Query 024854
Match_columns 261
No_of_seqs 195 out of 579
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 07:54:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3250 COP9 signalosome, subu 100.0 2.7E-68 5.9E-73 463.2 17.1 257 1-261 1-257 (258)
2 KOG2753 Uncharacterized conser 100.0 2.2E-32 4.7E-37 251.3 11.1 150 24-178 205-361 (378)
3 KOG2908 26S proteasome regulat 100.0 1.4E-30 2.9E-35 240.4 15.5 178 13-192 182-375 (380)
4 smart00753 PAM PCI/PINT associ 99.5 9.5E-14 2E-18 105.4 7.4 86 88-177 3-88 (88)
5 smart00088 PINT motif in prote 99.5 9.5E-14 2E-18 105.4 7.4 86 88-177 3-88 (88)
6 PF01399 PCI: PCI domain; Int 99.5 1.3E-13 2.9E-18 106.2 7.8 95 60-156 1-105 (105)
7 KOG1464 COP9 signalosome, subu 98.5 8.5E-07 1.8E-11 81.8 9.8 126 59-192 304-439 (440)
8 KOG2581 26S proteasome regulat 97.3 0.00034 7.5E-09 67.4 5.7 91 60-153 319-420 (493)
9 KOG1498 26S proteasome regulat 95.5 0.1 2.2E-06 50.5 9.7 128 58-197 286-429 (439)
10 KOG2758 Translation initiation 95.4 0.029 6.2E-07 53.2 5.5 95 92-193 332-426 (432)
11 KOG1497 COP9 signalosome, subu 94.9 0.049 1.1E-06 51.6 5.6 56 98-155 306-361 (399)
12 KOG0686 COP9 signalosome, subu 94.5 0.35 7.6E-06 47.1 10.2 100 61-162 307-416 (466)
13 KOG2688 Transcription-associat 94.3 0.091 2E-06 50.9 5.9 98 59-157 271-385 (394)
14 COG5071 RPN5 26S proteasome re 94.1 0.26 5.6E-06 46.6 8.2 75 105-191 349-423 (439)
15 KOG2582 COP9 signalosome, subu 92.1 1.1 2.4E-05 43.3 9.4 106 60-169 259-373 (422)
16 COG5600 Transcription-associat 90.0 1 2.2E-05 43.5 7.1 99 59-159 288-406 (413)
17 PF09756 DDRGK: DDRGK domain; 89.5 0.55 1.2E-05 41.2 4.5 57 97-155 101-157 (188)
18 PF10075 PCI_Csn8: COP9 signal 89.3 3.3 7.1E-05 33.9 8.8 108 24-132 5-119 (143)
19 KOG2072 Translation initiation 89.1 10 0.00022 40.2 13.8 49 106-155 444-492 (988)
20 KOG1463 26S proteasome regulat 87.5 1.6 3.4E-05 42.0 6.4 114 43-158 269-392 (411)
21 KOG0687 26S proteasome regulat 85.5 15 0.00032 35.4 11.6 110 44-156 242-362 (393)
22 COG3355 Predicted transcriptio 85.0 8.8 0.00019 31.6 8.8 80 105-190 38-120 (126)
23 KOG3054 Uncharacterized conser 81.6 2.4 5.3E-05 38.8 4.6 54 100-155 205-258 (299)
24 PF02082 Rrf2: Transcriptional 80.7 5.3 0.00012 29.7 5.6 58 95-155 11-68 (83)
25 PF09012 FeoC: FeoC like trans 79.6 1.6 3.5E-05 31.5 2.4 42 100-143 5-46 (69)
26 COG5159 RPN6 26S proteasome re 79.5 7.7 0.00017 36.8 7.2 100 59-160 283-392 (421)
27 PRK01919 tatB sec-independent 79.5 12 0.00025 32.4 7.8 59 161-220 19-77 (169)
28 smart00344 HTH_ASNC helix_turn 78.8 3.6 7.8E-05 31.6 4.3 42 100-143 8-49 (108)
29 PRK11179 DNA-binding transcrip 76.4 4 8.6E-05 33.9 4.2 48 99-148 13-63 (153)
30 PRK04098 sec-independent trans 76.3 18 0.0004 30.9 8.1 60 161-220 19-81 (158)
31 PRK04654 sec-independent trans 73.4 18 0.00039 32.4 7.6 36 161-196 19-54 (214)
32 TIGR02010 IscR iron-sulfur clu 70.8 12 0.00026 30.4 5.6 43 99-143 13-57 (135)
33 TIGR01410 tatB twin arginine-t 70.7 17 0.00036 27.5 5.9 35 161-195 18-52 (80)
34 COG1522 Lrp Transcriptional re 70.0 5.9 0.00013 32.2 3.7 42 101-144 14-55 (154)
35 PF13412 HTH_24: Winged helix- 69.7 9.1 0.0002 25.2 3.9 41 100-142 8-48 (48)
36 PRK14165 winged helix-turn-hel 69.3 20 0.00043 32.1 7.1 62 92-155 4-65 (217)
37 PF07389 DUF1500: Protein of u 68.8 5.2 0.00011 31.1 2.8 36 100-138 39-74 (100)
38 PRK11169 leucine-responsive tr 68.7 9.6 0.00021 32.0 4.8 43 99-143 18-60 (164)
39 PRK01770 sec-independent trans 66.4 23 0.0005 30.7 6.6 35 161-195 19-53 (171)
40 TIGR00738 rrf2_super rrf2 fami 65.8 22 0.00049 28.2 6.2 50 93-144 9-58 (132)
41 PRK10857 DNA-binding transcrip 63.7 18 0.00039 30.8 5.5 47 96-144 12-58 (164)
42 PF08280 HTH_Mga: M protein tr 62.8 6.8 0.00015 27.4 2.3 35 96-131 6-40 (59)
43 TIGR02944 suf_reg_Xantho FeS a 59.4 42 0.00091 26.7 6.7 37 106-144 22-58 (130)
44 smart00346 HTH_ICLR helix_turn 58.9 21 0.00045 26.2 4.5 46 96-143 6-52 (91)
45 PRK14858 tatA twin arginine tr 56.5 72 0.0016 25.6 7.4 38 161-198 19-56 (108)
46 COG1959 Predicted transcriptio 55.9 32 0.0007 28.7 5.6 52 95-148 11-62 (150)
47 PF08279 HTH_11: HTH domain; 54.0 19 0.00041 24.2 3.3 35 97-132 2-37 (55)
48 COG1777 Predicted transcriptio 53.6 1.4E+02 0.003 26.9 9.3 105 113-220 32-155 (217)
49 PRK10141 DNA-binding transcrip 52.8 28 0.00061 28.1 4.6 46 107-154 28-73 (117)
50 PF03399 SAC3_GANP: SAC3/GANP/ 52.7 57 0.0012 27.6 6.9 62 59-120 135-203 (204)
51 PF01726 LexA_DNA_bind: LexA D 52.5 27 0.00058 25.2 4.0 37 105-142 21-57 (65)
52 PF13730 HTH_36: Helix-turn-he 51.9 53 0.0011 21.9 5.3 47 93-141 7-55 (55)
53 PRK04214 rbn ribonuclease BN/u 51.6 1.1E+02 0.0024 29.6 9.3 60 106-174 307-366 (412)
54 PF13404 HTH_AsnC-type: AsnC-t 51.5 9.9 0.00021 25.0 1.5 28 100-128 8-35 (42)
55 PF09339 HTH_IclR: IclR helix- 51.4 38 0.00082 22.7 4.5 45 96-142 4-49 (52)
56 smart00550 Zalpha Z-DNA-bindin 50.8 26 0.00057 25.2 3.8 33 109-143 22-54 (68)
57 PF03962 Mnd1: Mnd1 family; I 50.5 1.1E+02 0.0025 26.5 8.4 103 117-228 23-134 (188)
58 PF05565 Sipho_Gp157: Siphovir 50.4 75 0.0016 26.8 7.1 56 180-237 44-99 (162)
59 PF13815 Dzip-like_N: Iguana/D 50.2 47 0.001 26.5 5.6 94 110-220 18-117 (118)
60 PRK00404 tatB sec-independent 50.0 1.1E+02 0.0024 25.7 7.8 37 161-197 19-55 (141)
61 cd00090 HTH_ARSR Arsenical Res 49.9 58 0.0012 21.9 5.4 36 110-147 21-56 (78)
62 PF12840 HTH_20: Helix-turn-he 49.3 32 0.00069 23.8 3.9 38 105-144 20-57 (61)
63 PF08281 Sigma70_r4_2: Sigma-7 48.5 24 0.00052 23.5 3.1 27 108-136 25-51 (54)
64 PRK11014 transcriptional repre 48.2 50 0.0011 26.9 5.5 50 96-147 12-61 (141)
65 PF11945 WASH_WAHD: WAHD domai 48.0 1.6E+02 0.0035 27.6 9.5 65 156-220 8-73 (297)
66 PF13601 HTH_34: Winged helix 47.6 24 0.00053 26.3 3.3 51 98-150 3-53 (80)
67 PRK11920 rirA iron-responsive 46.6 52 0.0011 27.4 5.5 39 106-146 21-59 (153)
68 PF08220 HTH_DeoR: DeoR-like h 46.5 31 0.00068 23.9 3.5 42 98-141 3-44 (57)
69 PF14947 HTH_45: Winged helix- 45.3 61 0.0013 23.8 5.1 50 99-155 10-59 (77)
70 PF01022 HTH_5: Bacterial regu 44.9 59 0.0013 21.3 4.5 33 108-142 14-46 (47)
71 PRK00708 sec-independent trans 44.5 79 0.0017 28.3 6.5 37 161-197 19-55 (209)
72 PHA01750 hypothetical protein 44.4 93 0.002 23.0 5.7 35 186-220 38-72 (75)
73 PF01325 Fe_dep_repress: Iron 43.7 58 0.0013 22.9 4.6 43 98-142 11-53 (60)
74 PF04967 HTH_10: HTH DNA bindi 43.5 1.1E+02 0.0023 21.3 5.8 27 105-132 19-45 (53)
75 PRK03100 sec-independent trans 43.4 55 0.0012 27.3 5.0 34 161-194 20-53 (136)
76 PRK09954 putative kinase; Prov 43.1 29 0.00063 32.5 3.8 54 100-155 8-64 (362)
77 PRK03573 transcriptional regul 43.0 1.7E+02 0.0037 23.4 8.3 56 100-157 37-92 (144)
78 PF14480 DNA_pol3_a_NI: DNA po 42.4 92 0.002 22.3 5.6 61 111-176 2-62 (76)
79 PF03979 Sigma70_r1_1: Sigma-7 42.0 20 0.00043 26.8 2.0 39 100-139 12-52 (82)
80 smart00420 HTH_DEOR helix_turn 41.1 46 0.00099 21.3 3.5 35 107-143 12-46 (53)
81 cd06445 ATase The DNA repair p 41.0 37 0.00081 25.1 3.4 30 98-127 6-36 (79)
82 PF09341 Pcc1: Transcription f 40.6 97 0.0021 22.5 5.5 47 138-190 30-76 (76)
83 PF13518 HTH_28: Helix-turn-he 40.5 34 0.00073 22.3 2.8 43 99-146 4-46 (52)
84 PF08784 RPA_C: Replication pr 40.0 74 0.0016 24.3 5.1 50 96-147 51-101 (102)
85 smart00418 HTH_ARSR helix_turn 38.1 1.1E+02 0.0024 19.8 5.2 38 107-146 8-45 (66)
86 smart00345 HTH_GNTR helix_turn 37.9 1.2E+02 0.0025 19.9 5.8 35 106-142 16-51 (60)
87 TIGR02919 accessory Sec system 37.8 1.1E+02 0.0024 30.1 7.0 86 112-201 341-432 (438)
88 PRK10265 chaperone-modulator p 37.8 1.1E+02 0.0024 23.8 5.7 39 105-149 3-41 (101)
89 COG4575 ElaB Uncharacterized c 37.4 1.5E+02 0.0033 23.7 6.4 56 159-220 2-57 (104)
90 PF10828 DUF2570: Protein of u 35.5 2.2E+02 0.0047 22.4 8.7 54 172-227 39-92 (110)
91 PF12802 MarR_2: MarR family; 34.5 1.4E+02 0.0031 19.9 5.5 41 108-150 20-60 (62)
92 PF05010 TACC: Transforming ac 34.3 2.7E+02 0.0059 24.7 8.3 52 167-218 120-172 (207)
93 PF01978 TrmB: Sugar-specific 33.8 67 0.0015 22.5 3.7 38 106-145 19-56 (68)
94 KOG2166 Cullins [Cell cycle co 33.8 5.3E+02 0.011 27.4 11.5 117 95-220 566-694 (725)
95 PF04545 Sigma70_r4: Sigma-70, 33.6 1.4E+02 0.003 19.5 5.2 28 107-136 18-45 (50)
96 PF04539 Sigma70_r3: Sigma-70 32.3 48 0.001 23.8 2.7 26 106-132 17-42 (78)
97 PRK10947 global DNA-binding tr 32.1 1.6E+02 0.0036 24.4 6.1 23 198-220 43-65 (135)
98 COG5187 RPN7 26S proteasome re 32.0 54 0.0012 31.3 3.6 63 92-156 314-376 (412)
99 PF06163 DUF977: Bacterial pro 31.8 1.2E+02 0.0025 25.2 5.1 52 87-141 5-56 (127)
100 PF01638 HxlR: HxlR-like helix 31.5 2.2E+02 0.0048 21.2 6.8 75 98-180 9-85 (90)
101 PF05615 THOC7: Tho complex su 31.4 2.8E+02 0.0061 22.4 8.2 57 164-220 41-97 (139)
102 PF13463 HTH_27: Winged helix 30.9 1.7E+02 0.0038 19.9 6.3 50 100-151 9-58 (68)
103 PF01047 MarR: MarR family; I 29.7 96 0.0021 20.8 3.8 44 105-150 13-56 (59)
104 PRK10884 SH3 domain-containing 29.5 1.8E+02 0.0039 25.8 6.4 13 233-245 172-184 (206)
105 PF09523 DUF2390: Protein of u 29.5 1.6E+02 0.0035 23.4 5.5 42 158-199 43-84 (109)
106 smart00347 HTH_MARR helix_turn 29.4 2.2E+02 0.0047 20.5 8.5 41 107-149 22-62 (101)
107 PF05331 DUF742: Protein of un 29.1 1.1E+02 0.0023 24.8 4.4 42 98-143 46-87 (114)
108 PRK00182 tatB sec-independent 28.6 2E+02 0.0042 24.8 6.1 33 161-193 20-52 (160)
109 PRK10328 DNA binding protein, 28.6 2E+02 0.0042 23.9 6.0 22 199-220 44-65 (134)
110 COG1497 Predicted transcriptio 28.1 4.9E+02 0.011 24.1 10.3 83 100-195 16-98 (260)
111 cd00092 HTH_CRP helix_turn_hel 28.1 1.2E+02 0.0027 20.5 4.2 35 107-143 23-57 (67)
112 PF07106 TBPIP: Tat binding pr 28.0 3.6E+02 0.0077 22.5 13.3 111 105-220 12-132 (169)
113 PF05791 Bacillus_HBL: Bacillu 27.8 2.2E+02 0.0048 24.4 6.6 56 165-220 124-179 (184)
114 PRK10870 transcriptional repre 27.3 3.8E+02 0.0083 22.6 8.3 55 100-156 61-116 (176)
115 TIGR03879 near_KaiC_dom probab 26.6 59 0.0013 24.3 2.3 24 108-132 31-54 (73)
116 KOG1076 Translation initiation 26.6 1.5E+02 0.0033 31.3 6.0 113 44-158 636-765 (843)
117 smart00419 HTH_CRP helix_turn_ 26.5 1.3E+02 0.0029 18.8 3.9 33 109-143 8-40 (48)
118 TIGR01884 cas_HTH CRISPR locus 26.2 1.9E+02 0.004 25.0 5.8 53 99-154 147-199 (203)
119 PF01920 Prefoldin_2: Prefoldi 25.1 2.8E+02 0.0061 20.7 6.1 42 152-193 45-86 (106)
120 cd01109 HTH_YyaN Helix-Turn-He 25.1 2.9E+02 0.0062 21.4 6.2 45 111-170 2-47 (113)
121 PF05377 FlaC_arch: Flagella a 25.0 2.3E+02 0.0049 20.1 4.9 33 188-220 5-37 (55)
122 COG1595 RpoE DNA-directed RNA 25.0 81 0.0018 26.3 3.2 28 107-136 141-168 (182)
123 PRK13182 racA polar chromosome 24.5 2.1E+02 0.0045 24.7 5.7 21 111-132 2-22 (175)
124 PRK10411 DNA-binding transcrip 24.2 1.2E+02 0.0026 27.2 4.3 45 96-142 5-49 (240)
125 PF07889 DUF1664: Protein of u 24.2 4E+02 0.0088 21.8 8.1 53 168-220 46-98 (126)
126 TIGR02337 HpaR homoprotocatech 24.1 3.4E+02 0.0073 20.9 8.5 45 106-152 39-83 (118)
127 PF09218 DUF1959: Domain of un 24.1 43 0.00093 27.3 1.3 41 114-182 18-58 (117)
128 COG1191 FliA DNA-directed RNA 23.7 3.3E+02 0.0071 24.9 7.1 113 9-132 27-148 (247)
129 PF09743 DUF2042: Uncharacteri 22.8 1.2E+02 0.0025 28.1 4.1 41 106-148 127-167 (272)
130 PF12999 PRKCSH-like: Glucosid 22.2 3.5E+02 0.0076 23.6 6.6 46 175-220 124-169 (176)
131 PF10668 Phage_terminase: Phag 22.1 98 0.0021 22.2 2.7 24 106-130 19-42 (60)
132 PRK12537 RNA polymerase sigma 21.5 1E+02 0.0022 25.7 3.1 27 108-136 148-174 (182)
133 TIGR02999 Sig-70_X6 RNA polyme 21.4 1.1E+02 0.0023 25.3 3.3 27 108-136 149-175 (183)
134 COG3413 Predicted DNA binding 21.2 2.8E+02 0.0061 24.1 6.0 80 61-143 127-209 (215)
135 cd06170 LuxR_C_like C-terminal 21.1 1.1E+02 0.0024 19.7 2.7 25 109-135 15-39 (57)
136 KOG3809 Microtubule-binding pr 21.1 2.4E+02 0.0053 28.2 6.0 60 161-220 503-562 (583)
137 PHA02943 hypothetical protein; 21.1 2.1E+02 0.0046 24.6 4.9 43 97-142 13-55 (165)
138 PF13022 HTH_Tnp_1_2: Helix-tu 20.7 1.9E+02 0.0041 24.4 4.5 45 86-131 10-55 (142)
139 PRK09802 DNA-binding transcrip 20.7 1.4E+02 0.0031 27.1 4.2 47 94-142 16-62 (269)
140 TIGR02702 SufR_cyano iron-sulf 20.6 5.4E+02 0.012 22.0 11.3 37 107-145 13-49 (203)
141 PF12324 HTH_15: Helix-turn-he 20.6 1.4E+02 0.0031 22.5 3.4 34 98-132 27-60 (77)
142 PF13542 HTH_Tnp_ISL3: Helix-t 20.5 1.3E+02 0.0028 19.7 2.9 31 99-132 19-49 (52)
143 PRK14857 tatA twin arginine tr 20.3 2.6E+02 0.0057 21.6 4.9 33 161-193 21-53 (90)
144 PF13591 MerR_2: MerR HTH fami 20.3 1.7E+02 0.0037 21.8 3.8 32 110-147 1-32 (84)
145 PF13384 HTH_23: Homeodomain-l 20.2 1.1E+02 0.0023 19.9 2.5 23 109-132 17-39 (50)
146 PF06394 Pepsin-I3: Pepsin inh 20.2 44 0.00095 25.2 0.6 38 148-185 26-66 (76)
147 PRK10884 SH3 domain-containing 20.1 6.1E+02 0.013 22.4 8.0 8 156-163 79-86 (206)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=2.7e-68 Score=463.17 Aligned_cols=257 Identities=41% Similarity=0.645 Sum_probs=252.9
Q ss_pred CchhHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 024854 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (261)
Q Consensus 1 ~~~~~~~~~~l~~fl~lak~a~~~aa~~lI~~AL~~p~vy~F~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~ 80 (261)
|++|+++++.+|||+++||+++|+|...+|.+||++|+||+|||||.+|+|.+|..+.++.+++||++||||||.||.++
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 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCC
Q 024854 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (261)
Q Consensus 81 ~~~l~~L~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~R 160 (261)
+-.+|.|+++++.||++||++|||+..++|||..+.+.|.+.|+++|||+|| +|||++|++|||||.+|+++|.|+++|
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 CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccccccCCccccccccccCCC
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~~~k~~~~~~~~~~~~~~~~~ 240 (261)
|+++.++++|..+|++||+.|+++|..|++++.|||++++...+++++.|.+|.++||+++.++|.|+++.++|..++ |
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 999999999999999999999999999999999999999999999999999999999999999999999999999998 8
Q ss_pred CCccccccCCCccccccCCCC
Q 024854 241 VMDYEEDRGRPKRCRRRHPLS 261 (261)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~ 261 (261)
.|++.++++||++ |+||++
T Consensus 239 ~~~qrqp~kk~sk--~kglv~ 257 (258)
T KOG3250|consen 239 VMDQRQPGKKPSK--RKGLVT 257 (258)
T ss_pred CccccCCCcCccc--ccCCCC
Confidence 8999999999999 778764
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=99.97 E-value=2.2e-32 Score=251.30 Aligned_cols=150 Identities=28% Similarity=0.538 Sum_probs=139.6
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhh----hhCCCCC---cchHHHHHHH
Q 024854 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----NAGHLPQ---LVPDQVLKLK 96 (261)
Q Consensus 24 ~aa~~lI~~AL~~p~vy~F~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~---L~~~~~~KLr 96 (261)
.+|.+||+.|+.+|++|.|+.|+.+|+|+.|+++. +|+||.||..|..++|.+ |++++.. ..+++.+|||
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 47999999999999999999999999999999765 899999999999999986 3444433 2367899999
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 024854 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (261)
Q Consensus 97 ~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~ 176 (261)
+||+++||+.+++|||++|+++|+|. .+|||.||| +||.+|+|.|||||.+++|.|+.+.+|.|+..||..|.++|..
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 024854 177 WL 178 (261)
Q Consensus 177 W~ 178 (261)
|.
T Consensus 360 w~ 361 (378)
T KOG2753|consen 360 WG 361 (378)
T ss_pred HH
Confidence 95
No 3
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=99.97 E-value=1.4e-30 Score=240.44 Aligned_cols=178 Identities=19% Similarity=0.367 Sum_probs=161.1
Q ss_pred HHHHhc------ccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh---hCC
Q 024854 13 HFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN---AGH 83 (261)
Q Consensus 13 ~fl~la------k~a~~~aa~~lI~~AL~~p~vy~F~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~---~~~ 83 (261)
.|+... .+.+-..|.+|..+||.+.+||||||||.+|+...|.||++.|++++|.+|+.||+..|... .+.
T Consensus 182 ~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~~ 261 (380)
T KOG2908|consen 182 LYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWGK 261 (380)
T ss_pred HHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhcc
Confidence 566655 44455789999999999999999999999999999999999999999999999999999974 345
Q ss_pred CCCcchH---HHHHHHHHHhhhccc----CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEe
Q 024854 84 LPQLVPD---QVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (261)
Q Consensus 84 l~~L~~~---~~~KLr~LTllsLa~----~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~ 156 (261)
.|.|... ..+|+++|+++.+|. ..|.+||++|+++++|| .++||.+|| +|++.|||+|.|||++++|+++|
T Consensus 262 ~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~sw 339 (380)
T KOG2908|consen 262 QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYMSW 339 (380)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEEec
Confidence 7777633 478999999998885 57999999999999999 999999999 99999999999999999999999
Q ss_pred ecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 157 AAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (261)
Q Consensus 157 ~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i 192 (261)
++||.++.+|+-.|.+++..|++.++++...++.+-
T Consensus 340 vqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~ 375 (380)
T KOG2908|consen 340 VQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRG 375 (380)
T ss_pred ccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 999999999999999999999999999999888654
No 4
>smart00753 PAM PCI/PINT associated module.
Probab=99.48 E-value=9.5e-14 Score=105.37 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.9
Q ss_pred chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcH
Q 024854 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (261)
Q Consensus 88 ~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (261)
.+....|++.++|.+++...++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++|
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 45678999999999999999999999999999998 789999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 024854 168 GSMIQTLSNW 177 (261)
Q Consensus 168 ~~L~~~L~~W 177 (261)
..+.++|..|
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=99.48 E-value=9.5e-14 Score=105.37 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.9
Q ss_pred chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcH
Q 024854 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (261)
Q Consensus 88 ~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (261)
.+....|++.++|.+++...++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++|
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 45678999999999999999999999999999998 789999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 024854 168 GSMIQTLSNW 177 (261)
Q Consensus 168 ~~L~~~L~~W 177 (261)
..+.++|..|
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=99.47 E-value=1.3e-13 Score=106.18 Aligned_cols=95 Identities=20% Similarity=0.402 Sum_probs=81.1
Q ss_pred hHHHHHHHHHhcCChhhHhhhhC----------CCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHH
Q 024854 60 SKYLDMLRLFAHGTWSDYKNNAG----------HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (261)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~~----------~l~~L~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~ 129 (261)
.|+.+|+++|..|++..|...-. .+..+.+....+++..++.+++...+.|+++.|++.|+++ ..+||.
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 37899999999999999986322 1222446678999999999999999999999999999998 899999
Q ss_pred HHHHHhHhcCceEEEecCCCCEEEEEe
Q 024854 130 FLINECMYTGIVRGKLDQLRRCFEVQF 156 (261)
Q Consensus 130 lvI~eAI~~gLI~GkIDQ~~~~v~V~~ 156 (261)
+|+ ++|..|.|.|+|||.+++|.++|
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=98.48 E-value=8.5e-07 Score=81.82 Aligned_cols=126 Identities=14% Similarity=0.372 Sum_probs=103.5
Q ss_pred chHHHHHHHHHhcCChhhHhh----hhCCC---C---CcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 024854 59 NSKYLDMLRLFAHGTWSDYKN----NAGHL---P---QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (261)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~----~~~~l---~---~L~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (261)
--.+.+|+..+...++..|.. +.+.+ | +..++.++++|.-.++.|..+...|...-|+++|+|+ ..+||
T Consensus 304 IlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~ 382 (440)
T KOG1464|consen 304 ILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVE 382 (440)
T ss_pred HHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHH
Confidence 345788999999999999986 33322 1 2447789999999999999999999999999999998 99999
Q ss_pred HHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (261)
Q Consensus 129 ~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i 192 (261)
.+++ .||-.+-|+|+|||+++.+....... .=..+.+.|+.|.+.++++.+.|-.++
T Consensus 383 ~LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr~ 439 (440)
T KOG1464|consen 383 SLLV-SCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSRV 439 (440)
T ss_pred HHHH-HHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999 99999999999999999988764321 112478999999999998887776543
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.33 E-value=0.00034 Score=67.41 Aligned_cols=91 Identities=10% Similarity=0.313 Sum_probs=69.4
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCCCCC-cc----hHHHHHHHHHH------hhhcccCCcccChHHHHHHcCCCChHHHH
Q 024854 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-LV----PDQVLKLKQLT------VLTLAETNKVLPYDELMEELDVTNVRELE 128 (261)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~~~l~~-L~----~~~~~KLr~LT------llsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (261)
.+||.|=+..--||++-|...-+.+.. +- =.....||+=. .+|| ..+.|||.+|+..|++.|..++|
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 569999999999999999874433221 11 11234444422 2233 47899999999999999999999
Q ss_pred HHHHHHhHhcCceEEEecCCCCEEE
Q 024854 129 DFLINECMYTGIVRGKLDQLRRCFE 153 (261)
Q Consensus 129 ~lvI~eAI~~gLI~GkIDQ~~~~v~ 153 (261)
.+|= +||..|+|+|+||..++.+.
T Consensus 397 yiVa-kAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 397 YIVA-KAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred HHHH-HHHHhccceeeeccccCcee
Confidence 9999 99999999999999999554
No 9
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=95.51 E-value=0.1 Score=50.53 Aligned_cols=128 Identities=21% Similarity=0.300 Sum_probs=92.5
Q ss_pred CchHHHHHHHHHhcCChhhHhhhh---------CCCCC---cchHH--HHHHHH--HHhhhcccCCcccChHHHHHHcCC
Q 024854 58 ENSKYLDMLRLFAHGTWSDYKNNA---------GHLPQ---LVPDQ--VLKLKQ--LTVLTLAETNKVLPYDELMEELDV 121 (261)
Q Consensus 58 ~~~~~~~LL~iFa~Gt~~dy~~~~---------~~l~~---L~~~~--~~KLr~--LTllsLa~~~k~Isy~~I~~~L~I 121 (261)
+.+.+-.+|.+|..|-+--|.... +.+.. ..+.. -.|.|. .-+--.|.=..+||+..+++-|++
T Consensus 286 e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl 365 (439)
T KOG1498|consen 286 ELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDL 365 (439)
T ss_pred cCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCC
Confidence 345678899999988765544211 11111 11111 122222 344444556889999999999999
Q ss_pred CChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024854 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (261)
Q Consensus 122 ~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~ 197 (261)
| .++.|.++= +.+..|.+.+|||+..+.+..... .++.+.|..|..++++++..++..-+-+.+
T Consensus 366 ~-~ee~E~~LS-~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~ll~K~~HLI~K 429 (439)
T KOG1498|consen 366 P-VEEMEKFLS-DLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGLLEKVSHLIHK 429 (439)
T ss_pred C-HHHHHHHHH-HHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHHHHHHHHHHHH
Confidence 8 999999999 899999999999999999987654 357889999999999999988866554444
No 10
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=95.38 E-value=0.029 Score=53.19 Aligned_cols=95 Identities=17% Similarity=0.240 Sum_probs=75.3
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHH
Q 024854 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMI 171 (261)
Q Consensus 92 ~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~ 171 (261)
+.--|++-+=+.|.-..+|+.+.+|+.|+++ .++.|.|++ +.|....+++|||..-++|.+.-... .--+.++
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 4555667777788889999999999999997 999999999 89999999999999999988764322 2245667
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 024854 172 QTLSNWLTTSDNLLISIQEKIK 193 (261)
Q Consensus 172 ~~L~~W~~~~~~~l~~ie~~i~ 193 (261)
++-....-+...+-..++.+++
T Consensus 405 e~tksLS~rsq~la~~lek~~~ 426 (432)
T KOG2758|consen 405 EKTKSLSFRSQNLAQQLEKKIQ 426 (432)
T ss_pred HhccccchhHHHHHHHHHHHHH
Confidence 7777777777777777766554
No 11
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=94.94 E-value=0.049 Score=51.56 Aligned_cols=56 Identities=14% Similarity=0.286 Sum_probs=50.0
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
-.|+++.+-...|+|+++..-|+|+ .+.+|...= +.|..|=+.|.|||.++.++..
T Consensus 306 hNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe 361 (399)
T KOG1497|consen 306 HNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFE 361 (399)
T ss_pred HhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeec
Confidence 4566666667889999999999998 999999999 8999999999999999999875
No 12
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=94.47 E-value=0.35 Score=47.12 Aligned_cols=100 Identities=15% Similarity=0.219 Sum_probs=76.3
Q ss_pred HHHHHHHHHhcCChhhHhh----hhCCCC---Ccc---hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 024854 61 KYLDMLRLFAHGTWSDYKN----NAGHLP---QLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (261)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~----~~~~l~---~L~---~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~l 130 (261)
.+.++|.-|..+-|..-.. .++.+- -|. .....++|.=.++.--.+...++++.++.+.+.+ +..+|.=
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 3566777777777665333 222211 122 2346788888888888889999999999999997 9999999
Q ss_pred HHHHhHhcCceEEEecCCCCEEEEEeecCCCC
Q 024854 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDL 162 (261)
Q Consensus 131 vI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl 162 (261)
|. +.|-.|-|.||||+.++++++.-+..|.-
T Consensus 386 l~-~LI~~~~i~~rIDs~~ki~~~~~~~~en~ 416 (466)
T KOG0686|consen 386 LL-ELILEGKISGRIDSHNKILYARDADSENA 416 (466)
T ss_pred HH-HHHHccchheeeccccceeeecccccccc
Confidence 99 99999999999999999999976655543
No 13
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=94.30 E-value=0.091 Score=50.86 Aligned_cols=98 Identities=15% Similarity=0.198 Sum_probs=71.8
Q ss_pred chHHHHHHHHHhcCChhhHhh----hhCCCCCcch-HHHHHHHHHHhhhccc-------CCcccChHHHHHHcCCCC---
Q 024854 59 NSKYLDMLRLFAHGTWSDYKN----NAGHLPQLVP-DQVLKLKQLTVLTLAE-------TNKVLPYDELMEELDVTN--- 123 (261)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~L~~-~~~~KLr~LTllsLa~-------~~k~Isy~~I~~~L~I~~--- 123 (261)
-..+-.|++..-.|++..|.. +...+....- -.+.|++.++.=.|.. +...+|++.+..++....
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 346778899999999999985 2222211110 0133455554443332 678999999999998875
Q ss_pred --hHHHHHHHHHHhHhcCceEEEecCCCCEEEEEee
Q 024854 124 --VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (261)
Q Consensus 124 --~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~ 157 (261)
.+|||-.+. .+|+.|.|+|.|+...+++.++..
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 689999999 899999999999999999998753
No 14
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=94.06 E-value=0.26 Score=46.65 Aligned_cols=75 Identities=16% Similarity=0.256 Sum_probs=64.6
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL 184 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~ 184 (261)
.=...|+-..|..-++++ ..+.|.+|= +.+..|.+.+||++..+.+..... ++..+.|..|..+++.+
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 346788999999999998 999999998 899999999999999999887533 34678899999999999
Q ss_pred HHHHHHH
Q 024854 185 LISIQEK 191 (261)
Q Consensus 185 l~~ie~~ 191 (261)
+..++.-
T Consensus 417 lgklek~ 423 (439)
T COG5071 417 LGKLEKV 423 (439)
T ss_pred HHHHHHH
Confidence 9888753
No 15
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=92.15 E-value=1.1 Score=43.26 Aligned_cols=106 Identities=11% Similarity=0.249 Sum_probs=77.9
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCCCC-----CcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 024854 60 SKYLDMLRLFAHGTWSDYKN----NAGHLP-----QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (261)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~----~~~~l~-----~L~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~l 130 (261)
.+|.++++++..+.-.+... +++.+- .|.-..+.-+.+-+|..|.+.-.+++.++|++..++.+..|+|..
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 36899999999988776553 222221 122233444555566677677778999999997777778999999
Q ss_pred HHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHH
Q 024854 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (261)
Q Consensus 131 vI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~ 169 (261)
|+ ..|..|=|-..|| +-|..+.-..-+..|+...+
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 77877776666666665554
No 16
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=90.01 E-value=1 Score=43.49 Aligned_cols=99 Identities=20% Similarity=0.314 Sum_probs=64.7
Q ss_pred chHHHHHHHHHhcCChhhHhhh----hCCCCC------cc---hH-HHHHHHHHHhhhcccCCcccChHHHHHHcCCCC-
Q 024854 59 NSKYLDMLRLFAHGTWSDYKNN----AGHLPQ------LV---PD-QVLKLKQLTVLTLAETNKVLPYDELMEELDVTN- 123 (261)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~------L~---~~-~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~- 123 (261)
.+.+--|.++.-+|++++|... ...+-+ |. |. +.+-|.. -+..++.+...+|++.+...++++.
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 4556678899999999999852 111110 00 10 1111111 2223333455577777766666653
Q ss_pred -----hHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecC
Q 024854 124 -----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (261)
Q Consensus 124 -----~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~ 159 (261)
..+||-.++ .+|..|+++|.|....+++.++...|
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 468999999 89999999999999999999986543
No 17
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=89.50 E-value=0.55 Score=41.18 Aligned_cols=57 Identities=14% Similarity=0.268 Sum_probs=40.8
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 97 ~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
+-.++......++++.++|+.++++. ..++-+-|- +....|.|.|-||...+-|+|+
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 778888888 8999999999999999889887
No 18
>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=89.33 E-value=3.3 Score=33.94 Aligned_cols=108 Identities=15% Similarity=0.187 Sum_probs=73.2
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhHhhhhCCC---CC---cchHHHHHHH
Q 024854 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNNAGHL---PQ---LVPDQVLKLK 96 (261)
Q Consensus 24 ~aa~~lI~~AL~~p~vy~F~eLL~lp~v~~L~~-~~~~~~~~LL~iFa~Gt~~dy~~~~~~l---~~---L~~~~~~KLr 96 (261)
.....+...+|..-.+-+|.-++..-.-...+. .+-..++.|.+.+-.|+|..|-+..... +. +-+.-...+|
T Consensus 5 ~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR 84 (143)
T PF10075_consen 5 EIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIR 84 (143)
T ss_dssp HHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHH
T ss_pred hHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHH
Confidence 344455566666666788888877444333332 4567789999999999999988732211 11 2344567777
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 97 ~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
.=++-.+......|+.+.+++-||++ ..+++.++.
T Consensus 85 ~~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~ 119 (143)
T PF10075_consen 85 ERIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK 119 (143)
T ss_dssp HHHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred HHHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence 76777777789999999999999998 999999887
No 19
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=89.11 E-value=10 Score=40.20 Aligned_cols=49 Identities=16% Similarity=0.212 Sum_probs=43.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
...+|+|+.|.+-.-.=|.-+||.+++ +|...+.+..+||...++|.+.
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 467888988888665556889999999 9999999999999999999987
No 20
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=87.52 E-value=1.6 Score=41.98 Aligned_cols=114 Identities=15% Similarity=0.244 Sum_probs=79.2
Q ss_pred hhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhhCCC-CCcch-----HHHHHH----HHHHhhhcccCCcccCh
Q 024854 43 SEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHL-PQLVP-----DQVLKL----KQLTVLTLAETNKVLPY 112 (261)
Q Consensus 43 ~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~~~~l-~~L~~-----~~~~KL----r~LTllsLa~~~k~Isy 112 (261)
+.|+.-.......+..-..+...=+.|..-++.||..--..+ ++|-+ .....| =---|+.+.++..++..
T Consensus 269 ~~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei 348 (411)
T KOG1463|consen 269 AALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEI 348 (411)
T ss_pred HHHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhH
Confidence 344444433334455556677777888888999998622211 22221 112221 11246667789999999
Q ss_pred HHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeec
Q 024854 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (261)
Q Consensus 113 ~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~ 158 (261)
+-|++-+|++ +..||.=+= ..|-...+.|.|||-++|+.|.--.
T Consensus 349 ~hIA~~IGl~-~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e~ 392 (411)
T KOG1463|consen 349 SHIAEVIGLD-VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEEP 392 (411)
T ss_pred HHHHHHHCCC-cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeCCC
Confidence 9999999998 999999888 8888899999999999999996443
No 21
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=85.54 E-value=15 Score=35.37 Aligned_cols=110 Identities=18% Similarity=0.291 Sum_probs=74.7
Q ss_pred hhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhh-----CCCC--C-cchH---HHHHHHHHHhhhcccCCcccCh
Q 024854 44 EILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNA-----GHLP--Q-LVPD---QVLKLKQLTVLTLAETNKVLPY 112 (261)
Q Consensus 44 eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~~-----~~l~--~-L~~~---~~~KLr~LTllsLa~~~k~Isy 112 (261)
-.+..|-|.+.-.+ -..+-+++.-+-.-+|++|-..- ..+. . |.|- -.+-||...--.|-+..|.++.
T Consensus 242 KVi~~~Evl~vl~~-l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l 320 (393)
T KOG0687|consen 242 KVIKCPEVLEVLHK-LPSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTL 320 (393)
T ss_pred hhcCcHHHHHHhhc-CchHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44445555443322 22345555555555666654311 1111 1 2332 2677888888888889999999
Q ss_pred HHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEe
Q 024854 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (261)
Q Consensus 113 ~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~ 156 (261)
+-.|++.|++ ++-++.=+= +-|-+|=++++||-++++|++++
T Consensus 321 ~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNr 362 (393)
T KOG0687|consen 321 ESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNR 362 (393)
T ss_pred HHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCC
Confidence 9999999997 887777777 77789999999999999999985
No 22
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.04 E-value=8.8 Score=31.64 Aligned_cols=80 Identities=19% Similarity=0.336 Sum_probs=58.6
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEE-ec-CCCCEEEEEeecCCCCCCCcHH-HHHHHHHHHHHHH
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK-LD-QLRRCFEVQFAAGRDLRPGQLG-SMIQTLSNWLTTS 181 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~Gk-ID-Q~~~~v~V~~~~~Rdl~~~q~~-~L~~~L~~W~~~~ 181 (261)
+.++.++-++|++.|+++ ...|..-|= +.+..|+|.=. .. ...+..++... ++++++. .+...|+.|++.+
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 368889999999999997 888888877 89999998633 33 23333333323 3456665 3688999999999
Q ss_pred HHHHHHHHH
Q 024854 182 DNLLISIQE 190 (261)
Q Consensus 182 ~~~l~~ie~ 190 (261)
...+...+.
T Consensus 112 ~~~i~~~~~ 120 (126)
T COG3355 112 KQLIEEFEK 120 (126)
T ss_pred HHHHHHHhc
Confidence 998887654
No 23
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.58 E-value=2.4 Score=38.78 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=42.9
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
++.-..++++++.++|+.+.++. ..+.=+-+= +.+..|++.|-||...+-++|+
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 44555689999999999999997 444333444 5666799999999999999997
No 24
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=80.66 E-value=5.3 Score=29.67 Aligned_cols=58 Identities=17% Similarity=0.230 Sum_probs=39.6
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 95 Lr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
++.|..+......+.++-.+|++.++++ ...|+.++= ....+|+|+..= ..++.+...
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 3444444443455569999999999998 999999877 888999987652 444554443
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=79.64 E-value=1.6 Score=31.49 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=32.7
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
|......++.+|+++|+.+++++ ...||.++= .-+..|-|+-
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 34444578899999999999998 999999887 8899998873
No 26
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=79.48 E-value=7.7 Score=36.82 Aligned_cols=100 Identities=18% Similarity=0.254 Sum_probs=71.6
Q ss_pred chHHHHHHHHHhcCChhhHhhh-hCCCCCcchH-----HH----HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 024854 59 NSKYLDMLRLFAHGTWSDYKNN-AGHLPQLVPD-----QV----LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (261)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~-~~~l~~L~~~-----~~----~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (261)
-..+...-+.|..-++.||... ...-|+|-.+ .+ .-|---.|+.+.++-.++..+-|++-+|++ +.+||
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 3456667778888889998752 2222222211 11 112122456667788999999999999997 99999
Q ss_pred HHHHHHhHhcCceEEEecCCCCEEEEEeecCC
Q 024854 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (261)
Q Consensus 129 ~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~R 160 (261)
.=+= ..|-..++-|.+||.++|+.|.--...
T Consensus 362 gKLs-qMILDKifyG~LDqg~gcLivy~ep~q 392 (421)
T COG5159 362 GKLS-QMILDKIFYGTLDQGDGCLIVYGEPAQ 392 (421)
T ss_pred HHHH-HHHHHHHHHhhhccCCceEEEeCCccc
Confidence 8888 888889999999999999999754433
No 27
>PRK01919 tatB sec-independent translocase; Provisional
Probab=79.47 E-value=12 Score=32.44 Aligned_cols=59 Identities=10% Similarity=0.261 Sum_probs=42.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.|+|+.+..+..++..|..++....+.+.+.+...-... +-.+.++++++...+++.++
T Consensus 19 V~GPekLP~~aRtlGk~i~k~Rr~~~d~K~ev~~E~e~d-Elrk~~~~~e~~~~~v~~si 77 (169)
T PRK01919 19 VIGPERLPRVARTAGALFGRAQRYINDVKAEVSREIELD-ELRKMKTDFESAARDVENTI 77 (169)
T ss_pred eeCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH-HHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999888887543332 22344555555555555554
No 28
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=78.84 E-value=3.6 Score=31.65 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=33.4
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
|+.....+..+||.+|++.++++ ...+-..+- .....|+|.+
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 33333445679999999999998 888888888 8888999883
No 29
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=76.40 E-value=4 Score=33.91 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=38.1
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE---EecCC
Q 024854 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQL 148 (261)
Q Consensus 99 TllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G---kIDQ~ 148 (261)
.|+.+-+.+...||.+|++.||++ ...|-.-+= +....|+|+| -+|..
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 344444667899999999999997 888888877 8888999985 45653
No 30
>PRK04098 sec-independent translocase; Provisional
Probab=76.31 E-value=18 Score=30.89 Aligned_cols=60 Identities=20% Similarity=0.292 Sum_probs=44.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD---SMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~---~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.|+|+.++.+...+..|...+......+.+.+...- ..++...+-++.++...+++++.+
T Consensus 19 vfGP~KLP~~~r~lGk~ir~~K~~~~~~k~~l~~Ei~~~elk~e~~k~k~~l~~~~~~l~~~~ 81 (158)
T PRK04098 19 FLGPDKLPQAMVDIAKFFKAVKKTINDAKSTLDKEINIEEIKEEALKYKKEFESAVESLKKKL 81 (158)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 489999999999999999988888888766665432 334444555777788888887744
No 31
>PRK04654 sec-independent translocase; Provisional
Probab=73.41 E-value=18 Score=32.36 Aligned_cols=36 Identities=14% Similarity=0.197 Sum_probs=30.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD 196 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~ 196 (261)
.|+|+.|..+...+..|..++.+....+.+.+.+--
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~El 54 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELEREL 54 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 479999999999999999998888888777776543
No 32
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=70.78 E-value=12 Score=30.39 Aligned_cols=43 Identities=19% Similarity=0.357 Sum_probs=35.2
Q ss_pred Hhhhcc--cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 99 TVLTLA--ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 99 TllsLa--~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
.++.|| ..++.++-++|++.+++| ...|+.++= ..-.+|||..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence 344444 345689999999999998 999999888 8888999985
No 33
>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=70.70 E-value=17 Score=27.46 Aligned_cols=35 Identities=11% Similarity=0.261 Sum_probs=30.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a 195 (261)
.|+|+.++.+...+..|........+.+++.+...
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~e 52 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDEE 52 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHHH
Confidence 47899999999999999999999988888877543
No 34
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=69.96 E-value=5.9 Score=32.20 Aligned_cols=42 Identities=17% Similarity=0.270 Sum_probs=33.5
Q ss_pred hhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEE
Q 024854 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (261)
Q Consensus 101 lsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~Gk 144 (261)
+.+-+.+..+||.+|++.+|++ ...+=.-|= +....|+|+|.
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 3333445559999999999998 888887777 88889999875
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=69.73 E-value=9.1 Score=25.18 Aligned_cols=41 Identities=20% Similarity=0.368 Sum_probs=30.1
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
|+.+...+..++-.+|++.++++ ...|-..+= +....|+|+
T Consensus 8 Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 8 ILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 44444456669999999999997 888887666 888888875
No 36
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=69.27 E-value=20 Score=32.09 Aligned_cols=62 Identities=11% Similarity=0.165 Sum_probs=49.3
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 92 ~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
+.=|+.|.++........+|..+|++.|+++ ...+=..|- +.-..|+|.-..+...+.+.++
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 3446666777666677789999999999997 777777777 8888999999999877666665
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=68.79 E-value=5.2 Score=31.05 Aligned_cols=36 Identities=17% Similarity=0.499 Sum_probs=27.8
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhc
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYT 138 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~ 138 (261)
|..|...-..+||++|-+. +||...||+||| +.+..
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 789999999999 77643
No 38
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.69 E-value=9.6 Score=32.02 Aligned_cols=43 Identities=12% Similarity=0.179 Sum_probs=35.8
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 99 TllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
.|+.+-+.+..+||.+|++.+|++ ...|-.-+= +....|+|+|
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~ 60 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQG 60 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEE
Confidence 455555788999999999999998 878877776 8888999976
No 39
>PRK01770 sec-independent translocase; Provisional
Probab=66.35 E-value=23 Score=30.67 Aligned_cols=35 Identities=20% Similarity=0.449 Sum_probs=31.1
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a 195 (261)
.|+|+.+..+..++..|...+..+...+++.+.+-
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~E 53 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQE 53 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999999999988777653
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=65.81 E-value=22 Score=28.16 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.7
Q ss_pred HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEE
Q 024854 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (261)
Q Consensus 93 ~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~Gk 144 (261)
.-++.|..+....+...++..+|++.+++| ...|..++= .....|+|...
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=63.65 E-value=18 Score=30.76 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=37.1
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEE
Q 024854 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (261)
Q Consensus 96 r~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~Gk 144 (261)
+.|..++.....+.++-++|++.+++| ..-|+.++- ..-.+|||...
T Consensus 12 ~~l~~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s~ 58 (164)
T PRK10857 12 TAMLDVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeC
Confidence 333333433456689999999999998 999999988 89999999973
No 42
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=62.84 E-value=6.8 Score=27.42 Aligned_cols=35 Identities=29% Similarity=0.481 Sum_probs=24.4
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHH
Q 024854 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (261)
Q Consensus 96 r~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lv 131 (261)
|++.|+.+....+.+++++|++.++++ .+.+-..|
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 444555544448899999999999997 76665543
No 43
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=59.39 E-value=42 Score=26.72 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=32.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEE
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~Gk 144 (261)
.+..++..+|++.++++ ...|...+= ....+|+|.+.
T Consensus 22 ~~~~~s~~eia~~l~is-~~~v~~~l~-~L~~~Gli~~~ 58 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLN-APTVSKILK-QLSLAGIVTSK 58 (130)
T ss_pred CCCCccHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 35679999999999998 999999887 88899999874
No 44
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=58.93 E-value=21 Score=26.21 Aligned_cols=46 Identities=24% Similarity=0.219 Sum_probs=35.4
Q ss_pred HHHHhhhcccC-CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 96 KQLTVLTLAET-NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 96 r~LTllsLa~~-~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
|.+.|+.+... ...++..+|++.++++ ...|-..+- .....|+|..
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 34555554443 3689999999999998 888888887 7788899875
No 45
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=56.46 E-value=72 Score=25.60 Aligned_cols=38 Identities=11% Similarity=0.147 Sum_probs=32.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSM 198 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~ 198 (261)
.|+|+.+..+...+..|..........+++.+..--..
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~E~~~ 56 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQEESRT 56 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999888887644333
No 46
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=55.89 E-value=32 Score=28.71 Aligned_cols=52 Identities=21% Similarity=0.236 Sum_probs=39.5
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCC
Q 024854 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (261)
Q Consensus 95 Lr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~ 148 (261)
++.|..++.-..++.++-++|++..+|+ ..-++.++- ..-.+|||+..=--.
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 3444444444455588999999999998 999999998 899999998654433
No 47
>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=53.99 E-value=19 Score=24.17 Aligned_cols=35 Identities=31% Similarity=0.400 Sum_probs=23.7
Q ss_pred HHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 97 QLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 97 ~LTllsLa-~~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
+..|+.+. +....+|-++|++.|+|+ .+.|..-|=
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHH
Confidence 34444443 455559999999999997 777766543
No 48
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=53.56 E-value=1.4e+02 Score=26.91 Aligned_cols=105 Identities=20% Similarity=0.260 Sum_probs=57.3
Q ss_pred HHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCC-------------EEEEE------eecCCCCCCCcHHHHHHH
Q 024854 113 DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR-------------CFEVQ------FAAGRDLRPGQLGSMIQT 173 (261)
Q Consensus 113 ~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~-------------~v~V~------~~~~Rdl~~~q~~~L~~~ 173 (261)
.+|++.+|++.-.-+++|=| .-.+|||..+++-..+ +++|+ |+...+....+++...-.
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 46888899985556777766 4678999999988777 34444 344444444444443333
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 174 LSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 174 L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
+..-.. ...-+..+..+...+|..-+.-.+.+.+++....++.+.+
T Consensus 110 ~~~~~~-s~~~~~~l~srl~~~~~~~e~l~~~~~~L~~~~~el~~ri 155 (217)
T COG1777 110 VSKLFK-SPEGISELISRLLEINREIEELSRAQTELQKQLNELMDRI 155 (217)
T ss_pred hhhhcc-cchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 221111 1112333334444455444444444555555555555555
No 49
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=52.77 E-value=28 Score=28.08 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=33.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEE
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V 154 (261)
....+..+|++.++++ ...|-.=+= ..-.+|||..+-+.......+
T Consensus 28 ~~~~~v~ela~~l~ls-qstvS~HL~-~L~~AGLV~~~r~Gr~~~Y~l 73 (117)
T PRK10141 28 SGELCVCDLCTALDQS-QPKISRHLA-LLRESGLLLDRKQGKWVHYRL 73 (117)
T ss_pred cCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEEEEcCEEEEEE
Confidence 4568889999999998 555554443 355689999998876655554
No 50
>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=52.73 E-value=57 Score=27.63 Aligned_cols=62 Identities=15% Similarity=0.222 Sum_probs=44.7
Q ss_pred chHHHHHHHHHhcCChhhHhhhh--CCCCCcc----hHHHHHHHHHHhhhcccCCcc-cChHHHHHHcC
Q 024854 59 NSKYLDMLRLFAHGTWSDYKNNA--GHLPQLV----PDQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (261)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~--~~l~~L~----~~~~~KLr~LTllsLa~~~k~-Isy~~I~~~L~ 120 (261)
....+++...+..|+|..|-... ...|.+. .....++|..++-+++...+. +|-+.+++-|+
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 45678899999999999998754 5555543 224778999888888887777 99999888775
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=52.48 E-value=27 Score=25.18 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=28.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
+.+..-|+.+|++.+++.|...|-..|- ..-..|+|+
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 3667789999999999998999998887 677777765
No 52
>PF13730 HTH_36: Helix-turn-helix domain
Probab=51.88 E-value=53 Score=21.91 Aligned_cols=47 Identities=21% Similarity=0.311 Sum_probs=35.7
Q ss_pred HHHHHHHhhhccc-CCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCce
Q 024854 93 LKLKQLTVLTLAE-TNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIV 141 (261)
Q Consensus 93 ~KLr~LTllsLa~-~~k~I-sy~~I~~~L~I~~~~evE~lvI~eAI~~gLI 141 (261)
.|+-.+.|.+.+. .+.+. |++.|++.++++ .+.|-..+= +....|+|
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 5666777888874 23344 799999999998 888888776 77777765
No 53
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=51.57 E-value=1.1e+02 Score=29.64 Aligned_cols=60 Identities=25% Similarity=0.338 Sum_probs=45.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHH
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTL 174 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L 174 (261)
.++.++-++|++.++++ .+.+++++= +...+|+|. +-++. .|+..||.+.=.+..+.+.+
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 788889997 33221 38888987666666655543
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=51.51 E-value=9.9 Score=25.03 Aligned_cols=28 Identities=29% Similarity=0.449 Sum_probs=18.7
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHH
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELE 128 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (261)
|+.+-+.+...||.+|++.+|++ ...|-
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 44444556889999999999997 65554
No 55
>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=51.42 E-value=38 Score=22.69 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=32.4
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 96 r~LTllsL-a~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
|-+.|+.. +.....++..+|+++++++ ...+-.++- .....|+|.
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 34556653 4456668999999999998 778887776 677777764
No 56
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=50.75 E-value=26 Score=25.16 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=29.7
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
.++-.+|+++|+|+ ...|-..+- .....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~-~~~v~r~L~-~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLP-KKEVNRVLY-SLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 49999999999998 889999999 8999999865
No 57
>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=50.46 E-value=1.1e+02 Score=26.48 Aligned_cols=103 Identities=18% Similarity=0.160 Sum_probs=55.4
Q ss_pred HHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH---HHH
Q 024854 117 EELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE---KIK 193 (261)
Q Consensus 117 ~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~---~i~ 193 (261)
+++||. ...|.++|- ..+..|+|+. ..=|+-.+.|+-|- .....+...+......++.+-..+.+ .+.
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 447887 788999888 7777776653 24456667787543 34444444444444444333333322 222
Q ss_pred HHHh------hhHHHHHHHHHHHHHHHHHHHhccccccCCc
Q 024854 194 WADS------MNEMDKKHRKDLEEKVEEAKKSLSHKADVDC 228 (261)
Q Consensus 194 ~a~~------~~~~~~~~~~~~~~~~~~~kk~~~~k~~~~~ 228 (261)
.+.. +........++++.+++.+++.+..-...|+
T Consensus 94 ~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el~~~~~~Dp 134 (188)
T PF03962_consen 94 EAKKGREESEEREELLEELEELKKELKELKKELEKYSENDP 134 (188)
T ss_pred HHHhcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCH
Confidence 2221 1122234445667777777777732234443
No 58
>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=50.44 E-value=75 Score=26.84 Aligned_cols=56 Identities=13% Similarity=0.258 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccccccCCcccccccccc
Q 024854 180 TSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSE 237 (261)
Q Consensus 180 ~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~~~k~~~~~~~~~~~~~~ 237 (261)
++-.++..++..+...+++...-..+++..+.+++.+|..+ ...++..|...+-+.
T Consensus 44 ~~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL--~~~m~~~g~~ki~t~ 99 (162)
T PF05565_consen 44 NIAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYL--LDAMEAAGIKKIKTP 99 (162)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHcCCceeecC
Confidence 33344555566666666777666777788899999999998 666666666655443
No 59
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=50.23 E-value=47 Score=26.50 Aligned_cols=94 Identities=19% Similarity=0.231 Sum_probs=50.3
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHH--HHHHHHHHHH----HHHHH
Q 024854 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG--SMIQTLSNWL----TTSDN 183 (261)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~--~L~~~L~~W~----~~~~~ 183 (261)
|.-+.|..+.+ ++.++.+|- .+.-|.|+...... .++|.=+. .|.+-.-+|. +.+..
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 44455666654 456776654 33455665544322 12222111 2333333443 44555
Q ss_pred HHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 184 LLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 184 ~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.+..+++.+..++...++....-++..+++..+|+.+
T Consensus 81 ~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~ 117 (118)
T PF13815_consen 81 QLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKES 117 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 5666667777777666665666666677777777665
No 60
>PRK00404 tatB sec-independent translocase; Provisional
Probab=50.01 E-value=1.1e+02 Score=25.72 Aligned_cols=37 Identities=16% Similarity=0.274 Sum_probs=30.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~ 197 (261)
.|+++.+..+..++..|..+..+....+.+.+.+--.
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 4799999999999999999988888877777665333
No 61
>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=49.91 E-value=58 Score=21.92 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=30.6
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecC
Q 024854 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (261)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ 147 (261)
+++.+|++.++++ ...+-..+- .....|+|...-+.
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 888887766 77789999987665
No 62
>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=49.28 E-value=32 Score=23.80 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=29.1
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEE
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~Gk 144 (261)
......+..+|++.++++ ...+-.=+= ....+|+|+..
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 766666555 56678998754
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=48.48 E-value=24 Score=23.54 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=20.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 024854 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (261)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~lvI~eAI 136 (261)
.-.||.+|++.++++ ...|..++- .|.
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 999998887 664
No 64
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=48.16 E-value=50 Score=26.86 Aligned_cols=50 Identities=12% Similarity=0.171 Sum_probs=37.1
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecC
Q 024854 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (261)
Q Consensus 96 r~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ 147 (261)
+.+..+.-...+..++-++|++.++|+ ..-|+..+- ..-..|+|..+=--
T Consensus 12 ~~~i~la~~~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~G~ 61 (141)
T PRK11014 12 RALIYMASLPEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVRGK 61 (141)
T ss_pred HHHHHHhcCCCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEecCC
Confidence 334444333456678999999999998 889999888 88888988765433
No 65
>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=48.03 E-value=1.6e+02 Score=27.59 Aligned_cols=65 Identities=14% Similarity=0.139 Sum_probs=47.0
Q ss_pred eecCCCCCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 156 FAAGRDLRPGQ-LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 156 ~~~~Rdl~~~q-~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
-.++.|++.++ +..+.+.|+..-.-++.+.+.|.+++..-...-+.-..+=...+++|+.++-+-
T Consensus 8 plI~~dLr~eEti~qi~~aL~~L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs~ 73 (297)
T PF11945_consen 8 PLIPPDLRREETILQIADALEYLDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGSK 73 (297)
T ss_pred cccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 35788888776 678899999999999999999999988655544443444444566777665543
No 66
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=47.55 E-value=24 Score=26.25 Aligned_cols=51 Identities=29% Similarity=0.315 Sum_probs=35.5
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCC
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~ 150 (261)
|.|+++-.....++|.+|.+.|+++ ...+-.-+= ....+|+|+-+=.-..+
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 4455544457889999999999997 766666655 67778999987665554
No 67
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=46.61 E-value=52 Score=27.45 Aligned_cols=39 Identities=18% Similarity=0.118 Sum_probs=33.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEec
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkID 146 (261)
.++.++-.+|++..+|| ..-|+.++- ....+|||...=-
T Consensus 21 ~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~rG 59 (153)
T PRK11920 21 DGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETVRG 59 (153)
T ss_pred CCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeecC
Confidence 34568999999999998 999999988 8888999987654
No 68
>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=46.50 E-value=31 Score=23.86 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=28.8
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCce
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI 141 (261)
-.|+.+....+.++..+|++.++++ ...+-.=+. ..-..|+|
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGLI 44 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCCE
Confidence 3456666778999999999999997 655544444 44445553
No 69
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=45.31 E-value=61 Score=23.75 Aligned_cols=50 Identities=14% Similarity=0.255 Sum_probs=33.8
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEE
Q 024854 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (261)
Q Consensus 99 TllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~ 155 (261)
.|+..+. ....++..|+..++++ ...+..++= ..+..|+|++ .++.+.+|
T Consensus 10 ~IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~-~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMYKANLN-YSTLKKYLK-ELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHHH--TT-B-HHHHHTTST---HHHHHHHHH-HHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCcCeeC----CCCEEEEC
Confidence 3444444 6778899999999997 889998877 8999999944 55555554
No 70
>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=44.91 E-value=59 Score=21.32 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=24.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
+..+..+|++.++++ ...|-.-+= .....|+|.
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 666665554 566677774
No 71
>PRK00708 sec-independent translocase; Provisional
Probab=44.54 E-value=79 Score=28.30 Aligned_cols=37 Identities=11% Similarity=0.136 Sum_probs=31.5
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~ 197 (261)
.|+|++|..|...+..|..++..+.+.+.+++...-.
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 5799999999999999999999888888887765433
No 72
>PHA01750 hypothetical protein
Probab=44.36 E-value=93 Score=22.96 Aligned_cols=35 Identities=23% Similarity=0.252 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 186 ISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 186 ~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
+.+.....+...+-+.-..++.++++.|+++|+-+
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 34455666666666666788888999999999876
No 73
>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=43.74 E-value=58 Score=22.90 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=32.5
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
.+|..|...+..++-.+|++.|+++ ...|=+.+= +.-..|+|.
T Consensus 11 ~~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~-~L~~~GlV~ 53 (60)
T PF01325_consen 11 KAIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLK-RLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEE
Confidence 3566666688999999999999997 666666666 677778775
No 74
>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=43.52 E-value=1.1e+02 Score=21.31 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=21.0
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
..-|.++..+|+++|||+ ...+-.-+=
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 356899999999999998 656555444
No 75
>PRK03100 sec-independent translocase; Provisional
Probab=43.42 E-value=55 Score=27.33 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=30.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~ 194 (261)
.|+|+.+..+...+..|........+.+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999888888877764
No 76
>PRK09954 putative kinase; Provisional
Probab=43.13 E-value=29 Score=32.46 Aligned_cols=54 Identities=19% Similarity=0.438 Sum_probs=41.1
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE---EecCCCCEEEEE
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQLRRCFEVQ 155 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G---kIDQ~~~~v~V~ 155 (261)
|+.+...+..+|+.+|++.|+++ ...|-..|- +....|+|.| .||.....+.|-
T Consensus 8 il~~l~~~~~~s~~~la~~l~~s-~~~v~~~i~-~L~~~g~i~~~~~~l~~~~~v~viG 64 (362)
T PRK09954 8 ILAILRRNPLIQQNEIADILQIS-RSRVAAHIM-DLMRKGRIKGKGYILTEQEYCVVVG 64 (362)
T ss_pred HHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCcCCcEEEEcCCccEEEEE
Confidence 45555577789999999999997 889998877 8888899875 456665554443
No 77
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=42.99 E-value=1.7e+02 Score=23.36 Aligned_cols=56 Identities=9% Similarity=-0.017 Sum_probs=40.9
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEee
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~ 157 (261)
|..|...+..++-.+|++.++++ ...|=..|- .....|+|.=.-|+.++....-+.
T Consensus 37 L~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~L 92 (144)
T PRK03573 37 LHNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKL 92 (144)
T ss_pred HHHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEE
Confidence 33444434456789999999997 666666666 888899999999987776555544
No 78
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=42.36 E-value=92 Score=22.30 Aligned_cols=61 Identities=11% Similarity=0.169 Sum_probs=47.8
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 024854 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (261)
Q Consensus 111 sy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~ 176 (261)
.|..+.+.+++++.. ..+++= + +.+-+-.++..+++.++....++.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~~~-~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPDEL-DNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCchh-hhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 367889999998332 344444 3 356778999999999999999999999999888887764
No 79
>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=42.00 E-value=20 Score=26.80 Aligned_cols=39 Identities=15% Similarity=0.296 Sum_probs=24.8
Q ss_pred hhhcccCCcccChHHHHHHcCC--CChHHHHHHHHHHhHhcC
Q 024854 100 VLTLAETNKVLPYDELMEELDV--TNVRELEDFLINECMYTG 139 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I--~~~~evE~lvI~eAI~~g 139 (261)
|+..+...+.|+|++|...|.= -+.+.++.++- ..-..|
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 13677777665 444444
No 80
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=41.10 E-value=46 Score=21.30 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=27.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
+..++-.+|++.++++ ...+...+= .....|+|.-
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~ 46 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTR 46 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 4569999999999997 888887766 6666777653
No 81
>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=40.98 E-value=37 Score=25.06 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=22.6
Q ss_pred HHhhhcccCCcccChHHHHHHcCCC-ChHHH
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVT-NVREL 127 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~-~~~ev 127 (261)
+.++.-...+++.||.+|++.++.+ ..+.|
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 4444445679999999999999996 35555
No 82
>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=40.65 E-value=97 Score=22.46 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=37.9
Q ss_pred cCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 138 TGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190 (261)
Q Consensus 138 ~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~ 190 (261)
.+-++..++-.++++.|.+.. .+...|...++.|...+.-+...+++
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 367889999999999999876 66789999999999988887777653
No 83
>PF13518 HTH_28: Helix-turn-helix domain
Probab=40.55 E-value=34 Score=22.35 Aligned_cols=43 Identities=12% Similarity=0.193 Sum_probs=28.3
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEec
Q 024854 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (261)
Q Consensus 99 TllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkID 146 (261)
.++.+...+ . |+.++++.++|+ ...|-.|+- .--..| +.|-.+
T Consensus 4 ~iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~-~y~~~G-~~~l~~ 46 (52)
T PF13518_consen 4 QIVELYLEG-E-SVREIAREFGIS-RSTVYRWIK-RYREGG-IEGLKP 46 (52)
T ss_pred HHHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH-HHHhcC-HHHhcc
Confidence 344444433 3 999999999995 899999976 433334 344333
No 84
>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=40.01 E-value=74 Score=24.28 Aligned_cols=50 Identities=18% Similarity=0.259 Sum_probs=37.0
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecC
Q 024854 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (261)
Q Consensus 96 r~LTllsL-a~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ 147 (261)
+.|.++.= +....=++.++|++.|+++ ..+|+..|= ..+..|.|=-.||.
T Consensus 51 ~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 51 KVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 34555544 4455569999999999997 999998877 88889998877775
No 85
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=38.10 E-value=1.1e+02 Score=19.82 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=29.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEec
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkID 146 (261)
...+++.+|++.++++ ...+-..+= .....|+|.-.=+
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 777777655 6777899874433
No 86
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=37.94 E-value=1.2e+02 Score=19.88 Aligned_cols=35 Identities=23% Similarity=0.284 Sum_probs=28.8
Q ss_pred CCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 106 TNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 106 ~~k~I-sy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
.+..+ |..+|++.++++ ...|-..+- .....|+|.
T Consensus 16 ~~~~l~s~~~la~~~~vs-~~tv~~~l~-~L~~~g~i~ 51 (60)
T smart00345 16 PGDKLPSERELAAQLGVS-RTTVREALS-RLEAEGLVQ 51 (60)
T ss_pred CCCcCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 45567 899999999997 888888877 777788875
No 87
>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=37.81 E-value=1.1e+02 Score=30.12 Aligned_cols=86 Identities=12% Similarity=0.210 Sum_probs=62.8
Q ss_pred hHHHHHHcCC----CChHHHHHHHHHHhHhcCceEEEecCC--CCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHH
Q 024854 112 YDELMEELDV----TNVRELEDFLINECMYTGIVRGKLDQL--RRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLL 185 (261)
Q Consensus 112 y~~I~~~L~I----~~~~evE~lvI~eAI~~gLI~GkIDQ~--~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l 185 (261)
.+++-+.|++ +.-+++...++ +|+..|+.----|.. .+.+... +..+..++.+.|.+++..-...-+.+-
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 4455565544 44578999999 999999877777765 3333333 666888999999999988877776777
Q ss_pred HHHHHHHHHHHhhhHH
Q 024854 186 ISIQEKIKWADSMNEM 201 (261)
Q Consensus 186 ~~ie~~i~~a~~~~~~ 201 (261)
..++.|-..||....+
T Consensus 417 ~~~~~q~~~a~~~~~~ 432 (438)
T TIGR02919 417 ELLEQQREHANDISKE 432 (438)
T ss_pred HHHHHHHHHhccCCHH
Confidence 7778888888876644
No 88
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=37.76 E-value=1.1e+02 Score=23.78 Aligned_cols=39 Identities=15% Similarity=0.080 Sum_probs=28.2
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCC
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~ 149 (261)
+....++.+++++.++++ .. ||. +.+..|+|.-.-+...
T Consensus 3 ~~~~~lt~~Elc~~~gi~-~~----~l~-eLve~GlIep~~~~~~ 41 (101)
T PRK10265 3 NVTVTFTITEFCLHTGVS-EE----ELN-EIVGLGVIEPREIQET 41 (101)
T ss_pred ceEEEeeHHHHHHHHCcC-HH----HHH-HHHHCCCeecCCCCcc
Confidence 344568999999999998 44 555 6666899986544433
No 89
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=37.35 E-value=1.5e+02 Score=23.67 Aligned_cols=56 Identities=20% Similarity=0.330 Sum_probs=35.9
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 159 GRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 159 ~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
+|.+.+..++.+..-|+.-.+.++.++.+ ++....++..+-|.+.+..+.++++.+
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 56677766777777776666666665554 233344555666667777777777776
No 90
>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=35.54 E-value=2.2e+02 Score=22.39 Aligned_cols=54 Identities=22% Similarity=0.276 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhccccccCC
Q 024854 172 QTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVD 227 (261)
Q Consensus 172 ~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~~~k~~~~ 227 (261)
+++.+=......+...+...-.............+.+-++..+.+|+.+ |.|.+
T Consensus 39 ~tI~qq~~~~~~L~~~~~~~r~~~~~~~~~~qq~r~~~e~~~e~ik~~l--k~d~C 92 (110)
T PF10828_consen 39 QTIQQQEDANQELKAQLQQNRQAVEEQQKREQQLRQQSEERRESIKTAL--KDDPC 92 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--ccCcc
Confidence 3333333333444444433333333333333344445566666777777 66655
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=34.50 E-value=1.4e+02 Score=19.94 Aligned_cols=41 Identities=22% Similarity=0.268 Sum_probs=32.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCC
Q 024854 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (261)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~ 150 (261)
..++..+|++.++++ ...|=..|= .....|+|.-.-|..++
T Consensus 20 ~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 20 EELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGDR 60 (62)
T ss_dssp SGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSST
T ss_pred CCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCCC
Confidence 359999999999998 788887776 88899999887776543
No 92
>PF05010 TACC: Transforming acidic coiled-coil-containing protein (TACC); InterPro: IPR007707 This family contains the proteins TACC 1, 2 and 3, found concentrated in the centrosomes of eukaryotes which may play a conserved role in organising centrosomal microtubules. The human TACC proteins have been linked to cancer and TACC2 has been identified as a possible tumour suppressor (AZU-1) [].
Probab=34.30 E-value=2.7e+02 Score=24.73 Aligned_cols=52 Identities=19% Similarity=0.180 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh-hHHHHHHHHHHHHHHHHHHH
Q 024854 167 LGSMIQTLSNWLTTSDNLLISIQEKIKWADSM-NEMDKKHRKDLEEKVEEAKK 218 (261)
Q Consensus 167 ~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~-~~~~~~~~~~~~~~~~~~kk 218 (261)
+.....++..|..+...+-...++++..||.+ ...+..|+.++..--+.+||
T Consensus 120 ~~ey~~~l~~~eqry~aLK~hAeekL~~ANeei~~v~~~~~~e~~aLqa~lkk 172 (207)
T PF05010_consen 120 IEEYEERLKKEEQRYQALKAHAEEKLEKANEEIAQVRSKHQAELLALQASLKK 172 (207)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Confidence 56678899999999999999999999999995 44456666666555455554
No 93
>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=33.83 E-value=67 Score=22.50 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=33.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEe
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkI 145 (261)
..+..+-.+|++.++++ ...|-..|= .....|+|.-.-
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 56789999999999998 889998877 899999997654
No 94
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=33.78 E-value=5.3e+02 Score=27.37 Aligned_cols=117 Identities=16% Similarity=0.171 Sum_probs=70.1
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHh--HhcCceEEEec--CCCCEEEEEee----cCCC----C
Q 024854 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINEC--MYTGIVRGKLD--QLRRCFEVQFA----AGRD----L 162 (261)
Q Consensus 95 Lr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eA--I~~gLI~GkID--Q~~~~v~V~~~----~~Rd----l 162 (261)
+-+++++-|-+..-.++|.+|++.++++ ..++=..+- .. +-..++.+..+ ..+..+.+++. ..|+ +
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 4567788888888889999999999998 888777665 43 22222222111 45677777752 2332 2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 163 RPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 163 ~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
...+-+....+++.|+.. .|++.|.++=+.. ++..|.+=+.+=++.+++..
T Consensus 644 ~~~e~~~~~~~ve~dRk~------~i~AaIVRIMK~r-K~l~h~~Lv~Ev~~ql~~RF 694 (725)
T KOG2166|consen 644 PMDERKKVVEDVDKDRKY------AIDAAIVRIMKSR-KVLGHQQLVSEVVEQLSERF 694 (725)
T ss_pred CchhHHHHHhhhhhHHHH------HHHHHHHHHHHhh-ccccHHHHHHHHHHHHhhhc
Confidence 233566778888888752 3444444433222 33555555555555555555
No 95
>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=33.55 E-value=1.4e+02 Score=19.52 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=21.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI 136 (261)
....||.+|++.+|++ ...|-.+.- .|+
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 877777665 665
No 96
>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=32.30 E-value=48 Score=23.77 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.2
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
.++.-+.++||+.|||+ ..+|..++-
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 47889999999999998 999997654
No 97
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=32.11 E-value=1.6e+02 Score=24.38 Aligned_cols=23 Identities=9% Similarity=0.153 Sum_probs=15.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhc
Q 024854 198 MNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 198 ~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
+.+....++++.++++++++..+
T Consensus 43 e~~~~~~~~~er~~kl~~~r~~m 65 (135)
T PRK10947 43 EESAAAAEVEERTRKLQQYREML 65 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344455556677888888888
No 98
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=31.97 E-value=54 Score=31.33 Aligned_cols=63 Identities=17% Similarity=0.267 Sum_probs=52.5
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEe
Q 024854 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (261)
Q Consensus 92 ~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~ 156 (261)
.+-||.=.-..|-+..+.++.+..|+..+++ ++-|+.=+= +-|-.|-+...||-+|++|++++
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg-~FIp~~~LncvIDRvnGvVetnr 376 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLG-EFIPEGRLNCVIDRVNGVVETNR 376 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHH-hhCCCCceeeeeecccceEeccC
Confidence 4666666667777889999999999999997 877776666 66667899999999999999875
No 99
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=31.75 E-value=1.2e+02 Score=25.16 Aligned_cols=52 Identities=13% Similarity=0.302 Sum_probs=42.1
Q ss_pred cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCce
Q 024854 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (261)
Q Consensus 87 L~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI 141 (261)
+++.+..+| ...|+.|+..++-+++.++...+|++ ...++.++- +++..|-|
T Consensus 5 ~T~eer~eL-k~rIvElVRe~GRiTi~ql~~~TGas-R~Tvk~~lr-eLVa~G~l 56 (127)
T PF06163_consen 5 FTPEEREEL-KARIVELVREHGRITIKQLVAKTGAS-RNTVKRYLR-ELVARGDL 56 (127)
T ss_pred CCHHHHHHH-HHHHHHHHHHcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCCe
Confidence 455544433 36788899999999999999999997 999999999 89887743
No 100
>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=31.50 E-value=2.2e+02 Score=21.18 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=49.2
Q ss_pred HHhhhcccCCcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEee-cCCCCCCCcHHHHHHHHH
Q 024854 98 LTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA-AGRDLRPGQLGSMIQTLS 175 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L-~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~-~~Rdl~~~q~~~L~~~L~ 175 (261)
+.|..|.. +...|.+|.+.+ +++ ...+-+-+= +....|||.=...... -..|.|. +++- .++..+...|.
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 34445544 789999999999 886 777777666 7888999987766433 3344442 2111 24566788888
Q ss_pred HHHHH
Q 024854 176 NWLTT 180 (261)
Q Consensus 176 ~W~~~ 180 (261)
.|...
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88753
No 101
>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=31.39 E-value=2.8e+02 Score=22.39 Aligned_cols=57 Identities=16% Similarity=0.194 Sum_probs=32.9
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 164 PGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 164 ~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.+++....+.+..+...++--+.-.+..+..-..+.+.......+++.+++.+|+.+
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 355666666666666666655555443333222255555666667777777777665
No 102
>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=30.89 E-value=1.7e+02 Score=19.85 Aligned_cols=50 Identities=16% Similarity=0.259 Sum_probs=32.7
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCE
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~ 151 (261)
|..++......+..+|++.++++ ...+=..|= +.+..|+|.=.=|..++.
T Consensus 9 L~~l~~~~~~~t~~~l~~~~~~~-~~~vs~~i~-~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 9 LRALAHSDGPMTQSDLAERLGIS-KSTVSRIIK-KLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp HHHHT--TS-BEHHHHHHHTT---HHHHHHHHH-HHHHTTSEEEEEESSCTT
T ss_pred HHHHHccCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEecCCCCcCC
Confidence 33444577888899999999997 777776554 888899997665554433
No 103
>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=29.66 E-value=96 Score=20.76 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=33.6
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCC
Q 024854 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~ 150 (261)
.....++..+|++.++++ ...+=.++= .....|+|.=.-|+.++
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 666766655 78889999988887665
No 104
>PRK10884 SH3 domain-containing protein; Provisional
Probab=29.54 E-value=1.8e+02 Score=25.76 Aligned_cols=13 Identities=23% Similarity=0.355 Sum_probs=7.4
Q ss_pred cccccCCCCCccc
Q 024854 233 EIYSEPGGVMDYE 245 (261)
Q Consensus 233 ~~~~~~~~~~~~~ 245 (261)
.++...+|+...+
T Consensus 172 ~wf~~Gg~v~~~G 184 (206)
T PRK10884 172 QWFMYGGGVAGIG 184 (206)
T ss_pred HHHHHchHHHHHH
Confidence 4566666664444
No 105
>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=29.49 E-value=1.6e+02 Score=23.37 Aligned_cols=42 Identities=19% Similarity=0.332 Sum_probs=36.4
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024854 158 AGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN 199 (261)
Q Consensus 158 ~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~ 199 (261)
.++.++++++..+.+.+..|.+.+-.=+..+...++......
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 578889999999999999999999888999988888766654
No 106
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=29.43 E-value=2.2e+02 Score=20.47 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=34.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCC
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~ 149 (261)
...++..+|++.++++ ...+-..|- +....|+|.-.-++.+
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 888888877 8999999987766544
No 107
>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=29.13 E-value=1.1e+02 Score=24.79 Aligned_cols=42 Identities=19% Similarity=0.288 Sum_probs=32.9
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
-.|+.||.. .+|-.||+..|++| ..-+--++= +.+..|+|.-
T Consensus 46 ~~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvs-DL~~~G~v~v 87 (114)
T PF05331_consen 46 RAILELCRR--PLSVAEIAARLGLP-LGVVRVLVS-DLADAGLVRV 87 (114)
T ss_pred HHHHHHHCC--CccHHHHHHhhCCC-chhhhhhHH-HHHhCCCEEE
Confidence 467888877 89999999999999 766665555 7888887653
No 108
>PRK00182 tatB sec-independent translocase; Provisional
Probab=28.63 E-value=2e+02 Score=24.76 Aligned_cols=33 Identities=12% Similarity=0.275 Sum_probs=27.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~ 193 (261)
.|+|+.+..+...+..|........+...+.+.
T Consensus 20 VfGPerLP~~~r~lg~~ir~~R~~~~~~k~el~ 52 (160)
T PRK00182 20 VIGPERLPRLIEDVRAALLAARTAINNAKQQLD 52 (160)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999988888777666655
No 109
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=28.61 E-value=2e+02 Score=23.90 Aligned_cols=22 Identities=14% Similarity=0.237 Sum_probs=15.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhc
Q 024854 199 NEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 199 ~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.++..+++++..+.++++++.+
T Consensus 44 ~~~~~~~~~er~~~l~~i~~~~ 65 (134)
T PRK10328 44 EEQQQRELAERQEKINTWLELM 65 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344566667778888888887
No 110
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=28.07 E-value=4.9e+02 Score=24.08 Aligned_cols=83 Identities=14% Similarity=0.300 Sum_probs=54.8
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHH
Q 024854 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179 (261)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~ 179 (261)
|.-++-....+.-.+|+++|+|+ ...|=+.+= +.+..|+|+- ..++.-.|| ++-.+-|.+.+.+.+.
T Consensus 16 L~ei~~~qp~v~q~eIA~~lgiT-~QaVsehiK-~Lv~eG~i~~---~gR~~Y~iT--------kkG~e~l~~~~~dlr~ 82 (260)
T COG1497 16 LSEIAVRQPRVKQKEIAKKLGIT-LQAVSEHIK-ELVKEGLIEK---EGRGEYEIT--------KKGAEWLLEQLSDLRR 82 (260)
T ss_pred HHHHHHhCCCCCHHHHHHHcCCC-HHHHHHHHH-HHHhccceee---cCCeeEEEe--------hhHHHHHHHHHHHHHH
Confidence 33344456778889999999997 988888888 7888777653 222244443 2334557777777766
Q ss_pred HHHHHHHHHHHHHHHH
Q 024854 180 TSDNLLISIQEKIKWA 195 (261)
Q Consensus 180 ~~~~~l~~ie~~i~~a 195 (261)
-++.+...+...+.|.
T Consensus 83 f~~ev~~~l~~~~vw~ 98 (260)
T COG1497 83 FSEEVELVLDYVMVWT 98 (260)
T ss_pred HHHHHHHHHhhHHHHH
Confidence 6666655555555554
No 111
>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=28.06 E-value=1.2e+02 Score=20.46 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=28.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
...++..+|++.++++ ...+...+= .....|+|.-
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 4568999999999997 888888766 7778888864
No 112
>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=27.98 E-value=3.6e+02 Score=22.51 Aligned_cols=111 Identities=19% Similarity=0.255 Sum_probs=66.2
Q ss_pred cCCcccChHHHHHHcC--CCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCC---CCCCcHHHHHHHHHHHHH
Q 024854 105 ETNKVLPYDELMEELD--VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRD---LRPGQLGSMIQTLSNWLT 179 (261)
Q Consensus 105 ~~~k~Isy~~I~~~L~--I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rd---l~~~q~~~L~~~L~~W~~ 179 (261)
..+|..+..+|...|+ ++ =..|...+= .+...|.|.+|.-... .|.|+.... ++++++..|-..+....+
T Consensus 12 ~qNRPys~~di~~nL~~~~~-K~~v~k~Ld-~L~~~g~i~~K~~GKq---kiY~~~Q~~~~~~s~eel~~ld~ei~~L~~ 86 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVG-KTAVQKALD-SLVEEGKIVEKEYGKQ---KIYFANQDELEVPSPEELAELDAEIKELRE 86 (169)
T ss_pred HcCCCCcHHHHHHHHHhhcc-HHHHHHHHH-HHHhCCCeeeeeecce---EEEeeCccccCCCCchhHHHHHHHHHHHHH
Confidence 4688899999999995 43 345555444 5666799999975544 444444333 457888888777777766
Q ss_pred HHHHHHHH---HHHHHHHHHhh--hHHHHHHHHHHHHHHHHHHHhc
Q 024854 180 TSDNLLIS---IQEKIKWADSM--NEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 180 ~~~~~l~~---ie~~i~~a~~~--~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.+..+-.. ++..++..++. .++-...-.+++++++.+...+
T Consensus 87 el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL 132 (169)
T PF07106_consen 87 ELAELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKL 132 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 55555444 34444444432 2222333344555555555554
No 113
>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=27.82 E-value=2.2e+02 Score=24.43 Aligned_cols=56 Identities=9% Similarity=0.204 Sum_probs=40.0
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 165 ~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
.....+...|..|...+..=...+......+...-.-....=..++.++++++..|
T Consensus 124 ~~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I 179 (184)
T PF05791_consen 124 DKVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEI 179 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHH
Confidence 34567788888888888887777777777776655555556667778888888777
No 114
>PRK10870 transcriptional repressor MprA; Provisional
Probab=27.34 E-value=3.8e+02 Score=22.62 Aligned_cols=55 Identities=16% Similarity=0.071 Sum_probs=40.9
Q ss_pred hhhccc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEe
Q 024854 100 VLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQF 156 (261)
Q Consensus 100 llsLa~-~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~ 156 (261)
|..|.. .+..++..+|++.++++ ...+=..|= +....|+|.=.-|..++....-.
T Consensus 61 L~~L~~~~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~ 116 (176)
T PRK10870 61 LITLESQENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQ 116 (176)
T ss_pred HHHHhcCCCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEE
Confidence 334443 46789999999999997 666665555 78889999999998876655444
No 115
>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=26.59 E-value=59 Score=24.26 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=20.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 024854 108 KVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
.-.||.+|++.++++ ...|..++-
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~ 54 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLK 54 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHh
Confidence 668999999999998 888887755
No 116
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=26.56 E-value=1.5e+02 Score=31.33 Aligned_cols=113 Identities=12% Similarity=0.254 Sum_probs=72.4
Q ss_pred hhhcCchhhhccCCCc---hHHHHHHHHHhcCChhhHhh---h----hCCCCCcc---hHHHHHHHHHH----hhhcccC
Q 024854 44 EILAVPNIAEFEGTEN---SKYLDMLRLFAHGTWSDYKN---N----AGHLPQLV---PDQVLKLKQLT----VLTLAET 106 (261)
Q Consensus 44 eLL~lp~v~~L~~~~~---~~~~~LL~iFa~Gt~~dy~~---~----~~~l~~L~---~~~~~KLr~LT----llsLa~~ 106 (261)
-.|..--=|.+.++|- .-+..-=+.+..|+|.+-.. + ++-+|.-. .-...+++-=+ |.+.+.-
T Consensus 636 r~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~ 715 (843)
T KOG1076|consen 636 RQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSV 715 (843)
T ss_pred HHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 3444333344455431 22455567788899987443 2 23455421 11133333322 3344445
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeec
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~ 158 (261)
+..+|.+.||+-.++| +..|=..|= +.|-..=|.+++||..+||.+.++.
T Consensus 716 Y~SvSl~~LA~mFdLp-~~~VhsIiS-kmiineEl~AslDqpt~~iv~hrvE 765 (843)
T KOG1076|consen 716 YDSVSLAKLADMFDLP-EPKVHSIIS-KMIINEELHASLDQPTQCIVMHRVE 765 (843)
T ss_pred hhhccHHHHHHHhCCC-chhHHHHHH-HHHHHHHhhhccCCCcceEEEeecc
Confidence 8899999999999998 878777666 7777788999999999999998754
No 117
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=26.55 E-value=1.3e+02 Score=18.81 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=27.4
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE
Q 024854 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (261)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G 143 (261)
.++..+|++.++++ ...+-..+- .....|+|.-
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~-~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLK-RLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 36789999999997 888888777 7888888863
No 118
>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=26.19 E-value=1.9e+02 Score=24.95 Aligned_cols=53 Identities=15% Similarity=0.214 Sum_probs=36.7
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEE
Q 024854 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (261)
Q Consensus 99 TllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V 154 (261)
.++.....++.++..+|++.++++ ...+-..+- .....|+|.-.-+ ..+.+.+
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEe
Confidence 333333344569999999999997 777887777 7788899986533 4444444
No 119
>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=25.12 E-value=2.8e+02 Score=20.71 Aligned_cols=42 Identities=12% Similarity=0.195 Sum_probs=26.6
Q ss_pred EEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 152 FEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (261)
Q Consensus 152 v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~ 193 (261)
-.|...+|+.|=....+.+...|..=...++.-+..++.+..
T Consensus 45 ~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~ 86 (106)
T PF01920_consen 45 RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLK 86 (106)
T ss_dssp -EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456788887778878777776666665555555554443
No 120
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.08 E-value=2.9e+02 Score=21.44 Aligned_cols=45 Identities=20% Similarity=0.309 Sum_probs=29.9
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCceEE-EecCCCCEEEEEeecCCCCCCCcHHHH
Q 024854 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLDQLRRCFEVQFAAGRDLRPGQLGSM 170 (261)
Q Consensus 111 sy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~G-kIDQ~~~~v~V~~~~~Rdl~~~q~~~L 170 (261)
+..++++.+||+ .+.+-.|- + .|+|.. .-+. .-.|.++++++..+
T Consensus 2 ~i~e~a~~~gvs-~~tlr~ye--~---~gll~~~~r~~---------~gyR~Y~~~~l~~l 47 (113)
T cd01109 2 TIKEVAEKTGLS-ADTLRYYE--K---EGLLPPVKRDE---------NGIRDFTEEDLEWL 47 (113)
T ss_pred CHHHHHHHHCcC-HHHHHHHH--H---CCCCCCCCcCC---------CCCccCCHHHHHHH
Confidence 578999999998 88888772 2 477742 1111 23577777776654
No 121
>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=25.02 E-value=2.3e+02 Score=20.08 Aligned_cols=33 Identities=18% Similarity=0.352 Sum_probs=15.6
Q ss_pred HHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 188 ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
||+.+......-.--++.-+++.+.++.++.++
T Consensus 5 lEn~~~~~~~~i~tvk~en~~i~~~ve~i~env 37 (55)
T PF05377_consen 5 LENELPRIESSINTVKKENEEISESVEKIEENV 37 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444333333444445555555555555
No 122
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=24.96 E-value=81 Score=26.32 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI 136 (261)
-..+||.+|++.++|+ +..|...+- .|.
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 123
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=24.53 E-value=2.1e+02 Score=24.71 Aligned_cols=21 Identities=10% Similarity=0.203 Sum_probs=17.2
Q ss_pred ChHHHHHHcCCCChHHHHHHHH
Q 024854 111 PYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 111 sy~~I~~~L~I~~~~evE~lvI 132 (261)
+..++++.+||+ ...|-.|.=
T Consensus 2 ti~evA~~lGVS-~~TLRrw~k 22 (175)
T PRK13182 2 KTPFVAKKLGVS-PKTVQRWVK 22 (175)
T ss_pred CHHHHHHHHCcC-HHHHHHHHH
Confidence 567899999997 888887765
No 124
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=24.22 E-value=1.2e+02 Score=27.17 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=34.0
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 96 r~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
|+..|+.+...++.++.++|++.|+++ ..-+...+- +.-..|+|.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~-~L~~~~~l~ 49 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLN-ELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 566677777788899999999999997 777777666 544445543
No 125
>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=24.19 E-value=4e+02 Score=21.84 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 168 GSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 168 ~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
..+-..|++-.+.+...-..+.++|...+..-++...-.+.+.++|.+++..+
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 44566666666677777777777777777766666777777777777777665
No 126
>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=24.12 E-value=3.4e+02 Score=20.90 Aligned_cols=45 Identities=11% Similarity=0.088 Sum_probs=35.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEE
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCF 152 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v 152 (261)
.+..++..+|++.++++ ...+=..|- +....|+|...-|..++..
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~ 83 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRR 83 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCe
Confidence 35568999999999997 556666666 8888999999988766543
No 127
>PF09218 DUF1959: Domain of unknown function (DUF1959); InterPro: IPR012056 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. This entry represents proteins that are predicted to be the hydrophilic EhaM subunits of Eha-type energy-converting [NiFe] hydrogenase complexes.; PDB: 1NXH_B.
Probab=24.08 E-value=43 Score=27.29 Aligned_cols=41 Identities=22% Similarity=0.254 Sum_probs=32.1
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHH
Q 024854 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182 (261)
Q Consensus 114 ~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~L~~~L~~W~~~~~ 182 (261)
.|+++|+|+ .+++++.+| +.. +...+.+|+.+.++|+-.|-
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 367889998 999999999 642 33557889999999987664
No 128
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=23.71 E-value=3.3e+02 Score=24.87 Aligned_cols=113 Identities=16% Similarity=0.286 Sum_probs=55.8
Q ss_pred HHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccC-----CCc-hHHHHHHHHHhcCChhhHhhhhC
Q 024854 9 ELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-----TEN-SKYLDMLRLFAHGTWSDYKNNAG 82 (261)
Q Consensus 9 ~~l~~fl~lak~a~~~aa~~lI~~AL~~p~vy~F~eLL~lp~v~~L~~-----~~~-~~~~~LL~iFa~Gt~~dy~~~~~ 82 (261)
..+++|+-|.+ ..|..+... .|. .|++|++.=.+--++. ... ......-...-.|-+-||....+
T Consensus 27 ~Li~~ylpLV~----~ia~k~~~r---~~~--~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~ 97 (247)
T COG1191 27 RLIERYLPLVK----SIARKFENR---GPS--EYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND 97 (247)
T ss_pred HHHHHHHHHHH----HHHHHHHhc---CCC--chhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC
Confidence 57778877765 344444333 333 6677776444432221 010 11111111223466666666555
Q ss_pred --CCCCcchHHHHHHHHHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 83 --HLPQLVPDQVLKLKQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 83 --~l~~L~~~~~~KLr~LTllsLa-~~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
.+|--.-...+++.. .+=.|. +.++.-+-++|+++|+|+ ..++-.++.
T Consensus 98 ~v~vpR~~~~~~~~i~~-~~~~l~~el~r~pt~~EIA~~L~i~-~ee~~~~~~ 148 (247)
T COG1191 98 SVKVPRSLRELGRRIEE-AIDELEQELGREPTDEEIAEELGID-KEEYIEALL 148 (247)
T ss_pred CccCcHHHHHHHHHHHH-HHHHHHHHhCCCCcHHHHHHHhCCC-HHHHHHHHH
Confidence 344211111111111 111122 357899999999999998 776665554
No 129
>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=22.83 E-value=1.2e+02 Score=28.08 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=36.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecCC
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ~ 148 (261)
..+.++..++++..++| .+=+-..++ +..-.++|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp-~efl~~~li-~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLP-SEFLKEELI-SKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCc-HHHHHHHHh-hhhcCcceeEEEeCC
Confidence 56899999999999999 777776788 787789999999998
No 130
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=22.18 E-value=3.5e+02 Score=23.56 Aligned_cols=46 Identities=26% Similarity=0.336 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 175 SNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 175 ~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
..|....+.....++..++.-..+.+...+.+++++.+++++++.+
T Consensus 124 ~~~~~~~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei 169 (176)
T PF12999_consen 124 KEYREELEEEEEIYKEGLKIRQELIEEAKKKREELEKKLEELEKEI 169 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555554444455555566677777777777776
No 131
>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=22.14 E-value=98 Score=22.20 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHH
Q 024854 106 TNKVLPYDELMEELDVTNVRELEDF 130 (261)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~l 130 (261)
.++.+++-+||+.|+|+ ...|-.|
T Consensus 19 ~~g~i~lkdIA~~Lgvs-~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVS-ESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCC-HHHHHHH
Confidence 46789999999999998 7776655
No 132
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.48 E-value=1e+02 Score=25.68 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=23.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 024854 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (261)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~lvI~eAI 136 (261)
...||++|++.+|++ +..|...+- .|.
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 568999999999998 999998887 765
No 133
>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=21.42 E-value=1.1e+02 Score=25.27 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=23.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 024854 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (261)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~lvI~eAI 136 (261)
...||.+|++.||++ +..|...+- .|.
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 568999999999998 999988776 664
No 134
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=21.23 E-value=2.8e+02 Score=24.06 Aligned_cols=80 Identities=13% Similarity=0.172 Sum_probs=49.1
Q ss_pred HHHHHHHHHhcCChhhHhhh--h-CCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 024854 61 KYLDMLRLFAHGTWSDYKNN--A-GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (261)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~~--~-~~l~~L~~~~~~KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~ 137 (261)
.+-.+.+++.+......... . ...+.|++.|.+=|+.--=+..-.--|.++-.+||++|||+ ...+.+-+= +|.
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 45555566655554433221 1 12346888766655555444555567999999999999997 666666555 554
Q ss_pred cCceEE
Q 024854 138 TGIVRG 143 (261)
Q Consensus 138 ~gLI~G 143 (261)
.+|+..
T Consensus 204 ~Kl~~~ 209 (215)
T COG3413 204 RKLIEA 209 (215)
T ss_pred HHHHHH
Confidence 344443
No 135
>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=21.14 E-value=1.1e+02 Score=19.67 Aligned_cols=25 Identities=12% Similarity=0.178 Sum_probs=20.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHh
Q 024854 109 VLPYDELMEELDVTNVRELEDFLINEC 135 (261)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~lvI~eA 135 (261)
..++.+|++.++++ ...|+.++= .+
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~-~~ 39 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLR-NI 39 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH-HH
Confidence 36999999999997 989988765 44
No 136
>KOG3809 consensus Microtubule-binding protein MIP-T3 [Cytoskeleton]
Probab=21.13 E-value=2.4e+02 Score=28.24 Aligned_cols=60 Identities=13% Similarity=0.193 Sum_probs=32.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHhc
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~~a~~~~~~~~~~~~~~~~~~~~~kk~~ 220 (261)
||-+++++.|..-|..|.+.-...-..++..-.......+--...-+++++.|.+.+.-|
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 344688999999999999766555555544333222222222222234444444444433
No 137
>PHA02943 hypothetical protein; Provisional
Probab=21.08 E-value=2.1e+02 Score=24.57 Aligned_cols=43 Identities=16% Similarity=0.205 Sum_probs=30.8
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 97 ~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
+..|+.+. ..++-+-++|++.||++ ..+++..+- -.-..|.|+
T Consensus 13 ~~eILE~L-k~G~~TtseIAkaLGlS-~~qa~~~Ly-vLErEG~Vk 55 (165)
T PHA02943 13 MIKTLRLL-ADGCKTTSRIANKLGVS-HSMARNALY-QLAKEGMVL 55 (165)
T ss_pred HHHHHHHH-hcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCceE
Confidence 33444444 77888999999999997 999997666 444555554
No 138
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=20.70 E-value=1.9e+02 Score=24.39 Aligned_cols=45 Identities=18% Similarity=0.138 Sum_probs=26.6
Q ss_pred CcchHHHHHHHHHHhhhccc-CCcccChHHHHHHcCCCChHHHHHHH
Q 024854 86 QLVPDQVLKLKQLTVLTLAE-TNKVLPYDELMEELDVTNVRELEDFL 131 (261)
Q Consensus 86 ~L~~~~~~KLr~LTllsLa~-~~k~Isy~~I~~~L~I~~~~evE~lv 131 (261)
.|++.|.+=...|..-.+.. .+...|+++||+++||+ ...+-.|-
T Consensus 10 ~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis-~~tLYrWr 55 (142)
T PF13022_consen 10 KLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGIS-RSTLYRWR 55 (142)
T ss_dssp TS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS--HHHHHHHH
T ss_pred HcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCC-HHHHHHHH
Confidence 36666666555666555554 45889999999999997 76666554
No 139
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=20.66 E-value=1.4e+02 Score=27.13 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=34.2
Q ss_pred HHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceE
Q 024854 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (261)
Q Consensus 94 KLr~LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~ 142 (261)
.-|+..|+.+....+.++..+|++.|+++ ..-+-.=+. ..-..|++.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~-~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLA-FLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHH-HHHhCCCeE
Confidence 45788888888888889999999999997 654443333 333457665
No 140
>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=20.62 E-value=5.4e+02 Score=22.01 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=29.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEe
Q 024854 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (261)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkI 145 (261)
...++..+|++.++|+ ...|=..+= .....|+|.-.-
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 3559999999999997 777776666 777789998663
No 141
>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=20.57 E-value=1.4e+02 Score=22.51 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=23.9
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 98 LTllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
..|+.+-..++.+|-++|+.+++.+ +++|...+=
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 3456555679999999999999998 999987654
No 142
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.54 E-value=1.3e+02 Score=19.68 Aligned_cols=31 Identities=16% Similarity=0.304 Sum_probs=22.7
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 024854 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 99 TllsLa~~~k~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
.|+.++... .|+.+|++.++++ ...|..++-
T Consensus 19 ~i~~~~~~~--~s~~~vA~~~~vs-~~TV~ri~~ 49 (52)
T PF13542_consen 19 YILKLLRES--RSFKDVARELGVS-WSTVRRIFD 49 (52)
T ss_pred HHHHHHhhc--CCHHHHHHHHCCC-HHHHHHHHH
Confidence 444444433 7999999999997 888877654
No 143
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=20.26 E-value=2.6e+02 Score=21.64 Aligned_cols=33 Identities=18% Similarity=0.206 Sum_probs=26.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024854 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (261)
Q Consensus 161 dl~~~q~~~L~~~L~~W~~~~~~~l~~ie~~i~ 193 (261)
.|+|+.+..+...|..|........+.+++.+.
T Consensus 21 vfGP~KLP~lar~lGk~i~~fkk~~~~~~~e~~ 53 (90)
T PRK14857 21 VFGPKKLPEIGRSLGKTLKGFQEASKEFENEIK 53 (90)
T ss_pred HcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999988887777655443
No 144
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=20.25 E-value=1.7e+02 Score=21.83 Aligned_cols=32 Identities=19% Similarity=0.380 Sum_probs=25.1
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCceEEEecC
Q 024854 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (261)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~lvI~eAI~~gLI~GkIDQ 147 (261)
||++++++.++++ .. ||. +.+..|+|.-.-.+
T Consensus 1 is~~e~~~~~~i~-~~----~l~-~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-PE----FLR-ELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-HH----HHH-HHHHCCCeeecCCC
Confidence 6899999999998 44 555 56668999887666
No 145
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.17 E-value=1.1e+02 Score=19.91 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=17.7
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 024854 109 VLPYDELMEELDVTNVRELEDFLI 132 (261)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~lvI 132 (261)
-.|+.+|++.|+++ ...|-.|+=
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 989988864
No 146
>PF06394 Pepsin-I3: Pepsin inhibitor-3-like repeated domain; InterPro: IPR010480 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The members of this group of proteins belong to MEROPS inhibitor family I33, clan IR; the nematode aspartyl protease inhibitors or Aspins. They are restricted to parasitic nematode species. Structural features common to the nematode Aspins include the presence of a signal peptide sequence and the conservation of all four cysteine residues in the mature protein. The Y[V.A]RDLT sequence motif has been suggested as being of crucial functional importance in several filarial nematode inhibitors [], this sequence is not conserved in Tco-API-1 from Trichostrongylus colubriformis (Black scour worm) and it has been demonstrated that Tco-API-1, is not an Aspin as it does not inhibit porcine pepsin []. Related inhibitors from Onchocerca volvulus, Ov33 [] and Ascaris suum (Pig roundworm), PI-3 [] inhibit the in vitro activity of aspartyl proteases such as pepsin and cathepsin E (MEROPS peptidase family A1). Aspin may facilitate the safe passage of the eggs of Ascaris through the host stomach without digestion by pepsin [, ]. The other parasitic nematodes known to express homologous proteins do not pass through the stomach of their hosts []. Several proteins in the family are potent allergens in mammals. The three-dimensional structures of pepsin inhibitor-3 (PI-3) from A. suum and of the complex between PI-3 and porcine pepsin at 1. 75 A and 2.45 A resolution, respectively, have revealed the mechanism of aspartic protease inhibition. PI-3 has a new fold consisting of two identical domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-strand of PI-3 pairs with one strand of the 'active site flap' (residues 70-82) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residues to occupy and therefore block the first three binding pockets in pepsin for substrate residues C-terminal to the scissile bond (S1'-S3') [].; PDB: 1F32_A 1F34_B.
Probab=20.16 E-value=44 Score=25.19 Aligned_cols=38 Identities=13% Similarity=0.179 Sum_probs=25.6
Q ss_pred CCCEEEEEeecCCCCCCCcHHHH---HHHHHHHHHHHHHHH
Q 024854 148 LRRCFEVQFAAGRDLRPGQLGSM---IQTLSNWLTTSDNLL 185 (261)
Q Consensus 148 ~~~~v~V~~~~~Rdl~~~q~~~L---~~~L~~W~~~~~~~l 185 (261)
.++.|+|.-.--|++.+++...| .+.+..|.+.+...+
T Consensus 26 ~~nklyvng~~~R~Lt~~E~~eL~~y~~~v~~y~~~l~~~i 66 (76)
T PF06394_consen 26 QNNKLYVNGKYARDLTPDEQQELKTYQKKVAAYKEQLQQQI 66 (76)
T ss_dssp ETTEEEETTCEEEE--HHHHHHHHHHHHHHHHHHHHHTT--
T ss_pred ECCEEEECCEeeccCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667788777899999887665 668888888766544
No 147
>PRK10884 SH3 domain-containing protein; Provisional
Probab=20.10 E-value=6.1e+02 Score=22.39 Aligned_cols=8 Identities=13% Similarity=0.256 Sum_probs=3.5
Q ss_pred eecCCCCC
Q 024854 156 FAAGRDLR 163 (261)
Q Consensus 156 ~~~~Rdl~ 163 (261)
|+..+.+.
T Consensus 79 WV~~~~Ls 86 (206)
T PRK10884 79 WIPLKQLS 86 (206)
T ss_pred eEEHHHhc
Confidence 44444443
Done!