Query 043780
Match_columns 386
No_of_seqs 209 out of 664
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 08:17:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043780.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043780hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2908 26S proteasome regulat 100.0 7E-101 1E-105 732.9 39.5 378 1-385 2-380 (380)
2 KOG2753 Uncharacterized conser 100.0 6.8E-41 1.5E-45 319.3 26.5 296 56-378 63-374 (378)
3 KOG3250 COP9 signalosome, subu 99.9 3.7E-26 8E-31 206.7 11.5 168 200-381 24-192 (258)
4 PF01399 PCI: PCI domain; Int 99.7 4.3E-16 9.4E-21 127.6 12.9 105 236-344 1-105 (105)
5 smart00753 PAM PCI/PINT associ 99.5 3.2E-14 6.9E-19 114.0 9.2 86 274-365 3-88 (88)
6 smart00088 PINT motif in prote 99.5 3.2E-14 6.9E-19 114.0 9.2 86 274-365 3-88 (88)
7 KOG2581 26S proteasome regulat 99.3 9.8E-10 2.1E-14 108.9 22.0 211 111-341 204-420 (493)
8 KOG1464 COP9 signalosome, subu 99.3 3.9E-10 8.5E-15 107.1 18.3 245 118-379 147-438 (440)
9 KOG1497 COP9 signalosome, subu 98.5 1.7E-05 3.6E-10 77.2 20.3 248 111-383 139-394 (399)
10 KOG0687 26S proteasome regulat 98.3 0.0031 6.7E-08 61.9 29.9 291 31-344 63-362 (393)
11 KOG1463 26S proteasome regulat 98.2 0.0001 2.2E-09 72.4 17.1 251 86-346 141-392 (411)
12 KOG1498 26S proteasome regulat 98.1 0.0053 1.1E-07 61.6 27.7 282 71-381 129-425 (439)
13 COG5600 Transcription-associat 98.1 0.00086 1.9E-08 66.8 21.0 218 113-348 174-407 (413)
14 KOG0686 COP9 signalosome, subu 98.0 0.00037 8E-09 70.0 16.7 223 128-361 199-427 (466)
15 KOG2688 Transcription-associat 97.9 0.00013 2.8E-09 73.5 12.7 220 111-347 158-387 (394)
16 COG5187 RPN7 26S proteasome re 97.6 0.032 7E-07 54.3 22.0 242 88-344 130-376 (412)
17 COG5159 RPN6 26S proteasome re 97.4 0.016 3.5E-07 56.3 18.3 249 88-346 140-390 (421)
18 KOG2582 COP9 signalosome, subu 97.3 0.21 4.4E-06 50.1 24.4 331 3-356 5-372 (422)
19 KOG2072 Translation initiation 96.3 0.4 8.8E-06 52.3 19.1 241 132-378 248-537 (988)
20 COG5071 RPN5 26S proteasome re 95.8 0.71 1.5E-05 45.4 16.8 87 276-381 339-425 (439)
21 KOG2758 Translation initiation 95.6 0.073 1.6E-06 52.5 9.3 126 245-379 299-424 (432)
22 KOG1076 Translation initiation 95.1 0.12 2.7E-06 55.4 9.7 131 218-348 634-767 (843)
23 PF14938 SNAP: Soluble NSF att 94.1 1.1 2.3E-05 43.4 13.2 173 81-261 83-261 (282)
24 PF10075 PCI_Csn8: COP9 signal 91.9 1.7 3.7E-05 37.7 9.8 80 233-323 39-121 (143)
25 COG3355 Predicted transcriptio 88.8 9.4 0.0002 32.9 11.4 80 297-380 40-122 (126)
26 PF09012 FeoC: FeoC like trans 88.1 0.83 1.8E-05 34.7 4.1 39 297-335 12-50 (69)
27 PF09756 DDRGK: DDRGK domain; 87.7 1.3 2.8E-05 40.7 5.9 58 282-343 100-157 (188)
28 TIGR02010 IscR iron-sulfur clu 82.5 5.1 0.00011 34.4 6.9 51 279-331 7-57 (135)
29 PF02082 Rrf2: Transcriptional 82.1 5.8 0.00013 31.0 6.5 61 281-344 9-69 (83)
30 PRK11179 DNA-binding transcrip 81.1 4 8.7E-05 35.8 5.9 35 297-331 21-55 (153)
31 COG1522 Lrp Transcriptional re 79.5 4.7 0.0001 34.9 5.7 36 297-332 20-55 (154)
32 PF13412 HTH_24: Winged helix- 79.3 6.9 0.00015 27.1 5.5 34 297-330 15-48 (48)
33 PF09976 TPR_21: Tetratricopep 78.5 41 0.00089 28.7 15.2 126 18-177 12-137 (145)
34 PF09339 HTH_IclR: IclR helix- 78.5 4.8 0.0001 28.6 4.5 46 282-330 4-49 (52)
35 PF01022 HTH_5: Bacterial regu 78.4 6.2 0.00013 27.4 5.0 34 297-330 13-46 (47)
36 smart00344 HTH_ASNC helix_turn 77.8 8.3 0.00018 31.3 6.4 34 298-331 16-49 (108)
37 PRK10857 DNA-binding transcrip 77.5 8.1 0.00018 34.6 6.7 52 279-332 7-58 (164)
38 PF12840 HTH_20: Helix-turn-he 74.0 15 0.00032 26.9 6.3 46 280-332 12-57 (61)
39 PRK11169 leucine-responsive tr 73.9 20 0.00044 31.7 8.3 36 296-331 25-60 (164)
40 PF08281 Sigma70_r4_2: Sigma-7 73.1 4.6 0.0001 28.6 3.3 28 298-325 25-52 (54)
41 PF09295 ChAPs: ChAPs (Chs5p-A 72.3 77 0.0017 32.5 13.1 129 34-191 169-297 (395)
42 KOG1126 DNA-binding cell divis 71.8 12 0.00026 40.3 7.3 90 69-175 517-608 (638)
43 KOG3682 Predicted membrane pro 71.0 67 0.0015 35.2 12.4 123 53-188 562-684 (930)
44 PF04545 Sigma70_r4: Sigma-70, 70.9 11 0.00024 26.3 4.8 28 298-325 19-46 (50)
45 PRK04214 rbn ribonuclease BN/u 70.1 21 0.00046 36.6 8.5 80 296-382 307-395 (412)
46 smart00346 HTH_ICLR helix_turn 69.6 16 0.00035 28.4 6.0 48 282-332 6-53 (91)
47 smart00347 HTH_MARR helix_turn 68.8 52 0.0011 25.4 9.4 71 298-373 23-93 (101)
48 TIGR00738 rrf2_super rrf2 fami 68.7 20 0.00042 30.2 6.8 50 281-332 9-58 (132)
49 PF03399 SAC3_GANP: SAC3/GANP/ 68.5 46 0.00099 30.0 9.6 66 236-310 136-203 (204)
50 PF10602 RPN7: 26S proteasome 68.3 91 0.002 28.0 12.9 117 86-212 49-168 (177)
51 TIGR02944 suf_reg_Xantho FeS a 67.9 14 0.00031 31.2 5.8 36 297-332 23-58 (130)
52 PRK10141 DNA-binding transcrip 67.7 25 0.00055 29.8 7.1 75 298-379 29-103 (117)
53 PRK03573 transcriptional regul 67.6 71 0.0015 27.2 10.2 50 299-348 46-95 (144)
54 PF13730 HTH_36: Helix-turn-he 66.5 27 0.00058 24.6 6.1 49 279-329 7-55 (55)
55 PF14559 TPR_19: Tetratricopep 66.5 17 0.00037 26.3 5.2 50 87-145 5-54 (68)
56 PF12569 NARP1: NMDA receptor- 66.4 1.9E+02 0.004 30.9 17.5 164 4-180 58-250 (517)
57 PF08280 HTH_Mga: M protein tr 65.6 12 0.00026 27.4 4.2 37 277-320 4-40 (59)
58 PRK10870 transcriptional repre 64.6 81 0.0018 28.3 10.3 51 297-347 69-119 (176)
59 KOG3054 Uncharacterized conser 64.5 16 0.00035 34.9 5.7 54 286-343 205-258 (299)
60 PF13404 HTH_AsnC-type: AsnC-t 64.5 10 0.00023 26.0 3.4 23 297-319 15-37 (42)
61 PF13429 TPR_15: Tetratricopep 64.4 77 0.0017 30.0 10.7 93 81-190 154-246 (280)
62 PRK11920 rirA iron-responsive 62.3 21 0.00047 31.4 5.9 47 283-332 11-57 (153)
63 cd00092 HTH_CRP helix_turn_hel 61.7 27 0.00058 25.3 5.6 35 297-331 23-57 (67)
64 PF07106 TBPIP: Tat binding pr 61.1 69 0.0015 28.4 9.1 82 296-380 13-99 (169)
65 TIGR02337 HpaR homoprotocatech 60.5 95 0.002 25.5 9.6 75 297-376 40-114 (118)
66 PF04967 HTH_10: HTH DNA bindi 59.8 16 0.00034 26.6 3.8 29 297-325 21-49 (53)
67 smart00550 Zalpha Z-DNA-bindin 59.5 35 0.00076 25.7 5.9 33 299-331 22-54 (68)
68 PF08784 RPA_C: Replication pr 58.8 22 0.00047 28.8 5.0 52 281-335 50-101 (102)
69 cd04761 HTH_MerR-SF Helix-Turn 58.2 18 0.0004 24.6 3.9 46 301-359 2-47 (49)
70 PF10255 Paf67: RNA polymerase 57.4 2.4E+02 0.0051 29.2 15.5 191 116-321 122-343 (404)
71 PF01978 TrmB: Sugar-specific 57.1 14 0.00031 27.5 3.4 37 297-333 20-56 (68)
72 PF12802 MarR_2: MarR family; 56.6 54 0.0012 23.4 6.4 41 298-338 20-60 (62)
73 KOG2004 Mitochondrial ATP-depe 56.5 2.5E+02 0.0054 31.4 13.5 135 56-193 231-395 (906)
74 PF13601 HTH_34: Winged helix 55.8 59 0.0013 25.4 6.8 42 297-338 12-53 (80)
75 PRK14165 winged helix-turn-hel 55.8 92 0.002 29.3 9.2 63 297-367 19-81 (217)
76 COG1959 Predicted transcriptio 55.0 47 0.001 29.2 6.8 50 281-332 9-58 (150)
77 cd00090 HTH_ARSR Arsenical Res 54.9 61 0.0013 23.2 6.6 36 300-335 21-56 (78)
78 PF13424 TPR_12: Tetratricopep 54.3 57 0.0012 24.2 6.5 63 119-182 8-70 (78)
79 PF12895 Apc3: Anaphase-promot 53.9 64 0.0014 24.5 6.8 76 55-141 8-83 (84)
80 smart00419 HTH_CRP helix_turn_ 53.1 46 0.001 22.2 5.2 33 299-331 8-40 (48)
81 PF14947 HTH_45: Winged helix- 52.9 51 0.0011 25.4 6.0 43 297-343 17-59 (77)
82 smart00418 HTH_ARSR helix_turn 51.7 47 0.001 23.1 5.3 37 298-334 9-45 (66)
83 PF10668 Phage_terminase: Phag 51.2 17 0.00036 27.2 2.8 23 297-319 20-42 (60)
84 TIGR02795 tol_pal_ybgF tol-pal 51.2 98 0.0021 24.2 7.8 59 81-145 47-105 (119)
85 TIGR03504 FimV_Cterm FimV C-te 51.1 15 0.00032 25.7 2.3 26 119-144 2-27 (44)
86 PF04218 CENP-B_N: CENP-B N-te 50.6 33 0.00071 24.6 4.2 36 276-320 8-43 (53)
87 PF12895 Apc3: Anaphase-promot 49.8 1.1E+02 0.0024 23.1 8.3 48 87-141 3-50 (84)
88 TIGR02795 tol_pal_ybgF tol-pal 49.5 1.2E+02 0.0027 23.6 9.1 95 86-191 15-109 (119)
89 PF09202 Rio2_N: Rio2, N-termi 49.0 55 0.0012 25.9 5.6 55 279-336 7-61 (82)
90 PRK09954 putative kinase; Prov 48.8 69 0.0015 31.8 7.8 46 297-342 15-63 (362)
91 PF09218 DUF1959: Domain of un 48.5 15 0.00033 31.1 2.5 41 304-370 18-58 (117)
92 PF09940 DUF2172: Domain of un 47.8 25 0.00055 35.7 4.3 46 279-330 341-386 (386)
93 PF10007 DUF2250: Uncharacteri 47.4 24 0.00052 28.7 3.4 27 304-330 26-52 (92)
94 PF14480 DNA_pol3_a_NI: DNA po 47.3 80 0.0017 23.9 6.3 61 301-364 2-62 (76)
95 PRK12537 RNA polymerase sigma 46.4 21 0.00046 31.7 3.3 28 298-325 148-175 (182)
96 PF13424 TPR_12: Tetratricopep 45.8 52 0.0011 24.5 5.0 60 81-143 13-73 (78)
97 COG1595 RpoE DNA-directed RNA 45.3 24 0.00051 31.5 3.5 28 298-325 142-169 (182)
98 COG2956 Predicted N-acetylgluc 44.4 3.5E+02 0.0077 27.4 17.0 155 20-191 110-282 (389)
99 PRK11014 transcriptional repre 43.0 68 0.0015 27.5 5.9 38 297-334 23-60 (141)
100 PF04539 Sigma70_r3: Sigma-70 42.0 26 0.00055 26.7 2.7 27 297-323 18-44 (78)
101 PF13518 HTH_28: Helix-turn-he 41.6 67 0.0015 22.0 4.7 27 301-327 14-40 (52)
102 PF08220 HTH_DeoR: DeoR-like h 41.3 73 0.0016 23.0 4.9 33 297-329 12-44 (57)
103 PRK12529 RNA polymerase sigma 41.0 30 0.00066 30.7 3.5 28 298-325 142-169 (178)
104 PF02002 TFIIE_alpha: TFIIE al 41.0 49 0.0011 26.9 4.5 35 298-332 26-60 (105)
105 PRK06759 RNA polymerase factor 40.3 33 0.00071 29.3 3.5 28 298-325 121-148 (154)
106 TIGR02999 Sig-70_X6 RNA polyme 39.9 32 0.0007 30.3 3.5 28 298-325 149-176 (183)
107 PF07381 DUF1495: Winged helix 39.8 1.8E+02 0.0039 23.5 7.3 62 278-342 7-79 (90)
108 PRK12523 RNA polymerase sigma 39.6 33 0.00072 30.1 3.5 28 298-325 134-161 (172)
109 PF03979 Sigma70_r1_1: Sigma-7 39.5 61 0.0013 25.4 4.5 40 285-328 11-53 (82)
110 TIGR02431 pcaR_pcaU beta-ketoa 38.9 74 0.0016 29.9 5.9 46 282-330 10-55 (248)
111 smart00421 HTH_LUXR helix_turn 38.9 45 0.00098 22.7 3.5 26 299-324 18-43 (58)
112 PRK09642 RNA polymerase sigma 38.7 36 0.00077 29.4 3.5 28 298-325 121-148 (160)
113 PF07389 DUF1500: Protein of u 38.7 34 0.00073 27.5 2.9 31 297-329 46-77 (100)
114 PF01726 LexA_DNA_bind: LexA D 38.5 52 0.0011 24.7 3.8 34 297-330 23-57 (65)
115 PF05331 DUF742: Protein of un 38.3 61 0.0013 27.4 4.6 41 286-332 48-88 (114)
116 PRK09651 RNA polymerase sigma 38.0 37 0.00079 29.9 3.5 28 298-325 134-161 (172)
117 TIGR02983 SigE-fam_strep RNA p 37.9 37 0.0008 29.3 3.4 28 298-325 125-152 (162)
118 PF08221 HTH_9: RNA polymerase 37.7 50 0.0011 24.5 3.6 35 297-331 25-59 (62)
119 PRK09047 RNA polymerase factor 37.6 38 0.00082 29.0 3.5 28 298-325 121-148 (161)
120 COG1414 IclR Transcriptional r 37.3 84 0.0018 29.8 6.0 57 282-343 5-61 (246)
121 PRK09191 two-component respons 37.2 1.8E+02 0.0038 26.8 8.2 28 298-325 103-130 (261)
122 cd06170 LuxR_C_like C-terminal 36.8 51 0.0011 22.6 3.5 26 299-324 15-40 (57)
123 TIGR03643 conserved hypothetic 36.7 67 0.0014 24.9 4.1 33 286-323 5-37 (72)
124 PF01047 MarR: MarR family; I 36.7 1.2E+02 0.0026 21.4 5.5 42 298-339 16-57 (59)
125 PF01325 Fe_dep_repress: Iron 36.1 1.5E+02 0.0032 21.8 5.9 44 283-330 10-53 (60)
126 smart00345 HTH_GNTR helix_turn 36.1 83 0.0018 21.8 4.5 33 298-330 18-51 (60)
127 PRK07037 extracytoplasmic-func 36.0 41 0.0009 29.0 3.5 27 298-324 124-150 (163)
128 TIGR03879 near_KaiC_dom probab 35.8 64 0.0014 25.1 4.0 30 298-327 31-60 (73)
129 KOG2047 mRNA splicing factor [ 35.6 1.7E+02 0.0037 32.2 8.3 101 22-147 174-279 (835)
130 PF06552 TOM20_plant: Plant sp 35.5 90 0.0019 28.7 5.5 76 110-185 21-103 (186)
131 PF10985 DUF2805: Protein of u 35.5 71 0.0015 24.8 4.1 33 286-323 4-36 (73)
132 PF10975 DUF2802: Protein of u 35.3 39 0.00085 25.9 2.7 22 299-320 44-65 (70)
133 PRK12527 RNA polymerase sigma 35.2 44 0.00096 28.8 3.5 27 298-324 120-146 (159)
134 PF00046 Homeobox: Homeobox do 35.1 36 0.00079 24.1 2.5 24 298-321 26-49 (57)
135 PF08279 HTH_11: HTH domain; 35.1 1.6E+02 0.0034 20.6 6.1 30 298-327 14-43 (55)
136 PF14493 HTH_40: Helix-turn-he 35.0 84 0.0018 24.9 4.8 55 298-367 12-67 (91)
137 TIGR02947 SigH_actino RNA poly 33.9 45 0.00097 29.9 3.4 27 298-324 146-172 (193)
138 PHA02943 hypothetical protein; 33.8 1.3E+02 0.0028 26.9 6.0 35 297-331 22-56 (165)
139 PF11972 HTH_13: HTH DNA bindi 33.7 77 0.0017 23.2 3.9 32 285-320 3-34 (54)
140 PRK12520 RNA polymerase sigma 33.6 46 0.001 29.7 3.5 27 298-324 146-172 (191)
141 PF13414 TPR_11: TPR repeat; P 33.5 1.7E+02 0.0038 20.8 6.1 59 120-186 7-66 (69)
142 PF09920 DUF2150: Uncharacteri 33.5 3.9E+02 0.0085 24.7 9.6 74 26-104 2-76 (190)
143 smart00422 HTH_MERR helix_turn 33.4 86 0.0019 22.9 4.4 48 301-360 2-49 (70)
144 PRK10747 putative protoheme IX 33.3 2.4E+02 0.0053 28.4 9.0 69 72-148 117-185 (398)
145 PRK12525 RNA polymerase sigma 33.1 49 0.0011 28.9 3.5 28 298-325 133-160 (168)
146 PRK10163 DNA-binding transcrip 33.0 1.1E+02 0.0023 29.5 6.0 58 281-343 25-82 (271)
147 PRK12543 RNA polymerase sigma 32.9 49 0.0011 29.3 3.4 27 298-324 132-158 (179)
148 PRK12522 RNA polymerase sigma 32.9 49 0.0011 29.0 3.4 28 298-325 134-161 (173)
149 PRK12514 RNA polymerase sigma 32.7 48 0.001 29.1 3.4 26 299-324 145-170 (179)
150 PRK12528 RNA polymerase sigma 32.7 51 0.0011 28.4 3.5 28 298-325 128-155 (161)
151 PF12569 NARP1: NMDA receptor- 32.6 6.4E+02 0.014 26.9 14.3 65 71-144 189-256 (517)
152 PRK11569 transcriptional repre 32.4 1.1E+02 0.0023 29.4 6.0 47 281-330 28-74 (274)
153 PRK12530 RNA polymerase sigma 32.4 50 0.0011 29.6 3.5 27 298-324 149-175 (189)
154 TIGR02787 codY_Gpos GTP-sensin 32.1 1.8E+02 0.004 27.9 7.2 37 297-333 196-232 (251)
155 PRK12511 RNA polymerase sigma 31.8 52 0.0011 29.5 3.4 28 298-325 126-153 (182)
156 PRK15090 DNA-binding transcrip 31.6 1.1E+02 0.0023 29.0 5.8 47 281-331 14-60 (257)
157 TIGR01764 excise DNA binding d 31.6 1.2E+02 0.0026 20.0 4.6 30 300-333 2-31 (49)
158 PF04703 FaeA: FaeA-like prote 31.6 76 0.0016 23.8 3.7 34 297-330 13-46 (62)
159 PF03444 HrcA_DNA-bdg: Winged 31.5 1.9E+02 0.0042 22.8 6.0 52 278-332 5-56 (78)
160 PF13542 HTH_Tnp_ISL3: Helix-t 31.3 60 0.0013 22.5 3.0 24 300-323 28-51 (52)
161 PRK12513 RNA polymerase sigma 31.3 53 0.0012 29.3 3.5 27 298-324 154-180 (194)
162 TIGR02147 Fsuc_second hypothet 30.9 3.1E+02 0.0066 26.7 8.8 75 298-372 136-249 (271)
163 PF13463 HTH_27: Winged helix 30.9 1.2E+02 0.0025 22.0 4.7 43 297-339 16-58 (68)
164 PRK08301 sporulation sigma fac 30.9 53 0.0011 30.5 3.5 28 298-325 197-224 (234)
165 PRK09645 RNA polymerase sigma 30.9 55 0.0012 28.6 3.4 27 298-324 133-159 (173)
166 cd00592 HTH_MerR-like Helix-Tu 30.8 97 0.0021 24.7 4.6 32 301-336 2-33 (100)
167 PRK12547 RNA polymerase sigma 30.7 58 0.0012 28.3 3.5 28 298-325 127-154 (164)
168 PF06163 DUF977: Bacterial pro 30.4 2.1E+02 0.0046 24.6 6.6 44 280-330 14-57 (127)
169 cd05804 StaR_like StaR_like; a 30.3 4.4E+02 0.0096 25.3 10.1 87 82-181 123-209 (355)
170 TIGR01884 cas_HTH CRISPR locus 30.2 2.4E+02 0.0051 25.7 7.6 45 298-343 156-200 (203)
171 smart00653 eIF2B_5 domain pres 29.7 2.5E+02 0.0053 23.5 6.9 51 300-358 22-72 (110)
172 cd01104 HTH_MlrA-CarA Helix-Tu 29.6 1E+02 0.0023 22.4 4.3 48 301-360 2-49 (68)
173 PRK12533 RNA polymerase sigma 29.4 59 0.0013 30.2 3.5 28 298-325 149-176 (216)
174 PRK12545 RNA polymerase sigma 28.8 61 0.0013 29.4 3.4 27 298-324 154-180 (201)
175 PRK12512 RNA polymerase sigma 28.7 63 0.0014 28.5 3.5 28 298-325 146-173 (184)
176 PRK09646 RNA polymerase sigma 28.7 61 0.0013 29.1 3.4 27 298-324 157-183 (194)
177 PLN03088 SGT1, suppressor of 28.6 3.7E+02 0.0081 26.8 9.3 88 87-191 16-103 (356)
178 TIGR02952 Sig70_famx2 RNA poly 28.6 65 0.0014 27.8 3.4 28 298-325 137-164 (170)
179 KOG2002 TPR-containing nuclear 28.4 7.9E+02 0.017 28.4 12.2 210 83-320 21-237 (1018)
180 COG1497 Predicted transcriptio 28.3 5.5E+02 0.012 24.8 11.3 77 280-373 12-88 (260)
181 PF00403 HMA: Heavy-metal-asso 28.2 2.1E+02 0.0046 20.3 5.7 38 318-356 14-53 (62)
182 PF06056 Terminase_5: Putative 28.2 62 0.0013 23.8 2.7 25 298-322 12-36 (58)
183 TIGR03302 OM_YfiO outer membra 28.2 4.5E+02 0.0097 23.7 9.8 95 86-190 46-147 (235)
184 PRK12517 RNA polymerase sigma 28.2 65 0.0014 28.9 3.5 27 298-324 143-169 (188)
185 PRK09649 RNA polymerase sigma 27.9 66 0.0014 28.7 3.5 27 298-324 145-171 (185)
186 PRK12516 RNA polymerase sigma 27.9 66 0.0014 28.9 3.4 27 298-324 131-157 (187)
187 KOG3252 Uncharacterized conser 27.8 3.2E+02 0.007 25.3 7.6 94 232-343 95-189 (217)
188 TIGR02943 Sig70_famx1 RNA poly 27.8 67 0.0015 28.8 3.5 27 298-324 146-172 (188)
189 KOG2003 TPR repeat-containing 27.6 7.7E+02 0.017 26.2 12.4 53 120-180 562-614 (840)
190 TIGR03001 Sig-70_gmx1 RNA poly 27.4 65 0.0014 30.6 3.4 27 298-324 176-202 (244)
191 PRK12519 RNA polymerase sigma 27.4 68 0.0015 28.6 3.5 28 298-325 156-183 (194)
192 PF08311 Mad3_BUB1_I: Mad3/BUB 27.4 3.8E+02 0.0082 22.6 10.2 80 52-141 42-124 (126)
193 COG3063 PilF Tfp pilus assembl 27.1 1.8E+02 0.0038 28.0 6.1 91 116-218 35-138 (250)
194 PRK12540 RNA polymerase sigma 27.0 71 0.0015 28.5 3.5 27 298-324 126-152 (182)
195 PF07721 TPR_4: Tetratricopept 27.0 93 0.002 18.5 2.9 23 119-141 4-26 (26)
196 PF09743 DUF2042: Uncharacteri 26.9 1.8E+02 0.0039 28.3 6.4 73 278-363 177-249 (272)
197 PRK09647 RNA polymerase sigma 26.8 70 0.0015 29.2 3.4 27 298-324 153-179 (203)
198 KOG3060 Uncharacterized conser 26.7 6.1E+02 0.013 24.8 13.9 178 31-229 8-188 (289)
199 PF14938 SNAP: Soluble NSF att 26.7 5.6E+02 0.012 24.4 21.3 156 53-215 91-250 (282)
200 COG2524 Predicted transcriptio 26.6 1.5E+02 0.0032 29.0 5.5 57 279-338 8-64 (294)
201 PF10771 DUF2582: Protein of u 26.4 1.8E+02 0.0038 22.1 4.9 45 296-342 19-63 (65)
202 PF03962 Mnd1: Mnd1 family; I 26.4 1.6E+02 0.0035 26.9 5.7 77 298-378 10-94 (188)
203 PF01873 eIF-5_eIF-2B: Domain 26.4 2.7E+02 0.0059 23.8 6.7 54 300-361 35-88 (125)
204 TIGR00540 hemY_coli hemY prote 26.4 5.3E+02 0.011 26.0 10.1 126 28-176 80-205 (409)
205 PRK15431 ferrous iron transpor 26.3 2.2E+02 0.0048 22.4 5.6 36 297-332 14-49 (78)
206 TIGR02954 Sig70_famx3 RNA poly 26.3 74 0.0016 27.6 3.4 28 298-325 134-161 (169)
207 PF04297 UPF0122: Putative hel 26.2 74 0.0016 26.3 3.1 27 297-323 31-57 (101)
208 TIGR02989 Sig-70_gvs1 RNA poly 25.9 78 0.0017 27.0 3.5 27 298-324 126-152 (159)
209 COG5290 IkappaB kinase complex 25.9 4.1E+02 0.0089 30.1 9.3 25 353-377 1157-1181(1243)
210 TIGR02702 SufR_cyano iron-sulf 25.7 5.1E+02 0.011 23.5 9.4 36 298-333 14-49 (203)
211 TIGR01610 phage_O_Nterm phage 25.6 3.4E+02 0.0074 21.6 6.9 46 296-343 44-89 (95)
212 cd00086 homeodomain Homeodomai 25.6 1E+02 0.0023 21.5 3.5 37 286-322 14-50 (59)
213 PF13384 HTH_23: Homeodomain-l 25.5 59 0.0013 22.3 2.1 29 299-327 17-45 (50)
214 PRK12539 RNA polymerase sigma 25.4 77 0.0017 28.1 3.4 27 298-324 146-172 (184)
215 TIGR02950 SigM_subfam RNA poly 25.3 82 0.0018 26.7 3.4 27 298-324 120-146 (154)
216 PRK12524 RNA polymerase sigma 25.3 1.1E+02 0.0024 27.4 4.5 27 298-324 151-177 (196)
217 PRK12536 RNA polymerase sigma 25.3 79 0.0017 27.9 3.5 27 298-324 144-170 (181)
218 PRK09652 RNA polymerase sigma 25.1 81 0.0018 27.3 3.4 27 298-324 143-169 (182)
219 TIGR02846 spore_sigmaK RNA pol 25.0 78 0.0017 29.4 3.5 27 298-324 193-219 (227)
220 PRK13919 putative RNA polymera 25.0 80 0.0017 27.9 3.4 27 298-324 150-176 (186)
221 PRK12542 RNA polymerase sigma 24.8 82 0.0018 27.9 3.5 27 298-324 137-163 (185)
222 PF13525 YfiO: Outer membrane 24.8 5.2E+02 0.011 23.3 11.3 74 86-169 18-91 (203)
223 TIGR02939 RpoE_Sigma70 RNA pol 24.8 81 0.0018 27.8 3.4 27 298-324 153-179 (190)
224 PRK12535 RNA polymerase sigma 24.7 81 0.0018 28.6 3.4 26 298-323 148-173 (196)
225 TIGR02835 spore_sigmaE RNA pol 24.5 85 0.0018 29.3 3.6 27 298-324 197-223 (234)
226 cd07377 WHTH_GntR Winged helix 24.5 1.8E+02 0.0039 20.5 4.7 31 300-330 26-56 (66)
227 PRK09648 RNA polymerase sigma 24.5 84 0.0018 27.9 3.5 28 298-325 154-181 (189)
228 PRK12532 RNA polymerase sigma 24.4 83 0.0018 28.1 3.5 27 298-324 151-177 (195)
229 TIGR00373 conserved hypothetic 24.4 5E+02 0.011 22.9 9.5 67 297-367 26-95 (158)
230 PF00325 Crp: Bacterial regula 23.9 1.5E+02 0.0032 19.3 3.5 30 300-329 3-32 (32)
231 TIGR02878 spore_ypjB sporulati 23.9 4.1E+02 0.009 25.3 7.9 112 125-258 14-128 (233)
232 PRK06704 RNA polymerase factor 23.9 83 0.0018 29.7 3.4 26 299-324 132-157 (228)
233 cd06171 Sigma70_r4 Sigma70, re 23.8 1.2E+02 0.0025 20.0 3.4 27 298-324 25-51 (55)
234 PF05920 Homeobox_KN: Homeobox 23.8 1E+02 0.0022 20.9 2.9 21 303-323 17-37 (40)
235 PRK12518 RNA polymerase sigma 23.7 88 0.0019 27.2 3.4 27 298-324 135-161 (175)
236 PF13432 TPR_16: Tetratricopep 23.5 2.7E+02 0.0058 19.6 6.5 61 121-189 2-62 (65)
237 PRK00118 putative DNA-binding 23.4 99 0.0022 25.6 3.4 26 298-323 32-57 (104)
238 PRK09638 RNA polymerase sigma 23.2 90 0.002 27.2 3.4 28 298-325 141-168 (176)
239 PF11817 Foie-gras_1: Foie gra 23.2 6.3E+02 0.014 23.7 10.5 95 86-185 151-245 (247)
240 PF12862 Apc5: Anaphase-promot 23.0 3.8E+02 0.0082 21.1 7.1 60 86-145 11-70 (94)
241 PRK07670 RNA polymerase sigma 22.7 1.3E+02 0.0028 28.4 4.5 28 298-325 216-243 (251)
242 PF06627 DUF1153: Protein of u 22.6 1.9E+02 0.0041 23.4 4.6 39 276-322 34-72 (90)
243 TIGR02985 Sig70_bacteroi1 RNA 22.5 1E+02 0.0022 26.0 3.5 27 298-324 128-154 (161)
244 COG3413 Predicted DNA binding 22.5 1E+02 0.0022 28.4 3.7 29 297-325 176-204 (215)
245 TIGR02959 SigZ RNA polymerase 22.3 1.4E+02 0.0031 26.0 4.5 27 298-324 115-141 (170)
246 PRK10430 DNA-binding transcrip 22.3 1.3E+02 0.0028 27.7 4.4 39 297-335 176-214 (239)
247 CHL00033 ycf3 photosystem I as 22.3 5E+02 0.011 22.3 9.8 56 84-145 46-101 (168)
248 PRK04217 hypothetical protein; 22.2 2.5E+02 0.0054 23.5 5.5 40 298-337 57-103 (110)
249 PF06619 DUF1149: Protein of u 22.1 1.9E+02 0.0041 24.9 4.8 49 328-376 68-116 (127)
250 smart00389 HOX Homeodomain. DN 22.1 1.6E+02 0.0034 20.4 3.9 36 287-322 15-50 (56)
251 TIGR02479 FliA_WhiG RNA polyme 22.1 1.4E+02 0.003 27.4 4.6 28 298-325 190-217 (224)
252 PRK12526 RNA polymerase sigma 21.9 99 0.0021 28.1 3.4 28 298-325 168-195 (206)
253 PRK09640 RNA polymerase sigma 21.7 1E+02 0.0022 27.4 3.5 27 298-324 149-175 (188)
254 PF09577 Spore_YpjB: Sporulati 21.7 6.1E+02 0.013 24.1 8.7 113 125-259 14-128 (232)
255 PRK06986 fliA flagellar biosyn 21.6 1.5E+02 0.0032 27.6 4.7 28 298-325 199-226 (236)
256 PRK10803 tol-pal system protei 21.4 7.3E+02 0.016 23.8 10.2 93 87-191 157-250 (263)
257 PRK09639 RNA polymerase sigma 21.3 1.1E+02 0.0024 26.3 3.5 28 298-325 126-153 (166)
258 PRK10803 tol-pal system protei 21.2 6.5E+02 0.014 24.1 9.1 55 85-145 192-246 (263)
259 TIGR02960 SigX5 RNA polymerase 21.1 99 0.0021 30.1 3.5 27 298-324 157-183 (324)
260 PRK12534 RNA polymerase sigma 21.1 1E+02 0.0022 27.2 3.3 27 298-324 152-178 (187)
261 cd04766 HTH_HspR Helix-Turn-He 21.0 1.5E+02 0.0033 23.3 4.0 46 300-358 2-47 (91)
262 PRK09415 RNA polymerase factor 20.9 1.1E+02 0.0024 27.0 3.5 27 298-324 142-168 (179)
263 PRK11924 RNA polymerase sigma 20.8 1.1E+02 0.0024 26.3 3.4 27 298-324 140-166 (179)
264 PRK12531 RNA polymerase sigma 20.8 1.1E+02 0.0023 27.4 3.4 27 298-324 156-182 (194)
265 PF04210 MtrG: Tetrahydrometha 20.8 1.8E+02 0.0039 22.4 4.0 35 346-380 4-39 (70)
266 PF13613 HTH_Tnp_4: Helix-turn 20.5 1.7E+02 0.0037 20.7 3.7 34 283-323 10-43 (53)
267 cd04762 HTH_MerR-trunc Helix-T 20.5 1.1E+02 0.0025 20.0 2.7 47 300-359 1-47 (49)
268 PRK08583 RNA polymerase sigma 20.4 1.5E+02 0.0033 27.9 4.5 28 298-325 220-247 (257)
269 PF02284 COX5A: Cytochrome c o 20.2 1.8E+02 0.0039 24.3 4.2 32 73-104 45-76 (108)
270 PRK12544 RNA polymerase sigma 20.1 1.1E+02 0.0025 27.9 3.4 27 298-324 163-189 (206)
271 PRK11923 algU RNA polymerase s 20.1 1.1E+02 0.0025 27.1 3.4 27 298-324 153-179 (193)
272 PF13371 TPR_9: Tetratricopept 20.1 3.1E+02 0.0067 19.6 5.3 60 123-190 2-61 (73)
273 PRK08558 adenine phosphoribosy 20.1 1.9E+02 0.004 27.5 5.0 33 276-314 6-38 (238)
274 PRK12336 translation initiatio 20.0 3.3E+02 0.0072 25.1 6.5 53 300-361 41-93 (201)
No 1
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.8e-101 Score=732.92 Aligned_cols=378 Identities=50% Similarity=0.797 Sum_probs=366.0
Q ss_pred CcHHHHHH-HHHhcCCchHHHHHHHHHHHHhhhHHHHHHHHHHHHhchhhcCchhHHHHHHHHHHHHHhhcChHHHHHHH
Q 043780 1 MAALQYLE-SLRNDHPELGEWYNALADLYQKKLWHQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETKINLLKLAHFA 79 (386)
Q Consensus 1 ~~~~~~L~-~~~~~~p~~~~~~~~~~~l~~~KLWhqLt~~l~~~~~~~~~~~~~~~~~ly~~fi~~f~~kin~l~l~~i~ 79 (386)
|++.+||+ +..+++|++++.|++++++|++|||||||.++.+|+++|.|++++.++++|.|||++|++||||+++|+|+
T Consensus 2 ~~~~~~L~~~~~~a~~~l~~ew~~leeLy~eKLW~QLt~~l~~fvd~~~f~~~~~~l~lY~NFvsefe~kINplslvei~ 81 (380)
T KOG2908|consen 2 MNAPDYLQTQLKSANPSLAAEWDRLEELYEEKLWHQLTLALVDFVDDPPFQAGDLLLQLYLNFVSEFETKINPLSLVEIL 81 (380)
T ss_pred CcHHHHHHHHHhhcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHhccccccchHHHHHHHHHHHHHhhccChHHHHHHH
Confidence 68999998 55666789999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHH
Q 043780 80 VIVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYAN 159 (386)
Q Consensus 80 ~~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~ 159 (386)
+.++++++|+++|++||+++.++++. .+.++|++|+.+.+++++|..||++++++.|++++..+|+..+|++.||+.
T Consensus 82 l~~~~~~~D~~~al~~Le~i~~~~~~---~~e~~av~~~~t~~~r~~L~i~DLk~~kk~ldd~~~~ld~~~~v~~~Vh~~ 158 (380)
T KOG2908|consen 82 LVVSEQISDKDEALEFLEKIIEKLKE---YKEPDAVIYILTEIARLKLEINDLKEIKKLLDDLKSMLDSLDGVTSNVHSS 158 (380)
T ss_pred HHHHHHhccHHHHHHHHHHHHHHHHh---hccchhHHHHHHHHHHHHHhcccHHHHHHHHHHHHHHHhcccCCChhhhhh
Confidence 99999999999999999999999963 344479999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHH
Q 043780 160 YYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLY 239 (386)
Q Consensus 160 ~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~ 239 (386)
||++++.||+..|+|++||+++|+||+|.+.+++|.++++++|++++++||+|++|||||||+.||++.+|+||++.|++
T Consensus 159 fY~lssqYyk~~~d~a~yYr~~L~YL~~~d~~~l~~se~~~lA~~L~~aALLGe~iyNfGELL~HPilesL~gT~~eWL~ 238 (380)
T KOG2908|consen 159 FYSLSSQYYKKIGDFASYYRHALLYLGCSDIDDLSESEKQDLAFDLSLAALLGENIYNFGELLAHPILESLKGTNREWLK 238 (380)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHhccccccccCHHHHHHHHHHHHHHHHhccccccHHHHHhhHHHHHhcCCcHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHH
Q 043780 240 YILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHL 319 (386)
Q Consensus 240 ~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~l 319 (386)
++|.+||.||+..|++.+ ..|.+.|+|.+++.+|++|||+||||++||.||++.|++||++||++|+||.++||++
T Consensus 239 dll~Afn~Gdl~~f~~l~----~~~~~~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~L 314 (380)
T KOG2908|consen 239 DLLIAFNSGDLKRFESLK----GVWGKQPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELL 314 (380)
T ss_pred HHHHHhccCCHHHHHHHH----HHhccCchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHH
Confidence 999999999999999996 4567799999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHHHHhhcccccc
Q 043780 320 LMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSIEAETPDLVA 385 (386)
Q Consensus 320 vikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l~~~~~~~~~ 385 (386)
||||+|.|||+|+||||+|+|+++|||||+++++||..|++|++.|+++|+++...|++.+.++++
T Consensus 315 VMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W~~~v~~me~~ve~~~~~i~~ 380 (380)
T KOG2908|consen 315 VMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEWNKDVKSMEGLVEHRGHEILT 380 (380)
T ss_pred HHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHHHHHHHHHHHHHHHhcccccC
Confidence 999999999999999999999999999999999999999999999999999999999999999974
No 2
>KOG2753 consensus Uncharacterized conserved protein, contains PCI domain [General function prediction only]
Probab=100.00 E-value=6.8e-41 Score=319.25 Aligned_cols=296 Identities=20% Similarity=0.291 Sum_probs=235.4
Q ss_pred HHHHHHHHHHHHhhcChHHHHHHHHHHHhcC----CC--hHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhc--
Q 043780 56 IQLYHNFITDFETKINLLKLAHFAVIVSRQY----PE--KQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKL-- 127 (386)
Q Consensus 56 ~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~----~d--~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l-- 127 (386)
+++--|-|.+.-..++|=+-..+++.+++++ .+ |.-+|..|.++..-+. +..+ ++..+..+.+.+
T Consensus 63 le~vlnsi~sLi~~~~~e~~e~~v~a~~ekva~q~n~~~~~l~L~vLsnLfn~~d------~~~~-aR~~Vy~~lv~la~ 135 (378)
T KOG2753|consen 63 LECVLNSIVSLIKNAPPEKVEEMVKAICEKVAKQPNDKTASLRLQVLSNLFNGVD------KPTP-ARYQVYMSLVTLAA 135 (378)
T ss_pred HHHHHHHHHHHHHhCCHHHhHHHHHHHHHHHhcCccCCCcccHHHHHHHHHhccC------CCch-HHHHHHHHHHHHHh
Confidence 5555555555555666766666666655543 22 3345666666665552 1111 333333333333
Q ss_pred -------ccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHH
Q 043780 128 -------EQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESLSDSFKLD 200 (386)
Q Consensus 128 -------~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~ 200 (386)
....++..++|+.+|.-. .+-+..+|++.++..+..+..++.-+....||+++..++ .+++++
T Consensus 136 ~~~~~~~i~~~lk~~~~~lkew~~~--------vedqrel~r~v~~al~~~k~~~~s~kvmt~lLgtyt~dn--as~Are 205 (378)
T KOG2753|consen 136 SCKLIEYIVPNLKQLDDWLKEWNIS--------VEDQRELLRAVHKALKDNKSVDESSKVMTELLGTYTEDN--ASEARE 205 (378)
T ss_pred hcceeeeecccHHHHHHHHHhCCCC--------HHHHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHhcccc--hhHHHH
Confidence 234778899999999764 445666777777776665556778888888998886665 678889
Q ss_pred HHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHH
Q 043780 201 LAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEK 280 (386)
Q Consensus 201 ~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~K 280 (386)
.|++|++.|+.+|++|.|++|+.+|+|+.|+++. +|+||.||.+|.+++|.+|.+.|++++.+++ ..+++.+ .|
T Consensus 206 dA~rcV~~av~dP~~F~fD~Ll~L~pV~qLE~d~---i~qLL~IF~s~~L~aYveF~~~N~~Fvqs~g--l~~E~~~-~K 279 (378)
T KOG2753|consen 206 DAMRCVVEAVKDPKIFLFDHLLTLPPVKQLEGDL---IHQLLKIFVSGKLDAYVEFVAANSGFVQSQG--LVHEQNM-AK 279 (378)
T ss_pred HHHHHHHHHHcCCceeccchhccCchHHHhccch---HHHHHHHHHhcchHHHHHHHHhChHHHHHhc--ccHHHHH-HH
Confidence 9999999999999999999999999999998876 9999999999999999999999999999887 3456666 99
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHH
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRD 360 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~ 360 (386)
|||||||+||. .+.+|||++|+++|+|.++|||.|||+||+.|+|.|||||++++|+|+.+++|+||++||+.|++
T Consensus 280 MRLLTlm~LA~----es~eisy~~l~k~LqI~edeVE~fVIdaI~aklV~~kidq~~~~viVs~~~hR~FG~~qW~~L~~ 355 (378)
T KOG2753|consen 280 MRLLTLMSLAE----ESNEISYDTLAKELQINEDEVELFVIDAIRAKLVEGKIDQMNRTVIVSSSTHRTFGKQQWQQLRD 355 (378)
T ss_pred HHHHHHHHHhc----cCCCCCHHHHHHHhccCHHHHHHHHHHHHHHHHHHhhHHhhcceEEeehhhhhhcccHHHHHHHH
Confidence 99999999997 36899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHH-HHHHHHHHHHHHh
Q 043780 361 RLDSW-LGKVHTALLSIEA 378 (386)
Q Consensus 361 ~L~~W-~~~v~~~~~~l~~ 378 (386)
+|..| +++++.+.+++..
T Consensus 356 kL~aw~k~~~stv~~~l~~ 374 (378)
T KOG2753|consen 356 KLAAWGKQNLSTVRENLQS 374 (378)
T ss_pred HHHHHHhhhhHHHHHHhhh
Confidence 99999 6666666665543
No 3
>KOG3250 consensus COP9 signalosome, subunit CSN7 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.93 E-value=3.7e-26 Score=206.68 Aligned_cols=168 Identities=23% Similarity=0.382 Sum_probs=152.2
Q ss_pred HHHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHH
Q 043780 200 DLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLE 279 (386)
Q Consensus 200 ~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~ 279 (386)
+..-.++.+|+.+|++|.|||||..|.+..|.++.++.+++||++|++|++.+|..- +...|.|.. ..+ .
T Consensus 24 ~al~~lIsqale~P~vf~F~ELl~l~nv~qlae~~dsa~lrlL~lFa~Gt~~Dy~ae-------a~rlp~Ls~--~q~-~ 93 (258)
T KOG3250|consen 24 EALEELISQALEAPGVFVFGELLILPNVVQLAEPIDSAYLRLLELFAYGTYRDYSAE-------ALRLPKLSL--AQL-N 93 (258)
T ss_pred hHHHHHHHHHhcCCCeeeHHHHHhhhhHHHHcccccHHHHHHHHHHhcCchhhhhhh-------hhcCCCCCH--HHH-H
Confidence 345678899999999999999999999999999889999999999999999999865 244565543 333 6
Q ss_pred HHHHHHHHHHHhhCCCCCCccChHHHHHHcCC-ChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHH
Q 043780 280 KINILCLMEIIFSRPSEDRTIPLSIIAERTKL-SIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSL 358 (386)
Q Consensus 280 KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i-~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L 358 (386)
|++-++..++|.. .+.|+|..+.+.+.+ +..++|++||+|++.++++|+|||.+|+++|.|+..|.+++.++..|
T Consensus 94 kLk~ltV~slas~----~k~lpy~~Ll~~l~~~nvrelEd~iieamya~IlrGkldqr~q~leV~faigRdlr~k~i~nm 169 (258)
T KOG3250|consen 94 KLKHLTVVSLASF----EKCLPYLVLLRLLPSRNVRELEDLIIEAMYADILRGKLDQRNQTLEVDFAIGRDLRSKDIDNM 169 (258)
T ss_pred hhhcceehhhhhh----chhhhHHHHHhhccCCchhHHHHHHHHHHHHHHHHhhHHhhcceEeechhhcccccHhHHHHH
Confidence 9999999999864 689999999999999 67999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcc
Q 043780 359 RDRLDSWLGKVHTALLSIEAETP 381 (386)
Q Consensus 359 ~~~L~~W~~~v~~~~~~l~~~~~ 381 (386)
.-.|++|++.+.+++-.++++.+
T Consensus 170 ~~TL~~w~~~cenvL~~ie~qv~ 192 (258)
T KOG3250|consen 170 KYTLDEWCEGCENVLFGIEAQVP 192 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHhccc
Confidence 99999999999999999998765
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=99.69 E-value=4.3e-16 Score=127.64 Aligned_cols=105 Identities=36% Similarity=0.419 Sum_probs=94.6
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhH
Q 043780 236 EWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIED 315 (386)
Q Consensus 236 ~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~e 315 (386)
+|+.+|+++|..||+..|.+..+++...+...+.+..+.+.++++++..+|..++. ..+++++++|++.++++.++
T Consensus 1 ~~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~----~y~~i~~~~ia~~l~~~~~~ 76 (105)
T PF01399_consen 1 PPYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSK----PYSSISISEIAKALQLSEEE 76 (105)
T ss_dssp HHHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHH----C-SEEEHHHHHHHHTCCHHH
T ss_pred CHHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHH----HhcccchHHHHHHhccchHH
Confidence 48999999999999999999999995556667777778889999999999999987 37999999999999999999
Q ss_pred HHHHHHHHhhccceEEeecCCCCEEEEEe
Q 043780 316 VEHLLMKSLSVHLIEGIIDQVEGTVHVSW 344 (386)
Q Consensus 316 VE~lvikAi~~gLI~G~IDqv~~~v~vt~ 344 (386)
||.+|+++|..|.|+|+|||++|+|+++|
T Consensus 77 vE~~l~~~I~~~~i~~~ID~~~~~v~~~k 105 (105)
T PF01399_consen 77 VESILIDLISNGLIKAKIDQVNGVVVFSK 105 (105)
T ss_dssp HHHHHHHHHHTTSSEEEEETTTTEEEE-S
T ss_pred HHHHHHHHHHCCCEEEEEECCCCEEEecC
Confidence 99999999999999999999999999987
No 5
>smart00753 PAM PCI/PINT associated module.
Probab=99.54 E-value=3.2e-14 Score=113.99 Aligned_cols=86 Identities=29% Similarity=0.370 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChh
Q 043780 274 EKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIP 353 (386)
Q Consensus 274 ~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~ 353 (386)
.+.+.+|+|..++..++.. .++|+|++|++.+++|.++||.+|+++|..|.|.|+|||.+++|.++|..||. .+
T Consensus 3 ~~~l~~~~~~~~l~~l~~~----y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~ 76 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEP----YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SE 76 (88)
T ss_pred HHHHHHHHHHHHHHHHhHH----hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hh
Confidence 4567799999999999873 68999999999999999999999999999999999999999999999999998 78
Q ss_pred hHHHHHHHHHHH
Q 043780 354 QIKSLRDRLDSW 365 (386)
Q Consensus 354 q~~~L~~~L~~W 365 (386)
+|..+.+++..|
T Consensus 77 ~~~~~~~~l~~~ 88 (88)
T smart00753 77 PLAQFAETLKKL 88 (88)
T ss_pred HHHHHHHHhhcC
Confidence 999999999988
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=99.54 E-value=3.2e-14 Score=113.99 Aligned_cols=86 Identities=29% Similarity=0.370 Sum_probs=80.8
Q ss_pred HHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChh
Q 043780 274 EKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIP 353 (386)
Q Consensus 274 ~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~ 353 (386)
.+.+.+|+|..++..++.. .++|+|++|++.+++|.++||.+|+++|..|.|.|+|||.+++|.++|..||. .+
T Consensus 3 ~~~l~~~~~~~~l~~l~~~----y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~~r~--~~ 76 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEP----YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVDPRR--SE 76 (88)
T ss_pred HHHHHHHHHHHHHHHHhHH----hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCchhh--hh
Confidence 4567799999999999873 68999999999999999999999999999999999999999999999999998 78
Q ss_pred hHHHHHHHHHHH
Q 043780 354 QIKSLRDRLDSW 365 (386)
Q Consensus 354 q~~~L~~~L~~W 365 (386)
+|..+.+++..|
T Consensus 77 ~~~~~~~~l~~~ 88 (88)
T smart00088 77 PLAQFAETLKKL 88 (88)
T ss_pred HHHHHHHHhhcC
Confidence 999999999988
No 7
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=99.26 E-value=9.8e-10 Score=108.91 Aligned_cols=211 Identities=18% Similarity=0.230 Sum_probs=152.3
Q ss_pred CCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCC
Q 043780 111 KEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSV 190 (386)
Q Consensus 111 ~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~ 190 (386)
+.++...+...+-+.+|..+.++.+.+.+....- ++.. .+.--++|.+..+...-.+++|++.-++.+..+.-.|.
T Consensus 204 d~e~qavLiN~LLr~yL~n~lydqa~~lvsK~~~--pe~~--snne~ARY~yY~GrIkaiqldYssA~~~~~qa~rkapq 279 (493)
T KOG2581|consen 204 DEEGQAVLINLLLRNYLHNKLYDQADKLVSKSVY--PEAA--SNNEWARYLYYLGRIKAIQLDYSSALEYFLQALRKAPQ 279 (493)
T ss_pred cchhHHHHHHHHHHHHhhhHHHHHHHHHhhcccC--cccc--ccHHHHHHHHHHhhHHHhhcchhHHHHHHHHHHHhCcc
Confidence 3445544455566788888889999988876642 1111 23466788888888888999999988888888876665
Q ss_pred CCCChhHHHHHHHH-HHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCch
Q 043780 191 ESLSDSFKLDLAFD-LSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPA 269 (386)
Q Consensus 191 ~~~~~~e~~~~a~~-l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~ 269 (386)
+...+.+++.-.- +++.-|+|| |-. --....|+++ . .-.+++.|-.++..||++.|...++++++.|.+++.
T Consensus 280 -~~alGf~q~v~k~~ivv~ll~ge-iPe-rs~F~Qp~~~---k-sL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~t 352 (493)
T KOG2581|consen 280 -HAALGFRQQVNKLMIVVELLLGE-IPE-RSVFRQPGMR---K-SLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGT 352 (493)
T ss_pred -hhhhhHHHHHHHHHHHHHHHcCC-Ccc-hhhhcCccHH---H-HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCc
Confidence 3445555553333 344555554 311 0111233332 1 235699999999999999999999999999988774
Q ss_pred hh----hhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCC-ChhHHHHHHHHHhhccceEEeecCCCCEEE
Q 043780 270 LV----ENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKL-SIEDVEHLLMKSLSVHLIEGIIDQVEGTVH 341 (386)
Q Consensus 270 L~----~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i-~~~eVE~lvikAi~~gLI~G~IDqv~~~v~ 341 (386)
.. -..++++.-||.++|. .+.||+.+||..|++ +++++|.+|-|||+.|+|+|+||..+|.+.
T Consensus 353 y~LivRLR~NVIkTgIR~ISls---------YSRISl~DIA~kL~l~Seed~EyiVakAIRDGvIea~Id~~~g~m~ 420 (493)
T KOG2581|consen 353 YTLIVRLRHNVIKTGIRKISLS---------YSRISLQDIAKKLGLNSEEDAEYIVAKAIRDGVIEAKIDHEDGFMQ 420 (493)
T ss_pred chHHHHHHHHHHHHhhhheeee---------eeeccHHHHHHHhcCCCchhHHHHHHHHHHhccceeeeccccCcee
Confidence 22 2467888888988775 468999999999999 567799999999999999999999998443
No 8
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.26 E-value=3.9e-10 Score=107.10 Aligned_cols=245 Identities=19% Similarity=0.325 Sum_probs=171.5
Q ss_pred HHHHHHHHhcccCChHHHHHHHHhccccccccCCCC--------HHHHH---HHHHHHHHHHHHhhcHHHHHHHHHHHhc
Q 043780 118 IKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDID--------PSVYA---NYYWVSSQYHKFHQEFAEFYKCALLYLA 186 (386)
Q Consensus 118 ~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~--------~~v~a---~~y~~~s~~~k~~~~~~~~y~~~l~yL~ 186 (386)
..+..+.++...+++....+++.++......-+|-+ .+++| ..|..- |........|..++..-+
T Consensus 147 TNtKLgkl~fd~~e~~kl~KIlkqLh~SCq~edGedD~kKGtQLLEiYAlEIQmYT~q----KnNKkLK~lYeqalhiKS 222 (440)
T KOG1464|consen 147 TNTKLGKLYFDRGEYTKLQKILKQLHQSCQTEDGEDDQKKGTQLLEIYALEIQMYTEQ----KNNKKLKALYEQALHIKS 222 (440)
T ss_pred ccchHhhhheeHHHHHHHHHHHHHHHHHhccccCchhhhccchhhhhHhhHhhhhhhh----cccHHHHHHHHHHHHhhc
Confidence 445677788888899999999987765543222221 23333 222221 222334556666665443
Q ss_pred cC-----------------------------------CCCCCChhHHHHHHHHHHHHHhcCC-CcccccccccChhhhcc
Q 043780 187 YT-----------------------------------SVESLSDSFKLDLAFDLSLSALLGD-NIYNFGELLAHPIINSL 230 (386)
Q Consensus 187 ~~-----------------------------------~~~~~~~~e~~~~a~~l~i~AL~~~-~iy~FgeLl~~p~v~~L 230 (386)
-+ +.++....-|......++++-++-. +|--|+.--+.|--
T Consensus 223 AIPHPlImGvIRECGGKMHlreg~fe~AhTDFFEAFKNYDEsGspRRttCLKYLVLANMLmkS~iNPFDsQEAKPyK--- 299 (440)
T KOG1464|consen 223 AIPHPLIMGVIRECGGKMHLREGEFEKAHTDFFEAFKNYDESGSPRRTTCLKYLVLANMLMKSGINPFDSQEAKPYK--- 299 (440)
T ss_pred cCCchHHHhHHHHcCCccccccchHHHHHhHHHHHHhcccccCCcchhHHHHHHHHHHHHHHcCCCCCcccccCCCC---
Confidence 21 2344444455567777887776643 34334332222211
Q ss_pred cCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcC
Q 043780 231 TGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTK 310 (386)
Q Consensus 231 ~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~ 310 (386)
.+++--.+.+|+.++...|+.+|+..+..|++.+-.+|.+..+.+.|.++||--.|+.|+ ||..+-.||| |+++++
T Consensus 300 NdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLI--kPYt~i~Ipf--is~~Ln 375 (440)
T KOG1464|consen 300 NDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLI--KPYTNIGIPF--ISKELN 375 (440)
T ss_pred CCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHh--ccccccCchh--hHhhcC
Confidence 123445677899999999999999999999999999999888877788999999999997 4755555555 999999
Q ss_pred CChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043780 311 LSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSIEAE 379 (386)
Q Consensus 311 i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l~~~ 379 (386)
||+.+||.+++.||-..-|+|+|||+++.+....... -=..+.+.|+.|.++++++.+.+-..
T Consensus 376 v~~~dV~~LLV~~ILD~~i~g~Ide~n~~l~~~~~~~------s~~k~~~al~kW~~ql~Sl~~~i~sr 438 (440)
T KOG1464|consen 376 VPEADVESLLVSCILDDTIDGRIDEVNQYLELDKSKN------SGSKLYKALDKWNNQLKSLQSNIVSR 438 (440)
T ss_pred CCHHHHHHHHHHHHhccccccchHHhhhHhccCccCC------cchHHHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999999999887654432 12347889999999999998877543
No 9
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=98.52 E-value=1.7e-05 Score=77.19 Aligned_cols=248 Identities=19% Similarity=0.244 Sum_probs=149.0
Q ss_pred CCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccC-C
Q 043780 111 KEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYT-S 189 (386)
Q Consensus 111 ~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~-~ 189 (386)
+.++-+...+.+++.||..||..++...+....-...... ++.+.-.|--..+...+.+++|-+..+.--. |++. -
T Consensus 139 d~~~kl~l~iriarlyLe~~d~veae~~inRaSil~a~~~--Ne~Lqie~kvc~ARvlD~krkFlEAAqrYye-ls~~ki 215 (399)
T KOG1497|consen 139 DVEQKLLLCIRIARLYLEDDDKVEAEAYINRASILQAESS--NEQLQIEYKVCYARVLDYKRKFLEAAQRYYE-LSQRKI 215 (399)
T ss_pred hhHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHhhhccc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHh
Confidence 3456677778899999999999999998888765433221 2333333222224444445443321111111 1111 1
Q ss_pred CCCCChhHHHHHHHHHHHHHhcCCCcccc-cccccChhhhcccCCCcHHHHHHH------HHHhcCCHHHHHHHHHHhhh
Q 043780 190 VESLSDSFKLDLAFDLSLSALLGDNIYNF-GELLAHPIINSLTGTKVEWLYYIL------QAFNSGDLVRYQELCRVHNA 262 (386)
Q Consensus 190 ~~~~~~~e~~~~a~~l~i~AL~~~~iy~F-geLl~~p~v~~L~~~~~~~l~~LL------~~f~~G~l~~f~~~~~~~~~ 262 (386)
.++...-++..-|..|.+-|.-||-.--| ..|...|.++.+ +.|.++ .+....+++.|..++.-|..
T Consensus 216 ~~e~~~~~aL~~a~~CtlLA~~gpqrsr~Latlfkder~~~l------~~y~ileKmyl~riI~k~el~ef~~~L~pHQk 289 (399)
T KOG1497|consen 216 VDESERLEALKKALQCTLLASAGPQRSRMLATLFKDERCQKL------PAYGILEKMYLERIIRKEELQEFEAFLQPHQK 289 (399)
T ss_pred cchHHHHHHHHHhHhheeecCCChHHHHHHHHHhcCcccccc------cchHHHHHHHHHHHhcchhHHHHHHHhcchhh
Confidence 22211233344566666666666654333 122222333222 233333 34445568899988876643
Q ss_pred hhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEE
Q 043780 263 ALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHV 342 (386)
Q Consensus 263 ~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~v 342 (386)
.=..++.-..+..++.+ -++++-.| ...|||++++..++||...+|..+-+.|..|-+.|.|||.++.+|+
T Consensus 290 a~~~dgssil~ra~~Eh--Nlls~Skl-------y~nisf~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihF 360 (399)
T KOG1497|consen 290 AHTMDGSSILDRAVIEH--NLLSASKL-------YNNISFEELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHF 360 (399)
T ss_pred hcccCcchhhhhHHHHH--hHHHHHHH-------HHhccHHHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEee
Confidence 21112211112334333 45666666 3579999999999999999999999999999999999999999998
Q ss_pred EeeccccCChhhHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Q 043780 343 SWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSIEAETPDL 383 (386)
Q Consensus 343 t~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l~~~~~~~ 383 (386)
.- |. ..+||. ..+..-++.|+++.+.+.+.+++.
T Consensus 361 e~---~e-~l~~wd---kqi~sl~~qvNki~~~i~~~~s~~ 394 (399)
T KOG1497|consen 361 ED---RE-ELPQWD---KQIQSLCNQVNKILDKISHYGSEW 394 (399)
T ss_pred cc---hh-hhhhhh---HHHHHHHHHHHHHHHHHHHhCcch
Confidence 73 21 234554 456667888899999998887764
No 10
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=98.30 E-value=0.0031 Score=61.93 Aligned_cols=291 Identities=17% Similarity=0.196 Sum_probs=182.8
Q ss_pred hhHHHHHHHHHHHHhchhhcCchhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhc---CCChHHHHHHHHHHHHHhhhcc
Q 043780 31 KLWHQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETKINLLKLAHFAVIVSRQ---YPEKQAAISYLEGVIEKLRATN 107 (386)
Q Consensus 31 KLWhqLt~~l~~~~~~~~~~~~~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~---~~d~~~al~fl~~~~~~~~~~~ 107 (386)
++|-++-..+..-+... +...++=.+.-|.+-+.++-..-..+.-+..++- +.|.+.|++.+.++.+|-...
T Consensus 63 ~~~i~~D~~~l~~m~~~----neeki~eld~~iedaeenlGE~ev~ea~~~kaeYycqigDkena~~~~~~t~~ktvs~- 137 (393)
T KOG0687|consen 63 SLVIKLDQDLLNSMKKA----NEEKIKELDEKIEDAEENLGESEVREAMLRKAEYYCQIGDKENALEALRKTYEKTVSL- 137 (393)
T ss_pred hcceeccHHHHHHHHHh----hHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHhhc-
Confidence 66666666655544432 3446777777788888777666666666666553 458999999998877764322
Q ss_pred ccCCCchHHHHHHHHHHHhcc----cCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHH
Q 043780 108 EQRKEEPILYIKMQIAMFKLE----QGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALL 183 (386)
Q Consensus 108 ~~~~~~a~~~~~~~~~~~~l~----~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~ 183 (386)
...=-++++++..|.+++. ...++.++.++++...= +.... -.++...|..+ ..+|.+.-...+.
T Consensus 138 --g~kiDVvf~~iRlglfy~D~~lV~~~iekak~liE~GgDW-eRrNR--lKvY~Gly~ms------vR~Fk~Aa~Lfld 206 (393)
T KOG0687|consen 138 --GHKIDVVFYKIRLGLFYLDHDLVTESIEKAKSLIEEGGDW-ERRNR--LKVYQGLYCMS------VRNFKEAADLFLD 206 (393)
T ss_pred --ccchhhHHHHHHHHHhhccHHHHHHHHHHHHHHHHhCCCh-hhhhh--HHHHHHHHHHH------HHhHHHHHHHHHH
Confidence 1222368888888888872 33455666666654321 11111 24555555444 3455555556666
Q ss_pred HhccCCCCCC-ChhHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHH-Hhh
Q 043780 184 YLAYTSVESL-SDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCR-VHN 261 (386)
Q Consensus 184 yL~~~~~~~~-~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~-~~~ 261 (386)
.+++|..-++ |-+.-..-++-++.-+|--+++= .-.+..|-+...-. ..+.+.+++..+-.-++++|-.-+. -..
T Consensus 207 ~vsTFtS~El~~Y~~~v~Ytv~~g~i~leR~dlk--tKVi~~~Evl~vl~-~l~~~~q~l~SLY~C~Y~~Ff~~L~~~~~ 283 (393)
T KOG0687|consen 207 SVSTFTSYELMSYETFVRYTVITGLIALERVDLK--TKVIKCPEVLEVLH-KLPSVSQLLNSLYECDYSDFFNDLAAVEA 283 (393)
T ss_pred HcccccceecccHHHHHHHHHHHhhheeccchHH--hhhcCcHHHHHHhh-cCchHHHHHHHHHhccHHHHHHHHHHHHH
Confidence 7777754433 43444343444444344333321 13334444433211 1345677777777777777765442 113
Q ss_pred hhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEE
Q 043780 262 AALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVH 341 (386)
Q Consensus 262 ~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~ 341 (386)
..+..+--|..|...--+-||+-+-.++-- ..|+++.+-.|++.|++++=++.=+=+-|..|-+.++||-|+|+|.
T Consensus 284 ~~lk~D~~l~~h~~yyvREMR~rvY~QlLE----SYrsl~l~~MA~aFgVSVefiDreL~rFI~~grL~ckIDrVnGVVE 359 (393)
T KOG0687|consen 284 KQLKDDRYLGPHYRYYVREMRRRVYAQLLE----SYRSLTLESMAKAFGVSVEFIDRELGRFIAAGRLHCKIDRVNGVVE 359 (393)
T ss_pred HhhccchhcchHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhCchHHHHHhHHHHhhccCceeeeeecccceee
Confidence 344444455667666557899998888765 2799999999999999999888888899999999999999999999
Q ss_pred EEe
Q 043780 342 VSW 344 (386)
Q Consensus 342 vt~ 344 (386)
+++
T Consensus 360 tNr 362 (393)
T KOG0687|consen 360 TNR 362 (393)
T ss_pred cCC
Confidence 984
No 11
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=98.18 E-value=0.0001 Score=72.44 Aligned_cols=251 Identities=16% Similarity=0.185 Sum_probs=163.3
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
.+...+|+..+..+...+++. +++.-.+=+.+.-+-.+-.+.++..++..|..++..-.. --++|.+.+..=..++
T Consensus 141 ~~~YteAlaL~~~L~rElKKl---DDK~lLvev~llESK~y~~l~Nl~KakasLTsART~Ana-iYcpPqlQa~lDLqSG 216 (411)
T KOG1463|consen 141 TKRYTEALALINDLLRELKKL---DDKILLVEVHLLESKAYHALRNLPKAKASLTSARTTANA-IYCPPQLQATLDLQSG 216 (411)
T ss_pred hHHHHHHHHHHHHHHHHHHhc---ccccceeeehhhhhHHHHHHhcchhHHHHHHHHHHhhcc-cccCHHHHHHHHHhcc
Confidence 345678888888887777532 122222223333344444567889999998887654222 2456777776655555
Q ss_pred HHHHHhhcHHHHHHHHHHHh-ccCCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHH
Q 043780 166 QYHKFHQEFAEFYKCALLYL-AYTSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQA 244 (386)
Q Consensus 166 ~~~k~~~~~~~~y~~~l~yL-~~~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~ 244 (386)
-++-...||.-.|.+-.... +|.+.++ ...+......+.++-+.-...=.-+.|+.-...-...+++-..+...-++
T Consensus 217 Ilha~ekDykTafSYFyEAfEgf~s~~~--~v~A~~sLKYMlLcKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavAeA 294 (411)
T KOG1463|consen 217 ILHAAEKDYKTAFSYFYEAFEGFDSLDD--DVKALTSLKYMLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVAEA 294 (411)
T ss_pred ceeecccccchHHHHHHHHHccccccCC--cHHHHHHHHHHHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHHHH
Confidence 55544566666666555544 4444332 22333334444444443332323334444332222566777778889999
Q ss_pred HhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 245 FNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 245 f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
|...++.+|+..+..|+..+..+|....|-..|..-|-=--|+.++- | ...+..+-||+-.|++...||.=+-+.|
T Consensus 295 ~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEknl~riIE--P--yS~Vei~hIA~~IGl~~~~VEkKLsqMI 370 (411)
T KOG1463|consen 295 FGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEKNLCRIIE--P--YSRVEISHIAEVIGLDVPQVEKKLSQMI 370 (411)
T ss_pred hcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHHhHHHHcC--c--hhhhhHHHHHHHHCCCcHHHHHHHHHHH
Confidence 99999999999999999999999976666555544332223444432 4 4566677799999999999999999999
Q ss_pred hccceEEeecCCCCEEEEEeec
Q 043780 325 SVHLIEGIIDQVEGTVHVSWVQ 346 (386)
Q Consensus 325 ~~gLI~G~IDqv~~~v~vt~v~ 346 (386)
=.+.+.|.+||.++++.|.--.
T Consensus 371 LDKkf~G~LDQg~g~Liv~~e~ 392 (411)
T KOG1463|consen 371 LDKKFYGTLDQGEGCLIVFEEP 392 (411)
T ss_pred HHHHhhcccccCCCeEEEeCCC
Confidence 9999999999999999987443
No 12
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=98.11 E-value=0.0053 Score=61.59 Aligned_cols=282 Identities=17% Similarity=0.195 Sum_probs=163.8
Q ss_pred ChHHHHHHHHHHHhcCCChHHHHHHHHHHH-HHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccccccc
Q 043780 71 NLLKLAHFAVIVSRQYPEKQAAISYLEGVI-EKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSM 149 (386)
Q Consensus 71 n~l~l~~i~~~v~~~~~d~~~al~fl~~~~-~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~ 149 (386)
---++.+++..+-+...|..+|.+.+..+. +..- .-.-.+- |=..+..-++-+..+|+-.+.-+...+..+.=+.
T Consensus 129 ERarlTk~L~~ike~~Gdi~~Aa~il~el~VETyg---sm~~~ek-V~fiLEQmrKOG~~~D~vra~i~skKI~~K~F~~ 204 (439)
T KOG1498|consen 129 ERARLTKMLAKIKEEQGDIAEAADILCELQVETYG---SMEKSEK-VAFILEQMRLCLLRLDYVRAQIISKKINKKFFEK 204 (439)
T ss_pred hHHHHHHHHHHHHHHcCCHHHHHHHHHhcchhhhh---hhHHHHH-HHHHHHHHHHHHHhhhHHHHHHHHHHhhHHhcCC
Confidence 345666777777777777777777775430 0000 0000011 1122344455556678888888777776653222
Q ss_pred CCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCC-ChhHH-HHHHHHHHHHHhcCCCcccccccccChhh
Q 043780 150 TDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESL-SDSFK-LDLAFDLSLSALLGDNIYNFGELLAHPII 227 (386)
Q Consensus 150 ~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~-~~~e~-~~~a~~l~i~AL~~~~iy~FgeLl~~p~v 227 (386)
+.+ -.+.--||.+.-.++-..+. |+.-+=.|=+..+.... +.+++ .+.....+..++++|-.--=.+|+.+-.-
T Consensus 205 ~~~-~~lKlkyY~lmI~l~lh~~~---Yl~v~~~Yraiy~t~~vk~d~~kw~~vL~~iv~f~~LAp~dneQsdll~~is~ 280 (439)
T KOG1498|consen 205 PDV-QELKLKYYELMIRLGLHDRA---YLNVCRSYRAIYDTGNVKEDPEKWIEVLRSIVSFCVLAPHDNEQSDLLARISN 280 (439)
T ss_pred ccH-HHHHHHHHHHHHHhcccccc---hhhHHHHHHHHhcccccccChhhhhhhhhhheeEEeecCCCcHHHHHHHHHhc
Confidence 222 34455676665544322222 22222222222221111 12222 23333333455556533222333333211
Q ss_pred -hcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhh-----------hhHHHHHHHHHHHHHHHHHhhCCC
Q 043780 228 -NSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALV-----------ENEKKLLEKINILCLMEIIFSRPS 295 (386)
Q Consensus 228 -~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~-----------~~~~~l~~KirlLaL~~L~~~r~~ 295 (386)
+.| +.-+..-++|..|.+|.+-.+..+-+++.+.+....... .....+.+-||+++=.
T Consensus 281 dKkL--~e~p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~y-------- 350 (439)
T KOG1498|consen 281 DKKL--SELPDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKY-------- 350 (439)
T ss_pred cccc--ccCccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHH--------
Confidence 112 233446689999999998888877666655554441000 0122445666766543
Q ss_pred CCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHH
Q 043780 296 EDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLS 375 (386)
Q Consensus 296 ~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~ 375 (386)
...||+.++++-++.|.++.|.++=..+..|-+.+|||+..+.+.+.-+ +.+.+-|..|..+|+++...
T Consensus 351 -YSrIt~~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~----------K~~~~~LneW~~nve~L~~l 419 (439)
T KOG1498|consen 351 -YSRITLKRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKV----------KDSNEILNEWASNVEKLLGL 419 (439)
T ss_pred -HhhccHHHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEec----------ccHHHHHHHHHhhHHHHHHH
Confidence 4689999999999999999999999999999999999999999988743 34567788999999998888
Q ss_pred HHhhcc
Q 043780 376 IEAETP 381 (386)
Q Consensus 376 l~~~~~ 381 (386)
++...+
T Consensus 420 l~K~~H 425 (439)
T KOG1498|consen 420 LEKVSH 425 (439)
T ss_pred HHHHHH
Confidence 876543
No 13
>COG5600 Transcription-associated recombination protein [DNA replication, recombination, and repair]
Probab=98.06 E-value=0.00086 Score=66.77 Aligned_cols=218 Identities=20% Similarity=0.269 Sum_probs=130.5
Q ss_pred chHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCC----HHHHHHHHHHHHHHHHHhhcHHHHHHHHHH-Hhcc
Q 043780 113 EPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDID----PSVYANYYWVSSQYHKFHQEFAEFYKCALL-YLAY 187 (386)
Q Consensus 113 ~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~----~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~-yL~~ 187 (386)
.+..|+--....+|++++..+-|+..+...+.. +..+.. +.++ .|.+..+.||=...++-+.|-+... ++.|
T Consensus 174 ~g~y~iaNlL~~iY~Rl~~~~l~~n~lka~~~v--s~~Di~~~~~sq~v-~f~YYLG~~~l~~en~heA~~~L~~aFl~c 250 (413)
T COG5600 174 VGLYYIANLLFQIYLRLGRFKLCENFLKASKEV--SMPDISEYQKSQVV-VFHYYLGIYYLLNENFHEAFLHLNEAFLQC 250 (413)
T ss_pred HHHHHHHHHHHHHHHHhccHHHHHHHHHhcccc--cccccchhhhccee-ehhhHHHHHHHHHHhHHHHHHHHHHHHHhC
Confidence 455666667788999999999999888876651 111111 1111 1222223333333344444444444 4455
Q ss_pred CCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCC-cHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhc
Q 043780 188 TSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTK-VEWLYYILQAFNSGDLVRYQELCRVHNAALRA 266 (386)
Q Consensus 188 ~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~-~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~ 266 (386)
-..- ...+..++-..+..+|+-.+.+ |--.-|...+ -+.+--|..++.+||+++|...+++|...+.+
T Consensus 251 ~~l~---~~n~~rIl~~~ipt~Llv~~~~--------Ptk~~L~r~~~~s~~~~LvkavrsGni~~~~~~l~~ner~~~~ 319 (413)
T COG5600 251 PWLI---TRNRKRILPYYIPTSLLVNKFP--------PTKDLLERFKRCSVYSPLVKAVRSGNIEDFDLALSRNERKFAK 319 (413)
T ss_pred hhhh---hcchheehhHHhhHHHHhCCCC--------CchHHHHhccccchhHHHHHHHHcCCHHHHHHHHHHhHHHHHH
Confidence 4321 2223344555566666655444 3222332211 22344577899999999999999999888877
Q ss_pred CchhhhhHHHHHHHHHHHHHHHHHhh---CCCCCCccChHH--HHHHcCC-C----hhHHHHHHHHHhhccceEEeecCC
Q 043780 267 QPALVENEKKLLEKINILCLMEIIFS---RPSEDRTIPLSI--IAERTKL-S----IEDVEHLLMKSLSVHLIEGIIDQV 336 (386)
Q Consensus 267 ~~~L~~~~~~l~~KirlLaL~~L~~~---r~~~~r~isf~~--Ia~~l~i-~----~~eVE~lvikAi~~gLI~G~IDqv 336 (386)
.+.. -.|..+.++++.-+|.-+ --..+..+|++- |+..+.. + .++||-.+..+|+.|+++|.|...
T Consensus 320 ~~l~----ltl~~~~~~V~~RNL~rk~w~~~~~qsrlp~sil~~~~qls~~dn~~~~~~VEciL~tlI~~G~lrgYis~s 395 (413)
T COG5600 320 RGLY----LTLLAHYPLVCFRNLFRKIWRLHGKQSRLPLSILLIVLQLSAIDNFHSFKEVECILVTLIGLGLLRGYISHS 395 (413)
T ss_pred cchH----HHHHhhccHHHHHHHHHHHHhhccccccCcHHHHHHHHHccCCCcccChHHHHHHHHHHHhhhhhhheeccc
Confidence 6642 234455666666655321 011233355554 4444444 2 468999999999999999999999
Q ss_pred CCEEEEEeeccc
Q 043780 337 EGTVHVSWVQPR 348 (386)
Q Consensus 337 ~~~v~vt~v~~R 348 (386)
.++|.++.-.|=
T Consensus 396 ~~~vV~sk~~pF 407 (413)
T COG5600 396 RRTVVFSKKDPF 407 (413)
T ss_pred ceEEEEecCCCC
Confidence 999999876653
No 14
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.97 E-value=0.00037 Score=69.97 Aligned_cols=223 Identities=18% Similarity=0.136 Sum_probs=145.3
Q ss_pred ccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhc-cCCCCCC-ChhHHHHHHHHH
Q 043780 128 EQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLA-YTSVESL-SDSFKLDLAFDL 205 (386)
Q Consensus 128 ~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~-~~~~~~~-~~~e~~~~a~~l 205 (386)
-.|++..+.....+.+...+....+...+++..+=+++...=..++|.+..++-+..-. .++.+++ ++ .+.+..-
T Consensus 199 ~~~nw~hv~sy~~~A~st~~~~~~~~q~v~~kl~C~agLa~L~lkkyk~aa~~fL~~~~~~~d~~~ivtp---sdv~iYg 275 (466)
T KOG0686|consen 199 YMGNWGHVLSYISKAESTPDANENLAQEVPAKLKCAAGLANLLLKKYKSAAKYFLLAEFDHCDYPEIVTP---SDVAIYG 275 (466)
T ss_pred hhcchhhhhhHHHHHHhCchhhhhHHHhcCcchHHHHHHHHHHHHHHHHHHHHHHhCCCCccCccceecc---hhhHHHH
Confidence 45677777777777776654444455666666555555443233344333333332111 1121121 22 2345555
Q ss_pred HHHHhcCCCccccccccc----ChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHH
Q 043780 206 SLSALLGDNIYNFGELLA----HPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKI 281 (386)
Q Consensus 206 ~i~AL~~~~iy~FgeLl~----~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~Ki 281 (386)
...||.. |+=.+|.. .-.++.+-+. .+-+.++|..|.++.++.--+.+.+.++.+.-++-|..|-..|-.+|
T Consensus 276 gLcALAt---fdr~~Lk~~vi~n~~Fk~flel-~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLaphVd~Ly~~I 351 (466)
T KOG0686|consen 276 GLCALAT---FDRQDLKLNVIKNESFKLFLEL-EPQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAPHVDNLYSLI 351 (466)
T ss_pred hhHhhcc---CCHHHHHHHHHcchhhhhHHhc-ChHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcchhHHHHHHHH
Confidence 5555543 11112221 1111111111 13488999999999999999999888888777888888988999999
Q ss_pred HHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHH
Q 043780 282 NILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDR 361 (386)
Q Consensus 282 rlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~ 361 (386)
|-=+|+..-. | ..++.++.+|.+.+.++...|.=|++.|-.|.|+||||+.++.+.+.-.-.|.=+-+.+..|.++
T Consensus 352 R~r~llqy~~--p--y~s~~m~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~~~en~~fe~~~~~~~~ 427 (466)
T KOG0686|consen 352 RNRALLQYLS--P--YSSADMSKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDADSENATFERVLPMGKR 427 (466)
T ss_pred HHhhHHHhcC--c--cccchHHHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeecccccccchhhhcchhhHH
Confidence 9999999743 4 68999999999999999999999999999999999999999999998885554444444444333
No 15
>KOG2688 consensus Transcription-associated recombination protein - Thp1p [Cell cycle control, cell division, chromosome partitioning]
Probab=97.92 E-value=0.00013 Score=73.54 Aligned_cols=220 Identities=17% Similarity=0.155 Sum_probs=144.3
Q ss_pred CCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccc-cCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCC
Q 043780 111 KEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDS-MTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTS 189 (386)
Q Consensus 111 ~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~-~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~ 189 (386)
.+-|..++-....++|.+.+.+.-|+..+...+..... .+..-+.++..-|++. .++--..|+.+.+..+......++
T Consensus 158 kk~~~~~i~n~lf~Iyfri~~~~L~k~l~ra~~~~~~~~~~~~l~~~v~y~YylG-r~a~~~~d~~~A~~~L~~af~~cp 236 (394)
T KOG2688|consen 158 KKVAMLYIVNQLFQIYFRIEKLLLCKNLIRAFDQSGSDISDFPLAQLVVYHYYLG-RYAMFESDFLNAFLQLNEAFRLCP 236 (394)
T ss_pred hhhHHHHHHHHHHHHHHHHhhHHHhHHHHHHhhccccchhhcccccceeeeeeee-eehhhhhhHHHHHHHHHHHHHhCc
Confidence 34578899999999999999999999988876654211 1111122222222222 222223445555555555444444
Q ss_pred CCCCChhHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCch
Q 043780 190 VESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPA 269 (386)
Q Consensus 190 ~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~ 269 (386)
..- ......+...++.-.+.-.. +|-..-|..-.-..+-.|+.++..||+..|....+.|...|.+.+.
T Consensus 237 ~~~--~~n~~~iliylip~~~llg~---------~Pt~~lL~~~~~~~~~~lv~aVr~Gnl~~f~~al~~~E~~f~~~gi 305 (394)
T KOG2688|consen 237 DLL--LKNKRLILIYLIPTGLLLGR---------IPTKELLDFYTLDKYSPLVQAVRSGNLRLFDLALADNERFFIRSGI 305 (394)
T ss_pred HHH--HhhhhhHHHHHhHHHHHhcc---------CcchhhHhHhhHHhHHHHHHHHHhccHHHHHHHHhhhHHHHHHhcc
Confidence 432 22334444444444333221 3444444321123456788999999999999999999888877764
Q ss_pred hhhhHHHHHHHHHHHHHHHHHhhC---CCCCCccChHHHHHHcCC-C-----hhHHHHHHHHHhhccceEEeecCCCCEE
Q 043780 270 LVENEKKLLEKINILCLMEIIFSR---PSEDRTIPLSIIAERTKL-S-----IEDVEHLLMKSLSVHLIEGIIDQVEGTV 340 (386)
Q Consensus 270 L~~~~~~l~~KirlLaL~~L~~~r---~~~~r~isf~~Ia~~l~i-~-----~~eVE~lvikAi~~gLI~G~IDqv~~~v 340 (386)
. .+..|.++++.-+|..+- -.....+|++.+..+++. + .+|||-.+..+|+.|.|+|.|+...+++
T Consensus 306 ~-----l~l~~l~lv~yrnL~kkv~~~~~~~~~lpls~~~~al~~~~~~~~~~deveciLa~lI~~G~ikgYish~~~~~ 380 (394)
T KOG2688|consen 306 Y-----LTLEKLPLVVYRNLFKKVIQLWGKTSQLPLSRFLTALQFSGVTDVDLDEVECILANLIDLGRIKGYISHQLQTL 380 (394)
T ss_pred H-----HHhhhhhHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHhhcCCCCCchhhHHHHHHhhhhhccccchhchhhheE
Confidence 3 233668888888875431 124578999999999877 3 5899999999999999999999999999
Q ss_pred EEEeecc
Q 043780 341 HVSWVQP 347 (386)
Q Consensus 341 ~vt~v~~ 347 (386)
.++.-.|
T Consensus 381 V~sK~~p 387 (394)
T KOG2688|consen 381 VFSKKDP 387 (394)
T ss_pred EEecCCC
Confidence 9987654
No 16
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=97.55 E-value=0.032 Score=54.29 Aligned_cols=242 Identities=17% Similarity=0.186 Sum_probs=141.2
Q ss_pred ChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHH
Q 043780 88 EKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQY 167 (386)
Q Consensus 88 d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~ 167 (386)
|.+.+.+.+.++.++-.....+ =-+.++++-.+.+ .||-..+++.|+.+...++. |-| +-+..=|.+..-.
T Consensus 130 D~~ng~~~~~~~~~~a~stg~K---iDv~l~kiRlg~~---y~d~~vV~e~lE~~~~~iEk--GgD-WeRrNRyK~Y~Gi 200 (412)
T COG5187 130 DIQNGFEWMRRLMRDAMSTGLK---IDVFLCKIRLGLI---YGDRKVVEESLEVADDIIEK--GGD-WERRNRYKVYKGI 200 (412)
T ss_pred hhhhHHHHHHHHHHHHHhcccc---hhhHHHHHHHHHh---hccHHHHHHHHHHHHHHHHh--CCC-HHhhhhHHHHHHH
Confidence 5666666665554443211111 1234555554444 46777777888877777664 222 2222223333333
Q ss_pred HH-HhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCccc-ccccccChhhhcccC--CCcHHHHHHHH
Q 043780 168 HK-FHQEFAEFYKCALLYLAYTSVESLSDSFKLDLAFDLSLSALLGDNIYN-FGELLAHPIINSLTG--TKVEWLYYILQ 243 (386)
Q Consensus 168 ~k-~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~-FgeLl~~p~v~~L~~--~~~~~l~~LL~ 243 (386)
|+ ...+|.+.-.-....|++|+..++..-++ .+...++..+..=+--. =.-++..|.+-++=+ .....+.++..
T Consensus 201 ~~m~~RnFkeAa~Ll~d~l~tF~S~El~sY~~--~vrYa~~~Gl~~leR~diktki~dspevl~vi~~~e~l~sl~~l~~ 278 (412)
T COG5187 201 FKMMRRNFKEAAILLSDILPTFESSELISYSR--AVRYAIFCGLLRLERRDIKTKILDSPEVLDVIGSSEKLGSLVQLAT 278 (412)
T ss_pred HHHHHHhhHHHHHHHHHHhccccccccccHHH--HHHHHHHhhhheeehhhhhhhhcCCHHHHHhccchhhhhhHHHHHH
Confidence 33 35677777777888888887665533222 23344444443211111 123444454333211 12233444444
Q ss_pred HHhcCCHH-HHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHH
Q 043780 244 AFNSGDLV-RYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMK 322 (386)
Q Consensus 244 ~f~~G~l~-~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvik 322 (386)
.+-.-|+. .|.....-+...+.....|..|.+.--+-||.=.-..+-- ..|.++.+..|+..|++++=|+.=+=+
T Consensus 279 SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLE----SYr~lsl~sMA~tFgVSV~yvdrDLg~ 354 (412)
T COG5187 279 SLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLE----SYRLLSLESMAQTFGVSVEYVDRDLGE 354 (412)
T ss_pred HHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHH----HHHHhhHHHHHHHhCccHHHHhhhHHh
Confidence 44444554 4555444333444444455666555557788877777754 268999999999999999988888888
Q ss_pred HhhccceEEeecCCCCEEEEEe
Q 043780 323 SLSVHLIEGIIDQVEGTVHVSW 344 (386)
Q Consensus 323 Ai~~gLI~G~IDqv~~~v~vt~ 344 (386)
-|-.|-+.+.||.++|+|..++
T Consensus 355 FIp~~~LncvIDRvnGvVetnr 376 (412)
T COG5187 355 FIPEGRLNCVIDRVNGVVETNR 376 (412)
T ss_pred hCCCCceeeeeecccceEeccC
Confidence 8899999999999999999984
No 17
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=97.43 E-value=0.016 Score=56.26 Aligned_cols=249 Identities=14% Similarity=0.160 Sum_probs=149.1
Q ss_pred ChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHH
Q 043780 88 EKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQY 167 (386)
Q Consensus 88 d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~ 167 (386)
...+||+.+..+...++.-|.+. ..+-+-+.-+.++-...++..++..|..++.. ..-.-.+|.+.+..=..++-+
T Consensus 140 ~YsdalalIn~ll~ElKk~DDK~---~Li~vhllESKvyh~irnv~KskaSLTaArt~-Ans~YCPpqlqa~lDL~sGIl 215 (421)
T COG5159 140 KYSDALALINPLLHELKKYDDKI---NLITVHLLESKVYHEIRNVSKSKASLTAARTL-ANSAYCPPQLQAQLDLLSGIL 215 (421)
T ss_pred cHHHHHHHHHHHHHHHHhhcCcc---ceeehhhhhHHHHHHHHhhhhhhhHHHHHHHH-hhccCCCHHHHHHHHHhccce
Confidence 45677777777766665322111 11111222233333445666777777665532 222234566666554444444
Q ss_pred HHHhhcHHHHHHHHHHHh-ccCCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccCh-hhhcccCCCcHHHHHHHHHH
Q 043780 168 HKFHQEFAEFYKCALLYL-AYTSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHP-IINSLTGTKVEWLYYILQAF 245 (386)
Q Consensus 168 ~k~~~~~~~~y~~~l~yL-~~~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p-~v~~L~~~~~~~l~~LL~~f 245 (386)
+-.-.+|.-.|.+-...+ +++.... ...+..-...+.++-+....+=.-+.++... .+...++..-..+...-++|
T Consensus 216 hcdd~dyktA~SYF~Ea~Egft~l~~--d~kAc~sLkYmlLSkIMlN~~~evk~vl~~K~t~~~y~~r~I~am~avaea~ 293 (421)
T COG5159 216 HCDDRDYKTASSYFIEALEGFTLLKM--DVKACVSLKYMLLSKIMLNRREEVKAVLRNKNTLKHYDDRMIRAMLAVAEAF 293 (421)
T ss_pred eeccccchhHHHHHHHHHhccccccc--hHHHHHHHHHHHHHHHHHhhHHHHHHHHccchhHhhhhhhhHHHHHHHHHHh
Confidence 433455555555555544 5554431 2334444444554444443333333333332 23334444455677788999
Q ss_pred hcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 246 NSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 246 ~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...++.+|...++.+.+.+.++|...+|-+.|..-+-=--|+..+- | ...+..+-||+-+|++..+||.=+-+.|-
T Consensus 294 ~NRsL~df~~aL~qY~~el~~D~~iRsHl~~LYD~LLe~Nl~kiiE--P--fs~VeishIa~viGldt~qvEgKLsqMIL 369 (421)
T COG5159 294 GNRSLKDFSDALAQYSDELHQDSFIRSHLQYLYDVLLEKNLVKIIE--P--FSVVEISHIADVIGLDTNQVEGKLSQMIL 369 (421)
T ss_pred CCCcHhhHHHHHHHhhHHhccCHHHHHHHHHHHHHHHHhhhhhhcC--c--ceeeehhHHHHHhcccHHHHHHHHHHHHH
Confidence 9999999999999999999888876666444433222223333332 4 34556666999999999999999999999
Q ss_pred ccceEEeecCCCCEEEEEeec
Q 043780 326 VHLIEGIIDQVEGTVHVSWVQ 346 (386)
Q Consensus 326 ~gLI~G~IDqv~~~v~vt~v~ 346 (386)
.+++-|.+||.++.+.|.--.
T Consensus 370 DKifyG~LDqg~gcLivy~ep 390 (421)
T COG5159 370 DKIFYGTLDQGDGCLIVYGEP 390 (421)
T ss_pred HHHHHhhhccCCceEEEeCCc
Confidence 999999999999999987543
No 18
>KOG2582 consensus COP9 signalosome, subunit CSN3 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.28 E-value=0.21 Score=50.10 Aligned_cols=331 Identities=17% Similarity=0.169 Sum_probs=174.3
Q ss_pred HHHHHHHHHhcC--C---chHHHHHHHHHHHHhhhHHHHHHHHH----------------HHHhchhhc-CchhHHHHHH
Q 043780 3 ALQYLESLRNDH--P---ELGEWYNALADLYQKKLWHQLTLKLE----------------QFVAHAVFQ-AGDALIQLYH 60 (386)
Q Consensus 3 ~~~~L~~~~~~~--p---~~~~~~~~~~~l~~~KLWhqLt~~l~----------------~~~~~~~~~-~~~~~~~ly~ 60 (386)
+++++.++++.. | ++++.+.+-.++.+|+.=|--+ .|. --+..|... ..+.++++++
T Consensus 5 l~a~i~~~~~~~~~~~~~eL~~~i~~~~ell~k~~~~~~~-~L~~ld~~~hSlgml~~l~~~f~~~~~~~~~~~li~~~~ 83 (422)
T KOG2582|consen 5 LEAAINELCSLSHSSNVGELAELIVKSKELLAKNSSDLDA-VLLHLDPQVHSLGMLAVLKVKFHTPSANPDPETLIELLN 83 (422)
T ss_pred HHHHHHHHHhhhcCCcHHHHHHHHHhhHHHHHhCcchHHH-HHHhcCccccchhhhhhhhccccCcccCCCHHHHHHHHH
Confidence 455665555443 3 6777777888888877443222 111 112222111 1346889999
Q ss_pred HHHHHHHhhcChHHHH-HHHHHHHh-------cCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCCh
Q 043780 61 NFITDFETKINLLKLA-HFAVIVSR-------QYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDR 132 (386)
Q Consensus 61 ~fi~~f~~kin~l~l~-~i~~~v~~-------~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l 132 (386)
.||...- --+++++ +++...++ +-+.|.=.+..+.+...++.. .....--+..-+...-|+.+++
T Consensus 84 ~FV~~~n--~eqlr~as~~f~~lc~~l~~~~~~~~~p~~gi~ii~~av~k~~~-----~~~qlT~~H~~l~~~~L~ak~y 156 (422)
T KOG2582|consen 84 DFVDENN--GEQLRLASEIFFPLCHDLTEAVVKKNKPLRGIRIIMQAVDKMQP-----SNGQLTSIHADLLQLCLEAKDY 156 (422)
T ss_pred HHHHhcC--hHHHhhHHHHHHHHHHHHHHHHHhcCCccccchHHHHHHHHhcc-----CccchhhhHHHHHHHHHHhhcc
Confidence 9987643 3344433 22222222 233565566777777777641 1111111112222233344444
Q ss_pred HHHHHHHHhccccc-cccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHH-HhccCCCCCCChhHHHHHHH-H-HHHH
Q 043780 133 KECKKLLEDGKSTL-DSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALL-YLAYTSVESLSDSFKLDLAF-D-LSLS 208 (386)
Q Consensus 133 ~~~~~~l~~~~~~l-~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~-yL~~~~~~~~~~~e~~~~a~-~-l~i~ 208 (386)
......++.--..+ ......++..--.|++..+-.+=..++|+ .++- |=.|+.....+-......|+ . +-+.
T Consensus 157 ~~~~p~ld~divei~~~n~h~~~k~fL~Y~yYgg~iciglk~fe----~Al~~~e~~v~~Pa~~vs~~hlEaYkkylLvs 232 (422)
T KOG2582|consen 157 ASVLPYLDDDIVEICKANPHLDPKYFLLYLYYGGMICIGLKRFE----RALYLLEICVTTPAMAVSHIHLEAYKKYLLVS 232 (422)
T ss_pred cccCCccchhHHHHhccCCCCCHHHHHHHHHhcceeeeccccHH----HHHHHHHHHHhcchhHHHHHHHHHHHHHHHHH
Confidence 43332222111000 00122333333333333332222233333 2222 22343211112222222222 2 3334
Q ss_pred HhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCch--hhhhHHHHHHHHHHHHH
Q 043780 209 ALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPA--LVENEKKLLEKINILCL 286 (386)
Q Consensus 209 AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~--L~~~~~~l~~KirlLaL 286 (386)
-+...+++...+=-...+....+ +--.++.+++.+...+.-.+.+....+|.+.|.++.. |....-...-|=+++.|
T Consensus 233 LI~~GK~~ql~k~ts~~~~r~~K-~ms~pY~ef~~~Y~~~~~~eLr~lVk~~~~rF~kDnnt~l~k~av~sl~k~nI~rl 311 (422)
T KOG2582|consen 233 LILTGKVFQLPKNTSQNAGRFFK-PMSNPYHEFLNVYLKDSSTELRTLVKKHSERFTKDNNTGLAKQAVSSLYKKNIQRL 311 (422)
T ss_pred hhhcCceeeccccchhhhHHhcc-cCCchHHHHHHHHhcCCcHHHHHHHHHHHHHHhhcCcHHHHHHHHHHHHHHHHHHH
Confidence 44444444322222111111222 2223688999999999999999999999888887662 22222222356677777
Q ss_pred HHHHhhCCCCCCccChHHHHHHcCC-ChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHH
Q 043780 287 MEIIFSRPSEDRTIPLSIIAERTKL-SIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIK 356 (386)
Q Consensus 287 ~~L~~~r~~~~r~isf~~Ia~~l~i-~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~ 356 (386)
.... -+++.++||+..++ +.+|||..|+.-|..|=|-++|| |.|.++.--..+-+++-..
T Consensus 312 tktF-------~sLsL~dIA~~vQLa~~qevek~Ilqmie~~~i~a~iN---G~v~f~~n~e~~~SpeM~~ 372 (422)
T KOG2582|consen 312 TKTF-------LSLSLSDIASRVQLASAQEVEKYILQMIEDGEIFASIN---GMVFFTDNPEKYNSPEMHE 372 (422)
T ss_pred HHHH-------HHhhHHHHHHHHHhcchHHHHHHHHHHhccCceEEEec---ceEEEecCcccCCCHHHHh
Confidence 7753 48999999999999 67899999999999999999999 7788777666777776555
No 19
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=96.28 E-value=0.4 Score=52.32 Aligned_cols=241 Identities=17% Similarity=0.162 Sum_probs=139.1
Q ss_pred hHHHHHHHHhccccc--cccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHH-HhccC-CC-CCCChhHHHHHHHHHH
Q 043780 132 RKECKKLLEDGKSTL--DSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALL-YLAYT-SV-ESLSDSFKLDLAFDLS 206 (386)
Q Consensus 132 l~~~~~~l~~~~~~l--~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~-yL~~~-~~-~~~~~~e~~~~a~~l~ 206 (386)
..+|-+.++++...+ .+. ..-|...+.||.=.+.++=.-|++- |...++. +-..+ +. ..++.++-+..|-...
T Consensus 248 WQEAyrSiEDIhgLm~lSKr-tPkp~~laNYY~KL~~VF~~sgn~L-fHAaAw~k~f~l~k~~~K~~Tqde~q~~as~Vl 325 (988)
T KOG2072|consen 248 WQEAYRSIEDIHGLMKLSKR-TPKPSTLANYYEKLAKVFWKSGNPL-FHAAAWLKLFKLYKNMNKNLTQDELQRMASRVL 325 (988)
T ss_pred HHHHHHHHHHHHHHHHHhcC-CCchhHHHHHHHHHHHHHHhcCcHH-HHHHHHHHHHHHHHHhcccccHHHHHHHHHHHH
Confidence 346666666665432 332 3347888999988888876666632 3333333 22222 22 2578899999999999
Q ss_pred HHHhcCCCcc---cccccccChhhh---c--------ccC--CCcHHHHHHHH----HHhcCCHHHHHHHHHHh------
Q 043780 207 LSALLGDNIY---NFGELLAHPIIN---S--------LTG--TKVEWLYYILQ----AFNSGDLVRYQELCRVH------ 260 (386)
Q Consensus 207 i~AL~~~~iy---~FgeLl~~p~v~---~--------L~~--~~~~~l~~LL~----~f~~G~l~~f~~~~~~~------ 260 (386)
++||.-|-.. .++-++..+..- . |.. |...-|.+++. -++..++.+.-.+++.+
T Consensus 326 LaaLSIP~~~~~~~~~r~~e~e~~~~ek~~rla~LL~L~~~PTR~~ll~e~v~~gV~~~v~qe~kdLY~iLEveF~PL~l 405 (988)
T KOG2072|consen 326 LAALSIPIPDARSDSARLIEIEDIGKEKNLRLANLLGLPAPPTRKGLLKEAVREGVLSKVDQEVKDLYNILEVEFHPLKL 405 (988)
T ss_pred HHHhcCCCCCcccccccccccccchhhHHHHHHHHhCCCCCccHHHHHHHHHHhccHhhhhHHHHHHHHHHHhcCCHHHH
Confidence 9999988322 233344333320 0 111 11111111111 01111222222222211
Q ss_pred -------hhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCC-ChhHHHHHHHHHhhccceEEe
Q 043780 261 -------NAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKL-SIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 261 -------~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i-~~~eVE~lvikAi~~gLI~G~ 332 (386)
=+.+++.|.-..+-+.| +++.++.|+.-++. -..+|+|+.+.+-.-. +.-++|.++|+|...+.+.-+
T Consensus 406 ~k~lq~ll~~ls~~~~~~QYI~sL-q~v~~~RllqQvSq---iY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~ir 481 (988)
T KOG2072|consen 406 CKKLQPLLDKLSESPDKSQYIPSL-QDVIILRLLQQVSQ---IYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIR 481 (988)
T ss_pred HHHHHHHHHHHHcCCCccccchhH-HHHHHHHHHHHHHH---HHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEE
Confidence 11244445444444555 66666666665553 2568999988876544 788999999999999999999
Q ss_pred ecCCCCEEEEE---eecccc-------CChhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 043780 333 IDQVEGTVHVS---WVQPRV-------LGIPQIKSLRDRLDSWLGKVHTALLSIEA 378 (386)
Q Consensus 333 IDqv~~~v~vt---~v~~R~-------l~~~q~~~L~~~L~~W~~~v~~~~~~l~~ 378 (386)
||....+|.+. ....|+ +...--+.+++.|....+.+..+.+.+..
T Consensus 482 iDH~~~~v~FgsDl~~s~~~~~~eg~~lqs~~sE~ir~~L~~m~~~L~~~~e~~dp 537 (988)
T KOG2072|consen 482 IDHESNSVSFGSDLFLSKEEDEPEGPELQSMPSEGIRSQLTAMAESLSKVVEELDP 537 (988)
T ss_pred eccccceeeeccccccccccccCCCchhhcCchHhHHHHHHHHHHHHHHHHHhhCh
Confidence 99999999998 322111 11123456777777777777777666543
No 20
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=95.81 E-value=0.71 Score=45.38 Aligned_cols=87 Identities=14% Similarity=0.176 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhH
Q 043780 276 KLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQI 355 (386)
Q Consensus 276 ~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~ 355 (386)
.+.+.+|+++=- ...|+-.+|..-++.|+.+.|..+-.....|.+.++|||..+.+.+..-+
T Consensus 339 viEHN~RvI~~y---------YSrI~~~rl~~lld~~~s~te~~ISdlVN~G~~yaKiNrpa~Ii~FEK~~--------- 400 (439)
T COG5071 339 VIEHNIRVIANY---------YSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQ--------- 400 (439)
T ss_pred HHHhhHhHHHHH---------hhhhhHHHHHHHHcCCHHHHHHHHHHHHhcCcEEEEecCccceEEeeccc---------
Confidence 445667766422 46799999999999999999999999999999999999999999887332
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcc
Q 043780 356 KSLRDRLDSWLGKVHTALLSIEAETP 381 (386)
Q Consensus 356 ~~L~~~L~~W~~~v~~~~~~l~~~~~ 381 (386)
...+.|..|..+|..++..++....
T Consensus 401 -n~~~~lneW~~NV~ellgklek~~H 425 (439)
T COG5071 401 -NVQEQLNEWGSNVTELLGKLEKVRH 425 (439)
T ss_pred -cHHHHHHHhcccHHHHHHHHHHHhH
Confidence 3457799999999999998886543
No 21
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=95.61 E-value=0.073 Score=52.46 Aligned_cols=126 Identities=16% Similarity=0.171 Sum_probs=86.1
Q ss_pred HhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 245 FNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 245 f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
+..-|+++-...+.+-..-+..++.|++--+-..+-.|++-.-..|- -+..|+.+.+|+.+.++.+|.|.|++..|
T Consensus 299 yvn~DFdgAq~kl~eCeeVl~nDfFLva~l~~F~E~ARl~ifEtfCR----IHqcIti~mLA~kLnm~~eeaErwivnlI 374 (432)
T KOG2758|consen 299 YVNYDFDGAQKKLRECEEVLVNDFFLVALLDEFLENARLLIFETFCR----IHQCITIDMLADKLNMDPEEAERWIVNLI 374 (432)
T ss_pred hhccchHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHHHHH----HHHheeHHHHHHHhcCCHHHHHHHHHHHH
Confidence 34445555554444434446666666654333348899998877774 36799999999999999999999999999
Q ss_pred hccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHHHHhh
Q 043780 325 SVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSIEAE 379 (386)
Q Consensus 325 ~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l~~~ 379 (386)
+...+.++||..-|.|.+.--++-. -+ ++-++-.+-.-+..++...++..
T Consensus 375 r~~rl~AkidSklg~Vvmg~~~~s~--~q---Q~ie~tksLS~rsq~la~~lek~ 424 (432)
T KOG2758|consen 375 RTARLDAKIDSKLGHVVMGHPTVSP--HQ---QLIEKTKSLSFRSQNLAQQLEKK 424 (432)
T ss_pred HHhhhhhhhccccCceeecCCCCCH--HH---HHHHhccccchhHHHHHHHHHHH
Confidence 9999999999999999887544332 12 33344444444444444444433
No 22
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=95.12 E-value=0.12 Score=55.36 Aligned_cols=131 Identities=20% Similarity=0.212 Sum_probs=99.0
Q ss_pred ccccccChhhhcccCCCc---HHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCC
Q 043780 218 FGELLAHPIINSLTGTKV---EWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRP 294 (386)
Q Consensus 218 FgeLl~~p~v~~L~~~~~---~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~ 294 (386)
|--.|.+---+++.|+|- .-+..--.+...||+.+-.+|+-.+-..|.-.|.-..-.+-|.+||+-=+|-..-|.-+
T Consensus 634 frr~Le~serqsf~gPPEn~RehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftYs 713 (843)
T KOG1076|consen 634 FRRQLEHSERQSFTGPPENTREHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTYS 713 (843)
T ss_pred HHHHHHHHhhccccCCchhHHHHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 334444444455566552 23344557888999999888765555556655532222445778999999988877655
Q ss_pred CCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccc
Q 043780 295 SEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPR 348 (386)
Q Consensus 295 ~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R 348 (386)
+-..++|.+.+|+...+|+..|-..|=+.|...=|.+++||+.++|.+++|.|-
T Consensus 714 s~Y~SvSl~~LA~mFdLp~~~VhsIiSkmiineEl~AslDqpt~~iv~hrvE~s 767 (843)
T KOG1076|consen 714 SVYDSVSLAKLADMFDLPEPKVHSIISKMIINEELHASLDQPTQCIVMHRVEPS 767 (843)
T ss_pred hhhhhccHHHHHHHhCCCchhHHHHHHHHHHHHHhhhccCCCcceEEEeeccch
Confidence 567899999999999999999999999999999999999999999999988764
No 23
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=94.12 E-value=1.1 Score=43.40 Aligned_cols=173 Identities=14% Similarity=0.118 Sum_probs=103.9
Q ss_pred HHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhccc-CChHHHHHHHHhccccccccCCCCHHHHHH
Q 043780 81 IVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQ-GDRKECKKLLEDGKSTLDSMTDIDPSVYAN 159 (386)
Q Consensus 81 ~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~-~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~ 159 (386)
.+.+.. +|++|++.+++..+-... .........+...+|.++-.. |+++.+-+...++-...+.-. .+.-...
T Consensus 83 ~~~k~~-~~~~Ai~~~~~A~~~y~~---~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~e~--~~~~a~~ 156 (282)
T PF14938_consen 83 NCYKKG-DPDEAIECYEKAIEIYRE---AGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQEG--SPHSAAE 156 (282)
T ss_dssp HHHHHT-THHHHHHHHHHHHHHHHH---CT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHHTT---HHHHHH
T ss_pred HHHHhh-CHHHHHHHHHHHHHHHHh---cCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHCC--ChhhHHH
Confidence 334444 789999999888776642 122334455666788888887 999999988887766544322 3555667
Q ss_pred HHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccC-----hhhhcccCCC
Q 043780 160 YYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAH-----PIINSLTGTK 234 (386)
Q Consensus 160 ~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~-----p~v~~L~~~~ 234 (386)
.+.-++.++-..++|.+.....-+.....-.+.+..-...+.....++..|..++...-...+.- |.+. .+.+
T Consensus 157 ~~~~~A~l~~~l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L~~~D~v~A~~~~~~~~~~~~~F~--~s~E 234 (282)
T PF14938_consen 157 CLLKAADLYARLGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHLAMGDYVAARKALERYCSQDPSFA--SSRE 234 (282)
T ss_dssp HHHHHHHHHHHTT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHGTTSTTST--TSHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHHHcCCHHHHHHHHHHHHhhCCCCC--CcHH
Confidence 77777777777788877666555544333222344444455555666666665444322221110 2221 1234
Q ss_pred cHHHHHHHHHHhcCCHHHHHHHHHHhh
Q 043780 235 VEWLYYILQAFNSGDLVRYQELCRVHN 261 (386)
Q Consensus 235 ~~~l~~LL~~f~~G~l~~f~~~~~~~~ 261 (386)
+.-+.+|++++..||.+.|.+.+..+.
T Consensus 235 ~~~~~~l~~A~~~~D~e~f~~av~~~d 261 (282)
T PF14938_consen 235 YKFLEDLLEAYEEGDVEAFTEAVAEYD 261 (282)
T ss_dssp HHHHHHHHHHHHTT-CCCHHHHCHHHT
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHc
Confidence 778889999999999999999876654
No 24
>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=91.86 E-value=1.7 Score=37.70 Aligned_cols=80 Identities=23% Similarity=0.306 Sum_probs=52.1
Q ss_pred CCcHHHHHHHHHHhcCCHHHHHHHHHHh---hhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHc
Q 043780 233 TKVEWLYYILQAFNSGDLVRYQELCRVH---NAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERT 309 (386)
Q Consensus 233 ~~~~~l~~LL~~f~~G~l~~f~~~~~~~---~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l 309 (386)
++-.-+..|.+.+-.|++.+|-...+.+ +......+.| .+.+| -++..+++.++ .+|+.+++++-|
T Consensus 39 ~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~iR--~~i~~~i~~aY------~sIs~~~la~~L 107 (143)
T PF10075_consen 39 PEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGF---EDTIR--ERIAHLISKAY------SSISLSDLAEML 107 (143)
T ss_dssp TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTH---HHHHH--HHHHHHHHHH-------SEE-HHHHHHHT
T ss_pred HHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHH---HHHHH--HHHHHHHHHHH------hHcCHHHHHHHh
Confidence 4445578899999999999998876553 2222223322 33332 34556666664 799999999999
Q ss_pred CCChhHHHHHHHHH
Q 043780 310 KLSIEDVEHLLMKS 323 (386)
Q Consensus 310 ~i~~~eVE~lvikA 323 (386)
|++.+|++.++.+-
T Consensus 108 g~~~~el~~~~~~~ 121 (143)
T PF10075_consen 108 GLSEEELEKFIKSR 121 (143)
T ss_dssp TS-HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHc
Confidence 99998999998875
No 25
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.78 E-value=9.4 Score=32.85 Aligned_cols=80 Identities=20% Similarity=0.258 Sum_probs=62.7
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEE-eecC-CCCEEEEEeeccccCChhhHH-HHHHHHHHHHHHHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG-IIDQ-VEGTVHVSWVQPRVLGIPQIK-SLRDRLDSWLGKVHTAL 373 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G-~IDq-v~~~v~vt~v~~R~l~~~q~~-~L~~~L~~W~~~v~~~~ 373 (386)
++.++-++||+.++++..-|..-|=+.+..|||.= +..- ..+..++= +..++++++ .+...|+.|.+++++++
T Consensus 40 ~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY----~~i~~ee~k~~i~~~l~~w~~~~~~~i 115 (126)
T COG3355 40 NGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLY----KPIDPEEIKKKILKDLDEWYDKMKQLI 115 (126)
T ss_pred cCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEE----ecCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57899999999999999999999999999999976 3432 23333332 345667765 57788999999999999
Q ss_pred HHHHhhc
Q 043780 374 LSIEAET 380 (386)
Q Consensus 374 ~~l~~~~ 380 (386)
+..+...
T Consensus 116 ~~~~~~~ 122 (126)
T COG3355 116 EEFEKKY 122 (126)
T ss_pred HHHhccc
Confidence 8877543
No 26
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=88.09 E-value=0.83 Score=34.68 Aligned_cols=39 Identities=21% Similarity=0.194 Sum_probs=32.1
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecC
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQ 335 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDq 335 (386)
.+.+|+++||.++++|++.||.++=.-+..|-|+-.-+.
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 579999999999999999999999999999999854433
No 27
>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=87.69 E-value=1.3 Score=40.69 Aligned_cols=58 Identities=17% Similarity=0.197 Sum_probs=42.1
Q ss_pred HHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 282 NILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 282 rlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
-|-.+++.+-. ++.+...++|..++++..+|-.-|-.....|.|.|-||.-.+-|+||
T Consensus 100 lL~~Fi~yIK~----~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKE----HKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-----SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHH----cceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 34456776654 58999999999999999999999999999999999999999999987
No 28
>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=82.46 E-value=5.1 Score=34.40 Aligned_cols=51 Identities=20% Similarity=0.386 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 279 EKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 279 ~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
.+.-+.+++.||+.. +.+.++-++||+.+++|..-|+.++=+.-..|||..
T Consensus 7 ~~YAl~~l~~La~~~--~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 7 GRYAVTAMLDLALNA--ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHHHHHHHHhCC--CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 345567788888752 346799999999999999999999999999999975
No 29
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=82.07 E-value=5.8 Score=31.01 Aligned_cols=61 Identities=20% Similarity=0.196 Sum_probs=43.4
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEe
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSW 344 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~ 344 (386)
.-+-.|+.|+... ..+.++-++||+.+++|..-|+..+=+.-..|+|+.+ -..++-.....
T Consensus 9 ~Al~~l~~la~~~--~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~-~G~~GGy~L~~ 69 (83)
T PF02082_consen 9 YALRILLYLARHP--DGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS-RGRGGGYRLAR 69 (83)
T ss_dssp HHHHHHHHHHCTT--TSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE-TSTTSEEEESS
T ss_pred HHHHHHHHHHhCC--CCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec-CCCCCceeecC
Confidence 3344555555432 3345999999999999999999999999999999764 35556555554
No 30
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=81.06 E-value=4 Score=35.82 Aligned_cols=35 Identities=17% Similarity=0.221 Sum_probs=33.4
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
+...||.+||+.+|+|...|-.-+=+....|+|+|
T Consensus 21 d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 21 NARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 57899999999999999999999999999999986
No 31
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=79.52 E-value=4.7 Score=34.86 Aligned_cols=36 Identities=28% Similarity=0.260 Sum_probs=33.1
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
+..+||.+||+.+++|...|=.-|=+....|+|+|.
T Consensus 20 d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 20 DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 345999999999999999999999999999999993
No 32
>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=79.26 E-value=6.9 Score=27.05 Aligned_cols=34 Identities=29% Similarity=0.270 Sum_probs=28.9
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
+..+|..+||+.++++..-|-..+=+....|+|+
T Consensus 15 ~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 15 NPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 3469999999999999999999999999999985
No 33
>PF09976 TPR_21: Tetratricopeptide repeat; InterPro: IPR018704 This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=78.54 E-value=41 Score=28.67 Aligned_cols=126 Identities=16% Similarity=0.083 Sum_probs=75.1
Q ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHHHhchhhcCchhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHHH
Q 043780 18 GEWYNALADLYQKKLWHQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYLE 97 (386)
Q Consensus 18 ~~~~~~~~~l~~~KLWhqLt~~l~~~~~~~~~~~~~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl~ 97 (386)
...|..+...+..+=|..+...+..++.+. . +. .... + =.|.++++.. .-++.++|.+.++
T Consensus 12 ~~~y~~~~~~~~~~~~~~~~~~~~~l~~~~--~-~s-~ya~---~--------A~l~lA~~~~----~~g~~~~A~~~l~ 72 (145)
T PF09976_consen 12 SALYEQALQALQAGDPAKAEAAAEQLAKDY--P-SS-PYAA---L--------AALQLAKAAY----EQGDYDEAKAALE 72 (145)
T ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHC--C-CC-hHHH---H--------HHHHHHHHHH----HCCCHHHHHHHHH
Confidence 345566666666666666655555555542 1 11 0110 0 1122222222 3458999999999
Q ss_pred HHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHH
Q 043780 98 GVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEF 177 (386)
Q Consensus 98 ~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~ 177 (386)
.+.++- +++.-.-..++..+.+++..|+++++.+.|+.... +.....++.+.++.+...|++.+.
T Consensus 73 ~~~~~~------~d~~l~~~a~l~LA~~~~~~~~~d~Al~~L~~~~~---------~~~~~~~~~~~Gdi~~~~g~~~~A 137 (145)
T PF09976_consen 73 KALANA------PDPELKPLARLRLARILLQQGQYDEALATLQQIPD---------EAFKALAAELLGDIYLAQGDYDEA 137 (145)
T ss_pred HHHhhC------CCHHHHHHHHHHHHHHHHHcCCHHHHHHHHHhccC---------cchHHHHHHHHHHHHHHCCCHHHH
Confidence 876644 12222344567788999999999999999976432 223445666788888888887653
No 34
>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=78.50 E-value=4.8 Score=28.55 Aligned_cols=46 Identities=24% Similarity=0.272 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 282 NILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 282 rlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
|-+.+++.... ..+.++..+|++.+++|...|-.++-.....|+|+
T Consensus 4 ral~iL~~l~~---~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 4 RALRILEALAE---SGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHCHHC---TBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHc---CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 44556665443 24568999999999999999999998888888875
No 35
>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=78.44 E-value=6.2 Score=27.40 Aligned_cols=34 Identities=32% Similarity=0.355 Sum_probs=30.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
.+..++.+|++.++++...|-+-+=.....|+|+
T Consensus 13 ~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 13 EGPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hCCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 3789999999999999999999998888899885
No 36
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=77.76 E-value=8.3 Score=31.29 Aligned_cols=34 Identities=24% Similarity=0.289 Sum_probs=32.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
..+|+.+|++.++++...|-..+-+....|+|+|
T Consensus 16 ~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 16 ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 5699999999999999999999999999999985
No 37
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.54 E-value=8.1 Score=34.61 Aligned_cols=52 Identities=19% Similarity=0.420 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 279 EKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 279 ~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
...-+.+++.||+.. +.+.+|-++||+.+++|..-|+.++-+.-..|||...
T Consensus 7 ~~yAl~~l~~lA~~~--~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 7 GRYAVTAMLDVALNS--EAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred HHHHHHHHHHHHhCC--CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 456677788888753 3467999999999999999999999999999999963
No 38
>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=74.01 E-value=15 Score=26.86 Aligned_cols=46 Identities=28% Similarity=0.283 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 280 KINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 280 KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
.++++..+. ..+..+..+|++.+++|...+-+-+=+....|||+..
T Consensus 12 R~~Il~~L~-------~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~ 57 (61)
T PF12840_consen 12 RLRILRLLA-------SNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVE 57 (61)
T ss_dssp HHHHHHHHH-------HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHh-------cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 455565552 1578999999999999999999999999999999864
No 39
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.88 E-value=20 Score=31.74 Aligned_cols=36 Identities=19% Similarity=0.172 Sum_probs=33.8
Q ss_pred CCCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 296 EDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 296 ~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
.+..+||.+||+.+|+|...|-.-+=+....|+|+|
T Consensus 25 ~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 25 KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 367999999999999999999999999999999987
No 40
>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=73.06 E-value=4.6 Score=28.59 Aligned_cols=28 Identities=21% Similarity=0.197 Sum_probs=21.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+++|+..|..++-+|..
T Consensus 25 ~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 25 QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 5799999999999999999999988863
No 41
>PF09295 ChAPs: ChAPs (Chs5p-Arf1p-binding proteins); InterPro: IPR015374 ChAPs (Chs5p-Arf1p-binding proteins) are required for the export of specialised cargo from the Golgi. They physically interact with Chs3, Chs5 and the small GTPase Arf1, and they also form interactions with each other [].
Probab=72.26 E-value=77 Score=32.54 Aligned_cols=129 Identities=19% Similarity=0.166 Sum_probs=80.2
Q ss_pred HHHHHHHHHHHhchhhcCchhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhccccCCCc
Q 043780 34 HQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATNEQRKEE 113 (386)
Q Consensus 34 hqLt~~l~~~~~~~~~~~~~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~ 113 (386)
.-|+..|..+++.- ...+..+++++...... |= .+-++..+.-.+++..+|+.++++....- ..+
T Consensus 169 NyLv~~Ll~~l~~t--~~~~~ai~lle~L~~~~-----pe-v~~~LA~v~l~~~~E~~AI~ll~~aL~~~-------p~d 233 (395)
T PF09295_consen 169 NYLVDTLLKYLSLT--QRYDEAIELLEKLRERD-----PE-VAVLLARVYLLMNEEVEAIRLLNEALKEN-------PQD 233 (395)
T ss_pred hHHHHHHHHHHhhc--ccHHHHHHHHHHHHhcC-----Cc-HHHHHHHHHHhcCcHHHHHHHHHHHHHhC-------CCC
Confidence 35788888888774 23345666666665443 32 22234444444566778888887765322 122
Q ss_pred hHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCC
Q 043780 114 PILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSVE 191 (386)
Q Consensus 114 a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~ 191 (386)
+.++ ...+.+++..++++.|.+...++-.. .|.-...+|.++-- |-..|+| .+||..|.++|..
T Consensus 234 ~~LL--~~Qa~fLl~k~~~~lAL~iAk~av~l-------sP~~f~~W~~La~~-Yi~~~d~----e~ALlaLNs~Pm~ 297 (395)
T PF09295_consen 234 SELL--NLQAEFLLSKKKYELALEIAKKAVEL-------SPSEFETWYQLAEC-YIQLGDF----ENALLALNSCPML 297 (395)
T ss_pred HHHH--HHHHHHHHhcCCHHHHHHHHHHHHHh-------CchhHHHHHHHHHH-HHhcCCH----HHHHHHHhcCcCC
Confidence 3333 46788999999999888888876543 23344455665544 4456665 4899999888764
No 42
>KOG1126 consensus DNA-binding cell division cycle control protein [Cell cycle control, cell division, chromosome partitioning]
Probab=71.83 E-value=12 Score=40.28 Aligned_cols=90 Identities=22% Similarity=0.156 Sum_probs=65.0
Q ss_pred hcChHHHHHHHHHHH--hcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccc
Q 043780 69 KINLLKLAHFAVIVS--RQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTL 146 (386)
Q Consensus 69 kin~l~l~~i~~~v~--~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l 146 (386)
.|||-..|-++..-. .+++..++||.++++... + +.--.+++...+.++...+++++|-..||+++...
T Consensus 517 ~INP~nsvi~~~~g~~~~~~k~~d~AL~~~~~A~~-l--------d~kn~l~~~~~~~il~~~~~~~eal~~LEeLk~~v 587 (638)
T KOG1126|consen 517 EINPSNSVILCHIGRIQHQLKRKDKALQLYEKAIH-L--------DPKNPLCKYHRASILFSLGRYVEALQELEELKELV 587 (638)
T ss_pred cCCccchhHHhhhhHHHHHhhhhhHHHHHHHHHHh-c--------CCCCchhHHHHHHHHHhhcchHHHHHHHHHHHHhC
Confidence 699999988876543 346788999999986421 1 11234567778888889999999999999999876
Q ss_pred cccCCCCHHHHHHHHHHHHHHHHHhhcHH
Q 043780 147 DSMTDIDPSVYANYYWVSSQYHKFHQEFA 175 (386)
Q Consensus 147 ~~~~~v~~~v~a~~y~~~s~~~k~~~~~~ 175 (386)
++ +..||+. .+..|+..|+..
T Consensus 588 P~----es~v~~l----lgki~k~~~~~~ 608 (638)
T KOG1126|consen 588 PQ----ESSVFAL----LGKIYKRLGNTD 608 (638)
T ss_pred cc----hHHHHHH----HHHHHHHHccch
Confidence 65 3455544 466777777655
No 43
>KOG3682 consensus Predicted membrane protein (associated with esophageal cancer in humans) [Function unknown]
Probab=70.98 E-value=67 Score=35.18 Aligned_cols=123 Identities=14% Similarity=0.170 Sum_probs=81.7
Q ss_pred hhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCCh
Q 043780 53 DALIQLYHNFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDR 132 (386)
Q Consensus 53 ~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l 132 (386)
...-.+.+-|++.|.+-|--..-++++++|++.+- +|..+++.=..| ..+.-++.-.+..+..- .++
T Consensus 562 svc~~il~~f~k~~~~~i~D~~~~q~L~evc~tl~---da~~~~~~ed~k---------R~~s~LI~~f~~mVdfg-~~~ 628 (930)
T KOG3682|consen 562 SVCSRILEIFSKTFTHTISDISACQFLIEVCRTLC---DAYRLEESEDVK---------RAASQLICSFLSMVDFG-TNL 628 (930)
T ss_pred HHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHH---HHhhhhhhhhhH---------HHHHHHHHHHHHHHhhc-ccH
Confidence 34566899999999999999999999999999753 455555421111 01222222222222222 588
Q ss_pred HHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccC
Q 043780 133 KECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYT 188 (386)
Q Consensus 133 ~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~ 188 (386)
+.+-..+-++++.......+---+....+.++-+-.|..++.+.|-+-.+.|+.-+
T Consensus 629 eq~L~f~vecRe~f~~~~~~li~LI~S~n~la~~t~K~gkK~a~Fvr~Cia~~~~T 684 (930)
T KOG3682|consen 629 EQCLEFIVECREDFGLRQNSLIHLIESLNQLAHRTQKSGKKKADFVRVCIANLSLT 684 (930)
T ss_pred HHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHhhee
Confidence 89989999998876554443222333445777777888888899999999999755
No 44
>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=70.90 E-value=11 Score=26.29 Aligned_cols=28 Identities=32% Similarity=0.436 Sum_probs=24.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...|+++||+.+|+|...|-.+.-+|+.
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 6899999999999999999988888864
No 45
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=70.11 E-value=21 Score=36.65 Aligned_cols=80 Identities=16% Similarity=0.271 Sum_probs=58.0
Q ss_pred CCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHH---------HHHH
Q 043780 296 EDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRL---------DSWL 366 (386)
Q Consensus 296 ~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L---------~~W~ 366 (386)
..+.+|-++|++.+++|.++|+.++=+....|+|. +-++ + .|+-.|+.+.=.+..+-+.+ ..|.
T Consensus 307 ~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~-~~~~--g----~~~l~rd~~~itL~dv~~~~~~~~~~~~~~~~~ 379 (412)
T PRK04214 307 HGKALDVDEIRRLEPMGYDELGELLCELARIGLLR-RGER--G----QWVLARDLDSVPLAELYELFVLRPLPCRDDHVG 379 (412)
T ss_pred cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE-ecCC--C----ceEecCCHHhCcHHHHHHhCCCCcCCCccchHH
Confidence 35689999999999999999999999999999997 3222 2 37776776554444444433 2678
Q ss_pred HHHHHHHHHHHhhccc
Q 043780 367 GKVHTALLSIEAETPD 382 (386)
Q Consensus 367 ~~v~~~~~~l~~~~~~ 382 (386)
.+++.+++.+++...+
T Consensus 380 ~~~~~~l~~~~~~~~~ 395 (412)
T PRK04214 380 QAADAALTQLRQPLRE 395 (412)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8888877777655443
No 46
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=69.61 E-value=16 Score=28.43 Aligned_cols=48 Identities=21% Similarity=0.205 Sum_probs=38.0
Q ss_pred HHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 282 NILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 282 rlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
|.+.++++.... .+.++..+|++.+++|...|-..+-.....|+|...
T Consensus 6 r~~~Il~~l~~~---~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 6 RGLAVLRALAEE---PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHHHhC---CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 344555554432 257999999999999999999999999999999863
No 47
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=68.76 E-value=52 Score=25.43 Aligned_cols=71 Identities=15% Similarity=0.114 Sum_probs=48.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTAL 373 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~ 373 (386)
..++..+|++.++++...|-..|-+....|+|.-.-++.++....-. ++..-+..+......|..-...+.
T Consensus 23 ~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~-----lT~~g~~~~~~~~~~~~~~~~~~~ 93 (101)
T smart00347 23 GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVS-----LTEEGRELIEELLEARHETLAELL 93 (101)
T ss_pred CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEE-----ECHhHHHHHHHHHHHHHHHHHHHH
Confidence 46999999999999999999999999999999987776554443322 234444444444444444333333
No 48
>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=68.69 E-value=20 Score=30.21 Aligned_cols=50 Identities=20% Similarity=0.370 Sum_probs=38.6
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
..+.+++.++.. .+...+|.++||+.+++|...|...+-+....|+|...
T Consensus 9 ~al~~l~~la~~--~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 9 YALRALLDLALN--PDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred HHHHHHHHHHhC--CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 344444455432 23458999999999999999999999999999999753
No 49
>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=68.51 E-value=46 Score=30.04 Aligned_cols=66 Identities=27% Similarity=0.452 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhh-HHHHHHHHHHHHHHHHHhhCCCCCCc-cChHHHHHHcC
Q 043780 236 EWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVEN-EKKLLEKINILCLMEIIFSRPSEDRT-IPLSIIAERTK 310 (386)
Q Consensus 236 ~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~-~~~l~~KirlLaL~~L~~~r~~~~r~-isf~~Ia~~l~ 310 (386)
.-..++..++..||+..|-+..++ .+.|.+... ....-.++|.-+|-.++.+ .+. +|.+.+++-|+
T Consensus 136 ~~al~l~~a~~~gny~~ff~l~~~-----~~~~~l~~~l~~~~~~~iR~~al~~i~~a----y~~~i~l~~l~~~L~ 203 (204)
T PF03399_consen 136 QFALELCRALMEGNYVRFFRLYRS-----KSAPYLFACLMERFFNRIRLRALQSISKA----YRSSIPLSFLAELLG 203 (204)
T ss_dssp HHHHHHHHHH--TTHHHHHHHHT------TTS-HHHHHHHGGGHHHHHHHHHHHHHHH----S-T-EEHHHHHHHTT
T ss_pred HHHHHHHHHHHcCCHHHHHHHHhc-----cCCChHHHHHHHHHHHHHHHHHHHHHHHH----cCCCCCHHHHHHHcC
Confidence 446788899999999999887621 122322211 1112368999999888764 344 88888877665
No 50
>PF10602 RPN7: 26S proteasome subunit RPN7; InterPro: IPR019585 This entry represents the regulatory subunit RPN7 (known as the non-ATPase regulatory subunit 6 in higher eukaryotes) of the 26S proteasome. This entry also matches the evolutionarily related subunit 1 of the COP9 signalosome complex (CSN) from Arabidopsis []. The 26S proteasome plays a major role in ATP-dependent degradation of ubiquitinated proteins. Substrate specificity is conferred by the regulatory particle (RP), which can dissociate into stable lid and base subcomplexes. The regulatory subunit RPN7 is one of the lid subunits of the 26S proteasome and has been shown in Saccharomyces cerevisiae (Baker's yeast) to be required for structural integrity []. The COP9 signalosome is a conserved protein complex composed of eight subunits, where Individual subunits of the complex have been linked to various signal transduction pathways leading to gene expression and cell cycle control []. The overall organisation and the amino acid sequences of the COP9 signalosome subunits resemble the lid subcomplex of the 19 S regulatory particle for the 26 S proteasome []. COP9 subunit 1 (CSN1 or GPS1) of the COP9 complex is an essential subunit of the complex with regard to both structural integrity and functionality. The N-terminal region of subunit 1 (CSN1-N) can inhibit c-fos expression from either a transfected template or a chromosomal transgene (fos-lacZ), and may contain the activity domain that confers most of the repression functions of CSN1. The C-terminal region of subunit 1 (CSN1-C) allows integration of the protein into the COP9 signalosome.
Probab=68.26 E-value=91 Score=28.05 Aligned_cols=117 Identities=15% Similarity=0.052 Sum_probs=70.2
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
+.|.++|++....+.++-. +....+=+-+.+.++.+..||...+.+.++.++..++.-. +......+--..+
T Consensus 49 ~Gd~~~A~k~y~~~~~~~~------~~~~~id~~l~~irv~i~~~d~~~v~~~i~ka~~~~~~~~--d~~~~nrlk~~~g 120 (177)
T PF10602_consen 49 IGDLEEALKAYSRARDYCT------SPGHKIDMCLNVIRVAIFFGDWSHVEKYIEKAESLIEKGG--DWERRNRLKVYEG 120 (177)
T ss_pred hhhHHHHHHHHHHHhhhcC------CHHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHhccc--hHHHHHHHHHHHH
Confidence 4478899999888777653 2233333445556666778999999999999998877622 3444444333333
Q ss_pred HHHHHhhcHHHHHHHHHHHhccCCC---CCCChhHHHHHHHHHHHHHhcC
Q 043780 166 QYHKFHQEFAEFYKCALLYLAYTSV---ESLSDSFKLDLAFDLSLSALLG 212 (386)
Q Consensus 166 ~~~k~~~~~~~~y~~~l~yL~~~~~---~~~~~~e~~~~a~~l~i~AL~~ 212 (386)
-++=..++|...-...+.-++++.. .++ -.-.+.|+..++.||.+
T Consensus 121 L~~l~~r~f~~AA~~fl~~~~t~~~~~~~el--~s~~d~a~Y~~l~aLat 168 (177)
T PF10602_consen 121 LANLAQRDFKEAAELFLDSLSTFTSLQYTEL--ISYNDFAIYGGLCALAT 168 (177)
T ss_pred HHHHHhchHHHHHHHHHccCcCCCCCchhhh--cCHHHHHHHHHHHHHHh
Confidence 3333456666655555555555532 221 12245567777777654
No 51
>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=67.90 E-value=14 Score=31.16 Aligned_cols=36 Identities=19% Similarity=0.216 Sum_probs=33.4
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
.+.+|..+|++.+++|..-|...+=+.-..|+|.+.
T Consensus 23 ~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 23 SQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred CCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 467999999999999999999999999999999874
No 52
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=67.67 E-value=25 Score=29.75 Aligned_cols=75 Identities=9% Similarity=0.046 Sum_probs=51.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSIE 377 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l~ 377 (386)
...+..+|++.++++..-|-+-+=..-.+|||..+-+.......+. |.+ .+.+..+-. ..|..+...+...++
T Consensus 29 ~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~---~~~--~~~~~~~~~--~~w~~~~~~l~~~l~ 101 (117)
T PRK10141 29 GELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLS---PHI--PAWAAKIIE--QAWLCEQEDVQAIVR 101 (117)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEEC---chH--HHHHHHHHH--HHHHHHHHHHHHHHH
Confidence 5688999999999999989888888888999999888655444442 321 222222122 267777777766665
Q ss_pred hh
Q 043780 378 AE 379 (386)
Q Consensus 378 ~~ 379 (386)
+.
T Consensus 102 ~l 103 (117)
T PRK10141 102 NL 103 (117)
T ss_pred HH
Confidence 54
No 53
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.58 E-value=71 Score=27.21 Aligned_cols=50 Identities=8% Similarity=-0.055 Sum_probs=45.0
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccc
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPR 348 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R 348 (386)
.++-.+|++.++++..-|=..|-+....|+|.=.-|..++....-..++.
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~ 95 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEK 95 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChH
Confidence 46789999999999999999999999999999999999998888777754
No 54
>PF13730 HTH_36: Helix-turn-helix domain
Probab=66.46 E-value=27 Score=24.64 Aligned_cols=49 Identities=16% Similarity=0.059 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccce
Q 043780 279 EKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLI 329 (386)
Q Consensus 279 ~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI 329 (386)
+|+-++.|...+-. . +.---|++.||+.++++.+.|...+=+....|+|
T Consensus 7 ~~~v~~~l~~~~~~-~-~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANK-N-GGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCC-C-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 56667777777632 1 2233489999999999999999999888888875
No 55
>PF14559 TPR_19: Tetratricopeptide repeat; PDB: 2R5S_A 3QDN_B 3QOU_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 3FP3_A 3LCA_A ....
Probab=66.45 E-value=17 Score=26.28 Aligned_cols=50 Identities=26% Similarity=0.336 Sum_probs=37.0
Q ss_pred CChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccc
Q 043780 87 PEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKST 145 (386)
Q Consensus 87 ~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~ 145 (386)
.++++|++.++++...- ..++.++ ...+.+++..|++++++.+++.+-..
T Consensus 5 ~~~~~A~~~~~~~l~~~-------p~~~~~~--~~la~~~~~~g~~~~A~~~l~~~~~~ 54 (68)
T PF14559_consen 5 GDYDEAIELLEKALQRN-------PDNPEAR--LLLAQCYLKQGQYDEAEELLERLLKQ 54 (68)
T ss_dssp THHHHHHHHHHHHHHHT-------TTSHHHH--HHHHHHHHHTT-HHHHHHHHHCCHGG
T ss_pred cCHHHHHHHHHHHHHHC-------CCCHHHH--HHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 36889999999876555 1233333 46788899999999999999988764
No 56
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=66.35 E-value=1.9e+02 Score=30.90 Aligned_cols=164 Identities=14% Similarity=0.225 Sum_probs=98.3
Q ss_pred HHHHHHHHhcCCchHHHHHHHHHHH---------HhhhHHHHHHHHHHHHhc---h-----hhcCchhHHHHHHHHHHHH
Q 043780 4 LQYLESLRNDHPELGEWYNALADLY---------QKKLWHQLTLKLEQFVAH---A-----VFQAGDALIQLYHNFITDF 66 (386)
Q Consensus 4 ~~~L~~~~~~~p~~~~~~~~~~~l~---------~~KLWhqLt~~l~~~~~~---~-----~~~~~~~~~~ly~~fi~~f 66 (386)
......+...+|+=...+..++... ..+-.-++=..+.+.+-. | .|.+|+.-.+..+.||.++
T Consensus 58 ~~~y~~Li~rNPdn~~Yy~~L~~~~g~~~~~~~~~~~~~~~~y~~l~~~yp~s~~~~rl~L~~~~g~~F~~~~~~yl~~~ 137 (517)
T PF12569_consen 58 EKIYRELIDRNPDNYDYYRGLEEALGLQLQLSDEDVEKLLELYDELAEKYPRSDAPRRLPLDFLEGDEFKERLDEYLRPQ 137 (517)
T ss_pred HHHHHHHHHHCCCcHHHHHHHHHHHhhhcccccccHHHHHHHHHHHHHhCccccchhHhhcccCCHHHHHHHHHHHHHHH
Confidence 3444566677787777777666665 122233333333333211 1 2345666677788888888
Q ss_pred HhhcChHHHHHHHHHHHhcCCChHHHHHHHHHHHH----Hhhhcc--------ccCCCchHHHHHHHHHHHhcccCChHH
Q 043780 67 ETKINLLKLAHFAVIVSRQYPEKQAAISYLEGVIE----KLRATN--------EQRKEEPILYIKMQIAMFKLEQGDRKE 134 (386)
Q Consensus 67 ~~kin~l~l~~i~~~v~~~~~d~~~al~fl~~~~~----~~~~~~--------~~~~~~a~~~~~~~~~~~~l~~~~l~~ 134 (386)
-.|==|--++.+--. ++|+.++ ..+.++.. .+.... ....+.+.+.+....|+++...|++++
T Consensus 138 l~KgvPslF~~lk~L----y~d~~K~-~~i~~l~~~~~~~l~~~~~~~~~~~~~~~~p~~~lw~~~~lAqhyd~~g~~~~ 212 (517)
T PF12569_consen 138 LRKGVPSLFSNLKPL----YKDPEKA-AIIESLVEEYVNSLESNGSFSNGDDEEKEPPSTLLWTLYFLAQHYDYLGDYEK 212 (517)
T ss_pred HhcCCchHHHHHHHH----HcChhHH-HHHHHHHHHHHHhhcccCCCCCccccccCCchHHHHHHHHHHHHHHHhCCHHH
Confidence 888666666655332 3345433 34444333 332110 123345667888899999999999999
Q ss_pred HHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHH
Q 043780 135 CKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKC 180 (386)
Q Consensus 135 ~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~ 180 (386)
+-+.++++=. ..+. + -.+|.+-+..+|..|++.+.+..
T Consensus 213 Al~~Id~aI~---htPt----~-~ely~~KarilKh~G~~~~Aa~~ 250 (517)
T PF12569_consen 213 ALEYIDKAIE---HTPT----L-VELYMTKARILKHAGDLKEAAEA 250 (517)
T ss_pred HHHHHHHHHh---cCCC----c-HHHHHHHHHHHHHCCCHHHHHHH
Confidence 8888886532 2211 1 24888999999999998876653
No 57
>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=65.60 E-value=12 Score=27.43 Aligned_cols=37 Identities=16% Similarity=0.311 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHH
Q 043780 277 LLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLL 320 (386)
Q Consensus 277 l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lv 320 (386)
+++++++|.++-= ++.+++++||+.++++...+-.-+
T Consensus 4 i~rq~~Ll~~L~~-------~~~~~~~ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 4 IKRQLKLLELLLK-------NKWITLKELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHHHH-------HTSBBHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHHHc-------CCCCcHHHHHHHHCCCHHHHHHHH
Confidence 4567777776642 478999999999999986554433
No 58
>PRK10870 transcriptional repressor MprA; Provisional
Probab=64.61 E-value=81 Score=28.31 Aligned_cols=51 Identities=10% Similarity=-0.067 Sum_probs=45.3
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeecc
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQP 347 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~ 347 (386)
+..++..+|++.++++...|=..|=+....|+|+=.-|..++.+..-..++
T Consensus 69 ~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~ 119 (176)
T PRK10870 69 NHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTE 119 (176)
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECH
Confidence 468999999999999999999999999999999999999998776666654
No 59
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=64.53 E-value=16 Score=34.87 Aligned_cols=54 Identities=22% Similarity=0.366 Sum_probs=44.0
Q ss_pred HHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 286 LMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 286 L~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
+++.+. .++.++.+++|.++++--.++=.-+=.-+..|++.|-||.-.+-++||
T Consensus 205 Fv~YIk----~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 205 FVEYIK----KNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHH----hcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 455553 478999999999999966555556666777899999999999999998
No 60
>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=64.52 E-value=10 Score=25.97 Aligned_cols=23 Identities=26% Similarity=0.185 Sum_probs=17.1
Q ss_pred CCccChHHHHHHcCCChhHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHL 319 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~l 319 (386)
+...||.+||+.+|++...|-.=
T Consensus 15 d~r~s~~~la~~lglS~~~v~~R 37 (42)
T PF13404_consen 15 DGRRSYAELAEELGLSESTVRRR 37 (42)
T ss_dssp -TTS-HHHHHHHHTS-HHHHHHH
T ss_pred cCCccHHHHHHHHCcCHHHHHHH
Confidence 46899999999999999887543
No 61
>PF13429 TPR_15: Tetratricopeptide repeat; PDB: 2VQ2_A 2PL2_B.
Probab=64.41 E-value=77 Score=29.97 Aligned_cols=93 Identities=13% Similarity=0.120 Sum_probs=54.2
Q ss_pred HHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHH
Q 043780 81 IVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANY 160 (386)
Q Consensus 81 ~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~ 160 (386)
.+..+..++++|++.+++..+.- |. ++.+ ....+..++..|+.++++..++.+....+.- +.++..|
T Consensus 154 ~~~~~~G~~~~A~~~~~~al~~~-----P~--~~~~--~~~l~~~li~~~~~~~~~~~l~~~~~~~~~~----~~~~~~l 220 (280)
T PF13429_consen 154 EIYEQLGDPDKALRDYRKALELD-----PD--DPDA--RNALAWLLIDMGDYDEAREALKRLLKAAPDD----PDLWDAL 220 (280)
T ss_dssp HHHHHCCHHHHHHHHHHHHHHH------TT---HHH--HHHHHHHHCTTCHHHHHHHHHHHHHHH-HTS----CCHCHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHcC-----CC--CHHH--HHHHHHHHHHCCChHHHHHHHHHHHHHCcCH----HHHHHHH
Confidence 34445678999999998876555 22 2222 2344556778899999999999888765332 2233322
Q ss_pred HHHHHHHHHHhhcHHHHHHHHHHHhccCCC
Q 043780 161 YWVSSQYHKFHQEFAEFYKCALLYLAYTSV 190 (386)
Q Consensus 161 y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~ 190 (386)
+..+...|++.+.....-+.+..-|.
T Consensus 221 ----a~~~~~lg~~~~Al~~~~~~~~~~p~ 246 (280)
T PF13429_consen 221 ----AAAYLQLGRYEEALEYLEKALKLNPD 246 (280)
T ss_dssp ----HHHHHHHT-HHHHHHHHHHHHHHSTT
T ss_pred ----HHHhcccccccccccccccccccccc
Confidence 33344556666555555555554443
No 62
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=62.29 E-value=21 Score=31.41 Aligned_cols=47 Identities=19% Similarity=0.101 Sum_probs=38.6
Q ss_pred HHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 283 ILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 283 lLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
+-+|+.||.. + .+.++-++||+..+||..-++.++-+.-..|+|+..
T Consensus 11 lr~L~~LA~~-~--~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 11 IRMLMYCAAN-D--GKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred HHHHHHHHhC-C--CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence 4456667643 2 356899999999999999999999999999999864
No 63
>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=61.65 E-value=27 Score=25.32 Aligned_cols=35 Identities=23% Similarity=0.140 Sum_probs=31.9
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
...++..+||+.++++...|...+-+....|+|.-
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~ 57 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISR 57 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 46799999999999999999999999999999974
No 64
>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=61.11 E-value=69 Score=28.45 Aligned_cols=82 Identities=9% Similarity=0.049 Sum_probs=60.7
Q ss_pred CCCccChHHHHHHcC--CChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccc---cCChhhHHHHHHHHHHHHHHHH
Q 043780 296 EDRTIPLSIIAERTK--LSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPR---VLGIPQIKSLRDRLDSWLGKVH 370 (386)
Q Consensus 296 ~~r~isf~~Ia~~l~--i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R---~l~~~q~~~L~~~L~~W~~~v~ 370 (386)
.+|..|-.+|...|| ++-..|...+=.....|.|.+|.=+.. .|=|+... +.+++++..|...+....+.+.
T Consensus 13 qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKq---kiY~~~Q~~~~~~s~eel~~ld~ei~~L~~el~ 89 (169)
T PF07106_consen 13 QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQ---KIYFANQDELEVPSPEELAELDAEIKELREELA 89 (169)
T ss_pred cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecce---EEEeeCccccCCCCchhHHHHHHHHHHHHHHHH
Confidence 578899999999995 676788888888888999999965444 44444443 4457788888888888888777
Q ss_pred HHHHHHHhhc
Q 043780 371 TALLSIEAET 380 (386)
Q Consensus 371 ~~~~~l~~~~ 380 (386)
.+...+....
T Consensus 90 ~l~~~~k~l~ 99 (169)
T PF07106_consen 90 ELKKEVKSLE 99 (169)
T ss_pred HHHHHHHHHH
Confidence 7766665443
No 65
>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=60.46 E-value=95 Score=25.51 Aligned_cols=75 Identities=5% Similarity=-0.042 Sum_probs=52.5
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSI 376 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l 376 (386)
+..++..+|++.++++...|=..|=+....|+|...-|..++....-..+| +-.+.+..-...|......+...+
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~-----~G~~~~~~~~~~~~~~~~~~~~~l 114 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTP-----KGQALYASLSPQIEEIYAAIEERL 114 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECH-----hHHHHHHHhhHHHHHHHHHHHHHc
Confidence 356899999999999988999999999999999999988887554443333 333344444444544444444443
No 66
>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=59.81 E-value=16 Score=26.59 Aligned_cols=29 Identities=28% Similarity=0.283 Sum_probs=25.1
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
.|.++..+||+.++|+..-+..-+-+|.+
T Consensus 21 PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 21 PRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 38999999999999999888887777754
No 67
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=59.51 E-value=35 Score=25.70 Aligned_cols=33 Identities=15% Similarity=0.060 Sum_probs=31.1
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
.++-.+||++++++...|...+-+....|+|.-
T Consensus 22 ~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 22 TSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 499999999999999999999999999999965
No 68
>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=58.80 E-value=22 Score=28.83 Aligned_cols=52 Identities=19% Similarity=0.233 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecC
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQ 335 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDq 335 (386)
-+++.++.- .+....=++.++|++.++++.++|+..|=..+..|.|=-.||.
T Consensus 50 ~~Vl~~i~~---~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 50 DKVLNFIKQ---QPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHHHC-------TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred HHHHHHHHh---cCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 344555543 1334567999999999999999999999999999999888885
No 69
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=58.21 E-value=18 Score=24.60 Aligned_cols=46 Identities=15% Similarity=0.146 Sum_probs=33.7
Q ss_pred ChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHH
Q 043780 301 PLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLR 359 (386)
Q Consensus 301 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~ 359 (386)
+-.++|+.++++...|..|+ ..|++.+.-+.. .+|.++.+++..|+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~----~~g~l~~~~~~~---------~~~~y~~~~v~~l~ 47 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE----RIGLLSPARTEG---------GYRLYSDADLERLR 47 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH----HCCCCCCCcCCC---------CCEEeCHHHHHHhh
Confidence 56789999999999999994 577776432221 35778888887765
No 70
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=57.43 E-value=2.4e+02 Score=29.17 Aligned_cols=191 Identities=18% Similarity=0.226 Sum_probs=104.5
Q ss_pred HHHHHHHHHHhcccCChHHHHHHHHhccccccc-cCCCCHHHHHHHHHHHHHHHHHhhcHHH---HHHHHHHHhccCC--
Q 043780 116 LYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDS-MTDIDPSVYANYYWVSSQYHKFHQEFAE---FYKCALLYLAYTS-- 189 (386)
Q Consensus 116 ~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~-~~~v~~~v~a~~y~~~s~~~k~~~~~~~---~y~~~l~yL~~~~-- 189 (386)
-+-.+...+++..+||+..|-+.|+.++-.-.. ...|.+.--+.||++.-.|. ..++|++ -+...|.|++-+.
T Consensus 122 YFSligLlRvh~LLGDY~~Alk~l~~idl~~~~l~~~V~~~~is~~YyvGFayl-MlrRY~DAir~f~~iL~yi~r~k~~ 200 (404)
T PF10255_consen 122 YFSLIGLLRVHCLLGDYYQALKVLENIDLNKKGLYTKVPACHISTYYYVGFAYL-MLRRYADAIRTFSQILLYIQRTKNQ 200 (404)
T ss_pred HHHHHHHHHHHHhccCHHHHHHHhhccCcccchhhccCcchheehHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 345577888888999999999999987643221 33453333346777766554 3344444 5556666764433
Q ss_pred -CCCCCh-----hHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHHh-hh
Q 043780 190 -VESLSD-----SFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRVH-NA 262 (386)
Q Consensus 190 -~~~~~~-----~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~~-~~ 262 (386)
....+. ....++-.-++++-.+.|.- +.-.+...+++. .-+=+.....||++.|+++-..- |.
T Consensus 201 ~~~~~~q~d~i~K~~eqMyaLlAic~~l~p~~------lde~i~~~lkek----y~ek~~kmq~gd~~~f~elF~~acPK 270 (404)
T PF10255_consen 201 YHQRSYQYDQINKKNEQMYALLAICLSLCPQR------LDESISSQLKEK----YGEKMEKMQRGDEEAFEELFSFACPK 270 (404)
T ss_pred hccccchhhHHHhHHHHHHHHHHHHHHhCCCC------CCHHHHHHHHHH----HHHHHHHHHccCHHHHHHHHHhhCCC
Confidence 010011 11122333445555566644 333445555543 33556667899999999886543 22
Q ss_pred hhhcC-chhhh----h---HHH----------HHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHH
Q 043780 263 ALRAQ-PALVE----N---EKK----------LLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLM 321 (386)
Q Consensus 263 ~~~~~-~~L~~----~---~~~----------l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvi 321 (386)
+++-. |.... + ++. +++-..+-+|-+... =..+|+.+.+|.-++++++++-..+|
T Consensus 271 FIsp~~pp~~~~~~~~~~~e~~~~Ql~~Fl~eV~~q~~l~~lRSyLK----LYtti~l~KLA~fl~vd~~~lr~~Ll 343 (404)
T PF10255_consen 271 FISPVSPPDYDGPSQNKNKEPYRRQLKLFLDEVKQQQKLPTLRSYLK----LYTTIPLEKLASFLDVDEEELRSQLL 343 (404)
T ss_pred ccCCCCCCCcccccchhhhhHHHHHHHHHHHHHHHhhhhhHHHHHHH----hhcCCCHHHHHHHcCCCHHHHHHHHH
Confidence 44322 21000 0 111 112222223322221 25799999999999998886554443
No 71
>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=57.14 E-value=14 Score=27.47 Aligned_cols=37 Identities=22% Similarity=0.065 Sum_probs=34.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEee
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGII 333 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 333 (386)
.+..+-++||+.+++|...|-..+=+....|+|+-.-
T Consensus 20 ~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 20 NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEE
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3689999999999999999999999999999998654
No 72
>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=56.64 E-value=54 Score=23.38 Aligned_cols=41 Identities=22% Similarity=0.205 Sum_probs=35.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCC
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEG 338 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~ 338 (386)
..++..+|++.++++..-|-..|=+....|+|+=.-|..++
T Consensus 20 ~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~~D~ 60 (62)
T PF12802_consen 20 EELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDPGDR 60 (62)
T ss_dssp SGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-SSST
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCCCC
Confidence 35999999999999999999999999999999988776654
No 73
>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]
Probab=56.47 E-value=2.5e+02 Score=31.44 Aligned_cols=135 Identities=19% Similarity=0.182 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHHhh---cChHHHHHHHHHHHhcCCChHHHHHHHHHH----------------------HHHhhhccccC
Q 043780 56 IQLYHNFITDFETK---INLLKLAHFAVIVSRQYPEKQAAISYLEGV----------------------IEKLRATNEQR 110 (386)
Q Consensus 56 ~~ly~~fi~~f~~k---in~l~l~~i~~~v~~~~~d~~~al~fl~~~----------------------~~~~~~~~~~~ 110 (386)
..+|..+|..|.+. .||-+|++|+..++.- +..+.+++|+.+ ..++.+..+++
T Consensus 231 n~l~r~~v~~~~~~~~~~~~~~LaD~~aai~~~--~~~elq~vL~~~di~~Rl~~al~llkke~e~~klq~ki~k~vE~k 308 (906)
T KOG2004|consen 231 NSLFREQVATLSQLIVEDNPIKLADFGAAISGA--EFHELQEVLEETDIEKRLEKALELLKKELELAKLQQKIGKEVEEK 308 (906)
T ss_pred hHHHHHHHHHHHHHhcccChhHHHHHHHHHhcc--CHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHhh
Confidence 45667776666553 5899999999999983 577777777532 22221111111
Q ss_pred --CCchHHHHHHHHHHHhcccCChHHHHH-HHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHH--HHHHHHHHh
Q 043780 111 --KEEPILYIKMQIAMFKLEQGDRKECKK-LLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAE--FYKCALLYL 185 (386)
Q Consensus 111 --~~~a~~~~~~~~~~~~l~~~~l~~~~~-~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~--~y~~~l~yL 185 (386)
......+++=++..++-.+|+=+.-+. +.+..++.+.. .+++..|+..++.-...+.......++ .-++.|.+|
T Consensus 309 ~~~~~r~ylL~eQlk~IKkeLg~e~Ddkd~~~~~~~er~~~-~~~P~~v~kv~~eEl~kL~~le~~~sEfnvtrNYLdwl 387 (906)
T KOG2004|consen 309 IKQDHREYLLREQLKAIKKELGIEKDDKDALVEKFRERIKS-LKMPDHVLKVIDEELTKLKLLEPSSSEFNVTRNYLDWL 387 (906)
T ss_pred hhHHHHHHHHHHHHHHHHHhhCCCccchhhHHHHHHHHhhh-ccCcHHHHHHHHHHHHHHhccCccccchhHHHHHHHHH
Confidence 111223333334444445553322222 33333333333 466667777666655554332222222 234556666
Q ss_pred ccCCCCCC
Q 043780 186 AYTSVESL 193 (386)
Q Consensus 186 ~~~~~~~~ 193 (386)
+..|=+..
T Consensus 388 t~LPWgk~ 395 (906)
T KOG2004|consen 388 TSLPWGKS 395 (906)
T ss_pred HhCCCCCC
Confidence 66655433
No 74
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=55.83 E-value=59 Score=25.37 Aligned_cols=42 Identities=14% Similarity=0.049 Sum_probs=34.4
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCC
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEG 338 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~ 338 (386)
.+.++|.+|.+.++++...+-.-+=+.-..|+|+-+-.-.++
T Consensus 12 ~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~ 53 (80)
T PF13601_consen 12 NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGR 53 (80)
T ss_dssp HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCC
Confidence 368999999999999999999999999999999987665554
No 75
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=55.75 E-value=92 Score=29.28 Aligned_cols=63 Identities=14% Similarity=0.086 Sum_probs=50.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLG 367 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~ 367 (386)
...+|-.+||+.++++..-+=..|-+.-..|+|+-..+.-.+.+.+| ..-.+.+..-...|..
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LT--------ekG~~ll~~~~~d~~~ 81 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITIT--------EKGLDVLYNEYADYSR 81 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEEC--------HHHHHHHHHHHHHHHH
Confidence 45799999999999999999999999999999999998876666666 3444455555556644
No 76
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=54.99 E-value=47 Score=29.20 Aligned_cols=50 Identities=22% Similarity=0.309 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
.-+-+|+.||.. | ..+.+|-++||+..+||+.=++.++-+.-..|||+..
T Consensus 9 yal~~L~~LA~~-~-~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~ 58 (150)
T COG1959 9 YALRALLYLALL-P-GGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSV 58 (150)
T ss_pred HHHHHHHHHHhC-C-CCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEee
Confidence 445677777764 2 2347889999999999999999999999999999865
No 77
>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=54.94 E-value=61 Score=23.20 Aligned_cols=36 Identities=31% Similarity=0.278 Sum_probs=32.7
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEeecC
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQ 335 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDq 335 (386)
+++.+|++.++++...+-..+=.....|+|...-+.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 999999999999999999998888899999987665
No 78
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=54.26 E-value=57 Score=24.20 Aligned_cols=63 Identities=16% Similarity=0.039 Sum_probs=41.2
Q ss_pred HHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHH
Q 043780 119 KMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCAL 182 (386)
Q Consensus 119 ~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l 182 (386)
-..+|.++...|+++++.+.++++-........ +....+..|.-.+..+...|++.+.-...-
T Consensus 8 ~~~la~~~~~~~~~~~A~~~~~~al~~~~~~~~-~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~ 70 (78)
T PF13424_consen 8 YNNLARVYRELGRYDEALDYYEKALDIEEQLGD-DHPDTANTLNNLGECYYRLGDYEEALEYYQ 70 (78)
T ss_dssp HHHHHHHHHHTT-HHHHHHHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHHHHTTHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 356788888999999999999987665333322 233335666666777777888775444433
No 79
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=53.86 E-value=64 Score=24.51 Aligned_cols=76 Identities=25% Similarity=0.160 Sum_probs=43.9
Q ss_pred HHHHHHHHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHH
Q 043780 55 LIQLYHNFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKE 134 (386)
Q Consensus 55 ~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~ 134 (386)
-+.+|+..+..-.++-|+.-+-. +..+.-+..+.++|++++++ .++. . ..+-+...+|+.++..|++++
T Consensus 8 Ai~~~~k~~~~~~~~~~~~~~~~-la~~~~~~~~y~~A~~~~~~--~~~~------~--~~~~~~~l~a~~~~~l~~y~e 76 (84)
T PF12895_consen 8 AIKYYEKLLELDPTNPNSAYLYN-LAQCYFQQGKYEEAIELLQK--LKLD------P--SNPDIHYLLARCLLKLGKYEE 76 (84)
T ss_dssp HHHHHHHHHHHHCGTHHHHHHHH-HHHHHHHTTHHHHHHHHHHC--HTHH------H--CHHHHHHHHHHHHHHTT-HHH
T ss_pred HHHHHHHHHHHCCCChhHHHHHH-HHHHHHHCCCHHHHHHHHHH--hCCC------C--CCHHHHHHHHHHHHHhCCHHH
Confidence 45556665554443112221111 34444456678899999987 3332 1 123334455899999999999
Q ss_pred HHHHHHh
Q 043780 135 CKKLLED 141 (386)
Q Consensus 135 ~~~~l~~ 141 (386)
+.+.+++
T Consensus 77 Ai~~l~~ 83 (84)
T PF12895_consen 77 AIKALEK 83 (84)
T ss_dssp HHHHHHH
T ss_pred HHHHHhc
Confidence 9988875
No 80
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=53.11 E-value=46 Score=22.23 Aligned_cols=33 Identities=27% Similarity=0.181 Sum_probs=29.9
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
.++..+||+.++++...|-..+-+....|+|.-
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 478899999999999999999999999999973
No 81
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=52.92 E-value=51 Score=25.40 Aligned_cols=43 Identities=14% Similarity=0.165 Sum_probs=33.1
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
....++.+|+..+++|...+...+=..+..|||++ .++...+|
T Consensus 17 ~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lT 59 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLT 59 (77)
T ss_dssp TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEEC
Confidence 36788999999999999999999999999999954 56677766
No 82
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=51.66 E-value=47 Score=23.14 Aligned_cols=37 Identities=27% Similarity=0.213 Sum_probs=31.8
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEeec
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIID 334 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ID 334 (386)
+.+++.+|++.++++...|-..+=+....|+|.-.-+
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 5689999999999999999888888888999985443
No 83
>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=51.20 E-value=17 Score=27.20 Aligned_cols=23 Identities=26% Similarity=0.294 Sum_probs=20.9
Q ss_pred CCccChHHHHHHcCCChhHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHL 319 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~l 319 (386)
++.+++.+||+.|+|+...|-.|
T Consensus 20 ~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 20 NGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCCccHHHHHHHHCCCHHHHHHH
Confidence 68999999999999999988766
No 84
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=51.17 E-value=98 Score=24.23 Aligned_cols=59 Identities=15% Similarity=0.107 Sum_probs=37.0
Q ss_pred HHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccc
Q 043780 81 IVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKST 145 (386)
Q Consensus 81 ~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~ 145 (386)
.+.....+.++|+..++.+...- +.+. ....+....+.++...|+.+++.+.++++-..
T Consensus 47 ~~~~~~~~~~~A~~~~~~~~~~~-----p~~~-~~~~~~~~~~~~~~~~~~~~~A~~~~~~~~~~ 105 (119)
T TIGR02795 47 EAYYAQGKYADAAKAFLAVVKKY-----PKSP-KAPDALLKLGMSLQELGDKEKAKATLQQVIKR 105 (119)
T ss_pred HHHHhhccHHHHHHHHHHHHHHC-----CCCC-cccHHHHHHHHHHHHhCChHHHHHHHHHHHHH
Confidence 33444557888998888776544 1111 11222345566777889999998888876554
No 85
>TIGR03504 FimV_Cterm FimV C-terminal domain. This protein is found at the extreme C-terminus of FimV from Pseudomonas aeruginosa, and of TspA of Neisseria meningitidis. Disruption of the former blocks twitching motility from type IV pili; Semmler, et al. suggest a role in peptidoglycan layer remodelling required by type IV fimbrial systems.
Probab=51.12 E-value=15 Score=25.65 Aligned_cols=26 Identities=31% Similarity=0.442 Sum_probs=22.2
Q ss_pred HHHHHHHhcccCChHHHHHHHHhccc
Q 043780 119 KMQIAMFKLEQGDRKECKKLLEDGKS 144 (386)
Q Consensus 119 ~~~~~~~~l~~~~l~~~~~~l~~~~~ 144 (386)
+...|..|...||.+.++++|+++-.
T Consensus 2 kLdLA~ayie~Gd~e~Ar~lL~evl~ 27 (44)
T TIGR03504 2 KLDLARAYIEMGDLEGARELLEEVIE 27 (44)
T ss_pred chHHHHHHHHcCChHHHHHHHHHHHH
Confidence 35678899999999999999998763
No 86
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=50.60 E-value=33 Score=24.65 Aligned_cols=36 Identities=28% Similarity=0.295 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHH
Q 043780 276 KLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLL 320 (386)
Q Consensus 276 ~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lv 320 (386)
.+.+|+.++...+ .+. +..+||+.+||+...|-.++
T Consensus 8 Tl~eK~~iI~~~e--------~g~-s~~~ia~~fgv~~sTv~~I~ 43 (53)
T PF04218_consen 8 TLEEKLEIIKRLE--------EGE-SKRDIAREFGVSRSTVSTIL 43 (53)
T ss_dssp -HHHHHHHHHHHH--------CTT--HHHHHHHHT--CCHHHHHH
T ss_pred CHHHHHHHHHHHH--------cCC-CHHHHHHHhCCCHHHHHHHH
Confidence 3568988888876 233 99999999999998887665
No 87
>PF12895 Apc3: Anaphase-promoting complex, cyclosome, subunit 3; PDB: 3KAE_D 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2XPI_A 3ULQ_A.
Probab=49.83 E-value=1.1e+02 Score=23.13 Aligned_cols=48 Identities=23% Similarity=0.313 Sum_probs=34.7
Q ss_pred CChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHh
Q 043780 87 PEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLED 141 (386)
Q Consensus 87 ~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~ 141 (386)
.+.+.|+.+.+++.+.-. .+.++..+. .+|.++...|+++.|-.+++.
T Consensus 3 ~~y~~Ai~~~~k~~~~~~-----~~~~~~~~~--~la~~~~~~~~y~~A~~~~~~ 50 (84)
T PF12895_consen 3 GNYENAIKYYEKLLELDP-----TNPNSAYLY--NLAQCYFQQGKYEEAIELLQK 50 (84)
T ss_dssp T-HHHHHHHHHHHHHHHC-----GTHHHHHHH--HHHHHHHHTTHHHHHHHHHHC
T ss_pred ccHHHHHHHHHHHHHHCC-----CChhHHHHH--HHHHHHHHCCCHHHHHHHHHH
Confidence 368899999998877762 111333332 368889999999999999988
No 88
>TIGR02795 tol_pal_ybgF tol-pal system protein YbgF. Members of this protein family are the product of one of seven genes regularly clustered in operons to encode the proteins of the tol-pal system, which is critical for maintaining the integrity of the bacterial outer membrane. The gene for this periplasmic protein has been designated orf2 and ybgF. All members of the seed alignment were from unique tol-pal gene regions from completed bacterial genomes. The architecture of this protein is a signal sequence, a low-complexity region usually rich in Asn and Gln, a well-conserved region with tandem repeats that resemble the tetratricopeptide (TPR) repeat, involved in protein-protein interaction.
Probab=49.52 E-value=1.2e+02 Score=23.60 Aligned_cols=95 Identities=6% Similarity=-0.080 Sum_probs=56.9
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
..+.++|++.++++.+.- +.+. .........+..+...|+++.+.+.++.+-..-+.... ....++..+.
T Consensus 15 ~~~~~~A~~~~~~~~~~~-----~~~~-~~~~~~~~l~~~~~~~~~~~~A~~~~~~~~~~~p~~~~----~~~~~~~~~~ 84 (119)
T TIGR02795 15 AGDYADAIQAFQAFLKKY-----PKST-YAPNAHYWLGEAYYAQGKYADAAKAFLAVVKKYPKSPK----APDALLKLGM 84 (119)
T ss_pred cCCHHHHHHHHHHHHHHC-----CCcc-ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHCCCCCc----ccHHHHHHHH
Confidence 347889999888876543 1111 11223455788899999999999999887654222111 1122333333
Q ss_pred HHHHHhhcHHHHHHHHHHHhccCCCC
Q 043780 166 QYHKFHQEFAEFYKCALLYLAYTSVE 191 (386)
Q Consensus 166 ~~~k~~~~~~~~y~~~l~yL~~~~~~ 191 (386)
.+...+++.+.....-..+...|.+
T Consensus 85 -~~~~~~~~~~A~~~~~~~~~~~p~~ 109 (119)
T TIGR02795 85 -SLQELGDKEKAKATLQQVIKRYPGS 109 (119)
T ss_pred -HHHHhCChHHHHHHHHHHHHHCcCC
Confidence 3445777777666666666665544
No 89
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=48.98 E-value=55 Score=25.91 Aligned_cols=55 Identities=22% Similarity=0.320 Sum_probs=43.2
Q ss_pred HHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCC
Q 043780 279 EKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQV 336 (386)
Q Consensus 279 ~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv 336 (386)
.-.|+|+-+++.-+ +..-+|.+.|.+..+++..+++.-+-+.+..|||.-+.-.-
T Consensus 7 ~d~rvL~aiE~gmk---~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y 61 (82)
T PF09202_consen 7 EDFRVLRAIEMGMK---NHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPY 61 (82)
T ss_dssp HHHHHHHHHHTTTT---T-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS
T ss_pred HHHHHHHHHHHccc---CCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCc
Confidence 34688888887653 57899999999999999999999999999999999854333
No 90
>PRK09954 putative kinase; Provisional
Probab=48.77 E-value=69 Score=31.85 Aligned_cols=46 Identities=26% Similarity=0.263 Sum_probs=38.7
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEE---eecCCCCEEEE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG---IIDQVEGTVHV 342 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G---~IDqv~~~v~v 342 (386)
+..+|..+||+.++++...|-..+.+....|+|+| .+|.....+.|
T Consensus 15 ~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v~vi 63 (362)
T PRK09954 15 NPLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYCVVV 63 (362)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccEEEE
Confidence 45899999999999999999999999999999987 56665555444
No 91
>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=48.55 E-value=15 Score=31.06 Aligned_cols=41 Identities=17% Similarity=0.294 Sum_probs=34.7
Q ss_pred HHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHH
Q 043780 304 IIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVH 370 (386)
Q Consensus 304 ~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~ 370 (386)
.|++++++|.++|+..+|+. ++..-+..|+.+.++|+..|-
T Consensus 18 plSk~lgi~~ee~~~ili~~--------------------------~DmssLe~lhar~E~Ak~~cl 58 (117)
T PF09218_consen 18 PLSKELGISIEEFIDILIEK--------------------------LDMSSLENLHARYEQAKMGCL 58 (117)
T ss_dssp TTTTTGGGTHHHHHHHHHHH--------------------------S-HHHHHHHHHHHHTTHHHHH
T ss_pred HHHHHhCcCHHHHHHHHHHh--------------------------cChHHHHhccHHHHHHhhhhh
Confidence 37899999999999999986 567888999999999988663
No 92
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=47.77 E-value=25 Score=35.73 Aligned_cols=46 Identities=24% Similarity=0.344 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 279 EKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 279 ~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
+.+-+|-++++| ++.-+.-+||+.+++|.+++...+-+.+..|||+
T Consensus 341 ~~~~~l~~L~~~------DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 341 QQMAMLWVLNYS------DGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -HHHHHHHHHH-------EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHhc------cCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 456677888875 6899999999999999999999999999999986
No 93
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=47.35 E-value=24 Score=28.65 Aligned_cols=27 Identities=37% Similarity=0.470 Sum_probs=25.3
Q ss_pred HHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 304 IIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 304 ~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
.||..+++|.++|+..+-+....|||+
T Consensus 26 ~ia~~l~~~~~~v~~~l~~Le~~GLle 52 (92)
T PF10007_consen 26 SIARRLKIPLEEVREALEKLEEMGLLE 52 (92)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 489999999999999999999999986
No 94
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=47.29 E-value=80 Score=23.87 Aligned_cols=61 Identities=8% Similarity=0.135 Sum_probs=48.0
Q ss_pred ChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHH
Q 043780 301 PLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDS 364 (386)
Q Consensus 301 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~ 364 (386)
.|.++.+.++++.+....+.=+| .+-+-.++..++..++.-..|+.++.+.+..+.++|..
T Consensus 2 ~F~~ll~ql~~~~~~~~~~f~~~---~I~kv~v~k~~~~w~f~l~~~~~l~~~~~~~~~~~l~~ 62 (76)
T PF14480_consen 2 RFFELLKQLQIPDELDNPLFEDA---EIEKVTVHKKSRKWRFHLSSPHILPFEVYQKFEEKLKK 62 (76)
T ss_pred chHHHHHHcCCCchhhhhhhccc---EEEEEEEEccCCEEEEEEEeCCcCCHHHHHHHHHHHHH
Confidence 36778888998876633333332 45555999999999999999999999999999998864
No 95
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=46.42 E-value=21 Score=31.70 Aligned_cols=28 Identities=21% Similarity=0.234 Sum_probs=25.7
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|++-|...+.+|..
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 4799999999999999999999999864
No 96
>PF13424 TPR_12: Tetratricopeptide repeat; PDB: 3RO2_A 3Q15_A 3ASG_A 3ASD_A 3AS5_A 3AS4_A 3ASH_B 4A1S_B 3CEQ_B 3EDT_H ....
Probab=45.80 E-value=52 Score=24.46 Aligned_cols=60 Identities=15% Similarity=0.186 Sum_probs=41.8
Q ss_pred HHHhcCCChHHHHHHHHHHHHHhhhccccCCCch-HHHHHHHHHHHhcccCChHHHHHHHHhcc
Q 043780 81 IVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEP-ILYIKMQIAMFKLEQGDRKECKKLLEDGK 143 (386)
Q Consensus 81 ~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a-~~~~~~~~~~~~l~~~~l~~~~~~l~~~~ 143 (386)
.+.....+.++|++++++..+..... .+..+ .+.+...+|.++...|+++++.+.++++-
T Consensus 13 ~~~~~~~~~~~A~~~~~~al~~~~~~---~~~~~~~a~~~~~lg~~~~~~g~~~~A~~~~~~al 73 (78)
T PF13424_consen 13 RVYRELGRYDEALDYYEKALDIEEQL---GDDHPDTANTLNNLGECYYRLGDYEEALEYYQKAL 73 (78)
T ss_dssp HHHHHTT-HHHHHHHHHHHHHHHHHT---TTHHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHH
T ss_pred HHHHHcCCHHHHHHHHHHHHHHHHHH---CCCCHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHH
Confidence 34445678999999999877664311 11222 35666778889999999999999888753
No 97
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=45.34 E-value=24 Score=31.45 Aligned_cols=28 Identities=21% Similarity=0.229 Sum_probs=25.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||+|||+.+++|...|...+-+|..
T Consensus 142 ~gls~~EIA~~l~i~~~tVks~l~ra~~ 169 (182)
T COG1595 142 EGLSYEEIAEILGISVGTVKSRLHRARK 169 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5799999999999999999999998853
No 98
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=44.42 E-value=3.5e+02 Score=27.37 Aligned_cols=155 Identities=15% Similarity=0.157 Sum_probs=95.3
Q ss_pred HHHHHHHHHHhhhHHHHHHHHHHHHhchhhcCc--hhHHHHHHHHHHHHHhhc-------------ChHHHHHHHHHHHh
Q 043780 20 WYNALADLYQKKLWHQLTLKLEQFVAHAVFQAG--DALIQLYHNFITDFETKI-------------NLLKLAHFAVIVSR 84 (386)
Q Consensus 20 ~~~~~~~l~~~KLWhqLt~~l~~~~~~~~~~~~--~~~~~ly~~fi~~f~~ki-------------n~l~l~~i~~~v~~ 84 (386)
.++--+||+...|..-=-.....+++.|.|..+ ..++.||..= ++++.-| +.+.+++|.|..+.
T Consensus 110 l~qL~~Dym~aGl~DRAE~~f~~L~de~efa~~AlqqLl~IYQ~t-reW~KAId~A~~L~k~~~q~~~~eIAqfyCELAq 188 (389)
T COG2956 110 LQQLGRDYMAAGLLDRAEDIFNQLVDEGEFAEGALQQLLNIYQAT-REWEKAIDVAERLVKLGGQTYRVEIAQFYCELAQ 188 (389)
T ss_pred HHHHHHHHHHhhhhhHHHHHHHHHhcchhhhHHHHHHHHHHHHHh-hHHHHHHHHHHHHHHcCCccchhHHHHHHHHHHH
Confidence 344456666666665554455555655666432 2466666532 3333322 45667888888887
Q ss_pred cC---CChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHH
Q 043780 85 QY---PEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYY 161 (386)
Q Consensus 85 ~~---~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y 161 (386)
+. +|.+.|.+.+++..+ .+.-.++..|..+.+.+..|+++.+-+.++.+... ....-++|-..+
T Consensus 189 ~~~~~~~~d~A~~~l~kAlq---------a~~~cvRAsi~lG~v~~~~g~y~~AV~~~e~v~eQ---n~~yl~evl~~L- 255 (389)
T COG2956 189 QALASSDVDRARELLKKALQ---------ADKKCVRASIILGRVELAKGDYQKAVEALERVLEQ---NPEYLSEVLEML- 255 (389)
T ss_pred HHhhhhhHHHHHHHHHHHHh---------hCccceehhhhhhHHHHhccchHHHHHHHHHHHHh---ChHHHHHHHHHH-
Confidence 64 356667777765322 12236778888999999999999988877766542 222224444443
Q ss_pred HHHHHHHHHhhcHHHHHHHHHHHhccCCCC
Q 043780 162 WVSSQYHKFHQEFAEFYKCALLYLAYTSVE 191 (386)
Q Consensus 162 ~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~ 191 (386)
...|...|+.+++-.++..+....+..
T Consensus 256 ---~~~Y~~lg~~~~~~~fL~~~~~~~~g~ 282 (389)
T COG2956 256 ---YECYAQLGKPAEGLNFLRRAMETNTGA 282 (389)
T ss_pred ---HHHHHHhCCHHHHHHHHHHHHHccCCc
Confidence 344667888888888888877666543
No 99
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=43.03 E-value=68 Score=27.54 Aligned_cols=38 Identities=11% Similarity=0.136 Sum_probs=33.3
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeec
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIID 334 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ID 334 (386)
...+|-++||+.+++|..=|+..+-+.-..|||+.+=-
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence 35789999999999999999999999999999976543
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=42.00 E-value=26 Score=26.65 Aligned_cols=27 Identities=37% Similarity=0.385 Sum_probs=21.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
.|.-+-++||+.++++.++|..++-.+
T Consensus 18 gr~Pt~eEiA~~lgis~~~v~~~l~~~ 44 (78)
T PF04539_consen 18 GREPTDEEIAEELGISVEEVRELLQAS 44 (78)
T ss_dssp SS--BHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHcccHHHHHHHHHhC
Confidence 688999999999999999999877544
No 101
>PF13518 HTH_28: Helix-turn-helix domain
Probab=41.58 E-value=67 Score=21.97 Aligned_cols=27 Identities=15% Similarity=0.028 Sum_probs=24.3
Q ss_pred ChHHHHHHcCCChhHHHHHHHHHhhcc
Q 043780 301 PLSIIAERTKLSIEDVEHLLMKSLSVH 327 (386)
Q Consensus 301 sf~~Ia~~l~i~~~eVE~lvikAi~~g 327 (386)
|+.++|+.++|+...|..|+-+--..|
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G 40 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGG 40 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcC
Confidence 999999999999999999998776666
No 102
>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=41.27 E-value=73 Score=23.03 Aligned_cols=33 Identities=21% Similarity=0.132 Sum_probs=27.7
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccce
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLI 329 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI 329 (386)
.+.++.+++|+.+++|...+-.=+.+.-..|+|
T Consensus 12 ~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i 44 (57)
T PF08220_consen 12 KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLI 44 (57)
T ss_pred cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 579999999999999998777777777677774
No 103
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=41.03 E-value=30 Score=30.66 Aligned_cols=28 Identities=11% Similarity=0.197 Sum_probs=25.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|+.-|...+-+|+.
T Consensus 142 ~g~s~~EIA~~lgis~~tVk~~l~rAl~ 169 (178)
T PRK12529 142 DGMKQKDIAQALDIALPTVKKYIHQAYV 169 (178)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988864
No 104
>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=40.99 E-value=49 Score=26.86 Aligned_cols=35 Identities=17% Similarity=0.147 Sum_probs=27.7
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
+.++-++||+.++++..+|-.++-+....|+|+.+
T Consensus 26 ~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 26 GELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp --B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 68999999999999999999999999999999775
No 105
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.34 E-value=33 Score=29.27 Aligned_cols=28 Identities=18% Similarity=0.190 Sum_probs=25.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...|+++||+.+|+|...|...+-+|+.
T Consensus 121 ~~~s~~EIA~~l~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALETEMTYYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999988854
No 106
>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=39.93 E-value=32 Score=30.28 Aligned_cols=28 Identities=21% Similarity=0.137 Sum_probs=25.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|+..|...+-+|..
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 149 AGLTVEEIAELLGVSVRTVERDWRFARA 176 (183)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988753
No 107
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=39.82 E-value=1.8e+02 Score=23.53 Aligned_cols=62 Identities=16% Similarity=-0.015 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHH----------Hhhccce-EEeecCCCCEEEE
Q 043780 278 LEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMK----------SLSVHLI-EGIIDQVEGTVHV 342 (386)
Q Consensus 278 ~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvik----------Ai~~gLI-~G~IDqv~~~v~v 342 (386)
+.|+|.-.|.-|+..-| +...-.+||+.++++...|=--+.- .++.||| ....+.-.+...+
T Consensus 7 rS~~R~~vl~~L~~~yp---~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~l 79 (90)
T PF07381_consen 7 RSKVRKKVLEYLCSIYP---EPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRL 79 (90)
T ss_pred HHHHHHHHHHHHHHcCC---CcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEe
Confidence 35677777788877544 6788899999999999888776664 6788999 4444444433333
No 108
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.56 E-value=33 Score=30.08 Aligned_cols=28 Identities=29% Similarity=0.350 Sum_probs=25.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+++|+.-|...+-+|+.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 161 (172)
T PRK12523 134 DGMGHAEIAERLGVSVSRVRQYLAQGLR 161 (172)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988864
No 109
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=39.50 E-value=61 Score=25.36 Aligned_cols=40 Identities=13% Similarity=0.063 Sum_probs=25.6
Q ss_pred HHHHHHhhCCCCCCccChHHHHHHcC---CChhHHHHHHHHHhhccc
Q 043780 285 CLMEIIFSRPSEDRTIPLSIIAERTK---LSIEDVEHLLMKSLSVHL 328 (386)
Q Consensus 285 aL~~L~~~r~~~~r~isf~~Ia~~l~---i~~~eVE~lvikAi~~gL 328 (386)
.|+....+ .+.|||++|.+.+. ++++.++.++...-..|+
T Consensus 11 ~Li~~gK~----~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI 53 (82)
T PF03979_consen 11 KLIEKGKK----KGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGI 53 (82)
T ss_dssp HHHHHHHH----HSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT--
T ss_pred HHHHHHhh----cCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCC
Confidence 36666543 47899999999987 567788888877666654
No 110
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=38.93 E-value=74 Score=29.93 Aligned_cols=46 Identities=20% Similarity=0.270 Sum_probs=37.9
Q ss_pred HHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 282 NILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 282 rlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
|-+.++++... ..+.++..||++.+++|...+-.++-.....|++.
T Consensus 10 ral~IL~~l~~---~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~ 55 (248)
T TIGR02431 10 RGLAVIEAFGA---ERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVT 55 (248)
T ss_pred HHHHHHHHHhc---CCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 45556665432 24679999999999999999999999999999997
No 111
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=38.89 E-value=45 Score=22.75 Aligned_cols=26 Identities=27% Similarity=0.243 Sum_probs=22.7
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
-.++.+||+.++++...|...+-++.
T Consensus 18 g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 18 GLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46999999999999999999877663
No 112
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.73 E-value=36 Score=29.35 Aligned_cols=28 Identities=21% Similarity=0.248 Sum_probs=25.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+|+++||+.+|+|+..|...+-+|..
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQEKIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988843
No 113
>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=38.66 E-value=34 Score=27.54 Aligned_cols=31 Identities=16% Similarity=0.299 Sum_probs=25.0
Q ss_pred CCccChHHHHHHcCCC-hhHHHHHHHHHhhccce
Q 043780 297 DRTIPLSIIAERTKLS-IEDVEHLLMKSLSVHLI 329 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~-~~eVE~lvikAi~~gLI 329 (386)
...++|.+|-+. +| ++.||+|||+.+..|..
T Consensus 46 ~~vi~Fd~iVr~--mpNes~v~qWV~dtln~i~~ 77 (100)
T PF07389_consen 46 CAVIPFDDIVRT--MPNESRVKQWVIDTLNDIMM 77 (100)
T ss_pred hccccHHHHHHh--CCCHHHHHHHHHHHHHhHhh
Confidence 357899999998 64 67999999999876553
No 114
>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=38.46 E-value=52 Score=24.73 Aligned_cols=34 Identities=21% Similarity=0.078 Sum_probs=27.2
Q ss_pred CCccChHHHHHHcCCC-hhHHHHHHHHHhhccceE
Q 043780 297 DRTIPLSIIAERTKLS-IEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~-~~eVE~lvikAi~~gLI~ 330 (386)
...-|+.||++.+++. ..-|-..+-..-..|+|+
T Consensus 23 G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 23 GYPPTVREIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp SS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred CCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 4567999999999995 899999998888888886
No 115
>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=38.28 E-value=61 Score=27.39 Aligned_cols=41 Identities=22% Similarity=0.266 Sum_probs=35.2
Q ss_pred HHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 286 LMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 286 L~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
+++||- +.+|-+|||..+++|..=|--+|=+.+..|+|.-+
T Consensus 48 Il~lC~------~~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 48 ILELCR------RPLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVR 88 (114)
T ss_pred HHHHHC------CCccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEe
Confidence 566773 47999999999999999999999999999998754
No 116
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=38.04 E-value=37 Score=29.90 Aligned_cols=28 Identities=21% Similarity=0.304 Sum_probs=25.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+|+|+..|...+-+|+.
T Consensus 134 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 134 DGLTYSEIAHKLGVSVSSVKKYVAKATE 161 (172)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5799999999999999999999988864
No 117
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=37.89 E-value=37 Score=29.25 Aligned_cols=28 Identities=21% Similarity=0.324 Sum_probs=25.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+|+++||+.+|+|.+.|...+-+|..
T Consensus 125 ~g~s~~eIA~~lgis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 125 EDLSEAQVAEALGISVGTVKSRLSRALA 152 (162)
T ss_pred hcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3799999999999999999999998854
No 118
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and 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 []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=37.74 E-value=50 Score=24.51 Aligned_cols=35 Identities=26% Similarity=0.302 Sum_probs=29.5
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
.+..|..+|.+.+++|.++|-.-++-.|..|++.-
T Consensus 25 ~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y 59 (62)
T PF08221_consen 25 RGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQY 59 (62)
T ss_dssp C-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCeee
Confidence 47899999999999999999999999999999864
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=37.64 E-value=38 Score=29.04 Aligned_cols=28 Identities=11% Similarity=0.019 Sum_probs=25.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|+.-|...+-+|+.
T Consensus 121 ~g~s~~EIA~~lgis~~tV~~~l~ra~~ 148 (161)
T PRK09047 121 EDMDVAETAAAMGCSEGSVKTHCSRATH 148 (161)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999888753
No 120
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=37.26 E-value=84 Score=29.83 Aligned_cols=57 Identities=23% Similarity=0.413 Sum_probs=41.7
Q ss_pred HHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 282 NILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 282 rlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
|-+.++++....| +.+++.+|++.+++|...|-.++......|+++= |..+++..++
T Consensus 5 ral~iL~~l~~~~---~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~--d~~~g~Y~Lg 61 (246)
T COG1414 5 RALAILDLLAEGP---GGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQ--DPEDGRYRLG 61 (246)
T ss_pred HHHHHHHHHHhCC---CCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEE--cCCCCcEeeh
Confidence 3445555544333 4599999999999999999999999999999863 3334455544
No 121
>PRK09191 two-component response regulator; Provisional
Probab=37.16 E-value=1.8e+02 Score=26.81 Aligned_cols=28 Identities=18% Similarity=0.135 Sum_probs=24.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+++|+..|...+-+|+.
T Consensus 103 ~~~s~~eIA~~l~~s~~tV~~~l~ra~~ 130 (261)
T PRK09191 103 EGFSVEEAAEILGVDPAEAEALLDDARA 130 (261)
T ss_pred hcCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999999999999999999888753
No 122
>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=36.84 E-value=51 Score=22.61 Aligned_cols=26 Identities=19% Similarity=0.074 Sum_probs=22.8
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..++.+||+.++++...|+.++-++.
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 47999999999999999999976653
No 123
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=36.72 E-value=67 Score=24.89 Aligned_cols=33 Identities=21% Similarity=0.455 Sum_probs=25.9
Q ss_pred HHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHH
Q 043780 286 LMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 286 L~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
+++||- .-..||+.|....|+++.||=.+.-+-
T Consensus 5 iIeMAw-----eDRtpFeaI~~~fGL~E~eVi~lMR~~ 37 (72)
T TIGR03643 5 IIEMAW-----EDRTPFEAIEQQFGLSEKEVIKLMRQN 37 (72)
T ss_pred HHHHHH-----ccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 677776 346899999999999999986665443
No 124
>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=36.71 E-value=1.2e+02 Score=21.42 Aligned_cols=42 Identities=24% Similarity=0.187 Sum_probs=36.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCE
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGT 339 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~ 339 (386)
+.++..+||+.++++..-+=.++=+....|+|.=.-|..++.
T Consensus 16 ~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~~D~R 57 (59)
T PF01047_consen 16 GGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDPDDRR 57 (59)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEETTETT
T ss_pred CCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCCCCCC
Confidence 459999999999999999999999999999999988887753
No 125
>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=36.10 E-value=1.5e+02 Score=21.80 Aligned_cols=44 Identities=25% Similarity=0.259 Sum_probs=34.5
Q ss_pred HHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 283 ILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 283 lLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
|.++..|.. ....++-.+||+.++++...|=..+=+.-..|+|.
T Consensus 10 L~~Iy~l~~----~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 10 LKAIYELSE----EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHHH----CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHc----CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 344555543 35789999999999999999999998888899886
No 126
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=36.09 E-value=83 Score=21.80 Aligned_cols=33 Identities=15% Similarity=0.134 Sum_probs=29.9
Q ss_pred Ccc-ChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 298 RTI-PLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 298 r~i-sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
..+ |..+||+.++++..-|...+-+.-..|+|.
T Consensus 18 ~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 18 DKLPSERELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 356 899999999999999999999999999986
No 127
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=35.98 E-value=41 Score=28.97 Aligned_cols=27 Identities=19% Similarity=0.094 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+|+|..-|...+-+|+
T Consensus 124 ~~~s~~EIA~~lgis~~tV~~~l~ra~ 150 (163)
T PRK07037 124 HGETQKDIARELGVSPTLVNFMIRDAL 150 (163)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478999999999999999999988874
No 128
>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=35.78 E-value=64 Score=25.07 Aligned_cols=30 Identities=20% Similarity=0.038 Sum_probs=24.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhcc
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVH 327 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~g 327 (386)
..+||++||+.+++|+.-|..++-+-.+.|
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~ 60 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKGETKAG 60 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhcCcccc
Confidence 579999999999999999988876544433
No 129
>KOG2047 consensus mRNA splicing factor [RNA processing and modification]
Probab=35.62 E-value=1.7e+02 Score=32.20 Aligned_cols=101 Identities=13% Similarity=0.206 Sum_probs=65.6
Q ss_pred HHHHHHHHhhhHHHHHHHHHHHHhchhhcCc--hhHHHHHH---HHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHH
Q 043780 22 NALADLYQKKLWHQLTLKLEQFVAHAVFQAG--DALIQLYH---NFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYL 96 (386)
Q Consensus 22 ~~~~~l~~~KLWhqLt~~l~~~~~~~~~~~~--~~~~~ly~---~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl 96 (386)
+-++-|.+...|-+-...+...++++.|.+. ..-..+|. +.|+...+|+--+.+=.|+..-.+.++
T Consensus 174 eyie~L~~~d~~~eaa~~la~vln~d~f~sk~gkSn~qlw~elcdlis~~p~~~~slnvdaiiR~gi~rft--------- 244 (835)
T KOG2047|consen 174 EYIEYLAKSDRLDEAAQRLATVLNQDEFVSKKGKSNHQLWLELCDLISQNPDKVQSLNVDAIIRGGIRRFT--------- 244 (835)
T ss_pred HHHHHHHhccchHHHHHHHHHhcCchhhhhhcccchhhHHHHHHHHHHhCcchhcccCHHHHHHhhcccCc---------
Confidence 4466778889999999999999999988652 22333333 234444444444444444433333332
Q ss_pred HHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccccc
Q 043780 97 EGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLD 147 (386)
Q Consensus 97 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~ 147 (386)
+-.-.+-+..|.+|.+.|.++.|+.+.++.=.++-
T Consensus 245 ----------------Dq~g~Lw~SLAdYYIr~g~~ekarDvyeeai~~v~ 279 (835)
T KOG2047|consen 245 ----------------DQLGFLWCSLADYYIRSGLFEKARDVYEEAIQTVM 279 (835)
T ss_pred ----------------HHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhhe
Confidence 12334557789999999999999999998755433
No 130
>PF06552 TOM20_plant: Plant specific mitochondrial import receptor subunit TOM20; InterPro: IPR010547 This family consists of several plant specific mitochondrial import receptor subunit TOM20 (translocase of outer membrane 20 kDa subunit) proteins. Most mitochondrial proteins are encoded by the nuclear genome, and are synthesised in the cytosol. TOM20 is a general import receptor that binds to mitochondrial pre-sequences in the early step of protein import into the mitochondria [].; GO: 0045040 protein import into mitochondrial outer membrane, 0005742 mitochondrial outer membrane translocase complex; PDB: 1ZU2_A.
Probab=35.53 E-value=90 Score=28.68 Aligned_cols=76 Identities=20% Similarity=0.287 Sum_probs=45.0
Q ss_pred CCCchHHHHHHHHHHHhc-ccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHH------HhhcHHHHHHHHH
Q 043780 110 RKEEPILYIKMQIAMFKL-EQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHK------FHQEFAEFYKCAL 182 (386)
Q Consensus 110 ~~~~a~~~~~~~~~~~~l-~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k------~~~~~~~~y~~~l 182 (386)
+..++..+.+--.++..| ...+..++++++++.-.+++.--.++|.-|.++|-..--|.. ...+.+++|..+.
T Consensus 21 nP~DadnL~~WG~ALLELAqfk~g~es~~miedAisK~eeAL~I~P~~hdAlw~lGnA~ts~A~l~~d~~~A~~~F~kA~ 100 (186)
T PF06552_consen 21 NPLDADNLTNWGGALLELAQFKQGPESKKMIEDAISKFEEALKINPNKHDALWCLGNAYTSLAFLTPDTAEAEEYFEKAT 100 (186)
T ss_dssp -TT-HHHHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHH-TT-HHHHHHHHHHHHHHHHH---HHHHHHHHHHHH
T ss_pred CcHhHHHHHHHHHHHHHHHhccCcchHHHHHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHhhcCChHHHHHHHHHHH
Confidence 344566666665555555 345667888888888777776555678888888766433321 2234566777777
Q ss_pred HHh
Q 043780 183 LYL 185 (386)
Q Consensus 183 ~yL 185 (386)
.|-
T Consensus 101 ~~F 103 (186)
T PF06552_consen 101 EYF 103 (186)
T ss_dssp HHH
T ss_pred HHH
Confidence 755
No 131
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=35.46 E-value=71 Score=24.84 Aligned_cols=33 Identities=24% Similarity=0.452 Sum_probs=25.7
Q ss_pred HHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHH
Q 043780 286 LMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 286 L~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
+++||- .-..||+.|....|+++.||=.+.-+-
T Consensus 4 iIeMAw-----eDRtpFeaI~~qfGl~E~eVi~lMR~~ 36 (73)
T PF10985_consen 4 IIEMAW-----EDRTPFEAIERQFGLSEKEVIKLMRKE 36 (73)
T ss_pred HHHHHH-----ccCCCHHHHHHHHCCCHHHHHHHHHhh
Confidence 577776 346899999999999999986655443
No 132
>PF10975 DUF2802: Protein of unknown function (DUF2802); InterPro: IPR021244 This bacterial family of proteins has no known function.
Probab=35.25 E-value=39 Score=25.92 Aligned_cols=22 Identities=27% Similarity=0.283 Sum_probs=19.4
Q ss_pred ccChHHHHHHcCCChhHHHHHH
Q 043780 299 TIPLSIIAERTKLSIEDVEHLL 320 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lv 320 (386)
=.+-++|++.|++|..|+|.++
T Consensus 44 Ga~~~el~~~CgL~~aEAeLl~ 65 (70)
T PF10975_consen 44 GASVEELMEECGLSRAEAELLL 65 (70)
T ss_pred CCCHHHHHHHcCCCHHHHHHHH
Confidence 3678999999999999999875
No 133
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=35.15 E-value=44 Score=28.77 Aligned_cols=27 Identities=22% Similarity=0.257 Sum_probs=24.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+.-|...+-+|+
T Consensus 120 ~~~s~~eIA~~lgis~~tv~~~l~ra~ 146 (159)
T PRK12527 120 EGLSHQQIAEHLGISRSLVEKHIVNAM 146 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 479999999999999999999988874
No 134
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=35.07 E-value=36 Score=24.08 Aligned_cols=24 Identities=13% Similarity=0.094 Sum_probs=20.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLM 321 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvi 321 (386)
..-...+||..++|+...|..|.-
T Consensus 26 ~~~~~~~la~~l~l~~~~V~~WF~ 49 (57)
T PF00046_consen 26 SKEEREELAKELGLTERQVKNWFQ 49 (57)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHH
T ss_pred cccccccccccccccccccccCHH
Confidence 445577899999999999999864
No 135
>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=35.07 E-value=1.6e+02 Score=20.55 Aligned_cols=30 Identities=13% Similarity=0.049 Sum_probs=21.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhcc
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVH 327 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~g 327 (386)
..+|-++||+.+++|...|..-+=..-..|
T Consensus 14 ~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 14 EPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp TSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 349999999999999887766655443344
No 136
>PF14493 HTH_40: Helix-turn-helix domain
Probab=35.04 E-value=84 Score=24.86 Aligned_cols=55 Identities=15% Similarity=0.194 Sum_probs=44.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccc-eEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHL-IEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLG 367 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gL-I~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~ 367 (386)
.-.|.++||+.-+++..-|+.-+++++..|- +. ..+.++.++.+.+.+.+..+..
T Consensus 12 ~G~si~eIA~~R~L~~sTI~~HL~~~~~~g~~~~---------------~~~~l~~e~~~~I~~~~~~~~~ 67 (91)
T PF14493_consen 12 KGLSIEEIAKIRGLKESTIYGHLAELIESGEPLD---------------IEELLSEEEIKQIEDAIEKLGS 67 (91)
T ss_pred cCCCHHHHHHHcCCCHHHHHHHHHHHHHhCCCCC---------------HHHhCCHHHHHHHHHHHHHcCc
Confidence 4589999999999999999999999998876 33 1256788888888777766543
No 137
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=33.94 E-value=45 Score=29.86 Aligned_cols=27 Identities=22% Similarity=0.111 Sum_probs=24.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+..|...+-+|.
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar 172 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGR 172 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999988874
No 138
>PHA02943 hypothetical protein; Provisional
Probab=33.78 E-value=1.3e+02 Score=26.91 Aligned_cols=35 Identities=17% Similarity=0.075 Sum_probs=30.8
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
.+.-|-++||+++|+|..+|+..+.-.=+.|-|+-
T Consensus 22 ~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~Vkr 56 (165)
T PHA02943 22 DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLK 56 (165)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEE
Confidence 46778899999999999999999998888888875
No 139
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=33.74 E-value=77 Score=23.20 Aligned_cols=32 Identities=19% Similarity=0.511 Sum_probs=28.1
Q ss_pred HHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHH
Q 043780 285 CLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLL 320 (386)
Q Consensus 285 aL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lv 320 (386)
.|+++++++| .+|-..++++++++..-+..+|
T Consensus 3 ~Lidll~~~P----~Vsa~mva~~L~vT~~~A~~li 34 (54)
T PF11972_consen 3 RLIDLLLSRP----LVSAPMVAKELGVTPQAAQRLI 34 (54)
T ss_pred HHHHHHHhCc----cccHHHHHHHhCCCHHHHHHHH
Confidence 4788899887 8999999999999999888875
No 140
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=33.61 E-value=46 Score=29.70 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=24.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|+.-|...+-+|.
T Consensus 146 ~g~s~~EIA~~lgis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQELQITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 369999999999999999999988774
No 141
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=33.49 E-value=1.7e+02 Score=20.81 Aligned_cols=59 Identities=19% Similarity=0.200 Sum_probs=37.5
Q ss_pred HHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhh-cHHHHHHHHHHHhc
Q 043780 120 MQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQ-EFAEFYKCALLYLA 186 (386)
Q Consensus 120 ~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~-~~~~~y~~~l~yL~ 186 (386)
...|..+...|+++++...++++=.. +|.-...+|.. +..+...| ++.+......+.++
T Consensus 7 ~~~g~~~~~~~~~~~A~~~~~~ai~~-------~p~~~~~~~~~-g~~~~~~~~~~~~A~~~~~~al~ 66 (69)
T PF13414_consen 7 YNLGQIYFQQGDYEEAIEYFEKAIEL-------DPNNAEAYYNL-GLAYMKLGKDYEEAIEDFEKALK 66 (69)
T ss_dssp HHHHHHHHHTTHHHHHHHHHHHHHHH-------STTHHHHHHHH-HHHHHHTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHc-------CCCCHHHHHHH-HHHHHHhCccHHHHHHHHHHHHH
Confidence 45677888889999999888877543 22222233333 44455566 68777777766664
No 142
>PF09920 DUF2150: Uncharacterized protein conserved in archaea (DUF2150); InterPro: IPR014518 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.49 E-value=3.9e+02 Score=24.68 Aligned_cols=74 Identities=18% Similarity=0.211 Sum_probs=53.4
Q ss_pred HHHHhhhHHHHHHHHHH-HHhchhhcCchhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhh
Q 043780 26 DLYQKKLWHQLTLKLEQ-FVAHAVFQAGDALIQLYHNFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLR 104 (386)
Q Consensus 26 ~l~~~KLWhqLt~~l~~-~~~~~~~~~~~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~ 104 (386)
.||+++.|.---.++.+ =+.+|.....+.-..+|.||..+.. +..++|+-..=+..=+.++|++-|+.+++-|-
T Consensus 2 eFYtqeRW~NWi~~lkE~~f~~~e~ed~~~~~avf~~~~dDv~-----lA~lKIi~~~~~~~l~keeAl~~L~~v~eIVl 76 (190)
T PF09920_consen 2 EFYTQERWQNWINRLKESDFDDPESEDSPRGGAVFDNFQDDVI-----LACLKIIAAYQNGELSKEEALEELEEVREIVL 76 (190)
T ss_pred ccccHHHHHHHHHHHHHccCCCcccccchhHHHHHHHHHHHHH-----HHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHh
Confidence 58999999998888886 3445644333333679999988876 55555555555544478999999999988875
No 143
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.39 E-value=86 Score=22.90 Aligned_cols=48 Identities=15% Similarity=0.150 Sum_probs=34.2
Q ss_pred ChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHH
Q 043780 301 PLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRD 360 (386)
Q Consensus 301 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~ 360 (386)
+-.++|+.+||+...+-.|. ..|++...-...+ ..|.++.+++..++.
T Consensus 2 s~~eva~~~gvs~~tlr~~~----~~gli~~~~~~~~--------g~r~y~~~dl~~l~~ 49 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE----RIGLLPPPIRTEG--------GYRLYSDEDLERLRF 49 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCC--------CCEecCHHHHHHHHH
Confidence 56789999999999999884 4788876422222 247788888765543
No 144
>PRK10747 putative protoheme IX biogenesis protein; Provisional
Probab=33.27 E-value=2.4e+02 Score=28.45 Aligned_cols=69 Identities=12% Similarity=0.074 Sum_probs=48.7
Q ss_pred hHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccc
Q 043780 72 LLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDS 148 (386)
Q Consensus 72 ~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~ 148 (386)
|.-.--+...++.+..+++.+.+++.+..+. .+++.+...+..+.+++..|+++.+...++.+...-++
T Consensus 117 p~l~~llaA~aA~~~g~~~~A~~~l~~A~~~--------~~~~~~~~~l~~a~l~l~~g~~~~Al~~l~~~~~~~P~ 185 (398)
T PRK10747 117 PVVNYLLAAEAAQQRGDEARANQHLERAAEL--------ADNDQLPVEITRVRIQLARNENHAARHGVDKLLEVAPR 185 (398)
T ss_pred hHHHHHHHHHHHHHCCCHHHHHHHHHHHHhc--------CCcchHHHHHHHHHHHHHCCCHHHHHHHHHHHHhcCCC
Confidence 3333334455556778999999999886432 33455555556689999999999999999998765333
No 145
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=33.10 E-value=49 Score=28.91 Aligned_cols=28 Identities=14% Similarity=0.348 Sum_probs=25.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+++|..-|...+-+|+.
T Consensus 133 eg~s~~EIA~~l~is~~tV~~~l~ra~~ 160 (168)
T PRK12525 133 EGLTYVEIGERLGVSLSRIHQYMVEAFK 160 (168)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999999999999999999888764
No 146
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=32.97 E-value=1.1e+02 Score=29.45 Aligned_cols=58 Identities=14% Similarity=0.130 Sum_probs=42.7
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
-|-+.++++... ..+.++..+|++++++|...|-.++-.....|++.= |..++...+.
T Consensus 25 ~r~l~IL~~~~~---~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~--~~~~~~Y~lG 82 (271)
T PRK10163 25 ERGIAILQYLEK---SGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQ--DSQLGWWHIG 82 (271)
T ss_pred HHHHHHHHHHHh---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE--cCCCCeEEec
Confidence 345556665432 246799999999999999999999999999999843 4445554443
No 147
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=32.89 E-value=49 Score=29.27 Aligned_cols=27 Identities=19% Similarity=0.213 Sum_probs=24.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+.-|...+-+|+
T Consensus 132 e~~s~~EIA~~lgis~~tV~~~l~ra~ 158 (179)
T PRK12543 132 HDYSQEEIAQLLQIPIGTVKSRIHAAL 158 (179)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 368999999999999999999988873
No 148
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=32.85 E-value=49 Score=28.97 Aligned_cols=28 Identities=14% Similarity=0.088 Sum_probs=25.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+|+|++-|...+-+|..
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKK 161 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 5799999999999999999999888743
No 149
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.73 E-value=48 Score=29.14 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=23.7
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..||++||+.+|+|+.-|...+-+|.
T Consensus 145 g~s~~eIA~~lgis~~tV~~~l~Rar 170 (179)
T PRK12514 145 GLSYKELAERHDVPLNTMRTWLRRSL 170 (179)
T ss_pred CCCHHHHHHHHCCChHHHHHHHHHHH
Confidence 58999999999999999998888774
No 150
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=32.68 E-value=51 Score=28.44 Aligned_cols=28 Identities=21% Similarity=0.220 Sum_probs=25.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|..-|...+-+|..
T Consensus 128 ~g~s~~EIA~~l~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 128 DGLGYGEIATELGISLATVKRYLNKAAM 155 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5799999999999999999999988853
No 151
>PF12569 NARP1: NMDA receptor-regulated protein 1 ; InterPro: IPR021183 This group represents N-terminal acetyltransferase A (NatA) auxiliary subunit and represents a non-catalytic component of the NatA N-terminal acetyltransferase, which catalyzes acetylation of proteins beginning with Met-Ser, Met-Gly and Met-Ala. N-terminal acetylation plays a role in normal eukaryotic translation and processing, protect against proteolytic degradation and protein turnover. NAT1 anchors ARD1 and NAT5 to the ribosome and may present the N- terminal of nascent polypeptides for acetylation [], [].
Probab=32.57 E-value=6.4e+02 Score=26.88 Aligned_cols=65 Identities=17% Similarity=0.261 Sum_probs=45.2
Q ss_pred ChHHHHHHHHHHHh---cCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccc
Q 043780 71 NLLKLAHFAVIVSR---QYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKS 144 (386)
Q Consensus 71 n~l~l~~i~~~v~~---~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~ 144 (386)
+|-.++-.....+. ...+.++|++++++..+.- |+ .+=+-+..|+++-..|++.+|-++++++..
T Consensus 189 ~p~~~lw~~~~lAqhyd~~g~~~~Al~~Id~aI~ht-----Pt----~~ely~~KarilKh~G~~~~Aa~~~~~Ar~ 256 (517)
T PF12569_consen 189 PPSTLLWTLYFLAQHYDYLGDYEKALEYIDKAIEHT-----PT----LVELYMTKARILKHAGDLKEAAEAMDEARE 256 (517)
T ss_pred CchHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHhcC-----CC----cHHHHHHHHHHHHHCCCHHHHHHHHHHHHh
Confidence 46554444444444 3568999999998643321 22 222446789999999999999999999986
No 152
>PRK11569 transcriptional repressor IclR; Provisional
Probab=32.43 E-value=1.1e+02 Score=29.45 Aligned_cols=47 Identities=19% Similarity=0.243 Sum_probs=38.2
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
-|-+.++++... ..+.++..+|++.+++|...|-.++-.....|++.
T Consensus 28 ~ral~IL~~l~~---~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~ 74 (274)
T PRK11569 28 TRGLKLLEWIAE---SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVR 74 (274)
T ss_pred HHHHHHHHHHHh---CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 345556665432 25679999999999999999999999999999996
No 153
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=32.36 E-value=50 Score=29.60 Aligned_cols=27 Identities=15% Similarity=0.250 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+..|...+-+|.
T Consensus 149 ~g~s~~EIA~~lgis~~tVk~~l~RAr 175 (189)
T PRK12530 149 LELSSEQICQECDISTSNLHVLLYRAR 175 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 379999999999999999999988774
No 154
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=32.12 E-value=1.8e+02 Score=27.91 Aligned_cols=37 Identities=24% Similarity=0.187 Sum_probs=33.3
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEee
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGII 333 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 333 (386)
+..++..+||+.+|++..-+-.-+-+.-+.|+|+++=
T Consensus 196 egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 196 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4789999999999999999888899999999999863
No 155
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=31.83 E-value=52 Score=29.48 Aligned_cols=28 Identities=7% Similarity=0.038 Sum_probs=25.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+++|+.-|...+-+|..
T Consensus 126 eg~s~~EIA~~lgis~~tV~~~l~Rar~ 153 (182)
T PRK12511 126 EGLSYQEAAAVLGIPIGTLMSRIGRARA 153 (182)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHHH
Confidence 4799999999999999999999988854
No 156
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=31.61 E-value=1.1e+02 Score=29.02 Aligned_cols=47 Identities=13% Similarity=0.294 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEE
Q 043780 281 INILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEG 331 (386)
Q Consensus 281 irlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G 331 (386)
-|-+.++++... .+.++..+|++.+++|...|-.++-.....|++.=
T Consensus 14 ~r~l~IL~~l~~----~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~ 60 (257)
T PRK15090 14 LKVFGILQALGE----EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQ 60 (257)
T ss_pred HHHHHHHHHhhc----CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 355666666432 34699999999999999999999999999999864
No 157
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=31.60 E-value=1.2e+02 Score=20.04 Aligned_cols=30 Identities=17% Similarity=0.105 Sum_probs=24.5
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEee
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGII 333 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 333 (386)
++..++|+.++++...+-.|+ ..|.+.+..
T Consensus 2 lt~~e~a~~lgis~~ti~~~~----~~g~i~~~~ 31 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI----HEGELPAYR 31 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH----HcCCCCeEE
Confidence 578999999999999988886 467777643
No 158
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=31.60 E-value=76 Score=23.77 Aligned_cols=34 Identities=24% Similarity=0.137 Sum_probs=29.3
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
+..++=.|||++|+++.-.+-.++...-..|.|+
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 3568889999999999999999999999999886
No 159
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=31.49 E-value=1.9e+02 Score=22.78 Aligned_cols=52 Identities=15% Similarity=0.160 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 278 LEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 278 ~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
+++--|-+|+++=.+ ..+.+.-.+|++.++++..-|---+.+.-..|||++.
T Consensus 5 rq~~IL~alV~~Y~~---~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 5 RQREILKALVELYIE---TGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHHHHHHh---cCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 366667788887543 4688999999999999988777666666778999764
No 160
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=31.34 E-value=60 Score=22.48 Aligned_cols=24 Identities=13% Similarity=0.135 Sum_probs=21.2
Q ss_pred cChHHHHHHcCCChhHHHHHHHHH
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
.|+.+||+.+|++.+.|..++-++
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 799999999999999998877553
No 161
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=31.30 E-value=53 Score=29.34 Aligned_cols=27 Identities=33% Similarity=0.281 Sum_probs=24.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|..-|...+-+|.
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~ 180 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYAL 180 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 579999999999999999998887774
No 162
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=30.93 E-value=3.1e+02 Score=26.68 Aligned_cols=75 Identities=17% Similarity=0.109 Sum_probs=51.0
Q ss_pred CccChHHHHHHcC--CChhHHHHHHHHHhhccceEE----eecCCCCEEEEEeec-------------------------
Q 043780 298 RTIPLSIIAERTK--LSIEDVEHLLMKSLSVHLIEG----IIDQVEGTVHVSWVQ------------------------- 346 (386)
Q Consensus 298 r~isf~~Ia~~l~--i~~~eVE~lvikAi~~gLI~G----~IDqv~~~v~vt~v~------------------------- 346 (386)
..-..++||+.|+ ||.++|..-+=-....|||+= +--|.+..+..+.-.
T Consensus 136 ~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~~~p~ 215 (271)
T TIGR02147 136 FADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALDALPP 215 (271)
T ss_pred CCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCccchHHHHHHHHHHHHHHHHHHHhCCc
Confidence 4445779999999 899999999988999999963 334444444422111
Q ss_pred -cc-------cCChhhHHHHHHHHHHHHHHHHHH
Q 043780 347 -PR-------VLGIPQIKSLRDRLDSWLGKVHTA 372 (386)
Q Consensus 347 -~R-------~l~~~q~~~L~~~L~~W~~~v~~~ 372 (386)
.| .++++..+.++..|...+.+|..+
T Consensus 216 ~eR~~S~lT~~i~~~~~~~i~~~i~~fRk~i~~i 249 (271)
T TIGR02147 216 SERDVSTVTFGISEEAYKEIVKKIQEFRKEVLAI 249 (271)
T ss_pred cccccceeeEecCHHHHHHHHHHHHHHHHHHHHH
Confidence 12 245667778888888888777543
No 163
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=30.93 E-value=1.2e+02 Score=21.96 Aligned_cols=43 Identities=26% Similarity=0.231 Sum_probs=34.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCE
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGT 339 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~ 339 (386)
.+.++..+|++.++++...+-..|=+....|+|+=.=|..++.
T Consensus 16 ~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R 58 (68)
T PF13463_consen 16 DGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKR 58 (68)
T ss_dssp TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTT
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCC
Confidence 6789999999999999999999999999999997666655544
No 164
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=30.91 E-value=53 Score=30.51 Aligned_cols=28 Identities=11% Similarity=0.076 Sum_probs=25.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|+..|...+-+|+.
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~ 224 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIK 224 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5899999999999999999999888753
No 165
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=30.86 E-value=55 Score=28.55 Aligned_cols=27 Identities=22% Similarity=0.143 Sum_probs=24.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+|+|+.-|...+-+|.
T Consensus 133 ~g~s~~EIA~~lgis~~tV~~~l~ra~ 159 (173)
T PRK09645 133 RGWSTAQIAADLGIPEGTVKSRLHYAL 159 (173)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999999988874
No 166
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=30.81 E-value=97 Score=24.65 Aligned_cols=32 Identities=9% Similarity=0.045 Sum_probs=25.1
Q ss_pred ChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCC
Q 043780 301 PLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQV 336 (386)
Q Consensus 301 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv 336 (386)
+-.++|+.+||+.+.+-+|. +.|++...-+..
T Consensus 2 ~~~eva~~~gi~~~tlr~~~----~~Gll~~~~~~~ 33 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYE----EKGLLPPERSEN 33 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HCCCcCCCcCCC
Confidence 56789999999999999994 578887654443
No 167
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=30.66 E-value=58 Score=28.33 Aligned_cols=28 Identities=4% Similarity=0.012 Sum_probs=25.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+|+++||+.+++|+..|...+-+|..
T Consensus 127 ~g~s~~eIA~~lgis~~tV~~~l~Rar~ 154 (164)
T PRK12547 127 SGFSYEDAAAICGCAVGTIKSRVSRARN 154 (164)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988753
No 168
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.39 E-value=2.1e+02 Score=24.63 Aligned_cols=44 Identities=20% Similarity=0.215 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 280 KINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 280 KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
|.|++.|+. .++.+|+.++...+|++.+.++..+-++...|-|-
T Consensus 14 k~rIvElVR-------e~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 14 KARIVELVR-------EHGRITIKQLVAKTGASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHHHH-------HcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeE
Confidence 555555554 36899999999999999999999999999988653
No 169
>cd05804 StaR_like StaR_like; a well-conserved protein found in bacteria, plants, and animals. A family member from Streptomyces toyocaensis, StaR is part of a gene cluster involved in the biosynthesis of glycopeptide antibiotics (GPAs), specifically A47934. It has been speculated that StaR could be a flavoprotein hydroxylating a tyrosine sidechain. Some family members have been annotated as proteins containing tetratricopeptide (TPR) repeats, which may at least indicate mostly alpha-helical secondary structure.
Probab=30.26 E-value=4.4e+02 Score=25.32 Aligned_cols=87 Identities=13% Similarity=0.083 Sum_probs=55.4
Q ss_pred HHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHH
Q 043780 82 VSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYY 161 (386)
Q Consensus 82 v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y 161 (386)
+.....+.++|++.+++..+.- ..++.. -...+.++...|+++++..+++++-...+. ++..+...|
T Consensus 123 ~~~~~G~~~~A~~~~~~al~~~-------p~~~~~--~~~la~i~~~~g~~~eA~~~l~~~l~~~~~----~~~~~~~~~ 189 (355)
T cd05804 123 GLEEAGQYDRAEEAARRALELN-------PDDAWA--VHAVAHVLEMQGRFKEGIAFMESWRDTWDC----SSMLRGHNW 189 (355)
T ss_pred HHHHcCCHHHHHHHHHHHHhhC-------CCCcHH--HHHHHHHHHHcCCHHHHHHHHHhhhhccCC----CcchhHHHH
Confidence 4445557788888887765543 122333 345588888899999999999987654332 233444445
Q ss_pred HHHHHHHHHhhcHHHHHHHH
Q 043780 162 WVSSQYHKFHQEFAEFYKCA 181 (386)
Q Consensus 162 ~~~s~~~k~~~~~~~~y~~~ 181 (386)
...+.++-..|++.+.....
T Consensus 190 ~~la~~~~~~G~~~~A~~~~ 209 (355)
T cd05804 190 WHLALFYLERGDYEAALAIY 209 (355)
T ss_pred HHHHHHHHHCCCHHHHHHHH
Confidence 56666777788877654433
No 170
>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=30.20 E-value=2.4e+02 Score=25.72 Aligned_cols=45 Identities=13% Similarity=0.046 Sum_probs=36.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
+.++..+||+.++++..-|-..+-+....|+|+-.-+ ..+.+.+|
T Consensus 156 g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT 200 (203)
T TIGR01884 156 GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLT 200 (203)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeC
Confidence 5699999999999999999999999889999986543 44444444
No 171
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=29.67 E-value=2.5e+02 Score=23.51 Aligned_cols=51 Identities=22% Similarity=0.320 Sum_probs=38.2
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHH
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSL 358 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L 358 (386)
..|.+|+++++-+++.|=.++..-++. .|+||.. +.+.|+ -.++.++++.+
T Consensus 22 ~Nf~~I~~~L~R~p~hv~kyl~~ELgt---~g~id~~-~rlii~----G~~~~~~i~~~ 72 (110)
T smart00653 22 VNFADIAKALNRPPDHVLKFLLAELGT---QGSIDGK-GRLIVN----GRFTPKKLQDL 72 (110)
T ss_pred EcHHHHHHHHCCCHHHHHHHHHHHhCC---ceeECCC-CeEEEE----EeeCHHHHHHH
Confidence 589999999999999988888887664 6888877 677666 23455544443
No 172
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=29.62 E-value=1e+02 Score=22.39 Aligned_cols=48 Identities=15% Similarity=0.084 Sum_probs=33.3
Q ss_pred ChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHH
Q 043780 301 PLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRD 360 (386)
Q Consensus 301 sf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~ 360 (386)
|..++|+.++|+...+-.|.=+ .|++...-+. -..|.++.+++..|+.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~---~g~~~~~r~~---------~~~r~yt~~~v~~l~~ 49 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR---YGLPAPQRTD---------GGHRLYSEADVARLRL 49 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh---CCCCCCCcCC---------CCCeecCHHHHHHHHH
Confidence 6689999999999999999633 2544332111 2458889998876653
No 173
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=29.38 E-value=59 Score=30.18 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=25.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|||+.-|...+-+|..
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~ 176 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARR 176 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988743
No 174
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=28.84 E-value=61 Score=29.40 Aligned_cols=27 Identities=15% Similarity=0.187 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|+.-|...+-+|.
T Consensus 154 eg~s~~EIA~~lgis~~tVk~~l~RAr 180 (201)
T PRK12545 154 LDFEIDDICTELTLTANHCSVLLYRAR 180 (201)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999998888774
No 175
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.71 E-value=63 Score=28.52 Aligned_cols=28 Identities=18% Similarity=0.182 Sum_probs=25.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+++|..-|...+-+|..
T Consensus 146 ~g~s~~eIA~~l~is~~tV~~~l~ra~~ 173 (184)
T PRK12512 146 EGASIKETAAKLSMSEGAVRVALHRGLA 173 (184)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999999999988754
No 176
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=28.69 E-value=61 Score=29.07 Aligned_cols=27 Identities=19% Similarity=0.277 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|..-|...+-+|.
T Consensus 157 ~~~s~~EIA~~Lgis~~tVk~~l~ra~ 183 (194)
T PRK09646 157 GGLTYREVAERLAVPLGTVKTRMRDGL 183 (194)
T ss_pred cCCCHHHHHHHhCCChHhHHHHHHHHH
Confidence 469999999999999999999988874
No 177
>PLN03088 SGT1, suppressor of G2 allele of SKP1; Provisional
Probab=28.62 E-value=3.7e+02 Score=26.82 Aligned_cols=88 Identities=14% Similarity=0.074 Sum_probs=56.4
Q ss_pred CChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHH
Q 043780 87 PEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQ 166 (386)
Q Consensus 87 ~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~ 166 (386)
.+.++|++.+.+....- ..++.++ ...|..++..|+++++...++.+-.. ++.-..+|++.+ .
T Consensus 16 ~~~~~Ai~~~~~Al~~~-------P~~~~a~--~~~a~~~~~~g~~~eAl~~~~~Al~l-------~P~~~~a~~~lg-~ 78 (356)
T PLN03088 16 DDFALAVDLYTQAIDLD-------PNNAELY--ADRAQANIKLGNFTEAVADANKAIEL-------DPSLAKAYLRKG-T 78 (356)
T ss_pred CCHHHHHHHHHHHHHhC-------CCCHHHH--HHHHHHHHHcCCHHHHHHHHHHHHHh-------CcCCHHHHHHHH-H
Confidence 47889998887765432 2334455 45567777889999999888776442 222233455444 4
Q ss_pred HHHHhhcHHHHHHHHHHHhccCCCC
Q 043780 167 YHKFHQEFAEFYKCALLYLAYTSVE 191 (386)
Q Consensus 167 ~~k~~~~~~~~y~~~l~yL~~~~~~ 191 (386)
.+-..|+|.+.....-+.+..-|.+
T Consensus 79 ~~~~lg~~~eA~~~~~~al~l~P~~ 103 (356)
T PLN03088 79 ACMKLEEYQTAKAALEKGASLAPGD 103 (356)
T ss_pred HHHHhCCHHHHHHHHHHHHHhCCCC
Confidence 4446788888777777777665543
No 178
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=28.57 E-value=65 Score=27.78 Aligned_cols=28 Identities=14% Similarity=0.280 Sum_probs=25.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...|+++||+.+|+|+.-|...+-+|..
T Consensus 137 ~g~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 137 QNLPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4699999999999999999999988753
No 179
>KOG2002 consensus TPR-containing nuclear phosphoprotein that regulates K(+) uptake [Inorganic ion transport and metabolism]
Probab=28.43 E-value=7.9e+02 Score=28.38 Aligned_cols=210 Identities=18% Similarity=0.171 Sum_probs=0.0
Q ss_pred HhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccccc-ccCCCCHHHHHHHH
Q 043780 83 SRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLD-SMTDIDPSVYANYY 161 (386)
Q Consensus 83 ~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~-~~~~v~~~v~a~~y 161 (386)
+.+++|+.+-+..|+.-...+. .=+.+|+-|-..|..++...+|++...... ...+++...+.+++
T Consensus 21 ~~~LPD~~ev~~IL~~e~a~le-------------~wi~~AleYy~~gk~eefi~iLE~g~~~~~~~y~d~~~~~~~a~~ 87 (1018)
T KOG2002|consen 21 CDQLPDATEVLSILKAEQAPLE-------------AWIEIALEYYKQGKTEEFIKILESGLIDANEEYADVKSDQMKALD 87 (1018)
T ss_pred hhcCCChHHHHHHHHHhcCchh-------------HHHHHHHHHHhcccHHHHHHHHHhhhhcccchhcchHHHHHHHHH
Q ss_pred HHHHHH----HHHhhcHH--HHHHHHHHHhccCCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccChhhhcccCCCc
Q 043780 162 WVSSQY----HKFHQEFA--EFYKCALLYLAYTSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINSLTGTKV 235 (386)
Q Consensus 162 ~~~s~~----~k~~~~~~--~~y~~~l~yL~~~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~ 235 (386)
.+++-| ++.+..-. ++..++..|+...+. +...+...+.++-+..-+.++.- -+-....-.-.|+.++.
T Consensus 88 ~laay~s~~a~kek~~~~k~e~~~~at~~~~~A~k--i~m~~~~~l~~~~~~~l~~~~~~---~~~A~a~F~~Vl~~sp~ 162 (1018)
T KOG2002|consen 88 ILAAYYSQLAMKEKKKDEKDELFDKATLLFDLADK--IDMYEDSHLLVQRGFLLLEGDKS---MDDADAQFHFVLKQSPD 162 (1018)
T ss_pred HHHHHHHHHHHHHHhcchhHHHHHHHHHHhhHHHH--hhccCcchhhhhhhhhhhcCCcc---HHHHHHHHHHHHhhCCc
Q ss_pred HHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhH
Q 043780 236 EWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIED 315 (386)
Q Consensus 236 ~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~e 315 (386)
.-+.=|..+-..=+=++|...+.=++..+-.+|....+.-...- .|+..| +..+.....+..++++++..
T Consensus 163 Nil~LlGkA~i~ynkkdY~~al~yyk~al~inp~~~aD~rIgig----~Cf~kl------~~~~~a~~a~~ralqLdp~~ 232 (1018)
T KOG2002|consen 163 NILALLGKARIAYNKKDYRGALKYYKKALRINPACKADVRIGIG----HCFWKL------GMSEKALLAFERALQLDPTC 232 (1018)
T ss_pred chHHHHHHHHHHhccccHHHHHHHHHHHHhcCcccCCCccchhh----hHHHhc------cchhhHHHHHHHHHhcChhh
Q ss_pred HHHHH
Q 043780 316 VEHLL 320 (386)
Q Consensus 316 VE~lv 320 (386)
|..+|
T Consensus 233 v~alv 237 (1018)
T KOG2002|consen 233 VSALV 237 (1018)
T ss_pred HHHHH
No 180
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=28.34 E-value=5.5e+02 Score=24.78 Aligned_cols=77 Identities=14% Similarity=0.169 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHH
Q 043780 280 KINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLR 359 (386)
Q Consensus 280 KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~ 359 (386)
+-.+|+.+ +-+. ..+.=.+||++++|++.-|-..+=..+..|+|+- .-.+.-.| +++-.+.|.
T Consensus 12 ~fqIL~ei--~~~q----p~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~---~gR~~Y~i--------TkkG~e~l~ 74 (260)
T COG1497 12 RFQILSEI--AVRQ----PRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK---EGRGEYEI--------TKKGAEWLL 74 (260)
T ss_pred HHHHHHHH--HHhC----CCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee---cCCeeEEE--------ehhHHHHHH
Confidence 44444444 4443 4788899999999999999999999999988864 22223334 456565666
Q ss_pred HHHHHHHHHHHHHH
Q 043780 360 DRLDSWLGKVHTAL 373 (386)
Q Consensus 360 ~~L~~W~~~v~~~~ 373 (386)
+.+...+.=++.+.
T Consensus 75 ~~~~dlr~f~~ev~ 88 (260)
T COG1497 75 EQLSDLRRFSEEVE 88 (260)
T ss_pred HHHHHHHHHHHHHH
Confidence 66666555555553
No 181
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=28.23 E-value=2.1e+02 Score=20.27 Aligned_cols=38 Identities=24% Similarity=0.202 Sum_probs=29.5
Q ss_pred HHHHHHhhc--cceEEeecCCCCEEEEEeeccccCChhhHH
Q 043780 318 HLLMKSLSV--HLIEGIIDQVEGTVHVSWVQPRVLGIPQIK 356 (386)
Q Consensus 318 ~lvikAi~~--gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~ 356 (386)
.-|.+++.. |+-...+|-.++++.|++..++ .+.+++.
T Consensus 14 ~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~-~~~~~i~ 53 (62)
T PF00403_consen 14 KKVEKALSKLPGVKSVKVDLETKTVTVTYDPDK-TSIEKII 53 (62)
T ss_dssp HHHHHHHHTSTTEEEEEEETTTTEEEEEESTTT-SCHHHHH
T ss_pred HHHHHHHhcCCCCcEEEEECCCCEEEEEEecCC-CCHHHHH
Confidence 344455554 9999999999999999998888 6766543
No 182
>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=28.22 E-value=62 Score=23.80 Aligned_cols=25 Identities=16% Similarity=0.064 Sum_probs=21.8
Q ss_pred CccChHHHHHHcCCChhHHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMK 322 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvik 322 (386)
+-.+..+||+.|++|..-|-.|+=+
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~~r 36 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWKDR 36 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHHHh
Confidence 3588999999999999999998755
No 183
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=28.17 E-value=4.5e+02 Score=23.71 Aligned_cols=95 Identities=13% Similarity=0.065 Sum_probs=55.0
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
..+.++|+..++++.+.- +.+. .........+..+...|+++++...++++-..-++. +.+...+|....
T Consensus 46 ~~~~~~A~~~~~~~~~~~-----p~~~-~~~~a~~~la~~~~~~~~~~~A~~~~~~~l~~~p~~----~~~~~a~~~~g~ 115 (235)
T TIGR03302 46 SGDYTEAIKYFEALESRY-----PFSP-YAEQAQLDLAYAYYKSGDYAEAIAAADRFIRLHPNH----PDADYAYYLRGL 115 (235)
T ss_pred cCCHHHHHHHHHHHHHhC-----CCch-hHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHCcCC----CchHHHHHHHHH
Confidence 347888988888765544 1111 112233556888888999999999999886544432 223334555555
Q ss_pred HHHHH-------hhcHHHHHHHHHHHhccCCC
Q 043780 166 QYHKF-------HQEFAEFYKCALLYLAYTSV 190 (386)
Q Consensus 166 ~~~k~-------~~~~~~~y~~~l~yL~~~~~ 190 (386)
.+++. .+++....+..-..+...|.
T Consensus 116 ~~~~~~~~~~~~~~~~~~A~~~~~~~~~~~p~ 147 (235)
T TIGR03302 116 SNYNQIDRVDRDQTAAREAFEAFQELIRRYPN 147 (235)
T ss_pred HHHHhcccccCCHHHHHHHHHHHHHHHHHCCC
Confidence 45442 24454444444444444443
No 184
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=28.17 E-value=65 Score=28.90 Aligned_cols=27 Identities=22% Similarity=0.113 Sum_probs=24.5
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+++.-|...+-+|.
T Consensus 143 ~g~s~~EIA~~lgis~~tV~~~l~Rar 169 (188)
T PRK12517 143 GGFSGEEIAEILDLNKNTVMTRLFRAR 169 (188)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999988874
No 185
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=27.94 E-value=66 Score=28.68 Aligned_cols=27 Identities=4% Similarity=0.005 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+++|+..|...+-+|.
T Consensus 145 ~g~s~~EIA~~lgis~~tVk~~l~Rar 171 (185)
T PRK09649 145 LGLSYADAAAVCGCPVGTIRSRVARAR 171 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999988774
No 186
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.86 E-value=66 Score=28.87 Aligned_cols=27 Identities=7% Similarity=0.048 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+++|+..|...+=+|.
T Consensus 131 ~g~s~~EIA~~Lgis~~tVk~~l~Rar 157 (187)
T PRK12516 131 SGFAYEEAAEICGCAVGTIKSRVNRAR 157 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999987774
No 187
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.77 E-value=3.2e+02 Score=25.31 Aligned_cols=94 Identities=14% Similarity=0.150 Sum_probs=64.9
Q ss_pred CCCcHHHHHHHHHHhcCCHHHHHHHHHHhhhhhhcCchhhhhHHHHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCC
Q 043780 232 GTKVEWLYYILQAFNSGDLVRYQELCRVHNAALRAQPALVENEKKLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKL 311 (386)
Q Consensus 232 ~~~~~~l~~LL~~f~~G~l~~f~~~~~~~~~~~~~~~~L~~~~~~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i 311 (386)
+.+..-+++|=..+-+|++..|=.-.+.|+..+...+++ ++.+|.=++ -++++.| ..|.=.-+|+.+|=
T Consensus 95 ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~mle~itGF---edsvr~yac--hvv~iTy------QkI~k~lLaellG~ 163 (217)
T KOG3252|consen 95 EEPFRSIIDLGDYLETCRFQQFWQEADENRDMLEGITGF---EDSVRKYAC--HVVGITY------QKIDKWLLAELLGG 163 (217)
T ss_pred ccchhHHHhHHHHHhhchHHHHhhhhccchHHhcCCCcH---HHHHHHHHH--HheechH------hhchHHHHHHhhCc
Confidence 345666888888888999999988888888888776654 556643222 2333333 23444556777765
Q ss_pred -ChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 312 -SIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 312 -~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
+..++|.|+-+- |++.+.+|.+.|-
T Consensus 164 ~sDs~le~~~~~~-------GW~a~e~G~ifv~ 189 (217)
T KOG3252|consen 164 LSDSQLEVWMTKY-------GWIADESGQIFVA 189 (217)
T ss_pred ccHHHHHHHHHHc-------cceecCCceEEEe
Confidence 677999999874 8888999866664
No 188
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=27.75 E-value=67 Score=28.77 Aligned_cols=27 Identities=15% Similarity=0.175 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|...|...+-+|.
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar 172 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRAR 172 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 479999999999999999999988773
No 189
>KOG2003 consensus TPR repeat-containing protein [General function prediction only]
Probab=27.58 E-value=7.7e+02 Score=26.22 Aligned_cols=53 Identities=19% Similarity=0.314 Sum_probs=36.1
Q ss_pred HHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHH
Q 043780 120 MQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKC 180 (386)
Q Consensus 120 ~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~ 180 (386)
++++.+|-...+...+-+|+-++...++. +|.+-+.+ +++|...|+-++.|.+
T Consensus 562 ~qianiye~led~aqaie~~~q~~slip~----dp~ilskl----~dlydqegdksqafq~ 614 (840)
T KOG2003|consen 562 VQIANIYELLEDPAQAIELLMQANSLIPN----DPAILSKL----ADLYDQEGDKSQAFQC 614 (840)
T ss_pred HHHHHHHHHhhCHHHHHHHHHHhcccCCC----CHHHHHHH----HHHhhcccchhhhhhh
Confidence 45666666677778888888888776665 56665543 6777777776665444
No 190
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=27.44 E-value=65 Score=30.58 Aligned_cols=27 Identities=7% Similarity=0.119 Sum_probs=24.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+.-|+..+-+|.
T Consensus 176 eg~S~~EIA~~Lgis~~TVk~rl~RAr 202 (244)
T TIGR03001 176 DGLSMDRIGAMYQVHRSTVSRWVAQAR 202 (244)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999999999884
No 191
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=27.42 E-value=68 Score=28.57 Aligned_cols=28 Identities=21% Similarity=0.216 Sum_probs=24.8
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+||++||+.+|+|..-|...+-+|+.
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLL 183 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4699999999999999999999888753
No 192
>PF08311 Mad3_BUB1_I: Mad3/BUB1 homology region 1; InterPro: IPR013212 Proteins containing this domain are checkpoint proteins involved in cell division. This region has been shown to be essential for the binding of BUB1 and MAD3 to CDC20p [].; PDB: 3ESL_B 4AEZ_I 4A1G_B 2LAH_A 2WVI_A 3SI5_B.
Probab=27.38 E-value=3.8e+02 Score=22.60 Aligned_cols=80 Identities=14% Similarity=0.240 Sum_probs=57.9
Q ss_pred chhHHHHHHHHHHHHHhh---cChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcc
Q 043780 52 GDALIQLYHNFITDFETK---INLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLE 128 (386)
Q Consensus 52 ~~~~~~ly~~fi~~f~~k---in~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~ 128 (386)
...+.++++.-++.|.+. -|=.+++.+.+.-++..+||.+...||.. ..+ ...=|..| +..|.++-.
T Consensus 42 ~~~L~~lLer~~~~f~~~~~Y~nD~RylkiWi~ya~~~~~~~~if~~l~~--~~I------G~~~A~fY--~~wA~~le~ 111 (126)
T PF08311_consen 42 QSGLLELLERCIRKFKDDERYKNDERYLKIWIKYADLSSDPREIFKFLYS--KGI------GTKLALFY--EEWAEFLEK 111 (126)
T ss_dssp CHHHHHHHHHHHHHHTTSGGGTT-HHHHHHHHHHHTTBSHHHHHHHHHHH--HTT------STTBHHHH--HHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHhhhHhhcCCHHHHHHHHHHHHHccCHHHHHHHHHH--cCc------cHHHHHHH--HHHHHHHHH
Confidence 345778888888888543 67889999999999988888888888754 122 23345666 567778888
Q ss_pred cCChHHHHHHHHh
Q 043780 129 QGDRKECKKLLED 141 (386)
Q Consensus 129 ~~~l~~~~~~l~~ 141 (386)
.|++++|.+++..
T Consensus 112 ~~~~~~A~~I~~~ 124 (126)
T PF08311_consen 112 RGNFKKADEIYQL 124 (126)
T ss_dssp TT-HHHHHHHHHH
T ss_pred cCCHHHHHHHHHh
Confidence 8999999988754
No 193
>COG3063 PilF Tfp pilus assembly protein PilF [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=27.06 E-value=1.8e+02 Score=27.98 Aligned_cols=91 Identities=27% Similarity=0.264 Sum_probs=56.9
Q ss_pred HHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcH---HHHHHHHHHHhccCCCC-
Q 043780 116 LYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEF---AEFYKCALLYLAYTSVE- 191 (386)
Q Consensus 116 ~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~---~~~y~~~l~yL~~~~~~- 191 (386)
.=+++..+.-||..||+..+++-|+++=.. ||..+.+ +.+.+.||...|.. .+.|+.++. --|.+
T Consensus 35 a~arlqLal~YL~~gd~~~A~~nlekAL~~-------DPs~~~a-~~~~A~~Yq~~Ge~~~A~e~YrkAls---l~p~~G 103 (250)
T COG3063 35 AKARLQLALGYLQQGDYAQAKKNLEKALEH-------DPSYYLA-HLVRAHYYQKLGENDLADESYRKALS---LAPNNG 103 (250)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHHh-------CcccHHH-HHHHHHHHHHcCChhhHHHHHHHHHh---cCCCcc
Confidence 336688899999999999999999876432 3444444 34456667666553 457777765 22211
Q ss_pred C-C--------ChhHHHHHHHHHHHHHhcCCCcccc
Q 043780 192 S-L--------SDSFKLDLAFDLSLSALLGDNIYNF 218 (386)
Q Consensus 192 ~-~--------~~~e~~~~a~~l~i~AL~~~~iy~F 218 (386)
+ + +.. +.+-|..--..|+.+|..+.=
T Consensus 104 dVLNNYG~FLC~qg-~~~eA~q~F~~Al~~P~Y~~~ 138 (250)
T COG3063 104 DVLNNYGAFLCAQG-RPEEAMQQFERALADPAYGEP 138 (250)
T ss_pred chhhhhhHHHHhCC-ChHHHHHHHHHHHhCCCCCCc
Confidence 0 0 011 345566666688999977653
No 194
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=27.00 E-value=71 Score=28.54 Aligned_cols=27 Identities=4% Similarity=-0.008 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+|+++||+.+++|+..|...+-+|.
T Consensus 126 ~g~s~~EIA~~Lgis~~tV~~~l~RAr 152 (182)
T PRK12540 126 SGFSYEDAAAICGCAVGTIKSRVNRAR 152 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999988774
No 195
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=26.97 E-value=93 Score=18.48 Aligned_cols=23 Identities=35% Similarity=0.553 Sum_probs=18.8
Q ss_pred HHHHHHHhcccCChHHHHHHHHh
Q 043780 119 KMQIAMFKLEQGDRKECKKLLED 141 (386)
Q Consensus 119 ~~~~~~~~l~~~~l~~~~~~l~~ 141 (386)
.+..+..+...|+++++..++++
T Consensus 4 ~~~la~~~~~~G~~~eA~~~l~~ 26 (26)
T PF07721_consen 4 RLALARALLAQGDPDEAERLLRR 26 (26)
T ss_pred HHHHHHHHHHcCCHHHHHHHHhC
Confidence 35668888999999999998863
No 196
>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=26.92 E-value=1.8e+02 Score=28.32 Aligned_cols=73 Identities=18% Similarity=0.189 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHH
Q 043780 278 LEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKS 357 (386)
Q Consensus 278 ~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~ 357 (386)
++|.++-..+..| .|.++.+.+.+.++++..=+-.++=+.+..|=+.|+|-. .--.|-++...|-+.
T Consensus 177 r~ka~iRG~l~a~------T~Pt~l~~l~~~~~~~~~l~~~il~~Li~~~~l~G~i~G-------~~yvP~iy~~~q~~~ 243 (272)
T PF09743_consen 177 RQKARIRGALSAI------TRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG-------ASYVPDIYSQAQQEW 243 (272)
T ss_pred HHHHHHHHHHhcC------ccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC-------CEEechHHHHHHHHH
Confidence 4677777777654 367999999999999988888888888899999999988 334577777777655
Q ss_pred HHHHHH
Q 043780 358 LRDRLD 363 (386)
Q Consensus 358 L~~~L~ 363 (386)
+.+-+.
T Consensus 244 V~~f~~ 249 (272)
T PF09743_consen 244 VDNFFK 249 (272)
T ss_pred HHHHHH
Confidence 554443
No 197
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=26.80 E-value=70 Score=29.23 Aligned_cols=27 Identities=11% Similarity=0.144 Sum_probs=24.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|+.-|...+-+|.
T Consensus 153 ~g~s~~EIA~~Lgis~~tV~~~l~RAr 179 (203)
T PRK09647 153 EGLSYEEIAATLGVKLGTVRSRIHRGR 179 (203)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999998874
No 198
>KOG3060 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.69 E-value=6.1e+02 Score=24.81 Aligned_cols=178 Identities=14% Similarity=0.079 Sum_probs=86.0
Q ss_pred hhHHHHHHHHHHHHhchhhcCchhHHHHHHHHHHHHHhh-c--ChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhcc
Q 043780 31 KLWHQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETK-I--NLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATN 107 (386)
Q Consensus 31 KLWhqLt~~l~~~~~~~~~~~~~~~~~ly~~fi~~f~~k-i--n~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~ 107 (386)
.-|.||-..+...-.-+.+. ++..+++++..+..-..+ . +.-.+-+-+..++=.+.-...|-.-++.+..++
T Consensus 8 ~~~~~l~~~~~~wr~~~~rn-seevv~l~~~~~~~~k~~~~g~e~w~l~EqV~IAAld~~~~~lAq~C~~~L~~~f---- 82 (289)
T KOG3060|consen 8 VSWEELRDQMRKWREETVRN-SEEVVQLGSEVLNYSKSGALGDEIWTLYEQVFIAALDTGRDDLAQKCINQLRDRF---- 82 (289)
T ss_pred HHHHHHHHHHHHHHhccccC-HHHHHHHHHHHHHHhhhcccCchHHHHHHHHHHHHHHhcchHHHHHHHHHHHHhC----
Confidence 33444444444333333222 234556666655555544 2 122233333333333322334445555555555
Q ss_pred ccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhcc
Q 043780 108 EQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAY 187 (386)
Q Consensus 108 ~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~ 187 (386)
+.+ -++....|..+=..|..+++.+..+..=. . + .-+..+|.=---..|.+|+-.+.-+....||..
T Consensus 83 -p~S----~RV~~lkam~lEa~~~~~~A~e~y~~lL~---d-d----pt~~v~~KRKlAilka~GK~l~aIk~ln~YL~~ 149 (289)
T KOG3060|consen 83 -PGS----KRVGKLKAMLLEATGNYKEAIEYYESLLE---D-D----PTDTVIRKRKLAILKAQGKNLEAIKELNEYLDK 149 (289)
T ss_pred -CCC----hhHHHHHHHHHHHhhchhhHHHHHHHHhc---c-C----cchhHHHHHHHHHHHHcCCcHHHHHHHHHHHHH
Confidence 122 23334455555567788888877765422 1 1 122223322222367788888889999999988
Q ss_pred CCCCCCChhHHHHHHHHHHHHHhcCCCcccccccccChhhhc
Q 043780 188 TSVESLSDSFKLDLAFDLSLSALLGDNIYNFGELLAHPIINS 229 (386)
Q Consensus 188 ~~~~~~~~~e~~~~a~~l~i~AL~~~~iy~FgeLl~~p~v~~ 229 (386)
|..| .+.-.++|---+-..--..-+|.+.|++.+.++..
T Consensus 150 F~~D---~EAW~eLaeiY~~~~~f~kA~fClEE~ll~~P~n~ 188 (289)
T KOG3060|consen 150 FMND---QEAWHELAEIYLSEGDFEKAAFCLEELLLIQPFNP 188 (289)
T ss_pred hcCc---HHHHHHHHHHHHhHhHHHHHHHHHHHHHHcCCCcH
Confidence 8665 33333322211111122233566667776655543
No 199
>PF14938 SNAP: Soluble NSF attachment protein, SNAP; PDB: 1QQE_A 2IFU_A.
Probab=26.69 E-value=5.6e+02 Score=24.37 Aligned_cols=156 Identities=12% Similarity=0.059 Sum_probs=92.4
Q ss_pred hhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhc---C-CChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcc
Q 043780 53 DALIQLYHNFITDFETKINLLKLAHFAVIVSRQ---Y-PEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLE 128 (386)
Q Consensus 53 ~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~---~-~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~ 128 (386)
+.-++.|+.-+.-|...=+|-.-++....+++- . .|+++|+++.++..+-... +.......-+...++.++..
T Consensus 91 ~~Ai~~~~~A~~~y~~~G~~~~aA~~~~~lA~~ye~~~~d~e~Ai~~Y~~A~~~y~~---e~~~~~a~~~~~~~A~l~~~ 167 (282)
T PF14938_consen 91 DEAIECYEKAIEIYREAGRFSQAAKCLKELAEIYEEQLGDYEKAIEYYQKAAELYEQ---EGSPHSAAECLLKAADLYAR 167 (282)
T ss_dssp HHHHHHHHHHHHHHHHCT-HHHHHHHHHHHHHHHCCTT--HHHHHHHHHHHHHHHHH---TT-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHH---CCChhhHHHHHHHHHHHHHH
Confidence 457888999888888777777777777776654 3 5889999999998888752 22223345566788889999
Q ss_pred cCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHHHHHHHHHH
Q 043780 129 QGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESLSDSFKLDLAFDLSLS 208 (386)
Q Consensus 129 ~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~~a~~l~i~ 208 (386)
.|+++++-+.++++....-+.......+...|...+-.+. ..||+...-+..=.|.+..|. ...+.-.. ...-++.
T Consensus 168 l~~y~~A~~~~e~~~~~~l~~~l~~~~~~~~~l~a~l~~L-~~~D~v~A~~~~~~~~~~~~~--F~~s~E~~-~~~~l~~ 243 (282)
T PF14938_consen 168 LGRYEEAIEIYEEVAKKCLENNLLKYSAKEYFLKAILCHL-AMGDYVAARKALERYCSQDPS--FASSREYK-FLEDLLE 243 (282)
T ss_dssp TT-HHHHHHHHHHHHHTCCCHCTTGHHHHHHHHHHHHHHH-HTT-HHHHHHHHHHHGTTSTT--STTSHHHH-HHHHHHH
T ss_pred hCCHHHHHHHHHHHHHHhhcccccchhHHHHHHHHHHHHH-HcCCHHHHHHHHHHHHhhCCC--CCCcHHHH-HHHHHHH
Confidence 9999999999998765432222222345555444433333 467766555555555543321 21222223 3444556
Q ss_pred HhcCCCc
Q 043780 209 ALLGDNI 215 (386)
Q Consensus 209 AL~~~~i 215 (386)
|....+.
T Consensus 244 A~~~~D~ 250 (282)
T PF14938_consen 244 AYEEGDV 250 (282)
T ss_dssp HHHTT-C
T ss_pred HHHhCCH
Confidence 7766555
No 200
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=26.60 E-value=1.5e+02 Score=28.97 Aligned_cols=57 Identities=21% Similarity=0.221 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCC
Q 043780 279 EKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEG 338 (386)
Q Consensus 279 ~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~ 338 (386)
||=-|.+|++|--+ ++|.+.=++||+.++-++.-|---++-.=++||++|+=-...+
T Consensus 8 QkeIL~aLi~LY~~---~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGG 64 (294)
T COG2524 8 QKEILQALINLYRR---KKRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGG 64 (294)
T ss_pred HHHHHHHHHHHHHh---cCCCcchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCC
Confidence 67778899999654 4789999999999999999888877777779999997544433
No 201
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=26.41 E-value=1.8e+02 Score=22.09 Aligned_cols=45 Identities=20% Similarity=0.134 Sum_probs=27.1
Q ss_pred CCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEE
Q 043780 296 EDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHV 342 (386)
Q Consensus 296 ~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~v 342 (386)
..+.+|+.+|++.++++..+|-.-+==..+-|=| .+++.++.++|
T Consensus 19 ~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI--~~~~~~~~~~v 63 (65)
T PF10771_consen 19 ENGEWSVSELKKATGLSDKEVYLAIGWLARENKI--EFEEKNGELYV 63 (65)
T ss_dssp CSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSE--EEEEETTEEEE
T ss_pred hCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCce--eEEeeCCEEEE
Confidence 3689999999999999888765432222223333 33455555544
No 202
>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=26.40 E-value=1.6e+02 Score=26.90 Aligned_cols=77 Identities=16% Similarity=0.216 Sum_probs=51.3
Q ss_pred CccChHHHH----HHcCCChhHHHHHHHHHhhccceEE-eecCCCCEEEEEeeccccCC---hhhHHHHHHHHHHHHHHH
Q 043780 298 RTIPLSIIA----ERTKLSIEDVEHLLMKSLSVHLIEG-IIDQVEGTVHVSWVQPRVLG---IPQIKSLRDRLDSWLGKV 369 (386)
Q Consensus 298 r~isf~~Ia----~~l~i~~~eVE~lvikAi~~gLI~G-~IDqv~~~v~vt~v~~R~l~---~~q~~~L~~~L~~W~~~v 369 (386)
...+..+|- +.+||+.-.|..+|-..+..|||+. || |+-.+=|+.|-.-. ...+..|...+..-+.++
T Consensus 10 ~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~EKi----Gssn~YWsFps~~~~~~~~~~~~l~~~~~~~~~~i 85 (188)
T PF03962_consen 10 DFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVEKI----GSSNYYWSFPSQAKQKRQNKLEKLQKEIEELEKKI 85 (188)
T ss_pred CcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhhhc----cCeeEEEecChHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555553 4489999999999999999999986 44 67778899874321 234555555555555555
Q ss_pred HHHHHHHHh
Q 043780 370 HTALLSIEA 378 (386)
Q Consensus 370 ~~~~~~l~~ 378 (386)
..+...++.
T Consensus 86 ~~l~~~i~~ 94 (188)
T PF03962_consen 86 EELEEKIEE 94 (188)
T ss_pred HHHHHHHHH
Confidence 555555543
No 203
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=26.37 E-value=2.7e+02 Score=23.80 Aligned_cols=54 Identities=24% Similarity=0.302 Sum_probs=41.8
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHH
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDR 361 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~ 361 (386)
..|.+|+++++-+++.|=.++..-++. .|+||.. +.+.|+ -.++.++++.+-.+
T Consensus 35 ~Nf~dI~~~L~R~p~~~~ky~~~ELgt---~~~id~~-~~lii~----G~~~~~~i~~~L~~ 88 (125)
T PF01873_consen 35 VNFVDICKALNRDPEHVLKYFGKELGT---QGSIDGK-GRLIIN----GRFSSKQIQDLLDK 88 (125)
T ss_dssp TTHHHHHHHHTSSHHHHHHHHHHHSSS---EEEEETT-TEEEEE----SSSSCCHHHHHHHH
T ss_pred ecHHHHHHHHCCCHHHHHHHHHHHHCC---ceEECCC-CEEEEE----EecCHHHHHHHHHH
Confidence 479999999999999999999888665 4899888 777776 35566766655444
No 204
>TIGR00540 hemY_coli hemY protein. This is an uncharacterized protein encoded next to a heme-biosynthetic enzyme in two gamma division proteobacteria (E. coli and H. influenzae). It is known in no other species. The gene symbol hemY is unfortunate in that an unrelated protein, protoporphyrinogen oxidase, is designated as HemG in E. coli but as HemY in Bacillus subtilis.
Probab=26.36 E-value=5.3e+02 Score=26.03 Aligned_cols=126 Identities=10% Similarity=-0.004 Sum_probs=77.1
Q ss_pred HHhhhHHHHHHHHHHHHhchhhcCchhHHHHHHHHHHHHHhhcChHHHHHHHHHHHhcCCChHHHHHHHHHHHHHhhhcc
Q 043780 28 YQKKLWHQLTLKLEQFVAHAVFQAGDALIQLYHNFITDFETKINLLKLAHFAVIVSRQYPEKQAAISYLEGVIEKLRATN 107 (386)
Q Consensus 28 ~~~KLWhqLt~~l~~~~~~~~~~~~~~~~~ly~~fi~~f~~kin~l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~~~~ 107 (386)
-.+|-...++..+..+.....-. -.+..... -...=+|.-..-+...++.+..+++.+.+++++..+..
T Consensus 80 ~~~k~~~~~~~glla~~~g~~~~----A~~~l~~~---~~~~~~~~~~~llaA~aa~~~g~~~~A~~~l~~a~~~~---- 148 (409)
T TIGR00540 80 KRRKAQKQTEEALLKLAEGDYAK----AEKLIAKN---ADHAAEPVLNLIKAAEAAQQRGDEARANQHLEEAAELA---- 148 (409)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHH----HHHHHHHH---hhcCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHhC----
Confidence 45577788888888888763111 11222221 11122344444456667777789999999998864333
Q ss_pred ccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHH
Q 043780 108 EQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAE 176 (386)
Q Consensus 108 ~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~ 176 (386)
+++.+.+.+..+++.+..|+++.+...++.+...-++ ++.+. ......+-..|++.+
T Consensus 149 ----p~~~l~~~~~~a~l~l~~~~~~~Al~~l~~l~~~~P~----~~~~l----~ll~~~~~~~~d~~~ 205 (409)
T TIGR00540 149 ----GNDNILVEIARTRILLAQNELHAARHGVDKLLEMAPR----HKEVL----KLAEEAYIRSGAWQA 205 (409)
T ss_pred ----CcCchHHHHHHHHHHHHCCCHHHHHHHHHHHHHhCCC----CHHHH----HHHHHHHHHHhhHHH
Confidence 2344445666689999999999999999888765333 23332 233444455666653
No 205
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=26.32 E-value=2.2e+02 Score=22.43 Aligned_cols=36 Identities=11% Similarity=0.044 Sum_probs=32.4
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEe
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGI 332 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~ 332 (386)
++..+-.+|+..++.|++-||..+-+-++.|-|+--
T Consensus 14 ~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred cCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 578999999999999999999999999999888643
No 206
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=26.31 E-value=74 Score=27.63 Aligned_cols=28 Identities=21% Similarity=0.259 Sum_probs=24.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...|+.+||+.+|+|+..|...+-+|..
T Consensus 134 ~g~s~~eiA~~lgis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 134 HDLTIKEIAEVMNKPEGTVKTYLHRALK 161 (169)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4699999999999999999988887753
No 207
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=26.20 E-value=74 Score=26.32 Aligned_cols=27 Identities=26% Similarity=0.322 Sum_probs=21.1
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
...+|+++||+.++||..-|-+++-+|
T Consensus 31 ~eDlSlsEIAe~~~iSRqaV~d~ikr~ 57 (101)
T PF04297_consen 31 EEDLSLSEIAEELGISRQAVYDSIKRA 57 (101)
T ss_dssp TS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 468999999999999999999998887
No 208
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=25.93 E-value=78 Score=26.96 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=24.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+|+|...|...+-+|.
T Consensus 126 ~g~~~~eIA~~l~is~~tv~~~l~Rar 152 (159)
T TIGR02989 126 RGVSLTALAEQLGRTVNAVYKALSRLR 152 (159)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 479999999999999999999887774
No 209
>COG5290 IkappaB kinase complex, IKAP component [Transcription]
Probab=25.90 E-value=4.1e+02 Score=30.12 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=21.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Q 043780 353 PQIKSLRDRLDSWLGKVHTALLSIE 377 (386)
Q Consensus 353 ~q~~~L~~~L~~W~~~v~~~~~~l~ 377 (386)
+.+..|..||.+|+..+..+.+.+.
T Consensus 1157 ~sirrli~rl~~~rpe~~rlve~l~ 1181 (1243)
T COG5290 1157 SSIRRLILRLVGWRPETERLVEILK 1181 (1243)
T ss_pred HHHHHHHHHHhccChhHHHHHHHHH
Confidence 4678899999999999999887763
No 210
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=25.74 E-value=5.1e+02 Score=23.51 Aligned_cols=36 Identities=22% Similarity=0.101 Sum_probs=32.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhhccceEEee
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGII 333 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I 333 (386)
..+|..+||+.++++..-|=..+=+....|+|.-.-
T Consensus 14 ~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 14 GQATAAALAEALAISPQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEee
Confidence 459999999999999999999998999999998663
No 211
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=25.60 E-value=3.4e+02 Score=21.61 Aligned_cols=46 Identities=24% Similarity=0.252 Sum_probs=36.8
Q ss_pred CCCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEE
Q 043780 296 EDRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVS 343 (386)
Q Consensus 296 ~~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt 343 (386)
....+|=.+||+.++++..-|-..+=+....|+|.- ....++|-|+
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r--~~~~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFR--QGMMGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee--ecCCceeecC
Confidence 456889999999999999999999999999999983 2334555554
No 212
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=25.58 E-value=1e+02 Score=21.46 Aligned_cols=37 Identities=14% Similarity=0.079 Sum_probs=24.9
Q ss_pred HHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHH
Q 043780 286 LMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMK 322 (386)
Q Consensus 286 L~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvik 322 (386)
+++-.|.....-..-..++||..++++..+|..|...
T Consensus 14 ~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (59)
T cd00086 14 ELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQN 50 (59)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 3344454321223445678999999999999999764
No 213
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.48 E-value=59 Score=22.30 Aligned_cols=29 Identities=17% Similarity=0.078 Sum_probs=18.7
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHhhcc
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSLSVH 327 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi~~g 327 (386)
-.|..+||+.+++|...|-.|+=+--..|
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 58999999999999999999986654444
No 214
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.37 E-value=77 Score=28.09 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|.+-|...+=+|.
T Consensus 146 ~g~s~~eIA~~lgis~~tV~~~l~ra~ 172 (184)
T PRK12539 146 EGLSVAEAATRSGMSESAVKVSVHRGL 172 (184)
T ss_pred cCCcHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999999988774
No 215
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=25.31 E-value=82 Score=26.69 Aligned_cols=27 Identities=26% Similarity=0.332 Sum_probs=23.6
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|+..|...+=+|.
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~ 146 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRAR 146 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478999999999999999988877764
No 216
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.28 E-value=1.1e+02 Score=27.38 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+++|...|...+=+|.
T Consensus 151 ~g~s~~eIA~~lgis~~tV~~~l~Ra~ 177 (196)
T PRK12524 151 EGLSNPEIAEVMEIGVEAVESLTARGK 177 (196)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 579999999999999999999988874
No 217
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=79 Score=27.93 Aligned_cols=27 Identities=22% Similarity=0.194 Sum_probs=24.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+++|+..|...+=+|.
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar 170 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGL 170 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999887774
No 218
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=25.12 E-value=81 Score=27.29 Aligned_cols=27 Identities=19% Similarity=0.192 Sum_probs=24.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+|+|+..|...+-+|.
T Consensus 143 ~~~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 143 EGLSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478999999999999999998887774
No 219
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=25.02 E-value=78 Score=29.37 Aligned_cols=27 Identities=22% Similarity=0.143 Sum_probs=23.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+|+++||+.+++|+..|...+-+|+
T Consensus 193 e~~S~~EIAe~lgis~~tV~~~~~rAl 219 (227)
T TIGR02846 193 RRKTQREIAKILGISRSYVSRIEKRAL 219 (227)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 579999999999999999988876664
No 220
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.00 E-value=80 Score=27.86 Aligned_cols=27 Identities=11% Similarity=0.070 Sum_probs=23.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+.-|...+=+|.
T Consensus 150 ~~~s~~eIA~~lgis~~~V~~~l~ra~ 176 (186)
T PRK13919 150 QGYTHREAAQLLGLPLGTLKTRARRAL 176 (186)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999998877764
No 221
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=24.82 E-value=82 Score=27.91 Aligned_cols=27 Identities=7% Similarity=0.112 Sum_probs=24.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+.-|...+-+|.
T Consensus 137 ~g~s~~EIA~~lgis~~tVk~~l~Rar 163 (185)
T PRK12542 137 YNLTYQEISSVMGITEANVRKQFERAR 163 (185)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 369999999999999999999888774
No 222
>PF13525 YfiO: Outer membrane lipoprotein; PDB: 3TGO_A 3Q5M_A 2YHC_A.
Probab=24.79 E-value=5.2e+02 Score=23.30 Aligned_cols=74 Identities=19% Similarity=0.195 Sum_probs=43.9
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
-++..+|++.++++....- .++. .--..+.++..+...|+++.+...++..-..-++. +.+-.++|..+-
T Consensus 18 ~g~y~~Ai~~f~~l~~~~P-----~s~~-a~~A~l~la~a~y~~~~y~~A~~~~~~fi~~yP~~----~~~~~A~Y~~g~ 87 (203)
T PF13525_consen 18 QGDYEEAIKLFEKLIDRYP-----NSPY-APQAQLMLAYAYYKQGDYEEAIAAYERFIKLYPNS----PKADYALYMLGL 87 (203)
T ss_dssp CT-HHHHHHHHHHHHHH-T-----TSTT-HHHHHHHHHHHHHHTT-HHHHHHHHHHHHHH-TT-----TTHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHCC-----CChH-HHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHCCCC----cchhhHHHHHHH
Confidence 3479999999999988872 2221 11233455667777899999999888876654443 233444555554
Q ss_pred HHHH
Q 043780 166 QYHK 169 (386)
Q Consensus 166 ~~~k 169 (386)
.+++
T Consensus 88 ~~~~ 91 (203)
T PF13525_consen 88 SYYK 91 (203)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 4443
No 223
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=24.79 E-value=81 Score=27.76 Aligned_cols=27 Identities=11% Similarity=0.148 Sum_probs=24.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+++..|...+-+|.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar 179 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAR 179 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999999887774
No 224
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=24.72 E-value=81 Score=28.56 Aligned_cols=26 Identities=4% Similarity=0.066 Sum_probs=23.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
...||++||+.+++|+.-|...+=+|
T Consensus 148 ~g~s~~EIAe~lgis~~tV~~~l~Ra 173 (196)
T PRK12535 148 LGYTYEEAAKIADVRVGTIRSRVARA 173 (196)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 47899999999999999999887655
No 225
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=24.54 E-value=85 Score=29.25 Aligned_cols=27 Identities=15% Similarity=0.085 Sum_probs=24.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|+.-|...+-+|+
T Consensus 197 eg~s~~EIA~~Lgis~~tV~~~l~ra~ 223 (234)
T TIGR02835 197 TEKTQKEVADMLGISQSYISRLEKRIL 223 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 579999999999999999998887664
No 226
>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=24.52 E-value=1.8e+02 Score=20.47 Aligned_cols=31 Identities=23% Similarity=0.115 Sum_probs=28.3
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceE
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIE 330 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~ 330 (386)
.+-.+||+.++++...|-..+-+.-..|+|.
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~ 56 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVE 56 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3499999999999999999999999999986
No 227
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.52 E-value=84 Score=27.89 Aligned_cols=28 Identities=14% Similarity=0.031 Sum_probs=24.7
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...|+++||+.+|+|..-|...+-+|+.
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 154 VGLSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3689999999999999999999888753
No 228
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=24.44 E-value=83 Score=28.12 Aligned_cols=27 Identities=7% Similarity=0.097 Sum_probs=23.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+|+++||+.+|+|+.-|...+-+|.
T Consensus 151 ~g~s~~EIA~~lgis~~tVk~~l~Rar 177 (195)
T PRK12532 151 LGFSSDEIQQMCGISTSNYHTIMHRAR 177 (195)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999998887763
No 229
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.39 E-value=5e+02 Score=22.93 Aligned_cols=67 Identities=13% Similarity=0.197 Sum_probs=46.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEee--cCCCCEEEEEeeccccCChhh-HHHHHHHHHHHHH
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGII--DQVEGTVHVSWVQPRVLGIPQ-IKSLRDRLDSWLG 367 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~I--Dqv~~~v~vt~v~~R~l~~~q-~~~L~~~L~~W~~ 367 (386)
++.++=++||+.+|++..+|-..+=+....||+.-+= |..+|...-.|- ++.++ ...++.++..-.+
T Consensus 26 ~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~----i~~~~i~d~Ik~~~~~~~~ 95 (158)
T TIGR00373 26 KGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWR----INYEKALDVLKRKLEETAK 95 (158)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEE----eCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999999995422 333355555553 24443 3344444443333
No 230
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=23.94 E-value=1.5e+02 Score=19.26 Aligned_cols=30 Identities=30% Similarity=0.237 Sum_probs=23.0
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccce
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLI 329 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI 329 (386)
+|=.+||+.+|++.+-|=..+=+.-..|+|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 566899999999999988888777777765
No 231
>TIGR02878 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set.
Probab=23.93 E-value=4.1e+02 Score=25.29 Aligned_cols=112 Identities=23% Similarity=0.208 Sum_probs=63.9
Q ss_pred HhcccCChHHHHHHHHhccccccccCCCCHH-HHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHH--H
Q 043780 125 FKLEQGDRKECKKLLEDGKSTLDSMTDIDPS-VYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESLSDSFKLD--L 201 (386)
Q Consensus 125 ~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~-v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~--~ 201 (386)
-+.+.|++++|+.+|...++.+-..+.-+.. .... .+ .--+..|..+.+.+... ++|..+|.. .
T Consensus 14 Ql~K~~~yeeAkqvL~yFs~~F~~~~~~~~~~~t~~------el----R~iT~~~e~a~~al~~~---~~~~~eki~~~t 80 (233)
T TIGR02878 14 QLTKQARYEEAKQVLEYFSKQFVSAGKEKDPMLTMD------QL----RTITLTYERAVQALTAT---DMSDDEKIRAVT 80 (233)
T ss_pred HHHHhhhHHHHHHHHHHHHHHHHhcccccCcccCHH------HH----HHHHHHHHHHHHHHhhc---cCCHHHHHHHHH
Confidence 3446789999999999887754322211111 1111 11 11144666777766654 456777775 5
Q ss_pred HHHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHH
Q 043780 202 AFDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCR 258 (386)
Q Consensus 202 a~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~ 258 (386)
++++++.|+.++.- .||. +...+=...+-++=++...||-..|.+-.+
T Consensus 81 ~fRLavDA~~s~~q----PLW~-----~~e~~im~~f~~mk~a~~~~~~~~f~~~ln 128 (233)
T TIGR02878 81 AFRLAVDAIVSRSQ----PLWG-----SLEKPVMEAFTELEKAAQKEDSQAFQEKLN 128 (233)
T ss_pred HHHHHHHHhcCCCc----chHH-----HHHHHHHHHHHHHHHHHHcCCHHHHHHHHH
Confidence 68899999999844 3332 222211122334445667788777765543
No 232
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=23.89 E-value=83 Score=29.65 Aligned_cols=26 Identities=23% Similarity=0.197 Sum_probs=23.7
Q ss_pred ccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 299 TIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 299 ~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..||++||+.+|+|++-|...+-+|.
T Consensus 132 g~S~~EIAe~LgiS~~tVksrL~Rar 157 (228)
T PRK06704 132 QYSIADIAKVCSVSEGAVKASLFRSR 157 (228)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 59999999999999999999988774
No 233
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=23.82 E-value=1.2e+02 Score=20.04 Aligned_cols=27 Identities=26% Similarity=0.265 Sum_probs=23.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...+..+||+.++++.+.|-.++-++.
T Consensus 25 ~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 25 EGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 458999999999999999988876653
No 234
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=23.78 E-value=1e+02 Score=20.92 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=16.7
Q ss_pred HHHHHHcCCChhHHHHHHHHH
Q 043780 303 SIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 303 ~~Ia~~l~i~~~eVE~lvikA 323 (386)
+.||+.+|++..+|..|.+.|
T Consensus 17 ~~L~~~tgls~~Qi~~WF~Na 37 (40)
T PF05920_consen 17 EELAKQTGLSRKQISNWFINA 37 (40)
T ss_dssp HHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHh
Confidence 457888899999999999876
No 235
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.73 E-value=88 Score=27.23 Aligned_cols=27 Identities=22% Similarity=0.295 Sum_probs=23.8
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|..-|...+-+|.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar 161 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYAR 161 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468899999999999999998888773
No 236
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=23.53 E-value=2.7e+02 Score=19.58 Aligned_cols=61 Identities=16% Similarity=0.142 Sum_probs=36.7
Q ss_pred HHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCC
Q 043780 121 QIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTS 189 (386)
Q Consensus 121 ~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~ 189 (386)
..+..++..|+++++.+.++++-..- |.-...+|.. +..+-..|++.+.-...-..+.-.|
T Consensus 2 ~~a~~~~~~g~~~~A~~~~~~~l~~~-------P~~~~a~~~l-g~~~~~~g~~~~A~~~~~~a~~~~P 62 (65)
T PF13432_consen 2 ALARALYQQGDYDEAIAAFEQALKQD-------PDNPEAWYLL-GRILYQQGRYDEALAYYERALELDP 62 (65)
T ss_dssp HHHHHHHHCTHHHHHHHHHHHHHCCS-------TTHHHHHHHH-HHHHHHTT-HHHHHHHHHHHHHHST
T ss_pred hHHHHHHHcCCHHHHHHHHHHHHHHC-------CCCHHHHHHH-HHHHHHcCCHHHHHHHHHHHHHHCc
Confidence 35778888999999999999876542 2223333333 3344467777766554444444433
No 237
>PRK00118 putative DNA-binding protein; Validated
Probab=23.43 E-value=99 Score=25.64 Aligned_cols=26 Identities=23% Similarity=0.217 Sum_probs=24.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHH
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
...|+++||+.+|+|..-|..++-+|
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RA 57 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRT 57 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 58999999999999999999998887
No 238
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=23.16 E-value=90 Score=27.18 Aligned_cols=28 Identities=11% Similarity=0.070 Sum_probs=24.5
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+++|...|...+-+|+.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIK 168 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHH
Confidence 3699999999999999999988887753
No 239
>PF11817 Foie-gras_1: Foie gras liver health family 1; InterPro: IPR021773 Mutating the gene foie gras in zebrafish has been shown to affect development; the mutants develop large, lipid-filled hepatocytes in the liver, resembling those in individuals with fatty liver disease []. Foie-gras protein is long and has several well-defined domains though none of them has a known function. We have annotated this one as the first []. THe C terminus of this region contains TPR repeats.
Probab=23.15 E-value=6.3e+02 Score=23.70 Aligned_cols=95 Identities=19% Similarity=0.249 Sum_probs=62.5
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
.......++.|++..+.+++. ....-.-++...+|..+...|+++.+.+.++.+-... ...+= ..+-...-....
T Consensus 151 ~~hs~~iI~lL~~A~~~f~~~---~~~R~~~~l~~~~A~ey~~~g~~~~A~~~l~~~~~~y-r~egW-~~l~~~~l~~l~ 225 (247)
T PF11817_consen 151 VDHSKLIIELLEKAYEQFKKY---GQNRMASYLSLEMAEEYFRLGDYDKALKLLEPAASSY-RREGW-WSLLTEVLWRLL 225 (247)
T ss_pred cchHHHHHHHHHHHHHHHHHh---ccchHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH-HhCCc-HHHHHHHHHHHH
Confidence 335567788888887777522 3355677888999999999999999999999883321 22232 333344444444
Q ss_pred HHHHHhhcHHHHHHHHHHHh
Q 043780 166 QYHKFHQEFAEFYKCALLYL 185 (386)
Q Consensus 166 ~~~k~~~~~~~~y~~~l~yL 185 (386)
..++..|+...|-..++.-+
T Consensus 226 ~Ca~~~~~~~~~l~~~leLl 245 (247)
T PF11817_consen 226 ECAKRLGDVEDYLTTSLELL 245 (247)
T ss_pred HHHHHhCCHHHHHHHHHHHh
Confidence 44556777777777666543
No 240
>PF12862 Apc5: Anaphase-promoting complex subunit 5
Probab=23.00 E-value=3.8e+02 Score=21.06 Aligned_cols=60 Identities=15% Similarity=0.219 Sum_probs=42.0
Q ss_pred CCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccc
Q 043780 86 YPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKST 145 (386)
Q Consensus 86 ~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~ 145 (386)
..|..+|++.|.+..+-......+.......+..+..+.++...|+.+++...++++=..
T Consensus 11 ~~dy~~A~d~L~~~fD~~~~~~~~~~~~~~~~all~lA~~~~~~G~~~~A~~~l~eAi~~ 70 (94)
T PF12862_consen 11 SGDYSEALDALHRYFDYAKQSNNSSSNSGLAYALLNLAELHRRFGHYEEALQALEEAIRL 70 (94)
T ss_pred cCCHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHH
Confidence 448889999998877665422122212245666677888888999999999988877554
No 241
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=22.69 E-value=1.3e+02 Score=28.36 Aligned_cols=28 Identities=21% Similarity=0.296 Sum_probs=25.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+++|..-|...+-+|+.
T Consensus 216 ~~~s~~EIA~~lgis~~tV~~~~~ra~~ 243 (251)
T PRK07670 216 EELTLTEIGQVLNLSTSRISQIHSKALF 243 (251)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5799999999999999999999888753
No 242
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=22.60 E-value=1.9e+02 Score=23.40 Aligned_cols=39 Identities=18% Similarity=0.114 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHH
Q 043780 276 KLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMK 322 (386)
Q Consensus 276 ~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvik 322 (386)
..++|.-+..=+. .+-+|.++-++..+++++|+|.|+-.
T Consensus 34 va~RKAaVV~aV~--------~Glis~~EA~~rY~Ls~eEf~~W~~a 72 (90)
T PF06627_consen 34 VARRKAAVVRAVR--------GGLISVEEACRRYGLSEEEFESWQRA 72 (90)
T ss_dssp -HHHHHHHHHHHH--------CTTS-HHHHHHCTTSSHHHHHHHHHH
T ss_pred hhhHHHHHHHHHH--------cCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 3456765554332 58999999999999999999999754
No 243
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=22.55 E-value=1e+02 Score=26.01 Aligned_cols=27 Identities=30% Similarity=0.309 Sum_probs=24.2
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+|+.+||+.+|+|...|...+-+|.
T Consensus 128 ~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 128 EGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478999999999999999999888874
No 244
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=22.48 E-value=1e+02 Score=28.42 Aligned_cols=29 Identities=17% Similarity=0.217 Sum_probs=25.6
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
.|.++-.+||+.+||+...+.+.+-+|.+
T Consensus 176 PR~~~l~dLA~~lGISkst~~ehLRrAe~ 204 (215)
T COG3413 176 PRRVSLKDLAKELGISKSTLSEHLRRAER 204 (215)
T ss_pred CccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 39999999999999999988888888754
No 245
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=22.34 E-value=1.4e+02 Score=26.03 Aligned_cols=27 Identities=19% Similarity=0.231 Sum_probs=23.8
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+++|+..|...+-+|.
T Consensus 115 ~g~s~~eIA~~lgis~~tV~~~l~Rar 141 (170)
T TIGR02959 115 EGLSQQEIAEKLGLSLSGAKSRVQRGR 141 (170)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 579999999999999999998877663
No 246
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.33 E-value=1.3e+02 Score=27.66 Aligned_cols=39 Identities=15% Similarity=0.175 Sum_probs=35.0
Q ss_pred CCccChHHHHHHcCCChhHHHHHHHHHhhccceEEeecC
Q 043780 297 DRTIPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQ 335 (386)
Q Consensus 297 ~r~isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDq 335 (386)
...+|-++||+.++++...|+..+..+...|++.=++.-
T Consensus 176 ~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 214 (239)
T PRK10430 176 DYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHY 214 (239)
T ss_pred CCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeec
Confidence 467899999999999999999999999999999766653
No 247
>CHL00033 ycf3 photosystem I assembly protein Ycf3
Probab=22.30 E-value=5e+02 Score=22.26 Aligned_cols=56 Identities=11% Similarity=0.073 Sum_probs=37.3
Q ss_pred hcCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccc
Q 043780 84 RQYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKST 145 (386)
Q Consensus 84 ~~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~ 145 (386)
....+.++|+..+.+...... +......+...++.++...|+++++...++.+-..
T Consensus 46 ~~~g~~~~A~~~~~~al~l~~------~~~~~~~~~~~lg~~~~~~g~~~eA~~~~~~Al~~ 101 (168)
T CHL00033 46 QSEGEYAEALQNYYEAMRLEI------DPYDRSYILYNIGLIHTSNGEHTKALEYYFQALER 101 (168)
T ss_pred HHcCCHHHHHHHHHHHHhccc------cchhhHHHHHHHHHHHHHcCCHHHHHHHHHHHHHh
Confidence 344578999998887654431 11122234456788888899999999988776543
No 248
>PRK04217 hypothetical protein; Provisional
Probab=22.16 E-value=2.5e+02 Score=23.52 Aligned_cols=40 Identities=18% Similarity=-0.008 Sum_probs=27.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHH-------HHhhccceEEeecCCC
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLM-------KSLSVHLIEGIIDQVE 337 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvi-------kAi~~gLI~G~IDqv~ 337 (386)
..+|+++||+.++++...|...+- +++..+-..+-+.+-+
T Consensus 57 eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre~L~~~~~~~~~~~~~ 103 (110)
T PRK04217 57 EGLTQEEAGKRMGVSRGTVWRALTSARKKVAQMLVEGRELIILPQGN 103 (110)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHhccceeEecCCc
Confidence 578999999999999986666554 4444444445444443
No 249
>PF06619 DUF1149: Protein of unknown function (DUF1149); InterPro: IPR009530 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 2HNG_A 2O2A_C.
Probab=22.10 E-value=1.9e+02 Score=24.95 Aligned_cols=49 Identities=18% Similarity=0.269 Sum_probs=35.4
Q ss_pred ceEEeecCCCCEEEEEeeccccCChhhHHHHHHHHHHHHHHHHHHHHHH
Q 043780 328 LIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDRLDSWLGKVHTALLSI 376 (386)
Q Consensus 328 LI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~L~~W~~~v~~~~~~l 376 (386)
.|.|.|.|+.+.+-=-.=.|-.|+.++|+.|..=|-...+++.-=...+
T Consensus 68 viSG~IsQiv~i~~r~~~~~sd~~~~e~~~Ls~PL~d~i~rLTYEVTeI 116 (127)
T PF06619_consen 68 VISGVISQIVHIKDRYVGEPSDLSQEEVELLSRPLLDYIERLTYEVTEI 116 (127)
T ss_dssp EEEEEEEEEEEEET---SSGGGS-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred EEEeeeeeeeeeeccccCChhhcCHHHHHHHHHHHHHHHHhheeEEEEE
Confidence 4789999887766544456889999999999999988888776544443
No 250
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=22.07 E-value=1.6e+02 Score=20.40 Aligned_cols=36 Identities=17% Similarity=0.125 Sum_probs=24.4
Q ss_pred HHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHH
Q 043780 287 MEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMK 322 (386)
Q Consensus 287 ~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvik 322 (386)
++-+|.+...-..-...+||+.++++..+|..|...
T Consensus 15 L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~n 50 (56)
T smart00389 15 LEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQN 50 (56)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHH
Confidence 344454322223445678999999999999999865
No 251
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=22.07 E-value=1.4e+02 Score=27.44 Aligned_cols=28 Identities=21% Similarity=0.252 Sum_probs=24.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+|+|..-|...+-+|+.
T Consensus 190 ~~~s~~eIA~~lgis~~tV~~~~~ra~~ 217 (224)
T TIGR02479 190 EELNLKEIGEVLGLTESRVSQIHSQALK 217 (224)
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4689999999999999999988877753
No 252
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=21.90 E-value=99 Score=28.12 Aligned_cols=28 Identities=14% Similarity=0.264 Sum_probs=24.5
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+|+++||+.+|+|+.-|...+=+|+.
T Consensus 168 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 168 QELSQEQLAQQLNVPLGTVKSRLRLALA 195 (206)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5799999999999999999988777643
No 253
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=21.71 E-value=1e+02 Score=27.39 Aligned_cols=27 Identities=11% Similarity=0.221 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|..-|...+=+|.
T Consensus 149 ~g~s~~EIA~~lgis~~tV~~~l~Ra~ 175 (188)
T PRK09640 149 AELEFQEIADIMHMGLSATKMRYKRAL 175 (188)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 468999999999999999999988874
No 254
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=21.68 E-value=6.1e+02 Score=24.14 Aligned_cols=113 Identities=21% Similarity=0.156 Sum_probs=65.8
Q ss_pred HhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCCCCCChhHHHH--HH
Q 043780 125 FKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSVESLSDSFKLD--LA 202 (386)
Q Consensus 125 ~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~~~~~~~e~~~--~a 202 (386)
-+.+.|++++|+..|+...+.+.+.+.-+..+.. . ..+-.+..|..+.+.+.-.+ ++.+++.. ..
T Consensus 14 qlvk~~~yeeA~q~l~~fs~~f~~~~~~~~~~t~------e----~iralT~t~~~a~~al~~~~---~~~~e~~~~at~ 80 (232)
T PF09577_consen 14 QLVKQGKYEEAKQLLEYFSEQFTSVDFKGRPLTM------E----EIRALTETIEEAKKALTSVS---MSEEEKIRAATQ 80 (232)
T ss_pred HHHHcccHHHHHHHHHHHHHHHhhccccccccCH------H----HHHHHHHHHHHHHHHHHccC---CCHHHHHHHHHH
Confidence 3447899999999999988765332210000110 0 11223556667777665543 45666665 45
Q ss_pred HHHHHHHhcCCCcccccccccChhhhcccCCCcHHHHHHHHHHhcCCHHHHHHHHHH
Q 043780 203 FDLSLSALLGDNIYNFGELLAHPIINSLTGTKVEWLYYILQAFNSGDLVRYQELCRV 259 (386)
Q Consensus 203 ~~l~i~AL~~~~iy~FgeLl~~p~v~~L~~~~~~~l~~LL~~f~~G~l~~f~~~~~~ 259 (386)
.+|++.||.++.- .||.. ...+=-..+-.+=++...|+-..|.+-.+.
T Consensus 81 ~RLavDAl~~~~q----PLW~~-----~e~~i~~~~~~mk~a~~~~~~~~f~~~~n~ 128 (232)
T PF09577_consen 81 FRLAVDALTHKHQ----PLWLQ-----YEKPIMEDFQRMKQAAQKGDKEAFRASLNE 128 (232)
T ss_pred HHHHHHHhcCCCC----CcHHH-----HHHHHHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 7789999999854 33332 111111224566778888887777665543
No 255
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.62 E-value=1.5e+02 Score=27.57 Aligned_cols=28 Identities=14% Similarity=0.177 Sum_probs=24.8
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
...||++||+.+|+|..-|...+-+|+.
T Consensus 199 ~g~s~~EIA~~lgis~~tV~~~~~ra~~ 226 (236)
T PRK06986 199 EELNLKEIGAVLGVSESRVSQIHSQAIK 226 (236)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4689999999999999999999888753
No 256
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=21.40 E-value=7.3e+02 Score=23.78 Aligned_cols=93 Identities=9% Similarity=0.090 Sum_probs=56.3
Q ss_pred CChHHHHHHHHHHHHHhhhccccCCCc-hHHHHHHHHHHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHH
Q 043780 87 PEKQAAISYLEGVIEKLRATNEQRKEE-PILYIKMQIAMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSS 165 (386)
Q Consensus 87 ~d~~~al~fl~~~~~~~~~~~~~~~~~-a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s 165 (386)
++.++|++.++++.++- +.+.. +. ....+|..+...|+++++......+-..-+. .+....++|.++.
T Consensus 157 ~~y~~Ai~af~~fl~~y-----P~s~~a~~--A~y~LG~~y~~~g~~~~A~~~f~~vv~~yP~----s~~~~dAl~klg~ 225 (263)
T PRK10803 157 SRQDDAIVAFQNFVKKY-----PDSTYQPN--ANYWLGQLNYNKGKKDDAAYYFASVVKNYPK----SPKAADAMFKVGV 225 (263)
T ss_pred CCHHHHHHHHHHHHHHC-----cCCcchHH--HHHHHHHHHHHcCCHHHHHHHHHHHHHHCCC----CcchhHHHHHHHH
Confidence 36777877777665555 22211 11 2346788888899999998887766443232 2445556666655
Q ss_pred HHHHHhhcHHHHHHHHHHHhccCCCC
Q 043780 166 QYHKFHQEFAEFYKCALLYLAYTSVE 191 (386)
Q Consensus 166 ~~~k~~~~~~~~y~~~l~yL~~~~~~ 191 (386)
.+. ..|++...-...-..+..+|.+
T Consensus 226 ~~~-~~g~~~~A~~~~~~vi~~yP~s 250 (263)
T PRK10803 226 IMQ-DKGDTAKAKAVYQQVIKKYPGT 250 (263)
T ss_pred HHH-HcCCHHHHHHHHHHHHHHCcCC
Confidence 444 4677776666555566666654
No 257
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.27 E-value=1.1e+02 Score=26.31 Aligned_cols=28 Identities=18% Similarity=0.119 Sum_probs=24.5
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
.-.|+++||+.+|+|+..|...+-+|..
T Consensus 126 ~g~s~~eIA~~lgis~~tV~~~i~ra~~ 153 (166)
T PRK09639 126 SGYSYKEIAEALGIKESSVGTTLARAKK 153 (166)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3689999999999999999999887753
No 258
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=21.18 E-value=6.5e+02 Score=24.14 Aligned_cols=55 Identities=15% Similarity=0.260 Sum_probs=35.9
Q ss_pred cCCChHHHHHHHHHHHHHhhhccccCCCchHHHHHHHHHHHhcccCChHHHHHHHHhcccc
Q 043780 85 QYPEKQAAISYLEGVIEKLRATNEQRKEEPILYIKMQIAMFKLEQGDRKECKKLLEDGKST 145 (386)
Q Consensus 85 ~~~d~~~al~fl~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~l~~~~l~~~~~~l~~~~~~ 145 (386)
..++.++|+...+++.++.- +.+ ..+..+.+ ++.++...|+.+++++.++++-..
T Consensus 192 ~~g~~~~A~~~f~~vv~~yP--~s~--~~~dAl~k--lg~~~~~~g~~~~A~~~~~~vi~~ 246 (263)
T PRK10803 192 NKGKKDDAAYYFASVVKNYP--KSP--KAADAMFK--VGVIMQDKGDTAKAKAVYQQVIKK 246 (263)
T ss_pred HcCCHHHHHHHHHHHHHHCC--CCc--chhHHHHH--HHHHHHHcCCHHHHHHHHHHHHHH
Confidence 34578889888887766662 122 22333333 355566789999999999877554
No 259
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.08 E-value=99 Score=30.06 Aligned_cols=27 Identities=19% Similarity=0.006 Sum_probs=24.7
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
-.+||++||+.+++|+.-|...+-+|.
T Consensus 157 ~g~s~~EIA~~lgis~~tV~~~l~Rar 183 (324)
T TIGR02960 157 LGWRAAETAELLGTSTASVNSALQRAR 183 (324)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 368999999999999999999999884
No 260
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.08 E-value=1e+02 Score=27.20 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=24.1
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|+..|...+=+|.
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar 178 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGL 178 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHH
Confidence 479999999999999999998887774
No 261
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.95 E-value=1.5e+02 Score=23.31 Aligned_cols=46 Identities=15% Similarity=0.116 Sum_probs=32.2
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHH
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSL 358 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L 358 (386)
++..++|+.+||++..+-.|. ..|+|...=+.. ..|.++..++..+
T Consensus 2 ~~i~e~A~~~gvs~~tLr~ye----~~Gli~p~r~~~---------g~R~y~~~dv~~l 47 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLYE----RLGLLSPSRTDG---------GTRRYSERDIERL 47 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHHH----HCCCcCCCcCCC---------CCeeECHHHHHHH
Confidence 467899999999999999994 478887521221 3466666655444
No 262
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=20.94 E-value=1.1e+02 Score=27.00 Aligned_cols=27 Identities=26% Similarity=0.260 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...||++||+.+|+|..-|...+-+|.
T Consensus 142 ~g~s~~EIA~~l~is~~tv~~~l~Ra~ 168 (179)
T PRK09415 142 EELSIKEIAEVTGVNENTVKTRLKKAK 168 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478999999999999999999888874
No 263
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.85 E-value=1.1e+02 Score=26.34 Aligned_cols=27 Identities=19% Similarity=0.192 Sum_probs=23.9
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...++.+||+.+|+|...|...+=+|.
T Consensus 140 ~~~~~~eIA~~lgis~~tv~~~~~ra~ 166 (179)
T PRK11924 140 EGLSYREIAEILGVPVGTVKSRLRRAR 166 (179)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 469999999999999999998887764
No 264
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.79 E-value=1.1e+02 Score=27.43 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=23.4
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|..-|...+=+|+
T Consensus 156 eg~s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 156 EELPHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred cCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 479999999999999999987776664
No 265
>PF04210 MtrG: Tetrahydromethanopterin S-methyltransferase, subunit G ; InterPro: IPR005866 This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane
Probab=20.76 E-value=1.8e+02 Score=22.39 Aligned_cols=35 Identities=23% Similarity=0.279 Sum_probs=28.9
Q ss_pred ccccC-ChhhHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 043780 346 QPRVL-GIPQIKSLRDRLDSWLGKVHTALLSIEAET 380 (386)
Q Consensus 346 ~~R~l-~~~q~~~L~~~L~~W~~~v~~~~~~l~~~~ 380 (386)
.|+++ +++|...+.+||+.-.++|+.+..-+.+..
T Consensus 4 iP~viv~~~~~~~i~~rLd~iEeKvEf~~~Ei~Qr~ 39 (70)
T PF04210_consen 4 IPQVIVDPDDFNEIMKRLDEIEEKVEFTNAEIAQRA 39 (70)
T ss_pred CCeeeeCHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 46665 889999999999999999998877775543
No 266
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=20.53 E-value=1.7e+02 Score=20.67 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=25.8
Q ss_pred HHHHHHHHhhCCCCCCccChHHHHHHcCCChhHHHHHHHHH
Q 043780 283 ILCLMEIIFSRPSEDRTIPLSIIAERTKLSIEDVEHLLMKS 323 (386)
Q Consensus 283 lLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~eVE~lvikA 323 (386)
+++|+-| ..-++|++||...||+...|-.++-+.
T Consensus 10 ll~L~~L-------R~~~~~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 10 LLTLMYL-------RLNLTFQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred HHHHHHH-------HcCCcHhHHhhheeecHHHHHHHHHHH
Confidence 5677777 257999999999999987666555443
No 267
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=20.48 E-value=1.1e+02 Score=20.00 Aligned_cols=47 Identities=13% Similarity=0.061 Sum_probs=30.5
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHH
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLR 359 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~ 359 (386)
++..++|+.++|+...|-.|+-+ |.+.+.-... ..|.++.+++..+.
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~----g~~~~~~~~~---------~~~~~~~~ei~~~~ 47 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE----GKLKAIRTPG---------GHRRFPEEDLERLL 47 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc----CCCCceeCCC---------CceecCHHHHHHHH
Confidence 46789999999999999988654 5444321111 23456777665543
No 268
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.38 E-value=1.5e+02 Score=27.89 Aligned_cols=28 Identities=18% Similarity=0.211 Sum_probs=24.5
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHhh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSLS 325 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi~ 325 (386)
..+|+.+||+.+++|..-|..++-+|+.
T Consensus 220 ~g~s~~eIA~~l~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 220 ENLSQKETGERLGISQMHVSRLQRQAIK 247 (257)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5789999999999999999988777653
No 269
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=20.18 E-value=1.8e+02 Score=24.35 Aligned_cols=32 Identities=25% Similarity=0.297 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhcCCChHHHHHHHHHHHHHhh
Q 043780 73 LKLAHFAVIVSRQYPEKQAAISYLEGVIEKLR 104 (386)
Q Consensus 73 l~l~~i~~~v~~~~~d~~~al~fl~~~~~~~~ 104 (386)
=+.++-++..|++.+|..-|+.||+.++.|..
T Consensus 45 P~ii~aALrAcRRvND~a~AVR~lE~iK~K~~ 76 (108)
T PF02284_consen 45 PKIIEAALRACRRVNDFALAVRILEGIKDKCG 76 (108)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHHHHHHHTT
T ss_pred hHHHHHHHHHHHHhhhHHHHHHHHHHHHHHcc
Confidence 36788899999999999999999999999994
No 270
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=20.11 E-value=1.1e+02 Score=27.91 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=24.0
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
..+||++||+.+|+|...|...+-+|.
T Consensus 163 ~g~s~~EIAe~lgis~~tV~~~l~RAr 189 (206)
T PRK12544 163 IELETNEICHAVDLSVSNLNVLLYRAR 189 (206)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 479999999999999999999887764
No 271
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=20.11 E-value=1.1e+02 Score=27.07 Aligned_cols=27 Identities=11% Similarity=0.154 Sum_probs=24.3
Q ss_pred CccChHHHHHHcCCChhHHHHHHHHHh
Q 043780 298 RTIPLSIIAERTKLSIEDVEHLLMKSL 324 (386)
Q Consensus 298 r~isf~~Ia~~l~i~~~eVE~lvikAi 324 (386)
...|+++||+.+|+|..-|...+-+|.
T Consensus 153 ~g~s~~eIA~~lgis~~tv~~~l~Rar 179 (193)
T PRK11923 153 DGLSYEDIASVMQCPVGTVRSRIFRAR 179 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 479999999999999999999988873
No 272
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=20.08 E-value=3.1e+02 Score=19.64 Aligned_cols=60 Identities=13% Similarity=0.033 Sum_probs=39.8
Q ss_pred HHHhcccCChHHHHHHHHhccccccccCCCCHHHHHHHHHHHHHHHHHhhcHHHHHHHHHHHhccCCC
Q 043780 123 AMFKLEQGDRKECKKLLEDGKSTLDSMTDIDPSVYANYYWVSSQYHKFHQEFAEFYKCALLYLAYTSV 190 (386)
Q Consensus 123 ~~~~l~~~~l~~~~~~l~~~~~~l~~~~~v~~~v~a~~y~~~s~~~k~~~~~~~~y~~~l~yL~~~~~ 190 (386)
..+++..++++.+.+.++.+-..-+. +...+...+..+-..|+|.+.....-.++.-.|.
T Consensus 2 ~~~~~~~~~~~~A~~~~~~~l~~~p~--------~~~~~~~~a~~~~~~g~~~~A~~~l~~~l~~~p~ 61 (73)
T PF13371_consen 2 KQIYLQQEDYEEALEVLERALELDPD--------DPELWLQRARCLFQLGRYEEALEDLERALELSPD 61 (73)
T ss_pred HHHHHhCCCHHHHHHHHHHHHHhCcc--------cchhhHHHHHHHHHhccHHHHHHHHHHHHHHCCC
Confidence 35677889999999888876543222 1222333444555688888888888888866553
No 273
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=20.07 E-value=1.9e+02 Score=27.48 Aligned_cols=33 Identities=12% Similarity=0.135 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHhhCCCCCCccChHHHHHHcCCChh
Q 043780 276 KLLEKINILCLMEIIFSRPSEDRTIPLSIIAERTKLSIE 314 (386)
Q Consensus 276 ~l~~KirlLaL~~L~~~r~~~~r~isf~~Ia~~l~i~~~ 314 (386)
.++-|+|...++.+.. +..||+|+++.+|||+.
T Consensus 6 ~~~~~~~~v~~lr~lk------~~~ty~el~~~~g~p~~ 38 (238)
T PRK08558 6 KVRLQLRAVRVLRSLK------KTYTYEELSSITGLPES 38 (238)
T ss_pred hHHHHHHHHHHHHHHh------cccCHHHHHHHHCCCHH
Confidence 3456888888888763 46799999999999875
No 274
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.02 E-value=3.3e+02 Score=25.12 Aligned_cols=53 Identities=17% Similarity=0.255 Sum_probs=40.3
Q ss_pred cChHHHHHHcCCChhHHHHHHHHHhhccceEEeecCCCCEEEEEeeccccCChhhHHHHHHH
Q 043780 300 IPLSIIAERTKLSIEDVEHLLMKSLSVHLIEGIIDQVEGTVHVSWVQPRVLGIPQIKSLRDR 361 (386)
Q Consensus 300 isf~~Ia~~l~i~~~eVE~lvikAi~~gLI~G~IDqv~~~v~vt~v~~R~l~~~q~~~L~~~ 361 (386)
..|.+|++.++-+++.|=.++..-++. .|+||. +.+.|+ .| ++..+++.+-++
T Consensus 41 ~N~~~i~~~l~R~~~~~~ky~~~ELgt---~~~~~~--~~~ii~---G~-~~~~~i~~~l~~ 93 (201)
T PRK12336 41 TNFGEIADALNRDPDHLMKFLQRELGT---AGKIEG--GRAVFN---GK-FTEEDIQAAIDA 93 (201)
T ss_pred ecHHHHHHHHCCCHHHHHHHHHHHhCC---cceecC--CEEEEE---ee-eCHHHHHHHHHH
Confidence 489999999999999999999988775 799984 555554 33 577766655444
Done!