Query psy6552
Match_columns 254
No_of_seqs 106 out of 297
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 20:55:16 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6552.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6552hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3341|consensus 100.0 1.2E-80 2.5E-85 533.4 23.4 246 1-252 1-247 (249)
2 PF04157 EAP30: EAP30/Vps36 fa 100.0 1.5E-64 3.2E-69 445.4 20.4 218 5-228 1-223 (223)
3 KOG2760|consensus 100.0 7E-45 1.5E-49 335.8 22.1 227 3-246 196-430 (432)
4 smart00550 Zalpha Z-DNA-bindin 96.8 0.0073 1.6E-07 43.6 7.0 56 181-240 8-64 (68)
5 PF13412 HTH_24: Winged helix- 96.7 0.0042 9.1E-08 41.3 5.2 47 177-225 1-47 (48)
6 PF05158 RNA_pol_Rpc34: RNA po 96.6 0.076 1.6E-06 49.8 14.5 119 95-227 7-132 (327)
7 PF04703 FaeA: FaeA-like prote 96.5 0.0088 1.9E-07 42.8 5.9 57 183-240 4-60 (62)
8 PF01978 TrmB: Sugar-specific 96.2 0.0063 1.4E-07 43.4 3.8 52 177-230 6-57 (68)
9 PF08220 HTH_DeoR: DeoR-like h 95.9 0.027 5.9E-07 39.2 5.7 47 181-229 2-48 (57)
10 PRK00135 scpB segregation and 95.3 0.17 3.7E-06 43.9 9.7 94 117-227 21-133 (188)
11 PF09339 HTH_IclR: IclR helix- 95.1 0.052 1.1E-06 36.8 4.8 46 183-229 7-52 (52)
12 smart00418 HTH_ARSR helix_turn 95.0 0.095 2.1E-06 35.3 6.1 46 194-241 9-54 (66)
13 PF12802 MarR_2: MarR family; 94.7 0.19 4.1E-06 34.5 6.9 55 177-231 3-57 (62)
14 PF09012 FeoC: FeoC like trans 94.7 0.051 1.1E-06 39.1 4.0 46 183-230 4-49 (69)
15 PRK09334 30S ribosomal protein 94.6 0.15 3.4E-06 38.8 6.6 38 193-230 39-77 (86)
16 PF01325 Fe_dep_repress: Iron 94.5 0.19 4E-06 35.5 6.5 47 182-230 11-57 (60)
17 COG3355 Predicted transcriptio 94.3 0.18 3.8E-06 41.1 6.7 54 177-232 25-79 (126)
18 smart00420 HTH_DEOR helix_turn 94.1 0.21 4.6E-06 32.6 5.8 47 182-230 3-49 (53)
19 PF01047 MarR: MarR family; I 94.0 0.12 2.7E-06 35.3 4.7 52 177-230 1-52 (59)
20 smart00347 HTH_MARR helix_turn 94.0 0.28 6.2E-06 36.2 7.0 54 175-230 6-59 (101)
21 PHA02943 hypothetical protein; 93.9 0.19 4.2E-06 42.2 6.4 55 182-241 14-68 (165)
22 COG2345 Predicted transcriptio 93.5 0.24 5.2E-06 44.0 6.7 49 182-232 14-62 (218)
23 TIGR01889 Staph_reg_Sar staphy 93.3 0.42 9.1E-06 37.2 7.2 55 177-231 23-79 (109)
24 smart00346 HTH_ICLR helix_turn 93.2 0.38 8.1E-06 35.6 6.4 46 183-229 9-54 (91)
25 PF09397 Ftsk_gamma: Ftsk gamm 93.1 0.28 6E-06 35.4 5.3 47 181-229 8-54 (65)
26 PF02002 TFIIE_alpha: TFIIE al 93.0 0.13 2.9E-06 39.8 3.8 64 177-242 11-78 (105)
27 PRK11179 DNA-binding transcrip 92.9 0.33 7E-06 40.2 6.2 49 177-227 7-55 (153)
28 PRK03573 transcriptional regul 92.8 0.55 1.2E-05 38.0 7.4 55 176-231 28-82 (144)
29 TIGR02147 Fsuc_second hypothet 92.7 0.67 1.5E-05 42.4 8.5 143 59-230 24-174 (271)
30 PRK11512 DNA-binding transcrip 92.6 0.58 1.3E-05 38.0 7.3 54 176-231 37-90 (144)
31 TIGR02698 CopY_TcrY copper tra 92.2 0.71 1.5E-05 37.4 7.3 62 177-242 2-67 (130)
32 PF08784 RPA_C: Replication pr 92.2 0.51 1.1E-05 36.2 6.1 50 177-226 45-96 (102)
33 PF12840 HTH_20: Helix-turn-he 92.1 0.36 7.8E-06 33.6 4.8 47 182-230 13-59 (61)
34 PF01726 LexA_DNA_bind: LexA D 92.0 0.55 1.2E-05 33.7 5.7 55 176-230 3-61 (65)
35 PRK11169 leucine-responsive tr 91.9 0.38 8.3E-06 40.3 5.5 50 176-227 11-60 (164)
36 cd00090 HTH_ARSR Arsenical Res 91.8 0.88 1.9E-05 31.2 6.6 49 179-230 7-55 (78)
37 COG4901 Ribosomal protein S25 91.8 0.22 4.9E-06 39.0 3.6 38 193-230 57-94 (107)
38 COG2512 Predicted membrane-ass 91.7 0.41 8.8E-06 43.5 5.9 55 175-230 191-245 (258)
39 PF13463 HTH_27: Winged helix 91.3 1.1 2.3E-05 31.2 6.6 49 179-228 3-51 (68)
40 PF01022 HTH_5: Bacterial regu 91.1 0.92 2E-05 30.0 5.7 41 182-225 5-45 (47)
41 PRK06266 transcription initiat 91.0 0.81 1.8E-05 39.3 6.7 45 180-226 23-67 (178)
42 PF03297 Ribosomal_S25: S25 ri 91.0 0.38 8.2E-06 38.0 4.3 35 193-227 57-91 (105)
43 PF09107 SelB-wing_3: Elongati 91.0 1.2 2.6E-05 30.4 6.2 43 186-230 3-45 (50)
44 TIGR01884 cas_HTH CRISPR locus 90.9 1 2.3E-05 38.9 7.4 53 176-230 140-192 (203)
45 PF06163 DUF977: Bacterial pro 90.8 0.35 7.5E-06 39.3 4.0 48 181-230 14-61 (127)
46 smart00344 HTH_ASNC helix_turn 90.6 0.73 1.6E-05 35.3 5.6 44 181-226 5-48 (108)
47 PRK10870 transcriptional repre 90.5 1.4 2.9E-05 37.5 7.6 55 177-231 53-107 (176)
48 smart00843 Ftsk_gamma This dom 90.5 0.57 1.2E-05 33.6 4.5 46 181-228 7-52 (63)
49 PRK10141 DNA-binding transcrip 90.5 0.8 1.7E-05 36.7 5.8 55 183-241 20-74 (117)
50 TIGR02337 HpaR homoprotocatech 90.4 1.2 2.6E-05 34.8 6.8 52 177-230 26-77 (118)
51 COG1349 GlpR Transcriptional r 90.4 0.6 1.3E-05 42.0 5.6 47 180-228 6-52 (253)
52 smart00419 HTH_CRP helix_turn_ 90.2 0.81 1.8E-05 29.4 4.8 35 195-229 8-42 (48)
53 PF08279 HTH_11: HTH domain; 90.2 1.1 2.4E-05 30.1 5.6 41 182-223 3-43 (55)
54 TIGR00373 conserved hypothetic 90.0 1.1 2.3E-05 37.7 6.5 61 179-241 14-78 (158)
55 PRK15466 carboxysome structura 89.6 0.57 1.2E-05 39.8 4.5 40 185-226 116-155 (166)
56 PRK10512 selenocysteinyl-tRNA- 89.4 13 0.00028 37.8 14.9 169 34-230 415-601 (614)
57 PRK10163 DNA-binding transcrip 89.0 1.2 2.5E-05 40.3 6.5 47 183-230 29-75 (271)
58 PF04079 DUF387: Putative tran 89.0 1.9 4.1E-05 36.4 7.3 96 117-230 14-128 (159)
59 PRK13509 transcriptional repre 88.9 1 2.2E-05 40.4 5.9 45 181-227 7-51 (251)
60 cd00092 HTH_CRP helix_turn_hel 88.8 1 2.2E-05 31.1 4.8 36 194-229 24-59 (67)
61 PRK10434 srlR DNA-bindng trans 88.8 0.97 2.1E-05 40.6 5.8 48 180-229 6-53 (256)
62 PF03965 Penicillinase_R: Peni 88.8 0.95 2.1E-05 35.5 5.0 61 178-242 2-66 (115)
63 PF04967 HTH_10: HTH DNA bindi 88.7 1.5 3.3E-05 30.3 5.3 43 177-221 1-49 (53)
64 TIGR00738 rrf2_super rrf2 fami 88.6 1.6 3.4E-05 34.7 6.3 45 185-229 15-59 (132)
65 smart00345 HTH_GNTR helix_turn 88.6 1.4 3.1E-05 29.3 5.2 37 193-229 17-54 (60)
66 PF02082 Rrf2: Transcriptional 88.4 2.2 4.8E-05 31.5 6.5 54 185-240 15-68 (83)
67 PRK13777 transcriptional regul 88.1 2.3 5E-05 36.7 7.3 54 176-231 42-95 (185)
68 PHA00738 putative HTH transcri 88.0 1.8 3.8E-05 34.4 6.0 55 183-241 16-70 (108)
69 COG1414 IclR Transcriptional r 88.0 1.5 3.3E-05 39.1 6.4 47 183-230 8-54 (246)
70 PRK03902 manganese transport t 87.7 1.8 3.9E-05 35.2 6.2 45 183-229 12-56 (142)
71 PRK10906 DNA-binding transcrip 87.6 1.3 2.9E-05 39.7 5.8 47 180-228 6-52 (252)
72 PF05331 DUF742: Protein of un 87.4 1.7 3.7E-05 34.8 5.7 53 175-231 39-91 (114)
73 PRK11569 transcriptional repre 87.3 1.6 3.4E-05 39.4 6.2 47 183-230 32-78 (274)
74 COG1522 Lrp Transcriptional re 86.8 1.7 3.7E-05 35.2 5.6 49 177-227 6-54 (154)
75 PRK15090 DNA-binding transcrip 86.7 2 4.3E-05 38.3 6.4 46 183-230 18-63 (257)
76 PF14947 HTH_45: Winged helix- 86.6 1.7 3.8E-05 31.8 5.0 41 182-225 9-49 (77)
77 COG3413 Predicted DNA binding 86.5 3.6 7.9E-05 35.8 7.9 45 176-222 155-205 (215)
78 COG4565 CitB Response regulato 86.3 2.1 4.6E-05 38.0 6.2 122 102-241 97-223 (224)
79 COG1846 MarR Transcriptional r 85.8 3.3 7.2E-05 31.3 6.5 53 177-231 20-72 (126)
80 PF00392 GntR: Bacterial regul 85.5 2.1 4.5E-05 29.9 4.8 38 193-230 21-59 (64)
81 PRK09954 putative kinase; Prov 85.4 1.8 3.8E-05 40.4 5.6 43 181-225 5-47 (362)
82 PRK00215 LexA repressor; Valid 85.0 4.8 0.0001 34.5 7.7 55 177-231 2-60 (205)
83 cd07377 WHTH_GntR Winged helix 84.9 1.7 3.6E-05 29.6 4.0 32 196-227 26-57 (66)
84 TIGR02702 SufR_cyano iron-sulf 84.9 3.5 7.6E-05 35.6 6.9 46 182-229 4-49 (203)
85 TIGR00281 segregation and cond 84.7 11 0.00023 32.7 9.7 96 117-228 18-131 (186)
86 TIGR02944 suf_reg_Xantho FeS a 84.6 2.3 5E-05 33.9 5.2 42 185-227 16-57 (130)
87 PF14394 DUF4423: Domain of un 84.4 3.2 7E-05 35.2 6.3 48 181-230 26-76 (171)
88 PRK09802 DNA-binding transcrip 84.1 2.4 5.2E-05 38.4 5.8 48 180-229 18-65 (269)
89 PRK00080 ruvB Holliday junctio 84.1 5.8 0.00013 36.6 8.4 74 137-229 236-311 (328)
90 PRK04424 fatty acid biosynthes 84.0 1.3 2.9E-05 38.0 3.8 46 180-227 8-53 (185)
91 TIGR00498 lexA SOS regulatory 84.0 3.1 6.8E-05 35.5 6.2 55 177-231 4-62 (199)
92 PRK11050 manganese transport r 83.7 3.5 7.6E-05 34.1 6.1 44 185-230 43-86 (152)
93 PRK09834 DNA-binding transcrip 83.7 3.3 7.1E-05 37.1 6.4 47 183-230 15-61 (263)
94 PF13730 HTH_36: Helix-turn-he 82.5 5.2 0.00011 26.8 5.6 32 194-225 24-55 (55)
95 TIGR00122 birA_repr_reg BirA b 82.2 7.6 0.00017 27.4 6.6 42 184-228 5-46 (69)
96 KOG1767|consensus 82.2 1.9 4.1E-05 34.0 3.6 46 180-225 44-90 (110)
97 TIGR02787 codY_Gpos GTP-sensin 82.0 3 6.5E-05 37.7 5.3 37 193-229 196-232 (251)
98 PF04558 tRNA_synt_1c_R1: Glut 81.5 7.5 0.00016 32.9 7.4 98 49-170 15-116 (164)
99 TIGR02010 IscR iron-sulfur clu 81.5 3.7 8E-05 33.1 5.4 44 184-227 14-57 (135)
100 TIGR02431 pcaR_pcaU beta-ketoa 81.4 3.7 8E-05 36.3 5.8 45 183-228 13-57 (248)
101 PRK10411 DNA-binding transcrip 81.1 4 8.7E-05 36.4 5.9 46 180-227 5-50 (240)
102 PF09743 DUF2042: Uncharacteri 80.9 13 0.00029 34.0 9.3 123 66-218 29-154 (272)
103 PRK11014 transcriptional repre 80.9 6.1 0.00013 32.1 6.5 45 193-239 23-67 (141)
104 PF13601 HTH_34: Winged helix 80.8 3.8 8.1E-05 30.4 4.7 46 184-231 5-50 (80)
105 PF00325 Crp: Bacterial regula 80.6 3.6 7.9E-05 25.5 3.8 30 196-225 3-32 (32)
106 PRK10263 DNA translocase FtsK; 80.4 4.5 9.8E-05 44.4 6.9 88 138-227 1247-1339(1355)
107 PF12324 HTH_15: Helix-turn-he 80.2 3.3 7.2E-05 30.9 4.2 43 183-230 28-70 (77)
108 cd08767 Cdt1_c The C-terminal 79.9 18 0.00039 29.2 8.8 78 97-186 45-123 (126)
109 COG1654 BirA Biotin operon rep 79.8 5.1 0.00011 30.0 5.1 49 178-230 5-53 (79)
110 PF08222 HTH_CodY: CodY helix- 79.4 2.9 6.2E-05 29.6 3.4 33 194-226 3-35 (61)
111 cd07153 Fur_like Ferric uptake 79.1 7.7 0.00017 29.9 6.3 48 182-230 4-56 (116)
112 PF13404 HTH_AsnC-type: AsnC-t 78.9 5.1 0.00011 26.1 4.3 38 181-220 5-42 (42)
113 PRK14165 winged helix-turn-hel 78.4 7.7 0.00017 34.4 6.7 38 193-230 19-56 (217)
114 PRK10857 DNA-binding transcrip 78.3 5.3 0.00011 33.7 5.4 43 185-227 15-57 (164)
115 PHA03103 double-strand RNA-bin 78.3 8.2 0.00018 33.4 6.6 46 193-241 25-70 (183)
116 PRK11414 colanic acid/biofilm 77.9 3.5 7.6E-05 35.6 4.4 38 193-230 32-69 (221)
117 COG1321 TroR Mn-dependent tran 77.8 5.3 0.00011 33.4 5.3 51 178-230 8-59 (154)
118 COG2996 Predicted RNA-bindinin 77.6 11 0.00025 34.6 7.6 62 166-228 209-279 (287)
119 PHA02701 ORF020 dsRNA-binding 77.6 9.3 0.0002 33.1 6.7 49 181-230 6-54 (183)
120 PRK04172 pheS phenylalanyl-tRN 77.3 7 0.00015 38.5 6.8 53 176-230 3-55 (489)
121 TIGR00635 ruvB Holliday juncti 77.3 38 0.00082 30.4 11.2 74 137-229 215-290 (305)
122 COG1386 scpB Chromosome segreg 77.0 36 0.00079 29.4 10.3 85 140-230 37-138 (184)
123 PF09681 Phage_rep_org_N: N-te 76.9 4.6 9.9E-05 32.6 4.4 53 195-251 53-105 (121)
124 PF10007 DUF2250: Uncharacteri 76.6 9.8 0.00021 29.3 6.0 53 177-231 5-57 (92)
125 COG1378 Predicted transcriptio 76.5 8.3 0.00018 34.7 6.5 57 177-239 14-71 (247)
126 PF09743 DUF2042: Uncharacteri 75.8 27 0.00058 32.0 9.7 100 119-228 2-105 (272)
127 TIGR01610 phage_O_Nterm phage 75.6 6.1 0.00013 30.1 4.7 38 193-230 45-82 (95)
128 COG1497 Predicted transcriptio 74.4 8.2 0.00018 35.0 5.7 44 182-227 14-57 (260)
129 cd05029 S-100A6 S-100A6: S-100 74.2 13 0.00029 27.8 6.2 51 100-153 10-62 (88)
130 PF03444 HrcA_DNA-bdg: Winged 73.8 12 0.00026 28.0 5.6 50 177-226 2-54 (78)
131 PF14502 HTH_41: Helix-turn-he 73.6 10 0.00022 25.8 4.7 36 195-230 6-41 (48)
132 PRK14999 histidine utilization 73.1 5.5 0.00012 35.0 4.4 34 197-230 38-71 (241)
133 PLN02198 glutathione gamma-glu 72.8 6.7 0.00014 39.6 5.4 33 90-126 217-250 (573)
134 PLN02180 gamma-glutamyl transp 72.8 7 0.00015 40.0 5.6 32 90-125 267-299 (639)
135 COG0055 AtpD F0F1-type ATP syn 72.8 7.7 0.00017 37.6 5.5 74 70-161 330-413 (468)
136 PRK10079 phosphonate metabolis 72.6 5.9 0.00013 34.8 4.5 35 196-230 36-70 (241)
137 PRK11534 DNA-binding transcrip 72.5 6.8 0.00015 33.8 4.8 38 193-230 28-65 (224)
138 TIGR02812 fadR_gamma fatty aci 72.1 7.1 0.00015 34.0 4.9 38 193-230 27-65 (235)
139 PF04545 Sigma70_r4: Sigma-70, 72.1 17 0.00037 23.8 5.7 43 176-221 4-46 (50)
140 TIGR03338 phnR_burk phosphonat 71.8 6 0.00013 33.8 4.3 38 193-230 32-69 (212)
141 TIGR01774 PFL2-3 pyruvate form 71.2 1.1E+02 0.0024 32.3 14.0 82 5-87 168-255 (786)
142 COG3682 Predicted transcriptio 71.1 10 0.00023 30.7 5.2 62 177-242 4-69 (123)
143 TIGR02018 his_ut_repres histid 71.0 6.8 0.00015 34.1 4.5 34 197-230 27-60 (230)
144 TIGR02404 trehalos_R_Bsub treh 70.6 7 0.00015 34.0 4.5 35 196-230 25-59 (233)
145 PF11994 DUF3489: Protein of u 70.6 22 0.00048 26.2 6.3 57 180-238 11-70 (72)
146 PRK15431 ferrous iron transpor 70.5 14 0.00031 27.6 5.4 37 192-228 13-49 (78)
147 smart00421 HTH_LUXR helix_turn 70.2 21 0.00046 22.9 5.9 41 176-220 3-43 (58)
148 PF01475 FUR: Ferric uptake re 69.9 16 0.00035 28.4 6.1 59 182-242 11-74 (120)
149 PF03962 Mnd1: Mnd1 family; I 69.6 6.6 0.00014 33.9 4.0 46 193-239 9-58 (188)
150 PRK06474 hypothetical protein; 69.6 18 0.00039 30.8 6.6 60 182-242 14-77 (178)
151 COG2188 PhnF Transcriptional r 69.4 7.5 0.00016 34.4 4.4 35 196-230 32-66 (236)
152 PF01019 G_glu_transpept: Gamm 69.3 9.4 0.0002 37.8 5.5 69 48-125 125-205 (510)
153 PF03428 RP-C: Replication pro 68.8 9.6 0.00021 32.7 4.8 42 195-238 70-112 (177)
154 TIGR01714 phage_rep_org_N phag 68.6 8.6 0.00019 31.0 4.2 51 196-250 52-102 (119)
155 PRK04984 fatty acid metabolism 68.3 9.7 0.00021 33.2 4.9 37 194-230 29-66 (239)
156 TIGR00066 g_glut_trans gamma-g 68.2 3.7 8E-05 40.8 2.4 32 90-125 191-223 (516)
157 PRK11402 DNA-binding transcrip 68.0 8.5 0.00018 33.7 4.5 36 195-230 33-68 (241)
158 cd01677 PFL2_DhaB_BssA Pyruvat 68.0 1.6E+02 0.0034 31.1 14.3 133 5-151 166-308 (781)
159 PF02295 z-alpha: Adenosine de 67.8 32 0.0007 24.6 6.7 56 181-239 6-61 (66)
160 KOG2165|consensus 67.7 20 0.00044 37.0 7.5 61 162-229 590-650 (765)
161 PRK09990 DNA-binding transcrip 67.5 10 0.00022 33.3 4.9 38 193-230 28-66 (251)
162 PF02901 PFL: Pyruvate formate 67.1 1.1E+02 0.0023 31.5 12.7 81 5-86 169-255 (648)
163 PF13545 HTH_Crp_2: Crp-like h 67.1 15 0.00033 25.9 4.9 35 195-229 28-62 (76)
164 COG2865 Predicted transcriptio 66.9 18 0.00039 35.8 6.8 58 180-241 403-460 (467)
165 COG4465 CodY Pleiotropic trans 66.8 11 0.00025 33.6 4.9 33 193-225 202-234 (261)
166 PRK09464 pdhR transcriptional 66.7 11 0.00024 33.2 4.9 38 193-230 31-69 (254)
167 PRK10421 DNA-binding transcrip 66.6 11 0.00024 33.3 4.9 38 193-230 23-61 (253)
168 PRK10681 DNA-binding transcrip 66.5 9.9 0.00021 34.0 4.7 41 181-223 9-49 (252)
169 PF07106 TBPIP: Tat binding pr 66.0 21 0.00045 29.9 6.3 58 181-240 3-62 (169)
170 COG1675 TFA1 Transcription ini 65.9 20 0.00043 30.9 6.1 60 181-242 20-83 (176)
171 TIGR02325 C_P_lyase_phnF phosp 65.8 10 0.00022 32.9 4.5 35 196-230 33-67 (238)
172 PRK11920 rirA iron-responsive 65.6 15 0.00033 30.4 5.3 53 184-239 14-66 (153)
173 KOG3233|consensus 65.2 66 0.0014 29.8 9.6 97 116-223 26-128 (297)
174 smart00753 PAM PCI/PINT associ 65.1 19 0.0004 26.3 5.2 46 183-230 14-61 (88)
175 smart00088 PINT motif in prote 65.1 19 0.0004 26.3 5.2 46 183-230 14-61 (88)
176 KOG1350|consensus 64.6 15 0.00032 35.0 5.5 82 67-163 377-465 (521)
177 PRK03837 transcriptional regul 64.4 11 0.00024 32.7 4.5 37 194-230 35-72 (241)
178 COG1241 MCM2 Predicted ATPase 64.1 1.2E+02 0.0025 31.6 12.2 153 60-229 507-675 (682)
179 PRK10225 DNA-binding transcrip 64.1 13 0.00028 32.9 4.9 38 193-230 30-68 (257)
180 PF03979 Sigma70_r1_1: Sigma-7 64.0 9.9 0.00021 28.2 3.5 46 184-231 12-60 (82)
181 PLN03083 E3 UFM1-protein ligas 64.0 1.5E+02 0.0033 31.4 13.1 170 31-242 4-177 (803)
182 PRK13558 bacterio-opsin activa 64.0 30 0.00066 34.7 8.1 80 140-221 564-656 (665)
183 PRK09764 DNA-binding transcrip 63.5 12 0.00025 32.9 4.5 36 195-230 28-64 (240)
184 PRK12423 LexA repressor; Provi 63.5 21 0.00045 30.8 6.0 54 177-230 4-61 (202)
185 PF05597 Phasin: Poly(hydroxya 63.1 60 0.0013 26.6 8.2 73 5-77 25-106 (132)
186 cd03319 L-Ala-DL-Glu_epimerase 62.9 16 0.00035 33.4 5.4 79 139-230 133-211 (316)
187 PF01399 PCI: PCI domain; Int 62.8 21 0.00045 26.3 5.2 44 185-230 52-97 (105)
188 PF08221 HTH_9: RNA polymerase 62.8 21 0.00045 25.1 4.8 34 193-226 25-58 (62)
189 smart00531 TFIIE Transcription 62.4 12 0.00026 30.8 4.1 36 193-228 13-48 (147)
190 PF05600 DUF773: Protein of un 62.3 16 0.00035 36.4 5.6 45 33-77 127-171 (507)
191 KOG1043|consensus 62.3 72 0.0016 31.8 10.0 111 34-155 257-378 (499)
192 PRK11523 DNA-binding transcrip 62.2 15 0.00032 32.5 4.9 38 193-230 29-67 (253)
193 PLN03083 E3 UFM1-protein ligas 61.6 30 0.00064 36.4 7.5 96 118-222 4-101 (803)
194 PF07818 HCNGP: HCNGP-like pro 61.5 17 0.00036 28.1 4.5 41 59-102 41-85 (96)
195 PRK05472 redox-sensing transcr 61.0 18 0.00038 31.3 5.1 43 180-224 17-61 (213)
196 PRK09615 ggt gamma-glutamyltra 60.0 6.6 0.00014 39.7 2.5 32 90-125 239-271 (581)
197 PRK04217 hypothetical protein; 60.0 19 0.00041 28.6 4.6 61 155-218 19-81 (110)
198 COG1802 GntR Transcriptional r 59.9 12 0.00026 32.5 3.9 38 193-230 37-74 (230)
199 PRK00411 cdc6 cell division co 59.7 40 0.00088 31.4 7.6 80 137-230 268-360 (394)
200 PF10771 DUF2582: Protein of u 59.7 23 0.0005 25.5 4.6 46 183-230 12-57 (65)
201 PRK10512 selenocysteinyl-tRNA- 59.5 2.1E+02 0.0045 29.3 13.1 133 92-243 413-550 (614)
202 COG1959 Predicted transcriptio 58.8 26 0.00057 28.9 5.5 45 184-228 14-58 (150)
203 COG4190 Predicted transcriptio 58.6 43 0.00093 27.7 6.5 67 177-245 62-129 (144)
204 PRK04214 rbn ribonuclease BN/u 58.5 21 0.00045 34.4 5.5 45 193-242 308-352 (412)
205 smart00529 HTH_DTXR Helix-turn 58.5 20 0.00044 26.4 4.4 33 198-230 2-34 (96)
206 PF09202 Rio2_N: Rio2, N-termi 58.4 55 0.0012 24.5 6.7 55 176-230 3-59 (82)
207 PF06969 HemN_C: HemN C-termin 58.2 20 0.00044 24.8 4.1 37 194-230 19-56 (66)
208 PRK10046 dpiA two-component re 57.9 36 0.00078 29.1 6.5 48 183-231 166-213 (225)
209 PF04182 B-block_TFIIIC: B-blo 57.9 34 0.00073 24.8 5.4 51 180-230 3-53 (75)
210 TIGR03337 phnR transcriptional 57.9 17 0.00036 31.4 4.4 35 196-230 26-60 (231)
211 TIGR03879 near_KaiC_dom probab 57.6 13 0.00027 27.5 3.0 48 176-225 15-62 (73)
212 PRK10430 DNA-binding transcrip 57.2 41 0.00088 29.0 6.8 63 177-239 159-224 (239)
213 PF07789 DUF1627: Protein of u 57.0 21 0.00046 29.9 4.6 48 193-241 4-51 (155)
214 COG5126 FRQ1 Ca2+-binding prot 56.8 66 0.0014 27.2 7.6 133 38-203 18-152 (160)
215 PF01638 HxlR: HxlR-like helix 56.7 52 0.0011 24.4 6.4 39 193-231 16-55 (90)
216 TIGR03793 TOMM_pelo TOMM prope 56.7 23 0.0005 26.3 4.3 24 56-79 12-40 (77)
217 COG3879 Uncharacterized protei 56.5 58 0.0013 29.5 7.6 64 58-155 89-152 (247)
218 PF05584 Sulfolobus_pRN: Sulfo 56.4 43 0.00093 24.7 5.6 44 182-228 8-51 (72)
219 PRK11886 bifunctional biotin-- 56.2 35 0.00075 31.4 6.4 46 183-230 8-53 (319)
220 COG0735 Fur Fe2+/Zn2+ uptake r 55.7 46 0.001 27.3 6.5 51 180-231 22-77 (145)
221 PRK00082 hrcA heat-inducible t 55.0 31 0.00068 32.4 6.0 66 177-244 4-82 (339)
222 PF12793 SgrR_N: Sugar transpo 54.8 20 0.00042 28.5 3.9 32 195-226 19-50 (115)
223 PF04492 Phage_rep_O: Bacterio 54.7 48 0.001 25.7 6.0 36 194-229 53-88 (100)
224 TIGR00475 selB selenocysteine- 54.5 1.1E+02 0.0023 31.0 10.1 76 139-230 500-575 (581)
225 COG1339 Transcriptional regula 54.0 18 0.00039 31.8 3.9 38 194-231 18-55 (214)
226 COG3877 Uncharacterized protei 53.9 39 0.00085 26.9 5.4 24 59-82 70-93 (122)
227 cd06170 LuxR_C_like C-terminal 53.4 55 0.0012 21.0 5.5 39 178-220 2-40 (57)
228 TIGR02716 C20_methyl_CrtF C-20 53.3 30 0.00065 31.4 5.5 37 193-229 21-57 (306)
229 KOG0624|consensus 53.2 8 0.00017 37.2 1.6 23 54-81 446-468 (504)
230 PRK13239 alkylmercury lyase; P 53.0 24 0.00052 31.1 4.5 46 181-231 24-69 (206)
231 PF08784 RPA_C: Replication pr 52.9 39 0.00084 25.6 5.3 52 95-158 45-96 (102)
232 PF08281 Sigma70_r4_2: Sigma-7 52.1 65 0.0014 21.1 5.7 41 177-220 11-51 (54)
233 PF02796 HTH_7: Helix-turn-hel 52.0 55 0.0012 21.2 5.2 39 174-216 3-42 (45)
234 cd08803 Death_ank3 Death domai 51.9 21 0.00045 26.8 3.5 67 66-148 6-83 (84)
235 PF07638 Sigma70_ECF: ECF sigm 51.2 1.5E+02 0.0032 24.9 13.6 152 31-219 15-175 (185)
236 PHA02591 hypothetical protein; 50.9 65 0.0014 24.2 5.8 49 161-218 33-82 (83)
237 COG2178 Predicted RNA-binding 50.6 44 0.00096 29.4 5.7 30 73-108 105-134 (204)
238 PRK15411 rcsA colanic acid cap 50.5 88 0.0019 26.8 7.7 74 138-223 107-181 (207)
239 TIGR02573 LcrG_PcrG type III s 50.4 13 0.00028 28.4 2.1 17 65-81 23-39 (90)
240 TIGR02844 spore_III_D sporulat 50.4 30 0.00066 25.8 4.1 33 181-216 8-40 (80)
241 TIGR00331 hrcA heat shock gene 50.3 38 0.00083 31.8 5.8 56 187-244 15-78 (337)
242 COG1725 Predicted transcriptio 50.2 26 0.00057 28.5 4.0 36 195-230 35-70 (125)
243 PF01645 Glu_synthase: Conserv 50.1 35 0.00075 32.7 5.5 108 113-230 150-282 (368)
244 PF09999 DUF2240: Uncharacteri 49.9 15 0.00031 30.7 2.5 29 202-230 28-57 (144)
245 TIGR02384 RelB_DinJ addiction 49.8 13 0.00029 27.8 2.1 24 57-80 7-30 (83)
246 PRK09430 djlA Dna-J like membr 49.7 2E+02 0.0044 26.0 10.7 31 116-153 196-226 (267)
247 PF09106 SelB-wing_2: Elongati 49.7 28 0.00062 23.9 3.7 38 193-230 15-55 (59)
248 COG2186 FadR Transcriptional r 49.3 24 0.00051 31.3 4.0 41 196-239 35-75 (241)
249 PF13518 HTH_28: Helix-turn-he 48.5 54 0.0012 21.1 4.8 37 184-224 5-41 (52)
250 COG0735 Fur Fe2+/Zn2+ uptake r 48.5 88 0.0019 25.6 7.0 59 101-170 25-83 (145)
251 smart00351 PAX Paired Box doma 48.5 61 0.0013 25.8 5.9 53 166-224 9-62 (125)
252 PF11662 DUF3263: Protein of u 48.4 55 0.0012 24.4 5.2 47 176-222 2-49 (77)
253 PRK10265 chaperone-modulator p 48.1 30 0.00064 26.7 3.9 41 195-241 7-47 (101)
254 PF08461 HTH_12: Ribonuclease 48.1 42 0.0009 23.9 4.4 43 184-227 3-50 (66)
255 PF10078 DUF2316: Uncharacteri 47.9 29 0.00063 26.6 3.7 42 177-218 3-46 (89)
256 PF08221 HTH_9: RNA polymerase 47.8 77 0.0017 22.2 5.7 48 92-155 8-55 (62)
257 COG1031 Uncharacterized Fe-S o 47.5 61 0.0013 32.3 6.7 100 94-230 292-399 (560)
258 KOG0027|consensus 47.3 98 0.0021 25.0 7.2 73 65-158 28-101 (151)
259 PF04157 EAP30: EAP30/Vps36 fa 47.0 11 0.00024 33.1 1.5 51 9-60 2-52 (223)
260 PF09756 DDRGK: DDRGK domain; 46.9 46 0.00099 28.9 5.3 111 66-206 74-184 (188)
261 COG4367 Uncharacterized protei 46.8 36 0.00078 26.2 4.0 50 177-226 3-54 (97)
262 COG2433 Uncharacterized conser 46.7 3.5E+02 0.0075 27.9 12.0 131 64-224 39-182 (652)
263 TIGR03697 NtcA_cyano global ni 46.2 35 0.00076 28.1 4.4 35 195-229 143-177 (193)
264 COG3398 Uncharacterized protei 45.3 58 0.0013 29.3 5.7 63 181-247 103-165 (240)
265 PF07216 LcrG: LcrG protein; 45.3 17 0.00038 27.9 2.1 17 65-81 26-42 (93)
266 smart00350 MCM minichromosome 45.0 46 0.001 32.9 5.7 53 97-153 441-506 (509)
267 PF10376 Mei5: Double-strand r 44.7 58 0.0013 29.0 5.7 46 31-78 168-215 (221)
268 PRK09191 two-component respons 44.5 34 0.00074 29.4 4.2 52 177-231 89-147 (261)
269 PRK10947 global DNA-binding tr 44.3 1.3E+02 0.0028 24.7 7.3 49 31-79 22-73 (135)
270 PF09336 Vps4_C: Vps4 C termin 44.1 40 0.00086 23.8 3.7 33 116-154 29-61 (62)
271 PRK11753 DNA-binding transcrip 43.6 44 0.00096 27.9 4.7 36 195-230 168-203 (211)
272 PRK05638 threonine synthase; V 43.6 55 0.0012 31.7 5.9 55 181-239 373-429 (442)
273 TIGR02865 spore_II_E stage II 42.4 1.3E+02 0.0029 31.4 8.8 137 27-170 431-583 (764)
274 COG4840 Uncharacterized protei 42.3 98 0.0021 22.6 5.4 47 101-154 12-69 (71)
275 COG1777 Predicted transcriptio 42.2 45 0.00099 29.6 4.5 59 183-244 19-80 (217)
276 COG0758 Smf Predicted Rossmann 42.2 1.2E+02 0.0026 28.9 7.7 47 181-230 298-344 (350)
277 PF09382 RQC: RQC domain; Int 41.9 82 0.0018 23.7 5.6 25 206-230 53-77 (106)
278 cd04761 HTH_MerR-SF Helix-Turn 41.8 41 0.00089 21.4 3.4 38 196-239 1-38 (49)
279 COG3432 Predicted transcriptio 41.7 33 0.00071 26.6 3.2 38 193-230 29-66 (95)
280 TIGR00762 DegV EDD domain prot 41.7 2.6E+02 0.0057 25.0 10.7 94 117-223 41-152 (275)
281 cd00213 S-100 S-100: S-100 dom 41.3 1.2E+02 0.0026 21.9 6.2 74 34-128 2-79 (88)
282 PRK10328 DNA binding protein, 41.3 1.5E+02 0.0033 24.3 7.3 49 31-79 22-73 (134)
283 PF10557 Cullin_Nedd8: Cullin 41.3 36 0.00078 24.2 3.2 48 182-231 11-66 (68)
284 PLN02964 phosphatidylserine de 41.2 80 0.0017 32.6 6.8 35 115-155 194-228 (644)
285 TIGR03060 PS_II_psb29 photosys 40.4 37 0.00081 30.1 3.8 16 65-80 75-90 (214)
286 KOG2607|consensus 40.3 68 0.0015 31.4 5.7 131 34-178 126-260 (505)
287 PF08280 HTH_Mga: M protein tr 40.2 59 0.0013 22.3 4.1 39 180-220 6-44 (59)
288 PF09079 Cdc6_C: CDC6, C termi 39.7 21 0.00046 26.1 1.9 20 62-81 20-39 (85)
289 PF00392 GntR: Bacterial regul 39.3 1.2E+02 0.0027 20.7 6.1 50 95-155 2-52 (64)
290 TIGR02941 Sigma_B RNA polymera 39.3 2.7E+02 0.0057 24.5 10.5 26 194-219 220-245 (255)
291 COG3177 Fic family protein [Fu 39.1 60 0.0013 30.5 5.2 45 193-239 302-346 (348)
292 PRK13918 CRP/FNR family transc 39.0 48 0.001 27.6 4.2 34 195-228 149-182 (202)
293 cd08317 Death_ank Death domain 38.9 44 0.00095 24.6 3.5 57 66-128 6-73 (84)
294 PF11972 HTH_13: HTH DNA bindi 38.8 82 0.0018 21.9 4.5 34 184-219 4-37 (54)
295 PTZ00111 DNA replication licen 38.8 1.8E+02 0.0039 31.3 9.0 34 194-227 858-903 (915)
296 PLN02853 Probable phenylalanyl 38.7 3.5E+02 0.0076 27.1 10.6 80 138-229 29-118 (492)
297 COG3888 Predicted transcriptio 38.5 1.3E+02 0.0027 28.0 6.9 48 195-242 20-67 (321)
298 PRK04158 transcriptional repre 38.3 59 0.0013 29.7 4.8 33 193-225 199-231 (256)
299 PF05873 Mt_ATP-synt_D: ATP sy 37.7 36 0.00078 28.7 3.2 109 31-151 26-143 (161)
300 TIGR03882 cyclo_dehyd_2 bacter 37.7 1.6E+02 0.0034 25.3 7.3 72 155-229 3-78 (193)
301 PF04221 RelB: RelB antitoxin; 37.4 22 0.00047 26.4 1.6 24 57-80 6-29 (83)
302 KOG1463|consensus 37.1 68 0.0015 30.8 5.1 24 51-74 308-331 (411)
303 COG4800 Predicted transcriptio 36.7 55 0.0012 27.4 4.0 77 52-128 6-90 (170)
304 COG2390 DeoR Transcriptional r 36.7 56 0.0012 30.7 4.5 37 194-230 25-61 (321)
305 PRK10840 transcriptional regul 36.7 1.9E+02 0.004 24.2 7.5 44 176-223 150-194 (216)
306 TIGR00667 aat leucyl/phenylala 36.5 1.9E+02 0.0042 25.1 7.4 81 137-232 79-159 (185)
307 PRK11235 bifunctional antitoxi 36.5 27 0.0006 26.1 2.0 24 57-80 6-29 (80)
308 KOG2410|consensus 36.4 24 0.00053 35.7 2.2 31 91-124 236-266 (579)
309 PF13833 EF-hand_8: EF-hand do 36.4 1.1E+02 0.0024 19.8 4.9 38 114-157 2-40 (54)
310 PRK09462 fur ferric uptake reg 36.2 1.5E+02 0.0033 23.9 6.7 48 180-227 18-70 (148)
311 KOG4302|consensus 36.2 1.6E+02 0.0034 30.5 7.9 48 33-80 155-203 (660)
312 PF08721 Tn7_Tnp_TnsA_C: TnsA 36.1 63 0.0014 22.8 3.9 43 184-228 32-78 (79)
313 PF12395 DUF3658: Protein of u 36.1 2.1E+02 0.0045 22.3 9.2 88 137-231 9-103 (111)
314 PF04914 DltD_C: DltD C-termin 36.0 44 0.00095 27.2 3.3 49 60-108 32-87 (130)
315 KOG3442|consensus 35.9 57 0.0012 26.6 3.9 50 112-174 52-101 (132)
316 PF09958 DUF2192: Uncharacteri 35.3 1.4E+02 0.003 26.8 6.6 54 42-105 158-222 (231)
317 PF13559 DUF4129: Domain of un 35.1 72 0.0016 21.9 4.0 34 118-154 39-72 (72)
318 PF14394 DUF4423: Domain of un 34.9 1.1E+02 0.0025 25.8 5.8 63 92-174 22-84 (171)
319 PRK15201 fimbriae regulatory p 34.8 1.2E+02 0.0025 26.6 5.8 44 173-220 130-173 (198)
320 KOG0403|consensus 34.5 61 0.0013 32.3 4.5 88 138-228 519-621 (645)
321 PRK15418 transcriptional regul 34.4 63 0.0014 30.0 4.5 37 194-230 28-64 (318)
322 KOG0040|consensus 34.2 3.4E+02 0.0073 31.4 10.2 76 65-158 2273-2349(2399)
323 PRK09333 30S ribosomal protein 34.1 1.6E+02 0.0035 24.7 6.4 90 137-229 5-115 (150)
324 smart00853 MutL_C MutL C termi 33.9 77 0.0017 24.8 4.4 40 138-177 60-100 (136)
325 PF07083 DUF1351: Protein of u 33.8 2E+02 0.0043 25.2 7.3 43 61-103 111-158 (215)
326 PF09733 VEFS-Box: VEFS-Box of 33.7 62 0.0014 26.7 3.9 30 45-74 93-122 (140)
327 PRK09391 fixK transcriptional 33.6 60 0.0013 28.1 4.0 34 195-228 179-212 (230)
328 PRK09983 pflD putative formate 33.5 1.7E+02 0.0038 30.7 7.9 74 5-87 167-246 (765)
329 PF06971 Put_DNA-bind_N: Putat 33.2 83 0.0018 21.4 3.8 32 183-214 16-47 (50)
330 PTZ00326 phenylalanyl-tRNA syn 33.2 1.1E+02 0.0023 30.6 6.1 50 180-230 7-56 (494)
331 cd07624 BAR_SNX7_30 The Bin/Am 33.0 2.4E+02 0.0051 24.2 7.6 59 12-71 117-180 (200)
332 PF14538 Raptor_N: Raptor N-te 33.0 1.3E+02 0.0028 25.2 5.7 28 137-164 70-98 (154)
333 PF08676 MutL_C: MutL C termin 32.9 1.3E+02 0.0029 23.9 5.7 52 138-189 59-113 (144)
334 cd00131 PAX Paired Box domain 32.6 1.4E+02 0.003 23.9 5.7 51 169-225 12-63 (128)
335 PF15208 Rab15_effector: Rab15 32.6 93 0.002 27.7 4.9 73 34-106 16-116 (236)
336 PRK12529 RNA polymerase sigma 32.3 94 0.002 25.6 4.9 41 177-220 128-168 (178)
337 PF07848 PaaX: PaaX-like prote 32.2 97 0.0021 22.4 4.3 44 193-238 18-64 (70)
338 PF02291 TFIID-31kDa: Transcri 32.1 1.1E+02 0.0023 25.0 4.9 49 92-150 28-76 (129)
339 COG1460 Uncharacterized protei 31.9 1.2E+02 0.0026 24.3 5.1 78 40-153 33-110 (114)
340 PRK03187 tgl transglutaminase; 31.9 27 0.00059 32.0 1.6 43 77-134 180-224 (272)
341 PLN02853 Probable phenylalanyl 31.7 1.2E+02 0.0027 30.2 6.2 49 180-230 4-53 (492)
342 TIGR03859 PQQ_PqqD coenzyme PQ 31.6 2.1E+02 0.0045 20.9 6.2 55 166-225 16-80 (81)
343 cd08805 Death_ank1 Death domai 31.6 85 0.0018 23.6 4.0 57 66-128 6-73 (84)
344 cd08804 Death_ank2 Death domai 31.5 80 0.0017 23.5 3.9 36 93-128 38-73 (84)
345 cd08318 Death_NMPP84 Death dom 31.4 54 0.0012 24.4 2.9 58 64-128 7-75 (86)
346 KOG0994|consensus 31.4 5.2E+02 0.011 29.1 10.9 104 35-153 1462-1577(1758)
347 PRK10736 hypothetical protein; 31.3 1E+02 0.0022 29.6 5.5 49 177-228 306-354 (374)
348 PF10108 DNA_pol_B_exo2: Predi 31.2 1E+02 0.0022 27.2 5.0 72 64-153 116-190 (209)
349 PRK00095 mutL DNA mismatch rep 31.1 2.7E+02 0.0059 28.3 8.8 92 138-229 488-596 (617)
350 PF06721 DUF1204: Protein of u 31.0 2.5E+02 0.0054 24.7 7.2 33 39-72 86-118 (228)
351 cd06171 Sigma70_r4 Sigma70, re 30.9 1.3E+02 0.0029 18.4 5.2 41 177-220 11-51 (55)
352 cd07669 BAR_SNX33 The Bin/Amph 30.9 1.3E+02 0.0028 26.6 5.5 75 48-128 37-113 (207)
353 cd03315 MLE_like Muconate lact 30.9 94 0.002 27.5 4.9 78 140-230 85-163 (265)
354 cd07153 Fur_like Ferric uptake 30.8 1.2E+02 0.0026 23.0 5.0 42 113-160 13-54 (116)
355 cd07668 BAR_SNX9 The Bin/Amphi 30.8 1.4E+02 0.003 26.5 5.7 74 48-127 37-112 (210)
356 TIGR00475 selB selenocysteine- 30.8 5.7E+02 0.012 25.8 11.8 116 92-229 404-523 (581)
357 KOG0031|consensus 30.8 3.4E+02 0.0074 23.2 8.3 89 36-157 28-116 (171)
358 PRK15481 transcriptional regul 30.6 64 0.0014 30.6 4.0 34 194-227 27-61 (431)
359 PF07766 LETM1: LETM1-like pro 30.5 1.5E+02 0.0032 26.9 6.1 78 64-154 173-254 (268)
360 TIGR00721 tfx DNA-binding prot 30.5 1.3E+02 0.0028 24.7 5.2 38 177-218 7-44 (137)
361 PF14848 HU-DNA_bdg: DNA-bindi 30.3 77 0.0017 25.2 3.9 54 111-171 23-81 (124)
362 PRK05773 3,4-dihydroxy-2-butan 30.2 83 0.0018 28.0 4.3 51 93-149 160-218 (219)
363 PF08429 PLU-1: PLU-1-like pro 30.2 4.3E+02 0.0093 24.2 9.4 55 65-132 138-195 (335)
364 PRK13824 replication initiatio 30.2 94 0.002 30.1 5.0 42 195-238 82-124 (404)
365 COG4189 Predicted transcriptio 30.2 96 0.0021 28.3 4.7 45 183-229 27-71 (308)
366 PF04539 Sigma70_r3: Sigma-70 30.1 1.2E+02 0.0026 21.4 4.6 44 185-231 11-54 (78)
367 COG1733 Predicted transcriptio 30.1 1.3E+02 0.0029 23.9 5.2 38 194-231 35-73 (120)
368 cd07622 BAR_SNX4 The Bin/Amphi 29.8 3.2E+02 0.0069 23.7 7.9 54 17-71 121-179 (201)
369 PRK11161 fumarate/nitrate redu 29.6 75 0.0016 27.2 4.0 35 195-229 184-218 (235)
370 PRK14981 DNA-directed RNA poly 29.5 1.1E+02 0.0023 24.2 4.4 47 92-153 63-109 (112)
371 PF05119 Terminase_4: Phage te 29.4 1.3E+02 0.0027 22.4 4.7 26 57-82 57-88 (100)
372 PRK14332 (dimethylallyl)adenos 29.1 4.8E+02 0.01 25.4 9.8 49 138-191 282-330 (449)
373 PF12307 DUF3631: Protein of u 29.0 3.5E+02 0.0076 23.4 7.9 99 36-153 20-131 (184)
374 COG1737 RpiR Transcriptional r 28.9 2.8E+02 0.006 25.0 7.7 82 65-154 37-130 (281)
375 TIGR02147 Fsuc_second hypothet 28.9 4.4E+02 0.0096 24.0 9.0 62 92-174 120-182 (271)
376 PF01475 FUR: Ferric uptake re 28.9 2.7E+02 0.0058 21.4 6.7 43 112-160 19-61 (120)
377 COG5340 Predicted transcriptio 28.7 1.8E+02 0.0038 26.4 6.1 83 101-200 15-102 (269)
378 PRK00301 aat leucyl/phenylalan 28.4 3.1E+02 0.0068 24.6 7.7 27 137-164 109-135 (233)
379 PRK09613 thiH thiamine biosynt 28.4 1.8E+02 0.0039 28.7 6.8 99 48-155 205-308 (469)
380 PF09824 ArsR: ArsR transcript 28.4 1.2E+02 0.0026 25.8 4.7 48 178-231 16-66 (160)
381 COG3612 Uncharacterized protei 28.0 64 0.0014 27.1 3.0 28 202-229 30-58 (157)
382 PF14948 RESP18: RESP18 domain 27.9 44 0.00095 26.4 1.9 21 211-231 23-43 (105)
383 PLN02859 glutamine-tRNA ligase 27.8 1.2E+02 0.0026 32.1 5.6 47 49-102 17-63 (788)
384 KOG2944|consensus 27.8 24 0.00052 30.0 0.5 28 130-159 114-141 (170)
385 cd07670 BAR_SNX18 The Bin/Amph 27.6 1.6E+02 0.0035 26.0 5.6 57 48-104 37-95 (207)
386 PF13405 EF-hand_6: EF-hand do 27.5 72 0.0016 18.6 2.5 13 138-150 16-28 (31)
387 PF09756 DDRGK: DDRGK domain; 27.4 83 0.0018 27.3 3.8 44 185-230 105-150 (188)
388 PF14762 HPS3_Mid: Hermansky-P 27.4 1.8E+02 0.0038 28.1 6.3 77 33-128 247-324 (374)
389 smart00576 BTP Bromodomain tra 27.3 1.7E+02 0.0036 21.2 4.9 15 137-151 57-71 (77)
390 PRK04172 pheS phenylalanyl-tRN 27.3 5.9E+02 0.013 25.0 10.2 98 115-230 19-122 (489)
391 PF00196 GerE: Bacterial regul 27.3 1.8E+02 0.0039 19.4 4.8 40 177-220 4-43 (58)
392 PRK10402 DNA-binding transcrip 27.1 83 0.0018 27.0 3.8 33 196-228 170-202 (226)
393 COG5159 RPN6 26S proteasome re 27.1 1.3E+02 0.0029 28.4 5.2 67 4-74 262-329 (421)
394 cd04766 HTH_HspR Helix-Turn-He 27.0 95 0.0021 23.0 3.6 31 195-229 1-31 (91)
395 COG2144 Selenophosphate synthe 26.8 1.4E+02 0.003 28.0 5.3 69 93-162 196-289 (324)
396 TIGR00288 conserved hypothetic 26.7 65 0.0014 27.3 2.9 82 65-155 69-156 (160)
397 PRK14333 (dimethylallyl)adenos 26.7 3.5E+02 0.0075 26.2 8.4 47 139-190 287-333 (448)
398 PRK11302 DNA-binding transcrip 26.3 3.2E+02 0.0069 24.1 7.5 82 66-154 36-128 (284)
399 KOG2278|consensus 26.3 2.2E+02 0.0048 24.8 6.0 69 97-174 9-83 (207)
400 TIGR00782 ccoP cytochrome c ox 26.2 4.9E+02 0.011 23.5 11.2 19 137-155 175-193 (285)
401 PF02847 MA3: MA3 domain; Int 26.2 1.5E+02 0.0032 22.4 4.7 51 91-151 30-81 (113)
402 PRK12523 RNA polymerase sigma 26.1 1.6E+02 0.0034 24.0 5.1 41 177-220 120-160 (172)
403 PF09907 DUF2136: Uncharacteri 26.1 1.4E+02 0.0031 22.0 4.3 40 118-164 5-44 (76)
404 PF04801 Sin_N: Sin-like prote 26.0 5.5E+02 0.012 24.6 9.6 88 113-219 281-375 (421)
405 PRK05660 HemN family oxidoredu 25.8 1.2E+02 0.0026 28.7 4.9 37 194-230 320-356 (378)
406 COG0640 ArsR Predicted transcr 25.7 2.3E+02 0.0051 19.6 5.9 44 194-239 38-81 (110)
407 PRK12539 RNA polymerase sigma 25.6 1.5E+02 0.0034 24.4 5.1 40 177-219 132-171 (184)
408 PRK00118 putative DNA-binding 25.6 1.8E+02 0.0038 22.8 5.0 39 177-218 18-56 (104)
409 TIGR02989 Sig-70_gvs1 RNA poly 25.6 1.7E+02 0.0037 23.1 5.2 40 177-219 112-151 (159)
410 PRK14335 (dimethylallyl)adenos 25.5 3.8E+02 0.0081 26.1 8.4 48 138-190 289-336 (455)
411 PRK13919 putative RNA polymera 25.3 1.6E+02 0.0035 24.1 5.1 40 177-219 136-175 (186)
412 PRK14703 glutaminyl-tRNA synth 25.2 6.1E+02 0.013 26.9 10.2 124 59-220 592-720 (771)
413 COG0078 ArgF Ornithine carbamo 25.2 68 0.0015 30.0 3.0 100 64-175 166-272 (310)
414 KOG2916|consensus 25.2 3.9E+02 0.0085 24.8 7.7 92 114-226 43-155 (304)
415 PF04697 Pinin_SDK_N: pinin/SD 24.9 1.1E+02 0.0024 25.1 3.8 32 31-62 4-35 (134)
416 PRK11639 zinc uptake transcrip 24.8 1.4E+02 0.003 25.0 4.7 48 180-228 27-79 (169)
417 PRK10361 DNA recombination pro 24.8 2.4E+02 0.0051 28.1 6.8 50 21-70 124-177 (475)
418 PF05732 RepL: Firmicute plasm 24.7 1.3E+02 0.0028 25.3 4.4 44 195-242 75-118 (165)
419 PRK09047 RNA polymerase factor 24.5 1.7E+02 0.0036 23.2 4.9 39 177-218 107-145 (161)
420 TIGR03358 VI_chp_5 type VI sec 24.4 1.6E+02 0.0036 24.9 4.9 38 30-72 107-144 (159)
421 PTZ00184 calmodulin; Provision 24.3 3.2E+02 0.007 20.8 9.2 13 138-150 100-112 (149)
422 TIGR02928 orc1/cdc6 family rep 24.0 3.3E+02 0.0072 24.9 7.4 116 92-225 219-347 (365)
423 cd03318 MLE Muconate Lactonizi 24.0 1.7E+02 0.0036 27.3 5.4 28 204-231 196-223 (365)
424 PRK09652 RNA polymerase sigma 23.9 1.7E+02 0.0038 23.4 5.0 40 177-219 129-168 (182)
425 PF11186 DUF2972: Protein of u 23.8 2.9E+02 0.0063 23.9 6.5 26 48-73 172-197 (199)
426 TIGR01558 sm_term_P27 phage te 23.7 1.7E+02 0.0038 22.7 4.7 27 57-83 66-98 (116)
427 cd01295 AdeC Adenine deaminase 23.5 1.3E+02 0.0028 28.8 4.7 33 139-174 330-362 (422)
428 PF09537 DUF2383: Domain of un 23.5 3.3E+02 0.0071 20.5 6.5 18 64-81 47-64 (111)
429 PRK12525 RNA polymerase sigma 23.4 1.8E+02 0.004 23.5 5.1 41 177-220 119-159 (168)
430 cd07979 TAF9 TATA Binding Prot 23.4 2.7E+02 0.0058 22.1 5.8 16 137-152 52-67 (117)
431 TIGR02193 heptsyl_trn_I lipopo 23.4 3.1E+02 0.0068 24.5 7.0 16 115-130 241-256 (319)
432 PF03374 ANT: Phage antirepres 23.3 1.9E+02 0.0042 21.9 4.9 33 193-228 22-54 (111)
433 CHL00081 chlI Mg-protoporyphyr 23.2 1.6E+02 0.0034 28.0 5.1 52 96-151 270-322 (350)
434 cd03324 rTSbeta_L-fuconate_deh 23.2 1.4E+02 0.003 28.9 4.8 77 139-230 195-274 (415)
435 PF13382 Adenine_deam_C: Adeni 23.1 1.3E+02 0.0029 25.5 4.2 33 139-174 73-105 (171)
436 PF14338 Mrr_N: Mrr N-terminal 23.0 2.5E+02 0.0053 20.8 5.3 41 95-146 2-42 (92)
437 PRK11642 exoribonuclease R; Pr 23.0 2.3E+02 0.005 30.1 6.7 49 181-230 21-73 (813)
438 PF13413 HTH_25: Helix-turn-he 22.9 87 0.0019 21.9 2.5 20 59-78 39-59 (62)
439 PF04458 DUF505: Protein of un 22.9 8.4E+02 0.018 25.0 11.0 125 91-225 413-574 (591)
440 PRK11337 DNA-binding transcrip 22.9 3.4E+02 0.0074 24.2 7.1 84 66-153 48-139 (292)
441 TIGR02959 SigZ RNA polymerase 22.7 2E+02 0.0042 23.5 5.1 38 177-217 101-138 (170)
442 PRK09642 RNA polymerase sigma 22.6 2E+02 0.0043 22.9 5.1 38 177-217 107-144 (160)
443 TIGR02985 Sig70_bacteroi1 RNA 22.5 2.1E+02 0.0045 22.3 5.1 40 177-219 114-153 (161)
444 KOG2199|consensus 22.3 2.8E+02 0.0061 27.1 6.5 56 27-83 84-149 (462)
445 smart00803 TAF TATA box bindin 22.3 2.9E+02 0.0063 19.5 6.6 59 66-149 7-65 (65)
446 TIGR02284 conserved hypothetic 22.1 1.9E+02 0.0042 23.4 4.9 17 65-81 47-63 (139)
447 TIGR03513 GldL_gliding gliding 22.1 5E+02 0.011 22.8 7.6 15 61-75 175-189 (202)
448 PF15292 Treslin_N: Treslin N- 21.8 96 0.0021 32.6 3.5 47 57-111 557-603 (803)
449 COG4519 Uncharacterized protei 21.7 1.3E+02 0.0028 22.9 3.3 39 193-231 20-58 (95)
450 PF07900 DUF1670: Protein of u 21.5 2.2E+02 0.0047 25.5 5.3 44 182-225 90-136 (220)
451 PF03102 NeuB: NeuB family; I 21.4 4.4E+02 0.0096 23.6 7.4 89 62-162 56-147 (241)
452 cd08768 Cdc6_C Winged-helix do 21.4 76 0.0016 22.9 2.1 20 62-81 27-46 (87)
453 PRK09649 RNA polymerase sigma 21.4 2E+02 0.0043 23.8 5.0 40 177-219 131-170 (185)
454 COG2255 RuvB Holliday junction 21.3 7E+02 0.015 23.6 8.9 117 93-230 179-313 (332)
455 TIGR02999 Sig-70_X6 RNA polyme 21.3 2.4E+02 0.0051 23.0 5.3 40 177-219 135-174 (183)
456 PF09279 EF-hand_like: Phospho 21.3 3.1E+02 0.0068 19.5 6.1 39 112-154 11-49 (83)
457 PF09454 Vps23_core: Vps23 cor 21.3 2.6E+02 0.0056 19.9 4.7 45 97-152 9-53 (65)
458 PRK11557 putative DNA-binding 21.2 5.3E+02 0.011 22.7 8.0 18 137-154 111-128 (278)
459 COG2183 Tex Transcriptional ac 21.2 1.7E+02 0.0036 30.9 5.1 89 31-119 149-243 (780)
460 PF11719 Drc1-Sld2: DNA replic 21.2 1.3E+02 0.0029 29.2 4.2 24 48-71 14-42 (426)
461 PRK14339 (dimethylallyl)adenos 21.1 2.5E+02 0.0054 27.0 6.1 48 138-190 261-308 (420)
462 PF02601 Exonuc_VII_L: Exonucl 21.0 4.4E+02 0.0095 24.0 7.6 25 140-164 56-82 (319)
463 TIGR02393 RpoD_Cterm RNA polym 21.0 2.4E+02 0.0052 24.6 5.6 27 194-220 195-221 (238)
464 COG1461 Predicted kinase relat 21.0 2.7E+02 0.0058 28.2 6.3 69 93-167 62-131 (542)
465 PF00493 MCM: MCM2/3/5 family 21.0 63 0.0014 30.1 1.9 33 114-153 296-328 (331)
466 PRK12547 RNA polymerase sigma 20.9 2.4E+02 0.0052 22.7 5.2 40 177-219 113-152 (164)
467 PF13012 MitMem_reg: Maintenan 20.9 32 0.0007 26.5 -0.0 67 3-75 4-74 (115)
468 cd08063 MPN_CSN6 Mpr1p, Pad1p 20.9 3.1E+02 0.0067 25.0 6.4 108 4-128 164-278 (288)
469 TIGR02937 sigma70-ECF RNA poly 20.8 2.4E+02 0.0052 21.3 5.0 41 177-220 111-151 (158)
470 PRK12528 RNA polymerase sigma 20.8 2.3E+02 0.005 22.6 5.1 41 177-220 114-154 (161)
471 PRK09462 fur ferric uptake reg 20.6 2.5E+02 0.0054 22.6 5.3 58 101-168 21-78 (148)
472 cd03316 MR_like Mandelate race 20.6 1.2E+02 0.0026 28.0 3.8 84 140-230 139-223 (357)
473 TIGR02030 BchI-ChlI magnesium 20.6 2E+02 0.0042 27.1 5.1 51 97-151 258-309 (337)
474 PRK11639 zinc uptake transcrip 20.5 2.3E+02 0.005 23.7 5.1 50 100-159 29-78 (169)
475 PRK12541 RNA polymerase sigma 20.5 2.1E+02 0.0046 22.8 4.8 40 177-219 113-152 (161)
476 COG4199 Uncharacterized protei 20.5 1.8E+02 0.0039 25.5 4.5 63 165-230 86-151 (201)
477 PRK09240 thiH thiamine biosynt 20.5 3.5E+02 0.0075 25.6 6.9 151 59-226 199-359 (371)
478 COG3793 TerB Tellurite resista 20.4 80 0.0017 26.3 2.2 21 60-80 121-141 (144)
479 PRK13626 transcriptional regul 20.4 1.2E+02 0.0026 30.1 3.9 36 193-228 21-56 (552)
480 PRK02363 DNA-directed RNA poly 20.3 4.1E+02 0.0089 21.6 6.4 65 101-172 4-69 (129)
481 TIGR00273 iron-sulfur cluster- 20.3 76 0.0016 31.0 2.4 126 18-149 32-172 (432)
482 cd07613 BAR_Endophilin_A1 The 20.3 2.4E+02 0.0052 25.1 5.4 43 24-67 2-44 (223)
483 KOG1900|consensus 20.3 8.4E+02 0.018 27.5 10.2 79 65-152 742-824 (1311)
484 PRK09645 RNA polymerase sigma 20.2 2.4E+02 0.0052 22.7 5.1 38 177-217 119-156 (173)
485 PRK09651 RNA polymerase sigma 20.2 2.1E+02 0.0047 23.3 4.9 40 177-219 120-159 (172)
486 cd04742 NPD_FabD 2-Nitropropan 20.2 2.5E+02 0.0054 27.5 5.8 43 118-160 26-72 (418)
487 TIGR01764 excise DNA binding d 20.1 1.3E+02 0.0028 18.6 2.8 28 195-226 1-28 (49)
No 1
>KOG3341|consensus
Probab=100.00 E-value=1.2e-80 Score=533.42 Aligned_cols=246 Identities=53% Similarity=0.931 Sum_probs=239.6
Q ss_pred CCcchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCccc
Q psy6552 1 MRRRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLA 80 (254)
Q Consensus 1 mrR~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~ 80 (254)
|||++|++||++.+ ...+|++.|+++.++|+.+|..||++|++.|++||+||+.+|++||+||++|+.||++|||||++
T Consensus 1 ~rrrvG~gAi~~~k-~~~ky~~~g~~l~e~Ql~q~~~Ql~~f~~~LeeFA~kH~~ei~knsqFR~~Fq~Mca~IGvDPla 79 (249)
T KOG3341|consen 1 MRRRVGLGAIQKKK-AAKKYKEVGTELAEQQLVQMSKQLEVFQEALEEFARKHKTEIRKNSQFRNQFQEMCASIGVDPLA 79 (249)
T ss_pred CccchhhhHHhhHH-HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHHcCCCccc
Confidence 89999999999997 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccc-ccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeE
Q psy6552 81 SRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFS 159 (254)
Q Consensus 81 s~kg~w~-~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~ 159 (254)
++||||+ ++|+|||||||+|||+|+|+++.+.|||+|++.||..++.+.|+..+ +.||+||++||+++|++||+||.
T Consensus 80 s~kgfw~~~lgvgdFYYelgVqviEvC~at~~~nGGlislqel~~~l~~~R~~~~--e~vt~dD~lrAi~kLk~LG~gFe 157 (249)
T KOG3341|consen 80 SGKGFWAELLGVGDFYYELGVQVIEVCLATKHTNGGLISLQELCNHLLQRRKKDH--EAVTEDDLLRAIDKLKVLGSGFE 157 (249)
T ss_pred cCcchHHHHhhhHHHHHHHhhHHHHHHHHhhcccCCeeeHHHHHHHHHHHhcccc--hhccHHHHHHHHHHhhccCCCeE
Confidence 9999999 99999999999999999999999999999999999999999998866 89999999999999999999999
Q ss_pred EEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 160 IIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 160 l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
|++++ |+++|||+|.|||+||+.||++|+ ..||||.+.|.++++|+..||+.+|++|+.+|++|+|.|.++|..|||
T Consensus 158 v~~ig-gK~~vrSVP~ELn~Dht~ILela~--~~gyvt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~e~~YW~ 234 (249)
T KOG3341|consen 158 VIKIG-GKKLVRSVPTELNMDHTVILELAE--ILGYVTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGDEAAYWF 234 (249)
T ss_pred EEEec-CEEeeecCcchhcccHHHHHHHHH--hcCceeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCcceeeec
Confidence 99999 999999999999999999999999 569999999999999999999999999999999999999888999999
Q ss_pred cccccCccccccc
Q psy6552 240 PSLFTECMNAEKE 252 (254)
Q Consensus 240 p~lf~~~~~~~~~ 252 (254)
|++|...++++..
T Consensus 235 ps~~~~~~~q~~~ 247 (249)
T KOG3341|consen 235 PSLFTDQYAQRSL 247 (249)
T ss_pred hhhhhHHHhhhhh
Confidence 9999999888753
No 2
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=100.00 E-value=1.5e-64 Score=445.43 Aligned_cols=218 Identities=46% Similarity=0.788 Sum_probs=184.9
Q ss_pred hhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCc
Q psy6552 5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKG 84 (254)
Q Consensus 5 vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg 84 (254)
+||+||+++.++++++++.+.+.+.+.+++|.+|++.|++++++||+||+++|++||+||++|++||++|||||+++++
T Consensus 1 ~GI~~l~~~~~~~~~~~~~~~~~a~~dl~~L~~qa~~~~~~l~~fa~k~~~~i~~~~~~r~~f~~~~~~lGvdp~~s~~- 79 (223)
T PF04157_consen 1 VGIAGLQRRQEQKRQYNELGMQLAFQDLEALMSQAKDFVELLENFARKHKSEIKSDPEFRSQFQSMCASLGVDPLASSK- 79 (223)
T ss_dssp --------------------TCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCSHHHHHHHHHHHHHHT--CHCCTT-
T ss_pred CchHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCCchHHHHHHHHHHHcCCCcccchh-
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999999998888
Q ss_pred ccc-cc-ccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhc-CCCCCCCCCCHHHHHHHHHHhhhhCCCeEEE
Q psy6552 85 FWS-LL-GMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSR-GKSLQHQDITNEDLLAAAKKLKIFGNGFSII 161 (254)
Q Consensus 85 ~w~-~l-g~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~R-g~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~ 161 (254)
+|+ .+ |.++||||||+||+|||..++++|||||+|+||||+|||+| |. ++|||+||++||++|++||.||+++
T Consensus 80 ~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~----~lISp~Di~~A~~~l~~lg~g~~l~ 155 (223)
T PF04157_consen 80 FWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGS----ELISPEDILRACKLLEVLGLGFRLR 155 (223)
T ss_dssp CCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTS----ST--HHHHHHHHHHHCCCTSSEEEE
T ss_pred hhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccC----CCcCHHHHHHHHHHHHHcCCCeEEE
Confidence 999 87 88999999999999999999999999999999999999999 66 7999999999999999999999999
Q ss_pred EeCCceEEEEccC-CCCChhHHHHHHHh-hccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 162 PIGQGQYLVQSIP-GELSLDHSLVLQQV-ASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 162 ~~~sg~~vv~s~p-~els~D~~~il~l~-~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
+|+||++||+++| .++|.|+.+|++++ .. ..||+|+.+|++++||++.||+++|+.|+++|++|||
T Consensus 156 ~~~sg~~vv~s~~~~e~~~~~~~il~~~~~~-~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~~D 223 (223)
T PF04157_consen 156 KFGSGVKVVQSVPYSELSKDQSRILELAEEE-NGGGVTASELAEKLGWSVERAKEALEELEREGLLWRD 223 (223)
T ss_dssp EETTTEEEEECST-CHH-HHHHHHHHHH--T-TTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEEEE
T ss_pred EeCCCcEEEEeCCchhhhHHHHHHHHHHHhh-cCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEeeC
Confidence 9999999999999 88999999999999 32 4899999999999999999999999999999999999
No 3
>KOG2760|consensus
Probab=100.00 E-value=7e-45 Score=335.82 Aligned_cols=227 Identities=27% Similarity=0.389 Sum_probs=199.2
Q ss_pred cchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHH---HHHHHhh---hhhhcCHHHHHHHHHHHHHcCC
Q psy6552 3 RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLE---SFASEYK---NEIKKDAQFRRHFQEMCASIGV 76 (254)
Q Consensus 3 R~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~---~FA~kh~---~~I~~dp~fr~~f~~mc~~lGV 76 (254)
|++||+||+|+.+.|.+.++.. |.. +|+||+++|+.||+|+. +||.|.+ ++|..|++. .|.++..++||
T Consensus 196 r~vGI~giEr~~e~q~~~td~~--i~~-AFqDLskLMs~Akemv~Lsk~~~~Km~~~~g~i~dDetv--~~ks~llsLGI 270 (432)
T KOG2760|consen 196 RMVGISGIERSLEEQLKKTDKT--INN-AFQDLSKLMSLAKEMVSLSKSIAEKMKSKTGEIQDDETV--RFKSYLLSLGI 270 (432)
T ss_pred eeechhHHHHHHHHHHHhcchh--HHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCchhhh--hhHHhhhhhcc
Confidence 5799999999999998888874 555 99999999999999997 8888884 678888887 89999999999
Q ss_pred C-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552 77 D-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 77 d-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg 155 (254)
+ |++... | -+....|+.+||+||.|+...+.++|||||+|.|+||+|||+||+ ++|||+|+.+||++|+.||
T Consensus 271 ~dpvt~~n-~--~~s~~~Y~~~Lakqlse~l~~~lee~ggmisLtdvY~~~NRaRG~----eLiSPedl~~ACe~le~l~ 343 (432)
T KOG2760|consen 271 LDPVTKDN-F--GLSLSLYHQELAKQLSEFLRLPLEENGGMISLTDVYCRYNRARGT----ELISPEDLVNACELLEHLG 343 (432)
T ss_pred CCcchhcc-c--cchHHHHHHHHHHHHHHHHhcchhhcCCEEEHHHHHHHHHHhccC----CCCCHHHHHHHHHHHHhcC
Confidence 8 998432 0 111248999999999999999999999999999999999999999 8999999999999999999
Q ss_pred CCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCc
Q psy6552 156 NGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQE 234 (254)
Q Consensus 156 ~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e 234 (254)
.|+++++|+||+.|||... .+ |..+++++.+.. ..+..|+++++..+||++..|+|+|..++++|.+|||++ .|
T Consensus 344 ~pl~L~kf~SGvlvvqlKs--~~-~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcRD~s--~e 418 (432)
T KOG2760|consen 344 VPLRLRKFNSGVLVVQLKS--HS-DEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCRDDS--VE 418 (432)
T ss_pred CceEEEEcCCceEEEEeec--cc-hHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeeeccC--cc
Confidence 9999999999999999775 44 666665555432 245678999999999999999999999999999999999 69
Q ss_pred ccceecccccCc
Q psy6552 235 HLYWFPSLFTEC 246 (254)
Q Consensus 235 ~~yw~p~lf~~~ 246 (254)
|+|||||+|...
T Consensus 419 GL~fY~N~f~e~ 430 (432)
T KOG2760|consen 419 GLRFYPNLFMES 430 (432)
T ss_pred ceeecccccccC
Confidence 999999999764
No 4
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.76 E-value=0.0073 Score=43.62 Aligned_cols=56 Identities=11% Similarity=0.135 Sum_probs=46.2
Q ss_pred HHHHHHHhhccCCC-cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552 181 HSLVLQQVASKNEA-HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240 (254)
Q Consensus 181 ~~~il~l~~~~~~g-~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p 240 (254)
...||++.... ++ .+|+.+|+..+|.+..-+..+|..|+++|+++.+.+ .+.+|.-
T Consensus 8 ~~~IL~~L~~~-g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~---~~~~W~i 64 (68)
T smart00550 8 EEKILEFLENS-GDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGG---TPPLWKL 64 (68)
T ss_pred HHHHHHHHHHC-CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCC---CCCceEe
Confidence 45788888843 23 399999999999999999999999999999999865 3457764
No 5
>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=96.73 E-value=0.0042 Score=41.33 Aligned_cols=47 Identities=17% Similarity=0.232 Sum_probs=38.2
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
||.-+..|+....+ .|.+|..+|++.+|+|..-+...|..|+++|++
T Consensus 1 l~~~~~~Il~~l~~--~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 1 LDETQRKILNYLRE--NPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp --HHHHHHHHHHHH--CTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 35556788888884 578999999999999999999999999999986
No 6
>PF05158 RNA_pol_Rpc34: RNA polymerase Rpc34 subunit; InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2DK8_A 2DK5_A 2YU3_A.
Probab=96.61 E-value=0.076 Score=49.78 Aligned_cols=119 Identities=16% Similarity=0.215 Sum_probs=89.3
Q ss_pred HHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC
Q psy6552 95 YYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP 174 (254)
Q Consensus 95 y~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p 174 (254)
..+|+.+|.+.|... ..+..++..||...+ ...+..++..|++.|-.-| -+++++-+ |..+.+-++
T Consensus 7 ~~~~~~~l~~~~~~~--~~~~~~~~~~L~~~~----------~~~~~~~~~~~in~Ll~~~-~~~~~~~~-~~l~~~~~~ 72 (327)
T PF05158_consen 7 LSELEKKLLELCREN--PSPKGFSQEDLQQLI----------PGLDLQELVKAINELLSSG-LLKLLKKG-GGLSYKAVS 72 (327)
T ss_dssp HHHHHHHHHHHHHH-----SS-EEHHHHHHH-----------TTS-HHHHHHHHHHHHHHT-SEEEEE-S-SSEEEEE--
T ss_pred HHHHHHHHHHHHHHh--cCCCCcCHHHHHhhc----------CCCCHHHHHHHHHHHHhCC-CEEEEEcC-CEEEEEEeC
Confidence 356888999999876 567899999999882 4679999999999987765 68888855 555555552
Q ss_pred -------CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 175 -------GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 175 -------~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
..++.|+..|+.+++..+.-+|-..+|..+.|.........|..|+..+++=-
T Consensus 73 ~~~a~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~ 132 (327)
T PF05158_consen 73 EEEAKKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKS 132 (327)
T ss_dssp SSS-----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHhhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence 45788899999998876567899999999999999999999999999998743
No 7
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.52 E-value=0.0088 Score=42.81 Aligned_cols=57 Identities=16% Similarity=0.232 Sum_probs=43.6
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p 240 (254)
.|++..... .+.+|+.++++.+|.|...|+..|+.|+++|.+-....-.+-..||.-
T Consensus 4 ~Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~l 60 (62)
T PF04703_consen 4 KILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWRL 60 (62)
T ss_dssp CHHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEEE
T ss_pred HHHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceeeee
Confidence 467777743 578999999999999999999999999999999776653344569964
No 8
>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=96.21 E-value=0.0063 Score=43.43 Aligned_cols=52 Identities=17% Similarity=0.174 Sum_probs=44.9
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+|..+..|+...-. .|..|+.+|++.+|++...+..+|+.|++.|++-+...
T Consensus 6 Ls~~E~~vy~~Ll~--~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 6 LSENEAKVYLALLK--NGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHHHHH--HCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 66677777655432 58999999999999999999999999999999999975
No 9
>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=95.91 E-value=0.027 Score=39.19 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=41.7
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+..|+++.. ..|.+|+.+|++.||.|..=++.-|..|++.|++-+--
T Consensus 2 ~~~Il~~l~--~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 2 QQQILELLK--EKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHH--HcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 457888888 46999999999999999999999999999999987653
No 10
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=95.31 E-value=0.17 Score=43.85 Aligned_cols=94 Identities=17% Similarity=0.189 Sum_probs=73.1
Q ss_pred eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh----hCCCeEEEEeCCceEEEEccCC---------------CC
Q psy6552 117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI----FGNGFSIIPIGQGQYLVQSIPG---------------EL 177 (254)
Q Consensus 117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~----Lg~g~~l~~~~sg~~vv~s~p~---------------el 177 (254)
+++.++-..++ ++++++..+++.|.. -+.|++|+.++ |...+++.|. .|
T Consensus 21 ls~~~La~~l~-----------~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~-~~y~l~tk~e~~~~v~~~~~~~~~~~L 88 (188)
T PRK00135 21 LSLEQLAEILE-----------LEPTEVQQLLEELQEKYEGDDRGLKLIEFN-DVYKLVTKEENADYLQKLVKTPIKQSL 88 (188)
T ss_pred CCHHHHHHHHC-----------CCHHHHHHHHHHHHHHHhhCCCCEEEEEEC-CEEEEEEcHHHHHHHHHHhcccccCCC
Confidence 67777776643 467899999999843 27899999999 7777777552 46
Q ss_pred ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
|.-...+|.++.. .+.||-.+|++..|.+. ..++..|++.|++-.
T Consensus 89 S~aaLEtLaiIay--~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e 133 (188)
T PRK00135 89 SQAALEVLAIIAY--KQPITRIEIDEIRGVNS---DGALQTLLAKGLIKE 133 (188)
T ss_pred CHHHHHHHHHHHH--cCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEE
Confidence 6555566766663 47899999999999996 688999999999875
No 11
>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=95.13 E-value=0.052 Score=36.76 Aligned_cols=46 Identities=22% Similarity=0.367 Sum_probs=38.0
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.||+..... .+.+|..+|++.+|+++.-+...|..|++.|++-.|.
T Consensus 7 ~iL~~l~~~-~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 7 RILEALAES-GGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHCHHCT-BSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecCc
Confidence 456655543 5668999999999999999999999999999998873
No 12
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.05 E-value=0.095 Score=35.31 Aligned_cols=46 Identities=17% Similarity=0.256 Sum_probs=38.6
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
+.+|..++++.+|+++.-+...|+.|++.|++..... +...||.++
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~--~~~~~~~~~ 54 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE--GKRVYYSLT 54 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec--CCEEEEEEc
Confidence 5789999999999999999999999999999997764 345555443
No 13
>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=94.70 E-value=0.19 Score=34.54 Aligned_cols=55 Identities=16% Similarity=0.178 Sum_probs=43.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++.-|-.||-.....+.+.+|+.+|++.+++++.-+...+..|++.|++.+....
T Consensus 3 lt~~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp STHHHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred cCHHHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 5666777776666432223999999999999999999999999999999988653
No 14
>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=94.66 E-value=0.051 Score=39.08 Aligned_cols=46 Identities=17% Similarity=0.289 Sum_probs=36.4
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.|.+.+. ..|.+|..+|+.+|++++.-.+..|+.+++.|.+-.-+.
T Consensus 4 ~i~~~l~--~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 4 EIRDYLR--ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHH--HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4556666 468999999999999999999999999999999876543
No 15
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=94.58 E-value=0.15 Score=38.77 Aligned_cols=38 Identities=13% Similarity=0.137 Sum_probs=34.8
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE-EEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYA-WIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l-wvD~q 230 (254)
..+||++.|++.+++...+|+.+|.+|+++|++ .|...
T Consensus 39 ~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~ 77 (86)
T PRK09334 39 EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKN 77 (86)
T ss_pred CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecC
Confidence 579999999999999999999999999999998 66544
No 16
>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=94.49 E-value=0.19 Score=35.48 Aligned_cols=47 Identities=9% Similarity=0.127 Sum_probs=40.5
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..|.++.+ .++.++..+|++.+|.++.=+.+.|..|.+.|++..+..
T Consensus 11 ~~Iy~l~~--~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 11 KAIYELSE--EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp HHHHHHHH--CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHc--CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCC
Confidence 35567777 578999999999999999999999999999999988754
No 17
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.31 E-value=0.18 Score=41.13 Aligned_cols=54 Identities=19% Similarity=0.144 Sum_probs=44.1
Q ss_pred CChhHHHH-HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC
Q psy6552 177 LSLDHSLV-LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP 232 (254)
Q Consensus 177 ls~D~~~i-l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~ 232 (254)
++.....| ..+.+ ..|..|+++|++.++.+...+...|+.|+..|++-+-..+-
T Consensus 25 Ls~~Dv~v~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~ 79 (126)
T COG3355 25 LSELDVEVYKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL 79 (126)
T ss_pred CcHHHHHHHHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc
Confidence 44433334 45565 36899999999999999999999999999999999987763
No 18
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=94.06 E-value=0.21 Score=32.64 Aligned_cols=47 Identities=19% Similarity=0.193 Sum_probs=39.3
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..++..... .+++|+.+|++.+++++.-+...|..|.+.|++-...+
T Consensus 3 ~~il~~l~~--~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 3 QQILELLAQ--QGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHH--cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 456666653 46799999999999999999999999999999876654
No 19
>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=93.99 E-value=0.12 Score=35.29 Aligned_cols=52 Identities=15% Similarity=0.176 Sum_probs=43.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+|..|-.+|..+.. .|.+|..+|++.++.++.-+...+..|++.|++-+-..
T Consensus 1 lt~~q~~iL~~l~~--~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 1 LTPSQFRILRILYE--NGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp STHHHHHHHHHHHH--HSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CCHHHHHHHHHHHH--cCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence 35567778877774 46799999999999999999999999999999987654
No 20
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.98 E-value=0.28 Score=36.23 Aligned_cols=54 Identities=26% Similarity=0.228 Sum_probs=46.8
Q ss_pred CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..++..+..|+.++. ..|.+|..+|++.++++..-....|..|++.|++-+...
T Consensus 6 ~~l~~~~~~il~~l~--~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 6 LGLTPTQFLVLRILY--EEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred cCCCHHHHHHHHHHH--HcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence 347878888888887 357899999999999999999999999999999987654
No 21
>PHA02943 hypothetical protein; Provisional
Probab=93.95 E-value=0.19 Score=42.21 Aligned_cols=55 Identities=22% Similarity=0.224 Sum_probs=47.1
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
..||++.. .|..|.+++++.+|.|...|+-.|..|+++|.+-.=.. +-..||.-+
T Consensus 14 ~eILE~Lk---~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~--G~~tyw~l~ 68 (165)
T PHA02943 14 IKTLRLLA---DGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEI--GRAAIWCLD 68 (165)
T ss_pred HHHHHHHh---cCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEee--cceEEEEEC
Confidence 45677773 68999999999999999999999999999999988665 567888744
No 22
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=93.52 E-value=0.24 Score=43.96 Aligned_cols=49 Identities=22% Similarity=0.279 Sum_probs=43.5
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP 232 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~ 232 (254)
..|+.++. ..|.+|+.+|++.+|+|+.-++.+|+.|+++|++-+-.+.+
T Consensus 14 ~~il~lL~--~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~ 62 (218)
T COG2345 14 ERILELLK--KSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQG 62 (218)
T ss_pred HHHHHHHh--ccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccC
Confidence 56788888 46899999999999999999999999999999998876654
No 23
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=93.31 E-value=0.42 Score=37.20 Aligned_cols=55 Identities=18% Similarity=0.301 Sum_probs=44.9
Q ss_pred CChhHHHHHHHhh--ccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVA--SKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~--~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++..|-.+|..+. ....|.+|..+|++.+++++.-.-..++.|++.|++.+-..+
T Consensus 23 ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~ 79 (109)
T TIGR01889 23 LSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSE 79 (109)
T ss_pred CCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCc
Confidence 6666766765543 222578999999999999999999999999999999986654
No 24
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.16 E-value=0.38 Score=35.56 Aligned_cols=46 Identities=24% Similarity=0.343 Sum_probs=39.6
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.|+++.... .+.+|+.+|++.+|.+..-+...|..|++.|++-.+.
T Consensus 9 ~Il~~l~~~-~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 9 AVLRALAEE-PGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHhC-CCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 456666532 4789999999999999999999999999999999874
No 25
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=93.09 E-value=0.28 Score=35.45 Aligned_cols=47 Identities=21% Similarity=0.260 Sum_probs=36.2
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
...+++++-. .+.+|++.|..+|++-..||...++.|+++|++==-+
T Consensus 8 y~~a~~~V~~--~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~ 54 (65)
T PF09397_consen 8 YEEAVEFVIE--EGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPAN 54 (65)
T ss_dssp HHHHHHHHHH--CTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---
T ss_pred HHHHHHHHHH--cCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCC
Confidence 4566666663 4789999999999999999999999999999985433
No 26
>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=92.97 E-value=0.13 Score=39.77 Aligned_cols=64 Identities=13% Similarity=0.272 Sum_probs=40.9
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE----eCCCCCcccceeccc
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI----DTQSPQEHLYWFPSL 242 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv----D~q~~~e~~yw~p~l 242 (254)
.++++..|+.+... .|.++.++|+..+|+++.-.+..|..|.++|++.. |++.+....|||.++
T Consensus 11 yg~~~~~Il~~L~~--~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~ 78 (105)
T PF02002_consen 11 YGEEAVRILDALLR--KGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDY 78 (105)
T ss_dssp S-STTHHHHHHHHH--H--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-TH
T ss_pred cCchHHHHHHHHHH--cCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcH
Confidence 34567788887763 47899999999999999999999999999999943 333223357888764
No 27
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=92.88 E-value=0.33 Score=40.17 Aligned_cols=49 Identities=14% Similarity=0.092 Sum_probs=43.4
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
++.-...||.+.+ ..|..|..+|++.+|+|..-+...++.|+++|+++.
T Consensus 7 lD~~D~~Il~~Lq--~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 7 IDNLDRGILEALM--ENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred cCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 5555667888888 459999999999999999999999999999999984
No 28
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=92.81 E-value=0.55 Score=38.00 Aligned_cols=55 Identities=18% Similarity=0.184 Sum_probs=45.6
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.++.-|-.+|..+... .+++|+.+|++.+++++.-....++.|++.|++.+-..+
T Consensus 28 glt~~q~~vL~~l~~~-~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~ 82 (144)
T PRK03573 28 ELTQTHWVTLHNIHQL-PPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA 82 (144)
T ss_pred CCCHHHHHHHHHHHHc-CCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC
Confidence 3666676776666532 467999999999999999999999999999999998664
No 29
>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=92.66 E-value=0.67 Score=42.39 Aligned_cols=143 Identities=10% Similarity=0.107 Sum_probs=83.3
Q ss_pred cCHHHHHHHHHHHHHcCCCc-ccCCCcccc-cc-ccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCC
Q psy6552 59 KDAQFRRHFQEMCASIGVDP-LASRKGFWS-LL-GMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQ 135 (254)
Q Consensus 59 ~dp~fr~~f~~mc~~lGVdP-l~s~kg~w~-~l-g~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~ 135 (254)
.+|.| .++.+|..+|++| - +.+ .+ |-...-..-+.+|++++--+-.+. +--++.-.+++
T Consensus 24 ~~p~f--S~R~fa~~~G~ss~s-----~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~----~yF~~lV~f~~------- 85 (271)
T TIGR02147 24 TDPAF--SWRFFAEKAGFSSTS-----YLNDIIKGKKNLTKRMIPKFAEALGLDEKEA----AYFEAMVNFGQ------- 85 (271)
T ss_pred cCcCc--CHHHHHHHhCCCCHH-----HHHHHHcCCCCCCHHHHHHHHHHcCCCHHHH----HHHHHHHHHhc-------
Confidence 68888 7899999999985 2 111 11 111122333444444442211110 00011112232
Q ss_pred CCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCC--ChhHHHHHHHhhccCCCcc-cHHHHHHhcC--CCHH
Q psy6552 136 HQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGEL--SLDHSLVLQQVASKNEAHI-SVSVLNNELN--WSTE 210 (254)
Q Consensus 136 ~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~el--s~D~~~il~l~~~~~~g~v-t~~~l~~~l~--ws~~ 210 (254)
.-|+++=.+|.+.+..+...-.++.++ ....+. +=-+..|.+++.- .++- ++..|++.++ +|.+
T Consensus 86 --ak~~~~k~~~~~~~~~~~~~~~~~~L~-------~~~~~y~~~W~~~virel~~~--~~~~~~~~~ia~~l~p~is~~ 154 (271)
T TIGR02147 86 --AKTDTEKQQFFEEMQALKPRPRLRVLA-------ADQFEYYRHWYNSVIRELLGV--MPFADDPEELAKRCFPKISAE 154 (271)
T ss_pred --cCCHHHHHHHHHHHHHHhhhchheecc-------HHHHHHHHHHHHHHHHHHhhc--CCCCCCHHHHHHHhCCCCCHH
Confidence 246777777777777664322222222 111111 1135778888884 4555 9999999999 9999
Q ss_pred HHHHHHHHHHHcCcEEEeCC
Q psy6552 211 RAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 211 ra~~~L~~l~~~G~lwvD~q 230 (254)
.+++.|+.|++-|++=.|..
T Consensus 155 ev~~sL~~L~~~glikk~~~ 174 (271)
T TIGR02147 155 QVKESLDLLERLGLIKKNED 174 (271)
T ss_pred HHHHHHHHHHHCCCeeECCC
Confidence 99999999999999998854
No 30
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=92.58 E-value=0.58 Score=38.02 Aligned_cols=54 Identities=19% Similarity=0.150 Sum_probs=46.2
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.++.-|-.||.... ..+.+|+.+|++.+++++.-.-..|+.|++.|++-+-..+
T Consensus 37 glt~~q~~vL~~l~--~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~ 90 (144)
T PRK11512 37 DITAAQFKVLCSIR--CAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP 90 (144)
T ss_pred CCCHHHHHHHHHHH--HcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence 36666777777665 2578999999999999999999999999999999997664
No 31
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=92.23 E-value=0.71 Score=37.42 Aligned_cols=62 Identities=13% Similarity=0.149 Sum_probs=47.5
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHh----cCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNE----LNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~----l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
+++-+..|+.+.= ..|.+|+.++.+. .+|++.-..+.|..|++.|++=++.. +...+|.|..
T Consensus 2 Lt~~E~~VM~vlW--~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~--gr~~~Y~p~v 67 (130)
T TIGR02698 2 ISDAEWEVMRVVW--TLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKE--GRKFIYTALV 67 (130)
T ss_pred CCHHHHHHHHHHH--cCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecC--CCcEEEEecC
Confidence 5555667777775 3567899995555 48999999999999999999988865 4556777643
No 32
>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=92.18 E-value=0.51 Score=36.23 Aligned_cols=50 Identities=28% Similarity=0.422 Sum_probs=41.3
Q ss_pred CChhHHHHHHHhhcc--CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 177 LSLDHSLVLQQVASK--NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 177 ls~D~~~il~l~~~~--~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
++.-+..|++++... ..-+|++.+|++.++.+....+.+|+.|..+|.+.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 666788999998751 13479999999999999999999999999999875
No 33
>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=92.10 E-value=0.36 Score=33.60 Aligned_cols=47 Identities=21% Similarity=0.276 Sum_probs=39.3
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..|+.... ..+..|+.+|++.+|++..-+..+|..|++.|++=+..+
T Consensus 13 ~~Il~~L~--~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 13 LRILRLLA--SNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHH--HCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHh--cCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 45677663 268899999999999999999999999999999877654
No 34
>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=92.00 E-value=0.55 Score=33.69 Aligned_cols=55 Identities=22% Similarity=0.271 Sum_probs=40.8
Q ss_pred CCChhHHHHHHHhhcc--CCC-cccHHHHHHhcCCC-HHHHHHHHHHHHHcCcEEEeCC
Q psy6552 176 ELSLDHSLVLQQVASK--NEA-HISVSVLNNELNWS-TERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 176 els~D~~~il~l~~~~--~~g-~vt~~~l~~~l~ws-~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+|+.-|..||+.+... ..| .-|+.+|++.+|++ +.-+...|..|++.|++=++..
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 3677788888876431 123 47999999999996 9999999999999999988865
No 35
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=91.88 E-value=0.38 Score=40.27 Aligned_cols=50 Identities=14% Similarity=0.195 Sum_probs=44.0
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
.++.-..+||.+.+ ..|.+|..+|++.+|.|..-+...++.|+++|+++.
T Consensus 11 ~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 11 DLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 35544668888888 569999999999999999999999999999999984
No 36
>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=91.78 E-value=0.88 Score=31.24 Aligned_cols=49 Identities=16% Similarity=0.183 Sum_probs=41.5
Q ss_pred hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..+..|+..+. ..+ ++..++++.++.+..-+...|+.|++.|++-+...
T Consensus 7 ~~~~~il~~l~--~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~ 55 (78)
T cd00090 7 PTRLRILRLLL--EGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE 55 (78)
T ss_pred hHHHHHHHHHH--HCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence 35667777766 245 99999999999999999999999999999998755
No 37
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=91.76 E-value=0.22 Score=39.01 Aligned_cols=38 Identities=18% Similarity=0.215 Sum_probs=34.4
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..+||+..|++.+|+....|+.+|.+|+++|.+-.=..
T Consensus 57 ~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvsk 94 (107)
T COG4901 57 ERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSK 94 (107)
T ss_pred ceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeecc
Confidence 57999999999999999999999999999998865444
No 38
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=91.74 E-value=0.41 Score=43.52 Aligned_cols=55 Identities=16% Similarity=0.219 Sum_probs=49.5
Q ss_pred CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..+++|...++++.... +|.++..+|.+.+|.|+.-....|..|++.|++=+=..
T Consensus 191 ~~L~~~e~~il~~i~~~-GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 191 YDLNEDEKEILDLIRER-GGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred CCCCHHHHHHHHHHHHh-CCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEe
Confidence 45999999999988865 77899999999999999999999999999999877655
No 39
>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=91.32 E-value=1.1 Score=31.18 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=36.0
Q ss_pred hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
..|-.||..+.. ..+..|..+|++.++.+..-+...|+.|++.|++=.-
T Consensus 3 ~~q~~vL~~l~~-~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 3 RPQWQVLRALAH-SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHHHHHHT---TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHc-cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 345555554442 3689999999999999999999999999999999443
No 40
>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=91.06 E-value=0.92 Score=29.96 Aligned_cols=41 Identities=27% Similarity=0.380 Sum_probs=35.0
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
..|+.+.. .|..++.+|++.+|.+..-...+|..|.+.|++
T Consensus 5 ~~Il~~L~---~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 5 LRILKLLS---EGPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp HHHHHHHT---TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHH---hCCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 35566666 378999999999999999999999999999986
No 41
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.04 E-value=0.81 Score=39.26 Aligned_cols=45 Identities=9% Similarity=0.064 Sum_probs=39.7
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
....|+.+.- ..|.+|.++|+..+|++..-++..|..|.++|++-
T Consensus 23 ~~~~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 23 EGFEVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred cHhHHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 3566777666 35899999999999999999999999999999998
No 42
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=90.98 E-value=0.38 Score=37.99 Aligned_cols=35 Identities=26% Similarity=0.199 Sum_probs=32.7
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
..+||++.|++.++++..+|+.+|++|++.|++-.
T Consensus 57 ~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~ 91 (105)
T PF03297_consen 57 MKLITPSVLSERLKINGSLARKALRELESKGLIKP 91 (105)
T ss_dssp SSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEE
T ss_pred CcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEE
Confidence 57899999999999999999999999999998754
No 43
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=90.96 E-value=1.2 Score=30.43 Aligned_cols=43 Identities=19% Similarity=0.262 Sum_probs=37.8
Q ss_pred HHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 186 QQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 186 ~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
++++ ..|.+|+.++.+.+|.|.--|...|+.+-+.|+.+++..
T Consensus 3 ~~~~--~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd 45 (50)
T PF09107_consen 3 ELLQ--KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGD 45 (50)
T ss_dssp HHHH--TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHh--cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCC
Confidence 4455 468999999999999999999999999999999999964
No 44
>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=90.93 E-value=1 Score=38.86 Aligned_cols=53 Identities=21% Similarity=0.172 Sum_probs=46.8
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.++..+..++.... ..|.+|..+|++.++.++.-+...|..|++.|++-++..
T Consensus 140 ~ls~~~~~IL~~l~--~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 140 GLSREELKVLEVLK--AEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred CCCHHHHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 46777788888887 347899999999999999999999999999999999863
No 45
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=90.82 E-value=0.35 Score=39.35 Aligned_cols=48 Identities=15% Similarity=0.204 Sum_probs=43.1
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
...|++++. ..|.+|..++...+|.+..-++.++.+|++.|-+..=..
T Consensus 14 k~rIvElVR--e~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~G~ 61 (127)
T PF06163_consen 14 KARIVELVR--EHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRHGR 61 (127)
T ss_pred HHHHHHHHH--HcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeCCC
Confidence 457899999 569999999999999999999999999999999998433
No 46
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=90.57 E-value=0.73 Score=35.30 Aligned_cols=44 Identities=18% Similarity=0.318 Sum_probs=39.1
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
...|+...+ ..|.+|..+|++.+|.++.-+...|..|+++|++.
T Consensus 5 D~~il~~L~--~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 5 DRKILEELQ--KDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHH--HhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 456777777 35789999999999999999999999999999987
No 47
>PRK10870 transcriptional repressor MprA; Provisional
Probab=90.53 E-value=1.4 Score=37.48 Aligned_cols=55 Identities=18% Similarity=0.152 Sum_probs=44.7
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++.-|-.+|........+.+|+.+|++.+++++.-+...++.|++.|++-+-..+
T Consensus 53 Lt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~ 107 (176)
T PRK10870 53 INETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESD 107 (176)
T ss_pred CCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence 5555666665554322578999999999999999999999999999999997665
No 48
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=90.51 E-value=0.57 Score=33.64 Aligned_cols=46 Identities=22% Similarity=0.223 Sum_probs=38.7
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
...+++++- ..+..|++.|..+|.+-..||...++.|+++|++=--
T Consensus 7 y~~a~~~V~--~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~ 52 (63)
T smart00843 7 YDEAVELVI--ETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPA 52 (63)
T ss_pred HHHHHHHHH--HhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCC
Confidence 345666666 3578999999999999999999999999999998543
No 49
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=90.50 E-value=0.8 Score=36.71 Aligned_cols=55 Identities=15% Similarity=0.156 Sum_probs=44.5
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
.|+.+.. ..|.+++.+|++.++.+..-+..+|..|.+.|++....+ +...||..+
T Consensus 20 ~IL~~L~--~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~--Gr~~~Y~l~ 74 (117)
T PRK10141 20 GIVLLLR--ESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQ--GKWVHYRLS 74 (117)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEE--cCEEEEEEC
Confidence 4555554 246799999999999999999999999999999999988 455555544
No 50
>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=90.40 E-value=1.2 Score=34.82 Aligned_cols=52 Identities=13% Similarity=0.106 Sum_probs=43.7
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
++.-|-.+|.... ..|.+|+.+|++.++++..-+...|+.|++.|++-+-..
T Consensus 26 lt~~q~~iL~~l~--~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~ 77 (118)
T TIGR02337 26 LTEQQWRILRILA--EQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKA 77 (118)
T ss_pred CCHHHHHHHHHHH--HcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccC
Confidence 5556767777666 357899999999999999999999999999999998543
No 51
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=90.37 E-value=0.6 Score=41.98 Aligned_cols=47 Identities=17% Similarity=0.222 Sum_probs=43.3
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
=|..|+++.+ ..|.+++++|++.|+.|.+=.+.=|..|++.|++-+=
T Consensus 6 R~~~Il~~l~--~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLK--EKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHH--HcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 3778999999 5699999999999999999999999999999999883
No 52
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=90.22 E-value=0.81 Score=29.43 Aligned_cols=35 Identities=14% Similarity=0.183 Sum_probs=32.2
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.+|..+|++.+|++..-+...|..|++.|++-.+.
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 48899999999999999999999999999997763
No 53
>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=90.21 E-value=1.1 Score=30.12 Aligned_cols=41 Identities=17% Similarity=0.234 Sum_probs=33.3
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEG 223 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G 223 (254)
..++.+... ..+++|..+|++.+|.|..-....|..|.+.|
T Consensus 3 ~~il~~L~~-~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLE-SKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHH-TTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHH-cCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 456665522 35679999999999999999999999999999
No 54
>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=89.98 E-value=1.1 Score=37.67 Aligned_cols=61 Identities=18% Similarity=0.187 Sum_probs=46.0
Q ss_pred hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE----EEeCCCCCcccceecc
Q psy6552 179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA----WIDTQSPQEHLYWFPS 241 (254)
Q Consensus 179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l----wvD~q~~~e~~yw~p~ 241 (254)
+++-.|+.+.- ..|.+|.++|+..+|++..-.+..|..|.+.|++ ..|+..+--+.||+.+
T Consensus 14 ~~~v~Vl~aL~--~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~ 78 (158)
T TIGR00373 14 EEVGLVLFSLG--IKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRIN 78 (158)
T ss_pred hhHHHHHHHHh--ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeC
Confidence 34566677555 3578999999999999999999999999999998 3555532234556544
No 55
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=89.64 E-value=0.57 Score=39.75 Aligned_cols=40 Identities=15% Similarity=0.302 Sum_probs=34.0
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
..+++ ...+.|+.+++.+|||+-++++.+|++|..+|.|-
T Consensus 116 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (166)
T PRK15466 116 ALLTS--VRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLR 155 (166)
T ss_pred HHHHH--HHccccHHHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence 34445 24579999999999999999999999999999874
No 56
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=89.40 E-value=13 Score=37.80 Aligned_cols=169 Identities=11% Similarity=0.122 Sum_probs=102.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhh-------hhhc-------CHHHHHHHHHHHHHcCCCcccCCCcccccc----ccchhH
Q psy6552 34 QLSQHLNTFRDKLESFASEYKN-------EIKK-------DAQFRRHFQEMCASIGVDPLASRKGFWSLL----GMGDFY 95 (254)
Q Consensus 34 ~L~~ql~~fk~~L~~FA~kh~~-------~I~~-------dp~fr~~f~~mc~~lGVdPl~s~kg~w~~l----g~gdfy 95 (254)
.++++.+...+.|+.|.++|.. ++++ .+-|..-...+|..=. +....++|+.- ..++-+
T Consensus 415 ~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~~~~~~~~~~~~~~l~~l~~~~~---i~~~~~~~~~~~~~~~~~~~~ 491 (614)
T PRK10512 415 VAARWQRKLLDTLATYHEQHRDEPGPGRERLRRMALPMEDEALVLLLIEKMRESGD---IHSHHGWLHLPDHKAGFSEEQ 491 (614)
T ss_pred HHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhhcccCCCHHHHHHHHHHHHhCCC---EEEeCCEEECCCCCCCCCHHH
Confidence 3455666667777788888743 2221 1112222233333211 22222344311 235667
Q ss_pred HHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCC
Q psy6552 96 YELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPG 175 (254)
Q Consensus 96 ~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~ 175 (254)
.++..+|.+.+.. .--.+.|++..+ .+.++++.+.+..|-..| .+++++ +..|+....
T Consensus 492 ~~~~~~l~~~~~~------~p~~~~~~~~~l-----------~~~~~~~~~~l~~l~~~g---~lv~l~-~~~~~~~~~- 549 (614)
T PRK10512 492 QALWQKAEPLFGD------EPWWVRDLAKET-----------GTDEQAMRLTLRQAAQQG---IITAIV-KDRYYRNDR- 549 (614)
T ss_pred HHHHHHHHHHHhc------CCCCHHHHHHHh-----------CCCHHHHHHHHHHHHHCC---CEEEec-CCEEECHHH-
Confidence 7777777775541 122344554432 356778888888887766 355666 444553332
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..--..+.++.+ ..|.+|+.++.+.+|.|.-.|...|+.+-+.|+.-++..
T Consensus 550 -~~~~~~~~~~~~~--~~~~~~~~~~r~~~g~sRK~~i~lLE~~D~~~~T~r~g~ 601 (614)
T PRK10512 550 -IVQFANMIRELDQ--ECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGN 601 (614)
T ss_pred -HHHHHHHHHHHHh--hCCcEeHHHHHHHhCccHHHHHHHHHHhccCCCEEEECC
Confidence 3333345566666 468999999999999999999999999999999999864
No 57
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.04 E-value=1.2 Score=40.29 Aligned_cols=47 Identities=19% Similarity=0.266 Sum_probs=41.0
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.||++.... .+.+|..+|++.+|+++.-+-..|..|++.|++-.|+.
T Consensus 29 ~IL~~~~~~-~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~ 75 (271)
T PRK10163 29 AILQYLEKS-GGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQ 75 (271)
T ss_pred HHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 557766543 56799999999999999999999999999999999865
No 58
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=89.04 E-value=1.9 Score=36.37 Aligned_cols=96 Identities=18% Similarity=0.321 Sum_probs=64.5
Q ss_pred eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhh-hh---CCCeEEEEeCCceEEEEccCC---------------CC
Q psy6552 117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLK-IF---GNGFSIIPIGQGQYLVQSIPG---------------EL 177 (254)
Q Consensus 117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~-~L---g~g~~l~~~~sg~~vv~s~p~---------------el 177 (254)
+++.++...+ . +++++.++++.|. .+ +.|++|+.++ |....++.|. .|
T Consensus 14 vs~~~La~~l-----------~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~-~~y~l~tk~~~~~~v~~~~~~~~~~~L 80 (159)
T PF04079_consen 14 VSIEELAEIL-----------G-SEDEVEEALEELQEEYNEEDRGLELVEVG-GGYRLQTKPEYAEYVEKLFKKPKPPKL 80 (159)
T ss_dssp B-HHHHHHHC-----------T--HHHHHHHHHHHHHHHHHCT-SEEEEEET-TEEEEEE-GGGHHHHHHHHCTCCCHHH
T ss_pred CCHHHHHHHh-----------C-CHHHHHHHHHHHHHHhccCCCCEEEEEEC-CEEEEEEhHHHHHHHHHHhccCccCCC
Confidence 6666666552 3 7899999999884 33 8999999999 8888888772 12
Q ss_pred ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
|.-...+|.++.- ..-||-.++.+--|.+ +..+|..|++.|++..=..
T Consensus 81 S~aalEtLAiIAY--~QPiTr~eIe~IRGv~---s~~~i~~L~e~glI~~~gr 128 (159)
T PF04079_consen 81 SQAALETLAIIAY--KQPITRAEIEEIRGVN---SDSVIKTLLERGLIEEVGR 128 (159)
T ss_dssp HHHHHHHHHHHHH--H-SEEHHHHHHHHTS-----HCHHHHHHHTTSEEEEEE
T ss_pred CHHHHHHHHHHHh--cCCcCHHHHHHHcCCC---hHHHHHHHHHCCCEEecCc
Confidence 2222223444443 2579999999999987 7788999999999987653
No 59
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=88.90 E-value=1 Score=40.44 Aligned_cols=45 Identities=18% Similarity=0.256 Sum_probs=41.4
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
+..|+++.. ..|.+++.+|++.+|+|..-++.-|..|++.|++-+
T Consensus 7 ~~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 7 HQILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 567888888 569999999999999999999999999999999976
No 60
>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=88.84 E-value=1 Score=31.08 Aligned_cols=36 Identities=14% Similarity=0.147 Sum_probs=34.1
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+.+|..+|++.+|.+..-+...|..|+++|++..+.
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 579999999999999999999999999999999875
No 61
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=88.83 E-value=0.97 Score=40.64 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=42.5
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
=+..|+++.. ..|.+++.+|++.|+.|..=++.-|..|+++|++-+=-
T Consensus 6 R~~~Il~~L~--~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 6 RQAAILEYLQ--KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHH--HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 3678899998 46899999999999999999999999999999886643
No 62
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=88.75 E-value=0.95 Score=35.53 Aligned_cols=61 Identities=15% Similarity=0.253 Sum_probs=43.9
Q ss_pred ChhHHHHHHHhhccCCCcccHHHHHHhc----CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 178 SLDHSLVLQQVASKNEAHISVSVLNNEL----NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 178 s~D~~~il~l~~~~~~g~vt~~~l~~~l----~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
++-+..|+++.=.. |.+|+.++.+.+ +|++.=..+.|..|++.|++-++.. +...+|.|..
T Consensus 2 s~~E~~IM~~lW~~--~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~--gr~~~Y~p~i 66 (115)
T PF03965_consen 2 SDLELEIMEILWES--GEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI--GRAYVYSPLI 66 (115)
T ss_dssp -HHHHHHHHHHHHH--SSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE--TTCEEEEESS
T ss_pred CHHHHHHHHHHHhC--CCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec--CCceEEEeCC
Confidence 33456677777643 559999888755 6889999999999999999999976 3455566543
No 63
>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=88.65 E-value=1.5 Score=30.30 Aligned_cols=43 Identities=19% Similarity=0.152 Sum_probs=35.3
Q ss_pred CChhHHHHHHHhhccCCCc------ccHHHHHHhcCCCHHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAH------ISVSVLNNELNWSTERAQHALDFMVQ 221 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~------vt~~~l~~~l~ws~~ra~~~L~~l~~ 221 (254)
|++.|..+|..|=. .|| +|..+|++.+|+|+.=+.+.|..+++
T Consensus 1 LT~~Q~e~L~~A~~--~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 1 LTDRQREILKAAYE--LGYFDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHHHHHH--cCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 35567888888873 454 89999999999999999999988765
No 64
>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=88.59 E-value=1.6 Score=34.65 Aligned_cols=45 Identities=16% Similarity=0.131 Sum_probs=36.8
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+.++...+.+.+|..+|++.++.++......|..|.+.|++....
T Consensus 15 ~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~ 59 (132)
T TIGR00738 15 LDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVR 59 (132)
T ss_pred HHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecc
Confidence 344442224589999999999999999999999999999988753
No 65
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=88.57 E-value=1.4 Score=29.33 Aligned_cols=37 Identities=22% Similarity=0.187 Sum_probs=32.4
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+..+ |..+|++.+|+|..-+..+|..|+++|++-+..
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3456 899999999999999999999999999976543
No 66
>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=88.37 E-value=2.2 Score=31.46 Aligned_cols=54 Identities=13% Similarity=0.099 Sum_probs=39.1
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p 240 (254)
+.++...+.+.+|..+|++.++.++......|..|.+.|++=--.. ..|-|+..
T Consensus 15 ~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G--~~GGy~L~ 68 (83)
T PF02082_consen 15 LYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRG--RGGGYRLA 68 (83)
T ss_dssp HHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETS--TTSEEEES
T ss_pred HHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCC--CCCceeec
Confidence 3445433233599999999999999999999999999999644333 35677663
No 67
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=88.08 E-value=2.3 Score=36.72 Aligned_cols=54 Identities=13% Similarity=0.089 Sum_probs=45.8
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.++.-|-.||..+. ..+++|..+|++.++.++.-+...|+.|++.|++-+-..+
T Consensus 42 gLt~~q~~iL~~L~--~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~ 95 (185)
T PRK13777 42 DLNINEHHILWIAY--HLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE 95 (185)
T ss_pred CCCHHHHHHHHHHH--hCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC
Confidence 36767778887776 3578999999999999999999999999999999986554
No 68
>PHA00738 putative HTH transcription regulator
Probab=88.00 E-value=1.8 Score=34.37 Aligned_cols=55 Identities=20% Similarity=0.258 Sum_probs=45.8
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
.|+++.. .++..++.+|++.++.+......+|..|.+.|++-.... +...||..+
T Consensus 16 ~IL~lL~--~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~--Gr~vyY~Ln 70 (108)
T PHA00738 16 KILELIA--ENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKE--GRTLYAKIR 70 (108)
T ss_pred HHHHHHH--HcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEE--CCEEEEEEC
Confidence 4577665 345699999999999999999999999999999999988 566666544
No 69
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=87.96 E-value=1.5 Score=39.14 Aligned_cols=47 Identities=21% Similarity=0.325 Sum_probs=40.4
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.||++.... .+.++..+|++.+|.++.-+...|..|++.|++..|..
T Consensus 8 ~iL~~l~~~-~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~ 54 (246)
T COG1414 8 AILDLLAEG-PGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPE 54 (246)
T ss_pred HHHHHHHhC-CCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 466666543 44589999999999999999999999999999999975
No 70
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=87.67 E-value=1.8 Score=35.15 Aligned_cols=45 Identities=9% Similarity=0.141 Sum_probs=38.8
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.|+.+.. ..|++++++|++.+++++.-+...|..|++.|++..+.
T Consensus 12 ~I~~l~~--~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 12 QIYLLIE--EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHh--cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 4455666 46899999999999999999999999999999998653
No 71
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=87.57 E-value=1.3 Score=39.73 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=42.1
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
-+..|+++.. ..|.+|+.+|++.|+.|.+=++.-|..|+++|++-+=
T Consensus 6 R~~~Il~~l~--~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 6 RHDAIIELVK--QQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHH--HcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3678899988 4689999999999999999999999999999999763
No 72
>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=87.40 E-value=1.7 Score=34.75 Aligned_cols=53 Identities=13% Similarity=0.219 Sum_probs=48.1
Q ss_pred CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 175 GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 175 ~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
..++.++..|+++|. . ..|+.|++..++.+...++-.+-+|.+.|++-+-...
T Consensus 39 ~~l~pE~~~Il~lC~--~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~~p~ 91 (114)
T PF05331_consen 39 AGLGPEHRAILELCR--R--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVRAPA 91 (114)
T ss_pred CCCCHHHHHHHHHHC--C--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEeCCC
Confidence 457888999999999 2 8999999999999999999999999999999997654
No 73
>PRK11569 transcriptional repressor IclR; Provisional
Probab=87.25 E-value=1.6 Score=39.45 Aligned_cols=47 Identities=15% Similarity=0.264 Sum_probs=40.7
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.||++.... .+.+|.++|++.+|.++.-+-..|..|++.|++-.|..
T Consensus 32 ~IL~~l~~~-~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~ 78 (274)
T PRK11569 32 KLLEWIAES-NGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGE 78 (274)
T ss_pred HHHHHHHhC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 456666543 56799999999999999999999999999999998865
No 74
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=86.83 E-value=1.7 Score=35.20 Aligned_cols=49 Identities=18% Similarity=0.161 Sum_probs=43.2
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
+++-...+|.+.+ ..+..+..+|++.+|.|+.-+...++.|+++|++-.
T Consensus 6 lD~~D~~IL~~L~--~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 6 LDDIDRRILRLLQ--EDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred ccHHHHHHHHHHH--HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceee
Confidence 6666778999999 457799999999999999999999999999998644
No 75
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=86.70 E-value=2 Score=38.28 Aligned_cols=46 Identities=22% Similarity=0.267 Sum_probs=39.9
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.||++... .+.+|.++|++.+|.++.-+-..|..|++.|++-.|..
T Consensus 18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~ 63 (257)
T PRK15090 18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE 63 (257)
T ss_pred HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 55776653 35699999999999999999999999999999999854
No 76
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=86.60 E-value=1.7 Score=31.80 Aligned_cols=41 Identities=10% Similarity=0.088 Sum_probs=32.4
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
..||+.+. .|..+.++|+...|.+..++...|+.|++.|++
T Consensus 9 ~~IL~~l~---~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 9 FDILKILS---KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp HHHHHHH----TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHH---cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCe
Confidence 45677776 478999999999999999999999999999999
No 77
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=86.55 E-value=3.6 Score=35.78 Aligned_cols=45 Identities=20% Similarity=0.143 Sum_probs=39.0
Q ss_pred CCChhHHHHHHHhhccCCCc------ccHHHHHHhcCCCHHHHHHHHHHHHHc
Q psy6552 176 ELSLDHSLVLQQVASKNEAH------ISVSVLNNELNWSTERAQHALDFMVQE 222 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~------vt~~~l~~~l~ws~~ra~~~L~~l~~~ 222 (254)
+|++=|..+|..|= ..|| +|..+||+.+|+|+.=+.++|+.+++.
T Consensus 155 ~LTdrQ~~vL~~A~--~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAY--KMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHH--HcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 58877999999998 3465 999999999999999999999988753
No 78
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=86.35 E-value=2.1 Score=37.98 Aligned_cols=122 Identities=16% Similarity=0.181 Sum_probs=75.7
Q ss_pred HHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChh-
Q psy6552 102 IVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD- 180 (254)
Q Consensus 102 ive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D- 180 (254)
+++++.++.+..- +.+....|.+.|-...-++.+|.+.|=.....-.+ .. -....|+.++.-
T Consensus 97 v~DYLiKPf~~eR----l~~aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k-~~------------~~~~LPkGi~~~T 159 (224)
T COG4565 97 VVDYLIKPFTFER----LQQALTRYRQKRHALESHQQLSQKELDQLFNIQSK-EQ------------PPDDLPKGLDELT 159 (224)
T ss_pred chhheecceeHHH----HHHHHHHHHHHHHHHhhhcccCHHHHHHHHhcccc-cc------------CcccCCCCcCHHH
Confidence 4555555443221 55666666666633221256787766554443222 11 112345545422
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC----Ccccceecc
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP----QEHLYWFPS 241 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~----~e~~yw~p~ 241 (254)
-..|.+..+. ..-..|++++++.+|.|..-|+..|+.|+..|.+-.+-+-+ .+..||.+.
T Consensus 160 l~~i~~~~~~-~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~yG~vGRP~r~Y~~~~ 223 (224)
T COG4565 160 LQKVREALKE-PDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIHYGKVGRPERRYRLKA 223 (224)
T ss_pred HHHHHHHHhC-cCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEeeccccCCcceeeeccC
Confidence 1345555553 24679999999999999999999999999999999997543 457888764
No 79
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=85.78 E-value=3.3 Score=31.30 Aligned_cols=53 Identities=17% Similarity=0.133 Sum_probs=43.5
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++.-|-.++..+.. .+..+..+|++.+++++.-....|+.|++.|++.+-..+
T Consensus 20 lt~~q~~~L~~l~~--~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~ 72 (126)
T COG1846 20 LTPPQYQVLLALYE--AGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDP 72 (126)
T ss_pred CCHHHHHHHHHHHH--hCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCc
Confidence 55567777766663 355555999999999999999999999999999998775
No 80
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=85.52 E-value=2.1 Score=29.94 Aligned_cols=38 Identities=18% Similarity=0.108 Sum_probs=32.6
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+-.+ |..+|++.+|.|..-++++|..|.++|++-+-..
T Consensus 21 g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 21 GDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp TSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 3468 9999999999999999999999999999988754
No 81
>PRK09954 putative kinase; Provisional
Probab=85.41 E-value=1.8 Score=40.38 Aligned_cols=43 Identities=14% Similarity=0.170 Sum_probs=38.5
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
..+||++.+ ..+++|..+|++.+|+|..-+...|..|+++|++
T Consensus 5 ~~~il~~l~--~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 5 EKEILAILR--RNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred HHHHHHHHH--HCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 456888888 4589999999999999999999999999999875
No 82
>PRK00215 LexA repressor; Validated
Probab=84.98 E-value=4.8 Score=34.54 Aligned_cols=55 Identities=15% Similarity=0.188 Sum_probs=44.0
Q ss_pred CChhHHHHHHHhhc---cCCCcccHHHHHHhcCC-CHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVAS---KNEAHISVSVLNNELNW-STERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~---~~~g~vt~~~l~~~l~w-s~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++.-|..+|+.+.. ......|..+|++.+|+ ++.-+...|..|++.|++-++...
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 34567778776542 11345899999999999 999999999999999999988764
No 83
>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=84.93 E-value=1.7 Score=29.63 Aligned_cols=32 Identities=28% Similarity=0.167 Sum_probs=29.1
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
.|..+|++.+++|..-+..+|..|.+.|++=.
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~ 57 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVER 57 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 56999999999999999999999999998643
No 84
>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=84.89 E-value=3.5 Score=35.56 Aligned_cols=46 Identities=15% Similarity=0.203 Sum_probs=39.5
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
..||.+... .|.+|+.+|++.+|+++.-+...|+.|++.|++-+..
T Consensus 4 ~~IL~~L~~--~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 4 EDILSYLLK--QGQATAAALAEALAISPQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEee
Confidence 456666652 4669999999999999999999999999999998773
No 85
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=84.66 E-value=11 Score=32.69 Aligned_cols=96 Identities=25% Similarity=0.273 Sum_probs=68.4
Q ss_pred eeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhh----CCCeEEEEeCCceEEEEccCC--------------CCC
Q psy6552 117 ILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIF----GNGFSIIPIGQGQYLVQSIPG--------------ELS 178 (254)
Q Consensus 117 i~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~L----g~g~~l~~~~sg~~vv~s~p~--------------els 178 (254)
+++.++-..++. + .++++..+++.|+.- +.|++|+.++ |...+++.|. .+|
T Consensus 18 ls~~~La~il~~--------~--~~~~~~~~l~~l~~~~~~~~~gl~l~~~~-~~y~l~tk~e~~~~i~~~~~~~~~~LS 86 (186)
T TIGR00281 18 VTLAELVRILGK--------E--KAEKLNAIMELLEDYLSRDTAGIEIIKFG-QSYSLVTKPAFADYIHRFLPAKLKNLN 86 (186)
T ss_pred CCHHHHHHHhCC--------C--chHHHHHHHHHHHHHHhcCCCCEEEEEEC-CEEEEEEhHHHHHHHHHHhccccccCC
Confidence 677777766532 1 145677777777554 5689999999 8777777661 144
Q ss_pred hhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 179 LDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 179 ~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.-...+|.++.- ..-||-.++.+--|.+ +..+|..|++.|++-+-
T Consensus 87 ~aaLEtLAIIAY--~QPITr~eIe~IRGv~---s~~~l~~L~ergLI~~~ 131 (186)
T TIGR00281 87 SASLEVLAIIAY--KQPITRARINEIRGVK---SYQIVDDLVEKGLVVEL 131 (186)
T ss_pred HHHHHHHHHHHH--cCCcCHHHHHHHcCCC---HHHHHHHHHHCCCeEec
Confidence 334444555553 3579999999999988 57899999999999775
No 86
>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=84.55 E-value=2.3 Score=33.85 Aligned_cols=42 Identities=7% Similarity=0.058 Sum_probs=35.6
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
..++.. ..+.+|..+|++.+|.+...+..+|..|.+.|++-.
T Consensus 16 ~~la~~-~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~ 57 (130)
T TIGR02944 16 TTLAQN-DSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTS 57 (130)
T ss_pred HHHHhC-CCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEe
Confidence 344443 256899999999999999999999999999999855
No 87
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=84.43 E-value=3.2 Score=35.24 Aligned_cols=48 Identities=17% Similarity=0.235 Sum_probs=42.7
Q ss_pred HHHHHHHhhccCCCcc-cHHHHHHhc--CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 181 HSLVLQQVASKNEAHI-SVSVLNNEL--NWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 181 ~~~il~l~~~~~~g~v-t~~~l~~~l--~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..|.+++. -.++- ++..|++.+ ++|.+.+++.|+.|++-|++=.|..
T Consensus 26 ~~~ir~l~~--l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 26 HPAIRELLP--LMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HHHHHHHhh--cCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 567888888 45666 999999999 9999999999999999999999965
No 88
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=84.15 E-value=2.4 Score=38.43 Aligned_cols=48 Identities=19% Similarity=0.261 Sum_probs=42.8
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
-+..|+++.+ ..|.+|+.+|++.||.|..=++.-|..|++.|++-+-.
T Consensus 18 R~~~Il~~L~--~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 18 RREQIIQRLR--QQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHH--HcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 4678888888 45889999999999999999999999999999998765
No 89
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=84.09 E-value=5.8 Score=36.57 Aligned_cols=74 Identities=15% Similarity=0.139 Sum_probs=53.4
Q ss_pred CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHH-HhhccCCCcccHHHHHHhcCCCHHHHHHH
Q psy6552 137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQ-QVASKNEAHISVSVLNNELNWSTERAQHA 215 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~-l~~~~~~g~vt~~~l~~~l~ws~~ra~~~ 215 (254)
..|+.+++..+.+.++. .+ ..++..+...+. ++..-.+|.++.+.++..+|++..-+.++
T Consensus 236 ~~I~~~~v~~~l~~~~~---~~----------------~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~ 296 (328)
T PRK00080 236 GVITKEIADKALDMLGV---DE----------------LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDV 296 (328)
T ss_pred CCCCHHHHHHHHHHhCC---Cc----------------CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHH
Confidence 46888888888865421 00 124444445554 55532267899999999999999999999
Q ss_pred HH-HHHHcCcEEEeC
Q psy6552 216 LD-FMVQEGYAWIDT 229 (254)
Q Consensus 216 L~-~l~~~G~lwvD~ 229 (254)
++ .|++.|++....
T Consensus 297 ~e~~Li~~~li~~~~ 311 (328)
T PRK00080 297 YEPYLIQQGFIQRTP 311 (328)
T ss_pred hhHHHHHcCCcccCC
Confidence 99 899999997443
No 90
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=84.01 E-value=1.3 Score=37.96 Aligned_cols=46 Identities=7% Similarity=-0.046 Sum_probs=41.2
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
-+..|++++. ..|.+++.+|++.+|.|..-++.=|..|+++|++-+
T Consensus 8 R~~~Il~~l~--~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r 53 (185)
T PRK04424 8 RQKALQELIE--ENPFITDEELAEKFGVSIQTIRLDRMELGIPELRER 53 (185)
T ss_pred HHHHHHHHHH--HCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHH
Confidence 4678899998 569999999999999999999999999999998744
No 91
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=84.01 E-value=3.1 Score=35.51 Aligned_cols=55 Identities=16% Similarity=0.228 Sum_probs=45.0
Q ss_pred CChhHHHHHHHhhcc--CCCc-ccHHHHHHhcCCC-HHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVASK--NEAH-ISVSVLNNELNWS-TERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~~--~~g~-vt~~~l~~~l~ws-~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++.-|..||+.+.+. ..|+ .|..+|++.+|.+ +.-+...|..|++.|++-.++..
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 666788898887632 1233 8899999999998 99999999999999999987653
No 92
>PRK11050 manganese transport regulator MntR; Provisional
Probab=83.72 E-value=3.5 Score=34.13 Aligned_cols=44 Identities=11% Similarity=0.110 Sum_probs=37.5
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+.+.. .+|.+++.+|++.+++++.-....|..|++.|++.++..
T Consensus 43 ~~~l~--~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~ 86 (152)
T PRK11050 43 ADLIA--EVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPY 86 (152)
T ss_pred HHHHH--hcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34455 357899999999999999999999999999999887643
No 93
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=83.67 E-value=3.3 Score=37.13 Aligned_cols=47 Identities=17% Similarity=0.301 Sum_probs=40.1
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.||+..... .+.+|..+|++.+|.++.-+-..|..|++.|++-+|..
T Consensus 15 ~iL~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~ 61 (263)
T PRK09834 15 MVLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSAS 61 (263)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 456665432 45699999999999999999999999999999999965
No 94
>PF13730 HTH_36: Helix-turn-helix domain
Probab=82.49 E-value=5.2 Score=26.75 Aligned_cols=32 Identities=22% Similarity=0.259 Sum_probs=29.1
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
-|-|.+.|++.+|.+..-...+|..|++.|++
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 35688999999999999999999999999975
No 95
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=82.23 E-value=7.6 Score=27.37 Aligned_cols=42 Identities=17% Similarity=0.189 Sum_probs=34.7
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
++++.. .+..|..+|++.+|.|..-+...|..|.+.|+.-..
T Consensus 5 il~~L~---~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 5 LLALLA---DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHH---cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 444444 356889999999999999999999999999995544
No 96
>KOG1767|consensus
Probab=82.21 E-value=1.9 Score=33.96 Aligned_cols=46 Identities=22% Similarity=0.201 Sum_probs=36.9
Q ss_pred hHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 180 DHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 180 D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
|+.+.-.+..+- ...+||++.|.+.+.+.-.+|+.+|.+|..+|++
T Consensus 44 dqatydkl~kevp~~k~it~svl~dRlkIngsLAr~alr~L~~kG~I 90 (110)
T KOG1767|consen 44 DQATYDKLLKEVPKYKLITPSVLSDRLKINGSLARAALRELSNKGVI 90 (110)
T ss_pred cHHHHHHHHHhcccceeecHHHhhhhhhhchHHHHHHHHHHHhcchH
Confidence 555554454421 1458999999999999999999999999999986
No 97
>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=81.98 E-value=3 Score=37.68 Aligned_cols=37 Identities=14% Similarity=0.112 Sum_probs=34.9
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.|.++..+|++.+|.|+.-+.+++..|++.|++-.-.
T Consensus 196 egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 196 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4899999999999999999999999999999998776
No 98
>PF04558 tRNA_synt_1c_R1: Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1 ; InterPro: IPR007639 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This is a domain found N-terminal to the catalytic domain of glutaminyl-tRNA synthetase (6.1.1.18 from EC) in eukaryotes but not in Escherichia coli. This domain is thought to bind RNA in a non-specific manner, enhancing interactions between the tRNA and enzyme, but is not essential for enzyme function [].; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3TL4_X.
Probab=81.55 E-value=7.5 Score=32.94 Aligned_cols=98 Identities=20% Similarity=0.240 Sum_probs=54.3
Q ss_pred HHHHhhhhhhcCHHHHHHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHH
Q psy6552 49 FASEYKNEIKKDAQFRRHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLV 127 (254)
Q Consensus 49 FA~kh~~~I~~dp~fr~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~n 127 (254)
|..+=..++-+||.+...|......-|++ |...+ .|..-|.||.++-.-+... .+-+...+.
T Consensus 15 L~e~kAket~KN~kls~~L~~iI~ea~~~~~~dk~--------~g~LLy~lAtk~k~~~~~~---------r~~iv~~I~ 77 (164)
T PF04558_consen 15 LSEKKAKETLKNKKLSASLKAIINEAGVDSGCDKK--------QGNLLYQLATKLKPQALPH---------RPFIVKYIV 77 (164)
T ss_dssp --HHHHHHHTTSHHHHHHHHHHHHTS-TT----HH--------HHHHHHHHHHHHTT---TT---------HHHHHHHHH
T ss_pred CChhhHHHHHhCHHHHHHHHHHHHHhcccCCCCHH--------HHHHHHHHHHhcCCCcchh---------HHHHHHHHH
Confidence 55566778889999999999999999988 66543 3677777877554433332 333333333
Q ss_pred HhcCCCCCCCCCCHHHHHHHHHHhhhhCC-CeEEEEeC--CceEEE
Q psy6552 128 KSRGKSLQHQDITNEDLLAAAKKLKIFGN-GFSIIPIG--QGQYLV 170 (254)
Q Consensus 128 r~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~-g~~l~~~~--sg~~vv 170 (254)
.. .+-|+..+-.|++.++.-+. ++..-.|+ .|+=|+
T Consensus 78 ~g-------klkt~~Ql~AA~~Yl~~~~~~~~d~~~Fe~~cGVGV~ 116 (164)
T PF04558_consen 78 DG-------KLKTNLQLDAALKYLKSNPSEPIDVAEFEKACGVGVV 116 (164)
T ss_dssp TT-------S--SHHHHHHHHHHHHHHGG-G--HHHHHHTTTTT--
T ss_pred hC-------CCCCHHHHHHHHHHHHHCCCCCCCHHHHHHHcCCCeE
Confidence 32 24466666666666666654 56655554 355444
No 99
>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=81.52 E-value=3.7 Score=33.12 Aligned_cols=44 Identities=7% Similarity=0.101 Sum_probs=36.8
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
++.+|.....+.+|..+|++.+++++.-....|..|.+.|++-.
T Consensus 14 l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 14 MLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 35666543345799999999999999999999999999998854
No 100
>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=81.43 E-value=3.7 Score=36.31 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=39.0
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.||++.... .+.+|..+|++.+|.++.-+-..|..|++.|++-.|
T Consensus 13 ~IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 13 AVIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 567766543 567999999999999999999999999999999775
No 101
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=81.09 E-value=4 Score=36.36 Aligned_cols=46 Identities=17% Similarity=0.277 Sum_probs=41.4
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
-+..|+++.. ..+++|+.+|++.|++|..-++.-|..|+..|++-+
T Consensus 5 R~~~Il~~l~--~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 5 RQQAIVDLLL--NHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHHH--HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 3667888888 468999999999999999999999999999999877
No 102
>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=80.94 E-value=13 Score=33.97 Aligned_cols=123 Identities=14% Similarity=0.244 Sum_probs=81.6
Q ss_pred HHHHHHHHcCCCcccCCCccccccccchhH--HHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHH
Q psy6552 66 HFQEMCASIGVDPLASRKGFWSLLGMGDFY--YELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNED 143 (254)
Q Consensus 66 ~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy--~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~D 143 (254)
-.+.++..=.+|-+.+..| ..|. .+|..+|.+-|.. +||=+++.||-..+ .|..+.
T Consensus 29 iv~kL~~~~~ldli~T~dG-------keyiT~~~L~~EI~~el~~----~gGRv~~~dL~~~L-----------nVd~~~ 86 (272)
T PF09743_consen 29 IVNKLIEKKLLDLIHTTDG-------KEYITPEQLEKEIKDELYV----HGGRVNLVDLAQAL-----------NVDLDH 86 (272)
T ss_pred HHHHHHHcCCeeEEEECCC-------CEEECHHHHHHHHHHHHHH----cCCceEHHHHHHhc-----------CcCHHH
Confidence 4456666667785543321 2343 4688888876653 79999999998664 488999
Q ss_pred HHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHH-HHHHH
Q psy6552 144 LLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQ-HALDF 218 (254)
Q Consensus 144 i~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~-~~L~~ 218 (254)
|.+.++.+-+=..++.+ ++ |. ++.... ++.--..+-+..+ +.|.+|.++|+..++.+.+-.+ ..+..
T Consensus 87 ie~~~~~i~~~~~~~~l--~~-ge-lit~~Y--ld~l~~Eine~Lq--e~G~vsi~eLa~~~~Lp~efl~~~li~~ 154 (272)
T PF09743_consen 87 IERRAQEIVKSDKSLQL--VQ-GE-LITDSY--LDSLAEEINEKLQ--ESGQVSISELAKQYDLPSEFLKEELISK 154 (272)
T ss_pred HHHHHHHHHhCCCcEEE--EC-CE-EccHHH--HHHHHHHHHHHHH--HcCeEeHHHHHHhcCCcHHHHHHHHhhh
Confidence 99999998776555543 33 43 332222 2222234445555 4699999999999999999988 44433
No 103
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=80.91 E-value=6.1 Score=32.05 Aligned_cols=45 Identities=11% Similarity=0.071 Sum_probs=38.3
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
+..+|..+|++.+|.|+.-.+++|..|.++|++..-... .|-|..
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~--~GG~~l 67 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGK--NGGIRL 67 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCC--CCCeee
Confidence 447899999999999999999999999999999988764 344444
No 104
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=80.82 E-value=3.8 Score=30.38 Aligned_cols=46 Identities=17% Similarity=0.292 Sum_probs=37.0
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
|+.+... .+.++..+|++.+|.+..-...+|..|+++|++=++...
T Consensus 5 Il~~L~~--~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~ 50 (80)
T PF13601_consen 5 ILALLYA--NEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEF 50 (80)
T ss_dssp HHHHHHH--HSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-
T ss_pred HHHHHhh--cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEec
Confidence 4444442 468999999999999999999999999999999999875
No 105
>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=80.63 E-value=3.6 Score=25.51 Aligned_cols=30 Identities=13% Similarity=0.234 Sum_probs=25.6
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
+|..+|++.+|.+++-+...|..+.++|++
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 678999999999999999999999999985
No 106
>PRK10263 DNA translocase FtsK; Provisional
Probab=80.45 E-value=4.5 Score=44.45 Aligned_cols=88 Identities=16% Similarity=0.107 Sum_probs=60.2
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEc-----cCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHH
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQS-----IPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERA 212 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s-----~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra 212 (254)
-||.+||.+-++.++.-|.+--+..+-.+..--.+ ...+.+.-...+++++- ..+.+|++.|.++|.+-..||
T Consensus 1247 fvsD~Ei~~vv~~~k~~~~p~y~~~~~~~~~~~~~~~~~~~~~~~D~l~~~a~~~v~--~~~~~S~S~lQR~~~iGynRA 1324 (1355)
T PRK10263 1247 FVRDQEVHAVVQDWKARGRPQYVDGITSDSESEGGAGGFDGAEELDPLFDQAVQFVT--EKRKASISGVQRQFRIGYNRA 1324 (1355)
T ss_pred cCCHHHHHHHHHHHHhcCCCchhhhhcccccccccccCcCCCccccHHHHHHHHHHH--hcCccCHHHHHHHhhcChHHH
Confidence 69999999999999988755322222100000000 00111112356677777 468899999999999999999
Q ss_pred HHHHHHHHHcCcEEE
Q psy6552 213 QHALDFMVQEGYAWI 227 (254)
Q Consensus 213 ~~~L~~l~~~G~lwv 227 (254)
...++.|+++|++==
T Consensus 1325 ariid~lE~~Giv~p 1339 (1355)
T PRK10263 1325 ARIIEQMEAQGIVSE 1339 (1355)
T ss_pred HHHHHHHHHCCcCCC
Confidence 999999999999854
No 107
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=80.23 E-value=3.3 Score=30.90 Aligned_cols=43 Identities=28% Similarity=0.363 Sum_probs=28.8
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+|.+.. .+.-||++.|+..+||+.+..+.+|..+- -.-.|++
T Consensus 28 ~LLr~LA--~G~PVt~~~LA~a~g~~~e~v~~~L~~~p---~tEyD~~ 70 (77)
T PF12324_consen 28 PLLRLLA--KGQPVTVEQLAAALGWPVEEVRAALAAMP---DTEYDDQ 70 (77)
T ss_dssp HHHHHHT--TTS-B-HHHHHHHHT--HHHHHHHHHH-T---TSEEETT
T ss_pred HHHHHHH--cCCCcCHHHHHHHHCCCHHHHHHHHHhCC---CceEcCC
Confidence 3455555 46789999999999999999999998863 2445555
No 108
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=79.92 E-value=18 Score=29.16 Aligned_cols=78 Identities=14% Similarity=0.124 Sum_probs=56.7
Q ss_pred HHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCC-eEEEEeCCceEEEEccCC
Q psy6552 97 ELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNG-FSIIPIGQGQYLVQSIPG 175 (254)
Q Consensus 97 eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g-~~l~~~~sg~~vv~s~p~ 175 (254)
+|+..|--++.+ .+.++||+.++...+-..- . .-+|++|+..-+..|..+=+. +.+.+++ |..+|....
T Consensus 45 ~la~~v~~if~s---~~k~~l~~e~l~~kl~~S~---~--~~~s~~E~E~~l~LL~el~P~Wis~~~~~-~~~~lk~~k- 114 (126)
T cd08767 45 ELARILRNIFVS---EKKTVLPLEELVYKLQASY---P--SILSRGEVEEHLRLLAELAPDWISEKSLR-KGDYLKIDK- 114 (126)
T ss_pred HHHHHHHHHHHh---cccccccHHHHHHHHHHhC---C--CCCCHHHHHHHHHHHHHhChHHheeeeeC-CceEEEECc-
Confidence 455555555555 7789999999998888743 1 579999999999999988644 6777777 566666553
Q ss_pred CCChhHHHHHH
Q psy6552 176 ELSLDHSLVLQ 186 (254)
Q Consensus 176 els~D~~~il~ 186 (254)
+.|...|.+
T Consensus 115 --~~~~~~V~~ 123 (126)
T cd08767 115 --KVDLEKVRK 123 (126)
T ss_pred --cccHHHHHH
Confidence 256666643
No 109
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=79.77 E-value=5.1 Score=29.96 Aligned_cols=49 Identities=22% Similarity=0.175 Sum_probs=38.4
Q ss_pred ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+.+...++.++. ..|+|=.+|++.+|+|..-...+++.|.+.|+ =||..
T Consensus 5 ~~~~~~ll~~~~---~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~-~I~s~ 53 (79)
T COG1654 5 SQMLLLLLLLLT---GNFVSGEKLAEELGISRTAVWKHIQQLREEGV-DIESV 53 (79)
T ss_pred HHHHHHHHHHcC---CCcccHHHHHHHHCccHHHHHHHHHHHHHhCC-ceEec
Confidence 334444444444 56999999999999999999999999999996 35554
No 110
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=79.44 E-value=2.9 Score=29.59 Aligned_cols=33 Identities=12% Similarity=0.120 Sum_probs=28.2
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
|-++++.+++..|++......+|..|+..|++=
T Consensus 3 g~lvas~iAd~~GiTRSvIVNALRKleSaGvIe 35 (61)
T PF08222_consen 3 GRLVASKIADRVGITRSVIVNALRKLESAGVIE 35 (61)
T ss_dssp EEE-HHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred ceehHHHHHHHhCccHHHHHHHHHHHHhcCcee
Confidence 679999999999999999999999999999875
No 111
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=79.11 E-value=7.7 Score=29.90 Aligned_cols=48 Identities=13% Similarity=0.218 Sum_probs=39.2
Q ss_pred HHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..|+++.... .+.+|+.+|.+.+ +++..=.-..|+.|++.|++=.=..
T Consensus 4 ~~Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~ 56 (116)
T cd07153 4 LAILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIEL 56 (116)
T ss_pred HHHHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEe
Confidence 3567776644 6789999999887 7899989999999999999987554
No 112
>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=78.92 E-value=5.1 Score=26.11 Aligned_cols=38 Identities=16% Similarity=0.216 Sum_probs=29.6
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
...|+.+.+. .|..+..+|++.+|+|..-+...+..|+
T Consensus 5 D~~Il~~Lq~--d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 5 DRKILRLLQE--DGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHH---TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHH--cCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 4567888873 5899999999999999999999888764
No 113
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=78.44 E-value=7.7 Score=34.40 Aligned_cols=38 Identities=26% Similarity=0.240 Sum_probs=35.3
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
...+|..+|++.++.|+.-+...|..|++.|++-+...
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~ 56 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIV 56 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEc
Confidence 45799999999999999999999999999999988765
No 114
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=78.32 E-value=5.3 Score=33.71 Aligned_cols=43 Identities=7% Similarity=0.103 Sum_probs=36.6
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
+.+|.....+.+|.++|++.++.++.-....|..|.+.|++-.
T Consensus 15 ~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 15 LDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred HHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 4555432346899999999999999999999999999999986
No 115
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=78.25 E-value=8.2 Score=33.41 Aligned_cols=46 Identities=17% Similarity=0.354 Sum_probs=37.8
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
++++|+.+|+..+|+++.-+-.+|-.|.+.|+++.-+.. +-.||-.
T Consensus 25 ~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~---pp~w~~~ 70 (183)
T PHA03103 25 GEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSN---PPKWFKT 70 (183)
T ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCC---CCCcccc
Confidence 689999999999999999999999999999999755442 3445543
No 116
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=77.88 E-value=3.5 Score=35.65 Aligned_cols=38 Identities=18% Similarity=0.121 Sum_probs=34.2
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..++..+|++.||.|..-.+++|..|+.+|++.+-..
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~ 69 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPA 69 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCC
Confidence 45688999999999999999999999999999988543
No 117
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=77.83 E-value=5.3 Score=33.43 Aligned_cols=51 Identities=10% Similarity=0.046 Sum_probs=42.0
Q ss_pred ChhHHHH-HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 178 SLDHSLV-LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 178 s~D~~~i-l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..|.-.+ ..+.+ ..|++...+|++.++.++.-+.+.|..|.+.|++=.+..
T Consensus 8 ~edYL~~Iy~l~~--~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y 59 (154)
T COG1321 8 EEDYLETIYELLE--EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPY 59 (154)
T ss_pred HHHHHHHHHHHHh--ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecC
Confidence 3455444 44555 479999999999999999999999999999999988654
No 118
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=77.57 E-value=11 Score=34.58 Aligned_cols=62 Identities=18% Similarity=0.205 Sum_probs=50.6
Q ss_pred ceEEEEccCC---CCChhHHHHHHHhhccCCC------cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 166 GQYLVQSIPG---ELSLDHSLVLQQVASKNEA------HISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 166 g~~vv~s~p~---els~D~~~il~l~~~~~~g------~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
|+.=+...|. .+++|...|+...+.. +| .-||+++.+.||+|+.-.+.+|-.|..+|.+-.|
T Consensus 209 g~lnLSl~p~~~E~l~~daq~Il~yL~~~-gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q~ 279 (287)
T COG2996 209 GKLNLSLRPRAHEMLDEDAQMILTYLESN-GGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQD 279 (287)
T ss_pred CeeecccccccHHhhhhhHHHHHHHHHHc-CCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEEc
Confidence 5555555552 4666788899888865 44 3799999999999999999999999999999985
No 119
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=77.55 E-value=9.3 Score=33.08 Aligned_cols=49 Identities=18% Similarity=0.230 Sum_probs=41.0
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
...|+.+.... +..+|+.+|+..+|+++.-+-.+|-.|.+.|.+..-+.
T Consensus 6 ~~~i~~~l~~~-~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~~ 54 (183)
T PHA02701 6 ASLILTLLSSS-GDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCEDG 54 (183)
T ss_pred HHHHHHHHHhc-CCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCCC
Confidence 46788888854 21599999999999999999999999999999965443
No 120
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=77.33 E-value=7 Score=38.52 Aligned_cols=53 Identities=17% Similarity=0.310 Sum_probs=46.9
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.++..|..+|.... ..|.+|+.+|++.+|++..-...+++.|++.|++-+.+.
T Consensus 3 ~Lt~~e~~vL~~L~--~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~ 55 (489)
T PRK04172 3 ELHPNEKKVLKALK--ELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEER 55 (489)
T ss_pred CCCHHHHHHHHHHH--hCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEee
Confidence 36777888888887 457899999999999999999999999999999999864
No 121
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=77.32 E-value=38 Score=30.44 Aligned_cols=74 Identities=14% Similarity=0.115 Sum_probs=50.3
Q ss_pred CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHH-HhhccCCCcccHHHHHHhcCCCHHHHHHH
Q psy6552 137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQ-QVASKNEAHISVSVLNNELNWSTERAQHA 215 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~-l~~~~~~g~vt~~~l~~~l~ws~~ra~~~ 215 (254)
..|+.+++.+++..+ +..+ ..++.-+...+. ++....++.+++.+++..+|+++.-+..+
T Consensus 215 ~~it~~~v~~~l~~l---~~~~----------------~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~ 275 (305)
T TIGR00635 215 KIINRDIALKALEML---MIDE----------------LGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDV 275 (305)
T ss_pred CCcCHHHHHHHHHHh---CCCC----------------CCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHh
Confidence 358888888887762 2111 113322333444 43322245699999999999999999999
Q ss_pred HH-HHHHcCcEEEeC
Q psy6552 216 LD-FMVQEGYAWIDT 229 (254)
Q Consensus 216 L~-~l~~~G~lwvD~ 229 (254)
++ .|++.|+++...
T Consensus 276 ~e~~Li~~~li~~~~ 290 (305)
T TIGR00635 276 YEPYLLQIGFLQRTP 290 (305)
T ss_pred hhHHHHHcCCcccCC
Confidence 99 599999997443
No 122
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=76.99 E-value=36 Score=29.36 Aligned_cols=85 Identities=16% Similarity=0.242 Sum_probs=61.1
Q ss_pred CHHHHHHHHHHhhhh--CCCeEEEEeCCceEEEEcc--------------C-CCCChhHHHHHHHhhccCCCcccHHHHH
Q psy6552 140 TNEDLLAAAKKLKIF--GNGFSIIPIGQGQYLVQSI--------------P-GELSLDHSLVLQQVASKNEAHISVSVLN 202 (254)
Q Consensus 140 S~~Di~rA~~~L~~L--g~g~~l~~~~sg~~vv~s~--------------p-~els~D~~~il~l~~~~~~g~vt~~~l~ 202 (254)
.+.++.+++..|..- +.|+.|+.++ +..-.++. | .++|.-...+|.++.-. + -||-+++.
T Consensus 37 ~~~~~~~~l~~l~~~y~~rg~~L~~~~-~~~r~~t~~~~~~~~~~l~~~~~~~~LSraalEtLAiIAY~-Q-PiTR~eI~ 113 (184)
T COG1386 37 SADAIIDALAELKEEYEDRGLELVEVA-EGWRLQTKQEYAEYLEKLQEQRPKRELSRAALETLAIIAYK-Q-PVTRSEIE 113 (184)
T ss_pred chHHHHHHHHHHHHhhcCCCeeEEEEc-CceeEEehHHHHHHHHHHhcccccccccHHHHHHHHHHHHc-C-CccHHHHH
Confidence 677788888777554 6888888888 42222232 2 24665555666666644 3 49999999
Q ss_pred HhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 203 NELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 203 ~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+--|....+ ++..|++.|+++--..
T Consensus 114 ~iRGv~~~~---~i~~L~e~glI~~~g~ 138 (184)
T COG1386 114 EIRGVAVSQ---VISTLLERGLIREVGR 138 (184)
T ss_pred HHhCccHHH---HHHHHHHCCCeEecCC
Confidence 999988887 7888999999987764
No 123
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=76.94 E-value=4.6 Score=32.57 Aligned_cols=53 Identities=15% Similarity=0.201 Sum_probs=45.9
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccccCcccccc
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAEK 251 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf~~~~~~~~ 251 (254)
-.|+++||..++-+.+-.+-+|..+.+-||+=+++ ++.|+.|++=....+.+.
T Consensus 53 py~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~e----d~~i~i~~~~~~~g~e~~ 105 (121)
T PF09681_consen 53 PYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDE----DGVIYIPNWEKHQGSETM 105 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec----CCeEEeecHHHHhCccch
Confidence 57999999999999999999999999999999985 488999998666655443
No 124
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=76.61 E-value=9.8 Score=29.28 Aligned_cols=53 Identities=15% Similarity=0.084 Sum_probs=44.9
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.++....||..+. ..|-=.+..++..++.+.+.+.++|+.|++.|++=+.+..
T Consensus 5 ~~~l~~~IL~hl~--~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 5 LDPLDLKILQHLK--KAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred cChhHHHHHHHHH--HHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 4556677887777 3467788899999999999999999999999999999863
No 125
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=76.51 E-value=8.3 Score=34.71 Aligned_cols=57 Identities=9% Similarity=0.043 Sum_probs=46.3
Q ss_pred CChhHHHH-HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 177 LSLDHSLV-LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 177 ls~D~~~i-l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
++..+.++ +.|.. .|-.|+.++++..|.+..+.-++|+.|+..|++-+-.+ .+.+|-
T Consensus 14 lt~yEa~vY~aLl~---~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g---~P~~y~ 71 (247)
T COG1378 14 LTEYEAKVYLALLC---LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEG---RPKKYR 71 (247)
T ss_pred CCHHHHHHHHHHHH---hCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCC---CCceEE
Confidence 66667777 34444 68999999999999999999999999999999999854 444443
No 126
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=75.83 E-value=27 Score=31.99 Aligned_cols=100 Identities=14% Similarity=0.234 Sum_probs=69.7
Q ss_pred HHHHHHHHHHhcCC-CCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHH-HHhhccCCCcc
Q psy6552 119 LDELRTRLVKSRGK-SLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVL-QQVASKNEAHI 196 (254)
Q Consensus 119 L~dl~~~~nr~Rg~-~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il-~l~~~~~~g~v 196 (254)
+.+|...|.++--. .+ ..+|+..+..=+.+|..++ .+.|+.-.+|+-|| +|..+ ...|. ++.. .+|.|
T Consensus 2 i~~L~~~~q~~Q~~~~~--~rLSErnciEiv~kL~~~~-~ldli~T~dGkeyi--T~~~L---~~EI~~el~~--~gGRv 71 (272)
T PF09743_consen 2 IEELQADFQRAQLASSS--QRLSERNCIEIVNKLIEKK-LLDLIHTTDGKEYI--TPEQL---EKEIKDELYV--HGGRV 71 (272)
T ss_pred HHHHHHHHHHHHHHhhh--hhcchhhHHHHHHHHHHcC-CeeEEEECCCCEEE--CHHHH---HHHHHHHHHH--cCCce
Confidence 34555555553311 12 5799999999999999888 66676665688888 44222 23454 4444 48999
Q ss_pred cHHHHHHhcCCCHHHHHHHHHHHHHcC--cEEEe
Q psy6552 197 SVSVLNNELNWSTERAQHALDFMVQEG--YAWID 228 (254)
Q Consensus 197 t~~~l~~~l~ws~~ra~~~L~~l~~~G--~lwvD 228 (254)
+..+|+..+|.+..-.+..+..++++- +..+.
T Consensus 72 ~~~dL~~~LnVd~~~ie~~~~~i~~~~~~~~l~~ 105 (272)
T PF09743_consen 72 NLVDLAQALNVDLDHIERRAQEIVKSDKSLQLVQ 105 (272)
T ss_pred EHHHHHHhcCcCHHHHHHHHHHHHhCCCcEEEEC
Confidence 999999999999999999999975543 55443
No 127
>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=75.63 E-value=6.1 Score=30.07 Aligned_cols=38 Identities=8% Similarity=0.169 Sum_probs=35.1
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
...+|..+|++.+|.++.-+..+|..|++.|++-++.+
T Consensus 45 ~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~ 82 (95)
T TIGR01610 45 QDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM 82 (95)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC
Confidence 45799999999999999999999999999999998864
No 128
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=74.36 E-value=8.2 Score=34.96 Aligned_cols=44 Identities=9% Similarity=0.183 Sum_probs=37.6
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
..+.+++. -++.+...++++++|+|+.-..+++..|+++|++--
T Consensus 14 qIL~ei~~--~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~ 57 (260)
T COG1497 14 QILSEIAV--RQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK 57 (260)
T ss_pred HHHHHHHH--hCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee
Confidence 34455666 369999999999999999999999999999999755
No 129
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=74.17 E-value=13 Score=27.81 Aligned_cols=51 Identities=10% Similarity=0.092 Sum_probs=36.0
Q ss_pred HHHHHHhhhhhh--hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 100 VQIVEVCLATNY--KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 100 vqive~c~~~r~--~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
..|++++.+.-. .+.|.|+..|+...+.+.+..+ ..+|++|+.+-++.+..
T Consensus 10 ~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg---~k~t~~ev~~m~~~~D~ 62 (88)
T cd05029 10 GLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIG---SKLQDAEIAKLMEDLDR 62 (88)
T ss_pred HHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHhcC
Confidence 356677666554 3458999999999997644222 46899999987776644
No 130
>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=73.78 E-value=12 Score=28.01 Aligned_cols=50 Identities=12% Similarity=0.163 Sum_probs=38.6
Q ss_pred CChhHHHHHHHhhcc---CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 177 LSLDHSLVLQQVASK---NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 177 ls~D~~~il~l~~~~---~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
|++-|..||..+-+. .+.-|....|++.++|+++-.+..+..|++.|++-
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve 54 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVE 54 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCcc
Confidence 455566665543110 25679999999999999999999999999999873
No 131
>PF14502 HTH_41: Helix-turn-helix domain
Probab=73.59 E-value=10 Score=25.81 Aligned_cols=36 Identities=19% Similarity=0.307 Sum_probs=33.0
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
--|++++++.|+.+.--.+.+|..|+++|.+-+..+
T Consensus 6 i~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~r 41 (48)
T PF14502_consen 6 IPTISEYSEKFGVSRGTIQNALKFLEENGAIKLESR 41 (48)
T ss_pred cCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeec
Confidence 358999999999999999999999999999988766
No 132
>PRK14999 histidine utilization repressor; Provisional
Probab=73.10 E-value=5.5 Score=34.97 Aligned_cols=34 Identities=21% Similarity=0.159 Sum_probs=32.3
Q ss_pred cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 197 SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 197 t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
|..+|++.+|.|..-++.+|..|+++|++.+-..
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 71 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQG 71 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 9999999999999999999999999999998754
No 133
>PLN02198 glutathione gamma-glutamylcysteinyltransferase
Probab=72.85 E-value=6.7 Score=39.60 Aligned_cols=33 Identities=33% Similarity=0.570 Sum_probs=27.2
Q ss_pred ccchhHH-HHHHHHHHHhhhhhhhcCCceeHHHHHHHH
Q psy6552 90 GMGDFYY-ELSVQIVEVCLATNYKNGGLILLDELRTRL 126 (254)
Q Consensus 90 g~gdfy~-eLavqive~c~~~r~~nGGii~L~dl~~~~ 126 (254)
|...||. ++|.+|++.|. .+||+|+++|+-..=
T Consensus 217 G~~~FY~G~iA~~iv~~~~----~~GG~lt~~DL~~y~ 250 (573)
T PLN02198 217 GPKAFYNGTVGVNLVRDIQ----KSGGIITLKDLQSYR 250 (573)
T ss_pred CcccccCCHHHHHHHHHHH----HcCCCCCHHHHhhCC
Confidence 5567877 69999999985 499999999998663
No 134
>PLN02180 gamma-glutamyl transpeptidase 4
Probab=72.82 E-value=7 Score=40.03 Aligned_cols=32 Identities=38% Similarity=0.721 Sum_probs=26.9
Q ss_pred ccchhHH-HHHHHHHHHhhhhhhhcCCceeHHHHHHH
Q psy6552 90 GMGDFYY-ELSVQIVEVCLATNYKNGGLILLDELRTR 125 (254)
Q Consensus 90 g~gdfy~-eLavqive~c~~~r~~nGGii~L~dl~~~ 125 (254)
|...||. ++|.+|++.+. .+||+|+++||-..
T Consensus 267 G~d~FY~G~iA~~iv~~~~----~~GG~lT~eDLa~Y 299 (639)
T PLN02180 267 GPGAFYNGTIGEKLVKDVK----KAGGIITMDDLRSY 299 (639)
T ss_pred CcccccCCHHHHHHHHHHH----HcCCCCCHHHHHhC
Confidence 5567887 89999999886 48999999999865
No 135
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=72.81 E-value=7.7 Score=37.55 Aligned_cols=74 Identities=24% Similarity=0.431 Sum_probs=53.1
Q ss_pred HHHHcCC----CcccCCCccccccc---cchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHH
Q psy6552 70 MCASIGV----DPLASRKGFWSLLG---MGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNE 142 (254)
Q Consensus 70 mc~~lGV----dPl~s~kg~w~~lg---~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~ 142 (254)
-.+++|+ |||.|++. +|. +|.=||++|+++-.++..+. +|.|++..+ |. +.+|++
T Consensus 330 ~ia~~GIyPAvDPL~StSr---~l~p~ivGe~Hy~va~~vq~iLqrYk-------eLqDIIaIL----Gm----dELsee 391 (468)
T COG0055 330 QIAALGIYPAVDPLDSTSR---ALDPKIVGEEHYEVAREVQSILQRYK-------ELQDIIAIL----GM----DELSEE 391 (468)
T ss_pred hHHhcCCCcccCccccccc---ccCcccccHHHHHHHHHHHHHHHHHH-------HHHHHHHHh----Cc----hhcChh
Confidence 3556664 89987543 332 68999999999999999865 477777775 34 789999
Q ss_pred H---HHHHHHHhhhhCCCeEEE
Q psy6552 143 D---LLAAAKKLKIFGNGFSII 161 (254)
Q Consensus 143 D---i~rA~~~L~~Lg~g~~l~ 161 (254)
| +.||-+.=+=|.-||-+-
T Consensus 392 dk~~V~rArki~~FlSQpF~vA 413 (468)
T COG0055 392 DKLTVARARKIQRFLSQPFFVA 413 (468)
T ss_pred HHHHHHHHHHHHHHhcCcchhh
Confidence 8 556666656667777553
No 136
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=72.58 E-value=5.9 Score=34.81 Aligned_cols=35 Identities=14% Similarity=0.192 Sum_probs=32.3
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
=|..+|++.+|.|..=++.+|+.|+++|++.+-..
T Consensus 36 PsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 70 (241)
T PRK10079 36 PAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG 70 (241)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 57888999999999999999999999999998754
No 137
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=72.52 E-value=6.8 Score=33.85 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=34.3
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..++..+|++.||.|..-.+++|..|+.+|++-+-.+
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence 44789999999999999999999999999999987644
No 138
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=72.13 E-value=7.1 Score=34.00 Aligned_cols=38 Identities=11% Similarity=0.193 Sum_probs=34.7
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..+ |..+|++.||.|..-.+++|..|+.+|++-+-.+
T Consensus 27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~ 65 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 65 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4468 8999999999999999999999999999998765
No 139
>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=72.12 E-value=17 Score=23.81 Aligned_cols=43 Identities=12% Similarity=0.123 Sum_probs=33.9
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHH
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQ 221 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~ 221 (254)
.|++.+..|+.+.- ....|..++++.+|+|...++..+..+++
T Consensus 4 ~L~~~er~vi~~~y---~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRY---FEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHH---TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh---cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 37778888888777 35789999999999999999988877653
No 140
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=71.83 E-value=6 Score=33.78 Aligned_cols=38 Identities=16% Similarity=0.179 Sum_probs=33.5
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..++..+|++.||.|..-.+++|..|+.+|++-+-.+
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~ 69 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKN 69 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecC
Confidence 45689999999999999999999999999999866533
No 141
>TIGR01774 PFL2-3 pyruvate formate-lyase. This model represents isoforms of the pyruvate-formate lyases found in a limited number of species including E. coli. This enzyme catalyzes the reaction pyruvate + CoA - acetyl-CoA + formate, which is a step in the fermentation of glucose.
Probab=71.20 E-value=1.1e+02 Score=32.25 Aligned_cols=82 Identities=6% Similarity=0.092 Sum_probs=52.7
Q ss_pred hhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhh------hhcCHHHHHHHHHHHHHcCCCc
Q psy6552 5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNE------IKKDAQFRRHFQEMCASIGVDP 78 (254)
Q Consensus 5 vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~------I~~dp~fr~~f~~mc~~lGVdP 78 (254)
.|+.||.+..+++.+..+....-..++.+-+++.+-.+.. +..||..|++. -..||+-+.++.+|....+-.|
T Consensus 168 ~G~~gi~~e~~~~~~~l~~~~~~~~~k~~fy~a~~i~~~a-~~~~a~R~a~lA~~~a~~e~d~~Rk~EL~~iA~~c~~vp 246 (786)
T TIGR01774 168 RGLRWLLEESERRIRALEESGVYEGEKYSFYQAAKIVLEA-VINHILRYAKLAEEMAASETGESRREELLKIAEICRKVA 246 (786)
T ss_pred HHHHHHHHHHHHHHHhccCCCchhhhHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHhccCc
Confidence 5888988865444332221111122345556666665554 44678887432 2368998999999999999999
Q ss_pred ccCCCcccc
Q psy6552 79 LASRKGFWS 87 (254)
Q Consensus 79 l~s~kg~w~ 87 (254)
--..++||-
T Consensus 247 ~~pa~tf~E 255 (786)
T TIGR01774 247 AEKPQTFWQ 255 (786)
T ss_pred ccCCCCHHH
Confidence 887776663
No 142
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=71.09 E-value=10 Score=30.72 Aligned_cols=62 Identities=16% Similarity=0.232 Sum_probs=48.0
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHH----HhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLN----NELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~----~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
+|.-...|.+..= ..|..|+.++. ....|+..=.+++|..|.+.|++-.+.+ +...+|.|.+
T Consensus 4 Is~aE~eVM~ilW--~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kd--gr~~~y~pL~ 69 (123)
T COG3682 4 ISAAEWEVMEILW--SRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKD--GRAFRYSPLL 69 (123)
T ss_pred ccHHHHHHHHHHH--HcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhc--CCeeeeeccc
Confidence 4545566677665 35789988865 4568999999999999999999999988 4566666654
No 143
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=70.98 E-value=6.8 Score=34.10 Aligned_cols=34 Identities=18% Similarity=0.054 Sum_probs=32.0
Q ss_pred cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 197 SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 197 t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
|..+|++.+|.|..=++.+|..|+++|++.+=..
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 60 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQG 60 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 8999999999999999999999999999988754
No 144
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=70.64 E-value=7 Score=34.05 Aligned_cols=35 Identities=23% Similarity=0.238 Sum_probs=32.4
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
=|..+|++.+|.|..-.+.+|+.|+++|++-+=..
T Consensus 25 PsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 59 (233)
T TIGR02404 25 PSEHELMDQYGASRETVRKALNLLTEAGYIQKIQG 59 (233)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 48899999999999999999999999999998754
No 145
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=70.60 E-value=22 Score=26.16 Aligned_cols=57 Identities=9% Similarity=0.191 Sum_probs=44.7
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH--HHcCcEEEeCCCCC-cccce
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM--VQEGYAWIDTQSPQ-EHLYW 238 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l--~~~G~lwvD~q~~~-e~~yw 238 (254)
-|..++.+.. ..++.|..+|++.+||.+.=++..|--+ -+.|+...-+..++ ...|.
T Consensus 11 Kqa~li~mL~--rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~s~k~~g~~r~Yr 70 (72)
T PF11994_consen 11 KQAQLIAMLR--RPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTITSEKVDGGGRRYR 70 (72)
T ss_pred HHHHHHHHHc--CCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEEeeecCCCeeeEe
Confidence 5778888888 4578999999999999999999999888 66788776665433 34443
No 146
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=70.55 E-value=14 Score=27.59 Aligned_cols=37 Identities=14% Similarity=0.053 Sum_probs=34.4
Q ss_pred CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 192 NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 192 ~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
..|.++..+|+..|+.++...+.-|+.+++.|.+..=
T Consensus 13 ~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 13 LRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 3689999999999999999999999999999999944
No 147
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=70.21 E-value=21 Score=22.92 Aligned_cols=41 Identities=17% Similarity=0.216 Sum_probs=32.3
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
.++.++..++.+.. .+.|..++++.+|+|..-....+..+.
T Consensus 3 ~l~~~e~~i~~~~~----~g~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 3 SLTPREREVLRLLA----EGLTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46777777776654 247999999999999999998888753
No 148
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=69.87 E-value=16 Score=28.42 Aligned_cols=59 Identities=14% Similarity=0.150 Sum_probs=43.1
Q ss_pred HHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
..|+++.... .+.+|+.+|.+.+ +.+.+=.-..|+.|++.|++..=... ....+|.++.
T Consensus 11 ~~Il~~l~~~-~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~-~~~~~Y~~~~ 74 (120)
T PF01475_consen 11 LAILELLKES-PEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG-DGESRYELST 74 (120)
T ss_dssp HHHHHHHHHH-SSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET-TSEEEEEESS
T ss_pred HHHHHHHHcC-CCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC-CCcceEeecC
Confidence 5678887765 5699999998866 56677778889999999999887654 3445555554
No 149
>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=69.64 E-value=6.6 Score=33.92 Aligned_cols=46 Identities=15% Similarity=0.369 Sum_probs=36.1
Q ss_pred CCcccHHHHHH----hcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 193 EAHISVSVLNN----ELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 193 ~g~vt~~~l~~----~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
..+-|..+|-. ..|++....+++|..|+.+|++.+|.=. ..-.||.
T Consensus 9 ~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~EKiG-ssn~YWs 58 (188)
T PF03962_consen 9 KDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVEKIG-SSNYYWS 58 (188)
T ss_pred CCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhhhcc-CeeEEEe
Confidence 45566666543 3699999999999999999999999874 3567773
No 150
>PRK06474 hypothetical protein; Provisional
Probab=69.59 E-value=18 Score=30.82 Aligned_cols=60 Identities=13% Similarity=0.107 Sum_probs=44.2
Q ss_pred HHHHHHhhccCCCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCCCC---Ccccceeccc
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQSP---QEHLYWFPSL 242 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q~~---~e~~yw~p~l 242 (254)
..|++..... .+..|+.+|++.+ +.+..-.-.+|..|++.|++.+..... +...||..+-
T Consensus 14 ~~Il~~L~~~-~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~ 77 (178)
T PRK06474 14 MKICQVLMRN-KEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINE 77 (178)
T ss_pred HHHHHHHHhC-CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEecc
Confidence 4667766532 3359999999999 788888889999999999999887531 1225555543
No 151
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=69.35 E-value=7.5 Score=34.35 Aligned_cols=35 Identities=26% Similarity=0.210 Sum_probs=32.5
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
=|..+|++.||.|..=++.+|..|+++|++.+-..
T Consensus 32 PsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G 66 (236)
T COG2188 32 PSERELAEQFGVSRMTVRKALDELVEEGLIVRRQG 66 (236)
T ss_pred CCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEec
Confidence 57788999999999999999999999999999865
No 152
>PF01019 G_glu_transpept: Gamma-glutamyltranspeptidase; InterPro: IPR000101 Gamma-glutamyltranspeptidase (2.3.2.2 from EC) (GGT) [] catalyzes the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate). GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification []. In prokaryotes and eukaryotes, it is an enzyme that consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. The active site of GGT is known to be located in the light subunit. The sequences of mammalian and bacterial GGT show a number of regions of high similarity []. Pseudomonas cephalosporin acylases (3.5.1 from EC) that convert 7-beta-(4-carboxybutanamido)-cephalosporanic acid (GL-7ACA) into 7-aminocephalosporanic acid (7ACA) and glutaric acid are evolutionary related to GGT and also show some GGT activity []. Like GGT, these GL-7ACA acylases, are also composed of two subunits. As an autocatalytic peptidase GGT belongs to MEROPS peptidase family T3 (gamma-glutamyltransferase family, clan PB(T)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. The type example is gamma-glutamyltransferase 1 from Escherichia coli. ; GO: 0003840 gamma-glutamyltransferase activity; PDB: 2DBX_A 2Z8K_D 2Z8I_B 2DBU_D 2E0X_B 2DBW_B 2E0W_B 2DG5_A 2E0Y_C 2Z8J_C ....
Probab=69.32 E-value=9.4 Score=37.79 Aligned_cols=69 Identities=26% Similarity=0.365 Sum_probs=39.0
Q ss_pred HHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCcccc-----------ccccchhHH-HHHHHHHHHhhhhhhhcCC
Q psy6552 48 SFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWS-----------LLGMGDFYY-ELSVQIVEVCLATNYKNGG 115 (254)
Q Consensus 48 ~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~-----------~lg~gdfy~-eLavqive~c~~~r~~nGG 115 (254)
.+....+..+..+|..|.-|.. =| .|+....-+-. .-|...||. +||.+|++... .+||
T Consensus 125 ~~l~~~~~~l~~~~~~~~~f~~----~G-~~~~~Gd~l~~p~LA~TL~~ia~~G~~~FY~G~lA~~iv~~~~----~~GG 195 (510)
T PF01019_consen 125 RALARNADKLRRDPGSRALFLP----DG-RPPREGDILRQPELADTLERIAEEGPDAFYRGELAEKIVADVQ----ANGG 195 (510)
T ss_dssp HHHHHHHHHHTTSHHHHHHHST----TS-SE--TTSEE--HHHHHHHHHHHHHTTHHHHSCHHHHHHHHHHH----HTT-
T ss_pred hHHHhHHHHHhhhhhHHHHhcc----CC-CcCCCCCEEEHHHHHHHHHHHHhcCchhhcCChHHHHHHHHHH----hccC
Confidence 4455556678888888776633 11 13221111100 114568888 79999888754 5899
Q ss_pred ceeHHHHHHH
Q psy6552 116 LILLDELRTR 125 (254)
Q Consensus 116 ii~L~dl~~~ 125 (254)
+|++.|+-..
T Consensus 196 ~lt~~Dla~Y 205 (510)
T PF01019_consen 196 LLTLEDLAAY 205 (510)
T ss_dssp S--HHHHHH-
T ss_pred CccHHHHhhc
Confidence 9999998865
No 153
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=68.84 E-value=9.6 Score=32.73 Aligned_cols=42 Identities=17% Similarity=0.136 Sum_probs=37.0
Q ss_pred cccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccce
Q psy6552 195 HISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYW 238 (254)
Q Consensus 195 ~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw 238 (254)
|-|...|+..+ |.+....+.+|..|++.|++++.|++ .+.+|
T Consensus 70 fpSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrDS~--NgkRy 112 (177)
T PF03428_consen 70 FPSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRDSP--NGKRY 112 (177)
T ss_pred ecCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeeccCC--CCCcc
Confidence 67888999999 99999999999999999999998885 45544
No 154
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=68.65 E-value=8.6 Score=30.98 Aligned_cols=51 Identities=8% Similarity=0.020 Sum_probs=43.5
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccccCccccc
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECMNAE 250 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf~~~~~~~ 250 (254)
-|+++||..++-+.+-.+-+|..+.+-||+=+++. +.|+.|+|=....+.+
T Consensus 52 y~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d~----g~i~i~~~~~~~g~es 102 (119)
T TIGR01714 52 YNAEMLATMFNRNVGDIRITLQTLESLGLIEKKNN----GDIFLENWEKHVGSDS 102 (119)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC----CcEEehhHHHHcCchh
Confidence 49999999999999999999999999999999964 5799999755544433
No 155
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=68.33 E-value=9.7 Score=33.18 Aligned_cols=37 Identities=11% Similarity=0.206 Sum_probs=33.6
Q ss_pred Ccc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 194 AHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 194 g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
-.+ |..+|++.||.|..-.+++|..|+.+|++-+-..
T Consensus 29 ~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g 66 (239)
T PRK04984 29 SILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 66 (239)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 357 8999999999999999999999999999998654
No 156
>TIGR00066 g_glut_trans gamma-glutamyltranspeptidase. Also called gamma-glutamyltranspeptidase (ggt). Some members of this family have antibiotic synthesis or resistance activities. In the case of a cephalosporin acylase from Pseudomonas sp., the enzyme was shown to retain some gamma-glutamyltranspeptidase activity. Other, more distantly related proteins have ggt-related activities and score below the trusted cutoff.
Probab=68.22 E-value=3.7 Score=40.79 Aligned_cols=32 Identities=28% Similarity=0.582 Sum_probs=26.9
Q ss_pred ccchhHH-HHHHHHHHHhhhhhhhcCCceeHHHHHHH
Q psy6552 90 GMGDFYY-ELSVQIVEVCLATNYKNGGLILLDELRTR 125 (254)
Q Consensus 90 g~gdfy~-eLavqive~c~~~r~~nGGii~L~dl~~~ 125 (254)
|...||. ++|.+|++.+. .+||+|+++||-..
T Consensus 191 G~~~FY~G~iA~~iv~~~~----~~GG~lt~~DL~~y 223 (516)
T TIGR00066 191 GPDAFYKGDIAESIIDTLQ----KNGGIMTKKDLAAY 223 (516)
T ss_pred CcccccCCHHHHHHHHHHH----HcCCCCCHHHHhhC
Confidence 5567888 89999999876 48999999999854
No 157
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=67.98 E-value=8.5 Score=33.73 Aligned_cols=36 Identities=17% Similarity=0.036 Sum_probs=33.4
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
-=|..+|++.||.|..=++.+|..|+++|++.+-..
T Consensus 33 LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 68 (241)
T PRK11402 33 IPTENELCTQYNVSRITIRKAISDLVADGVLIRWQG 68 (241)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 578899999999999999999999999999998854
No 158
>cd01677 PFL2_DhaB_BssA Pyruvate formate lyase 2 and related enzymes. This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. DhaB catalyzes the first step in the conversion of glycerol to 1,3-propanediol while BssA catalyzes the first step in the anaerobic mineralization of both toluene and m-xylene.
Probab=67.97 E-value=1.6e+02 Score=31.12 Aligned_cols=133 Identities=16% Similarity=0.210 Sum_probs=72.3
Q ss_pred hhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhh------hhcCHHHHHHHHHHHHHcCCCc
Q psy6552 5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNE------IKKDAQFRRHFQEMCASIGVDP 78 (254)
Q Consensus 5 vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~------I~~dp~fr~~f~~mc~~lGVdP 78 (254)
.|+.||.+..+++.+.......=..++.+-+++.+-.+. .+..||..|.+. ...||.-+.++.+|....+-.|
T Consensus 166 ~Gl~gi~~~~~~~~~~~~~~~~~~~~k~~fy~A~~i~~~-av~~~a~Rya~la~e~A~~e~d~~rk~EL~~iA~~c~~vp 244 (781)
T cd01677 166 KGLDGLIEEAKEAIEALDLTGPEDIDKIYFYQAMIIVCE-AVITYAKRYAELAKELAAKETDPKRKAELLEIAEICRRVP 244 (781)
T ss_pred HHHHHHHHHHHHHHhhccCCChhhhhHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhcccCHHHHHHHHHHHHHhccCc
Confidence 588888876544333222110001123444556555444 444688888432 2378999999999999999999
Q ss_pred ccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCcee---HHHHH-HHHHHhcCCCCCCCCCCHHHHHHHHHHh
Q psy6552 79 LASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLIL---LDELR-TRLVKSRGKSLQHQDITNEDLLAAAKKL 151 (254)
Q Consensus 79 l~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~---L~dl~-~~~nr~Rg~~~~~~~IS~~Di~rA~~~L 151 (254)
--..++||-.+- .-|+..|+.++- .||+-|+ ++.++ -.|.|--.. ..||+++...-++.|
T Consensus 245 ~~pp~tf~EAlQ-~~~~~~l~~~~e--------~n~~~~s~GR~Dq~L~Pyy~~Dl~~----G~it~eeA~Ell~~f 308 (781)
T cd01677 245 AHPPRTFWEALQ-SFWFIHLILQIE--------SNGHSISPGRFDQYLYPFYKQDIEE----GRLTREGAIELLECL 308 (781)
T ss_pred CCCCCCHHHHHH-HHHHHHHHHHHh--------cCCcccCCCcHHHHHHHHHHhHHhc----CCCCHHHHHHHHHHH
Confidence 887776763111 133333333322 2444333 34333 344443211 357777766665554
No 159
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=67.84 E-value=32 Score=24.58 Aligned_cols=56 Identities=9% Similarity=0.087 Sum_probs=40.0
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
+..|+++....+....++-.++..++.+.-..-.+|..|+++|.++..... +-.|+
T Consensus 6 ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~---PP~W~ 61 (66)
T PF02295_consen 6 EEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGT---PPKWS 61 (66)
T ss_dssp HHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSS---STEEE
T ss_pred HHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCC---CCceE
Confidence 567888887552235666666666666688899999999999999997653 44454
No 160
>KOG2165|consensus
Probab=67.72 E-value=20 Score=36.98 Aligned_cols=61 Identities=13% Similarity=0.255 Sum_probs=51.6
Q ss_pred EeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 162 PIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 162 ~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.|+ ++++..+|+ ..|..++-+-+ +....|.++|++.+|.++.+.+..|.-.++.|.++=-.
T Consensus 590 e~~-DRtl~~tVs----p~qA~iI~~Fq--ek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~ 650 (765)
T KOG2165|consen 590 EFE-DRTLVLTVS----PEQAAIINLFQ--EKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEP 650 (765)
T ss_pred EEc-CeEEEEeeC----HHHHHHHHHhc--CcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCC
Confidence 556 788888884 47888887777 44679999999999999999999999999999998543
No 161
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=67.50 E-value=10 Score=33.34 Aligned_cols=38 Identities=16% Similarity=0.155 Sum_probs=34.7
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..+ +..+|++.||.|..-.+++|..|+.+|++-+-.+
T Consensus 28 G~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 28 GQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4568 8999999999999999999999999999988755
No 162
>PF02901 PFL: Pyruvate formate lyase; InterPro: IPR004184 Pyruvate formate-lyase 2.3.1.54 from EC (also known as formate C-acetyltransferase) is an enzyme which converts acetyl-CoA and formate to CoA and pyruvate. Acetyl-CoA + formate = CoA + pyruvate In Escherichia coli, it uses a radical mechanism to reversibly cleave the C1-C2 bond of pyruvate using the Gly 734 radical and two cysteine residues (Cys 418, Cys 419) [].; GO: 0008861 formate C-acetyltransferase activity, 0006006 glucose metabolic process, 0005737 cytoplasm; PDB: 1QHM_A 1MZO_B 3PFL_B 1H18_A 2PFL_A 1CM5_B 1H16_A 1H17_A 1R9E_A 1R8W_A ....
Probab=67.10 E-value=1.1e+02 Score=31.51 Aligned_cols=81 Identities=12% Similarity=0.173 Sum_probs=51.8
Q ss_pred hhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh------hcCHHHHHHHHHHHHHcCCCc
Q psy6552 5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEI------KKDAQFRRHFQEMCASIGVDP 78 (254)
Q Consensus 5 vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I------~~dp~fr~~f~~mc~~lGVdP 78 (254)
-|+.||....+++.+-.+....-..+...-+++.+-++.. +..||.+|.+.. .+||.-+.++.+|.....-.|
T Consensus 169 ~Gl~gi~~~~e~~~~~~~~~~~~~~ek~~fy~a~~i~~~a-v~~~a~Rya~la~~~A~~e~d~~rk~EL~~iA~~c~~vp 247 (648)
T PF02901_consen 169 KGLDGIIEEIEEKLAALDPNDPEDAEKRDFYEAMIIVLEA-VIAYAKRYADLAEELAEEETDPERKAELLEIAEICRRVP 247 (648)
T ss_dssp HHHHHHHHHHHHHHHHCHCTTTTCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHCC-SSHHHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHhCCCCChhhhhHHHHHHHHHHHHHh-HHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhCcCc
Confidence 5899998876555443332221223355556676665555 446888885433 368999999999999999888
Q ss_pred ccCCCccc
Q psy6552 79 LASRKGFW 86 (254)
Q Consensus 79 l~s~kg~w 86 (254)
--..++||
T Consensus 248 ~~pa~tF~ 255 (648)
T PF02901_consen 248 ENPARTFR 255 (648)
T ss_dssp TS---SHH
T ss_pred CCCCCCHH
Confidence 87777666
No 163
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=67.09 E-value=15 Score=25.89 Aligned_cols=35 Identities=17% Similarity=0.203 Sum_probs=31.7
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.+|..+|++.+|.|..-+...|..|.++|++=++.
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcC
Confidence 58999999999999999999999999999876553
No 164
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=66.90 E-value=18 Score=35.75 Aligned_cols=58 Identities=14% Similarity=0.239 Sum_probs=48.6
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
-|..+++++. ..|++|..+|+..++.+..-+...|..|+..|++-.=.+ ...-||+-.
T Consensus 403 ~~~~il~~~~--en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~g~--~~~g~~~v~ 460 (467)
T COG2865 403 RQEKILELIK--ENGKVTARELREILGISSETIRRRIANLVKRGLLKQLGS--SGRGTWYVK 460 (467)
T ss_pred HHHHHHHHHh--hccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHhCc--CCCCcEEec
Confidence 3457788888 569999999999999999999999999999999877666 356677644
No 165
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=66.84 E-value=11 Score=33.62 Aligned_cols=33 Identities=15% Similarity=0.175 Sum_probs=31.0
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
.|.++++.++++.|++......+|..|+..|.+
T Consensus 202 EG~lvASkiADrvGITRSVIVNALRKlESAGvI 234 (261)
T COG4465 202 EGLLVASKIADRVGITRSVIVNALRKLESAGVI 234 (261)
T ss_pred cceeeehhhhhhhCchHHHHHHHHHHhhhcCce
Confidence 588999999999999999999999999999975
No 166
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=66.72 E-value=11 Score=33.23 Aligned_cols=38 Identities=11% Similarity=0.130 Sum_probs=34.1
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+-.+ |..+|++.||.|..-.+++|..|+.+|++-+-..
T Consensus 31 G~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 31 GEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3457 8999999999999999999999999999988754
No 167
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=66.63 E-value=11 Score=33.31 Aligned_cols=38 Identities=21% Similarity=0.185 Sum_probs=34.0
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+-.+ +..+|++.||.|..-.+++|..|+.+|++-+-.+
T Consensus 23 G~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~ 61 (253)
T PRK10421 23 GMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRG 61 (253)
T ss_pred CCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 3467 7899999999999999999999999999988754
No 168
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=66.52 E-value=9.9 Score=33.98 Aligned_cols=41 Identities=12% Similarity=0.038 Sum_probs=36.6
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEG 223 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G 223 (254)
+..|+++.. ..|.+++.+|++.||.|.+=.+.=|..|+..|
T Consensus 9 ~~~I~~~l~--~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 9 IGQLLQALK--RSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHH--HcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 678899998 56999999999999999999999999988654
No 169
>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=66.02 E-value=21 Score=29.86 Aligned_cols=58 Identities=19% Similarity=0.278 Sum_probs=44.3
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhc--CCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceec
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNEL--NWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFP 240 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l--~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p 240 (254)
...|++..... +.-.|+.+|.++| +.+...+..+|+.|+.+|.+-.=+-. --..||++
T Consensus 3 e~~Il~y~~~q-NRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~G-KqkiY~~~ 62 (169)
T PF07106_consen 3 EDAILEYMKEQ-NRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYG-KQKIYFAN 62 (169)
T ss_pred HHHHHHHHHHc-CCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeec-ceEEEeeC
Confidence 45678877654 5678899999988 58999999999999999988776652 23455544
No 170
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.90 E-value=20 Score=30.88 Aligned_cols=60 Identities=17% Similarity=0.266 Sum_probs=47.7
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE----EEeCCCCCcccceeccc
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA----WIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l----wvD~q~~~e~~yw~p~l 242 (254)
.-.|++... ..|-+|-++|+..+|+...-.+..|..|-++|++ |+|+-..-...||+++.
T Consensus 20 ~~~v~~~l~--~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~ 83 (176)
T COG1675 20 AVLVVDALL--EKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINY 83 (176)
T ss_pred hhHHHHHHH--hcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEech
Confidence 445666666 4578999999999999999999999999999987 46665434567888764
No 171
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=65.78 E-value=10 Score=32.92 Aligned_cols=35 Identities=11% Similarity=0.166 Sum_probs=32.4
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
=|..+|++.+|.|..=++.+|..|+++|++-+-..
T Consensus 33 PsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 67 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG 67 (238)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 48999999999999999999999999999988754
No 172
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=65.56 E-value=15 Score=30.45 Aligned_cols=53 Identities=9% Similarity=-0.032 Sum_probs=41.0
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
++.+|... .+.+|..+|++..++++.-....|..|.+.|++----.. .|=|+.
T Consensus 14 L~~LA~~~-~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~--~GGy~L 66 (153)
T PRK11920 14 LMYCAAND-GKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGR--NGGVRL 66 (153)
T ss_pred HHHHHhCC-CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCC--CCCeee
Confidence 35666543 557999999999999999999999999999987665542 344443
No 173
>KOG3233|consensus
Probab=65.16 E-value=66 Score=29.77 Aligned_cols=97 Identities=15% Similarity=0.161 Sum_probs=64.0
Q ss_pred ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC------CCCChhHHHHHHHhh
Q psy6552 116 LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP------GELSLDHSLVLQQVA 189 (254)
Q Consensus 116 ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p------~els~D~~~il~l~~ 189 (254)
-++..||-..+ +.+|..|...|++.|-.-| .+.+.+=+.|.++=.-.| ..++.+...++++++
T Consensus 26 git~q~L~~~~----------p~~~~~~~~salN~lLs~~-~l~llr~~~~l~yr~~d~~~a~~~~~~e~eEk~vy~lIe 94 (297)
T KOG3233|consen 26 GITQQELQSEM----------PQISATDRASALNILLSRG-LLDLLRQNTGLVYRAKDPKSASKGKGMENEEKLVYSLIE 94 (297)
T ss_pred cccHHHHHHHc----------CCCcHHHHHHHHHHHHhcC-cchhhccCCcceEeccCchhhcccccCChHHHHHHHHHH
Confidence 35666665442 3578888888887775544 233333332322222222 234446677889999
Q ss_pred ccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcC
Q psy6552 190 SKNEAHISVSVLNNELNWSTERAQHALDFMVQEG 223 (254)
Q Consensus 190 ~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G 223 (254)
.+++.++...+|..+.+.+.......|..|+..-
T Consensus 95 ~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKk 128 (297)
T KOG3233|consen 95 ESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKK 128 (297)
T ss_pred HcCCCceeeehhhhccCCCHHHHHHHHHHHHHHH
Confidence 7766789999999999999999998888887643
No 174
>smart00753 PAM PCI/PINT associated module.
Probab=65.10 E-value=19 Score=26.29 Aligned_cols=46 Identities=24% Similarity=0.209 Sum_probs=37.7
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE--EEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA--WIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l--wvD~q 230 (254)
.+..+++ ....++.++|++.++++.+-++..|-.|+.+|.+ .+|..
T Consensus 14 ~l~~l~~--~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00753 14 NLLQLSE--PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred HHHHHhH--HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 3456666 4678999999999999999999999999999975 56654
No 175
>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=65.10 E-value=19 Score=26.29 Aligned_cols=46 Identities=24% Similarity=0.209 Sum_probs=37.7
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE--EEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA--WIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l--wvD~q 230 (254)
.+..+++ ....++.++|++.++++.+-++..|-.|+.+|.+ .+|..
T Consensus 14 ~l~~l~~--~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00088 14 NLLQLSE--PYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred HHHHHhH--HhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 3456666 4678999999999999999999999999999975 56654
No 176
>KOG1350|consensus
Probab=64.61 E-value=15 Score=35.00 Aligned_cols=82 Identities=18% Similarity=0.293 Sum_probs=58.5
Q ss_pred HHHHHHHcCC----CcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHH
Q psy6552 67 FQEMCASIGV----DPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNE 142 (254)
Q Consensus 67 f~~mc~~lGV----dPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~ 142 (254)
+..-.+.+|| |||.|.+-...--=+|.=||.+|+++-..+..+. +|.|++..+- . +.+|++
T Consensus 377 LSR~iaelgIYPAVDPLDStSrimdp~ivG~eHY~vA~~Vqk~LQ~YK-------sLQDIIAILG----m----DELSEe 441 (521)
T KOG1350|consen 377 LSRGIAELGIYPAVDPLDSTSRIMDPNIVGEEHYNVARGVQKTLQDYK-------SLQDIIAILG----M----DELSEE 441 (521)
T ss_pred hhhhhHhcCCccccCCccccccccCccccchHHHHHHHHHHHHHHHHH-------HHHHHHHHhC----c----hhhchh
Confidence 3444566765 8898654322100157999999999999888754 4778887763 3 788999
Q ss_pred H---HHHHHHHhhhhCCCeEEEEe
Q psy6552 143 D---LLAAAKKLKIFGNGFSIIPI 163 (254)
Q Consensus 143 D---i~rA~~~L~~Lg~g~~l~~~ 163 (254)
| +.||-|.-+-|.-||.+-.+
T Consensus 442 DkLTV~RARKiqRFLSQPF~VAEv 465 (521)
T KOG1350|consen 442 DKLTVARARKIQRFLSQPFQVAEV 465 (521)
T ss_pred hhhhHHHHHHHHHHHcCchhhhhh
Confidence 8 56888888888999988665
No 177
>PRK03837 transcriptional regulator NanR; Provisional
Probab=64.39 E-value=11 Score=32.71 Aligned_cols=37 Identities=16% Similarity=0.150 Sum_probs=33.5
Q ss_pred Ccc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 194 AHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 194 g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
-.+ +..+|++.||.|..-.+++|..|+.+|++=+-..
T Consensus 35 ~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 35 DQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 357 8999999999999999999999999999888644
No 178
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=64.07 E-value=1.2e+02 Score=31.58 Aligned_cols=153 Identities=16% Similarity=0.179 Sum_probs=75.8
Q ss_pred CHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHH------HhhhhhhhcCCceeHHHHHHHHHHhcCCC
Q psy6552 60 DAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVE------VCLATNYKNGGLILLDELRTRLVKSRGKS 133 (254)
Q Consensus 60 dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive------~c~~~r~~nGGii~L~dl~~~~nr~Rg~~ 133 (254)
+++|-++.-.||.+- |.|.-+... .=-+.+||-++-..-.. +-..+|+. ..||-|++.++ |.|-+
T Consensus 507 ~~~~lrkYI~YAR~~-v~P~lt~ea---~e~l~~~Yv~~Rk~~~~~~~~~~~piT~RqL-EsiiRLaeA~A---k~rLS- 577 (682)
T COG1241 507 DFELLRKYISYARKN-VTPVLTEEA---REELEDYYVEMRKKSALVEEKRTIPITARQL-ESIIRLAEAHA---KMRLS- 577 (682)
T ss_pred cHHHHHHHHHHHhcc-CCcccCHHH---HHHHHHHHHHhhhccccccccCcccccHHHH-HHHHHHHHHHH---hhhcc-
Confidence 577777888888776 556643210 00023555554332211 00000110 12444454443 44544
Q ss_pred CCCCCCCHHHHHHHHHHhh-hhCC-CeEE--EEeCCceEEEEc-cCCCCChhHHHHH----HHhhccCCCcccHHHHHH-
Q psy6552 134 LQHQDITNEDLLAAAKKLK-IFGN-GFSI--IPIGQGQYLVQS-IPGELSLDHSLVL----QQVASKNEAHISVSVLNN- 203 (254)
Q Consensus 134 ~~~~~IS~~Di~rA~~~L~-~Lg~-g~~l--~~~~sg~~vv~s-~p~els~D~~~il----~l~~~~~~g~vt~~~l~~- 203 (254)
+.|+++|+..|++.+. .|.. .+.- -.++ ..++.+ .++.--.+...++ ++.+.. .+ ...++..
T Consensus 578 ---~~V~~eD~~eAi~lv~~~l~~v~~dp~~g~~d--~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~-~~--~~~~~~~~ 649 (682)
T COG1241 578 ---DVVEEEDVDEAIRLVDFSLKTVAVDPEKGKID--IDIIEPGKSKSKRDKIEKVLDIIKELVERS-ED--PVEEIIEE 649 (682)
T ss_pred ---CCCCHHHHHHHHHHHHHHHHHhhcCccCCcee--hhhhccCCcchhhhhHHHHHHHHHHHhhcc-cc--hHHHHHHH
Confidence 7899999999999986 2211 1110 0010 111112 1211111223333 334422 22 3333333
Q ss_pred hcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 204 ELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 204 ~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.-|.+...++++|..|...|.++-=.
T Consensus 650 ~~g~~~~~~e~~l~~l~~~g~i~~~~ 675 (682)
T COG1241 650 AEGISEKEVEEALEKLKKKGDILEPN 675 (682)
T ss_pred HcCCCHHHHHHHHHHHHhcCcEeccC
Confidence 22799999999999999999887543
No 179
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=64.06 E-value=13 Score=32.85 Aligned_cols=38 Identities=11% Similarity=0.122 Sum_probs=34.4
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..+ |..+|++.||.|..-.+++|..|+.+|++-+..+
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4467 7999999999999999999999999999988765
No 180
>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=63.99 E-value=9.9 Score=28.17 Aligned_cols=46 Identities=15% Similarity=0.317 Sum_probs=29.2
Q ss_pred HHHHhhccCCCcccHHHHHHhcC---CCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 184 VLQQVASKNEAHISVSVLNNELN---WSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~---ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
++.... ..||+|..+|.+.|. +++......+..|...|+-.+|+..
T Consensus 12 Li~~gK--~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI~Vvd~~~ 60 (82)
T PF03979_consen 12 LIEKGK--KKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGIEVVDEEE 60 (82)
T ss_dssp HHHHHH--HHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT----B--S-
T ss_pred HHHHHh--hcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence 355555 369999999999875 8999999999999999999999543
No 181
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=63.98 E-value=1.5e+02 Score=31.36 Aligned_cols=170 Identities=14% Similarity=0.163 Sum_probs=100.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHH--HcCCCcccCCCccccccccchhH--HHHHHHHHHHh
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCA--SIGVDPLASRKGFWSLLGMGDFY--YELSVQIVEVC 106 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~--~lGVdPl~s~kg~w~~lg~gdfy--~eLavqive~c 106 (254)
.+..|.++++.+|.. +-+.+... -+.-.-.+.+|. .|++|-+.+..| ..|+ .+|..+|.+-.
T Consensus 4 Ei~eLq~~fq~aQ~~--~ss~rLSE-----rNcIEiV~KLie~~~ld~dll~T~DG-------KEYiT~~qL~~EI~~El 69 (803)
T PLN03083 4 ELLELQRQFEFAQQA--KSSVRLSE-----RNVVELVQKLQELGIIDFDLLHTVSG-------KEYITQDQLRNEIEAEI 69 (803)
T ss_pred HHHHHHHHHHHHHHH--Hhhhhcch-----hhHHHHHHHHHHhcccCcceEEecCC-------ceeeCHHHHHHHHHHHH
Confidence 455666666665532 22222211 111134566666 456676654331 2454 45788887775
Q ss_pred hhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHH
Q psy6552 107 LATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQ 186 (254)
Q Consensus 107 ~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~ 186 (254)
. .||=+++.||-..+| |....|.+.++.+-.=+.++.+ +. |. +| +..+ ++.--..|=+
T Consensus 70 ~-----~gGRvnlvdLa~~Ln-----------VD~~hiEr~~~~iv~~d~~~~l--~~-Ge-Li-t~~Y-ld~iaeEIne 127 (803)
T PLN03083 70 K-----KLGRVSLVDLADTIG-----------VDLYHVERQAQQVVSDDPGLML--VQ-GE-II-SQSY-WDSIAEEINE 127 (803)
T ss_pred H-----hCCCeeHHHHhhhcC-----------CCHHHHHHHHHHHhcCCCceEE--ec-CE-ec-chHH-HHHHHHHHHH
Confidence 2 379999999976644 7889999999998554566655 33 54 22 2211 2212233444
Q ss_pred HhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 187 QVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 187 l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
..+ +.|.|++.+|+..++.+.+....+|... -|- -|+-.. ..+..|-|.+
T Consensus 128 ~Lq--E~G~isI~eLa~~~~Lpsefl~~~l~~r--lG~-iI~g~~-~g~~lyT~aY 177 (803)
T PLN03083 128 RLQ--ECSQIALAELARQLQVGSELVTSMLEPR--LGT-IVKARL-EGGQLYTPAY 177 (803)
T ss_pred HHH--HcCcChHHHHHHhcCChHHHHHHHHHHH--hcc-ceEEEe-cCCEEecHHH
Confidence 555 4799999999999999999999998654 443 344332 2334444444
No 182
>PRK13558 bacterio-opsin activator; Provisional
Probab=63.97 E-value=30 Score=34.66 Aligned_cols=80 Identities=14% Similarity=0.064 Sum_probs=59.1
Q ss_pred CHHHHHHHHHHhhhhCCCeEEEEeCCceEEEE-------ccCCCCChhHHHHHHHhhccCCCc------ccHHHHHHhcC
Q psy6552 140 TNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQ-------SIPGELSLDHSLVLQQVASKNEAH------ISVSVLNNELN 206 (254)
Q Consensus 140 S~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~-------s~p~els~D~~~il~l~~~~~~g~------vt~~~l~~~l~ 206 (254)
+.+|+...++.|..-...++|+.+..-..-.. .....|++-|-.+|++|- ..|| +|.++|++.+|
T Consensus 564 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~~q~e~l~~a~--~~gyf~~pr~~~~~e~a~~l~ 641 (665)
T PRK13558 564 TEAAGRAVVETLRDRYAGAELVSYTERDDPGETPDEFRASLENDLTDRQLTALQKAY--VSGYFEWPRRVEGEELAESMG 641 (665)
T ss_pred CCccHHHHHHHHHhhcCCcEEEEEEeecCCCcchhhHHHHhhhhCCHHHHHHHHHHH--HcCCCCCCccCCHHHHHHHhC
Confidence 56778888888887777888877651000000 001258888999999998 4577 69999999999
Q ss_pred CCHHHHHHHHHHHHH
Q psy6552 207 WSTERAQHALDFMVQ 221 (254)
Q Consensus 207 ws~~ra~~~L~~l~~ 221 (254)
+|..=+.++|..+++
T Consensus 642 is~~t~~~~lr~a~~ 656 (665)
T PRK13558 642 ISRSTFHQHLRAAER 656 (665)
T ss_pred CCHHHHHHHHHHHHH
Confidence 999999999988765
No 183
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=63.55 E-value=12 Score=32.92 Aligned_cols=36 Identities=19% Similarity=0.136 Sum_probs=32.9
Q ss_pred cc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 195 HI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 195 ~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+ |..+|++.+|.|..=.+.+|+.|+++|++-+=..
T Consensus 28 ~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G 64 (240)
T PRK09764 28 ALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQG 64 (240)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 35 8999999999999999999999999999988754
No 184
>PRK12423 LexA repressor; Provisional
Probab=63.54 E-value=21 Score=30.79 Aligned_cols=54 Identities=11% Similarity=0.233 Sum_probs=42.4
Q ss_pred CChhHHHHHHHhhcc--CCCc-ccHHHHHHhcCC-CHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 177 LSLDHSLVLQQVASK--NEAH-ISVSVLNNELNW-STERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 177 ls~D~~~il~l~~~~--~~g~-vt~~~l~~~l~w-s~~ra~~~L~~l~~~G~lwvD~q 230 (254)
|+..|..+++..... ..|+ -|..+|++.+|. +..-..++|+.|++.|++=++..
T Consensus 4 lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 4 LTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence 667788887765421 2333 499999999995 88888999999999999998765
No 185
>PF05597 Phasin: Poly(hydroxyalcanoate) granule associated protein (phasin); InterPro: IPR008769 Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=63.12 E-value=60 Score=26.56 Aligned_cols=73 Identities=21% Similarity=0.366 Sum_probs=49.8
Q ss_pred hhhHHHhccHHHHHH----HHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc-----CHHHHHHHHHHHHHcC
Q psy6552 5 AGVGAIQKQKLEQEK----YKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKK-----DAQFRRHFQEMCASIG 75 (254)
Q Consensus 5 vGi~~i~~~~~~~~~----~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~-----dp~fr~~f~~mc~~lG 75 (254)
+|++++-+..++-.+ .=..|..+....-..++.+++..++.++.++...++.+.. ...|-..+...+..||
T Consensus 25 AGLGA~ak~~~EG~k~F~~LVk~Ge~~e~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~dklE~~fd~rV~~aL~rLg 104 (132)
T PF05597_consen 25 AGLGAYAKAQEEGSKVFEALVKEGEKLEKKTRKKAEEQVEEARDQVKSRVDDVKERATGQWDKLEQAFDERVARALNRLG 104 (132)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 688888877644332 2245666777666778888888886666666555544432 2457778999999999
Q ss_pred CC
Q psy6552 76 VD 77 (254)
Q Consensus 76 Vd 77 (254)
|+
T Consensus 105 vP 106 (132)
T PF05597_consen 105 VP 106 (132)
T ss_pred CC
Confidence 98
No 186
>cd03319 L-Ala-DL-Glu_epimerase L-Ala-D/L-Glu epimerase catalyzes the epimerization of L-Ala-D/L-Glu and other dipeptides. The genomic context and the substrate specificity of characterized members of this family from E.coli and B.subtilis indicates a possible role in the metabolism of the murein peptide of peptidoglycan, of which L-Ala-D-Glu is a component. L-Ala-D/L-Glu epimerase is a member of the enolase-superfamily, which is characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=62.87 E-value=16 Score=33.38 Aligned_cols=79 Identities=24% Similarity=0.330 Sum_probs=49.4
Q ss_pred CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
-+|+++.+.++.+... ||+.++++ + ......|-.. ++.+.+. .|.+ .-.+--+-+|+...|.+.++.
T Consensus 133 ~~~~~~~~~~~~~~~~--Gf~~iKik-----~---g~~~~~d~~~-v~~lr~~-~g~~-~l~vD~n~~~~~~~A~~~~~~ 199 (316)
T cd03319 133 DTPEAMAAAAKKAAKR--GFPLLKIK-----L---GGDLEDDIER-IRAIREA-APDA-RLRVDANQGWTPEEAVELLRE 199 (316)
T ss_pred CCHHHHHHHHHHHHHc--CCCEEEEE-----e---CCChhhHHHH-HHHHHHh-CCCC-eEEEeCCCCcCHHHHHHHHHH
Confidence 3689998888887654 57766665 1 1112334333 3333321 2311 111223678999999999999
Q ss_pred HHHcCcEEEeCC
Q psy6552 219 MVQEGYAWIDTQ 230 (254)
Q Consensus 219 l~~~G~lwvD~q 230 (254)
+.+.|+.|+.+=
T Consensus 200 l~~~~l~~iEeP 211 (316)
T cd03319 200 LAELGVELIEQP 211 (316)
T ss_pred HHhcCCCEEECC
Confidence 999999999753
No 187
>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=62.83 E-value=21 Score=26.34 Aligned_cols=44 Identities=25% Similarity=0.235 Sum_probs=36.1
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE--EEeCC
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA--WIDTQ 230 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l--wvD~q 230 (254)
..++. ....++.+.+++.++++...++..|..|+.+|.+ -+|..
T Consensus 52 ~~l~~--~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~ 97 (105)
T PF01399_consen 52 RQLSK--PYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQV 97 (105)
T ss_dssp HHHHH--C-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETT
T ss_pred HHHHH--HhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECC
Confidence 34455 4678999999999999999999999999999986 45644
No 188
>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=62.78 E-value=21 Score=25.10 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=29.4
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
.|..|..+|.+..+.++...+..|--|++.|++.
T Consensus 25 ~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 25 RGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp C-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 6899999999999999999999999999999875
No 189
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.42 E-value=12 Score=30.77 Aligned_cols=36 Identities=17% Similarity=0.188 Sum_probs=32.3
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.|.+|.++|+..+|.+....+..|..|.+++++-+.
T Consensus 13 ~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~ 48 (147)
T smart00531 13 NGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKID 48 (147)
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhh
Confidence 578999999999999999999999999997776544
No 190
>PF05600 DUF773: Protein of unknown function (DUF773); InterPro: IPR008491 This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.
Probab=62.32 E-value=16 Score=36.38 Aligned_cols=45 Identities=16% Similarity=0.438 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCC
Q psy6552 33 EQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVD 77 (254)
Q Consensus 33 ~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVd 77 (254)
=.|++|+++.+..++..-+|...--+.--..+.+|..+|..+||.
T Consensus 127 P~lkKqi~k~~q~~~d~~kk~~e~~~~~~~~~~~~~~~c~~lGI~ 171 (507)
T PF05600_consen 127 PALKKQIAKCQQQLEDLDKKEEELQRSAAEARERYKKACKQLGIK 171 (507)
T ss_pred hHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence 368899999999998766666554455567899999999999998
No 191
>KOG1043|consensus
Probab=62.31 E-value=72 Score=31.82 Aligned_cols=111 Identities=18% Similarity=0.281 Sum_probs=74.3
Q ss_pred HHHHHHHHHH--------HHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHH
Q psy6552 34 QLSQHLNTFR--------DKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEV 105 (254)
Q Consensus 34 ~L~~ql~~fk--------~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~ 105 (254)
++.+.+.+++ +.+-.||.-+.++|.=|---|.++-.||..+++.|..+.+ -+-|.|-..|=++
T Consensus 257 ~fd~f~~kvr~~~~~~S~eeii~~aklf~de~~LdnLsR~qL~al~k~m~l~~~Gt~~---------~lr~~lr~kik~i 327 (499)
T KOG1043|consen 257 EFDRFLGKVRFIGLGVSTEEIIAFAKLFSDEITLDNLSRPQLVALCKYMDLNSFGTDK---------LLRYQLRKKIKEI 327 (499)
T ss_pred HHHHHHHHhcccCCCccHHHHHHHHHHhccchhhhccCHHHHHHHHHhhcccccCchH---------HHHHHHHHHHHHh
Confidence 6777777776 3444788888888887777789999999999999886532 4556666666666
Q ss_pred hhhhhhhc-CCceeHHHHHHHHHH--hcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552 106 CLATNYKN-GGLILLDELRTRLVK--SRGKSLQHQDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 106 c~~~r~~n-GGii~L~dl~~~~nr--~Rg~~~~~~~IS~~Di~rA~~~L~~Lg 155 (254)
--.-++.+ -|-+++..+...+.. .||+.+ ..++++++..-...+..|.
T Consensus 328 k~dD~~I~~eg~v~~ls~~el~~aC~~rgmra--~gv~~e~l~~ql~~wldls 378 (499)
T KOG1043|consen 328 KKDDKHIATEGAVESLSLLELQIACRERGMRA--LGVSEERLREQLRVWLDLS 378 (499)
T ss_pred cccccchhhhhhhhHhhHHHHHHHHHhhhcch--hccchhhhhHHHHHHHhhh
Confidence 55544432 343444444444444 456544 5788988877777766554
No 192
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=62.24 E-value=15 Score=32.45 Aligned_cols=38 Identities=18% Similarity=0.254 Sum_probs=34.2
Q ss_pred CCcc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..+ |..+|++.||.|..-.+++|..|+.+|++-+--+
T Consensus 29 G~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 29 GDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4467 6899999999999999999999999999988765
No 193
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=61.60 E-value=30 Score=36.43 Aligned_cols=96 Identities=14% Similarity=0.227 Sum_probs=66.1
Q ss_pred eHHHHHHHHHHhcCC-CCCCCCCCHHHHHHHHHHhhhhC-CCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCc
Q psy6552 118 LLDELRTRLVKSRGK-SLQHQDITNEDLLAAAKKLKIFG-NGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAH 195 (254)
Q Consensus 118 ~L~dl~~~~nr~Rg~-~~~~~~IS~~Di~rA~~~L~~Lg-~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~ 195 (254)
++.+|...|.++--. .. ..+|+..++.=+.+|..++ ..+.|+.--.|+-|| +|..+. ..|...+. .+|.
T Consensus 4 Ei~eLq~~fq~aQ~~~ss--~rLSErNcIEiV~KLie~~~ld~dll~T~DGKEYi--T~~qL~---~EI~~El~--~gGR 74 (803)
T PLN03083 4 ELLELQRQFEFAQQAKSS--VRLSERNVVELVQKLQELGIIDFDLLHTVSGKEYI--TQDQLR---NEIEAEIK--KLGR 74 (803)
T ss_pred HHHHHHHHHHHHHHHHhh--hhcchhhHHHHHHHHHHhcccCcceEEecCCceee--CHHHHH---HHHHHHHH--hCCC
Confidence 355666666664322 12 5799999999999998887 334455544488887 442222 23332233 2699
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHc
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQE 222 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~ 222 (254)
|++.+|+..+|.+...++..++.++++
T Consensus 75 vnlvdLa~~LnVD~~hiEr~~~~iv~~ 101 (803)
T PLN03083 75 VSLVDLADTIGVDLYHVERQAQQVVSD 101 (803)
T ss_pred eeHHHHhhhcCCCHHHHHHHHHHHhcC
Confidence 999999999999999999999987655
No 194
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=61.51 E-value=17 Score=28.12 Aligned_cols=41 Identities=17% Similarity=0.372 Sum_probs=29.0
Q ss_pred cCHHHHHHHHHHHHHcCCCcccCC--Ccccc--ccccchhHHHHHHHH
Q psy6552 59 KDAQFRRHFQEMCASIGVDPLASR--KGFWS--LLGMGDFYYELSVQI 102 (254)
Q Consensus 59 ~dp~fr~~f~~mc~~lGVdPl~s~--kg~w~--~lg~gdfy~eLavqi 102 (254)
.||. -+..++.-.|||-.+++ +.+|. .+...+||.+|+..=
T Consensus 41 rNP~---i~ekLi~~~~Ide~gTn~p~~i~dP~~~~~~~y~e~L~k~Q 85 (96)
T PF07818_consen 41 RNPS---ILEKLIEFFGIDEYGTNFPKDIFDPHGFPEEDYYEELAKAQ 85 (96)
T ss_pred CChH---HHHHHHHHcCCCcccCCCChhhcCCCCCCHHHHHHHHHHHH
Confidence 4555 46778888899987643 45776 555569999998653
No 195
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=61.01 E-value=18 Score=31.34 Aligned_cols=43 Identities=16% Similarity=0.207 Sum_probs=36.3
Q ss_pred hHHHHHHHhhccCCC--cccHHHHHHhcCCCHHHHHHHHHHHHHcCc
Q psy6552 180 DHSLVLQQVASKNEA--HISVSVLNNELNWSTERAQHALDFMVQEGY 224 (254)
Q Consensus 180 D~~~il~l~~~~~~g--~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~ 224 (254)
-+..+++.+. ..| ++|..+|++.+|.++...+.=|..+...|.
T Consensus 17 ~~~~il~~l~--~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 17 LYYRYLKELK--EEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHHHHHHH--HcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence 3567788888 457 999999999999999988888988887773
No 196
>PRK09615 ggt gamma-glutamyltranspeptidase; Reviewed
Probab=59.98 E-value=6.6 Score=39.73 Aligned_cols=32 Identities=38% Similarity=0.564 Sum_probs=27.1
Q ss_pred ccchhHH-HHHHHHHHHhhhhhhhcCCceeHHHHHHH
Q psy6552 90 GMGDFYY-ELSVQIVEVCLATNYKNGGLILLDELRTR 125 (254)
Q Consensus 90 g~gdfy~-eLavqive~c~~~r~~nGGii~L~dl~~~ 125 (254)
|...||. ++|.+|++.+. .+||+|+++||-..
T Consensus 239 G~~~FY~G~iA~~iv~~~~----~~GG~lt~~DLa~y 271 (581)
T PRK09615 239 GPDAFYKGTIADQIAQEMQ----KNGGLITKEDLAAY 271 (581)
T ss_pred CcccccCCHHHHHHHHHHH----HcCCCCCHHHHhhC
Confidence 5568888 79999999875 48999999999866
No 197
>PRK04217 hypothetical protein; Provisional
Probab=59.96 E-value=19 Score=28.58 Aligned_cols=61 Identities=11% Similarity=-0.056 Sum_probs=40.8
Q ss_pred CCCeEEEEeC-CceEEEEccC-CCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 155 GNGFSIIPIG-QGQYLVQSIP-GELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 155 g~g~~l~~~~-sg~~vv~s~p-~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
|--+.+++|. ++.-+....| .-++.++..++.+.. ...+|..++++.+|+|..-+...|..
T Consensus 19 ~~~~~~~~~~~~~~~~~~~~p~~~Lt~eereai~l~~---~eGlS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 19 GFIPQVRHFYPAIPPVGPPKPPIFMTYEEFEALRLVD---YEGLTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred eccCCcceEeCCCCCccCCCCcccCCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3345566664 4444444444 467777877777776 23579999999999998766666554
No 198
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=59.89 E-value=12 Score=32.49 Aligned_cols=38 Identities=26% Similarity=0.276 Sum_probs=35.3
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+-.++..+|+..||.|..-.+++|..|..+|++.+.-+
T Consensus 37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~ 74 (230)
T COG1802 37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPN 74 (230)
T ss_pred CCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCC
Confidence 45799999999999999999999999999999999854
No 199
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=59.70 E-value=40 Score=31.40 Aligned_cols=80 Identities=18% Similarity=0.215 Sum_probs=52.4
Q ss_pred CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHh-hcc--CCCcccHHHHHH-------hcC
Q psy6552 137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQV-ASK--NEAHISVSVLNN-------ELN 206 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~-~~~--~~g~vt~~~l~~-------~l~ 206 (254)
+.|+++||.+|++.+..- . -...++ .++.-|..+|.++ ... ..+.++..++.+ .+|
T Consensus 268 ~~I~~~~v~~a~~~~~~~--~--------~~~~~~----~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~ 333 (394)
T PRK00411 268 RKVTEEDVRKAYEKSEIV--H--------LSEVLR----TLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELG 333 (394)
T ss_pred CCcCHHHHHHHHHHHHHH--H--------HHHHHh----cCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcC
Confidence 689999999999988320 0 111232 2554555554433 211 125677777764 478
Q ss_pred CCH---HHHHHHHHHHHHcCcEEEeCC
Q psy6552 207 WST---ERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 207 ws~---~ra~~~L~~l~~~G~lwvD~q 230 (254)
+++ ......|..|+..|++-.-..
T Consensus 334 ~~~~~~~~~~~~l~~L~~~glI~~~~~ 360 (394)
T PRK00411 334 YEPRTHTRFYEYINKLDMLGIINTRYS 360 (394)
T ss_pred CCcCcHHHHHHHHHHHHhcCCeEEEEe
Confidence 855 888999999999999987543
No 200
>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=59.70 E-value=23 Score=25.45 Aligned_cols=46 Identities=20% Similarity=0.216 Sum_probs=39.7
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.|..+.. ..|..|.++|++..+.+..-..-+|-.|.++|.+.++..
T Consensus 12 ~Vw~~L~--~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~ 57 (65)
T PF10771_consen 12 KVWQLLN--ENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEK 57 (65)
T ss_dssp HHHHHHC--CSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEE
T ss_pred HHHHHHh--hCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEee
Confidence 4455666 468999999999999999999999999999999999977
No 201
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=59.53 E-value=2.1e+02 Score=29.25 Aligned_cols=133 Identities=11% Similarity=0.038 Sum_probs=83.8
Q ss_pred chhHHHHHHHHHHHhhhhhhhc--CCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEE
Q psy6552 92 GDFYYELSVQIVEVCLATNYKN--GGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYL 169 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~n--GGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~v 169 (254)
.++|.+|..++.+.+...-.+| ---|+..++.+++. ..+++.-+...++.|..=| .++ .-+ +.
T Consensus 413 ~~~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~~~---------~~~~~~~~~~~l~~l~~~~-~i~--~~~-~~-- 477 (614)
T PRK10512 413 APVAARWQRKLLDTLATYHEQHRDEPGPGRERLRRMAL---------PMEDEALVLLLIEKMRESG-DIH--SHH-GW-- 477 (614)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhhcc---------cCCCHHHHHHHHHHHHhCC-CEE--EeC-CE--
Confidence 4888999999999987543332 34577888875532 2467777777777775433 222 222 33
Q ss_pred EEccC--CCCChhHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccc
Q psy6552 170 VQSIP--GELSLDHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLF 243 (254)
Q Consensus 170 v~s~p--~els~D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf 243 (254)
|+... ..++.++..+.+..... ...--+..++.+.+|++...++++|..|+++|.+.+= .+..||-+..+
T Consensus 478 ~~~~~~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l----~~~~~~~~~~~ 550 (614)
T PRK10512 478 LHLPDHKAGFSEEQQALWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAI----VKDRYYRNDRI 550 (614)
T ss_pred EECCCCCCCCCHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe----cCCEEECHHHH
Confidence 33322 24566666553333211 1234566889999999999999999999999966532 23566655543
No 202
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=58.84 E-value=26 Score=28.95 Aligned_cols=45 Identities=11% Similarity=0.040 Sum_probs=36.4
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
++.+|...+.+-+|..+|++..|+|+.-....|..|.+.|++=-=
T Consensus 14 L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~ 58 (150)
T COG1959 14 LLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSV 58 (150)
T ss_pred HHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEee
Confidence 355665332336999999999999999999999999999998543
No 203
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=58.62 E-value=43 Score=27.73 Aligned_cols=67 Identities=16% Similarity=0.350 Sum_probs=54.3
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC-CcccceecccccC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP-QEHLYWFPSLFTE 245 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~-~e~~yw~p~lf~~ 245 (254)
||.+.-.+|+++. ..+--|..+|++.-|=.+.-.-.-|.+|+.-|++-..+..+ ..+..||-++..+
T Consensus 62 Lsp~nleLl~~Ia--~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~gq~k~P~~~y~~l~I~ 129 (144)
T COG4190 62 LSPRNLELLELIA--QEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEEDGQRKQPVVWYDELVID 129 (144)
T ss_pred hChhHHHHHHHHH--hcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEecCCcccCceeeccccEEe
Confidence 5656667777777 45789999999999999999999999999999999877422 4578999887553
No 204
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=58.53 E-value=21 Score=34.36 Aligned_cols=45 Identities=9% Similarity=0.055 Sum_probs=38.2
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
+..+|..+|++.++.++...++.|+.|.+.|++-++++ + .|.|+.
T Consensus 308 g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~----g-~~~l~r 352 (412)
T PRK04214 308 GKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGER----G-QWVLAR 352 (412)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCC----C-ceEecC
Confidence 55789999999999999999999999999999986543 1 377763
No 205
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=58.52 E-value=20 Score=26.44 Aligned_cols=33 Identities=18% Similarity=0.210 Sum_probs=29.8
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 198 VSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 198 ~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+.+|++.+|+++.-....|..|++.|++-++..
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 468999999999999999999999999888754
No 206
>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=58.41 E-value=55 Score=24.46 Aligned_cols=55 Identities=15% Similarity=0.145 Sum_probs=42.4
Q ss_pred CCChhHHHHHHHhhcc--CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 176 ELSLDHSLVLQQVASK--NEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 176 els~D~~~il~l~~~~--~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.++.++-+||..++.. .--+|-.+.+.+..|.+..-+...|..|...+++-.+..
T Consensus 3 ~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~ 59 (82)
T PF09202_consen 3 YLSKEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNK 59 (82)
T ss_dssp T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-S
T ss_pred cCCHHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCC
Confidence 3777888898888732 134899999999999999999999999999999999654
No 207
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=58.22 E-value=20 Score=24.77 Aligned_cols=37 Identities=19% Similarity=0.254 Sum_probs=29.1
Q ss_pred CcccHHHHHHhcCCCHHHH-HHHHHHHHHcCcEEEeCC
Q psy6552 194 AHISVSVLNNELNWSTERA-QHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra-~~~L~~l~~~G~lwvD~q 230 (254)
.+|+.+.+.+.+|-+..-. ...|+.++++|++.+|+.
T Consensus 19 ~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~ 56 (66)
T PF06969_consen 19 EGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDGG 56 (66)
T ss_dssp SEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-SS
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeCC
Confidence 4799999999999885555 777999999999999864
No 208
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=57.89 E-value=36 Score=29.09 Aligned_cols=48 Identities=10% Similarity=0.107 Sum_probs=40.3
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.|+.++.. ..++.|..++++.+++|+.=++.++..|++.|++--|-.-
T Consensus 166 ~Vl~~~~~-g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 166 AVRKLFKE-PGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred HHHHHHHc-CCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 67777762 1336899999999999999999999999999999888543
No 209
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=57.89 E-value=34 Score=24.77 Aligned_cols=51 Identities=16% Similarity=0.097 Sum_probs=41.1
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
++-.+|+.+.....-+++..+|...+|.++--.--.+..|++.|++-.=.-
T Consensus 3 ~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 3 IQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred hHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 466777776543345799999999999999999999999999999876543
No 210
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=57.87 E-value=17 Score=31.38 Aligned_cols=35 Identities=20% Similarity=0.227 Sum_probs=32.2
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
-|..+|++.||.|..-.+.+|..|+.+|++.+-..
T Consensus 26 PsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 26 PSERDLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 37899999999999999999999999999998754
No 211
>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=57.57 E-value=13 Score=27.50 Aligned_cols=48 Identities=15% Similarity=0.046 Sum_probs=38.4
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
++......+..+... ..+.|..++++.+|+|..-++..+..+.++|.+
T Consensus 15 ~l~~~~r~af~L~R~--~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 15 WVDSLAEAAAALARE--EAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred cCCHHHHHHHHHHHH--HcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 466666777777652 356899999999999999999999888887765
No 212
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=57.15 E-value=41 Score=28.99 Aligned_cols=63 Identities=16% Similarity=0.196 Sum_probs=45.1
Q ss_pred CChhHH-HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCC--Cccccee
Q psy6552 177 LSLDHS-LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSP--QEHLYWF 239 (254)
Q Consensus 177 ls~D~~-~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~--~e~~yw~ 239 (254)
++.-+. .++.++......+.|..++++.+++|..-++.++..|.+.|++-.+..-. +.+.|+|
T Consensus 159 Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (239)
T PRK10430 159 LTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHYGVTGRPVYRY 224 (239)
T ss_pred CCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeeccCCCCCCeee
Confidence 454333 34455542224578999999999999999999999999999996654321 4456666
No 213
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=57.04 E-value=21 Score=29.93 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=42.0
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
.|--|.++|+-.||.+.-+.-..|..+...|.|-+=.|. +--.|-.|+
T Consensus 4 ~Ga~T~eELA~~FGvttRkvaStLa~~ta~Grl~Rv~q~-gkfRy~iPg 51 (155)
T PF07789_consen 4 EGAKTAEELAGKFGVTTRKVASTLAMVTATGRLIRVNQN-GKFRYCIPG 51 (155)
T ss_pred cCcccHHHHHHHhCcchhhhHHHHHHHHhcceeEEecCC-CceEEeCCC
Confidence 588999999999999999999999999999999999995 344555665
No 214
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=56.84 E-value=66 Score=27.21 Aligned_cols=133 Identities=17% Similarity=0.270 Sum_probs=77.1
Q ss_pred HHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCce
Q psy6552 38 HLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLI 117 (254)
Q Consensus 38 ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii 117 (254)
|.+..++...-|...-.+-|. |..|..+..++|-.|-.+ ++-++.+..-+ +.|-|
T Consensus 18 qi~~lkeaF~l~D~d~~G~I~-----~~el~~ilr~lg~~~s~~----------------ei~~l~~~~d~----~~~~i 72 (160)
T COG5126 18 QIQELKEAFQLFDRDSDGLID-----RNELGKILRSLGFNPSEA----------------EINKLFEEIDA----GNETV 72 (160)
T ss_pred HHHHHHHHHHHhCcCCCCCCc-----HHHHHHHHHHcCCCCcHH----------------HHHHHHHhccC----CCCcc
Confidence 444445544444333233332 457888999999886542 12233333222 66899
Q ss_pred eHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHH--HHHHHhhccCCCc
Q psy6552 118 LLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHS--LVLQQVASKNEAH 195 (254)
Q Consensus 118 ~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~--~il~l~~~~~~g~ 195 (254)
++.+.++.+.+.... .-+++++..|.+.+..=+.|+- .++-=+.|+.+-...++ |+. .++..+.....|+
T Consensus 73 df~~Fl~~ms~~~~~-----~~~~Eel~~aF~~fD~d~dG~I--s~~eL~~vl~~lge~~~-deev~~ll~~~d~d~dG~ 144 (160)
T COG5126 73 DFPEFLTVMSVKLKR-----GDKEEELREAFKLFDKDHDGYI--SIGELRRVLKSLGERLS-DEEVEKLLKEYDEDGDGE 144 (160)
T ss_pred CHHHHHHHHHHHhcc-----CCcHHHHHHHHHHhCCCCCcee--cHHHHHHHHHhhcccCC-HHHHHHHHHhcCCCCCce
Confidence 999999999997654 3589999999999988777763 22211222332222232 221 2344444223788
Q ss_pred ccHHHHHH
Q psy6552 196 ISVSVLNN 203 (254)
Q Consensus 196 vt~~~l~~ 203 (254)
++-.+..+
T Consensus 145 i~~~eF~~ 152 (160)
T COG5126 145 IDYEEFKK 152 (160)
T ss_pred EeHHHHHH
Confidence 88887665
No 215
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=56.72 E-value=52 Score=24.42 Aligned_cols=39 Identities=15% Similarity=0.126 Sum_probs=34.3
Q ss_pred CCcccHHHHHHhc-CCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 193 EAHISVSVLNNEL-NWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 193 ~g~vt~~~l~~~l-~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.|...-.+|.+.+ |+|+..-...|..|++.|++-+....
T Consensus 16 ~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~ 55 (90)
T PF01638_consen 16 QGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYP 55 (90)
T ss_dssp TSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES
T ss_pred hCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccccc
Confidence 4789999999999 99999999999999999999998653
No 216
>TIGR03793 TOMM_pelo TOMM propeptide domain. This model represents a domain that is conserved among a large number of putative thiazole/oxazole-modified microcins (TOMM). Oddly, most of this seqence region appears homologous to nitrile hydratase subunits. This family is expanded especially in Pelotomaculum thermopropionicum SI.
Probab=56.67 E-value=23 Score=26.28 Aligned_cols=24 Identities=25% Similarity=0.450 Sum_probs=19.7
Q ss_pred hhhcCHHHHHHH----HHHHHHcCCC-cc
Q psy6552 56 EIKKDAQFRRHF----QEMCASIGVD-PL 79 (254)
Q Consensus 56 ~I~~dp~fr~~f----~~mc~~lGVd-Pl 79 (254)
.--+||+||+.+ ...|..+|++ |-
T Consensus 12 rAw~Dp~Fr~~Ll~DPraaL~e~G~~~P~ 40 (77)
T TIGR03793 12 KAWEDEAFKQALLTNPKEALEREGVQVPA 40 (77)
T ss_pred HHHcCHHHHHHHHHCHHHHHHHhCCCCCC
Confidence 334799999988 8889999999 54
No 217
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=56.54 E-value=58 Score=29.55 Aligned_cols=64 Identities=22% Similarity=0.294 Sum_probs=38.9
Q ss_pred hcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCC
Q psy6552 58 KKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQ 137 (254)
Q Consensus 58 ~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~ 137 (254)
..+-+.-++....-..+|--|++.+ |=+||++|.....+-.++. . +
T Consensus 89 t~~~~ie~~l~~l~~~aG~v~V~G~-------------------------------Gl~ITi~d~~~~~~~~~~~-~--~ 134 (247)
T COG3879 89 TDDAALEDRLEKLRMLAGSVPVTGP-------------------------------GLVITIDDPGYSPNGVGPN-S--Q 134 (247)
T ss_pred hHHHHHHHHHHHHHHHhccCCCcCC-------------------------------cEEEEecCCCCCcccCCCC-c--c
Confidence 3344444456666667787777732 3456666665554443322 1 5
Q ss_pred CCCHHHHHHHHHHhhhhC
Q psy6552 138 DITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg 155 (254)
.|.++|+..-++-|..-|
T Consensus 135 vv~~~dl~~viNeL~~sG 152 (247)
T COG3879 135 VVHDDDLQAVINELNISG 152 (247)
T ss_pred ccCHHHHHHHHHHHHhcc
Confidence 688888888888877766
No 218
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=56.42 E-value=43 Score=24.69 Aligned_cols=44 Identities=11% Similarity=0.074 Sum_probs=36.6
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
..|+..+. .+..|-++|.+..||+..-.--.|..|.++|++-+-
T Consensus 8 ~~IL~~ls---~~c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 8 QKILIILS---KRCCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHH---hccCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 34554444 248999999999999999999999999999998665
No 219
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=56.22 E-value=35 Score=31.41 Aligned_cols=46 Identities=17% Similarity=0.146 Sum_probs=38.6
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.++++.. ...+++..+|++.+|.|..-+..+|..|++.|+.-....
T Consensus 8 ~il~~L~--~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~ 53 (319)
T PRK11886 8 QLLSLLA--DGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVK 53 (319)
T ss_pred HHHHHHH--cCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEec
Confidence 5666666 357899999999999999999999999999999655543
No 220
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=55.67 E-value=46 Score=27.30 Aligned_cols=51 Identities=20% Similarity=0.229 Sum_probs=42.1
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
-...|+++.... .+++|+.+|-+.+ +++.+-.-..|+.|++.|++-+-+..
T Consensus 22 qR~~vl~~L~~~-~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~ 77 (145)
T COG0735 22 QRLAVLELLLEA-DGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFE 77 (145)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeC
Confidence 457788888765 5679999987654 58889999999999999999999884
No 221
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=54.99 E-value=31 Score=32.40 Aligned_cols=66 Identities=15% Similarity=0.202 Sum_probs=49.9
Q ss_pred CChhHHHHHH-----HhhccCCCcccHHHHHHh--cCCCHHHHHHHHHHHHHcCcEEEeCCCC-----Ccc-cceecccc
Q psy6552 177 LSLDHSLVLQ-----QVASKNEAHISVSVLNNE--LNWSTERAQHALDFMVQEGYAWIDTQSP-----QEH-LYWFPSLF 243 (254)
Q Consensus 177 ls~D~~~il~-----l~~~~~~g~vt~~~l~~~--l~ws~~ra~~~L~~l~~~G~lwvD~q~~-----~e~-~yw~p~lf 243 (254)
+++-+..||. .+. ..+.|+..+|++. +++|++=.+..|..|++.|++-.-.... ..| .||+-+++
T Consensus 4 l~~R~~~Il~~IV~~yi~--~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L~ 81 (339)
T PRK00082 4 LDERQREILRAIVEDYIA--TGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHLL 81 (339)
T ss_pred cCHHHHHHHHHHHHHHHh--cCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHhC
Confidence 5666778876 455 4688999999966 9999999999999999999998655431 113 45555565
Q ss_pred c
Q psy6552 244 T 244 (254)
Q Consensus 244 ~ 244 (254)
.
T Consensus 82 ~ 82 (339)
T PRK00082 82 E 82 (339)
T ss_pred C
Confidence 4
No 222
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=54.79 E-value=20 Score=28.54 Aligned_cols=32 Identities=25% Similarity=0.292 Sum_probs=29.7
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
.||.++|++.+..|.--|+..|..|.++|++.
T Consensus 19 ~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 19 EVTLDELAELLFCSRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred ceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 58999999999999999999999999999653
No 223
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=54.72 E-value=48 Score=25.73 Aligned_cols=36 Identities=22% Similarity=0.257 Sum_probs=33.3
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
-.||.+.++...|.++.-+..+|..|++.|++-+|.
T Consensus 53 d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~g 88 (100)
T PF04492_consen 53 DRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRDG 88 (100)
T ss_pred ceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC
Confidence 479999999999999999999999999999997664
No 224
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=54.47 E-value=1.1e+02 Score=30.98 Aligned_cols=76 Identities=12% Similarity=0.139 Sum_probs=56.5
Q ss_pred CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
+.++++.+.+..|-..|. ++.+. +..|.. ..+.++++ ..|.+|+.+..+.+|.|.-.|...|+.
T Consensus 500 ~~~~~~~~~l~~l~~~g~---~~~~~-~~~~~~----------~~~~~~~~--~~~~~~~~~~r~~~g~sRK~~i~lle~ 563 (581)
T TIGR00475 500 GDEKVMLKRVRKAGHRGG---ETLIV-KDRLLK----------KYINELKE--EGGTFNVQQARDKLGLGRKLLIQLLEY 563 (581)
T ss_pred CCHHHHHHHHHHHHhCCC---EEEEe-CCeEHH----------HHHHHHHh--cCCcCcHHHHHHHHCccHHHHHHHHHH
Confidence 456666666666665552 33444 332332 66667776 468999999999999999999999999
Q ss_pred HHHcCcEEEeCC
Q psy6552 219 MVQEGYAWIDTQ 230 (254)
Q Consensus 219 l~~~G~lwvD~q 230 (254)
+-+.|+.-|+..
T Consensus 564 ~D~~~~T~r~g~ 575 (581)
T TIGR00475 564 FDRLGFTRREGN 575 (581)
T ss_pred hhhCCCeEEeCC
Confidence 999999988864
No 225
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=54.02 E-value=18 Score=31.82 Aligned_cols=38 Identities=24% Similarity=0.285 Sum_probs=35.6
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
-++|.+++++.++.|...|...|.+|+.+|.+-++.+.
T Consensus 18 ~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~ 55 (214)
T COG1339 18 VKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISK 55 (214)
T ss_pred ccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecC
Confidence 46999999999999999999999999999999999864
No 226
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.90 E-value=39 Score=26.87 Aligned_cols=24 Identities=17% Similarity=0.353 Sum_probs=21.6
Q ss_pred cCHHHHHHHHHHHHHcCCCcccCC
Q psy6552 59 KDAQFRRHFQEMCASIGVDPLASR 82 (254)
Q Consensus 59 ~dp~fr~~f~~mc~~lGVdPl~s~ 82 (254)
+=|+.|.+|......+|..|.+..
T Consensus 70 sYptvR~kld~vlramgy~p~~e~ 93 (122)
T COG3877 70 SYPTVRTKLDEVLRAMGYNPDSEN 93 (122)
T ss_pred ccHHHHHHHHHHHHHcCCCCCCCC
Confidence 569999999999999999999854
No 227
>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=53.40 E-value=55 Score=21.00 Aligned_cols=39 Identities=15% Similarity=0.128 Sum_probs=29.5
Q ss_pred ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
++.+..++.+.. .+.|..++++.+|+++.-....+..+.
T Consensus 2 ~~~e~~i~~~~~----~~~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 2 TPREREVLRLLA----EGKTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHHHH----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 445555666654 347999999999999998888887753
No 228
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=53.29 E-value=30 Score=31.40 Aligned_cols=37 Identities=14% Similarity=0.115 Sum_probs=34.3
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.|..|+++|++.+|+++......|+.|+.-|++-.++
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 3689999999999999999999999999999998864
No 229
>KOG0624|consensus
Probab=53.17 E-value=8 Score=37.15 Aligned_cols=23 Identities=39% Similarity=0.710 Sum_probs=19.0
Q ss_pred hhhhhcCHHHHHHHHHHHHHcCCCcccC
Q psy6552 54 KNEIKKDAQFRRHFQEMCASIGVDPLAS 81 (254)
Q Consensus 54 ~~~I~~dp~fr~~f~~mc~~lGVdPl~s 81 (254)
.++.-+||+-|++|.. |.|||.+
T Consensus 446 AKEVLsd~EkRrqFDn-----GeDPLD~ 468 (504)
T KOG0624|consen 446 AKEVLSDPEKRRQFDN-----GEDPLDP 468 (504)
T ss_pred HHHhhcCHHHHhhccC-----CCCCCCh
Confidence 3566799999999975 9999964
No 230
>PRK13239 alkylmercury lyase; Provisional
Probab=52.96 E-value=24 Score=31.09 Aligned_cols=46 Identities=24% Similarity=0.337 Sum_probs=35.8
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
+..+|.+.. .+.-+|+.+|+..+||+.+.++.+|+.+- ..-.|++.
T Consensus 24 ~~~llr~la--~G~pvt~~~lA~~~~~~~~~v~~~L~~l~---~~~~d~~g 69 (206)
T PRK13239 24 LVPLLRLLA--KGRPVSVTTLAAALGWPVEEVEAVLEAMP---DTEYDEDG 69 (206)
T ss_pred HHHHHHHHH--cCCCCCHHHHHHHhCCCHHHHHHHHHhCC---CeEECCCC
Confidence 445566555 47789999999999999999999998863 44568763
No 231
>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=52.88 E-value=39 Score=25.61 Aligned_cols=52 Identities=15% Similarity=0.248 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCe
Q psy6552 95 YYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGF 158 (254)
Q Consensus 95 y~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~ 158 (254)
...+..+|.++|.......-| |++.++...+ .++++||..||+.|-.-|.=|
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~G-v~v~~I~~~l-----------~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEG-VHVDEIAQQL-----------GMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTT-EEHHHHHHHS-----------TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCc-ccHHHHHHHh-----------CcCHHHHHHHHHHHHhCCeEe
Confidence 467889999999994444445 8899999776 258999999999998877433
No 232
>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=52.09 E-value=65 Score=21.11 Aligned_cols=41 Identities=12% Similarity=-0.003 Sum_probs=29.5
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
|++.+..++.+.- ..+.|..++++.+|+|+.-++..|..+.
T Consensus 11 L~~~~r~i~~l~~---~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRY---FQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHH---TS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH---HHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 6667778888777 3579999999999999999988887654
No 233
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=52.03 E-value=55 Score=21.16 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=25.5
Q ss_pred CCCCCh-hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552 174 PGELSL-DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL 216 (254)
Q Consensus 174 p~els~-D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L 216 (254)
|.-+++ +...++++.+ .| .|+.++++.+|+|..=....|
T Consensus 3 p~~~~~~~~~~i~~l~~---~G-~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYA---EG-MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSSHCCHHHHHHHHH---TT---HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHH---CC-CCHHHHHHHHCcCHHHHHHHH
Confidence 334565 3467788887 45 999999999999987555444
No 234
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=51.87 E-value=21 Score=26.85 Aligned_cols=67 Identities=19% Similarity=0.189 Sum_probs=44.7
Q ss_pred HHHHHHHHcCCC--cccCCCccccccccc---------hhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCC
Q psy6552 66 HFQEMCASIGVD--PLASRKGFWSLLGMG---------DFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSL 134 (254)
Q Consensus 66 ~f~~mc~~lGVd--Pl~s~kg~w~~lg~g---------dfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~ 134 (254)
+...+|..||-| .|+. .||+. ++-..+..|+...+..=+.++|.--+..-|.+.+++
T Consensus 6 ~l~~ia~~LG~dW~~LA~------eLg~s~~dI~~i~~e~p~~~~~q~~~lL~~W~~r~g~~At~~~L~~aL~~------ 73 (84)
T cd08803 6 RMAIVADHLGLSWTELAR------ELNFSVDEINQIRVENPNSLIAQSFMLLKKWVTRDGKNATTDALTSVLTK------ 73 (84)
T ss_pred HHHHHHHHhhccHHHHHH------HcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHH------
Confidence 567788888888 4553 34443 233346667777777777777777777788877775
Q ss_pred CCCCCCHHHHHHHH
Q psy6552 135 QHQDITNEDLLAAA 148 (254)
Q Consensus 135 ~~~~IS~~Di~rA~ 148 (254)
|--+||+.++
T Consensus 74 ----i~R~DIv~~~ 83 (84)
T cd08803 74 ----INRIDIVTLL 83 (84)
T ss_pred ----CCcHHHHHhc
Confidence 4567777654
No 235
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=51.18 E-value=1.5e+02 Score=24.89 Aligned_cols=152 Identities=15% Similarity=0.112 Sum_probs=85.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhh----cCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHh
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEYKNEIK----KDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVC 106 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh~~~I~----~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c 106 (254)
.-+.++.++..+.+.|..+|.++-.... .+|..- -+..++.-.+-.+... .-+-..||.=++.-+--++
T Consensus 15 D~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~l-v~ea~lrl~~~~~~~~------~~~~~~f~~~~~~~~rr~l 87 (185)
T PF07638_consen 15 DEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTAL-VHEAFLRLARRGRFVQ------FSDRRHFWALLARIMRRKL 87 (185)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHH-HHHHHHHHhccccccC------CCCHHHHHHHHHHHHHHHH
Confidence 4456788888898999989988743322 223221 2344444444222210 0012456554444444444
Q ss_pred hh-----hhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhH
Q psy6552 107 LA-----TNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDH 181 (254)
Q Consensus 107 ~~-----~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~ 181 (254)
.. .+.+.||=....++-...-. . +.-+|++++.--+.|+.|-. +.+++
T Consensus 88 id~~R~~~a~KRg~~~~~~~l~~~~~~---~----~~~~~~~~~~l~e~l~~L~~--------------------l~~~~ 140 (185)
T PF07638_consen 88 IDHARRRQAQKRGGDQVRVELDERADS---G----DEPSPEELLELEEALERLLA--------------------LDPRQ 140 (185)
T ss_pred HHHHHHHHHHhcCCCCcccchhhhhcc---c----cCCCHHHHHHHHHHHHHHHc--------------------cCHHH
Confidence 33 22344433222222222111 1 34577777766666665320 34478
Q ss_pred HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 182 SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
..++++.- ..+.|..++++.+|+|+.-++..|..+
T Consensus 141 ~~~v~l~~---~~Gls~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 141 RRVVELRF---FEGLSVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred HHHHHHHH---HCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 88888866 346799999999999999888887764
No 236
>PHA02591 hypothetical protein; Provisional
Probab=50.91 E-value=65 Score=24.23 Aligned_cols=49 Identities=22% Similarity=0.329 Sum_probs=32.8
Q ss_pred EEeCCceEEEEccCCCCChhH-HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 161 IPIGQGQYLVQSIPGELSLDH-SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 161 ~~~~sg~~vv~s~p~els~D~-~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
+.++.-+++|.|-+ |. +..-+|.+ -+.|.+++|+.||.+..-.+..|+.
T Consensus 33 vqv~~~ryfi~~~d-----d~~~vA~eL~e----qGlSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 33 VQVGQTRYFVESED-----DLISVTHELAR----KGFTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred heeCCEEEEEeccc-----hHHHHHHHHHH----cCCCHHHHHHHhCCCHHHHHHHHhc
Confidence 44553455665442 33 23345555 3699999999999999988887753
No 237
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=50.60 E-value=44 Score=29.38 Aligned_cols=30 Identities=33% Similarity=0.556 Sum_probs=24.1
Q ss_pred HcCCCcccCCCccccccccchhHHHHHHHHHHHhhh
Q psy6552 73 SIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLA 108 (254)
Q Consensus 73 ~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~ 108 (254)
.|||+|... .+|++|+--||.+.+++....
T Consensus 105 EL~V~~~~Y------ilGl~D~vGELrR~~le~l~~ 134 (204)
T COG2178 105 ELGVPPIAY------ILGLADAVGELRRHVLELLRK 134 (204)
T ss_pred HcCCCHHHH------HHHHHHHHHHHHHHHHHHHHh
Confidence 377777764 778999999999999887765
No 238
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=50.52 E-value=88 Score=26.84 Aligned_cols=74 Identities=14% Similarity=0.008 Sum_probs=52.3
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHH
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALD 217 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~ 217 (254)
..+++++.+|+...-. |..+ +.+. ..+.|..|+.-+..||.++. .+.|..++++.+++|+.-.+.++.
T Consensus 107 ~~~~~~L~~aI~~v~~-g~~~----~~~~---~~~~~~~LT~RE~eVL~lla----~G~snkeIA~~L~iS~~TVk~h~~ 174 (207)
T PRK15411 107 SIKPESLDDLLGDILK-KETT----ITSF---LNLPTLSLSRTESSMLRMWM----AGQGTIQISDQMNIKAKTVSSHKG 174 (207)
T ss_pred cCCHHHHHHHHHHHHc-CCcc----cCcc---ccCCcccCCHHHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHHHH
Confidence 5699999999988643 2211 1100 11222348888889999888 357889999999999999999998
Q ss_pred HH-HHcC
Q psy6552 218 FM-VQEG 223 (254)
Q Consensus 218 ~l-~~~G 223 (254)
.+ .+-|
T Consensus 175 ~I~~KL~ 181 (207)
T PRK15411 175 NIKRKIK 181 (207)
T ss_pred HHHHHhC
Confidence 74 3444
No 239
>TIGR02573 LcrG_PcrG type III secretion protein LcrG. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the protein is believed to make a 1:1 complex with PcrV (LcrV). Mutants of LcrG cause premature secretion of effector proteins into the medium.
Probab=50.44 E-value=13 Score=28.42 Aligned_cols=17 Identities=35% Similarity=0.649 Sum_probs=15.2
Q ss_pred HHHHHHHHHcCCCcccC
Q psy6552 65 RHFQEMCASIGVDPLAS 81 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~s 81 (254)
.-|++||..|||.|.+.
T Consensus 23 ~llqEm~~gLgl~p~ag 39 (90)
T TIGR02573 23 DLLQEMWQGLGLGPVAG 39 (90)
T ss_pred HHHHHHHHHcCCChHHH
Confidence 57999999999999984
No 240
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=50.39 E-value=30 Score=25.84 Aligned_cols=33 Identities=6% Similarity=0.020 Sum_probs=29.4
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL 216 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L 216 (254)
+..|++++. . |.+|..++++.+|.|..-+...|
T Consensus 8 ~~~I~e~l~--~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 8 VLEIGKYIV--E-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHH--H-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 567888888 6 89999999999999999888876
No 241
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=50.29 E-value=38 Score=31.79 Aligned_cols=56 Identities=13% Similarity=0.171 Sum_probs=44.1
Q ss_pred HhhccCCCcccHHHHHHh--cCCCHHHHHHHHHHHHHcCcEEEeCCCCC--ccc----ceeccccc
Q psy6552 187 QVASKNEAHISVSVLNNE--LNWSTERAQHALDFMVQEGYAWIDTQSPQ--EHL----YWFPSLFT 244 (254)
Q Consensus 187 l~~~~~~g~vt~~~l~~~--l~ws~~ra~~~L~~l~~~G~lwvD~q~~~--e~~----yw~p~lf~ 244 (254)
.+. ..+.|+..+|++. +|+|.+=++..|..|++.|++-.-....+ ... ||.++++.
T Consensus 15 ~l~--~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~yv~~~~~ 78 (337)
T TIGR00331 15 YIK--TGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRYYVDHLLK 78 (337)
T ss_pred HHh--cCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHHHHHHhcc
Confidence 455 4689999999999 99999999999999999999988654321 123 66666665
No 242
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=50.24 E-value=26 Score=28.45 Aligned_cols=36 Identities=22% Similarity=0.177 Sum_probs=32.9
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
=-|+.+|+..+|.++.-+..+...|+++|++-..-.
T Consensus 35 LPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg 70 (125)
T COG1725 35 LPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG 70 (125)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 478999999999999999999999999999987754
No 243
>PF01645 Glu_synthase: Conserved region in glutamate synthase; InterPro: IPR002932 Ferredoxin-dependent glutamate synthases have been implicated in a number of functions including photorespiration in Arabidopsis where they may also play a role in primary nitrogen assimilation in roots []. This region is expressed as a seperate subunit in the glutamate synthase alpha subunit from archaebacteria, or part of a large multidomain enzyme in other organisms. The aligned region of these proteins contains a putative FMN binding site and Fe-S cluster.; GO: 0015930 glutamate synthase activity, 0016638 oxidoreductase activity, acting on the CH-NH2 group of donors, 0006537 glutamate biosynthetic process, 0055114 oxidation-reduction process; PDB: 1EA0_A 2VDC_E 1OFE_A 1LLW_A 1OFD_A 1LLZ_A 1LM1_A.
Probab=50.11 E-value=35 Score=32.71 Aligned_cols=108 Identities=18% Similarity=0.176 Sum_probs=60.4
Q ss_pred cCCceeHHHHHHHHHHhcCCCCC---------CCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHH
Q psy6552 113 NGGLILLDELRTRLVKSRGKSLQ---------HQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSL 183 (254)
Q Consensus 113 nGGii~L~dl~~~~nr~Rg~~~~---------~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~ 183 (254)
.||.++-..+-..+.+.|+...- ++.-|++|+.+-|+.|+.++.+..| ++|++-..+ -.+-..
T Consensus 150 ~GG~Lp~~KV~~~ia~~R~~~~g~~~iSP~~h~di~s~edl~~~I~~Lr~~~~~~pV-----gvKl~~~~~---~~~~~~ 221 (368)
T PF01645_consen 150 EGGHLPGEKVTEEIARIRGVPPGVDLISPPPHHDIYSIEDLAQLIEELRELNPGKPV-----GVKLVAGRG---VEDIAA 221 (368)
T ss_dssp T--EE-GGG--HHHHHHHTS-TT--EE--SS-TT-SSHHHHHHHHHHHHHH-TTSEE-----EEEEE-STT---HHHHHH
T ss_pred CcceechhhchHHHHHHhCCCCCCccccCCCCCCcCCHHHHHHHHHHHHhhCCCCcE-----EEEECCCCc---HHHHHH
Confidence 47999999999999999976311 3467889999999999999966665 566654332 212222
Q ss_pred HHHHhhcc----------CCCcccHHHHHHhcCCCHHHHHHHHH-HHHHcCc-----EEEeCC
Q psy6552 184 VLQQVASK----------NEAHISVSVLNNELNWSTERAQHALD-FMVQEGY-----AWIDTQ 230 (254)
Q Consensus 184 il~l~~~~----------~~g~vt~~~l~~~l~ws~~ra~~~L~-~l~~~G~-----lwvD~q 230 (254)
+ .+... .+-+-++..+.++.|.+...+-.... .|.++|+ |++|-.
T Consensus 222 ~--~~~ag~D~ItIDG~~GGTGAap~~~~d~~GlP~~~~l~~a~~~L~~~glr~~V~Li~sGg 282 (368)
T PF01645_consen 222 G--AAKAGADFITIDGAEGGTGAAPLTSMDHVGLPTEYALARAHQALVKNGLRDRVSLIASGG 282 (368)
T ss_dssp H--HHHTT-SEEEEE-TT---SSEECCHHHHC---HHHHHHHHHHHHHCTT-CCCSEEEEESS
T ss_pred h--hhhccCCEEEEeCCCCCCCCCchhHHhhCCCcHHHHHHHHHHHHHHcCCCCceEEEEeCC
Confidence 1 22110 12246777888999998877764444 4677774 555543
No 244
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=49.91 E-value=15 Score=30.67 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=24.7
Q ss_pred HHhcCC-CHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 202 NNELNW-STERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 202 ~~~l~w-s~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+-.+.| |++.|+.+++.++++|++-.++.
T Consensus 28 s~D~~WmspdqAk~li~~A~~eGLl~~~~~ 57 (144)
T PF09999_consen 28 SFDRKWMSPDQAKRLIDEAIEEGLLEEEGG 57 (144)
T ss_pred eeecCCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 345678 99999999999999999988643
No 245
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=49.84 E-value=13 Score=27.76 Aligned_cols=24 Identities=17% Similarity=0.461 Sum_probs=20.7
Q ss_pred hhcCHHHHHHHHHHHHHcCCCccc
Q psy6552 57 IKKDAQFRRHFQEMCASIGVDPLA 80 (254)
Q Consensus 57 I~~dp~fr~~f~~mc~~lGVdPl~ 80 (254)
++=|++.+.++...|..+|++|-.
T Consensus 7 ~Rvd~~lK~~a~~i~~~lGl~~s~ 30 (83)
T TIGR02384 7 IRIDEELKKEAYAVFEELGLTPST 30 (83)
T ss_pred EeeCHHHHHHHHHHHHHhCCCHHH
Confidence 456889999999999999999765
No 246
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=49.70 E-value=2e+02 Score=26.05 Aligned_cols=31 Identities=19% Similarity=0.103 Sum_probs=23.9
Q ss_pred ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 116 LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 116 ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
-+++.+.|..+.=. ...|+++|.+|-+.|-.
T Consensus 196 ~~~~~~ay~vLgv~-------~~as~~eIk~aYr~L~~ 226 (267)
T PRK09430 196 GPTLEDAYKVLGVS-------ESDDDQEIKRAYRKLMS 226 (267)
T ss_pred CCcHHhHHHHcCCC-------CCCCHHHHHHHHHHHHH
Confidence 46788888777643 46799999999998843
No 247
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=49.69 E-value=28 Score=23.89 Aligned_cols=38 Identities=16% Similarity=0.209 Sum_probs=32.2
Q ss_pred CCcccHHHHHHhc---CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNEL---NWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l---~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
..++..++|...+ +.+...+...|+.|+++|.+.++..
T Consensus 15 r~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~g~ 55 (59)
T PF09106_consen 15 RPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVEGD 55 (59)
T ss_dssp SS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEESS
T ss_pred ccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeECC
Confidence 5689999999887 7899999999999999999999864
No 248
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=49.28 E-value=24 Score=31.35 Aligned_cols=41 Identities=17% Similarity=0.082 Sum_probs=34.3
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
=+..+|++.||.|..-.+|+|..|+..|++.+=.. .|.|=.
T Consensus 35 P~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G---~Gt~V~ 75 (241)
T COG2186 35 PSERELAERFGVSRTVVREALKRLEAKGLVEIRQG---SGTFVR 75 (241)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCC---CceEec
Confidence 46788999999999999999999999999887644 455544
No 249
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.53 E-value=54 Score=21.08 Aligned_cols=37 Identities=16% Similarity=0.180 Sum_probs=30.2
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCc
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGY 224 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~ 224 (254)
++++.. .|. |..+++..+|++......-+....+.|.
T Consensus 5 iv~~~~---~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYL---EGE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHH---cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 455555 244 9999999999999999999988888885
No 250
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=48.50 E-value=88 Score=25.62 Aligned_cols=59 Identities=19% Similarity=0.215 Sum_probs=41.5
Q ss_pred HHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEE
Q psy6552 101 QIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLV 170 (254)
Q Consensus 101 qive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv 170 (254)
.|++++... .+. ++..|||..+...- +.||+.=|+|+++.|..+|.= ..+.+++|...-
T Consensus 25 ~vl~~L~~~---~~~-~sAeei~~~l~~~~------p~islaTVYr~L~~l~e~Glv-~~~~~~~~~~~y 83 (145)
T COG0735 25 AVLELLLEA---DGH-LSAEELYEELREEG------PGISLATVYRTLKLLEEAGLV-HRLEFEGGKTRY 83 (145)
T ss_pred HHHHHHHhc---CCC-CCHHHHHHHHHHhC------CCCCHhHHHHHHHHHHHCCCE-EEEEeCCCEEEE
Confidence 556665542 223 99999999999853 579999999999999999953 333444244433
No 251
>smart00351 PAX Paired Box domain.
Probab=48.47 E-value=61 Score=25.81 Aligned_cols=53 Identities=15% Similarity=0.187 Sum_probs=42.1
Q ss_pred ceEEEEccCCCCChhH-HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCc
Q psy6552 166 GQYLVQSIPGELSLDH-SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGY 224 (254)
Q Consensus 166 g~~vv~s~p~els~D~-~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~ 224 (254)
|..++...| ++.|. ..|+.++. ++.|..++++.||++..-+...+....+.|.
T Consensus 9 ~~~~~~~~~--~s~~~R~riv~~~~----~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~ 62 (125)
T smart00351 9 GGVFVNGRP--LPDEERQRIVELAQ----NGVRPCDISRQLCVSHGCVSKILGRYYETGS 62 (125)
T ss_pred CCeecCCCC--CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCC
Confidence 445666666 77765 56777776 2479999999999999999999999988886
No 252
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=48.39 E-value=55 Score=24.40 Aligned_cols=47 Identities=15% Similarity=0.166 Sum_probs=38.0
Q ss_pred CCChhHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHc
Q psy6552 176 ELSLDHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQE 222 (254)
Q Consensus 176 els~D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~ 222 (254)
+||+++..||.+-..- ..++-....|.+.||.|+.+--..|+.|++.
T Consensus 2 ~Ls~~d~~iL~fE~~ww~~~GaKe~aIre~fGls~~rYyq~Ln~LiD~ 49 (77)
T PF11662_consen 2 GLSDRDRAILDFERRWWRHGGAKEEAIREEFGLSPTRYYQRLNALIDD 49 (77)
T ss_pred CCCHHHHHHHHHHHHhCcCCCCcHHHHHHHHCCCHHHHHHHHHHHhCC
Confidence 4788888888876532 2567788899999999999999999998754
No 253
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=48.14 E-value=30 Score=26.73 Aligned_cols=41 Identities=20% Similarity=0.145 Sum_probs=32.7
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecc
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPS 241 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~ 241 (254)
.+|..++++..|.++. .|..+++.|++=.+.. +.+.|||++
T Consensus 7 ~lt~~Elc~~~gi~~~----~l~eLve~GlIep~~~--~~~~~~F~~ 47 (101)
T PRK10265 7 TFTITEFCLHTGVSEE----ELNEIVGLGVIEPREI--QETTWVFDD 47 (101)
T ss_pred EeeHHHHHHHHCcCHH----HHHHHHHCCCeecCCC--CcccceECH
Confidence 4889999999998876 5667889999887665 457888865
No 254
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=48.14 E-value=42 Score=23.89 Aligned_cols=43 Identities=23% Similarity=0.302 Sum_probs=31.0
Q ss_pred HHHHhhccCCCcccHHHHHHhc---CC--CHHHHHHHHHHHHHcCcEEE
Q psy6552 184 VLQQVASKNEAHISVSVLNNEL---NW--STERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l---~w--s~~ra~~~L~~l~~~G~lwv 227 (254)
||++..+. .+.++...|++.+ |+ |..-.+..|..|+++|++..
T Consensus 3 IL~~L~~~-~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~ 50 (66)
T PF08461_consen 3 ILRILAES-DKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRK 50 (66)
T ss_pred HHHHHHHc-CCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccc
Confidence 56665543 5678888888766 44 45778888999999996553
No 255
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=47.86 E-value=29 Score=26.59 Aligned_cols=42 Identities=17% Similarity=0.215 Sum_probs=31.2
Q ss_pred CChhHHHH--HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 177 LSLDHSLV--LQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 177 ls~D~~~i--l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
|+.+|... -||-+.-..-++|.++++..+|+|++....+|+.
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l 46 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNL 46 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcC
Confidence 66676544 4454432356899999999999999999888764
No 256
>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=47.76 E-value=77 Score=22.17 Aligned_cols=48 Identities=21% Similarity=0.285 Sum_probs=36.4
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg 155 (254)
.++|-+++.+|.+++.. -|-.|+.++... ..++++.|.+|+-.|-..|
T Consensus 8 ~~~fG~~~~~V~~~Ll~-----~G~ltl~~i~~~-----------t~l~~~~Vk~~L~~LiQh~ 55 (62)
T PF08221_consen 8 EEHFGEIVAKVGEVLLS-----RGRLTLREIVRR-----------TGLSPKQVKKALVVLIQHN 55 (62)
T ss_dssp HHHHHHHHHHHHHHHHH-----C-SEEHHHHHHH-----------HT--HHHHHHHHHHHHHTT
T ss_pred HHHcChHHHHHHHHHHH-----cCCcCHHHHHHH-----------hCCCHHHHHHHHHHHHHcC
Confidence 47889999999999876 478888888754 3479999999998887655
No 257
>COG1031 Uncharacterized Fe-S oxidoreductase [Energy production and conversion]
Probab=47.54 E-value=61 Score=32.28 Aligned_cols=100 Identities=24% Similarity=0.274 Sum_probs=63.8
Q ss_pred hHHHHHHHHHHHhhhhh----hhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCC--CeEEEE--eCC
Q psy6552 94 FYYELSVQIVEVCLATN----YKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGN--GFSIIP--IGQ 165 (254)
Q Consensus 94 fy~eLavqive~c~~~r----~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~--g~~l~~--~~s 165 (254)
=|.+=+++|+.+...+- -..=|+=|-++-..+.|- -+.||+|+++|++.+...|. |+.=++ +.
T Consensus 292 ~yp~eSr~i~K~ivky~TpGnVaAfGlEsaDp~V~r~Nn--------L~~spEEvl~AV~ivn~vG~~rg~nGlP~lLP- 362 (560)
T COG1031 292 RYPEESREIAKVIVKYGTPGNVAAFGLESADPRVARKNN--------LNASPEEVLEAVEIVNEVGGGRGYNGLPYLLP- 362 (560)
T ss_pred cChHHHHHHHHHHHhhCCCCceeeeeccccCHHHHhhcc--------ccCCHHHHHHHHHHHHHhcCccCcCCCccccc-
Confidence 35555677777666543 223466677776666664 37899999999999999986 331111 12
Q ss_pred ceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 166 GQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 166 g~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
|..+|.-.|+|-++ +..+-.+.|++++++|++.|--.
T Consensus 363 GINfv~GL~GEtke----------------------------T~~ln~efL~~ild~gllvRRIN 399 (560)
T COG1031 363 GINFVFGLPGETKE----------------------------TYELNYEFLKEILDEGLLVRRIN 399 (560)
T ss_pred cceeEecCCCccHH----------------------------HHHhhHHHHHHHHhcCceEEEee
Confidence 56666666655441 33445567777777887777654
No 258
>KOG0027|consensus
Probab=47.31 E-value=98 Score=24.98 Aligned_cols=73 Identities=18% Similarity=0.324 Sum_probs=41.8
Q ss_pred HHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCC-CCHHH
Q psy6552 65 RHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQD-ITNED 143 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~-IS~~D 143 (254)
.++.....++|..|-.. ++.++....-....|-|.+.+...++.+...... .. -+.++
T Consensus 28 ~el~~~lr~lg~~~t~~-------------------el~~~~~~~D~dg~g~I~~~eF~~l~~~~~~~~~--~~~~~~~e 86 (151)
T KOG0027|consen 28 EELGAVLRSLGQNPTEE-------------------ELRDLIKEIDLDGDGTIDFEEFLDLMEKLGEEKT--DEEASSEE 86 (151)
T ss_pred HHHHHHHHHcCCCCCHH-------------------HHHHHHHHhCCCCCCeEcHHHHHHHHHhhhcccc--cccccHHH
Confidence 46778888888886642 2333333333335677788888777777543311 11 24556
Q ss_pred HHHHHHHhhhhCCCe
Q psy6552 144 LLAAAKKLKIFGNGF 158 (254)
Q Consensus 144 i~rA~~~L~~Lg~g~ 158 (254)
+..|-+.+.+-|.||
T Consensus 87 l~eaF~~fD~d~~G~ 101 (151)
T KOG0027|consen 87 LKEAFRVFDKDGDGF 101 (151)
T ss_pred HHHHHHHHccCCCCc
Confidence 666666665555443
No 259
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=47.00 E-value=11 Score=33.09 Aligned_cols=51 Identities=14% Similarity=0.193 Sum_probs=26.1
Q ss_pred HHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcC
Q psy6552 9 AIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD 60 (254)
Q Consensus 9 ~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~d 60 (254)
||..-....++.....+...+.+++||+++|+.++++.+ .++++..+++++
T Consensus 2 GI~~l~~~~~~~~~~~~~~~~~a~~dl~~L~~qa~~~~~-~l~~fa~k~~~~ 52 (223)
T PF04157_consen 2 GIAGLQRRQEQKRQYNELGMQLAFQDLEALMSQAKDFVE-LLENFARKHKSE 52 (223)
T ss_dssp -------------------TCCCHHHHHHHHHHHHHHHH-HHHHHHHHHCCC
T ss_pred chHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhhcc
Confidence 455555555566666666667888899999999998776 688888877655
No 260
>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=46.89 E-value=46 Score=28.92 Aligned_cols=111 Identities=15% Similarity=0.200 Sum_probs=35.8
Q ss_pred HHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHH
Q psy6552 66 HFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLL 145 (254)
Q Consensus 66 ~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~ 145 (254)
.|..|=..+.|+-- |+- ...++.-.+|=...++++-. -=++.|.||-..|+ ++++|++
T Consensus 74 Ey~k~K~~f~veee----G~~--~~~~~~~~~lL~~Fi~yIK~-----~Kvv~ledla~~f~-----------l~t~~~i 131 (188)
T PF09756_consen 74 EYEKWKSAFSVEEE----GED--EEEEEEESQLLQEFINYIKE-----HKVVNLEDLAAEFG-----------LRTQDVI 131 (188)
T ss_dssp --------------------------------HHHHHHHHHHH------SEE-HHHHHHHH------------S-HHHHH
T ss_pred HHHHHHHhcccccc----chh--HHHhhHHHHHHHHHHHHHHH-----cceeeHHHHHHHcC-----------CCHHHHH
Confidence 55666666666621 110 00123333355555666544 24788999887765 6899999
Q ss_pred HHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcC
Q psy6552 146 AAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELN 206 (254)
Q Consensus 146 rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ 206 (254)
.-|+.|..-|.=..|+.= .| +||.-+|.|+ ..|...+. ..|.||.++|+...|
T Consensus 132 ~ri~~L~~~g~ltGv~Dd-rG-kfIyIs~eE~----~~va~fi~--~rGRvsi~el~~~~N 184 (188)
T PF09756_consen 132 NRIQELEAEGRLTGVIDD-RG-KFIYISEEEM----EAVAKFIK--QRGRVSISELAQESN 184 (188)
T ss_dssp HHHHHHHHHSSS-EEE-T-T---EEE-----------------------------------
T ss_pred HHHHHHHHCCCceeeEcC-CC-CeEEecHHHH----HHHHHHHH--HcCCccHHHHHHHHH
Confidence 999999999966666643 37 4665565444 35566666 479999999987654
No 261
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.81 E-value=36 Score=26.19 Aligned_cols=50 Identities=16% Similarity=0.277 Sum_probs=33.6
Q ss_pred CChhHHHH--HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 177 LSLDHSLV--LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 177 ls~D~~~i--l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
||..|..+ -++.+....--+|.++++..+||+..-.+..|..--+--.+|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW 54 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVW 54 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhH
Confidence 56666544 445443335679999999999999998888875543333333
No 262
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=46.73 E-value=3.5e+02 Score=27.91 Aligned_cols=131 Identities=17% Similarity=0.107 Sum_probs=86.0
Q ss_pred HHHHHHHHHHcCCCcccCCCccccccccchhHHHHH---HHHHHHhhhhh---------hhcCCceeHHHHHHHHHHhcC
Q psy6552 64 RRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELS---VQIVEVCLATN---------YKNGGLILLDELRTRLVKSRG 131 (254)
Q Consensus 64 r~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLa---vqive~c~~~r---------~~nGGii~L~dl~~~~nr~Rg 131 (254)
+++.-.||.+--.|-++. |=-|||+ .+|+.++-..= -.+|+--+|.+|-.++.
T Consensus 39 ~~rllrli~~~kpDIvAv-----------DnvyEL~~~~~~li~il~~lP~~tkLVQVTg~~g~~~sL~~lArr~G---- 103 (652)
T COG2433 39 LRRLLRLIWSYKPDIVAV-----------DNVYELGADKRDLIRILKRLPEGTKLVQVTGRPGEQESLWELARRHG---- 103 (652)
T ss_pred HHHHHHHHHhcCCCEEEe-----------ccHHHHhcChhHHHHHHHhCCCCceEEEEeCCCCCcchHHHHHHHhC----
Confidence 567778888888887763 4567888 88888876532 24566888877765543
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHH
Q psy6552 132 KSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTER 211 (254)
Q Consensus 132 ~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~r 211 (254)
.. ++...+|.|=-.||..|..+|-|+.+..|....++..|.- .| . +.|+-|..--..+..=..-+
T Consensus 104 ~~-~~~~~~P~eeA~~~A~LA~~GvG~ev~~fEdeT~I~VsR~--RS----------~--g~GGwSq~RY~R~vh~av~~ 168 (652)
T COG2433 104 IR-VNGKLNPYEEAYACARLASKGVGTEVSVFEDETKITVSRG--RS----------L--GPGGWSQNRYRRRVHGAVKR 168 (652)
T ss_pred CC-CCCCCChHHHHHHHHHHHhcCCCceeEeeeeeeEEEEEec--cc----------C--CCCCccHHHHHHHHHHHHHH
Confidence 31 1246899999999999999999999999984454554443 33 1 34545555554444444444
Q ss_pred HHHHHHH-HHHcCc
Q psy6552 212 AQHALDF-MVQEGY 224 (254)
Q Consensus 212 a~~~L~~-l~~~G~ 224 (254)
+...++. |.+.|+
T Consensus 169 ~~reIee~L~~agl 182 (652)
T COG2433 169 VVREIEEKLDEAGL 182 (652)
T ss_pred HHHHHHHHHHhcCC
Confidence 4455554 455554
No 263
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=46.16 E-value=35 Score=28.05 Aligned_cols=35 Identities=9% Similarity=0.073 Sum_probs=32.2
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.+|..+|++-+|.+++-.-..|..|.++|++-+..
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~ 177 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHK 177 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 37999999999999999999999999999998764
No 264
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=45.30 E-value=58 Score=29.26 Aligned_cols=63 Identities=14% Similarity=0.107 Sum_probs=51.0
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceecccccCcc
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSLFTECM 247 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~lf~~~~ 247 (254)
-..+++... +.++.+.++++.+++....-++=+|..|+.++++=-=.- ++...|||+-+.-..
T Consensus 103 R~~Iy~~i~--~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~--~g~~~yfpa~~t~~~ 165 (240)
T COG3398 103 RDGIYNYIK--PNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRV--GGALRYFPADMTYGE 165 (240)
T ss_pred HHHHHHHhc--cCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhcc--CCceEEccCCCCccc
Confidence 445677777 579999999999999999999999999999998744333 567899999776443
No 265
>PF07216 LcrG: LcrG protein; InterPro: IPR009863 This family consists of several bacterial LcrG proteins. Yersiniae are equipped with the Yop virulon, an apparatus that allows extracellular bacteria to deliver toxic Yop proteins inside the host cell cytosol in order to sabotage the communication networks of the host cell or even to cause cell death. LcrG is a component of the Yop virulon involved in the regulation of secretion of the Yops []. This protein is found in type III secretion operons, along with LcrR, H and V. Also known as PcrG in Pseudomonas, the prot ein is believed to make a 1:1 complex with PcrV (LcrV) []. Mutations in LcrG cause premature secretion of effector proteins into the medium [].
Probab=45.29 E-value=17 Score=27.90 Aligned_cols=17 Identities=35% Similarity=0.644 Sum_probs=15.2
Q ss_pred HHHHHHHHHcCCCcccC
Q psy6552 65 RHFQEMCASIGVDPLAS 81 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~s 81 (254)
.-|++||..|||+|.+.
T Consensus 26 ~llqEm~~gLg~~p~ag 42 (93)
T PF07216_consen 26 DLLQEMLEGLGLGPVAG 42 (93)
T ss_pred HHHHHHHHhcCCChhHH
Confidence 46999999999999984
No 266
>smart00350 MCM minichromosome maintenance proteins.
Probab=45.00 E-value=46 Score=32.88 Aligned_cols=53 Identities=17% Similarity=0.161 Sum_probs=32.9
Q ss_pred HHHHHHHHHhhhhhhhcC-------------CceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 97 ELSVQIVEVCLATNYKNG-------------GLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 97 eLavqive~c~~~r~~nG-------------Gii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
+...-|++++..+|.... .+++|-.+-...-|.++. +.|+++|+..|+++++.
T Consensus 441 ~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r----~~V~~~Dv~~ai~l~~~ 506 (509)
T smart00350 441 EAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLS----DVVEEADVEEAIRLLRE 506 (509)
T ss_pred HHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCC----CccCHHHHHHHHHHHHH
Confidence 444556677777774321 113343444444455555 78999999999999863
No 267
>PF10376 Mei5: Double-strand recombination repair protein ; InterPro: IPR018468 Mei5 is one of a pair of meiosis-specific proteins which facilitate the loading of Dmc1 on to Rad51 on DNA at double-strand breaks during recombination. Recombination is carried out by a large protein complex based around the two RecA homologues, Rad51 and Dmc1 []. This complex may play both a catalytic and a structural role in the interaction between homologous chromosomes during meiosis. Mei5 is seen to contain a coiled-coli region.
Probab=44.67 E-value=58 Score=28.96 Aligned_cols=46 Identities=24% Similarity=0.445 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhh--cCHHHHHHHHHHHHHcCCCc
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEYKNEIK--KDAQFRRHFQEMCASIGVDP 78 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh~~~I~--~dp~fr~~f~~mc~~lGVdP 78 (254)
..++|+.++.+.+..=+.-+.+...... .+|+| ...+++..+||||
T Consensus 168 ~~~~Lq~lI~Kwr~~~q~~l~eL~~~~~~~e~~~~--TM~eL~~~l~ID~ 215 (221)
T PF10376_consen 168 DLEQLQSLIKKWRSASQEALYELQSEMSEEEGEKF--TMGELIKRLGIDY 215 (221)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhhccccCc--cHHHHHHHhCCCc
Confidence 4456666665555444433444433333 35666 7889999999996
No 268
>PRK09191 two-component response regulator; Provisional
Probab=44.46 E-value=34 Score=29.43 Aligned_cols=52 Identities=15% Similarity=0.054 Sum_probs=39.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCH-------HHHHHHHHHHHHcCcEEEeCCC
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWST-------ERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~-------~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
|+.++..++.+.. ..+.|..++++.+|+|. .||...|......-++++|++.
T Consensus 89 L~~~~r~v~~l~~---~~~~s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~~liidd~~ 147 (261)
T PRK09191 89 LTPLPRQAFLLTA---LEGFSVEEAAEILGVDPAEAEALLDDARAEIARQVATRVLIIEDEP 147 (261)
T ss_pred CCHHHhHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCeEEEEcCcH
Confidence 6667777877776 34689999999999995 4666666665666788999874
No 269
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=44.25 E-value=1.3e+02 Score=24.68 Aligned_cols=49 Identities=22% Similarity=0.349 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh---hhhhhcCHHHHHHHHHHHHHcCCCcc
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEY---KNEIKKDAQFRRHFQEMCASIGVDPL 79 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh---~~~I~~dp~fr~~f~~mc~~lGVdPl 79 (254)
.+++|+..+++|...+++=-... ..++....+-..++.+|+...|+||-
T Consensus 22 ~~e~Lee~~ekl~~vv~er~ee~~~~~~~~~er~~kl~~~r~~m~~~Gis~~ 73 (135)
T PRK10947 22 TLETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDPN 73 (135)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCHH
Confidence 66788888888888776322222 33344444445889999999999954
No 270
>PF09336 Vps4_C: Vps4 C terminal oligomerisation domain; InterPro: IPR015415 This domain is found at the C-terminal of ATPase proteins involved in vacuolar sorting. It forms an alpha helix structure and is required for oligomerisation []. ; PDB: 1XWI_A 3EIH_C 2QPA_C 3EIE_A 2RKO_A 2QP9_X 3MHV_C 3CF3_C 3CF1_A 3CF2_A ....
Probab=44.11 E-value=40 Score=23.82 Aligned_cols=33 Identities=24% Similarity=0.337 Sum_probs=22.5
Q ss_pred ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhh
Q psy6552 116 LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 116 ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~L 154 (254)
-|++.|....+.+.|. -||++||.+=-+--+.+
T Consensus 29 ~it~~DF~~Al~~~kp------SVs~~dl~~ye~w~~~F 61 (62)
T PF09336_consen 29 PITMEDFEEALKKVKP------SVSQEDLKKYEEWTKEF 61 (62)
T ss_dssp HBCHHHHHHHHHTCGG------SS-HHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHcCC------CCCHHHHHHHHHHHHHc
Confidence 3678888888888874 48899987755544443
No 271
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=43.62 E-value=44 Score=27.94 Aligned_cols=36 Identities=14% Similarity=0.189 Sum_probs=33.2
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+|..+||+-+|.++.-.-..|..|.++|++-++..
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~ 203 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGK 203 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 588999999999999999999999999999988754
No 272
>PRK05638 threonine synthase; Validated
Probab=43.55 E-value=55 Score=31.66 Aligned_cols=55 Identities=9% Similarity=0.074 Sum_probs=42.5
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcC--CCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELN--WSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~--ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
...||.+.. .+-.+..+|.+.++ ++..-...+|..|++.|++-...+. +...||.
T Consensus 373 r~~IL~~L~---~~~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~-g~~~~Y~ 429 (442)
T PRK05638 373 KLEILKILS---EREMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRK-GRRVYYK 429 (442)
T ss_pred HHHHHHHHh---hCCccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecC-CCcEEEE
Confidence 345677777 34689999999998 9999999999999999999876432 3455554
No 273
>TIGR02865 spore_II_E stage II sporulation protein E. Stage II sporulation protein E (SpoIIE) is a multiple membrane spanning protein with two separable functions. It plays a role in the switch to polar cell division during sporulation. By means of it protein phosphatase activity, located in the C-terminal region, it activates sigma-F. All proteins that score above the trusted cutoff to this model are found in endospore-forming Gram-positive bacteria. Surprisingly, a sequence from the Cyanobacterium-like (and presumably non-spore-forming) photosynthesizer Heliobacillus mobilis is homologous, and scores between the trusted and noise cutoffs.
Probab=42.42 E-value=1.3e+02 Score=31.44 Aligned_cols=137 Identities=19% Similarity=0.166 Sum_probs=79.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCccc-----CCCcc-----cc--ccccchh
Q psy6552 27 IQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLA-----SRKGF-----WS--LLGMGDF 94 (254)
Q Consensus 27 l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~-----s~kg~-----w~--~lg~gdf 94 (254)
+.+ ..+-+..|+.-.-+.+++||+....++..|+....+..+.....|+.+-. ..+|= .. .-|-+.-
T Consensus 431 l~e-~R~~va~Ql~~~s~~l~~~a~e~~~~~~~~~~~e~~i~~~L~~~gi~v~~v~~~~~~~g~~~I~l~~~~~~g~~~~ 509 (764)
T TIGR02865 431 LEE-GRRLVAEQLKGVAESVEDIAKEINLEIVFHQLLEEKIIRALNKNGIPYEDVLAYNTEGGNIDVELTIAACGGRGEC 509 (764)
T ss_pred HHH-HHHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHCCCeeEEEEEEEcCCCcEEEEEEEcCCCCccch
Confidence 444 66778899999999999999999999999999999999999999995331 11110 00 1122345
Q ss_pred HHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCC---CCCCCHHHHHHHHHHhhhh-CCCeEEEEeCCceEEE
Q psy6552 95 YYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQ---HQDITNEDLLAAAKKLKIF-GNGFSIIPIGQGQYLV 170 (254)
Q Consensus 95 y~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~---~~~IS~~Di~rA~~~L~~L-g~g~~l~~~~sg~~vv 170 (254)
-.+++.-|.++|-.... .-.+-.+...+.+-+..+ ...--.-.+.++.+--+.. |..|.+.+.+.|+..+
T Consensus 510 ~k~i~~~ls~~~g~~~~------~~~~~~~~~~~~~~~i~f~e~~~~~~~~g~a~~~k~g~~vsGD~y~~~~l~~g~~~~ 583 (764)
T TIGR02865 510 EKKIAPIISEVTGELMC------VKDERCSIDPKGRCHLTFEETPKYHVSTGVARAAKDGELVSGDSYSFGKLSAGKYAV 583 (764)
T ss_pred HHHHHHHHHHHhCCceE------ecCCcccccCCCeEEEEEecCCceeehhhHHHhcCCCCcccCceEEEEEECCCEEEE
Confidence 55666666666644321 000001111110000000 0011234456666666555 5668888887666443
No 274
>COG4840 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.30 E-value=98 Score=22.55 Aligned_cols=47 Identities=21% Similarity=0.270 Sum_probs=32.9
Q ss_pred HHHHHhhhhhhhcCCce-----------eHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhh
Q psy6552 101 QIVEVCLATNYKNGGLI-----------LLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 101 qive~c~~~r~~nGGii-----------~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~L 154 (254)
.|.|+-.+..-.|+|++ .|.|+|..+.|+ +..||.++-.-...|..|
T Consensus 12 mi~eI~~KLnmvN~gvl~~e~~d~~~~edLtdiy~mvkkk-------enfSpsEmqaiA~eL~rl 69 (71)
T COG4840 12 MIEEIREKLNMVNVGVLDPEKYDNANYEDLTDIYDMVKKK-------ENFSPSEMQAIADELGRL 69 (71)
T ss_pred HHHHHHHHHhhhhhhccCHHhcccccHHHHHHHHHHHHHh-------ccCCHHHHHHHHHHHHHh
Confidence 44555555555678877 477899999887 678999987666665543
No 275
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=42.19 E-value=45 Score=29.57 Aligned_cols=59 Identities=20% Similarity=0.214 Sum_probs=44.3
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE--EeCCCCC-cccceeccccc
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAW--IDTQSPQ-EHLYWFPSLFT 244 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw--vD~q~~~-e~~yw~p~lf~ 244 (254)
.|+.+... .. .=+++++..+|.++.-.-++|+.|++.|++- +|++..+ ...||.|+-+.
T Consensus 19 ~Il~lLt~--~p-~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~~~ 80 (217)
T COG1777 19 RILQLLTR--RP-CYVSEISRELGVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISRNL 80 (217)
T ss_pred HHHHHHhc--Cc-hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccCCe
Confidence 45666553 23 5578899999999999999999999999983 7777532 24788877654
No 276
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=42.17 E-value=1.2e+02 Score=28.92 Aligned_cols=47 Identities=11% Similarity=-0.036 Sum_probs=40.3
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+..++.... ...+++..++..+|++.......|.+|+-+|.++++..
T Consensus 298 ~~~~~~~~~---~~~~~~d~l~~~~~~~~~~~~~~L~~lel~G~i~~~~g 344 (350)
T COG0758 298 FLALLANLG---DEPKEIDRLASCTGLTIAQVLAWLLELELEGKVKRLGG 344 (350)
T ss_pred HHHHHHHhc---CCCccHHHHHHHhCCCHHHHHHHHHHHHhcCcEEeeCC
Confidence 555666555 45799999999999999999999999999999998853
No 277
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=41.95 E-value=82 Score=23.69 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=22.0
Q ss_pred CCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 206 NWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 206 ~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+|+....+..+++|+.+|++.++..
T Consensus 53 ~~~~~~~~~li~~Li~~g~L~~~~~ 77 (106)
T PF09382_consen 53 DMSKDDWERLIRQLILEGYLSEDNG 77 (106)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEEC
T ss_pred cCCHHHHHHHHHHHHHcCCceecCC
Confidence 7899999999999999999988865
No 278
>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=41.78 E-value=41 Score=21.37 Aligned_cols=38 Identities=11% Similarity=0.093 Sum_probs=26.4
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
.|+.++++.+|.++. .|...+++|++..... ..+.++|
T Consensus 1 ~~~~e~a~~~gv~~~----tlr~~~~~g~l~~~~~--~~~~~~y 38 (49)
T cd04761 1 YTIGELAKLTGVSPS----TLRYYERIGLLSPART--EGGYRLY 38 (49)
T ss_pred CcHHHHHHHHCcCHH----HHHHHHHCCCCCCCcC--CCCCEEe
Confidence 367899999999887 4556789999874333 2255554
No 279
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=41.71 E-value=33 Score=26.60 Aligned_cols=38 Identities=21% Similarity=0.330 Sum_probs=32.2
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.|.+.+.-|.-..+.+..+|+..++.|++.|++-+++.
T Consensus 29 ~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~ 66 (95)
T COG3432 29 EGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDN 66 (95)
T ss_pred CCCCCceeeeeecCcCHHHHHHHHHHHHhCCCEEeccC
Confidence 57788888888889999999999999999996666654
No 280
>TIGR00762 DegV EDD domain protein, DegV family. This family of proteins is related to DegV of Bacillus subtilis and includes paralogous sets in several species (B. subtilis, Deinococcus radiodurans, Mycoplasma pneumoniae) that are closer in percent identity to each than to most homologs from other species. This suggests both recent paralogy and diversity of function. DegV itself is encoded immediately downstream of DegU, a transcriptional regulator of degradation, but is itself uncharacterized. Crystallography suggested a lipid-binding site, while comparison of the crystal structure to dihydroxyacetone kinase and to a mannose transporter EIIA domain suggests a conserved domain, EDD, with phosphotransferase activity.
Probab=41.66 E-value=2.6e+02 Score=25.05 Aligned_cols=94 Identities=19% Similarity=0.169 Sum_probs=56.7
Q ss_pred eeHHHHHHHHHHhcCC-CCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCC--
Q psy6552 117 ILLDELRTRLVKSRGK-SLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNE-- 193 (254)
Q Consensus 117 i~L~dl~~~~nr~Rg~-~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~-- 193 (254)
|+..++|..++..... .. ...||+|+.++.+.+..-|. .++.+. .+..+|.-.+.+..+++....
T Consensus 41 i~~~~~y~~~~~~~~~p~T--S~ps~~~~~~~~~~l~~~~~--~vi~i~--------iSs~lSgty~~a~~aa~~~~~~~ 108 (275)
T TIGR00762 41 ITPEEFYEKLKESKELPKT--SQPSPGEFLELYEKLLEEGD--EVLSIH--------LSSGLSGTYQSARQAAEMVDEAK 108 (275)
T ss_pred CCHHHHHHHHHhcCCCCCc--CCCCHHHHHHHHHHHHhCCC--eEEEEE--------cCCchhHHHHHHHHHHhhCCCCC
Confidence 8899999999775433 22 58999999999998877553 444443 223366555555444442100
Q ss_pred -------------Cc--ccHHHHHHhcCCCHHHHHHHHHHHHHcC
Q psy6552 194 -------------AH--ISVSVLNNELNWSTERAQHALDFMVQEG 223 (254)
Q Consensus 194 -------------g~--vt~~~l~~~l~ws~~ra~~~L~~l~~~G 223 (254)
|+ ..+..+. .-|.+.+-..+.|+.+.+.-
T Consensus 109 i~ViDS~~~s~~~g~~v~~a~~~~-~~G~s~~eI~~~l~~~~~~~ 152 (275)
T TIGR00762 109 VTVIDSKSASMGLGLLVLEAAKLA-EEGKSLEEILAKLEELRERT 152 (275)
T ss_pred EEEECChHHHHHHHHHHHHHHHHH-HcCCCHHHHHHHHHHHHhhc
Confidence 00 1112222 34788888888888776543
No 281
>cd00213 S-100 S-100: S-100 domain, which represents the largest family within the superfamily of proteins carrying the Ca-binding EF-hand motif. Note that this S-100 hierarchy contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins are expressed exclusively in vertebrates, and are implicated in intracellular and extracellular regulatory activities. Intracellularly, S100 proteins act as Ca-signaling or Ca-buffering proteins. The most unusual characteristic of certain S100 proteins is their occurrence in extracellular space, where they act in a cytokine-like manner through RAGE, the receptor for advanced glycation products. Structural data suggest that many S100 members exist within cells as homo- or heterodimers and even oligomers; oligomerization contributes to their functional diversification. Upon binding calcium, most S100 proteins change conformation to a more open structure exposing a hydrophobic cleft. This hydrophobic surface represents th
Probab=41.32 E-value=1.2e+02 Score=21.87 Aligned_cols=74 Identities=14% Similarity=0.221 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHHHHHH--HhhhhhhcCHHHHHHHHHHHHH-cCCCcccCCCccccccccchhHHHHHHHHHHHhhhhh
Q psy6552 34 QLSQHLNTFRDKLESFAS--EYKNEIKKDAQFRRHFQEMCAS-IGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATN 110 (254)
Q Consensus 34 ~L~~ql~~fk~~L~~FA~--kh~~~I~~dp~fr~~f~~mc~~-lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r 110 (254)
++++++..++.....|-+ ...+.|.. .+|..++.. +|..|-... ..+-++-.....
T Consensus 2 ~~~~~~~~l~~~F~~~D~~~~~~G~Is~-----~el~~~l~~~~g~~~~~~~----------------~~~ei~~i~~~~ 60 (88)
T cd00213 2 ELEKAIETIIDVFHKYSGKEGDKDTLSK-----KELKELLETELPNFLKNQK----------------DPEAVDKIMKDL 60 (88)
T ss_pred hHHHHHHHHHHHHHHHhhccCCCCcCcH-----HHHHHHHHHHhhhhccCCC----------------CHHHHHHHHHHh
Confidence 567788888888888877 46666633 245555554 443211000 011122223333
Q ss_pred h-hcCCceeHHHHHHHHHH
Q psy6552 111 Y-KNGGLILLDELRTRLVK 128 (254)
Q Consensus 111 ~-~nGGii~L~dl~~~~nr 128 (254)
. .+.|.|+..+.+..+.+
T Consensus 61 d~~~~g~I~f~eF~~~~~~ 79 (88)
T cd00213 61 DVNKDGKVDFQEFLVLIGK 79 (88)
T ss_pred ccCCCCcCcHHHHHHHHHH
Confidence 3 34578888888877765
No 282
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=41.29 E-value=1.5e+02 Score=24.27 Aligned_cols=49 Identities=18% Similarity=0.300 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh---hhhhhcCHHHHHHHHHHHHHcCCCcc
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEY---KNEIKKDAQFRRHFQEMCASIGVDPL 79 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh---~~~I~~dp~fr~~f~~mc~~lGVdPl 79 (254)
.+++|+..+++|...+++=-..+ ..+...-.+-..++.+|+..-|++|=
T Consensus 22 ~~e~Lee~~ekl~~vv~er~~~~~~~~~~~~er~~~l~~i~~~~~~~Git~e 73 (134)
T PRK10328 22 SIDVLEEMLEKFRVVTKERREEEEQQQRELAERQEKINTWLELMKADGINPE 73 (134)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHH
Confidence 67788888888888776333322 23333344556899999999999853
No 283
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=41.26 E-value=36 Score=24.17 Aligned_cols=48 Identities=13% Similarity=0.207 Sum_probs=32.0
Q ss_pred HHHHHHhhccCCCcccHHHHH--------HhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 182 SLVLQQVASKNEAHISVSVLN--------NELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 182 ~~il~l~~~~~~g~vt~~~l~--------~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
..|+.+... .+.++..+|. ..|.-+....+..|+.|++.|++=||+..
T Consensus 11 AaIVrimK~--~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d 66 (68)
T PF10557_consen 11 AAIVRIMKQ--EKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDD 66 (68)
T ss_dssp HHHHHHHHH--SSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSE
T ss_pred hheehhhhh--cCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCC
Confidence 344445542 3445555544 35678899999999999999999999874
No 284
>PLN02964 phosphatidylserine decarboxylase
Probab=41.22 E-value=80 Score=32.56 Aligned_cols=35 Identities=11% Similarity=0.096 Sum_probs=17.7
Q ss_pred CceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552 115 GLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 115 Gii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg 155 (254)
|-|++.|+...+.+.. ...+++|+..|.+.+..=|
T Consensus 194 G~IdfdEFl~lL~~lg------~~~seEEL~eaFk~fDkDg 228 (644)
T PLN02964 194 GQLSFSEFSDLIKAFG------NLVAANKKEELFKAADLNG 228 (644)
T ss_pred CeEcHHHHHHHHHHhc------cCCCHHHHHHHHHHhCCCC
Confidence 6666666666665431 1234444444444444433
No 285
>TIGR03060 PS_II_psb29 photosystem II biogenesis protein Psp29. Psp29, originally designated sll1414 in Synechocystis 6803, is found universally in Cyanobacteria and in Arabidopsis. It was isolated and partially sequenced from purified photosystem II (PS II) in Synechocystis. While its function is unknown, mutant studies show an impairment in photosystem II biogenesis and/or stability, rather than in PS II core function.
Probab=40.37 E-value=37 Score=30.10 Aligned_cols=16 Identities=38% Similarity=0.725 Sum_probs=14.2
Q ss_pred HHHHHHHHHcCCCccc
Q psy6552 65 RHFQEMCASIGVDPLA 80 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~ 80 (254)
.-|..+|.++|-||-.
T Consensus 75 ~IF~Alc~a~~~dp~~ 90 (214)
T TIGR03060 75 ALFDALCNSNGFDPEQ 90 (214)
T ss_pred HHHHHHHHhcCCCHHH
Confidence 5789999999999875
No 286
>KOG2607|consensus
Probab=40.27 E-value=68 Score=31.44 Aligned_cols=131 Identities=17% Similarity=0.234 Sum_probs=72.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCcccc-cccc-chhHHHHHHHHHHHhhhhhh
Q psy6552 34 QLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWS-LLGM-GDFYYELSVQIVEVCLATNY 111 (254)
Q Consensus 34 ~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~-gdfy~eLavqive~c~~~r~ 111 (254)
-|+.||++.+....+.-+||.+=-+.-..-|.+|...|..+|+--..-.+.+-. .-+. +.||.-+.+-+.++-
T Consensus 126 ~LkKQiaK~qQq~tE~~RKe~d~~k~aa~~r~qfe~~c~qlglkG~nvr~ElLelasdLPs~fyei~~v~i~~i~----- 200 (505)
T KOG2607|consen 126 YLKKQIAKVQQQMTELDRKEADIKKSAALSRTQFEDACRQLGLKGNNVRRELLELASDLPSTFYEILEVIISDIT----- 200 (505)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHhCCccchHHHHHHHHHhcCcHHHHHHHHHHHhhhh-----
Confidence 589999999999998877876543445667999999999999861110111111 1122 266766666655432
Q ss_pred hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeC--CceEEEEccCCCCC
Q psy6552 112 KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIG--QGQYLVQSIPGELS 178 (254)
Q Consensus 112 ~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~--sg~~vv~s~p~els 178 (254)
| --|+|..+...--.+. .=-..-|+--++.+..-|+...+-... -.-..|++.+.++.
T Consensus 201 ---~---aiDyYqa~v~~v~~g~---~k~~~qVLpiL~~i~Erg~n~Tvyew~~g~~pd~VE~p~~e~l 260 (505)
T KOG2607|consen 201 ---G---AIDYYQAYVQDVHTGK---DKPLRQVLPILKYIRERGPNLTVYEWSEGLDPDNVESPENENL 260 (505)
T ss_pred ---H---HHHHHHHHHHHHhccC---CccHHHHhHHHHHHHhcCCCcceeeccccCCcccccCCchhhh
Confidence 1 1255555443221111 111234566666666667555554442 12345666665444
No 287
>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=40.24 E-value=59 Score=22.31 Aligned_cols=39 Identities=15% Similarity=0.222 Sum_probs=31.0
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
.+..++++.-. .+.+|..+|++.+|.|.--.+..|..+-
T Consensus 6 rq~~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 6 RQLKLLELLLK--NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 45567777763 4799999999999999999999888764
No 288
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=39.72 E-value=21 Score=26.15 Aligned_cols=20 Identities=40% Similarity=0.893 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHcCCCcccC
Q psy6552 62 QFRRHFQEMCASIGVDPLAS 81 (254)
Q Consensus 62 ~fr~~f~~mc~~lGVdPl~s 81 (254)
+....++.+|..+|+||++.
T Consensus 20 ~vy~~Y~~lc~~~~~~pls~ 39 (85)
T PF09079_consen 20 EVYEVYEELCESLGVDPLSY 39 (85)
T ss_dssp HHHHHHHHHHHHTTS----H
T ss_pred HHHHHHHHHHHHcCCCCCCH
Confidence 44579999999999999984
No 289
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=39.33 E-value=1.2e+02 Score=20.67 Aligned_cols=50 Identities=20% Similarity=0.293 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHhhhhhhhcCCce-eHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC
Q psy6552 95 YYELSVQIVEVCLATNYKNGGLI-LLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 95 y~eLavqive~c~~~r~~nGGii-~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg 155 (254)
|.+++..|.+....-.-..|=.+ +..++-..+ .||..=+.+|+..|...|
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~-----------~vsr~tvr~al~~L~~~g 52 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERY-----------GVSRTTVREALRRLEAEG 52 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHH-----------TS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHh-----------ccCCcHHHHHHHHHHHCC
Confidence 66777777777777777778888 888888775 478899999999999887
No 290
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=39.32 E-value=2.7e+02 Score=24.46 Aligned_cols=26 Identities=12% Similarity=0.018 Sum_probs=22.3
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
.+.|..++++.+|+|...++..+..+
T Consensus 220 ~g~s~~eIA~~lgis~~~V~~~~~ra 245 (255)
T TIGR02941 220 ENLSQKETGERLGISQMHVSRLQRQA 245 (255)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 46899999999999999998877654
No 291
>COG3177 Fic family protein [Function unknown]
Probab=39.08 E-value=60 Score=30.50 Aligned_cols=45 Identities=13% Similarity=0.093 Sum_probs=39.6
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
.|++|+.++...++.+..-|...|.++++.|++-.+.. ....|.|
T Consensus 302 ~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~--~~r~~~~ 346 (348)
T COG3177 302 EGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKG--RGRSKLY 346 (348)
T ss_pred CCCccHHHHHHHhCccHHHHHHHHHHHHhCCCeeecCC--CCCceec
Confidence 68999999999999999999999999999999999987 3444443
No 292
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=38.96 E-value=48 Score=27.56 Aligned_cols=34 Identities=15% Similarity=0.165 Sum_probs=31.3
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.+|..+|++-+|.+++-.-..|..|.++|++.+.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC
Confidence 4789999999999999999999999999999754
No 293
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=38.86 E-value=44 Score=24.64 Aligned_cols=57 Identities=21% Similarity=0.188 Sum_probs=35.0
Q ss_pred HHHHHHHHcCCC--cccCCCccccccccc-----hhH----HHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHH
Q psy6552 66 HFQEMCASIGVD--PLASRKGFWSLLGMG-----DFY----YELSVQIVEVCLATNYKNGGLILLDELRTRLVK 128 (254)
Q Consensus 66 ~f~~mc~~lGVd--Pl~s~kg~w~~lg~g-----dfy----~eLavqive~c~~~r~~nGGii~L~dl~~~~nr 128 (254)
+|...|..||-| .|+. .||+. .+- ..+-.|..+.+..=+.++|.--|+..|.+.+.+
T Consensus 6 ~l~~ia~~lG~dW~~LAr------~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~at~~~L~~AL~~ 73 (84)
T cd08317 6 RLADISNLLGSDWPQLAR------ELGVSETDIDLIKAENPNSLAQQAQAMLKLWLEREGKKATGNSLEKALKK 73 (84)
T ss_pred hHHHHHHHHhhHHHHHHH------HcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcCCcchHHHHHHHHHH
Confidence 678888888877 4553 33432 121 123356666666666777777777777777665
No 294
>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=38.80 E-value=82 Score=21.90 Aligned_cols=34 Identities=15% Similarity=0.275 Sum_probs=28.0
Q ss_pred HHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 184 VLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
+++++- ..+.||+.++++.+|.|+.=|...++++
T Consensus 4 Lidll~--~~P~Vsa~mva~~L~vT~~~A~~li~eL 37 (54)
T PF11972_consen 4 LIDLLL--SRPLVSAPMVAKELGVTPQAAQRLIAEL 37 (54)
T ss_pred HHHHHH--hCccccHHHHHHHhCCCHHHHHHHHHHh
Confidence 456665 3689999999999999999998877664
No 295
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=38.79 E-value=1.8e+02 Score=31.33 Aligned_cols=34 Identities=21% Similarity=0.107 Sum_probs=28.2
Q ss_pred CcccHHHHHH------------hcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 194 AHISVSVLNN------------ELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 194 g~vt~~~l~~------------~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
+.++.++|.+ ..|++...++++|+.|.++|.+-.
T Consensus 858 ~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~l~~L~~~g~i~~ 903 (915)
T PTZ00111 858 KSLDLNEVLSLCHKTFKDNRDHKDGEIYKLISEVLNKMVQEGTAVR 903 (915)
T ss_pred CceeHHHHHHHHHhhccccchhccCCCHHHHHHHHHHHHhCCeEee
Confidence 5688888763 458999999999999999999643
No 296
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=38.68 E-value=3.5e+02 Score=27.05 Aligned_cols=80 Identities=15% Similarity=0.190 Sum_probs=53.0
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChh----------HHHHHHHhhccCCCcccHHHHHHhcCC
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD----------HSLVLQQVASKNEAHISVSVLNNELNW 207 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D----------~~~il~l~~~~~~g~vt~~~l~~~l~w 207 (254)
-+++++|.+|++.|+..| =+.+.... ...++ |+++ ...+++++. ..|.++.++|...++
T Consensus 29 g~~~~~v~~~~~~L~~kg-~v~~~~~~-~~~~~------LT~eG~~~l~~G~PE~rl~~~l~--~~~~~~~~eL~~~l~- 97 (492)
T PLN02853 29 GLDHNEVVGVIKSLHGFR-YVDAQDIK-RETWV------LTEEGKKYAAEGSPEVQLFAAVP--AEGSISKDELQKKLD- 97 (492)
T ss_pred CCCHHHHHHHHHHHHhCC-CEEEEEEE-EEEEE------ECHHHHHHHHcCCHHHHHHHHHh--hcCCccHHHHHHhhC-
Confidence 468999999999999986 22222222 22222 3322 234455555 346689999988774
Q ss_pred CHHHHHHHHHHHHHcCcEEEeC
Q psy6552 208 STERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 208 s~~ra~~~L~~l~~~G~lwvD~ 229 (254)
..-++-.+-.+.++|++-+|.
T Consensus 98 -~~~~~i~~g~a~k~gwi~i~~ 118 (492)
T PLN02853 98 -PAVFDIGFKQAMKNKWLEMGG 118 (492)
T ss_pred -chhHHHHHHHHHHCCcEEECC
Confidence 356677888999999999984
No 297
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=38.55 E-value=1.3e+02 Score=27.99 Aligned_cols=48 Identities=15% Similarity=0.212 Sum_probs=38.6
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
+|...++.+-.|.|+..+.|+|-+|+++|.+-|-.-...--.-|..-+
T Consensus 20 GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsGKs~rVwLaey 67 (321)
T COG3888 20 GIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSGKSKRVWLAEY 67 (321)
T ss_pred CccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeecCcceEEeeccc
Confidence 699999999999999999999999999999988865322234454333
No 298
>PRK04158 transcriptional repressor CodY; Validated
Probab=38.28 E-value=59 Score=29.67 Aligned_cols=33 Identities=15% Similarity=0.175 Sum_probs=30.7
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
.|-+.++.++++.|+|......+|..++..|.+
T Consensus 199 EG~lvASkiADrvgITRSVIVNALRK~ESAGvI 231 (256)
T PRK04158 199 EGLLVASKIADRVGITRSVIVNALRKLESAGVI 231 (256)
T ss_pred cceEEeeecccccCCchhhhhhhhhhhhcccce
Confidence 478999999999999999999999999999975
No 299
>PF05873 Mt_ATP-synt_D: ATP synthase D chain, mitochondrial (ATP5H); InterPro: IPR008689 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. F-ATPases (also known as F1F0-ATPase, or H(+)-transporting two-sector ATPase) (3.6.3.14 from EC) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), nine in mitochondria (A-G, F6, F8). Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the alpha(3)beta(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis []. These ATPases can also work in reverse to hydrolyse ATP to create a proton gradient. This entry represents subunit D from the F0 complex in F-ATPases found in mitochondria. The D subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D []. There is no homologue of subunit D in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0015078 hydrogen ion transmembrane transporter activity, 0015986 ATP synthesis coupled proton transport, 0000276 mitochondrial proton-transporting ATP synthase complex, coupling factor F(o); PDB: 2CLY_E 2WSS_U.
Probab=37.72 E-value=36 Score=28.68 Aligned_cols=109 Identities=14% Similarity=0.239 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--------HhhhhhhcCHHHHHHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHH
Q psy6552 31 QLEQLSQHLNTFRDKLESFAS--------EYKNEIKKDAQFRRHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQ 101 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~--------kh~~~I~~dp~fr~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavq 101 (254)
+|..+.+.=+.++..|..+.. .|+..|..||.+=.+|+....++-|+ |... . .-.+..|..++-..
T Consensus 26 ~~~afk~r~d~~~~~v~~~pe~pp~IDwa~Yk~~l~~~~~lVD~feK~y~s~kip~p~d~-~----~~~i~~~e~~~~~~ 100 (161)
T PF05873_consen 26 QFQAFKKRSDEYKRRVSKLPEQPPKIDWAHYKSVLKENPGLVDEFEKQYESFKIPYPVDK-Q----TKEIDAQEKEAIKE 100 (161)
T ss_dssp HHHHHHHHHHHHHHHHHHS-SS-----HHHHHHC-S-STTHHHHHHHHHCC--------T-T----TTHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHhCcCCCCCCCHHHHHHHhhhhHHHHHHHHHHHhccCCCCChHH-H----HHHHHHHHHHHHHH
Confidence 555555555555555553222 35777776898889999999999887 6521 1 11234666666666
Q ss_pred HHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHh
Q psy6552 102 IVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKL 151 (254)
Q Consensus 102 ive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L 151 (254)
+-+++.. .+..|-.+..-+..++..|.. +.+|.||+..|---+
T Consensus 101 ~~~~~~~---s~~~i~~l~keL~~i~~~~P~----e~mT~dd~~~a~Pe~ 143 (161)
T PF05873_consen 101 AKEFEAE---SKKRIAELEKELANIESARPF----EQMTVDDYAAAFPEI 143 (161)
T ss_dssp HHHHHHH---HHHHHHHHHHHHHHHT------------------------
T ss_pred HHHHHHH---HHHHHHHHHHHHHHHHcCCCh----HhCCHHHHHHhCccc
Confidence 6555544 445677788888888888877 789999998875443
No 300
>TIGR03882 cyclo_dehyd_2 bacteriocin biosynthesis cyclodehydratase domain. This model describes a ThiF-like domain of a fusion protein found in clusters associated with the production of TOMMs (thiazole/oxazole-modified microcins), small bacteriocins with characteristic heterocycle modifications. This domain is presumed to act as a cyclodehydratase, as do members of the SagC family modeled by TIGR03603.
Probab=37.71 E-value=1.6e+02 Score=25.27 Aligned_cols=72 Identities=22% Similarity=0.217 Sum_probs=45.9
Q ss_pred CCCeEEEEeCCceEEEEccC--CCCChhHHHHHHHhhccCCCcccHHHHHHhcC--CCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 155 GNGFSIIPIGQGQYLVQSIP--GELSLDHSLVLQQVASKNEAHISVSVLNNELN--WSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 155 g~g~~l~~~~sg~~vv~s~p--~els~D~~~il~l~~~~~~g~vt~~~l~~~l~--ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
...|.+..++++..++-+-. ..++ -..+.+++.-. .|.-|..+|.+.+. .+.....++|..|.+.|++--+.
T Consensus 3 K~~~~~~~~~~~~v~l~~e~~~~~l~--~~~~~~L~~lL-dG~rt~~eI~~~l~~~~p~~~v~~~L~~L~~~G~l~~~~ 78 (193)
T TIGR03882 3 KPHFSVEILGPEAVFLLSERGSFALS--GALYCQLAPLL-DGRRTLDEIIAALAGRFPAEEVLYALDRLERRGYLVEDA 78 (193)
T ss_pred CCCceeEEeCCCeEEEEeCCCcEEEc--chhHHHHHHHH-cCCCCHHHHHHHhhccCCHHHHHHHHHHHHHCCCEeccC
Confidence 34566666664433333322 2344 22344555543 57899999977663 46788999999999999988443
No 301
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=37.36 E-value=22 Score=26.36 Aligned_cols=24 Identities=8% Similarity=0.317 Sum_probs=17.8
Q ss_pred hhcCHHHHHHHHHHHHHcCCCccc
Q psy6552 57 IKKDAQFRRHFQEMCASIGVDPLA 80 (254)
Q Consensus 57 I~~dp~fr~~f~~mc~~lGVdPl~ 80 (254)
++=|++.+.++..+|..+|++|-+
T Consensus 6 ~Rid~~lK~~a~~il~~~Glt~s~ 29 (83)
T PF04221_consen 6 VRIDEELKEEAEAILEELGLTLSD 29 (83)
T ss_dssp EEE-HHHHHHHHHHHHHTT--HHH
T ss_pred EEcCHHHHHHHHHHHHHcCCCHHH
Confidence 456889999999999999999654
No 302
>KOG1463|consensus
Probab=37.13 E-value=68 Score=30.80 Aligned_cols=24 Identities=29% Similarity=0.654 Sum_probs=19.7
Q ss_pred HHhhhhhhcCHHHHHHHHHHHHHc
Q psy6552 51 SEYKNEIKKDAQFRRHFQEMCASI 74 (254)
Q Consensus 51 ~kh~~~I~~dp~fr~~f~~mc~~l 74 (254)
..|+.++..||-.|.+|+.+-.++
T Consensus 308 ~~yk~eL~~D~ivr~Hl~~Lyd~l 331 (411)
T KOG1463|consen 308 ADYKKELAEDPIVRSHLQSLYDNL 331 (411)
T ss_pred HHhHHHHhcChHHHHHHHHHHHHH
Confidence 368899999999999998876654
No 303
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=36.71 E-value=55 Score=27.37 Aligned_cols=77 Identities=19% Similarity=0.308 Sum_probs=54.3
Q ss_pred HhhhhhhcCHHHHHHHHHHHHHcCCCccc-CCC-c-----cccccccchhHHHHHHHHHHHhhhhh-hhcCCceeHHHHH
Q psy6552 52 EYKNEIKKDAQFRRHFQEMCASIGVDPLA-SRK-G-----FWSLLGMGDFYYELSVQIVEVCLATN-YKNGGLILLDELR 123 (254)
Q Consensus 52 kh~~~I~~dp~fr~~f~~mc~~lGVdPl~-s~k-g-----~w~~lg~gdfy~eLavqive~c~~~r-~~nGGii~L~dl~ 123 (254)
+....|.+++.|-..|+.....+|+.|.. +++ + .+..+...||-+.--.||+.-..+.. +.|||.|.+--..
T Consensus 6 rl~~~ies~E~F~~~l~~~l~Elglt~~eFak~anIP~StLYKil~G~dpr~~tl~~I~ktir~~ek~en~~fiA~IAAR 85 (170)
T COG4800 6 RLAECIESGEDFGSCLQKLLDELGLTPSEFAKRANIPLSTLYKILKGSDPRYDTLTRIFKTIRSYEKKENIGFIALIAAR 85 (170)
T ss_pred HHHHHHhchhHHHHHHHHHHHHcCCCHHHHHHHcCCCHHHHHHHHhCCCccHHHHHHHHHHHHHHHhccCCCeeeeeehH
Confidence 33446778999999999999999998773 111 1 23322226888887788888777665 5699999877666
Q ss_pred HHHHH
Q psy6552 124 TRLVK 128 (254)
Q Consensus 124 ~~~nr 128 (254)
..+++
T Consensus 86 ~vL~~ 90 (170)
T COG4800 86 YVLEE 90 (170)
T ss_pred HHHHH
Confidence 65554
No 304
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=36.67 E-value=56 Score=30.69 Aligned_cols=37 Identities=19% Similarity=0.180 Sum_probs=33.7
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.++|-+++++++|+|...+...|..+.++|++=|=-.
T Consensus 25 ~gltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~ 61 (321)
T COG2390 25 EGLTQSEIAERLGISRATVSRLLAKAREEGIVKISIN 61 (321)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence 4699999999999999999999999999999877544
No 305
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=36.67 E-value=1.9e+02 Score=24.21 Aligned_cols=44 Identities=25% Similarity=0.222 Sum_probs=36.4
Q ss_pred CCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH-HHcC
Q psy6552 176 ELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM-VQEG 223 (254)
Q Consensus 176 els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l-~~~G 223 (254)
.|+.-+..|+.++. .+.|..++++.+++|..-.+.++..+ .+-|
T Consensus 150 ~Lt~rE~evl~~~~----~G~s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 150 RLSPKESEVLRLFA----EGFLVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred cCCHHHHHHHHHHH----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 48877888998887 35999999999999999999998875 3444
No 306
>TIGR00667 aat leucyl/phenylalanyl-tRNA--protein transferase. The N-terminal residue controls the biological half-life of many proteins via the N-end rule pathway. This enzyme transfers a Leu or Phe to the amino end of certain proteins to enable degradation.
Probab=36.53 E-value=1.9e+02 Score=25.09 Aligned_cols=81 Identities=20% Similarity=0.202 Sum_probs=49.2
Q ss_pred CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHH
Q psy6552 137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHAL 216 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L 216 (254)
.-||| ||.+|-..|..+|....+.....| .+|=-.-+ .. - ++-|.-.++-+..-+=|+.--....
T Consensus 79 TWI~~-e~~~aY~~LH~~G~AHSvEvw~~~-~LvGGlYG-v~----------i--G~~F~GESMFs~~~nASKvAl~~L~ 143 (185)
T TIGR00667 79 TWISD-ELVEAYHRLHELGHAHSFEVWQGD-ELVGGMYG-IA----------Q--GGLFCGESMFSRMTNASKTALLVFC 143 (185)
T ss_pred CCCCH-HHHHHHHHHHHhCceEEEEEEECC-EEEEeeee-ee----------e--CCeEEeccccccCCChhHHHHHHHH
Confidence 47886 689999999999998888877623 23322110 00 0 1123344444444444555444455
Q ss_pred HHHHHcCcEEEeCCCC
Q psy6552 217 DFMVQEGYAWIDTQSP 232 (254)
Q Consensus 217 ~~l~~~G~lwvD~q~~ 232 (254)
+.|...|...+|-|..
T Consensus 144 ~~L~~~g~~liDcQ~~ 159 (185)
T TIGR00667 144 EHFIRHGGQLIDCQVQ 159 (185)
T ss_pred HHHHHCCCcEEEECCC
Confidence 5678889999998863
No 307
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=36.49 E-value=27 Score=26.12 Aligned_cols=24 Identities=17% Similarity=0.409 Sum_probs=20.4
Q ss_pred hhcCHHHHHHHHHHHHHcCCCccc
Q psy6552 57 IKKDAQFRRHFQEMCASIGVDPLA 80 (254)
Q Consensus 57 I~~dp~fr~~f~~mc~~lGVdPl~ 80 (254)
++=|++...+..+.|..+|++|-+
T Consensus 6 vRiD~~lK~~A~~vl~~lGls~S~ 29 (80)
T PRK11235 6 VRVDDELKARAYAVLEKLGVTPSE 29 (80)
T ss_pred EEeCHHHHHHHHHHHHHhCCCHHH
Confidence 345888899999999999999765
No 308
>KOG2410|consensus
Probab=36.42 E-value=24 Score=35.68 Aligned_cols=31 Identities=23% Similarity=0.393 Sum_probs=22.1
Q ss_pred cchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHH
Q psy6552 91 MGDFYYELSVQIVEVCLATNYKNGGLILLDELRT 124 (254)
Q Consensus 91 ~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~ 124 (254)
...||.. .+.+-+.+...++|||||++||-.
T Consensus 236 ~~~FY~G---~~a~~lvkdiq~~GGiiT~qDl~~ 266 (579)
T KOG2410|consen 236 PEAFYNG---ELAQKLVKDIQKAGGIITEQDLEN 266 (579)
T ss_pred cccccCh---HHHHHHHHHHHHhCCceEHHHHhh
Confidence 3467764 444444455678999999999987
No 309
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=36.38 E-value=1.1e+02 Score=19.82 Aligned_cols=38 Identities=24% Similarity=0.406 Sum_probs=23.4
Q ss_pred CCceeHHHHHHHHHHhcCCCCCCCC-CCHHHHHHHHHHhhhhCCC
Q psy6552 114 GGLILLDELRTRLVKSRGKSLQHQD-ITNEDLLAAAKKLKIFGNG 157 (254)
Q Consensus 114 GGii~L~dl~~~~nr~Rg~~~~~~~-IS~~Di~rA~~~L~~Lg~g 157 (254)
.|.|+..|+...+ +.-|. . +|++++..-...+..=+.|
T Consensus 2 ~G~i~~~~~~~~l-~~~g~-----~~~s~~e~~~l~~~~D~~~~G 40 (54)
T PF13833_consen 2 DGKITREEFRRAL-SKLGI-----KDLSEEEVDRLFREFDTDGDG 40 (54)
T ss_dssp SSEEEHHHHHHHH-HHTTS-----SSSCHHHHHHHHHHHTTSSSS
T ss_pred cCEECHHHHHHHH-HHhCC-----CCCCHHHHHHHHHhcccCCCC
Confidence 4677777777777 33233 3 6777777666666654444
No 310
>PRK09462 fur ferric uptake regulator; Provisional
Probab=36.21 E-value=1.5e+02 Score=23.93 Aligned_cols=48 Identities=15% Similarity=0.165 Sum_probs=36.4
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEE
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwv 227 (254)
--..|+++......+.+|+.+|-+.+ +++.+=.-..|+.|++.|++-.
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~ 70 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTR 70 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEE
Confidence 34677887764224699999988655 5677777789999999999963
No 311
>KOG4302|consensus
Probab=36.20 E-value=1.6e+02 Score=30.53 Aligned_cols=48 Identities=21% Similarity=0.503 Sum_probs=37.2
Q ss_pred HHHH-HHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCccc
Q psy6552 33 EQLS-QHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLA 80 (254)
Q Consensus 33 ~~L~-~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~ 80 (254)
.||. .-|+.|+..|..+=..+....++.-+|+......|..||+||..
T Consensus 155 ~dlsl~kLeelr~~L~~L~~ek~~Rlekv~~~~~~I~~l~~~Lg~~~~~ 203 (660)
T KOG4302|consen 155 SDLSLEKLEELREHLNELQKEKSDRLEKVLELKEEIKSLCSVLGLDFSM 203 (660)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCccc
Confidence 3444 66777777777666666667777788999999999999999874
No 312
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=36.09 E-value=63 Score=22.77 Aligned_cols=43 Identities=16% Similarity=0.253 Sum_probs=32.4
Q ss_pred HHHHhhccCCCcccHHHHHHhc----CCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 184 VLQQVASKNEAHISVSVLNNEL----NWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 184 il~l~~~~~~g~vt~~~l~~~l----~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
++.... ..|..|...+...+ +++...+-..+.+|+..+.+.+|
T Consensus 32 i~~~l~--~~~~~tl~~l~~~~d~~~~l~~g~~L~~l~~LiA~k~i~~D 78 (79)
T PF08721_consen 32 ILARLR--KNPTMTLRDLCKELDKDYELEPGTALPLLRHLIATKRIKVD 78 (79)
T ss_dssp HHHHHH--HTTTSBHHHHHHHHHHHCT--TTHHHHHHHHHHHTTSEE--
T ss_pred HHHHHH--HcCCCCHHHHHHHHHHhcCCCcCChHHHHHHHHhCChhccC
Confidence 555555 35679999998766 99999999999999999999887
No 313
>PF12395 DUF3658: Protein of unknown function ; InterPro: IPR022123 This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with PF08874 from PFAM. There are two completely conserved residues (D and R) that may be functionally important.
Probab=36.08 E-value=2.1e+02 Score=22.28 Aligned_cols=88 Identities=10% Similarity=0.145 Sum_probs=59.1
Q ss_pred CCCCHHHHHHHHHHhhhhC-CCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCcccHHHHH-----H-hcCCCH
Q psy6552 137 QDITNEDLLAAAKKLKIFG-NGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAHISVSVLN-----N-ELNWST 209 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg-~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~vt~~~l~-----~-~l~ws~ 209 (254)
..+|+++..+=++.++.|- ..-.|+.+..|+ |+|+| .+.-...|++.+. ..+..+..+. . ..+.+-
T Consensus 9 ~~ls~~~~~~l~~eW~~L~~~n~~LR~w~~g~--i~sv~--ed~yD~~Il~~~~---~~~~~~arvIg~vl~~~~~~i~D 81 (111)
T PF12395_consen 9 RPLSAEERQRLANEWEELKEENAPLRIWENGK--IVSVP--EDYYDDFILEQAP---DEFQKAARVIGEVLGHSDQGIGD 81 (111)
T ss_pred CCCCHHHHHHHHHHHHHHHhCCCceEEEECCe--EEecC--hHHhhHHHHhcCC---ccccHHHHHHHHHHHhcCcCCCh
Confidence 4799999999999999993 334444444353 77887 3433456666443 3344433322 1 246777
Q ss_pred HHHHHHHHHHHHcCcEEEeCCC
Q psy6552 210 ERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 210 ~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
.-..-.++.|++.|.+-....+
T Consensus 82 ~f~~~Ri~~Li~~G~le~~g~~ 103 (111)
T PF12395_consen 82 WFLEYRIRELISQGVLEIKGDP 103 (111)
T ss_pred HHHHHHHHHHHHCCCEEEecCC
Confidence 7777889999999999998775
No 314
>PF04914 DltD_C: DltD C-terminal region; InterPro: IPR006998 The dlt operon (dltA to dltD) of Lactobacillus rhamnosus 7469 encodes four proteins responsible for the esterification of lipoteichoic acid (LTA) by D-alanine. These esters play an important role in controlling the net anionic charge of the poly (GroP) moiety of LTA. DltA and DltC encode the D-alanine-D-alanyl carrier protein ligase (Dcl) and D-alanyl carrier protein (Dcp), respectively. Whereas the functions of DltA and DltC are defined, the functions of DltB and DltD are unknown. In vitro assays showed that DltD bound Dcp for ligation with D-alanine by Dcl in the presence of ATP. In contrast, the homologue of Dcp, the Escherichia coli acyl carrier protein (ACP), involved in fatty acid biosynthesis, was not bound to DltD and thus was not ligated with D-alanine. DltD also catalyzed the hydrolysis of the mischarged D-alanyl-ACP. The hydrophobic N-terminal sequence of DltD was required for anchoring the protein in the membrane. It is hypothesized that this membrane-associated DltD facilitates the binding of Dcp and Dcl for ligation of Dcp with D-alanine and that the resulting D-alanyl-Dcp is translocated to the primary site of D-alanylation []. These sequences contain the C-terminal region of DltD.; PDB: 3BMA_C.
Probab=36.02 E-value=44 Score=27.22 Aligned_cols=49 Identities=18% Similarity=0.417 Sum_probs=31.6
Q ss_pred CHHHH--HHHHHHHHHcCCCccc---CCCcccc-ccccc-hhHHHHHHHHHHHhhh
Q psy6552 60 DAQFR--RHFQEMCASIGVDPLA---SRKGFWS-LLGMG-DFYYELSVQIVEVCLA 108 (254)
Q Consensus 60 dp~fr--~~f~~mc~~lGVdPl~---s~kg~w~-~lg~g-dfy~eLavqive~c~~ 108 (254)
.||+. .-|.+.|...||+|+- +-.|-|. -.|+. +-+.+.-.+|-+.|.+
T Consensus 32 SpEy~Dl~l~L~~~k~~g~~~lfVi~PvNg~wydytG~~~~~r~~~y~kI~~~~~~ 87 (130)
T PF04914_consen 32 SPEYDDLQLLLDVCKELGIDVLFVIQPVNGKWYDYTGLSKEMRQEYYKKIKYQLKS 87 (130)
T ss_dssp -THHHHHHHHHHHHHHTT-EEEEEE----HHHHHHTT--HHHHHHHHHHHHHHHHT
T ss_pred CccHHHHHHHHHHHHHcCCceEEEecCCcHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46664 6778889999999985 4456787 66765 6667777777777765
No 315
>KOG3442|consensus
Probab=35.91 E-value=57 Score=26.62 Aligned_cols=50 Identities=24% Similarity=0.296 Sum_probs=37.8
Q ss_pred hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC
Q psy6552 112 KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP 174 (254)
Q Consensus 112 ~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p 174 (254)
.+|| |||.|...++|=. +..+++.|.+=-+.|=..+.+= -| |..|+||.-
T Consensus 52 ~~~~-iTlqEa~qILnV~-------~~ln~eei~k~yehLFevNdks----kG-GSFYLQSKV 101 (132)
T KOG3442|consen 52 SNGK-ITLQEAQQILNVK-------EPLNREEIEKRYEHLFEVNDKS----KG-GSFYLQSKV 101 (132)
T ss_pred cccc-ccHHHHhhHhCCC-------CCCCHHHHHHHHHHHHhccCcc----cC-cceeehHHH
Confidence 4678 9999999999964 6889999999888874433221 13 788888875
No 316
>PF09958 DUF2192: Uncharacterized protein conserved in archaea (DUF2192); InterPro: IPR018693 This family of various hypothetical archaeal proteins has no known function.
Probab=35.27 E-value=1.4e+02 Score=26.83 Aligned_cols=54 Identities=19% Similarity=0.367 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHh----------hhhhhcCHHHHHHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHHHHHH
Q psy6552 42 FRDKLESFASEY----------KNEIKKDAQFRRHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQIVEV 105 (254)
Q Consensus 42 fk~~L~~FA~kh----------~~~I~~dp~fr~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~ 105 (254)
.++.+.+|++-| .++|++..+-...=+.+|.+||+. |+-+ .+|-.+.|+.+-.+
T Consensus 158 ~~~t~~~y~rFY~AfKiAE~Ia~g~IR~r~~kea~K~alal~lG~~k~~P~----------d~yI~~IA~~Vf~V 222 (231)
T PF09958_consen 158 LKETARSYARFYIAFKIAEAIAEGEIRSREEKEAMKYALALRLGFEKCLPS----------DKYIAEIAKEVFKV 222 (231)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccCCHHHHHHHHHHHHHHcCCCCCCCc----------hHHHHHHHHHHhCC
Confidence 344444566555 355555555555667899999997 5543 47888888777544
No 317
>PF13559 DUF4129: Domain of unknown function (DUF4129)
Probab=35.08 E-value=72 Score=21.94 Aligned_cols=34 Identities=21% Similarity=0.264 Sum_probs=25.8
Q ss_pred eHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhh
Q psy6552 118 LLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 118 ~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~L 154 (254)
.+.++...|.+.|=.. ..+|++|+.++.+.++.|
T Consensus 39 ~~~~lt~~ye~~~Yg~---~~~~~~~~~~~~~~~~~l 72 (72)
T PF13559_consen 39 ALEELTRLYERARYGG---RPPSAEEFQRAREALRRL 72 (72)
T ss_pred HHHHHHHHHHHHHCCC---CCCCHHHHHHHHHHHhcC
Confidence 4677777788877221 479999999999988764
No 318
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=34.94 E-value=1.1e+02 Score=25.77 Aligned_cols=63 Identities=16% Similarity=0.132 Sum_probs=38.4
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEE
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQ 171 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~ 171 (254)
..||+-.-+.++++ .+|--+..++-.+++ +.||++++..|++.|..+| +++-+.+-.|++
T Consensus 22 ~~W~~~~ir~l~~l-------~~~~~d~~~iak~l~---------p~is~~ev~~sL~~L~~~g----li~k~~~g~y~~ 81 (171)
T PF14394_consen 22 SSWYHPAIRELLPL-------MPFAPDPEWIAKRLR---------PKISAEEVRDSLEFLEKLG----LIKKDGDGKYVQ 81 (171)
T ss_pred hhhHHHHHHHHhhc-------CCCCCCHHHHHHHhc---------CCCCHHHHHHHHHHHHHCC----CeEECCCCcEEE
Confidence 35666554444433 333334555544433 5799999999999999999 455542324555
Q ss_pred ccC
Q psy6552 172 SIP 174 (254)
Q Consensus 172 s~p 174 (254)
+.+
T Consensus 82 t~~ 84 (171)
T PF14394_consen 82 TDK 84 (171)
T ss_pred ecc
Confidence 553
No 319
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=34.82 E-value=1.2e+02 Score=26.56 Aligned_cols=44 Identities=16% Similarity=0.165 Sum_probs=36.6
Q ss_pred cCCCCChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 173 IPGELSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 173 ~p~els~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
.|..||.-+..|+.++. .+.|..++++.+++|+.-++..+..+.
T Consensus 130 ~~~~LSpRErEVLrLLA----qGkTnKEIAe~L~IS~rTVkth~srIm 173 (198)
T PRK15201 130 TTRHFSVTERHLLKLIA----SGYHLSETAALLSLSEEQTKSLRRSIM 173 (198)
T ss_pred CCCCCCHHHHHHHHHHH----CCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 34459988899999988 258899999999999999998887753
No 320
>KOG0403|consensus
Probab=34.51 E-value=61 Score=32.31 Aligned_cols=88 Identities=17% Similarity=0.157 Sum_probs=51.8
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhcc-CCCcccHHHHHHh----------cC
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASK-NEAHISVSVLNNE----------LN 206 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~-~~g~vt~~~l~~~----------l~ 206 (254)
-.+--||-.||..++.||-||==..+= .+.+|.-. |-..|.+.++.+.+.- ..|-||+.++.+- ++
T Consensus 519 Y~~~GdisEA~~CikeLgmPfFhHEvV-kkAlVm~m--Ekk~d~t~~ldLLk~cf~sglIT~nQMtkGf~RV~dsl~Dls 595 (645)
T KOG0403|consen 519 YELSGDISEACHCIKELGMPFFHHEVV-KKALVMVM--EKKGDSTMILDLLKECFKSGLITTNQMTKGFERVYDSLPDLS 595 (645)
T ss_pred HHhccchHHHHHHHHHhCCCcchHHHH-HHHHHHHH--HhcCcHHHHHHHHHHHHhcCceeHHHhhhhhhhhhccCcccc
Confidence 456778999999999999887321111 11111111 2233666777765531 2577888877653 34
Q ss_pred CCHHHHHHH----HHHHHHcCcEEEe
Q psy6552 207 WSTERAQHA----LDFMVQEGYAWID 228 (254)
Q Consensus 207 ws~~ra~~~----L~~l~~~G~lwvD 228 (254)
.++.-|.+. .+++.++|++|.-
T Consensus 596 LDvPna~ekf~~~Ve~~~~~G~i~~~ 621 (645)
T KOG0403|consen 596 LDVPNAYEKFERYVEECFQNGIISKQ 621 (645)
T ss_pred cCCCcHHHHHHHHHHHHHHcCchhHH
Confidence 444444544 4556778988864
No 321
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=34.45 E-value=63 Score=30.04 Aligned_cols=37 Identities=14% Similarity=0.172 Sum_probs=33.7
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+.|.+++++++|.|.......|..+.++|++=|.-.
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~ 64 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQIN 64 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEe
Confidence 5699999999999999999999999999999966643
No 322
>KOG0040|consensus
Probab=34.24 E-value=3.4e+02 Score=31.41 Aligned_cols=76 Identities=18% Similarity=0.365 Sum_probs=51.8
Q ss_pred HHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHH
Q psy6552 65 RHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNED 143 (254)
Q Consensus 65 ~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~D 143 (254)
.+|.+.+.++|-| |..-+ |.=-- ..-+++...=|-.-|-|++.|....+-+.-.. ...|.+.
T Consensus 2273 q~F~sCLrslgY~lpmvEe---------~~~~p----~fe~~ld~vDP~r~G~Vsl~dY~afmi~~ETe----NI~s~~e 2335 (2399)
T KOG0040|consen 2273 QHFKSCLRSLGYDLPMVEE---------GEPEP----EFEEILDLVDPNRDGYVSLQDYMAFMISKETE----NILSSEE 2335 (2399)
T ss_pred HHHHHHHHhcCCCCccccc---------CCCCh----hHHHHHHhcCCCCcCcccHHHHHHHHHhcccc----cccchHH
Confidence 5788888899999 88732 11000 11122222334557999999999887776444 4578889
Q ss_pred HHHHHHHhhhhCCCe
Q psy6552 144 LLAAAKKLKIFGNGF 158 (254)
Q Consensus 144 i~rA~~~L~~Lg~g~ 158 (254)
|..|.+.|.. |.||
T Consensus 2336 IE~AfraL~a-~~~y 2349 (2399)
T KOG0040|consen 2336 IEDAFRALDA-GKPY 2349 (2399)
T ss_pred HHHHHHHhhc-CCcc
Confidence 9999999988 7777
No 323
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=34.05 E-value=1.6e+02 Score=24.69 Aligned_cols=90 Identities=11% Similarity=0.000 Sum_probs=56.8
Q ss_pred CCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC-CCC---Chh--HHHHHHHhhcc-CCCcccHHHHHHhcCC--
Q psy6552 137 QDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP-GEL---SLD--HSLVLQQVASK-NEAHISVSVLNNELNW-- 207 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p-~el---s~D--~~~il~l~~~~-~~g~vt~~~l~~~l~w-- 207 (254)
-.|.++++.+++...=+-...+.+ ..=..+|.+.. .|+ +.| ...+++++..- ..|.+.+..|+..+|-
T Consensus 5 ~DVpa~~~I~~~A~~LK~~~ki~~---P~W~~~vKTg~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~k 81 (150)
T PRK09333 5 YDVPADLLIERLAEYLKNVDEIKP---PEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRK 81 (150)
T ss_pred ccCCHHHHHHHHHHHHHhcCCcCC---CcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCc
Confidence 368999999998766332222221 11222333332 233 334 35665555421 2678999999999988
Q ss_pred ------------CHHHHHHHHHHHHHcCcEEEeC
Q psy6552 208 ------------STERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 208 ------------s~~ra~~~L~~l~~~G~lwvD~ 229 (254)
|-...+..|++|++.|++=-|.
T Consensus 82 ~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 82 NRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred CCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 3445899999999999987765
No 324
>smart00853 MutL_C MutL C terminal dimerisation domain. MutL and MutS are key components of the DNA repair machinery that corrects replication errors. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signaling complex for repair. The N terminal region of MutL contains the ATPase domain and the C terminal is involved in dimerisation.
Probab=33.91 E-value=77 Score=24.81 Aligned_cols=40 Identities=18% Similarity=0.389 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHhhhh-CCCeEEEEeCCceEEEEccCCCC
Q psy6552 138 DITNEDLLAAAKKLKIF-GNGFSIIPIGQGQYLVQSIPGEL 177 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~L-g~g~~l~~~~sg~~vv~s~p~el 177 (254)
.+|+.+.....+..+.| ..||.+..++.+..+|+++|.-+
T Consensus 60 ~l~~~e~~~l~~~~~~l~~~Gf~~~~~~~~~~~i~~vP~~l 100 (136)
T smart00853 60 ELSPEEAALLEEHQELLARLGFELEIFGGQSVILRSVPALL 100 (136)
T ss_pred EcCHHHHHHHHHHHHHHHHcCeEEEccCCCEEEEEeECccc
Confidence 47888876666666556 47788888885667899999633
No 325
>PF07083 DUF1351: Protein of unknown function (DUF1351); InterPro: IPR009785 This entry is represented by Lactobacillus prophage Lj928, Orf309. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 230 residues in length. The function of this family is unknown.
Probab=33.84 E-value=2e+02 Score=25.22 Aligned_cols=43 Identities=28% Similarity=0.402 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHcCCCcccCC---Ccccc--ccccchhHHHHHHHHH
Q psy6552 61 AQFRRHFQEMCASIGVDPLASR---KGFWS--LLGMGDFYYELSVQIV 103 (254)
Q Consensus 61 p~fr~~f~~mc~~lGVdPl~s~---kg~w~--~lg~gdfy~eLavqiv 103 (254)
...+..|..+|...||||..-. ++-|- ..+....-.++.-.|.
T Consensus 111 ~~i~~~~~~~~~~~~v~~~~fe~~~~~~wlnks~s~kk~~eei~~~i~ 158 (215)
T PF07083_consen 111 EKIKEYFEEMAEEYGVDPEPFERIIKPKWLNKSYSLKKIEEEIDDQID 158 (215)
T ss_pred HHHHHHHHHHHHHcCCChHHHhhhcchHHhhcCCcHHHHHHHHHHHHH
Confidence 5678899999999999977532 33452 2233345555544443
No 326
>PF09733 VEFS-Box: VEFS-Box of polycomb protein; InterPro: IPR019135 The VEFS-Box is found in the the C-terminal region of the VRN2, EMF2, FIS2, and Su(z)12 polycomb proteins. This domain is characterised by an acidic cluster and a tryptophan/methionine-rich sequence, the acidic-W/M domain []. In some proteins the VEFS-Box is associated with a zinc-finger domain located roughly 100 residues towards the N terminus. These proteins are part of the polycomb cluster of proteins which control HOX gene transcription as it functions in heterochromatin-mediated repression [].
Probab=33.70 E-value=62 Score=26.69 Aligned_cols=30 Identities=20% Similarity=0.276 Sum_probs=23.7
Q ss_pred HHHHHHHHhhhhhhcCHHHHHHHHHHHHHc
Q psy6552 45 KLESFASEYKNEIKKDAQFRRHFQEMCASI 74 (254)
Q Consensus 45 ~L~~FA~kh~~~I~~dp~fr~~f~~mc~~l 74 (254)
..+.|++.|+..|.++|.++..|.--+.+|
T Consensus 93 ac~~Fv~~~~~~L~~~~~l~~~f~lHl~~L 122 (140)
T PF09733_consen 93 ACEAFVREHGQWLVEKPNLRREFLLHLINL 122 (140)
T ss_pred HHHHHHHHhHHHHhhChhHHHHHHHHHHHH
Confidence 345899999999999999988887655443
No 327
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=33.64 E-value=60 Score=28.11 Aligned_cols=34 Identities=18% Similarity=0.212 Sum_probs=30.7
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.+|..+|++-+|.+++-.-.+|..|.++|++=+.
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~ 212 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQLQDRGLIGLS 212 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEec
Confidence 3788999999999999999999999999988544
No 328
>PRK09983 pflD putative formate acetyltransferase 2; Provisional
Probab=33.46 E-value=1.7e+02 Score=30.74 Aligned_cols=74 Identities=15% Similarity=0.192 Sum_probs=47.9
Q ss_pred hhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhh------hhcCHHHHHHHHHHHHHcCCCc
Q psy6552 5 AGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNE------IKKDAQFRRHFQEMCASIGVDP 78 (254)
Q Consensus 5 vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~------I~~dp~fr~~f~~mc~~lGVdP 78 (254)
.|+.||.+..+++.+ .. .+.+-+++.+-.+. .+..||..|.+. ...||+-+.++.+|....+-.|
T Consensus 167 ~G~~gi~~e~~~~~~--~~------~~~~fy~a~~i~~~-av~~~a~Rya~lA~~~a~~e~d~~rk~EL~~iA~~c~~vp 237 (765)
T PRK09983 167 HGLGELVAQMQQHCQ--QQ------PENHFYQAALLLLE-ASQKHILRYAELAETMAANCTDAQRREELLTIAEISRHNA 237 (765)
T ss_pred HHHHHHHHHHHHHHh--cC------chHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHhccCc
Confidence 588888876543322 11 12234555554443 444688888432 2468998899999999999888
Q ss_pred ccCCCcccc
Q psy6552 79 LASRKGFWS 87 (254)
Q Consensus 79 l~s~kg~w~ 87 (254)
--..++||-
T Consensus 238 ~~pa~tF~E 246 (765)
T PRK09983 238 QHKPQTFWQ 246 (765)
T ss_pred ccCCCCHHH
Confidence 877777764
No 329
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=33.23 E-value=83 Score=21.36 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=21.3
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHH
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQH 214 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~ 214 (254)
.+|+.....+.-+|+..+|++.+||+++..+.
T Consensus 16 r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 16 RYLEQLKEEGVERVSSQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHcCCeeECHHHHHHHHCCCHHHhcc
Confidence 34555553334589999999999999988764
No 330
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=33.22 E-value=1.1e+02 Score=30.60 Aligned_cols=50 Identities=14% Similarity=0.268 Sum_probs=43.3
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+..||..++.. .+.+++.+|++.+|++..-...++..|...|++-++..
T Consensus 7 ~e~~iL~~l~~~-~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~ 56 (494)
T PTZ00326 7 EENTILSKLESE-NEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMK 56 (494)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEE
Confidence 567788887731 46799999999999999999999999999999999875
No 331
>cd07624 BAR_SNX7_30 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexins 7 and 30. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. This subfamily consists of SNX7, SNX30, and similar proteins. The specific functions of SNX7 and SNX30 have not been elucidated. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=32.99 E-value=2.4e+02 Score=24.23 Aligned_cols=59 Identities=17% Similarity=0.348 Sum_probs=38.3
Q ss_pred ccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh-----cCHHHHHHHHHHH
Q psy6552 12 KQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIK-----KDAQFRRHFQEMC 71 (254)
Q Consensus 12 ~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~-----~dp~fr~~f~~mc 71 (254)
++.+.+.+|+.....+.... ++|++.++.+++.++.|....+.|+. +.-+|+..|..++
T Consensus 117 ~R~~~q~~~e~~~e~L~~k~-~~l~~ev~~a~~~~e~~~~~~~~E~~rF~~~K~~d~k~~l~~~a 180 (200)
T cd07624 117 RRDQFQIEYELSVEELNKKR-LELLKEVEKLQDKLECANADLKADLERWKQNKRQDLKKILLDMA 180 (200)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445666777666676644 34888999999999888777776663 3344555554444
No 332
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=32.97 E-value=1.3e+02 Score=25.16 Aligned_cols=28 Identities=21% Similarity=0.133 Sum_probs=23.2
Q ss_pred CCCCHHHHHHHHHHhhhh-CCCeEEEEeC
Q psy6552 137 QDITNEDLLAAAKKLKIF-GNGFSIIPIG 164 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~L-g~g~~l~~~~ 164 (254)
-.-|.+|+.+.|..++.- +.+-.|.++.
T Consensus 70 ~dpt~e~~~~~~~~~R~~a~~~RvLFHYn 98 (154)
T PF14538_consen 70 LDPTVEDLKRLCQSLRRNAKDERVLFHYN 98 (154)
T ss_pred cCCCHHHHHHHHHHHHhhCCCceEEEEEC
Confidence 468999999999999776 6677788886
No 333
>PF08676 MutL_C: MutL C terminal dimerisation domain; InterPro: IPR014790 MutL and MutS are key components of the DNA repair machinery that corrects replication errors []. MutS recognises mispaired or unpaired bases in a DNA duplex and in the presence of ATP, recruits MutL to form a DNA signalling complex for repair. The N-terminal region of MutL contains the ATPase domain and the C-terminal is involved in dimerisation []. ; GO: 0005524 ATP binding, 0006298 mismatch repair; PDB: 3NCV_B 1X9Z_B 3GAB_C 3KDK_A 3KDG_A.
Probab=32.85 E-value=1.3e+02 Score=23.85 Aligned_cols=52 Identities=17% Similarity=0.326 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHhhhh-CCCeEEEEeCCceEEEEccCCCCChh--HHHHHHHhh
Q psy6552 138 DITNEDLLAAAKKLKIF-GNGFSIIPIGQGQYLVQSIPGELSLD--HSLVLQQVA 189 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~L-g~g~~l~~~~sg~~vv~s~p~els~D--~~~il~l~~ 189 (254)
.+|+.+....-+..+.| ..||++..++.+..+|+++|.-+... ...+.++++
T Consensus 59 ~ls~~e~~~l~~~~~~L~~~Gf~~~~~~~~~~~v~~vP~~l~~~~~~~~l~~ll~ 113 (144)
T PF08676_consen 59 ELSPQEAELLEENKEELEKLGFEIEEFGENSIIVRSVPAILREQDLEELLRELLE 113 (144)
T ss_dssp E--HHHHHHHHHHHHHHHHTT-EEEEESTTEEEEEEEECCCTTSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHhCCeEEEEecCCEEEEEEeCcccccccHHHHHHHHHH
Confidence 47888876666666666 46799888988899999999766532 333444443
No 334
>cd00131 PAX Paired Box domain
Probab=32.60 E-value=1.4e+02 Score=23.95 Aligned_cols=51 Identities=16% Similarity=0.171 Sum_probs=40.7
Q ss_pred EEEccCCCCChhH-HHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE
Q psy6552 169 LVQSIPGELSLDH-SLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 169 vv~s~p~els~D~-~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l 225 (254)
++-..| +|.|. ..|+.+++ .+.+..+++..||.+..-+...+....+.|-+
T Consensus 12 ~~m~~~--lS~d~R~rIv~~~~----~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v 63 (128)
T cd00131 12 FVNGRP--LPDSIRQRIVELAQ----SGIRPCDISRQLRVSHGCVSKILNRYYETGSI 63 (128)
T ss_pred ccCCCc--CCHHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCc
Confidence 443456 78765 57777776 35899999999999999999999999999954
No 335
>PF15208 Rab15_effector: Rab15 effector
Probab=32.56 E-value=93 Score=27.68 Aligned_cols=73 Identities=21% Similarity=0.393 Sum_probs=47.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhh---------h-----cCHHHHHHHHHHHHHcCCC-cccCCC---------c---cc
Q psy6552 34 QLSQHLNTFRDKLESFASEYKNEI---------K-----KDAQFRRHFQEMCASIGVD-PLASRK---------G---FW 86 (254)
Q Consensus 34 ~L~~ql~~fk~~L~~FA~kh~~~I---------~-----~dp~fr~~f~~mc~~lGVd-Pl~s~k---------g---~w 86 (254)
+....-++|-+.+..-|+|.+.=+ . -|+.|--+|-..|...||| -++..| | +|
T Consensus 16 e~~~~cev~S~avvhAsqklkEYLgFedP~skl~p~~~TLnEIFLi~fItfc~ekgv~e~ltttkMTk~Qa~LfGaDWIW 95 (236)
T PF15208_consen 16 EVLVICEVVSQAVVHASQKLKEYLGFEDPLSKLCPAPNTLNEIFLIHFITFCQEKGVDEWLTTTKMTKHQALLFGADWIW 95 (236)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHhCccCcHHhcCCCchhHHHHHHHHHHHHHHhcCchhheeecccCHHHHHHhccceee
Confidence 344455666666665555554322 1 2346778999999999999 676555 2 35
Q ss_pred cccccc-hhHHHHHHHHHHHh
Q psy6552 87 SLLGMG-DFYYELSVQIVEVC 106 (254)
Q Consensus 87 ~~lg~g-dfy~eLavqive~c 106 (254)
..+|.. .--.+||||..-.-
T Consensus 96 t~~g~dKqirlQiAVQtLqma 116 (236)
T PF15208_consen 96 TFWGPDKQIRLQIAVQTLQMA 116 (236)
T ss_pred eeecCCcchhhhhHHHHhhcc
Confidence 544543 67789999988773
No 336
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=32.30 E-value=94 Score=25.64 Aligned_cols=41 Identities=5% Similarity=-0.020 Sum_probs=34.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
|+..+-.|+.+.. ..+.|..++++.+|+|+.-++..|..+.
T Consensus 128 Lp~~~R~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~rAl 168 (178)
T PRK12529 128 LRPRVKQAFLMAT---LDGMKQKDIAQALDIALPTVKKYIHQAY 168 (178)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 7778888888876 3479999999999999999988877644
No 337
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=32.24 E-value=97 Score=22.39 Aligned_cols=44 Identities=20% Similarity=0.273 Sum_probs=32.4
Q ss_pred CCcccHHHHH---HhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccce
Q psy6552 193 EAHISVSVLN---NELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYW 238 (254)
Q Consensus 193 ~g~vt~~~l~---~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw 238 (254)
.+.+....|. ..+|++..-++.+|-.|.++|++-.... +...||
T Consensus 18 g~~i~~~~Li~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~--Gr~~~Y 64 (70)
T PF07848_consen 18 GGWIWVASLIRLLAAFGVSESAVRTALSRLVRRGWLESERR--GRRSYY 64 (70)
T ss_dssp TS-EEHHHHHHHHCCTT--HHHHHHHHHHHHHTTSEEEECC--CTEEEE
T ss_pred CCceeHHHHHHHHHHcCCChHHHHHHHHHHHHcCceeeeec--CccceE
Confidence 4566666544 5789999999999999999999999987 344454
No 338
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=32.13 E-value=1.1e+02 Score=25.02 Aligned_cols=49 Identities=14% Similarity=0.284 Sum_probs=28.0
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHH
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKK 150 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~ 150 (254)
.+|-...--|+.||...+-.. + |.|... |..-.|. ..|+.+||.-||+.
T Consensus 28 ~~yeprVv~qLLEfayRYt~~---v--L~DA~~-ya~hA~~----~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 28 TEYEPRVVNQLLEFAYRYTSD---V--LEDAQV-YADHAGR----STIDADDVRLAIQS 76 (129)
T ss_dssp --B-THHHHHHHHHHHHHHHH---H--HHHHHH-HHHHTT-----SSB-HHHHHHHHHH
T ss_pred cccCHHHHHHHHHHHHHHHHH---H--HHHHHH-HHHhccc----ccCChHHHHHHHHH
Confidence 367777778888888764322 2 233322 2222233 57999999999995
No 339
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=31.89 E-value=1.2e+02 Score=24.30 Aligned_cols=78 Identities=27% Similarity=0.313 Sum_probs=50.7
Q ss_pred HHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeH
Q psy6552 40 NTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILL 119 (254)
Q Consensus 40 ~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L 119 (254)
..++..|+ .|+|+.. =||+--+++..=..+++.. =..+|++|+++|-.+ .
T Consensus 33 y~~~~al~-y~~kFak---ldpe~a~e~veEL~~i~~~-----------------~e~~avkIadI~P~t---------~ 82 (114)
T COG1460 33 YEQREALE-YAEKFAK---LDPEKARELVEELLSIVKM-----------------SEKIAVKIADIMPRT---------P 82 (114)
T ss_pred HHHHHHHH-HHHHHhc---CCHHHHHHHHHHHHhhccc-----------------cHHHHHHHHHhCCCC---------H
Confidence 33455554 3444432 3566555666666666651 245799999999874 5
Q ss_pred HHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 120 DELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 120 ~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
.||...|-+.| -.+|++|+-+=...+.+
T Consensus 83 ~ElRsIla~e~------~~~s~E~l~~Ildiv~K 110 (114)
T COG1460 83 DELRSILAKER------VMLSDEELDKILDIVDK 110 (114)
T ss_pred HHHHHHHHHcc------CCCCHHHHHHHHHHHHH
Confidence 78889999887 34689888776666554
No 340
>PRK03187 tgl transglutaminase; Provisional
Probab=31.87 E-value=27 Score=32.01 Aligned_cols=43 Identities=23% Similarity=0.312 Sum_probs=31.3
Q ss_pred CcccCC-Ccccc-ccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCC
Q psy6552 77 DPLASR-KGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSL 134 (254)
Q Consensus 77 dPl~s~-kg~w~-~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~ 134 (254)
||-++. .|-|+ .||-|.||- ..=||.+-.+++..+|+.|-.++
T Consensus 180 ~p~tp~WqGeNaiyLgn~~yyG---------------HGiGI~t~~~iI~~LN~~R~~~a 224 (272)
T PRK03187 180 NPATPEWQGENVIYLGNGLYYG---------------HGIGIKTAEEIIYALNERRKPGA 224 (272)
T ss_pred CCCCCcccceeEEEecCCceee---------------cccccccHHHHHHHHHhccCCCc
Confidence 676554 45666 778665553 34499999999999999996654
No 341
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=31.73 E-value=1.2e+02 Score=30.18 Aligned_cols=49 Identities=4% Similarity=-0.016 Sum_probs=42.1
Q ss_pred hHHHHHHHhhccCCC-cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 180 DHSLVLQQVASKNEA-HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 180 D~~~il~l~~~~~~g-~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+..||..... .+ .++..+|++.+|++..-+..++..|...|++-+...
T Consensus 4 ~e~~iL~~l~~--~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~ 53 (492)
T PLN02853 4 AEEALLGALSN--NEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDI 53 (492)
T ss_pred HHHHHHHHHHh--cCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEE
Confidence 36678887773 35 489999999999999999999999999999998864
No 342
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=31.64 E-value=2.1e+02 Score=20.94 Aligned_cols=55 Identities=11% Similarity=0.082 Sum_probs=34.6
Q ss_pred ceEEEEccC--CCCChhHHHHHHHhhccCCCcccHHHHHH----hcCCCHHHHHH----HHHHHHHcCcE
Q psy6552 166 GQYLVQSIP--GELSLDHSLVLQQVASKNEAHISVSVLNN----ELNWSTERAQH----ALDFMVQEGYA 225 (254)
Q Consensus 166 g~~vv~s~p--~els~D~~~il~l~~~~~~g~vt~~~l~~----~l~ws~~ra~~----~L~~l~~~G~l 225 (254)
|..||.... ..+|.--..|.+++. |.-|+.+|.+ .++. ++.|.. .|..|.++|++
T Consensus 16 ~~~Vl~~p~~~~~Ln~~g~~Iw~lld----g~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~L~~~gli 80 (81)
T TIGR03859 16 DCYVLLYPEGMVKLNDSAGEILELCD----GKRSLAEIIQELAQRFPA-AEEIEDDVIAFLAVARAKHWL 80 (81)
T ss_pred CcEEEEcCCceeeeChHHHHHHHHcc----CCCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHHHHHCcCc
Confidence 666665544 246655678888888 3458877664 5588 665543 34456677764
No 343
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=31.57 E-value=85 Score=23.59 Aligned_cols=57 Identities=16% Similarity=0.088 Sum_probs=40.1
Q ss_pred HHHHHHHHcCCC--cccCCCccccccccc---------hhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHH
Q psy6552 66 HFQEMCASIGVD--PLASRKGFWSLLGMG---------DFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVK 128 (254)
Q Consensus 66 ~f~~mc~~lGVd--Pl~s~kg~w~~lg~g---------dfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr 128 (254)
+|..+|..||-| .|+. .||+. ++=..+..|+...+..=+.+.|.-=+...|+..+++
T Consensus 6 ~l~~Ia~~LG~dW~~Lar------~L~vs~~dI~~I~~e~p~~l~~Q~~~~L~~W~~r~g~~At~~~L~~AL~~ 73 (84)
T cd08805 6 KMAVIREHLGLSWAELAR------ELQFSVEDINRIRVENPNSLLEQSTALLNLWVDREGENAKMSPLYPALYS 73 (84)
T ss_pred HHHHHHHHhcchHHHHHH------HcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCccchHHHHHHHHHH
Confidence 677888888888 4443 34433 334447777777777777788888888888888776
No 344
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=31.45 E-value=80 Score=23.50 Aligned_cols=36 Identities=17% Similarity=-0.062 Sum_probs=25.6
Q ss_pred hhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHH
Q psy6552 93 DFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVK 128 (254)
Q Consensus 93 dfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr 128 (254)
++...+..|+.+.+..=+.+.|.=-+...|+..+++
T Consensus 38 ~~~~~~~eq~~~mL~~W~~r~g~~At~~~L~~aL~~ 73 (84)
T cd08804 38 ENPNSLQDQSHALLKYWLERDGKHATDTNLMKCLTK 73 (84)
T ss_pred HCcccHHHHHHHHHHHHHHccCCCchHHHHHHHHHH
Confidence 455667888888888877777766666666666665
No 345
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=31.41 E-value=54 Score=24.43 Aligned_cols=58 Identities=22% Similarity=0.263 Sum_probs=34.8
Q ss_pred HHHHHHHHHHcCCC--cccCCCccccccccc---------hhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHH
Q psy6552 64 RRHFQEMCASIGVD--PLASRKGFWSLLGMG---------DFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVK 128 (254)
Q Consensus 64 r~~f~~mc~~lGVd--Pl~s~kg~w~~lg~g---------dfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr 128 (254)
+.+|..+|.+||-| +|+. .||+. + |..+..|+.+.+..=+.++|+--|+.-|...+.+
T Consensus 7 ~~~l~~ia~~iG~~Wk~Lar------~LGls~~dI~~i~~~-~~~~~eq~~~mL~~W~~r~g~~AT~~~L~~aL~~ 75 (86)
T cd08318 7 GEQITVFANKLGEDWKTLAP------HLEMKDKEIRAIESD-SEDIKMQAKQLLVAWQDREGSQATPETLITALNA 75 (86)
T ss_pred HHHHHHHHHHHhhhHHHHHH------HcCCCHHHHHHHHhc-CCCHHHHHHHHHHHHHHhcCccccHHHHHHHHHH
Confidence 45677777777776 5554 34432 2 1234556666666666677766676666666655
No 346
>KOG0994|consensus
Probab=31.40 E-value=5.2e+02 Score=29.08 Aligned_cols=104 Identities=13% Similarity=0.286 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhh---cCHHHHHHHHHHHHH-cCCC-cccCCCccccccccchhHHHHHHHHHHHhhhh
Q psy6552 35 LSQHLNTFRDKLESFASEYKNEIK---KDAQFRRHFQEMCAS-IGVD-PLASRKGFWSLLGMGDFYYELSVQIVEVCLAT 109 (254)
Q Consensus 35 L~~ql~~fk~~L~~FA~kh~~~I~---~dp~fr~~f~~mc~~-lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~ 109 (254)
-..||+....-|+++++..++=+. .||+ ........ |+.+ |+++ +=...|+-+|-|...+.
T Consensus 1462 s~~q~~~s~~el~~Li~~v~~Flt~~~adp~---si~~vA~~vL~l~lp~tp-----------eqi~~L~~~I~e~v~sL 1527 (1758)
T KOG0994|consen 1462 SRSQMEESNRELRNLIQQVRDFLTQPDADPD---SIEEVAEEVLALELPLTP-----------EQIQQLTGEIQERVASL 1527 (1758)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCHH---HHHHHHHHHHhccCCCCH-----------HHHHHHHHHHHHHHHhc
Confidence 344455555555555555444332 2333 33333333 5666 6654 34455666666655442
Q ss_pred h------hhc-CCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 110 N------YKN-GGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 110 r------~~n-GGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
- .+. |-+--..-|...-+|+|.... ..+.+.+||..|++.-..
T Consensus 1528 ~nVd~IL~~T~~di~ra~~L~s~A~~a~~~A~-~v~~~ae~V~eaL~~Ad~ 1577 (1758)
T KOG0994|consen 1528 PNVDAILSRTKGDIARAENLQSEAERARSRAE-DVKGQAEDVVEALEEADV 1577 (1758)
T ss_pred ccHHHHHHhhhhhHHHHHHHHHHHHHHHhHHH-HHHHHHHHHHHHHHHHHH
Confidence 1 122 223233456666677765521 025778888888776543
No 347
>PRK10736 hypothetical protein; Provisional
Probab=31.28 E-value=1e+02 Score=29.58 Aligned_cols=49 Identities=14% Similarity=0.121 Sum_probs=39.3
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
++.+...++.... ...++.++|+..+||++...-..|-.|+-.|++-.-
T Consensus 306 ~~~~~~~v~~~l~---~~~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 306 VALPFPELLANVG---DEVTPVDVVAERAGQPVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred ccchHHHHHHhcC---CCCCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEc
Confidence 3434456666655 245899999999999999999999999999998664
No 348
>PF10108 DNA_pol_B_exo2: Predicted 3'-5' exonuclease related to the exonuclease domain of PolB; InterPro: IPR019288 This entry represents various prokaryotic 3'-5' exonucleases and hypothetical proteins.
Probab=31.21 E-value=1e+02 Score=27.19 Aligned_cols=72 Identities=25% Similarity=0.341 Sum_probs=49.1
Q ss_pred HHHHHHHHHHcCCCcccCCCccccccc--cchhHH-HHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCC
Q psy6552 64 RRHFQEMCASIGVDPLASRKGFWSLLG--MGDFYY-ELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDIT 140 (254)
Q Consensus 64 r~~f~~mc~~lGVdPl~s~kg~w~~lg--~gdfy~-eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS 140 (254)
+..+..+|..+||+ +|.- +-| +.+.|+ .==.+|.++|.. =+++.--||.+++..||. +|
T Consensus 116 ~~sLd~la~~lgiP----gK~~--idGs~V~~~y~~g~i~~I~~YCe~------DVl~T~~lylR~~~~~G~------l~ 177 (209)
T PF10108_consen 116 RTSLDELAALLGIP----GKDD--IDGSQVAELYQEGDIDEIREYCEK------DVLNTYLLYLRFELLRGR------LS 177 (209)
T ss_pred cCCHHHHHHHcCCC----CCCC--CCHHHHHHHHHcCCHHHHHHHHHH------HHHHHHHHHHHHHHhhCC------CC
Confidence 34678899999995 1210 112 224443 344679999987 466677788888887744 89
Q ss_pred HHHHHHHHHHhhh
Q psy6552 141 NEDLLAAAKKLKI 153 (254)
Q Consensus 141 ~~Di~rA~~~L~~ 153 (254)
+++-.+.+..++.
T Consensus 178 ~~~y~~~~~~~~~ 190 (209)
T PF10108_consen 178 PEDYQAEIAQLRD 190 (209)
T ss_pred HHHHHHHHHHHHH
Confidence 9998888887754
No 349
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=31.13 E-value=2.7e+02 Score=28.31 Aligned_cols=92 Identities=11% Similarity=0.173 Sum_probs=57.4
Q ss_pred CCCHHHHHHHHHHhhhh-CCCeEEEEeCCceEEEEccCCCCCh--hHHHHHHHhhcc-CCCcccHHH-------------
Q psy6552 138 DITNEDLLAAAKKLKIF-GNGFSIIPIGQGQYLVQSIPGELSL--DHSLVLQQVASK-NEAHISVSV------------- 200 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~L-g~g~~l~~~~sg~~vv~s~p~els~--D~~~il~l~~~~-~~g~vt~~~------------- 200 (254)
.+||.++...-+..+.| ..||.+..||.+..+|+++|.-+.. ....+.+++... ..+..+...
T Consensus 488 ~Ls~~e~~~l~~~~~~L~~lGf~~e~fg~~si~I~~vP~~l~~~~~~~~l~ell~~l~~~~~~~~~~~~~~las~ACr~A 567 (617)
T PRK00095 488 ELSEDEADRLEEHKELLARLGLELEPFGPNSFAVREVPALLGQQELEELIRDLLDELAEEGDSDTLKERELLATMACHGA 567 (617)
T ss_pred eeCHHHHHHHHHHHHHHHhCCcEEEEcCCCEEEEEecChhhcccCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHh
Confidence 47888877666666666 4779998998788899999963332 233344444321 112122222
Q ss_pred HHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 201 LNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 201 l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+...-.|+.+-++..|++|.+...-|-.-
T Consensus 568 Ik~g~~Ls~~E~~~Ll~~L~~~~~P~~CP 596 (617)
T PRK00095 568 IRAGRRLTLEEMNALLRQLEATENPGTCP 596 (617)
T ss_pred hhccCCCCHHHHHHHHHHHHhcccccCCC
Confidence 12233589999999999988877655443
No 350
>PF06721 DUF1204: Protein of unknown function (DUF1204); InterPro: IPR009596 This family represents the C terminus of a number of Arabidopsis thaliana hypothetical proteins of unknown function. Family members contain a conserved DFD motif.
Probab=31.04 E-value=2.5e+02 Score=24.68 Aligned_cols=33 Identities=9% Similarity=0.401 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHH
Q psy6552 39 LNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCA 72 (254)
Q Consensus 39 l~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~ 72 (254)
.+.||..+...-..+-+.|..+|-| -+|.+.|-
T Consensus 86 ~~l~QARidRvK~HiDdkia~ePkF-le~nQV~G 118 (228)
T PF06721_consen 86 ASLYQARIDRVKAHIDDKIADEPKF-LEFNQVKG 118 (228)
T ss_pred HHHHHHHHHHHHHHhhhhhhcchHH-HHHHHhhc
Confidence 3334444443222223455566766 34444443
No 351
>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=30.88 E-value=1.3e+02 Score=18.43 Aligned_cols=41 Identities=15% Similarity=0.061 Sum_probs=30.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
++..+..++.+.- ..+.|..++++.+|++.......+....
T Consensus 11 l~~~~~~~~~~~~---~~~~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPEREREVILLRF---GEGLSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred CCHHHHHHHHHHH---hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5555556665554 2457999999999999998888877653
No 352
>cd07669 BAR_SNX33 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 33. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX33 interacts with Wiskott-Aldrich syndrome protein (WASP) and plays a role in the maintenance of cell shape and cell cycle progression. It modulates the shedding and endocytosis of cellular prion protein (PrP(c)) and amyloid precursor protein (APP). BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in
Probab=30.87 E-value=1.3e+02 Score=26.62 Aligned_cols=75 Identities=19% Similarity=0.224 Sum_probs=40.4
Q ss_pred HHHHHhhhhhhcCHH-HHHHHHHHHHHcCCCcccCCCcccc-ccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHH
Q psy6552 48 SFASEYKNEIKKDAQ-FRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTR 125 (254)
Q Consensus 48 ~FA~kh~~~I~~dp~-fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~ 125 (254)
+|++|+....++.=. .=..|+.|+.++.+||-..+.++-. +-..|+=|.++|.-.+| .+++ -+++|.|....
T Consensus 37 e~~kk~~~~~kkEyqkiG~af~~LsqaFe~d~~~~s~~L~~Av~~tG~~y~~IG~~fae-----Qpk~-D~~pl~d~L~~ 110 (207)
T cd07669 37 ELVRKHLGGFRKEFQKLGNAFQAISHSFQLDPPYSSEALNNAISHTGRTYEAVGEMFAE-----QPKN-DLFQMLDTLSL 110 (207)
T ss_pred HHHHHHcccccHHHHHHHHHHHHHHHHHhcCCCccchHHHHHHHHHHHHHHHHHHHHHh-----cchh-hhhHHHHHHHH
Confidence 455555444444322 2245999999999995432222222 22246777765544433 2222 36667776666
Q ss_pred HHH
Q psy6552 126 LVK 128 (254)
Q Consensus 126 ~nr 128 (254)
|..
T Consensus 111 Y~G 113 (207)
T cd07669 111 YQG 113 (207)
T ss_pred HhC
Confidence 543
No 353
>cd03315 MLE_like Muconate lactonizing enzyme (MLE) like subgroup of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and residues that can function as general acid/base catalysts, a Lys-X-Lys motif and another conserved lysine. Despite these conserved residues, the members of the MLE subgroup, like muconate lactonizing enzyme, o-succinylbenzoate synthase (OSBS) and N-acylamino acid racemase (NAAAR), catalyze different reactions.
Probab=30.85 E-value=94 Score=27.54 Aligned_cols=78 Identities=14% Similarity=0.263 Sum_probs=47.1
Q ss_pred CHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCC-cccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 140 TNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEA-HISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 140 S~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g-~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
+|+++.+.++.+... ||+-++++=| .. ...|- .+++.+.+. .| .+.. .+--+-+|+...|.+.+..
T Consensus 85 ~~~~~~~~~~~~~~~--G~~~~KiKvg-----~~---~~~d~-~~v~~vr~~-~g~~~~l-~vDan~~~~~~~a~~~~~~ 151 (265)
T cd03315 85 EPAEVAEEARRALEA--GFRTFKLKVG-----RD---PARDV-AVVAALREA-VGDDAEL-RVDANRGWTPKQAIRALRA 151 (265)
T ss_pred CHHHHHHHHHHHHHC--CCCEEEEecC-----CC---HHHHH-HHHHHHHHh-cCCCCEE-EEeCCCCcCHHHHHHHHHH
Confidence 678888777776544 5776666511 11 12233 334443322 22 1110 1222678999999999999
Q ss_pred HHHcCcEEEeCC
Q psy6552 219 MVQEGYAWIDTQ 230 (254)
Q Consensus 219 l~~~G~lwvD~q 230 (254)
|...|+.|+.+-
T Consensus 152 l~~~~i~~iEeP 163 (265)
T cd03315 152 LEDLGLDYVEQP 163 (265)
T ss_pred HHhcCCCEEECC
Confidence 999999999853
No 354
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=30.84 E-value=1.2e+02 Score=23.03 Aligned_cols=42 Identities=21% Similarity=0.210 Sum_probs=34.2
Q ss_pred cCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEE
Q psy6552 113 NGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSI 160 (254)
Q Consensus 113 nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l 160 (254)
+++-++..||+..+.+.- ..||+.-|.|+++.|...|.=-++
T Consensus 13 ~~~~~sa~ei~~~l~~~~------~~i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 13 SDGHLTAEEIYERLRKKG------PSISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred CCCCCCHHHHHHHHHhcC------CCCCHHHHHHHHHHHHhCCCEEEE
Confidence 357789999999998752 469999999999999999854443
No 355
>cd07668 BAR_SNX9 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). It binds class I polyproline sequences found in dynamin 1/2 and the WASP/N-WASP actin regulators. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosi
Probab=30.81 E-value=1.4e+02 Score=26.53 Aligned_cols=74 Identities=15% Similarity=0.200 Sum_probs=39.5
Q ss_pred HHHHHhhhhhhcCHH-HHHHHHHHHHHcCCCcccCCCcccc-ccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHH
Q psy6552 48 SFASEYKNEIKKDAQ-FRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTR 125 (254)
Q Consensus 48 ~FA~kh~~~I~~dp~-fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~ 125 (254)
+|++|+...++++=. .=..|+.|+.++.+||-..+.+.-. +--.|+=|.++|.-.+| .+++ -+++|.|....
T Consensus 37 e~~kk~~~~~KkEyqkiG~af~~LsqaFe~d~~~~~~~L~~Ai~~tg~~y~~IG~~fae-----Qpk~-Dl~pl~d~L~~ 110 (210)
T cd07668 37 EHWKRCTGPLPKEYQKIGKALQSLATVFSTSGYQGETDLNDAITEAGKTYEEIASLVAE-----QPKK-DLHFLMETNHE 110 (210)
T ss_pred HHHHHHcccccHHHHHHHHHHHHHHHHHhcCCcccchHHHHHHHHHHHHHHHHHHHHHh-----cchh-hhHHHHHHHHH
Confidence 456666555554432 2245999999999996432222211 11235666655443333 2333 36666666555
Q ss_pred HH
Q psy6552 126 LV 127 (254)
Q Consensus 126 ~n 127 (254)
|.
T Consensus 111 Y~ 112 (210)
T cd07668 111 YK 112 (210)
T ss_pred Hh
Confidence 54
No 356
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=30.81 E-value=5.7e+02 Score=25.79 Aligned_cols=116 Identities=16% Similarity=0.052 Sum_probs=69.3
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEE
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQ 171 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~ 171 (254)
.++|.++-.++.+.+..-++ .--=|+..+|..++.. . +.-+...++.|.. +...+ +. |+
T Consensus 404 ~~~~~~~~~~~~~~l~~~~~-~~~g~~~~~l~~~~~~--------~---~~~~~~~l~~~~~------~~~~~-~~--~~ 462 (581)
T TIGR00475 404 IDFGEVEVKKILVKLGTEQH-DVKGVDKERLERMASL--------N---EELLKTAIEKLIG------TYKIG-GW--LH 462 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHh-hccCCCHHHHHhhccC--------C---hHHHHHHHHHHHH------heEeC-CE--EE
Confidence 48889999999998876222 3334667777655432 1 3333334444433 22333 22 22
Q ss_pred ccC--CCCChhHHHHHHHhhcc-CCCcccHHHHHHhcCCCHHHHHHHHHHHHHcC-cEEEeC
Q psy6552 172 SIP--GELSLDHSLVLQQVASK-NEAHISVSVLNNELNWSTERAQHALDFMVQEG-YAWIDT 229 (254)
Q Consensus 172 s~p--~els~D~~~il~l~~~~-~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G-~lwvD~ 229 (254)
... ..++.++. +.+..... .....++.+++..+|++....++.|..|.+.| ++-+++
T Consensus 463 ~~~~~~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~ 523 (581)
T TIGR00475 463 IPDHKSDFEKEED-IWQKIKGTFGTKGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVK 523 (581)
T ss_pred CCCCCCCCCHHHH-HHHHHHHHHhcCCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeC
Confidence 222 23565655 43322210 12458889999999999999999999999988 555553
No 357
>KOG0031|consensus
Probab=30.76 E-value=3.4e+02 Score=23.17 Aligned_cols=89 Identities=17% Similarity=0.203 Sum_probs=58.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCC
Q psy6552 36 SQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGG 115 (254)
Q Consensus 36 ~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGG 115 (254)
++|++.||+... +--+.++.|-.. ..++.|.++||-+|-- ++ +-+...+.+|
T Consensus 28 q~QIqEfKEAF~-~mDqnrDG~Idk----eDL~d~~aSlGk~~~d------------~e-----------lDaM~~Ea~g 79 (171)
T KOG0031|consen 28 QSQIQEFKEAFN-LMDQNRDGFIDK----EDLRDMLASLGKIASD------------EE-----------LDAMMKEAPG 79 (171)
T ss_pred HHHHHHHHHHHH-HHhccCCCcccH----HHHHHHHHHcCCCCCH------------HH-----------HHHHHHhCCC
Confidence 578999999885 555556655443 3567889999977321 11 1223346678
Q ss_pred ceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCC
Q psy6552 116 LILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNG 157 (254)
Q Consensus 116 ii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g 157 (254)
=|...-.+.++-.+-... =.++.|+.|.+.|.+-|.|
T Consensus 80 PINft~FLTmfGekL~gt-----dpe~~I~~AF~~FD~~~~G 116 (171)
T KOG0031|consen 80 PINFTVFLTMFGEKLNGT-----DPEEVILNAFKTFDDEGSG 116 (171)
T ss_pred CeeHHHHHHHHHHHhcCC-----CHHHHHHHHHHhcCccCCC
Confidence 888888888876654221 1367788898888876654
No 358
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=30.61 E-value=64 Score=30.58 Aligned_cols=34 Identities=24% Similarity=0.246 Sum_probs=30.3
Q ss_pred Ccc-cHHHHHHhcCCCHHHHHHHHHHHHHcCcEEE
Q psy6552 194 AHI-SVSVLNNELNWSTERAQHALDFMVQEGYAWI 227 (254)
Q Consensus 194 g~v-t~~~l~~~l~ws~~ra~~~L~~l~~~G~lwv 227 (254)
..+ |..+|++.+|.|..-.+++++.|+++|++..
T Consensus 27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~ 61 (431)
T PRK15481 27 DSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQS 61 (431)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 345 7899999999999999999999999998754
No 359
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=30.52 E-value=1.5e+02 Score=26.90 Aligned_cols=78 Identities=18% Similarity=0.303 Sum_probs=39.9
Q ss_pred HHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhh--hhcCC--ceeHHHHHHHHHHhcCCCCCCCCC
Q psy6552 64 RRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATN--YKNGG--LILLDELRTRLVKSRGKSLQHQDI 139 (254)
Q Consensus 64 r~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r--~~nGG--ii~L~dl~~~~nr~Rg~~~~~~~I 139 (254)
|.+...||..+|+.|..++ .-.-+.|...+-++...-+ .+. | -++..||. .....||... ..+
T Consensus 173 r~~L~~L~r~~~l~~~~~~---------~~lr~rL~~~~~~l~~dD~~i~~e-Gv~~Ls~~EL~-~Ac~~RGl~~--~~~ 239 (268)
T PF07766_consen 173 RPHLRALCRLLGLTPFGPS---------SLLRRRLRKRLRYLKQDDRLIKRE-GVDSLSEEELQ-DACYERGLRS--TGL 239 (268)
T ss_dssp HHHHHHHHHHTT----SSH---------HHHHHHHHHHHHHHHHHHHHHHHH--GGGS-HHHHH-HHHHHTT-----TT-
T ss_pred HHHHHHHHHHhccCcCCch---------HHHHHHHHHHHHHHHHHHHHHHHh-ccccCCHHHHH-HHHHHhCCCc--CCC
Confidence 6789999999999987532 1123445555555544433 222 4 34555555 3355677744 467
Q ss_pred CHHHHHHHHHHhhhh
Q psy6552 140 TNEDLLAAAKKLKIF 154 (254)
Q Consensus 140 S~~Di~rA~~~L~~L 154 (254)
|++++....+.+=.|
T Consensus 240 s~~~lr~~L~~WL~l 254 (268)
T PF07766_consen 240 SEEELREWLKQWLQL 254 (268)
T ss_dssp -HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHH
Confidence 888888888777554
No 360
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=30.46 E-value=1.3e+02 Score=24.75 Aligned_cols=38 Identities=16% Similarity=0.073 Sum_probs=29.7
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
|++.|..|+.+-. .+.|..++++.+|+|....+..+..
T Consensus 7 Lte~qr~VL~Lr~----~GlTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 7 LTERQIKVLELRE----KGLSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred CCHHHHHHHHHHH----cCCCHHHHHHHHCcCHHHHHHHHHh
Confidence 7878888988843 4689999999999998866654443
No 361
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=30.34 E-value=77 Score=25.23 Aligned_cols=54 Identities=24% Similarity=0.466 Sum_probs=40.4
Q ss_pred hhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhh-----hhCCCeEEEEeCCceEEEE
Q psy6552 111 YKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLK-----IFGNGFSIIPIGQGQYLVQ 171 (254)
Q Consensus 111 ~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~-----~Lg~g~~l~~~~sg~~vv~ 171 (254)
..+-|-+++.|+...+-+.+ ..+++.||+.+++.|. -|-.|+.|. +|-|...+.
T Consensus 23 ~~~~~~~tl~~Ia~~i~~~~------s~~t~~di~~vl~~~~~~~~~~l~~G~sV~-~glg~~sls 81 (124)
T PF14848_consen 23 VVSSGTLTLEDIAEEIAKEG------STLTRADIEAVLNALKDEMIEALMNGYSVN-LGLGYFSLS 81 (124)
T ss_pred EEecCccCHHHHHHHHHHhC------CCCCHHHHHHHHHHHHHHHHHHHhCCCEEE-cCCEEEEEE
Confidence 35678999999999998764 4689999999999884 466777775 354444443
No 362
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=30.23 E-value=83 Score=28.00 Aligned_cols=51 Identities=10% Similarity=0.074 Sum_probs=39.8
Q ss_pred hhHHHHHHHHHHHhhh-h-------hhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHH
Q psy6552 93 DFYYELSVQIVEVCLA-T-------NYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAK 149 (254)
Q Consensus 93 dfy~eLavqive~c~~-~-------r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~ 149 (254)
.=|-|+++-+++.+-- + .+ .||++.++++. .|-+..|. ..||-+||..+|+
T Consensus 160 ~GHTEasvdLa~lAGl~P~~vicEil~-~~~~~~~~~~~-~fA~~~~l----~~isi~dli~~~~ 218 (219)
T PRK05773 160 RGHTELSIALAQAAGLEPSAVIAEMLD-EKLSLSKEKAK-KIAKNLGF----PLVEGKEIFKEVV 218 (219)
T ss_pred CChhHHHHHHHHHcCCCccEEEEEEeC-CCCCcCHHHHH-HHHHHcCC----cEEEHHHHHHHhh
Confidence 3489999999998742 1 23 37899999994 67777777 6899999999986
No 363
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=30.20 E-value=4.3e+02 Score=24.16 Aligned_cols=55 Identities=24% Similarity=0.206 Sum_probs=36.4
Q ss_pred HHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCc--eeHHHHHHHHHHhcCC
Q psy6552 65 RHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGL--ILLDELRTRLVKSRGK 132 (254)
Q Consensus 65 ~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGi--i~L~dl~~~~nr~Rg~ 132 (254)
..+-....++||| |-. ...... ++-.++|...+..-++- ++|+++..++..+...
T Consensus 138 e~Ll~~g~s~~v~lpel-----------~~L~~~--l~~~~W~~~~~~~~~~~~~~tL~~l~~Ll~~g~~l 195 (335)
T PF08429_consen 138 EELLEEGESFGVDLPEL-----------DQLRRR--LEQLEWLEEAREILSDPDRLTLDELRELLDEGERL 195 (335)
T ss_pred HHHHHhcccCceeChhH-----------HHHHHH--HHHHHHHHHHHHHhccccCCcHHHHHHHHHhhhcC
Confidence 4555556667777 433 222332 34467888888776666 9999999999987544
No 364
>PRK13824 replication initiation protein RepC; Provisional
Probab=30.19 E-value=94 Score=30.11 Aligned_cols=42 Identities=12% Similarity=0.062 Sum_probs=36.1
Q ss_pred cccHHHHHHh-cCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccce
Q psy6552 195 HISVSVLNNE-LNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYW 238 (254)
Q Consensus 195 ~vt~~~l~~~-l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw 238 (254)
|-|-..|+.. .|.+....+.+|..|++.|++.+.|++ .|.+|
T Consensus 82 fpSN~~La~r~~Gms~~tlrRhla~LveaGLI~rrDSp--NGKRy 124 (404)
T PRK13824 82 FPSNAQLSLRAHGMAGATLRRHLAALVEAGLIIRRDSP--NGKRY 124 (404)
T ss_pred chhHHHHHHHHcCCCHHHHHHHHHHHHHCCCeEeecCC--CCccc
Confidence 6677788876 599999999999999999999999995 56655
No 365
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=30.18 E-value=96 Score=28.30 Aligned_cols=45 Identities=13% Similarity=0.265 Sum_probs=37.4
Q ss_pred HHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 183 LVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 183 ~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.||++.. ..|..++.++++.+|.+.......+..|++.|++--..
T Consensus 27 ~Il~lL~--~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t 71 (308)
T COG4189 27 AILQLLH--RKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTET 71 (308)
T ss_pred HHHHHHH--HhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeeee
Confidence 4466666 35789999999999999999999999999999875443
No 366
>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=30.09 E-value=1.2e+02 Score=21.37 Aligned_cols=44 Identities=14% Similarity=0.026 Sum_probs=30.0
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
-++.+.. +..-|..+|++.+|++.......|... ...+-+|...
T Consensus 11 ~~L~~~l-gr~Pt~eEiA~~lgis~~~v~~~l~~~--~~~~Sl~~~~ 54 (78)
T PF04539_consen 11 RELEQEL-GREPTDEEIAEELGISVEEVRELLQAS--RRPVSLDLPV 54 (78)
T ss_dssp HHHHHHH-SS--BHHHHHHHHTS-HHHHHHHHHHH--SCCEESSHCC
T ss_pred HHHHHHh-CCCCCHHHHHHHHcccHHHHHHHHHhC--CCCeEEeeee
Confidence 3444543 567999999999999999999998763 4456666544
No 367
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=30.05 E-value=1.3e+02 Score=23.88 Aligned_cols=38 Identities=11% Similarity=0.045 Sum_probs=30.9
Q ss_pred CcccHHHHHHhcC-CCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 194 AHISVSVLNNELN-WSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 194 g~vt~~~l~~~l~-ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
|-.--.+|....+ +|.-.-.+.|.+|++.|++.+...+
T Consensus 35 g~~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~ 73 (120)
T COG1733 35 GPKRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYP 73 (120)
T ss_pred CCCcHHHHHHHccccCHHHHHHHHHHHHHCCCEEeeecC
Confidence 4555667777776 8888888889999999999999875
No 368
>cd07622 BAR_SNX4 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 4. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX4 is involved in recycling traffic from the sorting endosome (post-Golgi endosome) back to the late Golgi. It is also implicated in the regulation of plasma membrane receptor trafficking and interacts with receptors for EGF, insulin, platelet-derived growth factor and leptin. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and
Probab=29.76 E-value=3.2e+02 Score=23.70 Aligned_cols=54 Identities=11% Similarity=0.225 Sum_probs=35.5
Q ss_pred HHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhh-----cCHHHHHHHHHHH
Q psy6552 17 QEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIK-----KDAQFRRHFQEMC 71 (254)
Q Consensus 17 ~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~-----~dp~fr~~f~~mc 71 (254)
+.++......+.. ..++++...+.+++..+.|..+-..|+. +.-+|+..|..++
T Consensus 121 q~~~e~~~~~L~~-k~~~l~~~ve~a~~~~e~f~~~~~~E~~rF~~~K~~dlk~~l~~~A 179 (201)
T cd07622 121 QYDLEKAEDALAN-KKQQGEEAVKEAKDELNEFVKKALEDVERFKKQKVRDLKEILISYA 179 (201)
T ss_pred HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333334333444 5677999999999999999888887773 4455555555544
No 369
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=29.62 E-value=75 Score=27.17 Aligned_cols=35 Identities=14% Similarity=0.171 Sum_probs=31.7
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
.+|..+|++-+|.+++-....|..|.++|++=+..
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~ 218 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKG 218 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC
Confidence 37999999999999999999999999999987654
No 370
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=29.47 E-value=1.1e+02 Score=24.19 Aligned_cols=47 Identities=26% Similarity=0.296 Sum_probs=35.7
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
+.+..+-+++|+++|-.+ .+|+...+.+-| ..+|++|+..-++.+..
T Consensus 63 ~~l~e~~a~~I~nL~P~~---------~dElrai~~~~~------~~~~~e~l~~ILd~l~k 109 (112)
T PRK14981 63 EKMKEKTAVKIADILPET---------RDELRAIFAKER------YTLSPEELDEILDIVKK 109 (112)
T ss_pred cCCCHHHHHHHHhcCCCC---------HHHHHHHHHHhc------cCCCHHHHHHHHHHHHH
Confidence 345677799999999885 567777777765 35899998887776654
No 371
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=29.39 E-value=1.3e+02 Score=22.38 Aligned_cols=26 Identities=15% Similarity=0.440 Sum_probs=21.5
Q ss_pred hhcCHHH------HHHHHHHHHHcCCCcccCC
Q psy6552 57 IKKDAQF------RRHFQEMCASIGVDPLASR 82 (254)
Q Consensus 57 I~~dp~f------r~~f~~mc~~lGVdPl~s~ 82 (254)
.+.+|.+ ..++.+++..||++|-+..
T Consensus 57 ~~~nP~~~~~~~~~~~~~~l~~~lGLtP~sR~ 88 (100)
T PF05119_consen 57 PKKNPAVSILNKAMKQMRSLASELGLTPASRA 88 (100)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHcCCCHHHHh
Confidence 6778866 4889999999999998754
No 372
>PRK14332 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=29.05 E-value=4.8e+02 Score=25.40 Aligned_cols=49 Identities=16% Similarity=0.242 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhcc
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASK 191 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~ 191 (254)
..|.+++.+|++.++....++.+. ..+|---|.|-.+|....++++...
T Consensus 282 ~~t~~~~~~~i~~lr~~~p~i~i~-----td~IvGfPgET~edf~~tl~~v~~l 330 (449)
T PRK14332 282 SYSKEEFLDVVKEIRNIVPDVGIT-----TDIIVGFPNETEEEFEDTLAVVREV 330 (449)
T ss_pred CCCHHHHHHHHHHHHHhCCCCEEE-----EEEEeeCCCCCHHHHHHHHHHHHhC
Confidence 469999999999999987777663 2367678988888888888887643
No 373
>PF12307 DUF3631: Protein of unknown function (DUF3631); InterPro: IPR022081 This domain is found in uncharacterised proteins and in tripartite motif containing (TRIM) protein 41. This protein functions as an E3 ligase that catalyzes the ubiquitin-mediated degradation of protein kinase C [].
Probab=28.95 E-value=3.5e+02 Score=23.41 Aligned_cols=99 Identities=23% Similarity=0.403 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCC-c--cc-CCCcccc-cccc----chhHHHHHHHHHHHh
Q psy6552 36 SQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVD-P--LA-SRKGFWS-LLGM----GDFYYELSVQIVEVC 106 (254)
Q Consensus 36 ~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVd-P--l~-s~kg~w~-~lg~----gdfy~eLavqive~c 106 (254)
..++...++.|..++..+...|..-. .+ | |. .....|- ++.+ |.=+-+.|++.+...
T Consensus 20 ~~~~~~Lr~rLa~W~~~~~~~v~~a~--------------P~mP~gv~DRaaD~WEPLlaVAd~AGg~WP~~Ar~A~~~l 85 (184)
T PF12307_consen 20 EPELHALRDRLAAWAADVADQVERAR--------------PDMPDGVEDRAADTWEPLLAVADLAGGHWPERARAAAIKL 85 (184)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhcC--------------CCCCcccccchhhhhHHHHHHHHHhcCcHHHHHHHHHHHH
Confidence 34555566667777888877664321 12 4 32 1123454 4432 333345555554444
Q ss_pred hh-h---hhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 107 LA-T---NYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 107 ~~-~---r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
.. . -..+-|+--|.|+...|.. .+. +-|+..||+.++...+.
T Consensus 86 ~~~~~~~~~~s~g~~LL~DIr~vf~~-~~~----~~i~T~dLl~~L~~~~e 131 (184)
T PF12307_consen 86 VAEADEEEEPSLGVRLLADIREVFEA-GGE----DRIPTADLLDALNADEE 131 (184)
T ss_pred HhhhcccccCCccchhHHHHHHHHcc-CCC----CcccHHHHHHHHHhCCC
Confidence 44 2 2467899999999999987 444 68999999999988764
No 374
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=28.92 E-value=2.8e+02 Score=25.05 Aligned_cols=82 Identities=22% Similarity=0.259 Sum_probs=46.5
Q ss_pred HHHHHHHHHcCCCcccCCCccccccc---cchhHHHHHHHHHHHhhhhh-----hhcCCceeHHH----HHHHHHHhcCC
Q psy6552 65 RHFQEMCASIGVDPLASRKGFWSLLG---MGDFYYELSVQIVEVCLATN-----YKNGGLILLDE----LRTRLVKSRGK 132 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~s~kg~w~~lg---~gdfy~eLavqive~c~~~r-----~~nGGii~L~d----l~~~~nr~Rg~ 132 (254)
...++++...||.|-|--+ |=..|| ..+|-..|+..+.+- .... ...+.--.+.. ....+.+..
T Consensus 37 ~si~elA~~a~VS~aTv~R-f~~kLGf~Gf~efk~~l~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~t~-- 112 (281)
T COG1737 37 LSIAELAERAGVSPATVVR-FARKLGFEGFSEFKLALAQELAEG-RAQLLREIAEDDGPESILEKLLAANIAALERTL-- 112 (281)
T ss_pred HHHHHHHHHhCCCHHHHHH-HHHHcCCCCHHHHHHHHHHHHhhc-cchhhcccCCCCCHHHHHHHHHHHHHHHHHHHH--
Confidence 4667888888988765222 111343 458888888888763 1100 01111101122 223333332
Q ss_pred CCCCCCCCHHHHHHHHHHhhhh
Q psy6552 133 SLQHQDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 133 ~~~~~~IS~~Di~rA~~~L~~L 154 (254)
..++++++.+||+.|..=
T Consensus 113 ----~~l~~~~l~~av~~L~~A 130 (281)
T COG1737 113 ----NLLDEEALERAVELLAKA 130 (281)
T ss_pred ----HhcCHHHHHHHHHHHHcC
Confidence 579999999999999763
No 375
>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=28.91 E-value=4.4e+02 Score=24.02 Aligned_cols=62 Identities=19% Similarity=0.231 Sum_probs=38.0
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEe-CCceEEE
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPI-GQGQYLV 170 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~-~sg~~vv 170 (254)
..||+-.-+.++.+ .+|--++.++-.+++ +.||.+++..|++.|..+| +++- ++| .|+
T Consensus 120 ~~W~~~virel~~~-------~~~~~~~~~ia~~l~---------p~is~~ev~~sL~~L~~~g----likk~~~g-~y~ 178 (271)
T TIGR02147 120 RHWYNSVIRELLGV-------MPFADDPEELAKRCF---------PKISAEQVKESLDLLERLG----LIKKNEDG-FYK 178 (271)
T ss_pred HHHHHHHHHHHhhc-------CCCCCCHHHHHHHhC---------CCCCHHHHHHHHHHHHHCC----CeeECCCC-cEE
Confidence 46666654444433 344444444443332 5799999999999999999 4443 334 466
Q ss_pred EccC
Q psy6552 171 QSIP 174 (254)
Q Consensus 171 ~s~p 174 (254)
++.+
T Consensus 179 ~t~~ 182 (271)
T TIGR02147 179 QTDK 182 (271)
T ss_pred eecc
Confidence 6544
No 376
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=28.87 E-value=2.7e+02 Score=21.41 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=33.0
Q ss_pred hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEE
Q psy6552 112 KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSI 160 (254)
Q Consensus 112 ~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l 160 (254)
.+++-++..|++..+.+. + ..||..=|.|+++.|...|.=-++
T Consensus 19 ~~~~~~ta~ei~~~l~~~-~-----~~is~~TVYR~L~~L~e~Gli~~~ 61 (120)
T PF01475_consen 19 ESPEHLTAEEIYDKLRKK-G-----PRISLATVYRTLDLLEEAGLIRKI 61 (120)
T ss_dssp HHSSSEEHHHHHHHHHHT-T-----TT--HHHHHHHHHHHHHTTSEEEE
T ss_pred cCCCCCCHHHHHHHhhhc-c-----CCcCHHHHHHHHHHHHHCCeEEEE
Confidence 445589999999999953 2 479999999999999999964444
No 377
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=28.71 E-value=1.8e+02 Score=26.41 Aligned_cols=83 Identities=19% Similarity=0.224 Sum_probs=54.1
Q ss_pred HHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCC-CCCh
Q psy6552 101 QIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPG-ELSL 179 (254)
Q Consensus 101 qive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~-els~ 179 (254)
.+.|.+...-.+.-+|||..|+-.. ..|+|.-+..+...|++-|.=.+ ++.|+++|+..|. |.+
T Consensus 15 ~~~e~l~~laae~hkiiTirdvae~-----------~ev~~n~lr~lasrLekkG~LeR---i~rG~YlI~~lpage~~- 79 (269)
T COG5340 15 RESELLSHLAAEGHKIITIRDVAET-----------LEVAPNTLRELASRLEKKGWLER---ILRGRYLIIPLPAGEEA- 79 (269)
T ss_pred HHHHHHHHHHHHhCceEEeHHhhhh-----------ccCCHHHHHHHHhhhhhcchhhh---hcCccEEEeecCCCccc-
Confidence 3344444444566789999998765 36899999999999888775444 4559999999885 444
Q ss_pred hHH----HHHHHhhccCCCcccHHH
Q psy6552 180 DHS----LVLQQVASKNEAHISVSV 200 (254)
Q Consensus 180 D~~----~il~l~~~~~~g~vt~~~ 200 (254)
+.. -+.+.+- ..|+|.-..
T Consensus 80 ~~t~he~~~~S~~~--~~gyIay~S 102 (269)
T COG5340 80 VYTTHEYLIASHVA--EPGYIAYYS 102 (269)
T ss_pred ceeehhHHHHHHHc--ccchhhHHH
Confidence 322 2344443 245655444
No 378
>PRK00301 aat leucyl/phenylalanyl-tRNA--protein transferase; Reviewed
Probab=28.43 E-value=3.1e+02 Score=24.65 Aligned_cols=27 Identities=22% Similarity=0.225 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHHHhhhhCCCeEEEEeC
Q psy6552 137 QDITNEDLLAAAKKLKIFGNGFSIIPIG 164 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg~g~~l~~~~ 164 (254)
.-||| ||.+|-..|..+|....|....
T Consensus 109 TWI~~-e~~~aY~~LH~~G~AHSVE~W~ 135 (233)
T PRK00301 109 TWITP-EIIEAYLELHELGHAHSVEVWQ 135 (233)
T ss_pred CCCCH-HHHHHHHHHHHcCceEEEEEEE
Confidence 57886 6999999999999988888775
No 379
>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=28.41 E-value=1.8e+02 Score=28.73 Aligned_cols=99 Identities=18% Similarity=0.243 Sum_probs=59.7
Q ss_pred HHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcC-Cc--eeHHHHHH
Q psy6552 48 SFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNG-GL--ILLDELRT 124 (254)
Q Consensus 48 ~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nG-Gi--i~L~dl~~ 124 (254)
.+.+-|...-+.|++.|-.-...+...|++-+.+.- ++|+++|.+|...-+... .......| |. |+++
T Consensus 205 ty~~~hp~g~k~~y~~Rl~t~~rA~~aGi~~Vg~G~----L~GLge~~~E~~~l~~hl-~~L~~~~gvgp~tIsvp---- 275 (469)
T PRK09613 205 TYEKMHPSGPKSDYDWRLTAMDRAMEAGIDDVGIGV----LFGLYDYKFEVLGLLMHA-EHLEERFGVGPHTISVP---- 275 (469)
T ss_pred HHHhcCCCCCCCCHHHHHHHHHHHHHcCCCeeCeEE----EEcCCCCHHHHHHHHHHH-HHHHHhhCCCCcccccc----
Confidence 344445444568899999999999999999776533 789999877643222111 11111221 22 3333
Q ss_pred HHHHhcCCC--CCCCCCCHHHHHHHHHHhhhhC
Q psy6552 125 RLVKSRGKS--LQHQDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 125 ~~nr~Rg~~--~~~~~IS~~Di~rA~~~L~~Lg 155 (254)
+++..-|+. .....||++|++|.+..++-+-
T Consensus 276 rl~P~~Gtpl~~~~~~vsd~e~lriiA~~RL~~ 308 (469)
T PRK09613 276 RLRPADGSDLENFPYLVSDEDFKKIVAILRLAV 308 (469)
T ss_pred ceecCCCCCcccCCCCCCHHHHHHHHHHHHHHC
Confidence 344444442 1112599999999999998653
No 380
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=28.40 E-value=1.2e+02 Score=25.76 Aligned_cols=48 Identities=13% Similarity=0.186 Sum_probs=35.3
Q ss_pred ChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE---EEeCCC
Q psy6552 178 SLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA---WIDTQS 231 (254)
Q Consensus 178 s~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l---wvD~q~ 231 (254)
|..+..|++... .++.|..+|.+.+|=...+|-..|. .-|++ ||=-.+
T Consensus 16 s~~~kkV~~~Ls---~~W~T~~El~e~~G~d~~~~L~~Lk---K~gLiE~qWrmP~p 66 (160)
T PF09824_consen 16 SEVYKKVYDELS---KGWMTEEELEEKYGKDVRESLLILK---KGGLIESQWRMPEP 66 (160)
T ss_pred CHHHHHHHHHHH---hccCCHHHHHHHHCcCHHHHHHHHH---HcCchhhccccCCC
Confidence 557888888877 5799999999999998865555555 45544 665543
No 381
>COG3612 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.97 E-value=64 Score=27.07 Aligned_cols=28 Identities=21% Similarity=0.336 Sum_probs=23.7
Q ss_pred HHhcCC-CHHHHHHHHHHHHHcCcEEEeC
Q psy6552 202 NNELNW-STERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 202 ~~~l~w-s~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+-.+.| +++-++.+++++.++|+|-.+.
T Consensus 30 Sfdrkw~spd~akr~vd~A~~eGLL~~k~ 58 (157)
T COG3612 30 SFDRKWFSPDVAKRVVDEALAEGLLVKKG 58 (157)
T ss_pred HhhhhhcChHHHHHHHHHHHhcccccccC
Confidence 334566 9999999999999999999884
No 382
>PF14948 RESP18: RESP18 domain
Probab=27.87 E-value=44 Score=26.41 Aligned_cols=21 Identities=29% Similarity=0.531 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHcCcEEEeCCC
Q psy6552 211 RAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 211 ra~~~L~~l~~~G~lwvD~q~ 231 (254)
+-+.+|..|+..|+.|-||=+
T Consensus 23 rLQ~vLqqL~~qGl~WqDDiT 43 (105)
T PF14948_consen 23 RLQVVLQQLMPQGLFWQDDIT 43 (105)
T ss_pred HHHHHHHHHHhcCCcccchHH
Confidence 456789999999999999743
No 383
>PLN02859 glutamine-tRNA ligase
Probab=27.81 E-value=1.2e+02 Score=32.09 Aligned_cols=47 Identities=9% Similarity=0.254 Sum_probs=33.2
Q ss_pred HHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHH
Q psy6552 49 FASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQI 102 (254)
Q Consensus 49 FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqi 102 (254)
|..+=..++-+||.+-+.+.......|++.-..++ .|..-|.||..+
T Consensus 17 L~e~kAketlKN~klt~~L~~iI~ea~~~~~~dk~-------~g~LLy~LAtk~ 63 (788)
T PLN02859 17 LDERTARNAIANNKVTSNLTAVIHEAGVTNGCDKT-------VGNLLYTVATKY 63 (788)
T ss_pred CChHHHHHHHhCHHHHHHHHHHHHhcCCccCCChH-------HHHHHHHHHHhc
Confidence 34455678888999988899999998887443221 466777777665
No 384
>KOG2944|consensus
Probab=27.78 E-value=24 Score=30.02 Aligned_cols=28 Identities=32% Similarity=0.357 Sum_probs=21.9
Q ss_pred cCCCCCCCCCCHHHHHHHHHHhhhhCCCeE
Q psy6552 130 RGKSLQHQDITNEDLLAAAKKLKIFGNGFS 159 (254)
Q Consensus 130 Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~ 159 (254)
||.++ -=|+-+||..||+.|+.+|-.|.
T Consensus 114 rGfgH--Ici~V~di~sac~~lkekGV~f~ 141 (170)
T KOG2944|consen 114 RGFGH--ICIEVDDINSACERLKEKGVRFK 141 (170)
T ss_pred Cccce--EEEEeCCHHHHHHHHHHhCceee
Confidence 45544 45899999999999999985543
No 385
>cd07670 BAR_SNX18 The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 18. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Sorting nexins (SNXs) are Phox homology (PX) domain containing proteins that are involved in regulating membrane traffic and protein sorting in the endosomal system. SNXs differ from each other in their lipid-binding specificity, subcellular localization and specific function in the endocytic pathway. A subset of SNXs also contain BAR domains. The PX-BAR structural unit determines the specific membrane targeting of SNXs. SNX18 is localized to peripheral endosomal structures, and acts in a trafficking pathway that is clathrin-independent but relies on AP-1 and PACS1. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=27.60 E-value=1.6e+02 Score=26.00 Aligned_cols=57 Identities=21% Similarity=0.299 Sum_probs=29.7
Q ss_pred HHHHHhhhhhhcCHH-HHHHHHHHHHHcCCCcccCCCcccc-ccccchhHHHHHHHHHH
Q psy6552 48 SFASEYKNEIKKDAQ-FRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVE 104 (254)
Q Consensus 48 ~FA~kh~~~I~~dp~-fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~gdfy~eLavqive 104 (254)
+|++|+....+++=. .=..|+.++.+..+||-..+.++-. +-..|+=|.++|.-.+|
T Consensus 37 e~~kk~~~~~KkEyqkiG~af~~LsqaF~~d~~~~s~~L~~Av~~tg~~y~~IG~~fae 95 (207)
T cd07670 37 EFARKQVTGFKKEYQKVGQSFKGLSQAFELDQQAFSAGLNQAIAFTGEAYEAIGELFAE 95 (207)
T ss_pred HHHHHHhccccHHHHHHHHHHHHHHHHHccCCcccchHHHHHHHHHHHHHHHHHHHHHh
Confidence 344454433333322 1245999999999996433332222 22246767665554443
No 386
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=27.50 E-value=72 Score=18.59 Aligned_cols=13 Identities=38% Similarity=0.279 Sum_probs=8.9
Q ss_pred CCCHHHHHHHHHH
Q psy6552 138 DITNEDLLAAAKK 150 (254)
Q Consensus 138 ~IS~~Di~rA~~~ 150 (254)
.||.+|+..++++
T Consensus 16 ~I~~~el~~~l~~ 28 (31)
T PF13405_consen 16 FIDFEELRAILRK 28 (31)
T ss_dssp EEEHHHHHHHHHH
T ss_pred cCcHHHHHHHHHH
Confidence 5777777777664
No 387
>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=27.44 E-value=83 Score=27.33 Aligned_cols=44 Identities=16% Similarity=0.252 Sum_probs=33.6
Q ss_pred HHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcE--EEeCC
Q psy6552 185 LQQVASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYA--WIDTQ 230 (254)
Q Consensus 185 l~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~l--wvD~q 230 (254)
+..+. ....|...+|+..||.+..-|...|..|+..|.+ .+|+.
T Consensus 105 i~yIK--~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~Ddr 150 (188)
T PF09756_consen 105 INYIK--EHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDR 150 (188)
T ss_dssp HHHHH--H-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT
T ss_pred HHHHH--HcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCC
Confidence 45566 3478999999999999999999999999999986 57876
No 388
>PF14762 HPS3_Mid: Hermansky-Pudlak syndrome 3, middle region
Probab=27.40 E-value=1.8e+02 Score=28.07 Aligned_cols=77 Identities=19% Similarity=0.289 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHH-HHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhh
Q psy6552 33 EQLSQHLNTFRDKLES-FASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNY 111 (254)
Q Consensus 33 ~~L~~ql~~fk~~L~~-FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~ 111 (254)
+-.-.+|..+--+|.. .......+-.++.+++..|++-|+.|| |||..+..+=...|...-.
T Consensus 247 ~~y~hLL~EaHlLLRsaL~~~~~~~~~~~~eL~~l~reSca~LG-----------------D~~~r~~~~d~~lA~pYYk 309 (374)
T PF14762_consen 247 QSYHHLLSEAHLLLRSALLDPSQEESEEKNELRELFRESCALLG-----------------DCYSRSDEKDYHLAAPYYK 309 (374)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhcccchHHHHHHHHHHHHHHHH-----------------hHhhccchHHHHHHHHHHH
Confidence 3455566666666652 111222222244567888888888876 5554444344444444444
Q ss_pred hcCCceeHHHHHHHHHH
Q psy6552 112 KNGGLILLDELRTRLVK 128 (254)
Q Consensus 112 ~nGGii~L~dl~~~~nr 128 (254)
..| .+++||+.+++.
T Consensus 310 MS~--l~i~~Vl~ri~~ 324 (374)
T PF14762_consen 310 MSG--LSISEVLNRIKL 324 (374)
T ss_pred hcC--CCHHHHHHHhhh
Confidence 443 346666666544
No 389
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=27.33 E-value=1.7e+02 Score=21.18 Aligned_cols=15 Identities=20% Similarity=0.248 Sum_probs=11.9
Q ss_pred CCCCHHHHHHHHHHh
Q psy6552 137 QDITNEDLLAAAKKL 151 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L 151 (254)
..+++.||..|.+.+
T Consensus 57 ~~~~~~Dv~~Al~~~ 71 (77)
T smart00576 57 TEPNLGDVVLALENL 71 (77)
T ss_pred CCCCHHHHHHHHHHh
Confidence 467899999888765
No 390
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=27.33 E-value=5.9e+02 Score=25.04 Aligned_cols=98 Identities=18% Similarity=0.193 Sum_probs=62.5
Q ss_pred CceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCC------CCChhHHHHHHHh
Q psy6552 115 GLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPG------ELSLDHSLVLQQV 188 (254)
Q Consensus 115 Gii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~------els~D~~~il~l~ 188 (254)
|-++..++-.. -.+++..|.++++.|+.-| +-.+.-. ....+..++. +.+. ...+++..
T Consensus 19 ~~~s~~eLA~~-----------l~l~~~tVt~~i~~Le~kG--lV~~~~~-~~~~i~LTeeG~~~~~~g~p-E~rl~~~l 83 (489)
T PRK04172 19 KEATLEELAEK-----------LGLPPEAVMRAAEWLEEKG--LVKVEER-VEEVYVLTEEGKKYAEEGLP-ERRLLNAL 83 (489)
T ss_pred CCCCHHHHHHH-----------hCcCHHHHHHHHHHHHhCC--CEEEEee-eEEEEEECHHHHHHHHhcCH-HHHHHHhh
Confidence 35677777543 3579999999999999976 3322221 2334443331 1111 22334444
Q ss_pred hccCCCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 189 ASKNEAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 189 ~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
. +.++++..+|.... ++..-+...+..|.+.|++-+|..
T Consensus 84 ~--~~~g~~~~el~~~a-L~~~~~~i~~~~l~k~g~i~i~~G 122 (489)
T PRK04172 84 K--DGGEVSLDELKEAL-LDKKEVGIALGNLARKGWAKIEKG 122 (489)
T ss_pred H--hcCCcCHHHHHHhh-ccchhHHHHHHHHHHCCCeecCCC
Confidence 4 24568899998875 566677888888999999999643
No 391
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=27.29 E-value=1.8e+02 Score=19.43 Aligned_cols=40 Identities=20% Similarity=0.170 Sum_probs=31.2
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
|+.-+..|+.+.. .+.|..++++.+|.++.-.+..+..+.
T Consensus 4 LT~~E~~vl~~l~----~G~~~~eIA~~l~is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 4 LTERELEVLRLLA----QGMSNKEIAEELGISEKTVKSHRRRIM 43 (58)
T ss_dssp S-HHHHHHHHHHH----TTS-HHHHHHHHTSHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHH----hcCCcchhHHhcCcchhhHHHHHHHHH
Confidence 6777778888777 358999999999999999888887753
No 392
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=27.12 E-value=83 Score=27.03 Aligned_cols=33 Identities=18% Similarity=0.099 Sum_probs=30.7
Q ss_pred ccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 196 ISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 196 vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.|..+||+.+|.|++-....|..|.++|++=+.
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~ 202 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKS 202 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEee
Confidence 688999999999999999999999999998765
No 393
>COG5159 RPN6 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=27.05 E-value=1.3e+02 Score=28.38 Aligned_cols=67 Identities=24% Similarity=0.362 Sum_probs=39.5
Q ss_pred chhhHHHhccHHHHHHHHhcccchHH-HHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHc
Q psy6552 4 RAGVGAIQKQKLEQEKYKDKGTSIQE-NQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASI 74 (254)
Q Consensus 4 ~vGi~~i~~~~~~~~~~~~~g~~l~~-~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~l 74 (254)
+--|.++.+.+.+.+.|...+-.... -+-.-=++-|..|.+.| .+|.+++..||-.|.+|+.+-..+
T Consensus 262 ~~evk~vl~~K~t~~~y~~r~I~am~avaea~~NRsL~df~~aL----~qY~~el~~D~~iRsHl~~LYD~L 329 (421)
T COG5159 262 REEVKAVLRNKNTLKHYDDRMIRAMLAVAEAFGNRSLKDFSDAL----AQYSDELHQDSFIRSHLQYLYDVL 329 (421)
T ss_pred HHHHHHHHccchhHhhhhhhhHHHHHHHHHHhCCCcHhhHHHHH----HHhhHHhccCHHHHHHHHHHHHHH
Confidence 34567777777777766655411111 00001122233344444 368899999999999999887654
No 394
>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=27.00 E-value=95 Score=23.02 Aligned_cols=31 Identities=13% Similarity=0.037 Sum_probs=24.3
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeC
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDT 229 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~ 229 (254)
+.|+.++++.+|.|+. .|...++.|++-...
T Consensus 1 ~~~i~e~A~~~gvs~~----tLr~ye~~Gli~p~r 31 (91)
T cd04766 1 VYVISVAAELSGMHPQ----TLRLYERLGLLSPSR 31 (91)
T ss_pred CcCHHHHHHHHCcCHH----HHHHHHHCCCcCCCc
Confidence 3588999999999986 556668899997643
No 395
>COG2144 Selenophosphate synthetase-related proteins [General function prediction only]
Probab=26.84 E-value=1.4e+02 Score=28.04 Aligned_cols=69 Identities=17% Similarity=0.096 Sum_probs=47.7
Q ss_pred hhHHHHHHHHHHHhhhhhh-hcCCceeHHHHHHHHHHh------------------------cCCCCCCCCCCHHHHHHH
Q psy6552 93 DFYYELSVQIVEVCLATNY-KNGGLILLDELRTRLVKS------------------------RGKSLQHQDITNEDLLAA 147 (254)
Q Consensus 93 dfy~eLavqive~c~~~r~-~nGGii~L~dl~~~~nr~------------------------Rg~~~~~~~IS~~Di~rA 147 (254)
+=|.++.+++++.|.+-.+ .|||++..-=..|.-.|. -|++ +=--+.|+|+.+.
T Consensus 196 ~~~~e~l~e~a~l~~AgKDvS~gG~iGtl~mlle~S~~ga~vdl~siP~p~~vd~~~wlk~ypg~g-fv~~v~pe~veev 274 (324)
T COG2144 196 RAQLELLREGAKLVKAGKDVSNGGLLGTLLMLLEKSRVGAGVDLDSIPYPADVDFRQWLKRYPGSG-FVLTVDPEDVEEV 274 (324)
T ss_pred HHHHHHHHHHHHHHhhcccccCccHHHHHHHHHHhhccCceeeecccCCcccccHHHHHHhCCCCc-EEEEeCHHHHHHH
Confidence 4578899999998877775 489988655444443311 1210 0024789999999
Q ss_pred HHHhhhhCCCeEEEE
Q psy6552 148 AKKLKIFGNGFSIIP 162 (254)
Q Consensus 148 ~~~L~~Lg~g~~l~~ 162 (254)
...++.-|.++.++-
T Consensus 275 ~~v~~~~g~~a~~~G 289 (324)
T COG2144 275 VDVFEEEGCPATVIG 289 (324)
T ss_pred HHHHHHcCCceEEEE
Confidence 999999999988754
No 396
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=26.73 E-value=65 Score=27.27 Aligned_cols=82 Identities=17% Similarity=0.248 Sum_probs=48.1
Q ss_pred HHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeH-HHHHHHHHHhcCCCCC----C-CC
Q psy6552 65 RHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILL-DELRTRLVKSRGKSLQ----H-QD 138 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L-~dl~~~~nr~Rg~~~~----~-~~ 138 (254)
.+|++.+..+|..|... | |+.=-+|++-..|++.+.+-..=-|+|= .|--.+++|.|..+.. + +.
T Consensus 69 ~~l~~~l~~~Gf~pv~~-k--------G~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~G~~V~v~g~~~ 139 (160)
T TIGR00288 69 DKLIEAVVNQGFEPIIV-A--------GDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKENGKETIVIGAEP 139 (160)
T ss_pred HHHHHHHHHCCceEEEe-c--------CcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHCCCEEEEEeCCC
Confidence 36889999999999853 3 4556678888888876532111112221 1444444444422100 0 45
Q ss_pred CCHHHHHHHHHHhhhhC
Q psy6552 139 ITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg 155 (254)
-|++++.+||..+-.|+
T Consensus 140 ~ts~~L~~acd~FI~L~ 156 (160)
T TIGR00288 140 GFSTALQNSADIAIILG 156 (160)
T ss_pred CChHHHHHhcCeEEeCC
Confidence 67777888877665554
No 397
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=26.67 E-value=3.5e+02 Score=26.20 Aligned_cols=47 Identities=21% Similarity=0.244 Sum_probs=37.5
Q ss_pred CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhc
Q psy6552 139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVAS 190 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~ 190 (254)
.|.+++.++++.++..+.++.+ +..+|---|.|-.+|....++++.+
T Consensus 287 ~t~e~~~~~i~~lr~~~p~i~i-----~~d~IvGfPgET~edf~~tl~~l~~ 333 (448)
T PRK14333 287 YTHEKYRRIIDKIREYMPDASI-----SADAIVGFPGETEAQFENTLKLVEE 333 (448)
T ss_pred CCHHHHHHHHHHHHHhCCCcEE-----EeeEEEECCCCCHHHHHHHHHHHHH
Confidence 5999999999999999777665 3346777898877788888888764
No 398
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=26.31 E-value=3.2e+02 Score=24.12 Aligned_cols=82 Identities=13% Similarity=0.144 Sum_probs=42.8
Q ss_pred HHHHHHHHcCCCcccCCCcccccccc---chhHHHHHHHHHHHhh-hhh--hhcCCcee-HHHHH----HHHHHhcCCCC
Q psy6552 66 HFQEMCASIGVDPLASRKGFWSLLGM---GDFYYELSVQIVEVCL-ATN--YKNGGLIL-LDELR----TRLVKSRGKSL 134 (254)
Q Consensus 66 ~f~~mc~~lGVdPl~s~kg~w~~lg~---gdfy~eLavqive~c~-~~r--~~nGGii~-L~dl~----~~~nr~Rg~~~ 134 (254)
..++++...||.|-|-.+ |...+|. .+|-++|...+.+--. ..+ ..+.+.-. +..++ ..+.+..
T Consensus 36 si~~lA~~~~vS~aTv~R-f~kklG~~gf~e~k~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~t~---- 110 (284)
T PRK11302 36 SIATLAKMANVSEPTVNR-FCRSLDTKGFPDFKLHLAQSLANGTPYVNRNVEEDDSVEAYTGKIFESAMASLDHAR---- 110 (284)
T ss_pred CHHHHHHHhCCCHHHHHH-HHHHcCCCCHHHHHHHHHHHhhccccccccCCCCCCCHHHHHHHHHHHHHHHHHHHH----
Confidence 456788888888766322 2224554 4777888766543100 001 11111111 11122 1222222
Q ss_pred CCCCCCHHHHHHHHHHhhhh
Q psy6552 135 QHQDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 135 ~~~~IS~~Di~rA~~~L~~L 154 (254)
..+.++++.++++.+..-
T Consensus 111 --~~id~~~i~~~~~~i~~a 128 (284)
T PRK11302 111 --QSLDPSAINRAVDLLTQA 128 (284)
T ss_pred --HhcCHHHHHHHHHHHHcC
Confidence 578999999999998653
No 399
>KOG2278|consensus
Probab=26.29 E-value=2.2e+02 Score=24.76 Aligned_cols=69 Identities=23% Similarity=0.351 Sum_probs=46.5
Q ss_pred HHHHHHHHHhhhhhh------hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEE
Q psy6552 97 ELSVQIVEVCLATNY------KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLV 170 (254)
Q Consensus 97 eLavqive~c~~~r~------~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv 170 (254)
.|++-+.-++.-|.. ..-|.+++.||+. +|+-||.. -|-|||.++++.=.+ .-|.+..- +|..+|
T Consensus 9 ~lskaLs~iLRHtA~~~~L~m~~dGfvpv~~lL~-lnq~r~~~-----~t~ddi~riVk~ndK--qRF~l~d~-~~el~I 79 (207)
T KOG2278|consen 9 ALSKALSRILRHTATELRLNMRGDGFVPVEDLLN-LNQFRGAN-----HTIDDIRRIVKRNDK--QRFSLIDE-AGELLI 79 (207)
T ss_pred HHHHHHHHHHHHHHHHhcccccCCCceEHHHHhc-cchhcccC-----CcHHHHHHHHhcccc--ceEEeecC-CCcEEE
Confidence 455555555554433 2469999999995 58888874 489999999987543 34666333 477777
Q ss_pred EccC
Q psy6552 171 QSIP 174 (254)
Q Consensus 171 ~s~p 174 (254)
+-..
T Consensus 80 rAnQ 83 (207)
T KOG2278|consen 80 RANQ 83 (207)
T ss_pred EecC
Confidence 7655
No 400
>TIGR00782 ccoP cytochrome c oxidase, cbb3-type, subunit III. This model describes a di-heme subunit of approximately 26 kDa of the cbb3 type copper and heme-containing cytochrome oxidase.
Probab=26.18 E-value=4.9e+02 Score=23.52 Aligned_cols=19 Identities=11% Similarity=0.108 Sum_probs=15.5
Q ss_pred CCCCHHHHHHHHHHhhhhC
Q psy6552 137 QDITNEDLLAAAKKLKIFG 155 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~Lg 155 (254)
..+|++||...+..+..+.
T Consensus 175 ~~LsdeeI~aVaaYv~sl~ 193 (285)
T TIGR00782 175 PLLEEADIKDVASYVMSLS 193 (285)
T ss_pred cccChHHHHHHHHHHHHhc
Confidence 3589999999998888875
No 401
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=26.18 E-value=1.5e+02 Score=22.36 Aligned_cols=51 Identities=20% Similarity=0.206 Sum_probs=32.2
Q ss_pred cchhHHHHHHHHHHHhhhh-hhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHh
Q psy6552 91 MGDFYYELSVQIVEVCLAT-NYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKL 151 (254)
Q Consensus 91 ~gdfy~eLavqive~c~~~-r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L 151 (254)
...|+.++..++++.|... ...+- -...|...+.+. ..+|++++.+|...+
T Consensus 30 ~~~~~~~vv~~~l~~~le~~~~~r~---~~~~Ll~~L~~~-------~~~~~~~~~~gf~~~ 81 (113)
T PF02847_consen 30 LPSQHHEVVKVILECALEEKKSYRE---YYSKLLSHLCKR-------KLISKEQFQEGFEDL 81 (113)
T ss_dssp -GGGHHHHHHHHHHHHHTSSHHHHH---HHHHHHHHHHHT-------TSS-HHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHhhccHHHHH---HHHHHHHHHHhc-------CCCCHHHHHHHHHHH
Confidence 3478888999999998875 21110 123444444443 578999999998765
No 402
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.12 E-value=1.6e+02 Score=24.01 Aligned_cols=41 Identities=15% Similarity=0.057 Sum_probs=33.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
|+.++..|+.+.- ..+.|..++++.+|+|..-.+..|..+.
T Consensus 120 Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ra~ 160 (172)
T PRK12523 120 LSSKARAAFLYNR---LDGMGHAEIAERLGVSVSRVRQYLAQGL 160 (172)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 6667888887766 3469999999999999998888877654
No 403
>PF09907 DUF2136: Uncharacterized protein conserved in bacteria (DUF2136); InterPro: IPR018669 HigB (YgjN) is the toxin of the HigB-HigA toxin-antitoxin system, acting as a translation-dependent mRNA interferase. HigB inhibits protein synthesis by cleaving translated mRNAs within the coding region []. ; GO: 0016788 hydrolase activity, acting on ester bonds
Probab=26.10 E-value=1.4e+02 Score=21.97 Aligned_cols=40 Identities=18% Similarity=0.155 Sum_probs=32.2
Q ss_pred eHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeC
Q psy6552 118 LLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIG 164 (254)
Q Consensus 118 ~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~ 164 (254)
+|...+..+.++ +-=||+||.+.......+|.++-+..++
T Consensus 5 ~L~~W~~~~~~a-------~w~~~~elk~~f~~ad~v~~~~~vFnI~ 44 (76)
T PF09907_consen 5 ALEAWYREVKKA-------DWKNPAELKQQFPSADIVKNNRVVFNIG 44 (76)
T ss_pred HHHHHHHHHHHc-------cCCCHHHHHHHCcchhhhcCCEEEEEcC
Confidence 356666666665 4669999999999999998888888886
No 404
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=26.02 E-value=5.5e+02 Score=24.59 Aligned_cols=88 Identities=22% Similarity=0.254 Sum_probs=59.0
Q ss_pred cCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChh----HHHH---H
Q psy6552 113 NGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLD----HSLV---L 185 (254)
Q Consensus 113 nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D----~~~i---l 185 (254)
+|=+|+.++|..++... .. |.++|++++.....|= . |.=|++|.. +-.+ .... +
T Consensus 281 ~~~v~~Fs~L~~ll~~~-------~~-~~~~lL~~L~~~AvLV--------~-G~WV~kS~l--l~~~~~~e~~~~aRD~ 341 (421)
T PF04801_consen 281 KARVISFSELRKLLPSN-------SD-TDEELLRALQQVAVLV--------Q-GNWVVKSEL--LYPDVPAEQLCRARDY 341 (421)
T ss_pred hCCcccHHHHHHHhccc-------cc-hHHHHHHHHHhheEEE--------e-eeEEEehhh--ccCCCcchhhhhhHHH
Confidence 45599999999888542 12 6999999998866542 2 566666643 1112 1111 1
Q ss_pred HHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 186 QQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 186 ~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
-|+......+|+.+++....+.+...+++.|..+
T Consensus 342 iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~ 375 (421)
T PF04801_consen 342 ILLLFTKSRYVKRKELMSATKLPPEDVKEILKEI 375 (421)
T ss_pred HHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHH
Confidence 1222223578999999999999999999999884
No 405
>PRK05660 HemN family oxidoreductase; Provisional
Probab=25.81 E-value=1.2e+02 Score=28.67 Aligned_cols=37 Identities=11% Similarity=0.066 Sum_probs=32.2
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
.+|+...+.+.+|.+.......|+.+++.|++.+|++
T Consensus 320 ~G~~~~~~~~~~g~~~~~~~~~l~~l~~~gl~~~~~~ 356 (378)
T PRK05660 320 EAAPRADFEAYTGLPESVIRPQLDEALAQGYLTETAD 356 (378)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4688899999999998877888999999999999864
No 406
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=25.70 E-value=2.3e+02 Score=19.62 Aligned_cols=44 Identities=16% Similarity=0.250 Sum_probs=36.8
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCccccee
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWF 239 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~ 239 (254)
+..++.+++..++.+..-...+|..+.+.|++-...+ +...||.
T Consensus 38 ~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~~--~~~~~~~ 81 (110)
T COG0640 38 GELTVGELAEALGLSQSTVSHHLKVLREAGLVELRRE--GRLRLYR 81 (110)
T ss_pred CCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEEec--ccEEEEe
Confidence 5788999999999999999999999999999999655 3444443
No 407
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.63 E-value=1.5e+02 Score=24.37 Aligned_cols=40 Identities=18% Similarity=0.094 Sum_probs=31.3
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..++.+.- ..+.|..++++.+|+|..-++..|..+
T Consensus 132 L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ra 171 (184)
T PRK12539 132 LPEKMRLAIQAVK---LEGLSVAEAATRSGMSESAVKVSVHRG 171 (184)
T ss_pred CCHHHHHHHHHHH---HcCCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 6667777777765 347999999999999998777776654
No 408
>PRK00118 putative DNA-binding protein; Validated
Probab=25.62 E-value=1.8e+02 Score=22.79 Aligned_cols=39 Identities=13% Similarity=0.094 Sum_probs=30.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
++.++..++.+.- ..+.|..++++.+|.|+.-+...|..
T Consensus 18 L~ekqRevl~L~y---~eg~S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 18 LTEKQRNYMELYY---LDDYSLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 5667777776665 35799999999999999877776654
No 409
>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=25.55 E-value=1.7e+02 Score=23.10 Aligned_cols=40 Identities=20% Similarity=0.227 Sum_probs=32.4
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|++++..|+.+.- ..+.|..++++.+|+|..-++..|..+
T Consensus 112 L~~~~r~v~~l~~---~~g~~~~eIA~~l~is~~tv~~~l~Ra 151 (159)
T TIGR02989 112 LPERQRELLQLRY---QRGVSLTALAEQLGRTVNAVYKALSRL 151 (159)
T ss_pred CCHHHHHHHHHHH---hcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 7778888888755 457999999999999998887776553
No 410
>PRK14335 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=25.46 E-value=3.8e+02 Score=26.08 Aligned_cols=48 Identities=23% Similarity=0.270 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhc
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVAS 190 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~ 190 (254)
..|.+|+.++++.++....++.+ +..+|---|.|-.+|....++++..
T Consensus 289 ~~t~e~~~~~v~~ir~~~pgi~i-----~~d~IvGfPgET~edf~~Tl~~i~~ 336 (455)
T PRK14335 289 SYTREHYLSLVGKLKASIPNVAL-----STDILIGFPGETEEDFEQTLDLMRE 336 (455)
T ss_pred CCCHHHHHHHHHHHHHhCCCCEE-----EEEEEEeCCCCCHHHHHHHHHHHHh
Confidence 46899999999999998666755 3336777898877788888887764
No 411
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.30 E-value=1.6e+02 Score=24.10 Aligned_cols=40 Identities=10% Similarity=-0.037 Sum_probs=30.7
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..|+.+.- ..+.|..++++.+|+|+.-++..|..+
T Consensus 136 L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~~V~~~l~ra 175 (186)
T PRK13919 136 LSPEERRVIEVLY---YQGYTHREAAQLLGLPLGTLKTRARRA 175 (186)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 6767777777655 346999999999999998777666554
No 412
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=25.23 E-value=6.1e+02 Score=26.86 Aligned_cols=124 Identities=15% Similarity=0.170 Sum_probs=69.5
Q ss_pred cCHHHHHHHHHHHHHcCCCcccCCCccccccc---cchhHHHHHHHHHHHhhhhh-hhcCCceeHHHHHHHHHHhcCCCC
Q psy6552 59 KDAQFRRHFQEMCASIGVDPLASRKGFWSLLG---MGDFYYELSVQIVEVCLATN-YKNGGLILLDELRTRLVKSRGKSL 134 (254)
Q Consensus 59 ~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg---~gdfy~eLavqive~c~~~r-~~nGGii~L~dl~~~~nr~Rg~~~ 134 (254)
-+|+-..++..+....|+++-...- +++ ..+||.+++.. |..+. ..| .-+.|+...+|+. ....
T Consensus 592 ~~~~~~~r~~Rlv~eyGLs~~dA~~----L~~d~~la~yFE~~v~~----~~~pk~aAN---Wl~~El~~~Lne~-~i~~ 659 (771)
T PRK14703 592 LNPEQRARFDRYLSELGLNEEDART----LARDPALAAFFEAALAA----GKSPVQLAN---WVVNDLAGLLRDR-ELAA 659 (771)
T ss_pred CCHhHHHHHHHHHHHcCCCHHHHHH----HHcChHHHHHHHHHHHc----CCCHHHHHH---HHHHHHHHHHhcC-CCcc
Confidence 4577777788888778887442110 111 23677776432 21111 111 1256777788875 2322
Q ss_pred CCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhH-HHHHHHhhccCCCcccHHHHHHhcCCCHHHHH
Q psy6552 135 QHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDH-SLVLQQVASKNEAHISVSVLNNELNWSTERAQ 213 (254)
Q Consensus 135 ~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~-~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~ 213 (254)
..|+|++|..-++++.. |+ +|... ..|++.+-. . .-++.++.+..||...--.
T Consensus 660 --~~l~pe~LaeLv~lV~~------------g~---------IS~~~AK~VL~~m~~--~-~~~p~~IIee~GL~qisDe 713 (771)
T PRK14703 660 --LPFTPAALARLVALVDA------------GR---------ISTRIAKDVLAELAA--S-GGDPEAIVEAKGLEQVSDA 713 (771)
T ss_pred --CCCCHHHHHHHHHHHHc------------CC---------ccHHHHHHHHHHHHh--c-CCCHHHHHHhcCCcccCCH
Confidence 46999999888888763 22 34333 345554431 2 3578889999888654333
Q ss_pred HHHHHHH
Q psy6552 214 HALDFMV 220 (254)
Q Consensus 214 ~~L~~l~ 220 (254)
+.|+.++
T Consensus 714 ~~Le~iV 720 (771)
T PRK14703 714 GALEPIV 720 (771)
T ss_pred HHHHHHH
Confidence 4444443
No 413
>COG0078 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism]
Probab=25.19 E-value=68 Score=30.04 Aligned_cols=100 Identities=16% Similarity=0.234 Sum_probs=68.8
Q ss_pred HHHHHHHHHHcCCC-cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHH-HHHHHHHHhcCCCCCCCCCCH
Q psy6552 64 RRHFQEMCASIGVD-PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLD-ELRTRLVKSRGKSLQHQDITN 141 (254)
Q Consensus 64 r~~f~~mc~~lGVd-Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~-dl~~~~nr~Rg~~~~~~~IS~ 141 (254)
-+.+-..|+.+|+| -++.++|+| .--.+++.|...-..+||=|++. |....+.-+--.+. .-.||.
T Consensus 166 ~nSl~~~~a~~G~dv~ia~Pk~~~-----------p~~~~~~~a~~~a~~~g~~i~~t~d~~eAv~gADvvyT-DvWvSM 233 (310)
T COG0078 166 ANSLLLAAAKLGMDVRIATPKGYE-----------PDPEVVEKAKENAKESGGKITLTEDPEEAVKGADVVYT-DVWVSM 233 (310)
T ss_pred HHHHHHHHHHhCCeEEEECCCcCC-----------cCHHHHHHHHHHHHhcCCeEEEecCHHHHhCCCCEEEe-cCcccC
Confidence 35777889999999 777788877 23467777777777888888877 66655544322221 136887
Q ss_pred HHHHHHHHHhhhhCCCeEEEE----e-CCceEEEEccCC
Q psy6552 142 EDLLAAAKKLKIFGNGFSIIP----I-GQGQYLVQSIPG 175 (254)
Q Consensus 142 ~Di~rA~~~L~~Lg~g~~l~~----~-~sg~~vv~s~p~ 175 (254)
.+-..+-+....+-.||+|-. . +.+.++.+-.|.
T Consensus 234 Gee~e~~~~~~~~~~~yQVn~~lm~~a~~~~ifmHCLPA 272 (310)
T COG0078 234 GEEAEAEERRIAFLPPYQVNEELMALAGPDAIFMHCLPA 272 (310)
T ss_pred cchhhhHHHHHhhCCCceeCHHHHhhcCCCeEEEeCCCC
Confidence 777777777788888888732 1 236788888884
No 414
>KOG2916|consensus
Probab=25.19 E-value=3.9e+02 Score=24.76 Aligned_cols=92 Identities=21% Similarity=0.327 Sum_probs=57.8
Q ss_pred CCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC--CCeEEEEeCCceEEEEccCCCCC-hhHHHHHH----
Q psy6552 114 GGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG--NGFSIIPIGQGQYLVQSIPGELS-LDHSLVLQ---- 186 (254)
Q Consensus 114 GGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg--~g~~l~~~~sg~~vv~s~p~els-~D~~~il~---- 186 (254)
-|||-|+||- |+| .|+|++|=..| -+.-+++++.++-||-..-.-.| .|-..|-+
T Consensus 43 EGmiLlsELS----rRR--------------IRSI~klirVGr~E~vvVlrVDkekGYIDLSkrrVs~ed~~kC~Er~~k 104 (304)
T KOG2916|consen 43 EGMILLSELS----RRR--------------IRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSPEDKEKCEERFAK 104 (304)
T ss_pred ccchhhhHHH----HHH--------------HHHHHHHHhcCCcceEEEEEEcCCCCceechhccCCHHHHHHHHHHHHH
Confidence 5788777764 444 57888888887 45777778767777754432222 23333311
Q ss_pred ----------HhhccCCCcccHHHHHHhcCCCHHH----HHHHHHHHHHcCcEE
Q psy6552 187 ----------QVASKNEAHISVSVLNNELNWSTER----AQHALDFMVQEGYAW 226 (254)
Q Consensus 187 ----------l~~~~~~g~vt~~~l~~~l~ws~~r----a~~~L~~l~~~G~lw 226 (254)
.|+ .=+++.++|-++.||+..+ |-++...++.++-+|
T Consensus 105 sK~v~sIlrhvAe---~~g~~LeeLY~~igW~~~rk~g~aYdaFK~~vtd~tV~ 155 (304)
T KOG2916|consen 105 SKLVYSILRHVAE---KLGYELEELYQRIGWPLERKYGHAYDAFKIAVTDPTVL 155 (304)
T ss_pred hHHHHHHHHHHHH---HhCCcHHHHHHHhCCchhhhhchHHHHHHHhccCcccc
Confidence 133 2246799999999999876 445555556665555
No 415
>PF04697 Pinin_SDK_N: pinin/SDK conserved region; InterPro: IPR006787 This conserved region is found at the N-terminal of the member proteins. It is located adjacent and N-terminal to the pinin/SKD/memA domain IPR006786 from INTERPRO. Members of this family have very varied localisations within the eukaryotic cell. Pinin is known to localise at the desmosomes and is implicated in anchoring intermediate filaments to the desmosomal plaque [, ]. SDK2/3 is a dynamically localised nuclear protein thought to be involved in modulation of alternative pre-mRNA splicing []. MemA is a tumour marker preferentially expressed in human melanoma cell lines. A common feature of the members of this family is that they may all participate in regulating protein-protein interactions [].
Probab=24.91 E-value=1.1e+02 Score=25.07 Aligned_cols=32 Identities=16% Similarity=0.305 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHH
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEYKNEIKKDAQ 62 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~ 62 (254)
+...|++||+++|+.|...=..+++-+-.||.
T Consensus 4 av~~Lq~qlE~Ake~Lk~vDenIkKltGRDp~ 35 (134)
T PF04697_consen 4 AVRTLQAQLEKAKESLKNVDENIKKLTGRDPS 35 (134)
T ss_pred hHHHHHHHHHHHHHHhhhhhHHHHHHhCCCcc
Confidence 56789999999999999776666666666764
No 416
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=24.83 E-value=1.4e+02 Score=25.00 Aligned_cols=48 Identities=23% Similarity=0.271 Sum_probs=36.5
Q ss_pred hHHHHHHHhhccCCCcccHHHHHHhc-----CCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 180 DHSLVLQQVASKNEAHISVSVLNNEL-----NWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 180 D~~~il~l~~~~~~g~vt~~~l~~~l-----~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
--..||++.... .+.+|+.+|.+.+ +.+.+=.-..|+.|++.|++-.=
T Consensus 27 qR~~IL~~l~~~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 27 QRLEVLRLMSLQ-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEE
Confidence 446778887754 6799999988755 35566666889999999999654
No 417
>PRK10361 DNA recombination protein RmuC; Provisional
Probab=24.80 E-value=2.4e+02 Score=28.09 Aligned_cols=50 Identities=14% Similarity=0.375 Sum_probs=32.2
Q ss_pred HhcccchHHHHHHHHHHHHHHHHHHHHHHHHHh----hhhhhcCHHHHHHHHHH
Q psy6552 21 KDKGTSIQENQLEQLSQHLNTFRDKLESFASEY----KNEIKKDAQFRRHFQEM 70 (254)
Q Consensus 21 ~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh----~~~I~~dp~fr~~f~~m 70 (254)
++.+..+.+.+-+.|+.+|.-+++.|+.|-.+. +.+++....++.+..++
T Consensus 124 e~k~~~f~~~~~~~l~~ll~Pl~e~l~~f~~~v~~~~~~~~~~~~~L~~qi~~L 177 (475)
T PRK10361 124 EHSNRRVDEQNRQSLNSLLSPLREQLDGFRRQVQDSFGKEAQERHTLAHEIRNL 177 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445566666778888999999998777665 44555555555555444
No 418
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=24.74 E-value=1.3e+02 Score=25.33 Aligned_cols=44 Identities=9% Similarity=0.022 Sum_probs=36.9
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCCCCcccceeccc
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQSPQEHLYWFPSL 242 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~~~e~~yw~p~l 242 (254)
..|..+|++.+|.|..=....+..|++.|++-+-. .+.|++.--
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~----~G~Y~iNP~ 118 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIR----NGAYMINPN 118 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEcc----CCeEEECcH
Confidence 47889999999999999999999999999997753 367887543
No 419
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.50 E-value=1.7e+02 Score=23.22 Aligned_cols=39 Identities=8% Similarity=-0.038 Sum_probs=29.2
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
|+..+-.|+.+.- ..+.|..++++.+|+|..-++..|..
T Consensus 107 Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~r 145 (161)
T PRK09047 107 LPARQREAFLLRY---WEDMDVAETAAAMGCSEGSVKTHCSR 145 (161)
T ss_pred CCHHHHHHHHHHH---HhcCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5666777777765 24689999999999998866665544
No 420
>TIGR03358 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=24.40 E-value=1.6e+02 Score=24.85 Aligned_cols=38 Identities=24% Similarity=0.457 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHH
Q psy6552 30 NQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCA 72 (254)
Q Consensus 30 ~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~ 72 (254)
.|...|.++|+ .|+.|.. .++.+-++|.||..++.+..
T Consensus 107 ~qVp~L~~Lle-lR~~L~~----L~~~l~~~~~~~~~l~~~l~ 144 (159)
T TIGR03358 107 KQVPELKKLLE-AREALRD----LKGPLDNNPDLRKLLQELLK 144 (159)
T ss_pred HHhHHHHHHHH-HHHHHHH----HHhhccCcHHHHHHHHHHHC
Confidence 37777887777 6776664 45556677888877777653
No 421
>PTZ00184 calmodulin; Provisional
Probab=24.34 E-value=3.2e+02 Score=20.79 Aligned_cols=13 Identities=15% Similarity=0.123 Sum_probs=8.5
Q ss_pred CCCHHHHHHHHHH
Q psy6552 138 DITNEDLLAAAKK 150 (254)
Q Consensus 138 ~IS~~Di~rA~~~ 150 (254)
.|+++|+.++++.
T Consensus 100 ~i~~~e~~~~l~~ 112 (149)
T PTZ00184 100 FISAAELRHVMTN 112 (149)
T ss_pred eEeHHHHHHHHHH
Confidence 5677777666654
No 422
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=23.98 E-value=3.3e+02 Score=24.86 Aligned_cols=116 Identities=14% Similarity=0.166 Sum_probs=0.0
Q ss_pred chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEE
Q psy6552 92 GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQ 171 (254)
Q Consensus 92 gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~ 171 (254)
+.|-.+....+++++..+.-.-.-.+.+-+....+-..++. +.||++||.+|+..+. .....
T Consensus 219 ~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~----~~it~~~v~~a~~~~~--------------~~~~~ 280 (365)
T TIGR02928 219 GVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGA----ERVTEDHVEKAQEKIE--------------KDRLL 280 (365)
T ss_pred CCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCC----CCCCHHHHHHHHHHHH--------------HHHHH
Q ss_pred ccCCCCChhHHHHHHHhh---ccCCCcccHH-------HHHHhcC---CCHHHHHHHHHHHHHcCcE
Q psy6552 172 SIPGELSLDHSLVLQQVA---SKNEAHISVS-------VLNNELN---WSTERAQHALDFMVQEGYA 225 (254)
Q Consensus 172 s~p~els~D~~~il~l~~---~~~~g~vt~~-------~l~~~l~---ws~~ra~~~L~~l~~~G~l 225 (254)
..=..++..+..+|..+. ....+.++.. .+++..| .+..+..++|..|+..|++
T Consensus 281 ~~i~~l~~~~~~~l~ai~~~~~~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~l~~l~~~gli 347 (365)
T TIGR02928 281 ELIRGLPTHSKLVLLAIANLAANDEDPFRTGEVYEVYKEVCEDIGVDPLTQRRISDLLNELDMLGLV 347 (365)
T ss_pred HHHHcCCHHHHHHHHHHHHHHhcCCCCccHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHhcCCe
No 423
>cd03318 MLE Muconate Lactonizing Enzyme (MLE), an homooctameric enzyme, catalyses the conversion of cis,cis-muconate (CCM) to muconolactone (ML) in the catechol branch of the beta-ketoadipate pathway. This pathway is used in soil microbes to breakdown lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates. Some bacterial species are also capable of dehalogenating chloroaromatic compounds by the action of chloromuconate lactonizing enzymes (Cl-MLEs). MLEs are members of the enolase superfamily characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and that is stabilized by coordination to the essential Mg2+ ion.
Probab=23.96 E-value=1.7e+02 Score=27.34 Aligned_cols=28 Identities=21% Similarity=0.337 Sum_probs=24.9
Q ss_pred hcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 204 ELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 204 ~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
|-+|+...|.+.+..|...|+.|+.+=.
T Consensus 196 N~~~~~~~A~~~~~~l~~~~~~~iEeP~ 223 (365)
T cd03318 196 NQAWDESTAIRALPRLEAAGVELIEQPV 223 (365)
T ss_pred CCCCCHHHHHHHHHHHHhcCcceeeCCC
Confidence 5679999999999999999999998644
No 424
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=23.86 E-value=1.7e+02 Score=23.38 Aligned_cols=40 Identities=5% Similarity=-0.037 Sum_probs=30.4
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..|+.+.- ..+.|..++++.+|+|+.-.+..+..+
T Consensus 129 L~~~~r~vl~l~~---~~~~s~~eIA~~lgis~~tV~~~l~ra 168 (182)
T PRK09652 129 LPEELRTAITLRE---IEGLSYEEIAEIMGCPIGTVRSRIFRA 168 (182)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6666777777665 246799999999999998877776554
No 425
>PF11186 DUF2972: Protein of unknown function (DUF2972); InterPro: IPR021353 Some members in this family of proteins with unknown function are annotated as sugar transferase proteins, however this cannot be confirmed.
Probab=23.82 E-value=2.9e+02 Score=23.95 Aligned_cols=26 Identities=15% Similarity=0.442 Sum_probs=11.3
Q ss_pred HHHHHhhhhhhcCHHHHHHHHHHHHH
Q psy6552 48 SFASEYKNEIKKDAQFRRHFQEMCAS 73 (254)
Q Consensus 48 ~FA~kh~~~I~~dp~fr~~f~~mc~~ 73 (254)
.+..+|+.+|-.-=.--.+|-.||-.
T Consensus 172 ~~IKq~rPDIVaSWKYYQEFEkmCke 197 (199)
T PF11186_consen 172 QHIKQHRPDIVASWKYYQEFEKMCKE 197 (199)
T ss_pred HHHHHhCHHHHHHHHHHHHHHHHHHh
Confidence 34444444443333334455555543
No 426
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=23.74 E-value=1.7e+02 Score=22.71 Aligned_cols=27 Identities=11% Similarity=0.393 Sum_probs=21.3
Q ss_pred hhcCHHH------HHHHHHHHHHcCCCcccCCC
Q psy6552 57 IKKDAQF------RRHFQEMCASIGVDPLASRK 83 (254)
Q Consensus 57 I~~dp~f------r~~f~~mc~~lGVdPl~s~k 83 (254)
++.||.+ ..++.+++..+|++|-+..+
T Consensus 66 ~k~nPa~~i~~~a~~~~~~l~~elGLtP~sR~k 98 (116)
T TIGR01558 66 PKANPALTVVEDAFKQLRSIGSALGLTPSSRSR 98 (116)
T ss_pred eecChHHHHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 4467765 47899999999999998544
No 427
>cd01295 AdeC Adenine deaminase (AdeC) directly deaminates adenine to form hypoxanthine. This reaction is part of one of the adenine salvage pathways, as well as the degradation pathway. It is important for adenine utilization as a purine, as well as a nitrogen source in bacteria and archea.
Probab=23.51 E-value=1.3e+02 Score=28.79 Aligned_cols=33 Identities=27% Similarity=0.578 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC
Q psy6552 139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP 174 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p 174 (254)
-+++|+..|++.|..+|+|+-+..= | +++-..|
T Consensus 330 ~~~~~~~~a~~~~~~~~gg~~~~~~--~-~~~~~~~ 362 (422)
T cd01295 330 TNDEDMALAVNRLKEIGGGIVVVKN--G-KVLAELP 362 (422)
T ss_pred CCHHHHHHHHHHHHHhCCcEEEEEC--C-EEEEEec
Confidence 4799999999999999999987652 3 4777777
No 428
>PF09537 DUF2383: Domain of unknown function (DUF2383); InterPro: IPR019052 This entry represents a functionally uncharacterised ferritin like domain.; PDB: 3FSE_B.
Probab=23.47 E-value=3.3e+02 Score=20.55 Aligned_cols=18 Identities=22% Similarity=0.327 Sum_probs=9.2
Q ss_pred HHHHHHHHHHcCCCcccC
Q psy6552 64 RRHFQEMCASIGVDPLAS 81 (254)
Q Consensus 64 r~~f~~mc~~lGVdPl~s 81 (254)
..+++++...+|.+|-.+
T Consensus 47 ~~~L~~~i~~~Gg~p~~~ 64 (111)
T PF09537_consen 47 AEELQAEIQELGGEPEES 64 (111)
T ss_dssp HHHHHHHHHHTT--H---
T ss_pred HHHHHHHHHHcCCCcCcc
Confidence 356677777888877764
No 429
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=23.42 E-value=1.8e+02 Score=23.51 Aligned_cols=41 Identities=12% Similarity=0.014 Sum_probs=32.5
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
|+.++..++.+.- ..+.|..++++.+|+|..-++..|..+.
T Consensus 119 L~~~~r~v~~L~~---~eg~s~~EIA~~l~is~~tV~~~l~ra~ 159 (168)
T PRK12525 119 LSGKARAAFLMSQ---LEGLTYVEIGERLGVSLSRIHQYMVEAF 159 (168)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 6667777777654 2468999999999999999988887654
No 430
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=23.42 E-value=2.7e+02 Score=22.07 Aligned_cols=16 Identities=19% Similarity=0.229 Sum_probs=13.5
Q ss_pred CCCCHHHHHHHHHHhh
Q psy6552 137 QDITNEDLLAAAKKLK 152 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~ 152 (254)
..|+.+||.-|++..-
T Consensus 52 ~tV~~eDV~lAi~~r~ 67 (117)
T cd07979 52 ANIDADDVKLAIQSRV 67 (117)
T ss_pred CCCCHHHHHHHHHHHh
Confidence 4799999999998854
No 431
>TIGR02193 heptsyl_trn_I lipopolysaccharide heptosyltransferase I. This family consists of examples of ADP-heptose:LPS heptosyltransferase I, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.
Probab=23.37 E-value=3.1e+02 Score=24.52 Aligned_cols=16 Identities=19% Similarity=0.156 Sum_probs=12.9
Q ss_pred CceeHHHHHHHHHHhc
Q psy6552 115 GLILLDELRTRLVKSR 130 (254)
Q Consensus 115 Gii~L~dl~~~~nr~R 130 (254)
|-.+|.|+.+.+.+++
T Consensus 241 g~~sL~el~ali~~a~ 256 (319)
T TIGR02193 241 PKMSLAEVAALLAGAD 256 (319)
T ss_pred CCCCHHHHHHHHHcCC
Confidence 4458888998888888
No 432
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=23.29 E-value=1.9e+02 Score=21.90 Aligned_cols=33 Identities=6% Similarity=0.263 Sum_probs=26.9
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
.|.+|+.+++..+|+.... ..+.|.+.|++..+
T Consensus 22 ~~~~ti~~~AK~L~i~~~~---l~~~Lr~~g~l~~~ 54 (111)
T PF03374_consen 22 DGLYTIREAAKLLGIGRNK---LFQWLREKGWLYRR 54 (111)
T ss_pred CCCccHHHHHHHhCCCHHH---HHHHHHhCCceEEC
Confidence 6899999999999998554 44456779999996
No 433
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=23.20 E-value=1.6e+02 Score=27.97 Aligned_cols=52 Identities=21% Similarity=0.402 Sum_probs=34.7
Q ss_pred HHHHHHHHHHhhhhhh-hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHh
Q psy6552 96 YELSVQIVEVCLATNY-KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKL 151 (254)
Q Consensus 96 ~eLavqive~c~~~r~-~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L 151 (254)
.++-.-|+++|.+++. ..-|-|.+...-..+--.+|. +.|+|+||..++...
T Consensus 270 ~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR----~~V~pdDv~~~a~~v 322 (350)
T CHL00081 270 YDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGR----TEVTPKDIFKVITLC 322 (350)
T ss_pred HHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCC----CCCCHHHHHHHHHHH
Confidence 4456678888888874 344455555444444444455 789999999998764
No 434
>cd03324 rTSbeta_L-fuconate_dehydratase Human rTS beta is encoded by the rTS gene which, through alternative RNA splicing, also encodes rTS alpha whose mRNA is complementary to thymidylate synthase mRNA. rTS beta expression is associated with the production of small molecules that appear to mediate the down-regulation of thymidylate synthase protein by a novel intercellular signaling mechanism. A member of this family, from Xanthomonas, has been characterized to be a L-fuconate dehydratase. rTS beta belongs to the enolase superfamily of enzymes, characterized by the presence of an enolate anion intermediate which is generated by abstraction of the alpha-proton of the carboxylate substrate by an active site residue and is stabilized by coordination to the essential Mg2+ ion.
Probab=23.20 E-value=1.4e+02 Score=28.91 Aligned_cols=77 Identities=16% Similarity=0.204 Sum_probs=48.1
Q ss_pred CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCCc---ccHHHHHHhcCCCHHHHHHH
Q psy6552 139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEAH---ISVSVLNNELNWSTERAQHA 215 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g~---vt~~~l~~~l~ws~~ra~~~ 215 (254)
.+++++.+.++.+.. .||+-++++=| .+ ...|-..|-.+-+. .|. +-++ .|-+|+...|...
T Consensus 195 ~~~~~~~~~a~~~~~--~Gf~~~KiKvg------~~--~~~d~~~v~avRe~--vG~~~~L~vD---aN~~w~~~~A~~~ 259 (415)
T cd03324 195 YSDEKLRRLCKEALA--QGFTHFKLKVG------AD--LEDDIRRCRLAREV--IGPDNKLMID---ANQRWDVPEAIEW 259 (415)
T ss_pred CCHHHHHHHHHHHHH--cCCCEEEEeCC------CC--HHHHHHHHHHHHHh--cCCCCeEEEE---CCCCCCHHHHHHH
Confidence 478888777766544 46877776511 11 23343443333331 221 2111 2568999999999
Q ss_pred HHHHHHcCcEEEeCC
Q psy6552 216 LDFMVQEGYAWIDTQ 230 (254)
Q Consensus 216 L~~l~~~G~lwvD~q 230 (254)
++.|..-|+.|+-+=
T Consensus 260 ~~~L~~~~l~~iEEP 274 (415)
T cd03324 260 VKQLAEFKPWWIEEP 274 (415)
T ss_pred HHHhhccCCCEEECC
Confidence 999999999999864
No 435
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=23.07 E-value=1.3e+02 Score=25.53 Aligned_cols=33 Identities=27% Similarity=0.621 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccC
Q psy6552 139 ITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIP 174 (254)
Q Consensus 139 IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p 174 (254)
-+++|+.+|++.+..+|+|+-+.. + |+ ++-..|
T Consensus 73 ~~~~dm~~A~n~l~~~gGG~vvv~-~-g~-v~a~lp 105 (171)
T PF13382_consen 73 TNDEDMALAANRLIEMGGGIVVVD-D-GE-VLAELP 105 (171)
T ss_dssp SSHHHHHHHHHHHHHTTSEEEEEE-T-TE-EEEEEE
T ss_pred CCHHHHHHHHHHHHHhCCCEEEEE-C-CE-EEEEEe
Confidence 379999999999999999998765 3 43 555666
No 436
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=22.97 E-value=2.5e+02 Score=20.82 Aligned_cols=41 Identities=24% Similarity=0.297 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHH
Q psy6552 95 YYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLA 146 (254)
Q Consensus 95 y~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~r 146 (254)
|.++-.-|.+++ ...||-++..|++..+-.. ..+|++|...
T Consensus 2 ~~~~~~piL~~L----~~~g~~~~~~ei~~~v~~~-------~~ls~e~~~~ 42 (92)
T PF14338_consen 2 YDELMPPILEAL----KDLGGSASRKEIYERVAER-------FGLSDEERNE 42 (92)
T ss_pred HHHHHHHHHHHH----HHcCCCcCHHHHHHHHHHH-------hCCCHHHHHH
Confidence 445555555555 4569999999999999776 3567776543
No 437
>PRK11642 exoribonuclease R; Provisional
Probab=22.95 E-value=2.3e+02 Score=30.06 Aligned_cols=49 Identities=22% Similarity=0.292 Sum_probs=39.0
Q ss_pred HHHHHHHhhccCCCcccHHHHHHhcCCCH----HHHHHHHHHHHHcCcEEEeCC
Q psy6552 181 HSLVLQQVASKNEAHISVSVLNNELNWST----ERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 181 ~~~il~l~~~~~~g~vt~~~l~~~l~ws~----~ra~~~L~~l~~~G~lwvD~q 230 (254)
...||++.... ...++..+|++.|+++. ...+.+|..|+++|.+-.+.+
T Consensus 21 ~~~Il~~l~~~-~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~ 73 (813)
T PRK11642 21 REFILEHLTKR-EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRR 73 (813)
T ss_pred HHHHHHHHHhc-CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCC
Confidence 44688887643 57899999999999984 347788999999999987654
No 438
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=22.92 E-value=87 Score=21.93 Aligned_cols=20 Identities=20% Similarity=0.507 Sum_probs=14.4
Q ss_pred cCHHH-HHHHHHHHHHcCCCc
Q psy6552 59 KDAQF-RRHFQEMCASIGVDP 78 (254)
Q Consensus 59 ~dp~f-r~~f~~mc~~lGVdP 78 (254)
.+|.| |.-++++|..||+||
T Consensus 39 p~~~y~rg~lr~Ya~~Lgld~ 59 (62)
T PF13413_consen 39 PSPVYARGYLRKYARFLGLDP 59 (62)
T ss_dssp SSHHHHHHHHHHHHHHTT--H
T ss_pred CcHHHHHHHHHHHHHHhCcCc
Confidence 34554 889999999999996
No 439
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=22.91 E-value=8.4e+02 Score=25.04 Aligned_cols=125 Identities=22% Similarity=0.334 Sum_probs=74.4
Q ss_pred cchhHHHHHHHHHHHhhhhhh--------hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhC------C
Q psy6552 91 MGDFYYELSVQIVEVCLATNY--------KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFG------N 156 (254)
Q Consensus 91 ~gdfy~eLavqive~c~~~r~--------~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg------~ 156 (254)
.|.||-+||.+|.---.-||- -..|++.-.++...+--. ..--+..+.+|+.+|+.-| +
T Consensus 413 sG~~ya~LA~~i~R~P~lTr~E~~vl~kiP~~~~i~~~~~~e~~~d~-------~~~ee~~i~~AL~kLEArGfI~~Lp~ 485 (591)
T PF04458_consen 413 SGRFYAELARHIKRLPHLTRYEMEVLHKIPDKGYIHREELVEFIKDH-------VGKEEEEIIEALEKLEARGFIEILPN 485 (591)
T ss_pred chHHHHHHHhhhhhcccccHHHHHHHHhCCccccccHHHHHHHhhcc-------cccchHHHHHHHHHHHhcchHHHcCC
Confidence 479999999999544333331 246666555555543322 2336778888999987654 4
Q ss_pred CeEEEEeCCceE---EEEccCC--------CCChhHHHHHHHhhccCCCc------------ccHHHHHHhcCCCHHHHH
Q psy6552 157 GFSIIPIGQGQY---LVQSIPG--------ELSLDHSLVLQQVASKNEAH------------ISVSVLNNELNWSTERAQ 213 (254)
Q Consensus 157 g~~l~~~~sg~~---vv~s~p~--------els~D~~~il~l~~~~~~g~------------vt~~~l~~~l~ws~~ra~ 213 (254)
|.-+.+=- |.. -+..+|. -.+.---.||+++.+. |. =+..++.+..|.+++-++
T Consensus 486 g~iilTea-G~~ik~Alsg~p~~e~~g~~~PVtP~~~rVL~Ai~~~--g~lyvKe~KvRi~pk~~ke~~K~sgL~~e~f~ 562 (591)
T PF04458_consen 486 GMIILTEA-GELIKRALSGVPEQEILGFGFPVTPTIYRVLKAIREV--GTLYVKEKKVRILPKNIKEAIKLSGLTPEEFK 562 (591)
T ss_pred CcEEEehh-hHHHHHHHhcCCcccccccCCCCCHHHHHHHHHHHHh--hhhhhhhhhhhcCccchHHHHHhcCCCHHHHH
Confidence 44333322 221 1222331 1222233556665532 22 244557789999999999
Q ss_pred HHHHHHHHcCcE
Q psy6552 214 HALDFMVQEGYA 225 (254)
Q Consensus 214 ~~L~~l~~~G~l 225 (254)
.+|..+-..|++
T Consensus 563 kaL~~aR~~~~i 574 (591)
T PF04458_consen 563 KALEVAREAGFI 574 (591)
T ss_pred HHHHHHHHhccc
Confidence 999999888876
No 440
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=22.85 E-value=3.4e+02 Score=24.20 Aligned_cols=84 Identities=8% Similarity=0.052 Sum_probs=40.0
Q ss_pred HHHHHHHHcCCCcccCCCcccccccc---chhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHH----HHh-cCCCCCCC
Q psy6552 66 HFQEMCASIGVDPLASRKGFWSLLGM---GDFYYELSVQIVEVCLATNYKNGGLILLDELRTRL----VKS-RGKSLQHQ 137 (254)
Q Consensus 66 ~f~~mc~~lGVdPl~s~kg~w~~lg~---gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~----nr~-Rg~~~~~~ 137 (254)
..+++....||.|-|-.+ |...+|. .+|-++|...+..--.........--+..+++..+ .+. ..+. .
T Consensus 48 si~~lA~~~~vS~aTi~R-f~kkLGf~gf~efk~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~t~---~ 123 (292)
T PRK11337 48 ALKDIAEALAVSEAMIVK-VAKKLGFSGFRNLRSALEDYFSQSEQVLHSELSFDDAPQDVVNKVFNTSLQAIEETQ---S 123 (292)
T ss_pred CHHHHHHHhCCChHHHHH-HHHHcCCCCHHHHHHHHHHHhccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHH---H
Confidence 346777778887665322 2224443 47777777654210000000000001223332221 111 0011 4
Q ss_pred CCCHHHHHHHHHHhhh
Q psy6552 138 DITNEDLLAAAKKLKI 153 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~ 153 (254)
.++++++.++++.+..
T Consensus 124 ~l~~~~l~~~~~~i~~ 139 (292)
T PRK11337 124 ILDVDEFHRAARFFYQ 139 (292)
T ss_pred hcCHHHHHHHHHHHHc
Confidence 6899999999999865
No 441
>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=22.69 E-value=2e+02 Score=23.49 Aligned_cols=38 Identities=13% Similarity=0.112 Sum_probs=28.7
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALD 217 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~ 217 (254)
|+.++-.++.+.- ..+.|..++++.+|+|+.-++..|.
T Consensus 101 L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 101 LPDEYREAIRLTE---LEGLSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHH
Confidence 6667777777765 3469999999999999876655543
No 442
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.57 E-value=2e+02 Score=22.89 Aligned_cols=38 Identities=11% Similarity=-0.073 Sum_probs=27.7
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALD 217 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~ 217 (254)
|+..+-.++.+.- ..+.|..++++.+|+|..-++..|.
T Consensus 107 Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 107 LPENYRDVVLAHY---LEEKSYQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred CCHHHHHHHHHHH---HhCCCHHHHHHHHCCCHHHHHHHHH
Confidence 6666777777665 2469999999999999865555443
No 443
>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=22.51 E-value=2.1e+02 Score=22.35 Aligned_cols=40 Identities=13% Similarity=0.017 Sum_probs=31.1
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..++.+.- ..+.|..++++.+|+|..-++..+..+
T Consensus 114 L~~~~r~il~l~~---~~~~~~~eIA~~lgis~~tv~~~~~ra 153 (161)
T TIGR02985 114 LPEQCRKIFILSR---FEGKSYKEIAEELGISVKTVEYHISKA 153 (161)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6667777777643 236799999999999999888887764
No 444
>KOG2199|consensus
Probab=22.33 E-value=2.8e+02 Score=27.14 Aligned_cols=56 Identities=18% Similarity=0.414 Sum_probs=36.7
Q ss_pred hHHHHHH-HHHHHHH-----HHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHc---CCC-cccCCC
Q psy6552 27 IQENQLE-QLSQHLN-----TFRDKLESFASEYKNEIKKDAQFRRHFQEMCASI---GVD-PLASRK 83 (254)
Q Consensus 27 l~~~~~~-~L~~ql~-----~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~l---GVd-Pl~s~k 83 (254)
++...|. .|.++++ +.++.+.....+..++-++||.+ +-...+|.+| |++ |...+|
T Consensus 84 VsSr~F~~el~al~~~~~h~kV~~k~~~lv~eWsee~K~Dp~l-sLi~~l~~klk~~g~~f~~~~~k 149 (462)
T KOG2199|consen 84 VSSRDFTTELRALIESKAHPKVCEKMRDLVKEWSEEFKKDPSL-SLISALYKKLKEEGITFLVAGSK 149 (462)
T ss_pred HhhhhHHHHHHHHHhhcccHHHHHHHHHHHHHHHHHhccCcch-hHHHHHHHHHHHcCCCcccCCCc
Confidence 4555555 4667766 34444455556666778899999 4678888775 887 665444
No 445
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=22.30 E-value=2.9e+02 Score=19.52 Aligned_cols=59 Identities=15% Similarity=0.204 Sum_probs=34.3
Q ss_pred HHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHH
Q psy6552 66 HFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLL 145 (254)
Q Consensus 66 ~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~ 145 (254)
-.+.+..+.||..+. .+=|.+|+..+-...... +.|.....+.++- ..++++||.
T Consensus 7 ~i~ria~~~Gi~ris-----------~~a~~~l~~~~e~rl~~i---------~~~A~k~~~hakR-----ktlt~~DI~ 61 (65)
T smart00803 7 TIKDVAESLGIGNLS-----------DEAAKLLAEDVEYRIKEI---------VQEALKFMRHSKR-----TTLTTSDID 61 (65)
T ss_pred HHHHHHHHCCCcccc-----------HHHHHHHHHHHHHHHHHH---------HHHHHHHHHHhCC-----CeecHHHHH
Confidence 456778889998764 355666665544443331 1233333333221 469999999
Q ss_pred HHHH
Q psy6552 146 AAAK 149 (254)
Q Consensus 146 rA~~ 149 (254)
.|++
T Consensus 62 ~Alk 65 (65)
T smart00803 62 SALR 65 (65)
T ss_pred HHhC
Confidence 8864
No 446
>TIGR02284 conserved hypothetical protein. Members of this protein family are found mostly in the Proteobacteria, although one member is found in the the marine planctomycete Pirellula sp. strain 1. The function is unknown.
Probab=22.14 E-value=1.9e+02 Score=23.39 Aligned_cols=17 Identities=29% Similarity=0.466 Sum_probs=11.2
Q ss_pred HHHHHHHHHcCCCcccC
Q psy6552 65 RHFQEMCASIGVDPLAS 81 (254)
Q Consensus 65 ~~f~~mc~~lGVdPl~s 81 (254)
.+++.+...+|-+|-.+
T Consensus 47 ~eL~~~v~~lGg~p~~~ 63 (139)
T TIGR02284 47 SELQQVVASLGGKPEDH 63 (139)
T ss_pred HHHHHHHHHhCCCCCCC
Confidence 46666667777777653
No 447
>TIGR03513 GldL_gliding gliding motility-associated protein GldL. This protein family, GldL, is named for the member from Flavobacterium johnsoniae, which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes. However, members are found also in several members of the Bacteriodetes that appear not to be motile
Probab=22.09 E-value=5e+02 Score=22.85 Aligned_cols=15 Identities=13% Similarity=0.470 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHHHcC
Q psy6552 61 AQFRRHFQEMCASIG 75 (254)
Q Consensus 61 p~fr~~f~~mc~~lG 75 (254)
..|+.+.+.|..+|.
T Consensus 175 ~~fkeQ~~kLa~NL~ 189 (202)
T TIGR03513 175 SSLKEEMEKMAANLT 189 (202)
T ss_pred HHHHHHHHHHHHHHH
Confidence 346777777776653
No 448
>PF15292 Treslin_N: Treslin N-terminus
Probab=21.82 E-value=96 Score=32.58 Aligned_cols=47 Identities=21% Similarity=0.355 Sum_probs=35.1
Q ss_pred hhcCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhh
Q psy6552 57 IKKDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNY 111 (254)
Q Consensus 57 I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~ 111 (254)
+.+||.+-+.|.+-...+=+|-+- + . .|+-|++|+.+|-+.|...++
T Consensus 557 lt~Dp~yLa~FLeeIl~~Yi~sip--k----~--L~~lY~sLg~~iP~~L~~vLP 603 (803)
T PF15292_consen 557 LTEDPAYLARFLEEILPLYIDSIP--K----T--LGELYHSLGTQIPQKLAGVLP 603 (803)
T ss_pred cccChHHHHHHHHHHHHHHHhhhH--H----H--HHHHHHHhccchHHHHhccCC
Confidence 568898888888776666655221 1 1 479999999999999988664
No 449
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.70 E-value=1.3e+02 Score=22.89 Aligned_cols=39 Identities=18% Similarity=0.181 Sum_probs=34.4
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCCC
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQS 231 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q~ 231 (254)
..-.++-+|....||+.--++.+|..|..-|+.|-=.|.
T Consensus 20 ~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l~FvQ~ 58 (95)
T COG4519 20 GETANVPELMAATGWPRRTAQDVIKALPGLGIVLEFVQE 58 (95)
T ss_pred cccCChHHHHHHcCCchhHHHHHHHhCcCCCeEEEeeec
Confidence 346889999999999999999999999999999976664
No 450
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=21.54 E-value=2.2e+02 Score=25.47 Aligned_cols=44 Identities=11% Similarity=0.096 Sum_probs=34.8
Q ss_pred HHHHHHhhcc--CCCcccHHHHHHhcCCCHHHHHHHHHHHHHc-CcE
Q psy6552 182 SLVLQQVASK--NEAHISVSVLNNELNWSTERAQHALDFMVQE-GYA 225 (254)
Q Consensus 182 ~~il~l~~~~--~~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~-G~l 225 (254)
..|+.++++. .+|-+|..+|+--||.|+......+..++++ |.+
T Consensus 90 ~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~v 136 (220)
T PF07900_consen 90 HRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVV 136 (220)
T ss_pred HHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCce
Confidence 3445555432 3678999999999999999999999999887 654
No 451
>PF03102 NeuB: NeuB family; InterPro: IPR013132 NeuB is the prokaryotic N-acetylneuraminic acid synthase (Neu5Ac). It catalyses the direct formation of Neu5Ac (the most common sialic acid) by condensation of phosphoenolpyruvate (PEP) and N-acetylmannosamine (ManNAc). This reaction has only been observed in prokaryotes; eukaryotes synthesise the 9-phosphate form, Neu5Ac-9-P, and utilise ManNAc-6-P instead of ManNAc. Such eukaryotic enzymes are not present in this family []. This family also contains SpsE spore coat polysaccharide biosynthesis proteins.; GO: 0016051 carbohydrate biosynthetic process; PDB: 3G8R_B 1XUU_A 1XUZ_A 3CM4_A 2ZDR_A 1VLI_A 2WQP_A.
Probab=21.40 E-value=4.4e+02 Score=23.56 Aligned_cols=89 Identities=19% Similarity=0.180 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHcCCCcccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCC--CCCC
Q psy6552 62 QFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQ--HQDI 139 (254)
Q Consensus 62 ~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~--~~~I 139 (254)
+.-.++.++|.+.||+.+++.=... .=+|..++.+ ...+...|-++=-.++..+-+.. .... ...-
T Consensus 56 e~~~~L~~~~~~~gi~f~stpfd~~----s~d~l~~~~~-------~~~KIaS~dl~n~~lL~~~A~tg-kPvIlSTG~s 123 (241)
T PF03102_consen 56 EQHKELFEYCKELGIDFFSTPFDEE----SVDFLEELGV-------PAYKIASGDLTNLPLLEYIAKTG-KPVILSTGMS 123 (241)
T ss_dssp HHHHHHHHHHHHTT-EEEEEE-SHH----HHHHHHHHT--------SEEEE-GGGTT-HHHHHHHHTT--S-EEEE-TT-
T ss_pred HHHHHHHHHHHHcCCEEEECCCCHH----HHHHHHHcCC-------CEEEeccccccCHHHHHHHHHhC-CcEEEECCCC
Confidence 3335889999999999887521000 0133333322 22233445555555555555532 1000 0235
Q ss_pred CHHHHHHHHHHh-hhhCCCeEEEE
Q psy6552 140 TNEDLLAAAKKL-KIFGNGFSIIP 162 (254)
Q Consensus 140 S~~Di~rA~~~L-~~Lg~g~~l~~ 162 (254)
|.+||.+|++.+ +.-+.++-|.+
T Consensus 124 tl~EI~~Av~~~~~~~~~~l~llH 147 (241)
T PF03102_consen 124 TLEEIERAVEVLREAGNEDLVLLH 147 (241)
T ss_dssp -HHHHHHHHHHHHHHCT--EEEEE
T ss_pred CHHHHHHHHHHHHhcCCCCEEEEe
Confidence 789999999999 44344455444
No 452
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=21.40 E-value=76 Score=22.89 Aligned_cols=20 Identities=40% Similarity=0.906 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHcCCCcccC
Q psy6552 62 QFRRHFQEMCASIGVDPLAS 81 (254)
Q Consensus 62 ~fr~~f~~mc~~lGVdPl~s 81 (254)
++...++.+|...|++|++.
T Consensus 27 ~vy~~Y~~~c~~~~~~~l~~ 46 (87)
T cd08768 27 EVYEVYEELCEEIGVDPLTQ 46 (87)
T ss_pred HHHHHHHHHHHHcCCCCCcH
Confidence 45589999999999999983
No 453
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.40 E-value=2e+02 Score=23.84 Aligned_cols=40 Identities=10% Similarity=-0.034 Sum_probs=31.6
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+-.|+.+.. ..+.|..++++.+|+|+.-++..|..+
T Consensus 131 Lp~~~r~v~~L~~---~~g~s~~EIA~~lgis~~tVk~~l~Ra 170 (185)
T PRK09649 131 LTTDQREALLLTQ---LLGLSYADAAAVCGCPVGTIRSRVARA 170 (185)
T ss_pred CCHHHhHHhhhHH---HcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5667777777766 347899999999999998888877654
No 454
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=21.34 E-value=7e+02 Score=23.57 Aligned_cols=117 Identities=16% Similarity=0.177 Sum_probs=73.8
Q ss_pred hhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCC----------------CCCCCHHHHHHHHHHhhhhCC
Q psy6552 93 DFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQ----------------HQDITNEDLLAAAKKLKIFGN 156 (254)
Q Consensus 93 dfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~----------------~~~IS~~Di~rA~~~L~~Lg~ 156 (254)
+||.. ..|.++...+-..-+==|+-......-.|+||+... ...|+.+=..+|.++|..-..
T Consensus 179 efY~~--~eL~~Iv~r~a~~l~i~i~~~~a~eIA~rSRGTPRIAnRLLrRVRDfa~V~~~~~I~~~ia~~aL~~L~Vd~~ 256 (332)
T COG2255 179 EFYTV--EELEEIVKRSAKILGIEIDEEAALEIARRSRGTPRIANRLLRRVRDFAQVKGDGDIDRDIADKALKMLDVDEL 256 (332)
T ss_pred ecCCH--HHHHHHHHHHHHHhCCCCChHHHHHHHHhccCCcHHHHHHHHHHHHHHHHhcCCcccHHHHHHHHHHhCcccc
Confidence 78873 356666665555444445566777778888887421 124555444445555443222
Q ss_pred CeEEEEeCCceEEEEccCCCCCh-hHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHH-HHHcCcEEEeCC
Q psy6552 157 GFSIIPIGQGQYLVQSIPGELSL-DHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDF-MVQEGYAWIDTQ 230 (254)
Q Consensus 157 g~~l~~~~sg~~vv~s~p~els~-D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~-l~~~G~lwvD~q 230 (254)
| ++. |..-+-.+++.-.+|-|-...|+..+|-+..-.+++++- |++.|++-+--.
T Consensus 257 G-------------------Ld~~D~k~L~~li~~f~GgPVGl~tia~~lge~~~TiEdv~EPyLiq~gfi~RTpR 313 (332)
T COG2255 257 G-------------------LDEIDRKYLRALIEQFGGGPVGLDTIAAALGEDRDTIEDVIEPYLIQQGFIQRTPR 313 (332)
T ss_pred c-------------------ccHHHHHHHHHHHHHhCCCCccHHHHHHHhcCchhHHHHHHhHHHHHhchhhhCCC
Confidence 2 332 333333334432368899999999999999999999996 999999876543
No 455
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=21.33 E-value=2.4e+02 Score=22.98 Aligned_cols=40 Identities=15% Similarity=0.131 Sum_probs=31.5
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|++.+..|+.+.- ..+.|..++++.+|+|+.-++..|..+
T Consensus 135 Lp~~~r~v~~l~~---~~g~s~~EIA~~lgis~~tVk~~l~Ra 174 (183)
T TIGR02999 135 VDPRQAEVVELRF---FAGLTVEEIAELLGVSVRTVERDWRFA 174 (183)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5667777777765 346999999999999998888777654
No 456
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=21.33 E-value=3.1e+02 Score=19.50 Aligned_cols=39 Identities=18% Similarity=0.253 Sum_probs=31.1
Q ss_pred hcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhh
Q psy6552 112 KNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 112 ~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~L 154 (254)
.+++.|++.++...++.-=+. ..++++++.+-+.+.++-
T Consensus 11 ~~~~~mt~~~f~~FL~~eQ~~----~~~~~~~~~~li~~~~~~ 49 (83)
T PF09279_consen 11 SDKEYMTAEEFRRFLREEQGE----PRLTDEQAKELIEKFEPD 49 (83)
T ss_dssp TTSSSEEHHHHHHHHHHTSS-----TTSSHHHHHHHHHHHHHH
T ss_pred CCCCcCCHHHHHHHHHHHhcc----ccCcHHHHHHHHHHHccc
Confidence 378999999999999876444 357999999999988654
No 457
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=21.30 E-value=2.6e+02 Score=19.92 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=30.9
Q ss_pred HHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhh
Q psy6552 97 ELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLK 152 (254)
Q Consensus 97 eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~ 152 (254)
.|..|+.|.+..- -++.|.+..+.++-.. +.|+.+..+|-+..|.
T Consensus 9 ~l~~Ql~el~Aed-------~AieDtiy~L~~al~~----g~I~~d~~lK~vR~La 53 (65)
T PF09454_consen 9 PLSNQLYELVAED-------HAIEDTIYYLDRALQR----GSIDLDTFLKQVRSLA 53 (65)
T ss_dssp HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHT----TSS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHc----CCCCHHHHHHHHHHHH
Confidence 3567888877763 3467777777776544 5689999888887764
No 458
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=21.19 E-value=5.3e+02 Score=22.71 Aligned_cols=18 Identities=17% Similarity=0.108 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHHHhhhh
Q psy6552 137 QDITNEDLLAAAKKLKIF 154 (254)
Q Consensus 137 ~~IS~~Di~rA~~~L~~L 154 (254)
..++++++.+||+.+..=
T Consensus 111 ~~~~~~~l~~~~~~i~~a 128 (278)
T PRK11557 111 DVNSEEKLHECVTMLRSA 128 (278)
T ss_pred HhcCHHHHHHHHHHHhcC
Confidence 468999999999998653
No 459
>COG2183 Tex Transcriptional accessory protein [Transcription]
Probab=21.16 E-value=1.7e+02 Score=30.91 Aligned_cols=89 Identities=17% Similarity=0.178 Sum_probs=52.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHHHHHHHHcCCCcccCCCcccc-ccccchhHHHHHHHHHHH----
Q psy6552 31 QLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFYYELSVQIVEV---- 105 (254)
Q Consensus 31 ~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~gdfy~eLavqive~---- 105 (254)
.|-..+.-.+..++.|.---..+..+|..||+||..+++...+=|+=-..-.+|.-. .-...+|||+-...|-.+
T Consensus 149 ~fi~~~~~v~s~~~Al~gA~dilae~is~da~lr~~lr~~~~~~g~~~~~~~~~~~~~e~~~f~~Y~d~~e~i~~~~~hr 228 (780)
T COG2183 149 DFISIEEGVSSSKLALDGARDILAERISEDAELREKLRDYLRKHGVLTSKVVKGKEDDEGAKFEDYYDHSEPIDNLPSHR 228 (780)
T ss_pred HHhhcccCcCCHHHHHHHHHHHHHHHHhhCHHHHHHHHHHHHhccEEEEeccCCcccccccceehhhhhhhHhhhhhHHH
Confidence 333344555556666654222337788999999999999999998852211121111 112347788776666543
Q ss_pred -hhhhhhhcCCceeH
Q psy6552 106 -CLATNYKNGGLILL 119 (254)
Q Consensus 106 -c~~~r~~nGGii~L 119 (254)
+.-.|..+-||+++
T Consensus 229 ~Lam~Rge~E~iL~v 243 (780)
T COG2183 229 ALAMNRGEKEGILSL 243 (780)
T ss_pred HHHHhhhcccCceEE
Confidence 23345566777654
No 460
>PF11719 Drc1-Sld2: DNA replication and checkpoint protein; InterPro: IPR021110 Genome duplication is precisely regulated by cyclin-dependent kinases CDKs, which bring about the onset of S phase by activating replication origins and then prevent relicensing of origins until mitosis is completed. The optimum sequence motif for CDK phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found to have at least 11 potential phosphorylation sites. Drc1 is required for DNA synthesis and S-M replication checkpoint control. Drc1 associates with Cdc2 and is phosphorylated at the onset of S phase when Cdc2 is activated. Thus Cdc2 promotes DNA replication by phosphorylating Drc1 and regulating its association with Cut5 []. Sld2 and Sld3 represent the minimal set of S-CDK substrates required for DNA replication []. This entry also includes ATP-dependent DNA helicase Q4, which may be involved in chromosome segregation and has been associated with various diseases.; PDB: 2KMU_A.
Probab=21.16 E-value=1.3e+02 Score=29.25 Aligned_cols=24 Identities=25% Similarity=0.522 Sum_probs=19.0
Q ss_pred HHHHHh-----hhhhhcCHHHHHHHHHHH
Q psy6552 48 SFASEY-----KNEIKKDAQFRRHFQEMC 71 (254)
Q Consensus 48 ~FA~kh-----~~~I~~dp~fr~~f~~mc 71 (254)
.|+.+| +.+|+.||+.+..+.+|-
T Consensus 14 ~F~~~hgRkP~k~DIk~~p~I~~~YK~Y~ 42 (426)
T PF11719_consen 14 AFAAQHGRKPSKEDIKANPEIAAKYKEYN 42 (426)
T ss_dssp HHHHHT-S---HHHHTTS-HHHHHHHHHH
T ss_pred HHHHHhCCCCCHHHHHhCHHHHHHHHHHH
Confidence 899999 789999999887766653
No 461
>PRK14339 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.09 E-value=2.5e+02 Score=27.01 Aligned_cols=48 Identities=25% Similarity=0.297 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhc
Q psy6552 138 DITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVAS 190 (254)
Q Consensus 138 ~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~ 190 (254)
..+.++++++++.++....++.+.+ .+|---|.|-.+|....++++..
T Consensus 261 ~~t~~~~~~~v~~lr~~~p~i~i~~-----d~IvGfPgETeedf~~Tl~fl~~ 308 (420)
T PRK14339 261 GYTKEWFLNRAEKLRALVPEVSIST-----DIIVGFPGESDKDFEDTMDVLEK 308 (420)
T ss_pred CCCHHHHHHHHHHHHHHCCCCEEEE-----EEEEECCCCCHHHHHHHHHHHHh
Confidence 3689999999999999877776533 36767798888888888888764
No 462
>PF02601 Exonuc_VII_L: Exonuclease VII, large subunit; InterPro: IPR020579 Exonuclease VII 3.1.11.6 from EC is composed of two nonidentical subunits; one large subunit and 4 small ones []. Exonuclease VII catalyses exonucleolytic cleavage in either 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. The large subunit also contains the OB-fold domains (IPR004365 from INTERPRO) that bind to nucleic acids at the N terminus. This entry represents Exonuclease VII, large subunit, C-terminal. ; GO: 0008855 exodeoxyribonuclease VII activity
Probab=21.05 E-value=4.4e+02 Score=23.99 Aligned_cols=25 Identities=24% Similarity=0.434 Sum_probs=21.2
Q ss_pred CHHHHHHHHHHhhhhC--CCeEEEEeC
Q psy6552 140 TNEDLLAAAKKLKIFG--NGFSIIPIG 164 (254)
Q Consensus 140 S~~Di~rA~~~L~~Lg--~g~~l~~~~ 164 (254)
++.+|.+|++.+...+ .+|.++.+.
T Consensus 56 A~~~I~~al~~~~~~~~~~~~Dviii~ 82 (319)
T PF02601_consen 56 AAASIVSALRKANEMGQADDFDVIIII 82 (319)
T ss_pred hHHHHHHHHHHHHhccccccccEEEEe
Confidence 8999999999999887 568777774
No 463
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=21.00 E-value=2.4e+02 Score=24.56 Aligned_cols=27 Identities=15% Similarity=0.171 Sum_probs=22.9
Q ss_pred CcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 194 AHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 194 g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
...|..++++.+|+|..+.+..+..++
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al 221 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKAL 221 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHH
Confidence 458999999999999999988766643
No 464
>COG1461 Predicted kinase related to dihydroxyacetone kinase [General function prediction only]
Probab=20.98 E-value=2.7e+02 Score=28.23 Aligned_cols=69 Identities=22% Similarity=0.212 Sum_probs=48.5
Q ss_pred hhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHH-HHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCce
Q psy6552 93 DFYYELSVQIVEVCLATNYKNGGLILLDELRTR-LVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQ 167 (254)
Q Consensus 93 dfy~eLavqive~c~~~r~~nGGii~L~dl~~~-~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~ 167 (254)
+...+|+.-+..-.+----=|.|+| |+.+++. ....++. ..|+.+|+..|...=......--+.++. |.
T Consensus 62 ~~~~~l~~~~s~g~LmGARGNSGVI-lSQilrGf~~~~~~~----~ei~~~~la~Af~~ave~AYkAVmkPVE-GT 131 (542)
T COG1461 62 SSIGELAKILSKGLLMGARGNSGVI-LSQILRGFAAAIADK----EEIDIEDLAKAFQRAVEVAYKAVMKPVE-GT 131 (542)
T ss_pred CcHHHHHHHHHHHHhhhccCcchhh-HHHHHHHHHHhcccc----cccCHHHHHHHHHHHHHHHHHHhcCCcC-ce
Confidence 5667787777776665555588999 8888884 4445444 6899999999998876665444444555 54
No 465
>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite.; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.
Probab=20.96 E-value=63 Score=30.08 Aligned_cols=33 Identities=27% Similarity=0.371 Sum_probs=24.1
Q ss_pred CCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhh
Q psy6552 114 GGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKI 153 (254)
Q Consensus 114 GGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~ 153 (254)
.+||-|++.+++++ .. ..|+++|+..||..++.
T Consensus 296 eSLIRLseA~AKl~---lr----~~V~~~Dv~~Ai~L~~~ 328 (331)
T PF00493_consen 296 ESLIRLSEAHAKLR---LR----DEVTEEDVEEAIRLFEE 328 (331)
T ss_dssp CHHHHHHHHHHHCT---TS----SECSHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHh---cc----CceeHHHHHHHHHHHHh
Confidence 45666666665543 33 78999999999999863
No 466
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.95 E-value=2.4e+02 Score=22.74 Aligned_cols=40 Identities=10% Similarity=0.017 Sum_probs=30.4
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..++.+.. ..+.|..++++.+|+|+.-++..|..+
T Consensus 113 L~~~~r~v~~l~~---~~g~s~~eIA~~lgis~~tV~~~l~Ra 152 (164)
T PRK12547 113 LSADQREAIILIG---ASGFSYEDAAAICGCAVGTIKSRVSRA 152 (164)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5556666666655 346899999999999998877777654
No 467
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=20.94 E-value=32 Score=26.54 Aligned_cols=67 Identities=25% Similarity=0.443 Sum_probs=8.8
Q ss_pred cchhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHH---HHHHHh-hhhhhcCHHHHHHHHHHHHHcC
Q psy6552 3 RRAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLE---SFASEY-KNEIKKDAQFRRHFQEMCASIG 75 (254)
Q Consensus 3 R~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~---~FA~kh-~~~I~~dp~fr~~f~~mc~~lG 75 (254)
+++||..|.|. .....+. .+. .+++.+...+.....++. .+..+. .+++..|++.-++++.+|..+-
T Consensus 4 Erigv~~l~~~-~~~~~~s----~~~-~~l~~~~~al~~L~~~l~~i~~Yl~~v~~g~~~~d~~i~r~l~~l~~~lp 74 (115)
T PF13012_consen 4 ERIGVDHLARG-LGDHYYS----SLS-SQLENEQNALKMLHKRLWQILDYLEDVISGEIPPDHEILRQLQDLLSSLP 74 (115)
T ss_dssp HHHHHHHHHHH---S--------------------------------------------------------------
T ss_pred HHHHHHHHHcc-CCCcccc----HHH-HHHHHHHHHHHHHHHhHHHHHHHHHHHHcCcCCCchhHHHHHHHHHHhcc
Confidence 56899999882 2222222 244 355555565655555555 223333 4567788888888888888764
No 468
>cd08063 MPN_CSN6 Mpr1p, Pad1p N-terminal (MPN) domains without catalytic isopeptidase activity, found in COP9 signalosome complex subunit 6. CSN6 (COP9 signalosome subunit 6; COP9 subunit 6; MOV34 homolog, 34 kD) is one of the eight subunits of COP9 signalosome, a highly conserved protein complex with diverse functions, including several important intracellular pathways such as the ubiquitin/proteasome system, DNA repair, cell cycle, developmental changes, and some aspects of immune responses. CSN6 is an MPN-domain protein that directly interacts with the MPN+-domain subunit CSN5. It is cleaved during apoptosis by activated caspases. CSN6 processing occurs in CSN/CRL (cullin-RING Ub ligase) complexes and is followed by the cleavage of Rbx1, the direct interaction partner of CSN6. CSN6 cleavage enhances CSN-mediated deneddylating activity (i.e. cleavage of ubiquitin-like protein Nedd8 (neural precursor cell expressed, developmentally downregulated 8)) in the cullin 1 in cells. The cleav
Probab=20.87 E-value=3.1e+02 Score=25.00 Aligned_cols=108 Identities=19% Similarity=0.281 Sum_probs=55.4
Q ss_pred chhhHHHhccHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHh-----hhhhhcCHHHHHHHHHHHHHcCCCc
Q psy6552 4 RAGVGAIQKQKLEQEKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEY-----KNEIKKDAQFRRHFQEMCASIGVDP 78 (254)
Q Consensus 4 ~vGi~~i~~~~~~~~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh-----~~~I~~dp~fr~~f~~mc~~lGVdP 78 (254)
++|+..|.+...... ........+++.+..-+...+++|.. ..+| .+++.-|+++-+..+++|.++-
T Consensus 164 rIgv~~l~~~~~~~~----~~~~~~~~~l~~~~~al~~L~~rl~~-i~~Yl~~V~~g~~~~d~~ilR~l~~~~~~lP--- 235 (288)
T cd08063 164 RIGVDHVARGGASGS----SEKSTVAAHLQAQHNAIKMLNSRVEL-ILEYLKAVPVGEVPPDHSILRSISALCSRLP--- 235 (288)
T ss_pred eeeHHHHHhcCCCCC----CcchHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCCCCCCCHHHHHHHHHHHHhCc---
Confidence 477888876542110 01111122445555555555555542 3333 3566778998889999997764
Q ss_pred ccCCCccccccccchhHHHHHHHHHHHhhhhh--hhcCCceeHHHHHHHHHH
Q psy6552 79 LASRKGFWSLLGMGDFYYELSVQIVEVCLATN--YKNGGLILLDELRTRLVK 128 (254)
Q Consensus 79 l~s~kg~w~~lg~gdfy~eLavqive~c~~~r--~~nGGii~L~dl~~~~nr 128 (254)
... ...|-.++..++=|+.+-+. ...-+..+|.|+...++=
T Consensus 236 ~~~---------~~~~~~~~~~~~~D~lmv~yLs~lt~~~~~l~~~~~k~~~ 278 (288)
T cd08063 236 VLK---------SEAFREELLAEYNDVLLVAYLATLTKGCNTLNELVDKFNV 278 (288)
T ss_pred cCC---------hHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 321 23455555555444433221 223345566666655543
No 469
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=20.83 E-value=2.4e+02 Score=21.26 Aligned_cols=41 Identities=17% Similarity=0.014 Sum_probs=29.9
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
+++.+..++.+.- ..+.|..++++.+|.|+......+..+.
T Consensus 111 L~~~~~~ii~~~~---~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 111 LPEREREVLVLRY---LEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred CCHHHHHHHhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4445555655443 2468999999999999999888877653
No 470
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.79 E-value=2.3e+02 Score=22.59 Aligned_cols=41 Identities=12% Similarity=0.019 Sum_probs=32.6
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFMV 220 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l~ 220 (254)
|+..+..|+.+-- ..+.|..++++.+|+|..-++..|..+.
T Consensus 114 L~~~~r~v~~L~~---~~g~s~~EIA~~l~is~~tV~~~l~ra~ 154 (161)
T PRK12528 114 LPPLVKRAFLLAQ---VDGLGYGEIATELGISLATVKRYLNKAA 154 (161)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 6667777777765 3479999999999999998888877653
No 471
>PRK09462 fur ferric uptake regulator; Provisional
Probab=20.64 E-value=2.5e+02 Score=22.64 Aligned_cols=58 Identities=16% Similarity=0.179 Sum_probs=40.9
Q ss_pred HHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceE
Q psy6552 101 QIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQY 168 (254)
Q Consensus 101 qive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~ 168 (254)
.|.++... ..++-++..||+..+.+.- ..||+.=|+|+++.|...|.=-++ .+++|..
T Consensus 21 ~Il~~l~~---~~~~h~sa~eI~~~l~~~~------~~i~~aTVYR~L~~L~e~Gli~~~-~~~~~~~ 78 (148)
T PRK09462 21 KILEVLQE---PDNHHVSAEDLYKRLIDMG------EEIGLATVYRVLNQFDDAGIVTRH-NFEGGKS 78 (148)
T ss_pred HHHHHHHh---CCCCCCCHHHHHHHHHhhC------CCCCHHHHHHHHHHHHHCCCEEEE-EcCCCcE
Confidence 55555553 2456789999999997642 469999999999999999963333 3433443
No 472
>cd03316 MR_like Mandelate racemase (MR)-like subfamily of the enolase superfamily. Enzymes of this subgroup share three conserved carboxylate ligands for the essential divalent metal ion (usually Mg2+), two aspartates and a glutamate, and conserved catalytic residues, a Lys-X-Lys motif and a conserved histidine-aspartate dyad. Members of the MR subgroup are mandelate racemase, D-glucarate/L-idarate dehydratase (GlucD), D-altronate/D-mannonate dehydratase , D-galactonate dehydratase (GalD) , D-gluconate dehydratase (GlcD), and L-rhamnonate dehydratase (RhamD).
Probab=20.63 E-value=1.2e+02 Score=27.96 Aligned_cols=84 Identities=17% Similarity=0.230 Sum_probs=48.2
Q ss_pred CHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhHHHHHHHhhccCCC-cccHHHHHHhcCCCHHHHHHHHHH
Q psy6552 140 TNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDHSLVLQQVASKNEA-HISVSVLNNELNWSTERAQHALDF 218 (254)
Q Consensus 140 S~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~~~il~l~~~~~~g-~vt~~~l~~~l~ws~~ra~~~L~~ 218 (254)
+++++.++++.+.. .||+.+++.-|...... .-...|-..+-.+.+.-... -+.++ -+-+|+.+.|.+.++.
T Consensus 139 ~~~~~~~~a~~~~~--~Gf~~~Kik~g~~~~~~--~~~~~d~~~v~~ir~~~g~~~~l~vD---aN~~~~~~~a~~~~~~ 211 (357)
T cd03316 139 SPEELAEEAKRAVA--EGFTAVKLKVGGPDSGG--EDLREDLARVRAVREAVGPDVDLMVD---ANGRWDLAEAIRLARA 211 (357)
T ss_pred CHHHHHHHHHHHHH--cCCCEEEEcCCCCCcch--HHHHHHHHHHHHHHHhhCCCCEEEEE---CCCCCCHHHHHHHHHH
Confidence 69999999988765 46776666511100000 00122323332222211011 13222 1669999999999999
Q ss_pred HHHcCcEEEeCC
Q psy6552 219 MVQEGYAWIDTQ 230 (254)
Q Consensus 219 l~~~G~lwvD~q 230 (254)
+.+.|+.|+.+-
T Consensus 212 l~~~~i~~iEqP 223 (357)
T cd03316 212 LEEYDLFWFEEP 223 (357)
T ss_pred hCccCCCeEcCC
Confidence 999999999854
No 473
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=20.58 E-value=2e+02 Score=27.11 Aligned_cols=51 Identities=20% Similarity=0.352 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhhhhhh-cCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHh
Q psy6552 97 ELSVQIVEVCLATNYK-NGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKL 151 (254)
Q Consensus 97 eLavqive~c~~~r~~-nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L 151 (254)
++-..|+++|.+++.. .-|-|.+-.+-..+--..|. +.|+|+||..|+...
T Consensus 258 ~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR----~~V~~dDv~~~a~~v 309 (337)
T TIGR02030 258 DVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGR----TEVTVDDIRRVAVLA 309 (337)
T ss_pred HHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCC----CCCCHHHHHHHHHHH
Confidence 4555677788877742 23344444443333333454 789999999998764
No 474
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=20.53 E-value=2.3e+02 Score=23.70 Aligned_cols=50 Identities=14% Similarity=0.074 Sum_probs=38.7
Q ss_pred HHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHhhhhCCCeE
Q psy6552 100 VQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKLKIFGNGFS 159 (254)
Q Consensus 100 vqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L~~Lg~g~~ 159 (254)
..|.++... +.+-++..||+..+.+.- ..||..-|+|.++.|...|.=-+
T Consensus 29 ~~IL~~l~~----~~~hlSa~eI~~~L~~~~------~~is~aTVYRtL~~L~e~Glv~~ 78 (169)
T PRK11639 29 LEVLRLMSL----QPGAISAYDLLDLLREAE------PQAKPPTVYRALDFLLEQGFVHK 78 (169)
T ss_pred HHHHHHHHh----cCCCCCHHHHHHHHHhhC------CCCCcchHHHHHHHHHHCCCEEE
Confidence 356666664 357889999999998753 46999999999999999885433
No 475
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=20.51 E-value=2.1e+02 Score=22.79 Aligned_cols=40 Identities=18% Similarity=0.043 Sum_probs=32.4
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..++.+.- ..+.|..++++.+|.|..-++..|..+
T Consensus 113 L~~~~r~v~~l~~---~~~~s~~eIA~~lgis~~tv~~~l~Ra 152 (161)
T PRK12541 113 LPLERRNVLLLRD---YYGFSYKEIAEMTGLSLAKVKIELHRG 152 (161)
T ss_pred CCHHHHHHhhhHH---hcCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6777888888766 346999999999999998888877654
No 476
>COG4199 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.46 E-value=1.8e+02 Score=25.52 Aligned_cols=63 Identities=19% Similarity=0.345 Sum_probs=42.4
Q ss_pred CceEEEEccCCCCChhH-HHHHHHhhccC--CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEeCC
Q psy6552 165 QGQYLVQSIPGELSLDH-SLVLQQVASKN--EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWIDTQ 230 (254)
Q Consensus 165 sg~~vv~s~p~els~D~-~~il~l~~~~~--~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD~q 230 (254)
+.-.++-..| +.|| ..+..++-... .=.---.+|++.+||+++.-.-.+.-..+-|++-+|+.
T Consensus 86 ~e~~yltg~p---tRd~Fa~lYk~i~kf~eFdi~k~~~~La~~l~~~~e~l~fM~KVF~eL~FVtiddG 151 (201)
T COG4199 86 SEDYYLTGIP---TRDHFAKLYKFIYKFPEFDIRKKGKRLAQYLGWNKETLVFMIKVFFELGFVTIDDG 151 (201)
T ss_pred CCCeeecCCC---cHHHHHHHHHHHHhcCCccHHHHHHHHHHHcCCCHHHHHHHHHHHHHcceeEeeCC
Confidence 3666776666 5565 45555543110 01123467999999999988888888888888888874
No 477
>PRK09240 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=20.45 E-value=3.5e+02 Score=25.58 Aligned_cols=151 Identities=13% Similarity=0.159 Sum_probs=74.8
Q ss_pred cCHHHHHHHHHHHHHcCCCcccCCCccccccccchhHHHH---HHHHHHHhhhhhhhcCCc-eeHHHHHHHHHHhcCCCC
Q psy6552 59 KDAQFRRHFQEMCASIGVDPLASRKGFWSLLGMGDFYYEL---SVQIVEVCLATNYKNGGL-ILLDELRTRLVKSRGKSL 134 (254)
Q Consensus 59 ~dp~fr~~f~~mc~~lGVdPl~s~kg~w~~lg~gdfy~eL---avqive~c~~~r~~nGGi-i~L~dl~~~~nr~Rg~~~ 134 (254)
.+.+.|-+--..+...|++.+.+.- ++|+|++..+. +..+.+...... .+++ |++..+.-. -|...
T Consensus 199 h~~~~rl~~i~~a~~aG~~~v~~g~----i~Glge~~~d~~~~a~~l~~L~~~~~--~~~~sv~~~~l~P~----~g~~~ 268 (371)
T PRK09240 199 RDFEYRLETPERAGRAGIRKIGLGA----LLGLSDWRTDALMTALHLRYLQRKYW--QAEYSISFPRLRPC----TGGIE 268 (371)
T ss_pred CCHHHHHHHHHHHHHcCCCeeceEE----EecCCccHHHHHHHHHHHHHHHHhCC--CCceeeecCccccC----CCCCC
Confidence 4677788888888889987554322 77888876443 333333332110 0111 222222111 11001
Q ss_pred CCCCCCHHHHHHHHHHhhhhCCCeEEEEeCCceEEEEccCCCCChhH----HHHHHHhhcc-CCCcccHHHHHHhcCCCH
Q psy6552 135 QHQDITNEDLLAAAKKLKIFGNGFSIIPIGQGQYLVQSIPGELSLDH----SLVLQQVASK-NEAHISVSVLNNELNWST 209 (254)
Q Consensus 135 ~~~~IS~~Di~rA~~~L~~Lg~g~~l~~~~sg~~vv~s~p~els~D~----~~il~l~~~~-~~g~vt~~~l~~~l~ws~ 209 (254)
....+|++|++|.+..++-+-+...| .+..|+ +..+.+.. ...+..+... .+||.|...-...|-++-
T Consensus 269 ~~~~~~~~e~l~~ia~~Rl~lP~~~i-~~s~g~------~~~lrd~~~~~~~~~~~ag~~~~~G~y~~~~~~~~qf~~~~ 341 (371)
T PRK09240 269 PASIVSDKQLVQLICAFRLFLPDVEI-SLSTRE------SPEFRDNLIPLGITKMSAGSSTQPGGYADDHKELEQFEISD 341 (371)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccccc-EEecCC------CHHHHHHHHhhcceeeccCccCCCCCcCCCCCCcCCccCCC
Confidence 12569999999999999876643333 333133 11122111 1112222111 377887622234455554
Q ss_pred HHHHHH-HHHHHHcCcEE
Q psy6552 210 ERAQHA-LDFMVQEGYAW 226 (254)
Q Consensus 210 ~ra~~~-L~~l~~~G~lw 226 (254)
.|..+. +.++.+.|+-.
T Consensus 342 ~r~~~~~~~~i~~~g~~~ 359 (371)
T PRK09240 342 DRSVEEVAAALRAKGLQP 359 (371)
T ss_pred CCCHHHHHHHHHHCCCee
Confidence 554443 44456678754
No 478
>COG3793 TerB Tellurite resistance protein [Inorganic ion transport and metabolism]
Probab=20.38 E-value=80 Score=26.34 Aligned_cols=21 Identities=24% Similarity=0.553 Sum_probs=17.7
Q ss_pred CHHHHHHHHHHHHHcCCCccc
Q psy6552 60 DAQFRRHFQEMCASIGVDPLA 80 (254)
Q Consensus 60 dp~fr~~f~~mc~~lGVdPl~ 80 (254)
||+-|.-..++|..||++|+-
T Consensus 121 d~~E~avl~eI~~aLGL~p~~ 141 (144)
T COG3793 121 EAEERAVLREIAGALGLSPAE 141 (144)
T ss_pred CHHHHHHHHHHHHHhCCCHHh
Confidence 466689999999999999973
No 479
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=20.35 E-value=1.2e+02 Score=30.09 Aligned_cols=36 Identities=22% Similarity=0.261 Sum_probs=31.9
Q ss_pred CCcccHHHHHHhcCCCHHHHHHHHHHHHHcCcEEEe
Q psy6552 193 EAHISVSVLNNELNWSTERAQHALDFMVQEGYAWID 228 (254)
Q Consensus 193 ~g~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lwvD 228 (254)
...+|..+|++.+..|.--|+..|..|.++|++.=-
T Consensus 21 ~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~w~ 56 (552)
T PRK13626 21 SQETTLNELAELLNCSRRHMRTLLNTMQQRGWLTWQ 56 (552)
T ss_pred cceeeHHHHHHHhcCChhHHHHHHHHHHHCCCeeee
Confidence 357999999999999999999999999999976433
No 480
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=20.35 E-value=4.1e+02 Score=21.55 Aligned_cols=65 Identities=14% Similarity=0.214 Sum_probs=49.5
Q ss_pred HHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHHHh-hhhCCCeEEEEeCCceEEEEc
Q psy6552 101 QIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAKKL-KIFGNGFSIIPIGQGQYLVQS 172 (254)
Q Consensus 101 qive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~~L-~~Lg~g~~l~~~~sg~~vv~s 172 (254)
.++++...-+.++|--|+..+|+..+.+..| +|.+++.+++..| ..|..-=+.+.+|.|+==+++
T Consensus 4 S~idvAy~iL~~~~~~m~f~dL~~ev~~~~~-------~s~e~~~~~iaq~YtdLn~DGRFi~lG~n~WgLr~ 69 (129)
T PRK02363 4 SLIEVAYEILKEKKEPMSFYDLVNEIQKYLG-------KSDEEIRERIAQFYTDLNLDGRFISLGDNKWGLRS 69 (129)
T ss_pred cHHHHHHHHHHHcCCcccHHHHHHHHHHHhC-------CCHHHHHHHHHHHHHHHhccCCeeEcCCCceeccc
Confidence 4677788878888999999999999999864 5899998888886 555555577777755544444
No 481
>TIGR00273 iron-sulfur cluster-binding protein. Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulfur clusters.
Probab=20.31 E-value=76 Score=30.98 Aligned_cols=126 Identities=14% Similarity=0.136 Sum_probs=67.1
Q ss_pred HHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcC-HHHHHHHHHHHHHcCCCcccCCCcccc-ccccchhH
Q psy6552 18 EKYKDKGTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKD-AQFRRHFQEMCASIGVDPLASRKGFWS-LLGMGDFY 95 (254)
Q Consensus 18 ~~~~~~g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~d-p~fr~~f~~mc~~lGVdPl~s~kg~w~-~lg~gdfy 95 (254)
+...+.+.++.+..+++|..+++.|.++++. .-..--.-++ .+.+.-..++|...|...+..+|+--. .+|+.+|.
T Consensus 32 ~~~r~~~~~ik~~~~~~ld~~l~~~~~~~~~--~g~~v~~a~t~~eA~~~v~~i~~~~~~~~vv~~kS~~~eeigl~~~L 109 (432)
T TIGR00273 32 EEWRELVKEIKLKVLENLDFYLDQLKENVTQ--RGGHVYYAKTAEEARKIIGKVAQEKNGKKVVKSKSMVSEEIGLNEVL 109 (432)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH--CCCEEEEECCHHHHHHHHHHHHHHhCCCEEEEcCchHHHHhCCHHHH
Confidence 3445556678888888899999988888762 1111111123 456677888999988886654442111 33444443
Q ss_pred HH---------HHHHHHHHhhhhhhhc----CCceeHHHHHHHHHHhcCCCCCCCCCCHHHHHHHHH
Q psy6552 96 YE---------LSVQIVEVCLATNYKN----GGLILLDELRTRLVKSRGKSLQHQDITNEDLLAAAK 149 (254)
Q Consensus 96 ~e---------Lavqive~c~~~r~~n----GGii~L~dl~~~~nr~Rg~~~~~~~IS~~Di~rA~~ 149 (254)
.+ |+..|+..--. .+.. .==++-.++-..|++..|.. ..-+|+++.++..
T Consensus 110 ~~~g~~~~etdlge~i~ql~~~-~pshiv~Paih~~r~~i~~~f~~~~~~~---~~~~~~~l~~~~r 172 (432)
T TIGR00273 110 EKIGIEVWETDLGELILQLDGD-PPSHIVVPALHKNRQQIGEILKERLGYE---GEESPEVLAREAR 172 (432)
T ss_pred HhCCCeeeeCccHHHHhhhccC-CCceeeeccccCCHHHHHHHHHHhccCC---CCCCHHHHHHHHH
Confidence 33 23222222100 0000 00023456777777766553 2346777666553
No 482
>cd07613 BAR_Endophilin_A1 The Bin/Amphiphysin/Rvs (BAR) domain of Endophilin-A1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. Endophilins play roles in synaptic vesicle formation, virus budding, mitochondrial morphology maintenance, receptor-mediated endocytosis inhibition, and endosomal sorting. Endophilins contain an N-terminal N-BAR domain (BAR domain with an additional N-terminal amphipathic helix), followed by a variable region containing proline clusters, and a C-terminal SH3 domain. They are classified into two types, A and B. Vertebrates contain three endophilin-A isoforms. Endophilin-A proteins are enriched in the brain and play multiple roles in receptor-mediated endocytosis. Endophilin-A1 (or endophilin-1) is also referred to as SH3P4 (SH3 domain containing protein 4) or SH3GL2 (SH3 domain containing Grb2-like protein 2). It is localized in presynaptic nerve terminals. It plays many roles i
Probab=20.29 E-value=2.4e+02 Score=25.13 Aligned_cols=43 Identities=7% Similarity=0.269 Sum_probs=36.4
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCHHHHHHH
Q psy6552 24 GTSIQENQLEQLSQHLNTFRDKLESFASEYKNEIKKDAQFRRHF 67 (254)
Q Consensus 24 g~~l~~~~~~~L~~ql~~fk~~L~~FA~kh~~~I~~dp~fr~~f 67 (254)
|+++.+ .|.+|++..+.-+..++++-.+-..=+..||..|.+-
T Consensus 2 ~t~ld~-~f~~le~k~D~t~~~~~~i~~~t~~~LQPNpa~r~k~ 44 (223)
T cd07613 2 GTKLDD-DFKEMERKVDVTSRAVMEIMTKTIEYLQPNPASRAKL 44 (223)
T ss_pred CCcccH-HHHHHHHHHHHHHHHHHHHHHHHHHHcCCChhHHHHH
Confidence 445555 9999999999999999999999989999999887543
No 483
>KOG1900|consensus
Probab=20.28 E-value=8.4e+02 Score=27.49 Aligned_cols=79 Identities=19% Similarity=0.242 Sum_probs=54.9
Q ss_pred HHHHHHHHHcCCC--cccCCCccccccccchhHHHHHHHHHHHhhhhhhhcCCceeHHHHHHHHHHhcCCCCCCCCCCHH
Q psy6552 65 RHFQEMCASIGVD--PLASRKGFWSLLGMGDFYYELSVQIVEVCLATNYKNGGLILLDELRTRLVKSRGKSLQHQDITNE 142 (254)
Q Consensus 65 ~~f~~mc~~lGVd--Pl~s~kg~w~~lg~gdfy~eLavqive~c~~~r~~nGGii~L~dl~~~~nr~Rg~~~~~~~IS~~ 142 (254)
++|..+|..++.| -..+.-.|-.+++.+| .||++.++.-.+..--..|| +.+++..++.+.=|. .=+.+
T Consensus 742 h~f~~Iv~els~~lqk~l~~ltF~dl~~~nd--kel~~~li~slin~~i~s~a--~vd~vs~~Lre~Cps-----~~s~~ 812 (1311)
T KOG1900|consen 742 HHFIDIVSELSADLQKELSCLTFHDLFTSND--KELTKELLISLINRYIMSGA--SVDYVSELLRERCPS-----FCSAS 812 (1311)
T ss_pred hHHHHHHHHhCHHHHHHHHhccHHHhcCcch--HHHHHHHHHHHHHHHhccCC--ChhHHHHHHHHhCcc-----cccch
Confidence 5778888888855 1112223433566678 89999999888887777777 778888777776554 44666
Q ss_pred HH--HHHHHHhh
Q psy6552 143 DL--LAAAKKLK 152 (254)
Q Consensus 143 Di--~rA~~~L~ 152 (254)
|+ .+|++.|+
T Consensus 813 D~l~ykA~E~L~ 824 (1311)
T KOG1900|consen 813 DILTYKAVELLE 824 (1311)
T ss_pred HHHHHHHHHHHH
Confidence 65 58999888
No 484
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.23 E-value=2.4e+02 Score=22.74 Aligned_cols=38 Identities=21% Similarity=0.201 Sum_probs=27.6
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALD 217 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~ 217 (254)
|+..+-.|+.+.- ..+.|..++++.+|+|..-++..|.
T Consensus 119 L~~~~r~vl~L~~---~~g~s~~EIA~~lgis~~tV~~~l~ 156 (173)
T PRK09645 119 LSPEHRAVLVRSY---YRGWSTAQIAADLGIPEGTVKSRLH 156 (173)
T ss_pred CCHHHHHHHHHHH---HcCCCHHHHHHHHCcCHHHHHHHHH
Confidence 6667777777765 2368999999999999865544433
No 485
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.22 E-value=2.1e+02 Score=23.26 Aligned_cols=40 Identities=10% Similarity=0.009 Sum_probs=29.8
Q ss_pred CChhHHHHHHHhhccCCCcccHHHHHHhcCCCHHHHHHHHHHH
Q psy6552 177 LSLDHSLVLQQVASKNEAHISVSVLNNELNWSTERAQHALDFM 219 (254)
Q Consensus 177 ls~D~~~il~l~~~~~~g~vt~~~l~~~l~ws~~ra~~~L~~l 219 (254)
|+..+..|+.+.- ..+.|..++++.+|+|..-++..|..+
T Consensus 120 L~~~~r~i~~l~~---~~g~s~~EIA~~lgis~~tV~~~l~Ra 159 (172)
T PRK09651 120 LNGKTREAFLLSQ---LDGLTYSEIAHKLGVSVSSVKKYVAKA 159 (172)
T ss_pred CCHHHhHHhhhhh---ccCCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5556666766655 457899999999999988777666543
No 486
>cd04742 NPD_FabD 2-Nitropropane dioxygenase (NPD)-like domain, associated with the (acyl-carrier-protein) S-malonyltransferase FabD. NPD is part of the nitroalkaneoxidizing enzyme family, that catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDPs are members of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.
Probab=20.18 E-value=2.5e+02 Score=27.46 Aligned_cols=43 Identities=12% Similarity=0.168 Sum_probs=29.5
Q ss_pred eHHHHHHHHHHhcCCCCCC-CCCCHHHHHHHHHHhhhh---CCCeEE
Q psy6552 118 LLDELRTRLVKSRGKSLQH-QDITNEDLLAAAKKLKIF---GNGFSI 160 (254)
Q Consensus 118 ~L~dl~~~~nr~Rg~~~~~-~~IS~~Di~rA~~~L~~L---g~g~~l 160 (254)
+-.+|...+.++-|.+.++ .-.||++|..+|..++.+ +.||-+
T Consensus 26 ss~eLVaAvs~AGgLG~lgag~l~~e~l~~~I~~ir~~lt~~~PfGV 72 (418)
T cd04742 26 ASAELVVAMGKAGMLGFFGAGGLPLDEVEQAIERIQAALGNGEPYGV 72 (418)
T ss_pred CCHHHHHHHHhCCCeeeecCCCCCHHHHHHHHHHHHHhccCCCCeEE
Confidence 5667777777766553221 357899999999999884 567744
No 487
>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=20.09 E-value=1.3e+02 Score=18.61 Aligned_cols=28 Identities=18% Similarity=0.137 Sum_probs=21.3
Q ss_pred cccHHHHHHhcCCCHHHHHHHHHHHHHcCcEE
Q psy6552 195 HISVSVLNNELNWSTERAQHALDFMVQEGYAW 226 (254)
Q Consensus 195 ~vt~~~l~~~l~ws~~ra~~~L~~l~~~G~lw 226 (254)
|+|..++++.+|.+..- |..++++|.+-
T Consensus 1 ~lt~~e~a~~lgis~~t----i~~~~~~g~i~ 28 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDT----VYRLIHEGELP 28 (49)
T ss_pred CCCHHHHHHHHCCCHHH----HHHHHHcCCCC
Confidence 57999999999988764 55566777543
Done!