~---e~~~~~~~~LTeE 64 (292)
.+...+|+.+-+.+..+++ .+++.++++...|.+.+-...|+=|++.+ .......|.|-|+
T Consensus 11 GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~ 78 (83)
T PF10826_consen 11 GIRRAVLKLFLKGKKFTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEK 78 (83)
T ss_pred cHHHHHHHHHHhCCCeeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHH
Confidence 3567788888777776654 45666788988899999999888899999 5567888888775
No 291
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=42.59 E-value=73 Score=31.85 Aligned_cols=63 Identities=24% Similarity=0.210 Sum_probs=42.6
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHH----HHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhcCChH
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVG----GMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDNGSHE 75 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~----~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~GlPE 75 (292)
++..|.....++...+....|.+.....+ .++.|... |++..+ ...+.||++|.-++.+=.++
T Consensus 371 ~~~~l~~~~gl~~~~~~~~~g~~~~~~~~~~~~~l~~l~~~-gll~~~---~~~~~lT~~G~~~~~~i~~~ 437 (455)
T TIGR00538 371 VIKSLMCNFKLDYSKIEEKFDLDFADYFAKELELLKPLEED-GLLDVD---EKGIEVTPKGRLLIRNIAMV 437 (455)
T ss_pred HHHHHHhcCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhC-CCEEEE---CCEEEECcCChHHHHHHHHH
Confidence 44444445567888888888888554333 45667776 998864 45799999999877543333
No 292
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=42.35 E-value=55 Score=29.41 Aligned_cols=37 Identities=11% Similarity=0.025 Sum_probs=32.3
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+||..+|++...|-+|+..|... |+|.-..-.-+++
T Consensus 37 ~eLa~~~~VSR~TvR~Al~~L~~e-Gli~r~~G~GTfV 73 (241)
T PRK11402 37 NELCTQYNVSRITIRKAISDLVAD-GVLIRWQGKGTFV 73 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCceeEE
Confidence 789999999999999999999986 9999776665555
No 293
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=41.72 E-value=59 Score=28.88 Aligned_cols=37 Identities=16% Similarity=0.166 Sum_probs=32.4
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+||+.+|++...|-+|+..|... |+|.-..-.-+++
T Consensus 36 ~eLa~~~~VSR~TvR~Al~~L~~e-Gli~r~~G~GtfV 72 (238)
T TIGR02325 36 MQLAERFGVNRHTVRRAIAALVER-GLLRAEQGRGTFV 72 (238)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCCEEEE
Confidence 699999999999999999999986 9999776666655
No 294
>KOG3054|consensus
Probab=41.66 E-value=65 Score=30.50 Aligned_cols=75 Identities=23% Similarity=0.295 Sum_probs=54.5
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE--eeeeEEEEEeChhHHHHhhcCChHHH--HHhhcC
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV--EPLSHKIWELTGEGNQVKDNGSHEVL--VFNNVP 83 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~--e~~~~~~~~LTeEG~~yl~~GlPE~r--l~~~l~ 83 (292)
....++.++..+..++||..+|+..+.+++-+..|... |+++- ..+-+-.| . |||.- +.++++
T Consensus 204 eFv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~e-g~ltGVmDDRGKfIY-I-----------S~eEl~AVAkfIk 270 (299)
T KOG3054|consen 204 EFVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAE-GLLTGVMDDRGKFIY-I-----------SMEELAAVAKFIK 270 (299)
T ss_pred HHHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHh-hhheeeecCCCceEE-e-----------cHHHHHHHHHHHH
Confidence 34566777888899999999999988888888888876 88764 22223333 2 45544 568888
Q ss_pred CCC-CChHHHhhc
Q psy10346 84 SEG-IGQKELLAT 95 (292)
Q Consensus 84 ~~~-~~~~el~~~ 95 (292)
..| +|+.+|.+.
T Consensus 271 qrGRVSIaelAe~ 283 (299)
T KOG3054|consen 271 QRGRVSIAELAEK 283 (299)
T ss_pred HcCceeHHHHHHh
Confidence 767 899998864
No 295
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=41.33 E-value=63 Score=27.41 Aligned_cols=47 Identities=11% Similarity=0.137 Sum_probs=41.3
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
.+..+|++.+..+|.++..+++..+|++...+-..+..|.+. |-|-.
T Consensus 12 eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~-G~l~~ 58 (127)
T PF06163_consen 12 ELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVAR-GDLYR 58 (127)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHc-CCeEe
Confidence 566789999999999999999999999999999999999987 66543
No 296
>PRK00037 hisS histidyl-tRNA synthetase; Reviewed
Probab=41.00 E-value=15 Score=35.91 Aligned_cols=36 Identities=19% Similarity=0.316 Sum_probs=30.4
Q ss_pred CCCCCCCChHHHHHHHHHHHhhhCCceecCCCCcccc
Q psy10346 214 SLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVES 250 (292)
Q Consensus 214 ~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves 250 (292)
...+...|+...+++.++++|...||.++. .|.+|.
T Consensus 12 d~~p~~~~~~~~i~~~i~~~~~~~Gy~ei~-tP~le~ 47 (412)
T PRK00037 12 DILPEESAKWQYVEDTIREVFERYGFSEIR-TPIFEY 47 (412)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHcCCeEee-ccccch
Confidence 455677889999999999999999999996 477755
No 297
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=40.88 E-value=95 Score=25.80 Aligned_cols=86 Identities=15% Similarity=0.252 Sum_probs=47.2
Q ss_pred HHHHHhhcCC-CCCChHHHhhcCC--------chhhHHHHHHHcCCeecccCcce--eeccCCCchHHHHHHHHHHh---
Q psy10346 75 EVLVFNNVPS-EGIGQKELLATFP--------NAKVGFSKAMAKGWISLDKATGK--VLRKVDSVTDELQAHLKLIA--- 140 (292)
Q Consensus 75 E~rl~~~l~~-~~~~~~el~~~~~--------~~~ig~~~a~k~gwi~i~~~~g~--v~~~~~~~~d~~~~~L~~i~--- 140 (292)
|..+++.|-. ++++..+|.+.++ ...--+..+.++|+|...+. |+ +....-.-.+..+..++.+.
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~-gr~~~Y~p~vs~ee~~~~~~~~~~~~~ 84 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKE-GRKFIYTALVSEDEAVENAAQELFSRI 84 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecC-CCcEEEEecCCHHHHHHHHHHHHHHHH
Confidence 6678888854 4588888665431 22334677889999987654 33 33332222233222222221
Q ss_pred -ccC----------CCCCChhhHHhhhcccceee
Q psy10346 141 -NNE----------YDKVPEANKVDYKKRKLLQE 163 (292)
Q Consensus 141 -~~~----------~~~l~~~~~~~LkkRkLv~~ 163 (292)
.|. .+.+++++++.|++ +|+.
T Consensus 85 f~gs~~~ll~~l~~~~~ls~eele~L~~--li~~ 116 (130)
T TIGR02698 85 CSRKVGAVIADLIEESPLSQTDIEKLEK--LLSE 116 (130)
T ss_pred HCCCHHHHHHHHHhcCCCCHHHHHHHHH--HHHh
Confidence 111 14678888887764 4544
No 298
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=40.73 E-value=1.1e+02 Score=24.22 Aligned_cols=45 Identities=13% Similarity=0.177 Sum_probs=36.2
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
-.+|++-+..-.-+++..+++.+++.-+-.-.+++.|+++ |+|..
T Consensus 29 ~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~k-G~Ik~ 73 (86)
T PRK09334 29 LKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKR-GVLVL 73 (86)
T ss_pred HHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHC-CCEEE
Confidence 3455555555556889999999999999899999999987 98865
No 299
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=40.66 E-value=11 Score=26.26 Aligned_cols=41 Identities=17% Similarity=0.252 Sum_probs=21.2
Q ss_pred HHHHHHhhhCCceecCC-CCccccceecccc-CCCCCCCCCCCC
Q psy10346 228 AEFRQIFLDMGFTEMPT-NNFVESSFWNFDA-LFQPQQHPARDA 269 (292)
Q Consensus 228 ~~i~~if~~mGF~e~~~-~~~Ves~f~NFD~-L~~PqdHPAR~~ 269 (292)
+++..+|...||++... |+.+-=...+-+. +.+| .||..++
T Consensus 2 ~el~k~L~~~G~~~~r~~GSH~~~~~~~~~~~~~vp-~h~~~ei 44 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVRQKGSHHIFRHPGGRKIVTVP-PHPGKEI 44 (56)
T ss_dssp HHHHHHHHHTT-EEEEEETTEEEEE-TTS-E-EEEE--SSS-S-
T ss_pred hHHHHHHHHCCCEEecCCCCEEEEEeCCCCcceEeC-CCCcccc
Confidence 57889999999987632 5654322222222 3455 6676654
No 300
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=40.47 E-value=61 Score=29.22 Aligned_cols=41 Identities=15% Similarity=0.045 Sum_probs=33.8
Q ss_pred CCCh-HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 18 PVDT-LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 18 ~~~~-~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+-+ .+||+.+|++...|-+|+..|... |+|.-..-.-+++
T Consensus 28 ~LPsE~eL~~~~~VSR~TvR~Al~~L~~e-Gli~r~~G~GtfV 69 (240)
T PRK09764 28 ALPTESALQTEFGVSRVTVRQALRQLVEQ-QILESIQGSGTYV 69 (240)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEecCceeEE
Confidence 3434 789999999999999999999986 9998766665554
No 301
>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 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=40.33 E-value=34 Score=25.65 Aligned_cols=40 Identities=23% Similarity=0.234 Sum_probs=29.4
Q ss_pred HHHHHHHHHhccCC----CCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346 4 DLTEKILKYLDTNP----PVDTLDLAKLFNEDHQKVVGGMKSIE 43 (292)
Q Consensus 4 ~~e~~iL~~L~~~~----~~~~~ela~~~~~~~~~v~~~~~~L~ 43 (292)
+.|++|...+-++. ..+..++|+.+|+++.+|+|-++.|-
T Consensus 16 ~~e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG 59 (77)
T PF01418_consen 16 PTEKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLG 59 (77)
T ss_dssp HHHHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCT
T ss_pred HHHHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhC
Confidence 45677777775433 35679999999999999999999995
No 302
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=38.94 E-value=1.1e+02 Score=29.56 Aligned_cols=53 Identities=13% Similarity=0.170 Sum_probs=37.6
Q ss_pred HHHHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChh
Q psy10346 7 EKILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGE 64 (292)
Q Consensus 7 ~~iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeE 64 (292)
..||..|.+ ...++..+++..+|+..++|+.++..| |+++... ....+.++.+
T Consensus 211 ~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l----~~l~~~~-g~~~i~~~~~ 264 (290)
T PLN03238 211 RVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL----NLIKYWK-GQHVIHVDQR 264 (290)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC----CcEEEEC-CcEEEEeCHH
Confidence 357777754 446788999999999999999998877 5776533 3334444433
No 303
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=38.87 E-value=29 Score=32.84 Aligned_cols=64 Identities=13% Similarity=0.108 Sum_probs=49.6
Q ss_pred HHHHHHHHHhc-c--CCCCChHHHHHhcCCCHHHHHHHHH-HhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 4 DLTEKILKYLD-T--NPPVDTLDLAKLFNEDHQKVVGGMK-SIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 4 ~~e~~iL~~L~-~--~~~~~~~ela~~~~~~~~~v~~~~~-~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
..+++.|.++. . ++.+..+.+|..+|.+.+.+...+. .|-.. |+|. ....--++|+.|.+|++.
T Consensus 259 ~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~-~li~---~~~~gr~~~~~~~~~~~~ 326 (328)
T PRK00080 259 EMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQ-GFIQ---RTPRGRVATPKAYEHLGL 326 (328)
T ss_pred HHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHc-CCcc---cCCchHHHHHHHHHHhCC
Confidence 35667776443 2 5568889999999999998888888 77765 8994 666667899999999864
No 304
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=38.18 E-value=52 Score=28.62 Aligned_cols=60 Identities=17% Similarity=0.187 Sum_probs=44.2
Q ss_pred HHHHHHhccCCCCChHHHHHhcCC-------CH-------HHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNE-------DH-------QKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~-------~~-------~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..||..+--.+.+-...++..+|. +. .-+-.++..|+.. |||+-.. .--+||+.|++.|.
T Consensus 56 AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~-glVek~~---~GR~lT~~G~~~LD 129 (150)
T PRK09333 56 ASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKA-GLVEKTK---KGRVITPKGRSLLD 129 (150)
T ss_pred HHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHC-CCeeeCC---CCCEeCHHHHHHHH
Confidence 356766655667778888888876 22 2367788999987 9998755 45579999998774
No 305
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=38.14 E-value=37 Score=31.04 Aligned_cols=37 Identities=19% Similarity=0.174 Sum_probs=33.0
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+|++.+|++...|-.+++.|+++ |+|++..-.-+++
T Consensus 38 reLae~fgVSR~~vREAl~~L~a~-Glve~r~G~Gt~V 74 (241)
T COG2186 38 RELAERFGVSRTVVREALKRLEAK-GLVEIRQGSGTFV 74 (241)
T ss_pred HHHHHHHCCCcHHHHHHHHHHHHC-CCeeecCCCceEe
Confidence 689999999999999999999997 9999877766655
No 306
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=37.58 E-value=99 Score=25.79 Aligned_cols=45 Identities=20% Similarity=0.301 Sum_probs=36.1
Q ss_pred HHHHHhccCC--------CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 8 KILKYLDTNP--------PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 8 ~iL~~L~~~~--------~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
-+|.++..+| +.+.+.+|..++-+.+.|.-|+.-++.. |+|.+.+
T Consensus 33 Lll~s~n~~G~L~~~~~ipy~~e~LA~~~~~~~~~V~~Al~~f~k~-glIe~~d 85 (119)
T TIGR01714 33 LLLLSLNDGGCIYLNELAPYNAEMLATMFNRNVGDIRITLQTLESL-GLIEKKN 85 (119)
T ss_pred HHHHHhcCCCEEEEcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEec
Confidence 3455565555 3577999999999999999999999987 9999764
No 307
>TIGR00442 hisS histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff.
Probab=37.10 E-value=21 Score=34.76 Aligned_cols=37 Identities=16% Similarity=0.300 Sum_probs=31.0
Q ss_pred CCCCCCCChHHHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346 214 SLPSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESS 251 (292)
Q Consensus 214 ~~~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~ 251 (292)
...+...|...++++.++++|..+||+++. .|.+|..
T Consensus 8 d~~p~~~~~~~~i~~~i~~~f~~~Gy~~i~-~P~le~~ 44 (397)
T TIGR00442 8 DFLPEEMIKWQYIEETIREVFELYGFKEIR-TPIFEYT 44 (397)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCCeEec-CcccchH
Confidence 445677888999999999999999999996 5777663
No 308
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=35.61 E-value=63 Score=26.75 Aligned_cols=44 Identities=16% Similarity=0.237 Sum_probs=32.9
Q ss_pred ChHHHHHhhcCC-CCCChHHHhhcC----CchhhHHHHHHHcCCeeccc
Q psy10346 73 SHEVLVFNNVPS-EGIGQKELLATF----PNAKVGFSKAMAKGWISLDK 116 (292)
Q Consensus 73 lPE~rl~~~l~~-~~~~~~el~~~~----~~~~ig~~~a~k~gwi~i~~ 116 (292)
.|++.++..|.. +++++.+|.+.+ +...-.+..+-++|||....
T Consensus 40 ~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 40 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 478888888864 469999998874 24455677888899999853
No 309
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=35.45 E-value=37 Score=30.33 Aligned_cols=36 Identities=14% Similarity=0.248 Sum_probs=31.5
Q ss_pred CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
.++.+.++++..+|++.+.|..+++.|+.- |+|.-.
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~-~lV~~~ 74 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKKLQDW-NLVKKV 74 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHHHHHHHHhc-chHHhh
Confidence 456788999999999999999999999986 888753
No 310
>PRK09462 fur ferric uptake regulator; Provisional
Probab=34.94 E-value=1.9e+02 Score=24.11 Aligned_cols=58 Identities=22% Similarity=0.216 Sum_probs=42.1
Q ss_pred HHHHHHHHHhcc--CCCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEeee--eEEEEEeC
Q psy10346 4 DLTEKILKYLDT--NPPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVEPL--SHKIWELT 62 (292)
Q Consensus 4 ~~e~~iL~~L~~--~~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e~~--~~~~~~LT 62 (292)
.....||..|.. ++..+.+++...+ +++...|-+.+..|... |+|.--.. ....|.++
T Consensus 17 ~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~-Gli~~~~~~~~~~~y~~~ 83 (148)
T PRK09462 17 LPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDA-GIVTRHNFEGGKSVFELT 83 (148)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHC-CCEEEEEcCCCcEEEEeC
Confidence 456779999964 2467777775543 57899999999999987 99875432 34567665
No 311
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=34.80 E-value=1.9e+02 Score=22.11 Aligned_cols=47 Identities=11% Similarity=0.186 Sum_probs=36.4
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHh--hccCCcEEE
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSI--ETLGEYLIV 51 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L--~s~~glv~~ 51 (292)
..+-+|+..|..-+..+..++++.+|+-+-.|-+++.-+ ... |+.-+
T Consensus 10 tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKkl-Gl~i~ 58 (72)
T PF11994_consen 10 TKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKL-GLTIT 58 (72)
T ss_pred cHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhc-CcEEE
Confidence 456788898976666788999999999988888888887 433 66444
No 312
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=34.49 E-value=96 Score=28.13 Aligned_cols=37 Identities=11% Similarity=0.098 Sum_probs=31.4
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.+||+.+|++...|-+|+..|.+. |+|.-..-.-+++
T Consensus 35 ~eLa~~f~VSR~TvRkAL~~L~~e-Gli~r~~G~GtfV 71 (236)
T COG2188 35 RELAEQFGVSRMTVRKALDELVEE-GLIVRRQGKGTFV 71 (236)
T ss_pred HHHHHHHCCcHHHHHHHHHHHHHC-CcEEEEecCeeEE
Confidence 689999999999999999999986 9998665555444
No 313
>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 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.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=34.24 E-value=76 Score=25.93 Aligned_cols=46 Identities=11% Similarity=0.107 Sum_probs=36.9
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
.-.+|++-+..-..+++..+|+.+++.-+-.-.+++.|+++ |+|..
T Consensus 46 ~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~Lr~L~~k-G~Ik~ 91 (105)
T PF03297_consen 46 TYDKLLKEVPKMKLITPSVLSERLKINGSLARKALRELESK-GLIKP 91 (105)
T ss_dssp HHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHHHHHHHHC-CSSEE
T ss_pred HHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHHHHHHHHC-CCEEE
Confidence 33455555555566899999999999999999999999997 88765
No 314
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.70 E-value=82 Score=24.16 Aligned_cols=39 Identities=15% Similarity=0.137 Sum_probs=30.9
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCc
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEY 48 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~gl 48 (292)
++|..+..+.. +..++|..+|++...|-++++..++. |+
T Consensus 3 ~~l~l~~~g~~-~~~~ia~~lg~s~~Tv~r~~~~~~~~-G~ 41 (112)
T PF13551_consen 3 QILLLLAEGVS-TIAEIARRLGISRRTVYRWLKRYREG-GI 41 (112)
T ss_pred HHHHHHHcCCC-cHHHHHHHHCcCHHHHHHHHHHHHcc-cH
Confidence 45666654432 57999999999999999999999875 74
No 315
>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional
Probab=33.41 E-value=52 Score=35.12 Aligned_cols=37 Identities=22% Similarity=0.307 Sum_probs=31.7
Q ss_pred CCCCCChHHHHHHHHHHHhhhCCceecCCCCccccce
Q psy10346 216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVESSF 252 (292)
Q Consensus 216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves~f 252 (292)
..|..+|...+.+.+|+.|.++||.|+-+-+.+..++
T Consensus 393 ~~~~~~~~~~~~~~ir~~L~~~Gf~Evitysf~s~~~ 429 (704)
T CHL00192 393 FIGRLDIDYNTRDKIRSYLRNLGLTELIHYSLVKQES 429 (704)
T ss_pred cCCCCCHHHHHHHHHHHHHHhCCCceEecccccChhh
Confidence 4578899999999999999999999998877775543
No 316
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=33.15 E-value=99 Score=30.15 Aligned_cols=59 Identities=17% Similarity=0.067 Sum_probs=40.4
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..++..|.....++...+....|.+.. ...+..|.+. |++..+. ...+.||++|..++.
T Consensus 314 e~~~~~Lr~~~gid~~~~~~~~g~~~~--~~~l~~l~~~-gl~~~~~--~~~~~lT~~G~~~~d 372 (380)
T PRK09057 314 EFLLMGLRLREGIDLARYAALSGRPLD--PERLADLIEE-GLIERDG--GSRLRATPAGRLVLD 372 (380)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHCCCch--HHHHHHHHHC-CCEEEcC--CCEEEECcchhHHHH
Confidence 334445554555788888888887754 2467788876 9988542 237999999987663
No 317
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=32.90 E-value=66 Score=25.91 Aligned_cols=35 Identities=9% Similarity=0.159 Sum_probs=30.4
Q ss_pred CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
.+....+++..|+++..|..+++.|... |+|..+.
T Consensus 54 ~Is~sq~~e~tg~~~~~V~~al~~Li~~-~vI~~~g 88 (100)
T PF04492_consen 54 RISNSQIAEMTGLSRDHVSKALNELIRR-GVIIRDG 88 (100)
T ss_pred eeeHHHHHHHHCcCHHHHHHHHHHHHHC-CCEEeCC
Confidence 4667889999999999999999999987 9996654
No 318
>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: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=32.68 E-value=63 Score=21.72 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=23.2
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHH
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMK 40 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~ 40 (292)
...|+..+.++ ....++|..+|++...|-+.+.
T Consensus 11 ~~~i~~l~~~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 11 IEEIKELYAEG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHHHTT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHHHCC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 35666766544 6789999999999999988764
No 319
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=32.15 E-value=74 Score=31.03 Aligned_cols=42 Identities=12% Similarity=0.101 Sum_probs=34.4
Q ss_pred CCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 17 PPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 17 ~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
..+ ...++|+.+|++...|.++...|++. |+|......-.++
T Consensus 27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~-g~i~~~~~~G~~v 69 (431)
T PRK15481 27 DSLPPVRELASELGVNRNTVAAAYKRLVTA-GLAQSQGRNGTVI 69 (431)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHC-CCEEEeCCCceEE
Confidence 344 45799999999999999999999987 9998776555444
No 320
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=31.96 E-value=1.2e+02 Score=26.50 Aligned_cols=47 Identities=9% Similarity=0.045 Sum_probs=37.6
Q ss_pred HHHHHHHhccCC-CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee
Q psy10346 6 TEKILKYLDTNP-PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP 53 (292)
Q Consensus 6 e~~iL~~L~~~~-~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~ 53 (292)
..+||..+..+. ..+..++|+.+|++...|-..+..|.+. |++..+-
T Consensus 164 ~r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~-~~~~~~~ 211 (225)
T PRK10046 164 LNAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASR-HLIIAEI 211 (225)
T ss_pred HHHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhC-CeEEEEe
Confidence 347888886532 2467999999999999999999999987 8887543
No 321
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=31.78 E-value=59 Score=31.22 Aligned_cols=37 Identities=11% Similarity=0.026 Sum_probs=32.4
Q ss_pred CChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE
Q psy10346 19 VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH 56 (292)
Q Consensus 19 ~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~ 56 (292)
.+-.++|+++|++...|.+.+..-+.. |+|+++-...
T Consensus 30 ~tQ~eIA~~lgiSR~~VsRlL~~Ar~~-GiV~I~I~~~ 66 (318)
T PRK15418 30 LTQSEIGERLGLTRLKVSRLLEKGRQS-GIIRVQINSR 66 (318)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHc-CcEEEEEeCC
Confidence 466899999999999999999999987 9999876543
No 322
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.62 E-value=79 Score=21.25 Aligned_cols=33 Identities=15% Similarity=0.195 Sum_probs=19.6
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHH
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMK 40 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~ 40 (292)
...+..|-+.| .+..++|..+|.+++.|.+.++
T Consensus 10 R~~I~~l~~~G-~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 10 RNQIEALLEQG-MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHHCS----HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHcC-CCHHHHHHHHCcCcHHHHHHHh
Confidence 33344444344 5678999999999999988775
No 323
>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.; PDB: 3SQN_A.
Probab=31.01 E-value=46 Score=25.11 Aligned_cols=41 Identities=24% Similarity=0.269 Sum_probs=31.4
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIE 43 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~ 43 (292)
+.....++..|-.++.++.+++|+.++++.+.+.+.++.+.
T Consensus 15 ~s~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~ 55 (87)
T PF05043_consen 15 ESLNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLN 55 (87)
T ss_dssp GSHHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45667788877667778899999999999999999888775
No 324
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=30.90 E-value=62 Score=30.77 Aligned_cols=59 Identities=10% Similarity=0.230 Sum_probs=43.9
Q ss_pred HHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE-EEEEeChhHHHHhhcCChHHHHHhhcC
Q psy10346 22 LDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH-KIWELTGEGNQVKDNGSHEVLVFNNVP 83 (292)
Q Consensus 22 ~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~-~~~~LTeEG~~yl~~GlPE~rl~~~l~ 83 (292)
..+.+..|++...|--++..+.. .|.+..+++-. .+|.|||.|..-...+ +++++..-.
T Consensus 32 I~il~~fG~sE~~vRaal~Rm~k-aG~l~~er~grks~Y~LSDkgl~r~~~a--~~riy~~~r 91 (291)
T COG3327 32 IQILAEFGISETTVRAALSRMVK-AGWLVGEREGRKSFYRLSDKGLARQRRA--ARRIYPRTR 91 (291)
T ss_pred HHHHHHcCccHHHHHHHHHHHHh-ccchheeecccccceeecHHHHHHHHHH--hhhhcCCCC
Confidence 55666789999999888888875 48877776554 4599999999876665 566665543
No 325
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=30.31 E-value=51 Score=29.42 Aligned_cols=43 Identities=14% Similarity=0.184 Sum_probs=36.2
Q ss_pred CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 16 NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 16 ~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
+..++-.++|..+|++..-|-.++..|++. |+|.+....-..+
T Consensus 37 G~~l~e~~La~~~gvSrtPVReAL~rL~~e-Glv~~~p~rG~~V 79 (230)
T COG1802 37 GERLSEEELAEELGVSRTPVREALRRLEAE-GLVEIEPNRGAFV 79 (230)
T ss_pred CCCccHHHHHHHhCCCCccHHHHHHHHHHC-CCeEecCCCCCee
Confidence 445778999999999999999999999986 9999986655444
No 326
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=30.14 E-value=1.2e+02 Score=30.74 Aligned_cols=56 Identities=9% Similarity=0.095 Sum_probs=43.4
Q ss_pred HHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhHHH
Q psy10346 8 KILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEGNQ 67 (292)
Q Consensus 8 ~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG~~ 67 (292)
.|+..|. +++....+|++.+|++...|++.+.-|. |+|.. .+-..+.|.|++..+-
T Consensus 4 ~~~~~L~-~g~~~~~eL~~~l~~sq~~~s~~L~~L~---~~V~~~~~gr~~~Y~l~~~~~g 60 (442)
T PRK09775 4 LLTTLLL-QGPLSAAELAARLGVSQATLSRLLAALG---DQVVRFGKARATRYALLRPLRG 60 (442)
T ss_pred HHHHHHh-cCCCCHHHHHHHhCCCHHHHHHHHHHhh---cceeEeccCceEEEEecccccC
Confidence 3555565 5677889999999999999999999992 66554 5666778888877653
No 327
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=30.04 E-value=1.7e+02 Score=29.29 Aligned_cols=59 Identities=10% Similarity=0.030 Sum_probs=42.9
Q ss_pred HHHHHHHhccCCCCChHHHHHhcCCCHHH-HHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 6 TEKILKYLDTNPPVDTLDLAKLFNEDHQK-VVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 6 e~~iL~~L~~~~~~~~~ela~~~~~~~~~-v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
...++..|. ...++...+.+..|.+... +...+..|+.. |++..+ ...+.||+.|+-++
T Consensus 347 ~~~~~~~L~-~~gld~~~f~~~~g~~~~~~~~~~l~~l~~~-Gll~~~---~~~l~lT~~G~~~~ 406 (433)
T PRK08629 347 QYRFLLGMF-SGRLSIKYFRETFGVNLDKALFKEMLLLKLI-GAIKND---PGDLIVTDFGKYLG 406 (433)
T ss_pred HHHHHHHHH-hCCcCHHHHHHHHCCCHHHHHHHHHHHHHHC-CCEEEE---CCEEEECcchhHHH
Confidence 344555564 4567888888889988555 55577788876 998864 45799999998765
No 328
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=29.85 E-value=1.6e+02 Score=29.07 Aligned_cols=57 Identities=16% Similarity=0.175 Sum_probs=40.5
Q ss_pred HHhccCCCCChHHHHHhcCCCH-HHHHHHHHHhhccCCcEEEeeeeEEE-EEeCh-hHHHHhhc
Q psy10346 11 KYLDTNPPVDTLDLAKLFNEDH-QKVVGGMKSIETLGEYLIVEPLSHKI-WELTG-EGNQVKDN 71 (292)
Q Consensus 11 ~~L~~~~~~~~~ela~~~~~~~-~~v~~~~~~L~s~~glv~~e~~~~~~-~~LTe-EG~~yl~~ 71 (292)
-.|.....++...+.+..|.+. +.....+..|... |++..+ ... +.||+ .|..++..
T Consensus 328 ~~Lr~~~Gl~~~~~~~~~g~~~~~~~~~~l~~l~~~-gll~~~---~~~~~~lT~~~G~~~~~~ 387 (400)
T PRK07379 328 LGLRLAEGVSLSALTERFGKEIVEQILQCLQPYFQQ-GWVELE---GDRRLRLTDPEGFLFSNT 387 (400)
T ss_pred hCCcccCCcCHHHHHHHHCCCHHHHHHHHHHHHHHC-CCEEEe---CCeEEEECchHHhHHHHH
Confidence 3344333478888888888885 5566788889876 998864 335 89995 89887644
No 329
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=29.70 E-value=1e+02 Score=29.88 Aligned_cols=38 Identities=8% Similarity=-0.007 Sum_probs=33.2
Q ss_pred CCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeE
Q psy10346 18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSH 56 (292)
Q Consensus 18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~ 56 (292)
..+-.++|+++|++...|.+.+...... |+|++.-...
T Consensus 26 gltQ~eIA~~LgiSR~~v~rlL~~Ar~~-GiV~I~i~~~ 63 (321)
T COG2390 26 GLTQSEIAERLGISRATVSRLLAKAREE-GIVKISINSP 63 (321)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHC-CeEEEEeCCC
Confidence 3567899999999999999999999987 9999877633
No 330
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=29.41 E-value=1.5e+02 Score=19.31 Aligned_cols=40 Identities=13% Similarity=0.205 Sum_probs=30.0
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
+.+.+++..+..+ .+..++|+.+|++...|-+.+..+..+
T Consensus 6 ~~e~~i~~~~~~g--~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 6 PREREVLRLLAEG--LTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred HHHHHHHHHHHcC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4566677665432 467999999999999998888876543
No 331
>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 []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=29.33 E-value=1.4e+02 Score=25.99 Aligned_cols=108 Identities=14% Similarity=0.127 Sum_probs=0.0
Q ss_pred HHHHHh--ccCCCCChHHHHHhcCCCHHHHHHHHHHhhccC-----CcEEEeeeeEEEEEeChhHHHHhhcCChH-----
Q psy10346 8 KILKYL--DTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLG-----EYLIVEPLSHKIWELTGEGNQVKDNGSHE----- 75 (292)
Q Consensus 8 ~iL~~L--~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~-----glv~~e~~~~~~~~LTeEG~~yl~~GlPE----- 75 (292)
.++.++ ..+.+++..++++.++ +...|..++..|..+. |+--++.-..-.+.+-++=..|++.=.+.
T Consensus 1 a~iEAlLF~s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~~~~~ 79 (159)
T PF04079_consen 1 AIIEALLFASGEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKPKPPK 79 (159)
T ss_dssp -HHHHHHHH-SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTCCCHH
T ss_pred ChhHhhHHHcCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccCccCC
Q ss_pred -----HHHHhhcC-CCCCChHHHhhc-CCchhhHHHHHHHcCCeeccc
Q psy10346 76 -----VLVFNNVP-SEGIGQKELLAT-FPNAKVGFSKAMAKGWISLDK 116 (292)
Q Consensus 76 -----~rl~~~l~-~~~~~~~el~~~-~~~~~ig~~~a~k~gwi~i~~ 116 (292)
...+..+. ..+++..|+.+. .-...-.+..++.+|||+..+
T Consensus 80 LS~aalEtLAiIAY~QPiTr~eIe~IRGv~s~~~i~~L~e~glI~~~g 127 (159)
T PF04079_consen 80 LSQAALETLAIIAYKQPITRAEIEEIRGVNSDSVIKTLLERGLIEEVG 127 (159)
T ss_dssp HHHHHHHHHHHHHHH-SEEHHHHHHHHTS--HCHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHHHHhcCCcCHHHHHHHcCCChHHHHHHHHHCCCEEecC
No 332
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=28.63 E-value=50 Score=25.73 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=18.6
Q ss_pred CCCh-HHHHHHHHHHHhhhCCc
Q psy10346 219 HLHP-LMKVRAEFRQIFLDMGF 239 (292)
Q Consensus 219 ~~Hp-l~~~~~~i~~if~~mGF 239 (292)
..|| +..++..|.+.+.+||+
T Consensus 64 ~~HP~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 64 ASHPKLAGILRNIMDSLANMGI 85 (85)
T ss_pred HhCCcHHHHHHHHHHHHHHCCC
Confidence 4688 89999999999999995
No 333
>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=28.54 E-value=70 Score=27.88 Aligned_cols=41 Identities=17% Similarity=0.272 Sum_probs=32.5
Q ss_pred CC-cHHHHHHHHHhccCCCCChHHHHHhcC-CCHHHHHHHHHHh
Q psy10346 1 MA-SDLTEKILKYLDTNPPVDTLDLAKLFN-EDHQKVVGGMKSI 42 (292)
Q Consensus 1 m~-~~~e~~iL~~L~~~~~~~~~ela~~~~-~~~~~v~~~~~~L 42 (292)
|+ .+.....|+.|-..| .+..+||..+| ++.++|++-+..|
T Consensus 1 M~Wtde~~~~L~~lw~~G-~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 1 MSWTDERVERLRKLWAEG-LSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCCHHHHHHHHHHHHcC-CCHHHHHHHhCCcchhhhhhhhhcc
Confidence 55 566667777775444 46789999999 9999999999987
No 334
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=27.95 E-value=1.5e+02 Score=24.93 Aligned_cols=56 Identities=18% Similarity=0.200 Sum_probs=41.5
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV 68 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y 68 (292)
.++-.+|...+.....+++...|.+. +..-|... -|==.++.+.-.|.||+.|+..
T Consensus 62 l~~A~~L~~~Gp~~~~~l~~~~~~~~-----A~~IL~~N-~YGWFeRv~rGvY~LT~~G~~a 117 (118)
T PF09929_consen 62 LRCAAALAEHGPSRPADLRKATGVPK-----ATSILRDN-HYGWFERVERGVYALTPAGRAA 117 (118)
T ss_pred HHHHHHHHHcCCCCHHHHHHhcCCCh-----HHHHHHhC-cccceeeeccceEecCcchhhc
Confidence 44567777778888888988877663 34445544 4666789999999999999864
No 335
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=27.12 E-value=1.1e+02 Score=28.94 Aligned_cols=62 Identities=15% Similarity=0.101 Sum_probs=49.2
Q ss_pred HHHHHHHHh-----ccCCCCChHHHHHhcC--CCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346 5 LTEKILKYL-----DTNPPVDTLDLAKLFN--EDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV 68 (292)
Q Consensus 5 ~e~~iL~~L-----~~~~~~~~~ela~~~~--~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y 68 (292)
.+..||.++ ..+.++.|..+++..+ +++..|-..+..|+.. |++. ...+..=-..|+.|-+|
T Consensus 4 R~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l~~SsATIRn~m~~LE~~-G~L~-qpHtSsGRIPT~~gyr~ 72 (260)
T PRK03911 4 KKDLLLDSIIQTYLQDNEPIGSNELKSLMNLKISAATIRNYFKKLSDE-GLLT-QLHISGGRIPTIKAMKN 72 (260)
T ss_pred HHHHHHHHHHHHHhccCCccCHHHHHHHcCCCCCcHHHHHHHHHHHHC-cCcc-CCcCCCCcCCCHHHHHH
Confidence 456677655 4577789999999865 5688999999999986 9976 66666667899999875
No 336
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry 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=26.50 E-value=1.2e+02 Score=24.59 Aligned_cols=34 Identities=15% Similarity=0.285 Sum_probs=27.9
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHh
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSI 42 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L 42 (292)
+...+.+++.....|+|..+|++++.|-.+++.|
T Consensus 62 L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lkrl 95 (119)
T PF01710_consen 62 LKALVEENPDATLRELAERLGVSPSTIWRALKRL 95 (119)
T ss_pred HHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHHHc
Confidence 4445566666788999999999999999998887
No 337
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=26.27 E-value=1.1e+02 Score=28.95 Aligned_cols=59 Identities=14% Similarity=0.102 Sum_probs=44.9
Q ss_pred HHHHHhccCCCC-ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHh
Q psy10346 8 KILKYLDTNPPV-DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVK 69 (292)
Q Consensus 8 ~iL~~L~~~~~~-~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl 69 (292)
+.+..+.+++.+ ..++-...+|+-...|-+.-.||.+- |+++-...... .||+.|+..+
T Consensus 17 K~~~~v~~~~~~F~~~~a~~~lGvGkNMV~siryWl~a~-gli~~~~~~~~--~~T~lG~~i~ 76 (286)
T PF13182_consen 17 KGYDAVENDPDVFSDEDAIVRLGVGKNMVKSIRYWLRAF-GLIEEDNKGKR--KLTPLGELIF 76 (286)
T ss_pred HHHHHHhcCcccccchhHHHHcCCCHhHHHHHHHHHHHc-CCcccCCCCCc--ccCHHHHHHH
Confidence 445555544433 34566667999999999999999997 99987665555 9999999988
No 338
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=26.18 E-value=89 Score=23.90 Aligned_cols=32 Identities=16% Similarity=0.189 Sum_probs=26.5
Q ss_pred CCChHHHHHhcCCCHHHHHHHHHHhhccCCcE
Q psy10346 18 PVDTLDLAKLFNEDHQKVVGGMKSIETLGEYL 49 (292)
Q Consensus 18 ~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv 49 (292)
..+..++|..+|++...|...+..+...+++|
T Consensus 32 GlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 32 GKTASEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 35779999999999999999999988764343
No 339
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=26.10 E-value=1.3e+02 Score=27.28 Aligned_cols=41 Identities=17% Similarity=0.148 Sum_probs=34.0
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
++.|.+||..+..+ .+..++|..++++...|-..+..+-.|
T Consensus 135 SpRErEVLrLLAqG--kTnKEIAe~L~IS~rTVkth~srImkK 175 (198)
T PRK15201 135 SVTERHLLKLIASG--YHLSETAALLSLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CHHHHHHHHHHHCC--CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 46799999999765 357899999999999998888877655
No 340
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=25.97 E-value=1.5e+02 Score=24.33 Aligned_cols=44 Identities=16% Similarity=0.102 Sum_probs=33.9
Q ss_pred HHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEE
Q psy10346 7 EKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIV 51 (292)
Q Consensus 7 ~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~ 51 (292)
.+|++-...-..+++..|++.+|++-+-.-.+++-|+.. |+|..
T Consensus 48 ~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~vLR~Leee-Gvv~l 91 (107)
T COG4901 48 DKIRKEVPRERVVTPYVLASRYGINGSVARIVLRHLEEE-GVVQL 91 (107)
T ss_pred HHHHHhcccceeecHHHHHHHhccchHHHHHHHHHHHhC-Cceee
Confidence 344444444445788999999999998888999999986 88765
No 341
>PRK13239 alkylmercury lyase; Provisional
Probab=25.93 E-value=1.4e+02 Score=27.30 Aligned_cols=39 Identities=21% Similarity=0.276 Sum_probs=33.7
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIE 43 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~ 43 (292)
+-..||..|..+..++..++|...|.+.+.|..++..|.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 456688889888889999999999999999998888874
No 342
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=25.53 E-value=1.8e+02 Score=29.71 Aligned_cols=52 Identities=10% Similarity=0.193 Sum_probs=37.6
Q ss_pred HHHHHHhccC-CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346 7 EKILKYLDTN-PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63 (292)
Q Consensus 7 ~~iL~~L~~~-~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe 63 (292)
..||..|... +.++..++++.+|+..++|+.++..| |+++.. .....+.+|.
T Consensus 362 ~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l----~~l~~~-kg~~~i~~~~ 414 (450)
T PLN00104 362 RVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL----NLIQYR-KGQHVICADP 414 (450)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC----CCEEec-CCcEEEEECH
Confidence 3577777544 46788999999999999999998888 577643 3334455554
No 343
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=25.42 E-value=2.2e+02 Score=25.38 Aligned_cols=61 Identities=8% Similarity=0.142 Sum_probs=44.2
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-----eEEEEEeChhHHHH
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-----SHKIWELTGEGNQV 68 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-----~~~~~~LTeEG~~y 68 (292)
....++|..+.-+.+++..+++...|++. -+.++.|..+ |+|....+ ....|.+|+.=..+
T Consensus 90 ~aaLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~~-gLI~e~gr~~~~Grp~ly~tT~~F~~~ 155 (188)
T PRK00135 90 QAALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLAK-GLIKEVGRKEVPGRPILYGTTDEFLDY 155 (188)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHC-CCeEEcCcCCCCCCCeeeehhHHHHHH
Confidence 34567888887788899999999999987 4677888876 99975221 24566777664443
No 344
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=25.22 E-value=1.6e+02 Score=25.46 Aligned_cols=48 Identities=10% Similarity=0.173 Sum_probs=36.2
Q ss_pred HHHHHHHHHhcc-CCCCChHHHHHhc-----CCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 4 DLTEKILKYLDT-NPPVDTLDLAKLF-----NEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 4 ~~e~~iL~~L~~-~~~~~~~ela~~~-----~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
.....||..|.. .+.++.+++...+ +++...|-+.|..|... |+|.--
T Consensus 26 ~qR~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~-Glv~~~ 79 (169)
T PRK11639 26 PQRLEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQ-GFVHKV 79 (169)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHC-CCEEEE
Confidence 455678888864 3457777776543 57889999999999987 998754
No 345
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=25.14 E-value=95 Score=28.36 Aligned_cols=47 Identities=21% Similarity=0.203 Sum_probs=37.6
Q ss_pred cHHHHHHHHHhccCCC----CChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 3 SDLTEKILKYLDTNPP----VDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~----~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
.+.|++|..++.++.. .+..++|+++|+++.+|+|-++.|-= .|+-.
T Consensus 15 t~~e~~Ia~yil~n~~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~-~gf~e 65 (284)
T PRK11302 15 SKSERKVAEVILASPQTAIHSSIATLAKMANVSEPTVNRFCRSLDT-KGFPD 65 (284)
T ss_pred CHHHHHHHHHHHhCHHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCC-CCHHH
Confidence 3678889988866543 46789999999999999999999964 37743
No 346
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=25.02 E-value=1e+02 Score=28.75 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=33.2
Q ss_pred HHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 9 ILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 9 iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
|+.-|.. .|..-..-+|...|+..+-++.|++.|+|. |+|+..
T Consensus 194 I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESA-GvIeSR 237 (261)
T COG4465 194 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA-GVIESR 237 (261)
T ss_pred HHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhc-Cceeec
Confidence 4444542 233456789999999999999999999997 999864
No 347
>PLN03239 histone acetyltransferase; Provisional
Probab=24.79 E-value=2.3e+02 Score=27.97 Aligned_cols=52 Identities=13% Similarity=0.145 Sum_probs=35.9
Q ss_pred HHHHHHhccC----CCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeCh
Q psy10346 7 EKILKYLDTN----PPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTG 63 (292)
Q Consensus 7 ~~iL~~L~~~----~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTe 63 (292)
..||..|... ..++..+++..+|+.+++|+.++..| |++.... ....+.++.
T Consensus 269 ~~il~~L~~~~~~~~~~si~dis~~Tgi~~~DIi~tL~~l----~~l~~~~-g~~~i~~~~ 324 (351)
T PLN03239 269 STIVDFLLNHSGNDSSLSIMDIAKKTSIMAEDIVFALNQL----GILKFIN-GIYFIAAEK 324 (351)
T ss_pred HHHHHHHHhccCCCCCccHHHHHHHhCCCHHHHHHHHHHC----CcEEEEC-CeEEEEeCH
Confidence 3566666432 34788999999999999999998888 5666433 333344553
No 348
>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.
Probab=24.79 E-value=63 Score=27.46 Aligned_cols=27 Identities=30% Similarity=0.609 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346 224 MKVRAEFRQIFLDMGFTEMPTNNFVESS 251 (292)
Q Consensus 224 ~~~~~~i~~if~~mGF~e~~~~~~Ves~ 251 (292)
..+.+.++++|.++||.|+.+ |.+++.
T Consensus 3 ~~~~~~~r~~l~~~Gf~Ev~t-~~l~~~ 29 (211)
T cd00768 3 SKIEQKLRRFMAELGFQEVET-PIVERE 29 (211)
T ss_pred HHHHHHHHHHHHHcCCEEeEc-ceecHH
Confidence 568899999999999999864 555554
No 349
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.66 E-value=1.8e+02 Score=27.10 Aligned_cols=58 Identities=17% Similarity=0.134 Sum_probs=45.0
Q ss_pred HHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEee-eeEEEEEeCh
Q psy10346 5 LTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEP-LSHKIWELTG 63 (292)
Q Consensus 5 ~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~-~~~~~~~LTe 63 (292)
.++.|+..+.+++......+|...|++...|.=.++.|+.- |+|.-.+ -....|..|+
T Consensus 175 ~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~-Gii~~~~~Gr~iiy~in~ 233 (240)
T COG3398 175 TSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEEL-GIIPEDREGRSIIYSINP 233 (240)
T ss_pred hHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHc-CCCcccccCceEEEEeCH
Confidence 45778888877766667899999999999999999999987 9987643 3344555554
No 350
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=24.56 E-value=2.1e+02 Score=18.73 Aligned_cols=39 Identities=13% Similarity=0.240 Sum_probs=29.2
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhc
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIET 44 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s 44 (292)
..+..++..+.. ..+..++|+.+|++...|-..+..+..
T Consensus 3 ~~e~~i~~~~~~--~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 3 PREREVLRLLAE--GKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHHHHHHHHc--CCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 345667766542 257799999999999999888887654
No 351
>COG2469 Uncharacterized conserved protein [Function unknown]
Probab=24.48 E-value=71 Score=30.57 Aligned_cols=63 Identities=19% Similarity=0.176 Sum_probs=45.9
Q ss_pred HHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhh
Q psy10346 4 DLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKD 70 (292)
Q Consensus 4 ~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~ 70 (292)
..|.+||-++-++ .++.+++.-+|++.+.|-.....|=.+ ||..+ -.......||++|+..+.
T Consensus 216 E~E~qiLvalYSg--~~~~sl~~~lGv~~~el~~l~drlI~~-gl~~i-V~iRk~ielt~~Gr~~vs 278 (284)
T COG2469 216 EIEKQILVALYSG--GDSASLELFLGVDTDELEILYDRLIDK-GLLKI-VKIRKEIELTPRGRAIVS 278 (284)
T ss_pred hhhheeeeeEecC--CCchhhhhHhCCcHHHHHHHHHHHHHh-chhhe-EeeehheecchhHHHHHH
Confidence 3456666666443 256667777999999999988888876 88764 344567799999998764
No 352
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=24.19 E-value=2.3e+02 Score=26.51 Aligned_cols=63 Identities=19% Similarity=0.257 Sum_probs=49.8
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeee-eEE-EEEeChhH
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPL-SHK-IWELTGEG 65 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~-~~~-~~~LTeEG 65 (292)
++....+..+|...|..+..++|.=+|++...+-.++..|.+.+.++.+.-. -.+ .|.+.+..
T Consensus 166 ea~~~Lv~Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 166 EALAELVRRYLRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHHHHHHHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEcCcceeEEechhhh
Confidence 3556677888888999999999999999999999999999754468888766 344 67666544
No 353
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=23.89 E-value=67 Score=30.54 Aligned_cols=27 Identities=22% Similarity=0.427 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhhhCCceecCCCCccccc
Q psy10346 224 MKVRAEFRQIFLDMGFTEMPTNNFVESS 251 (292)
Q Consensus 224 ~~~~~~i~~if~~mGF~e~~~~~~Ves~ 251 (292)
+.++..||++|.+.||.|+.+ |.+++.
T Consensus 5 s~i~~~ir~~f~~~gF~EV~T-P~l~~~ 31 (304)
T TIGR00462 5 ARLLAAIRAFFAERGVLEVET-PLLSPA 31 (304)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-CeEecC
Confidence 578899999999999999975 766644
No 354
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=23.47 E-value=5.3e+02 Score=22.98 Aligned_cols=103 Identities=11% Similarity=0.036 Sum_probs=60.9
Q ss_pred ccCCC-CChHHHHHhcCCCH-HHHHHHHHHhhcc-----CCcEEEeeeeEEEEEeChhHHHHhhcCChH---------HH
Q psy10346 14 DTNPP-VDTLDLAKLFNEDH-QKVVGGMKSIETL-----GEYLIVEPLSHKIWELTGEGNQVKDNGSHE---------VL 77 (292)
Q Consensus 14 ~~~~~-~~~~ela~~~~~~~-~~v~~~~~~L~s~-----~glv~~e~~~~~~~~LTeEG~~yl~~GlPE---------~r 77 (292)
..+.+ ++..++|+.++.+. +.+..++..|... .|+.-++.-..-.+.+-++=..|+..=.+. ..
T Consensus 12 ~sg~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~~~i~~~~~~~~~~LS~aaLE 91 (186)
T TIGR00281 12 VSGEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFADYIHRFLPAKLKNLNSASLE 91 (186)
T ss_pred HcCCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccccccCCHHHHH
Confidence 34565 89999999999884 4555566666432 144444444444556666655666542111 11
Q ss_pred HHhhcC-CCCCChHHHhhcCC-chhhHHHHHHHcCCeeccc
Q psy10346 78 VFNNVP-SEGIGQKELLATFP-NAKVGFSKAMAKGWISLDK 116 (292)
Q Consensus 78 l~~~l~-~~~~~~~el~~~~~-~~~ig~~~a~k~gwi~i~~ 116 (292)
.+..+. ..+++..++.+.-. ...-.+..++.+|||+..+
T Consensus 92 tLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~ergLI~~~G 132 (186)
T TIGR00281 92 VLAIIAYKQPITRARINEIRGVKSYQIVDDLVEKGLVVELG 132 (186)
T ss_pred HHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHHCCCeEecC
Confidence 222222 35688877777532 2344577899999998863
No 355
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=23.44 E-value=1e+02 Score=33.28 Aligned_cols=35 Identities=23% Similarity=0.430 Sum_probs=30.0
Q ss_pred CCCCCChHHHHHHHHHHHhhhCCceecCCCCcccc
Q psy10346 216 PSGHLHPLMKVRAEFRQIFLDMGFTEMPTNNFVES 250 (292)
Q Consensus 216 ~~g~~Hpl~~~~~~i~~if~~mGF~e~~~~~~Ves 250 (292)
..|..++...+.+.+|+.|.++||.|+-+-+.+..
T Consensus 482 ~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysf~~~ 516 (791)
T PRK00629 482 TMGGLTEAQRLLRRLRRALAALGYQEVITYSFVSP 516 (791)
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCcEEeccccCCH
Confidence 44688999999999999999999999987777644
No 356
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=23.40 E-value=1.1e+02 Score=21.59 Aligned_cols=63 Identities=11% Similarity=0.019 Sum_probs=38.4
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe-eeeEEEEEeChhHHHHhhcCChHHHHHhhcCCCCCChHHHhh
Q psy10346 20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE-PLSHKIWELTGEGNQVKDNGSHEVLVFNNVPSEGIGQKELLA 94 (292)
Q Consensus 20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e-~~~~~~~~LTeEG~~yl~~GlPE~rl~~~l~~~~~~~~el~~ 94 (292)
++.++|+.+|++.+.+-.+. .. |++... +........|++--. ..+.+..|.+.|++++++.+
T Consensus 2 s~~eva~~~gvs~~tlr~~~----~~-gli~~~~~~~~g~r~y~~~dl~-------~l~~i~~lr~~g~~~~~i~~ 65 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE----RI-GLLPPPIRTEGGYRLYSDEDLE-------RLRFIKRLKELGFSLEEIKE 65 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HC-CCCCCCccCCCCCEecCHHHHH-------HHHHHHHHHHcCCCHHHHHH
Confidence 45789999999997666553 34 888753 333333444443322 33445555557888877765
No 357
>PRK04158 transcriptional repressor CodY; Validated
Probab=23.11 E-value=58 Score=30.77 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=33.5
Q ss_pred HHHHhcc-CCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEe
Q psy10346 9 ILKYLDT-NPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVE 52 (292)
Q Consensus 9 iL~~L~~-~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e 52 (292)
|+..|+. .|.+-...+|...|+..+-++.|++.|+|- |+|+..
T Consensus 191 If~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESA-GvIESr 234 (256)
T PRK04158 191 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESA-GVIESR 234 (256)
T ss_pred HHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcc-cceeec
Confidence 5555543 223445778999999999999999999997 999864
No 358
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=22.51 E-value=1.9e+02 Score=25.40 Aligned_cols=43 Identities=9% Similarity=0.045 Sum_probs=31.9
Q ss_pred hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHH
Q psy10346 21 TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQ 67 (292)
Q Consensus 21 ~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~ 67 (292)
-.++|..+|+..+.|.++++.|+.. |+ .... .....+--+|.+
T Consensus 176 ~~~iA~~lG~tretvsR~l~~L~~~-gl-~~~~--~~i~I~d~~~L~ 218 (236)
T PRK09392 176 KRVLASYLGMTPENLSRAFAALASH-GV-HVDG--SAVTITDPAGLA 218 (236)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHhC-Ce-EeeC--CEEEEcCHHHHH
Confidence 3789999999999999999999987 86 4432 344445555543
No 359
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=22.28 E-value=78 Score=32.65 Aligned_cols=45 Identities=22% Similarity=0.319 Sum_probs=37.4
Q ss_pred hHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHH
Q psy10346 21 TLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQV 68 (292)
Q Consensus 21 ~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~y 68 (292)
.+++....|.+...|.-++.+|+|+ |+|+ .....-+.||+-|+..
T Consensus 445 iedi~~~~g~~eeev~~sl~klesk-gfve--eL~n~gv~LTeaGe~~ 489 (593)
T COG1542 445 IEDIQGHVGGDEEEVIKSLGKLESK-GFVE--ELPNKGVKLTEAGELV 489 (593)
T ss_pred HHHHHhhcCccHHHHHHHHHHHhhc-chHH--HhccCcEEeehhhHHH
Confidence 4677778899999999999999998 9976 4556678999999764
No 360
>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=22.21 E-value=2.9e+02 Score=26.43 Aligned_cols=61 Identities=16% Similarity=-0.016 Sum_probs=43.2
Q ss_pred CChHHHHHhcCCCH---------HHHHHHHHH-hhccCCcEEEeeeeE--------EEEEeChhHHHHhhcCChHHHHHh
Q psy10346 19 VDTLDLAKLFNEDH---------QKVVGGMKS-IETLGEYLIVEPLSH--------KIWELTGEGNQVKDNGSHEVLVFN 80 (292)
Q Consensus 19 ~~~~ela~~~~~~~---------~~v~~~~~~-L~s~~glv~~e~~~~--------~~~~LTeEG~~yl~~GlPE~rl~~ 80 (292)
.+.+++|.++|+++ .-+.+++.. |+.. |+|+.+..-. ..+.||+.+=..+ |-++.++..
T Consensus 96 ~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~-Gli~~~~~~D~~~~~~~Pk~I~lT~~ff~l~--gi~~~kl~~ 172 (281)
T PF02387_consen 96 ASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPL-GLITCEKEWDPYNGNYIPKHIWLTPLFFMLL--GISEDKLRR 172 (281)
T ss_pred ecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhc-CCeeeeeeechhhccccCeEEEECHHHHHHh--CCCHHHHHH
Confidence 46789999887654 456677755 7776 9998866533 3678999997655 777777665
Q ss_pred hc
Q psy10346 81 NV 82 (292)
Q Consensus 81 ~l 82 (292)
..
T Consensus 173 ~~ 174 (281)
T PF02387_consen 173 EQ 174 (281)
T ss_pred HH
Confidence 44
No 361
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=22.14 E-value=1.6e+02 Score=27.89 Aligned_cols=46 Identities=17% Similarity=0.159 Sum_probs=36.9
Q ss_pred CCCChHHHHHhcC--CCHHHHHHHHHHhhccCCcEEEeeeeEEEEEeChhH
Q psy10346 17 PPVDTLDLAKLFN--EDHQKVVGGMKSIETLGEYLIVEPLSHKIWELTGEG 65 (292)
Q Consensus 17 ~~~~~~ela~~~~--~~~~~v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG 65 (292)
+..++.++|+.++ ++.+.|-.++.-|... |+|+-.. ...|+.|+..
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~-glikk~~--~g~y~~t~~~ 183 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERL-GLIKKNE--DGFYKQTDKA 183 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHC-CCeeECC--CCcEEeecce
Confidence 3347889999998 7899999999999987 9998543 4578888754
No 362
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=22.08 E-value=2.4e+02 Score=19.22 Aligned_cols=41 Identities=12% Similarity=0.248 Sum_probs=33.2
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
.+.|..++..+..+ ....++|..++++...|..-+..+..|
T Consensus 6 t~rE~~v~~l~~~G--~s~~eia~~l~is~~tV~~h~~~i~~K 46 (65)
T COG2771 6 TPREREILRLVAQG--KSNKEIARILGISEETVKTHLRNIYRK 46 (65)
T ss_pred CHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 36688888888765 467999999999999998888887654
No 363
>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=21.78 E-value=3e+02 Score=23.58 Aligned_cols=60 Identities=18% Similarity=0.251 Sum_probs=43.5
Q ss_pred HHHHHHHHhcc-CCCCChHHHHHhc--CCCHHHHHHHHHHhhccCCcEEE-eeeeEEEEEeChhH
Q psy10346 5 LTEKILKYLDT-NPPVDTLDLAKLF--NEDHQKVVGGMKSIETLGEYLIV-EPLSHKIWELTGEG 65 (292)
Q Consensus 5 ~e~~iL~~L~~-~~~~~~~ela~~~--~~~~~~v~~~~~~L~s~~glv~~-e~~~~~~~~LTeEG 65 (292)
.+..||.+|.. +.+.+..++...+ ++....|..++..|.+. |-|.. .--+...|.....+
T Consensus 2 Ae~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~-g~i~~K~~GKqkiY~~~Q~~ 65 (169)
T PF07106_consen 2 AEDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEE-GKIVEKEYGKQKIYFANQDE 65 (169)
T ss_pred hHHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhC-CCeeeeeecceEEEeeCccc
Confidence 36679999965 5567777887765 47889999999999987 76666 44455566555443
No 364
>PF10623 PilI: Plasmid conjugative transfer protein PilI; InterPro: IPR018897 The thin pilus of plasmid R64 belongs to the type IV family and is required for liquid matings. PilI is one of 14 genes that have been identified as being involved in biogenesis of the R64 thin pilus [].
Probab=21.69 E-value=41 Score=26.29 Aligned_cols=8 Identities=75% Similarity=1.281 Sum_probs=7.3
Q ss_pred CCCCCCCC
Q psy10346 260 QPQQHPAR 267 (292)
Q Consensus 260 ~PqdHPAR 267 (292)
|||.||+|
T Consensus 1 m~~~~~gr 8 (83)
T PF10623_consen 1 MPQQHPGR 8 (83)
T ss_pred CCccCCCe
Confidence 79999998
No 365
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.35 E-value=1.8e+02 Score=24.88 Aligned_cols=36 Identities=11% Similarity=0.207 Sum_probs=28.3
Q ss_pred HHHHHHHhccCCC--CChHHHHHhcCCCHHHHHHHHHH
Q psy10346 6 TEKILKYLDTNPP--VDTLDLAKLFNEDHQKVVGGMKS 41 (292)
Q Consensus 6 e~~iL~~L~~~~~--~~~~ela~~~~~~~~~v~~~~~~ 41 (292)
=.+|-.+|.++.. .+..++++.+|++...|.++++.
T Consensus 32 f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~Ire 69 (137)
T TIGR03826 32 FEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIRE 69 (137)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHc
Confidence 3457788876665 78899999999999988776654
No 366
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=20.99 E-value=1.4e+02 Score=27.25 Aligned_cols=39 Identities=15% Similarity=0.243 Sum_probs=30.5
Q ss_pred HHHHHHHHhccCC--CCChHHHHHhcCCCHHHHHHHHHHhh
Q psy10346 5 LTEKILKYLDTNP--PVDTLDLAKLFNEDHQKVVGGMKSIE 43 (292)
Q Consensus 5 ~e~~iL~~L~~~~--~~~~~ela~~~~~~~~~v~~~~~~L~ 43 (292)
.=+++|+.|...+ .++|.++|...|++...|-+...-.-
T Consensus 17 ~YyR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfSYFG 57 (211)
T COG2344 17 LYYRVLERLHASGVERVSSKELSEALGVDSATIRRDFSYFG 57 (211)
T ss_pred HHHHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhHHHH
Confidence 4467888886554 47999999999999998877765553
No 367
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=20.47 E-value=1.9e+02 Score=25.57 Aligned_cols=41 Identities=15% Similarity=0.187 Sum_probs=33.4
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
++.|.+||..+.++. ...++|++++++...|-..+..+-.|
T Consensus 139 T~RE~eVL~lla~G~--snkeIA~~L~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 139 SRTESSMLRMWMAGQ--GTIQISDQMNIKAKTVSSHKGNIKRK 179 (207)
T ss_pred CHHHHHHHHHHHcCC--CHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 467999999997653 46899999999999888888777655
No 368
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.45 E-value=2e+02 Score=25.35 Aligned_cols=54 Identities=17% Similarity=0.214 Sum_probs=42.4
Q ss_pred HHHHhcCCCHHHHHHHHHHhhccCCcEEEee------------------eeEEEEEeChhHHHHhhcCChHHH
Q psy10346 23 DLAKLFNEDHQKVVGGMKSIETLGEYLIVEP------------------LSHKIWELTGEGNQVKDNGSHEVL 77 (292)
Q Consensus 23 ela~~~~~~~~~v~~~~~~L~s~~glv~~e~------------------~~~~~~~LTeEG~~yl~~GlPE~r 77 (292)
.++.-..++.-.|..+++-|... |+++.-. +-.+.|+||.||+-.+++=.||--
T Consensus 36 ~i~r~tkiPl~~i~e~l~dL~el-GLier~tgttiKrteAKfKksaEVHKHHTYYrl~rege~~lr~i~~~~l 107 (175)
T COG4344 36 NITRYTKIPLPRIREYLKDLKEL-GLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNREGEAVLREITPEWL 107 (175)
T ss_pred HHHHHccCChHHHHHHHHHHHHc-CCeeeccCchhhhhHHHHHHhHHHHhchhhheechhHHHHHHhcCHHHH
Confidence 34444678888999999999987 9987532 124689999999999999999764
No 369
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=20.45 E-value=2.4e+02 Score=28.28 Aligned_cols=56 Identities=16% Similarity=0.128 Sum_probs=38.0
Q ss_pred HHHHhccCCCCChHHHHHhcCCCHHH-HHHHHHHhhccCCcEEEeeeeEEEEEeChhHHHHhhc
Q psy10346 9 ILKYLDTNPPVDTLDLAKLFNEDHQK-VVGGMKSIETLGEYLIVEPLSHKIWELTGEGNQVKDN 71 (292)
Q Consensus 9 iL~~L~~~~~~~~~ela~~~~~~~~~-v~~~~~~L~s~~glv~~e~~~~~~~~LTeEG~~yl~~ 71 (292)
|...|.. +.++...+. .|.+... +...+..|... |++..+ ...+.||++|.-++.+
T Consensus 374 i~~~l~~-~~l~~~~~~--~g~~~~~~~~~~l~~~~~~-Gll~~~---~~~l~lT~~G~~~~~~ 430 (449)
T PRK09058 374 LKAGLER-GRLDLSELA--LGTPHADHLAPLLAQWQQA-GLVELS---SDCLRLTLAGRFWAVN 430 (449)
T ss_pred HHHHhhc-CCccHHHhh--cCCcHHHHHHHHHHHHHHC-CCEEEE---CCEEEECCCcccHHHH
Confidence 4444544 356766666 7777443 55577788876 998854 4579999999987643
No 370
>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: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=20.37 E-value=85 Score=31.75 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=38.1
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhccCCcEE
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETLGEYLI 50 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~~glv~ 50 (292)
...|..||.++.+...++.++++..+|++.+.+.+.+.+|-.. |++.
T Consensus 519 s~~q~~iLl~Fn~~~~~t~~ei~~~~~~~~~~l~~~L~~l~~~-~~l~ 565 (588)
T PF00888_consen 519 STLQAAILLLFNDNDSLTVEEISEKTGISEEELKRALKSLVKS-KILI 565 (588)
T ss_dssp EHHHHHHHHGGGSSSEEEHHHHHHHC---HHHHHHHHHCCCTT-TTCS
T ss_pred eHHHHHHHHHHccCCCccHHHHHHHHCcCHHHHHHHHHHHHhC-Ccce
Confidence 3578889999988888889999999999999999999999876 6654
No 371
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=20.32 E-value=1.7e+02 Score=25.76 Aligned_cols=39 Identities=15% Similarity=0.165 Sum_probs=32.2
Q ss_pred ChHHHHHhcCCCHHHHHHHHHHhhccCCcEEEeeeeEEEE
Q psy10346 20 DTLDLAKLFNEDHQKVVGGMKSIETLGEYLIVEPLSHKIW 59 (292)
Q Consensus 20 ~~~ela~~~~~~~~~v~~~~~~L~s~~glv~~e~~~~~~~ 59 (292)
.-.++|+.+|++...|.+++..|... |+|.-..-.-+++
T Consensus 27 sE~eLa~~~~Vsr~Tvr~Al~~L~~e-Gli~~~~g~Gt~V 65 (231)
T TIGR03337 27 SERDLGERFNTTRVTIREALQQLEAE-GLIYREDRRGWFV 65 (231)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC-CeEEEeCCCEEEE
Confidence 34789999999999999999999986 9998766554443
No 372
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=20.06 E-value=1.9e+02 Score=24.83 Aligned_cols=41 Identities=17% Similarity=0.184 Sum_probs=33.3
Q ss_pred cHHHHHHHHHhccCCCCChHHHHHhcCCCHHHHHHHHHHhhcc
Q psy10346 3 SDLTEKILKYLDTNPPVDTLDLAKLFNEDHQKVVGGMKSIETL 45 (292)
Q Consensus 3 ~~~e~~iL~~L~~~~~~~~~ela~~~~~~~~~v~~~~~~L~s~ 45 (292)
++.|.+||..+..+ ....++|+.++++...|-.-+..+-.|
T Consensus 152 t~rE~evl~~~~~G--~s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 152 SPKESEVLRLFAEG--FLVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred CHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 36789999999755 457899999999999888877777655
Done!