Query 025819
Match_columns 247
No_of_seqs 202 out of 577
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 09:56:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025819.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025819hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3250 COP9 signalosome, subu 100.0 2.7E-62 5.9E-67 420.0 15.8 239 1-241 1-248 (258)
2 KOG2753 Uncharacterized conser 100.0 3.7E-32 8.1E-37 246.5 11.6 150 24-178 205-361 (378)
3 KOG2908 26S proteasome regulat 100.0 6.2E-31 1.4E-35 239.5 14.9 180 12-193 181-376 (380)
4 PF01399 PCI: PCI domain; Int 99.5 3.1E-14 6.8E-19 108.6 7.7 95 60-156 1-105 (105)
5 smart00753 PAM PCI/PINT associ 99.5 3E-14 6.5E-19 106.9 7.3 87 87-177 2-88 (88)
6 smart00088 PINT motif in prote 99.5 3E-14 6.5E-19 106.9 7.3 87 87-177 2-88 (88)
7 KOG1464 COP9 signalosome, subu 98.9 2.3E-09 5E-14 97.2 7.5 126 59-192 304-439 (440)
8 KOG2581 26S proteasome regulat 97.7 0.00026 5.7E-09 67.3 10.6 93 60-153 319-420 (493)
9 KOG1498 26S proteasome regulat 96.5 0.03 6.6E-07 53.3 10.7 128 58-197 286-429 (439)
10 KOG2758 Translation initiation 96.4 0.0065 1.4E-07 56.7 5.6 98 89-193 329-426 (432)
11 KOG0686 COP9 signalosome, subu 96.3 0.031 6.7E-07 53.5 10.0 105 61-167 307-421 (466)
12 KOG1497 COP9 signalosome, subu 95.9 0.034 7.3E-07 51.9 7.8 155 26-190 228-389 (399)
13 COG5071 RPN5 26S proteasome re 95.6 0.06 1.3E-06 50.1 8.3 77 104-192 348-424 (439)
14 KOG2582 COP9 signalosome, subu 93.7 0.45 9.8E-06 45.2 9.2 106 60-169 259-373 (422)
15 KOG1463 26S proteasome regulat 93.3 0.21 4.6E-06 47.0 6.3 114 44-159 270-393 (411)
16 KOG2688 Transcription-associat 93.3 0.17 3.8E-06 48.3 5.7 98 59-157 271-385 (394)
17 COG5159 RPN6 26S proteasome re 91.0 1.7 3.6E-05 40.6 9.0 100 59-160 283-392 (421)
18 KOG2072 Translation initiation 90.5 5.1 0.00011 41.8 12.7 50 105-155 443-492 (988)
19 COG5600 Transcription-associat 90.2 0.95 2.1E-05 43.2 6.9 99 59-159 288-406 (413)
20 PF10075 PCI_Csn8: COP9 signal 90.1 2.5 5.5E-05 34.2 8.7 107 25-132 6-119 (143)
21 PF09756 DDRGK: DDRGK domain; 90.1 0.4 8.7E-06 41.5 4.1 57 97-155 101-157 (188)
22 KOG0687 26S proteasome regulat 89.0 1.8 3.8E-05 40.8 7.6 64 92-157 300-363 (393)
23 COG3355 Predicted transcriptio 86.1 7.1 0.00015 31.7 8.6 80 105-190 38-120 (126)
24 KOG3054 Uncharacterized conser 82.9 2 4.4E-05 38.7 4.6 54 100-155 205-258 (299)
25 PF09012 FeoC: FeoC like trans 82.9 1.3 2.9E-05 31.5 2.9 42 100-143 5-46 (69)
26 PF02082 Rrf2: Transcriptional 81.8 4.3 9.2E-05 29.8 5.4 58 95-155 11-68 (83)
27 smart00344 HTH_ASNC helix_turn 79.9 3.2 6.9E-05 31.5 4.3 42 100-143 8-49 (108)
28 PRK01919 tatB sec-independent 78.7 13 0.00029 31.6 7.9 59 161-220 19-77 (169)
29 PRK11179 DNA-binding transcrip 78.5 3.2 7E-05 34.0 4.1 47 100-148 14-63 (153)
30 TIGR02010 IscR iron-sulfur clu 74.1 8.6 0.00019 30.8 5.4 43 99-143 13-57 (135)
31 PRK04098 sec-independent trans 72.1 29 0.00064 29.2 8.2 59 161-219 19-80 (158)
32 COG1522 Lrp Transcriptional re 70.9 5.2 0.00011 32.1 3.5 43 100-144 13-55 (154)
33 PF13412 HTH_24: Winged helix- 70.4 8 0.00017 25.1 3.7 41 100-142 8-48 (48)
34 PRK11169 leucine-responsive tr 69.9 8.4 0.00018 32.0 4.6 48 99-148 18-68 (164)
35 PRK14165 winged helix-turn-hel 68.8 23 0.0005 31.3 7.3 62 92-155 4-65 (217)
36 TIGR01410 tatB twin arginine-t 68.7 20 0.00044 26.6 5.9 37 161-197 18-54 (80)
37 TIGR00738 rrf2_super rrf2 fami 68.2 18 0.00039 28.4 6.0 50 93-144 9-58 (132)
38 PF07389 DUF1500: Protein of u 67.4 5.9 0.00013 30.3 2.8 35 100-137 39-73 (100)
39 PRK10857 DNA-binding transcrip 67.0 14 0.00029 31.1 5.3 48 95-144 11-58 (164)
40 PRK04654 sec-independent trans 66.5 37 0.00079 30.0 7.9 35 161-195 19-53 (214)
41 TIGR02944 suf_reg_Xantho FeS a 62.2 35 0.00076 26.9 6.6 37 106-144 22-58 (130)
42 PF08280 HTH_Mga: M protein tr 62.0 7.1 0.00015 26.9 2.3 35 96-131 6-40 (59)
43 smart00346 HTH_ICLR helix_turn 60.9 18 0.00038 26.3 4.4 46 96-143 6-52 (91)
44 PRK14858 tatA twin arginine tr 59.3 64 0.0014 25.5 7.4 38 161-198 19-56 (108)
45 PF11945 WASH_WAHD: WAHD domai 57.2 96 0.0021 28.7 9.4 64 156-219 8-72 (297)
46 COG1959 Predicted transcriptio 57.1 28 0.00062 28.6 5.4 50 95-146 11-60 (150)
47 PRK04214 rbn ribonuclease BN/u 56.9 62 0.0013 30.9 8.5 60 106-174 307-366 (412)
48 PRK01770 sec-independent trans 55.8 67 0.0014 27.5 7.5 34 161-194 19-52 (171)
49 COG4575 ElaB Uncharacterized c 55.7 46 0.001 26.1 6.0 57 159-221 2-58 (104)
50 PF09339 HTH_IclR: IclR helix- 55.4 28 0.00061 23.0 4.3 45 96-142 4-49 (52)
51 PF01726 LexA_DNA_bind: LexA D 55.1 21 0.00046 25.3 3.8 37 105-142 21-57 (65)
52 PRK10141 DNA-binding transcrip 54.2 25 0.00054 28.0 4.5 46 107-154 28-73 (117)
53 PF13404 HTH_AsnC-type: AsnC-t 54.1 8.4 0.00018 25.0 1.4 28 100-128 8-35 (42)
54 PF08279 HTH_11: HTH domain; 53.3 20 0.00043 23.7 3.3 36 96-132 1-37 (55)
55 PRK11920 rirA iron-responsive 53.1 34 0.00074 28.2 5.3 49 95-146 11-59 (153)
56 PRK11014 transcriptional repre 53.0 36 0.00077 27.4 5.3 50 95-146 11-60 (141)
57 smart00550 Zalpha Z-DNA-bindin 52.8 22 0.00048 25.2 3.6 33 109-143 22-54 (68)
58 PHA01750 hypothetical protein 51.9 68 0.0015 23.3 5.8 35 186-220 38-72 (75)
59 PRK03573 transcriptional regul 51.8 1.1E+02 0.0025 24.1 8.1 56 101-158 38-93 (144)
60 PF13730 HTH_36: Helix-turn-he 50.2 58 0.0013 21.4 5.2 47 93-141 7-55 (55)
61 cd00090 HTH_ARSR Arsenical Res 50.2 53 0.0012 21.8 5.2 36 110-147 21-56 (78)
62 KOG1076 Translation initiation 49.8 18 0.0004 37.3 3.6 96 62-159 657-766 (843)
63 PF07106 TBPIP: Tat binding pr 49.6 1.5E+02 0.0032 24.5 12.0 114 105-220 12-132 (169)
64 PF12840 HTH_20: Helix-turn-he 49.5 29 0.00064 23.6 3.7 38 105-144 20-57 (61)
65 COG1777 Predicted transcriptio 48.9 1.5E+02 0.0032 26.3 8.7 38 111-150 29-67 (217)
66 PF01325 Fe_dep_repress: Iron 48.9 41 0.00089 23.3 4.4 42 99-142 12-53 (60)
67 PF03399 SAC3_GANP: SAC3/GANP/ 48.8 70 0.0015 26.8 6.7 62 59-120 135-203 (204)
68 PF08281 Sigma70_r4_2: Sigma-7 48.7 23 0.00051 23.3 3.0 27 108-136 25-51 (54)
69 PRK09954 putative kinase; Prov 47.5 23 0.0005 32.8 3.8 54 100-155 8-64 (362)
70 PF08220 HTH_DeoR: DeoR-like h 47.2 28 0.0006 23.8 3.3 42 97-140 2-43 (57)
71 PF13601 HTH_34: Winged helix 46.4 24 0.00052 25.9 3.1 51 98-150 3-53 (80)
72 PRK00708 sec-independent trans 45.6 76 0.0017 28.0 6.5 37 161-197 19-55 (209)
73 smart00345 HTH_GNTR helix_turn 45.6 82 0.0018 20.4 5.5 36 105-142 15-51 (60)
74 PRK10265 chaperone-modulator p 45.2 50 0.0011 25.4 4.8 38 106-149 4-41 (101)
75 COG5187 RPN7 26S proteasome re 45.1 75 0.0016 30.0 6.6 64 92-157 314-377 (412)
76 PRK00404 tatB sec-independent 44.9 1.5E+02 0.0033 24.5 7.8 35 161-195 19-53 (141)
77 PF04545 Sigma70_r4: Sigma-70, 44.7 74 0.0016 20.6 5.0 28 107-136 18-45 (50)
78 PF03962 Mnd1: Mnd1 family; I 44.6 1.7E+02 0.0036 25.1 8.4 64 116-188 22-85 (188)
79 smart00347 HTH_MARR helix_turn 44.5 1.1E+02 0.0025 21.7 7.8 41 107-149 22-62 (101)
80 PF01022 HTH_5: Bacterial regu 44.0 58 0.0013 21.0 4.3 33 108-142 14-46 (47)
81 cd06445 ATase The DNA repair p 43.9 32 0.00069 25.1 3.3 30 98-127 6-36 (79)
82 PF14947 HTH_45: Winged helix- 43.3 66 0.0014 23.2 5.0 49 100-155 11-59 (77)
83 PF04967 HTH_10: HTH DNA bindi 43.1 1.1E+02 0.0023 21.0 5.7 27 105-132 19-45 (53)
84 PF01638 HxlR: HxlR-like helix 42.5 1.4E+02 0.0029 22.0 6.8 75 98-180 9-85 (90)
85 PF03979 Sigma70_r1_1: Sigma-7 40.9 21 0.00045 26.3 2.0 38 100-139 12-52 (82)
86 PF14480 DNA_pol3_a_NI: DNA po 40.3 1E+02 0.0022 21.8 5.5 61 111-176 2-62 (76)
87 smart00420 HTH_DEOR helix_turn 39.5 73 0.0016 20.0 4.3 34 107-142 12-45 (53)
88 smart00418 HTH_ARSR helix_turn 39.2 1E+02 0.0022 19.8 5.1 38 107-146 8-45 (66)
89 PF09341 Pcc1: Transcription f 38.8 1.1E+02 0.0024 21.8 5.5 47 138-190 30-76 (76)
90 PF13815 Dzip-like_N: Iguana/D 38.6 97 0.0021 24.3 5.6 41 179-219 76-116 (118)
91 PHA03158 hypothetical protein; 38.4 39 0.00084 29.7 3.5 62 157-220 209-270 (273)
92 PF08784 RPA_C: Replication pr 37.4 79 0.0017 23.8 4.8 50 96-147 51-101 (102)
93 TIGR02337 HpaR homoprotocatech 36.4 1.9E+02 0.0042 22.0 8.4 46 106-153 39-84 (118)
94 PF13518 HTH_28: Helix-turn-he 35.7 50 0.0011 21.2 3.0 30 100-132 5-34 (52)
95 PF12802 MarR_2: MarR family; 35.5 1.1E+02 0.0024 20.2 4.9 42 107-150 19-60 (62)
96 PF06163 DUF977: Bacterial pro 34.8 93 0.002 25.4 4.9 52 87-141 5-56 (127)
97 PF05565 Sipho_Gp157: Siphovir 34.4 2.7E+02 0.0058 23.1 8.4 43 185-227 49-98 (162)
98 PF05331 DUF742: Protein of un 34.3 64 0.0014 25.7 3.9 40 99-142 47-86 (114)
99 PF01978 TrmB: Sugar-specific 34.3 59 0.0013 22.5 3.4 38 106-145 19-56 (68)
100 PF04539 Sigma70_r3: Sigma-70 33.6 44 0.00095 23.7 2.7 26 106-132 17-42 (78)
101 PRK10870 transcriptional repre 33.2 2.9E+02 0.0062 23.1 8.1 50 106-157 68-117 (176)
102 TIGR02919 accessory Sec system 33.0 1.5E+02 0.0032 28.8 7.0 87 112-202 341-433 (438)
103 PF01047 MarR: MarR family; I 32.5 62 0.0013 21.4 3.1 50 100-151 8-57 (59)
104 TIGR02702 SufR_cyano iron-sulf 32.5 3.1E+02 0.0067 23.2 10.6 37 107-145 13-49 (203)
105 PRK03100 sec-independent trans 31.9 2.6E+02 0.0055 23.0 7.1 34 161-194 20-53 (136)
106 PF09523 DUF2390: Protein of u 30.4 1.5E+02 0.0032 23.3 5.3 42 158-199 43-84 (109)
107 smart00419 HTH_CRP helix_turn_ 30.0 1.4E+02 0.003 18.4 5.0 32 109-142 8-39 (48)
108 TIGR03879 near_KaiC_dom probab 29.9 50 0.0011 24.3 2.4 24 108-132 31-54 (73)
109 PF13591 MerR_2: MerR HTH fami 29.8 84 0.0018 23.2 3.7 32 110-147 1-32 (84)
110 TIGR01884 cas_HTH CRISPR locus 28.5 1.5E+02 0.0033 25.2 5.6 52 100-154 148-199 (203)
111 COG1497 Predicted transcriptio 28.5 4.6E+02 0.0099 23.9 10.1 83 100-195 16-98 (260)
112 cd04784 HTH_CadR-PbrR Helix-Tu 27.9 1.6E+02 0.0034 23.2 5.2 43 111-168 2-45 (127)
113 cd00092 HTH_CRP helix_turn_hel 27.8 1.2E+02 0.0026 20.3 4.0 35 107-143 23-57 (67)
114 KOG2629 Peroxisomal membrane a 27.6 2.3E+02 0.0051 26.3 6.8 81 130-219 87-169 (300)
115 TIGR02051 MerR Hg(II)-responsi 27.1 3E+02 0.0066 21.5 6.8 27 111-143 1-27 (124)
116 PF01920 Prefoldin_2: Prefoldi 26.2 2.6E+02 0.0057 20.6 6.1 45 152-196 45-89 (106)
117 PF07889 DUF1664: Protein of u 25.9 3.6E+02 0.0077 21.8 7.9 53 168-220 46-98 (126)
118 PRK10411 DNA-binding transcrip 25.7 1E+02 0.0022 27.2 4.1 46 95-142 4-49 (240)
119 PRK00182 tatB sec-independent 25.6 2.4E+02 0.0052 23.9 6.1 34 161-194 20-53 (160)
120 COG1595 RpoE DNA-directed RNA 24.5 83 0.0018 25.9 3.2 28 107-136 141-168 (182)
121 PF02002 TFIIE_alpha: TFIIE al 24.3 66 0.0014 24.4 2.3 36 107-144 25-60 (105)
122 PF15290 Syntaphilin: Golgi-lo 24.2 3E+02 0.0064 25.6 6.8 22 202-223 122-143 (305)
123 PF12324 HTH_15: Helix-turn-he 23.9 1.1E+02 0.0024 22.7 3.4 34 98-132 27-60 (77)
124 cd07377 WHTH_GntR Winged helix 23.3 2.2E+02 0.0048 18.6 5.9 47 94-142 9-56 (66)
125 PF05615 THOC7: Tho complex su 23.0 3.9E+02 0.0085 21.2 8.2 56 165-220 42-97 (139)
126 PF09743 DUF2042: Uncharacteri 22.9 1.1E+02 0.0025 27.8 3.9 41 106-148 127-167 (272)
127 COG3413 Predicted DNA binding 22.9 2.5E+02 0.0053 24.1 6.0 79 61-142 127-208 (215)
128 PRK03887 methylated-DNA--prote 22.9 2.9E+02 0.0062 23.7 6.1 66 59-128 61-128 (175)
129 COG1191 FliA DNA-directed RNA 22.6 3.5E+02 0.0077 24.3 7.0 113 9-132 27-148 (247)
130 PF15397 DUF4618: Domain of un 22.4 2.5E+02 0.0055 25.5 6.0 40 164-203 62-101 (258)
131 PHA02943 hypothetical protein; 22.4 1.8E+02 0.004 24.6 4.7 44 96-142 12-55 (165)
132 cd01282 HTH_MerR-like_sg3 Heli 22.3 3.7E+02 0.0079 20.6 8.1 44 111-169 2-45 (112)
133 PF04703 FaeA: FaeA-like prote 22.2 1E+02 0.0022 21.8 2.8 34 107-142 13-46 (62)
134 PF10668 Phage_terminase: Phag 22.0 99 0.0022 21.8 2.7 24 106-130 19-42 (60)
135 PF05791 Bacillus_HBL: Bacillu 21.8 4E+02 0.0086 22.5 6.9 55 166-220 125-179 (184)
136 TIGR02999 Sig-70_X6 RNA polyme 21.7 1E+02 0.0023 25.0 3.2 27 108-136 149-175 (183)
137 PRK14857 tatA twin arginine tr 21.6 2.4E+02 0.0053 21.5 4.9 35 161-195 21-55 (90)
138 PRK14861 tatA twin arginine tr 21.6 2.2E+02 0.0047 20.1 4.3 33 161-193 20-52 (61)
139 PF09218 DUF1959: Domain of un 21.2 54 0.0012 26.3 1.3 42 114-183 18-59 (117)
140 PF05377 FlaC_arch: Flagella a 21.1 3E+02 0.0065 19.2 5.0 31 189-219 6-36 (55)
141 KOG3809 Microtubule-binding pr 21.0 2.4E+02 0.0052 27.9 5.8 30 162-191 504-533 (583)
142 cd06170 LuxR_C_like C-terminal 21.0 1.1E+02 0.0024 19.4 2.7 23 109-132 15-37 (57)
143 PRK09802 DNA-binding transcrip 20.9 1.3E+02 0.0029 27.0 4.0 47 94-142 16-62 (269)
144 PRK12537 RNA polymerase sigma 20.8 1.1E+02 0.0023 25.2 3.1 27 108-136 148-174 (182)
145 PRK15090 DNA-binding transcrip 20.8 1.8E+02 0.0039 25.6 4.7 45 96-142 15-59 (257)
146 KOG0971 Microtubule-associated 20.8 3E+02 0.0065 29.8 6.8 50 171-220 264-313 (1243)
147 PRK10434 srlR DNA-bindng trans 20.5 1.3E+02 0.0029 26.7 3.9 32 95-127 5-36 (256)
148 PF12999 PRKCSH-like: Glucosid 20.4 3.7E+02 0.0079 23.1 6.3 45 176-220 125-169 (176)
149 PF06056 Terminase_5: Putative 20.3 1.1E+02 0.0024 21.2 2.6 23 109-132 13-35 (58)
150 PRK15396 murein lipoprotein; P 20.1 3.7E+02 0.0081 19.9 7.5 49 165-213 25-73 (78)
No 1
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=100.00 E-value=2.7e-62 Score=419.99 Aligned_cols=239 Identities=40% Similarity=0.632 Sum_probs=233.9
Q ss_pred CchhHHHHhHHHHHHHhccCccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh
Q 025819 1 MDIEQRQAELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN 80 (247)
Q Consensus 1 ~~~~~~~~~~l~~f~~lak~~~~~~a~~lI~~AL~~p~vf~F~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~ 80 (247)
|++|+++++.++||+++||+.+|+|...+|.+||++|+||+|||||.+|+|.+|..+.++.+++||++||||||.||.++
T Consensus 1 m~~ek~~~~~~eqfvllak~~kg~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae 80 (258)
T KOG3250|consen 1 MDIEKKQAEIIEQFVLLAKTCKGEALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE 80 (258)
T ss_pred CCcchhhHHHHHHHHHHHhccchhHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh
Confidence 99999999999999999999999999999999999999999999999999999999889999999999999999999999
Q ss_pred hCCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025819 81 AGHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (247)
Q Consensus 81 ~~~l~~L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~R 160 (247)
+-.+|.|+++++.||++||+++||+..++|||+.+.+.|.+.|+++|||+|| +|||+++++|||||.+|+++|.|+++|
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 CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc---------CccccccccCC
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL---------SHKKLHTVSRP 231 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~---------~~~~~~~~~~~ 231 (247)
|+++.++++|..+|++||+.|+++|..|++++.|||++++...+++++.|.+|.++||++ +.|.|-++| |
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 999999999999999999999999999999999999999999999999999999999999 678888998 8
Q ss_pred Cccccccccc
Q 025819 232 TLTAEGTRRS 241 (247)
Q Consensus 232 ~~~~~~~~~~ 241 (247)
.|++.+++|.
T Consensus 239 ~~~qrqp~kk 248 (258)
T KOG3250|consen 239 VMDQRQPGKK 248 (258)
T ss_pred CccccCCCcC
Confidence 8999988764
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=99.97 E-value=3.7e-32 Score=246.52 Aligned_cols=150 Identities=28% Similarity=0.539 Sum_probs=139.7
Q ss_pred HHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhh----hhCCCCC---cchHHHHHHH
Q 025819 24 AALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKN----NAGHLPQ---LVPDQVLKLK 96 (247)
Q Consensus 24 ~~a~~lI~~AL~~p~vf~F~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~---L~~~~~~KLr 96 (247)
.+|.+||+.|+.+|++|.|++|+.+|+|+.|+++ .+|+||.||..|.+.+|.+ |++++.. ..+++.+|||
T Consensus 205 edA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d---~i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~gl~~E~~~~KMR 281 (378)
T KOG2753|consen 205 EDAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGD---LIHQLLKIFVSGKLDAYVEFVAANSGFVQSQGLVHEQNMAKMR 281 (378)
T ss_pred HHHHHHHHHHHcCCceeccchhccCchHHHhccc---hHHHHHHHHHhcchHHHHHHHHhChHHHHHhcccHHHHHHHHH
Confidence 5699999999999999999999999999999886 4999999999999999986 4444443 3367799999
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025819 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (247)
Q Consensus 97 ~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~ 176 (247)
+||+++||+.+.+|||+.|+++|+|. .+|||.||| +||.+|+|.|||||.+++|.|+++.+|.|+..||..|+++|..
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 025819 177 WL 178 (247)
Q Consensus 177 W~ 178 (247)
|.
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=6.2e-31 Score=239.54 Aligned_cols=180 Identities=18% Similarity=0.357 Sum_probs=162.6
Q ss_pred HHHHHhc------cCccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh---hC
Q 025819 12 DHFVKQA------SNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN---AG 82 (247)
Q Consensus 12 ~~f~~la------k~~~~~~a~~lI~~AL~~p~vf~F~eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~---~~ 82 (247)
-.|+... .+.+...|.+|..+||.+.++|||||||.+|+...|.||++.|++++|.+|+.||+..|... .+
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 4566655 44566889999999999999999999999999999999999999999999999999999974 34
Q ss_pred CCCCcchH---HHHHHHHHHhhhccc----CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 83 HLPQLVPD---QVLKLKQLTVLTLAE----TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 83 ~l~~L~~~---~~~KLr~LtllsLa~----~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
..|.|... ..+|+++++++-++. ..|.+||++|+++++|| .++||.+|+ +|++.|||+|.|||++++|+++
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 56777633 478999999998885 57999999999999999 899999999 9999999999999999999999
Q ss_pred eecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 156 FAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (247)
Q Consensus 156 ~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~ 193 (247)
|++||.++.+|+-.|.++++.|++.++++...++++.+
T Consensus 339 wvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~~ 376 (380)
T KOG2908|consen 339 WVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRGH 376 (380)
T ss_pred cccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 99999999999999999999999999999999887654
No 4
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=99.52 E-value=3.1e-14 Score=108.57 Aligned_cols=95 Identities=20% Similarity=0.399 Sum_probs=81.5
Q ss_pred hHHHHHHHHHhcCChhhHhhhh----------CCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHH
Q 025819 60 SKYLDMLRLFAHGTWSDYKNNA----------GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELED 129 (247)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~----------~~l~~L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~ 129 (247)
+|+.+|+++|..|++..|...- +.+..+.+....+++..++.+++..++.|+++.|++.|+++ ..+||.
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~-~~~vE~ 79 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLS-EEEVES 79 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCC-HHHHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccc-hHHHHH
Confidence 4789999999999999997621 12223456778999999999999999999999999999998 899999
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEe
Q 025819 130 FLINECMYTGIVRGKLDQLRRCFEVQF 156 (247)
Q Consensus 130 llI~~aI~~glI~GkIDQ~~~~v~V~~ 156 (247)
+++ ++|..|.|.|+|||.+++|.++|
T Consensus 80 ~l~-~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 80 ILI-DLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHH-HHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHH-HHHHCCCEEEEEECCCCEEEecC
Confidence 999 99999999999999999999875
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.52 E-value=3e-14 Score=106.91 Aligned_cols=87 Identities=23% Similarity=0.346 Sum_probs=81.3
Q ss_pred cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCc
Q 025819 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ 166 (247)
Q Consensus 87 L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q 166 (247)
+.+....|+|..++..++..+++|+|+.|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~ 77 (88)
T smart00753 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEP 77 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhH
Confidence 345678999999999999999999999999999998 789999999 9999999999999999999999999997 788
Q ss_pred HHHHHHHHHHH
Q 025819 167 LGSMIQTLSNW 177 (247)
Q Consensus 167 ~~~l~~~L~~W 177 (247)
|..+.++|..|
T Consensus 78 ~~~~~~~l~~~ 88 (88)
T smart00753 78 LAQFAETLKKL 88 (88)
T ss_pred HHHHHHHhhcC
Confidence 99999999887
No 6
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=99.52 E-value=3e-14 Score=106.91 Aligned_cols=87 Identities=23% Similarity=0.346 Sum_probs=81.3
Q ss_pred cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCc
Q 025819 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ 166 (247)
Q Consensus 87 L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q 166 (247)
+.+....|+|..++..++..+++|+|+.|++.++++ .+++|.+|+ ++|..|.|.|+|||.++++.+.+..+|. .++
T Consensus 2 ~~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~-~~~vE~~i~-~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~~ 77 (88)
T smart00088 2 LVERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLS-VPEVEKLVS-KAIRDGEISAKIDQVNGIVEFEEVDPRR--SEP 77 (88)
T ss_pred hHHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcC-HHHHHHHHH-HHHHCCCeEEEEcCcCCEEEECCCchhh--hhH
Confidence 345678999999999999999999999999999998 789999999 9999999999999999999999999997 788
Q ss_pred HHHHHHHHHHH
Q 025819 167 LGSMIQTLSNW 177 (247)
Q Consensus 167 ~~~l~~~L~~W 177 (247)
|..+.++|..|
T Consensus 78 ~~~~~~~l~~~ 88 (88)
T smart00088 78 LAQFAETLKKL 88 (88)
T ss_pred HHHHHHHhhcC
Confidence 99999999887
No 7
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.93 E-value=2.3e-09 Score=97.18 Aligned_cols=126 Identities=13% Similarity=0.346 Sum_probs=106.0
Q ss_pred chHHHHHHHHHhcCChhhHhh----hhC------CCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025819 59 NSKYLDMLRLFAHGTWSDYKN----NAG------HLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (247)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~----~~~------~l~~L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (247)
--.+.+|+..+...++..|+. |.+ ++-+..++.++++|...++.|..++..|....|+++|+|+ ..+||
T Consensus 304 IlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~-~~dV~ 382 (440)
T KOG1464|consen 304 ILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVP-EADVE 382 (440)
T ss_pred HHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCC-HHHHH
Confidence 346889999999999999986 332 2334567889999999999999999999999999999998 99999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKI 192 (247)
Q Consensus 129 ~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i 192 (247)
.+++ .||-.+-|+|+|||+++.+........ =..+.+.|+.|.+.++++.+.|-.++
T Consensus 383 ~LLV-~~ILD~~i~g~Ide~n~~l~~~~~~~s------~~k~~~al~kW~~ql~Sl~~~i~sr~ 439 (440)
T KOG1464|consen 383 SLLV-SCILDDTIDGRIDEVNQYLELDKSKNS------GSKLYKALDKWNNQLKSLQSNIVSRV 439 (440)
T ss_pred HHHH-HHHhccccccchHHhhhHhccCccCCc------chHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 9999 999999999999999999987643221 12378999999999999888776553
No 8
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=97.74 E-value=0.00026 Score=67.32 Aligned_cols=93 Identities=10% Similarity=0.305 Sum_probs=69.9
Q ss_pred hHHHHHHHHHhcCChhhHhhhhCCCCC-c----chHHHHHHHHHHhhh----cccCCcccChHHHHHHcCCCChHHHHHH
Q 025819 60 SKYLDMLRLFAHGTWSDYKNNAGHLPQ-L----VPDQVLKLKQLTVLT----LAETNKVLPYDELMEELDVTNVRELEDF 130 (247)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~~~~~l~~-L----~~~~~~KLr~Ltlls----La~~~k~Isy~~I~~~L~I~~~~evE~l 130 (247)
.+||.|-+....||++-|...-..+.+ + +=..+..||+=.|=+ +.-.++.|||.+|+..|+++|..++|.+
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 579999999999999999874332221 1 111234455532221 1125889999999999999999999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEE
Q 025819 131 LINECMYTGIVRGKLDQLRRCFE 153 (247)
Q Consensus 131 lI~~aI~~glI~GkIDQ~~~~v~ 153 (247)
|- +||+.|+|+|+||..++.+.
T Consensus 399 Va-kAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 399 VA-KAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred HH-HHHHhccceeeeccccCcee
Confidence 99 99999999999999999554
No 9
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=96.46 E-value=0.03 Score=53.31 Aligned_cols=128 Identities=21% Similarity=0.310 Sum_probs=92.2
Q ss_pred CchHHHHHHHHHhcCChhhHhhh---------hC-CCC--CcchHH--HHHHHH--HHhhhcccCCcccChHHHHHHcCC
Q 025819 58 ENSKYLDMLRLFAHGTWSDYKNN---------AG-HLP--QLVPDQ--VLKLKQ--LTVLTLAETNKVLPYDELMEELDV 121 (247)
Q Consensus 58 ~~~~~~~LL~iFa~Gt~~dy~~~---------~~-~l~--~L~~~~--~~KLr~--LtllsLa~~~k~Isy~~I~~~L~I 121 (247)
+.+.+-.+|.+|..|-+--|... .+ ++. ...+.. -.+.|. .-+--.|.=+.+||+..+++-|+.
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 34567789999998876655421 11 111 111111 122222 333344556899999999999999
Q ss_pred CChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025819 122 TNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (247)
Q Consensus 122 ~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (247)
| .++.|.++- +.+..|.+.+|||+..+.+.+... ..+.+.|..|..++++++..++..-+-..+
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 899999999999999999988754 347889999999999999998865555443
No 10
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=96.36 E-value=0.0065 Score=56.66 Aligned_cols=98 Identities=16% Similarity=0.229 Sum_probs=76.9
Q ss_pred hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHH
Q 025819 89 PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLG 168 (247)
Q Consensus 89 ~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~ 168 (247)
++=+..-|++-.=+.|.-..+|+.+-+++.|+++ .++.|.|++ +.|+...+.+|||..-++|.+.-...- --+
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 3445677888888888889999999999999997 999999999 899999999999999999888643322 245
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 169 SMIQTLSNWLTTSDNLLISIQEKIK 193 (247)
Q Consensus 169 ~l~~~L~~W~~~~~~vl~~Ie~~i~ 193 (247)
.++++-..-.-+..++-..++..++
T Consensus 402 Q~ie~tksLS~rsq~la~~lek~~~ 426 (432)
T KOG2758|consen 402 QLIEKTKSLSFRSQNLAQQLEKKIQ 426 (432)
T ss_pred HHHHhccccchhHHHHHHHHHHHHH
Confidence 5666666666666666666665544
No 11
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=96.31 E-value=0.031 Score=53.50 Aligned_cols=105 Identities=14% Similarity=0.204 Sum_probs=80.2
Q ss_pred HHHHHHHHHhcCChhhHhh----hhCCCC---Ccc---hHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025819 61 KYLDMLRLFAHGTWSDYKN----NAGHLP---QLV---PDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (247)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~----~~~~l~---~L~---~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~l 130 (247)
.+.++|.-|..+-|..-.. .++.+- -|. .....++|.=.++.--.++..++++.++.+.+.+ +..+|.=
T Consensus 307 qlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~s-v~~le~~ 385 (466)
T KOG0686|consen 307 QLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTS-VAILESE 385 (466)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHHHHhhHHHhcCccccchHHHHHHHhccc-HHHHHHH
Confidence 4566777777777665433 222211 122 4457899999999988999999999999999997 9999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcH
Q 025819 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQL 167 (247)
Q Consensus 131 lI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~ 167 (247)
|. +.|-.|.|+||||+.++++++.-+..|.-+-++.
T Consensus 386 l~-~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~ 421 (466)
T KOG0686|consen 386 LL-ELILEGKISGRIDSHNKILYARDADSENATFERV 421 (466)
T ss_pred HH-HHHHccchheeeccccceeeecccccccchhhhc
Confidence 99 9999999999999999999998765554333333
No 12
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=95.90 E-value=0.034 Score=51.91 Aligned_cols=155 Identities=11% Similarity=0.142 Sum_probs=91.3
Q ss_pred HHHHHHHHhcCCCcccc-hhhhcCchhhhccCCC-chHHHHHHHHHhcCChhhHhhh-----hCCCCCcchHHHHHHHHH
Q 025819 26 LGSVIVEATSQPSLFAF-SEILAVPNIAEFEGTE-NSKYLDMLRLFAHGTWSDYKNN-----AGHLPQLVPDQVLKLKQL 98 (247)
Q Consensus 26 a~~lI~~AL~~p~vf~F-~eLL~lp~v~~L~~~~-~~~~~~LL~iFa~Gt~~dy~~~-----~~~l~~L~~~~~~KLr~L 98 (247)
|..|..-|.-+|.+--| ..|...|.+++|..=+ -.++| |=++....+...|... +...+.=+.-.-+-+.--
T Consensus 228 a~~CtlLA~~gpqrsr~Latlfkder~~~l~~y~ileKmy-l~riI~k~el~ef~~~L~pHQka~~~dgssil~ra~~Eh 306 (399)
T KOG1497|consen 228 ALQCTLLASAGPQRSRMLATLFKDERCQKLPAYGILEKMY-LERIIRKEELQEFEAFLQPHQKAHTMDGSSILDRAVIEH 306 (399)
T ss_pred hHhheeecCCChHHHHHHHHHhcCcccccccchHHHHHHH-HHHHhcchhHHHHHHHhcchhhhcccCcchhhhhHHHHH
Confidence 44444445555555443 4555566666663211 12222 2223333345555541 111121111111233335
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHH
Q 025819 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWL 178 (247)
Q Consensus 99 tllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~ 178 (247)
.|+++.+-+..|+|+++...|+|+ .+.+|...- +.|..|-+.|.|||.++.+++.- |. ...+|+. ....-|
T Consensus 307 Nlls~Skly~nisf~~Lg~ll~i~-~ekaekiaa-~MI~qeRmng~IDQ~egiihFe~---~e-~l~~wdk---qi~sl~ 377 (399)
T KOG1497|consen 307 NLLSASKLYNNISFEELGALLKID-AEKAEKIAA-QMITQERMNGSIDQIEGIIHFED---RE-ELPQWDK---QIQSLC 377 (399)
T ss_pred hHHHHHHHHHhccHHHHHHHhCCC-HHHHHHHHH-HHHhHHHhccchHhhcceEeecc---hh-hhhhhhH---HHHHHH
Confidence 566777777889999999999998 999999999 89999999999999999999863 21 1134544 334456
Q ss_pred HHHHHHHHHHHH
Q 025819 179 TTSDNLLISIQE 190 (247)
Q Consensus 179 ~~~~~vl~~Ie~ 190 (247)
+.++++++.|..
T Consensus 378 ~qvNki~~~i~~ 389 (399)
T KOG1497|consen 378 NQVNKILDKISH 389 (399)
T ss_pred HHHHHHHHHHHH
Confidence 666666666554
No 13
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=95.61 E-value=0.06 Score=50.08 Aligned_cols=77 Identities=17% Similarity=0.250 Sum_probs=66.3
Q ss_pred ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHH
Q 025819 104 AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDN 183 (247)
Q Consensus 104 a~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~ 183 (247)
+.=+..|+-..|..-++.| ..+.|.+|- +.+..|++.+||++..+.+.+... ++..+.|..|..+++.
T Consensus 348 ~~yYSrI~~~rl~~lld~~-~s~te~~IS-dlVN~G~~yaKiNrpa~Ii~FEK~----------~n~~~~lneW~~NV~e 415 (439)
T COG5071 348 ANYYSRIHCSRLGVLLDMS-PSETEQFIS-DLVNKGHFYAKINRPAQIISFEKS----------QNVQEQLNEWGSNVTE 415 (439)
T ss_pred HHHhhhhhHHHHHHHHcCC-HHHHHHHHH-HHHhcCcEEEEecCccceEEeecc----------ccHHHHHHHhcccHHH
Confidence 3457889999999999998 999999999 899999999999999999987643 2367889999999999
Q ss_pred HHHHHHHHH
Q 025819 184 LLISIQEKI 192 (247)
Q Consensus 184 vl~~Ie~~i 192 (247)
++..++.--
T Consensus 416 llgklek~~ 424 (439)
T COG5071 416 LLGKLEKVR 424 (439)
T ss_pred HHHHHHHHh
Confidence 999887543
No 14
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=93.74 E-value=0.45 Score=45.20 Aligned_cols=106 Identities=11% Similarity=0.253 Sum_probs=79.2
Q ss_pred hHHHHHHHHHhcCChhhHhh----hhCCC-CC----cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHH
Q 025819 60 SKYLDMLRLFAHGTWSDYKN----NAGHL-PQ----LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDF 130 (247)
Q Consensus 60 ~~~~~LL~iFa~Gt~~dy~~----~~~~l-~~----L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~l 130 (247)
.+|.++++++..+.-...+. +++.+ .+ +.-..+.-+..-+|..|-....+++.++|++..++.+..|||..
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 48999999999998876554 23222 21 33333455556667777777788999999997777778999999
Q ss_pred HHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHH
Q 025819 131 LINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (247)
Q Consensus 131 lI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~ 169 (247)
|+ ..|..|=|-..|| |-+..+.-...+..|+...+
T Consensus 339 Il-qmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~n 373 (422)
T KOG2582|consen 339 IL-QMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHEN 373 (422)
T ss_pred HH-HHhccCceEEEec---ceEEEecCcccCCCHHHHhh
Confidence 99 8999999999999 77877776666666665554
No 15
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=93.31 E-value=0.21 Score=47.03 Aligned_cols=114 Identities=16% Similarity=0.225 Sum_probs=80.9
Q ss_pred hhhcCchhhhccCCCchHHHHHHHHHhcCChhhHhhh-hCCCCCcc-----hHHH----HHHHHHHhhhcccCCcccChH
Q 025819 44 EILAVPNIAEFEGTENSKYLDMLRLFAHGTWSDYKNN-AGHLPQLV-----PDQV----LKLKQLTVLTLAETNKVLPYD 113 (247)
Q Consensus 44 eLL~lp~v~~L~~~~~~~~~~LL~iFa~Gt~~dy~~~-~~~l~~L~-----~~~~----~KLr~LtllsLa~~~k~Isy~ 113 (247)
.|+.-.......+..-..+...=+.|..-++.||..- .+.-++|- ...+ ..|=---|+.+.+++.++..+
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 3443333333444445567777788999999999862 21111222 1112 223334577888999999999
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025819 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (247)
Q Consensus 114 ~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~ 159 (247)
-|++-+|++ +..||.=+- ..|-...+.|.|||-++++.|.--.+
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
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=93.27 E-value=0.17 Score=48.31 Aligned_cols=98 Identities=15% Similarity=0.195 Sum_probs=70.2
Q ss_pred chHHHHHHHHHhcCChhhHhh----hhCCCCCcchH-HHHHHHHHHhhhcc-------cCCcccChHHHHHHcCCCC---
Q 025819 59 NSKYLDMLRLFAHGTWSDYKN----NAGHLPQLVPD-QVLKLKQLTVLTLA-------ETNKVLPYDELMEELDVTN--- 123 (247)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~L~~~-~~~KLr~LtllsLa-------~~~k~Isy~~I~~~L~I~~--- 123 (247)
-..+-.|+.....|++..|.. |...+....-- .+.|++.++.=.|. .+...+|++.+..++....
T Consensus 271 ~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi~l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~ 350 (394)
T KOG2688|consen 271 LDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGIYLTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTD 350 (394)
T ss_pred HHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhccHHHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCC
Confidence 346777899999999999975 22222111100 12234444333332 2678999999999998765
Q ss_pred --hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025819 124 --VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (247)
Q Consensus 124 --~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~ 157 (247)
.+|||-.+. .+|+.|.|+|.|+...+++.+...
T Consensus 351 ~~~deveciLa-~lI~~G~ikgYish~~~~~V~sK~ 385 (394)
T KOG2688|consen 351 VDLDEVECILA-NLIDLGRIKGYISHQLQTLVFSKK 385 (394)
T ss_pred CchhhHHHHHH-hhhhhccccchhchhhheEEEecC
Confidence 689999999 899999999999999999998754
No 17
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=91.02 E-value=1.7 Score=40.58 Aligned_cols=100 Identities=17% Similarity=0.228 Sum_probs=74.0
Q ss_pred chHHHHHHHHHhcCChhhHhhh-hCCCCCcc-----hHH----HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHH
Q 025819 59 NSKYLDMLRLFAHGTWSDYKNN-AGHLPQLV-----PDQ----VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELE 128 (247)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~-~~~l~~L~-----~~~----~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (247)
-..+...-+.|..-++.||..- +..-|+|- -.. -..|---.|+.+.++..++..+-|++-+|++ ..+||
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 111 1222234577788899999999999999997 99999
Q ss_pred HHHHHHhHhcCccEEEecCCCCEEEEEeecCC
Q 025819 129 DFLINECMYTGIVRGKLDQLRRCFEVQFAAGR 160 (247)
Q Consensus 129 ~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~R 160 (247)
.=+- ..|-.+++-|.+||.++|+.|.-....
T Consensus 362 gKLs-qMILDKifyG~LDqg~gcLivy~ep~q 392 (421)
T COG5159 362 GKLS-QMILDKIFYGTLDQGDGCLIVYGEPAQ 392 (421)
T ss_pred HHHH-HHHHHHHHHhhhccCCceEEEeCCccc
Confidence 9888 889999999999999999999755433
No 18
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=90.48 E-value=5.1 Score=41.78 Aligned_cols=50 Identities=16% Similarity=0.219 Sum_probs=44.0
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
.-+.+|+|+.|.+-.-.=|.-+||.+++ +|...+.+..+||...++|.+.
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 3577899998887665556899999999 9999999999999999999987
No 19
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=90.18 E-value=0.95 Score=43.17 Aligned_cols=99 Identities=21% Similarity=0.336 Sum_probs=65.0
Q ss_pred chHHHHHHHHHhcCChhhHhh----hhCCCCC------cc---hH-HHHHHHHHHhhhcccCCcccChHHHHHHcCCC--
Q 025819 59 NSKYLDMLRLFAHGTWSDYKN----NAGHLPQ------LV---PD-QVLKLKQLTVLTLAETNKVLPYDELMEELDVT-- 122 (247)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~----~~~~l~~------L~---~~-~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~-- 122 (247)
.+.+--|.++.-+|++++|.. |...+-. |. |. +.+.|.. -+..++-....+|++.+...++++
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 455667889999999999975 2111110 00 11 1122211 233334455557777766666554
Q ss_pred C----hHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025819 123 N----VRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (247)
Q Consensus 123 ~----~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~ 159 (247)
+ ..+||-.++ .+|..|+++|.|....+++.+....|
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 89999999999999999999986543
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=90.12 E-value=2.5 Score=34.15 Aligned_cols=107 Identities=14% Similarity=0.180 Sum_probs=73.5
Q ss_pred HHHHHHHHHhcCCCcccchhhhcCchhhhccC-CCchHHHHHHHHHhcCChhhHhhh-hCC-----CCCcchHHHHHHHH
Q 025819 25 ALGSVIVEATSQPSLFAFSEILAVPNIAEFEG-TENSKYLDMLRLFAHGTWSDYKNN-AGH-----LPQLVPDQVLKLKQ 97 (247)
Q Consensus 25 ~a~~lI~~AL~~p~vf~F~eLL~lp~v~~L~~-~~~~~~~~LL~iFa~Gt~~dy~~~-~~~-----l~~L~~~~~~KLr~ 97 (247)
....+...+|..-.+-+|.-++..-.-...+. .+-..++.|.+.+-.|+|..|-+. .+. +..+.+.-..++|.
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 34445555666666788888876554443333 345778899999999999998772 221 11233555778888
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 98 LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
-++-.+...+..|+.+.+++-||++ ..+++.++.
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 7777888889999999999999998 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=90.11 E-value=0.4 Score=41.46 Aligned_cols=57 Identities=14% Similarity=0.268 Sum_probs=41.0
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 97 ~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
+-.++..+...++++.++|+.+.++. ..++-+-|- +....|.|.|-||...+-|+|+
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 788888888 8999999999999999889887
No 22
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=89.04 E-value=1.8 Score=40.84 Aligned_cols=64 Identities=17% Similarity=0.267 Sum_probs=56.5
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025819 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (247)
Q Consensus 92 ~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~ 157 (247)
.+-||...--.|-+.+|.++.+-.|+..|++ ++-++.=+= +-|-+|-+++|||-++++|++++-
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 5778888888888999999999999999997 887777677 778899999999999999999853
No 23
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=86.10 E-value=7.1 Score=31.73 Aligned_cols=80 Identities=20% Similarity=0.362 Sum_probs=57.7
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-EecCCC-CEEEEEeecCCCCCCCcHH-HHHHHHHHHHHHH
Q 025819 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLDQLR-RCFEVQFAAGRDLRPGQLG-SMIQTLSNWLTTS 181 (247)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G-kIDQ~~-~~v~V~~~~~Rdl~~~q~~-~l~~~L~~W~~~~ 181 (247)
+.++.++-++|++.|+++ -..|..-|= +.+..|+|.= |..-.. +-.++- +.++++++. .+...|+.|++++
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 333222 233332 234456665 4788999999999
Q ss_pred HHHHHHHHH
Q 025819 182 DNLLISIQE 190 (247)
Q Consensus 182 ~~vl~~Ie~ 190 (247)
...+...+.
T Consensus 112 ~~~i~~~~~ 120 (126)
T COG3355 112 KQLIEEFEK 120 (126)
T ss_pred HHHHHHHhc
Confidence 988876553
No 24
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.94 E-value=2 Score=38.71 Aligned_cols=54 Identities=19% Similarity=0.401 Sum_probs=44.0
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
++..+.++++++.++|+.+.++. ..+.=+-+= +.+..|+|.|-||...+-++|+
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 45556689999999999999998 444444445 5667899999999999999997
No 25
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=82.89 E-value=1.3 Score=31.48 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=33.0
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
|......++.+|+++|+.+++++ ...||.++= ..+..|-|+-
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s-~~~ve~mL~-~l~~kG~I~~ 46 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGIS-PEAVEAMLE-QLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT---HHHHHHHHH-HHHCCTSCEE
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEE
Confidence 44455578899999999999998 999999887 8999998883
No 26
>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=81.85 E-value=4.3 Score=29.79 Aligned_cols=58 Identities=17% Similarity=0.230 Sum_probs=39.6
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
++.|..+......+.++-.+|++.++++ ...|+.++= +...+|+|+.+= ..++.+...
T Consensus 11 l~~l~~la~~~~~~~~s~~eiA~~~~i~-~~~l~kil~-~L~~~Gli~s~~-G~~GGy~L~ 68 (83)
T PF02082_consen 11 LRILLYLARHPDGKPVSSKEIAERLGIS-PSYLRKILQ-KLKKAGLIESSR-GRGGGYRLA 68 (83)
T ss_dssp HHHHHHHHCTTTSC-BEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEET-STTSEEEES
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHCcC-HHHHHHHHH-HHhhCCeeEecC-CCCCceeec
Confidence 3444444333345569999999999998 999999877 889999987552 444555443
No 27
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=79.93 E-value=3.2 Score=31.54 Aligned_cols=42 Identities=12% Similarity=0.295 Sum_probs=33.2
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
|+.....+..+||.+|++.++++ ...+-..+- .....|+|.+
T Consensus 8 il~~L~~~~~~~~~~la~~l~~s-~~tv~~~l~-~L~~~g~i~~ 49 (108)
T smart00344 8 ILEELQKDARISLAELAKKVGLS-PSTVHNRVK-RLEEEGVIKG 49 (108)
T ss_pred HHHHHHHhCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeec
Confidence 33333445679999999999998 888888877 8888999883
No 28
>PRK01919 tatB sec-independent translocase; Provisional
Probab=78.66 E-value=13 Score=31.60 Aligned_cols=59 Identities=10% Similarity=0.263 Sum_probs=40.1
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
.|+|+.++.+..++..|..++....+.+.+.+..--.. ++-.+.+++++....+++.++
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 47899999999999999999999988888877754322 223333444444444444433
No 29
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=78.54 E-value=3.2 Score=34.03 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=37.6
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCC
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQL 148 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G---kIDQ~ 148 (247)
|+.+-+.+...||++|++.||++ ...|-.-+= +....|+|+| -+|..
T Consensus 14 Il~~Lq~d~R~s~~eiA~~lglS-~~tV~~Ri~-rL~~~GvI~~~~~~v~~~ 63 (153)
T PRK11179 14 ILEALMENARTPYAELAKQFGVS-PGTIHVRVE-KMKQAGIITGTRVDVNPK 63 (153)
T ss_pred HHHHHHHcCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeeeEEEEECHH
Confidence 44555667899999999999997 888887777 8888999984 46653
No 30
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=74.05 E-value=8.6 Score=30.83 Aligned_cols=43 Identities=19% Similarity=0.357 Sum_probs=35.1
Q ss_pred Hhhhcc--cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 99 TVLTLA--ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 99 tllsLa--~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
+++.|| ..++.++-++|++.++|| ...|+.++- ..-.+|+|..
T Consensus 13 ~l~~La~~~~~~~~s~~~ia~~~~ip-~~~l~kil~-~L~~~glv~s 57 (135)
T TIGR02010 13 AMLDLALNAETGPVTLADISERQGIS-LSYLEQLFA-KLRKAGLVKS 57 (135)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCceEE
Confidence 334444 345689999999999998 999999988 8888999985
No 31
>PRK04098 sec-independent translocase; Provisional
Probab=72.08 E-value=29 Score=29.24 Aligned_cols=59 Identities=19% Similarity=0.311 Sum_probs=43.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HhhhHHHHHHHHHHHHHHHHHHhh
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA---DSMNEMDKKHRKDLEEKVEEAKKS 219 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a---~~~~~~~~~~~~~~~~~~~~~k~~ 219 (247)
.|+|+.++.+...+..|...+......+.+.+... ...+.+..+-++.++...+++++.
T Consensus 19 vfGP~KLP~~~r~lGk~ir~~K~~~~~~k~~l~~Ei~~~elk~e~~k~k~~l~~~~~~l~~~ 80 (158)
T PRK04098 19 FLGPDKLPQAMVDIAKFFKAVKKTINDAKSTLDKEINIEEIKEEALKYKKEFESAVESLKKK 80 (158)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 47899999999999999998888887776665543 333444455567788888888773
No 32
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=70.94 E-value=5.2 Score=32.13 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=33.7
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~Gk 144 (247)
|+.+-+.+..+||.+|++.+|++ ...|=.-|= +....|+|+|-
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 33444555559999999999997 888877777 88889999864
No 33
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=70.35 E-value=8 Score=25.09 Aligned_cols=41 Identities=20% Similarity=0.368 Sum_probs=30.0
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
|+.+...+..++-.+|++.++++ ...|-..+= +....|+|+
T Consensus 8 Il~~l~~~~~~t~~ela~~~~is-~~tv~~~l~-~L~~~g~I~ 48 (48)
T PF13412_consen 8 ILNYLRENPRITQKELAEKLGIS-RSTVNRYLK-KLEEKGLIE 48 (48)
T ss_dssp HHHHHHHCTTS-HHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHHcCCCCHHHHHHHhCCC-HHHHHHHHH-HHHHCcCcC
Confidence 44444456669999999999997 888877665 888888875
No 34
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=69.92 E-value=8.4 Score=31.96 Aligned_cols=48 Identities=13% Similarity=0.175 Sum_probs=37.9
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCC
Q 025819 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQL 148 (247)
Q Consensus 99 tllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G---kIDQ~ 148 (247)
.|+.+-+.+..+||.+|++.+|++ ...|=.-+= +....|+|+| .+|..
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS-~~tv~~Ri~-rL~~~GvI~~~~~~v~p~ 68 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLS-PTPCLERVR-RLERQGFIQGYTALLNPH 68 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEEEEEECHH
Confidence 355566788999999999999997 788777766 8888999975 45543
No 35
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=68.76 E-value=23 Score=31.25 Aligned_cols=62 Identities=11% Similarity=0.165 Sum_probs=50.2
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 92 ~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
+.-|++|.++........+|..+|++.++++ ...+=..|- +.-..|+|.-..+...+.+.+|
T Consensus 4 ~~~Lk~iallg~l~~~~~IS~~eLA~~L~iS-~~Tvsr~Lk-~LEe~GlI~R~~~~r~~~v~LT 65 (217)
T PRK14165 4 IEALKKLALLGAVNNTVKISSSEFANHTGTS-SKTAARILK-QLEDEGYITRTIVPRGQLITIT 65 (217)
T ss_pred hHHHHHHHHHhccCCCCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEEcCCceEEEEC
Confidence 3456777777766677789999999999997 777777777 8888999999999877666665
No 36
>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=68.69 E-value=20 Score=26.63 Aligned_cols=37 Identities=11% Similarity=0.212 Sum_probs=31.2
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (247)
.|+|+.++.+..++..|........+.+.+.+...-.
T Consensus 18 v~GP~kLP~~~r~~G~~i~~~r~~~~~~~~~~~~e~~ 54 (80)
T TIGR01410 18 VLGPERLPVAIRAVGKFVRRLRGMASDVKNELDEELK 54 (80)
T ss_pred eECchHHHHHHHHHHHHHHHHHHhhHhHHHHHHHHhc
Confidence 4789999999999999999999988888887755443
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=68.20 E-value=18 Score=28.38 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.6
Q ss_pred HHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025819 93 LKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (247)
Q Consensus 93 ~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~Gk 144 (247)
.-++.+..+....+...++.++|++.+++| ...|...+= .....|+|...
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
>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=67.35 E-value=5.9 Score=30.31 Aligned_cols=35 Identities=17% Similarity=0.513 Sum_probs=27.3
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~ 137 (247)
|..+-..-..+||++|-+. +||...||+|+| +.+.
T Consensus 39 Iyrlftr~~vi~Fd~iVr~--mpNes~v~qWV~-dtln 73 (100)
T PF07389_consen 39 IYRLFTRCAVIPFDDIVRT--MPNESRVKQWVI-DTLN 73 (100)
T ss_pred HHHHHHhhccccHHHHHHh--CCCHHHHHHHHH-HHHH
Confidence 3344445567899999998 788999999999 7664
No 39
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=67.02 E-value=14 Score=31.10 Aligned_cols=48 Identities=15% Similarity=0.280 Sum_probs=37.7
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~Gk 144 (247)
|+.+..+......+.++-++|++.+++| ..-|+.++- ..-.+|||...
T Consensus 11 l~~l~~lA~~~~~~~vs~~eIA~~~~ip-~~~l~kIl~-~L~~aGLv~s~ 58 (164)
T PRK10857 11 VTAMLDVALNSEAGPVPLADISERQGIS-LSYLEQLFS-RLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHhCCCCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeC
Confidence 3333344444456689999999999998 999999988 89999999973
No 40
>PRK04654 sec-independent translocase; Provisional
Probab=66.51 E-value=37 Score=30.04 Aligned_cols=35 Identities=14% Similarity=0.241 Sum_probs=29.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a 195 (247)
.|+|+.|..+...+..|..++++....+.+.+.+-
T Consensus 19 V~GPerLPe~aRtlGk~irk~R~~~~~vk~El~~E 53 (214)
T PRK04654 19 VLGPERLPKAARFAGLWVRRARMQWDSVKQELERE 53 (214)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47999999999999999999888887777766543
No 41
>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=62.18 E-value=35 Score=26.85 Aligned_cols=37 Identities=19% Similarity=0.289 Sum_probs=32.4
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~Gk 144 (247)
.+..++..+|++.++++ ..-|...+= ....+|+|.+.
T Consensus 22 ~~~~~s~~eia~~l~is-~~~v~~~l~-~L~~~Gli~~~ 58 (130)
T TIGR02944 22 DSQPYSAAEIAEQTGLN-APTVSKILK-QLSLAGIVTSK 58 (130)
T ss_pred CCCCccHHHHHHHHCcC-HHHHHHHHH-HHHHCCcEEec
Confidence 45679999999999998 899999887 88899999774
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=62.02 E-value=7.1 Score=26.92 Aligned_cols=35 Identities=29% Similarity=0.481 Sum_probs=24.9
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHH
Q 025819 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFL 131 (247)
Q Consensus 96 r~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~ll 131 (247)
|++.|+.+.-..+.+++++|++.++++ .+.+-..|
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 445555555447899999999999997 77665543
No 43
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=60.87 E-value=18 Score=26.28 Aligned_cols=46 Identities=24% Similarity=0.232 Sum_probs=35.5
Q ss_pred HHHHhhhcccCC-cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 96 KQLTVLTLAETN-KVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 96 r~LtllsLa~~~-k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
|.+.|+.+.... ..++..+|++.++++ ...|-..+- .....|+|..
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 44
>PRK14858 tatA twin arginine translocase protein A; Provisional
Probab=59.30 E-value=64 Score=25.51 Aligned_cols=38 Identities=11% Similarity=0.147 Sum_probs=31.7
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSM 198 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~ 198 (247)
.|+|+.++.+...+..|........+.+++.+..--..
T Consensus 19 vfGPkKLPelar~lGk~i~~fk~~~~d~k~~i~~E~~~ 56 (108)
T PRK14858 19 VIGPQKLPDLARSLGRGLAEFKKATDDFKQSMQEESRT 56 (108)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999988888877654433
No 45
>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=57.21 E-value=96 Score=28.74 Aligned_cols=64 Identities=14% Similarity=0.152 Sum_probs=49.0
Q ss_pred eecCCCCCCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhh
Q 025819 156 FAAGRDLRPGQ-LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKS 219 (247)
Q Consensus 156 ~~~~Rdl~~~q-~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~ 219 (247)
-.+++|++.++ +..+.+.|+.--.-++.+.+.|.+++..-....+.-..+-...+++|+.++-+
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 35688888765 67889999999999999999999998887776665556666666777666543
No 46
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=57.11 E-value=28 Score=28.64 Aligned_cols=50 Identities=22% Similarity=0.264 Sum_probs=38.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkID 146 (247)
++-|..++.-..++.++-++|++..+|+ ..-++.++- ..-.+|+|+..=-
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 3444444444455588999999999998 999999998 8999999886543
No 47
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=56.87 E-value=62 Score=30.95 Aligned_cols=60 Identities=25% Similarity=0.338 Sum_probs=45.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHH
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTL 174 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L 174 (247)
.++.++-++|++.++++ .+.+++++= +...+|+|. +-++. .|+..||.+.=.+..+.+.+
T Consensus 307 ~g~~~t~~~La~~l~~~-~~~v~~iL~-~L~~agLI~-~~~~g------~~~l~rd~~~itL~dv~~~~ 366 (412)
T PRK04214 307 HGKALDVDEIRRLEPMG-YDELGELLC-ELARIGLLR-RGERG------QWVLARDLDSVPLAELYELF 366 (412)
T ss_pred cCCCCCHHHHHHHhCCC-HHHHHHHHH-HHHhCCCeE-ecCCC------ceEecCCHHhCcHHHHHHhC
Confidence 56788999999999998 999999877 888899997 33321 37888887655555555543
No 48
>PRK01770 sec-independent translocase; Provisional
Probab=55.78 E-value=67 Score=27.46 Aligned_cols=34 Identities=21% Similarity=0.462 Sum_probs=30.5
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (247)
.|+|+.+..+..++..|..+++.+...+++.+.+
T Consensus 19 V~GPerLP~~~r~lg~~i~~~R~~~~~~k~e~~~ 52 (171)
T PRK01770 19 VLGPQRLPVAVKTVAGWIRALRSLATTVQNELTQ 52 (171)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999988877665
No 49
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=55.67 E-value=46 Score=26.15 Aligned_cols=57 Identities=19% Similarity=0.327 Sum_probs=36.8
Q ss_pred CCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhcC
Q 025819 159 GRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSLS 221 (247)
Q Consensus 159 ~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~~ 221 (247)
+|.+.+..++.+..-|+.-.+.++.++.. +......+..+-|..++..+.++++.++
T Consensus 2 ~~~~~~~~~~~l~~el~~L~d~lEevL~s------sg~~a~~e~~~lR~r~~~~Lk~~r~rl~ 58 (104)
T COG4575 2 SREFTDDAIDQLLAELQELLDTLEEVLKS------SGSLAGDEAEELRSKAESALKEARDRLG 58 (104)
T ss_pred cccchhhhHHHHHHHHHHHHHHHHHHHHh------cccchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 56677777777777777766666666554 3333444556666667777777777763
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=55.35 E-value=28 Score=23.02 Aligned_cols=45 Identities=22% Similarity=0.332 Sum_probs=32.2
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 96 r~LtllsL-a~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
|-+.|+.. +.....++..+|++.++++ ...+-.++- .....|+|+
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 34556654 4455668999999999998 788887776 677777764
No 51
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=55.13 E-value=21 Score=25.33 Aligned_cols=37 Identities=19% Similarity=0.240 Sum_probs=28.0
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
+.+..-|+.+|++.+++.|..-|-..|- ..-..|.|+
T Consensus 21 ~~G~~Pt~rEIa~~~g~~S~~tv~~~L~-~Le~kG~I~ 57 (65)
T PF01726_consen 21 ENGYPPTVREIAEALGLKSTSTVQRHLK-ALERKGYIR 57 (65)
T ss_dssp HHSS---HHHHHHHHTSSSHHHHHHHHH-HHHHTTSEE
T ss_pred HcCCCCCHHHHHHHhCCCChHHHHHHHH-HHHHCcCcc
Confidence 3567789999999999998999988877 677777764
No 52
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=54.19 E-value=25 Score=28.00 Aligned_cols=46 Identities=13% Similarity=0.120 Sum_probs=33.1
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V 154 (247)
....+..+|++.++++ ...|-.=+= ..-.+|||..+-+.......+
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 3568888999999998 666654443 456689999988866544444
No 53
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=54.13 E-value=8.4 Score=25.00 Aligned_cols=28 Identities=29% Similarity=0.449 Sum_probs=18.8
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHH
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELE 128 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (247)
|+.+-..+...||.+|++.+|++ ...|-
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 54
>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=53.30 E-value=20 Score=23.73 Aligned_cols=36 Identities=31% Similarity=0.414 Sum_probs=24.1
Q ss_pred HHHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 96 KQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 96 r~LtllsLa-~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
|+..|+.+. .....+|-++|++.|+|+ .+.|..-+=
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~vS-~rTi~~~i~ 37 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELGVS-RRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCTS--HHHHHHHHH
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhCCC-HHHHHHHHH
Confidence 344455444 455559999999999997 777766543
No 55
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=53.09 E-value=34 Score=28.19 Aligned_cols=49 Identities=16% Similarity=0.124 Sum_probs=36.9
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkID 146 (247)
+|-|..++.. ..+.++-.+|++..+|| ..-|+.++- ..-.+|+|+..=-
T Consensus 11 lr~L~~LA~~-~~~~~s~~eIA~~~~is-~~~L~kIl~-~L~~aGlv~S~rG 59 (153)
T PRK11920 11 IRMLMYCAAN-DGKLSRIPEIARAYGVS-ELFLFKILQ-PLVEAGLVETVRG 59 (153)
T ss_pred HHHHHHHHhC-CCCcCcHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEeecC
Confidence 3434334322 34568999999999998 999999988 8889999886653
No 56
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=53.01 E-value=36 Score=27.37 Aligned_cols=50 Identities=14% Similarity=0.188 Sum_probs=37.3
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkID 146 (247)
+|.+..+.-..++..++-++|++.++|+ ..-|+..+- ..-..|+|..+=-
T Consensus 11 l~~~i~la~~~~g~~~s~~~ia~~~~is-~~~vrk~l~-~L~~~Glv~s~~G 60 (141)
T PRK11014 11 LRALIYMASLPEGRMTSISEVTEVYGVS-RNHMVKIIN-QLSRAGYVTAVRG 60 (141)
T ss_pred HHHHHHHhcCCCCCccCHHHHHHHHCcC-HHHHHHHHH-HHHhCCEEEEecC
Confidence 4444444444456688999999999998 889999888 8888898876543
No 57
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.75 E-value=22 Score=25.20 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=29.6
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
.++-.+|+++|+|+ ...|-..+- .....|+|.-
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 789999999 8999998864
No 58
>PHA01750 hypothetical protein
Probab=51.92 E-value=68 Score=23.30 Aligned_cols=35 Identities=23% Similarity=0.252 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 186 ISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 186 ~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
..+.....+...+.+.-..++.++++.|.++|+.+
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 34555677777777777788889999999999876
No 59
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=51.85 E-value=1.1e+02 Score=24.13 Aligned_cols=56 Identities=9% Similarity=-0.024 Sum_probs=40.9
Q ss_pred hhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeec
Q 025819 101 LTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAA 158 (247)
Q Consensus 101 lsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~ 158 (247)
..|...+..++-.+|++.++++ ...|=..|- .....|+|.=.-|..+++...-+.+
T Consensus 38 ~~l~~~~~~~t~~eLa~~l~~~-~~tvt~~v~-~Le~~GlV~r~~~~~DrR~~~l~LT 93 (144)
T PRK03573 38 HNIHQLPPEQSQIQLAKAIGIE-QPSLVRTLD-QLEEKGLISRQTCASDRRAKRIKLT 93 (144)
T ss_pred HHHHHcCCCCCHHHHHHHhCCC-hhhHHHHHH-HHHHCCCEeeecCCCCcCeeeeEEC
Confidence 3344333456789999999997 667766666 8888999999999877776655543
No 60
>PF13730 HTH_36: Helix-turn-helix domain
Probab=50.21 E-value=58 Score=21.37 Aligned_cols=47 Identities=21% Similarity=0.308 Sum_probs=34.9
Q ss_pred HHHHHHHhhhcccC-Cccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 025819 93 LKLKQLTVLTLAET-NKVL-PYDELMEELDVTNVRELEDFLINECMYTGIV 141 (247)
Q Consensus 93 ~KLr~LtllsLa~~-~k~I-sy~~I~~~L~I~~~~evE~llI~~aI~~glI 141 (247)
.|+-.+.|.+.+.+ +.+. |++.|++.++++ .+.|-..+= +....|+|
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 45666778888753 2344 699999999998 888888766 77777765
No 61
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=50.17 E-value=53 Score=21.82 Aligned_cols=36 Identities=22% Similarity=0.325 Sum_probs=30.5
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025819 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (247)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ 147 (247)
+++.+|++.++++ ...+-..+- .....|+|...-+.
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 77789999877665
No 62
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=49.77 E-value=18 Score=37.33 Aligned_cols=96 Identities=11% Similarity=0.244 Sum_probs=66.9
Q ss_pred HHHHHHHHhcCChhhHhh---h----hCCCCCcc---hHHHHHHHHHH----hhhcccCCcccChHHHHHHcCCCChHHH
Q 025819 62 YLDMLRLFAHGTWSDYKN---N----AGHLPQLV---PDQVLKLKQLT----VLTLAETNKVLPYDELMEELDVTNVREL 127 (247)
Q Consensus 62 ~~~LL~iFa~Gt~~dy~~---~----~~~l~~L~---~~~~~KLr~Lt----llsLa~~~k~Isy~~I~~~L~I~~~~ev 127 (247)
+..-=.+...|+|.+-.. + ++-+|.-. .-...+++-=+ |.+.+.-+..+|.+.||+-.++| +..|
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 444556788899987443 2 33445421 11233444322 34455568899999999999998 8888
Q ss_pred HHHHHHHhHhcCccEEEecCCCCEEEEEeecC
Q 025819 128 EDFLINECMYTGIVRGKLDQLRRCFEVQFAAG 159 (247)
Q Consensus 128 E~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~ 159 (247)
=..|- +.|-..=|.+++||..++|.++++.+
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 63
>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=49.62 E-value=1.5e+02 Score=24.52 Aligned_cols=114 Identities=16% Similarity=0.179 Sum_probs=66.5
Q ss_pred cCCcccChHHHHHHcC--CCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHH
Q 025819 105 ETNKVLPYDELMEELD--VTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSD 182 (247)
Q Consensus 105 ~~~k~Isy~~I~~~L~--I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~ 182 (247)
..+|..+..+|...|+ ++ =..|...+= .+...|.|.+|.=....+..+.-...-+++++++..|-..+....+.+.
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 4788899999999995 54 455555544 5666899999976555444433333444568888888777777766655
Q ss_pred HHHHHH---HHHHHHHHhhh--HHHHHHHHHHHHHHHHHHhhc
Q 025819 183 NLLISI---QEKIKWADSMN--EMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 183 ~vl~~I---e~~i~~a~~~~--~~~~~~~~~~~~~~~~~k~~~ 220 (247)
.+-..+ +..++..++.- ++-...-.+++.+++.+...+
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 33444333331 222333334444444444444
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=49.47 E-value=29 Score=23.65 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=28.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025819 105 ETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (247)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~Gk 144 (247)
......+..+|++.++++ ...+-.=+= ....+|+|+..
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 566889999999999998 676665555 56778888753
No 65
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=48.91 E-value=1.5e+02 Score=26.31 Aligned_cols=38 Identities=26% Similarity=0.477 Sum_probs=28.9
Q ss_pred Ch-HHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025819 111 PY-DELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (247)
Q Consensus 111 sy-~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~ 150 (247)
.| .+|++.+|++.-.-+++|=+ .-.+|||+.+++-..+
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 47888999984445677766 4678999999988777
No 66
>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=48.86 E-value=41 Score=23.34 Aligned_cols=42 Identities=19% Similarity=0.326 Sum_probs=32.1
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 99 tllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
+|..|...+..++-.+|++.|+++ ...|=+.+= +.-..|+|.
T Consensus 12 ~Iy~l~~~~~~v~~~~iA~~L~vs-~~tvt~ml~-~L~~~GlV~ 53 (60)
T PF01325_consen 12 AIYELSEEGGPVRTKDIAERLGVS-PPTVTEMLK-RLAEKGLVE 53 (60)
T ss_dssp HHHHHHHCTSSBBHHHHHHHHTS--HHHHHHHHH-HHHHTTSEE
T ss_pred HHHHHHcCCCCccHHHHHHHHCCC-hHHHHHHHH-HHHHCCCEE
Confidence 455555688999999999999997 777766666 777778775
No 67
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=48.81 E-value=70 Score=26.76 Aligned_cols=62 Identities=15% Similarity=0.222 Sum_probs=44.9
Q ss_pred chHHHHHHHHHhcCChhhHhhhh--CCCCCcc----hHHHHHHHHHHhhhcccCCcc-cChHHHHHHcC
Q 025819 59 NSKYLDMLRLFAHGTWSDYKNNA--GHLPQLV----PDQVLKLKQLTVLTLAETNKV-LPYDELMEELD 120 (247)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~--~~l~~L~----~~~~~KLr~LtllsLa~~~k~-Isy~~I~~~L~ 120 (247)
-...+++...+..|+|..|-... ...|.+. ..-..++|..++-+++...+. +|-+.+++-|+
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 45677899999999999998754 5555443 224679999999998887777 99999988775
No 68
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=48.71 E-value=23 Score=23.27 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=20.1
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025819 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (247)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~aI 136 (247)
.-.||.+|++.+|++ ...|..++- .|.
T Consensus 25 ~g~s~~eIa~~l~~s-~~~v~~~l~-ra~ 51 (54)
T PF08281_consen 25 QGMSYAEIAEILGIS-ESTVKRRLR-RAR 51 (54)
T ss_dssp S---HHHHHHHCTS--HHHHHHHHH-HHH
T ss_pred HCcCHHHHHHHHCcC-HHHHHHHHH-HHH
Confidence 568999999999997 999998877 664
No 69
>PRK09954 putative kinase; Provisional
Probab=47.46 E-value=23 Score=32.76 Aligned_cols=54 Identities=19% Similarity=0.438 Sum_probs=41.4
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE---EecCCCCEEEEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG---KLDQLRRCFEVQ 155 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G---kIDQ~~~~v~V~ 155 (247)
|+.+...+..+|+.+|++.|+++ ...|-..+- +....|+|+| .||....++.|-
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 889998877 8888899975 466666554443
No 70
>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=47.22 E-value=28 Score=23.75 Aligned_cols=42 Identities=24% Similarity=0.268 Sum_probs=28.8
Q ss_pred HHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCc
Q 025819 97 QLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGI 140 (247)
Q Consensus 97 ~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~gl 140 (247)
+-.|+.+....+.++..+|++.++++ ..-+-.=+. ..-..|+
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 34466666778999999999999997 655544333 3444454
No 71
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=46.40 E-value=24 Score=25.90 Aligned_cols=51 Identities=29% Similarity=0.315 Sum_probs=35.2
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025819 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (247)
Q Consensus 98 LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~ 150 (247)
|.|+++-.....++|.+|.+.|+++ ...+-.-+= ....+|+|+-+=.-..+
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 3445444446789999999999997 777766665 67778999977655544
No 72
>PRK00708 sec-independent translocase; Provisional
Probab=45.62 E-value=76 Score=27.98 Aligned_cols=37 Identities=11% Similarity=0.136 Sum_probs=31.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADS 197 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~ 197 (247)
.|+|+++..+...+..|..++..+.+.+.+++...-.
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 73
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=45.62 E-value=82 Score=20.36 Aligned_cols=36 Identities=22% Similarity=0.280 Sum_probs=29.0
Q ss_pred cCCccc-ChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 105 ETNKVL-PYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 105 ~~~k~I-sy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
.++..+ |..+|++.++++ ...|-..+- .....|+|.
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 799999999997 888888777 777788875
No 74
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=45.19 E-value=50 Score=25.35 Aligned_cols=38 Identities=18% Similarity=0.142 Sum_probs=28.8
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~ 149 (247)
....++.+++++.++++ +.||. +.+..|+|.-.-+...
T Consensus 4 ~~~~lt~~Elc~~~gi~-----~~~l~-eLve~GlIep~~~~~~ 41 (101)
T PRK10265 4 VTVTFTITEFCLHTGVS-----EEELN-EIVGLGVIEPREIQET 41 (101)
T ss_pred eEEEeeHHHHHHHHCcC-----HHHHH-HHHHCCCeecCCCCcc
Confidence 34568999999999998 55677 7777899986544433
No 75
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=45.06 E-value=75 Score=29.96 Aligned_cols=64 Identities=17% Similarity=0.265 Sum_probs=53.8
Q ss_pred HHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025819 92 VLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (247)
Q Consensus 92 ~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~ 157 (247)
.+-||.=.-..|-+.+|.++.+..++..+++ ++-|+.=+= +-|-.|-+.+.||-+|++|++++-
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 4667777777788899999999999999997 887776666 667789999999999999998753
No 76
>PRK00404 tatB sec-independent translocase; Provisional
Probab=44.87 E-value=1.5e+02 Score=24.52 Aligned_cols=35 Identities=17% Similarity=0.322 Sum_probs=29.3
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a 195 (247)
.|+++.+..+..++..|..++.+....+.+.+.+-
T Consensus 19 V~GPkkLP~laR~lG~~i~~~rr~~~~~k~ei~~E 53 (141)
T PRK00404 19 VLGPERLPGAARTAGLWIGRLKRSFNAIKQEVERE 53 (141)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47899999999999999998888777777666653
No 77
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=44.66 E-value=74 Score=20.58 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=21.7
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI 136 (247)
....||.+|++.+|++ ...|-.+.- .|+
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 5778999999999997 777776655 555
No 78
>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=44.55 E-value=1.7e+02 Score=25.13 Aligned_cols=64 Identities=13% Similarity=0.062 Sum_probs=37.9
Q ss_pred HHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHH
Q 025819 116 MEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISI 188 (247)
Q Consensus 116 ~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~I 188 (247)
.+++||. ...|.++|- ..+..|+|+. ..=|+-.+-|+-|- +....+...+......++.+-..+
T Consensus 22 pK~~gI~-~~~VKdvlq-~LvDDglV~~---EKiGssn~YWsFps----~~~~~~~~~~~~l~~~~~~~~~~i 85 (188)
T PF03962_consen 22 PKEKGIV-SMSVKDVLQ-SLVDDGLVHV---EKIGSSNYYWSFPS----QAKQKRQNKLEKLQKEIEELEKKI 85 (188)
T ss_pred ccccCCc-hhhHHHHHH-HHhccccchh---hhccCeeEEEecCh----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3447897 788999888 7887777763 13355667787543 344444444444444444433333
No 79
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=44.47 E-value=1.1e+02 Score=21.73 Aligned_cols=41 Identities=20% Similarity=0.187 Sum_probs=33.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCC
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLR 149 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~ 149 (247)
...++..+|++.++++ ...+-..|- +....|+|.-.-++.+
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 80
>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=43.96 E-value=58 Score=21.03 Aligned_cols=33 Identities=27% Similarity=0.341 Sum_probs=24.6
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 108 KVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
+..+..+|++.++++ ...|-.-+= .....|+|+
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 81
>cd06445 ATase The DNA repair protein O6-alkylguanine-DNA alkyltransferase (ATase; also known as AGT, AGAT and MGMT) reverses O6-alkylation DNA damage by transferring O6-alkyl adducts to an active site cysteine irreversibly, without inducing DNA strand breaks. ATases are specific for repair of guanines with O6-alkyl adducts, however human ATase is not limited to O6-methylguanine, repairing many other adducts at the O6-position of guanine as well. ATase is widely distributed among species. Most ATases have N- and C-terminal domains. The C-terminal domain contains the conserved active-site cysteine motif (PCHR), the O6-alkylguanine binding channel, and the helix-turn-helix (HTH) DNA-binding motif. The active site is located near the recognition helix of the HTH motif. While the C-terminal domain of ATase contains residues that are necessary for DNA binding and alkyl transfer, the function of the N-terminal domain is still unknown. Removal of the N-terminal domain abolishes the activity of
Probab=43.95 E-value=32 Score=25.10 Aligned_cols=30 Identities=13% Similarity=0.196 Sum_probs=22.8
Q ss_pred HHhhhcccCCcccChHHHHHHcCCC-ChHHH
Q 025819 98 LTVLTLAETNKVLPYDELMEELDVT-NVREL 127 (247)
Q Consensus 98 LtllsLa~~~k~Isy~~I~~~L~I~-~~~ev 127 (247)
+.++.-...++..||.+|++.++.+ ..+.|
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 35665
No 82
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=43.34 E-value=66 Score=23.21 Aligned_cols=49 Identities=14% Similarity=0.260 Sum_probs=33.3
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQ 155 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~ 155 (247)
|+..+. ....++..|+..++++ ...+..++= ..+..|+|++ .++.+.+|
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 899998877 8999999944 45555554
No 83
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=43.11 E-value=1.1e+02 Score=20.99 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=20.9
Q ss_pred cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 105 ETNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 105 ~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
..-|.++..+|+++|||+ ...+-.-+=
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 456899999999999998 666555443
No 84
>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=42.52 E-value=1.4e+02 Score=22.02 Aligned_cols=75 Identities=19% Similarity=0.298 Sum_probs=49.4
Q ss_pred HHhhhcccCCcccChHHHHHHc-CCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee-cCCCCCCCcHHHHHHHHH
Q 025819 98 LTVLTLAETNKVLPYDELMEEL-DVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA-AGRDLRPGQLGSMIQTLS 175 (247)
Q Consensus 98 LtllsLa~~~k~Isy~~I~~~L-~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~-~~Rdl~~~q~~~l~~~L~ 175 (247)
+.|..|.. +...|.+|.+.+ +|+ ...+-+-+= +....|+|.=...... -..|.|. +++- .++..+...|.
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 33445544 788999999999 887 778766666 7888999987766433 3344442 2111 23566788888
Q ss_pred HHHHH
Q 025819 176 NWLTT 180 (247)
Q Consensus 176 ~W~~~ 180 (247)
.|...
T Consensus 81 ~W~~~ 85 (90)
T PF01638_consen 81 EWGEE 85 (90)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 88754
No 85
>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=40.91 E-value=21 Score=26.30 Aligned_cols=38 Identities=16% Similarity=0.347 Sum_probs=24.6
Q ss_pred hhhcccCCcccChHHHHHHcC---CCChHHHHHHHHHHhHhcC
Q 025819 100 VLTLAETNKVLPYDELMEELD---VTNVRELEDFLINECMYTG 139 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~---I~~~~evE~llI~~aI~~g 139 (247)
|+......+.|+|++|...|. + +.+.++.++- ..-..|
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 444444
No 86
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=40.31 E-value=1e+02 Score=21.81 Aligned_cols=61 Identities=11% Similarity=0.178 Sum_probs=46.6
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHH
Q 025819 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSN 176 (247)
Q Consensus 111 sy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~ 176 (247)
.|..+.+.+++++ +...+++= + +.+-+-.++..+++.++....++.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~-~~~~~~f~-~---~~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPD-ELDNPLFE-D---AEIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCc-hhhhhhhc-c---cEEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 3678889999983 22343333 3 245668999999999999999999999999888887764
No 87
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=39.51 E-value=73 Score=19.99 Aligned_cols=34 Identities=21% Similarity=0.201 Sum_probs=26.8
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
+..++-.+|++.++++ ...+...+= .....|+|.
T Consensus 12 ~~~~s~~~l~~~l~~s-~~tv~~~l~-~L~~~g~i~ 45 (53)
T smart00420 12 QGKVSVEELAELLGVS-EMTIRRDLN-KLEEQGLLT 45 (53)
T ss_pred cCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 4569999999999997 888887766 666667765
No 88
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=39.18 E-value=1e+02 Score=19.81 Aligned_cols=38 Identities=21% Similarity=0.219 Sum_probs=29.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEec
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLD 146 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkID 146 (247)
...+++.+|++.++++ ...+-..+= .....|+|.-.=+
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 89
>PF09341 Pcc1: Transcription factor Pcc1; InterPro: IPR015419 Pcc1 is a proposed transcription factor involved in the expression of genes regulated by alpha-factor and galactose; component of the EKC/KEOPS protein complex with Kae1, Gon7, Bud32, and Cgi121; related to human cancer-testis antigens [].; PDB: 2BNR_C 2P5W_C 3KLA_C 2F54_C 2P5E_C 2F53_C 3ENO_E 3ENC_B.
Probab=38.85 E-value=1.1e+02 Score=21.84 Aligned_cols=47 Identities=17% Similarity=0.164 Sum_probs=37.2
Q ss_pred cCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 138 TGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQE 190 (247)
Q Consensus 138 ~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~ 190 (247)
.+-++..++-.++++.|.+.. .+...|+..+..|...+.-+...+++
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 56788999999999988877776653
No 90
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=38.58 E-value=97 Score=24.34 Aligned_cols=41 Identities=20% Similarity=0.192 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhh
Q 025819 179 TTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKS 219 (247)
Q Consensus 179 ~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~ 219 (247)
+.+...+..+++.+..++...++....-++..+++..+|+.
T Consensus 76 ~~L~~~~~~l~~~~~~~~~~~~~l~~~~~~~~~~~k~lk~E 116 (118)
T PF13815_consen 76 EYLSSQLEQLEERLQELQQEIEKLKQKLKKQKEEIKKLKKE 116 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44444555566666666666555555555556666666653
No 91
>PHA03158 hypothetical protein; Provisional
Probab=38.44 E-value=39 Score=29.70 Aligned_cols=62 Identities=24% Similarity=0.291 Sum_probs=42.3
Q ss_pred ecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 157 AAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 157 ~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
+..|++. =++.+...=--||-....=-..+-.|+-.+.+-+-..-+|.++++++++++.|++
T Consensus 209 V~y~sLp--f~ERl~Rs~pPWCv~t~~EK~~~~kQllka~kkc~~~s~~~~~leeei~eleks~ 270 (273)
T PHA03158 209 VRFDDLP--FMERIKRSGPPWCIKTAKEKAAILKQLLKAAKKCCKNSEHEKELEEEIEELEKSL 270 (273)
T ss_pred EEeccCc--HHHHHhccCCCcEeecHHHhHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHhh
Confidence 3445442 2344444445698666665556666666666666778899999999999999986
No 92
>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=37.44 E-value=79 Score=23.78 Aligned_cols=50 Identities=18% Similarity=0.259 Sum_probs=36.3
Q ss_pred HHHHhhhc-ccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025819 96 KQLTVLTL-AETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (247)
Q Consensus 96 r~LtllsL-a~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ 147 (247)
+.|.++.= +....=++.++|++.|+++ ..+|+.-|= ..+..|.|=-.||.
T Consensus 51 ~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~-~~~v~~al~-~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 51 KVLNFIKQQPNSEEGVHVDEIAQQLGMS-ENEVRKALD-FLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHC----TTTEEHHHHHHHSTS--HHHHHHHHH-HHHHTTSEEESSST
T ss_pred HHHHHHHhcCCCCCcccHHHHHHHhCcC-HHHHHHHHH-HHHhCCeEecccCC
Confidence 33445544 4445569999999999998 999998777 88889998777774
No 93
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=36.43 E-value=1.9e+02 Score=22.01 Aligned_cols=46 Identities=11% Similarity=0.073 Sum_probs=35.9
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEE
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFE 153 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~ 153 (247)
.+..++..+|++.++++ ...+=..|- +....|+|...-|..++...
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 556666665 88889999999887665533
No 94
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.72 E-value=50 Score=21.18 Aligned_cols=30 Identities=10% Similarity=0.206 Sum_probs=23.2
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
++.+...+ . |+.++++.++|+ ...|-.|+-
T Consensus 5 iv~~~~~g-~-s~~~~a~~~gis-~~tv~~w~~ 34 (52)
T PF13518_consen 5 IVELYLEG-E-SVREIAREFGIS-RSTVYRWIK 34 (52)
T ss_pred HHHHHHcC-C-CHHHHHHHHCCC-HhHHHHHHH
Confidence 44444433 3 999999999995 899999976
No 95
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=35.52 E-value=1.1e+02 Score=20.24 Aligned_cols=42 Identities=21% Similarity=0.265 Sum_probs=32.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCC
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRR 150 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~ 150 (247)
...++..+|++.++++ ...|=..|= .....|+|.-.-|..++
T Consensus 19 ~~~~t~~~la~~l~~~-~~~vs~~v~-~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 19 GEELTQSELAERLGIS-KSTVSRIVK-RLEKKGLVERERDPGDR 60 (62)
T ss_dssp TSGEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEE-SSST
T ss_pred CCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEeCCCCCC
Confidence 3359999999999998 788887766 88899999877766543
No 96
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=34.79 E-value=93 Score=25.35 Aligned_cols=52 Identities=13% Similarity=0.302 Sum_probs=41.7
Q ss_pred cchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCcc
Q 025819 87 LVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIV 141 (247)
Q Consensus 87 L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI 141 (247)
+++.+..+| ...|+.|+..++.+++.++...+|++ ...++.++- ++...|-|
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 555553333 25688999999999999999999997 999999999 89877743
No 97
>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=34.42 E-value=2.7e+02 Score=23.10 Aligned_cols=43 Identities=19% Similarity=0.322 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc-------Ccccccc
Q 025819 185 LISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL-------SHKKLHT 227 (247)
Q Consensus 185 l~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~-------~~~~~~~ 227 (247)
+..++..+....++..+-..+++..+.++..+|..+ |-+.+.+
T Consensus 49 Ik~~ea~~e~~k~E~krL~~rkk~~e~~~~~Lk~yL~~~m~~~g~~ki~t 98 (162)
T PF05565_consen 49 IKNLEADIEAIKAEIKRLQERKKSIENRIDRLKEYLLDAMEAAGIKKIKT 98 (162)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCceeec
Confidence 333344444455554555555566666666666665 5555544
No 98
>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=34.33 E-value=64 Score=25.66 Aligned_cols=40 Identities=20% Similarity=0.348 Sum_probs=32.2
Q ss_pred HhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 99 TVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 99 tllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
.|+.||.. .+|-.+|+..|++| ..-+--++= +.+..|+|.
T Consensus 47 ~Il~lC~~--~~SVAEiAA~L~lP-lgVvrVLvs-DL~~~G~v~ 86 (114)
T PF05331_consen 47 AILELCRR--PLSVAEIAARLGLP-LGVVRVLVS-DLADAGLVR 86 (114)
T ss_pred HHHHHHCC--CccHHHHHHhhCCC-chhhhhhHH-HHHhCCCEE
Confidence 47888887 89999999999999 766665655 788888764
No 99
>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=34.32 E-value=59 Score=22.49 Aligned_cols=38 Identities=21% Similarity=0.202 Sum_probs=32.7
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkI 145 (247)
..+..+-.+|++.++++ ...|-..|= .....|+|.-.-
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 45788999999999998 889998877 899999997554
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=33.64 E-value=44 Score=23.66 Aligned_cols=26 Identities=27% Similarity=0.457 Sum_probs=20.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
.+|.-+..+||+.|||+ ..+|..++-
T Consensus 17 lgr~Pt~eEiA~~lgis-~~~v~~~l~ 42 (78)
T PF04539_consen 17 LGREPTDEEIAEELGIS-VEEVRELLQ 42 (78)
T ss_dssp HSS--BHHHHHHHHTS--HHHHHHHHH
T ss_pred hCCCCCHHHHHHHHccc-HHHHHHHHH
Confidence 47889999999999998 999997654
No 101
>PRK10870 transcriptional repressor MprA; Provisional
Probab=33.19 E-value=2.9e+02 Score=23.06 Aligned_cols=50 Identities=14% Similarity=-0.005 Sum_probs=39.0
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEee
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFA 157 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~ 157 (247)
++..++..+|++.++++ ...+=..|= .....|+|.=.-|..+++...-..
T Consensus 68 ~~~~it~~eLa~~l~l~-~~tvsr~v~-rLe~kGlV~R~~~~~DrR~~~v~L 117 (176)
T PRK10870 68 ENHSIQPSELSCALGSS-RTNATRIAD-ELEKRGWIERRESDNDRRCLHLQL 117 (176)
T ss_pred CCCCcCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEEecCCCCCCCeeEEEE
Confidence 45789999999999998 666655544 788899999999988766654443
No 102
>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=33.01 E-value=1.5e+02 Score=28.82 Aligned_cols=87 Identities=11% Similarity=0.211 Sum_probs=61.9
Q ss_pred hHHHHHHcCC----CChHHHHHHHHHHhHhcCccEEEecCC--CCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHH
Q 025819 112 YDELMEELDV----TNVRELEDFLINECMYTGIVRGKLDQL--RRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLL 185 (247)
Q Consensus 112 y~~I~~~L~I----~~~~evE~llI~~aI~~glI~GkIDQ~--~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl 185 (247)
.+++-+.|++ +..+++...++ +|+..|+.----|.. .+.+... +..+..++.+.|.+++..-...-+.+-
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 4455555553 44578888888 999999877777765 3323322 566888899999999988877666777
Q ss_pred HHHHHHHHHHHhhhHHH
Q 025819 186 ISIQEKIKWADSMNEMD 202 (247)
Q Consensus 186 ~~Ie~~i~~a~~~~~~~ 202 (247)
..++.|...|+....+.
T Consensus 417 ~~~~~q~~~a~~~~~~~ 433 (438)
T TIGR02919 417 ELLEQQREHANDISKEQ 433 (438)
T ss_pred HHHHHHHHHhccCCHHH
Confidence 77777888887765543
No 103
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=32.49 E-value=62 Score=21.45 Aligned_cols=50 Identities=18% Similarity=0.245 Sum_probs=35.9
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRC 151 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~ 151 (247)
++........++..+|++.++++ ..-+=.++= .....|+|.=.-|+.+++
T Consensus 8 iL~~l~~~~~~~~~~la~~~~~~-~~~~t~~i~-~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 8 ILRILYENGGITQSELAEKLGIS-RSTVTRIIK-RLEKKGLIERERDPDDRR 57 (59)
T ss_dssp HHHHHHHHSSEEHHHHHHHHTS--HHHHHHHHH-HHHHTTSEEEEEETTETT
T ss_pred HHHHHHHcCCCCHHHHHHHHCCC-hhHHHHHHH-HHHHCCCEEeccCCCCCC
Confidence 33333344559999999999997 667666655 788899999888776653
No 104
>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=32.46 E-value=3.1e+02 Score=23.23 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=29.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEe
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKL 145 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkI 145 (247)
...++..+|++.++|+ ...|=..+= .....|+|.-+-
T Consensus 13 ~~~~t~~eLA~~lgis-~~tV~~~L~-~Le~~GlV~r~~ 49 (203)
T TIGR02702 13 QGQATAAALAEALAIS-PQAVRRHLK-DLETEGLIEYEA 49 (203)
T ss_pred cCCCCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCeEEee
Confidence 3559999999999997 777776666 777889998663
No 105
>PRK03100 sec-independent translocase; Provisional
Probab=31.94 E-value=2.6e+02 Score=23.02 Aligned_cols=34 Identities=15% Similarity=0.143 Sum_probs=30.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (247)
.|+|+.+..+...+..|....+...+.+++++..
T Consensus 20 v~GPkrLP~~~r~lG~~vr~~R~~~~~~~~~~~~ 53 (136)
T PRK03100 20 ILGPERLPGAIRWTARALRQARDYASGATSQLRE 53 (136)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999999999999999999988888887764
No 106
>PF09523 DUF2390: Protein of unknown function (DUF2390); InterPro: IPR012659 Members of this family are bacterial hypothetical proteins, about 160 amino acids in length, found in various proteobacteria, including members of the genera Pseudomonas and Vibrio. The C-terminal region is poorly conserved and is not included in the model.
Probab=30.41 E-value=1.5e+02 Score=23.25 Aligned_cols=42 Identities=19% Similarity=0.332 Sum_probs=36.1
Q ss_pred cCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 025819 158 AGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMN 199 (247)
Q Consensus 158 ~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~ 199 (247)
.++.++++++..+.+.+..|.+.+-.=+..+...++......
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 578889999999999999999998888888888888766554
No 107
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=30.02 E-value=1.4e+02 Score=18.44 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=26.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 109 VLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
.++..+|++.++++ ...+-..+- .....|+|.
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 36788999999997 888888777 788888886
No 108
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=29.88 E-value=50 Score=24.26 Aligned_cols=24 Identities=25% Similarity=0.221 Sum_probs=20.7
Q ss_pred cccChHHHHHHcCCCChHHHHHHHH
Q 025819 108 KVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
...||.+|++.++++ ...|..++-
T Consensus 31 eGlS~kEIAe~LGIS-~~TVk~~l~ 54 (73)
T TIGR03879 31 AGKTASEIAEELGRT-EQTVRNHLK 54 (73)
T ss_pred cCCCHHHHHHHHCcC-HHHHHHHHh
Confidence 678999999999998 888887755
No 109
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=29.82 E-value=84 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.418 Sum_probs=26.1
Q ss_pred cChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecC
Q 025819 110 LPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQ 147 (247)
Q Consensus 110 Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ 147 (247)
||+.++++.++++ +.||. +.+..|+|.-.-..
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 55666 67778999886666
No 110
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=28.53 E-value=1.5e+02 Score=25.17 Aligned_cols=52 Identities=15% Similarity=0.217 Sum_probs=36.5
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEE
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEV 154 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V 154 (247)
++.....+..++..+|++.++++ ..-+-..+- .....|+|.-.-+ ..+.+.+
T Consensus 148 IL~~l~~~g~~s~~eia~~l~is-~stv~r~L~-~Le~~GlI~r~~~-r~~~~~l 199 (203)
T TIGR01884 148 VLEVLKAEGEKSVKNIAKKLGKS-LSTISRHLR-ELEKKGLVEQKGR-KGKRYSL 199 (203)
T ss_pred HHHHHHHcCCcCHHHHHHHHCcC-HHHHHHHHH-HHHHCCCEEEEcC-CccEEEe
Confidence 33333444569999999999997 777877776 7788899885533 4444444
No 111
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=28.49 E-value=4.6e+02 Score=23.90 Aligned_cols=83 Identities=14% Similarity=0.300 Sum_probs=52.9
Q ss_pred hhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHH
Q 025819 100 VLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLT 179 (247)
Q Consensus 100 llsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~ 179 (247)
|.-++.....+.-.+|+++++|+ +..|=+.+= +.+..|+|+- .-++.-+|| ++-.+.|.+.+.+.+.
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 44444556678889999999998 898877777 7887777653 222244444 2223446666666666
Q ss_pred HHHHHHHHHHHHHHHH
Q 025819 180 TSDNLLISIQEKIKWA 195 (247)
Q Consensus 180 ~~~~vl~~Ie~~i~~a 195 (247)
-++.+...+.....|.
T Consensus 83 f~~ev~~~l~~~~vw~ 98 (260)
T COG1497 83 FSEEVELVLDYVMVWT 98 (260)
T ss_pred HHHHHHHHHhhHHHHH
Confidence 6666555555555554
No 112
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.85 E-value=1.6e+02 Score=23.16 Aligned_cols=43 Identities=16% Similarity=0.180 Sum_probs=27.3
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE-EecCCCCEEEEEeecCCCCCCCcHH
Q 025819 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG-KLDQLRRCFEVQFAAGRDLRPGQLG 168 (247)
Q Consensus 111 sy~~I~~~L~I~~~~evE~llI~~aI~~glI~G-kIDQ~~~~v~V~~~~~Rdl~~~q~~ 168 (247)
+..++++.+||+ .+.+=.| +- .|||.. +-+.. -.|.++.+++.
T Consensus 2 ~IgevA~~~gvs-~~tLRyY---e~--~GLl~p~~r~~~---------gyR~Y~~~~l~ 45 (127)
T cd04784 2 KIGELAKKTGCS-VETIRYY---EK--EGLLPAPARSAN---------NYRLYDEEHLE 45 (127)
T ss_pred CHHHHHHHHCcC-HHHHHHH---HH--CCCCCCCCcCCC---------CCeecCHHHHH
Confidence 568899999997 8887766 22 477752 33332 24556666654
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=27.84 E-value=1.2e+02 Score=20.28 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=28.5
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
...++..+|++.++++ ...|...+= .....|+|.-
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 7777888863
No 114
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=27.63 E-value=2.3e+02 Score=26.29 Aligned_cols=81 Identities=12% Similarity=0.258 Sum_probs=54.9
Q ss_pred HHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCc--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Q 025819 130 FLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQ--LGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRK 207 (247)
Q Consensus 130 llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q--~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~ 207 (247)
+++ -++.+|+.-|=.-=.+ .|+.||-|++.+ .......|+.=-.+++..+..|...+..+....... ++
T Consensus 87 ~vm-Avi~aGi~y~~y~~~K-----~YV~P~~l~~~~~k~e~~k~~Ld~~~~~~~~~~~~l~~~va~v~q~~~~q---q~ 157 (300)
T KOG2629|consen 87 FVM-AVILAGIAYAAYRFVK-----SYVLPRFLGESKDKLEADKRQLDDQFDKAAKSLNALMDEVAQVSQLLATQ---QS 157 (300)
T ss_pred HHH-HHHHhhHHHHHHHHHH-----HHHHHHhhCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HH
Confidence 444 7888886554322111 377888887665 578899999999999999999998888877654333 33
Q ss_pred HHHHHHHHHHhh
Q 025819 208 DLEEKVEEAKKS 219 (247)
Q Consensus 208 ~~~~~~~~~k~~ 219 (247)
++...+..++.+
T Consensus 158 Els~~L~~l~~~ 169 (300)
T KOG2629|consen 158 ELSRALASLKNT 169 (300)
T ss_pred HHHHHHHHHHHH
Confidence 555555555544
No 115
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=27.10 E-value=3e+02 Score=21.53 Aligned_cols=27 Identities=19% Similarity=0.334 Sum_probs=19.4
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEE
Q 025819 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRG 143 (247)
Q Consensus 111 sy~~I~~~L~I~~~~evE~llI~~aI~~glI~G 143 (247)
+..++++.+||+ .+.+=.| - + .|+|..
T Consensus 1 ~I~e~a~~~gvs-~~tlR~Y-e-~---~GLl~~ 27 (124)
T TIGR02051 1 TIGELAKAAGVN-VETIRYY-E-R---KGLLPE 27 (124)
T ss_pred CHHHHHHHHCcC-HHHHHHH-H-H---CCCCCC
Confidence 357899999997 8888666 2 2 577763
No 116
>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=26.18 E-value=2.6e+02 Score=20.57 Aligned_cols=45 Identities=11% Similarity=0.223 Sum_probs=27.8
Q ss_pred EEEEeecCCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 152 FEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWAD 196 (247)
Q Consensus 152 v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~ 196 (247)
-.|-...|+.|=....+.+...|..=...++.-+..++.+.....
T Consensus 45 ~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~ 89 (106)
T PF01920_consen 45 RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLE 89 (106)
T ss_dssp -EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334456788877777777777766666666665555555544444
No 117
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=25.93 E-value=3.6e+02 Score=21.83 Aligned_cols=53 Identities=15% Similarity=0.248 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 168 GSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 168 ~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
..+-..|++-.+.+...-..+.++|..++....+...-.+.+.++|.+++..+
T Consensus 46 ~~v~kql~~vs~~l~~tKkhLsqRId~vd~klDe~~ei~~~i~~eV~~v~~dv 98 (126)
T PF07889_consen 46 ASVSKQLEQVSESLSSTKKHLSQRIDRVDDKLDEQKEISKQIKDEVTEVREDV 98 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHhhH
Confidence 34555666666666666677777777777776777777777777777777665
No 118
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=25.72 E-value=1e+02 Score=27.23 Aligned_cols=46 Identities=22% Similarity=0.265 Sum_probs=34.2
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
-|+..|+.+...++.++.++|++.|+++ ..-+...+- +.-..|+|.
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 3666677777788899999999999997 777777665 444445443
No 119
>PRK00182 tatB sec-independent translocase; Provisional
Probab=25.63 E-value=2.4e+02 Score=23.85 Aligned_cols=34 Identities=12% Similarity=0.228 Sum_probs=28.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKW 194 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~ 194 (247)
.|+|+.+..+...+..|........+...+++..
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 120
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=24.50 E-value=83 Score=25.93 Aligned_cols=28 Identities=25% Similarity=0.343 Sum_probs=24.2
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECM 136 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI 136 (247)
...+||.+|++.++|+ +..|...+- .|.
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 4569999999999998 999998877 765
No 121
>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=24.30 E-value=66 Score=24.41 Aligned_cols=36 Identities=19% Similarity=0.333 Sum_probs=26.9
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEE
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGK 144 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~Gk 144 (247)
.++++-++|++.++++ ..+|-.++- .....|+|..+
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 4679999999999998 999999988 89999999655
No 122
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=24.18 E-value=3e+02 Score=25.58 Aligned_cols=22 Identities=32% Similarity=0.493 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHhhcCcc
Q 025819 202 DKKHRKDLEEKVEEAKKSLSHK 223 (247)
Q Consensus 202 ~~~~~~~~~~~~~~~k~~~~~~ 223 (247)
.+++-+++.+.|+.+|.+++++
T Consensus 122 ARkEIkQLkQvieTmrssL~ek 143 (305)
T PF15290_consen 122 ARKEIKQLKQVIETMRSSLAEK 143 (305)
T ss_pred HHHHHHHHHHHHHHHHhhhchh
Confidence 4566677888899999999776
No 123
>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=23.95 E-value=1.1e+02 Score=22.74 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=24.0
Q ss_pred HHhhhcccCCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 98 LTVLTLAETNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 98 LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
..|+.+-..++.+|-++|+.+++.+ +++|...+=
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 3466666679999999999999998 999987654
No 124
>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=23.31 E-value=2.2e+02 Score=18.56 Aligned_cols=47 Identities=28% Similarity=0.338 Sum_probs=32.4
Q ss_pred HHHHHHhhhcccCCcccC-hHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 94 KLKQLTVLTLAETNKVLP-YDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 94 KLr~LtllsLa~~~k~Is-y~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
.++..-+......+..++ -.+|++.++++ ...|-..+- ..-..|+|.
T Consensus 9 ~i~~~i~~~~~~~~~~~~~~~~la~~~~is-~~~v~~~l~-~L~~~G~i~ 56 (66)
T cd07377 9 QLREAILSGELKPGDRLPSERELAEELGVS-RTTVREALR-ELEAEGLVE 56 (66)
T ss_pred HHHHHHHcCCCCCCCCCCCHHHHHHHHCCC-HHHHHHHHH-HHHHCCCEE
Confidence 344433333233444555 99999999997 888888877 788888875
No 125
>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=23.00 E-value=3.9e+02 Score=21.24 Aligned_cols=56 Identities=16% Similarity=0.195 Sum_probs=28.3
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 165 ~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
+.+....+.+..+...++--+.-.......-..+.+.......+++..++.+|+.+
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 45555555555555555554444443333223333444445555666666655554
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=22.94 E-value=1.1e+02 Score=27.80 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=35.5
Q ss_pred CCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCC
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQL 148 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~ 148 (247)
..+.++.+++++..++| .+=+-..++ +....++|+|++|..
T Consensus 127 e~G~vsi~eLa~~~~Lp-~efl~~~li-~~~lg~~I~g~~d~~ 167 (272)
T PF09743_consen 127 ESGQVSISELAKQYDLP-SEFLKEELI-SKRLGKIIKGRLDGD 167 (272)
T ss_pred HcCeEeHHHHHHhcCCc-HHHHHHHHh-hhhcCcceeEEEeCC
Confidence 56899999999999999 676766778 777788999999998
No 127
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=22.93 E-value=2.5e+02 Score=24.11 Aligned_cols=79 Identities=13% Similarity=0.172 Sum_probs=48.6
Q ss_pred HHHHHHHHHhcCChhhHhhh--h-CCCCCcchHHHHHHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHh
Q 025819 61 KYLDMLRLFAHGTWSDYKNN--A-GHLPQLVPDQVLKLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMY 137 (247)
Q Consensus 61 ~~~~LL~iFa~Gt~~dy~~~--~-~~l~~L~~~~~~KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~ 137 (247)
.+-.+..++.+......... . ...+.|++.|.+=|+.--=+..-..-|.++-.+||++|||+ ...+.+-|= +|.
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 44455555555554433222 1 22346899886666655555555567999999999999997 666666554 454
Q ss_pred cCccE
Q 025819 138 TGIVR 142 (247)
Q Consensus 138 ~glI~ 142 (247)
.+|+.
T Consensus 204 ~Kl~~ 208 (215)
T COG3413 204 RKLIE 208 (215)
T ss_pred HHHHH
Confidence 34443
No 128
>PRK03887 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=22.86 E-value=2.9e+02 Score=23.74 Aligned_cols=66 Identities=20% Similarity=0.270 Sum_probs=39.7
Q ss_pred chHHHHHHHHHhcCChhhHhhhhC-CCCCcchHHHHHHHHHH-hhhcccCCcccChHHHHHHcCCCChHHHH
Q 025819 59 NSKYLDMLRLFAHGTWSDYKNNAG-HLPQLVPDQVLKLKQLT-VLTLAETNKVLPYDELMEELDVTNVRELE 128 (247)
Q Consensus 59 ~~~~~~LL~iFa~Gt~~dy~~~~~-~l~~L~~~~~~KLr~Lt-llsLa~~~k~Isy~~I~~~L~I~~~~evE 128 (247)
++.+-+++.-+..|...++..... .+..+++-+ -+... ++.-+..+++.||.+||+.++.+ .+.|=
T Consensus 61 ~~~~~~~l~~~l~g~~~~~~~~~~l~~~g~T~Fq---~rV~~~Lv~~IP~G~v~TYgqIA~~~G~a-aRAVG 128 (175)
T PRK03887 61 PSDYPELVFKVLIGKISNEEGLEELSFEGLTPFE---RKVYEWLTKNVKRGEVITYGELAKALNTS-PRAVG 128 (175)
T ss_pred ChhHHHHHHHHHcCCccccccCcccCcCCCCHHH---HHHHHHHHHhCCCCCCCcHHHHHHHHCch-HHHHH
Confidence 445667777777787777632111 112223433 22223 34445678999999999999974 66543
No 129
>COG1191 FliA DNA-directed RNA polymerase specialized sigma subunit [Transcription]
Probab=22.62 E-value=3.5e+02 Score=24.31 Aligned_cols=113 Identities=16% Similarity=0.285 Sum_probs=55.9
Q ss_pred hHHHHHHHhccCccHHHHHHHHHHHhcCCCcccchhhhcCchhhhccC----C-Cc-hHHHHHHHHHhcCChhhHhhhhC
Q 025819 9 ELIDHFVKQASNQKGAALGSVIVEATSQPSLFAFSEILAVPNIAEFEG----T-EN-SKYLDMLRLFAHGTWSDYKNNAG 82 (247)
Q Consensus 9 ~~l~~f~~lak~~~~~~a~~lI~~AL~~p~vf~F~eLL~lp~v~~L~~----~-~~-~~~~~LL~iFa~Gt~~dy~~~~~ 82 (247)
..+++|+-|.+ ..|.++... .|. .+.+|.+.=.|--++. + .. .....--...-.|-+-||....+
T Consensus 27 ~Li~~ylpLV~----~ia~k~~~r---~~~--~~dDLiqiG~iGLi~Aieryd~~kg~kF~tyA~~~I~Gei~d~LR~~~ 97 (247)
T COG1191 27 RLIERYLPLVK----SIARKFENR---GPS--EYDDLIQIGMIGLIKAIERYDPSKGTKFSTYAVRRIRGEILDYLRKND 97 (247)
T ss_pred HHHHHHHHHHH----HHHHHHHhc---CCC--chhHHHHHHHHHHHHHHHHcCcccCcchHHHHHHHHHHHHHHHHHhCC
Confidence 57777777765 344444333 343 6677776555433221 0 01 11111111223455666665444
Q ss_pred --CCCCcchHHHHHHHHHHhhhcc-cCCcccChHHHHHHcCCCChHHHHHHHH
Q 025819 83 --HLPQLVPDQVLKLKQLTVLTLA-ETNKVLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 83 --~l~~L~~~~~~KLr~LtllsLa-~~~k~Isy~~I~~~L~I~~~~evE~llI 132 (247)
.+|--.-...+++.. .+=.|. +-++.-+-.+|++.|+|+ ..++=.++.
T Consensus 98 ~v~vpR~~~~~~~~i~~-~~~~l~~el~r~pt~~EIA~~L~i~-~ee~~~~~~ 148 (247)
T COG1191 98 SVKVPRSLRELGRRIEE-AIDELEQELGREPTDEEIAEELGID-KEEYIEALL 148 (247)
T ss_pred CccCcHHHHHHHHHHHH-HHHHHHHHhCCCCcHHHHHHHhCCC-HHHHHHHHH
Confidence 344211111111111 111222 256889999999999998 777655544
No 130
>PF15397 DUF4618: Domain of unknown function (DUF4618)
Probab=22.44 E-value=2.5e+02 Score=25.52 Aligned_cols=40 Identities=18% Similarity=0.279 Sum_probs=33.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHH
Q 025819 164 PGQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDK 203 (247)
Q Consensus 164 ~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~ 203 (247)
..++..+...|..|.++.+.=++.++.++..+++......
T Consensus 62 ~~~l~~ak~eLqe~eek~e~~l~~Lq~ql~~l~akI~k~~ 101 (258)
T PF15397_consen 62 HKQLQQAKAELQEWEEKEESKLSKLQQQLEQLDAKIQKTQ 101 (258)
T ss_pred hHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3568889999999999999999999999998887755443
No 131
>PHA02943 hypothetical protein; Provisional
Probab=22.42 E-value=1.8e+02 Score=24.58 Aligned_cols=44 Identities=16% Similarity=0.221 Sum_probs=31.4
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 96 r~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
|...|+.+. ..++-+-++|++.||++ ..+++..+- -.-..|.|+
T Consensus 12 R~~eILE~L-k~G~~TtseIAkaLGlS-~~qa~~~Ly-vLErEG~Vk 55 (165)
T PHA02943 12 RMIKTLRLL-ADGCKTTSRIANKLGVS-HSMARNALY-QLAKEGMVL 55 (165)
T ss_pred HHHHHHHHH-hcCCccHHHHHHHHCCC-HHHHHHHHH-HHHHcCceE
Confidence 334444444 77888999999999997 899997665 455555544
No 132
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.25 E-value=3.7e+02 Score=20.65 Aligned_cols=44 Identities=23% Similarity=0.297 Sum_probs=28.7
Q ss_pred ChHHHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHH
Q 025819 111 PYDELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGS 169 (247)
Q Consensus 111 sy~~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~ 169 (247)
+..++++.+||+ .+.+-.|- + .|||...-+. .-.|.+++.++..
T Consensus 2 ~i~eva~~~gvs-~~tlR~Ye--~---~GLl~p~r~~---------~g~R~Y~~~~~~~ 45 (112)
T cd01282 2 RIGELAARTGVS-VRSLRYYE--E---QGLLVPERSA---------NGYRDYDEAAVDR 45 (112)
T ss_pred CHHHHHHHHCCC-HHHHHHHH--H---CCCCCCCcCC---------CCCeecCHHHHHH
Confidence 567899999998 88888772 2 4887642221 2356666666543
No 133
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=22.23 E-value=1e+02 Score=21.78 Aligned_cols=34 Identities=21% Similarity=0.271 Sum_probs=27.6
Q ss_pred CcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 107 NKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 107 ~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
+..++=.+||++|+++ ...+-.++- ..-..|.|+
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 6678889999999997 899999988 888777664
No 134
>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=22.02 E-value=99 Score=21.83 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=20.1
Q ss_pred CCcccChHHHHHHcCCCChHHHHHH
Q 025819 106 TNKVLPYDELMEELDVTNVRELEDF 130 (247)
Q Consensus 106 ~~k~Isy~~I~~~L~I~~~~evE~l 130 (247)
.++.+++-+||+.|+|+ ...|-.|
T Consensus 19 ~~g~i~lkdIA~~Lgvs-~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVS-ESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCC-HHHHHHH
Confidence 46789999999999998 7777665
No 135
>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=21.76 E-value=4e+02 Score=22.53 Aligned_cols=55 Identities=9% Similarity=0.207 Sum_probs=41.2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 166 QLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 166 q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
....+...|..|+..+..=...+......+.....-....-.+++.++++.+..|
T Consensus 125 ~~~~~i~~L~~f~~~l~~D~~~l~~~~~~l~~~l~~~~g~I~~L~~~I~~~~~~I 179 (184)
T PF05791_consen 125 KVQALINELNDFKDKLQKDSRNLKTDVDELQSILAGENGDIPQLQKQIENLNEEI 179 (184)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--HHHHHHHHHHHTGGG
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhcccCCHHHHHHHHHHHHHHH
Confidence 4566888888888888888888888887777776666677777778888777766
No 136
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=21.66 E-value=1e+02 Score=25.03 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=22.9
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025819 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (247)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~aI 136 (247)
...||.+|++.||++ +..|...+- .|.
T Consensus 149 ~g~s~~EIA~~lgis-~~tVk~~l~-Rar 175 (183)
T TIGR02999 149 AGLTVEEIAELLGVS-VRTVERDWR-FAR 175 (183)
T ss_pred cCCCHHHHHHHhCCC-HHHHHHHHH-HHH
Confidence 568999999999998 999988776 654
No 137
>PRK14857 tatA twin arginine translocase protein A; Provisional
Probab=21.64 E-value=2.4e+02 Score=21.49 Aligned_cols=35 Identities=17% Similarity=0.179 Sum_probs=28.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIKWA 195 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a 195 (247)
.|+|+.+..+...+..|....+...+.+++.+...
T Consensus 21 vfGP~KLP~lar~lGk~i~~fkk~~~~~~~e~~~~ 55 (90)
T PRK14857 21 VFGPKKLPEIGRSLGKTLKGFQEASKEFENEIKRE 55 (90)
T ss_pred HcCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999998888777766554443
No 138
>PRK14861 tatA twin arginine translocase protein A; Provisional
Probab=21.60 E-value=2.2e+02 Score=20.10 Aligned_cols=33 Identities=12% Similarity=0.069 Sum_probs=25.0
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 161 DLRPGQLGSMIQTLSNWLTTSDNLLISIQEKIK 193 (247)
Q Consensus 161 dl~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~ 193 (247)
.|+|+.++.+...+..|....++..+.+++...
T Consensus 20 vfGp~kLP~l~r~~G~~~~~fk~~~~~~~~~~~ 52 (61)
T PRK14861 20 IFGPKKLPELGKALGKTLREFKKATKELTDDDF 52 (61)
T ss_pred hcCchHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 478889999999999888777776666555444
No 139
>PF09218 DUF1959: Domain of unknown function (DUF1959); InterPro: IPR012056 [NiFe] hydrogenases function in H2 metabolism in a variety of microorganisms, enabling them to use H2 as a source of reducing equivalent under aerobic and anaerobic conditions [NiFe] hydrogenases consist of two subunits, hydrogenase large and hydrogenase small. The large subunit contains the binuclear [NiFe] active site, while the small subunit binds at least one [4Fe-4S] cluster []. Energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type) form a distinct group within the [NiFe] hydrogenase family [, ]. Members of this subgroup include: Hydrogenase 3 and 4 (Hyc and Hyf) from Escherichia coli CO-induced hydrogenase (Coo) from Rhodospirillum rubrum Mbh hydrogenase from Pyrococcus furiosus Eha and Ehb hydrogenases from Methanothermobacter species Ech hydrogenase from Methanosarcina barkeri Energy-converting [NiFe] hydrogenases are membrane-bound enzymes with a six-subunit core: the large and small hydrogenase subunits, plus two hydrophilic proteins and two integral membrane proteins. Their large and small subunits show little sequence similarity to other [NiFe] hydrogenases, except for key conserved residues coordinating the active site and [FeS] cluster. However, they show considerable sequence similarity to the six-subunit, energy-conserving NADH:quinone oxidoreductases (complex I), which are present in cytoplasmic membranes of many bacteria and in inner mitochondrial membranes. However, the reactions they catalyse differ significantly from complex I. Energy-converting [NiFe] hydrogenases function as ion pumps. Eha and Ehb hydrogenases contain extra subunits in addition to those shared by other energy-converting [NiFe] hydrogenases (or [NiFe]-hydrogenase-3-type). Eha contains a 6[4Fe-4S] polyferredoxin, a 10[4F-4S] polyferredoxin, ten other predicted integral membrane proteins (EhaA IPR011306 from INTERPRO, EhaB IPR011314 from INTERPRO, EhaC IPR011316 from INTERPRO, EhaD IPR011308 from INTERPRO, EhaE IPR011317 from INTERPRO, EhaF IPR011313 from INTERPRO, EhaG IPR011311 from INTERPRO, EhaI IPR011318 from INTERPRO, EhaK IPR011319 from INTERPRO, EhaL IPR011305 from INTERPRO) and four hydrophobic subunits (EhaM, EhaR IPR014502 from INTERPRO, EhS, EhT) []. The ten predicted integral membrane proteins are absent from Ech, Coo, Hyc and Hyf complexes, which may have simpler membrane components than Eha. Eha and Ehb catalyse the reduction of low-potential redox carriers (e.g. ferredoxins or polyferredoxins), which then might function as electron donors to oxidoreductases. This entry represents proteins that are predicted to be the hydrophilic EhaM subunits of Eha-type energy-converting [NiFe] hydrogenase complexes.; PDB: 1NXH_B.
Probab=21.23 E-value=54 Score=26.33 Aligned_cols=42 Identities=21% Similarity=0.252 Sum_probs=31.7
Q ss_pred HHHHHcCCCChHHHHHHHHHHhHhcCccEEEecCCCCEEEEEeecCCCCCCCcHHHHHHHHHHHHHHHHH
Q 025819 114 ELMEELDVTNVRELEDFLINECMYTGIVRGKLDQLRRCFEVQFAAGRDLRPGQLGSMIQTLSNWLTTSDN 183 (247)
Q Consensus 114 ~I~~~L~I~~~~evE~llI~~aI~~glI~GkIDQ~~~~v~V~~~~~Rdl~~~q~~~l~~~L~~W~~~~~~ 183 (247)
.|+++|+|+ .+++++.+| +.. +...+.+|..+.++|+-.|-.
T Consensus 18 plSk~lgi~-~ee~~~ili-~~~--------------------------DmssLe~lhar~E~Ak~~cl~ 59 (117)
T PF09218_consen 18 PLSKELGIS-IEEFIDILI-EKL--------------------------DMSSLENLHARYEQAKMGCLG 59 (117)
T ss_dssp TTTTTGGGT-HHHHHHHHH-HHS---------------------------HHHHHHHHHHHHTTHHHHHH
T ss_pred HHHHHhCcC-HHHHHHHHH-Hhc--------------------------ChHHHHhccHHHHHHhhhhhh
Confidence 367889998 999999999 642 234577888899999876643
No 140
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=21.05 E-value=3e+02 Score=19.16 Aligned_cols=31 Identities=19% Similarity=0.325 Sum_probs=12.1
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHHHHHHHhh
Q 025819 189 QEKIKWADSMNEMDKKHRKDLEEKVEEAKKS 219 (247)
Q Consensus 189 e~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~ 219 (247)
++.+........--++.-+++.+.++.++++
T Consensus 6 En~~~~~~~~i~tvk~en~~i~~~ve~i~en 36 (55)
T PF05377_consen 6 ENELPRIESSINTVKKENEEISESVEKIEEN 36 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333334444444444443
No 141
>KOG3809 consensus Microtubule-binding protein MIP-T3 [Cytoskeleton]
Probab=21.04 E-value=2.4e+02 Score=27.88 Aligned_cols=30 Identities=13% Similarity=0.254 Sum_probs=21.0
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025819 162 LRPGQLGSMIQTLSNWLTTSDNLLISIQEK 191 (247)
Q Consensus 162 l~~~q~~~l~~~L~~W~~~~~~vl~~Ie~~ 191 (247)
+-+++++.|..-|..|.+.-..--..+++.
T Consensus 504 ~i~eD~daMq~EL~mWrse~rq~~~elq~e 533 (583)
T KOG3809|consen 504 FINEDIDAMQKELEMWRSEQRQNEQELQNE 533 (583)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHhHHHHHhh
Confidence 446789999999999987655544444443
No 142
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=20.97 E-value=1.1e+02 Score=19.38 Aligned_cols=23 Identities=13% Similarity=0.196 Sum_probs=19.8
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025819 109 VLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI 132 (247)
..++.+|++.++++ ...|+.++=
T Consensus 15 ~~s~~eia~~l~~s-~~tv~~~~~ 37 (57)
T cd06170 15 GKTNKEIADILGIS-EKTVKTHLR 37 (57)
T ss_pred CCCHHHHHHHHCCC-HHHHHHHHH
Confidence 36999999999997 899888755
No 143
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=20.89 E-value=1.3e+02 Score=26.96 Aligned_cols=47 Identities=11% Similarity=0.085 Sum_probs=34.1
Q ss_pred HHHHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 94 KLKQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 94 KLr~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
.-|+..|+.+....+.++..+|++.|+++ ..-+-.=+. ..-..|++.
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS-~~TIRRDL~-~Le~~G~l~ 62 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVS-TVTIRNDLA-FLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCC-HHHHHHHHH-HHHhCCCeE
Confidence 45788888888888889999999999997 555543333 333456665
No 144
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=20.84 E-value=1.1e+02 Score=25.24 Aligned_cols=27 Identities=7% Similarity=0.208 Sum_probs=23.4
Q ss_pred cccChHHHHHHcCCCChHHHHHHHHHHhH
Q 025819 108 KVLPYDELMEELDVTNVRELEDFLINECM 136 (247)
Q Consensus 108 k~Isy~~I~~~L~I~~~~evE~llI~~aI 136 (247)
...||++|++.+|++ +..|...+- .|.
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 458999999999998 999998877 665
No 145
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=20.80 E-value=1.8e+02 Score=25.57 Aligned_cols=45 Identities=18% Similarity=0.208 Sum_probs=31.0
Q ss_pred HHHHhhhcccCCcccChHHHHHHcCCCChHHHHHHHHHHhHhcCccE
Q 025819 96 KQLTVLTLAETNKVLPYDELMEELDVTNVRELEDFLINECMYTGIVR 142 (247)
Q Consensus 96 r~LtllsLa~~~k~Isy~~I~~~L~I~~~~evE~llI~~aI~~glI~ 142 (247)
|-+.|+.+....+.++.++|++.+++| ...+=.++= .....|++.
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 334455443444578999999999998 777777666 666677664
No 146
>KOG0971 consensus Microtubule-associated protein dynactin DCTN1/Glued [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=20.76 E-value=3e+02 Score=29.79 Aligned_cols=50 Identities=10% Similarity=0.242 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 171 IQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 171 ~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
...+..|++++-.-...++.++.++..++.+...-+.+...+.+++-.++
T Consensus 264 leqlqEfkSkim~qqa~Lqrel~raR~e~keaqe~ke~~k~emad~ad~i 313 (1243)
T KOG0971|consen 264 LEQLQEFKSKIMEQQADLQRELKRARKEAKEAQEAKERYKEEMADTADAI 313 (1243)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56788999999999999999998888887777666665555544444433
No 147
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=20.54 E-value=1.3e+02 Score=26.67 Aligned_cols=32 Identities=19% Similarity=0.249 Sum_probs=26.7
Q ss_pred HHHHHhhhcccCCcccChHHHHHHcCCCChHHH
Q 025819 95 LKQLTVLTLAETNKVLPYDELMEELDVTNVREL 127 (247)
Q Consensus 95 Lr~LtllsLa~~~k~Isy~~I~~~L~I~~~~ev 127 (247)
=|+..|+.+...++.++..+|++.++++ ..-+
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 3777788888888999999999999997 5443
No 148
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=20.42 E-value=3.7e+02 Score=23.09 Aligned_cols=45 Identities=27% Similarity=0.343 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhc
Q 025819 176 NWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKVEEAKKSL 220 (247)
Q Consensus 176 ~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~~~~k~~~ 220 (247)
.|....+.....++..+..-....++..+.+++++.+++++++.+
T Consensus 125 ~~~~~~~~~~~~~~~G~~~r~~~i~~a~~~~~e~~~~l~~l~~ei 169 (176)
T PF12999_consen 125 EYREELEEEEEIYKEGLKIRQELIEEAKKKREELEKKLEELEKEI 169 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444444444455555566666555554
No 149
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=20.31 E-value=1.1e+02 Score=21.20 Aligned_cols=23 Identities=22% Similarity=0.172 Sum_probs=19.5
Q ss_pred ccChHHHHHHcCCCChHHHHHHHH
Q 025819 109 VLPYDELMEELDVTNVRELEDFLI 132 (247)
Q Consensus 109 ~Isy~~I~~~L~I~~~~evE~llI 132 (247)
-.++.+||+.|+++ ..-|-.|.=
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 150
>PRK15396 murein lipoprotein; Provisional
Probab=20.15 E-value=3.7e+02 Score=19.92 Aligned_cols=49 Identities=6% Similarity=0.128 Sum_probs=31.9
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHH
Q 025819 165 GQLGSMIQTLSNWLTTSDNLLISIQEKIKWADSMNEMDKKHRKDLEEKV 213 (247)
Q Consensus 165 ~q~~~l~~~L~~W~~~~~~vl~~Ie~~i~~a~~~~~~~~~~~~~~~~~~ 213 (247)
.+++.|...++.-..+++.+...+......+...+++..+.-+++...+
T Consensus 25 ~kvd~LssqV~~L~~kvdql~~dv~~~~~~~~~a~~eA~raN~RlDn~~ 73 (78)
T PRK15396 25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSDVQAAKDDAARANQRLDNQA 73 (78)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677777777777777777777777666666665555555544444443
Done!