Query 025901
Match_columns 246
No_of_seqs 204 out of 577
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 10:51:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3250 COP9 signalosome, subu 100.0 9.9E-63 2.1E-67 422.5 16.0 238 1-240 1-248 (258)
2 KOG2753 Uncharacterized conser 100.0 2.1E-32 4.6E-37 248.0 11.5 150 24-178 205-361 (378)
3 KOG2908 26S proteasome regulat 100.0 2.2E-31 4.7E-36 242.4 15.0 181 11-193 180-376 (380)
4 smart00753 PAM PCI/PINT associ 99.5 5.4E-14 1.2E-18 105.5 7.4 86 88-177 3-88 (88)
5 smart00088 PINT motif in prote 99.5 5.4E-14 1.2E-18 105.5 7.4 86 88-177 3-88 (88)
6 PF01399 PCI: PCI domain; Int 99.5 7.7E-14 1.7E-18 106.3 7.7 95 60-156 1-105 (105)
7 KOG1464 COP9 signalosome, subu 98.7 7.9E-08 1.7E-12 87.3 7.9 125 60-192 305-439 (440)
8 KOG2581 26S proteasome regulat 97.7 0.0002 4.3E-09 68.1 9.3 91 60-153 319-420 (493)
9 KOG1498 26S proteasome regulat 96.2 0.054 1.2E-06 51.6 10.8 127 59-197 287-429 (439)
10 KOG2758 Translation initiation 96.1 0.012 2.6E-07 54.9 5.7 95 92-193 332-426 (432)
11 KOG1497 COP9 signalosome, subu 95.4 0.03 6.5E-07 52.2 5.7 57 97-155 305-361 (399)
12 KOG0686 COP9 signalosome, subu 95.3 0.18 3.9E-06 48.4 10.5 99 61-161 307-415 (466)
13 COG5071 RPN5 26S proteasome re 94.9 0.14 3E-06 47.7 8.4 75 105-191 349-423 (439)
14 KOG2688 Transcription-associat 94.0 0.13 2.8E-06 49.2 6.3 98 59-157 271-385 (394)
15 KOG2582 COP9 signalosome, subu 92.7 0.87 1.9E-05 43.3 9.3 106 60-169 259-373 (422)
16 COG5600 Transcription-associat 92.0 0.48 1E-05 45.1 6.8 99 59-159 288-406 (413)
17 KOG1463 26S proteasome regulat 90.9 0.65 1.4E-05 43.9 6.4 113 44-158 270-392 (411)
18 PF09756 DDRGK: DDRGK domain; 90.1 0.43 9.4E-06 41.2 4.3 57 97-155 101-157 (188)
19 KOG2072 Translation initiation 89.2 8.5 0.00018 40.2 13.2 49 106-155 444-492 (988)
20 PF10075 PCI_Csn8: COP9 signal 89.1 3.7 7.9E-05 33.2 8.9 107 25-132 6-119 (143)
21 KOG0687 26S proteasome regulat 86.4 2.9 6.4E-05 39.4 7.4 64 92-157 300-363 (393)
22 COG5159 RPN6 26S proteasome re 86.0 5.9 0.00013 37.0 9.0 100 59-160 283-392 (421)
23 COG3355 Predicted transcriptio 85.3 8.4 0.00018 31.3 8.7 80 105-190 38-120 (126)
24 PRK04654 sec-independent trans 84.4 5.6 0.00012 35.0 7.8 61 161-222 19-79 (214)
25 PF09012 FeoC: FeoC like trans 82.0 1.3 2.8E-05 31.6 2.5 42 100-143 5-46 (69)
26 KOG3054 Uncharacterized conser 82.0 2.4 5.2E-05 38.2 4.7 54 100-155 205-258 (299)
27 PRK01919 tatB sec-independent 81.8 8.8 0.00019 32.7 7.8 61 161-222 19-79 (169)
28 TIGR01410 tatB twin arginine-t 81.1 6.3 0.00014 29.3 6.0 37 161-197 18-54 (80)
29 PF02082 Rrf2: Transcriptional 80.9 4.9 0.00011 29.4 5.4 58 95-155 11-68 (83)
30 smart00344 HTH_ASNC helix_turn 79.2 3.6 7.8E-05 31.2 4.3 42 100-143 8-49 (108)
31 PRK04098 sec-independent trans 77.5 17 0.00037 30.7 8.1 58 161-218 19-79 (158)
32 PRK11179 DNA-binding transcrip 77.0 3.9 8.5E-05 33.5 4.2 48 99-148 13-63 (153)
33 PRK01770 sec-independent trans 74.1 18 0.00038 31.0 7.4 36 161-196 19-54 (171)
34 TIGR02010 IscR iron-sulfur clu 72.1 10 0.00022 30.4 5.5 38 105-144 21-58 (135)
35 PF13412 HTH_24: Winged helix- 70.9 8.3 0.00018 25.0 3.9 42 99-142 7-48 (48)
36 COG1522 Lrp Transcriptional re 69.5 6.9 0.00015 31.4 3.9 42 101-144 14-55 (154)
37 PF07389 DUF1500: Protein of u 68.6 5.5 0.00012 30.5 2.8 36 100-138 39-74 (100)
38 PRK11169 leucine-responsive tr 68.3 9.8 0.00021 31.6 4.7 47 99-147 18-67 (164)
39 PRK14165 winged helix-turn-hel 68.2 24 0.00053 31.1 7.3 62 92-155 4-65 (217)
40 TIGR00738 rrf2_super rrf2 fami 66.5 22 0.00047 27.9 6.2 50 93-144 9-58 (132)
41 PRK10857 DNA-binding transcrip 65.3 15 0.00033 30.7 5.3 48 95-144 11-58 (164)
42 PRK04214 rbn ribonuclease BN/u 64.8 49 0.0011 31.6 9.3 60 106-174 307-366 (412)
43 PF13815 Dzip-like_N: Iguana/D 63.9 22 0.00048 28.0 5.7 95 110-221 18-118 (118)
44 PF08280 HTH_Mga: M protein tr 63.7 6.9 0.00015 27.0 2.5 35 96-131 6-40 (59)
45 COG1777 Predicted transcriptio 62.1 94 0.002 27.5 9.6 109 113-224 32-159 (217)
46 PF11945 WASH_WAHD: WAHD domai 61.8 70 0.0015 29.6 9.3 67 156-222 8-75 (297)
47 TIGR02944 suf_reg_Xantho FeS a 61.1 38 0.00082 26.6 6.7 37 106-144 22-58 (130)
48 smart00346 HTH_ICLR helix_turn 58.7 21 0.00045 25.8 4.5 46 96-143 6-52 (91)
49 PRK14858 tatA twin arginine tr 57.5 68 0.0015 25.3 7.3 37 161-197 19-55 (108)
50 PRK00708 sec-independent trans 56.7 50 0.0011 29.1 7.1 37 161-197 19-55 (209)
51 PF01726 LexA_DNA_bind: LexA D 56.5 21 0.00046 25.3 4.0 37 105-142 21-57 (65)
52 COG1959 Predicted transcriptio 55.6 31 0.00068 28.4 5.5 52 95-148 11-62 (150)
53 PRK10141 DNA-binding transcrip 54.1 26 0.00056 27.9 4.5 46 107-154 28-73 (117)
54 PF13404 HTH_AsnC-type: AsnC-t 54.0 9.2 0.0002 24.8 1.6 28 100-128 8-35 (42)
55 PF07106 TBPIP: Tat binding pr 53.5 1.3E+02 0.0028 24.9 13.4 115 105-221 12-133 (169)
56 PRK00404 tatB sec-independent 53.4 1E+02 0.0022 25.5 8.0 37 161-197 19-55 (141)
57 PF08279 HTH_11: HTH domain; 52.2 22 0.00047 23.5 3.3 34 97-131 2-36 (55)
58 PF03962 Mnd1: Mnd1 family; I 51.6 1.6E+02 0.0034 25.3 10.5 96 117-221 23-127 (188)
59 PF09339 HTH_IclR: IclR helix- 51.5 36 0.00079 22.4 4.3 45 96-142 4-49 (52)
60 PRK11920 rirA iron-responsive 50.6 40 0.00088 27.7 5.3 40 106-147 21-60 (153)
61 smart00550 Zalpha Z-DNA-bindin 50.4 26 0.00057 24.8 3.7 33 109-143 22-54 (68)
62 PRK11014 transcriptional repre 50.3 42 0.00092 26.9 5.3 51 95-147 11-61 (141)
63 PF08281 Sigma70_r4_2: Sigma-7 49.5 23 0.00049 23.3 3.1 27 108-136 25-51 (54)
64 cd00090 HTH_ARSR Arsenical Res 49.3 59 0.0013 21.6 5.3 36 110-147 21-56 (78)
65 PRK03573 transcriptional regul 48.6 1.3E+02 0.0029 23.7 8.2 56 101-158 38-93 (144)
66 PF03399 SAC3_GANP: SAC3/GANP/ 48.5 90 0.002 26.0 7.4 62 59-120 135-203 (204)
67 PF13730 HTH_36: Helix-turn-he 48.2 66 0.0014 21.1 5.3 47 93-141 7-55 (55)
68 KOG1076 Translation initiation 48.1 21 0.00044 37.0 3.7 96 62-159 657-766 (843)
69 PF12840 HTH_20: Helix-turn-he 48.1 35 0.00075 23.3 3.9 38 105-144 20-57 (61)
70 PF01325 Fe_dep_repress: Iron 46.6 48 0.001 23.0 4.4 42 99-142 12-53 (60)
71 PF13601 HTH_34: Winged helix 46.3 27 0.00058 25.7 3.3 51 98-150 3-53 (80)
72 cd06445 ATase The DNA repair p 45.4 29 0.00063 25.3 3.3 30 98-127 6-36 (79)
73 PF04545 Sigma70_r4: Sigma-70, 44.7 76 0.0016 20.5 5.0 28 107-136 18-45 (50)
74 PRK09954 putative kinase; Prov 44.1 29 0.00062 32.1 3.9 53 100-154 8-63 (362)
75 PF08220 HTH_DeoR: DeoR-like h 44.0 35 0.00077 23.2 3.4 41 98-140 3-43 (57)
76 smart00345 HTH_GNTR helix_turn 42.9 91 0.002 20.1 5.5 36 105-142 15-51 (60)
77 PF01022 HTH_5: Bacterial regu 42.8 65 0.0014 20.8 4.4 33 108-142 14-46 (47)
78 PF03979 Sigma70_r1_1: Sigma-7 42.2 21 0.00046 26.3 2.2 39 100-139 12-52 (82)
79 KOG3366 Mitochondrial F1F0-ATP 41.5 45 0.00098 28.5 4.3 80 154-238 53-139 (172)
80 PF14947 HTH_45: Winged helix- 41.1 77 0.0017 22.8 5.0 49 100-155 11-59 (77)
81 PF04967 HTH_10: HTH DNA bindi 40.1 1.2E+02 0.0026 20.7 5.7 27 105-132 19-45 (53)
82 COG5187 RPN7 26S proteasome re 39.4 34 0.00075 32.1 3.5 64 92-157 314-377 (412)
83 PHA01750 hypothetical protein 39.0 1.4E+02 0.003 21.7 5.8 35 186-220 38-72 (75)
84 PF09341 Pcc1: Transcription f 38.7 1.1E+02 0.0024 21.8 5.5 47 138-190 30-76 (76)
85 PF14480 DNA_pol3_a_NI: DNA po 38.5 1.1E+02 0.0025 21.5 5.5 61 111-176 2-62 (76)
86 COG4575 ElaB Uncharacterized c 38.0 1.6E+02 0.0034 23.2 6.5 56 159-220 2-57 (104)
87 PF13518 HTH_28: Helix-turn-he 37.6 46 0.001 21.3 3.1 31 99-132 4-34 (52)
88 smart00420 HTH_DEOR helix_turn 36.8 91 0.002 19.5 4.4 35 107-143 12-46 (53)
89 smart00418 HTH_ARSR helix_turn 36.7 1.1E+02 0.0025 19.5 5.1 38 107-146 8-45 (66)
90 PF05565 Sipho_Gp157: Siphovir 35.9 2.5E+02 0.0053 23.3 7.9 44 183-226 47-90 (162)
91 PF12802 MarR_2: MarR family; 35.7 1.2E+02 0.0025 20.1 5.0 40 108-149 20-59 (62)
92 PF12999 PRKCSH-like: Glucosid 35.3 1.8E+02 0.0039 24.9 7.1 48 175-222 124-171 (176)
93 PF08784 RPA_C: Replication pr 35.2 93 0.002 23.4 4.9 50 96-147 51-101 (102)
94 PRK00182 tatB sec-independent 35.0 1.4E+02 0.003 25.3 6.2 34 161-194 20-53 (160)
95 TIGR02919 accessory Sec system 35.0 1.3E+02 0.0028 29.2 6.9 87 112-202 341-433 (438)
96 KOG2629 Peroxisomal membrane a 34.6 1.6E+02 0.0035 27.3 7.0 82 129-219 86-169 (300)
97 PF05377 FlaC_arch: Flagella a 34.5 1.4E+02 0.0031 20.8 5.1 36 187-222 4-39 (55)
98 PRK10265 chaperone-modulator p 33.4 1.4E+02 0.003 22.9 5.6 38 106-149 4-41 (101)
99 PF04539 Sigma70_r3: Sigma-70 33.2 45 0.00098 23.6 2.7 26 106-132 17-42 (78)
100 PRK03100 sec-independent trans 32.5 2.5E+02 0.0054 23.1 7.2 34 161-194 20-53 (136)
101 PF08581 Tup_N: Tup N-terminal 32.0 2.1E+02 0.0046 21.2 8.6 56 166-221 12-74 (79)
102 PF01047 MarR: MarR family; I 32.0 71 0.0015 21.1 3.4 44 105-150 13-56 (59)
103 PF01978 TrmB: Sugar-specific 31.6 71 0.0015 22.0 3.4 38 106-145 19-56 (68)
104 PF09523 DUF2390: Protein of u 30.9 1.5E+02 0.0032 23.2 5.4 42 158-199 43-84 (109)
105 PF05791 Bacillus_HBL: Bacillu 30.8 2.2E+02 0.0047 24.1 6.9 59 165-223 124-182 (184)
106 KOG2166 Cullins [Cell cycle co 30.0 6.6E+02 0.014 26.3 11.5 118 95-221 566-695 (725)
107 PRK10870 transcriptional repre 29.7 3.3E+02 0.0072 22.7 8.1 50 106-157 68-117 (176)
108 PF01920 Prefoldin_2: Prefoldi 29.3 2.2E+02 0.0048 21.0 6.1 43 152-194 45-87 (106)
109 TIGR03879 near_KaiC_dom probab 29.3 52 0.0011 24.2 2.4 24 108-132 31-54 (73)
110 PF01638 HxlR: HxlR-like helix 28.0 2.4E+02 0.0053 20.6 6.7 75 98-180 9-85 (90)
111 PF05331 DUF742: Protein of un 27.9 1.1E+02 0.0025 24.2 4.3 48 85-142 39-86 (114)
112 cd00092 HTH_CRP helix_turn_hel 27.6 1.2E+02 0.0026 20.2 4.0 35 107-143 23-57 (67)
113 PF06163 DUF977: Bacterial pro 27.3 1.6E+02 0.0034 24.1 5.0 51 87-140 5-55 (127)
114 PF05615 THOC7: Tho complex su 27.2 3.2E+02 0.007 21.7 8.4 57 164-220 41-97 (139)
115 smart00419 HTH_CRP helix_turn_ 26.8 1.3E+02 0.0027 18.7 3.7 32 109-142 8-39 (48)
116 PF10828 DUF2570: Protein of u 26.2 2.6E+02 0.0056 21.6 6.1 56 171-226 38-93 (110)
117 PHA03158 hypothetical protein; 26.0 85 0.0018 27.6 3.5 62 157-220 209-270 (273)
118 PF09743 DUF2042: Uncharacteri 26.0 93 0.002 28.3 4.0 41 106-148 127-167 (272)
119 TIGR01884 cas_HTH CRISPR locus 25.5 1.9E+02 0.0042 24.5 5.7 52 100-154 148-199 (203)
120 PRK14857 tatA twin arginine tr 25.1 1.9E+02 0.0041 22.1 4.9 35 161-195 21-55 (90)
121 COG1595 RpoE DNA-directed RNA 24.9 82 0.0018 25.9 3.2 28 107-136 141-168 (182)
122 smart00347 HTH_MARR helix_turn 24.8 2.6E+02 0.0056 19.8 8.5 41 107-149 22-62 (101)
123 PRK15396 murein lipoprotein; P 24.7 3E+02 0.0064 20.4 7.3 49 165-213 25-73 (78)
124 PF10828 DUF2570: Protein of u 24.3 3.4E+02 0.0073 21.0 8.8 51 182-232 45-95 (110)
125 KOG3809 Microtubule-binding pr 24.2 2E+02 0.0044 28.3 6.0 60 161-220 503-562 (583)
126 PF07889 DUF1664: Protein of u 23.8 3.9E+02 0.0085 21.6 8.2 53 168-220 46-98 (126)
127 cd04784 HTH_CadR-PbrR Helix-Tu 23.6 2.3E+02 0.005 22.2 5.4 62 111-187 2-66 (127)
128 PRK10411 DNA-binding transcrip 23.5 1.2E+02 0.0027 26.7 4.2 46 95-142 4-49 (240)
129 PF02002 TFIIE_alpha: TFIIE al 23.4 76 0.0016 24.0 2.5 36 107-144 25-60 (105)
130 cd00632 Prefoldin_beta Prefold 22.9 2.9E+02 0.0063 20.9 5.8 37 156-192 50-86 (105)
131 TIGR02337 HpaR homoprotocatech 22.6 3.5E+02 0.0075 20.5 8.5 46 106-153 39-84 (118)
132 PF10668 Phage_terminase: Phag 22.6 96 0.0021 21.9 2.7 24 106-130 19-42 (60)
133 PF06013 WXG100: Proteins of 1 22.5 2E+02 0.0044 19.7 4.5 34 162-195 4-37 (86)
134 PF02416 MttA_Hcf106: mttA/Hcf 22.1 2.3E+02 0.0051 19.1 4.5 31 161-191 16-46 (53)
135 PF09218 DUF1959: Domain of un 22.1 32 0.00068 27.6 0.1 41 114-182 18-58 (117)
136 PRK14861 tatA twin arginine tr 22.0 2.1E+02 0.0045 20.2 4.3 33 161-193 20-52 (61)
137 KOG2235 Uncharacterized conser 21.8 1.8E+02 0.004 29.9 5.3 46 106-155 130-175 (776)
138 TIGR02999 Sig-70_X6 RNA polyme 21.7 1E+02 0.0023 25.0 3.3 27 108-136 149-175 (183)
139 PRK12537 RNA polymerase sigma 21.3 1E+02 0.0022 25.3 3.1 27 108-136 148-174 (182)
140 COG4741 Predicted secreted end 21.2 5.1E+02 0.011 22.0 8.3 33 188-220 47-79 (175)
141 cd06170 LuxR_C_like C-terminal 20.9 1.1E+02 0.0024 19.4 2.7 23 109-132 15-37 (57)
142 COG3413 Predicted DNA binding 20.8 2.9E+02 0.0063 23.6 6.0 80 61-143 127-209 (215)
143 PF13463 HTH_27: Winged helix 20.7 2.7E+02 0.0059 18.6 6.1 48 102-151 11-58 (68)
144 TIGR02702 SufR_cyano iron-sulf 20.7 5.2E+02 0.011 21.8 11.3 37 107-145 13-49 (203)
145 PF06056 Terminase_5: Putative 20.6 1.1E+02 0.0023 21.2 2.6 23 109-132 13-35 (58)
146 PF13384 HTH_23: Homeodomain-l 20.5 1E+02 0.0022 19.7 2.4 23 109-132 17-39 (50)
147 PF12324 HTH_15: Helix-turn-he 20.1 1.5E+02 0.0033 22.0 3.4 34 98-132 27-60 (77)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=9.9e-63 Score=422.51 Aligned_cols=238 Identities=40% Similarity=0.633 Sum_probs=232.7
Q ss_pred CchhHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 025901 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (246)
Q Consensus 1 ~~~~~~~~~~l~~f~~lak~a~~~aa~~li~~AL~~p~vf~F~eLL~~p~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~ 80 (246)
|++||++++.++||+++||+.+|+|...+|.+||.+|+||+|||||.+|+|.+|..+.++.+++||++||||||.||.++
T Consensus 1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae 80 (258)
T KOG3250|consen 1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE 80 (258)
T ss_pred CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999889999999999999999999999
Q ss_pred hCCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025901 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (246)
Q Consensus 81 ~~~l~~L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~R 160 (246)
+-.+|.|+++++.||++||++|||+..++|||..+.+.|.+.|+++|||+|| +|||+++++|||||.+|+++|.|+.+|
T Consensus 81 a~rlp~Ls~~q~~kLk~ltV~slas~~k~lpy~~Ll~~l~~~nvrelEd~ii-eamya~IlrGkldqr~q~leV~faigR 159 (258)
T KOG3250|consen 81 ALRLPKLSLAQLNKLKHLTVVSLASFEKCLPYLVLLRLLPSRNVRELEDLII-EAMYADILRGKLDQRNQTLEVDFAIGR 159 (258)
T ss_pred hhcCCCCCHHHHHhhhcceehhhhhhchhhhHHHHHhhccCCchhHHHHHHH-HHHHHHHHHhhHHhhcceEeechhhcc
Confidence 9999999999999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcch----------hccccCCC
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH----------KLHTVSRP 230 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~----------~~~~~~~~ 230 (246)
|+++.++++|..+|++||+.|+++|-.|++++.|||++++...+++++.|.+|.++||++|. +|.+++ |
T Consensus 160 dlr~k~i~nm~~TL~~w~~~cenvL~~ie~qv~~anq~~e~~~r~~qq~e~ev~~~kKtlk~~ad~d~~~~eq~l~ep-p 238 (258)
T KOG3250|consen 160 DLRSKDIDNMKYTLDEWCEGCENVLFGIEAQVPRANQSKERASRMSQQDEIEVMNFKKTLKPTADTDFQLNEQMLGEP-P 238 (258)
T ss_pred cccHhHHHHHHHHHHHHHHHHHHHHHHHHhccchhhhHHHHHHhhhhhhhhhHHhhhcccCCCccccccchHHHhCCC-C
Confidence 99999999999999999999999999999999999999999999999999999999999988 577787 8
Q ss_pred cccccccccc
Q 025901 231 TLTAEGTRRS 240 (246)
Q Consensus 231 ~~~~~~~~~~ 240 (246)
+|++.+++|.
T Consensus 239 ~~~qrqp~kk 248 (258)
T KOG3250|consen 239 VMDQRQPGKK 248 (258)
T ss_pred CccccCCCcC
Confidence 9999988764
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=99.98 E-value=2.1e-32 Score=247.98 Aligned_cols=150 Identities=28% Similarity=0.527 Sum_probs=139.3
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh----hCCCCC--c-chHHHHHHH
Q 025901 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN----AGHLPQ--L-VPDQVLKLK 96 (246)
Q Consensus 24 ~aa~~li~~AL~~p~vf~F~eLL~~p~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~--L-~~~~~~KLr 96 (246)
.+|.++|+.|+.+|++|.|+.|+.+|+|+.|+++. +|+||.||..|.+++|.++ ++++.. | .++..+|||
T Consensus 205 edA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMR 281 (378)
T KOG2753|consen 205 EDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMR 281 (378)
T ss_pred HHHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHH
Confidence 56999999999999999999999999999999875 8999999999999999874 344333 3 356789999
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025901 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (246)
Q Consensus 97 ~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~ 176 (246)
+||+++||+.++.|||++|+++|+|. .+|||.||| +||.+|+|.|||||.+++|.|+++.+|.||..||..|.++|..
T Consensus 282 LLTlm~LA~es~eisy~~l~k~LqI~-edeVE~fVI-daI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~kL~a 359 (378)
T KOG2753|consen 282 LLTLMSLAEESNEISYDTLAKELQIN-EDEVELFVI-DAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRDKLAA 359 (378)
T ss_pred HHHHHHHhccCCCCCHHHHHHHhccC-HHHHHHHHH-HHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHHHHHH
Confidence 99999999999999999999999996 999999999 9999999999999999999999999999999999999999999
Q ss_pred HH
Q 025901 177 WL 178 (246)
Q Consensus 177 W~ 178 (246)
|.
T Consensus 360 w~ 361 (378)
T KOG2753|consen 360 WG 361 (378)
T ss_pred HH
Confidence 96
No 3
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=2.2e-31 Score=242.39 Aligned_cols=181 Identities=18% Similarity=0.359 Sum_probs=163.5
Q ss_pred HHHHHHhc------ccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh---h
Q 025901 11 IDHFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN---A 81 (246)
Q Consensus 11 l~~f~~la------k~a~~~aa~~li~~AL~~p~vf~F~eLL~~p~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~---~ 81 (246)
.-.|+... .+.+...|.+|..+||.+.+||||||||.||+...|.||++.|++++|.+|+.||+..|... .
T Consensus 180 ~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~ 259 (380)
T KOG2908|consen 180 ALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVW 259 (380)
T ss_pred HHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHh
Confidence 34566666 55566889999999999999999999999999999999999999999999999999999874 3
Q ss_pred CCCCCcchHH---HHHHHHHHhhhccc----CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025901 82 GHLPQLVPDQ---VLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (246)
Q Consensus 82 ~~l~~L~~~~---~~KLr~LtllsLa~----~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V 154 (246)
+..|.|.... .+|+++++++-++. ..|.+||++|+++++|| .++||.+|| +|++.|||+|.|||++++|++
T Consensus 260 ~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~ 337 (380)
T KOG2908|consen 260 GKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYM 337 (380)
T ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEE
Confidence 4577776443 68999999998875 57999999999999998 999999998 999999999999999999999
Q ss_pred EeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 155 QFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (246)
Q Consensus 155 ~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~ 193 (246)
+|++||.++.+|+..|.+++..|++.+.++...++.+-+
T Consensus 338 swvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~~ 376 (380)
T KOG2908|consen 338 SWVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRGH 376 (380)
T ss_pred ecccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999999999999999999999987643
No 4
>smart00753 PAM PCI/PINT associated module.
Probab=99.50 E-value=5.4e-14 Score=105.45 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.6
Q ss_pred chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025901 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (246)
Q Consensus 88 ~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (246)
.+....|++.+++..++..+++|+|+.|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++|
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 35567899999999999999999999999999998 889999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 025901 168 GSMIQTLSNW 177 (246)
Q Consensus 168 ~~l~~~L~~W 177 (246)
..+.++|..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00753 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999999887
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=99.50 E-value=5.4e-14 Score=105.45 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.6
Q ss_pred chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025901 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (246)
Q Consensus 88 ~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (246)
.+....|++.+++..++..+++|+|+.|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++|
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~~ 78 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEPL 78 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhHH
Confidence 35567899999999999999999999999999998 889999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 025901 168 GSMIQTLSNW 177 (246)
Q Consensus 168 ~~l~~~L~~W 177 (246)
..+.++|..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00088 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999999887
No 6
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.49 E-value=7.7e-14 Score=106.34 Aligned_cols=95 Identities=20% Similarity=0.404 Sum_probs=80.7
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCC----------CCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHH
Q 025901 60 SKYLDMLRLFAHGTWSDYKNNAGH----------LPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (246)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~~~----------l~~L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~ 129 (246)
+|+.+|+++|..|++..|...-.. +..+.+....+++..++.+++...+.|+++.|++.|+++ .++||.
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 478999999999999999763221 122345568899999999999999999999999999998 899999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEe
Q 025901 130 FLINECMYTGIVRGKLDQLRRCFEVQF 156 (246)
Q Consensus 130 llI~~aI~~gLI~GkIDQ~~~~v~V~~ 156 (246)
+++ ++|..|.|.|+|||.+++|.++|
T Consensus 80 ~l~-~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILI-DLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHH-HHHHCCCEEEEEECCCCEEEecC
Confidence 999 99999999999999999999875
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.65 E-value=7.9e-08 Score=87.30 Aligned_cols=125 Identities=14% Similarity=0.360 Sum_probs=103.4
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCCC------CCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHH
Q 025901 60 SKYLDMLRLFAHGTWSDYKN----NAGHL------PQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (246)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~----~~~~l------~~L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~ 129 (246)
-.+.+|+..+...++..|+. |.+.+ -+..++.++++|.-.++.|..+...|....|+++|+|+ ..+||.
T Consensus 305 lAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~ 383 (440)
T KOG1464|consen 305 LAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVES 383 (440)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHH
Confidence 44788999999999999986 33332 22446678999999999999999999999999999998 999999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (246)
Q Consensus 130 llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i 192 (246)
+++ +||-.+-|+|+|||+++.+....... .-..+.+.|+.|.+.++++.+.|-.++
T Consensus 384 LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr~ 439 (440)
T KOG1464|consen 384 LLV-SCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSRV 439 (440)
T ss_pred HHH-HHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999 99999999999999999998764321 123478999999999998888776543
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.71 E-value=0.0002 Score=68.12 Aligned_cols=91 Identities=10% Similarity=0.346 Sum_probs=69.7
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCCCCC-cch----HHHHHHHH------HHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025901 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-LVP----DQVLKLKQ------LTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (246)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~~~l~~-L~~----~~~~KLr~------LtllsLa~~~k~isy~~I~~~L~i~~~~evE 128 (246)
.+|+.|=+..-.||++-|....+.+.+ +-. ..+..||+ +..+|| .++.|||.+|+..|+++|..++|
T Consensus 319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISl--sYSRISl~DIA~kL~l~Seed~E 396 (493)
T KOG2581|consen 319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISL--SYSRISLQDIAKKLGLNSEEDAE 396 (493)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheee--eeeeccHHHHHHHhcCCCchhHH
Confidence 569999999999999999875433322 111 11334444 223333 58899999999999999999999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEE
Q 025901 129 DFLINECMYTGIVRGKLDQLRRCFE 153 (246)
Q Consensus 129 ~llI~~aI~~gLI~GkIDQ~~~~v~ 153 (246)
.+|- +||+.|+|+|+||..++.+.
T Consensus 397 yiVa-kAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 397 YIVA-KAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred HHHH-HHHHhccceeeeccccCcee
Confidence 9998 99999999999999999554
No 9
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=96.19 E-value=0.054 Score=51.60 Aligned_cols=127 Identities=20% Similarity=0.294 Sum_probs=92.3
Q ss_pred chHHHHHHHHHhcCChhhHhhhh---------CCCCC---cchHHH--HHHHH--HHhhhcccCCcccChHHHHHHcCCC
Q 025901 59 NSKYLDMLRLFAHGTWSDYKNNA---------GHLPQ---LVPDQV--LKLKQ--LTVLTLAETNKVLPYDELMEELDVT 122 (246)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~---------~~l~~---L~~~~~--~KLr~--LtllsLa~~~k~isy~~I~~~L~i~ 122 (246)
.+.+-.+|.+|..|-+--|.... +.+.. ..+... .+.|. .-+--.|.=+.+||+..+++-|+.|
T Consensus 287 ~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~ 366 (439)
T KOG1498|consen 287 LPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLP 366 (439)
T ss_pred CccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCC
Confidence 45678899999988765554211 11111 111111 22222 3333445568899999999999998
Q ss_pred ChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025901 123 NVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (246)
Q Consensus 123 ~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~ 197 (246)
+++.|.++= +.+..|.+.+|||+..+.+..... ..+.+-|..|..+++++++.++..-+-+.+
T Consensus 367 -~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~ll~K~~HLI~K 429 (439)
T KOG1498|consen 367 -VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGLLEKVSHLIHK 429 (439)
T ss_pred -HHHHHHHHH-HHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 999999998 899999999999999999987654 347889999999999999998866555554
No 10
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=96.06 E-value=0.012 Score=54.95 Aligned_cols=95 Identities=17% Similarity=0.240 Sum_probs=74.1
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHH
Q 025901 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI 171 (246)
Q Consensus 92 ~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~ 171 (246)
+..-|++-.=+.|.-+.+|+.+.+|+.|+++ .++.|.|++ +.|+...|++|||..-+.|.+..... .--+.++
T Consensus 332 ~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~~~~-----s~~qQ~i 404 (432)
T KOG2758|consen 332 LENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGHPTV-----SPHQQLI 404 (432)
T ss_pred HHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecCCCC-----CHHHHHH
Confidence 3455666666777788999999999999997 999999999 89999999999999999988764332 2245567
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 025901 172 QTLSNWLTTSDNLLISIQEKIK 193 (246)
Q Consensus 172 ~~L~~W~~~~~~vl~~Ie~~i~ 193 (246)
++-....-+...+-..++..++
T Consensus 405 e~tksLS~rsq~la~~lek~~~ 426 (432)
T KOG2758|consen 405 EKTKSLSFRSQNLAQQLEKKIQ 426 (432)
T ss_pred HhccccchhHHHHHHHHHHHHH
Confidence 7766666666666666665543
No 11
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.43 E-value=0.03 Score=52.20 Aligned_cols=57 Identities=14% Similarity=0.290 Sum_probs=50.8
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 97 ~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
-..|+++++-...|+|+++...|+|+ .+.+|...= +.|..|-+.|.|||.++.+++.
T Consensus 305 EhNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe 361 (399)
T KOG1497|consen 305 EHNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFE 361 (399)
T ss_pred HHhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeec
Confidence 34566666667889999999999998 999999998 8999999999999999999975
No 12
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.30 E-value=0.18 Score=48.43 Aligned_cols=99 Identities=16% Similarity=0.253 Sum_probs=74.6
Q ss_pred HHHHHHHHHhcCChhhHhh----hhCCCC---Ccch---HHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025901 61 KYLDMLRLFAHGTWSDYKN----NAGHLP---QLVP---DQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (246)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~----~~~~l~---~L~~---~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~l 130 (246)
.+.++|.-|..+.|.--.. .++.+- -|.| ....++|.=.++.--.+...++++.++.+.+.+ +..+|.=
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 3556666666666654332 122110 1222 235788888888888899999999999999997 9999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeecCCC
Q 025901 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRD 161 (246)
Q Consensus 131 lI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rd 161 (246)
+. +.|-.|.|.||||+.++++++.-+..|.
T Consensus 386 l~-~LI~~~~i~~rIDs~~ki~~~~~~~~en 415 (466)
T KOG0686|consen 386 LL-ELILEGKISGRIDSHNKILYARDADSEN 415 (466)
T ss_pred HH-HHHHccchheeeccccceeeeccccccc
Confidence 99 9999999999999999999997665554
No 13
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=94.94 E-value=0.14 Score=47.68 Aligned_cols=75 Identities=16% Similarity=0.256 Sum_probs=65.2
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL 184 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~v 184 (246)
.=++.|+-..|..-++.+ ..+.|.+|- +.+..|.+.+||++..+.+.+... ++..+.|..|..+++.+
T Consensus 349 ~yYSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK~----------~n~~~~lneW~~NV~el 416 (439)
T COG5071 349 NYYSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEKS----------QNVQEQLNEWGSNVTEL 416 (439)
T ss_pred HHhhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeecc----------ccHHHHHHHhcccHHHH
Confidence 446789999999999998 999999998 899999999999999999987643 24678899999999999
Q ss_pred HHHHHHH
Q 025901 185 LISIQEK 191 (246)
Q Consensus 185 l~~Ie~~ 191 (246)
+..++.-
T Consensus 417 lgklek~ 423 (439)
T COG5071 417 LGKLEKV 423 (439)
T ss_pred HHHHHHH
Confidence 9988753
No 14
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=94.04 E-value=0.13 Score=49.17 Aligned_cols=98 Identities=14% Similarity=0.181 Sum_probs=70.5
Q ss_pred chHHHHHHHHHhcCChhhHhhh----hCCCCCcchH-HHHHHHHHHhhhcc-------cCCcccChHHHHHHcCCCC---
Q 025901 59 NSKYLDMLRLFAHGTWSDYKNN----AGHLPQLVPD-QVLKLKQLTVLTLA-------ETNKVLPYDELMEELDVTN--- 123 (246)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~L~~~-~~~KLr~LtllsLa-------~~~k~isy~~I~~~L~i~~--- 123 (246)
-..+-.|++....||+..|... ...+....-- .+.|++.++.=.|. .+...+|++.+..++....
T Consensus 271 ~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~ 350 (394)
T KOG2688|consen 271 LDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTD 350 (394)
T ss_pred HHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCC
Confidence 3467788999999999999752 2211111100 12234444333332 2678999999999998875
Q ss_pred --hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025901 124 --VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (246)
Q Consensus 124 --~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~ 157 (246)
.+|||-.+. .+|+.|.|+|.|+...+++.+...
T Consensus 351 ~~~deveciLa-~lI~~G~ikgYish~~~~~V~sK~ 385 (394)
T KOG2688|consen 351 VDLDEVECILA-NLIDLGRIKGYISHQLQTLVFSKK 385 (394)
T ss_pred CchhhHHHHHH-hhhhhccccchhchhhheEEEecC
Confidence 799999999 899999999999999999998754
No 15
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=92.67 E-value=0.87 Score=43.32 Aligned_cols=106 Identities=11% Similarity=0.249 Sum_probs=77.5
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCCCC-----CcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025901 60 SKYLDMLRLFAHGTWSDYKN----NAGHLP-----QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (246)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~----~~~~l~-----~L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~l 130 (246)
.+|.++++++..+.-..... +++.+- .|....+.-+..-+|..|-..-.+++.++|++..++.+..|||..
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 36999999999988776553 232221 133333445555667777777788999999997777778999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHH
Q 025901 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (246)
Q Consensus 131 lI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~ 169 (246)
|+ ..|..|=|...|| |-|..+.-..-+..|+...+
T Consensus 339 Il-qmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n 373 (422)
T KOG2582|consen 339 IL-QMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN 373 (422)
T ss_pred HH-HHhccCceEEEec---ceEEEecCcccCCCHHHHhh
Confidence 99 8999999999999 77777666666666665544
No 16
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=92.02 E-value=0.48 Score=45.07 Aligned_cols=99 Identities=20% Similarity=0.310 Sum_probs=65.3
Q ss_pred chHHHHHHHHHhcCChhhHhhhh----CCCCC------cc---hH-HHHHHHHHHhhhcccCCcccChHHHHHHcCCCC-
Q 025901 59 NSKYLDMLRLFAHGTWSDYKNNA----GHLPQ------LV---PD-QVLKLKQLTVLTLAETNKVLPYDELMEELDVTN- 123 (246)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~----~~l~~------L~---~~-~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~- 123 (246)
.+.+--|.++.-+|++++|.... ..+.+ |. |. ..+.|.. -+..++-+...+|++.+...++++.
T Consensus 288 ~s~~~~LvkavrsGni~~~~~~l~~ner~~~~~~l~ltl~~~~~~V~~RNL~r-k~w~~~~~qsrlp~sil~~~~qls~~ 366 (413)
T COG5600 288 CSVYSPLVKAVRSGNIEDFDLALSRNERKFAKRGLYLTLLAHYPLVCFRNLFR-KIWRLHGKQSRLPLSILLIVLQLSAI 366 (413)
T ss_pred cchhHHHHHHHHcCCHHHHHHHHHHhHHHHHHcchHHHHHhhccHHHHHHHHH-HHHhhccccccCcHHHHHHHHHccCC
Confidence 45667788999999999997521 11110 00 11 1122211 2233333455577777666666642
Q ss_pred -----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025901 124 -----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (246)
Q Consensus 124 -----~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~ 159 (246)
.++||-.++ .+|..|+++|.|....+++.+....|
T Consensus 367 dn~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 367 DNFHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred CcccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence 578999999 89999999999999999999986543
No 17
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=90.94 E-value=0.65 Score=43.86 Aligned_cols=113 Identities=15% Similarity=0.243 Sum_probs=79.6
Q ss_pred hhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhhCCCC-Ccc-----hHHHH----HHHHHHhhhcccCCcccChH
Q 025901 44 EILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLP-QLV-----PDQVL----KLKQLTVLTLAETNKVLPYD 113 (246)
Q Consensus 44 eLL~~p~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~~~~l~-~L~-----~~~~~----KLr~LtllsLa~~~k~isy~ 113 (246)
.|+.-.......+..-..+...=+.|..-++.||..--..++ +|- ...+. .|=---|+.+.++..++..+
T Consensus 270 ~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~ 349 (411)
T KOG1463|consen 270 ALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEIS 349 (411)
T ss_pred HHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHH
Confidence 344333333344444455777778888889999986322222 232 22222 22223577778899999999
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 025901 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (246)
Q Consensus 114 ~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~ 158 (246)
-|++-+|++ +..||.=+= ..|-...+.|.|||-++++.|.--.
T Consensus 350 hIA~~IGl~-~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e~ 392 (411)
T KOG1463|consen 350 HIAEVIGLD-VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEEP 392 (411)
T ss_pred HHHHHHCCC-cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeCCC
Confidence 999999998 999999887 8888899999999999999997443
No 18
>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=90.13 E-value=0.43 Score=41.24 Aligned_cols=57 Identities=14% Similarity=0.268 Sum_probs=40.8
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 97 ~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
+-.++.....+++++.++|+.++++. ..++-+-|- +....|.|.|-||...+-|+|+
T Consensus 101 L~~Fi~yIK~~Kvv~ledla~~f~l~-t~~~i~ri~-~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 101 LQEFINYIKEHKVVNLEDLAAEFGLR-TQDVINRIQ-ELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHH-S--HHHHHHHHH-HHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHcceeeHHHHHHHcCCC-HHHHHHHHH-HHHHCCCceeeEcCCCCeEEec
Confidence 34566677789999999999999998 888888887 8999999999999999999987
No 19
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=89.24 E-value=8.5 Score=40.21 Aligned_cols=49 Identities=16% Similarity=0.212 Sum_probs=43.2
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
.+..|+|+.|.+-.-.=|.-++|.+++ +|...+.+..+||...++|.+.
T Consensus 444 iY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 444 IYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence 467888988887655556899999999 9999999999999999999987
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=89.13 E-value=3.7 Score=33.20 Aligned_cols=107 Identities=15% Similarity=0.189 Sum_probs=72.2
Q ss_pred HHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhHhhhhCCC---CC---cchHHHHHHHH
Q 025901 25 ALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNNAGHL---PQ---LVPDQVLKLKQ 97 (246)
Q Consensus 25 aa~~li~~AL~~p~vf~F~eLL~~p~v~~L~~-~~~~~~~~LL~iFa~Gt~~dy~~~~~~l---~~---L~~~~~~KLr~ 97 (246)
....+...+|..-.+-+|.-++..-+-...+. .+-..++.|.+.+-.|+|..|.+..... +. +.+.-..++|.
T Consensus 6 ~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~ 85 (143)
T PF10075_consen 6 IYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRE 85 (143)
T ss_dssp HHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHH
T ss_pred HHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence 33445555566666788888877444443343 4457788999999999999987732221 11 23444677888
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025901 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 98 LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI 132 (246)
=++-.+...+..|+.+.+++-||++ ..+++.++.
T Consensus 86 ~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~ 119 (143)
T PF10075_consen 86 RIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK 119 (143)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred HHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence 7777777789999999999999998 999999887
No 21
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=86.42 E-value=2.9 Score=39.38 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=56.2
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025901 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (246)
Q Consensus 92 ~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~ 157 (246)
.+-||...--.|-+..|.++.+-.|+..|++ ++-++.=+= +-|-+|-+++|||-++++|++++-
T Consensus 300 vREMR~rvY~QlLESYrsl~l~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNrp 363 (393)
T KOG0687|consen 300 VREMRRRVYAQLLESYRSLTLESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNRP 363 (393)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCCc
Confidence 5778887777888899999999999999997 888877776 778899999999999999999854
No 22
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=85.95 E-value=5.9 Score=37.03 Aligned_cols=100 Identities=16% Similarity=0.242 Sum_probs=72.9
Q ss_pred chHHHHHHHHHhcCChhhHhhhhCC-CCCcc-----hHHH----HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025901 59 NSKYLDMLRLFAHGTWSDYKNNAGH-LPQLV-----PDQV----LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (246)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~~~-l~~L~-----~~~~----~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE 128 (246)
-..+...-+.|..-++.||...-.. -|+|- ...+ .-|---.|+.+.++..++..+-|++-+|++ +.+||
T Consensus 283 I~am~avaea~~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiEPfs~VeishIa~viGld-t~qvE 361 (421)
T COG5159 283 IRAMLAVAEAFGNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIEPFSVVEISHIADVIGLD-TNQVE 361 (421)
T ss_pred HHHHHHHHHHhCCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcCcceeeehhHHHHHhccc-HHHHH
Confidence 3456667778888889999763222 22232 2221 122223566777899999999999999997 99999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025901 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (246)
Q Consensus 129 ~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~R 160 (246)
.=+- ..|-..++-|.+||.++++.|.-....
T Consensus 362 gKLs-qMILDKifyG~LDqg~gcLivy~ep~q 392 (421)
T COG5159 362 GKLS-QMILDKIFYGTLDQGDGCLIVYGEPAQ 392 (421)
T ss_pred HHHH-HHHHHHHHHhhhccCCceEEEeCCccc
Confidence 8887 788888999999999999999754433
No 23
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.29 E-value=8.4 Score=31.27 Aligned_cols=80 Identities=20% Similarity=0.345 Sum_probs=58.2
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE-EEec-CCCCEEEEEeecCCCCCCCcHHH-HHHHHHHHHHHH
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR-GKLD-QLRRCFEVQFAAGRDLRPGQLGS-MIQTLSNWLTTS 181 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~-GkID-Q~~~~v~V~~~~~Rdl~~~q~~~-l~~~L~~W~~~~ 181 (246)
+.++.++-++|++.|+++ -..|..-|= +.+..|+|. =|.. ...+..++... ++++++.. +...|..|++++
T Consensus 38 ~~~~~~tvdelae~lnr~-rStv~rsl~-~L~~~GlV~Rek~~~~~Ggy~yiY~~----i~~ee~k~~i~~~l~~w~~~~ 111 (126)
T COG3355 38 EENGPLTVDELAEILNRS-RSTVYRSLQ-NLLEAGLVEREKVNLKGGGYYYLYKP----IDPEEIKKKILKDLDEWYDKM 111 (126)
T ss_pred hhcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeeeeeeccCCCceeEEEec----CCHHHHHHHHHHHHHHHHHHH
Confidence 367889999999999997 778888876 899999987 3333 23333333323 34566654 688999999999
Q ss_pred HHHHHHHHH
Q 025901 182 DNLLISIQE 190 (246)
Q Consensus 182 ~~vl~~Ie~ 190 (246)
...+...+.
T Consensus 112 ~~~i~~~~~ 120 (126)
T COG3355 112 KQLIEEFEK 120 (126)
T ss_pred HHHHHHHhc
Confidence 888877653
No 24
>PRK04654 sec-independent translocase; Provisional
Probab=84.42 E-value=5.6 Score=35.01 Aligned_cols=61 Identities=18% Similarity=0.309 Sum_probs=42.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcch
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 222 (246)
.|+|+.|..+...+..|..++++....+.+.+.+--...+- ++.-+++...+.+++..+|.
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~El~~~EL-rk~l~~~~~~i~~~~~~lk~ 79 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELERELEAEEL-KRSLQDVQASLREAEDQLRN 79 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH-HHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999998888888777654443322 22233444555555555555
No 25
>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=81.98 E-value=1.3 Score=31.57 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=32.7
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G 143 (246)
|..+...++.+|+++|+.+++++ ...||.++= .-+..|-|+-
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~ 46 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEE
Confidence 44445578899999999999997 999999886 8898998873
No 26
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.98 E-value=2.4 Score=38.23 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=43.3
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
++....++++++.++|+.+.++. ..+.=+-+= +.+..|++.|-||...+-++|+
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lr-tqd~inriq-~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLR-TQDSINRIQ-ELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCcc-HHHHHHHHH-HHHHhhhheeeecCCCceEEec
Confidence 44555689999999999999998 444444444 5666899999999999999997
No 27
>PRK01919 tatB sec-independent translocase; Provisional
Probab=81.80 E-value=8.8 Score=32.66 Aligned_cols=61 Identities=10% Similarity=0.256 Sum_probs=42.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcch
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 222 (246)
.|+|+.++.+...+..|..++....+.+.+.+..--.. ++-++.+++++....+++.++..
T Consensus 19 V~GPekLP~~aRtlGk~i~k~Rr~~~d~K~ev~~E~e~-dElrk~~~~~e~~~~~v~~si~~ 79 (169)
T PRK01919 19 VIGPERLPRVARTAGALFGRAQRYINDVKAEVSREIEL-DELRKMKTDFESAARDVENTIHD 79 (169)
T ss_pred eeCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999988887765432 22333445555555555555433
No 28
>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=81.11 E-value=6.3 Score=29.34 Aligned_cols=37 Identities=11% Similarity=0.212 Sum_probs=31.5
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~ 197 (246)
.|+|+.++.+...+..|........+.+.+++...-.
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~e~~ 54 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDEELK 54 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHhc
Confidence 4789999999999999999999999888887765444
No 29
>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=80.89 E-value=4.9 Score=29.43 Aligned_cols=58 Identities=17% Similarity=0.230 Sum_probs=39.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 95 Lr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
++.|..+......+.++-.+|++.++++ ...|+.++= ....+|+|+.+= ..++.+...
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~~-G~~GGy~L~ 68 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESSR-GRGGGYRLA 68 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEET-STTSEEEES
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEecC-CCCCceeec
Confidence 3444444333345569999999999998 999999876 888999987552 344444443
No 30
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=79.24 E-value=3.6 Score=31.23 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=33.2
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G 143 (246)
|+.....+..+||.+|++.++++ ...+-..+- .....|+|.+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~ 49 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG 49 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence 33333445679999999999997 888888877 8888999883
No 31
>PRK04098 sec-independent translocase; Provisional
Probab=77.48 E-value=17 Score=30.67 Aligned_cols=58 Identities=19% Similarity=0.316 Sum_probs=43.9
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HhhHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA---DSMNEMDKKHRKDLEEKVEEAKK 218 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~---~~~~~~~~~~~~~~~~~~~~~k~ 218 (246)
.|+|+.++.+...+..|...+....+.+...+... ...+++..+-++.++...+++++
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 58999999999999999999888888876666543 33344445667777777777776
No 32
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=77.02 E-value=3.9 Score=33.49 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=37.9
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCC
Q 025901 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQL 148 (246)
Q Consensus 99 tllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G---kIDQ~ 148 (246)
.|+.+-..+...||.+|++.||++ ...|-.-+= +....|+|+| -+|..
T Consensus 13 ~Il~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~~ 63 (153)
T PRK11179 13 GILEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNPK 63 (153)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECHH
Confidence 344445667899999999999997 888887776 8888999984 45653
No 33
>PRK01770 sec-independent translocase; Provisional
Probab=74.12 E-value=18 Score=30.95 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=31.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD 196 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~ 196 (246)
.|+|+.+..+..++..|..++.++...+++.+.+--
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~E~ 54 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQEL 54 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 579999999999999999999999999888776543
No 34
>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=72.10 E-value=10 Score=30.36 Aligned_cols=38 Identities=13% Similarity=0.279 Sum_probs=32.8
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
..++.++-++|++.+++| ...|+.++= ..-.+|+|...
T Consensus 21 ~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s~ 58 (135)
T TIGR02010 21 AETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKSV 58 (135)
T ss_pred CCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEE
Confidence 345689999999999998 999999887 88889999853
No 35
>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=70.91 E-value=8.3 Score=24.99 Aligned_cols=42 Identities=19% Similarity=0.360 Sum_probs=30.6
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 99 tllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
.|+.+...+..+|-.+|++.++++ ...|-..+= +....|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 344444456679999999999997 888887765 888888875
No 36
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=69.52 E-value=6.9 Score=31.41 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=33.1
Q ss_pred hhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 101 lsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
+.+-+.+..+||.+|++.+|++ ...+=.-|= +....|+|+|.
T Consensus 14 L~~L~~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~ 55 (154)
T COG1522 14 LRLLQEDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGY 55 (154)
T ss_pred HHHHHHhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeE
Confidence 3333455559999999999997 888877776 88889999864
No 37
>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=68.60 E-value=5.5 Score=30.45 Aligned_cols=36 Identities=17% Similarity=0.499 Sum_probs=27.7
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhc
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYT 138 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~ 138 (246)
|..+-..-..+||++|-+. +||...||+||| +.+..
T Consensus 39 Iyrlftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~ 74 (100)
T PF07389_consen 39 IYRLFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLND 74 (100)
T ss_pred HHHHHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHh
Confidence 3334445567899999998 688999999999 77643
No 38
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.27 E-value=9.8 Score=31.55 Aligned_cols=47 Identities=13% Similarity=0.192 Sum_probs=37.4
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecC
Q 025901 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQ 147 (246)
Q Consensus 99 tllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G---kIDQ 147 (246)
.|+.+-+.+..+||.+|++.+|++ ...|-.-+= +....|+|+| .+|.
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~~~~~v~p 67 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQGYTALLNP 67 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEEEEEECH
Confidence 455555788999999999999997 778777665 8888999975 4554
No 39
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=68.25 E-value=24 Score=31.09 Aligned_cols=62 Identities=11% Similarity=0.165 Sum_probs=50.0
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 92 ~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
+.-|+.|.++........+|..+|++.++++ ...+=..|- +.-..|+|.-..+...+.+.++
T Consensus 4 ~~~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk-~LEe~GlI~R~~~~r~~~v~LT 65 (217)
T PRK14165 4 IEALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILK-QLEDEGYITRTIVPRGQLITIT 65 (217)
T ss_pred hHHHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEEcCCceEEEEC
Confidence 3456777777766677789999999999997 777777777 8888999999999877666665
No 40
>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=66.52 E-value=22 Score=27.88 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.5
Q ss_pred HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 93 ~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
.-++.|..+....+...++..+|++.+++| ...|...+= .....|+|...
T Consensus 9 ~al~~l~~la~~~~~~~~s~~eia~~~~i~-~~~v~~il~-~L~~~gli~~~ 58 (132)
T TIGR00738 9 YALRALLDLALNPDEGPVSVKEIAERQGIS-RSYLEKILR-TLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 345555555543345589999999999998 999999887 88889998753
No 41
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=65.33 E-value=15 Score=30.74 Aligned_cols=48 Identities=15% Similarity=0.280 Sum_probs=37.6
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 95 Lr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
|+.+..++....++.+|-++|++.+++| ..-|+.++- ..-.+|||...
T Consensus 11 l~~l~~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s~ 58 (164)
T PRK10857 11 VTAMLDVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeC
Confidence 3333444444456689999999999998 999999988 88999999973
No 42
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=64.75 E-value=49 Score=31.63 Aligned_cols=60 Identities=25% Similarity=0.338 Sum_probs=45.6
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHH
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTL 174 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L 174 (246)
.++.++-++|++.++++ .+.+++++= ....+|+|. +-++. .|+..||.+.=.+..+.+.+
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~-~~~~g------~~~l~rd~~~itL~dv~~~~ 366 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR-RGERG------QWVLARDLDSVPLAELYELF 366 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE-ecCCC------ceEecCCHHhCcHHHHHHhC
Confidence 56788999999999998 999999876 888899997 33321 37888887666666665543
No 43
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=63.90 E-value=22 Score=28.02 Aligned_cols=95 Identities=19% Similarity=0.215 Sum_probs=50.9
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCc--HHHHHHHHHHHH----HHHHH
Q 025901 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ--LGSMIQTLSNWL----TTSDN 183 (246)
Q Consensus 110 isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q--~~~l~~~L~~W~----~~~~~ 183 (246)
|.-+.|.++.+ ++.++.+|- ++.-|.|+.....- ..+|.= +-.|.+-.-+|. +.+..
T Consensus 18 iDvd~i~~~~D---i~~Lq~~i~------~vtf~~l~~e~~~~--------~~dp~~~klfrLaQl~ieYLl~~q~~L~~ 80 (118)
T PF13815_consen 18 IDVDRIVRELD---IDTLQENIE------NVTFCDLENEDCQH--------FVDPNFLKLFRLAQLSIEYLLHCQEYLSS 80 (118)
T ss_pred cCHHHHHhccC---HHHHHHHHH------hcceeccChhhccC--------CCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455666554 456776654 33445555544322 122221 112333334443 44555
Q ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcc
Q 025901 184 LLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (246)
Q Consensus 184 vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~ 221 (246)
.+..+++.+..++...++-++.-+...+++..+|+.+|
T Consensus 81 ~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~k 118 (118)
T PF13815_consen 81 QLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKESK 118 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 56666667777777666666666666677777777654
No 44
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=63.74 E-value=6.9 Score=26.97 Aligned_cols=35 Identities=29% Similarity=0.481 Sum_probs=25.2
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHH
Q 025901 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (246)
Q Consensus 96 r~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~ll 131 (246)
|++.|+.+....+.+++++|++.++++ .+.+-.-|
T Consensus 6 rq~~Ll~~L~~~~~~~~~ela~~l~~S-~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLKNKWITLKELAKKLNIS-ERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHHHTSBBHHHHHHHCTS--HHHHHHHH
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHCCC-HHHHHHHH
Confidence 445555555457899999999999997 77766554
No 45
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=62.10 E-value=94 Score=27.53 Aligned_cols=109 Identities=18% Similarity=0.267 Sum_probs=59.4
Q ss_pred HHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC-----E--------EEEE------eecCCCCCCCcHHHHHHH
Q 025901 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR-----C--------FEVQ------FAAGRDLRPGQLGSMIQT 173 (246)
Q Consensus 113 ~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~-----~--------v~V~------~~~~Rdl~~~q~~~l~~~ 173 (246)
.+|++.+|++.-.-+++|=+ .-.+|||+.+++-..+ . ++|+ |+...+....+++...-.
T Consensus 32 sEiS~~lgvsqkAVl~HL~~--LE~AGlveS~ie~~~Rg~~rKYY~Is~~~rleV~lsp~~f~~~~~~~~~~~l~~~r~~ 109 (217)
T COG1777 32 SEISRELGVSQKAVLKHLRI--LERAGLVESRIEKIPRGRPRKYYMISRNLRLEVTLSPNFFGAERFDLEEDDLESERSE 109 (217)
T ss_pred HHHHhhcCcCHHHHHHHHHH--HHHcCCchhhccccccCCCcceeeccCCeEEEEEecCcccceeccCccccchhhhhcc
Confidence 46888899985555677766 4578999999988777 3 3443 344444444434333222
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcchhc
Q 025901 174 LSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKL 224 (246)
Q Consensus 174 L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~ 224 (246)
+..-..+ ..-++.+..+...+|..-+.=-+.+.+++....++.+.+|-++
T Consensus 110 ~~~~~~s-~~~~~~l~srl~~~~~~~e~l~~~~~~L~~~~~el~~rik~~i 159 (217)
T COG1777 110 VSKLFKS-PEGISELISRLLEINREIEELSRAQTELQKQLNELMDRIKEEI 159 (217)
T ss_pred hhhhccc-chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 2111111 1112333344445555444545555555555566665555543
No 46
>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=61.82 E-value=70 Score=29.63 Aligned_cols=67 Identities=13% Similarity=0.131 Sum_probs=51.3
Q ss_pred eecCCCCCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcch
Q 025901 156 FAAGRDLRPGQ-LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (246)
Q Consensus 156 ~~~~Rdl~~~q-~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 222 (246)
-.++.|++.++ +..+.+.|+..-.-++.+.+.|.+++..-....+.=..+-...+++|+.++-+=|+
T Consensus 8 plI~~dLr~eEti~qi~~aL~~L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs~kA 75 (297)
T PF11945_consen 8 PLIPPDLRREETILQIADALEYLDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGSKKA 75 (297)
T ss_pred cccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 45788888765 77899999999999999999999998887776655555556666777777655444
No 47
>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=61.08 E-value=38 Score=26.62 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=32.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
.+..++..+|++.++++ ..-|...+= ....+|+|.+.
T Consensus 22 ~~~~~s~~eia~~l~is-~~~v~~~l~-~L~~~Gli~~~ 58 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLN-APTVSKILK-QLSLAGIVTSK 58 (130)
T ss_pred CCCCccHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 45679999999999998 999999887 88899999874
No 48
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=58.65 E-value=21 Score=25.85 Aligned_cols=46 Identities=24% Similarity=0.232 Sum_probs=35.3
Q ss_pred HHHHhhhcccCC-cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025901 96 KQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (246)
Q Consensus 96 r~LtllsLa~~~-k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G 143 (246)
|.+.|+.+.... ..++..+|++.++++ ...|-..+- .....|+|..
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeee
Confidence 345555544433 689999999999998 888988877 7778898875
No 49
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=57.50 E-value=68 Score=25.34 Aligned_cols=37 Identities=11% Similarity=0.156 Sum_probs=31.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~ 197 (246)
.|+|+.++.+...+..|........+.+++.+..--.
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~E~~ 55 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQEESR 55 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5899999999999999999999999988887755444
No 50
>PRK00708 sec-independent translocase; Provisional
Probab=56.70 E-value=50 Score=29.12 Aligned_cols=37 Identities=11% Similarity=0.136 Sum_probs=32.1
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~ 197 (246)
.|+|+++..+...+..|..++..+.+.+.+++...-.
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 5799999999999999999999988888888776544
No 51
>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=56.53 E-value=21 Score=25.31 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=28.1
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
..+..-|+.+|++.+++.|...|-..|- ..-..|.|+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 3567789999999999998999988877 666777764
No 52
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=55.59 E-value=31 Score=28.36 Aligned_cols=52 Identities=21% Similarity=0.236 Sum_probs=39.1
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 025901 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (246)
Q Consensus 95 Lr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~ 148 (246)
++-|..++.-..++.++-++|++..+|+ ..-++.++- ..-.+|||+..=--.
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~-~L~kaGlV~S~rG~~ 62 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILS-KLRKAGLVKSVRGKG 62 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEeecCCC
Confidence 3444444444455588999999999997 999999998 899999988654433
No 53
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=54.10 E-value=26 Score=27.88 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=33.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V 154 (246)
....+..+|++.++++ ...|-.=+= ..-.+|||..+-+.......+
T Consensus 28 ~~~~~v~ela~~l~ls-qstvS~HL~-~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 28 SGELCVCDLCTALDQS-QPKISRHLA-LLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred cCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEEEEcCEEEEEE
Confidence 3568889999999998 666654443 456689999988866544444
No 54
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=53.96 E-value=9.2 Score=24.80 Aligned_cols=28 Identities=29% Similarity=0.449 Sum_probs=18.9
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHH
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELE 128 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE 128 (246)
|+.+-..+...||.+|++.+|++ ...|-
T Consensus 8 Il~~Lq~d~r~s~~~la~~lglS-~~~v~ 35 (42)
T PF13404_consen 8 ILRLLQEDGRRSYAELAEELGLS-ESTVR 35 (42)
T ss_dssp HHHHHHH-TTS-HHHHHHHHTS--HHHHH
T ss_pred HHHHHHHcCCccHHHHHHHHCcC-HHHHH
Confidence 44444566889999999999997 66653
No 55
>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=53.45 E-value=1.3e+02 Score=24.90 Aligned_cols=115 Identities=16% Similarity=0.178 Sum_probs=68.3
Q ss_pred cCCcccChHHHHHHcC--CCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHH
Q 025901 105 ETNKVLPYDELMEELD--VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~--i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~ 182 (246)
..+|..+..+|...|+ ++ =..|...+= .+...|.|.+|.-....+..+.-...-+.+++++..|-..+....+.+.
T Consensus 12 ~qNRPys~~di~~nL~~~~~-K~~v~k~Ld-~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~~el~ 89 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVG-KTAVQKALD-SLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAELDAEIKELREELA 89 (169)
T ss_pred HcCCCCcHHHHHHHHHhhcc-HHHHHHHHH-HHHhCCCeeeeeecceEEEeeCccccCCCCchhHHHHHHHHHHHHHHHH
Confidence 4788999999999995 44 355555554 6666899999976555333333233344568888888777777776665
Q ss_pred HHHHHHHH---HHHHHHhhH--HHHHHHHHHHHHHHHHHHHhcc
Q 025901 183 NLLISIQE---KIKWADSMN--EMDKKHRKDLEEKVEEAKKSLS 221 (246)
Q Consensus 183 ~vl~~Ie~---~i~~~~~~~--~~~~~~~~~~~~~~~~~k~~~~ 221 (246)
.+-..+.. .++..++.- ++-...-.+++.+++.+...+.
T Consensus 90 ~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL~ 133 (169)
T PF07106_consen 90 ELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKLE 133 (169)
T ss_pred HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55444433 333333322 2333444455555555555553
No 56
>PRK00404 tatB sec-independent translocase; Provisional
Probab=53.38 E-value=1e+02 Score=25.50 Aligned_cols=37 Identities=16% Similarity=0.274 Sum_probs=30.5
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~ 197 (246)
.|+++.+..+..++..|..++.+....+.+.+.+--.
T Consensus 19 V~GPkkLP~laR~lG~~i~~~rr~~~~~k~ei~~E~~ 55 (141)
T PRK00404 19 VLGPERLPGAARTAGLWIGRLKRSFNAIKQEVEREIG 55 (141)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 4799999999999999999988888777776665433
No 57
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=52.21 E-value=22 Score=23.52 Aligned_cols=34 Identities=32% Similarity=0.432 Sum_probs=23.6
Q ss_pred HHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHH
Q 025901 97 QLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFL 131 (246)
Q Consensus 97 ~LtllsLa-~~~k~isy~~I~~~L~i~~~~evE~ll 131 (246)
+..|+.+- .....+|-.+|++.|+++ .+.|..-|
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i 36 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS-RRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHH
Confidence 44444443 445559999999999997 87777654
No 58
>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=51.58 E-value=1.6e+02 Score=25.29 Aligned_cols=96 Identities=18% Similarity=0.142 Sum_probs=51.6
Q ss_pred HHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH---HH
Q 025901 117 EELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEK---IK 193 (246)
Q Consensus 117 ~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~---i~ 193 (246)
+++||. ...|.++|- ..+..|+|+. ..=|+-.+-|+-|- .....+...+......++.+-..+.+. +.
T Consensus 23 K~~gI~-~~~VKdvlq-~LvDDglV~~---EKiGssn~YWsFps----~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~i~ 93 (188)
T PF03962_consen 23 KEKGIV-SMSVKDVLQ-SLVDDGLVHV---EKIGSSNYYWSFPS----QAKQKRQNKLEKLQKEIEELEKKIEELEEKIE 93 (188)
T ss_pred cccCCc-hhhHHHHHH-HHhccccchh---hhccCeeEEEecCh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 447897 889999887 7777777652 13355667787543 444445555555554444444433332 22
Q ss_pred HHHhhH------HHHHHHHHHHHHHHHHHHHhcc
Q 025901 194 WADSMN------EMDKKHRKDLEEKVEEAKKSLS 221 (246)
Q Consensus 194 ~~~~~~------~~~~~~~~~~~~~~~~~k~~~~ 221 (246)
.+...+ .......++++.+++.+++.+.
T Consensus 94 ~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~ 127 (188)
T PF03962_consen 94 EAKKGREESEEREELLEELEELKKELKELKKELE 127 (188)
T ss_pred HHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 222211 1123334455555566665554
No 59
>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=51.49 E-value=36 Score=22.44 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=32.0
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 96 r~LtllsL-a~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
|-+.|+.. +.....++..+|++.++++ ...+-.++- .....|+|+
T Consensus 4 ral~iL~~l~~~~~~~t~~eia~~~gl~-~stv~r~L~-tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAESGGPLTLSEIARALGLP-KSTVHRLLQ-TLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHCTBSCEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCee
Confidence 33556653 4455668999999999998 878887776 667777664
No 60
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=50.57 E-value=40 Score=27.74 Aligned_cols=40 Identities=18% Similarity=0.128 Sum_probs=33.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ 147 (246)
.++.++-.+|++..+|| ..-|+.++- ..-.+|+|+..=-.
T Consensus 21 ~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~rG~ 60 (153)
T PRK11920 21 DGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETVRGR 60 (153)
T ss_pred CCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeecCC
Confidence 34568999999999998 999999988 88889999866543
No 61
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=50.43 E-value=26 Score=24.78 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=29.6
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025901 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (246)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G 143 (246)
.++-.+|+++|+++ ...|-..+- .....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~-~~~v~r~L~-~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLP-KKEVNRVLY-SLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 49999999999998 889999998 8999998864
No 62
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=50.30 E-value=42 Score=26.92 Aligned_cols=51 Identities=14% Similarity=0.194 Sum_probs=37.6
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025901 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (246)
Q Consensus 95 Lr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ 147 (246)
+|.+..+.-..++..+|-++|++.++|+ ..-|+..+- ..-..|+|+.+=--
T Consensus 11 l~~~i~la~~~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~G~ 61 (141)
T PRK11014 11 LRALIYMASLPEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVRGK 61 (141)
T ss_pred HHHHHHHhcCCCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEecCC
Confidence 3444444433456688999999999997 889999887 88888988765433
No 63
>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=49.51 E-value=23 Score=23.32 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=20.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025901 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (246)
Q Consensus 108 k~isy~~I~~~L~i~~~~evE~llI~~aI 136 (246)
.-.||.+|++.+|++ ...|..++- .|.
T Consensus 25 ~g~s~~eIa~~l~~s-~~~v~~~l~-ra~ 51 (54)
T PF08281_consen 25 QGMSYAEIAEILGIS-ESTVKRRLR-RAR 51 (54)
T ss_dssp S---HHHHHHHCTS--HHHHHHHHH-HHH
T ss_pred HCcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 568999999999997 999998886 664
No 64
>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=49.26 E-value=59 Score=21.60 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=30.5
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025901 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (246)
Q Consensus 110 isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ 147 (246)
+++.+|++.++++ ...+-..+- .....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~-~~~i~~~l~-~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLS-QSTVSRHLK-KLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcC-HhHHHHHHH-HHHHCCCeEEEEec
Confidence 9999999999997 888887765 77789999876665
No 65
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=48.56 E-value=1.3e+02 Score=23.69 Aligned_cols=56 Identities=9% Similarity=-0.024 Sum_probs=41.0
Q ss_pred hhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 025901 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (246)
Q Consensus 101 lsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~ 158 (246)
..+...+..++-.+|++.++++ ...|=..|- .....|+|.=.-|..+++...-+.+
T Consensus 38 ~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 38 HNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred HHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEEC
Confidence 3334333456789999999997 667777665 8888999999999877766555443
No 66
>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=48.50 E-value=90 Score=26.05 Aligned_cols=62 Identities=15% Similarity=0.226 Sum_probs=44.3
Q ss_pred chHHHHHHHHHhcCChhhHhhhh--CCCCCcch----HHHHHHHHHHhhhcccCCcc-cChHHHHHHcC
Q 025901 59 NSKYLDMLRLFAHGTWSDYKNNA--GHLPQLVP----DQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (246)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~--~~l~~L~~----~~~~KLr~LtllsLa~~~k~-isy~~I~~~L~ 120 (246)
....+++...+..|+|..|-... ...|.+.. .-..++|..++-+++...+. +|-+.+++-|+
T Consensus 135 i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~iR~~al~~i~~ay~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 135 IQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRIRLRALQSISKAYRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHHHHHHHHHHHHHS-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHcC
Confidence 45577899999999999988754 55554432 23678999888888887777 99999888775
No 67
>PF13730 HTH_36: Helix-turn-helix domain
Probab=48.20 E-value=66 Score=21.08 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=35.0
Q ss_pred HHHHHHHhhhcccC-Cccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 025901 93 LKLKQLTVLTLAET-NKVL-PYDELMEELDVTNVRELEDFLINECMYTGIV 141 (246)
Q Consensus 93 ~KLr~LtllsLa~~-~k~i-sy~~I~~~L~i~~~~evE~llI~~aI~~gLI 141 (246)
.|+-.+.|.+.+.+ +.+. |++.|++.++++ .+.|-..+= +....|+|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s-~~Tv~~~i~-~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVS-RRTVQRAIK-ELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCcCC
Confidence 35666777777752 2344 799999999997 999988876 77777765
No 68
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=48.10 E-value=21 Score=36.96 Aligned_cols=96 Identities=13% Similarity=0.267 Sum_probs=66.5
Q ss_pred HHHHHHHHhcCChhhHhh---h----hCCCCCcc--hHH-HHHHHHHH----hhhcccCCcccChHHHHHHcCCCChHHH
Q 025901 62 YLDMLRLFAHGTWSDYKN---N----AGHLPQLV--PDQ-VLKLKQLT----VLTLAETNKVLPYDELMEELDVTNVREL 127 (246)
Q Consensus 62 ~~~LL~iFa~Gt~~dy~~---~----~~~l~~L~--~~~-~~KLr~Lt----llsLa~~~k~isy~~I~~~L~i~~~~ev 127 (246)
+...=+....|+|.+-.. + ++-+|.-. -++ ..+++-=+ |.+.+.-+..+|.+.||+-.++| +..|
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 445556788899987444 2 23345421 111 23444322 34455568899999999999998 8888
Q ss_pred HHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025901 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (246)
Q Consensus 128 E~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~ 159 (246)
=..|= +.|-..=|.+++||..++|.++++.+
T Consensus 736 hsIiS-kmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 736 HSIIS-KMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred HHHHH-HHHHHHHhhhccCCCcceEEEeeccc
Confidence 77666 77777789999999999999997653
No 69
>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=48.07 E-value=35 Score=23.26 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=28.8
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
......+..+|++.++++ ...+-.=+= ....+|+|+..
T Consensus 20 ~~~~~~t~~ela~~l~~~-~~t~s~hL~-~L~~aGli~~~ 57 (61)
T PF12840_consen 20 ASNGPMTVSELAEELGIS-QSTVSYHLK-KLEEAGLIEVE 57 (61)
T ss_dssp HHCSTBEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEE
T ss_pred hcCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeEEe
Confidence 567889999999999998 766765554 56678988753
No 70
>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=46.65 E-value=48 Score=22.99 Aligned_cols=42 Identities=19% Similarity=0.326 Sum_probs=32.3
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 99 tllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
+|..|...+..++-.+|++.|+++ ...|=+.+= +.-..|+|.
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~-~L~~~GlV~ 53 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLK-RLAEKGLVE 53 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEE
Confidence 555555688999999999999997 777766665 777778775
No 71
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=46.34 E-value=27 Score=25.67 Aligned_cols=51 Identities=29% Similarity=0.315 Sum_probs=35.2
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025901 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (246)
Q Consensus 98 LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~ 150 (246)
|.|+++-.....++|.+|.+.|+++ ...+-.-+= ....+|+|+-+=.-..+
T Consensus 3 l~Il~~L~~~~~~~f~~L~~~l~lt-~g~Ls~hL~-~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 3 LAILALLYANEEATFSELKEELGLT-DGNLSKHLK-KLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HHHHHHHHHHSEEEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEE-SSS
T ss_pred HHHHHHHhhcCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCCCEEEEEeccCC
Confidence 4455544456789999999999997 777766655 67778999877655444
No 72
>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=45.37 E-value=29 Score=25.29 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=22.8
Q ss_pred HHhhhcccCCcccChHHHHHHcCCC-ChHHH
Q 025901 98 LTVLTLAETNKVLPYDELMEELDVT-NVREL 127 (246)
Q Consensus 98 LtllsLa~~~k~isy~~I~~~L~i~-~~~ev 127 (246)
+.++.-...++..||.+|++.++.+ +.+.|
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 4444445678999999999999996 45665
No 73
>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=44.73 E-value=76 Score=20.52 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=22.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI 136 (246)
....||.+|++.+|++ ...|-.+.- .|+
T Consensus 18 ~~~~t~~eIa~~lg~s-~~~V~~~~~-~al 45 (50)
T PF04545_consen 18 FEGLTLEEIAERLGIS-RSTVRRILK-RAL 45 (50)
T ss_dssp TST-SHHHHHHHHTSC-HHHHHHHHH-HHH
T ss_pred cCCCCHHHHHHHHCCc-HHHHHHHHH-HHH
Confidence 5678999999999997 888877665 665
No 74
>PRK09954 putative kinase; Provisional
Probab=44.09 E-value=29 Score=32.09 Aligned_cols=53 Identities=19% Similarity=0.453 Sum_probs=40.5
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCCCCEEEE
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQLRRCFEV 154 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G---kIDQ~~~~v~V 154 (246)
|+.+...+..+|+.+|++.|+++ ...|-..|- +....|+|.| .||....++.|
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~-~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIM-DLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCcCCcEEEEcCCccEEEE
Confidence 44555577799999999999997 889998876 8888899975 46666555433
No 75
>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=43.99 E-value=35 Score=23.21 Aligned_cols=41 Identities=22% Similarity=0.253 Sum_probs=28.6
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCc
Q 025901 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (246)
Q Consensus 98 LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gL 140 (246)
-.|+.+....+.++..+|++.++++ ..-+-.=+. ..-..|+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~ 43 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGL 43 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCC
Confidence 3456666778899999999999997 655544443 4444555
No 76
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=42.89 E-value=91 Score=20.11 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=29.1
Q ss_pred cCCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 105 ETNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 105 ~~~k~i-sy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
..+..+ |..+|++.++++ ...|-..+- .....|+|.
T Consensus 15 ~~~~~l~s~~~la~~~~vs-~~tv~~~l~-~L~~~g~i~ 51 (60)
T smart00345 15 RPGDKLPSERELAAQLGVS-RTTVREALS-RLEAEGLVQ 51 (60)
T ss_pred CCCCcCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 345567 899999999996 888888877 777788875
No 77
>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=42.78 E-value=65 Score=20.78 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=24.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 108 k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
+..+..+|++.++++ ...|-.-+= .....|+|+
T Consensus 14 ~~~~~~el~~~l~~s-~~~vs~hL~-~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLS-QSTVSHHLK-KLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred CCCchhhHHHhcccc-chHHHHHHH-HHHHCcCee
Confidence 778999999999997 777765554 566677764
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=42.23 E-value=21 Score=26.27 Aligned_cols=39 Identities=15% Similarity=0.296 Sum_probs=24.5
Q ss_pred hhhcccCCcccChHHHHHHcCC--CChHHHHHHHHHHhHhcC
Q 025901 100 VLTLAETNKVLPYDELMEELDV--TNVRELEDFLINECMYTG 139 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i--~~~~evE~llI~~aI~~g 139 (246)
|+..+...+.|+|++|...|.= -+.+.++.++- ..-..|
T Consensus 12 Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~-~L~~~g 52 (82)
T PF03979_consen 12 LIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYD-TLEDEG 52 (82)
T ss_dssp HHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHH-HHHTT-
T ss_pred HHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHH-HHHHCC
Confidence 6777777788999999999971 13677777655 444444
No 79
>KOG3366 consensus Mitochondrial F1F0-ATP synthase, subunit d/ATP7 [Energy production and conversion]
Probab=41.49 E-value=45 Score=28.49 Aligned_cols=80 Identities=14% Similarity=0.111 Sum_probs=39.5
Q ss_pred EEeecCCCCCCCcHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcchhccc
Q 025901 154 VQFAAGRDLRPGQLGSMIQTLSNWLTTSD-------NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKLHT 226 (246)
Q Consensus 154 V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~-------~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~ 226 (246)
|+|+..|-.= .-..+.++++.=.+++. ..+..|++..+.+.. .-..+......++.+++|.+..-...
T Consensus 53 IDwa~Yrk~v--a~a~~VD~~ek~y~slk~v~~~~~ky~~~vda~~k~~~~---~~ke~~~~s~~~iq~l~k~le~v~~~ 127 (172)
T KOG3366|consen 53 IDWAYYRKVV--ANAGLVDKYEKKYDSLKPVPVDEDKYLKEVDAEEKAAVK---EIKEYESLSKKRIQELEKELEKVKSA 127 (172)
T ss_pred cCHHHHHHHh--hhhHHHHHHHHHHHhccccCCCHHHHHHHhhHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4555544321 22234444444444443 455666666555555 33344455556666666666543333
Q ss_pred cCCCcccccccc
Q 025901 227 VSRPTLTAEGTR 238 (246)
Q Consensus 227 ~~~~~~~~~~~~ 238 (246)
-+-..||+++..
T Consensus 128 ~P~demT~ed~~ 139 (172)
T KOG3366|consen 128 RPFDEMTMEDLN 139 (172)
T ss_pred CCcccccHHHHH
Confidence 345556665543
No 80
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=41.14 E-value=77 Score=22.83 Aligned_cols=49 Identities=14% Similarity=0.260 Sum_probs=33.1
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
|+..+. ....++..|+..++++ ...+...+= ..+..|+|++ .++.+.+|
T Consensus 11 IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~-~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 11 ILKILS-KGGAKKTEIMYKANLN-YSTLKKYLK-ELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHH--TT-B-HHHHHTTST---HHHHHHHHH-HHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCcCeeC----CCCEEEEC
Confidence 333343 6778899999999997 999998886 8999999944 45555554
No 81
>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=40.10 E-value=1.2e+02 Score=20.72 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=20.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI 132 (246)
..-|.++..+|+++|||+ ...+-.-+=
T Consensus 19 d~PR~~tl~elA~~lgis-~st~~~~LR 45 (53)
T PF04967_consen 19 DVPRRITLEELAEELGIS-KSTVSEHLR 45 (53)
T ss_pred CCCCcCCHHHHHHHhCCC-HHHHHHHHH
Confidence 356899999999999997 666655443
No 82
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=39.42 E-value=34 Score=32.11 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=53.1
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025901 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (246)
Q Consensus 92 ~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~ 157 (246)
.+-||.=.-..|-+..|.++.+..|+..+++ ++-|+.=+= +-|-.|-+.+.||-++++|++++-
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg-~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLG-EFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHH-hhCCCCceeeeeecccceEeccCc
Confidence 4666666666777889999999999999997 888876666 677789999999999999998854
No 83
>PHA01750 hypothetical protein
Probab=38.96 E-value=1.4e+02 Score=21.72 Aligned_cols=35 Identities=23% Similarity=0.252 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 186 ISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 186 ~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
..+.....+...+-+.-...++++++.|.++|+-+
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 34455666666666666678888999999999865
No 84
>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=38.67 E-value=1.1e+02 Score=21.80 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=37.5
Q ss_pred cCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 138 TGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190 (246)
Q Consensus 138 ~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~ 190 (246)
.+-++..++-.++.+.|.+.. .+...|...+..|...+.-+...+++
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 367888999999999999876 56789999999999988877777653
No 85
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=38.46 E-value=1.1e+02 Score=21.50 Aligned_cols=61 Identities=11% Similarity=0.165 Sum_probs=46.7
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025901 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (246)
Q Consensus 111 sy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~ 176 (246)
.|..+.+.+++++. ...++.= + +.+-+-.++..+++.++....++.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~~-~~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPDE-LDNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCch-hhhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 36788899999832 2344333 3 245668999999999999999999999999888887764
No 86
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=37.98 E-value=1.6e+02 Score=23.18 Aligned_cols=56 Identities=20% Similarity=0.330 Sum_probs=34.0
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 159 GRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 159 ~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
+|.+.+..++.+..-|+.-.++++.++.. +......+..+-|..++..+.++++.+
T Consensus 2 ~~~~~~~~~~~l~~el~~L~d~lEevL~s------sg~~a~~e~~~lR~r~~~~Lk~~r~rl 57 (104)
T COG4575 2 SREFTDDAIDQLLAELQELLDTLEEVLKS------SGSLAGDEAEELRSKAESALKEARDRL 57 (104)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHh------cccchhhHHHHHHHHHHHHHHHHHHHH
Confidence 56777777777777777777766666654 222233444555555666666666655
No 87
>PF13518 HTH_28: Helix-turn-helix domain
Probab=37.64 E-value=46 Score=21.34 Aligned_cols=31 Identities=10% Similarity=0.200 Sum_probs=23.6
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025901 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 99 tllsLa~~~k~isy~~I~~~L~i~~~~evE~llI 132 (246)
.++.+...+ . |+.++++.++|+ ...|-.|+-
T Consensus 4 ~iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~ 34 (52)
T PF13518_consen 4 QIVELYLEG-E-SVREIAREFGIS-RSTVYRWIK 34 (52)
T ss_pred HHHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH
Confidence 344444443 3 999999999995 999999976
No 88
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=36.83 E-value=91 Score=19.52 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=27.3
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G 143 (246)
+..++-.+|++.++++ ...+...+= .....|+|.-
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~ 46 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTR 46 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 4569999999999996 888887765 6666677653
No 89
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=36.67 E-value=1.1e+02 Score=19.49 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=29.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkID 146 (246)
...+++.+|++.++++ ...+-..+= .....|+|.-.=+
T Consensus 8 ~~~~~~~~i~~~l~is-~~~v~~~l~-~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLS-QSTVSHHLK-KLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCC-HHHHHHHHH-HHHHCCCeeeeec
Confidence 5678999999999997 777777664 7777899874433
No 90
>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=35.90 E-value=2.5e+02 Score=23.33 Aligned_cols=44 Identities=11% Similarity=0.268 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcchhccc
Q 025901 183 NLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKLHT 226 (246)
Q Consensus 183 ~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~ 226 (246)
.++..++..+....++..+-..+++..+.++..+|..+...|..
T Consensus 47 ~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL~~~m~~ 90 (162)
T PF05565_consen 47 KVIKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYLLDAMEA 90 (162)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444445555555555566667778888888888888776554
No 91
>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=35.66 E-value=1.2e+02 Score=20.10 Aligned_cols=40 Identities=20% Similarity=0.236 Sum_probs=31.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025901 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (246)
Q Consensus 108 k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~ 149 (246)
..++..+|++.++++ ...|=..|= .....|+|.-.-|...
T Consensus 20 ~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 20 EELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGD 59 (62)
T ss_dssp SGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSS
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCC
Confidence 359999999999997 888888776 8899999987776554
No 92
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=35.35 E-value=1.8e+02 Score=24.93 Aligned_cols=48 Identities=25% Similarity=0.318 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcch
Q 025901 175 SNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (246)
Q Consensus 175 ~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 222 (246)
..|....+.....++..+..-..+..+..+.+++++.+++++++.+++
T Consensus 124 ~~~~~~~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei~~ 171 (176)
T PF12999_consen 124 KEYREELEEEEEIYKEGLKIRQELIEEAKKKREELEKKLEELEKEIQA 171 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555555666655555556666666777888888888887755
No 93
>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=35.22 E-value=93 Score=23.38 Aligned_cols=50 Identities=18% Similarity=0.259 Sum_probs=36.6
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025901 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (246)
Q Consensus 96 r~LtllsL-a~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ 147 (246)
+.|.++.= +....=++.++|++.|+++ ..+|+..|= +.+..|.|=-.||.
T Consensus 51 ~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 51 KVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 33455544 4445569999999999997 999998876 88889998777774
No 94
>PRK00182 tatB sec-independent translocase; Provisional
Probab=35.01 E-value=1.4e+02 Score=25.27 Aligned_cols=34 Identities=12% Similarity=0.228 Sum_probs=28.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (246)
.|+|+.+..+...+..|........+...+++..
T Consensus 20 VfGPerLP~~~r~lg~~ir~~R~~~~~~k~el~~ 53 (160)
T PRK00182 20 VIGPERLPRLIEDVRAALLAARTAINNAKQQLDG 53 (160)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4799999999999999999888877776665543
No 95
>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=34.98 E-value=1.3e+02 Score=29.20 Aligned_cols=87 Identities=11% Similarity=0.211 Sum_probs=61.9
Q ss_pred hHHHHHHcCC----CChHHHHHHHHHHhHhcCccEEEecCC--CCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHH
Q 025901 112 YDELMEELDV----TNVRELEDFLINECMYTGIVRGKLDQL--RRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLL 185 (246)
Q Consensus 112 y~~I~~~L~i----~~~~evE~llI~~aI~~gLI~GkIDQ~--~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl 185 (246)
.+++-+.|++ +..+++...++ +|+..|+.----|.. .+.+... +..+..++.+.|.+++..-...-+.+-
T Consensus 341 l~~ly~~~dlyLdin~~e~~~~al~-eA~~~G~pI~afd~t~~~~~~i~~---g~l~~~~~~~~m~~~i~~lL~d~~~~~ 416 (438)
T TIGR02919 341 IQELYQTCDIYLDINHGNEILNAVR-RAFEYNLLILGFEETAHNRDFIAS---ENIFEHNEVDQLISKLKDLLNDPNQFR 416 (438)
T ss_pred HHHHHHhccEEEEccccccHHHHHH-HHHHcCCcEEEEecccCCcccccC---CceecCCCHHHHHHHHHHHhcCHHHHH
Confidence 4455555544 44578888888 999999877666665 3323322 666888999999999988877766777
Q ss_pred HHHHHHHHHHHhhHHHH
Q 025901 186 ISIQEKIKWADSMNEMD 202 (246)
Q Consensus 186 ~~Ie~~i~~~~~~~~~~ 202 (246)
..++.|-..||....+.
T Consensus 417 ~~~~~q~~~a~~~~~~~ 433 (438)
T TIGR02919 417 ELLEQQREHANDISKEQ 433 (438)
T ss_pred HHHHHHHHHhccCCHHH
Confidence 77778888887765543
No 96
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=34.59 E-value=1.6e+02 Score=27.27 Aligned_cols=82 Identities=12% Similarity=0.242 Sum_probs=56.2
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCc--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Q 025901 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ--LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHR 206 (246)
Q Consensus 129 ~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q--~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~ 206 (246)
.+++ -++.+|+.-|=.-=.+ .|+.||-|++.+ .......|+.=-..++..++.|+..+..+.. +-...+
T Consensus 86 y~vm-Avi~aGi~y~~y~~~K-----~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q---~~~~qq 156 (300)
T KOG2629|consen 86 YFVM-AVILAGIAYAAYRFVK-----SYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQ---LLATQQ 156 (300)
T ss_pred HHHH-HHHHhhHHHHHHHHHH-----HHHHHHhhCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHH
Confidence 3454 7888886554322111 378899888665 5888999999999999999999988887766 333444
Q ss_pred HHHHHHHHHHHHh
Q 025901 207 KDLEEKVEEAKKS 219 (246)
Q Consensus 207 ~~~~~~~~~~k~~ 219 (246)
+++...+..++.+
T Consensus 157 ~Els~~L~~l~~~ 169 (300)
T KOG2629|consen 157 SELSRALASLKNT 169 (300)
T ss_pred HHHHHHHHHHHHH
Confidence 4666666666555
No 97
>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=34.52 E-value=1.4e+02 Score=20.76 Aligned_cols=36 Identities=17% Similarity=0.329 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcch
Q 025901 187 SIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSH 222 (246)
Q Consensus 187 ~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~ 222 (246)
.|++.+......-.--++.-+++...++.+++++|.
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ 39 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKD 39 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555555555666667777777777765
No 98
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=33.43 E-value=1.4e+02 Score=22.86 Aligned_cols=38 Identities=16% Similarity=0.074 Sum_probs=27.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~ 149 (246)
....++.+++++.++++ .. ||. +.+..|+|.-.-+...
T Consensus 4 ~~~~lt~~Elc~~~gi~-~~----~l~-eLve~GlIep~~~~~~ 41 (101)
T PRK10265 4 VTVTFTITEFCLHTGVS-EE----ELN-EIVGLGVIEPREIQET 41 (101)
T ss_pred eEEEeeHHHHHHHHCcC-HH----HHH-HHHHCCCeecCCCCcc
Confidence 44568999999999998 54 455 5566899986444433
No 99
>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=33.16 E-value=45 Score=23.56 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHH
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI 132 (246)
.++.-+..+||+.|||+ ..+|..++-
T Consensus 17 lgr~Pt~eEiA~~lgis-~~~v~~~l~ 42 (78)
T PF04539_consen 17 LGREPTDEEIAEELGIS-VEEVRELLQ 42 (78)
T ss_dssp HSS--BHHHHHHHHTS--HHHHHHHHH
T ss_pred hCCCCCHHHHHHHHccc-HHHHHHHHH
Confidence 47889999999999997 999997654
No 100
>PRK03100 sec-independent translocase; Provisional
Probab=32.46 E-value=2.5e+02 Score=23.09 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=30.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (246)
.|+|+.+..+...+..|........+.+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999888888877764
No 101
>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=32.03 E-value=2.1e+02 Score=21.18 Aligned_cols=56 Identities=14% Similarity=0.316 Sum_probs=39.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH-------HHHHHHHHHHHHHHHHHHHhcc
Q 025901 166 QLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN-------EMDKKHRKDLEEKVEEAKKSLS 221 (246)
Q Consensus 166 q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~-------~~~~~~~~~~~~~~~~~k~~~~ 221 (246)
+.+.+..-+..++...+..-..|.+++...+..+ ....+-|+.+|++|.-+|..+-
T Consensus 12 Ef~~~~~e~~~~k~~~~e~e~ki~~Qi~Em~~ir~~v~eLE~~h~kmK~~YEeEI~rLr~eLe 74 (79)
T PF08581_consen 12 EFENLSQEANSYKHQKDEYEHKINSQIQEMQQIRQKVYELEQAHRKMKQQYEEEIARLRRELE 74 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666777777777777777666554433 5667888899999999998873
No 102
>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=31.98 E-value=71 Score=21.14 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=33.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025901 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (246)
Q Consensus 105 ~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~ 150 (246)
.....++..+|++.++++ ..-+=.++= .....|+|.=.-|+.++
T Consensus 13 ~~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 13 YENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTET
T ss_pred HHcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCC
Confidence 344559999999999997 777776665 88889999988877655
No 103
>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=31.60 E-value=71 Score=22.05 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=32.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkI 145 (246)
..+..+-.+|++.++++ ...|-..+= +....|+|+-.=
T Consensus 19 ~~~~~t~~eIa~~l~i~-~~~v~~~L~-~L~~~GlV~~~~ 56 (68)
T PF01978_consen 19 KNGPATAEEIAEELGIS-RSTVYRALK-SLEEKGLVEREE 56 (68)
T ss_dssp HHCHEEHHHHHHHHTSS-HHHHHHHHH-HHHHTTSEEEEE
T ss_pred HcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEc
Confidence 55788999999999998 889998876 899999997554
No 104
>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=30.86 E-value=1.5e+02 Score=23.24 Aligned_cols=42 Identities=19% Similarity=0.332 Sum_probs=36.3
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhH
Q 025901 158 AGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN 199 (246)
Q Consensus 158 ~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~ 199 (246)
.++.++++++..+.+.+..|.+.+-.=+..+...++......
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 578889999999999999999998888888888888766544
No 105
>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=30.76 E-value=2.2e+02 Score=24.15 Aligned_cols=59 Identities=8% Similarity=0.201 Sum_probs=43.0
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcchh
Q 025901 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHK 223 (246)
Q Consensus 165 ~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~ 223 (246)
.....+...|..|+..+..=...+......+...-.-....-.+++.++++.+..|++.
T Consensus 124 ~~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I~~~ 182 (184)
T PF05791_consen 124 DKVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEIKKD 182 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG-GG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHHHhh
Confidence 34567888888888888888888888877777766666667777788888888777653
No 106
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=30.03 E-value=6.6e+02 Score=26.28 Aligned_cols=118 Identities=16% Similarity=0.177 Sum_probs=72.4
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHh--HhcCccEEEec--CCCCEEEEEee----cCCC----C
Q 025901 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINEC--MYTGIVRGKLD--QLRRCFEVQFA----AGRD----L 162 (246)
Q Consensus 95 Lr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~a--I~~gLI~GkID--Q~~~~v~V~~~----~~Rd----l 162 (246)
+-+++++-|-...-.++|.+|.++++++ .+++=..+- .. +-..++.+..+ ..+..+.+++. ..|+ +
T Consensus 566 t~Qm~VLlLFN~~d~lt~~eI~~~t~i~-~~~l~~~L~-Sl~~~K~~v~~~~~s~~~~~~~~~~N~~f~sk~~Rv~i~~~ 643 (725)
T KOG2166|consen 566 TYQMAVLLLFNNTEKLTYEEILEQTNLG-HEDLARLLQ-SLSCLKYKILLKPMSRTSPNDEFAFNSKFTSKMRRVKIPLP 643 (725)
T ss_pred hHHHHHHHHccchhhccHHHHHHHhCCC-HHHHHHHHH-HHHHHhHhhccCccccCCCCcEEEeeccccCcceeeccCCC
Confidence 4567777787888889999999999998 888877665 43 22222222111 45667777742 2232 2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcc
Q 025901 163 RPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (246)
Q Consensus 163 ~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~ 221 (246)
...+-+....+++.|+.. .|++.|.++=+ .+++..|.+=+.+-++.+++..+
T Consensus 644 ~~~e~~~~~~~ve~dRk~------~i~AaIVRIMK-~rK~l~h~~Lv~Ev~~ql~~RF~ 695 (725)
T KOG2166|consen 644 PMDERKKVVEDVDKDRKY------AIDAAIVRIMK-SRKVLGHQQLVSEVVEQLSERFK 695 (725)
T ss_pred CchhHHHHHhhhhhHHHH------HHHHHHHHHHH-hhccccHHHHHHHHHHHHhhhcC
Confidence 233556678888888864 45555555433 12345566655555555555554
No 107
>PRK10870 transcriptional repressor MprA; Provisional
Probab=29.66 E-value=3.3e+02 Score=22.67 Aligned_cols=50 Identities=14% Similarity=-0.005 Sum_probs=39.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~ 157 (246)
.+..++-.+|++.++++ ...+=..|= +....|+|.=.-|..+++...-..
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~L 117 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQL 117 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEE
Confidence 46789999999999997 667766554 888899999999988766654443
No 108
>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=29.31 E-value=2.2e+02 Score=20.98 Aligned_cols=43 Identities=12% Similarity=0.222 Sum_probs=26.6
Q ss_pred EEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 152 FEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (246)
Q Consensus 152 v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (246)
-.|....|+.|=....+.+...|..=...++.-+..++.+...
T Consensus 45 ~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~ 87 (106)
T PF01920_consen 45 RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKY 87 (106)
T ss_dssp -EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444567888877777777777766666555555555544433
No 109
>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=29.25 E-value=52 Score=24.17 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=20.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 025901 108 KVLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 108 k~isy~~I~~~L~i~~~~evE~llI 132 (246)
...||.+|++.++++ ...|..++-
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~ 54 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLK 54 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHh
Confidence 668999999999997 888887765
No 110
>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=27.98 E-value=2.4e+02 Score=20.60 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=49.1
Q ss_pred HHhhhcccCCcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee-cCCCCCCCcHHHHHHHHH
Q 025901 98 LTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA-AGRDLRPGQLGSMIQTLS 175 (246)
Q Consensus 98 LtllsLa~~~k~isy~~I~~~L-~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~-~~Rdl~~~q~~~l~~~L~ 175 (246)
+.|..|.. +...|.+|.+.+ +++ ...+-+-+= +....|||.=...... -..|.|. +++- .++..+...|.
T Consensus 9 ~IL~~l~~--g~~rf~el~~~l~~is-~~~L~~~L~-~L~~~GLv~r~~~~~~-p~~v~Y~LT~~G---~~l~~~l~~l~ 80 (90)
T PF01638_consen 9 LILRALFQ--GPMRFSELQRRLPGIS-PKVLSQRLK-ELEEAGLVERRVYPEV-PPRVEYSLTEKG---KELLPVLEALE 80 (90)
T ss_dssp HHHHHHTT--SSEEHHHHHHHSTTS--HHHHHHHHH-HHHHTTSEEEEEESSS-SSEEEEEE-HHH---HHHHHHHHHHH
T ss_pred HHHHHHHh--CCCcHHHHHHhcchhH-HHHHHHHHH-HHHHcchhhcccccCC-CCCCccCCCcCH---HHHHHHHHHHH
Confidence 33444544 788999999999 886 777766665 7888999987766432 3344442 2111 24567788888
Q ss_pred HHHHH
Q 025901 176 NWLTT 180 (246)
Q Consensus 176 ~W~~~ 180 (246)
.|...
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88764
No 111
>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=27.88 E-value=1.1e+02 Score=24.23 Aligned_cols=48 Identities=21% Similarity=0.356 Sum_probs=35.9
Q ss_pred CCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 85 PQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 85 ~~L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
+.+.+++. .|+.||.. .+|-.+|+..|++| ..-+--++= +.+..|+|.
T Consensus 39 ~~l~pE~~------~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvs-DL~~~G~v~ 86 (114)
T PF05331_consen 39 AGLGPEHR------AILELCRR--PLSVAEIAARLGLP-LGVVRVLVS-DLADAGLVR 86 (114)
T ss_pred CCCCHHHH------HHHHHHCC--CccHHHHHHhhCCC-chhhhhhHH-HHHhCCCEE
Confidence 34566552 67888877 89999999999999 766665555 778777754
No 112
>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=27.61 E-value=1.2e+02 Score=20.21 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=28.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G 143 (246)
...++..+|++.++++ ...+...+= .....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s-~~tv~r~l~-~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLT-RETVSRTLK-ELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 3568999999999997 888888775 7777888863
No 113
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=27.34 E-value=1.6e+02 Score=24.05 Aligned_cols=51 Identities=14% Similarity=0.296 Sum_probs=41.7
Q ss_pred cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCc
Q 025901 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (246)
Q Consensus 87 L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gL 140 (246)
+++++..+| ...|+.|+..++.+++.++...+|++ ...++..+- ++...|-
T Consensus 5 ~T~eer~eL-k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lr-eLVa~G~ 55 (127)
T PF06163_consen 5 FTPEEREEL-KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLR-ELVARGD 55 (127)
T ss_pred CCHHHHHHH-HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCC
Confidence 556553333 36788899999999999999999997 999999998 8887774
No 114
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=27.17 E-value=3.2e+02 Score=21.72 Aligned_cols=57 Identities=16% Similarity=0.194 Sum_probs=30.4
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 164 PGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 164 ~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
.+++....+.+..+...++.-+.-.......-..+.+.......+++..++++|+.+
T Consensus 41 ~e~~~~~~e~~l~~l~~~e~~~~k~q~~~~~n~~e~e~Y~~~~~~i~~~i~~~k~~i 97 (139)
T PF05615_consen 41 SEESQFLYERLLKELAQFEFSILKSQLILEMNKRERENYEQLNEEIEQEIEQAKKEI 97 (139)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 355566666666666665555444443333222333444555566666666666655
No 115
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=26.76 E-value=1.3e+02 Score=18.65 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=26.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
.++..+|++.++++ ...+-..+- .....|+|.
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~-~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLK-RLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 46789999999997 888888776 788888886
No 116
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=26.19 E-value=2.6e+02 Score=21.63 Aligned_cols=56 Identities=18% Similarity=0.234 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcchhccc
Q 025901 171 IQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKLHT 226 (246)
Q Consensus 171 ~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~ 226 (246)
.+++.+=....+.+...+.....-+..........+.+-+...+.+|+.+|...+.
T Consensus 38 ~~tI~qq~~~~~~L~~~~~~~r~~~~~~~~~~qq~r~~~e~~~e~ik~~lk~d~Ca 93 (110)
T PF10828_consen 38 AQTIQQQEDANQELKAQLQQNRQAVEEQQKREQQLRQQSEERRESIKTALKDDPCA 93 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCccc
Confidence 33343333433444444443333333333333333334445555555555554443
No 117
>PHA03158 hypothetical protein; Provisional
Probab=26.01 E-value=85 Score=27.62 Aligned_cols=62 Identities=24% Similarity=0.291 Sum_probs=40.5
Q ss_pred ecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 157 AAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 157 ~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
+..|++. =++.+...=--||-....=-..+-+|+-.+.+-.-..-+|.+++|++++++.|++
T Consensus 209 V~y~sLp--f~ERl~Rs~pPWCv~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~eleks~ 270 (273)
T PHA03158 209 VRFDDLP--FMERIKRSGPPWCIKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEKSL 270 (273)
T ss_pred EEeccCc--HHHHHhccCCCcEeecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhh
Confidence 4445542 2334444444588655555555555665566666677889999999999999986
No 118
>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=25.98 E-value=93 Score=28.35 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=35.9
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~ 148 (246)
..+.++..++++..++| .+=+-..++ +..-.++|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp-~efl~~~li-~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLP-SEFLKEELI-SKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCc-HHHHHHHHh-hhhcCcceeEEEeCC
Confidence 56899999999999998 777776788 787789999999998
No 119
>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=25.49 E-value=1.9e+02 Score=24.52 Aligned_cols=52 Identities=15% Similarity=0.217 Sum_probs=36.0
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025901 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (246)
Q Consensus 100 llsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V 154 (246)
++.....+..++..+|++.++++ ..-+-..+- .....|+|.-.-+ ..+.+.+
T Consensus 148 IL~~l~~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 148 VLEVLKAEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEe
Confidence 33333444569999999999997 777877776 7778899875532 3444443
No 120
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=25.05 E-value=1.9e+02 Score=22.07 Aligned_cols=35 Identities=17% Similarity=0.179 Sum_probs=28.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~ 195 (246)
.|+|+.+..+...+..|........+.+++.+...
T Consensus 21 vfGP~KLP~lar~lGk~i~~fkk~~~~~~~e~~~~ 55 (90)
T PRK14857 21 VFGPKKLPEIGRSLGKTLKGFQEASKEFENEIKRE 55 (90)
T ss_pred HcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999998888877776654443
No 121
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=24.89 E-value=82 Score=25.92 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI 136 (246)
-..+||.+|++.++|+ +..|...+- .|.
T Consensus 141 ~~gls~~EIA~~l~i~-~~tVks~l~-ra~ 168 (182)
T COG1595 141 LEGLSYEEIAEILGIS-VGTVKSRLH-RAR 168 (182)
T ss_pred hcCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 4579999999999998 999998887 765
No 122
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=24.80 E-value=2.6e+02 Score=19.78 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=33.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~ 149 (246)
...++..+|++.++++ ...+-..|- +....|+|.-.-++.+
T Consensus 22 ~~~~~~~~la~~~~~s-~~~i~~~l~-~L~~~g~v~~~~~~~~ 62 (101)
T smart00347 22 EGPLSVSELAKRLGVS-PSTVTRVLD-RLEKKGLIRRLPSPED 62 (101)
T ss_pred cCCcCHHHHHHHHCCC-chhHHHHHH-HHHHCCCeEecCCCCC
Confidence 4469999999999997 888888887 8999999987666543
No 123
>PRK15396 murein lipoprotein; Provisional
Probab=24.68 E-value=3e+02 Score=20.44 Aligned_cols=49 Identities=6% Similarity=0.128 Sum_probs=32.2
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Q 025901 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKV 213 (246)
Q Consensus 165 ~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~ 213 (246)
.+++.|...++.-..+++.+...+..--..+...+++..+.-++++..+
T Consensus 25 ~kvd~LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~RlDn~~ 73 (78)
T PRK15396 25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNQA 73 (78)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677777777777777777777777666666665555555555444433
No 124
>PF10828 DUF2570: Protein of unknown function (DUF2570); InterPro: IPR022538 This entry is represented by Bacteriophage IME08, pseT.3. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of proteins with unknown function.
Probab=24.26 E-value=3.4e+02 Score=20.97 Aligned_cols=51 Identities=14% Similarity=0.228 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhcchhccccCCCcc
Q 025901 182 DNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKLHTVSRPTL 232 (246)
Q Consensus 182 ~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~ 232 (246)
+.+...+.......+...++..+..++++.+.++.++.+|.-+..|+-...
T Consensus 45 ~~~~~~L~~~~~~~r~~~~~~~~~~qq~r~~~e~~~e~ik~~lk~d~Ca~~ 95 (110)
T PF10828_consen 45 EDANQELKAQLQQNRQAVEEQQKREQQLRQQSEERRESIKTALKDDPCANT 95 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCccccC
Confidence 334445555555555666677777788899999999999998888876644
No 125
>KOG3809 consensus Microtubule-binding protein MIP-T3 [Cytoskeleton]
Probab=24.19 E-value=2e+02 Score=28.35 Aligned_cols=60 Identities=13% Similarity=0.193 Sum_probs=33.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
|+-+++++.|..-|..|++.-..--..+++...-.....+--...-+++++.|...+..|
T Consensus 503 D~i~eD~daMq~EL~mWrse~rq~~~elq~eq~~t~~a~epL~~~la~lq~~I~d~~e~i 562 (583)
T KOG3809|consen 503 DFINEDIDAMQKELEMWRSEQRQNEQELQNEQAATFGASEPLYNILANLQKEINDTKEEI 562 (583)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHhHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 344688999999999999776655555554433322222222222334455555544444
No 126
>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=23.84 E-value=3.9e+02 Score=21.58 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 168 GSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 168 ~~l~~~L~~W~~~~~~vl~~Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
..+-..|++-.+.+...-..+.++|..++..-++...-.+.+.++|.+++..+
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 34556666666666666666667777777666666666666666666666554
No 127
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.56 E-value=2.3e+02 Score=22.18 Aligned_cols=62 Identities=13% Similarity=0.146 Sum_probs=35.5
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-EecCCCCEEEEEeecCCCCCCCcHHH--HHHHHHHHHHHHHHHHHH
Q 025901 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLDQLRRCFEVQFAAGRDLRPGQLGS--MIQTLSNWLTTSDNLLIS 187 (246)
Q Consensus 111 sy~~I~~~L~i~~~~evE~llI~~aI~~gLI~G-kIDQ~~~~v~V~~~~~Rdl~~~q~~~--l~~~L~~W~~~~~~vl~~ 187 (246)
+..++++.+||+ .+.+=.+- + .|||.. +-+. .-.|.++.+++.. ++..+...-=+++.+-..
T Consensus 2 ~IgevA~~~gvs-~~tLRyYe--~---~GLl~p~~r~~---------~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~ 66 (127)
T cd04784 2 KIGELAKKTGCS-VETIRYYE--K---EGLLPAPARSA---------NNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTL 66 (127)
T ss_pred CHHHHHHHHCcC-HHHHHHHH--H---CCCCCCCCcCC---------CCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHH
Confidence 578999999997 88777662 2 477752 2332 2346666666653 344444443333333333
No 128
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=23.49 E-value=1.2e+02 Score=26.69 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=34.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025901 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (246)
Q Consensus 95 Lr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~ 142 (246)
-|+..|+.+...++.++.++|++.|+++ ..-+...+- +.-..|+|.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~-~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLN-ELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 3566677777788899999999999997 877877665 444445543
No 129
>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=23.36 E-value=76 Score=24.04 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=26.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~Gk 144 (246)
.++++-++|++.++++ ..+|-.++- .....|+|..+
T Consensus 25 ~~~l~de~la~~~~l~-~~~vRkiL~-~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLK-PKEVRKILY-KLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S--HHHHHHHHH-HHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeEEE
Confidence 4679999999999997 999999987 89999999655
No 130
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=22.86 E-value=2.9e+02 Score=20.94 Aligned_cols=37 Identities=14% Similarity=0.052 Sum_probs=17.1
Q ss_pred eecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 156 FAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (246)
Q Consensus 156 ~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i 192 (246)
+..|+.|=....+.....|..=...++.-+..++.++
T Consensus 50 ~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~ 86 (105)
T cd00632 50 KLVGNVLVKQEKEEARTELKERLETIELRIKRLERQE 86 (105)
T ss_pred HHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445554444455555555544444444444444333
No 131
>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=22.64 E-value=3.5e+02 Score=20.52 Aligned_cols=46 Identities=11% Similarity=0.073 Sum_probs=35.9
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEE
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFE 153 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~ 153 (246)
.+..++..+|++.++++ ...+=..|- +....|+|...-|..++...
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~~ 84 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRRV 84 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCee
Confidence 34568999999999997 556766665 88889999999887665533
No 132
>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=22.56 E-value=96 Score=21.90 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHH
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDF 130 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~l 130 (246)
.++.+++-+||+.|+|+ ...|-.|
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 46789999999999997 7777655
No 133
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=22.54 E-value=2e+02 Score=19.66 Aligned_cols=34 Identities=21% Similarity=0.212 Sum_probs=30.8
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 162 LRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (246)
Q Consensus 162 l~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~~ 195 (246)
++++++..+...+......++..+..+...+...
T Consensus 4 vd~~~l~~~a~~~~~~~~~l~~~~~~l~~~~~~l 37 (86)
T PF06013_consen 4 VDPEQLRAAAQQLQAQADELQSQLQQLESSIDSL 37 (86)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5678899999999999999999999999999876
No 134
>PF02416 MttA_Hcf106: mttA/Hcf106 family; InterPro: IPR003369 Members of this protein family are involved in a sec-independent translocation mechanism. This pathway has been called the DeltapH pathway in chloroplasts []. Members of this family in Escherichia coli are involved in export of redox proteins with a "twin arginine" leader motif (S/T-R-R-X-F-L-K) []. This sec-independent pathway is termed TAT for twin-arginine translocation system. This system mainly transports proteins with bound cofactors that require folding prior to export.; GO: 0008565 protein transporter activity, 0015031 protein transport; PDB: 2L16_A.
Probab=22.13 E-value=2.3e+02 Score=19.15 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=23.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~ 191 (246)
.|+|+.++.+...+.+|.....+..+..++.
T Consensus 16 lfGp~kLP~~~r~lG~~ir~fk~~~~~~~~~ 46 (53)
T PF02416_consen 16 LFGPKKLPELARSLGKAIREFKKAINEAKEE 46 (53)
T ss_dssp HS-TTTHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HhCchHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3789999999999999988777766666554
No 135
>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=22.07 E-value=32 Score=27.63 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=31.7
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHH
Q 025901 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182 (246)
Q Consensus 114 ~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~ 182 (246)
.|+++|+|+ .+++++.+| +.. +...+.+|..+..+|+..|-
T Consensus 18 plSk~lgi~-~ee~~~ili-~~~--------------------------DmssLe~lhar~E~Ak~~cl 58 (117)
T PF09218_consen 18 PLSKELGIS-IEEFIDILI-EKL--------------------------DMSSLENLHARYEQAKMGCL 58 (117)
T ss_dssp TTTTTGGGT-HHHHHHHHH-HHS---------------------------HHHHHHHHHHHHTTHHHHH
T ss_pred HHHHHhCcC-HHHHHHHHH-Hhc--------------------------ChHHHHhccHHHHHHhhhhh
Confidence 367889997 999999999 642 23557889999999987664
No 136
>PRK14861 tatA twin arginine translocase protein A; Provisional
Probab=22.02 E-value=2.1e+02 Score=20.19 Aligned_cols=33 Identities=12% Similarity=0.069 Sum_probs=25.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025901 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (246)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~ 193 (246)
.|+|+.++.+...+..|.....+..+.+++.+.
T Consensus 20 vfGp~kLP~l~r~~G~~~~~fk~~~~~~~~~~~ 52 (61)
T PRK14861 20 IFGPKKLPELGKALGKTLREFKKATKELTDDDF 52 (61)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 478899999999999988877776666655443
No 137
>KOG2235 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.80 E-value=1.8e+02 Score=29.91 Aligned_cols=46 Identities=22% Similarity=0.381 Sum_probs=38.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025901 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (246)
Q Consensus 106 ~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~v~V~ 155 (246)
..+.++.++++..+++| .+=|...++ +=....+|+|++|- ++++-.
T Consensus 130 E~gqvtiaeLakq~dl~-sellqs~l~-ek~lg~iikgr~dg--gviyT~ 175 (776)
T KOG2235|consen 130 EQGQVTIAELAKQWDLP-SELLQSLLI-EKLLGSIIKGRVDG--GVIYTS 175 (776)
T ss_pred HhcchHHHHHHHhcCCc-HHHHHHHHH-HHhhccceeeeecC--CEEeeH
Confidence 56789999999999999 778899999 76667899999998 555533
No 138
>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=21.73 E-value=1e+02 Score=25.01 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025901 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (246)
Q Consensus 108 k~isy~~I~~~L~i~~~~evE~llI~~aI 136 (246)
...||.+|++.||++ +..|...+- .|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tVk~~l~-Rar 175 (183)
T TIGR02999 149 AGLTVEEIAELLGVS-VRTVERDWR-FAR 175 (183)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 568999999999997 999988776 654
No 139
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.35 E-value=1e+02 Score=25.32 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=23.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025901 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (246)
Q Consensus 108 k~isy~~I~~~L~i~~~~evE~llI~~aI 136 (246)
...||++|++.+|++ +..|...+- .|.
T Consensus 148 ~~~s~~eIA~~lgis-~~tV~~~l~-ra~ 174 (182)
T PRK12537 148 DGCSHAEIAQRLGAP-LGTVKAWIK-RSL 174 (182)
T ss_pred cCCCHHHHHHHHCCC-hhhHHHHHH-HHH
Confidence 468999999999997 999998877 665
No 140
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=21.22 E-value=5.1e+02 Score=21.96 Aligned_cols=33 Identities=24% Similarity=0.287 Sum_probs=25.3
Q ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHhc
Q 025901 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (246)
Q Consensus 188 Ie~~i~~~~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (246)
.+..+..+-.++++..|.++.+++++++++...
T Consensus 47 ~~r~v~ea~~~ke~~~Kl~E~iekkieeaR~da 79 (175)
T COG4741 47 RERLVNEAQARKEEEWKLKEWIEKKIEEAREDA 79 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356666777788888888888899998777654
No 141
>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=20.91 E-value=1.1e+02 Score=19.35 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=19.9
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025901 109 VLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~llI 132 (246)
..++.+|++.++++ .+.|..++=
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH
Confidence 36999999999997 999998764
No 142
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.81 E-value=2.9e+02 Score=23.62 Aligned_cols=80 Identities=13% Similarity=0.172 Sum_probs=48.7
Q ss_pred HHHHHHHHHhcCChhhHhhh--h-CCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 025901 61 KYLDMLRLFAHGTWSDYKNN--A-GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (246)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~~--~-~~l~~L~~~~~~KLr~LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~ 137 (246)
.+-.+..++.+......... . ...+.|++.|.+=|+.--=+..-..-|.++-.+||++|||+ ...+.+-+= +|.
T Consensus 127 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGIS-kst~~ehLR-rAe- 203 (215)
T COG3413 127 ELRDLLEILNFEDKEEVIESAFVEIGKNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGIS-KSTLSEHLR-RAE- 203 (215)
T ss_pred HHHHHHHHhcccceeeeccccccccccccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC-HHHHHHHHH-HHH-
Confidence 34455555555554432221 1 12346999886655554444555567999999999999997 666666554 554
Q ss_pred cCccEE
Q 025901 138 TGIVRG 143 (246)
Q Consensus 138 ~gLI~G 143 (246)
..|+.+
T Consensus 204 ~Kl~~~ 209 (215)
T COG3413 204 RKLIEA 209 (215)
T ss_pred HHHHHH
Confidence 344433
No 143
>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=20.69 E-value=2.7e+02 Score=18.56 Aligned_cols=48 Identities=17% Similarity=0.272 Sum_probs=32.4
Q ss_pred hcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 025901 102 TLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (246)
Q Consensus 102 sLa~~~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkIDQ~~~~ 151 (246)
.++..+...+..+|++.++++ ...+=..|= ++...|+|+=.=|..++.
T Consensus 11 ~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~-~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 11 ALAHSDGPMTQSDLAERLGIS-KSTVSRIIK-KLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHT--TS-BEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEESSCTT
T ss_pred HHHccCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecCCCCcCC
Confidence 344577888999999999997 777776654 889999997665554443
No 144
>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=20.67 E-value=5.2e+02 Score=21.81 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=29.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025901 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (246)
Q Consensus 107 ~k~isy~~I~~~L~i~~~~evE~llI~~aI~~gLI~GkI 145 (246)
...++..+|++.++|+ ...|=..+= .....|+|.-+-
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~-~Le~~GlV~r~~ 49 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLK-DLETEGLIEYEA 49 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEee
Confidence 3459999999999997 777776665 777889998663
No 145
>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=20.59 E-value=1.1e+02 Score=21.22 Aligned_cols=23 Identities=22% Similarity=0.172 Sum_probs=19.6
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025901 109 VLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~llI 132 (246)
-.++.+||+.|+++ ..-|-.|+=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 46889999999998 888888864
No 146
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.51 E-value=1e+02 Score=19.67 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=17.7
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025901 109 VLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 109 ~isy~~I~~~L~i~~~~evE~llI 132 (246)
-.|+.+|++.|+++ ...|-.|+=
T Consensus 17 G~s~~~ia~~lgvs-~~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVS-RSTVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS--HHHHHHHHT
T ss_pred CCCHHHHHHHHCcC-HHHHHHHHH
Confidence 57899999999997 999998864
No 147
>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=20.10 E-value=1.5e+02 Score=22.01 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=23.7
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025901 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (246)
Q Consensus 98 LtllsLa~~~k~isy~~I~~~L~i~~~~evE~llI 132 (246)
..|+.+-..++.+|-++|+.+++.+ +++|...+=
T Consensus 27 r~LLr~LA~G~PVt~~~LA~a~g~~-~e~v~~~L~ 60 (77)
T PF12324_consen 27 RPLLRLLAKGQPVTVEQLAAALGWP-VEEVRAALA 60 (77)
T ss_dssp HHHHHHHTTTS-B-HHHHHHHHT---HHHHHHHHH
T ss_pred HHHHHHHHcCCCcCHHHHHHHHCCC-HHHHHHHHH
Confidence 3455555669999999999999998 999987653
Done!