Query 030471
Match_columns 177
No_of_seqs 112 out of 562
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 14:13:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030471.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030471hhsearch_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 1.1E-39 2.4E-44 259.3 10.7 176 1-177 1-176 (258)
2 KOG2753 Uncharacterized conser 100.0 1.3E-36 2.8E-41 254.8 11.1 165 8-177 185-360 (378)
3 KOG2908 26S proteasome regulat 100.0 5.2E-36 1.1E-40 252.1 12.5 167 9-177 178-360 (380)
4 smart00088 PINT motif in prote 99.6 1.9E-15 4.1E-20 105.5 8.0 85 89-177 4-88 (88)
5 smart00753 PAM PCI/PINT associ 99.6 1.9E-15 4.1E-20 105.5 8.0 85 89-177 4-88 (88)
6 PF01399 PCI: PCI domain; Int 99.6 4E-15 8.6E-20 105.8 7.6 95 60-156 1-105 (105)
7 KOG1464 COP9 signalosome, subu 98.0 1.2E-05 2.6E-10 67.8 6.7 95 60-156 305-409 (440)
8 KOG2581 26S proteasome regulat 97.9 1.8E-05 3.9E-10 69.4 5.8 90 60-152 319-419 (493)
9 KOG2758 Translation initiation 96.5 0.0075 1.6E-07 52.0 6.6 63 92-156 332-394 (432)
10 KOG0686 COP9 signalosome, subu 96.3 0.03 6.6E-07 49.5 9.1 111 60-172 306-426 (466)
11 KOG2582 COP9 signalosome, subu 95.7 0.068 1.5E-06 46.8 8.2 105 60-168 259-372 (422)
12 KOG2688 Transcription-associat 95.6 0.028 6.2E-07 49.5 5.8 97 61-158 273-386 (394)
13 COG5600 Transcription-associat 95.3 0.057 1.2E-06 47.3 6.5 98 60-159 289-406 (413)
14 KOG1497 COP9 signalosome, subu 95.1 0.021 4.5E-07 49.3 3.4 128 25-156 227-362 (399)
15 PF10075 PCI_Csn8: COP9 signal 93.7 0.46 1E-05 35.6 7.8 108 24-132 5-119 (143)
16 PF09756 DDRGK: DDRGK domain; 92.9 0.19 4E-06 40.2 4.5 58 97-156 101-158 (188)
17 KOG1463 26S proteasome regulat 92.9 0.22 4.8E-06 43.4 5.2 104 54-159 280-393 (411)
18 PF02082 Rrf2: Transcriptional 91.4 0.6 1.3E-05 31.8 5.2 59 95-156 11-69 (83)
19 PF09012 FeoC: FeoC like trans 91.2 0.18 3.9E-06 33.3 2.3 46 100-147 5-50 (69)
20 KOG0687 26S proteasome regulat 88.2 0.71 1.5E-05 40.1 4.1 110 44-156 242-362 (393)
21 KOG1498 26S proteasome regulat 88.1 1.3 2.8E-05 39.3 5.7 111 59-171 287-413 (439)
22 PF13412 HTH_24: Winged helix- 87.3 1.2 2.6E-05 26.8 3.8 41 100-142 8-48 (48)
23 TIGR02010 IscR iron-sulfur clu 87.2 1.7 3.7E-05 32.3 5.3 46 96-143 12-57 (135)
24 PRK11179 DNA-binding transcrip 86.6 1.1 2.3E-05 34.2 4.0 46 100-147 14-62 (153)
25 PRK14165 winged helix-turn-hel 85.7 4.2 9.1E-05 33.1 7.2 62 93-156 5-66 (217)
26 smart00344 HTH_ASNC helix_turn 85.4 1.8 3.9E-05 30.5 4.4 37 105-143 13-49 (108)
27 COG5159 RPN6 26S proteasome re 85.1 1.1 2.5E-05 38.5 3.7 101 59-161 283-393 (421)
28 PF09339 HTH_IclR: IclR helix- 85.1 2.1 4.5E-05 26.4 4.1 45 96-142 4-49 (52)
29 KOG3054 Uncharacterized conser 85.0 1.7 3.7E-05 36.2 4.6 54 100-155 205-258 (299)
30 PRK11169 leucine-responsive tr 84.4 7.5 0.00016 29.8 7.8 43 99-143 18-60 (164)
31 PRK10857 DNA-binding transcrip 84.0 2.5 5.5E-05 32.8 5.0 47 95-143 11-57 (164)
32 TIGR00738 rrf2_super rrf2 fami 83.3 4.7 0.0001 29.4 6.1 49 94-144 10-58 (132)
33 COG1522 Lrp Transcriptional re 83.1 1.8 4E-05 32.3 3.8 42 102-145 15-56 (154)
34 COG1959 Predicted transcriptio 81.5 4.2 9.1E-05 31.0 5.3 48 95-144 11-58 (150)
35 smart00346 HTH_ICLR helix_turn 81.4 3.3 7.2E-05 28.0 4.3 55 96-154 6-61 (91)
36 PF01726 LexA_DNA_bind: LexA D 80.8 3.2 7E-05 27.2 3.9 37 105-142 21-57 (65)
37 COG5187 RPN7 26S proteasome re 80.5 9.4 0.0002 33.0 7.4 64 92-157 314-377 (412)
38 PF07389 DUF1500: Protein of u 78.8 3.3 7.2E-05 29.1 3.5 38 99-139 38-75 (100)
39 PF08220 HTH_DeoR: DeoR-like h 77.6 3.6 7.7E-05 26.1 3.3 42 98-141 3-44 (57)
40 PF12840 HTH_20: Helix-turn-he 77.2 5 0.00011 25.4 3.9 38 105-144 20-57 (61)
41 PRK11920 rirA iron-responsive 76.3 7.2 0.00016 29.8 5.2 48 95-145 11-58 (153)
42 PF08281 Sigma70_r4_2: Sigma-7 76.0 4 8.6E-05 25.0 3.1 27 108-136 25-51 (54)
43 PF01022 HTH_5: Bacterial regu 75.6 7.3 0.00016 23.4 4.2 33 108-142 14-46 (47)
44 TIGR02944 suf_reg_Xantho FeS a 75.4 7.7 0.00017 28.4 5.0 37 106-144 22-58 (130)
45 PRK11014 transcriptional repre 75.4 8.2 0.00018 28.8 5.3 48 96-145 12-59 (141)
46 smart00347 HTH_MARR helix_turn 75.0 10 0.00022 25.4 5.4 44 107-152 22-65 (101)
47 smart00550 Zalpha Z-DNA-bindin 75.0 5.5 0.00012 26.1 3.7 33 109-143 22-54 (68)
48 PF08280 HTH_Mga: M protein tr 75.0 2.9 6.3E-05 26.6 2.3 35 96-131 6-40 (59)
49 PF13730 HTH_36: Helix-turn-he 74.6 12 0.00026 22.8 5.1 47 93-141 7-55 (55)
50 KOG2072 Translation initiation 74.0 7.6 0.00017 37.6 5.6 49 106-155 444-492 (988)
51 PF01325 Fe_dep_repress: Iron 74.0 8.3 0.00018 24.8 4.3 43 98-142 11-53 (60)
52 smart00345 HTH_GNTR helix_turn 73.1 16 0.00035 22.1 5.5 36 105-142 15-51 (60)
53 PF04545 Sigma70_r4: Sigma-70, 71.7 16 0.00035 22.0 5.1 29 107-137 18-46 (50)
54 PF13404 HTH_AsnC-type: AsnC-t 70.9 2.9 6.4E-05 25.0 1.5 29 100-129 8-36 (42)
55 cd00090 HTH_ARSR Arsenical Res 69.8 18 0.00039 22.4 5.3 36 110-147 21-56 (78)
56 PF13601 HTH_34: Winged helix 69.3 6.3 0.00014 26.8 3.1 51 98-150 3-53 (80)
57 PF08279 HTH_11: HTH domain; 69.3 7.2 0.00016 23.9 3.1 35 97-132 2-37 (55)
58 PF12802 MarR_2: MarR family; 69.0 12 0.00025 23.3 4.2 41 108-150 20-60 (62)
59 PF14947 HTH_45: Winged helix- 68.6 16 0.00034 24.4 4.9 50 99-155 10-59 (77)
60 COG5071 RPN5 26S proteasome re 68.0 12 0.00026 32.6 5.1 50 105-156 349-398 (439)
61 TIGR02337 HpaR homoprotocatech 67.7 18 0.00039 25.8 5.4 48 106-155 39-86 (118)
62 PF01978 TrmB: Sugar-specific 67.3 8.9 0.00019 24.7 3.4 38 106-145 19-56 (68)
63 smart00420 HTH_DEOR helix_turn 67.2 16 0.00034 21.5 4.4 35 107-143 12-46 (53)
64 PF08784 RPA_C: Replication pr 67.1 14 0.00031 25.8 4.7 50 96-147 51-101 (102)
65 PRK09954 putative kinase; Prov 66.4 7.6 0.00016 33.3 3.7 50 100-151 8-60 (362)
66 PF01047 MarR: MarR family; I 65.4 9.7 0.00021 23.5 3.2 44 106-151 14-57 (59)
67 PRK03573 transcriptional regul 64.7 21 0.00045 26.4 5.4 57 101-159 38-94 (144)
68 KOG1076 Translation initiation 63.0 8.8 0.00019 36.6 3.6 117 42-160 634-767 (843)
69 smart00418 HTH_ARSR helix_turn 62.9 27 0.00059 20.9 5.0 38 107-146 8-45 (66)
70 smart00419 HTH_CRP helix_turn_ 62.8 28 0.0006 20.1 5.0 33 109-143 8-40 (48)
71 PF05331 DUF742: Protein of un 62.4 13 0.00029 27.2 3.8 42 99-144 47-88 (114)
72 PF04967 HTH_10: HTH DNA bindi 61.9 38 0.00081 21.3 5.7 30 105-136 19-48 (53)
73 PF13518 HTH_28: Helix-turn-he 61.0 13 0.00029 22.1 3.2 42 100-146 5-46 (52)
74 PF03979 Sigma70_r1_1: Sigma-7 59.5 7.7 0.00017 26.4 2.0 40 99-140 11-53 (82)
75 cd00092 HTH_CRP helix_turn_hel 58.3 22 0.00048 22.2 4.0 35 107-143 23-57 (67)
76 PF04539 Sigma70_r3: Sigma-70 57.4 12 0.00025 24.6 2.7 26 106-132 17-42 (78)
77 PF10668 Phage_terminase: Phag 56.8 13 0.00028 24.2 2.6 24 106-130 19-42 (60)
78 TIGR03879 near_KaiC_dom probab 56.5 11 0.00025 25.4 2.4 30 108-139 31-60 (73)
79 TIGR01884 cas_HTH CRISPR locus 56.3 35 0.00075 27.0 5.6 52 100-154 148-199 (203)
80 PF04703 FaeA: FaeA-like prote 56.2 15 0.00032 24.0 2.8 34 107-142 13-46 (62)
81 COG1595 RpoE DNA-directed RNA 55.9 14 0.0003 28.4 3.2 28 107-136 141-168 (182)
82 PF13463 HTH_27: Winged helix 54.8 45 0.00098 20.8 5.1 48 102-151 11-58 (68)
83 COG3355 Predicted transcriptio 53.4 22 0.00048 26.6 3.8 40 105-146 38-77 (126)
84 PHA02943 hypothetical protein; 53.1 33 0.00071 26.7 4.7 45 96-143 12-56 (165)
85 PRK10141 DNA-binding transcrip 52.9 19 0.00041 26.5 3.3 46 107-154 28-73 (117)
86 PRK10265 chaperone-modulator p 52.9 20 0.00042 25.5 3.3 39 106-150 4-42 (101)
87 PF02002 TFIIE_alpha: TFIIE al 51.9 16 0.00035 25.7 2.8 36 107-144 25-60 (105)
88 PRK15090 DNA-binding transcrip 51.8 29 0.00063 28.3 4.7 56 96-155 15-70 (257)
89 PRK15418 transcriptional regul 51.5 24 0.00053 30.2 4.3 40 108-149 28-67 (318)
90 PRK12537 RNA polymerase sigma 51.2 18 0.00039 27.7 3.2 27 108-136 148-174 (182)
91 cd06445 ATase The DNA repair p 50.5 18 0.00038 24.4 2.7 25 98-122 6-30 (79)
92 PRK10434 srlR DNA-bindng trans 49.8 24 0.00052 29.1 3.9 44 96-141 6-49 (256)
93 cd07377 WHTH_GntR Winged helix 49.8 58 0.0013 19.9 6.0 36 105-142 20-56 (66)
94 COG2390 DeoR Transcriptional r 49.3 26 0.00056 30.3 4.1 39 107-147 24-62 (321)
95 PRK10411 DNA-binding transcrip 49.0 28 0.00061 28.4 4.1 45 96-142 5-49 (240)
96 PRK12523 RNA polymerase sigma 48.9 22 0.00048 26.9 3.3 28 108-137 134-161 (172)
97 PF13591 MerR_2: MerR HTH fami 48.5 29 0.00062 23.7 3.5 32 110-147 1-32 (84)
98 PF06163 DUF977: Bacterial pro 48.3 29 0.00062 26.0 3.6 43 97-141 14-56 (127)
99 PRK04214 rbn ribonuclease BN/u 48.2 63 0.0014 28.6 6.5 56 106-170 307-362 (412)
100 TIGR02999 Sig-70_X6 RNA polyme 48.2 23 0.0005 26.9 3.3 28 107-136 148-175 (183)
101 PF13384 HTH_23: Homeodomain-l 48.0 20 0.00043 21.3 2.4 23 109-132 17-39 (50)
102 PF10975 DUF2802: Protein of u 47.8 22 0.00047 23.7 2.7 20 110-130 45-64 (70)
103 PRK09651 RNA polymerase sigma 46.8 24 0.00052 26.8 3.2 29 107-137 133-161 (172)
104 PF06056 Terminase_5: Putative 46.5 24 0.00051 22.6 2.6 23 109-132 13-35 (58)
105 PRK12529 RNA polymerase sigma 46.2 25 0.00055 26.8 3.3 27 108-136 142-168 (178)
106 PRK09642 RNA polymerase sigma 46.1 26 0.00057 25.9 3.3 28 107-136 120-147 (160)
107 PRK06759 RNA polymerase factor 46.0 27 0.00058 25.6 3.3 27 108-136 121-147 (154)
108 PRK13509 transcriptional repre 45.8 34 0.00075 28.1 4.2 47 95-143 5-51 (251)
109 PRK09802 DNA-binding transcrip 45.6 32 0.00069 28.6 4.0 47 94-142 16-62 (269)
110 PHA02763 hypothetical protein; 45.6 29 0.00064 24.4 3.1 52 108-162 51-102 (102)
111 PRK11512 DNA-binding transcrip 45.2 71 0.0015 23.5 5.5 52 107-160 52-103 (144)
112 PRK09047 RNA polymerase factor 45.1 28 0.00061 25.7 3.3 27 108-136 121-147 (161)
113 PRK12543 RNA polymerase sigma 44.7 27 0.00059 26.6 3.3 27 108-136 132-158 (179)
114 TIGR03541 reg_near_HchA LuxR f 44.6 29 0.00062 28.1 3.5 23 109-132 186-208 (232)
115 KOG3431 Apoptosis-related prot 44.5 14 0.00031 27.5 1.5 22 125-147 70-91 (129)
116 COG3413 Predicted DNA binding 44.3 35 0.00075 27.2 3.9 83 61-146 127-212 (215)
117 PF03399 SAC3_GANP: SAC3/GANP/ 44.2 1E+02 0.0022 23.8 6.6 62 59-120 135-203 (204)
118 PRK12525 RNA polymerase sigma 44.2 29 0.00063 26.1 3.3 29 107-137 132-160 (168)
119 PF09743 DUF2042: Uncharacteri 43.7 46 0.001 28.0 4.7 41 106-148 127-167 (272)
120 PRK12520 RNA polymerase sigma 43.2 28 0.00062 26.7 3.2 27 108-136 146-172 (191)
121 PRK07037 extracytoplasmic-func 42.7 32 0.00068 25.5 3.3 27 108-136 124-150 (163)
122 PF13542 HTH_Tnp_ISL3: Helix-t 42.7 34 0.00073 20.5 2.9 31 99-132 19-49 (52)
123 TIGR02431 pcaR_pcaU beta-ketoa 42.7 50 0.0011 26.7 4.7 45 96-142 10-55 (248)
124 smart00421 HTH_LUXR helix_turn 42.6 42 0.0009 19.7 3.3 24 110-135 19-42 (58)
125 PRK12527 RNA polymerase sigma 42.6 32 0.0007 25.5 3.3 28 107-136 119-146 (159)
126 cd06170 LuxR_C_like C-terminal 41.9 43 0.00094 19.7 3.3 25 109-135 15-39 (57)
127 TIGR02947 SigH_actino RNA poly 41.9 31 0.00068 26.5 3.2 28 107-136 145-172 (193)
128 PRK10870 transcriptional repre 41.9 74 0.0016 24.6 5.3 50 106-157 68-117 (176)
129 TIGR02983 SigE-fam_strep RNA p 41.2 34 0.00075 25.3 3.3 27 108-136 125-151 (162)
130 PRK12514 RNA polymerase sigma 41.0 33 0.00072 25.9 3.2 26 109-136 145-170 (179)
131 PRK12547 RNA polymerase sigma 40.5 36 0.00078 25.5 3.3 27 108-136 127-153 (164)
132 PF10007 DUF2250: Uncharacteri 40.5 39 0.00085 23.8 3.2 27 114-142 26-52 (92)
133 PF02406 MmoB_DmpM: MmoB/DmpM 39.9 30 0.00066 24.1 2.5 44 107-156 44-87 (87)
134 PRK12513 RNA polymerase sigma 39.8 36 0.00078 26.2 3.3 28 107-136 153-180 (194)
135 PRK12528 RNA polymerase sigma 39.8 38 0.00082 25.1 3.3 28 107-136 127-154 (161)
136 PF05920 Homeobox_KN: Homeobox 39.8 40 0.00087 19.8 2.7 21 113-135 17-37 (40)
137 PF14394 DUF4423: Domain of un 39.4 70 0.0015 24.9 4.8 57 111-172 41-102 (171)
138 PF14480 DNA_pol3_a_NI: DNA po 39.2 1.1E+02 0.0023 19.9 5.1 60 111-175 2-61 (76)
139 PRK12522 RNA polymerase sigma 38.4 40 0.00086 25.4 3.3 27 108-136 134-160 (173)
140 PRK12530 RNA polymerase sigma 38.3 40 0.00086 26.0 3.3 27 108-136 149-175 (189)
141 PRK09645 RNA polymerase sigma 37.9 38 0.00083 25.4 3.1 27 108-136 133-159 (173)
142 PRK09647 RNA polymerase sigma 37.9 40 0.00086 26.6 3.3 28 107-136 152-179 (203)
143 PF12728 HTH_17: Helix-turn-he 37.8 40 0.00087 20.1 2.6 29 110-144 2-30 (51)
144 cd04762 HTH_MerR-trunc Helix-T 37.8 41 0.00089 19.1 2.6 22 110-132 1-22 (49)
145 PF12324 HTH_15: Helix-turn-he 37.7 51 0.0011 22.5 3.3 33 99-132 28-60 (77)
146 PRK08301 sporulation sigma fac 37.7 40 0.00086 27.0 3.3 28 107-136 196-223 (234)
147 PRK09646 RNA polymerase sigma 37.5 40 0.00087 26.0 3.2 27 108-136 157-183 (194)
148 PRK10188 DNA-binding transcrip 37.4 59 0.0013 26.5 4.3 22 110-132 195-216 (240)
149 PRK10430 DNA-binding transcrip 37.3 56 0.0012 25.9 4.1 39 107-147 176-214 (239)
150 PRK12511 RNA polymerase sigma 37.2 42 0.00091 25.9 3.3 28 108-137 126-153 (182)
151 PRK12536 RNA polymerase sigma 37.2 42 0.00092 25.5 3.3 27 108-136 144-170 (181)
152 PRK12512 RNA polymerase sigma 37.1 41 0.00088 25.6 3.2 27 108-136 146-172 (184)
153 PRK10046 dpiA two-component re 36.9 63 0.0014 25.4 4.3 37 109-147 177-213 (225)
154 PRK12545 RNA polymerase sigma 36.7 42 0.00091 26.2 3.2 28 107-136 153-180 (201)
155 PF00325 Crp: Bacterial regula 36.3 72 0.0016 17.9 3.3 30 110-141 3-32 (32)
156 PRK10163 DNA-binding transcrip 36.2 69 0.0015 26.5 4.6 56 96-155 26-82 (271)
157 TIGR02950 SigM_subfam RNA poly 35.8 47 0.001 24.2 3.3 27 108-136 120-146 (154)
158 PRK12539 RNA polymerase sigma 35.8 45 0.00097 25.5 3.2 27 108-136 146-172 (184)
159 PF04297 UPF0122: Putative hel 35.4 45 0.00098 23.9 2.9 28 107-136 31-58 (101)
160 PRK10906 DNA-binding transcrip 35.2 57 0.0012 26.8 3.9 47 94-142 4-50 (252)
161 TIGR01764 excise DNA binding d 35.2 49 0.0011 18.9 2.7 30 110-145 2-31 (49)
162 PRK12540 RNA polymerase sigma 34.9 46 0.001 25.6 3.2 28 107-136 125-152 (182)
163 PRK12519 RNA polymerase sigma 34.5 49 0.0011 25.3 3.3 27 108-136 156-182 (194)
164 PRK12516 RNA polymerase sigma 34.5 49 0.0011 25.6 3.3 28 107-136 130-157 (187)
165 PRK11569 transcriptional repre 34.3 75 0.0016 26.3 4.5 55 96-154 29-84 (274)
166 PF04218 CENP-B_N: CENP-B N-te 34.3 41 0.0009 20.8 2.3 30 99-131 14-43 (53)
167 TIGR01889 Staph_reg_Sar staphy 34.2 1.6E+02 0.0034 20.6 5.7 52 106-159 40-91 (109)
168 TIGR02939 RpoE_Sigma70 RNA pol 34.2 50 0.0011 25.0 3.3 27 108-136 153-179 (190)
169 COG1414 IclR Transcriptional r 34.1 75 0.0016 26.0 4.4 55 97-155 6-61 (246)
170 cd04761 HTH_MerR-SF Helix-Turn 34.0 83 0.0018 18.2 3.6 46 111-171 2-47 (49)
171 TIGR02952 Sig70_famx2 RNA poly 33.8 53 0.0011 24.3 3.3 27 108-136 137-163 (170)
172 PRK13919 putative RNA polymera 33.7 49 0.0011 25.1 3.1 28 107-136 149-176 (186)
173 PRK09649 RNA polymerase sigma 33.6 50 0.0011 25.4 3.2 28 107-136 144-171 (185)
174 COG1339 Transcriptional regula 33.6 1.4E+02 0.003 24.3 5.7 58 95-155 6-63 (214)
175 TIGR02702 SufR_cyano iron-sulf 33.5 1.6E+02 0.0035 23.1 6.2 37 107-145 13-49 (203)
176 PF00888 Cullin: Cullin family 33.5 40 0.00087 30.6 3.0 43 98-142 523-565 (588)
177 PRK12535 RNA polymerase sigma 33.4 52 0.0011 25.7 3.3 27 108-136 148-174 (196)
178 PF06627 DUF1153: Protein of u 33.3 45 0.00098 23.5 2.5 31 106-139 46-76 (90)
179 PRK12524 RNA polymerase sigma 33.3 52 0.0011 25.5 3.2 28 107-136 150-177 (196)
180 KOG2235 Uncharacterized conser 33.2 65 0.0014 30.5 4.2 46 106-155 130-175 (776)
181 PF00403 HMA: Heavy-metal-asso 33.0 1E+02 0.0022 18.9 4.1 44 125-172 14-57 (62)
182 TIGR02943 Sig70_famx1 RNA poly 32.8 55 0.0012 25.2 3.3 27 108-136 146-172 (188)
183 PRK13870 transcriptional regul 32.6 56 0.0012 26.5 3.4 22 110-132 189-210 (234)
184 PRK12533 RNA polymerase sigma 32.5 54 0.0012 26.2 3.3 27 108-136 149-175 (216)
185 TIGR03001 Sig-70_gmx1 RNA poly 32.4 53 0.0011 26.9 3.3 27 108-136 176-202 (244)
186 PRK12542 RNA polymerase sigma 32.4 56 0.0012 24.9 3.3 27 108-136 137-163 (185)
187 PF08221 HTH_9: RNA polymerase 32.0 76 0.0016 20.3 3.3 36 106-143 24-59 (62)
188 PRK06266 transcription initiat 32.0 87 0.0019 24.6 4.3 51 105-157 32-84 (178)
189 PRK04239 hypothetical protein; 31.9 26 0.00056 25.6 1.2 22 125-147 67-88 (110)
190 TIGR02954 Sig70_famx3 RNA poly 31.8 58 0.0013 24.3 3.2 27 108-136 134-160 (169)
191 PRK09652 RNA polymerase sigma 31.8 59 0.0013 24.1 3.3 27 108-136 143-169 (182)
192 PRK12517 RNA polymerase sigma 31.7 58 0.0013 25.1 3.3 27 108-136 143-169 (188)
193 PRK06704 RNA polymerase factor 31.6 56 0.0012 26.6 3.2 26 109-136 132-157 (228)
194 PF02796 HTH_7: Helix-turn-hel 31.4 62 0.0014 19.1 2.7 20 110-130 22-41 (45)
195 PF00046 Homeobox: Homeobox do 31.3 54 0.0012 19.9 2.5 24 108-132 26-49 (57)
196 PF13545 HTH_Crp_2: Crp-like h 31.1 96 0.0021 19.8 3.8 33 108-142 27-59 (76)
197 TIGR02844 spore_III_D sporulat 31.0 50 0.0011 22.6 2.4 32 96-129 7-38 (80)
198 PF00392 GntR: Bacterial regul 31.0 1.4E+02 0.003 18.7 5.9 38 105-144 19-57 (64)
199 PF01984 dsDNA_bind: Double-st 30.8 27 0.00057 25.3 1.1 22 125-147 62-83 (107)
200 COG2345 Predicted transcriptio 30.7 94 0.002 25.4 4.4 47 100-148 16-62 (218)
201 TIGR02846 spore_sigmaK RNA pol 30.6 58 0.0013 26.0 3.2 27 108-136 193-219 (227)
202 smart00653 eIF2B_5 domain pres 30.6 2.1E+02 0.0046 20.7 6.0 53 110-172 22-74 (110)
203 PRK09638 RNA polymerase sigma 30.5 62 0.0013 24.2 3.2 27 108-136 141-167 (176)
204 PF09940 DUF2172: Domain of un 30.3 66 0.0014 28.6 3.6 45 94-142 342-386 (386)
205 PRK12532 RNA polymerase sigma 30.2 64 0.0014 24.8 3.3 27 108-136 151-177 (195)
206 PF05584 Sulfolobus_pRN: Sulfo 30.1 1.5E+02 0.0032 20.0 4.5 50 109-160 18-68 (72)
207 smart00422 HTH_MERR helix_turn 30.1 1E+02 0.0022 19.3 3.8 48 110-171 1-48 (70)
208 PRK03902 manganese transport t 29.9 95 0.0021 22.9 4.0 42 99-142 12-53 (142)
209 TIGR02989 Sig-70_gvs1 RNA poly 29.8 68 0.0015 23.5 3.3 27 108-136 126-152 (159)
210 TIGR02787 codY_Gpos GTP-sensin 29.7 99 0.0022 25.8 4.4 36 107-144 196-231 (251)
211 PRK09648 RNA polymerase sigma 29.7 67 0.0015 24.5 3.3 27 108-136 154-180 (189)
212 COG1349 GlpR Transcriptional r 29.6 74 0.0016 26.2 3.7 46 95-142 5-50 (253)
213 PRK09640 RNA polymerase sigma 29.5 68 0.0015 24.6 3.3 27 108-136 149-175 (188)
214 TIGR02835 spore_sigmaE RNA pol 29.2 69 0.0015 25.7 3.4 27 108-136 197-223 (234)
215 PF01035 DNA_binding_1: 6-O-me 29.2 49 0.0011 22.6 2.2 25 98-122 8-32 (85)
216 PF14493 HTH_40: Helix-turn-he 29.0 84 0.0018 21.4 3.4 30 109-140 13-42 (91)
217 PRK12534 RNA polymerase sigma 28.9 64 0.0014 24.5 3.0 27 108-136 152-178 (187)
218 COG2378 Predicted transcriptio 28.9 1.8E+02 0.0039 24.8 6.0 79 94-175 7-89 (311)
219 PRK12526 RNA polymerase sigma 28.8 68 0.0015 25.1 3.3 28 107-136 167-194 (206)
220 PRK09483 response regulator; P 28.2 1E+02 0.0022 23.2 4.2 21 110-131 164-184 (217)
221 PRK12518 RNA polymerase sigma 28.2 73 0.0016 23.8 3.2 27 108-136 135-161 (175)
222 PRK05602 RNA polymerase sigma 28.2 72 0.0016 24.2 3.3 27 108-136 143-169 (186)
223 TIGR02960 SigX5 RNA polymerase 28.1 65 0.0014 26.9 3.2 28 107-136 156-183 (324)
224 TIGR03209 P21_Cbot clostridium 27.9 42 0.00091 24.3 1.8 20 108-128 122-141 (142)
225 PRK12531 RNA polymerase sigma 27.6 75 0.0016 24.5 3.3 27 108-136 156-182 (194)
226 cd06171 Sigma70_r4 Sigma70, re 27.3 1E+02 0.0022 17.4 3.2 26 108-135 25-50 (55)
227 TIGR01610 phage_O_Nterm phage 27.2 1.7E+02 0.0037 20.1 4.7 46 106-155 44-89 (95)
228 PRK11924 RNA polymerase sigma 26.9 80 0.0017 23.3 3.2 27 108-136 140-166 (179)
229 PRK09639 RNA polymerase sigma 26.9 83 0.0018 23.2 3.3 27 108-136 126-152 (166)
230 PRK00118 putative DNA-binding 26.9 87 0.0019 22.5 3.2 26 109-136 33-58 (104)
231 PF06619 DUF1149: Protein of u 26.8 32 0.00069 25.8 0.9 35 140-174 68-102 (127)
232 PRK12544 RNA polymerase sigma 26.5 76 0.0017 25.0 3.2 27 108-136 163-189 (206)
233 TIGR00589 ogt O-6-methylguanin 26.5 77 0.0017 21.5 2.7 38 98-139 8-45 (80)
234 PRK11923 algU RNA polymerase s 26.4 81 0.0018 24.1 3.3 27 108-136 153-179 (193)
235 PF09202 Rio2_N: Rio2, N-termi 26.4 1.7E+02 0.0037 20.0 4.5 49 95-145 9-58 (82)
236 PRK04217 hypothetical protein; 26.0 87 0.0019 22.7 3.1 24 108-132 57-80 (110)
237 COG1321 TroR Mn-dependent tran 25.9 1.3E+02 0.0028 23.0 4.3 43 99-143 14-56 (154)
238 PRK09415 RNA polymerase factor 25.9 86 0.0019 23.8 3.3 27 108-136 142-168 (179)
239 PRK06986 fliA flagellar biosyn 25.8 82 0.0018 25.2 3.3 27 108-136 199-225 (236)
240 PRK09636 RNA polymerase sigma 25.8 76 0.0017 26.3 3.2 28 107-136 129-156 (293)
241 PRK04424 fatty acid biosynthes 25.6 75 0.0016 24.9 2.9 31 96-127 8-38 (185)
242 COG2963 Transposase and inacti 25.4 1.1E+02 0.0024 21.6 3.6 30 111-142 26-56 (116)
243 PF10078 DUF2316: Uncharacteri 25.3 79 0.0017 22.2 2.7 23 107-130 21-43 (89)
244 COG3415 Transposase and inacti 25.3 2.3E+02 0.0049 21.4 5.4 70 94-175 8-77 (138)
245 PRK15201 fimbriae regulatory p 25.3 1.2E+02 0.0027 24.3 4.0 35 98-136 139-173 (198)
246 PRK12515 RNA polymerase sigma 25.0 90 0.002 23.8 3.3 28 107-136 145-172 (189)
247 PRK15411 rcsA colanic acid cap 24.9 1.2E+02 0.0026 23.9 4.0 32 98-132 143-174 (207)
248 PRK10100 DNA-binding transcrip 24.9 1.1E+02 0.0025 24.4 3.9 35 98-136 161-195 (216)
249 PF01873 eIF-5_eIF-2B: Domain 24.8 2.9E+02 0.0063 20.4 6.6 53 111-173 36-88 (125)
250 PRK12538 RNA polymerase sigma 24.8 86 0.0019 25.3 3.2 28 107-136 185-212 (233)
251 TIGR02985 Sig70_bacteroi1 RNA 24.6 97 0.0021 22.3 3.3 27 108-136 128-154 (161)
252 cd00086 homeodomain Homeodomai 24.6 82 0.0018 18.9 2.5 23 109-132 27-49 (59)
253 PF10924 DUF2711: Protein of u 24.5 96 0.0021 25.4 3.4 32 105-137 51-82 (217)
254 PRK09644 RNA polymerase sigma 24.4 89 0.0019 23.2 3.1 27 107-135 122-148 (165)
255 TIGR02859 spore_sigH RNA polym 24.3 95 0.0021 23.7 3.3 27 107-135 163-189 (198)
256 PF13022 HTH_Tnp_1_2: Helix-tu 24.2 1.6E+02 0.0035 22.5 4.3 36 87-122 11-47 (142)
257 PRK09191 two-component respons 24.2 91 0.002 24.6 3.3 28 107-136 102-129 (261)
258 TIGR02959 SigZ RNA polymerase 24.2 98 0.0021 23.3 3.3 25 107-132 114-138 (170)
259 COG1846 MarR Transcriptional r 24.1 2.3E+02 0.0051 19.1 5.3 43 113-157 40-82 (126)
260 PF09218 DUF1959: Domain of un 24.0 36 0.00078 25.1 0.8 21 113-135 17-37 (117)
261 PRK12546 RNA polymerase sigma 23.3 1E+02 0.0022 23.9 3.3 28 107-136 127-154 (188)
262 PRK13239 alkylmercury lyase; P 23.2 1.1E+02 0.0023 24.9 3.4 47 98-151 25-71 (206)
263 TIGR02948 SigW_bacill RNA poly 23.2 1E+02 0.0022 23.2 3.3 27 108-136 151-177 (187)
264 PRK09641 RNA polymerase sigma 23.2 1E+02 0.0023 23.1 3.3 27 108-136 151-177 (187)
265 TIGR02997 Sig70-cyanoRpoD RNA 23.1 1.1E+02 0.0024 25.7 3.6 29 107-137 267-295 (298)
266 TIGR02394 rpoS_proteo RNA poly 22.9 95 0.0021 25.8 3.2 28 107-136 240-267 (285)
267 TIGR00373 conserved hypothetic 22.9 2.8E+02 0.0061 21.1 5.6 49 106-156 25-75 (158)
268 smart00389 HOX Homeodomain. DN 22.9 1E+02 0.0023 18.3 2.7 23 109-132 27-49 (56)
269 COG5647 Cullin, a subunit of E 22.7 1.1E+02 0.0023 29.6 3.7 58 96-155 609-670 (773)
270 PRK09834 DNA-binding transcrip 22.6 1.5E+02 0.0033 24.2 4.3 56 96-155 12-68 (263)
271 PRK09643 RNA polymerase sigma 22.5 1.1E+02 0.0023 23.6 3.3 26 108-135 149-174 (192)
272 PRK08295 RNA polymerase factor 22.4 1E+02 0.0022 23.7 3.2 27 108-136 169-195 (208)
273 cd04894 ACT_ACR-like_1 ACT dom 22.3 2.4E+02 0.0053 18.7 4.7 49 126-176 16-66 (69)
274 PRK06930 positive control sigm 22.2 1.1E+02 0.0023 23.7 3.2 27 108-136 129-155 (170)
275 PRK12541 RNA polymerase sigma 22.2 1.1E+02 0.0025 22.5 3.3 28 107-136 126-153 (161)
276 smart00342 HTH_ARAC helix_turn 22.0 2.1E+02 0.0046 17.8 4.2 37 95-132 37-73 (84)
277 PF14754 IFR3_antag: Papain-li 21.8 40 0.00086 26.5 0.7 22 35-56 83-104 (249)
278 COG1001 AdeC Adenine deaminase 21.8 3E+02 0.0065 25.9 6.4 43 24-70 157-199 (584)
279 TIGR03338 phnR_burk phosphonat 21.8 2.9E+02 0.0064 21.3 5.7 53 89-143 14-66 (212)
280 PRK03887 methylated-DNA--prote 21.6 3.2E+02 0.007 21.6 5.7 65 59-127 61-127 (175)
281 TIGR02937 sigma70-ECF RNA poly 21.6 1.2E+02 0.0027 21.1 3.3 27 108-136 125-151 (158)
282 PRK13777 transcriptional regul 21.6 2.9E+02 0.0062 21.8 5.5 51 107-159 57-107 (185)
283 PRK11534 DNA-binding transcrip 21.5 3.2E+02 0.0069 21.4 5.9 53 89-143 10-62 (224)
284 PRK06811 RNA polymerase factor 21.4 1.2E+02 0.0025 23.3 3.3 27 108-136 146-172 (189)
285 TIGR02393 RpoD_Cterm RNA polym 21.3 1.3E+02 0.0028 24.2 3.6 28 107-136 194-221 (238)
286 TIGR02957 SigX4 RNA polymerase 21.1 1.1E+02 0.0023 25.4 3.2 28 107-136 122-149 (281)
287 PRK07670 RNA polymerase sigma 21.1 1.1E+02 0.0024 24.7 3.3 28 107-136 215-242 (251)
288 TIGR02392 rpoH_proteo alternat 21.0 1.2E+02 0.0027 24.9 3.5 29 107-137 234-262 (270)
289 TIGR02479 FliA_WhiG RNA polyme 20.9 1.2E+02 0.0026 24.0 3.3 27 108-136 190-216 (224)
290 PRK10840 transcriptional regul 20.9 1.6E+02 0.0035 22.6 4.0 22 110-132 166-187 (216)
291 PRK08583 RNA polymerase sigma 20.8 1.2E+02 0.0025 24.7 3.3 28 107-136 219-246 (257)
292 cd00592 HTH_MerR-like Helix-Tu 20.8 2E+02 0.0044 19.5 4.1 46 111-171 2-47 (100)
293 PRK05803 sporulation sigma fac 20.7 1.2E+02 0.0025 24.3 3.2 27 108-136 194-220 (233)
294 PF11940 DUF3458: Domain of un 20.5 1.6E+02 0.0034 25.9 4.2 38 42-82 305-342 (367)
295 PRK09637 RNA polymerase sigma 20.5 1.2E+02 0.0026 23.2 3.2 28 107-136 120-147 (181)
296 PRK08241 RNA polymerase factor 20.4 1.1E+02 0.0024 25.8 3.2 28 107-136 167-194 (339)
297 PF13413 HTH_25: Helix-turn-he 20.4 1.1E+02 0.0024 19.6 2.5 21 107-128 8-28 (62)
298 PLN03083 E3 UFM1-protein ligas 20.4 1.6E+02 0.0034 28.8 4.4 42 106-152 131-172 (803)
299 COG4367 Uncharacterized protei 20.1 1.2E+02 0.0026 21.4 2.7 24 107-131 21-44 (97)
300 PRK11050 manganese transport r 20.1 2E+02 0.0043 21.6 4.2 38 105-144 47-84 (152)
301 PRK00215 LexA repressor; Valid 20.0 4.2E+02 0.0092 20.5 6.7 47 105-154 19-66 (205)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=1.1e-39 Score=259.26 Aligned_cols=176 Identities=48% Similarity=0.762 Sum_probs=173.0
Q ss_pred CchhHHHHHHHHHHHHhccccchHHHHHHHHHHhcCCCceehhhhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 030471 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (177)
Q Consensus 1 ~~~~~~~~~~~~~~l~~~~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~ 80 (177)
||+|+++++.+++|+.+++..++++...+|..|+.+|++|.|+|||.+|+|..|..+.++.++.||++|++||+.||...
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 99999999999999999999999999999999999999999999999999999998889999999999999999999999
Q ss_pred hCCCCCCchHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 030471 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (177)
Q Consensus 81 ~~~~~~L~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R 160 (177)
...+|.|+.+++.||+.+|+.++++..++|+|+.+.+.+.+.+..++|++|| +||+++++.|||||.+|+++|.|+..|
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 9999999999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred CCCcchHHHHHHHhccC
Q 030471 161 DLRPGQLGSMIQTLSNW 177 (177)
Q Consensus 161 ~~~~~~~~~L~~~L~~W 177 (177)
++++.++..|...|++|
T Consensus 160 dlr~k~i~nm~~TL~~w 176 (258)
T KOG3250|consen 160 DLRSKDIDNMKYTLDEW 176 (258)
T ss_pred cccHhHHHHHHHHHHHH
Confidence 99999999999999999
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=1.3e-36 Score=254.78 Aligned_cols=165 Identities=25% Similarity=0.509 Sum_probs=150.6
Q ss_pred HHHHHHHHHhccccc----hHHHHHHHHHHhcCCCceehhhhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhhh--
Q 030471 8 AELIDHFVKQASNQK----GAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA-- 81 (177)
Q Consensus 8 ~~~~~~~l~~~~~~~----~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~~-- 81 (177)
..+|-.||.+++..+ -++|.+||+.|+.+|++|.|++|+++|+|+.|+++ .+++||.||..|.+++|.++.
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 SKVMTELLGTYTEDNASEAREDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGD---LIHQLLKIFVSGKLDAYVEFVAA 261 (378)
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHHHHHHHcCCceeccchhccCchHHHhccc---hHHHHHHHHHhcchHHHHHHHHh
Confidence 467888899887643 25799999999999999999999999999999987 599999999999999999854
Q ss_pred --CCCCC--C-chHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 82 --GHLPQ--L-VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 82 --~~~~~--L-~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+++.. + .+++.+|||+||+|+||+.+++|||+++++.|+|. .++||.||| +||+.|+|.|||||.+++|.|++
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 33332 3 47789999999999999999999999999999997 999999999 99999999999999999999999
Q ss_pred ecCCCCCcchHHHHHHHhccC
Q 030471 157 AAGRDLRPGQLGSMIQTLSNW 177 (177)
Q Consensus 157 ~~~R~~~~~~~~~L~~~L~~W 177 (177)
+.+|.||+.||+.|+++|..|
T Consensus 340 ~~hR~FG~~qW~~L~~kL~aw 360 (378)
T KOG2753|consen 340 STHRTFGKQQWQQLRDKLAAW 360 (378)
T ss_pred hhhhhcccHHHHHHHHHHHHH
Confidence 999999999999999999999
No 3
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=5.2e-36 Score=252.13 Aligned_cols=167 Identities=20% Similarity=0.396 Sum_probs=152.9
Q ss_pred HHHHHHHHhc------cccchHHHHHHHHHHhcCCCceehhhhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhhh-
Q 030471 9 ELIDHFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA- 81 (177)
Q Consensus 9 ~~~~~~l~~~------~~~~~~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~~- 81 (177)
-....||... .+++.+.|.++..+||.+.++||||||+.||+..+|++++++|++++|.+|+.||+..|++..
T Consensus 178 r~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~ 257 (380)
T KOG2908|consen 178 RHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKG 257 (380)
T ss_pred HHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHH
Confidence 4556788887 555678999999999999999999999999999999999999999999999999999999865
Q ss_pred --CCCCCCchH---HHHHHHHHHhhcccc----CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEE
Q 030471 82 --GHLPQLVPD---QVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCF 152 (177)
Q Consensus 82 --~~~~~L~~~---~~~Klr~LtllsL~~----~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v 152 (177)
+..|.|.+. ..+|+|+++++.++. +.|++||++||++++|| .++||.+|| +|++.|||+|.|||++|+|
T Consensus 258 ~~~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v 335 (380)
T KOG2908|consen 258 VWGKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVV 335 (380)
T ss_pred HhccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEE
Confidence 456777532 478999999998886 67999999999999999 899999999 9999999999999999999
Q ss_pred EEEeecCCCCCcchHHHHHHHhccC
Q 030471 153 EVQFAAGRDLRPGQLGSMIQTLSNW 177 (177)
Q Consensus 153 ~v~~~~~R~~~~~~~~~L~~~L~~W 177 (177)
+++|++||.++.+|+..|++|++.|
T Consensus 336 ~~swvqPRvl~~~qI~~Mk~rl~~W 360 (380)
T KOG2908|consen 336 YMSWVQPRVLDRSQIVKMKDRLDEW 360 (380)
T ss_pred EEecccccccCHHHHHhHHHHHHHH
Confidence 9999999999999999999999998
No 4
>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=99.62 E-value=1.9e-15 Score=105.50 Aligned_cols=85 Identities=21% Similarity=0.325 Sum_probs=80.9
Q ss_pred hHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHH
Q 030471 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG 168 (177)
Q Consensus 89 ~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~ 168 (177)
+...+|+|..++..+++..++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++|.
T Consensus 4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~ 79 (88)
T smart00088 4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA 79 (88)
T ss_pred HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH
Confidence 4567899999999999999999999999999998 889999999 9999999999999999999999999997 78999
Q ss_pred HHHHHhccC
Q 030471 169 SMIQTLSNW 177 (177)
Q Consensus 169 ~L~~~L~~W 177 (177)
.+.+++..|
T Consensus 80 ~~~~~l~~~ 88 (88)
T smart00088 80 QFAETLKKL 88 (88)
T ss_pred HHHHHhhcC
Confidence 999999998
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.62 E-value=1.9e-15 Score=105.50 Aligned_cols=85 Identities=21% Similarity=0.325 Sum_probs=80.9
Q ss_pred hHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHH
Q 030471 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG 168 (177)
Q Consensus 89 ~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~ 168 (177)
+...+|+|..++..+++..++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++|.
T Consensus 4 ~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~ 79 (88)
T smart00753 4 ERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA 79 (88)
T ss_pred HHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH
Confidence 4567899999999999999999999999999998 889999999 9999999999999999999999999997 78999
Q ss_pred HHHHHhccC
Q 030471 169 SMIQTLSNW 177 (177)
Q Consensus 169 ~L~~~L~~W 177 (177)
.+.+++..|
T Consensus 80 ~~~~~l~~~ 88 (88)
T smart00753 80 QFAETLKKL 88 (88)
T ss_pred HHHHHhhcC
Confidence 999999998
No 6
>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=99.59 E-value=4e-15 Score=105.82 Aligned_cols=95 Identities=20% Similarity=0.394 Sum_probs=80.7
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCCC-------CC---CchHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHH
Q 030471 60 SKYLDMLRLFAHGTWSDYKNNAGHL-------PQ---LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (177)
Q Consensus 60 ~~l~~LL~if~~G~~~~~~~~~~~~-------~~---L~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~ 129 (177)
+|+.+++++|..|++..|.+.-... +. +.+....+++..++..++...+.+++++|++.++++ .++||.
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 3789999999999999998743222 11 235678999999999999999999999999999998 899999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 130 FLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 130 lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+++ +||..|.|+|+|||.+|+|+++|
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 99999999999999999999875
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.04 E-value=1.2e-05 Score=67.80 Aligned_cols=95 Identities=14% Similarity=0.384 Sum_probs=80.9
Q ss_pred hHHHHHHHHHhcCChhhHhhh----hCCC---CCC---chHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHH
Q 030471 60 SKYLDMLRLFAHGTWSDYKNN----AGHL---PQL---VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (177)
Q Consensus 60 ~~l~~LL~if~~G~~~~~~~~----~~~~---~~L---~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~ 129 (177)
-.+.+|+..+...++.+|+.. ++.+ |-+ .++.++++|.-.|+.|......|...-|+++|+|+ ..+||.
T Consensus 305 lAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~ 383 (440)
T KOG1464|consen 305 LAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVES 383 (440)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHH
Confidence 357899999999999999973 3322 112 36678999999999999988889999999999998 999999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 130 FLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 130 lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+++ .||-..-|+|+|||+++.+....
T Consensus 384 LLV-~~ILD~~i~g~Ide~n~~l~~~~ 409 (440)
T KOG1464|consen 384 LLV-SCILDDTIDGRIDEVNQYLELDK 409 (440)
T ss_pred HHH-HHHhccccccchHHhhhHhccCc
Confidence 999 99999999999999999987653
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.93 E-value=1.8e-05 Score=69.38 Aligned_cols=90 Identities=10% Similarity=0.331 Sum_probs=67.5
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCCCCC-Cc----hHHHHHHHH------HHhhccccCCcccChHHHHHHcCCCChHHHH
Q 030471 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-LV----PDQVLKLKQ------LTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (177)
Q Consensus 60 ~~l~~LL~if~~G~~~~~~~~~~~~~~-L~----~~~~~Klr~------LtllsL~~~~~~is~~~I~~~l~i~~~~evE 128 (177)
.++++|=.....||++-|....+.+.. +- -...-.||. ++.+|| ..+-||+.+||+.|++.|.+++|
T Consensus 319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISl--sYSRISl~DIA~kL~l~Seed~E 396 (493)
T KOG2581|consen 319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISL--SYSRISLQDIAKKLGLNSEEDAE 396 (493)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheee--eeeeccHHHHHHHhcCCCchhHH
Confidence 468999999999999999875432221 10 111122222 344444 36789999999999999888999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEE
Q 030471 129 DFLINECMYTGIVRGKLDQLRRCF 152 (177)
Q Consensus 129 ~lvI~~ai~~gLI~gkIDq~~~~v 152 (177)
.+|- +||+.|+|+|+||..+|.+
T Consensus 397 yiVa-kAIRDGvIea~Id~~~g~m 419 (493)
T KOG2581|consen 397 YIVA-KAIRDGVIEAKIDHEDGFM 419 (493)
T ss_pred HHHH-HHHHhccceeeeccccCce
Confidence 9999 9999999999999998854
No 9
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=96.54 E-value=0.0075 Score=52.00 Aligned_cols=63 Identities=16% Similarity=0.252 Sum_probs=57.1
Q ss_pred HHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 92 ~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+.--|++-+-..|.-+.+|+.+-+|+.|+++ .++.|.|++ +.|+...+++|||..-|.|.+..
T Consensus 332 ~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~ 394 (432)
T KOG2758|consen 332 LENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGH 394 (432)
T ss_pred HHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecC
Confidence 4666788888888889999999999999997 999999999 99999999999999999988753
No 10
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.31 E-value=0.03 Score=49.52 Aligned_cols=111 Identities=14% Similarity=0.200 Sum_probs=84.2
Q ss_pred hHHHHHHHHHhcCChhhHhhh-hCCCCC------Cc---hHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHH
Q 030471 60 SKYLDMLRLFAHGTWSDYKNN-AGHLPQ------LV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (177)
Q Consensus 60 ~~l~~LL~if~~G~~~~~~~~-~~~~~~------L~---~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~ 129 (177)
+.+.++|.-|..+.+..-... .+.-|. |. .+...++|.=.++.--.+..++.+..+|.+.+.+ ...+|.
T Consensus 306 Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~ 384 (466)
T KOG0686|consen 306 PQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILES 384 (466)
T ss_pred hHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHH
Confidence 346677777777777664432 111111 22 3457888888888887888999999999999997 999999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHHH
Q 030471 130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQ 172 (177)
Q Consensus 130 lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~ 172 (177)
=|. +.|-.|.|+||||+.++.+++.....|.=+-++...|.+
T Consensus 385 ~l~-~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~~~~~~ 426 (466)
T KOG0686|consen 385 ELL-ELILEGKISGRIDSHNKILYARDADSENATFERVLPMGK 426 (466)
T ss_pred HHH-HHHHccchheeeccccceeeecccccccchhhhcchhhH
Confidence 999 999999999999999999999887777655555555443
No 11
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.65 E-value=0.068 Score=46.79 Aligned_cols=105 Identities=11% Similarity=0.249 Sum_probs=79.5
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCCCC-----CCchHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHH
Q 030471 60 SKYLDMLRLFAHGTWSDYKN----NAGHLP-----QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (177)
Q Consensus 60 ~~l~~LL~if~~G~~~~~~~----~~~~~~-----~L~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~l 130 (177)
.++.++++++..+.-.+... +++.+. .+-...+.-+.+-+|..+.+.-.+++.++||+..++.+.+|||..
T Consensus 259 ~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rltktF~sLsL~dIA~~vQLa~~qevek~ 338 (422)
T KOG2582|consen 259 NPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRLTKTFLSLSLSDIASRVQLASAQEVEKY 338 (422)
T ss_pred chHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcchHHHHHH
Confidence 37889999999998887554 222221 233334455566677777777788999999998778778999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHH
Q 030471 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG 168 (177)
Q Consensus 131 vI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~ 168 (177)
|+ ..|..|=|-+.|| |-|..+.-...+.+++...
T Consensus 339 Il-qmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~ 372 (422)
T KOG2582|consen 339 IL-QMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHE 372 (422)
T ss_pred HH-HHhccCceEEEec---ceEEEecCcccCCCHHHHh
Confidence 99 9999999999999 7887776666777766655
No 12
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=95.59 E-value=0.028 Score=49.51 Aligned_cols=97 Identities=14% Similarity=0.189 Sum_probs=68.5
Q ss_pred HHHHHHHHHhcCChhhHhhhh----CCCCCCch-HHHHHHHHHHhhcccc-------CCcccChHHHHHHcCCCC-----
Q 030471 61 KYLDMLRLFAHGTWSDYKNNA----GHLPQLVP-DQVLKLKQLTVLTLAE-------TNKVLPYDELMEELDVTN----- 123 (177)
Q Consensus 61 ~l~~LL~if~~G~~~~~~~~~----~~~~~L~~-~~~~Klr~LtllsL~~-------~~~~is~~~I~~~l~i~~----- 123 (177)
.+-.++.....||+..|...- ..+....- -.+.|+++++.=.|.+ +...++++.+..+++...
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 566788999999999998621 11111000 0122334433333322 567899999999987754
Q ss_pred hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 030471 124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (177)
Q Consensus 124 ~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~ 158 (177)
.++||..+. .+|+.|.|+|.|+...+++.++...
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 689999999 9999999999999999999988643
No 13
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=95.28 E-value=0.057 Score=47.34 Aligned_cols=98 Identities=18% Similarity=0.284 Sum_probs=61.1
Q ss_pred hHHHHHHHHHhcCChhhHhhhhC----CCCC--C----c---h-HHHHHHHHHHhhccccCCcc--cChHHHHHHcCCCC
Q 030471 60 SKYLDMLRLFAHGTWSDYKNNAG----HLPQ--L----V---P-DQVLKLKQLTVLTLAETNKV--LPYDELMEELDVTN 123 (177)
Q Consensus 60 ~~l~~LL~if~~G~~~~~~~~~~----~~~~--L----~---~-~~~~Klr~LtllsL~~~~~~--is~~~I~~~l~i~~ 123 (177)
+.+.-|..+..+|++++|..--+ .+-+ | . + -+.+-+-. ....++-+... +|+-.++..+...+
T Consensus 289 s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~r-k~w~~~~~qsrlp~sil~~~~qls~~d 367 (413)
T COG5600 289 SVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFR-KIWRLHGKQSRLPLSILLIVLQLSAID 367 (413)
T ss_pred chhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHH-HHHhhccccccCcHHHHHHHHHccCCC
Confidence 34556788999999999986211 1110 0 0 0 01111111 22222223333 45555555555443
Q ss_pred ----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 030471 124 ----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (177)
Q Consensus 124 ----~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~ 159 (177)
.++||..++ .+|+.|+++|.|....+++.++...|
T Consensus 368 n~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 368 NFHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred cccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence 578999999 99999999999999999999987654
No 14
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.14 E-value=0.021 Score=49.26 Aligned_cols=128 Identities=10% Similarity=0.096 Sum_probs=80.5
Q ss_pred HHHHHHHHHhcCCCceehh-hhhcchhhhhccCCC-chHHHHHHHHHhcC-ChhhHhhh-hCC----CCCCchHHHHHHH
Q 030471 25 ALGSVIVEATSQPSLFAFS-EILAVPNIAEFEGTE-NSKYLDMLRLFAHG-TWSDYKNN-AGH----LPQLVPDQVLKLK 96 (177)
Q Consensus 25 ~a~~~i~~aL~~p~i~~f~-eLl~~~~v~~L~~~~-~~~l~~LL~if~~G-~~~~~~~~-~~~----~~~L~~~~~~Klr 96 (177)
.|..|...|.-+|.+-.|- .|...|.++.+..-. -+++| |+-|..+ +.+.|... .++ .+.=....-+-+.
T Consensus 227 ~a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmy--l~riI~k~el~ef~~~L~pHQka~~~dgssil~ra~~ 304 (399)
T KOG1497|consen 227 KALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMY--LERIIRKEELQEFEAFLQPHQKAHTMDGSSILDRAVI 304 (399)
T ss_pred HhHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHH--HHHHhcchhHHHHHHHhcchhhhcccCcchhhhhHHH
Confidence 3666666677777665543 444455555553210 11222 3333333 45555542 111 1110011113334
Q ss_pred HHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 97 ~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
-..|+++.+-...|||+++...++|+ ...+|.++= ++|..|=+.|.|||.++.++.-.
T Consensus 305 EhNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~ 362 (399)
T KOG1497|consen 305 EHNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED 362 (399)
T ss_pred HHhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc
Confidence 45667776666789999999999998 999999999 99999999999999999999864
No 15
>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=93.74 E-value=0.46 Score=35.65 Aligned_cols=108 Identities=15% Similarity=0.187 Sum_probs=71.6
Q ss_pred HHHHHHHHHHhcCCCceehhhhhcchhhhhccC-CCchHHHHHHHHHhcCChhhHhhhhCCC---CC---CchHHHHHHH
Q 030471 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNNAGHL---PQ---LVPDQVLKLK 96 (177)
Q Consensus 24 ~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~-~~~~~l~~LL~if~~G~~~~~~~~~~~~---~~---L~~~~~~Klr 96 (177)
.........+|..-.+-+|.-++..-+-...+. .+-..+..+.+.+-.|++.+|.+..... +. +-+....++|
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 344455556666666788887776444333332 3456788999999999999988733221 11 2244456777
Q ss_pred HHHhhccccCCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 97 ~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.=.+-.+......|+.+.+++-||++ .++++.++.
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 76666666778999999999999998 999999877
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=92.87 E-value=0.19 Score=40.19 Aligned_cols=58 Identities=14% Similarity=0.241 Sum_probs=40.7
Q ss_pred HHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 97 ~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+-.++...+..+.+..++||..+++. ..++-+-|- .....|.|.|-||..+.-|||+.
T Consensus 101 L~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs~ 158 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYISE 158 (188)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE---
T ss_pred HHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEecH
Confidence 34566666789999999999999998 788888888 89999999999999888888873
No 17
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=92.87 E-value=0.22 Score=43.38 Aligned_cols=104 Identities=15% Similarity=0.241 Sum_probs=76.1
Q ss_pred ccCCCchHHHHHHHHHhcCChhhHhhhhCCCC-CCch-----HHH----HHHHHHHhhccccCCcccChHHHHHHcCCCC
Q 030471 54 FEGTENSKYLDMLRLFAHGTWSDYKNNAGHLP-QLVP-----DQV----LKLKQLTVLTLAETNKVLPYDELMEELDVTN 123 (177)
Q Consensus 54 L~~~~~~~l~~LL~if~~G~~~~~~~~~~~~~-~L~~-----~~~----~Klr~LtllsL~~~~~~is~~~I~~~l~i~~ 123 (177)
..+..-..+...=+.|..-++++|++.-..++ +|.+ ..+ .-|---.|+.+.++.+.+...-||+-.|++
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 34444556777888999999999997432222 2221 111 122223566677888999999999999998
Q ss_pred hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 030471 124 VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (177)
Q Consensus 124 ~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~ 159 (177)
...||.=+= ++|-.+.+.|.+||-++++.|.--.+
T Consensus 359 ~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 359 VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeCCCC
Confidence 999999888 88889999999999999999875444
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=91.41 E-value=0.6 Score=31.78 Aligned_cols=59 Identities=17% Similarity=0.219 Sum_probs=41.6
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+|.|..+....+++.++.++||+.++++ ...++..+= +....|+|+.. -..++.+...+
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~-~G~~GGy~L~~ 69 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESS-RGRGGGYRLAR 69 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE-TSTTSEEEESS
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEec-CCCCCceeecC
Confidence 3444444433445569999999999998 999999888 89999998654 35566666554
No 19
>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=91.20 E-value=0.18 Score=33.30 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=35.0
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
|......++.+|+++||++++++ .+.||.++= ..++.|-|+-.-+.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEEEEEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEEecCC
Confidence 33444568899999999999998 999999988 89999998854443
No 20
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=88.17 E-value=0.71 Score=40.12 Aligned_cols=110 Identities=18% Similarity=0.289 Sum_probs=75.6
Q ss_pred hhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhhh-----CCCC-C--CchH---HHHHHHHHHhhccccCCcccCh
Q 030471 44 EILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA-----GHLP-Q--LVPD---QVLKLKQLTVLTLAETNKVLPY 112 (177)
Q Consensus 44 eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~~-----~~~~-~--L~~~---~~~Klr~LtllsL~~~~~~is~ 112 (177)
..+..|.|+..-.. -+.+.+++.-+-.-++++|-..- ..+. . +.+. -.+-||...-..+-+..|.++.
T Consensus 242 KVi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l 320 (393)
T KOG0687|consen 242 KVIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTL 320 (393)
T ss_pred hhcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555432211 22455555555555666655421 1111 1 2232 2477777777778889999999
Q ss_pred HHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 113 ~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
+-.|++.|++ .+-+++=+= +-|..|=+.++||-++|.|.+++
T Consensus 321 ~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNr 362 (393)
T KOG0687|consen 321 ESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNR 362 (393)
T ss_pred HHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCC
Confidence 9999999997 888888788 88889999999999999999886
No 21
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=88.15 E-value=1.3 Score=39.34 Aligned_cols=111 Identities=21% Similarity=0.264 Sum_probs=74.4
Q ss_pred chHHHHHHHHHhcCChhhHhhhh---------CCCCC---CchHH--HHHHHH--HHhhccccCCcccChHHHHHHcCCC
Q 030471 59 NSKYLDMLRLFAHGTWSDYKNNA---------GHLPQ---LVPDQ--VLKLKQ--LTVLTLAETNKVLPYDELMEELDVT 122 (177)
Q Consensus 59 ~~~l~~LL~if~~G~~~~~~~~~---------~~~~~---L~~~~--~~Klr~--LtllsL~~~~~~is~~~I~~~l~i~ 122 (177)
.+..-++|..|..|.+--|.... +.+.. ..+.. --|.|. ..+-=.+.-.+.|++.++++-+++|
T Consensus 287 ~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~ 366 (439)
T KOG1498|consen 287 LPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLP 366 (439)
T ss_pred CccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCC
Confidence 44567789999998876655321 11111 11111 122332 4444445568899999999999999
Q ss_pred ChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHH
Q 030471 123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI 171 (177)
Q Consensus 123 ~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~ 171 (177)
.++.|.++= +.+..|-+.+|||++.+.+....+..-.=-..+|...-
T Consensus 367 -~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nv 413 (439)
T KOG1498|consen 367 -VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNV 413 (439)
T ss_pred -HHHHHHHHH-HHHhccceEEEecCCCceEEEEecccHHHHHHHHHhhH
Confidence 999999999 99999999999999999998876543222223454433
No 22
>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=87.29 E-value=1.2 Score=26.84 Aligned_cols=41 Identities=20% Similarity=0.368 Sum_probs=30.8
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
++.....+..+|..+||+.++++ ...|-..+= +....|+|+
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 34433456679999999999997 888988777 888888875
No 23
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=87.21 E-value=1.7 Score=32.31 Aligned_cols=46 Identities=15% Similarity=0.292 Sum_probs=36.0
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
|.|..++...+++.++-++|++.+++| ...++.++= +.-.+|+|..
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s 57 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS 57 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence 333333333455689999999999998 999999888 8888999975
No 24
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=86.60 E-value=1.1 Score=34.16 Aligned_cols=46 Identities=22% Similarity=0.364 Sum_probs=37.8
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecC
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQ 147 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g---kIDq 147 (177)
|+.+.+.+...||.+||+.+|++ ...|-.-+= +....|+|+| .+|.
T Consensus 14 Il~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~ 62 (153)
T PRK11179 14 ILEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNP 62 (153)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECH
Confidence 44444667899999999999997 999988888 9999999984 4565
No 25
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=85.75 E-value=4.2 Score=33.15 Aligned_cols=62 Identities=11% Similarity=0.127 Sum_probs=51.2
Q ss_pred HHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 93 ~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
.-|..+.++....+...+|..+|++.++++ ...+=..+- +.-..|+|.-+.+...+.+++|-
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 455666777766677789999999999997 888888888 89999999999998777777663
No 26
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=85.37 E-value=1.8 Score=30.45 Aligned_cols=37 Identities=11% Similarity=0.308 Sum_probs=32.2
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
..+..+|+.+|++.++++ ...|-..+- +....|+|++
T Consensus 13 ~~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~ 49 (108)
T smart00344 13 QKDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG 49 (108)
T ss_pred HHhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence 445679999999999998 899998888 8999999884
No 27
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=85.09 E-value=1.1 Score=38.49 Aligned_cols=101 Identities=17% Similarity=0.265 Sum_probs=72.2
Q ss_pred chHHHHHHHHHhcCChhhHhhhhCCC-CCCch-----HHH----HHHHHHHhhccccCCcccChHHHHHHcCCCChHHHH
Q 030471 59 NSKYLDMLRLFAHGTWSDYKNNAGHL-PQLVP-----DQV----LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (177)
Q Consensus 59 ~~~l~~LL~if~~G~~~~~~~~~~~~-~~L~~-----~~~----~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE 128 (177)
-..+...-+.|.+.++.+|...-..+ ++|.. ..+ .-+---.|+.+.++-..+...-||+-+|++ ..+||
T Consensus 283 I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvE 361 (421)
T COG5159 283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVE 361 (421)
T ss_pred HHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHH
Confidence 34567777889999999998742222 22211 111 111122455566788888999999999997 99999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEeecCCC
Q 030471 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGRD 161 (177)
Q Consensus 129 ~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~ 161 (177)
-=+= ++|-.+++.|.+||.++++.|..-...+
T Consensus 362 gKLs-qMILDKifyG~LDqg~gcLivy~ep~qd 393 (421)
T COG5159 362 GKLS-QMILDKIFYGTLDQGDGCLIVYGEPAQD 393 (421)
T ss_pred HHHH-HHHHHHHHHhhhccCCceEEEeCCcccc
Confidence 8888 8888899999999999999998644433
No 28
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=85.07 E-value=2.1 Score=26.43 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=33.6
Q ss_pred HHHHhhcc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 96 r~LtllsL-~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
|-+.++.. +..+..++..+|++.+++| ...+-.++- .....|+++
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 44566654 4455668999999999998 888988887 777777764
No 29
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=84.98 E-value=1.7 Score=36.20 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=43.6
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
++.-.+.++++..+++|.+.++. ..++=+-+= +.+..|++.|-||....-+||+
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lr-tqd~inriq-~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLR-TQDSINRIQ-ELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCcc-HHHHHHHHH-HHHHhhhheeeecCCCceEEec
Confidence 44555689999999999999998 444444445 6677999999999999999997
No 30
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=84.37 E-value=7.5 Score=29.79 Aligned_cols=43 Identities=12% Similarity=0.179 Sum_probs=36.2
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
.|+.+-+.+.-+||.+||+.++++ ...|-.-+= +....|+|+|
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~ 60 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQG 60 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEE
Confidence 344455778899999999999997 888888877 8999999976
No 31
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=83.99 E-value=2.5 Score=32.80 Aligned_cols=47 Identities=15% Similarity=0.298 Sum_probs=37.6
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
+|.+..++...+++.+|-++||+.+++| ..-++.++- ..-.+|||..
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 3444444444456789999999999998 999999988 8999999996
No 32
>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=83.32 E-value=4.7 Score=29.38 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=38.1
Q ss_pred HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
-++.+..++...++..+|.++|++.+++| ...|...+= .....|+|...
T Consensus 10 al~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~-~L~~~gli~~~ 58 (132)
T TIGR00738 10 ALRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILR-TLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 44555555543345589999999999998 999999888 88889998753
No 33
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=83.06 E-value=1.8 Score=32.27 Aligned_cols=42 Identities=14% Similarity=0.228 Sum_probs=34.1
Q ss_pred ccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 102 TLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 102 sL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
.+.+.+...||.+||+.++++ ...|=.-+= +....|+|+|.-
T Consensus 15 ~~L~~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~~ 56 (154)
T COG1522 15 RLLQEDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGYT 56 (154)
T ss_pred HHHHHhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeEE
Confidence 333555569999999999997 889888888 899999988753
No 34
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=81.47 E-value=4.2 Score=31.03 Aligned_cols=48 Identities=23% Similarity=0.290 Sum_probs=37.6
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
++.|..++.-..++.+|-++||+..+++ ..-++.++- ..-.+|+|+..
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 3444444444455588999999999998 999999998 89999998765
No 35
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=81.44 E-value=3.3 Score=27.96 Aligned_cols=55 Identities=20% Similarity=0.198 Sum_probs=39.7
Q ss_pred HHHHhhcccc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 030471 96 KQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (177)
Q Consensus 96 r~LtllsL~~-~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v 154 (177)
|.+.++.+.. ..+.++..+|++.++++ ...|-..+- .....|+|... ..++...+
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~~--~~~~~y~l 61 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQD--GQNGRYRL 61 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeeec--CCCCceee
Confidence 3345555444 33689999999999998 899999888 78889999763 22444444
No 36
>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=80.77 E-value=3.2 Score=27.22 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=28.8
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
+.+..-|+.||++.+++.|...|-..+- ..-..|+|+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 3677889999999999998999998888 777777765
No 37
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=80.47 E-value=9.4 Score=33.05 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=54.4
Q ss_pred HHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 030471 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (177)
Q Consensus 92 ~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~ 157 (177)
.+-||.=.-..|.+..|.+|.+..|+..+++ ++-|+.=+= +-|-.|-+.+.||-++|.|..++-
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg-~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLG-EFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHH-hhCCCCceeeeeecccceEeccCc
Confidence 4667776666777889999999999999997 888887777 778889999999999999998763
No 38
>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=78.81 E-value=3.3 Score=29.09 Aligned_cols=38 Identities=16% Similarity=0.438 Sum_probs=28.5
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcC
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (177)
.+..+...-..++|++|-+. +|+++.||+||| +.+..+
T Consensus 38 NIyrlftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~i 75 (100)
T PF07389_consen 38 NIYRLFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLNDI 75 (100)
T ss_pred HHHHHHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHhH
Confidence 33444445567899999998 678899999999 877543
No 39
>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=77.56 E-value=3.6 Score=26.05 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=32.3
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI 141 (177)
-.|+.+...++.++.+++++.++++ ...+-.=+. ..-..|+|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGLI 44 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCCE
Confidence 3456666778899999999999997 888877666 66666663
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=77.24 E-value=5 Score=25.44 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=30.8
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
..++..+..+|++.++++ ...+-.=+= .....|+|+..
T Consensus 20 ~~~~~~t~~ela~~l~~~-~~t~s~hL~-~L~~aGli~~~ 57 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGIS-QSTVSYHLK-KLEEAGLIEVE 57 (61)
T ss_dssp HHCSTBEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred hcCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeEEe
Confidence 557899999999999998 788877666 67789998764
No 41
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=76.31 E-value=7.2 Score=29.78 Aligned_cols=48 Identities=17% Similarity=0.126 Sum_probs=36.5
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
+|.|..++.. .++.++-.+||+..++| ..-++.++- ....+|+|+..=
T Consensus 11 lr~L~~LA~~-~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~r 58 (153)
T PRK11920 11 IRMLMYCAAN-DGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETVR 58 (153)
T ss_pred HHHHHHHHhC-CCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeec
Confidence 3444444432 34568999999999998 999999988 888899987654
No 42
>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=75.99 E-value=4 Score=25.01 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=20.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
.-.||.+||+.++++ ...|..++- +|.
T Consensus 25 ~g~s~~eIa~~l~~s-~~~v~~~l~-ra~ 51 (54)
T PF08281_consen 25 QGMSYAEIAEILGIS-ESTVKRRLR-RAR 51 (54)
T ss_dssp S---HHHHHHHCTS--HHHHHHHHH-HHH
T ss_pred HCcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 458999999999997 999999887 775
No 43
>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=75.65 E-value=7.3 Score=23.39 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=26.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
+..+..+|++.++++ ...|-.-+= .....|+|+
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 779999999999997 888877666 677788875
No 44
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=75.36 E-value=7.7 Score=28.36 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=32.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
.+..+|.++|++.++++ ...|...+= .....|+|.+.
T Consensus 22 ~~~~~s~~eia~~l~is-~~~v~~~l~-~L~~~Gli~~~ 58 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLN-APTVSKILK-QLSLAGIVTSK 58 (130)
T ss_pred CCCCccHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 35679999999999998 999999888 89999999774
No 45
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=75.36 E-value=8.2 Score=28.77 Aligned_cols=48 Identities=13% Similarity=0.167 Sum_probs=36.4
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
|.+..+.-...+..+|-++||+.++++ ..-|+..+- ..-..|+|+.+=
T Consensus 12 ~~~i~la~~~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~ 59 (141)
T PRK11014 12 RALIYMASLPEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVR 59 (141)
T ss_pred HHHHHHhcCCCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEec
Confidence 443444433456678999999999998 899999888 888889887653
No 46
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=75.01 E-value=10 Score=25.42 Aligned_cols=44 Identities=20% Similarity=0.172 Sum_probs=36.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCF 152 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v 152 (177)
.+.++..+|++.++++ ...+-..+- +....|+|.-.-+..++..
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 4469999999999997 889999888 9999999998777654443
No 47
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=74.98 E-value=5.5 Score=26.12 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=30.0
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
.++-.+||+.++++ ...|...+- .....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~-~~~v~r~L~-~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLP-KKEVNRVLY-SLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 49999999999998 889999999 9999999865
No 48
>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=74.96 E-value=2.9 Score=26.63 Aligned_cols=35 Identities=29% Similarity=0.481 Sum_probs=24.8
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHH
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lv 131 (177)
|++.|+.+...++.++++++|+.++++ ...+-..+
T Consensus 6 rq~~Ll~~L~~~~~~~~~ela~~l~~S-~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLKNKWITLKELAKKLNIS-ERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHHHTSBBHHHHHHHCTS--HHHHHHHH
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHCCC-HHHHHHHH
Confidence 445555554457899999999999997 76665543
No 49
>PF13730 HTH_36: Helix-turn-helix domain
Probab=74.64 E-value=12 Score=22.84 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=35.5
Q ss_pred HHHHHHHhhccccC-Cccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 030471 93 LKLKQLTVLTLAET-NKVL-PYDELMEELDVTNVRELEDFLINECMYTGIV 141 (177)
Q Consensus 93 ~Klr~LtllsL~~~-~~~i-s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI 141 (177)
.|+-.+.|.+.+.+ +... |++.||+.++++ ...|...+= +....|+|
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 36666778888752 2233 899999999997 999998877 77777765
No 50
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=74.04 E-value=7.6 Score=37.58 Aligned_cols=49 Identities=16% Similarity=0.212 Sum_probs=42.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
...+|||+.+.+-.-.=|..++|.++| +|...+.+..+||...++|++.
T Consensus 444 iY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 444 IYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence 567899999887643335899999999 9999999999999999999987
No 51
>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=73.96 E-value=8.3 Score=24.75 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=34.2
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
-+|..+...+..++-.+||+.++++ ...|=..+= +.-..|+|.
T Consensus 11 ~~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~-~L~~~GlV~ 53 (60)
T PF01325_consen 11 KAIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLK-RLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEE
Confidence 3555555688899999999999997 888877777 888888875
No 52
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=73.15 E-value=16 Score=22.08 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=30.0
Q ss_pred cCCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 105 ETNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 105 ~~~~~i-s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
..+..+ |..+|++.++++ ...|...+- .....|+|.
T Consensus 15 ~~~~~l~s~~~la~~~~vs-~~tv~~~l~-~L~~~g~i~ 51 (60)
T smart00345 15 RPGDKLPSERELAAQLGVS-RTTVREALS-RLEAEGLVQ 51 (60)
T ss_pred CCCCcCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 345567 899999999997 899999888 888888875
No 53
>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=71.74 E-value=16 Score=21.96 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=23.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
....|+.+||+.++++ ...|-.+.- +|+.
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 5678999999999997 888888776 6663
No 54
>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=70.94 E-value=2.9 Score=24.97 Aligned_cols=29 Identities=28% Similarity=0.430 Sum_probs=19.5
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHH
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELED 129 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~ 129 (177)
|+.+...+...||.+|++.+|++ ...|-.
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 34444556889999999999997 777643
No 55
>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=69.75 E-value=18 Score=22.44 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=31.2
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
+++.+|++.++++ ...+-..+= .....|+|...-+.
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 9999999999997 888988777 77789999887655
No 56
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=69.35 E-value=6.3 Score=26.79 Aligned_cols=51 Identities=29% Similarity=0.315 Sum_probs=36.4
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~ 150 (177)
|.++++-......+|.+|.+.++++ ...+-.-+= ..-..|+|+-+-.-..+
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt-~g~Ls~hL~-~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLT-DGNLSKHLK-KLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEE-SSS
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEEEEeccCC
Confidence 4455544557789999999999997 777776666 77889999988765554
No 57
>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=69.29 E-value=7.2 Score=23.91 Aligned_cols=35 Identities=31% Similarity=0.400 Sum_probs=24.4
Q ss_pred HHHhhccc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 97 QLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 97 ~LtllsL~-~~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
+..++.+. +.+..+|-++||+.++++ ...|..-+=
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHH
Confidence 34444443 455559999999999997 888877644
No 58
>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=69.01 E-value=12 Score=23.25 Aligned_cols=41 Identities=22% Similarity=0.268 Sum_probs=33.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~ 150 (177)
..++..+|++.++++ ...|-..|= +....|+|.-.-|..++
T Consensus 20 ~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 20 EELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGDR 60 (62)
T ss_dssp SGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSST
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCCC
Confidence 359999999999998 888988888 99999999988776543
No 59
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=68.57 E-value=16 Score=24.44 Aligned_cols=50 Identities=14% Similarity=0.255 Sum_probs=33.9
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
.++..+. ++..++.+|+..++++ ...+..++= ..+..|+|++ .++...+|
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 3444444 6678899999999997 899999888 8999999944 45555554
No 60
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=67.96 E-value=12 Score=32.56 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=44.6
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
.-.+.|+..+|..-++.+ ..+.|..+= +.+..|.+-+||+++.+.+....
T Consensus 349 ~yYSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK 398 (439)
T COG5071 349 NYYSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEK 398 (439)
T ss_pred HHhhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeec
Confidence 346788999999999998 999999999 99999999999999999988753
No 61
>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=67.67 E-value=18 Score=25.81 Aligned_cols=48 Identities=10% Similarity=0.049 Sum_probs=39.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
.+..++..+|++.++++ ...|=..|- +....|+|...-|..++.....
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~~~v 86 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRRVYI 86 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCeeEE
Confidence 35578999999999997 677877777 8999999999998877654433
No 62
>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=67.29 E-value=8.9 Score=24.70 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=33.6
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
..+..+-.+|++.++++ ...|-..+= +....|+|+-.-
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 46789999999999998 999999888 999999997665
No 63
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=67.17 E-value=16 Score=21.46 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=28.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
+..++-.+|++.++++ ...|...+= .....|+|.-
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~ 46 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTR 46 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 4569999999999997 899988777 7777777764
No 64
>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=67.10 E-value=14 Score=25.81 Aligned_cols=50 Identities=18% Similarity=0.259 Sum_probs=37.7
Q ss_pred HHHHhhcc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 96 r~LtllsL-~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
+.+.++.= +....=++.++|++.|+++ .++|+..|= ..+..|.|=-.||+
T Consensus 51 ~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 51 KVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 34555544 4445569999999999998 999999888 89999999888875
No 65
>PRK09954 putative kinase; Provisional
Probab=66.43 E-value=7.6 Score=33.29 Aligned_cols=50 Identities=20% Similarity=0.504 Sum_probs=38.8
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE---ecCCCCE
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK---LDQLRRC 151 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk---IDq~~~~ 151 (177)
|+.+..++..+|..+|++.|+++ ...|...+- +....|+|+|+ +|.....
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~-~L~~~g~i~~~~~~l~~~~~v 60 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIM-DLMRKGRIKGKGYILTEQEYC 60 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCcCCcEEEEcCCccE
Confidence 44444567789999999999997 999999888 88888998754 4444444
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=65.40 E-value=9.7 Score=23.54 Aligned_cols=44 Identities=18% Similarity=0.234 Sum_probs=35.8
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~ 151 (177)
..+.++..+|++.++++ ...+=.++= +....|+|.-.-|+.+++
T Consensus 14 ~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 14 ENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDRR 57 (59)
T ss_dssp HHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTETT
T ss_pred HcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCCC
Confidence 34459999999999997 788888777 899999999998887653
No 67
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=64.70 E-value=21 Score=26.36 Aligned_cols=57 Identities=9% Similarity=-0.028 Sum_probs=43.9
Q ss_pred hccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 030471 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (177)
Q Consensus 101 lsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~ 159 (177)
..+...+..++-.+|++.++++ ...|=..|= +....|+|.-.-|+.+++......++
T Consensus 38 ~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~LT~ 94 (144)
T PRK03573 38 HNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKLTE 94 (144)
T ss_pred HHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEECh
Confidence 3344434457889999999997 788888877 89999999999998887766555443
No 68
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=63.01 E-value=8.8 Score=36.59 Aligned_cols=117 Identities=12% Similarity=0.229 Sum_probs=76.8
Q ss_pred hhhhhcchhhhhccCCC---chHHHHHHHHHhcCChhhHhhh-------hCCCCCCc---hHHHHHHHHH----Hhhccc
Q 030471 42 FSEILAVPNIAEFEGTE---NSKYLDMLRLFAHGTWSDYKNN-------AGHLPQLV---PDQVLKLKQL----TVLTLA 104 (177)
Q Consensus 42 f~eLl~~~~v~~L~~~~---~~~l~~LL~if~~G~~~~~~~~-------~~~~~~L~---~~~~~Klr~L----tllsL~ 104 (177)
|.-.|.+---|++.+++ -.-+..-=.+...|+|..-.++ ++-+|.-. .-..++++-= -|.+.+
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 33444444445555432 2335556677889999875552 22344321 1112333321 123333
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R 160 (177)
.-...+|.+.+|+-..+| +..|=..|= +.|...=+.+++||+.++|.+.++.|-
T Consensus 714 s~Y~SvSl~~LA~mFdLp-~~~VhsIiS-kmiineEl~AslDqpt~~iv~hrvE~s 767 (843)
T KOG1076|consen 714 SVYDSVSLAKLADMFDLP-EPKVHSIIS-KMIINEELHASLDQPTQCIVMHRVEPS 767 (843)
T ss_pred hhhhhccHHHHHHHhCCC-chhHHHHHH-HHHHHHHhhhccCCCcceEEEeeccch
Confidence 457899999999999998 889988777 888888899999999999999987764
No 69
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=62.94 E-value=27 Score=20.93 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=30.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkID 146 (177)
.+..++.+|++.++++ ...+-..+= +....|++.-.-+
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 5678999999999997 788877666 7788999985443
No 70
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=62.82 E-value=28 Score=20.12 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=28.3
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
.++..+|++.++++ ...+-..+- .....|+|.-
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 46889999999997 889988888 8888898863
No 71
>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=62.36 E-value=13 Score=27.23 Aligned_cols=42 Identities=19% Similarity=0.327 Sum_probs=34.4
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
.|+.||.. ..|-.|||..+++| ..-|--++= +.+..|+|..+
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 56778876 89999999999999 777777766 88888887654
No 72
>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=61.86 E-value=38 Score=21.35 Aligned_cols=30 Identities=20% Similarity=0.379 Sum_probs=23.7
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
..-|.++.++||+.++|+ ...+.+-+= +|.
T Consensus 19 d~PR~~tl~elA~~lgis-~st~~~~LR-rae 48 (53)
T PF04967_consen 19 DVPRRITLEELAEELGIS-KSTVSEHLR-RAE 48 (53)
T ss_pred CCCCcCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 357899999999999997 777766555 554
No 73
>PF13518 HTH_28: Helix-turn-helix domain
Probab=60.99 E-value=13 Score=22.14 Aligned_cols=42 Identities=12% Similarity=0.197 Sum_probs=28.4
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkID 146 (177)
++.+...+ . |+.++|+.++|+ ...|..|+- .--..| +.|-.+
T Consensus 5 iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~-~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 5 IVELYLEG-E-SVREIAREFGIS-RSTVYRWIK-RYREGG-IEGLKP 46 (52)
T ss_pred HHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH-HHHhcC-HHHhcc
Confidence 34444433 3 999999999996 899999976 544434 344333
No 74
>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=59.46 E-value=7.7 Score=26.42 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=25.2
Q ss_pred HhhccccCCcccChHHHHHHcC---CCChHHHHHHHHHHhHhcCc
Q 030471 99 TVLTLAETNKVLPYDELMEELD---VTNVRELEDFLINECMYTGI 140 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~---i~~~~evE~lvI~~ai~~gL 140 (177)
.|+...+..+.+||++|.++|. ++ .+.++.++- ..-..|+
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 3667777777899999999986 33 677887665 4444443
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=58.32 E-value=22 Score=22.18 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=29.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
...++..+|++.++++ ...|...+= .....|+|.-
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 4579999999999997 899998877 8888888864
No 76
>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=57.42 E-value=12 Score=24.64 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.2
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.+|.-+.++||+.|+++ .++|..++-
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 58899999999999998 999997644
No 77
>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=56.77 E-value=13 Score=24.16 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=21.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHH
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDF 130 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~l 130 (177)
.++.+++-+||+.|+++ ...|-.|
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 47789999999999998 8888776
No 78
>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=56.52 E-value=11 Score=25.42 Aligned_cols=30 Identities=23% Similarity=0.185 Sum_probs=23.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcC
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (177)
...||.+||+.++++ ...|..++- .-.+.|
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 568999999999998 899988765 434433
No 79
>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=56.34 E-value=35 Score=26.96 Aligned_cols=52 Identities=15% Similarity=0.217 Sum_probs=37.4
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v 154 (177)
++.....++.++..+|++.++++ ...+-..+- +....|+|.-.-+ ....+++
T Consensus 148 IL~~l~~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 148 VLEVLKAEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEe
Confidence 33333444579999999999997 888988888 8888999986543 3334443
No 80
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=56.21 E-value=15 Score=24.00 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=28.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
+..++=.|||++|+++ ..++-.++. ..-..|.|+
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 6678999999999997 999999999 888888774
No 81
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=55.92 E-value=14 Score=28.39 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-..+||+|||+.++++ ...|...+- +|.
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 4579999999999998 999999887 775
No 82
>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=54.81 E-value=45 Score=20.85 Aligned_cols=48 Identities=17% Similarity=0.272 Sum_probs=34.1
Q ss_pred ccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 030471 102 TLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (177)
Q Consensus 102 sL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~ 151 (177)
.++..++..+..+|++.++++ ...+-..|= +....|+|+=.=|..++.
T Consensus 11 ~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~-~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 11 ALAHSDGPMTQSDLAERLGIS-KSTVSRIIK-KLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHT--TS-BEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEESSCTT
T ss_pred HHHccCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecCCCCcCC
Confidence 333567889999999999997 788887665 889999997777765554
No 83
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=53.42 E-value=22 Score=26.56 Aligned_cols=40 Identities=28% Similarity=0.251 Sum_probs=34.4
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkID 146 (177)
+.++..+-++||+.++.+ ...|..-|= +.+..|+|.=.=.
T Consensus 38 ~~~~~~tvdelae~lnr~-rStv~rsl~-~L~~~GlV~Rek~ 77 (126)
T COG3355 38 EENGPLTVDELAEILNRS-RSTVYRSLQ-NLLEAGLVEREKV 77 (126)
T ss_pred hhcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeeeeee
Confidence 468899999999999997 899999988 9999999865433
No 84
>PHA02943 hypothetical protein; Provisional
Probab=53.08 E-value=33 Score=26.70 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=33.0
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
|+..++.+. ..++-|-.+||+++|++ ..+++..+- -.=+.|.|+-
T Consensus 12 R~~eILE~L-k~G~~TtseIAkaLGlS-~~qa~~~Ly-vLErEG~Vkr 56 (165)
T PHA02943 12 RMIKTLRLL-ADGCKTTSRIANKLGVS-HSMARNALY-QLAKEGMVLK 56 (165)
T ss_pred HHHHHHHHH-hcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCceEE
Confidence 444555544 56788899999999997 999998776 5666666553
No 85
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=52.93 E-value=19 Score=26.46 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=34.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v 154 (177)
++..+..+|++.++++ ...|-.-+= ..-.+|||..+-+.......+
T Consensus 28 ~~~~~v~ela~~l~ls-qstvS~HL~-~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 28 SGELCVCDLCTALDQS-QPKISRHLA-LLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred cCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEEEEcCEEEEEE
Confidence 4578999999999998 777765544 466799999998865544444
No 86
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=52.89 E-value=20 Score=25.48 Aligned_cols=39 Identities=18% Similarity=0.135 Sum_probs=28.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~ 150 (177)
....+|.+++++.++++ .+. |. +.+..|+|.-.-.+..+
T Consensus 4 ~~~~lt~~Elc~~~gi~-~~~----l~-eLve~GlIep~~~~~~~ 42 (101)
T PRK10265 4 VTVTFTITEFCLHTGVS-EEE----LN-EIVGLGVIEPREIQETT 42 (101)
T ss_pred eEEEeeHHHHHHHHCcC-HHH----HH-HHHHCCCeecCCCCccc
Confidence 34568999999999998 544 45 56669999975555433
No 87
>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=51.90 E-value=16 Score=25.69 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=27.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
++.++-++||+.++++ ..+|-.++- +....|+|+.+
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 4679999999999998 999999999 99999999766
No 88
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=51.83 E-value=29 Score=28.33 Aligned_cols=56 Identities=14% Similarity=0.173 Sum_probs=39.1
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
|-+.++.+....+.++..+|++.+++| ...|-.++= .....|++.=. ..++...+.
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~-kstv~Rll~-tL~~~G~l~~~--~~~~~Y~lG 70 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMS-KSTVYRFLQ-TMKTLGYVAQE--GESEKYSLT 70 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEc--CCCCcEEec
Confidence 345555544445679999999999998 889988887 77888887542 334444443
No 89
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=51.49 E-value=24 Score=30.16 Aligned_cols=40 Identities=23% Similarity=0.261 Sum_probs=35.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~ 149 (177)
.-.+=++||+.++++ .-.|=.++= +|...|+|+-+|+...
T Consensus 28 ~g~tQ~eIA~~lgiS-R~~VsRlL~-~Ar~~GiV~I~I~~~~ 67 (318)
T PRK15418 28 DGLTQSEIGERLGLT-RLKVSRLLE-KGRQSGIIRVQINSRF 67 (318)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHHHcCcEEEEEeCCC
Confidence 457789999999997 899999998 9999999999998753
No 90
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=51.17 E-value=18 Score=27.67 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=24.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
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 468999999999998 999999888 775
No 91
>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=50.48 E-value=18 Score=24.36 Aligned_cols=25 Identities=12% Similarity=0.151 Sum_probs=19.8
Q ss_pred HHhhccccCCcccChHHHHHHcCCC
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVT 122 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~ 122 (177)
+.++.-...+++.||.+||+.++.+
T Consensus 6 ~~~v~~IP~G~v~TYg~iA~~~g~p 30 (79)
T cd06445 6 WEALRQIPYGEVTTYGQIAKLAGTP 30 (79)
T ss_pred HHHHhcCCCCCcCcHHHHHHHHCCC
Confidence 3444444679999999999999996
No 92
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=49.85 E-value=24 Score=29.10 Aligned_cols=44 Identities=20% Similarity=0.232 Sum_probs=35.5
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI 141 (177)
|+-.|+.+...++.++..++++.++++ ...|-.=+. ..-..|+|
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TIRRDL~-~Le~~g~l 49 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTT-GTTIRKDLV-ILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHHHHHHH-HHHHCCCE
Confidence 777888888888899999999999997 777765555 55667754
No 93
>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=49.80 E-value=58 Score=19.87 Aligned_cols=36 Identities=33% Similarity=0.416 Sum_probs=29.2
Q ss_pred cCCcccC-hHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 105 ETNKVLP-YDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 105 ~~~~~is-~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
..+..++ -.+||+.++++ ...|-..+- +.-..|+|.
T Consensus 20 ~~~~~~~~~~~la~~~~is-~~~v~~~l~-~L~~~G~i~ 56 (66)
T cd07377 20 KPGDRLPSERELAEELGVS-RTTVREALR-ELEAEGLVE 56 (66)
T ss_pred CCCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 3444454 99999999997 899999888 888889875
No 94
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=49.32 E-value=26 Score=30.28 Aligned_cols=39 Identities=21% Similarity=0.308 Sum_probs=34.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
...++=++||+.++|+ ...|-.++= +|...|+|+-+|+.
T Consensus 24 ~~gltQ~eIA~~LgiS-R~~v~rlL~-~Ar~~GiV~I~i~~ 62 (321)
T COG2390 24 VEGLTQSEIAERLGIS-RATVSRLLA-KAREEGIVKISINS 62 (321)
T ss_pred hcCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCeEEEEeCC
Confidence 3457889999999997 899999999 99999999999984
No 95
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=49.01 E-value=28 Score=28.44 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=35.6
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
|+..|+.+...++.++.++|++.++++ ...|...+- +.-..|++.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~-~L~~~~~l~ 49 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLN-ELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 666677777778899999999999997 888988776 554556654
No 96
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=48.94 E-value=22 Score=26.87 Aligned_cols=28 Identities=21% Similarity=0.362 Sum_probs=24.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
...||.+||+.++++ ...|...+- +|+.
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 468999999999998 999998887 7763
No 97
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=48.52 E-value=29 Score=23.66 Aligned_cols=32 Identities=16% Similarity=0.267 Sum_probs=25.3
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
||++++++.++++ ...| . ..+..|+|.....+
T Consensus 1 is~~e~~~~~~i~-~~~l----~-~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-PEFL----R-ELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-HHHH----H-HHHHCCCeeecCCC
Confidence 6899999999998 5544 4 55669999987776
No 98
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=48.28 E-value=29 Score=26.01 Aligned_cols=43 Identities=12% Similarity=0.254 Sum_probs=38.0
Q ss_pred HHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 030471 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (177)
Q Consensus 97 ~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI 141 (177)
...|+.++..++-+|+.++...++++ .+.++..+- +++..|-|
T Consensus 14 k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lr-eLVa~G~l 56 (127)
T PF06163_consen 14 KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLR-ELVARGDL 56 (127)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCCe
Confidence 36888888999999999999999997 999999999 89877743
No 99
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=48.23 E-value=63 Score=28.56 Aligned_cols=56 Identities=27% Similarity=0.372 Sum_probs=40.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHH
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSM 170 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L 170 (177)
.++.++.+++++.+++| .+.+++++= +..+.|+|. +-++ + .|+..|+.+.=....+
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~-~~~~--g----~~~l~rd~~~itL~dv 362 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR-RGER--G----QWVLARDLDSVPLAEL 362 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE-ecCC--C----ceEecCCHHhCcHHHH
Confidence 56789999999999998 999999877 888899997 3222 2 2666666554433333
No 100
>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=48.16 E-value=23 Score=26.87 Aligned_cols=28 Identities=29% Similarity=0.178 Sum_probs=24.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.+|++ ...|...+- +|.
T Consensus 148 ~~g~s~~EIA~~lgis-~~tVk~~l~-Rar 175 (183)
T TIGR02999 148 FAGLTVEEIAELLGVS-VRTVERDWR-FAR 175 (183)
T ss_pred HcCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998877 764
No 101
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=48.04 E-value=20 Score=21.35 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=18.0
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI 132 (177)
-.|..+||+.++++ ...|-.|+=
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 57999999999997 999999865
No 102
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=47.84 E-value=22 Score=23.72 Aligned_cols=20 Identities=35% Similarity=0.388 Sum_probs=17.5
Q ss_pred cChHHHHHHcCCCChHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDF 130 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~l 130 (177)
.+-++|++.|++| ..|+|-+
T Consensus 45 a~~~el~~~CgL~-~aEAeLl 64 (70)
T PF10975_consen 45 ASVEELMEECGLS-RAEAELL 64 (70)
T ss_pred CCHHHHHHHcCCC-HHHHHHH
Confidence 6789999999998 8999954
No 103
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=46.78 E-value=24 Score=26.75 Aligned_cols=29 Identities=21% Similarity=0.395 Sum_probs=24.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
....||++||+.+|++ ...|...+- +|..
T Consensus 133 ~~g~s~~EIA~~lgis-~~tV~~~l~-Ra~~ 161 (172)
T PRK09651 133 LDGLTYSEIAHKLGVS-VSSVKKYVA-KATE 161 (172)
T ss_pred ccCCCHHHHHHHhCCC-HHHHHHHHH-HHHH
Confidence 4578999999999998 999998887 7763
No 104
>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=46.48 E-value=24 Score=22.59 Aligned_cols=23 Identities=22% Similarity=0.172 Sum_probs=19.9
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI 132 (177)
-.+..+||+.|+++ ...|-.|+=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 46899999999998 889988864
No 105
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=46.19 E-value=25 Score=26.81 Aligned_cols=27 Identities=7% Similarity=0.361 Sum_probs=23.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|+
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 458999999999998 999998877 776
No 106
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=46.08 E-value=26 Score=25.94 Aligned_cols=28 Identities=18% Similarity=0.195 Sum_probs=23.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.+|++ ...|...+- +|.
T Consensus 120 ~~g~s~~EIA~~lgis-~~tV~~~l~-Rar 147 (160)
T PRK09642 120 LEEKSYQEIALQEKIE-VKTVEMKLY-RAR 147 (160)
T ss_pred HhCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998877 664
No 107
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=45.98 E-value=27 Score=25.62 Aligned_cols=27 Identities=11% Similarity=0.056 Sum_probs=23.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.+|++ ...|...+- +|+
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 458999999999998 999999887 765
No 108
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=45.81 E-value=34 Score=28.07 Aligned_cols=47 Identities=11% Similarity=0.155 Sum_probs=38.4
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
-|+..|+.+...++.++..++++.++++ ...+...+- +.-..|+|.-
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 3666677777889999999999999997 888888877 7667788754
No 109
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=45.64 E-value=32 Score=28.65 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=37.7
Q ss_pred HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
.-|+..|+.+...++.++..++++.++++ ...+-.=+. ..-..|++.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~-~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLA-FLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHH-HHHhCCCeE
Confidence 44778888888878789999999999997 888876666 555678776
No 110
>PHA02763 hypothetical protein; Provisional
Probab=45.63 E-value=29 Score=24.36 Aligned_cols=52 Identities=19% Similarity=0.221 Sum_probs=41.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCC
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDL 162 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~ 162 (177)
-.+|-+-+++-++-+.-+.||+|+= +| ..|=.-+||...=.+.|.|+..|-|
T Consensus 51 ap~t~~~LsKYv~~SGFe~VEeWl~-eA--rrLh~~~id~~ryeiivi~in~~~f 102 (102)
T PHA02763 51 APVTEYCLSKYVKFSGFENVEEWLN-EA--RRLHNDKIDPERYEIIVIWINGRLF 102 (102)
T ss_pred cCchHHHHHHHhhhcchhhHHHHHH-HH--HHHhcCCCChhheEEEEEEEcCccC
Confidence 3566677777777776788999998 87 5566789999999999999987754
No 111
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=45.17 E-value=71 Score=23.51 Aligned_cols=52 Identities=15% Similarity=0.043 Sum_probs=42.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R 160 (177)
...++-.+|++.++++ ...|=..|= +....|+|.=.-|..+++....+.+++
T Consensus 52 ~~~~t~~eLa~~l~i~-~~tvsr~l~-~Le~~GlI~R~~~~~DrR~~~l~LT~~ 103 (144)
T PRK11512 52 AACITPVELKKVLSVD-LGALTRMLD-RLVCKGWVERLPNPNDKRGVLVKLTTS 103 (144)
T ss_pred cCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEeccCcccCCeeEeEEChh
Confidence 4569999999999997 777777766 888999999999988888776665543
No 112
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.10 E-value=28 Score=25.67 Aligned_cols=27 Identities=4% Similarity=0.030 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|.
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 468999999999998 999998776 664
No 113
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=44.73 E-value=27 Score=26.57 Aligned_cols=27 Identities=7% Similarity=0.224 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
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 457999999999998 999998876 664
No 114
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=44.62 E-value=29 Score=28.06 Aligned_cols=23 Identities=17% Similarity=0.208 Sum_probs=19.0
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI 132 (177)
-.|+.+||+.++++ ...|+..+-
T Consensus 186 G~t~~eIa~~l~is-~~Tv~~~l~ 208 (232)
T TIGR03541 186 GRRQADIAAILGIS-ERTVENHLR 208 (232)
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH
Confidence 37999999999997 888876554
No 115
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=44.49 E-value=14 Score=27.50 Aligned_cols=22 Identities=32% Similarity=0.554 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhHhcCccEEEecC
Q 030471 125 RELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 125 ~evE~lvI~~ai~~gLI~gkIDq 147 (177)
..||.++| ++...|-|.|||++
T Consensus 70 q~VE~~li-rma~~gQvs~Kise 91 (129)
T KOG3431|consen 70 QAVENYLI-RMAQTGQVSHKISE 91 (129)
T ss_pred HHHHHHHH-HHHHhCCccccccH
Confidence 56999999 99999999999985
No 116
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=44.34 E-value=35 Score=27.23 Aligned_cols=83 Identities=14% Similarity=0.209 Sum_probs=52.2
Q ss_pred HHHHHHHHHhcCChhhHhhhh--C-CCCCCchHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 61 KYLDMLRLFAHGTWSDYKNNA--G-HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 61 ~l~~LL~if~~G~~~~~~~~~--~-~~~~L~~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
.+-.+.+++............ . ..+.|++.|++-++..-=+..-.--|.++..+||+.+||+ ...+.+-+= +|.
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 444555555555544333221 1 2235888776655555555555578999999999999997 788877766 655
Q ss_pred cCccEEEec
Q 030471 138 TGIVRGKLD 146 (177)
Q Consensus 138 ~gLI~gkID 146 (177)
.+|+.+-++
T Consensus 204 ~Kl~~~~~~ 212 (215)
T COG3413 204 RKLIEAYFD 212 (215)
T ss_pred HHHHHHhhh
Confidence 566655444
No 117
>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=44.24 E-value=1e+02 Score=23.75 Aligned_cols=62 Identities=15% Similarity=0.222 Sum_probs=43.3
Q ss_pred chHHHHHHHHHhcCChhhHhhhh--CCCCCCc----hHHHHHHHHHHhhccccCCcc-cChHHHHHHcC
Q 030471 59 NSKYLDMLRLFAHGTWSDYKNNA--GHLPQLV----PDQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (177)
Q Consensus 59 ~~~l~~LL~if~~G~~~~~~~~~--~~~~~L~----~~~~~Klr~LtllsL~~~~~~-is~~~I~~~l~ 120 (177)
..-..++...+..|++..|.+.. ...|.+. .....++|.-++-+++...+. ++.+.+++-|+
T Consensus 135 i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 135 IQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 45577889999999999998865 4444432 224679999888888876666 88888888765
No 118
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=44.18 E-value=29 Score=26.13 Aligned_cols=29 Identities=24% Similarity=0.466 Sum_probs=24.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
-...||++||+.++++ ...|...+- +|+.
T Consensus 132 ~eg~s~~EIA~~l~is-~~tV~~~l~-ra~~ 160 (168)
T PRK12525 132 LEGLTYVEIGERLGVS-LSRIHQYMV-EAFK 160 (168)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHHH
Confidence 3468999999999998 999998887 7763
No 119
>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=43.68 E-value=46 Score=27.99 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=36.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~ 148 (177)
..+.++..++++..++| .+-+-.-++ ++.-.++|+|++|..
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 56899999999999999 677776788 888889999999997
No 120
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=43.24 E-value=28 Score=26.73 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
T Consensus 146 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 172 (191)
T PRK12520 146 LELETEEICQELQIT-ATNAWVLLY-RAR 172 (191)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 358999999999998 999998876 654
No 121
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=42.75 E-value=32 Score=25.53 Aligned_cols=27 Identities=11% Similarity=0.158 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|+
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 468999999999998 999998866 664
No 122
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=42.73 E-value=34 Score=20.50 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=23.2
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.++.++... .|+.+||+.++++ ...|..++-
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 344444433 7999999999997 888887654
No 123
>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=42.66 E-value=50 Score=26.74 Aligned_cols=45 Identities=20% Similarity=0.270 Sum_probs=36.8
Q ss_pred HHHHhhccc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 96 r~LtllsL~-~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
|-+.++.+. ...+.++..||++.+++| ...+-.++- .....|.+.
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 346666544 356789999999999998 889999988 788999987
No 124
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.57 E-value=42 Score=19.68 Aligned_cols=24 Identities=21% Similarity=0.379 Sum_probs=20.6
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHh
Q 030471 110 LPYDELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~a 135 (177)
.++.+||+.++++ ...|..++- ++
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 6999999999997 899998765 54
No 125
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=42.56 E-value=32 Score=25.46 Aligned_cols=28 Identities=18% Similarity=0.322 Sum_probs=23.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
....||++||+.++++ ...|...+- +|.
T Consensus 119 ~~~~s~~eIA~~lgis-~~tv~~~l~-ra~ 146 (159)
T PRK12527 119 LEGLSHQQIAEHLGIS-RSLVEKHIV-NAM 146 (159)
T ss_pred HcCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998877 664
No 126
>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=41.94 E-value=43 Score=19.74 Aligned_cols=25 Identities=12% Similarity=0.178 Sum_probs=21.0
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHh
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~a 135 (177)
..++.+||+.++++ ...|+.++= ++
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 36999999999997 999998865 54
No 127
>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=41.92 E-value=31 Score=26.53 Aligned_cols=28 Identities=14% Similarity=0.163 Sum_probs=23.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.+|++ ...|...+- +|.
T Consensus 145 ~~g~s~~EIA~~lgis-~~tVk~~l~-Rar 172 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTP-IGTVMSRLH-RGR 172 (193)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998877 664
No 128
>PRK10870 transcriptional repressor MprA; Provisional
Probab=41.88 E-value=74 Score=24.61 Aligned_cols=50 Identities=14% Similarity=-0.005 Sum_probs=41.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~ 157 (177)
++..++..+|++.++++ ...|=..|= +....|+|.-.-|..+++......
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~L 117 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQL 117 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEE
Confidence 46789999999999998 788877776 899999999999998877655544
No 129
>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=41.15 E-value=34 Score=25.29 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=23.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.+|++ ...|...+- +|.
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 368999999999998 999998887 765
No 130
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=41.02 E-value=33 Score=25.95 Aligned_cols=26 Identities=31% Similarity=0.517 Sum_probs=22.4
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
..||++||+.+|++ ...|...+- +|.
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 47999999999998 999988777 664
No 131
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=40.50 E-value=36 Score=25.47 Aligned_cols=27 Identities=7% Similarity=0.123 Sum_probs=23.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|.
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 468999999999998 999998887 765
No 132
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=40.48 E-value=39 Score=23.79 Aligned_cols=27 Identities=15% Similarity=0.329 Sum_probs=24.0
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 114 ELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 114 ~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
-||..++++ .++|+..+- +....|||+
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 488899998 999999988 999999975
No 133
>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=39.85 E-value=30 Score=24.08 Aligned_cols=44 Identities=16% Similarity=0.273 Sum_probs=35.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~ 156 (177)
.-.+.+++|.+.||=+ -++..+-+ ...+ ..|+|+.....+.+.|
T Consensus 44 ~l~i~~~tiee~LGr~--~~~~el~v-~mss---~~Gri~~~dD~~~~~w 87 (87)
T PF02406_consen 44 RLVIRRETIEEALGRP--FDLQELEV-NMSS---FYGRIDEDDDEFVLYW 87 (87)
T ss_dssp EEEEEHHHHHHHCTST--CHHHHHHH-TECE---EESEEEEESSEEEEES
T ss_pred eEEEEHHHHHHHhCCC--CcHHHHhh-hhhe---eeeEEEEeCCEEEEEC
Confidence 3478999999999965 67777777 6544 7899999999998876
No 134
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=39.83 E-value=36 Score=26.16 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=23.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.+|++ ...|...+- +|.
T Consensus 153 ~~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 180 (194)
T PRK12513 153 HGDLELEEIAELTGVP-EETVKSRLR-YAL 180 (194)
T ss_pred ccCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999987766 664
No 135
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=39.79 E-value=38 Score=25.15 Aligned_cols=28 Identities=21% Similarity=0.409 Sum_probs=24.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.++++ ...|...+- +|.
T Consensus 127 ~~g~s~~EIA~~l~is-~~tV~~~l~-ra~ 154 (161)
T PRK12528 127 VDGLGYGEIATELGIS-LATVKRYLN-KAA 154 (161)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998877 765
No 136
>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=39.75 E-value=40 Score=19.81 Aligned_cols=21 Identities=14% Similarity=0.528 Sum_probs=17.0
Q ss_pred HHHHHHcCCCChHHHHHHHHHHh
Q 030471 113 DELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 113 ~~I~~~l~i~~~~evE~lvI~~a 135 (177)
++|++.++++ ..+|..|.+ +|
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 4678889997 999999999 65
No 137
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=39.40 E-value=70 Score=24.87 Aligned_cols=57 Identities=12% Similarity=0.130 Sum_probs=38.5
Q ss_pred ChHHHHHHc--CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEe---ecCCCCCcchHHHHHH
Q 030471 111 PYDELMEEL--DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF---AAGRDLRPGQLGSMIQ 172 (177)
Q Consensus 111 s~~~I~~~l--~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~---~~~R~~~~~~~~~L~~ 172 (177)
.++.||+.| +|+ .++|+.-+- -....|+|+-.=| |...++. ..+-++.+.-+..++.
T Consensus 41 d~~~iak~l~p~is-~~ev~~sL~-~L~~~gli~k~~~---g~y~~t~~~l~~~~~~~~~avr~~h~ 102 (171)
T PF14394_consen 41 DPEWIAKRLRPKIS-AEEVRDSLE-FLEKLGLIKKDGD---GKYVQTDKSLTTSSEIPSEAVRSYHK 102 (171)
T ss_pred CHHHHHHHhcCCCC-HHHHHHHHH-HHHHCCCeEECCC---CcEEEecceeeCCCCCcHHHHHHHHH
Confidence 899999999 997 999998887 7888999975444 3333331 1334445444544443
No 138
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=39.23 E-value=1.1e+02 Score=19.92 Aligned_cols=60 Identities=12% Similarity=0.148 Sum_probs=46.5
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHHHHhc
Q 030471 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLS 175 (177)
Q Consensus 111 s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~~L~ 175 (177)
.|.++.+.++++ .+....+.= + ..+-+-.++..+++.++.-..++.+..+.+..+.++|.
T Consensus 2 ~F~~ll~ql~~~-~~~~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~ 61 (76)
T PF14480_consen 2 RFFELLKQLQIP-DELDNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLK 61 (76)
T ss_pred chHHHHHHcCCC-chhhhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHH
Confidence 367788889998 333243333 3 35667889999999999999999999999999998875
No 139
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=38.36 E-value=40 Score=25.40 Aligned_cols=27 Identities=19% Similarity=0.252 Sum_probs=23.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
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 568999999999998 999998877 664
No 140
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=38.30 E-value=40 Score=26.03 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+= +|.
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 468999999999998 999998766 654
No 141
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=37.92 E-value=38 Score=25.38 Aligned_cols=27 Identities=7% Similarity=0.131 Sum_probs=23.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ +..|...+- +|.
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 468999999999998 999988777 664
No 142
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=37.89 E-value=40 Score=26.60 Aligned_cols=28 Identities=18% Similarity=0.248 Sum_probs=23.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-.-.||.+||+.+|++ ...|...+- +|.
T Consensus 152 ~~g~s~~EIA~~Lgis-~~tV~~~l~-RAr 179 (203)
T PRK09647 152 IEGLSYEEIAATLGVK-LGTVRSRIH-RGR 179 (203)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3458999999999998 999998887 764
No 143
>PF12728 HTH_17: Helix-turn-helix domain
Probab=37.80 E-value=40 Score=20.15 Aligned_cols=29 Identities=17% Similarity=0.197 Sum_probs=21.9
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
+|.+|+|+.|+++ ...|..|+= .|-+.+-
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 5789999999997 888887643 5555444
No 144
>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=37.78 E-value=41 Score=19.11 Aligned_cols=22 Identities=27% Similarity=0.297 Sum_probs=18.3
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI 132 (177)
++..++|+.++++ ...+-.|+=
T Consensus 1 ~s~~e~a~~lgvs-~~tl~~~~~ 22 (49)
T cd04762 1 LTTKEAAELLGVS-PSTLRRWVK 22 (49)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH
Confidence 4678999999997 888888754
No 145
>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=37.66 E-value=51 Score=22.54 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=22.9
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.|+.+...++.+|-.++|.+++.+ .++|...+=
T Consensus 28 ~LLr~LA~G~PVt~~~LA~a~g~~-~e~v~~~L~ 60 (77)
T PF12324_consen 28 PLLRLLAKGQPVTVEQLAAALGWP-VEEVRAALA 60 (77)
T ss_dssp HHHHHHTTTS-B-HHHHHHHHT---HHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCC-HHHHHHHHH
Confidence 445544569999999999999998 999987654
No 146
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=37.65 E-value=40 Score=26.95 Aligned_cols=28 Identities=7% Similarity=0.095 Sum_probs=24.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
....||.+||+.+|++ ...|...+- +|+
T Consensus 196 ~eg~s~~EIA~~lgis-~~tVk~~~~-rA~ 223 (234)
T PRK08301 196 GEEKTQKEVADMLGIS-QSYISRLEK-RII 223 (234)
T ss_pred CCCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3578999999999998 999998876 665
No 147
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=37.48 E-value=40 Score=26.04 Aligned_cols=27 Identities=22% Similarity=0.341 Sum_probs=23.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
T Consensus 157 ~~~s~~EIA~~Lgis-~~tVk~~l~-ra~ 183 (194)
T PRK09646 157 GGLTYREVAERLAVP-LGTVKTRMR-DGL 183 (194)
T ss_pred cCCCHHHHHHHhCCC-hHhHHHHHH-HHH
Confidence 458999999999997 999998877 664
No 148
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=37.37 E-value=59 Score=26.50 Aligned_cols=22 Identities=9% Similarity=-0.019 Sum_probs=17.6
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI 132 (177)
.|..+||+.++|+ ...|+.-+-
T Consensus 195 ~t~~eIa~~l~is-~~TV~~h~~ 216 (240)
T PRK10188 195 KTSAEIAMILSIS-ENTVNFHQK 216 (240)
T ss_pred CCHHHHHHHhCCC-HHHHHHHHH
Confidence 6889999999997 888775444
No 149
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=37.26 E-value=56 Score=25.91 Aligned_cols=39 Identities=15% Similarity=0.208 Sum_probs=33.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
....|..+||+.++++ ...|+..+. .+...|++.-+++-
T Consensus 176 ~~g~s~~eIA~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~~ 214 (239)
T PRK10430 176 DYEFSTDELANAVNIS-RVSCRKYLI-WLVNCHILFTSIHY 214 (239)
T ss_pred CCCcCHHHHHHHhCch-HHHHHHHHH-HHHhCCEEEEEeec
Confidence 4567999999999997 999999999 99999998766654
No 150
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=37.15 E-value=42 Score=25.88 Aligned_cols=28 Identities=18% Similarity=0.177 Sum_probs=23.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
...||++||+.++++ ...|...+- +|..
T Consensus 126 eg~s~~EIA~~lgis-~~tV~~~l~-Rar~ 153 (182)
T PRK12511 126 EGLSYQEAAAVLGIP-IGTLMSRIG-RARA 153 (182)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HHHH
Confidence 468999999999998 999998877 6653
No 151
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=37.15 E-value=42 Score=25.53 Aligned_cols=27 Identities=7% Similarity=-0.021 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|.
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 458999999999998 999998876 654
No 152
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=37.11 E-value=41 Score=25.57 Aligned_cols=27 Identities=11% Similarity=0.057 Sum_probs=23.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|.
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 478999999999998 999998877 665
No 153
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=36.85 E-value=63 Score=25.37 Aligned_cols=37 Identities=8% Similarity=0.204 Sum_probs=31.9
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq 147 (177)
-.|..+||+.++|+ ...|+..+= .....|++...+.=
T Consensus 177 g~s~~eIa~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~~ 213 (225)
T PRK10046 177 QHTAETVAQALTIS-RTTARRYLE-YCASRHLIIAEIVH 213 (225)
T ss_pred CcCHHHHHHHhCcc-HHHHHHHHH-HHHhCCeEEEEeec
Confidence 47899999999997 999999888 78889988877653
No 154
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=36.74 E-value=42 Score=26.20 Aligned_cols=28 Identities=18% Similarity=0.179 Sum_probs=23.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.+|++ ...|...+- +|.
T Consensus 153 ~eg~s~~EIA~~lgis-~~tVk~~l~-RAr 180 (201)
T PRK12545 153 FLDFEIDDICTELTLT-ANHCSVLLY-RAR 180 (201)
T ss_pred HcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998776 664
No 155
>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=36.33 E-value=72 Score=17.94 Aligned_cols=30 Identities=13% Similarity=0.296 Sum_probs=20.9
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI 141 (177)
+|=.+||+.+++. .+.|=..+= +.-..|+|
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 888877666 66666654
No 156
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=36.21 E-value=69 Score=26.48 Aligned_cols=56 Identities=11% Similarity=0.141 Sum_probs=40.5
Q ss_pred HHHHhhccc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 96 r~LtllsL~-~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
|-+.|+.+. ..++.++..||++.+++| ...+=.++- .....|.+.= |...+...+.
T Consensus 26 r~l~IL~~~~~~~~~~tl~eIa~~lglp-kStv~RlL~-tL~~~G~l~~--~~~~~~Y~lG 82 (271)
T PRK10163 26 RGIAILQYLEKSGGSSSVSDISLNLDLP-LSTTFRLLK-VLQAADFVYQ--DSQLGWWHIG 82 (271)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE--cCCCCeEEec
Confidence 335555544 345679999999999998 889998888 7888888843 4455555544
No 157
>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=35.82 E-value=47 Score=24.19 Aligned_cols=27 Identities=22% Similarity=0.433 Sum_probs=22.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ +..|...+= +|.
T Consensus 120 ~g~s~~eIA~~lgis-~~tv~~~l~-Ra~ 146 (154)
T TIGR02950 120 KEFSYKEIAELLNLS-LAKVKSNLF-RAR 146 (154)
T ss_pred ccCcHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999998 999987766 553
No 158
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=35.78 E-value=45 Score=25.47 Aligned_cols=27 Identities=7% Similarity=0.003 Sum_probs=23.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+= +|.
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 468999999999997 999998877 664
No 159
>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=35.44 E-value=45 Score=23.92 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=19.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...+|+.+||+.++++ ...|=+.+- +|.
T Consensus 31 ~eDlSlsEIAe~~~iS-RqaV~d~ik-r~~ 58 (101)
T PF04297_consen 31 EEDLSLSEIAEELGIS-RQAVYDSIK-RAE 58 (101)
T ss_dssp TS---HHHHHHHCTS--HHHHHHHHH-HHH
T ss_pred ccCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4579999999999997 888887766 653
No 160
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=35.21 E-value=57 Score=26.83 Aligned_cols=47 Identities=13% Similarity=0.203 Sum_probs=38.2
Q ss_pred HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
+-|+-.|+.+...++.++..+|++.++++ ...+-.-+. ..-..|++.
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 34677778877888899999999999997 888887777 666777764
No 161
>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=35.20 E-value=49 Score=18.95 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=22.8
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
++..++|+.++++ ...+-.|+= .|.+.+..
T Consensus 2 lt~~e~a~~lgis-~~ti~~~~~-----~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KDTVYRLIH-----EGELPAYR 31 (49)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH-----cCCCCeEE
Confidence 5789999999997 888887643 56666643
No 162
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=34.88 E-value=46 Score=25.60 Aligned_cols=28 Identities=7% Similarity=0.103 Sum_probs=23.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.++++ ...|...+- +|.
T Consensus 125 ~~g~s~~EIA~~Lgis-~~tV~~~l~-RAr 152 (182)
T PRK12540 125 ASGFSYEDAAAICGCA-VGTIKSRVN-RAR 152 (182)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998876 664
No 163
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=34.55 E-value=49 Score=25.34 Aligned_cols=27 Identities=11% Similarity=0.185 Sum_probs=23.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+- +|+
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 468999999999997 999998877 765
No 164
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=34.45 E-value=49 Score=25.57 Aligned_cols=28 Identities=14% Similarity=0.156 Sum_probs=23.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.|+++ ...|...+= +|.
T Consensus 130 ~~g~s~~EIA~~Lgis-~~tVk~~l~-Rar 157 (187)
T PRK12516 130 ASGFAYEEAAEICGCA-VGTIKSRVN-RAR 157 (187)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998766 554
No 165
>PRK11569 transcriptional repressor IclR; Provisional
Probab=34.35 E-value=75 Score=26.27 Aligned_cols=55 Identities=18% Similarity=0.230 Sum_probs=40.5
Q ss_pred HHHHhhccc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 030471 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (177)
Q Consensus 96 r~LtllsL~-~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v 154 (177)
|-|.|+.+. +..+.++..+|++.++++ ...|=.++- .....|++. =|...++..+
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglp-ksTv~RlL~-tL~~~G~l~--~~~~~~~Y~l 84 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLP-NSTTHRLLT-TMQQQGFVR--QVGELGHWAI 84 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE--EcCCCCeEec
Confidence 345655543 456789999999999998 889999888 789999986 2444454443
No 166
>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=34.33 E-value=41 Score=20.84 Aligned_cols=30 Identities=13% Similarity=0.292 Sum_probs=19.6
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHH
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lv 131 (177)
.++...+.+. +..+||+.++++ ...|-.++
T Consensus 14 ~iI~~~e~g~--s~~~ia~~fgv~-~sTv~~I~ 43 (53)
T PF04218_consen 14 EIIKRLEEGE--SKRDIAREFGVS-RSTVSTIL 43 (53)
T ss_dssp HHHHHHHCTT---HHHHHHHHT---CCHHHHHH
T ss_pred HHHHHHHcCC--CHHHHHHHhCCC-HHHHHHHH
Confidence 4455556565 999999999998 77776654
No 167
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=34.16 E-value=1.6e+02 Score=20.63 Aligned_cols=52 Identities=10% Similarity=0.068 Sum_probs=42.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~ 159 (177)
.++.++-.+|++.++++ ...|=..|= +....|+|.=.-|..+++...-..++
T Consensus 40 ~~~~~t~~eL~~~l~~~-~stvs~~i~-~Le~kg~I~r~~~~~D~R~~~i~lT~ 91 (109)
T TIGR01889 40 NEGKLTLKEIIKEILIK-QSALVKIIK-KLSKKGYLSKERSEDDERKVIISINK 91 (109)
T ss_pred cCCcCcHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEeccCCcccCCeEEEEECH
Confidence 45789999999999997 788888777 88999999988888877665554444
No 168
>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=34.15 E-value=50 Score=25.00 Aligned_cols=27 Identities=15% Similarity=0.343 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
T Consensus 153 ~~~s~~EIA~~lgis-~~tv~~~l~-rar 179 (190)
T TIGR02939 153 EGLSYEDIARIMDCP-VGTVRSRIF-RAR 179 (190)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 568999999999998 999998876 654
No 169
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=34.10 E-value=75 Score=26.00 Aligned_cols=55 Identities=22% Similarity=0.257 Sum_probs=39.0
Q ss_pred HHHhhcccc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 97 QLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 97 ~LtllsL~~-~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
-|.|+.+.. ....+++.+|++.+++| ...+=.++. .....|+++= |..+++..+.
T Consensus 6 al~iL~~l~~~~~~l~l~ela~~~glp-ksT~~RlL~-tL~~~G~v~~--d~~~g~Y~Lg 61 (246)
T COG1414 6 ALAILDLLAEGPGGLSLAELAERLGLP-KSTVHRLLQ-TLVELGYVEQ--DPEDGRYRLG 61 (246)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEE--cCCCCcEeeh
Confidence 355555433 44448999999999998 899999998 8888888752 3334555544
No 170
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.98 E-value=83 Score=18.18 Aligned_cols=46 Identities=15% Similarity=0.093 Sum_probs=31.8
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHH
Q 030471 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI 171 (177)
Q Consensus 111 s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~ 171 (177)
+-.++|+.++++ ...|..|.= .|++.+.-+.. .+|.|+.+++..|+
T Consensus 2 ~~~e~a~~~gv~-~~tlr~~~~-----~g~l~~~~~~~---------~~~~y~~~~v~~l~ 47 (49)
T cd04761 2 TIGELAKLTGVS-PSTLRYYER-----IGLLSPARTEG---------GYRLYSDADLERLR 47 (49)
T ss_pred cHHHHHHHHCcC-HHHHHHHHH-----CCCCCCCcCCC---------CCEEeCHHHHHHhh
Confidence 568999999998 899998743 67765433222 24567777777665
No 171
>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=33.80 E-value=53 Score=24.33 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=23.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.++++ ...|...+- +|.
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 458999999999998 999998777 664
No 172
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=33.66 E-value=49 Score=25.11 Aligned_cols=28 Identities=11% Similarity=0.048 Sum_probs=23.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.+|++ ...|...+= +|.
T Consensus 149 ~~~~s~~eIA~~lgis-~~~V~~~l~-ra~ 176 (186)
T PRK13919 149 YQGYTHREAAQLLGLP-LGTLKTRAR-RAL 176 (186)
T ss_pred HcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 3568999999999998 999997766 554
No 173
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=33.61 E-value=50 Score=25.36 Aligned_cols=28 Identities=11% Similarity=0.051 Sum_probs=23.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.++++ ...|...+= +|.
T Consensus 144 ~~g~s~~EIA~~lgis-~~tVk~~l~-Rar 171 (185)
T PRK09649 144 LLGLSYADAAAVCGCP-VGTIRSRVA-RAR 171 (185)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998876 654
No 174
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=33.58 E-value=1.4e+02 Score=24.26 Aligned_cols=58 Identities=17% Similarity=0.190 Sum_probs=46.4
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
+..|..++-..+ -.+|-.++++.++++ ....-.++. +.-..|.|.=.+....+-+.++
T Consensus 6 lk~l~~~~a~~~-~~~t~~ela~~l~~S-~qta~R~l~-~le~~~~I~R~~~~~Gq~i~iT 63 (214)
T COG1339 6 LKKLALRGAVRG-VKVTSSELAKRLGVS-SQTAARKLK-ELEDEGYITRTISKRGQLITIT 63 (214)
T ss_pred HHHHHHhhhhcC-ccccHHHHHHHhCcC-cHHHHHHHH-hhccCCcEEEEecCCCcEEEeh
Confidence 344555555555 789999999999997 788888888 8888999998888888877776
No 175
>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=33.55 E-value=1.6e+02 Score=23.05 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=31.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
...+|..+|++.++++ ...|=..+= +....|+|.-+-
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 4459999999999997 888888777 888899998663
No 176
>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=33.48 E-value=40 Score=30.58 Aligned_cols=43 Identities=23% Similarity=0.301 Sum_probs=30.5
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
+.++.+-..+..+|+++|++.++++ .+++..-+- ..+..|++.
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 3444455668899999999999998 889988766 666777664
No 177
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=33.36 E-value=52 Score=25.68 Aligned_cols=27 Identities=19% Similarity=0.188 Sum_probs=22.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+= +|.
T Consensus 148 ~g~s~~EIAe~lgis-~~tV~~~l~-Rar 174 (196)
T PRK12535 148 LGYTYEEAAKIADVR-VGTIRSRVA-RAR 174 (196)
T ss_pred hCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 458999999999998 999997765 543
No 178
>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=33.32 E-value=45 Score=23.45 Aligned_cols=31 Identities=10% Similarity=0.184 Sum_probs=24.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcC
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (177)
.++.+|.+|-++..+++ .+|+|.|+= |+..+
T Consensus 46 ~~Glis~~EA~~rY~Ls-~eEf~~W~~--av~rh 76 (90)
T PF06627_consen 46 RGGLISVEEACRRYGLS-EEEFESWQR--AVDRH 76 (90)
T ss_dssp HCTTS-HHHHHHCTTSS-HHHHHHHHH--HCCT-
T ss_pred HcCCCCHHHHHHHhCCC-HHHHHHHHH--HHHHH
Confidence 37789999999999997 999999965 55443
No 179
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=33.28 E-value=52 Score=25.45 Aligned_cols=28 Identities=18% Similarity=0.227 Sum_probs=23.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.++++ ...|...+= +|.
T Consensus 150 ~~g~s~~eIA~~lgis-~~tV~~~l~-Ra~ 177 (196)
T PRK12524 150 IEGLSNPEIAEVMEIG-VEAVESLTA-RGK 177 (196)
T ss_pred HcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998877 664
No 180
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=33.23 E-value=65 Score=30.55 Aligned_cols=46 Identities=22% Similarity=0.381 Sum_probs=38.6
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
..+.++..++|+.+++| -+-+...++ .=.--.+|+|++|. ++++-.
T Consensus 130 E~gqvtiaeLakq~dl~-sellqs~l~-ek~lg~iikgr~dg--gviyT~ 175 (776)
T KOG2235|consen 130 EQGQVTIAELAKQWDLP-SELLQSLLI-EKLLGSIIKGRVDG--GVIYTS 175 (776)
T ss_pred HhcchHHHHHHHhcCCc-HHHHHHHHH-HHhhccceeeeecC--CEEeeH
Confidence 57799999999999999 688899999 66667899999998 666543
No 181
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=32.96 E-value=1e+02 Score=18.91 Aligned_cols=44 Identities=16% Similarity=0.252 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHHH
Q 030471 125 RELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQ 172 (177)
Q Consensus 125 ~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~ 172 (177)
..||.-+- .+ .|+-...+|-.++++.|.+..++ ++.+++..--+
T Consensus 14 ~~v~~~l~--~~-~GV~~v~vd~~~~~v~v~~~~~~-~~~~~i~~~i~ 57 (62)
T PF00403_consen 14 KKVEKALS--KL-PGVKSVKVDLETKTVTVTYDPDK-TSIEKIIEAIE 57 (62)
T ss_dssp HHHHHHHH--TS-TTEEEEEEETTTTEEEEEESTTT-SCHHHHHHHHH
T ss_pred HHHHHHHh--cC-CCCcEEEEECCCCEEEEEEecCC-CCHHHHHHHHH
Confidence 44565444 23 69999999999999999998888 66666554433
No 182
>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=32.78 E-value=55 Score=25.23 Aligned_cols=27 Identities=19% Similarity=0.276 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|.
T Consensus 146 ~g~s~~EIA~~lgis-~~tvk~rl~-Rar 172 (188)
T TIGR02943 146 LGFESDEICQELEIS-TSNCHVLLY-RAR 172 (188)
T ss_pred hCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 458999999999998 999988766 653
No 183
>PRK13870 transcriptional regulator TraR; Provisional
Probab=32.55 E-value=56 Score=26.52 Aligned_cols=22 Identities=14% Similarity=0.075 Sum_probs=17.0
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI 132 (177)
-|..||+..|+|+ +..|+.-+-
T Consensus 189 KT~~EIa~ILgIS-e~TV~~Hl~ 210 (234)
T PRK13870 189 KTMEEIADVEGVK-YNSVRVKLR 210 (234)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH
Confidence 3688999999997 888874433
No 184
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=32.54 E-value=54 Score=26.22 Aligned_cols=27 Identities=22% Similarity=0.258 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+- +|.
T Consensus 149 eg~s~~EIAe~LgiS-~~tVk~~L~-RAr 175 (216)
T PRK12533 149 EDMSYREIAAIADVP-VGTVMSRLA-RAR 175 (216)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999998776 654
No 185
>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=32.40 E-value=53 Score=26.88 Aligned_cols=27 Identities=11% Similarity=0.154 Sum_probs=23.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|+..+- +|.
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 468999999999998 999998877 764
No 186
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=32.38 E-value=56 Score=24.89 Aligned_cols=27 Identities=15% Similarity=0.215 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+- +|.
T Consensus 137 ~g~s~~EIA~~lgis-~~tVk~~l~-Rar 163 (185)
T PRK12542 137 YNLTYQEISSVMGIT-EANVRKQFE-RAR 163 (185)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999998 999998776 654
No 187
>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=31.97 E-value=76 Score=20.32 Aligned_cols=36 Identities=11% Similarity=0.238 Sum_probs=28.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
..+..|..+|.+..+++ .++|-.-++ -.|..|++.-
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 45688999999999998 999988887 7899998864
No 188
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=31.96 E-value=87 Score=24.56 Aligned_cols=51 Identities=10% Similarity=0.163 Sum_probs=38.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe--cCCCCEEEEEee
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL--DQLRRCFEVQFA 157 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI--Dq~~~~v~v~~~ 157 (177)
..++.+|=++||+.++++ ..+|-..+- +.-..|||..+- +...|..+-.|.
T Consensus 32 ~~~g~~tdeeLA~~Lgi~-~~~VRk~L~-~L~e~gLv~~~r~r~~~~Gr~~y~w~ 84 (178)
T PRK06266 32 IKKGEVTDEEIAEQTGIK-LNTVRKILY-KLYDARLADYKREKDEETNWYTYTWK 84 (178)
T ss_pred HHcCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeEEeeeeccCCCcEEEEEE
Confidence 355689999999999997 999999999 999999998544 223344444443
No 189
>PRK04239 hypothetical protein; Provisional
Probab=31.94 E-value=26 Score=25.61 Aligned_cols=22 Identities=27% Similarity=0.551 Sum_probs=19.9
Q ss_pred HHHHHHHHHHhHhcCccEEEecC
Q 030471 125 RELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 125 ~evE~lvI~~ai~~gLI~gkIDq 147 (177)
..||..+| .+...|-|.|+|++
T Consensus 67 ~~VE~~li-qlAq~G~i~~ki~e 88 (110)
T PRK04239 67 EQVEQQLI-QLAQSGRIQGPIDD 88 (110)
T ss_pred HHHHHHHH-HHHHcCCCCCCcCH
Confidence 57999999 89999999999986
No 190
>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=31.81 E-value=58 Score=24.30 Aligned_cols=27 Identities=15% Similarity=0.286 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+- +|.
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 458999999999997 999988777 664
No 191
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=31.78 E-value=59 Score=24.14 Aligned_cols=27 Identities=15% Similarity=0.334 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.+|++ ...|...+- +|.
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 567999999999997 999988776 654
No 192
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=31.67 E-value=58 Score=25.12 Aligned_cols=27 Identities=19% Similarity=0.170 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.||++ ...|...+- +|.
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 468999999999997 999998776 654
No 193
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=31.57 E-value=56 Score=26.61 Aligned_cols=26 Identities=8% Similarity=0.088 Sum_probs=22.0
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
..||.+||+.+|++ ...|...+- +|.
T Consensus 132 g~S~~EIAe~LgiS-~~tVksrL~-Rar 157 (228)
T PRK06704 132 QYSIADIAKVCSVS-EGAVKASLF-RSR 157 (228)
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 58999999999997 899887766 654
No 194
>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=31.41 E-value=62 Score=19.11 Aligned_cols=20 Identities=10% Similarity=0.325 Sum_probs=13.9
Q ss_pred cChHHHHHHcCCCChHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDF 130 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~l 130 (177)
.|..+||+.++|+ ...|-.+
T Consensus 22 ~si~~IA~~~gvs-r~TvyR~ 41 (45)
T PF02796_consen 22 MSIAEIAKQFGVS-RSTVYRY 41 (45)
T ss_dssp --HHHHHHHTTS--HHHHHHH
T ss_pred CCHHHHHHHHCcC-HHHHHHH
Confidence 9999999999997 7766543
No 195
>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=31.26 E-value=54 Score=19.92 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=19.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
..-...+||..|+|+ ...|..|.=
T Consensus 26 ~~~~~~~la~~l~l~-~~~V~~WF~ 49 (57)
T PF00046_consen 26 SKEEREELAKELGLT-ERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHHHHTSS-HHHHHHHHH
T ss_pred ccccccccccccccc-ccccccCHH
Confidence 345677899999998 999999864
No 196
>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=31.06 E-value=96 Score=19.80 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=27.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
-.+|.++||..++++ ...|-..+= +.-..|+|+
T Consensus 27 ~~lt~~~iA~~~g~s-r~tv~r~l~-~l~~~g~I~ 59 (76)
T PF13545_consen 27 LPLTQEEIADMLGVS-RETVSRILK-RLKDEGIIE 59 (76)
T ss_dssp EESSHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEE
T ss_pred ecCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 457899999999997 888988777 777788877
No 197
>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=31.03 E-value=50 Score=22.60 Aligned_cols=32 Identities=9% Similarity=0.061 Sum_probs=25.1
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHH
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~ 129 (177)
|+.-|+.+... +.++..+||+.+|++ ...|=.
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS-~~TVsr 38 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVS-KSTVHK 38 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCC-HHHHHH
Confidence 66777777777 889999999999996 655543
No 198
>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=31.00 E-value=1.4e+02 Score=18.71 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=29.3
Q ss_pred cCCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 105 ETNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 105 ~~~~~i-s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
..+..+ |-.+|++.++++ ...|-.-+- .....|+|.-+
T Consensus 19 ~~g~~lps~~~la~~~~vs-r~tvr~al~-~L~~~g~i~~~ 57 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVS-RTTVREALR-RLEAEGLIERR 57 (64)
T ss_dssp -TTSBE--HHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred CCCCEeCCHHHHHHHhccC-CcHHHHHHH-HHHHCCcEEEE
Confidence 356678 999999999997 888888777 78889988643
No 199
>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=30.77 E-value=27 Score=25.29 Aligned_cols=22 Identities=41% Similarity=0.729 Sum_probs=18.2
Q ss_pred HHHHHHHHHHhHhcCccEEEecC
Q 030471 125 RELEDFLINECMYTGIVRGKLDQ 147 (177)
Q Consensus 125 ~evE~lvI~~ai~~gLI~gkIDq 147 (177)
..||..+| .....|=|.|+||+
T Consensus 62 ~~VE~~Li-qlaq~G~l~~kI~d 83 (107)
T PF01984_consen 62 RQVENQLI-QLAQSGQLRGKIDD 83 (107)
T ss_dssp HHHHHHHH-HHHHCTSSSS-B-H
T ss_pred HHHHHHHH-HHHHcCCCCCCcCH
Confidence 67999999 99999999999986
No 200
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=30.72 E-value=94 Score=25.42 Aligned_cols=47 Identities=26% Similarity=0.286 Sum_probs=35.9
Q ss_pred hhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 030471 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (177)
Q Consensus 100 llsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~ 148 (177)
|+-+++.....|-++||+.|+|+ ...|-.=+- +....|+|..+.-+.
T Consensus 16 il~lL~~~g~~sa~elA~~Lgis-~~avR~HL~-~Le~~Glv~~~~~~~ 62 (218)
T COG2345 16 ILELLKKSGPVSADELAEELGIS-PMAVRRHLD-DLEAEGLVEVERQQG 62 (218)
T ss_pred HHHHHhccCCccHHHHHHHhCCC-HHHHHHHHH-HHHhCcceeeeeccC
Confidence 44455778899999999999998 777755555 667799999994444
No 201
>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=30.65 E-value=58 Score=26.01 Aligned_cols=27 Identities=7% Similarity=0.079 Sum_probs=22.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|+
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 568999999999998 999987765 554
No 202
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=30.56 E-value=2.1e+02 Score=20.68 Aligned_cols=53 Identities=15% Similarity=0.323 Sum_probs=36.9
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQ 172 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~ 172 (177)
..|.+|+++|+=+ .+-|=.++. .-++ ..|+||.. +.+.++. .|+.++++.+-+
T Consensus 22 ~Nf~~I~~~L~R~-p~hv~kyl~-~ELg---t~g~id~~-~rlii~G----~~~~~~i~~~l~ 74 (110)
T smart00653 22 VNFADIAKALNRP-PDHVLKFLL-AELG---TQGSIDGK-GRLIVNG----RFTPKKLQDLLR 74 (110)
T ss_pred EcHHHHHHHHCCC-HHHHHHHHH-HHhC---CceeECCC-CeEEEEE----eeCHHHHHHHHH
Confidence 4899999999987 777777777 4444 77999877 6776663 233445555443
No 203
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=30.46 E-value=62 Score=24.24 Aligned_cols=27 Identities=11% Similarity=0.215 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+= +|.
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 468999999999997 899987776 664
No 204
>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=30.25 E-value=66 Score=28.57 Aligned_cols=45 Identities=18% Similarity=0.293 Sum_probs=33.1
Q ss_pred HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
.+-+|.++.+| .++-|.-+||+.+++| .+++...+- +.+..|||+
T Consensus 342 ~~~~l~~L~~~--DG~~slldIA~~~~~~-~~~~~~~~~-~l~~~~Llk 386 (386)
T PF09940_consen 342 QMAMLWVLNYS--DGKNSLLDIAERIGLP-FDELADAAR-KLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHHH---EEEEEHHHHHHHHT---HHHHHHHHH-HHHHTT-EE
T ss_pred HHHHHHHHHhc--cCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHcCCCC
Confidence 34456666665 4567899999999998 999999888 899999885
No 205
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=30.15 E-value=64 Score=24.80 Aligned_cols=27 Identities=7% Similarity=0.126 Sum_probs=22.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
T Consensus 151 ~g~s~~EIA~~lgis-~~tVk~~l~-Rar 177 (195)
T PRK12532 151 LGFSSDEIQQMCGIS-TSNYHTIMH-RAR 177 (195)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999998 899987766 553
No 206
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=30.12 E-value=1.5e+02 Score=20.01 Aligned_cols=50 Identities=16% Similarity=0.134 Sum_probs=34.5
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE-ecCCCCEEEEEeecCC
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK-LDQLRRCFEVQFAAGR 160 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk-IDq~~~~v~v~~~~~R 160 (177)
+.|++++.+..+++ .+.+=-.+= +....|+|.=+ .--..+.+.+-+...|
T Consensus 18 c~TLeeL~ekTgi~-k~~LlV~Ls-rL~k~GiI~Rkw~~~~gkk~R~YclK~~ 68 (72)
T PF05584_consen 18 CCTLEELEEKTGIS-KNTLLVYLS-RLAKRGIIERKWRKFGGKKYREYCLKYK 68 (72)
T ss_pred cCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeeeEEecCeEEEEEEecch
Confidence 99999999999997 777765555 77778887643 3333345555444444
No 207
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=30.11 E-value=1e+02 Score=19.29 Aligned_cols=48 Identities=17% Similarity=0.164 Sum_probs=31.2
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI 171 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~ 171 (177)
++..++|+.++++ ...+-.| . + .|++...-...++ .|.|+.+++..++
T Consensus 1 ~s~~eva~~~gvs-~~tlr~~-~-~---~gli~~~~~~~~g--------~r~y~~~dl~~l~ 48 (70)
T smart00422 1 YTIGEVAKLAGVS-VRTLRYY-E-R---IGLLPPPIRTEGG--------YRLYSDEDLERLR 48 (70)
T ss_pred CCHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCccCCCC--------CEecCHHHHHHHH
Confidence 3678999999998 8888877 3 2 7887654222222 3556666666554
No 208
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=29.88 E-value=95 Score=22.89 Aligned_cols=42 Identities=12% Similarity=0.120 Sum_probs=32.7
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
+|..+...++..+..+|++.++++ ...|=..+= +....|+|.
T Consensus 12 ~I~~l~~~~~~~~~~ela~~l~vs-~~svs~~l~-~L~~~Gli~ 53 (142)
T PRK03902 12 QIYLLIEEKGYARVSDIAEALSVH-PSSVTKMVQ-KLDKDEYLI 53 (142)
T ss_pred HHHHHHhcCCCcCHHHHHHHhCCC-hhHHHHHHH-HHHHCCCEE
Confidence 334445566778999999999997 788877776 777788887
No 209
>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=29.84 E-value=68 Score=23.46 Aligned_cols=27 Identities=22% Similarity=0.190 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.++++ ...|...+- +|.
T Consensus 126 ~g~~~~eIA~~l~is-~~tv~~~l~-Rar 152 (159)
T TIGR02989 126 RGVSLTALAEQLGRT-VNAVYKALS-RLR 152 (159)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999998 899998776 654
No 210
>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=29.70 E-value=99 Score=25.84 Aligned_cols=36 Identities=11% Similarity=0.252 Sum_probs=30.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
+.-++..+||+.+|++ ..-+-.-+- +.-..|+|+++
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 4789999999999997 777766666 77889999886
No 211
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=29.66 E-value=67 Score=24.50 Aligned_cols=27 Identities=15% Similarity=0.035 Sum_probs=23.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+- +|.
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 358999999999998 999998877 665
No 212
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=29.61 E-value=74 Score=26.19 Aligned_cols=46 Identities=20% Similarity=0.214 Sum_probs=36.9
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~ 142 (177)
-|+-.|+.+....+.++.+++++.++++ ...+-.=+. +.=..|++.
T Consensus 5 eR~~~Il~~l~~~g~v~v~eLa~~~~VS-~~TIRRDL~-~Le~~g~l~ 50 (253)
T COG1349 5 ERHQKILELLKEKGKVSVEELAELFGVS-EMTIRRDLN-ELEEQGLLL 50 (253)
T ss_pred HHHHHHHHHHHHcCcEEHHHHHHHhCCC-HHHHHHhHH-HHHHCCcEE
Confidence 4788899999999999999999999997 777765555 555566654
No 213
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=29.47 E-value=68 Score=24.55 Aligned_cols=27 Identities=7% Similarity=0.169 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.++++ ...|...+- +|.
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 457999999999998 899998877 664
No 214
>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=29.24 E-value=69 Score=25.71 Aligned_cols=27 Identities=7% Similarity=0.084 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+- +|.
T Consensus 197 eg~s~~EIA~~Lgis-~~tV~~~l~-ra~ 223 (234)
T TIGR02835 197 TEKTQKEVADMLGIS-QSYISRLEK-RIL 223 (234)
T ss_pred CCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 579999999999998 999988765 543
No 215
>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=29.23 E-value=49 Score=22.56 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=17.2
Q ss_pred HHhhccccCCcccChHHHHHHcCCC
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVT 122 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~ 122 (177)
+..+.-...+++.||.+||+.++-+
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 4444445679999999999999954
No 216
>PF14493 HTH_40: Helix-turn-helix domain
Probab=28.98 E-value=84 Score=21.43 Aligned_cols=30 Identities=17% Similarity=0.174 Sum_probs=26.3
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCc
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai~~gL 140 (177)
-.|.++||+.-++. ...|+.-++ +++..|-
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 37899999999997 899999999 8987775
No 217
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=28.91 E-value=64 Score=24.54 Aligned_cols=27 Identities=15% Similarity=0.406 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+= +|.
T Consensus 152 ~g~s~~eIA~~lgis-~~~v~~~l~-Rar 178 (187)
T PRK12534 152 EGITYEELAARTDTP-IGTVKSWIR-RGL 178 (187)
T ss_pred cCCCHHHHHHHhCCC-hhHHHHHHH-HHH
Confidence 468999999999998 899988776 654
No 218
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=28.91 E-value=1.8e+02 Score=24.78 Aligned_cols=79 Identities=13% Similarity=0.142 Sum_probs=50.1
Q ss_pred HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE---e-ecCCCCCcchHHH
Q 030471 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ---F-AAGRDLRPGQLGS 169 (177)
Q Consensus 94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~---~-~~~R~~~~~~~~~ 169 (177)
-.|++.++.+...++.+|=.++|+.++++ ...+..=+= ..-..|+ --....-.+.-++. . ..|..|++++..+
T Consensus 7 a~RL~~ii~~L~~~~~vta~~lA~~~~VS-~RTi~RDi~-~L~~~gv-PI~~e~G~~~gy~~~~~~~L~pl~ft~~E~~A 83 (311)
T COG2378 7 AERLLQIIQILRAKETVTAAELADEFEVS-VRTIYRDIA-TLRAAGV-PIEGERGKGGGYRLRPGFKLPPLMFTEEEAEA 83 (311)
T ss_pred HHHHHHHHHHHHhCccchHHHHHHhcCCC-HHHHHHHHH-HHHHCCC-CeEeecCCCccEEEccCCCCCcccCCHHHHHH
Confidence 34678888877777779999999999997 777765432 2223443 32222221233332 2 4678899999888
Q ss_pred HHHHhc
Q 030471 170 MIQTLS 175 (177)
Q Consensus 170 L~~~L~ 175 (177)
+.-.+.
T Consensus 84 l~~~l~ 89 (311)
T COG2378 84 LLLALR 89 (311)
T ss_pred HHHHHH
Confidence 765543
No 219
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=28.82 E-value=68 Score=25.09 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=23.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.++++ ...|...+= +|.
T Consensus 167 ~~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 194 (206)
T PRK12526 167 FQELSQEQLAQQLNVP-LGTVKSRLR-LAL 194 (206)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999987766 554
No 220
>PRK09483 response regulator; Provisional
Probab=28.25 E-value=1e+02 Score=23.20 Aligned_cols=21 Identities=14% Similarity=0.408 Sum_probs=16.4
Q ss_pred cChHHHHHHcCCCChHHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFL 131 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lv 131 (177)
.+..+||+.++++ ...|+..+
T Consensus 164 ~~~~~Ia~~l~is-~~TV~~~~ 184 (217)
T PRK09483 164 QKVNEISEQLNLS-PKTVNSYR 184 (217)
T ss_pred CCHHHHHHHhCCC-HHHHHHHH
Confidence 6788999999996 77776543
No 221
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=28.24 E-value=73 Score=23.83 Aligned_cols=27 Identities=26% Similarity=0.352 Sum_probs=22.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+- +|.
T Consensus 135 ~g~s~~eIA~~lg~s-~~tv~~~l~-Rar 161 (175)
T PRK12518 135 EDLPQKEIAEILNIP-VGTVKSRLF-YAR 161 (175)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 457899999999998 899987766 553
No 222
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=28.22 E-value=72 Score=24.25 Aligned_cols=27 Identities=26% Similarity=0.278 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+= +|.
T Consensus 143 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 169 (186)
T PRK05602 143 QGLSNIEAAAVMDIS-VDALESLLA-RGR 169 (186)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HHH
Confidence 468999999999998 899988766 554
No 223
>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=28.11 E-value=65 Score=26.91 Aligned_cols=28 Identities=14% Similarity=-0.020 Sum_probs=23.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.++++ ...|...+- +|.
T Consensus 156 ~~g~s~~EIA~~lgis-~~tV~~~l~-Rar 183 (324)
T TIGR02960 156 VLGWRAAETAELLGTS-TASVNSALQ-RAR 183 (324)
T ss_pred HhCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3468999999999998 999998887 764
No 224
>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=27.94 E-value=42 Score=24.35 Aligned_cols=20 Identities=5% Similarity=0.152 Sum_probs=16.7
Q ss_pred cccChHHHHHHcCCCChHHHH
Q 030471 108 KVLPYDELMEELDVTNVRELE 128 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE 128 (177)
...||.|||+.+|++ ...|.
T Consensus 122 ~~~s~~EIA~~l~is-~~tV~ 141 (142)
T TIGR03209 122 EDMKEIDIAKKLHIS-RQSVY 141 (142)
T ss_pred cCCCHHHHHHHHCcC-HHhhc
Confidence 458999999999997 77663
No 225
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.63 E-value=75 Score=24.49 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=22.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+= +|+
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 458999999999998 888887665 554
No 226
>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=27.31 E-value=1e+02 Score=17.36 Aligned_cols=26 Identities=23% Similarity=0.365 Sum_probs=21.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHh
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~a 135 (177)
...++.+||+.++++ ...|-.++- ++
T Consensus 25 ~~~~~~~ia~~~~~s-~~~i~~~~~-~~ 50 (55)
T cd06171 25 EGLSYEEIAEILGIS-RSTVRQRLH-RA 50 (55)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HH
Confidence 347999999999998 888887765 54
No 227
>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=27.18 E-value=1.7e+02 Score=20.14 Aligned_cols=46 Identities=9% Similarity=0.043 Sum_probs=36.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
....+|-.+||+.++++ ...|-..+= +....|+|.- ..-.++|-|+
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 46688999999999997 788888776 8889999973 3335677665
No 228
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=26.94 E-value=80 Score=23.33 Aligned_cols=27 Identities=30% Similarity=0.340 Sum_probs=22.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...++.+||+.++++ ...|...+= +|.
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 899988776 654
No 229
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=26.87 E-value=83 Score=23.24 Aligned_cols=27 Identities=19% Similarity=0.270 Sum_probs=23.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
.-.|+.+||+.+|++ ...|...+- +|.
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 568999999999998 899988776 664
No 230
>PRK00118 putative DNA-binding protein; Validated
Probab=26.86 E-value=87 Score=22.50 Aligned_cols=26 Identities=19% Similarity=0.238 Sum_probs=22.1
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
..|+.+||+.+|++ ...|..++- +|.
T Consensus 33 g~S~~EIAe~lGIS-~~TV~r~L~-RAr 58 (104)
T PRK00118 33 DYSLGEIAEEFNVS-RQAVYDNIK-RTE 58 (104)
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 68999999999998 888888776 653
No 231
>PF06619 DUF1149: Protein of unknown function (DUF1149); InterPro: IPR009530 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2HNG_A 2O2A_C.
Probab=26.83 E-value=32 Score=25.77 Aligned_cols=35 Identities=14% Similarity=0.253 Sum_probs=22.8
Q ss_pred ccEEEecCCCCEEEEEeecCCCCCcchHHHHHHHh
Q 030471 140 IVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTL 174 (177)
Q Consensus 140 LI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~~L 174 (177)
.|+|.|.|+++...=..-.+-+|+.++|+.|..=|
T Consensus 68 viSG~IsQiv~i~~r~~~~~sd~~~~e~~~Ls~PL 102 (127)
T PF06619_consen 68 VISGVISQIVHIKDRYVGEPSDLSQEEVELLSRPL 102 (127)
T ss_dssp EEEEEEEEEEEEET---SSGGGS-HHHHHHHHHHH
T ss_pred EEEeeeeeeeeeeccccCChhhcCHHHHHHHHHHH
Confidence 37899988655443234577889999999987543
No 232
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=26.49 E-value=76 Score=25.00 Aligned_cols=27 Identities=22% Similarity=0.324 Sum_probs=22.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+- +|.
T Consensus 163 ~g~s~~EIAe~lgis-~~tV~~~l~-RAr 189 (206)
T PRK12544 163 IELETNEICHAVDLS-VSNLNVLLY-RAR 189 (206)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999998 999998766 553
No 233
>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=26.45 E-value=77 Score=21.51 Aligned_cols=38 Identities=8% Similarity=0.003 Sum_probs=24.8
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcC
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTG 139 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~g 139 (177)
+..+.-...+++.||.+||+.++-+. . -..|= .|+..+
T Consensus 8 ~~~l~~IP~G~v~TYg~iA~~~g~p~--~-~RaVg-~al~~n 45 (80)
T TIGR00589 8 WQALRTIPYGETKSYGQLAARIGNPK--A-VRAVG-GANGRN 45 (80)
T ss_pred HHHHhCCCCCCcCCHHHHHHHhCCCC--h-HHHHH-HHHHhC
Confidence 34444445799999999999999761 2 22344 566544
No 234
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=26.39 E-value=81 Score=24.07 Aligned_cols=27 Identities=11% Similarity=0.295 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
.-.|+++||+.+|++ ...|...+- +|.
T Consensus 153 ~g~s~~eIA~~lgis-~~tv~~~l~-Rar 179 (193)
T PRK11923 153 DGLSYEDIASVMQCP-VGTVRSRIF-RAR 179 (193)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 457999999999998 999998776 653
No 235
>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=26.37 E-value=1.7e+02 Score=19.97 Aligned_cols=49 Identities=12% Similarity=0.209 Sum_probs=36.4
Q ss_pred HHHHHhhccc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 030471 95 LKQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (177)
Q Consensus 95 lr~LtllsL~-~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI 145 (177)
.|.|+-+-.. .+..-++.+.|.+..+++ ..+++..+- +.+..|+|.-+.
T Consensus 9 ~rvL~aiE~gmk~hE~VP~~~I~~~s~l~-~~~~~~~L~-~L~~~kLv~~~~ 58 (82)
T PF09202_consen 9 FRVLRAIEMGMKNHEWVPLELIEKISGLS-EGEVEKRLK-RLVKLKLVSRRN 58 (82)
T ss_dssp HHHHHHHHTTTTT-SSEEHHHHHHHHT---HHHHHHHHH-HHHHTTSEEEE-
T ss_pred HHHHHHHHHcccCCccCCHHHHHHHhCcC-HHHHHHHHH-HHHhcCCccccC
Confidence 4555555443 467889999999999998 999999888 999999998744
No 236
>PRK04217 hypothetical protein; Provisional
Probab=26.03 E-value=87 Score=22.74 Aligned_cols=24 Identities=17% Similarity=0.093 Sum_probs=19.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
..+|+++||+.++++ ...|...+=
T Consensus 57 eGlS~~EIAk~LGIS-~sTV~r~L~ 80 (110)
T PRK04217 57 EGLTQEEAGKRMGVS-RGTVWRALT 80 (110)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH
Confidence 356999999999997 777765543
No 237
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=25.91 E-value=1.3e+02 Score=22.97 Aligned_cols=43 Identities=21% Similarity=0.271 Sum_probs=33.8
Q ss_pred HhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 99 tllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
+|..+...+..+.-.+||+.|+|. .-.|=.++= +.-+.|+|+=
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 344444578899999999999997 788877777 8888888753
No 238
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.90 E-value=86 Score=23.78 Aligned_cols=27 Identities=19% Similarity=0.174 Sum_probs=22.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+= +|.
T Consensus 142 ~g~s~~EIA~~l~is-~~tv~~~l~-Ra~ 168 (179)
T PRK09415 142 EELSIKEIAEVTGVN-ENTVKTRLK-KAK 168 (179)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 457999999999997 999988776 654
No 239
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.82 E-value=82 Score=25.20 Aligned_cols=27 Identities=15% Similarity=0.201 Sum_probs=23.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|+
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 457999999999998 999998877 665
No 240
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=25.76 E-value=76 Score=26.35 Aligned_cols=28 Identities=14% Similarity=0.185 Sum_probs=23.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||+|||+.++++ +..|...+- +|.
T Consensus 129 ~~g~s~~EIA~~lg~s-~~tVk~~l~-RAr 156 (293)
T PRK09636 129 VFGVPFDEIASTLGRS-PAACRQLAS-RAR 156 (293)
T ss_pred HhCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3468999999999997 999998887 764
No 241
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=25.58 E-value=75 Score=24.90 Aligned_cols=31 Identities=26% Similarity=0.461 Sum_probs=26.0
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHH
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVREL 127 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~ev 127 (177)
|+-.|+.+...++.++..++++.++++ ...+
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~vS-~~Ti 38 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFGVS-IQTI 38 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHCcC-HHHH
Confidence 777788888889999999999999997 5443
No 242
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.40 E-value=1.1e+02 Score=21.60 Aligned_cols=30 Identities=17% Similarity=0.257 Sum_probs=24.8
Q ss_pred ChHHHHHHcCC-CChHHHHHHHHHHhHhcCccE
Q 030471 111 PYDELMEELDV-TNVRELEDFLINECMYTGIVR 142 (177)
Q Consensus 111 s~~~I~~~l~i-~~~~evE~lvI~~ai~~gLI~ 142 (177)
|+.+||+.++| + ...+-.|++ .+...+...
T Consensus 26 sv~~vAr~~gv~~-~~~l~~W~~-~~~~~~~~~ 56 (116)
T COG2963 26 TVSEVAREFGIVS-ATQLYKWRI-QLQKGGGLA 56 (116)
T ss_pred cHHHHHHHhCCCC-hHHHHHHHH-HHHHccccc
Confidence 99999999996 6 889999999 877655443
No 243
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=25.34 E-value=79 Score=22.18 Aligned_cols=23 Identities=17% Similarity=0.300 Sum_probs=18.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDF 130 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~l 130 (177)
-..+|-++||..|+++ ...||..
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 4468889999999996 8898874
No 244
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.28 E-value=2.3e+02 Score=21.44 Aligned_cols=70 Identities=17% Similarity=0.198 Sum_probs=47.2
Q ss_pred HHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHHHH
Q 030471 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQT 173 (177)
Q Consensus 94 Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~~ 173 (177)
.+|.+.+...- ..-.|..+||+.++++ ...|..||= +-=..|+. - .. ...+=.|+-++.+|.+.+.+.
T Consensus 8 ~~R~~~~~~~~--~~G~S~re~Ak~~gvs-~sTvy~wv~-r~~e~G~~-l-~~------~~~~GrP~kl~~~q~~~l~e~ 75 (138)
T COG3415 8 DLRERVVDAVV--GEGLSCREAAKRFGVS-ISTVYRWVR-RYRETGLD-L-PP------KPRKGRPRKLSEEQLEILLER 75 (138)
T ss_pred HHHHHHHHHHH--HcCccHHHHHHHhCcc-HHHHHHHHH-Hhcccccc-c-cC------ccCCCCCcccCHHHHHHHHHH
Confidence 44554444432 3348999999999997 999999977 65444554 1 11 123457888888888887766
Q ss_pred hc
Q 030471 174 LS 175 (177)
Q Consensus 174 L~ 175 (177)
+.
T Consensus 76 ~~ 77 (138)
T COG3415 76 LR 77 (138)
T ss_pred Hh
Confidence 54
No 245
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=25.27 E-value=1.2e+02 Score=24.26 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=25.5
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
..++.+...| .|..+||+.++++ ...|+..+- +.+
T Consensus 139 rEVLrLLAqG--kTnKEIAe~L~IS-~rTVkth~s-rIm 173 (198)
T PRK15201 139 RHLLKLIASG--YHLSETAALLSLS-EEQTKSLRR-SIM 173 (198)
T ss_pred HHHHHHHHCC--CCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3444444444 6799999999997 899998776 543
No 246
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.97 E-value=90 Score=23.82 Aligned_cols=28 Identities=7% Similarity=0.033 Sum_probs=22.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.++++ ...|...+- +|.
T Consensus 145 ~~~~s~~eIA~~lgis-~~tV~~~l~-Rar 172 (189)
T PRK12515 145 YHEKSVEEVGEIVGIP-ESTVKTRMF-YAR 172 (189)
T ss_pred HcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 3568999999999997 889887765 543
No 247
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=24.87 E-value=1.2e+02 Score=23.89 Aligned_cols=32 Identities=3% Similarity=0.089 Sum_probs=23.8
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
..++.+...| .|..+||+.|+++ ...|+..+=
T Consensus 143 ~eVL~lla~G--~snkeIA~~L~iS-~~TVk~h~~ 174 (207)
T PRK15411 143 SSMLRMWMAG--QGTIQISDQMNIK-AKTVSSHKG 174 (207)
T ss_pred HHHHHHHHcC--CCHHHHHHHcCCC-HHHHHHHHH
Confidence 3444444444 6889999999997 899998765
No 248
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=24.86 E-value=1.1e+02 Score=24.38 Aligned_cols=35 Identities=11% Similarity=0.175 Sum_probs=25.8
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
..++.+...+ .|+.+||+.++++ ...|+..+- +++
T Consensus 161 ~~Vl~l~~~G--~s~~eIA~~L~iS-~~TVk~~~~-~i~ 195 (216)
T PRK10100 161 KEILNKLRIG--ASNNEIARSLFIS-ENTVKTHLY-NLF 195 (216)
T ss_pred HHHHHHHHcC--CCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3344443443 7899999999997 999998877 654
No 249
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=24.84 E-value=2.9e+02 Score=20.40 Aligned_cols=53 Identities=8% Similarity=0.185 Sum_probs=39.7
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHHHH
Q 030471 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQT 173 (177)
Q Consensus 111 s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~~~ 173 (177)
-|.+|+++|+-+ .+-|=.++. .-++ ..|+||.. +++.|+. .++.++++.+-++
T Consensus 36 Nf~dI~~~L~R~-p~~~~ky~~-~ELg---t~~~id~~-~~lii~G----~~~~~~i~~~L~~ 88 (125)
T PF01873_consen 36 NFVDICKALNRD-PEHVLKYFG-KELG---TQGSIDGK-GRLIING----RFSSKQIQDLLDK 88 (125)
T ss_dssp THHHHHHHHTSS-HHHHHHHHH-HHSS---SEEEEETT-TEEEEES----SSSCCHHHHHHHH
T ss_pred cHHHHHHHHCCC-HHHHHHHHH-HHHC---CceEECCC-CEEEEEE----ecCHHHHHHHHHH
Confidence 799999999987 788877777 4443 67999988 7777764 4556677776654
No 250
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.76 E-value=86 Score=25.33 Aligned_cols=28 Identities=25% Similarity=0.344 Sum_probs=23.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.+|++ ...|...+= +|.
T Consensus 185 ~eg~s~~EIA~~Lgis-~~tVk~~l~-RAr 212 (233)
T PRK12538 185 HENMSNGEIAEVMDTT-VAAVESLLK-RGR 212 (233)
T ss_pred hcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 3568999999999998 999988776 664
No 251
>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=24.64 E-value=97 Score=22.35 Aligned_cols=27 Identities=26% Similarity=0.496 Sum_probs=22.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.+|++ ...|...+- +|.
T Consensus 128 ~~~~~~eIA~~lgis-~~tv~~~~~-ra~ 154 (161)
T TIGR02985 128 EGKSYKEIAEELGIS-VKTVEYHIS-KAL 154 (161)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 467999999999997 899988776 653
No 252
>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=24.62 E-value=82 Score=18.91 Aligned_cols=23 Identities=26% Similarity=0.336 Sum_probs=19.2
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.-..++||..++++ ..+|..|.-
T Consensus 27 ~~~~~~la~~~~l~-~~qV~~WF~ 49 (59)
T cd00086 27 REEREELAKELGLT-ERQVKIWFQ 49 (59)
T ss_pred HHHHHHHHHHHCcC-HHHHHHHHH
Confidence 34567899999998 999999987
No 253
>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=24.50 E-value=96 Score=25.37 Aligned_cols=32 Identities=22% Similarity=0.350 Sum_probs=26.0
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
+.++.+|+.+|+..||+.|..|+-.-++ -+|+
T Consensus 51 ~~G~pVSWkeVms~~gL~s~~Ela~AL~-Tsig 82 (217)
T PF10924_consen 51 ENGKPVSWKEVMSKCGLNSYKELALALM-TSIG 82 (217)
T ss_pred hcCCcccHHHHHHHcCCCcHHHHHHHHH-HHhh
Confidence 5689999999999999998888876666 4553
No 254
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=24.39 E-value=89 Score=23.23 Aligned_cols=27 Identities=22% Similarity=0.356 Sum_probs=22.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~a 135 (177)
-...||.+||+.++++ ...|...+= +|
T Consensus 122 ~~g~s~~eIA~~lgis-~~tv~~~l~-Ra 148 (165)
T PRK09644 122 VHELTYEEAASVLDLK-LNTYKSHLF-RG 148 (165)
T ss_pred HhcCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 3568999999999997 999987765 54
No 255
>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=24.31 E-value=95 Score=23.65 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=22.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~a 135 (177)
-...||.+||+.+++| ...|...+- +|
T Consensus 163 ~~~~s~~eIA~~l~~s-~~tV~~~l~-r~ 189 (198)
T TIGR02859 163 LDGKSYQEIACDLNRH-VKSIDNALQ-RV 189 (198)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 3468999999999998 888987665 54
No 256
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=24.19 E-value=1.6e+02 Score=22.49 Aligned_cols=36 Identities=19% Similarity=0.157 Sum_probs=18.1
Q ss_pred CchHHHHHHHHHHhhcccc-CCcccChHHHHHHcCCC
Q 030471 87 LVPDQVLKLKQLTVLTLAE-TNKVLPYDELMEELDVT 122 (177)
Q Consensus 87 L~~~~~~Klr~LtllsL~~-~~~~is~~~I~~~l~i~ 122 (177)
|+..+.+-..+|..-.+.. ++..-|.++||+++||+
T Consensus 11 L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis 47 (142)
T PF13022_consen 11 LTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGIS 47 (142)
T ss_dssp S-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-
T ss_pred cCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCC
Confidence 4544433333344444443 45789999999999996
No 257
>PRK09191 two-component response regulator; Provisional
Probab=24.18 E-value=91 Score=24.63 Aligned_cols=28 Identities=25% Similarity=0.192 Sum_probs=22.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.++++ ...|...+- +|.
T Consensus 102 ~~~~s~~eIA~~l~~s-~~tV~~~l~-ra~ 129 (261)
T PRK09191 102 LEGFSVEEAAEILGVD-PAEAEALLD-DAR 129 (261)
T ss_pred HhcCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3468999999999998 888887776 665
No 258
>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=24.17 E-value=98 Score=23.29 Aligned_cols=25 Identities=16% Similarity=0.194 Sum_probs=20.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
-...++++||+.++++ ...|...+-
T Consensus 114 ~~g~s~~eIA~~lgis-~~tV~~~l~ 138 (170)
T TIGR02959 114 LEGLSQQEIAEKLGLS-LSGAKSRVQ 138 (170)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH
Confidence 3568999999999998 888887655
No 259
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=24.09 E-value=2.3e+02 Score=19.09 Aligned_cols=43 Identities=19% Similarity=0.139 Sum_probs=35.6
Q ss_pred HHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 030471 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (177)
Q Consensus 113 ~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~ 157 (177)
.+|++.++++ ...|=..|= +....|+|+=..|..+++..+...
T Consensus 40 ~~la~~l~i~-~~~vt~~l~-~Le~~glv~r~~~~~DrR~~~l~l 82 (126)
T COG1846 40 KELAERLGLD-RSTVTRLLK-RLEDKGLIERLRDPEDRRAVLVRL 82 (126)
T ss_pred HHHHHHHCCC-HHHHHHHHH-HHHHCCCeeecCCccccceeeEEE
Confidence 9999999997 788887766 888999999999998875544443
No 260
>PF09218 DUF1959: Domain of unknown function (DUF1959); InterPro: IPR012056 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. This entry represents proteins that are predicted to be the hydrophilic EhaM subunits of Eha-type energy-converting [NiFe] hydrogenase complexes.; PDB: 1NXH_B.
Probab=24.04 E-value=36 Score=25.14 Aligned_cols=21 Identities=38% Similarity=0.520 Sum_probs=17.4
Q ss_pred HHHHHHcCCCChHHHHHHHHHHh
Q 030471 113 DELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 113 ~~I~~~l~i~~~~evE~lvI~~a 135 (177)
..|+++++++ .++|+..+| +.
T Consensus 17 ~plSk~lgi~-~ee~~~ili-~~ 37 (117)
T PF09218_consen 17 IPLSKELGIS-IEEFIDILI-EK 37 (117)
T ss_dssp TTTTTTGGGT-HHHHHHHHH-HH
T ss_pred HHHHHHhCcC-HHHHHHHHH-Hh
Confidence 3478899998 999999999 64
No 261
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.32 E-value=1e+02 Score=23.87 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=23.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...|+++||+.+|++ ...|...+- +|.
T Consensus 127 ~~g~s~~EIA~~LgiS-~~tVk~~l~-Rar 154 (188)
T PRK12546 127 ASGFSYEEAAEMCGVA-VGTVKSRAN-RAR 154 (188)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 899987776 553
No 262
>PRK13239 alkylmercury lyase; Provisional
Probab=23.21 E-value=1.1e+02 Score=24.90 Aligned_cols=47 Identities=23% Similarity=0.271 Sum_probs=33.0
Q ss_pred HHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 030471 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (177)
Q Consensus 98 LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~ 151 (177)
++|+.+...++.++-.++|+.++.+ .++|+..+- ++. .-.+|...+.
T Consensus 25 ~~llr~la~G~pvt~~~lA~~~~~~-~~~v~~~L~--~l~----~~~~d~~g~i 71 (206)
T PRK13239 25 VPLLRLLAKGRPVSVTTLAAALGWP-VEEVEAVLE--AMP----DTEYDEDGRI 71 (206)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCC-HHHHHHHHH--hCC----CeEECCCCCE
Confidence 3444444489999999999999998 999997655 432 2256774443
No 263
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.17 E-value=1e+02 Score=23.15 Aligned_cols=27 Identities=22% Similarity=0.238 Sum_probs=22.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|-..+- +|.
T Consensus 151 ~g~s~~eIA~~lgis-~~~v~~~l~-Rar 177 (187)
T TIGR02948 151 EDLSLKEISEILDLP-VGTVKTRIH-RGR 177 (187)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999997 888887766 653
No 264
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=23.16 E-value=1e+02 Score=23.13 Aligned_cols=27 Identities=22% Similarity=0.238 Sum_probs=22.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+= +|.
T Consensus 151 ~~~s~~eIA~~lgis-~~~v~~~l~-Rar 177 (187)
T PRK09641 151 EDLSLKEISEILDLP-VGTVKTRIH-RGR 177 (187)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 578999999999998 888887655 543
No 265
>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=23.06 E-value=1.1e+02 Score=25.66 Aligned_cols=29 Identities=10% Similarity=0.218 Sum_probs=25.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
....|+++|++.+|++ ...|..+.- +|+.
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 5689999999999997 999999888 7764
No 266
>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=22.94 E-value=95 Score=25.75 Aligned_cols=28 Identities=14% Similarity=0.304 Sum_probs=23.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
....||.+||+.+|++ ...|...+- +|+
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 4568999999999998 999998877 665
No 267
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=22.91 E-value=2.8e+02 Score=21.14 Aligned_cols=49 Identities=18% Similarity=0.245 Sum_probs=37.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe--cCCCCEEEEEe
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL--DQLRRCFEVQF 156 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkI--Dq~~~~v~v~~ 156 (177)
.++.++=++||+.+|++ ..+|-..+= +....||+.-+= |..+|...-.|
T Consensus 25 ~~~~~tdEeLa~~Lgi~-~~~VRk~L~-~L~e~~Lv~~~r~r~~~~gw~~Y~w 75 (158)
T TIGR00373 25 IKGEFTDEEISLELGIK-LNEVRKALY-ALYDAGLADYKRRKDDETGWYEYTW 75 (158)
T ss_pred ccCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCceeeeeeecCCCcEEEEE
Confidence 45689999999999997 999999998 999999994332 23334444444
No 268
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=22.88 E-value=1e+02 Score=18.32 Aligned_cols=23 Identities=17% Similarity=0.283 Sum_probs=19.3
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 030471 109 VLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 109 ~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.-..++||+.++++ ..+|..|..
T Consensus 27 ~~~~~~la~~~~l~-~~qV~~WF~ 49 (56)
T smart00389 27 REEREELAAKLGLS-ERQVKVWFQ 49 (56)
T ss_pred HHHHHHHHHHHCcC-HHHHHHhHH
Confidence 44567899999998 999999987
No 269
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.70 E-value=1.1e+02 Score=29.62 Aligned_cols=58 Identities=24% Similarity=0.306 Sum_probs=43.9
Q ss_pred HHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE----EEecCCCCEEEEE
Q 030471 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR----GKLDQLRRCFEVQ 155 (177)
Q Consensus 96 r~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~----gkIDq~~~~v~v~ 155 (177)
-++.+..+++++.+++|++|.+..+++ .+++-..+. ....++++. ++.-.++-+++++
T Consensus 609 ~q~~vfll~n~~e~lt~eei~e~T~l~-~~dl~~~L~-sl~~ak~~~l~~~~~~~~p~~~fy~n 670 (773)
T COG5647 609 YQLLVFLLFNDHEELTFEEILELTKLS-TDDLKRVLQ-SLSCAKLVVLLKDDKLVSPNTKFYVN 670 (773)
T ss_pred HHHHHHHHhcCccceeHHHHHhhcCCC-hhhHHHHHH-HHHhhheeeeccccccCCCCceEEEc
Confidence 346677778899999999999999998 899988887 777776653 3334555666665
No 270
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=22.63 E-value=1.5e+02 Score=24.24 Aligned_cols=56 Identities=18% Similarity=0.143 Sum_probs=38.7
Q ss_pred HHHHhhccc-cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 030471 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (177)
Q Consensus 96 r~LtllsL~-~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~ 155 (177)
|-+.++... ..+..++..+|++.++++ ...+=.++- .....|++.- |...++..+.
T Consensus 12 ral~iL~~l~~~~~~ls~~eia~~lgl~-kstv~RlL~-tL~~~g~v~~--~~~~~~Y~Lg 68 (263)
T PRK09834 12 RGLMVLRALNRLDGGATVGLLAELTGLH-RTTVRRLLE-TLQEEGYVRR--SASDDSFRLT 68 (263)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE--ecCCCcEEEc
Confidence 335555433 445569999999999998 888888887 7888898863 2233444443
No 271
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.49 E-value=1.1e+02 Score=23.64 Aligned_cols=26 Identities=8% Similarity=-0.024 Sum_probs=21.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHh
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINEC 135 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~a 135 (177)
...||++||+.++++ ...|..-+= +|
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 458999999999998 899987764 44
No 272
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.42 E-value=1e+02 Score=23.72 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=22.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||++||+.+|++ ...|...+- +|.
T Consensus 169 e~~s~~EIA~~lgis-~~tV~~~l~-rar 195 (208)
T PRK08295 169 DGKSYQEIAEELNRH-VKSIDNALQ-RVK 195 (208)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 358999999999998 899987665 543
No 273
>cd04894 ACT_ACR-like_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.33 E-value=2.4e+02 Score=18.66 Aligned_cols=49 Identities=16% Similarity=0.149 Sum_probs=32.9
Q ss_pred HHHHHHHHHhHhcCccEEEecCCCCEEEE-EeecCCCCC-cchHHHHHHHhcc
Q 030471 126 ELEDFLINECMYTGIVRGKLDQLRRCFEV-QFAAGRDLR-PGQLGSMIQTLSN 176 (177)
Q Consensus 126 evE~lvI~~ai~~gLI~gkIDq~~~~v~v-~~~~~R~~~-~~~~~~L~~~L~~ 176 (177)
++=..+. + .+..+.+|-+.-..+=-+| -|+.||.=. +-.|..|++||.+
T Consensus 16 dlcr~il-~-fGl~i~rgd~sTDGkWCyiv~wVv~~~~~~~~rW~lLK~RL~~ 66 (69)
T cd04894 16 DLCRIIL-E-FGLNITRGDDSTDGRWCYIVFWVVPRPPSIKVRWDLLKNRLMS 66 (69)
T ss_pred HHHHHHH-H-hceEEEecccccCCcEEEEEEEEecCCCCCcccHHHHHHHHHh
Confidence 3444445 3 5666677777666665554 599998743 4789999999863
No 274
>PRK06930 positive control sigma-like factor; Validated
Probab=22.22 E-value=1.1e+02 Score=23.74 Aligned_cols=27 Identities=15% Similarity=0.310 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+- +|.
T Consensus 129 eg~s~~EIA~~lgiS-~~tVk~~l~-Ra~ 155 (170)
T PRK06930 129 YGLSYSEIADYLNIK-KSTVQSMIE-RAE 155 (170)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999997 999998876 654
No 275
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=22.16 E-value=1.1e+02 Score=22.47 Aligned_cols=28 Identities=14% Similarity=0.115 Sum_probs=22.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-..+|+++||+.+|++ ...|...+= +|.
T Consensus 126 ~~~~s~~eIA~~lgis-~~tv~~~l~-Rar 153 (161)
T PRK12541 126 YYGFSYKEIAEMTGLS-LAKVKIELH-RGR 153 (161)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 888887766 553
No 276
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.03 E-value=2.1e+02 Score=17.78 Aligned_cols=37 Identities=8% Similarity=0.007 Sum_probs=24.2
Q ss_pred HHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHH
Q 030471 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 95 lr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI 132 (177)
.|.-.++.....+ .++.++||..+|+.|...+-...-
T Consensus 37 ~r~~~a~~~l~~~-~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 37 RRLERARRLLRDT-DLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HHHHHHHHHHHcC-CCCHHHHHHHhCCCChHHHHHHHH
Confidence 3443344444444 899999999999965666655443
No 277
>PF14754 IFR3_antag: Papain-like auto-proteinase
Probab=21.84 E-value=40 Score=26.50 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=18.4
Q ss_pred cCCCceehhhhhcchhhhhccC
Q 030471 35 SQPSLFAFSEILAVPNIAEFEG 56 (177)
Q Consensus 35 ~~p~i~~f~eLl~~~~v~~L~~ 56 (177)
.-...|||-||+++|+...|+-
T Consensus 83 kvtgrynflellqhpafaqlrv 104 (249)
T PF14754_consen 83 KVTGRYNFLELLQHPAFAQLRV 104 (249)
T ss_pred hhcchhhHHHHHcCcchhheee
Confidence 4467899999999999988773
No 278
>COG1001 AdeC Adenine deaminase [Nucleotide transport and metabolism]
Probab=21.79 E-value=3e+02 Score=25.94 Aligned_cols=43 Identities=21% Similarity=0.376 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhcCCCceehhhhhcchhhhhccCCCchHHHHHHHHHh
Q 030471 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFA 70 (177)
Q Consensus 24 ~~a~~~i~~aL~~p~i~~f~eLl~~~~v~~L~~~~~~~l~~LL~if~ 70 (177)
....+-+...+..|+++-.+|..+.|.|. .+ +..+++-++.+.
T Consensus 157 ~l~a~~i~e~~~~p~Vigl~E~Mn~pgVi--~~--D~~~l~kl~a~~ 199 (584)
T COG1001 157 ELTAEDIKELLEHPEVIGLGEMMNFPGVI--EG--DPDMLAKLEAAR 199 (584)
T ss_pred eecHHHHHHHhhCCCccchhhhcCCchhc--cC--CHHHHHHHHHHH
Confidence 45667788899999999999999999995 22 345666677665
No 279
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=21.78 E-value=2.9e+02 Score=21.32 Aligned_cols=53 Identities=11% Similarity=0.082 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 89 ~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
+.....++..-+-.-...|..++=.++++.++|+ ..-|-+-+. ..-..|+|+-
T Consensus 14 ~~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVS-RtpVReAL~-~L~~eGlv~~ 66 (212)
T TIGR03338 14 TLVQDEIERAILSGELPPGAKLNESDIAARLGVS-RGPVREAFR-ALEEAGLVRN 66 (212)
T ss_pred HHHHHHHHHHHHcCCCCCCCEecHHHHHHHhCCC-hHHHHHHHH-HHHHCCCEEE
Confidence 3444566665444444567788999999999997 888877777 7888999874
No 280
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=21.64 E-value=3.2e+02 Score=21.58 Aligned_cols=65 Identities=20% Similarity=0.275 Sum_probs=37.7
Q ss_pred chHHHHHHHHHhcCChhhHhhhhC-CCCCCchHHHHHHHHHH-hhccccCCcccChHHHHHHcCCCChHHH
Q 030471 59 NSKYLDMLRLFAHGTWSDYKNNAG-HLPQLVPDQVLKLKQLT-VLTLAETNKVLPYDELMEELDVTNVREL 127 (177)
Q Consensus 59 ~~~l~~LL~if~~G~~~~~~~~~~-~~~~L~~~~~~Klr~Lt-llsL~~~~~~is~~~I~~~l~i~~~~ev 127 (177)
.+.+-+++.-+..|...++..... .+..+++- .-|... ++.-...+++.||.+||+.++.+ ...|
T Consensus 61 ~~~~~~~l~~~l~g~~~~~~~~~~l~~~g~T~F---q~rV~~~Lv~~IP~G~v~TYgqIA~~~G~a-aRAV 127 (175)
T PRK03887 61 PSDYPELVFKVLIGKISNEEGLEELSFEGLTPF---ERKVYEWLTKNVKRGEVITYGELAKALNTS-PRAV 127 (175)
T ss_pred ChhHHHHHHHHHcCCccccccCcccCcCCCCHH---HHHHHHHHHHhCCCCCCCcHHHHHHHHCch-HHHH
Confidence 345666777777788776643211 11112221 223333 44344679999999999999964 4333
No 281
>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=21.64 E-value=1.2e+02 Score=21.13 Aligned_cols=27 Identities=26% Similarity=0.357 Sum_probs=22.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...|+.+||+.+|++ ...|...+- ++.
T Consensus 125 ~g~s~~eIA~~l~~s-~~~v~~~~~-~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEILGIS-VGTVKRRLK-RAR 151 (158)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 357999999999997 899988766 553
No 282
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=21.59 E-value=2.9e+02 Score=21.78 Aligned_cols=51 Identities=10% Similarity=-0.141 Sum_probs=41.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~ 159 (177)
+..++-.+|++.+.++ ...|=.++= +.-..|+|.=.-|+.+++......++
T Consensus 57 ~~~itq~eLa~~l~l~-~sTvtr~l~-rLE~kGlI~R~~~~~DrR~~~I~LTe 107 (185)
T PRK13777 57 LKGASISEIAKFGVMH-VSTAFNFSK-KLEERGYLTFSKKEDDKRNTYIELTE 107 (185)
T ss_pred CCCcCHHHHHHHHCCC-HhhHHHHHH-HHHHCCCEEecCCCCCCCeeEEEECH
Confidence 4568999999999997 667777666 88899999999899888776665544
No 283
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=21.50 E-value=3.2e+02 Score=21.40 Aligned_cols=53 Identities=17% Similarity=0.071 Sum_probs=39.3
Q ss_pred hHHHHHHHHHHhhccccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 030471 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (177)
Q Consensus 89 ~~~~~Klr~LtllsL~~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~g 143 (177)
+.....+|..-+-.--..|..++-.++++.++++ ..-|-+-+. ..-..|+|+-
T Consensus 10 ~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVS-RtpVREAL~-~L~~eGlv~~ 62 (224)
T PRK11534 10 LDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALG-VGPLREALS-QLVAERLVTV 62 (224)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEEE
Confidence 3444566665454444567788889999999997 788877777 7888999974
No 284
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.36 E-value=1.2e+02 Score=23.26 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=22.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.++++ ...|...+= +|.
T Consensus 146 ~g~s~~EIAe~lgis-~~~V~~~l~-Ra~ 172 (189)
T PRK06811 146 LGEKIEEIAKKLGLT-RSAIDNRLS-RGR 172 (189)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 358999999999998 899987765 543
No 285
>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=21.25 E-value=1.3e+02 Score=24.16 Aligned_cols=28 Identities=14% Similarity=0.273 Sum_probs=24.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
....|+.+||+.+|++ ...|..+.- +|+
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 5779999999999998 888888876 665
No 286
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=21.09 E-value=1.1e+02 Score=25.37 Aligned_cols=28 Identities=11% Similarity=0.169 Sum_probs=23.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||++||+.++++ ...|...+- +|.
T Consensus 122 ~~g~s~~EIA~~lg~s-~~tVr~~l~-RAr 149 (281)
T TIGR02957 122 VFDYPYEEIASIVGKS-EANCRQLVS-RAR 149 (281)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4568999999999997 999998877 765
No 287
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=21.08 E-value=1.1e+02 Score=24.72 Aligned_cols=28 Identities=11% Similarity=0.267 Sum_probs=23.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
....||++||+.++++ ...|...+- +|+
T Consensus 215 ~~~~s~~EIA~~lgis-~~tV~~~~~-ra~ 242 (251)
T PRK07670 215 KEELTLTEIGQVLNLS-TSRISQIHS-KAL 242 (251)
T ss_pred hcCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 4578999999999998 999988876 665
No 288
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. 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 RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=20.95 E-value=1.2e+02 Score=24.88 Aligned_cols=29 Identities=21% Similarity=0.303 Sum_probs=24.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECMY 137 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai~ 137 (177)
....|+.+||+.++++ ...|..+.- +|+.
T Consensus 234 ~~~~t~~eIA~~lgvS-~~~V~q~~~-~Al~ 262 (270)
T TIGR02392 234 DDKLTLQELAAEYGVS-AERIRQIEK-NAMK 262 (270)
T ss_pred CCCcCHHHHHHHHCCC-HHHHHHHHH-HHHH
Confidence 3468999999999997 899998877 7763
No 289
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.88 E-value=1.2e+02 Score=24.00 Aligned_cols=27 Identities=19% Similarity=0.241 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+- +|+
T Consensus 190 ~~~s~~eIA~~lgis-~~tV~~~~~-ra~ 216 (224)
T TIGR02479 190 EELNLKEIGEVLGLT-ESRVSQIHS-QAL 216 (224)
T ss_pred CCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 467999999999998 899988766 665
No 290
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=20.87 E-value=1.6e+02 Score=22.64 Aligned_cols=22 Identities=9% Similarity=0.226 Sum_probs=19.7
Q ss_pred cChHHHHHHcCCCChHHHHHHHH
Q 030471 110 LPYDELMEELDVTNVRELEDFLI 132 (177)
Q Consensus 110 is~~~I~~~l~i~~~~evE~lvI 132 (177)
.|..+||+.++++ ...|+..+-
T Consensus 166 ~s~~eIA~~l~iS-~~TV~~h~~ 187 (216)
T PRK10840 166 FLVTEIAKKLNRS-IKTISSQKK 187 (216)
T ss_pred CCHHHHHHHHCCC-HHHHHHHHH
Confidence 8899999999997 899998766
No 291
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.82 E-value=1.2e+02 Score=24.66 Aligned_cols=28 Identities=14% Similarity=0.151 Sum_probs=23.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
....|+.+||+.++++ ...|..++- +|+
T Consensus 219 ~~g~s~~eIA~~l~is-~~tV~~~~~-ra~ 246 (257)
T PRK08583 219 IENLSQKETGERLGIS-QMHVSRLQR-QAI 246 (257)
T ss_pred hCCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3567999999999998 999988866 654
No 292
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.75 E-value=2e+02 Score=19.51 Aligned_cols=46 Identities=22% Similarity=0.239 Sum_probs=31.6
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCcchHHHHH
Q 030471 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI 171 (177)
Q Consensus 111 s~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v~~~~~R~~~~~~~~~L~ 171 (177)
+..++|+.||++ ...+-.| . + .|++...-+..+ .|.|+.+++..++
T Consensus 2 ~~~eva~~~gi~-~~tlr~~-~-~---~Gll~~~~~~~g---------~r~y~~~dv~~l~ 47 (100)
T cd00592 2 TIGEVAKLLGVS-VRTLRYY-E-E---KGLLPPERSENG---------YRLYSEEDLERLR 47 (100)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCcCCCcCCCC---------CcccCHHHHHHHH
Confidence 568999999998 8888887 3 3 688765444332 3566666665554
No 293
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=20.66 E-value=1.2e+02 Score=24.30 Aligned_cols=27 Identities=11% Similarity=0.119 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 108 ~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
...||.+||+.+|++ ...|...+- +|+
T Consensus 194 e~~S~~EIA~~lgis-~~tV~~~~~-rA~ 220 (233)
T PRK05803 194 KEKTQREIAKALGIS-RSYVSRIEK-RAL 220 (233)
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 567999999999998 899988765 554
No 294
>PF11940 DUF3458: Domain of unknown function (DUF3458); InterPro: IPR024601 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain, which contains a conserved FSAPV sequence motif, is found in the C-terminal of alanyl aminopeptidases that belong to MEROPS peptidase family M1 (aminopeptidase N, clan MA). ; PDB: 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A 3PUU_A 3B37_A 3B2P_A 3B3B_A ....
Probab=20.50 E-value=1.6e+02 Score=25.94 Aligned_cols=38 Identities=11% Similarity=0.329 Sum_probs=24.6
Q ss_pred hhhhhcchhhhhccCCCchHHHHHHHHHhcCChhhHhhhhC
Q 030471 42 FSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAG 82 (177)
Q Consensus 42 f~eLl~~~~v~~L~~~~~~~l~~LL~if~~G~~~~~~~~~~ 82 (177)
-..|++||... ++ +...+..|+-.|+.++...|+...+
T Consensus 305 V~~L~~Hp~F~-~~--NPNrvRaLig~Fa~~N~~~FH~~dG 342 (367)
T PF11940_consen 305 VKKLMQHPAFD-LK--NPNRVRALIGAFAQANPVQFHAADG 342 (367)
T ss_dssp HHHHTTSTTTT-TT---HHHHHHHHHHHHHC-HHHHT-TTS
T ss_pred HHHHhcCCCCC-CC--CCcHHHHHHHHHHhcChhhhcCCCC
Confidence 34555555552 22 2347899999999999999987554
No 295
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=20.47 E-value=1.2e+02 Score=23.16 Aligned_cols=28 Identities=14% Similarity=0.130 Sum_probs=23.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...++++||+.++++ ...|...+- +|.
T Consensus 120 ~~g~~~~EIA~~lgis-~~tV~~~l~-Rar 147 (181)
T PRK09637 120 LEGLSQKEIAEKLGLS-LSGAKSRVQ-RGR 147 (181)
T ss_pred hcCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 899987766 553
No 296
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=20.42 E-value=1.1e+02 Score=25.76 Aligned_cols=28 Identities=21% Similarity=0.125 Sum_probs=24.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lvI~~ai 136 (177)
-...||.+||+.++++ ...|...+- +|.
T Consensus 167 ~~g~s~~EIA~~lgis-~~tVk~~l~-RAr 194 (339)
T PRK08241 167 VLGWSAAEVAELLDTS-VAAVNSALQ-RAR 194 (339)
T ss_pred hhCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3568999999999998 999998887 765
No 297
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=20.38 E-value=1.1e+02 Score=19.56 Aligned_cols=21 Identities=33% Similarity=0.471 Sum_probs=13.3
Q ss_pred CcccChHHHHHHcCCCChHHHH
Q 030471 107 NKVLPYDELMEELDVTNVRELE 128 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE 128 (177)
.+-+|.+++++.++|+ ...++
T Consensus 8 ~~glsl~~va~~t~I~-~~~l~ 28 (62)
T PF13413_consen 8 AKGLSLEDVAEETKIS-VSYLE 28 (62)
T ss_dssp CTT--HHHHHHHCS---HHHHH
T ss_pred HcCCCHHHHHHHhCCC-HHHHH
Confidence 5678999999999998 65544
No 298
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=20.38 E-value=1.6e+02 Score=28.82 Aligned_cols=42 Identities=19% Similarity=0.240 Sum_probs=34.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEE
Q 030471 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCF 152 (177)
Q Consensus 106 ~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v 152 (177)
..+.|+..++++.+++| .+-+-..+. ..++ ++|+|+++ ++.+
T Consensus 131 E~G~isI~eLa~~~~Lp-sefl~~~l~-~rlG-~iI~g~~~--g~~l 172 (803)
T PLN03083 131 ECSQIALAELARQLQVG-SELVTSMLE-PRLG-TIVKARLE--GGQL 172 (803)
T ss_pred HcCcChHHHHHHhcCCh-HHHHHHHHH-HHhc-cceEEEec--CCEE
Confidence 57899999999999999 777888887 7776 79999994 3444
No 299
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.11 E-value=1.2e+02 Score=21.39 Aligned_cols=24 Identities=29% Similarity=0.263 Sum_probs=19.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHH
Q 030471 107 NKVLPYDELMEELDVTNVRELEDFL 131 (177)
Q Consensus 107 ~~~is~~~I~~~l~i~~~~evE~lv 131 (177)
-..+|-++||.+|++. +..+|..+
T Consensus 21 l~~LS~~~iA~~Ln~t-~~~lekil 44 (97)
T COG4367 21 LCPLSDEEIATALNWT-EVKLEKIL 44 (97)
T ss_pred hccccHHHHHHHhCCC-HHHHHHHH
Confidence 3468899999999997 78888643
No 300
>PRK11050 manganese transport regulator MntR; Provisional
Probab=20.08 E-value=2e+02 Score=21.62 Aligned_cols=38 Identities=13% Similarity=0.128 Sum_probs=30.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 030471 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i~~~~evE~lvI~~ai~~gLI~gk 144 (177)
..+..++..+|++.++++ ...|=.++- +.-..|+|.-+
T Consensus 47 ~~~~~~t~~eLA~~l~is-~stVsr~l~-~Le~~GlI~r~ 84 (152)
T PRK11050 47 AEVGEARQVDIAARLGVS-QPTVAKMLK-RLARDGLVEMR 84 (152)
T ss_pred HhcCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEEe
Confidence 345578999999999997 888888887 77788988754
No 301
>PRK00215 LexA repressor; Validated
Probab=20.02 E-value=4.2e+02 Score=20.51 Aligned_cols=47 Identities=21% Similarity=0.293 Sum_probs=36.9
Q ss_pred cCCcccChHHHHHHcCC-CChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 030471 105 ETNKVLPYDELMEELDV-TNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (177)
Q Consensus 105 ~~~~~is~~~I~~~l~i-~~~~evE~lvI~~ai~~gLI~gkIDq~~~~v~v 154 (177)
..+...+..+|++++++ + ...|=.++= .....|+|+..-+. .+.+.+
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 45778899999999999 6 788888777 77889999776555 455555
Done!