Query 032124
Match_columns 147
No_of_seqs 107 out of 328
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 09:54:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032124.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032124hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01090 Ribosomal_S19e: Ribos 100.0 3.7E-74 8E-79 445.2 8.5 133 5-137 1-133 (139)
2 PTZ00095 40S ribosomal protein 100.0 1.8E-72 3.9E-77 447.1 13.4 135 4-138 25-160 (169)
3 PRK09333 30S ribosomal protein 100.0 2.2E-71 4.9E-76 434.1 13.0 134 4-138 1-134 (150)
4 KOG3411 40S ribosomal protein 100.0 1.6E-71 3.5E-76 428.7 11.7 136 1-137 1-136 (143)
5 COG2238 RPS19A Ribosomal prote 100.0 4.9E-69 1.1E-73 418.0 11.5 133 4-137 1-133 (147)
6 PF08461 HTH_12: Ribonuclease 97.4 0.00044 9.6E-09 47.2 5.1 63 61-132 3-66 (66)
7 PF03444 HrcA_DNA-bdg: Winged 97.4 0.00044 9.5E-09 49.6 5.2 58 64-135 15-76 (78)
8 PF14947 HTH_45: Winged helix- 96.7 0.0055 1.2E-07 42.4 5.5 61 59-135 9-69 (77)
9 COG1420 HrcA Transcriptional r 96.6 0.0048 1E-07 54.3 5.8 68 57-136 7-81 (346)
10 TIGR02702 SufR_cyano iron-sulf 96.5 0.0067 1.5E-07 48.3 5.8 62 59-134 4-73 (203)
11 TIGR02337 HpaR homoprotocatech 96.5 0.014 3E-07 42.3 7.0 63 61-137 33-101 (118)
12 PRK11050 manganese transport r 96.4 0.013 2.8E-07 45.2 6.6 63 60-136 41-103 (152)
13 PF13463 HTH_27: Winged helix 96.4 0.0073 1.6E-07 39.2 4.5 54 61-128 8-68 (68)
14 PF01638 HxlR: HxlR-like helix 96.4 0.0075 1.6E-07 42.5 4.7 64 59-136 8-77 (90)
15 smart00529 HTH_DTXR Helix-turn 96.3 0.0068 1.5E-07 42.0 4.0 40 97-136 12-51 (96)
16 COG1846 MarR Transcriptional r 96.2 0.02 4.4E-07 39.5 6.4 65 59-137 25-95 (126)
17 PRK11512 DNA-binding transcrip 96.1 0.022 4.7E-07 42.7 6.4 62 60-135 44-111 (144)
18 smart00346 HTH_ICLR helix_turn 96.1 0.032 6.9E-07 38.0 6.7 60 56-129 5-66 (91)
19 PF05491 RuvB_C: Holliday junc 96.1 0.009 1.9E-07 42.7 4.0 68 52-133 7-74 (76)
20 smart00347 HTH_MARR helix_turn 95.9 0.044 9.6E-07 36.9 6.6 62 61-136 15-82 (101)
21 smart00418 HTH_ARSR helix_turn 95.9 0.042 9.1E-07 33.8 5.9 59 61-134 2-64 (66)
22 PRK10870 transcriptional repre 95.7 0.036 7.9E-07 43.6 6.3 62 61-136 60-129 (176)
23 PRK03902 manganese transport t 95.5 0.062 1.3E-06 40.4 6.7 61 61-135 13-73 (142)
24 PRK03911 heat-inducible transc 95.4 0.023 4.9E-07 48.8 4.6 70 58-139 5-81 (260)
25 PRK13777 transcriptional regul 95.2 0.067 1.5E-06 43.2 6.4 63 61-137 50-118 (185)
26 TIGR00331 hrcA heat shock gene 95.1 0.054 1.2E-06 47.1 5.9 57 67-135 18-76 (337)
27 PRK03573 transcriptional regul 95.0 0.11 2.3E-06 38.7 6.7 63 61-137 36-105 (144)
28 PF09339 HTH_IclR: IclR helix- 95.0 0.051 1.1E-06 34.6 4.2 49 56-118 3-52 (52)
29 PRK00082 hrcA heat-inducible t 95.0 0.059 1.3E-06 46.9 5.9 60 65-136 18-81 (339)
30 TIGR01889 Staph_reg_Sar staphy 94.8 0.11 2.3E-06 37.6 6.0 63 61-137 30-102 (109)
31 PRK09834 DNA-binding transcrip 94.6 0.15 3.3E-06 41.9 7.0 65 56-134 11-77 (263)
32 PF14338 Mrr_N: Mrr N-terminal 94.5 0.046 9.9E-07 38.7 3.3 36 98-133 54-89 (92)
33 PRK05638 threonine synthase; V 94.1 0.41 8.9E-06 42.5 9.3 93 25-135 337-441 (442)
34 COG3388 Predicted transcriptio 94.1 0.069 1.5E-06 40.1 3.6 64 57-135 15-78 (101)
35 TIGR03433 padR_acidobact trans 93.8 0.092 2E-06 37.7 3.8 45 93-137 34-86 (100)
36 TIGR01884 cas_HTH CRISPR locus 93.8 0.19 4.1E-06 40.0 5.9 55 60-128 147-203 (203)
37 COG3432 Predicted transcriptio 93.6 0.1 2.2E-06 38.7 3.7 42 94-135 41-85 (95)
38 cd07377 WHTH_GntR Winged helix 93.5 0.11 2.4E-06 32.7 3.4 39 73-125 28-66 (66)
39 PF02082 Rrf2: Transcriptional 93.3 0.26 5.6E-06 34.0 5.3 44 70-127 25-70 (83)
40 COG1321 TroR Mn-dependent tran 93.3 0.11 2.3E-06 40.8 3.7 50 68-131 22-71 (154)
41 PF01047 MarR: MarR family; I 93.0 0.25 5.4E-06 31.3 4.5 46 59-118 6-51 (59)
42 TIGR03338 phnR_burk phosphonat 93.0 0.14 2.9E-06 40.1 3.8 62 58-133 16-83 (212)
43 PF13601 HTH_34: Winged helix 92.9 0.26 5.7E-06 34.4 4.8 61 61-135 5-72 (80)
44 PF03551 PadR: Transcriptional 92.7 0.095 2.1E-06 35.4 2.3 41 93-133 26-74 (75)
45 PF10711 DUF2513: Hypothetical 92.7 0.2 4.3E-06 36.4 4.1 51 89-139 25-84 (102)
46 COG1733 Predicted transcriptio 92.6 0.31 6.7E-06 36.8 5.2 62 61-136 28-95 (120)
47 PF12802 MarR_2: MarR family; 92.6 0.29 6.3E-06 31.1 4.3 47 59-119 8-56 (62)
48 COG1693 Repressor of nif and g 92.5 0.096 2.1E-06 46.1 2.6 66 61-135 11-77 (325)
49 cd00092 HTH_CRP helix_turn_hel 92.5 0.75 1.6E-05 29.3 6.2 44 69-126 24-67 (67)
50 PF12840 HTH_20: Helix-turn-he 92.4 0.24 5.1E-06 32.3 3.8 46 59-118 13-58 (61)
51 PRK11014 transcriptional repre 92.1 0.34 7.5E-06 36.5 5.0 43 70-126 25-69 (141)
52 smart00345 HTH_GNTR helix_turn 91.8 0.22 4.7E-06 30.8 3.0 36 72-121 22-57 (60)
53 smart00550 Zalpha Z-DNA-bindin 91.7 0.66 1.4E-05 31.3 5.5 45 60-118 10-56 (68)
54 TIGR02812 fadR_gamma fatty aci 91.4 0.22 4.7E-06 39.7 3.4 41 72-126 32-72 (235)
55 PF00392 GntR: Bacterial regul 91.3 0.25 5.5E-06 32.4 3.1 38 72-123 26-63 (64)
56 COG1725 Predicted transcriptio 91.3 0.26 5.6E-06 38.0 3.5 36 99-134 50-85 (125)
57 TIGR02719 repress_PhaQ poly-be 91.3 0.31 6.8E-06 38.0 4.0 41 96-136 55-103 (138)
58 PRK15090 DNA-binding transcrip 91.2 0.56 1.2E-05 38.3 5.6 58 56-127 14-72 (257)
59 PF08220 HTH_DeoR: DeoR-like h 91.1 0.6 1.3E-05 30.5 4.7 52 57-123 1-52 (57)
60 PF06969 HemN_C: HemN C-termin 90.8 0.8 1.7E-05 29.8 5.1 55 61-129 11-65 (66)
61 PRK09990 DNA-binding transcrip 90.8 0.26 5.7E-06 39.7 3.3 45 72-130 33-77 (251)
62 cd00090 HTH_ARSR Arsenical Res 90.8 0.91 2E-05 28.3 5.2 61 60-136 11-74 (78)
63 PRK03837 transcriptional regul 90.6 1.7 3.6E-05 34.6 7.7 58 57-128 17-81 (241)
64 TIGR00738 rrf2_super rrf2 fami 90.3 0.78 1.7E-05 33.4 5.2 48 69-130 24-73 (132)
65 PF01726 LexA_DNA_bind: LexA D 90.3 1.3 2.7E-05 30.1 5.8 40 70-122 25-64 (65)
66 PRK04984 fatty acid metabolism 90.2 0.33 7.3E-06 38.7 3.4 41 72-126 33-73 (239)
67 PRK11569 transcriptional repre 90.2 0.85 1.9E-05 37.8 5.9 59 55-127 27-87 (274)
68 PRK10421 DNA-binding transcrip 90.1 0.32 6.9E-06 39.4 3.2 41 73-127 29-69 (253)
69 PRK10225 DNA-binding transcrip 90.0 0.31 6.8E-06 39.5 3.1 60 57-130 13-79 (257)
70 PRK11534 DNA-binding transcrip 89.9 0.44 9.6E-06 37.7 3.9 48 71-132 31-78 (224)
71 COG1802 GntR Transcriptional r 89.9 1.3 2.9E-05 35.3 6.6 65 57-135 20-90 (230)
72 smart00420 HTH_DEOR helix_turn 89.7 1.3 2.8E-05 26.5 5.1 45 60-118 4-48 (53)
73 PRK10163 DNA-binding transcrip 89.6 1 2.3E-05 37.3 6.0 58 56-127 25-84 (271)
74 PRK09464 pdhR transcriptional 89.5 0.38 8.3E-06 38.8 3.2 42 72-127 36-77 (254)
75 PRK11523 DNA-binding transcrip 89.1 0.41 9E-06 38.7 3.2 43 73-129 35-77 (253)
76 PRK11414 colanic acid/biofilm 89.1 0.53 1.2E-05 37.3 3.7 44 74-131 38-81 (221)
77 TIGR02944 suf_reg_Xantho FeS a 89.0 1.2 2.6E-05 32.8 5.3 57 58-128 11-71 (130)
78 PF10007 DUF2250: Uncharacteri 89.0 1.3 2.8E-05 32.5 5.4 48 61-124 12-59 (92)
79 COG1414 IclR Transcriptional r 88.9 1.2 2.7E-05 36.7 5.9 64 56-134 4-74 (246)
80 PF01978 TrmB: Sugar-specific 88.8 0.71 1.5E-05 30.4 3.6 46 59-118 11-56 (68)
81 TIGR02010 IscR iron-sulfur clu 88.7 1.3 2.7E-05 33.2 5.4 45 69-127 24-70 (135)
82 TIGR02018 his_ut_repres histid 88.7 1.6 3.5E-05 34.8 6.3 58 55-126 3-67 (230)
83 PF13412 HTH_24: Winged helix- 87.5 1.9 4E-05 26.5 4.8 42 60-115 7-48 (48)
84 TIGR02277 PaaX_trns_reg phenyl 86.9 0.75 1.6E-05 39.1 3.6 40 97-136 33-75 (280)
85 PRK14165 winged helix-turn-hel 86.2 0.77 1.7E-05 38.1 3.2 40 97-136 34-76 (217)
86 TIGR02325 C_P_lyase_phnF phosp 85.9 0.9 1.9E-05 36.0 3.4 61 54-128 9-76 (238)
87 COG2186 FadR Transcriptional r 85.9 0.87 1.9E-05 37.4 3.4 30 97-126 47-76 (241)
88 TIGR01610 phage_O_Nterm phage 85.7 3 6.5E-05 29.7 5.7 37 68-118 45-81 (95)
89 PF13814 Replic_Relax: Replica 85.5 2.2 4.8E-05 32.6 5.3 62 63-135 2-73 (191)
90 PF09382 RQC: RQC domain; Int 85.5 3.4 7.3E-05 29.1 5.8 77 59-135 7-97 (106)
91 PRK09416 lstR lineage-specific 85.5 1.2 2.7E-05 34.8 3.9 43 95-137 74-120 (135)
92 PRK10857 DNA-binding transcrip 84.6 2.6 5.7E-05 33.2 5.4 45 69-127 24-70 (164)
93 TIGR02787 codY_Gpos GTP-sensin 83.9 1.3 2.8E-05 38.0 3.6 39 96-134 210-250 (251)
94 PRK14999 histidine utilization 83.8 1.7 3.7E-05 35.0 4.1 60 54-127 13-79 (241)
95 COG4901 Ribosomal protein S25 83.6 1 2.2E-05 34.2 2.5 78 28-124 21-98 (107)
96 PRK11920 rirA iron-responsive 83.6 1.4 2.9E-05 34.2 3.3 45 70-128 24-70 (153)
97 smart00419 HTH_CRP helix_turn_ 83.2 1.8 4E-05 25.7 3.2 35 70-118 8-42 (48)
98 TIGR02431 pcaR_pcaU beta-ketoa 82.5 4 8.7E-05 33.0 5.8 57 56-127 9-66 (248)
99 PRK11886 bifunctional biotin-- 82.0 3.7 8E-05 34.7 5.6 59 55-127 3-62 (319)
100 TIGR02404 trehalos_R_Bsub treh 81.9 1.6 3.5E-05 34.8 3.3 41 73-127 27-67 (233)
101 COG1959 Predicted transcriptio 81.7 3.6 7.9E-05 31.8 5.1 44 70-127 25-70 (150)
102 PF09114 MotA_activ: Transcrip 81.4 7.7 0.00017 29.0 6.4 67 57-136 17-83 (96)
103 PRK09764 DNA-binding transcrip 81.4 1.8 3.9E-05 34.9 3.4 61 54-128 6-73 (240)
104 PRK04172 pheS phenylalanyl-tRN 81.3 3.5 7.5E-05 37.4 5.5 63 59-135 9-73 (489)
105 PRK09334 30S ribosomal protein 81.1 1.8 3.9E-05 31.6 2.9 22 97-118 54-75 (86)
106 COG3355 Predicted transcriptio 80.3 3.9 8.4E-05 31.7 4.7 38 67-118 39-76 (126)
107 PRK08599 coproporphyrinogen II 79.6 4.5 9.9E-05 34.8 5.5 38 99-137 334-371 (377)
108 PF01022 HTH_5: Bacterial regu 79.4 4.7 0.0001 25.0 4.1 42 60-116 6-47 (47)
109 PRK10079 phosphonate metabolis 79.3 2.1 4.7E-05 34.4 3.2 59 54-127 13-78 (241)
110 COG2255 RuvB Holliday junction 78.9 5.2 0.00011 35.6 5.6 71 52-136 259-329 (332)
111 PF14394 DUF4423: Domain of un 78.6 2.4 5.1E-05 33.7 3.2 33 95-127 52-84 (171)
112 PF12793 SgrR_N: Sugar transpo 78.5 2.5 5.4E-05 31.7 3.1 39 70-122 19-57 (115)
113 COG1695 Predicted transcriptio 78.4 2.3 5.1E-05 31.4 2.9 41 96-136 42-90 (138)
114 PRK06266 transcription initiat 77.9 5.6 0.00012 31.8 5.2 42 60-115 26-67 (178)
115 COG2524 Predicted transcriptio 77.4 2 4.3E-05 37.6 2.6 38 99-136 40-79 (294)
116 PRK13509 transcriptional repre 77.3 7.9 0.00017 32.0 6.0 51 57-122 6-56 (251)
117 PRK11402 DNA-binding transcrip 77.0 2.9 6.3E-05 33.6 3.3 60 55-128 11-77 (241)
118 PRK12423 LexA repressor; Provi 77.0 7.3 0.00016 31.1 5.6 37 70-119 25-61 (202)
119 PRK05283 deoxyribose-phosphate 76.6 2.6 5.6E-05 36.0 3.0 90 12-113 145-251 (257)
120 PRK09057 coproporphyrinogen II 76.4 8.2 0.00018 33.6 6.2 53 69-137 324-376 (380)
121 TIGR00122 birA_repr_reg BirA b 75.7 13 0.00028 24.4 5.7 52 60-126 4-55 (69)
122 PRK07379 coproporphyrinogen II 75.4 1.9 4.2E-05 37.9 2.0 37 99-137 351-390 (400)
123 PF04703 FaeA: FaeA-like prote 75.2 3.5 7.5E-05 28.1 2.8 37 68-118 13-49 (62)
124 PF03297 Ribosomal_S25: S25 ri 73.9 2.5 5.5E-05 31.7 2.1 35 70-118 59-93 (105)
125 PRK00215 LexA repressor; Valid 73.5 13 0.00029 29.2 6.2 52 70-134 23-76 (205)
126 PRK08208 coproporphyrinogen II 73.5 8.4 0.00018 34.2 5.6 56 68-138 359-414 (430)
127 COG2188 PhnF Transcriptional r 73.1 3.9 8.4E-05 33.3 3.1 73 55-141 9-96 (236)
128 PRK05799 coproporphyrinogen II 72.3 1.6 3.5E-05 37.4 0.8 37 100-137 334-370 (374)
129 PRK00080 ruvB Holliday junctio 71.9 6.7 0.00014 33.1 4.4 66 52-134 261-326 (328)
130 TIGR00498 lexA SOS regulatory 71.5 13 0.00028 29.1 5.7 45 62-119 15-61 (199)
131 PF07848 PaaX: PaaX-like prote 71.4 5.9 0.00013 27.3 3.3 61 57-128 1-70 (70)
132 TIGR02147 Fsuc_second hypothet 71.2 12 0.00026 31.9 5.8 59 52-126 121-181 (271)
133 TIGR00635 ruvB Holliday juncti 70.9 9.6 0.00021 31.2 5.0 50 68-132 253-303 (305)
134 PRK09802 DNA-binding transcrip 70.5 11 0.00025 31.5 5.5 55 56-125 17-71 (269)
135 PRK10906 DNA-binding transcrip 70.4 14 0.0003 30.6 5.9 55 57-126 6-60 (252)
136 PF01325 Fe_dep_repress: Iron 70.0 15 0.00033 24.2 5.0 40 68-121 20-59 (60)
137 PF00126 HTH_1: Bacterial regu 69.8 7 0.00015 25.2 3.2 32 97-129 26-60 (60)
138 COG2512 Predicted membrane-ass 69.4 18 0.00038 30.8 6.4 86 17-121 161-247 (258)
139 TIGR02698 CopY_TcrY copper tra 68.7 14 0.0003 27.9 5.1 52 60-122 8-59 (130)
140 PRK05628 coproporphyrinogen II 68.6 5.1 0.00011 34.6 3.1 35 102-137 337-371 (375)
141 PRK13347 coproporphyrinogen II 68.1 5.2 0.00011 35.7 3.1 35 102-137 402-436 (453)
142 PRK10434 srlR DNA-bindng trans 67.6 14 0.0003 30.7 5.3 54 57-125 6-59 (256)
143 PF09012 FeoC: FeoC like trans 66.7 10 0.00022 25.2 3.7 40 65-118 9-48 (69)
144 COG1542 Uncharacterized conser 66.1 3.8 8.2E-05 38.6 1.8 100 31-131 385-489 (593)
145 TIGR00373 conserved hypothetic 65.8 14 0.00031 28.8 4.8 43 59-115 17-59 (158)
146 PRK06582 coproporphyrinogen II 65.4 17 0.00036 32.1 5.7 56 67-137 330-386 (390)
147 TIGR01594 holin_lambda phage h 65.4 5.6 0.00012 29.7 2.3 35 46-84 1-44 (107)
148 PF09821 AAA_assoc_C: C-termin 65.2 7.4 0.00016 29.4 3.0 32 102-134 15-46 (120)
149 TIGR00637 ModE_repress ModE mo 65.1 11 0.00025 27.2 3.9 35 99-133 31-72 (99)
150 PRK06294 coproporphyrinogen II 63.7 7.3 0.00016 33.9 3.1 36 101-137 332-367 (370)
151 PF08222 HTH_CodY: CodY helix- 63.0 7.6 0.00017 26.8 2.4 21 98-118 18-38 (61)
152 PRK09249 coproporphyrinogen II 62.4 6.3 0.00014 35.1 2.5 33 104-137 404-436 (453)
153 PF13730 HTH_36: Helix-turn-he 61.8 7.2 0.00016 24.3 2.1 19 96-114 37-55 (55)
154 smart00344 HTH_ASNC helix_turn 61.7 23 0.0005 24.7 4.8 42 60-115 7-48 (108)
155 PF11313 DUF3116: Protein of u 60.7 9.9 0.00021 27.7 2.8 42 97-138 40-84 (85)
156 PRK08629 coproporphyrinogen II 60.6 20 0.00044 32.1 5.4 56 69-138 357-412 (433)
157 PF14337 DUF4393: Domain of un 59.3 8.1 0.00018 30.0 2.4 94 11-117 31-133 (186)
158 PRK05660 HemN family oxidoredu 59.0 10 0.00022 33.1 3.1 36 101-137 338-373 (378)
159 PF02522 Antibiotic_NAT: Amino 58.9 6.6 0.00014 32.1 1.9 86 11-104 15-107 (229)
160 TIGR00538 hemN oxygen-independ 58.7 7.9 0.00017 34.5 2.5 33 104-137 404-436 (455)
161 COG0635 HemN Coproporphyrinoge 58.7 27 0.00058 31.3 5.8 60 64-137 348-407 (416)
162 PRK13626 transcriptional regul 58.7 9.2 0.0002 34.7 2.9 40 69-122 22-61 (552)
163 PF03965 Penicillinase_R: Peni 58.6 20 0.00043 25.9 4.2 50 60-119 7-56 (115)
164 TIGR02424 TF_pcaQ pca operon t 57.8 13 0.00027 29.9 3.3 36 99-135 32-70 (300)
165 PF08279 HTH_11: HTH domain; 57.2 39 0.00084 20.9 4.9 48 57-118 1-50 (55)
166 PRK10141 DNA-binding transcrip 56.1 32 0.00069 25.9 5.0 60 60-134 20-83 (117)
167 PRK10411 DNA-binding transcrip 55.4 41 0.00089 27.7 6.0 51 57-121 5-55 (240)
168 PF07381 DUF1495: Winged helix 55.1 10 0.00022 27.7 2.2 28 107-134 58-89 (90)
169 PRK15481 transcriptional regul 55.0 15 0.00032 31.8 3.5 31 96-126 41-71 (431)
170 PRK08898 coproporphyrinogen II 54.9 13 0.00029 32.5 3.2 35 102-137 356-390 (394)
171 PRK11242 DNA-binding transcrip 54.5 17 0.00036 29.0 3.5 36 99-135 30-68 (296)
172 TIGR03337 phnR transcriptional 54.4 16 0.00034 28.8 3.3 42 73-128 28-69 (231)
173 PRK04424 fatty acid biosynthes 54.4 14 0.0003 29.4 3.0 65 57-137 8-79 (185)
174 PRK10082 cell density-dependen 54.3 14 0.00031 29.9 3.1 36 99-135 40-78 (303)
175 PRK04214 rbn ribonuclease BN/u 51.0 65 0.0014 28.5 6.9 56 56-125 292-351 (412)
176 COG4189 Predicted transcriptio 50.4 30 0.00064 30.4 4.5 49 61-123 28-76 (308)
177 TIGR03339 phn_lysR aminoethylp 50.4 22 0.00048 27.7 3.5 34 100-134 27-63 (279)
178 PRK09791 putative DNA-binding 50.3 19 0.00041 29.1 3.2 37 99-136 34-73 (302)
179 PRK08446 coproporphyrinogen II 50.3 13 0.00029 32.0 2.4 33 103-138 315-347 (350)
180 TIGR02647 DNA conserved hypoth 49.8 24 0.00052 25.5 3.3 37 93-132 29-65 (77)
181 PRK11716 DNA-binding transcrip 49.7 25 0.00054 27.2 3.7 37 99-136 6-45 (269)
182 PRK09058 coproporphyrinogen II 47.4 18 0.00038 32.5 2.8 36 101-137 398-433 (449)
183 PHA02943 hypothetical protein; 47.4 68 0.0015 26.1 5.9 55 51-120 6-60 (165)
184 COG1349 GlpR Transcriptional r 46.4 47 0.001 27.5 5.0 55 57-126 6-60 (253)
185 TIGR02036 dsdC D-serine deamin 46.3 30 0.00064 28.2 3.8 37 99-136 37-76 (302)
186 PF04408 HA2: Helicase associa 46.1 15 0.00033 26.0 1.9 26 103-132 1-26 (102)
187 PF09929 DUF2161: Uncharacteri 44.9 21 0.00045 27.6 2.5 59 57-132 60-118 (118)
188 PRK09986 DNA-binding transcrip 44.5 27 0.00058 27.7 3.2 35 100-135 37-74 (294)
189 COG4533 ABC-type uncharacteriz 43.6 23 0.00049 33.7 3.0 39 70-122 23-61 (564)
190 PRK11233 nitrogen assimilation 43.6 33 0.00073 27.9 3.7 35 99-134 30-67 (305)
191 PF14113 DUF4285: Domain of un 43.5 69 0.0015 23.7 5.1 45 19-69 11-55 (115)
192 PF14277 DUF4364: Domain of un 43.2 30 0.00065 27.4 3.3 35 100-134 35-73 (163)
193 PRK11151 DNA-binding transcrip 43.1 30 0.00065 27.9 3.4 35 99-134 30-67 (305)
194 COG2345 Predicted transcriptio 42.9 61 0.0013 27.2 5.2 57 60-130 15-79 (218)
195 KOG1767 40S ribosomal protein 42.8 16 0.00036 27.9 1.7 24 95-118 71-94 (110)
196 smart00847 HA2 Helicase associ 41.5 20 0.00043 24.3 1.8 25 104-132 2-26 (92)
197 PRK12681 cysB transcriptional 41.4 31 0.00067 28.8 3.3 35 100-135 32-70 (324)
198 COG0640 ArsR Predicted transcr 41.0 93 0.002 19.7 6.0 52 59-124 28-79 (110)
199 PRK03601 transcriptional regul 40.9 38 0.00083 27.2 3.6 36 100-136 31-69 (275)
200 PRK14997 LysR family transcrip 40.8 34 0.00073 27.5 3.3 35 100-135 32-69 (301)
201 PRK10094 DNA-binding transcrip 40.2 38 0.00082 27.8 3.6 36 99-135 31-69 (308)
202 PF08432 Vfa1: AAA-ATPase Vps4 40.2 7.6 0.00017 31.0 -0.5 13 46-58 28-40 (182)
203 COG1568 Predicted methyltransf 39.6 29 0.00062 31.1 2.9 38 95-133 45-82 (354)
204 TIGR03418 chol_sulf_TF putativ 39.4 28 0.0006 27.8 2.6 35 100-135 31-68 (291)
205 PF09681 Phage_rep_org_N: N-te 39.2 38 0.00082 25.7 3.2 48 65-126 46-95 (121)
206 PRK10837 putative DNA-binding 38.9 40 0.00088 26.7 3.4 35 100-135 33-70 (290)
207 CHL00180 rbcR LysR transcripti 38.8 36 0.00077 27.6 3.2 36 99-135 34-72 (305)
208 PRK09906 DNA-binding transcrip 38.6 31 0.00067 27.6 2.8 34 101-135 32-68 (296)
209 PF15129 FAM150: FAM150 family 38.4 20 0.00044 27.8 1.6 17 53-69 103-119 (123)
210 PF13182 DUF4007: Protein of u 38.3 25 0.00054 30.0 2.3 34 100-133 44-77 (286)
211 COG1510 Predicted transcriptio 38.3 28 0.00062 28.6 2.5 46 61-120 31-77 (177)
212 TIGR03298 argP transcriptional 38.2 34 0.00074 27.4 2.9 36 99-136 30-68 (292)
213 PRK10632 transcriptional regul 37.3 38 0.00082 27.7 3.1 36 99-135 31-69 (309)
214 PRK12684 transcriptional regul 37.3 30 0.00065 28.4 2.6 36 101-136 33-71 (313)
215 PRK15421 DNA-binding transcrip 37.2 43 0.00094 27.7 3.5 35 100-135 32-69 (317)
216 PRK06474 hypothetical protein; 36.8 1.1E+02 0.0023 24.3 5.5 46 60-118 15-61 (178)
217 PRK11013 DNA-binding transcrip 36.8 40 0.00088 27.5 3.2 36 99-135 33-71 (309)
218 PRK11062 nhaR transcriptional 35.9 50 0.0011 26.8 3.6 34 101-135 35-71 (296)
219 PRK12682 transcriptional regul 35.7 44 0.00095 27.2 3.3 37 99-136 31-71 (309)
220 PRK11139 DNA-binding transcrip 35.6 53 0.0011 26.4 3.7 36 99-135 35-73 (297)
221 PRK10086 DNA-binding transcrip 35.1 34 0.00074 28.0 2.5 34 101-135 45-81 (311)
222 TIGR02716 C20_methyl_CrtF C-20 34.8 53 0.0011 27.3 3.7 52 68-134 21-72 (306)
223 TIGR00988 hip integration host 34.7 30 0.00064 24.2 1.9 27 13-39 27-53 (94)
224 PF09202 Rio2_N: Rio2, N-termi 34.4 60 0.0013 23.0 3.4 37 96-132 36-74 (82)
225 PF04458 DUF505: Protein of un 34.2 27 0.00059 33.4 2.0 90 45-141 407-506 (591)
226 PHA00738 putative HTH transcri 34.1 1E+02 0.0022 23.4 4.7 48 61-123 17-64 (108)
227 PRK10341 DNA-binding transcrip 33.7 56 0.0012 26.7 3.6 35 99-134 36-73 (312)
228 PF07042 TrfA: TrfA protein; 33.5 22 0.00047 30.9 1.1 40 70-116 231-270 (282)
229 cd08768 Cdc6_C Winged-helix do 33.1 37 0.00079 22.8 2.0 22 97-118 45-66 (87)
230 COG1654 BirA Biotin operon rep 33.0 60 0.0013 23.1 3.2 30 97-126 32-62 (79)
231 PRK12680 transcriptional regul 32.5 46 0.00099 27.8 2.9 36 99-135 31-70 (327)
232 PF15522 Toxin_42: Putative to 32.5 40 0.00087 27.8 2.5 29 13-41 38-66 (205)
233 PRK09508 leuO leucine transcri 32.3 58 0.0013 26.6 3.4 31 101-132 53-86 (314)
234 PF02909 TetR_C: Tetracyclin r 32.2 1.2E+02 0.0027 21.4 4.8 58 47-115 2-61 (139)
235 smart00479 EXOIII exonuclease 31.8 1E+02 0.0022 22.4 4.4 53 55-110 113-165 (169)
236 PF10264 Stork_head: Winged he 31.5 2E+02 0.0043 20.7 5.7 53 69-127 28-80 (80)
237 PRK12683 transcriptional regul 30.8 58 0.0013 26.7 3.2 36 99-135 31-70 (309)
238 PF14178 YppF: YppF-like prote 30.7 46 0.00099 23.0 2.2 32 44-79 14-45 (60)
239 PF02002 TFIIE_alpha: TFIIE al 30.5 71 0.0015 22.6 3.3 45 58-116 15-59 (105)
240 PRK00199 ihfB integration host 30.5 38 0.00083 23.7 1.9 29 13-41 27-55 (94)
241 PRK12679 cbl transcriptional r 30.4 57 0.0012 26.8 3.1 34 100-134 32-69 (316)
242 PF04157 EAP30: EAP30/Vps36 fa 30.3 1.5E+02 0.0033 23.9 5.5 85 8-115 131-221 (223)
243 PF09079 Cdc6_C: CDC6, C termi 30.1 46 0.00099 22.6 2.2 20 99-118 40-59 (85)
244 PF04458 DUF505: Protein of un 29.6 36 0.00077 32.7 2.0 40 96-135 327-370 (591)
245 COG4754 Uncharacterized conser 29.5 53 0.0012 26.5 2.7 32 102-134 46-77 (157)
246 COG1339 Transcriptional regula 29.4 50 0.0011 27.9 2.6 32 102-133 37-71 (214)
247 PRK13348 chromosome replicatio 29.2 64 0.0014 25.8 3.2 35 100-136 32-69 (294)
248 COG3398 Uncharacterized protei 29.0 51 0.0011 28.3 2.6 27 96-123 200-226 (240)
249 TIGR01714 phage_rep_org_N phag 28.5 75 0.0016 24.2 3.2 27 99-125 66-92 (119)
250 COG3327 PaaX Phenylacetic acid 28.4 58 0.0013 28.6 2.9 39 98-136 42-83 (291)
251 PF07571 DUF1546: Protein of u 28.4 1.7E+02 0.0037 20.7 4.9 18 51-68 17-36 (92)
252 TIGR03042 PS_II_psbQ_bact phot 28.3 29 0.00064 27.4 1.0 59 50-119 61-119 (142)
253 PRK15092 DNA-binding transcrip 28.2 79 0.0017 26.2 3.6 34 101-135 42-78 (310)
254 PF09661 DUF2398: Protein of u 27.7 1.2E+02 0.0025 27.0 4.8 50 74-127 309-358 (368)
255 PRK11074 putative DNA-binding 26.8 78 0.0017 25.6 3.3 36 99-135 31-69 (300)
256 PF14629 ORC4_C: Origin recogn 26.8 64 0.0014 25.3 2.7 36 94-129 149-185 (203)
257 PRK00135 scpB segregation and 26.6 1.5E+02 0.0034 23.9 5.0 41 59-116 93-133 (188)
258 COG0583 LysR Transcriptional r 26.0 91 0.002 24.1 3.4 34 101-135 32-68 (297)
259 PF00216 Bac_DNA_binding: Bact 25.7 42 0.00091 22.7 1.3 26 13-38 26-51 (90)
260 PRK15243 transcriptional regul 25.5 1E+02 0.0022 26.0 3.8 35 99-134 33-70 (297)
261 COG0096 RpsH Ribosomal protein 25.3 68 0.0015 25.1 2.5 31 6-36 23-53 (132)
262 PF04182 B-block_TFIIIC: B-blo 25.1 54 0.0012 22.2 1.8 20 99-118 33-52 (75)
263 COG1485 Predicted ATPase [Gene 24.4 9.5 0.00021 34.4 -2.6 57 52-112 55-114 (367)
264 PRK11482 putative DNA-binding 24.2 88 0.0019 25.9 3.2 32 100-132 59-93 (317)
265 COG1497 Predicted transcriptio 24.2 58 0.0013 28.3 2.1 35 103-137 44-78 (260)
266 PRK10664 transcriptional regul 24.1 56 0.0012 23.1 1.8 26 13-38 26-51 (90)
267 PRK00285 ihfA integration host 24.1 60 0.0013 22.9 1.9 26 13-38 28-53 (99)
268 PTZ00134 40S ribosomal protein 23.9 80 0.0017 25.1 2.7 30 6-36 57-86 (154)
269 PF03953 Tubulin_C: Tubulin C- 23.4 80 0.0017 23.1 2.6 41 9-51 60-101 (126)
270 PRK11057 ATP-dependent DNA hel 23.2 1.4E+02 0.003 27.8 4.6 86 48-134 407-504 (607)
271 PRK07983 exodeoxyribonuclease 23.2 74 0.0016 26.0 2.5 88 55-142 96-205 (219)
272 cd01817 RGS12_RBD Ubiquitin do 22.8 86 0.0019 22.3 2.5 33 17-51 24-56 (73)
273 COG4465 CodY Pleiotropic trans 22.7 63 0.0014 27.9 2.1 22 97-118 217-238 (261)
274 TIGR03157 cas_Csc2 CRISPR-asso 22.6 61 0.0013 28.4 2.0 25 2-26 165-189 (282)
275 PF14502 HTH_41: Helix-turn-he 22.4 1E+02 0.0022 20.3 2.5 26 96-122 18-43 (48)
276 KOG2035 Replication factor C, 22.1 1.3E+02 0.0029 27.1 4.0 110 13-135 15-150 (351)
277 COG5631 Predicted transcriptio 21.9 82 0.0018 26.2 2.5 33 98-131 113-149 (199)
278 TIGR00987 himA integration hos 21.9 70 0.0015 22.5 1.9 25 13-37 27-51 (96)
279 PRK03635 chromosome replicatio 21.7 97 0.0021 25.0 2.9 36 100-137 32-70 (294)
280 PF06044 DRP: Dam-replacing fa 21.6 89 0.0019 27.1 2.8 23 99-122 228-250 (254)
281 PF09397 Ftsk_gamma: Ftsk gamm 21.4 96 0.0021 21.3 2.4 50 52-118 5-54 (65)
282 PF09911 DUF2140: Uncharacteri 21.2 90 0.0019 25.1 2.6 21 16-38 127-147 (187)
283 COG0735 Fur Fe2+/Zn2+ uptake r 21.2 1.1E+02 0.0024 23.4 3.0 26 96-121 53-78 (145)
284 PRK14493 putative bifunctional 21.1 1.6E+02 0.0034 25.0 4.2 46 8-59 10-55 (274)
285 KOG4068 Uncharacterized conser 21.1 87 0.0019 25.7 2.5 26 93-118 63-88 (174)
286 PF13545 HTH_Crp_2: Crp-like h 21.1 1.3E+02 0.0028 19.3 3.0 23 96-118 40-62 (76)
287 PF13835 DUF4194: Domain of un 20.8 2.1E+02 0.0045 21.8 4.5 64 52-119 73-145 (166)
288 COG3682 Predicted transcriptio 20.8 2E+02 0.0044 22.2 4.4 72 59-140 9-91 (123)
289 PF03180 Lipoprotein_9: NLPA l 20.8 88 0.0019 26.1 2.5 31 9-39 7-38 (237)
290 TIGR02928 orc1/cdc6 family rep 20.6 84 0.0018 26.3 2.4 21 97-117 330-350 (365)
291 COG4344 Uncharacterized protei 20.5 73 0.0016 26.0 1.9 20 99-118 46-65 (175)
292 PRK13239 alkylmercury lyase; P 20.5 2.7E+02 0.0058 23.2 5.3 47 60-124 26-72 (206)
293 TIGR00716 rnhC ribonuclease HI 20.1 1.7E+02 0.0036 25.2 4.1 50 53-113 221-271 (284)
294 COG1522 Lrp Transcriptional re 20.1 3.2E+02 0.007 19.8 5.2 44 60-117 12-55 (154)
295 PF05732 RepL: Firmicute plasm 20.0 1.4E+02 0.0031 23.5 3.5 32 96-127 87-118 (165)
No 1
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=100.00 E-value=3.7e-74 Score=445.18 Aligned_cols=133 Identities=56% Similarity=0.956 Sum_probs=122.5
Q ss_pred ccccccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCCC
Q 032124 5 KNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK 84 (147)
Q Consensus 5 ~tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~k 84 (147)
+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++||++|||+|
T Consensus 1 vtvkDV~a~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~~~DW~Y~RaASilRklY~~g~~GV~~lr~~YGg~k 80 (139)
T PF01090_consen 1 VTVKDVPADEFIKALAEFLKKSGKIEPPEWADIVKTGSHKELAPYDPDWWYIRAASILRKLYIRGPVGVGRLRKIYGGRK 80 (139)
T ss_dssp HCGGGSSHHHHHHHHHHHHTCSSTS--TSCGGGTSSSSS-SSTTCHHTHHHHHHHHHHHHHHHCTSB-HHHHHHHH--EE
T ss_pred CcceecCHHHHHHHHHHHHHHcCCcCCcchHHHHhhcccccCCCCCCCeeeeeHHHHHHHHHHhcCcchHHHHHHhCCCC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 85 RNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 85 rrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
|||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+||.
T Consensus 81 ~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~ 133 (139)
T PF01090_consen 81 RRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAG 133 (139)
T ss_dssp EETSSCCEE--CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999986
No 2
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=100.00 E-value=1.8e-72 Score=447.13 Aligned_cols=135 Identities=39% Similarity=0.655 Sum_probs=131.6
Q ss_pred CccccccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCC
Q 032124 4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG 83 (147)
Q Consensus 4 ~~tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~ 83 (147)
.+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++||++|||+
T Consensus 25 ~~tvkDVpa~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~YGg~ 104 (169)
T PTZ00095 25 NATLKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSSK 104 (169)
T ss_pred CCceeeCCHHHHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHHCCC
Confidence 45999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-CCeeeChhhhhhhhhhhcC
Q 032124 84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GQSLVLVERLHKLDCENSN 138 (147)
Q Consensus 84 krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~~LDri~~~ 138 (147)
||||++|+||++|||+|||+||||||++|||+++++ +||+|||+||++||+||..
T Consensus 105 krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~ 160 (169)
T PTZ00095 105 KRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQ 160 (169)
T ss_pred CCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHH
Confidence 999999999999999999999999999999999964 8999999999999999964
No 3
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=100.00 E-value=2.2e-71 Score=434.14 Aligned_cols=134 Identities=38% Similarity=0.650 Sum_probs=131.6
Q ss_pred CccccccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCC
Q 032124 4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG 83 (147)
Q Consensus 4 ~~tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~ 83 (147)
|+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+
T Consensus 1 m~tv~DVpa~~~I~~~A~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~ 80 (150)
T PRK09333 1 MVTVYDVPADLLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGR 80 (150)
T ss_pred CCCcccCCHHHHHHHHHHHHHhcCCcCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCC
Confidence 56999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhcC
Q 032124 84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENSN 138 (147)
Q Consensus 84 krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~~ 138 (147)
||||++|+||++|||+|||++|||||++|||++++ +||+||++||++||+||..
T Consensus 81 k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~iA~~ 134 (150)
T PRK09333 81 KNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNLAAE 134 (150)
T ss_pred cCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998 8999999999999999864
No 4
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-71 Score=428.65 Aligned_cols=136 Identities=56% Similarity=0.966 Sum_probs=134.7
Q ss_pred CCCCccccccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHh
Q 032124 1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY 80 (147)
Q Consensus 1 m~~~~tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~Y 80 (147)
||++ |||||+|++|+++||.|||++|||++|+|+|+||||.+||+||+||||||+|||||+||||++||+||++|+++|
T Consensus 1 m~gv-tVkdV~~~~f~~a~asfLK~sgkv~vp~~~DivKtg~~kElAP~D~dWfytRaASiaRhiylR~~~gvg~~~KiY 79 (143)
T KOG3411|consen 1 MPGV-TVKDVDPHKFTKAYASFLKRSGKVEVPQWVDIVKTGKGKELAPYDPDWYYTRAASIARHIYLRGPVGVGALTKIY 79 (143)
T ss_pred CCcc-chhhcCHHHHHHHHHHHHHhcCCccCcchhhhhhcccCcccCCCCccHHHHHHHHHHHHHHhccccchhHHHHHh
Confidence 8888 999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 81 GGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 81 Gg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
||+||||++|+||+.+||+|+|++||+||++||||++++|||+||++||+||||||+
T Consensus 80 Gg~krrGvrPsh~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~ 136 (143)
T KOG3411|consen 80 GGSKRRGVRPSHFCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAG 136 (143)
T ss_pred cccccCCCCChhhhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999986
No 5
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=4.9e-69 Score=417.96 Aligned_cols=133 Identities=41% Similarity=0.702 Sum_probs=131.0
Q ss_pred CccccccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCC
Q 032124 4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG 83 (147)
Q Consensus 4 ~~tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~ 83 (147)
|+||||||+|+||++||++||++++|++|+|++|||||+|||+||.++||||+||||||||||++||+||++||+.|||+
T Consensus 1 m~tv~dVpad~lI~~lA~~LK~~~kv~pP~wa~~vKTG~~kE~~P~~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~ 80 (147)
T COG2238 1 MVTVYDVPADLLIEALASYLKETGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGR 80 (147)
T ss_pred CCchhcCCHHHHHHHHHHHHHhcCCcCChhhhhhhhccccccCCCCCCchHHHHHHHHHHHHHhcCchhHHHHHHHHCcc
Confidence 56999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 84 krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
|+||++|+||.+|||+|+|++|||||++|||+|++ +||+|||+||++||+||.
T Consensus 81 k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ 133 (147)
T COG2238 81 KNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIAT 133 (147)
T ss_pred ccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHH
Confidence 99999999999999999999999999999999998 899999999999999985
No 6
>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=97.37 E-value=0.00044 Score=47.20 Aligned_cols=63 Identities=14% Similarity=0.159 Sum_probs=51.9
Q ss_pred HHHHHHHh-CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 61 i~RklYl~-g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
||+.|+-. +|+|=..|+....-. | ..-|-.-+|.-|.+||..|++++...+||.||++|...|
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~---g------~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLR---G------EELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc---C------hhhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence 77888875 699999999887642 3 234557899999999999999988778999999998765
No 7
>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=97.37 E-value=0.00044 Score=49.59 Aligned_cols=58 Identities=16% Similarity=0.324 Sum_probs=47.9
Q ss_pred HHHHh--CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCeeeChhhhhhhhhh
Q 032124 64 KIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSLVLVERLHKLDCE 135 (147)
Q Consensus 64 klYl~--g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~~LDri 135 (147)
.+|++ .|||=..+....+- |..-||..++.||++|||++.+ .+||+-|.+|-+.+++.
T Consensus 15 ~~Y~~~~~PVgSk~ia~~l~~--------------s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~~ 76 (78)
T PF03444_consen 15 ELYIETGEPVGSKTIAEELGR--------------SPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNRQ 76 (78)
T ss_pred HHHHhcCCCcCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHccc
Confidence 45775 59999999987541 3378999999999999999643 68999999999999875
No 8
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.67 E-value=0.0055 Score=42.40 Aligned_cols=61 Identities=13% Similarity=0.151 Sum_probs=43.0
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhh
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+.||.-+- .++.....+.. .+.=|-+.+.+.|..|++.|+|++. ++.-+||++|...|+.+
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHH
Confidence 34555554 67766665553 2456778999999999999999874 67999999999999876
No 9
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=96.57 E-value=0.0048 Score=54.30 Aligned_cols=68 Identities=18% Similarity=0.185 Sum_probs=53.3
Q ss_pred hHHHHHHH---HHHh--CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC-CCCeeeChhhhh
Q 032124 57 RAASMARK---IYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGQSLVLVERLH 130 (147)
Q Consensus 57 RaASi~Rk---lYl~--g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~ 130 (147)
|...|||. .|+. .|||=.+|.+.|+- .-|..-||..+++||++|+++|.. -.||+-|+.|-+
T Consensus 7 Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l------------~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr 74 (346)
T COG1420 7 RQRLILRAIVEDYLATGEPVGSKTLSEKYNL------------DLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYR 74 (346)
T ss_pred HHHHHHHHHHHHHHhcCCccchHHHHHHhCC------------CCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHH
Confidence 45556664 4775 59999999998762 456789999999999999999876 479999999976
Q ss_pred h-hhhhh
Q 032124 131 K-LDCEN 136 (147)
Q Consensus 131 ~-LDri~ 136 (147)
. .|..+
T Consensus 75 ~YVd~ll 81 (346)
T COG1420 75 YYVDHLL 81 (346)
T ss_pred HHHHHhc
Confidence 4 44443
No 10
>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=96.51 E-value=0.0067 Score=48.30 Aligned_cols=62 Identities=10% Similarity=0.117 Sum_probs=50.6
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC---CCCe-----eeChhhhh
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGQS-----LVLVERLH 130 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~---~~GR-----~lT~~G~~ 130 (147)
-+||..|.-.+++.+..|....|-. .+-+|+.|+.||+.|||++.+ ..|| .||++|+.
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis--------------~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~ 69 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAIS--------------PQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGRE 69 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhh
Confidence 3578888888999999999987643 368999999999999998762 3578 99999988
Q ss_pred hhhh
Q 032124 131 KLDC 134 (147)
Q Consensus 131 ~LDr 134 (147)
.+..
T Consensus 70 ~~~~ 73 (203)
T TIGR02702 70 QFPQ 73 (203)
T ss_pred hccc
Confidence 6653
No 11
>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=96.51 E-value=0.014 Score=42.31 Aligned_cols=63 Identities=10% Similarity=0.032 Sum_probs=49.7
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCe----eeChhhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQS----LVLVERLHKLDC 134 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~LDr 134 (147)
||..|+-.+++.+..|....|-.+ +-+-.+++.||+.|||++.+ .+.| .||++|+..++.
T Consensus 33 iL~~l~~~~~~t~~ela~~~~~~~--------------~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~ 98 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQACILR--------------PSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS 98 (118)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCc--------------hhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence 666777789999999999877543 34678999999999999755 3344 699999999988
Q ss_pred hhc
Q 032124 135 ENS 137 (147)
Q Consensus 135 i~~ 137 (147)
+..
T Consensus 99 ~~~ 101 (118)
T TIGR02337 99 LSP 101 (118)
T ss_pred hhH
Confidence 753
No 12
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.39 E-value=0.013 Score=45.17 Aligned_cols=63 Identities=13% Similarity=0.073 Sum_probs=51.2
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
.|++.++-.+++.+..|...+|-. .+-+..+|++||+.|+|...+.+|-.||++|+..+..+.
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is--------------~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~ 103 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVS--------------QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESR 103 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHH
Confidence 355666666888999999887643 378999999999999999877778999999999866554
No 13
>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=96.39 E-value=0.0073 Score=39.22 Aligned_cols=54 Identities=15% Similarity=0.261 Sum_probs=38.8
Q ss_pred HHHHHH-HhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCe----eeChhh
Q 032124 61 MARKIY-LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQS----LVLVER 128 (147)
Q Consensus 61 i~RklY-l~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR----~lT~~G 128 (147)
||+.|+ -.++.....|+...|-.+ .-+..++++|++.|||++.+ ..+| .|||+|
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~~--------------~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGISK--------------STVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT--H--------------HHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHccCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 677788 678999999999877543 56679999999999998664 3355 578887
No 14
>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=96.37 E-value=0.0075 Score=42.46 Aligned_cols=64 Identities=14% Similarity=0.174 Sum_probs=49.5
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC------CeeeChhhhhhh
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG------QSLVLVERLHKL 132 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~------GR~lT~~G~~~L 132 (147)
..|++.|.. ||...+.|.+.- ...|.+++-.-|+.||+.|+|++.... -..||++|++++
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 568888888 888888888743 246679999999999999999876432 278999999988
Q ss_pred hhhh
Q 032124 133 DCEN 136 (147)
Q Consensus 133 Dri~ 136 (147)
.-+.
T Consensus 74 ~~l~ 77 (90)
T PF01638_consen 74 PVLE 77 (90)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 7654
No 15
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.27 E-value=0.0068 Score=42.00 Aligned_cols=40 Identities=10% Similarity=0.071 Sum_probs=35.3
Q ss_pred chhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhh
Q 032124 97 SGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
|.+-++.+|+.||+.|||++.++++-.||++|+...+.+.
T Consensus 12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~ 51 (96)
T smart00529 12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLL 51 (96)
T ss_pred ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHH
Confidence 4578999999999999999998789999999999877664
No 16
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=96.24 E-value=0.02 Score=39.51 Aligned_cols=65 Identities=18% Similarity=0.213 Sum_probs=49.9
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC--CCe----eeChhhhhhh
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK--GQS----LVLVERLHKL 132 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~--~GR----~lT~~G~~~L 132 (147)
..++..||..++.+...|....+-. .+-+=.+++.||+.|||+...+ ++| .||++|+..+
T Consensus 25 ~~~L~~l~~~~~~~~~~la~~l~i~--------------~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~ 90 (126)
T COG1846 25 YQVLLALYEAGGITVKELAERLGLD--------------RSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELL 90 (126)
T ss_pred HHHHHHHHHhCCCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHH
Confidence 4578888888887656677765533 2667788999999999986653 455 7999999999
Q ss_pred hhhhc
Q 032124 133 DCENS 137 (147)
Q Consensus 133 Dri~~ 137 (147)
..+..
T Consensus 91 ~~~~~ 95 (126)
T COG1846 91 EQLLP 95 (126)
T ss_pred HHhcc
Confidence 88765
No 17
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.12 E-value=0.022 Score=42.69 Aligned_cols=62 Identities=6% Similarity=-0.009 Sum_probs=48.9
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCe----eeChhhhhhhh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQS----LVLVERLHKLD 133 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~LD 133 (147)
.||..|+-.+++....|+...|-.+ +-+=.+++.||+.|||++.+ .++| .||++|+..++
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~ 109 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVLSVDL--------------GALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE 109 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence 3667777788899999999877543 56677899999999999765 3455 58999999887
Q ss_pred hh
Q 032124 134 CE 135 (147)
Q Consensus 134 ri 135 (147)
.+
T Consensus 110 ~~ 111 (144)
T PRK11512 110 QC 111 (144)
T ss_pred HH
Confidence 74
No 18
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=96.11 E-value=0.032 Score=38.04 Aligned_cols=60 Identities=27% Similarity=0.346 Sum_probs=49.3
Q ss_pred HhHHHHHHHHHHh-CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC-CCCeeeChhhh
Q 032124 56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGQSLVLVERL 129 (147)
Q Consensus 56 iRaASi~RklYl~-g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~-~~GR~lT~~G~ 129 (147)
-|+-+|+..|.-. +++++..+....|- +.+-++..|+.||+.|+|++++ ++...|++...
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i--------------~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~ 66 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGL--------------SKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL 66 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence 3788899999887 79999999998864 3488999999999999999875 34567877654
No 19
>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=96.11 E-value=0.009 Score=42.69 Aligned_cols=68 Identities=15% Similarity=0.142 Sum_probs=43.8
Q ss_pred chhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 52 DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
|+.=.|.-..+..-|-.||||+.+|+..-|-.+ ..|.=.+===|-+.|++++++ .||++|++|..-
T Consensus 7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~-------------~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~ 72 (76)
T PF05491_consen 7 DELDRRYLKTLIENFKGGPVGLDTLAAALGEDK-------------ETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEH 72 (76)
T ss_dssp BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-H-------------HHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCH-------------hHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHH
Confidence 444455555666667789999999998766432 122222222456789999997 699999999887
Q ss_pred hh
Q 032124 132 LD 133 (147)
Q Consensus 132 LD 133 (147)
|.
T Consensus 73 l~ 74 (76)
T PF05491_consen 73 LG 74 (76)
T ss_dssp TT
T ss_pred hC
Confidence 64
No 20
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.90 E-value=0.044 Score=36.94 Aligned_cols=62 Identities=18% Similarity=0.195 Sum_probs=48.1
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC------CeeeChhhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG------QSLVLVERLHKLDC 134 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~------GR~lT~~G~~~LDr 134 (147)
|+..|+..+++.+..+....+-. ..-|..+|+.|++.|||++..++ .-.||++|.+.+..
T Consensus 15 il~~l~~~~~~~~~~la~~~~~s--------------~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 15 VLRILYEEGPLSVSELAKRLGVS--------------PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCC--------------chhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 67778888889999998875422 23478999999999999876542 35799999998876
Q ss_pred hh
Q 032124 135 EN 136 (147)
Q Consensus 135 i~ 136 (147)
+.
T Consensus 81 ~~ 82 (101)
T smart00347 81 LL 82 (101)
T ss_pred HH
Confidence 54
No 21
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.86 E-value=0.042 Score=33.78 Aligned_cols=59 Identities=22% Similarity=0.280 Sum_probs=44.4
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC---CeeeCh-hhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---QSLVLV-ERLHKLDC 134 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~---GR~lT~-~G~~~LDr 134 (147)
|++.|+ .+++.+..+...+|- |.+-++.+|++|++.|+|+...++ ...+|+ .|...++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~i--------------s~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGL--------------SQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 566777 889999999998872 336799999999999999966532 334777 66666554
No 22
>PRK10870 transcriptional repressor MprA; Provisional
Probab=95.70 E-value=0.036 Score=43.58 Aligned_cols=62 Identities=11% Similarity=0.063 Sum_probs=47.7
Q ss_pred HHHHHHHh--CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCee----eChhhhhhh
Q 032124 61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSL----VLVERLHKL 132 (147)
Q Consensus 61 i~RklYl~--g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~----lT~~G~~~L 132 (147)
||..|+-. +++.+..|+...|-.+ +-+=.+++.||+.|||++.+ .++|. ||++|+..+
T Consensus 60 iL~~L~~~~~~~it~~eLa~~l~l~~--------------~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~ 125 (176)
T PRK10870 60 ALITLESQENHSIQPSELSCALGSSR--------------TNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFL 125 (176)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence 56667653 4577788888877432 55667899999999999755 45777 999999999
Q ss_pred hhhh
Q 032124 133 DCEN 136 (147)
Q Consensus 133 Dri~ 136 (147)
+.+.
T Consensus 126 ~~i~ 129 (176)
T PRK10870 126 REVL 129 (176)
T ss_pred HHHH
Confidence 9874
No 23
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.49 E-value=0.062 Score=40.41 Aligned_cols=61 Identities=8% Similarity=-0.024 Sum_probs=44.7
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri 135 (147)
|.+.+.-.|++-+..|+...|-. .+-++.+|+.||+.|||.....++=.||++|+.....+
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs--------------~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVH--------------PSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCC--------------hhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence 44444445778788888765532 25577789999999999976667899999998765544
No 24
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=95.44 E-value=0.023 Score=48.77 Aligned_cols=70 Identities=13% Similarity=0.230 Sum_probs=53.1
Q ss_pred HHHHHHH---HHHh--CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC-CCCeeeChhhhhh
Q 032124 58 AASMARK---IYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGQSLVLVERLHK 131 (147)
Q Consensus 58 aASi~Rk---lYl~--g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~~ 131 (147)
.-.||+. -|+. .|||=..|.+.|+- .-|.+-||..++.||++|++++.. ..||+-|.+|-+.
T Consensus 5 ~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr~ 72 (260)
T PRK03911 5 KDLLLDSIIQTYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMKN 72 (260)
T ss_pred HHHHHHHHHHHHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHHH
Confidence 3344443 4775 59999999998763 446688999999999999999765 4799999999864
Q ss_pred -hhhhhcCC
Q 032124 132 -LDCENSNG 139 (147)
Q Consensus 132 -LDri~~~~ 139 (147)
.|.....-
T Consensus 73 Yvd~~l~~~ 81 (260)
T PRK03911 73 YWQKSLDFE 81 (260)
T ss_pred HHHhhcCcc
Confidence 56555443
No 25
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=95.21 E-value=0.067 Score=43.17 Aligned_cols=63 Identities=10% Similarity=0.025 Sum_probs=47.8
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCe----eeChhhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQS----LVLVERLHKLDC 134 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~LDr 134 (147)
||-.||-.+++....|++..+-.+ +-+-.+++.||+.|||+..+ +..| .||++|+..++.
T Consensus 50 iL~~L~~~~~itq~eLa~~l~l~~--------------sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~ 115 (185)
T PRK13777 50 ILWIAYHLKGASISEIAKFGVMHV--------------STAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE 115 (185)
T ss_pred HHHHHHhCCCcCHHHHHHHHCCCH--------------hhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 667778888999999998644321 33556999999999999653 4455 399999999998
Q ss_pred hhc
Q 032124 135 ENS 137 (147)
Q Consensus 135 i~~ 137 (147)
+..
T Consensus 116 l~~ 118 (185)
T PRK13777 116 TME 118 (185)
T ss_pred HHH
Confidence 753
No 26
>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=95.07 E-value=0.054 Score=47.06 Aligned_cols=57 Identities=16% Similarity=0.130 Sum_probs=46.5
Q ss_pred HhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-CCeeeChhhhhh-hhhh
Q 032124 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GQSLVLVERLHK-LDCE 135 (147)
Q Consensus 67 l~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~~-LDri 135 (147)
-.+|+|+..|.+.|+- .-|..-||.-|.+||+.|++++... .||.-|.+|-+. .|..
T Consensus 18 ~~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~yv~~~ 76 (337)
T TIGR00331 18 TGQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRYYVDHL 76 (337)
T ss_pred cCCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHHHHHHh
Confidence 3589999999998663 3456889999999999999998764 499999999876 4433
No 27
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=95.05 E-value=0.11 Score=38.67 Aligned_cols=63 Identities=10% Similarity=0.034 Sum_probs=46.0
Q ss_pred HHHHHHHh-CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCe----eeChhhhhhhh
Q 032124 61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQS----LVLVERLHKLD 133 (147)
Q Consensus 61 i~RklYl~-g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR----~lT~~G~~~LD 133 (147)
+|..|+-. ++.....|+...|-.+ +-+=.+++.||+.|||++.+ .+.| .||++|+..++
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~~~--------------~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~ 101 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGIEQ--------------PSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLIS 101 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCCh--------------hhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHH
Confidence 45666654 3567788888766543 45668999999999999765 3455 49999999988
Q ss_pred hhhc
Q 032124 134 CENS 137 (147)
Q Consensus 134 ri~~ 137 (147)
.+..
T Consensus 102 ~~~~ 105 (144)
T PRK03573 102 EVEA 105 (144)
T ss_pred HHHH
Confidence 7654
No 28
>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=94.99 E-value=0.051 Score=34.57 Aligned_cols=49 Identities=24% Similarity=0.316 Sum_probs=41.0
Q ss_pred HhHHHHHHHHHHhC-CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 56 iRaASi~RklYl~g-~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
-|+.+|++.|.-.+ ++++..+...-|-.+ +-+..+|+.|++.|||++++
T Consensus 3 ~ral~iL~~l~~~~~~~t~~eia~~~gl~~--------------stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 3 ERALRILEALAESGGPLTLSEIARALGLPK--------------STVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHHCHHCTBSCEEHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCcCeecCc
Confidence 48889999998865 579999999877533 78999999999999999874
No 29
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=94.99 E-value=0.059 Score=46.87 Aligned_cols=60 Identities=15% Similarity=0.207 Sum_probs=47.3
Q ss_pred HHH--hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-CCeeeChhhhhh-hhhhh
Q 032124 65 IYL--RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GQSLVLVERLHK-LDCEN 136 (147)
Q Consensus 65 lYl--~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-~GR~lT~~G~~~-LDri~ 136 (147)
.|+ .+|+|...|.+.|+- .-|..-||.-+..||++|++++... .||+-|.+|-+. +|...
T Consensus 18 ~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L~ 81 (339)
T PRK00082 18 DYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHLL 81 (339)
T ss_pred HHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHhC
Confidence 455 479999999987553 3355889999999999999997654 699999999774 45443
No 30
>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=94.81 E-value=0.11 Score=37.63 Aligned_cols=63 Identities=13% Similarity=0.083 Sum_probs=47.7
Q ss_pred HHHHHH----HhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCee----eChhhhh
Q 032124 61 MARKIY----LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSL----VLVERLH 130 (147)
Q Consensus 61 i~RklY----l~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~----lT~~G~~ 130 (147)
||..|+ -.+++....|+..-+-.+ +-+=.++..||+.|||.+.. ++.|. ||++|+.
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~~~--------------stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~ 95 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILIKQ--------------SALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS 95 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence 677777 346788999988765432 55667899999999999755 34553 9999999
Q ss_pred hhhhhhc
Q 032124 131 KLDCENS 137 (147)
Q Consensus 131 ~LDri~~ 137 (147)
.++.+.+
T Consensus 96 ~~~~~~~ 102 (109)
T TIGR01889 96 KIESLIS 102 (109)
T ss_pred HHHHHHH
Confidence 9988754
No 31
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=94.57 E-value=0.15 Score=41.94 Aligned_cols=65 Identities=15% Similarity=0.206 Sum_probs=52.7
Q ss_pred HhHHHHHHHHHHhC-CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC-CCCeeeChhhhhhhh
Q 032124 56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGQSLVLVERLHKLD 133 (147)
Q Consensus 56 iRaASi~RklYl~g-~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~-~~GR~lT~~G~~~LD 133 (147)
-|+..||+.|.-.+ ++++..+.+..|-.+ +-+..+|+.|++.|||++++ .+...|+++..+.-.
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~k--------------stv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLHR--------------TTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQLSE 76 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHHHH
Confidence 48889999997754 599999999886533 78999999999999999886 456889988876544
Q ss_pred h
Q 032124 134 C 134 (147)
Q Consensus 134 r 134 (147)
.
T Consensus 77 ~ 77 (263)
T PRK09834 77 G 77 (263)
T ss_pred h
Confidence 4
No 32
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=94.46 E-value=0.046 Score=38.66 Aligned_cols=36 Identities=17% Similarity=0.134 Sum_probs=31.5
Q ss_pred hhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhh
Q 032124 98 GSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLD 133 (147)
Q Consensus 98 gsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LD 133 (147)
-+-|+.+++-|.++|+|++...|--.||++|++.|-
T Consensus 54 ~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 54 KNRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA 89 (92)
T ss_pred HHhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence 367899999999999999876677999999998874
No 33
>PRK05638 threonine synthase; Validated
Probab=94.14 E-value=0.41 Score=42.54 Aligned_cols=93 Identities=12% Similarity=0.011 Sum_probs=63.0
Q ss_pred HcCCCCCCCceeeeccCCCCCC--------CCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCC
Q 032124 25 RSGKIELPTWNDIVKTGTLKEL--------APYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKS 96 (147)
Q Consensus 25 ~~gki~~P~W~d~vKTg~~kEl--------aP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~a 96 (147)
++|.|..-+=+-++=||.+-.- =+.++-+. .||+.|. +++.-+..|.+..+. .-
T Consensus 337 ~~g~i~~~~~Vv~i~tG~g~k~~~~~~~~~~~~~~~r~-----~IL~~L~-~~~~~~~el~~~l~~------------~~ 398 (442)
T PRK05638 337 EEGYIEKGDKVVLVVTGSGLKGYGEGGREKFTIGGTKL-----EILKILS-EREMYGYEIWKALGK------------PL 398 (442)
T ss_pred HcCCCCCCCeEEEEeCCCCCCCCCCCchhhhcccchHH-----HHHHHHh-hCCccHHHHHHHHcc------------cC
Confidence 4455555555556667766322 23344333 3667665 678889999998873 13
Q ss_pred chhHHHHHHHHhHhCCceeeCCCCCee----eChhhhhhhhhh
Q 032124 97 SGSVARHILHQLQDTNIIELDSKGQSL----VLVERLHKLDCE 135 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~~~GR~----lT~~G~~~LDri 135 (147)
|.+.++..|+.||++|||+.....||+ ||++|+..|..+
T Consensus 399 s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 399 KYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLENL 441 (442)
T ss_pred CcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHhc
Confidence 668999999999999999864223443 999999988753
No 34
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=94.09 E-value=0.069 Score=40.06 Aligned_cols=64 Identities=19% Similarity=0.215 Sum_probs=52.1
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhh
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri 135 (147)
|--+++..+.=.+|+|+..|+..-| .|+|. +|+.|.-||+.+++.-+ ..|-++|+.+-.+++-|
T Consensus 15 RHl~Vl~~v~eeqPiGI~klS~~TG-------mp~HK-------VRYSLRVLEq~~iI~PS-~~GAi~td~~~e~ie~i 78 (101)
T COG3388 15 RHLSVLKVVLEEQPIGIIKLSDETG-------MPEHK-------VRYSLRVLEQENIISPS-RQGAILTDDFPEFIEEI 78 (101)
T ss_pred HHHHHHHHHHHhCCceeEeechhcC-------Cchhh-------hhhhhhhhhhcCccCcc-ccCCccCccHHHHHHHH
Confidence 5556777777789999999999877 47776 89999999999999866 46999999987766544
No 35
>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=93.80 E-value=0.092 Score=37.72 Aligned_cols=45 Identities=13% Similarity=0.160 Sum_probs=33.2
Q ss_pred CCCCchhHHHHHHHHhHhCCceeeC--C-CCCe-----eeChhhhhhhhhhhc
Q 032124 93 FSKSSGSVARHILHQLQDTNIIELD--S-KGQS-----LVLVERLHKLDCENS 137 (147)
Q Consensus 93 ~~~asgsiiR~~LqqLE~~glV~k~--~-~~GR-----~lT~~G~~~LDri~~ 137 (147)
+..-+-+-+-.+|..||+.|||+.. + .+|| .||++|+..|+...+
T Consensus 34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~ 86 (100)
T TIGR03433 34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETE 86 (100)
T ss_pred ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHH
Confidence 3444556688899999999999972 2 2232 599999999987643
No 36
>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=93.78 E-value=0.19 Score=40.03 Aligned_cols=55 Identities=15% Similarity=0.161 Sum_probs=44.1
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC--CCeeeChhh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK--GQSLVLVER 128 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~--~GR~lT~~G 128 (147)
.|+..|.-+|++.+..+....|- |.+-+++.|+.||+.|||++..+ ..-.||++|
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~i--------------s~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGK--------------SLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 57888877789999999998864 34688999999999999998752 234578776
No 37
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=93.59 E-value=0.1 Score=38.70 Aligned_cols=42 Identities=12% Similarity=0.052 Sum_probs=33.4
Q ss_pred CCCchhHHHHHHHHhHhCCceeeCCCC---CeeeChhhhhhhhhh
Q 032124 94 SKSSGSVARHILHQLQDTNIIELDSKG---QSLVLVERLHKLDCE 135 (147)
Q Consensus 94 ~~asgsiiR~~LqqLE~~glV~k~~~~---GR~lT~~G~~~LDri 135 (147)
|.=+-.+++++++.|++.|++++...+ .-.||++|.++|-..
T Consensus 41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y 85 (95)
T COG3432 41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKY 85 (95)
T ss_pred cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHH
Confidence 444568999999999999988887543 357999999997653
No 38
>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=93.48 E-value=0.11 Score=32.74 Aligned_cols=39 Identities=18% Similarity=0.248 Sum_probs=30.9
Q ss_pred hhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeC
Q 032124 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVL 125 (147)
Q Consensus 73 V~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT 125 (147)
+..|+..||- |.+-+|++|+.|++.|+|+..+..|-.||
T Consensus 28 ~~~la~~~~i--------------s~~~v~~~l~~L~~~G~i~~~~~~~~~l~ 66 (66)
T cd07377 28 ERELAEELGV--------------SRTTVREALRELEAEGLVERRPGRGTFVA 66 (66)
T ss_pred HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 6677777653 45889999999999999998766676665
No 39
>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=93.35 E-value=0.26 Score=34.01 Aligned_cols=44 Identities=20% Similarity=0.214 Sum_probs=34.4
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCeeeChh
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSLVLVE 127 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~lT~~ 127 (147)
|+.+..++..+|-. -+.+|++|++|++.|+|+... .||-.|+..
T Consensus 25 ~~s~~eiA~~~~i~--------------~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~ 70 (83)
T PF02082_consen 25 PVSSKEIAERLGIS--------------PSYLRKILQKLKKAGLIESSRGRGGGYRLARP 70 (83)
T ss_dssp -BEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-
T ss_pred CCCHHHHHHHHCcC--------------HHHHHHHHHHHhhCCeeEecCCCCCceeecCC
Confidence 58899999887753 389999999999999999654 478888754
No 40
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=93.34 E-value=0.11 Score=40.83 Aligned_cols=50 Identities=14% Similarity=0.214 Sum_probs=41.2
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
.|++.++.++..-+ +.| +-+-..|+.|++.|||+..+.+|-.||++|.+.
T Consensus 22 ~~~~~~~diA~~L~------Vsp--------~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~ 71 (154)
T COG1321 22 KGFARTKDIAERLK------VSP--------PSVTEMLKRLERLGLVEYEPYGGVTLTEKGREK 71 (154)
T ss_pred cCcccHHHHHHHhC------CCc--------HHHHHHHHHHHHCCCeEEecCCCeEEChhhHHH
Confidence 47788888887654 344 567789999999999999999999999999854
No 41
>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=93.03 E-value=0.25 Score=31.34 Aligned_cols=46 Identities=22% Similarity=0.390 Sum_probs=38.4
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
..+|..||-.|++-+..|....+-. .+-+-.++++||+.|||++..
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~~--------------~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGIS--------------RSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCCC--------------hhHHHHHHHHHHHCCCEEecc
Confidence 3578889999999999999987753 367788999999999998654
No 42
>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=92.98 E-value=0.14 Score=40.13 Aligned_cols=62 Identities=16% Similarity=0.212 Sum_probs=44.7
Q ss_pred HHHHHHHHHHhCC------CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 58 AASMARKIYLRGG------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 58 aASi~RklYl~g~------vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
++..+|..-+.|- +.-..|+..||- |.+-+|.+|+.||..|||+..+..|-.+++-...+
T Consensus 16 v~~~l~~~I~~g~l~pG~~L~e~~La~~lgV--------------SRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~~ 81 (212)
T TIGR03338 16 VQDEIERAILSGELPPGAKLNESDIAARLGV--------------SRGPVREAFRALEEAGLVRNEKNRGVFVREISLAE 81 (212)
T ss_pred HHHHHHHHHHcCCCCCCCEecHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHH
Confidence 3444555555542 334568888774 44889999999999999999988898888766555
Q ss_pred hh
Q 032124 132 LD 133 (147)
Q Consensus 132 LD 133 (147)
+.
T Consensus 82 ~~ 83 (212)
T TIGR03338 82 AD 83 (212)
T ss_pred HH
Confidence 43
No 43
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=92.90 E-value=0.26 Score=34.43 Aligned_cols=61 Identities=10% Similarity=0.196 Sum_probs=42.4
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCC-----eeeChhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQ-----SLVLVERLHKLD 133 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~G-----R~lT~~G~~~LD 133 (147)
|+=-|+-.+.+-...|+..-| -+.+-+.+-|+.||++|+|+..+ .++ -.||++|+..+.
T Consensus 5 Il~~L~~~~~~~f~~L~~~l~--------------lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~ 70 (80)
T PF13601_consen 5 ILALLYANEEATFSELKEELG--------------LTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFE 70 (80)
T ss_dssp HHHHHHHHSEEEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHH
T ss_pred HHHHHhhcCCCCHHHHHHHhC--------------cCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHH
Confidence 444556667777777777644 34578899999999999998554 233 269999999876
Q ss_pred hh
Q 032124 134 CE 135 (147)
Q Consensus 134 ri 135 (147)
.-
T Consensus 71 ~~ 72 (80)
T PF13601_consen 71 RY 72 (80)
T ss_dssp HH
T ss_pred HH
Confidence 53
No 44
>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=92.75 E-value=0.095 Score=35.39 Aligned_cols=41 Identities=20% Similarity=0.150 Sum_probs=31.7
Q ss_pred CCCCchhHHHHHHHHhHhCCceeeCCCC---C-----eeeChhhhhhhh
Q 032124 93 FSKSSGSVARHILHQLQDTNIIELDSKG---Q-----SLVLVERLHKLD 133 (147)
Q Consensus 93 ~~~asgsiiR~~LqqLE~~glV~k~~~~---G-----R~lT~~G~~~LD 133 (147)
+..-|-+-+=.+|+.||+.|+|+..... | -.||++|+..|.
T Consensus 26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 3456678889999999999999855421 2 369999998774
No 45
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=92.70 E-value=0.2 Score=36.39 Aligned_cols=51 Identities=16% Similarity=0.094 Sum_probs=40.8
Q ss_pred CCCCCCCCchhHHHHHHHHhHhCCceeeCCCCC---------eeeChhhhhhhhhhhcCC
Q 032124 89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKGQ---------SLVLVERLHKLDCENSNG 139 (147)
Q Consensus 89 ~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~G---------R~lT~~G~~~LDri~~~~ 139 (147)
.+..+..-+-..|-+-+++|+++|+|+-..... ..||.+|..+||.|-++.
T Consensus 25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~IRd~~ 84 (102)
T PF10711_consen 25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAIRDDT 84 (102)
T ss_pred chhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHhcCch
Confidence 355666777789999999999999998665322 489999999999987653
No 46
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=92.59 E-value=0.31 Score=36.75 Aligned_cols=62 Identities=18% Similarity=0.193 Sum_probs=48.2
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC------CCeeeChhhhhhhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK------GQSLVLVERLHKLDC 134 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~------~GR~lT~~G~~~LDr 134 (147)
|+++|.- |+.--+.|++.-++ =|.+++=.-|+.||+.|+|++..- -...||+.|++++.-
T Consensus 28 Il~~L~~-g~~RF~eL~r~i~~-------------Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~v 93 (120)
T COG1733 28 ILRDLFD-GPKRFNELRRSIGG-------------ISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLPV 93 (120)
T ss_pred HHHHHhc-CCCcHHHHHHHccc-------------cCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHHH
Confidence 6777776 77777888776553 455888888999999999997652 367899999998765
Q ss_pred hh
Q 032124 135 EN 136 (147)
Q Consensus 135 i~ 136 (147)
+.
T Consensus 94 l~ 95 (120)
T COG1733 94 LL 95 (120)
T ss_pred HH
Confidence 43
No 47
>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=92.55 E-value=0.29 Score=31.08 Aligned_cols=47 Identities=17% Similarity=0.246 Sum_probs=38.6
Q ss_pred HHHHHHHHHhCC--CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC
Q 032124 59 ASMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (147)
Q Consensus 59 ASi~RklYl~g~--vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~ 119 (147)
+.||..|+-.++ +.+..|....|-.+ +-+-.+++.||+.|||++.+.
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~--------------~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISK--------------STVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEeCC
Confidence 358899999988 89999999877543 678889999999999997653
No 48
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=92.47 E-value=0.096 Score=46.06 Aligned_cols=66 Identities=14% Similarity=0.118 Sum_probs=50.5
Q ss_pred HHHHHHHhC-CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhh
Q 032124 61 MARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 61 i~RklYl~g-~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri 135 (147)
|||=|.-.+ |+|-......-- +||+. =+---+|+=||-||+.|++.|+.-.||.||.+|-+.|.+-
T Consensus 11 Il~il~esd~plgak~Ia~el~---kRGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~~ 77 (325)
T COG1693 11 ILRILAESDEPLGAKIIALELR---KRGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKRA 77 (325)
T ss_pred HHHHHHhcCCccchHHHHHHHH---hcccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhhh
Confidence 556565554 888877666542 23543 2345699999999999999999888999999999999883
No 49
>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=92.45 E-value=0.75 Score=29.32 Aligned_cols=44 Identities=16% Similarity=0.165 Sum_probs=32.2
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
+++....|....|- |.+-+.++|++|++.|+|+....++-.|+|
T Consensus 24 ~~~s~~ela~~~g~--------------s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLGL--------------TRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 35666666666553 457889999999999999987645566654
No 50
>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=92.41 E-value=0.24 Score=32.29 Aligned_cols=46 Identities=22% Similarity=0.308 Sum_probs=39.1
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
..|++.|-..+|..+..|....|- +-+-+.+=|+.||++|||+...
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~~--------------~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELGI--------------SQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEec
Confidence 468888888999999999999874 3377899999999999999774
No 51
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=92.14 E-value=0.34 Score=36.46 Aligned_cols=43 Identities=14% Similarity=0.156 Sum_probs=33.6
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC--CCeeeCh
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK--GQSLVLV 126 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~--~GR~lT~ 126 (147)
++.+..++..+|-. ...+|++|++|++.|||+..+. ||-.|+.
T Consensus 25 ~~s~~~ia~~~~is--------------~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 25 MTSISEVTEVYGVS--------------RNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred ccCHHHHHHHHCcC--------------HHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 56778888887753 4789999999999999997763 4656654
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=91.78 E-value=0.22 Score=30.83 Aligned_cols=36 Identities=14% Similarity=0.204 Sum_probs=27.9
Q ss_pred chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCC
Q 032124 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQ 121 (147)
Q Consensus 72 GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~G 121 (147)
.+..|+..||- |.+-+|++|++||+.|+|+..+.+|
T Consensus 22 s~~~la~~~~v--------------s~~tv~~~l~~L~~~g~i~~~~~~g 57 (60)
T smart00345 22 SERELAAQLGV--------------SRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCe
Confidence 56666776653 5589999999999999998776444
No 53
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.68 E-value=0.66 Score=31.33 Aligned_cols=45 Identities=11% Similarity=0.062 Sum_probs=38.2
Q ss_pred HHHHHHHHhCC--CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 60 SMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 60 Si~RklYl~g~--vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
.|+..|.-+|+ +....|.+.-|=.+ +.+|++|..||+.|+|++..
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~~--------------~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLPK--------------KEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEecC
Confidence 57777787877 99999999888543 68999999999999999865
No 54
>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=91.42 E-value=0.22 Score=39.73 Aligned_cols=41 Identities=12% Similarity=0.202 Sum_probs=34.7
Q ss_pred chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 72 GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
.-..|+..||- |.+-+|.||+.||..|||+..+..|-.+++
T Consensus 32 sE~~La~~lgV--------------SRtpVREAL~~Le~eGlV~~~~~~G~~V~~ 72 (235)
T TIGR02812 32 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNN 72 (235)
T ss_pred CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCccEecC
Confidence 45577887774 458999999999999999999888988887
No 55
>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=91.32 E-value=0.25 Score=32.38 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=29.8
Q ss_pred chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCee
Q 032124 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSL 123 (147)
Q Consensus 72 GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~ 123 (147)
....|...||- |...+|.+|+.|++.|+|+..+..|-.
T Consensus 26 s~~~la~~~~v--------------sr~tvr~al~~L~~~g~i~~~~~~G~~ 63 (64)
T PF00392_consen 26 SERELAERYGV--------------SRTTVREALRRLEAEGLIERRPGRGTF 63 (64)
T ss_dssp -HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETTTEEE
T ss_pred CHHHHHHHhcc--------------CCcHHHHHHHHHHHCCcEEEECCceEE
Confidence 66778888774 458999999999999999988766543
No 56
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=91.30 E-value=0.26 Score=38.03 Aligned_cols=36 Identities=17% Similarity=0.240 Sum_probs=31.6
Q ss_pred hHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhh
Q 032124 99 SVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDr 134 (147)
.-+.++.|.||..|+|+.....|..+|+++...+|.
T Consensus 50 nTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~ 85 (125)
T COG1725 50 NTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQ 85 (125)
T ss_pred HHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHH
Confidence 578999999999999998877899999998876543
No 57
>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=91.25 E-value=0.31 Score=37.95 Aligned_cols=41 Identities=15% Similarity=0.071 Sum_probs=30.8
Q ss_pred CchhHHHHHHHHhHhCCceeeC---CCCCe-----eeChhhhhhhhhhh
Q 032124 96 SSGSVARHILHQLQDTNIIELD---SKGQS-----LVLVERLHKLDCEN 136 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~---~~~GR-----~lT~~G~~~LDri~ 136 (147)
.+-+-+=.+|+.||+.|||+.. ..+|| .||++|+..|+...
T Consensus 55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~ 103 (138)
T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCA 103 (138)
T ss_pred CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHH
Confidence 4446677899999999999863 23344 49999999887654
No 58
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=91.21 E-value=0.56 Score=38.32 Aligned_cols=58 Identities=7% Similarity=0.144 Sum_probs=47.3
Q ss_pred HhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-CCeeeChh
Q 032124 56 IRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GQSLVLVE 127 (147)
Q Consensus 56 iRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-~GR~lT~~ 127 (147)
-|+..||..|.-.+++++..+.+.-|-.+ +-+..+|+.|++.|||++++. +...|+++
T Consensus 14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~k--------------stv~Rll~tL~~~G~l~~~~~~~~Y~lG~~ 72 (257)
T PRK15090 14 LKVFGILQALGEEREIGITELSQRVMMSK--------------STVYRFLQTMKTLGYVAQEGESEKYSLTLK 72 (257)
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence 48889999998778899999999877543 788999999999999998763 44566654
No 59
>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=91.06 E-value=0.6 Score=30.48 Aligned_cols=52 Identities=19% Similarity=0.325 Sum_probs=42.8
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCee
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSL 123 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~ 123 (147)
|-..|+..|--++.+.+..|...||- |..-||.=|+.||+.|+|.+.. ||=.
T Consensus 1 R~~~Il~~l~~~~~~s~~ela~~~~V--------------S~~TiRRDl~~L~~~g~i~r~~-GG~~ 52 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSVKELAEEFGV--------------SEMTIRRDLNKLEKQGLIKRTH-GGAV 52 (57)
T ss_pred CHHHHHHHHHHcCCEEHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEc-CEEE
Confidence 34567888888999999999999875 4478999999999999999885 4433
No 60
>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=90.84 E-value=0.8 Score=29.85 Aligned_cols=55 Identities=16% Similarity=0.303 Sum_probs=38.8
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhh
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERL 129 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~ 129 (147)
|+=.|=+..++-+..+...||.. --......|+.|++.|||+.+. +.=+||++|+
T Consensus 11 i~~~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~ 65 (66)
T PF06969_consen 11 IMLGLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDG-GRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred HHHHHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence 33444456788889999998854 2245588899999999999874 6778999996
No 61
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=90.82 E-value=0.26 Score=39.68 Aligned_cols=45 Identities=24% Similarity=0.095 Sum_probs=36.2
Q ss_pred chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhh
Q 032124 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLH 130 (147)
Q Consensus 72 GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~ 130 (147)
.-..|+..||- |.+-+|.+|+.||..|||+..+.+|-.+++-...
T Consensus 33 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~ 77 (251)
T PRK09990 33 SERRLCEKLGF--------------SRSALREGLTVLRGRGIIETAQGRGSFVARLNRV 77 (251)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence 44577777774 4589999999999999999998888888765443
No 62
>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=90.81 E-value=0.91 Score=28.28 Aligned_cols=61 Identities=16% Similarity=0.105 Sum_probs=44.6
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC---CCeeeChhhhhhhhhhh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GQSLVLVERLHKLDCEN 136 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~LDri~ 136 (147)
.|+..++-.+ +.+..+.+..|- +.+-++.+|.+|++.|++..... .-..+|+ |+..++-+.
T Consensus 11 ~il~~l~~~~-~~~~ei~~~~~i--------------~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~ 74 (78)
T cd00090 11 RILRLLLEGP-LTVSELAERLGL--------------SQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLE 74 (78)
T ss_pred HHHHHHHHCC-cCHHHHHHHHCc--------------CHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHH
Confidence 3666666555 889998887653 33678999999999999986542 2447888 888777654
No 63
>PRK03837 transcriptional regulator NanR; Provisional
Probab=90.64 E-value=1.7 Score=34.57 Aligned_cols=58 Identities=12% Similarity=0.223 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHhCC------C-chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhh
Q 032124 57 RAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVER 128 (147)
Q Consensus 57 RaASi~RklYl~g~------v-GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G 128 (147)
.++.-+|..-+.|- + ....|+..||= |.+.+|.||+.||..|||+..+..|-.+++-.
T Consensus 17 ~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gV--------------SRt~VREAL~~L~~eGlv~~~~~~G~~V~~~~ 81 (241)
T PRK03837 17 EVEERLEQMIRSGEFGPGDQLPSERELMAFFGV--------------GRPAVREALQALKRKGLVQISHGERARVSRPS 81 (241)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCceeEecCC
Confidence 34444555545542 3 45678888874 55899999999999999999887777776543
No 64
>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=90.28 E-value=0.78 Score=33.44 Aligned_cols=48 Identities=21% Similarity=0.179 Sum_probs=37.7
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeC--CCCCeeeChhhhh
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGQSLVLVERLH 130 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~--~~~GR~lT~~G~~ 130 (147)
+|+.+..|+..+|- +.+.+|++|+.|++.|||... ..||-.|+.....
T Consensus 24 ~~~s~~eia~~~~i--------------~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~ 73 (132)
T TIGR00738 24 GPVSVKEIAERQGI--------------SRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEE 73 (132)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHH
Confidence 48899999888765 348999999999999999864 3467788766653
No 65
>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=90.28 E-value=1.3 Score=30.15 Aligned_cols=40 Identities=20% Similarity=0.148 Sum_probs=30.8
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
|..|..++..+|- .|-+-+..-|++||+.|+|+.++...|
T Consensus 25 ~Pt~rEIa~~~g~-------------~S~~tv~~~L~~Le~kG~I~r~~~~~R 64 (65)
T PF01726_consen 25 PPTVREIAEALGL-------------KSTSTVQRHLKALERKGYIRRDPGKAR 64 (65)
T ss_dssp ---HHHHHHHHTS-------------SSHHHHHHHHHHHHHTTSEEEGCCSCC
T ss_pred CCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCcCccCCCCCCC
Confidence 6688888888774 467899999999999999999875443
No 66
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=90.22 E-value=0.33 Score=38.68 Aligned_cols=41 Identities=12% Similarity=0.202 Sum_probs=33.9
Q ss_pred chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 72 GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
.-..|+..||- |.+-+|.+|+.||..|+|+..+..|-.+++
T Consensus 33 sE~eLae~~gV--------------SRt~VReAL~~L~~eGlv~~~~g~G~~V~~ 73 (239)
T PRK04984 33 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNN 73 (239)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence 34567777774 558999999999999999998888888865
No 67
>PRK11569 transcriptional repressor IclR; Provisional
Probab=90.20 E-value=0.85 Score=37.80 Aligned_cols=59 Identities=14% Similarity=0.189 Sum_probs=47.7
Q ss_pred HHhHHHHHHHHHH-hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-CCeeeChh
Q 032124 55 YIRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GQSLVLVE 127 (147)
Q Consensus 55 YiRaASi~RklYl-~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-~GR~lT~~ 127 (147)
--|+..||+.|-- .+|+++..|.+.-|-.| +-+..+|+.|++.|||+++++ +...|.+.
T Consensus 27 l~ral~IL~~l~~~~~~~~lseia~~lglpk--------------sTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 87 (274)
T PRK11569 27 LTRGLKLLEWIAESNGSVALTELAQQAGLPN--------------STTHRLLTTMQQQGFVRQVGELGHWAIGAH 87 (274)
T ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence 4689999999987 46899999999877544 889999999999999998864 33455544
No 68
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=90.08 E-value=0.32 Score=39.40 Aligned_cols=41 Identities=15% Similarity=0.147 Sum_probs=33.7
Q ss_pred hhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 73 V~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
-..|+..||= |..-+|.||+.||..|||+..+.+|-.+++-
T Consensus 29 E~eLae~~gV--------------SRtpVREAL~~Le~~GlV~~~~~~G~~V~~~ 69 (253)
T PRK10421 29 ERQLAMQLGV--------------SRNSLREALAKLVSEGVLLSRRGGGTFIRWR 69 (253)
T ss_pred HHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence 4567777764 5589999999999999999888888888764
No 69
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=90.00 E-value=0.31 Score=39.46 Aligned_cols=60 Identities=17% Similarity=0.204 Sum_probs=43.6
Q ss_pred hHHHHHHHHHHhC------CC-chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhh
Q 032124 57 RAASMARKIYLRG------GL-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERL 129 (147)
Q Consensus 57 RaASi~RklYl~g------~v-GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~ 129 (147)
.++..+|..-+.| .+ ....|+..||= |..-+|.+|+.||..|||+..+..|-.+++...
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~ 78 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDV--------------TRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG 78 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence 3444455555554 23 35678888875 458999999999999999998888888876544
Q ss_pred h
Q 032124 130 H 130 (147)
Q Consensus 130 ~ 130 (147)
.
T Consensus 79 ~ 79 (257)
T PRK10225 79 S 79 (257)
T ss_pred c
Confidence 3
No 70
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=89.91 E-value=0.44 Score=37.70 Aligned_cols=48 Identities=17% Similarity=0.122 Sum_probs=37.1
Q ss_pred CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 71 LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 71 vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
+-...|+..||- |.+-+|.+|+.||..|||+..+..|-.+++-...++
T Consensus 31 L~e~eLae~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~ 78 (224)
T PRK11534 31 LRMSLLTSRYAL--------------GVGPLREALSQLVAERLVTVVNQKGYRVASMSEQEL 78 (224)
T ss_pred CCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHH
Confidence 345677887775 347899999999999999999888888876544443
No 71
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=89.89 E-value=1.3 Score=35.28 Aligned_cols=65 Identities=17% Similarity=0.235 Sum_probs=50.2
Q ss_pred hHHHHHHHHHHhC------CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhh
Q 032124 57 RAASMARKIYLRG------GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLH 130 (147)
Q Consensus 57 RaASi~RklYl~g------~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~ 130 (147)
.+...+|.--+.| .+....|...||-+. .-||.+|+.|+..|||+..+..|-.+++-...
T Consensus 20 ~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSr--------------tPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~ 85 (230)
T COG1802 20 QVYEELREAILSGELAPGERLSEEELAEELGVSR--------------TPVREALRRLEAEGLVEIEPNRGAFVAPLSLA 85 (230)
T ss_pred HHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCC--------------ccHHHHHHHHHHCCCeEecCCCCCeeCCCCHH
Confidence 3344555555554 578889999999643 57999999999999999999899998887776
Q ss_pred hhhhh
Q 032124 131 KLDCE 135 (147)
Q Consensus 131 ~LDri 135 (147)
++.-+
T Consensus 86 ~~~ei 90 (230)
T COG1802 86 EAREI 90 (230)
T ss_pred HHHHH
Confidence 66543
No 72
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.69 E-value=1.3 Score=26.53 Aligned_cols=45 Identities=16% Similarity=0.262 Sum_probs=36.1
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
.|++.|.-.+++.+..|+..+|- |-+-+++.|+.|++.|+|++..
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~--------------s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGV--------------SEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEee
Confidence 36666666788999999998853 3366899999999999999764
No 73
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.61 E-value=1 Score=37.30 Aligned_cols=58 Identities=16% Similarity=0.067 Sum_probs=46.5
Q ss_pred HhHHHHHHHHHHh-CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCC-eeeChh
Q 032124 56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQ-SLVLVE 127 (147)
Q Consensus 56 iRaASi~RklYl~-g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~G-R~lT~~ 127 (147)
-|+.+||+.|.-. +++++..+.+.-|-.| +-+..+|+.|+..|||++++..| -.|++.
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpk--------------Stv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 84 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDLPL--------------STTFRLLKVLQAADFVYQDSQLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEEecHH
Confidence 3889999999764 5799999999877644 78999999999999999986443 345554
No 74
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=89.48 E-value=0.38 Score=38.79 Aligned_cols=42 Identities=12% Similarity=0.196 Sum_probs=33.5
Q ss_pred chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 72 GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
.-..|+..||- |...+|.+|+.||..|||+..+.+|-.+++.
T Consensus 36 sE~eLa~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~ 77 (254)
T PRK09464 36 PERELAKQFDV--------------SRPSLREAIQRLEAKGLLLRRQGGGTFVQSS 77 (254)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEecC
Confidence 34567777764 5589999999999999999888888777653
No 75
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=89.13 E-value=0.41 Score=38.74 Aligned_cols=43 Identities=14% Similarity=0.052 Sum_probs=34.3
Q ss_pred hhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhh
Q 032124 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERL 129 (147)
Q Consensus 73 V~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~ 129 (147)
-..|+..||- |..-+|.+|+.||..|||+..+..|-.+++-..
T Consensus 35 E~eLae~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~ 77 (253)
T PRK11523 35 ERFIADEKNV--------------SRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQP 77 (253)
T ss_pred HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCeeEEecCCc
Confidence 4567777764 458999999999999999988887887776543
No 76
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=89.08 E-value=0.53 Score=37.26 Aligned_cols=44 Identities=14% Similarity=0.068 Sum_probs=34.2
Q ss_pred hhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 74 GSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 74 ~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
..|+..||-+ .+-+|.||+.||..|||+..+..|-.+++-...+
T Consensus 38 ~~La~~lgVS--------------RtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~ 81 (221)
T PRK11414 38 KNLAEQLGMS--------------ITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQ 81 (221)
T ss_pred HHHHHHHCCC--------------chhHHHHHHHHHHCCCEEecCCCceeecCCCHHH
Confidence 5688888753 4789999999999999999887777766544433
No 77
>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=89.02 E-value=1.2 Score=32.80 Aligned_cols=57 Identities=14% Similarity=0.117 Sum_probs=41.6
Q ss_pred HHHHHHHHHHh--CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCeeeChhh
Q 032124 58 AASMARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSLVLVER 128 (147)
Q Consensus 58 aASi~RklYl~--g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~lT~~G 128 (147)
|-.++..|... +++.+..|+..+|- |.+.++++|+.|++.|+|+... .+|..|....
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~i--------------s~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~ 71 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGL--------------NAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAP 71 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCc
Confidence 34456666654 46888999888775 3489999999999999998643 4666665433
No 78
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=88.98 E-value=1.3 Score=32.48 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=37.5
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeee
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLV 124 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~l 124 (147)
||.|||-.||-=...+++.. ..+-.-++.+|..||++|||+... |+.|
T Consensus 12 IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~--g~~i 59 (92)
T PF10007_consen 12 ILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE--GKTI 59 (92)
T ss_pred HHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec--Cccc
Confidence 89999999887666666643 344578999999999999999875 4444
No 79
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=88.93 E-value=1.2 Score=36.71 Aligned_cols=64 Identities=17% Similarity=0.140 Sum_probs=48.0
Q ss_pred HhHHHHHHHHHHhCCC--chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCC-eeeChh----h
Q 032124 56 IRAASMARKIYLRGGL--GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQ-SLVLVE----R 128 (147)
Q Consensus 56 iRaASi~RklYl~g~v--GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~G-R~lT~~----G 128 (147)
.|+..||..|.- +|. ++..|.+.-|-.| |=++..|+.|+..|||+++++.| -.|+++ |
T Consensus 4 ~ral~iL~~l~~-~~~~l~l~ela~~~glpk--------------sT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~~~~~lg 68 (246)
T COG1414 4 ERALAILDLLAE-GPGGLSLAELAERLGLPK--------------STVHRLLQTLVELGYVEQDPEDGRYRLGPRLLELG 68 (246)
T ss_pred HHHHHHHHHHHh-CCCCCCHHHHHHHhCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCcEeehHHHHHHH
Confidence 588899998887 454 4999999877533 78999999999999999998654 445543 4
Q ss_pred hhhhhh
Q 032124 129 LHKLDC 134 (147)
Q Consensus 129 ~~~LDr 134 (147)
...+++
T Consensus 69 ~~~l~~ 74 (246)
T COG1414 69 AAALSS 74 (246)
T ss_pred HHHHhc
Confidence 444443
No 80
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=88.75 E-value=0.71 Score=30.41 Aligned_cols=46 Identities=17% Similarity=0.205 Sum_probs=37.6
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
+.|...|--+|+..+..+.+.-|- +.+-++.+|+.|++.|||++.+
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i--------------~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGI--------------SRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTS--------------SHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEc
Confidence 445666666899999999998664 3488999999999999999875
No 81
>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=88.72 E-value=1.3 Score=33.21 Aligned_cols=45 Identities=13% Similarity=0.157 Sum_probs=35.1
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceee--CCCCCeeeChh
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSKGQSLVLVE 127 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k--~~~~GR~lT~~ 127 (147)
+++.+..++..++- +...++++|++|.++|||.. ...||-.|+..
T Consensus 24 ~~~s~~~ia~~~~i--------------p~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~ 70 (135)
T TIGR02010 24 GPVTLADISERQGI--------------SLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRP 70 (135)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEEEeCCCCCEeccCC
Confidence 47888888887653 44899999999999999984 33568788764
No 82
>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=88.68 E-value=1.6 Score=34.78 Aligned_cols=58 Identities=19% Similarity=0.191 Sum_probs=42.8
Q ss_pred HHhHHHHHHHHHHhCCC-------chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 55 YIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 55 YiRaASi~RklYl~g~v-------GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
|...+..||+--..|-. +-..|+..||- |..-+|+||+.|+..|+|.+.+..|-.+++
T Consensus 3 y~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~ 67 (230)
T TIGR02018 3 YQRIKQDILERIRSGEWPPGHRIPSEHELVAQYGC--------------SRMTVNRALRELTDAGLLERRQGVGTFVAE 67 (230)
T ss_pred HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEcc
Confidence 55556666655544422 45678888875 458999999999999999998877877764
No 83
>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=87.48 E-value=1.9 Score=26.54 Aligned_cols=42 Identities=17% Similarity=0.206 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCcee
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~ 115 (147)
.|+..|.-.|++.+..++...|- |.+-+++.|++|++.|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~i--------------s~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGI--------------SRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCcCcC
Confidence 47777888899999999998774 3478999999999999985
No 84
>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=86.93 E-value=0.75 Score=39.06 Aligned_cols=40 Identities=8% Similarity=0.102 Sum_probs=33.5
Q ss_pred chhHHHHHHHHhHhCCceeeCCC---CCeeeChhhhhhhhhhh
Q 032124 97 SGSVARHILHQLQDTNIIELDSK---GQSLVLVERLHKLDCEN 136 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~LDri~ 136 (147)
+...+|.+|.-|++.|||+.... +...||++|++.++...
T Consensus 33 ~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~ 75 (280)
T TIGR02277 33 NERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAA 75 (280)
T ss_pred CcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHh
Confidence 44689999999999999987653 57789999999998654
No 85
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=86.21 E-value=0.77 Score=38.11 Aligned_cols=40 Identities=28% Similarity=0.196 Sum_probs=32.1
Q ss_pred chhHHHHHHHHhHhCCceeeCCC---CCeeeChhhhhhhhhhh
Q 032124 97 SGSVARHILHQLQDTNIIELDSK---GQSLVLVERLHKLDCEN 136 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~LDri~ 136 (147)
|.+-+...|+.||+.|||++... .--.||++|+..|.++.
T Consensus 34 S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~ 76 (217)
T PRK14165 34 SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEY 76 (217)
T ss_pred CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHH
Confidence 45778889999999999987642 24579999999987765
No 86
>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=85.94 E-value=0.9 Score=36.03 Aligned_cols=61 Identities=13% Similarity=0.215 Sum_probs=45.2
Q ss_pred hHHhHHHHHHHHHHhCCC-------chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 54 ~YiRaASi~RklYl~g~v-------GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
-|...+..+|.-=..|-. .-..|+..||- |..-+|+||+.|+..|+|++.+..|-.+++
T Consensus 9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 74 (238)
T TIGR02325 9 LWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGV--------------NRHTVRRAIAALVERGLLRAEQGRGTFVAA 74 (238)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEECC
Confidence 466666666665555432 34567787775 458999999999999999998878888875
Q ss_pred hh
Q 032124 127 ER 128 (147)
Q Consensus 127 ~G 128 (147)
..
T Consensus 75 ~~ 76 (238)
T TIGR02325 75 RR 76 (238)
T ss_pred Cc
Confidence 43
No 87
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=85.94 E-value=0.87 Score=37.42 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=25.1
Q ss_pred chhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 97 SGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
|..++|.+|+.||..|||+..+..|=.+++
T Consensus 47 SR~~vREAl~~L~a~Glve~r~G~Gt~V~~ 76 (241)
T COG2186 47 SRTVVREALKRLEAKGLVEIRQGSGTFVRP 76 (241)
T ss_pred CcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence 558999999999999999987766666654
No 88
>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=85.70 E-value=3 Score=29.72 Aligned_cols=37 Identities=14% Similarity=0.126 Sum_probs=26.5
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
..++.-..|....|- |..-+.++|++||+.|||+...
T Consensus 45 ~~~is~~eLa~~~g~--------------sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 45 QDRVTATVIAELTGL--------------SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred CCccCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeeeec
Confidence 445555666666554 3356889999999999998753
No 89
>PF13814 Replic_Relax: Replication-relaxation
Probab=85.54 E-value=2.2 Score=32.64 Aligned_cols=62 Identities=15% Similarity=0.103 Sum_probs=46.0
Q ss_pred HHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC-----Ce-----eeChhhhhhh
Q 032124 63 RKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-----QS-----LVLVERLHKL 132 (147)
Q Consensus 63 RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~-----GR-----~lT~~G~~~L 132 (147)
+-||-.+.+....+...++...+. .+-+|..|++|++.|+|+..... |. .||++|...|
T Consensus 2 ~~L~~~r~lt~~Qi~~l~~~~~~~-----------~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l 70 (191)
T PF13814_consen 2 RLLARHRFLTTDQIARLLFPSSKS-----------ERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLL 70 (191)
T ss_pred hhHHHhcCcCHHHHHHHHcCCCcc-----------hHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHH
Confidence 456667778888888888764332 12789999999999999876531 22 6999999998
Q ss_pred hhh
Q 032124 133 DCE 135 (147)
Q Consensus 133 Dri 135 (147)
.-.
T Consensus 71 ~~~ 73 (191)
T PF13814_consen 71 ADL 73 (191)
T ss_pred Hhc
Confidence 643
No 90
>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=85.54 E-value=3.4 Score=29.08 Aligned_cols=77 Identities=12% Similarity=0.106 Sum_probs=51.0
Q ss_pred HHHHHHHHH-hCCCchhhHHHHhcCCCCCCCCCCC------CCCC---chhHHHHHHHHhHhCCceeeCCC----CCeee
Q 032124 59 ASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPH------FSKS---SGSVARHILHQLQDTNIIELDSK----GQSLV 124 (147)
Q Consensus 59 ASi~RklYl-~g~vGV~~lr~~YGg~krrG~~P~h------~~~a---sgsiiR~~LqqLE~~glV~k~~~----~GR~l 124 (147)
..|++-|+- .+.+|...+..++=|.+...+...+ |-.+ |..-++.++++|...|+++.... .-=.+
T Consensus 7 ~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~ 86 (106)
T PF09382_consen 7 KKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKL 86 (106)
T ss_dssp HHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEEE
Confidence 445666655 5689999999999998887754321 2222 45689999999999999975543 24578
Q ss_pred Chhhhhhhhhh
Q 032124 125 LVERLHKLDCE 135 (147)
Q Consensus 125 T~~G~~~LDri 135 (147)
|++|+..|...
T Consensus 87 ~~~~~~~l~g~ 97 (106)
T PF09382_consen 87 TPKGKELLNGK 97 (106)
T ss_dssp -GGGHHHHCTT
T ss_pred CHHHHHHHCCC
Confidence 99999988643
No 91
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=85.50 E-value=1.2 Score=34.78 Aligned_cols=43 Identities=12% Similarity=0.088 Sum_probs=32.8
Q ss_pred CCchhHHHHHHHHhHhCCceeeCCCC----CeeeChhhhhhhhhhhc
Q 032124 95 KSSGSVARHILHQLQDTNIIELDSKG----QSLVLVERLHKLDCENS 137 (147)
Q Consensus 95 ~asgsiiR~~LqqLE~~glV~k~~~~----GR~lT~~G~~~LDri~~ 137 (147)
..|-+-|=-+|+.||+.|||+....+ =-.||++|+..|+...+
T Consensus 74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~ 120 (135)
T PRK09416 74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEK 120 (135)
T ss_pred cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHh
Confidence 33556677899999999999864322 23699999999987765
No 92
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=84.56 E-value=2.6 Score=33.17 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=36.0
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceee--CCCCCeeeChh
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSKGQSLVLVE 127 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k--~~~~GR~lT~~ 127 (147)
+|+.+..++..+|- +...++++|++|.++|||+. .+.||-.|...
T Consensus 24 ~~vs~~eIA~~~~i--------------p~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~ 70 (164)
T PRK10857 24 GPVPLADISERQGI--------------SLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKD 70 (164)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCC
Confidence 47888888887764 44899999999999999984 44678888654
No 93
>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=83.87 E-value=1.3 Score=37.99 Aligned_cols=39 Identities=21% Similarity=0.198 Sum_probs=32.6
Q ss_pred CchhHHHHHHHHhHhCCceeeCC-C-CCeeeChhhhhhhhh
Q 032124 96 SSGSVARHILHQLQDTNIIELDS-K-GQSLVLVERLHKLDC 134 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~-~-~GR~lT~~G~~~LDr 134 (147)
=|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|-
T Consensus 210 VSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e 250 (251)
T TIGR02787 210 ITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE 250 (251)
T ss_pred CCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence 46689999999999999999887 5 488888877777763
No 94
>PRK14999 histidine utilization repressor; Provisional
Probab=83.82 E-value=1.7 Score=35.00 Aligned_cols=60 Identities=17% Similarity=0.082 Sum_probs=45.1
Q ss_pred hHHhHHHHHHHHHHhCC-------CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 54 YYIRAASMARKIYLRGG-------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 54 ~YiRaASi~RklYl~g~-------vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
.|...+..||+--..|. ..-..|+..||- |..-+|+||+.|+..|+|.+.+..|--+++
T Consensus 13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~GkGTfV~~ 78 (241)
T PRK14999 13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGF--------------SRMTINRALRELTDEGWLVRLQGVGTFVAE 78 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence 46666666666555542 145678888875 458999999999999999998877887765
Q ss_pred h
Q 032124 127 E 127 (147)
Q Consensus 127 ~ 127 (147)
.
T Consensus 79 ~ 79 (241)
T PRK14999 79 P 79 (241)
T ss_pred C
Confidence 3
No 95
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=83.59 E-value=1 Score=34.21 Aligned_cols=78 Identities=18% Similarity=0.268 Sum_probs=47.3
Q ss_pred CCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHH
Q 032124 28 KIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQ 107 (147)
Q Consensus 28 ki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~Lqq 107 (147)
.=+.-.|.+=-++...+--+-.|+.-+ ..|+.-+--..-+.+-.|...||- ++||.|.+|..
T Consensus 21 ~k~kKK~~~k~~k~~~~~av~vdee~~----~ki~KEV~~~r~VTpy~la~r~gI--------------~~SvAr~vLR~ 82 (107)
T COG4901 21 AKDKKKWSKKKKKEEARRAVTVDEELL----DKIRKEVPRERVVTPYVLASRYGI--------------NGSVARIVLRH 82 (107)
T ss_pred hhhhhccccccccchhhhhhhccHHHH----HHHHHhcccceeecHHHHHHHhcc--------------chHHHHHHHHH
Confidence 344456776555544333333343322 223333322345666777777764 47999999999
Q ss_pred hHhCCceeeCCCCCeee
Q 032124 108 LQDTNIIELDSKGQSLV 124 (147)
Q Consensus 108 LE~~glV~k~~~~GR~l 124 (147)
||+.|+|.... ++|+.
T Consensus 83 LeeeGvv~lvs-knrR~ 98 (107)
T COG4901 83 LEEEGVVQLVS-KNRRQ 98 (107)
T ss_pred HHhCCceeeec-cCccc
Confidence 99999998774 46654
No 96
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=83.59 E-value=1.4 Score=34.19 Aligned_cols=45 Identities=20% Similarity=0.172 Sum_probs=35.2
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCeeeChhh
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSLVLVER 128 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~lT~~G 128 (147)
++.+..++..+|- |.+.++++||+|.++|||+... .||-.|+..-
T Consensus 24 ~~s~~eIA~~~~i--------------s~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p 70 (153)
T PRK11920 24 LSRIPEIARAYGV--------------SELFLFKILQPLVEAGLVETVRGRNGGVRLGRPA 70 (153)
T ss_pred cCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCH
Confidence 5677778777654 4489999999999999998665 4788887544
No 97
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.25 E-value=1.8 Score=25.72 Aligned_cols=35 Identities=14% Similarity=0.244 Sum_probs=26.1
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
|+.+..++...|- |.+-++++|++|++.|+|++..
T Consensus 8 ~~s~~~la~~l~~--------------s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 8 PLTRQEIAELLGL--------------TRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred ccCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeC
Confidence 4555666666554 3467899999999999999763
No 98
>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=82.54 E-value=4 Score=33.04 Aligned_cols=57 Identities=16% Similarity=0.126 Sum_probs=45.7
Q ss_pred HhHHHHHHHHHH-hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 56 IRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 56 iRaASi~RklYl-~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
-|+-.||.-|-- .+|+++..|.+.-|-.| +-+..+|+.|+..|||+++ .+.-.|++.
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lglpk--------------sT~~RlL~tL~~~G~l~~~-~~~Y~lG~~ 66 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGLTR--------------AAARRFLLTLVELGYVTSD-GRLFWLTPR 66 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEeC-CCEEEecHH
Confidence 378888888875 57899999999877543 7889999999999999986 345566654
No 99
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=82.04 E-value=3.7 Score=34.70 Aligned_cols=59 Identities=7% Similarity=-0.090 Sum_probs=45.8
Q ss_pred HHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCc-eeeCCCCCeeeChh
Q 032124 55 YIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNI-IELDSKGQSLVLVE 127 (147)
Q Consensus 55 YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~gl-V~k~~~~GR~lT~~ 127 (147)
|-|...|++.|.-..++....|+..+|-. .+-+++.|+.|++.|+ +.....+|-.|.+.
T Consensus 3 ~~r~~~il~~L~~~~~~s~~~LA~~lgvs--------------r~tV~~~l~~L~~~G~~i~~~~~~Gy~L~~~ 62 (319)
T PRK11886 3 YTVMLQLLSLLADGDFHSGEQLGEELGIS--------------RAAIWKHIQTLEEWGLDIFSVKGKGYRLAEP 62 (319)
T ss_pred ccHHHHHHHHHHcCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCceEEecCCeEEecCc
Confidence 45788899988877788999999988854 3789999999999999 54444457776544
No 100
>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=81.87 E-value=1.6 Score=34.76 Aligned_cols=41 Identities=24% Similarity=0.277 Sum_probs=33.3
Q ss_pred hhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 73 V~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
=..|+..||- |..-+|+||+.|+..|+|++....|--+++.
T Consensus 27 E~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~G~GTfV~~~ 67 (233)
T TIGR02404 27 EHELMDQYGA--------------SRETVRKALNLLTEAGYIQKIQGKGSIVLNR 67 (233)
T ss_pred HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCceEEEecC
Confidence 3567777764 5589999999999999999998778888653
No 101
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=81.71 E-value=3.6 Score=31.81 Aligned_cols=44 Identities=16% Similarity=0.133 Sum_probs=34.6
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC--CCCeeeChh
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGQSLVLVE 127 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~--~~GR~lT~~ 127 (147)
++-+..++..+|- |.+.++++|++|.++|+|+... +||-+|...
T Consensus 25 ~~s~~~IA~~~~i--------------s~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~ 70 (150)
T COG1959 25 PVSSAEIAERQGI--------------SPSYLEKILSKLRKAGLVKSVRGKGGGYRLARP 70 (150)
T ss_pred cccHHHHHHHhCc--------------CHHHHHHHHHHHHHcCCEEeecCCCCCccCCCC
Confidence 5667888876654 3489999999999999998554 578888754
No 102
>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=81.43 E-value=7.7 Score=28.97 Aligned_cols=67 Identities=10% Similarity=0.087 Sum_probs=49.5
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhh
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
.+++|+-++|-+.=+..+.+|-.- +...+...+-+=++-|-+-|||||.. +|-++|.+|+..+-.+|
T Consensus 17 ~~~~ilI~v~Kk~Fit~~ev~e~l------------~~~~~~~~V~SNIGvLIKkglIEKSG-DGlv~T~~g~~Ii~~AA 83 (96)
T PF09114_consen 17 NAANILIQVAKKNFITASEVREAL------------ATEMNKASVNSNIGVLIKKGLIEKSG-DGLVITEEGMDIIIQAA 83 (96)
T ss_dssp HHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEET-TEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHccCCHHHHHHHH------------HHHhhhhHHHHhHHHHHHcCcccccC-CceEEechHHHHHHHHH
Confidence 568888888888777777777632 23455677777789999999999995 58999999998876655
No 103
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=81.36 E-value=1.8 Score=34.92 Aligned_cols=61 Identities=28% Similarity=0.337 Sum_probs=43.7
Q ss_pred hHHhHHHHHHHHHHhCCC-------chhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 54 ~YiRaASi~RklYl~g~v-------GV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
.|...+..|++--..|.. .-..|+..||- |..-+|+||+.|+..|+|.+.+..|-.+++
T Consensus 6 ly~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 71 (240)
T PRK09764 6 LYRQIADRIREQIARGELKPGDALPTESALQTEFGV--------------SRVTVRQALRQLVEQQILESIQGSGTYVKE 71 (240)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEcc
Confidence 356666666665555422 34567777764 558999999999999999988877877765
Q ss_pred hh
Q 032124 127 ER 128 (147)
Q Consensus 127 ~G 128 (147)
..
T Consensus 72 ~~ 73 (240)
T PRK09764 72 ER 73 (240)
T ss_pred cc
Confidence 43
No 104
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=81.28 E-value=3.5 Score=37.43 Aligned_cols=63 Identities=5% Similarity=0.029 Sum_probs=47.5
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC--CCeeeChhhhhhhhhh
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK--GQSLVLVERLHKLDCE 135 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~--~GR~lT~~G~~~LDri 135 (147)
..||..|.-.+++....|+...|-. -+-+-.++..||+.|||+.... ..-.||++|++.++.+
T Consensus 9 ~~vL~~L~~~~~~s~~eLA~~l~l~--------------~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g 73 (489)
T PRK04172 9 KKVLKALKELKEATLEELAEKLGLP--------------PEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEG 73 (489)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCcC--------------HHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhc
Confidence 4578888888888889998876632 1445567889999999996642 3557999999988753
No 105
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=81.08 E-value=1.8 Score=31.57 Aligned_cols=22 Identities=32% Similarity=0.457 Sum_probs=19.1
Q ss_pred chhHHHHHHHHhHhCCceeeCC
Q 032124 97 SGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~ 118 (147)
.||++|.+|+.||+-|+|....
T Consensus 54 ~~SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 54 KISVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred hHHHHHHHHHHHHHCCCEEEEe
Confidence 5799999999999999996553
No 106
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=80.31 E-value=3.9 Score=31.71 Aligned_cols=38 Identities=24% Similarity=0.325 Sum_probs=32.0
Q ss_pred HhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 67 l~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
.+||..|..|+..-+- +.|-+=++||.|..+|+|++.+
T Consensus 39 ~~~~~tvdelae~lnr--------------~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 39 ENGPLTVDELAEILNR--------------SRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred hcCCcCHHHHHHHHCc--------------cHHHHHHHHHHHHHcCCeeeee
Confidence 4899999999987543 4588999999999999998664
No 107
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=79.57 E-value=4.5 Score=34.83 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=32.3
Q ss_pred hHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 99 SVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
......+++|++.||++.+. +.=+||++|+-.+|.|++
T Consensus 334 ~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~ 371 (377)
T PRK08599 334 DVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFE 371 (377)
T ss_pred HHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHH
Confidence 45677889999999999763 567899999999999875
No 108
>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=79.39 E-value=4.7 Score=24.97 Aligned_cols=42 Identities=21% Similarity=0.327 Sum_probs=33.0
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceee
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k 116 (147)
.|+..|.- ||.-+..|....|-. -+.+.+=|..|+++|+|++
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s--------------~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLS--------------QSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHh-CCCchhhHHHhcccc--------------chHHHHHHHHHHHCcCeeC
Confidence 34444444 899999999988754 3789999999999999985
No 109
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=79.31 E-value=2.1 Score=34.40 Aligned_cols=59 Identities=19% Similarity=0.171 Sum_probs=41.2
Q ss_pred hHHhHHHHHHHHHHhCC-------CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 54 YYIRAASMARKIYLRGG-------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 54 ~YiRaASi~RklYl~g~-------vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
-|...|..||+- |.+- .+=..|+..||- |..-+|+||+.|++.|+|.+....|-.+++
T Consensus 13 ~Y~qi~~~L~~~-I~~~~~~G~~LPsE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~ 77 (241)
T PRK10079 13 RYQEIAAKLEQE-LRQHYRCGDYLPAEQQLAARYEV--------------NRHTLRRAIDQLVEKGWVQRRQGVGVLVLM 77 (241)
T ss_pred HHHHHHHHHHHH-HhcccCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEec
Confidence 456666666554 2221 133567777764 558999999999999999998877877764
Q ss_pred h
Q 032124 127 E 127 (147)
Q Consensus 127 ~ 127 (147)
.
T Consensus 78 ~ 78 (241)
T PRK10079 78 R 78 (241)
T ss_pred C
Confidence 3
No 110
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=78.94 E-value=5.2 Score=35.62 Aligned_cols=71 Identities=11% Similarity=0.113 Sum_probs=50.1
Q ss_pred chhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 52 DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
||.=.+--+.+-.-|--||||+++++-.-|--+. .|-=.+===|-..|++++++ .||++|+++...
T Consensus 259 d~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~-------------TiEdv~EPyLiq~gfi~RTp-RGR~aT~~ay~h 324 (332)
T COG2255 259 DEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRD-------------TIEDVIEPYLIQQGFIQRTP-RGRIATAKAYEH 324 (332)
T ss_pred cHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchh-------------HHHHHHhHHHHHhchhhhCC-CcceecHHHHHH
Confidence 6666665555666667799999999998775331 22222223466789999997 699999999888
Q ss_pred hhhhh
Q 032124 132 LDCEN 136 (147)
Q Consensus 132 LDri~ 136 (147)
|-...
T Consensus 325 l~~~~ 329 (332)
T COG2255 325 LGLPP 329 (332)
T ss_pred hccCC
Confidence 76543
No 111
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=78.64 E-value=2.4 Score=33.66 Aligned_cols=33 Identities=24% Similarity=0.284 Sum_probs=27.5
Q ss_pred CCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 95 KSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 95 ~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
.-|-.=+|.+|+-|+++|+++++.+|.-+.|.+
T Consensus 52 ~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~ 84 (171)
T PF14394_consen 52 KISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDK 84 (171)
T ss_pred CCCHHHHHHHHHHHHHCCCeEECCCCcEEEecc
Confidence 456678999999999999999998766676664
No 112
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=78.50 E-value=2.5 Score=31.68 Aligned_cols=39 Identities=13% Similarity=0.204 Sum_probs=32.1
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
++.+..|+.....+. .-+|.+|++|++.|||+-.|..||
T Consensus 19 ~vtl~elA~~l~cS~--------------Rn~r~lLkkm~~~gWi~W~pg~GR 57 (115)
T PF12793_consen 19 EVTLDELAELLFCSR--------------RNARTLLKKMQEEGWITWQPGRGR 57 (115)
T ss_pred ceeHHHHHHHhCCCH--------------HHHHHHHHHHHHCCCeeeeCCCCC
Confidence 467888888776544 568999999999999999997776
No 113
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=78.37 E-value=2.3 Score=31.44 Aligned_cols=41 Identities=17% Similarity=0.131 Sum_probs=30.5
Q ss_pred CchhHHHHHHHHhHhCCceeeCC--CCC------eeeChhhhhhhhhhh
Q 032124 96 SSGSVARHILHQLQDTNIIELDS--KGQ------SLVLVERLHKLDCEN 136 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~--~~G------R~lT~~G~~~LDri~ 136 (147)
.|-..|=-+|+.||+.|||+... .++ -.||++|+..|....
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~ 90 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELR 90 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHH
Confidence 34456677999999999998642 222 379999999988654
No 114
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.87 E-value=5.6 Score=31.85 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=36.6
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCcee
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~ 115 (147)
-|+..|.-+|++....|+..-|-+. .-+|++|+.|++.|||.
T Consensus 26 ~Vl~~L~~~g~~tdeeLA~~Lgi~~--------------~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALIKKGEVTDEEIAEQTGIKL--------------NTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCeE
Confidence 3788888889999999999877543 78999999999999998
No 115
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=77.42 E-value=2 Score=37.61 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=33.6
Q ss_pred hHHHHHHHHhHhCCceeeCC--CCCeeeChhhhhhhhhhh
Q 032124 99 SVARHILHQLQDTNIIELDS--KGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~--~~GR~lT~~G~~~LDri~ 136 (147)
.-+|..+|.|-++||||-.+ +||.+-|.+.-..|+.+-
T Consensus 40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~iqt 79 (294)
T COG2524 40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSIQT 79 (294)
T ss_pred chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhccCC
Confidence 46899999999999999766 699999999998888765
No 116
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=77.27 E-value=7.9 Score=31.97 Aligned_cols=51 Identities=16% Similarity=0.126 Sum_probs=42.9
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
|-..|++.|--+|.+.+..|...+|- |..-||+=|++||+.|++.+.. ||=
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~v--------------S~~TirRdL~~Le~~g~i~r~~-gga 56 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGI--------------SPATARRDINKLDESGKLKKVR-NGA 56 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEec-CCc
Confidence 66778888888999999999999874 4477899999999999999875 443
No 117
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=77.03 E-value=2.9 Score=33.56 Aligned_cols=60 Identities=12% Similarity=0.056 Sum_probs=43.0
Q ss_pred HHhHHHHHHHHHHhCC-------CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 55 YIRAASMARKIYLRGG-------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 55 YiRaASi~RklYl~g~-------vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
|...+..++.--..|- .+-..|+..||- |..-+|+||+.|++.|+|.+....|--+++.
T Consensus 11 y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GTfV~~~ 76 (241)
T PRK11402 11 YATVRQRLLDDIAQGVYQAGQQIPTENELCTQYNV--------------SRITIRKAISDLVADGVLIRWQGKGTFVQSQ 76 (241)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEECCC
Confidence 5555555555444442 234567777774 4589999999999999999988778888665
Q ss_pred h
Q 032124 128 R 128 (147)
Q Consensus 128 G 128 (147)
.
T Consensus 77 ~ 77 (241)
T PRK11402 77 K 77 (241)
T ss_pred c
Confidence 4
No 118
>PRK12423 LexA repressor; Provisional
Probab=76.99 E-value=7.3 Score=31.09 Aligned_cols=37 Identities=24% Similarity=0.369 Sum_probs=29.4
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~ 119 (147)
|..+..|...+|= .|.+.+|..|+.||+.|+|+..+.
T Consensus 25 ~Ps~~eia~~~g~-------------~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 25 PPSLAEIAQAFGF-------------ASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEEecCC
Confidence 3478888887662 244889999999999999998874
No 119
>PRK05283 deoxyribose-phosphate aldolase; Provisional
Probab=76.65 E-value=2.6 Score=36.03 Aligned_cols=90 Identities=17% Similarity=0.181 Sum_probs=53.0
Q ss_pred hhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHH----hCCCchh------hHHHH--
Q 032124 12 PHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYL----RGGLGVG------SFRRI-- 79 (147)
Q Consensus 12 ~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl----~g~vGV~------~lr~~-- 79 (147)
.++.|...++-..+.| +|||||+++..-.+-.++ ...++|..-- .+.+||. .+...
T Consensus 145 ~ee~i~~a~~~a~~aG-------ADFVKTSTGf~~~gAt~e-----dv~lm~~~i~~~~~~~~vgIKAsGGIrt~~~A~~ 212 (257)
T PRK05283 145 DEALIRKASEIAIKAG-------ADFIKTSTGKVPVNATLE-----AARIMLEVIRDMGVAKTVGFKPAGGVRTAEDAAQ 212 (257)
T ss_pred CHHHHHHHHHHHHHhC-------CCEEEcCCCCCCCCCCHH-----HHHHHHHHHHhcccCCCeeEEccCCCCCHHHHHH
Confidence 3444555555555555 899999999976666653 2334444321 1334442 22110
Q ss_pred -h-cCCCCCC---CCCCCCCCCchhHHHHHHHHhHhCCc
Q 032124 80 -Y-GGGKRNG---SRPPHFSKSSGSVARHILHQLQDTNI 113 (147)
Q Consensus 80 -Y-Gg~krrG---~~P~h~~~asgsiiR~~LqqLE~~gl 113 (147)
+ -|+-.=| ..|+.|+-|+.|++=.+|+.||....
T Consensus 213 ~i~ag~~~lg~~~~~~~~fR~G~Ssll~~~~~~~~~~~~ 251 (257)
T PRK05283 213 YLALADEILGADWADARHFRFGASSLLASLLKTLGHGDG 251 (257)
T ss_pred HHHHHHHHhChhhcCcccEeeehHHhHHHHHHHHhcccC
Confidence 0 1111122 46999999999999999998876543
No 120
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=76.41 E-value=8.2 Score=33.61 Aligned_cols=53 Identities=17% Similarity=0.189 Sum_probs=39.5
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
.++-...+...||-.- ....|+.|++.|+++.+.++.=+||++|+.++|.|++
T Consensus 324 ~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~ 376 (380)
T PRK09057 324 EGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVA 376 (380)
T ss_pred CCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHH
Confidence 4566677777777421 1257999999999997643247899999999999875
No 121
>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=75.67 E-value=13 Score=24.43 Aligned_cols=52 Identities=8% Similarity=0.012 Sum_probs=37.7
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
.|++.+. +++..+..|+..+|- |.+-|+..++.||+.|+..-..+.|..|.+
T Consensus 4 ~il~~L~-~~~~~~~eLa~~l~v--------------S~~tv~~~l~~L~~~g~~i~~~~~g~~l~~ 55 (69)
T TIGR00122 4 RLLALLA-DNPFSGEKLGEALGM--------------SRTAVNKHIQTLREWGVDVLTVGKGYRLPP 55 (69)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEecCCceEecC
Confidence 3555544 667788999998864 347899999999999995433356777644
No 122
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=75.38 E-value=1.9 Score=37.88 Aligned_cols=37 Identities=14% Similarity=0.083 Sum_probs=30.3
Q ss_pred hHHHHHHHHhHhCCceeeCCCCCe--eeCh-hhhhhhhhhhc
Q 032124 99 SVARHILHQLQDTNIIELDSKGQS--LVLV-ERLHKLDCENS 137 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~~~GR--~lT~-~G~~~LDri~~ 137 (147)
......|++|++.||++.+ ++| +||+ +|+-++|.|++
T Consensus 351 ~~~~~~l~~l~~~gll~~~--~~~~~~lT~~~G~~~~~~i~~ 390 (400)
T PRK07379 351 EQILQCLQPYFQQGWVELE--GDRRLRLTDPEGFLFSNTVLA 390 (400)
T ss_pred HHHHHHHHHHHHCCCEEEe--CCeEEEECchHHhHHHHHHHH
Confidence 4456788999999999875 456 8995 99999999875
No 123
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=75.15 E-value=3.5 Score=28.10 Aligned_cols=37 Identities=24% Similarity=0.210 Sum_probs=28.7
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
++|+-...+....|- |-.-+|+.|++||+.|.|++.+
T Consensus 13 ~~p~~T~eiA~~~gl--------------s~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 13 NGPLKTREIADALGL--------------SIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp TS-EEHHHHHHHHTS---------------HHHHHHHHHHHHHCTSEEEES
T ss_pred CCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEec
Confidence 567777777777664 3478999999999999999876
No 124
>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=73.89 E-value=2.5 Score=31.66 Aligned_cols=35 Identities=23% Similarity=0.245 Sum_probs=27.8
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
-+.+..|...|+- ++|+.|.+|+.||+-|+|....
T Consensus 59 ~ITp~~lserlkI--------------~~SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 59 LITPSVLSERLKI--------------NGSLARKALRELESKGLIKPVS 93 (105)
T ss_dssp CECHHHHHHHHCC--------------SCHHHHHHHHHHHHCCSSEEEE
T ss_pred EeeHHHHHHhHhh--------------HHHHHHHHHHHHHHCCCEEEEe
Confidence 4677777777764 4699999999999999997553
No 125
>PRK00215 LexA repressor; Validated
Probab=73.50 E-value=13 Score=29.16 Aligned_cols=52 Identities=17% Similarity=0.059 Sum_probs=37.7
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe--eeChhhhhhhhh
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS--LVLVERLHKLDC 134 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR--~lT~~G~~~LDr 134 (147)
|..+..|....|-+ +.+-+...|+.||+.|+|++.++.+| .|++.|+..+.+
T Consensus 23 ~~s~~ela~~~~~~-------------~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~~~~~~~~~ 76 (205)
T PRK00215 23 PPSRREIADALGLR-------------SPSAVHEHLKALERKGFIRRDPGRSRAIEVAAPAQLELPE 76 (205)
T ss_pred CCCHHHHHHHhCCC-------------ChHHHHHHHHHHHHCCCEEeCCCCcceEEecccccccccc
Confidence 56888999987752 22667789999999999999876554 355566655443
No 126
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=73.47 E-value=8.4 Score=34.17 Aligned_cols=56 Identities=23% Similarity=0.294 Sum_probs=41.4
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhcC
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENSN 138 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~~ 138 (147)
..++-...+...||.. + .. ....|++|++.|||+.+. +.=+||++|+-..|.|++.
T Consensus 359 ~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~ 414 (430)
T PRK08208 359 AQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPV 414 (430)
T ss_pred hCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHH
Confidence 4566667777777631 1 12 345889999999999763 4568999999999999864
No 127
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=73.09 E-value=3.9 Score=33.32 Aligned_cols=73 Identities=19% Similarity=0.196 Sum_probs=48.5
Q ss_pred HHhHHHHHHHHHHhCCCc-------hhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 55 YIRAASMARKIYLRGGLG-------VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 55 YiRaASi~RklYl~g~vG-------V~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
|.+.+.-++.-=..|-.. =..|+..||- |.--+|+||++|++.|+|......|--+++.
T Consensus 9 Y~qI~~~i~~~I~~G~~~~G~~LPsE~eLa~~f~V--------------SR~TvRkAL~~L~~eGli~r~~G~GtfV~~~ 74 (236)
T COG2188 9 YQQIAEDIRQRIESGELPPGDKLPSERELAEQFGV--------------SRMTVRKALDELVEEGLIVRRQGKGTFVASP 74 (236)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHHCC--------------cHHHHHHHHHHHHHCCcEEEEecCeeEEcCc
Confidence 455555555555554322 2356777764 5578999999999999999887778777764
Q ss_pred --------hhhhhhhhhcCCcc
Q 032124 128 --------RLHKLDCENSNGMD 141 (147)
Q Consensus 128 --------G~~~LDri~~~~~~ 141 (147)
-.++-+-+.+.|++
T Consensus 75 ~~~~~~~~~~~f~e~~~~~g~~ 96 (236)
T COG2188 75 KEQSPLLELTSFSEELKSQGLE 96 (236)
T ss_pred cccccccccccHHHHHHhCCCC
Confidence 22345555566665
No 128
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=72.29 E-value=1.6 Score=37.43 Aligned_cols=37 Identities=8% Similarity=0.094 Sum_probs=30.4
Q ss_pred HHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 100 VARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 100 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
.....|+.|++.|+++.+. +.=+||++|+-++|.|++
T Consensus 334 ~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~ 370 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSNSIMS 370 (374)
T ss_pred HHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHHHHHH
Confidence 4556789999999999753 346899999999999875
No 129
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=71.90 E-value=6.7 Score=33.08 Aligned_cols=66 Identities=14% Similarity=0.213 Sum_probs=45.1
Q ss_pred chhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 52 DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
|.-|+|+ +...|-.+|+|+..+...-|-... .+...+=..|-..|+|++.+ .||++|++|..-
T Consensus 261 ~~~~l~~---~~~~~~~~~~~~~~~a~~lg~~~~-------------~~~~~~e~~Li~~~li~~~~-~gr~~~~~~~~~ 323 (328)
T PRK00080 261 DRKYLRT---IIEKFGGGPVGLDTLAAALGEERD-------------TIEDVYEPYLIQQGFIQRTP-RGRVATPKAYEH 323 (328)
T ss_pred HHHHHHH---HHHHcCCCceeHHHHHHHHCCCcc-------------hHHHHhhHHHHHcCCcccCC-chHHHHHHHHHH
Confidence 4445542 334455679999999888764321 23333333888999998774 799999999988
Q ss_pred hhh
Q 032124 132 LDC 134 (147)
Q Consensus 132 LDr 134 (147)
|..
T Consensus 324 ~~~ 326 (328)
T PRK00080 324 LGL 326 (328)
T ss_pred hCC
Confidence 764
No 130
>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=71.48 E-value=13 Score=29.06 Aligned_cols=45 Identities=24% Similarity=0.175 Sum_probs=33.0
Q ss_pred HHHHHHhC--CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC
Q 032124 62 ARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (147)
Q Consensus 62 ~RklYl~g--~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~ 119 (147)
+++-|.++ |.++..|...+|- +|.+-++..|+.||+.|+|++...
T Consensus 15 l~~~~~~~~~~~~~~ela~~~~~-------------~s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 15 IRAHIESTGYPPSIREIARAVGL-------------RSPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred HHHHHHhcCCCCcHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEecCCC
Confidence 33444544 4567789887774 245889999999999999998754
No 131
>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=71.41 E-value=5.9 Score=27.34 Aligned_cols=61 Identities=28% Similarity=0.329 Sum_probs=39.3
Q ss_pred hHHHHHHHHH---Hh---CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC---CeeeChh
Q 032124 57 RAASMARKIY---LR---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---QSLVLVE 127 (147)
Q Consensus 57 RaASi~RklY---l~---g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~---GR~lT~~ 127 (147)
|+-|++--|| +. +++-++.|-...+. -| =+.+-+|.+|--|-+.||++....| .-.||++
T Consensus 1 ~a~Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~---~G--------v~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 1 RARSLIVTLLGDYLRPRGGWIWVASLIRLLAA---FG--------VSESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp -HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCC---TT----------HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred CcceehHHHHHHHhccCCCceeHHHHHHHHHH---cC--------CChHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 4556666666 32 35566666666542 12 2347899999999999999988654 3678887
Q ss_pred h
Q 032124 128 R 128 (147)
Q Consensus 128 G 128 (147)
|
T Consensus 70 g 70 (70)
T PF07848_consen 70 G 70 (70)
T ss_dssp H
T ss_pred C
Confidence 6
No 132
>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=71.17 E-value=12 Score=31.94 Aligned_cols=59 Identities=17% Similarity=0.175 Sum_probs=39.3
Q ss_pred chhHHhHHHHHHHHHH--hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 52 DWYYIRAASMARKIYL--RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 52 DW~YiRaASi~RklYl--~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
+|||. ++|-|-= .+-.-+..|.+.-+ | .=|-.=+|.+|+-|+++|+++++.+|.-+.|.
T Consensus 121 ~W~~~----virel~~~~~~~~~~~~ia~~l~--------p----~is~~ev~~sL~~L~~~glikk~~~g~y~~t~ 181 (271)
T TIGR02147 121 HWYNS----VIRELLGVMPFADDPEELAKRCF--------P----KISAEQVKESLDLLERLGLIKKNEDGFYKQTD 181 (271)
T ss_pred HHHHH----HHHHHhhcCCCCCCHHHHHHHhC--------C----CCCHHHHHHHHHHHHHCCCeeECCCCcEEeec
Confidence 78875 6776662 22223555666433 2 23557799999999999999998765455553
No 133
>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=70.92 E-value=9.6 Score=31.22 Aligned_cols=50 Identities=10% Similarity=0.190 Sum_probs=39.6
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHH-HhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILH-QLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~Lq-qLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
.+|+++..++...|-. ..-++.++. .|-+.|+|++. ..||+.|++|...|
T Consensus 253 ~~~~~~~~ia~~lg~~--------------~~~~~~~~e~~Li~~~li~~~-~~g~~~~~~~~~~~ 303 (305)
T TIGR00635 253 GGPVGLKTLAAALGED--------------ADTIEDVYEPYLLQIGFLQRT-PRGRIATELAYEHL 303 (305)
T ss_pred CCcccHHHHHHHhCCC--------------cchHHHhhhHHHHHcCCcccC-CchhhhhHHHHHHh
Confidence 4579999999888752 245677777 69999999865 57999999998765
No 134
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=70.51 E-value=11 Score=31.47 Aligned_cols=55 Identities=22% Similarity=0.325 Sum_probs=46.6
Q ss_pred HhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeC
Q 032124 56 IRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVL 125 (147)
Q Consensus 56 iRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT 125 (147)
-|-..|+..|--++.+.+..|...+|- |..-||.=|..||+.|++.+.. ||.++.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~V--------------S~~TIRRDL~~Le~~G~l~r~~-GGa~~~ 71 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGV--------------STVTIRNDLAFLEKQGIAVRAY-GGALIC 71 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCC--------------CHHHHHHHHHHHHhCCCeEEEe-CCEEec
Confidence 477888888888999999999999863 4478999999999999999875 677654
No 135
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=70.42 E-value=14 Score=30.64 Aligned_cols=55 Identities=16% Similarity=0.179 Sum_probs=44.7
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
|-..|+.-|--++.+.+..|...|+- |..-||.=|..||+.|++.+.. ||=.+.+
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~v--------------S~~TiRRdL~~Le~~g~l~r~~-GGa~~~~ 60 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSV--------------SPQTIRRDLNDLAEQNKILRHH-GGAALPS 60 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEec-CCEEecC
Confidence 66678888888899999999998853 4578999999999999999874 5655443
No 136
>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=69.99 E-value=15 Score=24.24 Aligned_cols=40 Identities=13% Similarity=0.255 Sum_probs=31.6
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCC
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQ 121 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~G 121 (147)
.+++....++...|-++ +-+=..|+.|++.|||+..+.+|
T Consensus 20 ~~~v~~~~iA~~L~vs~--------------~tvt~ml~~L~~~GlV~~~~y~g 59 (60)
T PF01325_consen 20 GGPVRTKDIAERLGVSP--------------PTVTEMLKRLAEKGLVEYEPYKG 59 (60)
T ss_dssp TSSBBHHHHHHHHTS-H--------------HHHHHHHHHHHHTTSEEEETTTE
T ss_pred CCCccHHHHHHHHCCCh--------------HHHHHHHHHHHHCCCEEecCCCC
Confidence 36888999998877532 55678999999999999887654
No 137
>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=69.81 E-value=7 Score=25.22 Aligned_cols=32 Identities=16% Similarity=0.108 Sum_probs=23.5
Q ss_pred chhHHHHHHHHhHhC---CceeeCCCCCeeeChhhh
Q 032124 97 SGSVARHILHQLQDT---NIIELDSKGQSLVLVERL 129 (147)
Q Consensus 97 sgsiiR~~LqqLE~~---glV~k~~~~GR~lT~~G~ 129 (147)
|-+-+.+.+++||+. .|++... +|=.||+.|+
T Consensus 26 s~~~vs~~i~~LE~~lg~~Lf~r~~-~~~~lT~~G~ 60 (60)
T PF00126_consen 26 SQSAVSRQIKQLEEELGVPLFERSG-RGLRLTEAGE 60 (60)
T ss_dssp SHHHHHHHHHHHHHHHTS-SEEECS-SSEEE-HHHH
T ss_pred cchHHHHHHHHHHHHhCCeEEEECC-CCeeEChhhC
Confidence 346778889999874 7888874 5899999996
No 138
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=69.40 E-value=18 Score=30.82 Aligned_cols=86 Identities=22% Similarity=0.251 Sum_probs=61.2
Q ss_pred HHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCC-CchhhHHHHhcCCCCCCCCCCCCCC
Q 032124 17 KAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGG-LGVGSFRRIYGGGKRNGSRPPHFSK 95 (147)
Q Consensus 17 ~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~-vGV~~lr~~YGg~krrG~~P~h~~~ 95 (147)
..++-.|...+.+..|.|....++..-.+..|.++|= -.|+.-|--+|+ +-=..|+++-|-.
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~e-----~~il~~i~~~GGri~Q~eL~r~lgls------------ 223 (258)
T COG2512 161 EALGVILIIYAPVIEPLLSRGDELRVLVNEYDLNEDE-----KEILDLIRERGGRITQAELRRALGLS------------ 223 (258)
T ss_pred hhhhhhhhhcchhhhhccccccccccccccCCCCHHH-----HHHHHHHHHhCCEEeHHHHHHhhCCC------------
Confidence 3444445555667778999988888887777777653 346665556666 6677888876643
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCCC
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKGQ 121 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~G 121 (147)
.+=+-.+|+.||+.|+||+.+.|+
T Consensus 224 --ktTvsR~L~~LEk~GlIe~~K~G~ 247 (258)
T COG2512 224 --KTTVSRILRRLEKRGLIEKEKKGR 247 (258)
T ss_pred --hHHHHHHHHHHHhCCceEEEEeCC
Confidence 356778999999999999986543
No 139
>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=68.73 E-value=14 Score=27.88 Aligned_cols=52 Identities=17% Similarity=0.226 Sum_probs=40.3
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
.||+.|+-.||+.+..+....+.. +|. +-+-++.+|..|++-|+|+... .||
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~--~~~--------~~tTv~T~L~rL~~KG~v~~~k-~gr 59 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEK--KDW--------SDSTIKTLLGRLVDKGCLTTEK-EGR 59 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhc--cCC--------cHHHHHHHHHHHHHCCceeeec-CCC
Confidence 588999999999999988776532 232 2367899999999999998764 455
No 140
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=68.59 E-value=5.1 Score=34.56 Aligned_cols=35 Identities=9% Similarity=0.116 Sum_probs=29.8
Q ss_pred HHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 102 RHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 102 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
+..|++|++.|++..+. +.=+||++|+-.+|.|++
T Consensus 337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~ 371 (375)
T PRK05628 337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADAVVR 371 (375)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHHHHH
Confidence 57889999999998763 457899999999999875
No 141
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=68.11 E-value=5.2 Score=35.71 Aligned_cols=35 Identities=17% Similarity=0.168 Sum_probs=29.5
Q ss_pred HHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 102 RHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 102 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
...|++|++.|||+.+. ++=+||++|+-++|.|+.
T Consensus 402 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~ 436 (453)
T PRK13347 402 LARLEPLAADGLVTIDG-GGIRVTPEGRPLIRAVAA 436 (453)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHH
Confidence 45789999999999763 456899999999999875
No 142
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=67.61 E-value=14 Score=30.67 Aligned_cols=54 Identities=17% Similarity=0.250 Sum_probs=45.2
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeC
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVL 125 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT 125 (147)
|-..|+..|--++.+-+..|...+|- |..-||.=|+.||+.|+|.+.. ||=+++
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~V--------------S~~TIRRDL~~Le~~g~l~r~~-Gga~~~ 59 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDT--------------TGTTIRKDLVILEHAGTVIRTY-GGVVLN 59 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEEE-CCEEcC
Confidence 67788888989999999999999875 4578999999999999998874 555443
No 143
>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=66.68 E-value=10 Score=25.21 Aligned_cols=40 Identities=23% Similarity=0.297 Sum_probs=31.7
Q ss_pred HHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 65 lYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
|--+|.+.+..|.+.++- |-..++..|.+||..|.|++..
T Consensus 9 l~~~~~~S~~eLa~~~~~--------------s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 9 LRERGRVSLAELAREFGI--------------SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHS-SEEHHHHHHHTT----------------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEec
Confidence 445688999999997764 4589999999999999999775
No 144
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=66.11 E-value=3.8 Score=38.63 Aligned_cols=100 Identities=13% Similarity=0.084 Sum_probs=56.2
Q ss_pred CCCceeee-ccCCCCCCCCCCCchhHHhHHHH-HHHHHHhCCCchhhHHHHhcCCCCCCCC---CCCCCCCchhHHHHHH
Q 032124 31 LPTWNDIV-KTGTLKELAPYDPDWYYIRAASM-ARKIYLRGGLGVGSFRRIYGGGKRNGSR---PPHFSKSSGSVARHIL 105 (147)
Q Consensus 31 ~P~W~d~v-KTg~~kElaP~~~DW~YiRaASi-~RklYl~g~vGV~~lr~~YGg~krrG~~---P~h~~~asgsiiR~~L 105 (147)
-|+|..-. +-|.-+.-||.+.-=+|.+.|.- =|+=|+.+- -+.-|.++=-+.-.||.- -+.+..+-..=++.+|
T Consensus 385 n~EW~eqa~~eglVs~gAiT~kGrl~akls~tikRkP~LT~~-e~kvl~kiP~~~ikrg~liedi~~~~g~~eeev~~sl 463 (593)
T COG1542 385 NAEWYEQAKEEGLVSRGAITEKGRLYAKLSKTIKRKPYLTKY-EIKVLIKIPRKYIKRGELIEDIQGHVGGDEEEVIKSL 463 (593)
T ss_pred CHHHHHHHHhcccccccCcCcchhHHHHHHHHHhcCcccchh-HHHHHHhccccccchhhHHHHHHhhcCccHHHHHHHH
Confidence 34554322 34455555677777777776532 233333221 122233321111222211 0111123346789999
Q ss_pred HHhHhCCceeeCCCCCeeeChhhhhh
Q 032124 106 HQLQDTNIIELDSKGQSLVLVERLHK 131 (147)
Q Consensus 106 qqLE~~glV~k~~~~GR~lT~~G~~~ 131 (147)
..||+-|+|+--+.+|=.||..||-.
T Consensus 464 ~kleskgfveeL~n~gv~LTeaGe~~ 489 (593)
T COG1542 464 GKLESKGFVEELPNKGVKLTEAGELV 489 (593)
T ss_pred HHHhhcchHHHhccCcEEeehhhHHH
Confidence 99999999998889999999999854
No 145
>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=65.84 E-value=14 Score=28.83 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=36.0
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCcee
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~ 115 (147)
.-|+..|..+|.+..+.|+..-|-+. +.+|++|+.|.+.|||.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi~~--------------~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGIKL--------------NEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCce
Confidence 34677777788899999999877544 78999999999999995
No 146
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=65.41 E-value=17 Score=32.08 Aligned_cols=56 Identities=13% Similarity=0.150 Sum_probs=40.0
Q ss_pred HhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHH-HHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVA-RHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 67 l~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsii-R~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
+..++-+..+...||-. + .... ...|+.|++.||++. . +.=+||++|+.+.|.|++
T Consensus 330 ~~~Gl~~~~~~~~~g~~------~-------~~~~~~~~l~~l~~~gll~~-~-~~l~lT~~G~~~~d~i~~ 386 (390)
T PRK06582 330 LSKGINISTLEQKLNTK------L-------ENILDMNNLKHYQALDLIRL-D-ENIYLTDKGLMLHSYIVP 386 (390)
T ss_pred hhCCCCHHHHHHHHCcC------H-------HHhhhHHHHHHHHHCCCEEE-C-CEEEECcchhHHHHHHHH
Confidence 34566667777777631 1 1122 467899999999997 3 457899999999999975
No 147
>TIGR01594 holin_lambda phage holin, lambda family. This model represents one of a large number of mutally dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda.
Probab=65.38 E-value=5.6 Score=29.73 Aligned_cols=35 Identities=29% Similarity=0.462 Sum_probs=22.3
Q ss_pred CCCCCCchhHHhHHHHHH--HHHHhCC-------CchhhHHHHhcCCC
Q 032124 46 LAPYDPDWYYIRAASMAR--KIYLRGG-------LGVGSFRRIYGGGK 84 (147)
Q Consensus 46 laP~~~DW~YiRaASi~R--klYl~g~-------vGV~~lr~~YGg~k 84 (147)
++|.+|||| |.++. +.+.++| ..+..||-.|+|..
T Consensus 1 mm~~~P~~W----~~ll~~l~~~~~~~i~g~~lA~~mA~LR~~Y~g~~ 44 (107)
T TIGR01594 1 MMIKEPDLW----AALLSWLQDAWRSQGQGALLALAIAYLRIRYMGGK 44 (107)
T ss_pred CCCCCccHH----HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHcCcc
Confidence 478899988 34433 3344433 34667889998754
No 148
>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=65.21 E-value=7.4 Score=29.43 Aligned_cols=32 Identities=9% Similarity=0.037 Sum_probs=26.9
Q ss_pred HHHHHHhHhCCceeeCCCCCeeeChhhhhhhhh
Q 032124 102 RHILHQLQDTNIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 102 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDr 134 (147)
=.++..+|-+|+|+.. +|-=.||+.|+++.+.
T Consensus 15 ~p~~eAaelLgf~~~~-~Gdi~LT~~G~~f~~a 46 (120)
T PF09821_consen 15 LPIVEAAELLGFAEVE-EGDIRLTPLGRRFAEA 46 (120)
T ss_pred HHHHHHHHHcCCeeec-CCcEEeccchHHHHHC
Confidence 3578899999999986 4778999999998764
No 149
>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=65.15 E-value=11 Score=27.20 Aligned_cols=35 Identities=9% Similarity=0.171 Sum_probs=26.6
Q ss_pred hHHHHHHHHhHhC---CceeeCC----CCCeeeChhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDS----KGQSLVLVERLHKLD 133 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~----~~GR~lT~~G~~~LD 133 (147)
+-+-..+++||+. .|++... .+|-.||+.|+.++.
T Consensus 31 stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~~ 72 (99)
T TIGR00637 31 KSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLIQ 72 (99)
T ss_pred HHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHHH
Confidence 5566778888875 6688774 258999999999864
No 150
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=63.69 E-value=7.3 Score=33.87 Aligned_cols=36 Identities=3% Similarity=-0.113 Sum_probs=29.8
Q ss_pred HHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 101 ARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 101 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
....|++|++.||++.+. +.=+||++|+-.+|.|++
T Consensus 332 ~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~~i~~ 367 (370)
T PRK06294 332 TSELIMHPIIQELFTKND-QALSLNKKGRLFHDTIAE 367 (370)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHH
Confidence 456788999999998763 456899999999999875
No 151
>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=62.96 E-value=7.6 Score=26.85 Aligned_cols=21 Identities=33% Similarity=0.414 Sum_probs=18.3
Q ss_pred hhHHHHHHHHhHhCCceeeCC
Q 032124 98 GSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 98 gsiiR~~LqqLE~~glV~k~~ 118 (147)
.|||=.+|+.||++|+++.-.
T Consensus 18 RSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 18 RSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHhcCceeecc
Confidence 489999999999999998543
No 152
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=62.36 E-value=6.3 Score=35.14 Aligned_cols=33 Identities=18% Similarity=0.110 Sum_probs=28.1
Q ss_pred HHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 104 ILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 104 ~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
.|++|++.|||+.+. +.=+||++|+-.+|.|+.
T Consensus 404 ~l~~l~~~gll~~~~-~~~~lT~~G~~~~d~i~~ 436 (453)
T PRK09249 404 RLAPLEADGLVELDE-NGITVTPKGRLLVRNIAM 436 (453)
T ss_pred HHHHHHHCCCEEEEC-CEEEECccchHHHHHHHH
Confidence 478999999999764 467899999999999874
No 153
>PF13730 HTH_36: Helix-turn-helix domain
Probab=61.79 E-value=7.2 Score=24.31 Aligned_cols=19 Identities=16% Similarity=0.391 Sum_probs=16.0
Q ss_pred CchhHHHHHHHHhHhCCce
Q 032124 96 SSGSVARHILHQLQDTNII 114 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV 114 (147)
-|.+=|+++++.||+.|||
T Consensus 37 ~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 37 VSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHHHHHHCcCC
Confidence 3457789999999999986
No 154
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=61.65 E-value=23 Score=24.72 Aligned_cols=42 Identities=12% Similarity=0.265 Sum_probs=35.5
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCcee
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~ 115 (147)
.|++.|.-++++....|....|- |.+-+++.++.|++.|+|.
T Consensus 7 ~il~~L~~~~~~~~~~la~~l~~--------------s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 7 KILEELQKDARISLAELAKKVGL--------------SPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCee
Confidence 47888888888889999888754 3478999999999999998
No 155
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=60.68 E-value=9.9 Score=27.71 Aligned_cols=42 Identities=10% Similarity=-0.037 Sum_probs=32.5
Q ss_pred chhHHHHHHHHhHhCCceeeCCC---CCeeeChhhhhhhhhhhcC
Q 032124 97 SGSVARHILHQLQDTNIIELDSK---GQSLVLVERLHKLDCENSN 138 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~~---~GR~lT~~G~~~LDri~~~ 138 (147)
+.+=+=.++=.||..|+|..... .--.+|++|..+|++|-++
T Consensus 40 TKNelL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~~~~~~ 84 (85)
T PF11313_consen 40 TKNELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLAEIKNE 84 (85)
T ss_pred cHHHHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHHHHHhc
Confidence 34556677889999999985542 2478999999999998764
No 156
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=60.59 E-value=20 Score=32.11 Aligned_cols=56 Identities=18% Similarity=0.090 Sum_probs=41.0
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhcC
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENSN 138 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~~ 138 (147)
+++-...+...||.. ........|++|+..|++..+. +.=.||++|+-.+|.|.+.
T Consensus 357 ~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d~i~~~ 412 (433)
T PRK08629 357 GRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGVVMMKE 412 (433)
T ss_pred CCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHH
Confidence 455566676766631 1345678889999999999753 3458999999999988763
No 157
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=59.28 E-value=8.1 Score=30.04 Aligned_cols=94 Identities=19% Similarity=0.224 Sum_probs=59.3
Q ss_pred ChhHHHHHHHHHHHHc-----CCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHh-cCCC
Q 032124 11 SPHEFVKAYAAHLKRS-----GKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY-GGGK 84 (147)
Q Consensus 11 ~~~~fI~~~A~~LK~~-----gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~Y-Gg~k 84 (147)
..+++-+.+|.-|-.+ ...--|.+++++| +|.|.+ |.||+.||-.+..-+...+..+ .+..
T Consensus 31 ~~e~Lremfa~LLass~d~~~~~~~hp~fv~Ii~-----qLsp~E--------A~iL~~l~~~~~~p~~~~~~~~~~~~~ 97 (186)
T PF14337_consen 31 DDEELREMFANLLASSMDKRKNDDVHPSFVEIIK-----QLSPDE--------ARILKYLYDNNQIPIVDVRLRRKNGPG 97 (186)
T ss_pred CcHHHHHHHHHHHHHHhCcCccccccHHHHHHHH-----hCCHHH--------HHHHHHHHhcCCCcceeeeeeecCCcc
Confidence 4556666666666554 2345688888875 788877 8999999966554444333332 1111
Q ss_pred CCCCCCCCCCCC---chhHHHHHHHHhHhCCceeeC
Q 032124 85 RNGSRPPHFSKS---SGSVARHILHQLQDTNIIELD 117 (147)
Q Consensus 85 rrG~~P~h~~~a---sgsiiR~~LqqLE~~glV~k~ 117 (147)
.+-..++.+.-+ +-..+-..|+.|+.+|||+-.
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~l~nL~rLGLi~~~ 133 (186)
T PF14337_consen 98 SRIVLSNISLVGEEASPDNIPSYLDNLERLGLIEIP 133 (186)
T ss_pred ceeecccccccccccchHHHHHHHHHHHHCCCceec
Confidence 111223222222 557889999999999999876
No 158
>PRK05660 HemN family oxidoreductase; Provisional
Probab=58.96 E-value=10 Score=33.10 Aligned_cols=36 Identities=8% Similarity=-0.086 Sum_probs=29.5
Q ss_pred HHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 101 ARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 101 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
....++.|++.||++.+. +.=+||++|+-++|.|++
T Consensus 338 ~~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d~i~~ 373 (378)
T PRK05660 338 IRPQLDEALAQGYLTETA-DHWQITEHGKLFLNDLLE 373 (378)
T ss_pred HHHHHHHHHHCCCEEEeC-CEEEECcchhHHHHHHHH
Confidence 346789999999998753 346789999999999875
No 159
>PF02522 Antibiotic_NAT: Aminoglycoside 3-N-acetyltransferase; InterPro: IPR003679 This family consists of bacterial aminoglycoside 3-N-acetyltransferases (2.3.1.81 from EC) that catalyse the reaction []: Acetyl-Co + a 2-deoxystreptamine antibiotic = CoA + N3'-acetyl-2-deoxystreptamine antibiotic The enzyme can use a range of antibiotics with 2-deoxystreptamine rings as acceptor for its acetyltransferase activity, this inactivates and confers resistance to gentamicin, kanamycin, tobramycin, neomycin and apramycin amongst others. For the kanamycin group antibiotics acetylation occurred at the 3"-amino group in arbekacin and amikacin, and at the 3-amino group in dibekacin as in the case of kanamycin reflecting the effect of the (S)-4-amino-2-hydroxybutyryl side chain which is present in arbekacin and amikacin, but absent in dibekacin and kanamycin [].; GO: 0046353 aminoglycoside 3-N-acetyltransferase activity, 0046677 response to antibiotic; PDB: 3SMA_D 3N0M_B 3IJW_B 3N0S_D 3SLB_C 3SLF_A 3KZL_D 3E4F_B 2NYG_E.
Probab=58.86 E-value=6.6 Score=32.11 Aligned_cols=86 Identities=14% Similarity=0.273 Sum_probs=50.6
Q ss_pred ChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHh----CCC-chhhHHHHhcCCC-
Q 032124 11 SPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLR----GGL-GVGSFRRIYGGGK- 84 (147)
Q Consensus 11 ~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~----g~v-GV~~lr~~YGg~k- 84 (147)
-|+.+|++|-+.+.++|-|-+|....-.-... ||..++||= .|..+.... .|. ++|.|...|--..
T Consensus 15 g~~~vi~aL~~~vg~~GTlvmPt~t~~~~~~~----~~~~~~~~~----~~~~~~~~fD~~~tps~~~G~l~E~fr~~pg 86 (229)
T PF02522_consen 15 GAETVIDALLEVVGPEGTLVMPTFTYSNSDPA----PPVPEEWWE----TIREEMPPFDPARTPSRGMGILPETFRTRPG 86 (229)
T ss_dssp HHHHHHHHHHHHHTTTSEEEEE---CCCS-GG----S---GGGHH----HHHHHS--B-TTT---SSS-HHHHHHCTSTT
T ss_pred cHHHHHHHHHHHhccCCeEEEEccCCccCCcc----cCCchhhhH----HHHhhCCCCCcccCccchhCHHHHHHHhCCC
Confidence 37899999999999999999998766433333 888889994 355555442 467 8999988886543
Q ss_pred -CCCCCCCCCCCCchhHHHHH
Q 032124 85 -RNGSRPPHFSKSSGSVARHI 104 (147)
Q Consensus 85 -rrG~~P~h~~~asgsiiR~~ 104 (147)
.|...|.|..-|-|.-...+
T Consensus 87 v~RS~HP~~Sfaa~G~~A~~l 107 (229)
T PF02522_consen 87 VVRSNHPTHSFAAWGPDAEEL 107 (229)
T ss_dssp EEE-S-TTT-EEEEETTHHHH
T ss_pred eEEecCCceEEEEECCCHHHh
Confidence 23345777777777766555
No 160
>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=58.74 E-value=7.9 Score=34.47 Aligned_cols=33 Identities=12% Similarity=0.153 Sum_probs=27.7
Q ss_pred HHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 104 ILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 104 ~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
+|++|++.|||+.+. +.=+||++|+-.+|.|+.
T Consensus 404 ~l~~l~~~gll~~~~-~~~~lT~~G~~~~~~i~~ 436 (455)
T TIGR00538 404 LLKPLEEDGLLDVDE-KGIEVTPKGRLLIRNIAM 436 (455)
T ss_pred HHHHHHhCCCEEEEC-CEEEECcCChHHHHHHHH
Confidence 477889999999763 567899999999998875
No 161
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=58.70 E-value=27 Score=31.33 Aligned_cols=60 Identities=15% Similarity=0.155 Sum_probs=47.8
Q ss_pred HHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 64 KIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 64 klYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
.|=+.-++-+..+...||- -. -..+...|+.+++.|++..+. +.-+||+.|+-++|.|++
T Consensus 348 gLr~~~gv~~~~~~~~~~~-~~------------~~~~~~~l~~~~~~Gll~~~~-~~~~lt~~g~~~~~~i~~ 407 (416)
T COG0635 348 GLRLNFGVDLAELEERFGI-FK------------FAEILELLAELIADGLLELDG-DRLRLTEKGRLLLRSIAE 407 (416)
T ss_pred HHHHhcCCCHHHHHHHhCc-ch------------hhhHHHHHHHHHhCCCEEecC-CEEEECCcchhHHHHHHH
Confidence 3444557888888888874 21 378899999999999999875 578999999888888875
No 162
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=58.70 E-value=9.2 Score=34.74 Aligned_cols=40 Identities=8% Similarity=0.194 Sum_probs=32.8
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
..+.+..|+....+.. .-+|.+|++|++.|||+-.+..||
T Consensus 22 ~~~~l~~la~~l~cs~--------------R~~~~~l~~~~~~gwl~w~~~~GR 61 (552)
T PRK13626 22 QETTLNELAELLNCSR--------------RHMRTLLNTMQQRGWLTWQAEAGR 61 (552)
T ss_pred ceeeHHHHHHHhcCCh--------------hHHHHHHHHHHHCCCeeeecCCCC
Confidence 3578888888877654 468999999999999999987676
No 163
>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=58.58 E-value=20 Score=25.93 Aligned_cols=50 Identities=10% Similarity=0.160 Sum_probs=40.5
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~ 119 (147)
-|++-|.-.|++.+..+....... ++. +-+-++..|..|++-|+|+....
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~l~~~--~~~--------~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEALPEE--RSW--------AYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHCTT--SS----------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHhCCCCCHHHHHHHHHhc--ccc--------chhHHHHHHHHHHhCCceeEeec
Confidence 478888999999999999988765 232 34889999999999999998754
No 164
>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=57.77 E-value=13 Score=29.91 Aligned_cols=36 Identities=14% Similarity=0.089 Sum_probs=26.9
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+=+.+++||+. .|.+.+ .+|-.||+.|+.+++.+
T Consensus 32 ~avS~~I~~LE~~lg~~LF~R~-~~~~~lT~~G~~l~~~a 70 (300)
T TIGR02424 32 PAVSKTLRELEEILGTPLFERD-RRGIRLTRYGELFLRHA 70 (300)
T ss_pred HHHHHHHHHHHHHhCCeEEEEc-CCCccccHhHHHHHHHH
Confidence 4456678888874 677776 46889999999888753
No 165
>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=57.20 E-value=39 Score=20.91 Aligned_cols=48 Identities=15% Similarity=0.155 Sum_probs=36.4
Q ss_pred hHHHHHHHHHHh-CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCC-ceeeCC
Q 032124 57 RAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTN-IIELDS 118 (147)
Q Consensus 57 RaASi~RklYl~-g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~g-lV~k~~ 118 (147)
|-..|++-|.-. +++....|+..+|- |..-|++-++.|++.+ .|+..+
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~v--------------S~rTi~~~i~~L~~~~~~I~~~~ 50 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGV--------------SRRTIRRDIKELREWGIPIESKR 50 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS---------------HHHHHHHHHHHHHTT-EEEEET
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeEEeeC
Confidence 456788888664 56999999998775 4478999999999999 444443
No 166
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=56.10 E-value=32 Score=25.90 Aligned_cols=60 Identities=8% Similarity=-0.020 Sum_probs=41.4
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe----eeChhhhhhhhh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS----LVLVERLHKLDC 134 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR----~lT~~G~~~LDr 134 (147)
+|++.|.-.++.-|+.|...+|-.+ +-+=+=|+.|+++|||+.... || .|.+.....++.
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsq--------------stvS~HL~~L~~AGLV~~~r~-Gr~~~Y~l~~~~~~~~~~ 83 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQ--------------PKISRHLALLRESGLLLDRKQ-GKWVHYRLSPHIPAWAAK 83 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCceEEEEE-cCEEEEEECchHHHHHHH
Confidence 5677666568899999999887532 345566899999999987754 44 455544443433
No 167
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=55.37 E-value=41 Score=27.67 Aligned_cols=51 Identities=16% Similarity=0.135 Sum_probs=41.0
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCC
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQ 121 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~G 121 (147)
|-..|+..|.-++.+.+..|...+| -|..=||.-|.+||+.|++.....++
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~--------------VS~~TiRRdL~~L~~~~~l~r~~Gga 55 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLN--------------VSKETIRRDLNELQTQGKILRNHGRA 55 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCeE
Confidence 4455777778889999999999996 34578999999999999998764333
No 168
>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=55.13 E-value=10 Score=27.69 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=20.5
Q ss_pred HhHhCCce-eeCCCC---CeeeChhhhhhhhh
Q 032124 107 QLQDTNII-ELDSKG---QSLVLVERLHKLDC 134 (147)
Q Consensus 107 qLE~~glV-~k~~~~---GR~lT~~G~~~LDr 134 (147)
+|..+||| ++...+ --+||++|.+..|.
T Consensus 58 SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 58 SLVGLGLVEEEEEKGGFKYYRLTEKGKRIAEM 89 (90)
T ss_pred hHHHcCCeeEeeecCCeeEEEeChhhhhHHhc
Confidence 58899999 444433 34799999988763
No 169
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=54.96 E-value=15 Score=31.81 Aligned_cols=31 Identities=3% Similarity=0.101 Sum_probs=26.5
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
-|.+-+|.++++||+.|+|+..+..|-.+.+
T Consensus 41 vsr~tv~~a~~~L~~~g~i~~~~~~G~~v~~ 71 (431)
T PRK15481 41 VNRNTVAAAYKRLVTAGLAQSQGRNGTVIRG 71 (431)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeCCCceEEcc
Confidence 4568999999999999999988777887764
No 170
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=54.86 E-value=13 Score=32.53 Aligned_cols=35 Identities=11% Similarity=-0.016 Sum_probs=28.2
Q ss_pred HHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 102 RHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 102 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
...|+.|++.|+|+.+. +.=+||++|+-++|.|++
T Consensus 356 ~~~l~~l~~~gll~~~~-~~~~LT~~G~~~~d~i~~ 390 (394)
T PRK08898 356 EPQLAAAEQRGLLERDH-TRIRPTPLGQRFLNDLQE 390 (394)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhHhHHHHHHHH
Confidence 45778899999998753 334899999999999875
No 171
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=54.51 E-value=17 Score=28.99 Aligned_cols=36 Identities=8% Similarity=0.071 Sum_probs=27.5
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+=+.|++||+. .|+..+ .+|-.||+.|+.+++.+
T Consensus 30 savS~~i~~LE~~lg~~Lf~R~-~~~~~lT~~G~~l~~~~ 68 (296)
T PRK11242 30 PTLSQQIRQLEESLGVQLFDRS-GRTVRLTDAGEVYLRYA 68 (296)
T ss_pred hHHHHHHHHHHHHhCCeeEeEc-CCceeechhHHHHHHHH
Confidence 3455678888864 777776 46899999999988764
No 172
>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=54.42 E-value=16 Score=28.78 Aligned_cols=42 Identities=17% Similarity=0.186 Sum_probs=33.7
Q ss_pred hhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhh
Q 032124 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVER 128 (147)
Q Consensus 73 V~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G 128 (147)
-..|+..||-. ...+|++|+.|+..|+|......|..+++..
T Consensus 28 E~eLa~~~~Vs--------------r~Tvr~Al~~L~~eGli~~~~g~Gt~V~~~~ 69 (231)
T TIGR03337 28 ERDLGERFNTT--------------RVTIREALQQLEAEGLIYREDRRGWFVSPPR 69 (231)
T ss_pred HHHHHHHHCCC--------------HHHHHHHHHHHHHCCeEEEeCCCEEEECCcc
Confidence 45677777753 5899999999999999998877788877543
No 173
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=54.39 E-value=14 Score=29.41 Aligned_cols=65 Identities=12% Similarity=-0.065 Sum_probs=50.8
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-------CCeeeChhhh
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-------GQSLVLVERL 129 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-------~GR~lT~~G~ 129 (147)
|-..|+..|--+|.+.+..|...||- |..-||.=|++||+.|+|.+... +=|.|-..
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~v--------------S~~TiRRDl~~L~~~g~~~r~~~~~~~~~~~~~~~~~~-- 71 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGV--------------SIQTIRLDRMELGIPELRERIKHVAEKNYDKVKSLPEE-- 71 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCc--------------CHHHHHHHHHHHhcchHHHHHHHHHHHhHHhhhcCCcc--
Confidence 77888889999999999999998874 55899999999999999986542 23444433
Q ss_pred hhhhhhhc
Q 032124 130 HKLDCENS 137 (147)
Q Consensus 130 ~~LDri~~ 137 (147)
..+|+|.+
T Consensus 72 ~~vD~i~e 79 (185)
T PRK04424 72 EVVGELID 79 (185)
T ss_pred cceeeEEE
Confidence 66777654
No 174
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=54.26 E-value=14 Score=29.94 Aligned_cols=36 Identities=3% Similarity=-0.096 Sum_probs=27.8
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+-+.+++||+. .|++.+. +|-.||++|+.+++.+
T Consensus 40 pavS~~I~~LE~~lG~~Lf~R~~-r~~~lT~~G~~l~~~a 78 (303)
T PRK10082 40 PAFSRRIRALEQAIGVELFNRQV-TPLQLSEQGKIFHSQI 78 (303)
T ss_pred HHHHHHHHHHHHHcCCEEEEecC-CCCccCHHHHHHHHHH
Confidence 4566778999864 6677763 6889999999988764
No 175
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=51.01 E-value=65 Score=28.52 Aligned_cols=56 Identities=14% Similarity=0.207 Sum_probs=39.1
Q ss_pred HhHHHHHHHHHH--h--CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeC
Q 032124 56 IRAASMARKIYL--R--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVL 125 (147)
Q Consensus 56 iRaASi~RklYl--~--g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT 125 (147)
..+-.|+.+++- + .|+....|++..+ .+-.+++.+|.+|+++|||...++++-.++
T Consensus 292 ~~al~iL~~l~~~~~~g~~~t~~~La~~l~--------------~~~~~v~~iL~~L~~agLI~~~~~g~~~l~ 351 (412)
T PRK04214 292 YDLLRLLGRLDQARKHGKALDVDEIRRLEP--------------MGYDELGELLCELARIGLLRRGERGQWVLA 351 (412)
T ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHhCCCeEecCCCceEec
Confidence 445568888873 2 3666777776533 344799999999999999987765544443
No 176
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=50.43 E-value=30 Score=30.36 Aligned_cols=49 Identities=14% Similarity=0.198 Sum_probs=37.9
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCee
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSL 123 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~ 123 (147)
||..|-..||.-|..++..-|=.+ |.+-.-+|.||++|+++....++|.
T Consensus 28 Il~lL~~k~plNvneiAe~lgLpq--------------st~s~~ik~Le~aGlirT~t~kark 76 (308)
T COG4189 28 ILQLLHRKGPLNVNEIAEALGLPQ--------------STMSANIKVLEKAGLIRTETVKARK 76 (308)
T ss_pred HHHHHHHhCCCCHHHHHHHhCCch--------------hhhhhhHHHHHhcCceeeeeecccc
Confidence 555667779999999999887533 6777789999999999866544443
No 177
>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=50.35 E-value=22 Score=27.74 Aligned_cols=34 Identities=6% Similarity=0.056 Sum_probs=24.1
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDr 134 (147)
-+=+.+++||+. .|++.. .+|=.||+.|+.++..
T Consensus 27 avS~~i~~LE~~lg~~Lf~R~-~~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 27 TVTDQVRKLEERYGVELFHRN-GRRLELTDAGHRLLPI 63 (279)
T ss_pred HHHHHHHHHHHHhCCccEEEc-CCeEEEChhHHHHHHH
Confidence 345667888764 677775 4678888888887754
No 178
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=50.35 E-value=19 Score=29.09 Aligned_cols=37 Identities=5% Similarity=-0.019 Sum_probs=27.9
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
+-+=+.+++||+. .|++... +|=.||++|+.++++..
T Consensus 34 ~avS~~i~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~ 73 (302)
T PRK09791 34 PALTKSIQELEEGLAAQLFFRRS-KGVTLTDAGESFYQHAS 73 (302)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCceECccHHHHHHHHH
Confidence 4456678888864 6777764 68899999999887653
No 179
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=50.26 E-value=13 Score=31.98 Aligned_cols=33 Identities=9% Similarity=0.014 Sum_probs=26.6
Q ss_pred HHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhcC
Q 032124 103 HILHQLQDTNIIELDSKGQSLVLVERLHKLDCENSN 138 (147)
Q Consensus 103 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~~ 138 (147)
..|++|++.||++.+ ++| ||++|.-+.|.|+.+
T Consensus 315 ~~l~~l~~~gl~~~~--~~~-l~~~g~~~~d~i~~~ 347 (350)
T PRK08446 315 KKVKILIEENKLFIK--NNR-LYNKDFFLADEIALF 347 (350)
T ss_pred HHHHHHHHCCCEEee--CCE-EcccchhhHHHHHHH
Confidence 567788999999865 344 999999999998754
No 180
>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=49.78 E-value=24 Score=25.45 Aligned_cols=37 Identities=11% Similarity=0.100 Sum_probs=28.6
Q ss_pred CCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 93 FSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 93 ~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
|..|+.++| .+++.|-+-|||.. ++ |..||+.|...-
T Consensus 29 H~dA~p~~i-~a~~RLheKGLI~~-pd-GgyLT~~G~~~a 65 (77)
T TIGR02647 29 HSTASPAAV-AAAARLHEKGLTTQ-PD-GGYLTSLGLEAA 65 (77)
T ss_pred cccCCHHHH-HHHHHHHHcCCccC-CC-CCEecHHHHHHH
Confidence 356777776 58899999999975 44 459999998654
No 181
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=49.70 E-value=25 Score=27.22 Aligned_cols=37 Identities=8% Similarity=0.045 Sum_probs=27.9
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
+-+=+.+++||+. .|.+.+. .|=.||+.|+.++++..
T Consensus 6 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 45 (269)
T PRK11716 6 STLSRQIQRLEEELGQPLFVRDN-RSVTLTEAGEELRPFAQ 45 (269)
T ss_pred HHHHHHHHHHHHHhCCeeEEecC-CceeECHhHHHHHHHHH
Confidence 3455677888864 7788764 68899999999988753
No 182
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=47.42 E-value=18 Score=32.47 Aligned_cols=36 Identities=17% Similarity=0.065 Sum_probs=29.8
Q ss_pred HHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 101 ARHILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 101 iR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
....|++|++.|||+.+. +.=+||++|+-..|.|+.
T Consensus 398 ~~~~l~~~~~~Gll~~~~-~~l~lT~~G~~~~~~i~~ 433 (449)
T PRK09058 398 LAPLLAQWQQAGLVELSS-DCLRLTLAGRFWAVNLTQ 433 (449)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECCCcccHHHHHHH
Confidence 345788999999999763 567899999999998874
No 183
>PHA02943 hypothetical protein; Provisional
Probab=47.39 E-value=68 Score=26.14 Aligned_cols=55 Identities=24% Similarity=0.186 Sum_probs=43.0
Q ss_pred CchhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC
Q 032124 51 PDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120 (147)
Q Consensus 51 ~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~ 120 (147)
.|=...|.--|++-| -.|...+..+.+.-|- |-+=+|.+|..||+.|.|++.+.|
T Consensus 6 sd~v~~R~~eILE~L-k~G~~TtseIAkaLGl--------------S~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 6 SDTVHTRMIKTLRLL-ADGCKTTSRIANKLGV--------------SHSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred hHHHHHHHHHHHHHH-hcCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHcCceEEEeec
Confidence 355567777888888 6666778888888774 336799999999999999998743
No 184
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=46.36 E-value=47 Score=27.54 Aligned_cols=55 Identities=16% Similarity=0.283 Sum_probs=45.0
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
|=-.|+..|--+|-+-|..|...||- |..-||.=|..||+.|++.+.. ||=.++.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~V--------------S~~TIRRDL~~Le~~g~l~R~h-GGa~~~~ 60 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGV--------------SEMTIRRDLNELEEQGLLLRVH-GGAVLPD 60 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCC--------------CHHHHHHhHHHHHHCCcEEEEe-CCEecCC
Confidence 55678888888899999999999875 4588999999999999999975 5555443
No 185
>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=46.26 E-value=30 Score=28.23 Aligned_cols=37 Identities=14% Similarity=0.075 Sum_probs=27.5
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
+-+=..+++||+. .|++.+. +|=.||+.|+.++....
T Consensus 37 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 76 (302)
T TIGR02036 37 SAISHRINQLEEELGIQLFVRSH-RKVELTHEGKRIYWALK 76 (302)
T ss_pred HHHHHHHHHHHHHhCCceEEECC-CceeECHhHHHHHHHHH
Confidence 3455668888864 6778774 68999999998886643
No 186
>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length. It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=46.08 E-value=15 Score=26.01 Aligned_cols=26 Identities=12% Similarity=0.069 Sum_probs=17.9
Q ss_pred HHHHHhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 103 HILHQLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 103 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
++++.|..+|.|+.+ + .||+-|+...
T Consensus 1 ~A~~~L~~Lgald~~--~--~lT~lG~~~~ 26 (102)
T PF04408_consen 1 KALELLKSLGALDEN--G--NLTPLGRKMS 26 (102)
T ss_dssp -HHHHHHHTTSB-TT--S---B-HHHHHHT
T ss_pred CHHHHHHHCCCCCCC--C--CcCHHHHHHH
Confidence 478999999999543 2 8999998753
No 187
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=44.93 E-value=21 Score=27.57 Aligned_cols=59 Identities=19% Similarity=0.126 Sum_probs=39.8
Q ss_pred hHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 57 RaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
.|-.++..|...||.-...+++.=|..+ ..+|++. --=||.|+.+.|=-.||++|+..|
T Consensus 60 ~Al~~A~~L~~~Gp~~~~~l~~~~~~~~------------A~~IL~~-----N~YGWFeRv~rGvY~LT~~G~~al 118 (118)
T PF09929_consen 60 DALRCAAALAEHGPSRPADLRKATGVPK------------ATSILRD-----NHYGWFERVERGVYALTPAGRAAL 118 (118)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHhcCCCh------------HHHHHHh-----CcccceeeeccceEecCcchhhcC
Confidence 4555666777788888888887533321 1223221 123999999988899999999765
No 188
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=44.49 E-value=27 Score=27.75 Aligned_cols=35 Identities=6% Similarity=0.004 Sum_probs=24.7
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
-+-+.|++||+. .|.+.+ .+|-.||+.|+.++...
T Consensus 37 avS~~i~~LE~~lg~~Lf~R~-~r~~~lT~~G~~l~~~a 74 (294)
T PRK09986 37 PLSIHIKELEDQLGTPLFIRH-SRSVVLTHAGKILMEES 74 (294)
T ss_pred HHHHHHHHHHHHhCCeeEeeC-CCceeECHhHHHHHHHH
Confidence 455677788764 677766 36788888888777643
No 189
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=43.63 E-value=23 Score=33.74 Aligned_cols=39 Identities=15% Similarity=0.196 Sum_probs=30.5
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
.+.+..|+....++ ..-+|.+|+||++.||++-.+.-||
T Consensus 23 ~~tl~eLA~~lfCS--------------~Rh~R~lL~q~q~~gWL~W~p~~GR 61 (564)
T COG4533 23 ETTLNELADILFCS--------------RRHARTLLRQMQEAGWLTWQPQAGR 61 (564)
T ss_pred eeeHHHHHHHhccC--------------HHHHHHHHHHHHHcCCEEeccCCCC
Confidence 35667777766554 4578999999999999999987665
No 190
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=43.59 E-value=33 Score=27.88 Aligned_cols=35 Identities=3% Similarity=-0.106 Sum_probs=24.8
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDr 134 (147)
+-+-+.+++||+. .|++++. .|=.||+.|+.++..
T Consensus 30 ~avS~~I~~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~ 67 (305)
T PRK11233 30 PALSQQVATLEGELNQQLLIRTK-RGVTPTEAGKILYTH 67 (305)
T ss_pred hHHHHHHHHHHHHhCCceEEeCC-CCceECHhHHHHHHH
Confidence 4566677888764 6777764 688889988776654
No 191
>PF14113 DUF4285: Domain of unknown function (DUF4285)
Probab=43.55 E-value=69 Score=23.75 Aligned_cols=45 Identities=22% Similarity=0.368 Sum_probs=33.3
Q ss_pred HHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhC
Q 032124 19 YAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRG 69 (147)
Q Consensus 19 ~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g 69 (147)
++--|-.+| +++|.-. ...+...|.|-.||++||..++--|..++
T Consensus 11 mS~aL~~~G-~~i~~~~-----~~~~~~~~~~g~~y~~ra~~l~~~L~~~~ 55 (115)
T PF14113_consen 11 MSYALNYSG-IPIKSFS-----TLGRTVSGADGKWYIYRAEELANWLKKKP 55 (115)
T ss_pred HHHHHHhCC-CccCccc-----ccceeccCCCCCchhhHHHHHHHHHHHCC
Confidence 444566666 5655544 34677788888999999999999888883
No 192
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=43.23 E-value=30 Score=27.39 Aligned_cols=35 Identities=17% Similarity=0.308 Sum_probs=27.4
Q ss_pred HHHHHHHHhHhCCceeeCC----CCCeeeChhhhhhhhh
Q 032124 100 VARHILHQLQDTNIIELDS----KGQSLVLVERLHKLDC 134 (147)
Q Consensus 100 iiR~~LqqLE~~glV~k~~----~~GR~lT~~G~~~LDr 134 (147)
-+..+|..|++.|+|.... ..=-.||++|+..|+-
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~ 73 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEF 73 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHH
Confidence 4678999999999998642 2356899999988754
No 193
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=43.09 E-value=30 Score=27.92 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=23.7
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDr 134 (147)
+-+-+.+++||+. .|.+.+ ..|=.||+.|+.+++.
T Consensus 30 pavS~~i~~LE~~lg~~LF~R~-~r~~~lT~~G~~l~~~ 67 (305)
T PRK11151 30 PTLSGQIRKLEDELGVMLLERT-SRKVLFTQAGLLLVDQ 67 (305)
T ss_pred hHHHHHHHHHHHHhCchheeeC-CCceeECccHHHHHHH
Confidence 3455667777764 666665 3678888888877664
No 194
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=42.89 E-value=61 Score=27.19 Aligned_cols=57 Identities=12% Similarity=0.205 Sum_probs=44.0
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC-C--Ce-----eeChhhhh
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-G--QS-----LVLVERLH 130 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~-~--GR-----~lT~~G~~ 130 (147)
.|+.-|--+||+.++.+..+-|=.+ .-+|.=|+.||+.|+|+.... + || .||.+|++
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis~--------------~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGISP--------------MAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCCH--------------HHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 4566566689999999999887532 578999999999999985532 2 55 68888876
No 195
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=42.84 E-value=16 Score=27.86 Aligned_cols=24 Identities=38% Similarity=0.523 Sum_probs=20.2
Q ss_pred CCchhHHHHHHHHhHhCCceeeCC
Q 032124 95 KSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 95 ~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
+=.||+.|.+|+.|+.-|+|....
T Consensus 71 kIngsLAr~alr~L~~kG~Ik~Vs 94 (110)
T KOG1767|consen 71 KINGSLARAALRELSNKGVIKQVS 94 (110)
T ss_pred hhchHHHHHHHHHHHhcchHHHHh
Confidence 345799999999999999997553
No 196
>smart00847 HA2 Helicase associated domain (HA2) Add an annotation. This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.
Probab=41.46 E-value=20 Score=24.32 Aligned_cols=25 Identities=12% Similarity=-0.011 Sum_probs=19.9
Q ss_pred HHHHhHhCCceeeCCCCCeeeChhhhhhh
Q 032124 104 ILHQLQDTNIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 104 ~LqqLE~~glV~k~~~~GR~lT~~G~~~L 132 (147)
+++.|..+|.++.+ | .||+-|+..-
T Consensus 2 A~~~L~~LgAld~~---~-~lT~lG~~m~ 26 (92)
T smart00847 2 ALELLYELGALDDD---G-RLTPLGRKMA 26 (92)
T ss_pred HHHHHHHCCCcCCC---C-CcCHHHHHHH
Confidence 67889999999653 3 8999999753
No 197
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=41.38 E-value=31 Score=28.76 Aligned_cols=35 Identities=11% Similarity=0.032 Sum_probs=24.8
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCe-eeChhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQS-LVLVERLHKLDCE 135 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~LDri 135 (147)
-+=+.+++||+. .|.+... +|- .||+.|+.+++..
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~~~~LT~~G~~l~~~a 70 (324)
T PRK12681 32 GISKQVRMLEDELGIQIFARSG-KHLTQVTPAGEEIIRIA 70 (324)
T ss_pred HHHHHHHHHHHHhCCEeEEECC-CCCCccCHHHHHHHHHH
Confidence 345667888864 7777764 343 6999999988754
No 198
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=40.96 E-value=93 Score=19.69 Aligned_cols=52 Identities=23% Similarity=0.326 Sum_probs=35.6
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeee
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLV 124 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~l 124 (147)
..|++.+.-..+..+..+.... .-+.+.+..-|..|+++|+|+...+++.++
T Consensus 28 ~~il~~l~~~~~~~~~~l~~~~--------------~~~~~~v~~hL~~L~~~glv~~~~~~~~~~ 79 (110)
T COG0640 28 LEILSLLAEGGELTVGELAEAL--------------GLSQSTVSHHLKVLREAGLVELRREGRLRL 79 (110)
T ss_pred HHHHHHHHhcCCccHHHHHHHH--------------CCChhHHHHHHHHHHHCCCeEEEecccEEE
Confidence 3445544444567788888877 344467778888899999999866555443
No 199
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=40.95 E-value=38 Score=27.18 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=26.2
Q ss_pred HHHHHHHHhHh---CCceeeCCCCCeeeChhhhhhhhhhh
Q 032124 100 VARHILHQLQD---TNIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 100 iiR~~LqqLE~---~glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
-|=+.|++||+ ..|.+.+. +|=.||++|+.+++...
T Consensus 31 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~ 69 (275)
T PRK03601 31 AVSFRIRQLENQLGVNLFTRHR-NNIRLTAAGERLLPYAE 69 (275)
T ss_pred HHHHHHHHHHHHhCCceEEECC-CceEECHhHHHHHHHHH
Confidence 34456788887 36778774 68889999998877653
No 200
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=40.82 E-value=34 Score=27.51 Aligned_cols=35 Identities=14% Similarity=0.013 Sum_probs=24.6
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
-+=+.+++||+. .|.+++ ..|-.||+.|+.++...
T Consensus 32 avS~~I~~LE~~lG~~LF~R~-~r~~~lT~~G~~l~~~a 69 (301)
T PRK14997 32 KLSRRIAQLEERLGVRLIQRT-TRQFNVTEVGQTFYEHC 69 (301)
T ss_pred HHHHHHHHHHHHhCCEeeeec-cCcceEcHhHHHHHHHH
Confidence 344567888864 566666 36889999998777654
No 201
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=40.24 E-value=38 Score=27.81 Aligned_cols=36 Identities=8% Similarity=0.047 Sum_probs=25.9
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+=..+|+||+. .|++.+. +|-.||+.|+.++++.
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 69 (308)
T PRK10094 31 ATISYRIKLLEENTGVALFFRTT-RSVTLTAAGEHLLSQA 69 (308)
T ss_pred HHHHHHHHHHHHHhCCEEEeeCC-CceeECHhHHHHHHHH
Confidence 3445678888864 6777763 6889999999887653
No 202
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=40.19 E-value=7.6 Score=31.00 Aligned_cols=13 Identities=23% Similarity=0.825 Sum_probs=10.3
Q ss_pred CCCCCCchhHHhH
Q 032124 46 LAPYDPDWYYIRA 58 (147)
Q Consensus 46 laP~~~DW~YiRa 58 (147)
..|.++||||+.-
T Consensus 28 ~t~~~~DfFY~C~ 40 (182)
T PF08432_consen 28 ITPDNKDFFYVCP 40 (182)
T ss_pred ecCCCCCeEEeCc
Confidence 3588999999863
No 203
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=39.57 E-value=29 Score=31.14 Aligned_cols=38 Identities=16% Similarity=0.219 Sum_probs=30.4
Q ss_pred CCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhh
Q 032124 95 KSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLD 133 (147)
Q Consensus 95 ~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LD 133 (147)
..+=-+.=.++..||..|+|+.++ +|=.||.+|..+..
T Consensus 45 ~~plp~v~~i~~~l~~egiv~~~~-g~v~~TekG~E~~e 82 (354)
T COG1568 45 DLPLPLVASILEILEDEGIVKIEE-GGVELTEKGEELAE 82 (354)
T ss_pred cCCchHHHHHHHHHHhcCcEEEec-CcEeehhhhHHHHH
Confidence 344456678899999999999885 67999999987653
No 204
>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=39.40 E-value=28 Score=27.79 Aligned_cols=35 Identities=6% Similarity=0.101 Sum_probs=22.1
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
-+=+.+|+||+. .|.+.+ .+|-.||+.|+.++++.
T Consensus 31 avS~~Ik~LE~~lg~~LF~R~-~r~~~lT~~G~~l~~~a 68 (291)
T TIGR03418 31 AVSQQVKRLEEELGTPLFERG-HRGIELTEDGQRLFEAV 68 (291)
T ss_pred HHHHHHHHHHHHhCcHHhhcC-CCceeEcHhHHHHHHHH
Confidence 344566777753 555555 35777888887776643
No 205
>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=39.25 E-value=38 Score=25.70 Aligned_cols=48 Identities=21% Similarity=0.301 Sum_probs=35.0
Q ss_pred HHHhC--CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeCh
Q 032124 65 IYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLV 126 (147)
Q Consensus 65 lYl~g--~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~ 126 (147)
||+.+ |.-.+.|+..+.- +-..+|.+|+-|++.|+|+..+++--.++.
T Consensus 46 L~~~~~ipy~~e~LA~~~~~--------------~~~~V~~AL~~f~k~glIe~~ed~~i~i~~ 95 (121)
T PF09681_consen 46 LYLSGNIPYTAEMLALEFDR--------------PVDTVRLALAVFQKLGLIEIDEDGVIYIPN 95 (121)
T ss_pred EEECCCCCCcHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCeEEeec
Confidence 44433 6677777777653 237999999999999999998766455543
No 206
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=38.86 E-value=40 Score=26.67 Aligned_cols=35 Identities=9% Similarity=0.004 Sum_probs=25.9
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
-+-+.+++||+. .|.+... +|=.||+.|+.+++.+
T Consensus 33 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 70 (290)
T PRK10837 33 AVSAALTDLEGQLGVQLFDRVG-KRLVVNEHGRLLYPRA 70 (290)
T ss_pred HHHHHHHHHHHHhCCccEeecC-CeEEECHhHHHHHHHH
Confidence 455677888864 7777764 5788999998887754
No 207
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=38.78 E-value=36 Score=27.65 Aligned_cols=36 Identities=6% Similarity=0.049 Sum_probs=26.7
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+-+.|++||+. .|++.+. .|=.||+.|+.++++.
T Consensus 34 pavS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 72 (305)
T CHL00180 34 PAVSLQIKNLEKQLNIPLFDRSK-NKASLTEAGELLLRYG 72 (305)
T ss_pred hHHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHHH
Confidence 3456678888864 6777763 6889999999986654
No 208
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=38.59 E-value=31 Score=27.57 Aligned_cols=34 Identities=12% Similarity=0.096 Sum_probs=24.9
Q ss_pred HHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 101 ARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 101 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+=+.+++||+. .|.+.. .+|=.||+.|+.+++..
T Consensus 32 vSr~i~~LE~~lg~~Lf~R~-~~~~~lT~~G~~l~~~a 68 (296)
T PRK09906 32 LSQQIKDLENCVGVPLLVRD-KRKVALTAAGEVFLQDA 68 (296)
T ss_pred HHHHHHHHHHHhCCeeeeeC-CCcceEcHhHHHHHHHH
Confidence 44567788764 677776 46889999999887654
No 209
>PF15129 FAM150: FAM150 family
Probab=38.38 E-value=20 Score=27.77 Aligned_cols=17 Identities=24% Similarity=0.432 Sum_probs=14.2
Q ss_pred hhHHhHHHHHHHHHHhC
Q 032124 53 WYYIRAASMARKIYLRG 69 (147)
Q Consensus 53 W~YiRaASi~RklYl~g 69 (147)
=||.|||++|-+|.+.+
T Consensus 103 ayykrcarlltrla~sp 119 (123)
T PF15129_consen 103 AYYKRCARLLTRLAVSP 119 (123)
T ss_pred HHHHHHHHHHHHhccCc
Confidence 58999999999887653
No 210
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=38.33 E-value=25 Score=29.96 Aligned_cols=34 Identities=24% Similarity=0.213 Sum_probs=27.2
Q ss_pred HHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhh
Q 032124 100 VARHILHQLQDTNIIELDSKGQSLVLVERLHKLD 133 (147)
Q Consensus 100 iiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LD 133 (147)
.+..+--=|.+.|+++.+.++++.+|+-|+..+|
T Consensus 44 MV~siryWl~a~gli~~~~~~~~~~T~lG~~i~~ 77 (286)
T PF13182_consen 44 MVKSIRYWLRAFGLIEEDNKGKRKLTPLGELIFD 77 (286)
T ss_pred HHHHHHHHHHHcCCcccCCCCCcccCHHHHHHHh
Confidence 3444445578899999887777799999999996
No 211
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=38.30 E-value=28 Score=28.57 Aligned_cols=46 Identities=26% Similarity=0.268 Sum_probs=36.2
Q ss_pred HHHHHHH-hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCC
Q 032124 61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120 (147)
Q Consensus 61 i~RklYl-~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~ 120 (147)
|.=-||+ +.|+.++.++.+-|-++ +-+=.+++.||..++|++....
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sk--------------s~vS~~lkkL~~~~lV~~~~~~ 77 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSK--------------SNVSMGLKKLQDWNLVKKVFEK 77 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCc--------------chHHHHHHHHHhcchHHhhhcc
Confidence 4445788 78999999999988764 3355689999999999977643
No 212
>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=38.25 E-value=34 Score=27.36 Aligned_cols=36 Identities=8% Similarity=0.051 Sum_probs=27.5
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
+-+=+.+++||+. .|++.. +|=.||+.|+.+++...
T Consensus 30 pavS~~I~~LE~~lg~~Lf~R~--r~~~lT~~G~~l~~~~~ 68 (292)
T TIGR03298 30 SAVSQRIKALEERLGQPLLVRT--QPCRATEAGQRLLRHAR 68 (292)
T ss_pred HHHHHHHHHHHHHhCchheecC--CCCcCCHhHHHHHHHHH
Confidence 3456678888864 778875 48999999999887654
No 213
>PRK10632 transcriptional regulator; Provisional
Probab=37.34 E-value=38 Score=27.70 Aligned_cols=36 Identities=8% Similarity=0.015 Sum_probs=26.3
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+=..+++||+. .|.+.+. +|-.||+.|+.++...
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~i~lT~~G~~l~~~a 69 (309)
T PRK10632 31 SSISQTVSKLEDELQVKLLNRST-RSIGLTEAGRIYYQGC 69 (309)
T ss_pred HHHHHHHHHHHHHhCCeeecccC-CCceechhHHHHHHHH
Confidence 4455678888864 6777763 6889999999887654
No 214
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=37.27 E-value=30 Score=28.40 Aligned_cols=36 Identities=14% Similarity=0.059 Sum_probs=24.6
Q ss_pred HHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhh
Q 032124 101 ARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 101 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
+=..|++||+. .|.+.+..+...||+.|+.+++...
T Consensus 33 vS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~ 71 (313)
T PRK12684 33 VSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVE 71 (313)
T ss_pred HHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHHH
Confidence 44567888864 6777764322469999999887654
No 215
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=37.19 E-value=43 Score=27.73 Aligned_cols=35 Identities=11% Similarity=0.032 Sum_probs=22.1
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
-+-+.+++||+. .|++... .|=.||+.|+.++++.
T Consensus 32 aVS~~Ik~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~a 69 (317)
T PRK15421 32 ALSHQFSDLEQRLGFRLFVRKS-QPLRFTPQGEILLQLA 69 (317)
T ss_pred HHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHHH
Confidence 345566777654 5566653 5677788887777543
No 216
>PRK06474 hypothetical protein; Provisional
Probab=36.83 E-value=1.1e+02 Score=24.26 Aligned_cols=46 Identities=11% Similarity=0.139 Sum_probs=34.5
Q ss_pred HHHHHHHHhCC-CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 60 SMARKIYLRGG-LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 60 Si~RklYl~g~-vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
.|++-|.-.++ ..+..+....+ .-|.+-+=.-|+.|+++|+|+..+
T Consensus 15 ~Il~~L~~~~~~~ta~el~~~l~-------------~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 15 KICQVLMRNKEGLTPLELVKILK-------------DVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 46677766554 88888887653 245567778899999999999765
No 217
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=36.81 E-value=40 Score=27.45 Aligned_cols=36 Identities=14% Similarity=0.163 Sum_probs=27.7
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+-+.+++||+. .|++.+. +|=.||+.|+.+++..
T Consensus 33 savS~~Ik~LE~~lg~~Lf~R~~-~~v~LT~~G~~l~~~a 71 (309)
T PRK11013 33 PTVSRELARFEKVIGLKLFERVR-GRLHPTVQGLRLFEEV 71 (309)
T ss_pred HHHHHHHHHHHHHhCceeeeecC-CCcccCHHHHHHHHHH
Confidence 5577788889875 6777764 5788999999888754
No 218
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=35.86 E-value=50 Score=26.76 Aligned_cols=34 Identities=3% Similarity=-0.103 Sum_probs=22.8
Q ss_pred HHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 101 ARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 101 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+=..+++||+. .|.+.. .+|-.||++|+.++...
T Consensus 35 vS~~I~~LE~~lg~~Lf~R~-~r~~~lT~~G~~l~~~a 71 (296)
T PRK11062 35 ITGQIKALEERLQGKLFKRK-GRGLEPTELGELVFRYA 71 (296)
T ss_pred HHHHHHHHHHHcCccceeec-CCceeECHhHHHHHHHH
Confidence 34456777764 666766 36788888888776543
No 219
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=35.75 E-value=44 Score=27.17 Aligned_cols=37 Identities=11% Similarity=0.025 Sum_probs=25.6
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCe-eeChhhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQS-LVLVERLHKLDCEN 136 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~LDri~ 136 (147)
+-+=+.+++||+. .|++... .|- .||+.|+.+++...
T Consensus 31 ~avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~~~ 71 (309)
T PRK12682 31 PGVSKAIIELEEELGIEIFIRHG-KRLKGLTEPGKAVLDVIE 71 (309)
T ss_pred HHHHHHHHHHHHHhCCeeEEECC-CCcCccCHhHHHHHHHHH
Confidence 3455667888864 6777663 354 69999999887653
No 220
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=35.56 E-value=53 Score=26.40 Aligned_cols=36 Identities=14% Similarity=0.107 Sum_probs=27.0
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+=+.+++||+. .|++... .|=.||+.|+.++..+
T Consensus 35 ~avS~~i~~LE~~lg~~Lf~R~~-r~l~lT~~G~~l~~~~ 73 (297)
T PRK11139 35 AAVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLDI 73 (297)
T ss_pred HHHHHHHHHHHHHhCchheEecC-CceeECHhHHHHHHHH
Confidence 4456678888875 6777764 6889999999887664
No 221
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=35.09 E-value=34 Score=27.98 Aligned_cols=34 Identities=12% Similarity=0.086 Sum_probs=23.3
Q ss_pred HHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 101 ARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 101 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+=+.+++||+. .|.+.+. +|=.||+.|+.+++..
T Consensus 45 vS~~I~~LE~~lG~~LF~R~~-r~~~LT~~G~~l~~~a 81 (311)
T PRK10086 45 VSHRINQLEEELGIKLFVRSH-RKVELTEEGKRVFWAL 81 (311)
T ss_pred HHHHHHHHHHHhCCeeEEEcC-CCcccCHhHHHHHHHH
Confidence 44556777763 5667663 5788888888877653
No 222
>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=34.84 E-value=53 Score=27.26 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=41.9
Q ss_pred hCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChhhhhhhhh
Q 032124 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 68 ~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDr 134 (147)
.||..+..|+..-| ....-++..|..|..+|+++++ ++.-.+|+.+...|+.
T Consensus 21 ~gp~t~~eLA~~~~--------------~~~~~~~~lL~~L~~lgll~~~-~~~y~~t~~~~~~l~~ 72 (306)
T TIGR02716 21 EGPKDLATLAADTG--------------SVPPRLEMLLETLRQMRVINLE-DGKWSLTEFADYMFSP 72 (306)
T ss_pred cCCCCHHHHHHHcC--------------CChHHHHHHHHHHHhCCCeEec-CCcEecchhHHhhccC
Confidence 47888888887543 2235799999999999999987 4789999999888865
No 223
>TIGR00988 hip integration host factor, beta subunit. This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU.
Probab=34.69 E-value=30 Score=24.16 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=24.0
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceeeec
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDIVK 39 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~vK 39 (147)
+.|.+.+++.|++.++|++|.+-.|.-
T Consensus 27 ~~~~~~i~~~L~~g~~V~l~gfG~F~~ 53 (94)
T TIGR00988 27 KTMLEHMASALAQGDRIEIRGFGSFSL 53 (94)
T ss_pred HHHHHHHHHHHHcCCeEEEcCcEEEEE
Confidence 678899999999999999999988843
No 224
>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=34.44 E-value=60 Score=23.02 Aligned_cols=37 Identities=14% Similarity=0.064 Sum_probs=26.4
Q ss_pred CchhHHHHHHHHhHhCCceeeCCC--CCeeeChhhhhhh
Q 032124 96 SSGSVARHILHQLQDTNIIELDSK--GQSLVLVERLHKL 132 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~--~GR~lT~~G~~~L 132 (147)
=+.+-+.++|++|-+.|+|..... .|-+||-.|-..|
T Consensus 36 l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~L 74 (82)
T PF09202_consen 36 LSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYL 74 (82)
T ss_dssp --HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHH
T ss_pred cCHHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHH
Confidence 345677889999999999997542 5999999986544
No 225
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=34.21 E-value=27 Score=33.40 Aligned_cols=90 Identities=16% Similarity=0.147 Sum_probs=55.9
Q ss_pred CCCCCCCchhHHhHHHHH-HHHHHhCCCchhhHHHHhcCCCCCCC-CC--------CCCCCCchhHHHHHHHHhHhCCce
Q 032124 45 ELAPYDPDWYYIRAASMA-RKIYLRGGLGVGSFRRIYGGGKRNGS-RP--------PHFSKSSGSVARHILHQLQDTNII 114 (147)
Q Consensus 45 ElaP~~~DW~YiRaASi~-RklYl~g~vGV~~lr~~YGg~krrG~-~P--------~h~~~asgsiiR~~LqqLE~~glV 114 (147)
.-.|.+.-+||.+.|.=+ |+-|+..- =+.-|.++ -++|. .. +|. -.-..=++.+|..||+-|+|
T Consensus 407 ~g~pT~sG~~ya~LA~~i~R~P~lTr~-E~~vl~ki----P~~~~i~~~~~~e~~~d~~-~~ee~~i~~AL~kLEArGfI 480 (591)
T PF04458_consen 407 TGEPTESGRFYAELARHIKRLPHLTRY-EMEVLHKI----PDKGYIHREELVEFIKDHV-GKEEEEIIEALEKLEARGFI 480 (591)
T ss_pred CCCCCcchHHHHHHHhhhhhcccccHH-HHHHHHhC----CccccccHHHHHHHhhccc-ccchHHHHHHHHHHHhcchH
Confidence 336888889998887764 55555320 01111111 01110 00 111 11123356799999999999
Q ss_pred eeCCCCCeeeChhhhhhhhhhhcCCcc
Q 032124 115 ELDSKGQSLVLVERLHKLDCENSNGMD 141 (147)
Q Consensus 115 ~k~~~~GR~lT~~G~~~LDri~~~~~~ 141 (147)
+--++|+=++|+.|+ +||+-.++.+.
T Consensus 481 ~~Lp~g~iilTeaG~-~ik~Alsg~p~ 506 (591)
T PF04458_consen 481 EILPNGMIILTEAGE-LIKRALSGVPE 506 (591)
T ss_pred HHcCCCcEEEehhhH-HHHHHHhcCCc
Confidence 999999999999997 67888877665
No 226
>PHA00738 putative HTH transcription regulator
Probab=34.08 E-value=1e+02 Score=23.43 Aligned_cols=48 Identities=15% Similarity=-0.020 Sum_probs=33.4
Q ss_pred HHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCee
Q 032124 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSL 123 (147)
Q Consensus 61 i~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~ 123 (147)
|+..|.-.+++-|..|...++-.+ +-|=+=|+.|+++|||+... .||.
T Consensus 17 IL~lL~~~e~~~V~eLae~l~lSQ--------------ptVS~HLKvLreAGLV~srK-~Gr~ 64 (108)
T PHA00738 17 ILELIAENYILSASLISHTLLLSY--------------TTVLRHLKILNEQGYIELYK-EGRT 64 (108)
T ss_pred HHHHHHHcCCccHHHHHHhhCCCH--------------HHHHHHHHHHHHCCceEEEE-ECCE
Confidence 555554445788999988776432 34455689999999998775 4554
No 227
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=33.70 E-value=56 Score=26.66 Aligned_cols=35 Identities=11% Similarity=0.117 Sum_probs=26.4
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDr 134 (147)
+-+-+.+++||+. .|.+.+. +|=.||+.|+.++..
T Consensus 36 pavS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~ 73 (312)
T PRK10341 36 PAVSKIINDIEDYFGVELIVRKN-TGVTLTPAGQVLLSR 73 (312)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCceEChhHHHHHHH
Confidence 3456678888875 5677764 688999999998874
No 228
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=33.50 E-value=22 Score=30.89 Aligned_cols=40 Identities=18% Similarity=0.341 Sum_probs=32.4
Q ss_pred CCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceee
Q 032124 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (147)
Q Consensus 70 ~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k 116 (147)
|+-|+.|+..-|+... ++.+|.. -+++||..|++.|+|+.
T Consensus 231 P~kvetl~~lcGS~~~---~l~~FR~----~Lk~AL~eL~~~g~v~~ 270 (282)
T PF07042_consen 231 PIKVETLRELCGSESS---RLRKFRQ----QLKKALDELVAVGFVSS 270 (282)
T ss_pred CccHHHHHHHcCCCcc---CHHHHHH----HHHHHHHHHHhcCceeE
Confidence 8999999998887542 4666654 49999999999999974
No 229
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=33.12 E-value=37 Score=22.79 Aligned_cols=22 Identities=14% Similarity=0.265 Sum_probs=17.9
Q ss_pred chhHHHHHHHHhHhCCceeeCC
Q 032124 97 SGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~ 118 (147)
+-.-++.+|+.||.+|+|+...
T Consensus 45 ~~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 45 TQRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred cHHHHHHHHHHHHHcCCeEEEE
Confidence 3367889999999999998544
No 230
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=32.97 E-value=60 Score=23.05 Aligned_cols=30 Identities=20% Similarity=0.194 Sum_probs=23.4
Q ss_pred chhHHHHHHHHhHhCCc-eeeCCCCCeeeCh
Q 032124 97 SGSVARHILHQLQDTNI-IELDSKGQSLVLV 126 (147)
Q Consensus 97 sgsiiR~~LqqLE~~gl-V~k~~~~GR~lT~ 126 (147)
|..-|=+.+|+|++.|+ |+.....|+.|.+
T Consensus 32 SRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~ 62 (79)
T COG1654 32 SRTAVWKHIQQLREEGVDIESVRGKGYLLPQ 62 (79)
T ss_pred cHHHHHHHHHHHHHhCCceEecCCCceeccC
Confidence 44667789999999998 5666666988864
No 231
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=32.49 E-value=46 Score=27.84 Aligned_cols=36 Identities=14% Similarity=0.074 Sum_probs=25.7
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCe-eeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQS-LVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~LDri 135 (147)
+-+=..+++||+. .|.+++. +|- .||+.|+.+++..
T Consensus 31 pavS~~I~~LE~~lG~~LF~R~~-r~v~~LT~~G~~l~~~a 70 (327)
T PRK12680 31 PGLSKQLKQLEDELGFLLFVRKG-RSLESVTPAGVEVIERA 70 (327)
T ss_pred hHHHHHHHHHHHHhCCeEEEECC-CcCCccCccHHHHHHHH
Confidence 3455677888864 6777774 344 3999999998874
No 232
>PF15522 Toxin_42: Putative toxin 42
Probab=32.46 E-value=40 Score=27.82 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceeeeccC
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDIVKTG 41 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~vKTg 41 (147)
+.||+.+-+-|..---=++|.|..|+||-
T Consensus 38 ~AF~rr~Rem~dA~~~~~v~~W~~Y~~T~ 66 (205)
T PF15522_consen 38 DAFIRRMREMLDAVAGGSVDTWENYTTTT 66 (205)
T ss_pred HHHHHHHHHHHHhccCCCCCchHhccccC
Confidence 47888888887765445789999999995
No 233
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=32.26 E-value=58 Score=26.60 Aligned_cols=31 Identities=3% Similarity=-0.069 Sum_probs=15.3
Q ss_pred HHHHHHHhHhC---CceeeCCCCCeeeChhhhhhh
Q 032124 101 ARHILHQLQDT---NIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 101 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~L 132 (147)
+-+.|++||+. .|++++. .|=.||+.|+.++
T Consensus 53 vS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~ 86 (314)
T PRK09508 53 VSNAVARLKVMFNDELFVRYG-RGIQPTARARQLF 86 (314)
T ss_pred HHHHHHHHHHhhCCCcEEEcC-CCCcCcHHHHHHH
Confidence 44445555543 4455442 3555555555543
No 234
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline []. Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein [] involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Y30_B 3ZQL_C 2Y31_B 2Y2Z_A 2VPR_A 3B6A_A 3B6C_A 2OPT_A 2NS7_B 2NS8_C ....
Probab=32.23 E-value=1.2e+02 Score=21.40 Aligned_cols=58 Identities=17% Similarity=0.138 Sum_probs=36.4
Q ss_pred CCCCCch--hHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCcee
Q 032124 47 APYDPDW--YYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (147)
Q Consensus 47 aP~~~DW--~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~ 115 (147)
|..+.|| +....|.-+|.+|++-|-.+.-+... | .....+-.++=.+|+.|.++|+=.
T Consensus 2 P~~~~~W~~~l~~~a~~~r~~~~~hP~~~~~~~~~----------~-~~~p~~l~~~e~~l~~L~~aG~~~ 61 (139)
T PF02909_consen 2 PDPGDDWRERLRALARAYRAALLRHPWLAELLLAR----------P-PPGPNALRLMEAMLRALRDAGFSP 61 (139)
T ss_dssp -CTTSEHHHHHHHHHHHHHHHHHTSTTHHHHHHTS----------S-CTSHHHHHHHHHHHHHHHHTTEEH
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHCcCHHHHHHhc----------C-CCChhHHHHHHHHHHHHHHcCcCH
Confidence 3444466 56677788999999988666554431 1 111223345558999999999754
No 235
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=31.81 E-value=1e+02 Score=22.37 Aligned_cols=53 Identities=11% Similarity=0.135 Sum_probs=33.1
Q ss_pred HHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHh
Q 032124 55 YIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQD 110 (147)
Q Consensus 55 YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~ 110 (147)
++-...+.++++-....++..|.+.||.....- .|.+..--...-.+++.|.+
T Consensus 113 ~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~---~H~A~~Da~~t~~l~~~~~~ 165 (169)
T smart00479 113 VIDTLKLARALNPGRKYSLKKLAERLGLEVIGR---AHRALDDARATAKLFKKLVE 165 (169)
T ss_pred eeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCC---CcCcHHHHHHHHHHHHHHHH
Confidence 455566777776444789999999999875422 35544444444555555543
No 236
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=31.53 E-value=2e+02 Score=20.70 Aligned_cols=53 Identities=17% Similarity=0.089 Sum_probs=38.2
Q ss_pred CCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 69 g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
.++.+++|+..-...- | +-..-|-.+++.+|.+|-+.+-|=.+..|=..+||+
T Consensus 28 ~~at~E~l~~~L~~~y-----p-~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivtP~ 80 (80)
T PF10264_consen 28 QPATQETLREHLRKHY-----P-GIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVTPQ 80 (80)
T ss_pred CcchHHHHHHHHHHhC-----C-CCCCCCHHHHHHHHHHHHHcCceeeCCCceEeeCCC
Confidence 4677777666544322 2 234567799999999999999998876666777875
No 237
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=30.80 E-value=58 Score=26.74 Aligned_cols=36 Identities=14% Similarity=0.057 Sum_probs=24.4
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCC-eeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQ-SLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~G-R~lT~~G~~~LDri 135 (147)
+-+=+.+++||+. .|++.+. +| ..||+.|+.+++..
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~~~~lT~~G~~l~~~a 70 (309)
T PRK12683 31 SGVSKQIKDLEDELGVEIFIRRG-KRLTGLTEPGKELLQIV 70 (309)
T ss_pred HHHHHHHHHHHHHhCCeeEeeCC-CCcCCcCHHHHHHHHHH
Confidence 3455677888864 5666653 34 36899999888764
No 238
>PF14178 YppF: YppF-like protein
Probab=30.74 E-value=46 Score=22.96 Aligned_cols=32 Identities=28% Similarity=0.638 Sum_probs=21.2
Q ss_pred CCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHH
Q 032124 44 KELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRI 79 (147)
Q Consensus 44 kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~ 79 (147)
|+..|.+-+=. --.+|++||.|-+-+...|..
T Consensus 14 k~y~p~~~NeL----LDFar~~Yi~gei~i~eYR~l 45 (60)
T PF14178_consen 14 KKYEPEDMNEL----LDFARKLYIQGEISINEYRNL 45 (60)
T ss_pred hccCcccHHHH----HHHHHHHHHhCcccHHHHHHH
Confidence 45556555322 235799999999988766553
No 239
>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=30.50 E-value=71 Score=22.60 Aligned_cols=45 Identities=18% Similarity=0.274 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceee
Q 032124 58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (147)
Q Consensus 58 aASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k 116 (147)
++-|++-|.-+|.+-=+.|+..-|- .-+.+|++|+.|.+.|+|..
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l--------------~~~~vRkiL~~L~~~~lv~~ 59 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGL--------------KPKEVRKILYKLYEDGLVSY 59 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S---------------HHHHHHHHHHHHHHSS-EE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeEE
Confidence 4557777776777776777765432 33899999999999999953
No 240
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=30.45 E-value=38 Score=23.70 Aligned_cols=29 Identities=17% Similarity=0.300 Sum_probs=25.2
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceeeeccC
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDIVKTG 41 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~vKTg 41 (147)
+.|.+.+++.|++.++|++|.|-.|..+-
T Consensus 27 ~~~~~~i~~~L~~g~~V~l~gfG~F~~~~ 55 (94)
T PRK00199 27 KEILEEMSDALARGDRIEIRGFGSFSLHY 55 (94)
T ss_pred HHHHHHHHHHHHcCCeEEEcCCEEEEEEE
Confidence 67889999999999999999998886543
No 241
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=30.45 E-value=57 Score=26.83 Aligned_cols=34 Identities=12% Similarity=-0.024 Sum_probs=22.3
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCe-eeChhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQS-LVLVERLHKLDC 134 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR-~lT~~G~~~LDr 134 (147)
-+=+.+++||+. .|.+... +|. .||+.|+.+++.
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~ 69 (316)
T PRK12679 32 GVSRHIRELEDELGIEIFIRRG-KRLLGMTEPGKALLVI 69 (316)
T ss_pred HHHHHHHHHHHHhCCEEEEECC-CcccccCHhHHHHHHH
Confidence 345567888764 5666653 232 699999988654
No 242
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=30.30 E-value=1.5e+02 Score=23.94 Aligned_cols=85 Identities=19% Similarity=0.236 Sum_probs=53.0
Q ss_pred cccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCC---CCCCCC-chhHHhHHHHHHHH--HHhCCCchhhHHHHhc
Q 032124 8 KDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKE---LAPYDP-DWYYIRAASMARKI--YLRGGLGVGSFRRIYG 81 (147)
Q Consensus 8 kDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kE---laP~~~-DW~YiRaASi~Rkl--Yl~g~vGV~~lr~~YG 81 (147)
.-|+|++|.+++ +.|+. +..| ..+++-++++- .+|..+ +=. ++.|+--+ -..|++.+..|+..+|
T Consensus 131 ~lISp~Di~~A~-~~l~~---lg~g--~~l~~~~sg~~vv~s~~~~e~~~~---~~~il~~~~~~~~g~vt~~~l~~~~~ 201 (223)
T PF04157_consen 131 ELISPEDILRAC-KLLEV---LGLG--FRLRKFGSGVKVVQSVPYSELSKD---QSRILELAEEENGGGVTASELAEKLG 201 (223)
T ss_dssp ST--HHHHHHHH-HHHCC---CTSS--EEEEEETTTEEEEECST-CHH-HH---HHHHHHHH--TTTSEEEHHHHHHHHT
T ss_pred CCcCHHHHHHHH-HHHHH---cCCC--eEEEEeCCCcEEEEeCCchhhhHH---HHHHHHHHHhhcCCCCCHHHHHHHhC
Confidence 368999999998 45554 4444 34444443322 233121 122 34555555 5578999999999988
Q ss_pred CCCCCCCCCCCCCCCchhHHHHHHHHhHhCCcee
Q 032124 82 GGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (147)
Q Consensus 82 g~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~ 115 (147)
= |-.+.+.+|..||..|++=
T Consensus 202 w--------------s~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 202 W--------------SVERAKEALEELEREGLLW 221 (223)
T ss_dssp B---------------HHHHHHHHHHHHHTTSEE
T ss_pred C--------------CHHHHHHHHHHHHhCCCEe
Confidence 3 3489999999999999873
No 243
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=30.13 E-value=46 Score=22.64 Aligned_cols=20 Identities=20% Similarity=0.220 Sum_probs=17.0
Q ss_pred hHHHHHHHHhHhCCceeeCC
Q 032124 99 SVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~ 118 (147)
.=++..|.+||.+|+|+...
T Consensus 40 ~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 40 RRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHhCCCeEEEe
Confidence 55788999999999998654
No 244
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=29.58 E-value=36 Score=32.66 Aligned_cols=40 Identities=15% Similarity=0.033 Sum_probs=32.2
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCC----CeeeChhhhhhhhhh
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKG----QSLVLVERLHKLDCE 135 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~----GR~lT~~G~~~LDri 135 (147)
..=.++|.+|..||+-+||+....+ --.||+-|++.|+.+
T Consensus 327 ~~~d~l~~~Ly~LEsf~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 327 KNFDDLRESLYSLESFGLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred cchhHHHHHHHHHHhhhhHHhhhhccCceeEEechhHHHHHHhh
Confidence 3445788999999999999876633 368999999999854
No 245
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=29.45 E-value=53 Score=26.54 Aligned_cols=32 Identities=9% Similarity=0.152 Sum_probs=26.5
Q ss_pred HHHHHHhHhCCceeeCCCCCeeeChhhhhhhhh
Q 032124 102 RHILHQLQDTNIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 102 R~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDr 134 (147)
=-|...++.+|+|+-. .|-=.||++|+..+++
T Consensus 46 ~piv~ta~~Lglv~~e-~GDiilT~~Gk~~v~~ 77 (157)
T COG4754 46 MPIVETASLLGLVTAE-SGDIILTDEGKEYVES 77 (157)
T ss_pred HHHHHHHHhcCceecc-CCCEEEehhhHHHHhC
Confidence 3467788999999865 5788999999999886
No 246
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=29.45 E-value=50 Score=27.90 Aligned_cols=32 Identities=19% Similarity=0.154 Sum_probs=23.7
Q ss_pred HHHHHHhHhCCceeeCC-CCC--eeeChhhhhhhh
Q 032124 102 RHILHQLQDTNIIELDS-KGQ--SLVLVERLHKLD 133 (147)
Q Consensus 102 R~~LqqLE~~glV~k~~-~~G--R~lT~~G~~~LD 133 (147)
=.+|++||+.|+|++.. +.| =.+|++|...|-
T Consensus 37 ~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~ 71 (214)
T COG1339 37 ARKLKELEDEGYITRTISKRGQLITITEKGIDLLY 71 (214)
T ss_pred HHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHH
Confidence 34789999999998654 334 367888887664
No 247
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=29.22 E-value=64 Score=25.81 Aligned_cols=35 Identities=6% Similarity=0.004 Sum_probs=25.4
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCEN 136 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~ 136 (147)
-+=+.+++||+. .|++.. +|-.||+.|+.+++++-
T Consensus 32 avS~~i~~LE~~lg~~Lf~R~--r~i~lT~~G~~l~~~a~ 69 (294)
T PRK13348 32 AVSQRIKALEESLGQPLLVRG--RPCRPTPAGQRLLRHLR 69 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccChhHHHHHHHHH
Confidence 355667888864 667664 48899999988877654
No 248
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.01 E-value=51 Score=28.29 Aligned_cols=27 Identities=22% Similarity=0.147 Sum_probs=22.2
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCCCee
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKGQSL 123 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~GR~ 123 (147)
=|..-+++.++.||..|++++++ .||+
T Consensus 200 ls~aTV~~~lk~l~~~Gii~~~~-~Gr~ 226 (240)
T COG3398 200 LSVATVAYHLKKLEELGIIPEDR-EGRS 226 (240)
T ss_pred ccHHHHHHHHHHHHHcCCCcccc-cCce
Confidence 36678999999999999998875 4554
No 249
>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=28.46 E-value=75 Score=24.24 Aligned_cols=27 Identities=22% Similarity=0.326 Sum_probs=22.0
Q ss_pred hHHHHHHHHhHhCCceeeCCCCCeeeC
Q 032124 99 SVARHILHQLQDTNIIELDSKGQSLVL 125 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~~~GR~lT 125 (147)
..+|.+|+-|++.|+|+...+|--.++
T Consensus 66 ~~V~~Al~~f~k~glIe~~d~g~i~i~ 92 (119)
T TIGR01714 66 GDIRITLQTLESLGLIEKKNNGDIFLE 92 (119)
T ss_pred HHHHHHHHHHHHCCCEEEecCCcEEeh
Confidence 689999999999999998865544444
No 250
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=28.40 E-value=58 Score=28.65 Aligned_cols=39 Identities=8% Similarity=0.036 Sum_probs=29.9
Q ss_pred hhHHHHHHHHhHhCCceeeCCC--CC-eeeChhhhhhhhhhh
Q 032124 98 GSVARHILHQLQDTNIIELDSK--GQ-SLVLVERLHKLDCEN 136 (147)
Q Consensus 98 gsiiR~~LqqLE~~glV~k~~~--~G-R~lT~~G~~~LDri~ 136 (147)
...+|.+|..|-++||+....+ ++ .+||.+|+..+=+.+
T Consensus 42 E~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkgl~r~~~a~ 83 (291)
T COG3327 42 ETTVRAALSRMVKAGWLVGEREGRKSFYRLSDKGLARQRRAA 83 (291)
T ss_pred HHHHHHHHHHHHhccchheeecccccceeecHHHHHHHHHHh
Confidence 3578999999999999976542 22 568999998776544
No 251
>PF07571 DUF1546: Protein of unknown function (DUF1546); InterPro: IPR011442 These proteins are associated with IPR004823 from INTERPRO in transcription initiation factor TFIID subunit 6 (TAF6).; GO: 0051090 regulation of sequence-specific DNA binding transcription factor activity, 0005634 nucleus
Probab=28.38 E-value=1.7e+02 Score=20.73 Aligned_cols=18 Identities=28% Similarity=0.438 Sum_probs=12.3
Q ss_pred CchhHHh--HHHHHHHHHHh
Q 032124 51 PDWYYIR--AASMARKIYLR 68 (147)
Q Consensus 51 ~DW~YiR--aASi~RklYl~ 68 (147)
+|-|.+| ||+++.+|.-+
T Consensus 17 ~~h~~LRd~AA~lL~~I~~~ 36 (92)
T PF07571_consen 17 DNHWALRDFAASLLAQICRK 36 (92)
T ss_pred cchHHHHHHHHHHHHHHHHH
Confidence 4677777 78887766543
No 252
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=28.26 E-value=29 Score=27.37 Aligned_cols=59 Identities=19% Similarity=0.267 Sum_probs=42.9
Q ss_pred CCchhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC
Q 032124 50 DPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (147)
Q Consensus 50 ~~DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~ 119 (147)
+.||-|+|- |||||.|--+.--.|=. ...|..-.+.-..+.++.+..|+++..-.+..+
T Consensus 61 kk~W~~vrn-------~irgp~g~Lr~dl~~l~----~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA~~kd 119 (142)
T TIGR03042 61 KEDWVFTRN-------LIHGPMGEVRREMTYLN----QSLLPKDQKEALALAKELKDDLEKLDEAARLQD 119 (142)
T ss_pred hcchHHHHH-------HHhccHHHHHHHHHHHH----HccCHHhHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 459999997 89999886443333321 224666777788899999999999988766644
No 253
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=28.22 E-value=79 Score=26.20 Aligned_cols=34 Identities=9% Similarity=0.218 Sum_probs=23.7
Q ss_pred HHHHHHHhHh---CCceeeCCCCCeeeChhhhhhhhhh
Q 032124 101 ARHILHQLQD---TNIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 101 iR~~LqqLE~---~glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+=+.+++||+ ..|++.+. .|-.||+.|+.++...
T Consensus 42 vS~~I~~LE~~lG~~LF~R~~-~~~~LT~~G~~l~~~a 78 (310)
T PRK15092 42 VSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYA 78 (310)
T ss_pred HHHHHHHHHHHhCcceEEECC-CCceECHhHHHHHHHH
Confidence 3345677775 36777764 5888999998887643
No 254
>PF09661 DUF2398: Protein of unknown function (DUF2398); InterPro: IPR013494 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=27.72 E-value=1.2e+02 Score=27.02 Aligned_cols=50 Identities=20% Similarity=0.358 Sum_probs=36.3
Q ss_pred hhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 74 GSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 74 ~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
..++..||..=++ .....+...+++.+|..|++.|+++..+++|=.|.|.
T Consensus 309 ~~l~~~~~~~W~k----~~~~~~~~~L~~~vl~~L~~~~L~~~~~~~~v~l~Pa 358 (368)
T PF09661_consen 309 AELRERYGSGWSK----EYREMDPEELAEEVLELLEEWGLARVDGDGGVVLLPA 358 (368)
T ss_pred HHHHHHhhccccc----ccccCCHHHHHHHHHHHHHHCCCceECCCCeEEEccc
Confidence 4556666654332 3445677889999999999999999887665666664
No 255
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=26.81 E-value=78 Score=25.58 Aligned_cols=36 Identities=11% Similarity=0.004 Sum_probs=23.5
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+-+-..+++||+. .|.+++ .+|=.||+.|+.++...
T Consensus 31 pavS~~I~~LE~~lg~~LF~R~-~r~~~lT~~G~~l~~~~ 69 (300)
T PRK11074 31 SAVSYTVRQLEEWLAVPLFERR-HRDVELTPAGEWFVKEA 69 (300)
T ss_pred HHHHHHHHHHHHHhCCeeEEeC-CCCceECccHHHHHHHH
Confidence 3455667777764 566665 35777888888776543
No 256
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=26.79 E-value=64 Score=25.29 Aligned_cols=36 Identities=17% Similarity=0.015 Sum_probs=26.5
Q ss_pred CCCchhHHHHHHHHhHhCCceee-CCCCCeeeChhhh
Q 032124 94 SKSSGSVARHILHQLQDTNIIEL-DSKGQSLVLVERL 129 (147)
Q Consensus 94 ~~asgsiiR~~LqqLE~~glV~k-~~~~GR~lT~~G~ 129 (147)
..-+..++++|++.|.++|+|.- ....+..+..+.|
T Consensus 149 ~~~~k~v~~~a~E~L~~l~Ll~~~~~~~~~~~~~e~r 185 (203)
T PF14629_consen 149 KVWSKPVALKAWEHLLSLELLKPNYDGSSNNVQKEFR 185 (203)
T ss_pred ccCCHHHHHHHHHHHHHCCCceecccCCCCccCccce
Confidence 45678999999999999999976 2234555555553
No 257
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=26.64 E-value=1.5e+02 Score=23.93 Aligned_cols=41 Identities=15% Similarity=0.099 Sum_probs=33.1
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceee
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k 116 (147)
--+|--|+.++|+.-..+..+.|-. + -.++++|-..|||+.
T Consensus 93 LEtLaiIay~qPiTr~eI~~irGv~------~-----------~~ii~~L~~~gLI~e 133 (188)
T PRK00135 93 LEVLAIIAYKQPITRIEIDEIRGVN------S-----------DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCC------H-----------HHHHHHHHHCCCeEE
Confidence 3468888999999999999987642 1 567889999999974
No 258
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=25.98 E-value=91 Score=24.14 Aligned_cols=34 Identities=9% Similarity=0.127 Sum_probs=22.8
Q ss_pred HHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhh
Q 032124 101 ARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCE 135 (147)
Q Consensus 101 iR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri 135 (147)
+=+.+++||+. .|.+... +|=.||+.|+.+++..
T Consensus 32 vS~~I~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a 68 (297)
T COG0583 32 VSRQIKRLEEELGVPLFERTT-RRVRLTEAGERLLERA 68 (297)
T ss_pred HHHHHHHHHHHhCchheeecC-CceeeCHhHHHHHHHH
Confidence 55677888873 4555442 3467999998887764
No 259
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=25.67 E-value=42 Score=22.70 Aligned_cols=26 Identities=15% Similarity=0.351 Sum_probs=22.0
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceeee
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDIV 38 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~v 38 (147)
+.|++.+++.|++.+.|.+|.|-.|-
T Consensus 26 ~~~~~~i~~~L~~g~~V~l~g~G~F~ 51 (90)
T PF00216_consen 26 DALFDVIKEALKEGESVKLPGFGTFS 51 (90)
T ss_dssp HHHHHHHHHHHHTT-EEEETTTEEEE
T ss_pred HHHHHHHHHHHhcCCeEEeeceeEEE
Confidence 67889999999999999999998773
No 260
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=25.54 E-value=1e+02 Score=26.00 Aligned_cols=35 Identities=6% Similarity=0.022 Sum_probs=25.7
Q ss_pred hHHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhh
Q 032124 99 SVARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDC 134 (147)
Q Consensus 99 siiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDr 134 (147)
+-+=..+++||+. .|.+.. .+|=.||+.|+.++..
T Consensus 33 pavS~~Ik~LE~eLG~~LF~R~-~r~~~LT~aG~~ll~~ 70 (297)
T PRK15243 33 TPLSRVISDLERELKQRLFIRK-NGTLIPTEFAQTIYRK 70 (297)
T ss_pred HHHHHHHHHHHHHhCCccEEeC-CCCeeECHHHHHHHHH
Confidence 3455678888864 677775 3688999999988764
No 261
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=25.32 E-value=68 Score=25.10 Aligned_cols=31 Identities=23% Similarity=0.162 Sum_probs=25.4
Q ss_pred cccccChhHHHHHHHHHHHHcCCCCCCCcee
Q 032124 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWND 36 (147)
Q Consensus 6 tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d 36 (147)
.+-++|+.+++.++++-||++|-|.==+..|
T Consensus 23 ~~v~~P~SKl~~~il~vLk~eGYI~~f~~~~ 53 (132)
T COG0096 23 EVVSMPASKLKGAILKVLKKEGYIKDFEVID 53 (132)
T ss_pred ceeecchHHHHHHHHHHHHHcCCcceEEEEe
Confidence 4568999999999999999999886444444
No 262
>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=25.14 E-value=54 Score=22.24 Aligned_cols=20 Identities=20% Similarity=0.150 Sum_probs=17.4
Q ss_pred hHHHHHHHHhHhCCceeeCC
Q 032124 99 SVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~ 118 (147)
.-+-+.++.||+.|||.+.+
T Consensus 33 r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 33 RSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred hHHHHHHHHHHHCCCEEEEE
Confidence 56778999999999999875
No 263
>COG1485 Predicted ATPase [General function prediction only]
Probab=24.37 E-value=9.5 Score=34.43 Aligned_cols=57 Identities=25% Similarity=0.486 Sum_probs=39.9
Q ss_pred chhHHhHHHHHHHHHHhCCCchhh---HHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCC
Q 032124 52 DWYYIRAASMARKIYLRGGLGVGS---FRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTN 112 (147)
Q Consensus 52 DW~YiRaASi~RklYl~g~vGV~~---lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~g 112 (147)
-|+|-|.+...|=||+.||||.|. |-..|.+-.-..-+.-||+ ..++.+-|.|..+.
T Consensus 55 ~~lf~r~~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh----~FM~~vH~~l~~l~ 114 (367)
T COG1485 55 GWLFGRDHGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFH----RFMARVHQRLHTLQ 114 (367)
T ss_pred ccccccCCCCCceEEEECCCCccHHHHHHHHHhhCCccccccccHH----HHHHHHHHHHHHHc
Confidence 589999888899999999999985 3455654332222334654 57777888877765
No 264
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=24.21 E-value=88 Score=25.89 Aligned_cols=32 Identities=6% Similarity=-0.065 Sum_probs=15.9
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhh
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKL 132 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~L 132 (147)
-+-+.+++||+. .|.+.. ..|=.||+.|+.++
T Consensus 59 avS~~I~~LE~~lG~~LF~R~-~r~v~lT~~G~~l~ 93 (317)
T PRK11482 59 AISQSIQKLRVIFPDPLFIRK-GQGVTPTAYATHLH 93 (317)
T ss_pred HHHHHHHHHHHHhCCcceEec-CCCccCCHHHHHHH
Confidence 344455555552 344444 24555666665443
No 265
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=24.18 E-value=58 Score=28.28 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=26.8
Q ss_pred HHHHHhHhCCceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 103 HILHQLQDTNIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 103 ~~LqqLE~~glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
.=++.|-+-|+|+++..+-.+||.+|-..|=+.++
T Consensus 44 ehiK~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~ 78 (260)
T COG1497 44 EHIKELVKEGLIEKEGRGEYEITKKGAEWLLEQLS 78 (260)
T ss_pred HHHHHHHhccceeecCCeeEEEehhHHHHHHHHHH
Confidence 44789999999998543345899999988766554
No 266
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=24.11 E-value=56 Score=23.15 Aligned_cols=26 Identities=12% Similarity=0.289 Sum_probs=23.1
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceeee
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDIV 38 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~v 38 (147)
+.|++.+.+.|++.++|++|.|-.|-
T Consensus 26 ~~~~~~i~~~L~~~~~v~l~gfG~F~ 51 (90)
T PRK10664 26 DAIIASVTESLKEGDDVALVGFGTFA 51 (90)
T ss_pred HHHHHHHHHHHhCCCEEEECCcEEEE
Confidence 67888999999999999999998873
No 267
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=24.09 E-value=60 Score=22.94 Aligned_cols=26 Identities=12% Similarity=0.302 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceeee
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDIV 38 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~v 38 (147)
+.|++.+++.|++.+.|++|.+-.|.
T Consensus 28 ~~~~~~i~~~L~~g~~V~l~gfG~F~ 53 (99)
T PRK00285 28 ELFFEEIRDALENGEQVKLSGFGNFQ 53 (99)
T ss_pred HHHHHHHHHHHHcCCeEEEcCCEEEE
Confidence 67899999999999999999999884
No 268
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=23.87 E-value=80 Score=25.14 Aligned_cols=30 Identities=10% Similarity=0.341 Sum_probs=24.2
Q ss_pred cccccChhHHHHHHHHHHHHcCCCCCCCcee
Q 032124 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWND 36 (147)
Q Consensus 6 tVkDV~~~~fI~~~A~~LK~~gki~~P~W~d 36 (147)
.+.|.+.++ |+.+.+.|.+..++.+|+|.-
T Consensus 57 ~~~~Lt~~q-i~~l~~~i~~~~~~~iP~w~~ 86 (154)
T PTZ00134 57 RAGELTAEE-IEKIVEIIANPLQFKIPDWFL 86 (154)
T ss_pred CcccCCHHH-HHHHHHHHhccccCCCChhHh
Confidence 788887777 788889998756688899864
No 269
>PF03953 Tubulin_C: Tubulin C-terminal domain; InterPro: IPR018316 This domain is found in the tubulin alpha, beta and gamma chains, as well as the bacterial FtsZ family of proteins. These proteins are GTPases and are involved in polymer formation. Tubulin is the major component of microtubules, while FtsZ is the polymer-forming protein of bacterial cell division, it is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in bacteria and archaea. This is the C-terminal domain.; GO: 0003924 GTPase activity, 0005525 GTP binding, 0006184 GTP catabolic process, 0051258 protein polymerization, 0043234 protein complex; PDB: 3RYH_A 3RYI_A 3HKE_C 3HKD_C 3HKB_A 3N2K_A 3N2G_A 3HKC_C 3RYF_C 3RYC_A ....
Probab=23.40 E-value=80 Score=23.13 Aligned_cols=41 Identities=34% Similarity=0.612 Sum_probs=29.3
Q ss_pred ccChhHHHHHHHHHHHHcCCCCCCCce-eeeccCCCCCCCCCCC
Q 032124 9 DVSPHEFVKAYAAHLKRSGKIELPTWN-DIVKTGTLKELAPYDP 51 (147)
Q Consensus 9 DV~~~~fI~~~A~~LK~~gki~~P~W~-d~vKTg~~kElaP~~~ 51 (147)
||++.+.-++++ .+|+...+..++|. +=+|+|..+ .||...
T Consensus 60 ~v~~~di~~~i~-~ik~~~~~~Fv~W~p~~~kv~~~~-~~p~~~ 101 (126)
T PF03953_consen 60 DVSPKDINEAIA-KIKQKNSIQFVDWIPTGFKVGICK-VPPYGQ 101 (126)
T ss_dssp SSTHHHHHHHHH-HHHCTSTTSB-SSSTTCEEEEEES-S-STST
T ss_pred ccccchhhhHHH-hhhhccccceeeecCchhhccccc-CCCccc
Confidence 678888777774 57877788999996 567998887 555543
No 270
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=23.23 E-value=1.4e+02 Score=27.78 Aligned_cols=86 Identities=15% Similarity=0.117 Sum_probs=57.6
Q ss_pred CCCCchhHHhHHHHHHHHHH-hCCCchhhHHHHhcCCCCCCCCCC------CCCC---CchhHHHHHHHHhHhCCceeeC
Q 032124 48 PYDPDWYYIRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPP------HFSK---SSGSVARHILHQLQDTNIIELD 117 (147)
Q Consensus 48 P~~~DW~YiRaASi~RklYl-~g~vGV~~lr~~YGg~krrG~~P~------h~~~---asgsiiR~~LqqLE~~glV~k~ 117 (147)
+..-|+. .-|..++.-+|- .+..|.+.+...+=|.++.-++-. .|-. -+..-++.++++|...|+++..
T Consensus 407 ~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~ 485 (607)
T PRK11057 407 PKQYDGL-EDAQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDYGHDKLKVYGIGRDKSHEHWVSVIRQLIHLGLVTQN 485 (607)
T ss_pred ccccccH-HHHHHHHHHHHHhcCCCCcceeeeeeeccCcchhhhcccccCCccCcCCcCCHHHHHHHHHHHHHcCCceec
Confidence 3334554 345556666664 467888888888877765544332 2222 2345889999999999999865
Q ss_pred CC--CCeeeChhhhhhhhh
Q 032124 118 SK--GQSLVLVERLHKLDC 134 (147)
Q Consensus 118 ~~--~GR~lT~~G~~~LDr 134 (147)
.. ..=.||++|+..|..
T Consensus 486 ~~~~~~l~~~~~~~~~l~~ 504 (607)
T PRK11057 486 IAQHSALQLTEAARPVLRG 504 (607)
T ss_pred cCccceEEECHHHHHHhcC
Confidence 42 355799999887764
No 271
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=23.19 E-value=74 Score=25.99 Aligned_cols=88 Identities=10% Similarity=-0.014 Sum_probs=50.2
Q ss_pred HHhHHHHHHHHHHhCCCchhhHHHHhcCCCCC-CCCCCCCCCCc----hhHHHHHHHH-----------hHhCCceeeCC
Q 032124 55 YIRAASMARKIYLRGGLGVGSFRRIYGGGKRN-GSRPPHFSKSS----GSVARHILHQ-----------LQDTNIIELDS 118 (147)
Q Consensus 55 YiRaASi~RklYl~g~vGV~~lr~~YGg~krr-G~~P~h~~~as----gsiiR~~Lqq-----------LE~~glV~k~~ 118 (147)
++....++|++|=.-+-+.+.|+..||-.... .....|.+.+- ..|..++++. .|+..+.+.-+
T Consensus 96 ~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~~~~~~~l~~~~~~~~~~~~~~ 175 (219)
T PRK07983 96 WICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTSGWTAEEMADITGRPSLLTTFT 175 (219)
T ss_pred cEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcCCccCCCcc
Confidence 36678889999966567889999999753211 00122333222 3333444422 33444554332
Q ss_pred ---CCCeeeChhh---hhhhhhhhcCCccc
Q 032124 119 ---KGQSLVLVER---LHKLDCENSNGMDI 142 (147)
Q Consensus 119 ---~~GR~lT~~G---~~~LDri~~~~~~~ 142 (147)
-+|+.+++-- ..-|....+|-+|.
T Consensus 176 fGk~kg~~~~~~~~~~~~yl~wl~~~~~d~ 205 (219)
T PRK07983 176 FGKYRGKAVSDVAERDPGYLRWLFNNLDDM 205 (219)
T ss_pred ccCccCcchhhhhhcchHHHHHHHhccccc
Confidence 2588888874 46677777775554
No 272
>cd01817 RGS12_RBD Ubiquitin domain of RGS12 and RGS14. RGS12 (regulator of G signalling 12), and RGS14, are members of a family of GTPase-activating proteins (GAP's) specific for the G-alpha subunit, which act as key inhibitors of G-protein-mediated cell responses in eukaryotes. Their domain architecture includes tandem RBD domains as well as PDZ , PTB, and RGS, and GoLoco domains.
Probab=22.84 E-value=86 Score=22.25 Aligned_cols=33 Identities=15% Similarity=0.075 Sum_probs=23.5
Q ss_pred HHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCC
Q 032124 17 KAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDP 51 (147)
Q Consensus 17 ~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~ 51 (147)
+.|..-||+.|. . |+-.+....|.-|-++..++
T Consensus 24 d~L~kllekRgl-~-~~~~~vf~~g~~k~l~~~qD 56 (73)
T cd01817 24 DLLSGLCEKRGI-N-YAAVDLFLVGGDKPLVLDQD 56 (73)
T ss_pred HHHHHHHHHcCC-C-hhHEEEEEecCCcccccCCc
Confidence 347888899884 4 67777778887777766554
No 273
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=22.68 E-value=63 Score=27.92 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=19.2
Q ss_pred chhHHHHHHHHhHhCCceeeCC
Q 032124 97 SGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~~ 118 (147)
..|||=.||..||++|++|...
T Consensus 217 TRSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 217 TRSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred hHHHHHHHHHHhhhcCceeecc
Confidence 3589999999999999998654
No 274
>TIGR03157 cas_Csc2 CRISPR-associated protein Csc2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc2 for CRISPR/Cas Subtype Cyano protein 2, as it is often the second gene upstream of the core cas genes, cas3-cas4-cas1-cas2.
Probab=22.56 E-value=61 Score=28.44 Aligned_cols=25 Identities=24% Similarity=0.377 Sum_probs=22.5
Q ss_pred CCCccccccChhHHHHHHHHHHHHc
Q 032124 2 ETAKNVKDVSPHEFVKAYAAHLKRS 26 (147)
Q Consensus 2 ~~~~tVkDV~~~~fI~~~A~~LK~~ 26 (147)
|.++|++||.+++|+-.+...|+..
T Consensus 165 p~~vTLkD~T~~e~~~~l~~~~rt~ 189 (282)
T TIGR03157 165 PCVVTLKDVTPAEFLYVVNNIARTA 189 (282)
T ss_pred ceEEEecCCCHHHHHHHHHHHHHhh
Confidence 5667999999999999999999875
No 275
>PF14502 HTH_41: Helix-turn-helix domain
Probab=22.37 E-value=1e+02 Score=20.34 Aligned_cols=26 Identities=23% Similarity=0.311 Sum_probs=20.7
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCCCe
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~GR 122 (147)
-|...|-++|+-||+.|-|.-.. .||
T Consensus 18 vs~GtiQ~Alk~Le~~gaI~Le~-rGh 43 (48)
T PF14502_consen 18 VSRGTIQNALKFLEENGAIKLES-RGH 43 (48)
T ss_pred cchhHHHHHHHHHHHCCcEEeee-cCc
Confidence 35578999999999999998664 344
No 276
>KOG2035 consensus Replication factor C, subunit RFC3 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=22.07 E-value=1.3e+02 Score=27.07 Aligned_cols=110 Identities=19% Similarity=0.238 Sum_probs=68.4
Q ss_pred hHHHHHHHHHHHHcCC-CCCCCceeeeccCCCCCCCCCCCchhHHhHHHHHHHHHHhCCCchhhHHHHhc-----CCCCC
Q 032124 13 HEFVKAYAAHLKRSGK-IELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYG-----GGKRN 86 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gk-i~~P~W~d~vKTg~~kElaP~~~DW~YiRaASi~RklYl~g~vGV~~lr~~YG-----g~krr 86 (147)
-.-.+..|++||..-- =+.|.-.-|=-+|++|. +|+-.++|+|| ++||..|+-.+- ++|+-
T Consensus 15 l~~~~e~~~~Lksl~~~~d~PHll~yGPSGaGKK----------TrimclL~elY---G~gveklki~~~t~~tpS~kkl 81 (351)
T KOG2035|consen 15 LIYHEELANLLKSLSSTGDFPHLLVYGPSGAGKK----------TRIMCLLRELY---GVGVEKLKIETRTFTTPSKKKL 81 (351)
T ss_pred cccHHHHHHHHHHhcccCCCCeEEEECCCCCCch----------hhHHHHHHHHh---CCCchheeeeeEEEecCCCceE
Confidence 3445778899988633 45799999999999997 79999999999 789998876542 22211
Q ss_pred C-----------CCCCCCCCCchhHHHHHHHHhHhCCceeeCCC---------CCeeeChhhhhhhhhh
Q 032124 87 G-----------SRPPHFSKSSGSVARHILHQLQDTNIIELDSK---------GQSLVLVERLHKLDCE 135 (147)
Q Consensus 87 G-----------~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~---------~GR~lT~~G~~~LDri 135 (147)
- +.|+-.-.-..-||-.+|++.-+..=|+..-. .+-.||...|.-|-|-
T Consensus 82 EistvsS~yHlEitPSDaG~~DRvViQellKevAQt~qie~~~qr~fKvvvi~ead~LT~dAQ~aLRRT 150 (351)
T KOG2035|consen 82 EISTVSSNYHLEITPSDAGNYDRVVIQELLKEVAQTQQIETQGQRPFKVVVINEADELTRDAQHALRRT 150 (351)
T ss_pred EEEEecccceEEeChhhcCcccHHHHHHHHHHHHhhcchhhccccceEEEEEechHhhhHHHHHHHHHH
Confidence 1 23433333333445555544433333332211 2446788888777664
No 277
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=21.90 E-value=82 Score=26.15 Aligned_cols=33 Identities=12% Similarity=-0.017 Sum_probs=25.3
Q ss_pred hhHHHHHHHHhHhCCceeeCCCCCe----eeChhhhhh
Q 032124 98 GSVARHILHQLQDTNIIELDSKGQS----LVLVERLHK 131 (147)
Q Consensus 98 gsiiR~~LqqLE~~glV~k~~~~GR----~lT~~G~~~ 131 (147)
-.+|-+.|..|++.|||+... .|+ .+|+.|-+-
T Consensus 113 th~itYslrKL~k~gLit~t~-~gkevTy~vTa~G~~a 149 (199)
T COG5631 113 THNITYSLRKLLKGGLITRTG-SGKEVTYEVTALGHRA 149 (199)
T ss_pred chhHHHHHHHHHhccceecCC-CCceEEEEEecchHHH
Confidence 357889999999999999774 344 567777654
No 278
>TIGR00987 himA integration host factor, alpha subunit. This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU.
Probab=21.86 E-value=70 Score=22.54 Aligned_cols=25 Identities=12% Similarity=0.329 Sum_probs=23.0
Q ss_pred hHHHHHHHHHHHHcCCCCCCCceee
Q 032124 13 HEFVKAYAAHLKRSGKIELPTWNDI 37 (147)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~W~d~ 37 (147)
+.|++.+++.|++.++|+++.+-.|
T Consensus 27 ~~~~~~i~~~L~~g~~V~l~gfG~F 51 (96)
T TIGR00987 27 ELFFEEIRRALENGEQVKLSGFGNF 51 (96)
T ss_pred HHHHHHHHHHHHcCCeEEecCCEEE
Confidence 6788999999999999999999888
No 279
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=21.65 E-value=97 Score=24.96 Aligned_cols=36 Identities=6% Similarity=0.003 Sum_probs=25.5
Q ss_pred HHHHHHHHhHhC---CceeeCCCCCeeeChhhhhhhhhhhc
Q 032124 100 VARHILHQLQDT---NIIELDSKGQSLVLVERLHKLDCENS 137 (147)
Q Consensus 100 iiR~~LqqLE~~---glV~k~~~~GR~lT~~G~~~LDri~~ 137 (147)
-+=..+++||+. .|.+.. .|-.||+.|+.++..+..
T Consensus 32 avS~~I~~LE~~lg~~LF~R~--~~~~lT~~G~~l~~~a~~ 70 (294)
T PRK03635 32 AVSQRIKALEERVGQVLLVRT--QPCRPTEAGQRLLRHARQ 70 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccCHHHHHHHHHHHH
Confidence 344567888864 566664 489999999998766543
No 280
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=21.56 E-value=89 Score=27.07 Aligned_cols=23 Identities=30% Similarity=0.355 Sum_probs=18.3
Q ss_pred hHHHHHHHHhHhCCceeeCCCCCe
Q 032124 99 SVARHILHQLQDTNIIELDSKGQS 122 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~~~GR 122 (147)
.=||.-||.|...|++|... .|+
T Consensus 228 ~KIRQqLQ~LRD~g~IeFl~-rG~ 250 (254)
T PF06044_consen 228 AKIRQQLQILRDKGIIEFLG-RGR 250 (254)
T ss_dssp HHHHHHHHHHHHTTSEEE-S-TTE
T ss_pred HHHHHHHHHHhhCCceEEec-CCc
Confidence 35999999999999999875 343
No 281
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=21.42 E-value=96 Score=21.25 Aligned_cols=50 Identities=22% Similarity=0.313 Sum_probs=31.4
Q ss_pred chhHHhHHHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 52 DW~YiRaASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
|=.|-.|..++. -.+-+.++.|.+.|.=. . .=.-.++.+||+.|+|.-..
T Consensus 5 D~ly~~a~~~V~---~~~~~S~S~lQR~~rIG-------------y-nrAariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 5 DPLYEEAVEFVI---EEGKASISLLQRKFRIG-------------Y-NRAARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp STTHHHHHHHHH---HCTCECHHHHHHHHT---------------H-HHHHHHHHHHHHCTSBE---
T ss_pred cHHHHHHHHHHH---HcCCccHHHHHHHhCCC-------------H-HHHHHHHHHHHHCCCCCCCC
Confidence 445666655543 36788888888866532 2 22346899999999997543
No 282
>PF09911 DUF2140: Uncharacterized protein conserved in bacteria (DUF2140); InterPro: IPR018672 This family of conserved hypothetical proteins has no known function.
Probab=21.21 E-value=90 Score=25.11 Aligned_cols=21 Identities=29% Similarity=0.523 Sum_probs=16.9
Q ss_pred HHHHHHHHHHcCCCCCCCceeee
Q 032124 16 VKAYAAHLKRSGKIELPTWNDIV 38 (147)
Q Consensus 16 I~~~A~~LK~~gki~~P~W~d~v 38 (147)
+..+-.++|++ .+.|+|+.+-
T Consensus 127 ~s~Vl~yi~~~--y~lP~wV~i~ 147 (187)
T PF09911_consen 127 ISFVLKYIKKS--YKLPKWVTIN 147 (187)
T ss_pred HHHHHHHHHhh--CCCCCcEEEc
Confidence 45567889988 8999999874
No 283
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=21.20 E-value=1.1e+02 Score=23.40 Aligned_cols=26 Identities=12% Similarity=0.041 Sum_probs=20.2
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCCC
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKGQ 121 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~G 121 (147)
.|-+-+-.+|++|+++|+|.+.+..|
T Consensus 53 islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 53 ISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred CCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 44456778999999999999877543
No 284
>PRK14493 putative bifunctional molybdopterin-guanine dinucleotide biosynthesis protein MobB/MoaE; Provisional
Probab=21.10 E-value=1.6e+02 Score=24.99 Aligned_cols=46 Identities=22% Similarity=0.162 Sum_probs=33.7
Q ss_pred cccChhHHHHHHHHHHHHcCCCCCCCceeeeccCCCCCCCCCCCchhHHhHH
Q 032124 8 KDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAA 59 (147)
Q Consensus 8 kDV~~~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~kElaP~~~DW~YiRaA 59 (147)
++.--.-|+..|+..|++.|+ +-++|.-.|.-..+...|||-.|.|
T Consensus 10 ~gSGKTTLi~~Li~~L~~~G~------V~~IKhd~h~~~~~~g~Ds~~~~~a 55 (274)
T PRK14493 10 KATGKTTLVERLVDRLSGRGR------VGTVKHMDTERLNPDGTDTGRHFDA 55 (274)
T ss_pred CCCCHHHHHHHHHHHHHhCCC------EEEEEEcCCCcCCCCCCCcHHHHHC
Confidence 455567899999999999983 6788886544223556789987765
No 285
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.08 E-value=87 Score=25.70 Aligned_cols=26 Identities=19% Similarity=0.248 Sum_probs=22.0
Q ss_pred CCCCchhHHHHHHHHhHhCCceeeCC
Q 032124 93 FSKSSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 93 ~~~asgsiiR~~LqqLE~~glV~k~~ 118 (147)
+++=|-.+|+.||++||+.|+.+-..
T Consensus 63 ~R~Ls~~~i~~Il~~l~k~g~~e~~D 88 (174)
T KOG4068|consen 63 QRRLSQEFIDEILEELEKKGLAEPTD 88 (174)
T ss_pred hccCCHHHHHHHHHHHHHccCCcccc
Confidence 45667899999999999999998653
No 286
>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=21.07 E-value=1.3e+02 Score=19.34 Aligned_cols=23 Identities=35% Similarity=0.511 Sum_probs=18.8
Q ss_pred CchhHHHHHHHHhHhCCceeeCC
Q 032124 96 SSGSVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~ 118 (147)
.|..-+=++|+.|++.|+|+...
T Consensus 40 ~sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 40 VSRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp SCHHHHHHHHHHHHHTTSEEEET
T ss_pred CCHHHHHHHHHHHHHCCCEEEcC
Confidence 45567888999999999999763
No 287
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=20.83 E-value=2.1e+02 Score=21.82 Aligned_cols=64 Identities=6% Similarity=-0.105 Sum_probs=44.3
Q ss_pred chhHHhHHHHHHHHHHhCC---------CchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCC
Q 032124 52 DWYYIRAASMARKIYLRGG---------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (147)
Q Consensus 52 DW~YiRaASi~RklYl~g~---------vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~ 119 (147)
...-+-..-+||.+|...- +.++.+...|..-.. -.+....+-.-++.+|..|++.|+++....
T Consensus 73 ~~~eTilLL~LR~~y~e~~~~~~~~~~~v~~~ei~e~~~~~~~----~~~d~~~~~~~~~~~l~~l~~~~ll~~~~~ 145 (166)
T PF13835_consen 73 SLEETILLLVLRLLYEEKESLSGSERVVVTREEIVEKLESFLP----ESRDEAPFKKRLDAALRRLKRYGLLRRLDG 145 (166)
T ss_pred CHHHHHHHHHHHHHHHHHhccCCCCcEEEeHHHHHHHHHHHcc----ccccccchHHHHHHHHHHHHHCCCeeccCC
Confidence 3445566779999999753 556666666655221 123345566789999999999999998753
No 288
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=20.83 E-value=2e+02 Score=22.19 Aligned_cols=72 Identities=17% Similarity=0.208 Sum_probs=50.7
Q ss_pred HHHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCee-----eC------hh
Q 032124 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSL-----VL------VE 127 (147)
Q Consensus 59 ASi~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~-----lT------~~ 127 (147)
+.|++.|.-+||..++.+-..-... + .=|-+-++..|+-|-+-|+|....+|++- +| ..
T Consensus 9 ~eVM~ilW~~~~~t~~eI~~~l~~~--~--------ews~sTV~TLl~RL~KKg~l~~~kdgr~~~y~pL~~~~~~~~~~ 78 (123)
T COG3682 9 WEVMEILWSRGPATVREIIEELPAD--R--------EWSYSTVKTLLNRLVKKGLLTRKKDGRAFRYSPLLTRDQYVAGE 78 (123)
T ss_pred HHHHHHHHHcCCccHHHHHHHHhhc--c--------cccHHHHHHHHHHHHhccchhhhhcCCeeeeecccCHHHHHHHH
Confidence 4689999999999999887766544 2 33457899999999999999877654332 11 12
Q ss_pred hhhhhhhhhcCCc
Q 032124 128 RLHKLDCENSNGM 140 (147)
Q Consensus 128 G~~~LDri~~~~~ 140 (147)
-+..||++-.-++
T Consensus 79 ~~~~l~k~~d~~~ 91 (123)
T COG3682 79 SQDLLDKICDGGL 91 (123)
T ss_pred HHHHHHHHHcccc
Confidence 3456676665554
No 289
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=20.78 E-value=88 Score=26.10 Aligned_cols=31 Identities=26% Similarity=0.443 Sum_probs=22.5
Q ss_pred ccChhHHHHHHHHHHHHcC-CCCCCCceeeec
Q 032124 9 DVSPHEFVKAYAAHLKRSG-KIELPTWNDIVK 39 (147)
Q Consensus 9 DV~~~~fI~~~A~~LK~~g-ki~~P~W~d~vK 39 (147)
-.|..++.+.+++.||+.| +|++=++.|++-
T Consensus 7 ~~~~~~i~~~v~~~~~~~Gi~vevv~f~D~~~ 38 (237)
T PF03180_consen 7 PGPDAEILEAVKEKLKKKGIDVEVVEFSDYVQ 38 (237)
T ss_dssp TTCHHHHHHHHHHHHHHTTEEEEEEEESSTTH
T ss_pred CCCHHHHHHHHHHHHHhcCCeEEEEEecchhh
Confidence 4567788888999999988 356666666653
No 290
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=20.58 E-value=84 Score=26.26 Aligned_cols=21 Identities=14% Similarity=0.309 Sum_probs=18.1
Q ss_pred chhHHHHHHHHhHhCCceeeC
Q 032124 97 SGSVARHILHQLQDTNIIELD 117 (147)
Q Consensus 97 sgsiiR~~LqqLE~~glV~k~ 117 (147)
+..-++.+|+.||.+|+|+..
T Consensus 330 ~~~~~~~~l~~l~~~gli~~~ 350 (365)
T TIGR02928 330 TQRRISDLLNELDMLGLVEAE 350 (365)
T ss_pred cHHHHHHHHHHHHhcCCeEEE
Confidence 348899999999999999854
No 291
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.53 E-value=73 Score=26.02 Aligned_cols=20 Identities=25% Similarity=0.363 Sum_probs=17.6
Q ss_pred hHHHHHHHHhHhCCceeeCC
Q 032124 99 SVARHILHQLQDTNIIELDS 118 (147)
Q Consensus 99 siiR~~LqqLE~~glV~k~~ 118 (147)
--||.+|+.|+++||++...
T Consensus 46 ~~i~e~l~dL~elGLier~t 65 (175)
T COG4344 46 PRIREYLKDLKELGLIERYT 65 (175)
T ss_pred HHHHHHHHHHHHcCCeeecc
Confidence 46899999999999999764
No 292
>PRK13239 alkylmercury lyase; Provisional
Probab=20.51 E-value=2.7e+02 Score=23.17 Aligned_cols=47 Identities=13% Similarity=0.139 Sum_probs=32.0
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeCCCCCeee
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGQSLV 124 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~~~~GR~l 124 (147)
+|+|.|---.|+.+..|.+..|.. ..-+|.+|++| ..++-++ .|+.+
T Consensus 26 ~llr~la~G~pvt~~~lA~~~~~~--------------~~~v~~~L~~l---~~~~~d~-~g~iv 72 (206)
T PRK13239 26 PLLRLLAKGRPVSVTTLAAALGWP--------------VEEVEAVLEAM---PDTEYDE-DGRII 72 (206)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCCC--------------HHHHHHHHHhC---CCeEECC-CCCEE
Confidence 489998855699999999987643 34566666665 5556665 35554
No 293
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=20.13 E-value=1.7e+02 Score=25.17 Aligned_cols=50 Identities=20% Similarity=0.168 Sum_probs=31.7
Q ss_pred hhHHhHHHHH-HHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCc
Q 032124 53 WYYIRAASMA-RKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNI 113 (147)
Q Consensus 53 W~YiRaASi~-RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~gl 113 (147)
-.=|-||||+ |-.+++ -+..|...||-....| ++..+.+.+-+.+++-|.
T Consensus 221 ~~aVAAASIiAR~~~l~---~l~~l~~~yg~~~pkG--------a~~~v~~~a~~~i~~~G~ 271 (284)
T TIGR00716 221 NLAVAAASIFARYKFLQ---SLKELERELGIKLPKG--------ASKEVKELAKSLILKKGP 271 (284)
T ss_pred chhhhHHHHHHHHHHHH---HHHHhCcccCCcCCCC--------CChHHHHHHHHHHHHhCc
Confidence 4457899985 555555 5677888888776555 333455555555655553
No 294
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.07 E-value=3.2e+02 Score=19.83 Aligned_cols=44 Identities=14% Similarity=0.148 Sum_probs=35.2
Q ss_pred HHHHHHHHhCCCchhhHHHHhcCCCCCCCCCCCCCCCchhHHHHHHHHhHhCCceeeC
Q 032124 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD 117 (147)
Q Consensus 60 Si~RklYl~g~vGV~~lr~~YGg~krrG~~P~h~~~asgsiiR~~LqqLE~~glV~k~ 117 (147)
.||+-|=-+++.....|.+..| -|.+-++.-++.||+.|++..-
T Consensus 12 ~IL~~L~~d~r~~~~eia~~lg--------------lS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 12 RILRLLQEDARISNAELAERVG--------------LSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHhCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCceeeE
Confidence 3666677778888999998877 3457788899999999999754
No 295
>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=20.02 E-value=1.4e+02 Score=23.53 Aligned_cols=32 Identities=19% Similarity=0.285 Sum_probs=24.5
Q ss_pred CchhHHHHHHHHhHhCCceeeCCCCCeeeChh
Q 032124 96 SSGSVARHILHQLQDTNIIELDSKGQSLVLVE 127 (147)
Q Consensus 96 asgsiiR~~LqqLE~~glV~k~~~~GR~lT~~ 127 (147)
-|-.-+..+++.||+.+++.+...|=-.|.|.
T Consensus 87 iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP~ 118 (165)
T PF05732_consen 87 ISKPTVSRAIKELEEKNIIKKIRNGAYMINPN 118 (165)
T ss_pred CCHHHHHHHHHHHHhCCcEEEccCCeEEECcH
Confidence 45567889999999999999875554566654
Done!