Query 025387
Match_columns 253
No_of_seqs 209 out of 579
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 05:17:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025387.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025387hhsearch_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 2.2E-65 4.7E-70 441.5 16.6 251 1-253 1-251 (258)
2 KOG2753 Uncharacterized conser 100.0 3.1E-32 6.8E-37 248.3 11.5 150 24-178 205-361 (378)
3 KOG2908 26S proteasome regulat 100.0 5.3E-31 1.1E-35 241.3 15.4 179 12-192 181-375 (380)
4 smart00088 PINT motif in prote 99.5 3.7E-14 7.9E-19 107.0 7.3 86 88-177 3-88 (88)
5 smart00753 PAM PCI/PINT associ 99.5 3.7E-14 7.9E-19 107.0 7.3 86 88-177 3-88 (88)
6 PF01399 PCI: PCI domain; Int 99.5 5.1E-14 1.1E-18 107.9 7.7 94 61-156 2-105 (105)
7 KOG1464 COP9 signalosome, subu 98.9 6.7E-09 1.5E-13 94.7 7.9 125 60-192 305-439 (440)
8 KOG2581 26S proteasome regulat 97.7 0.00018 3.9E-09 68.8 9.5 128 60-194 319-457 (493)
9 KOG1498 26S proteasome regulat 96.4 0.027 5.9E-07 53.9 10.4 128 58-197 286-429 (439)
10 KOG2758 Translation initiation 96.0 0.012 2.6E-07 55.2 5.6 97 89-192 329-425 (432)
11 KOG1497 COP9 signalosome, subu 95.7 0.02 4.3E-07 53.7 5.5 154 26-190 228-389 (399)
12 KOG0686 COP9 signalosome, subu 95.5 0.15 3.2E-06 49.3 10.7 98 62-161 308-415 (466)
13 COG5071 RPN5 26S proteasome re 95.3 0.08 1.7E-06 49.5 8.0 75 105-191 349-423 (439)
14 KOG2688 Transcription-associat 94.4 0.084 1.8E-06 50.7 5.9 109 48-157 260-385 (394)
15 KOG1463 26S proteasome regulat 93.1 0.25 5.4E-06 46.9 6.4 114 44-159 270-393 (411)
16 KOG2582 COP9 signalosome, subu 93.0 0.69 1.5E-05 44.2 9.2 106 60-169 259-373 (422)
17 COG5600 Transcription-associat 92.6 0.36 7.8E-06 46.2 6.8 99 59-159 288-406 (413)
18 KOG0687 26S proteasome regulat 90.9 3.5 7.5E-05 39.1 11.1 64 92-157 300-363 (393)
19 KOG2072 Translation initiation 90.6 3.4 7.3E-05 43.3 11.7 50 105-155 443-492 (988)
20 PF10075 PCI_Csn8: COP9 signal 90.4 2.7 5.9E-05 34.2 9.1 107 25-132 6-119 (143)
21 PF09756 DDRGK: DDRGK domain; 88.8 0.66 1.4E-05 40.3 4.5 57 97-155 101-157 (188)
22 COG5159 RPN6 26S proteasome re 88.1 3.8 8.2E-05 38.5 9.1 100 59-160 283-392 (421)
23 COG3355 Predicted transcriptio 85.8 7.1 0.00015 31.9 8.6 80 105-190 38-120 (126)
24 PF09012 FeoC: FeoC like trans 83.6 0.93 2E-05 32.5 2.3 43 99-143 4-46 (69)
25 PF02082 Rrf2: Transcriptional 81.4 4.6 9.9E-05 29.8 5.4 58 95-155 11-68 (83)
26 KOG3054 Uncharacterized conser 80.1 3 6.5E-05 37.9 4.6 54 100-155 205-258 (299)
27 PRK01919 tatB sec-independent 78.2 14 0.00029 31.8 7.8 59 161-220 19-77 (169)
28 smart00344 HTH_ASNC helix_turn 77.9 3.8 8.2E-05 31.3 4.1 42 100-143 8-49 (108)
29 PRK11179 DNA-binding transcrip 75.8 4.1 8.8E-05 33.6 4.0 48 99-148 13-63 (153)
30 PRK04098 sec-independent trans 74.6 22 0.00048 30.1 8.1 60 161-220 19-81 (158)
31 TIGR02010 IscR iron-sulfur clu 73.2 9.3 0.0002 30.8 5.5 44 99-144 13-58 (135)
32 PRK04654 sec-independent trans 72.3 14 0.00031 32.7 6.7 36 161-196 19-54 (214)
33 TIGR01410 tatB twin arginine-t 71.4 16 0.00034 27.3 5.9 37 161-197 18-54 (80)
34 PF13412 HTH_24: Winged helix- 71.2 7.5 0.00016 25.4 3.7 42 99-142 7-48 (48)
35 PF07389 DUF1500: Protein of u 69.8 4.8 0.0001 31.0 2.8 34 102-138 41-74 (100)
36 COG1522 Lrp Transcriptional re 69.7 6.5 0.00014 31.7 3.8 43 100-144 13-55 (154)
37 TIGR00738 rrf2_super rrf2 fami 68.9 17 0.00037 28.7 6.0 50 93-144 9-58 (132)
38 PRK11169 leucine-responsive tr 68.5 9.3 0.0002 31.9 4.6 44 98-143 17-60 (164)
39 PRK14165 winged helix-turn-hel 68.1 21 0.00045 31.7 6.9 62 92-155 4-65 (217)
40 PRK01770 sec-independent trans 67.3 21 0.00046 30.7 6.5 36 161-196 19-54 (171)
41 PRK10857 DNA-binding transcrip 66.7 14 0.0003 31.2 5.3 47 96-144 12-58 (164)
42 PF08280 HTH_Mga: M protein tr 62.9 6.7 0.00015 27.2 2.3 35 96-131 6-40 (59)
43 TIGR02944 suf_reg_Xantho FeS a 62.6 37 0.00081 26.8 6.9 37 106-144 22-58 (130)
44 smart00346 HTH_ICLR helix_turn 60.6 18 0.00038 26.4 4.4 46 96-143 6-52 (91)
45 PF01726 LexA_DNA_bind: LexA D 57.8 18 0.00039 25.8 3.8 36 106-142 22-57 (65)
46 PF11945 WASH_WAHD: WAHD domai 56.8 97 0.0021 28.9 9.4 64 156-219 8-72 (297)
47 PF03962 Mnd1: Mnd1 family; I 56.6 1.1E+02 0.0023 26.4 9.2 96 116-220 22-126 (188)
48 COG1959 Predicted transcriptio 56.5 30 0.00064 28.7 5.5 50 95-146 11-60 (150)
49 PF10828 DUF2570: Protein of u 55.6 99 0.0021 24.2 8.6 59 170-230 37-95 (110)
50 PF09339 HTH_IclR: IclR helix- 55.5 28 0.0006 23.2 4.3 45 96-142 4-49 (52)
51 PF13404 HTH_AsnC-type: AsnC-t 54.3 8.3 0.00018 25.2 1.4 28 100-128 8-35 (42)
52 PRK04214 rbn ribonuclease BN/u 54.2 93 0.002 29.9 9.2 59 106-173 307-365 (412)
53 PRK14858 tatA twin arginine tr 53.9 82 0.0018 25.1 7.2 37 161-197 19-55 (108)
54 COG1777 Predicted transcriptio 53.6 1E+02 0.0022 27.5 8.4 38 111-150 29-67 (217)
55 PRK10141 DNA-binding transcrip 53.6 27 0.00058 28.0 4.6 46 107-154 28-73 (117)
56 PF08279 HTH_11: HTH domain; 53.4 20 0.00042 23.9 3.3 35 97-132 2-37 (55)
57 smart00550 Zalpha Z-DNA-bindin 52.6 22 0.00048 25.3 3.6 33 109-143 22-54 (68)
58 PF03399 SAC3_GANP: SAC3/GANP/ 52.6 59 0.0013 27.4 6.9 62 59-120 135-203 (204)
59 PRK11920 rirA iron-responsive 52.4 36 0.00077 28.2 5.3 39 106-146 21-59 (153)
60 PF13730 HTH_36: Helix-turn-he 52.0 52 0.0011 21.7 5.3 47 93-141 7-55 (55)
61 KOG1076 Translation initiation 51.9 35 0.00075 35.6 6.0 96 62-159 657-766 (843)
62 PRK11014 transcriptional repre 51.7 39 0.00084 27.3 5.4 51 95-147 11-61 (141)
63 PF08281 Sigma70_r4_2: Sigma-7 50.2 22 0.00047 23.6 3.1 27 108-136 25-51 (54)
64 PF12840 HTH_20: Helix-turn-he 50.2 28 0.00062 23.9 3.8 38 105-144 20-57 (61)
65 cd00090 HTH_ARSR Arsenical Res 49.7 55 0.0012 21.9 5.3 36 110-147 21-56 (78)
66 PF13815 Dzip-like_N: Iguana/D 49.7 46 0.001 26.3 5.4 100 110-220 18-117 (118)
67 PF07106 TBPIP: Tat binding pr 48.6 1.6E+02 0.0034 24.5 11.9 114 105-220 12-132 (169)
68 PF08220 HTH_DeoR: DeoR-like h 48.4 26 0.00057 24.0 3.3 42 97-140 2-43 (57)
69 PF05565 Sipho_Gp157: Siphovir 48.4 72 0.0016 26.7 6.6 52 181-234 45-96 (162)
70 PF01022 HTH_5: Bacterial regu 48.2 46 0.00099 21.7 4.4 33 108-142 14-46 (47)
71 PF13601 HTH_34: Winged helix 47.7 23 0.00049 26.2 3.1 51 98-150 3-53 (80)
72 PF01325 Fe_dep_repress: Iron 47.6 44 0.00095 23.3 4.4 43 98-142 11-53 (60)
73 smart00345 HTH_GNTR helix_turn 47.2 76 0.0017 20.6 5.5 36 105-142 15-51 (60)
74 PRK00404 tatB sec-independent 47.0 1.3E+02 0.0029 25.0 7.7 37 161-197 19-55 (141)
75 PRK09954 putative kinase; Prov 46.4 24 0.00052 32.8 3.8 54 100-155 8-64 (362)
76 PRK00708 sec-independent trans 46.4 83 0.0018 27.9 6.8 37 161-197 19-55 (209)
77 PRK03573 transcriptional regul 45.9 1.5E+02 0.0033 23.5 8.0 57 100-158 37-93 (144)
78 COG5187 RPN7 26S proteasome re 44.4 25 0.00055 33.2 3.5 64 92-157 314-377 (412)
79 PRK10265 chaperone-modulator p 43.8 49 0.0011 25.5 4.6 39 105-149 3-41 (101)
80 cd06445 ATase The DNA repair p 42.9 33 0.00072 25.1 3.3 30 98-127 6-36 (79)
81 PF04967 HTH_10: HTH DNA bindi 42.3 1.1E+02 0.0024 21.0 5.7 27 105-132 19-45 (53)
82 PF14947 HTH_45: Winged helix- 41.0 76 0.0017 23.0 5.0 49 100-155 11-59 (77)
83 TIGR02919 accessory Sec system 40.8 96 0.0021 30.3 7.0 89 112-204 341-435 (438)
84 PF08784 RPA_C: Replication pr 40.0 69 0.0015 24.2 4.9 49 97-147 52-101 (102)
85 KOG2166 Cullins [Cell cycle co 39.6 3.9E+02 0.0085 28.1 11.5 117 95-220 566-694 (725)
86 PHA01750 hypothetical protein 39.1 1.3E+02 0.0028 22.0 5.7 35 186-220 38-72 (75)
87 PF01978 TrmB: Sugar-specific 39.0 51 0.0011 23.0 3.7 38 106-145 19-56 (68)
88 PF03979 Sigma70_r1_1: Sigma-7 39.0 23 0.0005 26.2 2.0 38 100-139 12-52 (82)
89 smart00420 HTH_DEOR helix_turn 38.6 77 0.0017 20.0 4.3 35 107-143 12-46 (53)
90 PF04545 Sigma70_r4: Sigma-70, 38.3 1.1E+02 0.0024 19.8 5.1 28 107-136 18-45 (50)
91 PF13518 HTH_28: Helix-turn-he 38.3 38 0.00082 21.9 2.8 31 99-132 4-34 (52)
92 smart00418 HTH_ARSR helix_turn 38.3 1.1E+02 0.0023 19.8 5.1 38 107-146 8-45 (66)
93 smart00347 HTH_MARR helix_turn 37.9 1.5E+02 0.0033 21.2 8.1 41 107-149 22-62 (101)
94 PF14480 DNA_pol3_a_NI: DNA po 37.7 1.1E+02 0.0025 21.6 5.5 61 111-176 2-62 (76)
95 PF09341 Pcc1: Transcription f 35.8 1.3E+02 0.0028 21.6 5.6 47 138-190 30-76 (76)
96 COG4575 ElaB Uncharacterized c 35.4 1.7E+02 0.0038 23.1 6.4 56 159-220 2-57 (104)
97 PF06163 DUF977: Bacterial pro 35.3 90 0.002 25.6 4.9 52 87-141 5-56 (127)
98 PF01638 HxlR: HxlR-like helix 34.9 1.9E+02 0.004 21.4 6.5 75 98-180 9-85 (90)
99 PF05331 DUF742: Protein of un 34.5 63 0.0014 25.9 3.9 41 98-142 46-86 (114)
100 PF04539 Sigma70_r3: Sigma-70 33.7 44 0.00094 23.8 2.7 26 106-132 17-42 (78)
101 TIGR02337 HpaR homoprotocatech 33.2 2.2E+02 0.0048 21.8 8.3 46 106-153 39-84 (118)
102 PRK13182 racA polar chromosome 33.1 1.5E+02 0.0033 25.4 6.3 21 111-132 2-22 (175)
103 PF12802 MarR_2: MarR family; 32.8 1.5E+02 0.0033 19.7 5.3 41 107-149 19-59 (62)
104 PHA03158 hypothetical protein; 32.5 53 0.0012 29.0 3.4 54 167-220 217-270 (273)
105 COG1191 FliA DNA-directed RNA 32.4 1.9E+02 0.004 26.2 7.0 113 9-132 27-148 (247)
106 PF01047 MarR: MarR family; I 30.8 69 0.0015 21.3 3.2 49 100-150 8-56 (59)
107 TIGR03879 near_KaiC_dom probab 30.4 48 0.001 24.5 2.4 24 108-132 31-54 (73)
108 PRK03100 sec-independent trans 29.2 2.9E+02 0.0063 22.8 7.1 34 161-194 20-53 (136)
109 KOG2629 Peroxisomal membrane a 28.6 2.2E+02 0.0048 26.6 6.8 85 127-219 83-169 (300)
110 PRK10870 transcriptional repre 28.4 3.5E+02 0.0077 22.6 8.0 56 100-157 61-117 (176)
111 PF05791 Bacillus_HBL: Bacillu 27.7 2.8E+02 0.0061 23.6 7.1 58 166-225 125-182 (184)
112 PF09523 DUF2390: Protein of u 27.7 1.9E+02 0.004 22.8 5.5 42 158-199 43-84 (109)
113 cd00092 HTH_CRP helix_turn_hel 27.2 1.2E+02 0.0027 20.3 4.0 35 107-143 23-57 (67)
114 TIGR01884 cas_HTH CRISPR locus 27.1 1.7E+02 0.0036 25.1 5.7 53 99-154 147-199 (203)
115 smart00419 HTH_CRP helix_turn_ 27.0 1.2E+02 0.0026 18.9 3.7 32 109-142 8-39 (48)
116 PRK00182 tatB sec-independent 26.7 2.2E+02 0.0048 24.2 6.1 34 161-194 20-53 (160)
117 COG1595 RpoE DNA-directed RNA 26.5 73 0.0016 26.4 3.2 28 107-136 141-168 (182)
118 PF05377 FlaC_arch: Flagella a 26.0 2E+02 0.0044 20.1 4.8 33 188-220 5-37 (55)
119 cd07377 WHTH_GntR Winged helix 25.9 2E+02 0.0043 18.9 5.9 48 93-142 8-56 (66)
120 TIGR02702 SufR_cyano iron-sulf 25.5 4.2E+02 0.0092 22.5 10.9 37 107-145 13-49 (203)
121 PRK10411 DNA-binding transcrip 25.4 1E+02 0.0022 27.3 4.1 46 95-142 4-49 (240)
122 PF13591 MerR_2: MerR HTH fami 25.4 1.1E+02 0.0024 22.6 3.7 32 110-147 1-32 (84)
123 PF12999 PRKCSH-like: Glucosid 24.6 2.8E+02 0.0061 23.9 6.5 46 175-220 124-169 (176)
124 COG4741 Predicted secreted end 23.8 4.6E+02 0.01 22.4 8.1 32 189-220 48-79 (175)
125 PF12324 HTH_15: Helix-turn-he 23.8 1.1E+02 0.0024 22.9 3.4 34 98-132 27-60 (77)
126 PF09743 DUF2042: Uncharacteri 23.8 1.1E+02 0.0023 28.1 4.0 41 106-148 127-167 (272)
127 PF01920 Prefoldin_2: Prefoldi 23.7 3E+02 0.0064 20.4 5.9 54 153-220 46-99 (106)
128 TIGR02999 Sig-70_X6 RNA polyme 23.1 94 0.002 25.4 3.2 27 108-136 149-175 (183)
129 PRK12537 RNA polymerase sigma 22.6 91 0.002 25.8 3.1 27 108-136 148-174 (182)
130 PF04703 FaeA: FaeA-like prote 22.5 1E+02 0.0022 21.9 2.8 34 107-142 13-46 (62)
131 PF02002 TFIIE_alpha: TFIIE al 22.2 88 0.0019 23.8 2.7 36 107-144 25-60 (105)
132 PF10668 Phage_terminase: Phag 22.0 99 0.0021 22.0 2.7 24 106-130 19-42 (60)
133 PRK15090 DNA-binding transcrip 21.4 1.7E+02 0.0037 25.9 4.7 45 96-142 15-59 (257)
134 cd06170 LuxR_C_like C-terminal 21.3 1.1E+02 0.0023 19.6 2.7 23 109-132 15-37 (57)
135 PF06056 Terminase_5: Putative 21.2 1E+02 0.0022 21.5 2.6 23 109-132 13-35 (58)
136 KOG3809 Microtubule-binding pr 21.1 2.5E+02 0.0054 27.9 6.0 59 162-220 504-562 (583)
137 PRK09802 DNA-binding transcrip 21.0 1.3E+02 0.0029 27.1 4.0 47 94-142 16-62 (269)
138 PRK12523 RNA polymerase sigma 21.0 1.1E+02 0.0024 25.0 3.2 27 108-136 134-160 (172)
139 PF10975 DUF2802: Protein of u 21.0 1E+02 0.0023 22.3 2.7 20 110-130 45-64 (70)
140 PRK14857 tatA twin arginine tr 21.0 2.5E+02 0.0054 21.6 4.9 34 161-194 21-54 (90)
141 cd08327 CARD_RAIDD Caspase act 21.0 2.3E+02 0.005 21.7 4.8 80 10-97 9-88 (94)
142 COG1497 Predicted transcriptio 20.9 6.5E+02 0.014 23.0 10.6 83 100-195 16-98 (260)
143 PF05615 THOC7: Tho complex su 20.6 4.5E+02 0.0097 21.0 8.1 56 165-220 42-97 (139)
144 COG3413 Predicted DNA binding 20.6 2.9E+02 0.0064 23.8 6.0 80 61-143 127-209 (215)
145 PRK10434 srlR DNA-bindng trans 20.5 1.3E+02 0.0029 26.8 3.9 32 95-127 5-36 (256)
146 PRK12543 RNA polymerase sigma 20.5 1.1E+02 0.0024 25.1 3.2 27 108-136 132-158 (179)
147 PRK09651 RNA polymerase sigma 20.5 1.1E+02 0.0025 24.9 3.3 28 107-136 133-160 (172)
148 PHA02943 hypothetical protein; 20.4 2.2E+02 0.0047 24.3 4.8 43 97-142 13-55 (165)
149 PRK14861 tatA twin arginine tr 20.4 2.3E+02 0.0049 20.1 4.3 33 161-193 20-52 (61)
150 PRK12529 RNA polymerase sigma 20.4 1.1E+02 0.0025 25.2 3.2 27 108-136 142-168 (178)
151 PRK09642 RNA polymerase sigma 20.4 1.2E+02 0.0025 24.3 3.2 27 108-136 121-147 (160)
152 PF06013 WXG100: Proteins of 1 20.4 2.3E+02 0.0049 19.5 4.4 34 162-195 4-37 (86)
153 PRK06759 RNA polymerase factor 20.2 1.2E+02 0.0026 24.0 3.2 27 108-136 121-147 (154)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=2.2e-65 Score=441.50 Aligned_cols=251 Identities=42% Similarity=0.652 Sum_probs=247.8
Q ss_pred CcHhHHHHHHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 025387 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (253)
Q Consensus 1 ~~~~~~~~~~l~~fl~lak~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~ 80 (253)
|++||++++.+|||+++||+.+|+|...+|.+||++|+||+|||||.+|+|.+|..+.++.+++||++||||||.||.++
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 hCCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025387 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (253)
Q Consensus 81 ~~~l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~R 160 (253)
+-.+|.|+++++.||++||++|||+..++|||..+.+.|.+.|+++||++|| +|||+++++|||||.+|+++|.|+.+|
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 CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhccccccCCccccchhhccCCC
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEIYSEPGG 240 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~~~k~~~~~~~~~~~~~~~~~ 240 (253)
|+++.++.+|..+|++||+.|+++|..|++++.|||++++...+++++.|.+|.++||+++.+++.|+++.+..+.+| |
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 999999999999999999999999999999999999999999999999999999999999999999999999999999 9
Q ss_pred ccccccccCCCCC
Q 025387 241 VMDYEEDRGRPKR 253 (253)
Q Consensus 241 ~~~~~~~~~~~~~ 253 (253)
+|++..++.+|++
T Consensus 239 ~~~qrqp~kk~sk 251 (258)
T KOG3250|consen 239 VMDQRQPGKKPSK 251 (258)
T ss_pred CccccCCCcCccc
Confidence 9999999999875
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=99.97 E-value=3.1e-32 Score=248.31 Aligned_cols=150 Identities=27% Similarity=0.523 Sum_probs=139.6
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh----hCCCCC---cchHHHHHHH
Q 025387 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN----AGHLPQ---LVPDQVLKLK 96 (253)
Q Consensus 24 ~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~---L~~~~~~KLr 96 (253)
.+|.+||+.|+.+|++|.|+.|+++|+|+.|+++. +|+||.||..|..++|.++ ++++.. ..+++.+|||
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 46999999999999999999999999999999765 8999999999999999874 444443 3367899999
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025387 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (253)
Q Consensus 97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~ 176 (253)
+||+++||+.+.+|||++|+++|+|. .+|||.||| +||.+++|.|||||.+++|.|+.+.+|.|+..||..|.++|..
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 025387 177 WL 178 (253)
Q Consensus 177 W~ 178 (253)
|.
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=5.3e-31 Score=241.29 Aligned_cols=179 Identities=18% Similarity=0.358 Sum_probs=161.9
Q ss_pred HHHHHhc------ccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh---hC
Q 025387 12 DHFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN---AG 82 (253)
Q Consensus 12 ~~fl~la------k~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~---~~ 82 (253)
-.|+... .+.+...|..|..+||.+.++|||||||.||+...|.||++.|++++|.+|+.||+..|... .+
T Consensus 181 L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~dll~Afn~Gdl~~f~~l~~~~~ 260 (380)
T KOG2908|consen 181 LLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLKDLLIAFNSGDLKRFESLKGVWG 260 (380)
T ss_pred HHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHHHHHHHhccCCHHHHHHHHHHhc
Confidence 3566665 44455789999999999999999999999999999999999999999999999999999974 34
Q ss_pred CCCCcchH---HHHHHHHHHhhhccc----CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 83 HLPQLVPD---QVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 83 ~l~~L~~~---~~~KLr~LtLlsLa~----~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
..|.|... ..+|+++++|+-++. ..|.+||++|+++++|| .++||.+|| +|++.|||+|.|||++++|+++
T Consensus 261 ~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip-~~eVE~LVM-KAlslgLikG~Idqv~~~v~~s 338 (380)
T KOG2908|consen 261 KQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIP-NKEVELLVM-KALSLGLIKGSIDQVEGVVYMS 338 (380)
T ss_pred cCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCC-HHHHHHHHH-HHHhccceeeeecccccEEEEe
Confidence 57777633 478999999998875 57999999999999999 899999998 9999999999999999999999
Q ss_pred eecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 156 FAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (253)
Q Consensus 156 ~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i 192 (253)
|++||.++.+|+..|.+++..|++.++++...++.+-
T Consensus 339 wvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~ 375 (380)
T KOG2908|consen 339 WVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRG 375 (380)
T ss_pred cccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 9999999999999999999999999999999998764
No 4
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.51 E-value=3.7e-14 Score=106.96 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.9
Q ss_pred chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025387 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (253)
Q Consensus 88 ~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (253)
.+....|++.+++.+++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+.+..+|. .++|
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 889999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 025387 168 GSMIQTLSNW 177 (253)
Q Consensus 168 ~~l~~~L~~W 177 (253)
..+.++|..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00088 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999998887
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.51 E-value=3.7e-14 Score=106.96 Aligned_cols=86 Identities=22% Similarity=0.335 Sum_probs=80.9
Q ss_pred chHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025387 88 VPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (253)
Q Consensus 88 ~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (253)
.+....|++.+++.+++..+++|+|++|++.++++ .+++|.+|+ ++|..|.|.|+|||.+++|.+.+..+|. .++|
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 889999999 9999999999999999999999999997 7889
Q ss_pred HHHHHHHHHH
Q 025387 168 GSMIQTLSNW 177 (253)
Q Consensus 168 ~~l~~~L~~W 177 (253)
..+.++|..|
T Consensus 79 ~~~~~~l~~~ 88 (88)
T smart00753 79 AQFAETLKKL 88 (88)
T ss_pred HHHHHHhhcC
Confidence 9999998887
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=99.51 E-value=5.1e-14 Score=107.87 Aligned_cols=94 Identities=20% Similarity=0.405 Sum_probs=80.9
Q ss_pred HHHHHHHHHhcCChhhHhhhhC----------CCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025387 61 KYLDMLRLFAHGTWSDYKNNAG----------HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (253)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~~~~----------~l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~l 130 (253)
|+.+|+++|..|++..|...-. .+..+.+....+++..++.+++..++.|+++.|++.|+++ .++||.+
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~~ 80 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVESI 80 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHHH
Confidence 6899999999999999986322 2223446678999999999999999999999999999998 8999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEe
Q 025387 131 LINECMYTGIVRGKLDQLRRCFEVQF 156 (253)
Q Consensus 131 lI~~AI~~gLI~GkIDQ~~~~v~V~~ 156 (253)
|+ ++|..|.|.|+|||.+++|+++|
T Consensus 81 l~-~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 81 LI-DLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred HH-HHHHCCCEEEEEECCCCEEEecC
Confidence 99 99999999999999999999875
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.86 E-value=6.7e-09 Score=94.72 Aligned_cols=125 Identities=14% Similarity=0.360 Sum_probs=105.1
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCC------CCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHH
Q 025387 60 SKYLDMLRLFAHGTWSDYKN----NAGH------LPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (253)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~----~~~~------l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~ 129 (253)
-.+.+|+..+...++..|+. |.+. +-+..++.++++|...|+.|..++..|....|+++|+|+ ..+||.
T Consensus 305 lAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~~ 383 (440)
T KOG1464|consen 305 LAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVES 383 (440)
T ss_pred HHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHHH
Confidence 45889999999999999986 3332 223557889999999999999999999999999999998 999999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (253)
Q Consensus 130 llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i 192 (253)
+++ .||..+-|+|+|||+++.+....... .-..+...|..|.+.++++.+.|-.++
T Consensus 384 LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr~ 439 (440)
T KOG1464|consen 384 LLV-SCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSRV 439 (440)
T ss_pred HHH-HHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 999 99999999999999999988764322 123378999999999999888776553
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.73 E-value=0.00018 Score=68.79 Aligned_cols=128 Identities=8% Similarity=0.183 Sum_probs=83.9
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCCCCC-c----chHHHHHHHHHHhhhc----ccCCcccChHHHHHHcCCCChHHHHHH
Q 025387 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-L----VPDQVLKLKQLTVLTL----AETNKVLPYDELMEELDVTNVRELEDF 130 (253)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~~~l~~-L----~~~~~~KLr~LtLlsL----a~~~k~Isy~~I~~~L~I~~~~evE~l 130 (253)
.+|+.|-+..-.||++-|....+.+.+ + +-...-.||+=.|=+= .-.++.|||.+|+..|+|+|..++|.+
T Consensus 319 ~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~Eyi 398 (493)
T KOG2581|consen 319 RPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDAEYI 398 (493)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhHHHH
Confidence 569999999999999999875433222 1 1112444555322221 115889999999999999999999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEe--ecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 131 LINECMYTGIVRGKLDQLRRCFEVQF--AAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (253)
Q Consensus 131 lI~~AI~~gLI~GkIDQ~~~~v~V~~--~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (253)
|- +||+.|+|+|+||..++.+.-.- -+.|.=. -...+..-..-|-++.+.....+.+
T Consensus 399 Va-kAIRDGvIea~Id~~~g~m~skE~~diy~t~e------pQ~~f~~rI~fCl~LhN~~vkamRy 457 (493)
T KOG2581|consen 399 VA-KAIRDGVIEAKIDHEDGFMQSKETFDIYSTRE------PQTAFDERIRFCLQLHNEAVKAMRY 457 (493)
T ss_pred HH-HHHHhccceeeeccccCceehhhhhhhhccCC------chhhHhHHHHHHHHHHHHHHHHhcC
Confidence 98 99999999999999999554321 1122111 1223334445555566666555543
No 9
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=96.44 E-value=0.027 Score=53.88 Aligned_cols=128 Identities=21% Similarity=0.300 Sum_probs=92.2
Q ss_pred CchHHHHHHHHHhcCChhhHhhhh---------CCCCC---cchHH--HHHHHH--HHhhhcccCCcccChHHHHHHcCC
Q 025387 58 ENSKYLDMLRLFAHGTWSDYKNNA---------GHLPQ---LVPDQ--VLKLKQ--LTVLTLAETNKVLPYDELMEELDV 121 (253)
Q Consensus 58 ~~~~~~~LL~iFa~Gt~~dy~~~~---------~~l~~---L~~~~--~~KLr~--LtLlsLa~~~k~Isy~~I~~~L~I 121 (253)
+.+.+-.+|.+|..|.+--+.... +.+.. ..+.. -.|.|. .-+-=.|.=+.+||+..+++-|+.
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 345577899999998766554211 11111 11111 122222 333344556889999999999999
Q ss_pred CChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (253)
Q Consensus 122 ~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (253)
| .++.|.+|- +.+..|.+.+|||+..+.+.+... ..+.+-|..|..++++++..++..-+-..+
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 899999999999999999988654 347888999999999999998876555544
No 10
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=96.04 E-value=0.012 Score=55.20 Aligned_cols=97 Identities=16% Similarity=0.226 Sum_probs=75.6
Q ss_pred hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHH
Q 025387 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG 168 (253)
Q Consensus 89 ~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~ 168 (253)
.+-+.--|++-.=+.|.-..+|+.+.+|+.|+++ .+|.|.|++ +.|+...|++|||..-++|.+.....- --+
T Consensus 329 ~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~-~eeaErwiv-nlIr~~rl~AkidSklg~Vvmg~~~~s-----~~q 401 (432)
T KOG2758|consen 329 DEFLENARLLIFETFCRIHQCITIDMLADKLNMD-PEEAERWIV-NLIRTARLDAKIDSKLGHVVMGHPTVS-----PHQ 401 (432)
T ss_pred HHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCC-HHHHHHHHH-HHHHHhhhhhhhccccCceeecCCCCC-----HHH
Confidence 4446677888888889889999999999999997 999999999 899999999999999999888643322 234
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 169 SMIQTLSNWLTTSDNLLISIQEKI 192 (253)
Q Consensus 169 ~l~~~L~~W~~~~~~vl~~Ie~~i 192 (253)
.++++-..-.-+...+-..++..+
T Consensus 402 Q~ie~tksLS~rsq~la~~lek~~ 425 (432)
T KOG2758|consen 402 QLIEKTKSLSFRSQNLAQQLEKKI 425 (432)
T ss_pred HHHHhccccchhHHHHHHHHHHHH
Confidence 566666666666666666665544
No 11
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.68 E-value=0.02 Score=53.66 Aligned_cols=154 Identities=11% Similarity=0.131 Sum_probs=89.7
Q ss_pred HHHHHHHHhcCCCcccc-hhhhcCchhhhccCCC-chHHHHHHHHHhcC-ChhhHhhh-----hCCCCCcchHHHHHHHH
Q 025387 26 LGSVIVEATSQPSLFAF-SEILAVPNIAEFEGTE-NSKYLDMLRLFAHG-TWSDYKNN-----AGHLPQLVPDQVLKLKQ 97 (253)
Q Consensus 26 a~~lI~~AL~~p~vf~F-~eLL~~p~v~~L~~t~-~~~~~~LL~iFa~G-t~~dy~~~-----~~~l~~L~~~~~~KLr~ 97 (253)
|..|..-|.-+|..--| ..|...|.+++|..=+ -.++| |+-|-.+ +...|... +...+.=+.-.-+-+.-
T Consensus 228 a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmy--l~riI~k~el~ef~~~L~pHQka~~~dgssil~ra~~E 305 (399)
T KOG1497|consen 228 ALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMY--LERIIRKEELQEFEAFLQPHQKAHTMDGSSILDRAVIE 305 (399)
T ss_pred hHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHH--HHHHhcchhHHHHHHHhcchhhhcccCcchhhhhHHHH
Confidence 44444444555544443 3555556666554211 12222 3444444 45556542 11112101111122333
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHH
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNW 177 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W 177 (253)
-.|+++++-+..|+|+++...|+|+ .+.+|...- +.|..+-+.|.|||.++.+++.- |. ...+|+. ....-
T Consensus 306 hNlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~---~e-~l~~wdk---qi~sl 376 (399)
T KOG1497|consen 306 HNLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED---RE-ELPQWDK---QIQSL 376 (399)
T ss_pred HhHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc---hh-hhhhhhH---HHHHH
Confidence 4566666778899999999999998 999999999 89999999999999999999763 21 1123443 33344
Q ss_pred HHHHHHHHHHHHH
Q 025387 178 LTTSDNLLISIQE 190 (253)
Q Consensus 178 ~~~~~~vl~~Ie~ 190 (253)
|+.++++++.|..
T Consensus 377 ~~qvNki~~~i~~ 389 (399)
T KOG1497|consen 377 CNQVNKILDKISH 389 (399)
T ss_pred HHHHHHHHHHHHH
Confidence 5555555555543
No 12
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.50 E-value=0.15 Score=49.31 Aligned_cols=98 Identities=15% Similarity=0.223 Sum_probs=76.5
Q ss_pred HHHHHHHHhcCChhhHhh----hhCCCC---Ccc---hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHH
Q 025387 62 YLDMLRLFAHGTWSDYKN----NAGHLP---QLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (253)
Q Consensus 62 ~~~LL~iFa~Gt~~dy~~----~~~~l~---~L~---~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~ll 131 (253)
+.++|.-|..+-|..-.. .++.+- -|. .....++|.=.++.--.++..++++.++.+.+.+ +..+|.=|
T Consensus 308 lr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~l 386 (466)
T KOG0686|consen 308 LREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESEL 386 (466)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHHH
Confidence 566777777776665333 222210 122 3457889998999988999999999999999997 99999999
Q ss_pred HHHhHhcCccEEEecCCCCEEEEEeecCCC
Q 025387 132 INECMYTGIVRGKLDQLRRCFEVQFAAGRD 161 (253)
Q Consensus 132 I~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rd 161 (253)
. +.|-.|.|.||||+.++++++.-+..|.
T Consensus 387 ~-~LI~~~~i~~rIDs~~ki~~~~~~~~en 415 (466)
T KOG0686|consen 387 L-ELILEGKISGRIDSHNKILYARDADSEN 415 (466)
T ss_pred H-HHHHccchheeeccccceeeeccccccc
Confidence 9 9999999999999999999987665554
No 13
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=95.30 E-value=0.08 Score=49.54 Aligned_cols=75 Identities=16% Similarity=0.256 Sum_probs=65.3
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHH
Q 025387 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNL 184 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~v 184 (253)
.=++.|+-..|..-++.| ..+.|.+|- +.+..|++.+||++..+.+.+... ++..+.|..|.++++.+
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 457889999999999998 999999999 899999999999999999987643 23577899999999999
Q ss_pred HHHHHHH
Q 025387 185 LISIQEK 191 (253)
Q Consensus 185 l~~Ie~~ 191 (253)
+..++.-
T Consensus 417 lgklek~ 423 (439)
T COG5071 417 LGKLEKV 423 (439)
T ss_pred HHHHHHH
Confidence 9988753
No 14
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=94.38 E-value=0.084 Score=50.68 Aligned_cols=109 Identities=15% Similarity=0.184 Sum_probs=74.7
Q ss_pred CchhhhccCCCchHHHHHHHHHhcCChhhHhh----hhCCCCCcch-HHHHHHHHHHhhhcc-------cCCcccChHHH
Q 025387 48 VPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----NAGHLPQLVP-DQVLKLKQLTVLTLA-------ETNKVLPYDEL 115 (253)
Q Consensus 48 ~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~L~~-~~~~KLr~LtLlsLa-------~~~k~Isy~~I 115 (253)
+|-..-|..-.-..+-.|+.....||+..|.. +...+....- -.+.|++.++.=.|. .+...+|++.+
T Consensus 260 ~Pt~~lL~~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~ 339 (394)
T KOG2688|consen 260 IPTKELLDFYTLDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRF 339 (394)
T ss_pred CcchhhHhHhhHHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHH
Confidence 34443343212345777999999999999985 2222211110 012334444433333 26789999999
Q ss_pred HHHcCCCC-----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387 116 MEELDVTN-----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (253)
Q Consensus 116 ~~~L~I~~-----~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~ 157 (253)
..++.... .+|||-.+. .+|+.|.|+|.|+...+++.+...
T Consensus 340 ~~al~~~~~~~~~~deveciLa-~lI~~G~ikgYish~~~~~V~sK~ 385 (394)
T KOG2688|consen 340 LTALQFSGVTDVDLDEVECILA-NLIDLGRIKGYISHQLQTLVFSKK 385 (394)
T ss_pred HHHHhhcCCCCCchhhHHHHHH-hhhhhccccchhchhhheEEEecC
Confidence 99998765 789999999 899999999999999999998854
No 15
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=93.10 E-value=0.25 Score=46.88 Aligned_cols=114 Identities=15% Similarity=0.230 Sum_probs=81.2
Q ss_pred hhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhhCCC-CCcc-----hHHH----HHHHHHHhhhcccCCcccChH
Q 025387 44 EILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHL-PQLV-----PDQV----LKLKQLTVLTLAETNKVLPYD 113 (253)
Q Consensus 44 eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~~~~l-~~L~-----~~~~----~KLr~LtLlsLa~~~k~Isy~ 113 (253)
.|+.-.......+..-..+...=+.|..-+++||..--..+ ++|- ...+ ..|=---|+.+.+++.++..+
T Consensus 270 ~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIEPyS~Vei~ 349 (411)
T KOG1463|consen 270 ALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIEPYSRVEIS 349 (411)
T ss_pred HHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcCchhhhhHH
Confidence 34443333334444556677788889999999998632212 1222 1122 222223577888899999999
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025387 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (253)
Q Consensus 114 ~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~ 159 (253)
-|++-+|++ +..||.=+- ..|-...+.|.|||-++++.|.--.+
T Consensus 350 hIA~~IGl~-~~~VEkKLs-qMILDKkf~G~LDQg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 350 HIAEVIGLD-VPQVEKKLS-QMILDKKFYGTLDQGEGCLIVFEEPP 393 (411)
T ss_pred HHHHHHCCC-cHHHHHHHH-HHHHHHHhhcccccCCCeEEEeCCCC
Confidence 999999998 999999988 89999999999999999999975443
No 16
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=93.01 E-value=0.69 Score=44.22 Aligned_cols=106 Identities=11% Similarity=0.247 Sum_probs=77.7
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCCC-C----CcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025387 60 SKYLDMLRLFAHGTWSDYKN----NAGHL-P----QLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (253)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~----~~~~l-~----~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~l 130 (253)
.+|.++++++..+.-.+.+. +++.+ . .|......-+..-+|..|-+...+++.++|++..++.+..|||..
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 36899999999988776554 22222 1 122333445555667777777788999999997777778999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHH
Q 025387 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (253)
Q Consensus 131 lI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~ 169 (253)
|+ ..|..|=|-..|| +-|..+.-...+..|+...+
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 77777766666666655543
No 17
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=92.61 E-value=0.36 Score=46.19 Aligned_cols=99 Identities=20% Similarity=0.317 Sum_probs=64.7
Q ss_pred chHHHHHHHHHhcCChhhHhhh----hCCCCC----cc-----hH-HHHHHHHHHhhhcccCCcccChHHHHHHcCCC--
Q 025387 59 NSKYLDMLRLFAHGTWSDYKNN----AGHLPQ----LV-----PD-QVLKLKQLTVLTLAETNKVLPYDELMEELDVT-- 122 (253)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~----~~~l~~----L~-----~~-~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~-- 122 (253)
.+.+--|.++.-+|++++|..- ...+-. ++ |. +.+.|.. -+..+.-....+|++.+...++++
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 1222222 223333345557777666555554
Q ss_pred C----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025387 123 N----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (253)
Q Consensus 123 ~----~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~ 159 (253)
+ ..+||-.++ .+|..|+++|.|....+++.+....|
T Consensus 367 dn~~~~~~VEciL~-tlI~~G~lrgYis~s~~~vV~sk~~p 406 (413)
T COG5600 367 DNFHSFKEVECILV-TLIGLGLLRGYISHSRRTVVFSKKDP 406 (413)
T ss_pred CcccChHHHHHHHH-HHHhhhhhhheecccceEEEEecCCC
Confidence 2 568999999 89999999999999999999986544
No 18
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=90.88 E-value=3.5 Score=39.14 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=56.3
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (253)
Q Consensus 92 ~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~ 157 (253)
.+-||+..--.|-+.+|.++.+..|+..|++ ++-++.=+= +-|-+|-++++||-++++|++++-
T Consensus 300 vREMR~rvY~QlLESYrsl~l~~MA~aFgVS-VefiDreL~-rFI~~grL~ckIDrVnGVVEtNrp 363 (393)
T KOG0687|consen 300 VREMRRRVYAQLLESYRSLTLESMAKAFGVS-VEFIDRELG-RFIAAGRLHCKIDRVNGVVETNRP 363 (393)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhCch-HHHHHhHHH-HhhccCceeeeeecccceeecCCc
Confidence 5778888888888899999999999999997 887777677 778899999999999999999854
No 19
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=90.62 E-value=3.4 Score=43.27 Aligned_cols=50 Identities=16% Similarity=0.219 Sum_probs=43.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
..+.+|+|+.|.+-.-.=|.-+||.+++ +|...+.+..+||....+|.+.
T Consensus 443 qiY~sIs~~~l~~La~F~~~~~lEk~~v-~a~k~~~v~iriDH~~~~v~Fg 492 (988)
T KOG2072|consen 443 QIYESISFERLYKLAPFFSAFELEKLLV-EAAKHNDVSIRIDHESNSVSFG 492 (988)
T ss_pred HHHHHHhHHHHHHHHhhcCHHHHHHHHH-HHHhccceeEEeccccceeeec
Confidence 3577899998887665556889999999 9999999999999999999987
No 20
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=90.38 E-value=2.7 Score=34.17 Aligned_cols=107 Identities=15% Similarity=0.185 Sum_probs=72.6
Q ss_pred HHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhHhhhhCCC---C---CcchHHHHHHHH
Q 025387 25 ALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNNAGHL---P---QLVPDQVLKLKQ 97 (253)
Q Consensus 25 aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~-t~~~~~~~LL~iFa~Gt~~dy~~~~~~l---~---~L~~~~~~KLr~ 97 (253)
....+...+|..-.+-+|.-++..-.-...+. .+-..++.|.+.+-.|+|..|-+..... + .+.+....++|.
T Consensus 6 ~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~iR~ 85 (143)
T PF10075_consen 6 IYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDTIRE 85 (143)
T ss_dssp HHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHHHHH
T ss_pred HHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHHHHH
Confidence 33445555555556788888877444333332 4557788999999999999987732211 1 233555778888
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
-++-.+...+..|+.+.+++-||++ ..+++.++.
T Consensus 86 ~i~~~i~~aY~sIs~~~la~~Lg~~-~~el~~~~~ 119 (143)
T PF10075_consen 86 RIAHLISKAYSSISLSDLAEMLGLS-EEELEKFIK 119 (143)
T ss_dssp HHHHHHHHH-SEE-HHHHHHHTTS--HHHHHHHHH
T ss_pred HHHHHHHHHHhHcCHHHHHHHhCCC-HHHHHHHHH
Confidence 7777777889999999999999998 999999877
No 21
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=88.79 E-value=0.66 Score=40.35 Aligned_cols=57 Identities=14% Similarity=0.268 Sum_probs=40.8
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
+-.++..+...++++.++||.++++. ..++-+-|- +....|.|.|-||...+-|+|+
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 34566777789999999999999998 788888877 8999999999999999989887
No 22
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=88.12 E-value=3.8 Score=38.51 Aligned_cols=100 Identities=17% Similarity=0.238 Sum_probs=73.5
Q ss_pred chHHHHHHHHHhcCChhhHhhh-hCCCCCcc-----hHHH----HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025387 59 NSKYLDMLRLFAHGTWSDYKNN-AGHLPQLV-----PDQV----LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (253)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~-~~~l~~L~-----~~~~----~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (253)
-..+...-+.|..-++.||..- +..-|+|- ...+ .-|---.|+.+.++..++..+-|++-+|++ ...||
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 3456667788888889999762 22222222 1111 222223567778899999999999999997 99999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025387 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (253)
Q Consensus 129 ~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~R 160 (253)
-=+- ..|-..++-|.+||.++|+.|.-....
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 889899999999999999999755433
No 23
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=85.85 E-value=7.1 Score=31.90 Aligned_cols=80 Identities=20% Similarity=0.365 Sum_probs=57.5
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-Eec-CCCCEEEEEeecCCCCCCCcHHH-HHHHHHHHHHHH
Q 025387 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLD-QLRRCFEVQFAAGRDLRPGQLGS-MIQTLSNWLTTS 181 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G-kID-Q~~~~v~V~~~~~Rdl~~~q~~~-l~~~L~~W~~~~ 181 (253)
+.++.++-++|++.|+++ -..|..-|= +.+..|+|.= |.. ...+..++- +.++++++.. +...|..|++++
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-NLLEAGLVEREKVNLKGGGYYYLY----KPIDPEEIKKKILKDLDEWYDKM 111 (126)
T ss_pred hhcCCcCHHHHHHHHCcc-HHHHHHHHH-HHHHcCCeeeeeeccCCCceeEEE----ecCCHHHHHHHHHHHHHHHHHHH
Confidence 367889999999999997 778888777 8999999873 333 223333332 2334556653 678999999999
Q ss_pred HHHHHHHHH
Q 025387 182 DNLLISIQE 190 (253)
Q Consensus 182 ~~vl~~Ie~ 190 (253)
...+...+.
T Consensus 112 ~~~i~~~~~ 120 (126)
T COG3355 112 KQLIEEFEK 120 (126)
T ss_pred HHHHHHHhc
Confidence 988876653
No 24
>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=83.62 E-value=0.93 Score=32.50 Aligned_cols=43 Identities=16% Similarity=0.287 Sum_probs=33.3
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
.|..+...++.+|+++|+.+++++ .+.||.++= ..+..|-|+-
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~ 46 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEE
Confidence 344455578899999999999997 999999887 8898998883
No 25
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=81.39 E-value=4.6 Score=29.80 Aligned_cols=58 Identities=17% Similarity=0.230 Sum_probs=39.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
++.|..+......+.++-.+|++.++++ ...|+.++= +...+|+|+.+= ..++.+...
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 3334444333344569999999999998 999998877 889999987552 444544443
No 26
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=80.10 E-value=3 Score=37.90 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=43.4
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
++..+.++++++.++|+.+.++. ..++=+-+= +.+..|+|.|-||...+-++|+
T Consensus 205 Fv~YIk~nKvV~ledLas~f~Lr-tqd~inriq-~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIKKNKVVPLEDLASEFGLR-TQDSINRIQ-ELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHhcCeeeHHHHHHHhCcc-HHHHHHHHH-HHHHhhhheeeecCCCceEEec
Confidence 44555689999999999999998 444444444 5666899999999999999997
No 27
>PRK01919 tatB sec-independent translocase; Provisional
Probab=78.25 E-value=14 Score=31.76 Aligned_cols=59 Identities=10% Similarity=0.263 Sum_probs=42.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
.|+|+.++.+..++..|..++....+.+.+.+..--.. ++-++.+++++....+++.++
T Consensus 19 V~GPekLP~~aRtlGk~i~k~Rr~~~d~K~ev~~E~e~-dElrk~~~~~e~~~~~v~~si 77 (169)
T PRK01919 19 VIGPERLPRVARTAGALFGRAQRYINDVKAEVSREIEL-DELRKMKTDFESAARDVENTI 77 (169)
T ss_pred eeCchHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH-HHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999988888765432 233334455555555555554
No 28
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=77.85 E-value=3.8 Score=31.28 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=33.0
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
|+.....+..+||.+|++.++++ ...+-..+- .....|+|.+
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 33333345679999999999997 888888777 8888999883
No 29
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.76 E-value=4.1 Score=33.62 Aligned_cols=48 Identities=21% Similarity=0.326 Sum_probs=37.6
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCC
Q 025387 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQL 148 (253)
Q Consensus 99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G---kIDQ~ 148 (253)
.|+.+-+.+...||.+|++.||++ ...|-.-+= +....|+|+| -+|..
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 344444567899999999999997 888887776 8888999984 45653
No 30
>PRK04098 sec-independent translocase; Provisional
Probab=74.56 E-value=22 Score=30.14 Aligned_cols=60 Identities=20% Similarity=0.328 Sum_probs=44.2
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---hhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA---DSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a---~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
.|+|+.++.+...+..|...+....+.+...+... ...+++..+-++.++...+++++.+
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 57999999999999999999888888876666543 3334444555677777777777643
No 31
>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=73.18 E-value=9.3 Score=30.79 Aligned_cols=44 Identities=18% Similarity=0.336 Sum_probs=35.4
Q ss_pred Hhhhcc--cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 99 TVLTLA--ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 99 tLlsLa--~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
.++.|| ..++.++-++|++.++|| ...|+.++- ..-.+|+|...
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s~ 58 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKSV 58 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEEE
Confidence 344444 345679999999999998 999999888 88889999853
No 32
>PRK04654 sec-independent translocase; Provisional
Probab=72.34 E-value=14 Score=32.70 Aligned_cols=36 Identities=14% Similarity=0.197 Sum_probs=30.4
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD 196 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~ 196 (253)
.|+++.|..+...+..|..++++....+.+.+.+--
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~El 54 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELEREL 54 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 579999999999999999998888888777765543
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=71.37 E-value=16 Score=27.35 Aligned_cols=37 Identities=11% Similarity=0.212 Sum_probs=31.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (253)
.|+|+.++.+...+..|........+.+.+++...-.
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~e~~ 54 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDEELK 54 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHhc
Confidence 4789999999999999999999999888887765444
No 34
>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=71.20 E-value=7.5 Score=25.38 Aligned_cols=42 Identities=19% Similarity=0.360 Sum_probs=30.2
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
.|+.+...+..++-.+|++.++++ ...|-..+= +....|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 344444446669999999999997 888877665 888888875
No 35
>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=69.85 E-value=4.8 Score=30.96 Aligned_cols=34 Identities=18% Similarity=0.498 Sum_probs=26.6
Q ss_pred hcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhc
Q 025387 102 TLAETNKVLPYDELMEELDVTNVRELEDFLINECMYT 138 (253)
Q Consensus 102 sLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~ 138 (253)
.+-..-..+||+.|-+. +||.+.||+||| +.+..
T Consensus 41 rlftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln~ 74 (100)
T PF07389_consen 41 RLFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLND 74 (100)
T ss_pred HHHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHHh
Confidence 33344457899999998 688999999999 77643
No 36
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=69.73 E-value=6.5 Score=31.74 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=33.4
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
|+.+-+.+..+||.+|++.++++ ...|=.-|= +....|+|+|.
T Consensus 13 IL~~L~~d~r~~~~eia~~lglS-~~~v~~Ri~-~L~~~GiI~~~ 55 (154)
T COG1522 13 ILRLLQEDARISNAELAERVGLS-PSTVLRRIK-RLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHhCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCceeeE
Confidence 33333445559999999999997 888877777 88889999864
No 37
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=68.90 E-value=17 Score=28.66 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.5
Q ss_pred HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 93 ~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
.-++.|..+....+...++.++|++.+++| ...|...+= .....|+|...
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 38
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.49 E-value=9.3 Score=31.86 Aligned_cols=44 Identities=11% Similarity=0.159 Sum_probs=35.7
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
..|+.+-+.+..+||.+|++.++++ ...|-.-+= +....|+|+|
T Consensus 17 ~~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~ 60 (164)
T PRK11169 17 RNILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQG 60 (164)
T ss_pred HHHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEE
Confidence 3455556688999999999999997 777776666 7888999975
No 39
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=68.08 E-value=21 Score=31.71 Aligned_cols=62 Identities=11% Similarity=0.165 Sum_probs=49.5
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 92 ~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
+.-|++|.++........+|..+|++.|+++ ...+=..|- +.-..|+|.-..+...+.+.++
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 4456667777766677789999999999997 777777777 8888999999999877666665
No 40
>PRK01770 sec-independent translocase; Provisional
Probab=67.30 E-value=21 Score=30.67 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=31.5
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD 196 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~ 196 (253)
.|+|+.++.+..++..|..+++++...+++.+.+--
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~E~ 54 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQEL 54 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 579999999999999999999999999888776533
No 41
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=66.66 E-value=14 Score=31.20 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=37.0
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 96 r~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
+.+..+......+.+|-++|++.++|| ..-|+.++- ..-.+|||...
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 333333433455689999999999998 999999888 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=62.91 E-value=6.7 Score=27.21 Aligned_cols=35 Identities=29% Similarity=0.481 Sum_probs=24.3
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHH
Q 025387 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (253)
Q Consensus 96 r~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~ll 131 (253)
|++.|+.+....+.+++++|++.++++ .+.+-..|
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 444555444347899999999999997 77665543
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=62.60 E-value=37 Score=26.82 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=32.3
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
.+..++..+|++.++++ ..-|...+= ....+|+|.+.
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 899998877 88899999874
No 44
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=60.64 E-value=18 Score=26.40 Aligned_cols=46 Identities=24% Similarity=0.232 Sum_probs=35.3
Q ss_pred HHHHhhhcccCC-cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 96 KQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 96 r~LtLlsLa~~~-k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
|.+.|+.+.... ..++..+|++.++++ ...|-..+- .....|+|..
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~~l~i~-~~tv~r~l~-~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLN-TLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeee
Confidence 345555544433 689999999999998 888888877 7778898875
No 45
>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=57.81 E-value=18 Score=25.84 Aligned_cols=36 Identities=17% Similarity=0.213 Sum_probs=27.6
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
.+..-|+.+|++.+++.|..-|-..|- ..-..|+|+
T Consensus 22 ~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 22 NGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred cCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 567789999999999998999988877 667777764
No 46
>PF11945 WASH_WAHD: WAHD domain of WASH complex; InterPro: IPR021854 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53. This entry represents the WASH subunit of the WASH complex. WASH genes duplicated to multiple chromosomal ends during primate evolution, with highest copy number reached in humans, whose WASH repertoires probably vary extensively among individuals []. It is therefore difficult to determine which gene is functional or not. The telomeric region of chromosome 9p is paralogous to the pericentromeric regions of chromosome 9 as well as to 2q. Paralogous regions contain 7 transcriptional units. Duplicated WASH genes are also present in the Xq/Yq pseudoautosomal region, as well as on chromosome 1 and 15. The chromosome 16 copy seems to be a pseudogene.
Probab=56.85 E-value=97 Score=28.87 Aligned_cols=64 Identities=14% Similarity=0.152 Sum_probs=48.0
Q ss_pred eecCCCCCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhh
Q 025387 156 FAAGRDLRPGQ-LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKS 219 (253)
Q Consensus 156 ~~~~Rdl~~~q-~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~ 219 (253)
-.++.|++.++ +..+.+.|+.--.-++.+.+.|.+++..-...-+.-..+-...+++|+.++-+
T Consensus 8 plI~~dLr~eEti~qi~~aL~~L~~v~~diF~rI~~Rv~~~~~~l~~i~~Ri~~~qaKi~~l~gs 72 (297)
T PF11945_consen 8 PLIPPDLRREETILQIADALEYLDKVSNDIFSRISARVERNRERLQAIQQRIEVAQAKIEKLQGS 72 (297)
T ss_pred cccCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 45688887765 67789999999999999999999998876665555555555566777766544
No 47
>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=56.63 E-value=1.1e+02 Score=26.43 Aligned_cols=96 Identities=19% Similarity=0.157 Sum_probs=52.6
Q ss_pred HHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH---HH
Q 025387 116 MEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE---KI 192 (253)
Q Consensus 116 ~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~---~i 192 (253)
.+++||. ...|.++|- ..+..|+|+. ..=|+-.+-|+-|- .....+...+......+..+-..+.. ++
T Consensus 22 pK~~gI~-~~~VKdvlq-~LvDDglV~~---EKiGssn~YWsFps----~~~~~~~~~~~~l~~~~~~~~~~i~~l~~~i 92 (188)
T PF03962_consen 22 PKEKGIV-SMSVKDVLQ-SLVDDGLVHV---EKIGSSNYYWSFPS----QAKQKRQNKLEKLQKEIEELEKKIEELEEKI 92 (188)
T ss_pred ccccCCc-hhhHHHHHH-HHhccccchh---hhccCeeEEEecCh----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3447886 788999888 7887777662 23456667787543 34444444444444444444333333 22
Q ss_pred HHHhh------hhHHHHHHHHHHHHHHHHHHhhc
Q 025387 193 KWADS------MNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 193 ~~a~~------~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
..+.. .........++++.+++.+++.+
T Consensus 93 ~~~~~~r~~~~eR~~~l~~l~~l~~~~~~l~~el 126 (188)
T PF03962_consen 93 EEAKKGREESEEREELLEELEELKKELKELKKEL 126 (188)
T ss_pred HHHHhcccccHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22221 11222344455667777777776
No 48
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=56.47 E-value=30 Score=28.70 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025387 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (253)
Q Consensus 95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkID 146 (253)
++-|..++.-..++.++-++|++..+|+ ..-++.++- ..-.+|||+..=-
T Consensus 11 l~~L~~LA~~~~~~~~s~~~IA~~~~is-~~~L~kil~-~L~kaGlV~S~rG 60 (150)
T COG1959 11 LRALLYLALLPGGGPVSSAEIAERQGIS-PSYLEKILS-KLRKAGLVKSVRG 60 (150)
T ss_pred HHHHHHHHhCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHHcCCEEeecC
Confidence 3444444444455588999999999997 999999988 8899999886544
No 49
>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=55.55 E-value=99 Score=24.19 Aligned_cols=59 Identities=20% Similarity=0.241 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhccccccCCccc
Q 025387 170 MIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRG 230 (253)
Q Consensus 170 l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~~~k~~~~~~~ 230 (253)
..+++.+=....+.+...+......+..........+.+-++..+.+|+.+ |.+.+.+-
T Consensus 37 q~~tI~qq~~~~~~L~~~~~~~r~~~~~~~~~~qq~r~~~e~~~e~ik~~l--k~d~Ca~~ 95 (110)
T PF10828_consen 37 QAQTIQQQEDANQELKAQLQQNRQAVEEQQKREQQLRQQSEERRESIKTAL--KDDPCANT 95 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--ccCccccC
Confidence 344555555555666666665555555555555666667778888888888 87776553
No 50
>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=55.55 E-value=28 Score=23.18 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=32.1
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 96 r~LtLlsL-a~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
|-+.|+.. +.....++..+|+++++++ ...+-.++- .....|+|+
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 34566654 4455668999999999998 778877776 667777664
No 51
>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=54.30 E-value=8.3 Score=25.17 Aligned_cols=28 Identities=29% Similarity=0.449 Sum_probs=18.6
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHH
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELE 128 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (253)
|+.+-..+...||.+|++.+|++ ...|-
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 66553
No 52
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=54.18 E-value=93 Score=29.91 Aligned_cols=59 Identities=25% Similarity=0.332 Sum_probs=44.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHH
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQT 173 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~ 173 (253)
.++.++-++|++.++++ .+.+++++= +...+|+|. +-++. .|+..||.+.=.+..+.+.
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~-~~~~g------~~~l~rd~~~itL~dv~~~ 365 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR-RGERG------QWVLARDLDSVPLAELYEL 365 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE-ecCCC------ceEecCCHHhCcHHHHHHh
Confidence 56788999999999998 999998877 888899997 32221 3788888766555555554
No 53
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=53.87 E-value=82 Score=25.08 Aligned_cols=37 Identities=11% Similarity=0.156 Sum_probs=31.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (253)
.|+|+.++.+...+..|........+.+++.+..--.
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~E~~ 55 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQEESR 55 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5789999999999999999999998888887755443
No 54
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=53.64 E-value=1e+02 Score=27.53 Aligned_cols=38 Identities=26% Similarity=0.477 Sum_probs=29.0
Q ss_pred Ch-HHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025387 111 PY-DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (253)
Q Consensus 111 sy-~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~ 150 (253)
.| .+|++.+|++.-.-+++|=+ .-.+|||+..++-..+
T Consensus 29 ~yvsEiS~~lgvsqkAVl~HL~~--LE~AGlveS~ie~~~R 67 (217)
T COG1777 29 CYVSEISRELGVSQKAVLKHLRI--LERAGLVESRIEKIPR 67 (217)
T ss_pred hHHHHHHhhcCcCHHHHHHHHHH--HHHcCCchhhcccccc
Confidence 44 47889999984445677766 4678999999988777
No 55
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=53.55 E-value=27 Score=27.97 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=33.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V 154 (253)
....+..+|++.++++ ...|-.=+= ..-.+|||..+-+.......+
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 3468889999999997 666654433 356689999988866544444
No 56
>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=53.36 E-value=20 Score=23.90 Aligned_cols=35 Identities=31% Similarity=0.400 Sum_probs=23.7
Q ss_pred HHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 97 QLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 97 ~LtLlsLa-~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
+..|+.+. .....+|-++||+.|+++ .+.|..-|=
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 44455443 444559999999999997 777766543
No 57
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.61 E-value=22 Score=25.33 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=29.5
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
.++-.+|+++|+|+ ...|-..+- .....|+|.-
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 789999998 8999998864
No 58
>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=52.55 E-value=59 Score=27.37 Aligned_cols=62 Identities=15% Similarity=0.222 Sum_probs=44.7
Q ss_pred chHHHHHHHHHhcCChhhHhhhh--CCCCCcc----hHHHHHHHHHHhhhcccCCcc-cChHHHHHHcC
Q 025387 59 NSKYLDMLRLFAHGTWSDYKNNA--GHLPQLV----PDQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (253)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~--~~l~~L~----~~~~~KLr~LtLlsLa~~~k~-Isy~~I~~~L~ 120 (253)
..-.+++...+..|+|..|-... ...|.+. .....++|..++-+++...+. +|-+.+++-|+
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 45567899999999999998754 5555543 224779999888888887777 99999888775
No 59
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=52.41 E-value=36 Score=28.24 Aligned_cols=39 Identities=18% Similarity=0.118 Sum_probs=33.2
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkID 146 (253)
..+.++-.+|++..+|| ..-|+.++- ..-.+|+|+..=-
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 44568999999999998 999999988 8888999886654
No 60
>PF13730 HTH_36: Helix-turn-helix domain
Probab=52.05 E-value=52 Score=21.74 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=35.1
Q ss_pred HHHHHHHhhhcccC-Cccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 025387 93 LKLKQLTVLTLAET-NKVL-PYDELMEELDVTNVRELEDFLINECMYTGIV 141 (253)
Q Consensus 93 ~KLr~LtLlsLa~~-~k~I-sy~~I~~~L~I~~~~evE~llI~~AI~~gLI 141 (253)
.|+-.+.|.+.+.+ +.+. |++.|++.++++ .+.|-..+= +....|+|
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 56666778888752 2344 799999999997 888888766 77777765
No 61
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=51.89 E-value=35 Score=35.57 Aligned_cols=96 Identities=11% Similarity=0.232 Sum_probs=67.1
Q ss_pred HHHHHHHHhcCChhhHhh---h----hCCCCCcc---hHHHHHHHHH----HhhhcccCCcccChHHHHHHcCCCChHHH
Q 025387 62 YLDMLRLFAHGTWSDYKN---N----AGHLPQLV---PDQVLKLKQL----TVLTLAETNKVLPYDELMEELDVTNVREL 127 (253)
Q Consensus 62 ~~~LL~iFa~Gt~~dy~~---~----~~~l~~L~---~~~~~KLr~L----tLlsLa~~~k~Isy~~I~~~L~I~~~~ev 127 (253)
+..-=.....|+|.+-.. + ++-+|.-. .-...+++-= -|.+.+.-+..+|.+.||+-.++| +..|
T Consensus 657 VvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYss~Y~SvSl~~LA~mFdLp-~~~V 735 (843)
T KOG1076|consen 657 VVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYSSVYDSVSLAKLADMFDLP-EPKV 735 (843)
T ss_pred HHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccHHHHHHHhCCC-chhH
Confidence 444556788899987444 2 23445421 1123333332 234555568999999999999998 8888
Q ss_pred HHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025387 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (253)
Q Consensus 128 E~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~ 159 (253)
=..|- +.|-..=|.+++||..+||.++++.+
T Consensus 736 hsIiS-kmiineEl~AslDqpt~~iv~hrvE~ 766 (843)
T KOG1076|consen 736 HSIIS-KMIINEELHASLDQPTQCIVMHRVEP 766 (843)
T ss_pred HHHHH-HHHHHHHhhhccCCCcceEEEeeccc
Confidence 77766 77877889999999999999987643
No 62
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=51.72 E-value=39 Score=27.32 Aligned_cols=51 Identities=14% Similarity=0.194 Sum_probs=37.4
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025387 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (253)
Q Consensus 95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ 147 (253)
+|.+..+.-..++..++-++|++.++|+ ..-|+..+- ..-..|+|+.+=--
T Consensus 11 l~~~i~la~~~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~G~ 61 (141)
T PRK11014 11 LRALIYMASLPEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVRGK 61 (141)
T ss_pred HHHHHHHhcCCCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEecCC
Confidence 3444444433456688999999999997 888998888 78888888765433
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=50.20 E-value=22 Score=23.59 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=20.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
.-.||.+|++.++++ ...|..++- .|.
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 468999999999997 999998877 664
No 64
>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=50.18 E-value=28 Score=23.87 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=28.7
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
......+..+|++.++++ ...+-.=+= ....+|+|+..
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 556889999999999998 767765555 56678888753
No 65
>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=49.74 E-value=55 Score=21.86 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=30.3
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025387 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (253)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ 147 (253)
+++.+|++.++++ ...+-..+- .....|+|...-+.
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 888877766 77788999876665
No 66
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=49.70 E-value=46 Score=26.34 Aligned_cols=100 Identities=20% Similarity=0.181 Sum_probs=50.8
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQ 189 (253)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie 189 (253)
|.-+.|.++.++ +.++.+|- .+.-|.|+.....-.+.-...+-|...|+ .++.|-.=.+.+...+..++
T Consensus 18 iDvd~i~~~~Di---~~Lq~~i~------~vtf~~l~~e~~~~~~dp~~~klfrLaQl--~ieYLl~~q~~L~~~~~~l~ 86 (118)
T PF13815_consen 18 IDVDRIVRELDI---DTLQENIE------NVTFCDLENEDCQHFVDPNFLKLFRLAQL--SIEYLLHCQEYLSSQLEQLE 86 (118)
T ss_pred cCHHHHHhccCH---HHHHHHHH------hcceeccChhhccCCCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHH
Confidence 444556665554 46666544 33456665544322111000011111111 23333333455566666677
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 190 EKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 190 ~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
+++..++...++-.+.-++..+++..+|+.+
T Consensus 87 ~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E~ 117 (118)
T PF13815_consen 87 ERLQELQQEIEKLKQKLKKQKEEIKKLKKES 117 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 7777777766666666666677777777654
No 67
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=48.64 E-value=1.6e+02 Score=24.51 Aligned_cols=114 Identities=16% Similarity=0.179 Sum_probs=65.6
Q ss_pred cCCcccChHHHHHHcC--CCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHH
Q 025387 105 ETNKVLPYDELMEELD--VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~--I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~ 182 (253)
..+|..+..+|...|+ ++ =..|...+= .+...|.|.+|.-....+..+.-...-+++++++..|-..+....+.+.
T Consensus 12 ~qNRPys~~di~~nL~~~~~-K~~v~k~Ld-~L~~~g~i~~K~~GKqkiY~~~Q~~~~~~s~eel~~ld~ei~~L~~el~ 89 (169)
T PF07106_consen 12 EQNRPYSAQDIFDNLHNKVG-KTAVQKALD-SLVEEGKIVEKEYGKQKIYFANQDELEVPSPEELAELDAEIKELREELA 89 (169)
T ss_pred HcCCCCcHHHHHHHHHhhcc-HHHHHHHHH-HHHhCCCeeeeeecceEEEeeCccccCCCCchhHHHHHHHHHHHHHHHH
Confidence 4788999999999996 54 345555544 5666799999976555433333333344567888888777777766555
Q ss_pred HHHHHH---HHHHHHHhhhh--HHHHHHHHHHHHHHHHHHhhc
Q 025387 183 NLLISI---QEKIKWADSMN--EMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 183 ~vl~~I---e~~i~~a~~~~--~~~~~~~~~~e~~v~~~k~~~ 220 (253)
.+-..+ +..++..++.- ++-...-.+++++++.+...+
T Consensus 90 ~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~~e~~~l~~kL 132 (169)
T PF07106_consen 90 ELKKEVKSLEAELASLSSEPTNEELREEIEELEEEIEELEEKL 132 (169)
T ss_pred HHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 544433 33444333322 122333334444444444444
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=48.42 E-value=26 Score=24.04 Aligned_cols=42 Identities=24% Similarity=0.268 Sum_probs=29.0
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCc
Q 025387 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (253)
Q Consensus 97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gL 140 (253)
+-.|+.+......++..+|++.++++ ..-+-.=+. ..-..|+
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS-~~TiRRDl~-~L~~~g~ 43 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVS-EMTIRRDLN-KLEKQGL 43 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcC-HHHHHHHHH-HHHHCCC
Confidence 34566666778899999999999997 655544334 3444454
No 69
>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=48.41 E-value=72 Score=26.73 Aligned_cols=52 Identities=13% Similarity=0.282 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhccccccCCccccchh
Q 025387 181 SDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKADVDCRGHEEI 234 (253)
Q Consensus 181 ~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~~~k~~~~~~~~~~~ 234 (253)
+..++..++..+....++..+-..+++..+.+++.+|..+ ...+...|...+
T Consensus 45 ~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL--~~~m~~~g~~ki 96 (162)
T PF05565_consen 45 IAKVIKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYL--LDAMEAAGIKKI 96 (162)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHcCCcee
Confidence 3334444555666666666666777788888899998888 666666666654
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=48.19 E-value=46 Score=21.68 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=24.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
+..+..+|++.++++ ...|-.-+= .....|+|+
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 777665544 566677764
No 71
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=47.74 E-value=23 Score=26.21 Aligned_cols=51 Identities=29% Similarity=0.315 Sum_probs=35.0
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~ 150 (253)
|.|+++-.....++|.+|.+.|+++ ...+-.-+= ....+|+|+-+-.-..+
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 4455544446789999999999997 667766655 67778999977655544
No 72
>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=47.60 E-value=44 Score=23.33 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=32.6
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
.+|..|...+..++-.+||+.|+++ ...|=..+= +.-..|+|.
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 3555566688999999999999997 777766666 777778775
No 73
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=47.24 E-value=76 Score=20.62 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=28.9
Q ss_pred cCCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 105 ETNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 105 ~~~k~I-sy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
.++..+ |..+|++.++++ ...|-..+- .....|+|.
T Consensus 15 ~~~~~l~s~~~la~~~~vs-~~tv~~~l~-~L~~~g~i~ 51 (60)
T smart00345 15 RPGDKLPSERELAAQLGVS-RTTVREALS-RLEAEGLVQ 51 (60)
T ss_pred CCCCcCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 345567 899999999996 888888777 777778875
No 74
>PRK00404 tatB sec-independent translocase; Provisional
Probab=46.97 E-value=1.3e+02 Score=25.03 Aligned_cols=37 Identities=16% Similarity=0.274 Sum_probs=30.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (253)
.|+++.+..+..++..|..+..+..+.+.+.+.+--.
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 5789999999999999999988888877777666433
No 75
>PRK09954 putative kinase; Provisional
Probab=46.43 E-value=24 Score=32.81 Aligned_cols=54 Identities=19% Similarity=0.438 Sum_probs=41.1
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCCCCEEEEE
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQLRRCFEVQ 155 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G---kIDQ~~~~v~V~ 155 (253)
|+.+...+..+|+.+|++.|+++ ...|-..|- +....|+|+| .||.....+.|-
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 55555577799999999999997 889988877 8888899875 466666554443
No 76
>PRK00708 sec-independent translocase; Provisional
Probab=46.39 E-value=83 Score=27.92 Aligned_cols=37 Identities=11% Similarity=0.136 Sum_probs=31.9
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (253)
.|+|+++..+...+..|..++..+.+.+.+++...-.
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 5789999999999999999999888888887766444
No 77
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=45.93 E-value=1.5e+02 Score=23.53 Aligned_cols=57 Identities=9% Similarity=-0.013 Sum_probs=41.0
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~ 158 (253)
|..|...+..++-.+|++.++++ ...|=..|- .....|+|.=.-|..+++...-+.+
T Consensus 37 L~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 37 LHNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred HHHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEEC
Confidence 33444333446789999999997 666666666 8888999999999877766555443
No 78
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=44.40 E-value=25 Score=33.16 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=53.3
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (253)
Q Consensus 92 ~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~ 157 (253)
.+-||.=.-..|-+.+|.++.+..|+..+++ ++-|+.=+= +-|-.|-+.+.||-++++|++++-
T Consensus 314 vREMRrrvYaQlLESYr~lsl~sMA~tFgVS-V~yvdrDLg-~FIp~~~LncvIDRvnGvVetnrp 377 (412)
T COG5187 314 VREMRRRVYAQLLESYRLLSLESMAQTFGVS-VEYVDRDLG-EFIPEGRLNCVIDRVNGVVETNRP 377 (412)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHhCcc-HHHHhhhHH-hhCCCCceeeeeecccceEeccCc
Confidence 4667776677777889999999999999997 877776666 667789999999999999998753
No 79
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=43.78 E-value=49 Score=25.53 Aligned_cols=39 Identities=18% Similarity=0.146 Sum_probs=29.0
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025387 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~ 149 (253)
+....++.+++++.++++ +.||. +.+..|+|.-.-+...
T Consensus 3 ~~~~~lt~~Elc~~~gi~-----~~~l~-eLve~GlIep~~~~~~ 41 (101)
T PRK10265 3 NVTVTFTITEFCLHTGVS-----EEELN-EIVGLGVIEPREIQET 41 (101)
T ss_pred ceEEEeeHHHHHHHHCcC-----HHHHH-HHHHCCCeecCCCCcc
Confidence 344578999999999998 45666 7777899986544433
No 80
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=42.92 E-value=33 Score=25.12 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=22.7
Q ss_pred HHhhhcccCCcccChHHHHHHcCCC-ChHHH
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVT-NVREL 127 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~-~~~ev 127 (253)
+.++.-.-.++..||.+|++.++.+ ..+.|
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 4445555678999999999999996 35554
No 81
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=42.30 E-value=1.1e+02 Score=21.01 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=20.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 105 ETNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
..-|.++..+|+++|||+ ...+-.-+=
T Consensus 19 d~PR~~tl~elA~~lgis-~st~~~~LR 45 (53)
T PF04967_consen 19 DVPRRITLEELAEELGIS-KSTVSEHLR 45 (53)
T ss_pred CCCCcCCHHHHHHHhCCC-HHHHHHHHH
Confidence 356899999999999997 666655444
No 82
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=40.99 E-value=76 Score=23.01 Aligned_cols=49 Identities=14% Similarity=0.260 Sum_probs=33.1
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~ 155 (253)
|+..+. ....++..|+..++++ ...+..++= ..+..|+|++ .++.+.+|
T Consensus 11 IL~~l~-~~~~~~t~i~~~~~L~-~~~~~~yL~-~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 11 ILKILS-KGGAKKTEIMYKANLN-YSTLKKYLK-ELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp HHHHH--TT-B-HHHHHTTST---HHHHHHHHH-HHHHTTSEEE----ETTEEEE-
T ss_pred HHHHHH-cCCCCHHHHHHHhCcC-HHHHHHHHH-HHHHCcCeeC----CCCEEEEC
Confidence 344443 6778899999999997 889998877 8999999944 45555554
No 83
>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=40.75 E-value=96 Score=30.31 Aligned_cols=89 Identities=12% Similarity=0.206 Sum_probs=64.6
Q ss_pred hHHHHHHcCC----CChHHHHHHHHHHhHhcCccEEEecCC--CCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHH
Q 025387 112 YDELMEELDV----TNVRELEDFLINECMYTGIVRGKLDQL--RRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLL 185 (253)
Q Consensus 112 y~~I~~~L~I----~~~~evE~llI~~AI~~gLI~GkIDQ~--~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl 185 (253)
.+++-+.|++ +..+++...++ +|+..|+.----|.. .+.+... +..+..++.+.|.+++..-...-+.+-
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 4456666554 44578888888 999999887777765 3323322 566888899999999988877777777
Q ss_pred HHHHHHHHHHhhhhHHHHH
Q 025387 186 ISIQEKIKWADSMNEMDKK 204 (253)
Q Consensus 186 ~~Ie~~i~~a~~~~~~~~~ 204 (253)
..++.|-..||....+.-+
T Consensus 417 ~~~~~q~~~a~~~~~~~~~ 435 (438)
T TIGR02919 417 ELLEQQREHANDISKEQFK 435 (438)
T ss_pred HHHHHHHHHhccCCHHHHH
Confidence 8888888888887666443
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=69 Score=24.23 Aligned_cols=49 Identities=16% Similarity=0.243 Sum_probs=36.1
Q ss_pred HHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025387 97 QLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (253)
Q Consensus 97 ~LtLlsL-a~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ 147 (253)
.|.++.= +....=++.++|++.|+++ ..+|+..|= ..+..|.|=-.||.
T Consensus 52 Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 52 VLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 3444444 4445569999999999997 999998777 88889998777775
No 85
>KOG2166 consensus Cullins [Cell cycle control, cell division, chromosome partitioning]
Probab=39.56 E-value=3.9e+02 Score=28.10 Aligned_cols=117 Identities=16% Similarity=0.178 Sum_probs=71.9
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHh--HhcCccEEEec--CCCCEEEEEee----cCCC----C
Q 025387 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINEC--MYTGIVRGKLD--QLRRCFEVQFA----AGRD----L 162 (253)
Q Consensus 95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~A--I~~gLI~GkID--Q~~~~v~V~~~----~~Rd----l 162 (253)
+-+++++-|-+..-.++|.+|.++++++ ..++=..+- .. +-..++.+.-+ ..+.++.+++. ..|+ +
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 888776655 43 22122222111 45667777742 2232 2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 163 RPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 163 ~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
...+-+....+++.|+.. .|++.|.+.=+ +.++..|.+=+.+-++.+++.+
T Consensus 644 ~~~e~~~~~~~ve~dRk~------~i~AaIVRIMK-~rK~l~h~~Lv~Ev~~ql~~RF 694 (725)
T KOG2166|consen 644 PMDERKKVVEDVDKDRKY------AIDAAIVRIMK-SRKVLGHQQLVSEVVEQLSERF 694 (725)
T ss_pred CchhHHHHHhhhhhHHHH------HHHHHHHHHHH-hhccccHHHHHHHHHHHHhhhc
Confidence 223556677788888752 34444444422 2244667777777777777776
No 86
>PHA01750 hypothetical protein
Probab=39.12 E-value=1.3e+02 Score=22.01 Aligned_cols=35 Identities=23% Similarity=0.252 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 186 ISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 186 ~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
..+.........+-+.-..+++++++.|.++|+-+
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 34455666666666666678888999999999876
No 87
>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=39.03 E-value=51 Score=22.96 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=32.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkI 145 (253)
..+..+-.+|++.++++ ...|-..|= .....|+|+-.-
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 45789999999999998 889998877 899999997554
No 88
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=39.02 E-value=23 Score=26.21 Aligned_cols=38 Identities=16% Similarity=0.347 Sum_probs=24.3
Q ss_pred hhhcccCCcccChHHHHHHcC---CCChHHHHHHHHHHhHhcC
Q 025387 100 VLTLAETNKVLPYDELMEELD---VTNVRELEDFLINECMYTG 139 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~---I~~~~evE~llI~~AI~~g 139 (253)
|+......+.|+|++|...|. + +.+.++.++- ..-..|
T Consensus 12 Li~~gK~~G~lT~~eI~~~L~~~~~-~~e~id~i~~-~L~~~g 52 (82)
T PF03979_consen 12 LIEKGKKKGYLTYDEINDALPEDDL-DPEQIDEIYD-TLEDEG 52 (82)
T ss_dssp HHHHHHHHSS-BHHHHHHH-S-S----HHHHHHHHH-HHHTT-
T ss_pred HHHHHhhcCcCCHHHHHHHcCccCC-CHHHHHHHHH-HHHHCC
Confidence 667777778899999999997 3 3677777655 444344
No 89
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=38.63 E-value=77 Score=20.00 Aligned_cols=35 Identities=20% Similarity=0.186 Sum_probs=27.0
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
+..++-.+|++.++++ ...+...+= .....|+|.-
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~~ 46 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLTR 46 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEE
Confidence 4569999999999996 888887765 6666677653
No 90
>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=38.33 E-value=1.1e+02 Score=19.84 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=21.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
....||.+|++.++++ ...|-.+.- .|+
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 887777665 565
No 91
>PF13518 HTH_28: Helix-turn-helix domain
Probab=38.32 E-value=38 Score=21.90 Aligned_cols=31 Identities=10% Similarity=0.200 Sum_probs=23.6
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
.++.+...+ . |+.+++++++|+ ...|-.|+-
T Consensus 4 ~iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~ 34 (52)
T PF13518_consen 4 QIVELYLEG-E-SVREIAREFGIS-RSTVYRWIK 34 (52)
T ss_pred HHHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH
Confidence 344444433 3 999999999995 899999976
No 92
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=38.28 E-value=1.1e+02 Score=19.79 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=29.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkID 146 (253)
...+++.+|++.++++ ...+-..+= .....|+|.-.=+
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 777776655 6777898874433
No 93
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=37.92 E-value=1.5e+02 Score=21.20 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=33.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~ 149 (253)
...++..+|++.++++ ...+-..|- +....|+|.-.-++.+
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 788888877 8999999987766543
No 94
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=37.69 E-value=1.1e+02 Score=21.61 Aligned_cols=61 Identities=11% Similarity=0.165 Sum_probs=46.1
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025387 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (253)
Q Consensus 111 sy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~ 176 (253)
.|..+.+.+++++. ....++= + +.+-+-.++..+++.++....++.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~~-~~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPDE-LDNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCch-hhhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 36788899999832 2233333 3 245668999999999999999999999988888777654
No 95
>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=35.79 E-value=1.3e+02 Score=21.56 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=37.4
Q ss_pred cCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 138 TGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190 (253)
Q Consensus 138 ~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~ 190 (253)
.+-+...++-.++++.|.+.. .+...|...+..|...+.-+...+++
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 367888999999999999875 56788999999999988887777653
No 96
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=35.41 E-value=1.7e+02 Score=23.12 Aligned_cols=56 Identities=20% Similarity=0.330 Sum_probs=35.6
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 159 GRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 159 ~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
+|.+.+..++.+..-|+.-.++++.++.. ++.....+..+-|..++..+.++++.+
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 56666666666776666666666665543 334444555666667777777777776
No 97
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=35.27 E-value=90 Score=25.57 Aligned_cols=52 Identities=13% Similarity=0.302 Sum_probs=42.0
Q ss_pred cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 025387 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (253)
Q Consensus 87 L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI 141 (253)
+++++..+| ...|+.|+..++.+++.++...++++ ...++.++- +++..|-|
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 455544443 36788999999999999999999997 999999999 89877743
No 98
>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=34.92 E-value=1.9e+02 Score=21.39 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=48.2
Q ss_pred HHhhhcccCCcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee-cCCCCCCCcHHHHHHHHH
Q 025387 98 LTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA-AGRDLRPGQLGSMIQTLS 175 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L-~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~-~~Rdl~~~q~~~l~~~L~ 175 (253)
+.|..|.. +...|.+|.+.+ +|+ ...+-+-+= +....|||.=...... -..|.|. +++- .++..+...|.
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 688999999999 786 777766666 7788999987766433 2334442 1111 23556777888
Q ss_pred HHHHH
Q 025387 176 NWLTT 180 (253)
Q Consensus 176 ~W~~~ 180 (253)
.|...
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88753
No 99
>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=34.47 E-value=63 Score=25.87 Aligned_cols=41 Identities=20% Similarity=0.322 Sum_probs=32.5
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
-.|+.||.. .+|-.||+..|++| ..-+--++= +.+..|+|.
T Consensus 46 ~~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvs-DL~~~G~v~ 86 (114)
T PF05331_consen 46 RAILELCRR--PLSVAEIAARLGLP-LGVVRVLVS-DLADAGLVR 86 (114)
T ss_pred HHHHHHHCC--CccHHHHHHhhCCC-chhhhhhHH-HHHhCCCEE
Confidence 467888877 89999999999999 766665555 788777764
No 100
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=33.74 E-value=44 Score=23.80 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
.+|.-+.++||+.|+|+ ..+|..++-
T Consensus 17 lgr~Pt~eEiA~~lgis-~~~v~~~l~ 42 (78)
T PF04539_consen 17 LGREPTDEEIAEELGIS-VEEVRELLQ 42 (78)
T ss_dssp HSS--BHHHHHHHHTS--HHHHHHHHH
T ss_pred hCCCCCHHHHHHHHccc-HHHHHHHHH
Confidence 47889999999999997 999997654
No 101
>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=33.18 E-value=2.2e+02 Score=21.77 Aligned_cols=46 Identities=11% Similarity=0.073 Sum_probs=35.6
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEE
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFE 153 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~ 153 (253)
.+..++..+|++.++++ ...+=..|- +....|+|...-|..++...
T Consensus 39 ~~~~~t~~ela~~~~~~-~~tvs~~l~-~Le~~GlI~r~~~~~D~R~~ 84 (118)
T TIGR02337 39 EQGSMEFTQLANQACIL-RPSLTGILA-RLERDGLVTRLKASNDQRRV 84 (118)
T ss_pred HcCCcCHHHHHHHhCCC-chhHHHHHH-HHHHCCCEEeccCCCCCCee
Confidence 34568999999999997 556666655 88889999999887665433
No 102
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=33.10 E-value=1.5e+02 Score=25.38 Aligned_cols=21 Identities=10% Similarity=0.203 Sum_probs=17.1
Q ss_pred ChHHHHHHcCCCChHHHHHHHH
Q 025387 111 PYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 111 sy~~I~~~L~I~~~~evE~llI 132 (253)
+..++|+.+||+ ...|-.|.=
T Consensus 2 ti~evA~~lGVS-~~TLRrw~k 22 (175)
T PRK13182 2 KTPFVAKKLGVS-PKTVQRWVK 22 (175)
T ss_pred CHHHHHHHHCcC-HHHHHHHHH
Confidence 567899999997 888887754
No 103
>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=32.78 E-value=1.5e+02 Score=19.67 Aligned_cols=41 Identities=20% Similarity=0.233 Sum_probs=31.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~ 149 (253)
...++..+|++.++++ ...|=..|= .....|+|.-.-|...
T Consensus 19 ~~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 19 GEELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGD 59 (62)
T ss_dssp TSGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSS
T ss_pred CCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCC
Confidence 3359999999999997 778887766 8889999987776554
No 104
>PHA03158 hypothetical protein; Provisional
Probab=32.53 E-value=53 Score=29.04 Aligned_cols=54 Identities=24% Similarity=0.339 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 167 LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 167 ~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
++.+...=--||-....=-..|-+|+-.+.+-+-..-+|.+++|++++++.|++
T Consensus 217 ~ERl~Rs~pPWCv~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~eleks~ 270 (273)
T PHA03158 217 MERIKRSGPPWCIKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEKSL 270 (273)
T ss_pred HHHHhccCCCcEeecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhh
Confidence 344444444588655555555556666666667778899999999999999987
No 105
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=32.40 E-value=1.9e+02 Score=26.24 Aligned_cols=113 Identities=16% Similarity=0.290 Sum_probs=56.3
Q ss_pred HHHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccC------CCchHHHHHHHHHhcCChhhHhhhhC
Q 025387 9 ELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEG------TENSKYLDMLRLFAHGTWSDYKNNAG 82 (253)
Q Consensus 9 ~~l~~fl~lak~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~------t~~~~~~~LL~iFa~Gt~~dy~~~~~ 82 (253)
..+++|+-|.+ ..|.++.. ..|. .+++|++.=.+--++. +.......--...-.|-+-||....+
T Consensus 27 ~Li~~ylpLV~----~ia~k~~~---r~~~--~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~ 97 (247)
T COG1191 27 RLIERYLPLVK----SIARKFEN---RGPS--EYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND 97 (247)
T ss_pred HHHHHHHHHHH----HHHHHHHh---cCCC--chhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC
Confidence 57778877765 34444433 3343 6777776544432221 11011111111223466666665555
Q ss_pred --CCCCcchHHHHHHHHHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 83 --HLPQLVPDQVLKLKQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 83 --~l~~L~~~~~~KLr~LtLlsLa-~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
.+|.-.-+..+++.. .+=.|. +-++.-+-.+|+++|+|+ ..|+-.++.
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 444322121222211 111122 357889999999999997 777655544
No 106
>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=30.78 E-value=69 Score=21.31 Aligned_cols=49 Identities=18% Similarity=0.265 Sum_probs=35.3
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~ 150 (253)
++........++..+|++.++++ ..-+=.++= .....|+|.=.-|+.++
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~ 56 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDR 56 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTET
T ss_pred HHHHHHHcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCC
Confidence 33333344559999999999997 666666655 78889999988877654
No 107
>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=30.41 E-value=48 Score=24.49 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=20.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
.-.||.+|++.++++ ...|..++-
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~ 54 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLK 54 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHh
Confidence 578999999999997 888887755
No 108
>PRK03100 sec-independent translocase; Provisional
Probab=29.16 E-value=2.9e+02 Score=22.84 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=30.1
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (253)
.|+++.+..+...+..|........+.+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999988888887764
No 109
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=28.59 E-value=2.2e+02 Score=26.61 Aligned_cols=85 Identities=12% Similarity=0.248 Sum_probs=56.6
Q ss_pred HHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCc--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHH
Q 025387 127 LEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ--LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKK 204 (253)
Q Consensus 127 vE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q--~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~ 204 (253)
.-++.+|-++.+|+.-|=.-=.. .|+.||-|+..+ .+.....|+.=-.++++.++.|+..+..... +-..
T Consensus 83 wrdy~vmAvi~aGi~y~~y~~~K-----~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q---~~~~ 154 (300)
T KOG2629|consen 83 WRDYFVMAVILAGIAYAAYRFVK-----SYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQ---LLAT 154 (300)
T ss_pred HHHHHHHHHHHhhHHHHHHHHHH-----HHHHHHhhCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHH
Confidence 33344438888886555332222 378888887665 4788889999999999999998888877666 3333
Q ss_pred HHHHHHHHHHHHHhh
Q 025387 205 HRKDLEEKVEEAKKS 219 (253)
Q Consensus 205 ~~~~~e~~v~~~k~~ 219 (253)
.+.++...+..+|.+
T Consensus 155 qq~Els~~L~~l~~~ 169 (300)
T KOG2629|consen 155 QQSELSRALASLKNT 169 (300)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344555555555555
No 110
>PRK10870 transcriptional repressor MprA; Provisional
Probab=28.44 E-value=3.5e+02 Score=22.62 Aligned_cols=56 Identities=16% Similarity=0.063 Sum_probs=41.1
Q ss_pred hhhccc-CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025387 100 VLTLAE-TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (253)
Q Consensus 100 LlsLa~-~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~ 157 (253)
|..|.. .+..++-.+|++.++++ ...+=..|= .....|+|.=.-|..+++...-..
T Consensus 61 L~~L~~~~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~L 117 (176)
T PRK10870 61 LITLESQENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQL 117 (176)
T ss_pred HHHHhcCCCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEE
Confidence 334433 45789999999999997 666655544 788899999999988766654443
No 111
>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=27.73 E-value=2.8e+02 Score=23.61 Aligned_cols=58 Identities=12% Similarity=0.240 Sum_probs=41.7
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhcccccc
Q 025387 166 QLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLSHKAD 225 (253)
Q Consensus 166 q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~~~k~~ 225 (253)
....+...|..|+..+..=...+......+...-.-.-..-..++.++++.+..| +.+
T Consensus 125 ~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I--~~~ 182 (184)
T PF05791_consen 125 KVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEI--KKD 182 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG---GG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHH--Hhh
Confidence 3566788888888888887777777777777766666666777788888888887 544
No 112
>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=27.70 E-value=1.9e+02 Score=22.79 Aligned_cols=42 Identities=19% Similarity=0.332 Sum_probs=36.0
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 025387 158 AGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN 199 (253)
Q Consensus 158 ~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~ 199 (253)
.++.++++++..+.+.+..|.+.+-.=+..+...++......
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 578889999999999999999998888888888888766654
No 113
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=27.18 E-value=1.2e+02 Score=20.31 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=28.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~G 143 (253)
...++..+|++.++++ ...|...+= .....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s-~~tv~r~l~-~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLT-RETVSRTLK-ELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEe
Confidence 3568999999999997 888887766 7777888763
No 114
>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=27.14 E-value=1.7e+02 Score=25.06 Aligned_cols=53 Identities=15% Similarity=0.214 Sum_probs=36.5
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025387 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (253)
Q Consensus 99 tLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V 154 (253)
.++.+...+..++..+|++.++++ ..-+-..+- .....|+|.-.-+ ..+.+.+
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 344433444579999999999997 777877766 7778899875533 3444443
No 115
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=27.05 E-value=1.2e+02 Score=18.86 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=26.7
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
.++..+|++.++++ ...+-..+- .....|+|.
T Consensus 8 ~~s~~~la~~l~~s-~~tv~~~l~-~L~~~g~l~ 39 (48)
T smart00419 8 PLTRQEIAELLGLT-RETVSRTLK-RLEKEGLIS 39 (48)
T ss_pred ccCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 46788999999997 888887777 788888886
No 116
>PRK00182 tatB sec-independent translocase; Provisional
Probab=26.70 E-value=2.2e+02 Score=24.20 Aligned_cols=34 Identities=12% Similarity=0.228 Sum_probs=28.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (253)
.|+|+.++.+...+..|........+...+++..
T Consensus 20 VfGPerLP~~~r~lg~~ir~~R~~~~~~k~el~~ 53 (160)
T PRK00182 20 VIGPERLPRLIEDVRAALLAARTAINNAKQQLDG 53 (160)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999888877776665543
No 117
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=26.46 E-value=73 Score=26.39 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...+||.+|++.++|| +..|...+- .|.
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 999998877 765
No 118
>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=26.00 E-value=2e+02 Score=20.13 Aligned_cols=33 Identities=18% Similarity=0.352 Sum_probs=16.3
Q ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 188 IQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 188 Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
||+.+......-..-++.-+++...|+.++.++
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 444444444444444444555555555555555
No 119
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=25.90 E-value=2e+02 Score=18.92 Aligned_cols=48 Identities=27% Similarity=0.304 Sum_probs=32.7
Q ss_pred HHHHHHHhhhcccCCcccC-hHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 93 LKLKQLTVLTLAETNKVLP-YDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 93 ~KLr~LtLlsLa~~~k~Is-y~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
..++..-+......+..++ -.+|++.++++ ...|-..+- ..-..|+|.
T Consensus 8 ~~i~~~i~~~~~~~~~~~~~~~~la~~~~is-~~~v~~~l~-~L~~~G~i~ 56 (66)
T cd07377 8 DQLREAILSGELKPGDRLPSERELAEELGVS-RTTVREALR-ELEAEGLVE 56 (66)
T ss_pred HHHHHHHHcCCCCCCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 3344433333233444555 99999999996 888888877 777888875
No 120
>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=25.53 E-value=4.2e+02 Score=22.53 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=29.4
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkI 145 (253)
...++..+|++.++|+ ...|=..+= .....|+|.-.-
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~-~Le~~GlV~r~~ 49 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLK-DLETEGLIEYEA 49 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEee
Confidence 3459999999999997 777766665 777889998663
No 121
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=25.42 E-value=1e+02 Score=27.34 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=34.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
-|+..|+.+...++.++.++|++.|+++ ..-+...+- +.-..|+|.
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS-~~TiRRdL~-~L~~~~~l~ 49 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVS-KETIRRDLN-ELQTQGKIL 49 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 3666777777788899999999999997 777776665 443445443
No 122
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=25.35 E-value=1.1e+02 Score=22.63 Aligned_cols=32 Identities=19% Similarity=0.418 Sum_probs=25.7
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025387 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (253)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ 147 (253)
||+.++++.++++ +.||. +.+..|+|.-.-..
T Consensus 1 is~~e~~~~~~i~-----~~~l~-~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIE-----PEFLR-ELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcC-----HHHHH-HHHHCCCeeecCCC
Confidence 6899999999998 44666 67778999886666
No 123
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=24.59 E-value=2.8e+02 Score=23.91 Aligned_cols=46 Identities=26% Similarity=0.336 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 175 SNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 175 ~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
..|....+.....+...+..-..+.++..+.+++++.+++++++.+
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 3445555555555555555444555555666777777777777776
No 124
>COG4741 Predicted secreted endonuclease distantly related to archaeal Holliday junction resolvase [Nucleotide transport and metabolism]
Probab=23.83 E-value=4.6e+02 Score=22.39 Aligned_cols=32 Identities=25% Similarity=0.321 Sum_probs=24.4
Q ss_pred HHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 189 QEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 189 e~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
+..+..+-.++++..|.++.+++++++++.-.
T Consensus 48 ~r~v~ea~~~ke~~~Kl~E~iekkieeaR~da 79 (175)
T COG4741 48 ERLVNEAQARKEEEWKLKEWIEKKIEEAREDA 79 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677777888888888888888887766543
No 125
>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=23.80 E-value=1.1e+02 Score=22.86 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=23.8
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025387 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 98 LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (253)
..|+.+-..++.+|-.+|+.+++.+ +++|...+=
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 3456655679999999999999998 999987654
No 126
>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=23.77 E-value=1.1e+02 Score=28.12 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=35.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~ 148 (253)
..+.++..++++..++| .+=+-..++ +....++|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp-~efl~~~li-~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLP-SEFLKEELI-SKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCc-HHHHHHHHh-hhhcCcceeEEEeCC
Confidence 56899999999999998 666766778 777789999999998
No 127
>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=23.74 E-value=3e+02 Score=20.41 Aligned_cols=54 Identities=24% Similarity=0.306 Sum_probs=31.2
Q ss_pred EEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 153 EVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 153 ~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
.|-...|+.|=....+.+...|..=...++.-+..++ +....++.++.++++.+
T Consensus 46 ~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~--------------~~~~~l~~~l~~~~~~l 99 (106)
T PF01920_consen 46 KVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLE--------------KQLKYLEKKLKELKKKL 99 (106)
T ss_dssp EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH
T ss_pred hhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHH
Confidence 3445667777666776666655555554444444444 44455556666666665
No 128
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=23.08 E-value=94 Score=25.45 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||.+||+.||++ +..|...+- .|.
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 468999999999998 999988776 654
No 129
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.62 E-value=91 Score=25.75 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=23.5
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||++|++.+||+ +..|...+- .|.
T Consensus 148 ~~~s~~eIA~~lgis-~~tV~~~l~-ra~ 174 (182)
T PRK12537 148 DGCSHAEIAQRLGAP-LGTVKAWIK-RSL 174 (182)
T ss_pred cCCCHHHHHHHHCCC-hhhHHHHHH-HHH
Confidence 468999999999997 999998877 665
No 130
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.53 E-value=1e+02 Score=21.93 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=27.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
+..++=.+||++|+++ ...+-.++- ..-..|.|+
T Consensus 13 ~~p~~T~eiA~~~gls-~~~aR~yL~-~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLS-IYQARYYLE-KLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS--HHHHHHHHH-HHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCEE
Confidence 6678899999999997 899999888 788777664
No 131
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=22.22 E-value=88 Score=23.83 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=26.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~Gk 144 (253)
.++++-++|++.++++ ..+|-.++- .....|+|..+
T Consensus 25 ~~~l~de~la~~~~l~-~~~vRkiL~-~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLK-PKEVRKILY-KLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S--HHHHHHHHH-HHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCC-HHHHHHHHH-HHHHCCCeEEE
Confidence 4679999999999997 999999888 89999999655
No 132
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=22.01 E-value=99 Score=21.98 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHH
Q 025387 106 TNKVLPYDELMEELDVTNVRELEDF 130 (253)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~l 130 (253)
.++.+++-+||++|+|+ ...|-.|
T Consensus 19 ~~g~i~lkdIA~~Lgvs-~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVS-ESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCC-HHHHHHH
Confidence 46789999999999997 7776655
No 133
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=21.44 E-value=1.7e+02 Score=25.86 Aligned_cols=45 Identities=18% Similarity=0.208 Sum_probs=30.1
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 96 r~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
|-|.|+.+....+.++..+|++.+++| ...+=.++= .....|++.
T Consensus 15 r~l~IL~~l~~~~~l~l~eia~~lgl~-kstv~Rll~-tL~~~G~l~ 59 (257)
T PRK15090 15 KVFGILQALGEEREIGITELSQRVMMS-KSTVYRFLQ-TMKTLGYVA 59 (257)
T ss_pred HHHHHHHHhhcCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEE
Confidence 334555443344578999999999997 667766665 566666664
No 134
>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=21.31 E-value=1.1e+02 Score=19.55 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=19.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025387 109 VLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI 132 (253)
-.++.+|++.++++ ...|+.++=
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH
Confidence 36999999999997 889888755
No 135
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=21.19 E-value=1e+02 Score=21.49 Aligned_cols=23 Identities=22% Similarity=0.172 Sum_probs=19.5
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025387 109 VLPYDELMEELDVTNVRELEDFLI 132 (253)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI 132 (253)
-.++.+||+.|+++ ..-|-.|.=
T Consensus 13 G~~~~eIA~~Lg~~-~~TV~~W~~ 35 (58)
T PF06056_consen 13 GWSIKEIAEELGVP-RSTVYSWKD 35 (58)
T ss_pred CCCHHHHHHHHCCC-hHHHHHHHH
Confidence 46889999999998 888888854
No 136
>KOG3809 consensus Microtubule-binding protein MIP-T3 [Cytoskeleton]
Probab=21.14 E-value=2.5e+02 Score=27.95 Aligned_cols=59 Identities=12% Similarity=0.169 Sum_probs=33.7
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 162 LRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 162 l~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
+-+++++.|..-|..|.+.-..--..+++.........+--...-+++++.|...+.-|
T Consensus 504 ~i~eD~daMq~EL~mWrse~rq~~~elq~eq~~t~~a~epL~~~la~lq~~I~d~~e~i 562 (583)
T KOG3809|consen 504 FINEDIDAMQKELEMWRSEQRQNEQELQNEQAATFGASEPLYNILANLQKEINDTKEEI 562 (583)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhHHHHHhhhhcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999766655555554433333333222233344555555554444
No 137
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=21.04 E-value=1.3e+02 Score=27.12 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=34.0
Q ss_pred HHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 94 KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
.-|+..|+.+...++.++..+|++.|+++ ..-+-.=+. ..-..|++.
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 45888888888888889999999999997 655533333 333456665
No 138
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=21.02 E-value=1.1e+02 Score=24.96 Aligned_cols=27 Identities=22% Similarity=0.398 Sum_probs=23.2
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||.+|++.|+++ +.-|...+- .|+
T Consensus 134 ~g~s~~EIA~~lgis-~~tV~~~l~-ra~ 160 (172)
T PRK12523 134 DGMGHAEIAERLGVS-VSRVRQYLA-QGL 160 (172)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 999998877 665
No 139
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=21.01 E-value=1e+02 Score=22.34 Aligned_cols=20 Identities=35% Similarity=0.388 Sum_probs=16.9
Q ss_pred cChHHHHHHcCCCChHHHHHH
Q 025387 110 LPYDELMEELDVTNVRELEDF 130 (253)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~l 130 (253)
-+-++|++.|+|| ..|.|-+
T Consensus 45 a~~~el~~~CgL~-~aEAeLl 64 (70)
T PF10975_consen 45 ASVEELMEECGLS-RAEAELL 64 (70)
T ss_pred CCHHHHHHHcCCC-HHHHHHH
Confidence 5778999999998 8999843
No 140
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=20.97 E-value=2.5e+02 Score=21.57 Aligned_cols=34 Identities=18% Similarity=0.184 Sum_probs=27.6
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (253)
.|+|+.++.+...+..|........+.+++.+..
T Consensus 21 vfGP~KLP~lar~lGk~i~~fkk~~~~~~~e~~~ 54 (90)
T PRK14857 21 VFGPKKLPEIGRSLGKTLKGFQEASKEFENEIKR 54 (90)
T ss_pred HcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999888877776655443
No 141
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=20.96 E-value=2.3e+02 Score=21.73 Aligned_cols=80 Identities=14% Similarity=0.142 Sum_probs=48.2
Q ss_pred HHHHHHHhcccccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhhhCCCCCcch
Q 025387 10 LIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNNAGHLPQLVP 89 (253)
Q Consensus 10 ~l~~fl~lak~~~~~aa~~lI~~AL~~p~vf~F~eLL~~p~v~~L~~t~~~~~~~LL~iFa~Gt~~dy~~~~~~l~~L~~ 89 (253)
.....+.|+++-+. .+.|...|.+.+|+.-.+.=. |.. +.|.......||.+.-.-....|..+.+.+.+ -|
T Consensus 9 Lr~~R~~Lv~dl~~---~~~v~~~L~~~gIlT~~~~e~---I~a-~~T~~~k~~~LLdiLp~RG~~AF~~F~~aL~e-~~ 80 (94)
T cd08327 9 LRSQRLELSAELLV---DGLVIQYLYQEGILTESHVEE---IES-QTTSRRKTMKLLDILPSRGPKAFHAFLDSLEE-FP 80 (94)
T ss_pred HHHHHHHHHHHccc---hHHHHHHHHhCCCCCHHHHHH---HHc-cCChHHHHHHHHHHHHhhChhHHHHHHHHHHH-HH
Confidence 34456666654322 246777788888887654432 222 33566778889999988888888776543333 23
Q ss_pred HHHHHHHH
Q 025387 90 DQVLKLKQ 97 (253)
Q Consensus 90 ~~~~KLr~ 97 (253)
-...||++
T Consensus 81 ~l~~~l~~ 88 (94)
T cd08327 81 WVRDKLLK 88 (94)
T ss_pred HHHHHHHH
Confidence 33444444
No 142
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=20.91 E-value=6.5e+02 Score=23.05 Aligned_cols=83 Identities=14% Similarity=0.300 Sum_probs=52.4
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHH
Q 025387 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179 (253)
Q Consensus 100 LlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~ 179 (253)
|+-++-....+.-.+|+++++|+ +..|=+.+= +.+..|+|+- ..++.-+|+ ++-.+-|.+.+.+.+.
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 33344455678889999999997 988877777 7887777653 222234443 2334446666666666
Q ss_pred HHHHHHHHHHHHHHHH
Q 025387 180 TSDNLLISIQEKIKWA 195 (253)
Q Consensus 180 ~~~~vl~~Ie~~i~~a 195 (253)
-++.+...+.....|.
T Consensus 83 f~~ev~~~l~~~~vw~ 98 (260)
T COG1497 83 FSEEVELVLDYVMVWT 98 (260)
T ss_pred HHHHHHHHHhhHHHHH
Confidence 6666655555555554
No 143
>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=20.64 E-value=4.5e+02 Score=21.01 Aligned_cols=56 Identities=16% Similarity=0.195 Sum_probs=25.8
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHhhc
Q 025387 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (253)
Q Consensus 165 ~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~e~~v~~~k~~~ 220 (253)
+.+....+.+..+...++.-+.-.+..+..-..+.+.-.....+++..++.+|+.|
T Consensus 42 e~~~~~~e~~l~~l~~~e~~~~k~q~~~~~n~~e~e~Y~~~~~~i~~~i~~~k~~i 97 (139)
T PF05615_consen 42 EESQFLYERLLKELAQFEFSILKSQLILEMNKRERENYEQLNEEIEQEIEQAKKEI 97 (139)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555555544433332222222233333444455566666655554
No 144
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=20.60 E-value=2.9e+02 Score=23.76 Aligned_cols=80 Identities=13% Similarity=0.172 Sum_probs=48.5
Q ss_pred HHHHHHHHHhcCChhhHhhh--h-CCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 025387 61 KYLDMLRLFAHGTWSDYKNN--A-GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (253)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~~--~-~~l~~L~~~~~~KLr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~ 137 (253)
.+-.+.+++.+......... . ...+.|++.|.+=|+.-.=+..-..-|.++-.+||++|||+ ...+.+-|= +|.
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 34455555555554433321 1 12346888766655554444444567999999999999997 666666555 554
Q ss_pred cCccEE
Q 025387 138 TGIVRG 143 (253)
Q Consensus 138 ~gLI~G 143 (253)
.+|+..
T Consensus 204 ~Kl~~~ 209 (215)
T COG3413 204 RKLIEA 209 (215)
T ss_pred HHHHHH
Confidence 344443
No 145
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=20.53 E-value=1.3e+02 Score=26.80 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=26.9
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHH
Q 025387 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVREL 127 (253)
Q Consensus 95 Lr~LtLlsLa~~~k~Isy~~I~~~L~I~~~~ev 127 (253)
-|+..|+.+...++.++..+|++.|+++ ..-+
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS-~~TI 36 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTT-GTTI 36 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCC-HHHH
Confidence 3778888888888999999999999997 5444
No 146
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.52 E-value=1.1e+02 Score=25.14 Aligned_cols=27 Identities=7% Similarity=0.224 Sum_probs=22.3
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||++||+.|||+ +.-|...+- .|.
T Consensus 132 e~~s~~EIA~~lgis-~~tV~~~l~-ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIP-IGTVKSRIH-AAL 158 (179)
T ss_pred ccCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 457999999999998 888887766 554
No 147
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.47 E-value=1.1e+02 Score=24.94 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=23.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
....||.+|++.||++ +..|...+- .|.
T Consensus 133 ~~g~s~~EIA~~lgis-~~tV~~~l~-Ra~ 160 (172)
T PRK09651 133 LDGLTYSEIAHKLGVS-VSSVKKYVA-KAT 160 (172)
T ss_pred ccCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 3578999999999997 999988776 665
No 148
>PHA02943 hypothetical protein; Provisional
Probab=20.41 E-value=2.2e+02 Score=24.33 Aligned_cols=43 Identities=16% Similarity=0.205 Sum_probs=30.0
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025387 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (253)
Q Consensus 97 ~LtLlsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~AI~~gLI~ 142 (253)
...|+.+. ..++-|-++|++.||++ ..+++..+- -.-..|.|+
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 67888899999999997 899996655 444445443
No 149
>PRK14861 tatA twin arginine translocase protein A; Provisional
Probab=20.40 E-value=2.3e+02 Score=20.13 Aligned_cols=33 Identities=12% Similarity=0.069 Sum_probs=25.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (253)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~ 193 (253)
.|+|+.++.+...+..|.....+..+.+++.+.
T Consensus 20 vfGp~kLP~l~r~~G~~~~~fk~~~~~~~~~~~ 52 (61)
T PRK14861 20 IFGPKKLPELGKALGKTLREFKKATKELTDDDF 52 (61)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 478889999999999988877776666655444
No 150
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.38 E-value=1.1e+02 Score=25.16 Aligned_cols=27 Identities=7% Similarity=0.361 Sum_probs=22.8
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||++|++.||++ +..|...+- .|+
T Consensus 142 ~g~s~~EIA~~lgis-~~tVk~~l~-rAl 168 (178)
T PRK12529 142 DGMKQKDIAQALDIA-LPTVKKYIH-QAY 168 (178)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999998 999988776 665
No 151
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.36 E-value=1.2e+02 Score=24.31 Aligned_cols=27 Identities=19% Similarity=0.239 Sum_probs=22.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||.+||+.||++ +..|...+- .|.
T Consensus 121 ~g~s~~EIA~~lgis-~~tV~~~l~-Rar 147 (160)
T PRK09642 121 EEKSYQEIALQEKIE-VKTVEMKLY-RAR 147 (160)
T ss_pred hCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 468999999999997 888887766 554
No 152
>PF06013 WXG100: Proteins of 100 residues with WXG; InterPro: IPR010310 ESAT-6 is a small protein appears to be of fundamental importance in virulence and protective immunity in Mycobacterium tuberculosis. Homologues have been detected in other Gram-positive bacterial species. It may represent a novel secretion system potentially driven by the PF01580 from PFAM domains in the YukA-like proteins []. Members of this protein family include secretion targets for type main variants of type VII secretion systems (T7SS), one found in the Actinobacteria, one found in the Firmicutes. This model was derived through iteration from PF06013 from PFAM. The best characterised member of this family is ESAT-6 from Mycobacterium tuberculosis. Members of this family usually are ~100 amino acids in length but occasionally have long C-terminal extension. ; PDB: 3FAV_A 1WA8_A 3Q4H_B 2KG7_A 2VRZ_B 2VS0_B 3OGI_A 3H6P_B 3GVM_B 3GWK_C ....
Probab=20.36 E-value=2.3e+02 Score=19.51 Aligned_cols=34 Identities=21% Similarity=0.212 Sum_probs=29.9
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025387 162 LRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (253)
Q Consensus 162 l~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a 195 (253)
++++++..+...+......++..+..+...+...
T Consensus 4 vd~~~l~~~a~~~~~~~~~l~~~~~~l~~~~~~l 37 (86)
T PF06013_consen 4 VDPEQLRAAAQQLQAQADELQSQLQQLESSIDSL 37 (86)
T ss_dssp SCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677888999999999999999999999988876
No 153
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=20.16 E-value=1.2e+02 Score=23.96 Aligned_cols=27 Identities=11% Similarity=0.056 Sum_probs=23.0
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025387 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (253)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~AI 136 (253)
...||.+||+.||++ ...|...+- .|+
T Consensus 121 ~~~s~~EIA~~l~is-~~tV~~~~~-ra~ 147 (154)
T PRK06759 121 VGKTMGEIALETEMT-YYQVRWIYR-QAL 147 (154)
T ss_pred cCCCHHHHHHHHCCC-HHHHHHHHH-HHH
Confidence 358899999999997 999998877 665
Done!