Query 044757
Match_columns 227
No_of_seqs 145 out of 577
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 06:30:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044757.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044757hhsearch_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 1.7E-50 3.7E-55 338.5 15.6 222 1-225 1-222 (258)
2 KOG2753 Uncharacterized conser 100.0 5.5E-35 1.2E-39 258.5 12.0 158 26-188 205-370 (378)
3 KOG2908 26S proteasome regulat 100.0 2E-34 4.3E-39 256.0 14.7 169 25-195 198-376 (380)
4 PF01399 PCI: PCI domain; Int 99.6 6.3E-15 1.4E-19 110.4 8.9 95 62-158 1-105 (105)
5 smart00753 PAM PCI/PINT associ 99.6 8.1E-15 1.8E-19 107.8 7.9 86 90-179 3-88 (88)
6 smart00088 PINT motif in prote 99.6 8.1E-15 1.8E-19 107.8 7.9 86 90-179 3-88 (88)
7 KOG1464 COP9 signalosome, subu 99.0 8.5E-10 1.8E-14 97.5 8.7 125 62-194 305-439 (440)
8 KOG2581 26S proteasome regulat 98.3 9.5E-06 2.1E-10 75.0 11.3 90 62-154 319-419 (493)
9 KOG0686 COP9 signalosome, subu 96.9 0.0095 2.1E-07 55.5 10.5 99 63-163 307-415 (466)
10 KOG1498 26S proteasome regulat 96.8 0.0094 2E-07 55.3 10.0 131 60-202 286-432 (439)
11 KOG1497 COP9 signalosome, subu 96.7 0.0042 9.1E-08 56.3 6.2 153 28-192 228-389 (399)
12 KOG2758 Translation initiation 96.6 0.0068 1.5E-07 55.1 7.0 94 94-194 332-425 (432)
13 COG5071 RPN5 26S proteasome re 96.0 0.073 1.6E-06 48.3 10.3 79 106-196 348-426 (439)
14 KOG2582 COP9 signalosome, subu 96.0 0.079 1.7E-06 48.9 10.5 105 62-170 259-372 (422)
15 KOG2688 Transcription-associat 95.5 0.044 9.4E-07 51.1 7.2 98 63-161 273-387 (394)
16 KOG1463 26S proteasome regulat 95.2 0.075 1.6E-06 48.8 7.3 115 45-161 269-393 (411)
17 COG5600 Transcription-associat 94.3 0.18 3.8E-06 46.8 7.5 99 61-161 288-406 (413)
18 KOG0687 26S proteasome regulat 93.0 0.53 1.2E-05 43.1 8.2 64 94-159 300-363 (393)
19 PF09756 DDRGK: DDRGK domain; 92.9 0.22 4.7E-06 42.1 5.2 57 99-157 101-157 (188)
20 KOG2072 Translation initiation 92.2 4.4 9.5E-05 41.3 13.9 50 107-157 443-492 (988)
21 PF10075 PCI_Csn8: COP9 signal 92.2 1.5 3.3E-05 34.7 9.1 107 27-134 6-119 (143)
22 COG5159 RPN6 26S proteasome re 91.8 0.5 1.1E-05 42.8 6.4 99 61-161 283-391 (421)
23 PF09012 FeoC: FeoC like trans 91.1 0.26 5.7E-06 34.4 3.2 47 101-149 4-50 (69)
24 COG3355 Predicted transcriptio 90.8 3.3 7.1E-05 32.8 9.4 79 108-192 39-120 (126)
25 PF02082 Rrf2: Transcriptional 87.3 2.1 4.6E-05 30.7 5.7 54 108-165 22-75 (83)
26 KOG3054 Uncharacterized conser 85.7 1.6 3.5E-05 38.3 5.0 55 101-157 204-258 (299)
27 KOG1076 Translation initiation 84.0 11 0.00025 37.8 10.5 115 45-161 635-766 (843)
28 PF13412 HTH_24: Winged helix- 84.0 3.1 6.7E-05 26.4 4.7 42 101-144 7-48 (48)
29 PRK11179 DNA-binding transcrip 82.4 2.5 5.5E-05 33.9 4.7 48 101-150 13-63 (153)
30 smart00344 HTH_ASNC helix_turn 82.4 3.5 7.6E-05 30.6 5.2 42 102-145 8-49 (108)
31 PRK01919 tatB sec-independent 81.5 9 0.00019 31.8 7.5 61 163-224 19-79 (169)
32 TIGR02010 IscR iron-sulfur clu 81.0 4.7 0.0001 31.7 5.6 43 101-145 13-57 (135)
33 PRK14165 winged helix-turn-hel 79.8 9.1 0.0002 33.0 7.4 61 95-157 5-65 (217)
34 PF09339 HTH_IclR: IclR helix- 78.5 6.5 0.00014 25.5 4.9 45 98-144 4-49 (52)
35 PF01726 LexA_DNA_bind: LexA D 77.9 6.3 0.00014 27.3 4.8 36 108-144 22-57 (65)
36 COG1522 Lrp Transcriptional re 77.5 4.4 9.6E-05 31.9 4.5 43 102-146 13-55 (154)
37 PRK11169 leucine-responsive tr 77.2 5.4 0.00012 32.4 5.1 47 101-149 18-67 (164)
38 smart00346 HTH_ICLR helix_turn 76.8 6.7 0.00014 27.9 5.0 46 98-145 6-52 (91)
39 TIGR00738 rrf2_super rrf2 fami 76.7 7.2 0.00016 30.0 5.4 48 97-146 11-58 (132)
40 PRK04654 sec-independent trans 76.6 18 0.00039 31.1 8.1 34 163-196 19-52 (214)
41 PRK03573 transcriptional regul 76.2 31 0.00068 26.8 9.1 57 103-161 38-94 (144)
42 PRK10857 DNA-binding transcrip 76.1 7.2 0.00016 32.0 5.5 43 102-146 16-58 (164)
43 PF07389 DUF1500: Protein of u 75.8 3.6 7.9E-05 30.5 3.2 36 103-141 40-75 (100)
44 COG5187 RPN7 26S proteasome re 73.7 15 0.00032 33.6 7.2 64 94-159 314-377 (412)
45 PF12840 HTH_20: Helix-turn-he 72.4 11 0.00023 25.2 4.8 38 107-146 20-57 (61)
46 PF08280 HTH_Mga: M protein tr 72.3 5.1 0.00011 27.0 3.1 35 98-133 6-40 (59)
47 PRK10141 DNA-binding transcrip 72.0 13 0.00029 28.8 5.8 46 109-156 28-73 (117)
48 TIGR01410 tatB twin arginine-t 71.9 18 0.00039 26.2 6.1 37 163-199 18-54 (80)
49 PF08220 HTH_DeoR: DeoR-like h 71.9 8.2 0.00018 25.8 4.1 43 99-143 2-44 (57)
50 PF01022 HTH_5: Bacterial regu 71.6 14 0.00031 23.4 5.0 33 110-144 14-46 (47)
51 smart00550 Zalpha Z-DNA-bindin 71.3 9.5 0.00021 26.4 4.4 33 111-145 22-54 (68)
52 PRK04098 sec-independent trans 70.6 37 0.00081 27.9 8.3 58 163-220 19-79 (158)
53 PF13404 HTH_AsnC-type: AsnC-t 70.1 4.6 0.0001 25.5 2.4 29 101-130 7-35 (42)
54 PF03962 Mnd1: Mnd1 family; I 69.3 52 0.0011 27.6 9.2 73 110-191 10-86 (188)
55 TIGR02944 suf_reg_Xantho FeS a 68.7 14 0.0003 28.5 5.4 37 108-146 22-58 (130)
56 COG1959 Predicted transcriptio 68.1 15 0.00033 29.5 5.6 45 101-147 13-59 (150)
57 PF08281 Sigma70_r4_2: Sigma-7 67.8 6.9 0.00015 25.3 3.0 27 110-138 25-51 (54)
58 TIGR02337 HpaR homoprotocatech 67.6 50 0.0011 24.8 9.0 50 108-159 39-88 (118)
59 cd00090 HTH_ARSR Arsenical Res 67.1 26 0.00057 22.9 5.9 36 112-149 21-56 (78)
60 PF01325 Fe_dep_repress: Iron 66.9 19 0.00041 24.4 5.1 43 100-144 11-53 (60)
61 PF13730 HTH_36: Helix-turn-he 66.9 22 0.00048 22.9 5.4 47 95-143 7-55 (55)
62 PRK10265 chaperone-modulator p 66.7 21 0.00046 26.8 5.8 39 108-152 4-42 (101)
63 smart00347 HTH_MARR helix_turn 66.2 43 0.00093 23.5 8.7 44 109-154 22-65 (101)
64 PRK11920 rirA iron-responsive 65.8 18 0.00039 29.2 5.6 45 101-147 13-58 (153)
65 PF03399 SAC3_GANP: SAC3/GANP/ 64.6 17 0.00036 30.0 5.4 61 62-122 136-203 (204)
66 PF08279 HTH_11: HTH domain; 64.5 13 0.00027 24.1 3.7 36 98-134 1-37 (55)
67 PF04967 HTH_10: HTH DNA bindi 64.4 21 0.00045 23.8 4.8 30 107-138 19-48 (53)
68 PF04703 FaeA: FaeA-like prote 64.4 13 0.00029 25.6 3.9 34 109-144 13-46 (62)
69 PRK11014 transcriptional repre 63.8 20 0.00044 28.2 5.5 40 107-148 21-60 (141)
70 PF13601 HTH_34: Winged helix 63.6 14 0.00031 26.5 4.1 51 100-152 3-53 (80)
71 PF14947 HTH_45: Winged helix- 62.9 25 0.00055 24.8 5.3 51 100-157 9-59 (77)
72 PRK01770 sec-independent trans 62.6 38 0.00082 28.2 7.0 34 163-196 19-52 (171)
73 PF01978 TrmB: Sugar-specific 62.6 21 0.00045 24.3 4.7 38 108-147 19-56 (68)
74 PF04539 Sigma70_r3: Sigma-70 62.3 19 0.0004 25.0 4.5 26 108-134 17-42 (78)
75 PRK04214 rbn ribonuclease BN/u 62.2 74 0.0016 29.7 9.8 79 108-195 307-394 (412)
76 smart00345 HTH_GNTR helix_turn 61.7 35 0.00076 21.7 5.6 36 107-144 15-51 (60)
77 smart00420 HTH_DEOR helix_turn 61.6 30 0.00065 21.4 5.1 37 108-146 11-47 (53)
78 PF04545 Sigma70_r4: Sigma-70, 61.6 31 0.00067 21.9 5.2 28 109-138 18-45 (50)
79 PRK09954 putative kinase; Prov 59.4 14 0.0003 33.5 4.3 54 102-157 8-64 (362)
80 COG1777 Predicted transcriptio 59.1 1.1E+02 0.0025 26.3 9.4 38 113-152 29-67 (217)
81 PRK14858 tatA twin arginine tr 58.5 79 0.0017 24.3 7.6 34 163-196 19-52 (108)
82 PF08784 RPA_C: Replication pr 58.4 26 0.00057 25.8 5.0 49 99-149 52-101 (102)
83 PF07106 TBPIP: Tat binding pr 58.2 99 0.0021 25.0 13.4 79 107-190 12-95 (169)
84 smart00418 HTH_ARSR helix_turn 57.6 46 0.00099 21.0 5.6 38 109-148 8-45 (66)
85 TIGR03879 near_KaiC_dom probab 57.5 21 0.00045 25.6 4.0 31 109-141 30-60 (73)
86 PRK10870 transcriptional repre 57.5 1.1E+02 0.0023 25.1 9.4 51 108-160 68-118 (176)
87 PF01047 MarR: MarR family; I 57.2 33 0.00072 22.3 4.9 49 102-152 8-56 (59)
88 PF03979 Sigma70_r1_1: Sigma-7 55.5 14 0.0003 26.6 2.9 33 101-134 11-46 (82)
89 PF11945 WASH_WAHD: WAHD domai 55.2 1.3E+02 0.0027 27.3 9.6 67 158-224 8-75 (297)
90 PF05331 DUF742: Protein of un 53.8 26 0.00056 27.2 4.4 42 101-146 47-88 (114)
91 PF13518 HTH_28: Helix-turn-he 53.6 25 0.00054 22.1 3.7 43 101-148 4-46 (52)
92 KOG2629 Peroxisomal membrane a 53.4 44 0.00095 30.2 6.2 83 130-221 85-169 (300)
93 PF12802 MarR_2: MarR family; 52.5 58 0.0013 21.1 5.5 40 110-151 20-59 (62)
94 TIGR01884 cas_HTH CRISPR locus 50.2 57 0.0012 27.2 6.3 53 101-156 147-199 (203)
95 PHA01750 hypothetical protein 50.2 78 0.0017 22.3 5.8 36 187-222 37-72 (75)
96 PF06163 DUF977: Bacterial pro 50.2 52 0.0011 26.1 5.5 52 89-143 5-56 (127)
97 smart00419 HTH_CRP helix_turn_ 49.8 57 0.0012 19.8 5.2 33 111-145 8-40 (48)
98 PF05791 Bacillus_HBL: Bacillu 48.3 94 0.002 25.8 7.3 61 167-227 124-184 (184)
99 TIGR02051 MerR Hg(II)-responsi 45.7 1.3E+02 0.0029 23.0 7.3 95 113-216 1-107 (124)
100 cd00092 HTH_CRP helix_turn_hel 45.3 47 0.001 21.8 4.2 35 109-145 23-57 (67)
101 PF02002 TFIIE_alpha: TFIIE al 43.6 33 0.00071 25.5 3.5 36 109-146 25-60 (105)
102 PHA02943 hypothetical protein; 43.5 66 0.0014 26.5 5.3 45 98-145 12-56 (165)
103 COG1595 RpoE DNA-directed RNA 43.3 29 0.00062 28.1 3.4 28 109-138 141-168 (182)
104 PF10668 Phage_terminase: Phag 43.1 29 0.00062 23.9 2.8 24 108-132 19-42 (60)
105 COG4575 ElaB Uncharacterized c 42.8 1.3E+02 0.0027 23.1 6.4 29 161-189 2-30 (104)
106 cd01109 HTH_YyaN Helix-Turn-He 42.7 1.4E+02 0.003 22.4 6.9 44 113-171 2-46 (113)
107 KOG1861 Leucine permease trans 42.6 1E+02 0.0022 29.8 7.2 64 63-126 425-493 (540)
108 cd06445 ATase The DNA repair p 42.6 28 0.00061 24.7 2.8 25 100-124 6-30 (79)
109 PRK15090 DNA-binding transcrip 42.0 57 0.0012 28.1 5.2 46 98-145 15-60 (257)
110 TIGR02702 SufR_cyano iron-sulf 41.9 2E+02 0.0044 23.8 11.9 44 102-147 6-49 (203)
111 PF01638 HxlR: HxlR-like helix 41.8 1.3E+02 0.0028 21.6 7.2 75 100-182 9-85 (90)
112 PRK10411 DNA-binding transcrip 41.6 52 0.0011 28.4 4.9 45 98-144 5-49 (240)
113 PRK10434 srlR DNA-bindng trans 40.3 51 0.0011 28.7 4.7 45 98-144 6-50 (256)
114 PF05565 Sipho_Gp157: Siphovir 39.8 2E+02 0.0044 23.3 8.2 43 182-224 44-86 (162)
115 KOG2166 Cullins [Cell cycle co 39.4 4.4E+02 0.0095 27.0 11.5 119 97-224 566-696 (725)
116 KOG3809 Microtubule-binding pr 39.3 87 0.0019 30.1 6.1 59 164-222 504-562 (583)
117 COG3413 Predicted DNA binding 38.3 39 0.00085 28.5 3.5 81 64-147 128-211 (215)
118 PF14480 DNA_pol3_a_NI: DNA po 38.2 1.3E+02 0.0029 20.6 6.1 61 113-178 2-62 (76)
119 PRK12537 RNA polymerase sigma 38.2 37 0.0008 27.4 3.3 27 110-138 148-174 (182)
120 TIGR02999 Sig-70_X6 RNA polyme 37.4 41 0.00088 26.9 3.4 28 109-138 148-175 (183)
121 PRK00708 sec-independent trans 37.3 1.8E+02 0.004 25.0 7.4 35 163-197 19-53 (209)
122 PRK09802 DNA-binding transcrip 37.1 62 0.0013 28.4 4.7 47 96-144 16-62 (269)
123 TIGR00373 conserved hypothetic 37.0 2.2E+02 0.0049 23.0 9.2 50 108-159 25-76 (158)
124 cd04784 HTH_CadR-PbrR Helix-Tu 36.8 1.9E+02 0.0042 22.1 7.0 26 113-144 2-27 (127)
125 PRK12523 RNA polymerase sigma 36.3 43 0.00094 26.7 3.4 27 110-138 134-160 (172)
126 PF13542 HTH_Tnp_ISL3: Helix-t 36.2 58 0.0013 20.6 3.4 31 101-134 19-49 (52)
127 PF13384 HTH_23: Homeodomain-l 35.9 41 0.00088 21.1 2.6 23 111-134 17-39 (50)
128 KOG0971 Microtubule-associated 35.6 1.5E+02 0.0033 31.1 7.5 50 173-222 264-313 (1243)
129 PRK13509 transcriptional repre 35.6 74 0.0016 27.6 4.9 47 97-145 5-51 (251)
130 PF13591 MerR_2: MerR HTH fami 35.4 63 0.0014 23.2 3.8 32 112-149 1-32 (84)
131 PRK09642 RNA polymerase sigma 35.3 47 0.001 26.0 3.4 28 109-138 120-147 (160)
132 PRK12529 RNA polymerase sigma 35.1 46 0.001 26.8 3.4 27 110-138 142-168 (178)
133 TIGR02431 pcaR_pcaU beta-ketoa 35.1 86 0.0019 26.8 5.2 45 98-144 10-55 (248)
134 PF06056 Terminase_5: Putative 34.5 47 0.001 22.4 2.7 23 111-134 13-35 (58)
135 PF13463 HTH_27: Winged helix 34.2 1.4E+02 0.003 19.6 6.4 49 103-153 10-58 (68)
136 PRK09651 RNA polymerase sigma 34.2 49 0.0011 26.4 3.4 28 109-138 133-160 (172)
137 PRK06759 RNA polymerase factor 34.2 51 0.0011 25.5 3.4 27 110-138 121-147 (154)
138 PRK09047 RNA polymerase factor 33.7 52 0.0011 25.6 3.4 27 110-138 121-147 (161)
139 PRK12543 RNA polymerase sigma 33.4 50 0.0011 26.5 3.3 27 110-138 132-158 (179)
140 PF05377 FlaC_arch: Flagella a 33.0 1.6E+02 0.0034 20.0 5.2 16 207-222 22-37 (55)
141 PRK12520 RNA polymerase sigma 32.8 52 0.0011 26.7 3.4 27 110-138 146-172 (191)
142 PRK07037 extracytoplasmic-func 32.7 54 0.0012 25.6 3.4 27 110-138 124-150 (163)
143 PRK12525 RNA polymerase sigma 32.3 56 0.0012 26.0 3.4 28 109-138 132-159 (168)
144 cd07377 WHTH_GntR Winged helix 32.3 1.4E+02 0.003 19.1 6.0 35 108-144 21-56 (66)
145 PRK15418 transcriptional regul 32.1 68 0.0015 29.0 4.2 39 110-150 28-66 (318)
146 PF10975 DUF2802: Protein of u 32.1 50 0.0011 23.2 2.7 20 112-132 45-64 (70)
147 smart00421 HTH_LUXR helix_turn 32.0 74 0.0016 19.6 3.4 25 111-137 18-42 (58)
148 PRK12527 RNA polymerase sigma 31.7 58 0.0013 25.4 3.4 28 109-138 119-146 (159)
149 PRK12514 RNA polymerase sigma 31.6 56 0.0012 26.1 3.3 27 110-138 144-170 (179)
150 PF04218 CENP-B_N: CENP-B N-te 31.6 67 0.0015 21.1 3.1 31 100-133 13-43 (53)
151 PHA02763 hypothetical protein; 31.4 67 0.0015 23.9 3.3 51 111-164 52-102 (102)
152 PF09341 Pcc1: Transcription f 31.1 1.7E+02 0.0037 20.3 5.4 47 140-192 30-76 (76)
153 PF15397 DUF4618: Domain of un 30.9 1.7E+02 0.0036 26.1 6.3 39 166-204 62-100 (258)
154 PF10007 DUF2250: Uncharacteri 30.9 68 0.0015 23.9 3.3 27 116-144 26-52 (92)
155 TIGR02947 SigH_actino RNA poly 30.8 59 0.0013 26.4 3.3 28 109-138 145-172 (193)
156 cd01107 HTH_BmrR Helix-Turn-He 30.4 2.3E+02 0.005 21.1 7.4 45 113-171 2-47 (108)
157 TIGR02983 SigE-fam_strep RNA p 30.2 63 0.0014 25.2 3.3 27 110-138 125-151 (162)
158 PF06394 Pepsin-I3: Pepsin inh 30.2 29 0.00063 25.0 1.2 38 151-188 27-67 (76)
159 PRK12547 RNA polymerase sigma 30.2 62 0.0013 25.6 3.3 27 110-138 127-153 (164)
160 cd00592 HTH_MerR-like Helix-Tu 30.0 1.3E+02 0.0028 21.8 4.8 43 113-170 2-44 (100)
161 PF09743 DUF2042: Uncharacteri 29.9 97 0.0021 27.6 4.7 41 108-150 127-167 (272)
162 PF10828 DUF2570: Protein of u 29.8 2.5E+02 0.0053 21.2 8.3 52 173-224 38-89 (110)
163 PF14523 Syntaxin_2: Syntaxin- 29.8 2.2E+02 0.0047 20.6 8.2 55 167-221 26-83 (102)
164 cd04786 HTH_MerR-like_sg7 Heli 29.5 2.7E+02 0.0059 21.7 8.9 95 113-221 2-114 (131)
165 cd06170 LuxR_C_like C-terminal 29.5 87 0.0019 19.4 3.4 25 111-137 15-39 (57)
166 PRK15431 ferrous iron transpor 29.4 1.3E+02 0.0029 21.7 4.5 38 105-144 10-47 (78)
167 PRK12513 RNA polymerase sigma 29.2 66 0.0014 26.1 3.4 28 109-138 153-180 (194)
168 PRK12528 RNA polymerase sigma 29.2 68 0.0015 25.1 3.4 28 109-138 127-154 (161)
169 PRK10046 dpiA two-component re 29.0 1.1E+02 0.0023 25.4 4.7 38 110-149 176-213 (225)
170 COG2378 Predicted transcriptio 28.9 4.3E+02 0.0093 23.7 9.9 82 97-181 8-93 (311)
171 PF01920 Prefoldin_2: Prefoldi 28.8 2.3E+02 0.0049 20.5 6.6 47 154-200 45-91 (106)
172 PRK15396 murein lipoprotein; P 28.8 2.3E+02 0.0049 20.5 7.6 50 167-216 25-74 (78)
173 PF12324 HTH_15: Helix-turn-he 28.6 1E+02 0.0022 22.3 3.8 34 100-134 27-60 (77)
174 PRK10163 DNA-binding transcrip 28.5 1.3E+02 0.0027 26.4 5.2 56 98-157 26-82 (271)
175 cd01282 HTH_MerR-like_sg3 Heli 28.5 2.6E+02 0.0055 21.0 8.6 43 113-170 2-44 (112)
176 PRK12530 RNA polymerase sigma 28.2 70 0.0015 26.0 3.4 27 110-138 149-175 (189)
177 PF07889 DUF1664: Protein of u 28.1 3E+02 0.0065 21.7 8.1 52 170-221 46-97 (126)
178 PRK12539 RNA polymerase sigma 28.0 69 0.0015 25.8 3.2 27 110-138 146-172 (184)
179 COG1414 IclR Transcriptional r 27.6 1.3E+02 0.0028 26.0 5.1 56 98-157 5-61 (246)
180 PRK09645 RNA polymerase sigma 27.6 73 0.0016 25.2 3.3 27 110-138 133-159 (173)
181 PRK12536 RNA polymerase sigma 27.4 72 0.0016 25.6 3.3 27 110-138 144-170 (181)
182 PRK12522 RNA polymerase sigma 27.4 73 0.0016 25.3 3.3 27 110-138 134-160 (173)
183 PRK09646 RNA polymerase sigma 27.4 72 0.0016 26.0 3.3 27 110-138 157-183 (194)
184 PRK11569 transcriptional repre 27.2 1.3E+02 0.0029 26.2 5.1 45 98-144 29-74 (274)
185 PRK11512 DNA-binding transcrip 27.1 2.4E+02 0.0052 21.8 6.2 52 109-162 52-103 (144)
186 PF10771 DUF2582: Protein of u 27.0 2.2E+02 0.0048 19.8 5.3 49 105-157 16-64 (65)
187 PRK09647 RNA polymerase sigma 27.0 74 0.0016 26.5 3.4 28 109-138 152-179 (203)
188 PRK12511 RNA polymerase sigma 26.9 74 0.0016 25.9 3.3 27 110-138 126-152 (182)
189 TIGR02844 spore_III_D sporulat 26.9 80 0.0017 22.8 3.0 31 98-130 7-37 (80)
190 PF13815 Dzip-like_N: Iguana/D 26.9 2.9E+02 0.0062 21.1 8.3 50 174-223 69-118 (118)
191 PRK12545 RNA polymerase sigma 26.8 75 0.0016 26.2 3.3 28 109-138 153-180 (201)
192 PRK12512 RNA polymerase sigma 26.5 79 0.0017 25.3 3.4 27 110-138 146-172 (184)
193 PRK08301 sporulation sigma fac 26.4 76 0.0017 26.7 3.4 28 109-138 196-223 (234)
194 PRK09514 zntR zinc-responsive 26.3 3.2E+02 0.007 21.4 9.3 97 112-217 2-113 (140)
195 COG2390 DeoR Transcriptional r 26.0 1E+02 0.0022 28.2 4.2 38 110-149 25-62 (321)
196 PRK12516 RNA polymerase sigma 25.9 81 0.0018 25.7 3.4 28 109-138 130-157 (187)
197 KOG2235 Uncharacterized conser 25.7 1E+02 0.0022 30.9 4.3 46 108-157 130-175 (776)
198 PF12999 PRKCSH-like: Glucosid 25.7 3.4E+02 0.0074 22.7 7.0 46 178-223 125-170 (176)
199 PRK00404 tatB sec-independent 25.6 3.6E+02 0.0078 21.7 7.6 34 163-196 19-52 (141)
200 PF09218 DUF1959: Domain of un 25.6 42 0.00092 26.2 1.4 79 116-222 18-112 (117)
201 PRK12540 RNA polymerase sigma 25.5 84 0.0018 25.5 3.4 27 110-138 126-152 (182)
202 PF09940 DUF2172: Domain of un 25.5 1.1E+02 0.0025 28.6 4.5 45 96-144 342-386 (386)
203 TIGR02950 SigM_subfam RNA poly 25.5 88 0.0019 24.0 3.3 27 110-138 120-146 (154)
204 PRK13919 putative RNA polymera 25.3 85 0.0018 25.1 3.3 28 109-138 149-176 (186)
205 PF01035 DNA_binding_1: 6-O-me 24.9 74 0.0016 22.9 2.6 25 100-124 8-32 (85)
206 TIGR02919 accessory Sec system 24.9 2.3E+02 0.005 26.9 6.6 88 113-204 340-433 (438)
207 PRK10906 DNA-binding transcrip 24.8 1.4E+02 0.0029 26.0 4.7 47 96-144 4-50 (252)
208 cd01106 HTH_TipAL-Mta Helix-Tu 24.8 2.8E+02 0.0061 20.3 7.7 26 113-144 2-27 (103)
209 cd00632 Prefoldin_beta Prefold 24.8 2.9E+02 0.0063 20.4 6.1 15 207-221 85-99 (105)
210 PRK00182 tatB sec-independent 24.6 3E+02 0.0066 22.6 6.3 33 163-195 20-52 (160)
211 cd04770 HTH_HMRTR Helix-Turn-H 24.6 3.1E+02 0.0067 20.7 10.0 89 112-215 1-109 (123)
212 KOG3431 Apoptosis-related prot 24.6 46 0.001 26.2 1.5 22 127-149 70-91 (129)
213 PRK00478 scpA segregation and 24.5 6.6E+02 0.014 24.4 9.7 100 109-209 360-465 (505)
214 PF05584 Sulfolobus_pRN: Sulfo 24.4 2.7E+02 0.0058 19.9 7.1 57 102-162 11-68 (72)
215 PF02796 HTH_7: Helix-turn-hel 24.4 1.1E+02 0.0024 19.1 3.0 19 112-131 22-40 (45)
216 TIGR02952 Sig70_famx2 RNA poly 24.4 93 0.002 24.3 3.4 27 110-138 137-163 (170)
217 PRK10430 DNA-binding transcrip 24.4 2E+02 0.0044 23.9 5.6 39 109-149 176-214 (239)
218 TIGR02939 RpoE_Sigma70 RNA pol 24.4 91 0.002 24.9 3.4 27 110-138 153-179 (190)
219 PRK12519 RNA polymerase sigma 24.4 91 0.002 25.2 3.4 27 110-138 156-182 (194)
220 cd04762 HTH_MerR-trunc Helix-T 24.3 95 0.0021 18.5 2.7 28 112-145 1-28 (49)
221 PF00046 Homeobox: Homeobox do 24.3 87 0.0019 20.1 2.7 23 111-134 27-49 (57)
222 PRK12535 RNA polymerase sigma 24.1 91 0.002 25.7 3.3 27 110-138 148-174 (196)
223 PRK12533 RNA polymerase sigma 24.0 91 0.002 26.4 3.4 27 110-138 149-175 (216)
224 cd08327 CARD_RAIDD Caspase act 23.9 1.2E+02 0.0026 22.5 3.6 54 30-87 24-77 (94)
225 PF06013 WXG100: Proteins of 1 23.9 2.3E+02 0.0049 19.0 4.9 34 164-197 4-37 (86)
226 TIGR02943 Sig70_famx1 RNA poly 23.8 94 0.002 25.3 3.4 27 110-138 146-172 (188)
227 PRK12524 RNA polymerase sigma 23.7 92 0.002 25.4 3.3 28 109-138 150-177 (196)
228 TIGR03001 Sig-70_gmx1 RNA poly 23.6 90 0.002 27.0 3.3 27 110-138 176-202 (244)
229 TIGR02787 codY_Gpos GTP-sensin 23.6 1.6E+02 0.0034 26.1 4.7 36 109-146 196-231 (251)
230 PRK09652 RNA polymerase sigma 23.5 99 0.0021 24.2 3.4 27 110-138 143-169 (182)
231 TIGR02954 Sig70_famx3 RNA poly 23.4 96 0.0021 24.4 3.3 27 110-138 134-160 (169)
232 PF06619 DUF1149: Protein of u 23.2 1.3E+02 0.0028 23.8 3.8 44 142-185 68-111 (127)
233 cd01110 HTH_SoxR Helix-Turn-He 23.2 3.7E+02 0.0081 21.1 7.0 31 112-148 2-32 (139)
234 PRK12542 RNA polymerase sigma 23.2 97 0.0021 24.9 3.3 27 110-138 137-163 (185)
235 PF13545 HTH_Crp_2: Crp-like h 23.2 1.6E+02 0.0036 19.8 4.1 42 110-157 27-68 (76)
236 PRK12517 RNA polymerase sigma 23.1 99 0.0021 25.2 3.4 27 110-138 143-169 (188)
237 PRK09649 RNA polymerase sigma 23.1 1E+02 0.0022 25.0 3.4 28 109-138 144-171 (185)
238 PRK09638 RNA polymerase sigma 22.8 1E+02 0.0022 24.4 3.3 27 110-138 141-167 (176)
239 COG1339 Transcriptional regula 22.8 2.8E+02 0.006 23.9 5.9 58 97-157 6-63 (214)
240 PRK03100 sec-independent trans 22.7 4E+02 0.0087 21.3 7.2 34 163-196 20-53 (136)
241 PF00325 Crp: Bacterial regula 22.4 1.8E+02 0.004 17.3 3.5 30 112-143 3-32 (32)
242 PF05920 Homeobox_KN: Homeobox 22.4 1.2E+02 0.0025 18.9 2.8 21 115-137 17-37 (40)
243 PF09202 Rio2_N: Rio2, N-termi 22.4 2.6E+02 0.0057 20.2 5.1 49 97-147 9-58 (82)
244 TIGR02047 CadR-PbrR Cd(II)/Pb( 22.3 3.7E+02 0.0079 20.7 6.5 27 113-145 2-28 (127)
245 cd06171 Sigma70_r4 Sigma70, re 22.3 1.8E+02 0.004 17.2 4.3 24 110-134 25-48 (55)
246 PRK10884 SH3 domain-containing 22.1 4.9E+02 0.011 22.1 8.0 21 169-189 95-115 (206)
247 PF12728 HTH_17: Helix-turn-he 22.1 1.1E+02 0.0023 19.3 2.7 29 112-146 2-30 (51)
248 PF01984 dsDNA_bind: Double-st 22.1 53 0.0012 25.1 1.4 22 127-149 62-83 (107)
249 TIGR01764 excise DNA binding d 21.9 1.1E+02 0.0025 18.3 2.8 30 112-147 2-31 (49)
250 PRK09640 RNA polymerase sigma 21.9 1.1E+02 0.0024 24.7 3.4 27 110-138 149-175 (188)
251 PF08221 HTH_9: RNA polymerase 21.7 1.8E+02 0.0039 19.6 3.9 37 108-146 24-60 (62)
252 PF06323 Phage_antiter_Q: Phag 21.6 1.1E+02 0.0024 26.7 3.4 55 70-124 106-180 (230)
253 PRK06704 RNA polymerase factor 21.6 1.1E+02 0.0023 26.4 3.3 26 111-138 132-157 (228)
254 PRK12534 RNA polymerase sigma 21.6 1E+02 0.0023 24.7 3.2 27 110-138 152-178 (187)
255 PRK12532 RNA polymerase sigma 21.6 1.1E+02 0.0024 24.8 3.4 27 110-138 151-177 (195)
256 PRK15002 redox-sensitivie tran 21.4 4.4E+02 0.0095 21.2 6.9 35 108-148 8-42 (154)
257 TIGR02989 Sig-70_gvs1 RNA poly 21.3 1.2E+02 0.0026 23.4 3.3 27 110-138 126-152 (159)
258 PF00403 HMA: Heavy-metal-asso 21.2 1.7E+02 0.0037 18.9 3.7 38 128-169 15-52 (62)
259 cd04773 HTH_TioE_rpt2 Second H 21.2 3.5E+02 0.0077 20.1 8.3 31 112-148 1-31 (108)
260 PF04297 UPF0122: Putative hel 21.2 1E+02 0.0023 23.3 2.8 27 109-137 31-57 (101)
261 PRK12526 RNA polymerase sigma 21.0 1.1E+02 0.0025 25.2 3.4 28 109-138 167-194 (206)
262 TIGR00589 ogt O-6-methylguanin 21.0 1.1E+02 0.0024 21.9 2.9 25 100-124 8-32 (80)
263 PRK04239 hypothetical protein; 21.0 58 0.0013 25.1 1.4 22 127-149 67-88 (110)
264 PF00196 GerE: Bacterial regul 20.8 2.5E+02 0.0054 18.1 4.6 23 111-134 18-40 (58)
265 PRK14857 tatA twin arginine tr 20.8 3.1E+02 0.0067 20.4 5.2 38 163-200 21-58 (90)
266 PF00888 Cullin: Cullin family 20.8 1E+02 0.0022 29.6 3.3 45 98-144 521-565 (588)
267 PRK13182 racA polar chromosome 20.7 4.5E+02 0.0097 21.8 6.8 21 113-134 2-22 (175)
268 PF02787 CPSase_L_D3: Carbamoy 20.7 1.3E+02 0.0028 23.4 3.4 77 55-134 4-94 (123)
269 PRK09648 RNA polymerase sigma 20.6 1.2E+02 0.0026 24.4 3.4 27 110-138 154-180 (189)
270 PRK12518 RNA polymerase sigma 20.5 1.1E+02 0.0024 24.1 3.1 27 110-138 135-161 (175)
271 TIGR03209 P21_Cbot clostridium 20.5 73 0.0016 24.4 1.9 19 110-129 122-140 (142)
272 PF13022 HTH_Tnp_1_2: Helix-tu 20.3 2.4E+02 0.0052 22.8 4.8 44 88-132 10-54 (142)
273 PRK12531 RNA polymerase sigma 20.2 1.2E+02 0.0026 24.6 3.3 27 110-138 156-182 (194)
274 TIGR02338 gimC_beta prefoldin, 20.1 3.8E+02 0.0083 20.0 6.1 45 158-202 54-98 (110)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=1.7e-50 Score=338.47 Aligned_cols=222 Identities=42% Similarity=0.652 Sum_probs=218.4
Q ss_pred ChhhhchhhhHHHHHHHhccCCCchHHHHHHHHHHhcCCCceechhhhcChhhhhccCCCchHHHHHHHHHhcCCHhhHH
Q 044757 1 MEIEQKQAPLIEQFVKQASTLNGPGPALVKLIVEATSHPSLFAFSEILSVPNLLQLQGTESSVYIDLLRLFAHGTWTDYK 80 (227)
Q Consensus 1 ~~~~~~~~~~~e~f~~l~~~~~~~~~~a~~li~~aL~~p~if~F~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~dy~ 80 (227)
|.|||++++-+|+|+.+||+.+ |.+...+|.+||.+|++|.|||||.+|+|..|.++.++.+++||++|++|||.||.
T Consensus 1 m~~ek~~~~~~eqfvllak~~k--g~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ 78 (258)
T KOG3250|consen 1 MDIEKKQAEIIEQFVLLAKTCK--GEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYS 78 (258)
T ss_pred CCcchhhHHHHHHHHHHHhccc--hhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhh
Confidence 8899999999999999999999 99999999999999999999999999999999998899999999999999999999
Q ss_pred hhhhcCCCcchHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeec
Q 044757 81 SNAAHLPQLVPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAA 160 (227)
Q Consensus 81 ~~~~~~~~l~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~ 160 (227)
...-.+|.|+.+++.||+.++++++++..++|+|..+.+.+.+.+..+||++|| +||+++++.|||||.+|+++|.|+.
T Consensus 79 aea~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~fai 157 (258)
T KOG3250|consen 79 AEALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAI 157 (258)
T ss_pred hhhhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhh
Confidence 999999999999999999999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhccc
Q 044757 161 GRDLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHSK 225 (227)
Q Consensus 161 ~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 225 (227)
+|++++.++.+|...|.+|++.|++++-.|++++.+|++.++.+.+++++.+..+.++||++|..
T Consensus 158 gRdlr~k~i~nm~~TL~~w~~~cenvL~~ie~qv~~anq~~e~~~r~~qq~e~ev~~~kKtlk~~ 222 (258)
T KOG3250|consen 158 GRDLRSKDIDNMKYTLDEWCEGCENVLFGIEAQVPRANQSKERASRMSQQDEIEVMNFKKTLKPT 222 (258)
T ss_pred cccccHhHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHhhhhhhhhhHHhhhcccCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999874
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=5.5e-35 Score=258.48 Aligned_cols=158 Identities=27% Similarity=0.503 Sum_probs=145.1
Q ss_pred HHHHHHHHHHhcCCCceechhhhcChhhhhccCCCchHHHHHHHHHhcCCHhhHHhhhhcCCCc-------chHHHHHHH
Q 044757 26 PALVKLIVEATSHPSLFAFSEILSVPNLLQLQGTESSVYIDLLRLFAHGTWTDYKSNAAHLPQL-------VPDQAVKLK 98 (227)
Q Consensus 26 ~~a~~li~~aL~~p~if~F~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~dy~~~~~~~~~l-------~~~~~~Klr 98 (227)
..|.++|+.|+.+|++|.|++|+++|+|+.|+++ .+|+||.||..|.+++|..|....+.+ .+++.+|||
T Consensus 205 edA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d---~i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMR 281 (378)
T KOG2753|consen 205 EDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGD---LIHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMR 281 (378)
T ss_pred HHHHHHHHHHHcCCceeccchhccCchHHHhccc---hHHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHH
Confidence 6799999999999999999999999999999987 699999999999999999986555443 367789999
Q ss_pred HHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHH
Q 044757 99 QLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTN 178 (227)
Q Consensus 99 ~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~ 178 (227)
+||+++||+++.+|||++|++.|+|. .+|||.||| +||+.|+|.|||||.+++|.|+++.+|.||..||+.|+++|..
T Consensus 282 LLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI-daI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~a 359 (378)
T KOG2753|consen 282 LLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI-DAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAA 359 (378)
T ss_pred HHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH-HHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHH
Confidence 99999999999999999999999998 899999999 9999999999999999999999999999999999999999999
Q ss_pred H-HHHHHHHHH
Q 044757 179 W-LDTSDNILS 188 (227)
Q Consensus 179 W-~~~~~~~l~ 188 (227)
| ++++.++..
T Consensus 360 w~k~~~stv~~ 370 (378)
T KOG2753|consen 360 WGKQNLSTVRE 370 (378)
T ss_pred HHhhhhHHHHH
Confidence 9 454444433
No 3
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=2e-34 Score=256.01 Aligned_cols=169 Identities=20% Similarity=0.396 Sum_probs=156.0
Q ss_pred hHHHHHHHHHHhcCCCceechhhhcChhhhhccCCCchHHHHHHHHHhcCCHhhHHhhh---hcCCCcchH---HHHHHH
Q 044757 25 GPALVKLIVEATSHPSLFAFSEILSVPNLLQLQGTESSVYIDLLRLFAHGTWTDYKSNA---AHLPQLVPD---QAVKLK 98 (227)
Q Consensus 25 ~~~a~~li~~aL~~p~if~F~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~dy~~~~---~~~~~l~~~---~~~Klr 98 (227)
-..|+.+..+||.+.+|||||||+.||+..+|.||.+.|++++|.+|+.||+..|+... ...|.|... ..+|++
T Consensus 198 ~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e~~L~qKI~ 277 (380)
T KOG2908|consen 198 QDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNEDFLLQKIR 277 (380)
T ss_pred HHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999864 456777533 368999
Q ss_pred HHHhhhhhc----cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHH
Q 044757 99 QLSVLTLAE----MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQ 174 (227)
Q Consensus 99 ~LtLlsLa~----~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~ 174 (227)
+|+|+.++- ..|.+||++||++++|| .++||.+|| +|++.|||+|.|||++++|+++|++||+++.+|+-.|.+
T Consensus 278 LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~ 355 (380)
T KOG2908|consen 278 LLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKD 355 (380)
T ss_pred HHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEEecccccccCHHHHHhHHH
Confidence 999998874 57999999999999999 799999998 999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 044757 175 SLTNWLDTSDNILSVIQDKIK 195 (227)
Q Consensus 175 ~L~~W~~~~~~~l~~ie~~~~ 195 (227)
++..|.++++++...|+++..
T Consensus 356 rl~~W~~~v~~me~~ve~~~~ 376 (380)
T KOG2908|consen 356 RLDEWNKDVKSMEGLVEHRGH 376 (380)
T ss_pred HHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999987643
No 4
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.59 E-value=6.3e-15 Score=110.39 Aligned_cols=95 Identities=22% Similarity=0.385 Sum_probs=81.7
Q ss_pred hHHHHHHHHHhcCCHhhHHhhhhcC-------CC---cchHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHH
Q 044757 62 SVYIDLLRLFAHGTWTDYKSNAAHL-------PQ---LVPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELED 131 (227)
Q Consensus 62 ~~l~~LL~iF~~G~~~dy~~~~~~~-------~~---l~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~ 131 (227)
+|+.+|+++|..|++..|......+ +. +.+....+++..++.+++..++.+++++|++.|+++ .++||.
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 4789999999999999998754333 22 235667899999999999999999999999999999 899999
Q ss_pred HHHHHhHhcCceEEEecccCcEEEEEe
Q 044757 132 FLINECMYVGIVKGKLNQLRRCFEVQF 158 (227)
Q Consensus 132 lvI~~ai~~gLI~gkIDQ~~~~v~V~~ 158 (227)
+++ ++|..|.|.|+|||.+++|+++|
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 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.57 E-value=8.1e-15 Score=107.81 Aligned_cols=86 Identities=22% Similarity=0.308 Sum_probs=80.5
Q ss_pred chHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchH
Q 044757 90 VPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQL 169 (227)
Q Consensus 90 ~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~ 169 (227)
.+...+++|..++.+++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+++..+|. .++|
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 34567899999999999999999999999999999 789999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 044757 170 ENMMQSLTNW 179 (227)
Q Consensus 170 ~~l~~~L~~W 179 (227)
..+.++|..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00753 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999999887
No 6
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.57 E-value=8.1e-15 Score=107.81 Aligned_cols=86 Identities=22% Similarity=0.308 Sum_probs=80.5
Q ss_pred chHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchH
Q 044757 90 VPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQL 169 (227)
Q Consensus 90 ~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~ 169 (227)
.+...+++|..++.+++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+++..+|. .++|
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 34567899999999999999999999999999999 789999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 044757 170 ENMMQSLTNW 179 (227)
Q Consensus 170 ~~l~~~L~~W 179 (227)
..+.++|..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00088 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999999887
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.04 E-value=8.5e-10 Score=97.49 Aligned_cols=125 Identities=14% Similarity=0.363 Sum_probs=104.5
Q ss_pred hHHHHHHHHHhcCCHhhHHhh----hhcC---C---CcchHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHH
Q 044757 62 SVYIDLLRLFAHGTWTDYKSN----AAHL---P---QLVPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELED 131 (227)
Q Consensus 62 ~~l~~LL~iF~~G~~~dy~~~----~~~~---~---~l~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~ 131 (227)
-.+.+|+.++...++.+|+.. ++.+ | ...++.++++|.-.|+.|..++..|....|+++|+|+ ..+||.
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 458899999999999999984 2222 1 1246778999999999999999999999999999999 899999
Q ss_pred HHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 132 FLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDNILSVIQDKI 194 (227)
Q Consensus 132 lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~ 194 (227)
++| +||...-|+|+|||+++.+....... .-..+...|+.|.+.+.++.+.|-.++
T Consensus 384 LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr~ 439 (440)
T KOG1464|consen 384 LLV-SCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSRV 439 (440)
T ss_pred HHH-HHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999 99999999999999999888764422 123378999999999999888776543
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=98.26 E-value=9.5e-06 Score=75.02 Aligned_cols=90 Identities=14% Similarity=0.321 Sum_probs=68.1
Q ss_pred hHHHHHHHHHhcCCHhhHHhhhhcCCC-cchH----HHHHHHH------HHhhhhhccCccccHHHHHHHhCCCChhHHH
Q 044757 62 SVYIDLLRLFAHGTWTDYKSNAAHLPQ-LVPD----QAVKLKQ------LSVLTLAEMNKVLSYDQLLKELEVANVRELE 130 (227)
Q Consensus 62 ~~l~~LL~iF~~G~~~dy~~~~~~~~~-l~~~----~~~Klr~------LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE 130 (227)
.+++.|-.+.-.||++-|....+.+.. |-.+ ..-.||+ ++.++| .++.||+.+||..|++.|..++|
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 478999999999999999986544322 1110 1122222 333344 38999999999999999888899
Q ss_pred HHHHHHhHhcCceEEEecccCcEE
Q 044757 131 DFLINECMYVGIVKGKLNQLRRCF 154 (227)
Q Consensus 131 ~lvI~~ai~~gLI~gkIDQ~~~~v 154 (227)
.+|- +||+.|+|+|+||..++.+
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 9999999999999999843
No 9
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.91 E-value=0.0095 Score=55.54 Aligned_cols=99 Identities=14% Similarity=0.209 Sum_probs=76.9
Q ss_pred HHHHHHHHHhcCCHhhHHhhh-hcCCCc---------chHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHH
Q 044757 63 VYIDLLRLFAHGTWTDYKSNA-AHLPQL---------VPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDF 132 (227)
Q Consensus 63 ~l~~LL~iF~~G~~~dy~~~~-~~~~~l---------~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~l 132 (227)
.+.++|..|..+.++.-...- +.-|.| ..+...++|.=+++..-.++.++.++.+|.+.+.+ ...+|.=
T Consensus 307 qlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~ 385 (466)
T KOG0686|consen 307 QLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESE 385 (466)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHH
Confidence 455666777776666433321 111221 14456899999999999999999999999999998 8999999
Q ss_pred HHHHhHhcCceEEEecccCcEEEEEeecCCC
Q 044757 133 LINECMYVGIVKGKLNQLRRCFEVQFAAGRD 163 (227)
Q Consensus 133 vI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~ 163 (227)
|. +.|-.|.|.||||+.++.+++.-...|.
T Consensus 386 l~-~LI~~~~i~~rIDs~~ki~~~~~~~~en 415 (466)
T KOG0686|consen 386 LL-ELILEGKISGRIDSHNKILYARDADSEN 415 (466)
T ss_pred HH-HHHHccchheeeccccceeeeccccccc
Confidence 99 9999999999999999999998765554
No 10
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=96.85 E-value=0.0094 Score=55.29 Aligned_cols=131 Identities=18% Similarity=0.277 Sum_probs=95.9
Q ss_pred CchHHHHHHHHHhcCCHhhHHhhhhc---------CCC---cchHHH--HHHHH--HHhhhhhccCccccHHHHHHHhCC
Q 044757 60 ESSVYIDLLRLFAHGTWTDYKSNAAH---------LPQ---LVPDQA--VKLKQ--LSVLTLAEMNKVLSYDQLLKELEV 123 (227)
Q Consensus 60 ~~~~l~~LL~iF~~G~~~dy~~~~~~---------~~~---l~~~~~--~Klr~--LtLlsLa~~~~~isy~~I~~~L~i 123 (227)
+.+..-.+|..|..|-+--|...... +-. ..+... -+.|. .-+-=.+.-+..|++..+++-++.
T Consensus 286 e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl 365 (439)
T KOG1498|consen 286 ELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDL 365 (439)
T ss_pred cCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCC
Confidence 34567789999999977665532111 100 111111 12232 333334556899999999999999
Q ss_pred CChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 044757 124 ANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCE 202 (227)
Q Consensus 124 ~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~ 202 (227)
| .++.|.++- +.+..|-+.+|||+..+.+.+..+ +.+.+-|..|..++++++..++..-.-+.++..
T Consensus 366 ~-~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~ll~K~~HLI~KEem 432 (439)
T KOG1498|consen 366 P-VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGLLEKVSHLIHKEEM 432 (439)
T ss_pred C-HHHHHHHHH-HHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHH
Confidence 9 899999999 899999999999999999998765 337789999999999999999877666655443
No 11
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.67 E-value=0.0042 Score=56.32 Aligned_cols=153 Identities=10% Similarity=0.150 Sum_probs=91.0
Q ss_pred HHHHHHHHhcCCCceec-hhhhcChhhhhccCCC-chHHHHHHHHHhcC-CHhhHHhhh-h----cCCC-cchHHHHHHH
Q 044757 28 LVKLIVEATSHPSLFAF-SEILSVPNLLQLQGTE-SSVYIDLLRLFAHG-TWTDYKSNA-A----HLPQ-LVPDQAVKLK 98 (227)
Q Consensus 28 a~~li~~aL~~p~if~F-~eLl~~p~v~~L~~~~-~~~l~~LL~iF~~G-~~~dy~~~~-~----~~~~-l~~~~~~Klr 98 (227)
|..|..-|.-+|..--| ..|.-.|.++.|..=+ -+.+ .|+-|..+ +...|..+- + ..+. .+... +-+-
T Consensus 228 a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKm--yl~riI~k~el~ef~~~L~pHQka~~~dgssil~-ra~~ 304 (399)
T KOG1497|consen 228 ALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKM--YLERIIRKEELQEFEAFLQPHQKAHTMDGSSILD-RAVI 304 (399)
T ss_pred hHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHH--HHHHHhcchhHHHHHHHhcchhhhcccCcchhhh-hHHH
Confidence 33444445555555443 4555556655553210 0111 23334444 566666541 1 1111 11111 2222
Q ss_pred HHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHH
Q 044757 99 QLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTN 178 (227)
Q Consensus 99 ~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~ 178 (227)
-..|+++.+-+..|||+++...|+|+ ...+|..+- +.|..|-+.|.|||.++.+++....+ ..+|+ .....
T Consensus 305 EhNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~~e~----l~~wd---kqi~s 375 (399)
T KOG1497|consen 305 EHNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFEDREE----LPQWD---KQIQS 375 (399)
T ss_pred HHhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecchhh----hhhhh---HHHHH
Confidence 34566777778889999999999999 899999999 99999999999999999999864211 12343 34444
Q ss_pred HHHHHHHHHHHHHH
Q 044757 179 WLDTSDNILSVIQD 192 (227)
Q Consensus 179 W~~~~~~~l~~ie~ 192 (227)
-++.++++++.|..
T Consensus 376 l~~qvNki~~~i~~ 389 (399)
T KOG1497|consen 376 LCNQVNKILDKISH 389 (399)
T ss_pred HHHHHHHHHHHHHH
Confidence 56666666666654
No 12
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=96.60 E-value=0.0068 Score=55.12 Aligned_cols=94 Identities=13% Similarity=0.205 Sum_probs=73.5
Q ss_pred HHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHH
Q 044757 94 AVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMM 173 (227)
Q Consensus 94 ~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~ 173 (227)
+.--|++-.=+.|.-+.+|+.+.+|+.|+++ .++.|.|++ +.|+...+++|||..-+.|.+..-.+. --+.+.
T Consensus 332 ~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~~~~s-----~~qQ~i 404 (432)
T KOG2758|consen 332 LENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGHPTVS-----PHQQLI 404 (432)
T ss_pred HHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecCCCCC-----HHHHHH
Confidence 4666777777888889999999999999998 899999999 999999999999999999888754332 234556
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 044757 174 QSLTNWLDTSDNILSVIQDKI 194 (227)
Q Consensus 174 ~~L~~W~~~~~~~l~~ie~~~ 194 (227)
++-....-+..++-..++..+
T Consensus 405 e~tksLS~rsq~la~~lek~~ 425 (432)
T KOG2758|consen 405 EKTKSLSFRSQNLAQQLEKKI 425 (432)
T ss_pred HhccccchhHHHHHHHHHHHH
Confidence 666655556666555555443
No 13
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=96.03 E-value=0.073 Score=48.31 Aligned_cols=79 Identities=16% Similarity=0.271 Sum_probs=67.4
Q ss_pred hccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHH
Q 044757 106 AEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDN 185 (227)
Q Consensus 106 a~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~ 185 (227)
+.-+..|+-..|..-++.| ..+.|.++- +.+..|.+.+||++..+.+.+... ++..+.|..|..++..
T Consensus 348 ~~yYSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK~----------~n~~~~lneW~~NV~e 415 (439)
T COG5071 348 ANYYSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEKS----------QNVQEQLNEWGSNVTE 415 (439)
T ss_pred HHHhhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeecc----------ccHHHHHHHhcccHHH
Confidence 3447889999999999998 899999999 999999999999999999987643 2356789999999999
Q ss_pred HHHHHHHHHHH
Q 044757 186 ILSVIQDKIKW 196 (227)
Q Consensus 186 ~l~~ie~~~~~ 196 (227)
++..++.--.-
T Consensus 416 llgklek~~HL 426 (439)
T COG5071 416 LLGKLEKVRHL 426 (439)
T ss_pred HHHHHHHHhHH
Confidence 99999754433
No 14
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.98 E-value=0.079 Score=48.93 Aligned_cols=105 Identities=13% Similarity=0.199 Sum_probs=79.5
Q ss_pred hHHHHHHHHHhcCCHhhHHhh----h-----hcCCCcchHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHH
Q 044757 62 SVYIDLLRLFAHGTWTDYKSN----A-----AHLPQLVPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDF 132 (227)
Q Consensus 62 ~~l~~LL~iF~~G~~~dy~~~----~-----~~~~~l~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~l 132 (227)
.++.++++++..+...+.... + +..-.|....+.-+.+-+|.+|.+...+++.++||+..++.+..|||..
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 478999999999988876653 1 2222344444566667788888888889999999997777667999999
Q ss_pred HHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHH
Q 044757 133 LINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLE 170 (227)
Q Consensus 133 vI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~ 170 (227)
|+ ..|..|=|-+.|| |-|.++.-...+..|+...
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 7777765555555555444
No 15
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=95.54 E-value=0.044 Score=51.10 Aligned_cols=98 Identities=16% Similarity=0.198 Sum_probs=70.7
Q ss_pred HHHHHHHHHhcCCHhhHHhhhhcCCCcchH-----HHHHHHHHHhhhhhc-------cCccccHHHHHHHhCCCC-----
Q 044757 63 VYIDLLRLFAHGTWTDYKSNAAHLPQLVPD-----QAVKLKQLSVLTLAE-------MNKVLSYDQLLKELEVAN----- 125 (227)
Q Consensus 63 ~l~~LL~iF~~G~~~dy~~~~~~~~~l~~~-----~~~Klr~LtLlsLa~-------~~~~isy~~I~~~L~i~~----- 125 (227)
.+..|+.+...||+..|...-+....+.-. .+.|++.++.=.|.+ ....+|++.+..+++..+
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 556689999999999998642211111100 123344444433332 567899999999998765
Q ss_pred hhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecC
Q 044757 126 VRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAG 161 (227)
Q Consensus 126 ~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~ 161 (227)
.++||-.+. .+|+.|.|+|.|+...+++.++.-.|
T Consensus 353 ~deveciLa-~lI~~G~ikgYish~~~~~V~sK~~p 387 (394)
T KOG2688|consen 353 LDEVECILA-NLIDLGRIKGYISHQLQTLVFSKKDP 387 (394)
T ss_pred hhhHHHHHH-hhhhhccccchhchhhheEEEecCCC
Confidence 689999999 89999999999999999999986543
No 16
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=95.18 E-value=0.075 Score=48.77 Aligned_cols=115 Identities=17% Similarity=0.218 Sum_probs=84.1
Q ss_pred hhhhcChhhhhccCCCchHHHHHHHHHhcCCHhhHHhhhhcCC-Cc-----chHHHHHH----HHHHhhhhhccCccccH
Q 044757 45 SEILSVPNLLQLQGTESSVYIDLLRLFAHGTWTDYKSNAAHLP-QL-----VPDQAVKL----KQLSVLTLAEMNKVLSY 114 (227)
Q Consensus 45 ~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~dy~~~~~~~~-~l-----~~~~~~Kl----r~LtLlsLa~~~~~isy 114 (227)
+-|+.-.......+..-..+...=++|..-++.||+..-..++ .| ....+..| ----|+.+.+|+..+..
T Consensus 269 ~~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei 348 (411)
T KOG1463|consen 269 AALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEI 348 (411)
T ss_pred HHHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhH
Confidence 4455444333344544567788889999999999997533322 12 22222222 22357778889999999
Q ss_pred HHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecC
Q 044757 115 DQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAG 161 (227)
Q Consensus 115 ~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~ 161 (227)
+-||+-+|++ ...||.=+- +.|-.+.+.|.|||-++++.|.--.+
T Consensus 349 ~hIA~~IGl~-~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 349 SHIAEVIGLD-VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred HHHHHHHCCC-cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeCCCC
Confidence 9999999999 899999999 99999999999999999999975443
No 17
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=94.31 E-value=0.18 Score=46.80 Aligned_cols=99 Identities=19% Similarity=0.260 Sum_probs=62.6
Q ss_pred chHHHHHHHHHhcCCHhhHHhhhhcCCCcc--------------hHHHHHHHHHHhhhhhccCccccHHHHHHHhCCC--
Q 044757 61 SSVYIDLLRLFAHGTWTDYKSNAAHLPQLV--------------PDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVA-- 124 (227)
Q Consensus 61 ~~~l~~LL~iF~~G~~~dy~~~~~~~~~l~--------------~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~-- 124 (227)
.+.+--|..+.-+|++++|.........+. .-+.+.+-. ....++-....+|++.+...++++
T Consensus 288 ~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~r-k~w~~~~~qsrlp~sil~~~~qls~~ 366 (413)
T COG5600 288 CSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFR-KIWRLHGKQSRLPLSILLIVLQLSAI 366 (413)
T ss_pred cchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHH-HHHhhccccccCcHHHHHHHHHccCC
Confidence 345556889999999999987422111110 001111111 112222234446666655555554
Q ss_pred C----hhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecC
Q 044757 125 N----VRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAG 161 (227)
Q Consensus 125 ~----~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~ 161 (227)
+ .++||-.++ .+|..|+++|.|....++|.++...|
T Consensus 367 dn~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 367 DNFHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred CcccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence 2 468999999 89999999999999999999987654
No 18
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=93.05 E-value=0.53 Score=43.11 Aligned_cols=64 Identities=16% Similarity=0.224 Sum_probs=56.5
Q ss_pred HHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEee
Q 044757 94 AVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFA 159 (227)
Q Consensus 94 ~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~ 159 (227)
.+-||...--.+-+.+|.++.+..|++.|++ ++-++.=+= +-|-.|-+.++||-++++|.+++-
T Consensus 300 vREMR~rvY~QlLESYrsl~l~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNrp 363 (393)
T KOG0687|consen 300 VREMRRRVYAQLLESYRSLTLESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNRP 363 (393)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCCc
Confidence 4677777777888899999999999999998 888887777 888899999999999999998754
No 19
>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=92.91 E-value=0.22 Score=42.08 Aligned_cols=57 Identities=12% Similarity=0.222 Sum_probs=41.7
Q ss_pred HHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 99 QLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 99 ~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
+-.++..+...+.+..++||..+|+. ..++-+-|- +....|.|.|-||...+-||||
T Consensus 101 L~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEec
Confidence 45677888889999999999999999 788888888 8999999999999999999988
No 20
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=92.20 E-value=4.4 Score=41.25 Aligned_cols=50 Identities=18% Similarity=0.248 Sum_probs=43.6
Q ss_pred ccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 107 EMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 107 ~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
.-+.+|+|+.|.+-.-.=|..++|.++| +|...+.+..+||...++|.+.
T Consensus 443 qiY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 443 QIYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence 3578899999887654444789999999 9999999999999999999998
No 21
>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=92.16 E-value=1.5 Score=34.70 Aligned_cols=107 Identities=15% Similarity=0.176 Sum_probs=68.9
Q ss_pred HHHHHHHHHhcCCCceechhhhcChhhhhccC-CCchHHHHHHHHHhcCCHhhHHhhhhcC---CC---cchHHHHHHHH
Q 044757 27 ALVKLIVEATSHPSLFAFSEILSVPNLLQLQG-TESSVYIDLLRLFAHGTWTDYKSNAAHL---PQ---LVPDQAVKLKQ 99 (227)
Q Consensus 27 ~a~~li~~aL~~p~if~F~eLl~~p~v~~L~~-~~~~~l~~LL~iF~~G~~~dy~~~~~~~---~~---l~~~~~~Klr~ 99 (227)
....+...+|..-.+-+|.-+|..-.-...+. .+-..+..|...+-.|++..|-...... +. +.+.-..++|.
T Consensus 6 ~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~ 85 (143)
T PF10075_consen 6 IYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRE 85 (143)
T ss_dssp HHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHH
T ss_pred HHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence 33444455555555788887776432222232 3456788899999999999988743221 11 23444567777
Q ss_pred HHhhhhhccCccccHHHHHHHhCCCChhHHHHHHH
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
-.+-.+...+.+|+.+.+++-||++ .++++.++.
T Consensus 86 ~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~ 119 (143)
T PF10075_consen 86 RIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK 119 (143)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred HHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence 6666667779999999999999999 899999877
No 22
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=91.81 E-value=0.5 Score=42.81 Aligned_cols=99 Identities=15% Similarity=0.230 Sum_probs=74.8
Q ss_pred chHHHHHHHHHhcCCHhhHHhhhhcC-CCc-----chHHHH----HHHHHHhhhhhccCccccHHHHHHHhCCCChhHHH
Q 044757 61 SSVYIDLLRLFAHGTWTDYKSNAAHL-PQL-----VPDQAV----KLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELE 130 (227)
Q Consensus 61 ~~~l~~LL~iF~~G~~~dy~~~~~~~-~~l-----~~~~~~----Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE 130 (227)
-..+...-++|...++.||......+ |.+ ....++ .|---.|+.+.++...+..+-|++-+|++ ..+||
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 34677778889999999998753322 222 222221 22223566777899999999999999998 89999
Q ss_pred HHHHHHhHhcCceEEEecccCcEEEEEeecC
Q 044757 131 DFLINECMYVGIVKGKLNQLRRCFEVQFAAG 161 (227)
Q Consensus 131 ~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~ 161 (227)
.=+- +.|-.+++-|.+||.++++.|.--..
T Consensus 362 gKLs-qMILDKifyG~LDqg~gcLivy~ep~ 391 (421)
T COG5159 362 GKLS-QMILDKIFYGTLDQGDGCLIVYGEPA 391 (421)
T ss_pred HHHH-HHHHHHHHHhhhccCCceEEEeCCcc
Confidence 9999 89999999999999999999985543
No 23
>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=91.12 E-value=0.26 Score=34.36 Aligned_cols=47 Identities=13% Similarity=0.173 Sum_probs=36.0
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
.|.++...++.+|+++||.+++++ .+.||.++= ..+..|-|+-.-+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEEEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEEecCC
Confidence 455666678999999999999999 899999988 89999998844333
No 24
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=90.85 E-value=3.3 Score=32.80 Aligned_cols=79 Identities=16% Similarity=0.324 Sum_probs=58.9
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE-Eec-ccCcEEEEEeecCCCCCcchH-HHHHHHHHHHHHHHH
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG-KLN-QLRRCFEVQFAAGRDLRHGQL-ENMMQSLTNWLDTSD 184 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g-kID-Q~~~~v~V~~~~~R~~~~~q~-~~l~~~L~~W~~~~~ 184 (227)
.++..+-++||+.++++ ...|..-|= +.+..|+|.= +.. ...+-.++. +.++++++ +.+...|+.|++++.
T Consensus 39 ~~~~~tvdelae~lnr~-rStv~rsl~-~L~~~GlV~Rek~~~~~Ggy~yiY----~~i~~ee~k~~i~~~l~~w~~~~~ 112 (126)
T COG3355 39 ENGPLTVDELAEILNRS-RSTVYRSLQ-NLLEAGLVEREKVNLKGGGYYYLY----KPIDPEEIKKKILKDLDEWYDKMK 112 (126)
T ss_pred hcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeeeeeeccCCCceeEEE----ecCCHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999998 889998888 9999999973 333 223333333 23445666 347789999999999
Q ss_pred HHHHHHHH
Q 044757 185 NILSVIQD 192 (227)
Q Consensus 185 ~~l~~ie~ 192 (227)
..+...+.
T Consensus 113 ~~i~~~~~ 120 (126)
T COG3355 113 QLIEEFEK 120 (126)
T ss_pred HHHHHHhc
Confidence 98877653
No 25
>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=87.26 E-value=2.1 Score=30.69 Aligned_cols=54 Identities=11% Similarity=0.180 Sum_probs=37.8
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCC
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLR 165 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~ 165 (227)
..+.++.++||+.+++| ...|+..+= +....|+|+.. -..++-+...+ .|.+++
T Consensus 22 ~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~-~G~~GGy~L~~-~~~~It 75 (83)
T PF02082_consen 22 DGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESS-RGRGGGYRLAR-PPEEIT 75 (83)
T ss_dssp TSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE-TSTTSEEEESS--CCGSB
T ss_pred CCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEec-CCCCCceeecC-CHHHCC
Confidence 34459999999999999 899998877 88899998765 34556555543 344433
No 26
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=85.65 E-value=1.6 Score=38.32 Aligned_cols=55 Identities=15% Similarity=0.299 Sum_probs=44.8
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
-++..++.+++++.++++.++++-+ .++=+-+= +.+..|++.|-||...+-+||+
T Consensus 204 eFv~YIk~nKvV~ledLas~f~Lrt-qd~inriq-~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 204 EFVEYIKKNKVVPLEDLASEFGLRT-QDSINRIQ-ELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHhcCeeeHHHHHHHhCccH-HHHHHHHH-HHHHhhhheeeecCCCceEEec
Confidence 3556677899999999999999984 44444445 6677899999999999999998
No 27
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=84.02 E-value=11 Score=37.81 Aligned_cols=115 Identities=10% Similarity=0.198 Sum_probs=77.3
Q ss_pred hhhhcChhhhhccCCC---chHHHHHHHHHhcCCHhhHHhhh-------hcCCCcc--hH-HHHHHHHH----Hhhhhhc
Q 044757 45 SEILSVPNLLQLQGTE---SSVYIDLLRLFAHGTWTDYKSNA-------AHLPQLV--PD-QAVKLKQL----SVLTLAE 107 (227)
Q Consensus 45 ~eLl~~p~v~~L~~~~---~~~l~~LL~iF~~G~~~dy~~~~-------~~~~~l~--~~-~~~Klr~L----tLlsLa~ 107 (227)
--.|.+--=|.+.++| ...+..-=.+...|+|.+-..+. +-+|.-. -+ ..++++-- -|.+.+.
T Consensus 635 rr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss 714 (843)
T KOG1076|consen 635 RRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSS 714 (843)
T ss_pred HHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 3444444444455543 23355667788999998765531 2233311 11 12333322 3455666
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecC
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAG 161 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~ 161 (227)
-+.++|.+.+|+-..+| ...|=..|- +.|...=+.+++||+.++|.++++.|
T Consensus 715 ~Y~SvSl~~LA~mFdLp-~~~VhsIiS-kmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 715 VYDSVSLAKLADMFDLP-EPKVHSIIS-KMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred hhhhccHHHHHHHhCCC-chhHHHHHH-HHHHHHHhhhccCCCcceEEEeeccc
Confidence 78999999999999999 888887777 88888889999999999999998755
No 28
>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=83.97 E-value=3.1 Score=26.42 Aligned_cols=42 Identities=14% Similarity=0.300 Sum_probs=31.3
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.++.+...+..+|..+||+.++++ ...|-..+= +....|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 445555556679999999999998 788887766 888888875
No 29
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=82.39 E-value=2.5 Score=33.88 Aligned_cols=48 Identities=21% Similarity=0.272 Sum_probs=38.1
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE---Eeccc
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG---KLNQL 150 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g---kIDQ~ 150 (227)
.|+.+-..+...||.+||+.+|++ ...|-.-+= +....|+|.| -+|..
T Consensus 13 ~Il~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~~ 63 (153)
T PRK11179 13 GILEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNPK 63 (153)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECHH
Confidence 445555567899999999999999 788888777 8889999984 46653
No 30
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=82.37 E-value=3.5 Score=30.61 Aligned_cols=42 Identities=17% Similarity=0.274 Sum_probs=33.4
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
++.....+..+||.+|++.++++ ...|-..+- +....|+|.+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~ 49 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG 49 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence 33333345679999999999999 788888888 8888999883
No 31
>PRK01919 tatB sec-independent translocase; Provisional
Probab=81.48 E-value=9 Score=31.80 Aligned_cols=61 Identities=13% Similarity=0.245 Sum_probs=44.3
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcc
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHS 224 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (227)
+|+|+.++.+...+..|..++......+.+.+..-. ...+.++.+++++....+++.+++.
T Consensus 19 V~GPekLP~~aRtlGk~i~k~Rr~~~d~K~ev~~E~-e~dElrk~~~~~e~~~~~v~~si~~ 79 (169)
T PRK01919 19 VIGPERLPRVARTAGALFGRAQRYINDVKAEVSREI-ELDELRKMKTDFESAARDVENTIHD 79 (169)
T ss_pred eeCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999888887776543 2234455556666666666665543
No 32
>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=81.04 E-value=4.7 Score=31.66 Aligned_cols=43 Identities=19% Similarity=0.309 Sum_probs=34.9
Q ss_pred Hhhhhh--ccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 101 SVLTLA--EMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 101 tLlsLa--~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
.++.|+ ..++.++-++|++.+++| ...|+..+- ..-..|+|..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence 444455 345679999999999999 899999887 8888999985
No 33
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=79.78 E-value=9.1 Score=32.99 Aligned_cols=61 Identities=11% Similarity=0.128 Sum_probs=49.5
Q ss_pred HHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 95 VKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 95 ~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
.-|+.|.++........+|..+|++.++++ ...+=..|- +.-..|+|.-..+...+.+++|
T Consensus 5 ~~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk-~LEe~GlI~R~~~~r~~~v~LT 65 (217)
T PRK14165 5 EALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILK-QLEDEGYITRTIVPRGQLITIT 65 (217)
T ss_pred HHHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEEcCCceEEEEC
Confidence 456667777766667789999999999998 677877777 8888999999999877666665
No 34
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=78.51 E-value=6.5 Score=25.51 Aligned_cols=45 Identities=20% Similarity=0.308 Sum_probs=33.8
Q ss_pred HHHHhhhh-hccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 98 KQLSVLTL-AEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 98 r~LtLlsL-a~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
|-+.++.. +.....++..+|++.+++| ...+-.++- .....|+++
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 44666654 4455668999999999999 888888877 777778764
No 35
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=77.90 E-value=6.3 Score=27.32 Aligned_cols=36 Identities=8% Similarity=0.109 Sum_probs=28.0
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.+..-|+.+|++.+|+.|...|-..|- ..-..|+|+
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 567789999999999998899988877 677778775
No 36
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=77.49 E-value=4.4 Score=31.87 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=33.5
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
++.+-..+..+||.+|++.+|++ ...|=.-+= +....|+|+|.
T Consensus 13 IL~~L~~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~ 55 (154)
T COG1522 13 ILRLLQEDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeE
Confidence 34444445559999999999999 788877777 88889999864
No 37
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=77.16 E-value=5.4 Score=32.36 Aligned_cols=47 Identities=17% Similarity=0.184 Sum_probs=37.3
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE---Eecc
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG---KLNQ 149 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g---kIDQ 149 (227)
.|+.+-..+..+||.+||+.+|++ ...|-.-+= +....|+|+| .+|.
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQGYTALLNP 67 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEEEEEECH
Confidence 455555678899999999999999 788877766 8888999975 4554
No 38
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=76.84 E-value=6.7 Score=27.93 Aligned_cols=46 Identities=20% Similarity=0.216 Sum_probs=36.5
Q ss_pred HHHHhhhhhccC-ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 98 KQLSVLTLAEMN-KVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 98 r~LtLlsLa~~~-~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
|.+.++.+.... +.++..+|++.++++ ...|-..+- .....|+|..
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeee
Confidence 445666655443 689999999999999 889988887 7778999975
No 39
>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=76.68 E-value=7.2 Score=30.01 Aligned_cols=48 Identities=21% Similarity=0.223 Sum_probs=36.6
Q ss_pred HHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 97 LKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 97 lr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
++.|..+....+...++.++|++.+++| ...|...+= .....|+|...
T Consensus 11 l~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~-~L~~~gli~~~ 58 (132)
T TIGR00738 11 LRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILR-TLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 4444444433334589999999999999 899999887 88889999753
No 40
>PRK04654 sec-independent translocase; Provisional
Probab=76.60 E-value=18 Score=31.15 Aligned_cols=34 Identities=9% Similarity=0.160 Sum_probs=28.4
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKW 196 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~ 196 (227)
.|+++.+..+...+..|..++++....+.+.+..
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~ 52 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELER 52 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999988877777665543
No 41
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=76.17 E-value=31 Score=26.83 Aligned_cols=57 Identities=14% Similarity=0.015 Sum_probs=42.7
Q ss_pred hhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecC
Q 044757 103 LTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAG 161 (227)
Q Consensus 103 lsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~ 161 (227)
..+......++-.+|++.++++ ...|=..|- +....|+|.=.-|+.++....-..++
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 3444333456789999999998 677777776 88899999999998777766655543
No 42
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=76.08 E-value=7.2 Score=32.00 Aligned_cols=43 Identities=12% Similarity=0.151 Sum_probs=35.1
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
.+....+.+.+|-++|++.+++| ..-|+..+- ..-..|||...
T Consensus 16 ~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s~ 58 (164)
T PRK10857 16 DVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSSV 58 (164)
T ss_pred HHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeC
Confidence 33333455689999999999999 899999888 88899999973
No 43
>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=75.84 E-value=3.6 Score=30.53 Aligned_cols=36 Identities=14% Similarity=0.330 Sum_probs=27.4
Q ss_pred hhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcC
Q 044757 103 LTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVG 141 (227)
Q Consensus 103 lsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~g 141 (227)
..+...-..++|++|-+. +|+.+.||+||| +.+..+
T Consensus 40 yrlftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~i 75 (100)
T PF07389_consen 40 YRLFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLNDI 75 (100)
T ss_pred HHHHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHhH
Confidence 334444467899999998 677899999999 877544
No 44
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=73.74 E-value=15 Score=33.59 Aligned_cols=64 Identities=16% Similarity=0.208 Sum_probs=54.5
Q ss_pred HHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEee
Q 044757 94 AVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFA 159 (227)
Q Consensus 94 ~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~ 159 (227)
.+-||.=.--.|-+.+|.++.+..|+..|++ ++-|+.=+= +-|-.|-+.+.||-++++|..++-
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 4667766666777889999999999999998 888887777 778889999999999999998754
No 45
>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=72.38 E-value=11 Score=25.23 Aligned_cols=38 Identities=16% Similarity=0.228 Sum_probs=29.8
Q ss_pred ccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 107 EMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 107 ~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
......+..+|++.++++ ...+-.=+= .....|+|+..
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 557889999999999999 777766655 66788998764
No 46
>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=72.30 E-value=5.1 Score=26.95 Aligned_cols=35 Identities=29% Similarity=0.460 Sum_probs=25.3
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHH
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFL 133 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lv 133 (227)
|++.|+.+.-..+.+++++|++.++++ ...+-..+
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 455666655457899999999999998 66665543
No 47
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=71.98 E-value=13 Score=28.81 Aligned_cols=46 Identities=11% Similarity=0.091 Sum_probs=33.6
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEE
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEV 156 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V 156 (227)
....+..+|++.++++ ...|-.-+= ..-.+|||..+-+.......+
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 4568889999999998 677755544 456699999988865443333
No 48
>TIGR01410 tatB twin arginine-targeting protein translocase TatB. This model represents the TatB protein of a Sec-independent system for transporting folded proteins, often with a bound redox cofactor, across the bacterial inner membrane. TatC is the multiple membrane spanning component. TatB, like the related TatA/E proteins, appears to span the membrane one time. The tat system recognizes proteins with an elongated signal sequence containing a conserved R-R in a motif approximated by RRxFLK N-terminal to the transmembrane helix. TIGRFAMs model TIGR01409 describes this twin-Arg signal sequence. A similar system, termed Delta-pH-dependent transport, operates on chloroplast-encoded proteins.
Probab=71.94 E-value=18 Score=26.20 Aligned_cols=37 Identities=8% Similarity=0.135 Sum_probs=31.0
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAET 199 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~ 199 (227)
.|+|+.++.+...+..|..+.......+++.+...-.
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~e~~ 54 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDEELK 54 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHhc
Confidence 4789999999999999999999988888877655433
No 49
>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=71.90 E-value=8.2 Score=25.76 Aligned_cols=43 Identities=21% Similarity=0.228 Sum_probs=32.0
Q ss_pred HHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCce
Q 044757 99 QLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIV 143 (227)
Q Consensus 99 ~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI 143 (227)
+-.|+.+....+.++.+++++.++++ ...+-.=+. ..-..|+|
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~i 44 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGLI 44 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCCE
Confidence 34566777778999999999999998 676665555 55556654
No 50
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=71.56 E-value=14 Score=23.41 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=26.3
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
+..++.+|++.++++ ...|-.-+= .....|+|+
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 789999999999998 778776665 677788875
No 51
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=71.26 E-value=9.5 Score=26.42 Aligned_cols=33 Identities=24% Similarity=0.158 Sum_probs=30.0
Q ss_pred cccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 111 VLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
.++-.+|++.||++ ...|-..+- .....|+|.-
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 49999999999999 789999999 8999999865
No 52
>PRK04098 sec-independent translocase; Provisional
Probab=70.60 E-value=37 Score=27.89 Aligned_cols=58 Identities=21% Similarity=0.271 Sum_probs=39.7
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHhhHHHHHHHHHHHHHHHHHHh
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKW---AETMCEEDKKHKMEVKSHLQDVKK 220 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~ 220 (227)
.|||+.++.+...+..|...+......+.+.+.. +..-+.+...-++.++..++++++
T Consensus 19 vfGP~KLP~~~r~lGk~ir~~K~~~~~~k~~l~~Ei~~~elk~e~~k~k~~l~~~~~~l~~ 79 (158)
T PRK04098 19 FLGPDKLPQAMVDIAKFFKAVKKTINDAKSTLDKEINIEEIKEEALKYKKEFESAVESLKK 79 (158)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5899999999999999999998888777665553 223333334445555666665655
No 53
>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=70.09 E-value=4.6 Score=25.52 Aligned_cols=29 Identities=24% Similarity=0.363 Sum_probs=19.4
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHH
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELE 130 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE 130 (227)
.|+.+-..+...||.+|++.+|++ ...|-
T Consensus 7 ~Il~~Lq~d~r~s~~~la~~lglS-~~~v~ 35 (42)
T PF13404_consen 7 KILRLLQEDGRRSYAELAEELGLS-ESTVR 35 (42)
T ss_dssp HHHHHHHH-TTS-HHHHHHHHTS--HHHHH
T ss_pred HHHHHHHHcCCccHHHHHHHHCcC-HHHHH
Confidence 345545556889999999999998 66654
No 54
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=69.28 E-value=52 Score=27.58 Aligned_cols=73 Identities=12% Similarity=0.109 Sum_probs=44.4
Q ss_pred ccccHHHH----HHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHH
Q 044757 110 KVLSYDQL----LKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDN 185 (227)
Q Consensus 110 ~~isy~~I----~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~ 185 (227)
...+..+| .+.+||. ...|.++|- ..+..|+|.. ..=|+-.+.|+-|- +....+...+......+..
T Consensus 10 ~~y~lKELEK~~pK~~gI~-~~~VKdvlq-~LvDDglV~~---EKiGssn~YWsFps----~~~~~~~~~~~~l~~~~~~ 80 (188)
T PF03962_consen 10 DFYTLKELEKLAPKEKGIV-SMSVKDVLQ-SLVDDGLVHV---EKIGSSNYYWSFPS----QAKQKRQNKLEKLQKEIEE 80 (188)
T ss_pred CcccHHHHHHHcccccCCc-hhhHHHHHH-HHhccccchh---hhccCeeEEEecCh----HHHHHHHHHHHHHHHHHHH
Confidence 34455554 3448998 688999888 7887777763 13356667788553 4445555555555555555
Q ss_pred HHHHHH
Q 044757 186 ILSVIQ 191 (227)
Q Consensus 186 ~l~~ie 191 (227)
+...+.
T Consensus 81 ~~~~i~ 86 (188)
T PF03962_consen 81 LEKKIE 86 (188)
T ss_pred HHHHHH
Confidence 544443
No 55
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=68.74 E-value=14 Score=28.49 Aligned_cols=37 Identities=16% Similarity=0.218 Sum_probs=32.4
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
+...++..+|++.+++| ...|...+= .....|+|.+.
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 35679999999999999 899999887 88899999874
No 56
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=68.06 E-value=15 Score=29.52 Aligned_cols=45 Identities=22% Similarity=0.196 Sum_probs=36.1
Q ss_pred Hhhhhhc--cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe
Q 044757 101 SVLTLAE--MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL 147 (227)
Q Consensus 101 tLlsLa~--~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI 147 (227)
.|+.||. ..+.++-++||+..+|| ..-++.++- ..-.+|||+..=
T Consensus 13 ~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~-~L~kaGlV~S~r 59 (150)
T COG1959 13 ALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILS-KLRKAGLVKSVR 59 (150)
T ss_pred HHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEeec
Confidence 4445554 34478899999999999 899999988 888999998653
No 57
>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=67.79 E-value=6.9 Score=25.29 Aligned_cols=27 Identities=15% Similarity=0.224 Sum_probs=20.4
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|..++- +|.
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 468999999999999 899999887 765
No 58
>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=67.61 E-value=50 Score=24.78 Aligned_cols=50 Identities=12% Similarity=-0.000 Sum_probs=38.4
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEee
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFA 159 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~ 159 (227)
.+..++..+|++.++++ ...|=..|- +....|+|...-|..++....-..
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~~~v~L 88 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRRVYISL 88 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCeeEEEE
Confidence 35678999999999998 567776666 888999999998876665444333
No 59
>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=67.12 E-value=26 Score=22.93 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=30.7
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
+++.+|++.++++ ...+-..+- .....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~-~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLK-KLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHH-HHHHCCCeEEEEec
Confidence 9999999999998 788887766 77789999987665
No 60
>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=66.95 E-value=19 Score=24.38 Aligned_cols=43 Identities=16% Similarity=0.243 Sum_probs=33.4
Q ss_pred HHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.+|..|...+..++-.+||+.|+++ ...|=..+= +.-..|+|.
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 3555666688899999999999998 777766766 777788875
No 61
>PF13730 HTH_36: Helix-turn-helix domain
Probab=66.91 E-value=22 Score=22.88 Aligned_cols=47 Identities=26% Similarity=0.309 Sum_probs=34.7
Q ss_pred HHHHHHHhhhhhcc-Cccc-cHHHHHHHhCCCChhHHHHHHHHHhHhcCce
Q 044757 95 VKLKQLSVLTLAEM-NKVL-SYDQLLKELEVANVRELEDFLINECMYVGIV 143 (227)
Q Consensus 95 ~Klr~LtLlsLa~~-~~~i-sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI 143 (227)
.|+-.+.|.+.+.+ +... |++.|++.+|++ .+.|-..+= +....|+|
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 35566777788742 2233 799999999999 888888776 77777764
No 62
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=66.70 E-value=21 Score=26.78 Aligned_cols=39 Identities=15% Similarity=0.178 Sum_probs=29.0
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCc
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRR 152 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~ 152 (227)
....+|.+++++.++++ +.||. +.+..|+|+-.-+...+
T Consensus 4 ~~~~lt~~Elc~~~gi~-----~~~l~-eLve~GlIep~~~~~~~ 42 (101)
T PRK10265 4 VTVTFTITEFCLHTGVS-----EEELN-EIVGLGVIEPREIQETT 42 (101)
T ss_pred eEEEeeHHHHHHHHCcC-----HHHHH-HHHHCCCeecCCCCccc
Confidence 34568999999999998 34566 66779999975555443
No 63
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=66.25 E-value=43 Score=23.54 Aligned_cols=44 Identities=20% Similarity=0.148 Sum_probs=35.7
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEE
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCF 154 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v 154 (227)
...++..+|++.++++ ...+-..+- +....|+|.-.-++.++.-
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 4569999999999998 788888888 8999999987766544333
No 64
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=65.79 E-value=18 Score=29.17 Aligned_cols=45 Identities=16% Similarity=0.093 Sum_probs=35.3
Q ss_pred Hhhhhhc-cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe
Q 044757 101 SVLTLAE-MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL 147 (227)
Q Consensus 101 tLlsLa~-~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI 147 (227)
.++-|+. +.+.++-.+||+..+|| ..-++..+- ..-..|+|+..=
T Consensus 13 ~L~~LA~~~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~r 58 (153)
T PRK11920 13 MLMYCAANDGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETVR 58 (153)
T ss_pred HHHHHHhCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeec
Confidence 3344443 34568999999999999 899999888 888899998654
No 65
>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=64.61 E-value=17 Score=29.96 Aligned_cols=61 Identities=11% Similarity=0.200 Sum_probs=44.6
Q ss_pred hHHHHHHHHHhcCCHhhHHhhh--hcCCCcc----hHHHHHHHHHHhhhhhccCcc-ccHHHHHHHhC
Q 044757 62 SVYIDLLRLFAHGTWTDYKSNA--AHLPQLV----PDQAVKLKQLSVLTLAEMNKV-LSYDQLLKELE 122 (227)
Q Consensus 62 ~~l~~LL~iF~~G~~~dy~~~~--~~~~~l~----~~~~~Klr~LtLlsLa~~~~~-isy~~I~~~L~ 122 (227)
.-..++..++..|++..|-... ...|.+. .....++|..++-+++..++. +|.+.+++-|+
T Consensus 136 ~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 136 QFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 4567888999999999998865 4555543 334679999999999988887 99999988775
No 66
>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=64.51 E-value=13 Score=24.12 Aligned_cols=36 Identities=25% Similarity=0.346 Sum_probs=24.4
Q ss_pred HHHHhhhhh-ccCccccHHHHHHHhCCCChhHHHHHHH
Q 044757 98 KQLSVLTLA-EMNKVLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 98 r~LtLlsLa-~~~~~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
|+..++.+. +....+|-++||+.|+|+ ...|..-+=
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~ 37 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHH
Confidence 344455444 444559999999999998 777776644
No 67
>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=64.37 E-value=21 Score=23.84 Aligned_cols=30 Identities=13% Similarity=0.345 Sum_probs=22.7
Q ss_pred ccCccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 107 EMNKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 107 ~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
..-|.++..+||+.|||+ ...+-.-+= +|.
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 456899999999999998 666655544 443
No 68
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=64.36 E-value=13 Score=25.63 Aligned_cols=34 Identities=18% Similarity=0.211 Sum_probs=28.7
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
+..++=.+||++|+++ ...+-.++. ..-..|.|+
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 6779999999999999 899999999 888888775
No 69
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=63.79 E-value=20 Score=28.17 Aligned_cols=40 Identities=10% Similarity=0.108 Sum_probs=32.9
Q ss_pred ccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEec
Q 044757 107 EMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLN 148 (227)
Q Consensus 107 ~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkID 148 (227)
.++..+|-++|++.++|| ..-|+..+- ..-..|+|+.+=-
T Consensus 21 ~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~G 60 (141)
T PRK11014 21 PEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVRG 60 (141)
T ss_pred CCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEecC
Confidence 355678999999999999 888998888 7888898876543
No 70
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=63.59 E-value=14 Score=26.48 Aligned_cols=51 Identities=24% Similarity=0.259 Sum_probs=35.2
Q ss_pred HHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCc
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRR 152 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~ 152 (227)
|.+|++-.....++|.+|.+.|+++ ...+-.-+= ..-..|+|+-+-.-..+
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 4455544446789999999999998 677766655 67789999987655444
No 71
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=62.94 E-value=25 Score=24.81 Aligned_cols=51 Identities=12% Similarity=0.231 Sum_probs=34.8
Q ss_pred HHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
..++..++ ....++.+|+..++++ ...+..++= ..+..|||++ .++.+.+|
T Consensus 9 ~~IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~-~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 9 FDILKILS-KGGAKKTEIMYKANLN-YSTLKKYLK-ELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHHHH--TT-B-HHHHHTTST---HHHHHHHHH-HHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCcCeeC----CCCEEEEC
Confidence 34455554 6778899999999999 889999888 8999999944 45566655
No 72
>PRK01770 sec-independent translocase; Provisional
Probab=62.63 E-value=38 Score=28.20 Aligned_cols=34 Identities=12% Similarity=0.352 Sum_probs=29.8
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKW 196 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~ 196 (227)
+||++.+..+...+..|..++.++...+++.+..
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~ 52 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQ 52 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999999998888766554
No 73
>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=62.55 E-value=21 Score=24.26 Aligned_cols=38 Identities=16% Similarity=0.139 Sum_probs=33.3
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL 147 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI 147 (227)
..+..+-.+|++.++++ ...|-..+= +....|+|+-.-
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 46789999999999999 899998887 899999997654
No 74
>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=62.26 E-value=19 Score=25.03 Aligned_cols=26 Identities=19% Similarity=0.450 Sum_probs=20.0
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHH
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
.+|.-+.++||+.||++ .++|..++-
T Consensus 17 lgr~Pt~eEiA~~lgis-~~~v~~~l~ 42 (78)
T PF04539_consen 17 LGREPTDEEIAEELGIS-VEEVRELLQ 42 (78)
T ss_dssp HSS--BHHHHHHHHTS--HHHHHHHHH
T ss_pred hCCCCCHHHHHHHHccc-HHHHHHHHH
Confidence 47899999999999999 999997644
No 75
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=62.15 E-value=74 Score=29.74 Aligned_cols=79 Identities=19% Similarity=0.337 Sum_probs=52.4
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHH---------HH
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSL---------TN 178 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L---------~~ 178 (227)
.++.++.++|++.+++| .+.+++++= +....|+|. +-++ + .|+..||.+.=.+..+.+.+ ..
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~-~~~~--g----~~~l~rd~~~itL~dv~~~~~~~~~~~~~~~ 377 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR-RGER--G----QWVLARDLDSVPLAELYELFVLRPLPCRDDH 377 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE-ecCC--C----ceEecCCHHhCcHHHHHHhCCCCcCCCccch
Confidence 56788999999999999 899999877 788889997 3332 1 26666765433333333322 25
Q ss_pred HHHHHHHHHHHHHHHHH
Q 044757 179 WLDTSDNILSVIQDKIK 195 (227)
Q Consensus 179 W~~~~~~~l~~ie~~~~ 195 (227)
|..+++.+++.+++...
T Consensus 378 ~~~~~~~~l~~~~~~~~ 394 (412)
T PRK04214 378 VGQAADAALTQLRQPLR 394 (412)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66666666666654433
No 76
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=61.72 E-value=35 Score=21.68 Aligned_cols=36 Identities=22% Similarity=0.219 Sum_probs=29.4
Q ss_pred ccCccc-cHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 107 EMNKVL-SYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 107 ~~~~~i-sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.++..+ |..+|++.++++ ...|-..+- .....|+|.
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 899999999998 788888877 777788875
No 77
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=61.63 E-value=30 Score=21.38 Aligned_cols=37 Identities=16% Similarity=0.102 Sum_probs=28.8
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
.+..++-.+|++.++++ ...|...+= .....|+|.-.
T Consensus 11 ~~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~~ 47 (53)
T smart00420 11 QQGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTRV 47 (53)
T ss_pred HcCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEEe
Confidence 34569999999999998 788887766 66677777643
No 78
>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=61.56 E-value=31 Score=21.88 Aligned_cols=28 Identities=11% Similarity=0.258 Sum_probs=22.5
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+|++.+|++ ...|-.+.- +|+
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~-~al 45 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILK-RAL 45 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHH-HHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHH-HHH
Confidence 5678999999999998 888877766 665
No 79
>PRK09954 putative kinase; Provisional
Probab=59.44 E-value=14 Score=33.51 Aligned_cols=54 Identities=19% Similarity=0.400 Sum_probs=42.0
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE---EecccCcEEEEE
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG---KLNQLRRCFEVQ 157 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g---kIDQ~~~~v~V~ 157 (227)
|+.+...+..+|+.+|++.|+++ ...|-..+- +....|+|+| .+|.....+.|.
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~-~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIM-DLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCcCCcEEEEcCCccEEEEE
Confidence 55555566789999999999998 899998887 8888899875 466666555554
No 80
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=59.10 E-value=1.1e+02 Score=26.34 Aligned_cols=38 Identities=24% Similarity=0.478 Sum_probs=29.6
Q ss_pred cH-HHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCc
Q 044757 113 SY-DQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRR 152 (227)
Q Consensus 113 sy-~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~ 152 (227)
.| .+|++.+|++.-.-+++|=+ .=.+|||+.+++-..+
T Consensus 29 ~yvsEiS~~lgvsqkAVl~HL~~--LE~AGlveS~ie~~~R 67 (217)
T COG1777 29 CYVSEISRELGVSQKAVLKHLRI--LERAGLVESRIEKIPR 67 (217)
T ss_pred hHHHHHHhhcCcCHHHHHHHHHH--HHHcCCchhhcccccc
Confidence 45 47899999994444688766 4679999999998877
No 81
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=58.51 E-value=79 Score=24.34 Aligned_cols=34 Identities=12% Similarity=0.098 Sum_probs=29.2
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKW 196 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~ 196 (227)
.|+++.++.+...+..|..+.......+++.+..
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~ 52 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQE 52 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5889999999999999999999988887776654
No 82
>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=58.42 E-value=26 Score=25.84 Aligned_cols=49 Identities=12% Similarity=0.174 Sum_probs=36.6
Q ss_pred HHHhhhh-hccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 99 QLSVLTL-AEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 99 ~LtLlsL-a~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
.|.++.= +....=++.++|++.|+++ .++|+.-|= ..+..|.|=-.||.
T Consensus 52 Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 52 VLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 3455544 4345569999999999998 899998877 88999999888875
No 83
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=58.16 E-value=99 Score=25.01 Aligned_cols=79 Identities=14% Similarity=0.151 Sum_probs=54.0
Q ss_pred ccCccccHHHHHHHhC--CCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCC---CCCcchHHHHHHHHHHHHH
Q 044757 107 EMNKVLSYDQLLKELE--VANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGR---DLRHGQLENMMQSLTNWLD 181 (227)
Q Consensus 107 ~~~~~isy~~I~~~L~--i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R---~~~~~q~~~l~~~L~~W~~ 181 (227)
..+|..+..+|...|+ ++ -..|...+= .+...|.|.+|.=... .|.++... +++++++..|...+....+
T Consensus 12 ~qNRPys~~di~~nL~~~~~-K~~v~k~Ld-~L~~~g~i~~K~~GKq---kiY~~~Q~~~~~~s~eel~~ld~ei~~L~~ 86 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVG-KTAVQKALD-SLVEEGKIVEKEYGKQ---KIYFANQDELEVPSPEELAELDAEIKELRE 86 (169)
T ss_pred HcCCCCcHHHHHHHHHhhcc-HHHHHHHHH-HHHhCCCeeeeeecce---EEEeeCccccCCCCchhHHHHHHHHHHHHH
Confidence 3789999999999996 55 456666555 6677899999964433 44444433 3457777777777777777
Q ss_pred HHHHHHHHH
Q 044757 182 TSDNILSVI 190 (227)
Q Consensus 182 ~~~~~l~~i 190 (227)
.+..+-..+
T Consensus 87 el~~l~~~~ 95 (169)
T PF07106_consen 87 ELAELKKEV 95 (169)
T ss_pred HHHHHHHHH
Confidence 666655444
No 84
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=57.56 E-value=46 Score=21.05 Aligned_cols=38 Identities=16% Similarity=0.181 Sum_probs=29.7
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEec
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLN 148 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkID 148 (227)
.+.+++.+|++.++++ ...+-..+= .....|++.-.=+
T Consensus 8 ~~~~~~~~i~~~l~is-~~~v~~~l~-~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLS-QSTVSHHLK-KLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeeec
Confidence 5678999999999998 677776655 6777899985443
No 85
>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=57.52 E-value=21 Score=25.55 Aligned_cols=31 Identities=13% Similarity=0.117 Sum_probs=23.8
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcC
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVG 141 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~g 141 (227)
....||.+||+.++++ ...|..++- .-.+.|
T Consensus 30 ~eGlS~kEIAe~LGIS-~~TVk~~l~-~~~~~~ 60 (73)
T TIGR03879 30 EAGKTASEIAEELGRT-EQTVRNHLK-GETKAG 60 (73)
T ss_pred HcCCCHHHHHHHHCcC-HHHHHHHHh-cCcccc
Confidence 3678999999999999 888888765 433333
No 86
>PRK10870 transcriptional repressor MprA; Provisional
Probab=57.49 E-value=1.1e+02 Score=25.12 Aligned_cols=51 Identities=12% Similarity=-0.039 Sum_probs=40.9
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeec
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAA 160 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~ 160 (227)
+...++..+|++.++++ ...|=..|= +....|+|.=.-|..++....-..+
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~LT 118 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQLT 118 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEEC
Confidence 45779999999999998 677766655 8888999999999888766555443
No 87
>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=57.25 E-value=33 Score=22.26 Aligned_cols=49 Identities=12% Similarity=0.196 Sum_probs=36.7
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCc
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRR 152 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~ 152 (227)
+|........++..+|++.++++ ...+=.++= +....|+|.=.-|+.++
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTET
T ss_pred HHHHHHHcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCC
Confidence 33333345559999999999998 677777666 88889999988887665
No 88
>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=55.46 E-value=14 Score=26.61 Aligned_cols=33 Identities=12% Similarity=0.326 Sum_probs=22.9
Q ss_pred HhhhhhccCccccHHHHHHHhC---CCChhHHHHHHH
Q 044757 101 SVLTLAEMNKVLSYDQLLKELE---VANVRELEDFLI 134 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~---i~~~~eVE~lvI 134 (227)
.|+...+..+.+||++|.+.|. ++ .+.++.++-
T Consensus 11 ~Li~~gK~~G~lT~~eI~~~L~~~~~~-~e~id~i~~ 46 (82)
T PF03979_consen 11 KLIEKGKKKGYLTYDEINDALPEDDLD-PEQIDEIYD 46 (82)
T ss_dssp HHHHHHHHHSS-BHHHHHHH-S-S----HHHHHHHHH
T ss_pred HHHHHHhhcCcCCHHHHHHHcCccCCC-HHHHHHHHH
Confidence 4777888788899999999987 33 566776654
No 89
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=55.24 E-value=1.3e+02 Score=27.28 Aligned_cols=67 Identities=13% Similarity=0.184 Sum_probs=54.5
Q ss_pred eecCCCCCcch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcc
Q 044757 158 FAAGRDLRHGQ-LENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHS 224 (227)
Q Consensus 158 ~~~~R~~~~~q-~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (227)
-..+.|++.++ +..+.+.|+....-++.+-..|.++++.-+++.+.-.++-...+++|+.++.+-|+
T Consensus 8 plI~~dLr~eEti~qi~~aL~~L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs~kA 75 (297)
T PF11945_consen 8 PLIPPDLRREETILQIADALEYLDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGSKKA 75 (297)
T ss_pred cccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 45678888766 67789999999999999999999999988888887777777778888877665444
No 90
>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=53.79 E-value=26 Score=27.18 Aligned_cols=42 Identities=17% Similarity=0.286 Sum_probs=34.3
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
.|+.||.. ..|-.|||..|++| ..-|--++= +.+..|+|.-+
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 67788875 89999999999999 777776766 88888887643
No 91
>PF13518 HTH_28: Helix-turn-helix domain
Probab=53.55 E-value=25 Score=22.11 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=28.3
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEec
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLN 148 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkID 148 (227)
.++.+... +. |+.++|..++|+ ...|-.|+- .--..| +.|-.+
T Consensus 4 ~iv~~~~~-g~-s~~~~a~~~gis-~~tv~~w~~-~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 4 QIVELYLE-GE-SVREIAREFGIS-RSTVYRWIK-RYREGG-IEGLKP 46 (52)
T ss_pred HHHHHHHc-CC-CHHHHHHHHCCC-HhHHHHHHH-HHHhcC-HHHhcc
Confidence 34444443 33 999999999997 899999976 433334 344433
No 92
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=53.43 E-value=44 Score=30.17 Aligned_cols=83 Identities=17% Similarity=0.324 Sum_probs=58.5
Q ss_pred HHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcch--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH
Q 044757 130 EDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQ--LENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKH 207 (227)
Q Consensus 130 E~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q--~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~ 207 (227)
+.+++ -++..|+.-|=.-=++ .|+.||.|+..+ .+..+..|+.=-.++++.+..++..+..+.+.-..++.
T Consensus 85 dy~vm-Avi~aGi~y~~y~~~K-----~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q~~~~qq~- 157 (300)
T KOG2629|consen 85 DYFVM-AVILAGIAYAAYRFVK-----SYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQLLATQQS- 157 (300)
T ss_pred HHHHH-HHHHhhHHHHHHHHHH-----HHHHHHhhCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-
Confidence 33444 7888885544332222 378899888665 58888999999999999999999988888777765544
Q ss_pred HHHHHHHHHHHHhh
Q 044757 208 KMEVKSHLQDVKKS 221 (227)
Q Consensus 208 ~~~~~~~~~~~~~~ 221 (227)
++...++.++.+
T Consensus 158 --Els~~L~~l~~~ 169 (300)
T KOG2629|consen 158 --ELSRALASLKNT 169 (300)
T ss_pred --HHHHHHHHHHHH
Confidence 566666666655
No 93
>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=52.55 E-value=58 Score=21.13 Aligned_cols=40 Identities=13% Similarity=0.168 Sum_probs=32.2
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccC
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLR 151 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~ 151 (227)
..++..+|++.++++ ...|=..|= .....|+|.-.-|..+
T Consensus 20 ~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 20 EELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGD 59 (62)
T ss_dssp SGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSS
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCC
Confidence 359999999999998 788888777 8889999988777654
No 94
>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=50.23 E-value=57 Score=27.21 Aligned_cols=53 Identities=19% Similarity=0.214 Sum_probs=37.9
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEE
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEV 156 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V 156 (227)
.++.+...++.++..+|++.++++ ...+-..+- .....|+|.-.-+ ....+++
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEe
Confidence 444444444679999999999998 788887777 7788899986543 4444444
No 95
>PHA01750 hypothetical protein
Probab=50.17 E-value=78 Score=22.29 Aligned_cols=36 Identities=17% Similarity=0.305 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhh
Q 044757 187 LSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSV 222 (227)
Q Consensus 187 l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (227)
-+.+...+++...+..+-..+++.+++.+.++|+-+
T Consensus 37 keIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 37 KEIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 345667888888888888899999999999999865
No 96
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=50.17 E-value=52 Score=26.07 Aligned_cols=52 Identities=15% Similarity=0.299 Sum_probs=42.2
Q ss_pred cchHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCce
Q 044757 89 LVPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIV 143 (227)
Q Consensus 89 l~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI 143 (227)
+++.+..+| +..|+.|+..++.+++.++...+|++ .+.++.++- ++...|-|
T Consensus 5 ~T~eer~eL-k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lr-eLVa~G~l 56 (127)
T PF06163_consen 5 FTPEEREEL-KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLR-ELVARGDL 56 (127)
T ss_pred CCHHHHHHH-HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCCe
Confidence 455543333 47899999999999999999999998 899999999 88877744
No 97
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=49.85 E-value=57 Score=19.80 Aligned_cols=33 Identities=12% Similarity=0.146 Sum_probs=27.8
Q ss_pred cccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 111 VLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
.++..+|++.++++ ...|-..+- .....|+|.-
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 46889999999998 788888877 7888898863
No 98
>PF05791 Bacillus_HBL: Bacillus haemolytic enterotoxin (HBL); InterPro: IPR008414 This family consists of several Bacillus haemolytic enterotoxins (HblC, HblD, HblA, NheA, and NheB), which can cause food poisoning in humans []. Haemolysin BL (encoded by HBL) and non-haemolytic enterotoxin (encoded by NHE), represent the major enterotoxins produced by Bacillus cereus. Most of the cytotoxic activity of B. cereus isolates has been attributed to the level of Nhe, which may indicate a highly diarrheic potential []. The exact mechanism by which B. cereus causes diarrhoea is unknown. Hbl, cytotoxin K (CytK) and Nhe are all putative causes. Both Hbl and Nhe are three-component cytotoxins and maximal cytotoxicity of Nhe against epithelia is dependent on all three components. Nhe has haemolytic activity against erythrocytes from a variety of species. It is possible that the common structural and functional properties of these toxins indicate that the Hbl/Nhe and ClyA families of toxins constitute a superfamily of pore-forming cytotoxins []. The high virulence of some strains is thought to be due to the greater cytotoxic activity of CytK-1 compared to CytK-2, and to a high level of cytK expression []. Haemolysin BL and non-haemolytic enterotoxin production are both influenced by pH and micro []. This entry is found in cytotoxic proteins that form part of the enterotoxin complex and bind to erythrocytes. HblA is composed of a binding component, B, and two lytic components, L1 and L2. All three subunits act synergically to cause hemolysis.; GO: 0009405 pathogenesis, 0016020 membrane; PDB: 2NRJ_A.
Probab=48.35 E-value=94 Score=25.77 Aligned_cols=61 Identities=5% Similarity=0.257 Sum_probs=48.5
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcccCC
Q 044757 167 GQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHSKVN 227 (227)
Q Consensus 167 ~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 227 (227)
...+.+...|..|+..+..=...+......+..--.-....-...+..+++.+.+++...|
T Consensus 124 ~~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I~~~~~ 184 (184)
T PF05791_consen 124 DKVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEIKKDLN 184 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG-GG--
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHHHhhcC
Confidence 4467788999999999999999998888888888877778888899999999999887664
No 99
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=45.68 E-value=1.3e+02 Score=23.04 Aligned_cols=95 Identities=9% Similarity=0.058 Sum_probs=50.2
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE-----------eecCCCCCcchHHHHHHHHHHHH-
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ-----------FAAGRDLRHGQLENMMQSLTNWL- 180 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~-----------~~~~R~~~~~q~~~l~~~L~~W~- 180 (227)
+..++|+.+||+ .+.+=.| - + .||+...-+..++.-.-+ ....-.|+.+++..+.+ .+.
T Consensus 1 ~I~e~a~~~gvs-~~tlR~Y-e-~---~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~---~~~~ 71 (124)
T TIGR02051 1 TIGELAKAAGVN-VETIRYY-E-R---KGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLG---LVDG 71 (124)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHh---cccC
Confidence 357899999998 7888666 3 3 688863323323322212 00111233333333322 221
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 044757 181 DTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQ 216 (227)
Q Consensus 181 ~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~ 216 (227)
..+..+...+++++..++++.++-...+..++....
T Consensus 72 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~ 107 (124)
T TIGR02051 72 THCREMYELASRKLKSVQAKMADLLRIERLLEELLE 107 (124)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 234555666667777777666666555555554444
No 100
>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=45.34 E-value=47 Score=21.81 Aligned_cols=35 Identities=14% Similarity=0.144 Sum_probs=29.3
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
...++..+|++.++++ ...|...+= .....|+|.-
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 3568999999999998 888988776 7788888874
No 101
>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=43.58 E-value=33 Score=25.49 Aligned_cols=36 Identities=22% Similarity=0.306 Sum_probs=27.2
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
++.++-++|++.++++ ..+|-.++- .....|+|..+
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 5679999999999999 899999998 99999999765
No 102
>PHA02943 hypothetical protein; Provisional
Probab=43.49 E-value=66 Score=26.48 Aligned_cols=45 Identities=16% Similarity=0.190 Sum_probs=33.0
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
|+.-++.+. ..++-|-.+||++||++ ..+++..+. -.=+.|.|+-
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 444555555 56788899999999999 899997666 5556676653
No 103
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=43.33 E-value=29 Score=28.11 Aligned_cols=28 Identities=21% Similarity=0.292 Sum_probs=24.6
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...+||++||+.++|| ...|...+- .|.
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 4569999999999999 899999887 775
No 104
>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=43.12 E-value=29 Score=23.88 Aligned_cols=24 Identities=13% Similarity=0.289 Sum_probs=20.8
Q ss_pred cCccccHHHHHHHhCCCChhHHHHH
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDF 132 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~l 132 (227)
.++.+++-+||+.|+|+ ...|-.|
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 46789999999999999 7887766
No 105
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=42.77 E-value=1.3e+02 Score=23.09 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=19.3
Q ss_pred CCCCCcchHHHHHHHHHHHHHHHHHHHHH
Q 044757 161 GRDLRHGQLENMMQSLTNWLDTSDNILSV 189 (227)
Q Consensus 161 ~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ 189 (227)
+|.++...++.+...|..-.+.++.++..
T Consensus 2 ~~~~~~~~~~~l~~el~~L~d~lEevL~s 30 (104)
T COG4575 2 SREFTDDAIDQLLAELQELLDTLEEVLKS 30 (104)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 56677766677777777666666666554
No 106
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of 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=42.71 E-value=1.4e+02 Score=22.36 Aligned_cols=44 Identities=16% Similarity=0.268 Sum_probs=29.2
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE-EecccCcEEEEEeecCCCCCcchHHH
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKG-KLNQLRRCFEVQFAAGRDLRHGQLEN 171 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g-kIDQ~~~~v~V~~~~~R~~~~~q~~~ 171 (227)
+..++|+.+||+ ...+-.| - + .|++.. .-+. ...|.++++++..
T Consensus 2 ~i~e~a~~~gvs-~~tlr~y-e-~---~gll~~~~r~~---------~gyR~Y~~~~l~~ 46 (113)
T cd01109 2 TIKEVAEKTGLS-ADTLRYY-E-K---EGLLPPVKRDE---------NGIRDFTEEDLEW 46 (113)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCCCcCC---------CCCccCCHHHHHH
Confidence 678999999999 8888877 2 3 577742 2222 2357777776543
No 107
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=42.65 E-value=1e+02 Score=29.84 Aligned_cols=64 Identities=8% Similarity=0.145 Sum_probs=48.0
Q ss_pred HHHHHHHHHhcCCHhhHHhhhhcCCCcc----hHHHHHHHHHHhhhhhccCc-cccHHHHHHHhCCCCh
Q 044757 63 VYIDLLRLFAHGTWTDYKSNAAHLPQLV----PDQAVKLKQLSVLTLAEMNK-VLSYDQLLKELEVANV 126 (227)
Q Consensus 63 ~l~~LL~iF~~G~~~dy~~~~~~~~~l~----~~~~~Klr~LtLlsLa~~~~-~isy~~I~~~L~i~~~ 126 (227)
..+++=.+.+.|++--|-.+--..|... +--+.+.|+.+|.-+|+.++ +|+++.|+..|...+.
T Consensus 425 hAL~vR~A~~~GNY~kFFrLY~~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~ 493 (540)
T KOG1861|consen 425 HALEVRSAVTLGNYHKFFRLYLTAPNMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSM 493 (540)
T ss_pred HHHHHHHHHHhccHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchH
Confidence 3566777888888888776654555543 44467888888888888888 9999999999987643
No 108
>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=42.62 E-value=28 Score=24.72 Aligned_cols=25 Identities=20% Similarity=0.221 Sum_probs=19.9
Q ss_pred HHhhhhhccCccccHHHHHHHhCCC
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVA 124 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~ 124 (227)
+.++.-...++..||.+||+.++.+
T Consensus 6 ~~~v~~IP~G~v~TYg~iA~~~g~p 30 (79)
T cd06445 6 WEALRQIPYGEVTTYGQIAKLAGTP 30 (79)
T ss_pred HHHHhcCCCCCcCcHHHHHHHHCCC
Confidence 4444445578999999999999996
No 109
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=42.01 E-value=57 Score=28.12 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=34.8
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
|-+.|+.+....+.++..+|++.+++| ...|=.++- .....|++.=
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~-kstv~Rll~-tL~~~G~l~~ 60 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMS-KSTVYRFLQ-TMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEE
Confidence 445666554445679999999999999 788888877 6777888754
No 110
>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=41.90 E-value=2e+02 Score=23.84 Aligned_cols=44 Identities=11% Similarity=0.150 Sum_probs=32.9
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL 147 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI 147 (227)
++.+......++..+|++.++|+ ...|=..+= .....|+|.-+-
T Consensus 6 IL~~L~~~~~~t~~eLA~~lgis-~~tV~~~L~-~Le~~GlV~r~~ 49 (203)
T TIGR02702 6 ILSYLLKQGQATAAALAEALAIS-PQAVRRHLK-DLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEee
Confidence 33333334559999999999998 778877666 777899998663
No 111
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=41.80 E-value=1.3e+02 Score=21.58 Aligned_cols=75 Identities=17% Similarity=0.312 Sum_probs=47.9
Q ss_pred HHhhhhhccCccccHHHHHHHh-CCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEee-cCCCCCcchHHHHHHHHH
Q 044757 100 LSVLTLAEMNKVLSYDQLLKEL-EVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFA-AGRDLRHGQLENMMQSLT 177 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L-~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~-~~R~~~~~q~~~l~~~L~ 177 (227)
+-|..|.. +...|.+|.+.+ +++ ...+-.-+= +....|||.=...... -..+.+. +++- .++..+...|.
T Consensus 9 ~IL~~l~~--g~~rf~el~~~l~~is-~~~L~~~L~-~L~~~GLv~r~~~~~~-p~~v~Y~LT~~G---~~l~~~l~~l~ 80 (90)
T PF01638_consen 9 LILRALFQ--GPMRFSELQRRLPGIS-PKVLSQRLK-ELEEAGLVERRVYPEV-PPRVEYSLTEKG---KELLPVLEALE 80 (90)
T ss_dssp HHHHHHTT--SSEEHHHHHHHSTTS--HHHHHHHHH-HHHHTTSEEEEEESSS-SSEEEEEE-HHH---HHHHHHHHHHH
T ss_pred HHHHHHHh--CCCcHHHHHHhcchhH-HHHHHHHHH-HHHHcchhhcccccCC-CCCCccCCCcCH---HHHHHHHHHHH
Confidence 33444554 789999999999 787 666655555 6788999987776533 2333332 2221 34556777888
Q ss_pred HHHHH
Q 044757 178 NWLDT 182 (227)
Q Consensus 178 ~W~~~ 182 (227)
.|..+
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88765
No 112
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=41.58 E-value=52 Score=28.43 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=35.4
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
|+..|+.+...++.++.++|++.++++ ...|...+- +.-..|++.
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 666777777778899999999999998 788888766 544456554
No 113
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=40.32 E-value=51 Score=28.68 Aligned_cols=45 Identities=16% Similarity=0.166 Sum_probs=34.6
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
|+..|+.+...++.++..++++.|+++ ...|-.=+. ..-..|+|.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TIRRDL~-~Le~~g~l~ 50 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTT-GTTIRKDLV-ILEHAGTVI 50 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 778888888888999999999999998 666644444 444567553
No 114
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=39.84 E-value=2e+02 Score=23.26 Aligned_cols=43 Identities=7% Similarity=0.188 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcc
Q 044757 182 TSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHS 224 (227)
Q Consensus 182 ~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (227)
++..++..++..+..+.++.++-..+++..+..+...|..|..
T Consensus 44 ~~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL~~ 86 (162)
T PF05565_consen 44 NIAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYLLD 86 (162)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555667777777777778888888888777776543
No 115
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=39.36 E-value=4.4e+02 Score=26.97 Aligned_cols=119 Identities=13% Similarity=0.154 Sum_probs=69.7
Q ss_pred HHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHh--HhcCceEEEec--ccCcEEEEEee----cCCC----C
Q 044757 97 LKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINEC--MYVGIVKGKLN--QLRRCFEVQFA----AGRD----L 164 (227)
Q Consensus 97 lr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~a--i~~gLI~gkID--Q~~~~v~V~~~----~~R~----~ 164 (227)
+.+++++-|-+..-.++|++|.+.++++ ..++-..|- .. +...++.+..+ ..+.++.+.+- .+|+ +
T Consensus 566 t~Qm~VLlLFN~~d~lt~~eI~~~t~i~-~~~l~~~L~-Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~~~ 643 (725)
T KOG2166|consen 566 TYQMAVLLLFNNTEKLTYEEILEQTNLG-HEDLARLLQ-SLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIPLP 643 (725)
T ss_pred hHHHHHHHHccchhhccHHHHHHHhCCC-HHHHHHHHH-HHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccCCC
Confidence 4567788888888889999999999999 777776655 43 22112222111 45667777742 2232 2
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcc
Q 044757 165 RHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHS 224 (227)
Q Consensus 165 ~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (227)
...+-+.....++.|+.. .|++.+.++=++++ ...|.+=+.+-++..++.++.
T Consensus 644 ~~~e~~~~~~~ve~dRk~------~i~AaIVRIMK~rK-~l~h~~Lv~Ev~~ql~~RF~p 696 (725)
T KOG2166|consen 644 PMDERKKVVEDVDKDRKY------AIDAAIVRIMKSRK-VLGHQQLVSEVVEQLSERFKP 696 (725)
T ss_pred CchhHHHHHhhhhhHHHH------HHHHHHHHHHHhhc-cccHHHHHHHHHHHHhhhcCC
Confidence 233556667777777764 33444444332222 345666666666666665553
No 116
>KOG3809 consensus Microtubule-binding protein MIP-T3 [Cytoskeleton]
Probab=39.29 E-value=87 Score=30.07 Aligned_cols=59 Identities=12% Similarity=0.171 Sum_probs=41.5
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhh
Q 044757 164 LRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSV 222 (227)
Q Consensus 164 ~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (227)
|-+++++.|..-|..|.+.-..--..+++..+......+-.+..-.+++..+++.++.|
T Consensus 504 ~i~eD~daMq~EL~mWrse~rq~~~elq~eq~~t~~a~epL~~~la~lq~~I~d~~e~i 562 (583)
T KOG3809|consen 504 FINEDIDAMQKELEMWRSEQRQNEQELQNEQAATFGASEPLYNILANLQKEINDTKEEI 562 (583)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999988777777776666555555555555556666666666554
No 117
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=38.33 E-value=39 Score=28.46 Aligned_cols=81 Identities=17% Similarity=0.185 Sum_probs=49.4
Q ss_pred HHHHHHHHhcCCHhhHHhhh---hcCCCcchHHHHHHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhc
Q 044757 64 YIDLLRLFAHGTWTDYKSNA---AHLPQLVPDQAVKLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYV 140 (227)
Q Consensus 64 l~~LL~iF~~G~~~dy~~~~---~~~~~l~~~~~~Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~ 140 (227)
+-.+..++............ ...+.|++.|.+-|+.--=+..-..-|.++-.+||+.+||+ ...+.+-+= +|. .
T Consensus 128 l~~~~~~~~~~~~~~~~~~~~~~~~~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGIS-kst~~ehLR-rAe-~ 204 (215)
T COG3413 128 LRDLLEILNFEDKEEVIESAFVEIGKNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGIS-KSTLSEHLR-RAE-R 204 (215)
T ss_pred HHHHHHHhcccceeeeccccccccccccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC-HHHHHHHHH-HHH-H
Confidence 34445555555444222221 12345888876666554445555567999999999999998 677776655 555 5
Q ss_pred CceEEEe
Q 044757 141 GIVKGKL 147 (227)
Q Consensus 141 gLI~gkI 147 (227)
+|+.+-+
T Consensus 205 Kl~~~~~ 211 (215)
T COG3413 205 KLIEAYF 211 (215)
T ss_pred HHHHHhh
Confidence 5554433
No 118
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=38.20 E-value=1.3e+02 Score=20.62 Aligned_cols=61 Identities=15% Similarity=0.241 Sum_probs=46.1
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHH
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTN 178 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~ 178 (227)
.|..+.+.+++++ +....++= + ..+-+-.++..+++.++.-..++.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~-~~~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPD-ELDNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCc-hhhhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 3678888999983 33233333 3 345568999999999999999999999999888877754
No 119
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=38.17 E-value=37 Score=27.39 Aligned_cols=27 Identities=7% Similarity=0.190 Sum_probs=24.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 568999999999999 899999888 775
No 120
>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=37.36 E-value=41 Score=26.93 Aligned_cols=28 Identities=21% Similarity=0.122 Sum_probs=23.9
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.||++ ...|...+- +|.
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 3569999999999999 899998877 664
No 121
>PRK00708 sec-independent translocase; Provisional
Probab=37.27 E-value=1.8e+02 Score=24.97 Aligned_cols=35 Identities=9% Similarity=0.098 Sum_probs=29.9
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWA 197 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~ 197 (227)
+|+++++..+...+..|..++..+.+.+.+++...
T Consensus 19 V~GPkrLP~~~R~lGk~v~k~R~~a~e~r~~~~e~ 53 (209)
T PRK00708 19 VVGPKDLPPMLRAFGKMTARMRKMAGEFRRQFDEA 53 (209)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999998888887766543
No 122
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=37.11 E-value=62 Score=28.45 Aligned_cols=47 Identities=11% Similarity=0.044 Sum_probs=36.7
Q ss_pred HHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 96 KLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 96 Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.-|+..|+.+...++.++..+|++.|+++ ...+-.=+. ..-..|++.
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 44788889888878889999999999998 666655555 444577776
No 123
>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=37.05 E-value=2.2e+02 Score=22.96 Aligned_cols=50 Identities=14% Similarity=0.230 Sum_probs=37.4
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe--cccCcEEEEEee
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL--NQLRRCFEVQFA 159 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI--DQ~~~~v~V~~~ 159 (227)
.++.++=++||..||++ ..+|=..+- .....||+.-+= |..++...-.|.
T Consensus 25 ~~~~~tdEeLa~~Lgi~-~~~VRk~L~-~L~e~~Lv~~~r~r~~~~gw~~Y~w~ 76 (158)
T TIGR00373 25 IKGEFTDEEISLELGIK-LNEVRKALY-ALYDAGLADYKRRKDDETGWYEYTWR 76 (158)
T ss_pred ccCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCceeeeeeecCCCcEEEEEE
Confidence 45689999999999998 899999988 899999994222 233344444454
No 124
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.77 E-value=1.9e+02 Score=22.09 Aligned_cols=26 Identities=15% Similarity=0.307 Sum_probs=20.4
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
+..++|+.+||+ ...+-.| - + .||+.
T Consensus 2 ~IgevA~~~gvs-~~tLRyY-e-~---~GLl~ 27 (127)
T cd04784 2 KIGELAKKTGCS-VETIRYY-E-K---EGLLP 27 (127)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCC
Confidence 578999999998 7888776 2 2 68886
No 125
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=36.32 E-value=43 Score=26.66 Aligned_cols=27 Identities=15% Similarity=0.347 Sum_probs=23.8
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.||++ ...|...+- +|+
T Consensus 134 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 160 (172)
T PRK12523 134 DGMGHAEIAERLGVS-VSRVRQYLA-QGL 160 (172)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 899998887 776
No 126
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=36.18 E-value=58 Score=20.57 Aligned_cols=31 Identities=19% Similarity=0.289 Sum_probs=23.0
Q ss_pred HhhhhhccCccccHHHHHHHhCCCChhHHHHHHH
Q 044757 101 SVLTLAEMNKVLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 101 tLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
.++.++... .|+.+||+.+|++ .+.|..++-
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 445555433 7999999999999 788887654
No 127
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=35.92 E-value=41 Score=21.12 Aligned_cols=23 Identities=17% Similarity=0.185 Sum_probs=17.8
Q ss_pred cccHHHHHHHhCCCChhHHHHHHH
Q 044757 111 VLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
-.|+.+||+.||++ ...|-.|+=
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 68999999999999 899998854
No 128
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=35.62 E-value=1.5e+02 Score=31.11 Aligned_cols=50 Identities=16% Similarity=0.248 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhh
Q 044757 173 MQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSV 222 (227)
Q Consensus 173 ~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 222 (227)
...+..|+.++-.-+..++.++..++.++++....+.++..+.+++..++
T Consensus 264 leqlqEfkSkim~qqa~Lqrel~raR~e~keaqe~ke~~k~emad~ad~i 313 (1243)
T KOG0971|consen 264 LEQLQEFKSKIMEQQADLQRELKRARKEAKEAQEAKERYKEEMADTADAI 313 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46889999999999999999999999999999888888887777765554
No 129
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=35.55 E-value=74 Score=27.59 Aligned_cols=47 Identities=11% Similarity=0.113 Sum_probs=38.0
Q ss_pred HHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 97 LKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 97 lr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
-|+..++.+...++.++-.+|++.++++ ...+-..+- +.-..|+|.-
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 3666788888889999999999999998 788877766 6656777754
No 130
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=35.37 E-value=63 Score=23.24 Aligned_cols=32 Identities=16% Similarity=0.335 Sum_probs=25.4
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
||+++++..++++ . .||. ..+..|+|.-...+
T Consensus 1 is~~e~~~~~~i~-~----~~l~-~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-P----EFLR-ELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-H----HHHH-HHHHCCCeeecCCC
Confidence 6899999999998 3 3555 56668999987766
No 131
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=35.27 E-value=47 Score=25.96 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=23.8
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||++||+.+|++ ...|...+- .|.
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 3568999999999999 899998877 664
No 132
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=35.09 E-value=46 Score=26.80 Aligned_cols=27 Identities=7% Similarity=0.336 Sum_probs=23.6
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.||++ ...|...+- .|+
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 458999999999999 899998877 765
No 133
>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=35.08 E-value=86 Score=26.82 Aligned_cols=45 Identities=16% Similarity=0.234 Sum_probs=36.9
Q ss_pred HHHHhhhhhc-cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 98 KQLSVLTLAE-MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 98 r~LtLlsLa~-~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
|-+.++.+.. ..+.++..+|++.+++| ...+-.++- .....|.+.
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 4467776543 46789999999999999 889999888 788899987
No 134
>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=34.47 E-value=47 Score=22.44 Aligned_cols=23 Identities=17% Similarity=0.118 Sum_probs=19.9
Q ss_pred cccHHHHHHHhCCCChhHHHHHHH
Q 044757 111 VLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
-.++.+||+.|+++ ...|-.|.=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 47899999999999 888988854
No 135
>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=34.24 E-value=1.4e+02 Score=19.63 Aligned_cols=49 Identities=12% Similarity=0.177 Sum_probs=32.8
Q ss_pred hhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcE
Q 044757 103 LTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRC 153 (227)
Q Consensus 103 lsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~ 153 (227)
..++...+..+..+|++.++++ ...+=..|= ++...|+|+=.=|..++.
T Consensus 10 ~~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~-~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 10 RALAHSDGPMTQSDLAERLGIS-KSTVSRIIK-KLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHT--TS-BEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEESSCTT
T ss_pred HHHHccCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecCCCCcCC
Confidence 3344567889999999999998 677776655 888899997665554443
No 136
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=34.23 E-value=49 Score=26.44 Aligned_cols=28 Identities=18% Similarity=0.417 Sum_probs=24.3
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||++||+.+|++ ...|...+- +|+
T Consensus 133 ~~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 160 (172)
T PRK09651 133 LDGLTYSEIAHKLGVS-VSSVKKYVA-KAT 160 (172)
T ss_pred ccCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 4568999999999999 899998887 766
No 137
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.16 E-value=51 Score=25.48 Aligned_cols=27 Identities=7% Similarity=0.040 Sum_probs=23.6
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- +|+
T Consensus 121 ~~~s~~EIA~~l~is-~~tV~~~~~-ra~ 147 (154)
T PRK06759 121 VGKTMGEIALETEMT-YYQVRWIYR-QAL 147 (154)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999999 899998887 765
No 138
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.72 E-value=52 Score=25.58 Aligned_cols=27 Identities=0% Similarity=-0.006 Sum_probs=23.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
..+||++||+.||++ ...|...+- +|.
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 899988776 665
No 139
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=33.36 E-value=50 Score=26.54 Aligned_cols=27 Identities=7% Similarity=0.226 Sum_probs=22.9
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|+
T Consensus 132 e~~s~~EIA~~lgis-~~tV~~~l~-ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIP-IGTVKSRIH-AAL 158 (179)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999999 888988877 664
No 140
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=33.01 E-value=1.6e+02 Score=19.95 Aligned_cols=16 Identities=13% Similarity=0.414 Sum_probs=6.6
Q ss_pred HHHHHHHHHHHHHhhh
Q 044757 207 HKMEVKSHLQDVKKSV 222 (227)
Q Consensus 207 ~~~~~~~~~~~~~~~~ 222 (227)
.-+++...++.+++++
T Consensus 22 en~~i~~~ve~i~env 37 (55)
T PF05377_consen 22 ENEEISESVEKIEENV 37 (55)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3334444444444443
No 141
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=32.83 E-value=52 Score=26.67 Aligned_cols=27 Identities=15% Similarity=0.192 Sum_probs=23.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 358999999999999 899998877 654
No 142
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=32.74 E-value=54 Score=25.62 Aligned_cols=27 Identities=11% Similarity=0.159 Sum_probs=23.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|+
T Consensus 124 ~~~s~~EIA~~lgis-~~tV~~~l~-ra~ 150 (163)
T PRK07037 124 HGETQKDIARELGVS-PTLVNFMIR-DAL 150 (163)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 899998866 665
No 143
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=32.30 E-value=56 Score=25.96 Aligned_cols=28 Identities=18% Similarity=0.447 Sum_probs=24.0
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||++||+.||++ ...|...+- +|+
T Consensus 132 ~eg~s~~EIA~~l~is-~~tV~~~l~-ra~ 159 (168)
T PRK12525 132 LEGLTYVEIGERLGVS-LSRIHQYMV-EAF 159 (168)
T ss_pred HcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 3568999999999999 899988877 776
No 144
>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=32.25 E-value=1.4e+02 Score=19.14 Aligned_cols=35 Identities=26% Similarity=0.257 Sum_probs=28.3
Q ss_pred cCcccc-HHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 108 MNKVLS-YDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 108 ~~~~is-y~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.+..++ -.+|++.++++ ...|-..+- ..-..|+|.
T Consensus 21 ~~~~~~~~~~la~~~~is-~~~v~~~l~-~L~~~G~i~ 56 (66)
T cd07377 21 PGDRLPSERELAEELGVS-RTTVREALR-ELEAEGLVE 56 (66)
T ss_pred CCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 344455 99999999998 888988887 777888875
No 145
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=32.10 E-value=68 Score=29.03 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=34.9
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEeccc
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQL 150 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~ 150 (227)
.-.+=++||+.||++ ...|=.++= +|...|+|+-+|+..
T Consensus 28 ~g~tQ~eIA~~lgiS-R~~VsRlL~-~Ar~~GiV~I~I~~~ 66 (318)
T PRK15418 28 DGLTQSEIGERLGLT-RLKVSRLLE-KGRQSGIIRVQINSR 66 (318)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHHHcCcEEEEEeCC
Confidence 457888999999998 889999988 999999999999864
No 146
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=32.08 E-value=50 Score=23.24 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=17.3
Q ss_pred ccHHHHHHHhCCCChhHHHHH
Q 044757 112 LSYDQLLKELEVANVRELEDF 132 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~l 132 (227)
.+-++|++.|++| ..|.|-+
T Consensus 45 a~~~el~~~CgL~-~aEAeLl 64 (70)
T PF10975_consen 45 ASVEELMEECGLS-RAEAELL 64 (70)
T ss_pred CCHHHHHHHcCCC-HHHHHHH
Confidence 6779999999999 8999943
No 147
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.03 E-value=74 Score=19.62 Aligned_cols=25 Identities=12% Similarity=0.258 Sum_probs=20.8
Q ss_pred cccHHHHHHHhCCCChhHHHHHHHHHh
Q 044757 111 VLSYDQLLKELEVANVRELEDFLINEC 137 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI~~a 137 (227)
-.++.+|++.++++ ...|..++- .+
T Consensus 18 g~s~~eia~~l~is-~~tv~~~~~-~~ 42 (58)
T smart00421 18 GLTNKEIAERLGIS-EKTVKTHLS-NI 42 (58)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 36999999999998 889988765 54
No 148
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.70 E-value=58 Score=25.43 Aligned_cols=28 Identities=21% Similarity=0.305 Sum_probs=23.6
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||++||+.+|++ ...|...+- .|+
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 3568999999999999 888988876 665
No 149
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.59 E-value=56 Score=26.08 Aligned_cols=27 Identities=22% Similarity=0.454 Sum_probs=22.8
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- .|.
T Consensus 144 ~g~s~~eIA~~lgis-~~tV~~~l~-Rar 170 (179)
T PRK12514 144 EGLSYKELAERHDVP-LNTMRTWLR-RSL 170 (179)
T ss_pred cCCCHHHHHHHHCCC-hHHHHHHHH-HHH
Confidence 358999999999999 899988777 664
No 150
>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=31.59 E-value=67 Score=21.05 Aligned_cols=31 Identities=19% Similarity=0.313 Sum_probs=20.1
Q ss_pred HHhhhhhccCccccHHHHHHHhCCCChhHHHHHH
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVANVRELEDFL 133 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lv 133 (227)
+.++...+.+. +..+||+.+||+ ...|-.++
T Consensus 13 ~~iI~~~e~g~--s~~~ia~~fgv~-~sTv~~I~ 43 (53)
T PF04218_consen 13 LEIIKRLEEGE--SKRDIAREFGVS-RSTVSTIL 43 (53)
T ss_dssp HHHHHHHHCTT---HHHHHHHHT---CCHHHHHH
T ss_pred HHHHHHHHcCC--CHHHHHHHhCCC-HHHHHHHH
Confidence 35555555554 999999999999 67777654
No 151
>PHA02763 hypothetical protein; Provisional
Probab=31.43 E-value=67 Score=23.89 Aligned_cols=51 Identities=20% Similarity=0.227 Sum_probs=40.6
Q ss_pred cccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCC
Q 044757 111 VLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDL 164 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~ 164 (227)
.++-+-+++-++.+.-+.||.|+- +| ..|=.-+||.-.=.+.|-|+..|-|
T Consensus 52 p~t~~~LsKYv~~SGFe~VEeWl~-eA--rrLh~~~id~~ryeiivi~in~~~f 102 (102)
T PHA02763 52 PVTEYCLSKYVKFSGFENVEEWLN-EA--RRLHNDKIDPERYEIIVIWINGRLF 102 (102)
T ss_pred CchHHHHHHHhhhcchhhHHHHHH-HH--HHHhcCCCChhheEEEEEEEcCccC
Confidence 456666777788877788999998 77 4566789999999999999987754
No 152
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=31.09 E-value=1.7e+02 Score=20.25 Aligned_cols=47 Identities=19% Similarity=0.205 Sum_probs=37.0
Q ss_pred cCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 140 VGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDNILSVIQD 192 (227)
Q Consensus 140 ~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~ 192 (227)
.+-+...++-.++.+.|++.. .+...|+..+..|...+.-+...+++
T Consensus 30 ~~~~~~~~~~~~~~L~i~~~A------~d~~~LRasvns~l~~l~l~~~~i~e 76 (76)
T PF09341_consen 30 PSRVKRELSVDGNKLVITIEA------EDLRSLRASVNSFLDLLKLAEETIEE 76 (76)
T ss_dssp S-SSEEEEEEESSEEEEEEEE------SSHHHHHHHHHHHHHHHHHHCHHH--
T ss_pred CCcEEEEEEEeCCEEEEEEEE------CCHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 467888888888899998764 45788999999999999888877753
No 153
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=30.90 E-value=1.7e+02 Score=26.06 Aligned_cols=39 Identities=21% Similarity=0.419 Sum_probs=33.3
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHH
Q 044757 166 HGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEED 204 (227)
Q Consensus 166 ~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~ 204 (227)
..+++.++..|..|.++.+.=+..++.++..+++.....
T Consensus 62 ~~~l~~ak~eLqe~eek~e~~l~~Lq~ql~~l~akI~k~ 100 (258)
T PF15397_consen 62 HKQLQQAKAELQEWEEKEESKLSKLQQQLEQLDAKIQKT 100 (258)
T ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 356888999999999999999999999998888776644
No 154
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=30.88 E-value=68 Score=23.90 Aligned_cols=27 Identities=15% Similarity=0.399 Sum_probs=23.9
Q ss_pred HHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 116 QLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 116 ~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.||..++++ .++|+..+- +....|||+
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 478889999 999999888 899999986
No 155
>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=30.80 E-value=59 Score=26.43 Aligned_cols=28 Identities=7% Similarity=0.107 Sum_probs=23.8
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.||++ ...|...+- +|.
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 3568999999999999 899998877 664
No 156
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.42 E-value=2.3e+02 Score=21.07 Aligned_cols=45 Identities=18% Similarity=0.281 Sum_probs=29.6
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE-ecccCcEEEEEeecCCCCCcchHHH
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKGK-LNQLRRCFEVQFAAGRDLRHGQLEN 171 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk-IDQ~~~~v~V~~~~~R~~~~~q~~~ 171 (227)
+..++++.+||+ ...+=.| - + .|||... .+..+ ..|.++..++..
T Consensus 2 ~i~eva~~~gis-~~tlR~y-e-~---~GLi~p~~~~~~n--------gyR~Y~~~~i~~ 47 (108)
T cd01107 2 TIGEFAKLSNLS-IKALRYY-D-K---IGLLKPAYVDPDT--------GYRYYSAEQLER 47 (108)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---cCCCCCCcCCCCC--------CccccCHHHHHH
Confidence 578999999999 7888777 2 3 5888763 33322 246666665443
No 157
>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=30.22 E-value=63 Score=25.21 Aligned_cols=27 Identities=22% Similarity=0.272 Sum_probs=23.6
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- .|.
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 468999999999999 899998887 765
No 158
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=30.21 E-value=29 Score=25.04 Aligned_cols=38 Identities=11% Similarity=0.174 Sum_probs=25.4
Q ss_pred CcEEEEEeecCCCCCcchHHHH---HHHHHHHHHHHHHHHH
Q 044757 151 RRCFEVQFAAGRDLRHGQLENM---MQSLTNWLDTSDNILS 188 (227)
Q Consensus 151 ~~~v~V~~~~~R~~~~~q~~~l---~~~L~~W~~~~~~~l~ 188 (227)
++.|+|...--|++++++.++| .+++..|++.+...+.
T Consensus 27 ~nklyvng~~~R~Lt~~E~~eL~~y~~~v~~y~~~l~~~iq 67 (76)
T PF06394_consen 27 NNKLYVNGKYARDLTPDEQQELKTYQKKVAAYKEQLQQQIQ 67 (76)
T ss_dssp TTEEEETTCEEEE--HHHHHHHHHHHHHHHHHHHHHTT---
T ss_pred CCEEEECCEeeccCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777899999887665 4688889888776543
No 159
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=30.15 E-value=62 Score=25.57 Aligned_cols=27 Identities=15% Similarity=0.123 Sum_probs=23.5
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 568999999999999 899998887 765
No 160
>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=29.99 E-value=1.3e+02 Score=21.79 Aligned_cols=43 Identities=26% Similarity=0.284 Sum_probs=29.2
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHH
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLE 170 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~ 170 (227)
+..++++.|||+ ...+-.| . + .|++...-+..+ .|.++..++.
T Consensus 2 ~~~eva~~~gi~-~~tlr~~-~-~---~Gll~~~~~~~g---------~r~y~~~dv~ 44 (100)
T cd00592 2 TIGEVAKLLGVS-VRTLRYY-E-E---KGLLPPERSENG---------YRLYSEEDLE 44 (100)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCcCCCcCCCC---------CcccCHHHHH
Confidence 567899999999 7888877 3 3 688765443332 3556666654
No 161
>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=29.93 E-value=97 Score=27.58 Aligned_cols=41 Identities=24% Similarity=0.277 Sum_probs=35.8
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEeccc
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQL 150 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~ 150 (227)
..+.++..++++..++| .+-+-..++ +....++|+|++|..
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 666766778 787899999999998
No 162
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=29.81 E-value=2.5e+02 Score=21.22 Aligned_cols=52 Identities=10% Similarity=0.213 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhcc
Q 044757 173 MQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVHS 224 (227)
Q Consensus 173 ~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (227)
.+.+.+=.+-...+...+......+.+..+...+.+.+-+...+.+|..+|.
T Consensus 38 ~~tI~qq~~~~~~L~~~~~~~r~~~~~~~~~~qq~r~~~e~~~e~ik~~lk~ 89 (110)
T PF10828_consen 38 AQTIQQQEDANQELKAQLQQNRQAVEEQQKREQQLRQQSEERRESIKTALKD 89 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 3344444444455555555544455555554455555555666666666654
No 163
>PF14523 Syntaxin_2: Syntaxin-like protein; PDB: 2DNX_A.
Probab=29.77 E-value=2.2e+02 Score=20.58 Aligned_cols=55 Identities=11% Similarity=0.322 Sum_probs=36.1
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh---hHHHHHHHHHHHHHHHHHHhh
Q 044757 167 GQLENMMQSLTNWLDTSDNILSVIQDKIKWAETM---CEEDKKHKMEVKSHLQDVKKS 221 (227)
Q Consensus 167 ~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~ 221 (227)
.+-..+++++......+..+...+...+...... .......+...+....+.+.+
T Consensus 26 ~Ds~~lR~~i~~~~~~~~~l~k~~~~~l~~l~~~~~~~~~~~~~k~~~~KL~~df~~~ 83 (102)
T PF14523_consen 26 RDSQELREKIHQLIQKTNQLIKEISELLKKLNSLSSDRSNDRQQKLQREKLSRDFKEA 83 (102)
T ss_dssp S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSH----HHHHHHHHHHHHHHHHHHH
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 4467799999999999999999999988887776 333334444444444444433
No 164
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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 su
Probab=29.52 E-value=2.7e+02 Score=21.67 Aligned_cols=95 Identities=14% Similarity=0.138 Sum_probs=55.2
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchH----------------HHHHHHH
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQL----------------ENMMQSL 176 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~----------------~~l~~~L 176 (227)
+..++++.+||+ .+.+-.|- ..||+.-.-...++ .|.++..++ +.++.-|
T Consensus 2 ~Ige~a~~~gvs-~~tLRyYE-----~~GLl~p~~r~~~g--------yR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll 67 (131)
T cd04786 2 KIGELAKRSGMA-ASRIRFYE-----AEGLLSSVERSANG--------YRDYPPETVWVLEIISSAQQAGFSLDEIRQLL 67 (131)
T ss_pred CHHHHHHHHCcC-HHHHHHHH-----HCCCCCCCCcCCCC--------CeecCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 578899999998 77877762 26888643222222 233333332 1222222
Q ss_pred HHHH--HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhh
Q 044757 177 TNWL--DTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKS 221 (227)
Q Consensus 177 ~~W~--~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (227)
..+. ..+..+...++.++..+.++.++..+.+..++..+......
T Consensus 68 ~~~~~~~~~~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~~~ 114 (131)
T cd04786 68 PADASNWQHDELLAALERKVADIEALEARLAQNKAQLLVLIDLIESK 114 (131)
T ss_pred hcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 2221 12355666777777777777777777777777666655443
No 165
>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=29.51 E-value=87 Score=19.43 Aligned_cols=25 Identities=8% Similarity=0.118 Sum_probs=21.0
Q ss_pred cccHHHHHHHhCCCChhHHHHHHHHHh
Q 044757 111 VLSYDQLLKELEVANVRELEDFLINEC 137 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI~~a 137 (227)
..++.+|++.++++ ...|..++= ++
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 46999999999998 889998865 44
No 166
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=29.42 E-value=1.3e+02 Score=21.73 Aligned_cols=38 Identities=13% Similarity=0.149 Sum_probs=31.6
Q ss_pred hhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 105 LAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 105 La~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
....++..+-.+|+..++.| .+-||.++- ..+..|-|+
T Consensus 10 ~l~~~gr~s~~~Ls~~~~~p-~~~VeaMLe-~l~~kGkve 47 (78)
T PRK15431 10 LLALRGRMEAAQISQTLNTP-QPMINAMLQ-QLESMGKAV 47 (78)
T ss_pred HHHHcCcccHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeE
Confidence 33467889999999999999 889998888 888777765
No 167
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.19 E-value=66 Score=26.11 Aligned_cols=28 Identities=11% Similarity=0.101 Sum_probs=23.3
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.+|++ ...|...+- +|.
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 3568999999999999 899987766 665
No 168
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=29.17 E-value=68 Score=25.09 Aligned_cols=28 Identities=18% Similarity=0.392 Sum_probs=23.9
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.+|++ ...|...+- +|.
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 3568999999999999 899998877 664
No 169
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=28.95 E-value=1.1e+02 Score=25.43 Aligned_cols=38 Identities=8% Similarity=0.179 Sum_probs=32.2
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
.-.+..+||+.|+|+ ...|+..+- .+-..|++.-.++=
T Consensus 176 ~g~s~~eIa~~l~iS-~~Tv~~~~~-~~~~~~~~~~~~~~ 213 (225)
T PRK10046 176 VQHTAETVAQALTIS-RTTARRYLE-YCASRHLIIAEIVH 213 (225)
T ss_pred CCcCHHHHHHHhCcc-HHHHHHHHH-HHHhCCeEEEEeec
Confidence 357899999999999 899999888 78888998877653
No 170
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=28.95 E-value=4.3e+02 Score=23.74 Aligned_cols=82 Identities=12% Similarity=0.070 Sum_probs=54.8
Q ss_pred HHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEe----ecCCCCCcchHHHH
Q 044757 97 LKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQF----AAGRDLRHGQLENM 172 (227)
Q Consensus 97 lr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~----~~~R~~~~~q~~~l 172 (227)
.|++.++.+...++.++=.++|+.++++ ...+..=+ +++..--+.-..+.-.+.-++.. ..|..|++++...+
T Consensus 8 ~RL~~ii~~L~~~~~vta~~lA~~~~VS-~RTi~RDi--~~L~~~gvPI~~e~G~~~gy~~~~~~~L~pl~ft~~E~~Al 84 (311)
T COG2378 8 ERLLQIIQILRAKETVTAAELADEFEVS-VRTIYRDI--ATLRAAGVPIEGERGKGGGYRLRPGFKLPPLMFTEEEAEAL 84 (311)
T ss_pred HHHHHHHHHHHhCccchHHHHHHhcCCC-HHHHHHHH--HHHHHCCCCeEeecCCCccEEEccCCCCCcccCCHHHHHHH
Confidence 4678888887777779999999999998 67665542 23332223322222222333332 25778999999999
Q ss_pred HHHHHHHHH
Q 044757 173 MQSLTNWLD 181 (227)
Q Consensus 173 ~~~L~~W~~ 181 (227)
...+..|.+
T Consensus 85 ~~~l~~l~~ 93 (311)
T COG2378 85 LLALRALAS 93 (311)
T ss_pred HHHHHHHHh
Confidence 998888886
No 171
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=28.81 E-value=2.3e+02 Score=20.46 Aligned_cols=47 Identities=13% Similarity=0.263 Sum_probs=26.9
Q ss_pred EEEEeecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 044757 154 FEVQFAAGRDLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETM 200 (227)
Q Consensus 154 v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~ 200 (227)
-.|....++.|=..+.+.+...|..=...+..-+..++.+.....+.
T Consensus 45 ~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~ 91 (106)
T PF01920_consen 45 RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKK 91 (106)
T ss_dssp -EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445567777666676666666666666666555555444444333
No 172
>PRK15396 murein lipoprotein; Provisional
Probab=28.75 E-value=2.3e+02 Score=20.48 Aligned_cols=50 Identities=2% Similarity=0.104 Sum_probs=34.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 044757 167 GQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQ 216 (227)
Q Consensus 167 ~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~ 216 (227)
++++.|...+..-..+++.+...+..-...+.+.++|..+.-+++.-.+.
T Consensus 25 ~kvd~LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~RlDn~~~ 74 (78)
T PRK15396 25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNQAT 74 (78)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36777888888888888888877777666666666666565555554443
No 173
>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=28.62 E-value=1e+02 Score=22.28 Aligned_cols=34 Identities=24% Similarity=0.260 Sum_probs=23.4
Q ss_pred HHhhhhhccCccccHHHHHHHhCCCChhHHHHHHH
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
..|+.+-..++.+|-+++|.+++.+ .++|...+=
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~-~e~v~~~L~ 60 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWP-VEEVRAALA 60 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT---HHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCC-HHHHHHHHH
Confidence 3456555568999999999999999 899987643
No 174
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=28.52 E-value=1.3e+02 Score=26.35 Aligned_cols=56 Identities=11% Similarity=0.110 Sum_probs=39.7
Q ss_pred HHHHhhhhhc-cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 98 KQLSVLTLAE-MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 98 r~LtLlsLa~-~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
|-+.|+.+.. ..+.++..+|++.+++| ...+=.++- .....|++.- |...+...+.
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 4456665543 45679999999999999 788888888 7788888843 4444444433
No 175
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=28.50 E-value=2.6e+02 Score=21.00 Aligned_cols=43 Identities=21% Similarity=0.301 Sum_probs=28.9
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHH
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLE 170 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~ 170 (227)
+..++|+.+||+ ...+-.| - + .|||...-+. ...|.++..++.
T Consensus 2 ~i~eva~~~gvs-~~tlR~Y-e-~---~GLl~p~r~~---------~g~R~Y~~~~~~ 44 (112)
T cd01282 2 RIGELAARTGVS-VRSLRYY-E-E---QGLLVPERSA---------NGYRDYDEAAVD 44 (112)
T ss_pred CHHHHHHHHCCC-HHHHHHH-H-H---CCCCCCCcCC---------CCCeecCHHHHH
Confidence 578999999999 8888877 2 3 5888753222 234666666543
No 176
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.22 E-value=70 Score=26.04 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=23.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 468999999999999 899988876 654
No 177
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=28.06 E-value=3e+02 Score=21.68 Aligned_cols=52 Identities=12% Similarity=0.260 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhh
Q 044757 170 ENMMQSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKS 221 (227)
Q Consensus 170 ~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (227)
..+...|++-.+.+...-..+.+++..+...-.+..+-.+.+.++|.+++..
T Consensus 46 ~~v~kql~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~d 97 (126)
T PF07889_consen 46 ASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVRED 97 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 3455566666666666666666666666666666666666666666666543
No 178
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=27.96 E-value=69 Score=25.85 Aligned_cols=27 Identities=7% Similarity=-0.018 Sum_probs=23.5
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.||+| ...|...+- +|+
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 568999999999998 899998877 665
No 179
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=27.62 E-value=1.3e+02 Score=26.03 Aligned_cols=56 Identities=18% Similarity=0.243 Sum_probs=39.0
Q ss_pred HHHHhhhhhc-cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 98 KQLSVLTLAE-MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 98 r~LtLlsLa~-~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
|-|.|+++.. ....++..+|++.+++| ...+=.++. .....|+++= |..+++..+.
T Consensus 5 ral~iL~~l~~~~~~l~l~ela~~~glp-ksT~~RlL~-tL~~~G~v~~--d~~~g~Y~Lg 61 (246)
T COG1414 5 RALAILDLLAEGPGGLSLAELAERLGLP-KSTVHRLLQ-TLVELGYVEQ--DPEDGRYRLG 61 (246)
T ss_pred HHHHHHHHHHhCCCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEE--cCCCCcEeeh
Confidence 3456665543 33448999999999999 889998988 7888888753 2223444444
No 180
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=27.56 E-value=73 Score=25.19 Aligned_cols=27 Identities=15% Similarity=0.145 Sum_probs=23.2
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.||++ ...|...+- +|.
T Consensus 133 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 159 (173)
T PRK09645 133 RGWSTAQIAADLGIP-EGTVKSRLH-YAL 159 (173)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 468999999999999 899988877 665
No 181
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=27.41 E-value=72 Score=25.63 Aligned_cols=27 Identities=7% Similarity=-0.047 Sum_probs=23.1
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 458999999999999 899988876 654
No 182
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=27.37 E-value=73 Score=25.31 Aligned_cols=27 Identities=15% Similarity=0.199 Sum_probs=23.2
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 568999999999999 899988877 654
No 183
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=27.36 E-value=72 Score=26.01 Aligned_cols=27 Identities=15% Similarity=0.305 Sum_probs=23.1
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.||++ ...|...+- +|.
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 458999999999998 899998877 664
No 184
>PRK11569 transcriptional repressor IclR; Provisional
Probab=27.22 E-value=1.3e+02 Score=26.19 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=36.2
Q ss_pred HHHHhhhhh-ccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 98 KQLSVLTLA-EMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 98 r~LtLlsLa-~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
|-|.|+.+. +..+.++..+|++.+++| ...|=.++- .....|++.
T Consensus 29 ral~IL~~l~~~~~~~~lseia~~lglp-ksTv~RlL~-tL~~~G~l~ 74 (274)
T PRK11569 29 RGLKLLEWIAESNGSVALTELAQQAGLP-NSTTHRLLT-TMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 446666544 446779999999999999 788988888 788899886
No 185
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=27.10 E-value=2.4e+02 Score=21.82 Aligned_cols=52 Identities=17% Similarity=0.048 Sum_probs=41.6
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCC
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGR 162 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R 162 (227)
...++-.+|++.++++ ...|=..|= .....|+|.=.-|..++....-+.++.
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 4569999999999998 667766655 778899999999988877777666543
No 186
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=27.05 E-value=2.2e+02 Score=19.76 Aligned_cols=49 Identities=14% Similarity=-0.000 Sum_probs=28.5
Q ss_pred hhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 105 LAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 105 La~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
+-+..+..|+.+|++.++++ ..+|-.-+= =..+.|-| .+++.++.++|.
T Consensus 16 ~L~~~~~~s~~el~k~~~l~-~~~~~~AiG-WLarE~KI--~~~~~~~~~~v~ 64 (65)
T PF10771_consen 16 LLNENGEWSVSELKKATGLS-DKEVYLAIG-WLARENKI--EFEEKNGELYVS 64 (65)
T ss_dssp HHCCSSSEEHHHHHHHCT-S-CHHHHHHHH-HHHCTTSE--EEEEETTEEEEE
T ss_pred HHhhCCCcCHHHHHHHhCcC-HHHHHHHHH-HHhccCce--eEEeeCCEEEEE
Confidence 33457899999999999998 455432111 11235545 344566666553
No 187
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=26.99 E-value=74 Score=26.46 Aligned_cols=28 Identities=18% Similarity=0.220 Sum_probs=23.9
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
..-.||.+||+.||++ ...|...+- +|.
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 3568999999999999 899998887 764
No 188
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=26.90 E-value=74 Score=25.90 Aligned_cols=27 Identities=19% Similarity=0.190 Sum_probs=23.5
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
T Consensus 126 eg~s~~EIA~~lgis-~~tV~~~l~-Rar 152 (182)
T PRK12511 126 EGLSYQEAAAVLGIP-IGTLMSRIG-RAR 152 (182)
T ss_pred cCCCHHHHHHHhCcC-HHHHHHHHH-HHH
Confidence 468999999999999 899998877 665
No 189
>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=26.89 E-value=80 Score=22.84 Aligned_cols=31 Identities=10% Similarity=0.037 Sum_probs=25.4
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHH
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELE 130 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE 130 (227)
|+.-|+.+... +.++..+||+.+|++ ...|=
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS-~~TVs 37 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVS-KSTVH 37 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCC-HHHHH
Confidence 77778888877 999999999999998 55443
No 190
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=26.85 E-value=2.9e+02 Score=21.06 Aligned_cols=50 Identities=14% Similarity=0.190 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhc
Q 044757 174 QSLTNWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVH 223 (227)
Q Consensus 174 ~~L~~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (227)
+-|..=.+.+...+..+++++..++++.++....-+...+++..+|+.+|
T Consensus 69 eYLl~~q~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~k 118 (118)
T PF13815_consen 69 EYLLHCQEYLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKESK 118 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 33344445566666667777777777777766666677777777777654
No 191
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.83 E-value=75 Score=26.20 Aligned_cols=28 Identities=14% Similarity=0.138 Sum_probs=23.5
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.+|++ ...|...+- +|.
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 3568999999999999 889988777 664
No 192
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.47 E-value=79 Score=25.33 Aligned_cols=27 Identities=11% Similarity=0.036 Sum_probs=23.4
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.||++ ...|...+- +|.
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 568999999999999 899998877 665
No 193
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=26.37 E-value=76 Score=26.74 Aligned_cols=28 Identities=4% Similarity=0.042 Sum_probs=24.0
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.+|++ ...|...+- +|+
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 3678999999999999 899988876 665
No 194
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=26.32 E-value=3.2e+02 Score=21.43 Aligned_cols=97 Identities=13% Similarity=0.143 Sum_probs=51.9
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE-ecccCcEEEEE----------eecCCCCCcchHHHHHHHHHHHH
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGK-LNQLRRCFEVQ----------FAAGRDLRHGQLENMMQSLTNWL 180 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk-IDQ~~~~v~V~----------~~~~R~~~~~q~~~l~~~L~~W~ 180 (227)
.+..++|+.+||+ ...+-.| - + .|||... =+..+...+=. ....-.|+.+++..+ +..+.
T Consensus 2 ~~I~e~a~~~gvs-~~tlR~Y-e-~---~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~---l~~~~ 72 (140)
T PRK09514 2 YRIGELAKLAEVT-PDTLRFY-E-K---QGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIREL---LSIRL 72 (140)
T ss_pred CcHHHHHHHHCcC-HHHHHHH-H-H---CCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHH---HHhcc
Confidence 4678999999999 8888887 2 2 5888753 23322222211 001112223333322 22221
Q ss_pred ----HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Q 044757 181 ----DTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQD 217 (227)
Q Consensus 181 ----~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (227)
..+..+...++.++..+.++.++..+.+..++..++.
T Consensus 73 ~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 113 (140)
T PRK09514 73 DPEHHTCQEVKGIVDEKLAEVEAKIAELQHMRRSLQRLNDA 113 (140)
T ss_pred cCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 1345556666777777777666666655555554443
No 195
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=26.01 E-value=1e+02 Score=28.21 Aligned_cols=38 Identities=21% Similarity=0.297 Sum_probs=33.7
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
--++=++||+.|+|+ ..-|=.+|= +|...|+|+-+|+.
T Consensus 25 ~gltQ~eIA~~LgiS-R~~v~rlL~-~Ar~~GiV~I~i~~ 62 (321)
T COG2390 25 EGLTQSEIAERLGIS-RATVSRLLA-KAREEGIVKISINS 62 (321)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCeEEEEeCC
Confidence 457788999999999 788999888 99999999999983
No 196
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=25.85 E-value=81 Score=25.73 Aligned_cols=28 Identities=11% Similarity=0.119 Sum_probs=23.8
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.||++ ...|...+- +|.
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 3568999999999999 899998876 665
No 197
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.74 E-value=1e+02 Score=30.91 Aligned_cols=46 Identities=20% Similarity=0.331 Sum_probs=39.1
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
..+.++.++++..+++| -+-+...++ +=....+|+|++|. ++++-.
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 56889999999999999 578899999 76678899999999 666644
No 198
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=25.68 E-value=3.4e+02 Score=22.66 Aligned_cols=46 Identities=17% Similarity=0.400 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHhhhc
Q 044757 178 NWLDTSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHLQDVKKSVH 223 (227)
Q Consensus 178 ~W~~~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 223 (227)
.|....+.....++..+..-.+...+..+.+.+++..++++++.++
T Consensus 125 ~~~~~~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei~ 170 (176)
T PF12999_consen 125 EYREELEEEEEIYKEGLKIRQELIEEAKKKREELEKKLEELEKEIQ 170 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333334444433333333333334445555566666655554
No 199
>PRK00404 tatB sec-independent translocase; Provisional
Probab=25.56 E-value=3.6e+02 Score=21.74 Aligned_cols=34 Identities=12% Similarity=0.266 Sum_probs=27.6
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKW 196 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~ 196 (227)
.||++.+..+...+..|..++.+....+.+.+..
T Consensus 19 V~GPkkLP~laR~lG~~i~~~rr~~~~~k~ei~~ 52 (141)
T PRK00404 19 VLGPERLPGAARTAGLWIGRLKRSFNAIKQEVER 52 (141)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999988877766555443
No 200
>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=25.56 E-value=42 Score=26.19 Aligned_cols=79 Identities=23% Similarity=0.262 Sum_probs=48.7
Q ss_pred HHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHHHH--------
Q 044757 116 QLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDNIL-------- 187 (227)
Q Consensus 116 ~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~~l-------- 187 (227)
.|+++|+|+ .++|++.+| +.. +..-..+|+.+.++|+..|-.=-
T Consensus 18 plSk~lgi~-~ee~~~ili-~~~--------------------------DmssLe~lhar~E~Ak~~cl~~~vd~dL~L~ 69 (117)
T PF09218_consen 18 PLSKELGIS-IEEFIDILI-EKL--------------------------DMSSLENLHARYEQAKMGCLGRKVDIDLGLC 69 (117)
T ss_dssp TTTTTGGGT-HHHHHHHHH-HHS---------------------------HHHHHHHHHHHHTTHHHHHHHHHHHHTTHH
T ss_pred HHHHHhCcC-HHHHHHHHH-Hhc--------------------------ChHHHHhccHHHHHHhhhhhhhhhhHHhhHH
Confidence 467889999 999999999 642 34567889999999987653211
Q ss_pred ------HHH-HHHHHHHHHhhHHH-HHHHHHHHHHHHHHHhhh
Q 044757 188 ------SVI-QDKIKWAETMCEED-KKHKMEVKSHLQDVKKSV 222 (227)
Q Consensus 188 ------~~i-e~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~ 222 (227)
..| ++....+.....+. -.+.+.+++++++=++.+
T Consensus 70 wl~d~~~lis~edAd~ir~kv~~~~i~~~~~y~eAl~eGR~~~ 112 (117)
T PF09218_consen 70 WLSDVMGLISEEDADLIRKKVVEDTIIHGKPYEEALEEGRKDI 112 (117)
T ss_dssp HHTTTS--S-HHHHHHHHHHHHHH-HHTT--HHHHHHHHHHHH
T ss_pred HHHHHHHHccHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 111 12333344444444 666777777777766654
No 201
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=25.54 E-value=84 Score=25.53 Aligned_cols=27 Identities=15% Similarity=0.111 Sum_probs=23.4
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.|+++ ...|...+- +|.
T Consensus 126 ~g~s~~EIA~~Lgis-~~tV~~~l~-RAr 152 (182)
T PRK12540 126 SGFSYEDAAAICGCA-VGTIKSRVN-RAR 152 (182)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 568999999999999 899998877 665
No 202
>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=25.51 E-value=1.1e+02 Score=28.63 Aligned_cols=45 Identities=20% Similarity=0.271 Sum_probs=33.3
Q ss_pred HHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 96 KLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 96 Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
.+-+|-++.+|. +.-+.-+||+.+++| .+++.+.+- ..+..|||+
T Consensus 342 ~~~~l~~L~~~D--G~~slldIA~~~~~~-~~~~~~~~~-~l~~~~Llk 386 (386)
T PF09940_consen 342 QMAMLWVLNYSD--GKNSLLDIAERIGLP-FDELADAAR-KLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHHH-E--EEEEHHHHHHHHT---HHHHHHHHH-HHHHTT-EE
T ss_pred HHHHHHHHHhcc--CCCcHHHHHHHHCcC-HHHHHHHHH-HHHHcCCCC
Confidence 344577777774 667889999999999 899999888 888899885
No 203
>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=25.46 E-value=88 Score=24.04 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=22.4
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- .|.
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 568999999999999 888887766 553
No 204
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.27 E-value=85 Score=25.14 Aligned_cols=28 Identities=7% Similarity=0.025 Sum_probs=23.4
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||++||+.+|++ ...|...+= +|.
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 4568999999999999 889988766 654
No 205
>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=24.88 E-value=74 Score=22.95 Aligned_cols=25 Identities=16% Similarity=0.240 Sum_probs=17.5
Q ss_pred HHhhhhhccCccccHHHHHHHhCCC
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVA 124 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~ 124 (227)
+..+.-...++..||.+||+.++-+
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 4455555678999999999999954
No 206
>TIGR02919 accessory Sec system glycosyltransferase GtfB. Members of this protein family are found only in Gram-positive bacteria of the Firmicutes lineage, including several species of Staphylococcus, Streptococcus, and Lactobacillus.
Probab=24.87 E-value=2.3e+02 Score=26.88 Aligned_cols=88 Identities=10% Similarity=0.258 Sum_probs=60.6
Q ss_pred cHHHHHHHhCC----CChhHHHHHHHHHhHhcCceEEEeccc--CcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHHH
Q 044757 113 SYDQLLKELEV----ANVRELEDFLINECMYVGIVKGKLNQL--RRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDNI 186 (227)
Q Consensus 113 sy~~I~~~L~i----~~~~eVE~lvI~~ai~~gLI~gkIDQ~--~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~~ 186 (227)
..+++-+.|++ +.-+++...++ +|++.|+.----|.. .+.+... +..+..++.+.|.+++..-...-+.+
T Consensus 340 ~l~~ly~~~dlyLdin~~e~~~~al~-eA~~~G~pI~afd~t~~~~~~i~~---g~l~~~~~~~~m~~~i~~lL~d~~~~ 415 (438)
T TIGR02919 340 KIQELYQTCDIYLDINHGNEILNAVR-RAFEYNLLILGFEETAHNRDFIAS---ENIFEHNEVDQLISKLKDLLNDPNQF 415 (438)
T ss_pred HHHHHHHhccEEEEccccccHHHHHH-HHHHcCCcEEEEecccCCcccccC---CceecCCCHHHHHHHHHHHhcCHHHH
Confidence 34566666554 33468888888 999999977766654 2222222 45577788899999988877776677
Q ss_pred HHHHHHHHHHHHHhhHHH
Q 044757 187 LSVIQDKIKWAETMCEED 204 (227)
Q Consensus 187 l~~ie~~~~~~~~~~~~~ 204 (227)
...++.+...|+....++
T Consensus 416 ~~~~~~q~~~a~~~~~~~ 433 (438)
T TIGR02919 416 RELLEQQREHANDISKEQ 433 (438)
T ss_pred HHHHHHHHHHhccCCHHH
Confidence 777777777777666654
No 207
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=24.84 E-value=1.4e+02 Score=26.03 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=37.2
Q ss_pred HHHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 96 KLKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 96 Klr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
+-|+-.|+.+...++.++..+|++.|+++ ...+=.-+. ..-..|++.
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 34777788888888999999999999998 777776666 555667764
No 208
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=24.81 E-value=2.8e+02 Score=20.27 Aligned_cols=26 Identities=31% Similarity=0.483 Sum_probs=20.1
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
+..++|+.+||+ ...+-.| . + .|++.
T Consensus 2 ti~eva~~~gvs-~~tlR~y-e-~---~Gll~ 27 (103)
T cd01106 2 TVGEVAKLTGVS-VRTLHYY-D-E---IGLLK 27 (103)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCC
Confidence 567899999999 7888877 3 2 67764
No 209
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=24.77 E-value=2.9e+02 Score=20.41 Aligned_cols=15 Identities=7% Similarity=0.446 Sum_probs=5.8
Q ss_pred HHHHHHHHHHHHHhh
Q 044757 207 HKMEVKSHLQDVKKS 221 (227)
Q Consensus 207 ~~~~~~~~~~~~~~~ 221 (227)
..+.++..+.+.+..
T Consensus 85 ~~~~l~~~~~elk~~ 99 (105)
T cd00632 85 QEEDLQEKLKELQEK 99 (105)
T ss_pred HHHHHHHHHHHHHHH
Confidence 333333344443333
No 210
>PRK00182 tatB sec-independent translocase; Provisional
Probab=24.62 E-value=3e+02 Score=22.65 Aligned_cols=33 Identities=6% Similarity=0.169 Sum_probs=26.6
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIK 195 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~ 195 (227)
.|+++.+..+...+..|...+........+.+.
T Consensus 20 VfGPerLP~~~r~lg~~ir~~R~~~~~~k~el~ 52 (160)
T PRK00182 20 VIGPERLPRLIEDVRAALLAARTAINNAKQQLD 52 (160)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999888887776655444
No 211
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located 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=24.60 E-value=3.1e+02 Score=20.65 Aligned_cols=89 Identities=16% Similarity=0.224 Sum_probs=48.4
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE-EEecccCcEEEEEeecCCCCCcchHHHH----------------HH
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVK-GKLNQLRRCFEVQFAAGRDLRHGQLENM----------------MQ 174 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~-gkIDQ~~~~v~V~~~~~R~~~~~q~~~l----------------~~ 174 (227)
++..++|+.+||+ ...+-.| +- .||+. ..-+. + ..|.++.+++..+ +.
T Consensus 1 ~~I~eva~~~gvs-~~tLRyY---e~--~GLl~p~~r~~-~--------gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~ 65 (123)
T cd04770 1 MKIGELAKAAGVS-PDTIRYY---ER--IGLLPPPQRSE-N--------GYRLYGEADLARLRFIRRAQALGFSLAEIRE 65 (123)
T ss_pred CCHHHHHHHHCcC-HHHHHHH---HH--CCCCCCCCCCC-C--------CCccCCHHHHHHHHHHHHHHHCCCCHHHHHH
Confidence 3678999999999 7888766 22 68887 44443 2 2455555554322 22
Q ss_pred HHHHHHH---HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Q 044757 175 SLTNWLD---TSDNILSVIQDKIKWAETMCEEDKKHKMEVKSHL 215 (227)
Q Consensus 175 ~L~~W~~---~~~~~l~~ie~~~~~~~~~~~~~~~~~~~~~~~~ 215 (227)
-+..+.. .+..+...++++...+.++.++....+..+...+
T Consensus 66 ~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~ 109 (123)
T cd04770 66 LLSLRDDGAAPCAEVRALLEEKLAEVEAKIAELQALRAELAGLL 109 (123)
T ss_pred HHHhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2222211 1334455555566666555555555554444433
No 212
>KOG3431 consensus Apoptosis-related protein/predicted DNA-binding protein [Cell cycle control, cell division, chromosome partitioning]
Probab=24.58 E-value=46 Score=26.25 Aligned_cols=22 Identities=27% Similarity=0.526 Sum_probs=19.7
Q ss_pred hHHHHHHHHHhHhcCceEEEecc
Q 044757 127 RELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 127 ~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
.-||.+|| ++...|-|.|||+.
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 46999999 99999999999975
No 213
>PRK00478 scpA segregation and condensation protein A/unknown domain fusion protein; Provisional
Probab=24.49 E-value=6.6e+02 Score=24.43 Aligned_cols=100 Identities=9% Similarity=0.008 Sum_probs=68.7
Q ss_pred CccccHHHHHHHhC-CCChhHH---HHHHHHHhHhcCceEEEecccCcEEEEEeecC-CCCCcc-hHHHHHHHHHHHHHH
Q 044757 109 NKVLSYDQLLKELE-VANVREL---EDFLINECMYVGIVKGKLNQLRRCFEVQFAAG-RDLRHG-QLENMMQSLTNWLDT 182 (227)
Q Consensus 109 ~~~isy~~I~~~L~-i~~~~eV---E~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~-R~~~~~-q~~~l~~~L~~W~~~ 182 (227)
++.++|.++-..+. -++..+| =--|. +.++.|.|...=+..-+.+.|.+..| |..+.+ ..+.|.++...=...
T Consensus 360 ~~~~~F~~L~~~~~~~~sr~evVvtFLAlL-EL~K~~~I~i~Q~~~f~~I~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (505)
T PRK00478 360 YNQVSLKRVLLKINHKISLMYFVTAFVALL-VLVNNQKIDLEQKNDDEELYICLLDPTKIVNSQESPQEMVQRQQEQEQA 438 (505)
T ss_pred CCeEEhHHHhhhcccCCCcceEehHHHHHH-HHhccCeEEEEEcCCCCeEEEEEcCcchhhhhhhCHHHHHHHHHHHHHH
Confidence 46799999988542 1122222 23345 77889999988888888999887654 333322 256788888888888
Q ss_pred HHHHHHHHHHHHHHHHHhhHHHHHHHH
Q 044757 183 SDNILSVIQDKIKWAETMCEEDKKHKM 209 (227)
Q Consensus 183 ~~~~l~~ie~~~~~~~~~~~~~~~~~~ 209 (227)
....+..+.+.-+..|.++++....++
T Consensus 439 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 465 (505)
T PRK00478 439 LKESIKQIQEERAISNFQKREEYLKKK 465 (505)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHh
Confidence 888888888777777777777665543
No 214
>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=24.44 E-value=2.7e+02 Score=19.87 Aligned_cols=57 Identities=11% Similarity=0.095 Sum_probs=38.1
Q ss_pred hhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE-EEecccCcEEEEEeecCC
Q 044757 102 VLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK-GKLNQLRRCFEVQFAAGR 162 (227)
Q Consensus 102 LlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~-gkIDQ~~~~v~V~~~~~R 162 (227)
|+.++.. +.+++++.+..+++ .+.+=-.+= +....|+|. +..---.+.+.+-+...|
T Consensus 11 L~~ls~~--c~TLeeL~ekTgi~-k~~LlV~Ls-rL~k~GiI~Rkw~~~~gkk~R~YclK~~ 68 (72)
T PF05584_consen 11 LIILSKR--CCTLEELEEKTGIS-KNTLLVYLS-RLAKRGIIERKWRKFGGKKYREYCLKYK 68 (72)
T ss_pred HHHHHhc--cCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeeeEEecCeEEEEEEecch
Confidence 4444443 99999999999998 676655555 667788887 434444456666555544
No 215
>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=24.44 E-value=1.1e+02 Score=19.10 Aligned_cols=19 Identities=16% Similarity=0.254 Sum_probs=13.1
Q ss_pred ccHHHHHHHhCCCChhHHHH
Q 044757 112 LSYDQLLKELEVANVRELED 131 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~ 131 (227)
.|..+||+.++|+ ...|-.
T Consensus 22 ~si~~IA~~~gvs-r~TvyR 40 (45)
T PF02796_consen 22 MSIAEIAKQFGVS-RSTVYR 40 (45)
T ss_dssp --HHHHHHHTTS--HHHHHH
T ss_pred CCHHHHHHHHCcC-HHHHHH
Confidence 9999999999998 666543
No 216
>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=24.42 E-value=93 Score=24.29 Aligned_cols=27 Identities=7% Similarity=0.103 Sum_probs=23.1
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.||++ ...|...+- +|.
T Consensus 137 ~g~s~~eIA~~l~is-~~tv~~~l~-ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARILGKT-EGAVKILQF-RAI 163 (170)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999999 899988776 664
No 217
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.39 E-value=2e+02 Score=23.94 Aligned_cols=39 Identities=15% Similarity=0.198 Sum_probs=33.4
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecc
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
..-++..+||+.++++ ...|+..+. .+...|++.=+++-
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 4668999999999998 899999999 99999988666553
No 218
>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=24.39 E-value=91 Score=24.90 Aligned_cols=27 Identities=15% Similarity=0.343 Sum_probs=22.8
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...+|++||+.||++ ...|...+- .|.
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 568999999999999 899988876 654
No 219
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=24.36 E-value=91 Score=25.21 Aligned_cols=27 Identities=15% Similarity=0.193 Sum_probs=23.3
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- +|+
T Consensus 156 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 182 (194)
T PRK12519 156 EGLSQSEIAKRLGIP-LGTVKARAR-QGL 182 (194)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 468999999999998 899998877 665
No 220
>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=24.31 E-value=95 Score=18.52 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=20.8
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
++..++++.|+|+ ...|-.|+= .|.+.+
T Consensus 1 ~s~~e~a~~lgvs-~~tl~~~~~-----~g~~~~ 28 (49)
T cd04762 1 LTTKEAAELLGVS-PSTLRRWVK-----EGKLKA 28 (49)
T ss_pred CCHHHHHHHHCcC-HHHHHHHHH-----cCCCCc
Confidence 4678999999998 788887744 455544
No 221
>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=24.29 E-value=87 Score=20.10 Aligned_cols=23 Identities=22% Similarity=0.391 Sum_probs=19.0
Q ss_pred cccHHHHHHHhCCCChhHHHHHHH
Q 044757 111 VLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
.-....||..|||+ ...|..|.-
T Consensus 27 ~~~~~~la~~l~l~-~~~V~~WF~ 49 (57)
T PF00046_consen 27 KEEREELAKELGLT-ERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHHHTSS-HHHHHHHHH
T ss_pred cccccccccccccc-ccccccCHH
Confidence 44577899999999 899999864
No 222
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.10 E-value=91 Score=25.69 Aligned_cols=27 Identities=15% Similarity=0.171 Sum_probs=22.7
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.++++ ...|...+- +|.
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 558999999999999 899988866 554
No 223
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=24.01 E-value=91 Score=26.36 Aligned_cols=27 Identities=19% Similarity=0.224 Sum_probs=23.3
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+|++.|||+ ...|...+- +|.
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 568999999999999 899998876 654
No 224
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=23.91 E-value=1.2e+02 Score=22.53 Aligned_cols=54 Identities=13% Similarity=0.175 Sum_probs=36.7
Q ss_pred HHHHHHhcCCCceechhhhcChhhhhccCCCchHHHHHHHHHhcCCHhhHHhhhhcCC
Q 044757 30 KLIVEATSHPSLFAFSEILSVPNLLQLQGTESSVYIDLLRLFAHGTWTDYKSNAAHLP 87 (227)
Q Consensus 30 ~li~~aL~~p~if~F~eLl~~p~v~~L~~~~~~~l~~LL~iF~~G~~~dy~~~~~~~~ 87 (227)
+.|...|.+.+|+.-.+.=... + ++|.......||.+.-......|..|...+.
T Consensus 24 ~~v~~~L~~~gIlT~~~~e~I~---a-~~T~~~k~~~LLdiLp~RG~~AF~~F~~aL~ 77 (94)
T cd08327 24 GLVIQYLYQEGILTESHVEEIE---S-QTTSRRKTMKLLDILPSRGPKAFHAFLDSLE 77 (94)
T ss_pred HHHHHHHHhCCCCCHHHHHHHH---c-cCChHHHHHHHHHHHHhhChhHHHHHHHHHH
Confidence 4566777778887765443222 2 2345667888999999988888988865543
No 225
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=23.87 E-value=2.3e+02 Score=18.95 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=29.4
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 164 LRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWA 197 (227)
Q Consensus 164 ~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~ 197 (227)
++++++..+...+....+.+.+.+..+...+..+
T Consensus 4 vd~~~l~~~a~~~~~~~~~l~~~~~~l~~~~~~l 37 (86)
T PF06013_consen 4 VDPEQLRAAAQQLQAQADELQSQLQQLESSIDSL 37 (86)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678888899999999999999999998888865
No 226
>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=23.84 E-value=94 Score=25.28 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=22.9
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 468999999999999 899988876 653
No 227
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=23.75 E-value=92 Score=25.40 Aligned_cols=28 Identities=18% Similarity=0.221 Sum_probs=23.7
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||++||+.||++ ...|...+- +|.
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 3568999999999999 889988877 664
No 228
>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=23.62 E-value=90 Score=26.96 Aligned_cols=27 Identities=15% Similarity=0.177 Sum_probs=24.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+||+ ...|+..+- +|.
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 568999999999999 899999888 775
No 229
>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=23.58 E-value=1.6e+02 Score=26.08 Aligned_cols=36 Identities=8% Similarity=0.214 Sum_probs=28.3
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
...++..+||+.+||+ ..-+=.-+- +.-..|+|+++
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 4789999999999998 555544455 66788999886
No 230
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.53 E-value=99 Score=24.23 Aligned_cols=27 Identities=11% Similarity=0.288 Sum_probs=22.9
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- +|.
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 568999999999998 899988776 654
No 231
>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=23.39 E-value=96 Score=24.44 Aligned_cols=27 Identities=7% Similarity=0.230 Sum_probs=22.9
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.||++ ...|...+- .|.
T Consensus 134 ~g~s~~eiA~~lgis-~~tv~~~l~-Ra~ 160 (169)
T TIGR02954 134 HDLTIKEIAEVMNKP-EGTVKTYLH-RAL 160 (169)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999998 888888776 664
No 232
>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=23.23 E-value=1.3e+02 Score=23.82 Aligned_cols=44 Identities=14% Similarity=0.301 Sum_probs=29.3
Q ss_pred ceEEEecccCcEEEEEeecCCCCCcchHHHHHHHHHHHHHHHHH
Q 044757 142 IVKGKLNQLRRCFEVQFAAGRDLRHGQLENMMQSLTNWLDTSDN 185 (227)
Q Consensus 142 LI~gkIDQ~~~~v~V~~~~~R~~~~~q~~~l~~~L~~W~~~~~~ 185 (227)
.|.|.|.|+.+.+.=..-.+-+|..++|+.|..=|-...+++..
T Consensus 68 viSG~IsQiv~i~~r~~~~~sd~~~~e~~~Ls~PL~d~i~rLTY 111 (127)
T PF06619_consen 68 VISGVISQIVHIKDRYVGEPSDLSQEEVELLSRPLLDYIERLTY 111 (127)
T ss_dssp EEEEEEEEEEEEET---SSGGGS-HHHHHHHHHHHHHHHHHHHH
T ss_pred EEEeeeeeeeeeeccccCChhhcCHHHHHHHHHHHHHHHHhhee
Confidence 47899988766554233467888999999888877766665543
No 233
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=23.22 E-value=3.7e+02 Score=21.07 Aligned_cols=31 Identities=29% Similarity=0.324 Sum_probs=23.6
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEec
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLN 148 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkID 148 (227)
++..++|+.+||+ ...+=.|- + .|||...=+
T Consensus 2 ~~I~EvA~~~Gvs-~~tLRyYE--~---~GLl~p~r~ 32 (139)
T cd01110 2 LSVGEVAKRSGVA-VSALHFYE--Q---KGLIASWRN 32 (139)
T ss_pred CCHHHHHHHHCcC-HHHHHHHH--H---CCCCCCCcC
Confidence 6789999999999 78888772 2 488876433
No 234
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=23.18 E-value=97 Score=24.92 Aligned_cols=27 Identities=7% Similarity=0.165 Sum_probs=22.9
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- +|.
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 458999999999999 899998776 654
No 235
>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=23.17 E-value=1.6e+02 Score=19.76 Aligned_cols=42 Identities=17% Similarity=0.159 Sum_probs=31.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
-.++.++||+.+|++ ...|-..+= +.-..|+|+ -.++.+.|.
T Consensus 27 ~~lt~~~iA~~~g~s-r~tv~r~l~-~l~~~g~I~----~~~~~i~I~ 68 (76)
T PF13545_consen 27 LPLTQEEIADMLGVS-RETVSRILK-RLKDEGIIE----VKRGKIIIL 68 (76)
T ss_dssp EESSHHHHHHHHTSC-HHHHHHHHH-HHHHTTSEE----EETTEEEES
T ss_pred ecCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE----EcCCEEEEC
Confidence 357899999999998 788888766 777778877 234455553
No 236
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=23.14 E-value=99 Score=25.20 Aligned_cols=27 Identities=11% Similarity=0.099 Sum_probs=22.8
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.||++ ...|...+- .|.
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 468999999999999 899988776 654
No 237
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=23.09 E-value=1e+02 Score=25.02 Aligned_cols=28 Identities=14% Similarity=0.032 Sum_probs=23.6
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
....||.+||+.+|++ ...|...+- .|.
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 3568999999999999 899998876 654
No 238
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=22.82 E-value=1e+02 Score=24.38 Aligned_cols=27 Identities=11% Similarity=0.214 Sum_probs=22.7
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|+
T Consensus 141 ~g~s~~eIA~~l~is-~~~V~~~l~-ra~ 167 (176)
T PRK09638 141 YGYTYEEIAKMLNIP-EGTVKSRVH-HGI 167 (176)
T ss_pred cCCCHHHHHHHHCCC-hhHHHHHHH-HHH
Confidence 468999999999998 888888776 665
No 239
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=22.76 E-value=2.8e+02 Score=23.87 Aligned_cols=58 Identities=17% Similarity=0.171 Sum_probs=45.8
Q ss_pred HHHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEecccCcEEEEE
Q 044757 97 LKQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLNQLRRCFEVQ 157 (227)
Q Consensus 97 lr~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~ 157 (227)
|+.|.+++-..+ -.+|-+++++.++++ ....=.|+. +.-..|+|.=++....+.+.++
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 779999999999998 567777888 8888899999888888888876
No 240
>PRK03100 sec-independent translocase; Provisional
Probab=22.68 E-value=4e+02 Score=21.29 Aligned_cols=34 Identities=12% Similarity=0.049 Sum_probs=28.7
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKW 196 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~ 196 (227)
.|+++.+..+...+..|..++......+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999887777766653
No 241
>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=22.39 E-value=1.8e+02 Score=17.26 Aligned_cols=30 Identities=10% Similarity=0.214 Sum_probs=19.2
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCce
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIV 143 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI 143 (227)
++-.+||+.+|+. .+.|=..+= +.-..|+|
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 5678999999998 666666555 55555554
No 242
>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=22.38 E-value=1.2e+02 Score=18.85 Aligned_cols=21 Identities=14% Similarity=0.501 Sum_probs=16.4
Q ss_pred HHHHHHhCCCChhHHHHHHHHHh
Q 044757 115 DQLLKELEVANVRELEDFLINEC 137 (227)
Q Consensus 115 ~~I~~~L~i~~~~eVE~lvI~~a 137 (227)
+.|++.+|++ ..+|..|++ .+
T Consensus 17 ~~L~~~tgls-~~Qi~~WF~-Na 37 (40)
T PF05920_consen 17 EELAKQTGLS-RKQISNWFI-NA 37 (40)
T ss_dssp HHHHHHHTS--HHHHHHHHH-HH
T ss_pred HHHHHHcCCC-HHHHHHHHH-Hh
Confidence 4578888998 899999998 54
No 243
>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=22.37 E-value=2.6e+02 Score=20.15 Aligned_cols=49 Identities=12% Similarity=0.165 Sum_probs=36.0
Q ss_pred HHHHHhhhh-hccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe
Q 044757 97 LKQLSVLTL-AEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL 147 (227)
Q Consensus 97 lr~LtLlsL-a~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI 147 (227)
.|.|+-+-. ..++.-+|.+.|.+..+++ ..+++.-+- +.+..|||.-+.
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 344454443 3477889999999999999 899998877 999999998854
No 244
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.30 E-value=3.7e+02 Score=20.66 Aligned_cols=27 Identities=15% Similarity=0.279 Sum_probs=20.9
Q ss_pred cHHHHHHHhCCCChhHHHHHHHHHhHhcCceEE
Q 044757 113 SYDQLLKELEVANVRELEDFLINECMYVGIVKG 145 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~g 145 (227)
+..++|+.+||+ ...+-.|- + .||+..
T Consensus 2 ~I~e~a~~~gvs-~~tlR~Ye--~---~GLl~~ 28 (127)
T TIGR02047 2 KIGELAQKTGVS-VETIRFYE--K---QGLLPP 28 (127)
T ss_pred cHHHHHHHHCcC-HHHHHHHH--H---CCCCCC
Confidence 568999999999 78888772 2 688863
No 245
>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=22.28 E-value=1.8e+02 Score=17.21 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=20.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
...++.+|++.++++ ...|-.++-
T Consensus 25 ~~~~~~~ia~~~~~s-~~~i~~~~~ 48 (55)
T cd06171 25 EGLSYEEIAEILGIS-RSTVRQRLH 48 (55)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHH
Confidence 447999999999998 788877765
No 246
>PRK10884 SH3 domain-containing protein; Provisional
Probab=22.11 E-value=4.9e+02 Score=22.09 Aligned_cols=21 Identities=14% Similarity=0.243 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 044757 169 LENMMQSLTNWLDTSDNILSV 189 (227)
Q Consensus 169 ~~~l~~~L~~W~~~~~~~l~~ 189 (227)
++.+...+..-+.+++++...
T Consensus 95 lp~le~el~~l~~~l~~~~~~ 115 (206)
T PRK10884 95 VPDLENQVKTLTDKLNNIDNT 115 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHhH
Confidence 455555555554444444333
No 247
>PF12728 HTH_17: Helix-turn-helix domain
Probab=22.08 E-value=1.1e+02 Score=19.26 Aligned_cols=29 Identities=10% Similarity=0.137 Sum_probs=21.6
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
+|.+++++.|+|+ ...|..|+ ..|-+.+-
T Consensus 2 lt~~e~a~~l~is-~~tv~~~~-----~~g~i~~~ 30 (51)
T PF12728_consen 2 LTVKEAAELLGIS-RSTVYRWI-----RQGKIPPF 30 (51)
T ss_pred CCHHHHHHHHCcC-HHHHHHHH-----HcCCCCeE
Confidence 5788999999998 77777664 35666554
No 248
>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=22.05 E-value=53 Score=25.09 Aligned_cols=22 Identities=32% Similarity=0.623 Sum_probs=18.1
Q ss_pred hHHHHHHHHHhHhcCceEEEecc
Q 044757 127 RELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 127 ~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
..||+.|| .....|-|.|+||.
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 57999999 89999999999986
No 249
>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=21.87 E-value=1.1e+02 Score=18.31 Aligned_cols=30 Identities=13% Similarity=0.128 Sum_probs=22.5
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEe
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGKL 147 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkI 147 (227)
++..++++.|+++ ...+-.|+ ..|.+.+..
T Consensus 2 lt~~e~a~~lgis-~~ti~~~~-----~~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KDTVYRLI-----HEGELPAYR 31 (49)
T ss_pred CCHHHHHHHHCCC-HHHHHHHH-----HcCCCCeEE
Confidence 5789999999998 77777653 367777654
No 250
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=21.86 E-value=1.1e+02 Score=24.72 Aligned_cols=27 Identities=4% Similarity=0.140 Sum_probs=23.1
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- .|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 175 (188)
T PRK09640 149 AELEFQEIADIMHMG-LSATKMRYK-RAL 175 (188)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 458999999999999 889988877 665
No 251
>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=21.68 E-value=1.8e+02 Score=19.64 Aligned_cols=37 Identities=8% Similarity=0.167 Sum_probs=28.6
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEE
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGK 146 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gk 146 (227)
.++..|..+|.+..++| .++|-.-++ -.|..|++...
T Consensus 24 ~~G~ltl~~i~~~t~l~-~~~Vk~~L~-~LiQh~~v~y~ 60 (62)
T PF08221_consen 24 SRGRLTLREIVRRTGLS-PKQVKKALV-VLIQHNLVQYF 60 (62)
T ss_dssp HC-SEEHHHHHHHHT---HHHHHHHHH-HHHHTTSEEEE
T ss_pred HcCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHcCCeeee
Confidence 46789999999999999 899987777 78999988643
No 252
>PF06323 Phage_antiter_Q: Phage antitermination protein Q; InterPro: IPR010455 This entry is represented by Bacteriophage 82, GpQ. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage antitermination protein Q and related bacterial sequences. Phage 82 gene Q encodes a phage-specific positive regulator of late gene expression, thought, by analogy to the corresponding gene of phage lambda, to be a transcription antiterminator. GpQ positively regulates expression of the phage late gene operons. Bacterial host RNA polymerase modified by antitermination proteins transcribes through termination sites that otherwise prevent expression of the regulated genes [].
Probab=21.61 E-value=1.1e+02 Score=26.68 Aligned_cols=55 Identities=18% Similarity=0.288 Sum_probs=34.8
Q ss_pred HHhcCCHhhHHh-----------hhhcCC--CcchHHHHHHHHHHhhhhhc-----cCc--cccHHHHHHHhCCC
Q 044757 70 LFAHGTWTDYKS-----------NAAHLP--QLVPDQAVKLKQLSVLTLAE-----MNK--VLSYDQLLKELEVA 124 (227)
Q Consensus 70 iF~~G~~~dy~~-----------~~~~~~--~l~~~~~~Klr~LtLlsLa~-----~~~--~isy~~I~~~L~i~ 124 (227)
.+|||+--.|.. |....+ .+...-..+|+.|..+..-. .++ ..+|++||+-+||+
T Consensus 106 lyCYs~~~~~~~Q~~I~~~~W~~F~~~~~~~ki~~Kt~~rLk~LiwLA~Q~vk~~l~~~~~~y~~~~LA~L~GV~ 180 (230)
T PF06323_consen 106 LYCYSENLNWEHQVLICQWLWSEFQAQLGGKKIAKKTKKRLKSLIWLAAQDVKAELNGREYKYTYAELAELVGVS 180 (230)
T ss_pred HHHhcCCCCchhHHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHcCCCccccHHHHHHHhCCC
Confidence 588887665553 223333 24555567777777775422 222 27899999999998
No 253
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=21.59 E-value=1.1e+02 Score=26.42 Aligned_cols=26 Identities=15% Similarity=0.098 Sum_probs=22.5
Q ss_pred cccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 111 VLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
..||++||+.||+| ...|...+- +|.
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 58999999999998 888988877 665
No 254
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.58 E-value=1e+02 Score=24.66 Aligned_cols=27 Identities=7% Similarity=0.367 Sum_probs=22.8
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.||++ ...|...+= +|.
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 568999999999999 888888776 654
No 255
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.58 E-value=1.1e+02 Score=24.80 Aligned_cols=27 Identities=7% Similarity=0.099 Sum_probs=22.5
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.+|++ ...|...+- +|.
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 458999999999999 888988776 654
No 256
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=21.43 E-value=4.4e+02 Score=21.25 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=26.2
Q ss_pred cCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEec
Q 044757 108 MNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLN 148 (227)
Q Consensus 108 ~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkID 148 (227)
....++..++|+.+||+ ...+=.|- ..|||...=+
T Consensus 8 ~~~~~~IgevAk~~gvs-~~TlRyYE-----~~GLi~~~r~ 42 (154)
T PRK15002 8 IKALLTPGEVAKRSGVA-VSALHFYE-----SKGLITSIRN 42 (154)
T ss_pred hcccccHHHHHHHHCcC-HHHHHHHH-----HCCCCCCccC
Confidence 34568999999999999 77777662 2788887433
No 257
>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=21.26 E-value=1.2e+02 Score=23.43 Aligned_cols=27 Identities=19% Similarity=0.139 Sum_probs=22.8
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...+|.+||+.+|++ ...|...+- +|.
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 568999999999999 889988766 654
No 258
>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=21.25 E-value=1.7e+02 Score=18.89 Aligned_cols=38 Identities=13% Similarity=0.229 Sum_probs=28.4
Q ss_pred HHHHHHHHHhHhcCceEEEecccCcEEEEEeecCCCCCcchH
Q 044757 128 ELEDFLINECMYVGIVKGKLNQLRRCFEVQFAAGRDLRHGQL 169 (227)
Q Consensus 128 eVE~lvI~~ai~~gLI~gkIDQ~~~~v~V~~~~~R~~~~~q~ 169 (227)
.|+.-|- .+ .|+-...+|-.++++.|.+..++ ++.+++
T Consensus 15 ~v~~~l~--~~-~GV~~v~vd~~~~~v~v~~~~~~-~~~~~i 52 (62)
T PF00403_consen 15 KVEKALS--KL-PGVKSVKVDLETKTVTVTYDPDK-TSIEKI 52 (62)
T ss_dssp HHHHHHH--TS-TTEEEEEEETTTTEEEEEESTTT-SCHHHH
T ss_pred HHHHHHh--cC-CCCcEEEEECCCCEEEEEEecCC-CCHHHH
Confidence 4555443 33 69999999999999999998777 555544
No 259
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=21.22 E-value=3.5e+02 Score=20.09 Aligned_cols=31 Identities=16% Similarity=0.266 Sum_probs=23.1
Q ss_pred ccHHHHHHHhCCCChhHHHHHHHHHhHhcCceEEEec
Q 044757 112 LSYDQLLKELEVANVRELEDFLINECMYVGIVKGKLN 148 (227)
Q Consensus 112 isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~gkID 148 (227)
++..++|+.+||+ ...+-.|- + .|++...-+
T Consensus 1 ~~i~eva~~~gvs-~~tlR~ye--~---~Gll~p~~~ 31 (108)
T cd04773 1 MTIGELAHLLGVP-PSTLRHWE--K---EGLLSPDRE 31 (108)
T ss_pred CCHHHHHHHHCcC-HHHHHHHH--H---CCCCCCCcC
Confidence 3678999999999 78888772 2 588865433
No 260
>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=21.20 E-value=1e+02 Score=23.33 Aligned_cols=27 Identities=19% Similarity=0.292 Sum_probs=19.0
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHh
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINEC 137 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~a 137 (227)
...+|+++||+.++|+ ...|=+++- +|
T Consensus 31 ~eDlSlsEIAe~~~iS-RqaV~d~ik-r~ 57 (101)
T PF04297_consen 31 EEDLSLSEIAEELGIS-RQAVYDSIK-RA 57 (101)
T ss_dssp TS---HHHHHHHCTS--HHHHHHHHH-HH
T ss_pred ccCCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 4679999999999998 778887766 54
No 261
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=21.04 E-value=1.1e+02 Score=25.20 Aligned_cols=28 Identities=25% Similarity=0.288 Sum_probs=23.4
Q ss_pred CccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 109 NKVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 109 ~~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...+||++||+.+|++ ...|...+= +|+
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 3568999999999999 899988766 554
No 262
>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=21.02 E-value=1.1e+02 Score=21.91 Aligned_cols=25 Identities=20% Similarity=0.212 Sum_probs=19.6
Q ss_pred HHhhhhhccCccccHHHHHHHhCCC
Q 044757 100 LSVLTLAEMNKVLSYDQLLKELEVA 124 (227)
Q Consensus 100 LtLlsLa~~~~~isy~~I~~~L~i~ 124 (227)
+..+.-...++..||.+||+.++-+
T Consensus 8 ~~~l~~IP~G~v~TYg~iA~~~g~p 32 (80)
T TIGR00589 8 WQALRTIPYGETKSYGQLAARIGNP 32 (80)
T ss_pred HHHHhCCCCCCcCCHHHHHHHhCCC
Confidence 4444445578999999999999976
No 263
>PRK04239 hypothetical protein; Provisional
Probab=20.96 E-value=58 Score=25.14 Aligned_cols=22 Identities=23% Similarity=0.475 Sum_probs=19.7
Q ss_pred hHHHHHHHHHhHhcCceEEEecc
Q 044757 127 RELEDFLINECMYVGIVKGKLNQ 149 (227)
Q Consensus 127 ~eVE~lvI~~ai~~gLI~gkIDQ 149 (227)
..||++|| .+...|-|.|+||.
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 47999999 89999999999986
No 264
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=20.84 E-value=2.5e+02 Score=18.13 Aligned_cols=23 Identities=13% Similarity=0.231 Sum_probs=17.8
Q ss_pred cccHHHHHHHhCCCChhHHHHHHH
Q 044757 111 VLSYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 111 ~isy~~I~~~L~i~~~~eVE~lvI 134 (227)
-.+..+||+.++++ ...|...+-
T Consensus 18 G~~~~eIA~~l~is-~~tV~~~~~ 40 (58)
T PF00196_consen 18 GMSNKEIAEELGIS-EKTVKSHRR 40 (58)
T ss_dssp TS-HHHHHHHHTSH-HHHHHHHHH
T ss_pred cCCcchhHHhcCcc-hhhHHHHHH
Confidence 36788999999998 788887655
No 265
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=20.84 E-value=3.1e+02 Score=20.35 Aligned_cols=38 Identities=16% Similarity=0.096 Sum_probs=30.5
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 044757 163 DLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETM 200 (227)
Q Consensus 163 ~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~ 200 (227)
.|+++.+..+...+..|.....+....+++.+......
T Consensus 21 vfGP~KLP~lar~lGk~i~~fkk~~~~~~~e~~~~~~~ 58 (90)
T PRK14857 21 VFGPKKLPEIGRSLGKTLKGFQEASKEFENEIKREMAE 58 (90)
T ss_pred HcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47899999999999999999998888877666554433
No 266
>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=20.83 E-value=1e+02 Score=29.63 Aligned_cols=45 Identities=20% Similarity=0.221 Sum_probs=31.3
Q ss_pred HHHHhhhhhccCccccHHHHHHHhCCCChhHHHHHHHHHhHhcCceE
Q 044757 98 KQLSVLTLAEMNKVLSYDQLLKELEVANVRELEDFLINECMYVGIVK 144 (227)
Q Consensus 98 r~LtLlsLa~~~~~isy~~I~~~L~i~~~~eVE~lvI~~ai~~gLI~ 144 (227)
-+++++.+-.....+|+++|++.+|++ .+++..-+- ..+..|++.
T Consensus 521 ~q~~iLl~Fn~~~~~t~~ei~~~~~~~-~~~l~~~L~-~l~~~~~l~ 565 (588)
T PF00888_consen 521 LQAAILLLFNDNDSLTVEEISEKTGIS-EEELKRALK-SLVKSKILI 565 (588)
T ss_dssp HHHHHHHGGGSSSEEEHHHHHHHC----HHHHHHHHH-CCCTTTTCS
T ss_pred HHHHHHHHHccCCCccHHHHHHHHCcC-HHHHHHHHH-HHHhCCcce
Confidence 345566666678899999999999999 788887666 666666664
No 267
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=20.71 E-value=4.5e+02 Score=21.77 Aligned_cols=21 Identities=14% Similarity=0.238 Sum_probs=17.6
Q ss_pred cHHHHHHHhCCCChhHHHHHHH
Q 044757 113 SYDQLLKELEVANVRELEDFLI 134 (227)
Q Consensus 113 sy~~I~~~L~i~~~~eVE~lvI 134 (227)
+..++|+.+||+ ...|-.|.=
T Consensus 2 ti~evA~~lGVS-~~TLRrw~k 22 (175)
T PRK13182 2 KTPFVAKKLGVS-PKTVQRWVK 22 (175)
T ss_pred CHHHHHHHHCcC-HHHHHHHHH
Confidence 568999999999 788888854
No 268
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=20.65 E-value=1.3e+02 Score=23.37 Aligned_cols=77 Identities=14% Similarity=0.216 Sum_probs=38.6
Q ss_pred hccCCCchHHHHHHHHHhcC-CHhhHHhhhhcCCCcch-------HHHHHHHHHHhhhhh----ccCccccHH--HHHHH
Q 044757 55 QLQGTESSVYIDLLRLFAHG-TWTDYKSNAAHLPQLVP-------DQAVKLKQLSVLTLA----EMNKVLSYD--QLLKE 120 (227)
Q Consensus 55 ~L~~~~~~~l~~LL~iF~~G-~~~dy~~~~~~~~~l~~-------~~~~Klr~LtLlsLa----~~~~~isy~--~I~~~ 120 (227)
.|....+..++.+.++|..| ++++.... ..+..+.- +..++|+.. .-.+. ..-+..-|+ .||+-
T Consensus 4 ~L~~Ptd~Rlf~i~eAlrrG~sveeI~e~-T~ID~wFL~~i~~Iv~~e~~L~~~-~~~~~~~~L~~aK~~GFsD~~IA~l 81 (123)
T PF02787_consen 4 KLRHPTDERLFAIAEALRRGYSVEEIHEL-TKIDPWFLEQIKNIVDMEKELKEY-LNELDPELLRKAKRLGFSDRQIARL 81 (123)
T ss_dssp HHHSTBTTHHHHHHHHHHTTB-HHHHHHH-H---HHHHHHHHHHHHHHHHHHHH-GGG--HHHHHHHHHTT--HHHHHHH
T ss_pred hhCCCCCcHHHHHHHHHHcCCCHHHHHHH-HCccHHHHHHHHHHHHHHHHHHHh-hccchHHHHHHHHHcCCCHHHHHhc
Confidence 34554566899999999999 56655542 22222211 111333331 11111 122334444 58888
Q ss_pred hCCCChhHHHHHHH
Q 044757 121 LEVANVRELEDFLI 134 (227)
Q Consensus 121 L~i~~~~eVE~lvI 134 (227)
++++ ..+|..+-.
T Consensus 82 ~~~~-e~~vr~~R~ 94 (123)
T PF02787_consen 82 WGVS-EEEVRELRK 94 (123)
T ss_dssp HTS--HHHHHHHHH
T ss_pred cCCC-HHHHHHHHH
Confidence 9987 788887655
No 269
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.58 E-value=1.2e+02 Score=24.38 Aligned_cols=27 Identities=7% Similarity=-0.037 Sum_probs=23.0
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- +|+
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 358999999999999 899988877 665
No 270
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.46 E-value=1.1e+02 Score=24.09 Aligned_cols=27 Identities=15% Similarity=0.191 Sum_probs=22.1
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||.+||+.+|++ ...|...+- +|.
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 457899999999999 888887766 553
No 271
>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=20.46 E-value=73 Score=24.40 Aligned_cols=19 Identities=11% Similarity=0.207 Sum_probs=16.2
Q ss_pred ccccHHHHHHHhCCCChhHH
Q 044757 110 KVLSYDQLLKELEVANVREL 129 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eV 129 (227)
...||.+||+.||++ ...|
T Consensus 122 ~~~s~~EIA~~l~is-~~tV 140 (142)
T TIGR03209 122 EDMKEIDIAKKLHIS-RQSV 140 (142)
T ss_pred cCCCHHHHHHHHCcC-HHhh
Confidence 568999999999998 6655
No 272
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=20.27 E-value=2.4e+02 Score=22.77 Aligned_cols=44 Identities=14% Similarity=0.108 Sum_probs=23.6
Q ss_pred CcchHHHHHHHHHHhhhhhc-cCccccHHHHHHHhCCCChhHHHHH
Q 044757 88 QLVPDQAVKLKQLSVLTLAE-MNKVLSYDQLLKELEVANVRELEDF 132 (227)
Q Consensus 88 ~l~~~~~~Klr~LtLlsLa~-~~~~isy~~I~~~L~i~~~~eVE~l 132 (227)
.|+..|.+-...|..-.+.. .+..-|+++||+++||+ ...+=.|
T Consensus 10 ~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis-~~tLYrW 54 (142)
T PF13022_consen 10 KLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGIS-RSTLYRW 54 (142)
T ss_dssp TS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS--HHHHHHH
T ss_pred HcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCC-HHHHHHH
Confidence 35566644444455555554 45789999999999998 5544444
No 273
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.16 E-value=1.2e+02 Score=24.61 Aligned_cols=27 Identities=11% Similarity=0.186 Sum_probs=22.1
Q ss_pred ccccHHHHHHHhCCCChhHHHHHHHHHhH
Q 044757 110 KVLSYDQLLKELEVANVRELEDFLINECM 138 (227)
Q Consensus 110 ~~isy~~I~~~L~i~~~~eVE~lvI~~ai 138 (227)
...||++||+.||++ ...|...+- .|+
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 468999999999999 888877665 554
No 274
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=20.14 E-value=3.8e+02 Score=20.03 Aligned_cols=45 Identities=16% Similarity=0.102 Sum_probs=22.2
Q ss_pred eecCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 044757 158 FAAGRDLRHGQLENMMQSLTNWLDTSDNILSVIQDKIKWAETMCE 202 (227)
Q Consensus 158 ~~~~R~~~~~q~~~l~~~L~~W~~~~~~~l~~ie~~~~~~~~~~~ 202 (227)
...++.|=..+...+...|..=.+.++..+..++.+.....+...
T Consensus 54 k~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~ 98 (110)
T TIGR02338 54 KSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLK 98 (110)
T ss_pred HHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455544445555555555555555555555544444444443
Done!