Query 032244
Match_columns 144
No_of_seqs 109 out of 329
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 11:31:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032244.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032244hhsearch_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 1.3E-75 2.8E-80 450.5 9.6 138 5-142 1-138 (139)
2 PTZ00095 40S ribosomal protein 100.0 3.1E-74 6.7E-79 454.2 15.2 141 1-141 22-163 (169)
3 PRK09333 30S ribosomal protein 100.0 5.3E-73 1.1E-77 440.6 14.6 138 4-142 1-138 (150)
4 KOG3411 40S ribosomal protein 100.0 5.7E-72 1.2E-76 427.6 13.4 141 1-142 1-141 (143)
5 COG2238 RPS19A Ribosomal prote 100.0 7.5E-71 1.6E-75 424.8 13.3 137 4-141 1-137 (147)
6 PF03444 HrcA_DNA-bdg: Winged 97.5 0.00024 5.2E-09 50.5 5.1 57 64-134 15-75 (78)
7 PF08461 HTH_12: Ribonuclease 97.4 0.00029 6.4E-09 47.8 4.8 63 61-132 3-66 (66)
8 PF14947 HTH_45: Winged helix- 97.0 0.002 4.3E-08 44.4 5.7 62 59-136 9-70 (77)
9 COG3388 Predicted transcriptio 96.9 0.0024 5.2E-08 47.3 5.0 68 57-139 15-82 (101)
10 COG1420 HrcA Transcriptional r 96.8 0.003 6.6E-08 55.3 6.1 63 57-131 7-75 (346)
11 TIGR02337 HpaR homoprotocatech 96.7 0.011 2.3E-07 42.7 7.6 65 61-139 33-103 (118)
12 PRK11512 DNA-binding transcrip 96.5 0.017 3.8E-07 43.1 7.7 63 61-137 45-113 (144)
13 TIGR02702 SufR_cyano iron-sulf 96.5 0.0069 1.5E-07 48.1 5.7 60 60-133 5-72 (203)
14 PRK11050 manganese transport r 96.4 0.02 4.3E-07 44.0 7.9 63 61-137 42-104 (152)
15 smart00418 HTH_ARSR helix_turn 96.4 0.017 3.7E-07 35.5 6.1 59 61-134 2-64 (66)
16 smart00529 HTH_DTXR Helix-turn 96.3 0.0093 2E-07 41.2 4.9 42 97-138 12-53 (96)
17 smart00347 HTH_MARR helix_turn 96.3 0.035 7.5E-07 37.4 7.6 65 61-139 15-85 (101)
18 PF13463 HTH_27: Winged helix 96.3 0.011 2.3E-07 38.3 4.7 54 61-128 8-68 (68)
19 PF01638 HxlR: HxlR-like helix 96.1 0.017 3.6E-07 40.5 5.4 65 58-136 7-77 (90)
20 PF05491 RuvB_C: Holliday junc 96.1 0.0057 1.2E-07 43.3 3.0 68 52-133 7-74 (76)
21 PRK03911 heat-inducible transc 96.0 0.018 3.8E-07 49.1 6.1 63 57-131 4-72 (260)
22 COG1846 MarR Transcriptional r 95.9 0.043 9.3E-07 37.8 6.9 65 59-137 25-95 (126)
23 PRK10870 transcriptional repre 95.9 0.042 9.2E-07 43.0 7.3 64 61-138 60-131 (176)
24 smart00346 HTH_ICLR helix_turn 95.8 0.055 1.2E-06 36.7 6.6 60 56-129 5-66 (91)
25 TIGR01889 Staph_reg_Sar staphy 95.6 0.062 1.3E-06 38.7 6.9 66 61-140 30-105 (109)
26 PRK03573 transcriptional regul 95.6 0.077 1.7E-06 39.3 7.5 65 61-139 36-107 (144)
27 PRK13777 transcriptional regul 95.5 0.07 1.5E-06 42.8 7.5 65 61-139 50-120 (185)
28 PRK03902 manganese transport t 95.1 0.094 2E-06 39.3 6.6 61 61-135 13-73 (142)
29 PF13601 HTH_34: Winged helix 95.0 0.09 2E-06 36.6 5.7 65 61-139 5-76 (80)
30 TIGR03433 padR_acidobact trans 94.8 0.067 1.5E-06 38.2 4.9 47 93-139 34-88 (100)
31 TIGR00331 hrcA heat shock gene 94.8 0.079 1.7E-06 45.8 6.1 52 68-131 19-71 (337)
32 PF14338 Mrr_N: Mrr N-terminal 94.8 0.035 7.5E-07 39.1 3.2 35 99-133 55-89 (92)
33 PRK00082 hrcA heat-inducible t 94.7 0.086 1.9E-06 45.6 6.1 63 57-131 7-75 (339)
34 PF09339 HTH_IclR: IclR helix- 94.7 0.072 1.6E-06 33.7 4.2 49 56-118 3-52 (52)
35 PRK05638 threonine synthase; V 94.6 0.24 5.1E-06 43.9 8.8 93 25-135 337-441 (442)
36 COG3432 Predicted transcriptio 94.4 0.063 1.4E-06 39.5 3.9 43 94-136 41-86 (95)
37 PF12840 HTH_20: Helix-turn-he 94.1 0.13 2.9E-06 33.3 4.6 48 60-122 14-61 (61)
38 PF02082 Rrf2: Transcriptional 93.9 0.13 2.9E-06 35.3 4.6 46 70-129 25-72 (83)
39 COG1693 Repressor of nif and g 93.9 0.059 1.3E-06 47.0 3.4 65 61-134 11-76 (325)
40 PF10711 DUF2513: Hypothetical 93.8 0.12 2.5E-06 37.4 4.3 47 89-135 25-80 (102)
41 TIGR03338 phnR_burk phosphonat 93.5 0.11 2.5E-06 40.4 4.2 65 57-135 15-85 (212)
42 COG1321 TroR Mn-dependent tran 93.5 0.15 3.2E-06 39.8 4.7 54 68-135 22-75 (154)
43 TIGR02944 suf_reg_Xantho FeS a 93.4 0.46 1E-05 34.8 7.0 68 58-139 11-83 (130)
44 TIGR02719 repress_PhaQ poly-be 93.2 0.19 4.1E-06 38.9 4.9 44 96-139 55-106 (138)
45 cd00090 HTH_ARSR Arsenical Res 93.1 0.46 1E-05 29.6 5.8 62 60-137 11-75 (78)
46 PRK09834 DNA-binding transcrip 93.1 0.36 7.9E-06 39.5 6.7 62 56-131 11-74 (263)
47 PF01047 MarR: MarR family; I 93.1 0.36 7.7E-06 30.5 5.3 51 59-123 6-58 (59)
48 TIGR01884 cas_HTH CRISPR locus 93.0 0.34 7.3E-06 38.4 6.2 55 60-128 147-203 (203)
49 PF12802 MarR_2: MarR family; 92.9 0.27 5.8E-06 31.1 4.6 46 59-118 8-55 (62)
50 COG1733 Predicted transcriptio 92.8 0.37 7.9E-06 36.1 5.8 62 61-136 28-95 (120)
51 PF00392 GntR: Bacterial regul 92.8 0.55 1.2E-05 30.6 6.0 39 70-122 23-62 (64)
52 cd07377 WHTH_GntR Winged helix 92.5 0.16 3.6E-06 31.9 3.1 39 73-125 28-66 (66)
53 PF03551 PadR: Transcriptional 92.5 0.094 2E-06 35.2 2.1 42 93-134 26-75 (75)
54 PRK11014 transcriptional repre 92.5 0.33 7.2E-06 36.4 5.2 43 70-126 25-69 (141)
55 TIGR02277 PaaX_trns_reg phenyl 92.3 0.19 4E-06 42.5 4.1 61 70-141 17-80 (280)
56 COG1725 Predicted transcriptio 92.0 0.3 6.5E-06 37.4 4.5 38 98-135 49-86 (125)
57 cd00092 HTH_CRP helix_turn_hel 91.6 1.2 2.7E-05 28.2 6.5 44 69-126 24-67 (67)
58 COG1802 GntR Transcriptional r 91.6 1 2.2E-05 35.9 7.3 65 57-135 20-90 (230)
59 TIGR00738 rrf2_super rrf2 fami 91.4 1.2 2.7E-05 32.3 7.1 49 69-131 24-74 (132)
60 TIGR02812 fadR_gamma fatty aci 91.2 0.37 8.1E-06 38.3 4.5 42 72-127 32-73 (235)
61 PRK11534 DNA-binding transcrip 91.2 0.35 7.6E-06 38.2 4.3 51 71-135 31-81 (224)
62 PF08220 HTH_DeoR: DeoR-like h 91.0 0.71 1.5E-05 30.0 4.9 48 58-119 2-49 (57)
63 PF10007 DUF2250: Uncharacteri 90.9 0.75 1.6E-05 33.5 5.5 44 61-118 12-55 (92)
64 smart00550 Zalpha Z-DNA-bindin 90.8 0.79 1.7E-05 30.8 5.1 45 60-118 10-56 (68)
65 smart00345 HTH_GNTR helix_turn 90.7 0.3 6.4E-06 30.1 2.8 36 72-121 22-57 (60)
66 PRK09990 DNA-binding transcrip 90.7 0.33 7.1E-06 39.0 3.7 45 72-130 33-77 (251)
67 PF09114 MotA_activ: Transcrip 90.6 1.6 3.5E-05 32.2 6.9 70 57-139 17-86 (96)
68 PRK11414 colanic acid/biofilm 90.3 0.46 9.9E-06 37.5 4.2 49 73-135 37-85 (221)
69 PF06969 HemN_C: HemN C-termin 90.2 0.84 1.8E-05 29.6 4.8 55 61-129 11-65 (66)
70 smart00420 HTH_DEOR helix_turn 90.1 0.93 2E-05 27.1 4.7 46 60-119 4-49 (53)
71 PRK03837 transcriptional regul 90.1 2.3 5.1E-05 33.6 8.2 57 57-127 17-80 (241)
72 PRK15090 DNA-binding transcrip 89.7 0.92 2E-05 36.9 5.7 58 56-127 14-72 (257)
73 TIGR02010 IscR iron-sulfur clu 89.7 1.1 2.5E-05 33.3 5.7 46 69-128 24-71 (135)
74 PF13412 HTH_24: Winged helix- 89.7 1.4 3.1E-05 26.9 5.3 42 60-115 7-48 (48)
75 PRK08599 coproporphyrinogen II 89.2 1.4 3.1E-05 37.8 6.7 59 68-140 316-374 (377)
76 PRK09057 coproporphyrinogen II 88.9 2 4.3E-05 37.3 7.4 57 68-140 323-379 (380)
77 PRK11569 transcriptional repre 88.4 1.4 2.9E-05 36.5 5.9 59 55-127 27-87 (274)
78 PRK10163 DNA-binding transcrip 88.1 1.5 3.3E-05 36.2 5.9 57 56-126 25-83 (271)
79 PRK14165 winged helix-turn-hel 88.0 0.72 1.6E-05 38.1 4.0 55 71-139 22-79 (217)
80 COG1414 IclR Transcriptional r 88.0 1.6 3.4E-05 35.9 5.9 51 56-121 4-56 (246)
81 TIGR02018 his_ut_repres histid 87.9 1.9 4.2E-05 34.2 6.3 58 55-126 3-67 (230)
82 PRK09464 pdhR transcriptional 87.9 0.88 1.9E-05 36.6 4.3 41 72-126 36-76 (254)
83 PF01978 TrmB: Sugar-specific 87.9 0.7 1.5E-05 30.3 3.1 47 59-119 11-57 (68)
84 COG3355 Predicted transcriptio 87.8 1.4 2.9E-05 33.9 5.1 60 67-140 39-112 (126)
85 PRK10421 DNA-binding transcrip 87.8 0.54 1.2E-05 38.0 3.0 41 73-127 29-69 (253)
86 PRK04984 fatty acid metabolism 87.7 0.61 1.3E-05 37.1 3.3 41 72-126 33-73 (239)
87 PRK10225 DNA-binding transcrip 87.6 0.53 1.2E-05 38.0 2.9 59 57-129 13-78 (257)
88 PF12793 SgrR_N: Sugar transpo 87.2 0.84 1.8E-05 34.0 3.6 39 70-122 19-57 (115)
89 PRK09416 lstR lineage-specific 86.8 1.1 2.3E-05 34.9 4.1 44 95-138 74-121 (135)
90 PRK11920 rirA iron-responsive 86.8 0.75 1.6E-05 35.4 3.2 46 70-129 24-71 (153)
91 COG1695 Predicted transcriptio 86.7 1.1 2.3E-05 33.2 3.9 44 96-139 42-93 (138)
92 TIGR02325 C_P_lyase_phnF phosp 86.6 2.8 6.1E-05 33.1 6.5 61 54-128 9-76 (238)
93 PF13814 Replic_Relax: Replica 86.6 1.8 4E-05 33.0 5.3 62 62-134 1-72 (191)
94 PRK10857 DNA-binding transcrip 86.5 2.2 4.8E-05 33.4 5.8 46 69-128 24-71 (164)
95 PRK11523 DNA-binding transcrip 86.3 0.72 1.6E-05 37.2 3.0 41 73-127 35-75 (253)
96 PF09382 RQC: RQC domain; Int 86.2 3 6.4E-05 29.3 5.8 76 58-133 6-95 (106)
97 PRK13347 coproporphyrinogen II 86.1 2.5 5.4E-05 37.6 6.6 63 65-139 376-438 (453)
98 PRK08208 coproporphyrinogen II 85.8 2.8 6E-05 37.0 6.7 59 67-140 358-416 (430)
99 PRK00080 ruvB Holliday junctio 85.5 1.1 2.4E-05 37.6 3.9 57 62-133 268-325 (328)
100 COG4901 Ribosomal protein S25 85.3 0.77 1.7E-05 34.5 2.5 77 29-124 22-98 (107)
101 TIGR01610 phage_O_Nterm phage 84.9 3.6 7.9E-05 29.1 5.8 48 57-118 26-81 (95)
102 PRK05628 coproporphyrinogen II 84.3 1.4 3.1E-05 37.9 4.0 38 102-140 337-374 (375)
103 TIGR02404 trehalos_R_Bsub treh 83.9 4.3 9.2E-05 32.3 6.4 58 55-126 2-66 (233)
104 PRK14999 histidine utilization 83.7 7.9 0.00017 31.0 7.9 60 54-127 13-79 (241)
105 PF01726 LexA_DNA_bind: LexA D 83.2 1.4 3.1E-05 29.6 2.9 40 70-122 25-64 (65)
106 PRK05799 coproporphyrinogen II 83.0 1.8 4E-05 37.0 4.2 40 100-140 334-373 (374)
107 PRK09334 30S ribosomal protein 82.4 1.5 3.3E-05 31.7 2.9 36 70-119 41-76 (86)
108 PRK06294 coproporphyrinogen II 82.2 1.9 4.1E-05 37.3 4.0 39 101-140 332-370 (370)
109 PRK09764 DNA-binding transcrip 82.0 6.7 0.00014 31.5 6.9 61 54-128 6-73 (240)
110 COG2255 RuvB Holliday junction 81.9 3.5 7.6E-05 36.4 5.5 68 52-133 259-326 (332)
111 smart00419 HTH_CRP helix_turn_ 81.7 1.9 4.2E-05 25.5 2.8 35 70-118 8-42 (48)
112 PF07848 PaaX: PaaX-like prote 81.4 6 0.00013 27.1 5.5 61 57-128 1-70 (70)
113 TIGR02787 codY_Gpos GTP-sensin 81.3 1.6 3.5E-05 37.1 3.2 60 61-134 188-250 (251)
114 PRK08898 coproporphyrinogen II 81.0 7.7 0.00017 33.9 7.4 39 101-140 355-393 (394)
115 COG2186 FadR Transcriptional r 80.7 1.8 3.9E-05 35.4 3.2 40 73-126 37-76 (241)
116 COG2188 PhnF Transcriptional r 80.6 7.1 0.00015 31.6 6.6 71 55-139 9-90 (236)
117 PRK05660 HemN family oxidoredu 80.5 2.6 5.6E-05 36.6 4.3 39 102-141 339-377 (378)
118 COG1959 Predicted transcriptio 79.9 2 4.2E-05 33.1 3.0 45 70-128 25-71 (150)
119 PRK06582 coproporphyrinogen II 79.6 7.5 0.00016 34.1 6.9 61 65-140 328-389 (390)
120 PRK09249 coproporphyrinogen II 79.5 2.2 4.9E-05 37.8 3.6 36 104-140 404-439 (453)
121 PRK06266 transcription initiat 79.4 4.1 8.9E-05 32.5 4.8 42 60-115 26-67 (178)
122 PRK08629 coproporphyrinogen II 79.3 6.8 0.00015 35.0 6.6 59 68-140 356-414 (433)
123 COG2524 Predicted transcriptio 79.3 1.6 3.4E-05 37.9 2.5 35 99-133 40-76 (294)
124 PRK11402 DNA-binding transcrip 79.2 7.3 0.00016 31.1 6.2 61 54-128 10-77 (241)
125 TIGR00635 ruvB Holliday juncti 79.1 5 0.00011 32.8 5.3 50 68-132 253-303 (305)
126 PF01022 HTH_5: Bacterial regu 78.8 6.6 0.00014 24.1 4.7 41 61-116 7-47 (47)
127 TIGR00538 hemN oxygen-independ 78.0 2.7 5.8E-05 37.3 3.7 36 104-140 404-439 (455)
128 PRK04172 pheS phenylalanyl-tRN 77.8 4.3 9.2E-05 36.7 4.9 66 59-138 9-76 (489)
129 PF04703 FaeA: FaeA-like prote 76.9 2.7 5.8E-05 28.4 2.6 38 68-119 13-50 (62)
130 PF09012 FeoC: FeoC like trans 76.4 5.9 0.00013 26.3 4.2 40 65-118 9-48 (69)
131 PRK11886 bifunctional biotin-- 76.4 8.2 0.00018 32.5 6.0 59 55-127 3-62 (319)
132 PRK09058 coproporphyrinogen II 76.3 3.6 7.7E-05 36.7 4.0 40 101-141 398-437 (449)
133 PF14394 DUF4423: Domain of un 75.9 3 6.5E-05 32.9 3.1 33 95-127 52-84 (171)
134 PRK07379 coproporphyrinogen II 75.8 2.7 5.9E-05 36.8 3.1 41 99-141 351-394 (400)
135 PRK13626 transcriptional regul 75.6 4.8 0.0001 36.4 4.7 40 69-122 22-61 (552)
136 PF03297 Ribosomal_S25: S25 ri 75.6 2.6 5.6E-05 31.4 2.5 37 69-119 58-94 (105)
137 TIGR02431 pcaR_pcaU beta-ketoa 75.3 7.5 0.00016 31.3 5.3 56 56-126 9-65 (248)
138 TIGR00122 birA_repr_reg BirA b 74.7 17 0.00038 23.7 6.1 53 60-127 4-56 (69)
139 PRK13509 transcriptional repre 74.3 11 0.00025 30.9 6.2 50 57-120 6-55 (251)
140 PF00126 HTH_1: Bacterial regu 73.9 4.8 0.0001 25.9 3.1 32 97-129 26-60 (60)
141 PRK09802 DNA-binding transcrip 73.1 11 0.00024 31.4 5.9 55 56-125 17-71 (269)
142 PRK10079 phosphonate metabolis 72.7 3.8 8.2E-05 32.9 3.0 59 54-127 13-78 (241)
143 COG0635 HemN Coproporphyrinoge 72.0 17 0.00037 32.4 7.2 80 42-140 331-410 (416)
144 PRK12423 LexA repressor; Provi 71.5 13 0.00027 29.6 5.7 45 62-119 15-61 (202)
145 COG2512 Predicted membrane-ass 71.4 19 0.00041 30.4 7.0 87 17-122 161-248 (258)
146 TIGR00373 conserved hypothetic 71.2 8.8 0.00019 29.8 4.6 43 59-115 17-59 (158)
147 PF09821 AAA_assoc_C: C-termin 70.9 7.3 0.00016 29.2 4.0 32 102-134 15-46 (120)
148 PRK05283 deoxyribose-phosphate 68.8 7.5 0.00016 33.0 4.0 86 12-112 145-250 (257)
149 PF14277 DUF4364: Domain of un 68.5 7.4 0.00016 30.6 3.7 40 100-139 35-78 (163)
150 PRK00215 LexA repressor; Valid 67.8 17 0.00036 28.5 5.6 49 70-131 23-73 (205)
151 TIGR00498 lexA SOS regulatory 67.4 17 0.00037 28.2 5.6 45 62-119 15-61 (199)
152 PRK10434 srlR DNA-bindng trans 67.1 15 0.00033 30.3 5.4 53 57-124 6-58 (256)
153 TIGR02698 CopY_TcrY copper tra 66.8 18 0.0004 27.0 5.4 52 60-122 8-59 (130)
154 COG1542 Uncharacterized conser 65.7 5.7 0.00012 37.2 2.9 93 30-136 384-494 (593)
155 PRK04424 fatty acid biosynthes 65.6 8.1 0.00018 30.5 3.5 48 57-118 8-55 (185)
156 TIGR02424 TF_pcaQ pca operon t 64.9 9.4 0.0002 30.6 3.8 37 99-136 32-71 (300)
157 TIGR00637 ModE_repress ModE mo 64.4 18 0.00039 26.0 4.8 36 97-132 29-71 (99)
158 PRK09791 putative DNA-binding 64.2 12 0.00027 30.1 4.3 38 99-137 34-74 (302)
159 PRK11242 DNA-binding transcrip 63.7 11 0.00023 30.0 3.9 37 99-136 30-69 (296)
160 PF08222 HTH_CodY: CodY helix- 63.6 10 0.00022 26.0 3.1 21 98-118 18-38 (61)
161 PF11313 DUF3116: Protein of u 63.1 10 0.00022 27.4 3.3 42 97-138 40-84 (85)
162 PRK11716 DNA-binding transcrip 62.4 14 0.00031 28.5 4.2 38 99-137 6-46 (269)
163 PRK10082 cell density-dependen 62.3 9.9 0.00021 30.8 3.5 37 99-136 40-79 (303)
164 PF13730 HTH_36: Helix-turn-he 62.3 7.5 0.00016 24.1 2.2 19 96-114 37-55 (55)
165 TIGR03339 phn_lysR aminoethylp 62.0 13 0.00028 29.0 4.0 34 100-134 27-63 (279)
166 PF14337 DUF4393: Domain of un 61.8 8.9 0.00019 29.7 3.0 94 11-117 31-133 (186)
167 smart00344 HTH_ASNC helix_turn 61.7 26 0.00057 24.3 5.2 68 60-141 7-86 (108)
168 PRK08446 coproporphyrinogen II 61.4 12 0.00025 32.1 3.9 35 103-140 315-349 (350)
169 TIGR02647 DNA conserved hypoth 60.7 18 0.0004 25.8 4.1 39 93-134 29-67 (77)
170 PRK03601 transcriptional regul 60.7 13 0.00027 29.9 3.8 37 100-137 31-70 (275)
171 PRK11151 DNA-binding transcrip 60.4 14 0.0003 29.8 4.0 37 99-136 30-69 (305)
172 PF01325 Fe_dep_repress: Iron 60.4 40 0.00086 22.1 5.5 40 68-121 20-59 (60)
173 PRK10086 DNA-binding transcrip 60.2 12 0.00025 30.6 3.6 33 101-134 45-80 (311)
174 TIGR02036 dsdC D-serine deamin 59.5 19 0.00042 29.2 4.7 38 99-137 37-77 (302)
175 TIGR01594 holin_lambda phage h 59.2 9.4 0.0002 28.3 2.6 36 46-85 1-45 (107)
176 PRK10141 DNA-binding transcrip 58.6 29 0.00063 25.9 5.2 55 60-129 20-78 (117)
177 PRK11233 nitrogen assimilation 58.5 18 0.0004 29.3 4.4 37 99-136 30-69 (305)
178 PRK14997 LysR family transcrip 58.3 11 0.00024 30.3 3.0 36 100-136 32-70 (301)
179 COG1485 Predicted ATPase [Gene 56.3 4.7 0.0001 36.1 0.7 57 52-112 55-114 (367)
180 PF07381 DUF1495: Winged helix 56.3 9.2 0.0002 27.7 2.0 28 107-134 58-89 (90)
181 PF08279 HTH_11: HTH domain; 56.1 28 0.00062 21.4 4.1 42 57-112 1-43 (55)
182 PF14178 YppF: YppF-like prote 56.1 17 0.00036 24.8 3.2 20 61-80 27-46 (60)
183 PRK04214 rbn ribonuclease BN/u 55.9 43 0.00094 29.5 6.6 56 56-125 292-351 (412)
184 COG4533 ABC-type uncharacteriz 55.2 25 0.00054 33.2 5.2 58 70-141 23-86 (564)
185 PRK10094 DNA-binding transcrip 55.1 13 0.00028 30.5 3.0 36 100-136 32-70 (308)
186 PF09681 Phage_rep_org_N: N-te 54.1 13 0.00028 28.0 2.6 48 65-126 46-95 (121)
187 TIGR03418 chol_sulf_TF putativ 53.9 17 0.00038 28.9 3.5 36 100-136 31-69 (291)
188 PRK12681 cysB transcriptional 53.1 16 0.00036 30.3 3.4 37 100-136 32-71 (324)
189 PRK11062 nhaR transcriptional 53.1 19 0.00042 29.1 3.7 37 100-137 34-73 (296)
190 PRK09986 DNA-binding transcrip 53.0 25 0.00054 27.8 4.3 36 100-136 37-75 (294)
191 PRK10632 transcriptional regul 52.7 23 0.00049 28.9 4.1 38 99-137 31-71 (309)
192 PRK10837 putative DNA-binding 52.5 21 0.00046 28.2 3.8 35 100-135 33-70 (290)
193 PHA02943 hypothetical protein; 52.4 55 0.0012 26.4 6.0 54 52-120 7-60 (165)
194 PRK09906 DNA-binding transcrip 52.2 22 0.00048 28.4 3.9 34 101-135 32-68 (296)
195 CHL00180 rbcR LysR transcripti 51.4 24 0.00051 28.6 4.0 36 100-136 35-73 (305)
196 PRK10906 DNA-binding transcrip 51.0 45 0.00099 27.5 5.6 54 57-125 6-59 (252)
197 PRK11013 DNA-binding transcrip 50.6 23 0.00051 28.8 3.8 37 99-136 33-72 (309)
198 PRK15092 DNA-binding transcrip 50.2 23 0.00049 29.3 3.8 36 100-136 41-79 (310)
199 PRK10411 DNA-binding transcrip 49.7 55 0.0012 26.8 5.9 52 57-122 5-56 (240)
200 PRK15421 DNA-binding transcrip 48.9 25 0.00053 29.1 3.8 35 100-135 32-69 (317)
201 PRK10341 DNA-binding transcrip 48.9 27 0.00058 28.5 3.9 35 100-135 37-74 (312)
202 PRK12680 transcriptional regul 48.6 25 0.00054 29.3 3.8 37 100-137 32-72 (327)
203 COG2345 Predicted transcriptio 48.3 40 0.00086 28.1 4.9 58 60-131 15-80 (218)
204 PRK15481 transcriptional regul 47.8 21 0.00046 30.8 3.3 41 72-126 31-71 (431)
205 PRK12682 transcriptional regul 47.3 29 0.00063 28.2 3.9 38 100-138 32-73 (309)
206 KOG1767 40S ribosomal protein 46.8 13 0.00028 28.2 1.6 23 96-118 72-94 (110)
207 PRK11139 DNA-binding transcrip 46.6 35 0.00076 27.4 4.2 37 99-136 35-74 (297)
208 PRK12684 transcriptional regul 46.5 29 0.00063 28.4 3.8 38 100-137 32-72 (313)
209 TIGR02147 Fsuc_second hypothet 46.3 21 0.00045 30.4 3.0 58 52-125 121-180 (271)
210 TIGR03337 phnR transcriptional 45.5 24 0.00052 27.6 3.1 42 73-128 28-69 (231)
211 PF15522 Toxin_42: Putative to 44.1 24 0.00051 28.9 2.8 81 13-105 38-123 (205)
212 PRK09508 leuO leucine transcri 43.9 45 0.00098 27.1 4.6 34 100-134 52-88 (314)
213 TIGR03298 argP transcriptional 43.6 31 0.00067 27.5 3.5 37 99-137 30-69 (292)
214 PF03965 Penicillinase_R: Peni 43.6 58 0.0013 23.3 4.6 50 60-119 7-56 (115)
215 PHA00738 putative HTH transcri 43.1 72 0.0016 24.0 5.1 48 61-123 17-64 (108)
216 PF09202 Rio2_N: Rio2, N-termi 42.3 31 0.00066 24.3 2.9 35 98-132 38-74 (82)
217 PF04408 HA2: Helicase associa 42.3 19 0.00041 25.4 1.9 25 103-131 1-25 (102)
218 PF14502 HTH_41: Helix-turn-he 41.0 31 0.00067 22.5 2.5 26 96-122 18-43 (48)
219 COG3327 PaaX Phenylacetic acid 40.9 36 0.00079 29.6 3.6 43 99-141 43-88 (291)
220 PRK11074 putative DNA-binding 40.8 60 0.0013 26.2 4.8 38 99-137 31-71 (300)
221 COG1339 Transcriptional regula 40.8 41 0.00088 28.2 3.8 43 97-139 32-77 (214)
222 PF06163 DUF977: Bacterial pro 40.2 1.7E+02 0.0038 22.6 7.1 67 59-139 15-81 (127)
223 PF02002 TFIIE_alpha: TFIIE al 39.8 62 0.0014 22.8 4.2 44 58-115 15-58 (105)
224 PRK09213 pur operon repressor; 39.8 1.3E+02 0.0028 25.7 6.8 78 57-142 8-94 (271)
225 cd08768 Cdc6_C Winged-helix do 39.3 26 0.00057 23.4 2.1 23 96-118 44-66 (87)
226 PF02522 Antibiotic_NAT: Amino 39.2 11 0.00023 30.7 0.2 86 11-104 15-107 (229)
227 PF14113 DUF4285: Domain of un 39.2 89 0.0019 23.0 5.1 44 19-68 11-54 (115)
228 PRK11482 putative DNA-binding 38.9 56 0.0012 27.0 4.4 35 100-135 59-96 (317)
229 COG0583 LysR Transcriptional r 38.7 60 0.0013 25.1 4.3 36 101-137 32-70 (297)
230 PF15129 FAM150: FAM150 family 38.2 22 0.00047 27.3 1.7 17 53-69 103-119 (123)
231 PRK13239 alkylmercury lyase; P 37.9 99 0.0021 25.5 5.6 52 53-124 21-72 (206)
232 COG1349 GlpR Transcriptional r 37.8 97 0.0021 25.5 5.7 49 57-119 6-54 (253)
233 COG1568 Predicted methyltransf 37.8 35 0.00076 30.3 3.1 39 94-133 44-82 (354)
234 PRK06474 hypothetical protein; 37.6 1.1E+02 0.0023 24.1 5.6 45 61-118 16-61 (178)
235 PF08432 Vfa1: AAA-ATPase Vps4 37.5 8.2 0.00018 30.6 -0.7 14 46-59 28-41 (182)
236 smart00847 HA2 Helicase associ 37.4 25 0.00053 23.7 1.8 24 104-131 2-25 (92)
237 PRK09801 transcriptional activ 37.4 33 0.00072 28.2 2.8 37 99-136 35-74 (310)
238 TIGR02716 C20_methyl_CrtF C-20 37.2 48 0.001 27.4 3.8 51 68-133 21-71 (306)
239 COG3398 Uncharacterized protei 37.1 33 0.00072 29.2 2.8 27 96-123 200-226 (240)
240 PRK05974 phosphoribosylformylg 36.2 38 0.00083 23.3 2.6 42 98-143 18-69 (80)
241 PRK15243 transcriptional regul 36.2 56 0.0012 27.4 4.1 37 99-136 33-72 (297)
242 PF04458 DUF505: Protein of un 36.0 87 0.0019 29.9 5.6 72 46-131 408-497 (591)
243 COG4521 TauA ABC-type taurine 35.7 33 0.00072 30.1 2.6 30 13-42 297-328 (334)
244 PRK13348 chromosome replicatio 35.7 49 0.0011 26.4 3.5 36 100-137 32-70 (294)
245 PRK12683 transcriptional regul 35.6 59 0.0013 26.6 4.0 37 99-136 31-71 (309)
246 PRK12679 cbl transcriptional r 35.6 55 0.0012 26.8 3.8 36 100-136 32-71 (316)
247 PF04458 DUF505: Protein of un 34.9 21 0.00046 33.9 1.4 40 96-135 327-370 (591)
248 COG4189 Predicted transcriptio 34.5 85 0.0018 27.3 4.9 44 61-118 28-71 (308)
249 PRK00135 scpB segregation and 33.4 1.1E+02 0.0023 24.7 5.1 41 59-116 93-133 (188)
250 PRK00199 ihfB integration host 33.1 27 0.00058 24.4 1.4 28 13-40 27-54 (94)
251 PF09079 Cdc6_C: CDC6, C termi 32.4 38 0.00083 22.9 2.1 22 97-118 38-59 (85)
252 PF09107 SelB-wing_3: Elongati 32.3 1.4E+02 0.003 19.1 5.1 43 67-124 7-49 (50)
253 PF06044 DRP: Dam-replacing fa 30.9 45 0.00097 28.6 2.6 20 100-119 229-248 (254)
254 KOG4068 Uncharacterized conser 30.9 48 0.001 26.9 2.6 27 93-119 63-89 (174)
255 PRK03635 chromosome replicatio 30.7 57 0.0012 26.2 3.2 36 100-137 32-70 (294)
256 TIGR00988 hip integration host 30.6 28 0.00061 24.1 1.2 26 13-38 27-52 (94)
257 COG0640 ArsR Predicted transcr 30.4 1.4E+02 0.0031 18.7 7.3 51 60-124 29-79 (110)
258 PF02909 TetR_C: Tetracyclin r 30.4 2E+02 0.0042 20.3 6.1 58 47-115 2-61 (139)
259 TIGR01743 purR_Bsub pur operon 30.2 2.1E+02 0.0046 24.4 6.6 77 57-141 6-91 (268)
260 PF07042 TrfA: TrfA protein; 29.5 29 0.00062 29.9 1.2 40 70-116 231-270 (282)
261 PF10264 Stork_head: Winged he 29.1 1.4E+02 0.0031 21.3 4.5 53 69-127 28-80 (80)
262 PRK10664 transcriptional regul 29.0 33 0.00071 24.2 1.3 25 13-37 26-50 (90)
263 PRK06423 phosphoribosylformylg 28.9 61 0.0013 21.9 2.6 40 103-143 20-63 (73)
264 COG0096 RpsH Ribosomal protein 28.8 54 0.0012 25.4 2.5 31 6-36 23-53 (132)
265 PF09929 DUF2161: Uncharacteri 28.6 1.4E+02 0.0031 22.8 4.8 59 57-132 60-118 (118)
266 smart00501 BRIGHT BRIGHT, ARID 28.1 1.2E+02 0.0026 20.9 4.1 17 12-28 3-19 (93)
267 PF09106 SelB-wing_2: Elongati 27.9 88 0.0019 20.0 3.1 43 65-118 12-54 (59)
268 PF00727 IL4: Interleukin 4 Th 27.8 23 0.00049 27.0 0.3 52 9-68 4-58 (117)
269 PF15398 DUF4619: Domain of un 27.7 13 0.00029 32.3 -1.1 67 41-131 56-126 (296)
270 PF09397 Ftsk_gamma: Ftsk gamm 27.5 62 0.0013 22.0 2.4 50 52-118 5-54 (65)
271 PRK11057 ATP-dependent DNA hel 27.4 90 0.002 28.9 4.2 82 51-133 410-503 (607)
272 COG1510 Predicted transcriptio 27.1 67 0.0015 26.2 2.9 49 61-123 31-81 (177)
273 smart00479 EXOIII exonuclease 27.1 1.3E+02 0.0027 21.8 4.2 53 55-110 113-165 (169)
274 PRK10402 DNA-binding transcrip 26.9 91 0.002 24.4 3.6 41 97-140 182-222 (226)
275 TIGR03703 plsB glycerol-3-phos 26.7 1.7E+02 0.0037 28.7 6.0 50 87-140 742-791 (799)
276 smart00190 IL4_13 Interleukins 26.4 1.9E+02 0.0042 22.7 5.2 59 9-73 28-88 (138)
277 PRK02539 hypothetical protein; 26.2 65 0.0014 23.4 2.4 27 102-131 42-68 (85)
278 COG4754 Uncharacterized conser 25.9 58 0.0013 26.1 2.3 32 102-134 46-77 (157)
279 COG5631 Predicted transcriptio 25.6 1.1E+02 0.0024 25.2 3.8 39 98-136 113-154 (199)
280 PF14629 ORC4_C: Origin recogn 24.9 77 0.0017 24.7 2.8 37 93-129 148-185 (203)
281 PF04182 B-block_TFIIIC: B-blo 24.9 56 0.0012 22.0 1.8 36 70-119 18-53 (75)
282 COG1654 BirA Biotin operon rep 24.7 1E+02 0.0022 21.7 3.1 43 70-126 19-62 (79)
283 PF09661 DUF2398: Protein of u 24.3 1.5E+02 0.0032 26.2 4.8 50 74-127 309-358 (368)
284 PRK01546 hypothetical protein; 24.1 76 0.0016 22.7 2.4 26 102-130 43-68 (79)
285 COG4465 CodY Pleiotropic trans 23.8 1E+02 0.0022 26.4 3.5 22 97-118 217-238 (261)
286 KOG0345 ATP-dependent RNA heli 23.7 39 0.00084 31.9 1.1 19 46-64 333-351 (567)
287 PRK10216 DNA-binding transcrip 23.7 1.1E+02 0.0025 24.8 3.8 9 121-129 61-69 (319)
288 TIGR01714 phage_rep_org_N phag 23.5 94 0.002 23.5 3.0 42 70-125 51-92 (119)
289 PF09639 YjcQ: YjcQ protein; 23.5 77 0.0017 22.2 2.4 36 99-134 25-69 (88)
290 PRK10676 DNA-binding transcrip 23.5 1.2E+02 0.0025 25.4 3.8 66 52-133 15-87 (263)
291 PF08221 HTH_9: RNA polymerase 23.4 1.7E+02 0.0036 19.2 3.9 47 56-116 13-59 (62)
292 COG4344 Uncharacterized protei 23.3 59 0.0013 26.3 1.9 39 99-137 46-104 (175)
293 PF13835 DUF4194: Domain of un 23.3 1.7E+02 0.0037 22.2 4.4 63 53-119 74-145 (166)
294 TIGR00987 himA integration hos 23.1 52 0.0011 23.1 1.4 25 13-37 27-51 (96)
295 TIGR03042 PS_II_psbQ_bact phot 22.8 44 0.00096 26.2 1.1 59 50-119 61-119 (142)
296 PF14357 DUF4404: Domain of un 22.7 71 0.0015 22.5 2.1 19 95-113 67-85 (85)
297 COG3189 Uncharacterized conser 22.5 46 0.001 25.5 1.1 31 44-84 43-73 (117)
298 COG2443 Sss1 Preprotein transl 22.4 62 0.0013 22.4 1.6 26 13-41 12-37 (65)
299 PF13545 HTH_Crp_2: Crp-like h 22.3 1.1E+02 0.0023 19.7 2.7 23 96-118 40-62 (76)
300 PLN00146 40S ribosomal protein 22.2 1E+02 0.0022 23.4 3.0 26 6-31 24-49 (130)
301 COG1497 Predicted transcriptio 22.2 1.1E+02 0.0023 26.4 3.4 36 103-138 44-79 (260)
302 cd06590 RNaseH_typeII_bacteria 22.0 1.6E+02 0.0034 23.5 4.2 36 51-88 138-173 (208)
303 PF00216 Bac_DNA_binding: Bact 21.9 39 0.00084 22.7 0.6 25 13-37 26-50 (90)
304 PF13518 HTH_28: Helix-turn-he 21.9 1.8E+02 0.004 17.1 4.9 36 65-115 8-43 (52)
305 PF13182 DUF4007: Protein of u 21.5 1.1E+02 0.0023 26.0 3.3 33 100-132 44-76 (286)
306 PF05979 DUF896: Bacterial pro 21.4 64 0.0014 22.2 1.5 22 103-127 41-62 (65)
307 PRK15431 ferrous iron transpor 21.4 2.6E+02 0.0056 19.9 4.7 41 64-118 10-50 (78)
308 PF03953 Tubulin_C: Tubulin C- 21.3 92 0.002 22.7 2.5 40 9-50 60-100 (126)
309 PRK00285 ihfA integration host 21.2 54 0.0012 23.0 1.2 25 13-37 28-52 (99)
310 smart00843 Ftsk_gamma This dom 20.8 2.8E+02 0.0061 18.8 5.6 50 52-118 4-53 (63)
311 PF06348 DUF1059: Protein of u 20.8 83 0.0018 20.5 1.9 31 11-41 21-53 (57)
312 PRK10263 DNA translocase FtsK; 20.7 5.3E+02 0.012 27.3 8.3 87 12-118 1249-1341(1355)
313 PF03428 RP-C: Replication pro 20.5 78 0.0017 25.4 2.1 22 96-117 83-104 (177)
314 COG4483 Uncharacterized protei 20.3 70 0.0015 22.4 1.5 10 55-64 48-57 (68)
315 COG3398 Uncharacterized protei 20.2 2E+02 0.0043 24.6 4.5 48 62-123 107-154 (240)
316 PF14557 AphA_like: Putative A 20.2 1.6E+02 0.0035 24.0 3.9 45 94-138 42-92 (175)
317 COG1522 Lrp Transcriptional re 20.2 3.2E+02 0.007 19.7 5.3 44 61-118 13-56 (154)
318 TIGR00475 selB selenocysteine- 20.1 2.7E+02 0.0059 25.9 5.8 89 15-124 476-579 (581)
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=1.3e-75 Score=450.49 Aligned_cols=138 Identities=62% Similarity=1.084 Sum_probs=126.8
Q ss_pred CceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCC
Q 032244 5 KNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK 84 (144)
Q Consensus 5 ~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k 84 (144)
+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+|
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 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244 85 RNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV 142 (144)
Q Consensus 85 ~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~ 142 (144)
|||++|+||++|||+|||+||||||++|||++++++||+||++||++||+||.||++.
T Consensus 81 ~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~~v~~~ 138 (139)
T PF01090_consen 81 RRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAGQVAKE 138 (139)
T ss_dssp EETSSCCEE--CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHHHHHHc
Confidence 9999999999999999999999999999999999889999999999999999999863
No 2
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=100.00 E-value=3.1e-74 Score=454.24 Aligned_cols=141 Identities=41% Similarity=0.724 Sum_probs=137.0
Q ss_pred CCCCCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHh
Q 032244 1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY 80 (144)
Q Consensus 1 m~~~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~Y 80 (144)
|..++||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|
T Consensus 22 ~~~~~tvkDVpa~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~Y 101 (169)
T PTZ00095 22 RRKNATLKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRF 101 (169)
T ss_pred ccCCCceeeCCHHHHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHH
Confidence 44679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHhhHHHHHHHHhh
Q 032244 81 GGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 81 Gg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~~lD~iA~~i~~ 141 (144)
||+||||++|+||++|||+|||+||||||++|||++++ ++||+||++||++||+||.+|++
T Consensus 102 Gg~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~ 163 (169)
T PTZ00095 102 SSKKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTI 163 (169)
T ss_pred CCCCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999996 48999999999999999999975
No 3
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=100.00 E-value=5.3e-73 Score=440.59 Aligned_cols=138 Identities=41% Similarity=0.708 Sum_probs=135.6
Q ss_pred CCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCC
Q 032244 4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG 83 (144)
Q Consensus 4 ~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~ 83 (144)
|+||||||||+||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244 84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV 142 (144)
Q Consensus 84 k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~ 142 (144)
||||++|+||++|||+|||++|||||++|||++++ +||+||++||++||+||.+|++.
T Consensus 81 k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~iA~~i~~~ 138 (150)
T PRK09333 81 KNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNLAAEVKKE 138 (150)
T ss_pred cCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999 79999999999999999999754
No 4
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.7e-72 Score=427.61 Aligned_cols=141 Identities=62% Similarity=1.080 Sum_probs=138.4
Q ss_pred CCCCCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHh
Q 032244 1 METAKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY 80 (144)
Q Consensus 1 m~~~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~Y 80 (144)
||. +|||||+|++|+++||.|||++|||++|+|+|+||||.+||+||+||||||+|||||+||||+++++|||.|+++|
T Consensus 1 m~g-vtVkdV~~~~f~~a~asfLK~sgkv~vp~~~DivKtg~~kElAP~D~dWfytRaASiaRhiylR~~~gvg~~~KiY 79 (143)
T KOG3411|consen 1 MPG-VTVKDVDPHKFTKAYASFLKRSGKVEVPQWVDIVKTGKGKELAPYDPDWYYTRAASIARHIYLRGPVGVGALTKIY 79 (143)
T ss_pred CCc-cchhhcCHHHHHHHHHHHHHhcCCccCcchhhhhhcccCcccCCCCccHHHHHHHHHHHHHHhccccchhHHHHHh
Confidence 774 8999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhhc
Q 032244 81 GGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAVV 142 (144)
Q Consensus 81 Gg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~~ 142 (144)
||+||||++|+||+.+||+|+|++||+||++||||++++|||+||++||++||+||++|.+.
T Consensus 80 Gg~krrGvrPsh~~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~ 141 (143)
T KOG3411|consen 80 GGSKRRGVRPSHFCDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE 141 (143)
T ss_pred cccccCCCCChhhhccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999764
No 5
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.5e-71 Score=424.85 Aligned_cols=137 Identities=44% Similarity=0.768 Sum_probs=135.0
Q ss_pred CCceeccCchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCC
Q 032244 4 AKNVKDVSPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGG 83 (144)
Q Consensus 4 ~~tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~ 83 (144)
|+||||||+|+||+++|++||++++|++|+|++|||||+|||+||+|+||||+||||||||||++||+||++|++.|||+
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 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhh
Q 032244 84 KRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 84 k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~ 141 (144)
|+||++|+||++|||+|+|++|||||++|||++++ +||+|||+||++||+||.+|++
T Consensus 81 k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ei~e 137 (147)
T COG2238 81 KNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIATEIKE 137 (147)
T ss_pred ccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHHHHHH
Confidence 99999999999999999999999999999999999 5999999999999999999975
No 6
>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=97.49 E-value=0.00024 Score=50.52 Aligned_cols=57 Identities=23% Similarity=0.440 Sum_probs=47.1
Q ss_pred HHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCceeCcchHhhHHH
Q 032244 64 KIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 64 klYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR~lT~~G~~~lD~ 134 (144)
..|++ .|||=..+....+ -|..-||+.++.||++|||++. +.+||+-|.+|-+.+++
T Consensus 15 ~~Y~~~~~PVgSk~ia~~l~--------------~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~ 75 (78)
T PF03444_consen 15 ELYIETGEPVGSKTIAEELG--------------RSPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR 75 (78)
T ss_pred HHHHhcCCCcCHHHHHHHHC--------------CChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence 45775 5999999998764 1346899999999999999964 47899999999998864
No 7
>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=97.43 E-value=0.00029 Score=47.78 Aligned_cols=63 Identities=21% Similarity=0.243 Sum_probs=51.3
Q ss_pred HHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244 61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDL 132 (144)
Q Consensus 61 ilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l 132 (144)
||+.|+-. +|+|=..|+....-. | ..-|-.-+|.-|..||..||+++...+||.||++|...|
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 78888875 689999999988632 2 233456799999999999999988778999999998764
No 8
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=97.04 E-value=0.002 Score=44.40 Aligned_cols=62 Identities=18% Similarity=0.305 Sum_probs=44.5
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+.||.-+- .++.+..++.. .+.=|-+.+...|+.|++.|+|++ .++.-.||++|...|+.+-
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~lTekG~~~l~~l~ 70 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKK-KDGKYRLTEKGKEFLEELE 70 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEE-ETTEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeC-CCCEEEECccHHHHHHHHH
Confidence 34555444 67777777764 556778899999999999999977 4458999999999999883
No 9
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=96.85 E-value=0.0024 Score=47.33 Aligned_cols=68 Identities=22% Similarity=0.320 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
|--+||..+.=.+|+|+..|+..-| .|.|. +|+.|.-||..+++.-+.. |-.+|+.+-.++++|.
T Consensus 15 RHl~Vl~~v~eeqPiGI~klS~~TG-------mp~HK-------VRYSLRVLEq~~iI~PS~~-GAi~td~~~e~ie~i~ 79 (101)
T COG3388 15 RHLSVLKVVLEEQPIGIIKLSDETG-------MPEHK-------VRYSLRVLEQENIISPSRQ-GAILTDDFPEFIEEII 79 (101)
T ss_pred HHHHHHHHHHHhCCceeEeechhcC-------Cchhh-------hhhhhhhhhhcCccCcccc-CCccCccHHHHHHHHH
Confidence 5556676667789999999999999 67664 7899999999999987776 9999999999998887
Q ss_pred HHH
Q 032244 137 GRI 139 (144)
Q Consensus 137 ~~i 139 (144)
+++
T Consensus 80 ~dl 82 (101)
T COG3388 80 GDL 82 (101)
T ss_pred HHH
Confidence 765
No 10
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=96.79 E-value=0.003 Score=55.26 Aligned_cols=63 Identities=27% Similarity=0.379 Sum_probs=51.6
Q ss_pred HHHHHHHHH---HHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHh
Q 032244 57 RAASMARKI---YLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQR 130 (144)
Q Consensus 57 RaASilRkl---Yl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~ 130 (144)
|...|||.| |+. .|||=..|.+.|+ -.-|.+-||+.+++||++||++|.. .+||+-|+.|-+
T Consensus 7 Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~------------l~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr 74 (346)
T COG1420 7 RQRLILRAIVEDYLATGEPVGSKTLSEKYN------------LDLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYR 74 (346)
T ss_pred HHHHHHHHHHHHHHhcCCccchHHHHHHhC------------CCCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHH
Confidence 556677654 775 5999999999886 2346788999999999999999876 569999999976
Q ss_pred h
Q 032244 131 D 131 (144)
Q Consensus 131 ~ 131 (144)
.
T Consensus 75 ~ 75 (346)
T COG1420 75 Y 75 (346)
T ss_pred H
Confidence 4
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=96.72 E-value=0.011 Score=42.71 Aligned_cols=65 Identities=15% Similarity=0.172 Sum_probs=52.2
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~ 134 (144)
||..|+-.+++.+..|.+..|-.+ +-+-.+++.||+.|||++.+ .+.| .||++|++.+++
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 677778889999999999887433 35678999999999999765 3345 699999999998
Q ss_pred HHHHH
Q 032244 135 VAGRI 139 (144)
Q Consensus 135 iA~~i 139 (144)
+....
T Consensus 99 ~~~~~ 103 (118)
T TIGR02337 99 LSPQI 103 (118)
T ss_pred hhHHH
Confidence 87654
No 12
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.49 E-value=0.017 Score=43.07 Aligned_cols=63 Identities=14% Similarity=0.143 Sum_probs=50.5
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD~ 134 (144)
||..|+-.+++....|+...|-.+ +-+=.+++.||+.|||++.+ .++| .||++|+..+++
T Consensus 45 vL~~l~~~~~~t~~eLa~~l~i~~--------------~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~ 110 (144)
T PRK11512 45 VLCSIRCAACITPVELKKVLSVDL--------------GALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQ 110 (144)
T ss_pred HHHHHHHcCCCCHHHHHHHHCCCH--------------HHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHH
Confidence 677788888999999999887533 45777899999999999765 4455 589999999888
Q ss_pred HHH
Q 032244 135 VAG 137 (144)
Q Consensus 135 iA~ 137 (144)
+..
T Consensus 111 ~~~ 113 (144)
T PRK11512 111 CHQ 113 (144)
T ss_pred HHH
Confidence 643
No 13
>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=96.48 E-value=0.0069 Score=48.06 Aligned_cols=60 Identities=17% Similarity=0.316 Sum_probs=49.5
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhh
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGGR-----RITSSGQRD 131 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gGR-----~lT~~G~~~ 131 (144)
+||.-|.-.+++.+..|....|- +..-+|..|+.||+.|||+... ..|| .||++|+..
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgi--------------s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~ 70 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAI--------------SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ 70 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence 57877877899999999998874 3468999999999999998763 2478 999999876
Q ss_pred HH
Q 032244 132 LD 133 (144)
Q Consensus 132 lD 133 (144)
+.
T Consensus 71 ~~ 72 (203)
T TIGR02702 71 FP 72 (203)
T ss_pred cc
Confidence 54
No 14
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.44 E-value=0.02 Score=43.96 Aligned_cols=63 Identities=17% Similarity=0.194 Sum_probs=52.2
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
|++.++-.+++.+..|...+|- |.+-+..+|++||+.|||...+.+|-.||++|+..+..+..
T Consensus 42 I~~~l~~~~~~t~~eLA~~l~i--------------s~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~ 104 (152)
T PRK11050 42 IADLIAEVGEARQVDIAARLGV--------------SQPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE 104 (152)
T ss_pred HHHHHHhcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence 5556666788999999998874 34689999999999999998876689999999999777654
No 15
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.41 E-value=0.017 Score=35.54 Aligned_cols=59 Identities=24% Similarity=0.329 Sum_probs=44.1
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC---CceeCc-chHhhHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---GRRITS-SGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~-~G~~~lD~ 134 (144)
|++.|+ .+++.+..+...+|- |.+-++.+|++|++.|+|+...++ ...+|. .|...++.
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 567777 889999999999872 445799999999999999976642 234666 55555543
No 16
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.31 E-value=0.0093 Score=41.17 Aligned_cols=42 Identities=19% Similarity=0.378 Sum_probs=36.4
Q ss_pred chhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q 032244 97 SGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGR 138 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~ 138 (144)
|.+-++.+|+.||+.|||++.+.++-.||+.|+...+.+...
T Consensus 12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~ 53 (96)
T smart00529 12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRK 53 (96)
T ss_pred ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHH
Confidence 456899999999999999999877999999999988776543
No 17
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.28 E-value=0.035 Score=37.41 Aligned_cols=65 Identities=18% Similarity=0.280 Sum_probs=51.7
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC------CceeCcchHhhHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG------GRRITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g------GR~lT~~G~~~lD~ 134 (144)
||..|+..+++.+..+....+-. ..-|..+|+.|++.|||+...++ .-.||++|.+.+..
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 67778888999999999876522 23478999999999999876542 35699999999988
Q ss_pred HHHHH
Q 032244 135 VAGRI 139 (144)
Q Consensus 135 iA~~i 139 (144)
+...+
T Consensus 81 ~~~~~ 85 (101)
T smart00347 81 LLEAR 85 (101)
T ss_pred HHHHH
Confidence 77665
No 18
>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=96.25 E-value=0.011 Score=38.26 Aligned_cols=54 Identities=22% Similarity=0.399 Sum_probs=39.5
Q ss_pred HHHHHH-HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcch
Q 032244 61 MARKIY-LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSG 128 (144)
Q Consensus 61 ilRklY-l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G 128 (144)
||+.|+ -.++.....|+...+- +..-+..++++|++.|||++.+ .++| .||++|
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~--------------~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGI--------------SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHccCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 688888 7789999999998774 3346779999999999998664 3365 578877
No 19
>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=96.11 E-value=0.017 Score=40.49 Aligned_cols=65 Identities=17% Similarity=0.260 Sum_probs=49.8
Q ss_pred HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC------CceeCcchHhh
Q 032244 58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG------GRRITSSGQRD 131 (144)
Q Consensus 58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g------GR~lT~~G~~~ 131 (144)
+..||+.|.. |+...+.|.+.- ...|.+++-.-|+.||+.|+|++.... -..||+.|+++
T Consensus 7 ~~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l 72 (90)
T PF01638_consen 7 TLLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKEL 72 (90)
T ss_dssp HHHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHH
T ss_pred HHHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHH
Confidence 3568888888 888888888743 246788999999999999999986422 27899999998
Q ss_pred HHHHH
Q 032244 132 LDQVA 136 (144)
Q Consensus 132 lD~iA 136 (144)
+.-+.
T Consensus 73 ~~~l~ 77 (90)
T PF01638_consen 73 LPVLE 77 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 86554
No 20
>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=96.10 E-value=0.0057 Score=43.32 Aligned_cols=68 Identities=19% Similarity=0.224 Sum_probs=43.0
Q ss_pred chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRD 131 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~ 131 (144)
|+.-.|.-..|..-|-.||+|+..|+..-|-.+. .|.=.+===|-+.|+|+++++ ||++|++|.+-
T Consensus 7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~-------------Tie~v~EPyLiq~G~I~RT~r-GR~~T~~a~~~ 72 (76)
T PF05491_consen 7 DELDRRYLKTLIENFKGGPVGLDTLAAALGEDKE-------------TIEDVIEPYLIQIGFIQRTPR-GRVATPKAYEH 72 (76)
T ss_dssp BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HH-------------HHHHTTHHHHHHTTSEEEETT-EEEE-HHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHh-------------HHHHHhhHHHHHhhhHhhCcc-HHHhHHHHHHH
Confidence 3444455555666677899999999987774332 111111123456899999998 99999999876
Q ss_pred HH
Q 032244 132 LD 133 (144)
Q Consensus 132 lD 133 (144)
|.
T Consensus 73 l~ 74 (76)
T PF05491_consen 73 LG 74 (76)
T ss_dssp TT
T ss_pred hC
Confidence 53
No 21
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=96.02 E-value=0.018 Score=49.07 Aligned_cols=63 Identities=19% Similarity=0.343 Sum_probs=49.7
Q ss_pred HHHHHHHH---HHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHh
Q 032244 57 RAASMARK---IYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQR 130 (144)
Q Consensus 57 RaASilRk---lYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~ 130 (144)
|.-.||+. -|+. .|||-..|.+.|+- .-|.+-||+.++.||++|++++.. .+||+-|.+|-+
T Consensus 4 R~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr 71 (260)
T PRK03911 4 KKDLLLDSIIQTYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMK 71 (260)
T ss_pred HHHHHHHHHHHHHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHH
Confidence 34445554 4775 59999999998872 346678999999999999999765 569999999986
Q ss_pred h
Q 032244 131 D 131 (144)
Q Consensus 131 ~ 131 (144)
.
T Consensus 72 ~ 72 (260)
T PRK03911 72 N 72 (260)
T ss_pred H
Confidence 3
No 22
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=95.95 E-value=0.043 Score=37.84 Aligned_cols=65 Identities=26% Similarity=0.392 Sum_probs=50.5
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhH
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDL 132 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~l 132 (144)
..+|..||..++.+.+.|....+- +.+-+=.+++.||+.|||+... .++| .||++|+..+
T Consensus 25 ~~~L~~l~~~~~~~~~~la~~l~i--------------~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~ 90 (126)
T COG1846 25 YQVLLALYEAGGITVKELAERLGL--------------DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELL 90 (126)
T ss_pred HHHHHHHHHhCCCcHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHH
Confidence 457888888888776778876663 3356778899999999998665 4455 7999999999
Q ss_pred HHHHH
Q 032244 133 DQVAG 137 (144)
Q Consensus 133 D~iA~ 137 (144)
.++..
T Consensus 91 ~~~~~ 95 (126)
T COG1846 91 EQLLP 95 (126)
T ss_pred HHhcc
Confidence 88755
No 23
>PRK10870 transcriptional repressor MprA; Provisional
Probab=95.88 E-value=0.042 Score=43.01 Aligned_cols=64 Identities=17% Similarity=0.178 Sum_probs=49.5
Q ss_pred HHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCce----eCcchHhhH
Q 032244 61 MARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRR----ITSSGQRDL 132 (144)
Q Consensus 61 ilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~----lT~~G~~~l 132 (144)
||..|+-. +++.+..|+...|-. .+-+=.+++.||+.|||++.+ .++|. ||++|+..+
T Consensus 60 iL~~L~~~~~~~it~~eLa~~l~l~--------------~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~ 125 (176)
T PRK10870 60 ALITLESQENHSIQPSELSCALGSS--------------RTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFL 125 (176)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence 57777753 467778999988743 246677899999999999764 45777 999999999
Q ss_pred HHHHHH
Q 032244 133 DQVAGR 138 (144)
Q Consensus 133 D~iA~~ 138 (144)
+++-..
T Consensus 126 ~~i~~~ 131 (176)
T PRK10870 126 REVLPP 131 (176)
T ss_pred HHHHHH
Confidence 998544
No 24
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.76 E-value=0.055 Score=36.75 Aligned_cols=60 Identities=27% Similarity=0.362 Sum_probs=49.0
Q ss_pred HHHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchH
Q 032244 56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQ 129 (144)
Q Consensus 56 ~RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~ 129 (144)
-|+-.|+..|.-. +++++..+....|- +.+-++..|+.||+.|+|++++ ++...|++...
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 3788899988887 79999999998863 4578999999999999999875 44567777543
No 25
>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=95.65 E-value=0.062 Score=38.70 Aligned_cols=66 Identities=12% Similarity=0.142 Sum_probs=51.6
Q ss_pred HHHHHH----HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHh
Q 032244 61 MARKIY----LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQR 130 (144)
Q Consensus 61 ilRklY----l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~ 130 (144)
||..|+ -.+++....|+...+-. .+-+=.++..||+.|||++.+ ++.| .||++|++
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~~--------------~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~ 95 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILIK--------------QSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS 95 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence 677777 34789999999977732 245777899999999999765 4355 39999999
Q ss_pred hHHHHHHHHh
Q 032244 131 DLDQVAGRIA 140 (144)
Q Consensus 131 ~lD~iA~~i~ 140 (144)
.++.+..++-
T Consensus 96 ~~~~~~~~~~ 105 (109)
T TIGR01889 96 KIESLISEIE 105 (109)
T ss_pred HHHHHHHHHH
Confidence 9999988764
No 26
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=95.63 E-value=0.077 Score=39.33 Aligned_cols=65 Identities=15% Similarity=0.173 Sum_probs=48.7
Q ss_pred HHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCc----eeCcchHhhHH
Q 032244 61 MARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGR----RITSSGQRDLD 133 (144)
Q Consensus 61 ilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR----~lT~~G~~~lD 133 (144)
+|..|+-. +++....|+...|-.+ +-+=.+++.||+.|||++.+ .+.| .||++|+..++
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 56667754 4578889998877433 34668999999999999765 4455 49999999998
Q ss_pred HHHHHH
Q 032244 134 QVAGRI 139 (144)
Q Consensus 134 ~iA~~i 139 (144)
.+....
T Consensus 102 ~~~~~~ 107 (144)
T PRK03573 102 EVEAVI 107 (144)
T ss_pred HHHHHH
Confidence 866543
No 27
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=95.55 E-value=0.07 Score=42.83 Aligned_cols=65 Identities=14% Similarity=0.152 Sum_probs=49.9
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGR----RITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR----~lT~~G~~~lD~ 134 (144)
||-.||-.+++....|++..+-. .+-+=.+++.||+.|||++. +++.| .||++|++.+++
T Consensus 50 iL~~L~~~~~itq~eLa~~l~l~--------------~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~ 115 (185)
T PRK13777 50 ILWIAYHLKGASISEIAKFGVMH--------------VSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLE 115 (185)
T ss_pred HHHHHHhCCCcCHHHHHHHHCCC--------------HhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 67778888999999999965532 13366699999999999965 44455 399999999998
Q ss_pred HHHHH
Q 032244 135 VAGRI 139 (144)
Q Consensus 135 iA~~i 139 (144)
+...+
T Consensus 116 l~~~~ 120 (185)
T PRK13777 116 TMEEY 120 (185)
T ss_pred HHHHH
Confidence 86543
No 28
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.12 E-value=0.094 Score=39.26 Aligned_cols=61 Identities=13% Similarity=0.144 Sum_probs=45.8
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
|.+.+.-.|++-+..|+...|- |.+-++..|+.||+.|||.....+|=.||++|+.....+
T Consensus 13 I~~l~~~~~~~~~~ela~~l~v--------------s~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSV--------------HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCC--------------ChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence 3333444577888888886663 335678889999999999976656899999998876655
No 29
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.96 E-value=0.09 Score=36.58 Aligned_cols=65 Identities=12% Similarity=0.318 Sum_probs=46.5
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCC-----ceeCcchHhhHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGG-----RRITSSGQRDLD 133 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gG-----R~lT~~G~~~lD 133 (144)
|+=-|+-.+.+-...|+..-| -+.+-+.+-|+.||++|+|+..+ .++ -.||++|++.+.
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 444455567777788887554 46678999999999999998654 333 269999999998
Q ss_pred HHHHHH
Q 032244 134 QVAGRI 139 (144)
Q Consensus 134 ~iA~~i 139 (144)
+.-..+
T Consensus 71 ~~~~~L 76 (80)
T PF13601_consen 71 RYVAAL 76 (80)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 876654
No 30
>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=94.81 E-value=0.067 Score=38.23 Aligned_cols=47 Identities=19% Similarity=0.309 Sum_probs=35.8
Q ss_pred CCCCchhhHHHHHHHHHhCCcceec--C-CCCc-----eeCcchHhhHHHHHHHH
Q 032244 93 FSKSSGSVARHILHQLQDTNIIELD--S-KGGR-----RITSSGQRDLDQVAGRI 139 (144)
Q Consensus 93 ~~~asg~iiR~~LqqLE~~glv~k~--~-~gGR-----~lT~~G~~~lD~iA~~i 139 (144)
+..-+-+-+-.+|..||+.|||+.. + .+|| .||++|+..|+......
T Consensus 34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~ 88 (100)
T TIGR03433 34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW 88 (100)
T ss_pred ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 3444556688999999999999973 2 2232 59999999999987765
No 31
>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=94.78 E-value=0.079 Score=45.85 Aligned_cols=52 Identities=25% Similarity=0.275 Sum_probs=44.1
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC-CceeCcchHhh
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG-GRRITSSGQRD 131 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g-GR~lT~~G~~~ 131 (144)
.+|+|+..|.+.|+- .-|..-||+-|.+||+.|++++...+ ||.-|.+|-+.
T Consensus 19 ~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~ 71 (337)
T TIGR00331 19 GQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRY 71 (337)
T ss_pred CCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHH
Confidence 589999999998762 34567899999999999999987644 99999998776
No 32
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=94.77 E-value=0.035 Score=39.09 Aligned_cols=35 Identities=29% Similarity=0.388 Sum_probs=31.4
Q ss_pred hhHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q 032244 99 SVARHILHQLQDTNIIELDSKGGRRITSSGQRDLD 133 (144)
Q Consensus 99 ~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD 133 (144)
+-|+++++-|.++|+|++..+|--.||++|++.|-
T Consensus 55 ~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 55 NRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA 89 (92)
T ss_pred HhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence 46899999999999999888877999999999874
No 33
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=94.70 E-value=0.086 Score=45.65 Aligned_cols=63 Identities=24% Similarity=0.376 Sum_probs=48.3
Q ss_pred HHHHHHH---HHHH--hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHh
Q 032244 57 RAASMAR---KIYL--RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQR 130 (144)
Q Consensus 57 RaASilR---klYl--~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~ 130 (144)
|--.||. ..|+ .+|+|...|.+.|+- .-|..-||+-+..||++|++++.. ..||.-|.+|-+
T Consensus 7 R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR 74 (339)
T PRK00082 7 RQREILRAIVEDYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYR 74 (339)
T ss_pred HHHHHHHHHHHHHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHH
Confidence 3344554 2456 479999999987652 235678999999999999999765 459999999976
Q ss_pred h
Q 032244 131 D 131 (144)
Q Consensus 131 ~ 131 (144)
.
T Consensus 75 ~ 75 (339)
T PRK00082 75 Y 75 (339)
T ss_pred H
Confidence 4
No 34
>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=94.66 E-value=0.072 Score=33.68 Aligned_cols=49 Identities=22% Similarity=0.300 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 56 ~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
-|+.+||+.|.-.+ ++++..+...-|- +.+-+..+|+.|++.|||++++
T Consensus 3 ~ral~iL~~l~~~~~~~t~~eia~~~gl--------------~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 3 ERALRILEALAESGGPLTLSEIARALGL--------------PKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHHCHHCTBSCEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCcCeecCc
Confidence 48899999888865 5799999998884 3468999999999999999875
No 35
>PRK05638 threonine synthase; Validated
Probab=94.63 E-value=0.24 Score=43.88 Aligned_cols=93 Identities=19% Similarity=0.209 Sum_probs=62.3
Q ss_pred HcCCCCCCCcchhcccCCC--------ccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCC
Q 032244 25 RSGKIELPTWNDIVKTGTL--------KELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKS 96 (144)
Q Consensus 25 ~~gki~~P~w~d~vKTg~~--------kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~a 96 (144)
++|.|..-+=+=++=||.+ ||.-..++-+. .||+.|. +++.-+..|.+..+. .-
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 4444444344444555554 33334455433 3666555 678999999998883 13
Q ss_pred chhhHHHHHHHHHhCCcceecCCCCce----eCcchHhhHHHH
Q 032244 97 SGSVARHILHQLQDTNIIELDSKGGRR----ITSSGQRDLDQV 135 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~~gGR~----lT~~G~~~lD~i 135 (144)
|...++..|+.||++|||+...+.||+ ||++|+..+..+
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 677999999999999999864222444 999999998764
No 36
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=94.40 E-value=0.063 Score=39.47 Aligned_cols=43 Identities=19% Similarity=0.271 Sum_probs=34.7
Q ss_pred CCCchhhHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHHH
Q 032244 94 SKSSGSVARHILHQLQDTNIIELDSKG---GRRITSSGQRDLDQVA 136 (144)
Q Consensus 94 ~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~~G~~~lD~iA 136 (144)
+.=+=.+++++++.|++.|++++.+.+ .-.||++|.++|.++-
T Consensus 41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence 344557999999999999988888764 3579999999987653
No 37
>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=94.08 E-value=0.13 Score=33.32 Aligned_cols=48 Identities=25% Similarity=0.390 Sum_probs=40.4
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
.|++.|-..+|..++.|....|- +-+-+.+=|+.||++|||+.... ||
T Consensus 14 ~Il~~L~~~~~~t~~ela~~l~~--------------~~~t~s~hL~~L~~aGli~~~~~-gr 61 (61)
T PF12840_consen 14 RILRLLASNGPMTVSELAEELGI--------------SQSTVSYHLKKLEEAGLIEVERE-GR 61 (61)
T ss_dssp HHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEEE-TT
T ss_pred HHHHHHhcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEecc-CC
Confidence 58888888999999999999983 44679999999999999998775 44
No 38
>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=93.88 E-value=0.13 Score=35.29 Aligned_cols=46 Identities=26% Similarity=0.364 Sum_probs=36.0
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchH
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQ 129 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~ 129 (144)
++.+..++..+|- |-..+|++|++|++.|+|+..+ .||-.|+..-.
T Consensus 25 ~~s~~eiA~~~~i--------------~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 25 PVSSKEIAERLGI--------------SPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPE 72 (83)
T ss_dssp -BEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CC
T ss_pred CCCHHHHHHHHCc--------------CHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHH
Confidence 4899999998874 4469999999999999999664 57888876543
No 39
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=93.88 E-value=0.059 Score=46.97 Aligned_cols=65 Identities=20% Similarity=0.277 Sum_probs=50.4
Q ss_pred HHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q 032244 61 MARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
|||=|.-.+ |+|-+.....-- +||+. =+---+|+=||-||+.||++|+--.||.||.+|-+.|.+
T Consensus 11 Il~il~esd~plgak~Ia~el~---kRGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~ 76 (325)
T COG1693 11 ILRILAESDEPLGAKIIALELR---KRGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKR 76 (325)
T ss_pred HHHHHHhcCCccchHHHHHHHH---hcccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhh
Confidence 566555554 888877766554 23432 233468999999999999999998899999999999998
No 40
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=93.78 E-value=0.12 Score=37.41 Aligned_cols=47 Identities=28% Similarity=0.344 Sum_probs=38.2
Q ss_pred CCCCCCCCchhhHHHHHHHHHhCCcceecCCC---C------ceeCcchHhhHHHH
Q 032244 89 RPPHFSKSSGSVARHILHQLQDTNIIELDSKG---G------RRITSSGQRDLDQV 135 (144)
Q Consensus 89 ~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---G------R~lT~~G~~~lD~i 135 (144)
....+..-+-.-|-+-+++|+++|||+..... | ..||.+|..+||.|
T Consensus 25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~I 80 (102)
T PF10711_consen 25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAI 80 (102)
T ss_pred chhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHh
Confidence 44556667777999999999999999976632 2 48999999999986
No 41
>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=93.54 E-value=0.11 Score=40.44 Aligned_cols=65 Identities=14% Similarity=0.242 Sum_probs=48.4
Q ss_pred HHHHHHHHHHHhCC------CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244 57 RAASMARKIYLRGG------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR 130 (144)
Q Consensus 57 RaASilRklYl~g~------~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~ 130 (144)
.++..||..-+.|. +.-..|+..|| -|.+-+|.+|+.||..|||+..+..|-.+++-...
T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lg--------------VSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~ 80 (212)
T TIGR03338 15 LVQDEIERAILSGELPPGAKLNESDIAARLG--------------VSRGPVREAFRALEEAGLVRNEKNRGVFVREISLA 80 (212)
T ss_pred HHHHHHHHHHHcCCCCCCCEecHHHHHHHhC--------------CChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence 34445555555543 44567888888 36679999999999999999998889888887776
Q ss_pred hHHHH
Q 032244 131 DLDQV 135 (144)
Q Consensus 131 ~lD~i 135 (144)
++..+
T Consensus 81 ~~~ei 85 (212)
T TIGR03338 81 EADEI 85 (212)
T ss_pred HHHHH
Confidence 66543
No 42
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=93.52 E-value=0.15 Score=39.84 Aligned_cols=54 Identities=17% Similarity=0.295 Sum_probs=43.3
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
.|++.++.++..-+= |.+-+-..|+.|++.|||+..+.+|-.||++|.+..-++
T Consensus 22 ~~~~~~~diA~~L~V--------------sp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~ 75 (154)
T COG1321 22 KGFARTKDIAERLKV--------------SPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKEL 75 (154)
T ss_pred cCcccHHHHHHHhCC--------------CcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHH
Confidence 467888888886652 234677889999999999999999999999999654443
No 43
>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=93.38 E-value=0.46 Score=34.83 Aligned_cols=68 Identities=13% Similarity=0.193 Sum_probs=49.6
Q ss_pred HHHHHHHHHHh--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcch-HhhH
Q 032244 58 AASMARKIYLR--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSG-QRDL 132 (144)
Q Consensus 58 aASilRklYl~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G-~~~l 132 (144)
|-.+|..|... +++.+..|+..+|- |.+.++++|+.|++.|+|+... .||..|.... +-.+
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~i--------------s~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~ 76 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTGL--------------NAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITV 76 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCH
Confidence 44566666554 46899999998874 5579999999999999998653 5687887665 3346
Q ss_pred HHHHHHH
Q 032244 133 DQVAGRI 139 (144)
Q Consensus 133 D~iA~~i 139 (144)
.+|...|
T Consensus 77 ~~v~~~l 83 (130)
T TIGR02944 77 ADIVKAV 83 (130)
T ss_pred HHHHHHH
Confidence 6666555
No 44
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=93.25 E-value=0.19 Score=38.92 Aligned_cols=44 Identities=23% Similarity=0.338 Sum_probs=33.9
Q ss_pred CchhhHHHHHHHHHhCCcceec---CCCCc-----eeCcchHhhHHHHHHHH
Q 032244 96 SSGSVARHILHQLQDTNIIELD---SKGGR-----RITSSGQRDLDQVAGRI 139 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~---~~gGR-----~lT~~G~~~lD~iA~~i 139 (144)
.+-+-+=.+|+.||+.|||+.. ..+|| .||+.|++.|+....++
T Consensus 55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w 106 (138)
T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF 106 (138)
T ss_pred CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence 4456678899999999999863 23354 49999999988877664
No 45
>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=93.12 E-value=0.46 Score=29.60 Aligned_cols=62 Identities=19% Similarity=0.209 Sum_probs=46.6
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHH
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSGQRDLDQVA 136 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G~~~lD~iA 136 (144)
.|+..++-.+ +....+.+..|- +.+-++.+|.+|++.|++..... .-..+|+ |+..++.+.
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 3566666555 999999997763 34678999999999999986543 2457898 888888765
Q ss_pred H
Q 032244 137 G 137 (144)
Q Consensus 137 ~ 137 (144)
.
T Consensus 75 ~ 75 (78)
T cd00090 75 S 75 (78)
T ss_pred H
Confidence 3
No 46
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=93.09 E-value=0.36 Score=39.55 Aligned_cols=62 Identities=19% Similarity=0.249 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHHhC-CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCceeCcchHhh
Q 032244 56 IRAASMARKIYLRG-GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRRITSSGQRD 131 (144)
Q Consensus 56 ~RaASilRklYl~g-~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~lT~~G~~~ 131 (144)
-|+..||+.|.-.+ ++++..|.+..|- +.+-+..+|+.|++.|||++++ .+...||++..+.
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl--------------~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l 74 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGL--------------HRTTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHH
Confidence 38889999887654 5999999998874 3468999999999999999986 4467788876543
No 47
>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=93.06 E-value=0.36 Score=30.47 Aligned_cols=51 Identities=24% Similarity=0.402 Sum_probs=40.8
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCce
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRR 123 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~ 123 (144)
..+|..||-.+++.+..|....+- +.+-+-.++++||+.|||++.. ++.|.
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~--------------~~~~~t~~i~~L~~~g~I~r~~~~~D~R~ 58 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGI--------------SRSTVTRIIKRLEKKGLIERERDPDDRRQ 58 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEEETTETTS
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEeccCCCCCCc
Confidence 347888999999999999998874 4467888999999999998654 44553
No 48
>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=93.01 E-value=0.34 Score=38.40 Aligned_cols=55 Identities=18% Similarity=0.248 Sum_probs=44.5
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC--CceeCcch
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG--GRRITSSG 128 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g--GR~lT~~G 128 (144)
.||..|.-++++.+..+....|- |.+-+++.|+.||+.|||++..+. .-.||++|
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 57877777789999999998874 456889999999999999988622 34578876
No 49
>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=92.93 E-value=0.27 Score=31.11 Aligned_cols=46 Identities=15% Similarity=0.217 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCC--CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 59 ASMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 59 ASilRklYl~g~--~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
..||..|+-.++ +.++.|....|-. .+-+-.+++.||+.|||++.+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~--------------~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGIS--------------KSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEeC
Confidence 358999999998 9999999988843 357888999999999999775
No 50
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=92.79 E-value=0.37 Score=36.14 Aligned_cols=62 Identities=23% Similarity=0.347 Sum_probs=48.3
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC------CCCceeCcchHhhHHH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS------KGGRRITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~------~gGR~lT~~G~~~lD~ 134 (144)
||+++.- |+.--+.|++.-++ =|.+++=.-|+.||+.|+|++.. +-...||+.|++++.-
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 6777766 77777777776554 56678888899999999999775 2268899999998765
Q ss_pred HH
Q 032244 135 VA 136 (144)
Q Consensus 135 iA 136 (144)
+.
T Consensus 94 l~ 95 (120)
T COG1733 94 LL 95 (120)
T ss_pred HH
Confidence 54
No 51
>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=92.78 E-value=0.55 Score=30.59 Aligned_cols=39 Identities=26% Similarity=0.386 Sum_probs=31.0
Q ss_pred CC-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 70 GL-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 70 ~~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
.+ ....|...|| -|...+|.+|+.|++.|+|+..+..|-
T Consensus 23 ~lps~~~la~~~~--------------vsr~tvr~al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 23 RLPSERELAERYG--------------VSRTTVREALRRLEAEGLIERRPGRGT 62 (64)
T ss_dssp BE--HHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred EeCCHHHHHHHhc--------------cCCcHHHHHHHHHHHCCcEEEECCceE
Confidence 35 7788888888 466799999999999999998886553
No 52
>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=92.54 E-value=0.16 Score=31.87 Aligned_cols=39 Identities=18% Similarity=0.267 Sum_probs=31.4
Q ss_pred hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125 (144)
Q Consensus 73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT 125 (144)
+..|+..||- |..-++++|+.|++.|+|+..+..|-.||
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 7778887763 55799999999999999997775576665
No 53
>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=92.50 E-value=0.094 Score=35.24 Aligned_cols=42 Identities=31% Similarity=0.431 Sum_probs=32.9
Q ss_pred CCCCchhhHHHHHHHHHhCCcceecCC---CC-----ceeCcchHhhHHH
Q 032244 93 FSKSSGSVARHILHQLQDTNIIELDSK---GG-----RRITSSGQRDLDQ 134 (144)
Q Consensus 93 ~~~asg~iiR~~LqqLE~~glv~k~~~---gG-----R~lT~~G~~~lD~ 134 (144)
+..-|-+-|=.+|+.||+.|||+.... +| -.||++|+..|..
T Consensus 26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 456677889999999999999986542 22 4699999998763
No 54
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=92.47 E-value=0.33 Score=36.39 Aligned_cols=43 Identities=21% Similarity=0.339 Sum_probs=34.6
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCc
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITS 126 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~ 126 (144)
++.+..|+..+|- |...+|++|++|++.|||+..+ .||-.|+.
T Consensus 25 ~~s~~~ia~~~~i--------------s~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 25 MTSISEVTEVYGV--------------SRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred ccCHHHHHHHHCc--------------CHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 5778889998884 4569999999999999999776 34666654
No 55
>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=92.35 E-value=0.19 Score=42.49 Aligned_cols=61 Identities=18% Similarity=0.203 Sum_probs=46.6
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHHhh
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G~~~lD~iA~~i~~ 141 (144)
.+.++.|-..-+ ...=+...+|.+|.-|++.|||+.... ....||++|++.++..+.-|..
T Consensus 17 ~i~~~~Li~l~~-----------~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~ 80 (280)
T TIGR02277 17 AIWLGSLIEFLA-----------GLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD 80 (280)
T ss_pred ceeHHHHHHHHH-----------hcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC
Confidence 455566655554 223345689999999999999997654 3678999999999999888865
No 56
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=91.97 E-value=0.3 Score=37.38 Aligned_cols=38 Identities=21% Similarity=0.336 Sum_probs=32.8
Q ss_pred hhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244 98 GSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 98 g~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
-.-+.++.|.||..|+|+.....|..+|++|+..+|..
T Consensus 49 pnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~ 86 (125)
T COG1725 49 PNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQL 86 (125)
T ss_pred HHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHH
Confidence 35788999999999999988877999999999877654
No 57
>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=91.62 E-value=1.2 Score=28.16 Aligned_cols=44 Identities=16% Similarity=0.239 Sum_probs=33.8
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
+++....|....|- |.+-+..+|++|++.|+|+....++-.|+|
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 45677777777763 556889999999999999988755666654
No 58
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=91.58 E-value=1 Score=35.88 Aligned_cols=65 Identities=17% Similarity=0.288 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHhC------CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244 57 RAASMARKIYLRG------GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR 130 (144)
Q Consensus 57 RaASilRklYl~g------~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~ 130 (144)
.+...||.--+.| .+....|...||- |..-||.+|++|+..|||+..+..|-.+++-..+
T Consensus 20 ~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gv--------------SrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~ 85 (230)
T COG1802 20 QVYEELREAILSGELAPGERLSEEELAEELGV--------------SRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLA 85 (230)
T ss_pred HHHHHHHHHHHhCCCCCCCCccHHHHHHHhCC--------------CCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHH
Confidence 4445556555554 5788999999995 4468999999999999999999889999988888
Q ss_pred hHHHH
Q 032244 131 DLDQV 135 (144)
Q Consensus 131 ~lD~i 135 (144)
++..+
T Consensus 86 ~~~ei 90 (230)
T COG1802 86 EAREI 90 (230)
T ss_pred HHHHH
Confidence 87774
No 59
>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=91.39 E-value=1.2 Score=32.26 Aligned_cols=49 Identities=24% Similarity=0.312 Sum_probs=39.3
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceec--CCCCceeCcchHhh
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELD--SKGGRRITSSGQRD 131 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~--~~gGR~lT~~G~~~ 131 (144)
+++.+..|+..+|- +.+.+|++|+.|++.|||... ..||-.|+......
T Consensus 24 ~~~s~~eia~~~~i--------------~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~i 74 (132)
T TIGR00738 24 GPVSVKEIAERQGI--------------SRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI 74 (132)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHC
Confidence 38999999998774 457999999999999999864 35678888776544
No 60
>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=91.23 E-value=0.37 Score=38.30 Aligned_cols=42 Identities=10% Similarity=0.256 Sum_probs=35.8
Q ss_pred chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
.-..|+..|| -|..-+|-+|+.||..|||+..+..|-.+++-
T Consensus 32 sE~~La~~lg--------------VSRtpVREAL~~Le~eGlV~~~~~~G~~V~~~ 73 (235)
T TIGR02812 32 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNNF 73 (235)
T ss_pred CHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEeCCCccEecCc
Confidence 4667888888 46789999999999999999998778888773
No 61
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=91.16 E-value=0.35 Score=38.18 Aligned_cols=51 Identities=20% Similarity=0.289 Sum_probs=40.2
Q ss_pred CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244 71 LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 71 ~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
+....|+..||- |..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus 31 L~e~eLae~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~ei 81 (224)
T PRK11534 31 LRMSLLTSRYAL--------------GVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLDI 81 (224)
T ss_pred CCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHHHHH
Confidence 455688888883 557999999999999999999877888877666555443
No 62
>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=91.02 E-value=0.71 Score=29.96 Aligned_cols=48 Identities=17% Similarity=0.253 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
-..|+..|--++.+.+..|...||- |-.=||.=|+.||+.|+|.+.-.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~V--------------S~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGV--------------SEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcC
Confidence 3457888888999999999999984 55689999999999999998875
No 63
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=90.94 E-value=0.75 Score=33.46 Aligned_cols=44 Identities=18% Similarity=0.160 Sum_probs=37.7
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
||.|||--||--...+++.. ..+-.-++.+|..||++||||...
T Consensus 12 IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 12 ILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred HHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec
Confidence 89999999998888887754 455578999999999999999877
No 64
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.75 E-value=0.79 Score=30.76 Aligned_cols=45 Identities=11% Similarity=0.062 Sum_probs=38.3
Q ss_pred HHHHHHHHhCC--CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 60 SMARKIYLRGG--LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 60 SilRklYl~g~--~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
.||..|.-+|+ +....|.+..|=.+ +.++.+|..||+.|+|++..
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 47777777877 99999999988543 58999999999999999865
No 65
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=90.73 E-value=0.3 Score=30.08 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=29.1
Q ss_pred chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC
Q 032244 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG 121 (144)
Q Consensus 72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG 121 (144)
.+..|+..|| -|..-+|.+|++||+.|+|+..+.+|
T Consensus 22 s~~~la~~~~--------------vs~~tv~~~l~~L~~~g~i~~~~~~g 57 (60)
T smart00345 22 SERELAAQLG--------------VSRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCe
Confidence 6777788776 35679999999999999998776544
No 66
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=90.65 E-value=0.33 Score=39.01 Aligned_cols=45 Identities=22% Similarity=0.170 Sum_probs=36.9
Q ss_pred chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQR 130 (144)
Q Consensus 72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~ 130 (144)
.-..|+..|| -|..-+|.+|+.||..|||+..+..|-.+++-...
T Consensus 33 sE~eLa~~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~ 77 (251)
T PRK09990 33 SERRLCEKLG--------------FSRSALREGLTVLRGRGIIETAQGRGSFVARLNRV 77 (251)
T ss_pred CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence 4567888888 46789999999999999999998778777765543
No 67
>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=90.64 E-value=1.6 Score=32.23 Aligned_cols=70 Identities=17% Similarity=0.141 Sum_probs=53.9
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
.+++|+-++|-+.=+..+.++-.- +...+...+-+=++-|-+-|||||.-+ |-++|..|+..+-++|
T Consensus 17 ~~~~ilI~v~Kk~Fit~~ev~e~l------------~~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~~AA 83 (96)
T PF09114_consen 17 NAANILIQVAKKNFITASEVREAL------------ATEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIIIQAA 83 (96)
T ss_dssp HHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHccCCHHHHHHHH------------HHHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHHHHH
Confidence 578899888888888888888733 234455677777899999999999998 8999999999999887
Q ss_pred HHH
Q 032244 137 GRI 139 (144)
Q Consensus 137 ~~i 139 (144)
.--
T Consensus 84 ~l~ 86 (96)
T PF09114_consen 84 ELW 86 (96)
T ss_dssp HHH
T ss_pred HHH
Confidence 643
No 68
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=90.28 E-value=0.46 Score=37.53 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=37.8
Q ss_pred hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q 032244 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
...|+..||- |..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus 37 e~~La~~lgV--------------SRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei 85 (221)
T PRK11414 37 TKNLAEQLGM--------------SITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI 85 (221)
T ss_pred HHHHHHHHCC--------------CchhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence 3568888883 557899999999999999998877877766555555443
No 69
>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=90.22 E-value=0.84 Score=29.60 Aligned_cols=55 Identities=20% Similarity=0.386 Sum_probs=39.2
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchH
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQ 129 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~ 129 (144)
|+=.|=+..++-+..+...||.. --......|++|++.|||+.+.. .=+||++|+
T Consensus 11 i~~~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~~-~l~lT~~G~ 65 (66)
T PF06969_consen 11 IMLGLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDGG-RLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-SS-EEEE-TTTG
T ss_pred HHHHHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeCC-EEEECcccC
Confidence 34445556788999999999854 22355788999999999998774 778999996
No 70
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=90.13 E-value=0.93 Score=27.08 Aligned_cols=46 Identities=15% Similarity=0.248 Sum_probs=37.0
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
.|+..|.-++++.+..|...+|- |-.-+++.|+.|++.|+|+....
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~--------------s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGV--------------SEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeec
Confidence 36666666788999999999863 34568999999999999997664
No 71
>PRK03837 transcriptional regulator NanR; Provisional
Probab=90.12 E-value=2.3 Score=33.62 Aligned_cols=57 Identities=12% Similarity=0.292 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 57 RAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 57 RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
..+.-||.--+.|. + ....|+..|| -|...+|.+|+.||..|||+..+..|-.+++-
T Consensus 17 ~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~g--------------VSRt~VREAL~~L~~eGlv~~~~~~G~~V~~~ 80 (241)
T PRK03837 17 EVEERLEQMIRSGEFGPGDQLPSERELMAFFG--------------VGRPAVREALQALKRKGLVQISHGERARVSRP 80 (241)
T ss_pred HHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCCceeEecC
Confidence 34444454444542 4 4667899888 47789999999999999999888667666653
No 72
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=89.74 E-value=0.92 Score=36.93 Aligned_cols=58 Identities=7% Similarity=0.115 Sum_probs=46.4
Q ss_pred HHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-CCceeCcc
Q 032244 56 IRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-GGRRITSS 127 (144)
Q Consensus 56 ~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-gGR~lT~~ 127 (144)
-|+-.||..|.-.+++++..|.+.-|-. .+-+..+|+.|++.|||++++. +...|+++
T Consensus 14 ~r~l~IL~~l~~~~~l~l~eia~~lgl~--------------kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~~ 72 (257)
T PRK15090 14 LKVFGILQALGEEREIGITELSQRVMMS--------------KSTVYRFLQTMKTLGYVAQEGESEKYSLTLK 72 (257)
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence 4888999999877889999999977743 4689999999999999998863 43455543
No 73
>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=89.71 E-value=1.1 Score=33.32 Aligned_cols=46 Identities=15% Similarity=0.305 Sum_probs=36.6
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee--cCCCCceeCcch
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSKGGRRITSSG 128 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k--~~~gGR~lT~~G 128 (144)
+++.+..++..++ -+...++++|++|.++|||+. ...||-.|+..-
T Consensus 24 ~~~s~~~ia~~~~--------------ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~ 71 (135)
T TIGR02010 24 GPVTLADISERQG--------------ISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPA 71 (135)
T ss_pred CcCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCH
Confidence 4789999998776 455799999999999999985 346687887643
No 74
>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=89.67 E-value=1.4 Score=26.93 Aligned_cols=42 Identities=17% Similarity=0.206 Sum_probs=34.8
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~ 115 (144)
.||..|.-++++.+..++...|- |.+-+++.|++|++.|+|+
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 47777888899999999998884 5578999999999999986
No 75
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=89.22 E-value=1.4 Score=37.79 Aligned_cols=59 Identities=20% Similarity=0.331 Sum_probs=44.8
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
..++-...+...||.. -.......+++|++.||++.+.. .=+||++|+-.+|.|+.+++
T Consensus 316 ~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~~-~~~lt~~G~~~~~~i~~~~~ 374 (377)
T PRK08599 316 KSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDDD-HVRLTKKGKFLGNEVFEAFL 374 (377)
T ss_pred hCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEECC-EEEECccHhHHHHHHHHHHh
Confidence 4455566666666521 13456778899999999997654 67999999999999999875
No 76
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=88.85 E-value=2 Score=37.25 Aligned_cols=57 Identities=26% Similarity=0.387 Sum_probs=44.2
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
..++-...+...||-.- ....|+.|++.||++.+.++.=+||++|+-.+|.|+.+++
T Consensus 323 ~~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~ 379 (380)
T PRK09057 323 REGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA 379 (380)
T ss_pred hCCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence 35677788888888421 1257999999999986553246899999999999999876
No 77
>PRK11569 transcriptional repressor IclR; Provisional
Probab=88.43 E-value=1.4 Score=36.46 Aligned_cols=59 Identities=15% Similarity=0.196 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC-ceeCcc
Q 032244 55 YIRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG-RRITSS 127 (144)
Q Consensus 55 y~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG-R~lT~~ 127 (144)
--|+..||+.|-- .+++++..|.+.-|-.| +-+..+|+.|++.|||+++++.| ..|.+.
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 3599999999876 46899999999887543 68999999999999999887433 345443
No 78
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=88.07 E-value=1.5 Score=36.20 Aligned_cols=57 Identities=19% Similarity=0.144 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC-ceeCc
Q 032244 56 IRAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG-RRITS 126 (144)
Q Consensus 56 ~RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG-R~lT~ 126 (144)
-|+.+||+.|.-. +++++..+.+.-|-.| +-+..+|+.|+..|||++++..| ..|++
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglpk--------------Stv~RlL~tL~~~G~l~~~~~~~~Y~lG~ 83 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDLPL--------------STTFRLLKVLQAADFVYQDSQLGWWHIGL 83 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence 3888999998764 5799999999888544 67899999999999999987433 33443
No 79
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=88.02 E-value=0.72 Score=38.05 Aligned_cols=55 Identities=25% Similarity=0.204 Sum_probs=42.7
Q ss_pred CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHH
Q 032244 71 LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK---GGRRITSSGQRDLDQVAGRI 139 (144)
Q Consensus 71 ~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~---gGR~lT~~G~~~lD~iA~~i 139 (144)
+..+.|.+..|- |.+-+-..|++||+.|||++... .--.||++|+..+.+...+.
T Consensus 22 IS~~eLA~~L~i--------------S~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~ 79 (217)
T PRK14165 22 ISSSEFANHTGT--------------SSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADY 79 (217)
T ss_pred cCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHH
Confidence 446788886653 55678899999999999987652 23579999999998887664
No 80
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=87.97 E-value=1.6 Score=35.92 Aligned_cols=51 Identities=20% Similarity=0.254 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHhCCC--chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC
Q 032244 56 IRAASMARKIYLRGGL--GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG 121 (144)
Q Consensus 56 ~RaASilRklYl~g~~--Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG 121 (144)
.|+..||..|.- +|. ++..|.+.-|- +.+=++.+|+.|++.|||++++++|
T Consensus 4 ~ral~iL~~l~~-~~~~l~l~ela~~~gl--------------pksT~~RlL~tL~~~G~v~~d~~~g 56 (246)
T COG1414 4 ERALAILDLLAE-GPGGLSLAELAERLGL--------------PKSTVHRLLQTLVELGYVEQDPEDG 56 (246)
T ss_pred HHHHHHHHHHHh-CCCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHHCCCEEEcCCCC
Confidence 488899988887 444 59999998774 3467999999999999999999654
No 81
>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=87.92 E-value=1.9 Score=34.21 Aligned_cols=58 Identities=19% Similarity=0.216 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 55 YIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 55 y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
|..-+..||+-=..|.. +-..|+..||- |..-+|++|+.|+..|+|.+.+..|-.+++
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 55666666665555532 45678898884 667999999999999999999866766654
No 82
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=87.88 E-value=0.88 Score=36.58 Aligned_cols=41 Identities=15% Similarity=0.259 Sum_probs=33.9
Q ss_pred chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
.-..|+..|| -|...+|.+|+.||..|||+..+..|-.+++
T Consensus 36 sE~eLa~~lg--------------VSRtpVREAL~~L~~eGlv~~~~~~G~~V~~ 76 (254)
T PRK09464 36 PERELAKQFD--------------VSRPSLREAIQRLEAKGLLLRRQGGGTFVQS 76 (254)
T ss_pred CHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEEec
Confidence 4556888888 4678999999999999999988877866665
No 83
>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=87.87 E-value=0.7 Score=30.29 Aligned_cols=47 Identities=17% Similarity=0.193 Sum_probs=38.3
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
+.|+..|--+|+..+..+.+.-|- +.+-++.+|+.|++.|||++.+.
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i--------------~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGI--------------SRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTS--------------SHHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcC
Confidence 445656656899999999997764 45789999999999999998773
No 84
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=87.83 E-value=1.4 Score=33.95 Aligned_cols=60 Identities=27% Similarity=0.388 Sum_probs=47.4
Q ss_pred HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC---CCCc-----------eeCcchHhhH
Q 032244 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS---KGGR-----------RITSSGQRDL 132 (144)
Q Consensus 67 l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~---~gGR-----------~lT~~G~~~l 132 (144)
-+||.+|..|+..-+ =+.+-+=++||.|..+|+|++.+ ++|| .++....++|
T Consensus 39 ~~~~~tvdelae~ln--------------r~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l 104 (126)
T COG3355 39 ENGPLTVDELAEILN--------------RSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDL 104 (126)
T ss_pred hcCCcCHHHHHHHHC--------------ccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHH
Confidence 489999999999765 35678999999999999998665 4443 3567788888
Q ss_pred HHHHHHHh
Q 032244 133 DQVAGRIA 140 (144)
Q Consensus 133 D~iA~~i~ 140 (144)
|..|.++.
T Consensus 105 ~~w~~~~~ 112 (126)
T COG3355 105 DEWYDKMK 112 (126)
T ss_pred HHHHHHHH
Confidence 88887763
No 85
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=87.75 E-value=0.54 Score=37.96 Aligned_cols=41 Identities=20% Similarity=0.184 Sum_probs=34.5
Q ss_pred hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
-..|+..|| -|..-+|.+|+.||..|||+..+..|-.+++-
T Consensus 29 E~eLae~~g--------------VSRtpVREAL~~Le~~GlV~~~~~~G~~V~~~ 69 (253)
T PRK10421 29 ERQLAMQLG--------------VSRNSLREALAKLVSEGVLLSRRGGGTFIRWR 69 (253)
T ss_pred HHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence 457888888 46789999999999999999888778888764
No 86
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=87.72 E-value=0.61 Score=37.10 Aligned_cols=41 Identities=10% Similarity=0.285 Sum_probs=34.5
Q ss_pred chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
.-..|+..|| -|..-+|.+|+.||..|||+..+..|-.+++
T Consensus 33 sE~eLae~~g--------------VSRt~VReAL~~L~~eGlv~~~~g~G~~V~~ 73 (239)
T PRK04984 33 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNN 73 (239)
T ss_pred CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence 4557888888 4678999999999999999998877877765
No 87
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=87.57 E-value=0.53 Score=37.99 Aligned_cols=59 Identities=17% Similarity=0.259 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHhC------CC-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchH
Q 032244 57 RAASMARKIYLRG------GL-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQ 129 (144)
Q Consensus 57 RaASilRklYl~g------~~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~ 129 (144)
..+..||.--+.| .+ ....|+..||= |..-+|.+|+.||..|||+..+..|-.+++...
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 4445555555555 24 36689999983 668999999999999999998877877766543
No 88
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=87.20 E-value=0.84 Score=33.99 Aligned_cols=39 Identities=21% Similarity=0.353 Sum_probs=33.2
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
++.+..|+....+..| -.|.+|++|++.|||+-.+.-||
T Consensus 19 ~vtl~elA~~l~cS~R--------------n~r~lLkkm~~~gWi~W~pg~GR 57 (115)
T PF12793_consen 19 EVTLDELAELLFCSRR--------------NARTLLKKMQEEGWITWQPGRGR 57 (115)
T ss_pred ceeHHHHHHHhCCCHH--------------HHHHHHHHHHHCCCeeeeCCCCC
Confidence 5789999998887665 68999999999999999985565
No 89
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=86.85 E-value=1.1 Score=34.86 Aligned_cols=44 Identities=18% Similarity=0.335 Sum_probs=33.7
Q ss_pred CCchhhHHHHHHHHHhCCcceecCCC-C---ceeCcchHhhHHHHHHH
Q 032244 95 KSSGSVARHILHQLQDTNIIELDSKG-G---RRITSSGQRDLDQVAGR 138 (144)
Q Consensus 95 ~asg~iiR~~LqqLE~~glv~k~~~g-G---R~lT~~G~~~lD~iA~~ 138 (144)
..|-+-|=-+|+.||+.|||+....+ . -.||+.|+..|+....+
T Consensus 74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~ 121 (135)
T PRK09416 74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKN 121 (135)
T ss_pred cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhC
Confidence 33556677899999999999865432 2 36999999999987653
No 90
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=86.83 E-value=0.75 Score=35.43 Aligned_cols=46 Identities=24% Similarity=0.323 Sum_probs=37.4
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcchH
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSGQ 129 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~ 129 (144)
++.+..++..++- |...+++|||+|.++|||+... .||-.|+..-.
T Consensus 24 ~~s~~eIA~~~~i--------------s~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~ 71 (153)
T PRK11920 24 LSRIPEIARAYGV--------------SELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAA 71 (153)
T ss_pred cCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHH
Confidence 5778888887763 5579999999999999998665 67999987654
No 91
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=86.71 E-value=1.1 Score=33.17 Aligned_cols=44 Identities=25% Similarity=0.419 Sum_probs=32.9
Q ss_pred CchhhHHHHHHHHHhCCcceecC--CCC------ceeCcchHhhHHHHHHHH
Q 032244 96 SSGSVARHILHQLQDTNIIELDS--KGG------RRITSSGQRDLDQVAGRI 139 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~--~gG------R~lT~~G~~~lD~iA~~i 139 (144)
.|-+.|=-+|+.||+.|||+... .+| -.||++|+..|.+...+.
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~ 93 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEW 93 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 34445667999999999999652 222 379999999999876553
No 92
>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=86.64 E-value=2.8 Score=33.10 Aligned_cols=61 Identities=11% Similarity=0.211 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
-|..-+..|+.-=..|.. .-..|+..|| -|..-+|++|+.|+..|+|++.+..|-.+++
T Consensus 9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 74 (238)
T TIGR02325 9 LWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFG--------------VNRHTVRRAIAALVERGLLRAEQGRGTFVAA 74 (238)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEECC
Confidence 466777777666555533 3457888888 4667999999999999999998866877775
Q ss_pred ch
Q 032244 127 SG 128 (144)
Q Consensus 127 ~G 128 (144)
..
T Consensus 75 ~~ 76 (238)
T TIGR02325 75 RR 76 (238)
T ss_pred Cc
Confidence 43
No 93
>PF13814 Replic_Relax: Replication-relaxation
Probab=86.62 E-value=1.8 Score=33.00 Aligned_cols=62 Identities=21% Similarity=0.285 Sum_probs=46.9
Q ss_pred HHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC-----CC-----ceeCcchHhh
Q 032244 62 ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK-----GG-----RRITSSGQRD 131 (144)
Q Consensus 62 lRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~-----gG-----R~lT~~G~~~ 131 (144)
|+-||-.+-+....|...++...++ ..-+|..|++|++.|+|+.... +| -.||++|.+.
T Consensus 1 L~~L~~~r~lt~~Qi~~l~~~~~~~-----------~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~ 69 (191)
T PF13814_consen 1 LRLLARHRFLTTDQIARLLFPSSKS-----------ERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARL 69 (191)
T ss_pred ChhHHHhcCcCHHHHHHHHcCCCcc-----------hHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHH
Confidence 3556777788888898888854432 1279999999999999987653 13 3799999998
Q ss_pred HHH
Q 032244 132 LDQ 134 (144)
Q Consensus 132 lD~ 134 (144)
|..
T Consensus 70 l~~ 72 (191)
T PF13814_consen 70 LAD 72 (191)
T ss_pred HHh
Confidence 874
No 94
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=86.48 E-value=2.2 Score=33.39 Aligned_cols=46 Identities=15% Similarity=0.255 Sum_probs=37.5
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee--cCCCCceeCcch
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL--DSKGGRRITSSG 128 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k--~~~gGR~lT~~G 128 (144)
+++.+..++..+|- +...++++|++|.++|||+. .+.||-.|...-
T Consensus 24 ~~vs~~eIA~~~~i--------------p~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p 71 (164)
T PRK10857 24 GPVPLADISERQGI--------------SLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDA 71 (164)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCH
Confidence 47899999997774 55699999999999999985 456788887654
No 95
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=86.30 E-value=0.72 Score=37.22 Aligned_cols=41 Identities=17% Similarity=0.165 Sum_probs=33.6
Q ss_pred hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
-..|+..|| -|..-+|.+|+.||..|||+..+..|-.+++-
T Consensus 35 E~eLae~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~ 75 (253)
T PRK11523 35 ERFIADEKN--------------VSRTVVREAIIMLEVEGYVEVRKGSGIHVVSN 75 (253)
T ss_pred HHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCeeEEecC
Confidence 457888888 46789999999999999999888667666654
No 96
>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=86.16 E-value=3 Score=29.25 Aligned_cols=76 Identities=16% Similarity=0.176 Sum_probs=50.3
Q ss_pred HHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCC------CCC---chhhHHHHHHHHHhCCcceecCC----CCce
Q 032244 58 AASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHF------SKS---SGSVARHILHQLQDTNIIELDSK----GGRR 123 (144)
Q Consensus 58 aASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~------~~a---sg~iiR~~LqqLE~~glv~k~~~----gGR~ 123 (144)
|..||+-|+- .+.+|...+..++=|.++....-.++ -.+ |..-++.++++|...|+++.... .-=.
T Consensus 6 a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~ 85 (106)
T PF09382_consen 6 AKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLK 85 (106)
T ss_dssp HHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEE
T ss_pred HHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEE
Confidence 3446666665 46899999999999998877543322 222 44689999999999999965543 1357
Q ss_pred eCcchHhhHH
Q 032244 124 ITSSGQRDLD 133 (144)
Q Consensus 124 lT~~G~~~lD 133 (144)
+|++|++.|.
T Consensus 86 ~~~~~~~~l~ 95 (106)
T PF09382_consen 86 LTPKGKELLN 95 (106)
T ss_dssp E-GGGHHHHC
T ss_pred ECHHHHHHHC
Confidence 8999998875
No 97
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=86.12 E-value=2.5 Score=37.56 Aligned_cols=63 Identities=16% Similarity=0.109 Sum_probs=44.7
Q ss_pred HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHH
Q 032244 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRI 139 (144)
Q Consensus 65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i 139 (144)
|-...++-...+...||-.. .. -.-....|++|++.|||+.+.. +=+||++|+-.+|.|+..+
T Consensus 376 L~~~~~ld~~~~~~~~g~~~------~~-----~~~~~~~l~~l~~~gl~~~~~~-~~~lT~~G~~~~~~i~~~f 438 (453)
T PRK13347 376 LMCNFPVDLAAIAARHGFFA------RY-----FLDELARLEPLAADGLVTIDGG-GIRVTPEGRPLIRAVAAAF 438 (453)
T ss_pred HHhhCCcCHHHHHHHHCCCH------HH-----HHHHHHHHHHHHHCCCEEEECC-EEEECcchhHHHHHHHHHH
Confidence 44455666777888887320 00 0012457899999999997654 6799999999999999865
No 98
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=85.80 E-value=2.8 Score=37.04 Aligned_cols=59 Identities=22% Similarity=0.293 Sum_probs=45.2
Q ss_pred HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 67 l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
+..++-...+...||.. + .. ....|++|++.|||+.+.+ .=+||++|+-..|.|+.+++
T Consensus 358 ~~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~~-~l~lT~~G~~~~d~i~~~~~ 416 (430)
T PRK08208 358 QAQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNGG-RLRLTEEGLALSDAIGPVFI 416 (430)
T ss_pred HhCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEECC-EEEECcchhhHHHHHHHHHc
Confidence 34677777888888731 1 12 3458899999999987653 56899999999999999885
No 99
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=85.46 E-value=1.1 Score=37.62 Aligned_cols=57 Identities=16% Similarity=0.281 Sum_probs=42.3
Q ss_pred HHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHH-HHHhCCcceecCCCCceeCcchHhhHH
Q 032244 62 ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILH-QLQDTNIIELDSKGGRRITSSGQRDLD 133 (144)
Q Consensus 62 lRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~Lq-qLE~~glv~k~~~gGR~lT~~G~~~lD 133 (144)
+...|-.+++|+..+...-|-... -+-.++. .|-+.|||++++. ||++|++|.+.|.
T Consensus 268 ~~~~~~~~~~~~~~~a~~lg~~~~--------------~~~~~~e~~Li~~~li~~~~~-gr~~~~~~~~~~~ 325 (328)
T PRK00080 268 IIEKFGGGPVGLDTLAAALGEERD--------------TIEDVYEPYLIQQGFIQRTPR-GRVATPKAYEHLG 325 (328)
T ss_pred HHHHcCCCceeHHHHHHHHCCCcc--------------hHHHHhhHHHHHcCCcccCCc-hHHHHHHHHHHhC
Confidence 344455679999999998885443 2333333 8889999997776 9999999998774
No 100
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=85.31 E-value=0.77 Score=34.53 Aligned_cols=77 Identities=22% Similarity=0.340 Sum_probs=47.6
Q ss_pred CCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHH
Q 032244 29 IELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQL 108 (144)
Q Consensus 29 i~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqL 108 (144)
=+.-.|.+=-++...+--.-.|+.-+ ..|+--+--..-|.+..|...||- ++||.|.+|..|
T Consensus 22 k~kKK~~~k~~k~~~~~av~vdee~~----~ki~KEV~~~r~VTpy~la~r~gI--------------~~SvAr~vLR~L 83 (107)
T COG4901 22 KDKKKWSKKKKKEEARRAVTVDEELL----DKIRKEVPRERVVTPYVLASRYGI--------------NGSVARIVLRHL 83 (107)
T ss_pred hhhhccccccccchhhhhhhccHHHH----HHHHHhcccceeecHHHHHHHhcc--------------chHHHHHHHHHH
Confidence 34456766544443333333333221 123333333345778888888883 679999999999
Q ss_pred HhCCcceecCCCCcee
Q 032244 109 QDTNIIELDSKGGRRI 124 (144)
Q Consensus 109 E~~glv~k~~~gGR~l 124 (144)
|+.|+|....+ +|+.
T Consensus 84 eeeGvv~lvsk-nrR~ 98 (107)
T COG4901 84 EEEGVVQLVSK-NRRQ 98 (107)
T ss_pred HhCCceeeecc-Cccc
Confidence 99999988776 5554
No 101
>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=84.95 E-value=3.6 Score=29.12 Aligned_cols=48 Identities=15% Similarity=0.106 Sum_probs=34.5
Q ss_pred HHHHHHHHHH--------HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 57 RAASMARKIY--------LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 57 RaASilRklY--------l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
|-|++|-.|. ...++.-..|....|- |..-+.++|++||+.|||+...
T Consensus 26 r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~--------------sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 26 REFRVLLAIIRLTYGWNKKQDRVTATVIAELTGL--------------SRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHHHHHHHHHHHhCccccCCccCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeeeec
Confidence 5566665554 4456677777777763 3456889999999999998654
No 102
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=84.25 E-value=1.4 Score=37.86 Aligned_cols=38 Identities=13% Similarity=0.130 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 102 RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
+..|++|++.|++..+.. .=+||++|+-.+|.|+.+++
T Consensus 337 ~~~l~~l~~~gl~~~~~~-~~~lT~~G~~~~~~i~~~~~ 374 (375)
T PRK05628 337 RARAARVVADGLLAAEGG-RLVLTLRGRLLADAVVRDLL 374 (375)
T ss_pred HHHHHHHHHCCCEEEECC-EEEEChhhhHHHHHHHHHHh
Confidence 468899999999987654 57899999999999998864
No 103
>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=83.95 E-value=4.3 Score=32.25 Aligned_cols=58 Identities=17% Similarity=0.206 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 55 YIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 55 y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
|...+..|++-=..|.. .=..|+..|| -|..-+|++|+.|+..|+|++.+..|--+++
T Consensus 2 y~qi~~~l~~~I~~g~~~~G~~LPsE~eLa~~~g--------------VSR~TVR~Al~~L~~eGli~r~~G~GTfV~~ 66 (233)
T TIGR02404 2 YEQIYQDLEQKITHGQYKEGDYLPSEHELMDQYG--------------ASRETVRKALNLLTEAGYIQKIQGKGSIVLN 66 (233)
T ss_pred HHHHHHHHHHHHHhCCCCCCCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCceEEEec
Confidence 44455555554444433 2456888888 4678999999999999999999866877754
No 104
>PRK14999 histidine utilization repressor; Provisional
Probab=83.75 E-value=7.9 Score=31.01 Aligned_cols=60 Identities=17% Similarity=0.153 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHhCC------C-chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 54 YYIRAASMARKIYLRGG------L-GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 54 ~y~RaASilRklYl~g~------~-Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
.|...+..|++-=..|. + +-..|+..|| -|..-+|++|+.|+..|+|.+.+..|--+++
T Consensus 13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~g--------------VSR~TVR~Al~~L~~eGli~r~~GkGTfV~~ 78 (241)
T PRK14999 13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYG--------------FSRMTINRALRELTDEGWLVRLQGVGTFVAE 78 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence 46677777766555542 2 5678899998 4667999999999999999988866777765
Q ss_pred c
Q 032244 127 S 127 (144)
Q Consensus 127 ~ 127 (144)
.
T Consensus 79 ~ 79 (241)
T PRK14999 79 P 79 (241)
T ss_pred C
Confidence 4
No 105
>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=83.23 E-value=1.4 Score=29.65 Aligned_cols=40 Identities=23% Similarity=0.194 Sum_probs=30.7
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
|-.|..+...+|- .|-+-+..-|++||+.|+|+.++...|
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 5588888888883 367889999999999999999885433
No 106
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=83.02 E-value=1.8 Score=37.02 Aligned_cols=40 Identities=5% Similarity=0.090 Sum_probs=33.0
Q ss_pred hHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 100 VARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 100 iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
.....|++|++.||++.+.. .=+||++|+-.+|.|+.+++
T Consensus 334 ~~~~~l~~l~~~gl~~~~~~-~~~lT~~G~~~~~~i~~~~~ 373 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEKEG-RIYLSERGIEVSNSIMSDFL 373 (374)
T ss_pred HHHHHHHHHHHCCCEEEECC-EEEEChhHHHHHHHHHHHHh
Confidence 35567899999999986543 46899999999999998874
No 107
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=82.35 E-value=1.5 Score=31.68 Aligned_cols=36 Identities=28% Similarity=0.343 Sum_probs=27.3
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
-+....|...|+ =.||+.|.+|++||+-|+|.....
T Consensus 41 ~ITps~lserlk--------------I~~SlAr~~Lr~L~~kG~Ik~V~~ 76 (86)
T PRK09334 41 IVTPYTLASKYG--------------IKISVAKKVLRELEKRGVLVLYSK 76 (86)
T ss_pred EEcHHHHHHHhc--------------chHHHHHHHHHHHHHCCCEEEEec
Confidence 355666666665 357899999999999999976554
No 108
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=82.18 E-value=1.9 Score=37.32 Aligned_cols=39 Identities=10% Similarity=0.166 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 101 ARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 101 iR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
....+++|++.||++.+.+ .=.||++|+-.+|.|+.+++
T Consensus 332 ~~~~l~~~~~~gll~~~~~-~i~lT~~G~~~~~~i~~~~~ 370 (370)
T PRK06294 332 TSELIMHPIIQELFTKNDQ-ALSLNKKGRLFHDTIAEEIM 370 (370)
T ss_pred HHHHHHHHHHCCCEEEECC-EEEECcchhhHHHHHHHHhC
Confidence 4567889999999986653 56899999999999998763
No 109
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=81.97 E-value=6.7 Score=31.49 Aligned_cols=61 Identities=25% Similarity=0.344 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
.|...+..|++-=..|.. .-..|+..|| -|..-+|.+|+.|+..|+|.+.+..|-.+++
T Consensus 6 ly~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 71 (240)
T PRK09764 6 LYRQIADRIREQIARGELKPGDALPTESALQTEFG--------------VSRVTVRQALRQLVEQQILESIQGSGTYVKE 71 (240)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEEcc
Confidence 466677777666555532 3467888888 3668999999999999999988866877765
Q ss_pred ch
Q 032244 127 SG 128 (144)
Q Consensus 127 ~G 128 (144)
..
T Consensus 72 ~~ 73 (240)
T PRK09764 72 ER 73 (240)
T ss_pred cc
Confidence 44
No 110
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=81.92 E-value=3.5 Score=36.36 Aligned_cols=68 Identities=16% Similarity=0.196 Sum_probs=48.0
Q ss_pred chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRD 131 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~ 131 (144)
||.=.+--+.+-.-|--||||+..++-.-|--+. .|-=.+===|-..|+++++++ ||++|+++.+.
T Consensus 259 d~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~-------------TiEdv~EPyLiq~gfi~RTpR-GR~aT~~ay~h 324 (332)
T COG2255 259 DEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRD-------------TIEDVIEPYLIQQGFIQRTPR-GRIATAKAYEH 324 (332)
T ss_pred cHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchh-------------HHHHHHhHHHHHhchhhhCCC-cceecHHHHHH
Confidence 5666666556666666799999999998885432 121122223556899999998 99999999876
Q ss_pred HH
Q 032244 132 LD 133 (144)
Q Consensus 132 lD 133 (144)
|-
T Consensus 325 l~ 326 (332)
T COG2255 325 LG 326 (332)
T ss_pred hc
Confidence 53
No 111
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.71 E-value=1.9 Score=25.50 Aligned_cols=35 Identities=14% Similarity=0.244 Sum_probs=26.7
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
++.+..+....|- |..-++.+|++|++.|+|+...
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 4556666676663 4467899999999999998765
No 112
>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=81.42 E-value=6 Score=27.09 Aligned_cols=61 Identities=31% Similarity=0.390 Sum_probs=41.4
Q ss_pred HHHHHHHHHH---Hh---CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC---CceeCcc
Q 032244 57 RAASMARKIY---LR---GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG---GRRITSS 127 (144)
Q Consensus 57 RaASilRklY---l~---g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g---GR~lT~~ 127 (144)
|+-|++--|| +. +++-++.|-...+. --=+-+-+|.+|--|-+.||++....| +-.||++
T Consensus 1 ~a~Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~-----------~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 1 RARSLIVTLLGDYLRPRGGWIWVASLIRLLAA-----------FGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp -HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCC-----------TT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred CcceehHHHHHHHhccCCCceeHHHHHHHHHH-----------cCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 4567777777 43 46677777776662 223456899999999999999998874 3678887
Q ss_pred h
Q 032244 128 G 128 (144)
Q Consensus 128 G 128 (144)
|
T Consensus 70 g 70 (70)
T PF07848_consen 70 G 70 (70)
T ss_dssp H
T ss_pred C
Confidence 6
No 113
>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=81.27 E-value=1.6 Score=37.14 Aligned_cols=60 Identities=20% Similarity=0.228 Sum_probs=44.3
Q ss_pred HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-C-CCceeCcchHhhHHH
Q 032244 61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-K-GGRRITSSGQRDLDQ 134 (144)
Q Consensus 61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~-gGR~lT~~G~~~lD~ 134 (144)
||+.|=- +|-+.-..|+..+| =|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|.
T Consensus 188 IL~~L~~~egrlse~eLAerlG--------------VSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e 250 (251)
T TIGR02787 188 IFEELDGNEGLLVASKIADRVG--------------ITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE 250 (251)
T ss_pred HHHHhccccccccHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence 4444444 24555666666666 47789999999999999999888 4 377888877777775
No 114
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=81.03 E-value=7.7 Score=33.88 Aligned_cols=39 Identities=23% Similarity=0.235 Sum_probs=32.4
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 101 ARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 101 iR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
+...|+.|++.||++.+.+ .=+||++|+-.+|.|+.+++
T Consensus 355 ~~~~l~~l~~~gll~~~~~-~~~LT~~G~~~~d~i~~~~~ 393 (394)
T PRK08898 355 IEPQLAAAEQRGLLERDHT-RIRPTPLGQRFLNDLQELFL 393 (394)
T ss_pred HHHHHHHHHHCCCEEEECC-EEEEChhHhHHHHHHHHHHh
Confidence 4568899999999986542 34899999999999999875
No 115
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=80.67 E-value=1.8 Score=35.38 Aligned_cols=40 Identities=20% Similarity=0.400 Sum_probs=31.5
Q ss_pred hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
-..|...|| -|..++|-+|+.||..|||+.-+..|=.+++
T Consensus 37 EreLae~fg--------------VSR~~vREAl~~L~a~Glve~r~G~Gt~V~~ 76 (241)
T COG2186 37 ERELAERFG--------------VSRTVVREALKRLEAKGLVEIRQGSGTFVRP 76 (241)
T ss_pred HHHHHHHHC--------------CCcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence 346777777 4668999999999999999988765655544
No 116
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=80.57 E-value=7.1 Score=31.63 Aligned_cols=71 Identities=21% Similarity=0.274 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHhCCCchh-------HHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 55 YIRAASMARKIYLRGGLGVG-------SFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 55 y~RaASilRklYl~g~~Gv~-------~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
|.+-+.-|+.-=..|-...| .|+..||- |.--+|++|++|++.|+|......|--+++.
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 45555566665555543333 67888874 6679999999999999999888668777764
Q ss_pred ----hHhhHHHHHHHH
Q 032244 128 ----GQRDLDQVAGRI 139 (144)
Q Consensus 128 ----G~~~lD~iA~~i 139 (144)
....+..+...+
T Consensus 75 ~~~~~~~~~~~f~e~~ 90 (236)
T COG2188 75 KEQSPLLELTSFSEEL 90 (236)
T ss_pred cccccccccccHHHHH
Confidence 333344444443
No 117
>PRK05660 HemN family oxidoreductase; Provisional
Probab=80.45 E-value=2.6 Score=36.59 Aligned_cols=39 Identities=15% Similarity=0.147 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhh
Q 032244 102 RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~ 141 (144)
...+++|++.||++.+.. .=+||++|+-++|.|+.+++.
T Consensus 339 ~~~l~~l~~~gl~~~~~~-~~~lt~~G~~~~d~i~~~~~~ 377 (378)
T PRK05660 339 RPQLDEALAQGYLTETAD-HWQITEHGKLFLNDLLELFLA 377 (378)
T ss_pred HHHHHHHHHCCCEEEeCC-EEEECcchhHHHHHHHHHHhc
Confidence 467899999999986543 467999999999999998864
No 118
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=79.87 E-value=2 Score=33.13 Aligned_cols=45 Identities=20% Similarity=0.267 Sum_probs=36.5
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcch
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSSG 128 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G 128 (144)
++.+..++..+|- |-+.++++|++|.++|||+... +||-+|...-
T Consensus 25 ~~s~~~IA~~~~i--------------s~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~ 71 (150)
T COG1959 25 PVSSAEIAERQGI--------------SPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPP 71 (150)
T ss_pred cccHHHHHHHhCc--------------CHHHHHHHHHHHHHcCCEEeecCCCCCccCCCCh
Confidence 5778888887763 5579999999999999998554 7899988654
No 119
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=79.56 E-value=7.5 Score=34.09 Aligned_cols=61 Identities=15% Similarity=0.230 Sum_probs=45.1
Q ss_pred HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhH-HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVA-RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~ii-R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
|-+..++-+..+...||-.- .... ...|++|++.||++. . +.=.||++|+-..|.|+.+++
T Consensus 328 LR~~~Gl~~~~~~~~~g~~~-------------~~~~~~~~l~~l~~~gll~~-~-~~l~lT~~G~~~~d~i~~~~~ 389 (390)
T PRK06582 328 LRLSKGINISTLEQKLNTKL-------------ENILDMNNLKHYQALDLIRL-D-ENIYLTDKGLMLHSYIVPRLI 389 (390)
T ss_pred HHhhCCCCHHHHHHHHCcCH-------------HHhhhHHHHHHHHHCCCEEE-C-CEEEECcchhHHHHHHHHHHh
Confidence 33456777888888887311 1112 467889999999997 3 457899999999999998864
No 120
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=79.47 E-value=2.2 Score=37.81 Aligned_cols=36 Identities=25% Similarity=0.389 Sum_probs=31.0
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 104 ILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 104 ~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
.|++|++.||++.+.+ .=+||++|+-.+|.|+..+-
T Consensus 404 ~l~~l~~~gll~~~~~-~~~lT~~G~~~~d~i~~~f~ 439 (453)
T PRK09249 404 RLAPLEADGLVELDEN-GITVTPKGRLLVRNIAMAFD 439 (453)
T ss_pred HHHHHHHCCCEEEECC-EEEECccchHHHHHHHHHHH
Confidence 4789999999997764 67899999999999998764
No 121
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=79.41 E-value=4.1 Score=32.45 Aligned_cols=42 Identities=17% Similarity=0.245 Sum_probs=37.0
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~ 115 (144)
-||..|.-+|.+....|+..-|-.. .-+|++|+.|++.|||.
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 3788888889999999999888544 58999999999999998
No 122
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=79.35 E-value=6.8 Score=34.96 Aligned_cols=59 Identities=17% Similarity=0.111 Sum_probs=45.8
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
.+++-...+...||.. ........|++|+..|++..+.+ .=.||++|+-.+|.|+.+++
T Consensus 356 ~~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~~-~l~lT~~G~~~~d~i~~~f~ 414 (433)
T PRK08629 356 SGRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDPG-DLIVTDFGKYLGVVMMKEFY 414 (433)
T ss_pred hCCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEECC-EEEECcchhHHHHHHHHHHH
Confidence 4567777888888732 13456788899999999987543 45899999999999999875
No 123
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=79.29 E-value=1.6 Score=37.92 Aligned_cols=35 Identities=26% Similarity=0.368 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHhCCcceecC--CCCceeCcchHhhHH
Q 032244 99 SVARHILHQLQDTNIIELDS--KGGRRITSSGQRDLD 133 (144)
Q Consensus 99 ~iiR~~LqqLE~~glv~k~~--~gGR~lT~~G~~~lD 133 (144)
+-+|+.+|.|..+||||-.+ +||.+-|.+.-..|+
T Consensus 40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~ 76 (294)
T COG2524 40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALS 76 (294)
T ss_pred chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhc
Confidence 46899999999999999665 899999999877665
No 124
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=79.18 E-value=7.3 Score=31.14 Aligned_cols=61 Identities=13% Similarity=0.079 Sum_probs=44.5
Q ss_pred HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
-|...+..|+.-=..|-. +=..|+..|| -|..-+|++|+.|++.|||.+....|--+++
T Consensus 10 ~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GTfV~~ 75 (241)
T PRK11402 10 LYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYN--------------VSRITIRKAISDLVADGVLIRWQGKGTFVQS 75 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEECC
Confidence 356666666665555533 3356888888 3667999999999999999988866777765
Q ss_pred ch
Q 032244 127 SG 128 (144)
Q Consensus 127 ~G 128 (144)
..
T Consensus 76 ~~ 77 (241)
T PRK11402 76 QK 77 (241)
T ss_pred Cc
Confidence 54
No 125
>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=79.05 E-value=5 Score=32.81 Aligned_cols=50 Identities=16% Similarity=0.296 Sum_probs=40.1
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHH-HHHhCCcceecCCCCceeCcchHhhH
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILH-QLQDTNIIELDSKGGRRITSSGQRDL 132 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~Lq-qLE~~glv~k~~~gGR~lT~~G~~~l 132 (144)
.+++++..++...|-.. .-++.++. .|-+.|+|++... ||..|++|...|
T Consensus 253 ~~~~~~~~ia~~lg~~~--------------~~~~~~~e~~Li~~~li~~~~~-g~~~~~~~~~~~ 303 (305)
T TIGR00635 253 GGPVGLKTLAAALGEDA--------------DTIEDVYEPYLLQIGFLQRTPR-GRIATELAYEHL 303 (305)
T ss_pred CCcccHHHHHHHhCCCc--------------chHHHhhhHHHHHcCCcccCCc-hhhhhHHHHHHh
Confidence 45799999999888522 35677777 6999999986665 999999998876
No 126
>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=78.80 E-value=6.6 Score=24.10 Aligned_cols=41 Identities=24% Similarity=0.377 Sum_probs=32.4
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k 116 (144)
|+..|. .|+..+..|....|- |-+.+.+=|..|+++|+|++
T Consensus 7 Il~~L~-~~~~~~~el~~~l~~--------------s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLS-EGPLTVSELAEELGL--------------SQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHT-TSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHH-hCCCchhhHHHhccc--------------cchHHHHHHHHHHHCcCeeC
Confidence 444443 489999999998884 45789999999999999985
No 127
>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=77.99 E-value=2.7 Score=37.30 Aligned_cols=36 Identities=22% Similarity=0.470 Sum_probs=30.5
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 104 ILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 104 ~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
.|++|++.|||+.+.. .=+||++|+-.+|.|+.++-
T Consensus 404 ~l~~l~~~gll~~~~~-~~~lT~~G~~~~~~i~~~f~ 439 (455)
T TIGR00538 404 LLKPLEEDGLLDVDEK-GIEVTPKGRLLIRNIAMVFD 439 (455)
T ss_pred HHHHHHhCCCEEEECC-EEEECcCChHHHHHHHHHHH
Confidence 4778999999997654 67899999999999998763
No 128
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=77.83 E-value=4.3 Score=36.70 Aligned_cols=66 Identities=6% Similarity=0.091 Sum_probs=50.4
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC--CCceeCcchHhhHHHHH
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK--GGRRITSSGQRDLDQVA 136 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~--gGR~lT~~G~~~lD~iA 136 (144)
..||..|.-.+++....|+...|- +-+-+-.++..||+.|||+...+ ..-.||++|++.++++.
T Consensus 9 ~~vL~~L~~~~~~s~~eLA~~l~l--------------~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g~ 74 (489)
T PRK04172 9 KKVLKALKELKEATLEELAEKLGL--------------PPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEGL 74 (489)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhcC
Confidence 357888888889999999987773 22345567889999999997652 25679999999998765
Q ss_pred HH
Q 032244 137 GR 138 (144)
Q Consensus 137 ~~ 138 (144)
.+
T Consensus 75 pE 76 (489)
T PRK04172 75 PE 76 (489)
T ss_pred HH
Confidence 43
No 129
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=76.90 E-value=2.7 Score=28.40 Aligned_cols=38 Identities=24% Similarity=0.190 Sum_probs=29.6
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
++|+-...+....|= |-.-+|+.|++||+.|.|++.+-
T Consensus 13 ~~p~~T~eiA~~~gl--------------s~~~aR~yL~~Le~eG~V~~~~~ 50 (62)
T PF04703_consen 13 NGPLKTREIADALGL--------------SIYQARYYLEKLEKEGKVERSPV 50 (62)
T ss_dssp TS-EEHHHHHHHHTS---------------HHHHHHHHHHHHHCTSEEEES-
T ss_pred CCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecC
Confidence 677888888887763 45689999999999999998773
No 130
>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=76.40 E-value=5.9 Score=26.25 Aligned_cols=40 Identities=23% Similarity=0.320 Sum_probs=32.3
Q ss_pred HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
|=-++.+.+..|++.|+ .|-..++..|.+||..|.|++..
T Consensus 9 l~~~~~~S~~eLa~~~~--------------~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 9 LRERGRVSLAELAREFG--------------ISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHS-SEEHHHHHHHTT----------------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHcCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEEec
Confidence 44578899999999777 46679999999999999999776
No 131
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=76.37 E-value=8.2 Score=32.50 Aligned_cols=59 Identities=10% Similarity=-0.002 Sum_probs=45.2
Q ss_pred HHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce-ecCCCCceeCcc
Q 032244 55 YIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE-LDSKGGRRITSS 127 (144)
Q Consensus 55 y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~-k~~~gGR~lT~~ 127 (144)
|-|...||+.|.-..++....|+..+|- |.+-+++.++.|++.|++- ..+..|-.|.+.
T Consensus 3 ~~r~~~il~~L~~~~~~s~~~LA~~lgv--------------sr~tV~~~l~~L~~~G~~i~~~~~~Gy~L~~~ 62 (319)
T PRK11886 3 YTVMLQLLSLLADGDFHSGEQLGEELGI--------------SRAAIWKHIQTLEEWGLDIFSVKGKGYRLAEP 62 (319)
T ss_pred ccHHHHHHHHHHcCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCceEEecCCeEEecCc
Confidence 3578889988877778899999999885 4568999999999999944 434336666444
No 132
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=76.33 E-value=3.6 Score=36.67 Aligned_cols=40 Identities=23% Similarity=0.235 Sum_probs=33.4
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHhh
Q 032244 101 ARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 101 iR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~~ 141 (144)
....|++|++.|||+.+.+ .=+||++|+-..|.|+.++..
T Consensus 398 ~~~~l~~~~~~Gll~~~~~-~l~lT~~G~~~~~~i~~~~~~ 437 (449)
T PRK09058 398 LAPLLAQWQQAGLVELSSD-CLRLTLAGRFWAVNLTQGLIE 437 (449)
T ss_pred HHHHHHHHHHCCCEEEECC-EEEECCCcccHHHHHHHHHHH
Confidence 3457889999999997654 679999999999999998753
No 133
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=75.87 E-value=3 Score=32.86 Aligned_cols=33 Identities=27% Similarity=0.277 Sum_probs=26.7
Q ss_pred CCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 95 KSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 95 ~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
.-|-.=+|.+|+-|+++|+|+++.+|.-..|.+
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 345678999999999999999999866565553
No 134
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=75.79 E-value=2.7 Score=36.81 Aligned_cols=41 Identities=20% Similarity=0.209 Sum_probs=33.4
Q ss_pred hhHHHHHHHHHhCCcceecCCCCc--eeCc-chHhhHHHHHHHHhh
Q 032244 99 SVARHILHQLQDTNIIELDSKGGR--RITS-SGQRDLDQVAGRIAV 141 (144)
Q Consensus 99 ~iiR~~LqqLE~~glv~k~~~gGR--~lT~-~G~~~lD~iA~~i~~ 141 (144)
......|++|++.||++.+. +| +||+ +|+-.+|.|+.+++.
T Consensus 351 ~~~~~~l~~l~~~gll~~~~--~~~~~lT~~~G~~~~~~i~~~~~~ 394 (400)
T PRK07379 351 EQILQCLQPYFQQGWVELEG--DRRLRLTDPEGFLFSNTVLASLFE 394 (400)
T ss_pred HHHHHHHHHHHHCCCEEEeC--CeEEEECchHHhHHHHHHHHHHHH
Confidence 34567789999999998654 55 8995 999999999998863
No 135
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=75.64 E-value=4.8 Score=36.41 Aligned_cols=40 Identities=15% Similarity=0.339 Sum_probs=34.4
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
..+.+..|+....+..| -+|.+|++|++.|||+-.+.-||
T Consensus 22 ~~~~l~~la~~l~cs~R--------------~~~~~l~~~~~~gwl~w~~~~GR 61 (552)
T PRK13626 22 QETTLNELAELLNCSRR--------------HMRTLLNTMQQRGWLTWQAEAGR 61 (552)
T ss_pred ceeeHHHHHHHhcCChh--------------HHHHHHHHHHHCCCeeeecCCCC
Confidence 46889999999887776 58999999999999999886565
No 136
>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=75.63 E-value=2.6 Score=31.38 Aligned_cols=37 Identities=24% Similarity=0.250 Sum_probs=30.1
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
.-|.+..|...|+= ++|+.|.+|+.||+-|+|.....
T Consensus 58 K~ITp~~lserlkI--------------~~SlAr~~Lr~L~~kG~Ik~V~k 94 (105)
T PF03297_consen 58 KLITPSVLSERLKI--------------NGSLARKALRELESKGLIKPVSK 94 (105)
T ss_dssp SCECHHHHHHHHCC--------------SCHHHHHHHHHHHHCCSSEEEEC
T ss_pred cEeeHHHHHHhHhh--------------HHHHHHHHHHHHHHCCCEEEEec
Confidence 34788888888873 57899999999999999976543
No 137
>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=75.34 E-value=7.5 Score=31.35 Aligned_cols=56 Identities=18% Similarity=0.152 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 56 IRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 56 ~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
-|+-.||.-|-- .+++++..|.+.-|-.| +-+..+|+.|++.|||+++. +.-.|++
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lglpk--------------sT~~RlL~tL~~~G~l~~~~-~~Y~lG~ 65 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGLTR--------------AAARRFLLTLVELGYVTSDG-RLFWLTP 65 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCCEEeCC-CEEEecH
Confidence 378888988865 56899999999887543 67899999999999999864 3344444
No 138
>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=74.71 E-value=17 Score=23.66 Aligned_cols=53 Identities=11% Similarity=0.141 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
.|++.+- +++..+..|+..+|- |..-|+..++.||+.|+..-....|..|.+.
T Consensus 4 ~il~~L~-~~~~~~~eLa~~l~v--------------S~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~ 56 (69)
T TIGR00122 4 RLLALLA-DNPFSGEKLGEALGM--------------SRTAVNKHIQTLREWGVDVLTVGKGYRLPPP 56 (69)
T ss_pred HHHHHHH-cCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEecCCceEecCc
Confidence 3555544 677889999998874 4578999999999999954333557777443
No 139
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=74.26 E-value=11 Score=30.87 Aligned_cols=50 Identities=18% Similarity=0.175 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g 120 (144)
|-..|+..|--++.+.+..|...+|- |..-||+=|++||+.|++.+...|
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~v--------------S~~TirRdL~~Le~~g~i~r~~gg 55 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGI--------------SPATARRDINKLDESGKLKKVRNG 55 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecCC
Confidence 66778888888899999999999883 556789999999999999987753
No 140
>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=73.88 E-value=4.8 Score=25.85 Aligned_cols=32 Identities=28% Similarity=0.506 Sum_probs=24.0
Q ss_pred chhhHHHHHHHHHh---CCcceecCCCCceeCcchH
Q 032244 97 SGSVARHILHQLQD---TNIIELDSKGGRRITSSGQ 129 (144)
Q Consensus 97 sg~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~ 129 (144)
|-+-+.+.+++||+ ..|++...+ |=.||+.|+
T Consensus 26 s~~~vs~~i~~LE~~lg~~Lf~r~~~-~~~lT~~G~ 60 (60)
T PF00126_consen 26 SQSAVSRQIKQLEEELGVPLFERSGR-GLRLTEAGE 60 (60)
T ss_dssp SHHHHHHHHHHHHHHHTS-SEEECSS-SEEE-HHHH
T ss_pred cchHHHHHHHHHHHHhCCeEEEECCC-CeeEChhhC
Confidence 44578888999998 578887776 799999996
No 141
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=73.09 E-value=11 Score=31.37 Aligned_cols=55 Identities=24% Similarity=0.349 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244 56 IRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125 (144)
Q Consensus 56 ~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT 125 (144)
-|-..|+..|--++.+.+..|...+| -|..-||.=|..||+.|++.+.. ||..+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~--------------VS~~TIRRDL~~Le~~G~l~r~~-GGa~~~ 71 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYG--------------VSTVTIRNDLAFLEKQGIAVRAY-GGALIC 71 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHC--------------CCHHHHHHHHHHHHhCCCeEEEe-CCEEec
Confidence 47788898888899999999999997 35578999999999999999877 576554
No 142
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=72.72 E-value=3.8 Score=32.86 Aligned_cols=59 Identities=15% Similarity=0.148 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHhCCC-------chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 54 YYIRAASMARKIYLRGGL-------GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 54 ~y~RaASilRklYl~g~~-------Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
-|...|..||+- |.+.. +=..|+..|| -|..-+|++|++|+..|+|++.+..|-.+++
T Consensus 13 ~Y~qi~~~L~~~-I~~~~~~G~~LPsE~eLa~~~~--------------VSR~TVR~Al~~L~~eGli~r~~G~GtfV~~ 77 (241)
T PRK10079 13 RYQEIAAKLEQE-LRQHYRCGDYLPAEQQLAARYE--------------VNRHTLRRAIDQLVEKGWVQRRQGVGVLVLM 77 (241)
T ss_pred HHHHHHHHHHHH-HhcccCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEEec
Confidence 455555555554 22221 2356888888 4667999999999999999988866866654
Q ss_pred c
Q 032244 127 S 127 (144)
Q Consensus 127 ~ 127 (144)
.
T Consensus 78 ~ 78 (241)
T PRK10079 78 R 78 (241)
T ss_pred C
Confidence 3
No 143
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=72.04 E-value=17 Score=32.42 Aligned_cols=80 Identities=25% Similarity=0.326 Sum_probs=58.8
Q ss_pred CCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC
Q 032244 42 TLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG 121 (144)
Q Consensus 42 ~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG 121 (144)
...+++|.|. +|-+ ++-.|=+.-++-+..+...||- -. -..+...|+.+++.|+++.+.+ .
T Consensus 331 ~~~~l~~~d~----~~e~-~i~gLr~~~gv~~~~~~~~~~~-~~------------~~~~~~~l~~~~~~Gll~~~~~-~ 391 (416)
T COG0635 331 EGEELTPDDL----IREA-LILGLRLNFGVDLAELEERFGI-FK------------FAEILELLAELIADGLLELDGD-R 391 (416)
T ss_pred eeeeCCHHHH----HHHH-HHHHHHHhcCCCHHHHHHHhCc-ch------------hhhHHHHHHHHHhCCCEEecCC-E
Confidence 3456666664 2222 2333445568889999999883 11 4678899999999999998885 7
Q ss_pred ceeCcchHhhHHHHHHHHh
Q 032244 122 RRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 122 R~lT~~G~~~lD~iA~~i~ 140 (144)
-+||+.|+-++|.||....
T Consensus 392 ~~lt~~g~~~~~~i~~~f~ 410 (416)
T COG0635 392 LRLTEKGRLLLRSIAEAFD 410 (416)
T ss_pred EEECCcchhHHHHHHHHHH
Confidence 8999999999999998764
No 144
>PRK12423 LexA repressor; Provisional
Probab=71.49 E-value=13 Score=29.58 Aligned_cols=45 Identities=24% Similarity=0.390 Sum_probs=33.2
Q ss_pred HHHHHHhCCC--chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 62 ARKIYLRGGL--GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 62 lRklYl~g~~--Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
|+..+..++. .+..|...+|= .|.+.+|..|+.||+.|+|+..+.
T Consensus 15 l~~~i~~~g~~Ps~~eia~~~g~-------------~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 15 IRERIAQAGQPPSLAEIAQAFGF-------------ASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEEecCC
Confidence 4444444443 78888887772 244688999999999999998875
No 145
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=71.42 E-value=19 Score=30.45 Aligned_cols=87 Identities=23% Similarity=0.245 Sum_probs=61.6
Q ss_pred HHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCC-CchhHHHHHhcCCCCCCCCCCCCCC
Q 032244 17 KAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGG-LGVGSFRRIYGGGKRNGSRPPHFSK 95 (144)
Q Consensus 17 ~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~-~Gv~~l~~~YGg~k~rG~~P~h~~~ 95 (144)
..++-.+-..+.+..|.|....++...-+..+.++|= ..|+.-|--+|+ +-=..|++.-|=
T Consensus 161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~e-----~~il~~i~~~GGri~Q~eL~r~lgl------------- 222 (258)
T COG2512 161 EALGVILIIYAPVIEPLLSRGDELRVLVNEYDLNEDE-----KEILDLIRERGGRITQAELRRALGL------------- 222 (258)
T ss_pred hhhhhhhhhcchhhhhccccccccccccccCCCCHHH-----HHHHHHHHHhCCEEeHHHHHHhhCC-------------
Confidence 3444444455557778899888888887777777642 346655555666 667788887773
Q ss_pred CchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 96 SSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
|..=+=.+|+.||++|+||+.++|++
T Consensus 223 -sktTvsR~L~~LEk~GlIe~~K~G~~ 248 (258)
T COG2512 223 -SKTTVSRILRRLEKRGLIEKEKKGRT 248 (258)
T ss_pred -ChHHHHHHHHHHHhCCceEEEEeCCe
Confidence 34567789999999999999998543
No 146
>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=71.16 E-value=8.8 Score=29.84 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=37.2
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~ 115 (144)
.-|+..|..++.+....|+..-|-++ +.+|++|+.|.+.|||.
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 34777788889999999999998655 48999999999999995
No 147
>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=70.90 E-value=7.3 Score=29.25 Aligned_cols=32 Identities=22% Similarity=0.304 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q 032244 102 RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
=.++..+|-+|+|+... |-=.||+.|+++.+.
T Consensus 15 ~p~~eAaelLgf~~~~~-Gdi~LT~~G~~f~~a 46 (120)
T PF09821_consen 15 LPIVEAAELLGFAEVEE-GDIRLTPLGRRFAEA 46 (120)
T ss_pred HHHHHHHHHcCCeeecC-CcEEeccchHHHHHC
Confidence 35788999999999765 578999999998864
No 148
>PRK05283 deoxyribose-phosphate aldolase; Provisional
Probab=68.82 E-value=7.5 Score=33.02 Aligned_cols=86 Identities=19% Similarity=0.247 Sum_probs=52.4
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHH----hCCCch------hHH-----
Q 032244 12 PHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYL----RGGLGV------GSF----- 76 (144)
Q Consensus 12 ~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl----~g~~Gv------~~l----- 76 (144)
.++.|...++-..+.| +|||||+++..-.+-.++ ...++|..-- .+.+|| ..+
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 899999999976665552 3344544321 123433 222
Q ss_pred -----HHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCC
Q 032244 77 -----RRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTN 112 (144)
Q Consensus 77 -----~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~g 112 (144)
+...| +.=..|+.|+-|+.+++=.+|+.||...
T Consensus 213 ~i~ag~~~lg---~~~~~~~~fR~G~Ssll~~~~~~~~~~~ 250 (257)
T PRK05283 213 YLALADEILG---ADWADARHFRFGASSLLASLLKTLGHGD 250 (257)
T ss_pred HHHHHHHHhC---hhhcCcccEeeehHHhHHHHHHHHhccc
Confidence 22223 1124799999999999999999886543
No 149
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=68.48 E-value=7.4 Score=30.64 Aligned_cols=40 Identities=28% Similarity=0.450 Sum_probs=31.8
Q ss_pred hHHHHHHHHHhCCcceec--CC--CCceeCcchHhhHHHHHHHH
Q 032244 100 VARHILHQLQDTNIIELD--SK--GGRRITSSGQRDLDQVAGRI 139 (144)
Q Consensus 100 iiR~~LqqLE~~glv~k~--~~--gGR~lT~~G~~~lD~iA~~i 139 (144)
-+..+|..|++.|+|... .+ .=-.||++|+..|+-+..+|
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~~I 78 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFENRI 78 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHHhC
Confidence 467789999999999965 22 24689999999998877765
No 150
>PRK00215 LexA repressor; Validated
Probab=67.78 E-value=17 Score=28.46 Aligned_cols=49 Identities=18% Similarity=0.185 Sum_probs=35.9
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc--eeCcchHhh
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR--RITSSGQRD 131 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR--~lT~~G~~~ 131 (144)
+.++..|....|-+ +.+-+-..|+.||+.|+|++.++++| .|++.|+..
T Consensus 23 ~~s~~ela~~~~~~-------------~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~~~~~~ 73 (205)
T PRK00215 23 PPSRREIADALGLR-------------SPSAVHEHLKALERKGFIRRDPGRSRAIEVAAPAQLE 73 (205)
T ss_pred CCCHHHHHHHhCCC-------------ChHHHHHHHHHHHHCCCEEeCCCCcceEEeccccccc
Confidence 56888999988841 22467789999999999999886554 355555543
No 151
>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=67.39 E-value=17 Score=28.25 Aligned_cols=45 Identities=24% Similarity=0.175 Sum_probs=33.4
Q ss_pred HHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 62 ARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 62 lRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
|++-|.++ +.++..|...+|- .|.+-++..|+.||+.|+|++...
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 34444544 4567799998883 245789999999999999998763
No 152
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=67.09 E-value=15 Score=30.26 Aligned_cols=53 Identities=17% Similarity=0.265 Sum_probs=44.9
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l 124 (144)
|-..|+..|--++.+.+..|...|| -|..-||+=|+.||+.|+|.+... |=++
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~--------------VS~~TIRRDL~~Le~~g~l~r~~G-ga~~ 58 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFD--------------TTGTTIRKDLVILEHAGTVIRTYG-GVVL 58 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEEEC-CEEc
Confidence 7778888888899999999999998 366789999999999999988763 5433
No 153
>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=66.79 E-value=18 Score=27.03 Aligned_cols=52 Identities=23% Similarity=0.334 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
.|++.|+-.+++.+..+....+..+ | =+-+-++++|.-|++-|+|+.... ||
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~~--~--------~~~tTv~T~L~rL~~KG~v~~~k~-gr 59 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEKK--D--------WSDSTIKTLLGRLVDKGCLTTEKE-GR 59 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhcc--C--------CcHHHHHHHHHHHHHCCceeeecC-CC
Confidence 5888899999999999888776321 1 234579999999999999987765 65
No 154
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=65.71 E-value=5.7 Score=37.18 Aligned_cols=93 Identities=17% Similarity=0.292 Sum_probs=65.1
Q ss_pred CCCCcchhc-ccCCCccCCCCCCchHHHHHHH--------------HHHHH---HHhCCCchhHHHHHhcCCCCCCCCCC
Q 032244 30 ELPTWNDIV-KTGTLKELAPYDPDWYYIRAAS--------------MARKI---YLRGGLGVGSFRRIYGGGKRNGSRPP 91 (144)
Q Consensus 30 ~~P~w~d~v-KTg~~kE~~P~d~DW~y~RaAS--------------ilRkl---Yl~g~~Gv~~l~~~YGg~k~rG~~P~ 91 (144)
.-|+|..-. +-|--+.-||.+.-=+|.+.|- +|+++ ||+.+.=|..+...||+-+
T Consensus 384 Pn~EW~eqa~~eglVs~gAiT~kGrl~akls~tikRkP~LT~~e~kvl~kiP~~~ikrg~liedi~~~~g~~e------- 456 (593)
T COG1542 384 PNAEWYEQAKEEGLVSRGAITEKGRLYAKLSKTIKRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQGHVGGDE------- 456 (593)
T ss_pred CCHHHHHHHHhcccccccCcCcchhHHHHHHHHHhcCcccchhHHHHHHhccccccchhhHHHHHHhhcCccH-------
Confidence 445665433 3455566678888888888764 44443 3444555666666666533
Q ss_pred CCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q 032244 92 HFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 92 h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
.=++.+|..||+-|+|+--+.+|=.||..||-.=--|.
T Consensus 457 -------eev~~sl~kleskgfveeL~n~gv~LTeaGe~~KtAis 494 (593)
T COG1542 457 -------EEVIKSLGKLESKGFVEELPNKGVKLTEAGELVKTAIS 494 (593)
T ss_pred -------HHHHHHHHHHhhcchHHHhccCcEEeehhhHHHHHHHH
Confidence 46899999999999999888889999999986544443
No 155
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=65.60 E-value=8.1 Score=30.53 Aligned_cols=48 Identities=15% Similarity=-0.002 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
|-..|+..|--++.+.+..|...|| -|..-||.=|++||+.|+|.+..
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~--------------vS~~TiRRDl~~L~~~g~~~r~~ 55 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFG--------------VSIQTIRLDRMELGIPELRERIK 55 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHC--------------cCHHHHHHHHHHHhcchHHHHHH
Confidence 7788898888899999999999888 57789999999999999998654
No 156
>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=64.95 E-value=9.4 Score=30.56 Aligned_cols=37 Identities=27% Similarity=0.436 Sum_probs=28.6
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+=+.+++||+ ..|.+.+.. |-.||+.|+.+++.+.
T Consensus 32 ~avS~~I~~LE~~lg~~LF~R~~~-~~~lT~~G~~l~~~a~ 71 (300)
T TIGR02424 32 PAVSKTLRELEEILGTPLFERDRR-GIRLTRYGELFLRHAG 71 (300)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcCC-CccccHhHHHHHHHHH
Confidence 356678889998 467777765 8999999999887643
No 157
>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=64.42 E-value=18 Score=25.99 Aligned_cols=36 Identities=25% Similarity=0.373 Sum_probs=26.9
Q ss_pred chhhHHHHHHHHHh---CCcceecCC----CCceeCcchHhhH
Q 032244 97 SGSVARHILHQLQD---TNIIELDSK----GGRRITSSGQRDL 132 (144)
Q Consensus 97 sg~iiR~~LqqLE~---~glv~k~~~----gGR~lT~~G~~~l 132 (144)
|-+-+-..+++||+ ..|++.... +|-.||+.|+..+
T Consensus 29 S~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 29 SYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred CHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 33456677889988 356777752 4899999999986
No 158
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=64.23 E-value=12 Score=30.06 Aligned_cols=38 Identities=16% Similarity=0.264 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
+-+=+.+++||+ ..|+++..+ |=.||+.|+.+++.+..
T Consensus 34 ~avS~~i~~LE~~lG~~LF~R~~r-~~~lT~~G~~l~~~a~~ 74 (302)
T PRK09791 34 PALTKSIQELEEGLAAQLFFRRSK-GVTLTDAGESFYQHASL 74 (302)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcCC-CceECccHHHHHHHHHH
Confidence 356677889987 467777665 89999999999887654
No 159
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=63.72 E-value=11 Score=30.01 Aligned_cols=37 Identities=16% Similarity=0.316 Sum_probs=28.7
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+=+.+++||+ ..|+..+.+ |-.||+.|+.+++.+-
T Consensus 30 savS~~i~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l~~~~~ 69 (296)
T PRK11242 30 PTLSQQIRQLEESLGVQLFDRSGR-TVRLTDAGEVYLRYAR 69 (296)
T ss_pred hHHHHHHHHHHHHhCCeeEeEcCC-ceeechhHHHHHHHHH
Confidence 346677889988 467777765 8999999999887654
No 160
>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=63.56 E-value=10 Score=25.97 Aligned_cols=21 Identities=33% Similarity=0.414 Sum_probs=18.3
Q ss_pred hhhHHHHHHHHHhCCcceecC
Q 032244 98 GSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 98 g~iiR~~LqqLE~~glv~k~~ 118 (144)
.++|=++|..||.+|++|.-.
T Consensus 18 RSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 18 RSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHhcCceeecc
Confidence 479999999999999999554
No 161
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=63.11 E-value=10 Score=27.36 Aligned_cols=42 Identities=14% Similarity=0.156 Sum_probs=32.0
Q ss_pred chhhHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHHHHH
Q 032244 97 SGSVARHILHQLQDTNIIELDSKG---GRRITSSGQRDLDQVAGR 138 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~~g---GR~lT~~G~~~lD~iA~~ 138 (144)
+.+=+=.++=.||..|+|.....+ --.+|++|...|++|-.+
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 334455777899999999866521 468999999999998643
No 162
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=62.38 E-value=14 Score=28.54 Aligned_cols=38 Identities=13% Similarity=0.207 Sum_probs=29.5
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
+-+=+.+++||+ ..|.+...+ |=.||+.|+.+++.+..
T Consensus 6 pavS~~I~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a~~ 46 (269)
T PRK11716 6 STLSRQIQRLEEELGQPLFVRDNR-SVTLTEAGEELRPFAQQ 46 (269)
T ss_pred HHHHHHHHHHHHHhCCeeEEecCC-ceeECHhHHHHHHHHHH
Confidence 345567889987 467787765 89999999999887654
No 163
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=62.34 E-value=9.9 Score=30.80 Aligned_cols=37 Identities=8% Similarity=0.153 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
.-+-+.+++||+ ..|++.+.+ |-.||+.|+.+++.+-
T Consensus 40 pavS~~I~~LE~~lG~~Lf~R~~r-~~~lT~~G~~l~~~a~ 79 (303)
T PRK10082 40 PAFSRRIRALEQAIGVELFNRQVT-PLQLSEQGKIFHSQIR 79 (303)
T ss_pred HHHHHHHHHHHHHcCCEEEEecCC-CCccCHHHHHHHHHHH
Confidence 457778899998 356676765 8999999999988743
No 164
>PF13730 HTH_36: Helix-turn-helix domain
Probab=62.32 E-value=7.5 Score=24.09 Aligned_cols=19 Identities=16% Similarity=0.391 Sum_probs=15.9
Q ss_pred CchhhHHHHHHHHHhCCcc
Q 032244 96 SSGSVARHILHQLQDTNII 114 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv 114 (144)
-|..=|+++++.||+.|||
T Consensus 37 ~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 37 VSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHHHHHHCcCC
Confidence 3456799999999999986
No 165
>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=62.01 E-value=13 Score=29.04 Aligned_cols=34 Identities=15% Similarity=0.324 Sum_probs=25.9
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
-+=+.+++||+ ..|++...+ |=.||+.|+.++..
T Consensus 27 avS~~i~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 27 TVTDQVRKLEERYGVELFHRNGR-RLELTDAGHRLLPI 63 (279)
T ss_pred HHHHHHHHHHHHhCCccEEEcCC-eEEEChhHHHHHHH
Confidence 45567888988 467777665 88999999988854
No 166
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=61.84 E-value=8.9 Score=29.69 Aligned_cols=94 Identities=19% Similarity=0.224 Sum_probs=58.7
Q ss_pred CchHHHHHHHHHHHHc-----CCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHh-cCCC
Q 032244 11 SPHEFVKAYAAHLKRS-----GKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIY-GGGK 84 (144)
Q Consensus 11 ~~~~fI~~~A~~LK~~-----gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~Y-Gg~k 84 (144)
..+.+-+.+|.-|-++ ...--|.+++++| ++.|.| |.||+.||-.+..-+...+..+ .+..
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 4455555555555443 2346788888875 788877 8899999966554444433333 2221
Q ss_pred CCCCCCCCCCCC---chhhHHHHHHHHHhCCcceec
Q 032244 85 RNGSRPPHFSKS---SGSVARHILHQLQDTNIIELD 117 (144)
Q Consensus 85 ~rG~~P~h~~~a---sg~iiR~~LqqLE~~glv~k~ 117 (144)
.+-..++....+ +-..+-..|+.|+.+|||+..
T Consensus 98 ~~~~~~~~~~~~~~~~~~~~~~~l~nL~rLGLi~~~ 133 (186)
T PF14337_consen 98 SRIVLSNISLVGEEASPDNIPSYLDNLERLGLIEIP 133 (186)
T ss_pred ceeecccccccccccchHHHHHHHHHHHHCCCceec
Confidence 221223322222 557889999999999999877
No 167
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=61.74 E-value=26 Score=24.30 Aligned_cols=68 Identities=12% Similarity=0.210 Sum_probs=47.9
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC------CCCce------eCcc
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS------KGGRR------ITSS 127 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~------~gGR~------lT~~ 127 (144)
.|++.|.-++++....|.+..|- |-.-++..++.|++.|+|.... .-|.. ++-.
T Consensus 7 ~il~~L~~~~~~~~~~la~~l~~--------------s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~ 72 (108)
T smart00344 7 KILEELQKDARISLAELAKKVGL--------------SPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLE 72 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEEC
Confidence 47888888899999999998763 4568999999999999998321 11321 2222
Q ss_pred hHhhHHHHHHHHhh
Q 032244 128 GQRDLDQVAGRIAV 141 (144)
Q Consensus 128 G~~~lD~iA~~i~~ 141 (144)
.....|+++..+.+
T Consensus 73 ~~~~~~~v~~~l~~ 86 (108)
T smart00344 73 SPDKLEEFLEKLEK 86 (108)
T ss_pred ChhHHHHHHHHHhC
Confidence 12467888887753
No 168
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=61.38 E-value=12 Score=32.14 Aligned_cols=35 Identities=14% Similarity=0.102 Sum_probs=28.3
Q ss_pred HHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 103 HILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 103 ~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
..|++|++.||++.+. + +||++|.-+.|.|+..+.
T Consensus 315 ~~l~~l~~~gl~~~~~--~-~l~~~g~~~~d~i~~~~~ 349 (350)
T PRK08446 315 KKVKILIEENKLFIKN--N-RLYNKDFFLADEIALFLL 349 (350)
T ss_pred HHHHHHHHCCCEEeeC--C-EEcccchhhHHHHHHHhh
Confidence 5677889999998543 4 499999999999998764
No 169
>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=60.69 E-value=18 Score=25.77 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=30.1
Q ss_pred CCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q 032244 93 FSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 93 ~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
|..|+-++| .+++.|=+-|||. +++ |..||+.|.+.-+.
T Consensus 29 H~dA~p~~i-~a~~RLheKGLI~-~pd-GgyLT~~G~~~aEh 67 (77)
T TIGR02647 29 HSTASPAAV-AAAARLHEKGLTT-QPD-GGYLTSLGLEAAEH 67 (77)
T ss_pred cccCCHHHH-HHHHHHHHcCCcc-CCC-CCEecHHHHHHHHH
Confidence 566776666 5789999999996 565 45999999876554
No 170
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=60.66 E-value=13 Score=29.89 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=28.3
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
-|=+.+++||+ ..|++.+.+ |=.||++|+.+++.+..
T Consensus 31 avS~~I~~LE~~lG~~LF~R~~r-~~~lT~~G~~l~~~a~~ 70 (275)
T PRK03601 31 AVSFRIRQLENQLGVNLFTRHRN-NIRLTAAGERLLPYAET 70 (275)
T ss_pred HHHHHHHHHHHHhCCceEEECCC-ceEECHhHHHHHHHHHH
Confidence 34456788988 467787775 88999999998877654
No 171
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=60.45 E-value=14 Score=29.80 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=28.2
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+-+.+++||+ ..|.+.+.+ |-.||+.|+..++..-
T Consensus 30 pavS~~i~~LE~~lg~~LF~R~~r-~~~lT~~G~~l~~~a~ 69 (305)
T PRK11151 30 PTLSGQIRKLEDELGVMLLERTSR-KVLFTQAGLLLVDQAR 69 (305)
T ss_pred hHHHHHHHHHHHHhCchheeeCCC-ceeECccHHHHHHHHH
Confidence 356678889988 467777665 8999999999887643
No 172
>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=60.36 E-value=40 Score=22.08 Aligned_cols=40 Identities=18% Similarity=0.325 Sum_probs=31.7
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCC
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGG 121 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gG 121 (144)
.+++....++...|= |.+-+=..|+.|++.|||+..+.+|
T Consensus 20 ~~~v~~~~iA~~L~v--------------s~~tvt~ml~~L~~~GlV~~~~y~g 59 (60)
T PF01325_consen 20 GGPVRTKDIAERLGV--------------SPPTVTEMLKRLAEKGLVEYEPYKG 59 (60)
T ss_dssp TSSBBHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred CCCccHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEecCCCC
Confidence 368999999998883 2345678899999999999888654
No 173
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=60.24 E-value=12 Score=30.63 Aligned_cols=33 Identities=18% Similarity=0.315 Sum_probs=23.7
Q ss_pred HHHHHHHHHh---CCcceecCCCCceeCcchHhhHHH
Q 032244 101 ARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 101 iR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
+=+.+++||+ .-|.+.+.+ |=.||+.|+.+++.
T Consensus 45 vS~~I~~LE~~lG~~LF~R~~r-~~~LT~~G~~l~~~ 80 (311)
T PRK10086 45 VSHRINQLEEELGIKLFVRSHR-KVELTEEGKRVFWA 80 (311)
T ss_pred HHHHHHHHHHHhCCeeEEEcCC-CcccCHhHHHHHHH
Confidence 4456778877 456666665 78888888888876
No 174
>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=59.54 E-value=19 Score=29.20 Aligned_cols=38 Identities=18% Similarity=0.272 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
+-+=..+++||+ ..|++.+.+ |-.||+.|+.++..+..
T Consensus 37 pavS~~I~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a~~ 77 (302)
T TIGR02036 37 SAISHRINQLEEELGIQLFVRSHR-KVELTHEGKRIYWALKS 77 (302)
T ss_pred HHHHHHHHHHHHHhCCceEEECCC-ceeECHhHHHHHHHHHH
Confidence 345567889998 467787776 89999999988876543
No 175
>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=59.25 E-value=9.4 Score=28.31 Aligned_cols=36 Identities=28% Similarity=0.420 Sum_probs=21.9
Q ss_pred CCCCCCchHHHHHHHHHH--HHHHhCC-------CchhHHHHHhcCCCC
Q 032244 46 LAPYDPDWYYIRAASMAR--KIYLRGG-------LGVGSFRRIYGGGKR 85 (144)
Q Consensus 46 ~~P~d~DW~y~RaASilR--klYl~g~-------~Gv~~l~~~YGg~k~ 85 (144)
++|.||||| |.++. +.+.+++ +.+.-||-.|+|.+.
T Consensus 1 mm~~~P~~W----~~ll~~l~~~~~~~i~g~~lA~~mA~LR~~Y~g~~~ 45 (107)
T TIGR01594 1 MMIKEPDLW----AALLSWLQDAWRSQGQGALLALAIAYLRIRYMGGKF 45 (107)
T ss_pred CCCCCccHH----HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHcCccH
Confidence 478899987 33332 3344432 345678888987553
No 176
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=58.61 E-value=29 Score=25.93 Aligned_cols=55 Identities=13% Similarity=0.171 Sum_probs=39.5
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc----eeCcchH
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR----RITSSGQ 129 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR----~lT~~G~ 129 (144)
.||+.|.-.++..|+.|...+|-.+ +-+=+=|+.|+++|||+...+ || .|-+...
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsq--------------stvS~HL~~L~~AGLV~~~r~-Gr~~~Y~l~~~~~ 78 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQ--------------PKISRHLALLRESGLLLDRKQ-GKWVHYRLSPHIP 78 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCceEEEEE-cCEEEEEECchHH
Confidence 4666665558999999999887432 345566889999999998887 54 4555433
No 177
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=58.47 E-value=18 Score=29.33 Aligned_cols=37 Identities=11% Similarity=0.159 Sum_probs=28.4
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+-+.+++||+ ..|++++.+ |=.||+.|+.++....
T Consensus 30 ~avS~~I~~LE~~lg~~LF~R~~r-~v~lT~~G~~l~~~a~ 69 (305)
T PRK11233 30 PALSQQVATLEGELNQQLLIRTKR-GVTPTEAGKILYTHAR 69 (305)
T ss_pred hHHHHHHHHHHHHhCCceEEeCCC-CceECHhHHHHHHHHH
Confidence 356778889988 467787775 8999999988776543
No 178
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=58.34 E-value=11 Score=30.28 Aligned_cols=36 Identities=17% Similarity=0.261 Sum_probs=26.7
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+=+.+++||+ ..|.+++.. |-.||+.|+.++..+-
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~r-~~~lT~~G~~l~~~a~ 70 (301)
T PRK14997 32 KLSRRIAQLEERLGVRLIQRTTR-QFNVTEVGQTFYEHCK 70 (301)
T ss_pred HHHHHHHHHHHHhCCEeeeeccC-cceEcHhHHHHHHHHH
Confidence 34456889988 356677665 8999999998886643
No 179
>COG1485 Predicted ATPase [General function prediction only]
Probab=56.31 E-value=4.7 Score=36.07 Aligned_cols=57 Identities=25% Similarity=0.486 Sum_probs=42.8
Q ss_pred chHHHHHHHHHHHHHHhCCCchhH---HHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCC
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGS---FRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTN 112 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~---l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~g 112 (144)
-|+|-|.+...|=||+.||||.|. |-..|.+-.-..-+.-||. ..++.+-|.|..+.
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 589999888899999999999986 5566766444433445554 47888888888765
No 180
>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=56.26 E-value=9.2 Score=27.71 Aligned_cols=28 Identities=32% Similarity=0.547 Sum_probs=21.2
Q ss_pred HHHhCCcc-eecCCCC---ceeCcchHhhHHH
Q 032244 107 QLQDTNII-ELDSKGG---RRITSSGQRDLDQ 134 (144)
Q Consensus 107 qLE~~glv-~k~~~gG---R~lT~~G~~~lD~ 134 (144)
+|..+||| +....+| -+||++|.+..|-
T Consensus 58 SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 58 SLVGLGLVEEEEEKGGFKYYRLTEKGKRIAEM 89 (90)
T ss_pred hHHHcCCeeEeeecCCeeEEEeChhhhhHHhc
Confidence 79999999 4444334 5799999988763
No 181
>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=56.11 E-value=28 Score=21.39 Aligned_cols=42 Identities=12% Similarity=0.151 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHh-CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCC
Q 032244 57 RAASMARKIYLR-GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTN 112 (144)
Q Consensus 57 RaASilRklYl~-g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~g 112 (144)
|-..|+.-|.-. +++....|+..+|- |..-|++-++.|++.|
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~v--------------S~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGV--------------SRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS---------------HHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCC
Confidence 456688888664 56999999998885 4458999999999999
No 182
>PF14178 YppF: YppF-like protein
Probab=56.08 E-value=17 Score=24.83 Aligned_cols=20 Identities=30% Similarity=0.855 Sum_probs=16.9
Q ss_pred HHHHHHHhCCCchhHHHHHh
Q 032244 61 MARKIYLRGGLGVGSFRRIY 80 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~Y 80 (144)
.+|+.||.|.+.+...|..+
T Consensus 27 Far~~Yi~gei~i~eYR~lv 46 (60)
T PF14178_consen 27 FARKLYIQGEISINEYRNLV 46 (60)
T ss_pred HHHHHHHhCcccHHHHHHHH
Confidence 58999999999998887643
No 183
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=55.89 E-value=43 Score=29.49 Aligned_cols=56 Identities=13% Similarity=0.189 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHH--h--CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244 56 IRAASMARKIYL--R--GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125 (144)
Q Consensus 56 ~RaASilRklYl--~--g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT 125 (144)
..+-.++.+++- + .|++...|++..+ .+-.+++.+|.+|+++|||...++|+-.++
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 3667777777544 455699999999999999987776544443
No 184
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=55.25 E-value=25 Score=33.21 Aligned_cols=58 Identities=21% Similarity=0.281 Sum_probs=46.1
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc------eeCcchHhhHHHHHHHHhh
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR------RITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR------~lT~~G~~~lD~iA~~i~~ 141 (144)
.+.+..|+....+..| -+|.+|+||++.||++-.+.-|| .+...+...+-..|+++++
T Consensus 23 ~~tl~eLA~~lfCS~R--------------h~R~lL~q~q~~gWL~W~p~~GRGkrSrL~flr~~e~L~~q~a~~~le 86 (564)
T COG4533 23 ETTLNELADILFCSRR--------------HARTLLRQMQEAGWLTWQPQAGRGKRSRLTFLRTPEALLLQLAEKLLE 86 (564)
T ss_pred eeeHHHHHHHhccCHH--------------HHHHHHHHHHHcCCEEeccCCCCCcceeEEEecChHHHHHHHHHHHHh
Confidence 5778888888877655 69999999999999999885555 3556788888888887754
No 185
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=55.15 E-value=13 Score=30.48 Aligned_cols=36 Identities=14% Similarity=0.219 Sum_probs=28.0
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+=..+|+||+ ..|++.+.+ |-.||+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a~ 70 (308)
T PRK10094 32 TISYRIKLLEENTGVALFFRTTR-SVTLTAAGEHLLSQAR 70 (308)
T ss_pred HHHHHHHHHHHHhCCEEEeeCCC-ceeECHhHHHHHHHHH
Confidence 45567889998 467777766 8999999999887654
No 186
>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=54.15 E-value=13 Score=28.04 Aligned_cols=48 Identities=23% Similarity=0.302 Sum_probs=36.2
Q ss_pred HHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 65 IYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 65 lYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
||+.+ |.....|+..++-. -..+|.+|+-|++.|+|+..++|--.++.
T Consensus 46 L~~~~~ipy~~e~LA~~~~~~--------------~~~V~~AL~~f~k~glIe~~ed~~i~i~~ 95 (121)
T PF09681_consen 46 LYLSGNIPYTAEMLALEFDRP--------------VDTVRLALAVFQKLGLIEIDEDGVIYIPN 95 (121)
T ss_pred EEECCCCCCcHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCeEEeec
Confidence 45543 77888888887733 35899999999999999998875444543
No 187
>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=53.91 E-value=17 Score=28.87 Aligned_cols=36 Identities=25% Similarity=0.454 Sum_probs=25.2
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+=+.+|+||+ ..|.+.+.+ |-.||+.|+.+++.+.
T Consensus 31 avS~~Ik~LE~~lg~~LF~R~~r-~~~lT~~G~~l~~~a~ 69 (291)
T TIGR03418 31 AVSQQVKRLEEELGTPLFERGHR-GIELTEDGQRLFEAVR 69 (291)
T ss_pred HHHHHHHHHHHHhCcHHhhcCCC-ceeEcHhHHHHHHHHH
Confidence 45566788887 355666554 7888999988877544
No 188
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=53.12 E-value=16 Score=30.29 Aligned_cols=37 Identities=16% Similarity=0.189 Sum_probs=26.8
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+=+.+++||+ ..|.+...++...||+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~r~~~~LT~~G~~l~~~a~ 71 (324)
T PRK12681 32 GISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRIAR 71 (324)
T ss_pred HHHHHHHHHHHHhCCEeEEECCCCCCccCHHHHHHHHHHH
Confidence 45567889988 46777776522369999999987644
No 189
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=53.11 E-value=19 Score=29.07 Aligned_cols=37 Identities=11% Similarity=0.165 Sum_probs=26.0
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
-+=..+++||+ ..|.+...+ |-.||+.|+.++..+..
T Consensus 34 avS~~I~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a~~ 73 (296)
T PRK11062 34 TITGQIKALEERLQGKLFKRKGR-GLEPTELGELVFRYADK 73 (296)
T ss_pred HHHHHHHHHHHHcCccceeecCC-ceeECHhHHHHHHHHHH
Confidence 34456778887 466777665 88899999888766543
No 190
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=53.04 E-value=25 Score=27.85 Aligned_cols=36 Identities=17% Similarity=0.220 Sum_probs=27.4
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+-+.+++||+ ..|++.+.+ |-.||+.|+..+..+.
T Consensus 37 avS~~i~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a~ 75 (294)
T PRK09986 37 PLSIHIKELEDQLGTPLFIRHSR-SVVLTHAGKILMEESR 75 (294)
T ss_pred HHHHHHHHHHHHhCCeeEeeCCC-ceeECHhHHHHHHHHH
Confidence 56677888987 467777765 8899999998886543
No 191
>PRK10632 transcriptional regulator; Provisional
Probab=52.66 E-value=23 Score=28.92 Aligned_cols=38 Identities=13% Similarity=0.255 Sum_probs=28.9
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
+-+=..+++||+ ..|.+.+.+ |-.||+.|+.++..+..
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~r-~i~lT~~G~~l~~~a~~ 71 (309)
T PRK10632 31 SSISQTVSKLEDELQVKLLNRSTR-SIGLTEAGRIYYQGCRR 71 (309)
T ss_pred HHHHHHHHHHHHHhCCeeecccCC-CceechhHHHHHHHHHH
Confidence 356677899997 467777776 89999999998766543
No 192
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=52.51 E-value=21 Score=28.22 Aligned_cols=35 Identities=11% Similarity=0.152 Sum_probs=27.5
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
-+-+.+++||+ ..|.+...+ |=.||+.|+.+++.+
T Consensus 33 avS~~I~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a 70 (290)
T PRK10837 33 AVSAALTDLEGQLGVQLFDRVGK-RLVVNEHGRLLYPRA 70 (290)
T ss_pred HHHHHHHHHHHHhCCccEeecCC-eEEECHhHHHHHHHH
Confidence 46677888988 467777776 888999999988864
No 193
>PHA02943 hypothetical protein; Provisional
Probab=52.41 E-value=55 Score=26.43 Aligned_cols=54 Identities=24% Similarity=0.187 Sum_probs=43.5
Q ss_pred chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCC
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKG 120 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~g 120 (144)
|=...|---||+-| -.|...+..+.+..|= |-+=+|++|..||+.|.|++.+.|
T Consensus 7 d~v~~R~~eILE~L-k~G~~TtseIAkaLGl--------------S~~qa~~~LyvLErEG~VkrV~~G 60 (165)
T PHA02943 7 DTVHTRMIKTLRLL-ADGCKTTSRIANKLGV--------------SHSMARNALYQLAKEGMVLKVEIG 60 (165)
T ss_pred HHHHHHHHHHHHHH-hcCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHcCceEEEeec
Confidence 44556777788877 6677778899998873 456899999999999999998873
No 194
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=52.23 E-value=22 Score=28.37 Aligned_cols=34 Identities=15% Similarity=0.293 Sum_probs=20.9
Q ss_pred HHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHH
Q 032244 101 ARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 101 iR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
+=+.+++||+ ..|.+...+ |=.||+.|+..++.+
T Consensus 32 vSr~i~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l~~~a 68 (296)
T PRK09906 32 LSQQIKDLENCVGVPLLVRDKR-KVALTAAGEVFLQDA 68 (296)
T ss_pred HHHHHHHHHHHhCCeeeeeCCC-cceEcHhHHHHHHHH
Confidence 3345666666 355666554 677777777777643
No 195
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=51.44 E-value=24 Score=28.60 Aligned_cols=36 Identities=11% Similarity=0.149 Sum_probs=27.9
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+-+.+++||+ ..|++.+.+ |=.||+.|+.+++...
T Consensus 35 avS~~i~~LE~~lg~~Lf~R~~r-~~~lT~~G~~l~~~a~ 73 (305)
T CHL00180 35 AVSLQIKNLEKQLNIPLFDRSKN-KASLTEAGELLLRYGN 73 (305)
T ss_pred HHHHHHHHHHHHhCCEEEEecCC-CceECHhHHHHHHHHH
Confidence 56678889988 466777665 8999999999976644
No 196
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=51.00 E-value=45 Score=27.46 Aligned_cols=54 Identities=17% Similarity=0.216 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT 125 (144)
|-..|+.-|--++.+.+..|...|+ -|-.-||+=|..||+.|++.+.-. |=.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~--------------vS~~TiRRdL~~Le~~g~l~r~~G-Ga~~~ 59 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFS--------------VSPQTIRRDLNDLAEQNKILRHHG-GAALP 59 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecC-CEEec
Confidence 6667888888889999999999885 355789999999999999988764 54433
No 197
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=50.59 E-value=23 Score=28.77 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=29.6
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+-+.+++||+ ..|++.+.+ |=.||+.|+.+++.+.
T Consensus 33 savS~~Ik~LE~~lg~~Lf~R~~~-~v~LT~~G~~l~~~a~ 72 (309)
T PRK11013 33 PTVSRELARFEKVIGLKLFERVRG-RLHPTVQGLRLFEEVQ 72 (309)
T ss_pred HHHHHHHHHHHHHhCceeeeecCC-CcccCHHHHHHHHHHH
Confidence 467788999998 467777765 7899999999988654
No 198
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=50.23 E-value=23 Score=29.32 Aligned_cols=36 Identities=11% Similarity=0.259 Sum_probs=25.9
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
-+=+-+++||+ ..|++.+.+ |-.||+.|+.++..+.
T Consensus 41 avS~~I~~LE~~lG~~LF~R~~~-~~~LT~~G~~l~~~a~ 79 (310)
T PRK15092 41 AVSQQMQRLEQLVGKELFARHGR-NKLLTEHGIQLLGYAR 79 (310)
T ss_pred HHHHHHHHHHHHhCcceEEECCC-CceECHhHHHHHHHHH
Confidence 34455778887 467777765 8889999998877654
No 199
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.73 E-value=55 Score=26.79 Aligned_cols=52 Identities=15% Similarity=0.155 Sum_probs=42.0
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
|-..|+..|--++.+.+..|...+| -|-.=||+-|.+||+.|++.....|+.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~--------------VS~~TiRRdL~~L~~~~~l~r~~Gga~ 56 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLN--------------VSKETIRRDLNELQTQGKILRNHGRAK 56 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCeEE
Confidence 4556777777889999999999996 455689999999999999987654343
No 200
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=48.95 E-value=25 Score=29.08 Aligned_cols=35 Identities=20% Similarity=0.234 Sum_probs=23.4
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
-+-+.+++||+ ..|++...+ |=.||+.|+.+++.+
T Consensus 32 aVS~~Ik~LE~~lg~~LF~R~~r-~v~lT~~G~~l~~~a 69 (317)
T PRK15421 32 ALSHQFSDLEQRLGFRLFVRKSQ-PLRFTPQGEILLQLA 69 (317)
T ss_pred HHHHHHHHHHHHhCCEEEEecCC-CceECHhHHHHHHHH
Confidence 45566777776 355666554 678888888777654
No 201
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=48.90 E-value=27 Score=28.46 Aligned_cols=35 Identities=23% Similarity=0.414 Sum_probs=27.7
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
-+-+.+++||+ ..|.+.+.+ |=.||+.|+.++..+
T Consensus 37 avS~~I~~LE~~lg~~LF~R~~r-~~~lT~~G~~l~~~a 74 (312)
T PRK10341 37 AVSKIINDIEDYFGVELIVRKNT-GVTLTPAGQVLLSRS 74 (312)
T ss_pred HHHHHHHHHHHHhCCeEEEEcCC-CceEChhHHHHHHHH
Confidence 56677889988 356777776 899999999998853
No 202
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=48.62 E-value=25 Score=29.33 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=27.7
Q ss_pred hHHHHHHHHHh---CCcceecCCCCc-eeCcchHhhHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGR-RITSSGQRDLDQVAG 137 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR-~lT~~G~~~lD~iA~ 137 (144)
-+=..+++||+ ..|++++.+ |- .||+.|+.+++.+..
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~r-~v~~LT~~G~~l~~~a~~ 72 (327)
T PRK12680 32 GLSKQLKQLEDELGFLLFVRKGR-SLESVTPAGVEVIERARA 72 (327)
T ss_pred HHHHHHHHHHHHhCCeEEEECCC-cCCccCccHHHHHHHHHH
Confidence 45567889987 456777765 55 499999999988654
No 203
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=48.30 E-value=40 Score=28.07 Aligned_cols=58 Identities=21% Similarity=0.410 Sum_probs=44.9
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CC--Cc-----eeCcchHhh
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KG--GR-----RITSSGQRD 131 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~g--GR-----~lT~~G~~~ 131 (144)
.|+.-+--++|+.++.+..+-|=. ..-+|.=|+.||+.|+|+... .+ || .||.+|.+.
T Consensus 15 ~il~lL~~~g~~sa~elA~~Lgis--------------~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~ 80 (218)
T COG2345 15 RILELLKKSGPVSADELAEELGIS--------------PMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQ 80 (218)
T ss_pred HHHHHHhccCCccHHHHHHHhCCC--------------HHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhh
Confidence 355555558999999999998853 347899999999999998654 22 54 799998863
No 204
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=47.77 E-value=21 Score=30.76 Aligned_cols=41 Identities=12% Similarity=0.197 Sum_probs=32.3
Q ss_pred chhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCc
Q 032244 72 GVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITS 126 (144)
Q Consensus 72 Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~ 126 (144)
.+..|++.|| -|.+-+|.++++||+.|+|+..+..|-.+.+
T Consensus 31 s~r~la~~~~--------------vsr~tv~~a~~~L~~~g~i~~~~~~G~~v~~ 71 (431)
T PRK15481 31 PVRELASELG--------------VNRNTVAAAYKRLVTAGLAQSQGRNGTVIRG 71 (431)
T ss_pred CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCceEEcc
Confidence 4556777676 4667999999999999999988766776654
No 205
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=47.33 E-value=29 Score=28.16 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=27.7
Q ss_pred hHHHHHHHHHh---CCcceecCCCCc-eeCcchHhhHHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGR-RITSSGQRDLDQVAGR 138 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR-~lT~~G~~~lD~iA~~ 138 (144)
-+=+.+++||+ ..|+++..+ |- .||+.|+.+++.+..-
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~~-~~~~lT~~G~~l~~~~~~~ 73 (309)
T PRK12682 32 GVSKAIIELEEELGIEIFIRHGK-RLKGLTEPGKAVLDVIERI 73 (309)
T ss_pred HHHHHHHHHHHHhCCeeEEECCC-CcCccCHhHHHHHHHHHHH
Confidence 45667889987 456676665 54 6999999998876543
No 206
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=46.78 E-value=13 Score=28.17 Aligned_cols=23 Identities=35% Similarity=0.499 Sum_probs=19.8
Q ss_pred CchhhHHHHHHHHHhCCcceecC
Q 032244 96 SSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~ 118 (144)
=.||+.|.+|+.|+.-|+|....
T Consensus 72 IngsLAr~alr~L~~kG~Ik~Vs 94 (110)
T KOG1767|consen 72 INGSLARAALRELSNKGVIKQVS 94 (110)
T ss_pred hchHHHHHHHHHHHhcchHHHHh
Confidence 35789999999999999998654
No 207
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=46.65 E-value=35 Score=27.35 Aligned_cols=37 Identities=19% Similarity=0.343 Sum_probs=28.3
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+=+.+++||+ ..|++.... |=.||+.|+.++..+.
T Consensus 35 ~avS~~i~~LE~~lg~~Lf~R~~r-~l~lT~~G~~l~~~~~ 74 (297)
T PRK11139 35 AAVSHQIKALEDFLGLKLFRRRNR-SLLLTEEGQRYFLDIR 74 (297)
T ss_pred HHHHHHHHHHHHHhCchheEecCC-ceeECHhHHHHHHHHH
Confidence 356677889988 367777765 8899999999887753
No 208
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=46.47 E-value=29 Score=28.42 Aligned_cols=38 Identities=24% Similarity=0.257 Sum_probs=26.3
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
-+=..+++||+ ..|++.+.++...||+.|+..++.+..
T Consensus 32 avS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~ 72 (313)
T PRK12684 32 GVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVER 72 (313)
T ss_pred HHHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHHHH
Confidence 34556788887 466676665335799999998876543
No 209
>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=46.34 E-value=21 Score=30.35 Aligned_cols=58 Identities=17% Similarity=0.174 Sum_probs=38.1
Q ss_pred chHHHHHHHHHHHHHH--hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244 52 DWYYIRAASMARKIYL--RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125 (144)
Q Consensus 52 DW~y~RaASilRklYl--~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT 125 (144)
+|||. ++|-|-= .+-.-+..|.+.-+. .=|-.=+|.+|+-|+++|||+++.+|--+.|
T Consensus 121 ~W~~~----virel~~~~~~~~~~~~ia~~l~p------------~is~~ev~~sL~~L~~~glikk~~~g~y~~t 180 (271)
T TIGR02147 121 HWYNS----VIRELLGVMPFADDPEELAKRCFP------------KISAEQVKESLDLLERLGLIKKNEDGFYKQT 180 (271)
T ss_pred HHHHH----HHHHHhhcCCCCCCHHHHHHHhCC------------CCCHHHHHHHHHHHHHCCCeeECCCCcEEee
Confidence 68875 5665552 222245667765442 1245679999999999999999987434443
No 210
>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=45.50 E-value=24 Score=27.64 Aligned_cols=42 Identities=14% Similarity=0.245 Sum_probs=33.4
Q ss_pred hhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcch
Q 032244 73 VGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSG 128 (144)
Q Consensus 73 v~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G 128 (144)
-..|+..||- |...+|.+|+.|+..|+|......|..+++..
T Consensus 28 E~eLa~~~~V--------------sr~Tvr~Al~~L~~eGli~~~~g~Gt~V~~~~ 69 (231)
T TIGR03337 28 ERDLGERFNT--------------TRVTIREALQQLEAEGLIYREDRRGWFVSPPR 69 (231)
T ss_pred HHHHHHHHCC--------------CHHHHHHHHHHHHHCCeEEEeCCCEEEECCcc
Confidence 4567888874 36799999999999999998886677776543
No 211
>PF15522 Toxin_42: Putative toxin 42
Probab=44.14 E-value=24 Score=28.87 Aligned_cols=81 Identities=19% Similarity=0.291 Sum_probs=46.6
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhC-----CCchhHHHHHhcCCCCCC
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRG-----GLGVGSFRRIYGGGKRNG 87 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g-----~~Gv~~l~~~YGg~k~rG 87 (144)
+.||+.+-+-|..---=++|.|.+|+||-..-- ..+= -|| +=++| +.|--.+++.-|..---=
T Consensus 38 ~AF~rr~Rem~dA~~~~~v~~W~~Y~~T~~~S~-----atfg------glr-VG~HGQltG~~~G~~~~~~~~G~~~Gmm 105 (205)
T PF15522_consen 38 DAFIRRMREMLDAVAGGSVDTWENYTTTTEVSN-----ATFG------GLR-VGTHGQLTGRPTGDVDLEPVSGEGAGMM 105 (205)
T ss_pred HHHHHHHHHHHHhccCCCCCchHhccccCcccc-----cccc------cce-eeecceeccccccccccccCCccccccc
Confidence 478888888887664457899999999953211 0000 011 22222 334444444444222222
Q ss_pred CCCCCCCCCchhhHHHHH
Q 032244 88 SRPPHFSKSSGSVARHIL 105 (144)
Q Consensus 88 ~~P~h~~~asg~iiR~~L 105 (144)
++|...-++|-.+..+.|
T Consensus 106 srpar~~R~SHH~~QYLL 123 (205)
T PF15522_consen 106 SRPARAGRQSHHIPQYLL 123 (205)
T ss_pred cCcccccccccchHHHHH
Confidence 578888888888777765
No 212
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=43.90 E-value=45 Score=27.15 Aligned_cols=34 Identities=9% Similarity=0.142 Sum_probs=21.1
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
-+=+.+++||+ ..|++++.+ |=.||+.|+.++..
T Consensus 52 avS~~I~~LE~~lg~~LF~R~~r-~~~lT~~G~~l~~~ 88 (314)
T PRK09508 52 AVSNAVARLKVMFNDELFVRYGR-GIQPTARARQLFGP 88 (314)
T ss_pred HHHHHHHHHHHhhCCCcEEEcCC-CCcCcHHHHHHHHH
Confidence 45556667766 356666654 66777777766554
No 213
>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=43.62 E-value=31 Score=27.54 Aligned_cols=37 Identities=22% Similarity=0.290 Sum_probs=28.5
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
+-+=+.+++||+ ..|++.. + |=.||+.|+.+++.+-.
T Consensus 30 pavS~~I~~LE~~lg~~Lf~R~-r-~~~lT~~G~~l~~~~~~ 69 (292)
T TIGR03298 30 SAVSQRIKALEERLGQPLLVRT-Q-PCRATEAGQRLLRHARQ 69 (292)
T ss_pred HHHHHHHHHHHHHhCchheecC-C-CCcCCHhHHHHHHHHHH
Confidence 346677889997 4677875 4 89999999999877544
No 214
>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=43.59 E-value=58 Score=23.31 Aligned_cols=50 Identities=10% Similarity=0.172 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
-|++-|.-.|++.+..+.......+. -+-+-++..|.-|++-|+|+....
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~l~~~~~----------~~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEALPEERS----------WAYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHCTTSS------------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHhCCCCCHHHHHHHHHhccc----------cchhHHHHHHHHHHhCCceeEeec
Confidence 47888888999999999999876521 245789999999999999998876
No 215
>PHA00738 putative HTH transcription regulator
Probab=43.10 E-value=72 Score=24.02 Aligned_cols=48 Identities=21% Similarity=0.087 Sum_probs=34.5
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCce
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRR 123 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~ 123 (144)
||..|.-.+++.|+.|...++- |..-+=+=|+.|+++|||+.... ||.
T Consensus 17 IL~lL~~~e~~~V~eLae~l~l--------------SQptVS~HLKvLreAGLV~srK~-Gr~ 64 (108)
T PHA00738 17 ILELIAENYILSASLISHTLLL--------------SYTTVLRHLKILNEQGYIELYKE-GRT 64 (108)
T ss_pred HHHHHHHcCCccHHHHHHhhCC--------------CHHHHHHHHHHHHHCCceEEEEE-CCE
Confidence 5554543457999999998863 33455566899999999998776 654
No 216
>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=42.31 E-value=31 Score=24.33 Aligned_cols=35 Identities=23% Similarity=0.273 Sum_probs=26.1
Q ss_pred hhhHHHHHHHHHhCCcceecCC--CCceeCcchHhhH
Q 032244 98 GSVARHILHQLQDTNIIELDSK--GGRRITSSGQRDL 132 (144)
Q Consensus 98 g~iiR~~LqqLE~~glv~k~~~--gGR~lT~~G~~~l 132 (144)
.+-+.++|++|-+.|+|..... .|-+||-.|-..|
T Consensus 38 ~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~L 74 (82)
T PF09202_consen 38 EGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYL 74 (82)
T ss_dssp HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHH
T ss_pred HHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHH
Confidence 4567789999999999997552 3999999996543
No 217
>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=42.29 E-value=19 Score=25.40 Aligned_cols=25 Identities=20% Similarity=0.384 Sum_probs=17.0
Q ss_pred HHHHHHHhCCcceecCCCCceeCcchHhh
Q 032244 103 HILHQLQDTNIIELDSKGGRRITSSGQRD 131 (144)
Q Consensus 103 ~~LqqLE~~glv~k~~~gGR~lT~~G~~~ 131 (144)
++++.|..+|.|+. ++ .||+-|+..
T Consensus 1 ~A~~~L~~Lgald~--~~--~lT~lG~~~ 25 (102)
T PF04408_consen 1 KALELLKSLGALDE--NG--NLTPLGRKM 25 (102)
T ss_dssp -HHHHHHHTTSB-T--TS---B-HHHHHH
T ss_pred CHHHHHHHCCCCCC--CC--CcCHHHHHH
Confidence 47899999999943 32 899999865
No 218
>PF14502 HTH_41: Helix-turn-helix domain
Probab=41.00 E-value=31 Score=22.50 Aligned_cols=26 Identities=27% Similarity=0.465 Sum_probs=21.6
Q ss_pred CchhhHHHHHHHHHhCCcceecCCCCc
Q 032244 96 SSGSVARHILHQLQDTNIIELDSKGGR 122 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~~gGR 122 (144)
-|...|-++|+-||+.|-|.-..+ ||
T Consensus 18 vs~GtiQ~Alk~Le~~gaI~Le~r-Gh 43 (48)
T PF14502_consen 18 VSRGTIQNALKFLEENGAIKLESR-GH 43 (48)
T ss_pred cchhHHHHHHHHHHHCCcEEeeec-Cc
Confidence 456789999999999999987766 44
No 219
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=40.89 E-value=36 Score=29.60 Aligned_cols=43 Identities=19% Similarity=0.280 Sum_probs=35.5
Q ss_pred hhHHHHHHHHHhCCcceecCCC--C-ceeCcchHhhHHHHHHHHhh
Q 032244 99 SVARHILHQLQDTNIIELDSKG--G-RRITSSGQRDLDQVAGRIAV 141 (144)
Q Consensus 99 ~iiR~~LqqLE~~glv~k~~~g--G-R~lT~~G~~~lD~iA~~i~~ 141 (144)
..+|.+|.-|-++|++....+| + .+||.+|...+-+-+..|..
T Consensus 43 ~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkgl~r~~~a~~riy~ 88 (291)
T COG3327 43 TTVRAALSRMVKAGWLVGEREGRKSFYRLSDKGLARQRRAARRIYP 88 (291)
T ss_pred HHHHHHHHHHHhccchheeecccccceeecHHHHHHHHHHhhhhcC
Confidence 4789999999999999866642 2 57899999999988888764
No 220
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=40.82 E-value=60 Score=26.16 Aligned_cols=38 Identities=16% Similarity=0.272 Sum_probs=28.3
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
.-+-..+++||+ .-|..++.+ |=.||+.|+.++..+-.
T Consensus 31 pavS~~I~~LE~~lg~~LF~R~~r-~~~lT~~G~~l~~~~~~ 71 (300)
T PRK11074 31 SAVSYTVRQLEEWLAVPLFERRHR-DVELTPAGEWFVKEARS 71 (300)
T ss_pred HHHHHHHHHHHHHhCCeeEEeCCC-CceECccHHHHHHHHHH
Confidence 356678889988 466777665 78999999998766543
No 221
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=40.75 E-value=41 Score=28.18 Aligned_cols=43 Identities=28% Similarity=0.258 Sum_probs=31.6
Q ss_pred chhhHHHHHHHHHhCCcceecC-CCC--ceeCcchHhhHHHHHHHH
Q 032244 97 SGSVARHILHQLQDTNIIELDS-KGG--RRITSSGQRDLDQVAGRI 139 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~-~gG--R~lT~~G~~~lD~iA~~i 139 (144)
|+.-.=.+|++||+.|+|++.. +.| =.+|++|.+.|-..-.++
T Consensus 32 S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~~~d~ 77 (214)
T COG1339 32 SSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKEYEDL 77 (214)
T ss_pred CcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHHHHHH
Confidence 3334445789999999999765 345 478999999987765554
No 222
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=40.22 E-value=1.7e+02 Score=22.61 Aligned_cols=67 Identities=13% Similarity=0.230 Sum_probs=54.3
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGR 138 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~ 138 (144)
+.|+--+=-+|.+.+..+....| +|..-++..|.+|.+-|-|-.+-.-|--.+++...|-|+...+
T Consensus 15 ~rIvElVRe~GRiTi~ql~~~TG--------------asR~Tvk~~lreLVa~G~l~~~G~~GvF~seqA~~dw~~~~~~ 80 (127)
T PF06163_consen 15 ARIVELVREHGRITIKQLVAKTG--------------ASRNTVKRYLRELVARGDLYRHGRSGVFPSEQARKDWDKARKK 80 (127)
T ss_pred HHHHHHHHHcCCccHHHHHHHHC--------------CCHHHHHHHHHHHHHcCCeEeCCCccccccHHHHHHHHHhHHh
Confidence 34555555689999999999888 5667899999999999999887655778888888888887765
Q ss_pred H
Q 032244 139 I 139 (144)
Q Consensus 139 i 139 (144)
.
T Consensus 81 ~ 81 (127)
T PF06163_consen 81 L 81 (127)
T ss_pred h
Confidence 4
No 223
>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=39.84 E-value=62 Score=22.77 Aligned_cols=44 Identities=18% Similarity=0.280 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244 58 AASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (144)
Q Consensus 58 aASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~ 115 (144)
++-|++-|..+|.+-=..|...-|- +-+.+|++|+.|.+.|+|.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l--------------~~~~vRkiL~~L~~~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGL--------------KPKEVRKILYKLYEDGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S---------------HHHHHHHHHHHHHHSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeE
Confidence 4567777777888888888885553 4479999999999999995
No 224
>PRK09213 pur operon repressor; Provisional
Probab=39.77 E-value=1.3e+02 Score=25.70 Aligned_cols=78 Identities=14% Similarity=0.238 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCc-----c
Q 032244 57 RAASMARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITS-----S 127 (144)
Q Consensus 57 RaASilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~-----~ 127 (144)
|...|-+.|-=++ -+.+..|+..|+..|- .-.-.=.||+.+|++ +.+|.|+..+ .||-+.+| +
T Consensus 8 r~~~~~~~l~~~p~~~~~l~~f~~~~~~aks-------~ised~~i~~~~~~~-~~~g~~~t~~ga~ggv~~~p~~~~~~ 79 (271)
T PRK09213 8 RLVDMTKYLLENPNKLISLTFFAERYGAAKS-------SISEDLVIIKETFEK-QGIGTLETVPGAAGGVKYIPSISEEE 79 (271)
T ss_pred HHHHHHHHHHhCCCceEcHHHHHHHhccccc-------hhhhhHHHHHHHHHh-cCCceEEEeCCCCCCeEEEcCCCHHH
Confidence 4444554444343 4899999999997663 112223489999977 4689999887 56766665 3
Q ss_pred hHhhHHHHHHHHhhc
Q 032244 128 GQRDLDQVAGRIAVV 142 (144)
Q Consensus 128 G~~~lD~iA~~i~~~ 142 (144)
.++.|+.++.++.+.
T Consensus 80 a~~~~~~L~~~L~~~ 94 (271)
T PRK09213 80 AREFVEELCERLSEP 94 (271)
T ss_pred HHHHHHHHHHHHHhC
Confidence 788899998887543
No 225
>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=39.32 E-value=26 Score=23.38 Aligned_cols=23 Identities=13% Similarity=0.224 Sum_probs=18.4
Q ss_pred CchhhHHHHHHHHHhCCcceecC
Q 032244 96 SSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~ 118 (144)
-+-.-++.+|+.||.+|+|+...
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEEE
Confidence 34467888999999999998554
No 226
>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=39.19 E-value=11 Score=30.74 Aligned_cols=86 Identities=15% Similarity=0.303 Sum_probs=50.8
Q ss_pred CchHHHHHHHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHH----hCCC-chhHHHHHhcCCC-
Q 032244 11 SPHEFVKAYAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYL----RGGL-GVGSFRRIYGGGK- 84 (144)
Q Consensus 11 ~~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl----~g~~-Gv~~l~~~YGg~k- 84 (144)
-|+.+|++|-+.+.++|-|-+|....---... ||..++||= .|..+... ..|. ++|.|...|-...
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 37899999999999999999998765433333 888889984 23333333 2467 9999999887644
Q ss_pred -CCCCCCCCCCCCchhhHHHH
Q 032244 85 -RNGSRPPHFSKSSGSVARHI 104 (144)
Q Consensus 85 -~rG~~P~h~~~asg~iiR~~ 104 (144)
.|...|.|.--|-|.-...+
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 34567777777777766655
No 227
>PF14113 DUF4285: Domain of unknown function (DUF4285)
Probab=39.17 E-value=89 Score=22.98 Aligned_cols=44 Identities=23% Similarity=0.388 Sum_probs=32.3
Q ss_pred HHHHHHHcCCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHh
Q 032244 19 YAAHLKRSGKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLR 68 (144)
Q Consensus 19 ~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~ 68 (144)
++--|-.+| +++|.-. ...+...+.|-.||++|+..++--|..+
T Consensus 11 mS~aL~~~G-~~i~~~~-----~~~~~~~~~~g~~y~~ra~~l~~~L~~~ 54 (115)
T PF14113_consen 11 MSYALNYSG-IPIKSFS-----TLGRTVSGADGKWYIYRAEELANWLKKK 54 (115)
T ss_pred HHHHHHhCC-CccCccc-----ccceeccCCCCCchhhHHHHHHHHHHHC
Confidence 444566666 5555544 3477788889999999999999877777
No 228
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=38.90 E-value=56 Score=26.98 Aligned_cols=35 Identities=9% Similarity=0.096 Sum_probs=21.0
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQV 135 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~i 135 (144)
-+-+.+++||+ ..|.+...+ |=.||+.|+.++..+
T Consensus 59 avS~~I~~LE~~lG~~LF~R~~r-~v~lT~~G~~l~~~~ 96 (317)
T PRK11482 59 AISQSIQKLRVIFPDPLFIRKGQ-GVTPTAYATHLHEYI 96 (317)
T ss_pred HHHHHHHHHHHHhCCcceEecCC-CccCCHHHHHHHHHH
Confidence 45566667776 345555543 667777777665543
No 229
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=38.68 E-value=60 Score=25.13 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=24.8
Q ss_pred HHHHHHHHHh-C--CcceecCCCCceeCcchHhhHHHHHH
Q 032244 101 ARHILHQLQD-T--NIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 101 iR~~LqqLE~-~--glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
+=..+++||+ + .|.+.... |=.||+.|+..++.+-.
T Consensus 32 vS~~I~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l~~~a~~ 70 (297)
T COG0583 32 VSRQIKRLEEELGVPLFERTTR-RVRLTEAGERLLERARR 70 (297)
T ss_pred HHHHHHHHHHHhCchheeecCC-ceeeCHhHHHHHHHHHH
Confidence 5567889988 3 44444444 46799999988876543
No 230
>PF15129 FAM150: FAM150 family
Probab=38.20 E-value=22 Score=27.34 Aligned_cols=17 Identities=24% Similarity=0.432 Sum_probs=13.9
Q ss_pred hHHHHHHHHHHHHHHhC
Q 032244 53 WYYIRAASMARKIYLRG 69 (144)
Q Consensus 53 W~y~RaASilRklYl~g 69 (144)
=||.|||++|-+|.+.+
T Consensus 103 ayykrcarlltrla~sp 119 (123)
T PF15129_consen 103 AYYKRCARLLTRLAVSP 119 (123)
T ss_pred HHHHHHHHHHHHhccCc
Confidence 48999999998887653
No 231
>PRK13239 alkylmercury lyase; Provisional
Probab=37.89 E-value=99 Score=25.54 Aligned_cols=52 Identities=17% Similarity=0.150 Sum_probs=34.6
Q ss_pred hHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244 53 WYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124 (144)
Q Consensus 53 W~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l 124 (144)
++..++ |||.|-.-.|+.+..|.+..|.. ..-+|.+|++| ..++-+++ |+.+
T Consensus 21 ~~~~~~--llr~la~G~pvt~~~lA~~~~~~--------------~~~v~~~L~~l---~~~~~d~~-g~iv 72 (206)
T PRK13239 21 ATLLVP--LLRLLAKGRPVSVTTLAAALGWP--------------VEEVEAVLEAM---PDTEYDED-GRII 72 (206)
T ss_pred hHHHHH--HHHHHHcCCCCCHHHHHHHhCCC--------------HHHHHHHHHhC---CCeEECCC-CCEE
Confidence 444444 78887755699999999987743 34566665554 56666775 5553
No 232
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=37.83 E-value=97 Score=25.52 Aligned_cols=49 Identities=16% Similarity=0.276 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
|=-.|+.-|=-+|-+-|..|...||= |..=||+=|..||+.|++.+...
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~V--------------S~~TIRRDL~~Le~~g~l~R~hG 54 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGV--------------SEMTIRRDLNELEEQGLLLRVHG 54 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCC--------------CHHHHHHhHHHHHHCCcEEEEeC
Confidence 55668888888899999999999883 56789999999999999999875
No 233
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=37.76 E-value=35 Score=30.34 Aligned_cols=39 Identities=23% Similarity=0.386 Sum_probs=31.2
Q ss_pred CCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q 032244 94 SKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLD 133 (144)
Q Consensus 94 ~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD 133 (144)
+..+=-+.=.++..||..|+|+.++. |=.||.+|..+..
T Consensus 44 s~~plp~v~~i~~~l~~egiv~~~~g-~v~~TekG~E~~e 82 (354)
T COG1568 44 SDLPLPLVASILEILEDEGIVKIEEG-GVELTEKGEELAE 82 (354)
T ss_pred ccCCchHHHHHHHHHHhcCcEEEecC-cEeehhhhHHHHH
Confidence 34444567788999999999998885 7999999998754
No 234
>PRK06474 hypothetical protein; Provisional
Probab=37.63 E-value=1.1e+02 Score=24.12 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=34.6
Q ss_pred HHHHHHHhCC-CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 61 MARKIYLRGG-LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 61 ilRklYl~g~-~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
|++-|.-.++ ..+..+....+ .-|.+-+=+-|+.|++.|+|+..+
T Consensus 16 Il~~L~~~~~~~ta~el~~~l~-------------~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 16 ICQVLMRNKEGLTPLELVKILK-------------DVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHhCCCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 6666666554 89999988764 255667778899999999999765
No 235
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=37.46 E-value=8.2 Score=30.63 Aligned_cols=14 Identities=21% Similarity=0.793 Sum_probs=10.9
Q ss_pred CCCCCCchHHHHHH
Q 032244 46 LAPYDPDWYYIRAA 59 (144)
Q Consensus 46 ~~P~d~DW~y~RaA 59 (144)
..|.++||||+.-.
T Consensus 28 ~t~~~~DfFY~C~~ 41 (182)
T PF08432_consen 28 ITPDNKDFFYVCPS 41 (182)
T ss_pred ecCCCCCeEEeCcc
Confidence 46889999997653
No 236
>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=37.40 E-value=25 Score=23.71 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=19.4
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhh
Q 032244 104 ILHQLQDTNIIELDSKGGRRITSSGQRD 131 (144)
Q Consensus 104 ~LqqLE~~glv~k~~~gGR~lT~~G~~~ 131 (144)
+++.|..+|.++. + | .||+-|+..
T Consensus 2 A~~~L~~LgAld~--~-~-~lT~lG~~m 25 (92)
T smart00847 2 ALELLYELGALDD--D-G-RLTPLGRKM 25 (92)
T ss_pred HHHHHHHCCCcCC--C-C-CcCHHHHHH
Confidence 6788999999964 3 3 899999975
No 237
>PRK09801 transcriptional activator TtdR; Provisional
Probab=37.39 E-value=33 Score=28.16 Aligned_cols=37 Identities=22% Similarity=0.417 Sum_probs=27.3
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+=..+++||+ .-|.+...+ |=.||+.|+.++..+-
T Consensus 35 pavS~~I~~LE~~LG~~Lf~R~~r-~~~lT~~G~~l~~~a~ 74 (310)
T PRK09801 35 AFVTKRIQILENTLATTLLNRSAR-GVALTESGQRCYEHAL 74 (310)
T ss_pred HHHHHHHHHHHHHhCCEeeeecCC-CCcccHhHHHHHHHHH
Confidence 345567889988 356677665 8999999998877643
No 238
>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=37.19 E-value=48 Score=27.38 Aligned_cols=51 Identities=16% Similarity=0.244 Sum_probs=41.2
Q ss_pred hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q 032244 68 RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLD 133 (144)
Q Consensus 68 ~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD 133 (144)
.||..+..|+..-|- +-.-++..|..|..+|++++.. +.-.+|+.+...|+
T Consensus 21 ~gp~t~~eLA~~~~~--------------~~~~~~~lL~~L~~lgll~~~~-~~y~~t~~~~~~l~ 71 (306)
T TIGR02716 21 EGPKDLATLAADTGS--------------VPPRLEMLLETLRQMRVINLED-GKWSLTEFADYMFS 71 (306)
T ss_pred cCCCCHHHHHHHcCC--------------ChHHHHHHHHHHHhCCCeEecC-CcEecchhHHhhcc
Confidence 478899999886553 2347999999999999999865 58999999977665
No 239
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=37.10 E-value=33 Score=29.16 Aligned_cols=27 Identities=30% Similarity=0.348 Sum_probs=22.8
Q ss_pred CchhhHHHHHHHHHhCCcceecCCCCce
Q 032244 96 SSGSVARHILHQLQDTNIIELDSKGGRR 123 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~~gGR~ 123 (144)
=|..-+++.+..||..|++..++. ||.
T Consensus 200 ls~aTV~~~lk~l~~~Gii~~~~~-Gr~ 226 (240)
T COG3398 200 LSVATVAYHLKKLEELGIIPEDRE-GRS 226 (240)
T ss_pred ccHHHHHHHHHHHHHcCCCccccc-Cce
Confidence 366789999999999999998876 554
No 240
>PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed
Probab=36.23 E-value=38 Score=23.28 Aligned_cols=42 Identities=17% Similarity=0.302 Sum_probs=24.3
Q ss_pred hhhHHHHHHHHHhCCc--ceecCCCCceeCcc--h------HhhHHHHHHHHhhcC
Q 032244 98 GSVARHILHQLQDTNI--IELDSKGGRRITSS--G------QRDLDQVAGRIAVVA 143 (144)
Q Consensus 98 g~iiR~~LqqLE~~gl--v~k~~~gGR~lT~~--G------~~~lD~iA~~i~~~~ 143 (144)
|.-|++.|+. +|+ |+...- |+.++=. | ...++.||.+++.|+
T Consensus 18 G~ai~~~l~~---lg~~~v~~Vr~-~k~~~l~~~~~~~~~a~~~v~~i~~~lL~Np 69 (80)
T PRK05974 18 GQAIKGALGS---LGYDGVEDVRQ-GKYFELELEGESEEKAEADLKEMCEKLLANP 69 (80)
T ss_pred HHHHHHHHHH---cCCCCcceEEE-EEEEEEEEcCCchhhhHHHHHHHHHHhcCCc
Confidence 3444445544 455 333333 5555544 4 677899999887653
No 241
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=36.21 E-value=56 Score=27.38 Aligned_cols=37 Identities=11% Similarity=0.051 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA 136 (144)
+-+=..+++||+ ..|.+...+ |=.||+.|+.++...-
T Consensus 33 pavS~~Ik~LE~eLG~~LF~R~~r-~~~LT~aG~~ll~~a~ 72 (297)
T PRK15243 33 TPLSRVISDLERELKQRLFIRKNG-TLIPTEFAQTIYRKVK 72 (297)
T ss_pred HHHHHHHHHHHHHhCCccEEeCCC-CeeECHHHHHHHHHHH
Confidence 346677889988 356676665 8899999999887643
No 242
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=36.04 E-value=87 Score=29.91 Aligned_cols=72 Identities=19% Similarity=0.212 Sum_probs=48.7
Q ss_pred CCCCCCchHHHHHHHHH-HHHHHh----------CCCc---hhHH----HHHhcCCCCCCCCCCCCCCCchhhHHHHHHH
Q 032244 46 LAPYDPDWYYIRAASMA-RKIYLR----------GGLG---VGSF----RRIYGGGKRNGSRPPHFSKSSGSVARHILHQ 107 (144)
Q Consensus 46 ~~P~d~DW~y~RaASil-RklYl~----------g~~G---v~~l----~~~YGg~k~rG~~P~h~~~asg~iiR~~Lqq 107 (144)
-.|.+.-+||.+.|.=+ |+-|+. +.-| -+.+ ...+|+-. .=++++|..
T Consensus 408 g~pT~sG~~ya~LA~~i~R~P~lTr~E~~vl~kiP~~~~i~~~~~~e~~~d~~~~ee--------------~~i~~AL~k 473 (591)
T PF04458_consen 408 GEPTESGRFYAELARHIKRLPHLTRYEMEVLHKIPDKGYIHREELVEFIKDHVGKEE--------------EEIIEALEK 473 (591)
T ss_pred CCCCcchHHHHHHHhhhhhcccccHHHHHHHHhCCccccccHHHHHHHhhcccccch--------------HHHHHHHHH
Confidence 36889999999988743 555553 1111 1111 12222221 235679999
Q ss_pred HHhCCcceecCCCCceeCcchHhh
Q 032244 108 LQDTNIIELDSKGGRRITSSGQRD 131 (144)
Q Consensus 108 LE~~glv~k~~~gGR~lT~~G~~~ 131 (144)
||.-|+|+--++|+=.+|+.|+..
T Consensus 474 LEArGfI~~Lp~g~iilTeaG~~i 497 (591)
T PF04458_consen 474 LEARGFIEILPNGMIILTEAGELI 497 (591)
T ss_pred HHhcchHHHcCCCcEEEehhhHHH
Confidence 999999999999999999999753
No 243
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=35.68 E-value=33 Score=30.07 Aligned_cols=30 Identities=23% Similarity=0.317 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHHHcCCCC--CCCcchhcccCC
Q 032244 13 HEFVKAYAAHLKRSGKIE--LPTWNDIVKTGT 42 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~--~P~w~d~vKTg~ 42 (144)
..-|..-|+|||++|||. .+++++||-..-
T Consensus 297 ~kAi~~ta~FLkeQgkv~avl~DYs~yVts~f 328 (334)
T COG4521 297 VKAIADTAEFLKEQGKVPAVLNDYSPYVTSRF 328 (334)
T ss_pred HHHHHHHHHHHHHcCCCcccccchhhHhHHHH
Confidence 345788899999999985 688888885543
No 244
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=35.67 E-value=49 Score=26.38 Aligned_cols=36 Identities=19% Similarity=0.290 Sum_probs=26.7
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
-+=+.+++||+ ..|++.. + |-.||+.|+.+++.+-.
T Consensus 32 avS~~i~~LE~~lg~~Lf~R~-r-~i~lT~~G~~l~~~a~~ 70 (294)
T PRK13348 32 AVSQRIKALEESLGQPLLVRG-R-PCRPTPAGQRLLRHLRQ 70 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC-C-CCccChhHHHHHHHHHH
Confidence 45567888987 3566664 4 89999999888876553
No 245
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=35.64 E-value=59 Score=26.60 Aligned_cols=37 Identities=24% Similarity=0.282 Sum_probs=26.2
Q ss_pred hhHHHHHHHHHh---CCcceecCCCC-ceeCcchHhhHHHHH
Q 032244 99 SVARHILHQLQD---TNIIELDSKGG-RRITSSGQRDLDQVA 136 (144)
Q Consensus 99 ~iiR~~LqqLE~---~glv~k~~~gG-R~lT~~G~~~lD~iA 136 (144)
+-+=+.+++||+ ..|++.+.+ | ..||+.|+.+++.+-
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~r-~~~~lT~~G~~l~~~a~ 71 (309)
T PRK12683 31 SGVSKQIKDLEDELGVEIFIRRGK-RLTGLTEPGKELLQIVE 71 (309)
T ss_pred HHHHHHHHHHHHHhCCeeEeeCCC-CcCCcCHHHHHHHHHHH
Confidence 346677889988 356666554 4 369999999887654
No 246
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=35.56 E-value=55 Score=26.82 Aligned_cols=36 Identities=19% Similarity=0.172 Sum_probs=24.3
Q ss_pred hHHHHHHHHHh---CCcceecCCCC-ceeCcchHhhHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGG-RRITSSGQRDLDQVA 136 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gG-R~lT~~G~~~lD~iA 136 (144)
-+=+.+++||+ ..|.+.... | -.||+.|+.+++.+.
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~~-~~~~lT~~G~~l~~~a~ 71 (316)
T PRK12679 32 GVSRHIRELEDELGIEIFIRRGK-RLLGMTEPGKALLVIAE 71 (316)
T ss_pred HHHHHHHHHHHHhCCEEEEECCC-cccccCHhHHHHHHHHH
Confidence 45567888987 345555543 4 379999999876543
No 247
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=34.86 E-value=21 Score=33.86 Aligned_cols=40 Identities=20% Similarity=0.191 Sum_probs=32.5
Q ss_pred CchhhHHHHHHHHHhCCcceecCCC----CceeCcchHhhHHHH
Q 032244 96 SSGSVARHILHQLQDTNIIELDSKG----GRRITSSGQRDLDQV 135 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~~g----GR~lT~~G~~~lD~i 135 (144)
..=.++|.+|..||+-+||+....+ -..||+-|++.|+..
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 3445789999999999999876632 378999999999965
No 248
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=34.51 E-value=85 Score=27.33 Aligned_cols=44 Identities=16% Similarity=0.242 Sum_probs=34.8
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
||..|-..||.-|..++..-|=. .+.+-.-+|.||++||++...
T Consensus 28 Il~lL~~k~plNvneiAe~lgLp--------------qst~s~~ik~Le~aGlirT~t 71 (308)
T COG4189 28 ILQLLHRKGPLNVNEIAEALGLP--------------QSTMSANIKVLEKAGLIRTET 71 (308)
T ss_pred HHHHHHHhCCCCHHHHHHHhCCc--------------hhhhhhhHHHHHhcCceeeee
Confidence 55566667999999999988843 356667789999999998665
No 249
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=33.41 E-value=1.1e+02 Score=24.68 Aligned_cols=41 Identities=15% Similarity=0.097 Sum_probs=33.7
Q ss_pred HHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee
Q 032244 59 ASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (144)
Q Consensus 59 ASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k 116 (144)
--+|--|+.++|+.-..+..+.|-.. -.++++|.+.|||+.
T Consensus 93 LEtLaiIay~qPiTr~eI~~irGv~~-----------------~~ii~~L~~~gLI~e 133 (188)
T PRK00135 93 LEVLAIIAYKQPITRIEIDEIRGVNS-----------------DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCH-----------------HHHHHHHHHCCCeEE
Confidence 34788899999999999999887321 567889999999974
No 250
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=33.09 E-value=27 Score=24.38 Aligned_cols=28 Identities=18% Similarity=0.359 Sum_probs=24.5
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchhccc
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDIVKT 40 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~vKT 40 (144)
+.|.+.+++.|++.++|++|.|-.|.-+
T Consensus 27 ~~~~~~i~~~L~~g~~V~l~gfG~F~~~ 54 (94)
T PRK00199 27 KEILEEMSDALARGDRIEIRGFGSFSLH 54 (94)
T ss_pred HHHHHHHHHHHHcCCeEEEcCCEEEEEE
Confidence 6788999999999999999999887544
No 251
>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=32.44 E-value=38 Score=22.91 Aligned_cols=22 Identities=23% Similarity=0.173 Sum_probs=17.6
Q ss_pred chhhHHHHHHHHHhCCcceecC
Q 032244 97 SGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~ 118 (144)
|-.=++..|.+||.+|+|+...
T Consensus 38 s~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 38 SYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHHHHhCCCeEEEe
Confidence 3456788999999999998665
No 252
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=32.31 E-value=1.4e+02 Score=19.13 Aligned_cols=43 Identities=26% Similarity=0.309 Sum_probs=34.7
Q ss_pred HhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244 67 LRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124 (144)
Q Consensus 67 l~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l 124 (144)
-.+++.|+.++...|. |.+.+--+|.-|.+.|+.....+ .|+|
T Consensus 7 ~~~~itv~~~rd~lg~--------------sRK~ai~lLE~lD~~g~T~R~gd-~Rvl 49 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGL--------------SRKYAIPLLEYLDREGITRRVGD-KRVL 49 (50)
T ss_dssp TTSSBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETT-EEEE
T ss_pred cCCcCcHHHHHHHHCc--------------cHHHHHHHHHHHhccCCEEEeCC-EEee
Confidence 3789999999998884 66788889999999999987765 5654
No 253
>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=30.87 E-value=45 Score=28.64 Aligned_cols=20 Identities=35% Similarity=0.471 Sum_probs=17.5
Q ss_pred hHHHHHHHHHhCCcceecCC
Q 032244 100 VARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 100 iiR~~LqqLE~~glv~k~~~ 119 (144)
=||.-||.|...|++|....
T Consensus 229 KIRQqLQ~LRD~g~IeFl~r 248 (254)
T PF06044_consen 229 KIRQQLQILRDKGIIEFLGR 248 (254)
T ss_dssp HHHHHHHHHHHTTSEEE-ST
T ss_pred HHHHHHHHHhhCCceEEecC
Confidence 49999999999999998876
No 254
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.86 E-value=48 Score=26.91 Aligned_cols=27 Identities=22% Similarity=0.278 Sum_probs=23.5
Q ss_pred CCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 93 FSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 93 ~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
+++=|-..|+.||++||+.|+.+-..+
T Consensus 63 ~R~Ls~~~i~~Il~~l~k~g~~e~~Dk 89 (174)
T KOG4068|consen 63 QRRLSQEFIDEILEELEKKGLAEPTDK 89 (174)
T ss_pred hccCCHHHHHHHHHHHHHccCCccccc
Confidence 566788899999999999999987765
No 255
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=30.75 E-value=57 Score=26.20 Aligned_cols=36 Identities=19% Similarity=0.249 Sum_probs=25.9
Q ss_pred hHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q 032244 100 VARHILHQLQD---TNIIELDSKGGRRITSSGQRDLDQVAG 137 (144)
Q Consensus 100 iiR~~LqqLE~---~glv~k~~~gGR~lT~~G~~~lD~iA~ 137 (144)
-+=..+++||+ ..|.++. + |-.||+.|+.++..+-.
T Consensus 32 avS~~I~~LE~~lg~~LF~R~-~-~~~lT~~G~~l~~~a~~ 70 (294)
T PRK03635 32 AVSQRIKALEERVGQVLLVRT-Q-PCRPTEAGQRLLRHARQ 70 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC-C-CCccCHHHHHHHHHHHH
Confidence 34456788987 3566664 5 89999999998766543
No 256
>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=30.63 E-value=28 Score=24.15 Aligned_cols=26 Identities=15% Similarity=0.360 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchhc
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDIV 38 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~v 38 (144)
+.|.+.+++.|++.++|++|.+-.|-
T Consensus 27 ~~~~~~i~~~L~~g~~V~l~gfG~F~ 52 (94)
T TIGR00988 27 KTMLEHMASALAQGDRIEIRGFGSFS 52 (94)
T ss_pred HHHHHHHHHHHHcCCeEEEcCcEEEE
Confidence 67889999999999999999998774
No 257
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=30.45 E-value=1.4e+02 Score=18.73 Aligned_cols=51 Identities=25% Similarity=0.375 Sum_probs=35.7
Q ss_pred HHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244 60 SMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124 (144)
Q Consensus 60 SilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l 124 (144)
.|++.+.-..+..+..+.... .-+.+.+.+-|..|+++|+|+...+++..+
T Consensus 29 ~il~~l~~~~~~~~~~l~~~~--------------~~~~~~v~~hL~~L~~~glv~~~~~~~~~~ 79 (110)
T COG0640 29 EILSLLAEGGELTVGELAEAL--------------GLSQSTVSHHLKVLREAGLVELRREGRLRL 79 (110)
T ss_pred HHHHHHHhcCCccHHHHHHHH--------------CCChhHHHHHHHHHHHCCCeEEEecccEEE
Confidence 344444433577788888877 345567778888899999999877655443
No 258
>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=30.40 E-value=2e+02 Score=20.27 Aligned_cols=58 Identities=17% Similarity=0.138 Sum_probs=36.6
Q ss_pred CCCCCch--HHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244 47 APYDPDW--YYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (144)
Q Consensus 47 ~P~d~DW--~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~ 115 (144)
|..+.|| +....|.-+|.+|++-|-.+.-+... | ......-.++=.+|+.|.++|+=.
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 3334466 55677778999999988666555431 0 122233345558999999999864
No 259
>TIGR01743 purR_Bsub pur operon repressor, Bacillus subtilis type. This model represents the puring operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.
Probab=30.21 E-value=2.1e+02 Score=24.38 Aligned_cols=77 Identities=8% Similarity=0.123 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHhC--CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC--CCCceeCcc-----
Q 032244 57 RAASMARKIYLRG--GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS--KGGRRITSS----- 127 (144)
Q Consensus 57 RaASilRklYl~g--~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~--~gGR~lT~~----- 127 (144)
|...+-+.|--++ -+.+..|+..|+..|- .-.-.=.|||.+|++ +.+|.++..+ .||-+.+|.
T Consensus 6 r~~~~t~~l~~~p~~~~~l~~f~~~~~~aks-------~ised~~i~~~~~~~-~~~g~~~t~~ga~ggv~~~p~~~~~~ 77 (268)
T TIGR01743 6 RLVDLTNYLITNPNKLIPLNFFSERYESAKS-------SISEDIVIIKETFEK-FGIGKLLTVPGAAGGVKYIPKMSQAE 77 (268)
T ss_pred HHHHHHHHHHhCCCceEcHHHHHHHhccccc-------hhhhhHHHHHHHHHh-cCCceEEEeCCCCCCeEEEeCCCHHH
Confidence 4444554444443 4899999999997663 111223489999977 4689999887 567766653
Q ss_pred hHhhHHHHHHHHhh
Q 032244 128 GQRDLDQVAGRIAV 141 (144)
Q Consensus 128 G~~~lD~iA~~i~~ 141 (144)
.+.+|++++..+.+
T Consensus 78 ~~~~~~~l~~~l~~ 91 (268)
T TIGR01743 78 AEEFVEELCQSLSE 91 (268)
T ss_pred HHHHHHHHHHHHHH
Confidence 66778888777654
No 260
>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=29.48 E-value=29 Score=29.93 Aligned_cols=40 Identities=18% Similarity=0.356 Sum_probs=32.7
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k 116 (144)
|+.|+.|+..-|+.-. ++.+|... ++.+|..|++.|+|+.
T Consensus 231 P~kvetl~~lcGS~~~---~l~~FR~~----Lk~AL~eL~~~g~v~~ 270 (282)
T PF07042_consen 231 PIKVETLRELCGSESS---RLRKFRQQ----LKKALDELVAVGFVSS 270 (282)
T ss_pred CccHHHHHHHcCCCcc---CHHHHHHH----HHHHHHHHHhcCceeE
Confidence 8999999998887542 46666654 8999999999999974
No 261
>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=29.07 E-value=1.4e+02 Score=21.26 Aligned_cols=53 Identities=15% Similarity=0.013 Sum_probs=37.2
Q ss_pred CCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 69 GGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 69 g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
.++.++.|+..-...-. +-..-|-.+++.+|.+|-+.+-|=.+..|=..+||+
T Consensus 28 ~~at~E~l~~~L~~~yp------~i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivtP~ 80 (80)
T PF10264_consen 28 QPATQETLREHLRKHYP------GIAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVTPQ 80 (80)
T ss_pred CcchHHHHHHHHHHhCC------CCCCCCHHHHHHHHHHHHHcCceeeCCCceEeeCCC
Confidence 45666665554442222 244567789999999999999998887766778875
No 262
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=29.05 E-value=33 Score=24.18 Aligned_cols=25 Identities=12% Similarity=0.299 Sum_probs=22.5
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchh
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDI 37 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~ 37 (144)
|.|++.+.+.|++.++|++|.|--|
T Consensus 26 ~~~~~~i~~~L~~~~~v~l~gfG~F 50 (90)
T PRK10664 26 DAIIASVTESLKEGDDVALVGFGTF 50 (90)
T ss_pred HHHHHHHHHHHhCCCEEEECCcEEE
Confidence 6788999999999999999999777
No 263
>PRK06423 phosphoribosylformylglycinamidine synthase; Provisional
Probab=28.92 E-value=61 Score=21.85 Aligned_cols=40 Identities=23% Similarity=0.236 Sum_probs=21.0
Q ss_pred HHHHHHHhCCc--ceecCCCCceeCc--chHhhHHHHHHHHhhcC
Q 032244 103 HILHQLQDTNI--IELDSKGGRRITS--SGQRDLDQVAGRIAVVA 143 (144)
Q Consensus 103 ~~LqqLE~~gl--v~k~~~gGR~lT~--~G~~~lD~iA~~i~~~~ 143 (144)
.+.++|..+|+ |+...- |+.++= .....++.+|.+++.|+
T Consensus 20 ti~~~l~~lg~~~v~~Vr~-~k~~~l~~~~~~~~~~i~~~lL~Np 63 (73)
T PRK06423 20 TILKNLNILGYNGIKGVSI-SKVYYFDADSYNEVDEIAGKILTNP 63 (73)
T ss_pred HHHHHHHHcCCCCcceEEE-EEEEEEecCCHHHHHHHHHHhcCCc
Confidence 33344444454 232222 444443 33556888888887664
No 264
>COG0096 RpsH Ribosomal protein S8 [Translation, ribosomal structure and biogenesis]
Probab=28.80 E-value=54 Score=25.42 Aligned_cols=31 Identities=23% Similarity=0.162 Sum_probs=25.7
Q ss_pred ceeccCchHHHHHHHHHHHHcCCCCCCCcch
Q 032244 6 NVKDVSPHEFVKAYAAHLKRSGKIELPTWND 36 (144)
Q Consensus 6 tv~DV~~~~fI~~~A~~LK~~gki~~P~w~d 36 (144)
..-++|+..++.++++-||++|-|.==+..|
T Consensus 23 ~~v~~P~SKl~~~il~vLk~eGYI~~f~~~~ 53 (132)
T COG0096 23 EVVSMPASKLKGAILKVLKKEGYIKDFEVID 53 (132)
T ss_pred ceeecchHHHHHHHHHHHHHcCCcceEEEEe
Confidence 4568999999999999999999987544444
No 265
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=28.63 E-value=1.4e+02 Score=22.79 Aligned_cols=59 Identities=22% Similarity=0.231 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244 57 RAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDL 132 (144)
Q Consensus 57 RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l 132 (144)
.|-.++..|...||.-...|++.-|..+ ..+|++. --=||.|+.++|=-.||++|+..|
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 3445555667788888888887655322 1222221 124999999998799999999754
No 266
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=28.06 E-value=1.2e+02 Score=20.88 Aligned_cols=17 Identities=12% Similarity=0.221 Sum_probs=15.3
Q ss_pred chHHHHHHHHHHHHcCC
Q 032244 12 PHEFVKAYAAHLKRSGK 28 (144)
Q Consensus 12 ~~~fI~~~A~~LK~~gk 28 (144)
.+.|++.|.+|++.+|.
T Consensus 3 ~~~F~~~L~~F~~~~g~ 19 (93)
T smart00501 3 RVLFLDRLYKFMEERGS 19 (93)
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 57899999999999986
No 267
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=27.93 E-value=88 Score=19.99 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=30.2
Q ss_pred HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
--++.+++-++|++.+.. ..-..++...+|++|++.|.|..+.
T Consensus 12 ~Plr~G~~keeLrsrl~~-----------~~l~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 12 NPLRPGMPKEELRSRLFK-----------PRLPPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp -TTSS-EEHHHHHHHCST------------TS-HCCHHHHHHHHHHTTSEEEES
T ss_pred CcCccCcCHHHHHHHHhh-----------ccCCHHHHHHHHHHHHHCCCeeeEC
Confidence 334568888999976653 1234678999999999999997654
No 268
>PF00727 IL4: Interleukin 4 This family is a subset of the SCOP family; InterPro: IPR002354 Cytokines are protein messengers that carry information from cell to cell []. Interleukin is one such molecule, and participates in several B-cell activation processes: e.g., it enhances production and secretion of IgG1 and IgE []; it induces expression of class II major histocompatability complex (MHC) molecules on resting B-cells; and it regulates expression of the low affinity Fc receptor for IgE on lymphocytes and monocytes. Interleukin-4 (IL4) has a compact, globular fold (similar to other cytokines), stabilised by 3 disulphide bonds []. One half of the structure is dominated by a 4 alpha-helix bundle with a left-handed twist []. The helices are anti-parallel, with 2 overhand connections, which fall into a 2-stranded anti-parallel beta-sheet [].; GO: 0005136 interleukin-4 receptor binding, 0008083 growth factor activity, 0006955 immune response, 0005576 extracellular region; PDB: 1HIK_A 1HZI_A 1ITI_A 2INT_A 1RCB_A 1CYL_A 3QB7_A 1BBN_A 2B8Z_A 1ITM_A ....
Probab=27.84 E-value=23 Score=27.03 Aligned_cols=52 Identities=25% Similarity=0.319 Sum_probs=32.3
Q ss_pred ccCchHHHHHHHHHHHHc---CCCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHh
Q 032244 9 DVSPHEFVKAYAAHLKRS---GKIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLR 68 (144)
Q Consensus 9 DV~~~~fI~~~A~~LK~~---gki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~ 68 (144)
|+.=.+.|+.+-.-..+. .++.||+=..--|..+-+|+ +-|||.+||++|..
T Consensus 4 ~~~L~EIIk~lN~Lt~kk~~C~el~V~Dvfa~~KnttekEl--------lCrAatvLr~~y~~ 58 (117)
T PF00727_consen 4 DITLKEIIKTLNILTEKKTPCMELTVADVFAAPKNTTEKEL--------LCRAATVLRQFYSH 58 (117)
T ss_dssp STHHHHHHHHHHHHHTS-SSSTTSEEE-GGGSSSSSSHHHH--------HHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHhcCCCccchhhhhHHhccCCCCCcchh--------hhHHHHHHHHHHhc
Confidence 334455566555444432 45666665555576666664 56999999999985
No 269
>PF15398 DUF4619: Domain of unknown function (DUF4619)
Probab=27.71 E-value=13 Score=32.29 Aligned_cols=67 Identities=18% Similarity=0.377 Sum_probs=48.2
Q ss_pred CCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHH----HHHHHHHhCCccee
Q 032244 41 GTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVAR----HILHQLQDTNIIEL 116 (144)
Q Consensus 41 g~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR----~~LqqLE~~glv~k 116 (144)
....+|||.-+.|| =|..++=|-+|++=| ...+..|||+ .=||.||.+++-..
T Consensus 56 ~~egQLPPLret~y-Grys~v~r~m~FDIp----------------------le~~EtSIIKrHPPRRlQkLEp~~lP~~ 112 (296)
T PF15398_consen 56 ALEGQLPPLRETWY-GRYSTVPRAMYFDIP----------------------LENGETSIIKRHPPRRLQKLEPIDLPQV 112 (296)
T ss_pred ccccCCCchhhccc-cccccCCCceeeeec----------------------ccCCcccccccCCCccccccCCCCCCcc
Confidence 34589999999886 588889999999865 3346678888 46899999877654
Q ss_pred cCCCCceeCcchHhh
Q 032244 117 DSKGGRRITSSGQRD 131 (144)
Q Consensus 117 ~~~gGR~lT~~G~~~ 131 (144)
..- +|.++++..+.
T Consensus 113 its-~rll~q~e~~~ 126 (296)
T PF15398_consen 113 ITS-ERLLSQQEART 126 (296)
T ss_pred cch-hhhhhHHHhhh
Confidence 443 56666665543
No 270
>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=27.48 E-value=62 Score=21.99 Aligned_cols=50 Identities=22% Similarity=0.308 Sum_probs=32.4
Q ss_pred chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
|=.|-.|..++. -.+.+.++.|.+.|.=--+ =.=.++.|||+.|+|....
T Consensus 5 D~ly~~a~~~V~---~~~~~S~S~lQR~~rIGyn--------------rAariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 5 DPLYEEAVEFVI---EEGKASISLLQRKFRIGYN--------------RAARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp STTHHHHHHHHH---HCTCECHHHHHHHHT--HH--------------HHHHHHHHHHHCTSBE---
T ss_pred cHHHHHHHHHHH---HcCCccHHHHHHHhCCCHH--------------HHHHHHHHHHHCCCCCCCC
Confidence 445666666543 3678888989887763222 2346899999999997554
No 271
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=27.44 E-value=90 Score=28.89 Aligned_cols=82 Identities=16% Similarity=0.150 Sum_probs=55.6
Q ss_pred CchHHHHHHHHHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCC------C---CchhhHHHHHHHHHhCCcceecCC-
Q 032244 51 PDWYYIRAASMARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFS------K---SSGSVARHILHQLQDTNIIELDSK- 119 (144)
Q Consensus 51 ~DW~y~RaASilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~------~---asg~iiR~~LqqLE~~glv~k~~~- 119 (144)
-|+. .-|..++.-+|- .+..|.+.+...+-|.++.-.+-.++. . -+..-++.+++||...|+++....
T Consensus 410 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 488 (607)
T PRK11057 410 YDGL-EDAQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDYGHDKLKVYGIGRDKSHEHWVSVIRQLIHLGLVTQNIAQ 488 (607)
T ss_pred cccH-HHHHHHHHHHHHhcCCCCcceeeeeeeccCcchhhhcccccCCccCcCCcCCHHHHHHHHHHHHHcCCceeccCc
Confidence 3654 345556666664 567888888888888766554332222 2 234578999999999999986542
Q ss_pred -CCceeCcchHhhHH
Q 032244 120 -GGRRITSSGQRDLD 133 (144)
Q Consensus 120 -gGR~lT~~G~~~lD 133 (144)
..=.||++|+..|.
T Consensus 489 ~~~l~~~~~~~~~l~ 503 (607)
T PRK11057 489 HSALQLTEAARPVLR 503 (607)
T ss_pred cceEEECHHHHHHhc
Confidence 24578888887765
No 272
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=27.12 E-value=67 Score=26.20 Aligned_cols=49 Identities=29% Similarity=0.352 Sum_probs=37.5
Q ss_pred HHHHHHH-hCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC-CCCce
Q 032244 61 MARKIYL-RGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS-KGGRR 123 (144)
Q Consensus 61 ilRklYl-~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~-~gGR~ 123 (144)
|.=-||+ +.|+.+..++.+-|-.+- -+=.++..||..++|++.. +|-|+
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sks--------------~vS~~lkkL~~~~lV~~~~~~G~Rk 81 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSKS--------------NVSMGLKKLQDWNLVKKVFEKGDRK 81 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCcc--------------hHHHHHHHHHhcchHHhhhccCcch
Confidence 3445789 889999999999995442 3556789999999999775 44454
No 273
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=27.06 E-value=1.3e+02 Score=21.78 Aligned_cols=53 Identities=11% Similarity=0.135 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHh
Q 032244 55 YIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQD 110 (144)
Q Consensus 55 y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~ 110 (144)
++-...+.++++-....++..|.+.||....+- .|.+..--...-.+++.|.+
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 345566666666444789999999999876432 34444444444555555543
No 274
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=26.91 E-value=91 Score=24.42 Aligned_cols=41 Identities=15% Similarity=0.118 Sum_probs=27.3
Q ss_pred chhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 97 SGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
+.--+=.+|++|++.|+|+... +.|+=.=...|.++|..+.
T Consensus 182 sretvsR~L~~L~~~G~I~~~~---~~i~I~d~~~L~~~~~~~~ 222 (226)
T PRK10402 182 SYRHLLYVLAQFIQDGYLKKSK---RGYLIKNRKQLSGLALELK 222 (226)
T ss_pred cHHHHHHHHHHHHHCCCEEeeC---CEEEEeCHHHHHHHHHHhc
Confidence 3344556999999999998754 3454434556666776654
No 275
>TIGR03703 plsB glycerol-3-phosphate O-acyltransferase. Members of this protein family are PlsB, glycerol-3-phosphate O-acyltransferase, present in E. coli and numerous related species. In many bacteria, PlsB is not found, and appears to be replaced by a two enzyme system for 1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y system.
Probab=26.70 E-value=1.7e+02 Score=28.73 Aligned_cols=50 Identities=16% Similarity=0.273 Sum_probs=39.2
Q ss_pred CCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHh
Q 032244 87 GSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGRIA 140 (144)
Q Consensus 87 G~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~i~ 140 (144)
-..|+.|. ..+.+.++|.|.+.|++.++.+ |-....+-...++..|..++
T Consensus 742 i~~pef~d---k~lf~~~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~l 791 (799)
T TIGR03703 742 INAPEFFD---KAVFSTFIATLREQGYLDDDGD-GKLIFDEKLEELADQLKALL 791 (799)
T ss_pred CCCccccc---HHHHHHHHHHHHHCCCCCcccc-cchhhHHHHHHHHHHHHHhc
Confidence 34677776 6799999999999999976565 77777888888877776665
No 276
>smart00190 IL4_13 Interleukins 4 and 13. Interleukins-4 and -13 are cytokines involved in inflammatory and immune responses. IL-4 stimulates B and T cells.
Probab=26.36 E-value=1.9e+02 Score=22.66 Aligned_cols=59 Identities=14% Similarity=0.214 Sum_probs=35.0
Q ss_pred ccCchHHHHHHHHHHHHcC--CCCCCCcchhcccCCCccCCCCCCchHHHHHHHHHHHHHHhCCCch
Q 032244 9 DVSPHEFVKAYAAHLKRSG--KIELPTWNDIVKTGTLKELAPYDPDWYYIRAASMARKIYLRGGLGV 73 (144)
Q Consensus 9 DV~~~~fI~~~A~~LK~~g--ki~~P~w~d~vKTg~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv 73 (144)
|+.=.|+|+.+-.--+++- =.+.+.|.-|..+-.. .+.=.|-||+-+||++|.+.--+|
T Consensus 28 ~~~LkEIIk~Ln~lT~~~~~~C~e~~V~dV~~~~kNt------Te~e~~CrA~~vLr~~y~~~~s~i 88 (138)
T smart00190 28 DITLREIIETLNNVTQKGTNLCTEMMVPDVLAATKNT------TEKELFCRALKVLRNFYFHNCSAI 88 (138)
T ss_pred cchHHHHHHHHHHHccCCCCCcccccHHHHhcccCCC------cchhHhhHHHHHHHHHHHhhhhHH
Confidence 6666778888776555431 1344555554422111 122358999999999998743333
No 277
>PRK02539 hypothetical protein; Provisional
Probab=26.16 E-value=65 Score=23.36 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhh
Q 032244 102 RHILHQLQDTNIIELDSKGGRRITSSGQRD 131 (144)
Q Consensus 102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~ 131 (144)
....+||+.+.+| +++ |--+||+=-..
T Consensus 42 ~~~~~~L~~i~iv--D~~-G~dVTP~Klk~ 68 (85)
T PRK02539 42 RSVRHHIEGIKIV--DEE-GNDVTPEKLRQ 68 (85)
T ss_pred HHHHHHhccceEE--CCC-CCCCCHHHHHH
Confidence 3456799999999 454 77899974443
No 278
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=25.92 E-value=58 Score=26.06 Aligned_cols=32 Identities=16% Similarity=0.265 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q 032244 102 RHILHQLQDTNIIELDSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~ 134 (144)
=.|.-.++.+|+|+-.. |.=.||++|+..+++
T Consensus 46 ~piv~ta~~Lglv~~e~-GDiilT~~Gk~~v~~ 77 (157)
T COG4754 46 MPIVETASLLGLVTAES-GDIILTDEGKEYVES 77 (157)
T ss_pred HHHHHHHHhcCceeccC-CCEEEehhhHHHHhC
Confidence 35677888899997544 578999999999875
No 279
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=25.64 E-value=1.1e+02 Score=25.20 Aligned_cols=39 Identities=21% Similarity=0.230 Sum_probs=30.0
Q ss_pred hhhHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHHH
Q 032244 98 GSVARHILHQLQDTNIIELDSKG---GRRITSSGQRDLDQVA 136 (144)
Q Consensus 98 g~iiR~~LqqLE~~glv~k~~~g---GR~lT~~G~~~lD~iA 136 (144)
-.+|-+.|..|++.|||+....| --.+|+.|.+.--+.|
T Consensus 113 th~itYslrKL~k~gLit~t~~gkevTy~vTa~G~~acarYa 154 (199)
T COG5631 113 THNITYSLRKLLKGGLITRTGSGKEVTYEVTALGHRACARYA 154 (199)
T ss_pred chhHHHHHHHHHhccceecCCCCceEEEEEecchHHHHHHHH
Confidence 35788999999999999977752 2467899987666544
No 280
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=24.93 E-value=77 Score=24.72 Aligned_cols=37 Identities=11% Similarity=0.062 Sum_probs=27.7
Q ss_pred CCCCchhhHHHHHHHHHhCCccee-cCCCCceeCcchH
Q 032244 93 FSKSSGSVARHILHQLQDTNIIEL-DSKGGRRITSSGQ 129 (144)
Q Consensus 93 ~~~asg~iiR~~LqqLE~~glv~k-~~~gGR~lT~~G~ 129 (144)
...-+..+++++++.|.++|+|.- ....|..+....|
T Consensus 148 ~~~~~k~v~~~a~E~L~~l~Ll~~~~~~~~~~~~~e~r 185 (203)
T PF14629_consen 148 IKVWSKPVALKAWEHLLSLELLKPNYDGSSNNVQKEFR 185 (203)
T ss_pred cccCCHHHHHHHHHHHHHCCCceecccCCCCccCccce
Confidence 346688899999999999999987 2333556666654
No 281
>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=24.91 E-value=56 Score=22.03 Aligned_cols=36 Identities=17% Similarity=0.213 Sum_probs=25.5
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
++-...|.+.+|-. ..-+-+.++.||+.|||.+.+-
T Consensus 18 Gi~q~~L~~~~~~D--------------~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 18 GITQSDLSKLLGID--------------PRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred CEehhHHHHHhCCC--------------chHHHHHHHHHHHCCCEEEEEe
Confidence 34445666666632 2367789999999999987763
No 282
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=24.67 E-value=1e+02 Score=21.72 Aligned_cols=43 Identities=14% Similarity=0.082 Sum_probs=30.2
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcc-eecCCCCceeCc
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNII-ELDSKGGRRITS 126 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv-~k~~~gGR~lT~ 126 (144)
++.=..|+..-|- |..-|=+.+|+|++.|+= +.....|+.|..
T Consensus 19 ~~SGe~La~~Lgi--------------SRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~ 62 (79)
T COG1654 19 FVSGEKLAEELGI--------------SRTAVWKHIQQLREEGVDIESVRGKGYLLPQ 62 (79)
T ss_pred cccHHHHHHHHCc--------------cHHHHHHHHHHHHHhCCceEecCCCceeccC
Confidence 4555666666663 456778899999999984 555555888864
No 283
>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=24.30 E-value=1.5e+02 Score=26.18 Aligned_cols=50 Identities=20% Similarity=0.370 Sum_probs=36.2
Q ss_pred hHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeCcc
Q 032244 74 GSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 74 ~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
..++..||..=++ .....+...+++.+|..|++.||++...++|=.|.|.
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 3455666653332 4456677889999999999999999888765666654
No 284
>PRK01546 hypothetical protein; Provisional
Probab=24.11 E-value=76 Score=22.67 Aligned_cols=26 Identities=15% Similarity=0.529 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHh
Q 032244 102 RHILHQLQDTNIIELDSKGGRRITSSGQR 130 (144)
Q Consensus 102 R~~LqqLE~~glv~k~~~gGR~lT~~G~~ 130 (144)
....+||+.+.+| +++ |--+||+=-.
T Consensus 43 ~~~~~~L~~i~vv--D~~-G~dVTP~Klk 68 (79)
T PRK01546 43 QNMLNELKGIKVV--NEQ-GTDVTPAKLK 68 (79)
T ss_pred HHHHHHhccceEE--CCC-CCCCCHHHHH
Confidence 3456799999999 454 7789997443
No 285
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=23.84 E-value=1e+02 Score=26.44 Aligned_cols=22 Identities=32% Similarity=0.418 Sum_probs=19.2
Q ss_pred chhhHHHHHHHHHhCCcceecC
Q 032244 97 SGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 97 sg~iiR~~LqqLE~~glv~k~~ 118 (144)
..|||=++|..||.+|++|...
T Consensus 217 TRSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 217 TRSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred hHHHHHHHHHHhhhcCceeecc
Confidence 4689999999999999999665
No 286
>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=23.70 E-value=39 Score=31.89 Aligned_cols=19 Identities=32% Similarity=0.434 Sum_probs=17.0
Q ss_pred CCCCCCchHHHHHHHHHHH
Q 032244 46 LAPYDPDWYYIRAASMARK 64 (144)
Q Consensus 46 ~~P~d~DW~y~RaASilRk 64 (144)
-||.|||||-.||..-+|.
T Consensus 333 DpP~~~~~FvHR~GRTaR~ 351 (567)
T KOG0345|consen 333 DPPKDPSSFVHRCGRTARA 351 (567)
T ss_pred CCCCChhHHHhhcchhhhc
Confidence 5899999999999998874
No 287
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=23.68 E-value=1.1e+02 Score=24.84 Aligned_cols=9 Identities=22% Similarity=-0.093 Sum_probs=4.5
Q ss_pred CceeCcchH
Q 032244 121 GRRITSSGQ 129 (144)
Q Consensus 121 GR~lT~~G~ 129 (144)
|=.+|+.|+
T Consensus 61 ~~~lT~~G~ 69 (319)
T PRK10216 61 GLSPTPLMV 69 (319)
T ss_pred CcccCHHHH
Confidence 444555554
No 288
>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=23.54 E-value=94 Score=23.49 Aligned_cols=42 Identities=14% Similarity=0.207 Sum_probs=30.7
Q ss_pred CCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCceeC
Q 032244 70 GLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRIT 125 (144)
Q Consensus 70 ~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~lT 125 (144)
|--.+.|+..++- +=..+|.+|+-|++.|+|+...+|--.|+
T Consensus 51 py~~e~LA~~~~~--------------~~~~V~~Al~~f~k~glIe~~d~g~i~i~ 92 (119)
T TIGR01714 51 PYNAEMLATMFNR--------------NVGDIRITLQTLESLGLIEKKNNGDIFLE 92 (119)
T ss_pred CCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCcEEeh
Confidence 5556677777662 23589999999999999998876533443
No 289
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=23.52 E-value=77 Score=22.18 Aligned_cols=36 Identities=33% Similarity=0.324 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHhCCcce--------e-cCCCCceeCcchHhhHHH
Q 032244 99 SVARHILHQLQDTNIIE--------L-DSKGGRRITSSGQRDLDQ 134 (144)
Q Consensus 99 ~iiR~~LqqLE~~glv~--------k-~~~gGR~lT~~G~~~lD~ 134 (144)
.=.-.+|++|.+.|+|+ . .....=.||.+|...|-.
T Consensus 25 ~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~E 69 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEE 69 (88)
T ss_dssp HHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHH
Confidence 56678999999999995 1 112255799999988864
No 290
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=23.46 E-value=1.2e+02 Score=25.37 Aligned_cols=66 Identities=21% Similarity=0.301 Sum_probs=41.3
Q ss_pred chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHh-C--CcceecC----CCCcee
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQD-T--NIIELDS----KGGRRI 124 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~-~--glv~k~~----~gGR~l 124 (144)
.+|=.|-..+++.|.-.|.+ ..-.+.-|- |-+-+=..+++||+ + -|++... .+|=.|
T Consensus 15 ~~~~~~~l~~l~~v~~~gS~--s~AA~~l~~--------------s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~~l 78 (263)
T PRK10676 15 LFADPRRISLLKQIALTGSI--SQGAKLAGI--------------SYKSAWDAINEMNQLSEHILVERATGGKGGGGAVL 78 (263)
T ss_pred cccCHHHHHHHHHHHHHCCH--HHHHHHhCC--------------CHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCcEE
Confidence 35556677777777777652 333333332 22345567888888 3 4577663 236789
Q ss_pred CcchHhhHH
Q 032244 125 TSSGQRDLD 133 (144)
Q Consensus 125 T~~G~~~lD 133 (144)
|+.|+.++.
T Consensus 79 T~~G~~l~~ 87 (263)
T PRK10676 79 TRYGERLIQ 87 (263)
T ss_pred CHHHHHHHH
Confidence 999999983
No 291
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=23.39 E-value=1.7e+02 Score=19.18 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCccee
Q 032244 56 IRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIEL 116 (144)
Q Consensus 56 ~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k 116 (144)
-.|+.|...|--+|...+..+.+.=+ =+-+.+|++|-.|...++|.-
T Consensus 13 ~~~~~V~~~Ll~~G~ltl~~i~~~t~--------------l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 13 EIVAKVGEVLLSRGRLTLREIVRRTG--------------LSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp HHHHHHHHHHHHC-SEEHHHHHHHHT----------------HHHHHHHHHHHHHTTSEEE
T ss_pred hHHHHHHHHHHHcCCcCHHHHHHHhC--------------CCHHHHHHHHHHHHHcCCeee
Confidence 35788888888899999999988433 456799999999999999874
No 292
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.34 E-value=59 Score=26.28 Aligned_cols=39 Identities=21% Similarity=0.292 Sum_probs=27.7
Q ss_pred hhHHHHHHHHHhCCcceecCCC--------------------CceeCcchHhhHHHHHH
Q 032244 99 SVARHILHQLQDTNIIELDSKG--------------------GRRITSSGQRDLDQVAG 137 (144)
Q Consensus 99 ~iiR~~LqqLE~~glv~k~~~g--------------------GR~lT~~G~~~lD~iA~ 137 (144)
--||.+|..|+++||++..... =-+||.+|..+|-.|-.
T Consensus 46 ~~i~e~l~dL~elGLier~tgttiKrteAKfKksaEVHKHHTYYrl~rege~~lr~i~~ 104 (175)
T COG4344 46 PRIREYLKDLKELGLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNREGEAVLREITP 104 (175)
T ss_pred HHHHHHHHHHHHcCCeeeccCchhhhhHHHHHHhHHHHhchhhheechhHHHHHHhcCH
Confidence 4689999999999999966521 14567777766655543
No 293
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=23.28 E-value=1.7e+02 Score=22.21 Aligned_cols=63 Identities=6% Similarity=-0.109 Sum_probs=44.1
Q ss_pred hHHHHHHHHHHHHHHhCC---------CchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 53 WYYIRAASMARKIYLRGG---------LGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 53 W~y~RaASilRklYl~g~---------~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
..-+-..-+||.+|...- +.+..+...|..-.. -.+.....-.-++.+|..|++.|+++....
T Consensus 74 ~~eTilLL~LR~~y~e~~~~~~~~~~~v~~~ei~e~~~~~~~----~~~d~~~~~~~~~~~l~~l~~~~ll~~~~~ 145 (166)
T PF13835_consen 74 LEETILLLVLRLLYEEKESLSGSERVVVTREEIVEKLESFLP----ESRDEAPFKKRLDAALRRLKRYGLLRRLDG 145 (166)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCCcEEEeHHHHHHHHHHHcc----ccccccchHHHHHHHHHHHHHCCCeeccCC
Confidence 444556669999999753 566777766664211 123445666789999999999999997764
No 294
>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=23.09 E-value=52 Score=23.07 Aligned_cols=25 Identities=12% Similarity=0.329 Sum_probs=22.8
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchh
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDI 37 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~ 37 (144)
+.|++.+++.|++.++|+++.+--|
T Consensus 27 ~~~~~~i~~~L~~g~~V~l~gfG~F 51 (96)
T TIGR00987 27 ELFFEEIRRALENGEQVKLSGFGNF 51 (96)
T ss_pred HHHHHHHHHHHHcCCeEEecCCEEE
Confidence 6788999999999999999999877
No 295
>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=22.76 E-value=44 Score=26.17 Aligned_cols=59 Identities=20% Similarity=0.286 Sum_probs=43.8
Q ss_pred CCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCC
Q 032244 50 DPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSK 119 (144)
Q Consensus 50 d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~ 119 (144)
+.||-|+|- |||||.|--+.--.|= ....|..-.+.-..+.+..+..|+++..--+..+
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-------LIHGPMGEVRREMTYL----NQSLLPKDQKEALALAKELKDDLEKLDEAARLQD 119 (142)
T ss_pred hcchHHHHH-------HHhccHHHHHHHHHHH----HHccCHHhHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 569999886 7899988654433331 2235777778888899999999999988776665
No 296
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=22.75 E-value=71 Score=22.51 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=15.8
Q ss_pred CCchhhHHHHHHHHHhCCc
Q 032244 95 KSSGSVARHILHQLQDTNI 113 (144)
Q Consensus 95 ~asg~iiR~~LqqLE~~gl 113 (144)
..-..++|.+++.|-.||+
T Consensus 67 P~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 67 PKLAGILRNIMDSLANMGI 85 (85)
T ss_pred CcHHHHHHHHHHHHHHCCC
Confidence 3455799999999999996
No 297
>COG3189 Uncharacterized conserved protein [Function unknown]
Probab=22.54 E-value=46 Score=25.48 Aligned_cols=31 Identities=26% Similarity=0.347 Sum_probs=26.8
Q ss_pred ccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCC
Q 032244 44 KELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGK 84 (144)
Q Consensus 44 kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k 84 (144)
|+.+|.++ ||+-|-+-|.+-..|++.|.---
T Consensus 43 KdiAPS~e----------LRkwf~Hdp~~w~~F~~rY~~EL 73 (117)
T COG3189 43 KDIAPSTE----------LRKWFHHDPKKWDEFRERYRAEL 73 (117)
T ss_pred hhcCCCHH----------HHHHHcCCHHHHHHHHHHHHHHH
Confidence 67899997 99999999999999999997433
No 298
>COG2443 Sss1 Preprotein translocase subunit Sss1 [Intracellular trafficking and secretion]
Probab=22.41 E-value=62 Score=22.36 Aligned_cols=26 Identities=35% Similarity=0.669 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchhcccC
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDIVKTG 41 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~vKTg 41 (144)
.+|++++...|+.. .-|+|-+|.|+.
T Consensus 12 ~~~lke~~rvl~~a---rKP~~eEy~~~a 37 (65)
T COG2443 12 REFLKEYRRVLKVA---RKPDWEEYSKIA 37 (65)
T ss_pred HHHHHHHHHHHHHH---hCCCHHHHHHHH
Confidence 46777778888775 569999998764
No 299
>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=22.25 E-value=1.1e+02 Score=19.66 Aligned_cols=23 Identities=35% Similarity=0.511 Sum_probs=18.9
Q ss_pred CchhhHHHHHHHHHhCCcceecC
Q 032244 96 SSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~~ 118 (144)
.|..-+=.+|+.|++.|+|+...
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 45567888999999999999655
No 300
>PLN00146 40S ribosomal protein S15a; Provisional
Probab=22.23 E-value=1e+02 Score=23.38 Aligned_cols=26 Identities=15% Similarity=0.158 Sum_probs=22.6
Q ss_pred ceeccCchHHHHHHHHHHHHcCCCCC
Q 032244 6 NVKDVSPHEFVKAYAAHLKRSGKIEL 31 (144)
Q Consensus 6 tv~DV~~~~fI~~~A~~LK~~gki~~ 31 (144)
+|..+|...+..+++.-|+++|-|+=
T Consensus 24 ~v~~~p~Skl~~~il~iL~~eGyI~~ 49 (130)
T PLN00146 24 QVLIRPSSKVVIKFLKVMQKHGYIGE 49 (130)
T ss_pred eEEEEcChHHHHHHHHHHHHCCCCcc
Confidence 44557999999999999999999874
No 301
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=22.19 E-value=1.1e+02 Score=26.43 Aligned_cols=36 Identities=22% Similarity=0.303 Sum_probs=25.9
Q ss_pred HHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q 032244 103 HILHQLQDTNIIELDSKGGRRITSSGQRDLDQVAGR 138 (144)
Q Consensus 103 ~~LqqLE~~glv~k~~~gGR~lT~~G~~~lD~iA~~ 138 (144)
.=+++|-+-|+|+++..+-..||.+|-..|-+-+.+
T Consensus 44 ehiK~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~d 79 (260)
T COG1497 44 EHIKELVKEGLIEKEGRGEYEITKKGAEWLLEQLSD 79 (260)
T ss_pred HHHHHHHhccceeecCCeeEEEehhHHHHHHHHHHH
Confidence 346799999999985544458999998766544333
No 302
>cd06590 RNaseH_typeII_bacteria_HIII_like bacterial Ribonuclease HIII-like. Ribonuclease H (RNase H) is classified into two families, type I (prokaryotic RNase HI, eukaryotic RNase H1 and viral RNase H) and type II (prokaryotic RNase HII and HIII, and eukaryotic RNase H2). RNase H endonucleolytically hydrolyzes an RNA strand when it is annealed to a complementary DNA strand in the presence of divalent cations, in DNA replication and repair. Several bacteria, such as Bacillus subtilis, have two different type II RNases H, RNases HII and HIII. RNases HIII are distinguished by having a large (70-90 residues) N-terminal extension of unknown function. In addition, the active site of RNase HIII differs from that of other RNases H; replacing the fourth residue (aspartate) of the acidic "DEDD" motif with a glutamate. Most prokaryotic and eukaryotic genomes contain multiple RNase H genes, however, no prokaryotic genomes contain the combination of both RNase HI and HIII. This mutual exclusive gen
Probab=21.97 E-value=1.6e+02 Score=23.53 Aligned_cols=36 Identities=17% Similarity=0.230 Sum_probs=27.3
Q ss_pred CchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCC
Q 032244 51 PDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGS 88 (144)
Q Consensus 51 ~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~ 88 (144)
..-.=|-||||+-|++.+.- +..|...||-..+.|+
T Consensus 138 ~~~~~VaAASIlAKv~Rd~~--m~~l~~~yg~~~~~G~ 173 (208)
T cd06590 138 SKHLAVAAASILARYAFLEK--MEKLSKQYGMKLPKGA 173 (208)
T ss_pred ccchHHHHHHHHHHHHHHHH--HHHHHHHhCCCCCCCC
Confidence 45677999999999988754 4778888986666553
No 303
>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=21.92 E-value=39 Score=22.75 Aligned_cols=25 Identities=16% Similarity=0.379 Sum_probs=21.2
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchh
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDI 37 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~ 37 (144)
+.|++.+++.|.+.+.|.+|.|--|
T Consensus 26 ~~~~~~i~~~L~~g~~V~l~g~G~F 50 (90)
T PF00216_consen 26 DALFDVIKEALKEGESVKLPGFGTF 50 (90)
T ss_dssp HHHHHHHHHHHHTT-EEEETTTEEE
T ss_pred HHHHHHHHHHHhcCCeEEeeceeEE
Confidence 6788899999999999999998766
No 304
>PF13518 HTH_28: Helix-turn-helix domain
Probab=21.90 E-value=1.8e+02 Score=17.08 Aligned_cols=36 Identities=25% Similarity=0.398 Sum_probs=28.0
Q ss_pred HHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcce
Q 032244 65 IYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIE 115 (144)
Q Consensus 65 lYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~ 115 (144)
.|++|- ++..++..||= |-+-++..+++.++-|+-.
T Consensus 8 ~~~~g~-s~~~~a~~~gi--------------s~~tv~~w~~~y~~~G~~~ 43 (52)
T PF13518_consen 8 LYLEGE-SVREIAREFGI--------------SRSTVYRWIKRYREGGIEG 43 (52)
T ss_pred HHHcCC-CHHHHHHHHCC--------------CHhHHHHHHHHHHhcCHHH
Confidence 466665 99999999993 3457799999999988644
No 305
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=21.54 E-value=1.1e+02 Score=25.98 Aligned_cols=33 Identities=30% Similarity=0.422 Sum_probs=26.9
Q ss_pred hHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q 032244 100 VARHILHQLQDTNIIELDSKGGRRITSSGQRDL 132 (144)
Q Consensus 100 iiR~~LqqLE~~glv~k~~~gGR~lT~~G~~~l 132 (144)
.+..+--=|...|+++.+.++++.+|+-|+..+
T Consensus 44 MV~siryWl~a~gli~~~~~~~~~~T~lG~~i~ 76 (286)
T PF13182_consen 44 MVKSIRYWLRAFGLIEEDNKGKRKLTPLGELIF 76 (286)
T ss_pred HHHHHHHHHHHcCCcccCCCCCcccCHHHHHHH
Confidence 444455567889999999887779999999999
No 306
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=21.44 E-value=64 Score=22.17 Aligned_cols=22 Identities=23% Similarity=0.518 Sum_probs=6.7
Q ss_pred HHHHHHHhCCcceecCCCCceeCcc
Q 032244 103 HILHQLQDTNIIELDSKGGRRITSS 127 (144)
Q Consensus 103 ~~LqqLE~~glv~k~~~gGR~lT~~ 127 (144)
..-+||+...+|+ ++ |--+||+
T Consensus 41 ~~~~~L~~i~ivD--~~-G~dVTP~ 62 (65)
T PF05979_consen 41 NFRSQLENIKIVD--PD-GNDVTPE 62 (65)
T ss_dssp HHHHCSSTT----------------
T ss_pred HHHHHhcceeEEC--CC-CCCCChh
Confidence 3556899999874 44 6678885
No 307
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=21.40 E-value=2.6e+02 Score=19.86 Aligned_cols=41 Identities=15% Similarity=0.206 Sum_probs=34.5
Q ss_pred HHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 64 KIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 64 klYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
.|-++|-+....|+..|+ .+-..|+-.|.+|+.+|-|++.+
T Consensus 10 ~l~~~gr~s~~~Ls~~~~--------------~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 10 LLALRGRMEAAQISQTLN--------------TPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHcCcccHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeEeec
Confidence 456678889999998776 45569999999999999999886
No 308
>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=21.28 E-value=92 Score=22.70 Aligned_cols=40 Identities=35% Similarity=0.620 Sum_probs=28.0
Q ss_pred ccCchHHHHHHHHHHHHcCCCCCCCcc-hhcccCCCccCCCCC
Q 032244 9 DVSPHEFVKAYAAHLKRSGKIELPTWN-DIVKTGTLKELAPYD 50 (144)
Q Consensus 9 DV~~~~fI~~~A~~LK~~gki~~P~w~-d~vKTg~~kE~~P~d 50 (144)
||.+.+.-++++. +|+...+..++|. +=+|+|..+ .||..
T Consensus 60 ~v~~~di~~~i~~-ik~~~~~~Fv~W~p~~~kv~~~~-~~p~~ 100 (126)
T PF03953_consen 60 DVSPKDINEAIAK-IKQKNSIQFVDWIPTGFKVGICK-VPPYG 100 (126)
T ss_dssp SSTHHHHHHHHHH-HHCTSTTSB-SSSTTCEEEEEES-S-STS
T ss_pred ccccchhhhHHHh-hhhccccceeeecCchhhccccc-CCCcc
Confidence 6777777776665 7777789999996 567888887 55544
No 309
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=21.25 E-value=54 Score=23.00 Aligned_cols=25 Identities=12% Similarity=0.333 Sum_probs=23.2
Q ss_pred hHHHHHHHHHHHHcCCCCCCCcchh
Q 032244 13 HEFVKAYAAHLKRSGKIELPTWNDI 37 (144)
Q Consensus 13 ~~fI~~~A~~LK~~gki~~P~w~d~ 37 (144)
+.|++.+++.|++.+.|++|.+-.|
T Consensus 28 ~~~~~~i~~~L~~g~~V~l~gfG~F 52 (99)
T PRK00285 28 ELFFEEIRDALENGEQVKLSGFGNF 52 (99)
T ss_pred HHHHHHHHHHHHcCCeEEEcCCEEE
Confidence 6789999999999999999999888
No 310
>smart00843 Ftsk_gamma 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.
Probab=20.80 E-value=2.8e+02 Score=18.77 Aligned_cols=50 Identities=18% Similarity=0.215 Sum_probs=34.5
Q ss_pred chHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 52 DWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 52 DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
|=.|-.|+.++.. .+-..++.|-+.|.---+ =.-.++.+||+.|+|....
T Consensus 4 D~ly~~a~~~V~~---~~~~S~S~lQR~~~IGyn--------------rAariid~lE~~GiV~p~~ 53 (63)
T smart00843 4 DELYDEAVELVIE---TQKASTSLLQRRLRIGYN--------------RAARLIDQLEEEGIVGPAN 53 (63)
T ss_pred cHHHHHHHHHHHH---hCCCChHHHHHHHhcchh--------------HHHHHHHHHHHCcCCCCCC
Confidence 4467777666533 577788888886654333 2457899999999997543
No 311
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=20.79 E-value=83 Score=20.53 Aligned_cols=31 Identities=16% Similarity=0.396 Sum_probs=25.3
Q ss_pred CchHHHHHHHHHHHHc-CCCCC-CCcchhcccC
Q 032244 11 SPHEFVKAYAAHLKRS-GKIEL-PTWNDIVKTG 41 (144)
Q Consensus 11 ~~~~fI~~~A~~LK~~-gki~~-P~w~d~vKTg 41 (144)
.-+++++.+++|++.. |.-.+ |++.+-||..
T Consensus 21 tedEll~~~~~Ha~~~Hg~~~~~~el~~~ir~~ 53 (57)
T PF06348_consen 21 TEDELLEAVVEHAREVHGMTEIPEELREKIRSA 53 (57)
T ss_pred CHHHHHHHHHHHHHHhcCCccCCHHHHHHHHHH
Confidence 4589999999999999 76664 5888888764
No 312
>PRK10263 DNA translocase FtsK; Provisional
Probab=20.74 E-value=5.3e+02 Score=27.28 Aligned_cols=87 Identities=16% Similarity=0.182 Sum_probs=56.9
Q ss_pred chHHHHHHHHHHHHcCCCCCCCcchhcccCCC------ccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHHhcCCCC
Q 032244 12 PHEFVKAYAAHLKRSGKIELPTWNDIVKTGTL------KELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRIYGGGKR 85 (144)
Q Consensus 12 ~~~fI~~~A~~LK~~gki~~P~w~d~vKTg~~------kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~YGg~k~ 85 (144)
.|+=|+++.+|+|.++ .|++.+-+-.... ....-.+.|=.|-.|.+++ --.+-+.++.|-+.|.---|
T Consensus 1249 sD~Ei~~vv~~~k~~~---~p~y~~~~~~~~~~~~~~~~~~~~~~~D~l~~~a~~~v---~~~~~~S~S~lQR~~~iGyn 1322 (1355)
T PRK10263 1249 RDQEVHAVVQDWKARG---RPQYVDGITSDSESEGGAGGFDGAEELDPLFDQAVQFV---TEKRKASISGVQRQFRIGYN 1322 (1355)
T ss_pred CHHHHHHHHHHHHhcC---CCchhhhhcccccccccccCcCCCccccHHHHHHHHHH---HhcCccCHHHHHHHhhcChH
Confidence 4566889999999986 4666543321111 1111224466787776654 34678899999887753332
Q ss_pred CCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 86 NGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 86 rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
-..+++.|||+.|+|....
T Consensus 1323 --------------RAariid~lE~~Giv~p~~ 1341 (1355)
T PRK10263 1323 --------------RAARIIEQMEAQGIVSEQG 1341 (1355)
T ss_pred --------------HHHHHHHHHHHCCcCCCCC
Confidence 3567999999999998654
No 313
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=20.54 E-value=78 Score=25.36 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=18.6
Q ss_pred CchhhHHHHHHHHHhCCcceec
Q 032244 96 SSGSVARHILHQLQDTNIIELD 117 (144)
Q Consensus 96 asg~iiR~~LqqLE~~glv~k~ 117 (144)
-|.+-+|..|-.|.++|||...
T Consensus 83 ~s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 83 MSERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred CCHHHHHHHHHHHHHCCCeeec
Confidence 3567899999999999999753
No 314
>COG4483 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.33 E-value=70 Score=22.35 Aligned_cols=10 Identities=40% Similarity=0.790 Sum_probs=8.4
Q ss_pred HHHHHHHHHH
Q 032244 55 YIRAASMARK 64 (144)
Q Consensus 55 y~RaASilRk 64 (144)
|.||++|||+
T Consensus 48 yl~a~~IL~r 57 (68)
T COG4483 48 YLRARLILRR 57 (68)
T ss_pred HHHHHHHHHH
Confidence 5699999985
No 315
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.25 E-value=2e+02 Score=24.56 Aligned_cols=48 Identities=23% Similarity=0.213 Sum_probs=32.7
Q ss_pred HHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCce
Q 032244 62 ARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRR 123 (144)
Q Consensus 62 lRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~ 123 (144)
.-.||-+++..+..+++.-+ . ..+-+|+-|.+||+.++++....+|+.
T Consensus 107 y~~i~~nPG~~lsEl~~nl~--i------------~R~TlRyhlriLe~~~li~a~~~~g~~ 154 (240)
T COG3398 107 YNYIKPNPGFSLSELRANLY--I------------NRSTLRYHLRILESNPLIEAGRVGGAL 154 (240)
T ss_pred HHHhccCCCccHHHHHHhcC--C------------ChHHHHHHHHHHHhCcchhhhccCCce
Confidence 33444556666666665333 2 236789999999999999988766654
No 316
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=20.23 E-value=1.6e+02 Score=23.96 Aligned_cols=45 Identities=20% Similarity=0.250 Sum_probs=34.6
Q ss_pred CCCchhhHHHHHHHHHhCCcceecCC-C-----CceeCcchHhhHHHHHHH
Q 032244 94 SKSSGSVARHILHQLQDTNIIELDSK-G-----GRRITSSGQRDLDQVAGR 138 (144)
Q Consensus 94 ~~asg~iiR~~LqqLE~~glv~k~~~-g-----GR~lT~~G~~~lD~iA~~ 138 (144)
.-.|-.++=.++.-|+..|+|+-... + =-.||++||..|+..-.+
T Consensus 42 ~gps~~Ll~~sie~Lr~eGlve~~~g~g~e~~a~l~iT~~Gr~~l~~Llt~ 92 (175)
T PF14557_consen 42 WGPSLDLLGTSIELLREEGLVEAVDGEGMEDNALLAITDAGRRELQTLLTA 92 (175)
T ss_pred ccCchhhhhhHHHHHHhcCCcccccccCCCccceeeeCcchHHHHHHHHhC
Confidence 34556688889999999999997731 1 247999999999987554
No 317
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.17 E-value=3.2e+02 Score=19.73 Aligned_cols=44 Identities=14% Similarity=0.161 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCchhHHHHHhcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecC
Q 032244 61 MARKIYLRGGLGVGSFRRIYGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDS 118 (144)
Q Consensus 61 ilRklYl~g~~Gv~~l~~~YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~ 118 (144)
||+-|=-++......|.+..| -|-+-++.-++.||+.|++....
T Consensus 13 IL~~L~~d~r~~~~eia~~lg--------------lS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 13 ILRLLQEDARISNAELAERVG--------------LSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HHHHHHHhCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCceeeEE
Confidence 666666788899999999887 45667899999999999998543
No 318
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=20.06 E-value=2.7e+02 Score=25.89 Aligned_cols=89 Identities=9% Similarity=0.035 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHcCCCCCCCcchhccc---------------CCCccCCCCCCchHHHHHHHHHHHHHHhCCCchhHHHHH
Q 032244 15 FVKAYAAHLKRSGKIELPTWNDIVKT---------------GTLKELAPYDPDWYYIRAASMARKIYLRGGLGVGSFRRI 79 (144)
Q Consensus 15 fI~~~A~~LK~~gki~~P~w~d~vKT---------------g~~kE~~P~d~DW~y~RaASilRklYl~g~~Gv~~l~~~ 79 (144)
+.+.+.+.|+ ..+|...|+... ....++-+.++|.||. ..+..++-..+.+.+..+|..
T Consensus 476 ~~~~i~~~~~----~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~r~~ 549 (581)
T TIGR00475 476 IWQKIKGTFG----TKGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVKDRLLK--KYINELKEEGGTFNVQQARDK 549 (581)
T ss_pred HHHHHHHHHh----cCCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeCCeEHH--HHHHHHHhcCCcCcHHHHHHH
Confidence 4555555554 578888887652 1234577888999998 344444444689999999999
Q ss_pred hcCCCCCCCCCCCCCCCchhhHHHHHHHHHhCCcceecCCCCcee
Q 032244 80 YGGGKRNGSRPPHFSKSSGSVARHILHQLQDTNIIELDSKGGRRI 124 (144)
Q Consensus 80 YGg~k~rG~~P~h~~~asg~iiR~~LqqLE~~glv~k~~~gGR~l 124 (144)
.|. |.+.+--+|.-|.+.|+-....+ -|+|
T Consensus 550 ~g~--------------sRK~~i~lle~~D~~~~T~r~g~-~r~~ 579 (581)
T TIGR00475 550 LGL--------------GRKLLIQLLEYFDRLGFTRREGN-DHRL 579 (581)
T ss_pred HCc--------------cHHHHHHHHHHhhhCCCeEEeCC-EEEe
Confidence 984 44566666666777777654433 4443
Done!