Query psy10889
Match_columns 267
No_of_seqs 201 out of 584
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 21:02:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10889.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10889hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3250|consensus 100.0 6E-61 1.3E-65 416.3 16.5 250 8-259 5-258 (258)
2 KOG2753|consensus 100.0 1.2E-32 2.7E-37 252.5 13.6 159 26-188 204-368 (378)
3 KOG2908|consensus 100.0 1.4E-31 3E-36 246.6 16.8 174 22-196 194-375 (380)
4 PF01399 PCI: PCI domain; Int 99.5 7.3E-14 1.6E-18 108.0 10.4 97 63-160 1-105 (105)
5 smart00088 PINT motif in prote 99.5 6.8E-14 1.5E-18 106.4 7.4 86 93-181 3-88 (88)
6 smart00753 PAM PCI/PINT associ 99.5 6.8E-14 1.5E-18 106.4 7.4 86 93-181 3-88 (88)
7 KOG1464|consensus 98.7 1E-07 2.2E-12 87.6 10.2 126 64-196 306-439 (440)
8 KOG2581|consensus 97.8 0.00053 1.2E-08 66.0 13.7 95 63-158 319-421 (493)
9 KOG0686|consensus 96.8 0.012 2.6E-07 56.9 11.1 110 64-174 307-424 (466)
10 KOG1498|consensus 96.3 0.024 5.3E-07 54.6 9.4 82 109-201 348-429 (439)
11 KOG2758|consensus 95.8 0.028 6E-07 53.2 7.0 95 96-196 331-425 (432)
12 COG5071 RPN5 26S proteasome re 95.5 0.09 1.9E-06 49.5 9.0 74 112-196 351-424 (439)
13 KOG1497|consensus 95.5 0.028 6E-07 53.1 5.7 82 105-194 308-389 (399)
14 KOG2688|consensus 95.0 0.12 2.6E-06 50.0 8.5 98 63-161 272-385 (394)
15 KOG2582|consensus 94.7 0.35 7.6E-06 46.5 10.8 108 63-173 259-373 (422)
16 KOG1463|consensus 93.9 0.33 7.2E-06 46.3 8.6 106 57-163 280-393 (411)
17 COG5600 Transcription-associat 93.7 0.33 7.1E-06 46.8 8.3 101 63-163 289-406 (413)
18 COG5159 RPN6 26S proteasome re 92.7 1.3 2.8E-05 41.8 10.4 102 63-165 284-393 (421)
19 KOG0687|consensus 90.6 2.7 5.9E-05 40.1 10.2 112 48-161 243-363 (393)
20 PF10075 PCI_Csn8: COP9 signal 90.5 1.8 4E-05 35.5 8.3 110 29-139 7-121 (143)
21 PF09756 DDRGK: DDRGK domain; 89.8 0.5 1.1E-05 41.4 4.4 58 101-159 100-157 (188)
22 PF09012 FeoC: FeoC like trans 88.5 0.46 1E-05 34.4 2.9 45 104-149 4-48 (69)
23 COG3355 Predicted transcriptio 86.7 7.3 0.00016 32.0 9.1 79 111-194 39-120 (126)
24 PF02082 Rrf2: Transcriptional 84.3 3.1 6.7E-05 31.0 5.5 58 100-159 11-68 (83)
25 KOG2072|consensus 83.4 15 0.00032 39.0 11.5 48 112-159 445-492 (988)
26 smart00344 HTH_ASNC helix_turn 82.4 2.3 5.1E-05 32.7 4.3 37 110-147 13-49 (108)
27 KOG3054|consensus 82.3 2.3 4.9E-05 38.9 4.7 54 105-159 205-258 (299)
28 KOG1076|consensus 81.3 9.7 0.00021 39.7 9.2 98 65-163 657-766 (843)
29 PRK11179 DNA-binding transcrip 79.9 2.8 6.1E-05 34.9 4.3 43 109-152 18-63 (153)
30 PRK01919 tatB sec-independent 79.5 18 0.0004 31.2 9.0 59 165-224 19-77 (169)
31 PF13412 HTH_24: Winged helix- 76.9 4.9 0.00011 26.5 4.0 41 105-146 8-48 (48)
32 PF07389 DUF1500: Protein of u 76.7 2.8 6E-05 32.4 2.9 33 110-144 44-76 (100)
33 TIGR02010 IscR iron-sulfur clu 74.7 8.2 0.00018 31.4 5.5 44 103-147 12-57 (135)
34 COG1522 Lrp Transcriptional re 73.8 4.5 9.7E-05 33.0 3.8 38 110-148 18-55 (154)
35 PRK14165 winged helix-turn-hel 73.1 14 0.0003 33.1 6.9 60 99-159 6-65 (217)
36 PRK11169 leucine-responsive tr 71.8 7.7 0.00017 32.6 4.8 42 105-147 19-60 (164)
37 PF13730 HTH_36: Helix-turn-he 71.2 15 0.00032 24.7 5.4 47 98-145 7-55 (55)
38 TIGR00738 rrf2_super rrf2 fami 68.8 15 0.00033 29.2 5.8 49 99-148 10-58 (132)
39 PRK10947 global DNA-binding tr 68.2 37 0.0008 28.2 8.0 23 205-227 46-68 (135)
40 PRK04654 sec-independent trans 68.2 30 0.00066 30.9 7.8 35 165-199 19-53 (214)
41 smart00346 HTH_ICLR helix_turn 67.8 11 0.00024 27.8 4.5 46 101-147 6-52 (91)
42 PF08280 HTH_Mga: M protein tr 67.2 4.7 0.0001 28.2 2.2 38 96-137 4-41 (59)
43 TIGR02944 suf_reg_Xantho FeS a 66.6 26 0.00056 28.0 6.7 37 111-148 22-58 (130)
44 PRK10857 DNA-binding transcrip 65.6 15 0.00033 31.2 5.4 38 110-148 21-58 (164)
45 PF09339 HTH_IclR: IclR helix- 65.1 15 0.00033 24.7 4.3 45 101-146 4-49 (52)
46 PF03962 Mnd1: Mnd1 family; I 64.8 76 0.0017 27.6 9.7 96 121-225 22-127 (188)
47 PRK04098 sec-independent trans 63.9 48 0.001 28.3 8.0 58 165-222 19-79 (158)
48 PRK03573 transcriptional regul 63.3 64 0.0014 26.0 8.6 56 106-162 38-93 (144)
49 TIGR01410 tatB twin arginine-t 62.0 30 0.00064 26.1 5.8 34 165-198 18-51 (80)
50 PRK04214 rbn ribonuclease BN/u 61.9 51 0.0011 31.9 9.0 60 111-178 307-366 (412)
51 PF01325 Fe_dep_repress: Iron 60.5 21 0.00046 25.1 4.5 44 102-146 10-53 (60)
52 PF08784 RPA_C: Replication pr 60.0 21 0.00046 27.4 4.9 51 100-151 50-101 (102)
53 smart00550 Zalpha Z-DNA-bindin 58.8 17 0.00036 26.2 3.8 33 114-147 22-54 (68)
54 COG5187 RPN7 26S proteasome re 58.2 74 0.0016 30.3 8.8 64 97-161 314-377 (412)
55 PF08279 HTH_11: HTH domain; 58.1 27 0.00058 23.4 4.6 41 102-143 2-43 (55)
56 PRK10328 DNA binding protein, 57.5 74 0.0016 26.4 7.9 22 206-227 47-68 (134)
57 COG1959 Predicted transcriptio 57.4 28 0.00061 29.1 5.5 48 101-149 12-59 (150)
58 cd00090 HTH_ARSR Arsenical Res 57.0 35 0.00077 23.1 5.3 36 115-151 21-56 (78)
59 PF08281 Sigma70_r4_2: Sigma-7 56.8 15 0.00032 24.6 3.1 27 113-140 25-51 (54)
60 COG1777 Predicted transcriptio 56.7 1.2E+02 0.0027 27.1 9.6 109 118-228 32-159 (217)
61 PRK01770 sec-independent trans 56.4 62 0.0013 28.0 7.5 34 165-198 19-52 (171)
62 PF13404 HTH_AsnC-type: AsnC-t 56.1 8 0.00017 25.4 1.6 27 106-133 9-35 (42)
63 PRK10265 chaperone-modulator p 54.6 18 0.00039 28.2 3.7 39 110-153 3-41 (101)
64 PF01726 LexA_DNA_bind: LexA D 54.5 23 0.0005 25.5 4.0 37 110-146 21-57 (65)
65 PF13601 HTH_34: Winged helix 54.2 15 0.00034 27.3 3.1 51 103-154 3-53 (80)
66 smart00347 HTH_MARR helix_turn 53.0 86 0.0019 22.7 8.5 41 112-153 22-62 (101)
67 PF12840 HTH_20: Helix-turn-he 52.8 28 0.0006 24.1 4.1 38 110-148 20-57 (61)
68 PRK11920 rirA iron-responsive 52.4 36 0.00078 28.4 5.4 38 112-150 22-59 (153)
69 PF14947 HTH_45: Winged helix- 52.0 40 0.00087 24.7 5.0 49 105-159 11-59 (77)
70 smart00420 HTH_DEOR helix_turn 51.8 43 0.00093 21.4 4.8 36 112-148 12-47 (53)
71 PF08220 HTH_DeoR: DeoR-like h 51.8 25 0.00054 24.3 3.7 42 103-145 3-44 (57)
72 PRK10141 DNA-binding transcrip 51.5 29 0.00063 28.0 4.5 46 112-158 28-73 (117)
73 PF01022 HTH_5: Bacterial regu 51.3 39 0.00085 22.2 4.4 33 113-146 14-46 (47)
74 PRK11014 transcriptional repre 50.3 43 0.00093 27.3 5.5 40 110-150 21-60 (141)
75 PF13815 Dzip-like_N: Iguana/D 50.2 49 0.0011 26.4 5.6 43 183-225 76-118 (118)
76 PRK09954 putative kinase; Prov 49.8 20 0.00044 33.6 3.9 53 105-158 8-63 (362)
77 smart00418 HTH_ARSR helix_turn 49.2 58 0.0013 21.3 5.2 38 112-150 8-45 (66)
78 PF03979 Sigma70_r1_1: Sigma-7 49.0 14 0.00031 27.6 2.2 38 105-143 12-52 (82)
79 PF07106 TBPIP: Tat binding pr 48.6 1.6E+02 0.0035 24.6 13.2 84 110-194 12-97 (169)
80 PF13518 HTH_28: Helix-turn-he 48.1 23 0.00051 23.1 3.0 37 104-143 4-40 (52)
81 PHA03158 hypothetical protein; 48.0 23 0.00049 31.5 3.6 52 174-225 220-271 (273)
82 PF04967 HTH_10: HTH DNA bindi 47.6 77 0.0017 22.0 5.5 30 110-140 19-48 (53)
83 PF11945 WASH_WAHD: WAHD domai 47.1 1.6E+02 0.0034 27.7 9.2 66 160-225 8-74 (297)
84 smart00345 HTH_GNTR helix_turn 47.1 80 0.0017 20.7 5.7 35 111-146 16-51 (60)
85 PF03399 SAC3_GANP: SAC3/GANP/ 46.9 41 0.00089 28.6 5.1 61 63-125 136-203 (204)
86 PF01638 HxlR: HxlR-like helix 46.4 1.1E+02 0.0025 22.8 6.9 72 104-184 10-85 (90)
87 PRK14858 tatA twin arginine tr 45.7 1.3E+02 0.0028 24.1 7.3 34 165-198 19-52 (108)
88 PRK10870 transcriptional repre 45.0 1.8E+02 0.0039 24.7 8.7 50 111-161 68-117 (176)
89 PF12802 MarR_2: MarR family; 44.3 74 0.0016 21.4 5.2 39 114-153 21-59 (62)
90 PF13591 MerR_2: MerR HTH fami 44.2 39 0.00085 25.3 4.0 32 115-151 1-32 (84)
91 PF05331 DUF742: Protein of un 41.9 45 0.00097 26.9 4.2 41 104-147 47-87 (114)
92 PF14480 DNA_pol3_a_NI: DNA po 41.9 79 0.0017 22.7 5.2 61 116-180 2-62 (76)
93 TIGR02337 HpaR homoprotocatech 41.7 1.6E+02 0.0036 22.7 8.8 47 111-158 39-85 (118)
94 PF01978 TrmB: Sugar-specific 41.2 43 0.00092 23.5 3.6 38 111-149 19-56 (68)
95 KOG2235|consensus 39.9 1.8E+02 0.0038 30.4 8.8 164 92-262 239-451 (776)
96 PRK00708 sec-independent trans 39.7 1.3E+02 0.0028 26.9 7.1 37 165-201 19-55 (209)
97 PF01047 MarR: MarR family; I 39.6 47 0.001 22.3 3.5 44 111-155 14-57 (59)
98 TIGR02919 accessory Sec system 39.6 89 0.0019 30.8 6.7 86 117-205 341-432 (438)
99 cd00592 HTH_MerR-like Helix-Tu 39.4 1.6E+02 0.0035 22.1 6.9 45 116-174 2-46 (100)
100 PHA01750 hypothetical protein 38.4 1.4E+02 0.0031 21.9 5.8 35 190-224 38-72 (75)
101 smart00419 HTH_CRP helix_turn_ 38.4 65 0.0014 20.3 3.9 33 114-147 8-40 (48)
102 PF04539 Sigma70_r3: Sigma-70 38.2 34 0.00073 24.6 2.7 27 112-139 18-44 (78)
103 PRK00404 tatB sec-independent 38.1 2.2E+02 0.0047 24.0 7.7 34 165-198 19-52 (141)
104 PF04545 Sigma70_r4: Sigma-70, 37.6 63 0.0014 21.2 3.8 29 112-141 18-46 (50)
105 cd07377 WHTH_GntR Winged helix 37.4 1.3E+02 0.0027 20.1 6.4 36 110-146 20-56 (66)
106 cd00092 HTH_CRP helix_turn_hel 37.2 71 0.0015 21.7 4.2 35 112-147 23-57 (67)
107 cd04766 HTH_HspR Helix-Turn-He 36.1 1.8E+02 0.004 21.7 7.0 46 115-174 2-47 (91)
108 PF05565 Sipho_Gp157: Siphovir 36.1 2.6E+02 0.0057 23.5 8.3 43 185-227 45-87 (162)
109 cd06445 ATase The DNA repair p 35.2 50 0.0011 24.4 3.3 30 103-132 6-36 (79)
110 TIGR03879 near_KaiC_dom probab 34.7 32 0.0007 25.6 2.1 29 113-142 31-59 (73)
111 KOG2166|consensus 34.4 1.6E+02 0.0034 31.2 7.8 118 100-225 566-695 (725)
112 TIGR02702 SufR_cyano iron-sulf 34.2 3E+02 0.0066 23.6 11.6 37 112-149 13-49 (203)
113 PHA02763 hypothetical protein; 32.9 54 0.0012 25.4 3.1 50 115-166 53-102 (102)
114 PF09341 Pcc1: Transcription f 32.7 1.5E+02 0.0032 21.4 5.5 47 142-194 30-76 (76)
115 PF05010 TACC: Transforming ac 32.7 3.1E+02 0.0068 24.4 8.4 53 170-222 119-172 (207)
116 KOG4348|consensus 32.5 1.8E+02 0.004 29.0 7.4 50 176-225 569-625 (627)
117 PF09218 DUF1959: Domain of un 31.7 27 0.00058 28.4 1.3 40 120-186 19-58 (117)
118 PRK10411 DNA-binding transcrip 31.6 71 0.0015 28.6 4.3 45 101-146 5-49 (240)
119 COG1595 RpoE DNA-directed RNA 30.7 60 0.0013 27.1 3.5 27 113-140 142-168 (182)
120 PF13542 HTH_Tnp_ISL3: Helix-t 30.4 64 0.0014 21.2 2.9 33 104-139 19-51 (52)
121 PRK15090 DNA-binding transcrip 29.9 97 0.0021 27.7 4.9 45 102-147 16-60 (257)
122 TIGR01884 cas_HTH CRISPR locus 28.9 1.5E+02 0.0032 25.6 5.7 46 111-158 154-199 (203)
123 PRK12537 RNA polymerase sigma 28.5 67 0.0015 26.8 3.4 27 113-140 148-174 (182)
124 PF06163 DUF977: Bacterial pro 28.3 87 0.0019 25.8 3.8 51 93-145 6-56 (127)
125 PF05377 FlaC_arch: Flagella a 28.0 2.1E+02 0.0046 20.2 5.2 34 192-225 5-38 (55)
126 PF01920 Prefoldin_2: Prefoldi 27.5 2.6E+02 0.0055 21.0 6.3 59 154-226 43-101 (106)
127 PF04703 FaeA: FaeA-like prote 27.3 82 0.0018 22.6 3.1 34 112-146 13-46 (62)
128 TIGR02999 Sig-70_X6 RNA polyme 27.3 73 0.0016 26.3 3.4 27 113-140 149-175 (183)
129 cd01106 HTH_TipAL-Mta Helix-Tu 27.2 2.8E+02 0.0061 21.1 7.1 92 116-224 2-96 (103)
130 PF02002 TFIIE_alpha: TFIIE al 27.1 56 0.0012 25.2 2.5 36 112-148 25-60 (105)
131 smart00421 HTH_LUXR helix_turn 27.0 1E+02 0.0022 19.7 3.5 25 114-139 18-42 (58)
132 PF09202 Rio2_N: Rio2, N-termi 26.9 1.6E+02 0.0034 22.2 4.8 49 100-149 9-58 (82)
133 PRK12523 RNA polymerase sigma 26.6 80 0.0017 26.0 3.5 28 113-141 134-161 (172)
134 PF13022 HTH_Tnp_1_2: Helix-tu 26.4 1.1E+02 0.0025 25.6 4.2 46 91-137 10-56 (142)
135 PF08581 Tup_N: Tup N-terminal 26.2 2.8E+02 0.0062 20.8 8.6 57 170-226 12-75 (79)
136 PRK12529 RNA polymerase sigma 25.9 83 0.0018 26.2 3.5 27 113-140 142-168 (178)
137 PRK09047 RNA polymerase factor 25.8 86 0.0019 25.2 3.5 27 113-140 121-147 (161)
138 PHA02943 hypothetical protein; 25.7 1.5E+02 0.0032 25.4 4.8 45 97-146 11-55 (165)
139 TIGR02051 MerR Hg(II)-responsi 25.6 3.3E+02 0.0072 21.6 6.8 26 117-147 2-27 (124)
140 PRK06759 RNA polymerase factor 25.3 89 0.0019 25.0 3.5 28 113-141 121-148 (154)
141 COG4575 ElaB Uncharacterized c 25.3 3.2E+02 0.0069 21.8 6.4 57 163-225 2-58 (104)
142 cd06170 LuxR_C_like C-terminal 25.1 1.2E+02 0.0025 19.6 3.5 25 114-139 15-39 (57)
143 PRK09642 RNA polymerase sigma 25.0 90 0.002 25.2 3.5 27 113-140 121-147 (160)
144 PF02796 HTH_7: Helix-turn-hel 25.0 79 0.0017 20.6 2.5 26 107-135 16-41 (45)
145 PRK09651 RNA polymerase sigma 25.0 89 0.0019 25.8 3.5 28 113-141 134-161 (172)
146 PF13384 HTH_23: Homeodomain-l 24.7 76 0.0017 20.6 2.5 25 114-139 17-41 (50)
147 PF09743 DUF2042: Uncharacteri 24.6 99 0.0021 28.6 4.0 41 111-152 127-167 (272)
148 PRK09802 DNA-binding transcrip 24.6 1E+02 0.0022 28.1 4.1 47 99-146 16-62 (269)
149 PRK07037 extracytoplasmic-func 24.6 93 0.002 25.2 3.5 27 113-140 124-150 (163)
150 PF04297 UPF0122: Putative hel 24.5 82 0.0018 24.9 2.9 26 113-139 32-57 (101)
151 PF00392 GntR: Bacterial regul 24.4 2.4E+02 0.0053 19.4 6.4 37 110-147 19-56 (64)
152 cd01109 HTH_YyaN Helix-Turn-He 24.4 3.2E+02 0.0069 21.2 6.4 95 116-224 2-102 (113)
153 PF10668 Phage_terminase: Phag 24.0 87 0.0019 22.4 2.7 24 111-135 19-42 (60)
154 PRK15418 transcriptional regul 23.8 1.1E+02 0.0024 28.7 4.2 39 113-152 28-66 (318)
155 PF09523 DUF2390: Protein of u 23.8 1.7E+02 0.0037 23.2 4.7 42 162-203 43-84 (109)
156 PRK12543 RNA polymerase sigma 23.8 92 0.002 25.9 3.4 26 113-139 132-157 (179)
157 PRK11020 hypothetical protein; 23.7 3.3E+02 0.007 22.2 6.2 47 177-223 6-53 (118)
158 PRK00182 tatB sec-independent 23.5 2.9E+02 0.0062 23.7 6.2 33 165-197 20-52 (160)
159 KOG1861|consensus 23.1 2.7E+02 0.0058 28.2 6.7 65 65-131 426-495 (540)
160 PRK12520 RNA polymerase sigma 23.1 1E+02 0.0022 25.9 3.5 25 114-139 147-171 (191)
161 PRK12527 RNA polymerase sigma 23.0 1E+02 0.0023 24.8 3.5 27 113-140 120-146 (159)
162 PF10007 DUF2250: Uncharacteri 22.9 1.1E+02 0.0024 23.7 3.3 27 119-146 26-52 (92)
163 PF13463 HTH_27: Winged helix 22.8 2.5E+02 0.0055 19.0 6.6 47 108-155 12-58 (68)
164 PF14203 DUF4319: Domain of un 22.8 1.3E+02 0.0029 21.8 3.5 27 65-92 6-32 (64)
165 COG1497 Predicted transcriptio 22.7 6.1E+02 0.013 23.4 10.6 83 105-199 16-98 (260)
166 PF06056 Terminase_5: Putative 22.5 95 0.0021 21.8 2.7 23 114-137 13-35 (58)
167 PRK12525 RNA polymerase sigma 22.4 1.1E+02 0.0023 25.2 3.5 28 113-141 133-160 (168)
168 PF00403 HMA: Heavy-metal-asso 22.4 1.4E+02 0.003 20.2 3.5 30 142-172 24-53 (62)
169 PRK12547 RNA polymerase sigma 22.2 1.1E+02 0.0023 25.1 3.4 27 113-140 127-153 (164)
170 PRK12513 RNA polymerase sigma 22.1 1.1E+02 0.0023 25.7 3.5 27 113-140 154-180 (194)
171 PRK12514 RNA polymerase sigma 22.0 1.1E+02 0.0023 25.3 3.4 27 113-140 144-170 (179)
172 COG2963 Transposase and inacti 22.0 3.7E+02 0.0081 20.7 7.8 31 116-146 26-56 (116)
173 PRK03100 sec-independent trans 21.8 4.5E+02 0.0097 21.9 6.9 34 165-198 20-53 (136)
174 PF07889 DUF1664: Protein of u 21.6 4.6E+02 0.0099 21.5 8.2 53 172-224 46-98 (126)
175 TIGR02947 SigH_actino RNA poly 21.5 1.1E+02 0.0023 25.8 3.3 27 113-140 146-172 (193)
176 PF12324 HTH_15: Helix-turn-he 21.5 1.3E+02 0.0027 22.7 3.3 35 104-139 28-62 (77)
177 TIGR02431 pcaR_pcaU beta-ketoa 21.4 1.7E+02 0.0037 25.8 4.8 45 101-146 10-55 (248)
178 PF13936 HTH_38: Helix-turn-he 21.3 1.2E+02 0.0027 19.7 2.9 39 89-135 2-40 (44)
179 COG3413 Predicted DNA binding 21.3 2.3E+02 0.0049 24.7 5.5 52 88-140 152-203 (215)
180 TIGR02983 SigE-fam_strep RNA p 21.3 1.2E+02 0.0026 24.5 3.5 27 113-140 125-151 (162)
181 PF10975 DUF2802: Protein of u 21.1 99 0.0022 22.6 2.6 21 115-136 45-65 (70)
182 COG5647 Cullin, a subunit of E 21.1 7.9E+02 0.017 26.2 9.8 59 100-159 608-670 (773)
183 PRK13509 transcriptional repre 20.9 1.4E+02 0.0029 26.9 4.0 47 100-147 5-51 (251)
184 KOG3438|consensus 20.9 2.6E+02 0.0056 22.3 5.0 42 161-203 62-103 (105)
185 TIGR03092 SASP_sspI small, aci 20.8 1.2E+02 0.0027 22.1 3.0 24 120-143 6-29 (65)
186 cd00280 TRFH Telomeric Repeat 20.7 1.3E+02 0.0028 26.7 3.7 48 66-113 18-70 (200)
187 PRK12536 RNA polymerase sigma 20.7 1.2E+02 0.0025 25.3 3.4 27 113-140 144-170 (181)
188 KOG2629|consensus 20.6 4.2E+02 0.0092 24.9 7.2 65 133-202 85-151 (300)
189 PRK10434 srlR DNA-bindng trans 20.6 1.3E+02 0.0029 27.0 4.0 44 101-145 6-49 (256)
190 PRK12539 RNA polymerase sigma 20.4 1.2E+02 0.0025 25.4 3.3 27 113-140 146-172 (184)
191 PF05791 Bacillus_HBL: Bacillu 20.4 4.2E+02 0.009 22.7 6.8 57 170-226 125-181 (184)
192 KOG3431|consensus 20.3 71 0.0015 26.2 1.8 22 130-151 70-91 (129)
193 PRK09646 RNA polymerase sigma 20.2 1.1E+02 0.0024 25.8 3.2 26 113-139 157-182 (194)
No 1
>KOG3250|consensus
Probab=100.00 E-value=6e-61 Score=416.27 Aligned_cols=250 Identities=45% Similarity=0.694 Sum_probs=235.5
Q ss_pred cCCcchHHHHHhhcccchHHHHHHHHHHHHhCCCeeechhhhcChhhhhhcCCCchhHHHHHHHHhcCCHhHHHhhhhhc
Q psy10889 8 GVGTNPLEQFVLLAKTTKGAAAVELIKQVLEAPGIFMFKELIDMPLIKELDTSPHAGYYHLLKLFAHGTYQDYLKQKEEL 87 (267)
Q Consensus 8 ~~~~~~le~fl~lak~~k~~aa~~lI~~aL~~p~vf~F~eLL~~p~vq~L~~s~~~~~~~LL~lFa~Gt~~dy~~~~~~~ 87 (267)
....+.++||+++||+.+|+|+..+|.+||++|+||+|+|||.+|+|.+|.++.++.+++||++||||||.||.++..
T Consensus 5 k~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~aea~-- 82 (258)
T KOG3250|consen 5 KKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAEAL-- 82 (258)
T ss_pred hhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhhhh--
Confidence 345678999999999999999999999999999999999999999999999998999999999999999999999887
Q ss_pred cCchhHHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCC
Q psy10889 88 KLPEMTQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDIN 167 (267)
Q Consensus 88 ~~p~L~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~ 167 (267)
.+|.|+++++.||++||++|||+..++|||+.|++.|.+.|+++||++||+|||++++.|||||.+++++|.|+++||++
T Consensus 83 rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr 162 (258)
T KOG3250|consen 83 RLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLR 162 (258)
T ss_pred cCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhccccCCCCCccccccCCCCc---
Q psy10889 168 PGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLKNQTNQSQDTDDMMGSDNVV--- 244 (267)
Q Consensus 168 ~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~d~~~--- 244 (267)
+.++.+|..+|++||+.|+++|-.|++++++||.+++...+++++.|.++.|+||++|...+..-+.-++|-.+.+.
T Consensus 163 ~k~i~nm~~TL~~w~~~cenvL~~ie~qv~~anq~~e~~~r~~qq~e~ev~~~kKtlk~~ad~d~~~~eq~l~epp~~~q 242 (258)
T KOG3250|consen 163 SKDIDNMKYTLDEWCEGCENVLFGIEAQVPRANQSKERASRMSQQDEIEVMNFKKTLKPTADTDFQLNEQMLGEPPVMDQ 242 (258)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHhhhhhhhhhHHhhhcccCCCccccccchHHHhCCCCCccc
Confidence 99999999999999999999999999999999999999999999999999999999999865444455566666644
Q ss_pred cccccc-cccCCCCCC
Q psy10889 245 DKIGKK-YKIKSNRGT 259 (267)
Q Consensus 245 ~~~~~~-~~~~~~~~~ 259 (267)
++|+|| +|.||++++
T Consensus 243 rqp~kk~sk~kglv~s 258 (258)
T KOG3250|consen 243 RQPGKKPSKRKGLVTS 258 (258)
T ss_pred cCCCcCcccccCCCCC
Confidence 689999 999998853
No 2
>KOG2753|consensus
Probab=100.00 E-value=1.2e-32 Score=252.50 Aligned_cols=159 Identities=26% Similarity=0.481 Sum_probs=144.2
Q ss_pred HHHHHHHHHHHHhCCCeeechhhhcChhhhhhcCCCchhHHHHHHHHhcCCHhHHHhhhh----hccCchhH-HHHHHHH
Q psy10889 26 GAAAVELIKQVLEAPGIFMFKELIDMPLIKELDTSPHAGYYHLLKLFAHGTYQDYLKQKE----ELKLPEMT-QLQKKKL 100 (267)
Q Consensus 26 ~~aa~~lI~~aL~~p~vf~F~eLL~~p~vq~L~~s~~~~~~~LL~lFa~Gt~~dy~~~~~----~~~~p~L~-~~~~~KL 100 (267)
...|.++|+.|+.+|+.|.|++|+.+|+|+.|+++. +|+||.||..|.+++|.++.. +++.-+|. +++.+||
T Consensus 204 redA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KM 280 (378)
T KOG2753|consen 204 REDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKM 280 (378)
T ss_pred HHHHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHH
Confidence 356899999999999999999999999999999986 999999999999999998854 23333444 5679999
Q ss_pred HhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHH
Q psy10889 101 QNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQA 180 (267)
Q Consensus 101 r~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~ 180 (267)
|+||+++||+.+..|||++|+++|+|. .+|||.|||+||.+++|.|||||.+++|.|+.+.+|.|+..||..|.++|..
T Consensus 281 RLLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~a 359 (378)
T KOG2753|consen 281 RLLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAA 359 (378)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHH
Confidence 999999999999999999999999997 9999999999999999999999999999999999999999999999999999
Q ss_pred HH-HHHHHH
Q psy10889 181 WS-DSCANV 188 (267)
Q Consensus 181 W~-~~~~~v 188 (267)
|. +.+.++
T Consensus 360 w~k~~~stv 368 (378)
T KOG2753|consen 360 WGKQNLSTV 368 (378)
T ss_pred HHhhhhHHH
Confidence 95 433333
No 3
>KOG2908|consensus
Probab=99.98 E-value=1.4e-31 Score=246.63 Aligned_cols=174 Identities=18% Similarity=0.377 Sum_probs=162.7
Q ss_pred ccchHHHHHHHHHHHHhCCCeeechhhhcChhhhhhcCCCchhHHHHHHHHhcCCHhHHHhhhhhc-cCchhHH---HHH
Q psy10889 22 KTTKGAAAVELIKQVLEAPGIFMFKELIDMPLIKELDTSPHAGYYHLLKLFAHGTYQDYLKQKEEL-KLPEMTQ---LQK 97 (267)
Q Consensus 22 k~~k~~aa~~lI~~aL~~p~vf~F~eLL~~p~vq~L~~s~~~~~~~LL~lFa~Gt~~dy~~~~~~~-~~p~L~~---~~~ 97 (267)
.+.+...|.+|..+||.+.++|||||||.||+...|.+|++.|++++|.+|+.||+..|......+ ..|.|.. ...
T Consensus 194 ~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~~p~L~~~e~~L~ 273 (380)
T KOG2908|consen 194 ESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGKQPDLASNEDFLL 273 (380)
T ss_pred HHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhccCchHHHHHHHHH
Confidence 456678899999999999999999999999999999999999999999999999999999987655 7788853 369
Q ss_pred HHHHhHHhhhccc----CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHH
Q psy10889 98 KKLQNLTIVTLSL----ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTN 173 (267)
Q Consensus 98 ~KLr~LtLlsLa~----~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~ 173 (267)
+|+++|+|+.+|- ..|.+||++|+++++|| .++||.+||+|++.|||+|.|||++++|+++|++||.++.+|+..
T Consensus 274 qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~ 352 (380)
T KOG2908|consen 274 QKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVK 352 (380)
T ss_pred HHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHh
Confidence 9999999999984 57999999999999999 899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 174 MITEFQAWSDSCANVLKAIETQI 196 (267)
Q Consensus 174 L~~~L~~W~~~~~~vl~~ie~~i 196 (267)
|.+++..|++.+.++...|+.+.
T Consensus 353 Mk~rl~~W~~~v~~me~~ve~~~ 375 (380)
T KOG2908|consen 353 MKDRLDEWNKDVKSMEGLVEHRG 375 (380)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999988754
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=99.53 E-value=7.3e-14 Score=107.97 Aligned_cols=97 Identities=26% Similarity=0.396 Sum_probs=83.0
Q ss_pred hhHHHHHHHHhcCCHhHHHhhhhhc-----cCchh---HHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHH
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQKEEL-----KLPEM---TQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLED 134 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~~~~-----~~p~L---~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~ 134 (267)
+|+.+|+++|..|++..|....... ..|.+ .+.+..+++..+|.+++...+.|++++|++.|+++ ..+||.
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 3789999999999999998764311 22333 46789999999999999999999999999999999 899999
Q ss_pred HHHHHHhcCccEEEecCCCCeEEEEe
Q psy10889 135 LIIEAIYSDIIHGKLDQRNSSLELDF 160 (267)
Q Consensus 135 lvI~aI~~gLI~GkIDQ~~~~v~V~~ 160 (267)
+|+++|..|.|.|+|||.+++|+++|
T Consensus 80 ~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999875
No 5
>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=99.49 E-value=6.8e-14 Score=106.35 Aligned_cols=86 Identities=23% Similarity=0.303 Sum_probs=81.1
Q ss_pred HHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHH
Q psy10889 93 TQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVT 172 (267)
Q Consensus 93 ~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~ 172 (267)
.+.+.+|++.++|+.++..+++|+|++|++.++++ .+++|.+|+++|..|.|.|+|||.+++|.+.+..+|. .++|.
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~ 79 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA 79 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH
Confidence 45678999999999999999999999999999999 7899999999999999999999999999999999996 78899
Q ss_pred HHHHHHHHH
Q psy10889 173 NMITEFQAW 181 (267)
Q Consensus 173 ~L~~~L~~W 181 (267)
.+.++|..|
T Consensus 80 ~~~~~l~~~ 88 (88)
T smart00088 80 QFAETLKKL 88 (88)
T ss_pred HHHHHhhcC
Confidence 999998887
No 6
>smart00753 PAM PCI/PINT associated module.
Probab=99.49 E-value=6.8e-14 Score=106.35 Aligned_cols=86 Identities=23% Similarity=0.303 Sum_probs=81.1
Q ss_pred HHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHH
Q psy10889 93 TQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVT 172 (267)
Q Consensus 93 ~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~ 172 (267)
.+.+.+|++.++|+.++..+++|+|++|++.++++ .+++|.+|+++|..|.|.|+|||.+++|.+.+..+|. .++|.
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~~ 79 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPLA 79 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hhHHH
Confidence 45678999999999999999999999999999999 7899999999999999999999999999999999996 78899
Q ss_pred HHHHHHHHH
Q psy10889 173 NMITEFQAW 181 (267)
Q Consensus 173 ~L~~~L~~W 181 (267)
.+.++|..|
T Consensus 80 ~~~~~l~~~ 88 (88)
T smart00753 80 QFAETLKKL 88 (88)
T ss_pred HHHHHhhcC
Confidence 999998887
No 7
>KOG1464|consensus
Probab=98.70 E-value=1e-07 Score=87.63 Aligned_cols=126 Identities=17% Similarity=0.334 Sum_probs=106.3
Q ss_pred hHHHHHHHHhcCCHhHHHhhh----hhc-cCchhH---HHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHH
Q psy10889 64 GYYHLLKLFAHGTYQDYLKQK----EEL-KLPEMT---QLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDL 135 (267)
Q Consensus 64 ~~~~LL~lFa~Gt~~dy~~~~----~~~-~~p~L~---~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~l 135 (267)
.+.+|+..+...++.+|+... +.+ ..|.+. ++.++++|.-.|+.|......|....|+++|.|+ +.+||.|
T Consensus 306 AMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~L 384 (440)
T KOG1464|consen 306 AMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVESL 384 (440)
T ss_pred HHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHHH
Confidence 478899999999999998753 234 557764 5679999999999999999999999999999999 9999999
Q ss_pred HHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 136 IIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCANVLKAIETQI 196 (267)
Q Consensus 136 vI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i 196 (267)
++.||-.+-|+|+|||+++.+....... .-..+...|..|.++++++.+.|-.++
T Consensus 385 LV~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr~ 439 (440)
T KOG1464|consen 385 LVSCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSRV 439 (440)
T ss_pred HHHHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999999999999999999998764321 122388999999999999988876543
No 8
>KOG2581|consensus
Probab=97.79 E-value=0.00053 Score=66.04 Aligned_cols=95 Identities=20% Similarity=0.341 Sum_probs=69.6
Q ss_pred hhHHHHHHHHhcCCHhHHHhhhhhccCchhH----HHHHHHHHhHHh----hhcccCCcccCHHHHHHHhCCCChhhHHH
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQKEELKLPEMT----QLQKKKLQNLTI----VTLSLESKCIPYDKLLKELDISNVRDLED 134 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~~~~~~p~L~----~~~~~KLr~LtL----lsLa~~~k~IsY~~I~~~L~I~~~~evE~ 134 (267)
.+|+.|-+..--||++-|.....+.. +.|- -..+-.||+=.| -.+.-.++.|||.+|+..|+|+|..++|.
T Consensus 319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k-~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~Ey 397 (493)
T KOG2581|consen 319 RPYFKLTQAVRLGDLKKFNETLEQFK-DKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEY 397 (493)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHH-HHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHH
Confidence 46999999999999999988755210 1111 112333333222 12222478999999999999999899999
Q ss_pred HHHHHHhcCccEEEecCCCCeEEE
Q psy10889 135 LIIEAIYSDIIHGKLDQRNSSLEL 158 (267)
Q Consensus 135 lvI~aI~~gLI~GkIDQ~~~~v~V 158 (267)
+|-+||..|+|+|+||..++.+.-
T Consensus 398 iVakAIRDGvIea~Id~~~g~m~s 421 (493)
T KOG2581|consen 398 IVAKAIRDGVIEAKIDHEDGFMQS 421 (493)
T ss_pred HHHHHHHhccceeeeccccCceeh
Confidence 999999999999999999995543
No 9
>KOG0686|consensus
Probab=96.85 E-value=0.012 Score=56.90 Aligned_cols=110 Identities=20% Similarity=0.204 Sum_probs=83.9
Q ss_pred hHHHHHHHHhcCCHhHHHhhhhhc--cC---chhHH---HHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHH
Q psy10889 64 GYYHLLKLFAHGTYQDYLKQKEEL--KL---PEMTQ---LQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDL 135 (267)
Q Consensus 64 ~~~~LL~lFa~Gt~~dy~~~~~~~--~~---p~L~~---~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~l 135 (267)
.+.++|.-|..+-|..-...-..+ .+ +-|.| ....++|.=+++..-.....++++.+|.+.+.+ +..+|.=
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 366677777777766544432211 11 33444 468889999999999999999999999999998 9999999
Q ss_pred HHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHH
Q psy10889 136 IIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNM 174 (267)
Q Consensus 136 vI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L 174 (267)
|.+.|-.|.|.||||+.++++.+.-+..|.-+-+....|
T Consensus 386 l~~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~~~~ 424 (466)
T KOG0686|consen 386 LLELILEGKISGRIDSHNKILYARDADSENATFERVLPM 424 (466)
T ss_pred HHHHHHccchheeeccccceeeecccccccchhhhcchh
Confidence 999999999999999999999998776664433333333
No 10
>KOG1498|consensus
Probab=96.33 E-value=0.024 Score=54.57 Aligned_cols=82 Identities=15% Similarity=0.283 Sum_probs=71.1
Q ss_pred ccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHH
Q psy10889 109 SLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCANV 188 (267)
Q Consensus 109 a~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~v 188 (267)
|.-+.+||+..+++-|+++ .++.|.+|=+.+..|.|.+|||+..+.+.+.-+ ..+.+-|.+|..+++++
T Consensus 348 A~yYSrIt~~rl~eLLdl~-~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L 416 (439)
T KOG1498|consen 348 AKYYSRITLKRLAELLDLP-VEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKL 416 (439)
T ss_pred HHHHhhccHHHHHHHhCCC-HHHHHHHHHHHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHH
Confidence 3447899999999999999 999999999999999999999999999988633 44788899999999999
Q ss_pred HHHHHHHHHHHHH
Q psy10889 189 LKAIETQIGKANS 201 (267)
Q Consensus 189 l~~ie~~i~~a~~ 201 (267)
+..++.--.-..+
T Consensus 417 ~~ll~K~~HLI~K 429 (439)
T KOG1498|consen 417 LGLLEKVSHLIHK 429 (439)
T ss_pred HHHHHHHHHHHHH
Confidence 9988875555544
No 11
>KOG2758|consensus
Probab=95.81 E-value=0.028 Score=53.17 Aligned_cols=95 Identities=18% Similarity=0.265 Sum_probs=76.2
Q ss_pred HHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHH
Q psy10889 96 QKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMI 175 (267)
Q Consensus 96 ~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~ 175 (267)
-+.-.|+|-.-+.|.-+.+|+.+.||+.|+++ ..|.|.|++..|....|++|||..-+.|.+..... .--++++
T Consensus 331 F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwivnlIr~~rl~AkidSklg~Vvmg~~~~-----s~~qQ~i 404 (432)
T KOG2758|consen 331 FLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIVNLIRTARLDAKIDSKLGHVVMGHPTV-----SPHQQLI 404 (432)
T ss_pred HHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHHHHHHHhhhhhhhccccCceeecCCCC-----CHHHHHH
Confidence 36777888888888889999999999999998 99999999999999999999999999988764322 1344566
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q psy10889 176 TEFQAWSDSCANVLKAIETQI 196 (267)
Q Consensus 176 ~~L~~W~~~~~~vl~~ie~~i 196 (267)
++-..-.-+..++-..++..+
T Consensus 405 e~tksLS~rsq~la~~lek~~ 425 (432)
T KOG2758|consen 405 EKTKSLSFRSQNLAQQLEKKI 425 (432)
T ss_pred HhccccchhHHHHHHHHHHHH
Confidence 666666666666666666554
No 12
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=95.49 E-value=0.09 Score=49.53 Aligned_cols=74 Identities=16% Similarity=0.287 Sum_probs=64.4
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHH
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCANVLKA 191 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ 191 (267)
+..|+-..|..-|+.+ ..+.|.+|-+.+..|.+.+||+|..+.+.+.-. .+..+.|..|.++++.++..
T Consensus 351 YSrI~~~rl~~lld~~-~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~----------~n~~~~lneW~~NV~ellgk 419 (439)
T COG5071 351 YSRIHCSRLGVLLDMS-PSETEQFISDLVNKGHFYAKINRPAQIISFEKS----------QNVQEQLNEWGSNVTELLGK 419 (439)
T ss_pred hhhhhHHHHHHHHcCC-HHHHHHHHHHHHhcCcEEEEecCccceEEeecc----------ccHHHHHHHhcccHHHHHHH
Confidence 5778999999999998 999999999999999999999999999988633 23567889999999999988
Q ss_pred HHHHH
Q psy10889 192 IETQI 196 (267)
Q Consensus 192 ie~~i 196 (267)
++.--
T Consensus 420 lek~~ 424 (439)
T COG5071 420 LEKVR 424 (439)
T ss_pred HHHHh
Confidence 87643
No 13
>KOG1497|consensus
Probab=95.47 E-value=0.028 Score=53.05 Aligned_cols=82 Identities=16% Similarity=0.241 Sum_probs=60.1
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHH
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDS 184 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~ 184 (267)
|+++..-...|+|++|...|+|+ ...+|.++=++|..+=++|.|||.++.+++.-.-+ -.+|+. .+..-|..
T Consensus 308 lls~Skly~nisf~~Lg~ll~i~-~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~----l~~wdk---qi~sl~~q 379 (399)
T KOG1497|consen 308 LLSASKLYNNISFEELGALLKID-AEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREE----LPQWDK---QIQSLCNQ 379 (399)
T ss_pred HHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHHHHHhHHHhccchHhhcceEeecchhh----hhhhhH---HHHHHHHH
Confidence 34444446789999999999999 99999999999999999999999999999863211 124443 33344555
Q ss_pred HHHHHHHHHH
Q psy10889 185 CANVLKAIET 194 (267)
Q Consensus 185 ~~~vl~~ie~ 194 (267)
+++++..|..
T Consensus 380 vNki~~~i~~ 389 (399)
T KOG1497|consen 380 VNKILDKISH 389 (399)
T ss_pred HHHHHHHHHH
Confidence 5555555543
No 14
>KOG2688|consensus
Probab=94.96 E-value=0.12 Score=49.98 Aligned_cols=98 Identities=16% Similarity=0.216 Sum_probs=72.4
Q ss_pred hhHHHHHHHHhcCCHhHHHhhhhhccCchhHH----HHHHHHHhHHhhhcc-------cCCcccCHHHHHHHhCCCC---
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQKEELKLPEMTQ----LQKKKLQNLTIVTLS-------LESKCIPYDKLLKELDISN--- 128 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~~~~~~p~L~~----~~~~KLr~LtLlsLa-------~~~k~IsY~~I~~~L~I~~--- 128 (267)
..+-.|+.....|++..|....+. +.--+.. -.+.|+++++.=.|. .+...+|++.+..+|....
T Consensus 272 ~~~~~lv~aVr~Gnl~~f~~al~~-~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~ 350 (394)
T KOG2688|consen 272 DKYSPLVQAVRSGNLRLFDLALAD-NERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTD 350 (394)
T ss_pred HhHHHHHHHHHhccHHHHHHHHhh-hHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCC
Confidence 356778999999999999875331 0000100 124446666544433 2568899999999998765
Q ss_pred --hhhHHHHHHHHHhcCccEEEecCCCCeEEEEee
Q psy10889 129 --VRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFA 161 (267)
Q Consensus 129 --~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~ 161 (267)
.+|||-.+..+|+.|.|+|.|+...+++.+...
T Consensus 351 ~~~deveciLa~lI~~G~ikgYish~~~~~V~sK~ 385 (394)
T KOG2688|consen 351 VDLDEVECILANLIDLGRIKGYISHQLQTLVFSKK 385 (394)
T ss_pred CchhhHHHHHHhhhhhccccchhchhhheEEEecC
Confidence 689999999999999999999999999999754
No 15
>KOG2582|consensus
Probab=94.73 E-value=0.35 Score=46.46 Aligned_cols=108 Identities=10% Similarity=0.167 Sum_probs=80.9
Q ss_pred hhHHHHHHHHhcCCHhHHHhhhh----hc---cCchhHHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHH
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQKE----EL---KLPEMTQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDL 135 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~~----~~---~~p~L~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~l 135 (267)
.+|.++++++..+.-.+.+.... .+ +.-+|....+.-+.+=+|..|....-+|+.++|++..++.+..|||..
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 36999999999988776655321 11 334455444555555566666666778999999997777778999999
Q ss_pred HHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHH
Q psy10889 136 IIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTN 173 (267)
Q Consensus 136 vI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~ 173 (267)
|+..|..|=|-+.|| +-|..+.-...+..|+...+
T Consensus 339 Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n 373 (422)
T KOG2582|consen 339 ILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN 373 (422)
T ss_pred HHHHhccCceEEEec---ceEEEecCcccCCCHHHHhh
Confidence 999999999999999 88888777777777766554
No 16
>KOG1463|consensus
Probab=93.85 E-value=0.33 Score=46.31 Aligned_cols=106 Identities=14% Similarity=0.149 Sum_probs=76.2
Q ss_pred hcCCCchhHHHHHHHHhcCCHhHHHhhhh----hc-cCchhHHH---HHHHHHhHHhhhcccCCcccCHHHHHHHhCCCC
Q psy10889 57 LDTSPHAGYYHLLKLFAHGTYQDYLKQKE----EL-KLPEMTQL---QKKKLQNLTIVTLSLESKCIPYDKLLKELDISN 128 (267)
Q Consensus 57 L~~s~~~~~~~LL~lFa~Gt~~dy~~~~~----~~-~~p~L~~~---~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~ 128 (267)
..+..-..+...-+.|..-+++||...-. ++ ..|....+ .-.-|----|+.+.++..++..+-|++-+|++
T Consensus 280 y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~hIA~~IGl~- 358 (411)
T KOG1463|consen 280 YAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEISHIAEVIGLD- 358 (411)
T ss_pred ccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHHHHHHHHCCC-
Confidence 33433455777778888889999986432 11 22222111 11111112367777889999999999999998
Q ss_pred hhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecC
Q psy10889 129 VRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIG 163 (267)
Q Consensus 129 ~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~ 163 (267)
+..||.=+-.+|-...+.|.|||-++|+.|.--.+
T Consensus 359 ~~~VEkKLsqMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 359 VPQVEKKLSQMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred cHHHHHHHHHHHHHHHhhcccccCCCeEEEeCCCC
Confidence 99999999999999999999999999999974433
No 17
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=93.66 E-value=0.33 Score=46.75 Aligned_cols=101 Identities=15% Similarity=0.187 Sum_probs=65.9
Q ss_pred hhHHHHHHHHhcCCHhHHHhhhhh----ccCchhHHHHHHHHHhH-------HhhhcccCCcccCHHHHHHHhCCCC---
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQKEE----LKLPEMTQLQKKKLQNL-------TIVTLSLESKCIPYDKLLKELDISN--- 128 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~~~----~~~p~L~~~~~~KLr~L-------tLlsLa~~~k~IsY~~I~~~L~I~~--- 128 (267)
+.+--|..+.-+|++++|....+. +---+|-=.+..+...+ .+..++-....+||+.+...++++.
T Consensus 289 s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn 368 (413)
T COG5600 289 SVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDN 368 (413)
T ss_pred chhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCc
Confidence 445668899999999999875321 00000100111222222 2334444455577777666666543
Q ss_pred ---hhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecC
Q psy10889 129 ---VRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIG 163 (267)
Q Consensus 129 ---~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~ 163 (267)
..+||-++..+|..|+++|.|....++++++...|
T Consensus 369 ~~~~~~VEciL~tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 369 FHSFKEVECILVTLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred ccChHHHHHHHHHHHhhhhhhheecccceEEEEecCCC
Confidence 46899999999999999999999999999986543
No 18
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=92.74 E-value=1.3 Score=41.79 Aligned_cols=102 Identities=15% Similarity=0.195 Sum_probs=73.6
Q ss_pred hhHHHHHHHHhcCCHhHHHhhhh----hc-cCchhHHH---HHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHH
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQKE----EL-KLPEMTQL---QKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLED 134 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~~----~~-~~p~L~~~---~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~ 134 (267)
..+...-+.|...++.||...-. ++ +.|.+..+ .-.-|----|+.+.+...++..+-|++-+|++ ...||.
T Consensus 284 ~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvEg 362 (421)
T COG5159 284 RAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVEG 362 (421)
T ss_pred HHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHHH
Confidence 44666777788888999986532 11 12222111 11111122366777888899999999999998 999999
Q ss_pred HHHHHHhcCccEEEecCCCCeEEEEeecCCC
Q psy10889 135 LIIEAIYSDIIHGKLDQRNSSLELDFAIGRD 165 (267)
Q Consensus 135 lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd 165 (267)
=+-..|-..++-|.+||.++|+.|.--...|
T Consensus 363 KLsqMILDKifyG~LDqg~gcLivy~ep~qd 393 (421)
T COG5159 363 KLSQMILDKIFYGTLDQGDGCLIVYGEPAQD 393 (421)
T ss_pred HHHHHHHHHHHHhhhccCCceEEEeCCcccc
Confidence 9999999999999999999999998654443
No 19
>KOG0687|consensus
Probab=90.58 E-value=2.7 Score=40.11 Aligned_cols=112 Identities=17% Similarity=0.235 Sum_probs=78.2
Q ss_pred hhcChhhhhhcCCCchhHHHHHHHHhcCCHhHHHhhh-----hhccC-chhHHH---HHHHHHhHHhhhcccCCcccCHH
Q psy10889 48 LIDMPLIKELDTSPHAGYYHLLKLFAHGTYQDYLKQK-----EELKL-PEMTQL---QKKKLQNLTIVTLSLESKCIPYD 118 (267)
Q Consensus 48 LL~~p~vq~L~~s~~~~~~~LL~lFa~Gt~~dy~~~~-----~~~~~-p~L~~~---~~~KLr~LtLlsLa~~~k~IsY~ 118 (267)
++.-|-|++.-.+ -+..-+++.-+-.-+|.+|-..- ..+.. --|.|. -.+-||+..-..+-+..|.++.+
T Consensus 243 Vi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~ 321 (393)
T KOG0687|consen 243 VIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLE 321 (393)
T ss_pred hcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444443332 22355555555555666654321 11111 123443 36778888888888899999999
Q ss_pred HHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEee
Q psy10889 119 KLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFA 161 (267)
Q Consensus 119 ~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~ 161 (267)
..|+..||+ ++-++.=+=+-|-+|-++++||-++++|++++-
T Consensus 322 ~MA~aFgVS-VefiDreL~rFI~~grL~ckIDrVnGVVEtNrp 363 (393)
T KOG0687|consen 322 SMAKAFGVS-VEFIDRELGRFIAAGRLHCKIDRVNGVVETNRP 363 (393)
T ss_pred HHHHHhCch-HHHHHhHHHHhhccCceeeeeecccceeecCCc
Confidence 999999998 988888888899999999999999999999854
No 20
>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=90.55 E-value=1.8 Score=35.49 Aligned_cols=110 Identities=14% Similarity=0.123 Sum_probs=70.4
Q ss_pred HHHHHHHHHhCCCeeechhhhcChhhhhhcC-CCchhHHHHHHHHhcCCHhHHHhhhhhc-cCchhH---HHHHHHHHhH
Q psy10889 29 AVELIKQVLEAPGIFMFKELIDMPLIKELDT-SPHAGYYHLLKLFAHGTYQDYLKQKEEL-KLPEMT---QLQKKKLQNL 103 (267)
Q Consensus 29 a~~lI~~aL~~p~vf~F~eLL~~p~vq~L~~-s~~~~~~~LL~lFa~Gt~~dy~~~~~~~-~~p~L~---~~~~~KLr~L 103 (267)
...++..+|..-.+-+|.-++..-.-...+. .+-..++.|.+.+-.|+|..|......- -.|.+. +.....+|.=
T Consensus 7 ~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~~ 86 (143)
T PF10075_consen 7 YALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRER 86 (143)
T ss_dssp HHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHHH
T ss_pred HHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHHH
Confidence 3444555555555677887776533333332 3456788899999999999998743310 012332 2346677776
Q ss_pred HhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 104 TIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
.+-.+...+..|+-+.+++-|+++ ..+++.++.+-
T Consensus 87 i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~~~ 121 (143)
T PF10075_consen 87 IAHLISKAYSSISLSDLAEMLGLS-EEELEKFIKSR 121 (143)
T ss_dssp HHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHHHH
T ss_pred HHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHHHc
Confidence 666677779999999999999999 99999998765
No 21
>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=89.76 E-value=0.5 Score=41.40 Aligned_cols=58 Identities=17% Similarity=0.240 Sum_probs=43.2
Q ss_pred HhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEE
Q psy10889 101 QNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELD 159 (267)
Q Consensus 101 r~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~ 159 (267)
-+-.++......++++.++|+.++++. ..++-+-|-+....|.|.|-||...+-|+|+
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 344577888889999999999999998 8899999999999999999999999999987
No 22
>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=88.54 E-value=0.46 Score=34.36 Aligned_cols=45 Identities=20% Similarity=0.193 Sum_probs=35.5
Q ss_pred HhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEe
Q psy10889 104 TIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKL 149 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkI 149 (267)
.|..+...++.+++++|+.+++++ ...||.+|=..+..|-|+-.-
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEEec
Confidence 345555678899999999999998 999999999999999998433
No 23
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=86.67 E-value=7.3 Score=32.04 Aligned_cols=79 Identities=15% Similarity=0.325 Sum_probs=58.1
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE-Eec-CCCCeEEEEeecCCCCCCCcHHH-HHHHHHHHHHHHHH
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG-KLD-QRNSSLELDFAIGRDINPGDVTN-MITEFQAWSDSCAN 187 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G-kID-Q~~~~v~V~~~~~Rd~~~~q~~~-L~~~L~~W~~~~~~ 187 (267)
.+..++-++|++.|+++ ...|..-|=..+..|||.= |.. ...+-.++-.+ ++++++.. |...|..|++++..
T Consensus 39 ~~~~~tvdelae~lnr~-rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~----i~~ee~k~~i~~~l~~w~~~~~~ 113 (126)
T COG3355 39 ENGPLTVDELAEILNRS-RSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKP----IDPEEIKKKILKDLDEWYDKMKQ 113 (126)
T ss_pred hcCCcCHHHHHHHHCcc-HHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEec----CCHHHHHHHHHHHHHHHHHHHHH
Confidence 57889999999999998 8899999999999999863 222 12223333222 34456654 67899999999998
Q ss_pred HHHHHHH
Q psy10889 188 VLKAIET 194 (267)
Q Consensus 188 vl~~ie~ 194 (267)
.+...+.
T Consensus 114 ~i~~~~~ 120 (126)
T COG3355 114 LIEEFEK 120 (126)
T ss_pred HHHHHhc
Confidence 8876654
No 24
>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=84.28 E-value=3.1 Score=30.96 Aligned_cols=58 Identities=17% Similarity=0.218 Sum_probs=40.9
Q ss_pred HHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEE
Q psy10889 100 LQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELD 159 (267)
Q Consensus 100 Lr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~ 159 (267)
++.|..+......+.++-.+|++.++++ ...|+.++=....+|+|+..= ..++-+...
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~~L~~~Gli~s~~-G~~GGy~L~ 68 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQKLKKAGLIESSR-GRGGGYRLA 68 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEET-STTSEEEES
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHHHHhhCCeeEecC-CCCCceeec
Confidence 4444444443445569999999999998 999999999999999987652 334444443
No 25
>KOG2072|consensus
Probab=83.41 E-value=15 Score=39.00 Aligned_cols=48 Identities=21% Similarity=0.370 Sum_probs=43.6
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEE
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELD 159 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~ 159 (267)
+..|+|+.|.+-.-+=|.-+||.+|++|...+.+..+||....+|.+.
T Consensus 445 Y~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 445 YESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEeccccceeeec
Confidence 678999998887766668999999999999999999999999999986
No 26
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=82.38 E-value=2.3 Score=32.75 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=32.7
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
..+..+||.+|++.++++ ...+-..+-.....|+|.+
T Consensus 13 ~~~~~~~~~~la~~l~~s-~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 13 QKDARISLAELAKKVGLS-PSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHhCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeec
Confidence 345679999999999998 9999999999999999983
No 27
>KOG3054|consensus
Probab=82.32 E-value=2.3 Score=38.88 Aligned_cols=54 Identities=20% Similarity=0.384 Sum_probs=46.4
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEE
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELD 159 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~ 159 (267)
++....++++++.++|+.+.++. ..+.=+-+=+.+..|+|.|-||...+-++|+
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lr-tqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLR-TQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCcc-HHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 66777889999999999999998 4555556667778999999999999999997
No 28
>KOG1076|consensus
Probab=81.32 E-value=9.7 Score=39.71 Aligned_cols=98 Identities=16% Similarity=0.263 Sum_probs=71.9
Q ss_pred HHHHHHHHhcCCHhHHHhhh----hhcc-CchhHH---HHHHHHHhHH----hhhcccCCcccCHHHHHHHhCCCChhhH
Q psy10889 65 YYHLLKLFAHGTYQDYLKQK----EELK-LPEMTQ---LQKKKLQNLT----IVTLSLESKCIPYDKLLKELDISNVRDL 132 (267)
Q Consensus 65 ~~~LL~lFa~Gt~~dy~~~~----~~~~-~p~L~~---~~~~KLr~Lt----LlsLa~~~k~IsY~~I~~~L~I~~~~ev 132 (267)
+..-=.++..|+|.+-..+. .-|. +|.-.. -...+++-=+ |++.++-+..+|.+.||+-.++| +..|
T Consensus 657 VvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp-~~~V 735 (843)
T KOG1076|consen 657 VVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLP-EPKV 735 (843)
T ss_pred HHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCC-chhH
Confidence 45566788899998766532 1122 243221 1244444433 55566668899999999999999 9999
Q ss_pred HHHHHHHHhcCccEEEecCCCCeEEEEeecC
Q psy10889 133 EDLIIEAIYSDIIHGKLDQRNSSLELDFAIG 163 (267)
Q Consensus 133 E~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~ 163 (267)
-.+|=+.|-..=|.+.+||..+||.++.+.+
T Consensus 736 hsIiSkmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 736 HSIISKMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred HHHHHHHHHHHHhhhccCCCcceEEEeeccc
Confidence 9999899999999999999999999997643
No 29
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=79.91 E-value=2.8 Score=34.86 Aligned_cols=43 Identities=21% Similarity=0.376 Sum_probs=36.6
Q ss_pred ccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE---EecCC
Q psy10889 109 SLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG---KLDQR 152 (267)
Q Consensus 109 a~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G---kIDQ~ 152 (267)
-..+..+||.+|++.|+++ ...|-.-+=.....|+|+| -+|..
T Consensus 18 Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~rL~~~GvI~~~~~~v~~~ 63 (153)
T PRK11179 18 LMENARTPYAELAKQFGVS-PGTIHVRVEKMKQAGIITGTRVDVNPK 63 (153)
T ss_pred HHHcCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeeeEEEEECHH
Confidence 3456889999999999998 9999999999999999984 45654
No 30
>PRK01919 tatB sec-independent translocase; Provisional
Probab=79.49 E-value=18 Score=31.18 Aligned_cols=59 Identities=5% Similarity=0.137 Sum_probs=39.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhh
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSL 224 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 224 (267)
.|+|+.+..+...+..|..++....+.+.+.+.+.-.. ++-.+.+++++....+++.++
T Consensus 19 V~GPekLP~~aRtlGk~i~k~Rr~~~d~K~ev~~E~e~-dElrk~~~~~e~~~~~v~~si 77 (169)
T PRK01919 19 VIGPERLPRVARTAGALFGRAQRYINDVKAEVSREIEL-DELRKMKTDFESAARDVENTI 77 (169)
T ss_pred eeCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999888888777644322 222223344444444444443
No 31
>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=76.88 E-value=4.9 Score=26.46 Aligned_cols=41 Identities=20% Similarity=0.215 Sum_probs=31.8
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
|+.+...+..++-.+|++.++++ ...|-..+=+....|+|+
T Consensus 8 Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 8 ILNYLRENPRITQKELAEKLGIS-RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCcCcC
Confidence 34444446679999999999998 899999998999999885
No 32
>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=76.69 E-value=2.8 Score=32.44 Aligned_cols=33 Identities=15% Similarity=0.470 Sum_probs=27.2
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCc
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDI 144 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gL 144 (267)
+..-.+||++|-+. ++|.+.||+|||+.+..+.
T Consensus 44 tr~~vi~Fd~iVr~--mpNes~v~qWV~dtln~i~ 76 (100)
T PF07389_consen 44 TRCAVIPFDDIVRT--MPNESRVKQWVIDTLNDIM 76 (100)
T ss_pred HhhccccHHHHHHh--CCCHHHHHHHHHHHHHhHh
Confidence 44457999999998 7789999999999876554
No 33
>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=74.73 E-value=8.2 Score=31.37 Aligned_cols=44 Identities=16% Similarity=0.258 Sum_probs=36.6
Q ss_pred HHhhhcc--cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 103 LTIVTLS--LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 103 LtLlsLa--~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
.+++.|| ..++.++-++|++.++|| ...|+.++-..-.+|||..
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGIS-LSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCceEE
Confidence 3444455 345679999999999999 9999999999999999985
No 34
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=73.75 E-value=4.5 Score=32.99 Aligned_cols=38 Identities=18% Similarity=0.158 Sum_probs=33.2
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
..+..+||.+|++.++++ ...|=.-|=+....|+|.|.
T Consensus 18 ~~d~r~~~~eia~~lglS-~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 18 QEDARISNAELAERVGLS-PSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHhCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCceeeE
Confidence 344459999999999998 99999999999999999875
No 35
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=73.07 E-value=14 Score=33.12 Aligned_cols=60 Identities=10% Similarity=0.129 Sum_probs=49.5
Q ss_pred HHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEE
Q psy10889 99 KLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELD 159 (267)
Q Consensus 99 KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~ 159 (267)
=|+.|.++....+...+|..+|++.|+++ ...+=..|-+.-..|+|.-..+...+.+.++
T Consensus 6 ~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LT 65 (217)
T PRK14165 6 ALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILKQLEDEGYITRTIVPRGQLITIT 65 (217)
T ss_pred HHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEEcCCceEEEEC
Confidence 35566666655667789999999999998 8899999999999999999999877666665
No 36
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=71.83 E-value=7.7 Score=32.65 Aligned_cols=42 Identities=17% Similarity=0.112 Sum_probs=35.8
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
|+.+-..+..+||.+|++.++++ ...|-.-|=+....|+|+|
T Consensus 19 IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 19 ILNELQKDGRISNVELSKRVGLS-PTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEE
Confidence 33444578899999999999998 8899999999999999975
No 37
>PF13730 HTH_36: Helix-turn-helix domain
Probab=71.20 E-value=15 Score=24.70 Aligned_cols=47 Identities=26% Similarity=0.368 Sum_probs=37.2
Q ss_pred HHHHhHHhhhcccC-Cccc-CHHHHHHHhCCCChhhHHHHHHHHHhcCcc
Q psy10889 98 KKLQNLTIVTLSLE-SKCI-PYDKLLKELDISNVRDLEDLIIEAIYSDII 145 (267)
Q Consensus 98 ~KLr~LtLlsLa~~-~k~I-sY~~I~~~L~I~~~~evE~lvI~aI~~gLI 145 (267)
.|+-.+.|.+.+.+ +.+. |++.|++.++++ .+.|-..+=+....|+|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s-~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVS-RRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCcCC
Confidence 46667778888743 2344 799999999998 99999999888888875
No 38
>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=68.77 E-value=15 Score=29.18 Aligned_cols=49 Identities=14% Similarity=0.182 Sum_probs=38.8
Q ss_pred HHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 99 KLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 99 KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
=++.|..+....+...++-.+|++.++++ ...|..++-.....|+|...
T Consensus 10 al~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 10 ALRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEec
Confidence 34555555443335589999999999999 99999999999999999753
No 39
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=68.19 E-value=37 Score=28.20 Aligned_cols=23 Identities=9% Similarity=0.058 Sum_probs=14.9
Q ss_pred HHHHhHhHHHHHHHHHHHhhccc
Q psy10889 205 QHLAHSNAIDMEILNIKKSLKNQ 227 (267)
Q Consensus 205 ~~~~~~~~~~~~~~~~k~~~~~~ 227 (267)
+..++.++.++.++.+++.+...
T Consensus 46 ~~~~~~~er~~kl~~~r~~m~~~ 68 (135)
T PRK10947 46 AAAAEVEERTRKLQQYREMLIAD 68 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Confidence 34445555667788888887654
No 40
>PRK04654 sec-independent translocase; Provisional
Probab=68.17 E-value=30 Score=30.92 Aligned_cols=35 Identities=6% Similarity=0.191 Sum_probs=29.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGKA 199 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a 199 (267)
.|+++.|..+...+..|..++++....+.+.+.+-
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~E 53 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELERE 53 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 57899999999999999999988888777766543
No 41
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=67.79 E-value=11 Score=27.76 Aligned_cols=46 Identities=13% Similarity=0.144 Sum_probs=36.9
Q ss_pred HhHHhhhcccCC-cccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 101 QNLTIVTLSLES-KCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 101 r~LtLlsLa~~~-k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
|.+.|+.+.... ..++..+|++.++++ ...|-..+-.....|+|.-
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHHHHHHCCCeee
Confidence 344455544443 689999999999998 8999999999999999975
No 42
>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=67.24 E-value=4.7 Score=28.23 Aligned_cols=38 Identities=32% Similarity=0.449 Sum_probs=25.8
Q ss_pred HHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHH
Q psy10889 96 QKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLII 137 (267)
Q Consensus 96 ~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI 137 (267)
..+++++|.++. ..+.++|++|++.++++ .+.+-.-|-
T Consensus 4 i~rq~~Ll~~L~---~~~~~~~~ela~~l~~S-~rti~~~i~ 41 (59)
T PF08280_consen 4 IKRQLKLLELLL---KNKWITLKELAKKLNIS-ERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHH---HHTSBBHHHHHHHCTS--HHHHHHHHH
T ss_pred HHHHHHHHHHHH---cCCCCcHHHHHHHHCCC-HHHHHHHHH
Confidence 345555555543 37899999999999998 666555544
No 43
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=66.61 E-value=26 Score=27.98 Aligned_cols=37 Identities=8% Similarity=0.220 Sum_probs=33.5
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
.+..++..+|++.++++ ...|...+=....+|+|.+.
T Consensus 22 ~~~~~s~~eia~~l~is-~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLN-APTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred CCCCccHHHHHHHHCcC-HHHHHHHHHHHHHCCcEEec
Confidence 35679999999999998 99999999999999999874
No 44
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=65.63 E-value=15 Score=31.19 Aligned_cols=38 Identities=18% Similarity=0.238 Sum_probs=34.3
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
.....++-++|++.++|| ..-|+.++-..-.+|||...
T Consensus 21 ~~~~~vs~~eIA~~~~ip-~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 21 SEAGPVPLADISERQGIS-LSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEeC
Confidence 445689999999999999 99999999999999999973
No 45
>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=65.15 E-value=15 Score=24.69 Aligned_cols=45 Identities=9% Similarity=0.182 Sum_probs=34.2
Q ss_pred HhHHhhhcc-cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 101 QNLTIVTLS-LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 101 r~LtLlsLa-~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
|-+.|+... .....++..+|+++++++ ...+-.++-.....|+|.
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~-~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLP-KSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCcCee
Confidence 345555544 345568999999999998 889999998888888875
No 46
>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=64.76 E-value=76 Score=27.58 Aligned_cols=96 Identities=19% Similarity=0.279 Sum_probs=56.7
Q ss_pred HHHhCCCChhhHHHHHHHHHhcCccEE-EecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH---HH
Q psy10889 121 LKELDISNVRDLEDLIIEAIYSDIIHG-KLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCANVLKAIET---QI 196 (267)
Q Consensus 121 ~~~L~I~~~~evE~lvI~aI~~gLI~G-kIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~---~i 196 (267)
.+++||. ...|.++|-..+..|+|+. || ++-.+-|+-|- +....+...+......+..+...+.+ .+
T Consensus 22 pK~~gI~-~~~VKdvlq~LvDDglV~~EKi----Gssn~YWsFps----~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~i 92 (188)
T PF03962_consen 22 PKEKGIV-SMSVKDVLQSLVDDGLVHVEKI----GSSNYYWSFPS----QAKQKRQNKLEKLQKEIEELEKKIEELEEKI 92 (188)
T ss_pred ccccCCc-hhhHHHHHHHHhccccchhhhc----cCeeEEEecCh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3447897 8999999999999998873 44 67777888554 34444555555555544444443333 22
Q ss_pred HHHHH------HHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 197 GKANS------EKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 197 ~~a~~------~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
..+.. ++...+..-++++.+++.+++.+.
T Consensus 93 ~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~ 127 (188)
T PF03962_consen 93 EEAKKGREESEEREELLEELEELKKELKELKKELE 127 (188)
T ss_pred HHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22221 122233445566666666666665
No 47
>PRK04098 sec-independent translocase; Provisional
Probab=63.86 E-value=48 Score=28.34 Aligned_cols=58 Identities=10% Similarity=0.247 Sum_probs=42.2
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHhHhHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGKAN---SEKHQHLAHSNAIDMEILNIKK 222 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~---~~~~~~~~~~~~~~~~~~~~k~ 222 (267)
.|+|+.+..+...+..|...+......+.+.+...- ..++...+-++.++...+++++
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 578999999999999999998888777766554332 2233334456777777777776
No 48
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=63.27 E-value=64 Score=25.95 Aligned_cols=56 Identities=9% Similarity=-0.075 Sum_probs=43.5
Q ss_pred hhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeec
Q psy10889 106 VTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAI 162 (267)
Q Consensus 106 lsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~ 162 (267)
..+...+..++-.+|++.++++ ...|=..|-.....|+|.=.-|+..+....-+.+
T Consensus 38 ~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 38 HNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred HHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEC
Confidence 3333333456789999999998 8888899999999999999999887766655443
No 49
>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=62.03 E-value=30 Score=26.06 Aligned_cols=34 Identities=6% Similarity=0.193 Sum_probs=29.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGK 198 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~ 198 (267)
.|+|+.+..+...+..|........+.+.+++..
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~ 51 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDE 51 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHH
Confidence 4789999999999999999999988888877643
No 50
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=61.87 E-value=51 Score=31.95 Aligned_cols=60 Identities=13% Similarity=0.325 Sum_probs=47.1
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHH
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEF 178 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L 178 (267)
.++.++-++|++.++++ .+.+++++=+...+|+|. +-++. .|+..||.+.=.+..+.+.+
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~~L~~agLI~-~~~~g------~~~l~rd~~~itL~dv~~~~ 366 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLCELARIGLLR-RGERG------QWVLARDLDSVPLAELYELF 366 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHHHHHhCCCeE-ecCCC------ceEecCCHHhCcHHHHHHhC
Confidence 46788999999999998 999999999999999997 33322 38888987766666665544
No 51
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=60.47 E-value=21 Score=25.14 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=35.5
Q ss_pred hHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 102 NLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 102 ~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
+.+|..|...+..++-.+|++.|+++ ...|=+.+=+.-..|+|.
T Consensus 10 L~~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 10 LKAIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHHHHHHCCCEE
Confidence 34555666688899999999999998 888888888888888875
No 52
>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=60.04 E-value=21 Score=27.36 Aligned_cols=51 Identities=12% Similarity=0.145 Sum_probs=39.1
Q ss_pred HHhHHhhhc-ccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecC
Q psy10889 100 LQNLTIVTL-SLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQ 151 (267)
Q Consensus 100 Lr~LtLlsL-a~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ 151 (267)
-+.|.++.- +....=++.++|++.|+++ ..+|+..|=..+..|.|=-.||.
T Consensus 50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 50 DKVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHHHHHHTTSEEESSST
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHHHHHhCCeEecccCC
Confidence 344555554 4445569999999999998 99999999999999999888875
No 53
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.79 E-value=17 Score=26.18 Aligned_cols=33 Identities=9% Similarity=0.106 Sum_probs=30.5
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
.++-.+|+++|+|+ ...|...+......|+|.-
T Consensus 22 ~~ta~eLa~~lgl~-~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLP-KKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEe
Confidence 49999999999999 7899999999999999865
No 54
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=58.20 E-value=74 Score=30.34 Aligned_cols=64 Identities=13% Similarity=0.171 Sum_probs=54.8
Q ss_pred HHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEee
Q psy10889 97 KKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFA 161 (267)
Q Consensus 97 ~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~ 161 (267)
.+-||.=.-..|-+..|.++.+..|+..+++ ++-|+.=+=+-|-.|-+.+.||-++++|++++-
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLGEFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHHhhCCCCceeeeeecccceEeccCc
Confidence 5566666667777788999999999999998 888888888888899999999999999999854
No 55
>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=58.08 E-value=27 Score=23.40 Aligned_cols=41 Identities=24% Similarity=0.166 Sum_probs=26.5
Q ss_pred hHHhhhcc-cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcC
Q psy10889 102 NLTIVTLS-LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSD 143 (267)
Q Consensus 102 ~LtLlsLa-~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~g 143 (267)
+..|+.+- .....++-++||+.|+|+ .+.|..-|=..-..|
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHHHHHHCC
Confidence 34444443 444559999999999998 777766665543333
No 56
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=57.47 E-value=74 Score=26.36 Aligned_cols=22 Identities=9% Similarity=-0.028 Sum_probs=14.5
Q ss_pred HHHhHhHHHHHHHHHHHhhccc
Q psy10889 206 HLAHSNAIDMEILNIKKSLKNQ 227 (267)
Q Consensus 206 ~~~~~~~~~~~~~~~k~~~~~~ 227 (267)
..+++++.++.++.+++.+...
T Consensus 47 ~~~~~~er~~~l~~i~~~~~~~ 68 (134)
T PRK10328 47 QQRELAERQEKINTWLELMKAD 68 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3445566677788888877654
No 57
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=57.37 E-value=28 Score=29.07 Aligned_cols=48 Identities=13% Similarity=0.126 Sum_probs=37.3
Q ss_pred HhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEe
Q psy10889 101 QNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKL 149 (267)
Q Consensus 101 r~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkI 149 (267)
+.|..+..-..++.++-++|++..+|+ ..-|+.++-..-.+|||+..=
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~~L~kaGlV~S~r 59 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILSKLRKAGLVKSVR 59 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHHHHHHcCCEEeec
Confidence 333333333344478899999999998 999999999999999998654
No 58
>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=56.99 E-value=35 Score=23.08 Aligned_cols=36 Identities=8% Similarity=0.192 Sum_probs=32.4
Q ss_pred cCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecC
Q psy10889 115 IPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQ 151 (267)
Q Consensus 115 IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ 151 (267)
+++.+|++.++++ ...+-..+-.....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHHHHHHCCCeEEEEec
Confidence 9999999999998 89999998888899999987665
No 59
>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=56.76 E-value=15 Score=24.64 Aligned_cols=27 Identities=19% Similarity=0.257 Sum_probs=20.5
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
.-.||.+|++.++++ ...|..++-.|.
T Consensus 25 ~g~s~~eIa~~l~~s-~~~v~~~l~ra~ 51 (54)
T PF08281_consen 25 QGMSYAEIAEILGIS-ESTVKRRLRRAR 51 (54)
T ss_dssp S---HHHHHHHCTS--HHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcC-HHHHHHHHHHHH
Confidence 468999999999998 999999988774
No 60
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=56.72 E-value=1.2e+02 Score=27.14 Aligned_cols=109 Identities=14% Similarity=0.202 Sum_probs=63.1
Q ss_pred HHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCC-------------eEEEE------eecCCCCCCCcHHHHHHHH
Q psy10889 118 DKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNS-------------SLELD------FAIGRDINPGDVTNMITEF 178 (267)
Q Consensus 118 ~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~-------------~v~V~------~~~~Rd~~~~q~~~L~~~L 178 (267)
.+|++.++|+.-.-+++|=| .-.+|||+.+++-..+ +++|+ |+...+....+++...-.+
T Consensus 32 sEiS~~lgvsqkAVl~HL~~-LE~AGlveS~ie~~~Rg~~rKYY~Is~~~rleV~lsp~~f~~~~~~~~~~~l~~~r~~~ 110 (217)
T COG1777 32 SEISRELGVSQKAVLKHLRI-LERAGLVESRIEKIPRGRPRKYYMISRNLRLEVTLSPNFFGAERFDLEEDDLESERSEV 110 (217)
T ss_pred HHHHhhcCcCHHHHHHHHHH-HHHcCCchhhccccccCCCcceeeccCCeEEEEEecCcccceeccCccccchhhhhcch
Confidence 47888899983333455443 4458999998888777 44444 3334444444444332222
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhcccc
Q psy10889 179 QAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLKNQT 228 (267)
Q Consensus 179 ~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~~~~ 228 (267)
..-.. ...-+..+......+|.+-++-.+.+.+++....++.+.+|...
T Consensus 111 ~~~~~-s~~~~~~l~srl~~~~~~~e~l~~~~~~L~~~~~el~~rik~~i 159 (217)
T COG1777 111 SKLFK-SPEGISELISRLLEINREIEELSRAQTELQKQLNELMDRIKEEI 159 (217)
T ss_pred hhhcc-cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 11111 12223444445555666666666677777778888888887765
No 61
>PRK01770 sec-independent translocase; Provisional
Probab=56.39 E-value=62 Score=28.00 Aligned_cols=34 Identities=6% Similarity=0.321 Sum_probs=30.2
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGK 198 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~ 198 (267)
.|+|+.+..+..++..|..++..+...+.+.+.+
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~ 52 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQ 52 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999999888876654
No 62
>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=56.07 E-value=8 Score=25.43 Aligned_cols=27 Identities=26% Similarity=0.325 Sum_probs=17.5
Q ss_pred hhcccCCcccCHHHHHHHhCCCChhhHH
Q psy10889 106 VTLSLESKCIPYDKLLKELDISNVRDLE 133 (267)
Q Consensus 106 lsLa~~~k~IsY~~I~~~L~I~~~~evE 133 (267)
+.+-..+...||.+|++.++++ ...|-
T Consensus 9 l~~Lq~d~r~s~~~la~~lglS-~~~v~ 35 (42)
T PF13404_consen 9 LRLLQEDGRRSYAELAEELGLS-ESTVR 35 (42)
T ss_dssp HHHHHH-TTS-HHHHHHHHTS--HHHHH
T ss_pred HHHHHHcCCccHHHHHHHHCcC-HHHHH
Confidence 3333455789999999999998 55543
No 63
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=54.57 E-value=18 Score=28.21 Aligned_cols=39 Identities=13% Similarity=0.070 Sum_probs=31.8
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCC
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRN 153 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~ 153 (267)
+....++.+++++.++++ +.||.+.+..|+|.-.-....
T Consensus 3 ~~~~~lt~~Elc~~~gi~-----~~~l~eLve~GlIep~~~~~~ 41 (101)
T PRK10265 3 NVTVTFTITEFCLHTGVS-----EEELNEIVGLGVIEPREIQET 41 (101)
T ss_pred ceEEEeeHHHHHHHHCcC-----HHHHHHHHHCCCeecCCCCcc
Confidence 345578999999999999 889999999999996555433
No 64
>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=54.49 E-value=23 Score=25.45 Aligned_cols=37 Identities=5% Similarity=0.016 Sum_probs=29.9
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
..+..-++.+|++.+++.|...|-..|-..-..|+|+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 3466789999999999998999999999888888875
No 65
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=54.16 E-value=15 Score=27.31 Aligned_cols=51 Identities=14% Similarity=0.199 Sum_probs=37.3
Q ss_pred HHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCC
Q psy10889 103 LTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNS 154 (267)
Q Consensus 103 LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~ 154 (267)
|.|+++-.....++|.+|.+.|+++ ...+-.-+=....+|+|+-+-.-..+
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt-~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLT-DGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcC-HHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 3444444446789999999999998 88888888888889999987655444
No 66
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=53.05 E-value=86 Score=22.75 Aligned_cols=41 Identities=12% Similarity=0.127 Sum_probs=35.1
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCC
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRN 153 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~ 153 (267)
...++..+|++.++++ ...+-..|-+....|+|.-.-++..
T Consensus 22 ~~~~~~~~la~~~~~s-~~~i~~~l~~L~~~g~v~~~~~~~~ 62 (101)
T smart00347 22 EGPLSVSELAKRLGVS-PSTVTRVLDRLEKKGLIRRLPSPED 62 (101)
T ss_pred cCCcCHHHHHHHHCCC-chhHHHHHHHHHHCCCeEecCCCCC
Confidence 3469999999999998 8899999999999999987766543
No 67
>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=52.79 E-value=28 Score=24.12 Aligned_cols=38 Identities=16% Similarity=0.125 Sum_probs=31.1
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
......+..+|++.|+++ ...+-.=|=.....|||+..
T Consensus 20 ~~~~~~t~~ela~~l~~~-~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGIS-QSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHCSTBEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEE
T ss_pred hcCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCeEEe
Confidence 556889999999999998 78888877788888998754
No 68
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=52.36 E-value=36 Score=28.43 Aligned_cols=38 Identities=8% Similarity=0.054 Sum_probs=33.5
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEec
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLD 150 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkID 150 (267)
.+.++-.+|++..+|+ ..-|+.++-....+|||+..=-
T Consensus 22 ~~~~s~~eIA~~~~is-~~~L~kIl~~L~~aGlv~S~rG 59 (153)
T PRK11920 22 GKLSRIPEIARAYGVS-ELFLFKILQPLVEAGLVETVRG 59 (153)
T ss_pred CCcCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEeecC
Confidence 4568999999999998 9999999999999999987653
No 69
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=52.00 E-value=40 Score=24.70 Aligned_cols=49 Identities=10% Similarity=0.186 Sum_probs=34.4
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEE
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELD 159 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~ 159 (267)
|+..++ ....++.+|+..++++ ...+...+=..+..|+|++ ..+.+.+|
T Consensus 11 IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 11 ILKILS-KGGAKKTEIMYKANLN-YSTLKKYLKELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHH--TT-B-HHHHHTTST---HHHHHHHHHHHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHHHHHHCcCeeC----CCCEEEEC
Confidence 344444 6778899999999998 9999999999999999944 45566555
No 70
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=51.83 E-value=43 Score=21.43 Aligned_cols=36 Identities=8% Similarity=0.058 Sum_probs=30.1
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
+..++-.+|++.++++ ...+...+-.....|+|.-.
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEe
Confidence 4568999999999997 89999888888888887643
No 71
>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=51.81 E-value=25 Score=24.33 Aligned_cols=42 Identities=17% Similarity=0.164 Sum_probs=31.0
Q ss_pred HHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCcc
Q psy10889 103 LTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDII 145 (267)
Q Consensus 103 LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI 145 (267)
-.|+.+......++..+|++.++|+ ...+-.=+...-..|+|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLNKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHHHHHHCCCE
Confidence 3456666678899999999999998 66666666655556653
No 72
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=51.51 E-value=29 Score=27.97 Aligned_cols=46 Identities=15% Similarity=0.048 Sum_probs=35.4
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEE
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLEL 158 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V 158 (267)
....+..+|++.++++ ...|-.=+=..-.+|||..+-+.......+
T Consensus 28 ~~~~~v~ela~~l~ls-qstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 28 SGELCVCDLCTALDQS-QPKISRHLALLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred cCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCceEEEEEcCEEEEEE
Confidence 3468888999999998 677777666677799999988866544444
No 73
>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=51.30 E-value=39 Score=22.17 Aligned_cols=33 Identities=12% Similarity=0.183 Sum_probs=26.9
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
+..+..+|++.++++ ...|-.-+=.....|+|+
T Consensus 14 ~~~~~~el~~~l~~s-~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLS-QSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhcccc-chHHHHHHHHHHHCcCee
Confidence 678899999999998 788877777777788874
No 74
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=50.27 E-value=43 Score=27.27 Aligned_cols=40 Identities=8% Similarity=0.090 Sum_probs=34.2
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEec
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLD 150 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkID 150 (267)
..+..++-++|++.++|+ ..-|+..+-..-..|||..+=-
T Consensus 21 ~~g~~~s~~~ia~~~~is-~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 21 PEGRMTSISEVTEVYGVS-RNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCCCccCHHHHHHHHCcC-HHHHHHHHHHHHhCCEEEEecC
Confidence 345678999999999998 8999999999999999986643
No 75
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=50.24 E-value=49 Score=26.41 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 183 DSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 183 ~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
+.+...+..+++.+..++.+.++-...-++..+++..+|+-+|
T Consensus 76 ~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~k 118 (118)
T PF13815_consen 76 EYLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKESK 118 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3445555666667777777666555555666677777766543
No 76
>PRK09954 putative kinase; Provisional
Probab=49.82 E-value=20 Score=33.55 Aligned_cols=53 Identities=17% Similarity=0.258 Sum_probs=42.1
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE---EecCCCCeEEE
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG---KLDQRNSSLEL 158 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G---kIDQ~~~~v~V 158 (267)
|+.+..++..+|+.+|++.|+|+ ...|-..|-+....|+|.| .||....++.|
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEE
Confidence 44444567789999999999998 9999999999999999975 46666655544
No 77
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=49.23 E-value=58 Score=21.32 Aligned_cols=38 Identities=8% Similarity=0.078 Sum_probs=31.6
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEec
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLD 150 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkID 150 (267)
...+++.+|++.++++ ...+-..|=.....|+|.-.=+
T Consensus 8 ~~~~~~~~i~~~l~is-~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLS-QSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCC-HHHHHHHHHHHHHCCCeeeeec
Confidence 5678999999999998 8888888888888999984433
No 78
>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=48.99 E-value=14 Score=27.57 Aligned_cols=38 Identities=8% Similarity=0.219 Sum_probs=25.7
Q ss_pred hhhcccCCcccCHHHHHHHhC---CCChhhHHHHHHHHHhcC
Q psy10889 105 IVTLSLESKCIPYDKLLKELD---ISNVRDLEDLIIEAIYSD 143 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~---I~~~~evE~lvI~aI~~g 143 (267)
|+..+...+.|+|++|...|. ++ .+.++.++-..-..|
T Consensus 12 Li~~gK~~G~lT~~eI~~~L~~~~~~-~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 12 LIEKGKKKGYLTYDEINDALPEDDLD-PEQIDEIYDTLEDEG 52 (82)
T ss_dssp HHHHHHHHSS-BHHHHHHH-S-S----HHHHHHHHHHHHTT-
T ss_pred HHHHHhhcCcCCHHHHHHHcCccCCC-HHHHHHHHHHHHHCC
Confidence 666777778899999999997 33 677887777665555
No 79
>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=48.60 E-value=1.6e+02 Score=24.64 Aligned_cols=84 Identities=8% Similarity=0.094 Sum_probs=57.5
Q ss_pred cCCcccCHHHHHHHhC--CCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHH
Q psy10889 110 LESKCIPYDKLLKELD--ISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCAN 187 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~--I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~ 187 (267)
..+|..+..+|...|+ |+ =..|...+=.+...|.|.+|.-....+..+.=...-+++++++..|-..+....+.+..
T Consensus 12 ~qNRPys~~di~~nL~~~~~-K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~~el~~ 90 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVG-KTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAELDAEIKELREELAE 90 (169)
T ss_pred HcCCCCcHHHHHHHHHhhcc-HHHHHHHHHHHHhCCCeeeeeecceEEEeeCccccCCCCchhHHHHHHHHHHHHHHHHH
Confidence 4688899999999995 55 46777777778889999999765543333322223344577888887777777777666
Q ss_pred HHHHHHH
Q psy10889 188 VLKAIET 194 (267)
Q Consensus 188 vl~~ie~ 194 (267)
+-..+..
T Consensus 91 l~~~~k~ 97 (169)
T PF07106_consen 91 LKKEVKS 97 (169)
T ss_pred HHHHHHH
Confidence 5554433
No 80
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.06 E-value=23 Score=23.14 Aligned_cols=37 Identities=24% Similarity=0.202 Sum_probs=27.2
Q ss_pred HhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcC
Q psy10889 104 TIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSD 143 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~g 143 (267)
.++.+...+ . |+.++++.++|+ ...|..|+-.--..|
T Consensus 4 ~iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 4 QIVELYLEG-E-SVREIAREFGIS-RSTVYRWIKRYREGG 40 (52)
T ss_pred HHHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHHHHHhcC
Confidence 344444443 3 999999999996 899999987654445
No 81
>PHA03158 hypothetical protein; Provisional
Probab=47.95 E-value=23 Score=31.48 Aligned_cols=52 Identities=25% Similarity=0.266 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 174 MITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 174 L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
+...=--||-....=-..|-+|+-.|....-+.-+|..++|++++++.|++.
T Consensus 220 l~Rs~pPWCv~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~eleks~a 271 (273)
T PHA03158 220 IKRSGPPWCIKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEKSLA 271 (273)
T ss_pred HhccCCCcEeecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhhc
Confidence 3333334887766666666677767777777788899999999999999873
No 82
>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=47.61 E-value=77 Score=21.99 Aligned_cols=30 Identities=23% Similarity=0.249 Sum_probs=23.0
Q ss_pred cCCcccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 110 LESKCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 110 ~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
..-|.++..+|+++|+|+ ...+-.-|=.|.
T Consensus 19 d~PR~~tl~elA~~lgis-~st~~~~LRrae 48 (53)
T PF04967_consen 19 DVPRRITLEELAEELGIS-KSTVSEHLRRAE 48 (53)
T ss_pred CCCCcCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 345899999999999998 666666655553
No 83
>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=47.07 E-value=1.6e+02 Score=27.71 Aligned_cols=66 Identities=9% Similarity=0.167 Sum_probs=47.6
Q ss_pred eecCCCCCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 160 FAIGRDINPGD-VTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 160 ~~~~Rd~~~~q-~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
-.++.|++.++ +..+.+.|+....-++.+...|.+++..-...-+.=..|=...+++|+.++-+-|
T Consensus 8 plI~~dLr~eEti~qi~~aL~~L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs~k 74 (297)
T PF11945_consen 8 PLIPPDLRREETILQIADALEYLDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGSKK 74 (297)
T ss_pred cccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCc
Confidence 34688888765 7889999999999999999999998876665555444444555666666654433
No 84
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=47.06 E-value=80 Score=20.69 Aligned_cols=35 Identities=9% Similarity=0.161 Sum_probs=30.1
Q ss_pred CCccc-CHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 111 ESKCI-PYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 111 ~~k~I-sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
.+..+ +..+|++.++++ ...|...+-.....|+|.
T Consensus 16 ~~~~l~s~~~la~~~~vs-~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 16 PGDKLPSERELAAQLGVS-RTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CCCcCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 34567 799999999997 899999999998899886
No 85
>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=46.88 E-value=41 Score=28.58 Aligned_cols=61 Identities=15% Similarity=0.218 Sum_probs=45.9
Q ss_pred hhHHHHHHHHhcCCHhHHHhhh--hhccCchhHHH----HHHHHHhHHhhhcccCCcc-cCHHHHHHHhC
Q psy10889 63 AGYYHLLKLFAHGTYQDYLKQK--EELKLPEMTQL----QKKKLQNLTIVTLSLESKC-IPYDKLLKELD 125 (267)
Q Consensus 63 ~~~~~LL~lFa~Gt~~dy~~~~--~~~~~p~L~~~----~~~KLr~LtLlsLa~~~k~-IsY~~I~~~L~ 125 (267)
.-.+++...+..|+|..|-... . ..|.+... ...++|..++-.++...+. +|-+.+++-|+
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 QFALELCRALMEGNYVRFFRLYRSK--SAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHH--TTHHHHHHHHT-T--TS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCHHHHHHHHhcc--CCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 4567888999999999998866 4 56666543 3779999999999988777 99999988775
No 86
>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=46.44 E-value=1.1e+02 Score=22.77 Aligned_cols=72 Identities=13% Similarity=0.323 Sum_probs=51.5
Q ss_pred HhhhcccCCcccCHHHHHHHh-CCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEee---cCCCCCCCcHHHHHHHHH
Q psy10889 104 TIVTLSLESKCIPYDKLLKEL-DISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFA---IGRDINPGDVTNMITEFQ 179 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L-~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~---~~Rd~~~~q~~~L~~~L~ 179 (267)
-|..|.. +...|.+|.+.+ +|+ ...+-+-+=+....|||.=...... -..|.|. .|+ ++..+...|.
T Consensus 10 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 10 ILRALFQ--GPMRFSELQRRLPGIS-PKVLSQRLKELEEAGLVERRVYPEV-PPRVEYSLTEKGK-----ELLPVLEALE 80 (90)
T ss_dssp HHHHHTT--SSEEHHHHHHHSTTS--HHHHHHHHHHHHHTTSEEEEEESSS-SSEEEEEE-HHHH-----HHHHHHHHHH
T ss_pred HHHHHHh--CCCcHHHHHHhcchhH-HHHHHHHHHHHHHcchhhcccccCC-CCCCccCCCcCHH-----HHHHHHHHHH
Confidence 3444444 688999999999 787 8888888888999999988776433 3455554 222 5666788888
Q ss_pred HHHHH
Q psy10889 180 AWSDS 184 (267)
Q Consensus 180 ~W~~~ 184 (267)
.|...
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88765
No 87
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=45.65 E-value=1.3e+02 Score=24.08 Aligned_cols=34 Identities=6% Similarity=0.126 Sum_probs=29.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGK 198 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~ 198 (267)
.|+|+.+..+...+..|..........+.+.+..
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~ 52 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQE 52 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999998888877743
No 88
>PRK10870 transcriptional repressor MprA; Provisional
Probab=45.04 E-value=1.8e+02 Score=24.68 Aligned_cols=50 Identities=14% Similarity=-0.022 Sum_probs=42.2
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEee
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFA 161 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~ 161 (267)
.+..++-.+|++.++++ ...+=.+|=.....|+|.=.-|...+....-..
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~L 117 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIADELEKRGWIERRESDNDRRCLHLQL 117 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEE
Confidence 35779999999999998 788888888999999999999988876655444
No 89
>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=44.35 E-value=74 Score=21.43 Aligned_cols=39 Identities=13% Similarity=0.197 Sum_probs=33.1
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCC
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRN 153 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~ 153 (267)
.++..+|++.++++ ...|-..|=.....|+|.-.-|...
T Consensus 21 ~~t~~~la~~l~~~-~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 21 ELTQSELAERLGIS-KSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp GEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred CcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 58999999999998 8999999999999999988776654
No 90
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=44.23 E-value=39 Score=25.31 Aligned_cols=32 Identities=13% Similarity=0.286 Sum_probs=28.9
Q ss_pred cCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecC
Q psy10889 115 IPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQ 151 (267)
Q Consensus 115 IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ 151 (267)
||+.++++.++++ +.||.+.+..|+|.-.-.+
T Consensus 1 is~~e~~~~~~i~-----~~~l~~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-----PEFLRELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-----HHHHHHHHHCCCeeecCCC
Confidence 6899999999999 8899999999999987766
No 91
>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=41.94 E-value=45 Score=26.92 Aligned_cols=41 Identities=10% Similarity=0.182 Sum_probs=34.0
Q ss_pred HhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 104 TIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
.|+.||.. .+|-+||+..|+++ ..-+--|+=+.+..|+|.-
T Consensus 47 ~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 47 AILELCRR--PLSVAEIAARLGLP-LGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred HHHHHHCC--CccHHHHHHhhCCC-chhhhhhHHHHHhCCCEEE
Confidence 57788877 89999999999999 7777777778888887654
No 92
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=41.93 E-value=79 Score=22.67 Aligned_cols=61 Identities=13% Similarity=0.164 Sum_probs=46.5
Q ss_pred CHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHH
Q psy10889 116 PYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQA 180 (267)
Q Consensus 116 sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~ 180 (267)
.|..+.+.+++++ +....++=+| .+-+-.++..+++.+++...++.++.+.+..+.+.|..
T Consensus 2 ~F~~ll~ql~~~~-~~~~~~f~~~---~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPD-ELDNPLFEDA---EIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCc-hhhhhhhccc---EEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 3678899999983 2223333332 46668999999999999999999999999888887764
No 93
>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=41.66 E-value=1.6e+02 Score=22.72 Aligned_cols=47 Identities=9% Similarity=0.106 Sum_probs=38.6
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEE
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLEL 158 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V 158 (267)
.+..++..+|++.++++ ...+=..|-.....|+|...-|...+....
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~ 85 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILARLERDGLVTRLKASNDQRRVY 85 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHHHHHHCCCEEeccCCCCCCeeE
Confidence 34578999999999998 678888888999999999998877654333
No 94
>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=41.17 E-value=43 Score=23.55 Aligned_cols=38 Identities=11% Similarity=0.083 Sum_probs=33.9
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEe
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKL 149 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkI 149 (267)
.....+-.+|++.++++ ...|-..|=.....|+|+-.-
T Consensus 19 ~~~~~t~~eIa~~l~i~-~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 19 KNGPATAEEIAEELGIS-RSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHCHEEHHHHHHHHTSS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HcCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEc
Confidence 45778999999999999 999999999999999997655
No 95
>KOG2235|consensus
Probab=39.94 E-value=1.8e+02 Score=30.37 Aligned_cols=164 Identities=18% Similarity=0.228 Sum_probs=0.0
Q ss_pred hHHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCC-----------------------ChhhHHHHHHHHHhcCccEEE
Q psy10889 92 MTQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDIS-----------------------NVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 92 L~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~-----------------------~~~evE~lvI~aI~~gLI~Gk 148 (267)
+.|.+..+.+.=++-+.-..+.-|.|+.|.+ |||+ ....||+.++.|....+
T Consensus 239 yvP~iya~tqk~cVds~yrQNsfleydalqk-LGIsdA~syl~kryp~~e~l~lk~v~~~~~lve~qv~~Aveeai---- 313 (776)
T KOG2235|consen 239 YVPMIYAHTQKSCVDSFYRQNSFLEYDALQK-LGISDAKSYLEKRYPSSEKLVLKRVMFGTKLVEDQVINAVEEAI---- 313 (776)
T ss_pred echHHHHHHHHHHHHHHHhcccceeHHHHHh-cCcchHHHHHHHHCCCchHHHHHHHHHHHHHHHHHHHHHHHHHH----
Q ss_pred ecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhHhHHH
Q psy10889 149 LDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCAN--------------VLKAIETQIGKANSEKHQHLAHSNAID 214 (267)
Q Consensus 149 IDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~--------------vl~~ie~~i~~a~~~~~~~~~~~~~~~ 214 (267)
|.++.+-|+-+.|-.+.+++...+...+..=..+... +-..++.--+-|+..+.+...+----.
T Consensus 314 --~~~~w~D~~~~LpSsls~eDa~~ll~~im~~~~k~ek~~vf~e~~Vfs~~fl~~~~~~i~klad~~a~~a~d~~vh~~ 391 (776)
T KOG2235|consen 314 --QKSGWSDVHLALPSSLSPEDAMALLDEIMSKVAKVEKDSVFAEGFVFSGAFLTEALRSIDKLADVRAHEAVDRLVHPS 391 (776)
T ss_pred --hhcCcchhHHhccccCChhhHHHHHHHHHHHHhcCccceeeecceeechHHHHHHHHHHHHHHHHHHHHHHhcccCch
Q ss_pred HHHHHHHHhhccccC------------CCCCccccccCCCCccccccccccCCCCCCCCC
Q psy10889 215 MEILNIKKSLKNQTN------------QSQDTDDMMGSDNVVDKIGKKYKIKSNRGTSNT 262 (267)
Q Consensus 215 ~~~~~~k~~~~~~~~------------~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~ 262 (267)
...++-.+++-+.+. +..-.+++-+.+++.+.+.|+++.|++|.+++.
T Consensus 392 ~i~ee~~kq~~st~e~gs~~kkdk~derr~ka~eg~~~~g~~grekk~ks~KkGrkss~~ 451 (776)
T KOG2235|consen 392 SIEEEKLKQIPSTTEKGSKGKKDKVDERREKADEGDGGGGGKGREKKAKSVKKGRKSSSS 451 (776)
T ss_pred hhhhHHHhcCcccccccccccchhHHHHHhhcccCCCCCCcccccccchhhhcccccccc
No 96
>PRK00708 sec-independent translocase; Provisional
Probab=39.69 E-value=1.3e+02 Score=26.88 Aligned_cols=37 Identities=16% Similarity=0.266 Sum_probs=31.2
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGKANS 201 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~ 201 (267)
.|+|++|..|...|..|..++..+.+.+.+++...-.
T Consensus 19 V~GPkrLP~~~R~lGk~v~k~R~~a~e~r~~~~e~~~ 55 (209)
T PRK00708 19 VVGPKDLPPMLRAFGKMTARMRKMAGEFRRQFDEALR 55 (209)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 5789999999999999999999888888777765443
No 97
>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=39.64 E-value=47 Score=22.35 Aligned_cols=44 Identities=20% Similarity=0.234 Sum_probs=36.5
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCe
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSS 155 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~ 155 (267)
....++..+|++.++++ ...+=.++=.....|+|.=.-|+.++.
T Consensus 14 ~~~~~~~~~la~~~~~~-~~~~t~~i~~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 14 ENGGITQSELAEKLGIS-RSTVTRIIKRLEKKGLIERERDPDDRR 57 (59)
T ss_dssp HHSSEEHHHHHHHHTS--HHHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred HcCCCCHHHHHHHHCCC-hhHHHHHHHHHHHCCCEEeccCCCCCC
Confidence 44559999999999998 888888888999999999888877653
No 98
>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=39.63 E-value=89 Score=30.78 Aligned_cols=86 Identities=13% Similarity=0.196 Sum_probs=62.7
Q ss_pred HHHHHHHhC----CCChhhHHHHHHHHHhcCccEEEecCC--CCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHH
Q psy10889 117 YDKLLKELD----ISNVRDLEDLIIEAIYSDIIHGKLDQR--NSSLELDFAIGRDINPGDVTNMITEFQAWSDSCANVLK 190 (267)
Q Consensus 117 Y~~I~~~L~----I~~~~evE~lvI~aI~~gLI~GkIDQ~--~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~ 190 (267)
.+++-+.|+ ++.-+++...+++|+..|+.----|.. .+.+... +..+..++.+.|.+++..-...-+.+-.
T Consensus 341 l~~ly~~~dlyLdin~~e~~~~al~eA~~~G~pI~afd~t~~~~~~i~~---g~l~~~~~~~~m~~~i~~lL~d~~~~~~ 417 (438)
T TIGR02919 341 IQELYQTCDIYLDINHGNEILNAVRRAFEYNLLILGFEETAHNRDFIAS---ENIFEHNEVDQLISKLKDLLNDPNQFRE 417 (438)
T ss_pred HHHHHHhccEEEEccccccHHHHHHHHHHcCCcEEEEecccCCcccccC---CceecCCCHHHHHHHHHHHhcCHHHHHH
Confidence 445666655 454578999999999999887777766 3333333 6668888999999999888777767777
Q ss_pred HHHHHHHHHHHHHHH
Q psy10889 191 AIETQIGKANSEKHQ 205 (267)
Q Consensus 191 ~ie~~i~~a~~~~~~ 205 (267)
.|+.|-..||....+
T Consensus 418 ~~~~q~~~a~~~~~~ 432 (438)
T TIGR02919 418 LLEQQREHANDISKE 432 (438)
T ss_pred HHHHHHHHhccCCHH
Confidence 777777777765443
No 99
>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=39.36 E-value=1.6e+02 Score=22.05 Aligned_cols=45 Identities=18% Similarity=0.155 Sum_probs=30.2
Q ss_pred CHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHH
Q psy10889 116 PYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNM 174 (267)
Q Consensus 116 sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L 174 (267)
+-.++++.|+|+ ...|-.| ...|++...-+.. -.|.++..++..+
T Consensus 2 ~~~eva~~~gi~-~~tlr~~----~~~Gll~~~~~~~---------g~r~y~~~dv~~l 46 (100)
T cd00592 2 TIGEVAKLLGVS-VRTLRYY----EEKGLLPPERSEN---------GYRLYSEEDLERL 46 (100)
T ss_pred CHHHHHHHHCcC-HHHHHHH----HHCCCcCCCcCCC---------CCcccCHHHHHHH
Confidence 457899999998 7787777 4578776543332 2456666666643
No 100
>PHA01750 hypothetical protein
Probab=38.38 E-value=1.4e+02 Score=21.89 Aligned_cols=35 Identities=11% Similarity=0.313 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhh
Q psy10889 190 KAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSL 224 (267)
Q Consensus 190 ~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 224 (267)
..+.....+...+-+.-..+++.++++|.++|+-+
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 33445555555565556678888999999999865
No 101
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=38.38 E-value=65 Score=20.32 Aligned_cols=33 Identities=6% Similarity=0.086 Sum_probs=29.2
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
.++..+|++.++++ ...+-..+-.....|+|.-
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEE
Confidence 46789999999998 8999999999999999963
No 102
>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=38.23 E-value=34 Score=24.61 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=21.1
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
++.-+..+||+.|+|+ +.+|..++-.+
T Consensus 18 gr~Pt~eEiA~~lgis-~~~v~~~l~~~ 44 (78)
T PF04539_consen 18 GREPTDEEIAEELGIS-VEEVRELLQAS 44 (78)
T ss_dssp SS--BHHHHHHHHTS--HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHccc-HHHHHHHHHhC
Confidence 7889999999999998 99999887644
No 103
>PRK00404 tatB sec-independent translocase; Provisional
Probab=38.08 E-value=2.2e+02 Score=23.95 Aligned_cols=34 Identities=12% Similarity=0.292 Sum_probs=28.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGK 198 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~ 198 (267)
.|+++.+..+...+..|..++.+....+.+.+.+
T Consensus 19 V~GPkkLP~laR~lG~~i~~~rr~~~~~k~ei~~ 52 (141)
T PRK00404 19 VLGPERLPGAARTAGLWIGRLKRSFNAIKQEVER 52 (141)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999988877777665544
No 104
>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=37.56 E-value=63 Score=21.23 Aligned_cols=29 Identities=14% Similarity=0.271 Sum_probs=23.1
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHh
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIY 141 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~ 141 (267)
....||.+|++.++++ ...|-.+.-.|+.
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~~al~ 46 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILKRALK 46 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHHHHHH
Confidence 5678999999999998 8888777777653
No 105
>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=37.36 E-value=1.3e+02 Score=20.14 Aligned_cols=36 Identities=17% Similarity=0.258 Sum_probs=30.0
Q ss_pred cCCcccC-HHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 110 LESKCIP-YDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 110 ~~~k~Is-Y~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
..+..++ -.+|++.++++ ...|-..+-..-..|+|.
T Consensus 20 ~~~~~~~~~~~la~~~~is-~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 20 KPGDRLPSERELAEELGVS-RTTVREALRELEAEGLVE 56 (66)
T ss_pred CCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEE
Confidence 3344555 99999999997 899999999999999986
No 106
>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=37.17 E-value=71 Score=21.74 Aligned_cols=35 Identities=9% Similarity=0.082 Sum_probs=30.9
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
...++..+|++.++++ ...|...+=.....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s-~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLT-RETVSRTLKELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEe
Confidence 3568999999999998 8999999999999999874
No 107
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is 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 dissimilar C-terminal domains bind specific coactivator molecules.
Probab=36.11 E-value=1.8e+02 Score=21.66 Aligned_cols=46 Identities=7% Similarity=-0.020 Sum_probs=31.4
Q ss_pred cCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHH
Q psy10889 115 IPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNM 174 (267)
Q Consensus 115 IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L 174 (267)
.+..++|+.++|+ +..|-.| ...|+|...=++ .-.|.+++.++..+
T Consensus 2 ~~i~e~A~~~gvs-~~tLr~y----e~~Gli~p~r~~---------~g~R~y~~~dv~~l 47 (91)
T cd04766 2 YVISVAAELSGMH-PQTLRLY----ERLGLLSPSRTD---------GGTRRYSERDIERL 47 (91)
T ss_pred cCHHHHHHHHCcC-HHHHHHH----HHCCCcCCCcCC---------CCCeeECHHHHHHH
Confidence 4678999999998 8888887 346888642111 13466777777643
No 108
>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=36.10 E-value=2.6e+02 Score=23.48 Aligned_cols=43 Identities=23% Similarity=0.312 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhccc
Q psy10889 185 CANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLKNQ 227 (267)
Q Consensus 185 ~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 227 (267)
+..++..++..+.....+...-..+++..+.++..+|..|...
T Consensus 45 ~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL~~~ 87 (162)
T PF05565_consen 45 IAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYLLDA 87 (162)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555566666666666666677888889999998888654
No 109
>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=35.21 E-value=50 Score=24.36 Aligned_cols=30 Identities=10% Similarity=0.100 Sum_probs=21.8
Q ss_pred HHhhhcccCCcccCHHHHHHHhCCC-ChhhH
Q psy10889 103 LTIVTLSLESKCIPYDKLLKELDIS-NVRDL 132 (267)
Q Consensus 103 LtLlsLa~~~k~IsY~~I~~~L~I~-~~~ev 132 (267)
+.++.-.-.+++.||.+|++.++.+ ..+.|
T Consensus 6 ~~~v~~IP~G~v~TYg~iA~~~g~p~~~R~V 36 (79)
T cd06445 6 WEALRQIPYGEVTTYGQIAKLAGTPKAARAV 36 (79)
T ss_pred HHHHhcCCCCCcCcHHHHHHHHCCCCcHHHH
Confidence 3344444568999999999999996 35554
No 110
>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=34.75 E-value=32 Score=25.59 Aligned_cols=29 Identities=7% Similarity=0.061 Sum_probs=22.9
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHhc
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIYS 142 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~~ 142 (267)
...||.+|++.|+++ ...|..++-.-...
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~~~~~~ 59 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLKGETKA 59 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHhcCccc
Confidence 678999999999998 88888776543333
No 111
>KOG2166|consensus
Probab=34.37 E-value=1.6e+02 Score=31.17 Aligned_cols=118 Identities=12% Similarity=0.239 Sum_probs=70.8
Q ss_pred HHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHH--HhcCccEEEec--CCCCeEEEEee----cCCC----CC
Q psy10889 100 LQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEA--IYSDIIHGKLD--QRNSSLELDFA----IGRD----IN 167 (267)
Q Consensus 100 Lr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~a--I~~gLI~GkID--Q~~~~v~V~~~----~~Rd----~~ 167 (267)
+-+++++-|-.+.-.++|.+|.++++++ ..++=..|-.. +...++....+ ..+..+.+++. ..|+ +.
T Consensus 566 t~Qm~VLlLFN~~d~lt~~eI~~~t~i~-~~~l~~~L~Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~~~~ 644 (725)
T KOG2166|consen 566 TYQMAVLLLFNNTEKLTYEEILEQTNLG-HEDLARLLQSLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIPLPP 644 (725)
T ss_pred hHHHHHHHHccchhhccHHHHHHHhCCC-HHHHHHHHHHHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccCCCC
Confidence 4456677777777889999999999999 88888877755 33222222111 45778888743 2332 22
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 168 PGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 168 ~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
..+-+.....++.|+... |++.|.+.-+ .+++..|.+=+.+=++.+++..+
T Consensus 645 ~~e~~~~~~~ve~dRk~~------i~AaIVRIMK-~rK~l~h~~Lv~Ev~~ql~~RF~ 695 (725)
T KOG2166|consen 645 MDERKKVVEDVDKDRKYA------IDAAIVRIMK-SRKVLGHQQLVSEVVEQLSERFK 695 (725)
T ss_pred chhHHHHHhhhhhHHHHH------HHHHHHHHHH-hhccccHHHHHHHHHHHHhhhcC
Confidence 234555677777777652 3344433322 22355677766666666655554
No 112
>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=34.24 E-value=3e+02 Score=23.63 Aligned_cols=37 Identities=14% Similarity=0.070 Sum_probs=31.9
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEe
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKL 149 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkI 149 (267)
...++..+|++.++|+ ...|=..+-.....|+|.-.-
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCeEEee
Confidence 3459999999999998 888888888888999998663
No 113
>PHA02763 hypothetical protein; Provisional
Probab=32.92 E-value=54 Score=25.38 Aligned_cols=50 Identities=20% Similarity=0.246 Sum_probs=41.8
Q ss_pred cCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCC
Q psy10889 115 IPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDI 166 (267)
Q Consensus 115 IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~ 166 (267)
++-+-|++-++.+.-+.||.|+-+| ..|=.-+||...=.+.|-|+.+|-|
T Consensus 53 ~t~~~LsKYv~~SGFe~VEeWl~eA--rrLh~~~id~~ryeiivi~in~~~f 102 (102)
T PHA02763 53 VTEYCLSKYVKFSGFENVEEWLNEA--RRLHNDKIDPERYEIIVIWINGRLF 102 (102)
T ss_pred chHHHHHHHhhhcchhhHHHHHHHH--HHHhcCCCChhheEEEEEEEcCccC
Confidence 4556678888888788999999999 6777889999999999999988743
No 114
>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=32.72 E-value=1.5e+02 Score=21.42 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=37.8
Q ss_pred cCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 142 SDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCANVLKAIET 194 (267)
Q Consensus 142 ~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~ 194 (267)
.+-+...++-.++.+.|++.. .+...|+..+..|...+.-+...+++
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 367888899889999998875 47889999999999999888877764
No 115
>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].
Probab=32.69 E-value=3.1e+02 Score=24.36 Aligned_cols=53 Identities=15% Similarity=0.107 Sum_probs=38.6
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhHhHHHHHHHHHHH
Q psy10889 170 DVTNMITEFQAWSDSCANVLKAIETQIGKANSEKH-QHLAHSNAIDMEILNIKK 222 (267)
Q Consensus 170 q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~-~~~~~~~~~~~~~~~~k~ 222 (267)
.+.....+|..|..+...+-...++++..||.+-+ -+..|+.++..--+.+||
T Consensus 119 ~~~ey~~~l~~~eqry~aLK~hAeekL~~ANeei~~v~~~~~~e~~aLqa~lkk 172 (207)
T PF05010_consen 119 CIEEYEERLKKEEQRYQALKAHAEEKLEKANEEIAQVRSKHQAELLALQASLKK 172 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 45567889999999999999999999999999855 344555554444444443
No 116
>KOG4348|consensus
Probab=32.55 E-value=1.8e+02 Score=29.05 Aligned_cols=50 Identities=16% Similarity=0.290 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 176 TEFQAWSDSCANVLKAIET-------QIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 176 ~~L~~W~~~~~~vl~~ie~-------~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
+.|+..+..+..++..|+. .+.+...+-++...-+-.++.+|+.+||++-
T Consensus 569 ~s~delr~qi~el~~ive~lk~~~~kel~kl~~dleeek~mr~~lemei~~lkka~~ 625 (627)
T KOG4348|consen 569 NSLDELRAQIIELLCIVEALKKDHGKELEKLRKDLEEEKTMRSNLEMEIEKLKKAVL 625 (627)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHhhHHHHHHHhh
Confidence 3444455555555555543 4555566666666677789999999999874
No 117
>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=31.68 E-value=27 Score=28.41 Aligned_cols=40 Identities=28% Similarity=0.529 Sum_probs=32.2
Q ss_pred HHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHH
Q psy10889 120 LLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDSCA 186 (267)
Q Consensus 120 I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~ 186 (267)
|+++|+|+ .++|++.+|+.. +...+.+|..+..+|+..|-
T Consensus 19 lSk~lgi~-~ee~~~ili~~~--------------------------DmssLe~lhar~E~Ak~~cl 58 (117)
T PF09218_consen 19 LSKELGIS-IEEFIDILIEKL--------------------------DMSSLENLHARYEQAKMGCL 58 (117)
T ss_dssp TTTTGGGT-HHHHHHHHHHHS---------------------------HHHHHHHHHHHHTTHHHHH
T ss_pred HHHHhCcC-HHHHHHHHHHhc--------------------------ChHHHHhccHHHHHHhhhhh
Confidence 67889998 999999999872 23468888999999988764
No 118
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=31.60 E-value=71 Score=28.62 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=35.4
Q ss_pred HhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 101 QNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 101 r~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
|+..|+.+...++.++.++|++.|+++ ...+...+-+.-..|+|.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~~L~~~~~l~ 49 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLNELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHHHHHHCCCEE
Confidence 556677776678899999999999998 888877777765666554
No 119
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=30.68 E-value=60 Score=27.14 Aligned_cols=27 Identities=22% Similarity=0.362 Sum_probs=24.2
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
..+||.+|++.|+|+ +..|...+-.|.
T Consensus 142 ~gls~~EIA~~l~i~-~~tVks~l~ra~ 168 (182)
T COG1595 142 EGLSYEEIAEILGIS-VGTVKSRLHRAR 168 (182)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 579999999999999 999999988774
No 120
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=30.42 E-value=64 Score=21.20 Aligned_cols=33 Identities=21% Similarity=0.276 Sum_probs=24.0
Q ss_pred HhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 104 TIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
.++.++... .|+.+|++.++|+ ...|..++-++
T Consensus 19 ~i~~~~~~~--~s~~~vA~~~~vs-~~TV~ri~~~~ 51 (52)
T PF13542_consen 19 YILKLLRES--RSFKDVARELGVS-WSTVRRIFDRY 51 (52)
T ss_pred HHHHHHhhc--CCHHHHHHHHCCC-HHHHHHHHHhh
Confidence 344444443 7999999999998 78887776543
No 121
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=29.85 E-value=97 Score=27.66 Aligned_cols=45 Identities=11% Similarity=0.033 Sum_probs=32.6
Q ss_pred hHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 102 NLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 102 ~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
-|.|+.+....+.++..+|++.++++ ...+-.++-.....|++.=
T Consensus 16 ~l~IL~~l~~~~~l~l~eia~~lgl~-kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 16 VFGILQALGEEREIGITELSQRVMMS-KSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEE
Confidence 33344333344578999999999998 8888888888888887753
No 122
>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=28.91 E-value=1.5e+02 Score=25.59 Aligned_cols=46 Identities=13% Similarity=0.121 Sum_probs=35.9
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEE
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLEL 158 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V 158 (267)
.+..++..+|++.++++ ...+-..|-.....|+|.-.-+ ..+.+.+
T Consensus 154 ~~g~~s~~eia~~l~is-~stv~r~L~~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 154 AEGEKSVKNIAKKLGKS-LSTISRHLRELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HcCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEEEcC-CccEEEe
Confidence 44568999999999998 8889988889889999986533 4444444
No 123
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.54 E-value=67 Score=26.80 Aligned_cols=27 Identities=7% Similarity=0.159 Sum_probs=24.1
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||++|++.+||+ +..|...+-.|.
T Consensus 148 ~~~s~~eIA~~lgis-~~tV~~~l~ra~ 174 (182)
T PRK12537 148 DGCSHAEIAQRLGAP-LGTVKAWIKRSL 174 (182)
T ss_pred cCCCHHHHHHHHCCC-hhhHHHHHHHHH
Confidence 468999999999998 999999988774
No 124
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=28.32 E-value=87 Score=25.84 Aligned_cols=51 Identities=20% Similarity=0.222 Sum_probs=40.8
Q ss_pred HHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCcc
Q psy10889 93 TQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDII 145 (267)
Q Consensus 93 ~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI 145 (267)
++++..+| ...|+.|+..+..+++.++...++++ ...++.++-+++..|-|
T Consensus 6 T~eer~eL-k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lreLVa~G~l 56 (127)
T PF06163_consen 6 TPEEREEL-KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLRELVARGDL 56 (127)
T ss_pred CHHHHHHH-HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHHHHHHcCCe
Confidence 44443333 34577888889999999999999998 99999999999888743
No 125
>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=28.04 E-value=2.1e+02 Score=20.17 Aligned_cols=34 Identities=15% Similarity=0.275 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 192 IETQIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 192 ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
||+.++.....-..-.+.-+++...++.++++++
T Consensus 5 lEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk 38 (55)
T PF05377_consen 5 LENELPRIESSINTVKKENEEISESVEKIEENVK 38 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444333333333344455555555555553
No 126
>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=27.52 E-value=2.6e+02 Score=20.96 Aligned_cols=59 Identities=17% Similarity=0.282 Sum_probs=35.4
Q ss_pred CeEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhcc
Q psy10889 154 SSLELDFAIGRDINPGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLKN 226 (267)
Q Consensus 154 ~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~~ 226 (267)
.--.|-...|+.|=..+.+.+...|..=...++.-+..++.+. ..++.++.++++.|+.
T Consensus 43 ~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~--------------~~l~~~l~~~~~~l~~ 101 (106)
T PF01920_consen 43 DDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQL--------------KYLEKKLKELKKKLYE 101 (106)
T ss_dssp TT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHC
T ss_pred CcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHH
Confidence 3344445678887777887777777766666655555555444 4445555666665543
No 127
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=27.30 E-value=82 Score=22.56 Aligned_cols=34 Identities=6% Similarity=0.048 Sum_probs=28.7
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
+..++=.+||++|+|+ ...+-.++...-..|.|+
T Consensus 13 ~~p~~T~eiA~~~gls-~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLS-IYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS--HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHHHHHHCCCEE
Confidence 5678889999999998 999999999998888775
No 128
>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=27.26 E-value=73 Score=26.35 Aligned_cols=27 Identities=22% Similarity=0.172 Sum_probs=23.6
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||.+||+.|+++ +..|...+-.|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tVk~~l~Rar 175 (183)
T TIGR02999 149 AGLTVEEIAELLGVS-VRTVERDWRFAR 175 (183)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 468999999999998 999998887764
No 129
>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=27.20 E-value=2.8e+02 Score=21.08 Aligned_cols=92 Identities=10% Similarity=0.064 Sum_probs=47.4
Q ss_pred CHHHHHHHhCCCChhhHHHHHHHHHhcCccEE-EecCCCCeEEEEeecCCCCCCCcHHHHHH--HHHHHHHHHHHHHHHH
Q psy10889 116 PYDKLLKELDISNVRDLEDLIIEAIYSDIIHG-KLDQRNSSLELDFAIGRDINPGDVTNMIT--EFQAWSDSCANVLKAI 192 (267)
Q Consensus 116 sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G-kIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~--~L~~W~~~~~~vl~~i 192 (267)
+..++++.+||+ .+.+-.|. ..|++.- +-++.+ .|.++++++..+.. .|..-.=.+..+...+
T Consensus 2 ti~eva~~~gvs-~~tlR~ye----~~Gll~~~~~~~~g---------~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~ 67 (103)
T cd01106 2 TVGEVAKLTGVS-VRTLHYYD----EIGLLKPSRRTENG---------YRLYTEEDLERLQQILFLKELGFSLKEIKELL 67 (103)
T ss_pred CHHHHHHHHCcC-HHHHHHHH----HCCCCCCCccCCCC---------ceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 457899999998 78887763 3677632 233322 35566666654422 2222111233333333
Q ss_pred HHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhh
Q psy10889 193 ETQIGKANSEKHQHLAHSNAIDMEILNIKKSL 224 (267)
Q Consensus 193 e~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 224 (267)
+... ....+.-..+.++++.++++++.++
T Consensus 68 ~~~~---~~~~~~l~~~~~~l~~~i~~l~~~~ 96 (103)
T cd01106 68 KDPS---EDLLEALREQKELLEEKKERLDKLI 96 (103)
T ss_pred HcCc---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2211 2223333446666666666666554
No 130
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=27.15 E-value=56 Score=25.15 Aligned_cols=36 Identities=8% Similarity=0.245 Sum_probs=27.7
Q ss_pred CcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEE
Q psy10889 112 SKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGK 148 (267)
Q Consensus 112 ~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~Gk 148 (267)
.++++-++|++.++++ ..+|-.++-.....|+|..+
T Consensus 25 ~~~l~de~la~~~~l~-~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLK-PKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S--HHHHHHHHHHHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCC-HHHHHHHHHHHHHCCCeEEE
Confidence 4679999999999998 99999999999999999665
No 131
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=27.03 E-value=1e+02 Score=19.69 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=21.2
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
-.++.+|++.++++ ...|...+-.+
T Consensus 18 g~s~~eia~~l~is-~~tv~~~~~~~ 42 (58)
T smart00421 18 GLTNKEIAERLGIS-EKTVKTHLSNI 42 (58)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHHHH
Confidence 36999999999998 88888877655
No 132
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=26.89 E-value=1.6e+02 Score=22.20 Aligned_cols=49 Identities=10% Similarity=0.248 Sum_probs=38.8
Q ss_pred HHhHHhhhccc-CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEe
Q psy10889 100 LQNLTIVTLSL-ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKL 149 (267)
Q Consensus 100 Lr~LtLlsLa~-~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkI 149 (267)
.|.|+.+.... +..-+|.+.|.+..+++ ..+++..+-+.+..++|.-+.
T Consensus 9 ~rvL~aiE~gmk~hE~VP~~~I~~~s~l~-~~~~~~~L~~L~~~kLv~~~~ 58 (82)
T PF09202_consen 9 FRVLRAIEMGMKNHEWVPLELIEKISGLS-EGEVEKRLKRLVKLKLVSRRN 58 (82)
T ss_dssp HHHHHHHHTTTTT-SSEEHHHHHHHHT---HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHHHHcccCCccCCHHHHHHHhCcC-HHHHHHHHHHHHhcCCccccC
Confidence 56777777664 46789999999999998 999999999999999998743
No 133
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.60 E-value=80 Score=26.04 Aligned_cols=28 Identities=11% Similarity=0.262 Sum_probs=24.0
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHh
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIY 141 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~ 141 (267)
...||.+|++.|+++ +..|...+-.|+.
T Consensus 134 ~g~s~~EIA~~lgis-~~tV~~~l~ra~~ 161 (172)
T PRK12523 134 DGMGHAEIAERLGVS-VSRVRQYLAQGLR 161 (172)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHHH
Confidence 468999999999998 9999988877753
No 134
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=26.45 E-value=1.1e+02 Score=25.64 Aligned_cols=46 Identities=24% Similarity=0.129 Sum_probs=28.5
Q ss_pred hhHHHHHHHHHhHHhhhcccC-CcccCHHHHHHHhCCCChhhHHHHHH
Q psy10889 91 EMTQLQKKKLQNLTIVTLSLE-SKCIPYDKLLKELDISNVRDLEDLII 137 (267)
Q Consensus 91 ~L~~~~~~KLr~LtLlsLa~~-~k~IsY~~I~~~L~I~~~~evE~lvI 137 (267)
.|++.|.+=..+|..-.+-.. +...++++||+++||+ ...+-.|-=
T Consensus 10 ~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis-~~tLYrWr~ 56 (142)
T PF13022_consen 10 KLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGIS-RSTLYRWRQ 56 (142)
T ss_dssp TS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS--HHHHHHHHH
T ss_pred HcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCC-HHHHHHHHh
Confidence 366777766777776665543 4789999999999998 777666653
No 135
>PF08581 Tup_N: Tup N-terminal; InterPro: IPR013890 The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor []. ; PDB: 3VP9_B 3VP8_B.
Probab=26.25 E-value=2.8e+02 Score=20.79 Aligned_cols=57 Identities=16% Similarity=0.281 Sum_probs=41.4
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHhHhHHHHHHHHHHHhhcc
Q psy10889 170 DVTNMITEFQAWSDSCANVLKAIETQIGKANSEKH-------QHLAHSNAIDMEILNIKKSLKN 226 (267)
Q Consensus 170 q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~-------~~~~~~~~~~~~~~~~k~~~~~ 226 (267)
+.+.+...+..++...+..=..|.+++...+..++ ...+-++..|++|..++..|-.
T Consensus 12 Ef~~~~~e~~~~k~~~~e~e~ki~~Qi~Em~~ir~~v~eLE~~h~kmK~~YEeEI~rLr~eLe~ 75 (79)
T PF08581_consen 12 EFENLSQEANSYKHQKDEYEHKINSQIQEMQQIRQKVYELEQAHRKMKQQYEEEIARLRRELEQ 75 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45556666667777777777777777776665554 4667788999999999988743
No 136
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=25.86 E-value=83 Score=26.24 Aligned_cols=27 Identities=19% Similarity=0.325 Sum_probs=23.3
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||++|++.|+++ +..|...+-.|+
T Consensus 142 ~g~s~~EIA~~lgis-~~tVk~~l~rAl 168 (178)
T PRK12529 142 DGMKQKDIAQALDIA-LPTVKKYIHQAY 168 (178)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 458999999999998 999988887664
No 137
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.79 E-value=86 Score=25.19 Aligned_cols=27 Identities=7% Similarity=-0.013 Sum_probs=23.1
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
..+||.+|++.|+++ +..|...+-.|.
T Consensus 121 ~g~s~~EIA~~lgis-~~tV~~~l~ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAMGCS-EGSVKTHCSRAT 147 (161)
T ss_pred hcCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 468999999999998 888888877664
No 138
>PHA02943 hypothetical protein; Provisional
Probab=25.69 E-value=1.5e+02 Score=25.43 Aligned_cols=45 Identities=9% Similarity=0.272 Sum_probs=34.5
Q ss_pred HHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 97 KKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 97 ~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
.+|...|.++ ...+-+-++|++.||++ ..+++..|.-.=..|.|.
T Consensus 11 ~R~~eILE~L----k~G~~TtseIAkaLGlS-~~qa~~~LyvLErEG~Vk 55 (165)
T PHA02943 11 TRMIKTLRLL----ADGCKTTSRIANKLGVS-HSMARNALYQLAKEGMVL 55 (165)
T ss_pred HHHHHHHHHH----hcCCccHHHHHHHHCCC-HHHHHHHHHHHHHcCceE
Confidence 3444455554 67788899999999998 899998888776677665
No 139
>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=25.64 E-value=3.3e+02 Score=21.59 Aligned_cols=26 Identities=12% Similarity=0.170 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 117 YDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 117 Y~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
..++++.++|+ .+.|=.| -..|||..
T Consensus 2 I~e~a~~~gvs-~~tlR~Y----e~~GLl~~ 27 (124)
T TIGR02051 2 IGELAKAAGVN-VETIRYY----ERKGLLPE 27 (124)
T ss_pred HHHHHHHHCcC-HHHHHHH----HHCCCCCC
Confidence 56899999998 8888666 44788863
No 140
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.34 E-value=89 Score=24.95 Aligned_cols=28 Identities=7% Similarity=0.036 Sum_probs=24.0
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHh
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIY 141 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~ 141 (267)
...||.+||+.|+++ +..|...+-.|+.
T Consensus 121 ~~~s~~EIA~~l~is-~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALETEMT-YYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHHH
Confidence 458999999999998 9999998887753
No 141
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=25.32 E-value=3.2e+02 Score=21.78 Aligned_cols=57 Identities=14% Similarity=0.246 Sum_probs=35.3
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhc
Q psy10889 163 GRDINPGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLK 225 (267)
Q Consensus 163 ~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 225 (267)
+|.+.+..++.+...|+.-.+.++.++..= +..-.++-.+-+..++..+.++++.+.
T Consensus 2 ~~~~~~~~~~~l~~el~~L~d~lEevL~ss------g~~a~~e~~~lR~r~~~~Lk~~r~rl~ 58 (104)
T COG4575 2 SREFTDDAIDQLLAELQELLDTLEEVLKSS------GSLAGDEAEELRSKAESALKEARDRLG 58 (104)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHhc------ccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 567777777778888887777777776532 222233334455555666666666654
No 142
>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=25.14 E-value=1.2e+02 Score=19.56 Aligned_cols=25 Identities=12% Similarity=0.114 Sum_probs=21.3
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
..++.+|++.++++ .+.|+..+=.+
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~~~ 39 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLRNI 39 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHHHH
Confidence 46999999999997 88888887655
No 143
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.03 E-value=90 Score=25.20 Aligned_cols=27 Identities=19% Similarity=0.229 Sum_probs=23.4
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||.+||+.||++ +..|...+-.|.
T Consensus 121 ~g~s~~EIA~~lgis-~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIE-VKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 468999999999998 899988887764
No 144
>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=24.98 E-value=79 Score=20.61 Aligned_cols=26 Identities=15% Similarity=0.238 Sum_probs=15.9
Q ss_pred hcccCCcccCHHHHHHHhCCCChhhHHHH
Q psy10889 107 TLSLESKCIPYDKLLKELDISNVRDLEDL 135 (267)
Q Consensus 107 sLa~~~k~IsY~~I~~~L~I~~~~evE~l 135 (267)
.|...+ .|+.+||+.++|+ ...|-.+
T Consensus 16 ~l~~~G--~si~~IA~~~gvs-r~TvyR~ 41 (45)
T PF02796_consen 16 ELYAEG--MSIAEIAKQFGVS-RSTVYRY 41 (45)
T ss_dssp HHHHTT----HHHHHHHTTS--HHHHHHH
T ss_pred HHHHCC--CCHHHHHHHHCcC-HHHHHHH
Confidence 344444 8999999999998 6655443
No 145
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=24.98 E-value=89 Score=25.84 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=24.0
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHh
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIY 141 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~ 141 (267)
...||.+|++.||++ +..|...+-.|+.
T Consensus 134 ~g~s~~EIA~~lgis-~~tV~~~l~Ra~~ 161 (172)
T PRK09651 134 DGLTYSEIAHKLGVS-VSSVKKYVAKATE 161 (172)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHHHHHH
Confidence 568999999999998 9999888877643
No 146
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.66 E-value=76 Score=20.62 Aligned_cols=25 Identities=16% Similarity=0.101 Sum_probs=17.9
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
-.|+.+|++.|+++ ...|-.|+=.-
T Consensus 17 G~s~~~ia~~lgvs-~~Tv~~w~kr~ 41 (50)
T PF13384_consen 17 GWSIREIAKRLGVS-RSTVYRWIKRY 41 (50)
T ss_dssp T--HHHHHHHHTS--HHHHHHHHT--
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHHHc
Confidence 67899999999998 88998887543
No 147
>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=24.63 E-value=99 Score=28.57 Aligned_cols=41 Identities=29% Similarity=0.430 Sum_probs=36.1
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCC
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQR 152 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~ 152 (267)
..+.++..++++..++| .+=+-..+++....++|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp-~efl~~~li~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLP-SEFLKEELISKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCc-HHHHHHHHhhhhcCcceeEEEeCC
Confidence 46889999999999999 677777888888889999999998
No 148
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=24.61 E-value=1e+02 Score=28.08 Aligned_cols=47 Identities=9% Similarity=-0.002 Sum_probs=35.3
Q ss_pred HHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 99 KLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 99 KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
.-|+..|+.+....+.++..+|++.|+|+ ..-+-.=|...-..|++.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHHHHHhCCCeE
Confidence 35788888888778889999999999998 655555554444567665
No 149
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.58 E-value=93 Score=25.17 Aligned_cols=27 Identities=19% Similarity=0.213 Sum_probs=23.0
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||++|++.|+++ ...|...+-.|+
T Consensus 124 ~~~s~~EIA~~lgis-~~tV~~~l~ra~ 150 (163)
T PRK07037 124 HGETQKDIARELGVS-PTLVNFMIRDAL 150 (163)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 468999999999998 899988877663
No 150
>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=24.55 E-value=82 Score=24.90 Aligned_cols=26 Identities=27% Similarity=0.325 Sum_probs=19.7
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
..+|+++||+.++|+ ...|-+.|-+|
T Consensus 32 eDlSlsEIAe~~~iS-RqaV~d~ikr~ 57 (101)
T PF04297_consen 32 EDLSLSEIAEELGIS-RQAVYDSIKRA 57 (101)
T ss_dssp S---HHHHHHHCTS--HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHH
Confidence 468999999999998 88888888877
No 151
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=24.44 E-value=2.4e+02 Score=19.37 Aligned_cols=37 Identities=8% Similarity=0.091 Sum_probs=28.9
Q ss_pred cCCccc-CHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 110 LESKCI-PYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 110 ~~~k~I-sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
..+..+ +-.+|++.++++ ..-|-.-+-.....|+|.-
T Consensus 19 ~~g~~lps~~~la~~~~vs-r~tvr~al~~L~~~g~i~~ 56 (64)
T PF00392_consen 19 PPGDRLPSERELAERYGVS-RTTVREALRRLEAEGLIER 56 (64)
T ss_dssp -TTSBE--HHHHHHHHTS--HHHHHHHHHHHHHTTSEEE
T ss_pred CCCCEeCCHHHHHHHhccC-CcHHHHHHHHHHHCCcEEE
Confidence 345567 899999999998 8888888888888998864
No 152
>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=24.40 E-value=3.2e+02 Score=21.18 Aligned_cols=95 Identities=13% Similarity=0.117 Sum_probs=49.1
Q ss_pred CHHHHHHHhCCCChhhHHHHHHHHHhcCccEE-EecCCCCeEEEEeecCCCCCCCcHHHHH--HHHHHHHHHHHHHHHHH
Q psy10889 116 PYDKLLKELDISNVRDLEDLIIEAIYSDIIHG-KLDQRNSSLELDFAIGRDINPGDVTNMI--TEFQAWSDSCANVLKAI 192 (267)
Q Consensus 116 sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G-kIDQ~~~~v~V~~~~~Rd~~~~q~~~L~--~~L~~W~~~~~~vl~~i 192 (267)
+..++++.+||+ .+.|-.|- ..|+|.. .-+. .-.|.++++++..|. ..|..--=++..+...+
T Consensus 2 ~i~e~a~~~gvs-~~tlr~ye----~~gll~~~~r~~---------~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l 67 (113)
T cd01109 2 TIKEVAEKTGLS-ADTLRYYE----KEGLLPPVKRDE---------NGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYA 67 (113)
T ss_pred CHHHHHHHHCcC-HHHHHHHH----HCCCCCCCCcCC---------CCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 568999999998 88887773 3677742 1121 235777777776542 22222222233333333
Q ss_pred HHHHH---HHHHHHHHHHHhHhHHHHHHHHHHHhh
Q psy10889 193 ETQIG---KANSEKHQHLAHSNAIDMEILNIKKSL 224 (267)
Q Consensus 193 e~~i~---~a~~~~~~~~~~~~~~~~~~~~~k~~~ 224 (267)
+..-. ......+.-..+.++++.+++.++..+
T Consensus 68 ~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~l~~~~ 102 (113)
T cd01109 68 ELRREGDSTIPERLELLEEHREELEEQIAELQETL 102 (113)
T ss_pred HHHccCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 32100 011122223345566666666666554
No 153
>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=23.96 E-value=87 Score=22.42 Aligned_cols=24 Identities=13% Similarity=0.223 Sum_probs=19.3
Q ss_pred CCcccCHHHHHHHhCCCChhhHHHH
Q psy10889 111 ESKCIPYDKLLKELDISNVRDLEDL 135 (267)
Q Consensus 111 ~~k~IsY~~I~~~L~I~~~~evE~l 135 (267)
.++.+++-+||+.|+|+ ...|-.|
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 46789999999999998 6665544
No 154
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=23.85 E-value=1.1e+02 Score=28.67 Aligned_cols=39 Identities=15% Similarity=0.245 Sum_probs=34.9
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCC
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQR 152 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~ 152 (267)
.-++=++|+++|+|+ .-.|=.+|=+|...|+|+-+|+..
T Consensus 28 ~g~tQ~eIA~~lgiS-R~~VsRlL~~Ar~~GiV~I~I~~~ 66 (318)
T PRK15418 28 DGLTQSEIGERLGLT-RLKVSRLLEKGRQSGIIRVQINSR 66 (318)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHHHHHHcCcEEEEEeCC
Confidence 456778999999998 889999999999999999999854
No 155
>PF09523 DUF2390: Protein of unknown function (DUF2390); InterPro: IPR012659 Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model.
Probab=23.82 E-value=1.7e+02 Score=23.20 Aligned_cols=42 Identities=17% Similarity=0.412 Sum_probs=35.0
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 162 IGRDINPGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEK 203 (267)
Q Consensus 162 ~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~ 203 (267)
.++.++++++..+.+.+..|.+.+-.-+..+...++..+...
T Consensus 43 ~g~~l~~~~l~~l~~~~~~W~~~vv~PLR~lRr~lk~~~~~~ 84 (109)
T PF09523_consen 43 QGRSLDAERLAALDAAVAPWREEVVQPLRALRRALKAAAPED 84 (109)
T ss_pred cCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCC
Confidence 567888899999999999999998888888887777665543
No 156
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=23.79 E-value=92 Score=25.89 Aligned_cols=26 Identities=15% Similarity=0.213 Sum_probs=22.4
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
...||++||+.|+|+ +..|...+-.|
T Consensus 132 e~~s~~EIA~~lgis-~~tV~~~l~ra 157 (179)
T PRK12543 132 HDYSQEEIAQLLQIP-IGTVKSRIHAA 157 (179)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHHHH
Confidence 458999999999998 88888887766
No 157
>PRK11020 hypothetical protein; Provisional
Probab=23.68 E-value=3.3e+02 Score=22.15 Aligned_cols=47 Identities=19% Similarity=0.261 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhHhHHHHHHHHHHHh
Q psy10889 177 EFQAWSDSCANVLKAIETQIGKANSEKH-QHLAHSNAIDMEILNIKKS 223 (267)
Q Consensus 177 ~L~~W~~~~~~vl~~ie~~i~~a~~~~~-~~~~~~~~~~~~~~~~k~~ 223 (267)
.|++..++++.+...+.....+-+.+.- +-.+..+.++.+|+++|..
T Consensus 6 Eiq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~~ 53 (118)
T PRK11020 6 EIKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIARLKEV 53 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444444422 3444556677777776643
No 158
>PRK00182 tatB sec-independent translocase; Provisional
Probab=23.53 E-value=2.9e+02 Score=23.71 Aligned_cols=33 Identities=15% Similarity=0.252 Sum_probs=27.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIG 197 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~ 197 (267)
.|+|+.+..+...+..|........+...+++.
T Consensus 20 VfGPerLP~~~r~lg~~ir~~R~~~~~~k~el~ 52 (160)
T PRK00182 20 VIGPERLPRLIEDVRAALLAARTAINNAKQQLD 52 (160)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999988888777666553
No 159
>KOG1861|consensus
Probab=23.11 E-value=2.7e+02 Score=28.17 Aligned_cols=65 Identities=15% Similarity=0.283 Sum_probs=46.0
Q ss_pred HHHHHHHHhcCCHhHHHhhhhhccCchhHH----HHHHHHHhHHhhhcccCCc-ccCHHHHHHHhCCCChhh
Q psy10889 65 YYHLLKLFAHGTYQDYLKQKEELKLPEMTQ----LQKKKLQNLTIVTLSLESK-CIPYDKLLKELDISNVRD 131 (267)
Q Consensus 65 ~~~LL~lFa~Gt~~dy~~~~~~~~~p~L~~----~~~~KLr~LtLlsLa~~~k-~IsY~~I~~~L~I~~~~e 131 (267)
.+++=.+.+-|+|--|-.+-- ..|.... --+.+.|.-+|.-+|...+ +|+++.|++.|...+..+
T Consensus 426 AL~vR~A~~~GNY~kFFrLY~--~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~fi~~~laf~~~e~ 495 (540)
T KOG1861|consen 426 ALEVRSAVTLGNYHKFFRLYL--TAPNMSGYLMDLFLERERKKALTIICKSYRPTITVDFIASELAFDSMED 495 (540)
T ss_pred HHHHHHHHHhccHHHHHHHHh--hcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHHHHhhhhhhchHHH
Confidence 556666777888777655433 4455443 3377788888888888877 999999999999874333
No 160
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=23.06 E-value=1e+02 Score=25.92 Aligned_cols=25 Identities=20% Similarity=0.278 Sum_probs=22.3
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
..||++|++.|+++ +..|...+-.|
T Consensus 147 g~s~~EIA~~lgis-~~tV~~~l~Ra 171 (191)
T PRK12520 147 ELETEEICQELQIT-ATNAWVLLYRA 171 (191)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHHHH
Confidence 58999999999998 99998887766
No 161
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=22.98 E-value=1e+02 Score=24.84 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=23.3
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||++|++.|+++ +..|...+-.|.
T Consensus 120 ~~~s~~eIA~~lgis-~~tv~~~l~ra~ 146 (159)
T PRK12527 120 EGLSHQQIAEHLGIS-RSLVEKHIVNAM 146 (159)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 468999999999998 888888877764
No 162
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=22.93 E-value=1.1e+02 Score=23.70 Aligned_cols=27 Identities=7% Similarity=0.270 Sum_probs=24.4
Q ss_pred HHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 119 KLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 119 ~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
.||..++++ ..+|++.+-+....|||+
T Consensus 26 ~ia~~l~~~-~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 26 SIARRLKIP-LEEVREALEKLEEMGLLE 52 (92)
T ss_pred HHHHHHCCC-HHHHHHHHHHHHHCCCeE
Confidence 378889999 999999999999999986
No 163
>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=22.81 E-value=2.5e+02 Score=19.00 Aligned_cols=47 Identities=15% Similarity=0.193 Sum_probs=34.1
Q ss_pred cccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCe
Q psy10889 108 LSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSS 155 (267)
Q Consensus 108 La~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~ 155 (267)
++..+..++..+|++.++++ ...+-..|=+++..|+|+=.=|..++.
T Consensus 12 l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 12 LAHSDGPMTQSDLAERLGIS-KSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HT--TS-BEHHHHHHHTT---HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred HHccCCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 33567888999999999998 888888888999999997666654443
No 164
>PF14203 DUF4319: Domain of unknown function (DUF4319); PDB: 2L7K_A.
Probab=22.79 E-value=1.3e+02 Score=21.75 Aligned_cols=27 Identities=19% Similarity=0.348 Sum_probs=18.0
Q ss_pred HHHHHHHHhcCCHhHHHhhhhhccCchh
Q psy10889 65 YYHLLKLFAHGTYQDYLKQKEELKLPEM 92 (267)
Q Consensus 65 ~~~LL~lFa~Gt~~dy~~~~~~~~~p~L 92 (267)
-.+|+.+|..|+-.+-.+.... .+|.+
T Consensus 6 E~nL~~iy~~g~R~~~i~~l~~-~lp~m 32 (64)
T PF14203_consen 6 EENLMCIYHTGSREGTIENLTA-ALPYM 32 (64)
T ss_dssp HHHHHHHH--SHHHHHHHHHHH-STTTS
T ss_pred HHHHHHHHcCCCHHHHHHHHHH-HHHHh
Confidence 4689999999998877665332 46776
No 165
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=22.66 E-value=6.1e+02 Score=23.38 Aligned_cols=83 Identities=10% Similarity=0.190 Sum_probs=53.3
Q ss_pred hhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCcHHHHHHHHHHHHHH
Q psy10889 105 IVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGDVTNMITEFQAWSDS 184 (267)
Q Consensus 105 LlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~~L~~~L~~W~~~ 184 (267)
|.-++.....+.=.+|+++|+|+ +..|=+-+=+.+..|+|+- ..+..-+|| ..-.+-|.+.+.+.+.=
T Consensus 16 L~ei~~~qp~v~q~eIA~~lgiT-~QaVsehiK~Lv~eG~i~~---~gR~~Y~iT--------kkG~e~l~~~~~dlr~f 83 (260)
T COG1497 16 LSEIAVRQPRVKQKEIAKKLGIT-LQAVSEHIKELVKEGLIEK---EGRGEYEIT--------KKGAEWLLEQLSDLRRF 83 (260)
T ss_pred HHHHHHhCCCCCHHHHHHHcCCC-HHHHHHHHHHHHhccceee---cCCeeEEEe--------hhHHHHHHHHHHHHHHH
Confidence 44455566778889999999998 9999999999999988864 222244444 22344455555555555
Q ss_pred HHHHHHHHHHHHHHH
Q psy10889 185 CANVLKAIETQIGKA 199 (267)
Q Consensus 185 ~~~vl~~ie~~i~~a 199 (267)
++.+...+.....|.
T Consensus 84 ~~ev~~~l~~~~vw~ 98 (260)
T COG1497 84 SEEVELVLDYVMVWT 98 (260)
T ss_pred HHHHHHHHhhHHHHH
Confidence 555544444444443
No 166
>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=22.48 E-value=95 Score=21.78 Aligned_cols=23 Identities=9% Similarity=0.037 Sum_probs=19.6
Q ss_pred ccCHHHHHHHhCCCChhhHHHHHH
Q psy10889 114 CIPYDKLLKELDISNVRDLEDLII 137 (267)
Q Consensus 114 ~IsY~~I~~~L~I~~~~evE~lvI 137 (267)
-.++.+||+.|+++ ...|-.|+=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 47889999999998 888888764
No 167
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=22.39 E-value=1.1e+02 Score=25.18 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=23.8
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHHh
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAIY 141 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI~ 141 (267)
...||++|++.|+++ +..|...+-.|+.
T Consensus 133 eg~s~~EIA~~l~is-~~tV~~~l~ra~~ 160 (168)
T PRK12525 133 EGLTYVEIGERLGVS-LSRIHQYMVEAFK 160 (168)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHHH
Confidence 468999999999998 8888888877653
No 168
>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=22.36 E-value=1.4e+02 Score=20.20 Aligned_cols=30 Identities=7% Similarity=0.191 Sum_probs=24.1
Q ss_pred cCccEEEecCCCCeEEEEeecCCCCCCCcHH
Q psy10889 142 SDIIHGKLDQRNSSLELDFAIGRDINPGDVT 172 (267)
Q Consensus 142 ~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q~~ 172 (267)
.|+....+|-.++++.|.+..++ +.++++.
T Consensus 24 ~GV~~v~vd~~~~~v~v~~~~~~-~~~~~i~ 53 (62)
T PF00403_consen 24 PGVKSVKVDLETKTVTVTYDPDK-TSIEKII 53 (62)
T ss_dssp TTEEEEEEETTTTEEEEEESTTT-SCHHHHH
T ss_pred CCCcEEEEECCCCEEEEEEecCC-CCHHHHH
Confidence 58999999999999999998777 4444433
No 169
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.18 E-value=1.1e+02 Score=25.11 Aligned_cols=27 Identities=11% Similarity=0.126 Sum_probs=23.6
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...+|.+|++.|+|+ ...|...+-+|.
T Consensus 127 ~g~s~~eIA~~lgis-~~tV~~~l~Rar 153 (164)
T PRK12547 127 SGFSYEDAAAICGCA-VGTIKSRVSRAR 153 (164)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 468999999999998 999998888774
No 170
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.08 E-value=1.1e+02 Score=25.74 Aligned_cols=27 Identities=4% Similarity=0.087 Sum_probs=23.0
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||.+|++.|+++ +..|...+-.|.
T Consensus 154 ~g~s~~EIA~~lgis-~~tV~~~l~ra~ 180 (194)
T PRK12513 154 GDLELEEIAELTGVP-EETVKSRLRYAL 180 (194)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 468999999999998 899988777664
No 171
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.03 E-value=1.1e+02 Score=25.31 Aligned_cols=27 Identities=11% Similarity=0.395 Sum_probs=22.6
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
.-.||++|++.||++ +..|...+-.|.
T Consensus 144 ~g~s~~eIA~~lgis-~~tV~~~l~Rar 170 (179)
T PRK12514 144 EGLSYKELAERHDVP-LNTMRTWLRRSL 170 (179)
T ss_pred cCCCHHHHHHHHCCC-hHHHHHHHHHHH
Confidence 358999999999998 888888877663
No 172
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.98 E-value=3.7e+02 Score=20.66 Aligned_cols=31 Identities=13% Similarity=0.127 Sum_probs=25.7
Q ss_pred CHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 116 PYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 116 sY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
++..|+.+++|-+...+-.|++.+...+...
T Consensus 26 sv~~vAr~~gv~~~~~l~~W~~~~~~~~~~~ 56 (116)
T COG2963 26 TVSEVAREFGIVSATQLYKWRIQLQKGGGLA 56 (116)
T ss_pred cHHHHHHHhCCCChHHHHHHHHHHHHccccc
Confidence 9999999999733899999999997766444
No 173
>PRK03100 sec-independent translocase; Provisional
Probab=21.85 E-value=4.5e+02 Score=21.88 Aligned_cols=34 Identities=9% Similarity=0.051 Sum_probs=29.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 165 DINPGDVTNMITEFQAWSDSCANVLKAIETQIGK 198 (267)
Q Consensus 165 d~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~ 198 (267)
.|+++.+..+...+..|........+.+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999888888877754
No 174
>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=21.57 E-value=4.6e+02 Score=21.49 Aligned_cols=53 Identities=13% Similarity=0.278 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhh
Q psy10889 172 TNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSL 224 (267)
Q Consensus 172 ~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 224 (267)
..+-..|++-.+.+...-..+.++|...+..-++..+-.+.+..++.+++..+
T Consensus 46 ~~v~kql~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv 98 (126)
T PF07889_consen 46 ASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDV 98 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhH
Confidence 34556666666666666666777777777766666667777777777776654
No 175
>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=21.54 E-value=1.1e+02 Score=25.79 Aligned_cols=27 Identities=4% Similarity=0.151 Sum_probs=23.4
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
..+||.+|++.|+|+ +..|...+-.|.
T Consensus 146 ~g~s~~EIA~~lgis-~~tVk~~l~Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTP-IGTVMSRLHRGR 172 (193)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 468999999999998 999988887763
No 176
>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=21.54 E-value=1.3e+02 Score=22.73 Aligned_cols=35 Identities=11% Similarity=0.241 Sum_probs=24.0
Q ss_pred HhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 104 TIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 104 tLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
.|+.+-..++.++-.+|+.+++.+ +++|...+=.+
T Consensus 28 ~LLr~LA~G~PVt~~~LA~a~g~~-~e~v~~~L~~~ 62 (77)
T PF12324_consen 28 PLLRLLAKGQPVTVEQLAAALGWP-VEEVRAALAAM 62 (77)
T ss_dssp HHHHHHTTTS-B-HHHHHHHHT---HHHHHHHHHH-
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCC-HHHHHHHHHhC
Confidence 455555669999999999999998 89988876543
No 177
>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=21.38 E-value=1.7e+02 Score=25.84 Aligned_cols=45 Identities=4% Similarity=0.120 Sum_probs=36.1
Q ss_pred HhHHhhhccc-CCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE
Q psy10889 101 QNLTIVTLSL-ESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH 146 (267)
Q Consensus 101 r~LtLlsLa~-~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~ 146 (267)
|-|.|+.+.. ....++..+|++.++++ ...+-.++-.....|++.
T Consensus 10 ral~IL~~l~~~~~~~~l~eia~~lglp-ksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGAERPRLTLTDVAEATGLT-RAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEE
Confidence 4455555443 46679999999999998 889999999999999887
No 178
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.32 E-value=1.2e+02 Score=19.67 Aligned_cols=39 Identities=13% Similarity=0.210 Sum_probs=15.2
Q ss_pred CchhHHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHH
Q psy10889 89 LPEMTQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDL 135 (267)
Q Consensus 89 ~p~L~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~l 135 (267)
++.|++++...+..| . . .-.|+.+||+.|+++ ...|-..
T Consensus 2 ~~~Lt~~eR~~I~~l--~---~--~G~s~~~IA~~lg~s-~sTV~re 40 (44)
T PF13936_consen 2 YKHLTPEERNQIEAL--L---E--QGMSIREIAKRLGRS-RSTVSRE 40 (44)
T ss_dssp ----------HHHHH--H---C--S---HHHHHHHTT---HHHHHHH
T ss_pred ccchhhhHHHHHHHH--H---H--cCCCHHHHHHHHCcC-cHHHHHH
Confidence 355666655554443 1 1 338999999999997 6555443
No 179
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=21.32 E-value=2.3e+02 Score=24.66 Aligned_cols=52 Identities=21% Similarity=0.130 Sum_probs=36.4
Q ss_pred cCchhHHHHHHHHHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 88 KLPEMTQLQKKKLQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 88 ~~p~L~~~~~~KLr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
..+.|++.|.+=|+.--=+-.-.--|.++-.+||++|||+ ...+.+-|=+|.
T Consensus 152 ~~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGIS-kst~~ehLRrAe 203 (215)
T COG3413 152 GKNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGIS-KSTLSEHLRRAE 203 (215)
T ss_pred ccccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 3356888775555544444444557999999999999998 777776666653
No 180
>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=21.28 E-value=1.2e+02 Score=24.51 Aligned_cols=27 Identities=19% Similarity=0.274 Sum_probs=23.7
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
.-.+|.+|++.++++ +..|...+-.|.
T Consensus 125 ~g~s~~eIA~~lgis-~~tV~~~l~ra~ 151 (162)
T TIGR02983 125 EDLSEAQVAEALGIS-VGTVKSRLSRAL 151 (162)
T ss_pred hcCCHHHHHHHhCCC-HHHHHHHHHHHH
Confidence 368999999999998 999999888774
No 181
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=21.10 E-value=99 Score=22.60 Aligned_cols=21 Identities=24% Similarity=0.365 Sum_probs=17.7
Q ss_pred cCHHHHHHHhCCCChhhHHHHH
Q psy10889 115 IPYDKLLKELDISNVRDLEDLI 136 (267)
Q Consensus 115 IsY~~I~~~L~I~~~~evE~lv 136 (267)
.+-++|++.|+|+ ..|.|-++
T Consensus 45 a~~~el~~~CgL~-~aEAeLl~ 65 (70)
T PF10975_consen 45 ASVEELMEECGLS-RAEAELLL 65 (70)
T ss_pred CCHHHHHHHcCCC-HHHHHHHH
Confidence 5678999999998 88888665
No 182
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.09 E-value=7.9e+02 Score=26.23 Aligned_cols=59 Identities=15% Similarity=0.296 Sum_probs=47.2
Q ss_pred HHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccE----EEecCCCCeEEEE
Q psy10889 100 LQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIH----GKLDQRNSSLELD 159 (267)
Q Consensus 100 Lr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~----GkIDQ~~~~v~V~ 159 (267)
.-++.++.|+..+-+|+|.+|.+-.+++ ++++-..+...+.+.++. +++-..+-.+.|+
T Consensus 608 ~~q~~vfll~n~~e~lt~eei~e~T~l~-~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~fy~n 670 (773)
T COG5647 608 VYQLLVFLLFNDHEELTFEEILELTKLS-TDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVN 670 (773)
T ss_pred HHHHHHHHHhcCccceeHHHHHhhcCCC-hhhHHHHHHHHHhhheeeeccccccCCCCceEEEc
Confidence 4456677788899999999999999999 899999999887777654 4555666677776
No 183
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=20.89 E-value=1.4e+02 Score=26.92 Aligned_cols=47 Identities=15% Similarity=0.116 Sum_probs=37.1
Q ss_pred HHhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCccEE
Q psy10889 100 LQNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDIIHG 147 (267)
Q Consensus 100 Lr~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI~G 147 (267)
-|+..|+.+...++.++-.+|++.++++ ..-+..-+-+.-..|+|.-
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS-~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 5 QRHQILLELLAQLGFVTVEKVIERLGIS-PATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHHHHHHCCCEEE
Confidence 3566677777788999999999999998 7777777776666777754
No 184
>KOG3438|consensus
Probab=20.86 E-value=2.6e+02 Score=22.27 Aligned_cols=42 Identities=19% Similarity=0.262 Sum_probs=33.7
Q ss_pred ecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 161 AIGRDINPGDVTNMITEFQAWSDSCANVLKAIETQIGKANSEK 203 (267)
Q Consensus 161 ~~~Rd~~~~q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~ 203 (267)
++.|+ +..-.+.|...|..-.+-|+.+.+..++++.+-+.++
T Consensus 62 IQt~~-~~~A~evl~kgl~el~~~c~~v~~kF~~~i~~~k~~~ 103 (105)
T KOG3438|consen 62 IQTRD-GDPAVEVLKKGLEELMQLCDHVRSKFEEEIEEYKDQK 103 (105)
T ss_pred EEecC-CCcchHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 34455 5566888999999999999999999999998766543
No 185
>TIGR03092 SASP_sspI small, acid-soluble spore protein I. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. It is a minor SASP (small, acid-soluble spore protein) designated SspI. The gene in Bacillus subtilis previously was designated ysfA.
Probab=20.83 E-value=1.2e+02 Score=22.05 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=18.2
Q ss_pred HHHHhCCCChhhHHHHHHHHHhcC
Q psy10889 120 LLKELDISNVRDLEDLIIEAIYSD 143 (267)
Q Consensus 120 I~~~L~I~~~~evE~lvI~aI~~g 143 (267)
|+..+.=++.+++|+.|.+||.+|
T Consensus 6 i~~nv~~~s~~elk~~I~daI~sg 29 (65)
T TIGR03092 6 ILANISNNTKEQLEATIVDAIQSG 29 (65)
T ss_pred HHHHhcCCCHHHHHHHHHHHHhcc
Confidence 444455556899999999999865
No 186
>cd00280 TRFH Telomeric Repeat binding Factor or TTAGGG Repeat binding Factor, central (dimerization) domain Homology; TRFH. Telomeres are protein/DNA complexes that make up the physical ends of eukaryotic linear chromosomes and are essential for chromosome stability, protecting the chromosome ends from degradation and end-to-end fusion. Proteins TRF1, TRF2 and Taz1 bind telomeric DNA and are also involved in recruiting interacting proteins, TIN2, and Rap1, to the telomeres. It has also been demonstrated that PARP1 associates with TRF2 and is capable of poly(ADP-ribosyl)ation of TRF2, which affects binding of TRF2 to telomeric DNA. TRF1, TRF2 and Taz1 proteins contain three functional domains: an N-terminal acidic domain, a central TRF-specific/dimerization domain, and a C-terminal DNA binding domain with a single Myb-like repeat. Homodimerization, a prerequisite to DNA binding, results in the juxtaposition of two Myb DNA binding domains.
Probab=20.71 E-value=1.3e+02 Score=26.66 Aligned_cols=48 Identities=21% Similarity=0.320 Sum_probs=36.6
Q ss_pred HHHHHHHhcCCHhHHHhhhhhc-----cCchhHHHHHHHHHhHHhhhcccCCc
Q psy10889 66 YHLLKLFAHGTYQDYLKQKEEL-----KLPEMTQLQKKKLQNLTIVTLSLESK 113 (267)
Q Consensus 66 ~~LL~lFa~Gt~~dy~~~~~~~-----~~p~L~~~~~~KLr~LtLlsLa~~~k 113 (267)
+.+.+.|..|.+.||....+-+ ....++..+..|+|..-.++-...++
T Consensus 18 ~~~c~aFR~~r~~dFr~~rdi~e~ll~~~~~~~a~~~k~l~i~QfLsRI~eG~ 70 (200)
T cd00280 18 HSACRAFREGRYEDFRRTRDIAEALLVGPLKLTATQLKTLRIMQFLSRIAEGK 70 (200)
T ss_pred HHHHHHHHccChHHHHHHHHHHHHHHhccccccccchhHhHHHHHHHHHHcCC
Confidence 4588999999999999886521 33456677889999999888776544
No 187
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=1.2e+02 Score=25.33 Aligned_cols=27 Identities=7% Similarity=0.015 Sum_probs=23.3
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
...||++|++.|+++ +..|...+-.|.
T Consensus 144 ~g~s~~EIA~~l~is-~~tV~~~l~rar 170 (181)
T PRK12536 144 EGLSVAETAQLTGLS-ESAVKVGIHRGL 170 (181)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 458999999999998 999988887664
No 188
>KOG2629|consensus
Probab=20.65 E-value=4.2e+02 Score=24.95 Aligned_cols=65 Identities=11% Similarity=0.196 Sum_probs=46.1
Q ss_pred HHHHHHHHhcCccEEEecCCCCeEEEEeecCCCCCCCc--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy10889 133 EDLIIEAIYSDIIHGKLDQRNSSLELDFAIGRDINPGD--VTNMITEFQAWSDSCANVLKAIETQIGKANSE 202 (267)
Q Consensus 133 E~lvI~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd~~~~q--~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~ 202 (267)
+.+++-+|.+|+.-|=.- |+=.|+.||-|+..+ .+.....|+.=-..+++.+..|+..+......
T Consensus 85 dy~vmAvi~aGi~y~~y~-----~~K~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q~ 151 (300)
T KOG2629|consen 85 DYFVMAVILAGIAYAAYR-----FVKSYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQL 151 (300)
T ss_pred HHHHHHHHHhhHHHHHHH-----HHHHHHHHHhhCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446778888886554321 122478899888654 57888888888888888888888877665543
No 189
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=20.65 E-value=1.3e+02 Score=27.04 Aligned_cols=44 Identities=7% Similarity=0.077 Sum_probs=32.3
Q ss_pred HhHHhhhcccCCcccCHHHHHHHhCCCChhhHHHHHHHHHhcCcc
Q psy10889 101 QNLTIVTLSLESKCIPYDKLLKELDISNVRDLEDLIIEAIYSDII 145 (267)
Q Consensus 101 r~LtLlsLa~~~k~IsY~~I~~~L~I~~~~evE~lvI~aI~~gLI 145 (267)
|+..|+.+...++.++..+|++.|+++ ...+-.=|...-..|+|
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TIRRDL~~Le~~g~l 49 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFDTT-GTTIRKDLVILEHAGTV 49 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHHHHHHHHHHHCCCE
Confidence 777788888888999999999999998 54444444444456644
No 190
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.40 E-value=1.2e+02 Score=25.39 Aligned_cols=27 Identities=4% Similarity=0.042 Sum_probs=23.5
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEAI 140 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~aI 140 (267)
.-.+|.+|++.|+++ +..|...+-.|.
T Consensus 146 ~g~s~~eIA~~lgis-~~tV~~~l~ra~ 172 (184)
T PRK12539 146 EGLSVAEAATRSGMS-ESAVKVSVHRGL 172 (184)
T ss_pred cCCcHHHHHHHHCcC-HHHHHHHHHHHH
Confidence 468999999999998 999998887764
No 191
>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=20.38 E-value=4.2e+02 Score=22.73 Aligned_cols=57 Identities=16% Similarity=0.265 Sum_probs=36.4
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhhcc
Q psy10889 170 DVTNMITEFQAWSDSCANVLKAIETQIGKANSEKHQHLAHSNAIDMEILNIKKSLKN 226 (267)
Q Consensus 170 q~~~L~~~L~~W~~~~~~vl~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~~ 226 (267)
....+...|..|+..+..=...+......+...-...-..=..++.+|+++...|+.
T Consensus 125 ~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I~~ 181 (184)
T PF05791_consen 125 KVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEIKK 181 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG-G
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHHHh
Confidence 456677777777777777777777766666665554445555667777777666654
No 192
>KOG3431|consensus
Probab=20.29 E-value=71 Score=26.24 Aligned_cols=22 Identities=14% Similarity=0.338 Sum_probs=19.9
Q ss_pred hhHHHHHHHHHhcCccEEEecC
Q psy10889 130 RDLEDLIIEAIYSDIIHGKLDQ 151 (267)
Q Consensus 130 ~evE~lvI~aI~~gLI~GkIDQ 151 (267)
..||.+||.++..|=|.|||+.
T Consensus 70 q~VE~~lirma~~gQvs~Kise 91 (129)
T KOG3431|consen 70 QAVENYLIRMAQTGQVSHKISE 91 (129)
T ss_pred HHHHHHHHHHHHhCCccccccH
Confidence 5799999999999999999964
No 193
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=20.19 E-value=1.1e+02 Score=25.81 Aligned_cols=26 Identities=8% Similarity=0.294 Sum_probs=22.7
Q ss_pred cccCHHHHHHHhCCCChhhHHHHHHHH
Q psy10889 113 KCIPYDKLLKELDISNVRDLEDLIIEA 139 (267)
Q Consensus 113 k~IsY~~I~~~L~I~~~~evE~lvI~a 139 (267)
...+|++|++.|+++ ...|...+-.|
T Consensus 157 ~~~s~~EIA~~Lgis-~~tVk~~l~ra 182 (194)
T PRK09646 157 GGLTYREVAERLAVP-LGTVKTRMRDG 182 (194)
T ss_pred cCCCHHHHHHHhCCC-hHhHHHHHHHH
Confidence 458999999999997 89998888766
Done!