Query 033029
Match_columns 129
No_of_seqs 106 out of 326
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 08:56:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033029.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033029hhsearch_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 6.7E-67 1.4E-71 395.4 8.9 124 5-128 1-138 (139)
2 PTZ00095 40S ribosomal protein 100.0 7.4E-66 1.6E-70 399.7 13.5 126 3-128 24-164 (169)
3 PRK09333 30S ribosomal protein 100.0 1.5E-64 3.3E-69 386.5 13.1 124 4-128 1-138 (150)
4 KOG3411 40S ribosomal protein 100.0 2.2E-64 4.8E-69 379.7 12.8 127 1-128 1-141 (143)
5 COG2238 RPS19A Ribosomal prote 100.0 9.8E-63 2.1E-67 373.7 12.4 124 4-128 1-138 (147)
6 PF08461 HTH_12: Ribonuclease 97.5 0.00019 4.1E-09 47.9 4.7 63 47-118 3-66 (66)
7 PF03444 HrcA_DNA-bdg: Winged 97.2 0.00027 5.8E-09 49.4 2.8 57 50-120 15-75 (78)
8 COG1420 HrcA Transcriptional r 97.0 0.0015 3.3E-08 56.0 5.7 63 43-117 7-75 (346)
9 PF14947 HTH_45: Winged helix- 97.0 0.0026 5.7E-08 43.0 5.6 62 45-122 9-70 (77)
10 smart00529 HTH_DTXR Helix-turn 96.6 0.0059 1.3E-07 41.4 5.0 41 83-123 12-52 (96)
11 TIGR02337 HpaR homoprotocatech 96.5 0.016 3.4E-07 41.0 7.2 65 47-125 33-103 (118)
12 TIGR02702 SufR_cyano iron-sulf 96.5 0.0059 1.3E-07 47.5 5.2 60 46-119 5-72 (203)
13 PRK10870 transcriptional repre 96.4 0.021 4.5E-07 43.9 7.9 64 47-124 60-131 (176)
14 PF13463 HTH_27: Winged helix 96.4 0.0035 7.5E-08 39.8 3.0 54 47-114 8-68 (68)
15 PRK11050 manganese transport r 96.3 0.02 4.3E-07 43.1 7.1 64 46-123 41-104 (152)
16 COG3388 Predicted transcriptio 96.3 0.0093 2E-07 43.5 5.0 69 42-125 14-82 (101)
17 PF05491 RuvB_C: Holliday junc 96.3 0.0049 1.1E-07 42.9 3.3 68 38-119 7-74 (76)
18 PRK11512 DNA-binding transcrip 96.2 0.028 6E-07 41.2 7.2 64 46-123 44-113 (144)
19 smart00347 HTH_MARR helix_turn 96.2 0.039 8.3E-07 36.4 7.3 65 47-125 15-85 (101)
20 smart00418 HTH_ARSR helix_turn 96.1 0.026 5.7E-07 34.0 5.7 59 47-120 2-64 (66)
21 PRK03911 heat-inducible transc 96.0 0.0099 2.1E-07 49.7 4.5 55 51-117 15-72 (260)
22 PF01638 HxlR: HxlR-like helix 95.9 0.028 6.1E-07 38.6 5.6 64 45-122 8-77 (90)
23 smart00346 HTH_ICLR helix_turn 95.9 0.046 1E-06 36.4 6.5 60 42-115 5-66 (91)
24 PRK03573 transcriptional regul 95.8 0.081 1.8E-06 38.4 8.1 64 47-124 36-106 (144)
25 COG1846 MarR Transcriptional r 95.8 0.053 1.1E-06 36.6 6.6 65 45-123 25-95 (126)
26 PRK03902 manganese transport t 95.6 0.068 1.5E-06 39.3 6.9 61 47-121 13-73 (142)
27 TIGR01889 Staph_reg_Sar staphy 95.2 0.11 2.5E-06 36.6 6.8 66 47-126 30-105 (109)
28 PRK13777 transcriptional regul 95.0 0.12 2.6E-06 40.7 7.2 66 46-125 49-120 (185)
29 TIGR03433 padR_acidobact trans 94.9 0.056 1.2E-06 37.9 4.6 45 81-125 36-88 (100)
30 PF14338 Mrr_N: Mrr N-terminal 94.9 0.033 7.2E-07 38.5 3.3 36 84-119 54-89 (92)
31 COG3432 Predicted transcriptio 94.8 0.049 1.1E-06 39.3 4.1 42 81-122 42-86 (95)
32 TIGR00331 hrcA heat shock gene 94.8 0.075 1.6E-06 45.1 5.8 53 53-117 18-71 (337)
33 PRK00082 hrcA heat-inducible t 94.6 0.087 1.9E-06 44.7 5.8 55 51-117 18-75 (339)
34 TIGR03338 phnR_burk phosphonat 94.5 0.063 1.4E-06 41.1 4.3 51 57-121 35-85 (212)
35 PF09339 HTH_IclR: IclR helix- 94.4 0.092 2E-06 32.6 4.2 49 42-104 3-52 (52)
36 PF13601 HTH_34: Winged helix 94.3 0.095 2.1E-06 35.8 4.5 65 47-125 5-76 (80)
37 PRK05638 threonine synthase; V 94.3 0.11 2.5E-06 44.9 5.9 75 29-121 363-441 (442)
38 COG1725 Predicted transcriptio 94.2 0.082 1.8E-06 39.8 4.3 37 85-121 50-86 (125)
39 PRK11414 colanic acid/biofilm 94.2 0.28 6E-06 38.0 7.4 85 1-121 1-85 (221)
40 PF10711 DUF2513: Hypothetical 94.1 0.097 2.1E-06 37.1 4.3 47 75-121 25-80 (102)
41 COG1693 Repressor of nif and g 94.0 0.053 1.1E-06 46.5 3.3 65 47-120 11-76 (325)
42 TIGR02719 repress_PhaQ poly-be 94.0 0.082 1.8E-06 40.2 3.9 43 83-125 56-106 (138)
43 COG1321 TroR Mn-dependent tran 93.8 0.13 2.8E-06 39.4 4.8 54 54-121 22-75 (154)
44 PF03551 PadR: Transcriptional 93.7 0.063 1.4E-06 35.4 2.6 41 80-120 27-75 (75)
45 TIGR01884 cas_HTH CRISPR locus 93.6 0.23 5.1E-06 38.5 6.1 55 46-114 147-203 (203)
46 PF02082 Rrf2: Transcriptional 93.4 0.19 4E-06 33.9 4.6 45 56-114 25-71 (83)
47 cd07377 WHTH_GntR Winged helix 93.4 0.12 2.5E-06 31.9 3.3 39 59-111 28-66 (66)
48 PF12840 HTH_20: Helix-turn-he 93.0 0.27 5.9E-06 31.2 4.6 46 45-104 13-58 (61)
49 TIGR02812 fadR_gamma fatty aci 92.8 0.2 4.3E-06 39.0 4.6 42 58-113 32-73 (235)
50 PRK11534 DNA-binding transcrip 92.8 0.19 4.2E-06 38.9 4.4 51 57-121 31-81 (224)
51 PRK09834 DNA-binding transcrip 92.6 0.42 9E-06 38.4 6.3 62 42-117 11-74 (263)
52 PF01047 MarR: MarR family; I 92.5 0.46 9.9E-06 29.4 5.1 51 45-109 6-58 (59)
53 PRK09990 DNA-binding transcrip 92.4 0.18 4E-06 39.6 3.9 45 58-116 33-77 (251)
54 COG1733 Predicted transcriptio 92.0 0.54 1.2E-05 34.6 5.7 62 47-122 28-95 (120)
55 TIGR02944 suf_reg_Xantho FeS a 92.0 0.68 1.5E-05 33.3 6.2 68 44-125 11-83 (130)
56 cd00090 HTH_ARSR Arsenical Res 91.9 0.83 1.8E-05 27.8 5.8 61 47-123 12-75 (78)
57 smart00345 HTH_GNTR helix_turn 91.9 0.21 4.6E-06 30.1 3.0 36 58-107 22-57 (60)
58 TIGR02277 PaaX_trns_reg phenyl 91.7 0.26 5.6E-06 40.8 4.2 44 84-127 34-80 (280)
59 PF00392 GntR: Bacterial regul 91.5 0.24 5.2E-06 31.7 3.1 37 58-108 26-62 (64)
60 PRK11014 transcriptional repre 91.4 0.41 8.8E-06 35.2 4.5 43 56-112 25-69 (141)
61 PF12802 MarR_2: MarR family; 91.3 0.43 9.4E-06 29.5 4.0 46 45-104 8-55 (62)
62 PF09114 MotA_activ: Transcrip 91.2 1.4 3E-05 32.0 6.9 71 42-125 16-86 (96)
63 COG1802 GntR Transcriptional r 91.1 0.33 7.1E-06 37.9 4.0 52 56-121 39-90 (230)
64 PF08220 HTH_DeoR: DeoR-like h 90.8 0.6 1.3E-05 29.7 4.3 48 43-104 1-48 (57)
65 PRK10421 DNA-binding transcrip 90.4 0.29 6.2E-06 38.8 3.2 41 59-113 29-69 (253)
66 TIGR00738 rrf2_super rrf2 fami 90.4 1.2 2.7E-05 31.6 6.2 49 55-117 24-74 (132)
67 PF10007 DUF2250: Uncharacteri 90.4 0.87 1.9E-05 32.5 5.3 48 47-110 12-59 (92)
68 PRK04984 fatty acid metabolism 90.3 0.33 7.2E-06 37.8 3.4 41 58-112 33-73 (239)
69 PRK10225 DNA-binding transcrip 90.3 0.28 6.2E-06 38.8 3.1 44 58-115 35-78 (257)
70 PRK15090 DNA-binding transcrip 90.1 0.85 1.8E-05 36.4 5.6 58 42-113 14-72 (257)
71 cd00092 HTH_CRP helix_turn_hel 90.1 0.47 1E-05 29.6 3.4 45 54-112 23-67 (67)
72 smart00550 Zalpha Z-DNA-bindin 89.9 0.98 2.1E-05 29.7 4.9 45 46-104 10-56 (68)
73 PF06969 HemN_C: HemN C-termin 89.9 0.93 2E-05 28.8 4.7 52 50-115 14-65 (66)
74 PRK03837 transcriptional regul 89.9 0.38 8.2E-06 37.4 3.4 43 58-114 39-81 (241)
75 PRK09464 pdhR transcriptional 89.7 0.36 7.9E-06 38.0 3.2 42 58-113 36-77 (254)
76 PRK09416 lstR lineage-specific 89.6 0.41 8.9E-06 36.5 3.3 42 83-124 76-121 (135)
77 PRK11523 DNA-binding transcrip 89.3 0.4 8.7E-06 37.9 3.2 42 59-114 35-76 (253)
78 smart00420 HTH_DEOR helix_turn 89.2 1.7 3.8E-05 25.3 5.3 45 46-104 4-48 (53)
79 PRK14165 winged helix-turn-hel 88.9 0.67 1.4E-05 37.5 4.2 55 57-125 22-79 (217)
80 PF09382 RQC: RQC domain; Int 88.6 2 4.2E-05 29.6 5.9 76 45-120 7-96 (106)
81 PF12793 SgrR_N: Sugar transpo 88.5 0.61 1.3E-05 34.1 3.4 39 56-108 19-57 (115)
82 PRK11569 transcriptional repre 88.4 1.4 3E-05 35.7 5.8 59 41-113 27-87 (274)
83 PRK09057 coproporphyrinogen II 88.3 2.2 4.7E-05 36.3 7.1 57 54-126 323-379 (380)
84 COG3355 Predicted transcriptio 88.0 1.6 3.4E-05 33.0 5.5 60 53-126 39-112 (126)
85 PF01726 LexA_DNA_bind: LexA D 87.7 0.8 1.7E-05 30.3 3.3 40 56-108 25-64 (65)
86 PF13814 Replic_Relax: Replica 87.5 1.5 3.3E-05 32.7 5.2 62 48-120 1-72 (191)
87 PRK08599 coproporphyrinogen II 87.4 2.2 4.9E-05 35.8 6.6 62 53-128 315-376 (377)
88 PF13412 HTH_24: Winged helix- 87.3 2.5 5.4E-05 25.3 5.1 42 46-101 7-48 (48)
89 PRK10163 DNA-binding transcrip 87.2 1.9 4.1E-05 34.9 5.9 57 42-112 25-83 (271)
90 TIGR02325 C_P_lyase_phnF phosp 87.2 0.73 1.6E-05 35.7 3.4 61 40-114 9-76 (238)
91 TIGR02010 IscR iron-sulfur clu 87.1 1.5 3.3E-05 32.0 4.9 46 55-114 24-71 (135)
92 COG1695 Predicted transcriptio 87.0 0.99 2.1E-05 32.7 3.8 40 85-124 45-92 (138)
93 PRK07379 coproporphyrinogen II 86.9 0.8 1.7E-05 39.3 3.7 40 85-126 351-393 (400)
94 COG1414 IclR Transcriptional r 86.8 2 4.4E-05 34.6 5.9 56 42-112 4-62 (246)
95 TIGR02787 codY_Gpos GTP-sensin 86.5 0.76 1.6E-05 38.4 3.3 60 47-120 188-250 (251)
96 PRK11920 rirA iron-responsive 86.4 0.88 1.9E-05 34.4 3.4 46 56-115 24-71 (153)
97 TIGR02018 his_ut_repres histid 86.0 0.85 1.8E-05 35.6 3.2 59 41-113 3-68 (230)
98 PRK00080 ruvB Holliday junctio 85.9 1.6 3.5E-05 35.9 4.9 64 38-119 261-325 (328)
99 PF01978 TrmB: Sugar-specific 85.7 1.4 3.1E-05 28.3 3.6 46 45-104 11-56 (68)
100 PRK05799 coproporphyrinogen II 85.5 0.67 1.5E-05 38.9 2.6 40 86-126 334-373 (374)
101 COG2186 FadR Transcriptional r 85.4 0.96 2.1E-05 36.3 3.3 30 83-112 47-76 (241)
102 COG4901 Ribosomal protein S25 84.5 0.96 2.1E-05 33.5 2.6 40 56-110 59-98 (107)
103 smart00419 HTH_CRP helix_turn_ 84.4 1.5 3.3E-05 25.5 3.1 22 83-104 21-42 (48)
104 PRK05628 coproporphyrinogen II 83.9 1.6 3.5E-05 36.8 4.1 38 88-126 337-374 (375)
105 PRK05660 HemN family oxidoredu 83.9 1.8 3.9E-05 36.8 4.5 40 88-128 339-378 (378)
106 PRK09764 DNA-binding transcrip 83.6 1.3 2.9E-05 34.8 3.4 60 41-114 7-73 (240)
107 TIGR02404 trehalos_R_Bsub treh 83.5 1.3 2.9E-05 34.5 3.2 40 60-113 28-67 (233)
108 PRK09334 30S ribosomal protein 82.5 1.6 3.6E-05 30.9 3.1 22 83-104 54-75 (86)
109 PRK10857 DNA-binding transcrip 82.4 3.1 6.8E-05 31.9 4.9 46 55-114 24-71 (164)
110 TIGR01610 phage_O_Nterm phage 82.3 4.4 9.4E-05 28.2 5.2 48 43-104 26-81 (95)
111 PRK08208 coproporphyrinogen II 82.2 1.9 4E-05 37.4 4.0 59 54-127 359-417 (430)
112 COG0635 HemN Coproporphyrinoge 81.6 8 0.00017 33.8 7.7 79 29-126 332-410 (416)
113 PRK13347 coproporphyrinogen II 81.4 2.3 5.1E-05 37.0 4.3 63 51-125 376-438 (453)
114 PRK14999 histidine utilization 81.3 1.8 3.9E-05 34.0 3.3 61 40-114 13-80 (241)
115 COG2255 RuvB Holliday junction 81.2 3.5 7.6E-05 35.7 5.2 68 38-119 259-326 (332)
116 PRK10079 phosphonate metabolis 81.1 1.8 3.8E-05 34.1 3.2 40 60-113 39-78 (241)
117 PRK06294 coproporphyrinogen II 81.0 2.4 5.2E-05 36.0 4.2 38 87-125 332-369 (370)
118 COG2524 Predicted transcriptio 80.1 1.4 3.1E-05 37.5 2.4 36 85-120 40-77 (294)
119 COG1959 Predicted transcriptio 79.9 2.1 4.5E-05 32.3 3.1 46 56-115 25-72 (150)
120 PRK06582 coproporphyrinogen II 79.9 7.5 0.00016 33.4 6.8 59 53-126 330-389 (390)
121 COG2188 PhnF Transcriptional r 79.8 2.3 4.9E-05 33.8 3.4 31 83-113 44-74 (236)
122 PF04703 FaeA: FaeA-like prote 79.7 2.6 5.5E-05 28.0 3.1 37 54-104 13-49 (62)
123 PF14394 DUF4423: Domain of un 79.3 2.1 4.7E-05 33.1 3.1 61 37-113 22-84 (171)
124 PRK11402 DNA-binding transcrip 79.3 2.4 5.2E-05 33.3 3.4 41 60-114 37-77 (241)
125 PRK09249 coproporphyrinogen II 79.1 2.5 5.5E-05 36.7 3.7 36 90-126 404-439 (453)
126 PRK08898 coproporphyrinogen II 78.2 3.5 7.6E-05 35.3 4.3 38 88-126 356-393 (394)
127 TIGR00538 hemN oxygen-independ 77.9 2.9 6.3E-05 36.3 3.8 35 90-125 404-438 (455)
128 PRK06266 transcription initiat 77.8 4.8 0.0001 31.5 4.6 65 9-101 3-67 (178)
129 PRK11886 bifunctional biotin-- 77.6 7.2 0.00016 32.2 5.9 59 41-113 3-62 (319)
130 PRK04172 pheS phenylalanyl-tRN 77.2 4 8.6E-05 36.2 4.5 66 45-124 9-76 (489)
131 PF03297 Ribosomal_S25: S25 ri 76.1 2.5 5.4E-05 30.9 2.4 35 56-104 59-93 (105)
132 TIGR02431 pcaR_pcaU beta-ketoa 76.0 7.3 0.00016 30.8 5.3 57 42-113 9-66 (248)
133 TIGR00635 ruvB Holliday juncti 76.0 6.3 0.00014 31.5 5.0 50 54-118 253-303 (305)
134 TIGR02147 Fsuc_second hypothet 74.1 9 0.00019 31.9 5.6 58 38-111 121-180 (271)
135 PRK09058 coproporphyrinogen II 73.8 5.1 0.00011 35.0 4.2 39 87-126 398-436 (449)
136 COG2512 Predicted membrane-ass 72.6 3.6 7.8E-05 34.1 2.9 48 46-107 199-247 (258)
137 PRK08629 coproporphyrinogen II 72.0 6.7 0.00015 34.3 4.6 59 54-126 356-414 (433)
138 TIGR00122 birA_repr_reg BirA b 72.0 21 0.00045 22.8 5.9 53 46-113 4-56 (69)
139 PF14337 DUF4393: Domain of un 71.6 5 0.00011 30.5 3.3 85 11-103 31-133 (186)
140 TIGR01594 holin_lambda phage h 71.4 3.4 7.4E-05 30.1 2.2 35 32-70 1-44 (107)
141 PRK13626 transcriptional regul 71.4 4.8 0.0001 35.7 3.6 58 55-126 22-85 (552)
142 PRK08446 coproporphyrinogen II 70.3 6.1 0.00013 33.2 3.8 35 89-126 315-349 (350)
143 TIGR02698 CopY_TcrY copper tra 69.6 12 0.00025 27.6 4.7 52 46-108 8-59 (130)
144 PF14277 DUF4364: Domain of un 68.9 7.9 0.00017 29.9 3.9 40 86-125 35-78 (163)
145 PRK12423 LexA repressor; Provi 68.8 6.2 0.00013 30.7 3.3 35 58-105 27-61 (202)
146 PRK09802 DNA-binding transcrip 68.7 15 0.00033 30.0 5.7 55 42-111 17-71 (269)
147 PF09821 AAA_assoc_C: C-termin 68.5 6.4 0.00014 29.0 3.2 31 89-120 16-46 (120)
148 COG1485 Predicted ATPase [Gene 67.9 2.6 5.5E-05 37.1 1.1 57 38-98 55-114 (367)
149 PRK13509 transcriptional repre 67.9 19 0.00041 29.0 6.1 49 43-105 6-54 (251)
150 PF09012 FeoC: FeoC like trans 67.3 12 0.00025 24.3 3.9 40 51-104 9-48 (69)
151 TIGR00498 lexA SOS regulatory 65.8 10 0.00023 28.9 4.0 44 49-105 16-61 (199)
152 PF11313 DUF3116: Protein of u 65.7 9.1 0.0002 27.2 3.3 41 84-124 41-84 (85)
153 TIGR00373 conserved hypothetic 65.5 12 0.00027 28.5 4.3 43 45-101 17-59 (158)
154 PF07848 PaaX: PaaX-like prote 65.4 8.1 0.00018 26.0 2.9 61 43-114 1-70 (70)
155 TIGR00637 ModE_repress ModE mo 65.3 16 0.00035 25.7 4.6 35 84-118 30-71 (99)
156 PF00126 HTH_1: Bacterial regu 64.8 8.4 0.00018 24.2 2.8 32 83-115 26-60 (60)
157 PF13730 HTH_36: Helix-turn-he 64.1 6.6 0.00014 23.9 2.2 19 82-100 37-55 (55)
158 PRK10434 srlR DNA-bindng trans 63.8 21 0.00045 28.8 5.6 53 43-110 6-58 (256)
159 PF08222 HTH_CodY: CodY helix- 63.5 8 0.00017 26.0 2.5 21 84-104 18-38 (61)
160 PF07381 DUF1495: Winged helix 62.8 6.2 0.00014 28.1 2.1 28 93-120 58-89 (90)
161 COG1542 Uncharacterized conser 61.7 4.7 0.0001 37.1 1.5 82 27-122 396-494 (593)
162 PF08279 HTH_11: HTH domain; 60.6 25 0.00055 21.2 4.4 48 43-104 1-50 (55)
163 PRK00215 LexA repressor; Valid 58.8 11 0.00025 28.8 3.1 49 56-117 23-73 (205)
164 TIGR02424 TF_pcaQ pca operon t 58.7 14 0.00031 28.9 3.7 36 86-122 33-71 (300)
165 PRK04214 rbn ribonuclease BN/u 58.4 76 0.0016 27.4 8.4 56 42-111 292-351 (412)
166 TIGR03337 phnR transcriptional 58.2 13 0.00028 28.6 3.3 42 59-114 28-69 (231)
167 PRK10906 DNA-binding transcrip 57.5 36 0.00077 27.5 5.9 54 43-111 6-59 (252)
168 PF01022 HTH_5: Bacterial regu 57.1 14 0.0003 22.2 2.7 41 47-102 7-47 (47)
169 COG4533 ABC-type uncharacteriz 56.9 24 0.00052 32.7 5.3 58 56-127 23-86 (564)
170 PRK15481 transcriptional regul 56.8 13 0.00029 31.3 3.4 31 82-112 41-71 (431)
171 PRK09791 putative DNA-binding 55.7 21 0.00046 28.1 4.3 38 85-123 34-74 (302)
172 PF01325 Fe_dep_repress: Iron 54.9 15 0.00033 23.6 2.7 40 54-107 20-59 (60)
173 PRK10411 DNA-binding transcrip 54.6 41 0.00089 27.0 5.8 51 43-107 5-55 (240)
174 PRK04424 fatty acid biosynthes 54.1 17 0.00036 28.2 3.3 48 43-104 8-55 (185)
175 PF03965 Penicillinase_R: Peni 54.1 21 0.00046 25.1 3.7 52 46-108 7-58 (115)
176 PRK10082 cell density-dependen 52.9 18 0.00039 28.7 3.4 37 85-122 40-79 (303)
177 PRK11242 DNA-binding transcrip 51.8 22 0.00047 27.6 3.7 36 86-122 31-69 (296)
178 smart00344 HTH_ASNC helix_turn 51.5 35 0.00075 23.2 4.3 68 46-127 7-86 (108)
179 PF03836 RasGAP_C: RasGAP C-te 51.1 5.1 0.00011 29.9 0.0 33 86-126 8-40 (142)
180 KOG1767 40S ribosomal protein 50.6 10 0.00022 28.2 1.5 23 82-104 72-94 (110)
181 TIGR03339 phn_lysR aminoethylp 50.1 25 0.00054 26.8 3.7 34 86-120 27-63 (279)
182 TIGR00462 genX lysyl-tRNA synt 49.8 28 0.00061 28.9 4.3 58 10-71 237-297 (304)
183 PRK11151 DNA-binding transcrip 48.5 27 0.00058 27.6 3.8 35 86-121 31-68 (305)
184 PF04408 HA2: Helicase associa 48.4 13 0.00029 25.7 1.8 25 89-117 1-25 (102)
185 COG3327 PaaX Phenylacetic acid 48.1 23 0.00051 30.2 3.5 43 85-127 43-88 (291)
186 PRK14997 LysR family transcrip 47.9 19 0.00042 28.2 2.9 36 86-122 32-70 (301)
187 TIGR02036 dsdC D-serine deamin 47.6 39 0.00084 26.9 4.6 36 86-122 38-76 (302)
188 PF08432 Vfa1: AAA-ATPase Vps4 47.3 4.9 0.00011 31.3 -0.6 12 33-44 29-40 (182)
189 PRK03601 transcriptional regul 47.1 27 0.00058 27.4 3.6 37 86-123 31-70 (275)
190 PRK11716 DNA-binding transcrip 47.0 36 0.00077 25.7 4.1 38 85-123 6-46 (269)
191 PRK11233 nitrogen assimilation 46.4 37 0.0008 27.0 4.3 35 86-121 31-68 (305)
192 PF02909 TetR_C: Tetracyclin r 46.2 66 0.0014 22.3 5.2 59 33-102 2-62 (139)
193 TIGR03042 PS_II_psbQ_bact phot 45.7 9.2 0.0002 29.4 0.7 59 36-105 61-119 (142)
194 PRK09986 DNA-binding transcrip 44.6 34 0.00073 26.6 3.7 35 86-121 37-74 (294)
195 COG1568 Predicted methyltransf 44.3 26 0.00056 30.6 3.2 35 84-119 48-82 (354)
196 PF15129 FAM150: FAM150 family 43.7 15 0.00033 27.7 1.6 17 39-55 103-119 (123)
197 PRK09350 poxB regulator PoxA; 43.4 48 0.001 27.6 4.7 58 10-71 242-302 (306)
198 smart00847 HA2 Helicase associ 42.8 18 0.00038 24.0 1.7 24 90-117 2-25 (92)
199 PRK12684 transcriptional regul 42.6 34 0.00074 27.4 3.6 37 87-123 33-72 (313)
200 PRK12681 cysB transcriptional 42.5 33 0.0007 27.9 3.5 36 86-122 32-71 (324)
201 TIGR02647 DNA conserved hypoth 42.4 51 0.0011 23.1 3.9 39 79-120 29-67 (77)
202 PF03969 AFG1_ATPase: AFG1-lik 42.2 31 0.00067 29.7 3.5 86 7-98 17-111 (362)
203 cd08768 Cdc6_C Winged-helix do 42.1 24 0.00053 23.1 2.3 21 84-104 46-66 (87)
204 PRK09906 DNA-binding transcrip 42.0 29 0.00063 27.1 3.0 36 86-122 31-69 (296)
205 PRK10094 DNA-binding transcrip 41.0 40 0.00087 27.0 3.8 36 86-122 32-70 (308)
206 PF03537 Glyco_hydro_114: Glyc 40.3 18 0.00039 24.2 1.4 37 4-40 26-69 (74)
207 PRK10632 transcriptional regul 40.1 44 0.00095 26.7 3.9 38 85-123 31-71 (309)
208 PRK12680 transcriptional regul 40.1 41 0.00089 27.4 3.7 37 86-123 32-72 (327)
209 COG2345 Predicted transcriptio 39.7 64 0.0014 26.4 4.7 58 46-117 15-80 (218)
210 PRK10141 DNA-binding transcrip 39.6 74 0.0016 23.3 4.7 59 46-119 20-82 (117)
211 TIGR03418 chol_sulf_TF putativ 39.5 34 0.00075 26.6 3.1 36 86-122 31-69 (291)
212 KOG1392 Acetyl-CoA acetyltrans 39.2 22 0.00048 31.4 2.1 56 5-73 359-418 (465)
213 PRK10086 DNA-binding transcrip 39.0 31 0.00068 27.5 2.8 34 86-120 44-80 (311)
214 COG1654 BirA Biotin operon rep 38.8 45 0.00097 23.1 3.2 30 83-112 32-62 (79)
215 PRK10402 DNA-binding transcrip 38.8 43 0.00094 25.7 3.5 39 85-126 184-222 (226)
216 TIGR03298 argP transcriptional 38.6 41 0.00089 26.2 3.4 37 85-123 30-69 (292)
217 PRK11013 DNA-binding transcrip 38.5 47 0.001 26.4 3.8 37 85-122 33-72 (309)
218 PRK12682 transcriptional regul 38.4 50 0.0011 26.2 3.9 38 86-124 32-73 (309)
219 PRK14137 recX recombination re 38.4 38 0.00081 26.9 3.2 56 34-97 127-182 (195)
220 PHA02943 hypothetical protein; 38.2 1.3E+02 0.0029 23.8 6.1 53 38-105 7-59 (165)
221 PRK15421 DNA-binding transcrip 38.0 48 0.001 26.8 3.8 34 86-120 32-68 (317)
222 CHL00180 rbcR LysR transcripti 38.0 51 0.0011 26.1 3.9 36 86-122 35-73 (305)
223 PRK15092 DNA-binding transcrip 37.8 44 0.00096 27.1 3.6 35 87-122 42-79 (310)
224 PRK06474 hypothetical protein; 37.8 1E+02 0.0023 23.7 5.5 46 46-104 15-61 (178)
225 PRK11062 nhaR transcriptional 37.5 60 0.0013 25.7 4.2 35 87-122 35-72 (296)
226 COG1339 Transcriptional regula 37.5 45 0.00098 27.4 3.5 39 86-124 35-76 (214)
227 PF09202 Rio2_N: Rio2, N-termi 37.4 49 0.0011 22.9 3.2 36 83-118 37-74 (82)
228 PRK10341 DNA-binding transcrip 37.4 54 0.0012 26.1 4.0 35 86-121 37-74 (312)
229 PRK10837 putative DNA-binding 37.4 46 0.001 25.7 3.5 35 86-121 33-70 (290)
230 PF09079 Cdc6_C: CDC6, C termi 36.7 36 0.00078 22.6 2.5 20 85-104 40-59 (85)
231 smart00479 EXOIII exonuclease 36.2 88 0.0019 22.2 4.6 53 41-96 113-165 (169)
232 PF09681 Phage_rep_org_N: N-te 36.1 45 0.00097 24.6 3.1 48 51-112 46-95 (121)
233 PF04458 DUF505: Protein of un 35.6 33 0.00072 32.1 2.7 92 8-117 388-497 (591)
234 PRK11139 DNA-binding transcrip 35.3 66 0.0014 25.2 4.1 36 86-122 36-74 (297)
235 PF10264 Stork_head: Winged he 34.9 1.4E+02 0.0031 20.9 5.3 53 55-113 28-80 (80)
236 COG3398 Uncharacterized protei 34.4 39 0.00084 28.2 2.7 28 82-110 200-227 (240)
237 PF07042 TrfA: TrfA protein; 33.7 26 0.00057 29.6 1.7 40 56-102 231-270 (282)
238 PRK09508 leuO leucine transcri 33.5 81 0.0018 25.1 4.4 39 58-96 56-98 (314)
239 PF14178 YppF: YppF-like prote 33.3 32 0.0007 23.1 1.7 33 29-65 13-45 (60)
240 PRK00135 scpB segregation and 33.0 1E+02 0.0022 24.3 4.8 40 46-102 94-133 (188)
241 PRK13348 chromosome replicatio 32.9 63 0.0014 25.2 3.6 36 86-123 32-70 (294)
242 COG1349 GlpR Transcriptional r 32.7 1.3E+02 0.0028 24.3 5.4 55 43-112 6-60 (253)
243 PRK12683 transcriptional regul 32.5 61 0.0013 26.0 3.5 36 86-122 32-71 (309)
244 TIGR02716 C20_methyl_CrtF C-20 32.1 42 0.00091 27.2 2.6 51 54-119 21-71 (306)
245 PF06208 BDV_G: Borna disease 31.9 30 0.00064 30.9 1.7 38 11-51 92-132 (503)
246 PF02985 HEAT: HEAT repeat; I 31.0 36 0.00078 18.6 1.4 11 36-47 11-21 (31)
247 PRK10676 DNA-binding transcrip 30.9 79 0.0017 25.8 4.0 66 38-119 15-87 (263)
248 PF09661 DUF2398: Protein of u 30.6 95 0.0021 26.9 4.6 50 60-113 309-358 (368)
249 PF14605 Nup35_RRM_2: Nup53/35 30.3 21 0.00045 22.5 0.4 38 4-43 3-42 (53)
250 PRK12679 cbl transcriptional r 30.1 75 0.0016 25.5 3.7 35 86-121 32-70 (316)
251 PF09397 Ftsk_gamma: Ftsk gamm 30.1 52 0.0011 22.0 2.3 50 38-104 5-54 (65)
252 PRK11057 ATP-dependent DNA hel 30.1 88 0.0019 28.4 4.5 82 38-120 411-504 (607)
253 COG4189 Predicted transcriptio 30.0 1.1E+02 0.0024 26.2 4.7 48 47-108 28-75 (308)
254 PF04458 DUF505: Protein of un 29.7 39 0.00084 31.6 2.2 41 81-121 326-370 (591)
255 PRK13239 alkylmercury lyase; P 29.3 2.3E+02 0.005 22.9 6.4 53 38-110 20-72 (206)
256 COG4754 Uncharacterized conser 29.1 48 0.001 26.1 2.3 31 89-120 47-77 (157)
257 PF14502 HTH_41: Helix-turn-he 29.1 69 0.0015 20.5 2.6 25 83-108 19-43 (48)
258 COG0583 LysR Transcriptional r 28.6 1.1E+02 0.0023 23.2 4.1 37 86-123 31-70 (297)
259 PHA00738 putative HTH transcri 27.8 1.8E+02 0.0039 21.5 5.0 48 47-109 17-64 (108)
260 PRK11074 putative DNA-binding 27.8 1.3E+02 0.0028 23.7 4.6 37 85-122 31-70 (300)
261 PRK06063 DNA polymerase III su 27.6 1.5E+02 0.0033 24.8 5.2 58 42-99 126-184 (313)
262 PRK11482 putative DNA-binding 27.5 1E+02 0.0023 24.8 4.1 32 87-119 60-94 (317)
263 TIGR01714 phage_rep_org_N phag 27.2 80 0.0017 23.4 3.1 27 85-111 66-92 (119)
264 PF09929 DUF2161: Uncharacteri 27.1 48 0.001 24.9 1.9 58 44-118 61-118 (118)
265 PF02002 TFIIE_alpha: TFIIE al 27.0 46 0.00099 23.0 1.7 45 44-102 15-59 (105)
266 PF14629 ORC4_C: Origin recogn 27.0 67 0.0015 24.5 2.8 36 80-115 149-185 (203)
267 PRK03635 chromosome replicatio 26.9 78 0.0017 24.9 3.2 35 86-122 32-69 (294)
268 PRK09213 pur operon repressor; 26.8 2.3E+02 0.005 23.7 6.1 77 43-127 8-93 (271)
269 PF13545 HTH_Crp_2: Crp-like h 26.3 90 0.0019 19.6 2.9 23 82-104 40-62 (76)
270 PF10396 TrmE_N: GTP-binding p 26.0 54 0.0012 24.2 2.0 27 77-103 75-101 (114)
271 PF04182 B-block_TFIIIC: B-blo 25.8 57 0.0012 21.5 2.0 20 85-104 33-52 (75)
272 PRK09391 fixK transcriptional 25.6 84 0.0018 24.3 3.2 18 86-103 195-212 (230)
273 PF15398 DUF4619: Domain of un 25.4 12 0.00026 32.0 -1.7 64 29-116 58-125 (296)
274 KOG0345 ATP-dependent RNA heli 25.4 34 0.00074 31.7 1.0 19 32-50 333-351 (567)
275 PRK09801 transcriptional activ 25.3 68 0.0015 25.8 2.7 37 85-122 35-74 (310)
276 PF02923 BamHI: Restriction en 24.8 30 0.00065 27.3 0.5 36 56-101 36-71 (158)
277 PF12964 DUF3853: Protein of u 24.6 66 0.0014 23.4 2.2 32 58-93 47-78 (96)
278 PF14357 DUF4404: Domain of un 24.5 65 0.0014 22.3 2.1 18 82-99 68-85 (85)
279 PF13182 DUF4007: Protein of u 24.5 88 0.0019 26.0 3.2 33 86-118 44-76 (286)
280 PRK08561 rps15p 30S ribosomal 24.4 85 0.0018 24.5 2.9 20 9-28 83-107 (151)
281 smart00190 IL4_13 Interleukins 24.0 2E+02 0.0044 22.1 4.9 51 9-59 28-88 (138)
282 PRK15243 transcriptional regul 23.9 1.2E+02 0.0026 24.9 3.9 36 85-121 33-71 (297)
283 TIGR02928 orc1/cdc6 family rep 23.9 73 0.0016 26.0 2.6 43 56-103 307-350 (365)
284 TIGR03157 cas_Csc2 CRISPR-asso 23.6 81 0.0018 27.0 2.9 38 2-39 165-221 (282)
285 PF10231 DUF2315: Uncharacteri 23.6 25 0.00055 26.4 -0.1 32 8-41 75-106 (126)
286 PF03849 Tfb2: Transcription f 23.6 1.6E+02 0.0035 25.5 4.7 56 29-104 25-80 (366)
287 PF02513 Spin-Ssty: Spin/Ssty 23.6 19 0.0004 23.3 -0.7 13 31-43 25-37 (50)
288 COG5631 Predicted transcriptio 23.6 1.3E+02 0.0029 24.3 3.9 37 85-122 114-154 (199)
289 COG0735 Fur Fe2+/Zn2+ uptake r 23.6 94 0.002 23.1 3.0 26 82-107 53-78 (145)
290 PF05209 MinC_N: Septum format 23.4 35 0.00076 23.6 0.6 54 6-63 19-82 (99)
291 COG4465 CodY Pleiotropic trans 23.0 65 0.0014 27.1 2.1 21 84-104 218-238 (261)
292 PF14493 HTH_40: Helix-turn-he 23.0 94 0.002 21.0 2.7 40 6-45 45-89 (91)
293 COG2738 Predicted Zn-dependent 22.7 43 0.00093 27.7 1.0 25 75-104 164-188 (226)
294 PF03180 Lipoprotein_9: NLPA l 22.6 76 0.0016 25.8 2.5 27 85-111 107-133 (237)
295 smart00501 BRIGHT BRIGHT, ARID 22.6 1.1E+02 0.0024 20.6 3.0 24 12-35 3-26 (93)
296 PF09639 YjcQ: YjcQ protein; 22.6 94 0.002 21.3 2.6 36 85-120 25-69 (88)
297 COG4344 Uncharacterized protei 22.5 66 0.0014 25.6 2.0 20 85-104 46-65 (175)
298 COG1710 Uncharacterized protei 22.4 45 0.00099 25.6 1.1 27 69-99 52-78 (139)
299 PF05746 DALR_1: DALR anticodo 22.4 57 0.0012 22.3 1.5 16 40-55 4-19 (119)
300 PF05106 Phage_holin_3: Phage 22.1 63 0.0014 23.0 1.7 32 34-69 2-41 (100)
301 PRK05974 phosphoribosylformylg 22.0 1E+02 0.0023 20.7 2.7 45 81-129 15-69 (80)
302 PF08357 SEFIR: SEFIR domain; 22.0 94 0.002 22.2 2.7 32 9-40 10-52 (150)
303 COG0640 ArsR Predicted transcr 22.0 2E+02 0.0044 17.6 7.1 51 46-110 29-79 (110)
304 smart00843 Ftsk_gamma This dom 21.8 77 0.0017 21.2 2.0 49 38-103 4-52 (63)
305 PF05732 RepL: Firmicute plasm 21.8 1.1E+02 0.0025 23.4 3.2 32 82-113 87-118 (165)
306 PF01805 Surp: Surp module; I 21.8 37 0.00079 21.2 0.4 31 14-44 3-38 (55)
307 PF10746 Phage_holin_6: Phage 21.6 47 0.001 22.7 0.9 11 38-50 35-45 (66)
308 PF13835 DUF4194: Domain of un 21.5 1.9E+02 0.0041 21.5 4.3 63 39-105 74-145 (166)
309 PRK14134 recX recombination re 21.5 1.2E+02 0.0027 25.1 3.6 54 35-96 151-208 (283)
310 PF10987 DUF2806: Protein of u 21.5 38 0.00081 27.2 0.5 20 85-104 137-156 (219)
311 TIGR00876 tal_mycobact transal 21.5 75 0.0016 27.8 2.3 60 33-99 264-323 (350)
312 PF02980 FokI_C: Restriction e 21.4 98 0.0021 24.0 2.7 43 79-121 77-135 (142)
313 COG4483 Uncharacterized protei 21.3 62 0.0013 22.2 1.4 10 41-50 48-57 (68)
314 cd07153 Fur_like Ferric uptake 21.3 74 0.0016 21.8 1.9 49 47-104 6-55 (116)
315 TIGR03703 plsB glycerol-3-phos 21.3 1.7E+02 0.0037 28.2 4.8 49 74-126 743-791 (799)
316 PF00727 IL4: Interleukin 4 Th 21.2 73 0.0016 23.9 1.9 17 39-55 43-59 (117)
317 PF03376 Adeno_E3B: Adenovirus 21.0 45 0.00098 22.8 0.7 8 38-45 41-48 (67)
318 KOG4068 Uncharacterized conser 20.7 95 0.0021 24.8 2.6 26 79-104 63-88 (174)
319 COG1510 Predicted transcriptio 20.7 94 0.002 24.9 2.6 71 13-109 9-81 (177)
320 PF05158 RNA_pol_Rpc34: RNA po 20.6 1E+02 0.0022 26.3 2.9 44 47-104 89-134 (327)
321 cd00772 ProRS_core Prolyl-tRNA 20.4 1.3E+02 0.0029 24.3 3.5 35 91-125 7-42 (264)
322 TIGR01743 purR_Bsub pur operon 20.3 3.6E+02 0.0078 22.5 6.1 77 43-127 6-91 (268)
323 COG1497 Predicted transcriptio 20.3 1.3E+02 0.0028 25.5 3.4 32 89-120 44-75 (260)
324 KOG4226 Adaptor protein NCK/Do 20.2 41 0.00088 29.3 0.5 18 29-46 218-235 (379)
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=6.7e-67 Score=395.37 Aligned_cols=124 Identities=59% Similarity=1.064 Sum_probs=114.5
Q ss_pred CcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccC
Q 033029 5 RTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSK 70 (129)
Q Consensus 5 ~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k 70 (129)
+||||||||+||++||+|||++|+ +||+||+||||||+|||||||||||+||+||++||++|||+|
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 599999999999999999999987 999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029 71 RNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 71 ~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
|||++|+||++|||+|||+||||||++|||++++++||+|||+||++||+||.||+++
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 9999999999999999999999999999999999899999999999999999999864
No 2
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=100.00 E-value=7.4e-66 Score=399.75 Aligned_cols=126 Identities=42% Similarity=0.781 Sum_probs=121.8
Q ss_pred CCCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcc
Q 033029 3 TARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGG 68 (129)
Q Consensus 3 ~~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg 68 (129)
.++||||||||+||++||+|||++|+ +||+||+||||||+||||||||||++||+||++||++|||
T Consensus 24 ~~~tvkDVpa~~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~YGg 103 (169)
T PTZ00095 24 KNATLKDVSPWRFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSS 103 (169)
T ss_pred CCCceeeCCHHHHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHHCC
Confidence 46899999999999999999999987 9999999999999999999999999999999999999999
Q ss_pred cCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhhHHHHHHHhhhC
Q 033029 69 SKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 69 ~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
+||||++|+||++|||+|||+||||||++|||++++ ++||+|||+||++||+||.+|+++
T Consensus 104 ~krrG~~P~h~~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~~ 164 (169)
T PTZ00095 104 KKRRGSAPNHTVRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIR 164 (169)
T ss_pred CCCCCCCCCcccCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999999999996 489999999999999999999764
No 3
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=100.00 E-value=1.5e-64 Score=386.49 Aligned_cols=124 Identities=40% Similarity=0.667 Sum_probs=120.9
Q ss_pred CCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhccc
Q 033029 4 ARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGS 69 (129)
Q Consensus 4 ~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~ 69 (129)
|+||||||||+||++||+|||++|+ +||+||+||||||+||||||||||++||+||++|+++|||+
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 7899999999999999999999987 99999999999999999999999999999999999999999
Q ss_pred CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029 70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
||||++|+||++|||+|||++|||||++|||++++ +||+||++||++||+||.+|+.+
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 99999999999999999999999999999999998 89999999999999999999753
No 4
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.2e-64 Score=379.75 Aligned_cols=127 Identities=65% Similarity=1.116 Sum_probs=124.7
Q ss_pred CCCCCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHh
Q 033029 1 MATARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIY 66 (129)
Q Consensus 1 m~~~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~Y 66 (129)
||+ +|||||+|++|+++||.|||++|| +||+||+||||||+|||||+||||++||+||++|+++|
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 787 899999999999999999999998 99999999999999999999999999999999999999
Q ss_pred cccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029 67 GGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 67 Gg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
||+|||||+|+||+.+||+|+|++||+||++||||++++|||+||++||++||+||++|..+
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 99999999999999999999999999999999999999999999999999999999999875
No 5
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.8e-63 Score=373.67 Aligned_cols=124 Identities=43% Similarity=0.717 Sum_probs=121.1
Q ss_pred CCcccccChhHHHHHHHHHHHhcCC--------------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhccc
Q 033029 4 ARTVKDVSPHEFVKAYSAHLKRSGK--------------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGS 69 (129)
Q Consensus 4 ~~tv~DV~~~~fI~~~A~~LK~~gk--------------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~ 69 (129)
|+||||||+|+||++||++||++++ |||+||+++||||+|||||||||||+|||||++||+.|||+
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 7899999999999999999999976 99999999999999999999999999999999999999999
Q ss_pred CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029 70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
+|||++|+||.+|||+|+|++|||||++|||+|++ +||+|||+||++||+||.+|+++
T Consensus 81 k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ei~ee 138 (147)
T COG2238 81 KNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIATEIKEE 138 (147)
T ss_pred ccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHHHHHHH
Confidence 99999999999999999999999999999999998 79999999999999999999764
No 6
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=97.52 E-value=0.00019 Score=47.86 Aligned_cols=63 Identities=21% Similarity=0.238 Sum_probs=51.1
Q ss_pred HHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029 47 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL 118 (129)
Q Consensus 47 ilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l 118 (129)
||+.|+-. +|+|-..|+....-. |. .-|-.-+|+-|..||..||+++...+||.||++|...|
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---GE------ELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc---Ch------hhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence 67777775 689999999987653 32 33456899999999999999987778999999998764
No 7
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=97.23 E-value=0.00027 Score=49.43 Aligned_cols=57 Identities=25% Similarity=0.514 Sum_probs=46.2
Q ss_pred HHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchHhhHHH
Q 033029 50 KIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ 120 (129)
Q Consensus 50 ~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~~~lD~ 120 (129)
..|++ .|||-..+....+- |-.-||+.++.||++|||++.+ .+||+-|.+|-+.+++
T Consensus 15 ~~Y~~~~~PVgSk~ia~~l~~--------------s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~ 75 (78)
T PF03444_consen 15 ELYIETGEPVGSKTIAEELGR--------------SPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR 75 (78)
T ss_pred HHHHhcCCCcCHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence 45775 49999999987531 2368999999999999999643 6899999999998864
No 8
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=96.98 E-value=0.0015 Score=56.03 Aligned_cols=63 Identities=27% Similarity=0.402 Sum_probs=50.6
Q ss_pred hHHHHHHHH---HHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHh
Q 033029 43 RAASMARKI---YLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQR 116 (129)
Q Consensus 43 R~ASilR~l---Yl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~ 116 (129)
|-..|||.| |+. -|||-..|.+.|+- .-|..-||+.+++||++|+++|.. ..||+-|+.|-+
T Consensus 7 Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~l------------~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr 74 (346)
T COG1420 7 RQRLILRAIVEDYLATGEPVGSKTLSEKYNL------------DLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYR 74 (346)
T ss_pred HHHHHHHHHHHHHHhcCCccchHHHHHHhCC------------CCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHH
Confidence 455566654 775 49999999998763 345678999999999999999865 479999999976
Q ss_pred h
Q 033029 117 D 117 (129)
Q Consensus 117 ~ 117 (129)
.
T Consensus 75 ~ 75 (346)
T COG1420 75 Y 75 (346)
T ss_pred H
Confidence 4
No 9
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.96 E-value=0.0026 Score=42.98 Aligned_cols=62 Identities=15% Similarity=0.247 Sum_probs=43.7
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHH
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+.||.-+- .++.....+... +.=|-+.+.+.|..|++.|+|++. ++.-.||++|...|+.+-
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~--------------~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l~ 70 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYK--------------ANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEELE 70 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTT--------------ST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHH-cCCCCHHHHHHH--------------hCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHHH
Confidence 34555554 677777666532 345667999999999999999774 578999999999999874
No 10
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.55 E-value=0.0059 Score=41.36 Aligned_cols=41 Identities=22% Similarity=0.398 Sum_probs=35.9
Q ss_pred chhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029 83 SGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
+.+-+..+|+.||+.|||++.++++-.||+.|+...+.+..
T Consensus 12 s~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~ 52 (96)
T smart00529 12 SPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLR 52 (96)
T ss_pred ChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHH
Confidence 45689999999999999999887799999999998877654
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=96.52 E-value=0.016 Score=41.04 Aligned_cols=65 Identities=14% Similarity=0.133 Sum_probs=51.2
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLDQ 120 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD~ 120 (129)
||..|+-++++.+..|+...|-.+ +-+-.+++.||+.|||+..+ ...| .||++|+..+++
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 666777889999999999876532 24568999999999999754 3344 699999999998
Q ss_pred HHHHh
Q 033029 121 VAGRI 125 (129)
Q Consensus 121 iA~~i 125 (129)
+....
T Consensus 99 ~~~~~ 103 (118)
T TIGR02337 99 LSPQI 103 (118)
T ss_pred hhHHH
Confidence 87654
No 12
>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=0.0059 Score=47.51 Aligned_cols=60 Identities=15% Similarity=0.256 Sum_probs=49.1
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCCc-----eeCcchHhh
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----RITSSGQRD 117 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~GR-----~lT~~G~~~ 117 (129)
+||..|.-.|++.+..|....|-. ..-+|+.|+.||+.|||+... ..|| .||++|...
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgis--------------~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~ 70 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAIS--------------PQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ 70 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence 578888778999999999987543 358999999999999998762 3578 999999876
Q ss_pred HH
Q 033029 118 LD 119 (129)
Q Consensus 118 lD 119 (129)
+.
T Consensus 71 ~~ 72 (203)
T TIGR02702 71 FP 72 (203)
T ss_pred cc
Confidence 54
No 13
>PRK10870 transcriptional repressor MprA; Provisional
Probab=96.42 E-value=0.021 Score=43.88 Aligned_cols=64 Identities=17% Similarity=0.184 Sum_probs=49.1
Q ss_pred HHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce----eCcchHhhH
Q 033029 47 MARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQRDL 118 (129)
Q Consensus 47 ilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~----lT~~G~~~l 118 (129)
||..|+-. +++.+..|+...|-. .+-+=.+++.||+.|||++.+ +.+|. ||++|+..+
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 56777753 467778999987753 235667899999999999754 45777 999999999
Q ss_pred HHHHHH
Q 033029 119 DQVAGR 124 (129)
Q Consensus 119 D~iA~~ 124 (129)
+++-..
T Consensus 126 ~~i~~~ 131 (176)
T PRK10870 126 REVLPP 131 (176)
T ss_pred HHHHHH
Confidence 998544
No 14
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=96.42 E-value=0.0035 Score=39.84 Aligned_cols=54 Identities=19% Similarity=0.322 Sum_probs=38.4
Q ss_pred HHHHHH-HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcch
Q 033029 47 MARKIY-LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSG 114 (129)
Q Consensus 47 ilR~lY-l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G 114 (129)
||+.|+ -+++.....|+...+-. ..-+.+++++|++.|||++.+ ..+| .|||+|
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~~--------------~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGIS--------------KSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHccCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 777788 67899999999987653 245669999999999998654 3455 578877
No 15
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.32 E-value=0.02 Score=43.13 Aligned_cols=64 Identities=16% Similarity=0.164 Sum_probs=52.2
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHH
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
.|++.++-.+++.+..|...+|-. .+-+..+++.||+.|+|...+.+|-.||++|+..+..+..
T Consensus 41 ~I~~~l~~~~~~t~~eLA~~l~is--------------~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~ 104 (152)
T PRK11050 41 LIADLIAEVGEARQVDIAARLGVS--------------QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE 104 (152)
T ss_pred HHHHHHHhcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence 366666667889999999887643 3589999999999999998776789999999999777653
No 16
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=96.30 E-value=0.0093 Score=43.51 Aligned_cols=69 Identities=23% Similarity=0.294 Sum_probs=57.8
Q ss_pred HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
.|--+++..+-=.+|+|+..|+..-|- |+|. +|+.|.=||+.+++.-+. .|-++|+.+-..+++|
T Consensus 14 ~RHl~Vl~~v~eeqPiGI~klS~~TGm-------p~HK-------VRYSLRVLEq~~iI~PS~-~GAi~td~~~e~ie~i 78 (101)
T COG3388 14 KRHLSVLKVVLEEQPIGIIKLSDETGM-------PEHK-------VRYSLRVLEQENIISPSR-QGAILTDDFPEFIEEI 78 (101)
T ss_pred HHHHHHHHHHHHhCCceeEeechhcCC-------chhh-------hhhhhhhhhhcCccCccc-cCCccCccHHHHHHHH
Confidence 355677777777899999999998774 8776 799999999999998664 5999999999998888
Q ss_pred HHHh
Q 033029 122 AGRI 125 (129)
Q Consensus 122 A~~i 125 (129)
.+.+
T Consensus 79 ~~dl 82 (101)
T COG3388 79 IGDL 82 (101)
T ss_pred HHHH
Confidence 7664
No 17
>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=96.27 E-value=0.0049 Score=42.93 Aligned_cols=68 Identities=21% Similarity=0.216 Sum_probs=44.9
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhh
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD 117 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~ 117 (129)
|+.=.|.-..+...|-.||||+..|+..-|--+ ..|.=.+===|-+.|+|++++ .||++|++|.+-
T Consensus 7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~-------------~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~ 72 (76)
T PF05491_consen 7 DELDRRYLKTLIENFKGGPVGLDTLAAALGEDK-------------ETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEH 72 (76)
T ss_dssp BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-H-------------HHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCH-------------hHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHH
Confidence 445556566677777889999999998765421 123322333467899999998 599999999876
Q ss_pred HH
Q 033029 118 LD 119 (129)
Q Consensus 118 lD 119 (129)
|.
T Consensus 73 l~ 74 (76)
T PF05491_consen 73 LG 74 (76)
T ss_dssp TT
T ss_pred hC
Confidence 53
No 18
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.21 E-value=0.028 Score=41.18 Aligned_cols=64 Identities=14% Similarity=0.163 Sum_probs=50.2
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD 119 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD 119 (129)
.||..|+-.+++....|+...|-. .+-+=.+++.||+.|||++.+ ..+| .||++|+..++
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l~i~--------------~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~ 109 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVLSVD--------------LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE 109 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence 367778888999999999987653 235667899999999999754 3455 58999999988
Q ss_pred HHHH
Q 033029 120 QVAG 123 (129)
Q Consensus 120 ~iA~ 123 (129)
++..
T Consensus 110 ~~~~ 113 (144)
T PRK11512 110 QCHQ 113 (144)
T ss_pred HHHH
Confidence 8643
No 19
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.19 E-value=0.039 Score=36.44 Aligned_cols=65 Identities=18% Similarity=0.276 Sum_probs=50.7
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC------CceeCcchHhhHHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSGQRDLDQ 120 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~------GR~lT~~G~~~lD~ 120 (129)
|+..|+..+++.+..+....+-. ..-|..+|+.|++.|||++..++ .-.||++|...+..
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 77778888899999998875421 22478999999999999876532 35699999999988
Q ss_pred HHHHh
Q 033029 121 VAGRI 125 (129)
Q Consensus 121 iA~~i 125 (129)
+...+
T Consensus 81 ~~~~~ 85 (101)
T smart00347 81 LLEAR 85 (101)
T ss_pred HHHHH
Confidence 77664
No 20
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.12 E-value=0.026 Score=33.95 Aligned_cols=59 Identities=19% Similarity=0.260 Sum_probs=43.1
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC---CceeCc-chHhhHHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITS-SGQRDLDQ 120 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~-~G~~~lD~ 120 (129)
|++.|+ .+++.+..+...+|- |.+-++.+|++|++.|+|+...++ .-.+|+ .|...++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~i--------------s~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGL--------------SQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 566777 889999999999872 335799999999999999976532 233666 55555543
No 21
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=96.01 E-value=0.0099 Score=49.68 Aligned_cols=55 Identities=22% Similarity=0.383 Sum_probs=45.2
Q ss_pred HHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029 51 IYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD 117 (129)
Q Consensus 51 lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~ 117 (129)
-|+. -|||-..|.+.|+- .-|.+-||+.++.||++|++++.. ..||+-|.+|-+.
T Consensus 15 ~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr~ 72 (260)
T PRK03911 15 TYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMKN 72 (260)
T ss_pred HHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHHH
Confidence 3775 49999999998764 334578999999999999999754 4799999999863
No 22
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=95.88 E-value=0.028 Score=38.58 Aligned_cols=64 Identities=13% Similarity=0.182 Sum_probs=48.5
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC------CceeCcchHhhH
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG------GRRITSSGQRDL 118 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~------GR~lT~~G~~~l 118 (129)
..|++.|.. |+...+.|.+.- ...|.+++-.-|..||+.|+|++.... -..||+.|++++
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 568888888 888878877753 245678999999999999999976422 268999999988
Q ss_pred HHHH
Q 033029 119 DQVA 122 (129)
Q Consensus 119 D~iA 122 (129)
.-+.
T Consensus 74 ~~l~ 77 (90)
T PF01638_consen 74 PVLE 77 (90)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6554
No 23
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.85 E-value=0.046 Score=36.38 Aligned_cols=60 Identities=20% Similarity=0.297 Sum_probs=48.5
Q ss_pred HhHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchH
Q 033029 42 VRAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQ 115 (129)
Q Consensus 42 ~R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~ 115 (129)
-|+-.|+..|.-. +++++..+....|- +.+-+++.|+.||+.|+|++++ ++...|++...
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 3788899998887 79999999998754 3468999999999999999875 34567777544
No 24
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=95.81 E-value=0.081 Score=38.43 Aligned_cols=64 Identities=14% Similarity=0.146 Sum_probs=47.5
Q ss_pred HHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhHH
Q 033029 47 MARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDLD 119 (129)
Q Consensus 47 ilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~lD 119 (129)
+|..|+-. ++.....|+...|-.+ +-+=.++..||+.|||++.+ +..| .||++|+..++
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 56666654 4577889998876542 24558999999999999764 3455 49999999998
Q ss_pred HHHHH
Q 033029 120 QVAGR 124 (129)
Q Consensus 120 ~iA~~ 124 (129)
.+...
T Consensus 102 ~~~~~ 106 (144)
T PRK03573 102 EVEAV 106 (144)
T ss_pred HHHHH
Confidence 86654
No 25
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=95.79 E-value=0.053 Score=36.62 Aligned_cols=65 Identities=20% Similarity=0.326 Sum_probs=49.7
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCc----eeCcchHhhH
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGR----RITSSGQRDL 118 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR----~lT~~G~~~l 118 (129)
..++..||..++.+.+.|....+- +.+-+=.+++.||+.|||+... ..+| .||++|+..+
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 568888899888765677766443 2346678899999999998655 3455 7999999999
Q ss_pred HHHHH
Q 033029 119 DQVAG 123 (129)
Q Consensus 119 D~iA~ 123 (129)
.++..
T Consensus 91 ~~~~~ 95 (126)
T COG1846 91 EQLLP 95 (126)
T ss_pred HHhcc
Confidence 88755
No 26
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=95.56 E-value=0.068 Score=39.25 Aligned_cols=61 Identities=13% Similarity=0.077 Sum_probs=44.1
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
|.+.+.-.|++-+..|+...|-. .+-++..|+.||+.|||.....+|=.||++|+.....+
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs--------------~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVH--------------PSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCC--------------hhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence 44444445667777777765432 23577889999999999876667899999998876655
No 27
>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=95.16 E-value=0.11 Score=36.58 Aligned_cols=66 Identities=11% Similarity=0.106 Sum_probs=50.6
Q ss_pred HHHHHH----HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce----eCcchHh
Q 033029 47 MARKIY----LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR----ITSSGQR 116 (129)
Q Consensus 47 ilR~lY----l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~----lT~~G~~ 116 (129)
+|..|+ -.+++....|+..-+-. .+-+=.++..||+.|||++.. +..|. ||++|++
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 34789999999876542 235667899999999999754 34553 8999999
Q ss_pred hHHHHHHHhh
Q 033029 117 DLDQVAGRIV 126 (129)
Q Consensus 117 ~lD~iA~~i~ 126 (129)
.++.+..++-
T Consensus 96 ~~~~~~~~~~ 105 (109)
T TIGR01889 96 KIESLISEIE 105 (109)
T ss_pred HHHHHHHHHH
Confidence 9999988763
No 28
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=95.01 E-value=0.12 Score=40.72 Aligned_cols=66 Identities=12% Similarity=0.137 Sum_probs=49.8
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCc----eeCcchHhhHH
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGR----RITSSGQRDLD 119 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR----~lT~~G~~~lD 119 (129)
.||-.||-++++....|++..+-. .+-+=.+++.||+.|||+.. ++..| .||++|+..++
T Consensus 49 ~iL~~L~~~~~itq~eLa~~l~l~--------------~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~ 114 (185)
T PRK13777 49 HILWIAYHLKGASISEIAKFGVMH--------------VSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL 114 (185)
T ss_pred HHHHHHHhCCCcCHHHHHHHHCCC--------------HhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence 367778888999999999964432 12355699999999999964 34455 39999999999
Q ss_pred HHHHHh
Q 033029 120 QVAGRI 125 (129)
Q Consensus 120 ~iA~~i 125 (129)
++...+
T Consensus 115 ~l~~~~ 120 (185)
T PRK13777 115 ETMEEY 120 (185)
T ss_pred HHHHHH
Confidence 886543
No 29
>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=94.92 E-value=0.056 Score=37.90 Aligned_cols=45 Identities=20% Similarity=0.293 Sum_probs=34.1
Q ss_pred CCchhHHHHHHHHHHhCCceeec--C-CCCc-----eeCcchHhhHHHHHHHh
Q 033029 81 KSSGAIARHILQQLQNMNIIDIE--P-KGGR-----RITSSGQRDLDQVAGRI 125 (129)
Q Consensus 81 ~asg~iiR~~lqqLE~~g~vek~--~-~~GR-----~lT~~G~~~lD~iA~~i 125 (129)
.-+-+-+=.+|..||+.|||+.. + .+|| .||++|+..|+......
T Consensus 36 ~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~ 88 (100)
T TIGR03433 36 QVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW 88 (100)
T ss_pred ccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 34445688899999999999973 2 2232 59999999999887654
No 30
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=94.87 E-value=0.033 Score=38.45 Aligned_cols=36 Identities=25% Similarity=0.332 Sum_probs=31.6
Q ss_pred hhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHH
Q 033029 84 GAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 119 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD 119 (129)
-+-++++++-|.++|+|++...|--.||+.|++.|-
T Consensus 54 ~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 54 KNRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA 89 (92)
T ss_pred HHhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence 357999999999999999877667899999999874
No 31
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=94.80 E-value=0.049 Score=39.33 Aligned_cols=42 Identities=19% Similarity=0.233 Sum_probs=33.5
Q ss_pred CCchhHHHHHHHHHHhCCceeecCCC---CceeCcchHhhHHHHH
Q 033029 81 KSSGAIARHILQQLQNMNIIDIEPKG---GRRITSSGQRDLDQVA 122 (129)
Q Consensus 81 ~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~~G~~~lD~iA 122 (129)
.=+-.+++++++.|++.|++++...+ .-.||++|.++|..+-
T Consensus 42 Nlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y~ 86 (95)
T COG3432 42 NLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKYS 86 (95)
T ss_pred CcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHHH
Confidence 33457899999999999988877643 2579999999987653
No 32
>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=94.77 E-value=0.075 Score=45.09 Aligned_cols=53 Identities=25% Similarity=0.293 Sum_probs=44.0
Q ss_pred HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcchHhh
Q 033029 53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSSGQRD 117 (129)
Q Consensus 53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~G~~~ 117 (129)
-.+|||+..|.+.|+- .-|..-||+-+.+||+.|++++... .||.-|.+|-+.
T Consensus 18 ~~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~ 71 (337)
T TIGR00331 18 TGQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRY 71 (337)
T ss_pred cCCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHH
Confidence 3579999999998664 3345689999999999999998653 599999998776
No 33
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=94.60 E-value=0.087 Score=44.73 Aligned_cols=55 Identities=24% Similarity=0.389 Sum_probs=44.2
Q ss_pred HHH--hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029 51 IYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD 117 (129)
Q Consensus 51 lYl--~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~ 117 (129)
.|+ .+|+|+..|.+.|+- .-|-.-||+-+..||++|++++.. ..||+-|.+|-+.
T Consensus 18 ~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~ 75 (339)
T PRK00082 18 DYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRY 75 (339)
T ss_pred HHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHH
Confidence 355 579999999987654 233468999999999999999755 4699999999764
No 34
>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=94.48 E-value=0.063 Score=41.05 Aligned_cols=51 Identities=16% Similarity=0.229 Sum_probs=40.7
Q ss_pred CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
+.-..|+..||- |.+-+|.+|+.||..|||+..++.|-.+++-...++..+
T Consensus 35 L~e~~La~~lgV--------------SRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~ei 85 (212)
T TIGR03338 35 LNESDIAARLGV--------------SRGPVREAFRALEEAGLVRNEKNRGVFVREISLAEADEI 85 (212)
T ss_pred ecHHHHHHHhCC--------------ChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHHHHHHH
Confidence 344578888765 446899999999999999999888999988777766543
No 35
>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=94.41 E-value=0.092 Score=32.57 Aligned_cols=49 Identities=18% Similarity=0.255 Sum_probs=40.3
Q ss_pred HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
-|+..||+.|.-.+ ++++..+...-|- +.+-+.++|+.|++.|||++++
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 48889999888865 4799999998664 2367899999999999999874
No 36
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.33 E-value=0.095 Score=35.79 Aligned_cols=65 Identities=12% Similarity=0.320 Sum_probs=43.2
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCC-----ceeCcchHhhHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGG-----RRITSSGQRDLD 119 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~G-----R~lT~~G~~~lD 119 (129)
|+=-|+-.+.+-...|+..-| -+.+-+.+-|+.||++|+|+..+ .++ -.||++|+..+.
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 344445556666666666533 34567889999999999998654 233 269999999998
Q ss_pred HHHHHh
Q 033029 120 QVAGRI 125 (129)
Q Consensus 120 ~iA~~i 125 (129)
+.-..+
T Consensus 71 ~~~~~L 76 (80)
T PF13601_consen 71 RYVAAL 76 (80)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 766543
No 37
>PRK05638 threonine synthase; Validated
Probab=94.28 E-value=0.11 Score=44.95 Aligned_cols=75 Identities=15% Similarity=0.198 Sum_probs=54.6
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
++|.-+.++-+. .||+.|. +++.-+..|.+..+. .-|...++..|+.||+.|||+...+.||
T Consensus 363 ~~~~~~~~~~r~-----~IL~~L~-~~~~~~~el~~~l~~------------~~s~~~v~~hL~~Le~~GLV~~~~~~g~ 424 (442)
T PRK05638 363 GREKFTIGGTKL-----EILKILS-EREMYGYEIWKALGK------------PLKYQAVYQHIKELEELGLIEEAYRKGR 424 (442)
T ss_pred chhhhcccchHH-----HHHHHHh-hCCccHHHHHHHHcc------------cCCcchHHHHHHHHHHCCCEEEeecCCC
Confidence 555555566443 3666665 668889999998873 1366799999999999999986422344
Q ss_pred e----eCcchHhhHHHH
Q 033029 109 R----ITSSGQRDLDQV 121 (129)
Q Consensus 109 ~----lT~~G~~~lD~i 121 (129)
+ ||++|+..+..+
T Consensus 425 ~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 425 RVYYKLTEKGRRLLENL 441 (442)
T ss_pred cEEEEECcHHHHHHHhc
Confidence 4 999999998764
No 38
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=94.19 E-value=0.082 Score=39.75 Aligned_cols=37 Identities=22% Similarity=0.343 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 85 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
+-+.++.|.||..|+|+.....|..+|++|+..+|..
T Consensus 50 nTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~ 86 (125)
T COG1725 50 NTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQL 86 (125)
T ss_pred HHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHH
Confidence 4889999999999999988878999999999877654
No 39
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=94.19 E-value=0.28 Score=38.00 Aligned_cols=85 Identities=19% Similarity=0.228 Sum_probs=57.7
Q ss_pred CCCCCcccccChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCccc
Q 033029 1 MATARTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFC 80 (129)
Q Consensus 1 m~~~~tv~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~ 80 (129)
||+..+ ++...+-+.++++|++.=...+++|-+. +-...|+..||-.
T Consensus 1 ~~~~~~---~~~~~~~e~v~~~l~~~I~~g~l~pG~~-------------------L~e~~La~~lgVS----------- 47 (221)
T PRK11414 1 MPGTEK---TQHISLTLQVENDLKHQLSIGALKPGAR-------------------LITKNLAEQLGMS----------- 47 (221)
T ss_pred CCCCcc---cCCCCHHHHHHHHHHHHHHhCCCCCCCc-------------------cCHHHHHHHHCCC-----------
Confidence 555333 3344455666777776544567788663 2235688888753
Q ss_pred CCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 81 KSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 81 ~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus 48 ---RtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei 85 (221)
T PRK11414 48 ---ITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI 85 (221)
T ss_pred ---chhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence 35899999999999999998877877776655555443
No 40
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=94.11 E-value=0.097 Score=37.10 Aligned_cols=47 Identities=26% Similarity=0.280 Sum_probs=37.6
Q ss_pred CCCcccCCchhHHHHHHHHHHhCCceeecCCC---C------ceeCcchHhhHHHH
Q 033029 75 RPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---G------RRITSSGQRDLDQV 121 (129)
Q Consensus 75 ~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---G------R~lT~~G~~~lD~i 121 (129)
.+..+..-+-.-|-+-+++|.++|||+-.... | ..||.+|..+||.|
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 34555666677999999999999999866532 1 48999999999986
No 41
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=94.01 E-value=0.053 Score=46.46 Aligned_cols=65 Identities=20% Similarity=0.230 Sum_probs=48.9
Q ss_pred HHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029 47 MARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 47 ilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
|||=|.=.+ |+|-......--- ||+.- +---+|+=||-||+.||++|+.-.||.||++|-+.|.+
T Consensus 11 Il~il~esd~plgak~Ia~el~k---RGy~i------geRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~ 76 (325)
T COG1693 11 ILRILAESDEPLGAKIIALELRK---RGYNI------GERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKR 76 (325)
T ss_pred HHHHHHhcCCccchHHHHHHHHh---cccch------hHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhh
Confidence 555555544 7887766655422 25432 23469999999999999999988899999999999998
No 42
>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=93.96 E-value=0.082 Score=40.17 Aligned_cols=43 Identities=21% Similarity=0.332 Sum_probs=32.6
Q ss_pred chhHHHHHHHHHHhCCceeec---CCCCc-----eeCcchHhhHHHHHHHh
Q 033029 83 SGAIARHILQQLQNMNIIDIE---PKGGR-----RITSSGQRDLDQVAGRI 125 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~---~~~GR-----~lT~~G~~~lD~iA~~i 125 (129)
+-+-+=.+|+.||+.|||+.. ..+|| .||+.|+..|+....++
T Consensus 56 ~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w 106 (138)
T TIGR02719 56 DQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF 106 (138)
T ss_pred CcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence 334677899999999999863 23354 49999999888876654
No 43
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=93.81 E-value=0.13 Score=39.40 Aligned_cols=54 Identities=17% Similarity=0.374 Sum_probs=43.2
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
.|++.++.++..-+ +.| +-+-..++.|++.|||+..+.+|=.||++|....-.+
T Consensus 22 ~~~~~~~diA~~L~------Vsp--------~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~ 75 (154)
T COG1321 22 KGFARTKDIAERLK------VSP--------PSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKEL 75 (154)
T ss_pred cCcccHHHHHHHhC------CCc--------HHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHH
Confidence 56788888887643 445 3677899999999999999999999999999655443
No 44
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=93.74 E-value=0.063 Score=35.43 Aligned_cols=41 Identities=27% Similarity=0.362 Sum_probs=31.6
Q ss_pred cCCchhHHHHHHHHHHhCCceeecCC---CC-----ceeCcchHhhHHH
Q 033029 80 CKSSGAIARHILQQLQNMNIIDIEPK---GG-----RRITSSGQRDLDQ 120 (129)
Q Consensus 80 ~~asg~iiR~~lqqLE~~g~vek~~~---~G-----R~lT~~G~~~lD~ 120 (129)
..-|-+-+=.+|+.||+.|+|+.... +| -.||++|+..|.+
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 45566788999999999999986442 22 3699999998763
No 45
>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=93.64 E-value=0.23 Score=38.55 Aligned_cols=55 Identities=13% Similarity=0.175 Sum_probs=43.7
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC--CceeCcch
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG--GRRITSSG 114 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~--GR~lT~~G 114 (129)
.|+..|.-+|++.+..+....|- |.+-+++.|+.||+.|||++..+. .-.||++|
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 57877777789999999998864 345789999999999999987522 34578776
No 46
>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=93.44 E-value=0.19 Score=33.90 Aligned_cols=45 Identities=24% Similarity=0.346 Sum_probs=34.7
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcch
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG 114 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G 114 (129)
++.+..++..+|-. -..+|+++++|++.|+|+..+ .||-.|+..-
T Consensus 25 ~~s~~eiA~~~~i~--------------~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 25 PVSSKEIAERLGIS--------------PSYLRKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp -BEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred CCCHHHHHHHHCcC--------------HHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 48888999887653 358999999999999999654 4788887654
No 47
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=93.37 E-value=0.12 Score=31.94 Aligned_cols=39 Identities=18% Similarity=0.303 Sum_probs=30.3
Q ss_pred hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
+..|+..||- |..-++++|+.|++.|+|+..++.|-.||
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 6677777644 34689999999999999997765666665
No 48
>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=93.01 E-value=0.27 Score=31.24 Aligned_cols=46 Identities=17% Similarity=0.229 Sum_probs=38.9
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
..|++.|-..+|..++.|....|- +-+-+.+=|+.||++|+|+...
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~~--------------~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELGI--------------SQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeEEec
Confidence 358888888999999999999873 3357899999999999999875
No 49
>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=92.83 E-value=0.2 Score=39.04 Aligned_cols=42 Identities=14% Similarity=0.229 Sum_probs=34.9
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
.-..|+..||- |..-+|.+|+.||..|+|+..++.|-.+++-
T Consensus 32 sE~~La~~lgV--------------SRtpVREAL~~Le~eGlV~~~~~~G~~V~~~ 73 (235)
T TIGR02812 32 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNNF 73 (235)
T ss_pred CHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCCCccEecCc
Confidence 45577777765 4578999999999999999988889998873
No 50
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=92.76 E-value=0.19 Score=38.86 Aligned_cols=51 Identities=20% Similarity=0.279 Sum_probs=40.0
Q ss_pred CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
+-...|+..||- |..-+|.+|+.||..|+|+..+..|-.+++-...++..+
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 345678888875 336899999999999999998888888887766655443
No 51
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=92.64 E-value=0.42 Score=38.42 Aligned_cols=62 Identities=19% Similarity=0.226 Sum_probs=49.7
Q ss_pred HhHHHHHHHHHHhC-CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-CCCceeCcchHhh
Q 033029 42 VRAASMARKIYLRQ-GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-KGGRRITSSGQRD 117 (129)
Q Consensus 42 ~R~ASilR~lYl~g-~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~~GR~lT~~G~~~ 117 (129)
-|+..||+.|.-++ ++++..|.+..|-. .+-+.++|+.|++.|||++++ ++...||++....
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lgl~--------------kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l 74 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTGLH--------------RTTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQL 74 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHH
Confidence 48889999987755 59999999987542 357899999999999999886 4567788877543
No 52
>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=92.45 E-value=0.46 Score=29.38 Aligned_cols=51 Identities=20% Similarity=0.333 Sum_probs=40.0
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCce
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRR 109 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~ 109 (129)
..+|..||-.|++.+..|....+- +.+-+-.++++||+.|||++.. +..|.
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 357888999999999999998765 3356778999999999998654 34443
No 53
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=92.36 E-value=0.18 Score=39.63 Aligned_cols=45 Identities=18% Similarity=0.129 Sum_probs=36.3
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHh
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQR 116 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~ 116 (129)
.-..|+..||- |...+|.+|+.||..|||+..++.|-.+++-...
T Consensus 33 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~ 77 (251)
T PRK09990 33 SERRLCEKLGF--------------SRSALREGLTVLRGRGIIETAQGRGSFVARLNRV 77 (251)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence 45677887775 4579999999999999999988888888776544
No 54
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=92.03 E-value=0.54 Score=34.59 Aligned_cols=62 Identities=19% Similarity=0.282 Sum_probs=47.7
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC------CCCceeCcchHhhHHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGRRITSSGQRDLDQ 120 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~------~~GR~lT~~G~~~lD~ 120 (129)
|++++.- |+.--+.|++.-++ =|-+++=.-|+.||+.|+|++.. +-...||+.|++++.-
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 7777776 77777777776544 45578888899999999999765 2367899999998765
Q ss_pred HH
Q 033029 121 VA 122 (129)
Q Consensus 121 iA 122 (129)
+.
T Consensus 94 l~ 95 (120)
T COG1733 94 LL 95 (120)
T ss_pred HH
Confidence 43
No 55
>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=92.02 E-value=0.68 Score=33.27 Aligned_cols=68 Identities=15% Similarity=0.212 Sum_probs=48.1
Q ss_pred HHHHHHHHHHh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcch-HhhH
Q 033029 44 AASMARKIYLR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSG-QRDL 118 (129)
Q Consensus 44 ~ASilR~lYl~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G-~~~l 118 (129)
|-.+|..|... +++.+..|+..+|- |.+.++++|+.|++.|+|+... .+|..|.... +-.+
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 34456666554 46888889888765 3469999999999999998643 5677777655 3336
Q ss_pred HHHHHHh
Q 033029 119 DQVAGRI 125 (129)
Q Consensus 119 D~iA~~i 125 (129)
..|...|
T Consensus 77 ~~v~~~l 83 (130)
T TIGR02944 77 ADIVKAV 83 (130)
T ss_pred HHHHHHH
Confidence 6666554
No 56
>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=91.91 E-value=0.83 Score=27.84 Aligned_cols=61 Identities=16% Similarity=0.197 Sum_probs=45.1
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHH
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~ 123 (129)
|+..++-.+ +.+..+.+..|- +.+-++.+|.+|++.|+|..... .-..+|+ |+..++.+..
T Consensus 12 il~~l~~~~-~~~~ei~~~~~i--------------~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~~ 75 (78)
T cd00090 12 ILRLLLEGP-LTVSELAERLGL--------------SQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLES 75 (78)
T ss_pred HHHHHHHCC-cCHHHHHHHHCc--------------CHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHHH
Confidence 666666655 889999887643 23578999999999999986542 2447898 8888877653
No 57
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=91.90 E-value=0.21 Score=30.15 Aligned_cols=36 Identities=19% Similarity=0.310 Sum_probs=27.4
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G 107 (129)
.+..|+..||- |..-+|++|++|++.|+|+..+++|
T Consensus 22 s~~~la~~~~v--------------s~~tv~~~l~~L~~~g~i~~~~~~g 57 (60)
T smart00345 22 SERELAAQLGV--------------SRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCe
Confidence 56666776643 4568999999999999998776444
No 58
>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=91.70 E-value=0.26 Score=40.82 Aligned_cols=44 Identities=23% Similarity=0.271 Sum_probs=37.5
Q ss_pred hhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHHHhhh
Q 033029 84 GAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRIVV 127 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~~i~~ 127 (129)
...+|.+|.-|++.|+|+.... ....||++|++.++..+.-|..
T Consensus 34 ~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~ 80 (280)
T TIGR02277 34 ERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD 80 (280)
T ss_pred cchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC
Confidence 3589999999999999997653 4678999999999998887764
No 59
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=91.53 E-value=0.24 Score=31.71 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=28.8
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
....|...||- |...+|.+|+.|++.|+|+..+..|-
T Consensus 26 s~~~la~~~~v--------------sr~tvr~al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 26 SERELAERYGV--------------SRTTVREALRRLEAEGLIERRPGRGT 62 (64)
T ss_dssp -HHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred CHHHHHHHhcc--------------CCcHHHHHHHHHHHCCcEEEECCceE
Confidence 56677777764 45699999999999999998876553
No 60
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=91.38 E-value=0.41 Score=35.23 Aligned_cols=43 Identities=21% Similarity=0.310 Sum_probs=33.4
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCceeCc
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITS 112 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR~lT~ 112 (129)
++.+..|+..+|- |...+|++|++|++.|+|+..+. ||-.|+.
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 5677888888775 34589999999999999997763 4656654
No 61
>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=91.33 E-value=0.43 Score=29.54 Aligned_cols=46 Identities=15% Similarity=0.219 Sum_probs=38.1
Q ss_pred HHHHHHHHHhCC--CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 45 ASMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 45 ASilR~lYl~g~--vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
..||..|+-+++ +.+..|+...|-. .+-+-.+++.||+.|||++.+
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 358899999998 8999999987653 346788999999999999765
No 62
>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=91.20 E-value=1.4 Score=32.03 Aligned_cols=71 Identities=17% Similarity=0.106 Sum_probs=53.3
Q ss_pred HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
=.+|+|+=+||-+.=+..+.++-.- +...+...+-+=++-|-+-|||||..| |-++|..|+..+-++
T Consensus 16 E~~~~ilI~v~Kk~Fit~~ev~e~l------------~~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~~A 82 (96)
T PF09114_consen 16 ENAANILIQVAKKNFITASEVREAL------------ATEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIIIQA 82 (96)
T ss_dssp HHHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHccCCHHHHHHHH------------HHHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHHHH
Confidence 3578899999988888888887742 224455667777899999999999964 899999999999998
Q ss_pred HHHh
Q 033029 122 AGRI 125 (129)
Q Consensus 122 A~~i 125 (129)
|.--
T Consensus 83 A~l~ 86 (96)
T PF09114_consen 83 AELW 86 (96)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 8643
No 63
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=91.06 E-value=0.33 Score=37.90 Aligned_cols=52 Identities=19% Similarity=0.324 Sum_probs=45.1
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHH
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
.+....|+..||-. ..-||.+|+.|+..|+|+..+..|-.+++-..+++..+
T Consensus 39 ~l~e~~La~~~gvS--------------rtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~~~~ei 90 (230)
T COG1802 39 RLSEEELAEELGVS--------------RTPVREALRRLEAEGLVEIEPNRGAFVAPLSLAEAREI 90 (230)
T ss_pred CccHHHHHHHhCCC--------------CccHHHHHHHHHHCCCeEecCCCCCeeCCCCHHHHHHH
Confidence 57788899999864 24799999999999999999989999999888888774
No 64
>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=90.77 E-value=0.6 Score=29.74 Aligned_cols=48 Identities=17% Similarity=0.220 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|-..|+..|--++.+.+..|...||- |-.-||+=|+.||+.|+|.+.-
T Consensus 1 R~~~Il~~l~~~~~~s~~ela~~~~V--------------S~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 1 RQQQILELLKEKGKVSVKELAEEFGV--------------SEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred CHHHHHHHHHHcCCEEHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEc
Confidence 34567888888999999999999875 3458999999999999999875
No 65
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=90.45 E-value=0.29 Score=38.76 Aligned_cols=41 Identities=20% Similarity=0.135 Sum_probs=33.5
Q ss_pred hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
-..|+..||= |..-+|.+|+.||..|||+..+.+|-.+++-
T Consensus 29 E~eLae~~gV--------------SRtpVREAL~~Le~~GlV~~~~~~G~~V~~~ 69 (253)
T PRK10421 29 ERQLAMQLGV--------------SRNSLREALAKLVSEGVLLSRRGGGTFIRWR 69 (253)
T ss_pred HHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence 4567777764 5579999999999999999888788888764
No 66
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=90.39 E-value=1.2 Score=31.61 Aligned_cols=49 Identities=20% Similarity=0.308 Sum_probs=38.5
Q ss_pred CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCceeCcchHhh
Q 033029 55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSGQRD 117 (129)
Q Consensus 55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR~lT~~G~~~ 117 (129)
+++.+..|+..+|- +.+.++++|+.|++.|||... ..||-.|+......
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 37889999888765 346999999999999999864 34677888776544
No 67
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=90.36 E-value=0.87 Score=32.52 Aligned_cols=48 Identities=19% Similarity=0.203 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l 110 (129)
||.|+|--||---..+++.. ...-.-++.+|..||++||||... |..|
T Consensus 12 IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~--g~~i 59 (92)
T PF10007_consen 12 ILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE--GKTI 59 (92)
T ss_pred HHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec--Cccc
Confidence 78888888876555565543 344468999999999999999875 4444
No 68
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=90.35 E-value=0.33 Score=37.83 Aligned_cols=41 Identities=15% Similarity=0.257 Sum_probs=33.8
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
.-..|+..||- |.+-+|.+|+.||..|+|+..+..|-.+++
T Consensus 33 sE~eLae~~gV--------------SRt~VReAL~~L~~eGlv~~~~g~G~~V~~ 73 (239)
T PRK04984 33 AERELSELIGV--------------TRTTLREVLQRLARDGWLTIQHGKPTKVNN 73 (239)
T ss_pred CHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence 34567787765 557999999999999999998878888865
No 69
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=90.31 E-value=0.28 Score=38.77 Aligned_cols=44 Identities=11% Similarity=0.186 Sum_probs=35.8
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ 115 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~ 115 (129)
....|+..||= |..-+|.+|+.||..|+|+..++.|-.+++...
T Consensus 35 sE~eLa~~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~ 78 (257)
T PRK10225 35 PEREIAEMLDV--------------TRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG 78 (257)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence 35678888875 456899999999999999988877888876543
No 70
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=90.07 E-value=0.85 Score=36.37 Aligned_cols=58 Identities=10% Similarity=0.149 Sum_probs=45.9
Q ss_pred HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcc
Q 033029 42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS 113 (129)
Q Consensus 42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~ 113 (129)
-|+..||..|.-.+++++..|++.-|-. .+-+..+|+.|++.|||++++. +...|+++
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 4888899999877889999999986653 3578999999999999998753 44455544
No 71
>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=90.07 E-value=0.47 Score=29.57 Aligned_cols=45 Identities=16% Similarity=0.230 Sum_probs=33.4
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
.+++....|....|- |.+-+.++|++|++.|+|+....++-.|||
T Consensus 23 ~~~~s~~ela~~~g~--------------s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 23 QLPLTRQEIADYLGL--------------TRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred cCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 356677777777664 346789999999999999987645566654
No 72
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.91 E-value=0.98 Score=29.73 Aligned_cols=45 Identities=7% Similarity=-0.036 Sum_probs=37.1
Q ss_pred HHHHHHHHhCC--CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 46 SMARKIYLRQG--LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 46 SilR~lYl~g~--vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
.||..|.-+|+ +....|.+..|=. .+.++++|..||+.|+|++..
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl~--------------~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGLP--------------KKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEecC
Confidence 46777777777 9999999987753 248999999999999999865
No 73
>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=89.88 E-value=0.93 Score=28.81 Aligned_cols=52 Identities=21% Similarity=0.425 Sum_probs=36.6
Q ss_pred HHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchH
Q 033029 50 KIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQ 115 (129)
Q Consensus 50 ~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~ 115 (129)
.|=+..++-+..+...||.. --......|+.|++.|||+.+. +.=+||++|+
T Consensus 14 ~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~ 65 (66)
T PF06969_consen 14 GLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDG-GRLRLTEKGR 65 (66)
T ss_dssp HHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred HHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence 34446688888899988864 1235578899999999999875 5778999996
No 74
>PRK03837 transcriptional regulator NanR; Provisional
Probab=89.86 E-value=0.38 Score=37.38 Aligned_cols=43 Identities=16% Similarity=0.294 Sum_probs=34.4
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 114 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G 114 (129)
....|+..||= |.+.+|.+|+.||..|+|+..++.|-.+++-.
T Consensus 39 ~E~~Lae~~gV--------------SRt~VREAL~~L~~eGlv~~~~~~G~~V~~~~ 81 (241)
T PRK03837 39 SERELMAFFGV--------------GRPAVREALQALKRKGLVQISHGERARVSRPS 81 (241)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCCceeEecCC
Confidence 45678888764 55799999999999999998887777776543
No 75
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=89.68 E-value=0.36 Score=38.02 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=33.4
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
.-..|+..||- |...+|.+|+.||..|||+..+.+|-.+++.
T Consensus 36 sE~eLa~~lgV--------------SRtpVREAL~~L~~eGlv~~~~~~G~~V~~~ 77 (254)
T PRK09464 36 PERELAKQFDV--------------SRPSLREAIQRLEAKGLLLRRQGGGTFVQSS 77 (254)
T ss_pred CHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEecC
Confidence 34567777764 4579999999999999999888778777653
No 76
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=89.63 E-value=0.41 Score=36.51 Aligned_cols=42 Identities=17% Similarity=0.253 Sum_probs=32.1
Q ss_pred chhHHHHHHHHHHhCCceeecCCC-C---ceeCcchHhhHHHHHHH
Q 033029 83 SGAIARHILQQLQNMNIIDIEPKG-G---RRITSSGQRDLDQVAGR 124 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~~~-G---R~lT~~G~~~lD~iA~~ 124 (129)
|-+-|=-+|+.||+.|||+....+ . -.||+.|+..|+....+
T Consensus 76 s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~ 121 (135)
T PRK09416 76 NEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKN 121 (135)
T ss_pred CCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhC
Confidence 445677899999999999864322 2 36999999999987653
No 77
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=89.28 E-value=0.4 Score=37.91 Aligned_cols=42 Identities=12% Similarity=0.122 Sum_probs=33.5
Q ss_pred hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029 59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 114 (129)
Q Consensus 59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G 114 (129)
-..|+..||= |..-+|.+|+.||..|+|+..+..|-.+++-.
T Consensus 35 E~eLae~~gV--------------SRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~ 76 (253)
T PRK11523 35 ERFIADEKNV--------------SRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQ 76 (253)
T ss_pred HHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCeeEEecCC
Confidence 4567777765 45689999999999999998887787776643
No 78
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.24 E-value=1.7 Score=25.35 Aligned_cols=45 Identities=13% Similarity=0.182 Sum_probs=35.5
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
.|+..+.-++++.+..|+..+|- |-+-+++.|+.|++.|+|+...
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~~--------------s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLGV--------------SEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEee
Confidence 35666666788999999998843 2346899999999999999765
No 79
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=88.87 E-value=0.67 Score=37.54 Aligned_cols=55 Identities=24% Similarity=0.170 Sum_probs=40.7
Q ss_pred CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHHHh
Q 033029 57 LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGRI 125 (129)
Q Consensus 57 vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~~i 125 (129)
+..+.|++..|- |.+-+-+.|+.||+.|||++... .--.||++|+..+.+.....
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 335577776543 45678889999999999987642 24579999999998877553
No 80
>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=88.57 E-value=2 Score=29.59 Aligned_cols=76 Identities=16% Similarity=0.144 Sum_probs=50.0
Q ss_pred HHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcc------cC---CchhHHHHHHHHHHhCCceeecCC----CCcee
Q 033029 45 ASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHF------CK---SSGAIARHILQQLQNMNIIDIEPK----GGRRI 110 (129)
Q Consensus 45 ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~------~~---asg~iiR~~lqqLE~~g~vek~~~----~GR~l 110 (129)
..|++-|+- .+.+|...+..++=|.++......++ -. =+..-++.++++|...|+++...+ .-=.+
T Consensus 7 ~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~ 86 (106)
T PF09382_consen 7 KKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKL 86 (106)
T ss_dssp HHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEEE
Confidence 345555555 56899999999999988877543322 11 255789999999999999976543 13468
Q ss_pred CcchHhhHHH
Q 033029 111 TSSGQRDLDQ 120 (129)
Q Consensus 111 T~~G~~~lD~ 120 (129)
|++|++.|..
T Consensus 87 ~~~~~~~l~g 96 (106)
T PF09382_consen 87 TPKGKELLNG 96 (106)
T ss_dssp -GGGHHHHCT
T ss_pred CHHHHHHHCC
Confidence 9999988753
No 81
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=88.48 E-value=0.61 Score=34.10 Aligned_cols=39 Identities=26% Similarity=0.399 Sum_probs=32.4
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
++.+..|+....+..| -+|.+|++|++.|||+-.+..||
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 5788888888776544 68999999999999999987676
No 82
>PRK11569 transcriptional repressor IclR; Provisional
Probab=88.37 E-value=1.4 Score=35.67 Aligned_cols=59 Identities=12% Similarity=0.157 Sum_probs=46.0
Q ss_pred HHhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-CCceeCcc
Q 033029 41 YVRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-GGRRITSS 113 (129)
Q Consensus 41 Y~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-~GR~lT~~ 113 (129)
--|+..||+.|-- .+++++..|.+.-|-. .+-+..+|+.|++.|||+++++ +...|.+.
T Consensus 27 l~ral~IL~~l~~~~~~~~lseia~~lglp--------------ksTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 87 (274)
T PRK11569 27 LTRGLKLLEWIAESNGSVALTELAQQAGLP--------------NSTTHRLLTTMQQQGFVRQVGELGHWAIGAH 87 (274)
T ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence 3588999999876 4689999999986653 3688999999999999998764 33345443
No 83
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=88.29 E-value=2.2 Score=36.30 Aligned_cols=57 Identities=21% Similarity=0.351 Sum_probs=44.0
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
..++-...+...||-. . ....|+.|++.|+++.+.++.=+||++|+-.+|.|+..++
T Consensus 323 ~~gid~~~~~~~~g~~------~----------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~ 379 (380)
T PRK09057 323 REGIDLARYAALSGRP------L----------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA 379 (380)
T ss_pred hCCCCHHHHHHHHCCC------c----------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence 4567778888888743 1 1247999999999997542246899999999999999875
No 84
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.04 E-value=1.6 Score=32.97 Aligned_cols=60 Identities=25% Similarity=0.315 Sum_probs=46.2
Q ss_pred HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC---CCCc-----------eeCcchHhhH
Q 033029 53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP---KGGR-----------RITSSGQRDL 118 (129)
Q Consensus 53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~---~~GR-----------~lT~~G~~~l 118 (129)
.+||..|..|+..-+ =+.|-+=++||.|..+|+|++.+ ++|| .++....++|
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 489999999998743 35578899999999999998655 3444 2566788888
Q ss_pred HHHHHHhh
Q 033029 119 DQVAGRIV 126 (129)
Q Consensus 119 D~iA~~i~ 126 (129)
|..+.++.
T Consensus 105 ~~w~~~~~ 112 (126)
T COG3355 105 DEWYDKMK 112 (126)
T ss_pred HHHHHHHH
Confidence 88887763
No 85
>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=87.67 E-value=0.8 Score=30.35 Aligned_cols=40 Identities=20% Similarity=0.216 Sum_probs=29.3
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
|-.|..++..+|- .|-+-+..-|++||+.|+|+.++...|
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 3467777777765 355789999999999999999875443
No 86
>PF13814 Replic_Relax: Replication-relaxation
Probab=87.51 E-value=1.5 Score=32.75 Aligned_cols=62 Identities=24% Similarity=0.338 Sum_probs=46.2
Q ss_pred HHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC-----CCc-----eeCcchHhh
Q 033029 48 ARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK-----GGR-----RITSSGQRD 117 (129)
Q Consensus 48 lR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~-----~GR-----~lT~~G~~~ 117 (129)
|+-||-.+-+....|...++...+. ..-++..|++|++.|+|+.... +|. .||++|...
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 3456677778888888888765332 1278999999999999987653 122 699999998
Q ss_pred HHH
Q 033029 118 LDQ 120 (129)
Q Consensus 118 lD~ 120 (129)
|..
T Consensus 70 l~~ 72 (191)
T PF13814_consen 70 LAD 72 (191)
T ss_pred HHh
Confidence 874
No 87
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=87.37 E-value=2.2 Score=35.84 Aligned_cols=62 Identities=18% Similarity=0.300 Sum_probs=46.3
Q ss_pred HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029 53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
...++=...+...||.. ........+++|++.|+++.+. +.=+||++|+-.+|.|+.+++.+
T Consensus 315 ~~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~~~~~~ 376 (377)
T PRK08599 315 KKSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFEAFLLD 376 (377)
T ss_pred hhCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHHHHhhh
Confidence 34556666666666531 1345677889999999999764 46789999999999999987643
No 88
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=87.30 E-value=2.5 Score=25.32 Aligned_cols=42 Identities=12% Similarity=0.177 Sum_probs=34.3
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCcee
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 101 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ve 101 (129)
.|+..|.-+|++.+..++...|- |.+-+++.|++|++.|+|+
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 47777888899999999998765 4468999999999999985
No 89
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=87.17 E-value=1.9 Score=34.95 Aligned_cols=57 Identities=12% Similarity=0.066 Sum_probs=44.6
Q ss_pred HhHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC-ceeCc
Q 033029 42 VRAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITS 112 (129)
Q Consensus 42 ~R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G-R~lT~ 112 (129)
-|+.+||+.|.-. +++++..|++.-|-. .+-+..+|+.|+..|||++++..| -.|++
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lglp--------------kStv~RlL~tL~~~G~l~~~~~~~~Y~lG~ 83 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDLP--------------LSTTFRLLKVLQAADFVYQDSQLGWWHIGL 83 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence 3889999998764 579999999987653 357899999999999999876433 33444
No 90
>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=87.16 E-value=0.73 Score=35.71 Aligned_cols=61 Identities=11% Similarity=0.139 Sum_probs=43.3
Q ss_pred HHHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 40 YYVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 40 ~Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
-|...+..++.-=..|.. .-..|+..||- |..-+|++|+.|++.|+|++.+..|-.+++
T Consensus 9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 74 (238)
T TIGR02325 9 LWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFGV--------------NRHTVRRAIAALVERGLLRAEQGRGTFVAA 74 (238)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEECC
Confidence 355555555554444432 33567777775 456899999999999999998877888876
Q ss_pred ch
Q 033029 113 SG 114 (129)
Q Consensus 113 ~G 114 (129)
..
T Consensus 75 ~~ 76 (238)
T TIGR02325 75 RR 76 (238)
T ss_pred Cc
Confidence 54
No 91
>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=87.14 E-value=1.5 Score=32.00 Aligned_cols=46 Identities=13% Similarity=0.257 Sum_probs=35.4
Q ss_pred CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec--CCCCceeCcch
Q 033029 55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE--PKGGRRITSSG 114 (129)
Q Consensus 55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~--~~~GR~lT~~G 114 (129)
+++.+..++..++- +...++++|++|.++|||+.. ..||-.|+..-
T Consensus 24 ~~~s~~~ia~~~~i--------------p~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~~ 71 (135)
T TIGR02010 24 GPVTLADISERQGI--------------SLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRPA 71 (135)
T ss_pred CcCcHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEEEeCCCCCEeccCCH
Confidence 47888888887654 346899999999999999853 35687887643
No 92
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=87.03 E-value=0.99 Score=32.69 Aligned_cols=40 Identities=23% Similarity=0.444 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHhCCceeecC--CCC------ceeCcchHhhHHHHHHH
Q 033029 85 AIARHILQQLQNMNIIDIEP--KGG------RRITSSGQRDLDQVAGR 124 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~--~~G------R~lT~~G~~~lD~iA~~ 124 (129)
..|=-+|+.||+.|||+... .++ -.||++|+..|.+...+
T Consensus 45 gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~ 92 (138)
T COG1695 45 GTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREE 92 (138)
T ss_pred CcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHH
Confidence 35667999999999998642 222 37999999999987655
No 93
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=86.87 E-value=0.8 Score=39.30 Aligned_cols=40 Identities=23% Similarity=0.289 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHhCCceeecCCCCc--eeCc-chHhhHHHHHHHhh
Q 033029 85 AIARHILQQLQNMNIIDIEPKGGR--RITS-SGQRDLDQVAGRIV 126 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~GR--~lT~-~G~~~lD~iA~~i~ 126 (129)
......|++|++.||++.+ ++| +||+ +|.-.+|.|+.+++
T Consensus 351 ~~~~~~l~~l~~~gll~~~--~~~~~~lT~~~G~~~~~~i~~~~~ 393 (400)
T PRK07379 351 EQILQCLQPYFQQGWVELE--GDRRLRLTDPEGFLFSNTVLASLF 393 (400)
T ss_pred HHHHHHHHHHHHCCCEEEe--CCeEEEECchHHhHHHHHHHHHHH
Confidence 3456778999999999865 456 8995 99999999999875
No 94
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=86.85 E-value=2 Score=34.56 Aligned_cols=56 Identities=16% Similarity=0.257 Sum_probs=43.5
Q ss_pred HhHHHHHHHHHHhCCC--chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC-ceeCc
Q 033029 42 VRAASMARKIYLRQGL--GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG-RRITS 112 (129)
Q Consensus 42 ~R~ASilR~lYl~g~v--GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G-R~lT~ 112 (129)
.|+..||..|.- +|. ++..|.+.-|-. .+=++.+|+.|++.|||+++++.| -.|++
T Consensus 4 ~ral~iL~~l~~-~~~~l~l~ela~~~glp--------------ksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~ 62 (246)
T COG1414 4 ERALAILDLLAE-GPGGLSLAELAERLGLP--------------KSTVHRLLQTLVELGYVEQDPEDGRYRLGP 62 (246)
T ss_pred HHHHHHHHHHHh-CCCCCCHHHHHHHhCcC--------------HHHHHHHHHHHHHCCCEEEcCCCCcEeehH
Confidence 588899998887 454 499999986642 357899999999999999998554 34444
No 95
>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=86.55 E-value=0.76 Score=38.42 Aligned_cols=60 Identities=12% Similarity=0.169 Sum_probs=42.9
Q ss_pred HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-C-CCceeCcchHhhHHH
Q 033029 47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-K-GGRRITSSGQRDLDQ 120 (129)
Q Consensus 47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~-~GR~lT~~G~~~lD~ 120 (129)
|++.|=- +|-+.-..|+..+| -|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|.
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 4444433 24455555555554 35679999999999999999887 5 488888888888775
No 96
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=86.44 E-value=0.88 Score=34.40 Aligned_cols=46 Identities=24% Similarity=0.325 Sum_probs=35.8
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchH
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ 115 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~ 115 (129)
++.+..++..++- |.+.++++||+|.++|||+... +||-.|+..-.
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 4677777777654 3468999999999999998665 57989986554
No 97
>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=85.97 E-value=0.85 Score=35.56 Aligned_cols=59 Identities=14% Similarity=0.153 Sum_probs=41.3
Q ss_pred HHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 41 YVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 41 Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
|...+..|++-=..|.. +-..|+..||- |..-+|++|+.|++.|+|.+.+..|-.+++.
T Consensus 3 y~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~~ 68 (230)
T TIGR02018 3 YQRIKQDILERIRSGEWPPGHRIPSEHELVAQYGC--------------SRMTVNRALRELTDAGLLERRQGVGTFVAEP 68 (230)
T ss_pred HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEccC
Confidence 44445555544334422 44577888875 4569999999999999999988778777643
No 98
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=85.93 E-value=1.6 Score=35.95 Aligned_cols=64 Identities=19% Similarity=0.309 Sum_probs=45.2
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHH-HHHhCCceeecCCCCceeCcchHh
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQR 116 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lq-qLE~~g~vek~~~~GR~lT~~G~~ 116 (129)
|..|+|+ +...|-.+|+|+..+...-|-... -+-.++. .|-..|+|++.+ .||++|++|.+
T Consensus 261 ~~~~l~~---~~~~~~~~~~~~~~~a~~lg~~~~--------------~~~~~~e~~Li~~~li~~~~-~gr~~~~~~~~ 322 (328)
T PRK00080 261 DRKYLRT---IIEKFGGGPVGLDTLAAALGEERD--------------TIEDVYEPYLIQQGFIQRTP-RGRVATPKAYE 322 (328)
T ss_pred HHHHHHH---HHHHcCCCceeHHHHHHHHCCCcc--------------hHHHHhhHHHHHcCCcccCC-chHHHHHHHHH
Confidence 4556643 233355779999999988765322 2333444 889999999775 69999999998
Q ss_pred hHH
Q 033029 117 DLD 119 (129)
Q Consensus 117 ~lD 119 (129)
.|.
T Consensus 323 ~~~ 325 (328)
T PRK00080 323 HLG 325 (328)
T ss_pred HhC
Confidence 774
No 99
>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=85.71 E-value=1.4 Score=28.26 Aligned_cols=46 Identities=13% Similarity=0.114 Sum_probs=36.4
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
+.|...|--+|+..+..+.+.-|- +.+-++.+|+.|++.|||++.+
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l~i--------------~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEELGI--------------SRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHHTS--------------SHHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEc
Confidence 345555556889999999987554 4468999999999999999875
No 100
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=85.53 E-value=0.67 Score=38.87 Aligned_cols=40 Identities=5% Similarity=0.200 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 86 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 86 iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
.....|+.|++.|+++.+. +.=+||++|+-.+|.|+.+++
T Consensus 334 ~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~ 373 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSNSIMSDFL 373 (374)
T ss_pred HHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHHHHHHHHh
Confidence 4556789999999999753 346889999999999998864
No 101
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=85.38 E-value=0.96 Score=36.28 Aligned_cols=30 Identities=20% Similarity=0.438 Sum_probs=24.8
Q ss_pred chhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 83 SGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
|..++|-+|+.||..|||+..++.|=.+++
T Consensus 47 SR~~vREAl~~L~a~Glve~r~G~Gt~V~~ 76 (241)
T COG2186 47 SRTVVREALKRLEAKGLVEIRQGSGTFVRP 76 (241)
T ss_pred CcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence 456999999999999999987766666654
No 102
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=84.47 E-value=0.96 Score=33.45 Aligned_cols=40 Identities=23% Similarity=0.384 Sum_probs=30.5
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l 110 (129)
-|.+..|...||- ++||.|.+|..||+.|+|.... ++|+.
T Consensus 59 ~VTpy~la~r~gI--------------~~SvAr~vLR~LeeeGvv~lvs-knrR~ 98 (107)
T COG4901 59 VVTPYVLASRYGI--------------NGSVARIVLRHLEEEGVVQLVS-KNRRQ 98 (107)
T ss_pred eecHHHHHHHhcc--------------chHHHHHHHHHHHhCCceeeec-cCccc
Confidence 4556667777664 4789999999999999998775 35553
No 103
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=84.36 E-value=1.5 Score=25.49 Aligned_cols=22 Identities=18% Similarity=0.283 Sum_probs=18.5
Q ss_pred chhHHHHHHHHHHhCCceeecC
Q 033029 83 SGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~ 104 (129)
|.+-++++|++|++.|+|+...
T Consensus 21 s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 21 TRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred CHHHHHHHHHHHHHCCCEEEeC
Confidence 3457899999999999999764
No 104
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=83.89 E-value=1.6 Score=36.77 Aligned_cols=38 Identities=18% Similarity=0.194 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 88 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 88 R~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
+..|++|++.|++..+. +.=+||++|+-.+|.|+..++
T Consensus 337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~ 374 (375)
T PRK05628 337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADAVVRDLL 374 (375)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHHHHHHHh
Confidence 46889999999998764 356899999999999998764
No 105
>PRK05660 HemN family oxidoreductase; Provisional
Probab=83.87 E-value=1.8 Score=36.79 Aligned_cols=40 Identities=15% Similarity=0.155 Sum_probs=33.2
Q ss_pred HHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhhC
Q 033029 88 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVVA 128 (129)
Q Consensus 88 R~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~~ 128 (129)
...++.|++.||++.+. +.=+||++|+-++|.|+..++.+
T Consensus 339 ~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d~i~~~~~~~ 378 (378)
T PRK05660 339 RPQLDEALAQGYLTETA-DHWQITEHGKLFLNDLLELFLAE 378 (378)
T ss_pred HHHHHHHHHCCCEEEeC-CEEEECcchhHHHHHHHHHHhcC
Confidence 45789999999998753 34578999999999999988754
No 106
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=83.65 E-value=1.3 Score=34.80 Aligned_cols=60 Identities=22% Similarity=0.290 Sum_probs=41.7
Q ss_pred HHhHHHHHHHHHHhCCC-------chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 41 YVRAASMARKIYLRQGL-------GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 41 Y~R~ASilR~lYl~g~v-------GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
|...+..|+.-=..|.. .-..|+..||- |..-+|+||+.|++.|+|.+.+..|-.+++.
T Consensus 7 y~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GtfV~~~ 72 (240)
T PRK09764 7 YRQIADRIREQIARGELKPGDALPTESALQTEFGV--------------SRVTVRQALRQLVEQQILESIQGSGTYVKEE 72 (240)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEEccc
Confidence 45555555554444422 33567777764 4568999999999999999888778787765
Q ss_pred h
Q 033029 114 G 114 (129)
Q Consensus 114 G 114 (129)
.
T Consensus 73 ~ 73 (240)
T PRK09764 73 R 73 (240)
T ss_pred c
Confidence 4
No 107
>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=83.47 E-value=1.3 Score=34.47 Aligned_cols=40 Identities=20% Similarity=0.237 Sum_probs=32.5
Q ss_pred hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 60 GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 60 ~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
..|+..||- |..-+|++|+.|++.|+|++.+..|-.+++.
T Consensus 28 ~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~G~GTfV~~~ 67 (233)
T TIGR02404 28 HELMDQYGA--------------SRETVRKALNLLTEAGYIQKIQGKGSIVLNR 67 (233)
T ss_pred HHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEeCCceEEEecC
Confidence 457777764 5569999999999999999988778888653
No 108
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=82.52 E-value=1.6 Score=30.94 Aligned_cols=22 Identities=14% Similarity=0.373 Sum_probs=19.1
Q ss_pred chhHHHHHHHHHHhCCceeecC
Q 033029 83 SGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~ 104 (129)
.||++|.+|..||+-|+|.-..
T Consensus 54 ~~SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 54 KISVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred hHHHHHHHHHHHHHCCCEEEEe
Confidence 4789999999999999997554
No 109
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=82.38 E-value=3.1 Score=31.93 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=36.3
Q ss_pred CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee--cCCCCceeCcch
Q 033029 55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI--EPKGGRRITSSG 114 (129)
Q Consensus 55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek--~~~~GR~lT~~G 114 (129)
+++.+..++..+|- +...++++|++|.++|||+. .++||-.|...-
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 47888888888765 34689999999999999985 346788887553
No 110
>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=82.30 E-value=4.4 Score=28.18 Aligned_cols=48 Identities=15% Similarity=0.090 Sum_probs=33.1
Q ss_pred hHHHHHHHHH--------HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 43 RAASMARKIY--------LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 43 R~ASilR~lY--------l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|-|++|-.|. ...++.-..|....|-. ..-+.++|++||+.|+|+...
T Consensus 26 r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~s--------------r~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 26 REFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLS--------------RTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCeeeec
Confidence 5556555554 44566666777766553 335889999999999998753
No 111
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=82.21 E-value=1.9 Score=37.36 Aligned_cols=59 Identities=22% Similarity=0.342 Sum_probs=43.7
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhhh
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIVV 127 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~~ 127 (129)
..++-...+...||.. + .. ....|++|++.|||+.+. +.=+||++|+-..|.|+.+++.
T Consensus 359 ~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~~~~ 417 (430)
T PRK08208 359 AQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPVFIS 417 (430)
T ss_pred hCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHHcC
Confidence 3566667777777642 1 12 345789999999999764 3558999999999999998754
No 112
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=81.58 E-value=8 Score=33.80 Aligned_cols=79 Identities=22% Similarity=0.288 Sum_probs=58.5
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
..+++|.|. +|-+ ++=.+=+.-++-+..+...||- -. -..+...|+.+++.|+++.+. +.-
T Consensus 332 ~~~l~~~d~----~~e~-~i~gLr~~~gv~~~~~~~~~~~-~~------------~~~~~~~l~~~~~~Gll~~~~-~~~ 392 (416)
T COG0635 332 GEELTPDDL----IREA-LILGLRLNFGVDLAELEERFGI-FK------------FAEILELLAELIADGLLELDG-DRL 392 (416)
T ss_pred eeeCCHHHH----HHHH-HHHHHHHhcCCCHHHHHHHhCc-ch------------hhhHHHHHHHHHhCCCEEecC-CEE
Confidence 677888774 2221 2223334558888899998875 22 357889999999999999875 578
Q ss_pred eeCcchHhhHHHHHHHhh
Q 033029 109 RITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 109 ~lT~~G~~~lD~iA~~i~ 126 (129)
.||+.|+-++|.||....
T Consensus 393 ~lt~~g~~~~~~i~~~f~ 410 (416)
T COG0635 393 RLTEKGRLLLRSIAEAFD 410 (416)
T ss_pred EECCcchhHHHHHHHHHH
Confidence 999999999999998753
No 113
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=81.39 E-value=2.3 Score=37.00 Aligned_cols=63 Identities=19% Similarity=0.221 Sum_probs=42.7
Q ss_pred HHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHh
Q 033029 51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI 125 (129)
Q Consensus 51 lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i 125 (129)
|-...++-...+...||-. +..+ .-....|++|++.|||+.+. ++=+||++|+-.+|.|+..+
T Consensus 376 L~~~~~ld~~~~~~~~g~~------~~~~-----~~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~f 438 (453)
T PRK13347 376 LMCNFPVDLAAIAARHGFF------ARYF-----LDELARLEPLAADGLVTIDG-GGIRVTPEGRPLIRAVAAAF 438 (453)
T ss_pred HHhhCCcCHHHHHHHHCCC------HHHH-----HHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHH
Confidence 3344555556666666632 1111 01245789999999999764 45689999999999999864
No 114
>PRK14999 histidine utilization repressor; Provisional
Probab=81.33 E-value=1.8 Score=34.01 Aligned_cols=61 Identities=13% Similarity=0.073 Sum_probs=43.5
Q ss_pred HHHhHHHHHHHHHHhCC------C-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 40 YYVRAASMARKIYLRQG------L-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 40 ~Y~R~ASilR~lYl~g~------v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
.|...+..|++-=..|. + .-..|+..||- |..-+|++|+.|+..|+|.+.+..|--+++
T Consensus 13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~gV--------------SR~TVR~Al~~L~~eGli~r~~GkGTfV~~ 78 (241)
T PRK14999 13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYGF--------------SRMTINRALRELTDEGWLVRLQGVGTFVAE 78 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence 35555555555444432 2 45678888875 456899999999999999998877888865
Q ss_pred ch
Q 033029 113 SG 114 (129)
Q Consensus 113 ~G 114 (129)
..
T Consensus 79 ~~ 80 (241)
T PRK14999 79 PK 80 (241)
T ss_pred CC
Confidence 43
No 115
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=81.24 E-value=3.5 Score=35.74 Aligned_cols=68 Identities=18% Similarity=0.173 Sum_probs=48.8
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhh
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD 117 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~ 117 (129)
||.=.+--+.+-.-|--||||+..++-.-|--.. .|-=.+===|-..|++++++ .||++|+++.+-
T Consensus 259 d~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~-------------TiEdv~EPyLiq~gfi~RTp-RGR~aT~~ay~h 324 (332)
T COG2255 259 DEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRD-------------TIEDVIEPYLIQQGFIQRTP-RGRIATAKAYEH 324 (332)
T ss_pred cHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchh-------------HHHHHHhHHHHHhchhhhCC-CcceecHHHHHH
Confidence 6666666666666677899999999998775322 12222333466789999998 599999999776
Q ss_pred HH
Q 033029 118 LD 119 (129)
Q Consensus 118 lD 119 (129)
|-
T Consensus 325 l~ 326 (332)
T COG2255 325 LG 326 (332)
T ss_pred hc
Confidence 53
No 116
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=81.06 E-value=1.8 Score=34.09 Aligned_cols=40 Identities=13% Similarity=0.086 Sum_probs=32.3
Q ss_pred hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 60 GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 60 ~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
..|+..||- |..-+|++|+.|++.|+|+..+..|-.+++.
T Consensus 39 ~eLa~~~~V--------------SR~TVR~Al~~L~~eGli~r~~G~GtfV~~~ 78 (241)
T PRK10079 39 QQLAARYEV--------------NRHTLRRAIDQLVEKGWVQRRQGVGVLVLMR 78 (241)
T ss_pred HHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCCEEEEecC
Confidence 467777765 4569999999999999999988778777643
No 117
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=81.04 E-value=2.4 Score=35.96 Aligned_cols=38 Identities=11% Similarity=0.136 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHh
Q 033029 87 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI 125 (129)
Q Consensus 87 iR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i 125 (129)
....+++|++.||++.+. +.=.||++|+-.+|.|+.++
T Consensus 332 ~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~~i~~~~ 369 (370)
T PRK06294 332 TSELIMHPIIQELFTKND-QALSLNKKGRLFHDTIAEEI 369 (370)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHh
Confidence 456788999999998763 35689999999999999875
No 118
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=80.11 E-value=1.4 Score=37.52 Aligned_cols=36 Identities=28% Similarity=0.454 Sum_probs=31.0
Q ss_pred hHHHHHHHHHHhCCceeecC--CCCceeCcchHhhHHH
Q 033029 85 AIARHILQQLQNMNIIDIEP--KGGRRITSSGQRDLDQ 120 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~~~lD~ 120 (129)
.-+|+.+|.|-++||||-.+ +||.+-|.+.-..|+.
T Consensus 40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~i 77 (294)
T COG2524 40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSI 77 (294)
T ss_pred chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhcc
Confidence 36899999999999999765 7999999998877653
No 119
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=79.95 E-value=2.1 Score=32.34 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=35.4
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcchH
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSSGQ 115 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~G~ 115 (129)
++-+..++..+|- |-+.++++|++|.++|+|+... +||-+|...-.
T Consensus 25 ~~s~~~IA~~~~i--------------s~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~ 72 (150)
T COG1959 25 PVSSAEIAERQGI--------------SPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPE 72 (150)
T ss_pred cccHHHHHHHhCc--------------CHHHHHHHHHHHHHcCCEEeecCCCCCccCCCChH
Confidence 5667888876654 3468999999999999998654 58999886543
No 120
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=79.91 E-value=7.5 Score=33.45 Aligned_cols=59 Identities=15% Similarity=0.283 Sum_probs=43.8
Q ss_pred HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHH-HHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 53 LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIA-RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 53 l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~ii-R~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
+..++-+..+...||-. + .... ...|++|++.||++. . +.=.||++|+-..|.|+.+++
T Consensus 330 ~~~Gl~~~~~~~~~g~~------~-------~~~~~~~~l~~l~~~gll~~-~-~~l~lT~~G~~~~d~i~~~~~ 389 (390)
T PRK06582 330 LSKGINISTLEQKLNTK------L-------ENILDMNNLKHYQALDLIRL-D-ENIYLTDKGLMLHSYIVPRLI 389 (390)
T ss_pred hhCCCCHHHHHHHHCcC------H-------HHhhhHHHHHHHHHCCCEEE-C-CEEEECcchhHHHHHHHHHHh
Confidence 44677777888877742 1 1112 467899999999997 3 457899999999999998864
No 121
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=79.77 E-value=2.3 Score=33.84 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=26.8
Q ss_pred chhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 83 SGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
|.--+|++|++|++.|+|......|--+++.
T Consensus 44 SR~TvRkAL~~L~~eGli~r~~G~GtfV~~~ 74 (236)
T COG2188 44 SRMTVRKALDELVEEGLIVRRQGKGTFVASP 74 (236)
T ss_pred cHHHHHHHHHHHHHCCcEEEEecCeeEEcCc
Confidence 4568999999999999999888778888775
No 122
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=79.68 E-value=2.6 Score=28.00 Aligned_cols=37 Identities=22% Similarity=0.185 Sum_probs=27.5
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
++|+-...+....|= |-.-+|+.|++||+.|.|++.+
T Consensus 13 ~~p~~T~eiA~~~gl--------------s~~~aR~yL~~Le~eG~V~~~~ 49 (62)
T PF04703_consen 13 NGPLKTREIADALGL--------------SIYQARYYLEKLEKEGKVERSP 49 (62)
T ss_dssp TS-EEHHHHHHHHTS---------------HHHHHHHHHHHHHCTSEEEES
T ss_pred CCCCCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCEEEec
Confidence 566666666666543 3457999999999999999876
No 123
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=79.34 E-value=2.1 Score=33.05 Aligned_cols=61 Identities=21% Similarity=0.275 Sum_probs=39.8
Q ss_pred CchHHHhHHHHHHHHHH-hCCC-chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 37 PDWYYVRAASMARKIYL-RQGL-GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 37 ~DW~Y~R~ASilR~lYl-~g~v-GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
++|||. ++|-+-= .+.. -+..|.+.- +| .-|-.=+|.+|+-|+++|+|+++.+|.-..|.+
T Consensus 22 ~~W~~~----~ir~l~~l~~~~~d~~~iak~l--------~p----~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~ 84 (171)
T PF14394_consen 22 SSWYHP----AIRELLPLMPFAPDPEWIAKRL--------RP----KISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDK 84 (171)
T ss_pred hhhHHH----HHHHHhhcCCCCCCHHHHHHHh--------cC----CCCHHHHHHHHHHHHHCCCeEECCCCcEEEecc
Confidence 468876 4554432 2222 455555542 22 345568999999999999999998766666654
No 124
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=79.26 E-value=2.4 Score=33.25 Aligned_cols=41 Identities=15% Similarity=0.090 Sum_probs=33.3
Q ss_pred hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029 60 GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 114 (129)
Q Consensus 60 ~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G 114 (129)
..|+..||- |..-+|++|+.|++.|+|.+....|--+++..
T Consensus 37 ~eLa~~~~V--------------SR~TvR~Al~~L~~eGli~r~~G~GTfV~~~~ 77 (241)
T PRK11402 37 NELCTQYNV--------------SRITIRKAISDLVADGVLIRWQGKGTFVQSQK 77 (241)
T ss_pred HHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEecCceeEECCCc
Confidence 457777765 45689999999999999999887788887654
No 125
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=79.05 E-value=2.5 Score=36.75 Aligned_cols=36 Identities=17% Similarity=0.295 Sum_probs=30.7
Q ss_pred HHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 90 ILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 90 ~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
.|++|++.|||+.+. +.=+||++|+-.+|.|+..+-
T Consensus 404 ~l~~l~~~gll~~~~-~~~~lT~~G~~~~d~i~~~f~ 439 (453)
T PRK09249 404 RLAPLEADGLVELDE-NGITVTPKGRLLVRNIAMAFD 439 (453)
T ss_pred HHHHHHHCCCEEEEC-CEEEECccchHHHHHHHHHHH
Confidence 478999999999765 467899999999999998753
No 126
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=78.17 E-value=3.5 Score=35.25 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=31.3
Q ss_pred HHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 88 RHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 88 R~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
...|+.|++.|+|+.+. +.=+||++|+-.+|.|+.+++
T Consensus 356 ~~~l~~l~~~gll~~~~-~~~~LT~~G~~~~d~i~~~~~ 393 (394)
T PRK08898 356 EPQLAAAEQRGLLERDH-TRIRPTPLGQRFLNDLQELFL 393 (394)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhHhHHHHHHHHHHh
Confidence 45788999999998753 234799999999999998875
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=77.86 E-value=2.9 Score=36.34 Aligned_cols=35 Identities=20% Similarity=0.414 Sum_probs=29.8
Q ss_pred HHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHh
Q 033029 90 ILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRI 125 (129)
Q Consensus 90 ~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i 125 (129)
.|++|++.|||+.+. +.=+||++|+-.+|.|+.++
T Consensus 404 ~l~~l~~~gll~~~~-~~~~lT~~G~~~~~~i~~~f 438 (455)
T TIGR00538 404 LLKPLEEDGLLDVDE-KGIEVTPKGRLLIRNIAMVF 438 (455)
T ss_pred HHHHHHhCCCEEEEC-CEEEECcCChHHHHHHHHHH
Confidence 467889999999764 46789999999999999875
No 128
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.82 E-value=4.8 Score=31.47 Aligned_cols=65 Identities=11% Similarity=0.112 Sum_probs=48.1
Q ss_pred ccChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHH
Q 033029 9 DVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIAR 88 (129)
Q Consensus 9 DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR 88 (129)
++-.+..|..|+.++=.. + ++ +--|+..|.-+|.+....|+..-|-. .+-+|
T Consensus 3 ~~~~~~~v~~~l~~~~~~-------~-~~------~~~Vl~~L~~~g~~tdeeLA~~Lgi~--------------~~~VR 54 (178)
T PRK06266 3 TMLNNPLVQKVLFEIMEG-------D-EE------GFEVLKALIKKGEVTDEEIAEQTGIK--------------LNTVR 54 (178)
T ss_pred hhhcCHHHHHHHHHHhcC-------C-cc------HhHHHHHHHHcCCcCHHHHHHHHCCC--------------HHHHH
Confidence 344567777776665531 1 11 23478888888999999999987654 35899
Q ss_pred HHHHHHHhCCcee
Q 033029 89 HILQQLQNMNIID 101 (129)
Q Consensus 89 ~~lqqLE~~g~ve 101 (129)
++|+.|++.|||.
T Consensus 55 k~L~~L~e~gLv~ 67 (178)
T PRK06266 55 KILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHCCCeE
Confidence 9999999999998
No 129
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=77.60 E-value=7.2 Score=32.17 Aligned_cols=59 Identities=15% Similarity=0.057 Sum_probs=45.2
Q ss_pred HHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCc-eeecCCCCceeCcc
Q 033029 41 YVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI-IDIEPKGGRRITSS 113 (129)
Q Consensus 41 Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~-vek~~~~GR~lT~~ 113 (129)
|.|...|++.|.-+.++....|+..+|- |.+-+++.++.|++.|+ |.....+|-.|.+.
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 4578889998887778888899998875 34589999999999999 54444447776544
No 130
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=77.17 E-value=4 Score=36.17 Aligned_cols=66 Identities=9% Similarity=0.138 Sum_probs=49.2
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC--CCceeCcchHhhHHHHH
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK--GGRRITSSGQRDLDQVA 122 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~--~GR~lT~~G~~~lD~iA 122 (129)
..||..|.-.+++....|+...|-. | +-+-.++..||+.|||+...+ ..-.||++|++.++++.
T Consensus 9 ~~vL~~L~~~~~~s~~eLA~~l~l~------~--------~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g~ 74 (489)
T PRK04172 9 KKVLKALKELKEATLEELAEKLGLP------P--------EAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEGL 74 (489)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCcC------H--------HHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhcC
Confidence 4578888888888888998876532 1 345557889999999986542 35579999999998755
Q ss_pred HH
Q 033029 123 GR 124 (129)
Q Consensus 123 ~~ 124 (129)
.+
T Consensus 75 pE 76 (489)
T PRK04172 75 PE 76 (489)
T ss_pred HH
Confidence 43
No 131
>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=76.13 E-value=2.5 Score=30.91 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=27.7
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
-|.+..|+..|+- ++|+.|.+|+.||+-|+|....
T Consensus 59 ~ITp~~lserlkI--------------~~SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 59 LITPSVLSERLKI--------------NGSLARKALRELESKGLIKPVS 93 (105)
T ss_dssp CECHHHHHHHHCC--------------SCHHHHHHHHHHHHCCSSEEEE
T ss_pred EeeHHHHHHhHhh--------------HHHHHHHHHHHHHHCCCEEEEe
Confidence 3667777777654 4689999999999999997654
No 132
>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=76.02 E-value=7.3 Score=30.77 Aligned_cols=57 Identities=18% Similarity=0.152 Sum_probs=44.0
Q ss_pred HhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 42 VRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 42 ~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
.|+-.||.-|-- .+|+++..|.+.-|-. .+-+..+|+.|++.|||+++. +.-.|++.
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lglp--------------ksT~~RlL~tL~~~G~l~~~~-~~Y~lG~~ 66 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGLT--------------RAAARRFLLTLVELGYVTSDG-RLFWLTPR 66 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCcC--------------HHHHHHHHHHHHHCCCEEeCC-CEEEecHH
Confidence 378888888865 5689999999986653 357899999999999999863 44455543
No 133
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=75.95 E-value=6.3 Score=31.53 Aligned_cols=50 Identities=16% Similarity=0.288 Sum_probs=39.6
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHH-HHHhCCceeecCCCCceeCcchHhhH
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQ-QLQNMNIIDIEPKGGRRITSSGQRDL 118 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lq-qLE~~g~vek~~~~GR~lT~~G~~~l 118 (129)
.+++++..++...|-. | .-++.++. .|-+.|+|++.. .||+.|++|...|
T Consensus 253 ~~~~~~~~ia~~lg~~------~--------~~~~~~~e~~Li~~~li~~~~-~g~~~~~~~~~~~ 303 (305)
T TIGR00635 253 GGPVGLKTLAAALGED------A--------DTIEDVYEPYLLQIGFLQRTP-RGRIATELAYEHL 303 (305)
T ss_pred CCcccHHHHHHHhCCC------c--------chHHHhhhHHHHHcCCcccCC-chhhhhHHHHHHh
Confidence 4579999999987763 2 35677777 699999998664 7999999998866
No 134
>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=74.13 E-value=9 Score=31.92 Aligned_cols=58 Identities=17% Similarity=0.205 Sum_probs=38.5
Q ss_pred chHHHhHHHHHHHHHH--hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 38 DWYYVRAASMARKIYL--RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl--~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
+|||. ++|-+-= .+..-+..|.+.-+. .-|-.=+|.+|+-|+++|+|+++.+|--+.|
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 79986 6676652 222245566665332 2344579999999999999999876434444
No 135
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=73.79 E-value=5.1 Score=35.00 Aligned_cols=39 Identities=15% Similarity=0.244 Sum_probs=32.8
Q ss_pred HHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 87 ARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 87 iR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
....|++|++.|||+.+. +.=+||++|+-..|.|+..+.
T Consensus 398 ~~~~l~~~~~~Gll~~~~-~~l~lT~~G~~~~~~i~~~~~ 436 (449)
T PRK09058 398 LAPLLAQWQQAGLVELSS-DCLRLTLAGRFWAVNLTQGLI 436 (449)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECCCcccHHHHHHHHHH
Confidence 345789999999999764 467899999999999998764
No 136
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=72.63 E-value=3.6 Score=34.10 Aligned_cols=48 Identities=29% Similarity=0.414 Sum_probs=32.6
Q ss_pred HHHHHHHHhCC-CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC
Q 033029 46 SMARKIYLRQG-LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107 (129)
Q Consensus 46 SilR~lYl~g~-vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G 107 (129)
.|+.-|=-+|+ +-=..|++.-|- |..=+=++|+.||+.|+||+.+.|+
T Consensus 199 ~il~~i~~~GGri~Q~eL~r~lgl--------------sktTvsR~L~~LEk~GlIe~~K~G~ 247 (258)
T COG2512 199 EILDLIRERGGRITQAELRRALGL--------------SKTTVSRILRRLEKRGLIEKEKKGR 247 (258)
T ss_pred HHHHHHHHhCCEEeHHHHHHhhCC--------------ChHHHHHHHHHHHhCCceEEEEeCC
Confidence 45555555555 555666666543 3345778999999999999987544
No 137
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=71.98 E-value=6.7 Score=34.29 Aligned_cols=59 Identities=17% Similarity=0.164 Sum_probs=44.6
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
.+++-...+...||.. ........+++|+..|++..+. +.=.||++|+-.+|.|..+++
T Consensus 356 ~~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d~i~~~f~ 414 (433)
T PRK08629 356 SGRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGVVMMKEFY 414 (433)
T ss_pred hCCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHHH
Confidence 3566667777777642 1235677889999999999753 345899999999999998875
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=71.98 E-value=21 Score=22.80 Aligned_cols=53 Identities=11% Similarity=0.125 Sum_probs=38.0
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
.|++.+- +++..+..|+..+|- |..-|+..++.|++.|+.....+.|..|.+.
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 667788899998765 3368999999999999954333567777543
No 139
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=71.56 E-value=5 Score=30.49 Aligned_cols=85 Identities=18% Similarity=0.221 Sum_probs=53.4
Q ss_pred ChhHHHHHHHHHHHhc----CC----------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHh-cccCCCCCC
Q 033029 11 SPHEFVKAYSAHLKRS----GK----------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIY-GGSKRNGSR 75 (129)
Q Consensus 11 ~~~~fI~~~A~~LK~~----gk----------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~Y-Gg~k~rG~~ 75 (129)
.-+++-+.+|.-|-++ .. -+++.|.| |.||+.||-.+..-+...+..+ .+...+-+.
T Consensus 31 ~~e~Lremfa~LLass~d~~~~~~~hp~fv~Ii~qLsp~E--------A~iL~~l~~~~~~p~~~~~~~~~~~~~~~~~~ 102 (186)
T PF14337_consen 31 DDEELREMFANLLASSMDKRKNDDVHPSFVEIIKQLSPDE--------ARILKYLYDNNQIPIVDVRLRRKNGPGSRIVL 102 (186)
T ss_pred CcHHHHHHHHHHHHHHhCcCccccccHHHHHHHHhCCHHH--------HHHHHHHHhcCCCcceeeeeeecCCccceeec
Confidence 4456666666666554 11 67899987 9999999966654444444333 222122222
Q ss_pred CCcccCC---chhHHHHHHHHHHhCCceeec
Q 033029 76 PPHFCKS---SGAIARHILQQLQNMNIIDIE 103 (129)
Q Consensus 76 P~h~~~a---sg~iiR~~lqqLE~~g~vek~ 103 (129)
++.+.-+ +-..+-..|+.|+.+|+|+-.
T Consensus 103 ~~~~~~~~~~~~~~~~~~l~nL~rLGLi~~~ 133 (186)
T PF14337_consen 103 SNISLVGEEASPDNIPSYLDNLERLGLIEIP 133 (186)
T ss_pred ccccccccccchHHHHHHHHHHHHCCCceec
Confidence 3322222 557889999999999999876
No 140
>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=71.44 E-value=3.4 Score=30.10 Aligned_cols=35 Identities=26% Similarity=0.401 Sum_probs=22.4
Q ss_pred CCCCCCchHHHhHHHHHH--HHHHhCC-------CchhhhHHHhcccC
Q 033029 32 LAPYDPDWYYVRAASMAR--KIYLRQG-------LGVGSFRRIYGGSK 70 (129)
Q Consensus 32 ~aP~d~DW~Y~R~ASilR--~lYl~g~-------vGV~~lr~~YGg~k 70 (129)
++|.||||| |.++. +.++++| +.+.-||-.|+|..
T Consensus 1 mm~~~P~~W----~~ll~~l~~~~~~~i~g~~lA~~mA~LR~~Y~g~~ 44 (107)
T TIGR01594 1 MMIKEPDLW----AALLSWLQDAWRSQGQGALLALAIAYLRIRYMGGK 44 (107)
T ss_pred CCCCCccHH----HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHcCcc
Confidence 478999988 44443 3344432 44667888898754
No 141
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=71.38 E-value=4.8 Score=35.66 Aligned_cols=58 Identities=19% Similarity=0.273 Sum_probs=40.9
Q ss_pred CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCce------eCcchHhhHHHHHHHhh
Q 033029 55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR------ITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~------lT~~G~~~lD~iA~~i~ 126 (129)
..+.+..|+....+..| -+|.+|++|++.|||+-.+..||- +-....+.+-..|.+++
T Consensus 22 ~~~~l~~la~~l~cs~R--------------~~~~~l~~~~~~gwl~w~~~~GRg~~s~l~~~~~~~~~~~~~~~~~~ 85 (552)
T PRK13626 22 QETTLNELAELLNCSRR--------------HMRTLLNTMQQRGWLTWQAEAGRGKRSRLTFLYTGLALQQQRAEDLL 85 (552)
T ss_pred ceeeHHHHHHHhcCChh--------------HHHHHHHHHHHCCCeeeecCCCCCCceEEEEEECHHHHHHHHHHHHH
Confidence 36788888888877644 689999999999999998876762 22333444444444443
No 142
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=70.29 E-value=6.1 Score=33.21 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=28.4
Q ss_pred HHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 89 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 89 ~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
..|++|++.|||+.+ ++| ||++|.-+.|.|+..+.
T Consensus 315 ~~l~~l~~~gl~~~~--~~~-l~~~g~~~~d~i~~~~~ 349 (350)
T PRK08446 315 KKVKILIEENKLFIK--NNR-LYNKDFFLADEIALFLL 349 (350)
T ss_pred HHHHHHHHCCCEEee--CCE-EcccchhhHHHHHHHhh
Confidence 457788999999865 344 99999999999998754
No 143
>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=69.64 E-value=12 Score=27.59 Aligned_cols=52 Identities=17% Similarity=0.238 Sum_probs=40.3
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
.|+.-|+-.|++.+..+....+.. +|. +-+-++.+|.-|++-|+|+... .||
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~--~~~--------~~tTv~T~L~rL~~KG~v~~~k-~gr 59 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEK--KDW--------SDSTIKTLLGRLVDKGCLTTEK-EGR 59 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhc--cCC--------cHHHHHHHHHHHHHCCceeeec-CCC
Confidence 588999999999999988876543 222 2357999999999999998764 466
No 144
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=68.88 E-value=7.9 Score=29.92 Aligned_cols=40 Identities=28% Similarity=0.415 Sum_probs=32.0
Q ss_pred HHHHHHHHHHhCCceeec--C--CCCceeCcchHhhHHHHHHHh
Q 033029 86 IARHILQQLQNMNIIDIE--P--KGGRRITSSGQRDLDQVAGRI 125 (129)
Q Consensus 86 iiR~~lqqLE~~g~vek~--~--~~GR~lT~~G~~~lD~iA~~i 125 (129)
-+..+|..|++.|+|... . +.=-.||++|+..|+-+...|
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 467789999999999864 2 234589999999998887765
No 145
>PRK12423 LexA repressor; Provisional
Probab=68.78 E-value=6.2 Score=30.72 Aligned_cols=35 Identities=23% Similarity=0.480 Sum_probs=26.3
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 105 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~ 105 (129)
.+..|+..+|= .|.+.+|..|+.||+.|+|+..+.
T Consensus 27 s~~eia~~~g~-------------~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 27 SLAEIAQAFGF-------------ASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEEecCC
Confidence 55666666552 233678899999999999998874
No 146
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=68.70 E-value=15 Score=29.98 Aligned_cols=55 Identities=22% Similarity=0.283 Sum_probs=46.1
Q ss_pred HhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 42 VRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 42 ~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
-|-..|+..|--++.+.+..|...||- |..-||+=|..||+.|++.+.. ||.++.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~V--------------S~~TIRRDL~~Le~~G~l~r~~-GGa~~~ 71 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGV--------------STVTIRNDLAFLEKQGIAVRAY-GGALIC 71 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCC--------------CHHHHHHHHHHHHhCCCeEEEe-CCEEec
Confidence 477788888888999999999999854 3468999999999999999876 677654
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=68.54 E-value=6.4 Score=29.02 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=26.2
Q ss_pred HHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029 89 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 89 ~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
.++..+|-+|+|+... |-=.||+.|+++.+.
T Consensus 16 p~~eAaelLgf~~~~~-Gdi~LT~~G~~f~~a 46 (120)
T PF09821_consen 16 PIVEAAELLGFAEVEE-GDIRLTPLGRRFAEA 46 (120)
T ss_pred HHHHHHHHcCCeeecC-CcEEeccchHHHHHC
Confidence 5788999999999864 677999999998764
No 148
>COG1485 Predicted ATPase [General function prediction only]
Probab=67.91 E-value=2.6 Score=37.06 Aligned_cols=57 Identities=25% Similarity=0.494 Sum_probs=43.6
Q ss_pred chHHHhHHHHHHHHHHhCCCchhh---hHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCC
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGS---FRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMN 98 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~---lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g 98 (129)
-|+|-|.+...|=||+.||||.|. |-..|.+-.-..-+.-||+ ..++.+-|.|..+.
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 699999889999999999999986 4566766444333445664 47888989888876
No 149
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=67.85 E-value=19 Score=28.98 Aligned_cols=49 Identities=16% Similarity=0.049 Sum_probs=41.6
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 105 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~ 105 (129)
|-..|+..|--+|.+.+..|...+|- |..-||+=|++||+.|+|++.-.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~v--------------S~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGI--------------SPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEecC
Confidence 66678888888899999999999864 44578999999999999998753
No 150
>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=67.33 E-value=12 Score=24.33 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=31.5
Q ss_pred HHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 51 IYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 51 lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|=-+|.+.+..|.+.|+- +-..++..|.+||..|.|++..
T Consensus 9 l~~~~~~S~~eLa~~~~~--------------s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 9 LRERGRVSLAELAREFGI--------------SPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHS-SEEHHHHHHHTT----------------HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCcEEEec
Confidence 445788899999998765 4469999999999999999765
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=65.76 E-value=10 Score=28.89 Aligned_cols=44 Identities=20% Similarity=0.209 Sum_probs=31.9
Q ss_pred HHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029 49 RKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 105 (129)
Q Consensus 49 R~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~ 105 (129)
++.|.++ |.++..|...+|-. |.+-++..|+.||+.|+|++..+
T Consensus 16 ~~~~~~~~~~~~~~ela~~~~~~-------------s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 16 RAHIESTGYPPSIREIARAVGLR-------------SPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred HHHHHhcCCCCcHHHHHHHhCCC-------------ChHHHHHHHHHHHHCCCEecCCC
Confidence 3334544 45667888877642 34688999999999999998763
No 152
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=65.74 E-value=9.1 Score=27.15 Aligned_cols=41 Identities=12% Similarity=0.050 Sum_probs=31.2
Q ss_pred hhHHHHHHHHHHhCCceeecCC---CCceeCcchHhhHHHHHHH
Q 033029 84 GAIARHILQQLQNMNIIDIEPK---GGRRITSSGQRDLDQVAGR 124 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~~---~GR~lT~~G~~~lD~iA~~ 124 (129)
.+=+=.++=.||..|+|..... .--.+|++|...|++|-.+
T Consensus 41 KNelL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~~~~~~ 84 (85)
T PF11313_consen 41 KNELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLAEIKNE 84 (85)
T ss_pred HHHHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHHHHHhc
Confidence 3445577889999999985442 2468999999999998653
No 153
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=65.50 E-value=12 Score=28.45 Aligned_cols=43 Identities=12% Similarity=0.050 Sum_probs=36.1
Q ss_pred HHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCcee
Q 033029 45 ASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 101 (129)
Q Consensus 45 ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ve 101 (129)
.-|+..|..+|.+....|+..-|-+. +.+|++|+.|.+.|||.
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 44777788889999999999876643 48999999999999994
No 154
>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=65.41 E-value=8.1 Score=25.97 Aligned_cols=61 Identities=28% Similarity=0.362 Sum_probs=38.1
Q ss_pred hHHHHHHHHH---Hh---CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCC---CceeCcc
Q 033029 43 RAASMARKIY---LR---QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKG---GRRITSS 113 (129)
Q Consensus 43 R~ASilR~lY---l~---g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~---GR~lT~~ 113 (129)
|+-|++--|| +. +++-++.|-...+.- |+. -+-+|.+|--|-+.||++....| +-.||++
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 RARSLIVTLLGDYLRPRGGWIWVASLIRLLAAF---GVS--------ESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp -HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCCT---T----------HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred CcceehHHHHHHHhccCCCceeHHHHHHHHHHc---CCC--------hHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 3445666665 32 355666666665432 332 35899999999999999988643 3678887
Q ss_pred h
Q 033029 114 G 114 (129)
Q Consensus 114 G 114 (129)
|
T Consensus 70 g 70 (70)
T PF07848_consen 70 G 70 (70)
T ss_dssp H
T ss_pred C
Confidence 6
No 155
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=65.31 E-value=16 Score=25.70 Aligned_cols=35 Identities=23% Similarity=0.380 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHhC---CceeecC----CCCceeCcchHhhH
Q 033029 84 GAIARHILQQLQNM---NIIDIEP----KGGRRITSSGQRDL 118 (129)
Q Consensus 84 g~iiR~~lqqLE~~---g~vek~~----~~GR~lT~~G~~~l 118 (129)
-+-+-..+++||+. .|++... .+|-.|||.|+..+
T Consensus 30 ~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 30 YKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred HHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 34566778888875 5677764 24899999999986
No 156
>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=64.78 E-value=8.4 Score=24.21 Aligned_cols=32 Identities=22% Similarity=0.382 Sum_probs=23.1
Q ss_pred chhHHHHHHHHHHhC---CceeecCCCCceeCcchH
Q 033029 83 SGAIARHILQQLQNM---NIIDIEPKGGRRITSSGQ 115 (129)
Q Consensus 83 sg~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~ 115 (129)
|-+-+.+.+++||+. .|++... +|=.||+.|+
T Consensus 26 s~~~vs~~i~~LE~~lg~~Lf~r~~-~~~~lT~~G~ 60 (60)
T PF00126_consen 26 SQSAVSRQIKQLEEELGVPLFERSG-RGLRLTEAGE 60 (60)
T ss_dssp SHHHHHHHHHHHHHHHTS-SEEECS-SSEEE-HHHH
T ss_pred cchHHHHHHHHHHHHhCCeEEEECC-CCeeEChhhC
Confidence 345778889999974 6788765 5889999986
No 157
>PF13730 HTH_36: Helix-turn-helix domain
Probab=64.05 E-value=6.6 Score=23.87 Aligned_cols=19 Identities=16% Similarity=0.331 Sum_probs=16.0
Q ss_pred CchhHHHHHHHHHHhCCce
Q 033029 82 SSGAIARHILQQLQNMNII 100 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~v 100 (129)
-|.+=|+++++.||+.|||
T Consensus 37 ~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 37 VSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHHHHHHCcCC
Confidence 3456789999999999986
No 158
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=63.77 E-value=21 Score=28.84 Aligned_cols=53 Identities=17% Similarity=0.224 Sum_probs=44.3
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l 110 (129)
|-..|+..|--+|.+-+..|...||- |..-||+=|+.||+.|+|.+.- ||=++
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~V--------------S~~TIRRDL~~Le~~g~l~r~~-Gga~~ 58 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDT--------------TGTTIRKDLVILEHAGTVIRTY-GGVVL 58 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEEEE-CCEEc
Confidence 66778888888999999999999875 4468999999999999998875 55444
No 159
>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=63.49 E-value=8 Score=26.02 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.1
Q ss_pred hhHHHHHHHHHHhCCceeecC
Q 033029 84 GAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~ 104 (129)
.|+|=++|..||.+|+||.-.
T Consensus 18 RSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 18 RSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHhcCceeecc
Confidence 478999999999999999543
No 160
>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=62.84 E-value=6.2 Score=28.06 Aligned_cols=28 Identities=29% Similarity=0.466 Sum_probs=20.7
Q ss_pred HHHhCCce-eecCCC---CceeCcchHhhHHH
Q 033029 93 QLQNMNII-DIEPKG---GRRITSSGQRDLDQ 120 (129)
Q Consensus 93 qLE~~g~v-ek~~~~---GR~lT~~G~~~lD~ 120 (129)
+|..+||| ++...+ --+||++|.+..|-
T Consensus 58 SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 58 SLVGLGLVEEEEEKGGFKYYRLTEKGKRIAEM 89 (90)
T ss_pred hHHHcCCeeEeeecCCeeEEEeChhhhhHHhc
Confidence 68899999 444433 34799999988763
No 161
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=61.65 E-value=4.7 Score=37.09 Aligned_cols=82 Identities=18% Similarity=0.301 Sum_probs=56.2
Q ss_pred CCCCCCCCCCCchHHHhHHHH-HHHHH----------------HhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHH
Q 033029 27 GKFKELAPYDPDWYYVRAASM-ARKIY----------------LRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARH 89 (129)
Q Consensus 27 gk~kE~aP~d~DW~Y~R~ASi-lR~lY----------------l~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~ 89 (129)
|--+.-||.+.-=+|.+.|-- =|+=| |+-+.=|+.++..||+ --.=++.
T Consensus 396 glVs~gAiT~kGrl~akls~tikRkP~LT~~e~kvl~kiP~~~ikrg~liedi~~~~g~--------------~eeev~~ 461 (593)
T COG1542 396 GLVSRGAITEKGRLYAKLSKTIKRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQGHVGG--------------DEEEVIK 461 (593)
T ss_pred ccccccCcCcchhHHHHHHHHHhcCcccchhHHHHHHhccccccchhhHHHHHHhhcCc--------------cHHHHHH
Confidence 335666788887788776532 23333 3334445555555554 2346889
Q ss_pred HHHHHHhCCceeecCCCCceeCcchHhhHHHHH
Q 033029 90 ILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 90 ~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+|..||+-|+|+--+.+|=+||..||-.=--|.
T Consensus 462 sl~kleskgfveeL~n~gv~LTeaGe~~KtAis 494 (593)
T COG1542 462 SLGKLESKGFVEELPNKGVKLTEAGELVKTAIS 494 (593)
T ss_pred HHHHHhhcchHHHhccCcEEeehhhHHHHHHHH
Confidence 999999999999988899999999986544433
No 162
>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=60.57 E-value=25 Score=21.19 Aligned_cols=48 Identities=13% Similarity=0.172 Sum_probs=35.9
Q ss_pred hHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCC-ceeecC
Q 033029 43 RAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMN-IIDIEP 104 (129)
Q Consensus 43 R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g-~vek~~ 104 (129)
|-..|+.-|.-. +++....|+..+|- |-.-|++-++.|++.| .|+..+
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~v--------------S~rTi~~~i~~L~~~~~~I~~~~ 50 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGV--------------SRRTIRRDIKELREWGIPIESKR 50 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS---------------HHHHHHHHHHHHHTT-EEEEET
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeEEeeC
Confidence 455678888654 46999999998765 3458999999999999 444444
No 163
>PRK00215 LexA repressor; Validated
Probab=58.79 E-value=11 Score=28.82 Aligned_cols=49 Identities=16% Similarity=0.199 Sum_probs=35.2
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCce--eCcchHhh
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR--ITSSGQRD 117 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~--lT~~G~~~ 117 (129)
+..+..|+...|-+ +.+-+-..|+.||+.|+|++.++.+|. |++.|+..
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 56788999987752 224577899999999999988765543 55555543
No 164
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=58.71 E-value=14 Score=28.92 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|.+.+. +|-.||+.|+.+++.+-
T Consensus 33 avS~~I~~LE~~lg~~LF~R~~-~~~~lT~~G~~l~~~a~ 71 (300)
T TIGR02424 33 AVSKTLRELEEILGTPLFERDR-RGIRLTRYGELFLRHAG 71 (300)
T ss_pred HHHHHHHHHHHHhCCeEEEEcC-CCccccHhHHHHHHHHH
Confidence 566778888875 6677764 68899999998887543
No 165
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=58.43 E-value=76 Score=27.42 Aligned_cols=56 Identities=13% Similarity=0.189 Sum_probs=38.8
Q ss_pred HhHHHHHHHHH--Hh--CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 42 VRAASMARKIY--LR--QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 42 ~R~ASilR~lY--l~--g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
..+-.++.+++ .+ .|+....|++..+ .+-.+++.+|.+|+++|+|...++++-.++
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 44556888886 22 3666777777543 233599999999999999987665544443
No 166
>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=58.18 E-value=13 Score=28.59 Aligned_cols=42 Identities=19% Similarity=0.241 Sum_probs=33.5
Q ss_pred hhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcch
Q 033029 59 VGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSG 114 (129)
Q Consensus 59 V~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G 114 (129)
-..|+..||-. ...+|.+|+.|+..|+|......|-.+++..
T Consensus 28 E~eLa~~~~Vs--------------r~Tvr~Al~~L~~eGli~~~~g~Gt~V~~~~ 69 (231)
T TIGR03337 28 ERDLGERFNTT--------------RVTIREALQQLEAEGLIYREDRRGWFVSPPR 69 (231)
T ss_pred HHHHHHHHCCC--------------HHHHHHHHHHHHHCCeEEEeCCCEEEECCcc
Confidence 45677777753 4699999999999999998887788777543
No 167
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=57.51 E-value=36 Score=27.54 Aligned_cols=54 Identities=17% Similarity=0.176 Sum_probs=43.7
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
|-..|+.-|--++.+.+..|...|+ -|-.-||+=|..||+.|++.+.- ||=.+.
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~--------------vS~~TiRRdL~~Le~~g~l~r~~-GGa~~~ 59 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFS--------------VSPQTIRRDLNDLAEQNKILRHH-GGAALP 59 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEec-CCEEec
Confidence 5667888888889999999999884 34468999999999999998875 555443
No 168
>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=57.06 E-value=14 Score=22.22 Aligned_cols=41 Identities=17% Similarity=0.250 Sum_probs=31.8
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 102 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek 102 (129)
|+..|.- ||..+..|....|- |-+.+.+=|..|+++|+|++
T Consensus 7 Il~~L~~-~~~~~~el~~~l~~--------------s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE-GPLTVSELAEELGL--------------SQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT-SSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh-CCCchhhHHHhccc--------------cchHHHHHHHHHHHCcCeeC
Confidence 4444443 88999999998765 34688999999999999975
No 169
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=56.88 E-value=24 Score=32.71 Aligned_cols=58 Identities=22% Similarity=0.304 Sum_probs=43.6
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc------eeCcchHhhHHHHHHHhhh
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR------RITSSGQRDLDQVAGRIVV 127 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR------~lT~~G~~~lD~iA~~i~~ 127 (129)
.+.+..|+....+.. .-+|.+|+||++.||++-.+.-|| .+...+..++-..|++.++
T Consensus 23 ~~tl~eLA~~lfCS~--------------Rh~R~lL~q~q~~gWL~W~p~~GRGkrSrL~flr~~e~L~~q~a~~~le 86 (564)
T COG4533 23 ETTLNELADILFCSR--------------RHARTLLRQMQEAGWLTWQPQAGRGKRSRLTFLRTPEALLLQLAEKLLE 86 (564)
T ss_pred eeeHHHHHHHhccCH--------------HHHHHHHHHHHHcCCEEeccCCCCCcceeEEEecChHHHHHHHHHHHHh
Confidence 456677777766543 478999999999999998886565 3556777888888877654
No 170
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=56.77 E-value=13 Score=31.32 Aligned_cols=31 Identities=10% Similarity=0.158 Sum_probs=25.9
Q ss_pred CchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 82 SSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
-|.+-+|.++++||+.|+|+..+..|-.+.+
T Consensus 41 vsr~tv~~a~~~L~~~g~i~~~~~~G~~v~~ 71 (431)
T PRK15481 41 VNRNTVAAAYKRLVTAGLAQSQGRNGTVIRG 71 (431)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeCCCceEEcc
Confidence 3567899999999999999987777877754
No 171
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=55.68 E-value=21 Score=28.08 Aligned_cols=38 Identities=13% Similarity=0.163 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
+-+=+.+++||+. .|++... +|=.||+.|+.+++.+..
T Consensus 34 ~avS~~i~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~~ 74 (302)
T PRK09791 34 PALTKSIQELEEGLAAQLFFRRS-KGVTLTDAGESFYQHASL 74 (302)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCceECccHHHHHHHHHH
Confidence 3566778889864 6677764 688999999998887654
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=54.86 E-value=15 Score=23.65 Aligned_cols=40 Identities=20% Similarity=0.366 Sum_probs=30.7
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G 107 (129)
.+++....++...|=+ | +-+=..|+.|++.|||+..+.+|
T Consensus 20 ~~~v~~~~iA~~L~vs------~--------~tvt~ml~~L~~~GlV~~~~y~g 59 (60)
T PF01325_consen 20 GGPVRTKDIAERLGVS------P--------PTVTEMLKRLAEKGLVEYEPYKG 59 (60)
T ss_dssp TSSBBHHHHHHHHTS-------H--------HHHHHHHHHHHHTTSEEEETTTE
T ss_pred CCCccHHHHHHHHCCC------h--------HHHHHHHHHHHHCCCEEecCCCC
Confidence 3688888888887653 2 35668899999999999887654
No 173
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=54.62 E-value=41 Score=26.98 Aligned_cols=51 Identities=16% Similarity=0.112 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCC
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGG 107 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~G 107 (129)
|-..|+..|--++.+.+..|...+| -|-.=||+-|.+||+.|+|.....++
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~--------------VS~~TiRRdL~~L~~~~~l~r~~Gga 55 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLN--------------VSKETIRRDLNELQTQGKILRNHGRA 55 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCeE
Confidence 4455777777889999999999995 34468999999999999998765333
No 174
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=54.14 E-value=17 Score=28.19 Aligned_cols=48 Identities=13% Similarity=-0.029 Sum_probs=41.8
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|-..|+-.|--+|.+.+..|...||- |..-||+=|++||+.|+|....
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~v--------------S~~TiRRDl~~L~~~g~~~r~~ 55 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGV--------------SIQTIRLDRMELGIPELRERIK 55 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCc--------------CHHHHHHHHHHHhcchHHHHHH
Confidence 77788888999999999999999875 5578999999999999998543
No 175
>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=54.11 E-value=21 Score=25.12 Aligned_cols=52 Identities=12% Similarity=0.149 Sum_probs=41.2
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
-|++-|.-.|++.+..+....... ++. +-+-++..|.-|++-|+|+.... ||
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~l~~~--~~~--------~~sTv~t~L~rL~~Kg~l~~~~~-gr 58 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEALPEE--RSW--------AYSTVQTLLNRLVEKGFLTREKI-GR 58 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHCTT--SS----------HHHHHHHHHHHHHTTSEEEEEE-TT
T ss_pred HHHHHHHhCCCCCHHHHHHHHHhc--ccc--------chhHHHHHHHHHHhCCceeEeec-CC
Confidence 478888899999999999988765 222 33689999999999999998764 44
No 176
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=52.93 E-value=18 Score=28.69 Aligned_cols=37 Identities=8% Similarity=0.143 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+-+-+.+++||+. .|++.+. +|-.||+.|+.+++.+-
T Consensus 40 pavS~~I~~LE~~lG~~Lf~R~~-r~~~lT~~G~~l~~~a~ 79 (303)
T PRK10082 40 PAFSRRIRALEQAIGVELFNRQV-TPLQLSEQGKIFHSQIR 79 (303)
T ss_pred HHHHHHHHHHHHHcCCEEEEecC-CCCccCHHHHHHHHHHH
Confidence 3567788999975 5666664 58899999999888743
No 177
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=51.76 E-value=22 Score=27.65 Aligned_cols=36 Identities=19% Similarity=0.260 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|+..+ .+|-.||+.|+.+++.+-
T Consensus 31 avS~~i~~LE~~lg~~Lf~R~-~~~~~lT~~G~~l~~~~~ 69 (296)
T PRK11242 31 TLSQQIRQLEESLGVQLFDRS-GRTVRLTDAGEVYLRYAR 69 (296)
T ss_pred HHHHHHHHHHHHhCCeeEeEc-CCceeechhHHHHHHHHH
Confidence 456778888875 677776 368999999999887654
No 178
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=51.52 E-value=35 Score=23.21 Aligned_cols=68 Identities=10% Similarity=0.165 Sum_probs=46.7
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC------CCCce------eCcc
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP------KGGRR------ITSS 113 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~------~~GR~------lT~~ 113 (129)
.|++.|.-++++....|.+..|- |-+-+++.++.|++.|+|.... .-|.. ++-.
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 47788888888889999888754 3358999999999999998321 11321 2222
Q ss_pred hHhhHHHHHHHhhh
Q 033029 114 GQRDLDQVAGRIVV 127 (129)
Q Consensus 114 G~~~lD~iA~~i~~ 127 (129)
....+|+++..+..
T Consensus 73 ~~~~~~~v~~~l~~ 86 (108)
T smart00344 73 SPDKLEEFLEKLEK 86 (108)
T ss_pred ChhHHHHHHHHHhC
Confidence 12467888887754
No 179
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=51.05 E-value=5.1 Score=29.88 Aligned_cols=33 Identities=21% Similarity=0.228 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 86 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 86 iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
-+..-|..||.+|+|....+ =|..|+.||..|.
T Consensus 8 ~~l~~l~~LE~~G~v~~~n~--------yQ~lln~IA~dI~ 40 (142)
T PF03836_consen 8 KILENLKELESLGIVSRSNN--------YQDLLNDIAKDIR 40 (142)
T ss_dssp -----------------------------------------
T ss_pred HHHHHHHHHHHCCCCCCccc--------HHHHHHHHHHHHh
Confidence 45666789999999986632 2458888988874
No 180
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=50.56 E-value=10 Score=28.21 Aligned_cols=23 Identities=30% Similarity=0.486 Sum_probs=19.7
Q ss_pred CchhHHHHHHHHHHhCCceeecC
Q 033029 82 SSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~vek~~ 104 (129)
=.||+.|.+|+.|+.-|+|....
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 181
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=50.10 E-value=25 Score=26.82 Aligned_cols=34 Identities=15% Similarity=0.222 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
-+=+.+++||+. .|++... +|=.||+.|+.++..
T Consensus 27 avS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 27 TVTDQVRKLEERYGVELFHRNG-RRLELTDAGHRLLPI 63 (279)
T ss_pred HHHHHHHHHHHHhCCccEEEcC-CeEEEChhHHHHHHH
Confidence 455667888875 6666653 578888888887754
No 182
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=49.79 E-value=28 Score=28.94 Aligned_cols=58 Identities=17% Similarity=0.148 Sum_probs=37.3
Q ss_pred cChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHH-HHHhC--CCchhhhHHHhcccCC
Q 033029 10 VSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARK-IYLRQ--GLGVGSFRRIYGGSKR 71 (129)
Q Consensus 10 V~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~-lYl~g--~vGV~~lr~~YGg~k~ 71 (129)
.++++..+.+.+.+++.. .+...|.+-||||+.|.. . +.=++ ++|+.+|...+-|..+
T Consensus 237 ~d~~~~~~r~~~~~~~~~-~~g~~~~~~d~~yl~~~~---~G~pP~~G~GiGieRL~m~l~g~~~ 297 (304)
T TIGR00462 237 TDAAEQRRRFEADNAERK-ALGLPRYPLDERFLAALE---AGLPECSGVALGVDRLLMLALGADS 297 (304)
T ss_pred CCHHHHHHHHHHHHHHHH-hCCCCcchhhHHHHHHHH---cCCCCCCceEEcHHHHHHHHhCCCc
Confidence 456677777776655432 233555566899998865 1 22233 5888999998888644
No 183
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=48.53 E-value=27 Score=27.57 Aligned_cols=35 Identities=14% Similarity=0.164 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
-+-+.+++||+. .|.+.+. .|=.||+.|+..++..
T Consensus 31 avS~~i~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a 68 (305)
T PRK11151 31 TLSGQIRKLEDELGVMLLERTS-RKVLFTQAGLLLVDQA 68 (305)
T ss_pred HHHHHHHHHHHHhCchheeeCC-CceeECccHHHHHHHH
Confidence 566677888764 5666653 5888888888877654
No 184
>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=48.39 E-value=13 Score=25.68 Aligned_cols=25 Identities=24% Similarity=0.490 Sum_probs=17.3
Q ss_pred HHHHHHHhCCceeecCCCCceeCcchHhh
Q 033029 89 HILQQLQNMNIIDIEPKGGRRITSSGQRD 117 (129)
Q Consensus 89 ~~lqqLE~~g~vek~~~~GR~lT~~G~~~ 117 (129)
++++.|..+|.|+.+ + .||+-|+..
T Consensus 1 ~A~~~L~~Lgald~~--~--~lT~lG~~~ 25 (102)
T PF04408_consen 1 KALELLKSLGALDEN--G--NLTPLGRKM 25 (102)
T ss_dssp -HHHHHHHTTSB-TT--S---B-HHHHHH
T ss_pred CHHHHHHHCCCCCCC--C--CcCHHHHHH
Confidence 478999999999543 2 899999865
No 185
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=48.05 E-value=23 Score=30.21 Aligned_cols=43 Identities=21% Similarity=0.265 Sum_probs=34.9
Q ss_pred hHHHHHHHHHHhCCceeecCCC--C-ceeCcchHhhHHHHHHHhhh
Q 033029 85 AIARHILQQLQNMNIIDIEPKG--G-RRITSSGQRDLDQVAGRIVV 127 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~--G-R~lT~~G~~~lD~iA~~i~~ 127 (129)
..+|.+|.-|-++|++....+| + -+||.+|...+-+-+..|..
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 4689999999999999765522 2 56899999999998888764
No 186
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=47.93 E-value=19 Score=28.25 Aligned_cols=36 Identities=17% Similarity=0.173 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|++++. .|-.||+.|+.++..+-
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~ 70 (301)
T PRK14997 32 KLSRRIAQLEERLGVRLIQRTT-RQFNVTEVGQTFYEHCK 70 (301)
T ss_pred HHHHHHHHHHHHhCCEeeeecc-CcceEcHhHHHHHHHHH
Confidence 444568899875 4566664 58999999988876543
No 187
>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=47.56 E-value=39 Score=26.89 Aligned_cols=36 Identities=17% Similarity=0.164 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=..+++||+. .|++.+. +|=.||+.|+.++..+.
T Consensus 38 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 76 (302)
T TIGR02036 38 AISHRINQLEEELGIQLFVRSH-RKVELTHEGKRIYWALK 76 (302)
T ss_pred HHHHHHHHHHHHhCCceEEECC-CceeECHhHHHHHHHHH
Confidence 455678899874 6777764 68899999988886654
No 188
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=47.28 E-value=4.9 Score=31.29 Aligned_cols=12 Identities=33% Similarity=0.825 Sum_probs=9.7
Q ss_pred CCCCCchHHHhH
Q 033029 33 APYDPDWYYVRA 44 (129)
Q Consensus 33 aP~d~DW~Y~R~ 44 (129)
.|.++||||+.-
T Consensus 29 t~~~~DfFY~C~ 40 (182)
T PF08432_consen 29 TPDNKDFFYVCP 40 (182)
T ss_pred cCCCCCeEEeCc
Confidence 578999999853
No 189
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=47.13 E-value=27 Score=27.40 Aligned_cols=37 Identities=24% Similarity=0.335 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
-|=+.+++||+. .|++.+. +|=.||++|+.+++.+..
T Consensus 31 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~~ 70 (275)
T PRK03601 31 AVSFRIRQLENQLGVNLFTRHR-NNIRLTAAGERLLPYAET 70 (275)
T ss_pred HHHHHHHHHHHHhCCceEEECC-CceEECHhHHHHHHHHHH
Confidence 344567888873 6777764 578899999988876554
No 190
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=47.03 E-value=36 Score=25.74 Aligned_cols=38 Identities=11% Similarity=0.096 Sum_probs=28.5
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
+-+=+.+++||+. .|++... .|=.||+.|+.+++.+..
T Consensus 6 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~~ 46 (269)
T PRK11716 6 STLSRQIQRLEEELGQPLFVRDN-RSVTLTEAGEELRPFAQQ 46 (269)
T ss_pred HHHHHHHHHHHHHhCCeeEEecC-CceeECHhHHHHHHHHHH
Confidence 3455678888874 6777764 588999999999887654
No 191
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=46.45 E-value=37 Score=26.98 Aligned_cols=35 Identities=11% Similarity=0.096 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
-+-+.+++||+. .|++.+. .|=.||+.|+.++...
T Consensus 31 avS~~I~~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~a 68 (305)
T PRK11233 31 ALSQQVATLEGELNQQLLIRTK-RGVTPTEAGKILYTHA 68 (305)
T ss_pred HHHHHHHHHHHHhCCceEEeCC-CCceECHhHHHHHHHH
Confidence 566677888864 5666664 5788888887776654
No 192
>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=46.17 E-value=66 Score=22.28 Aligned_cols=59 Identities=15% Similarity=0.110 Sum_probs=38.9
Q ss_pred CCCCCch--HHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee
Q 033029 33 APYDPDW--YYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 102 (129)
Q Consensus 33 aP~d~DW--~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek 102 (129)
|+.+.|| +....|.-+|.+|++-|-.+.-+... | ......-.++-.+|+.|..+|+=..
T Consensus 2 P~~~~~W~~~l~~~a~~~r~~~~~hP~~~~~~~~~----------~-~~~p~~l~~~e~~l~~L~~aG~~~~ 62 (139)
T PF02909_consen 2 PDPGDDWRERLRALARAYRAALLRHPWLAELLLAR----------P-PPGPNALRLMEAMLRALRDAGFSPE 62 (139)
T ss_dssp -CTTSEHHHHHHHHHHHHHHHHHTSTTHHHHHHTS----------S-CTSHHHHHHHHHHHHHHHHTTEEHH
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHCcCHHHHHHhc----------C-CCChhHHHHHHHHHHHHHHcCcCHH
Confidence 4444467 66778888999999988665554431 1 1223344566689999999998643
No 193
>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=45.68 E-value=9.2 Score=29.42 Aligned_cols=59 Identities=19% Similarity=0.255 Sum_probs=44.3
Q ss_pred CCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029 36 DPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 105 (129)
Q Consensus 36 d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~ 105 (129)
+.||-|+|- |||||.|--+.--.|=. ...|..-.+.-..+.+..+..|+++..-.+.++
T Consensus 61 kk~W~~vrn-------~irgp~g~Lr~dl~~l~----~sl~p~dqk~a~~L~~~Lf~~L~~LD~AA~~kd 119 (142)
T TIGR03042 61 KEDWVFTRN-------LIHGPMGEVRREMTYLN----QSLLPKDQKEALALAKELKDDLEKLDEAARLQD 119 (142)
T ss_pred hcchHHHHH-------HHhccHHHHHHHHHHHH----HccCHHhHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 568999998 99999886443333311 224666677788999999999999998877654
No 194
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=44.63 E-value=34 Score=26.55 Aligned_cols=35 Identities=9% Similarity=0.112 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
-+-+.+++||+. .|++... +|-.||+.|+..+..+
T Consensus 37 avS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 74 (294)
T PRK09986 37 PLSIHIKELEDQLGTPLFIRHS-RSVVLTHAGKILMEES 74 (294)
T ss_pred HHHHHHHHHHHHhCCeeEeeCC-CceeECHhHHHHHHHH
Confidence 456677888865 5666653 5788888888877654
No 195
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=44.27 E-value=26 Score=30.63 Aligned_cols=35 Identities=29% Similarity=0.479 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHH
Q 033029 84 GAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 119 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD 119 (129)
=-+.=.++..||..|+|+.++ +|=.||++|..+..
T Consensus 48 lp~v~~i~~~l~~egiv~~~~-g~v~~TekG~E~~e 82 (354)
T COG1568 48 LPLVASILEILEDEGIVKIEE-GGVELTEKGEELAE 82 (354)
T ss_pred chHHHHHHHHHHhcCcEEEec-CcEeehhhhHHHHH
Confidence 346667889999999999886 67999999998764
No 196
>PF15129 FAM150: FAM150 family
Probab=43.72 E-value=15 Score=27.67 Aligned_cols=17 Identities=24% Similarity=0.468 Sum_probs=14.3
Q ss_pred hHHHhHHHHHHHHHHhC
Q 033029 39 WYYVRAASMARKIYLRQ 55 (129)
Q Consensus 39 W~Y~R~ASilR~lYl~g 55 (129)
=||.|||++|-+|.+.+
T Consensus 103 ayykrcarlltrla~sp 119 (123)
T PF15129_consen 103 AYYKRCARLLTRLAVSP 119 (123)
T ss_pred HHHHHHHHHHHHhccCc
Confidence 58999999999987653
No 197
>PRK09350 poxB regulator PoxA; Provisional
Probab=43.45 E-value=48 Score=27.60 Aligned_cols=58 Identities=14% Similarity=0.126 Sum_probs=37.8
Q ss_pred cChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHH-HHHhC--CCchhhhHHHhcccCC
Q 033029 10 VSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARK-IYLRQ--GLGVGSFRRIYGGSKR 71 (129)
Q Consensus 10 V~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~-lYl~g--~vGV~~lr~~YGg~k~ 71 (129)
.+++++.+.+.+..++.. ..-..|.+-||||+.|.. . +.=++ ++||.+|.-.+-|..+
T Consensus 242 ~d~~~~~~r~~~~~~~~~-~~g~~~~~~d~~~l~a~~---~G~pp~~G~giGidRL~m~~~g~~~ 302 (306)
T PRK09350 242 TDAREQRQRFEQDNRKRA-ARGLPQQPIDENLIAALE---AGLPDCSGVALGVDRLIMLALGAES 302 (306)
T ss_pred CCHHHHHHHHHHHHHHHH-hCCCCcccCcHHHHHHHH---cCCCCCCceEecHHHHHHHHcCCCC
Confidence 567778888877665422 122456667899998865 1 22233 5889999998888654
No 198
>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=42.76 E-value=18 Score=23.95 Aligned_cols=24 Identities=29% Similarity=0.529 Sum_probs=19.5
Q ss_pred HHHHHHhCCceeecCCCCceeCcchHhh
Q 033029 90 ILQQLQNMNIIDIEPKGGRRITSSGQRD 117 (129)
Q Consensus 90 ~lqqLE~~g~vek~~~~GR~lT~~G~~~ 117 (129)
+++.|..+|.|+.+ | .||+-|+..
T Consensus 2 A~~~L~~LgAld~~---~-~lT~lG~~m 25 (92)
T smart00847 2 ALELLYELGALDDD---G-RLTPLGRKM 25 (92)
T ss_pred HHHHHHHCCCcCCC---C-CcCHHHHHH
Confidence 67889999999652 3 899999875
No 199
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=42.58 E-value=34 Score=27.40 Aligned_cols=37 Identities=22% Similarity=0.237 Sum_probs=24.4
Q ss_pred HHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 87 ARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 87 iR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
+=..+++||+. .|++.+.++...||+.|+..++.+..
T Consensus 33 vS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a~~ 72 (313)
T PRK12684 33 VSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASVER 72 (313)
T ss_pred HHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHHHH
Confidence 44567888864 56666543224689999988876543
No 200
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=42.54 E-value=33 Score=27.94 Aligned_cols=36 Identities=11% Similarity=0.112 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhC---CceeecCCCCc-eeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR-~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|.+... +|- .||+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~~~~LT~~G~~l~~~a~ 71 (324)
T PRK12681 32 GISKQVRMLEDELGIQIFARSG-KHLTQVTPAGEEIIRIAR 71 (324)
T ss_pred HHHHHHHHHHHHhCCEeEEECC-CCCCccCHHHHHHHHHHH
Confidence 455678888874 6677664 343 69999999987643
No 201
>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=42.41 E-value=51 Score=23.13 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=29.8
Q ss_pred ccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029 79 FCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 79 ~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
|..|+-++| .+++.|=+-|+|.. ++ |..||+.|...-+.
T Consensus 29 H~dA~p~~i-~a~~RLheKGLI~~-pd-GgyLT~~G~~~aEh 67 (77)
T TIGR02647 29 HSTASPAAV-AAAARLHEKGLTTQ-PD-GGYLTSLGLEAAEH 67 (77)
T ss_pred cccCCHHHH-HHHHHHHHcCCccC-CC-CCEecHHHHHHHHH
Confidence 356777776 57899999999975 44 44999999876543
No 202
>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP. AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding
Probab=42.23 E-value=31 Score=29.70 Aligned_cols=86 Identities=14% Similarity=0.213 Sum_probs=46.5
Q ss_pred ccccChhHHHHHHHHHHHhcCCCCCCCCCCC----chHHHh--HHHHHHHHHHhCCCchhh---hHHHhcccCCCCCCCC
Q 033029 7 VKDVSPHEFVKAYSAHLKRSGKFKELAPYDP----DWYYVR--AASMARKIYLRQGLGVGS---FRRIYGGSKRNGSRPP 77 (129)
Q Consensus 7 v~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~----DW~Y~R--~ASilR~lYl~g~vGV~~---lr~~YGg~k~rG~~P~ 77 (129)
..|..+...++.+.....+- .+..+|... .|++-+ ..+.-|-|||.||||.|. |--.|..-.-..-+.-
T Consensus 17 ~~D~~q~~~~~~l~~l~~~l--~~~~~~~~~~~~~~~~~~~~~~~~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~ 94 (362)
T PF03969_consen 17 FPDPAQRQAIEHLDRLYQEL--QKYKPARQSKSRLRKLFGRKPPPPPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRV 94 (362)
T ss_pred CCCHHHHHHHHhHHHHHHHH--HhccccchhhHHHHHHhcCCccCCCCceEEEECCCCCchhHHHHHHHHhCCccccccc
Confidence 45777777777665544432 112222221 233332 334578899999999985 3444554333233455
Q ss_pred cccCCchhHHHHHHHHHHhCC
Q 033029 78 HFCKSSGAIARHILQQLQNMN 98 (129)
Q Consensus 78 h~~~asg~iiR~~lqqLE~~g 98 (129)
||. ..+..+-+.|-+..
T Consensus 95 HFh----~Fm~~vh~~l~~~~ 111 (362)
T PF03969_consen 95 HFH----EFMLDVHSRLHQLR 111 (362)
T ss_pred ccc----HHHHHHHHHHHHHh
Confidence 664 35555556665554
No 203
>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=42.09 E-value=24 Score=23.09 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=17.4
Q ss_pred hhHHHHHHHHHHhCCceeecC
Q 033029 84 GAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~ 104 (129)
-.-++.+|+.||.+|+|+...
T Consensus 46 ~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 46 QRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred HHHHHHHHHHHHHcCCeEEEE
Confidence 357889999999999998544
No 204
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=42.03 E-value=29 Score=27.10 Aligned_cols=36 Identities=14% Similarity=0.199 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|++... +|=.+|+.|+..++.+-
T Consensus 31 avSr~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~ 69 (296)
T PRK09906 31 SLSQQIKDLENCVGVPLLVRDK-RKVALTAAGEVFLQDAR 69 (296)
T ss_pred HHHHHHHHHHHHhCCeeeeeCC-CcceEcHhHHHHHHHHH
Confidence 344567888864 6777764 68899999998887543
No 205
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=40.98 E-value=40 Score=27.01 Aligned_cols=36 Identities=14% Similarity=0.130 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=..+|+||+. .|++.+. +|-.||+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 70 (308)
T PRK10094 32 TISYRIKLLEENTGVALFFRTT-RSVTLTAAGEHLLSQAR 70 (308)
T ss_pred HHHHHHHHHHHHhCCEEEeeCC-CceeECHhHHHHHHHHH
Confidence 455678888875 5666664 58899999998877643
No 206
>PF03537 Glyco_hydro_114: Glycoside-hydrolase family GH114; InterPro: IPR004352 Eighty-one archaeal-like genes, ranging in size from 4-20kb, are clustered in 15 regions of the Thermotoga maritima genome []. Conservation of gene order between T. maritima and Archaea in many of these regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea []. One of the T. maritima sequences (hypothetical protein TM1410) shares similarity with Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ1477 and with hypothetical protein DR0705 from Deinococcus radiodurans. The sequences are characterised by relatively variable N- and C-terminal domains, and a more conserved central domain. They share no similarity with any other known, functionally or structurally characterised proteins. ; PDB: 2AAM_F.
Probab=40.28 E-value=18 Score=24.19 Aligned_cols=37 Identities=30% Similarity=0.455 Sum_probs=23.7
Q ss_pred CCcccccChhHHHHHHHHHHHhcCC-------CCCCCCCCCchH
Q 033029 4 ARTVKDVSPHEFVKAYSAHLKRSGK-------FKELAPYDPDWY 40 (129)
Q Consensus 4 ~~tv~DV~~~~fI~~~A~~LK~~gk-------~kE~aP~d~DW~ 40 (129)
.+.|.||++..|-.+--+.||.+|+ .=+.-|..|||.
T Consensus 26 ~~~v~~iD~~~~~~~~I~~L~~~G~~vicY~s~Gs~E~~R~d~~ 69 (74)
T PF03537_consen 26 DVDVVVIDLFDFSKEEIARLKAQGKKVICYFSIGSAEDWRPDWD 69 (74)
T ss_dssp S-SEEEE-SBS--HHHHHHHHHTT-EEEEEEESSEEETTSTT--
T ss_pred CCCEEEECCccCCHHHHHHHHHCCCEEEEEEeCceecCCccchh
Confidence 4689999999999888899999998 445556666664
No 207
>PRK10632 transcriptional regulator; Provisional
Probab=40.12 E-value=44 Score=26.66 Aligned_cols=38 Identities=8% Similarity=0.165 Sum_probs=27.6
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
+-+=..+++||+. .|++.+. +|-.||+.|+.+++....
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~i~lT~~G~~l~~~a~~ 71 (309)
T PRK10632 31 SSISQTVSKLEDELQVKLLNRST-RSIGLTEAGRIYYQGCRR 71 (309)
T ss_pred HHHHHHHHHHHHHhCCeeecccC-CCceechhHHHHHHHHHH
Confidence 3566778899864 5666664 588999999988766543
No 208
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=40.07 E-value=41 Score=27.44 Aligned_cols=37 Identities=14% Similarity=0.144 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhC---CceeecCCCCc-eeCcchHhhHHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQVAG 123 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR-~lT~~G~~~lD~iA~ 123 (129)
-+=..+++||+. .|++.+. +|- .||+.|+.+++....
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~v~~LT~~G~~l~~~a~~ 72 (327)
T PRK12680 32 GLSKQLKQLEDELGFLLFVRKG-RSLESVTPAGVEVIERARA 72 (327)
T ss_pred HHHHHHHHHHHHhCCeEEEECC-CcCCccCccHHHHHHHHHH
Confidence 455678889864 5667664 344 399999999988654
No 209
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=39.75 E-value=64 Score=26.37 Aligned_cols=58 Identities=19% Similarity=0.328 Sum_probs=44.2
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC-C--CCc-----eeCcchHhh
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP-K--GGR-----RITSSGQRD 117 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~-~--~GR-----~lT~~G~~~ 117 (129)
.|+.-+--+||+.++.+...-|=. ..-+|.=|+.||+.|+|+... . -|| .||.+|.+.
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 456555568999999999987753 247899999999999998543 2 255 689998763
No 210
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=39.64 E-value=74 Score=23.30 Aligned_cols=59 Identities=12% Similarity=0.054 Sum_probs=40.6
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHH
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLD 119 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD 119 (129)
.|++.|.-.++..|+.|...+|-.+ +-+=+=|+-|+++|||+.... || .|.+.....++
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~lsq--------------stvS~HL~~L~~AGLV~~~r~-Gr~~~Y~l~~~~~~~~~ 82 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQSQ--------------PKISRHLALLRESGLLLDRKQ-GKWVHYRLSPHIPAWAA 82 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCH--------------HHHHHHHHHHHHCCceEEEEE-cCEEEEEECchHHHHHH
Confidence 4777666568999999999876531 234556899999999987764 55 45554433333
No 211
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=39.54 E-value=34 Score=26.60 Aligned_cols=36 Identities=19% Similarity=0.335 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=+.+|+||+. .|.+.+. +|-.||+.|+.+++.+.
T Consensus 31 avS~~Ik~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a~ 69 (291)
T TIGR03418 31 AVSQQVKRLEEELGTPLFERGH-RGIELTEDGQRLFEAVR 69 (291)
T ss_pred HHHHHHHHHHHHhCcHHhhcCC-CceeEcHhHHHHHHHHH
Confidence 344556777754 4455543 46777777777766543
No 212
>KOG1392 consensus Acetyl-CoA acetyltransferase [Lipid transport and metabolism]
Probab=39.24 E-value=22 Score=31.39 Aligned_cols=56 Identities=27% Similarity=0.574 Sum_probs=39.4
Q ss_pred CcccccChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHH--hCCCchhhhHHH--hcccCCCC
Q 033029 5 RTVKDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYL--RQGLGVGSFRRI--YGGSKRNG 73 (129)
Q Consensus 5 ~tv~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl--~g~vGV~~lr~~--YGg~k~rG 73 (129)
.|++||+.-+|-+++|...--+ +--.|.|||-. -|+ .+.+|.--|.+. +||.-.-|
T Consensus 359 ltlkdid~feiheafagqilan-----lkamdsdwfck--------~ymgr~~kvg~ppl~k~nnwggslsig 418 (465)
T KOG1392|consen 359 LTLKDIDVFEIHEAFAGQILAN-----LKAMDSDWFCK--------EYMGRSGKVGRPPLDKLNNWGGSLSIG 418 (465)
T ss_pred CcccccchhhhHHHHhHHHHhh-----hhhhcchHHHH--------HHhcccCccCCCChHHhcccCcceecC
Confidence 6999999999999999876544 33469999943 355 456776666553 56655544
No 213
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=39.05 E-value=31 Score=27.54 Aligned_cols=34 Identities=18% Similarity=0.202 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
-+=+.+++||+. -|++.+. +|=.||+.|+.+++.
T Consensus 44 avS~~I~~LE~~lG~~LF~R~~-r~~~LT~~G~~l~~~ 80 (311)
T PRK10086 44 AVSHRINQLEEELGIKLFVRSH-RKVELTEEGKRVFWA 80 (311)
T ss_pred HHHHHHHHHHHHhCCeeEEEcC-CCcccCHhHHHHHHH
Confidence 344567788864 5666654 578888888888876
No 214
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=38.82 E-value=45 Score=23.07 Aligned_cols=30 Identities=20% Similarity=0.220 Sum_probs=23.3
Q ss_pred chhHHHHHHHHHHhCCc-eeecCCCCceeCc
Q 033029 83 SGAIARHILQQLQNMNI-IDIEPKGGRRITS 112 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~-vek~~~~GR~lT~ 112 (129)
|..-|=+.+|+|++.|+ |+.....|+.|.+
T Consensus 32 SRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~ 62 (79)
T COG1654 32 SRTAVWKHIQQLREEGVDIESVRGKGYLLPQ 62 (79)
T ss_pred cHHHHHHHHHHHHHhCCceEecCCCceeccC
Confidence 44567789999999998 5666666998864
No 215
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=38.76 E-value=43 Score=25.74 Aligned_cols=39 Identities=13% Similarity=0.082 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 85 AIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
.-+=++|++|++.|+|+.. |+.|+=.=...|.++|..+.
T Consensus 184 etvsR~L~~L~~~G~I~~~---~~~i~I~d~~~L~~~~~~~~ 222 (226)
T PRK10402 184 RHLLYVLAQFIQDGYLKKS---KRGYLIKNRKQLSGLALELK 222 (226)
T ss_pred HHHHHHHHHHHHCCCEEee---CCEEEEeCHHHHHHHHHHhc
Confidence 3455699999999999875 33455444566666676643
No 216
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=38.65 E-value=41 Score=26.24 Aligned_cols=37 Identities=19% Similarity=0.214 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
+-+=+.+++||+. .|++.. +|=.||+.|+.+++.+-.
T Consensus 30 pavS~~I~~LE~~lg~~Lf~R~--r~~~lT~~G~~l~~~~~~ 69 (292)
T TIGR03298 30 SAVSQRIKALEERLGQPLLVRT--QPCRATEAGQRLLRHARQ 69 (292)
T ss_pred HHHHHHHHHHHHHhCchheecC--CCCcCCHhHHHHHHHHHH
Confidence 3466778889875 677774 488999999998876543
No 217
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=38.47 E-value=47 Score=26.43 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=28.0
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+-+-+.+++||+. .|++.+. +|=.||+.|+.+++.+.
T Consensus 33 savS~~Ik~LE~~lg~~Lf~R~~-~~v~LT~~G~~l~~~a~ 72 (309)
T PRK11013 33 PTVSRELARFEKVIGLKLFERVR-GRLHPTVQGLRLFEEVQ 72 (309)
T ss_pred HHHHHHHHHHHHHhCceeeeecC-CCcccCHHHHHHHHHHH
Confidence 4677888899875 6677664 57889999998887653
No 218
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=38.45 E-value=50 Score=26.18 Aligned_cols=38 Identities=16% Similarity=0.116 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhC---CceeecCCCCc-eeCcchHhhHHHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQVAGR 124 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR-~lT~~G~~~lD~iA~~ 124 (129)
-+=+.+++||+. .|++... .|- .||+.|+.+++.+..-
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~~~~~ 73 (309)
T PRK12682 32 GVSKAIIELEEELGIEIFIRHG-KRLKGLTEPGKAVLDVIERI 73 (309)
T ss_pred HHHHHHHHHHHHhCCeeEEECC-CCcCccCHhHHHHHHHHHHH
Confidence 455678888864 5666653 354 6999999988876543
No 219
>PRK14137 recX recombination regulator RecX; Provisional
Probab=38.39 E-value=38 Score=26.90 Aligned_cols=56 Identities=13% Similarity=0.097 Sum_probs=39.1
Q ss_pred CCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhC
Q 033029 34 PYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNM 97 (129)
Q Consensus 34 P~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~ 97 (129)
-.++|||+-.|..++.+-|-.-.---..-.+.|.--.++|+.. .+|+.++..+...
T Consensus 127 ~~d~ede~e~a~~l~~KK~~~~~~~~~~k~K~~~~L~rRGFs~--------~~I~~al~~~~~~ 182 (195)
T PRK14137 127 ARDPQEEQQEARNLLERRWSSFARKRDPRASAYAFLARRGFSG--------AVIWPAIREVAAL 182 (195)
T ss_pred hcCchhHHHHHHHHHHHhccccCcchhHHHHHHHHHHHCCCCH--------HHHHHHHHHHHHh
Confidence 3467788899999998887431100133467788888888755 5999999887665
No 220
>PHA02943 hypothetical protein; Provisional
Probab=38.19 E-value=1.3e+02 Score=23.80 Aligned_cols=53 Identities=19% Similarity=0.091 Sum_probs=41.1
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 105 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~ 105 (129)
|-...|.--||+-| -.|...+..+.+.-|= |-+=+|++|..||+.|.|++.+.
T Consensus 7 d~v~~R~~eILE~L-k~G~~TtseIAkaLGl--------------S~~qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 7 DTVHTRMIKTLRLL-ADGCKTTSRIANKLGV--------------SHSMARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred HHHHHHHHHHHHHH-hcCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHcCceEEEee
Confidence 45566777788877 5666778888887664 33579999999999999999874
No 221
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=38.02 E-value=48 Score=26.81 Aligned_cols=34 Identities=18% Similarity=0.191 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
-+-+.+++||+. .|++... .|=.||+.|+.+++.
T Consensus 32 aVS~~Ik~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~ 68 (317)
T PRK15421 32 ALSHQFSDLEQRLGFRLFVRKS-QPLRFTPQGEILLQL 68 (317)
T ss_pred HHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHH
Confidence 344556666654 4455543 466677777766654
No 222
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=38.01 E-value=51 Score=26.12 Aligned_cols=36 Identities=14% Similarity=0.152 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+-+.+++||+. .|++.+. .|=.||+.|+.+++...
T Consensus 35 avS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 73 (305)
T CHL00180 35 AVSLQIKNLEKQLNIPLFDRSK-NKASLTEAGELLLRYGN 73 (305)
T ss_pred HHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHHHH
Confidence 566778888875 5666654 58899999999966543
No 223
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=37.82 E-value=44 Score=27.05 Aligned_cols=35 Identities=14% Similarity=0.245 Sum_probs=23.7
Q ss_pred HHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 87 ARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 87 iR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+=+-+++||+. .|++.+. +|-.||+.|+.++..+.
T Consensus 42 vS~~I~~LE~~lG~~LF~R~~-~~~~LT~~G~~l~~~a~ 79 (310)
T PRK15092 42 VSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYAR 79 (310)
T ss_pred HHHHHHHHHHHhCcceEEECC-CCceECHhHHHHHHHHH
Confidence 44456777754 6676654 57788888888776544
No 224
>PRK06474 hypothetical protein; Provisional
Probab=37.77 E-value=1e+02 Score=23.69 Aligned_cols=46 Identities=13% Similarity=0.146 Sum_probs=34.3
Q ss_pred HHHHHHHHhCC-CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 46 SMARKIYLRQG-LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 46 SilR~lYl~g~-vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
.|++-|.-.++ ..+..|....+ .-|.+-+=+.|+.|++.|+|+..+
T Consensus 15 ~Il~~L~~~~~~~ta~el~~~l~-------------~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 15 KICQVLMRNKEGLTPLELVKILK-------------DVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 36676766654 88888887653 245567778899999999999755
No 225
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=37.51 E-value=60 Score=25.65 Aligned_cols=35 Identities=11% Similarity=0.115 Sum_probs=21.7
Q ss_pred HHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 87 ARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 87 iR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+=+.+++||+. .|.+... +|-.||+.|+.++..+.
T Consensus 35 vS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~ 72 (296)
T PRK11062 35 ITGQIKALEERLQGKLFKRKG-RGLEPTELGELVFRYAD 72 (296)
T ss_pred HHHHHHHHHHHcCccceeecC-CceeECHhHHHHHHHHH
Confidence 34456677764 5555553 57777777777765543
No 226
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=37.49 E-value=45 Score=27.44 Aligned_cols=39 Identities=26% Similarity=0.226 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhCCceeecC-CCCc--eeCcchHhhHHHHHHH
Q 033029 86 IARHILQQLQNMNIIDIEP-KGGR--RITSSGQRDLDQVAGR 124 (129)
Q Consensus 86 iiR~~lqqLE~~g~vek~~-~~GR--~lT~~G~~~lD~iA~~ 124 (129)
-.=++|++||+.|+|++.. +.|- .+|++|...|-..-..
T Consensus 35 ta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~~~d 76 (214)
T COG1339 35 TAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKEYED 76 (214)
T ss_pred HHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHHHHH
Confidence 3445789999999998654 3443 6899999988765444
No 227
>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=37.45 E-value=49 Score=22.87 Aligned_cols=36 Identities=25% Similarity=0.319 Sum_probs=26.0
Q ss_pred chhHHHHHHHHHHhCCceeecCC--CCceeCcchHhhH
Q 033029 83 SGAIARHILQQLQNMNIIDIEPK--GGRRITSSGQRDL 118 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~~--~GR~lT~~G~~~l 118 (129)
+.+-+.++|++|-+.|+|..... .|-+||-.|-..|
T Consensus 37 ~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~L 74 (82)
T PF09202_consen 37 SEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYL 74 (82)
T ss_dssp -HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHH
T ss_pred CHHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHH
Confidence 34567789999999999997542 4999999986543
No 228
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=37.43 E-value=54 Score=26.13 Aligned_cols=35 Identities=20% Similarity=0.341 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
-+-+.+++||+. .|.+.+. +|=.||+.|+.++..+
T Consensus 37 avS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a 74 (312)
T PRK10341 37 AVSKIINDIEDYFGVELIVRKN-TGVTLTPAGQVLLSRS 74 (312)
T ss_pred HHHHHHHHHHHHhCCeEEEEcC-CCceEChhHHHHHHHH
Confidence 566778889875 5666664 5889999999988753
No 229
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=37.42 E-value=46 Score=25.71 Aligned_cols=35 Identities=11% Similarity=0.106 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
-+-+.+++||+. .|.+... +|=.||+.|+.+++.+
T Consensus 33 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a 70 (290)
T PRK10837 33 AVSAALTDLEGQLGVQLFDRVG-KRLVVNEHGRLLYPRA 70 (290)
T ss_pred HHHHHHHHHHHHhCCccEeecC-CeEEECHhHHHHHHHH
Confidence 455677888874 6677654 5788999998888753
No 230
>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=36.70 E-value=36 Score=22.57 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=16.9
Q ss_pred hHHHHHHHHHHhCCceeecC
Q 033029 85 AIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~ 104 (129)
.=++..|.+||.+|+|+...
T Consensus 40 ~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 40 RRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHhCCCeEEEe
Confidence 45788999999999998654
No 231
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=36.24 E-value=88 Score=22.17 Aligned_cols=53 Identities=9% Similarity=0.134 Sum_probs=34.2
Q ss_pred HHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHh
Q 033029 41 YVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQN 96 (129)
Q Consensus 41 Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~ 96 (129)
++-...+.++++-....++..|++.||.....- .|.+..--..+-.+++.|.+
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 455667777776544789999999999875421 35555444455555555544
No 232
>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=36.11 E-value=45 Score=24.64 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=35.0
Q ss_pred HHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 51 IYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 51 lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
||+.+ |.-.+.|+..++-. -..++.+|+-|++.|+|+..+++--.++.
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 55544 67777788776542 35899999999999999998765444443
No 233
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=35.65 E-value=33 Score=32.05 Aligned_cols=92 Identities=20% Similarity=0.254 Sum_probs=62.3
Q ss_pred cccChhHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHH-HHHHHhC----------CCc---hhhh----HHHhccc
Q 033029 8 KDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMA-RKIYLRQ----------GLG---VGSF----RRIYGGS 69 (129)
Q Consensus 8 ~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASil-R~lYl~g----------~vG---V~~l----r~~YGg~ 69 (129)
.++|..++|+.- ++.|--..-.|.+.-+||.+.|.-+ |+-||.. .-| -+.+ +..+|+
T Consensus 388 f~~P~~eWv~~A----~eeglvg~g~pT~sG~~ya~LA~~i~R~P~lTr~E~~vl~kiP~~~~i~~~~~~e~~~d~~~~- 462 (591)
T PF04458_consen 388 FSAPNREWVEEA----REEGLVGTGEPTESGRFYAELARHIKRLPHLTRYEMEVLHKIPDKGYIHREELVEFIKDHVGK- 462 (591)
T ss_pred CCCCcHHHHHHH----HHccccCCCCCCcchHHHHHHHhhhhhcccccHHHHHHHHhCCccccccHHHHHHHhhccccc-
Confidence 688888888753 3334455668999999999988765 6666542 111 0111 111221
Q ss_pred CCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhh
Q 033029 70 KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRD 117 (129)
Q Consensus 70 k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~ 117 (129)
--.=++++|..||+-|+|+--++++=++|+.|+-.
T Consensus 463 -------------ee~~i~~AL~kLEArGfI~~Lp~g~iilTeaG~~i 497 (591)
T PF04458_consen 463 -------------EEEEIIEALEKLEARGFIEILPNGMIILTEAGELI 497 (591)
T ss_pred -------------chHHHHHHHHHHHhcchHHHcCCCcEEEehhhHHH
Confidence 11234669999999999999999999999999854
No 234
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=35.30 E-value=66 Score=25.22 Aligned_cols=36 Identities=17% Similarity=0.293 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|++... .|=.||+.|+.++..+.
T Consensus 36 avS~~i~~LE~~lg~~Lf~R~~-r~l~lT~~G~~l~~~~~ 74 (297)
T PRK11139 36 AVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLDIR 74 (297)
T ss_pred HHHHHHHHHHHHhCchheEecC-CceeECHhHHHHHHHHH
Confidence 556678888875 6666664 57889999988877653
No 235
>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=34.93 E-value=1.4e+02 Score=20.87 Aligned_cols=53 Identities=17% Similarity=0.063 Sum_probs=37.6
Q ss_pred CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 55 QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 55 g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
.++.+++|+..-...-. | -..-|-.+++.+|.+|-+.+-|=.+..|=..+||+
T Consensus 28 ~~at~E~l~~~L~~~yp-~-----i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivtP~ 80 (80)
T PF10264_consen 28 QPATQETLREHLRKHYP-G-----IAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVTPQ 80 (80)
T ss_pred CcchHHHHHHHHHHhCC-C-----CCCCCHHHHHHHHHHHHHcCceeeCCCceEeeCCC
Confidence 46666666655444322 2 33456689999999999999998877666788875
No 236
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.45 E-value=39 Score=28.25 Aligned_cols=28 Identities=32% Similarity=0.373 Sum_probs=22.5
Q ss_pred CchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029 82 SSGAIARHILQQLQNMNIIDIEPKGGRRI 110 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~vek~~~~GR~l 110 (129)
=|..-+++.+..||..|+|.+++ .||.+
T Consensus 200 ls~aTV~~~lk~l~~~Gii~~~~-~Gr~i 227 (240)
T COG3398 200 LSVATVAYHLKKLEELGIIPEDR-EGRSI 227 (240)
T ss_pred ccHHHHHHHHHHHHHcCCCcccc-cCceE
Confidence 36678999999999999999875 46643
No 237
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=33.69 E-value=26 Score=29.60 Aligned_cols=40 Identities=18% Similarity=0.352 Sum_probs=33.0
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 102 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek 102 (129)
|+-|+.|+..-|+... ++.+|.. -++.+|..|++.|+|+.
T Consensus 231 P~kvetl~~lcGS~~~---~l~~FR~----~Lk~AL~eL~~~g~v~~ 270 (282)
T PF07042_consen 231 PIKVETLRELCGSESS---RLRKFRQ----QLKKALDELVAVGFVSS 270 (282)
T ss_pred CccHHHHHHHcCCCcc---CHHHHHH----HHHHHHHHHHhcCceeE
Confidence 8999999998887542 4667754 49999999999999974
No 238
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=33.47 E-value=81 Score=25.13 Aligned_cols=39 Identities=21% Similarity=0.297 Sum_probs=19.2
Q ss_pred chhhhHHHhcc----cCCCCCCCCcccCCchhHHHHHHHHHHh
Q 033029 58 GVGSFRRIYGG----SKRNGSRPPHFCKSSGAIARHILQQLQN 96 (129)
Q Consensus 58 GV~~lr~~YGg----~k~rG~~P~h~~~asg~iiR~~lqqLE~ 96 (129)
-+..|...+|. |..+|+.|......--..++.++++++.
T Consensus 56 ~I~~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~~~~~l~~~~~ 98 (314)
T PRK09508 56 AVARLKVMFNDELFVRYGRGIQPTARARQLFGPVRQALQLVQN 98 (314)
T ss_pred HHHHHHHhhCCCcEEEcCCCCcCcHHHHHHHHHHHHHHHHHHH
Confidence 34555555553 4555555554433333344555555553
No 239
>PF14178 YppF: YppF-like protein
Probab=33.26 E-value=32 Score=23.05 Aligned_cols=33 Identities=24% Similarity=0.509 Sum_probs=24.0
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHH
Q 033029 29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRI 65 (129)
Q Consensus 29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~ 65 (129)
-|+..|.+-+=. --.+|+.||.|-+.+...|..
T Consensus 13 ~k~y~p~~~NeL----LDFar~~Yi~gei~i~eYR~l 45 (60)
T PF14178_consen 13 KKKYEPEDMNEL----LDFARKLYIQGEISINEYRNL 45 (60)
T ss_pred HhccCcccHHHH----HHHHHHHHHhCcccHHHHHHH
Confidence 356778776433 337899999999988877654
No 240
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=33.01 E-value=1e+02 Score=24.33 Aligned_cols=40 Identities=20% Similarity=0.141 Sum_probs=32.9
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 102 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek 102 (129)
-+|--|+.++|+.-..+..+.|-. + -.++++|.+.|||+.
T Consensus 94 EtLaiIay~qPiTr~eI~~irGv~------~-----------~~ii~~L~~~gLI~e 133 (188)
T PRK00135 94 EVLAIIAYKQPITRIEIDEIRGVN------S-----------DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCCC------H-----------HHHHHHHHHCCCeEE
Confidence 468888999999999999986653 2 567889999999974
No 241
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=32.94 E-value=63 Score=25.23 Aligned_cols=36 Identities=19% Similarity=0.207 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
-+=+.+++||+. .|++.. +|-.||+.|+.+++.+-.
T Consensus 32 avS~~i~~LE~~lg~~Lf~R~--r~i~lT~~G~~l~~~a~~ 70 (294)
T PRK13348 32 AVSQRIKALEESLGQPLLVRG--RPCRPTPAGQRLLRHLRQ 70 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccChhHHHHHHHHHH
Confidence 455677888865 566664 488999999888876543
No 242
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=32.67 E-value=1.3e+02 Score=24.34 Aligned_cols=55 Identities=16% Similarity=0.264 Sum_probs=44.5
Q ss_pred hHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCc
Q 033029 43 RAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITS 112 (129)
Q Consensus 43 R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~ 112 (129)
|=-.|+..|=-+|-+-|..|...||- |..-||+=|..||+.|++.+.- ||=.++.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~V--------------S~~TIRRDL~~Le~~g~l~R~h-GGa~~~~ 60 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGV--------------SEMTIRRDLNELEEQGLLLRVH-GGAVLPD 60 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCC--------------CHHHHHHhHHHHHHCCcEEEEe-CCEecCC
Confidence 55568888888899999999999875 4568999999999999999875 4544433
No 243
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=32.48 E-value=61 Score=25.99 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhC---CceeecCCCC-ceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGG-RRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~G-R~lT~~G~~~lD~iA 122 (129)
-+=+.+++||+. .|++.+. +| ..||+.|+.+++.+-
T Consensus 32 avS~~I~~LE~~lg~~Lf~R~~-r~~~~lT~~G~~l~~~a~ 71 (309)
T PRK12683 32 GVSKQIKDLEDELGVEIFIRRG-KRLTGLTEPGKELLQIVE 71 (309)
T ss_pred HHHHHHHHHHHHhCCeeEeeCC-CCcCCcCHHHHHHHHHHH
Confidence 456678888875 5666553 34 368999998887644
No 244
>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=32.10 E-value=42 Score=27.17 Aligned_cols=51 Identities=18% Similarity=0.282 Sum_probs=40.3
Q ss_pred hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHH
Q 033029 54 RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLD 119 (129)
Q Consensus 54 ~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD 119 (129)
.||..+..|...-|- .| .-++..|..|..+|+++++. +.-.+|+.+...|+
T Consensus 21 ~gp~t~~eLA~~~~~------~~--------~~~~~lL~~L~~lgll~~~~-~~y~~t~~~~~~l~ 71 (306)
T TIGR02716 21 EGPKDLATLAADTGS------VP--------PRLEMLLETLRQMRVINLED-GKWSLTEFADYMFS 71 (306)
T ss_pred cCCCCHHHHHHHcCC------Ch--------HHHHHHHHHHHhCCCeEecC-CcEecchhHHhhcc
Confidence 478888888875432 22 37999999999999999874 78999999976665
No 245
>PF06208 BDV_G: Borna disease virus G protein; InterPro: IPR009344 This family consists of Borna disease virus G glycoprotein sequences. Borna disease virus (BDV) infection produces a variety of clinical diseases, from behavioural illnesses to classical fatal encephalitis []. G protein is important for viral entry into the host cell [,].
Probab=31.87 E-value=30 Score=30.86 Aligned_cols=38 Identities=26% Similarity=0.665 Sum_probs=28.3
Q ss_pred ChhHHHHHHHHHHHhcCCCCCCCCCCC---chHHHhHHHHHHHH
Q 033029 11 SPHEFVKAYSAHLKRSGKFKELAPYDP---DWYYVRAASMARKI 51 (129)
Q Consensus 11 ~~~~fI~~~A~~LK~~gk~kE~aP~d~---DW~Y~R~ASilR~l 51 (129)
.+|.+|+.|...+++- -.|-+|+|| +|||- |.+|.--|
T Consensus 92 S~DrlI~R~tG~~~~C--iN~s~~EDPFvCNWyYC-CSAI~n~i 132 (503)
T PF06208_consen 92 SADRLINRYTGDPKQC--INESTVEDPFVCNWYYC-CSAIVNEI 132 (503)
T ss_pred chhHHHHHhcCChHHh--hcCCCCCCCeeechhhh-hHHHhhhh
Confidence 5789999998877765 678889999 78875 55555443
No 246
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=30.95 E-value=36 Score=18.62 Aligned_cols=11 Identities=45% Similarity=0.480 Sum_probs=7.0
Q ss_pred CCchHHHhHHHH
Q 033029 36 DPDWYYVRAASM 47 (129)
Q Consensus 36 d~DW~Y~R~ASi 47 (129)
||+|. +|.|++
T Consensus 11 D~~~~-VR~~a~ 21 (31)
T PF02985_consen 11 DPSPE-VRQAAA 21 (31)
T ss_dssp -SSHH-HHHHHH
T ss_pred CCCHH-HHHHHH
Confidence 78887 776654
No 247
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=30.91 E-value=79 Score=25.84 Aligned_cols=66 Identities=18% Similarity=0.250 Sum_probs=41.0
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHh-CC--ceeecC----CCCcee
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQN-MN--IIDIEP----KGGRRI 110 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~-~g--~vek~~----~~GR~l 110 (129)
.+|=.|-..+++.|.-.|.+ ..-++.-|- |-+-+=..+++||+ +| +++... .+|=.|
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 35556677777777777754 223333222 22345567788887 34 577652 246789
Q ss_pred CcchHhhHH
Q 033029 111 TSSGQRDLD 119 (129)
Q Consensus 111 T~~G~~~lD 119 (129)
|+.|+.++.
T Consensus 79 T~~G~~l~~ 87 (263)
T PRK10676 79 TRYGERLIQ 87 (263)
T ss_pred CHHHHHHHH
Confidence 999999983
No 248
>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=30.55 E-value=95 Score=26.88 Aligned_cols=50 Identities=16% Similarity=0.304 Sum_probs=37.2
Q ss_pred hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 60 GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 60 ~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
..|+..||..=++ .....+...+++.++..|++.|+++...++|=.|.|.
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 4566777775443 3345677899999999999999999887655666664
No 249
>PF14605 Nup35_RRM_2: Nup53/35/40-type RNA recognition motif
Probab=30.30 E-value=21 Score=22.45 Aligned_cols=38 Identities=16% Similarity=0.283 Sum_probs=27.4
Q ss_pred CCcccccChhHHHHHHHHHHHhcCC--CCCCCCCCCchHHHh
Q 033029 4 ARTVKDVSPHEFVKAYSAHLKRSGK--FKELAPYDPDWYYVR 43 (129)
Q Consensus 4 ~~tv~DV~~~~fI~~~A~~LK~~gk--~kE~aP~d~DW~Y~R 43 (129)
.++|..++++.. +.+-.|+++-|. +.+.+ .+.+|+|++
T Consensus 3 wI~V~Gf~~~~~-~~vl~~F~~fGeI~~~~~~-~~~~~~~l~ 42 (53)
T PF14605_consen 3 WISVSGFPPDLA-EEVLEHFASFGEIVDIYVP-ESTNWMYLK 42 (53)
T ss_pred EEEEEeECchHH-HHHHHHHHhcCCEEEEEcC-CCCcEEEEE
Confidence 468888997766 445557888898 55555 467899986
No 250
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=30.15 E-value=75 Score=25.48 Aligned_cols=35 Identities=14% Similarity=0.072 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhC---CceeecCCCCc-eeCcchHhhHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGR-RITSSGQRDLDQV 121 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR-~lT~~G~~~lD~i 121 (129)
-+=+.+++||+. .|++... +|. .||+.|+.+++.+
T Consensus 32 avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~a 70 (316)
T PRK12679 32 GVSRHIRELEDELGIEIFIRRG-KRLLGMTEPGKALLVIA 70 (316)
T ss_pred HHHHHHHHHHHHhCCEEEEECC-CcccccCHhHHHHHHHH
Confidence 455677888875 4555543 232 6999999887654
No 251
>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=30.13 E-value=52 Score=21.98 Aligned_cols=50 Identities=18% Similarity=0.188 Sum_probs=32.0
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|=.|-.|..++. -.+.+.++.|-+.|.=--+ =.=+++.+||+.|+|.-..
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 445666666544 3678888888887754221 2346899999999997543
No 252
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=30.08 E-value=88 Score=28.39 Aligned_cols=82 Identities=17% Similarity=0.187 Sum_probs=55.1
Q ss_pred chHHHhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCccc---------CCchhHHHHHHHHHHhCCceeecCC--
Q 033029 38 DWYYVRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFC---------KSSGAIARHILQQLQNMNIIDIEPK-- 105 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~---------~asg~iiR~~lqqLE~~g~vek~~~-- 105 (129)
|+. .-|..++.-+|- .+..|.+.+..++-|.++.-++-.++. .-+..-++.+++||...|+++....
T Consensus 411 ~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~ 489 (607)
T PRK11057 411 DGL-EDAQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDYGHDKLKVYGIGRDKSHEHWVSVIRQLIHLGLVTQNIAQH 489 (607)
T ss_pred ccH-HHHHHHHHHHHHhcCCCCcceeeeeeeccCcchhhhcccccCCccCcCCcCCHHHHHHHHHHHHHcCCceeccCcc
Confidence 443 334556666664 567888888888888766554432221 2245678999999999999986542
Q ss_pred CCceeCcchHhhHHH
Q 033029 106 GGRRITSSGQRDLDQ 120 (129)
Q Consensus 106 ~GR~lT~~G~~~lD~ 120 (129)
..=.||++|+..|..
T Consensus 490 ~~l~~~~~~~~~l~~ 504 (607)
T PRK11057 490 SALQLTEAARPVLRG 504 (607)
T ss_pred ceEEECHHHHHHhcC
Confidence 245788888877753
No 253
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=29.99 E-value=1.1e+02 Score=26.22 Aligned_cols=48 Identities=17% Similarity=0.239 Sum_probs=37.3
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCc
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
||..|-..||.-|..+...-|= |. +++-.-+|.||++|+++...-.+|
T Consensus 28 Il~lL~~k~plNvneiAe~lgL-------pq-------st~s~~ik~Le~aGlirT~t~kar 75 (308)
T COG4189 28 ILQLLHRKGPLNVNEIAEALGL-------PQ-------STMSANIKVLEKAGLIRTETVKAR 75 (308)
T ss_pred HHHHHHHhCCCCHHHHHHHhCC-------ch-------hhhhhhHHHHHhcCceeeeeeccc
Confidence 6777888899999999998774 33 466677899999999986543344
No 254
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=29.70 E-value=39 Score=31.60 Aligned_cols=41 Identities=20% Similarity=0.229 Sum_probs=32.6
Q ss_pred CCchhHHHHHHHHHHhCCceeecCCC----CceeCcchHhhHHHH
Q 033029 81 KSSGAIARHILQQLQNMNIIDIEPKG----GRRITSSGQRDLDQV 121 (129)
Q Consensus 81 ~asg~iiR~~lqqLE~~g~vek~~~~----GR~lT~~G~~~lD~i 121 (129)
+..-.++|.+|..||+-+||+....+ --.||+-|++.|+..
T Consensus 326 ~~~~d~l~~~Ly~LEsf~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 326 RKNFDDLRESLYSLESFGLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred hcchhHHHHHHHHHHhhhhHHhhhhccCceeEEechhHHHHHHhh
Confidence 34445789999999999999866532 368999999999865
No 255
>PRK13239 alkylmercury lyase; Provisional
Probab=29.29 E-value=2.3e+02 Score=22.93 Aligned_cols=53 Identities=15% Similarity=0.154 Sum_probs=34.6
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l 110 (129)
+|+..++ |||.|---.|+.+..|.+..|.. ..-+|.+|++ +..++-+++ |+++
T Consensus 20 ~~~~~~~--llr~la~G~pvt~~~lA~~~~~~--------------~~~v~~~L~~---l~~~~~d~~-g~iv 72 (206)
T PRK13239 20 TATLLVP--LLRLLAKGRPVSVTTLAAALGWP--------------VEEVEAVLEA---MPDTEYDED-GRII 72 (206)
T ss_pred chHHHHH--HHHHHHcCCCCCHHHHHHHhCCC--------------HHHHHHHHHh---CCCeEECCC-CCEE
Confidence 3444544 89997755599999999986653 2345555555 556666663 6654
No 256
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=29.09 E-value=48 Score=26.07 Aligned_cols=31 Identities=16% Similarity=0.353 Sum_probs=25.7
Q ss_pred HHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029 89 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 89 ~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
-|.-.++.+|+|+-. .|-=.||+.|+..++.
T Consensus 47 piv~ta~~Lglv~~e-~GDiilT~~Gk~~v~~ 77 (157)
T COG4754 47 PIVETASLLGLVTAE-SGDIILTDEGKEYVES 77 (157)
T ss_pred HHHHHHHhcCceecc-CCCEEEehhhHHHHhC
Confidence 467788999999865 4678999999999875
No 257
>PF14502 HTH_41: Helix-turn-helix domain
Probab=29.05 E-value=69 Score=20.50 Aligned_cols=25 Identities=24% Similarity=0.356 Sum_probs=20.2
Q ss_pred chhHHHHHHHHHHhCCceeecCCCCc
Q 033029 83 SGAIARHILQQLQNMNIIDIEPKGGR 108 (129)
Q Consensus 83 sg~iiR~~lqqLE~~g~vek~~~~GR 108 (129)
|...|-++|+-||+.|-|.-.. .||
T Consensus 19 s~GtiQ~Alk~Le~~gaI~Le~-rGh 43 (48)
T PF14502_consen 19 SRGTIQNALKFLEENGAIKLES-RGH 43 (48)
T ss_pred chhHHHHHHHHHHHCCcEEeee-cCc
Confidence 4568999999999999998665 354
No 258
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=28.64 E-value=1.1e+02 Score=23.23 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVAG 123 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA~ 123 (129)
-+=..+++||+. .|.+... +|=.||+.|+..++.+-.
T Consensus 31 avS~~I~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a~~ 70 (297)
T COG0583 31 AVSRQIKRLEEELGVPLFERTT-RRVRLTEAGERLLERARR 70 (297)
T ss_pred HHHHHHHHHHHHhCchheeecC-CceeeCHhHHHHHHHHHH
Confidence 355677888873 3444432 345799999888776543
No 259
>PHA00738 putative HTH transcription regulator
Probab=27.77 E-value=1.8e+02 Score=21.48 Aligned_cols=48 Identities=17% Similarity=0.047 Sum_probs=33.5
Q ss_pred HHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCce
Q 033029 47 MARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRR 109 (129)
Q Consensus 47 ilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~ 109 (129)
|+..|.-.++..|+.|...++-. ..-+=+=|+.|+++|+|+... .||.
T Consensus 17 IL~lL~~~e~~~V~eLae~l~lS--------------QptVS~HLKvLreAGLV~srK-~Gr~ 64 (108)
T PHA00738 17 ILELIAENYILSASLISHTLLLS--------------YTTVLRHLKILNEQGYIELYK-EGRT 64 (108)
T ss_pred HHHHHHHcCCccHHHHHHhhCCC--------------HHHHHHHHHHHHHCCceEEEE-ECCE
Confidence 55555444578899999887543 234455689999999998775 4664
No 260
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=27.77 E-value=1.3e+02 Score=23.72 Aligned_cols=37 Identities=11% Similarity=0.196 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
.-+-..+++||+. -|+.++. +|=.||+.|+.++..+-
T Consensus 31 pavS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~~~ 70 (300)
T PRK11074 31 SAVSYTVRQLEEWLAVPLFERRH-RDVELTPAGEWFVKEAR 70 (300)
T ss_pred HHHHHHHHHHHHHhCCeeEEeCC-CCceECccHHHHHHHHH
Confidence 3566778888874 5666653 57788888888876543
No 261
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=27.58 E-value=1.5e+02 Score=24.79 Aligned_cols=58 Identities=14% Similarity=0.229 Sum_probs=37.9
Q ss_pred HhHHHHHHHHHHh-CCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCc
Q 033029 42 VRAASMARKIYLR-QGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI 99 (129)
Q Consensus 42 ~R~ASilR~lYl~-g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ 99 (129)
+-.-.++|+++.. ....+..|+..||-...+-++--.-+.+-..|...+++++++.++
T Consensus 126 ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~~~H~Al~DA~ata~l~~~ll~~~~~~~~ 184 (313)
T PRK06063 126 MCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVLAGILRPSLERARERDV 184 (313)
T ss_pred EehHHHHHHhccCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHHhcCC
Confidence 4455688888763 567899999999875332222222233445677888888888775
No 262
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=27.50 E-value=1e+02 Score=24.84 Aligned_cols=32 Identities=13% Similarity=0.085 Sum_probs=13.8
Q ss_pred HHHHHHHHHhC---CceeecCCCCceeCcchHhhHH
Q 033029 87 ARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLD 119 (129)
Q Consensus 87 iR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD 119 (129)
+-+.+++||+. -|.+... .|=.||+.|+.++.
T Consensus 60 vS~~I~~LE~~lG~~LF~R~~-r~v~lT~~G~~l~~ 94 (317)
T PRK11482 60 ISQSIQKLRVIFPDPLFIRKG-QGVTPTAYATHLHE 94 (317)
T ss_pred HHHHHHHHHHHhCCcceEecC-CCccCCHHHHHHHH
Confidence 34444555542 2333332 34455555554443
No 263
>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=27.16 E-value=80 Score=23.43 Aligned_cols=27 Identities=22% Similarity=0.330 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 85 AIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
..+|.+|+-|++.|+|+...+|--.|+
T Consensus 66 ~~V~~Al~~f~k~glIe~~d~g~i~i~ 92 (119)
T TIGR01714 66 GDIRITLQTLESLGLIEKKNNGDIFLE 92 (119)
T ss_pred HHHHHHHHHHHHCCCEEEecCCcEEeh
Confidence 589999999999999998865533443
No 264
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=27.07 E-value=48 Score=24.89 Aligned_cols=58 Identities=17% Similarity=0.196 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029 44 AASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDL 118 (129)
Q Consensus 44 ~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l 118 (129)
|-.++..|...||.-...|++.=|.. ...+|++. --=||.|+.++|=-.||++|+..|
T Consensus 61 Al~~A~~L~~~Gp~~~~~l~~~~~~~------------~A~~IL~~-----N~YGWFeRv~rGvY~LT~~G~~al 118 (118)
T PF09929_consen 61 ALRCAAALAEHGPSRPADLRKATGVP------------KATSILRD-----NHYGWFERVERGVYALTPAGRAAL 118 (118)
T ss_pred HHHHHHHHHHcCCCCHHHHHHhcCCC------------hHHHHHHh-----CcccceeeeccceEecCcchhhcC
Confidence 33444455668898888888753321 12233332 224999999988889999999754
No 265
>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=27.00 E-value=46 Score=23.02 Aligned_cols=45 Identities=16% Similarity=0.174 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceee
Q 033029 44 AASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDI 102 (129)
Q Consensus 44 ~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek 102 (129)
++-|++-|.-+|.+-=..|...-|- .-+.+|++|+.|.+.|+|..
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~~l--------------~~~~vRkiL~~L~~~~lv~~ 59 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKLGL--------------KPKEVRKILYKLYEDGLVSY 59 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT-S---------------HHHHHHHHHHHHHHSS-EE
T ss_pred HHHHHHHHHHcCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeEE
Confidence 4556777766777766777765433 23699999999999999953
No 266
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=26.99 E-value=67 Score=24.53 Aligned_cols=36 Identities=8% Similarity=0.058 Sum_probs=27.0
Q ss_pred cCCchhHHHHHHHHHHhCCceee-cCCCCceeCcchH
Q 033029 80 CKSSGAIARHILQQLQNMNIIDI-EPKGGRRITSSGQ 115 (129)
Q Consensus 80 ~~asg~iiR~~lqqLE~~g~vek-~~~~GR~lT~~G~ 115 (129)
..-+..+++++++.|.++|+|.- ....+..+....+
T Consensus 149 ~~~~k~v~~~a~E~L~~l~Ll~~~~~~~~~~~~~e~r 185 (203)
T PF14629_consen 149 KVWSKPVALKAWEHLLSLELLKPNYDGSSNNVQKEFR 185 (203)
T ss_pred ccCCHHHHHHHHHHHHHCCCceecccCCCCccCccce
Confidence 45577899999999999999976 2234566666554
No 267
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=26.86 E-value=78 Score=24.90 Aligned_cols=35 Identities=20% Similarity=0.196 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 86 IARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 86 iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
-+=..+++||+. .|.+.. .|-.||+.|+.++..+-
T Consensus 32 avS~~I~~LE~~lg~~LF~R~--~~~~lT~~G~~l~~~a~ 69 (294)
T PRK03635 32 AVSQRIKALEERVGQVLLVRT--QPCRPTEAGQRLLRHAR 69 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccCHHHHHHHHHHH
Confidence 344567888864 455664 48999999998876553
No 268
>PRK09213 pur operon repressor; Provisional
Probab=26.78 E-value=2.3e+02 Score=23.68 Aligned_cols=77 Identities=16% Similarity=0.316 Sum_probs=53.5
Q ss_pred hHHHHHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcc-----
Q 033029 43 RAASMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSS----- 113 (129)
Q Consensus 43 R~ASilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~----- 113 (129)
|...+.+.|-=++ -+.+..|+..|+..|-. - .-.=.||+.+|++. .+|.|+..+ .||-+.+|.
T Consensus 8 r~~~~~~~l~~~p~~~~~l~~f~~~~~~aks~-----i--sed~~i~~~~~~~~-~~g~~~t~~ga~ggv~~~p~~~~~~ 79 (271)
T PRK09213 8 RLVDMTKYLLENPNKLISLTFFAERYGAAKSS-----I--SEDLVIIKETFEKQ-GIGTLETVPGAAGGVKYIPSISEEE 79 (271)
T ss_pred HHHHHHHHHHhCCCceEcHHHHHHHhccccch-----h--hhhHHHHHHHHHhc-CCceEEEeCCCCCCeEEEcCCCHHH
Confidence 4445555444444 48899999999987531 1 11235899999874 689999887 367777664
Q ss_pred hHhhHHHHHHHhhh
Q 033029 114 GQRDLDQVAGRIVV 127 (129)
Q Consensus 114 G~~~lD~iA~~i~~ 127 (129)
.++.|+.++.++.+
T Consensus 80 a~~~~~~L~~~L~~ 93 (271)
T PRK09213 80 AREFVEELCERLSE 93 (271)
T ss_pred HHHHHHHHHHHHHh
Confidence 78889999888754
No 269
>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=26.32 E-value=90 Score=19.63 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=18.4
Q ss_pred CchhHHHHHHHHHHhCCceeecC
Q 033029 82 SSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~vek~~ 104 (129)
.|..-+=++|+.|++.|+|+...
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 34456778999999999999753
No 270
>PF10396 TrmE_N: GTP-binding protein TrmE N-terminus; InterPro: IPR018948 This family represents the shorter, B, chain of the homo-dimeric structure which is a guanine nucleotide-binding protein that binds and hydrolyses GTP. TrmE is homologous to the tetrahydrofolate-binding domain of N,N-dimethylglycine oxidase and indeed binds formyl-tetrahydrofolate. TrmE actively participates in the formylation reaction of uridine and regulates the ensuing hydrogenation reaction of a Schiff's base intermediate. This B chain is the N-terminal portion of the protein consisting of five beta-strands and three alpha helices and is necessary for mediating dimer formation within the protein []. ; PDB: 1XZQ_B 1XZP_A 3GEE_A 3GEI_B 3GEH_A.
Probab=25.95 E-value=54 Score=24.15 Aligned_cols=27 Identities=26% Similarity=0.340 Sum_probs=20.9
Q ss_pred CcccCCchhHHHHHHHHHHhCCceeec
Q 033029 77 PHFCKSSGAIARHILQQLQNMNIIDIE 103 (129)
Q Consensus 77 ~h~~~asg~iiR~~lqqLE~~g~vek~ 103 (129)
+-|+.|+-.|++.+|+.|.++|.=.-.
T Consensus 75 Ei~~HGg~~v~~~il~~l~~~G~R~A~ 101 (114)
T PF10396_consen 75 EIHCHGGPAVVRRILEALLKAGARLAE 101 (114)
T ss_dssp EEEEESSHHHHHHHHHHHHHTT-EE--
T ss_pred EEEcCCCHHHHHHHHHHHHHcCceEcC
Confidence 457789999999999999999865443
No 271
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=25.78 E-value=57 Score=21.54 Aligned_cols=20 Identities=15% Similarity=0.092 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHhCCceeecC
Q 033029 85 AIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~ 104 (129)
.-+-+.++.||+.|+|.+.+
T Consensus 33 r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 33 RSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred hHHHHHHHHHHHCCCEEEEE
Confidence 46778999999999998765
No 272
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=25.57 E-value=84 Score=24.31 Aligned_cols=18 Identities=28% Similarity=0.436 Sum_probs=14.5
Q ss_pred HHHHHHHHHHhCCceeec
Q 033029 86 IARHILQQLQNMNIIDIE 103 (129)
Q Consensus 86 iiR~~lqqLE~~g~vek~ 103 (129)
-+=++|++|++.|+|+..
T Consensus 195 tlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 195 TVSRALSQLQDRGLIGLS 212 (230)
T ss_pred HHHHHHHHHHHCCcEEec
Confidence 344579999999999864
No 273
>PF15398 DUF4619: Domain of unknown function (DUF4619)
Probab=25.44 E-value=12 Score=31.97 Aligned_cols=64 Identities=22% Similarity=0.431 Sum_probs=45.0
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHH----HHHHHHHhCCceeecC
Q 033029 29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIAR----HILQQLQNMNIIDIEP 104 (129)
Q Consensus 29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR----~~lqqLE~~g~vek~~ 104 (129)
..++||.-+.|| =|..++=|-+|++=|+ ..+..|||+ .=||.||-+++=...
T Consensus 58 egQLPPLret~y-Grys~v~r~m~FDIpl----------------------e~~EtSIIKrHPPRRlQkLEp~~lP~~i- 113 (296)
T PF15398_consen 58 EGQLPPLRETWY-GRYSTVPRAMYFDIPL----------------------ENGETSIIKRHPPRRLQKLEPIDLPQVI- 113 (296)
T ss_pred ccCCCchhhccc-cccccCCCceeeeecc----------------------cCCcccccccCCCccccccCCCCCCccc-
Confidence 689999998775 8888888888887654 234567777 468999988765433
Q ss_pred CCCceeCcchHh
Q 033029 105 KGGRRITSSGQR 116 (129)
Q Consensus 105 ~~GR~lT~~G~~ 116 (129)
..+|.++++...
T Consensus 114 ts~rll~q~e~~ 125 (296)
T PF15398_consen 114 TSERLLSQQEAR 125 (296)
T ss_pred chhhhhhHHHhh
Confidence 235666665544
No 274
>KOG0345 consensus ATP-dependent RNA helicase [RNA processing and modification]
Probab=25.42 E-value=34 Score=31.68 Aligned_cols=19 Identities=32% Similarity=0.438 Sum_probs=17.1
Q ss_pred CCCCCCchHHHhHHHHHHH
Q 033029 32 LAPYDPDWYYVRAASMARK 50 (129)
Q Consensus 32 ~aP~d~DW~Y~R~ASilR~ 50 (129)
-||.||+||--||-..+|.
T Consensus 333 DpP~~~~~FvHR~GRTaR~ 351 (567)
T KOG0345|consen 333 DPPKDPSSFVHRCGRTARA 351 (567)
T ss_pred CCCCChhHHHhhcchhhhc
Confidence 4899999999999998884
No 275
>PRK09801 transcriptional activator TtdR; Provisional
Probab=25.29 E-value=68 Score=25.78 Aligned_cols=37 Identities=27% Similarity=0.404 Sum_probs=26.7
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQVA 122 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~iA 122 (129)
+-+=..+++||+. -|++... +|=.||+.|+..+...-
T Consensus 35 pavS~~I~~LE~~LG~~Lf~R~~-r~~~lT~~G~~l~~~a~ 74 (310)
T PRK09801 35 AFVTKRIQILENTLATTLLNRSA-RGVALTESGQRCYEHAL 74 (310)
T ss_pred HHHHHHHHHHHHHhCCEeeeecC-CCCcccHhHHHHHHHHH
Confidence 3455678889875 4566654 58899999998877643
No 276
>PF02923 BamHI: Restriction endonuclease BamHI; InterPro: IPR004194 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents BamHI restriction endonucleases, which recognises the DNA sequence GGATCC and cleaves after G-1 [, ].; PDB: 1ESG_A 3BAM_B 1BHM_B 2BAM_A 1BAM_A.
Probab=24.79 E-value=30 Score=27.25 Aligned_cols=36 Identities=25% Similarity=0.335 Sum_probs=25.5
Q ss_pred CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCcee
Q 033029 56 GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIID 101 (129)
Q Consensus 56 ~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ve 101 (129)
|.|-+.|. +|.++|.+||+| |=-.|.+.|++.||.-
T Consensus 36 P~~~~~F~-InPt~K~NGVKP---------IKe~cm~~L~~~gW~l 71 (158)
T PF02923_consen 36 PAGNDNFT-INPTRKGNGVKP---------IKEACMAHLEKHGWYL 71 (158)
T ss_dssp STTSSSBE-EE-SSTTB-SHH---------HHHHHHHHHHTT--EE
T ss_pred CCCCCeEE-ECCccccCCCcc---------hHHHHHHHHHhcCceE
Confidence 66655554 689999999999 6778999999889864
No 277
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=24.61 E-value=66 Score=23.39 Aligned_cols=32 Identities=31% Similarity=0.486 Sum_probs=21.1
Q ss_pred chhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHH
Q 033029 58 GVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQ 93 (129)
Q Consensus 58 GV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqq 93 (129)
|+..|++.||+...--+| -+.||.|-+.|.|-
T Consensus 47 G~~GlAklfgcSv~Ta~R----iK~sG~id~AI~Q~ 78 (96)
T PF12964_consen 47 GLKGLAKLFGCSVPTANR----IKKSGKIDPAITQI 78 (96)
T ss_pred hHHHHHHHhCCCchhHHH----HHhcCCccHHHHHc
Confidence 788889999986432221 25667777777663
No 278
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=24.55 E-value=65 Score=22.28 Aligned_cols=18 Identities=39% Similarity=0.591 Sum_probs=15.3
Q ss_pred CchhHHHHHHHHHHhCCc
Q 033029 82 SSGAIARHILQQLQNMNI 99 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~ 99 (129)
.-..++|.+++.|-.||+
T Consensus 68 ~l~~~lr~i~~sLa~MGI 85 (85)
T PF14357_consen 68 KLAGILRNIMDSLANMGI 85 (85)
T ss_pred cHHHHHHHHHHHHHHCCC
Confidence 345799999999999996
No 279
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=24.50 E-value=88 Score=25.97 Aligned_cols=33 Identities=24% Similarity=0.428 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhCCceeecCCCCceeCcchHhhH
Q 033029 86 IARHILQQLQNMNIIDIEPKGGRRITSSGQRDL 118 (129)
Q Consensus 86 iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~l 118 (129)
.+..+--=|.+.|+++.+.++++.+|+-|+..+
T Consensus 44 MV~siryWl~a~gli~~~~~~~~~~T~lG~~i~ 76 (286)
T PF13182_consen 44 MVKSIRYWLRAFGLIEEDNKGKRKLTPLGELIF 76 (286)
T ss_pred HHHHHHHHHHHcCCcccCCCCCcccCHHHHHHH
Confidence 444455568889999988777779999999999
No 280
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=24.41 E-value=85 Score=24.52 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=14.0
Q ss_pred ccChhHH-----HHHHHHHHHhcCC
Q 033029 9 DVSPHEF-----VKAYSAHLKRSGK 28 (129)
Q Consensus 9 DV~~~~f-----I~~~A~~LK~~gk 28 (129)
+||-|.+ |..+.+||+.+.|
T Consensus 83 ~iPEDL~~L~~ri~~L~~HL~~nkK 107 (151)
T PRK08561 83 EIPEDLRNLIKKAVNLRKHLEENPK 107 (151)
T ss_pred CCcHHHHHHHHHHHHHHHHHHhCCC
Confidence 5665554 5678888888866
No 281
>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=23.96 E-value=2e+02 Score=22.11 Aligned_cols=51 Identities=14% Similarity=0.283 Sum_probs=29.9
Q ss_pred ccChhHHHHHHHHHHHhcC-CCCCCC-------CC--CCchHHHhHHHHHHHHHHhCCCch
Q 033029 9 DVSPHEFVKAYSAHLKRSG-KFKELA-------PY--DPDWYYVRAASMARKIYLRQGLGV 59 (129)
Q Consensus 9 DV~~~~fI~~~A~~LK~~g-k~kE~a-------P~--d~DW~Y~R~ASilR~lYl~g~vGV 59 (129)
|+.=.|+|+.|-.--+++. ---|+. |- .+.=.|-||+-+||++|.+.--+|
T Consensus 28 ~~~LkEIIk~Ln~lT~~~~~~C~e~~V~dV~~~~kNtTe~e~~CrA~~vLr~~y~~~~s~i 88 (138)
T smart00190 28 DITLREIIETLNNVTQKGTNLCTEMMVPDVLAATKNTTEKELFCRALKVLRNFYFHNCSAI 88 (138)
T ss_pred cchHHHHHHHHHHHccCCCCCcccccHHHHhcccCCCcchhHhhHHHHHHHHHHHhhhhHH
Confidence 6666777777766554432 111111 11 123458999999999998743333
No 282
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=23.88 E-value=1.2e+02 Score=24.89 Aligned_cols=36 Identities=14% Similarity=0.080 Sum_probs=26.3
Q ss_pred hHHHHHHHHHHhC---CceeecCCCCceeCcchHhhHHHH
Q 033029 85 AIARHILQQLQNM---NIIDIEPKGGRRITSSGQRDLDQV 121 (129)
Q Consensus 85 ~iiR~~lqqLE~~---g~vek~~~~GR~lT~~G~~~lD~i 121 (129)
+-+=..+++||+. .|.+... +|=.||+.|+.++...
T Consensus 33 pavS~~Ik~LE~eLG~~LF~R~~-r~~~LT~aG~~ll~~a 71 (297)
T PRK15243 33 TPLSRVISDLERELKQRLFIRKN-GTLIPTEFAQTIYRKV 71 (297)
T ss_pred HHHHHHHHHHHHHhCCccEEeCC-CCeeECHHHHHHHHHH
Confidence 3456778888875 5666653 5888999999888754
No 283
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=23.86 E-value=73 Score=25.96 Aligned_cols=43 Identities=16% Similarity=0.350 Sum_probs=27.8
Q ss_pred CCchhhhHHHhccc-CCCCCCCCcccCCchhHHHHHHHHHHhCCceeec
Q 033029 56 GLGVGSFRRIYGGS-KRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 103 (129)
Q Consensus 56 ~vGV~~lr~~YGg~-k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~ 103 (129)
++..+.+-..|--- ..-|..|- +..-++.+|+.||.+|+|+..
T Consensus 307 ~~~~~~~~~~y~~~~~~~~~~~~-----~~~~~~~~l~~l~~~gli~~~ 350 (365)
T TIGR02928 307 PFRTGEVYEVYKEVCEDIGVDPL-----TQRRISDLLNELDMLGLVEAE 350 (365)
T ss_pred CccHHHHHHHHHHHHHhcCCCCC-----cHHHHHHHHHHHHhcCCeEEE
Confidence 45555555544321 22344453 347899999999999999854
No 284
>TIGR03157 cas_Csc2 CRISPR-associated protein Csc2. CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This protein family is a CRISPR-associated (Cas) family strictly associated with the Cyano subtype of CRISPR/Cas locus, found in several species of Cyanobacteria and several archaeal species. This family is designated Csc2 for CRISPR/Cas Subtype Cyano protein 2, as it is often the second gene upstream of the core cas genes, cas3-cas4-cas1-cas2.
Probab=23.64 E-value=81 Score=26.97 Aligned_cols=38 Identities=21% Similarity=0.289 Sum_probs=31.3
Q ss_pred CCCCcccccChhHHHHHHHHHHHhcC---------C----------CCCCCCCCCch
Q 033029 2 ATARTVKDVSPHEFVKAYSAHLKRSG---------K----------FKELAPYDPDW 39 (129)
Q Consensus 2 ~~~~tv~DV~~~~fI~~~A~~LK~~g---------k----------~kE~aP~d~DW 39 (129)
|..+|++||.+++|+-.+...|+... + +..-.|.+-+|
T Consensus 165 p~~vTLkD~T~~e~~~~l~~~~rt~RYGa~ttr~G~v~N~IlgV~~~~~E~~Snl~~ 221 (282)
T TIGR03157 165 PCVVTLKDVTPAEFLYVVNNIARTARYGANTTRFGRVRNRILGVFLSPYEGPSNLEL 221 (282)
T ss_pred ceEEEecCCCHHHHHHHHHHHHHhhhccccccccceeeeEEEEEEecCCCCcchHHH
Confidence 44579999999999999999999762 2 67777888777
No 285
>PF10231 DUF2315: Uncharacterised conserved protein (DUF2315); InterPro: IPR018796 This entry consists of small conserved proteins found from worms to humans. Their function is not known.
Probab=23.62 E-value=25 Score=26.37 Aligned_cols=32 Identities=25% Similarity=0.599 Sum_probs=25.8
Q ss_pred cccChhHHHHHHHHHHHhcCCCCCCCCCCCchHH
Q 033029 8 KDVSPHEFVKAYSAHLKRSGKFKELAPYDPDWYY 41 (129)
Q Consensus 8 ~DV~~~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y 41 (129)
.+++++++-+-|.+||.++ .+...=||-+||-
T Consensus 75 ~~l~a~~mseFYk~FL~~n--~~~h~~YN~eWyr 106 (126)
T PF10231_consen 75 QELSADEMSEFYKEFLDKN--RKRHMQYNREWYR 106 (126)
T ss_pred CCCCHHHHHHHHHHHHHHH--HHHHHHHHHHHHH
Confidence 4689999999999999988 5556667878873
No 286
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.62 E-value=1.6e+02 Score=25.45 Aligned_cols=56 Identities=18% Similarity=0.399 Sum_probs=41.9
Q ss_pred CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 29 FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 29 ~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
+|++||.-..+ |+|=||+.+|+-...+...- +|++ .+-...+++.|.++.++...+
T Consensus 25 fR~LP~LAK~~-------VmrLL~~~~pv~~~~l~~Wv--------~~~~-----~~~~~~al~~L~~L~Ii~~~~ 80 (366)
T PF03849_consen 25 FRSLPPLAKQY-------VMRLLFVEQPVPQADLESWV--------KPES-----KKEHDEALKRLRSLHIIQESE 80 (366)
T ss_pred HHhccHHHHHH-------HHHHHhcCCCcCHHHHHHHh--------Cccc-----hHHHHHHHHHHhhCeeEeecc
Confidence 56677654321 78889999999999998763 3433 467789999999999997554
No 287
>PF02513 Spin-Ssty: Spin/Ssty Family; InterPro: IPR003671 Spindlin (Spin) and Ssty were first identified for their involvement in gametogenesis. Spindlin was identified as a maternal transcript present in the unfertilised egg and early embryo, and was subsequently shown to interact with the spindle apparatus during oogenesis, and may therefore be important for mitosis []. In addition, spindlin appears to be a target for cell cycle-dependent phosphorylation, and as such may play a role in cell cycle regulation during the transition from gamete to embryo []. Ssty is a multi-copy, Y-linked spermatogenesis-specific transcript that appears to be required for normal spermatogenesis []. Ssty may play an analogous role to spindlin in sperm cells, namely during the transition from sperm cells to early embryo, and in mitosis.; GO: 0007276 gamete generation; PDB: 2NS2_A.
Probab=23.62 E-value=19 Score=23.28 Aligned_cols=13 Identities=31% Similarity=0.861 Sum_probs=9.9
Q ss_pred CCCCCCCchHHHh
Q 033029 31 ELAPYDPDWYYVR 43 (129)
Q Consensus 31 E~aP~d~DW~Y~R 43 (129)
...|.+|+||||.
T Consensus 25 ~Qvp~~ps~y~Ik 37 (50)
T PF02513_consen 25 HQVPAKPSLYYIK 37 (50)
T ss_dssp EE-TTSTTEEEEE
T ss_pred EEeecCCcEEEEE
Confidence 3689999999984
No 288
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=23.61 E-value=1.3e+02 Score=24.30 Aligned_cols=37 Identities=22% Similarity=0.264 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHhCCceeecCCCCc----eeCcchHhhHHHHH
Q 033029 85 AIARHILQQLQNMNIIDIEPKGGR----RITSSGQRDLDQVA 122 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~GR----~lT~~G~~~lD~iA 122 (129)
.+|-+.|..|++.|||+... .|+ .+|+.|.+.--+.|
T Consensus 114 h~itYslrKL~k~gLit~t~-~gkevTy~vTa~G~~acarYa 154 (199)
T COG5631 114 HNITYSLRKLLKGGLITRTG-SGKEVTYEVTALGHRACARYA 154 (199)
T ss_pred hhHHHHHHHHHhccceecCC-CCceEEEEEecchHHHHHHHH
Confidence 47889999999999999765 344 57888987655544
No 289
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=23.60 E-value=94 Score=23.14 Aligned_cols=26 Identities=19% Similarity=0.123 Sum_probs=20.0
Q ss_pred CchhHHHHHHHHHHhCCceeecCCCC
Q 033029 82 SSGAIARHILQQLQNMNIIDIEPKGG 107 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~vek~~~~G 107 (129)
.|-+-+-++|++|+++|+|.+....|
T Consensus 53 islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 53 ISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred CCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 34456778999999999999776433
No 290
>PF05209 MinC_N: Septum formation inhibitor MinC, N-terminal domain; InterPro: IPR007874 In Escherichia coli FtsZ (P0A9A6 from SWISSPROT) assembles into a Z ring at midcell. Its assembly at polar sites is prevented by the min system. MinC P18196 from SWISSPROT, a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with the MinDE proteins. MinC is an oligomer, probably a dimer []. The C-terminal half of MinC is the most conserved and interacts with MinD. The N-terminal half is thought to interact with FtsZ. MinC rapidly oscillates between the poles of the cell to destabilise FtsZ filaments that have formed before they mature into polar Z rings; GO: 0051302 regulation of cell division; PDB: 3GHF_A 1HF2_C.
Probab=23.40 E-value=35 Score=23.63 Aligned_cols=54 Identities=19% Similarity=0.315 Sum_probs=36.5
Q ss_pred cccccChhHHHHHHHHHHHhcCC----------CCCCCCCCCchHHHhHHHHHHHHHHhCCCchhhhH
Q 033029 6 TVKDVSPHEFVKAYSAHLKRSGK----------FKELAPYDPDWYYVRAASMARKIYLRQGLGVGSFR 63 (129)
Q Consensus 6 tv~DV~~~~fI~~~A~~LK~~gk----------~kE~aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr 63 (129)
.+.+.+.++|.+++.+.+++... ..++ +...|| -..-.++|..-+. |+||...+
T Consensus 19 ~l~~~d~~~l~~~L~~ki~~ap~FF~~~pvvldl~~l-~~~~dl--~~L~~~l~~~gl~-~vgv~~~~ 82 (99)
T PF05209_consen 19 RLRSADLDELLQALDEKIAQAPDFFKNAPVVLDLSNL-PDELDL--AALVELLRRHGLR-PVGVRGGN 82 (99)
T ss_dssp EECSS-HHHHHHHHHHHHHHTHHHCTTTEEEEEEEEE-ETTHHH--HHHHHHHHCCCHC-CCCEHHHH
T ss_pred EeCCCCHHHHHHHHHHHHHhChHhHcCCCeEEehhhc-CChhhH--HHHHHHHHHcCCE-EEEecccH
Confidence 35788999999999999998865 3334 334455 4445677766666 88984443
No 291
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=23.04 E-value=65 Score=27.12 Aligned_cols=21 Identities=14% Similarity=0.365 Sum_probs=18.5
Q ss_pred hhHHHHHHHHHHhCCceeecC
Q 033029 84 GAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 84 g~iiR~~lqqLE~~g~vek~~ 104 (129)
.|||=++|..||.+|+||...
T Consensus 218 RSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 218 RSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred HHHHHHHHHHhhhcCceeecc
Confidence 579999999999999998654
No 292
>PF14493 HTH_40: Helix-turn-helix domain
Probab=22.98 E-value=94 Score=21.00 Aligned_cols=40 Identities=20% Similarity=0.395 Sum_probs=29.3
Q ss_pred cccccChhHHHHHHHHHHHhcCC-----CCCCCCCCCchHHHhHH
Q 033029 6 TVKDVSPHEFVKAYSAHLKRSGK-----FKELAPYDPDWYYVRAA 45 (129)
Q Consensus 6 tv~DV~~~~fI~~~A~~LK~~gk-----~kE~aP~d~DW~Y~R~A 45 (129)
.+.++-+.+.++.+.+.+++.+. -+|.-|.+=||+-+|++
T Consensus 45 ~~~~~l~~e~~~~I~~~~~~~~~~~lk~i~e~l~~~~sy~~iRl~ 89 (91)
T PF14493_consen 45 DIEELLSEEEIKQIEDAIEKLGSEKLKPIKEALPGDYSYFEIRLV 89 (91)
T ss_pred CHHHhCCHHHHHHHHHHHHHcCcccHHHHHHHCCCCCCHHHHHHH
Confidence 44555556667777777776654 67788888899999986
No 293
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=22.75 E-value=43 Score=27.69 Aligned_cols=25 Identities=32% Similarity=0.505 Sum_probs=19.0
Q ss_pred CCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 75 RPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 75 ~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
-|--| +|| |+++||||..|++..++
T Consensus 164 LPVEF-DAS----~RA~~~l~~~gii~~~E 188 (226)
T COG2738 164 LPVEF-DAS----SRALKQLESLGIIRENE 188 (226)
T ss_pred cceee-cch----HHHHHHHHhcCCcCcch
Confidence 45555 333 68999999999998665
No 294
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=22.64 E-value=76 Score=25.81 Aligned_cols=27 Identities=22% Similarity=0.250 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHhCCceeecCCCCceeC
Q 033029 85 AIARHILQQLQNMNIIDIEPKGGRRIT 111 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~~~GR~lT 111 (129)
+-.=++|.-||++|||+-.++.|-..|
T Consensus 107 sN~~RaL~lLq~aGLI~Lk~~~~~~~t 133 (237)
T PF03180_consen 107 SNQARALKLLQEAGLITLKDGVGLTAT 133 (237)
T ss_dssp HHHHHHHHHHHHTTSEEE-TT-GCC-S
T ss_pred cchhHHHHHHHhCCeEEEcCCCCCccC
Confidence 344578999999999997655554555
No 295
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=22.56 E-value=1.1e+02 Score=20.64 Aligned_cols=24 Identities=13% Similarity=0.146 Sum_probs=19.7
Q ss_pred hhHHHHHHHHHHHhcCCCCCCCCC
Q 033029 12 PHEFVKAYSAHLKRSGKFKELAPY 35 (129)
Q Consensus 12 ~~~fI~~~A~~LK~~gk~kE~aP~ 35 (129)
.+.|++.|.+|++.+|..-+.+|.
T Consensus 3 ~~~F~~~L~~F~~~~g~~~~~~P~ 26 (93)
T smart00501 3 RVLFLDRLYKFMEERGSPLKKIPV 26 (93)
T ss_pred HHHHHHHHHHHHHHcCCcCCcCCe
Confidence 578999999999999875556664
No 296
>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=22.56 E-value=94 Score=21.32 Aligned_cols=36 Identities=28% Similarity=0.278 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHhCCcee--------e-cCCCCceeCcchHhhHHH
Q 033029 85 AIARHILQQLQNMNIID--------I-EPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~ve--------k-~~~~GR~lT~~G~~~lD~ 120 (129)
.=.-.+|++|.+.|+|+ - .....=.||++|...|-+
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 112345799999988864
No 297
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.46 E-value=66 Score=25.56 Aligned_cols=20 Identities=20% Similarity=0.368 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHhCCceeecC
Q 033029 85 AIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~ 104 (129)
--||.+|..|+++|+++...
T Consensus 46 ~~i~e~l~dL~elGLier~t 65 (175)
T COG4344 46 PRIREYLKDLKELGLIERYT 65 (175)
T ss_pred HHHHHHHHHHHHcCCeeecc
Confidence 36899999999999999654
No 298
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.43 E-value=45 Score=25.57 Aligned_cols=27 Identities=30% Similarity=0.417 Sum_probs=19.7
Q ss_pred cCCCCCCCCcccCCchhHHHHHHHHHHhCCc
Q 033029 69 SKRNGSRPPHFCKSSGAIARHILQQLQNMNI 99 (129)
Q Consensus 69 ~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ 99 (129)
-|.-|+-|+.+.+.|.+|+| +||++|+
T Consensus 52 vK~Ig~P~s~y~k~skkvlk----aleq~gI 78 (139)
T COG1710 52 VKVIGCPPSLYPKVSKKVLK----ALEQMGI 78 (139)
T ss_pred cceecCCchhhhHHHHHHHH----HHHhCCc
Confidence 45667788888877777666 7777775
No 299
>PF05746 DALR_1: DALR anticodon binding domain; InterPro: IPR008909 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This all alpha helical domain is the anticodon binding domain of Arginyl tRNA synthetase. This domain is known as the DALR domain after characteristic conserved amino acids [].; GO: 0004814 arginine-tRNA ligase activity, 0005524 ATP binding, 0006420 arginyl-tRNA aminoacylation; PDB: 2ZUE_A 2ZUF_A 3FNR_A 1F7V_A 1F7U_A 1BS2_A 1IQ0_A.
Probab=22.37 E-value=57 Score=22.33 Aligned_cols=16 Identities=31% Similarity=0.306 Sum_probs=12.3
Q ss_pred HHHhHHHHHHHHHHhC
Q 033029 40 YYVRAASMARKIYLRQ 55 (129)
Q Consensus 40 ~Y~R~ASilR~lYl~g 55 (129)
-|.|+.||+|+.=-.+
T Consensus 4 a~aRi~sIl~k~~~~~ 19 (119)
T PF05746_consen 4 AYARISSILRKAEESG 19 (119)
T ss_dssp HHHHHHHHHHHCTCTT
T ss_pred HHHHHHHHHHcCCCcC
Confidence 3789999999765544
No 300
>PF05106 Phage_holin_3: Phage holin family (Lysis protein S); InterPro: IPR006481 This entry is represented by the Bacteriophage lambda, GpS. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually 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=22.15 E-value=63 Score=22.98 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=19.7
Q ss_pred CCCCchHHHhHHHHHHHHHHhC-C-------CchhhhHHHhccc
Q 033029 34 PYDPDWYYVRAASMARKIYLRQ-G-------LGVGSFRRIYGGS 69 (129)
Q Consensus 34 P~d~DW~Y~R~ASilR~lYl~g-~-------vGV~~lr~~YGg~ 69 (129)
|.|||+| |.++--+.-+- + +-+.-||..|++.
T Consensus 2 ~k~P~~W----~~ll~wl~~~~~~~~~a~lA~~mA~LR~~Y~g~ 41 (100)
T PF05106_consen 2 DKNPDFW----AQLLAWLQSHWPQIYGALLAFVMALLRGAYGGG 41 (100)
T ss_pred CCCccHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 5688888 55665555332 2 3356778888654
No 301
>PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed
Probab=22.02 E-value=1e+02 Score=20.66 Aligned_cols=45 Identities=18% Similarity=0.391 Sum_probs=25.7
Q ss_pred CCchhHHHHHHHHHHhCCc--eeecCCCCceeCcc--h------HhhHHHHHHHhhhCC
Q 033029 81 KSSGAIARHILQQLQNMNI--IDIEPKGGRRITSS--G------QRDLDQVAGRIVVAP 129 (129)
Q Consensus 81 ~asg~iiR~~lqqLE~~g~--vek~~~~GR~lT~~--G------~~~lD~iA~~i~~~~ 129 (129)
..-|.-|++.|+.| |+ |+... -|+.++=. | ...++.||.+++.+|
T Consensus 15 Dp~G~ai~~~l~~l---g~~~v~~Vr-~~k~~~l~~~~~~~~~a~~~v~~i~~~lL~Np 69 (80)
T PRK05974 15 DPQGQAIKGALGSL---GYDGVEDVR-QGKYFELELEGESEEKAEADLKEMCEKLLANP 69 (80)
T ss_pred ChHHHHHHHHHHHc---CCCCcceEE-EEEEEEEEEcCCchhhhHHHHHHHHHHhcCCc
Confidence 33455555566655 54 33222 35555443 3 677899999887654
No 302
>PF08357 SEFIR: SEFIR domain; InterPro: IPR013568 This domain is found in IL17 receptors (IL17Rs, e.g. Q60943 from SWISSPROT) and SEF proteins (e.g. Q8QHJ9 from SWISSPROT). The latter are feedback inhibitors of FGF signalling and are also thought to be receptors. Due to its similarity to the TIR domain (IPR000157 from INTERPRO), the SEFIR region is thought to be involved in homotypic interactions with other SEFIR/TIR-domain-containing proteins. Thus, SEFs and IL17Rs may be involved in TOLL/IL1R-like signalling pathways [].
Probab=22.01 E-value=94 Score=22.24 Aligned_cols=32 Identities=34% Similarity=0.676 Sum_probs=23.6
Q ss_pred ccChh-HHHHHHHHHHHhc-CC--------CCCCCCCCCc-hH
Q 033029 9 DVSPH-EFVKAYSAHLKRS-GK--------FKELAPYDPD-WY 40 (129)
Q Consensus 9 DV~~~-~fI~~~A~~LK~~-gk--------~kE~aP~d~D-W~ 40 (129)
|-+.+ +.|.+||++|.+. |- ..+.++.++. |.
T Consensus 10 d~~~h~~~V~~la~~L~~~~g~~V~lD~~~~~~i~~~g~~~W~ 52 (150)
T PF08357_consen 10 DSEEHKEWVLALAEFLRQNCGIDVILDQWELNEIARQGPPRWM 52 (150)
T ss_pred CCHHHHHHHHHHHHHHHhccCCceeecHHhhcccccCCHHHHH
Confidence 33444 7799999999999 75 4566787875 55
No 303
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=21.98 E-value=2e+02 Score=17.61 Aligned_cols=51 Identities=18% Similarity=0.287 Sum_probs=34.6
Q ss_pred HHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCCCCcee
Q 033029 46 SMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRI 110 (129)
Q Consensus 46 SilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~l 110 (129)
.|++.+.-..+..+..+.... .-+.+.+..-|..|+++|+|+....++.++
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 344444443566778888776 344557777888899999999866554443
No 304
>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=21.84 E-value=77 Score=21.16 Aligned_cols=49 Identities=18% Similarity=0.184 Sum_probs=33.2
Q ss_pred chHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeec
Q 033029 38 DWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIE 103 (129)
Q Consensus 38 DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~ 103 (129)
|=.|-.|+.++.. .+-+.++.|-+.|.---+ =.-+++.+||+.|+|.-.
T Consensus 4 D~ly~~a~~~V~~---~~~~S~S~lQR~~~IGyn--------------rAariid~lE~~GiV~p~ 52 (63)
T smart00843 4 DELYDEAVELVIE---TQKASTSLLQRRLRIGYN--------------RAARLIDQLEEEGIVGPA 52 (63)
T ss_pred cHHHHHHHHHHHH---hCCCChHHHHHHHhcchh--------------HHHHHHHHHHHCcCCCCC
Confidence 3467766665443 567778888876654222 245789999999999754
No 305
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=21.82 E-value=1.1e+02 Score=23.43 Aligned_cols=32 Identities=22% Similarity=0.280 Sum_probs=24.7
Q ss_pred CchhHHHHHHHHHHhCCceeecCCCCceeCcc
Q 033029 82 SSGAIARHILQQLQNMNIIDIEPKGGRRITSS 113 (129)
Q Consensus 82 asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~ 113 (129)
-|-.-+.++++.||+.+++.+...|=-.|.|.
T Consensus 87 iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP~ 118 (165)
T PF05732_consen 87 ISKPTVSRAIKELEEKNIIKKIRNGAYMINPN 118 (165)
T ss_pred CCHHHHHHHHHHHHhCCcEEEccCCeEEECcH
Confidence 34557889999999999999876554666664
No 306
>PF01805 Surp: Surp module; InterPro: IPR000061 SWAP is derived from the Suppressor-of-White-APricot splicing regulator from Drosophila melanogaster. The domain is found in regulators responsible for pervasive, nonsex-specific alternative pre-mRNA splicing characteristics and has been found in splicing regulatory proteins []. These ancient, conserved SWAP proteins share a colinearly arrayed series of novel sequence motifs [].; GO: 0003723 RNA binding, 0006396 RNA processing; PDB: 2E5Z_A 2DT7_B 2DT6_A 1UG0_A 1X4P_A 2E60_A 1X4O_A 4DGW_B.
Probab=21.78 E-value=37 Score=21.20 Aligned_cols=31 Identities=13% Similarity=0.416 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHhcCC-----CCCCCCCCCchHHHhH
Q 033029 14 EFVKAYSAHLKRSGK-----FKELAPYDPDWYYVRA 44 (129)
Q Consensus 14 ~fI~~~A~~LK~~gk-----~kE~aP~d~DW~Y~R~ 44 (129)
.+|+..|++..++|. -++.-..||.|.|+.-
T Consensus 3 ~~I~~tA~~Va~~G~~fE~~l~~~~~~np~F~FL~~ 38 (55)
T PF01805_consen 3 EIIDKTAEFVAKNGPEFEEKLRERERNNPQFNFLFP 38 (55)
T ss_dssp HHHHHHHHHHHHCSHHHHHHHHHHTTTSGGGGGGST
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHhcCCCCCCcCcCC
Confidence 679999999999986 3444466777776653
No 307
>PF10746 Phage_holin_6: Phage holin family 6; InterPro: IPR019682 This entry represents a protein conserved in Caudovirales (known as tailed bacteriophages). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis.
Probab=21.62 E-value=47 Score=22.66 Aligned_cols=11 Identities=36% Similarity=1.210 Sum_probs=8.0
Q ss_pred chHHHhHHHHHHH
Q 033029 38 DWYYVRAASMARK 50 (129)
Q Consensus 38 DW~Y~R~ASilR~ 50 (129)
||||+ |+|+--
T Consensus 35 eWfyi--ati~Yt 45 (66)
T PF10746_consen 35 EWFYI--ATIAYT 45 (66)
T ss_pred HHHHH--HHHHHH
Confidence 69998 666643
No 308
>PF13835 DUF4194: Domain of unknown function (DUF4194)
Probab=21.54 E-value=1.9e+02 Score=21.49 Aligned_cols=63 Identities=6% Similarity=-0.089 Sum_probs=43.3
Q ss_pred hHHHhHHHHHHHHHHhCC---------CchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecCC
Q 033029 39 WYYVRAASMARKIYLRQG---------LGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEPK 105 (129)
Q Consensus 39 W~Y~R~ASilR~lYl~g~---------vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~ 105 (129)
..-+=..-+||.+|...- |.++.+...|..-.. -.+-...+-.-++.+|..|++.|+|+....
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 444556779999999763 556666666655222 012234556788999999999999997753
No 309
>PRK14134 recX recombination regulator RecX; Provisional
Probab=21.50 E-value=1.2e+02 Score=25.08 Aligned_cols=54 Identities=20% Similarity=0.091 Sum_probs=39.0
Q ss_pred CCCchHHHhHHHHHHHHHHhCC-Cch---hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHh
Q 033029 35 YDPDWYYVRAASMARKIYLRQG-LGV---GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQN 96 (129)
Q Consensus 35 ~d~DW~Y~R~ASilR~lYl~g~-vGV---~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~ 96 (129)
.+++|++-.|..++.+.|-.-. ..- ....+.++--.++|+.. .+|+.+|+.|..
T Consensus 151 ~~~e~e~e~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~--------~~I~~vl~~~~~ 208 (283)
T PRK14134 151 IDEEKEKKVAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSS--------NIAEWILNELIK 208 (283)
T ss_pred CChhhHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCH--------HHHHHHHHHHHh
Confidence 4667888999999988874321 111 23467888888999866 599999999854
No 310
>PF10987 DUF2806: Protein of unknown function (DUF2806); InterPro: IPR021254 This bacterial family of proteins has no known function.
Probab=21.47 E-value=38 Score=27.17 Aligned_cols=20 Identities=15% Similarity=0.242 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHhCCceeecC
Q 033029 85 AIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 85 ~iiR~~lqqLE~~g~vek~~ 104 (129)
.|--.-|-.|+++|+|..++
T Consensus 137 gl~y~~ll~L~elGLI~~~e 156 (219)
T PF10987_consen 137 GLPYSSLLTLEELGLIHGSE 156 (219)
T ss_pred CCCHHHHHHHHHCCCccccc
Confidence 45566788999999997665
No 311
>TIGR00876 tal_mycobact transaldolase, mycobacterial type. This model describes one of three related but easily separable famiiles of known and putative transaldolases. This family and the family typified by E. coli TalA and TalB both contain experimentally verified examples.
Probab=21.45 E-value=75 Score=27.79 Aligned_cols=60 Identities=13% Similarity=0.063 Sum_probs=35.2
Q ss_pred CCCCCchHHHhHHHHHHHHHHhCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCc
Q 033029 33 APYDPDWYYVRAASMARKIYLRQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNI 99 (129)
Q Consensus 33 aP~d~DW~Y~R~ASilR~lYl~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~ 99 (129)
-|..||++|+..---=--|---++..+..++.. |......-.+...-++..|.+|+++|+
T Consensus 264 ~p~~~d~~YV~~Ligp~tVnT~P~~Tl~Af~dh-------g~~~~~~l~~~~~~a~~~l~~l~~~GI 323 (350)
T TIGR00876 264 NNDLADDLYIKALCAKHSINTAPEEAIDAVADD-------GNIECDTPLGTASDAEAFFDELGAHGI 323 (350)
T ss_pred CCcccccccHHHhcCCCccccCCHHHHHHHHHc-------CCcCCCCCCCcHHHHHHHHHHHHHcCC
Confidence 578899999965221112233344555555552 222222233444579999999999986
No 312
>PF02980 FokI_C: Restriction endonuclease FokI, catalytic domain; InterPro: IPR004233 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition (IPR004234 from INTERPRO) and cleavage functions, respectively. The catalytic domain contains only a single catalytic centre, raising the question of how monomeric FokI manages to cleave both DNA strands. The catalytic domain is sequestered in a 'piggyback' fashion by the recognition domain [].; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=21.40 E-value=98 Score=24.00 Aligned_cols=43 Identities=26% Similarity=0.403 Sum_probs=29.7
Q ss_pred ccCCchhHHHHHHHHHHhCCceeecCC------C----------CceeCcchHhhHHHH
Q 033029 79 FCKSSGAIARHILQQLQNMNIIDIEPK------G----------GRRITSSGQRDLDQV 121 (129)
Q Consensus 79 ~~~asg~iiR~~lqqLE~~g~vek~~~------~----------GR~lT~~G~~~lD~i 121 (129)
+.-.|.+-+|.|.-=|.++|||++..+ + .-+||-+|...|.+.
T Consensus 77 ~EgTSDKYaR~I~~wL~k~glv~~~~k~vt~~~~~~~~~~~i~~~YkIT~~Gl~aL~~~ 135 (142)
T PF02980_consen 77 WEGTSDKYARMICGWLKKVGLVEQKTKKVTRTIGGRKYKETIGQSYKITGKGLTALKRA 135 (142)
T ss_dssp ---HHHHHHHHHHHHHHHTTSEEE--EEEE-BTTBTT-EEEESSEEEE-HHHHHHHHHH
T ss_pred cccchHHHHHHHHHHHHHhchheecceEEEeeccCccccccccceEEEeccHHHHHHHh
Confidence 345678899999999999999996542 1 446788888877664
No 313
>COG4483 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.35 E-value=62 Score=22.21 Aligned_cols=10 Identities=40% Similarity=0.757 Sum_probs=8.6
Q ss_pred HHhHHHHHHH
Q 033029 41 YVRAASMARK 50 (129)
Q Consensus 41 Y~R~ASilR~ 50 (129)
|.||++|||+
T Consensus 48 yl~a~~IL~r 57 (68)
T COG4483 48 YLRARLILRR 57 (68)
T ss_pred HHHHHHHHHH
Confidence 5899999995
No 314
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=21.34 E-value=74 Score=21.83 Aligned_cols=49 Identities=12% Similarity=0.034 Sum_probs=30.1
Q ss_pred HHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 47 MARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 47 ilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|+.-|.- .+++.+..+-..-... + ..-|-+-+=+.|+.|++.|+|.+..
T Consensus 6 Il~~l~~~~~~~sa~ei~~~l~~~---~------~~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 6 ILEVLLESDGHLTAEEIYERLRKK---G------PSISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHhCCCCCCHHHHHHHHHhc---C------CCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 4444444 3466666665543221 2 1233456677899999999998765
No 315
>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=21.26 E-value=1.7e+02 Score=28.20 Aligned_cols=49 Identities=16% Similarity=0.281 Sum_probs=38.3
Q ss_pred CCCCcccCCchhHHHHHHHHHHhCCceeecCCCCceeCcchHhhHHHHHHHhh
Q 033029 74 SRPPHFCKSSGAIARHILQQLQNMNIIDIEPKGGRRITSSGQRDLDQVAGRIV 126 (129)
Q Consensus 74 ~~P~h~~~asg~iiR~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~iA~~i~ 126 (129)
..|+.|. ..+.+.++|.|.+.|+|+++. .|-....+-...++..|..++
T Consensus 743 ~~pef~d---k~lf~~~~~~l~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~l 791 (799)
T TIGR03703 743 NAPEFFD---KAVFSTFIATLREQGYLDDDG-DGKLIFDEKLEELADQLKALL 791 (799)
T ss_pred CCccccc---HHHHHHHHHHHHHCCCCCccc-ccchhhHHHHHHHHHHHHHhc
Confidence 4677775 679999999999999997654 577777777777777666654
No 316
>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=21.20 E-value=73 Score=23.85 Aligned_cols=17 Identities=29% Similarity=0.429 Sum_probs=14.2
Q ss_pred hHHHhHHHHHHHHHHhC
Q 033029 39 WYYVRAASMARKIYLRQ 55 (129)
Q Consensus 39 W~Y~R~ASilR~lYl~g 55 (129)
=.+-|||.+||++|..-
T Consensus 43 EllCrAatvLr~~y~~h 59 (117)
T PF00727_consen 43 ELLCRAATVLRQFYSHH 59 (117)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred hhhhHHHHHHHHHHhcc
Confidence 35789999999999853
No 317
>PF03376 Adeno_E3B: Adenovirus E3B protein; InterPro: IPR005041 Adenoviruses are medium-sized, non-enveloped viruses containing double-stranded DNA. They can cause a variety of diseases including pneumonia, cystitis, conjunctivitis and diarrhoea, all of which can be fatal to patients who are immunocompromised []. These viruses have many mechanisms to evade the host immune response, including several proteins which are expressed as part of the early transcription unit 3 (E3) []. One of the regions of E3, known as the E3B region, encodes three proteins known as 10.4K, 14.5K and 14.7K. Two of these proteins, 10.4K and 14.5K, form the RID complex (receptor internalisation and degradation) which protects the infected cell from host-induced lysis by clearing the the TNF and Fas receptors from the cell surface []. Other receptors, such as the epidermal growth factor receptor, are also known to be cleared by RID []. This entry represents the E3B region 10.4K protein, also known as the RID alpha subunit.; GO: 0016020 membrane
Probab=21.04 E-value=45 Score=22.81 Aligned_cols=8 Identities=63% Similarity=1.065 Sum_probs=6.7
Q ss_pred chHHHhHH
Q 033029 38 DWYYVRAA 45 (129)
Q Consensus 38 DW~Y~R~A 45 (129)
||+|+|-|
T Consensus 41 Dy~~vR~~ 48 (67)
T PF03376_consen 41 DYIYVRIA 48 (67)
T ss_pred HHHHHHHH
Confidence 89999865
No 318
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.73 E-value=95 Score=24.79 Aligned_cols=26 Identities=15% Similarity=0.201 Sum_probs=21.6
Q ss_pred ccCCchhHHHHHHHHHHhCCceeecC
Q 033029 79 FCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 79 ~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
+++-|-..|+.||++||+.|+.+-..
T Consensus 63 ~R~Ls~~~i~~Il~~l~k~g~~e~~D 88 (174)
T KOG4068|consen 63 QRRLSQEFIDEILEELEKKGLAEPTD 88 (174)
T ss_pred hccCCHHHHHHHHHHHHHccCCcccc
Confidence 34567789999999999999998654
No 319
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=20.70 E-value=94 Score=24.91 Aligned_cols=71 Identities=23% Similarity=0.362 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHhcCCCCCCCCCCCchHHHhHHHHHHHHHH-hCCCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHH
Q 033029 13 HEFVKAYSAHLKRSGKFKELAPYDPDWYYVRAASMARKIYL-RQGLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHIL 91 (129)
Q Consensus 13 ~~fI~~~A~~LK~~gk~kE~aP~d~DW~Y~R~ASilR~lYl-~g~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~l 91 (129)
+.||+.+|+-...-|-.+- .-.|.=-+|+ +.|..++.++.+-|-.+- -+=.++
T Consensus 9 ~~~Ie~fae~m~r~G~nrt------------VG~iYgilyls~~Pmtl~Ei~E~lg~Sks--------------~vS~~l 62 (177)
T COG1510 9 DIFIEHFAETMSRWGINRT------------VGQIYGILYLSRKPLTLDEIAEALGMSKS--------------NVSMGL 62 (177)
T ss_pred HHHHHHHHHHHHHhCCcch------------HHHHhhhheecCCCccHHHHHHHHCCCcc--------------hHHHHH
Confidence 5677777777766553111 1234455799 889999999999887532 244678
Q ss_pred HHHHhCCceeecCC-CCce
Q 033029 92 QQLQNMNIIDIEPK-GGRR 109 (129)
Q Consensus 92 qqLE~~g~vek~~~-~GR~ 109 (129)
..||..++|++... |-|+
T Consensus 63 kkL~~~~lV~~~~~~G~Rk 81 (177)
T COG1510 63 KKLQDWNLVKKVFEKGDRK 81 (177)
T ss_pred HHHHhcchHHhhhccCcch
Confidence 99999999997653 3343
No 320
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=20.56 E-value=1e+02 Score=26.31 Aligned_cols=44 Identities=14% Similarity=0.147 Sum_probs=27.5
Q ss_pred HHHHHHHhCCCch--hhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC
Q 033029 47 MARKIYLRQGLGV--GSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP 104 (129)
Q Consensus 47 ilR~lYl~g~vGV--~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~ 104 (129)
|.-.|--.|.-|+ ..|++.=+ =.-+++.+||++||.-++|...+
T Consensus 89 vy~~I~~ag~~GIw~~~i~~~t~--------------l~~~~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 89 VYQLIEEAGNKGIWTKDIKKKTN--------------LHQTQLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHHTTT-EEHHHHHHHCT----------------HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHhCCCCCcHHHHHHHcC--------------CCHHHHHHHHHHHHhCCCEEEec
Confidence 4444445566555 45555421 12369999999999999998654
No 321
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=20.35 E-value=1.3e+02 Score=24.34 Aligned_cols=35 Identities=14% Similarity=0.239 Sum_probs=29.5
Q ss_pred HHHHHhCCceeec-CCCCceeCcchHhhHHHHHHHh
Q 033029 91 LQQLQNMNIIDIE-PKGGRRITSSGQRDLDQVAGRI 125 (129)
Q Consensus 91 lqqLE~~g~vek~-~~~GR~lT~~G~~~lD~iA~~i 125 (129)
-|=|.++|+|+.. .+|-..+.|.|...+++|-..|
T Consensus 7 ~~~l~~ag~~~~~~~~G~~~~lP~g~~i~~~I~~~i 42 (264)
T cd00772 7 LEHIGKAELADQGPGRGIINFLPLAKAILDKIENVL 42 (264)
T ss_pred HHHHHhcCCccccCCCCEEEECCcHHHHHHHHHHHH
Confidence 4668899999987 5788999999999999887665
No 322
>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=20.32 E-value=3.6e+02 Score=22.53 Aligned_cols=77 Identities=10% Similarity=0.199 Sum_probs=52.7
Q ss_pred hHHHHHHHHHHhC--CCchhhhHHHhcccCCCCCCCCcccCCchhHHHHHHHHHHhCCceeecC--CCCceeCcc-----
Q 033029 43 RAASMARKIYLRQ--GLGVGSFRRIYGGSKRNGSRPPHFCKSSGAIARHILQQLQNMNIIDIEP--KGGRRITSS----- 113 (129)
Q Consensus 43 R~ASilR~lYl~g--~vGV~~lr~~YGg~k~rG~~P~h~~~asg~iiR~~lqqLE~~g~vek~~--~~GR~lT~~----- 113 (129)
|...+.+.|-=++ -+.+..|+..|+..|-. - .-.=.||+.+|++ +.+|.|+..+ .||-+.+|.
T Consensus 6 r~~~~t~~l~~~p~~~~~l~~f~~~~~~aks~-----i--sed~~i~~~~~~~-~~~g~~~t~~ga~ggv~~~p~~~~~~ 77 (268)
T TIGR01743 6 RLVDLTNYLITNPNKLIPLNFFSERYESAKSS-----I--SEDIVIIKETFEK-FGIGKLLTVPGAAGGVKYIPKMSQAE 77 (268)
T ss_pred HHHHHHHHHHhCCCceEcHHHHHHHhccccch-----h--hhhHHHHHHHHHh-cCCceEEEeCCCCCCeEEEeCCCHHH
Confidence 4445555544444 48899999999987531 1 1123589999987 4689999887 368777764
Q ss_pred hHhhHHHHHHHhhh
Q 033029 114 GQRDLDQVAGRIVV 127 (129)
Q Consensus 114 G~~~lD~iA~~i~~ 127 (129)
.+.+|++++..+..
T Consensus 78 ~~~~~~~l~~~l~~ 91 (268)
T TIGR01743 78 AEEFVEELCQSLSE 91 (268)
T ss_pred HHHHHHHHHHHHHH
Confidence 67778888877654
No 323
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=20.31 E-value=1.3e+02 Score=25.51 Aligned_cols=32 Identities=25% Similarity=0.339 Sum_probs=23.6
Q ss_pred HHHHHHHhCCceeecCCCCceeCcchHhhHHH
Q 033029 89 HILQQLQNMNIIDIEPKGGRRITSSGQRDLDQ 120 (129)
Q Consensus 89 ~~lqqLE~~g~vek~~~~GR~lT~~G~~~lD~ 120 (129)
.=++.|-+.|+|++...+-..||.+|-..|-+
T Consensus 44 ehiK~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~ 75 (260)
T COG1497 44 EHIKELVKEGLIEKEGRGEYEITKKGAEWLLE 75 (260)
T ss_pred HHHHHHHhccceeecCCeeEEEehhHHHHHHH
Confidence 44789999999998533334799999866543
No 324
>KOG4226 consensus Adaptor protein NCK/Dock, contains SH2 and SH3 domains [Signal transduction mechanisms]
Probab=20.24 E-value=41 Score=29.34 Aligned_cols=18 Identities=33% Similarity=0.708 Sum_probs=14.5
Q ss_pred CCCCCCCCCchHHHhHHH
Q 033029 29 FKELAPYDPDWYYVRAAS 46 (129)
Q Consensus 29 ~kE~aP~d~DW~Y~R~AS 46 (129)
--|.|-.|||||--|-|+
T Consensus 218 ivd~Pe~DPdWwkarn~~ 235 (379)
T KOG4226|consen 218 IVDKPENDPDWWKARNAR 235 (379)
T ss_pred eccCCCCCchHHhhcccC
Confidence 457788999999887765
Done!