Query 031323
Match_columns 161
No_of_seqs 118 out of 517
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 12:28:55 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031323.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031323hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3250 COP9 signalosome, subu 100.0 2.6E-36 5.7E-41 239.7 9.5 159 1-160 1-159 (258)
2 KOG2753 Uncharacterized conser 100.0 1.9E-33 4.1E-38 235.1 9.4 149 8-161 185-344 (378)
3 KOG2908 26S proteasome regulat 100.0 8.3E-32 1.8E-36 226.0 11.4 147 13-161 182-344 (380)
4 PF01399 PCI: PCI domain; Int 99.6 1.5E-15 3.3E-20 106.7 7.7 95 60-156 1-105 (105)
5 smart00753 PAM PCI/PINT associ 99.4 6.8E-13 1.5E-17 91.7 7.5 70 89-160 4-73 (88)
6 smart00088 PINT motif in prote 99.4 6.8E-13 1.5E-17 91.7 7.5 70 89-160 4-73 (88)
7 KOG1464 COP9 signalosome, subu 97.7 0.00012 2.7E-09 61.7 7.3 92 61-154 306-407 (440)
8 KOG2581 26S proteasome regulat 97.6 0.00026 5.6E-09 62.1 7.6 92 60-152 319-419 (493)
9 KOG2688 Transcription-associat 96.0 0.019 4E-07 50.3 6.3 97 61-158 273-386 (394)
10 KOG2758 Translation initiation 95.8 0.016 3.5E-07 49.9 4.9 66 89-156 329-394 (432)
11 KOG0686 COP9 signalosome, subu 95.3 0.14 3.1E-06 45.2 9.2 97 61-159 307-413 (466)
12 KOG1497 COP9 signalosome, subu 95.3 0.075 1.6E-06 45.7 7.3 127 26-156 228-362 (399)
13 COG5600 Transcription-associat 95.0 0.059 1.3E-06 47.0 5.8 99 60-159 289-406 (413)
14 KOG2582 COP9 signalosome, subu 93.1 0.4 8.6E-06 42.0 7.1 90 61-154 260-358 (422)
15 PF09012 FeoC: FeoC like trans 92.5 0.17 3.7E-06 33.2 3.3 47 99-147 4-50 (69)
16 PF09756 DDRGK: DDRGK domain; 92.3 0.4 8.6E-06 38.1 5.7 59 96-156 100-158 (188)
17 PF10075 PCI_Csn8: COP9 signal 91.5 1.4 3.1E-05 32.7 7.7 108 24-132 5-119 (143)
18 PF02082 Rrf2: Transcriptional 90.7 0.8 1.7E-05 30.9 5.2 37 106-144 22-58 (83)
19 KOG1463 26S proteasome regulat 88.8 0.66 1.4E-05 40.4 4.3 101 54-156 280-390 (411)
20 PRK14165 winged helix-turn-hel 88.0 2.4 5.2E-05 34.4 6.9 62 93-156 5-66 (217)
21 PF13412 HTH_24: Winged helix- 87.5 2.2 4.7E-05 25.5 5.0 41 100-142 8-48 (48)
22 TIGR02010 IscR iron-sulfur clu 86.7 2.1 4.5E-05 31.6 5.5 45 97-143 11-57 (135)
23 KOG1498 26S proteasome regulat 86.7 1.7 3.7E-05 38.4 5.7 124 31-158 260-400 (439)
24 KOG0687 26S proteasome regulat 86.1 1.4 2.9E-05 38.3 4.7 109 45-156 243-362 (393)
25 PF13730 HTH_36: Helix-turn-he 84.9 4.2 9.1E-05 24.9 5.5 47 93-141 7-55 (55)
26 PF07389 DUF1500: Protein of u 84.6 1.5 3.3E-05 30.8 3.5 35 103-140 42-76 (100)
27 PRK11179 DNA-binding transcrip 84.5 2.4 5.2E-05 31.9 5.0 45 101-147 15-62 (153)
28 smart00346 HTH_ICLR helix_turn 83.6 3.8 8.2E-05 27.4 5.3 47 96-144 6-53 (91)
29 TIGR00738 rrf2_super rrf2 fami 83.4 3.4 7.4E-05 29.8 5.3 48 95-144 11-58 (132)
30 PF09339 HTH_IclR: IclR helix- 82.8 3.8 8.3E-05 25.0 4.6 45 96-142 4-49 (52)
31 KOG3054 Uncharacterized conser 82.6 3.4 7.4E-05 34.4 5.4 54 100-155 205-258 (299)
32 smart00344 HTH_ASNC helix_turn 82.5 3.3 7.1E-05 28.8 4.7 36 106-143 14-49 (108)
33 PRK10857 DNA-binding transcrip 82.4 3.5 7.5E-05 31.8 5.2 45 97-143 11-57 (164)
34 COG1522 Lrp Transcriptional re 80.3 4.1 8.9E-05 30.0 4.8 37 106-144 19-55 (154)
35 PF01726 LexA_DNA_bind: LexA D 79.7 6.4 0.00014 25.7 5.0 36 106-142 22-57 (65)
36 COG5159 RPN6 26S proteasome re 79.6 3.5 7.6E-05 35.5 4.6 95 60-156 284-388 (421)
37 COG1959 Predicted transcriptio 78.3 6.8 0.00015 29.7 5.5 46 97-144 11-58 (150)
38 PRK11169 leucine-responsive tr 78.0 5.8 0.00012 30.2 5.1 42 100-143 19-60 (164)
39 TIGR02944 suf_reg_Xantho FeS a 77.5 7.1 0.00015 28.3 5.3 36 107-144 23-58 (130)
40 PF12840 HTH_20: Helix-turn-he 76.9 8.1 0.00017 24.3 4.8 46 94-144 12-57 (61)
41 cd00090 HTH_ARSR Arsenical Res 76.6 15 0.00032 22.6 6.3 36 110-147 21-56 (78)
42 PF08784 RPA_C: Replication pr 76.2 7 0.00015 27.2 4.8 52 94-147 49-101 (102)
43 PRK11920 rirA iron-responsive 75.9 8.6 0.00019 29.1 5.5 45 98-144 12-57 (153)
44 PF08280 HTH_Mga: M protein tr 75.6 4.4 9.6E-05 25.6 3.3 34 96-130 6-39 (59)
45 KOG2072 Translation initiation 75.5 5.6 0.00012 38.3 5.1 63 92-155 429-492 (988)
46 PF08281 Sigma70_r4_2: Sigma-7 75.3 4.3 9.3E-05 24.7 3.1 26 109-136 26-51 (54)
47 smart00550 Zalpha Z-DNA-bindin 75.3 8 0.00017 25.2 4.6 45 95-143 9-54 (68)
48 PF14947 HTH_45: Winged helix- 74.9 14 0.00029 24.6 5.7 50 99-155 10-59 (77)
49 PF01325 Fe_dep_repress: Iron 74.2 12 0.00026 23.9 5.1 44 97-142 10-53 (60)
50 smart00347 HTH_MARR helix_turn 73.2 23 0.0005 23.4 6.7 44 107-152 22-65 (101)
51 PF04539 Sigma70_r3: Sigma-70 72.2 10 0.00022 24.8 4.6 26 106-132 17-42 (78)
52 PF13518 HTH_28: Helix-turn-he 72.0 9 0.00019 22.8 3.9 38 98-139 3-40 (52)
53 PF01022 HTH_5: Bacterial regu 71.8 14 0.0003 22.1 4.7 33 108-142 14-46 (47)
54 TIGR02337 HpaR homoprotocatech 71.7 22 0.00048 25.1 6.6 47 106-154 39-85 (118)
55 PF13404 HTH_AsnC-type: AsnC-t 71.6 5 0.00011 23.9 2.7 29 100-129 8-36 (42)
56 PF08220 HTH_DeoR: DeoR-like h 70.5 11 0.00023 23.7 4.2 41 99-141 4-44 (57)
57 PF03979 Sigma70_r1_1: Sigma-7 69.4 7.6 0.00017 26.3 3.5 40 99-140 11-53 (82)
58 PF13601 HTH_34: Winged helix 69.0 21 0.00046 24.0 5.6 50 99-150 4-53 (80)
59 PRK11014 transcriptional repre 68.5 15 0.00032 27.2 5.2 37 106-144 22-58 (141)
60 COG5071 RPN5 26S proteasome re 67.0 13 0.00028 32.3 5.1 48 107-156 351-398 (439)
61 PF12802 MarR_2: MarR family; 65.6 28 0.00062 21.3 6.0 40 109-150 21-60 (62)
62 PF08279 HTH_11: HTH domain; 65.5 27 0.00058 21.1 5.2 41 97-139 2-43 (55)
63 PF01978 TrmB: Sugar-specific 65.5 9 0.00019 24.5 3.1 38 106-145 19-56 (68)
64 smart00420 HTH_DEOR helix_turn 65.5 24 0.00053 20.4 5.4 37 106-144 11-47 (53)
65 PRK09954 putative kinase; Prov 65.1 12 0.00027 31.6 4.8 53 100-154 8-63 (362)
66 PF01047 MarR: MarR family; I 65.0 20 0.00044 21.9 4.6 43 106-150 14-56 (59)
67 PRK03573 transcriptional regul 64.5 33 0.00072 25.0 6.4 58 100-159 37-94 (144)
68 smart00345 HTH_GNTR helix_turn 64.3 28 0.00061 20.8 5.2 34 107-142 17-51 (60)
69 smart00419 HTH_CRP helix_turn_ 64.2 25 0.00055 20.2 5.0 33 109-143 8-40 (48)
70 PRK10265 chaperone-modulator p 62.7 4 8.6E-05 28.9 1.1 37 105-147 3-39 (101)
71 PHA02763 hypothetical protein; 62.2 9.8 0.00021 26.7 2.9 50 109-161 52-101 (102)
72 KOG1076 Translation initiation 62.0 11 0.00025 35.7 4.1 116 42-159 634-766 (843)
73 smart00418 HTH_ARSR helix_turn 61.9 31 0.00068 20.4 5.7 38 107-146 8-45 (66)
74 TIGR01884 cas_HTH CRISPR locus 60.9 40 0.00086 26.4 6.6 47 106-155 154-200 (203)
75 cd00092 HTH_CRP helix_turn_hel 59.0 22 0.00049 22.0 4.1 35 107-143 23-57 (67)
76 COG5187 RPN7 26S proteasome re 58.5 16 0.00034 31.6 4.1 63 92-156 314-376 (412)
77 PF04545 Sigma70_r4: Sigma-70, 57.9 20 0.00042 21.5 3.5 29 107-137 18-46 (50)
78 PF05331 DUF742: Protein of un 57.5 23 0.0005 25.8 4.4 42 99-144 47-88 (114)
79 PF13463 HTH_27: Winged helix 57.2 45 0.00096 20.7 5.8 47 103-151 12-58 (68)
80 PF06163 DUF977: Bacterial pro 56.3 28 0.0006 26.0 4.6 51 88-141 6-56 (127)
81 PRK15090 DNA-binding transcrip 55.7 30 0.00066 27.9 5.3 46 96-143 15-60 (257)
82 PF13591 MerR_2: MerR HTH fami 53.9 22 0.00048 24.1 3.6 32 110-147 1-32 (84)
83 cd07377 WHTH_GntR Winged helix 53.6 49 0.0011 20.1 5.7 35 106-142 21-56 (66)
84 TIGR03879 near_KaiC_dom probab 53.2 22 0.00048 24.0 3.4 30 108-139 31-60 (73)
85 PF09202 Rio2_N: Rio2, N-termi 53.0 38 0.00083 23.1 4.6 50 94-145 8-58 (82)
86 COG1595 RpoE DNA-directed RNA 52.7 17 0.00037 27.6 3.2 28 107-136 141-168 (182)
87 COG1339 Transcriptional regula 52.2 49 0.0011 26.8 5.7 59 94-155 5-63 (214)
88 PF04703 FaeA: FaeA-like prote 51.6 31 0.00068 22.4 3.8 34 107-142 13-46 (62)
89 PF13542 HTH_Tnp_ISL3: Helix-t 51.4 28 0.0006 20.8 3.5 31 99-132 19-49 (52)
90 PRK15418 transcriptional regul 51.2 29 0.00062 29.5 4.6 39 108-148 28-66 (318)
91 PF14394 DUF4423: Domain of un 50.4 36 0.00078 26.3 4.7 33 110-144 40-74 (171)
92 PHA02943 hypothetical protein; 50.2 52 0.0011 25.5 5.4 44 93-142 12-55 (165)
93 PF02002 TFIIE_alpha: TFIIE al 49.7 27 0.00059 24.3 3.7 36 107-144 25-60 (105)
94 PF03399 SAC3_GANP: SAC3/GANP/ 49.6 81 0.0017 24.1 6.6 61 60-120 136-203 (204)
95 PRK12537 RNA polymerase sigma 49.2 20 0.00044 27.1 3.1 27 108-136 148-174 (182)
96 PF10668 Phage_terminase: Phag 48.4 22 0.00047 23.1 2.7 24 106-130 19-42 (60)
97 cd06445 ATase The DNA repair p 48.1 21 0.00045 23.9 2.7 30 98-127 6-36 (79)
98 KOG3431 Apoptosis-related prot 47.9 12 0.00026 27.8 1.6 23 124-147 69-91 (129)
99 PRK10411 DNA-binding transcrip 47.7 46 0.00099 27.0 5.1 46 95-142 4-49 (240)
100 TIGR02431 pcaR_pcaU beta-ketoa 47.2 51 0.0011 26.4 5.3 45 96-142 10-55 (248)
101 PF13384 HTH_23: Homeodomain-l 46.7 21 0.00046 21.1 2.3 23 109-132 17-39 (50)
102 TIGR02999 Sig-70_X6 RNA polyme 45.9 26 0.00056 26.3 3.2 27 108-136 149-175 (183)
103 PRK12523 RNA polymerase sigma 45.8 27 0.00059 26.1 3.3 28 108-137 134-161 (172)
104 PRK10870 transcriptional repre 45.4 1.1E+02 0.0023 23.5 6.7 51 106-158 68-118 (176)
105 PF04218 CENP-B_N: CENP-B N-te 45.0 37 0.0008 21.0 3.3 33 93-131 11-43 (53)
106 PF04967 HTH_10: HTH DNA bindi 45.0 77 0.0017 19.9 5.3 28 106-135 20-47 (53)
107 PRK09642 RNA polymerase sigma 44.1 29 0.00063 25.4 3.2 27 108-136 121-147 (160)
108 PRK11512 DNA-binding transcrip 44.0 1.1E+02 0.0025 22.2 6.4 51 107-159 52-102 (144)
109 COG2390 DeoR Transcriptional r 43.1 40 0.00087 28.9 4.3 37 109-147 26-62 (321)
110 PRK06759 RNA polymerase factor 43.0 33 0.00071 24.9 3.3 27 108-136 121-147 (154)
111 PRK09047 RNA polymerase factor 42.6 32 0.00069 25.1 3.2 27 108-136 121-147 (161)
112 PRK12529 RNA polymerase sigma 42.3 33 0.00071 25.9 3.3 27 108-136 142-168 (178)
113 PRK09651 RNA polymerase sigma 42.3 33 0.00072 25.7 3.4 28 107-136 133-160 (172)
114 PRK10163 DNA-binding transcrip 42.0 69 0.0015 26.2 5.4 54 96-153 26-80 (271)
115 PF10007 DUF2250: Uncharacteri 42.0 36 0.00077 23.9 3.2 27 114-142 26-52 (92)
116 smart00421 HTH_LUXR helix_turn 41.9 45 0.00097 19.4 3.3 24 110-135 19-42 (58)
117 COG2963 Transposase and inacti 41.7 62 0.0013 22.7 4.5 42 98-142 14-56 (116)
118 PF05491 RuvB_C: Holliday junc 41.5 53 0.0012 22.3 3.8 41 97-142 13-57 (76)
119 PRK12520 RNA polymerase sigma 41.5 32 0.0007 26.1 3.2 26 108-135 146-171 (191)
120 COG3355 Predicted transcriptio 41.5 64 0.0014 24.0 4.6 36 106-143 39-74 (126)
121 PF10975 DUF2802: Protein of u 41.0 31 0.00068 22.9 2.6 21 110-131 45-65 (70)
122 PRK10046 dpiA two-component re 40.8 57 0.0012 25.4 4.6 36 109-146 177-212 (225)
123 PRK09802 DNA-binding transcrip 40.6 61 0.0013 26.7 4.9 48 93-142 15-62 (269)
124 PRK13509 transcriptional repre 40.2 63 0.0014 26.3 4.9 47 95-143 5-51 (251)
125 PRK12543 RNA polymerase sigma 40.0 37 0.0008 25.5 3.3 27 108-136 132-158 (179)
126 PRK12525 RNA polymerase sigma 39.9 37 0.00079 25.3 3.2 28 108-137 133-160 (168)
127 PF09940 DUF2172: Domain of un 39.8 39 0.00085 29.8 3.7 47 92-142 340-386 (386)
128 PRK07037 extracytoplasmic-func 39.8 39 0.00084 24.8 3.3 27 108-136 124-150 (163)
129 PRK12514 RNA polymerase sigma 39.7 36 0.00078 25.5 3.2 26 109-136 145-170 (179)
130 cd06170 LuxR_C_like C-terminal 39.3 52 0.0011 19.2 3.3 25 109-135 15-39 (57)
131 PRK12527 RNA polymerase sigma 39.3 40 0.00088 24.7 3.3 27 108-136 120-146 (159)
132 TIGR02983 SigE-fam_strep RNA p 39.0 39 0.00084 24.7 3.2 27 108-136 125-151 (162)
133 TIGR02947 SigH_actino RNA poly 38.7 37 0.00081 25.8 3.2 27 108-136 146-172 (193)
134 PRK11569 transcriptional repre 38.6 81 0.0018 25.8 5.3 45 96-142 29-74 (274)
135 PRK12547 RNA polymerase sigma 38.5 40 0.00087 25.0 3.2 27 108-136 127-153 (164)
136 PRK10430 DNA-binding transcrip 37.8 98 0.0021 24.2 5.5 38 107-146 176-213 (239)
137 PRK13505 formate--tetrahydrofo 37.7 29 0.00063 32.1 2.7 55 101-159 6-65 (557)
138 PRK10434 srlR DNA-bindng trans 37.7 69 0.0015 26.1 4.8 45 95-141 5-49 (256)
139 PF06056 Terminase_5: Putative 37.2 40 0.00087 21.4 2.6 23 109-132 13-35 (58)
140 PRK12513 RNA polymerase sigma 37.1 44 0.00094 25.4 3.3 27 108-136 154-180 (194)
141 PRK12528 RNA polymerase sigma 36.7 47 0.001 24.4 3.3 27 108-136 128-154 (161)
142 PF02796 HTH_7: Helix-turn-hel 36.4 64 0.0014 19.0 3.3 24 103-129 17-40 (45)
143 PRK12530 RNA polymerase sigma 35.5 46 0.001 25.4 3.2 27 108-136 149-175 (189)
144 PF05920 Homeobox_KN: Homeobox 35.2 50 0.0011 19.4 2.6 21 113-135 17-37 (40)
145 COG1414 IclR Transcriptional r 35.2 1E+02 0.0022 25.0 5.3 44 97-142 6-50 (246)
146 PRK09646 RNA polymerase sigma 35.2 48 0.001 25.3 3.3 26 108-135 157-182 (194)
147 PRK09647 RNA polymerase sigma 35.1 48 0.001 25.9 3.3 27 108-136 153-179 (203)
148 PRK08301 sporulation sigma fac 35.1 49 0.0011 26.1 3.4 27 108-136 197-223 (234)
149 PRK12522 RNA polymerase sigma 35.1 48 0.001 24.7 3.2 27 108-136 134-160 (173)
150 PRK12511 RNA polymerase sigma 35.0 47 0.001 25.3 3.2 27 108-136 126-152 (182)
151 PRK09645 RNA polymerase sigma 34.5 49 0.0011 24.5 3.2 27 108-136 133-159 (173)
152 PRK04239 hypothetical protein; 34.2 23 0.00049 25.8 1.2 23 124-147 66-88 (110)
153 PF00046 Homeobox: Homeobox do 34.0 45 0.00097 20.2 2.4 23 109-132 27-49 (57)
154 PRK12545 RNA polymerase sigma 33.7 50 0.0011 25.5 3.2 26 108-135 154-179 (201)
155 TIGR02702 SufR_cyano iron-sulf 33.6 1.8E+02 0.004 22.6 6.5 37 107-145 13-49 (203)
156 PRK12536 RNA polymerase sigma 33.6 52 0.0011 24.8 3.2 27 108-136 144-170 (181)
157 PF01984 dsDNA_bind: Double-st 33.5 23 0.0005 25.5 1.2 23 124-147 61-83 (107)
158 PRK12540 RNA polymerase sigma 33.4 52 0.0011 25.1 3.2 27 108-136 126-152 (182)
159 PRK12512 RNA polymerase sigma 32.9 54 0.0012 24.6 3.2 27 108-136 146-172 (184)
160 PRK04214 rbn ribonuclease BN/u 32.6 1.1E+02 0.0025 26.7 5.6 35 106-142 307-341 (412)
161 TIGR02952 Sig70_famx2 RNA poly 32.5 56 0.0012 23.9 3.2 27 108-136 137-163 (170)
162 PRK12519 RNA polymerase sigma 32.3 58 0.0013 24.6 3.3 27 108-136 156-182 (194)
163 PRK13919 putative RNA polymera 32.2 55 0.0012 24.5 3.2 26 108-135 150-175 (186)
164 TIGR02939 RpoE_Sigma70 RNA pol 32.1 56 0.0012 24.4 3.2 26 108-135 153-178 (190)
165 PF13545 HTH_Crp_2: Crp-like h 32.0 1.1E+02 0.0025 19.3 4.3 42 108-155 27-68 (76)
166 PRK12516 RNA polymerase sigma 31.9 59 0.0013 24.9 3.3 27 108-136 131-157 (187)
167 PRK12539 RNA polymerase sigma 31.9 56 0.0012 24.7 3.2 27 108-136 146-172 (184)
168 PF08221 HTH_9: RNA polymerase 31.7 98 0.0021 19.7 3.8 36 106-143 24-59 (62)
169 TIGR02950 SigM_subfam RNA poly 31.6 60 0.0013 23.3 3.2 26 108-135 120-145 (154)
170 PF09743 DUF2042: Uncharacteri 31.5 70 0.0015 26.7 3.9 41 106-148 127-167 (272)
171 PRK12533 RNA polymerase sigma 31.4 60 0.0013 25.7 3.3 26 108-135 149-174 (216)
172 TIGR02943 Sig70_famx1 RNA poly 31.2 60 0.0013 24.8 3.2 26 108-135 146-171 (188)
173 PF13936 HTH_38: Helix-turn-he 31.2 86 0.0019 18.4 3.3 21 109-130 20-40 (44)
174 PRK09649 RNA polymerase sigma 31.2 60 0.0013 24.7 3.2 26 108-135 145-170 (185)
175 PRK09652 RNA polymerase sigma 30.9 65 0.0014 23.6 3.3 27 108-136 143-169 (182)
176 PF13022 HTH_Tnp_1_2: Helix-tu 30.8 1.3E+02 0.0027 23.0 4.8 44 86-130 10-54 (142)
177 cd04762 HTH_MerR-trunc Helix-T 30.6 63 0.0014 18.1 2.6 29 110-144 1-29 (49)
178 PF00325 Crp: Bacterial regula 30.5 99 0.0022 17.4 3.2 30 110-141 3-32 (32)
179 PRK12517 RNA polymerase sigma 30.1 64 0.0014 24.7 3.2 27 108-136 143-169 (188)
180 PF12324 HTH_15: Helix-turn-he 30.1 1E+02 0.0023 21.0 3.8 34 98-132 27-60 (77)
181 TIGR03001 Sig-70_gmx1 RNA poly 30.1 60 0.0013 26.3 3.2 27 108-136 176-202 (244)
182 cd06171 Sigma70_r4 Sigma70, re 29.8 99 0.0021 17.3 3.4 26 108-135 25-50 (55)
183 PRK12542 RNA polymerase sigma 29.7 66 0.0014 24.2 3.2 26 108-135 137-162 (185)
184 PRK10906 DNA-binding transcrip 29.6 1E+02 0.0022 25.1 4.5 47 94-142 4-50 (252)
185 PRK06704 RNA polymerase factor 29.5 63 0.0014 26.1 3.2 25 109-135 132-156 (228)
186 TIGR02787 codY_Gpos GTP-sensin 29.4 2.1E+02 0.0046 23.8 6.2 36 107-144 196-231 (251)
187 PRK12524 RNA polymerase sigma 29.3 65 0.0014 24.6 3.2 26 108-135 151-176 (196)
188 PRK12535 RNA polymerase sigma 29.2 66 0.0014 24.8 3.2 24 108-132 148-171 (196)
189 PF12728 HTH_17: Helix-turn-he 28.9 68 0.0015 19.0 2.6 29 110-144 2-30 (51)
190 TIGR02846 spore_sigmaK RNA pol 28.6 70 0.0015 25.3 3.3 27 108-136 193-219 (227)
191 PRK09638 RNA polymerase sigma 28.3 74 0.0016 23.5 3.3 27 108-136 141-167 (176)
192 TIGR02954 Sig70_famx3 RNA poly 28.2 76 0.0017 23.4 3.3 27 108-136 134-160 (169)
193 PF00888 Cullin: Cullin family 28.2 57 0.0012 29.2 3.0 43 98-142 523-565 (588)
194 PRK03902 manganese transport t 27.7 1.6E+02 0.0034 21.5 4.9 41 100-142 13-53 (142)
195 COG2524 Predicted transcriptio 27.4 1.6E+02 0.0035 25.0 5.2 52 92-145 7-59 (294)
196 PF06627 DUF1153: Protein of u 27.2 69 0.0015 22.5 2.6 30 106-138 46-75 (90)
197 PRK11050 manganese transport r 27.2 1.8E+02 0.0038 21.7 5.1 43 100-144 42-84 (152)
198 PRK10100 DNA-binding transcrip 27.1 1.4E+02 0.0029 23.7 4.7 34 99-136 162-195 (216)
199 TIGR02844 spore_III_D sporulat 27.1 99 0.0021 21.0 3.4 31 96-128 7-37 (80)
200 TIGR02835 spore_sigmaE RNA pol 27.0 80 0.0017 25.0 3.4 26 108-135 197-222 (234)
201 TIGR02989 Sig-70_gvs1 RNA poly 27.0 81 0.0018 22.8 3.2 26 108-135 126-151 (159)
202 PRK09640 RNA polymerase sigma 26.8 83 0.0018 23.8 3.3 27 108-136 149-175 (188)
203 PF01035 DNA_binding_1: 6-O-me 26.6 52 0.0011 22.3 1.9 25 98-122 8-32 (85)
204 TIGR01610 phage_O_Nterm phage 26.5 2.2E+02 0.0047 19.5 5.7 46 106-155 44-89 (95)
205 PRK12532 RNA polymerase sigma 26.5 84 0.0018 23.9 3.3 26 108-135 151-176 (195)
206 PRK12534 RNA polymerase sigma 26.4 79 0.0017 23.7 3.1 26 108-135 152-177 (187)
207 TIGR03209 P21_Cbot clostridium 26.4 47 0.001 23.8 1.8 19 108-127 122-140 (142)
208 TIGR02960 SigX5 RNA polymerase 26.4 75 0.0016 26.2 3.2 27 108-136 157-183 (324)
209 PRK05602 RNA polymerase sigma 26.4 81 0.0018 23.7 3.2 26 108-135 143-168 (186)
210 PRK12518 RNA polymerase sigma 26.4 85 0.0018 23.2 3.3 26 108-135 135-160 (175)
211 PF14493 HTH_40: Helix-turn-he 26.3 1E+02 0.0022 20.8 3.4 30 109-140 13-42 (91)
212 PF10924 DUF2711: Protein of u 26.3 1E+02 0.0023 25.1 3.9 34 103-137 49-82 (217)
213 PRK00215 LexA repressor; Valid 26.1 3.1E+02 0.0066 21.1 7.7 47 105-154 19-66 (205)
214 COG2345 Predicted transcriptio 26.0 1.7E+02 0.0037 23.8 5.1 42 102-145 18-59 (218)
215 PRK12526 RNA polymerase sigma 25.7 87 0.0019 24.2 3.3 27 108-136 168-194 (206)
216 PRK09648 RNA polymerase sigma 25.6 87 0.0019 23.6 3.2 27 108-136 154-180 (189)
217 PRK12531 RNA polymerase sigma 25.5 89 0.0019 23.8 3.3 27 108-136 156-182 (194)
218 TIGR00589 ogt O-6-methylguanin 25.2 85 0.0018 21.2 2.8 25 98-122 8-32 (80)
219 PRK09834 DNA-binding transcrip 25.0 1.8E+02 0.004 23.5 5.2 46 96-143 12-58 (263)
220 PRK11924 RNA polymerase sigma 24.8 96 0.0021 22.6 3.3 27 108-136 140-166 (179)
221 PRK15411 rcsA colanic acid cap 24.8 1.6E+02 0.0035 22.9 4.7 30 100-132 145-174 (207)
222 cd00086 homeodomain Homeodomai 24.6 80 0.0017 18.8 2.4 22 110-132 28-49 (59)
223 TIGR02997 Sig70-cyanoRpoD RNA 24.5 1.3E+02 0.0029 24.9 4.4 29 107-137 267-295 (298)
224 PF10078 DUF2316: Uncharacteri 24.5 83 0.0018 22.0 2.6 23 107-130 21-43 (89)
225 COG1846 MarR Transcriptional r 24.2 2.3E+02 0.0049 18.9 6.1 44 113-158 40-83 (126)
226 COG1321 TroR Mn-dependent tran 24.2 2E+02 0.0044 21.8 5.0 43 99-143 14-56 (154)
227 PRK12544 RNA polymerase sigma 24.2 92 0.002 24.3 3.2 26 108-135 163-188 (206)
228 TIGR02393 RpoD_Cterm RNA polym 24.1 1.8E+02 0.0039 23.1 4.9 28 107-136 194-221 (238)
229 PRK09639 RNA polymerase sigma 24.0 1E+02 0.0023 22.4 3.3 27 108-136 126-152 (166)
230 COG1497 Predicted transcriptio 23.8 2.1E+02 0.0046 23.9 5.3 47 93-143 11-57 (260)
231 PRK04217 hypothetical protein; 23.7 1E+02 0.0023 22.2 3.1 38 109-147 58-101 (110)
232 PRK15431 ferrous iron transpor 23.6 2.5E+02 0.0054 19.2 4.8 39 104-144 11-49 (78)
233 PRK09636 RNA polymerase sigma 23.5 92 0.002 25.6 3.2 26 108-135 130-155 (293)
234 PRK06986 fliA flagellar biosyn 23.3 1E+02 0.0022 24.4 3.3 27 108-136 199-225 (236)
235 PRK09415 RNA polymerase factor 23.3 1.1E+02 0.0023 23.0 3.3 26 108-135 142-167 (179)
236 PRK09644 RNA polymerase sigma 23.1 1E+02 0.0023 22.6 3.2 26 108-135 123-148 (165)
237 TIGR01764 excise DNA binding d 23.1 1.5E+02 0.0033 16.6 4.7 30 110-145 2-31 (49)
238 TIGR03643 conserved hypothetic 23.1 1.6E+02 0.0035 19.8 3.7 27 100-128 5-31 (72)
239 PRK00118 putative DNA-binding 22.9 1.2E+02 0.0026 21.6 3.3 25 109-135 33-57 (104)
240 PRK09191 two-component respons 22.9 1E+02 0.0023 24.0 3.3 27 108-136 103-129 (261)
241 TIGR02985 Sig70_bacteroi1 RNA 22.8 1.1E+02 0.0025 21.7 3.3 26 108-135 128-153 (161)
242 PF04297 UPF0122: Putative hel 22.7 1E+02 0.0022 22.0 2.9 27 107-135 31-57 (101)
243 PRK12538 RNA polymerase sigma 22.6 99 0.0021 24.7 3.1 27 108-136 186-212 (233)
244 PRK11923 algU RNA polymerase s 22.5 1.1E+02 0.0024 23.0 3.3 26 108-135 153-178 (193)
245 PRK15201 fimbriae regulatory p 22.4 2.1E+02 0.0044 23.0 4.7 31 99-132 140-170 (198)
246 PRK13239 alkylmercury lyase; P 22.4 1.5E+02 0.0033 23.8 4.2 47 98-151 25-71 (206)
247 PF00392 GntR: Bacterial regul 22.2 2.1E+02 0.0045 17.8 4.3 37 106-144 20-57 (64)
248 PF10985 DUF2805: Protein of u 22.1 1.7E+02 0.0036 19.8 3.6 27 100-128 4-30 (73)
249 PRK07405 RNA polymerase sigma 22.0 1.6E+02 0.0034 24.9 4.4 28 107-136 274-301 (317)
250 PF12833 HTH_18: Helix-turn-he 22.0 2.2E+02 0.0047 18.2 4.3 40 92-131 28-67 (81)
251 TIGR02394 rpoS_proteo RNA poly 21.9 1.9E+02 0.0042 23.7 4.8 28 107-136 240-267 (285)
252 COG1349 GlpR Transcriptional r 21.9 1.6E+02 0.0034 24.0 4.2 47 94-142 4-50 (253)
253 COG2901 Fis Factor for inversi 21.8 1.7E+02 0.0038 20.6 3.8 33 5-37 29-61 (98)
254 COG2118 DNA-binding protein [G 21.7 54 0.0012 24.1 1.3 23 124-147 69-91 (116)
255 PRK12546 RNA polymerase sigma 21.6 1.2E+02 0.0026 23.3 3.3 26 108-135 128-153 (188)
256 smart00389 HOX Homeodomain. DN 21.4 1.1E+02 0.0025 18.0 2.6 22 110-132 28-49 (56)
257 PF02186 TFIIE_beta: TFIIE bet 21.4 1.9E+02 0.0042 18.7 3.8 27 106-132 17-43 (65)
258 TIGR00498 lexA SOS regulatory 21.3 3.8E+02 0.0082 20.5 6.5 47 106-154 22-68 (199)
259 PRK06811 RNA polymerase factor 21.3 2.4E+02 0.0053 21.2 5.0 26 108-135 146-171 (189)
260 TIGR02948 SigW_bacill RNA poly 21.3 1.2E+02 0.0027 22.4 3.3 26 108-135 151-176 (187)
261 PRK06266 transcription initiat 21.2 2.4E+02 0.0052 21.9 5.0 38 106-145 33-70 (178)
262 COG3413 Predicted DNA binding 21.2 2.2E+02 0.0047 22.3 4.8 80 61-143 127-209 (215)
263 COG4565 CitB Response regulato 21.0 2.3E+02 0.005 23.2 4.9 39 106-146 170-208 (224)
264 PRK09641 RNA polymerase sigma 20.9 1.3E+02 0.0028 22.4 3.3 26 108-135 151-176 (187)
265 TIGR02959 SigZ RNA polymerase 20.8 1.3E+02 0.0028 22.4 3.3 24 108-132 115-138 (170)
266 TIGR02859 spore_sigH RNA polym 20.8 1.3E+02 0.0028 22.7 3.3 26 108-135 164-189 (198)
267 PRK12515 RNA polymerase sigma 20.7 1.3E+02 0.0028 22.7 3.3 26 108-135 146-171 (189)
268 PRK09643 RNA polymerase sigma 20.7 1.2E+02 0.0026 23.1 3.2 26 108-135 149-174 (192)
269 PRK10840 transcriptional regul 20.5 2.3E+02 0.0049 21.5 4.7 22 110-132 166-187 (216)
270 TIGR02937 sigma70-ECF RNA poly 20.5 1.4E+02 0.0031 20.5 3.3 26 108-135 125-150 (158)
271 PF02406 MmoB_DmpM: MmoB/DmpM 20.2 1.2E+02 0.0027 20.9 2.8 43 108-156 45-87 (87)
272 PRK10141 DNA-binding transcrip 20.2 3.5E+02 0.0075 19.6 6.1 56 94-154 18-73 (117)
273 PRK06930 positive control sigm 20.1 1.3E+02 0.0028 23.1 3.2 26 108-135 129-154 (170)
274 PRK12541 RNA polymerase sigma 20.1 1.3E+02 0.0029 21.9 3.2 26 108-135 127-152 (161)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=2.6e-36 Score=239.71 Aligned_cols=159 Identities=47% Similarity=0.714 Sum_probs=156.0
Q ss_pred CcHhHHHHHHHHHHHHHhcccchHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhc
Q 031323 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (161)
Q Consensus 1 ~~~~~~~~~~l~~~l~~~~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~ 80 (161)
||+++.+.+-+|.|+.+++..++++...+|..|+.+|++|.|+|||.+|+|..|..+.++.++.||++|++|||.||.++
T Consensus 1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae 80 (258)
T KOG3250|consen 1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE 80 (258)
T ss_pred CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999998888999999999999999999998
Q ss_pred cCCCCCCCHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR 160 (161)
Q Consensus 81 ~~~~~~L~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R 160 (161)
...+|.|++.++.||+.||+.++|+..+.++|+.+.+.+...+..++|+++| +||+++++.|||||.+|+++|.|+.+|
T Consensus 81 a~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~faigR 159 (258)
T KOG3250|consen 81 ALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAIGR 159 (258)
T ss_pred hhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhhcc
Confidence 8899999999999999999999999999999999999999998999999999 999999999999999999999999998
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=1.9e-33 Score=235.06 Aligned_cols=149 Identities=28% Similarity=0.541 Sum_probs=133.9
Q ss_pred HHHHHHHHHHhcccc----hHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhh----
Q 031323 8 AELIDHFVKQASNQK----GAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN---- 79 (161)
Q Consensus 8 ~~~l~~~l~~~~~~~----~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~---- 79 (161)
..++-+||.++...+ -++|.+||+.|+.+|++|.|++|+++|+|+.|+++. +|+||+||.+|.+++|.+
T Consensus 185 ~kvmt~lLgtyt~dnas~AredA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~ 261 (378)
T KOG2753|consen 185 SKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAA 261 (378)
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHh
Confidence 456678888887643 356999999999999999999999999999999865 899999999999999997
Q ss_pred ccCCCCC--CC-HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 80 NAGHLPQ--LV-PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 80 ~~~~~~~--L~-~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
|++++.. +. +.++.|||+||+|+||+.+++|||+++++.|+|+ .+|||.||| +||++|+|+|||||.+++|+|++
T Consensus 262 N~~Fvqs~gl~~E~~~~KMRLLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI-daI~aklV~~kidq~~~~viVs~ 339 (378)
T KOG2753|consen 262 NSGFVQSQGLVHEQNMAKMRLLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI-DAIRAKLVEGKIDQMNRTVIVSS 339 (378)
T ss_pred ChHHHHHhcccHHHHHHHHHHHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH-HHHHHHHHHhhHHhhcceEEeeh
Confidence 4444433 33 7789999999999999999999999999999998 999999999 99999999999999999999999
Q ss_pred eeccC
Q 031323 157 VLVRL 161 (161)
Q Consensus 157 ~~~Rv 161 (161)
+++|.
T Consensus 340 ~~hR~ 344 (378)
T KOG2753|consen 340 STHRT 344 (378)
T ss_pred hhhhh
Confidence 99984
No 3
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=8.3e-32 Score=226.03 Aligned_cols=147 Identities=20% Similarity=0.382 Sum_probs=134.1
Q ss_pred HHHHHh------cccchHHHHHHHHHHhcCCCcccchhhhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhcc---CC
Q 031323 13 HFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA---GH 83 (161)
Q Consensus 13 ~~l~~~------~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~~---~~ 83 (161)
.||... .+++.+.|..+..+||.+.++||||||+.||+...|+|+++.|++++|..|+.||+..|++.. +.
T Consensus 182 ~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~ 261 (380)
T KOG2908|consen 182 LYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGK 261 (380)
T ss_pred HHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhcc
Confidence 566666 444668899999999999999999999999999999999999999999999999999999843 34
Q ss_pred CCCCC--H-HHHHHHHHHHHHHhhh----cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 84 LPQLV--P-DQVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 84 ~~~L~--~-~~~~KlrlLtL~sLa~----~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
.|.|. + -..+|+++|+|+.+|+ +.|.+||++||++++|| .++||.+|| +|++.|||+|.|||++|+|+++|
T Consensus 262 ~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~sw 339 (380)
T KOG2908|consen 262 QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYMSW 339 (380)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEEec
Confidence 67774 3 3689999999999998 46999999999999999 999999999 99999999999999999999999
Q ss_pred eeccC
Q 031323 157 VLVRL 161 (161)
Q Consensus 157 ~~~Rv 161 (161)
++|||
T Consensus 340 vqPRv 344 (380)
T KOG2908|consen 340 VQPRV 344 (380)
T ss_pred ccccc
Confidence 99997
No 4
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.62 E-value=1.5e-15 Score=106.72 Aligned_cols=95 Identities=21% Similarity=0.433 Sum_probs=80.9
Q ss_pred hhHHHHHHHHhcCCHhHHhhccCC-----C--CCC---CHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHH
Q 031323 60 SKYLDMLRLFAHGTWSDYKNNAGH-----L--PQL---VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (161)
Q Consensus 60 ~~l~~LL~iF~~G~~~dy~~~~~~-----~--~~L---~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~ 129 (161)
.|+.+++++|..|++.+|.+.-.. + +.+ .+.+.+|++..++.+++...+.+++++|++.++++ .++||.
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHH
Confidence 378999999999999999862111 1 222 26678999999999999999999999999999999 999999
Q ss_pred HHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 130 FLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 130 lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
+++ ++|..|.|.|+|||.+|+|+++|
T Consensus 80 ~l~-~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILI-DLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHH-HHHHCCCEEEEEECCCCEEEecC
Confidence 999 99999999999999999999986
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.42 E-value=6.8e-13 Score=91.65 Aligned_cols=70 Identities=23% Similarity=0.326 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR 160 (161)
Q Consensus 89 ~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R 160 (161)
+...+|+|.+++..++...+.++|++|++.++++ .+++|.+++ ++|..|.+.|+|||.+++|.+++..+|
T Consensus 4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00753 4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 4578999999999999999999999999999999 889999999 999999999999999999999999887
No 6
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.42 E-value=6.8e-13 Score=91.65 Aligned_cols=70 Identities=23% Similarity=0.326 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeecc
Q 031323 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVR 160 (161)
Q Consensus 89 ~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~R 160 (161)
+...+|+|.+++..++...+.++|++|++.++++ .+++|.+++ ++|..|.+.|+|||.+++|.+++..+|
T Consensus 4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r 73 (88)
T smart00088 4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPR 73 (88)
T ss_pred HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchh
Confidence 4578999999999999999999999999999999 889999999 999999999999999999999999887
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.72 E-value=0.00012 Score=61.70 Aligned_cols=92 Identities=14% Similarity=0.413 Sum_probs=78.1
Q ss_pred hHHHHHHHHhcCCHhHHhh----ccCCCCC---C---CHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323 61 KYLDMLRLFAHGTWSDYKN----NAGHLPQ---L---VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 61 ~l~~LL~iF~~G~~~dy~~----~~~~~~~---L---~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l 130 (161)
.+-+|+..+...++.+|+. |++.+-+ + .++.++++|.-.|+.|......|...-|+++|.++ ..+||.+
T Consensus 306 AMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~L 384 (440)
T KOG1464|consen 306 AMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVESL 384 (440)
T ss_pred HHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHHH
Confidence 3678999999999999996 3333211 1 27789999999999999987788888899999999 9999999
Q ss_pred HHHHhHhcCCcEEEecCCCCEEEE
Q 031323 131 LINECMYTGIVRGKLDQLRRCFEV 154 (161)
Q Consensus 131 vI~~ai~~gLi~gkIDq~~~~v~V 154 (161)
++ +||-..-|+|+|||+++.+..
T Consensus 385 LV-~~ILD~~i~g~Ide~n~~l~~ 407 (440)
T KOG1464|consen 385 LV-SCILDDTIDGRIDEVNQYLEL 407 (440)
T ss_pred HH-HHHhccccccchHHhhhHhcc
Confidence 99 999999999999999987654
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.58 E-value=0.00026 Score=62.06 Aligned_cols=92 Identities=9% Similarity=0.295 Sum_probs=65.2
Q ss_pred hhHHHHHHHHhcCCHhHHhhccCCCCC-C----CHHHHHHHHH----HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-L----VPDQVLKLKQ----LTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 60 ~~l~~LL~iF~~G~~~dy~~~~~~~~~-L----~~~~~~Klrl----LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l 130 (161)
.++|+|=...-.||++-|...-+.+.+ + +-...-.||. =.+-.+.-..+-||+.+||+.|+++|.+++|-+
T Consensus 319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~Eyi 398 (493)
T KOG2581|consen 319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYI 398 (493)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHH
Confidence 458999999999999999964322211 1 1111222221 111111113678999999999999988999999
Q ss_pred HHHHhHhcCCcEEEecCCCCEE
Q 031323 131 LINECMYTGIVRGKLDQLRRCF 152 (161)
Q Consensus 131 vI~~ai~~gLi~gkIDq~~~~v 152 (161)
|= +||+.|+|+|+||..++.+
T Consensus 399 Va-kAIRDGvIea~Id~~~g~m 419 (493)
T KOG2581|consen 399 VA-KAIRDGVIEAKIDHEDGFM 419 (493)
T ss_pred HH-HHHHhccceeeeccccCce
Confidence 99 9999999999999998844
No 9
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=95.99 E-value=0.019 Score=50.34 Aligned_cols=97 Identities=15% Similarity=0.200 Sum_probs=73.7
Q ss_pred hHHHHHHHHhcCCHhHHhh----ccCCCCCCC-HHHHHHHHHHHHHHhhh-------cCCccCHHHHHHhcCCCC-----
Q 031323 61 KYLDMLRLFAHGTWSDYKN----NAGHLPQLV-PDQVLKLKQLTVLTLAE-------TNKVLPYDELMEELDVTN----- 123 (161)
Q Consensus 61 ~l~~LL~iF~~G~~~dy~~----~~~~~~~L~-~~~~~KlrlLtL~sLa~-------~~~~isy~~I~~~l~i~~----- 123 (161)
.+-.++.....||+..|.. |...+.... =-.+.|+++++.-.|.. ....+|++.+..+++..+
T Consensus 273 ~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~ 352 (394)
T KOG2688|consen 273 KYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVD 352 (394)
T ss_pred hHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCc
Confidence 5677899999999999985 222222211 11245566666665554 457899999999998764
Q ss_pred hhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323 124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL 158 (161)
Q Consensus 124 ~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~ 158 (161)
.+|||-.+. .+|+.|.|+|.|+...+++.++.--
T Consensus 353 ~deveciLa-~lI~~G~ikgYish~~~~~V~sK~~ 386 (394)
T KOG2688|consen 353 LDEVECILA-NLIDLGRIKGYISHQLQTLVFSKKD 386 (394)
T ss_pred hhhHHHHHH-hhhhhccccchhchhhheEEEecCC
Confidence 789999999 9999999999999999999988643
No 10
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=95.79 E-value=0.016 Score=49.90 Aligned_cols=66 Identities=15% Similarity=0.232 Sum_probs=59.1
Q ss_pred HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 89 ~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
++-++--|++-.-..|.-+..|+.+-+|+.|.++ .+|.|.|++ +.|+...+++|||..-|+|.+..
T Consensus 329 ~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~ 394 (432)
T KOG2758|consen 329 DEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGH 394 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecC
Confidence 3346777888888889888999999999999998 999999999 99999999999999999987753
No 11
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.34 E-value=0.14 Score=45.19 Aligned_cols=97 Identities=14% Similarity=0.198 Sum_probs=78.2
Q ss_pred hHHHHHHHHhcCCHhHHhh----ccCCC---CCCC---HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323 61 KYLDMLRLFAHGTWSDYKN----NAGHL---PQLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 61 ~l~~LL~iF~~G~~~dy~~----~~~~~---~~L~---~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l 130 (161)
.+.++|.-|..+.++.-.. .++.+ +-|. +....|+|.=+++..-....++.+..+|.+.+.+ ...+|.=
T Consensus 307 qlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~ 385 (466)
T KOG0686|consen 307 QLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESE 385 (466)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHH
Confidence 3777888888887775554 22221 1122 5568999999999988888999999999999998 9999999
Q ss_pred HHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323 131 LINECMYTGIVRGKLDQLRRCFEVCTVLV 159 (161)
Q Consensus 131 vI~~ai~~gLi~gkIDq~~~~v~V~~~~~ 159 (161)
|. +.|-.|-|.||||+-++.+++.-.-.
T Consensus 386 l~-~LI~~~~i~~rIDs~~ki~~~~~~~~ 413 (466)
T KOG0686|consen 386 LL-ELILEGKISGRIDSHNKILYARDADS 413 (466)
T ss_pred HH-HHHHccchheeeccccceeeeccccc
Confidence 99 99999999999999999999876543
No 12
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.34 E-value=0.075 Score=45.74 Aligned_cols=127 Identities=10% Similarity=0.105 Sum_probs=84.7
Q ss_pred HHHHHHHHhcCCCcccc-hhhhcCcccccccCCC-chhHHHHHHHHhcC-CHhHHhhc-cC----CCCCCCHHHHHHHHH
Q 031323 26 LGSVIVEATSQPSLFAF-SEILAVPNIAEFEGTE-NSKYLDMLRLFAHG-TWSDYKNN-AG----HLPQLVPDQVLKLKQ 97 (161)
Q Consensus 26 a~~~i~~aL~~p~i~~f-~eLl~~~~v~~L~~s~-~~~l~~LL~iF~~G-~~~dy~~~-~~----~~~~L~~~~~~Klrl 97 (161)
|..|.+-|.-+|..-.| ..|...|.++.+..=. -+++| |+-|..+ .++.|... .+ +.+.=+...-+-+.-
T Consensus 228 a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmy--l~riI~k~el~ef~~~L~pHQka~~~dgssil~ra~~E 305 (399)
T KOG1497|consen 228 ALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMY--LERIIRKEELQEFEAFLQPHQKAHTMDGSSILDRAVIE 305 (399)
T ss_pred hHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHH--HHHHhcchhHHHHHHHhcchhhhcccCcchhhhhHHHH
Confidence 66666777778887765 5677778777765311 12233 4555555 57777752 11 111111111122333
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
-.|+++..-...+||+++.+.++|+ ...+|..+= ++|..|=+.|.|||.++.+|...
T Consensus 306 hNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~ 362 (399)
T KOG1497|consen 306 HNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED 362 (399)
T ss_pred HhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc
Confidence 3445555545579999999999999 999999999 99999999999999999999764
No 13
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=95.00 E-value=0.059 Score=47.05 Aligned_cols=99 Identities=19% Similarity=0.307 Sum_probs=61.2
Q ss_pred hhHHHHHHHHhcCCHhHHhh----ccCCCCC--CCHHHHHHHHHHH-------HHHhhhcCCccCHHHHHHhcCCC--C-
Q 031323 60 SKYLDMLRLFAHGTWSDYKN----NAGHLPQ--LVPDQVLKLKQLT-------VLTLAETNKVLPYDELMEELDVT--N- 123 (161)
Q Consensus 60 ~~l~~LL~iF~~G~~~dy~~----~~~~~~~--L~~~~~~KlrlLt-------L~sLa~~~~~isy~~I~~~l~i~--~- 123 (161)
+.+--|.++..+|++++|.. |...+.+ |---+..+.+.++ ...++.....+|++-+...++++ +
T Consensus 289 s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn 368 (413)
T COG5600 289 SVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDN 368 (413)
T ss_pred chhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCc
Confidence 34556889999999999985 2111111 0000111111121 12222233445566555555443 3
Q ss_pred ---hhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323 124 ---VRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV 159 (161)
Q Consensus 124 ---~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~ 159 (161)
.++||-.+. .+|+.|+++|.|....++|.+++-.|
T Consensus 369 ~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 369 FHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred ccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence 578999999 99999999999999999999987543
No 14
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=93.09 E-value=0.4 Score=41.96 Aligned_cols=90 Identities=11% Similarity=0.277 Sum_probs=67.4
Q ss_pred hHHHHHHHHhcCCHhHHhh----ccCCC-CCCC----HHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHH
Q 031323 61 KYLDMLRLFAHGTWSDYKN----NAGHL-PQLV----PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (161)
Q Consensus 61 ~l~~LL~iF~~G~~~dy~~----~~~~~-~~L~----~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lv 131 (161)
++.+++++...+.-.+... +.+.+ .+-+ -..+.-+.+-+|.++...-.+++.++||+..++.+..|||..|
T Consensus 260 pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~I 339 (422)
T KOG2582|consen 260 PYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKYI 339 (422)
T ss_pred hHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHHH
Confidence 5788999999888776654 22222 2222 2235556666677777777789999999988888889999999
Q ss_pred HHHhHhcCCcEEEecCCCCEEEE
Q 031323 132 INECMYTGIVRGKLDQLRRCFEV 154 (161)
Q Consensus 132 I~~ai~~gLi~gkIDq~~~~v~V 154 (161)
+ +.|..|=|-+.|| |-|..
T Consensus 340 l-qmie~~~i~a~iN---G~v~f 358 (422)
T KOG2582|consen 340 L-QMIEDGEIFASIN---GMVFF 358 (422)
T ss_pred H-HHhccCceEEEec---ceEEE
Confidence 9 9999999999999 55544
No 15
>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=92.46 E-value=0.17 Score=33.19 Aligned_cols=47 Identities=15% Similarity=0.203 Sum_probs=36.1
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
.|.+....++.+|+++||.+++++ ...||.++= ..++.|-|+-.-++
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEEecCC
Confidence 445555578899999999999999 999999988 99999999844433
No 16
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=92.30 E-value=0.4 Score=38.11 Aligned_cols=59 Identities=14% Similarity=0.246 Sum_probs=41.3
Q ss_pred HHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 96 rlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
-+-.+++....++.+..+++|.++++. ..++-+-|- +....|.|.|-||...+=|+||.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs~ 158 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYISE 158 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE---
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEecH
Confidence 455667777789999999999999998 777777777 89999999999999988888874
No 17
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=91.47 E-value=1.4 Score=32.67 Aligned_cols=108 Identities=15% Similarity=0.205 Sum_probs=69.7
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCcccccccC-CCchhHHHHHHHHhcCCHhHHhhc-cCC-C-CC---CCHHHHHHHH
Q 031323 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNN-AGH-L-PQ---LVPDQVLKLK 96 (161)
Q Consensus 24 ~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~-s~~~~l~~LL~iF~~G~~~dy~~~-~~~-~-~~---L~~~~~~Klr 96 (161)
.........+|..-.+-+|.-+|..-+-...+. .+-..+..|.+.+-.|++.+|.+. ++. . +. +-+....++|
T Consensus 5 ~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR 84 (143)
T PF10075_consen 5 EIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIR 84 (143)
T ss_dssp HHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHH
T ss_pred hHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence 344455556666656678887775443333332 345668899999999999999872 221 1 11 1244577788
Q ss_pred HHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 97 lLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
.=.+-.+......|+-+.+++-||++ .++++.++.
T Consensus 85 ~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~ 119 (143)
T PF10075_consen 85 ERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK 119 (143)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred HHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence 66666666678899999999999999 999999877
No 18
>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=90.69 E-value=0.8 Score=30.94 Aligned_cols=37 Identities=19% Similarity=0.312 Sum_probs=30.7
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
+++.++-++||+.++++ ...++..+= +....|+|+.+
T Consensus 22 ~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~ 58 (83)
T PF02082_consen 22 DGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESS 58 (83)
T ss_dssp TSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred CCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEec
Confidence 34459999999999999 999999877 99999998764
No 19
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=88.77 E-value=0.66 Score=40.36 Aligned_cols=101 Identities=18% Similarity=0.301 Sum_probs=70.9
Q ss_pred ccCCCchhHHHHHHHHhcCCHhHHhhc-cCCCCCCC--H---HHHH----HHHHHHHHHhhhcCCccCHHHHHHhcCCCC
Q 031323 54 FEGTENSKYLDMLRLFAHGTWSDYKNN-AGHLPQLV--P---DQVL----KLKQLTVLTLAETNKVLPYDELMEELDVTN 123 (161)
Q Consensus 54 L~~s~~~~l~~LL~iF~~G~~~dy~~~-~~~~~~L~--~---~~~~----KlrlLtL~sLa~~~~~isy~~I~~~l~i~~ 123 (161)
..+..-..+...=+.|..-++.||+.- .+.-++|. + ...+ -|--=-|+.+.+..+.+..+-||+-.|++
T Consensus 280 y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~- 358 (411)
T KOG1463|consen 280 YAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLD- 358 (411)
T ss_pred ccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCC-
Confidence 444444557778888999999999962 21112232 1 1111 11112344555566777888899999999
Q ss_pred hhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 124 ~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
...||.=+= ++|-.+-+.|.+||-++++.|.-
T Consensus 359 ~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~ 390 (411)
T KOG1463|consen 359 VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFE 390 (411)
T ss_pred cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeC
Confidence 999999988 99999999999999999999854
No 20
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=87.96 E-value=2.4 Score=34.37 Aligned_cols=62 Identities=11% Similarity=0.145 Sum_probs=50.2
Q ss_pred HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
.=|+.|.++....+...+|..+|++.++++ ...+=..+- +.-..|+|+-+.+...+.+++|.
T Consensus 5 ~~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk-~LEe~GlI~R~~~~r~~~v~LTe 66 (217)
T PRK14165 5 EALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILK-QLEDEGYITRTIVPRGQLITITE 66 (217)
T ss_pred HHHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEEcCCceEEEECH
Confidence 445566666655566789999999999998 888888888 99999999999998877777763
No 21
>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=87.45 E-value=2.2 Score=25.53 Aligned_cols=41 Identities=20% Similarity=0.368 Sum_probs=30.7
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
++.....+..+|..+||+.++++ ...|-..+= +....|+|+
T Consensus 8 Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 8 ILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 33444456679999999999998 888888766 888899875
No 22
>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=86.71 E-value=2.1 Score=31.59 Aligned_cols=45 Identities=18% Similarity=0.300 Sum_probs=37.6
Q ss_pred HHHHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 97 QLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 97 lLtL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
+..++.||. +++.++-++|++.+++| ...++..+= ..-..|+|..
T Consensus 11 l~~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s 57 (135)
T TIGR02010 11 VTAMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence 455666664 45579999999999999 999999887 8999999975
No 23
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=86.71 E-value=1.7 Score=38.38 Aligned_cols=124 Identities=20% Similarity=0.248 Sum_probs=78.0
Q ss_pred HHHhcCCCcccchhhhcCccc-ccccCCCchhHHHHHHHHhcCCHhHHhhc---------cCCCCC---CCHHH----HH
Q 031323 31 VEATSQPSLFAFSEILAVPNI-AEFEGTENSKYLDMLRLFAHGTWSDYKNN---------AGHLPQ---LVPDQ----VL 93 (161)
Q Consensus 31 ~~aL~~p~i~~f~eLl~~~~v-~~L~~s~~~~l~~LL~iF~~G~~~dy~~~---------~~~~~~---L~~~~----~~ 93 (161)
..++..|..---.+|++.-.. +.|+ +.+..-.+|.+|..|-+--|... .+.+-. ..+.. ..
T Consensus 260 ~f~~LAp~dneQsdll~~is~dKkL~--e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~ 337 (439)
T KOG1498|consen 260 SFCVLAPHDNEQSDLLARISNDKKLS--ELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKL 337 (439)
T ss_pred eEEeecCCCcHHHHHHHHHhcccccc--cCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHH
Confidence 344555554434455533321 1132 33446789999999976655521 111111 11111 11
Q ss_pred HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL 158 (161)
Q Consensus 94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~ 158 (161)
.+--.-+-=+|.-...||+.++++-++.+ .++.|.++= ..+..|-+.+|||+..+.+....+.
T Consensus 338 RIiEHNiRiiA~yYSrIt~~rl~eLLdl~-~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~K 400 (439)
T KOG1498|consen 338 RIIEHNIRIIAKYYSRITLKRLAELLDLP-VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKVK 400 (439)
T ss_pred HHHHHHHHHHHHHHhhccHHHHHHHhCCC-HHHHHHHHH-HHHhccceEEEecCCCceEEEEecc
Confidence 12223333334446789999999999999 999999999 9999999999999999999877653
No 24
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=86.12 E-value=1.4 Score=38.30 Aligned_cols=109 Identities=18% Similarity=0.289 Sum_probs=75.7
Q ss_pred hhcCcccccccCCCchhHHHHHHHHhcCCHhHHhhcc-----CCC-CC--CCHH---HHHHHHHHHHHHhhhcCCccCHH
Q 031323 45 ILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA-----GHL-PQ--LVPD---QVLKLKQLTVLTLAETNKVLPYD 113 (161)
Q Consensus 45 Ll~~~~v~~L~~s~~~~l~~LL~iF~~G~~~dy~~~~-----~~~-~~--L~~~---~~~KlrlLtL~sLa~~~~~isy~ 113 (161)
.+..|-|...-.. -..+.+++..+-.-++++|-..- ..+ ++ +.+. -.+-||...-..+-+..|.++.+
T Consensus 243 Vi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~ 321 (393)
T KOG0687|consen 243 VIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLE 321 (393)
T ss_pred hcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555432211 12355666666666777666421 111 11 2332 25777777777777788999999
Q ss_pred HHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 114 ~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
-.|++.|++ .+-+++=+= +-|-.|=+.++||-+++.|.+++
T Consensus 322 ~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNr 362 (393)
T KOG0687|consen 322 SMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNR 362 (393)
T ss_pred HHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCC
Confidence 999999998 888888887 88889999999999999999875
No 25
>PF13730 HTH_36: Helix-turn-helix domain
Probab=84.87 E-value=4.2 Score=24.86 Aligned_cols=47 Identities=21% Similarity=0.277 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhhhc-CCc-cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323 93 LKLKQLTVLTLAET-NKV-LPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (161)
Q Consensus 93 ~KlrlLtL~sLa~~-~~~-isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi 141 (161)
.|+-.+.|.+.+.+ +.. -|++.||+.++++ ...|-..+= +....|+|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s-~~Tv~~~i~-~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVS-RRTVQRAIK-ELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCC
Confidence 67788888888853 223 3799999999998 999999877 88888875
No 26
>PF07389 DUF1500: Protein of unknown function (DUF1500); InterPro: IPR009974 This family consists of several Orthopoxvirus specific proteins, which include Vaccinia virus, B6 protein, they are around 100 residues in length. The function of this family is unknown.
Probab=84.57 E-value=1.5 Score=30.80 Aligned_cols=35 Identities=17% Similarity=0.467 Sum_probs=26.7
Q ss_pred hhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCC
Q 031323 103 LAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (161)
Q Consensus 103 La~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gL 140 (161)
+.+.-..++|++|-+. +|+.+.||+||| +.+..+.
T Consensus 42 lftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~i~ 76 (100)
T PF07389_consen 42 LFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLNDIM 76 (100)
T ss_pred HHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHhHh
Confidence 3334457899999999 667899999999 8765443
No 27
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=84.46 E-value=2.4 Score=31.89 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=36.1
Q ss_pred HHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE---EecC
Q 031323 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQ 147 (161)
Q Consensus 101 ~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g---kIDq 147 (161)
+..-..+.-.||.+||+.+|++ ...|-.-+= +....|+|+| .+|+
T Consensus 15 l~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 15 LEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNP 62 (153)
T ss_pred HHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECH
Confidence 3333456789999999999998 999888877 9999999984 4554
No 28
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=83.60 E-value=3.8 Score=27.42 Aligned_cols=47 Identities=23% Similarity=0.231 Sum_probs=37.3
Q ss_pred HHHHHHHhhhcC-CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 96 KQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 96 rlLtL~sLa~~~-~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
|.+.++...... +.++..+|++.++++ ...|-..+- .....|++...
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~~ 53 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeeec
Confidence 345555544443 689999999999999 999999888 88899999763
No 29
>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=83.40 E-value=3.4 Score=29.83 Aligned_cols=48 Identities=23% Similarity=0.277 Sum_probs=37.1
Q ss_pred HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
++.|..+....++..+|-++|++.++++ ...|.+.+= .....|+|...
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~-~L~~~gli~~~ 58 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILR-TLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 4444444433234589999999999999 999999887 89999999753
No 30
>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=82.83 E-value=3.8 Score=25.04 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=34.8
Q ss_pred HHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 96 rlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
|-+.+++.-. .+..++..+|++.++++ ...+-.++- .....|+++
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~-~stv~r~L~-tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLP-KSTVHRLLQ-TLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCee
Confidence 4566666554 45568999999999999 999999887 888888875
No 31
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.57 E-value=3.4 Score=34.37 Aligned_cols=54 Identities=19% Similarity=0.425 Sum_probs=42.3
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
++....++++++.++++.+.++-+.+.+-. += +.+..|++.|-||...+-++|+
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lrtqd~inr-iq-~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLRTQDSINR-IQ-ELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCccHHHHHHH-HH-HHHHhhhheeeecCCCceEEec
Confidence 456666889999999999999974433332 23 5556899999999999999987
No 32
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=82.49 E-value=3.3 Score=28.84 Aligned_cols=36 Identities=11% Similarity=0.301 Sum_probs=31.7
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
.+..+|+.+|++.++++ ...|-..+- +....|+|++
T Consensus 14 ~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~ 49 (108)
T smart00344 14 KDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG 49 (108)
T ss_pred HhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence 44579999999999999 999999888 9999999884
No 33
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=82.43 E-value=3.5 Score=31.79 Aligned_cols=45 Identities=18% Similarity=0.298 Sum_probs=37.2
Q ss_pred HHHHHHhhh--cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 97 QLTVLTLAE--TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 97 lLtL~sLa~--~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
+..++-+|+ +++.+|-++||+.+++| ..-+++.+- ..-..|||..
T Consensus 11 l~~l~~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s 57 (164)
T PRK10857 11 VTAMLDVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSS 57 (164)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEe
Confidence 444555554 45689999999999999 999999888 9999999986
No 34
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=80.26 E-value=4.1 Score=29.99 Aligned_cols=37 Identities=14% Similarity=0.232 Sum_probs=31.3
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
.+..+||.+||+.++++ ...|=.-+= +....|+|+|.
T Consensus 19 ~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~ 55 (154)
T COG1522 19 EDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGY 55 (154)
T ss_pred HhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeE
Confidence 44459999999999998 888887777 88999998874
No 35
>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=79.67 E-value=6.4 Score=25.69 Aligned_cols=36 Identities=17% Similarity=0.213 Sum_probs=29.7
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
++..-|+.+|++.+++.|...|-..+- ..-..|+|+
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 577889999999999998999999988 888888886
No 36
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=79.63 E-value=3.5 Score=35.50 Aligned_cols=95 Identities=17% Similarity=0.265 Sum_probs=66.7
Q ss_pred hhHHHHHHHHhcCCHhHHhhccCC-CCCCC--HHHHHHHH-------HHHHHHhhhcCCccCHHHHHHhcCCCChhhHHH
Q 031323 60 SKYLDMLRLFAHGTWSDYKNNAGH-LPQLV--PDQVLKLK-------QLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (161)
Q Consensus 60 ~~l~~LL~iF~~G~~~dy~~~~~~-~~~L~--~~~~~Klr-------lLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~ 129 (161)
..+...-+.|..-++.||..--.. -++|. +-...-+. --.|+.+.+.-..+...-|++-+|++ .++||.
T Consensus 284 ~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvEg 362 (421)
T COG5159 284 RAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVEG 362 (421)
T ss_pred HHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHHH
Confidence 446677788888899999852111 12231 11111111 12344455566777888899999998 999999
Q ss_pred HHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 130 FLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 130 lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
=+= ++|-.+++-|.+||.++++.|..
T Consensus 363 KLs-qMILDKifyG~LDqg~gcLivy~ 388 (421)
T COG5159 363 KLS-QMILDKIFYGTLDQGDGCLIVYG 388 (421)
T ss_pred HHH-HHHHHHHHHhhhccCCceEEEeC
Confidence 988 99999999999999999998863
No 37
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=78.31 E-value=6.8 Score=29.68 Aligned_cols=46 Identities=22% Similarity=0.224 Sum_probs=37.6
Q ss_pred HHHHHHhhhc--CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 97 QLTVLTLAET--NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 97 lLtL~sLa~~--~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
+-.|+.||.. ++.+|-++||+..+++ ..-+|+++- ..-.+|||+..
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~-~L~kaGlV~S~ 58 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILS-KLRKAGLVKSV 58 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEee
Confidence 4455666653 3478899999999999 999999988 99999998764
No 38
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=77.97 E-value=5.8 Score=30.19 Aligned_cols=42 Identities=12% Similarity=0.180 Sum_probs=34.0
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
|+.+-..+.-+||.+||+.+|++ ...|=.-+= +....|+|+|
T Consensus 19 IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~ 60 (164)
T PRK11169 19 ILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQG 60 (164)
T ss_pred HHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEE
Confidence 33333467789999999999998 888888776 8899999975
No 39
>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=77.50 E-value=7.1 Score=28.27 Aligned_cols=36 Identities=19% Similarity=0.297 Sum_probs=32.5
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
+..+|.++|++.++++ ..-|...+= .....|+|.+.
T Consensus 23 ~~~~s~~eia~~l~is-~~~v~~~l~-~L~~~Gli~~~ 58 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLN-APTVSKILK-QLSLAGIVTSK 58 (130)
T ss_pred CCCccHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 5679999999999999 999999887 99999999874
No 40
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=76.92 E-value=8.1 Score=24.30 Aligned_cols=46 Identities=24% Similarity=0.365 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
.+++|..+ ..++..+..+|++.++++ ...+-.-+= .....|+|+..
T Consensus 12 R~~Il~~L---~~~~~~t~~ela~~l~~~-~~t~s~hL~-~L~~aGli~~~ 57 (61)
T PF12840_consen 12 RLRILRLL---ASNGPMTVSELAEELGIS-QSTVSYHLK-KLEEAGLIEVE 57 (61)
T ss_dssp HHHHHHHH---HHCSTBEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred HHHHHHHH---hcCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeEEe
Confidence 44445444 456799999999999998 777777766 78889998764
No 41
>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=76.62 E-value=15 Score=22.59 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=31.8
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
+++.+|++.++++ ...+-..+= .....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~-~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLK-KLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHH-HHHHCCCeEEEEec
Confidence 9999999999998 889988876 88899999987665
No 42
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=76.25 E-value=7 Score=27.21 Aligned_cols=52 Identities=17% Similarity=0.233 Sum_probs=39.9
Q ss_pred HHHHHHHHHh-hhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323 94 KLKQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 94 KlrlLtL~sL-a~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
+-+.|.++.- +....=++.++|++.|+++ .++|+.-+= ..+..|.|=-.||+
T Consensus 49 ~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 49 QDKVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 4456666665 4445569999999999998 999999877 99999999888885
No 43
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=75.92 E-value=8.6 Score=29.14 Aligned_cols=45 Identities=18% Similarity=0.124 Sum_probs=36.2
Q ss_pred HHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 98 LTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 98 LtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
..++-||. .++.++-++||+..+++ ..-++..+- ....+|+|+..
T Consensus 12 r~L~~LA~~~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~ 57 (153)
T PRK11920 12 RMLMYCAANDGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETV 57 (153)
T ss_pred HHHHHHHhCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEee
Confidence 34445554 34568999999999999 999999998 99999998765
No 44
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=75.63 E-value=4.4 Score=25.64 Aligned_cols=34 Identities=29% Similarity=0.468 Sum_probs=23.1
Q ss_pred HHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHH
Q 031323 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 96 rlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~l 130 (161)
|++.|+.+....+.++++++|+.++++ ...+-..
T Consensus 6 rq~~Ll~~L~~~~~~~~~ela~~l~~S-~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLKNKWITLKELAKKLNIS-ERTIKND 39 (59)
T ss_dssp HHHHHHHHHHHHTSBBHHHHHHHCTS--HHHHHHH
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHCCC-HHHHHHH
Confidence 344445544457789999999999998 6555444
No 45
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=75.54 E-value=5.6 Score=38.27 Aligned_cols=63 Identities=16% Similarity=0.196 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 92 VLKLKQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 92 ~~KlrlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
++++.++.++.=++ -..+|+|+.+.+-.-.=+..++|.+++ +|...+.+..+||..+++|...
T Consensus 429 Lq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 429 LQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence 44455555554444 356899999888766545899999999 9999999999999999999876
No 46
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=75.34 E-value=4.3 Score=24.70 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=20.0
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
..||++||+.++++ ...|..++- +|.
T Consensus 26 g~s~~eIa~~l~~s-~~~v~~~l~-ra~ 51 (54)
T PF08281_consen 26 GMSYAEIAEILGIS-ESTVKRRLR-RAR 51 (54)
T ss_dssp ---HHHHHHHCTS--HHHHHHHHH-HHH
T ss_pred CcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 68999999999998 999999987 764
No 47
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=75.32 E-value=8 Score=25.22 Aligned_cols=45 Identities=20% Similarity=0.182 Sum_probs=35.3
Q ss_pred HHHHHHHHhhhcCC-ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 95 LKQLTVLTLAETNK-VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 95 lrlLtL~sLa~~~~-~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
-++|.++. ..+. .++=.+|++.++++ ...|...+- .....|+|.-
T Consensus 9 ~~IL~~L~--~~g~~~~ta~eLa~~lgl~-~~~v~r~L~-~L~~~G~V~~ 54 (68)
T smart00550 9 EKILEFLE--NSGDETSTALQLAKNLGLP-KKEVNRVLY-SLEKKGKVCK 54 (68)
T ss_pred HHHHHHHH--HCCCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 34454444 2233 49999999999999 889999999 9999999865
No 48
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=74.89 E-value=14 Score=24.64 Aligned_cols=50 Identities=14% Similarity=0.252 Sum_probs=34.1
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
.++..+. ++..++.+|+..++++ ...+..++= ..+..|||++ .++...+|
T Consensus 10 ~IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~-~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMYKANLN-YSTLKKYLK-ELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHHH--TT-B-HHHHHTTST---HHHHHHHHH-HHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCcCeeC----CCCEEEEC
Confidence 3445554 5678899999999998 999999887 9999999954 45555544
No 49
>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=74.24 E-value=12 Score=23.90 Aligned_cols=44 Identities=18% Similarity=0.283 Sum_probs=34.6
Q ss_pred HHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 97 lLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+-++..+...+..++-.+||+.++++ ...|=..+= +.-..|+|+
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~-~L~~~GlV~ 53 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLK-RLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEE
Confidence 34555566678899999999999998 888877776 888888876
No 50
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=73.19 E-value=23 Score=23.39 Aligned_cols=44 Identities=20% Similarity=0.172 Sum_probs=36.2
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEE
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCF 152 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v 152 (161)
.+.++..+|++.++++ ...+-..+- ++...|+|.-.-++..+..
T Consensus 22 ~~~~~~~~la~~~~~s-~~~i~~~l~-~L~~~g~v~~~~~~~~~r~ 65 (101)
T smart00347 22 EGPLSVSELAKRLGVS-PSTVTRVLD-RLEKKGLIRRLPSPEDRRS 65 (101)
T ss_pred cCCcCHHHHHHHHCCC-chhHHHHHH-HHHHCCCeEecCCCCCCCe
Confidence 4479999999999998 888998887 9999999987766544333
No 51
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=72.19 E-value=10 Score=24.75 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.2
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
.+|.-+.++||+.|+++ ..+|..++-
T Consensus 17 lgr~Pt~eEiA~~lgis-~~~v~~~l~ 42 (78)
T PF04539_consen 17 LGREPTDEEIAEELGIS-VEEVRELLQ 42 (78)
T ss_dssp HSS--BHHHHHHHHTS--HHHHHHHHH
T ss_pred hCCCCCHHHHHHHHccc-HHHHHHHHH
Confidence 47899999999999999 999998644
No 52
>PF13518 HTH_28: Helix-turn-helix domain
Probab=71.96 E-value=9 Score=22.77 Aligned_cols=38 Identities=13% Similarity=0.207 Sum_probs=27.8
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcC
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (161)
+.++.+..++ . |+.++|+.++|+ ...|..|+- .--..|
T Consensus 3 ~~iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~-~y~~~G 40 (52)
T PF13518_consen 3 LQIVELYLEG-E-SVREIAREFGIS-RSTVYRWIK-RYREGG 40 (52)
T ss_pred HHHHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH-HHHhcC
Confidence 3445555544 4 999999999997 999999976 544445
No 53
>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=71.80 E-value=14 Score=22.06 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=27.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+..+..+|++.++++ ...|-.-+= .....|+|+
T Consensus 14 ~~~~~~el~~~l~~s-~~~vs~hL~-~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLS-QSTVSHHLK-KLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred CCCchhhHHHhcccc-chHHHHHHH-HHHHCcCee
Confidence 689999999999998 888887766 777888875
No 54
>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=71.66 E-value=22 Score=25.07 Aligned_cols=47 Identities=11% Similarity=0.063 Sum_probs=37.9
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V 154 (161)
.+..++..+|++.++++ ...|=..+- +....|+|...-|...+....
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~~~ 85 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRRVY 85 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCeeE
Confidence 34579999999999998 667777766 999999999998876665443
No 55
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=71.65 E-value=5 Score=23.88 Aligned_cols=29 Identities=28% Similarity=0.430 Sum_probs=18.9
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHH
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELED 129 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~ 129 (161)
|+.+-..+...||.+|++.+|++ ...|-.
T Consensus 8 Il~~Lq~d~r~s~~~la~~lglS-~~~v~~ 36 (42)
T PF13404_consen 8 ILRLLQEDGRRSYAELAEELGLS-ESTVRR 36 (42)
T ss_dssp HHHHHHH-TTS-HHHHHHHHTS--HHHHHH
T ss_pred HHHHHHHcCCccHHHHHHHHCcC-HHHHHH
Confidence 34444455789999999999998 666543
No 56
>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=70.47 E-value=11 Score=23.70 Aligned_cols=41 Identities=22% Similarity=0.291 Sum_probs=32.1
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi 141 (161)
.++.+...++.++.+++++.++++ ...+-.=+. ..-..|++
T Consensus 4 ~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~i 44 (57)
T PF08220_consen 4 QILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGLI 44 (57)
T ss_pred HHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCCE
Confidence 456666678899999999999998 777777666 66667764
No 57
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=69.44 E-value=7.6 Score=26.27 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=26.3
Q ss_pred HHHHhhhcCCccCHHHHHHhcC---CCChhhHHHHHHHHhHhcCC
Q 031323 99 TVLTLAETNKVLPYDELMEELD---VTNVRELEDFLINECMYTGI 140 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~---i~~~~evE~lvI~~ai~~gL 140 (161)
.|+..+...+.+||++|...|. ++ .+.+|.++- ..-..|+
T Consensus 11 ~Li~~gK~~G~lT~~eI~~~L~~~~~~-~e~id~i~~-~L~~~gI 53 (82)
T PF03979_consen 11 KLIEKGKKKGYLTYDEINDALPEDDLD-PEQIDEIYD-TLEDEGI 53 (82)
T ss_dssp HHHHHHHHHSS-BHHHHHHH-S-S----HHHHHHHHH-HHHTT--
T ss_pred HHHHHHhhcCcCCHHHHHHHcCccCCC-HHHHHHHHH-HHHHCCC
Confidence 3777777777899999999987 33 778888765 5555554
No 58
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=69.03 E-value=21 Score=24.01 Aligned_cols=50 Identities=28% Similarity=0.295 Sum_probs=35.5
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCC
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~ 150 (161)
.++++-.....++|.+|++.++++ ...+-.-+= ..-..|+|+-+-.-..+
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt-~g~Ls~hL~-~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLT-DGNLSKHLK-KLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEE-SSS
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEEEEeccCC
Confidence 344443345689999999999998 777777666 78889999988765554
No 59
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=68.51 E-value=15 Score=27.16 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=32.4
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
.+..+|-++||+.++++ ..-|++.+- ..-..|+|+.+
T Consensus 22 ~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~ 58 (141)
T PRK11014 22 EGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAV 58 (141)
T ss_pred CCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEe
Confidence 45578999999999999 999999988 89999998765
No 60
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=67.03 E-value=13 Score=32.26 Aligned_cols=48 Identities=17% Similarity=0.207 Sum_probs=43.0
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
.+.|+-.+|..-++.+ ..+.|.++= ..+..|.+-+||++..+.+....
T Consensus 351 YSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK 398 (439)
T COG5071 351 YSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEK 398 (439)
T ss_pred hhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeec
Confidence 4678888888999998 999999998 99999999999999999988754
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=65.65 E-value=28 Score=21.26 Aligned_cols=40 Identities=23% Similarity=0.265 Sum_probs=32.9
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCC
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~ 150 (161)
.++..+|++.++++ ...|-..|= +....|+|+-+-|+..+
T Consensus 21 ~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 21 ELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGDR 60 (62)
T ss_dssp GEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSST
T ss_pred CcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCCC
Confidence 49999999999998 888988777 99999999988776543
No 62
>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=65.55 E-value=27 Score=21.10 Aligned_cols=41 Identities=32% Similarity=0.349 Sum_probs=26.6
Q ss_pred HHHHHHhh-hcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcC
Q 031323 97 QLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (161)
Q Consensus 97 lLtL~sLa-~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (161)
+..++.+- ..+..+|-++||+.++++ ...|..-+= ..-..|
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~-~L~~~~ 43 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIK-ELREWG 43 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHH-HHHHTT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCC
Confidence 34444444 445559999999999998 877777644 443334
No 63
>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=65.49 E-value=9 Score=24.51 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=33.4
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
..+..+-++|++.++++ ...|-..+= +....|+|+-.-
T Consensus 19 ~~~~~t~~eIa~~l~i~-~~~v~~~L~-~L~~~GlV~~~~ 56 (68)
T PF01978_consen 19 KNGPATAEEIAEELGIS-RSTVYRALK-SLEEKGLVEREE 56 (68)
T ss_dssp HHCHEEHHHHHHHHTSS-HHHHHHHHH-HHHHTTSEEEEE
T ss_pred HcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEc
Confidence 35689999999999999 999999887 999999997665
No 64
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=65.47 E-value=24 Score=20.43 Aligned_cols=37 Identities=19% Similarity=0.161 Sum_probs=30.4
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
.+..++-.+|++.++++ ...|...+= .....|+|.-.
T Consensus 11 ~~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~~ 47 (53)
T smart00420 11 QQGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTRV 47 (53)
T ss_pred HcCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEEe
Confidence 34569999999999998 999988876 77788887643
No 65
>PRK09954 putative kinase; Provisional
Probab=65.08 E-value=12 Score=31.58 Aligned_cols=53 Identities=21% Similarity=0.486 Sum_probs=40.2
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE---ecCCCCEEEE
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK---LDQLRRCFEV 154 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk---IDq~~~~v~V 154 (161)
++++-.++..+|+.+|++.|+++ ...|-..+- +....|+|+|+ +|+....+.|
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~-~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIM-DLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCcCCcEEEEcCCccEEEE
Confidence 44444466789999999999998 999999988 88889998753 5555544443
No 66
>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=65.05 E-value=20 Score=21.86 Aligned_cols=43 Identities=19% Similarity=0.257 Sum_probs=35.1
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCC
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~ 150 (161)
..+.++..+|++.++++ ...+=.++= +....|+|+=.-|+.++
T Consensus 14 ~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 14 ENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTET
T ss_pred HcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCC
Confidence 44459999999999998 888877766 89999999998887765
No 67
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=64.54 E-value=33 Score=24.98 Aligned_cols=58 Identities=9% Similarity=0.007 Sum_probs=44.3
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV 159 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~ 159 (161)
|..+...+..++-.+|++.++++ ...|=..|= +....|+|.-.-|+..+....-..++
T Consensus 37 L~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~LT~ 94 (144)
T PRK03573 37 LHNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKLTE 94 (144)
T ss_pred HHHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEECh
Confidence 33444444457889999999998 788888776 99999999999998887766655443
No 68
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=64.30 E-value=28 Score=20.75 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=29.5
Q ss_pred CCcc-CHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 107 NKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 107 ~~~i-sy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+..+ |..++++.++++ ...|...+- .....|+|.
T Consensus 17 ~~~l~s~~~la~~~~vs-~~tv~~~l~-~L~~~g~i~ 51 (60)
T smart00345 17 GDKLPSERELAAQLGVS-RTTVREALS-RLEAEGLVQ 51 (60)
T ss_pred CCcCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 4456 899999999998 999999888 888899986
No 69
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=64.18 E-value=25 Score=20.15 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=28.9
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
.++..+|++.++++ ...+-..+- .....|+++-
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~-~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLK-RLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 47889999999998 899999887 9999999974
No 70
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=62.75 E-value=4 Score=28.91 Aligned_cols=37 Identities=16% Similarity=0.132 Sum_probs=27.5
Q ss_pred hcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 105 ~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
+....+|.+++++.++++ . .|+. +.+..|+|+-.-..
T Consensus 3 ~~~~~lt~~Elc~~~gi~-~----~~l~-eLve~GlIep~~~~ 39 (101)
T PRK10265 3 NVTVTFTITEFCLHTGVS-E----EELN-EIVGLGVIEPREIQ 39 (101)
T ss_pred ceEEEeeHHHHHHHHCcC-H----HHHH-HHHHCCCeecCCCC
Confidence 334568999999999999 4 4555 66679999865444
No 71
>PHA02763 hypothetical protein; Provisional
Probab=62.23 E-value=9.8 Score=26.74 Aligned_cols=50 Identities=20% Similarity=0.173 Sum_probs=42.3
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeeccC
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLVRL 161 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~Rv 161 (161)
.+|-+-+++-++.+.-+.||+|+= +| ..|=.-+||...=.+.|-|+..|.
T Consensus 52 p~t~~~LsKYv~~SGFe~VEeWl~-eA--rrLh~~~id~~ryeiivi~in~~~ 101 (102)
T PHA02763 52 PVTEYCLSKYVKFSGFENVEEWLN-EA--RRLHNDKIDPERYEIIVIWINGRL 101 (102)
T ss_pred CchHHHHHHHhhhcchhhHHHHHH-HH--HHHhcCCCChhheEEEEEEEcCcc
Confidence 556667778888887899999998 88 677788999999999999998773
No 72
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=62.04 E-value=11 Score=35.69 Aligned_cols=116 Identities=13% Similarity=0.245 Sum_probs=78.8
Q ss_pred chhhhcCcccccccCCC---chhHHHHHHHHhcCCHhHHhhc-cCC------CCCCC---HHHHHHHHHHHHHHhh----
Q 031323 42 FSEILAVPNIAEFEGTE---NSKYLDMLRLFAHGTWSDYKNN-AGH------LPQLV---PDQVLKLKQLTVLTLA---- 104 (161)
Q Consensus 42 f~eLl~~~~v~~L~~s~---~~~l~~LL~iF~~G~~~dy~~~-~~~------~~~L~---~~~~~KlrlLtL~sLa---- 104 (161)
|...|.+---+.+.+++ -.-+..-=+.+..|+|.+-.++ .+. +|.-. ....+|++-=+|-+.-
T Consensus 634 frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYs 713 (843)
T KOG1076|consen 634 FRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYS 713 (843)
T ss_pred HHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44455555555555543 1225556678889999877662 122 23221 2234566654444433
Q ss_pred hcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV 159 (161)
Q Consensus 105 ~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~ 159 (161)
.-...+|.+.+|+-..+| ...|=..|= ++|...=|.+++||+.++|.+.++.|
T Consensus 714 s~Y~SvSl~~LA~mFdLp-~~~VhsIiS-kmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 714 SVYDSVSLAKLADMFDLP-EPKVHSIIS-KMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred hhhhhccHHHHHHHhCCC-chhHHHHHH-HHHHHHHhhhccCCCcceEEEeeccc
Confidence 346789999999999999 888888776 88888889999999999999999865
No 73
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=61.87 E-value=31 Score=20.44 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=30.7
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEec
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkID 146 (161)
.+.+++.+|++.++++ ...+-..+= .....|++.-.=+
T Consensus 8 ~~~~~~~~i~~~l~is-~~~v~~~l~-~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLS-QSTVSHHLK-KLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeeec
Confidence 5678999999999998 778877655 8888999985544
No 74
>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=60.86 E-value=40 Score=26.37 Aligned_cols=47 Identities=13% Similarity=0.172 Sum_probs=36.9
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
.++.++..+|++.++++ ...+-..+- +....|+|+-.-+ ..+.+++|
T Consensus 154 ~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~lT 200 (203)
T TIGR01884 154 AEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSLT 200 (203)
T ss_pred HcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEeC
Confidence 44579999999999998 888888877 8889999986643 45555554
No 75
>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=58.96 E-value=22 Score=21.97 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=30.5
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
...++..+|++.++++ ...|...+= .....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s-~~tv~r~l~-~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLT-RETVSRTLK-ELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 3579999999999998 999998877 8888999874
No 76
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=58.50 E-value=16 Score=31.61 Aligned_cols=63 Identities=17% Similarity=0.270 Sum_probs=53.1
Q ss_pred HHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 92 ~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
.+-||.=.-..+-+..|.+|.+..|+..|++ .+-|+.=+= +-|-.|=+.+.||.+++.|.+++
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg-~FIp~~~LncvIDRvnGvVetnr 376 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLG-EFIPEGRLNCVIDRVNGVVETNR 376 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHH-hhCCCCceeeeeecccceEeccC
Confidence 4666666666666778899999999999998 888888777 77889999999999999999876
No 77
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=57.85 E-value=20 Score=21.45 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=22.9
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHh
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~ 137 (161)
....||.+|++.+|++ ...|-.+.- +|+.
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~-~al~ 46 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILK-RALK 46 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHH-HHHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHH-HHHH
Confidence 4578999999999998 888888766 6653
No 78
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=57.55 E-value=23 Score=25.84 Aligned_cols=42 Identities=19% Similarity=0.327 Sum_probs=34.1
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
.++++|.. ..|-+|||..+++| ..-|--++= +.+..|++..+
T Consensus 47 ~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvs-DL~~~G~v~v~ 88 (114)
T PF05331_consen 47 AILELCRR--PLSVAEIAARLGLP-LGVVRVLVS-DLADAGLVRVR 88 (114)
T ss_pred HHHHHHCC--CccHHHHHHhhCCC-chhhhhhHH-HHHhCCCEEEe
Confidence 46677766 89999999999999 766666666 89999998764
No 79
>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=57.19 E-value=45 Score=20.71 Aligned_cols=47 Identities=17% Similarity=0.274 Sum_probs=33.1
Q ss_pred hhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCE
Q 031323 103 LAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (161)
Q Consensus 103 La~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~ 151 (161)
++..++..+..+|++.++++ ...+=..+= ++...|+|+=.=|+..+.
T Consensus 12 l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~-~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 12 LAHSDGPMTQSDLAERLGIS-KSTVSRIIK-KLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HT--TS-BEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEESSCTT
T ss_pred HHccCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecCCCCcCC
Confidence 33467789999999999998 888877544 899999997776665554
No 80
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=56.29 E-value=28 Score=26.03 Aligned_cols=51 Identities=14% Similarity=0.295 Sum_probs=41.7
Q ss_pred CHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (161)
Q Consensus 88 ~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi 141 (161)
++++..+| +..+++++..++-+|+.++...+|++ .+.++.++- +++..|-+
T Consensus 6 T~eer~eL-k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lr-eLVa~G~l 56 (127)
T PF06163_consen 6 TPEEREEL-KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLR-ELVARGDL 56 (127)
T ss_pred CHHHHHHH-HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCCe
Confidence 44433333 46788899999999999999999998 999999999 99888765
No 81
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=55.68 E-value=30 Score=27.92 Aligned_cols=46 Identities=17% Similarity=0.196 Sum_probs=36.2
Q ss_pred HHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 96 rlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
|-|.++.+-...+.++..+|++.++++ ...+=.++= .....|++.=
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~-kstv~Rll~-tL~~~G~l~~ 60 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMS-KSTVYRFLQ-TMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence 445555544445679999999999999 999999887 8888999864
No 82
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=53.91 E-value=22 Score=24.12 Aligned_cols=32 Identities=19% Similarity=0.404 Sum_probs=25.5
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
||++++++.++++ . .|+. +.+..|+|+-...+
T Consensus 1 is~~e~~~~~~i~-~----~~l~-~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-P----EFLR-ELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-H----HHHH-HHHHCCCeeecCCC
Confidence 6899999999998 4 4455 66669999987766
No 83
>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=53.65 E-value=49 Score=20.08 Aligned_cols=35 Identities=34% Similarity=0.416 Sum_probs=29.4
Q ss_pred cCCccC-HHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 106 TNKVLP-YDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 106 ~~~~is-y~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
.+..++ -.+|++.++++ ...|-..+- +.-..|+|.
T Consensus 21 ~~~~~~~~~~la~~~~is-~~~v~~~l~-~L~~~G~i~ 56 (66)
T cd07377 21 PGDRLPSERELAEELGVS-RTTVREALR-ELEAEGLVE 56 (66)
T ss_pred CCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 344454 99999999998 999999888 999999986
No 84
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=53.23 E-value=22 Score=23.95 Aligned_cols=30 Identities=23% Similarity=0.185 Sum_probs=23.6
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHhcC
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (161)
...||.+||+.++++ ...|..++- .-.+.|
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~-~~~~~~ 60 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLK-GETKAG 60 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHh-cCcccc
Confidence 468999999999998 999988765 433333
No 85
>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=52.96 E-value=38 Score=23.12 Aligned_cols=50 Identities=12% Similarity=0.187 Sum_probs=39.3
Q ss_pred HHHHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 94 KLKQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 94 KlrlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
-.|.|+-+.+.- ++.-+|.+.|.+..+++ ..+++.-+- +.+..|+|.-+.
T Consensus 8 d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~-~~~~~~~L~-~L~~~kLv~~~~ 58 (82)
T PF09202_consen 8 DFRVLRAIEMGMKNHEWVPLELIEKISGLS-EGEVEKRLK-RLVKLKLVSRRN 58 (82)
T ss_dssp HHHHHHHHHTTTTT-SSEEHHHHHHHHT---HHHHHHHHH-HHHHTTSEEEE-
T ss_pred HHHHHHHHHHcccCCccCCHHHHHHHhCcC-HHHHHHHHH-HHHhcCCccccC
Confidence 467788887776 56788999999999999 999999877 999999998743
No 86
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=52.74 E-value=17 Score=27.56 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.5
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
-..+||++||+.++++ ...|...+- .|.
T Consensus 141 ~~gls~~EIA~~l~i~-~~tVks~l~-ra~ 168 (182)
T COG1595 141 LEGLSYEEIAEILGIS-VGTVKSRLH-RAR 168 (182)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3579999999999999 999999887 764
No 87
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=52.21 E-value=49 Score=26.77 Aligned_cols=59 Identities=17% Similarity=0.173 Sum_probs=48.8
Q ss_pred HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
-+++|.+++-..+ -.+|-.++++.++++ ....=.|+. +.-..|.|.=++....+-+.+|
T Consensus 5 ~lk~l~~~~a~~~-~~~t~~ela~~l~~S-~qta~R~l~-~le~~~~I~R~~~~~Gq~i~iT 63 (214)
T COG1339 5 LLKKLALRGAVRG-VKVTSSELAKRLGVS-SQTAARKLK-ELEDEGYITRTISKRGQLITIT 63 (214)
T ss_pred HHHHHHHhhhhcC-ccccHHHHHHHhCcC-cHHHHHHHH-hhccCCcEEEEecCCCcEEEeh
Confidence 3455666665556 789999999999998 788888999 9889999999998888888776
No 88
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=51.59 E-value=31 Score=22.37 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=29.0
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+..++=.+||++|+++ ...+-.++. ..-..|.|+
T Consensus 13 ~~p~~T~eiA~~~gls-~~~aR~yL~-~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLS-IYQARYYLE-KLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS--HHHHHHHHH-HHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCEE
Confidence 5678889999999998 999999999 999999875
No 89
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=51.40 E-value=28 Score=20.75 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=23.6
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
.++.++... .|+.+||+.++++ .+.|..++-
T Consensus 19 ~i~~~~~~~--~s~~~vA~~~~vs-~~TV~ri~~ 49 (52)
T PF13542_consen 19 YILKLLRES--RSFKDVARELGVS-WSTVRRIFD 49 (52)
T ss_pred HHHHHHhhc--CCHHHHHHHHCCC-HHHHHHHHH
Confidence 444555443 7999999999998 888888654
No 90
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=51.16 E-value=29 Score=29.48 Aligned_cols=39 Identities=23% Similarity=0.295 Sum_probs=35.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCC
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~ 148 (161)
.-++-++||+.++++ .-.|=.++= +|...|+++-+|+..
T Consensus 28 ~g~tQ~eIA~~lgiS-R~~VsRlL~-~Ar~~GiV~I~I~~~ 66 (318)
T PRK15418 28 DGLTQSEIGERLGLT-RLKVSRLLE-KGRQSGIIRVQINSR 66 (318)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHHHcCcEEEEEeCC
Confidence 468999999999998 999999988 999999999999865
No 91
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=50.37 E-value=36 Score=26.32 Aligned_cols=33 Identities=15% Similarity=0.188 Sum_probs=28.6
Q ss_pred cCHHHHHHhc--CCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 110 LPYDELMEEL--DVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 110 isy~~I~~~l--~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
-.++.||+.| +|+ .++|+.-+- -....|+|+=.
T Consensus 40 ~d~~~iak~l~p~is-~~ev~~sL~-~L~~~gli~k~ 74 (171)
T PF14394_consen 40 PDPEWIAKRLRPKIS-AEEVRDSLE-FLEKLGLIKKD 74 (171)
T ss_pred CCHHHHHHHhcCCCC-HHHHHHHHH-HHHHCCCeEEC
Confidence 3899999999 998 999999877 88899998743
No 92
>PHA02943 hypothetical protein; Provisional
Probab=50.23 E-value=52 Score=25.55 Aligned_cols=44 Identities=18% Similarity=0.227 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+|...|.++ ..+.-|-.+||+++|++ ..+++..+- -.-+.|.|+
T Consensus 12 R~~eILE~L----k~G~~TtseIAkaLGlS-~~qa~~~Ly-vLErEG~Vk 55 (165)
T PHA02943 12 RMIKTLRLL----ADGCKTTSRIANKLGVS-HSMARNALY-QLAKEGMVL 55 (165)
T ss_pred HHHHHHHHH----hcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCceE
Confidence 344444444 55678889999999998 999998877 666666665
No 93
>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=49.74 E-value=27 Score=24.31 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=27.5
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
++.++-++|++.++++ ..+|-.++- .....|+|..+
T Consensus 25 ~~~l~de~la~~~~l~-~~~vRkiL~-~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLK-PKEVRKILY-KLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S--HHHHHHHHH-HHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeEEE
Confidence 4579999999999999 999999988 99999999665
No 94
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=49.58 E-value=81 Score=24.11 Aligned_cols=61 Identities=15% Similarity=0.241 Sum_probs=43.3
Q ss_pred hhHHHHHHHHhcCCHhHHhhcc--CCCCCCC----HHHHHHHHHHHHHHhhhcCCc-cCHHHHHHhcC
Q 031323 60 SKYLDMLRLFAHGTWSDYKNNA--GHLPQLV----PDQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (161)
Q Consensus 60 ~~l~~LL~iF~~G~~~dy~~~~--~~~~~L~----~~~~~KlrlLtL~sLa~~~~~-isy~~I~~~l~ 120 (161)
.-..++...+..|++..|.+.- ...|.+. +....++|.-++-.++...+. +|-+.+++-|+
T Consensus 136 ~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 136 QFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 4467888999999999999744 3344332 224789999999999987776 88888888765
No 95
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=49.23 E-value=20 Score=27.10 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=24.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ .+.|..++- +|.
T Consensus 148 ~~~s~~eIA~~lgis-~~tV~~~l~-ra~ 174 (182)
T PRK12537 148 DGCSHAEIAQRLGAP-LGTVKAWIK-RSL 174 (182)
T ss_pred cCCCHHHHHHHHCCC-hhhHHHHHH-HHH
Confidence 468999999999999 999999988 774
No 96
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=48.40 E-value=22 Score=23.09 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.7
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHH
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~l 130 (161)
.++.+++.+||+.|+++ ...|-.|
T Consensus 19 ~~g~i~lkdIA~~Lgvs-~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVS-ESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCC-HHHHHHH
Confidence 36789999999999998 8888776
No 97
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=48.12 E-value=21 Score=23.89 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=20.9
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCC-ChhhH
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVT-NVREL 127 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~-~~~ev 127 (161)
+.++.-..-++..||.+||+.++.+ ....|
T Consensus 6 ~~~v~~IP~G~v~TYg~iA~~~g~p~~~R~V 36 (79)
T cd06445 6 WEALRQIPYGEVTTYGQIAKLAGTPKAARAV 36 (79)
T ss_pred HHHHhcCCCCCcCcHHHHHHHHCCCCcHHHH
Confidence 3334334468899999999999986 23444
No 98
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=47.92 E-value=12 Score=27.84 Aligned_cols=23 Identities=30% Similarity=0.531 Sum_probs=20.6
Q ss_pred hhhHHHHHHHHhHhcCCcEEEecC
Q 031323 124 VRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 124 ~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
..-||.++| ++...|-|.+||++
T Consensus 69 Aq~VE~~li-rma~~gQvs~Kise 91 (129)
T KOG3431|consen 69 AQAVENYLI-RMAQTGQVSHKISE 91 (129)
T ss_pred HHHHHHHHH-HHHHhCCccccccH
Confidence 356999999 99999999999975
No 99
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=47.68 E-value=46 Score=26.96 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=36.4
Q ss_pred HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
-|+..++.+-..++.++.++|++.++++ ...|...+- +.-..|++.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~-~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLN-ELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 3566677777778899999999999998 888888877 665666664
No 100
>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=47.22 E-value=51 Score=26.40 Aligned_cols=45 Identities=20% Similarity=0.265 Sum_probs=37.6
Q ss_pred HHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 96 rlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
|-|.++++.. ..+.++..+|++.++++ ...+-.++- .....|+++
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglp-ksT~~RlL~-tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLT-RAAARRFLL-TLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 4566666544 46789999999999999 999999988 889999997
No 101
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=46.70 E-value=21 Score=21.12 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=18.0
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHH
Q 031323 109 VLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI 132 (161)
-.|+.+||+.++++ ...|-.|+=
T Consensus 17 G~s~~~ia~~lgvs-~~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVS-RSTVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS--HHHHHHHHT
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH
Confidence 58999999999998 999999864
No 102
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=45.87 E-value=26 Score=26.28 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=23.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tVk~~l~-Rar 175 (183)
T TIGR02999 149 AGLTVEEIAELLGVS-VRTVERDWR-FAR 175 (183)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 469999999999999 999998877 664
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=45.78 E-value=27 Score=26.07 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=24.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMY 137 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~ 137 (161)
...||.+||+.+|++ ...|...+- +|+.
T Consensus 134 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~~ 161 (172)
T PRK12523 134 DGMGHAEIAERLGVS-VSRVRQYLA-QGLR 161 (172)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHHH
Confidence 468999999999999 999999877 7653
No 104
>PRK10870 transcriptional repressor MprA; Provisional
Probab=45.38 E-value=1.1e+02 Score=23.48 Aligned_cols=51 Identities=14% Similarity=0.023 Sum_probs=41.6
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL 158 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~ 158 (161)
++..++..+|++.++++ ...|=..|= +....|+|+=.-|...+.+..-..+
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~LT 118 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQLT 118 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEEC
Confidence 35679999999999998 788877655 8999999999999888776655444
No 105
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=45.00 E-value=37 Score=21.01 Aligned_cols=33 Identities=18% Similarity=0.272 Sum_probs=20.5
Q ss_pred HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHH
Q 031323 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (161)
Q Consensus 93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lv 131 (161)
+|+..+ .....+. +..+||+.+|++ ...|-.|+
T Consensus 11 eK~~iI---~~~e~g~--s~~~ia~~fgv~-~sTv~~I~ 43 (53)
T PF04218_consen 11 EKLEII---KRLEEGE--SKRDIAREFGVS-RSTVSTIL 43 (53)
T ss_dssp HHHHHH---HHHHCTT---HHHHHHHHT---CCHHHHHH
T ss_pred HHHHHH---HHHHcCC--CHHHHHHHhCCC-HHHHHHHH
Confidence 454444 4444554 999999999998 77777654
No 106
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=44.98 E-value=77 Score=19.86 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=21.6
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
..|.++.++||+.++|+ ...+..-+= +|
T Consensus 20 ~PR~~tl~elA~~lgis-~st~~~~LR-ra 47 (53)
T PF04967_consen 20 VPRRITLEELAEELGIS-KSTVSEHLR-RA 47 (53)
T ss_pred CCCcCCHHHHHHHhCCC-HHHHHHHHH-HH
Confidence 35899999999999998 666665544 44
No 107
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.12 E-value=29 Score=25.42 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=23.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- .|.
T Consensus 121 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIE-VKTVEMKLY-RAR 147 (160)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 469999999999999 999998876 663
No 108
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=44.02 E-value=1.1e+02 Score=22.17 Aligned_cols=51 Identities=16% Similarity=0.091 Sum_probs=41.6
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeeec
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVLV 159 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~~ 159 (161)
...++-.+|++.++++ ...|=..|= .....|+|.=.-|+..+....-+.++
T Consensus 52 ~~~~t~~eLa~~l~i~-~~tvsr~l~-~Le~~GlI~R~~~~~DrR~~~l~LT~ 102 (144)
T PRK11512 52 AACITPVELKKVLSVD-LGALTRMLD-RLVCKGWVERLPNPNDKRGVLVKLTT 102 (144)
T ss_pred cCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEeccCcccCCeeEeEECh
Confidence 4569999999999998 777777655 88899999999998888776665554
No 109
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=43.12 E-value=40 Score=28.87 Aligned_cols=37 Identities=22% Similarity=0.334 Sum_probs=34.3
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
.++-++||+.++|+ ..-|=.++= +|...|+|+-+|+.
T Consensus 26 gltQ~eIA~~LgiS-R~~v~rlL~-~Ar~~GiV~I~i~~ 62 (321)
T COG2390 26 GLTQSEIAERLGIS-RATVSRLLA-KAREEGIVKISINS 62 (321)
T ss_pred CCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCeEEEEeCC
Confidence 68999999999998 999999988 99999999999984
No 110
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=43.02 E-value=33 Score=24.85 Aligned_cols=27 Identities=11% Similarity=0.056 Sum_probs=23.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...|+.+||+.+|++ ...|..++- +|+
T Consensus 121 ~~~s~~EIA~~l~is-~~tV~~~~~-ra~ 147 (154)
T PRK06759 121 VGKTMGEIALETEMT-YYQVRWIYR-QAL 147 (154)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999999 999999877 764
No 111
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=42.62 E-value=32 Score=25.06 Aligned_cols=27 Identities=4% Similarity=0.030 Sum_probs=22.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 121 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAMGCS-EGSVKTHCS-RAT 147 (161)
T ss_pred hcCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 368999999999998 999988876 654
No 112
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=42.30 E-value=33 Score=25.92 Aligned_cols=27 Identities=7% Similarity=0.361 Sum_probs=23.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- .|+
T Consensus 142 ~g~s~~EIA~~lgis-~~tVk~~l~-rAl 168 (178)
T PRK12529 142 DGMKQKDIAQALDIA-LPTVKKYIH-QAY 168 (178)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998877 664
No 113
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=42.28 E-value=33 Score=25.66 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=24.0
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
....||++||+.+|++ ...|...+= +|.
T Consensus 133 ~~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 160 (172)
T PRK09651 133 LDGLTYSEIAHKLGVS-VSSVKKYVA-KAT 160 (172)
T ss_pred ccCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3578999999999999 999998877 764
No 114
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=42.03 E-value=69 Score=26.21 Aligned_cols=54 Identities=13% Similarity=0.148 Sum_probs=39.5
Q ss_pred HHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEE
Q 031323 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFE 153 (161)
Q Consensus 96 rlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~ 153 (161)
|-|.++++-. .++.++..+|+++++++ ...+=.++- .....|++.- |..++...
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglp-kStv~RlL~-tL~~~G~l~~--~~~~~~Y~ 80 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLP-LSTTFRLLK-VLQAADFVYQ--DSQLGWWH 80 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE--cCCCCeEE
Confidence 3455555443 45679999999999999 999999888 8889999843 44444443
No 115
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=41.96 E-value=36 Score=23.93 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=24.2
Q ss_pred HHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 114 ELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 114 ~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
.||..++++ .++|+..+- +....|||+
T Consensus 26 ~ia~~l~~~-~~~v~~~l~-~Le~~GLle 52 (92)
T PF10007_consen 26 SIARRLKIP-LEEVREALE-KLEEMGLLE 52 (92)
T ss_pred HHHHHHCCC-HHHHHHHHH-HHHHCCCeE
Confidence 488899999 999999988 999999975
No 116
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=41.95 E-value=45 Score=19.36 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=20.8
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 110 LPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
.++.+|++.++++ ...|..++= ++
T Consensus 19 ~s~~eia~~l~is-~~tv~~~~~-~~ 42 (58)
T smart00421 19 LTNKEIAERLGIS-EKTVKTHLS-NI 42 (58)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 6999999999998 999998765 54
No 117
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=41.75 E-value=62 Score=22.71 Aligned_cols=42 Identities=17% Similarity=0.197 Sum_probs=30.9
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCC-CChhhHHHHHHHHhHhcCCcE
Q 031323 98 LTVLTLAETNKVLPYDELMEELDV-TNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i-~~~~evE~lvI~~ai~~gLi~ 142 (161)
+.++.++...+. |+..||+.++| + ...+-.|++ ++...+...
T Consensus 14 ~~iv~~~~~~g~-sv~~vAr~~gv~~-~~~l~~W~~-~~~~~~~~~ 56 (116)
T COG2963 14 LEAVALYLRGGD-TVSEVAREFGIVS-ATQLYKWRI-QLQKGGGLA 56 (116)
T ss_pred HHHHHHHHhcCc-cHHHHHHHhCCCC-hHHHHHHHH-HHHHccccc
Confidence 344555554333 99999999997 6 999999999 887665544
No 118
>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=41.51 E-value=53 Score=22.33 Aligned_cols=41 Identities=22% Similarity=0.291 Sum_probs=26.7
Q ss_pred HHHHHHhhhcCCccCHHHHHHhcCCCChh----hHHHHHHHHhHhcCCcE
Q 031323 97 QLTVLTLAETNKVLPYDELMEELDVTNVR----ELEDFLINECMYTGIVR 142 (161)
Q Consensus 97 lLtL~sLa~~~~~isy~~I~~~l~i~~~~----evE~lvI~~ai~~gLi~ 142 (161)
.|..+--.++++.+..+.||..++.+ .+ .+|.++| + .|+|.
T Consensus 13 yL~~l~~~f~ggPvGl~tlA~~l~ed-~~Tie~v~EPyLi-q---~G~I~ 57 (76)
T PF05491_consen 13 YLKTLIENFKGGPVGLDTLAAALGED-KETIEDVIEPYLI-Q---IGFIQ 57 (76)
T ss_dssp HHHHHHHCSTTS-B-HHHHHHHTTS--HHHHHHTTHHHHH-H---TTSEE
T ss_pred HHHHHHHHcCCCCeeHHHHHHHHCCC-HhHHHHHhhHHHH-H---hhhHh
Confidence 34444444578899999999999987 44 4667777 4 78775
No 119
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=41.50 E-value=32 Score=26.11 Aligned_cols=26 Identities=23% Similarity=0.261 Sum_probs=22.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 146 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra 171 (191)
T PRK12520 146 LELETEEICQELQIT-ATNAWVLLY-RA 171 (191)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 358999999999999 999998876 65
No 120
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=41.45 E-value=64 Score=24.03 Aligned_cols=36 Identities=28% Similarity=0.280 Sum_probs=32.2
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
.++..+-++||+.++.+ ...|..-|= +.+..|+|.=
T Consensus 39 ~~~~~tvdelae~lnr~-rStv~rsl~-~L~~~GlV~R 74 (126)
T COG3355 39 ENGPLTVDELAEILNRS-RSTVYRSLQ-NLLEAGLVER 74 (126)
T ss_pred hcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeee
Confidence 56789999999999998 999999888 9999999863
No 121
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=41.02 E-value=31 Score=22.85 Aligned_cols=21 Identities=38% Similarity=0.433 Sum_probs=18.0
Q ss_pred cCHHHHHHhcCCCChhhHHHHH
Q 031323 110 LPYDELMEELDVTNVRELEDFL 131 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lv 131 (161)
.+-++|++.|+++ ..|+|-++
T Consensus 45 a~~~el~~~CgL~-~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLS-RAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCC-HHHHHHHH
Confidence 6779999999999 99999653
No 122
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=40.84 E-value=57 Score=25.36 Aligned_cols=36 Identities=8% Similarity=0.198 Sum_probs=32.0
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEec
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkID 146 (161)
-.|..+||+.++|+ ...|+..+= -+...|++...+.
T Consensus 177 g~s~~eIa~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~ 212 (225)
T PRK10046 177 QHTAETVAQALTIS-RTTARRYLE-YCASRHLIIAEIV 212 (225)
T ss_pred CcCHHHHHHHhCcc-HHHHHHHHH-HHHhCCeEEEEee
Confidence 47899999999998 999999988 8888999887775
No 123
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=40.59 E-value=61 Score=26.68 Aligned_cols=48 Identities=10% Similarity=0.074 Sum_probs=37.8
Q ss_pred HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+.-|+..++.+...++.++..++++.++++ ..-+-.=+. ..-..|++.
T Consensus 15 ~~eR~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~-~Le~~G~l~ 62 (269)
T PRK09802 15 TSERREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLA-FLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHH-HHHhCCCeE
Confidence 345788888888877789999999999998 777766666 555677765
No 124
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=40.22 E-value=63 Score=26.28 Aligned_cols=47 Identities=11% Similarity=0.155 Sum_probs=38.3
Q ss_pred HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
-|+..++.+...++.++-.++++.++++ ...+-..+- +.-..|+|.-
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS-~~TirRdL~-~Le~~g~i~r 51 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGIS-PATARRDIN-KLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence 3556677777788899999999999998 888888877 7777888754
No 125
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=40.01 E-value=37 Score=25.54 Aligned_cols=27 Identities=7% Similarity=0.224 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 132 e~~s~~EIA~~lgis-~~tV~~~l~-ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIP-IGTVKSRIH-AAL 158 (179)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999999 999988866 653
No 126
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=39.89 E-value=37 Score=25.29 Aligned_cols=28 Identities=25% Similarity=0.519 Sum_probs=23.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMY 137 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~ 137 (161)
...||++||+.++++ ...|...+- .|+.
T Consensus 133 eg~s~~EIA~~l~is-~~tV~~~l~-ra~~ 160 (168)
T PRK12525 133 EGLTYVEIGERLGVS-LSRIHQYMV-EAFK 160 (168)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHHH
Confidence 468999999999999 999998877 7653
No 127
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=39.81 E-value=39 Score=29.80 Aligned_cols=47 Identities=17% Similarity=0.273 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 92 ~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
.+.+-+|.++++|-+ +-|.-+||+.++++ .+++...+- +....||++
T Consensus 340 ~~~~~~l~~L~~~DG--~~slldIA~~~~~~-~~~~~~~~~-~l~~~~Llk 386 (386)
T PF09940_consen 340 AQQMAMLWVLNYSDG--KNSLLDIAERIGLP-FDELADAAR-KLLEAGLLK 386 (386)
T ss_dssp --HHHHHHHHHH-EE--EEEHHHHHHHHT---HHHHHHHHH-HHHHTT-EE
T ss_pred HHHHHHHHHHHhccC--CCcHHHHHHHHCcC-HHHHHHHHH-HHHHcCCCC
Confidence 455667888888854 56789999999999 999999888 999999985
No 128
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=39.76 E-value=39 Score=24.76 Aligned_cols=27 Identities=11% Similarity=0.158 Sum_probs=22.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+= +|+
T Consensus 124 ~~~s~~EIA~~lgis-~~tV~~~l~-ra~ 150 (163)
T PRK07037 124 HGETQKDIARELGVS-PTLVNFMIR-DAL 150 (163)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998865 553
No 129
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=39.66 E-value=36 Score=25.47 Aligned_cols=26 Identities=31% Similarity=0.517 Sum_probs=22.4
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
..||++||+.+|++ ...|...+- .|.
T Consensus 145 g~s~~eIA~~lgis-~~tV~~~l~-Rar 170 (179)
T PRK12514 145 GLSYKELAERHDVP-LNTMRTWLR-RSL 170 (179)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH-HHH
Confidence 58999999999999 999988876 653
No 130
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=39.31 E-value=52 Score=19.20 Aligned_cols=25 Identities=12% Similarity=0.178 Sum_probs=21.2
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
..++.+||+.++++ ...|+.++= ++
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~-~~ 39 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLR-NI 39 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 37999999999998 999998865 44
No 131
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=39.27 E-value=40 Score=24.65 Aligned_cols=27 Identities=19% Similarity=0.370 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- .|.
T Consensus 120 ~~~s~~eIA~~lgis-~~tv~~~l~-ra~ 146 (159)
T PRK12527 120 EGLSHQQIAEHLGIS-RSLVEKHIV-NAM 146 (159)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999988876 663
No 132
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=39.03 E-value=39 Score=24.74 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=23.6
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- .|.
T Consensus 125 ~g~s~~eIA~~lgis-~~tV~~~l~-ra~ 151 (162)
T TIGR02983 125 EDLSEAQVAEALGIS-VGTVKSRLS-RAL 151 (162)
T ss_pred hcCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 368999999999999 999999887 764
No 133
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=38.74 E-value=37 Score=25.81 Aligned_cols=27 Identities=15% Similarity=0.196 Sum_probs=23.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||.+||+.+|++ ...|...+- +|.
T Consensus 146 ~g~s~~EIA~~lgis-~~tVk~~l~-Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTP-IGTVMSRLH-RGR 172 (193)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 653
No 134
>PRK11569 transcriptional repressor IclR; Provisional
Probab=38.61 E-value=81 Score=25.79 Aligned_cols=45 Identities=20% Similarity=0.299 Sum_probs=36.8
Q ss_pred HHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 96 rlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
|-|.++.+.. ..+.++..+|++.++++ ...|=.++- .....|++.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglp-ksTv~RlL~-tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLP-NSTTHRLLT-TMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 4455555444 46789999999999999 999999988 999999996
No 135
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=38.49 E-value=40 Score=24.96 Aligned_cols=27 Identities=7% Similarity=0.123 Sum_probs=23.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+- +|.
T Consensus 127 ~g~s~~eIA~~lgis-~~tV~~~l~-Rar 153 (164)
T PRK12547 127 SGFSYEDAAAICGCA-VGTIKSRVS-RAR 153 (164)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998877 664
No 136
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=37.76 E-value=98 Score=24.19 Aligned_cols=38 Identities=16% Similarity=0.228 Sum_probs=33.4
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEec
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkID 146 (161)
...+|.++||+.++++ ...|+..+. .+...|++.-+++
T Consensus 176 ~~g~s~~eIA~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~ 213 (239)
T PRK10430 176 DYEFSTDELANAVNIS-RVSCRKYLI-WLVNCHILFTSIH 213 (239)
T ss_pred CCCcCHHHHHHHhCch-HHHHHHHHH-HHHhCCEEEEEee
Confidence 4568999999999998 999999999 9999999866554
No 137
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=37.69 E-value=29 Score=32.07 Aligned_cols=55 Identities=16% Similarity=0.242 Sum_probs=36.9
Q ss_pred HHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecC-----CCCEEEEEeeec
Q 031323 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ-----LRRCFEVCTVLV 159 (161)
Q Consensus 101 ~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq-----~~~~v~V~~~~~ 159 (161)
+.++......+..+|++.++|+ .+++|.+ .-.++++--..++. ..+.|.||++.|
T Consensus 6 ~eia~~~~~~~i~~ia~~~gl~-~~~~e~Y---g~~kaki~~~~~~~~~~~~~~k~IlVTS~~P 65 (557)
T PRK13505 6 IEIAQEATLKPITEIAAKLGIP-EDDLEPY---GKYKAKISLDKIKALKDKKDGKLILVTAINP 65 (557)
T ss_pred HHHHhhCCCcCHHHHHHHcCCC-HHHHHhc---cCcceeeCHHHHhhhccCCCCeEEEEecCCC
Confidence 4556555677999999999999 8898876 33333332222233 357889988776
No 138
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=37.66 E-value=69 Score=26.10 Aligned_cols=45 Identities=20% Similarity=0.215 Sum_probs=34.6
Q ss_pred HHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (161)
Q Consensus 95 lrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi 141 (161)
-|+-.++++-..++.++..++++.++++ ...|=.=+. +.-..|++
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TIRRDL~-~Le~~g~l 49 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTT-GTTIRKDLV-ILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHHHHHHH-HHHHCCCE
Confidence 3777778888888899999999999998 666655555 55567754
No 139
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=37.18 E-value=40 Score=21.44 Aligned_cols=23 Identities=22% Similarity=0.172 Sum_probs=19.7
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHH
Q 031323 109 VLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI 132 (161)
-.+..+||+.|+++ ...|-.|.=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 47899999999999 888888854
No 140
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=37.14 E-value=44 Score=25.41 Aligned_cols=27 Identities=19% Similarity=0.149 Sum_probs=22.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 154 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 180 (194)
T PRK12513 154 GDLELEEIAELTGVP-EETVKSRLR-YAL 180 (194)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999998 999988766 653
No 141
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=36.73 E-value=47 Score=24.37 Aligned_cols=27 Identities=22% Similarity=0.452 Sum_probs=23.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 128 ~g~s~~EIA~~l~is-~~tV~~~l~-ra~ 154 (161)
T PRK12528 128 DGLGYGEIATELGIS-LATVKRYLN-KAA 154 (161)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999999 999998877 664
No 142
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=36.44 E-value=64 Score=18.98 Aligned_cols=24 Identities=13% Similarity=0.230 Sum_probs=15.4
Q ss_pred hhhcCCccCHHHHHHhcCCCChhhHHH
Q 031323 103 LAETNKVLPYDELMEELDVTNVRELED 129 (161)
Q Consensus 103 La~~~~~isy~~I~~~l~i~~~~evE~ 129 (161)
|...+ .|..+||+.++|+ ...|-.
T Consensus 17 l~~~G--~si~~IA~~~gvs-r~TvyR 40 (45)
T PF02796_consen 17 LYAEG--MSIAEIAKQFGVS-RSTVYR 40 (45)
T ss_dssp HHHTT----HHHHHHHTTS--HHHHHH
T ss_pred HHHCC--CCHHHHHHHHCcC-HHHHHH
Confidence 33444 9999999999998 666544
No 143
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.52 E-value=46 Score=25.40 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=22.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+= +|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tVk~~l~-RAr 175 (189)
T PRK12530 149 LELSSEQICQECDIS-TSNLHVLLY-RAR 175 (189)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 368999999999999 999988866 553
No 144
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=35.23 E-value=50 Score=19.36 Aligned_cols=21 Identities=14% Similarity=0.528 Sum_probs=16.5
Q ss_pred HHHHHhcCCCChhhHHHHHHHHh
Q 031323 113 DELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 113 ~~I~~~l~i~~~~evE~lvI~~a 135 (161)
+.|++.+|++ ..+|..|++ .+
T Consensus 17 ~~L~~~tgls-~~Qi~~WF~-Na 37 (40)
T PF05920_consen 17 EELAKQTGLS-RKQISNWFI-NA 37 (40)
T ss_dssp HHHHHHHTS--HHHHHHHHH-HH
T ss_pred HHHHHHcCCC-HHHHHHHHH-Hh
Confidence 4578888998 999999999 65
No 145
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=35.23 E-value=1e+02 Score=25.04 Aligned_cols=44 Identities=25% Similarity=0.294 Sum_probs=34.9
Q ss_pred HHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 97 QLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 97 lLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
-|.++++-. ....++..+|++.++++ ...+=.++. .....|+++
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glp-ksT~~RlL~-tL~~~G~v~ 50 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLP-KSTVHRLLQ-TLVELGYVE 50 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEE
Confidence 345555443 34448999999999999 999999999 999999986
No 146
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=35.19 E-value=48 Score=25.33 Aligned_cols=26 Identities=23% Similarity=0.318 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 157 ~~~s~~EIA~~Lgis-~~tVk~~l~-ra 182 (194)
T PRK09646 157 GGLTYREVAERLAVP-LGTVKTRMR-DG 182 (194)
T ss_pred cCCCHHHHHHHhCCC-hHhHHHHHH-HH
Confidence 459999999999998 999998876 65
No 147
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=35.15 E-value=48 Score=25.86 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=23.3
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 153 ~g~s~~EIA~~Lgis-~~tV~~~l~-RAr 179 (203)
T PRK09647 153 EGLSYEEIAATLGVK-LGTVRSRIH-RGR 179 (203)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998877 663
No 148
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=35.09 E-value=49 Score=26.13 Aligned_cols=27 Identities=7% Similarity=0.094 Sum_probs=23.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|+
T Consensus 197 eg~s~~EIA~~lgis-~~tVk~~~~-rA~ 223 (234)
T PRK08301 197 EEKTQKEVADMLGIS-QSYISRLEK-RII 223 (234)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 578999999999999 999988876 664
No 149
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=35.06 E-value=48 Score=24.68 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 134 ~~~s~~EIA~~lgis-~~tV~~~l~-Ra~ 160 (173)
T PRK12522 134 EQYSYKEMSEILNIP-IGTVKYRLN-YAK 160 (173)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 653
No 150
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=35.02 E-value=47 Score=25.35 Aligned_cols=27 Identities=19% Similarity=0.211 Sum_probs=23.3
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+- .|.
T Consensus 126 eg~s~~EIA~~lgis-~~tV~~~l~-Rar 152 (182)
T PRK12511 126 EGLSYQEAAAVLGIP-IGTLMSRIG-RAR 152 (182)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 654
No 151
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=34.45 E-value=49 Score=24.51 Aligned_cols=27 Identities=7% Similarity=0.131 Sum_probs=23.0
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||.+||+.+|++ ...|...+- +|.
T Consensus 133 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 159 (173)
T PRK09645 133 RGWSTAQIAADLGIP-EGTVKSRLH-YAL 159 (173)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999999 999988876 663
No 152
>PRK04239 hypothetical protein; Provisional
Probab=34.17 E-value=23 Score=25.82 Aligned_cols=23 Identities=26% Similarity=0.528 Sum_probs=20.5
Q ss_pred hhhHHHHHHHHhHhcCCcEEEecC
Q 031323 124 VRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 124 ~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
...||..+| .+...|=|.|+||+
T Consensus 66 A~~VE~~li-qlAq~G~i~~ki~e 88 (110)
T PRK04239 66 AEQVEQQLI-QLAQSGRIQGPIDD 88 (110)
T ss_pred HHHHHHHHH-HHHHcCCCCCCcCH
Confidence 368999999 99999999999975
No 153
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=34.01 E-value=45 Score=20.18 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=19.1
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHH
Q 031323 109 VLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI 132 (161)
.-....||..|+++ ...|..|.=
T Consensus 27 ~~~~~~la~~l~l~-~~~V~~WF~ 49 (57)
T PF00046_consen 27 KEEREELAKELGLT-ERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHHHTSS-HHHHHHHHH
T ss_pred cccccccccccccc-ccccccCHH
Confidence 34567799999999 999999975
No 154
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=50 Score=25.52 Aligned_cols=26 Identities=19% Similarity=0.254 Sum_probs=22.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 154 eg~s~~EIA~~lgis-~~tVk~~l~-RA 179 (201)
T PRK12545 154 LDFEIDDICTELTLT-ANHCSVLLY-RA 179 (201)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 468999999999999 999998766 65
No 155
>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=33.65 E-value=1.8e+02 Score=22.55 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=31.4
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
.+.+|..+|++.++++ ...|=..+= +....|+|+-+-
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~-~Le~~GlV~r~~ 49 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLK-DLETEGLIEYEA 49 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEee
Confidence 3459999999999998 888888776 888999998663
No 156
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.59 E-value=52 Score=24.78 Aligned_cols=27 Identities=7% Similarity=-0.021 Sum_probs=23.0
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+= .|.
T Consensus 144 ~g~s~~EIA~~l~is-~~tV~~~l~-rar 170 (181)
T PRK12536 144 EGLSVAETAQLTGLS-ESAVKVGIH-RGL 170 (181)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 653
No 157
>PF01984 dsDNA_bind: Double-stranded DNA-binding domain; InterPro: IPR002836 This protein family is found in archaea and eukaryota. The human TFAR19 (TF-1 cell apoptosis-related protein 19) encodes a protein which shares significant homology to the corresponding proteins of species ranging from yeast to mice. TFAR19 exhibits a ubiquitous expression pattern and its expression is up-regulated in the tumour cells undergoing apoptosis. TFAR19 may play a general role in the apoptotic process []. Also included in this family is a DNA-binding protein from the archaea, Methanobacterium thermoautotrophicum.; GO: 0003677 DNA binding; PDB: 1EIJ_A 2K6B_A 2CRU_A 1YYB_A 2JXN_A 2FH0_A.
Probab=33.50 E-value=23 Score=25.48 Aligned_cols=23 Identities=39% Similarity=0.699 Sum_probs=18.8
Q ss_pred hhhHHHHHHHHhHhcCCcEEEecC
Q 031323 124 VRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 124 ~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
...||..+| .....|=|.++||+
T Consensus 61 A~~VE~~Li-qlaq~G~l~~kI~d 83 (107)
T PF01984_consen 61 ARQVENQLI-QLAQSGQLRGKIDD 83 (107)
T ss_dssp HHHHHHHHH-HHHHCTSSSS-B-H
T ss_pred HHHHHHHHH-HHHHcCCCCCCcCH
Confidence 467999999 99999999999985
No 158
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=33.40 E-value=52 Score=25.05 Aligned_cols=27 Identities=7% Similarity=0.111 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+- +|.
T Consensus 126 ~g~s~~EIA~~Lgis-~~tV~~~l~-RAr 152 (182)
T PRK12540 126 SGFSYEDAAAICGCA-VGTIKSRVN-RAR 152 (182)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 653
No 159
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=32.85 E-value=54 Score=24.58 Aligned_cols=27 Identities=11% Similarity=0.057 Sum_probs=23.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+= +|.
T Consensus 146 ~g~s~~eIA~~l~is-~~tV~~~l~-ra~ 172 (184)
T PRK12512 146 EGASIKETAAKLSMS-EGAVRVALH-RGL 172 (184)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 478999999999999 999998876 654
No 160
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=32.63 E-value=1.1e+02 Score=26.67 Aligned_cols=35 Identities=29% Similarity=0.358 Sum_probs=31.4
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+++.+|-+++++.++++ .+.+++++= +..+.|+|.
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~ 341 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR 341 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE
Confidence 46788999999999999 999999876 888999997
No 161
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=32.49 E-value=56 Score=23.88 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 137 ~g~s~~eIA~~l~is-~~tv~~~l~-ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARILGKT-EGAVKILQF-RAI 163 (170)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 653
No 162
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=32.32 E-value=58 Score=24.64 Aligned_cols=27 Identities=11% Similarity=0.185 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|+
T Consensus 156 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 182 (194)
T PRK12519 156 EGLSQSEIAKRLGIP-LGTVKARAR-QGL 182 (194)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999998876 664
No 163
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=32.25 E-value=55 Score=24.53 Aligned_cols=26 Identities=12% Similarity=0.033 Sum_probs=22.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+= +|
T Consensus 150 ~~~s~~eIA~~lgis-~~~V~~~l~-ra 175 (186)
T PRK13919 150 QGYTHREAAQLLGLP-LGTLKTRAR-RA 175 (186)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 578999999999999 999988765 55
No 164
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=32.06 E-value=56 Score=24.42 Aligned_cols=26 Identities=15% Similarity=0.378 Sum_probs=22.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- .|
T Consensus 153 ~~~s~~EIA~~lgis-~~tv~~~l~-ra 178 (190)
T TIGR02939 153 EGLSYEDIARIMDCP-VGTVRSRIF-RA 178 (190)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 468999999999999 999998876 65
No 165
>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=31.97 E-value=1.1e+02 Score=19.27 Aligned_cols=42 Identities=19% Similarity=0.189 Sum_probs=33.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
-.+|.++||..+|++ ...|-..+= +.-..|+|+- .++.+.|.
T Consensus 27 ~~lt~~~iA~~~g~s-r~tv~r~l~-~l~~~g~I~~----~~~~i~I~ 68 (76)
T PF13545_consen 27 LPLTQEEIADMLGVS-RETVSRILK-RLKDEGIIEV----KRGKIIIL 68 (76)
T ss_dssp EESSHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEEE----ETTEEEES
T ss_pred ecCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE----cCCEEEEC
Confidence 367899999999998 888999877 8888999873 34455553
No 166
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=31.95 E-value=59 Score=24.87 Aligned_cols=27 Identities=15% Similarity=0.165 Sum_probs=22.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.|+++ ...|...+= +|.
T Consensus 131 ~g~s~~EIA~~Lgis-~~tVk~~l~-Rar 157 (187)
T PRK12516 131 SGFAYEEAAEICGCA-VGTIKSRVN-RAR 157 (187)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 479999999999999 999998865 553
No 167
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=31.94 E-value=56 Score=24.67 Aligned_cols=27 Identities=7% Similarity=0.003 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ .+.|...+= +|.
T Consensus 146 ~g~s~~eIA~~lgis-~~tV~~~l~-ra~ 172 (184)
T PRK12539 146 EGLSVAEAATRSGMS-ESAVKVSVH-RGL 172 (184)
T ss_pred cCCcHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999998 999998876 653
No 168
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=31.69 E-value=98 Score=19.70 Aligned_cols=36 Identities=11% Similarity=0.238 Sum_probs=29.2
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
..+..|..+|.+..+++ .++|-.-+. -.|..|++..
T Consensus 24 ~~G~ltl~~i~~~t~l~-~~~Vk~~L~-~LiQh~~v~y 59 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLS-PKQVKKALV-VLIQHNLVQY 59 (62)
T ss_dssp HC-SEEHHHHHHHHT---HHHHHHHHH-HHHHTTSEEE
T ss_pred HcCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHcCCeee
Confidence 45688999999999999 999999888 8999998865
No 169
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=31.57 E-value=60 Score=23.35 Aligned_cols=26 Identities=23% Similarity=0.471 Sum_probs=22.0
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+= .|
T Consensus 120 ~g~s~~eIA~~lgis-~~tv~~~l~-Ra 145 (154)
T TIGR02950 120 KEFSYKEIAELLNLS-LAKVKSNLF-RA 145 (154)
T ss_pred ccCcHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999999 888888765 55
No 170
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=31.53 E-value=70 Score=26.71 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=36.0
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCC
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~ 148 (161)
..+.++..++++..++| .+-+-..++ +..-.++|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp-~efl~~~li-~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLP-SEFLKEELI-SKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCc-HHHHHHHHh-hhhcCcceeEEEeCC
Confidence 45799999999999999 777776788 888899999999987
No 171
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=31.37 E-value=60 Score=25.73 Aligned_cols=26 Identities=23% Similarity=0.290 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 149 eg~s~~EIAe~LgiS-~~tVk~~L~-RA 174 (216)
T PRK12533 149 EDMSYREIAAIADVP-VGTVMSRLA-RA 174 (216)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999999 999998876 65
No 172
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=31.22 E-value=60 Score=24.77 Aligned_cols=26 Identities=19% Similarity=0.308 Sum_probs=22.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 146 ~g~s~~EIA~~lgis-~~tvk~rl~-Ra 171 (188)
T TIGR02943 146 LGFESDEICQELEIS-TSNCHVLLY-RA 171 (188)
T ss_pred hCCCHHHHHHHhCCC-HHHHHHHHH-HH
Confidence 368999999999999 999988866 55
No 173
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.19 E-value=86 Score=18.42 Aligned_cols=21 Identities=10% Similarity=0.086 Sum_probs=13.1
Q ss_pred ccCHHHHHHhcCCCChhhHHHH
Q 031323 109 VLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~l 130 (161)
-.|+.+||+.++.+ ...|-..
T Consensus 20 G~s~~~IA~~lg~s-~sTV~re 40 (44)
T PF13936_consen 20 GMSIREIAKRLGRS-RSTVSRE 40 (44)
T ss_dssp ---HHHHHHHTT---HHHHHHH
T ss_pred CCCHHHHHHHHCcC-cHHHHHH
Confidence 38999999999998 7766554
No 174
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.18 E-value=60 Score=24.67 Aligned_cols=26 Identities=12% Similarity=0.115 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|...+= .|
T Consensus 145 ~g~s~~EIA~~lgis-~~tVk~~l~-Ra 170 (185)
T PRK09649 145 LGLSYADAAAVCGCP-VGTIRSRVA-RA 170 (185)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 568999999999999 999998866 55
No 175
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.87 E-value=65 Score=23.62 Aligned_cols=27 Identities=15% Similarity=0.334 Sum_probs=22.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...|+++||+.+|++ ...|..++- +|.
T Consensus 143 ~~~s~~eIA~~lgis-~~tV~~~l~-ra~ 169 (182)
T PRK09652 143 EGLSYEEIAEIMGCP-IGTVRSRIF-RAR 169 (182)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999988866 553
No 176
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=30.83 E-value=1.3e+02 Score=22.97 Aligned_cols=44 Identities=18% Similarity=0.157 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHH
Q 031323 86 QLVPDQVLKLKQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 86 ~L~~~~~~KlrlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~l 130 (161)
.|+..+.+=..+|..-.+-. ++..-|+++||+++||+ ...+=.|
T Consensus 10 ~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis-~~tLYrW 54 (142)
T PF13022_consen 10 KLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGIS-RSTLYRW 54 (142)
T ss_dssp TS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS--HHHHHHH
T ss_pred HcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCC-HHHHHHH
Confidence 35555555555666666555 35789999999999997 5555444
No 177
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=30.58 E-value=63 Score=18.13 Aligned_cols=29 Identities=24% Similarity=0.310 Sum_probs=22.0
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
++..++|+.++++ ...+-.|+= .|.+.+.
T Consensus 1 ~s~~e~a~~lgvs-~~tl~~~~~-----~g~~~~~ 29 (49)
T cd04762 1 LTTKEAAELLGVS-PSTLRRWVK-----EGKLKAI 29 (49)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH-----cCCCCce
Confidence 4678999999998 888888754 5666543
No 178
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=30.53 E-value=99 Score=17.38 Aligned_cols=30 Identities=13% Similarity=0.296 Sum_probs=20.4
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCc
Q 031323 110 LPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi 141 (161)
+|-.+||+.+|+. .+-|=..+= +.-..|+|
T Consensus 3 mtr~diA~~lG~t-~ETVSR~l~-~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLT-RETVSRILK-KLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS--HHHHHHHHH-HHHHTTSE
T ss_pred cCHHHHHHHhCCc-HHHHHHHHH-HHHHcCCC
Confidence 5678999999997 777777665 66666664
No 179
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=30.13 E-value=64 Score=24.67 Aligned_cols=27 Identities=19% Similarity=0.170 Sum_probs=22.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||.+||+.+|++ ...|...+- .|.
T Consensus 143 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 169 (188)
T PRK12517 143 GGFSGEEIAEILDLN-KNTVMTRLF-RAR 169 (188)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999998866 553
No 180
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=30.09 E-value=1e+02 Score=20.98 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=23.3
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
..|+.+-..++.+|-+++|.+++.+ .++|...+=
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~-~e~v~~~L~ 60 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWP-VEEVRAALA 60 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT---HHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCC-HHHHHHHHH
Confidence 3455555568999999999999998 999988654
No 181
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=30.08 E-value=60 Score=26.31 Aligned_cols=27 Identities=11% Similarity=0.154 Sum_probs=23.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|+..+- +|.
T Consensus 176 eg~S~~EIA~~Lgis-~~TVk~rl~-RAr 202 (244)
T TIGR03001 176 DGLSMDRIGAMYQVH-RSTVSRWVA-QAR 202 (244)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999999 999998876 653
No 182
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=29.76 E-value=99 Score=17.29 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=21.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...++.+|++.++++ ...|-.++= .+
T Consensus 25 ~~~~~~~ia~~~~~s-~~~i~~~~~-~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGIS-RSTVRQRLH-RA 50 (55)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 357999999999998 888887765 44
No 183
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.69 E-value=66 Score=24.24 Aligned_cols=26 Identities=15% Similarity=0.245 Sum_probs=22.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|...+- +|
T Consensus 137 ~g~s~~EIA~~lgis-~~tVk~~l~-Ra 162 (185)
T PRK12542 137 YNLTYQEISSVMGIT-EANVRKQFE-RA 162 (185)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 359999999999999 999998766 65
No 184
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=29.58 E-value=1e+02 Score=25.07 Aligned_cols=47 Identities=13% Similarity=0.203 Sum_probs=38.2
Q ss_pred HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+-|+-.++++-..++.++-.++++.++++ ...+=..+. +.-..|++.
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS-~~TiRRdL~-~Le~~g~l~ 50 (252)
T PRK10906 4 TQRHDAIIELVKQQGYVSTEELVEHFSVS-PQTIRRDLN-DLAEQNKIL 50 (252)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHhCCC-HHHHHHHHH-HHHHCCCEE
Confidence 44677777777888899999999999998 888877777 777788864
No 185
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=29.46 E-value=63 Score=26.10 Aligned_cols=25 Identities=8% Similarity=0.114 Sum_probs=21.4
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
..||++||+.+|++ .+.|...+- +|
T Consensus 132 g~S~~EIAe~LgiS-~~tVksrL~-Ra 156 (228)
T PRK06704 132 QYSIADIAKVCSVS-EGAVKASLF-RS 156 (228)
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 58999999999998 888888765 55
No 186
>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=29.44 E-value=2.1e+02 Score=23.83 Aligned_cols=36 Identities=11% Similarity=0.252 Sum_probs=29.2
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
+.-++..+||+.+|++ ..-+=+-+- +.-..|+|+++
T Consensus 196 egrlse~eLAerlGVS-Rs~ireAlr-kLE~aGvIe~r 231 (251)
T TIGR02787 196 EGLLVASKIADRVGIT-RSVIVNALR-KLESAGVIESR 231 (251)
T ss_pred cccccHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEec
Confidence 4689999999999998 666655566 77789999886
No 187
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=29.33 E-value=65 Score=24.61 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=22.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|...+= +|
T Consensus 151 ~g~s~~eIA~~lgis-~~tV~~~l~-Ra 176 (196)
T PRK12524 151 EGLSNPEIAEVMEIG-VEAVESLTA-RG 176 (196)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 468999999999999 999998876 65
No 188
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=29.24 E-value=66 Score=24.83 Aligned_cols=24 Identities=21% Similarity=0.223 Sum_probs=21.0
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
...||++||+.++++ .+.|...+=
T Consensus 148 ~g~s~~EIAe~lgis-~~tV~~~l~ 171 (196)
T PRK12535 148 LGYTYEEAAKIADVR-VGTIRSRVA 171 (196)
T ss_pred hCCCHHHHHHHhCCC-HHHHHHHHH
Confidence 468999999999998 999998854
No 189
>PF12728 HTH_17: Helix-turn-helix domain
Probab=28.94 E-value=68 Score=18.98 Aligned_cols=29 Identities=17% Similarity=0.197 Sum_probs=21.9
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
+|.+++|+.|+++ ...|..|+= .|-+.+-
T Consensus 2 lt~~e~a~~l~is-~~tv~~~~~-----~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGIS-RSTVYRWIR-----QGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH-----cCCCCeE
Confidence 5788999999998 888887653 5655444
No 190
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=28.60 E-value=70 Score=25.28 Aligned_cols=27 Identities=7% Similarity=0.079 Sum_probs=22.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|..++= .|+
T Consensus 193 e~~S~~EIAe~lgis-~~tV~~~~~-rAl 219 (227)
T TIGR02846 193 RRKTQREIAKILGIS-RSYVSRIEK-RAL 219 (227)
T ss_pred CCcCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999999 999988754 543
No 191
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=28.32 E-value=74 Score=23.53 Aligned_cols=27 Identities=11% Similarity=0.215 Sum_probs=22.6
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+= +|.
T Consensus 141 ~g~s~~eIA~~l~is-~~~V~~~l~-ra~ 167 (176)
T PRK09638 141 YGYTYEEIAKMLNIP-EGTVKSRVH-HGI 167 (176)
T ss_pred cCCCHHHHHHHHCCC-hhHHHHHHH-HHH
Confidence 468999999999998 888888766 653
No 192
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=28.25 E-value=76 Score=23.40 Aligned_cols=27 Identities=15% Similarity=0.286 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||.+||+.+|++ ...|...+- .|.
T Consensus 134 ~g~s~~eiA~~lgis-~~tv~~~l~-Ra~ 160 (169)
T TIGR02954 134 HDLTIKEIAEVMNKP-EGTVKTYLH-RAL 160 (169)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999998 999988776 653
No 193
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=28.25 E-value=57 Score=29.20 Aligned_cols=43 Identities=23% Similarity=0.301 Sum_probs=31.2
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
++++-+-.++..+|+++|++.++++ ..++..-+- ..+..|++.
T Consensus 523 ~~iLl~Fn~~~~~t~~ei~~~~~~~-~~~l~~~L~-~l~~~~~l~ 565 (588)
T PF00888_consen 523 AAILLLFNDNDSLTVEEISEKTGIS-EEELKRALK-SLVKSKILI 565 (588)
T ss_dssp HHHHHGGGSSSEEEHHHHHHHC----HHHHHHHHH-CCCTTTTCS
T ss_pred HHHHHHHccCCCccHHHHHHHHCcC-HHHHHHHHH-HHHhCCcce
Confidence 4444445567799999999999999 889998777 777777775
No 194
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=27.71 E-value=1.6e+02 Score=21.51 Aligned_cols=41 Identities=12% Similarity=0.122 Sum_probs=32.1
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
+..+...++..+..+|++.++++ ...|=..+= +....|+|.
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs-~~svs~~l~-~L~~~Gli~ 53 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVH-PSSVTKMVQ-KLDKDEYLI 53 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCC-hhHHHHHHH-HHHHCCCEE
Confidence 34445566778999999999998 777777766 777889987
No 195
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=27.41 E-value=1.6e+02 Score=24.96 Aligned_cols=52 Identities=15% Similarity=0.160 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHhhh-cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 92 VLKLKQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 92 ~~KlrlLtL~sLa~-~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
.+|=-+.+|++|-. .++.+.=.+||+.++-+ +..|-..+. ..-+.||++|+=
T Consensus 7 ~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rn-pGTVRNqmq-~LkaLgLVegvp 59 (294)
T COG2524 7 SQKEILQALINLYRRKKRPIKGEEIAEVLNRN-PGTVRNQMQ-SLKALGLVEGVP 59 (294)
T ss_pred HHHHHHHHHHHHHHhcCCCcchHHHHHHHccC-cchHHHHHH-HHHhcCcccccc
Confidence 47777889999987 47899999999999987 888888766 677799999863
No 196
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=27.23 E-value=69 Score=22.50 Aligned_cols=30 Identities=10% Similarity=0.205 Sum_probs=24.2
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhc
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYT 138 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~ 138 (161)
.++.+|.++-++..+++ .+|+|.|+= ++..
T Consensus 46 ~~Glis~~EA~~rY~Ls-~eEf~~W~~--av~r 75 (90)
T PF06627_consen 46 RGGLISVEEACRRYGLS-EEEFESWQR--AVDR 75 (90)
T ss_dssp HCTTS-HHHHHHCTTSS-HHHHHHHHH--HCCT
T ss_pred HcCCCCHHHHHHHhCCC-HHHHHHHHH--HHHH
Confidence 36799999999999998 999999965 5443
No 197
>PRK11050 manganese transport regulator MntR; Provisional
Probab=27.18 E-value=1.8e+02 Score=21.74 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=33.6
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
|..+...+..++..+|++.++++ ...|=.++- +....|+|.-+
T Consensus 42 I~~~l~~~~~~t~~eLA~~l~is-~stVsr~l~-~Le~~GlI~r~ 84 (152)
T PRK11050 42 IADLIAEVGEARQVDIAARLGVS-QPTVAKMLK-RLARDGLVEMR 84 (152)
T ss_pred HHHHHHhcCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEEe
Confidence 34344445578999999999998 888888887 88888998754
No 198
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=27.11 E-value=1.4e+02 Score=23.70 Aligned_cols=34 Identities=12% Similarity=0.165 Sum_probs=25.5
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
.++.+... -.|+.+||+.++++ ...|+..+- .++
T Consensus 162 ~Vl~l~~~--G~s~~eIA~~L~iS-~~TVk~~~~-~i~ 195 (216)
T PRK10100 162 EILNKLRI--GASNNEIARSLFIS-ENTVKTHLY-NLF 195 (216)
T ss_pred HHHHHHHc--CCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 34444444 38899999999998 999998876 544
No 199
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=27.07 E-value=99 Score=21.05 Aligned_cols=31 Identities=10% Similarity=0.057 Sum_probs=23.6
Q ss_pred HHHHHHHhhhcCCccCHHHHHHhcCCCChhhHH
Q 031323 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (161)
Q Consensus 96 rlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE 128 (161)
|+.-++.+... +.++..+||+.+|++ ...|=
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS-~~TVs 37 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVS-KSTVH 37 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCC-HHHHH
Confidence 66667777777 888999999999987 44443
No 200
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=27.01 E-value=80 Score=25.05 Aligned_cols=26 Identities=8% Similarity=0.051 Sum_probs=22.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+= .|
T Consensus 197 eg~s~~EIA~~Lgis-~~tV~~~l~-ra 222 (234)
T TIGR02835 197 TEKTQKEVADMLGIS-QSYISRLEK-RI 222 (234)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 569999999999999 999988765 54
No 201
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=26.98 E-value=81 Score=22.78 Aligned_cols=26 Identities=23% Similarity=0.218 Sum_probs=22.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...|+.+||+.+|++ ...|...+- +|
T Consensus 126 ~g~~~~eIA~~l~is-~~tv~~~l~-Ra 151 (159)
T TIGR02989 126 RGVSLTALAEQLGRT-VNAVYKALS-RL 151 (159)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HH
Confidence 468999999999999 999988866 65
No 202
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=26.75 E-value=83 Score=23.77 Aligned_cols=27 Identities=7% Similarity=0.169 Sum_probs=22.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+= .|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 175 (188)
T PRK09640 149 AELEFQEIADIMHMG-LSATKMRYK-RAL 175 (188)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999999 899988876 663
No 203
>PF01035 DNA_binding_1: 6-O-methylguanine DNA methyltransferase, DNA binding domain; InterPro: IPR014048 Synonym(s): 6-O-methylguanine-DNA methyltransferase, O-6-methylguanine-DNA-alkyltransferase This entry represents the DNA binding region of 6-O-methylguanine-DNA methyltransferases. The repair of DNA containing O6-alkylated guanine is carried out by DNA-[protein]-cysteine S-methyltransferase (2.1.1.63 from EC). The major mutagenic and carcinogenic effect of methylating agents in DNA is the formation of O6-alkylguanine. The alkyl group at the O-6 position is transferred to a cysteine residue in the enzyme []. This is a suicide reaction since the enzyme is irreversibly inactivated and the methylated protein accumulates as a dead-end product. Most, but not all of the methyltransferases are also able to repair O-4-methylthymine. DNA-[protein]-cysteine S-methyltransferases are widely distributed and are found in various prokaryotic and eukaryotic sources [].; GO: 0003824 catalytic activity, 0006281 DNA repair; PDB: 1SFE_A 1T39_B 1T38_A 1EH7_A 1EH6_A 1YFH_C 1EH8_A 1QNT_A 2KIM_A 2KIF_A ....
Probab=26.61 E-value=52 Score=22.33 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=16.3
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCC
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVT 122 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~ 122 (161)
+..+.-..-++..||.+||+.++-+
T Consensus 8 ~~~v~~IP~G~v~TYg~iA~~~g~p 32 (85)
T PF01035_consen 8 WEAVRQIPYGKVTTYGEIARLLGRP 32 (85)
T ss_dssp HHHHTTS-TT-BEEHHHHHHHTT-T
T ss_pred HHHHHcCCCCceEeHHHHHHHHhhc
Confidence 3333334467899999999999944
No 204
>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=26.51 E-value=2.2e+02 Score=19.50 Aligned_cols=46 Identities=9% Similarity=0.025 Sum_probs=35.8
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVC 155 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~ 155 (161)
....+|-.+|++.++++ ..-|=..+= +....|+|.- +...++|-|+
T Consensus 44 ~~~~is~~eLa~~~g~s-r~tVsr~L~-~Le~~GlI~r--~~~~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLS-RTHVSDAIK-SLARRRIIFR--QGMMGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeee--ecCCceeecC
Confidence 35688999999999998 778888665 8899999973 3445666665
No 205
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.48 E-value=84 Score=23.87 Aligned_cols=26 Identities=8% Similarity=0.152 Sum_probs=21.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 151 ~g~s~~EIA~~lgis-~~tVk~~l~-Ra 176 (195)
T PRK12532 151 LGFSSDEIQQMCGIS-TSNYHTIMH-RA 176 (195)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 358999999999999 999988765 54
No 206
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=26.42 E-value=79 Score=23.75 Aligned_cols=26 Identities=15% Similarity=0.386 Sum_probs=22.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+= .|
T Consensus 152 ~g~s~~eIA~~lgis-~~~v~~~l~-Ra 177 (187)
T PRK12534 152 EGITYEELAARTDTP-IGTVKSWIR-RG 177 (187)
T ss_pred cCCCHHHHHHHhCCC-hhHHHHHHH-HH
Confidence 468999999999999 899888765 55
No 207
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=26.42 E-value=47 Score=23.83 Aligned_cols=19 Identities=5% Similarity=0.207 Sum_probs=16.2
Q ss_pred CccCHHHHHHhcCCCChhhH
Q 031323 108 KVLPYDELMEELDVTNVREL 127 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~ev 127 (161)
...||++||+.+|++ ...|
T Consensus 122 ~~~s~~EIA~~l~is-~~tV 140 (142)
T TIGR03209 122 EDMKEIDIAKKLHIS-RQSV 140 (142)
T ss_pred cCCCHHHHHHHHCcC-HHhh
Confidence 468999999999998 6655
No 208
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.41 E-value=75 Score=26.22 Aligned_cols=27 Identities=15% Similarity=0.006 Sum_probs=23.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+- +|.
T Consensus 157 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 183 (324)
T TIGR02960 157 LGWRAAETAELLGTS-TASVNSALQ-RAR 183 (324)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999999877 663
No 209
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.37 E-value=81 Score=23.71 Aligned_cols=26 Identities=27% Similarity=0.311 Sum_probs=22.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+= .|
T Consensus 143 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra 168 (186)
T PRK05602 143 QGLSNIEAAAVMDIS-VDALESLLA-RG 168 (186)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HH
Confidence 468999999999999 999888765 55
No 210
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=26.37 E-value=85 Score=23.18 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=21.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||.+||+.+|++ ...|...+- +|
T Consensus 135 ~g~s~~eIA~~lg~s-~~tv~~~l~-Ra 160 (175)
T PRK12518 135 EDLPQKEIAEILNIP-VGTVKSRLF-YA 160 (175)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 457999999999999 888888765 54
No 211
>PF14493 HTH_40: Helix-turn-helix domain
Probab=26.35 E-value=1e+02 Score=20.82 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=25.1
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHhHhcCC
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~ai~~gL 140 (161)
-.|.++||+.-++. ...|+.-++ +++..|-
T Consensus 13 G~si~eIA~~R~L~-~sTI~~HL~-~~~~~g~ 42 (91)
T PF14493_consen 13 GLSIEEIAKIRGLK-ESTIYGHLA-ELIESGE 42 (91)
T ss_pred CCCHHHHHHHcCCC-HHHHHHHHH-HHHHhCC
Confidence 37888999999988 888888888 8887776
No 212
>PF10924 DUF2711: Protein of unknown function (DUF2711); InterPro: IPR024250 Some members in this family of proteins are annotated as ywbB. The function of these proteins is unknown.
Probab=26.29 E-value=1e+02 Score=25.06 Aligned_cols=34 Identities=21% Similarity=0.349 Sum_probs=26.7
Q ss_pred hhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHh
Q 031323 103 LAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (161)
Q Consensus 103 La~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~ 137 (161)
+...++.+|+.+|...||+.+..|+-.-++ .+|.
T Consensus 49 Ii~~G~pVSWkeVms~~gL~s~~Ela~AL~-Tsig 82 (217)
T PF10924_consen 49 IIENGKPVSWKEVMSKCGLNSYKELALALM-TSIG 82 (217)
T ss_pred HHhcCCcccHHHHHHHcCCCcHHHHHHHHH-HHhh
Confidence 344688999999999999998888877666 5543
No 213
>PRK00215 LexA repressor; Validated
Probab=26.13 E-value=3.1e+02 Score=21.12 Aligned_cols=47 Identities=21% Similarity=0.293 Sum_probs=37.4
Q ss_pred hcCCccCHHHHHHhcCC-CChhhHHHHHHHHhHhcCCcEEEecCCCCEEEE
Q 031323 105 ETNKVLPYDELMEELDV-TNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (161)
Q Consensus 105 ~~~~~isy~~I~~~l~i-~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V 154 (161)
.++...+..+|++++++ + ...|=.++= .....|+|+..-+. .+.++|
T Consensus 19 ~~~~~~s~~ela~~~~~~~-~~tv~~~l~-~L~~~g~i~~~~~~-~r~~~l 66 (205)
T PRK00215 19 ETGYPPSRREIADALGLRS-PSAVHEHLK-ALERKGFIRRDPGR-SRAIEV 66 (205)
T ss_pred HhCCCCCHHHHHHHhCCCC-hHHHHHHHH-HHHHCCCEEeCCCC-cceEEe
Confidence 35678899999999999 6 888888776 88889999776555 456666
No 214
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=25.96 E-value=1.7e+02 Score=23.75 Aligned_cols=42 Identities=24% Similarity=0.270 Sum_probs=31.2
Q ss_pred HhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 102 TLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 102 sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
-++.....+|-++||+.|+|+ ...|=.=+= +....|+++.+.
T Consensus 18 ~lL~~~g~~sa~elA~~Lgis-~~avR~HL~-~Le~~Glv~~~~ 59 (218)
T COG2345 18 ELLKKSGPVSADELAEELGIS-PMAVRRHLD-DLEAEGLVEVER 59 (218)
T ss_pred HHHhccCCccHHHHHHHhCCC-HHHHHHHHH-HHHhCcceeeee
Confidence 344467899999999999998 665544444 566689998883
No 215
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.73 E-value=87 Score=24.24 Aligned_cols=27 Identities=19% Similarity=0.325 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+= +|.
T Consensus 168 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 194 (206)
T PRK12526 168 QELSQEQLAQQLNVP-LGTVKSRLR-LAL 194 (206)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 999988765 553
No 216
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.56 E-value=87 Score=23.60 Aligned_cols=27 Identities=15% Similarity=0.035 Sum_probs=23.0
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||.+||+.+|++ ...|...+- +|.
T Consensus 154 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 180 (189)
T PRK09648 154 VGLSAEETAEAVGST-PGAVRVAQH-RAL 180 (189)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 368999999999999 999988876 664
No 217
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.45 E-value=89 Score=23.78 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=21.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+= .|.
T Consensus 156 eg~s~~EIA~~lgis-~~tVk~rl~-ra~ 182 (194)
T PRK12531 156 EELPHQQVAEMFDIP-LGTVKSRLR-LAV 182 (194)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HHH
Confidence 468999999999998 888877655 553
No 218
>TIGR00589 ogt O-6-methylguanine DNA methyltransferase. All proteins in this family for which functions are known are involved alkyl-DNA transferases which remove alkyl groups from DNA as part of alkylation DNA repair. Some of the proteins in this family are also transcription regulators and have a distinct transcription regulatory domain. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.15 E-value=85 Score=21.21 Aligned_cols=25 Identities=12% Similarity=0.171 Sum_probs=18.4
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCC
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVT 122 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~ 122 (161)
+..+.-..-+++.||.+||+.++-+
T Consensus 8 ~~~l~~IP~G~v~TYg~iA~~~g~p 32 (80)
T TIGR00589 8 WQALRTIPYGETKSYGQLAARIGNP 32 (80)
T ss_pred HHHHhCCCCCCcCCHHHHHHHhCCC
Confidence 3333334458899999999999975
No 219
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=25.01 E-value=1.8e+02 Score=23.47 Aligned_cols=46 Identities=20% Similarity=0.124 Sum_probs=35.2
Q ss_pred HHHHHHHhh-hcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 96 rlLtL~sLa-~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
|-|.++..- ..+..++-.+|++.++++ ...+=.++= .....|++.-
T Consensus 12 ral~iL~~l~~~~~~ls~~eia~~lgl~-kstv~RlL~-tL~~~g~v~~ 58 (263)
T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLH-RTTVRRLLE-TLQEEGYVRR 58 (263)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence 344555433 344569999999999999 888988877 8888999874
No 220
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=24.78 E-value=96 Score=22.60 Aligned_cols=27 Identities=30% Similarity=0.340 Sum_probs=22.6
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...++++||+.+|++ ...|..++= +|.
T Consensus 140 ~~~~~~eIA~~lgis-~~tv~~~~~-ra~ 166 (179)
T PRK11924 140 EGLSYREIAEILGVP-VGTVKSRLR-RAR 166 (179)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999988865 553
No 221
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.78 E-value=1.6e+02 Score=22.90 Aligned_cols=30 Identities=3% Similarity=0.101 Sum_probs=22.5
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
++.+..+| .|..+||++|+++ ...|+..+=
T Consensus 145 VL~lla~G--~snkeIA~~L~iS-~~TVk~h~~ 174 (207)
T PRK15411 145 MLRMWMAG--QGTIQISDQMNIK-AKTVSSHKG 174 (207)
T ss_pred HHHHHHcC--CCHHHHHHHcCCC-HHHHHHHHH
Confidence 34444444 7889999999998 888888764
No 222
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=24.61 E-value=80 Score=18.81 Aligned_cols=22 Identities=27% Similarity=0.382 Sum_probs=18.5
Q ss_pred cCHHHHHHhcCCCChhhHHHHHH
Q 031323 110 LPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI 132 (161)
-..+.||..++++ ..+|..|+-
T Consensus 28 ~~~~~la~~~~l~-~~qV~~WF~ 49 (59)
T cd00086 28 EEREELAKELGLT-ERQVKIWFQ 49 (59)
T ss_pred HHHHHHHHHHCcC-HHHHHHHHH
Confidence 3467788999998 999999987
No 223
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=24.49 E-value=1.3e+02 Score=24.88 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=25.0
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhHh
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai~ 137 (161)
....||++|++.+|++ ..-|.++.- +|+.
T Consensus 267 ~~~~Tl~EIa~~lgiS-~erVrq~~~-rAl~ 295 (298)
T TIGR02997 267 GEPLTLAEIGRRLNLS-RERVRQIEA-KALR 295 (298)
T ss_pred CCCcCHHHHHHHHCcC-HHHHHHHHH-HHHH
Confidence 4689999999999998 999998877 7753
No 224
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=24.47 E-value=83 Score=22.01 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=19.2
Q ss_pred CCccCHHHHHHhcCCCChhhHHHH
Q 031323 107 NKVLPYDELMEELDVTNVRELEDF 130 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~l 130 (161)
...+|-++||+.|+++ ..+||+.
T Consensus 21 ~~~ls~~~ia~dL~~s-~~~le~v 43 (89)
T PF10078_consen 21 LSGLSLEQIAADLGTS-PEHLEQV 43 (89)
T ss_pred HcCCCHHHHHHHhCCC-HHHHHHH
Confidence 4578899999999998 8888873
No 225
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.22 E-value=2.3e+02 Score=18.95 Aligned_cols=44 Identities=18% Similarity=0.183 Sum_probs=36.0
Q ss_pred HHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEeee
Q 031323 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCTVL 158 (161)
Q Consensus 113 ~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~~~ 158 (161)
.+|++.++++ ...|=..+= +....|+|+=.-|+.++...+-..+
T Consensus 40 ~~la~~l~i~-~~~vt~~l~-~Le~~glv~r~~~~~DrR~~~l~lT 83 (126)
T COG1846 40 KELAERLGLD-RSTVTRLLK-RLEDKGLIERLRDPEDRRAVLVRLT 83 (126)
T ss_pred HHHHHHHCCC-HHHHHHHHH-HHHHCCCeeecCCccccceeeEEEC
Confidence 9999999998 888887655 8889999999999988765554443
No 226
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=24.20 E-value=2e+02 Score=21.78 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=33.3
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
++-.+-.++..+.-.+||+.|+++ .-.|=..+= +.-+.|+|+=
T Consensus 14 ~Iy~l~~~~~~~~~~diA~~L~Vs-p~sVt~ml~-rL~~~GlV~~ 56 (154)
T COG1321 14 TIYELLEEKGFARTKDIAERLKVS-PPSVTEMLK-RLERLGLVEY 56 (154)
T ss_pred HHHHHHhccCcccHHHHHHHhCCC-cHHHHHHHH-HHHHCCCeEE
Confidence 334444477889999999999998 788877666 8888998863
No 227
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=24.16 E-value=92 Score=24.29 Aligned_cols=26 Identities=23% Similarity=0.358 Sum_probs=22.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+- +|
T Consensus 163 ~g~s~~EIAe~lgis-~~tV~~~l~-RA 188 (206)
T PRK12544 163 IELETNEICHAVDLS-VSNLNVLLY-RA 188 (206)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 468999999999999 999988765 54
No 228
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=24.15 E-value=1.8e+02 Score=23.09 Aligned_cols=28 Identities=14% Similarity=0.273 Sum_probs=23.4
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
....||.+||+.+|++ ...|.++.- +|+
T Consensus 194 ~~~~t~~EIA~~lgis-~~~V~q~~~-~al 221 (238)
T TIGR02393 194 GRPHTLEEVGKEFNVT-RERIRQIES-KAL 221 (238)
T ss_pred CCCccHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4679999999999998 888888765 554
No 229
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.98 E-value=1e+02 Score=22.42 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=22.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|.
T Consensus 126 ~g~s~~eIA~~lgis-~~tV~~~i~-ra~ 152 (166)
T PRK09639 126 SGYSYKEIAEALGIK-ESSVGTTLA-RAK 152 (166)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999999 888888766 653
No 230
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=23.77 E-value=2.1e+02 Score=23.88 Aligned_cols=47 Identities=15% Similarity=0.338 Sum_probs=35.2
Q ss_pred HHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEE
Q 031323 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (161)
Q Consensus 93 ~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~g 143 (161)
.|-+.|+. ++-....+.-.+||++++|. ...|=+.+= +.+..|+|+-
T Consensus 11 t~fqIL~e--i~~~qp~v~q~eIA~~lgiT-~QaVsehiK-~Lv~eG~i~~ 57 (260)
T COG1497 11 TRFQILSE--IAVRQPRVKQKEIAKKLGIT-LQAVSEHIK-ELVKEGLIEK 57 (260)
T ss_pred hHHHHHHH--HHHhCCCCCHHHHHHHcCCC-HHHHHHHHH-HHHhccceee
Confidence 34444443 44456678999999999998 888888777 8888888764
No 231
>PRK04217 hypothetical protein; Provisional
Probab=23.71 E-value=1e+02 Score=22.22 Aligned_cols=38 Identities=18% Similarity=0.063 Sum_probs=24.7
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHH------HHhHhcCCcEEEecC
Q 031323 109 VLPYDELMEELDVTNVRELEDFLI------NECMYTGIVRGKLDQ 147 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI------~~ai~~gLi~gkIDq 147 (161)
.+|+++||+.++++ ...|...+= .+++..+-..+.+.+
T Consensus 58 GlS~~EIAk~LGIS-~sTV~r~L~RArkkLre~L~~~~~~~~~~~ 101 (110)
T PRK04217 58 GLTQEEAGKRMGVS-RGTVWRALTSARKKVAQMLVEGRELIILPQ 101 (110)
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHHHHHHHHHHHHHhccceeEecC
Confidence 57999999999998 776665533 044444444444443
No 232
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=23.56 E-value=2.5e+02 Score=19.16 Aligned_cols=39 Identities=8% Similarity=0.032 Sum_probs=32.2
Q ss_pred hhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 104 AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 104 a~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
-..++-.+-.+|+..++.| .+-||.++- ..+..|-|+--
T Consensus 11 l~~~gr~s~~~Ls~~~~~p-~~~VeaMLe-~l~~kGkverv 49 (78)
T PRK15431 11 LALRGRMEAAQISQTLNTP-QPMINAMLQ-QLESMGKAVRI 49 (78)
T ss_pred HHHcCcccHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEee
Confidence 3356788999999999999 999999988 88888877643
No 233
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=23.46 E-value=92 Score=25.57 Aligned_cols=26 Identities=15% Similarity=0.249 Sum_probs=23.0
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|...+- +|
T Consensus 130 ~g~s~~EIA~~lg~s-~~tVk~~l~-RA 155 (293)
T PRK09636 130 FGVPFDEIASTLGRS-PAACRQLAS-RA 155 (293)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999998 999998877 66
No 234
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.33 E-value=1e+02 Score=24.41 Aligned_cols=27 Identities=15% Similarity=0.201 Sum_probs=23.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+- +|+
T Consensus 199 ~g~s~~EIA~~lgis-~~tV~~~~~-ra~ 225 (236)
T PRK06986 199 EELNLKEIGAVLGVS-ESRVSQIHS-QAI 225 (236)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999998876 664
No 235
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.27 E-value=1.1e+02 Score=23.01 Aligned_cols=26 Identities=19% Similarity=0.198 Sum_probs=22.1
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||.+||+.++++ ...|...+= +|
T Consensus 142 ~g~s~~EIA~~l~is-~~tv~~~l~-Ra 167 (179)
T PRK09415 142 EELSIKEIAEVTGVN-ENTVKTRLK-KA 167 (179)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999998 999988766 55
No 236
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.11 E-value=1e+02 Score=22.59 Aligned_cols=26 Identities=23% Similarity=0.397 Sum_probs=21.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|..++= +|
T Consensus 123 ~g~s~~eIA~~lgis-~~tv~~~l~-Ra 148 (165)
T PRK09644 123 HELTYEEAASVLDLK-LNTYKSHLF-RG 148 (165)
T ss_pred hcCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999998 898888765 54
No 237
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=23.08 E-value=1.5e+02 Score=16.56 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=22.8
Q ss_pred cCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
++..++|+.++++ ...+-.|+ ..|.+.+..
T Consensus 2 lt~~e~a~~lgis-~~ti~~~~-----~~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KDTVYRLI-----HEGELPAYR 31 (49)
T ss_pred CCHHHHHHHHCCC-HHHHHHHH-----HcCCCCeEE
Confidence 5788999999998 88877764 367666654
No 238
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=23.05 E-value=1.6e+02 Score=19.82 Aligned_cols=27 Identities=11% Similarity=0.421 Sum_probs=20.2
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHH
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELE 128 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE 128 (161)
++.||-.. -.||+.|....|++ +.+|=
T Consensus 5 iIeMAweD-RtpFeaI~~~fGL~-E~eVi 31 (72)
T TIGR03643 5 IIEMAWED-RTPFEAIEQQFGLS-EKEVI 31 (72)
T ss_pred HHHHHHcc-CCCHHHHHHHHCCC-HHHHH
Confidence 56666555 46999999999998 66653
No 239
>PRK00118 putative DNA-binding protein; Validated
Probab=22.88 E-value=1.2e+02 Score=21.64 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=21.6
Q ss_pred ccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 109 VLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 109 ~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
..|+++||+.+|++ ...|..++- ++
T Consensus 33 g~S~~EIAe~lGIS-~~TV~r~L~-RA 57 (104)
T PRK00118 33 DYSLGEIAEEFNVS-RQAVYDNIK-RT 57 (104)
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 68999999999998 888888766 54
No 240
>PRK09191 two-component response regulator; Provisional
Probab=22.88 E-value=1e+02 Score=23.98 Aligned_cols=27 Identities=26% Similarity=0.236 Sum_probs=22.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.++++ ...|...+- +|.
T Consensus 103 ~~~s~~eIA~~l~~s-~~tV~~~l~-ra~ 129 (261)
T PRK09191 103 EGFSVEEAAEILGVD-PAEAEALLD-DAR 129 (261)
T ss_pred hcCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 368999999999998 888888876 664
No 241
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=22.82 E-value=1.1e+02 Score=21.68 Aligned_cols=26 Identities=27% Similarity=0.479 Sum_probs=22.2
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...|+.+||+.+|++ ...|...+- .|
T Consensus 128 ~~~~~~eIA~~lgis-~~tv~~~~~-ra 153 (161)
T TIGR02985 128 EGKSYKEIAEELGIS-VKTVEYHIS-KA 153 (161)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 368999999999998 999888766 55
No 242
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=22.69 E-value=1e+02 Score=22.03 Aligned_cols=27 Identities=22% Similarity=0.345 Sum_probs=18.2
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...+|+.+||+.++++ ...|=+++- +|
T Consensus 31 ~eDlSlsEIAe~~~iS-RqaV~d~ik-r~ 57 (101)
T PF04297_consen 31 EEDLSLSEIAEELGIS-RQAVYDSIK-RA 57 (101)
T ss_dssp TS---HHHHHHHCTS--HHHHHHHHH-HH
T ss_pred ccCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 3579999999999998 777777665 54
No 243
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=22.56 E-value=99 Score=24.73 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=22.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
...||++||+.+|++ ...|...+= +|.
T Consensus 186 eg~s~~EIA~~Lgis-~~tVk~~l~-RAr 212 (233)
T PRK12538 186 ENMSNGEIAEVMDTT-VAAVESLLK-RGR 212 (233)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 568999999999999 999988766 653
No 244
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.46 E-value=1.1e+02 Score=23.04 Aligned_cols=26 Identities=12% Similarity=0.328 Sum_probs=22.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...|+++||+.+|++ ...|...+- +|
T Consensus 153 ~g~s~~eIA~~lgis-~~tv~~~l~-Ra 178 (193)
T PRK11923 153 DGLSYEDIASVMQCP-VGTVRSRIF-RA 178 (193)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999998 999988876 65
No 245
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=22.40 E-value=2.1e+02 Score=22.98 Aligned_cols=31 Identities=13% Similarity=0.160 Sum_probs=23.4
Q ss_pred HHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 99 tL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
.++.+..+| .+..+||+.++++ ...|+..+-
T Consensus 140 EVLrLLAqG--kTnKEIAe~L~IS-~rTVkth~s 170 (198)
T PRK15201 140 HLLKLIASG--YHLSETAALLSLS-EEQTKSLRR 170 (198)
T ss_pred HHHHHHHCC--CCHHHHHHHhCCC-HHHHHHHHH
Confidence 344444444 6799999999998 889988765
No 246
>PRK13239 alkylmercury lyase; Provisional
Probab=22.38 E-value=1.5e+02 Score=23.80 Aligned_cols=47 Identities=21% Similarity=0.241 Sum_probs=33.2
Q ss_pred HHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCE
Q 031323 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (161)
Q Consensus 98 LtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~ 151 (161)
++|+.+-..++.++-.++++.++.+ .++|+..+= ++ + .-.+|...+.
T Consensus 25 ~~llr~la~G~pvt~~~lA~~~~~~-~~~v~~~L~-~l---~--~~~~d~~g~i 71 (206)
T PRK13239 25 VPLLRLLAKGRPVSVTTLAAALGWP-VEEVEAVLE-AM---P--DTEYDEDGRI 71 (206)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCC-HHHHHHHHH-hC---C--CeEECCCCCE
Confidence 3444444488999999999999998 999998655 42 2 2256764443
No 247
>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=22.20 E-value=2.1e+02 Score=17.75 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=28.9
Q ss_pred cCCcc-CHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEE
Q 031323 106 TNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (161)
Q Consensus 106 ~~~~i-sy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gk 144 (161)
.+..+ |-.+|++.++++ ..-|-.-+- .....|+|.-+
T Consensus 20 ~g~~lps~~~la~~~~vs-r~tvr~al~-~L~~~g~i~~~ 57 (64)
T PF00392_consen 20 PGDRLPSERELAERYGVS-RTTVREALR-RLEAEGLIERR 57 (64)
T ss_dssp TTSBE--HHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred CCCEeCCHHHHHHHhccC-CcHHHHHHH-HHHHCCcEEEE
Confidence 35577 999999999998 888888777 88889998643
No 248
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=22.07 E-value=1.7e+02 Score=19.79 Aligned_cols=27 Identities=11% Similarity=0.405 Sum_probs=20.1
Q ss_pred HHHhhhcCCccCHHHHHHhcCCCChhhHH
Q 031323 100 VLTLAETNKVLPYDELMEELDVTNVRELE 128 (161)
Q Consensus 100 L~sLa~~~~~isy~~I~~~l~i~~~~evE 128 (161)
++.||-.. -.||+.|....|++ +.+|=
T Consensus 4 iIeMAweD-RtpFeaI~~qfGl~-E~eVi 30 (73)
T PF10985_consen 4 IIEMAWED-RTPFEAIERQFGLS-EKEVI 30 (73)
T ss_pred HHHHHHcc-CCCHHHHHHHHCCC-HHHHH
Confidence 55666554 46999999999998 66543
No 249
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=22.05 E-value=1.6e+02 Score=24.90 Aligned_cols=28 Identities=14% Similarity=0.285 Sum_probs=23.9
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
+...|+++|++.+|++ ..-|-++.- +|+
T Consensus 274 ~~~~Tl~EIa~~lgiS-~erVRqi~~-rAl 301 (317)
T PRK07405 274 GQPLTLAKIGERLNIS-RERVRQIER-EAL 301 (317)
T ss_pred CCCcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 4679999999999998 888888766 665
No 250
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=22.03 E-value=2.2e+02 Score=18.17 Aligned_cols=40 Identities=18% Similarity=0.201 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHH
Q 031323 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (161)
Q Consensus 92 ~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lv 131 (161)
+..+|+.....+-.++...|..+|+..+|.++....-...
T Consensus 28 ~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~f 67 (81)
T PF12833_consen 28 LRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAF 67 (81)
T ss_dssp HHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHH
Confidence 5677777777655334579999999999998766554433
No 251
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=21.88 E-value=1.9e+02 Score=23.66 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=23.8
Q ss_pred CCccCHHHHHHhcCCCChhhHHHHHHHHhH
Q 031323 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (161)
Q Consensus 107 ~~~isy~~I~~~l~i~~~~evE~lvI~~ai 136 (161)
....||.+||+.+|++ ...|...+- .|+
T Consensus 240 ~e~~s~~EIA~~Lgis-~~tVk~~l~-rAl 267 (285)
T TIGR02394 240 YEPATLEEVAAEVGLT-RERVRQIQV-EAL 267 (285)
T ss_pred CCCccHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4568999999999999 999998876 664
No 252
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=21.86 E-value=1.6e+02 Score=24.01 Aligned_cols=47 Identities=19% Similarity=0.218 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcE
Q 031323 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (161)
Q Consensus 94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~ 142 (161)
.-|.-.++++...++.++-+++++.++++ ...+=.=+. +.-..|++.
T Consensus 4 ~eR~~~Il~~l~~~g~v~v~eLa~~~~VS-~~TIRRDL~-~Le~~g~l~ 50 (253)
T COG1349 4 EERHQKILELLKEKGKVSVEELAELFGVS-EMTIRRDLN-ELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHHHHHcCcEEHHHHHHHhCCC-HHHHHHhHH-HHHHCCcEE
Confidence 44888899999999999999999999998 665555444 555566654
No 253
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=21.77 E-value=1.7e+02 Score=20.63 Aligned_cols=33 Identities=12% Similarity=0.265 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHhcccchHHHHHHHHHHhcCC
Q 031323 5 QRQAELIDHFVKQASNQKGAALGSVIVEATSQP 37 (161)
Q Consensus 5 ~~~~~~l~~~l~~~~~~~~~~a~~~i~~aL~~p 37 (161)
+....+|+.|++-..+..+...++++...++.|
T Consensus 29 dsV~~~L~~Y~~~L~G~~v~~lY~mVL~evE~P 61 (98)
T COG2901 29 DSVKQALKNYFADLNGQDVNDLYEMVLAEVEQP 61 (98)
T ss_pred HHHHHHHHHHHHHcCCCChhhHHHHHHHHHHhH
Confidence 445667888888888888888888888887766
No 254
>COG2118 DNA-binding protein [General function prediction only]
Probab=21.65 E-value=54 Score=24.10 Aligned_cols=23 Identities=30% Similarity=0.463 Sum_probs=20.6
Q ss_pred hhhHHHHHHHHhHhcCCcEEEecC
Q 031323 124 VRELEDFLINECMYTGIVRGKLDQ 147 (161)
Q Consensus 124 ~~evE~lvI~~ai~~gLi~gkIDq 147 (161)
.+.||..+| .....|=|..+||+
T Consensus 69 AeavE~qLi-~LaqtGri~~~I~e 91 (116)
T COG2118 69 AEAVENQLI-QLAQTGRITHKIDE 91 (116)
T ss_pred HHHHHHHHH-HHHHcCCCCCCCCH
Confidence 367999999 99999999999986
No 255
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=21.63 E-value=1.2e+02 Score=23.26 Aligned_cols=26 Identities=19% Similarity=0.196 Sum_probs=22.3
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...|+++||+.+|++ ...|...+= +|
T Consensus 128 ~g~s~~EIA~~LgiS-~~tVk~~l~-Ra 153 (188)
T PRK12546 128 SGFSYEEAAEMCGVA-VGTVKSRAN-RA 153 (188)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 468999999999999 998888765 54
No 256
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=21.38 E-value=1.1e+02 Score=18.01 Aligned_cols=22 Identities=18% Similarity=0.326 Sum_probs=18.8
Q ss_pred cCHHHHHHhcCCCChhhHHHHHH
Q 031323 110 LPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI 132 (161)
-..+.|++.++++ ..+|..|+.
T Consensus 28 ~~~~~la~~~~l~-~~qV~~WF~ 49 (56)
T smart00389 28 EEREELAAKLGLS-ERQVKVWFQ 49 (56)
T ss_pred HHHHHHHHHHCcC-HHHHHHhHH
Confidence 3467789999998 999999987
No 257
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=21.37 E-value=1.9e+02 Score=18.73 Aligned_cols=27 Identities=19% Similarity=0.402 Sum_probs=17.4
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHH
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
.+..+|+++|.+.+.++-...+.+|+-
T Consensus 17 r~~Plt~~eI~d~l~~d~~~~~~~~Lk 43 (65)
T PF02186_consen 17 RDHPLTLEEILDYLSLDIGKKLKQWLK 43 (65)
T ss_dssp H-S-B-HHHHHHHHTSSS-HHHHHHHH
T ss_pred cCCCcCHHHHHHHHcCCCCHHHHHHHH
Confidence 377999999999999874455666543
No 258
>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=21.30 E-value=3.8e+02 Score=20.47 Aligned_cols=47 Identities=13% Similarity=0.157 Sum_probs=35.8
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEE
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V 154 (161)
++...+..+||+.+++++...|-..+- .....|+|+..=.... .+.+
T Consensus 22 ~~~~~~~~ela~~~~~~s~~tv~~~l~-~L~~~g~i~~~~~~~~-~~~~ 68 (199)
T TIGR00498 22 TGYPPSIREIARAVGLRSPSAAEEHLK-ALERKGYIERDPGKPR-AIRI 68 (199)
T ss_pred cCCCCcHHHHHHHhCCCChHHHHHHHH-HHHHCCCEecCCCCCC-eEEe
Confidence 455688999999999986788888877 8888999987644333 4443
No 259
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.27 E-value=2.4e+02 Score=21.20 Aligned_cols=26 Identities=15% Similarity=0.164 Sum_probs=21.9
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||.+||+.+|++ ...|...+= +|
T Consensus 146 ~g~s~~EIAe~lgis-~~~V~~~l~-Ra 171 (189)
T PRK06811 146 LGEKIEEIAKKLGLT-RSAIDNRLS-RG 171 (189)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 359999999999999 888888765 54
No 260
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=21.26 E-value=1.2e+02 Score=22.45 Aligned_cols=26 Identities=23% Similarity=0.268 Sum_probs=21.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|-..+- +|
T Consensus 151 ~g~s~~eIA~~lgis-~~~v~~~l~-Ra 176 (187)
T TIGR02948 151 EDLSLKEISEILDLP-VGTVKTRIH-RG 176 (187)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 358999999999998 888887765 55
No 261
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.23 E-value=2.4e+02 Score=21.91 Aligned_cols=38 Identities=11% Similarity=0.156 Sum_probs=33.5
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEe
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkI 145 (161)
.++.+|=++||+.++++ ..+|=..+- ..-..||+..+-
T Consensus 33 ~~g~~tdeeLA~~Lgi~-~~~VRk~L~-~L~e~gLv~~~r 70 (178)
T PRK06266 33 KKGEVTDEEIAEQTGIK-LNTVRKILY-KLYDARLADYKR 70 (178)
T ss_pred HcCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeEEee
Confidence 45689999999999998 999999988 999999998543
No 262
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=21.20 E-value=2.2e+02 Score=22.34 Aligned_cols=80 Identities=13% Similarity=0.188 Sum_probs=45.7
Q ss_pred hHHHHHHHHhcCCHhHHhhc--cC-CCCCCCHHHHHHHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHh
Q 031323 61 KYLDMLRLFAHGTWSDYKNN--AG-HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (161)
Q Consensus 61 ~l~~LL~iF~~G~~~dy~~~--~~-~~~~L~~~~~~KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~ 137 (161)
.+-.+.+++........... .. ..++|++.|++=++.=-=+..-.-.|.++-.+||+.+||+ ...+++-+= +|.
T Consensus 127 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGIS-kst~~ehLR-rAe- 203 (215)
T COG3413 127 ELRDLLEILNFEDKEEVIESAFVEIGKNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGIS-KSTLSEHLR-RAE- 203 (215)
T ss_pred HHHHHHHHhcccceeeeccccccccccccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC-HHHHHHHHH-HHH-
Confidence 45566666666655543332 11 2235777544433322222222246899999999999998 777777655 553
Q ss_pred cCCcEE
Q 031323 138 TGIVRG 143 (161)
Q Consensus 138 ~gLi~g 143 (161)
.+|+.+
T Consensus 204 ~Kl~~~ 209 (215)
T COG3413 204 RKLIEA 209 (215)
T ss_pred HHHHHH
Confidence 444443
No 263
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=20.97 E-value=2.3e+02 Score=23.19 Aligned_cols=39 Identities=18% Similarity=0.332 Sum_probs=34.2
Q ss_pred cCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEec
Q 031323 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (161)
Q Consensus 106 ~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkID 146 (161)
.....|=++++++++++ ...+-.++. =+++.|.+++.|.
T Consensus 170 ~~~~~Taeela~~~giS-RvTaRRYLe-yl~~~~~l~a~i~ 208 (224)
T COG4565 170 PDQELTAEELAQALGIS-RVTARRYLE-YLVSNGILEAEIH 208 (224)
T ss_pred cCCccCHHHHHHHhCcc-HHHHHHHHH-HHHhcCeeeEEee
Confidence 45689999999999998 888888888 8889999998875
No 264
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=20.88 E-value=1.3e+02 Score=22.37 Aligned_cols=26 Identities=23% Similarity=0.268 Sum_probs=21.5
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.+|++ ...|...+= .|
T Consensus 151 ~~~s~~eIA~~lgis-~~~v~~~l~-Ra 176 (187)
T PRK09641 151 EDLSLKEISEILDLP-VGTVKTRIH-RG 176 (187)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 578999999999998 888887654 44
No 265
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=20.82 E-value=1.3e+02 Score=22.37 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=20.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHH
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI 132 (161)
...|+++||+.++++ ...|...+=
T Consensus 115 ~g~s~~eIA~~lgis-~~tV~~~l~ 138 (170)
T TIGR02959 115 EGLSQQEIAEKLGLS-LSGAKSRVQ 138 (170)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH
Confidence 468999999999998 888887754
No 266
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=20.80 E-value=1.3e+02 Score=22.67 Aligned_cols=26 Identities=19% Similarity=0.356 Sum_probs=21.7
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|...+- .|
T Consensus 164 ~~~s~~eIA~~l~~s-~~tV~~~l~-r~ 189 (198)
T TIGR02859 164 DGKSYQEIACDLNRH-VKSIDNALQ-RV 189 (198)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 479999999999998 888887655 54
No 267
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=20.74 E-value=1.3e+02 Score=22.72 Aligned_cols=26 Identities=8% Similarity=0.075 Sum_probs=21.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|...+= .|
T Consensus 146 ~~~s~~eIA~~lgis-~~tV~~~l~-Ra 171 (189)
T PRK12515 146 HEKSVEEVGEIVGIP-ESTVKTRMF-YA 171 (189)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 569999999999998 888887755 54
No 268
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=20.66 E-value=1.2e+02 Score=23.09 Aligned_cols=26 Identities=8% Similarity=-0.024 Sum_probs=21.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||++||+.++++ ...|..-+= .|
T Consensus 149 ~g~s~~EIA~~lg~s-~~tV~~rl~-ra 174 (192)
T PRK09643 149 QGYSVADAARMLGVA-EGTVKSRCA-RG 174 (192)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 468999999999998 998888764 44
No 269
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=20.48 E-value=2.3e+02 Score=21.55 Aligned_cols=22 Identities=9% Similarity=0.226 Sum_probs=19.7
Q ss_pred cCHHHHHHhcCCCChhhHHHHHH
Q 031323 110 LPYDELMEELDVTNVRELEDFLI 132 (161)
Q Consensus 110 isy~~I~~~l~i~~~~evE~lvI 132 (161)
.|..+||+.++++ ...|+..+-
T Consensus 166 ~s~~eIA~~l~iS-~~TV~~h~~ 187 (216)
T PRK10840 166 FLVTEIAKKLNRS-IKTISSQKK 187 (216)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH
Confidence 8999999999998 899998765
No 270
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=20.45 E-value=1.4e+02 Score=20.54 Aligned_cols=26 Identities=27% Similarity=0.392 Sum_probs=21.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...|+.+||+.++++ ...|..++- ++
T Consensus 125 ~g~s~~eIA~~l~~s-~~~v~~~~~-~~ 150 (158)
T TIGR02937 125 EGLSYKEIAEILGIS-VGTVKRRLK-RA 150 (158)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 357999999999998 888888766 54
No 271
>PF02406 MmoB_DmpM: MmoB/DmpM family ; InterPro: IPR003454 This family consists of monooxygenase components such as MmoB methane monooxygenase (1.14.13.25 from EC) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen []. Also found in this family is DmpM or Phenol hydroxylase (1.14.13.7 from EC) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase []. Phenol hydroxylase catabolises phenol and some of its methylated derivatives in the first step of phenol biodegradation, and is required for growth on phenol. The multicomponent enzyme is made up of P0, P1, P2, P3, P4 and P5 polypeptides.; GO: 0004497 monooxygenase activity, 0006725 cellular aromatic compound metabolic process; PDB: 2INN_L 2INP_L 1CKV_A 3Q3M_H 3GE3_E 1G11_A 2BF2_B 3I5J_E 3Q3O_E 3I63_E ....
Probab=20.18 E-value=1.2e+02 Score=20.93 Aligned_cols=43 Identities=16% Similarity=0.248 Sum_probs=34.6
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEEEe
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVCT 156 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V~~ 156 (161)
-.+.+++|.+.||=+ -++.++-+ . .--.-|+|+.....+.++|
T Consensus 45 l~i~~~tiee~LGr~--~~~~el~v-~---mss~~Gri~~~dD~~~~~w 87 (87)
T PF02406_consen 45 LVIRRETIEEALGRP--FDLQELEV-N---MSSFYGRIDEDDDEFVLYW 87 (87)
T ss_dssp EEEEHHHHHHHCTST--CHHHHHHH-T---ECEEESEEEEESSEEEEES
T ss_pred EEEEHHHHHHHhCCC--CcHHHHhh-h---hheeeeEEEEeCCEEEEEC
Confidence 378999999999965 67777766 4 3347899999999999887
No 272
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=20.16 E-value=3.5e+02 Score=19.58 Aligned_cols=56 Identities=14% Similarity=0.156 Sum_probs=37.0
Q ss_pred HHHHHHHHHhhhcCCccCHHHHHHhcCCCChhhHHHHHHHHhHhcCCcEEEecCCCCEEEE
Q 031323 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (161)
Q Consensus 94 KlrlLtL~sLa~~~~~isy~~I~~~l~i~~~~evE~lvI~~ai~~gLi~gkIDq~~~~v~V 154 (161)
.+++|.++. +++..+-.+|++.++++ ...|-.-+= ..-.+|||+.+-+......++
T Consensus 18 Rl~IL~~L~---~~~~~~v~ela~~l~ls-qstvS~HL~-~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 18 RLGIVLLLR---ESGELCVCDLCTALDQS-QPKISRHLA-LLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred HHHHHHHHH---HcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEEEEcCEEEEEE
Confidence 344444432 33468888999999998 777766654 566799998877655444433
No 273
>PRK06930 positive control sigma-like factor; Validated
Probab=20.11 E-value=1.3e+02 Score=23.11 Aligned_cols=26 Identities=15% Similarity=0.348 Sum_probs=22.4
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
...||.+||+.++++ ...|...+- +|
T Consensus 129 eg~s~~EIA~~lgiS-~~tVk~~l~-Ra 154 (170)
T PRK06930 129 YGLSYSEIADYLNIK-KSTVQSMIE-RA 154 (170)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 468999999999998 999998866 55
No 274
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=1.3e+02 Score=21.87 Aligned_cols=26 Identities=15% Similarity=0.164 Sum_probs=21.8
Q ss_pred CccCHHHHHHhcCCCChhhHHHHHHHHh
Q 031323 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (161)
Q Consensus 108 ~~isy~~I~~~l~i~~~~evE~lvI~~a 135 (161)
..+||++||+.+|++ ...|...+= .|
T Consensus 127 ~~~s~~eIA~~lgis-~~tv~~~l~-Ra 152 (161)
T PRK12541 127 YGFSYKEIAEMTGLS-LAKVKIELH-RG 152 (161)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 469999999999998 888887765 54
Done!