Query 025599
Match_columns 250
No_of_seqs 109 out of 228
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 07:29:06 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025599.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025599hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3341 RNA polymerase II tran 100.0 5.1E-93 1.1E-97 616.5 21.2 244 1-246 1-244 (249)
2 PF04157 EAP30: EAP30/Vps36 fa 100.0 2.8E-66 6.1E-71 457.2 18.9 218 5-224 1-223 (223)
3 KOG2760 Vacuolar sorting prote 100.0 9.6E-37 2.1E-41 284.4 20.4 224 3-244 196-431 (432)
4 PF13412 HTH_24: Winged helix- 96.8 0.0045 9.8E-08 41.5 5.6 47 175-221 1-47 (48)
5 PRK00135 scpB segregation and 96.5 0.031 6.7E-07 48.8 10.1 107 102-223 7-133 (188)
6 PF05158 RNA_pol_Rpc34: RNA po 96.2 0.084 1.8E-06 49.7 12.0 115 97-222 8-131 (327)
7 PF01978 TrmB: Sugar-specific 96.0 0.018 3.8E-07 41.3 5.3 53 174-226 5-57 (68)
8 smart00550 Zalpha Z-DNA-bindin 95.9 0.034 7.5E-07 40.4 6.5 55 179-237 8-64 (68)
9 PF08220 HTH_DeoR: DeoR-like h 95.6 0.036 7.7E-07 38.9 5.3 45 179-223 2-46 (57)
10 PF09012 FeoC: FeoC like trans 95.3 0.039 8.4E-07 40.0 4.8 44 181-224 4-47 (69)
11 smart00418 HTH_ARSR helix_turn 95.2 0.081 1.8E-06 35.7 6.1 53 182-238 2-54 (66)
12 PF04703 FaeA: FaeA-like prote 94.8 0.1 2.2E-06 37.8 5.7 56 181-237 4-60 (62)
13 PF01726 LexA_DNA_bind: LexA D 94.6 0.087 1.9E-06 38.2 5.1 53 174-226 3-61 (65)
14 PF12802 MarR_2: MarR family; 94.0 0.17 3.7E-06 34.9 5.5 53 175-227 3-57 (62)
15 smart00420 HTH_DEOR helix_turn 94.0 0.2 4.3E-06 32.9 5.5 46 179-224 2-47 (53)
16 PF01047 MarR: MarR family; I 93.9 0.15 3.3E-06 35.0 5.0 50 175-224 1-50 (59)
17 smart00347 HTH_MARR helix_turn 93.7 0.38 8.3E-06 35.5 7.3 54 173-226 6-59 (101)
18 TIGR02147 Fsuc_second hypothet 93.7 0.19 4.1E-06 46.3 6.5 160 40-225 8-173 (271)
19 PRK11179 DNA-binding transcrip 93.1 0.27 6E-06 40.8 6.1 49 175-223 7-55 (153)
20 PF04079 DUF387: Putative tran 92.8 0.48 1E-05 40.2 7.3 96 118-226 14-128 (159)
21 TIGR00281 segregation and cond 92.6 1.5 3.3E-05 38.2 10.2 108 102-224 4-131 (186)
22 PF02002 TFIIE_alpha: TFIIE al 92.2 0.27 5.8E-06 38.3 4.6 64 175-239 11-78 (105)
23 PRK11169 leucine-responsive tr 91.8 0.35 7.5E-06 40.7 5.2 51 173-223 10-60 (164)
24 TIGR01889 Staph_reg_Sar staphy 91.6 0.87 1.9E-05 35.6 7.0 56 174-229 22-81 (109)
25 COG3355 Predicted transcriptio 91.2 0.92 2E-05 37.3 6.9 48 180-227 31-78 (126)
26 PHA02943 hypothetical protein; 91.1 0.72 1.6E-05 39.3 6.3 58 176-237 10-67 (165)
27 PF08784 RPA_C: Replication pr 91.1 0.64 1.4E-05 35.8 5.6 49 174-222 44-96 (102)
28 COG1349 GlpR Transcriptional r 90.7 0.46 1E-05 42.9 5.2 46 178-223 6-51 (253)
29 PF13463 HTH_27: Winged helix 90.0 0.93 2E-05 31.7 5.3 47 175-221 1-48 (68)
30 PRK11512 DNA-binding transcrip 89.9 1.6 3.6E-05 35.4 7.4 56 172-227 35-90 (144)
31 TIGR02698 CopY_TcrY copper tra 89.9 1.5 3.2E-05 35.8 7.0 62 175-239 2-67 (130)
32 PRK15466 carboxysome structura 89.8 0.52 1.1E-05 40.4 4.4 39 184-222 117-155 (166)
33 PF09397 Ftsk_gamma: Ftsk gamm 89.6 0.95 2E-05 33.1 5.1 43 180-222 9-51 (65)
34 TIGR02337 HpaR homoprotocatech 89.6 1.8 3.9E-05 33.9 7.2 51 174-224 25-75 (118)
35 PF03965 Penicillinase_R: Peni 89.5 1.2 2.6E-05 35.2 6.1 61 176-239 2-66 (115)
36 COG2345 Predicted transcriptio 89.3 0.73 1.6E-05 41.3 5.2 57 180-236 14-71 (218)
37 smart00344 HTH_ASNC helix_turn 89.3 1.1 2.4E-05 34.4 5.6 44 179-222 5-48 (108)
38 PRK09334 30S ribosomal protein 89.2 0.68 1.5E-05 35.7 4.3 39 188-226 38-77 (86)
39 PRK13509 transcriptional repre 89.1 0.84 1.8E-05 41.1 5.5 46 178-223 6-51 (251)
40 COG2512 Predicted membrane-ass 88.8 0.95 2E-05 41.4 5.6 54 172-225 190-244 (258)
41 PF09107 SelB-wing_3: Elongati 88.5 1.7 3.6E-05 30.1 5.4 43 183-225 2-44 (50)
42 PF01325 Fe_dep_repress: Iron 88.5 1.7 3.7E-05 30.8 5.7 44 182-225 13-56 (60)
43 cd00090 HTH_ARSR Arsenical Res 88.5 2.7 5.8E-05 28.7 6.7 49 177-226 7-55 (78)
44 PRK10434 srlR DNA-bindng trans 88.3 0.95 2.1E-05 40.8 5.4 47 177-223 5-51 (256)
45 PRK03573 transcriptional regul 88.1 2.4 5.3E-05 34.3 7.2 56 172-227 26-82 (144)
46 smart00346 HTH_ICLR helix_turn 88.1 2.1 4.6E-05 31.5 6.3 45 181-225 9-54 (91)
47 PF06163 DUF977: Bacterial pro 88.0 0.95 2.1E-05 37.3 4.6 46 179-224 14-59 (127)
48 PF09339 HTH_IclR: IclR helix- 87.8 1.3 2.8E-05 30.0 4.6 44 181-224 7-51 (52)
49 PRK09954 putative kinase; Prov 86.9 1.4 3.1E-05 41.1 5.8 43 179-221 5-47 (362)
50 TIGR01884 cas_HTH CRISPR locus 86.9 2 4.3E-05 37.2 6.4 53 173-225 139-191 (203)
51 PRK04424 fatty acid biosynthes 86.7 0.98 2.1E-05 38.9 4.3 46 177-222 7-52 (185)
52 TIGR00373 conserved hypothetic 86.7 2.4 5.3E-05 35.8 6.6 62 176-238 13-78 (158)
53 PRK10906 DNA-binding transcrip 86.5 1.4 3.1E-05 39.7 5.4 46 178-223 6-51 (252)
54 cd00092 HTH_CRP helix_turn_hel 86.1 2.5 5.4E-05 29.2 5.4 36 190-225 24-59 (67)
55 cd08767 Cdt1_c The C-terminal 86.1 5.6 0.00012 32.4 8.2 78 98-184 45-123 (126)
56 PF12840 HTH_20: Helix-turn-he 86.0 2.7 5.9E-05 29.3 5.6 47 179-225 12-58 (61)
57 PF08279 HTH_11: HTH domain; 86.0 3 6.5E-05 28.1 5.7 40 180-219 3-43 (55)
58 COG1522 Lrp Transcriptional re 85.9 2.2 4.8E-05 34.6 5.8 48 174-221 5-52 (154)
59 PRK06266 transcription initiat 85.6 3.1 6.7E-05 35.9 6.8 44 179-222 24-67 (178)
60 smart00345 HTH_GNTR helix_turn 85.5 1.6 3.4E-05 29.3 4.0 33 189-221 17-50 (60)
61 PF05331 DUF742: Protein of un 85.3 1.8 4E-05 34.9 4.9 54 172-227 38-91 (114)
62 PF03297 Ribosomal_S25: S25 ri 85.2 1.6 3.4E-05 34.8 4.4 36 188-223 56-91 (105)
63 PRK03902 manganese transport t 84.8 2.3 4.9E-05 34.7 5.4 43 182-224 13-55 (142)
64 smart00843 Ftsk_gamma This dom 84.2 2.4 5.3E-05 30.8 4.6 43 181-223 9-51 (63)
65 PLN02180 gamma-glutamyl transp 84.2 1.7 3.6E-05 44.7 5.2 74 44-126 215-299 (639)
66 PLN02198 glutathione gamma-glu 83.8 1.7 3.6E-05 44.1 4.9 74 45-127 166-250 (573)
67 PRK10411 DNA-binding transcrip 83.7 2.5 5.3E-05 37.9 5.6 47 177-223 4-50 (240)
68 PF09743 DUF2042: Uncharacteri 83.1 7.5 0.00016 35.8 8.6 94 120-219 2-98 (272)
69 PF01022 HTH_5: Bacterial regu 82.5 4.1 8.8E-05 27.0 5.0 40 181-221 6-45 (47)
70 COG1846 MarR Transcriptional r 82.4 6 0.00013 29.8 6.6 55 175-229 20-74 (126)
71 COG5126 FRQ1 Ca2+-binding prot 82.4 5.1 0.00011 34.2 6.7 40 36-80 16-55 (160)
72 PF14394 DUF4423: Domain of un 82.4 3.1 6.8E-05 35.6 5.4 49 178-226 25-76 (171)
73 TIGR00066 g_glut_trans gamma-g 82.3 3.3 7.1E-05 41.3 6.3 32 91-126 191-223 (516)
74 PRK09802 DNA-binding transcrip 82.3 2.7 6E-05 38.2 5.4 49 176-224 16-64 (269)
75 PRK00080 ruvB Holliday junctio 82.1 6.9 0.00015 36.1 8.1 71 136-224 236-310 (328)
76 PF09756 DDRGK: DDRGK domain; 81.8 2.1 4.6E-05 37.5 4.2 117 56-202 68-184 (188)
77 smart00419 HTH_CRP helix_turn_ 81.5 2.6 5.6E-05 27.1 3.7 34 191-224 8-41 (48)
78 PF04967 HTH_10: HTH DNA bindi 81.4 5.7 0.00012 27.8 5.5 43 175-217 1-49 (53)
79 COG0055 AtpD F0F1-type ATP syn 81.4 1.8 4E-05 42.1 4.0 124 19-162 252-415 (468)
80 TIGR02702 SufR_cyano iron-sulf 80.6 3.8 8.2E-05 35.5 5.4 45 180-224 4-48 (203)
81 PF12324 HTH_15: Helix-turn-he 80.4 3 6.6E-05 31.5 4.1 38 179-216 26-63 (77)
82 PF01019 G_glu_transpept: Gamm 80.2 2.2 4.8E-05 42.3 4.3 76 44-128 121-207 (510)
83 PF13404 HTH_AsnC-type: AsnC-t 80.1 5.9 0.00013 26.1 5.0 38 179-216 5-42 (42)
84 TIGR00498 lexA SOS regulatory 80.0 4.7 0.0001 34.5 5.8 52 175-226 4-61 (199)
85 PRK10141 DNA-binding transcrip 79.4 6.9 0.00015 31.6 6.2 56 180-238 19-74 (117)
86 KOG1767 40S ribosomal protein 79.0 3.2 7E-05 33.2 4.0 44 178-221 44-90 (110)
87 PRK13777 transcriptional regul 78.7 9.4 0.0002 33.2 7.2 56 172-227 40-95 (185)
88 COG4901 Ribosomal protein S25 78.7 3.2 6.9E-05 33.1 3.9 40 188-227 56-95 (107)
89 PF13730 HTH_36: Helix-turn-he 78.6 9.6 0.00021 25.6 5.9 48 174-221 2-55 (55)
90 PRK10870 transcriptional repre 78.4 9.4 0.0002 32.5 7.1 55 174-228 52-108 (176)
91 PLN03083 E3 UFM1-protein ligas 77.6 8.3 0.00018 40.7 7.6 96 119-219 4-102 (803)
92 PF14947 HTH_45: Winged helix- 77.5 5.7 0.00012 29.3 4.8 40 181-221 10-49 (77)
93 cd07377 WHTH_GntR Winged helix 77.2 3.9 8.5E-05 27.8 3.7 30 192-221 26-55 (66)
94 PF13601 HTH_34: Winged helix 76.9 7.9 0.00017 28.9 5.5 56 181-236 4-59 (80)
95 PF11994 DUF3489: Protein of u 76.4 11 0.00024 28.2 5.9 60 176-235 9-70 (72)
96 PRK00215 LexA repressor; Valid 76.0 15 0.00033 31.4 7.9 53 175-227 2-60 (205)
97 PF00392 GntR: Bacterial regul 75.2 4.3 9.2E-05 28.5 3.5 36 190-225 22-58 (64)
98 PRK09615 ggt gamma-glutamyltra 75.0 7.1 0.00015 39.7 6.2 33 91-127 239-272 (581)
99 PF02082 Rrf2: Transcriptional 74.4 6.1 0.00013 29.3 4.3 45 189-236 23-67 (83)
100 KOG2165 Anaphase-promoting com 74.3 11 0.00024 39.2 7.3 81 140-224 553-649 (765)
101 PRK15090 DNA-binding transcrip 73.6 10 0.00023 33.7 6.4 45 182-226 19-63 (257)
102 PF10007 DUF2250: Uncharacteri 73.1 12 0.00026 29.2 5.7 54 174-227 4-57 (92)
103 cd05029 S-100A6 S-100A6: S-100 73.0 12 0.00027 28.2 5.8 54 101-155 10-65 (88)
104 PF03979 Sigma70_r1_1: Sigma-7 72.9 7.4 0.00016 29.1 4.5 46 182-227 12-60 (82)
105 COG1386 scpB Chromosome segreg 72.9 54 0.0012 28.5 10.4 85 139-226 37-138 (184)
106 PF08784 RPA_C: Replication pr 72.8 7 0.00015 30.0 4.4 52 96-157 45-96 (102)
107 PF09743 DUF2042: Uncharacteri 72.8 9.6 0.00021 35.1 6.0 122 67-214 30-154 (272)
108 COG1414 IclR Transcriptional r 72.7 11 0.00024 33.8 6.3 47 181-227 8-55 (246)
109 PRK11050 manganese transport r 72.6 10 0.00022 31.5 5.7 44 182-225 42-85 (152)
110 TIGR02944 suf_reg_Xantho FeS a 72.3 8.1 0.00018 30.8 4.9 38 184-221 17-55 (130)
111 TIGR00738 rrf2_super rrf2 fami 71.8 11 0.00024 29.8 5.6 36 189-224 23-58 (132)
112 COG3682 Predicted transcriptio 71.1 13 0.00029 30.4 5.8 63 174-239 3-69 (123)
113 PF08221 HTH_9: RNA polymerase 71.1 12 0.00026 26.6 5.0 42 181-222 17-58 (62)
114 TIGR01610 phage_O_Nterm phage 70.9 15 0.00031 28.2 5.8 53 174-226 22-82 (95)
115 PRK10512 selenocysteinyl-tRNA- 70.6 1.3E+02 0.0028 30.8 15.2 114 92-225 487-600 (614)
116 PRK11569 transcriptional repre 70.4 11 0.00024 34.0 5.9 46 182-227 33-79 (274)
117 COG2865 Predicted transcriptio 70.4 8 0.00017 38.4 5.2 62 174-238 399-460 (467)
118 PRK10163 DNA-binding transcrip 70.3 13 0.00028 33.6 6.3 46 182-227 30-76 (271)
119 PRK15431 ferrous iron transpor 70.1 14 0.0003 28.0 5.3 43 182-224 7-49 (78)
120 TIGR02787 codY_Gpos GTP-sensin 70.0 8.5 0.00019 35.2 4.9 37 189-225 196-232 (251)
121 PHA00738 putative HTH transcri 69.9 18 0.0004 29.0 6.3 55 181-238 16-70 (108)
122 PRK04172 pheS phenylalanyl-tRN 69.9 13 0.00027 36.8 6.5 53 174-226 3-55 (489)
123 PF10771 DUF2582: Protein of u 69.4 13 0.00027 27.2 4.8 47 181-227 12-58 (65)
124 PRK10681 DNA-binding transcrip 69.3 8.7 0.00019 34.5 4.9 43 177-219 7-49 (252)
125 PF05584 Sulfolobus_pRN: Sulfo 69.3 15 0.00032 27.5 5.2 42 181-223 9-50 (72)
126 COG2996 Predicted RNA-bindinin 69.0 22 0.00047 33.1 7.3 51 174-224 222-279 (287)
127 PTZ00111 DNA replication licen 68.8 12 0.00026 40.1 6.4 151 60-221 698-901 (915)
128 PTZ00184 calmodulin; Provision 68.5 53 0.0012 25.4 9.7 15 189-203 134-148 (149)
129 PHA03103 double-strand RNA-bin 68.3 21 0.00045 31.2 6.8 39 189-227 25-63 (183)
130 COG1321 TroR Mn-dependent tran 68.1 12 0.00025 31.6 5.1 49 177-225 9-58 (154)
131 PRK14999 histidine utilization 67.2 7.4 0.00016 34.2 3.9 33 193-225 38-70 (241)
132 smart00088 PINT motif in prote 67.1 16 0.00035 26.8 5.2 47 180-226 13-61 (88)
133 smart00753 PAM PCI/PINT associ 67.1 16 0.00035 26.8 5.2 47 180-226 13-61 (88)
134 PRK12423 LexA repressor; Provi 67.1 17 0.00036 31.5 6.1 53 174-226 3-61 (202)
135 TIGR00635 ruvB Holliday juncti 67.1 24 0.00053 31.7 7.4 71 136-224 215-289 (305)
136 TIGR03793 TOMM_pelo TOMM prope 66.5 15 0.00032 27.6 4.8 22 59-80 15-40 (77)
137 PF03444 HrcA_DNA-bdg: Winged 66.1 24 0.00051 26.8 5.9 48 174-221 1-53 (78)
138 PF05600 DUF773: Protein of un 66.1 8.4 0.00018 38.5 4.5 66 34-103 128-197 (507)
139 COG1675 TFA1 Transcription ini 65.6 20 0.00043 31.2 6.1 60 179-239 20-83 (176)
140 PRK10079 phosphonate metabolis 64.6 9.1 0.0002 33.7 4.0 34 192-225 36-69 (241)
141 PF03428 RP-C: Replication pro 64.6 82 0.0018 27.2 9.8 73 136-228 21-108 (177)
142 smart00421 HTH_LUXR helix_turn 64.3 23 0.0005 22.8 5.1 43 172-216 1-43 (58)
143 PRK11414 colanic acid/biofilm 64.0 9.9 0.00022 32.9 4.1 37 189-225 32-68 (221)
144 TIGR02404 trehalos_R_Bsub treh 64.0 8.6 0.00019 33.5 3.7 34 192-225 25-58 (233)
145 PHA02701 ORF020 dsRNA-binding 64.0 18 0.0004 31.6 5.6 49 179-227 6-55 (183)
146 PF04558 tRNA_synt_1c_R1: Glut 63.9 8.4 0.00018 32.9 3.5 93 48-162 14-107 (164)
147 PF04545 Sigma70_r4: Sigma-70, 63.7 27 0.0006 23.0 5.4 43 174-217 4-46 (50)
148 COG4190 Predicted transcriptio 63.7 30 0.00064 29.0 6.5 68 174-241 61-128 (144)
149 cd07153 Fur_like Ferric uptake 63.5 18 0.0004 27.9 5.1 47 181-227 5-57 (116)
150 PF09202 Rio2_N: Rio2, N-termi 63.2 30 0.00064 26.2 6.0 52 174-225 3-58 (82)
151 TIGR02325 C_P_lyase_phnF phosp 63.0 9.2 0.0002 33.2 3.7 33 192-224 33-65 (238)
152 PRK11402 DNA-binding transcrip 62.8 10 0.00022 33.3 4.0 35 191-225 33-67 (241)
153 PF14848 HU-DNA_bdg: DNA-bindi 62.6 20 0.00044 28.8 5.3 52 113-169 24-81 (124)
154 TIGR02018 his_ut_repres histid 62.5 11 0.00023 33.0 4.0 34 192-225 26-59 (230)
155 cd03319 L-Ala-DL-Glu_epimerase 62.3 15 0.00032 33.7 5.0 77 139-227 134-212 (316)
156 TIGR00122 birA_repr_reg BirA b 62.0 24 0.00052 24.9 5.1 41 182-223 5-45 (69)
157 COG2188 PhnF Transcriptional r 61.9 11 0.00023 33.5 3.9 36 191-226 31-66 (236)
158 COG1654 BirA Biotin operon rep 61.6 21 0.00045 27.0 4.9 50 176-227 5-54 (79)
159 PRK09764 DNA-binding transcrip 61.5 10 0.00022 33.4 3.7 33 193-225 31-63 (240)
160 PRK13239 alkylmercury lyase; P 61.3 16 0.00034 32.6 4.8 47 178-227 23-69 (206)
161 COG4367 Uncharacterized protei 60.6 27 0.00059 27.2 5.4 66 175-240 3-90 (97)
162 TIGR02010 IscR iron-sulfur clu 60.6 19 0.00041 29.1 4.9 40 182-221 14-55 (135)
163 PRK03187 tgl transglutaminase; 60.5 15 0.00032 34.1 4.6 43 77-134 180-223 (272)
164 PF01399 PCI: PCI domain; Int 60.4 22 0.00047 26.3 4.9 40 182-221 51-90 (105)
165 PRK00082 hrcA heat-inducible t 60.1 22 0.00047 33.6 5.9 52 174-225 3-61 (339)
166 PF02295 z-alpha: Adenosine de 60.0 13 0.00028 27.0 3.4 49 179-227 6-56 (66)
167 PLN02964 phosphatidylserine de 59.5 27 0.00058 36.2 6.7 93 35-157 138-231 (644)
168 COG1378 Predicted transcriptio 59.0 33 0.00071 31.1 6.6 51 175-225 14-64 (247)
169 PF14538 Raptor_N: Raptor N-te 58.6 21 0.00045 30.1 4.9 80 69-165 10-100 (154)
170 PF11662 DUF3263: Protein of u 58.5 31 0.00067 26.1 5.3 45 174-218 2-49 (77)
171 COG3413 Predicted DNA binding 58.1 24 0.00053 30.7 5.5 45 173-217 154-204 (215)
172 PF09079 Cdc6_C: CDC6, C termi 57.9 11 0.00024 27.9 2.8 30 51-81 10-39 (85)
173 PRK09834 DNA-binding transcrip 57.5 31 0.00067 30.9 6.2 47 181-227 15-62 (263)
174 PRK05472 redox-sensing transcr 57.2 23 0.0005 30.8 5.1 42 178-219 17-60 (213)
175 PF09733 VEFS-Box: VEFS-Box of 57.1 13 0.00028 31.0 3.4 32 43-74 91-122 (140)
176 PF14502 HTH_41: Helix-turn-he 56.6 18 0.0004 24.9 3.4 36 192-227 7-42 (48)
177 PRK13558 bacterio-opsin activa 56.1 30 0.00064 34.7 6.4 79 139-217 564-656 (665)
178 TIGR00331 hrcA heat shock gene 56.0 26 0.00057 33.0 5.7 63 179-241 4-78 (337)
179 PRK11014 transcriptional repre 55.8 36 0.00079 27.6 5.8 39 189-227 23-61 (141)
180 TIGR03338 phnR_burk phosphonat 55.4 16 0.00034 31.2 3.8 35 189-223 32-66 (212)
181 PRK10263 DNA translocase FtsK; 55.4 28 0.0006 38.9 6.3 88 136-223 1246-1339(1355)
182 PF04801 Sin_N: Sin-like prote 55.2 99 0.0022 29.8 9.6 100 99-217 271-377 (421)
183 PF04337 DUF480: Protein of un 55.1 1E+02 0.0023 26.1 8.4 101 118-219 25-135 (148)
184 cd08803 Death_ank3 Death domai 55.0 21 0.00046 27.1 4.0 66 67-147 7-83 (84)
185 PF07638 Sigma70_ECF: ECF sigm 54.9 1.3E+02 0.0028 25.4 12.7 154 29-215 13-175 (185)
186 PRK06474 hypothetical protein; 54.7 51 0.0011 28.2 6.8 60 179-238 13-76 (178)
187 PRK11534 DNA-binding transcrip 54.6 18 0.00039 31.3 4.0 38 189-226 28-65 (224)
188 COG0735 Fur Fe2+/Zn2+ uptake r 54.6 83 0.0018 25.9 7.8 54 101-163 24-77 (145)
189 PRK04984 fatty acid metabolism 54.2 16 0.00035 31.8 3.7 37 190-226 29-66 (239)
190 PRK10857 DNA-binding transcrip 53.9 28 0.0006 29.5 5.0 42 182-223 14-57 (164)
191 PF13382 Adenine_deam_C: Adeni 53.9 26 0.00057 30.1 4.8 33 138-172 73-105 (171)
192 PF00325 Crp: Bacterial regula 52.8 26 0.00056 22.0 3.4 30 192-221 3-32 (32)
193 TIGR02812 fadR_gamma fatty aci 52.5 22 0.00048 30.9 4.3 39 189-227 27-66 (235)
194 PF13545 HTH_Crp_2: Crp-like h 51.9 24 0.00053 24.9 3.7 31 191-221 28-58 (76)
195 PF03962 Mnd1: Mnd1 family; I 51.6 23 0.0005 30.7 4.2 49 188-238 8-61 (188)
196 COG4565 CitB Response regulato 51.5 45 0.00097 30.1 6.0 91 136-238 128-223 (224)
197 PF09907 DUF2136: Uncharacteri 51.3 31 0.00066 25.8 4.3 40 119-163 5-44 (76)
198 TIGR03879 near_KaiC_dom probab 51.2 24 0.00052 26.4 3.6 49 173-221 14-62 (73)
199 PRK14165 winged helix-turn-hel 50.6 43 0.00093 29.9 5.8 38 189-226 19-56 (217)
200 PRK02899 adaptor protein; Prov 50.3 1.5E+02 0.0033 25.9 9.2 76 138-215 111-191 (197)
201 KOG0027 Calmodulin and related 50.2 1.4E+02 0.0029 24.2 8.6 96 37-157 5-101 (151)
202 PF13413 HTH_25: Helix-turn-he 50.1 22 0.00048 25.3 3.2 46 32-78 13-59 (62)
203 KOG1350 F0F1-type ATP synthase 50.1 22 0.00047 34.4 4.0 109 34-162 326-465 (521)
204 COG1497 Predicted transcriptio 50.0 40 0.00087 30.9 5.6 48 172-221 7-55 (260)
205 TIGR02844 spore_III_D sporulat 49.8 33 0.00071 26.0 4.2 34 178-212 7-40 (80)
206 COG3877 Uncharacterized protei 49.6 52 0.0011 26.6 5.5 25 58-82 69-93 (122)
207 PRK04172 pheS phenylalanyl-tRN 49.5 1.2E+02 0.0027 29.9 9.4 97 116-225 19-121 (489)
208 PRK04217 hypothetical protein; 48.9 53 0.0012 26.3 5.6 42 172-214 40-81 (110)
209 cd01295 AdeC Adenine deaminase 48.9 39 0.00085 32.4 5.7 33 139-173 331-363 (422)
210 PRK09464 pdhR transcriptional 48.5 26 0.00055 30.9 4.1 37 190-226 32-69 (254)
211 TIGR02833 spore_III_AB stage I 48.3 19 0.00042 30.6 3.1 55 15-76 105-159 (170)
212 cd07668 BAR_SNX9 The Bin/Amphi 48.1 38 0.00082 30.3 5.0 60 44-104 33-94 (210)
213 PRK11886 bifunctional biotin-- 47.7 39 0.00084 31.2 5.3 44 181-224 8-51 (319)
214 COG1241 MCM2 Predicted ATPase 47.1 1.3E+02 0.0028 31.5 9.4 152 60-225 507-675 (682)
215 PRK08307 stage III sporulation 47.1 21 0.00044 30.5 3.1 55 15-76 106-160 (171)
216 cd07669 BAR_SNX33 The Bin/Amph 46.8 39 0.00084 30.2 4.8 61 44-105 33-95 (207)
217 PF07818 HCNGP: HCNGP-like pro 46.3 21 0.00046 27.8 2.8 41 59-102 41-84 (96)
218 TIGR02431 pcaR_pcaU beta-ketoa 46.3 47 0.001 29.3 5.5 43 181-223 13-56 (248)
219 PRK09990 DNA-binding transcrip 46.0 32 0.0007 30.2 4.3 39 189-227 28-67 (251)
220 PRK10225 DNA-binding transcrip 45.8 29 0.00064 30.6 4.1 39 189-227 30-69 (257)
221 PRK11920 rirA iron-responsive 45.8 44 0.00095 27.8 4.9 40 182-221 14-54 (153)
222 PRK10421 DNA-binding transcrip 45.7 30 0.00064 30.6 4.1 37 190-226 24-61 (253)
223 PF09681 Phage_rep_org_N: N-te 45.6 33 0.00072 27.8 4.0 51 190-245 52-102 (121)
224 PF08280 HTH_Mga: M protein tr 45.4 63 0.0014 22.4 4.9 40 177-216 5-44 (59)
225 PRK00411 cdc6 cell division co 45.3 57 0.0012 30.4 6.1 79 135-226 267-360 (394)
226 PF01475 FUR: Ferric uptake re 45.0 82 0.0018 24.5 6.1 60 178-239 9-74 (120)
227 PF15112 DUF4559: Domain of un 44.5 99 0.0022 29.2 7.4 98 35-152 161-264 (307)
228 TIGR01558 sm_term_P27 phage te 44.2 1E+02 0.0022 24.2 6.6 24 57-80 66-95 (116)
229 PRK03837 transcriptional regul 44.0 34 0.00074 29.7 4.1 35 190-224 35-70 (241)
230 KOG0624 dsRNA-activated protei 43.8 14 0.00029 36.0 1.6 36 54-95 446-491 (504)
231 PRK09191 two-component respons 43.8 33 0.00071 29.6 4.0 53 174-227 88-147 (261)
232 COG3879 Uncharacterized protei 43.5 89 0.0019 28.6 6.8 97 44-175 74-176 (247)
233 COG3710 CadC DNA-binding winge 43.4 30 0.00066 28.9 3.5 57 93-154 26-83 (148)
234 COG1802 GntR Transcriptional r 43.1 24 0.00053 30.7 3.1 39 189-227 37-75 (230)
235 cd00213 S-100 S-100: S-100 dom 43.1 1.3E+02 0.0028 21.9 7.1 75 34-129 2-79 (88)
236 cd07291 PX_SNX5 The phosphoino 43.0 39 0.00085 28.4 4.1 31 38-69 104-139 (141)
237 PRK10512 selenocysteinyl-tRNA- 42.7 3.4E+02 0.0074 27.8 11.6 132 93-240 413-550 (614)
238 PRK11523 DNA-binding transcrip 42.1 37 0.00079 30.0 4.1 39 189-227 29-68 (253)
239 TIGR02941 Sigma_B RNA polymera 41.8 1.9E+02 0.0042 25.4 8.7 44 32-75 28-72 (255)
240 TIGR01714 phage_rep_org_N phag 41.7 54 0.0012 26.7 4.6 49 190-244 51-99 (119)
241 TIGR03337 phnR transcriptional 41.7 36 0.00077 29.3 3.9 34 192-225 26-59 (231)
242 TIGR02384 RelB_DinJ addiction 41.3 22 0.00048 26.8 2.2 25 56-80 6-30 (83)
243 smart00531 TFIIE Transcription 41.2 52 0.0011 27.1 4.6 43 182-224 6-48 (147)
244 PF01638 HxlR: HxlR-like helix 41.2 1.1E+02 0.0024 22.7 6.1 45 182-227 10-55 (90)
245 PF07240 Turandot: Stress-indu 40.8 24 0.00052 27.2 2.3 29 75-105 49-77 (85)
246 cd07670 BAR_SNX18 The Bin/Amph 40.6 54 0.0012 29.3 4.8 61 44-105 33-95 (207)
247 COG0735 Fur Fe2+/Zn2+ uptake r 40.5 95 0.0021 25.6 6.1 61 176-237 20-86 (145)
248 cd06170 LuxR_C_like C-terminal 40.5 99 0.0021 19.8 5.2 40 176-217 2-41 (57)
249 PF07216 LcrG: LcrG protein; 40.4 18 0.00039 28.2 1.6 45 66-133 27-71 (93)
250 PF08281 Sigma70_r4_2: Sigma-7 40.2 1.1E+02 0.0023 20.2 5.5 42 174-216 10-51 (54)
251 PHA02591 hypothetical protein; 39.7 71 0.0015 24.4 4.6 49 159-213 32-81 (83)
252 PF08721 Tn7_Tnp_TnsA_C: TnsA 38.9 82 0.0018 22.3 4.9 43 182-224 32-78 (79)
253 TIGR02573 LcrG_PcrG type III s 38.4 20 0.00044 27.7 1.6 17 66-82 24-40 (90)
254 PF14948 RESP18: RESP18 domain 38.1 24 0.00053 28.2 2.0 22 207-228 23-44 (105)
255 TIGR02716 C20_methyl_CrtF C-20 37.9 62 0.0013 29.4 5.0 37 189-225 21-57 (306)
256 PF09824 ArsR: ArsR transcript 37.6 73 0.0016 27.3 4.9 46 176-225 16-64 (160)
257 PF06136 DUF966: Domain of unk 37.5 18 0.00038 34.4 1.4 27 118-144 29-73 (337)
258 cd08317 Death_ank Death domain 37.4 57 0.0012 24.2 3.9 67 66-147 6-83 (84)
259 COG1725 Predicted transcriptio 37.2 49 0.0011 27.2 3.7 36 191-226 35-70 (125)
260 TIGR01774 PFL2-3 pyruvate form 36.9 2.7E+02 0.0058 29.6 10.0 133 5-150 168-310 (786)
261 PF07862 Nif11: Nitrogen fixat 36.6 39 0.00085 22.5 2.7 22 44-69 4-25 (49)
262 PF00888 Cullin: Cullin family 36.0 35 0.00077 33.6 3.3 81 140-224 471-567 (588)
263 PLN02853 Probable phenylalanyl 35.8 2.6E+02 0.0057 28.1 9.3 107 101-224 6-117 (492)
264 PF04221 RelB: RelB antitoxin; 35.6 24 0.00052 26.4 1.6 23 57-79 6-28 (83)
265 PF07352 Phage_Mu_Gam: Bacteri 35.6 85 0.0018 25.9 5.1 29 30-58 39-67 (149)
266 PRK15201 fimbriae regulatory p 35.4 1E+02 0.0022 27.3 5.5 45 171-217 130-174 (198)
267 COG1959 Predicted transcriptio 35.2 93 0.002 25.8 5.2 40 182-221 14-55 (150)
268 PF08221 HTH_9: RNA polymerase 35.0 83 0.0018 22.2 4.3 48 93-154 8-55 (62)
269 PRK07598 RNA polymerase sigma 34.9 3.8E+02 0.0083 26.3 10.1 168 27-213 75-300 (415)
270 PRK15411 rcsA colanic acid cap 34.8 1.7E+02 0.0037 25.1 7.1 71 137-216 107-177 (207)
271 PF08461 HTH_12: Ribonuclease 34.8 95 0.0021 22.3 4.6 39 182-220 3-47 (66)
272 PHA02047 phage lambda Rz1-like 34.5 1E+02 0.0022 24.4 4.9 29 30-58 41-72 (101)
273 PRK14339 (dimethylallyl)adenos 34.3 1.1E+02 0.0024 29.6 6.3 48 137-188 261-308 (420)
274 PRK10947 global DNA-binding tr 34.1 92 0.002 25.8 5.0 47 32-78 23-72 (135)
275 smart00350 MCM minichromosome 34.0 71 0.0015 31.7 5.1 52 98-151 441-505 (509)
276 smart00529 HTH_DTXR Helix-turn 33.6 60 0.0013 23.9 3.5 31 194-224 2-32 (96)
277 smart00803 TAF TATA box bindin 33.5 1.4E+02 0.0031 21.4 5.3 13 136-148 53-65 (65)
278 PF07106 TBPIP: Tat binding pr 33.4 1.5E+02 0.0033 24.7 6.3 56 179-237 3-62 (169)
279 PF04977 DivIC: Septum formati 33.3 1.4E+02 0.0031 21.1 5.4 46 17-62 23-73 (80)
280 COG0309 HypE Hydrogenase matur 33.1 30 0.00065 33.1 2.1 37 44-80 232-271 (339)
281 cd08768 Cdc6_C Winged-helix do 33.1 54 0.0012 23.8 3.1 26 55-81 21-46 (87)
282 PF04914 DltD_C: DltD C-termin 33.0 22 0.00047 29.2 1.1 54 56-109 28-87 (130)
283 PF06721 DUF1204: Protein of u 32.9 1.5E+02 0.0033 26.3 6.3 18 114-131 128-147 (228)
284 PF08222 HTH_CodY: CodY helix- 32.9 51 0.0011 23.8 2.8 33 190-222 3-35 (61)
285 COG0405 Ggt Gamma-glutamyltran 32.6 93 0.002 31.6 5.6 34 92-129 207-241 (539)
286 PRK11557 putative DNA-binding 32.6 1E+02 0.0022 27.5 5.4 17 136-152 111-127 (278)
287 cd03036 ArsC_like Arsenate Red 32.5 63 0.0014 25.2 3.6 40 43-82 12-58 (111)
288 PF09336 Vps4_C: Vps4 C termin 32.4 65 0.0014 23.0 3.3 26 118-147 30-55 (62)
289 cd08804 Death_ank2 Death domai 32.4 89 0.0019 23.5 4.3 46 94-147 38-83 (84)
290 PF09756 DDRGK: DDRGK domain; 32.3 75 0.0016 27.8 4.4 46 182-227 104-151 (188)
291 TIGR01617 arsC_related transcr 32.1 65 0.0014 25.2 3.7 39 44-82 13-58 (117)
292 COG3398 Uncharacterized protei 32.1 1.5E+02 0.0033 26.9 6.3 59 181-242 105-163 (240)
293 TIGR00475 selB selenocysteine- 32.0 1.6E+02 0.0035 29.9 7.3 75 138-225 500-574 (581)
294 COG2186 FadR Transcriptional r 32.0 60 0.0013 28.9 3.8 33 192-224 35-67 (241)
295 PRK10328 DNA binding protein, 31.9 1.3E+02 0.0027 25.0 5.4 47 32-78 23-72 (134)
296 PF05597 Phasin: Poly(hydroxya 31.6 2.1E+02 0.0045 23.6 6.6 71 5-77 25-106 (132)
297 COG1709 Predicted transcriptio 31.3 90 0.0019 28.4 4.7 140 43-208 8-172 (241)
298 PRK14333 (dimethylallyl)adenos 31.3 1.1E+02 0.0025 29.6 5.9 48 138-189 287-334 (448)
299 cd08805 Death_ank1 Death domai 31.2 1E+02 0.0023 23.3 4.5 67 66-147 6-83 (84)
300 PF09106 SelB-wing_2: Elongati 31.1 81 0.0018 21.8 3.6 37 189-225 15-54 (59)
301 PF12793 SgrR_N: Sugar transpo 30.8 71 0.0015 25.5 3.7 36 190-227 18-53 (115)
302 PRK14332 (dimethylallyl)adenos 30.7 1.4E+02 0.0031 29.1 6.5 49 137-189 282-330 (449)
303 PF10078 DUF2316: Uncharacteri 30.6 1E+02 0.0022 23.9 4.3 50 174-223 2-56 (89)
304 PF05796 Chordopox_G2: Chordop 30.3 69 0.0015 28.7 3.8 105 57-175 16-120 (216)
305 cd07153 Fur_like Ferric uptake 30.2 1.3E+02 0.0027 23.0 5.0 46 102-155 5-50 (116)
306 PF08279 HTH_11: HTH domain; 30.2 1.4E+02 0.003 19.7 4.6 36 118-164 16-51 (55)
307 PF04182 B-block_TFIIIC: B-blo 30.1 1.5E+02 0.0032 21.5 5.0 47 177-223 2-50 (75)
308 PLN03083 E3 UFM1-protein ligas 30.1 92 0.002 33.1 5.2 124 67-215 33-158 (803)
309 TIGR01837 PHA_granule_1 poly(h 29.8 1.9E+02 0.004 23.2 6.0 71 5-77 12-93 (118)
310 KOG2607 CDK5 activator-binding 29.8 86 0.0019 31.1 4.6 127 34-176 126-260 (505)
311 PF06296 DUF1044: Protein of u 29.8 2.6E+02 0.0056 22.7 6.8 63 136-198 16-109 (120)
312 TIGR02147 Fsuc_second hypothet 29.7 2.1E+02 0.0046 26.3 7.1 77 93-187 120-207 (271)
313 cd03316 MR_like Mandelate race 29.6 96 0.0021 28.7 4.9 82 139-227 139-224 (357)
314 PRK10430 DNA-binding transcrip 29.6 2.3E+02 0.0049 24.3 7.0 63 174-236 158-224 (239)
315 TIGR03697 NtcA_cyano global ni 29.6 80 0.0017 25.9 4.0 33 192-224 144-176 (193)
316 PF14106 DUF4279: Domain of un 29.5 89 0.0019 24.0 4.0 29 28-56 53-81 (118)
317 PF08726 EFhand_Ca_insen: Ca2+ 29.3 30 0.00066 25.4 1.2 19 185-203 15-33 (69)
318 CHL00053 rps7 ribosomal protei 29.3 2.9E+02 0.0063 23.1 7.3 70 141-222 60-135 (155)
319 KOG1463 26S proteasome regulat 29.0 1.2E+02 0.0026 29.4 5.4 42 32-73 285-330 (411)
320 PRK14329 (dimethylallyl)adenos 28.7 1.4E+02 0.0031 29.3 6.1 48 137-188 304-351 (467)
321 KOG1106 Uncharacterized conser 28.7 45 0.00097 29.1 2.3 40 88-130 94-133 (177)
322 PRK12529 RNA polymerase sigma 28.6 1.5E+02 0.0032 24.5 5.5 42 174-216 127-168 (178)
323 PF09114 MotA_activ: Transcrip 28.5 2.3E+02 0.005 22.2 5.9 48 174-221 13-62 (96)
324 KOG1043 Ca2+-binding transmemb 28.4 3.5E+02 0.0076 27.3 8.7 102 34-146 257-370 (499)
325 cd03315 MLE_like Muconate lact 28.3 1.1E+02 0.0023 27.3 4.8 75 139-227 85-164 (265)
326 PF04458 DUF505: Protein of un 28.2 2.7E+02 0.0059 28.7 8.0 123 92-221 413-574 (591)
327 KOG4302 Microtubule-associated 28.0 56 0.0012 34.0 3.2 46 34-79 156-202 (660)
328 cd03320 OSBS o-Succinylbenzoat 27.8 1E+02 0.0022 27.5 4.6 66 154-227 95-162 (263)
329 smart00411 BHL bacterial (prok 27.8 1.9E+02 0.0041 21.1 5.4 50 118-172 1-56 (90)
330 TIGR02933 nifM_nitrog nitrogen 27.7 4.4E+02 0.0096 23.5 13.2 108 12-152 4-116 (256)
331 cd04871 ACT_PSP_2 ACT domains 27.7 46 0.001 24.8 2.0 17 61-77 63-79 (84)
332 PRK00888 ftsB cell division pr 27.6 1.6E+02 0.0035 23.1 5.2 35 29-63 47-84 (105)
333 PF10410 DnaB_bind: DnaB-helic 27.5 1.2E+02 0.0026 20.3 4.0 24 54-78 32-56 (59)
334 COG1001 AdeC Adenine deaminase 27.4 1.1E+02 0.0025 31.3 5.2 34 138-173 481-514 (584)
335 PTZ00326 phenylalanyl-tRNA syn 27.3 1.3E+02 0.0029 30.2 5.6 50 178-227 7-57 (494)
336 PF10557 Cullin_Nedd8: Cullin 27.0 2.2E+02 0.0048 20.2 5.5 45 184-228 15-67 (68)
337 COG0758 Smf Predicted Rossmann 26.9 2.3E+02 0.0051 27.1 7.0 46 179-225 298-343 (350)
338 PF14394 DUF4423: Domain of un 26.9 34 0.00074 29.2 1.3 48 6-53 108-155 (171)
339 KOG0027 Calmodulin and related 26.9 3.4E+02 0.0073 21.9 7.7 74 66-158 65-138 (151)
340 TIGR00762 DegV EDD domain prot 26.7 4.7E+02 0.01 23.5 10.4 62 118-188 41-103 (275)
341 cd08318 Death_NMPP84 Death dom 26.7 1.2E+02 0.0026 22.7 4.2 61 61-129 4-75 (86)
342 PF13518 HTH_28: Helix-turn-he 26.5 1.8E+02 0.0039 18.6 4.7 38 182-221 5-42 (52)
343 cd05022 S-100A13 S-100A13: S-1 26.5 78 0.0017 24.1 3.1 37 34-75 2-40 (89)
344 KOG1956 DNA topoisomerase III 26.4 54 0.0012 34.1 2.8 41 98-152 122-162 (758)
345 PF03837 RecT: RecT family; I 26.1 48 0.001 28.3 2.1 21 60-80 21-41 (199)
346 COG4396 Mu-like prophage host- 26.1 1.8E+02 0.0039 24.7 5.3 31 31-61 55-85 (170)
347 PF09548 Spore_III_AB: Stage I 25.9 65 0.0014 27.2 2.8 56 14-76 104-159 (170)
348 PRK09841 cryptic autophosphory 25.7 1.5E+02 0.0032 30.8 5.9 46 10-55 254-299 (726)
349 PRK02363 DNA-directed RNA poly 25.7 1.1E+02 0.0025 25.1 4.1 63 103-170 5-69 (129)
350 cd03324 rTSbeta_L-fuconate_deh 25.7 1.1E+02 0.0023 29.8 4.5 79 138-227 195-275 (415)
351 TIGR02865 spore_II_E stage II 25.5 8.1E+02 0.018 25.8 12.7 47 32-78 435-481 (764)
352 cd03318 MLE Muconate Lactonizi 25.2 1.4E+02 0.0031 27.8 5.3 66 155-228 156-224 (365)
353 COG1777 Predicted transcriptio 25.2 1.4E+02 0.003 26.9 4.8 61 180-241 18-80 (217)
354 PF13833 EF-hand_8: EF-hand do 25.1 2E+02 0.0043 18.7 4.6 35 116-154 3-38 (54)
355 PRK14337 (dimethylallyl)adenos 25.0 1.7E+02 0.0038 28.4 5.9 49 137-189 280-328 (446)
356 TIGR02928 orc1/cdc6 family rep 25.0 1.7E+02 0.0036 26.9 5.6 19 63-81 313-331 (365)
357 PRK09613 thiH thiamine biosynt 25.0 2.3E+02 0.0051 28.1 6.9 96 47-152 204-306 (469)
358 PRK14338 (dimethylallyl)adenos 24.9 2.1E+02 0.0046 28.0 6.5 49 138-190 287-335 (459)
359 PF09382 RQC: RQC domain; Int 24.8 2.6E+02 0.0055 21.0 5.8 25 202-226 53-77 (106)
360 PRK13717 conjugal transfer pro 24.6 1.5E+02 0.0033 24.5 4.6 40 24-63 65-105 (128)
361 cd03032 ArsC_Spx Arsenate Redu 24.6 1E+02 0.0023 24.0 3.6 38 45-82 15-59 (115)
362 PLN02853 Probable phenylalanyl 24.6 1.7E+02 0.0036 29.5 5.7 49 179-227 5-54 (492)
363 PF14338 Mrr_N: Mrr N-terminal 24.6 1.6E+02 0.0035 22.0 4.5 42 96-146 2-43 (92)
364 PF05491 RuvB_C: Holliday junc 24.5 2E+02 0.0043 21.7 4.9 51 175-225 6-60 (76)
365 PRK10027 cryptic adenine deami 24.5 1.4E+02 0.003 30.6 5.3 33 138-172 483-515 (588)
366 PF04433 SWIRM: SWIRM domain; 24.4 2.5E+02 0.0054 20.7 5.5 40 182-221 42-84 (86)
367 TIGR00273 iron-sulfur cluster- 24.3 76 0.0016 31.2 3.3 80 17-97 31-110 (432)
368 PRK11235 bifunctional antitoxi 24.2 61 0.0013 24.6 2.1 23 57-79 6-28 (80)
369 COG2433 Uncharacterized conser 23.9 4.4E+02 0.0094 27.5 8.5 92 63-169 38-141 (652)
370 PRK14017 galactonate dehydrata 23.9 62 0.0013 30.7 2.6 86 139-227 124-212 (382)
371 cd01677 PFL2_DhaB_BssA Pyruvat 23.9 7.2E+02 0.016 26.4 10.5 96 58-165 224-341 (781)
372 PF10376 Mei5: Double-strand r 23.9 2E+02 0.0042 25.8 5.6 18 59-78 198-215 (221)
373 PRK14101 bifunctional glucokin 23.6 1.1E+02 0.0023 31.2 4.4 111 32-152 347-467 (638)
374 PRK13918 CRP/FNR family transc 23.5 1.1E+02 0.0023 25.5 3.7 34 191-224 149-182 (202)
375 PRK09462 fur ferric uptake reg 23.5 2.3E+02 0.005 23.0 5.6 47 175-221 15-68 (148)
376 PRK12523 RNA polymerase sigma 23.4 2.1E+02 0.0045 23.3 5.4 42 174-216 119-160 (172)
377 PF13443 HTH_26: Cro/C1-type H 23.4 2.1E+02 0.0045 19.3 4.6 42 32-78 13-54 (63)
378 PF10136 SpecificRecomb: Site- 23.4 1.1E+02 0.0023 31.9 4.2 66 57-129 42-111 (643)
379 PF07870 DUF1657: Protein of u 23.3 2.4E+02 0.0053 19.2 4.8 33 37-74 7-39 (50)
380 PHA02095 hypothetical protein 23.2 73 0.0016 24.0 2.3 23 166-188 58-80 (84)
381 PRK14331 (dimethylallyl)adenos 23.2 1.6E+02 0.0035 28.5 5.3 49 137-189 276-324 (437)
382 PF14528 LAGLIDADG_3: LAGLIDAD 23.2 64 0.0014 22.9 2.0 22 58-79 28-49 (77)
383 KOG2410 Gamma-glutamyltransfer 23.1 52 0.0011 33.6 1.9 32 91-125 235-266 (579)
384 PF11972 HTH_13: HTH DNA bindi 23.1 2.1E+02 0.0046 20.2 4.5 35 182-216 4-38 (54)
385 PF05119 Terminase_4: Phage te 23.1 2.8E+02 0.006 20.6 5.6 25 56-80 56-86 (100)
386 PF03102 NeuB: NeuB family; I 23.0 2E+02 0.0043 26.0 5.5 84 65-160 59-146 (241)
387 cd00051 EFh EF-hand, calcium b 23.0 2E+02 0.0043 17.8 5.2 33 115-151 14-46 (63)
388 TIGR00721 tfx DNA-binding prot 23.0 1.7E+02 0.0037 24.3 4.7 38 174-213 6-43 (137)
389 TIGR03017 EpsF chain length de 22.8 2E+02 0.0044 27.4 5.9 41 15-55 163-203 (444)
390 PF13814 Replic_Relax: Replica 22.8 1E+02 0.0022 25.6 3.4 42 185-226 3-47 (191)
391 PRK11519 tyrosine kinase; Prov 22.7 1.8E+02 0.0039 30.2 5.8 45 11-55 255-299 (719)
392 PRK14335 (dimethylallyl)adenos 22.7 2.4E+02 0.0052 27.6 6.4 49 137-189 289-337 (455)
393 PF00392 GntR: Bacterial regul 22.7 2.6E+02 0.0057 19.2 5.2 50 96-154 2-52 (64)
394 cd05031 S-100A10_like S-100A10 22.7 3.2E+02 0.007 20.2 6.3 75 34-129 2-79 (94)
395 PHA03078 transcriptional elong 22.5 61 0.0013 29.1 2.0 101 57-175 13-117 (219)
396 PF13012 MitMem_reg: Maintenan 22.4 18 0.00038 28.2 -1.2 69 3-75 4-74 (115)
397 PF12381 Peptidase_C3G: Tungro 22.4 48 0.001 30.0 1.4 18 135-152 213-230 (231)
398 PRK15481 transcriptional regul 22.4 1E+02 0.0022 29.3 3.7 33 193-227 31-63 (431)
399 PF06969 HemN_C: HemN C-termin 22.4 1.8E+02 0.0038 20.0 4.1 37 189-225 18-55 (66)
400 cd03329 MR_like_4 Mandelate ra 22.4 1.1E+02 0.0025 28.7 4.0 79 139-228 143-225 (368)
401 PF04492 Phage_rep_O: Bacterio 22.4 1.3E+02 0.0028 23.5 3.7 51 174-224 29-87 (100)
402 KOG3233 RNA polymerase III, su 22.3 5.5E+02 0.012 24.2 8.2 109 99-220 12-129 (297)
403 PRK14330 (dimethylallyl)adenos 22.2 2.4E+02 0.0051 27.3 6.2 48 138-189 272-319 (434)
404 PF06407 BDV_P40: Borna diseas 22.2 1.6E+02 0.0034 27.8 4.7 43 34-76 132-175 (370)
405 PRK10046 dpiA two-component re 22.2 1.7E+02 0.0036 24.9 4.7 51 175-227 162-213 (225)
406 TIGR00475 selB selenocysteine- 22.1 7.2E+02 0.016 25.2 9.9 115 93-224 404-522 (581)
407 PRK09430 djlA Dna-J like membr 22.1 2E+02 0.0044 26.2 5.5 100 46-151 111-225 (267)
408 smart00576 BTP Bromodomain tra 21.9 1.7E+02 0.0037 21.3 4.1 16 136-151 57-72 (77)
409 TIGR01178 ade adenine deaminas 21.9 1.7E+02 0.0036 29.6 5.3 34 138-173 451-484 (552)
410 PRK14340 (dimethylallyl)adenos 21.8 1.9E+02 0.0042 28.2 5.6 49 137-189 279-327 (445)
411 COG5014 Predicted Fe-S oxidore 21.7 5.7E+02 0.012 22.7 10.4 99 113-223 69-190 (228)
412 PRK09047 RNA polymerase factor 21.7 2.4E+02 0.0052 22.3 5.3 39 174-213 106-144 (161)
413 PF06224 HTH_42: Winged helix 21.5 2.2E+02 0.0048 25.9 5.7 121 114-238 96-228 (327)
414 PRK14325 (dimethylallyl)adenos 21.5 2.2E+02 0.0048 27.5 5.9 49 137-189 280-328 (444)
415 PF05633 DUF793: Protein of un 21.2 1.4E+02 0.0031 29.1 4.4 79 66-153 82-163 (389)
416 CHL00073 chlN photochlorophyll 21.1 6.1E+02 0.013 25.2 8.9 73 5-81 271-343 (457)
417 PF08227 DASH_Hsk3: DASH compl 21.1 1.3E+02 0.0027 20.5 2.9 18 32-49 4-21 (45)
418 cd03323 D-glucarate_dehydratas 21.1 1.4E+02 0.003 28.7 4.3 78 138-227 167-247 (395)
419 COG1737 RpiR Transcriptional r 21.0 1E+02 0.0022 28.0 3.3 111 34-152 11-129 (281)
420 PF01710 HTH_Tnp_IS630: Transp 20.9 4.2E+02 0.009 20.8 8.3 90 96-213 4-93 (119)
421 smart00544 MA3 Domain in DAP-5 20.9 2.2E+02 0.0047 21.6 4.7 53 90-150 28-81 (113)
422 cd02646 R3H_G-patch R3H domain 20.8 1.7E+02 0.0036 20.3 3.6 38 40-77 2-42 (58)
423 PF11719 Drc1-Sld2: DNA replic 20.8 70 0.0015 31.3 2.3 35 34-71 3-42 (426)
424 PRK03525 crotonobetainyl-CoA:c 20.7 6.7E+02 0.015 24.1 9.0 144 66-224 255-404 (405)
425 PRK09645 RNA polymerase sigma 20.7 2.6E+02 0.0056 22.6 5.4 38 174-212 118-155 (173)
426 PRK11337 DNA-binding transcrip 20.7 2.2E+02 0.0047 25.6 5.3 110 33-152 20-139 (292)
427 cd07626 BAR_SNX9_like The Bin/ 20.6 1.4E+02 0.003 26.3 3.9 48 35-82 16-64 (199)
428 COG1339 Transcriptional regula 20.6 1.3E+02 0.0028 26.9 3.6 40 189-228 17-56 (214)
429 COG5201 SKP1 SCF ubiquitin lig 20.4 2.8E+02 0.0061 23.3 5.4 77 45-149 53-136 (158)
430 PRK14334 (dimethylallyl)adenos 20.4 2.9E+02 0.0063 26.8 6.5 48 138-189 269-316 (440)
431 PF01088 Peptidase_C12: Ubiqui 20.4 67 0.0015 28.3 1.9 31 56-94 4-34 (214)
432 TIGR00288 conserved hypothetic 20.4 3E+02 0.0065 23.5 5.8 80 65-155 69-157 (160)
433 PRK12539 RNA polymerase sigma 20.3 2.4E+02 0.0052 23.3 5.2 41 174-215 131-171 (184)
434 TIGR02959 SigZ RNA polymerase 20.3 2.6E+02 0.0056 22.9 5.3 39 174-213 100-138 (170)
435 COG3888 Predicted transcriptio 20.3 1.9E+02 0.0041 27.2 4.8 46 182-227 9-56 (321)
436 PRK10550 tRNA-dihydrouridine s 20.2 1.8E+02 0.004 27.0 4.9 84 65-148 151-238 (312)
437 PRK09642 RNA polymerase sigma 20.2 2.6E+02 0.0057 22.2 5.3 38 174-212 106-143 (160)
438 PF03849 Tfb2: Transcription f 20.1 1.4E+02 0.003 28.7 4.1 59 177-240 211-269 (366)
439 PF13267 DUF4058: Protein of u 20.1 69 0.0015 29.4 1.9 29 75-109 7-35 (254)
440 PRK00095 mutL DNA mismatch rep 20.0 4.4E+02 0.0096 27.0 7.9 86 137-224 488-595 (617)
No 1
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=100.00 E-value=5.1e-93 Score=616.46 Aligned_cols=244 Identities=59% Similarity=0.974 Sum_probs=238.1
Q ss_pred CCCCcchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCC
Q 025599 1 MRRRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 1 mrR~~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~ 80 (250)
||||+|++||++++ +..+|++.|++++++|+.+|++||++|+.+|++||+||+.||++||+||++|+.||++||||||+
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 89999999999987 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEE
Q 025599 81 SNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVI 160 (250)
Q Consensus 81 s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi 160 (250)
|+||||++++|+|||||||+|||||||++|.+.|||+|++.||++++.+.|+...+.||+||++|||++|++||+||+|+
T Consensus 80 s~kgfw~~~lgvgdFYYelgVqviEvC~at~~~nGGlislqel~~~l~~~R~~~~e~vt~dD~lrAi~kLk~LG~gFev~ 159 (249)
T KOG3341|consen 80 SGKGFWAELLGVGDFYYELGVQVIEVCLATKHTNGGLISLQELCNHLLQRRKKDHEAVTEDDLLRAIDKLKVLGSGFEVI 159 (249)
T ss_pred cCcchHHHHhhhHHHHHHHhhHHHHHHHHhhcccCCeeeHHHHHHHHHHHhcccchhccHHHHHHHHHHhhccCCCeEEE
Confidence 99999999999999999999999999999999999999999999999999998889999999999999999999999999
Q ss_pred EECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCcc
Q 025599 161 SVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240 (250)
Q Consensus 161 ~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~ 240 (250)
+|||+++|||||.|||+||+.|||+|+..||||.+.|+++|+|+..||+.+|++|+++|++|+|.|+++ |..|||||+|
T Consensus 160 ~iggK~~vrSVP~ELn~Dht~ILela~~~gyvt~s~l~~~l~We~~Ra~qaLe~lv~egL~WiD~q~g~-e~~YW~ps~~ 238 (249)
T KOG3341|consen 160 KIGGKKLVRSVPTELNMDHTVILELAEILGYVTISLLKANLGWERSRAIQALEHLVKEGLAWIDLQAGD-EAAYWFPSLF 238 (249)
T ss_pred EecCEEeeecCcchhcccHHHHHHHHHhcCceeHHHHHHhccchHHHHHHHHHHHHhccceeeeccCCc-ceeeechhhh
Confidence 999999999999999999999999999999999999999999999999999999999999999999965 9999999999
Q ss_pred CCCccC
Q 025599 241 SISSSM 246 (250)
Q Consensus 241 ~~~~~~ 246 (250)
...-++
T Consensus 239 ~~~~~q 244 (249)
T KOG3341|consen 239 TDQYAQ 244 (249)
T ss_pred hHHHhh
Confidence 865443
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=2.8e-66 Score=457.17 Aligned_cols=218 Identities=49% Similarity=0.789 Sum_probs=187.6
Q ss_pred cchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCc
Q 025599 5 PGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKG 84 (250)
Q Consensus 5 ~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~ 84 (250)
+||+||+++.+++++|++.+.+.+.+++++|..|+++|++.+++|+++|+++|++||+||++|++||++|||||+++++
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 6999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccccc-ccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC
Q 025599 85 FWAELL-GIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG 163 (250)
Q Consensus 85 ~ws~~l-G~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig 163 (250)
+|++.+ |.++||||||+||+|||..+++.|||||+|+||+|++||+|+. ...|||+||++||++|++||.||++++++
T Consensus 80 ~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g-~~lISp~Di~~A~~~l~~lg~g~~l~~~~ 158 (223)
T PF04157_consen 80 FWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGG-SELISPEDILRACKLLEVLGLGFRLRKFG 158 (223)
T ss_dssp CCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTT-SST--HHHHHHHHHHHCCCTSSEEEEEET
T ss_pred hhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhccc-CCCcCHHHHHHHHHHHHHcCCCeEEEEeC
Confidence 999999 9999999999999999999999999999999999999999931 57999999999999999999999999999
Q ss_pred -CEEEEEecC-CccchhHHHHHHHH--HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 164 -KKKLVRSVP-TELNKDHNQILELA--QAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 164 -~~~~v~svp-~El~~D~~~vLela--~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
|++||+++| .|++.||++||+++ +..||+|+.+|++++||+..||+++|+.|+++|++|||
T Consensus 159 sg~~vv~s~~~~e~~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~~D 223 (223)
T PF04157_consen 159 SGVKVVQSVPYSELSKDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLWRD 223 (223)
T ss_dssp TTEEEEECST-CHH-HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCcEEEEeCCchhhhHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEeeC
Confidence 999999999 89999999999999 67999999999999999999999999999999999999
No 3
>KOG2760 consensus Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport]
Probab=100.00 E-value=9.6e-37 Score=284.42 Aligned_cols=224 Identities=20% Similarity=0.266 Sum_probs=195.5
Q ss_pred CCcchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHH------HHHHHHHHhcccccccChhHHHHHHHHHHHcCC
Q 025599 3 RRPGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFR------SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGV 76 (250)
Q Consensus 3 R~~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~------~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGV 76 (250)
|++||++|+|+.+++.+-++...+.+ |++|++.|+..+ +++.++.+..+++|.+|++.| |+++..++||
T Consensus 196 r~vGI~giEr~~e~q~~~td~~i~~A---FqDLskLMs~Akemv~Lsk~~~~Km~~~~g~i~dDetv~--~ks~llsLGI 270 (432)
T KOG2760|consen 196 RMVGISGIERSLEEQLKKTDKTINNA---FQDLSKLMSLAKEMVSLSKSIAEKMKSKTGEIQDDETVR--FKSYLLSLGI 270 (432)
T ss_pred eeechhHHHHHHHHHHHhcchhHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcCchhhhh--hHHhhhhhcc
Confidence 57999999999999999999887777 777777777766 688899999999999999997 9999999999
Q ss_pred CCCCCCCccccccccc--ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccC
Q 025599 77 DPLASNKGFWAELLGI--GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLG 154 (250)
Q Consensus 77 DPL~s~k~~ws~~lG~--gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG 154 (250)
+...+..+ +|+ .-|+-+||.||.|+...+.++|||||+|.|+||++||+|| +++|||+|+.+||+.|+.||
T Consensus 271 ~dpvt~~n-----~~~s~~~Y~~~Lakqlse~l~~~lee~ggmisLtdvY~~~NRaRG--~eLiSPedl~~ACe~le~l~ 343 (432)
T KOG2760|consen 271 LDPVTKDN-----FGLSLSLYHQELAKQLSEFLRLPLEENGGMISLTDVYCRYNRARG--TELISPEDLVNACELLEHLG 343 (432)
T ss_pred CCcchhcc-----ccchHHHHHHHHHHHHHHHHhcchhhcCCEEEHHHHHHHHHHhcc--CCCCCHHHHHHHHHHHHhcC
Confidence 74443422 231 5789999999999999999999999999999999999998 79999999999999999999
Q ss_pred CCeEEEEEC-CEEEEEecCCccchhHHHHHHHHH---hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCC
Q 025599 155 NGYEVISVG-KKKLVRSVPTELNKDHNQILELAQ---AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDR 230 (250)
Q Consensus 155 ~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~---~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~ 230 (250)
.|+++.+++ |..+||.- -..|..+++.+.+ ..+.+|+++++..+||+...|+++|..++++|.+|+|++.
T Consensus 344 ~pl~L~kf~SGvlvvqlK---s~~~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcRD~s~--- 417 (432)
T KOG2760|consen 344 VPLRLRKFNSGVLVVQLK---SHSDEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCRDDSV--- 417 (432)
T ss_pred CceEEEEcCCceEEEEee---ccchHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeeeccCc---
Confidence 999999999 88888833 3444445555444 4678899999999999999999999999999999999999
Q ss_pred CcceeecCccCCCc
Q 025599 231 KRRYWFPCASSISS 244 (250)
Q Consensus 231 e~~Yw~P~l~~~~~ 244 (250)
|++|||||+|.+..
T Consensus 418 eGL~fY~N~f~e~~ 431 (432)
T KOG2760|consen 418 EGLRFYPNLFMESS 431 (432)
T ss_pred cceeecccccccCC
Confidence 89999999998753
No 4
>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=96.77 E-value=0.0045 Score=41.47 Aligned_cols=47 Identities=23% Similarity=0.326 Sum_probs=40.0
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
||.-+..||.+....|.+|..+|++.+|++..-+...|..|+++|++
T Consensus 1 l~~~~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 1 LDETQRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp --HHHHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 45667889999998899999999999999999999999999999975
No 5
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=96.46 E-value=0.031 Score=48.77 Aligned_cols=107 Identities=20% Similarity=0.266 Sum_probs=83.9
Q ss_pred HHHHHhhhhcccCCCc-eeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecC----
Q 025599 102 QIVEICLATRPHNGGL-INLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVP---- 172 (250)
Q Consensus 102 qIvevC~~tr~~nGGl-i~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp---- 172 (250)
.+||.++=. .|-= +++.+|...+. +++++|..+++.|.. -+.|++|+.++|.+.+++-|
T Consensus 7 ~~iEA~LF~---sg~pgls~~~La~~l~---------~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~ 74 (188)
T PRK00135 7 SIIEALLFV---SGEEGLSLEQLAEILE---------LEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENAD 74 (188)
T ss_pred HHHHHHHHH---cCCCCCCHHHHHHHHC---------CCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHH
Confidence 345555443 3332 67888876542 567899999999953 48899999999988888732
Q ss_pred -----------CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 173 -----------TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 173 -----------~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
..||.....+|.++.-++-||-.++.+..|-+. -..|..|+..|++=.
T Consensus 75 ~v~~~~~~~~~~~LS~aaLEtLaiIay~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e 133 (188)
T PRK00135 75 YLQKLVKTPIKQSLSQAALEVLAIIAYKQPITRIEIDEIRGVNS---DGALQTLLAKGLIKE 133 (188)
T ss_pred HHHHHhcccccCCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEE
Confidence 269988888899888889999999999999985 788999999999864
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=96.15 E-value=0.084 Score=49.75 Aligned_cols=115 Identities=15% Similarity=0.243 Sum_probs=87.9
Q ss_pred hhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEec-----
Q 025599 97 YELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSV----- 171 (250)
Q Consensus 97 ~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~sv----- 171 (250)
.+++.+|.+.|.+. ..+..++.+||...+ ...+..+++.|++.|-.-|. +++++-++....+-+
T Consensus 8 ~~~~~~l~~~~~~~--~~~~~~~~~~L~~~~--------~~~~~~~~~~~in~Ll~~~~-~~~~~~~~~l~~~~~~~~~a 76 (327)
T PF05158_consen 8 SELEKKLLELCREN--PSPKGFSQEDLQQLI--------PGLDLQELVKAINELLSSGL-LKLLKKGGGLSYKAVSEEEA 76 (327)
T ss_dssp HHHHHHHHHHHHH-----SS-EEHHHHHHH---------TTS-HHHHHHHHHHHHHHTS-EEEEE-SSSEEEEE--SSS-
T ss_pred HHHHHHHHHHHHHh--cCCCCcCHHHHHhhc--------CCCCHHHHHHHHHHHHhCCC-EEEEEcCCEEEEEEeCHHHH
Confidence 57899999999987 667889999998773 34799999999999977554 888887776666666
Q ss_pred --CCccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 172 --PTELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 172 --p~El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
...|+.|+..|+.+++. +-.+...+|+...|-.......+|..|+..+++=
T Consensus 77 ~k~~~l~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK 131 (327)
T PF05158_consen 77 KKLKGLSDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIK 131 (327)
T ss_dssp ----SSSCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEE
T ss_pred hhhcCCCHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEE
Confidence 34789999999999984 5568999999999999999999999999999863
No 7
>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=95.99 E-value=0.018 Score=41.33 Aligned_cols=53 Identities=23% Similarity=0.344 Sum_probs=47.5
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
.|+..+.+|+...-..|..|+++|++.+|.+...+..+|+.|++.|++=+...
T Consensus 5 gLs~~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 5 GLSENEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp CHHHHHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred CcCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 46788888887766778999999999999999999999999999999988873
No 8
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.90 E-value=0.034 Score=40.40 Aligned_cols=55 Identities=20% Similarity=0.259 Sum_probs=46.7
Q ss_pred HHHHHHHHHhCCC--ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025599 179 HNQILELAQAQGF--VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237 (250)
Q Consensus 179 ~~~vLela~~~g~--vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P 237 (250)
...||++....|. +|+.+|++.+|-++.-+...|..|.++|++..+.+. +.+|.-
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~----~~~W~i 64 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGT----PPLWKL 64 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCC----CCceEe
Confidence 3468998887777 999999999999999999999999999999887654 457753
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=95.59 E-value=0.036 Score=38.93 Aligned_cols=45 Identities=29% Similarity=0.364 Sum_probs=41.6
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
+..|+++....|.+|+++|++.+|-|..=++.-|+.|.+.|++-+
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r 46 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKR 46 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 456899999999999999999999999999999999999999754
No 10
>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=95.27 E-value=0.039 Score=40.00 Aligned_cols=44 Identities=18% Similarity=0.293 Sum_probs=37.1
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.|.++...+|.+|..+|+..+++++.-.+..|+.|++.|.+=.-
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~ 47 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKV 47 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEe
Confidence 47788888999999999999999999999999999999987543
No 11
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.20 E-value=0.081 Score=35.69 Aligned_cols=53 Identities=28% Similarity=0.313 Sum_probs=42.7
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~ 238 (250)
|+++.. .+.+|.+++++.++++..-+..+|+.|.+.|++...... ...||.++
T Consensus 2 il~~l~-~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~---~~~~~~~~ 54 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREG---KRVYYSLT 54 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecC---CEEEEEEc
Confidence 455555 678999999999999999999999999999999876432 45566544
No 12
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.79 E-value=0.1 Score=37.80 Aligned_cols=56 Identities=25% Similarity=0.281 Sum_probs=43.5
Q ss_pred HHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025599 181 QILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237 (250)
Q Consensus 181 ~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P 237 (250)
.||++... .+.+|..++++.+|.+...|+.-|+.|+++|.+=..... .|-..||.-
T Consensus 4 ~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~-rG~~~~W~l 60 (62)
T PF04703_consen 4 KILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVR-RGKSTYWRL 60 (62)
T ss_dssp CHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-S-SSSS-EEEE
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC-CCcceeeee
Confidence 48888886 888999999999999999999999999999988544433 235679964
No 13
>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=94.63 E-value=0.087 Score=38.25 Aligned_cols=53 Identities=26% Similarity=0.445 Sum_probs=41.3
Q ss_pred ccchhHHHHHHHHH----hCCC-ccHHHHHHhcCCC-hHHHHHHHHHHHHcCCceeecC
Q 025599 174 ELNKDHNQILELAQ----AQGF-VTVDEVERRLSWT-SGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 174 El~~D~~~vLela~----~~g~-vt~~~L~~~l~W~-~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
+|+.-|..||+++. ..|| .|+.+|++.+|++ ..-+...|..|++.|++=.+..
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 57888999999876 2565 7999999999997 9999999999999999866643
No 14
>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=94.05 E-value=0.17 Score=34.92 Aligned_cols=53 Identities=17% Similarity=0.174 Sum_probs=44.0
Q ss_pred cchhHHHHHHHHHhCCC--ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 175 LNKDHNQILELAQAQGF--VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 175 l~~D~~~vLela~~~g~--vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|+.-|-.||-.....+- +|+.+|++.++.++.-+...+..|++.|++-.....
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 56667778887776555 999999999999999999999999999999877544
No 15
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=93.95 E-value=0.2 Score=32.93 Aligned_cols=46 Identities=35% Similarity=0.361 Sum_probs=39.2
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
+..+++.....+.+|+.+|++.++.+..-+...|..|.++|++=..
T Consensus 2 ~~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 2 QQQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3457777776788999999999999999999999999999986443
No 16
>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=93.94 E-value=0.15 Score=35.05 Aligned_cols=50 Identities=20% Similarity=0.288 Sum_probs=43.4
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
||..|-.+|..+...|.+|..+|++.++-+..-.-..+..|++.|++=.-
T Consensus 1 lt~~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 1 LTPSQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp STHHHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 46678889988888788999999999999999999999999999987543
No 17
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.71 E-value=0.38 Score=35.53 Aligned_cols=54 Identities=22% Similarity=0.280 Sum_probs=48.0
Q ss_pred CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
.+++..+..+|.+....|.+|..+|++.++.+..-....|..|++.|++=....
T Consensus 6 ~~l~~~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 6 LGLTPTQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCC
Confidence 367888889999988888899999999999999999999999999999965543
No 18
>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=93.68 E-value=0.19 Score=46.26 Aligned_cols=160 Identities=16% Similarity=0.223 Sum_probs=88.7
Q ss_pred HHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccc-cccchhhhHHHHHHHhhhhcccCCCce
Q 025599 40 ATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLG-IGDFYYELGVQIVEICLATRPHNGGLI 118 (250)
Q Consensus 40 ~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG-~gdfy~eLavqIvevC~~tr~~nGGli 118 (250)
..++.-|..|-.+++. .||.|- ++.+|..+|++|. ++.+.++- -...--.-+.+|++++--+-.+.
T Consensus 8 ~dYR~fl~d~ye~rk~---~~p~fS--~R~fa~~~G~ss~----s~L~~v~~Gkr~Ls~~~~~k~a~~l~L~~~E~---- 74 (271)
T TIGR02147 8 TDYRKYLRDYYEERKK---TDPAFS--WRFFAEKAGFSST----SYLNDIIKGKKNLTKRMIPKFAEALGLDEKEA---- 74 (271)
T ss_pred hhHHHHHHHHHHHHhc---cCcCcC--HHHHHHHhCCCCH----HHHHHHHcCCCCCCHHHHHHHHHHcCCCHHHH----
Confidence 4566777777766663 799995 8999999999863 22222211 01111222333333332111110
Q ss_pred eHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCc--cchhHHHHHHHHHhCCCc-cHH
Q 025599 119 NLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTE--LNKDHNQILELAQAQGFV-TVD 195 (250)
Q Consensus 119 ~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~E--l~~D~~~vLela~~~g~v-t~~ 195 (250)
+.-+++-.+++ .-|+++=.+|.+++..+-..-.+..+++. -.+ -+=-|..|.+++.-.++- +++
T Consensus 75 ~yF~~lV~f~~-------ak~~~~k~~~~~~~~~~~~~~~~~~L~~~------~~~y~~~W~~~virel~~~~~~~~~~~ 141 (271)
T TIGR02147 75 AYFEAMVNFGQ-------AKTDTEKQQFFEEMQALKPRPRLRVLAAD------QFEYYRHWYNSVIRELLGVMPFADDPE 141 (271)
T ss_pred HHHHHHHHHhc-------cCCHHHHHHHHHHHHHHhhhchheeccHH------HHHHHHHHHHHHHHHHhhcCCCCCCHH
Confidence 00011112222 23555555555555543221111111110 000 023466788888865555 999
Q ss_pred HHHHhcC--CChHHHHHHHHHHHHcCCceeec
Q 025599 196 EVERRLS--WTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 196 ~L~~~l~--W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|++.++ .+...++++|+-|++-|++=.|.
T Consensus 142 ~ia~~l~p~is~~ev~~sL~~L~~~glikk~~ 173 (271)
T TIGR02147 142 ELAKRCFPKISAEQVKESLDLLERLGLIKKNE 173 (271)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC
Confidence 9999998 89999999999999999997774
No 19
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.07 E-value=0.27 Score=40.77 Aligned_cols=49 Identities=12% Similarity=0.186 Sum_probs=44.6
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
|+.-..++|++.+..|..|.++|++.+|+|..-+..+++.|+.+|.+|.
T Consensus 7 lD~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 7 IDNLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred cCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 4555667999999899999999999999999999999999999999984
No 20
>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=92.82 E-value=0.48 Score=40.23 Aligned_cols=96 Identities=24% Similarity=0.344 Sum_probs=72.8
Q ss_pred eeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc----cCCCeEEEEECCEEEEEecCC---------------ccchh
Q 025599 118 INLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVPT---------------ELNKD 178 (250)
Q Consensus 118 i~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp~---------------El~~D 178 (250)
+++++|...+ . ++++|.++++.|+. -+.|++|+.++|.+.+++-|. .||..
T Consensus 14 vs~~~La~~l--------~--~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~~~~~LS~a 83 (159)
T PF04079_consen 14 VSIEELAEIL--------G--SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKPKPPKLSQA 83 (159)
T ss_dssp B-HHHHHHHC--------T---HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTCCCHHHHHH
T ss_pred CCHHHHHHHh--------C--CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccCccCCCCHH
Confidence 6777775542 2 78999999999963 589999999999988888542 67877
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
...+|.++.=+.-||-.++.+--|-+ +..+|..|+..|++-+=..
T Consensus 84 alEtLAiIAY~QPiTr~eIe~IRGv~---s~~~i~~L~e~glI~~~gr 128 (159)
T PF04079_consen 84 ALETLAIIAYKQPITRAEIEEIRGVN---SDSVIKTLLERGLIEEVGR 128 (159)
T ss_dssp HHHHHHHHHHH-SEEHHHHHHHHTS-----HCHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHhcCCcCHHHHHHHcCCC---hHHHHHHHHHCCCEEecCc
Confidence 77788888767789999999988876 7889999999999877653
No 21
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=92.58 E-value=1.5 Score=38.23 Aligned_cols=108 Identities=21% Similarity=0.272 Sum_probs=78.9
Q ss_pred HHHHHhhhhcccCCCc-eeHHHHHHHHHhhcCCCCCCCC-HHHHHHHHhhccc----cCCCeEEEEECCEEEEEecC---
Q 025599 102 QIVEICLATRPHNGGL-INLQELCNLLRQRRKSNREAVS-EDDCLRAISKLKV----LGNGYEVISVGKKKLVRSVP--- 172 (250)
Q Consensus 102 qIvevC~~tr~~nGGl-i~l~el~~~v~k~R~~~~~~IS-~~DI~rAik~L~~----LG~g~~vi~ig~~~~v~svp--- 172 (250)
.+||.++=.. |-= +++.++...+. ++ ++++..+++.|+. -+.|++|+.++|.+.+++-|
T Consensus 4 ~~iEAlLF~s---g~pgls~~~La~il~---------~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~ 71 (186)
T TIGR00281 4 AIIEALLFVS---GEPGVTLAELVRILG---------KEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFA 71 (186)
T ss_pred HHHHHHHHHc---CCCCCCHHHHHHHhC---------CCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHH
Confidence 3455544433 332 67888876653 23 4567777777754 36799999999988888743
Q ss_pred -----------CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 173 -----------TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 173 -----------~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
..||.....+|.++.=+.-||-.++.+-.|-+ +..+|..|+..|++=+-
T Consensus 72 ~~i~~~~~~~~~~LS~aaLEtLAIIAY~QPITr~eIe~IRGv~---s~~~l~~L~ergLI~~~ 131 (186)
T TIGR00281 72 DYIHRFLPAKLKNLNSASLEVLAIIAYKQPITRARINEIRGVK---SYQIVDDLVEKGLVVEL 131 (186)
T ss_pred HHHHHHhccccccCCHHHHHHHHHHHHcCCcCHHHHHHHcCCC---HHHHHHHHHHCCCeEec
Confidence 13777777888888877899999999988887 67899999999988654
No 22
>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=92.20 E-value=0.27 Score=38.26 Aligned_cols=64 Identities=23% Similarity=0.388 Sum_probs=42.2
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee----ecCCCCCCcceeecCc
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV----DDGHRDRKRRYWFPCA 239 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv----D~q~~~~e~~Yw~P~l 239 (250)
...++..|+.+.-..|.+|.++|+..+|.+.--.+..|..|..+|++-+ |++.+ -...|||.++
T Consensus 11 yg~~~~~Il~~L~~~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~-~~~~yw~i~~ 78 (105)
T PF02002_consen 11 YGEEAVRILDALLRKGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERG-WTRYYWYIDY 78 (105)
T ss_dssp S-STTHHHHHHHHHH--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE---------EEEEE-TH
T ss_pred cCchHHHHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCc-EEEEEEEEcH
Confidence 3456778888888789999999999999999999999999999999843 32221 1357888764
No 23
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=91.78 E-value=0.35 Score=40.68 Aligned_cols=51 Identities=18% Similarity=0.302 Sum_probs=46.3
Q ss_pred CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
..|+.-..++|.+.+..|.+|.++|++.+|.|..-+..+++.|+++|.++.
T Consensus 10 ~~lD~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 10 KDLDRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hhHHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 356666778999999999999999999999999999999999999999984
No 24
>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=91.62 E-value=0.87 Score=35.60 Aligned_cols=56 Identities=16% Similarity=0.238 Sum_probs=47.5
Q ss_pred ccchhHHHHHHHHH----hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025599 174 ELNKDHNQILELAQ----AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD 229 (250)
Q Consensus 174 El~~D~~~vLela~----~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~ 229 (250)
.++.-|-.+|.... ..|.+|..+|++.+++++.-.-..++.|++.|++..-....|
T Consensus 22 ~ls~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D 81 (109)
T TIGR01889 22 NLSLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDD 81 (109)
T ss_pred CCCHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCccc
Confidence 56777877887666 468899999999999999999999999999999997655533
No 25
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=91.21 E-value=0.92 Score=37.34 Aligned_cols=48 Identities=27% Similarity=0.327 Sum_probs=42.1
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.....+.+.+|-.|+++|++.++-++..+..+|+-|+..|++=+-...
T Consensus 31 ~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 31 EVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeec
Confidence 334455667899999999999999999999999999999999998666
No 26
>PHA02943 hypothetical protein; Provisional
Probab=91.07 E-value=0.72 Score=39.31 Aligned_cols=58 Identities=22% Similarity=0.298 Sum_probs=48.1
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P 237 (250)
.+--..|||+. ..|+.|.+++++.+|-|...|+-.|..|+++|.+=.=... ...||.-
T Consensus 10 ~~R~~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G---~~tyw~l 67 (165)
T PHA02943 10 HTRMIKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIG---RAAIWCL 67 (165)
T ss_pred HHHHHHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeec---ceEEEEE
Confidence 33345578888 7899999999999999999999999999999998774443 6788864
No 27
>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=91.06 E-value=0.64 Score=35.84 Aligned_cols=49 Identities=27% Similarity=0.394 Sum_probs=41.4
Q ss_pred ccchhHHHHHHHHHh----CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 174 ELNKDHNQILELAQA----QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 174 El~~D~~~vLela~~----~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
.++.-+.+||+++.. .-.|++.+|.+.++.+....+.+|+.|..+|.+.
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 477788999999885 3459999999999999999999999999999875
No 28
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=90.69 E-value=0.46 Score=42.87 Aligned_cols=46 Identities=30% Similarity=0.417 Sum_probs=43.6
Q ss_pred hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
-|..|+++.+..|.|++++|++.++-|..=.+.=|..|++.|++=+
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R 51 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLR 51 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence 4788999999999999999999999999999999999999999866
No 29
>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=90.00 E-value=0.93 Score=31.68 Aligned_cols=47 Identities=23% Similarity=0.347 Sum_probs=36.9
Q ss_pred cchhHHHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 175 LNKDHNQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 175 l~~D~~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
|+..|..||..+. ..+..|..+|++.++-+..-+-..|+.|+..|++
T Consensus 1 lt~~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv 48 (68)
T PF13463_consen 1 LTRPQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLV 48 (68)
T ss_dssp --HHHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSE
T ss_pred CCHHHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 3455777777776 7899999999999999999999999999999988
No 30
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=89.87 E-value=1.6 Score=35.44 Aligned_cols=56 Identities=20% Similarity=0.202 Sum_probs=48.5
Q ss_pred CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|..|+.-|-.||......|.+|..+|++.++.++.-.-..|+.|++.|++=+-...
T Consensus 35 ~~glt~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~ 90 (144)
T PRK11512 35 PLDITAAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNP 90 (144)
T ss_pred ccCCCHHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCc
Confidence 44567778888887777788999999999999999999999999999999876544
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=89.85 E-value=1.5 Score=35.82 Aligned_cols=62 Identities=11% Similarity=0.243 Sum_probs=47.7
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHh----cCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERR----LSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA 239 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~----l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l 239 (250)
|+.-+..|+++.=..|-+|+.++.+. .+|+..-..+.|..|+++|++=++... ...+|.|..
T Consensus 2 Lt~~E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~g---r~~~Y~p~v 67 (130)
T TIGR02698 2 ISDAEWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEG---RKFIYTALV 67 (130)
T ss_pred CCHHHHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCC---CcEEEEecC
Confidence 45566778887766778999996655 489999999999999999998666332 466777753
No 32
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=89.81 E-value=0.52 Score=40.41 Aligned_cols=39 Identities=26% Similarity=0.371 Sum_probs=33.4
Q ss_pred HHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 184 ELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 184 ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
.+++.+-..|+.++..++||+.++|+.+|++|..+|.+-
T Consensus 117 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (166)
T PRK15466 117 LLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLR 155 (166)
T ss_pred HHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence 445555566999999999999999999999999999764
No 33
>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=89.61 E-value=0.95 Score=33.06 Aligned_cols=43 Identities=23% Similarity=0.392 Sum_probs=36.1
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
..+.+++-..+.+|++.|+..|+.-=.||-..++.|+.+|++=
T Consensus 9 ~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs 51 (65)
T PF09397_consen 9 EEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVS 51 (65)
T ss_dssp HHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE
T ss_pred HHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCC
Confidence 3466666678999999999999999999999999999999873
No 34
>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=89.59 E-value=1.8 Score=33.93 Aligned_cols=51 Identities=18% Similarity=0.192 Sum_probs=45.2
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.++.-|-.+|......|.+|..+|++.++.++.-+-..|+.|+++|++=+-
T Consensus 25 ~lt~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 25 GLTEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred CCCHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence 456678788888887888999999999999999999999999999988764
No 35
>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=89.47 E-value=1.2 Score=35.16 Aligned_cols=61 Identities=23% Similarity=0.329 Sum_probs=45.9
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhc----CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRL----SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA 239 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l----~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l 239 (250)
+.-...|+++.=..|.+|+.++.+.+ +|+..=.++.|..|+++|++-++... ...+|.|..
T Consensus 2 s~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~g---r~~~Y~p~i 66 (115)
T PF03965_consen 2 SDLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIG---RAYVYSPLI 66 (115)
T ss_dssp -HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEET---TCEEEEESS
T ss_pred CHHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecC---CceEEEeCC
Confidence 44456688887777779999888765 58899999999999999999999764 455666653
No 36
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=89.31 E-value=0.73 Score=41.25 Aligned_cols=57 Identities=28% Similarity=0.351 Sum_probs=47.3
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC-CCcceee
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD-RKRRYWF 236 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~-~e~~Yw~ 236 (250)
..+|.++.+.|-+|+.+|++.||.++.-++.-|+.|+++|++=+-.+.++ |.+.+.|
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y 71 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLY 71 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceee
Confidence 45888888889999999999999999999999999999999877766542 3444444
No 37
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=89.25 E-value=1.1 Score=34.39 Aligned_cols=44 Identities=20% Similarity=0.341 Sum_probs=40.6
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
...||.+.+..|.+|.++|++.+|-+..-+...|..|+++|++-
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 45688888888899999999999999999999999999999987
No 38
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=89.16 E-value=0.68 Score=35.68 Aligned_cols=39 Identities=15% Similarity=0.147 Sum_probs=34.9
Q ss_pred hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc-eeecC
Q 025599 188 AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA-MVDDG 226 (250)
Q Consensus 188 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~-WvD~q 226 (250)
..-+||++.|++.++.....|+.+|.+|+.+|++ .|...
T Consensus 38 ~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~ 77 (86)
T PRK09334 38 KEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKN 77 (86)
T ss_pred cCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecC
Confidence 4578999999999999999999999999999998 66533
No 39
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=89.08 E-value=0.84 Score=41.08 Aligned_cols=46 Identities=35% Similarity=0.432 Sum_probs=42.3
Q ss_pred hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
-+..++++....|++|+++|++.+|.+..-++.-|..|+++|++=+
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4677999999999999999999999999999999999999999854
No 40
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=88.76 E-value=0.95 Score=41.42 Aligned_cols=54 Identities=28% Similarity=0.390 Sum_probs=48.2
Q ss_pred CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+..|+.|...|+++... +|-++.++|++.+|-++.-.-..|..|++.|++=+-.
T Consensus 190 ~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 190 EYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred cCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEE
Confidence 46899999999998885 7779999999999999999999999999999975543
No 41
>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=88.48 E-value=1.7 Score=30.08 Aligned_cols=43 Identities=33% Similarity=0.314 Sum_probs=38.7
Q ss_pred HHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 183 LELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 183 Lela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-++++..|.+|+.++++.+|-|.--|...|+.|-+.|+.+++.
T Consensus 2 ~~~~~~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~g 44 (50)
T PF09107_consen 2 RELLQKNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVG 44 (50)
T ss_dssp HHHHHTTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred hHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeC
Confidence 3566778999999999999999999999999999999999985
No 42
>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=88.48 E-value=1.7 Score=30.81 Aligned_cols=44 Identities=27% Similarity=0.407 Sum_probs=38.7
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
|+++.+.++.|+..+|++.+|-++.=+-+.|..|.++|++-.+.
T Consensus 13 Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 56666778999999999999999999999999999999987664
No 43
>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=88.45 E-value=2.7 Score=28.73 Aligned_cols=49 Identities=27% Similarity=0.277 Sum_probs=41.7
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
..+..|+..+...+ ++.+++++.++-+..-+...|+.|++.|++-....
T Consensus 7 ~~~~~il~~l~~~~-~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~ 55 (78)
T cd00090 7 PTRLRILRLLLEGP-LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRRE 55 (78)
T ss_pred hHHHHHHHHHHHCC-cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEe
Confidence 45667887766666 99999999999999999999999999999977543
No 44
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=88.31 E-value=0.95 Score=40.84 Aligned_cols=47 Identities=28% Similarity=0.310 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
.-+..|+++.+..|.+++.+|++.++-|..=++.-|..|+++|++=+
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r 51 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIR 51 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 34678999999999999999999999999999999999999997633
No 45
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=88.11 E-value=2.4 Score=34.25 Aligned_cols=56 Identities=20% Similarity=0.190 Sum_probs=47.3
Q ss_pred CCccchhHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 172 PTELNKDHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 172 p~El~~D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|..|+.-|-.+|..+.. .+..|..+|++.+++++.-.-..++.|++.|++-+-...
T Consensus 26 ~~glt~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~ 82 (144)
T PRK03573 26 PLELTQTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCA 82 (144)
T ss_pred hcCCCHHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCC
Confidence 44667778778877764 467899999999999999999999999999999987554
No 46
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=88.06 E-value=2.1 Score=31.55 Aligned_cols=45 Identities=27% Similarity=0.336 Sum_probs=39.5
Q ss_pred HHHHHHHhC-CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 181 QILELAQAQ-GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 181 ~vLela~~~-g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|+++.... +.+|+.+|++.+|.+..-+...|..|++.|++-.+.
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 467766654 789999999999999999999999999999998763
No 47
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=88.04 E-value=0.95 Score=37.29 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=43.1
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
...|+|++...|.+|..++....|-+..-++..+.+|+..|-++.=
T Consensus 14 k~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 14 KARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeC
Confidence 5668999999999999999999999999999999999999999874
No 48
>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=87.84 E-value=1.3 Score=30.04 Aligned_cols=44 Identities=32% Similarity=0.425 Sum_probs=36.0
Q ss_pred HHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 181 QILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 181 ~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.||++.. ..+.+|..+|++.+|+++.-+...|..|+..|++=.|
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 3566555 3566899999999999999999999999999998655
No 49
>PRK09954 putative kinase; Provisional
Probab=86.95 E-value=1.4 Score=41.06 Aligned_cols=43 Identities=16% Similarity=0.291 Sum_probs=39.9
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
..+||++.+..+++|..+|++.+|+++..++..|..|+++|.+
T Consensus 5 ~~~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i 47 (362)
T PRK09954 5 EKEILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRI 47 (362)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 3468999999999999999999999999999999999999975
No 50
>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=86.95 E-value=2 Score=37.21 Aligned_cols=53 Identities=21% Similarity=0.322 Sum_probs=48.6
Q ss_pred CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
..++..+..+|.+....|.+|..+|++.++.+...+...|..|++.|++-.+.
T Consensus 139 ~~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 139 AGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred cCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 36788888999998887899999999999999999999999999999998885
No 51
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=86.71 E-value=0.98 Score=38.95 Aligned_cols=46 Identities=15% Similarity=0.091 Sum_probs=42.5
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
.-+..|++++...|++++.+|++.+|-|..-++.=|..|.++|++=
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~ 52 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRE 52 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHH
Confidence 3577899999999999999999999999999999999999999873
No 52
>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=86.66 E-value=2.4 Score=35.77 Aligned_cols=62 Identities=23% Similarity=0.201 Sum_probs=48.3
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc----eeecCCCCCCcceeecC
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA----MVDDGHRDRKRRYWFPC 238 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~----WvD~q~~~~e~~Yw~P~ 238 (250)
..++..|+++.-..|-+|.++|+..+|.+..-.+..|..|..+|++ ..|+..+ --..||+.+
T Consensus 13 g~~~v~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~g-w~~Y~w~i~ 78 (158)
T TIGR00373 13 EEEVGLVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETG-WYEYTWRIN 78 (158)
T ss_pred ChhHHHHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCC-cEEEEEEeC
Confidence 3456667776666789999999999999999999999999999998 4565542 135566543
No 53
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.53 E-value=1.4 Score=39.71 Aligned_cols=46 Identities=26% Similarity=0.416 Sum_probs=42.3
Q ss_pred hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
-+..++++....|.+|+.+|++.++-|..=++.-|..|+++|++=+
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r 51 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILR 51 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 4677999999999999999999999999999999999999999743
No 54
>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=86.06 E-value=2.5 Score=29.19 Aligned_cols=36 Identities=28% Similarity=0.183 Sum_probs=33.8
Q ss_pred CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+.+|..+|++.+|-+..-+...|..|.++|++..+.
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 579999999999999999999999999999998875
No 55
>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=86.05 E-value=5.6 Score=32.36 Aligned_cols=78 Identities=17% Similarity=0.184 Sum_probs=60.0
Q ss_pred hhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCC-eEEEEECCEEEEEecCCccc
Q 025599 98 ELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNG-YEVISVGKKKLVRSVPTELN 176 (250)
Q Consensus 98 eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g-~~vi~ig~~~~v~svp~El~ 176 (250)
+|+-.|--+|.+ ++-..|++++|+..+... +...+|.+|+..-++.|.-+=.. +.++++++..||+..-.
T Consensus 45 ~la~~v~~if~s---~~k~~l~~e~l~~kl~~S---~~~~~s~~E~E~~l~LL~el~P~Wis~~~~~~~~~lk~~k~--- 115 (126)
T cd08767 45 ELARILRNIFVS---EKKTVLPLEELVYKLQAS---YPSILSRGEVEEHLRLLAELAPDWISEKSLRKGDYLKIDKK--- 115 (126)
T ss_pred HHHHHHHHHHHh---cccccccHHHHHHHHHHh---CCCCCCHHHHHHHHHHHHHhChHHheeeeeCCceEEEECcc---
Confidence 566666666766 778999999999999874 34679999999999999865533 67777888889987743
Q ss_pred hhHHHHHH
Q 025599 177 KDHNQILE 184 (250)
Q Consensus 177 ~D~~~vLe 184 (250)
.|...|.+
T Consensus 116 ~~~~~V~~ 123 (126)
T cd08767 116 VDLEKVRK 123 (126)
T ss_pred ccHHHHHH
Confidence 56666654
No 56
>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=86.00 E-value=2.7 Score=29.29 Aligned_cols=47 Identities=30% Similarity=0.348 Sum_probs=39.4
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-..||.+....+..|+.+|++.+|.+..-+...|..|++.|++=+..
T Consensus 12 R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 12 RLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 34577777667889999999999999999999999999999975554
No 57
>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=85.99 E-value=3 Score=28.15 Aligned_cols=40 Identities=25% Similarity=0.285 Sum_probs=34.2
Q ss_pred HHHHHHH-HhCCCccHHHHHHhcCCChHHHHHHHHHHHHcC
Q 025599 180 NQILELA-QAQGFVTVDEVERRLSWTSGRAIDALDILLEEG 219 (250)
Q Consensus 180 ~~vLela-~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G 219 (250)
..++.+. +..+++|.++|++.++-|.-=++.-|..|...|
T Consensus 3 ~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4566666 667789999999999999999999999999998
No 58
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=85.90 E-value=2.2 Score=34.57 Aligned_cols=48 Identities=23% Similarity=0.373 Sum_probs=44.1
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.|+.-..++|++.+..|-.|..+|++.+|-|..-+..++..|+++|++
T Consensus 5 ~lD~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 5 KLDDIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred cccHHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCce
Confidence 466677889999998889999999999999999999999999999975
No 59
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=85.58 E-value=3.1 Score=35.92 Aligned_cols=44 Identities=20% Similarity=0.157 Sum_probs=40.9
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
+..||.+.-..|.+|.++|+..+|.+..-++..|..|..+|++=
T Consensus 24 ~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 24 GFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 56688887788999999999999999999999999999999987
No 60
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=85.55 E-value=1.6 Score=29.26 Aligned_cols=33 Identities=24% Similarity=0.258 Sum_probs=30.2
Q ss_pred CCCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 189 QGFV-TVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 189 ~g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
...+ |..+|++.+|.+..-++.+|..|.++|++
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i 50 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLV 50 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 4456 99999999999999999999999999985
No 61
>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=85.29 E-value=1.8 Score=34.94 Aligned_cols=54 Identities=30% Similarity=0.394 Sum_probs=49.4
Q ss_pred CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+..++.+|..|+++|.. ..|+.|++..++-...-+|-.+.+|+..|++=|-...
T Consensus 38 ~~~l~pE~~~Il~lC~~--~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~~p~ 91 (114)
T PF05331_consen 38 PAGLGPEHRAILELCRR--PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVRAPA 91 (114)
T ss_pred CCCCCHHHHHHHHHHCC--CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEeCCC
Confidence 35799999999999998 8999999999999999999999999999999887554
No 62
>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=85.18 E-value=1.6 Score=34.84 Aligned_cols=36 Identities=25% Similarity=0.219 Sum_probs=32.8
Q ss_pred hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 188 AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 188 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
..-+||+..|++.|+.+...|+.+|.+|+..|++=.
T Consensus 56 ~~K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~ 91 (105)
T PF03297_consen 56 KMKLITPSVLSERLKINGSLARKALRELESKGLIKP 91 (105)
T ss_dssp TSSCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEE
T ss_pred cCcEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEE
Confidence 356899999999999999999999999999998743
No 63
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=84.79 E-value=2.3 Score=34.71 Aligned_cols=43 Identities=16% Similarity=0.300 Sum_probs=37.9
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
++.+....|++|+++|++.+++++.-+...|..|.+.|++-.+
T Consensus 13 I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 13 IYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 4455667899999999999999999999999999999998754
No 64
>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=84.18 E-value=2.4 Score=30.77 Aligned_cols=43 Identities=28% Similarity=0.302 Sum_probs=37.6
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
.+++++-..+.+|++.|++.|..-=.||-..++.|+.+|++=-
T Consensus 9 ~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p 51 (63)
T smart00843 9 EAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGP 51 (63)
T ss_pred HHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCC
Confidence 3566666778999999999999999999999999999999744
No 65
>PLN02180 gamma-glutamyl transpeptidase 4
Probab=84.18 E-value=1.7 Score=44.71 Aligned_cols=74 Identities=27% Similarity=0.450 Sum_probs=48.8
Q ss_pred HHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCccccc----c------cccccchh-hhHHHHHHHhhhhcc
Q 025599 44 SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAE----L------LGIGDFYY-ELGVQIVEICLATRP 112 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~----~------lG~gdfy~-eLavqIvevC~~tr~ 112 (250)
..|.......+..+.++|.+|.-|.. =| .|+....-+... + -|...||. ++|.+|++-+.+
T Consensus 215 ~~la~~l~~~~~~l~~~p~~~~~f~~----~G-~~~~~Gd~l~qp~LA~TLe~IA~~G~d~FY~G~iA~~iv~~~~~--- 286 (639)
T PLN02180 215 PYLGKAISSHAAMILKDPGLRSVFSR----NG-QVLKPGETCYNPELAQSLETISEQGPGAFYNGTIGEKLVKDVKK--- 286 (639)
T ss_pred HHHHHHHHHHHHHHhcChhHHHHhCc----CC-ccCCCCCeeccHHHHHHHHHHHHhCcccccCCHHHHHHHHHHHH---
Confidence 34555555666667778888766653 13 454322111111 1 25678888 999999999874
Q ss_pred cCCCceeHHHHHHH
Q 025599 113 HNGGLINLQELCNL 126 (250)
Q Consensus 113 ~nGGli~l~el~~~ 126 (250)
+||+|+++||-..
T Consensus 287 -~GG~lT~eDLa~Y 299 (639)
T PLN02180 287 -AGGIITMDDLRSY 299 (639)
T ss_pred -cCCCCCHHHHHhC
Confidence 8999999999755
No 66
>PLN02198 glutathione gamma-glutamylcysteinyltransferase
Probab=83.79 E-value=1.7 Score=44.07 Aligned_cols=74 Identities=22% Similarity=0.275 Sum_probs=46.1
Q ss_pred HHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccc----cc------cccccchh-hhHHHHHHHhhhhccc
Q 025599 45 QLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWA----EL------LGIGDFYY-ELGVQIVEICLATRPH 113 (250)
Q Consensus 45 ~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws----~~------lG~gdfy~-eLavqIvevC~~tr~~ 113 (250)
.|.......+..|+.+|.+|+-|.. =| .|+....-+.. ++ -|...||. ++|.+|++-|. .
T Consensus 166 ~la~~l~~~~~~l~~~p~~~~~f~~----~G-~~~~~Gd~l~~p~LA~TL~~iA~~G~~~FY~G~iA~~iv~~~~----~ 236 (573)
T PLN02198 166 YLYMQMNATRSDILADKGLSDLFVS----NG-ELKKPGTICHNPKLALTLRLIGEYGPKAFYNGTVGVNLVRDIQ----K 236 (573)
T ss_pred HHHHHHHHHHHHHhcChhHHHHcCc----CC-CcCCCCCeecCHHHHHHHHHHHHhCcccccCCHHHHHHHHHHH----H
Confidence 3444455556666677777766642 12 34332211110 11 25678887 79999999996 4
Q ss_pred CCCceeHHHHHHHH
Q 025599 114 NGGLINLQELCNLL 127 (250)
Q Consensus 114 nGGli~l~el~~~v 127 (250)
+||+|+++||-..=
T Consensus 237 ~GG~lt~~DL~~y~ 250 (573)
T PLN02198 237 SGGIITLKDLQSYR 250 (573)
T ss_pred cCCCCCHHHHhhCC
Confidence 99999999997653
No 67
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=83.72 E-value=2.5 Score=37.88 Aligned_cols=47 Identities=15% Similarity=0.211 Sum_probs=42.1
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
.-+..++++....+++|+++|++.+++|..-++.-|..|...|++=+
T Consensus 4 ~R~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 4 ARQQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 34667999999899999999999999999999999999999998744
No 68
>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=83.12 E-value=7.5 Score=35.80 Aligned_cols=94 Identities=19% Similarity=0.301 Sum_probs=68.7
Q ss_pred HHHHHHHHHhhc-CCCCCCCCHHHHHHHHhhccccCCCeEEEEE-CCEEEEEecCCccchhHHHHH-HHHHhCCCccHHH
Q 025599 120 LQELCNLLRQRR-KSNREAVSEDDCLRAISKLKVLGNGYEVISV-GKKKLVRSVPTELNKDHNQIL-ELAQAQGFVTVDE 196 (250)
Q Consensus 120 l~el~~~v~k~R-~~~~~~IS~~DI~rAik~L~~LG~g~~vi~i-g~~~~v~svp~El~~D~~~vL-ela~~~g~vt~~~ 196 (250)
+.+|...+.++- ......+|+-.++.=+.+|..++ .+.|+.. +|+-|| +|..|. ..|- |+...+|.|+.-+
T Consensus 2 i~~L~~~~q~~Q~~~~~~rLSErnciEiv~kL~~~~-~ldli~T~dGkeyi--T~~~L~---~EI~~el~~~gGRv~~~d 75 (272)
T PF09743_consen 2 IEELQADFQRAQLASSSQRLSERNCIEIVNKLIEKK-LLDLIHTTDGKEYI--TPEQLE---KEIKDELYVHGGRVNLVD 75 (272)
T ss_pred HHHHHHHHHHHHHHhhhhhcchhhHHHHHHHHHHcC-CeeEEEECCCCEEE--CHHHHH---HHHHHHHHHcCCceEHHH
Confidence 455665555532 12357899999999999998887 4666655 577665 344442 3344 4445689999999
Q ss_pred HHHhcCCChHHHHHHHHHHHHcC
Q 025599 197 VERRLSWTSGRAIDALDILLEEG 219 (250)
Q Consensus 197 L~~~l~W~~~Ra~~~L~~l~~~G 219 (250)
|...+|-+..-+...+..++++-
T Consensus 76 L~~~LnVd~~~ie~~~~~i~~~~ 98 (272)
T PF09743_consen 76 LAQALNVDLDHIERRAQEIVKSD 98 (272)
T ss_pred HHHhcCcCHHHHHHHHHHHHhCC
Confidence 99999999999999999988865
No 69
>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=82.52 E-value=4.1 Score=27.03 Aligned_cols=40 Identities=33% Similarity=0.442 Sum_probs=34.3
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.|+.+... |..++.+|++.+|-+..-...-|..|...|++
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV 45 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELGLSQSTVSHHLKKLREAGLV 45 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHh-CCCchhhHHHhccccchHHHHHHHHHHHCcCe
Confidence 45655556 88999999999999999999999999999985
No 70
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=82.44 E-value=6 Score=29.82 Aligned_cols=55 Identities=25% Similarity=0.254 Sum_probs=46.3
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCC
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRD 229 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~ 229 (250)
++.-|..+|......+..+..+|++.++.++.-.-..|+.|++.|++.+-....|
T Consensus 20 lt~~q~~~L~~l~~~~~~~~~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~D 74 (126)
T COG1846 20 LTPPQYQVLLALYEAGGITVKELAERLGLDRSTVTRLLKRLEDKGLIERLRDPED 74 (126)
T ss_pred CCHHHHHHHHHHHHhCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccc
Confidence 6777888888777666666599999999999999999999999999998766543
No 71
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=82.42 E-value=5.1 Score=34.23 Aligned_cols=40 Identities=20% Similarity=0.446 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCC
Q 025599 36 KEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 36 ~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~ 80 (250)
..|.+.++++..-|..+..+-|..+ .|..|..++|-.|..
T Consensus 16 ~~qi~~lkeaF~l~D~d~~G~I~~~-----el~~ilr~lg~~~s~ 55 (160)
T COG5126 16 EEQIQELKEAFQLFDRDSDGLIDRN-----ELGKILRSLGFNPSE 55 (160)
T ss_pred HHHHHHHHHHHHHhCcCCCCCCcHH-----HHHHHHHHcCCCCcH
Confidence 4566778888888988888888876 688999999998864
No 72
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=82.38 E-value=3.1 Score=35.57 Aligned_cols=49 Identities=27% Similarity=0.324 Sum_probs=43.4
Q ss_pred hHHHHHHHHHhCCCc-cHHHHHHhc--CCChHHHHHHHHHHHHcCCceeecC
Q 025599 178 DHNQILELAQAQGFV-TVDEVERRL--SWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 178 D~~~vLela~~~g~v-t~~~L~~~l--~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
-|..|++++.-.++- ++..|++.+ +.+.+.++++|+-|++-|++=.|..
T Consensus 25 ~~~~ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 25 YHPAIRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HHHHHHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 366788999976676 999999999 9999999999999999999988754
No 73
>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=82.35 E-value=3.3 Score=41.30 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=27.5
Q ss_pred ccccchh-hhHHHHHHHhhhhcccCCCceeHHHHHHH
Q 025599 91 GIGDFYY-ELGVQIVEICLATRPHNGGLINLQELCNL 126 (250)
Q Consensus 91 G~gdfy~-eLavqIvevC~~tr~~nGGli~l~el~~~ 126 (250)
|...||. ++|.+|++-+.+ +||+|+++||...
T Consensus 191 G~~~FY~G~iA~~iv~~~~~----~GG~lt~~DL~~y 223 (516)
T TIGR00066 191 GPDAFYKGDIAESIIDTLQK----NGGIMTKKDLAAY 223 (516)
T ss_pred CcccccCCHHHHHHHHHHHH----cCCCCCHHHHhhC
Confidence 5678888 999999998874 9999999999754
No 74
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=82.34 E-value=2.7 Score=38.22 Aligned_cols=49 Identities=20% Similarity=0.312 Sum_probs=43.6
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
..-+..|+++.+..|.+|+.+|++.|+-|..=++.=|..|+++|++=+-
T Consensus 16 ~eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~ 64 (269)
T PRK09802 16 SERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEE
Confidence 3457789999999999999999999999999999999999999998543
No 75
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=82.13 E-value=6.9 Score=36.13 Aligned_cols=71 Identities=17% Similarity=0.255 Sum_probs=55.6
Q ss_pred CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHH-HHHh--CCCccHHHHHHhcCCChHHHHHHH
Q 025599 136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILE-LAQA--QGFVTVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLe-la~~--~g~vt~~~L~~~l~W~~~Ra~~~L 212 (250)
..||.+++..+++.+.. . ...|+.-+...|. ++.. .|.++.+.++..+|++..-+..++
T Consensus 236 ~~I~~~~v~~~l~~~~~---~---------------~~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~ 297 (328)
T PRK00080 236 GVITKEIADKALDMLGV---D---------------ELGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVY 297 (328)
T ss_pred CCCCHHHHHHHHHHhCC---C---------------cCCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHh
Confidence 57999999999976522 1 1234555566675 6664 788999999999999999999999
Q ss_pred H-HHHHcCCceee
Q 025599 213 D-ILLEEGLAMVD 224 (250)
Q Consensus 213 ~-~l~~~Gl~WvD 224 (250)
+ .|++.|+++..
T Consensus 298 e~~Li~~~li~~~ 310 (328)
T PRK00080 298 EPYLIQQGFIQRT 310 (328)
T ss_pred hHHHHHcCCcccC
Confidence 9 99999999743
No 76
>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=81.85 E-value=2.1 Score=37.48 Aligned_cols=117 Identities=15% Similarity=0.218 Sum_probs=35.9
Q ss_pred ccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCC
Q 025599 56 DIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNR 135 (250)
Q Consensus 56 eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~ 135 (250)
+.+++++| ..|=..+.|+-=.+ -|. .++.-.+|-...|+...... ++.|.||-..++
T Consensus 68 e~rE~eEy----~k~K~~f~veeeG~---~~~----~~~~~~~lL~~Fi~yIK~~K-----vv~ledla~~f~------- 124 (188)
T PF09756_consen 68 ERREQEEY----EKWKSAFSVEEEGE---DEE----EEEEESQLLQEFINYIKEHK-----VVNLEDLAAEFG------- 124 (188)
T ss_dssp -------------------------------------------HHHHHHHHHHH-S-----EE-HHHHHHHH--------
T ss_pred HHHHHHHH----HHHHHhccccccch---hHH----HhhHHHHHHHHHHHHHHHcc-----eeeHHHHHHHcC-------
Confidence 44455554 46666667763211 111 12332235555555555433 667888877765
Q ss_pred CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcC
Q 025599 136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLS 202 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~ 202 (250)
++..|++.-|+.|..-|.=.-|+.=.| +||--+|.||. +|-.++..+|.||.++|....|
T Consensus 125 --l~t~~~i~ri~~L~~~g~ltGv~DdrG-kfIyIs~eE~~----~va~fi~~rGRvsi~el~~~~N 184 (188)
T PF09756_consen 125 --LRTQDVINRIQELEAEGRLTGVIDDRG-KFIYISEEEME----AVAKFIKQRGRVSISELAQESN 184 (188)
T ss_dssp --S-HHHHHHHHHHHHHHSSS-EEE-TT---EEE---------------------------------
T ss_pred --CCHHHHHHHHHHHHHCCCceeeEcCCC-CeEEecHHHHH----HHHHHHHHcCCccHHHHHHHHH
Confidence 799999999999999887666665447 58888888885 3667777899999999987654
No 77
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=81.53 E-value=2.6 Score=27.15 Aligned_cols=34 Identities=26% Similarity=0.248 Sum_probs=31.0
Q ss_pred CccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 191 FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.+|..+|++.+|.+..-+...|..|.++|++=.+
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 4789999999999999999999999999998554
No 78
>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=81.44 E-value=5.7 Score=27.77 Aligned_cols=43 Identities=21% Similarity=0.353 Sum_probs=35.7
Q ss_pred cchhHHHHHHHHHhCCC------ccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 175 LNKDHNQILELAQAQGF------VTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 175 l~~D~~~vLela~~~g~------vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
|+..|..+|..|=..|| +|.++|++.+|.++.=+-..|...++
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 56778899999988887 78999999999999887777765543
No 79
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=81.44 E-value=1.8 Score=42.07 Aligned_cols=124 Identities=24% Similarity=0.419 Sum_probs=83.8
Q ss_pred HHHhhcHhHHHHH---------HHHHHHHHHHHHHHHHHHHHhccccccc------------ChhHHHHHHHH-------
Q 025599 19 QYRLLGENVAKLR---------TDLMKEQLATFRSQLEDFARKHKNDIRK------------NPTFRSQFHEM------- 70 (250)
Q Consensus 19 ~~~~~g~~l~~~~---------~~~l~~qL~~F~~~L~~Fa~~h~~eI~~------------dp~fR~~F~~m------- 70 (250)
+|+..|.+++.-- .-.|.+.|..+|+.+. +..++.|++ ||.=-.-|.-+
T Consensus 252 RftQAGsEVSalLGr~PSavGYQpTLatemg~lQERIt---stk~GSITSiQavyvPaDDlTDPapattFaHLDat~vLs 328 (468)
T COG0055 252 RFTQAGSEVSALLGRMPSAVGYQPTLATEMGQLQERIT---STKKGSITSVQAVYVPADDLTDPAPATTFAHLDATTVLS 328 (468)
T ss_pred HHhhcchHHHHHhccCccccccCchhHHHHHHHHHHHh---cCCCCceEEEEEEEeccccCCCcchhhhhhhcccceeee
Confidence 5667776665311 0157788888888774 466677764 77655556433
Q ss_pred --HHHcC----CCCCCCCCcccccccc---cccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHH
Q 025599 71 --CAKVG----VDPLASNKGFWAELLG---IGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSED 141 (250)
Q Consensus 71 --C~siG----VDPL~s~k~~ws~~lG---~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~ 141 (250)
.+++| ||||.|++ .+|- +|+=+|++|.++-.+.+.. .+|.|++..+ | ++++|++
T Consensus 329 R~ia~~GIyPAvDPL~StS----r~l~p~ivGe~Hy~va~~vq~iLqrY-------keLqDIIaIL----G--mdELsee 391 (468)
T COG0055 329 RQIAALGIYPAVDPLDSTS----RALDPKIVGEEHYEVAREVQSILQRY-------KELQDIIAIL----G--MDELSEE 391 (468)
T ss_pred HhHHhcCCCcccCcccccc----cccCcccccHHHHHHHHHHHHHHHHH-------HHHHHHHHHh----C--chhcChh
Confidence 45667 59999773 3443 6899999999999999984 3456665554 3 6899999
Q ss_pred H---HHHHHhhccccCCCeEEEEE
Q 025599 142 D---CLRAISKLKVLGNGYEVISV 162 (250)
Q Consensus 142 D---I~rAik~L~~LG~g~~vi~i 162 (250)
| |.||-+.=+=|.-+|-+-..
T Consensus 392 dk~~V~rArki~~FlSQpF~vAE~ 415 (468)
T COG0055 392 DKLTVARARKIQRFLSQPFFVAEV 415 (468)
T ss_pred HHHHHHHHHHHHHHhcCcchhhhe
Confidence 9 55666655667777765443
No 80
>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=80.59 E-value=3.8 Score=35.46 Aligned_cols=45 Identities=24% Similarity=0.243 Sum_probs=40.1
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
..||.+....|.+|+.+|++.+|.+..-+...|+.|+++|++=..
T Consensus 4 ~~IL~~L~~~~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQGQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 458887776677999999999999999999999999999998765
No 81
>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=80.45 E-value=3 Score=31.52 Aligned_cols=38 Identities=24% Similarity=0.323 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
...+|.+...+.-||++.|+..+||+.++.+.+|..+-
T Consensus 26 ~r~LLr~LA~G~PVt~~~LA~a~g~~~e~v~~~L~~~p 63 (77)
T PF12324_consen 26 LRPLLRLLAKGQPVTVEQLAAALGWPVEEVRAALAAMP 63 (77)
T ss_dssp HHHHHHHHTTTS-B-HHHHHHHHT--HHHHHHHHHH-T
T ss_pred HHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHhCC
Confidence 33456666667889999999999999999999998874
No 82
>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=80.22 E-value=2.2 Score=42.35 Aligned_cols=76 Identities=26% Similarity=0.396 Sum_probs=46.0
Q ss_pred HHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccc----cc------cccccchh-hhHHHHHHHhhhhcc
Q 025599 44 SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWA----EL------LGIGDFYY-ELGVQIVEICLATRP 112 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws----~~------lG~gdfy~-eLavqIvevC~~tr~ 112 (250)
..|..++++.+..|+.+|..|+-|.. +=.|+....-+-. ++ -|...||- +||.+|++...+
T Consensus 121 ~~la~~l~~~~~~l~~~~~~~~~f~~-----~G~~~~~Gd~l~~p~LA~TL~~ia~~G~~~FY~G~lA~~iv~~~~~--- 192 (510)
T PF01019_consen 121 PSLARALARNADKLRRDPGSRALFLP-----DGRPPREGDILRQPELADTLERIAEEGPDAFYRGELAEKIVADVQA--- 192 (510)
T ss_dssp HHHHHHHHHHHHHHTTSHHHHHHHST-----TSSE--TTSEE--HHHHHHHHHHHHHTTHHHHSCHHHHHHHHHHHH---
T ss_pred hhHHhHHHhHHHHHhhhhhHHHHhcc-----CCCcCCCCCEEEHHHHHHHHHHHHhcCchhhcCChHHHHHHHHHHh---
Confidence 57777788888888999999877743 1123332211100 01 25668888 799999998665
Q ss_pred cCCCceeHHHHHHHHH
Q 025599 113 HNGGLINLQELCNLLR 128 (250)
Q Consensus 113 ~nGGli~l~el~~~v~ 128 (250)
+||+|+++|+-..-.
T Consensus 193 -~GG~lt~~Dla~Y~~ 207 (510)
T PF01019_consen 193 -NGGLLTLEDLAAYQV 207 (510)
T ss_dssp -TT-S--HHHHHH---
T ss_pred -ccCCccHHHHhhcCC
Confidence 899999999976533
No 83
>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=80.05 E-value=5.9 Score=26.14 Aligned_cols=38 Identities=21% Similarity=0.251 Sum_probs=30.8
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
..++|.+.+..|-.|..+|.+.+|+|..-+..++..|.
T Consensus 5 D~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 5 DRKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 34688888988999999999999999999999998763
No 84
>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=80.05 E-value=4.7 Score=34.49 Aligned_cols=52 Identities=25% Similarity=0.458 Sum_probs=44.6
Q ss_pred cchhHHHHHHHHHh----CCC-ccHHHHHHhcCCC-hHHHHHHHHHHHHcCCceeecC
Q 025599 175 LNKDHNQILELAQA----QGF-VTVDEVERRLSWT-SGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 175 l~~D~~~vLela~~----~g~-vt~~~L~~~l~W~-~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
|+.-|..||++.+. .|+ .|+.+|++.+|-+ +.-+...|..|+++|++=.++.
T Consensus 4 lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 4 LTARQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred cCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCC
Confidence 67789999998883 455 8899999999998 9999999999999999877643
No 85
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=79.42 E-value=6.9 Score=31.59 Aligned_cols=56 Identities=20% Similarity=0.148 Sum_probs=46.1
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~ 238 (250)
..||.+....|.+++.+|.+.++-+..-+-.-|..|.+.|+++...+. ...||..+
T Consensus 19 l~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~G---r~~~Y~l~ 74 (117)
T PRK10141 19 LGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQG---KWVHYRLS 74 (117)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEc---CEEEEEEC
Confidence 346766665678999999999999999999999999999999999876 45555433
No 86
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=78.98 E-value=3.2 Score=33.16 Aligned_cols=44 Identities=23% Similarity=0.233 Sum_probs=36.1
Q ss_pred hHHHHHHHHHh---CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 178 DHNQILELAQA---QGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 178 D~~~vLela~~---~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
||...=.+..+ --+||++.|.+.+...-..|+.+|.+|..+|++
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 45444444443 468999999999999999999999999999986
No 87
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=78.75 E-value=9.4 Score=33.16 Aligned_cols=56 Identities=20% Similarity=0.189 Sum_probs=47.6
Q ss_pred CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|-.|+.-|-.||..+...+.+|.++|++.++-++.-+-..|+.|++.|++-+-...
T Consensus 40 ~~gLt~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~ 95 (185)
T PRK13777 40 PYDLNINEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKE 95 (185)
T ss_pred HCCCCHHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCC
Confidence 34567778889988887788999999999999998899999999999999876444
No 88
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=78.68 E-value=3.2 Score=33.10 Aligned_cols=40 Identities=23% Similarity=0.144 Sum_probs=34.9
Q ss_pred hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 188 AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 188 ~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
...+||+..|.+.+|.....|+.+|.+|..+|.+=.=++.
T Consensus 56 ~~r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~lvskn 95 (107)
T COG4901 56 RERVVTPYVLASRYGINGSVARIVLRHLEEEGVVQLVSKN 95 (107)
T ss_pred cceeecHHHHHHHhccchHHHHHHHHHHHhCCceeeeccC
Confidence 3679999999999999999999999999999987544443
No 89
>PF13730 HTH_36: Helix-turn-helix domain
Probab=78.59 E-value=9.6 Score=25.60 Aligned_cols=48 Identities=17% Similarity=0.208 Sum_probs=36.3
Q ss_pred ccchhHHHHHHHHH----h--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 174 ELNKDHNQILELAQ----A--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 174 El~~D~~~vLela~----~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.|+.....|+-... . .-|.|.+.|++.+|-++.-++.+|..|++.|++
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 35555555543322 1 245689999999999999999999999999975
No 90
>PRK10870 transcriptional repressor MprA; Provisional
Probab=78.43 E-value=9.4 Score=32.45 Aligned_cols=55 Identities=15% Similarity=0.084 Sum_probs=45.1
Q ss_pred ccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCC
Q 025599 174 ELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHR 228 (250)
Q Consensus 174 El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~ 228 (250)
.|+.-|-.+|-.... .+.+|+.+|++.+++++.-+-..++.|++.|++=+-....
T Consensus 52 gLt~~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~ 108 (176)
T PRK10870 52 GINETLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDN 108 (176)
T ss_pred CCCHHHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 345557677766653 5789999999999999999999999999999998865553
No 91
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=77.65 E-value=8.3 Score=40.68 Aligned_cols=96 Identities=17% Similarity=0.224 Sum_probs=68.9
Q ss_pred eHHHHHHHHHhhc-CCCCCCCCHHHHHHHHhhccccCC-Ce-EEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHH
Q 025599 119 NLQELCNLLRQRR-KSNREAVSEDDCLRAISKLKVLGN-GY-EVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVD 195 (250)
Q Consensus 119 ~l~el~~~v~k~R-~~~~~~IS~~DI~rAik~L~~LG~-g~-~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~ 195 (250)
++.+|..++.++- ......+|+-.++.=+.+|..++. +| -|.+.+|+-|| +|..|- ..|-.....+|.|++-
T Consensus 4 Ei~eLq~~fq~aQ~~~ss~rLSErNcIEiV~KLie~~~ld~dll~T~DGKEYi--T~~qL~---~EI~~El~~gGRvnlv 78 (803)
T PLN03083 4 ELLELQRQFEFAQQAKSSVRLSERNVVELVQKLQELGIIDFDLLHTVSGKEYI--TQDQLR---NEIEAEIKKLGRVSLV 78 (803)
T ss_pred HHHHHHHHHHHHHHHHhhhhcchhhHHHHHHHHHHhcccCcceEEecCCceee--CHHHHH---HHHHHHHHhCCCeeHH
Confidence 4667777777632 233578999999999999987772 22 35555788665 354553 2232222458999999
Q ss_pred HHHHhcCCChHHHHHHHHHHHHcC
Q 025599 196 EVERRLSWTSGRAIDALDILLEEG 219 (250)
Q Consensus 196 ~L~~~l~W~~~Ra~~~L~~l~~~G 219 (250)
+|...+|.+...+...+..+++++
T Consensus 79 dLa~~LnVD~~hiEr~~~~iv~~d 102 (803)
T PLN03083 79 DLADTIGVDLYHVERQAQQVVSDD 102 (803)
T ss_pred HHhhhcCCCHHHHHHHHHHHhcCC
Confidence 999999999999999999988763
No 92
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=77.51 E-value=5.7 Score=29.26 Aligned_cols=40 Identities=23% Similarity=0.246 Sum_probs=31.9
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.||+.++ .|..+.+.|....+-+..+++..|+.|+..|++
T Consensus 10 ~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI 49 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLI 49 (77)
T ss_dssp HHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCe
Confidence 4677776 688899999999999999999999999999999
No 93
>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=77.24 E-value=3.9 Score=27.81 Aligned_cols=30 Identities=27% Similarity=0.277 Sum_probs=28.0
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.|..+|++.++.+..-+..+|..|.+.|++
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i 55 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLV 55 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 469999999999999999999999999974
No 94
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=76.86 E-value=7.9 Score=28.89 Aligned_cols=56 Identities=30% Similarity=0.447 Sum_probs=42.2
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF 236 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~ 236 (250)
.|+.+....+.++..+|++.+|-+.......|..|+.+|++=+.....++.+.-|+
T Consensus 4 ~Il~~L~~~~~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~ 59 (80)
T PF13601_consen 4 AILALLYANEEATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWY 59 (80)
T ss_dssp HHHHHHHHHSEEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEE
T ss_pred HHHHHHhhcCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEE
Confidence 45666566788999999999999999999999999999999998776443345444
No 95
>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=76.40 E-value=11 Score=28.18 Aligned_cols=60 Identities=20% Similarity=0.308 Sum_probs=47.3
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHH--HHcCCceeecCCCCCCccee
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDIL--LEEGLAMVDDGHRDRKRRYW 235 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l--~~~Gl~WvD~q~~~~e~~Yw 235 (250)
++-|..++++...-+..|+.+|.+..||...-++.+|--+ -+.|+.-.-+-.+++...|.
T Consensus 9 ~tKqa~li~mL~rp~GATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~s~k~~g~~r~Yr 70 (72)
T PF11994_consen 9 GTKQAQLIAMLRRPEGATIAEICEATGWQPHTVRGALSGLLKKKLGLTITSEKVDGGGRRYR 70 (72)
T ss_pred ccHHHHHHHHHcCCCCCCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEEeeecCCCeeeEe
Confidence 4557779999887777899999999999999999999988 55688776665543356664
No 96
>PRK00215 LexA repressor; Validated
Probab=76.00 E-value=15 Score=31.44 Aligned_cols=53 Identities=21% Similarity=0.288 Sum_probs=43.7
Q ss_pred cchhHHHHHHHHHh-----CCCccHHHHHHhcCC-ChHHHHHHHHHHHHcCCceeecCC
Q 025599 175 LNKDHNQILELAQA-----QGFVTVDEVERRLSW-TSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 175 l~~D~~~vLela~~-----~g~vt~~~L~~~l~W-~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|+..|..+|++... .-..|..+|++.+|+ ++.-+...|..|+++|++=.+...
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 45668888887652 334799999999999 999999999999999999776544
No 97
>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=75.16 E-value=4.3 Score=28.51 Aligned_cols=36 Identities=22% Similarity=0.187 Sum_probs=31.0
Q ss_pred CCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 190 GFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 190 g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-.+ |..+|++.++-+..-++++|..|..+|++-+-.
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEEC
Confidence 467 999999999999999999999999999987664
No 98
>PRK09615 ggt gamma-glutamyltranspeptidase; Reviewed
Probab=74.99 E-value=7.1 Score=39.66 Aligned_cols=33 Identities=33% Similarity=0.502 Sum_probs=28.0
Q ss_pred ccccchh-hhHHHHHHHhhhhcccCCCceeHHHHHHHH
Q 025599 91 GIGDFYY-ELGVQIVEICLATRPHNGGLINLQELCNLL 127 (250)
Q Consensus 91 G~gdfy~-eLavqIvevC~~tr~~nGGli~l~el~~~v 127 (250)
|...||. ++|.+|++.+.+ +||+|+++||-..=
T Consensus 239 G~~~FY~G~iA~~iv~~~~~----~GG~lt~~DLa~y~ 272 (581)
T PRK09615 239 GPDAFYKGTIADQIAQEMQK----NGGLITKEDLAAYK 272 (581)
T ss_pred CcccccCCHHHHHHHHHHHH----cCCCCCHHHHhhCC
Confidence 5678888 799999999874 89999999997663
No 99
>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=74.36 E-value=6.1 Score=29.25 Aligned_cols=45 Identities=22% Similarity=0.293 Sum_probs=35.1
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceee
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWF 236 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~ 236 (250)
.+.+|..+|++.++-++...+..|..|.+.|++ .... +..+-|+.
T Consensus 23 ~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli--~s~~-G~~GGy~L 67 (83)
T PF02082_consen 23 GKPVSSKEIAERLGISPSYLRKILQKLKKAGLI--ESSR-GRGGGYRL 67 (83)
T ss_dssp SC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSE--EEET-STTSEEEE
T ss_pred CCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCee--EecC-CCCCceee
Confidence 345999999999999999999999999999994 5433 22466765
No 100
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=74.32 E-value=11 Score=39.21 Aligned_cols=81 Identities=20% Similarity=0.235 Sum_probs=63.6
Q ss_pred HHHHHHHHhhc----------------cccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCC
Q 025599 140 EDDCLRAISKL----------------KVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSW 203 (250)
Q Consensus 140 ~~DI~rAik~L----------------~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W 203 (250)
|.||.++.++- +.+|.==-=|.++++++..+| +.-|..++-+-+..-..|.++|++.+|.
T Consensus 553 P~pl~~el~~Y~~~Y~~~K~~RkL~w~~~lG~Veieie~~DRtl~~tV----sp~qA~iI~~Fqek~twt~eelse~l~i 628 (765)
T KOG2165|consen 553 PGPLEAELDKYAEIYEQLKRGRKLQWLKNLGKVEIEIEFEDRTLVLTV----SPEQAAIINLFQEKNTWTLEELSESLGI 628 (765)
T ss_pred ChhHHHHHHHHHHHHHHhccCCeeeeecccCeEEEEEEEcCeEEEEee----CHHHHHHHHHhcCcccccHHHHHHHhCC
Confidence 67777776542 235532222445799999999 5668888888787777899999999999
Q ss_pred ChHHHHHHHHHHHHcCCceee
Q 025599 204 TSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 204 ~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
++.+-+.+|+..++.|.++=-
T Consensus 629 p~~~lrrrL~fWi~~GvL~e~ 649 (765)
T KOG2165|consen 629 PVPALRRRLSFWIQKGVLREE 649 (765)
T ss_pred CHHHHHHHHHHHHHcCeeecC
Confidence 999999999999999999854
No 101
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=73.55 E-value=10 Score=33.75 Aligned_cols=45 Identities=13% Similarity=0.199 Sum_probs=39.1
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
||++....+.+|+++|++.+|.++.-+...|..|+..|++=.|..
T Consensus 19 IL~~l~~~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~ 63 (257)
T PRK15090 19 ILQALGEEREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE 63 (257)
T ss_pred HHHHhhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 666665556799999999999999999999999999999877744
No 102
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=73.11 E-value=12 Score=29.15 Aligned_cols=54 Identities=26% Similarity=0.243 Sum_probs=46.5
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.++.....||......|-=.+..++..++.+...++.+|+.|++.|++=..+..
T Consensus 4 ~~~~l~~~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 4 ILDPLDLKILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred ccChhHHHHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 345667778988888788899999999999999999999999999999887643
No 103
>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=73.04 E-value=12 Score=28.24 Aligned_cols=54 Identities=11% Similarity=0.138 Sum_probs=38.1
Q ss_pred HHHHHHhhhhcccC--CCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCC
Q 025599 101 VQIVEICLATRPHN--GGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGN 155 (250)
Q Consensus 101 vqIvevC~~tr~~n--GGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~ 155 (250)
+.||+++.+--..| .|.|+..|+...+.+.+.. ...+|++||.+-++.+..=|.
T Consensus 10 ~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~l-g~k~t~~ev~~m~~~~D~d~d 65 (88)
T cd05029 10 GLLVAIFHKYSGREGDKNTLSKKELKELIQKELTI-GSKLQDAEIAKLMEDLDRNKD 65 (88)
T ss_pred HHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhcCCCC
Confidence 45777777666544 4799999999988753221 366899999998887655443
No 104
>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=72.93 E-value=7.4 Score=29.08 Aligned_cols=46 Identities=26% Similarity=0.520 Sum_probs=30.2
Q ss_pred HHHHHHhCCCccHHHHHHhcC---CChHHHHHHHHHHHHcCCceeecCC
Q 025599 182 ILELAQAQGFVTVDEVERRLS---WTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~---W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+++.+..+||||.++|.+.|. +++.....++..|...|+-=+|+..
T Consensus 12 Li~~gK~~G~lT~~eI~~~L~~~~~~~e~id~i~~~L~~~gI~Vvd~~~ 60 (82)
T PF03979_consen 12 LIEKGKKKGYLTYDEINDALPEDDLDPEQIDEIYDTLEDEGIEVVDEEE 60 (82)
T ss_dssp HHHHHHHHSS-BHHHHHHH-S-S---HHHHHHHHHHHHTT----B--S-
T ss_pred HHHHHhhcCcCCHHHHHHHcCccCCCHHHHHHHHHHHHHCCCEEecCCC
Confidence 455566799999999999875 8999999999999999999999543
No 105
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=72.90 E-value=54 Score=28.51 Aligned_cols=85 Identities=25% Similarity=0.307 Sum_probs=66.0
Q ss_pred CHHHHHHHHhhccc--cCCCeEEEEECCEEEEEec--------------C-CccchhHHHHHHHHHhCCCccHHHHHHhc
Q 025599 139 SEDDCLRAISKLKV--LGNGYEVISVGKKKLVRSV--------------P-TELNKDHNQILELAQAQGFVTVDEVERRL 201 (250)
Q Consensus 139 S~~DI~rAik~L~~--LG~g~~vi~ig~~~~v~sv--------------p-~El~~D~~~vLela~~~g~vt~~~L~~~l 201 (250)
...++..++..|+. =+.|+.++.+++..-.++. | .+||.-...+|.++.-+--||-+++.+-.
T Consensus 37 ~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t~~~~~~~~~~l~~~~~~~~LSraalEtLAiIAY~QPiTR~eI~~iR 116 (184)
T COG1386 37 SADAIIDALAELKEEYEDRGLELVEVAEGWRLQTKQEYAEYLEKLQEQRPKRELSRAALETLAIIAYKQPVTRSEIEEIR 116 (184)
T ss_pred chHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEehHHHHHHHHHHhcccccccccHHHHHHHHHHHHcCCccHHHHHHHh
Confidence 56677777777764 5788999999875555552 3 36998888889888865669999999999
Q ss_pred CCChHHHHHHHHHHHHcCCceeecC
Q 025599 202 SWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 202 ~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
|-...+ ++..|+..|++..-..
T Consensus 117 Gv~~~~---~i~~L~e~glI~~~g~ 138 (184)
T COG1386 117 GVAVSQ---VISTLLERGLIREVGR 138 (184)
T ss_pred CccHHH---HHHHHHHCCCeEecCC
Confidence 987776 8888999998887654
No 106
>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=72.80 E-value=7 Score=29.99 Aligned_cols=52 Identities=19% Similarity=0.313 Sum_probs=38.5
Q ss_pred hhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCe
Q 025599 96 YYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGY 157 (250)
Q Consensus 96 y~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~ 157 (250)
...+..+|.++|.......-| +++.+|...+ + ++++||..||..|..-|-=|
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~G-v~v~~I~~~l----~-----~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEG-VHVDEIAQQL----G-----MSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp S-HHHHHHHHHHHC----TTT-EEHHHHHHHS----T-----S-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHhcCCCCCc-ccHHHHHHHh----C-----cCHHHHHHHHHHHHhCCeEe
Confidence 467899999999994444445 8899999887 2 79999999999998877533
No 107
>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=72.77 E-value=9.6 Score=35.11 Aligned_cols=122 Identities=20% Similarity=0.278 Sum_probs=78.3
Q ss_pred HHHHHHHcCCCCCCCCCcccccccccccch--hhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHH
Q 025599 67 FHEMCAKVGVDPLASNKGFWAELLGIGDFY--YELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCL 144 (250)
Q Consensus 67 F~~mC~siGVDPL~s~k~~ws~~lG~gdfy--~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~ 144 (250)
...++..=.+|-+.|..| ..|+ -+|..+|.+-|.. +||=+++.||-..+| |..+.|.
T Consensus 30 v~kL~~~~~ldli~T~dG--------keyiT~~~L~~EI~~el~~----~gGRv~~~dL~~~Ln---------Vd~~~ie 88 (272)
T PF09743_consen 30 VNKLIEKKLLDLIHTTDG--------KEYITPEQLEKEIKDELYV----HGGRVNLVDLAQALN---------VDLDHIE 88 (272)
T ss_pred HHHHHHcCCeeEEEECCC--------CEEECHHHHHHHHHHHHHH----cCCceEHHHHHHhcC---------cCHHHHH
Confidence 445666667786655533 1222 3677888866654 699999999976654 8999999
Q ss_pred HHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHH-HHHHH
Q 025599 145 RAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAI-DALDI 214 (250)
Q Consensus 145 rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~-~~L~~ 214 (250)
+.++.+-.=..++.+ ++|. ++..-. ++.=-..+-+..+..|.||+++|+..++-+.+-.+ ..+..
T Consensus 89 ~~~~~i~~~~~~~~l--~~ge-lit~~Y--ld~l~~Eine~Lqe~G~vsi~eLa~~~~Lp~efl~~~li~~ 154 (272)
T PF09743_consen 89 RRAQEIVKSDKSLQL--VQGE-LITDSY--LDSLAEEINEKLQESGQVSISELAKQYDLPSEFLKEELISK 154 (272)
T ss_pred HHHHHHHhCCCcEEE--ECCE-EccHHH--HHHHHHHHHHHHHHcCeEeHHHHHHhcCCcHHHHHHHHhhh
Confidence 999998765555543 2343 111110 11001223334456899999999999999998888 44443
No 108
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=72.71 E-value=11 Score=33.80 Aligned_cols=47 Identities=26% Similarity=0.340 Sum_probs=39.8
Q ss_pred HHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 181 QILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 181 ~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.||++... .+.+|..+|++.+|-++.-+..-|..|+..|++..|+..
T Consensus 8 ~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~ 55 (246)
T COG1414 8 AILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPED 55 (246)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 46666554 333899999999999999999999999999999999754
No 109
>PRK11050 manganese transport regulator MntR; Provisional
Probab=72.61 E-value=10 Score=31.52 Aligned_cols=44 Identities=20% Similarity=0.253 Sum_probs=37.3
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
++.+....|.+|..+|++.++++..-....|..|++.|++..+.
T Consensus 42 I~~~l~~~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~ 85 (152)
T PRK11050 42 IADLIAEVGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRP 85 (152)
T ss_pred HHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 33455567889999999999999999999999999999876653
No 110
>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=72.33 E-value=8.1 Score=30.80 Aligned_cols=38 Identities=18% Similarity=0.180 Sum_probs=33.5
Q ss_pred HHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 184 ELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 184 ela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.+++. .+.+|+.+|++.++-+..-+..+|..|.+.|++
T Consensus 17 ~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli 55 (130)
T TIGR02944 17 TLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIV 55 (130)
T ss_pred HHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcE
Confidence 34443 568999999999999999999999999999987
No 111
>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=71.80 E-value=11 Score=29.76 Aligned_cols=36 Identities=25% Similarity=0.260 Sum_probs=33.2
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.+.+|.++|++.++-+.......|..|.+.|++...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 458999999999999999999999999999998764
No 112
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=71.14 E-value=13 Score=30.44 Aligned_cols=63 Identities=17% Similarity=0.301 Sum_probs=48.9
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHh----cCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERR----LSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA 239 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~----l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l 239 (250)
.++.-...|+++.=..|..|++++.+. ..|+..-.++.|..|+++|++=.+.+. ...+|.|-+
T Consensus 3 ~Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~kdg---r~~~y~pL~ 69 (123)
T COG3682 3 SISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRKKDG---RAFRYSPLL 69 (123)
T ss_pred cccHHHHHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhhhcC---Ceeeeeccc
Confidence 344455567777777899999887754 569999999999999999999888765 466666643
No 113
>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=71.08 E-value=12 Score=26.58 Aligned_cols=42 Identities=24% Similarity=0.374 Sum_probs=33.5
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
+|.+..-..|..|..+|.+..+-+....+.+|-.|++.|++.
T Consensus 17 ~V~~~Ll~~G~ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 17 KVGEVLLSRGRLTLREIVRRTGLSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHC-SEEHHHHHHHHT--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCcCHHHHHHHhCCCHHHHHHHHHHHHHcCCee
Confidence 344444468999999999999999999999999999999875
No 114
>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=70.85 E-value=15 Score=28.19 Aligned_cols=53 Identities=15% Similarity=0.161 Sum_probs=42.0
Q ss_pred ccchhHHHHHH-HHH-------hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 174 ELNKDHNQILE-LAQ-------AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 174 El~~D~~~vLe-la~-------~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
.++.-+..+|- ++. ....+|.++|++.+|-++.-+..+|..|++.|++=++.+
T Consensus 22 ~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~ 82 (95)
T TIGR01610 22 DLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM 82 (95)
T ss_pred CCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC
Confidence 34444555554 553 356799999999999999999999999999999977653
No 115
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=70.65 E-value=1.3e+02 Score=30.79 Aligned_cols=114 Identities=16% Similarity=0.106 Sum_probs=78.9
Q ss_pred cccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEec
Q 025599 92 IGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSV 171 (250)
Q Consensus 92 ~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~sv 171 (250)
.++-+-++..+|.+.+. . ---.+.|++..++ +.+++..+.++.|-.-| .++.+++..|+-
T Consensus 487 ~~~~~~~~~~~l~~~~~-~-----~p~~~~~~~~~l~---------~~~~~~~~~l~~l~~~g---~lv~l~~~~~~~-- 546 (614)
T PRK10512 487 FSEEQQALWQKAEPLFG-D-----EPWWVRDLAKETG---------TDEQAMRLTLRQAAQQG---IITAIVKDRYYR-- 546 (614)
T ss_pred CCHHHHHHHHHHHHHHh-c-----CCCCHHHHHHHhC---------CCHHHHHHHHHHHHHCC---CEEEecCCEEEC--
Confidence 35566677777776554 1 1223455554432 56777777787777655 366777443332
Q ss_pred CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+.-+..--..+.++.+..|.+|+.++++.+|-+.-.|...|+.|=+.|+.=++.
T Consensus 547 ~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~g~sRK~~i~lLE~~D~~~~T~r~g 600 (614)
T PRK10512 547 NDRIVQFANMIRELDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRG 600 (614)
T ss_pred HHHHHHHHHHHHHHHhhCCcEeHHHHHHHhCccHHHHHHHHHHhccCCCEEEEC
Confidence 223333345567777778999999999999999999999999999999997764
No 116
>PRK11569 transcriptional repressor IclR; Provisional
Probab=70.41 E-value=11 Score=34.03 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=39.7
Q ss_pred HHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 182 ILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 182 vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
||++... .+-+|.++|++.+|-++.-+...|..|+..|++-.|...
T Consensus 33 IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~ 79 (274)
T PRK11569 33 LLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGEL 79 (274)
T ss_pred HHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 6666553 567999999999999999999999999999999887543
No 117
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=70.38 E-value=8 Score=38.40 Aligned_cols=62 Identities=26% Similarity=0.356 Sum_probs=51.4
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~ 238 (250)
.++.-|..+++++...|++|..+|+..++-+..-+...|..|++.|++=-=.+. ..-||+-.
T Consensus 399 ~~~~~~~~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~g~~---~~g~~~v~ 460 (467)
T COG2865 399 SLSERQEKILELIKENGKVTARELREILGISSETIRRRIANLVKRGLLKQLGSS---GRGTWYVK 460 (467)
T ss_pred ChhHHHHHHHHHHhhccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHhCcC---CCCcEEec
Confidence 355556789999999999999999999999999999999999999998655554 45666643
No 118
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=70.28 E-value=13 Score=33.61 Aligned_cols=46 Identities=17% Similarity=0.263 Sum_probs=39.6
Q ss_pred HHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 182 ILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 182 vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
||++... .+.+|..+|++.+|.++..+-.-|..|+..|++=.|+..
T Consensus 30 IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~ 76 (271)
T PRK10163 30 ILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQL 76 (271)
T ss_pred HHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 6666653 467999999999999999999999999999999777543
No 119
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=70.10 E-value=14 Score=28.04 Aligned_cols=43 Identities=16% Similarity=0.129 Sum_probs=38.2
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
|-++.+.+|.++..+|+..++-+..-.+.-|+.+++.|.+-.=
T Consensus 7 lRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 4455667899999999999999999999999999999999843
No 120
>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=69.99 E-value=8.5 Score=35.17 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=34.3
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|.++..+|++.+|-|+.-+++++..|+..|++=.-.
T Consensus 196 egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 196 EGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred cccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4899999999999999999999999999999987664
No 121
>PHA00738 putative HTH transcription regulator
Probab=69.89 E-value=18 Score=29.00 Aligned_cols=55 Identities=20% Similarity=0.197 Sum_probs=46.3
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecC
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPC 238 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~ 238 (250)
.||++...++..++.+|.+.++.+....-.-|..|...|++-...+. .+.||..+
T Consensus 16 ~IL~lL~~~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~G---r~vyY~Ln 70 (108)
T PHA00738 16 KILELIAENYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEG---RTLYAKIR 70 (108)
T ss_pred HHHHHHHHcCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEEC---CEEEEEEC
Confidence 36776666667999999999999999999999999999999998876 56666543
No 122
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=69.88 E-value=13 Score=36.83 Aligned_cols=53 Identities=23% Similarity=0.377 Sum_probs=48.1
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
.|+.-|..||......|.+|..+|++.++.+..-+-.+++.|.+.|++=+.+.
T Consensus 3 ~Lt~~e~~vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~ 55 (489)
T PRK04172 3 ELHPNEKKVLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEER 55 (489)
T ss_pred CCCHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEee
Confidence 57778889999988888999999999999999999999999999999988753
No 123
>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=69.36 E-value=13 Score=27.17 Aligned_cols=47 Identities=15% Similarity=0.218 Sum_probs=41.5
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.|..+....|..|+++|.+..+-+..-.-.+|-.|.+||.+-++...
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~ 58 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKN 58 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEET
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeC
Confidence 36666777899999999999999999999999999999999999776
No 124
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=69.32 E-value=8.7 Score=34.48 Aligned_cols=43 Identities=9% Similarity=0.027 Sum_probs=38.9
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcC
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEG 219 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G 219 (250)
.-|..|+++.+..|.|++.+|++.+|-|..=++.=|..|++.|
T Consensus 7 eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 7 ERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 4577899999999999999999999999999999999988655
No 125
>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=69.28 E-value=15 Score=27.48 Aligned_cols=42 Identities=19% Similarity=0.277 Sum_probs=35.4
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
.+|..++.+ +.|.++|.+..||++.-.---|..|.++|++=+
T Consensus 9 ~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~R 50 (72)
T PF05584_consen 9 KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIER 50 (72)
T ss_pred HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 355555544 999999999999999999999999999999743
No 126
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=69.05 E-value=22 Score=33.14 Aligned_cols=51 Identities=22% Similarity=0.384 Sum_probs=45.5
Q ss_pred ccchhHHHHHHHHHh-CCC------ccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 174 ELNKDHNQILELAQA-QGF------VTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 174 El~~D~~~vLela~~-~g~------vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.++.|...||+..+. +|+ -|++++.+.+|.|+.-+|.||-.|+++|.+-.|
T Consensus 222 ~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q~ 279 (287)
T COG2996 222 MLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQD 279 (287)
T ss_pred hhhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEEc
Confidence 589999999999885 444 589999999999999999999999999999874
No 127
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=68.85 E-value=12 Score=40.08 Aligned_cols=151 Identities=14% Similarity=0.153 Sum_probs=82.4
Q ss_pred ChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHH-------------h---hhhcccCCCc--eeHH
Q 025599 60 NPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEI-------------C---LATRPHNGGL--INLQ 121 (250)
Q Consensus 60 dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvev-------------C---~~tr~~nGGl--i~l~ 121 (250)
++++-+++-.||..- +.|.-|.... +. +-+||.+|-.+-... | .... ..++- |+..
T Consensus 698 ~~~lLrkYI~YAR~~-~~P~Ls~eA~--~~--i~~~Yv~mR~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~i~iT~R 771 (915)
T PTZ00111 698 DLDMLRMYIKFSKLH-CFPKLSDEAK--KV--ITREYVKMRQGNFQTSNLDELEHAQEDDDDDLYYQS-SGTRMIYVSSR 771 (915)
T ss_pred CHHHHHHHHHHHhcc-CCCCCCHHHH--HH--HHHHHHHHhhhhcccccccccccccccccccccccc-ccCCcccccHH
Confidence 567767888899763 7886554211 11 358999987542211 0 0001 11122 3333
Q ss_pred HHH--HHHHhhcC--CCCCCCCHHHHHHHHhhccc-c-CC------C---eEEEEECCEEEEEecCC-c-cchhHHHHHH
Q 025599 122 ELC--NLLRQRRK--SNREAVSEDDCLRAISKLKV-L-GN------G---YEVISVGKKKLVRSVPT-E-LNKDHNQILE 184 (250)
Q Consensus 122 el~--~~v~k~R~--~~~~~IS~~DI~rAik~L~~-L-G~------g---~~vi~ig~~~~v~svp~-E-l~~D~~~vLe 184 (250)
.|- =||..++. .....|+++|+.+||+.++. | .. | +.++..|. +.+. + +..=...+.+
T Consensus 772 qLEsLIRLsEA~AK~rLs~~Vt~~Dv~~Ai~L~~~sl~~~~~DpetG~iD~d~~~~G~-----s~~~r~~~~~~~~~i~~ 846 (915)
T PTZ00111 772 MISSIIRISVSLARMRLSTVVTPADALQAVQIVKSSTFQSLVDPTTGKIDFDQLHQGI-----TTNKMQQLNQMYEQVLS 846 (915)
T ss_pred HHHHHHHHHHHHhhhcCcCcccHHHHHHHHHHHHHHHhhhcccccCCcccceeeccCC-----cHHHHHHHHHHHHHHHH
Confidence 332 23333332 23578999999999999872 1 11 1 12222121 0010 1 1000111333
Q ss_pred HHHh------CCCccHHHHHHh------------cCCChHHHHHHHHHHHHcCCc
Q 025599 185 LAQA------QGFVTVDEVERR------------LSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 185 la~~------~g~vt~~~L~~~------------l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
+... .+.++.++|.+. .|.+...++++|+.|.++|.+
T Consensus 847 ~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~i~~~~~~~~l~~L~~~g~i 901 (915)
T PTZ00111 847 VLTRSSNQDSNKSLDLNEVLSLCHKTFKDNRDHKDGEIYKLISEVLNKMVQEGTA 901 (915)
T ss_pred HHHhhhccccCCceeHHHHHHHHHhhccccchhccCCCHHHHHHHHHHHHhCCeE
Confidence 3321 257899988744 489999999999999999985
No 128
>PTZ00184 calmodulin; Provisional
Probab=68.46 E-value=53 Score=25.41 Aligned_cols=15 Identities=13% Similarity=0.246 Sum_probs=10.8
Q ss_pred CCCccHHHHHHhcCC
Q 025599 189 QGFVTVDEVERRLSW 203 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W 203 (250)
.|.||.++...-+.|
T Consensus 134 ~g~i~~~ef~~~~~~ 148 (149)
T PTZ00184 134 DGQINYEEFVKMMMS 148 (149)
T ss_pred CCcCcHHHHHHHHhc
Confidence 577888777766665
No 129
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=68.29 E-value=21 Score=31.24 Aligned_cols=39 Identities=23% Similarity=0.291 Sum_probs=35.6
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
++++|+-+|+..+|.++.-+-..|-.|.+.|++..-+..
T Consensus 25 ~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~ 63 (183)
T PHA03103 25 GEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSN 63 (183)
T ss_pred CCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCC
Confidence 689999999999999999999999999999999766554
No 130
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=68.07 E-value=12 Score=31.57 Aligned_cols=49 Identities=24% Similarity=0.372 Sum_probs=39.8
Q ss_pred hhHHH-HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 177 KDHNQ-ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 177 ~D~~~-vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|... |+.+.+..|+++..+|++.++-++.-+.+.|..|.+.|++=.+.
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 34433 34455578999999999999999999999999999999876543
No 131
>PRK14999 histidine utilization repressor; Provisional
Probab=67.25 E-value=7.4 Score=34.25 Aligned_cols=33 Identities=18% Similarity=0.154 Sum_probs=31.4
Q ss_pred cHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 193 TVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 193 t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
|..+|++.+|-+..-++.||+.|+.+|++.+-.
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 999999999999999999999999999998763
No 132
>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=67.12 E-value=16 Score=26.78 Aligned_cols=47 Identities=11% Similarity=0.258 Sum_probs=39.5
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc--eeecC
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA--MVDDG 226 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~--WvD~q 226 (250)
..+..+++....+|.+.|++.++.+.+-++..|-.|+.+|.+ -+|..
T Consensus 13 ~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00088 13 TNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred HHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 346677787888999999999999999999999999999965 45543
No 133
>smart00753 PAM PCI/PINT associated module.
Probab=67.12 E-value=16 Score=26.78 Aligned_cols=47 Identities=11% Similarity=0.258 Sum_probs=39.5
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc--eeecC
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA--MVDDG 226 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~--WvD~q 226 (250)
..+..+++....+|.+.|++.++.+.+-++..|-.|+.+|.+ -+|..
T Consensus 13 ~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~ 61 (88)
T smart00753 13 TNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV 61 (88)
T ss_pred HHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc
Confidence 346677787888999999999999999999999999999965 45543
No 134
>PRK12423 LexA repressor; Provisional
Probab=67.10 E-value=17 Score=31.54 Aligned_cols=53 Identities=21% Similarity=0.311 Sum_probs=43.4
Q ss_pred ccchhHHHHHHHHH----hCCC-ccHHHHHHhcCC-ChHHHHHHHHHHHHcCCceeecC
Q 025599 174 ELNKDHNQILELAQ----AQGF-VTVDEVERRLSW-TSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 174 El~~D~~~vLela~----~~g~-vt~~~L~~~l~W-~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
+|+..|..+|++.. ..|+ -|..+|++.+|- +..-.+..|..|.+.|++=++..
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCC
Confidence 37888999988766 3555 499999999995 78778899999999999977644
No 135
>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=67.10 E-value=24 Score=31.72 Aligned_cols=71 Identities=20% Similarity=0.237 Sum_probs=52.0
Q ss_pred CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHH-HHH--hCCCccHHHHHHhcCCChHHHHHHH
Q 025599 136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILE-LAQ--AQGFVTVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLe-la~--~~g~vt~~~L~~~l~W~~~Ra~~~L 212 (250)
..||.+++..++..+ +-.+ ..++.-+...|. ++. ..+.++.+++++.+|++...+..++
T Consensus 215 ~~it~~~v~~~l~~l---~~~~---------------~~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~ 276 (305)
T TIGR00635 215 KIINRDIALKALEML---MIDE---------------LGLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVY 276 (305)
T ss_pred CCcCHHHHHHHHHHh---CCCC---------------CCCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhh
Confidence 468999999988873 2221 123333444555 444 3556999999999999999999999
Q ss_pred H-HHHHcCCceee
Q 025599 213 D-ILLEEGLAMVD 224 (250)
Q Consensus 213 ~-~l~~~Gl~WvD 224 (250)
+ .|+..|+++..
T Consensus 277 e~~Li~~~li~~~ 289 (305)
T TIGR00635 277 EPYLLQIGFLQRT 289 (305)
T ss_pred hHHHHHcCCcccC
Confidence 9 69999999743
No 136
>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=66.47 E-value=15 Score=27.63 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=19.4
Q ss_pred cChhHHHHH----HHHHHHcCCCCCC
Q 025599 59 KNPTFRSQF----HEMCAKVGVDPLA 80 (250)
Q Consensus 59 ~dp~fR~~F----~~mC~siGVDPL~ 80 (250)
+||+||+++ +..|..+|++...
T Consensus 15 ~Dp~Fr~~Ll~DPraaL~e~G~~~P~ 40 (77)
T TIGR03793 15 EDEAFKQALLTNPKEALEREGVQVPA 40 (77)
T ss_pred cCHHHHHHHHHCHHHHHHHhCCCCCC
Confidence 799999999 8899999999654
No 137
>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=66.11 E-value=24 Score=26.76 Aligned_cols=48 Identities=19% Similarity=0.227 Sum_probs=39.3
Q ss_pred ccchhHHHHHHH-HH----hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 174 ELNKDHNQILEL-AQ----AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 174 El~~D~~~vLel-a~----~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
+|+.-|..||.. ++ ...-|....|++.++|+..-.++.+..|+..|++
T Consensus 1 ~Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlv 53 (78)
T PF03444_consen 1 MLTERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLV 53 (78)
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCc
Confidence 356667777754 22 3677899999999999999999999999999986
No 138
>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=66.09 E-value=8.4 Score=38.52 Aligned_cols=66 Identities=26% Similarity=0.480 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccc----cccchhhhHHHH
Q 025599 34 LMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLG----IGDFYYELGVQI 103 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG----~gdfy~eLavqI 103 (250)
.+++|+...+..+++.-+|...--+.-..++.+|+++|..+||.. +.+-.+++. +-.+|-+++..|
T Consensus 128 ~lkKqi~k~~q~~~d~~kk~~e~~~~~~~~~~~~~~~c~~lGI~G----~nir~ELl~l~~~LP~~~~~i~~~i 197 (507)
T PF05600_consen 128 ALKKQIAKCQQQLEDLDKKEEELQRSAAEARERYKKACKQLGIKG----ENIREELLELVKELPSLFDEIVEAI 197 (507)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhCCcc----chhHHHHHHHHHhhHHHHHHHHHHH
Confidence 789999999999988666655444555579999999999999983 334344332 345554444433
No 139
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=65.58 E-value=20 Score=31.16 Aligned_cols=60 Identities=18% Similarity=0.238 Sum_probs=49.6
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc----eeecCCCCCCcceeecCc
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA----MVDDGHRDRKRRYWFPCA 239 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~----WvD~q~~~~e~~Yw~P~l 239 (250)
...|+++..++|-+|-++|+..+|...--.+.+|..|-.+|++ |+|+-.+ -+..||+++.
T Consensus 20 ~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~-~~~y~w~~~~ 83 (176)
T COG1675 20 AVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESG-WEEYTWYINY 83 (176)
T ss_pred hhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCC-cEEEEEEech
Confidence 5557777778889999999999999999999999999999986 5676653 2677888764
No 140
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=64.64 E-value=9.1 Score=33.69 Aligned_cols=34 Identities=18% Similarity=0.198 Sum_probs=31.5
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-|..+|++.+|-|..=++.||+.|+++|++.+-.
T Consensus 36 PsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 69 (241)
T PRK10079 36 PAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ 69 (241)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4888999999999999999999999999998764
No 141
>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=64.62 E-value=82 Score=27.24 Aligned_cols=73 Identities=22% Similarity=0.272 Sum_probs=54.0
Q ss_pred CCCCHHHHHHHHhhccc-cCCCeEEEEECCEEEEEecCCccchhHHHHHHH-HH------------hCCCccHHHHHHhc
Q 025599 136 EAVSEDDCLRAISKLKV-LGNGYEVISVGKKKLVRSVPTELNKDHNQILEL-AQ------------AQGFVTVDEVERRL 201 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~-LG~g~~vi~ig~~~~v~svp~El~~D~~~vLel-a~------------~~g~vt~~~L~~~l 201 (250)
..++.-+++++++...+ ||- +.-...+|.. .. .--|.|...|+..+
T Consensus 21 ~~~~k~~ll~~l~~a~~~lgl--------------------~~~~l~vL~aLls~~~~~d~~~~~~piVfpSN~~La~r~ 80 (177)
T PF03428_consen 21 AGVTKWQLLRALKEARPALGL--------------------SDRALAVLDALLSFTPPDDWEPGRRPIVFPSNAQLAERL 80 (177)
T ss_pred CCCCHHHHHHHHHHHHHhcCC--------------------ChhHHHHHHHHHHhCCcccccCCCCceeecCHHHHHHHH
Confidence 45999999999999876 331 1112223322 11 12578899999999
Q ss_pred -CCChHHHHHHHHHHHHcCCceeecCCC
Q 025599 202 -SWTSGRAIDALDILLEEGLAMVDDGHR 228 (250)
Q Consensus 202 -~W~~~Ra~~~L~~l~~~Gl~WvD~q~~ 228 (250)
|.+.-..+..|-.|+..|+++..|+.+
T Consensus 81 ~G~s~~tlrR~l~~LveaGLI~rrDS~N 108 (177)
T PF03428_consen 81 NGMSERTLRRHLARLVEAGLIVRRDSPN 108 (177)
T ss_pred cCCCHHHHHHHHHHHHHCCCeeeccCCC
Confidence 999999999999999999999988773
No 142
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=64.26 E-value=23 Score=22.82 Aligned_cols=43 Identities=23% Similarity=0.369 Sum_probs=33.8
Q ss_pred CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
|..|+.++..++.+. ..| .|..++++.+|++..-.+..+..+.
T Consensus 1 ~~~l~~~e~~i~~~~-~~g-~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 1 LASLTPREREVLRLL-AEG-LTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCCCHHHHHHHHHH-HcC-CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 346788888887765 334 5999999999999999988887653
No 143
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=64.03 E-value=9.9 Score=32.86 Aligned_cols=37 Identities=14% Similarity=0.067 Sum_probs=33.5
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+..++..+|++.||-|..-.++||..|..+|++.+-.
T Consensus 32 G~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 32 GARLITKNLAEQLGMSITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred CCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence 4568899999999999999999999999999998753
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=64.02 E-value=8.6 Score=33.54 Aligned_cols=34 Identities=18% Similarity=0.159 Sum_probs=31.4
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-|..+|++.+|-|..=++.||+.|+.+|++=+=.
T Consensus 25 PsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 25 PSEHELMDQYGASRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 4899999999999999999999999999987653
No 145
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=63.97 E-value=18 Score=31.57 Aligned_cols=49 Identities=24% Similarity=0.321 Sum_probs=42.6
Q ss_pred HHHHHHHHHhCC-CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 179 HNQILELAQAQG-FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 179 ~~~vLela~~~g-~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.+.||.+....| -+|+-+++..||.++.-+-..|-.|.+.|++..-+..
T Consensus 6 ~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~~~ 55 (183)
T PHA02701 6 ASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCEDGC 55 (183)
T ss_pred HHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCCCC
Confidence 456888888777 6999999999999999999999999999999765444
No 146
>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=63.85 E-value=8.4 Score=32.91 Aligned_cols=93 Identities=15% Similarity=0.224 Sum_probs=51.9
Q ss_pred HHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHH
Q 025599 48 DFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLL 127 (250)
Q Consensus 48 ~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v 127 (250)
-|..+...|+-+||.+.+.|...-..-|++.-... . .|..-|.||.++-.-+... ...|...+
T Consensus 14 GL~e~kAket~KN~kls~~L~~iI~ea~~~~~~dk-----~---~g~LLy~lAtk~k~~~~~~---------r~~iv~~I 76 (164)
T PF04558_consen 14 GLSEKKAKETLKNKKLSASLKAIINEAGVDSGCDK-----K---QGNLLYQLATKLKPQALPH---------RPFIVKYI 76 (164)
T ss_dssp T--HHHHHHHTTSHHHHHHHHHHHHTS-TT----H-----H---HHHHHHHHHHHHTT---TT---------HHHHHHHH
T ss_pred CCChhhHHHHHhCHHHHHHHHHHHHHhcccCCCCH-----H---HHHHHHHHHHhcCCCcchh---------HHHHHHHH
Confidence 34556677899999999999999999888722211 1 4678889988665544333 34445555
Q ss_pred HhhcCCCCCCCCHHHHHHHHhhccccCC-CeEEEEE
Q 025599 128 RQRRKSNREAVSEDDCLRAISKLKVLGN-GYEVISV 162 (250)
Q Consensus 128 ~k~R~~~~~~IS~~DI~rAik~L~~LG~-g~~vi~i 162 (250)
... ..-|+..|-.|++.|+.-+. ++..-.|
T Consensus 77 ~~g-----klkt~~Ql~AA~~Yl~~~~~~~~d~~~F 107 (164)
T PF04558_consen 77 VDG-----KLKTNLQLDAALKYLKSNPSEPIDVAEF 107 (164)
T ss_dssp HTT-----S--SHHHHHHHHHHHHHHGG-G--HHHH
T ss_pred HhC-----CCCCHHHHHHHHHHHHHCCCCCCCHHHH
Confidence 442 12356666666666655444 4443333
No 147
>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=63.69 E-value=27 Score=23.01 Aligned_cols=43 Identities=19% Similarity=0.280 Sum_probs=33.7
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
.|+.++..|+.+.-.. ..|.+++++.+|.+..+++..+...++
T Consensus 4 ~L~~~er~vi~~~y~~-~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-GLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHHTS-T-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-CCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 5788888888877654 459999999999999999988876543
No 148
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=63.68 E-value=30 Score=29.02 Aligned_cols=68 Identities=15% Similarity=0.271 Sum_probs=57.9
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccC
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASS 241 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~ 241 (250)
-|+.+...+|+++...+-.|..+|++..|=+..-.-.-|..|..-|++-..+......+..||-.+..
T Consensus 61 vLsp~nleLl~~Ia~~~P~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~~gq~k~P~~~y~~l~I 128 (144)
T COG4190 61 VLSPRNLELLELIAQEEPASINELAELVGRDVKNVHRTLSTLADLGLIFFEEDGQRKQPVVWYDELVI 128 (144)
T ss_pred HhChhHHHHHHHHHhcCcccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEecCCcccCceeeccccEE
Confidence 57778888888888888899999999999999999999999999999999874433468899988654
No 149
>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=63.49 E-value=18 Score=27.86 Aligned_cols=47 Identities=30% Similarity=0.372 Sum_probs=38.4
Q ss_pred HHHHHHHh-CCCccHHHHHHhc-----CCChHHHHHHHHHHHHcCCceeecCC
Q 025599 181 QILELAQA-QGFVTVDEVERRL-----SWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 181 ~vLela~~-~g~vt~~~L~~~l-----~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.||++... .+.+|+++|.+.+ +++..=.-..|+.|++.|++=.=+..
T Consensus 5 ~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~ 57 (116)
T cd07153 5 AILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELG 57 (116)
T ss_pred HHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeC
Confidence 47777664 6789999999887 68999999999999999998765443
No 150
>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=63.20 E-value=30 Score=26.21 Aligned_cols=52 Identities=17% Similarity=0.265 Sum_probs=42.6
Q ss_pred ccchhHHHHHHHHHh----CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 174 ELNKDHNQILELAQA----QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 174 El~~D~~~vLela~~----~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|+.|+-.||..++. --+|..+.+.+..|-+..-+...|..|.+.+++-.+.
T Consensus 3 ~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~ 58 (82)
T PF09202_consen 3 YLSKEDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRN 58 (82)
T ss_dssp T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-
T ss_pred cCCHHHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccC
Confidence 578889999999993 4789999999999999999999999999999999954
No 151
>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=63.02 E-value=9.2 Score=33.22 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=30.9
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
-|..+|++.+|-+..=++.||+.|+.+|++=.-
T Consensus 33 PsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~ 65 (238)
T TIGR02325 33 PAEMQLAERFGVNRHTVRRAIAALVERGLLRAE 65 (238)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 499999999999999999999999999998765
No 152
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=62.78 E-value=10 Score=33.27 Aligned_cols=35 Identities=14% Similarity=0.114 Sum_probs=32.6
Q ss_pred CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 191 FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.-|..+|++.||-+..=++.||+.|+.+|++-.-.
T Consensus 33 LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 33 IPTENELCTQYNVSRITIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 47999999999999999999999999999998773
No 153
>PF14848 HU-DNA_bdg: DNA-binding domain
Probab=62.65 E-value=20 Score=28.84 Aligned_cols=52 Identities=21% Similarity=0.365 Sum_probs=40.7
Q ss_pred cCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhcc-----ccCCCeEEEEEC-CEEEEE
Q 025599 113 HNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK-----VLGNGYEVISVG-KKKLVR 169 (250)
Q Consensus 113 ~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~-----~LG~g~~vi~ig-~~~~v~ 169 (250)
.+-|-++++|+..++.+.+ ..+|+.||+.+++.|. -|-+|+.|- +| +...+.
T Consensus 24 ~~~~~~tl~~Ia~~i~~~~----s~~t~~di~~vl~~~~~~~~~~l~~G~sV~-~glg~~sls 81 (124)
T PF14848_consen 24 VSSGTLTLEDIAEEIAKEG----STLTRADIEAVLNALKDEMIEALMNGYSVN-LGLGYFSLS 81 (124)
T ss_pred EecCccCHHHHHHHHHHhC----CCCCHHHHHHHHHHHHHHHHHHHhCCCEEE-cCCEEEEEE
Confidence 5678999999999998763 3589999999999996 378888876 46 443333
No 154
>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=62.54 E-value=11 Score=32.96 Aligned_cols=34 Identities=18% Similarity=0.114 Sum_probs=31.4
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-|..+|++.+|-+..=++.||..|+.+|++-+=.
T Consensus 26 PsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 59 (230)
T TIGR02018 26 PSEHELVAQYGCSRMTVNRALRELTDAGLLERRQ 59 (230)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 3999999999999999999999999999987763
No 155
>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=62.31 E-value=15 Score=33.74 Aligned_cols=77 Identities=19% Similarity=0.369 Sum_probs=49.9
Q ss_pred CHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccchhHHHHHHHHHhCCCccHH-HHHHhcCCChHHHHHHHHHHH
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELNKDHNQILELAQAQGFVTVD-EVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~~~g~vt~~-~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
+++++.+.++.+.. .||..+++. |. ....|-..|-.+.+..| ... .+-.|-+|+...|...+..|.
T Consensus 134 ~~~~~~~~~~~~~~--~Gf~~iKik~g~--------~~~~d~~~v~~lr~~~g--~~~l~vD~n~~~~~~~A~~~~~~l~ 201 (316)
T cd03319 134 TPEAMAAAAKKAAK--RGFPLLKIKLGG--------DLEDDIERIRAIREAAP--DARLRVDANQGWTPEEAVELLRELA 201 (316)
T ss_pred CHHHHHHHHHHHHH--cCCCEEEEEeCC--------ChhhHHHHHHHHHHhCC--CCeEEEeCCCCcCHHHHHHHHHHHH
Confidence 67888888877754 468888875 32 12333322333333344 111 122367899999999999999
Q ss_pred HcCCceeecCC
Q 025599 217 EEGLAMVDDGH 227 (250)
Q Consensus 217 ~~Gl~WvD~q~ 227 (250)
..|+.|+.+-.
T Consensus 202 ~~~l~~iEeP~ 212 (316)
T cd03319 202 ELGVELIEQPV 212 (316)
T ss_pred hcCCCEEECCC
Confidence 99999998544
No 156
>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=62.00 E-value=24 Score=24.91 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=34.4
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
++++.. .++.|.++|++.+|-+..-+...|..|.+.|+.=.
T Consensus 5 il~~L~-~~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~ 45 (69)
T TIGR00122 5 LLALLA-DNPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVL 45 (69)
T ss_pred HHHHHH-cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 555544 45789999999999999999999999999998433
No 157
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=61.86 E-value=11 Score=33.50 Aligned_cols=36 Identities=28% Similarity=0.375 Sum_probs=32.8
Q ss_pred CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 191 FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
--|..+|++.+|-|..=++.||..|+.+|++.+-.-
T Consensus 31 LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G 66 (236)
T COG2188 31 LPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQG 66 (236)
T ss_pred CCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEec
Confidence 368899999999999999999999999999998743
No 158
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=61.64 E-value=21 Score=26.98 Aligned_cols=50 Identities=18% Similarity=0.252 Sum_probs=37.6
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+.+...++.++ ...|+|=+.|.+.||.+..-.-..++.|.++|+= ||...
T Consensus 5 ~~~~~~ll~~~-~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~-I~s~~ 54 (79)
T COG1654 5 SQMLLLLLLLL-TGNFVSGEKLAEELGISRTAVWKHIQQLREEGVD-IESVR 54 (79)
T ss_pred HHHHHHHHHHc-CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCc-eEecC
Confidence 33343333332 4569999999999999999999999999999963 55444
No 159
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=61.51 E-value=10 Score=33.41 Aligned_cols=33 Identities=15% Similarity=0.113 Sum_probs=30.8
Q ss_pred cHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 193 TVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 193 t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
|..+|++.+|-+..=++.||+.|+.+|++=+=.
T Consensus 31 sE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVEQQILESIQ 63 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 899999999999999999999999999987653
No 160
>PRK13239 alkylmercury lyase; Provisional
Probab=61.29 E-value=16 Score=32.56 Aligned_cols=47 Identities=17% Similarity=0.206 Sum_probs=36.8
Q ss_pred hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
=+..+|.+...+.-||+++|...+||+.+.++.+|+.|- ... .|++.
T Consensus 23 ~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~--~~~-~d~~g 69 (206)
T PRK13239 23 LLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP--DTE-YDEDG 69 (206)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC--CeE-ECCCC
Confidence 355566666677889999999999999999999999873 333 46654
No 161
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.61 E-value=27 Score=27.24 Aligned_cols=66 Identities=21% Similarity=0.298 Sum_probs=45.6
Q ss_pred cchhHHHH--HHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee-----------cCCC-------CCCc
Q 025599 175 LNKDHNQI--LELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD-----------DGHR-------DRKR 232 (250)
Q Consensus 175 l~~D~~~v--Lela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD-----------~q~~-------~~e~ 232 (250)
||..|... -|+.+ ..--+|.++++..|+|+....+..|..--+--.+|+= -|+| +.-.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lekil~~tqr~~dvW~lRd~l~~~i~e~GqtP~PfT~Lsgdk~ 82 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKILQVTQRPADVWRLRDFLVQAIRESGQTPVPFTALSGDKH 82 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHHHHHhhccchhHHHHHHHHHHHHhcCCCCCCeeeecCccc
Confidence 45555443 34444 3577999999999999999999988766666666642 3444 2247
Q ss_pred ceeecCcc
Q 025599 233 RYWFPCAS 240 (250)
Q Consensus 233 ~Yw~P~l~ 240 (250)
.|||-++-
T Consensus 83 ~yWFl~~~ 90 (97)
T COG4367 83 QYWFLSWT 90 (97)
T ss_pred cceeeccc
Confidence 89998764
No 162
>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=60.58 E-value=19 Score=29.12 Aligned_cols=40 Identities=25% Similarity=0.330 Sum_probs=34.5
Q ss_pred HHHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 182 ILELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 182 vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
++.+|. ..+.+|.++|++.++.+..-.+..|..|.+.|++
T Consensus 14 l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv 55 (135)
T TIGR02010 14 MLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLV 55 (135)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCce
Confidence 455565 2457999999999999999999999999999976
No 163
>PRK03187 tgl transglutaminase; Provisional
Probab=60.55 E-value=15 Score=34.05 Aligned_cols=43 Identities=30% Similarity=0.579 Sum_probs=30.6
Q ss_pred CCCCCC-CcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCC
Q 025599 77 DPLASN-KGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSN 134 (250)
Q Consensus 77 DPL~s~-k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~ 134 (250)
||-++. .|-|+-.|| +++||..+. ||++-++++..||+.|...
T Consensus 180 ~p~tp~WqGeNaiyLg-n~~yyGHGi--------------GI~t~~~iI~~LN~~R~~~ 223 (272)
T PRK03187 180 NPATPEWQGENVIYLG-NGLYYGHGI--------------GIKTAEEIIYALNERRKPG 223 (272)
T ss_pred CCCCCcccceeEEEec-CCceeeccc--------------ccccHHHHHHHHHhccCCC
Confidence 665433 455555677 557776543 9999999999999988643
No 164
>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=60.39 E-value=22 Score=26.29 Aligned_cols=40 Identities=18% Similarity=0.319 Sum_probs=34.3
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
+..++..-..++.+.+++.++++...++..|..|+.+|.+
T Consensus 51 l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i 90 (105)
T PF01399_consen 51 LRQLSKPYSSISISEIAKALQLSEEEVESILIDLISNGLI 90 (105)
T ss_dssp HHHHHHC-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHhcccchHHHHHHhccchHHHHHHHHHHHHCCCE
Confidence 3455555678999999999999999999999999999986
No 165
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=60.11 E-value=22 Score=33.62 Aligned_cols=52 Identities=21% Similarity=0.210 Sum_probs=45.0
Q ss_pred ccchhHHHHHH-----HHHhCCCccHHHHHHh--cCCChHHHHHHHHHHHHcCCceeec
Q 025599 174 ELNKDHNQILE-----LAQAQGFVTVDEVERR--LSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 174 El~~D~~~vLe-----la~~~g~vt~~~L~~~--l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|+.-|..||. +++..+.|+...|++. +++|..-.+.-+..|++.|++=.-.
T Consensus 3 ~l~~R~~~Il~~IV~~yi~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~h 61 (339)
T PRK00082 3 MLDERQREILRAIVEDYIATGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKPH 61 (339)
T ss_pred ccCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCCc
Confidence 56777888997 6777899999999955 9999999999999999999987543
No 166
>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=59.96 E-value=13 Score=26.97 Aligned_cols=49 Identities=20% Similarity=0.215 Sum_probs=35.2
Q ss_pred HHHHHHHHHhCCCccHHHHH--HhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 179 HNQILELAQAQGFVTVDEVE--RRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~--~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
...||++....|-.|+-.++ ..++-++-..-.+|-.|.++|.++.....
T Consensus 6 ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~ 56 (66)
T PF02295_consen 6 EEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGT 56 (66)
T ss_dssp HHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSS
T ss_pred HHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCC
Confidence 45688888865544444444 45555578888999999999999987654
No 167
>PLN02964 phosphatidylserine decarboxylase
Probab=59.51 E-value=27 Score=36.15 Aligned_cols=93 Identities=13% Similarity=0.280 Sum_probs=55.8
Q ss_pred HHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcC-CCCCCCCCcccccccccccchhhhHHHHHHHhhhhccc
Q 025599 35 MKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVG-VDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPH 113 (250)
Q Consensus 35 l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siG-VDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~ 113 (250)
+++|++.+++.+..|-.++.+.| +...+.++| .+|-.....||. ++++.. -..
T Consensus 138 ~~kqi~elkeaF~lfD~dgdG~i---------Lg~ilrslG~~~pte~e~~fi~--------------~mf~~~---D~D 191 (644)
T PLN02964 138 VTQEPESACESFDLLDPSSSNKV---------VGSIFVSCSIEDPVETERSFAR--------------RILAIV---DYD 191 (644)
T ss_pred cHHHHHHHHHHHHHHCCCCCCcC---------HHHHHHHhCCCCCCHHHHHHHH--------------HHHHHh---CCC
Confidence 45677888888888888777665 556777888 476542222222 222221 112
Q ss_pred CCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCe
Q 025599 114 NGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGY 157 (250)
Q Consensus 114 nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~ 157 (250)
+-|.|+++|+...+.+.. ...+++||..|.+.+..=|.|+
T Consensus 192 gdG~IdfdEFl~lL~~lg----~~~seEEL~eaFk~fDkDgdG~ 231 (644)
T PLN02964 192 EDGQLSFSEFSDLIKAFG----NLVAANKKEELFKAADLNGDGV 231 (644)
T ss_pred CCCeEcHHHHHHHHHHhc----cCCCHHHHHHHHHHhCCCCCCc
Confidence 347888888877776531 2356666777766666555543
No 168
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=58.96 E-value=33 Score=31.05 Aligned_cols=51 Identities=20% Similarity=0.196 Sum_probs=43.4
Q ss_pred cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 175 LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 175 l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
|+....+++-..=..|-.|+.++++..|-+..|.-.+|+.|++.|++=+-.
T Consensus 14 lt~yEa~vY~aLl~~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~ 64 (247)
T COG1378 14 LTEYEAKVYLALLCLGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIE 64 (247)
T ss_pred CCHHHHHHHHHHHHhCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeC
Confidence 466666676555556899999999999999999999999999999988773
No 169
>PF14538 Raptor_N: Raptor N-terminal CASPase like domain
Probab=58.57 E-value=21 Score=30.11 Aligned_cols=80 Identities=19% Similarity=0.265 Sum_probs=48.1
Q ss_pred HHHHHcCCCCCCCCC-------ccccccccc--ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHh-hcCCCCCCC
Q 025599 69 EMCAKVGVDPLASNK-------GFWAELLGI--GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQ-RRKSNREAV 138 (250)
Q Consensus 69 ~mC~siGVDPL~s~k-------~~ws~~lG~--gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k-~R~~~~~~I 138 (250)
-||+.+|+||.-..+ -.|-+.... .++-.+++.+ |..-|.+++. .|-+..-.-
T Consensus 10 ~lcln~g~dppd~~~~~~~ar~~cW~dp~~~~~~~~~~~I~~~-----------------l~~qY~~~~~~~~~~~~~dp 72 (154)
T PF14538_consen 10 VLCLNIGVDPPDVVKTSPCARLECWIDPSNMPPSKASEEIGKN-----------------LQSQYESWQPRARYKQSLDP 72 (154)
T ss_pred EEeecCCCCCCCccccCCCceEEEecCCcccCchhHHHHHHHH-----------------HHHHHHHhCccCcEEEecCC
Confidence 489999999886332 257543322 1222222221 3334444421 233334688
Q ss_pred CHHHHHHHHhhccc-cCCCeEEEEECCE
Q 025599 139 SEDDCLRAISKLKV-LGNGYEVISVGKK 165 (250)
Q Consensus 139 S~~DI~rAik~L~~-LG~g~~vi~ig~~ 165 (250)
|.+|+.+.|..++. -+++-.|+..+|.
T Consensus 73 t~e~~~~~~~~~R~~a~~~RvLFHYnGh 100 (154)
T PF14538_consen 73 TVEDLKRLCQSLRRNAKDERVLFHYNGH 100 (154)
T ss_pred CHHHHHHHHHHHHhhCCCceEEEEECCC
Confidence 99999999999974 5678888888755
No 170
>PF11662 DUF3263: Protein of unknown function (DUF3263); InterPro: IPR021678 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=58.52 E-value=31 Score=26.10 Aligned_cols=45 Identities=16% Similarity=0.361 Sum_probs=39.6
Q ss_pred ccchhHHHHHHHHHh---CCCccHHHHHHhcCCChHHHHHHHHHHHHc
Q 025599 174 ELNKDHNQILELAQA---QGFVTVDEVERRLSWTSGRAIDALDILLEE 218 (250)
Q Consensus 174 El~~D~~~vLela~~---~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~ 218 (250)
+||.++..||++-.. .|....+.+.+.||.|+.|--..|+.|+..
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 688999999999873 677799999999999999999999999754
No 171
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=58.09 E-value=24 Score=30.68 Aligned_cols=45 Identities=18% Similarity=0.343 Sum_probs=40.2
Q ss_pred CccchhHHHHHHHHHhCCC------ccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 173 TELNKDHNQILELAQAQGF------VTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 173 ~El~~D~~~vLela~~~g~------vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
.+|+.-|.++|..|=..|| +|..+|++.+|.++.=+.+.|...++
T Consensus 154 ~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~ 204 (215)
T COG3413 154 NDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAER 204 (215)
T ss_pred ccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 4799999999999999888 79999999999999988888876655
No 172
>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=57.87 E-value=11 Score=27.90 Aligned_cols=30 Identities=27% Similarity=0.691 Sum_probs=18.6
Q ss_pred HhcccccccChhHHHHHHHHHHHcCCCCCCC
Q 025599 51 RKHKNDIRKNPTFRSQFHEMCAKVGVDPLAS 81 (250)
Q Consensus 51 ~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s 81 (250)
..+..+++.-..+ ...+..|.++|+||++.
T Consensus 10 ~~~~~~~~~~~vy-~~Y~~lc~~~~~~pls~ 39 (85)
T PF09079_consen 10 EGGKEEVTTGEVY-EVYEELCESLGVDPLSY 39 (85)
T ss_dssp HCTSSSEEHHHHH-HHHHHHHHHTTS----H
T ss_pred hCCCCceeHHHHH-HHHHHHHHHcCCCCCCH
Confidence 3334566665555 48999999999999984
No 173
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=57.46 E-value=31 Score=30.90 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=39.7
Q ss_pred HHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 181 QILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 181 ~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.||++... .+-+|..+|.+.+|.++.-+...|..|++.|++=.|...
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~ 62 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASD 62 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCC
Confidence 35666543 455999999999999999999999999999999988644
No 174
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=57.21 E-value=23 Score=30.76 Aligned_cols=42 Identities=21% Similarity=0.171 Sum_probs=36.6
Q ss_pred hHHHHHHHHHhCC--CccHHHHHHhcCCChHHHHHHHHHHHHcC
Q 025599 178 DHNQILELAQAQG--FVTVDEVERRLSWTSGRAIDALDILLEEG 219 (250)
Q Consensus 178 D~~~vLela~~~g--~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G 219 (250)
-+..+|+.....| +||..+|++.+|-+....+.=|..+...|
T Consensus 17 ~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G 60 (213)
T PRK05472 17 LYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFG 60 (213)
T ss_pred HHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcC
Confidence 3566888888889 99999999999999988888888887777
No 175
>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=57.07 E-value=13 Score=31.01 Aligned_cols=32 Identities=22% Similarity=0.326 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcccccccChhHHHHHHHHHHHc
Q 025599 43 RSQLEDFARKHKNDIRKNPTFRSQFHEMCAKV 74 (250)
Q Consensus 43 ~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~si 74 (250)
-.+.+.|++.|+.+|.++|.++..|.-.+.+|
T Consensus 91 p~ac~~Fv~~~~~~L~~~~~l~~~f~lHl~~L 122 (140)
T PF09733_consen 91 PWACEAFVREHGQWLVEKPNLRREFLLHLINL 122 (140)
T ss_pred HHHHHHHHHHhHHHHhhChhHHHHHHHHHHHH
Confidence 37899999999999999999999998765543
No 176
>PF14502 HTH_41: Helix-turn-helix domain
Probab=56.58 E-value=18 Score=24.94 Aligned_cols=36 Identities=22% Similarity=0.339 Sum_probs=32.4
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
-|++++++.++-+.--.+.+|..|+.+|-+=+..+.
T Consensus 7 ~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rG 42 (48)
T PF14502_consen 7 PTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRG 42 (48)
T ss_pred CCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecC
Confidence 589999999999999999999999999988776554
No 177
>PRK13558 bacterio-opsin activator; Provisional
Probab=56.13 E-value=30 Score=34.72 Aligned_cols=79 Identities=16% Similarity=0.187 Sum_probs=59.2
Q ss_pred CHHHHHHHHhhccccCCCeEEEEECCEE-EEE-------ecCCccchhHHHHHHHHHhCCC------ccHHHHHHhcCCC
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVGKKK-LVR-------SVPTELNKDHNQILELAQAQGF------VTVDEVERRLSWT 204 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig~~~-~v~-------svp~El~~D~~~vLela~~~g~------vt~~~L~~~l~W~ 204 (250)
+.+|+-..+..|..-..+++++.+.... =.. .....|+..|..+|++|-..|| +|.++|++.+|.+
T Consensus 564 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is 643 (665)
T PRK13558 564 TEAAGRAVVETLRDRYAGAELVSYTERDDPGETPDEFRASLENDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGIS 643 (665)
T ss_pred CCccHHHHHHHHHhhcCCcEEEEEEeecCCCcchhhHHHHhhhhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCC
Confidence 5677777778887766688888765321 000 1113799999999999999999 5999999999999
Q ss_pred hHHHHHHHHHHHH
Q 025599 205 SGRAIDALDILLE 217 (250)
Q Consensus 205 ~~Ra~~~L~~l~~ 217 (250)
+.=+-+.|...++
T Consensus 644 ~~t~~~~lr~a~~ 656 (665)
T PRK13558 644 RSTFHQHLRAAER 656 (665)
T ss_pred HHHHHHHHHHHHH
Confidence 9887777765543
No 178
>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=56.04 E-value=26 Score=33.05 Aligned_cols=63 Identities=14% Similarity=0.139 Sum_probs=48.2
Q ss_pred HHHHH-----HHHHhCCCccHHHHHHh--cCCChHHHHHHHHHHHHcCCceeecCCCC-CCcc----eeecCccC
Q 025599 179 HNQIL-----ELAQAQGFVTVDEVERR--LSWTSGRAIDALDILLEEGLAMVDDGHRD-RKRR----YWFPCASS 241 (250)
Q Consensus 179 ~~~vL-----ela~~~g~vt~~~L~~~--l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~-~e~~----Yw~P~l~~ 241 (250)
|..|| +++...+.|+...|++. +++|..-++.-|..|++.|++=.-....+ -... ||.++++.
T Consensus 4 ~~~il~aIV~~~l~~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~yv~~~~~ 78 (337)
T TIGR00331 4 QRKILKAIVEEYIKTGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRYYVDHLLK 78 (337)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHHHHHHhcc
Confidence 45566 46667899999999999 99999999999999999999977543321 0233 67776665
No 179
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=55.75 E-value=36 Score=27.59 Aligned_cols=39 Identities=13% Similarity=0.239 Sum_probs=35.5
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
...+|.++|++.+|.+..-.+.+|..|.++|++-.-...
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~ 61 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGK 61 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCC
Confidence 357899999999999999999999999999999887655
No 180
>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=55.44 E-value=16 Score=31.19 Aligned_cols=35 Identities=23% Similarity=0.298 Sum_probs=31.4
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
+..++..+|++.||-|..-.+++|..|..+|++=+
T Consensus 32 G~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~ 66 (212)
T TIGR03338 32 GAKLNESDIAARLGVSRGPVREAFRALEEAGLVRN 66 (212)
T ss_pred CCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEE
Confidence 45689999999999999999999999999999633
No 181
>PRK10263 DNA translocase FtsK; Provisional
Probab=55.37 E-value=28 Score=38.89 Aligned_cols=88 Identities=14% Similarity=0.183 Sum_probs=58.3
Q ss_pred CCCCHHHHHHHHhhccccCCCeEEEEEC-CEEEEEe-----cCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHH
Q 025599 136 EAVSEDDCLRAISKLKVLGNGYEVISVG-KKKLVRS-----VPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAI 209 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~s-----vp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~ 209 (250)
.-||++||.+-++.++.-|.+--+-.+- ...--.+ ...+.+.=...+++++-..|.+|.+.|++.+..---||-
T Consensus 1246 afvsD~Ei~~vv~~~k~~~~p~y~~~~~~~~~~~~~~~~~~~~~~~D~l~~~a~~~v~~~~~~S~S~lQR~~~iGynRAa 1325 (1355)
T PRK10263 1246 AFVRDQEVHAVVQDWKARGRPQYVDGITSDSESEGGAGGFDGAEELDPLFDQAVQFVTEKRKASISGVQRQFRIGYNRAA 1325 (1355)
T ss_pred ccCCHHHHHHHHHHHHhcCCCchhhhhcccccccccccCcCCCccccHHHHHHHHHHHhcCccCHHHHHHHhhcChHHHH
Confidence 4689999999999888755432111110 0000000 001122222446666667899999999999999999999
Q ss_pred HHHHHHHHcCCcee
Q 025599 210 DALDILLEEGLAMV 223 (250)
Q Consensus 210 ~~L~~l~~~Gl~Wv 223 (250)
..++.|+.+|++==
T Consensus 1326 riid~lE~~Giv~p 1339 (1355)
T PRK10263 1326 RIIEQMEAQGIVSE 1339 (1355)
T ss_pred HHHHHHHHCCcCCC
Confidence 99999999999743
No 182
>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=55.24 E-value=99 Score=29.80 Aligned_cols=100 Identities=25% Similarity=0.327 Sum_probs=67.1
Q ss_pred hHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEec---CC--
Q 025599 99 LGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSV---PT-- 173 (250)
Q Consensus 99 LavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~sv---p~-- 173 (250)
|.-||-.+... |=+|++++|+..+... .. |.++|++++.....| |.|.-+++|- |+
T Consensus 271 l~eqi~~ll~~-----~~v~~Fs~L~~ll~~~-----~~-~~~~lL~~L~~~AvL--------V~G~WV~kS~ll~~~~~ 331 (421)
T PF04801_consen 271 LEEQIKALLKK-----ARVISFSELRKLLPSN-----SD-TDEELLRALQQVAVL--------VQGNWVVKSELLYPDVP 331 (421)
T ss_pred HHHHHHHHHHh-----CCcccHHHHHHHhccc-----cc-hHHHHHHHHHhheEE--------EeeeEEEehhhccCCCc
Confidence 34455555443 4499999998887643 11 799999999997764 4555566663 33
Q ss_pred -c-cchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 174 -E-LNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 174 -E-l~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
| +-.--.-||-+-....+|+.++|....+-+...+++.|..+-.
T Consensus 332 ~e~~~~aRD~iL~~F~~~~~v~r~~l~~~~~l~~~~~~eiL~~~a~ 377 (421)
T PF04801_consen 332 AEQLCRARDYILLLFTKSRYVKRKELMSATKLPPEDVKEILKEIAV 377 (421)
T ss_pred chhhhhhHHHHHHHhcCCCceeHHHhhhhcCCCHHHHHHHHHHHhh
Confidence 2 1111112443334457899999999999999999999987643
No 183
>PF04337 DUF480: Protein of unknown function, DUF480; InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3BZ6_A.
Probab=55.07 E-value=1e+02 Score=26.08 Aligned_cols=101 Identities=21% Similarity=0.235 Sum_probs=58.4
Q ss_pred eeHHHHHHHHHhhcCCC-CCCCCHHHHHHHHhhccccCCCeEEEEECCE--EEEEecC--CccchhHHHHHHHHHhCCCc
Q 025599 118 INLQELCNLLRQRRKSN-REAVSEDDCLRAISKLKVLGNGYEVISVGKK--KLVRSVP--TELNKDHNQILELAQAQGFV 192 (250)
Q Consensus 118 i~l~el~~~v~k~R~~~-~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~--~~v~svp--~El~~D~~~vLela~~~g~v 192 (250)
++|.-|...-|..-+.. .-.+|++||..|++.|+..|-=.. ...|++ +|=.-.. -.++..+.+|+-+.--+|-=
T Consensus 25 LtLNaL~~aCNQKsnR~PVm~l~e~eV~~ald~L~~~~Lv~~-~~~gsRv~ky~Hr~~~~l~l~~~e~All~~LlLRGpQ 103 (148)
T PF04337_consen 25 LTLNALTTACNQKSNREPVMNLSESEVQAALDELRAKGLVRE-SGFGSRVAKYEHRFCNTLQLSPQELALLCLLLLRGPQ 103 (148)
T ss_dssp EEHHHHHHHHT-SSS-SS-----HHHHHHHHHHHHHTTSEEE--E--SS--EEEE-HHHHHT--HHHHHHHHHHHHH-SB
T ss_pred chHHHHHHHhccccccCccccCCHHHHHHHHHHHHHCcCeee-cCCCcchHHHHhhhhhhcCCCHHHHHHHHHHHHcCCC
Confidence 45556666666532211 246899999999999998774333 244443 2222221 26777887777666668999
Q ss_pred cHHHHHHhcC----C-ChHHHHHHHHHHHHcC
Q 025599 193 TVDEVERRLS----W-TSGRAIDALDILLEEG 219 (250)
Q Consensus 193 t~~~L~~~l~----W-~~~Ra~~~L~~l~~~G 219 (250)
|+.+|+.+.+ + +..-.+++|+.|...+
T Consensus 104 T~GELR~Rs~Rl~~F~d~~~Ve~~L~~L~~r~ 135 (148)
T PF04337_consen 104 TPGELRTRSERLHEFADVAEVEAVLERLAERE 135 (148)
T ss_dssp -HHHHHHHHTTTS--SSHHHHHHHHHHHHHTT
T ss_pred chhHHHhhhccccCCCCHHHHHHHHHHHHhcc
Confidence 9999997654 2 6677888999998877
No 184
>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=55.05 E-value=21 Score=27.08 Aligned_cols=66 Identities=15% Similarity=0.142 Sum_probs=49.2
Q ss_pred HHHHHHHcCCC--CCCCCCccccccccc---------ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCC
Q 025599 67 FHEMCAKVGVD--PLASNKGFWAELLGI---------GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNR 135 (250)
Q Consensus 67 F~~mC~siGVD--PL~s~k~~ws~~lG~---------gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~ 135 (250)
....|..||-| .|+ .-||+ .++-..+..|+.++...=+..+|.--++..|++.+.+
T Consensus 7 l~~ia~~LG~dW~~LA-------~eLg~s~~dI~~i~~e~p~~~~~q~~~lL~~W~~r~g~~At~~~L~~aL~~------ 73 (84)
T cd08803 7 MAIVADHLGLSWTELA-------RELNFSVDEINQIRVENPNSLIAQSFMLLKKWVTRDGKNATTDALTSVLTK------ 73 (84)
T ss_pred HHHHHHHhhccHHHHH-------HHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhhCCCcHHHHHHHHHHH------
Confidence 56788888888 344 23443 3556678888888888888888888888888888887
Q ss_pred CCCCHHHHHHHH
Q 025599 136 EAVSEDDCLRAI 147 (250)
Q Consensus 136 ~~IS~~DI~rAi 147 (250)
|-.+||+.++
T Consensus 74 --i~R~DIv~~~ 83 (84)
T cd08803 74 --INRIDIVTLL 83 (84)
T ss_pred --CCcHHHHHhc
Confidence 6778888765
No 185
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=54.95 E-value=1.3e+02 Score=25.36 Aligned_cols=154 Identities=15% Similarity=0.160 Sum_probs=83.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhccccc----ccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHH
Q 025599 29 KLRTDLMKEQLATFRSQLEDFARKHKNDI----RKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIV 104 (250)
Q Consensus 29 ~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI----~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIv 104 (250)
.-+-+.+...+..+...|..+|+.+-... ..+|+.- -|-.++.-.+-++... |+ +-.+||.=++.-+-
T Consensus 13 ~GD~~A~~~L~~~~y~~L~~~a~~~l~~~~~~~~~~~~~l-v~ea~lrl~~~~~~~~----~~---~~~~f~~~~~~~~r 84 (185)
T PF07638_consen 13 QGDEAALDQLFERYYPELRRLARRRLRRERRGHDLQDTAL-VHEAFLRLARRGRFVQ----FS---DRRHFWALLARIMR 84 (185)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHhccccCCchhHHHH-HHHHHHHHhccccccC----CC---CHHHHHHHHHHHHH
Confidence 33455677788888889999998764333 3445432 2455555554332211 11 12466554444444
Q ss_pred HHhhh-----hcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhH
Q 025599 105 EICLA-----TRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDH 179 (250)
Q Consensus 105 evC~~-----tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~ 179 (250)
-++.. .+...||=....++-..... .+.-++++++.--..|..|- .+..++
T Consensus 85 r~lid~~R~~~a~KRg~~~~~~~l~~~~~~-----~~~~~~~~~~~l~e~l~~L~-------------------~l~~~~ 140 (185)
T PF07638_consen 85 RKLIDHARRRQAQKRGGDQVRVELDERADS-----GDEPSPEELLELEEALERLL-------------------ALDPRQ 140 (185)
T ss_pred HHHHHHHHHHHHHhcCCCCcccchhhhhcc-----ccCCCHHHHHHHHHHHHHHH-------------------ccCHHH
Confidence 44322 22223322212222111111 12345666555444444422 145667
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHH
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDIL 215 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l 215 (250)
..++++.-..|+ |.+++++.+|.|+.-++..|..+
T Consensus 141 ~~~v~l~~~~Gl-s~~EIA~~lgiS~~tV~r~l~~a 175 (185)
T PF07638_consen 141 RRVVELRFFEGL-SVEEIAERLGISERTVRRRLRRA 175 (185)
T ss_pred HHHHHHHHHCCC-CHHHHHHHHCcCHHHHHHHHHHH
Confidence 778888777676 99999999999999888887654
No 186
>PRK06474 hypothetical protein; Provisional
Probab=54.73 E-value=51 Score=28.19 Aligned_cols=60 Identities=13% Similarity=0.160 Sum_probs=44.0
Q ss_pred HHHHHHHHHhCC-CccHHHHHHhc-CCChHHHHHHHHHHHHcCCceeecCCC--CCCcceeecC
Q 025599 179 HNQILELAQAQG-FVTVDEVERRL-SWTSGRAIDALDILLEEGLAMVDDGHR--DRKRRYWFPC 238 (250)
Q Consensus 179 ~~~vLela~~~g-~vt~~~L~~~l-~W~~~Ra~~~L~~l~~~Gl~WvD~q~~--~~e~~Yw~P~ 238 (250)
-..||++....+ .+|+.+|.+.+ +.+..-.-..|..|.+.|++.+.+... ++...||..+
T Consensus 13 R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~ 76 (178)
T PRK06474 13 RMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAIN 76 (178)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEec
Confidence 345777666544 49999999998 677788888999999999999987632 2234566554
No 187
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=54.58 E-value=18 Score=31.26 Aligned_cols=38 Identities=21% Similarity=0.226 Sum_probs=33.9
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
+..++..+|++.||-|..-.+++|..|..+|++-+-.+
T Consensus 28 G~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 28 DEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred CCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence 45689999999999999999999999999999977533
No 188
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=54.55 E-value=83 Score=25.94 Aligned_cols=54 Identities=20% Similarity=0.328 Sum_probs=40.4
Q ss_pred HHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC
Q 025599 101 VQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG 163 (250)
Q Consensus 101 vqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig 163 (250)
..|+++....... ++..|||..+.+. .+.||+.=|.|+++.|.-+|- +..+.++
T Consensus 24 ~~vl~~L~~~~~~----~sAeei~~~l~~~----~p~islaTVYr~L~~l~e~Gl-v~~~~~~ 77 (145)
T COG0735 24 LAVLELLLEADGH----LSAEELYEELREE----GPGISLATVYRTLKLLEEAGL-VHRLEFE 77 (145)
T ss_pred HHHHHHHHhcCCC----CCHHHHHHHHHHh----CCCCCHhHHHHHHHHHHHCCC-EEEEEeC
Confidence 4566666653333 9999999999985 367999999999999998885 4444443
No 189
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=54.17 E-value=16 Score=31.83 Aligned_cols=37 Identities=16% Similarity=0.269 Sum_probs=33.2
Q ss_pred CCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 190 GFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 190 g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
-.+ |..+|++.||-|..-.++||..|+.+|++-+-..
T Consensus 29 ~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g 66 (239)
T PRK04984 29 SILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 66 (239)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 346 8999999999999999999999999999987644
No 190
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=53.94 E-value=28 Score=29.53 Aligned_cols=42 Identities=19% Similarity=0.268 Sum_probs=35.4
Q ss_pred HHHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 182 ILELAQ--AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 182 vLela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
++.+|. ..+.+|.++|++.++.+..-...+|..|.+.|++=.
T Consensus 14 l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s 57 (164)
T PRK10857 14 MLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSS 57 (164)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 344554 246899999999999999999999999999998764
No 191
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=53.90 E-value=26 Score=30.12 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=26.8
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVP 172 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp 172 (250)
-+++|+.+|++.|..+|+|+.++. +|+ ++-.+|
T Consensus 73 ~~~~dm~~A~n~l~~~gGG~vvv~-~g~-v~a~lp 105 (171)
T PF13382_consen 73 TNDEDMALAANRLIEMGGGIVVVD-DGE-VLAELP 105 (171)
T ss_dssp SSHHHHHHHHHHHHHTTSEEEEEE-TTE-EEEEEE
T ss_pred CCHHHHHHHHHHHHHhCCCEEEEE-CCE-EEEEEe
Confidence 379999999999999999998875 555 455554
No 192
>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=52.79 E-value=26 Score=22.03 Aligned_cols=30 Identities=23% Similarity=0.273 Sum_probs=25.2
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
+|..++++-+|-+.+-+-.+|..|.++|++
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 578899999999999999999999999974
No 193
>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=52.53 E-value=22 Score=30.92 Aligned_cols=39 Identities=15% Similarity=0.252 Sum_probs=34.9
Q ss_pred CCCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+..+ |..+|++.||-|..-.++||..|..+|++-+-.+.
T Consensus 27 G~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~ 66 (235)
T TIGR02812 27 GSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHGK 66 (235)
T ss_pred CCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 4567 89999999999999999999999999999887543
No 194
>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=51.88 E-value=24 Score=24.91 Aligned_cols=31 Identities=23% Similarity=0.266 Sum_probs=28.8
Q ss_pred CccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 191 FVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.+|.++|++-+|-+...+-..|..|.++|++
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I 58 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGII 58 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCE
Confidence 4799999999999999999999999999954
No 195
>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=51.58 E-value=23 Score=30.73 Aligned_cols=49 Identities=31% Similarity=0.546 Sum_probs=39.7
Q ss_pred hCCCccHHHHHHh----cCCChHHHHHHHHHHHHcCCceeecCCCCCCccee-ecC
Q 025599 188 AQGFVTVDEVERR----LSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYW-FPC 238 (250)
Q Consensus 188 ~~g~vt~~~L~~~----l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw-~P~ 238 (250)
...+-|..+|... .|....-+|++|..|+.+|++-+|.-+. -..|| |||
T Consensus 8 ~~~~y~lKELEK~~pK~~gI~~~~VKdvlq~LvDDglV~~EKiGs--sn~YWsFps 61 (188)
T PF03962_consen 8 SKDFYTLKELEKLAPKEKGIVSMSVKDVLQSLVDDGLVHVEKIGS--SNYYWSFPS 61 (188)
T ss_pred cCCcccHHHHHHHcccccCCchhhHHHHHHHHhccccchhhhccC--eeEEEecCh
Confidence 3567777777643 6999999999999999999999998764 58888 454
No 196
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=51.54 E-value=45 Score=30.08 Aligned_cols=91 Identities=15% Similarity=0.202 Sum_probs=61.9
Q ss_pred CCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhH-HHHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHH
Q 025599 136 EAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDH-NQILELAQ-AQGFVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~-~~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
+.+|.+.|=...+.-.. ..+ .+-+|+.++.-- .+|.+..+ ..-..|+++|.+.+|.|..-|+.-|+
T Consensus 128 ~~~sQ~~lD~l~~~~~k-~~~-----------~~~LPkGi~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLe 195 (224)
T COG4565 128 QQLSQKELDQLFNIQSK-EQP-----------PDDLPKGLDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLE 195 (224)
T ss_pred cccCHHHHHHHHhcccc-ccC-----------cccCCCCcCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHH
Confidence 67888887766654432 111 122465554211 12444444 24567999999999999999999999
Q ss_pred HHHHcCCceeecCCC---CCCcceeecC
Q 025599 214 ILLEEGLAMVDDGHR---DRKRRYWFPC 238 (250)
Q Consensus 214 ~l~~~Gl~WvD~q~~---~~e~~Yw~P~ 238 (250)
.|+..|.+=.+-+-+ ..+..||.+.
T Consensus 196 yl~~~~~l~a~i~yG~vGRP~r~Y~~~~ 223 (224)
T COG4565 196 YLVSNGILEAEIHYGKVGRPERRYRLKA 223 (224)
T ss_pred HHHhcCeeeEEeeccccCCcceeeeccC
Confidence 999999999996643 2368888764
No 197
>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=51.32 E-value=31 Score=25.84 Aligned_cols=40 Identities=10% Similarity=0.211 Sum_probs=33.0
Q ss_pred eHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC
Q 025599 119 NLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG 163 (250)
Q Consensus 119 ~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig 163 (250)
+|...+..+.++ ..=|++||.+.......+++++-|+.|+
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 456666666664 5679999999999999999999999996
No 198
>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=51.25 E-value=24 Score=26.35 Aligned_cols=49 Identities=18% Similarity=0.081 Sum_probs=39.9
Q ss_pred CccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 173 TELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 173 ~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.+|..+...++.++......|.+++++.+|.|..-++..+..+.++|.+
T Consensus 14 ~~l~~~~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 14 TWVDSLAEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred hcCCHHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 3677788888888764334499999999999999999999888877754
No 199
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=50.57 E-value=43 Score=29.90 Aligned_cols=38 Identities=18% Similarity=0.062 Sum_probs=34.3
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
...+|.++|++.++-+..-+-..|..|+++|++=+...
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 45699999999999999999999999999999977644
No 200
>PRK02899 adaptor protein; Provisional
Probab=50.32 E-value=1.5e+02 Score=25.87 Aligned_cols=76 Identities=16% Similarity=0.131 Sum_probs=49.1
Q ss_pred CCHHHHHHHHhhccccCCC-eEEEEECCEEEEEecCCccchh-HHHHHHHHHh---CCCccHHHHHHhcCCChHHHHHHH
Q 025599 138 VSEDDCLRAISKLKVLGNG-YEVISVGKKKLVRSVPTELNKD-HNQILELAQA---QGFVTVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g-~~vi~ig~~~~v~svp~El~~D-~~~vLela~~---~g~vt~~~L~~~l~W~~~Ra~~~L 212 (250)
=+-+||+.+++.|.+.+.+ =.+-+..|++|+...+.+.+.+ ...++.++.+ ...+|..-|.+. | ...-...||
T Consensus 111 ~~fEdvi~la~~l~~~~~~~s~LY~~~~~YYL~l~~~~~~~~~~~~~~ail~EYg~~s~~t~~~l~Eh-G-k~I~~~~Al 188 (197)
T PRK02899 111 ATFEDVINLSHRLYNLGVTGGKLYSYDGRFYLWLEEEELIQLLKADFIAILAEYGNPSTVTIYRLEEY-G-KELMASQAV 188 (197)
T ss_pred CCHHHHHHHHHhhcccCCCCcceEEECCEEEEEEecCCCCHhhHHHHHHHHHhhCCCCcccHHHHHHh-h-HHHhHhhHH
Confidence 3689999999999765533 5677789999998777666654 4456666654 344566555533 3 344455555
Q ss_pred HHH
Q 025599 213 DIL 215 (250)
Q Consensus 213 ~~l 215 (250)
+.+
T Consensus 189 ~~l 191 (197)
T PRK02899 189 EQI 191 (197)
T ss_pred HHH
Confidence 544
No 201
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=50.24 E-value=1.4e+02 Score=24.23 Aligned_cols=96 Identities=15% Similarity=0.350 Sum_probs=59.6
Q ss_pred HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCC
Q 025599 37 EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGG 116 (250)
Q Consensus 37 ~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGG 116 (250)
.+...++.....|-..+.+-|... .+.....++|..|-.. .+.++-...-....|
T Consensus 5 ~~~~el~~~F~~fD~d~~G~i~~~-----el~~~lr~lg~~~t~~--------------------el~~~~~~~D~dg~g 59 (151)
T KOG0027|consen 5 EQILELKEAFQLFDKDGDGKISVE-----ELGAVLRSLGQNPTEE--------------------ELRDLIKEIDLDGDG 59 (151)
T ss_pred HHHHHHHHHHHHHCCCCCCcccHH-----HHHHHHHHcCCCCCHH--------------------HHHHHHHHhCCCCCC
Confidence 455667888888888777777654 5778888888886531 112222222223678
Q ss_pred ceeHHHHHHHHHhhcCCCCCC-CCHHHHHHHHhhccccCCCe
Q 025599 117 LINLQELCNLLRQRRKSNREA-VSEDDCLRAISKLKVLGNGY 157 (250)
Q Consensus 117 li~l~el~~~v~k~R~~~~~~-IS~~DI~rAik~L~~LG~g~ 157 (250)
-|++.|....+.+.-...... -+.+++..|-+.+-.=|.||
T Consensus 60 ~I~~~eF~~l~~~~~~~~~~~~~~~~el~eaF~~fD~d~~G~ 101 (151)
T KOG0027|consen 60 TIDFEEFLDLMEKLGEEKTDEEASSEELKEAFRVFDKDGDGF 101 (151)
T ss_pred eEcHHHHHHHHHhhhcccccccccHHHHHHHHHHHccCCCCc
Confidence 899999988888753321111 24556777766666655555
No 202
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=50.12 E-value=22 Score=25.26 Aligned_cols=46 Identities=22% Similarity=0.257 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccChh-HHHHHHHHHHHcCCCC
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKNDIRKNPT-FRSQFHEMCAKVGVDP 78 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~-fR~~F~~mC~siGVDP 78 (250)
+++++.++..=...|+.. .+..-+.-.+|. .|.-+++||.-+|+||
T Consensus 13 l~~va~~t~I~~~~l~ai-E~~~~~~lp~~~y~rg~lr~Ya~~Lgld~ 59 (62)
T PF13413_consen 13 LEDVAEETKISVSYLEAI-ENGDFDSLPSPVYARGYLRKYARFLGLDP 59 (62)
T ss_dssp HHHHHHHCS--HHHHHHH-HCT-GCCSSSHHHHHHHHHHHHHHTT--H
T ss_pred HHHHHHHhCCCHHHHHHH-HCcChhhCCcHHHHHHHHHHHHHHhCcCc
Confidence 445555555544455442 223333344555 5889999999999996
No 203
>KOG1350 consensus F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=50.09 E-value=22 Score=34.35 Aligned_cols=109 Identities=23% Similarity=0.432 Sum_probs=72.3
Q ss_pred HHHHHHHHHHHHHHHHHHhccccccc------------ChhHHHHH---------HHHHHHcC----CCCCCCCCccccc
Q 025599 34 LMKEQLATFRSQLEDFARKHKNDIRK------------NPTFRSQF---------HEMCAKVG----VDPLASNKGFWAE 88 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~~h~~eI~~------------dp~fR~~F---------~~mC~siG----VDPL~s~k~~ws~ 88 (250)
.|.+.|-..|+.+.+ .+++.|++ ||.=-..| .+=.+.+| ||||-|.+ .
T Consensus 326 TLaTdMG~mQERITt---TkkGSiTSvQAvYVPADDLtDPaPattFaHLDAttVLSR~iaelgIYPAVDPLDStS----r 398 (521)
T KOG1350|consen 326 TLATDMGTMQERITT---TKKGSITSVQAVYVPADDLTDPAPATTFAHLDATTVLSRGIAELGIYPAVDPLDSTS----R 398 (521)
T ss_pred ccccchhhhhHhhhc---cccCceeEEEEEEeehhccCCCCccceeeccchhhhhhhhhHhcCCccccCCccccc----c
Confidence 456667777766643 55566653 55322223 23345566 58887653 3
Q ss_pred ccc---cccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHH---HHHHHhhccccCCCeEEEEE
Q 025599 89 LLG---IGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDD---CLRAISKLKVLGNGYEVISV 162 (250)
Q Consensus 89 ~lG---~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~D---I~rAik~L~~LG~g~~vi~i 162 (250)
++- +|.=+|.+|.++-++.+... +|.|++..+ | +.++|++| +.||-|.=+-|.-+|.|-.+
T Consensus 399 imdp~ivG~eHY~vA~~Vqk~LQ~YK-------sLQDIIAIL----G--mDELSEeDkLTV~RARKiqRFLSQPF~VAEv 465 (521)
T KOG1350|consen 399 IMDPNIVGEEHYNVARGVQKTLQDYK-------SLQDIIAIL----G--MDELSEEDKLTVARARKIQRFLSQPFQVAEV 465 (521)
T ss_pred ccCccccchHHHHHHHHHHHHHHHHH-------HHHHHHHHh----C--chhhchhhhhhHHHHHHHHHHHcCchhhhhh
Confidence 332 57889999999999988744 456666554 2 68899999 56788877889999988766
No 204
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=50.04 E-value=40 Score=30.93 Aligned_cols=48 Identities=29% Similarity=0.377 Sum_probs=39.5
Q ss_pred CCccchhHHHHH-HHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 172 PTELNKDHNQIL-ELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 172 p~El~~D~~~vL-ela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
|.++..-| || +++...+++...++++++|.+.--.-+-+..|+++|++
T Consensus 7 kk~~t~fq--IL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i 55 (260)
T COG1497 7 KKNLTRFQ--ILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLI 55 (260)
T ss_pred cccchHHH--HHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccce
Confidence 55555444 55 44556799999999999999999999999999999986
No 205
>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=49.76 E-value=33 Score=25.96 Aligned_cols=34 Identities=12% Similarity=0.022 Sum_probs=30.8
Q ss_pred hHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHH
Q 025599 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L 212 (250)
-+..|++++.. |.+|..++++.+|-|...+..+|
T Consensus 7 R~~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 7 RVLEIGKYIVE-TKATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHh
Confidence 46778999999 99999999999999999988877
No 206
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.58 E-value=52 Score=26.58 Aligned_cols=25 Identities=28% Similarity=0.498 Sum_probs=22.3
Q ss_pred ccChhHHHHHHHHHHHcCCCCCCCC
Q 025599 58 RKNPTFRSQFHEMCAKVGVDPLASN 82 (250)
Q Consensus 58 ~~dp~fR~~F~~mC~siGVDPL~s~ 82 (250)
.+-|++|.+|-+....+|..|.+-.
T Consensus 69 ~sYptvR~kld~vlramgy~p~~e~ 93 (122)
T COG3877 69 ISYPTVRTKLDEVLRAMGYNPDSEN 93 (122)
T ss_pred CccHHHHHHHHHHHHHcCCCCCCCC
Confidence 3679999999999999999999854
No 207
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=49.54 E-value=1.2e+02 Score=29.93 Aligned_cols=97 Identities=21% Similarity=0.225 Sum_probs=65.6
Q ss_pred CceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCC------ccchhHHHHHHHHHhC
Q 025599 116 GLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPT------ELNKDHNQILELAQAQ 189 (250)
Q Consensus 116 Gli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~------El~~D~~~vLela~~~ 189 (250)
|-++..+|...+. +++..|.++++.|+.-| |..+.-.....+..++. +.+..+ .++++....
T Consensus 19 ~~~s~~eLA~~l~---------l~~~tVt~~i~~Le~kG--lV~~~~~~~~~i~LTeeG~~~~~~g~pE~-rl~~~l~~~ 86 (489)
T PRK04172 19 KEATLEELAEKLG---------LPPEAVMRAAEWLEEKG--LVKVEERVEEVYVLTEEGKKYAEEGLPER-RLLNALKDG 86 (489)
T ss_pred CCCCHHHHHHHhC---------cCHHHHHHHHHHHHhCC--CEEEEeeeEEEEEECHHHHHHHHhcCHHH-HHHHhhHhc
Confidence 3467888855433 79999999999999865 54444333445555543 233322 344444444
Q ss_pred CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+.++.++|.+.+ ++..-++.++..|.+.|.+.+|.
T Consensus 87 ~g~~~~el~~~a-L~~~~~~i~~~~l~k~g~i~i~~ 121 (489)
T PRK04172 87 GEVSLDELKEAL-LDKKEVGIALGNLARKGWAKIEK 121 (489)
T ss_pred CCcCHHHHHHhh-ccchhHHHHHHHHHHCCCeecCC
Confidence 557899999875 56677888889999999999964
No 208
>PRK04217 hypothetical protein; Provisional
Probab=48.94 E-value=53 Score=26.27 Aligned_cols=42 Identities=24% Similarity=0.379 Sum_probs=33.1
Q ss_pred CCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHH
Q 025599 172 PTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDI 214 (250)
Q Consensus 172 p~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~ 214 (250)
|..|+.++..++.+....|. |.+++++.+|.+..-++..|..
T Consensus 40 ~~~Lt~eereai~l~~~eGl-S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHHHH
Confidence 45789999888877776555 9999999999998766666554
No 209
>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=48.88 E-value=39 Score=32.37 Aligned_cols=33 Identities=27% Similarity=0.559 Sum_probs=27.2
Q ss_pred CHHHHHHHHhhccccCCCeEEEEECCEEEEEecCC
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPT 173 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~ 173 (250)
+++|+..|++.|..+|+|+.++. +|+ ++-.+|-
T Consensus 331 ~~~~~~~a~~~~~~~~gg~~~~~-~~~-~~~~~~l 363 (422)
T cd01295 331 NDEDMALAVNRLKEIGGGIVVVK-NGK-VLAELPL 363 (422)
T ss_pred CHHHHHHHHHHHHHhCCcEEEEE-CCE-EEEEecc
Confidence 69999999999999999998875 444 6667664
No 210
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=48.49 E-value=26 Score=30.91 Aligned_cols=37 Identities=16% Similarity=0.247 Sum_probs=33.3
Q ss_pred CCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 190 GFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 190 g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
-.+ |..+|++.||-|..-.+++|..|..+|++-+-..
T Consensus 32 ~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 32 EKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred CcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 446 8999999999999999999999999999987643
No 211
>TIGR02833 spore_III_AB stage III sporulation protein AB. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is designated stage III sporulation protein AB.
Probab=48.28 E-value=19 Score=30.64 Aligned_cols=55 Identities=15% Similarity=0.253 Sum_probs=44.1
Q ss_pred HHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCC
Q 025599 15 VARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGV 76 (250)
Q Consensus 15 ~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGV 76 (250)
++.+-..++|.+|-..+.+.-.++++...+.|+.-..+.+.+.++| .+|+.++||
T Consensus 105 ~d~eiL~~lG~~LG~~D~e~Q~k~i~L~~~~L~~~~~~a~~~~~k~-------~Kmy~~LGv 159 (170)
T TIGR02833 105 SEKEILLQFGKTLGESDREGQQKHINLTLEHLERQLTEAEDEQKKN-------EKMYRYLGV 159 (170)
T ss_pred HHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------ccHHHHHHH
Confidence 5678888999999988888888888888888888777777776666 578888886
No 212
>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=48.06 E-value=38 Score=30.28 Aligned_cols=60 Identities=7% Similarity=0.174 Sum_probs=40.3
Q ss_pred HHHHHHHHhcccccccChh-HHHHHHHHHHHcCCCCCCCCCcccccccc-cccchhhhHHHHH
Q 025599 44 SQLEDFARKHKNDIRKNPT-FRSQFHEMCAKVGVDPLASNKGFWAELLG-IGDFYYELGVQIV 104 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~-fR~~F~~mC~siGVDPL~s~k~~ws~~lG-~gdfy~eLavqIv 104 (250)
....+|++++.+.++++=+ +=..|+.|+.++.+||-..+.+. ++.++ .|+=|-++|.-..
T Consensus 33 ~~~~e~~kk~~~~~KkEyqkiG~af~~LsqaFe~d~~~~~~~L-~~Ai~~tg~~y~~IG~~fa 94 (210)
T cd07668 33 TVGQEHWKRCTGPLPKEYQKIGKALQSLATVFSTSGYQGETDL-NDAITEAGKTYEEIASLVA 94 (210)
T ss_pred HHHHHHHHHHcccccHHHHHHHHHHHHHHHHHhcCCcccchHH-HHHHHHHHHHHHHHHHHHH
Confidence 5567889999998888765 33449999999999986544332 23333 2666666654433
No 213
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=47.74 E-value=39 Score=31.17 Aligned_cols=44 Identities=20% Similarity=0.293 Sum_probs=38.3
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.+|++.....+++.++|++.+|-++.-+..+|..|..+|+.=..
T Consensus 8 ~il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~ 51 (319)
T PRK11886 8 QLLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS 51 (319)
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence 46777777789999999999999999999999999999994433
No 214
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=47.12 E-value=1.3e+02 Score=31.47 Aligned_cols=152 Identities=15% Similarity=0.206 Sum_probs=81.1
Q ss_pred ChhHHHHHHHHHHHcCCCCCCCCCcccccccc-cccchhhhHHHHHHHhhhhcccCCCceeHHHHHH------HHHhhcC
Q 025599 60 NPTFRSQFHEMCAKVGVDPLASNKGFWAELLG-IGDFYYELGVQIVEICLATRPHNGGLINLQELCN------LLRQRRK 132 (250)
Q Consensus 60 dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG-~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~------~v~k~R~ 132 (250)
+|+|-++.-.||.+- |-|.-+. ++-. +.+||.++-..-.. .. +.+=-.|+...|-. ...|.|
T Consensus 507 ~~~~lrkYI~YAR~~-v~P~lt~-----ea~e~l~~~Yv~~Rk~~~~---~~-~~~~~piT~RqLEsiiRLaeA~Ak~r- 575 (682)
T COG1241 507 DFELLRKYISYARKN-VTPVLTE-----EAREELEDYYVEMRKKSAL---VE-EKRTIPITARQLESIIRLAEAHAKMR- 575 (682)
T ss_pred cHHHHHHHHHHHhcc-CCcccCH-----HHHHHHHHHHHHhhhcccc---cc-ccCcccccHHHHHHHHHHHHHHHhhh-
Confidence 688888889999886 6677544 1111 35788877544322 11 11112333333321 122222
Q ss_pred CCCCCCCHHHHHHHHhhcc-ccCC-CeEE--EEECCEEEEEe-cCCccchhHHHHHHH----HHhCCCccHHHHHHhc-C
Q 025599 133 SNREAVSEDDCLRAISKLK-VLGN-GYEV--ISVGKKKLVRS-VPTELNKDHNQILEL----AQAQGFVTVDEVERRL-S 202 (250)
Q Consensus 133 ~~~~~IS~~DI~rAik~L~-~LG~-g~~v--i~ig~~~~v~s-vp~El~~D~~~vLel----a~~~g~vt~~~L~~~l-~ 202 (250)
.++.|+++|+.+|++.+. .|.. ++.- ..++ ..++.+ .|..--.+...++.. .+.... .++++.... |
T Consensus 576 -LS~~V~~eD~~eAi~lv~~~l~~v~~dp~~g~~d-~~~~~~~~~~~~~~~~~~~~~~i~e~~~~~~~-~~~~~~~~~~g 652 (682)
T COG1241 576 -LSDVVEEEDVDEAIRLVDFSLKTVAVDPEKGKID-IDIIEPGKSKSKRDKIEKVLDIIKELVERSED-PVEEIIEEAEG 652 (682)
T ss_pred -ccCCCCHHHHHHHHHHHHHHHHHhhcCccCCcee-hhhhccCCcchhhhhHHHHHHHHHHHhhcccc-hHHHHHHHHcC
Confidence 358899999999999987 2221 1110 0000 111111 132222223334443 333222 333443333 6
Q ss_pred CChHHHHHHHHHHHHcCCceeec
Q 025599 203 WTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 203 W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.+...++++|+.|...|.++-=.
T Consensus 653 ~~~~~~e~~l~~l~~~g~i~~~~ 675 (682)
T COG1241 653 ISEKEVEEALEKLKKKGDILEPN 675 (682)
T ss_pred CCHHHHHHHHHHHHhcCcEeccC
Confidence 99999999999999999887543
No 215
>PRK08307 stage III sporulation protein SpoAB; Provisional
Probab=47.07 E-value=21 Score=30.50 Aligned_cols=55 Identities=13% Similarity=0.185 Sum_probs=44.4
Q ss_pred HHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCC
Q 025599 15 VARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGV 76 (250)
Q Consensus 15 ~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGV 76 (250)
++.+...++|.+|-..+.+.-.++++...+.|+.-..+.+.+.++|. +|+.++||
T Consensus 106 ~d~eiL~~lg~~LG~~D~e~Q~k~i~L~~e~L~~~~~~a~~~~~k~~-------Kmy~~LGv 160 (171)
T PRK08307 106 EDIEILLQFGKTLGQSDREGQQKHIRLALEHLEREEEEAEEEQKKNE-------KMYKYLGF 160 (171)
T ss_pred HHHHHHHHHHHHHCcCcHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-------cHHHHHHH
Confidence 66788889999999888888888888888888888777777777664 77778775
No 216
>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=46.77 E-value=39 Score=30.16 Aligned_cols=61 Identities=21% Similarity=0.385 Sum_probs=40.3
Q ss_pred HHHHHHHHhcccccccChh-HHHHHHHHHHHcCCCCCCCCCcccccccc-cccchhhhHHHHHH
Q 025599 44 SQLEDFARKHKNDIRKNPT-FRSQFHEMCAKVGVDPLASNKGFWAELLG-IGDFYYELGVQIVE 105 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~-fR~~F~~mC~siGVDPL~s~k~~ws~~lG-~gdfy~eLavqIve 105 (250)
....+|++++.+..+++=+ +=..|+.|+.++.+||-..+.++ ++.++ .|+=|-++|.-..|
T Consensus 33 ~~~~e~~kk~~~~~kkEyqkiG~af~~LsqaFe~d~~~~s~~L-~~Av~~tG~~y~~IG~~fae 95 (207)
T cd07669 33 NVASELVRKHLGGFRKEFQKLGNAFQAISHSFQLDPPYSSEAL-NNAISHTGRTYEAVGEMFAE 95 (207)
T ss_pred HHHHHHHHHHcccccHHHHHHHHHHHHHHHHHhcCCCccchHH-HHHHHHHHHHHHHHHHHHHh
Confidence 4567888888888887755 33349999999999986544222 22333 36777776654433
No 217
>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=46.31 E-value=21 Score=27.84 Aligned_cols=41 Identities=24% Similarity=0.489 Sum_probs=29.1
Q ss_pred cChhHHHHHHHHHHHcCCCCCCCC--Ccccc-cccccccchhhhHHH
Q 025599 59 KNPTFRSQFHEMCAKVGVDPLASN--KGFWA-ELLGIGDFYYELGVQ 102 (250)
Q Consensus 59 ~dp~fR~~F~~mC~siGVDPL~s~--k~~ws-~~lG~gdfy~eLavq 102 (250)
.||.+ +..+..-.|||...|+ +.+|. ..+.-.+||-+|+..
T Consensus 41 rNP~i---~ekLi~~~~Ide~gTn~p~~i~dP~~~~~~~y~e~L~k~ 84 (96)
T PF07818_consen 41 RNPSI---LEKLIEFFGIDEYGTNFPKDIFDPHGFPEEDYYEELAKA 84 (96)
T ss_pred CChHH---HHHHHHHcCCCcccCCCChhhcCCCCCCHHHHHHHHHHH
Confidence 48888 6778888899998766 44453 223347999999864
No 218
>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=46.26 E-value=47 Score=29.28 Aligned_cols=43 Identities=21% Similarity=0.177 Sum_probs=37.1
Q ss_pred HHHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 181 QILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 181 ~vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
.||++.. ..+-+|..+|++.+|-++.-+-.-|..|+..|++=.
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 3677665 366799999999999999999999999999998854
No 219
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=45.96 E-value=32 Score=30.20 Aligned_cols=39 Identities=13% Similarity=0.264 Sum_probs=34.9
Q ss_pred CCCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+..+ |..+|++.||-|..-.+++|..|..+|++-+-.+.
T Consensus 28 G~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~ 67 (251)
T PRK09990 28 GQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGR 67 (251)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 4568 89999999999999999999999999999887543
No 220
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=45.77 E-value=29 Score=30.63 Aligned_cols=39 Identities=26% Similarity=0.204 Sum_probs=34.4
Q ss_pred CCCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+-.+ |..+|++.||-|..-.+++|..|..+|++-+-...
T Consensus 30 G~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~ 69 (257)
T PRK10225 30 GERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGA 69 (257)
T ss_pred CCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3567 79999999999999999999999999999877543
No 221
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=45.77 E-value=44 Score=27.83 Aligned_cols=40 Identities=20% Similarity=0.243 Sum_probs=34.3
Q ss_pred HHHHHH-hCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 182 ILELAQ-AQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 182 vLela~-~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
++.+|. ..+.+|.++|++.++.+..-.+..|..|.+.|++
T Consensus 14 L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv 54 (153)
T PRK11920 14 LMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLV 54 (153)
T ss_pred HHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 456665 3457899999999999999999999999999965
No 222
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=45.72 E-value=30 Score=30.58 Aligned_cols=37 Identities=19% Similarity=0.251 Sum_probs=33.4
Q ss_pred CCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 190 GFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 190 g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
-.+ |..+|++.||-|..-.+++|..|..+|++-+-..
T Consensus 24 ~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~ 61 (253)
T PRK10421 24 MKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRRG 61 (253)
T ss_pred CcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 457 7999999999999999999999999999987644
No 223
>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=45.57 E-value=33 Score=27.80 Aligned_cols=51 Identities=16% Similarity=0.125 Sum_probs=43.4
Q ss_pred CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccCCCcc
Q 025599 190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSISSS 245 (250)
Q Consensus 190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~~~~~ 245 (250)
.-.|+++|+..++=+..-.+.+|..+.+-||+=+++ ++.|+.|+|-...++
T Consensus 52 ipy~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~e-----d~~i~i~~~~~~~g~ 102 (121)
T PF09681_consen 52 IPYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDE-----DGVIYIPNWEKHQGS 102 (121)
T ss_pred CCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-----CCeEEeecHHHHhCc
Confidence 345999999999999999999999999999998875 478999997665444
No 224
>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=45.37 E-value=63 Score=22.37 Aligned_cols=40 Identities=20% Similarity=0.348 Sum_probs=33.0
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
.++..++++.-..+.+|..+|+..+|-|.--.+.-|+.+-
T Consensus 5 ~rq~~Ll~~L~~~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 5 KRQLKLLELLLKNKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHHHHHHHTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3566788887778999999999999999999998888764
No 225
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=45.26 E-value=57 Score=30.43 Aligned_cols=79 Identities=19% Similarity=0.196 Sum_probs=53.9
Q ss_pred CCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHH-h----CCCccHHHHHHh-------cC
Q 025599 135 REAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQ-A----QGFVTVDEVERR-------LS 202 (250)
Q Consensus 135 ~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~-~----~g~vt~~~L~~~-------l~ 202 (250)
...|+++||.+|++.+.. +.+ ...+ ..|+.-|..+|..+. . .+.++..++.+. .|
T Consensus 267 ~~~I~~~~v~~a~~~~~~--~~~-------~~~~----~~L~~~~k~~L~ai~~~~~~~~~~~~~~~i~~~y~~l~~~~~ 333 (394)
T PRK00411 267 SRKVTEEDVRKAYEKSEI--VHL-------SEVL----RTLPLHEKLLLRAIVRLLKKGGDEVTTGEVYEEYKELCEELG 333 (394)
T ss_pred CCCcCHHHHHHHHHHHHH--HHH-------HHHH----hcCCHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHHHHHHcC
Confidence 468999999999998732 000 1112 255666666665433 2 256788888754 68
Q ss_pred CCh---HHHHHHHHHHHHcCCceeecC
Q 025599 203 WTS---GRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 203 W~~---~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
.++ .+....|..|+..|++-.-..
T Consensus 334 ~~~~~~~~~~~~l~~L~~~glI~~~~~ 360 (394)
T PRK00411 334 YEPRTHTRFYEYINKLDMLGIINTRYS 360 (394)
T ss_pred CCcCcHHHHHHHHHHHHhcCCeEEEEe
Confidence 855 788889999999999987654
No 226
>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=45.00 E-value=82 Score=24.48 Aligned_cols=60 Identities=23% Similarity=0.244 Sum_probs=43.1
Q ss_pred hHHHHHHHHHh-CCCccHHHHHHhc-----CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCc
Q 025599 178 DHNQILELAQA-QGFVTVDEVERRL-----SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCA 239 (250)
Q Consensus 178 D~~~vLela~~-~g~vt~~~L~~~l-----~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l 239 (250)
-...||++... .+++|+++|-+.+ ..+..=.-..|+.|++.|++..=... + ...+|.++.
T Consensus 9 ~R~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~-~-~~~~Y~~~~ 74 (120)
T PF01475_consen 9 QRLAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG-D-GESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET-T-SEEEEEESS
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC-C-CcceEeecC
Confidence 34568888774 6799999999876 45666678899999999999987554 2 445555554
No 227
>PF15112 DUF4559: Domain of unknown function (DUF4559)
Probab=44.55 E-value=99 Score=29.20 Aligned_cols=98 Identities=19% Similarity=0.271 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHHHHHHHhcccccccChh---HHHHHHHHHH---HcCCCCCCCCCcccccccccccchhhhHHHHHHHhh
Q 025599 35 MKEQLATFRSQLEDFARKHKNDIRKNPT---FRSQFHEMCA---KVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICL 108 (250)
Q Consensus 35 l~~qL~~F~~~L~~Fa~~h~~eI~~dp~---fR~~F~~mC~---siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~ 108 (250)
-+.+|..|..+|.+|++ +.+.+|+ +..+-.+|.. .++++++.-..|.-+ -.++|.+.. +|.|+|+
T Consensus 161 s~~wm~~~~~~i~nll~----~f~~ipe~~~a~~~Ie~ll~~d~~v~~~~~d~~Dg~~~----~~~~~~~~~-~i~e~e~ 231 (307)
T PF15112_consen 161 SSQWMRDFQMKIQNLLN----EFRNIPEIVAAGSRIEQLLTSDWAVHIPEEDQRDGCES----ETDVYLSES-QILEIEM 231 (307)
T ss_pred CHHHHHHHHHHHHHHHH----HhccChHHHHHHHHHHHHHhhhhhhcCchhhccchhhh----ccchhhhHH-HHHHHHH
Confidence 46789999999999999 5556886 4455556653 478887765444322 256776654 4778887
Q ss_pred hhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc
Q 025599 109 ATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV 152 (250)
Q Consensus 109 ~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~ 152 (250)
+...+- +.|+|..+. .+.++++.+...++.++.
T Consensus 232 e~Lke~-----lqel~~~~e------~~~~~~ee~~~~l~~~~~ 264 (307)
T PF15112_consen 232 ELLKEK-----LQELYLQAE------EQEVLPEEDSKRLEVLKE 264 (307)
T ss_pred HHHHHH-----HHHHHHHHh------hccccchhhhHHHHHHHH
Confidence 754443 334433322 245666666666666653
No 228
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=44.17 E-value=1e+02 Score=24.18 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=19.5
Q ss_pred cccChhH------HHHHHHHHHHcCCCCCC
Q 025599 57 IRKNPTF------RSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 57 I~~dp~f------R~~F~~mC~siGVDPL~ 80 (250)
++.||.+ .++++++|..+|.+|-+
T Consensus 66 ~k~nPa~~i~~~a~~~~~~l~~elGLtP~s 95 (116)
T TIGR01558 66 PKANPALTVVEDAFKQLRSIGSALGLTPSS 95 (116)
T ss_pred eecChHHHHHHHHHHHHHHHHHHcCCCHHH
Confidence 5578865 46788999999999976
No 229
>PRK03837 transcriptional regulator NanR; Provisional
Probab=44.01 E-value=34 Score=29.70 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=31.6
Q ss_pred CCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 190 GFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 190 g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
-.+ +..+|++.||-|..-+++||..|..+|++=+-
T Consensus 35 ~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 35 DQLPSERELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 346 99999999999999999999999999997664
No 230
>KOG0624 consensus dsRNA-activated protein kinase inhibitor P58, contains TPR and DnaJ domains [Defense mechanisms]
Probab=43.84 E-value=14 Score=36.04 Aligned_cols=36 Identities=36% Similarity=0.757 Sum_probs=26.5
Q ss_pred ccccccChhHHHHHHHHHHHcCCCCCCC----------CCcccccccccccc
Q 025599 54 KNDIRKNPTFRSQFHEMCAKVGVDPLAS----------NKGFWAELLGIGDF 95 (250)
Q Consensus 54 ~~eI~~dp~fR~~F~~mC~siGVDPL~s----------~k~~ws~~lG~gdf 95 (250)
.++.-+||+-|++|-. |.|||-+ +.|||. ..|+|-|
T Consensus 446 AKEVLsd~EkRrqFDn-----GeDPLD~Es~q~GGGg~~Hgf~n-~hgF~~F 491 (504)
T KOG0624|consen 446 AKEVLSDPEKRRQFDN-----GEDPLDPESQQGGGGGPFHGFWN-EHGFNPF 491 (504)
T ss_pred HHHhhcCHHHHhhccC-----CCCCCChhhccCCCCCCCCCCcc-ccCCCCC
Confidence 3577899999999975 9999942 245886 5666554
No 231
>PRK09191 two-component response regulator; Provisional
Probab=43.83 E-value=33 Score=29.56 Aligned_cols=53 Identities=19% Similarity=0.252 Sum_probs=39.6
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCCh-------HHHHHHHHHHHHcCCceeecCC
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTS-------GRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~-------~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.|+.++..++.+....|+ |..++++.+|.+. .||+..|......-++++|++.
T Consensus 88 ~L~~~~r~v~~l~~~~~~-s~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~~~~liidd~~ 147 (261)
T PRK09191 88 GLTPLPRQAFLLTALEGF-SVEEAAEILGVDPAEAEALLDDARAEIARQVATRVLIIEDEP 147 (261)
T ss_pred hCCHHHhHHHHHHHHhcC-CHHHHHHHHCCCHHHHHHHHHHHHHHHhccCCCeEEEEcCcH
Confidence 556678888888776554 8999999999984 4666666655666788999765
No 232
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.53 E-value=89 Score=28.62 Aligned_cols=97 Identities=22% Similarity=0.350 Sum_probs=54.4
Q ss_pred HHHHHHHHhcc-cccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHH
Q 025599 44 SQLEDFARKHK-NDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQE 122 (250)
Q Consensus 44 ~~L~~Fa~~h~-~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~e 122 (250)
+.+++++...+ .+++.+-+.-++...+-..+|--|.... |. ...+.|=+|.-+-
T Consensus 74 ~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~aG~v~V~G~-Gl---~ITi~d~~~~~~~--------------------- 128 (247)
T COG3879 74 EDLENKLDSVRRSVLTDDAALEDRLEKLRMLAGSVPVTGP-GL---VITIDDPGYSPNG--------------------- 128 (247)
T ss_pred HHHHHHHHHHHHhHHhHHHHHHHHHHHHHHHhccCCCcCC-cE---EEEecCCCCCccc---------------------
Confidence 34455544443 5667777777778888888998887733 32 2223344433211
Q ss_pred HHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC-----CEEEEEecCCcc
Q 025599 123 LCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG-----KKKLVRSVPTEL 175 (250)
Q Consensus 123 l~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig-----~~~~v~svp~El 175 (250)
. +...+.|.++||..=|+-|..-| -+-|.|+ ..++|+.++.-+
T Consensus 129 -------~-~~~~~vv~~~dl~~viNeL~~sG--AEaIsIn~~RI~~~t~Ir~v~g~~ 176 (247)
T COG3879 129 -------V-GPNSQVVHDDDLQAVINELNISG--AEAISINGQRIGSNTTIRCVGGTL 176 (247)
T ss_pred -------C-CCCccccCHHHHHHHHHHHHhcc--chheeECCEEeecceEEEecCCeE
Confidence 1 11236678888777777777644 3444443 344556655433
No 233
>COG3710 CadC DNA-binding winged-HTH domains [Transcription]
Probab=43.42 E-value=30 Score=28.85 Aligned_cols=57 Identities=25% Similarity=0.295 Sum_probs=46.1
Q ss_pred ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc-cC
Q 025599 93 GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV-LG 154 (250)
Q Consensus 93 gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~-LG 154 (250)
+|=-+.|+-+-..+....-+.-|.+++=+||..+|=..|. +++.++-.+|..|+. |+
T Consensus 26 ~~~~v~l~~~~~~lL~~L~e~~geVvsk~eL~~~VW~~~~-----v~~~~Ltq~I~~LRr~L~ 83 (148)
T COG3710 26 GDEVVKLGPRELKLLSLLLERAGEVVSKDELLDAVWPGRI-----VTVNTLTQAISALRRALR 83 (148)
T ss_pred CCeEEEecHHHHHHHHHHHhccCceecHHHHHHHhCCCce-----EccChHHHHHHHHHHHHh
Confidence 3444556777777777777789999999999999998877 888999999999974 44
No 234
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=43.09 E-value=24 Score=30.66 Aligned_cols=39 Identities=21% Similarity=0.259 Sum_probs=35.2
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+-.++..+|++.||-|..-.+++|..|..+|++-+..+-
T Consensus 37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~r 75 (230)
T COG1802 37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNR 75 (230)
T ss_pred CCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCC
Confidence 466999999999999999999999999999999887443
No 235
>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=43.06 E-value=1.3e+02 Score=21.88 Aligned_cols=75 Identities=12% Similarity=0.181 Sum_probs=46.1
Q ss_pred HHHHHHHHHHHHHHHHHH--hcccccccChhHHHHHHHHHHH-cCCCCCCCCCcccccccccccchhhhHHHHHHHhhhh
Q 025599 34 LMKEQLATFRSQLEDFAR--KHKNDIRKNPTFRSQFHEMCAK-VGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLAT 110 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~--~h~~eI~~dp~fR~~F~~mC~s-iGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~t 110 (250)
++.++++.++.....|-+ .+.+-|..+ .|.+++.. +|..|-. . ++ -..|-++....
T Consensus 2 ~~~~~~~~l~~~F~~~D~~~~~~G~Is~~-----el~~~l~~~~g~~~~~-~---~~------------~~ei~~i~~~~ 60 (88)
T cd00213 2 ELEKAIETIIDVFHKYSGKEGDKDTLSKK-----ELKELLETELPNFLKN-Q---KD------------PEAVDKIMKDL 60 (88)
T ss_pred hHHHHHHHHHHHHHHHhhccCCCCcCcHH-----HHHHHHHHHhhhhccC-C---CC------------HHHHHHHHHHh
Confidence 467899999999999999 688888764 45566654 4432110 0 00 11222233333
Q ss_pred cccCCCceeHHHHHHHHHh
Q 025599 111 RPHNGGLINLQELCNLLRQ 129 (250)
Q Consensus 111 r~~nGGli~l~el~~~v~k 129 (250)
-..+.|.|++.+.+..+.+
T Consensus 61 d~~~~g~I~f~eF~~~~~~ 79 (88)
T cd00213 61 DVNKDGKVDFQEFLVLIGK 79 (88)
T ss_pred ccCCCCcCcHHHHHHHHHH
Confidence 3445688999998877765
No 236
>cd07291 PX_SNX5 The phosphoinositide binding Phox Homology domain of Sorting Nexin 5. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting
Probab=43.01 E-value=39 Score=28.37 Aligned_cols=31 Identities=29% Similarity=0.484 Sum_probs=22.4
Q ss_pred HHHHHHHH---HHHHHHhccc--ccccChhHHHHHHH
Q 025599 38 QLATFRSQ---LEDFARKHKN--DIRKNPTFRSQFHE 69 (250)
Q Consensus 38 qL~~F~~~---L~~Fa~~h~~--eI~~dp~fR~~F~~ 69 (250)
=|++|++. |+.|.+.=.. -+++||.|| .|.+
T Consensus 104 ~~~~~kk~~a~lE~fL~Ria~HP~l~~d~~f~-~FLe 139 (141)
T cd07291 104 YLAVFKKTVQVHEVFLQRLSSHPSLSKDRNFH-IFLE 139 (141)
T ss_pred hhhHHHHHHHHHHHHHHHHhhCCeeccCcchh-hhcc
Confidence 37778865 8888775443 688899998 5764
No 237
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=42.69 E-value=3.4e+02 Score=27.82 Aligned_cols=132 Identities=11% Similarity=0.040 Sum_probs=81.4
Q ss_pred ccchhhhHHHHHHHhhhhc--ccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEe
Q 025599 93 GDFYYELGVQIVEICLATR--PHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRS 170 (250)
Q Consensus 93 gdfy~eLavqIvevC~~tr--~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~s 170 (250)
.++|.++..++.+....-- +-.---|+..|+.+++.+ .+++.-+...++.|..=| . +..-++...+..
T Consensus 413 ~~~~~~~~~~~~~~l~~~h~~~p~~~g~~~~~l~~~~~~-------~~~~~~~~~~l~~l~~~~--~-i~~~~~~~~~~~ 482 (614)
T PRK10512 413 APVAARWQRKLLDTLATYHEQHRDEPGPGRERLRRMALP-------MEDEALVLLLIEKMRESG--D-IHSHHGWLHLPD 482 (614)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCcccCCCHHHHHhhccc-------CCCHHHHHHHHHHHHhCC--C-EEEeCCEEECCC
Confidence 5777788888888875321 112234778888766433 366776666667665322 1 222344322221
Q ss_pred cCCccchhHHHHHHHHHh---CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc-eeecCCCCCCcceeecCcc
Q 025599 171 VPTELNKDHNQILELAQA---QGFVTVDEVERRLSWTSGRAIDALDILLEEGLA-MVDDGHRDRKRRYWFPCAS 240 (250)
Q Consensus 171 vp~El~~D~~~vLela~~---~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~-WvD~q~~~~e~~Yw~P~l~ 240 (250)
--..++.++..+.+.... ..-.+.++|.+.++.+...++++|..|+++|.+ =++ +..|+-|..+
T Consensus 483 ~~~~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~------~~~~~~~~~~ 550 (614)
T PRK10512 483 HKAGFSEEQQALWQKAEPLFGDEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIV------KDRYYRNDRI 550 (614)
T ss_pred CCCCCCHHHHHHHHHHHHHHhcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec------CCEEECHHHH
Confidence 113567777666444332 244577889999999999999999999999954 333 4667766543
No 238
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=42.12 E-value=37 Score=30.00 Aligned_cols=39 Identities=15% Similarity=0.101 Sum_probs=34.3
Q ss_pred CCCc-cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 189 QGFV-TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 189 ~g~v-t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+..+ |..+|++.||-|..-.+++|..|..+|++-+-...
T Consensus 29 G~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~ 68 (253)
T PRK11523 29 GDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGS 68 (253)
T ss_pred CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 3467 68999999999999999999999999999877544
No 239
>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=41.75 E-value=1.9e+02 Score=25.42 Aligned_cols=44 Identities=5% Similarity=0.061 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccc-cccChhHHHHHHHHHHHcC
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKND-IRKNPTFRSQFHEMCAKVG 75 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~e-I~~dp~fR~~F~~mC~siG 75 (250)
.+........+...+..||.++.++ .-.+.-+..-|-.+..++.
T Consensus 28 ~~a~~~l~~~y~~~v~~~a~~~~~~~~~aeDlvQe~~i~l~~a~~ 72 (255)
T TIGR02941 28 GEAQEKLVDHYQNLVYSIAYKYSKGGPMHEDLVQVGMLGLLGAIR 72 (255)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 4567888888999999999988753 2334446667777776655
No 240
>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=41.72 E-value=54 Score=26.66 Aligned_cols=49 Identities=10% Similarity=0.091 Sum_probs=41.7
Q ss_pred CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccCCCc
Q 025599 190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSISS 244 (250)
Q Consensus 190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~~~~ 244 (250)
.| |+++|+..++-+..-.+-||..+.+.||+=+++ .+.|+.|+|-...+
T Consensus 51 py-~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d-----~g~i~i~~~~~~~g 99 (119)
T TIGR01714 51 PY-NAEMLATMFNRNVGDIRITLQTLESLGLIEKKN-----NGDIFLENWEKHVG 99 (119)
T ss_pred CC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-----CCcEEehhHHHHcC
Confidence 44 999999999999999999999999999999885 25699998755433
No 241
>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=41.70 E-value=36 Score=29.35 Aligned_cols=34 Identities=26% Similarity=0.288 Sum_probs=31.5
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
-|..+|++.+|-+..-.+.+|..|..+|++..-.
T Consensus 26 PsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 26 PSERDLGERFNTTRVTIREALQQLEAEGLIYRED 59 (231)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC
Confidence 3899999999999999999999999999999764
No 242
>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=41.35 E-value=22 Score=26.84 Aligned_cols=25 Identities=16% Similarity=0.388 Sum_probs=21.7
Q ss_pred ccccChhHHHHHHHHHHHcCCCCCC
Q 025599 56 DIRKNPTFRSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 56 eI~~dp~fR~~F~~mC~siGVDPL~ 80 (250)
.|+=|++.+.++.+.|.++|++|-.
T Consensus 6 ~~Rvd~~lK~~a~~i~~~lGl~~s~ 30 (83)
T TIGR02384 6 SIRIDEELKKEAYAVFEELGLTPST 30 (83)
T ss_pred EEeeCHHHHHHHHHHHHHhCCCHHH
Confidence 4677999999999999999999743
No 243
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.17 E-value=52 Score=27.14 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=35.9
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
|+...-..|.+|.++|+..+|.+.-..+..|..|..++++-+.
T Consensus 6 v~d~L~~~~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~ 48 (147)
T smart00531 6 VLDALMRNGCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKID 48 (147)
T ss_pred ehHHHHhcCCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhh
Confidence 4554445689999999999999999999999999997775444
No 244
>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=41.16 E-value=1.1e+02 Score=22.74 Aligned_cols=45 Identities=27% Similarity=0.211 Sum_probs=36.2
Q ss_pred HHHHHHhCCCccHHHHHHhc-CCChHHHHHHHHHHHHcCCceeecCC
Q 025599 182 ILELAQAQGFVTVDEVERRL-SWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l-~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
||..+.. |...-++|.+.+ |.+..---.+|.+|++.|++......
T Consensus 10 IL~~l~~-g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~ 55 (90)
T PF01638_consen 10 ILRALFQ-GPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYP 55 (90)
T ss_dssp HHHHHTT-SSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES
T ss_pred HHHHHHh-CCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccccc
Confidence 3433333 889999999999 88988888999999999999998654
No 245
>PF07240 Turandot: Stress-inducible humoral factor Turandot; InterPro: IPR010825 This family consists of several Drosophila species specific Turandot proteins. The Turandot A (TotA) gene encodes a humoral factor, which is secreted from the fat body and accumulates in the body fluids. TotA is strongly induced upon bacterial challenge, as well as by other types of stress such as high temperature, mechanical pressure, dehydration, UV irradiation, and oxidative agents. It is also upregulated during metamorphosis and at high age. Flies that overexpress TotA show prolonged survival and retain normal activity at otherwise lethal temperatures. Although TotA is only induced by severe stress, it responds to a much wider range of stimuli than heat shock genes such as hsp70 or immune genes such as Cecropin A1 [].
Probab=40.84 E-value=24 Score=27.17 Aligned_cols=29 Identities=17% Similarity=0.461 Sum_probs=19.8
Q ss_pred CCCCCCCCCcccccccccccchhhhHHHHHH
Q 025599 75 GVDPLASNKGFWAELLGIGDFYYELGVQIVE 105 (250)
Q Consensus 75 GVDPL~s~k~~ws~~lG~gdfy~eLavqIve 105 (250)
=||=+-+..|+|+..++ .+--.+|+.|+.
T Consensus 49 lVDGvPaQGG~~~~i~~--~~i~~~a~~v~~ 77 (85)
T PF07240_consen 49 LVDGVPAQGGFWGKIVK--KIISPAAKSVAD 77 (85)
T ss_pred cccCcCCCCCchHHHHH--HHHHHHHHHHHH
Confidence 47866678899986653 555666666654
No 246
>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=40.56 E-value=54 Score=29.25 Aligned_cols=61 Identities=21% Similarity=0.390 Sum_probs=39.5
Q ss_pred HHHHHHHHhcccccccChh-HHHHHHHHHHHcCCCCCCCCCcccccccc-cccchhhhHHHHHH
Q 025599 44 SQLEDFARKHKNDIRKNPT-FRSQFHEMCAKVGVDPLASNKGFWAELLG-IGDFYYELGVQIVE 105 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~-fR~~F~~mC~siGVDPL~s~k~~ws~~lG-~gdfy~eLavqIve 105 (250)
..-.+|++++.+..+++=+ +=..|+.++.+..+||-..+.++ ++.++ .|+=|-++|.-..|
T Consensus 33 ~~~~e~~kk~~~~~KkEyqkiG~af~~LsqaF~~d~~~~s~~L-~~Av~~tg~~y~~IG~~fae 95 (207)
T cd07670 33 HTANEFARKQVTGFKKEYQKVGQSFKGLSQAFELDQQAFSAGL-NQAIAFTGEAYEAIGELFAE 95 (207)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHHHHHccCCcccchHH-HHHHHHHHHHHHHHHHHHHh
Confidence 4556788888888877765 33349999999999976544222 22333 36777766654443
No 247
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=40.53 E-value=95 Score=25.58 Aligned_cols=61 Identities=23% Similarity=0.290 Sum_probs=46.9
Q ss_pred chhHHHHHHHHHh-CCCccHHHHHHhc-----CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025599 176 NKDHNQILELAQA-QGFVTVDEVERRL-----SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237 (250)
Q Consensus 176 ~~D~~~vLela~~-~g~vt~~~L~~~l-----~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P 237 (250)
+.-..+||++... .+++|+++|-+.+ +.+..-.-.+|+.|...|++=.-+..+ +...|..+
T Consensus 20 T~qR~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~-~~~~y~~~ 86 (145)
T COG0735 20 TPQRLAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG-GKTRYELN 86 (145)
T ss_pred CHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC-CEEEEecC
Confidence 4456778988874 5779999987655 477888899999999999999988773 24555544
No 248
>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=40.53 E-value=99 Score=19.84 Aligned_cols=40 Identities=15% Similarity=0.138 Sum_probs=30.1
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
+.++..++.+.. ...|..++++.++++..-.+..+..+.+
T Consensus 2 ~~~e~~i~~~~~--~~~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 2 TPREREVLRLLA--EGKTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CHHHHHHHHHHH--cCCCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 455666776653 3469999999999999988888876543
No 249
>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=40.36 E-value=18 Score=28.23 Aligned_cols=45 Identities=29% Similarity=0.403 Sum_probs=28.9
Q ss_pred HHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCC
Q 025599 66 QFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKS 133 (250)
Q Consensus 66 ~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~ 133 (250)
=|++||..|||+|.+.. .+||..+= + .++.+ =.||+..|+|.|..
T Consensus 27 llqEm~~gLg~~p~ag~-----lLf~~~~~--~-~~k~A---------------EqELL~Ei~Rrr~~ 71 (93)
T PF07216_consen 27 LLQEMLEGLGLGPVAGE-----LLFGGSSP--E-LMKQA---------------EQELLEEIQRRRQQ 71 (93)
T ss_pred HHHHHHHhcCCChhHHH-----HHhcCCCH--H-HHHHH---------------HHHHHHHHHHHHHc
Confidence 49999999999999854 33433221 1 22222 25788888888763
No 250
>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=40.15 E-value=1.1e+02 Score=20.19 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=30.1
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
.|+..+..++.+.-..|+ |..++++.+|.+..-++..|....
T Consensus 10 ~L~~~~r~i~~l~~~~g~-s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQGM-SYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp CS-HHHHHHHHHHHTS----HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHCc-CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467778888888777665 999999999999998888876543
No 251
>PHA02591 hypothetical protein; Provisional
Probab=39.74 E-value=71 Score=24.40 Aligned_cols=49 Identities=29% Similarity=0.416 Sum_probs=29.9
Q ss_pred EEEEC-CEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHH
Q 025599 159 VISVG-KKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 159 vi~ig-~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
++.+| .++||-|-.++.|.- -++. ..|+ |.+.+++.||.+..-.+.-|+
T Consensus 32 ~vqv~~~ryfi~~~dd~~~vA----~eL~-eqGl-SqeqIA~~LGVsqetVrKYL~ 81 (83)
T PHA02591 32 VVQVGQTRYFVESEDDLISVT----HELA-RKGF-TVEKIASLLGVSVRKVRRYLE 81 (83)
T ss_pred hheeCCEEEEEeccchHHHHH----HHHH-HcCC-CHHHHHHHhCCCHHHHHHHHh
Confidence 45566 455555543333211 1222 3565 999999999999887776554
No 252
>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=38.92 E-value=82 Score=22.28 Aligned_cols=43 Identities=23% Similarity=0.289 Sum_probs=34.0
Q ss_pred HHHHHHhCCCccHHHHHHhc----CCChHHHHHHHHHHHHcCCceee
Q 025599 182 ILELAQAQGFVTVDEVERRL----SWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l----~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
++...+..|..|...|...+ +++...+-..+.+|+..+.+-+|
T Consensus 32 i~~~l~~~~~~tl~~l~~~~d~~~~l~~g~~L~~l~~LiA~k~i~~D 78 (79)
T PF08721_consen 32 ILARLRKNPTMTLRDLCKELDKDYELEPGTALPLLRHLIATKRIKVD 78 (79)
T ss_dssp HHHHHHHTTTSBHHHHHHHHHHHCT--TTHHHHHHHHHHHTTSEE--
T ss_pred HHHHHHHcCCCCHHHHHHHHHHhcCCCcCChHHHHHHHHhCChhccC
Confidence 66667777889999998765 99999999999999999988777
No 253
>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=38.36 E-value=20 Score=27.75 Aligned_cols=17 Identities=29% Similarity=0.600 Sum_probs=14.7
Q ss_pred HHHHHHHHcCCCCCCCC
Q 025599 66 QFHEMCAKVGVDPLASN 82 (250)
Q Consensus 66 ~F~~mC~siGVDPL~s~ 82 (250)
=|++||.+|||-|.+..
T Consensus 24 llqEm~~gLgl~p~ag~ 40 (90)
T TIGR02573 24 LLQEMWQGLGLGPVAGE 40 (90)
T ss_pred HHHHHHHHcCCChHHHH
Confidence 49999999999998743
No 254
>PF14948 RESP18: RESP18 domain
Probab=38.07 E-value=24 Score=28.18 Aligned_cols=22 Identities=32% Similarity=0.330 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHcCCceeecCCC
Q 025599 207 RAIDALDILLEEGLAMVDDGHR 228 (250)
Q Consensus 207 Ra~~~L~~l~~~Gl~WvD~q~~ 228 (250)
|-+.+|..|+..|+.|-||=+.
T Consensus 23 rLQ~vLqqL~~qGl~WqDDiTQ 44 (105)
T PF14948_consen 23 RLQVVLQQLMPQGLFWQDDITQ 44 (105)
T ss_pred HHHHHHHHHHhcCCcccchHHH
Confidence 5567999999999999997654
No 255
>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=37.86 E-value=62 Score=29.41 Aligned_cols=37 Identities=14% Similarity=0.100 Sum_probs=34.1
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
.|..|+++|++.+|+++...+.-|+.|+.-|++-.++
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 3789999999999999999999999999999998763
No 256
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=37.58 E-value=73 Score=27.31 Aligned_cols=46 Identities=20% Similarity=0.254 Sum_probs=37.1
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc---eeec
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA---MVDD 225 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~---WvD~ 225 (250)
|..|.+|++.... |+.|.++|.+.+|=+. ..+|.-|-+-||+ |+=-
T Consensus 16 s~~~kkV~~~Ls~-~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE~qWrmP 64 (160)
T PF09824_consen 16 SEVYKKVYDELSK-GWMTEEELEEKYGKDV---RESLLILKKGGLIESQWRMP 64 (160)
T ss_pred CHHHHHHHHHHHh-ccCCHHHHHHHHCcCH---HHHHHHHHHcCchhhccccC
Confidence 5568888887776 7999999999999887 6677777777876 7765
No 257
>PF06136 DUF966: Domain of unknown function (DUF966); InterPro: IPR010369 This is a family of plant proteins confined to monocotyledons and mosses, with unknown function
Probab=37.54 E-value=18 Score=34.41 Aligned_cols=27 Identities=22% Similarity=0.370 Sum_probs=24.1
Q ss_pred eeHHHHHHHHHhhcCCCC------------------CCCCHHHHH
Q 025599 118 INLQELCNLLRQRRKSNR------------------EAVSEDDCL 144 (250)
Q Consensus 118 i~l~el~~~v~k~R~~~~------------------~~IS~~DI~ 144 (250)
+-|.||..||+-.||+.| +++++||++
T Consensus 29 L~LRDV~~RL~~LRGkGMp~~ySWS~KRsYKnGfVW~DL~ddD~I 73 (337)
T PF06136_consen 29 LYLRDVKDRLTALRGKGMPDMYSWSCKRSYKNGFVWHDLSDDDLI 73 (337)
T ss_pred cCHHHHHHHHHHhhCCCcceeeEEeeeccccCCceeccCcCCCee
Confidence 779999999999999875 589999976
No 258
>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=37.39 E-value=57 Score=24.22 Aligned_cols=67 Identities=19% Similarity=0.244 Sum_probs=42.1
Q ss_pred HHHHHHHHcCCC--CCCCCCcccccccccc---------cchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCC
Q 025599 66 QFHEMCAKVGVD--PLASNKGFWAELLGIG---------DFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSN 134 (250)
Q Consensus 66 ~F~~mC~siGVD--PL~s~k~~ws~~lG~g---------dfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~ 134 (250)
+|...|..||-| .|+ .-||+. ++-..+-.|+.++...=+..+|.--++..|.+.+.+
T Consensus 6 ~l~~ia~~lG~dW~~LA-------r~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~at~~~L~~AL~~----- 73 (84)
T cd08317 6 RLADISNLLGSDWPQLA-------RELGVSETDIDLIKAENPNSLAQQAQAMLKLWLEREGKKATGNSLEKALKK----- 73 (84)
T ss_pred hHHHHHHHHhhHHHHHH-------HHcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcCCcchHHHHHHHHHH-----
Confidence 588999999977 444 234432 222234466666666667777777777777777665
Q ss_pred CCCCCHHHHHHHH
Q 025599 135 REAVSEDDCLRAI 147 (250)
Q Consensus 135 ~~~IS~~DI~rAi 147 (250)
|-..||...|
T Consensus 74 ---i~r~Di~~~~ 83 (84)
T cd08317 74 ---IGRDDIVEKC 83 (84)
T ss_pred ---cChHHHHHHh
Confidence 4556666554
No 259
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=37.20 E-value=49 Score=27.16 Aligned_cols=36 Identities=22% Similarity=0.312 Sum_probs=32.5
Q ss_pred CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecC
Q 025599 191 FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
--|+.+|+..+|-++.-++.+...|+++|++-..-.
T Consensus 35 LPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg 70 (125)
T COG1725 35 LPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRG 70 (125)
T ss_pred CCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 369999999999999999999999999999977643
No 260
>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=36.95 E-value=2.7e+02 Score=29.65 Aligned_cols=133 Identities=8% Similarity=0.069 Sum_probs=68.2
Q ss_pred cchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccc------cccChhHHHHHHHHHHHcCCCC
Q 025599 5 PGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKND------IRKNPTFRSQFHEMCAKVGVDP 78 (250)
Q Consensus 5 ~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~e------I~~dp~fR~~F~~mC~siGVDP 78 (250)
-|+.+|-+..+++.+-.+.+..-..++.+-++..+.++ ..+.+||..|+.. -..||+-++.+.+|....+-+|
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 RGLRWLLEESERRIRALEESGVYEGEKYSFYQAAKIVL-EAVINHILRYAKLAEEMAASETGESRREELLKIAEICRKVA 246 (786)
T ss_pred HHHHHHHHHHHHHHHhccCCCchhhhHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHhccCc
Confidence 37777776544333222211111122333333333332 2333444444321 3569999999999999999998
Q ss_pred CCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHH---H-HHHHhhcCCCCCCCCHHHHHHHHhhc
Q 025599 79 LASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQEL---C-NLLRQRRKSNREAVSEDDCLRAISKL 150 (250)
Q Consensus 79 L~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el---~-~~v~k~R~~~~~~IS~~DI~rAik~L 150 (250)
--.-+.||- ++= -=|++.|+++ .+.||.-|++--+ + -.+.|- .....||+++...-++.|
T Consensus 247 ~~pa~tf~E-AlQ-~~wf~~l~~~--------~E~ng~~~s~GR~Dq~L~Pyy~~D--l~~G~it~e~A~ELl~~~ 310 (786)
T TIGR01774 247 AEKPQTFWQ-AVQ-LVWLVQSILQ--------QESNEQSISMGRIDQYLYPFYKKD--IGEGRIDRELAFEILASL 310 (786)
T ss_pred ccCCCCHHH-HHH-HHHHHHHHHH--------HhccccccCCCchHHHHHHHHHhH--HhcCCCCHHHHHHHHHHH
Confidence 876667774 321 2233333333 2456766665433 2 223331 112347888866665544
No 261
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=36.61 E-value=39 Score=22.46 Aligned_cols=22 Identities=27% Similarity=0.644 Sum_probs=15.0
Q ss_pred HHHHHHHHhcccccccChhHHHHHHH
Q 025599 44 SQLEDFARKHKNDIRKNPTFRSQFHE 69 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~fR~~F~~ 69 (250)
+.|+.|..+ +++||+||.++++
T Consensus 4 ~~l~~Fl~~----~~~d~~l~~~l~~ 25 (49)
T PF07862_consen 4 ESLKAFLEK----VKSDPELREQLKA 25 (49)
T ss_pred HHHHHHHHH----HhcCHHHHHHHHh
Confidence 345555553 3479999988887
No 262
>PF00888 Cullin: Cullin family; InterPro: IPR001373 Cullins are a family of hydrophobic proteins that act as scaffolds for ubiquitin ligases (E3). Cullins are found throughout eukaryotes. Humans express seven cullins (Cul1, 2, 3, 4A, 4B, 5 and 7), each forming part of a multi-subunit ubiquitin complex. Cullin-RING ubiquitin ligases (CRLs), such as Cul1 (SCF) [], play an essential role in targeting proteins for ubiquitin-mediated destruction; as such, they are diverse in terms of composition and function, regulating many different processes from glucose sensing and DNA replication to limb patterning and circadian rhythms. The catalytic core of CRLs consists of a RING protein and a cullin family member. For Cul1, the C-terminal cullin-homology domain binds the RING protein. The RING protein appears to function as a docking site for ubiquitin-conjugating enzymes (E2s). Other proteins contain a cullin-homology domain, such as the APC2 subunit of the anaphase-promoting complex/cyclosome and the p53 cytoplasmic anchor PARC; both APC2 and PARC have ubiquitin ligase activity. The N-terminal region of cullins is more variable, and is used to interact with specific adaptor proteins [, , ]. This entry represents the N-terminal region of cullin proteins, which consists of several domains, including cullin repeat domain, a 4-helical bundle domain, an alpha+beta domain, and a winged helix-like domain.; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 2WZK_A 3DQV_D 3DPL_C 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_A 1U6G_A 4A0K_A ....
Probab=36.01 E-value=35 Score=33.56 Aligned_cols=81 Identities=16% Similarity=0.167 Sum_probs=56.0
Q ss_pred HHHHHHHHhhcc----------------ccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCC
Q 025599 140 EDDCLRAISKLK----------------VLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSW 203 (250)
Q Consensus 140 ~~DI~rAik~L~----------------~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W 203 (250)
|+.+..+++..+ .||.+---..+++.++.-.+ +.-|..||-+-.....+|+++|.+..|.
T Consensus 471 P~~l~~~~~~f~~~Y~~~~~~R~L~w~~~l~~~~i~~~~~~~~~~l~~----s~~q~~iLl~Fn~~~~~t~~ei~~~~~~ 546 (588)
T PF00888_consen 471 PPELQQALDSFEKFYKEKHKGRKLTWLPSLSSVEIEFNFNNGKYELTV----STLQAAILLLFNDNDSLTVEEISEKTGI 546 (588)
T ss_dssp -HHHHHHHHHHHHHHHTTSTTEEEEEEGGGEEEEEEEESSSSEEEEEE----EHHHHHHHHGGGSSSEEEHHHHHHHC--
T ss_pred CHHHHHHHHHHHHHHHhcCCCcEEEEecccCcEEEEEEecCCceeEEe----eHHHHHHHHHHccCCCccHHHHHHHHCc
Confidence 566776666554 24443333333344343344 7779888877777888999999999999
Q ss_pred ChHHHHHHHHHHHHcCCceee
Q 025599 204 TSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 204 ~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
+....+.+|..|+..|++-..
T Consensus 547 ~~~~l~~~L~~l~~~~~l~~~ 567 (588)
T PF00888_consen 547 SEEELKRALKSLVKSKILILL 567 (588)
T ss_dssp -HHHHHHHHHCCCTTTTCSEE
T ss_pred CHHHHHHHHHHHHhCCcceee
Confidence 999999999999999999865
No 263
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=35.83 E-value=2.6e+02 Score=28.11 Aligned_cols=107 Identities=10% Similarity=0.111 Sum_probs=64.8
Q ss_pred HHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCC-----cc
Q 025599 101 VQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPT-----EL 175 (250)
Q Consensus 101 vqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~-----El 175 (250)
.+|.+.+.. +|..++..++-.. ..++.++|.+|++.|+.-| +.-+.--....+...+. +-
T Consensus 6 ~~iL~~l~~----~~~~~~~~~la~~---------~g~~~~~v~~~~~~L~~kg--~v~~~~~~~~~~~LT~eG~~~l~~ 70 (492)
T PLN02853 6 EALLGALSN----NEEISDSGQFAAS---------HGLDHNEVVGVIKSLHGFR--YVDAQDIKRETWVLTEEGKKYAAE 70 (492)
T ss_pred HHHHHHHHh----cCCCCCHHHHHHH---------cCCCHHHHHHHHHHHHhCC--CEEEEEEEEEEEEECHHHHHHHHc
Confidence 445544433 3434566666332 2378999999999999875 33332222222322221 00
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
..=...+++++...|.++.++|...++ ..-++-++-.+.++|.+-+|
T Consensus 71 G~PE~rl~~~l~~~~~~~~~eL~~~l~--~~~~~i~~g~a~k~gwi~i~ 117 (492)
T PLN02853 71 GSPEVQLFAAVPAEGSISKDELQKKLD--PAVFDIGFKQAMKNKWLEMG 117 (492)
T ss_pred CCHHHHHHHHHhhcCCccHHHHHHhhC--chhHHHHHHHHHHCCcEEEC
Confidence 011233566666557789999998773 35678899999999988886
No 264
>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=35.60 E-value=24 Score=26.36 Aligned_cols=23 Identities=9% Similarity=0.291 Sum_probs=17.9
Q ss_pred cccChhHHHHHHHHHHHcCCCCC
Q 025599 57 IRKNPTFRSQFHEMCAKVGVDPL 79 (250)
Q Consensus 57 I~~dp~fR~~F~~mC~siGVDPL 79 (250)
||=|++.+.++.++|..+|++|-
T Consensus 6 ~Rid~~lK~~a~~il~~~Glt~s 28 (83)
T PF04221_consen 6 VRIDEELKEEAEAILEELGLTLS 28 (83)
T ss_dssp EEE-HHHHHHHHHHHHHTT--HH
T ss_pred EEcCHHHHHHHHHHHHHcCCCHH
Confidence 56799999999999999999973
No 265
>PF07352 Phage_Mu_Gam: Bacteriophage Mu Gam like protein; InterPro: IPR009951 The Gam protein, originally characterised in Bacteriophage Mu, protects linear double stranded DNA from exonuclease degradation in vitro and in vivo []. This protein is also found in many bacterial species as part of a suspected prophage. Further studies have shown that Gam is a functional counterpart of the eukaryotic Ku protein, which has key roles in DNA repair and in certain transposition events. Gam displays DNA binding characteristics remarkably similar to those of human Ku []. In addition, Gam can interfere with Ty1 retrotransposition in Saccharomyces cerevisiae (Baker's yeast). These data reveal structural and functional parallels between bacteriophage Gam and eukaryotic Ku and suggest that their functions have been evolutionarily conserved [].; GO: 0003690 double-stranded DNA binding, 0042262 DNA protection; PDB: 2P2U_B.
Probab=35.57 E-value=85 Score=25.89 Aligned_cols=29 Identities=7% Similarity=0.336 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccccc
Q 025599 30 LRTDLMKEQLATFRSQLEDFARKHKNDIR 58 (250)
Q Consensus 30 ~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~ 58 (250)
.+...+..+++.|...|..|+..|+.+..
T Consensus 39 ~~~~~l~~~i~~l~~~l~~y~e~~r~e~~ 67 (149)
T PF07352_consen 39 AEIAPLQNRIEYLEGLLQAYAEANRDELT 67 (149)
T ss_dssp HHCHHHHHHHHHHHHHHHHHHHCTHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCHHhcc
Confidence 34567888888899999999999987654
No 266
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=35.36 E-value=1e+02 Score=27.30 Aligned_cols=45 Identities=13% Similarity=0.279 Sum_probs=37.4
Q ss_pred cCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 171 VPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 171 vp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
.|..||..+..||.++.. |+ |..++++.++++..-++.-+..+.+
T Consensus 130 ~~~~LSpRErEVLrLLAq-Gk-TnKEIAe~L~IS~rTVkth~srImk 174 (198)
T PRK15201 130 TTRHFSVTERHLLKLIAS-GY-HLSETAALLSLSEEQTKSLRRSIMR 174 (198)
T ss_pred CCCCCCHHHHHHHHHHHC-CC-CHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 477899999999998886 44 8999999999999988887775443
No 267
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=35.18 E-value=93 Score=25.84 Aligned_cols=40 Identities=28% Similarity=0.287 Sum_probs=34.3
Q ss_pred HHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 182 ILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 182 vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
++.+|.. .+-+|.++|++..|.++.=....|-.|.+.|++
T Consensus 14 L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV 55 (150)
T COG1959 14 LLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLV 55 (150)
T ss_pred HHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCE
Confidence 4555653 337999999999999999999999999999997
No 268
>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=34.99 E-value=83 Score=22.22 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=35.3
Q ss_pred ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccC
Q 025599 93 GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLG 154 (250)
Q Consensus 93 gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG 154 (250)
.|.|-+++.+|+++... -|-.++.++.+..+ ++++.|..|+-.|--.+
T Consensus 8 ~~~fG~~~~~V~~~Ll~-----~G~ltl~~i~~~t~---------l~~~~Vk~~L~~LiQh~ 55 (62)
T PF08221_consen 8 EEHFGEIVAKVGEVLLS-----RGRLTLREIVRRTG---------LSPKQVKKALVVLIQHN 55 (62)
T ss_dssp HHHHHHHHHHHHHHHHH-----C-SEEHHHHHHHHT-----------HHHHHHHHHHHHHTT
T ss_pred HHHcChHHHHHHHHHHH-----cCCcCHHHHHHHhC---------CCHHHHHHHHHHHHHcC
Confidence 57899999999999976 46788888875432 79999999988775433
No 269
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=34.92 E-value=3.8e+02 Score=26.28 Aligned_cols=168 Identities=13% Similarity=0.205 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHH-------------------HHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC------CC
Q 025599 27 VAKLRTDLMKEQLATFRS-------------------QLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL------AS 81 (250)
Q Consensus 27 l~~~~~~~l~~qL~~F~~-------------------~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL------~s 81 (250)
|+.++--+|.+|.+.+-. .|++.=.+-..++-..|++- +.+..+|+|+- ..
T Consensus 75 L~~~eEv~l~~~vq~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~g~~pt~~----ewa~~~~~~~~~l~~~l~~ 150 (415)
T PRK07598 75 LGRDEEVSEAQKVQRYMKLIVLANAAKEGDEVIKPYLRLIEVRERLTSELGHRPSLE----RWAKTADISLADLKPTLAE 150 (415)
T ss_pred CCHHHHHHHHHHHHHHHHHhhhhhhhhcccchhhhHHHHHHHHHHHHHHhCCCCCHH----HHHHHhCCcHHHHHHhhhh
Q ss_pred CCcccccccccc----------------cchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHH
Q 025599 82 NKGFWAELLGIG----------------DFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLR 145 (250)
Q Consensus 82 ~k~~ws~~lG~g----------------dfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~r 145 (250)
++..|++..|++ ..+..---.|+-||..-...+ +++.||++-.+-. +.+
T Consensus 151 ~~~~~~~~~~l~~~eL~~~l~~G~~A~e~LI~~nlrLVvsiAkky~~~g---~~~eDLiQEG~iG------------L~r 215 (415)
T PRK07598 151 GKRRWAEIAKLTVEELEQIQKQGLRAKEHMIKANLRLVVSVAKKYQNRG---LELLDLVQEGTLG------------LER 215 (415)
T ss_pred hhhhhhhhccCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHccCC---CCHHHHHHHHHHH------------HHH
Q ss_pred HHhhcccc-CCCeEEEEE-----------CCEEEEEecCCccchhHHHHHHHHHh-----CCCccHHHHHHhcCCChHHH
Q 025599 146 AISKLKVL-GNGYEVISV-----------GKKKLVRSVPTELNKDHNQILELAQA-----QGFVTVDEVERRLSWTSGRA 208 (250)
Q Consensus 146 Aik~L~~L-G~g~~vi~i-----------g~~~~v~svp~El~~D~~~vLela~~-----~g~vt~~~L~~~l~W~~~Ra 208 (250)
|++++.+= |..|..--+ ........+|.-++.-...+-..-.. +..-|.++|++.+|++..+.
T Consensus 216 avekFDp~rG~rFSTYa~wwIRqaI~r~i~~~srtIrlP~~i~e~l~~lrk~~r~L~~~lgR~pt~~EiA~~l~is~~~v 295 (415)
T PRK07598 216 AVEKFDPTKGYRFSTYAYWWIRQGITRAIATQSRTIRLPVHITEKLNKIKKAQRKISQEKGRTPTIEDIAQELEMTPTQV 295 (415)
T ss_pred HHHHcCcccCCCHHHHHHHHHHHHHHHHHHHcCCceehhHHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHH
Q ss_pred HHHHH
Q 025599 209 IDALD 213 (250)
Q Consensus 209 ~~~L~ 213 (250)
++++.
T Consensus 296 r~~l~ 300 (415)
T PRK07598 296 REVLL 300 (415)
T ss_pred HHHHH
No 270
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=34.81 E-value=1.7e+02 Score=25.09 Aligned_cols=71 Identities=7% Similarity=0.093 Sum_probs=50.6
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
..+++++..||+.... |..| + .. ...+-|..|+.-+..||.+... |+ |..++++.++.+..-++..+..+.
T Consensus 107 ~~~~~~L~~aI~~v~~-g~~~--~--~~--~~~~~~~~LT~RE~eVL~lla~-G~-snkeIA~~L~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 107 SIKPESLDDLLGDILK-KETT--I--TS--FLNLPTLSLSRTESSMLRMWMA-GQ-GTIQISDQMNIKAKTVSSHKGNIK 177 (207)
T ss_pred cCCHHHHHHHHHHHHc-CCcc--c--Cc--cccCCcccCCHHHHHHHHHHHc-CC-CHHHHHHHcCCCHHHHHHHHHHHH
Confidence 5689999999988643 2111 1 10 0112234599999999998876 44 889999999999999998887543
No 271
>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=34.80 E-value=95 Score=22.26 Aligned_cols=39 Identities=15% Similarity=0.199 Sum_probs=29.1
Q ss_pred HHHHHHh-CCCccHHHHHHhc---CC--ChHHHHHHHHHHHHcCC
Q 025599 182 ILELAQA-QGFVTVDEVERRL---SW--TSGRAIDALDILLEEGL 220 (250)
Q Consensus 182 vLela~~-~g~vt~~~L~~~l---~W--~~~Ra~~~L~~l~~~Gl 220 (250)
||++... .+-++...|++.+ |+ +..-.+..|..|.++|+
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Gl 47 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGL 47 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCC
Confidence 5666553 5668888887766 44 45888999999999993
No 272
>PHA02047 phage lambda Rz1-like protein
Probab=34.48 E-value=1e+02 Score=24.43 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHH---HHHHHHHHhcccccc
Q 025599 30 LRTDLMKEQLATFR---SQLEDFARKHKNDIR 58 (250)
Q Consensus 30 ~~~~~l~~qL~~F~---~~L~~Fa~~h~~eI~ 58 (250)
.|+++++.++...+ ..|+..+.+...||+
T Consensus 41 ~qLE~a~~r~~~~Q~~V~~l~~kae~~t~Ei~ 72 (101)
T PHA02047 41 ARLEALEVRYATLQRHVQAVEARTNTQRQEVD 72 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666666666 456666666655554
No 273
>PRK14339 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=34.32 E-value=1.1e+02 Score=29.59 Aligned_cols=48 Identities=17% Similarity=0.309 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHh
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQA 188 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~ 188 (250)
..|.+++++++++++....|+.+.+ .+|--.|+|=..|....++++..
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 4689999999999998876766543 36666799999999999999885
No 274
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=34.14 E-value=92 Score=25.84 Aligned_cols=47 Identities=17% Similarity=0.301 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccccc---ccChhHHHHHHHHHHHcCCCC
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKNDI---RKNPTFRSQFHEMCAKVGVDP 78 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~eI---~~dp~fR~~F~~mC~siGVDP 78 (250)
+++|...++.|...+++--.+..... .+-.+-..++++|....|+||
T Consensus 23 ~e~Lee~~ekl~~vv~er~ee~~~~~~~~~er~~kl~~~r~~m~~~Gis~ 72 (135)
T PRK10947 23 LETLEEMLEKLEVVVNERREEESAAAAEVEERTRKLQQYREMLIADGIDP 72 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCH
Confidence 66777777777766666555444433 333344678999999999996
No 275
>smart00350 MCM minichromosome maintenance proteins.
Probab=34.02 E-value=71 Score=31.70 Aligned_cols=52 Identities=23% Similarity=0.288 Sum_probs=30.8
Q ss_pred hhHHHHHHHhhhhcccCCC-------------ceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhcc
Q 025599 98 ELGVQIVEICLATRPHNGG-------------LINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK 151 (250)
Q Consensus 98 eLavqIvevC~~tr~~nGG-------------li~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~ 151 (250)
+....|++++.++|..... +++|-.+-+...|.++ ...|+++|+..|++.+.
T Consensus 441 ~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~--r~~V~~~Dv~~ai~l~~ 505 (509)
T smart00350 441 EAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRL--SDVVEEADVEEAIRLLR 505 (509)
T ss_pred HHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcC--CCccCHHHHHHHHHHHH
Confidence 4455566677777753321 1223333333333334 47899999999999874
No 276
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=33.64 E-value=60 Score=23.95 Aligned_cols=31 Identities=23% Similarity=0.348 Sum_probs=27.1
Q ss_pred HHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 194 VDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 194 ~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
+.+|++.++.++.-....|..|++.|++=.+
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~ 32 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYE 32 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEc
Confidence 4689999999999999999999999966554
No 277
>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=33.46 E-value=1.4e+02 Score=21.40 Aligned_cols=13 Identities=15% Similarity=0.222 Sum_probs=11.1
Q ss_pred CCCCHHHHHHHHh
Q 025599 136 EAVSEDDCLRAIS 148 (250)
Q Consensus 136 ~~IS~~DI~rAik 148 (250)
..||.+||..|++
T Consensus 53 ktlt~~DI~~Alk 65 (65)
T smart00803 53 TTLTTSDIDSALR 65 (65)
T ss_pred CeecHHHHHHHhC
Confidence 5699999999875
No 278
>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=33.36 E-value=1.5e+02 Score=24.73 Aligned_cols=56 Identities=21% Similarity=0.346 Sum_probs=42.5
Q ss_pred HHHHHHHHHh--CCCccHHHHHHhc--CCChHHHHHHHHHHHHcCCceeecCCCCCCcceeec
Q 025599 179 HNQILELAQA--QGFVTVDEVERRL--SWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFP 237 (250)
Q Consensus 179 ~~~vLela~~--~g~vt~~~L~~~l--~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P 237 (250)
...|+++... ++| |+.++.+|| +.++.-+..+|+.|+.+|.+=.=.-+ .-..||.+
T Consensus 3 e~~Il~y~~~qNRPy-s~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~G--KqkiY~~~ 62 (169)
T PF07106_consen 3 EDAILEYMKEQNRPY-SAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYG--KQKIYFAN 62 (169)
T ss_pred HHHHHHHHHHcCCCC-cHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeec--ceEEEeeC
Confidence 3468888773 555 999999999 58999999999999999988666543 23455543
No 279
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=33.28 E-value=1.4e+02 Score=21.11 Aligned_cols=46 Identities=15% Similarity=0.309 Sum_probs=26.7
Q ss_pred HHHHHhhcHhHHHH--HHHHHHHHHHHH---HHHHHHHHHhcccccccChh
Q 025599 17 RDQYRLLGENVAKL--RTDLMKEQLATF---RSQLEDFARKHKNDIRKNPT 62 (250)
Q Consensus 17 ~~~~~~~g~~l~~~--~~~~l~~qL~~F---~~~L~~Fa~~h~~eI~~dp~ 62 (250)
+++.+++-.++.+. +.++|+.+++.. .+.++.+|++.-+=++.|+.
T Consensus 23 ~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR~~lgm~~~~E~ 73 (80)
T PF04977_consen 23 NQEIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAREKLGMVKPGEI 73 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcCCcCCCCE
Confidence 44444444444332 345677777777 36777777766665665554
No 280
>COG0309 HypE Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.15 E-value=30 Score=33.05 Aligned_cols=37 Identities=24% Similarity=0.492 Sum_probs=30.1
Q ss_pred HHHHHHHHhcccccccChh---HHHHHHHHHHHcCCCCCC
Q 025599 44 SQLEDFARKHKNDIRKNPT---FRSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 44 ~~L~~Fa~~h~~eI~~dp~---fR~~F~~mC~siGVDPL~ 80 (250)
..|.++|.+-...|+=+++ +|..-+.+|.-+|+|||.
T Consensus 232 ~aLnEmA~aSgvgi~I~ee~Ipv~~eVr~vce~lGiDPl~ 271 (339)
T COG0309 232 GALNEMAEASGVGISIEEEKIPVREEVRGVCELLGLDPLE 271 (339)
T ss_pred HHHHHHHHHcCCeEEEeeccccccHHHHHHHHHhCCCHHH
Confidence 6788999988876655543 777788999999999996
No 281
>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=33.07 E-value=54 Score=23.85 Aligned_cols=26 Identities=27% Similarity=0.784 Sum_probs=19.6
Q ss_pred cccccChhHHHHHHHHHHHcCCCCCCC
Q 025599 55 NDIRKNPTFRSQFHEMCAKVGVDPLAS 81 (250)
Q Consensus 55 ~eI~~dp~fR~~F~~mC~siGVDPL~s 81 (250)
.+++....+ ..++.+|...|+||+..
T Consensus 21 ~~~~~~~vy-~~Y~~~c~~~~~~~l~~ 46 (87)
T cd08768 21 EEATTGEVY-EVYEELCEEIGVDPLTQ 46 (87)
T ss_pred CCccHHHHH-HHHHHHHHHcCCCCCcH
Confidence 455544444 58999999999999874
No 282
>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=32.95 E-value=22 Score=29.25 Aligned_cols=54 Identities=20% Similarity=0.413 Sum_probs=35.6
Q ss_pred ccccChhHH--HHHHHHHHHcCCCCCC---CCCccccccccc-ccchhhhHHHHHHHhhh
Q 025599 56 DIRKNPTFR--SQFHEMCAKVGVDPLA---SNKGFWAELLGI-GDFYYELGVQIVEICLA 109 (250)
Q Consensus 56 eI~~dp~fR--~~F~~mC~siGVDPL~---s~k~~ws~~lG~-gdfy~eLavqIvevC~~ 109 (250)
+-.+.|||. .-|...|...|||||. .-.|.|.+-.|+ -+-+.+.-.+|-++|.+
T Consensus 28 ~y~~SpEy~Dl~l~L~~~k~~g~~~lfVi~PvNg~wydytG~~~~~r~~~y~kI~~~~~~ 87 (130)
T PF04914_consen 28 SYTKSPEYDDLQLLLDVCKELGIDVLFVIQPVNGKWYDYTGLSKEMRQEYYKKIKYQLKS 87 (130)
T ss_dssp --SS-THHHHHHHHHHHHHHTT-EEEEEE----HHHHHHTT--HHHHHHHHHHHHHHHHT
T ss_pred cccCCccHHHHHHHHHHHHHcCCceEEEecCCcHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 344567653 2467789999999994 336889988887 47778888888888876
No 283
>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=32.90 E-value=1.5e+02 Score=26.27 Aligned_cols=18 Identities=17% Similarity=0.311 Sum_probs=10.7
Q ss_pred CCCceeH--HHHHHHHHhhc
Q 025599 114 NGGLINL--QELCNLLRQRR 131 (250)
Q Consensus 114 nGGli~l--~el~~~v~k~R 131 (250)
.+|.|+| .+.+|++.--|
T Consensus 128 e~G~~E~KSte~M~rL~aD~ 147 (228)
T PF06721_consen 128 ENGEMEMKSTERMCRLKADK 147 (228)
T ss_pred hcCceeecccchHHHHHccH
Confidence 3567744 47777766543
No 284
>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=32.87 E-value=51 Score=23.78 Aligned_cols=33 Identities=21% Similarity=0.316 Sum_probs=27.4
Q ss_pred CCccHHHHHHhcCCChHHHHHHHHHHHHcCCce
Q 025599 190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAM 222 (250)
Q Consensus 190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~W 222 (250)
|.++++.+++..|.+..-...+|.-|+..|++=
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 678999999999999999999999999999863
No 285
>COG0405 Ggt Gamma-glutamyltransferase [Amino acid transport and metabolism]
Probab=32.58 E-value=93 Score=31.59 Aligned_cols=34 Identities=29% Similarity=0.486 Sum_probs=25.1
Q ss_pred cccch-hhhHHHHHHHhhhhcccCCCceeHHHHHHHHHh
Q 025599 92 IGDFY-YELGVQIVEICLATRPHNGGLINLQELCNLLRQ 129 (250)
Q Consensus 92 ~gdfy-~eLavqIvevC~~tr~~nGGli~l~el~~~v~k 129 (250)
...|| -+||.+|++...+. ||+|+++|+-..=.+
T Consensus 207 ~~~FY~G~iA~~iv~~~~~~----gG~lt~eDla~Y~~~ 241 (539)
T COG0405 207 PDAFYKGEIADAIVKAVQKA----GGLLTLEDLAGYRVE 241 (539)
T ss_pred cccccCcHHHHHHHHHHHHc----CCcccHHHHhhCCce
Confidence 34566 47888888877654 999999999765333
No 286
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=32.56 E-value=1e+02 Score=27.46 Aligned_cols=17 Identities=18% Similarity=0.315 Sum_probs=14.2
Q ss_pred CCCCHHHHHHHHhhccc
Q 025599 136 EAVSEDDCLRAISKLKV 152 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~ 152 (250)
..++++++.++++.|..
T Consensus 111 ~~~~~~~l~~~~~~i~~ 127 (278)
T PRK11557 111 DVNSEEKLHECVTMLRS 127 (278)
T ss_pred HhcCHHHHHHHHHHHhc
Confidence 45899999999999864
No 287
>cd03036 ArsC_like Arsenate Reductase (ArsC) family, unknown subfamily; uncharacterized proteins containing a CXXC motif with similarity to thioredoxin (TRX)-fold arsenic reductases, ArsC. Proteins containing a redox active CXXC motif like TRX and glutaredoxin (GRX) function as protein disulfide oxidoreductases, altering the redox state of target proteins via the reversible oxidation of the active site dithiol. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via GRX, through a single catalytic cysteine.
Probab=32.46 E-value=63 Score=25.16 Aligned_cols=40 Identities=15% Similarity=0.303 Sum_probs=28.3
Q ss_pred HHHHHHHHHhcc-----cccccChhHHHHHHHHHHHcCC--CCCCCC
Q 025599 43 RSQLEDFARKHK-----NDIRKNPTFRSQFHEMCAKVGV--DPLASN 82 (250)
Q Consensus 43 ~~~L~~Fa~~h~-----~eI~~dp~fR~~F~~mC~siGV--DPL~s~ 82 (250)
.....+|..+|. .+|.+||.-+..+++++...|+ +.+.+.
T Consensus 12 c~ka~~~L~~~~i~~~~idi~~~~~~~~el~~~~~~~~~~~~~l~~~ 58 (111)
T cd03036 12 CRKAKKWLDEHGVDYTAIDIVEEPPSKEELKKWLEKSGLPLKKFFNT 58 (111)
T ss_pred HHHHHHHHHHcCCceEEecccCCcccHHHHHHHHHHcCCCHHHHHhc
Confidence 334445555554 4788999999999999999885 455433
No 288
>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=32.45 E-value=65 Score=22.97 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=13.3
Q ss_pred eeHHHHHHHHHhhcCCCCCCCCHHHHHHHH
Q 025599 118 INLQELCNLLRQRRKSNREAVSEDDCLRAI 147 (250)
Q Consensus 118 i~l~el~~~v~k~R~~~~~~IS~~DI~rAi 147 (250)
|++.|....+.+.|.+ ||++||.+=.
T Consensus 30 it~~DF~~Al~~~kpS----Vs~~dl~~ye 55 (62)
T PF09336_consen 30 ITMEDFEEALKKVKPS----VSQEDLKKYE 55 (62)
T ss_dssp BCHHHHHHHHHTCGGS----S-HHHHHHHH
T ss_pred CCHHHHHHHHHHcCCC----CCHHHHHHHH
Confidence 4455555555555442 5666665543
No 289
>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=32.35 E-value=89 Score=23.47 Aligned_cols=46 Identities=13% Similarity=0.035 Sum_probs=36.2
Q ss_pred cchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHH
Q 025599 94 DFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAI 147 (250)
Q Consensus 94 dfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAi 147 (250)
+++..+.-|+.+....=+...|.=-+...|+..+.+ |-..||+..+
T Consensus 38 ~~~~~~~eq~~~mL~~W~~r~g~~At~~~L~~aL~~--------i~r~Div~~~ 83 (84)
T cd08804 38 ENPNSLQDQSHALLKYWLERDGKHATDTNLMKCLTK--------INRMDIVHLM 83 (84)
T ss_pred HCcccHHHHHHHHHHHHHHccCCCchHHHHHHHHHH--------cChHHHHHHh
Confidence 667788999999998888888877777778777776 5667887654
No 290
>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=32.34 E-value=75 Score=27.83 Aligned_cols=46 Identities=15% Similarity=0.338 Sum_probs=33.9
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc--eeecCC
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA--MVDDGH 227 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~--WvD~q~ 227 (250)
.++++...-.|..++|+..+|.+..-+..+|..|..+|.+ =+||..
T Consensus 104 Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrG 151 (188)
T PF09756_consen 104 FINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRG 151 (188)
T ss_dssp HHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT-
T ss_pred HHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCC
Confidence 3455556779999999999999999999999999999987 467753
No 291
>TIGR01617 arsC_related transcriptional regulator, Spx/MgsR family. This model represents a portion of the proteins within the larger set covered by Pfam model pfam03960. That larger family includes a glutaredoxin-dependent arsenate reductase (TIGR00014). Characterized members of this family include Spx and MgsR from Bacillus subtili. Spx is a global regulator for response to thiol-specific oxidative stress. It interacts with RNA polymerase. MgsR (modulator of the general stress response, also called YqgZ) provides a second level of regulation for more than a third of the proteins in the B. subtilis general stress regulon controlled by Sigma-B.
Probab=32.14 E-value=65 Score=25.19 Aligned_cols=39 Identities=15% Similarity=0.323 Sum_probs=29.5
Q ss_pred HHHHHHHHhcc-----cccccChhHHHHHHHHHHHcC--CCCCCCC
Q 025599 44 SQLEDFARKHK-----NDIRKNPTFRSQFHEMCAKVG--VDPLASN 82 (250)
Q Consensus 44 ~~L~~Fa~~h~-----~eI~~dp~fR~~F~~mC~siG--VDPL~s~ 82 (250)
.....|..+|. -+|.++|.-+.++.+++..+| ++++.+.
T Consensus 13 ~ka~~~L~~~~i~~~~idi~~~~~~~~el~~l~~~~~~~~~~lin~ 58 (117)
T TIGR01617 13 KKARRWLEANGIEYQFIDIGEDGPTREELLDILSLLEDGIDPLLNT 58 (117)
T ss_pred HHHHHHHHHcCCceEEEecCCChhhHHHHHHHHHHcCCCHHHheeC
Confidence 34445556655 578899999999999999998 6767644
No 292
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.07 E-value=1.5e+02 Score=26.91 Aligned_cols=59 Identities=15% Similarity=0.115 Sum_probs=49.3
Q ss_pred HHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCccCC
Q 025599 181 QILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCASSI 242 (250)
Q Consensus 181 ~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~~~ 242 (250)
.+++....++..+.+|++++++..+.-++=-|..|+.++++=-=. .+....+||+=+.-
T Consensus 105 ~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~---~~g~~~yfpa~~t~ 163 (240)
T COG3398 105 GIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGR---VGGALRYFPADMTY 163 (240)
T ss_pred HHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhc---cCCceEEccCCCCc
Confidence 388888888999999999999999999999999999999874332 23588889986654
No 293
>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=32.04 E-value=1.6e+02 Score=29.86 Aligned_cols=75 Identities=20% Similarity=0.240 Sum_probs=56.8
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHH
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLE 217 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~ 217 (250)
+.++++.+.+..|...|. ++.+.+..|+- ..+.++++..|-+|+.++++.+|-+.-.|...|+.+-+
T Consensus 500 ~~~~~~~~~l~~l~~~g~---~~~~~~~~~~~----------~~~~~~~~~~~~~~~~~~r~~~g~sRK~~i~lle~~D~ 566 (581)
T TIGR00475 500 GDEKVMLKRVRKAGHRGG---ETLIVKDRLLK----------KYINELKEEGGTFNVQQARDKLGLGRKLLIQLLEYFDR 566 (581)
T ss_pred CCHHHHHHHHHHHHhCCC---EEEEeCCeEHH----------HHHHHHHhcCCcCcHHHHHHHHCccHHHHHHHHHHhhh
Confidence 456666666666666552 44454332322 56788888889999999999999999999999999999
Q ss_pred cCCceeec
Q 025599 218 EGLAMVDD 225 (250)
Q Consensus 218 ~Gl~WvD~ 225 (250)
.|+.=++.
T Consensus 567 ~~~T~r~g 574 (581)
T TIGR00475 567 LGFTRREG 574 (581)
T ss_pred CCCeEEeC
Confidence 99987664
No 294
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=31.98 E-value=60 Score=28.89 Aligned_cols=33 Identities=21% Similarity=0.252 Sum_probs=30.4
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
-|..+|++.||-|..-.+++|..|...|++.+=
T Consensus 35 P~EreLae~fgVSR~~vREAl~~L~a~Glve~r 67 (241)
T COG2186 35 PSERELAERFGVSRTVVREALKRLEAKGLVEIR 67 (241)
T ss_pred CCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeec
Confidence 478999999999999999999999999988765
No 295
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=31.93 E-value=1.3e+02 Score=25.01 Aligned_cols=47 Identities=17% Similarity=0.376 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccc---ccccChhHHHHHHHHHHHcCCCC
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKN---DIRKNPTFRSQFHEMCAKVGVDP 78 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~---eI~~dp~fR~~F~~mC~siGVDP 78 (250)
+++|...++.|..-+++--.++.. +..+-.+...++++|...-|+||
T Consensus 23 ~e~Lee~~ekl~~vv~er~~~~~~~~~~~~er~~~l~~i~~~~~~~Git~ 72 (134)
T PRK10328 23 IDVLEEMLEKFRVVTKERREEEEQQQRELAERQEKINTWLELMKADGINP 72 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCH
Confidence 666777777777665554443333 33334467789999999999996
No 296
>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=31.62 E-value=2.1e+02 Score=23.63 Aligned_cols=71 Identities=18% Similarity=0.286 Sum_probs=39.8
Q ss_pred cchhhhhccHHHHHHHH----hhcHhHHHHHHHHHHHHHHHHH-------HHHHHHHHhcccccccChhHHHHHHHHHHH
Q 025599 5 PGIGGLQSAAVARDQYR----LLGENVAKLRTDLMKEQLATFR-------SQLEDFARKHKNDIRKNPTFRSQFHEMCAK 73 (250)
Q Consensus 5 ~Gi~ai~~~~~~~~~~~----~~g~~l~~~~~~~l~~qL~~F~-------~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~s 73 (250)
.|+||+.+..++-.+|= ..|..+....-.....+++..+ ..+..-|...-+.+ .-.|-..+...+..
T Consensus 25 AGLGA~ak~~~EG~k~F~~LVk~Ge~~e~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~dkl--E~~fd~rV~~aL~r 102 (132)
T PF05597_consen 25 AGLGAYAKAQEEGSKVFEALVKEGEKLEKKTRKKAEEQVEEARDQVKSRVDDVKERATGQWDKL--EQAFDERVARALNR 102 (132)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHh
Confidence 58899888765533322 3344444444444444444444 44444444333333 23576778999999
Q ss_pred cCCC
Q 025599 74 VGVD 77 (250)
Q Consensus 74 iGVD 77 (250)
|||-
T Consensus 103 LgvP 106 (132)
T PF05597_consen 103 LGVP 106 (132)
T ss_pred cCCC
Confidence 9985
No 297
>COG1709 Predicted transcriptional regulator [Transcription]
Probab=31.32 E-value=90 Score=28.35 Aligned_cols=140 Identities=26% Similarity=0.345 Sum_probs=84.7
Q ss_pred HHHHHHHHHhccccc--ccCh--h---HHHHH----HHHHHHcCCCCCCCC---C---cccccccccccchhhhHHHHHH
Q 025599 43 RSQLEDFARKHKNDI--RKNP--T---FRSQF----HEMCAKVGVDPLASN---K---GFWAELLGIGDFYYELGVQIVE 105 (250)
Q Consensus 43 ~~~L~~Fa~~h~~eI--~~dp--~---fR~~F----~~mC~siGVDPL~s~---k---~~ws~~lG~gdfy~eLavqIve 105 (250)
...-+.-|.+-.+|| .+|| + -|.-| .+++..|||-|-.-+ + .+.. -..-.++|+
T Consensus 8 ~~~~~~va~rIaGdIvlS~~pge~lrKWR~~F~vSQ~elA~~l~vSpSVISDYE~GRRk~Pg---------~~~vkk~V~ 78 (241)
T COG1709 8 SYPRELLAKRIAGDIVLSEDPGETLRKWREIFNVSQTELARELGVSPSVISDYESGRRKSPG---------IAFVKKFVE 78 (241)
T ss_pred HHHHHHHHHHhhcceEecCChhHHHHHHHHHhCccHHHHHHHhCCCcceeehhhccCccCcc---------HHHHHHHHH
Confidence 334455566667777 4566 2 23333 356777999987533 0 1111 234578899
Q ss_pred HhhhhcccCCCceeHHHHHHHHHhhcCC--------CCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccch
Q 025599 106 ICLATRPHNGGLINLQELCNLLRQRRKS--------NREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNK 177 (250)
Q Consensus 106 vC~~tr~~nGGli~l~el~~~v~k~R~~--------~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~ 177 (250)
..+..-.+.||-. ++.+-..+...-.. +...|+.+++.+|++-=-+-+.+.. ..+-|.++|-|+
T Consensus 79 ALIeID~eRGg~v-ik~l~~~l~~~~~~~aildirEf~~pv~l~~~~~aidg~~v~~~~~~-~~v~GyTVvDSi------ 150 (241)
T COG1709 79 ALIEIDEERGGKV-IKALARVLGSEFPSKAILDIREFDIPVTLEELVEAIDGEIVVHDGAD-RDVYGYTVVDSI------ 150 (241)
T ss_pred HHHhhhHhhcchH-HHHHHHHhccCCchhheEehhhcCCCcCHHHHHHHhcceEecccCCC-cceeeeEEehhH------
Confidence 9999999999976 56665555552221 1257999999999986433222222 123355555444
Q ss_pred hHHHHHHHHHhCCCccHHHHHHhcCCChHHH
Q 025599 178 DHNQILELAQAQGFVTVDEVERRLSWTSGRA 208 (250)
Q Consensus 178 D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra 208 (250)
.+||+ +|..++...|||+..||
T Consensus 151 --kAIL~-------ls~~ef~~LyG~~t~Ra 172 (241)
T COG1709 151 --KAILE-------LSGLEFYRLYGWTTERA 172 (241)
T ss_pred --HHHHh-------cchhhHHHHhcCCcceE
Confidence 44554 35667788899999986
No 298
>PRK14333 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=31.26 E-value=1.1e+02 Score=29.64 Aligned_cols=48 Identities=15% Similarity=0.239 Sum_probs=39.1
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
.|.+++.++++.++..+.|+.+ +..+|--.|+|=..|....++++...
T Consensus 287 ~t~e~~~~~i~~lr~~~p~i~i----~~d~IvGfPgET~edf~~tl~~l~~~ 334 (448)
T PRK14333 287 YTHEKYRRIIDKIREYMPDASI----SADAIVGFPGETEAQFENTLKLVEEI 334 (448)
T ss_pred CCHHHHHHHHHHHHHhCCCcEE----EeeEEEECCCCCHHHHHHHHHHHHHc
Confidence 6899999999999988766654 22466677999999999999998854
No 299
>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=31.17 E-value=1e+02 Score=23.34 Aligned_cols=67 Identities=13% Similarity=0.075 Sum_probs=48.8
Q ss_pred HHHHHHHHcCCC--CCCCCCccccccccc---------ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCC
Q 025599 66 QFHEMCAKVGVD--PLASNKGFWAELLGI---------GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSN 134 (250)
Q Consensus 66 ~F~~mC~siGVD--PL~s~k~~ws~~lG~---------gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~ 134 (250)
+|...|..||-| .|+ .-||+ .++=..+..|+.+....=+...|.-=+...|++.+++
T Consensus 6 ~l~~Ia~~LG~dW~~La-------r~L~vs~~dI~~I~~e~p~~l~~Q~~~~L~~W~~r~g~~At~~~L~~AL~~----- 73 (84)
T cd08805 6 KMAVIREHLGLSWAELA-------RELQFSVEDINRIRVENPNSLLEQSTALLNLWVDREGENAKMSPLYPALYS----- 73 (84)
T ss_pred HHHHHHHHhcchHHHHH-------HHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCccchHHHHHHHHHH-----
Confidence 388899999988 333 12443 2555668888888888888888888888888888887
Q ss_pred CCCCCHHHHHHHH
Q 025599 135 REAVSEDDCLRAI 147 (250)
Q Consensus 135 ~~~IS~~DI~rAi 147 (250)
|...||+..+
T Consensus 74 ---i~R~div~~~ 83 (84)
T cd08805 74 ---IDRLTIVNML 83 (84)
T ss_pred ---CChHHHHHhh
Confidence 5677887643
No 300
>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=31.07 E-value=81 Score=21.76 Aligned_cols=37 Identities=22% Similarity=0.224 Sum_probs=30.8
Q ss_pred CCCccHHHHHHhc---CCChHHHHHHHHHHHHcCCceeec
Q 025599 189 QGFVTVDEVERRL---SWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 189 ~g~vt~~~L~~~l---~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+..++.++|+..+ +-+..-+...|+.|+++|.+.++.
T Consensus 15 r~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 15 RPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp SS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEES
T ss_pred ccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeEC
Confidence 4567999999877 778888999999999999999885
No 301
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=30.76 E-value=71 Score=25.54 Aligned_cols=36 Identities=28% Similarity=0.193 Sum_probs=31.2
Q ss_pred CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 190 GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 190 g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
..||.++|++.+.-|.--|+..|..|..+| ||+=++
T Consensus 18 ~~vtl~elA~~l~cS~Rn~r~lLkkm~~~g--Wi~W~p 53 (115)
T PF12793_consen 18 VEVTLDELAELLFCSRRNARTLLKKMQEEG--WITWQP 53 (115)
T ss_pred cceeHHHHHHHhCCCHHHHHHHHHHHHHCC--CeeeeC
Confidence 458999999999999999999999999998 555444
No 302
>PRK14332 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=30.73 E-value=1.4e+02 Score=29.12 Aligned_cols=49 Identities=10% Similarity=0.314 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
..|.+++.++++.++..+.++.+. ..+|--.|+|=-.|....++++...
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 479999999999999877777653 2466667999999999999998864
No 303
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=30.62 E-value=1e+02 Score=23.95 Aligned_cols=50 Identities=12% Similarity=0.139 Sum_probs=34.6
Q ss_pred ccchhHHHH--HHHHH--hCCCccHHHHHHhcCCChHHHHHHHHHH-HHcCCcee
Q 025599 174 ELNKDHNQI--LELAQ--AQGFVTVDEVERRLSWTSGRAIDALDIL-LEEGLAMV 223 (250)
Q Consensus 174 El~~D~~~v--Lela~--~~g~vt~~~L~~~l~W~~~Ra~~~L~~l-~~~Gl~Wv 223 (250)
.||.+|... -|+-+ ..-.+|.+++++.||+|....+.+|+.= -.-..+|+
T Consensus 2 SLn~~Q~~~T~~ELq~nf~~~~ls~~~ia~dL~~s~~~le~vL~l~~~~~~~vW~ 56 (89)
T PF10078_consen 2 SLNPEQRRATRQELQANFELSGLSLEQIAADLGTSPEHLEQVLNLKQPFPEDVWI 56 (89)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhCCCHHHHHHHHcCCCCCcccchH
Confidence 356667665 24444 3667899999999999999999988632 22344553
No 304
>PF05796 Chordopox_G2: Chordopoxvirus protein G2; InterPro: IPR008446 This family consists of several Chordopoxvirus isatin-beta-thiosemicarbazone dependent protein (protein G2) sequences. Inactivation of the gene coding for this protein renders the virus dependent upon isatin-beta-thiosemicarbazone (IBT) for growth [].
Probab=30.26 E-value=69 Score=28.72 Aligned_cols=105 Identities=17% Similarity=0.255 Sum_probs=56.0
Q ss_pred cccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCC
Q 025599 57 IRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNRE 136 (250)
Q Consensus 57 I~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~ 136 (250)
.++||+.-.+|.++|...|||.-.-=..|. +.=|+..--++++ |...-++-- +.=+++++..+-+.|=-
T Consensus 16 lTed~~s~~~~~SLCrgF~id~~~li~~f~------~~k~~k~iskal~-~~~ll~Ei~-~~FP~dil~eLv~LRL~--- 84 (216)
T PF05796_consen 16 LTEDEESMKMFISLCRGFGIDFEELISEFY------NKKYLKKISKALN-CADLLPEIS-LEFPDDILRELVRLRLC--- 84 (216)
T ss_pred hcCCHHHHHHHHHHhcccCCCHHHHHHHhh------hhHHHHHHHHHhh-ccccCHHHh-eeCCHHHHHHHHHHHHH---
Confidence 479999999999999999999543111111 1123333333332 222222211 11123344444443310
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCcc
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTEL 175 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El 175 (250)
.- .-.+++.-+|..=+.|..+|. |+.-+|+...+||
T Consensus 85 kf--~k~IK~SykL~~~m~Giaivk-~~~V~v~~aNd~l 120 (216)
T PF05796_consen 85 KF--SKTIKRSYKLPASMKGIAIVK-DRNVYVRRANDEL 120 (216)
T ss_pred HH--HHhhhHHhcCCcccCcEEEEc-CCEEEEEcCCHHH
Confidence 01 123566677777788998884 6666777775544
No 305
>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=30.24 E-value=1.3e+02 Score=23.04 Aligned_cols=46 Identities=24% Similarity=0.403 Sum_probs=36.0
Q ss_pred HHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCC
Q 025599 102 QIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGN 155 (250)
Q Consensus 102 qIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~ 155 (250)
.|+++... +++-++..||+..+.+. ...||..-|.|+++.|...|-
T Consensus 5 ~Il~~l~~----~~~~~sa~ei~~~l~~~----~~~i~~~TVYR~L~~L~~~Gl 50 (116)
T cd07153 5 AILEVLLE----SDGHLTAEEIYERLRKK----GPSISLATVYRTLELLEEAGL 50 (116)
T ss_pred HHHHHHHh----CCCCCCHHHHHHHHHhc----CCCCCHHHHHHHHHHHHhCCC
Confidence 34555443 35778999999999875 256999999999999998885
No 306
>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=30.23 E-value=1.4e+02 Score=19.72 Aligned_cols=36 Identities=31% Similarity=0.320 Sum_probs=27.3
Q ss_pred eeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECC
Q 025599 118 INLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGK 164 (250)
Q Consensus 118 i~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~ 164 (250)
++..++-..++ ||+.-|.+-++.|+..| +.|....+
T Consensus 16 it~~eLa~~l~---------vS~rTi~~~i~~L~~~~--~~I~~~~~ 51 (55)
T PF08279_consen 16 ITAKELAEELG---------VSRRTIRRDIKELREWG--IPIESKRG 51 (55)
T ss_dssp BEHHHHHHHCT---------S-HHHHHHHHHHHHHTT---EEEEETT
T ss_pred cCHHHHHHHhC---------CCHHHHHHHHHHHHHCC--CeEEeeCC
Confidence 88998877654 89999999999999988 65555444
No 307
>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=30.15 E-value=1.5e+02 Score=21.53 Aligned_cols=47 Identities=17% Similarity=0.132 Sum_probs=36.9
Q ss_pred hhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCcee
Q 025599 177 KDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMV 223 (250)
Q Consensus 177 ~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~Wv 223 (250)
++|-.+||.+.. .-.++..+|...+|-+.--.=-.+..|+..|++=.
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k 50 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVK 50 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEE
Confidence 456778887663 23368888999999988888889999999998743
No 308
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=30.10 E-value=92 Score=33.14 Aligned_cols=124 Identities=17% Similarity=0.165 Sum_probs=79.7
Q ss_pred HHHHHH--HcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHH
Q 025599 67 FHEMCA--KVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCL 144 (250)
Q Consensus 67 F~~mC~--siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~ 144 (250)
...||. .|++|-+.+..|. +.+.-. +|-.+|.+-. . .||=+++.||-..+| |..+.|.
T Consensus 33 V~KLie~~~ld~dll~T~DGK--EYiT~~----qL~~EI~~El-~----~gGRvnlvdLa~~Ln---------VD~~hiE 92 (803)
T PLN03083 33 VQKLQELGIIDFDLLHTVSGK--EYITQD----QLRNEIEAEI-K----KLGRVSLVDLADTIG---------VDLYHVE 92 (803)
T ss_pred HHHHHHhcccCcceEEecCCc--eeeCHH----HHHHHHHHHH-H----hCCCeeHHHHhhhcC---------CCHHHHH
Confidence 567776 4677877766442 222222 4555555543 1 379999999976655 8899999
Q ss_pred HHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHH
Q 025599 145 RAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDIL 215 (250)
Q Consensus 145 rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l 215 (250)
|.++.+-.=+.++.+ +.|. ++. +.=++.=-..|=+..+..|.|++.+|+..+.-+.+-.+..|..-
T Consensus 93 r~~~~iv~~d~~~~l--~~Ge-Lit--~~Yld~iaeEIne~LqE~G~isI~eLa~~~~Lpsefl~~~l~~r 158 (803)
T PLN03083 93 RQAQQVVSDDPGLML--VQGE-IIS--QSYWDSIAEEINERLQECSQIALAELARQLQVGSELVTSMLEPR 158 (803)
T ss_pred HHHHHHhcCCCceEE--ecCE-ecc--hHHHHHHHHHHHHHHHHcCcChHHHHHHhcCChHHHHHHHHHHH
Confidence 999998544566655 3443 111 11111111223344556899999999999999999999998654
No 309
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein. This model describes a domain found in some proteins associated with polyhydroxyalkanoate (PHA) granules in a subset of species that have PHA inclusion granules. Included are two tandem proteins of Pseudomonas oleovorans, PhaI and PhaF, and their homologs in related species. PhaF proteins have a low-complexity C-terminal region with repeats similar to AAAKP.
Probab=29.82 E-value=1.9e+02 Score=23.17 Aligned_cols=71 Identities=14% Similarity=0.282 Sum_probs=38.8
Q ss_pred cchhhhhccHHHHHHHH----hhcHhHHHHHHHHHHHHHHHHHHHHHH-------HHHhcccccccChhHHHHHHHHHHH
Q 025599 5 PGIGGLQSAAVARDQYR----LLGENVAKLRTDLMKEQLATFRSQLED-------FARKHKNDIRKNPTFRSQFHEMCAK 73 (250)
Q Consensus 5 ~Gi~ai~~~~~~~~~~~----~~g~~l~~~~~~~l~~qL~~F~~~L~~-------Fa~~h~~eI~~dp~fR~~F~~mC~s 73 (250)
.|||++-+..+.-.++- ..|....++.-.-+...++..+..+.. -+..+.+++ ++.|..++++++..
T Consensus 12 AGLGa~a~~~ek~~k~~~~LVkkGe~~~ee~k~~~~e~~~~~~e~~~~~~~~~~~~~~~~~~~l--e~~~~~~v~~~L~~ 89 (118)
T TIGR01837 12 AGIGALARVQEEGSKFFNRLVKEGELAEKRGQKRFDESVDAAREEVKTALEQTRDQVQRNWDKL--EKAFDERVEQALNR 89 (118)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHhhHHHH--HHHHHHHHHHHHHH
Confidence 47888877655443332 445444433333344444444432221 222333333 35788899999999
Q ss_pred cCCC
Q 025599 74 VGVD 77 (250)
Q Consensus 74 iGVD 77 (250)
||+-
T Consensus 90 lg~~ 93 (118)
T TIGR01837 90 LNIP 93 (118)
T ss_pred cCCC
Confidence 9974
No 310
>KOG2607 consensus CDK5 activator-binding protein [Signal transduction mechanisms]
Probab=29.78 E-value=86 Score=31.09 Aligned_cols=127 Identities=24% Similarity=0.349 Sum_probs=72.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccc----c-ccchhhhHHHHHHHhh
Q 025599 34 LMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLG----I-GDFYYELGVQIVEICL 108 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG----~-gdfy~eLavqIvevC~ 108 (250)
-|++|++..+....+..+||..==+.-..-|.+|-.-|..+|+- +.+.-.++|- + +.||--+.|-|..|-
T Consensus 126 ~LkKQiaK~qQq~tE~~RKe~d~~k~aa~~r~qfe~~c~qlglk----G~nvr~ElLelasdLPs~fyei~~v~i~~i~- 200 (505)
T KOG2607|consen 126 YLKKQIAKVQQQMTELDRKEADIKKSAALSRTQFEDACRQLGLK----GNNVRRELLELASDLPSTFYEILEVIISDIT- 200 (505)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCccHHHHHHHHHHHHHHhCCc----cchHHHHHHHHHhcCcHHHHHHHHHHHhhhh-
Confidence 79999999999999988877643344456999999999999986 2122223332 2 367776666665432
Q ss_pred hhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEE--C-CEEEEEecCCccc
Q 025599 109 ATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISV--G-KKKLVRSVPTELN 176 (250)
Q Consensus 109 ~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~i--g-~~~~v~svp~El~ 176 (250)
|-| |+|..+..-=.. +..=--.-|+--++.+...|....|... | .-..|.+-|.|+.
T Consensus 201 -------~ai---DyYqa~v~~v~~-g~~k~~~qVLpiL~~i~Erg~n~Tvyew~~g~~pd~VE~p~~e~l 260 (505)
T KOG2607|consen 201 -------GAI---DYYQAYVQDVHT-GKDKPLRQVLPILKYIRERGPNLTVYEWSEGLDPDNVESPENENL 260 (505)
T ss_pred -------HHH---HHHHHHHHHHhc-cCCccHHHHhHHHHHHHhcCCCcceeeccccCCcccccCCchhhh
Confidence 222 444444321000 0111223466666666666655555544 2 2233455455554
No 311
>PF06296 DUF1044: Protein of unknown function (DUF1044); InterPro: IPR009387 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=29.77 E-value=2.6e+02 Score=22.72 Aligned_cols=63 Identities=27% Similarity=0.421 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHhhcc------ccCC----------------CeEEEEE---CCEEEEEec-----CCccchhHHHHHH-
Q 025599 136 EAVSEDDCLRAISKLK------VLGN----------------GYEVISV---GKKKLVRSV-----PTELNKDHNQILE- 184 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~------~LG~----------------g~~vi~i---g~~~~v~sv-----p~El~~D~~~vLe- 184 (250)
..+|++|+..|++.+. -||+ |+++|.+ ++..+.-.. ..+++.++...|.
T Consensus 16 ~~~sd~~L~~ai~el~~G~~~adLGGgv~K~Ria~~g~GKsGG~R~I~~~~~~~~~~~l~~y~K~~~~nis~~El~~lk~ 95 (120)
T PF06296_consen 16 EGLSDDDLCEAIEELEQGLIDADLGGGVRKKRIARKGKGKSGGYRVIYFFKQEDRIFFLYIYAKNEKANISDKELKALKK 95 (120)
T ss_pred cCCCHHHHHHHHHHHHhCCcccchhccEEEEEeccCCCCCCCceEEEEEEEeCCEEEEEEEEcccccCCCCHHHHHHHHH
Confidence 4589999999999886 2665 4555544 222222222 3477777766653
Q ss_pred HHHhCCCccHHHHH
Q 025599 185 LAQAQGFVTVDEVE 198 (250)
Q Consensus 185 la~~~g~vt~~~L~ 198 (250)
+|+..-..|.++|.
T Consensus 96 la~~l~~~~~~~l~ 109 (120)
T PF06296_consen 96 LAKELLNLSEEQLE 109 (120)
T ss_pred HHHHHHHhCHHHHH
Confidence 33333344555444
No 312
>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=29.74 E-value=2.1e+02 Score=26.31 Aligned_cols=77 Identities=16% Similarity=0.179 Sum_probs=48.2
Q ss_pred ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEE-CCEEEEEec
Q 025599 93 GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISV-GKKKLVRSV 171 (250)
Q Consensus 93 gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~i-g~~~~v~sv 171 (250)
.+|||-.--.++ +..+|=-.+.++-.+++ +.||.++|..|++.|..+| +++- +.-.|+++.
T Consensus 120 ~~W~~~virel~-------~~~~~~~~~~~ia~~l~-------p~is~~ev~~sL~~L~~~g----likk~~~g~y~~t~ 181 (271)
T TIGR02147 120 RHWYNSVIRELL-------GVMPFADDPEELAKRCF-------PKISAEQVKESLDLLERLG----LIKKNEDGFYKQTD 181 (271)
T ss_pred HHHHHHHHHHHh-------hcCCCCCCHHHHHHHhC-------CCCCHHHHHHHHHHHHHCC----CeeECCCCcEEeec
Confidence 577877433333 34455555666555543 5699999999999999988 3333 333577764
Q ss_pred -----CCcc-----chhHHHHHHHHH
Q 025599 172 -----PTEL-----NKDHNQILELAQ 187 (250)
Q Consensus 172 -----p~El-----~~D~~~vLela~ 187 (250)
|.+. -.=|..++++|.
T Consensus 182 ~~l~~~~~~~~~avr~~h~q~l~lA~ 207 (271)
T TIGR02147 182 KAVSTGDEVIPLAVRQYQKQMIDLAK 207 (271)
T ss_pred ceeecCCccchHHHHHHHHHHHHHHH
Confidence 2222 223666777777
No 313
>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=29.62 E-value=96 Score=28.73 Aligned_cols=82 Identities=17% Similarity=0.231 Sum_probs=50.3
Q ss_pred CHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccchhHHHHHHHHHhCC---CccHHHHHHhcCCChHHHHHHHHH
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELNKDHNQILELAQAQG---FVTVDEVERRLSWTSGRAIDALDI 214 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~~~g---~vt~~~L~~~l~W~~~Ra~~~L~~ 214 (250)
+++++.++++.+.. .||..+++. +...... .-+..|-..+-.+-+..| -+.++. |-+|+.+.|...+..
T Consensus 139 ~~~~~~~~a~~~~~--~Gf~~~Kik~g~~~~~~--~~~~~d~~~v~~ir~~~g~~~~l~vDa---N~~~~~~~a~~~~~~ 211 (357)
T cd03316 139 SPEELAEEAKRAVA--EGFTAVKLKVGGPDSGG--EDLREDLARVRAVREAVGPDVDLMVDA---NGRWDLAEAIRLARA 211 (357)
T ss_pred CHHHHHHHHHHHHH--cCCCEEEEcCCCCCcch--HHHHHHHHHHHHHHHhhCCCCEEEEEC---CCCCCHHHHHHHHHH
Confidence 68888888887764 678888874 3210000 001222222323333223 243332 779999999999999
Q ss_pred HHHcCCceeecCC
Q 025599 215 LLEEGLAMVDDGH 227 (250)
Q Consensus 215 l~~~Gl~WvD~q~ 227 (250)
|...|+.|+.+-.
T Consensus 212 l~~~~i~~iEqP~ 224 (357)
T cd03316 212 LEEYDLFWFEEPV 224 (357)
T ss_pred hCccCCCeEcCCC
Confidence 9989999998544
No 314
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=29.60 E-value=2.3e+02 Score=24.30 Aligned_cols=63 Identities=11% Similarity=0.069 Sum_probs=45.3
Q ss_pred ccchhHHH-HHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCC-CCCcceee
Q 025599 174 ELNKDHNQ-ILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHR-DRKRRYWF 236 (250)
Q Consensus 174 El~~D~~~-vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~-~~e~~Yw~ 236 (250)
.|+.-+.. ++.++.. ....|.+++++.++++..-++.-+..|++.|++-.+-.-. .|.+.|.|
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~s~~eIA~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 224 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEFSTDELANAVNISRVSCRKYLIWLVNCHILFTSIHYGVTGRPVYRY 224 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCcCHHHHHHHhCchHHHHHHHHHHHHhCCEEEEEeeccCCCCCCeee
Confidence 46655533 4455552 2345999999999999999999999999999996664321 23566666
No 315
>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=29.56 E-value=80 Score=25.89 Aligned_cols=33 Identities=12% Similarity=0.099 Sum_probs=31.2
Q ss_pred ccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 192 VTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 192 vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
+|.++|++-+|.+.+-.-.+|..|.++|++-+.
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 176 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIH 176 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 799999999999999999999999999998765
No 316
>PF14106 DUF4279: Domain of unknown function (DUF4279)
Probab=29.45 E-value=89 Score=24.04 Aligned_cols=29 Identities=10% Similarity=0.164 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccc
Q 025599 28 AKLRTDLMKEQLATFRSQLEDFARKHKND 56 (250)
Q Consensus 28 ~~~~~~~l~~qL~~F~~~L~~Fa~~h~~e 56 (250)
-+.|+++|-.+|+-.++.|.+++++|.-+
T Consensus 53 l~~~l~~ll~~L~~~~~~i~~l~~~~~~~ 81 (118)
T PF14106_consen 53 LEDHLEELLDRLEPKREIIKELKEKYNLE 81 (118)
T ss_pred HHHHHHHHHHHHcccHHHHHHHHHhcCcc
Confidence 34678888888888889999999988876
No 317
>PF08726 EFhand_Ca_insen: Ca2+ insensitive EF hand; InterPro: IPR014837 EF hands are helix-loop-helix binding motifs involved in the regulation of many cellular processes. EF hands usually bind to Ca2+ ions, which cause a major conformational change that allows the protein to interact with its designated targets. This protein corresponds to an EF hand which has partially or entirely lost its calcium-binding properties. The calcium insensitive EF hand is still able to mediate protein-protein recognition []. ; PDB: 1H8B_A 1SJJ_B.
Probab=29.35 E-value=30 Score=25.44 Aligned_cols=19 Identities=32% Similarity=0.483 Sum_probs=15.0
Q ss_pred HHHhCCCccHHHHHHhcCC
Q 025599 185 LAQAQGFVTVDEVERRLSW 203 (250)
Q Consensus 185 la~~~g~vt~~~L~~~l~W 203 (250)
+|..++|||.++|+..+-=
T Consensus 15 lA~~KpyVT~~dLr~~l~p 33 (69)
T PF08726_consen 15 LAGGKPYVTEEDLRRSLTP 33 (69)
T ss_dssp HCTSSSCEEHHHHHHHS-C
T ss_pred HHcCCCcccHHHHHHHcCc
Confidence 3667999999999988643
No 318
>CHL00053 rps7 ribosomal protein S7
Probab=29.27 E-value=2.9e+02 Score=23.14 Aligned_cols=70 Identities=16% Similarity=0.122 Sum_probs=44.8
Q ss_pred HHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHH------HHHhCCCccHHHHHHhcCCChHHHHHHHHH
Q 025599 141 DDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILE------LAQAQGFVTVDEVERRLSWTSGRAIDALDI 214 (250)
Q Consensus 141 ~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLe------la~~~g~vt~~~L~~~l~W~~~Ra~~~L~~ 214 (250)
+=+..||..+.|+= ...-+.+||..+ -||.+++.++..-|. .|.....-+ ...-.|.+.++.
T Consensus 60 ~vl~~Ai~N~~P~~-evk~~r~gG~~~--qvPv~v~~~rr~~lAirWil~~ar~r~~~~---------~~~~La~Eii~A 127 (155)
T CHL00053 60 SVLRQAIRNVTPDV-EVKARRVGGSTY--QVPIEIGSTRGKALAIRWLLKASRKRSGRN---------MAFKLSSELVDA 127 (155)
T ss_pred HHHHHHHHhCCCcE-EEEEEeeCCEEE--EEeeEcCHHHHHHHHHHHHHHHHHhcCCCC---------HHHHHHHHHHHH
Confidence 34567999999872 345566688855 568888888876543 344333222 234677777877
Q ss_pred HHHcCCce
Q 025599 215 LLEEGLAM 222 (250)
Q Consensus 215 l~~~Gl~W 222 (250)
.-..|-++
T Consensus 128 ~~~~g~ai 135 (155)
T CHL00053 128 AKGSGNAI 135 (155)
T ss_pred HhCCCchh
Confidence 77777654
No 319
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=29.02 E-value=1.2e+02 Score=29.44 Aligned_cols=42 Identities=24% Similarity=0.409 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHH-HH---HHHHHhcccccccChhHHHHHHHHHHH
Q 025599 32 TDLMKEQLATFRS-QL---EDFARKHKNDIRKNPTFRSQFHEMCAK 73 (250)
Q Consensus 32 ~~~l~~qL~~F~~-~L---~~Fa~~h~~eI~~dp~fR~~F~~mC~s 73 (250)
++.|..--+.|++ +| +.=..+|+.++..||.+|.+|+.+-..
T Consensus 285 i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~ 330 (411)
T KOG1463|consen 285 IDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDN 330 (411)
T ss_pred hHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHH
Confidence 3445555555541 22 233467899999999999999887544
No 320
>PRK14329 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=28.70 E-value=1.4e+02 Score=29.26 Aligned_cols=48 Identities=19% Similarity=0.340 Sum_probs=39.5
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHh
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQA 188 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~ 188 (250)
..|.+++.++++.++..+.++.+.. .+|--.|+|=..|....++++..
T Consensus 304 ~~t~~~~~~~i~~ir~~~~~~~i~~----d~IvGfPgET~edf~~tl~~i~~ 351 (467)
T PRK14329 304 KYTREWYLDRIDAIRRIIPDCGIST----DMIAGFPTETEEDHQDTLSLMEE 351 (467)
T ss_pred CCCHHHHHHHHHHHHHhCCCCEEEE----eEEEeCCCCCHHHHHHHHHHHHh
Confidence 4788999999999998877765443 46777799999999999999885
No 321
>KOG1106 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.69 E-value=45 Score=29.06 Aligned_cols=40 Identities=23% Similarity=0.377 Sum_probs=30.1
Q ss_pred cccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhh
Q 025599 88 ELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQR 130 (250)
Q Consensus 88 ~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~ 130 (250)
++.+++-+||++|.|+ |.--+.+|=|++-..-+++|+...
T Consensus 94 dL~s~~phFY~fg~kl---~~l~s~~~l~~~~se~l~~R~~~~ 133 (177)
T KOG1106|consen 94 DLRSLCPHFYEFGMKL---LPLDSGENLGIILSETLRSRVREI 133 (177)
T ss_pred eccccccHHHHHHHHH---hhcccCcchhHHHHHHHHHHHHHH
Confidence 4556799999999886 566677886666667788887764
No 322
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=28.60 E-value=1.5e+02 Score=24.55 Aligned_cols=42 Identities=12% Similarity=0.144 Sum_probs=34.4
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
.|+..+..|+.+....|+ |.+++++.+|++..-++..|...+
T Consensus 127 ~Lp~~~R~v~~L~~~~g~-s~~EIA~~lgis~~tVk~~l~rAl 168 (178)
T PRK12529 127 TLRPRVKQAFLMATLDGM-KQKDIAQALDIALPTVKKYIHQAY 168 (178)
T ss_pred hCCHHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 567788888888776555 999999999999998888776543
No 323
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=28.47 E-value=2.3e+02 Score=22.24 Aligned_cols=48 Identities=23% Similarity=0.418 Sum_probs=33.6
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhc--CCChHHHHHHHHHHHHcCCc
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRL--SWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l--~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
.||..-..++-..-++-|+|++++++.+ ..+..-.-.-+-.|++.|++
T Consensus 13 alsE~~~~ilI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglI 62 (96)
T PF09114_consen 13 ALSENAANILIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKGLI 62 (96)
T ss_dssp SS-HHHHHHHHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSE
T ss_pred hhhHHHHHHHHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcc
Confidence 4665555566556678899999999977 56676666778899999985
No 324
>KOG1043 consensus Ca2+-binding transmembrane protein LETM1/MRS7 [Function unknown]
Probab=28.39 E-value=3.5e+02 Score=27.34 Aligned_cols=102 Identities=22% Similarity=0.314 Sum_probs=69.1
Q ss_pred HHHHHHHHHH--------HHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHH
Q 025599 34 LMKEQLATFR--------SQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVE 105 (250)
Q Consensus 34 ~l~~qL~~F~--------~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIve 105 (250)
++...+..|+ ..|..||+=-..||.=|---|.+.-.||.-++..|..+. .=+-|.|-.+|=+
T Consensus 257 ~fd~f~~kvr~~~~~~S~eeii~~aklf~de~~LdnLsR~qL~al~k~m~l~~~Gt~----------~~lr~~lr~kik~ 326 (499)
T KOG1043|consen 257 EFDRFLGKVRFIGLGVSTEEIIAFAKLFSDEITLDNLSRPQLVALCKYMDLNSFGTD----------KLLRYQLRKKIKE 326 (499)
T ss_pred HHHHHHHHhcccCCCccHHHHHHHHHHhccchhhhccCHHHHHHHHHhhcccccCch----------HHHHHHHHHHHHH
Confidence 6777777776 688999999999999999999999999999999987653 2345666667766
Q ss_pred Hhhhhcc--cCCCc--eeHHHHHHHHHhhcCCCCCCCCHHHHHHH
Q 025599 106 ICLATRP--HNGGL--INLQELCNLLRQRRKSNREAVSEDDCLRA 146 (250)
Q Consensus 106 vC~~tr~--~nGGl--i~l~el~~~v~k~R~~~~~~IS~~DI~rA 146 (250)
+--.-++ .-|+. .++.|++..-+ .||..+.-++++++..-
T Consensus 327 ik~dD~~I~~eg~v~~ls~~el~~aC~-~rgmra~gv~~e~l~~q 370 (499)
T KOG1043|consen 327 IKKDDKHIATEGAVESLSLLELQIACR-ERGMRALGVSEERLREQ 370 (499)
T ss_pred hcccccchhhhhhhhHhhHHHHHHHHH-hhhcchhccchhhhhHH
Confidence 6654333 33433 33334443332 44544566777764433
No 325
>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=28.28 E-value=1.1e+02 Score=27.28 Aligned_cols=75 Identities=23% Similarity=0.368 Sum_probs=47.8
Q ss_pred CHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccchhHHHHHHHHH-hCC---CccHHHHHHhcCCChHHHHHHHH
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELNKDHNQILELAQ-AQG---FVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~-~~g---~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
+++++.+.++.+. ..||..+++. |. -| ..|- ..++.+. ..| .+.++ .|-+|+...|...+.
T Consensus 85 ~~~~~~~~~~~~~--~~G~~~~KiKvg~-----~~---~~d~-~~v~~vr~~~g~~~~l~vD---an~~~~~~~a~~~~~ 150 (265)
T cd03315 85 EPAEVAEEARRAL--EAGFRTFKLKVGR-----DP---ARDV-AVVAALREAVGDDAELRVD---ANRGWTPKQAIRALR 150 (265)
T ss_pred CHHHHHHHHHHHH--HCCCCEEEEecCC-----CH---HHHH-HHHHHHHHhcCCCCEEEEe---CCCCcCHHHHHHHHH
Confidence 5677777666654 4478888874 31 12 2222 3343333 233 23222 377899999999999
Q ss_pred HHHHcCCceeecCC
Q 025599 214 ILLEEGLAMVDDGH 227 (250)
Q Consensus 214 ~l~~~Gl~WvD~q~ 227 (250)
.|...|+.|+.+-.
T Consensus 151 ~l~~~~i~~iEeP~ 164 (265)
T cd03315 151 ALEDLGLDYVEQPL 164 (265)
T ss_pred HHHhcCCCEEECCC
Confidence 99999999998543
No 326
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=28.21 E-value=2.7e+02 Score=28.66 Aligned_cols=123 Identities=23% Similarity=0.384 Sum_probs=80.2
Q ss_pred cccchhhhHHHHH----------HHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc------cCC
Q 025599 92 IGDFYYELGVQIV----------EICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV------LGN 155 (250)
Q Consensus 92 ~gdfy~eLavqIv----------evC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~------LG~ 155 (250)
.|-||-+||..|. +|...+ -+.|++.-.++...|.-.-+ --+..|.+|+.+|+. |.+
T Consensus 413 sG~~ya~LA~~i~R~P~lTr~E~~vl~ki--P~~~~i~~~~~~e~~~d~~~-----~ee~~i~~AL~kLEArGfI~~Lp~ 485 (591)
T PF04458_consen 413 SGRFYAELARHIKRLPHLTRYEMEVLHKI--PDKGYIHREELVEFIKDHVG-----KEEEEIIEALEKLEARGFIEILPN 485 (591)
T ss_pred chHHHHHHHhhhhhcccccHHHHHHHHhC--CccccccHHHHHHHhhcccc-----cchHHHHHHHHHHHhcchHHHcCC
Confidence 4799999999993 444444 45566766666665444322 467788899999984 777
Q ss_pred CeEEEEECCEEE---EEecCC--------ccchhHHHHHHHHHhCCCc------------cHHHHHHhcCCChHHHHHHH
Q 025599 156 GYEVISVGKKKL---VRSVPT--------ELNKDHNQILELAQAQGFV------------TVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 156 g~~vi~ig~~~~---v~svp~--------El~~D~~~vLela~~~g~v------------t~~~L~~~l~W~~~Ra~~~L 212 (250)
|.-+.+=-|+.+ |.-+|. -.|.=--.||++....|.. +..++.+..|-+++-++.+|
T Consensus 486 g~iilTeaG~~ik~Alsg~p~~e~~g~~~PVtP~~~rVL~Ai~~~g~lyvKe~KvRi~pk~~ke~~K~sgL~~e~f~kaL 565 (591)
T PF04458_consen 486 GMIILTEAGELIKRALSGVPEQEILGFGFPVTPTIYRVLKAIREVGTLYVKEKKVRILPKNIKEAIKLSGLTPEEFKKAL 565 (591)
T ss_pred CcEEEehhhHHHHHHHhcCCcccccccCCCCCHHHHHHHHHHHHhhhhhhhhhhhhcCccchHHHHHhcCCCHHHHHHHH
Confidence 776666434322 223343 2333344567666554443 44557788899999999999
Q ss_pred HHHHHcCCc
Q 025599 213 DILLEEGLA 221 (250)
Q Consensus 213 ~~l~~~Gl~ 221 (250)
..+-.-|++
T Consensus 566 ~~aR~~~~i 574 (591)
T PF04458_consen 566 EVAREAGFI 574 (591)
T ss_pred HHHHHhccc
Confidence 988877765
No 327
>KOG4302 consensus Microtubule-associated protein essential for anaphase spindle elongation [Cell cycle control, cell division, chromosome partitioning; Cytoskeleton]
Probab=27.99 E-value=56 Score=33.97 Aligned_cols=46 Identities=17% Similarity=0.471 Sum_probs=40.1
Q ss_pred HHH-HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCC
Q 025599 34 LMK-EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPL 79 (250)
Q Consensus 34 ~l~-~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL 79 (250)
+++ .-|+.|+..|.+.=.++..-.++.-+|+...+..|..||+||-
T Consensus 156 dlsl~kLeelr~~L~~L~~ek~~Rlekv~~~~~~I~~l~~~Lg~~~~ 202 (660)
T KOG4302|consen 156 DLSLEKLEELREHLNELQKEKSDRLEKVLELKEEIKSLCSVLGLDFS 202 (660)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 444 6688888899888888888888999999999999999999987
No 328
>cd03320 OSBS o-Succinylbenzoate synthase (OSBS) catalyzes the conversion of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB), a reaction in the menaquinone biosynthetic pathway. Menaquinone is an essential cofactor for anaerobic growth in eubacteria and some archaea. OSBS 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=27.84 E-value=1e+02 Score=27.51 Aligned_cols=66 Identities=17% Similarity=0.352 Sum_probs=41.8
Q ss_pred CCCeEEEEEC-CEEEEEecCCccchhHHHHHHHHHhCCC-ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 154 GNGYEVISVG-KKKLVRSVPTELNKDHNQILELAQAQGF-VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 154 G~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~~~g~-vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
..||+.+++. | +.....|-..+-.+.+..|. +.. .+=.|-+|+...|...+..|...++.|+.+=.
T Consensus 95 ~~Gf~~~KiKvg-------~~~~~~d~~~v~~vr~~~g~~~~l-~vDaN~~w~~~~A~~~~~~l~~~~i~~iEqP~ 162 (263)
T cd03320 95 GGGYRTVKLKVG-------ATSFEEDLARLRALREALPADAKL-RLDANGGWSLEEALAFLEALAAGRIEYIEQPL 162 (263)
T ss_pred hCCCCEEEEEEC-------CCChHHHHHHHHHHHHHcCCCCeE-EEeCCCCCCHHHHHHHHHhhcccCCceEECCC
Confidence 4589888863 2 11223444444444444442 111 12247789999999999999999999999644
No 329
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=27.82 E-value=1.9e+02 Score=21.13 Aligned_cols=50 Identities=22% Similarity=0.254 Sum_probs=34.8
Q ss_pred eeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhcc-----ccCCCeEEEEEC-CEEEEEecC
Q 025599 118 INLQELCNLLRQRRKSNREAVSEDDCLRAISKLK-----VLGNGYEVISVG-KKKLVRSVP 172 (250)
Q Consensus 118 i~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~-----~LG~g~~vi~ig-~~~~v~svp 172 (250)
|+-+||+.+|.+..+ +|..|+...++.|- .|..|-.|.--| |.-.+...|
T Consensus 1 mtk~eli~~ia~~~~-----~~~~~v~~vl~~l~~~i~~~L~~g~~V~i~g~G~F~~~~~~ 56 (90)
T smart00411 1 MTKSELIDAIAEKAG-----LSKKDAKAAVDAFLEIITEALKKGEKVELRGFGTFEVRERK 56 (90)
T ss_pred CCHHHHHHHHHHHhC-----CCHHHHHHHHHHHHHHHHHHHhCCCeEEEeCcEEEEEEeec
Confidence 567899999988644 89999999998875 466676544223 555555443
No 330
>TIGR02933 nifM_nitrog nitrogen fixation protein NifM. Members of this protein family, found in a subset of nitrogen-fixing bacteria, are the nitrogen fixation protein NifM. NifM, homologous to peptidyl-prolyl cis-trans isomerases, appears to be an accessory protein for NifH, the Fe protein, also called component II or dinitrogenase reductase, of nitrogenase.
Probab=27.72 E-value=4.4e+02 Score=23.50 Aligned_cols=108 Identities=6% Similarity=-0.004 Sum_probs=66.3
Q ss_pred ccHHHHHHHHhhcHhHHHHHHHHHHHHHHH---HHHHHHHHHHhcccccccChh--HHHHHHHHHHHcCCCCCCCCCccc
Q 025599 12 SAAVARDQYRLLGENVAKLRTDLMKEQLAT---FRSQLEDFARKHKNDIRKNPT--FRSQFHEMCAKVGVDPLASNKGFW 86 (250)
Q Consensus 12 ~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~---F~~~L~~Fa~~h~~eI~~dp~--fR~~F~~mC~siGVDPL~s~k~~w 86 (250)
+-+.+.+.|...+..++.++..++..|... -...+.+.|.+..=.|..+.. -..+|++.+..-|+++
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lI~e~l~lq~A~~~gi~v~~~ev~~~~e~~~~~L~~~G~~~-------- 75 (256)
T TIGR02933 4 RWKLAHEMWNCAPGELSPDQLQQFDQAWQRQRHIEQAVVRAADEIGVVIPPSLLEEAPQALAQALDEQALDA-------- 75 (256)
T ss_pred HHHHHHHHhCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHcCCCH--------
Confidence 445667788888888888887777666443 223334455555433333321 1257888888888763
Q ss_pred ccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc
Q 025599 87 AELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV 152 (250)
Q Consensus 87 s~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~ 152 (250)
.+|...|-.+| .+..+...+.+.| ..||++||....+..+.
T Consensus 76 ------~~~r~~ir~~i---------------~~~~~~~~~~~~~----i~ise~ei~~yy~~~~~ 116 (256)
T TIGR02933 76 ------AERRAMLAHHL---------------RLEAQLACVCAQA----PQPDDADVEAWYRRHAE 116 (256)
T ss_pred ------HHHHHHHHHHH---------------HHHHHHHHHhcCC----CCCCHHHHHHHHHHHHH
Confidence 35555554442 2445555554432 46899999999887653
No 331
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=27.70 E-value=46 Score=24.80 Aligned_cols=17 Identities=24% Similarity=0.536 Sum_probs=15.4
Q ss_pred hhHHHHHHHHHHHcCCC
Q 025599 61 PTFRSQFHEMCAKVGVD 77 (250)
Q Consensus 61 p~fR~~F~~mC~siGVD 77 (250)
+.+|..|.+.+..+|||
T Consensus 63 ~~lr~~L~~la~elgvD 79 (84)
T cd04871 63 EALRAALLELASELNVD 79 (84)
T ss_pred HHHHHHHHHHhcccCce
Confidence 36999999999999998
No 332
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=27.58 E-value=1.6e+02 Score=23.07 Aligned_cols=35 Identities=23% Similarity=0.411 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHH---HHHHHHHhcccccccChhH
Q 025599 29 KLRTDLMKEQLATFRS---QLEDFARKHKNDIRKNPTF 63 (250)
Q Consensus 29 ~~~~~~l~~qL~~F~~---~L~~Fa~~h~~eI~~dp~f 63 (250)
+.+.++|..+++.+++ .+++-|+++=+=++.|+++
T Consensus 47 ~~~n~~L~~eI~~L~~~~dyiEe~AR~~Lg~vk~gEiv 84 (105)
T PRK00888 47 KARNDQLFAEIDDLKGGQEAIEERARNELGMVKPGETF 84 (105)
T ss_pred HHHHHHHHHHHHHhhCcHHHHHHHHHHHcCCCCCCCEE
Confidence 3456688888888874 7999999999999999986
No 333
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=27.52 E-value=1.2e+02 Score=20.29 Aligned_cols=24 Identities=17% Similarity=0.365 Sum_probs=14.1
Q ss_pred ccccccChhHHHHHHHH-HHHcCCCC
Q 025599 54 KNDIRKNPTFRSQFHEM-CAKVGVDP 78 (250)
Q Consensus 54 ~~eI~~dp~fR~~F~~m-C~siGVDP 78 (250)
=..|. ||..|..+.+. +..+|||+
T Consensus 32 i~~i~-~~i~r~~y~~~la~~~~i~~ 56 (59)
T PF10410_consen 32 IAQIP-DPIERELYIRELAERLGISE 56 (59)
T ss_dssp HTT---SHHHHHHHHHHHHHHCT-SS
T ss_pred HHHCC-CHHHHHHHHHHHHHHhCcCc
Confidence 33444 88888777655 44589886
No 334
>COG1001 AdeC Adenine deaminase [Nucleotide transport and metabolism]
Probab=27.45 E-value=1.1e+02 Score=31.27 Aligned_cols=34 Identities=26% Similarity=0.542 Sum_probs=27.2
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPT 173 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~ 173 (250)
.+++|+..|++.|.-.|+|+.++.= |+ ++-.+|-
T Consensus 481 ~n~~Dm~~Avn~l~e~gGGivvv~~-Ge-v~~~lpL 514 (584)
T COG1001 481 VNDEDMALAVNRLKEIGGGIVVVEN-GE-VLEELPL 514 (584)
T ss_pred CCHHHHHHHHHHHHhcCCcEEEEEC-CE-EEEEecc
Confidence 5799999999999999999988764 43 4555653
No 335
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=27.28 E-value=1.3e+02 Score=30.16 Aligned_cols=50 Identities=14% Similarity=0.187 Sum_probs=43.8
Q ss_pred hHHHHHHHHHh-CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 178 DHNQILELAQA-QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 178 D~~~vLela~~-~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
.+.+||...+. .+.++.++|++.+|.+...+..++..|...|++=++...
T Consensus 7 ~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~ 57 (494)
T PTZ00326 7 EENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKK 57 (494)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence 35668888876 677999999999999999999999999999999888654
No 336
>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=27.05 E-value=2.2e+02 Score=20.18 Aligned_cols=45 Identities=13% Similarity=0.198 Sum_probs=30.3
Q ss_pred HHHHhCCCccHHHHHH--------hcCCChHHHHHHHHHHHHcCCceeecCCC
Q 025599 184 ELAQAQGFVTVDEVER--------RLSWTSGRAIDALDILLEEGLAMVDDGHR 228 (250)
Q Consensus 184 ela~~~g~vt~~~L~~--------~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~ 228 (250)
.+......++..+|.. .+.-+..-.+.+|+.|+..|++=+|+..+
T Consensus 15 rimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~d~ 67 (68)
T PF10557_consen 15 RIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDEDDP 67 (68)
T ss_dssp HHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESSEC
T ss_pred hhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCCCC
Confidence 3334445555555542 45677888999999999999999998763
No 337
>COG0758 Smf Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]
Probab=26.89 E-value=2.3e+02 Score=27.14 Aligned_cols=46 Identities=15% Similarity=-0.027 Sum_probs=38.7
Q ss_pred HHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeec
Q 025599 179 HNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDD 225 (250)
Q Consensus 179 ~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~ 225 (250)
+.+++..... ..++++.|....|++..-....|.+|+-+|.++.+.
T Consensus 298 ~~~~~~~~~~-~~~~~d~l~~~~~~~~~~~~~~L~~lel~G~i~~~~ 343 (350)
T COG0758 298 FLALLANLGD-EPKEIDRLASCTGLTIAQVLAWLLELELEGKVKRLG 343 (350)
T ss_pred HHHHHHHhcC-CCccHHHHHHHhCCCHHHHHHHHHHHHhcCcEEeeC
Confidence 5455544443 678999999999999999999999999999999873
No 338
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=26.88 E-value=34 Score=29.19 Aligned_cols=48 Identities=15% Similarity=0.258 Sum_probs=38.6
Q ss_pred chhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025599 6 GIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKH 53 (250)
Q Consensus 6 Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h 53 (250)
+..+|++---+...|..+.-.+..+.++++.+.+..|+..+..+|.+-
T Consensus 108 A~~al~~~p~~~R~~s~~T~~vs~~~~~ki~~~i~~fRk~i~~i~~~~ 155 (171)
T PF14394_consen 108 AQEALDRVPPEERDFSGLTMSVSREDYEKIKKEIREFRKKIIAIAEED 155 (171)
T ss_pred HHHHHHhCCccccceeeeEEEeCHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 455666555556677777777889999999999999999999999974
No 339
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=26.88 E-value=3.4e+02 Score=21.86 Aligned_cols=74 Identities=20% Similarity=0.371 Sum_probs=49.8
Q ss_pred HHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHH
Q 025599 66 QFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLR 145 (250)
Q Consensus 66 ~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~r 145 (250)
.|..||.+.+..+.... +=...+.++=..-=..+-|.|+..||...+.+. ++..|.+++..
T Consensus 65 eF~~l~~~~~~~~~~~~---------------~~~~el~eaF~~fD~d~~G~Is~~el~~~l~~l----g~~~~~~e~~~ 125 (151)
T KOG0027|consen 65 EFLDLMEKLGEEKTDEE---------------ASSEELKEAFRVFDKDGDGFISASELKKVLTSL----GEKLTDEECKE 125 (151)
T ss_pred HHHHHHHhhhccccccc---------------ccHHHHHHHHHHHccCCCCcCcHHHHHHHHHHh----CCcCCHHHHHH
Confidence 68888888776643311 112233333333334566999999999888886 35688999999
Q ss_pred HHhhccccCCCeE
Q 025599 146 AISKLKVLGNGYE 158 (250)
Q Consensus 146 Aik~L~~LG~g~~ 158 (250)
-++...+=|.|..
T Consensus 126 mi~~~d~d~dg~i 138 (151)
T KOG0027|consen 126 MIREVDVDGDGKV 138 (151)
T ss_pred HHHhcCCCCCCeE
Confidence 9988887666653
No 340
>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=26.71 E-value=4.7e+02 Score=23.47 Aligned_cols=62 Identities=21% Similarity=0.232 Sum_probs=43.5
Q ss_pred eeHHHHHHHHHhhcCC-CCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHh
Q 025599 118 INLQELCNLLRQRRKS-NREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQA 188 (250)
Q Consensus 118 i~l~el~~~v~k~R~~-~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~ 188 (250)
|+.+++++++...... .....|++|+.++.+.|..=| ..|+. -++...||.-...+..+++.
T Consensus 41 i~~~~~y~~~~~~~~~p~TS~ps~~~~~~~~~~l~~~~--~~vi~-------i~iSs~lSgty~~a~~aa~~ 103 (275)
T TIGR00762 41 ITPEEFYEKLKESKELPKTSQPSPGEFLELYEKLLEEG--DEVLS-------IHLSSGLSGTYQSARQAAEM 103 (275)
T ss_pred CCHHHHHHHHHhcCCCCCcCCCCHHHHHHHHHHHHhCC--CeEEE-------EEcCCchhHHHHHHHHHHhh
Confidence 7899999999875432 346899999999999887644 44543 34455677666666666553
No 341
>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=26.67 E-value=1.2e+02 Score=22.71 Aligned_cols=61 Identities=23% Similarity=0.297 Sum_probs=38.1
Q ss_pred hhHHHHHHHHHHHcCCC--CCCCCCcccccccccc---------cchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHh
Q 025599 61 PTFRSQFHEMCAKVGVD--PLASNKGFWAELLGIG---------DFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQ 129 (250)
Q Consensus 61 p~fR~~F~~mC~siGVD--PL~s~k~~ws~~lG~g---------dfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k 129 (250)
|-=+.+|...|..||-| +|+ ..||+. + |..+..|+.++...=+..+|+--++.-|...+.+
T Consensus 4 ~~t~~~l~~ia~~iG~~Wk~La-------r~LGls~~dI~~i~~~-~~~~~eq~~~mL~~W~~r~g~~AT~~~L~~aL~~ 75 (86)
T cd08318 4 PVTGEQITVFANKLGEDWKTLA-------PHLEMKDKEIRAIESD-SEDIKMQAKQLLVAWQDREGSQATPETLITALNA 75 (86)
T ss_pred CCCHHHHHHHHHHHhhhHHHHH-------HHcCCCHHHHHHHHhc-CCCHHHHHHHHHHHHHHhcCccccHHHHHHHHHH
Confidence 44456788888888877 444 224432 3 3346667777777777777766666666666655
No 342
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.54 E-value=1.8e+02 Score=18.63 Aligned_cols=38 Identities=24% Similarity=0.343 Sum_probs=30.8
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
+++++. .|. |..+++..+|.+......-+......|..
T Consensus 5 iv~~~~-~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~~ 42 (52)
T PF13518_consen 5 IVELYL-EGE-SVREIAREFGISRSTVYRWIKRYREGGIE 42 (52)
T ss_pred HHHHHH-cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCHH
Confidence 455555 466 99999999999999999988888888853
No 343
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=26.45 E-value=78 Score=24.05 Aligned_cols=37 Identities=14% Similarity=0.293 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHHHHHHH-hcccccccChhHHHHHHHHHHH-cC
Q 025599 34 LMKEQLATFRSQLEDFAR-KHKNDIRKNPTFRSQFHEMCAK-VG 75 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~-~h~~eI~~dp~fR~~F~~mC~s-iG 75 (250)
+|++-|...+.....|++ .+.+-|..+ .|+.++.+ +|
T Consensus 2 ~lE~ai~~l~~~F~~fd~~~~~g~i~~~-----ELk~ll~~elg 40 (89)
T cd05022 2 ELEKAIETLVSNFHKASVKGGKESLTAS-----EFQELLTQQLP 40 (89)
T ss_pred hHHHHHHHHHHHHHHHhCCCCCCeECHH-----HHHHHHHHHhh
Confidence 577888889999999999 888888876 67788888 87
No 344
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=26.42 E-value=54 Score=34.07 Aligned_cols=41 Identities=20% Similarity=0.404 Sum_probs=30.4
Q ss_pred hhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc
Q 025599 98 ELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV 152 (250)
Q Consensus 98 eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~ 152 (250)
-+|.+|++||.+..+.- . |.|+| ...||+.||..|++.|.-
T Consensus 122 ~Ig~eI~~v~~~~~~~~----~-------V~RA~---Fs~it~~~I~sA~~nlre 162 (758)
T KOG1956|consen 122 NIGWEIIDVCRAVKRLL----Q-------VRRAR---FSEITRSAIKSAARNLRE 162 (758)
T ss_pred hhhHHHHHHHHhhCccc----e-------eehhh---hhcccHHHHHHHHhCccc
Confidence 47999999999865432 1 55554 357999999999998764
No 345
>PF03837 RecT: RecT family; InterPro: IPR018330 All proteins in this family for which functions are known bind single-stranded DNA and are involved in the the pairing of homologous DNA. RecT from Escherichia coli is a homotetramer which binds to single-stranded DNA and promotes the renaturation of complementary single-stranded DNA, and also plays a role in recombination. It is able to promote the annealing of complementary single DNA strands and can catalyze the formation of joint molecules [].; GO: 0003677 DNA binding, 0006259 DNA metabolic process
Probab=26.14 E-value=48 Score=28.29 Aligned_cols=21 Identities=19% Similarity=0.346 Sum_probs=16.2
Q ss_pred ChhHHHHHHHHHHHcCCCCCC
Q 025599 60 NPTFRSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 60 dp~fR~~F~~mC~siGVDPL~ 80 (250)
||+=-..|--.|+.+|.||+.
T Consensus 21 ~~~s~~~a~~~~a~~GL~P~~ 41 (199)
T PF03837_consen 21 TPESIAGALMQAAQLGLNPFK 41 (199)
T ss_pred CHHHHHHHHHHHHHhCcCCCc
Confidence 443224688899999999997
No 346
>COG4396 Mu-like prophage host-nuclease inhibitor protein Gam [General function prediction only]
Probab=26.09 E-value=1.8e+02 Score=24.66 Aligned_cols=31 Identities=6% Similarity=0.408 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcccccccCh
Q 025599 31 RTDLMKEQLATFRSQLEDFARKHKNDIRKNP 61 (250)
Q Consensus 31 ~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp 61 (250)
|+..|.+....+.+.++.+...|++++++|-
T Consensus 55 q~~~lk~EI~~L~k~vq~yCeanrDELTe~G 85 (170)
T COG4396 55 QAAPLKAEIMSLTKRVQAYCEANRDELTENG 85 (170)
T ss_pred hhHHHHHHHHHHHHHHHHHHHhCHHHHhcCC
Confidence 5567777777788888888888888887764
No 347
>PF09548 Spore_III_AB: Stage III sporulation protein AB (spore_III_AB); InterPro: IPR014198 This entry represents the stage III sporulation protein AB, which is encoded in a spore formation operon: spoIIIAABCDEFGH that is under sigma G regulation []. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=25.88 E-value=65 Score=27.18 Aligned_cols=56 Identities=14% Similarity=0.315 Sum_probs=40.2
Q ss_pred HHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCC
Q 025599 14 AVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGV 76 (250)
Q Consensus 14 ~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGV 76 (250)
.++.+-..++|..|-..+.+.-.++++.+.+.|+.-..+-+.+.+++ .+|+.++||
T Consensus 104 ~~d~e~L~~lg~~LG~~D~~~Q~k~i~l~~~~L~~~~~~a~~~~~~~-------~Klyr~LGv 159 (170)
T PF09548_consen 104 KEDKEILLELGKSLGYSDREMQEKHIELYLEQLEQQLEEAREEAKKK-------GKLYRSLGV 159 (170)
T ss_pred HHHHHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-------ccHHHHHHH
Confidence 46788888999999877777777777777777777666555554444 466666665
No 348
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=25.74 E-value=1.5e+02 Score=30.84 Aligned_cols=46 Identities=9% Similarity=0.112 Sum_probs=36.7
Q ss_pred hhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 025599 10 LQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKN 55 (250)
Q Consensus 10 i~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~ 55 (250)
++.+.+++.+-+..+.+.-++|+.+++++|+.-...|++|-++|+-
T Consensus 254 i~~~l~~k~~~a~~a~~fL~~qL~~l~~~L~~aE~~l~~fr~~~~~ 299 (726)
T PRK09841 254 LQQNIARQAAQDSQSLEFLQRQLPEVRSELDQAEEKLNVYRQQRDS 299 (726)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3445566666777778888889999999999999999999998853
No 349
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=25.66 E-value=1.1e+02 Score=25.08 Aligned_cols=63 Identities=19% Similarity=0.255 Sum_probs=46.6
Q ss_pred HHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc-cCCCeEEEEEC-CEEEEEe
Q 025599 103 IVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV-LGNGYEVISVG-KKKLVRS 170 (250)
Q Consensus 103 IvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~-LG~g~~vi~ig-~~~~v~s 170 (250)
+|++..+-...+|--|++.+|...|.+..+ +|.+++.+++..|=. |.--=+.|.+| |+-=+|+
T Consensus 5 ~idvAy~iL~~~~~~m~f~dL~~ev~~~~~-----~s~e~~~~~iaq~YtdLn~DGRFi~lG~n~WgLr~ 69 (129)
T PRK02363 5 LIEVAYEILKEKKEPMSFYDLVNEIQKYLG-----KSDEEIRERIAQFYTDLNLDGRFISLGDNKWGLRS 69 (129)
T ss_pred HHHHHHHHHHHcCCcccHHHHHHHHHHHhC-----CCHHHHHHHHHHHHHHHhccCCeeEcCCCceeccc
Confidence 566777777778999999999999999877 799999988888642 32222567777 5544555
No 350
>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=25.65 E-value=1.1e+02 Score=29.81 Aligned_cols=79 Identities=14% Similarity=0.147 Sum_probs=49.4
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccchhHHHHHHHHHhCCCccHHHHH-HhcCCChHHHHHHHHHH
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVE-RRLSWTSGRAIDALDIL 215 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~-~~l~W~~~Ra~~~L~~l 215 (250)
.+++++.+.++.+. ..||+.+++. | .....|-..|-.+-+..|- .+.... .|-+|+...|...+..|
T Consensus 195 ~~~~~~~~~a~~~~--~~Gf~~~KiKvg--------~~~~~d~~~v~avRe~vG~-~~~L~vDaN~~w~~~~A~~~~~~L 263 (415)
T cd03324 195 YSDEKLRRLCKEAL--AQGFTHFKLKVG--------ADLEDDIRRCRLAREVIGP-DNKLMIDANQRWDVPEAIEWVKQL 263 (415)
T ss_pred CCHHHHHHHHHHHH--HcCCCEEEEeCC--------CCHHHHHHHHHHHHHhcCC-CCeEEEECCCCCCHHHHHHHHHHh
Confidence 46777766665553 3589998874 3 1223333333333333333 111111 36789999999999999
Q ss_pred HHcCCceeecCC
Q 025599 216 LEEGLAMVDDGH 227 (250)
Q Consensus 216 ~~~Gl~WvD~q~ 227 (250)
..-|+.|+-+=.
T Consensus 264 ~~~~l~~iEEP~ 275 (415)
T cd03324 264 AEFKPWWIEEPT 275 (415)
T ss_pred hccCCCEEECCC
Confidence 999999999644
No 351
>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=25.53 E-value=8.1e+02 Score=25.84 Aligned_cols=47 Identities=21% Similarity=0.251 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCC
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDP 78 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDP 78 (250)
-+-++.||.-+...+++||++-+.++..||....+..+.....|+.+
T Consensus 435 R~~va~Ql~~~s~~l~~~a~e~~~~~~~~~~~e~~i~~~L~~~gi~v 481 (764)
T TIGR02865 435 RRLVAEQLKGVAESVEDIAKEINLEIVFHQLLEEKIIRALNKNGIPY 481 (764)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhccHHHHHHHHHHHHHCCCee
Confidence 45688999999999999999999999999999999999999999954
No 352
>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=25.24 E-value=1.4e+02 Score=27.83 Aligned_cols=66 Identities=20% Similarity=0.277 Sum_probs=41.5
Q ss_pred CC-eEEEEEC-CEEEEEecCCccchhHHHHHHHHHhCCCccHHH-HHHhcCCChHHHHHHHHHHHHcCCceeecCCC
Q 025599 155 NG-YEVISVG-KKKLVRSVPTELNKDHNQILELAQAQGFVTVDE-VERRLSWTSGRAIDALDILLEEGLAMVDDGHR 228 (250)
Q Consensus 155 ~g-~~vi~ig-~~~~v~svp~El~~D~~~vLela~~~g~vt~~~-L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~ 228 (250)
.| |+.+++. |. ..+..|-..|-.+-+..|. .+.. +=.|-+|+...|...+..|...|+.|+.+=.+
T Consensus 156 ~G~f~~~KiKvg~-------~~~~~d~~~v~avr~~~g~-~~~l~iDaN~~~~~~~A~~~~~~l~~~~~~~iEeP~~ 224 (365)
T cd03318 156 AGRHRRFKLKMGA-------RPPADDLAHVEAIAKALGD-RASVRVDVNQAWDESTAIRALPRLEAAGVELIEQPVP 224 (365)
T ss_pred CCCceEEEEEeCC-------CChHHHHHHHHHHHHHcCC-CcEEEEECCCCCCHHHHHHHHHHHHhcCcceeeCCCC
Confidence 46 9988874 21 1233344334333344443 1111 11366899999999999999999999996554
No 353
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=25.21 E-value=1.4e+02 Score=26.90 Aligned_cols=61 Identities=26% Similarity=0.416 Sum_probs=45.3
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCc-e-eecCCCCCCcceeecCccC
Q 025599 180 NQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLA-M-VDDGHRDRKRRYWFPCASS 241 (250)
Q Consensus 180 ~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~-W-vD~q~~~~e~~Yw~P~l~~ 241 (250)
-.+|.+.....| =+++++..+|-+.--.-..|..|++.|++ + +|++..+..+-||.|+-+.
T Consensus 18 R~Il~lLt~~p~-yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~~~ 80 (217)
T COG1777 18 RRILQLLTRRPC-YVSEISRELGVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISRNL 80 (217)
T ss_pred HHHHHHHhcCch-HHHHHHhhcCcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccCCe
Confidence 346666554443 46789999999998888889999999998 3 7877653346798887554
No 354
>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=25.08 E-value=2e+02 Score=18.68 Aligned_cols=35 Identities=23% Similarity=0.283 Sum_probs=17.5
Q ss_pred CceeHHHHHHHHHhhcCCCCCC-CCHHHHHHHHhhccccC
Q 025599 116 GLINLQELCNLLRQRRKSNREA-VSEDDCLRAISKLKVLG 154 (250)
Q Consensus 116 Gli~l~el~~~v~k~R~~~~~~-IS~~DI~rAik~L~~LG 154 (250)
|.|+.+++...+.+. | .. +|++++..-++.+-+=+
T Consensus 3 G~i~~~~~~~~l~~~-g---~~~~s~~e~~~l~~~~D~~~ 38 (54)
T PF13833_consen 3 GKITREEFRRALSKL-G---IKDLSEEEVDRLFREFDTDG 38 (54)
T ss_dssp SEEEHHHHHHHHHHT-T---SSSSCHHHHHHHHHHHTTSS
T ss_pred CEECHHHHHHHHHHh-C---CCCCCHHHHHHHHHhcccCC
Confidence 556666666555332 1 23 55555555555544433
No 355
>PRK14337 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=25.01 E-value=1.7e+02 Score=28.41 Aligned_cols=49 Identities=18% Similarity=0.268 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
..|.+|+.++++.++..+.|+.+. ..+|--.|+|=-.|....++++...
T Consensus 280 ~~t~e~~~~~v~~lr~~~~~i~i~----~d~IvG~PgET~ed~~~tl~~l~~~ 328 (446)
T PRK14337 280 KYDMARYLDIVTDLRAARPDIALT----TDLIVGFPGETEEDFEQTLEAMRTV 328 (446)
T ss_pred CCCHHHHHHHHHHHHHhCCCCeEE----EeEEEECCCCCHHHHHHHHHHHHhc
Confidence 478999999999999887676432 3467777999999999999998853
No 356
>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=24.98 E-value=1.7e+02 Score=26.92 Aligned_cols=19 Identities=37% Similarity=0.878 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHcCCCCCCC
Q 025599 63 FRSQFHEMCAKVGVDPLAS 81 (250)
Q Consensus 63 fR~~F~~mC~siGVDPL~s 81 (250)
+-.+++.+|..+|++|+..
T Consensus 313 ~~~~y~~~~~~~~~~~~~~ 331 (365)
T TIGR02928 313 VYEVYKEVCEDIGVDPLTQ 331 (365)
T ss_pred HHHHHHHHHHhcCCCCCcH
Confidence 4457889999999999863
No 357
>PRK09613 thiH thiamine biosynthesis protein ThiH; Reviewed
Probab=24.98 E-value=2.3e+02 Score=28.14 Aligned_cols=96 Identities=19% Similarity=0.314 Sum_probs=61.2
Q ss_pred HHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCC-Cc--eeHHHH
Q 025599 47 EDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNG-GL--INLQEL 123 (250)
Q Consensus 47 ~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nG-Gl--i~l~el 123 (250)
+.|.+=|...-+.|+..|-.-...+...|+|-+.+. -++|++++-+|..--+... ......-| |. |++.
T Consensus 204 ety~~~hp~g~k~~y~~Rl~t~~rA~~aGi~~Vg~G-----~L~GLge~~~E~~~l~~hl-~~L~~~~gvgp~tIsvp-- 275 (469)
T PRK09613 204 PTYEKMHPSGPKSDYDWRLTAMDRAMEAGIDDVGIG-----VLFGLYDYKFEVLGLLMHA-EHLEERFGVGPHTISVP-- 275 (469)
T ss_pred HHHHhcCCCCCCCCHHHHHHHHHHHHHcCCCeeCeE-----EEEcCCCCHHHHHHHHHHH-HHHHHhhCCCCcccccc--
Confidence 556666766678999999999999999999977765 5899999988754432222 11111111 11 3332
Q ss_pred HHHHHhhcCCC---C-CCCCHHHHHHHHhhccc
Q 025599 124 CNLLRQRRKSN---R-EAVSEDDCLRAISKLKV 152 (250)
Q Consensus 124 ~~~v~k~R~~~---~-~~IS~~DI~rAik~L~~ 152 (250)
+++-.-|.. . ..||++|+++.|-.++-
T Consensus 276 --rl~P~~Gtpl~~~~~~vsd~e~lriiA~~RL 306 (469)
T PRK09613 276 --RLRPADGSDLENFPYLVSDEDFKKIVAILRL 306 (469)
T ss_pred --ceecCCCCCcccCCCCCCHHHHHHHHHHHHH
Confidence 333322321 1 25899999999998874
No 358
>PRK14338 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=24.92 E-value=2.1e+02 Score=27.98 Aligned_cols=49 Identities=8% Similarity=0.139 Sum_probs=38.1
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhCC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQG 190 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~g 190 (250)
.|.+|+.++++.++..+.|+.+. ..+|--.|+|=-.|....++++...+
T Consensus 287 ~t~e~~~~~i~~lr~~~pgi~i~----~d~IvG~PgET~ed~~~ti~~l~~l~ 335 (459)
T PRK14338 287 YTVARYRELIARIREAIPDVSLT----TDIIVGHPGETEEQFQRTYDLLEEIR 335 (459)
T ss_pred CCHHHHHHHHHHHHHhCCCCEEE----EEEEEECCCCCHHHHHHHHHHHHHcC
Confidence 58999999999999876676542 23555669998999999999988543
No 359
>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=24.85 E-value=2.6e+02 Score=21.01 Aligned_cols=25 Identities=20% Similarity=0.227 Sum_probs=21.6
Q ss_pred CCChHHHHHHHHHHHHcCCceeecC
Q 025599 202 SWTSGRAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 202 ~W~~~Ra~~~L~~l~~~Gl~WvD~q 226 (250)
+|+....+..+++|+.+|.+-++..
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 6999999999999999999977754
No 360
>PRK13717 conjugal transfer protein TrbI; Provisional
Probab=24.65 E-value=1.5e+02 Score=24.49 Aligned_cols=40 Identities=13% Similarity=0.357 Sum_probs=30.3
Q ss_pred cHhHHHHHHHHHHHHHH-HHHHHHHHHHHhcccccccChhH
Q 025599 24 GENVAKLRTDLMKEQLA-TFRSQLEDFARKHKNDIRKNPTF 63 (250)
Q Consensus 24 g~~l~~~~~~~l~~qL~-~F~~~L~~Fa~~h~~eI~~dp~f 63 (250)
..++++.|.++++++.. ..+..|.+|+++|+-=|--.|.+
T Consensus 65 ~~~lte~q~e~lt~rF~~aL~~~L~~yq~~H~~VILVspAV 105 (128)
T PRK13717 65 QKQLSEAQSKALSARFNTALEASLQAWQQKHHAVILVSPAV 105 (128)
T ss_pred ccCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCEEEEechhh
Confidence 45577777777776543 36689999999999888888876
No 361
>cd03032 ArsC_Spx Arsenate Reductase (ArsC) family, Spx subfamily; Spx is a unique RNA polymerase (RNAP)-binding protein present in bacilli and some mollicutes. It inhibits transcription by binding to the C-terminal domain of the alpha subunit of RNAP, disrupting complex formation between RNAP and certain transcriptional activator proteins like ResD and ComA. In response to oxidative stress, Spx can also activate transcription, making it a general regulator that exerts both positive and negative control over transcription initiation. Spx has been shown to exert redox-sensitive transcriptional control over genes like trxA (TRX) and trxB (TRX reductase), genes that function in thiol homeostasis. This redox-sensitive activity is dependent on the presence of a CXXC motif, present in some members of the Spx subfamily, that acts as a thiol/disulfide switch. Spx has also been shown to repress genes in a sulfate-dependent manner independent of the presence of the CXXC motif.
Probab=24.60 E-value=1e+02 Score=23.99 Aligned_cols=38 Identities=18% Similarity=0.453 Sum_probs=26.7
Q ss_pred HHHHHHHhcc-----cccccChhHHHHHHHHHHHc--CCCCCCCC
Q 025599 45 QLEDFARKHK-----NDIRKNPTFRSQFHEMCAKV--GVDPLASN 82 (250)
Q Consensus 45 ~L~~Fa~~h~-----~eI~~dp~fR~~F~~mC~si--GVDPL~s~ 82 (250)
...+|..+|. .+|.++|-=+.++.+++..+ |++.|.+.
T Consensus 15 ka~~~L~~~gi~~~~idi~~~~~~~~el~~~~~~~~~~~~~l~n~ 59 (115)
T cd03032 15 KAKQWLEEHQIPFEERNLFKQPLTKEELKEILSLTENGVEDIIST 59 (115)
T ss_pred HHHHHHHHCCCceEEEecCCCcchHHHHHHHHHHhcCCHHHHHhc
Confidence 3444555554 57889998889999999988 55555433
No 362
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=24.58 E-value=1.7e+02 Score=29.51 Aligned_cols=49 Identities=6% Similarity=0.024 Sum_probs=42.9
Q ss_pred HHHHHHHHHhCC-CccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 179 HNQILELAQAQG-FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 179 ~~~vLela~~~g-~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
+.+||...+..+ .++.++|++.+|++...+..++..|...|++=+....
T Consensus 5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~ 54 (492)
T PLN02853 5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIK 54 (492)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence 567888888766 5899999999999999999999999999999888654
No 363
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=24.56 E-value=1.6e+02 Score=22.03 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=29.8
Q ss_pred hhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHH
Q 025599 96 YYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRA 146 (250)
Q Consensus 96 y~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rA 146 (250)
|.++-.-|+++. ...||-++.+|++.+|.+.- .+|++|...-
T Consensus 2 ~~~~~~piL~~L----~~~g~~~~~~ei~~~v~~~~-----~ls~e~~~~~ 43 (92)
T PF14338_consen 2 YDELMPPILEAL----KDLGGSASRKEIYERVAERF-----GLSDEERNER 43 (92)
T ss_pred HHHHHHHHHHHH----HHcCCCcCHHHHHHHHHHHh-----CCCHHHHHHH
Confidence 445555566655 45699999999999998863 3788866543
No 364
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=24.52 E-value=2e+02 Score=21.66 Aligned_cols=51 Identities=18% Similarity=0.232 Sum_probs=38.0
Q ss_pred cchhHHHHHHHH-H--hCCCccHHHHHHhcCCChHHHHHHHH-HHHHcCCceeec
Q 025599 175 LNKDHNQILELA-Q--AQGFVTVDEVERRLSWTSGRAIDALD-ILLEEGLAMVDD 225 (250)
Q Consensus 175 l~~D~~~vLela-~--~~g~vt~~~L~~~l~W~~~Ra~~~L~-~l~~~Gl~WvD~ 225 (250)
|+.-+.+.|+.. + .+|.|..+-|+..+|-++.-...+.+ -|++.|++=+-.
T Consensus 6 Ld~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~ 60 (76)
T PF05491_consen 6 LDELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTP 60 (76)
T ss_dssp -BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEET
T ss_pred CCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCc
Confidence 555556666654 4 38999999999999999999999999 799999986643
No 365
>PRK10027 cryptic adenine deaminase; Provisional
Probab=24.46 E-value=1.4e+02 Score=30.57 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=26.9
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVP 172 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp 172 (250)
-+++|+..|++.|..+|+|+.++. +|+ ++-.+|
T Consensus 483 ~~~~dm~~A~~~l~~~~GG~vvv~-~g~-v~a~lp 515 (588)
T PRK10027 483 RSAEEMALAVNQVIQDGGGLCVVR-NGQ-VQSHLP 515 (588)
T ss_pred CCHHHHHHHHHHHHHhCCcEEEEE-CCE-EEEEec
Confidence 479999999999999999998874 443 566665
No 366
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=24.40 E-value=2.5e+02 Score=20.66 Aligned_cols=40 Identities=18% Similarity=0.239 Sum_probs=30.6
Q ss_pred HHHH--HHhCCCccHHHHHHhcC-CChHHHHHHHHHHHHcCCc
Q 025599 182 ILEL--AQAQGFVTVDEVERRLS-WTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 182 vLel--a~~~g~vt~~~L~~~l~-W~~~Ra~~~L~~l~~~Gl~ 221 (250)
++.. +...+++|.++....+. -+...+..+.+-|++.|++
T Consensus 42 il~~w~~n~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~I 84 (86)
T PF04433_consen 42 ILAEWRKNPNKYLTKTDARKLIKGIDVNKIRRIYDFLERWGLI 84 (86)
T ss_dssp HHHHHHHHTTS---HHHHHHHTTSSSHHHHHHHHHHHHHTTSS
T ss_pred HHHHHHHCCCCcccHHHHHHHccccCHHHHHHHHHHHHHcCcc
Confidence 4544 34589999999999999 5899999999999999974
No 367
>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=24.34 E-value=76 Score=31.16 Aligned_cols=80 Identities=10% Similarity=0.146 Sum_probs=52.6
Q ss_pred HHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccch
Q 025599 17 RDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFY 96 (250)
Q Consensus 17 ~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy 96 (250)
-+...+....+...-++.|...++.|.++++. ..-|-.-.+...+.+....++|...|...++-+|+-=.+-.|++++.
T Consensus 31 ~~~~r~~~~~ik~~~~~~ld~~l~~~~~~~~~-~g~~v~~a~t~~eA~~~v~~i~~~~~~~~vv~~kS~~~eeigl~~~L 109 (432)
T TIGR00273 31 WEEWRELVKEIKLKVLENLDFYLDQLKENVTQ-RGGHVYYAKTAEEARKIIGKVAQEKNGKKVVKSKSMVSEEIGLNEVL 109 (432)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH-CCCEEEEECCHHHHHHHHHHHHHHhCCCEEEEcCchHHHHhCCHHHH
Confidence 34455666777777788888899999888854 22233333444667778899999999887764444333445555554
Q ss_pred h
Q 025599 97 Y 97 (250)
Q Consensus 97 ~ 97 (250)
-
T Consensus 110 ~ 110 (432)
T TIGR00273 110 E 110 (432)
T ss_pred H
Confidence 3
No 368
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=24.21 E-value=61 Score=24.55 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=20.6
Q ss_pred cccChhHHHHHHHHHHHcCCCCC
Q 025599 57 IRKNPTFRSQFHEMCAKVGVDPL 79 (250)
Q Consensus 57 I~~dp~fR~~F~~mC~siGVDPL 79 (250)
++=|++...++.+.|..+|++|-
T Consensus 6 vRiD~~lK~~A~~vl~~lGls~S 28 (80)
T PRK11235 6 VRVDDELKARAYAVLEKLGVTPS 28 (80)
T ss_pred EEeCHHHHHHHHHHHHHhCCCHH
Confidence 56789999999999999999974
No 369
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=23.92 E-value=4.4e+02 Score=27.46 Aligned_cols=92 Identities=21% Similarity=0.163 Sum_probs=69.1
Q ss_pred HHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhH---HHHHHHhhhhcc---------cCCCceeHHHHHHHHHhh
Q 025599 63 FRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELG---VQIVEICLATRP---------HNGGLINLQELCNLLRQR 130 (250)
Q Consensus 63 fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLa---vqIvevC~~tr~---------~nGGli~l~el~~~v~k~ 130 (250)
=+++.-.||.+--.|-+|. |=-|||+ .+++.+....-+ .+|+.-+|.+|-.+..=.
T Consensus 38 s~~rllrli~~~kpDIvAv------------DnvyEL~~~~~~li~il~~lP~~tkLVQVTg~~g~~~sL~~lArr~G~~ 105 (652)
T COG2433 38 SLRRLLRLIWSYKPDIVAV------------DNVYELGADKRDLIRILKRLPEGTKLVQVTGRPGEQESLWELARRHGIR 105 (652)
T ss_pred hHHHHHHHHHhcCCCEEEe------------ccHHHHhcChhHHHHHHHhCCCCceEEEEeCCCCCcchHHHHHHHhCCC
Confidence 3556778999988887772 5568898 788888766544 567788888776554321
Q ss_pred cCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEE
Q 025599 131 RKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVR 169 (250)
Q Consensus 131 R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~ 169 (250)
.....+|.|=-.+|..|..+|-|+.+.-+-..+.|.
T Consensus 106 ---~~~~~~P~eeA~~~A~LA~~GvG~ev~~fEdeT~I~ 141 (652)
T COG2433 106 ---VNGKLNPYEEAYACARLASKGVGTEVSVFEDETKIT 141 (652)
T ss_pred ---CCCCCChHHHHHHHHHHHhcCCCceeEeeeeeeEEE
Confidence 124689999999999999999999999887665443
No 370
>PRK14017 galactonate dehydratase; Provisional
Probab=23.91 E-value=62 Score=30.66 Aligned_cols=86 Identities=10% Similarity=0.084 Sum_probs=49.1
Q ss_pred CHHHHHHHHhhccccCCCeEEEEEC--CEEEEEecCCccchhHHHHHHHHHhCCC-ccHHHHHHhcCCChHHHHHHHHHH
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVG--KKKLVRSVPTELNKDHNQILELAQAQGF-VTVDEVERRLSWTSGRAIDALDIL 215 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig--~~~~v~svp~El~~D~~~vLela~~~g~-vt~~~L~~~l~W~~~Ra~~~L~~l 215 (250)
+++++...+..+. ..||+.+++. ++.-+...+.....|-..|-.+-+..|. +.. .+=.|-+|+...|...+..|
T Consensus 124 ~~~~~~~~a~~~~--~~Gf~~~KiKv~~~~~~~~~~~~~~~d~~~i~avr~~~g~~~~l-~vDaN~~w~~~~A~~~~~~l 200 (382)
T PRK14017 124 RPADVAEAARARV--ERGFTAVKMNGTEELQYIDSPRKVDAAVARVAAVREAVGPEIGI-GVDFHGRVHKPMAKVLAKEL 200 (382)
T ss_pred CHHHHHHHHHHHH--HcCCCEEEEcCcCCccccccHHHHHHHHHHHHHHHHHhCCCCeE-EEECCCCCCHHHHHHHHHhh
Confidence 6677765555543 3589999884 1100000011223343333333333332 111 12236689999999999999
Q ss_pred HHcCCceeecCC
Q 025599 216 LEEGLAMVDDGH 227 (250)
Q Consensus 216 ~~~Gl~WvD~q~ 227 (250)
..-|+.|+.+=.
T Consensus 201 ~~~~~~~iEeP~ 212 (382)
T PRK14017 201 EPYRPMFIEEPV 212 (382)
T ss_pred cccCCCeEECCC
Confidence 999999999644
No 371
>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=23.91 E-value=7.2e+02 Score=26.42 Aligned_cols=96 Identities=18% Similarity=0.377 Sum_probs=57.5
Q ss_pred ccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHH---HHHH-HHHhhcCC
Q 025599 58 RKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQ---ELCN-LLRQRRKS 133 (250)
Q Consensus 58 ~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~---el~~-~v~k~R~~ 133 (250)
..||.=++++.+|....+-.|--.-+.||- ++- .=|++.|+.++ ..||+-|++- .++- .+.|- .
T Consensus 224 e~d~~rk~EL~~iA~~c~~vp~~pp~tf~E-AlQ-~~~~~~l~~~~--------e~n~~~~s~GR~Dq~L~Pyy~~D--l 291 (781)
T cd01677 224 ETDPKRKAELLEIAEICRRVPAHPPRTFWE-ALQ-SFWFIHLILQI--------ESNGHSISPGRFDQYLYPFYKQD--I 291 (781)
T ss_pred ccCHHHHHHHHHHHHHhccCcCCCCCCHHH-HHH-HHHHHHHHHHH--------hcCCcccCCCcHHHHHHHHHHhH--H
Confidence 479999999999999999988776667774 331 23333444332 2355555544 3332 23321 1
Q ss_pred CCCCCCHHHHHHHHhhccc-------c----------C-CCeEEEEECCE
Q 025599 134 NREAVSEDDCLRAISKLKV-------L----------G-NGYEVISVGKK 165 (250)
Q Consensus 134 ~~~~IS~~DI~rAik~L~~-------L----------G-~g~~vi~ig~~ 165 (250)
....+|+++...-++.+-. + | ..|..+++||.
T Consensus 292 ~~G~it~eeA~Ell~~f~ik~~~~~~~~~~~~~~~~~G~~~~~~i~iGG~ 341 (781)
T cd01677 292 EEGRLTREGAIELLECLWIKINEINKVRSGASAKYFAGYNTFQNLTIGGQ 341 (781)
T ss_pred hcCCCCHHHHHHHHHHHHHHhcccccccCccccccccCCCCcceEEECCc
Confidence 1235899888777655321 1 1 23778889886
No 372
>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=23.90 E-value=2e+02 Score=25.82 Aligned_cols=18 Identities=22% Similarity=0.540 Sum_probs=15.2
Q ss_pred cChhHHHHHHHHHHHcCCCC
Q 025599 59 KNPTFRSQFHEMCAKVGVDP 78 (250)
Q Consensus 59 ~dp~fR~~F~~mC~siGVDP 78 (250)
++|.| -..+|+..+||||
T Consensus 198 e~~~~--TM~eL~~~l~ID~ 215 (221)
T PF10376_consen 198 EGEKF--TMGELIKRLGIDY 215 (221)
T ss_pred cccCc--cHHHHHHHhCCCc
Confidence 57777 4889999999996
No 373
>PRK14101 bifunctional glucokinase/RpiR family transcriptional regulator; Provisional
Probab=23.64 E-value=1.1e+02 Score=31.21 Aligned_cols=111 Identities=18% Similarity=0.253 Sum_probs=57.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCC-CCCcccccccc---cccchhhhHHHHHHHh
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLA-SNKGFWAELLG---IGDFYYELGVQIVEIC 107 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~-s~k~~ws~~lG---~gdfy~eLavqIvevC 107 (250)
+.+...+|..=...+.+|+.+|..++..- --+++....||.|-+ ++ ++..|| +.||-++|...+.+-=
T Consensus 347 I~~~~~~Lt~~E~~IA~yIl~n~~~v~~~-----si~eLA~~~~vS~aTV~R---f~kkLGf~Gf~efK~~L~~~~~~~~ 418 (638)
T PRK14101 347 IRQMRDALTPAERRVADLALNHPRSIIND-----PIVDIARKADVSQPTVIR---FCRSLGCQGLSDFKLKLATGLTGTI 418 (638)
T ss_pred HHHHHhhcCHHHHHHHHHHHhCHHHHHhc-----cHHHHHHHhCCCHHHHHH---HHHHhCCCCHHHHHHHHHHHhhhcc
Confidence 33444444455678889999888776533 233666666666543 11 122344 3688888886654310
Q ss_pred hh-hcc-cCCCceeHHHHHHHHHh----hcCCCCCCCCHHHHHHHHhhccc
Q 025599 108 LA-TRP-HNGGLINLQELCNLLRQ----RRKSNREAVSEDDCLRAISKLKV 152 (250)
Q Consensus 108 ~~-tr~-~nGGli~l~el~~~v~k----~R~~~~~~IS~~DI~rAik~L~~ 152 (250)
.. .+. .++. +..++...+.. .-......++++++.++++.|..
T Consensus 419 ~~~~~~~~~~~--~~~~~~~~~~~~~~~~i~~t~~~id~~~l~~aa~~L~~ 467 (638)
T PRK14101 419 PMSHSQVHLGD--TATDFGAKVLDNTVSAILQLREHLNFEHVEQAIDILNN 467 (638)
T ss_pred ccccccCCCCC--CHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHhc
Confidence 00 000 0111 12232222211 00001246899999999999863
No 374
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=23.46 E-value=1.1e+02 Score=25.46 Aligned_cols=34 Identities=18% Similarity=0.215 Sum_probs=30.9
Q ss_pred CccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 191 FVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 191 ~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.+|.++|++-+|-+++-+-.+|..|.++|++-+.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~ 182 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIRSG 182 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC
Confidence 3789999999999999999999999999998653
No 375
>PRK09462 fur ferric uptake regulator; Provisional
Probab=23.46 E-value=2.3e+02 Score=22.98 Aligned_cols=47 Identities=19% Similarity=0.299 Sum_probs=0.0
Q ss_pred cchhHHHHHHHHHhC--CCccHHHHHHhc-----CCChHHHHHHHHHHHHcCCc
Q 025599 175 LNKDHNQILELAQAQ--GFVTVDEVERRL-----SWTSGRAIDALDILLEEGLA 221 (250)
Q Consensus 175 l~~D~~~vLela~~~--g~vt~~~L~~~l-----~W~~~Ra~~~L~~l~~~Gl~ 221 (250)
++.-...||++.... +.+|+++|-+.+ +.+..=.-..|+.|+..|++
T Consensus 15 ~T~qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli 68 (148)
T PRK09462 15 VTLPRLKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIV 68 (148)
T ss_pred CCHHHHHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCE
No 376
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.45 E-value=2.1e+02 Score=23.33 Aligned_cols=42 Identities=19% Similarity=0.217 Sum_probs=33.3
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
+|+.++..|+.+.-..| .|..++++.+|++..-++..|...+
T Consensus 119 ~Lp~~~r~v~~L~~~~g-~s~~EIA~~lgis~~tV~~~l~ra~ 160 (172)
T PRK12523 119 KLSSKARAAFLYNRLDG-MGHAEIAERLGVSVSRVRQYLAQGL 160 (172)
T ss_pred hCCHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 56777888888877655 4999999999999988888776543
No 377
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=23.45 E-value=2.1e+02 Score=19.28 Aligned_cols=42 Identities=14% Similarity=0.294 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCC
Q 025599 32 TDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDP 78 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDP 78 (250)
..+|++.+..=+..|....... ..+|.+- .+..+|..+||+|
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~----~~~~~~~-~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGK----PSNPSLD-TLEKIAKALNCSP 54 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT---------HH-HHHHHHHHHT--H
T ss_pred HHHHHHHHCcCHHHHHHHHhcc----cccccHH-HHHHHHHHcCCCH
Confidence 4467788888888888877744 2467664 7999999999987
No 378
>PF10136 SpecificRecomb: Site-specific recombinase; InterPro: IPR011385 This group represents a site-specific recombinase Gcr. Please see the following relevant reference: [].
Probab=23.40 E-value=1.1e+02 Score=31.89 Aligned_cols=66 Identities=24% Similarity=0.440 Sum_probs=46.1
Q ss_pred cccChhHHHHHHHHHHH--cCCCC--CCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHh
Q 025599 57 IRKNPTFRSQFHEMCAK--VGVDP--LASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQ 129 (250)
Q Consensus 57 I~~dp~fR~~F~~mC~s--iGVDP--L~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k 129 (250)
++.||+.|.+|+.+... -++|+ |.+.-|+-+ -..|+.||..++-+=-+..-+... ++.||...+-.
T Consensus 42 L~~~p~~~~~l~~~l~~~l~~~~~~~L~~d~Gi~~----~~gF~~El~~Rl~~r~lP~~~d~~---~l~~lf~~lF~ 111 (643)
T PF10136_consen 42 LERNPELRAALRRYLRRLLRERRQYPLLTDSGILS----RSGFFSELSRRLYERLLPAPPDPN---DLSDLFNLLFP 111 (643)
T ss_pred HHhCHHHHHHHHHHHHHHHhcCCcchHHHhcCCCC----CccHHHHHHHHHHhhcCCCCCChh---HHHHHHHHHCC
Confidence 34699999999998777 36664 334445544 378999999999988777665554 46666655553
No 379
>PF07870 DUF1657: Protein of unknown function (DUF1657); InterPro: IPR012452 This domain appears to be restricted to the Bacillales.
Probab=23.29 E-value=2.4e+02 Score=19.20 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHc
Q 025599 37 EQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKV 74 (250)
Q Consensus 37 ~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~si 74 (250)
.-|...+..|+.||-.. +|++-+..|.++...+
T Consensus 7 AslK~~qA~Le~fal~T-----~d~~AK~~y~~~a~~l 39 (50)
T PF07870_consen 7 ASLKKAQADLETFALQT-----QDQEAKQMYEQAAQQL 39 (50)
T ss_pred HHHHHHHhhHHHHHhhc-----CCHHHHHHHHHHHHHH
Confidence 45666778999999864 5999998998887654
No 380
>PHA02095 hypothetical protein
Probab=23.24 E-value=73 Score=23.98 Aligned_cols=23 Identities=30% Similarity=0.502 Sum_probs=20.1
Q ss_pred EEEEecCCccchhHHHHHHHHHh
Q 025599 166 KLVRSVPTELNKDHNQILELAQA 188 (250)
Q Consensus 166 ~~v~svp~El~~D~~~vLela~~ 188 (250)
..|..||.+++.|.+.|++.|+.
T Consensus 58 ~~ii~vp~~~~~dyn~ii~wa~~ 80 (84)
T PHA02095 58 EHIVEVPDEMAGDYNEIISWAEK 80 (84)
T ss_pred eeeeeCchhhcccHHHHHHHHHh
Confidence 35778999999999999999885
No 381
>PRK14331 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=23.22 E-value=1.6e+02 Score=28.46 Aligned_cols=49 Identities=18% Similarity=0.298 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
..|.+|+.++++.++....|+.+. ..+|--.|+|=-.|....++++...
T Consensus 276 ~~t~~~~~~~v~~lr~~~~gi~i~----~d~IvG~PgET~ed~~~tl~~l~~l 324 (437)
T PRK14331 276 GYTKEEYLEKIELLKEYIPDITFS----TDIIVGFPTETEEDFEETLDVLKKV 324 (437)
T ss_pred CCCHHHHHHHHHHHHHhCCCCEEe----cCEEEECCCCCHHHHHHHHHHHHhc
Confidence 479999999999999875666532 2355666999899999999998854
No 382
>PF14528 LAGLIDADG_3: LAGLIDADG-like domain; PDB: 2CW7_A 2CW8_A 2VS8_F 2VS7_G 1B24_A 1DQ3_A 2DCH_X.
Probab=23.21 E-value=64 Score=22.94 Aligned_cols=22 Identities=9% Similarity=0.298 Sum_probs=16.9
Q ss_pred ccChhHHHHHHHHHHHcCCCCC
Q 025599 58 RKNPTFRSQFHEMCAKVGVDPL 79 (250)
Q Consensus 58 ~~dp~fR~~F~~mC~siGVDPL 79 (250)
+.|++|...++.++.++||.|-
T Consensus 28 ~~s~~ll~~v~~lL~~lGi~~~ 49 (77)
T PF14528_consen 28 SKSKELLEDVQKLLLRLGIKAS 49 (77)
T ss_dssp ES-HHHHHHHHHHHHHTT--EE
T ss_pred ECCHHHHHHHHHHHHHCCCeeE
Confidence 5678999999999999999974
No 383
>KOG2410 consensus Gamma-glutamyltransferase [Amino acid transport and metabolism]
Probab=23.11 E-value=52 Score=33.65 Aligned_cols=32 Identities=28% Similarity=0.472 Sum_probs=22.9
Q ss_pred ccccchhhhHHHHHHHhhhhcccCCCceeHHHHHH
Q 025599 91 GIGDFYYELGVQIVEICLATRPHNGGLINLQELCN 125 (250)
Q Consensus 91 G~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~ 125 (250)
|...||.. .+.+-..+....+||+|+++||-+
T Consensus 235 g~~~FY~G---~~a~~lvkdiq~~GGiiT~qDl~~ 266 (579)
T KOG2410|consen 235 GPEAFYNG---ELAQKLVKDIQKAGGIITEQDLEN 266 (579)
T ss_pred CcccccCh---HHHHHHHHHHHHhCCceEHHHHhh
Confidence 45678775 444444455667999999999976
No 384
>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=23.10 E-value=2.1e+02 Score=20.17 Aligned_cols=35 Identities=20% Similarity=0.219 Sum_probs=29.2
Q ss_pred HHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHH
Q 025599 182 ILELAQAQGFVTVDEVERRLSWTSGRAIDALDILL 216 (250)
Q Consensus 182 vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~ 216 (250)
+++++-....||+.++.+.+|-|..=|..-+.+|-
T Consensus 4 Lidll~~~P~Vsa~mva~~L~vT~~~A~~li~eLg 38 (54)
T PF11972_consen 4 LIDLLLSRPLVSAPMVAKELGVTPQAAQRLIAELG 38 (54)
T ss_pred HHHHHHhCccccHHHHHHHhCCCHHHHHHHHHHhh
Confidence 56667778999999999999999998888776653
No 385
>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=23.07 E-value=2.8e+02 Score=20.59 Aligned_cols=25 Identities=24% Similarity=0.593 Sum_probs=20.6
Q ss_pred ccccChhH------HHHHHHHHHHcCCCCCC
Q 025599 56 DIRKNPTF------RSQFHEMCAKVGVDPLA 80 (250)
Q Consensus 56 eI~~dp~f------R~~F~~mC~siGVDPL~ 80 (250)
.++.||.+ ..++++++..+|..|-+
T Consensus 56 ~~~~nP~~~~~~~~~~~~~~l~~~lGLtP~s 86 (100)
T PF05119_consen 56 NPKKNPAVSILNKAMKQMRSLASELGLTPAS 86 (100)
T ss_pred CcccCHHHHHHHHHHHHHHHHHHHcCCCHHH
Confidence 37899964 46789999999999976
No 386
>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=23.02 E-value=2e+02 Score=25.97 Aligned_cols=84 Identities=19% Similarity=0.261 Sum_probs=44.3
Q ss_pred HHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCC---CCCCCCHH
Q 025599 65 SQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKS---NREAVSED 141 (250)
Q Consensus 65 ~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~---~~~~IS~~ 141 (250)
.++.++|.+.||+.++|-=...+ =||.-++.+.. .+.--|-++=-.+++.+.+.... ...--|.+
T Consensus 59 ~~L~~~~~~~gi~f~stpfd~~s-----~d~l~~~~~~~-------~KIaS~dl~n~~lL~~~A~tgkPvIlSTG~stl~ 126 (241)
T PF03102_consen 59 KELFEYCKELGIDFFSTPFDEES-----VDFLEELGVPA-------YKIASGDLTNLPLLEYIAKTGKPVILSTGMSTLE 126 (241)
T ss_dssp HHHHHHHHHTT-EEEEEE-SHHH-----HHHHHHHT-SE-------EEE-GGGTT-HHHHHHHHTT-S-EEEE-TT--HH
T ss_pred HHHHHHHHHcCCEEEECCCCHHH-----HHHHHHcCCCE-------EEeccccccCHHHHHHHHHhCCcEEEECCCCCHH
Confidence 46999999999998875422111 24444443322 22333444455677777774210 01345899
Q ss_pred HHHHHHhhc-cccCCCeEEE
Q 025599 142 DCLRAISKL-KVLGNGYEVI 160 (250)
Q Consensus 142 DI~rAik~L-~~LG~g~~vi 160 (250)
||.+|++.+ +.-+..+.++
T Consensus 127 EI~~Av~~~~~~~~~~l~ll 146 (241)
T PF03102_consen 127 EIERAVEVLREAGNEDLVLL 146 (241)
T ss_dssp HHHHHHHHHHHHCT--EEEE
T ss_pred HHHHHHHHHHhcCCCCEEEE
Confidence 999999999 4444445444
No 387
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=23.00 E-value=2e+02 Score=17.80 Aligned_cols=33 Identities=27% Similarity=0.364 Sum_probs=16.0
Q ss_pred CCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhcc
Q 025599 115 GGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK 151 (250)
Q Consensus 115 GGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~ 151 (250)
-|.|+..|+...+... + ...+.+.+.+..+.+.
T Consensus 14 ~g~l~~~e~~~~l~~~-~---~~~~~~~~~~~~~~~~ 46 (63)
T cd00051 14 DGTISADELKAALKSL-G---EGLSEEEIDEMIREVD 46 (63)
T ss_pred CCcCcHHHHHHHHHHh-C---CCCCHHHHHHHHHHhC
Confidence 3555666655555443 1 2344555554444443
No 388
>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=22.98 E-value=1.7e+02 Score=24.29 Aligned_cols=38 Identities=18% Similarity=0.199 Sum_probs=29.3
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
-|+..|..|+.+- .. ..|.+++++.+|+|....+..+.
T Consensus 6 ~Lte~qr~VL~Lr-~~-GlTq~EIAe~LgiS~stV~~~e~ 43 (137)
T TIGR00721 6 FLTERQIKVLELR-EK-GLSQKEIAKELKTTRANVSAIEK 43 (137)
T ss_pred CCCHHHHHHHHHH-Hc-CCCHHHHHHHHCcCHHHHHHHHH
Confidence 3788888999884 34 45999999999999886664443
No 389
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=22.78 E-value=2e+02 Score=27.40 Aligned_cols=41 Identities=12% Similarity=0.059 Sum_probs=32.8
Q ss_pred HHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 025599 15 VARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKN 55 (250)
Q Consensus 15 ~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~ 55 (250)
+.+..-+..+...-++++.++.++|+.-...|++|-++|+-
T Consensus 163 ~~~~~~~~~~~~fl~~ql~~~~~~l~~ae~~l~~fr~~~~i 203 (444)
T TIGR03017 163 ELKVEPAQKAALWFVQQIAALREDLARAQSKLSAYQQEKGI 203 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 33444455667777889999999999999999999999864
No 390
>PF13814 Replic_Relax: Replication-relaxation
Probab=22.77 E-value=1e+02 Score=25.62 Aligned_cols=42 Identities=31% Similarity=0.222 Sum_probs=34.8
Q ss_pred HHHhCCCccHHHHHHhcCCChH---HHHHHHHHHHHcCCceeecC
Q 025599 185 LAQAQGFVTVDEVERRLSWTSG---RAIDALDILLEEGLAMVDDG 226 (250)
Q Consensus 185 la~~~g~vt~~~L~~~l~W~~~---Ra~~~L~~l~~~Gl~WvD~q 226 (250)
+....+++|.+.|..-+.-+.. .+..+|..|.+.|++-.-..
T Consensus 3 ~L~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~ 47 (191)
T PF13814_consen 3 LLARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRR 47 (191)
T ss_pred hHHHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecc
Confidence 4455689999999988877766 69999999999999977765
No 391
>PRK11519 tyrosine kinase; Provisional
Probab=22.71 E-value=1.8e+02 Score=30.19 Aligned_cols=45 Identities=7% Similarity=0.090 Sum_probs=35.1
Q ss_pred hccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Q 025599 11 QSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKN 55 (250)
Q Consensus 11 ~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~ 55 (250)
+...+.+.+-+..+...-++|+.+++++|+.-...|++|-++|+-
T Consensus 255 ~~~~~~k~~~a~~a~~fL~~ql~~l~~~L~~aE~~l~~fr~~~~~ 299 (719)
T PRK11519 255 EQNIERKSEEASKSLAFLAQQLPEVRSRLDVAENKLNAFRQDKDS 299 (719)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Confidence 344455556666777788889999999999999999999888764
No 392
>PRK14335 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=22.70 E-value=2.4e+02 Score=27.55 Aligned_cols=49 Identities=20% Similarity=0.306 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
..|.+|+.++++.++....|+.+- ..+|-=.|+|=..|....++++...
T Consensus 289 ~~t~e~~~~~v~~ir~~~pgi~i~----~d~IvGfPgET~edf~~Tl~~i~~l 337 (455)
T PRK14335 289 SYTREHYLSLVGKLKASIPNVALS----TDILIGFPGETEEDFEQTLDLMREV 337 (455)
T ss_pred CCCHHHHHHHHHHHHHhCCCCEEE----EEEEEeCCCCCHHHHHHHHHHHHhc
Confidence 478999999999999876666432 2355556999999999999998853
No 393
>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=22.68 E-value=2.6e+02 Score=19.15 Aligned_cols=50 Identities=24% Similarity=0.296 Sum_probs=36.4
Q ss_pred hhhhHHHHHHHhhhhcccCCCce-eHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccC
Q 025599 96 YYELGVQIVEICLATRPHNGGLI-NLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLG 154 (250)
Q Consensus 96 y~eLavqIvevC~~tr~~nGGli-~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG 154 (250)
|.+++..|.+--..-.-..|=.+ +..+|..++. ||..=+.+|++.|...|
T Consensus 2 ~~~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~---------vsr~tvr~al~~L~~~g 52 (64)
T PF00392_consen 2 YEQIYDQLRQAILSGRLPPGDRLPSERELAERYG---------VSRTTVREALRRLEAEG 52 (64)
T ss_dssp HHHHHHHHHHHHHTTSS-TTSBE--HHHHHHHHT---------S-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhc---------cCCcHHHHHHHHHHHCC
Confidence 55666677776667666777788 7888877654 88999999999999876
No 394
>cd05031 S-100A10_like S-100A10_like: S-100A10 domain found in proteins similar to S100A10. S100A10 is a member of the S100 family of EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A1_like group belongs, 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. A unique feature of S100A10 is that it contains mutation in both of the calcium binding sites, making it calcium insensitive. S100A10 has been detected in brain, heart, gastrointestinal tract, kidney, liver, lung, spleen, testes, epidermis, aorta, and thymus. Structural data supports the homo- and hetero-dimeric as well as hetero-tetrameric nature of the protein. S100A10 has multiple binding partners in its calcium free state and is therefore involved in many diverse biological functions.
Probab=22.65 E-value=3.2e+02 Score=20.18 Aligned_cols=75 Identities=11% Similarity=0.239 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHHHHHHH-hc-ccccccChhHHHHHHHHHHH-cCCCCCCCCCcccccccccccchhhhHHHHHHHhhhh
Q 025599 34 LMKEQLATFRSQLEDFAR-KH-KNDIRKNPTFRSQFHEMCAK-VGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLAT 110 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~-~h-~~eI~~dp~fR~~F~~mC~s-iGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~t 110 (250)
++..-+..++..+..|.. ++ .+.|..+ +++.-+++++-. +|.+|-. ..|-+++...
T Consensus 2 ~~~~~~~~l~~~F~~~D~~dg~dG~Is~~-El~~~l~~~~g~~lg~~~s~--------------------~ei~~~~~~~ 60 (94)
T cd05031 2 ELEHAMESLILTFHRYAGKDGDKNTLSRK-ELKKLMEKELSEFLKNQKDP--------------------MAVDKIMKDL 60 (94)
T ss_pred hHHHHHHHHHHHHHHHhccCCCCCeECHH-HHHHHHHHHhHHHhhccccH--------------------HHHHHHHHHh
Confidence 355667888899999997 65 5777765 344333333322 4544321 0222233333
Q ss_pred cccCCCceeHHHHHHHHHh
Q 025599 111 RPHNGGLINLQELCNLLRQ 129 (250)
Q Consensus 111 r~~nGGli~l~el~~~v~k 129 (250)
-..+.|.|+..|.+..+..
T Consensus 61 D~~~dg~I~f~eF~~l~~~ 79 (94)
T cd05031 61 DQNRDGKVNFEEFVSLVAG 79 (94)
T ss_pred CCCCCCcCcHHHHHHHHHH
Confidence 3344588888888766654
No 395
>PHA03078 transcriptional elongation factor; Provisional
Probab=22.49 E-value=61 Score=29.13 Aligned_cols=101 Identities=22% Similarity=0.304 Sum_probs=53.8
Q ss_pred cccChhHHHHHHHHHHHcCCCCCCCCCcccccccccccch----hhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcC
Q 025599 57 IRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGDFY----YELGVQIVEICLATRPHNGGLINLQELCNLLRQRRK 132 (250)
Q Consensus 57 I~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy----~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~ 132 (250)
.++||+.-.+|.+.|...|||.-. ++ .+|| ..+.-++.+ |-..-++- -+.=..+++..+-+.|=
T Consensus 13 lTede~s~~~f~SLCrgF~i~~~~--------li--~~f~~kk~~k~itkvl~-c~~ll~Ei-~l~FP~di~reLv~LRL 80 (219)
T PHA03078 13 LTEDEESLRMFISLCRGFNIDLEE--------LI--TEFYNKKYLKKITKVLE-CADLLPEL-SLEFPDDILRELVRLRL 80 (219)
T ss_pred hcCCHHHHHHHHHHhcccCCCHHH--------HH--HHHhhhhhHHHHHHHhc-ccccCHHH-heeCChHHHHHHHHHHH
Confidence 478999999999999999999542 11 2343 222222221 11111111 11123344444444432
Q ss_pred CCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCcc
Q 025599 133 SNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTEL 175 (250)
Q Consensus 133 ~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El 175 (250)
- .-| =.+|+.-+|..=+.|..+|. |+.-+|+-..+||
T Consensus 81 ~---kf~--k~Ik~SykL~~~m~Gia~i~-~~~V~v~~aNd~l 117 (219)
T PHA03078 81 Y---KFS--KTIKRSYKLPNNMKGIAVIK-DRNVYVRRANDEL 117 (219)
T ss_pred H---hhh--HhhHHhhcCCcccCceEEEc-CCEEEEEcCCHHH
Confidence 1 011 13455566666678888874 5555577775444
No 396
>PF13012 MitMem_reg: Maintenance of mitochondrial structure and function; PDB: 2O96_B 2O95_A.
Probab=22.44 E-value=18 Score=28.19 Aligned_cols=69 Identities=16% Similarity=0.291 Sum_probs=8.1
Q ss_pred CCcchhhhhccHHHHHHHHhhcHhHHHH--HHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcC
Q 025599 3 RRPGIGGLQSAAVARDQYRLLGENVAKL--RTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVG 75 (250)
Q Consensus 3 R~~Gi~ai~~~~~~~~~~~~~g~~l~~~--~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siG 75 (250)
+|+||.++-|. .....|......+... -+..|.+.+......|+.+. .+++.-|++.-++.+.+|.++-
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-LGDHYYSSLSSQLENEQNALKMLHKRLWQILDYLEDVI---SGEIPPDHEILRQLQDLLSSLP 74 (115)
T ss_dssp HHHHHHHHHHH---S------------------------------------------------------------
T ss_pred HHHHHHHHHcc-CCCccccHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH---cCcCCCchhHHHHHHHHHHhcc
Confidence 45788888772 2233333332222211 22345555555556666652 4677889998889999999874
No 397
>PF12381 Peptidase_C3G: Tungro spherical virus-type peptidase; InterPro: IPR024387 This entry represents a rice tungro spherical waikavirus-type peptidase that belongs to MEROPS peptidase family C3G. It is a picornain 3C-type protease, and is responsible for the self-cleavage of the positive single-stranded polyproteins of a number of plant viral genomes. The location of the protease activity of the polyprotein is at the C-terminal end, adjacent and N-terminal to the putative RNA polymerase [, ].
Probab=22.41 E-value=48 Score=29.97 Aligned_cols=18 Identities=39% Similarity=0.700 Sum_probs=16.4
Q ss_pred CCCCCHHHHHHHHhhccc
Q 025599 135 REAVSEDDCLRAISKLKV 152 (250)
Q Consensus 135 ~~~IS~~DI~rAik~L~~ 152 (250)
++-||+|||.+|+.+|++
T Consensus 213 Ae~itQEDL~~A~~~l~~ 230 (231)
T PF12381_consen 213 AESITQEDLMRAINKLEK 230 (231)
T ss_pred hhhhhHHHHHHHHHhhcC
Confidence 578999999999999975
No 398
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=22.41 E-value=1e+02 Score=29.29 Aligned_cols=33 Identities=24% Similarity=0.287 Sum_probs=29.5
Q ss_pred cHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 193 TVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 193 t~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|..+|++.+|-+..-++++++.|+.+|++ +.+.
T Consensus 31 s~r~la~~~~vsr~tv~~a~~~L~~~g~i--~~~~ 63 (431)
T PRK15481 31 PVRELASELGVNRNTVAAAYKRLVTAGLA--QSQG 63 (431)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCE--EEeC
Confidence 89999999999999999999999999965 4444
No 399
>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=22.41 E-value=1.8e+02 Score=19.99 Aligned_cols=37 Identities=24% Similarity=0.352 Sum_probs=28.6
Q ss_pred CCCccHHHHHHhcCCChHHH-HHHHHHHHHcCCceeec
Q 025599 189 QGFVTVDEVERRLSWTSGRA-IDALDILLEEGLAMVDD 225 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra-~~~L~~l~~~Gl~WvD~ 225 (250)
...|+.+.+.+.+|-+-... ...|..++++|++-+|+
T Consensus 18 ~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~ 55 (66)
T PF06969_consen 18 NEGIDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDG 55 (66)
T ss_dssp HSEEEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-S
T ss_pred HCCcCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeC
Confidence 45789999999999875555 77899999999998874
No 400
>cd03329 MR_like_4 Mandelate racemase (MR)-like subfamily of the enolase superfamily, subgroup 4. 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. This subgroup's function is unknown.
Probab=22.37 E-value=1.1e+02 Score=28.66 Aligned_cols=79 Identities=20% Similarity=0.172 Sum_probs=49.2
Q ss_pred CHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHH-hCCC---ccHHHHHHhcCCChHHHHHHHHH
Q 025599 139 SEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQ-AQGF---VTVDEVERRLSWTSGRAIDALDI 214 (250)
Q Consensus 139 S~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~-~~g~---vt~~~L~~~l~W~~~Ra~~~L~~ 214 (250)
++++..+.++... ..||+.+++-. ..+..+..|- ..++.+. ..|. +.++ .|-+|+...|...+..
T Consensus 143 ~~~~~~~~a~~~~--~~Gf~~~Kik~-----~~~~~~~~di-~~i~~vR~~~G~~~~l~vD---an~~~~~~~A~~~~~~ 211 (368)
T cd03329 143 SPEAYADFAEECK--ALGYRAIKLHP-----WGPGVVRRDL-KACLAVREAVGPDMRLMHD---GAHWYSRADALRLGRA 211 (368)
T ss_pred CHHHHHHHHHHHH--HcCCCEEEEec-----CCchhHHHHH-HHHHHHHHHhCCCCeEEEE---CCCCcCHHHHHHHHHH
Confidence 7777776666554 35899988720 0011122232 2343333 2332 2222 3678999999999999
Q ss_pred HHHcCCceeecCCC
Q 025599 215 LLEEGLAMVDDGHR 228 (250)
Q Consensus 215 l~~~Gl~WvD~q~~ 228 (250)
|..-++.|+.+-.+
T Consensus 212 l~~~~l~~iEeP~~ 225 (368)
T cd03329 212 LEELGFFWYEDPLR 225 (368)
T ss_pred hhhcCCCeEeCCCC
Confidence 99999999996553
No 401
>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=22.36 E-value=1.3e+02 Score=23.53 Aligned_cols=51 Identities=16% Similarity=0.227 Sum_probs=40.4
Q ss_pred ccchhHHHHHHHHHh--------CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 174 ELNKDHNQILELAQA--------QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 174 El~~D~~~vLela~~--------~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
.|+.-|..|+-++-. .-.||.+.+.+..|-++..+..+|+.|++.|++=+|
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~ 87 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELIRRGVIIRD 87 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 455556666655442 246999999999999999999999999999999544
No 402
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=22.30 E-value=5.5e+02 Score=24.17 Aligned_cols=109 Identities=16% Similarity=0.139 Sum_probs=70.7
Q ss_pred hHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecC-----
Q 025599 99 LGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVP----- 172 (250)
Q Consensus 99 LavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp----- 172 (250)
.-.++.++| ..+ +-.++..||.+. +..+|..|...|++.|=.-| .+.++.=+ +-.|=.-.|
T Consensus 12 ~~~~~~~~~-~~~---p~git~q~L~~~--------~p~~~~~~~~salN~lLs~~-~l~llr~~~~l~yr~~d~~~a~~ 78 (297)
T KOG3233|consen 12 IENILIQIV-KQI---PEGITQQELQSE--------MPQISATDRASALNILLSRG-LLDLLRQNTGLVYRAKDPKSASK 78 (297)
T ss_pred HHHHHHHHH-Hhc---cccccHHHHHHH--------cCCCcHHHHHHHHHHHHhcC-cchhhccCCcceEeccCchhhcc
Confidence 344555555 222 234667776544 34589999999999886544 35555544 222222223
Q ss_pred -CccchhHHHHHHHHHh--CCCccHHHHHHhcCCChHHHHHHHHHHHHcCC
Q 025599 173 -TELNKDHNQILELAQA--QGFVTVDEVERRLSWTSGRAIDALDILLEEGL 220 (250)
Q Consensus 173 -~El~~D~~~vLela~~--~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl 220 (250)
..+..+...|+.+++. +-.++..+|+..-+.........|.-|+..-+
T Consensus 79 ~~~~e~eEk~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkL 129 (297)
T KOG3233|consen 79 GKGMENEEKLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKL 129 (297)
T ss_pred cccCChHHHHHHHHHHHcCCCceeeehhhhccCCCHHHHHHHHHHHHHHHH
Confidence 3456677778889995 45689999999999988888888887776433
No 403
>PRK14330 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=22.22 E-value=2.4e+02 Score=27.27 Aligned_cols=48 Identities=17% Similarity=0.325 Sum_probs=37.9
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
.+.+|+.++++.++..+.|+.+- ..+|--.|+|=-.|....++++...
T Consensus 272 ~~~~~~~~~i~~lr~~~~~i~i~----~d~IvGfPgET~edf~~tl~fi~~~ 319 (434)
T PRK14330 272 YTREEYLELIEKIRSKVPDASIS----SDIIVGFPTETEEDFMETVDLVEKA 319 (434)
T ss_pred CCHHHHHHHHHHHHHhCCCCEEE----EEEEEECCCCCHHHHHHHHHHHHhc
Confidence 68899999999999876665432 2356667999889999999998854
No 404
>PF06407 BDV_P40: Borna disease virus P40 protein; InterPro: IPR009441 This entry represents P40 nucleoproteins from several Borna disease virus (BDV) strains. BDV is an RNA virus that is a member of the Mononegavirales family, which includes such members as Measles virus and Ebola virus sp.. BDV causes an infection of the central nervous system in a wide range of vertebrates, which can progress to an often fatal immune-mediated disease. Viral nucleoproteins are central to transcription, replication, and packaging of the RNA genome. P40 nucleoprotein from BDV is multi-helical in structure and can be divided into two subdomains, each of which has an alpha-bundle topology []. The nucleoprotein assembles into a planar homotetramer, with the RNA genome either wrapping around the outside of the tetramer or possibly fitting within the charged central channel of the tetramer [].; PDB: 1N93_X 1PP1_X.
Probab=22.21 E-value=1.6e+02 Score=27.82 Aligned_cols=43 Identities=16% Similarity=0.139 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccccChh-HHHHHHHHHHHcCC
Q 025599 34 LMKEQLATFRSQLEDFARKHKNDIRKNPT-FRSQFHEMCAKVGV 76 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~-fR~~F~~mC~siGV 76 (250)
+++..+..+++-|..-+.--.+.|..+.. +.++|+.|.++||-
T Consensus 132 e~SSi~~HCC~lLIGv~~gSS~kI~a~s~qI~RRfkAMmAsinr 175 (370)
T PF06407_consen 132 EKSSILRHCCDLLIGVAAGSSDKICAGSLQIQRRFKAMMASINR 175 (370)
T ss_dssp HHHHHHHHHHHHHHHHHHT-SHHHHS--HHHHHHHHHHHHHTT-
T ss_pred HHHHHHHHHHHHHHhhhhcCcccccccHHHHHHHHHHHHHhcCC
Confidence 57888999999999999999999988764 66699999999994
No 405
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=22.20 E-value=1.7e+02 Score=24.95 Aligned_cols=51 Identities=18% Similarity=0.147 Sum_probs=41.3
Q ss_pred cchhHHHHHHHHHhC-CCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 175 LNKDHNQILELAQAQ-GFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 175 l~~D~~~vLela~~~-g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
|+.. .||.+...+ +..|..++++.++.+..=++.-+..|+..|++=-|-.-
T Consensus 162 Lt~r--~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 162 LTLN--AVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred HHHH--HHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEeec
Confidence 5554 578777642 24699999999999999999999999999999777543
No 406
>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=22.15 E-value=7.2e+02 Score=25.21 Aligned_cols=115 Identities=13% Similarity=0.043 Sum_probs=68.6
Q ss_pred ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecC
Q 025599 93 GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVP 172 (250)
Q Consensus 93 gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp 172 (250)
.++|-++-.++.+.....++ .--=|+..+|.+++... +.-+...++.|.. +...++...+..--
T Consensus 404 ~~~~~~~~~~~~~~l~~~~~-~~~g~~~~~l~~~~~~~---------~~~~~~~l~~~~~------~~~~~~~~~~~~~~ 467 (581)
T TIGR00475 404 IDFGEVEVKKILVKLGTEQH-DVKGVDKERLERMASLN---------EELLKTAIEKLIG------TYKIGGWLHIPDHK 467 (581)
T ss_pred HHHHHHHHHHHHHHHHHHHh-hccCCCHHHHHhhccCC---------hHHHHHHHHHHHH------heEeCCEEECCCCC
Confidence 67888888888888766222 33346777887765432 2222222232222 22233322111111
Q ss_pred CccchhHHHHHHHHH---hCCCccHHHHHHhcCCChHHHHHHHHHHHHcC-Cceee
Q 025599 173 TELNKDHNQILELAQ---AQGFVTVDEVERRLSWTSGRAIDALDILLEEG-LAMVD 224 (250)
Q Consensus 173 ~El~~D~~~vLela~---~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G-l~WvD 224 (250)
..++.++. +.+... .....+++++...++.+....++.|..|.+.| ++=++
T Consensus 468 ~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~ 522 (581)
T TIGR00475 468 SDFEKEED-IWQKIKGTFGTKGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIV 522 (581)
T ss_pred CCCCHHHH-HHHHHHHHHhcCCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEe
Confidence 25566655 333322 13568999999999999999999999999988 55555
No 407
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=22.14 E-value=2e+02 Score=26.16 Aligned_cols=100 Identities=21% Similarity=0.292 Sum_probs=57.8
Q ss_pred HHHHHHhcccccccChhHHHHHHHHHHHcCC-C-CCCCCC----cccccccccccchhhhHHHHHHH--hhhhcccCCC-
Q 025599 46 LEDFARKHKNDIRKNPTFRSQFHEMCAKVGV-D-PLASNK----GFWAELLGIGDFYYELGVQIVEI--CLATRPHNGG- 116 (250)
Q Consensus 46 L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGV-D-PL~s~k----~~ws~~lG~gdfy~eLavqIvev--C~~tr~~nGG- 116 (250)
|..|++..+......|.....|..+|-.+-. | .+.... --+++.||++..-++-....++. +.. +..||+
T Consensus 111 l~~~~~~~~~~~~~r~~l~~~lL~~l~~vA~ADG~l~~~E~~~L~~Ia~~Lgis~~df~~~~~~~~~~~~f~-~~~~~~~ 189 (267)
T PRK09430 111 LREKLRQFRSVCGGRFDLLRMFLEIQIQAAFADGSLHPNERQVLYVIAEELGFSRFQFDQLLRMMQAGFRFQ-QQQGGGG 189 (267)
T ss_pred HHHHHHHHHHHhcccHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhc-ccccccc
Confidence 6777777776667777776666554444321 2 221110 12456678766555555555443 221 111111
Q ss_pred ------ceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhcc
Q 025599 117 ------LINLQELCNLLRQRRKSNREAVSEDDCLRAISKLK 151 (250)
Q Consensus 117 ------li~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~ 151 (250)
-+++.+.|..+.=. ...|+++|.+|-++|-
T Consensus 190 ~~~~~~~~~~~~ay~vLgv~-----~~as~~eIk~aYr~L~ 225 (267)
T PRK09430 190 YQQAQRGPTLEDAYKVLGVS-----ESDDDQEIKRAYRKLM 225 (267)
T ss_pred cccccCCCcHHhHHHHcCCC-----CCCCHHHHHHHHHHHH
Confidence 36778888776643 4589999999999984
No 408
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=21.91 E-value=1.7e+02 Score=21.34 Aligned_cols=16 Identities=19% Similarity=0.204 Sum_probs=12.8
Q ss_pred CCCCHHHHHHHHhhcc
Q 025599 136 EAVSEDDCLRAISKLK 151 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~ 151 (250)
..+++.||..|++.+.
T Consensus 57 ~~~~~~Dv~~Al~~~g 72 (77)
T smart00576 57 TEPNLGDVVLALENLG 72 (77)
T ss_pred CCCCHHHHHHHHHHhC
Confidence 3578999999988764
No 409
>TIGR01178 ade adenine deaminase. The family described by this model includes an experimentally characterized adenine deaminase of Bacillus subtilis. It also include a member from Methanobacterium thermoautotrophicum, in which adenine deaminase activity has been detected.
Probab=21.91 E-value=1.7e+02 Score=29.63 Aligned_cols=34 Identities=21% Similarity=0.336 Sum_probs=27.4
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPT 173 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~ 173 (250)
-+++|+..|++.|..+|+|+.++. +|+ ++-.+|-
T Consensus 451 ~~~~dm~~A~~~l~~~~GG~~~v~-~g~-v~~~l~L 484 (552)
T TIGR01178 451 SNDEDLALAVNKLIQIGGGLCAAK-NGE-VTIILPL 484 (552)
T ss_pred CCHHHHHHHHHHHHHhCCcEEEEE-CCE-EEEEecc
Confidence 369999999999999999998874 444 5666653
No 410
>PRK14340 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.77 E-value=1.9e+02 Score=28.16 Aligned_cols=49 Identities=18% Similarity=0.262 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
..|.+|+.+++++++..-.|+.+. ..+|--.|+|=-.|....+++++..
T Consensus 279 ~~t~~~~~~~v~~lr~~~pgi~i~----td~IvGfPgET~edf~~tl~~~~~~ 327 (445)
T PRK14340 279 GHTIEEYLEKIALIRSAIPGVTLS----TDLIAGFCGETEEDHRATLSLMEEV 327 (445)
T ss_pred CCCHHHHHHHHHHHHHhCCCCEEe----ccEEEECCCCCHHHHHHHHHHHHhc
Confidence 478999999999999875566532 2356667999999999999998853
No 411
>COG5014 Predicted Fe-S oxidoreductase [General function prediction only]
Probab=21.71 E-value=5.7e+02 Score=22.70 Aligned_cols=99 Identities=18% Similarity=0.259 Sum_probs=60.8
Q ss_pred cCCCceeHHHHHHHH---HhhcCC-------CCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHH
Q 025599 113 HNGGLINLQELCNLL---RQRRKS-------NREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQI 182 (250)
Q Consensus 113 ~nGGli~l~el~~~v---~k~R~~-------~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~v 182 (250)
..|-.++..||..|+ .|.||- ..+.+-++.|+.-|..|. ..-| |+..+|. =+..|-+-+
T Consensus 69 rag~f~~P~eVaeRL~ei~K~~g~d~vRiSG~EP~l~~EHvlevIeLl~--~~tF-vlETNG~--------~~g~drslv 137 (228)
T COG5014 69 RAGDFLSPEEVAERLLEISKKRGCDLVRISGAEPILGREHVLEVIELLV--NNTF-VLETNGL--------MFGFDRSLV 137 (228)
T ss_pred ccccccCHHHHHHHHHHHHHhcCCcEEEeeCCCccccHHHHHHHHHhcc--CceE-EEEeCCe--------EEecCHHHH
Confidence 567788888888887 345542 124677888888888871 1222 2222332 234455666
Q ss_pred HHHHH---------hCCCccHHHHHHhcCCChHHHH---HHHHHHHHcCC-cee
Q 025599 183 LELAQ---------AQGFVTVDEVERRLSWTSGRAI---DALDILLEEGL-AMV 223 (250)
Q Consensus 183 Lela~---------~~g~vt~~~L~~~l~W~~~Ra~---~~L~~l~~~Gl-~Wv 223 (250)
-+++. .+|+ +++...+--|-+++=.. .+|..|..+|+ .|.
T Consensus 138 ~el~nr~nv~vRVsvKG~-dpesF~kIT~asp~~F~~QL~aLr~L~~~g~rf~p 190 (228)
T COG5014 138 DELVNRLNVLVRVSVKGW-DPESFEKITGASPEYFRYQLKALRHLHGKGHRFWP 190 (228)
T ss_pred HHHhcCCceEEEEEecCC-CHHHHHHHhcCChHHHHHHHHHHHHHHhcCceeee
Confidence 66665 1455 67777766666665444 46778889998 664
No 412
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.71 E-value=2.4e+02 Score=22.35 Aligned_cols=39 Identities=13% Similarity=0.162 Sum_probs=28.4
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
.|+..+..|+.+.-..|+ |.+++++.+|++..-++..|.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~-s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWEDM-DVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhcC-CHHHHHHHHCCCHHHHHHHHH
Confidence 345567778777665544 999999999999876665554
No 413
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=21.55 E-value=2.2e+02 Score=25.87 Aligned_cols=121 Identities=21% Similarity=0.137 Sum_probs=66.7
Q ss_pred CCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEEC-C--EEEEEe---cCCccchhHHHHHHHHH
Q 025599 114 NGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVG-K--KKLVRS---VPTELNKDHNQILELAQ 187 (250)
Q Consensus 114 nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig-~--~~~v~s---vp~El~~D~~~vLela~ 187 (250)
.+|-++-+||...+... +.....-.....-.++..|..-|- +.+..-. | +.|.-. +|.....+...+-+++.
T Consensus 96 ~~gplt~~eL~~~l~~~-~~~~~~~~~~~~~~~l~~l~~~G~-l~~~~~~~g~~~~y~l~~~~lP~~~~~~~ea~~~Lv~ 173 (327)
T PF06224_consen 96 ADGPLTRAELREALAEA-GWWGWGGPSSPWKHLLEYLWYRGL-LCVGPRPRGRWRTYDLTERWLPAPDDDREEALAELVR 173 (327)
T ss_pred hcCCCCHHHHHHHhhhc-cccCCCCCCchHHHHHHHHHhCCe-EEEeccCCCceEEEechHHhCCCCcCCHHHHHHHHHH
Confidence 36777888888777765 100011112233444444443221 1111111 2 222222 25444234444555555
Q ss_pred ----hCCCccHHHHHHhcCCChHHHHHHHHHHHHcC-CceeecCCCCCCc-ceeecC
Q 025599 188 ----AQGFVTVDEVERRLSWTSGRAIDALDILLEEG-LAMVDDGHRDRKR-RYWFPC 238 (250)
Q Consensus 188 ----~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G-l~WvD~q~~~~e~-~Yw~P~ 238 (250)
..|-+|..+++.=+|.++..++.+|..|+..| ++=+.... |.. .|..|.
T Consensus 174 Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~~--G~~~~~~~~~ 228 (327)
T PF06224_consen 174 RYLRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVEG--GKEPLYDLPE 228 (327)
T ss_pred HHHHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEcC--cceeEEechh
Confidence 47999999999999999999999999998653 43333221 233 566665
No 414
>PRK14325 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=21.51 E-value=2.2e+02 Score=27.48 Aligned_cols=49 Identities=14% Similarity=0.238 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 137 AVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 137 ~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
..|.+|+.++++.++..+.|+.+. ..+|--.|+|=-.|...+++++...
T Consensus 280 ~~~~~~~~~~i~~lr~~~~gi~v~----~~~IvG~PgET~ed~~~tl~~i~~~ 328 (444)
T PRK14325 280 GHTALEYKSIIRKLRAARPDIAIS----SDFIVGFPGETDEDFEATMKLIEDV 328 (444)
T ss_pred CCCHHHHHHHHHHHHHHCCCCEEE----eeEEEECCCCCHHHHHHHHHHHHhc
Confidence 368999999999999887776542 2356666999999999999998853
No 415
>PF05633 DUF793: Protein of unknown function (DUF793); InterPro: IPR008511 This entry includes Protein BYPASS 1 which is required for normal root and shoot development. Prevents constitutive production of a root mobile carotenoid-derived signaling compound that is capable of arresting shoot and leaf development [, ].
Probab=21.19 E-value=1.4e+02 Score=29.10 Aligned_cols=79 Identities=24% Similarity=0.416 Sum_probs=46.6
Q ss_pred HHHHHHHHcCCCCCCCC-CcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcC--CCCCCCCHHH
Q 025599 66 QFHEMCAKVGVDPLASN-KGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRK--SNREAVSEDD 142 (250)
Q Consensus 66 ~F~~mC~siGVDPL~s~-k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~--~~~~~IS~~D 142 (250)
.|+.....+..-|++.. -.-|- +.|.+-+|+..+||.+-++ ||=.+..-+..+.-+=. .....+++.-
T Consensus 82 efr~li~~~~~~~~s~~~~dk~v------~eylD~sVKlLDvCNA~~~---gi~~lr~~~~ll~~al~~L~~~~~~~~~~ 152 (389)
T PF05633_consen 82 EFRALITNLRDLPLSKPPDDKWV------DEYLDRSVKLLDVCNAIRD---GISQLRQWQLLLQIALHALDSSRPLGEGQ 152 (389)
T ss_pred HHHHHHhcccccccCCchHHHHH------HHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHhcCCCCCcHHH
Confidence 36666666654366632 12343 8899999999999999654 33222221111111000 0024799999
Q ss_pred HHHHHhhcccc
Q 025599 143 CLRAISKLKVL 153 (250)
Q Consensus 143 I~rAik~L~~L 153 (250)
+.||-+.|.-|
T Consensus 153 ~rRAr~aL~dl 163 (389)
T PF05633_consen 153 LRRARKALSDL 163 (389)
T ss_pred HHHHHHHHHHH
Confidence 99999988753
No 416
>CHL00073 chlN photochlorophyllide reductase subunit N
Probab=21.15 E-value=6.1e+02 Score=25.22 Aligned_cols=73 Identities=10% Similarity=-0.003 Sum_probs=46.7
Q ss_pred cchhhhhccHHHHHHHHhhcHhHHHHHHHHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCC
Q 025599 5 PGIGGLQSAAVARDQYRLLGENVAKLRTDLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLAS 81 (250)
Q Consensus 5 ~Gi~ai~~~~~~~~~~~~~g~~l~~~~~~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s 81 (250)
+|+.+-++-..+-.++..+-.+--+.+..++-..|+.++..| .-| +--+--||..=-...+.+..+|+.|...
T Consensus 271 iGi~~Td~fLr~Ia~~~G~~pe~l~~Er~rl~dal~d~~~~L---~GK-rvai~Gdp~~~i~LarfL~elGmevV~v 343 (457)
T CHL00073 271 IGPDGTRAWIEKICSVFGIEPQGLEEREEQIWESLKDYLDLV---RGK-SVFFMGDNLLEISLARFLIRCGMIVYEI 343 (457)
T ss_pred CcHHHHHHHHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHHH---CCC-EEEEECCCcHHHHHHHHHHHCCCEEEEE
Confidence 577777777766666654332111334444555555555544 222 3348889887778999999999999964
No 417
>PF08227 DASH_Hsk3: DASH complex subunit Hsk3 like; InterPro: IPR013183 This is a family of fungal proteins of unknown function.
Probab=21.15 E-value=1.3e+02 Score=20.47 Aligned_cols=18 Identities=28% Similarity=0.375 Sum_probs=8.1
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 025599 32 TDLMKEQLATFRSQLEDF 49 (250)
Q Consensus 32 ~~~l~~qL~~F~~~L~~F 49 (250)
..+|..||+....+|.+|
T Consensus 4 ~s~L~~qL~qL~aNL~~t 21 (45)
T PF08227_consen 4 YSHLASQLAQLQANLADT 21 (45)
T ss_pred HHHHHHHHHHHHHhHHHH
Confidence 344444444444444443
No 418
>cd03323 D-glucarate_dehydratase D-Glucarate dehydratase (GlucD) catalyzes the dehydration of both D-glucarate and L-idarate to form 5-keto-4-deoxy-D-glucarate (5-KDG) , the initial reaction of the catabolic pathway for (D)-glucarate. GlucD 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 that is stabilized by coordination to the essential Mg2+ ion.
Probab=21.07 E-value=1.4e+02 Score=28.68 Aligned_cols=78 Identities=13% Similarity=0.061 Sum_probs=48.0
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEEC-CEEEEEecCCccchhHHHHHHHHH-hCCCccHHHHH-HhcCCChHHHHHHHHH
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVG-KKKLVRSVPTELNKDHNQILELAQ-AQGFVTVDEVE-RRLSWTSGRAIDALDI 214 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig-~~~~v~svp~El~~D~~~vLela~-~~g~vt~~~L~-~~l~W~~~Ra~~~L~~ 214 (250)
.+++++.+.++.+.. ..||+.+++. |. .....|-. .+..+. ..+- ..... .|-+|+...|...+..
T Consensus 167 ~~~e~~~~~a~~~~~-~~Gf~~~KiKvG~-------~~~~~di~-~v~avRea~~~--~~l~vDaN~~w~~~~A~~~~~~ 235 (395)
T cd03323 167 LTPEGVVRLARAAID-RYGFKSFKLKGGV-------LPGEEEIE-AVKALAEAFPG--ARLRLDPNGAWSLETAIRLAKE 235 (395)
T ss_pred CCHHHHHHHHHHHHH-hcCCcEEEEecCC-------CCHHHHHH-HHHHHHHhCCC--CcEEEeCCCCcCHHHHHHHHHh
Confidence 478888776665532 3489988874 21 11223322 333332 2221 11222 4788999999999999
Q ss_pred HHHcCCceeecCC
Q 025599 215 LLEEGLAMVDDGH 227 (250)
Q Consensus 215 l~~~Gl~WvD~q~ 227 (250)
|.. ++.|+.+=.
T Consensus 236 l~~-~l~~iEeP~ 247 (395)
T cd03323 236 LEG-VLAYLEDPC 247 (395)
T ss_pred cCc-CCCEEECCC
Confidence 999 999998644
No 419
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=20.95 E-value=1e+02 Score=27.98 Aligned_cols=111 Identities=18% Similarity=0.227 Sum_probs=59.4
Q ss_pred HHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCcccccccc---cccchhhhHHHHHHHhhhh
Q 025599 34 LMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLG---IGDFYYELGVQIVEICLAT 110 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG---~gdfy~eLavqIvevC~~t 110 (250)
+.-.+|..-...+.+|+-+|.+++.. ..-++++...||-|-+-. =++..|| +.||...|+..+.+- ...
T Consensus 11 ~~~~~Lt~~er~iA~yil~~~~~~~~-----~si~elA~~a~VS~aTv~--Rf~~kLGf~Gf~efk~~l~~~l~~~-~~~ 82 (281)
T COG1737 11 ERYDSLTKSERKIADYILANPDEVAL-----LSIAELAERAGVSPATVV--RFARKLGFEGFSEFKLALAQELAEG-RAQ 82 (281)
T ss_pred HHHhcCCHHHHHHHHHHHhCHHHHHH-----HHHHHHHHHhCCCHHHHH--HHHHHcCCCCHHHHHHHHHHHHhhc-cch
Confidence 33344444456677777777754432 235678888888766411 0223444 468999998888764 110
Q ss_pred c-----ccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccc
Q 025599 111 R-----PHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKV 152 (250)
Q Consensus 111 r-----~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~ 152 (250)
. ...+.---+..+.......-......++++++.+|+..|..
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~t~~~l~~~~l~~av~~L~~ 129 (281)
T COG1737 83 LLREIAEDDGPESILEKLLAANIAALERTLNLLDEEALERAVELLAK 129 (281)
T ss_pred hhcccCCCCCHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHc
Confidence 0 11111001122222221111111246899999999999974
No 420
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.94 E-value=4.2e+02 Score=20.80 Aligned_cols=90 Identities=19% Similarity=0.302 Sum_probs=55.8
Q ss_pred hhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCcc
Q 025599 96 YYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTEL 175 (250)
Q Consensus 96 y~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El 175 (250)
=+.|-.+|++.+.. |+ +..++..++ .||..-|.+-++. ...|. +.. ...+. + .+
T Consensus 4 S~DlR~rVl~~~~~-----g~--s~~eaa~~F---------~VS~~Tv~~W~k~-~~~G~-~~~-k~r~~------~-Ki 57 (119)
T PF01710_consen 4 SLDLRQRVLAYIEK-----GK--SIREAAKRF---------GVSRNTVYRWLKR-KETGD-LEP-KPRGR------K-KI 57 (119)
T ss_pred CHHHHHHHHHHHHc-----cc--hHHHHHHHh---------CcHHHHHHHHHHh-ccccc-ccc-ccccc------c-cc
Confidence 35566777776654 33 556665443 3888889998883 33342 221 11111 1 44
Q ss_pred chhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHH
Q 025599 176 NKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 176 ~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
+.| .+.++++..+-+|..||++.||.+..-.-.+|.
T Consensus 58 d~~--~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~~Lk 93 (119)
T PF01710_consen 58 DRD--ELKALVEENPDATLRELAERLGVSPSTIWRALK 93 (119)
T ss_pred cHH--HHHHHHHHCCCcCHHHHHHHcCCCHHHHHHHHH
Confidence 434 478888889999999999999976554444443
No 421
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=20.88 E-value=2.2e+02 Score=21.62 Aligned_cols=53 Identities=15% Similarity=0.124 Sum_probs=35.2
Q ss_pred cccccchhhhHHHHHHHhhhhc-ccCCCceeHHHHHHHHHhhcCCCCCCCCHHHHHHHHhhc
Q 025599 90 LGIGDFYYELGVQIVEICLATR-PHNGGLINLQELCNLLRQRRKSNREAVSEDDCLRAISKL 150 (250)
Q Consensus 90 lG~gdfy~eLavqIvevC~~tr-~~nGGli~l~el~~~v~k~R~~~~~~IS~~DI~rAik~L 150 (250)
|+..+|+.++...+++.|+... ..|- -...|..++.+. ..+|++++..|+..+
T Consensus 28 L~~~~~~~~vv~~~i~~~le~~~~~~~---~~~~Ll~~L~~~-----~~~~~~~~~~~f~~~ 81 (113)
T smart00544 28 LKLPEQHHEVVKVLLTCALEEKRTYRE---MYSVLLSRLCQA-----NVISTKQFEKGFWRL 81 (113)
T ss_pred hCCCcchHHHHHHHHHHHHcCCccHHH---HHHHHHHHHHHc-----CCcCHHHHHHHHHHH
Confidence 3445799999999999999752 1221 122333444332 469999999999874
No 422
>cd02646 R3H_G-patch R3H domain of a group of fungal and plant proteins with unknown function, who also contain a G-patch domain. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the R3H domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=20.80 E-value=1.7e+02 Score=20.29 Aligned_cols=38 Identities=11% Similarity=0.251 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhcccccccC---hhHHHHHHHHHHHcCCC
Q 025599 40 ATFRSQLEDFARKHKNDIRKN---PTFRSQFHEMCAKVGVD 77 (250)
Q Consensus 40 ~~F~~~L~~Fa~~h~~eI~~d---p~fR~~F~~mC~siGVD 77 (250)
+.++..|++|+...+..+.-. |.-|+..+++|...|+-
T Consensus 2 ~~i~~~i~~F~~~~~~~~~fppm~~~~R~~vH~lA~~~~L~ 42 (58)
T cd02646 2 EDIKDEIEAFLLDSRDSLSFPPMDKHGRKTIHKLANCYNLK 42 (58)
T ss_pred hHHHHHHHHHHhCCCceEecCCCCHHHHHHHHHHHHHcCCc
Confidence 456778888888877666554 46788899999999865
No 423
>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=20.78 E-value=70 Score=31.29 Aligned_cols=35 Identities=26% Similarity=0.591 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcc-----cccccChhHHHHHHHHH
Q 025599 34 LMKEQLATFRSQLEDFARKHK-----NDIRKNPTFRSQFHEMC 71 (250)
Q Consensus 34 ~l~~qL~~F~~~L~~Fa~~h~-----~eI~~dp~fR~~F~~mC 71 (250)
+|..+|-.+. ..|+.+|. .||+.||+++..+++|-
T Consensus 3 ~Lr~eLK~WE---~~F~~~hgRkP~k~DIk~~p~I~~~YK~Y~ 42 (426)
T PF11719_consen 3 QLRAELKQWE---RAFAAQHGRKPSKEDIKANPEIAAKYKEYN 42 (426)
T ss_dssp HHHHHHHHHH---HHHHHHT-S---HHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHHH---HHHHHHhCCCCCHHHHHhCHHHHHHHHHHH
Confidence 3455554444 46889994 59999999999999884
No 424
>PRK03525 crotonobetainyl-CoA:carnitine CoA-transferase; Provisional
Probab=20.68 E-value=6.7e+02 Score=24.11 Aligned_cols=144 Identities=11% Similarity=0.081 Sum_probs=71.5
Q ss_pred HHHHHHHHcCCCCCCCCCccccccc---cc-ccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCCCCCCCCHH
Q 025599 66 QFHEMCAKVGVDPLASNKGFWAELL---GI-GDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKSNREAVSED 141 (250)
Q Consensus 66 ~F~~mC~siGVDPL~s~k~~ws~~l---G~-gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~~~~~IS~~ 141 (250)
+|..+|..||...+.....|..... .. ..-+.||-..|.+++.. -+..|+..++.+++--.....|.+
T Consensus 255 ~w~~l~~~lg~~~l~~d~~f~~~~~~~~r~~~~~~~el~~~l~~~~~~--------~t~~ew~~~l~~~~vp~~pV~~~~ 326 (405)
T PRK03525 255 QIKECFKDIGLAHLLGTPEIPEGTQLIHRIECPYGPLVEEKLDAWLAA--------HTIAEVEARFAELNIACAKVLTIP 326 (405)
T ss_pred HHHHHHHHhCCcccccCccccCccccchhhhhhhHHHHHHHHHHHHHh--------CCHHHHHHHHHHcCCCEEecCCHH
Confidence 6899999999765543322211100 00 12345665555555444 357888888887654334455667
Q ss_pred HHHHHHhhccccCCCeEEEEEC--CEEEEEecCCccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcC
Q 025599 142 DCLRAISKLKVLGNGYEVISVG--KKKLVRSVPTELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEG 219 (250)
Q Consensus 142 DI~rAik~L~~LG~g~~vi~ig--~~~~v~svp~El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~G 219 (250)
|++.-=.. ..-|. |.-+... +...+..+|--++.....+-..+-..|-=|.+.|++ +|++.. .++.|.++|
T Consensus 327 e~~~dp~~-~~r~~-~~~~~~~~g~~~~~~~~p~~~~~~~~~~~~~aP~lGeht~~vL~~-lG~~~~----ei~~L~~~g 399 (405)
T PRK03525 327 ELESNPQY-VARES-ITQWQTMDGRTCKGPNIMPKFKNNPGQIWRGMPSHGMDTAAILKN-IGYSEE----DIQELVAKG 399 (405)
T ss_pred HHhhCHHH-HHhCC-EEEEecCCCCeeEeecCCcccCCCCCCCCCCCCCCCCCHHHHHHH-cCCCHH----HHHHHHHCc
Confidence 76542211 11110 1111111 121122334333321111111122356668888876 888864 566778888
Q ss_pred Cceee
Q 025599 220 LAMVD 224 (250)
Q Consensus 220 l~WvD 224 (250)
.+=|.
T Consensus 400 vi~~~ 404 (405)
T PRK03525 400 LAKVE 404 (405)
T ss_pred CEeCC
Confidence 76543
No 425
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=20.65 E-value=2.6e+02 Score=22.62 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=27.8
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L 212 (250)
.|+..+..|+.+.-..|+ |.+++++.+|.+..-++..|
T Consensus 118 ~L~~~~r~vl~L~~~~g~-s~~EIA~~lgis~~tV~~~l 155 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRGW-STAQIAADLGIPEGTVKSRL 155 (173)
T ss_pred hCCHHHHHHHHHHHHcCC-CHHHHHHHHCcCHHHHHHHH
Confidence 456677788887665555 99999999999875444433
No 426
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=20.65 E-value=2.2e+02 Score=25.59 Aligned_cols=110 Identities=13% Similarity=0.142 Sum_probs=57.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCCccccccccc---ccchhhhHHHHHHH-h-
Q 025599 33 DLMKEQLATFRSQLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGI---GDFYYELGVQIVEI-C- 107 (250)
Q Consensus 33 ~~l~~qL~~F~~~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~---gdfy~eLavqIvev-C- 107 (250)
...-.+|..-...+.+|+-+|.+++.... -+++....||.|-+-. .| +..||. .||-++|...+-.- .
T Consensus 20 ~~~~~~Lt~~e~~Ia~yil~~~~~v~~~s-----i~~lA~~~~vS~aTi~-Rf-~kkLGf~gf~efk~~l~~~~~~~~~~ 92 (292)
T PRK11337 20 RMKQEGLTPLESRVVEWLLKPGDLSEATA-----LKDIAEALAVSEAMIV-KV-AKKLGFSGFRNLRSALEDYFSQSEQV 92 (292)
T ss_pred HHHHhhcCHHHHHHHHHHHhCHHHHHhcC-----HHHHHHHhCCChHHHH-HH-HHHcCCCCHHHHHHHHHHHhcccccc
Confidence 33344444456788889988887765552 3467777777765411 11 234443 57888887654210 0
Q ss_pred -hhhcccCCCceeHHHHHHHHHhhc----CCCCCCCCHHHHHHHHhhccc
Q 025599 108 -LATRPHNGGLINLQELCNLLRQRR----KSNREAVSEDDCLRAISKLKV 152 (250)
Q Consensus 108 -~~tr~~nGGli~l~el~~~v~k~R----~~~~~~IS~~DI~rAik~L~~ 152 (250)
......+. +..++...+...- ......++++++.++++.|..
T Consensus 93 ~~~~~~~~~---~~~~~~~~~~~~~~~~i~~t~~~l~~~~l~~~~~~i~~ 139 (292)
T PRK11337 93 LHSELSFDD---APQDVVNKVFNTSLQAIEETQSILDVDEFHRAARFFYQ 139 (292)
T ss_pred ccCCCCCCC---CHHHHHHHHHHHHHHHHHHHHHhcCHHHHHHHHHHHHc
Confidence 00001111 2334433322100 001246899999999999863
No 427
>cd07626 BAR_SNX9_like The Bin/Amphiphysin/Rvs (BAR) domain of Sorting Nexin 9 and Similar Proteins. 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 SNX9, SNX18, SNX33, and similar proteins. SNX9 is localized to plasma membrane endocytic sites and acts primarily in clathrin-mediated endocytosis, while 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 for
Probab=20.63 E-value=1.4e+02 Score=26.34 Aligned_cols=48 Identities=15% Similarity=0.293 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHhcccccccChh-HHHHHHHHHHHcCCCCCCCC
Q 025599 35 MKEQLATFRSQLEDFARKHKNDIRKNPT-FRSQFHEMCAKVGVDPLASN 82 (250)
Q Consensus 35 l~~qL~~F~~~L~~Fa~~h~~eI~~dp~-fR~~F~~mC~siGVDPL~s~ 82 (250)
|..=+..+.....+++++|.+-.+++=. +=..|+.|+.++.+|+-..+
T Consensus 16 md~svk~l~~~~~~~~kk~~~~~kkeyqk~G~af~~L~~af~~d~~~~~ 64 (199)
T cd07626 16 MDDSVKNLINIAQEQAKKHQGPYKKEYQKIGQAFTSLGTAFELDETPTS 64 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHccCCCccc
Confidence 4444445777888899999888877654 55569999999999976544
No 428
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=20.55 E-value=1.3e+02 Score=26.92 Aligned_cols=40 Identities=30% Similarity=0.253 Sum_probs=36.3
Q ss_pred CCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCC
Q 025599 189 QGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHR 228 (250)
Q Consensus 189 ~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~ 228 (250)
+-++|.++|++.++-|.-.|-..|.+|+.+|.+-++...+
T Consensus 17 ~~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~ 56 (214)
T COG1339 17 GVKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKR 56 (214)
T ss_pred CccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCC
Confidence 3579999999999999999999999999999999887653
No 429
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=20.41 E-value=2.8e+02 Score=23.34 Aligned_cols=77 Identities=21% Similarity=0.462 Sum_probs=51.3
Q ss_pred HHHHHHHhcccccccChhHHHHHHHHHHHcCCCCCCCCC----cccccccccccchhhhHHH-HHHHhhhhcccCCCcee
Q 025599 45 QLEDFARKHKNDIRKNPTFRSQFHEMCAKVGVDPLASNK----GFWAELLGIGDFYYELGVQ-IVEICLATRPHNGGLIN 119 (250)
Q Consensus 45 ~L~~Fa~~h~~eI~~dp~fR~~F~~mC~siGVDPL~s~k----~~ws~~lG~gdfy~eLavq-IvevC~~tr~~nGGli~ 119 (250)
.+.+++..|++....|. ||+-++| .||- .||.+.-.+ +.|||++..-.+ +=+
T Consensus 53 kv~ew~ehh~~s~sede---------------~d~~~rks~p~D~wd------r~Fm~vDqemL~eI~laaNYL~--ikp 109 (158)
T COG5201 53 KVQEWMEHHTSSLSEDE---------------NDLEIRKSKPSDFWD------RFFMEVDQEMLLEICLAANYLE--IKP 109 (158)
T ss_pred HHHHHHHhccccCCCcc---------------ChHhhhccCCccHHH------HHHHHhhHHHHHHHHHhhcccc--chH
Confidence 35677888887666654 4554443 3553 577777655 579999976665 566
Q ss_pred HHHHHHHHHh--hcCCCCCCCCHHHHHHHHhh
Q 025599 120 LQELCNLLRQ--RRKSNREAVSEDDCLRAISK 149 (250)
Q Consensus 120 l~el~~~v~k--~R~~~~~~IS~~DI~rAik~ 149 (250)
|-|+.|.+-. -||+ ||+||.+-++.
T Consensus 110 LLd~gCKivaemirgk-----Speeir~tfni 136 (158)
T COG5201 110 LLDLGCKIVAEMIRGK-----SPEEIRETFNI 136 (158)
T ss_pred HHHHHHHHHHHHHccC-----CHHHHHHHhCC
Confidence 7788777643 6664 88888877654
No 430
>PRK14334 (dimethylallyl)adenosine tRNA methylthiotransferase; Provisional
Probab=20.41 E-value=2.9e+02 Score=26.78 Aligned_cols=48 Identities=15% Similarity=0.250 Sum_probs=37.4
Q ss_pred CCHHHHHHHHhhccccCCCeEEEEECCEEEEEecCCccchhHHHHHHHHHhC
Q 025599 138 VSEDDCLRAISKLKVLGNGYEVISVGKKKLVRSVPTELNKDHNQILELAQAQ 189 (250)
Q Consensus 138 IS~~DI~rAik~L~~LG~g~~vi~ig~~~~v~svp~El~~D~~~vLela~~~ 189 (250)
.+.++++++++.++..|.++.+ +..+|--.|+|=-.|....++++...
T Consensus 269 ~~~~~~~~~v~~lr~~~~~i~i----~~d~IvG~PgEt~ed~~~tl~~i~~l 316 (440)
T PRK14334 269 YRREKYLERIAEIREALPDVVL----STDIIVGFPGETEEDFQETLSLYDEV 316 (440)
T ss_pred CCHHHHHHHHHHHHHhCCCcEE----EEeEEEECCCCCHHHHHHHHHHHHhc
Confidence 6899999999999988766422 22366677999888898999988753
No 431
>PF01088 Peptidase_C12: Ubiquitin carboxyl-terminal hydrolase, family 1; InterPro: IPR001578 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C12 (ubiquitin C-terminal hydrolase family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. The type example is the human ubiquitin C-terminal hydrolase UCH-L1. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa and 100-200 kDa, IPR001394 from INTERPRO) []: this family are the 20-30 kDa ppeptides which includes the yeast yuh1. Yeast yuh1 protease is known to be active only against small ubiquitin conjugates, being inactive against conjugated beta-galactosidase []. A mammalian homologue, UCH (ubiquitin conjugate hydrolase), is one of the most abundant proteins in the brain []. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process, 0005622 intracellular; PDB: 1CMX_A 4DM9_A 2ETL_A 3IRT_A 3KW5_A 3IFW_A 2LEN_A 3KVF_A 2WDT_C 2WE6_B ....
Probab=20.41 E-value=67 Score=28.35 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=22.5
Q ss_pred ccccChhHHHHHHHHHHHcCCCCCCCCCccccccccccc
Q 025599 56 DIRKNPTFRSQFHEMCAKVGVDPLASNKGFWAELLGIGD 94 (250)
Q Consensus 56 eI~~dp~fR~~F~~mC~siGVDPL~s~k~~ws~~lG~gd 94 (250)
.|-+||++ |+.++..||| |-.. +.+++++.+
T Consensus 4 pLESnP~v---fn~l~~~lGv-~~~~----f~Dv~sld~ 34 (214)
T PF01088_consen 4 PLESNPEV---FNELLRKLGV-SGVQ----FEDVYSLDD 34 (214)
T ss_dssp -EESSHHH---HHHHHHHTTB-TSEE----EEEESTSSH
T ss_pred cccCCHHH---HHHHHHHcCC-ceeE----EEEcccccc
Confidence 36789999 9999999999 4321 236666765
No 432
>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=20.37 E-value=3e+02 Score=23.47 Aligned_cols=80 Identities=15% Similarity=0.245 Sum_probs=50.9
Q ss_pred HHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCce----eHHHHHHHHHhhcCCC-----C
Q 025599 65 SQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLI----NLQELCNLLRQRRKSN-----R 135 (250)
Q Consensus 65 ~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli----~l~el~~~v~k~R~~~-----~ 135 (250)
.+|++.+..+|.-|.... |+.=.+|++-.+|++.+.+-..=-|+ ..+.|..++... |.. .
T Consensus 69 ~~l~~~l~~~Gf~pv~~k----------G~~Dv~laIDame~~~~~~iD~~vLvSgD~DF~~Lv~~lre~-G~~V~v~g~ 137 (160)
T TIGR00288 69 DKLIEAVVNQGFEPIIVA----------GDVDVRMAVEAMELIYNPNIDAVALVTRDADFLPVINKAKEN-GKETIVIGA 137 (160)
T ss_pred HHHHHHHHHCCceEEEec----------CcccHHHHHHHHHHhccCCCCEEEEEeccHhHHHHHHHHHHC-CCEEEEEeC
Confidence 368899999999998532 46678899999999865332211222 344455555443 331 2
Q ss_pred CCCCHHHHHHHHhhccccCC
Q 025599 136 EAVSEDDCLRAISKLKVLGN 155 (250)
Q Consensus 136 ~~IS~~DI~rAik~L~~LG~ 155 (250)
+.-|++++.+||...-.|+.
T Consensus 138 ~~~ts~~L~~acd~FI~L~~ 157 (160)
T TIGR00288 138 EPGFSTALQNSADIAIILGE 157 (160)
T ss_pred CCCChHHHHHhcCeEEeCCC
Confidence 55778888888887655543
No 433
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=20.33 E-value=2.4e+02 Score=23.26 Aligned_cols=41 Identities=10% Similarity=0.059 Sum_probs=31.1
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDIL 215 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l 215 (250)
.|+..+..++.+.-.. ..|.+++++.+|.+..-++..|...
T Consensus 131 ~L~~~~r~v~~l~~~~-g~s~~eIA~~lgis~~tV~~~l~ra 171 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-GLSVAEAATRSGMSESAVKVSVHRG 171 (184)
T ss_pred hCCHHHHHHHHHHHHc-CCcHHHHHHHHCcCHHHHHHHHHHH
Confidence 4567777788776654 4599999999999988777776643
No 434
>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=20.29 E-value=2.6e+02 Score=22.87 Aligned_cols=39 Identities=18% Similarity=0.374 Sum_probs=28.2
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALD 213 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~ 213 (250)
.|+.++..++.+.-..|+ |.+++++.+|.+...++..|.
T Consensus 100 ~L~~~~r~v~~l~~~~g~-s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL-SQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-CHHHHHHHHCCCHHHHHHHHH
Confidence 456667778877665554 999999999998766555443
No 435
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=20.25 E-value=1.9e+02 Score=27.18 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=36.4
Q ss_pred HHHHHHhCCC--ccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCC
Q 025599 182 ILELAQAQGF--VTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGH 227 (250)
Q Consensus 182 vLela~~~g~--vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~ 227 (250)
++...+..|- +...++.+.-|.++.++-++|.+|++.|.+=+-.-.
T Consensus 9 lir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~Rrkvs 56 (321)
T COG3888 9 LIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVS 56 (321)
T ss_pred HHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeec
Confidence 4444444344 899999999999999999999999999998766433
No 436
>PRK10550 tRNA-dihydrouridine synthase C; Provisional
Probab=20.23 E-value=1.8e+02 Score=27.03 Aligned_cols=84 Identities=11% Similarity=0.049 Sum_probs=48.1
Q ss_pred HHHHHHHHHcCCCCCCCCCcccccccccccchhhhHHHHHHHhhhhcccCCCceeHHHHHHHHHhhcCC----CCCCCCH
Q 025599 65 SQFHEMCAKVGVDPLASNKGFWAELLGIGDFYYELGVQIVEICLATRPHNGGLINLQELCNLLRQRRKS----NREAVSE 140 (250)
Q Consensus 65 ~~F~~mC~siGVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~tr~~nGGli~l~el~~~v~k~R~~----~~~~IS~ 140 (250)
.+|-+++..-|+|-++-......+.+......++...+|.+.+--+---|||+.+..+....+....-. +...+..
T Consensus 151 ~~~a~~l~~~Gvd~i~Vh~Rt~~~~y~g~~~~~~~i~~ik~~~~iPVi~nGdI~t~~da~~~l~~~g~DgVmiGRg~l~n 230 (312)
T PRK10550 151 FEIADAVQQAGATELVVHGRTKEDGYRAEHINWQAIGEIRQRLTIPVIANGEIWDWQSAQQCMAITGCDAVMIGRGALNI 230 (312)
T ss_pred HHHHHHHHhcCCCEEEECCCCCccCCCCCcccHHHHHHHHhhcCCcEEEeCCcCCHHHHHHHHhccCCCEEEEcHHhHhC
Confidence 368888888888877533222222221112234666666666655666788888888888777543110 0124455
Q ss_pred HHHHHHHh
Q 025599 141 DDCLRAIS 148 (250)
Q Consensus 141 ~DI~rAik 148 (250)
-++.+-++
T Consensus 231 P~lf~~~~ 238 (312)
T PRK10550 231 PNLSRVVK 238 (312)
T ss_pred cHHHHHhh
Confidence 56666554
No 437
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.17 E-value=2.6e+02 Score=22.23 Aligned_cols=38 Identities=11% Similarity=0.023 Sum_probs=27.7
Q ss_pred ccchhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHH
Q 025599 174 ELNKDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDAL 212 (250)
Q Consensus 174 El~~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L 212 (250)
.|+.++..++.+.-..|+ |.+++++.+|++..-++..|
T Consensus 106 ~Lp~~~r~v~~l~~~~g~-s~~EIA~~lgis~~tV~~~l 143 (160)
T PRK09642 106 ELPENYRDVVLAHYLEEK-SYQEIALQEKIEVKTVEMKL 143 (160)
T ss_pred hCCHHHHHHHHHHHHhCC-CHHHHHHHHCCCHHHHHHHH
Confidence 456677778877665554 99999999999885554443
No 438
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.15 E-value=1.4e+02 Score=28.68 Aligned_cols=59 Identities=17% Similarity=0.221 Sum_probs=34.9
Q ss_pred hhHHHHHHHHHhCCCccHHHHHHhcCCChHHHHHHHHHHHHcCCceeecCCCCCCcceeecCcc
Q 025599 177 KDHNQILELAQAQGFVTVDEVERRLSWTSGRAIDALDILLEEGLAMVDDGHRDRKRRYWFPCAS 240 (250)
Q Consensus 177 ~D~~~vLela~~~g~vt~~~L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD~q~~~~e~~Yw~P~l~ 240 (250)
.|...+|.+.-..|+.+...--..-+++.. .+..|.+|..-|+++..... ..+|||.-+
T Consensus 211 ~~~~~~l~flf~L~~~~~g~~Y~~~~ls~~-q~~~L~~l~~~GLvy~~~~~----~~~fypT~L 269 (366)
T PF03849_consen 211 MDLVEVLSFLFQLSFLELGKAYSTEGLSET-QKNMLQDLRELGLVYQRKRK----SRRFYPTRL 269 (366)
T ss_pred CCHHHHHHHHHHhcccccCCcCcCCCCCHH-HHHHHHHHHHCCeEEEecCC----CCeEechHH
Confidence 344444444333333333322222245554 48899999999999999764 456668744
No 439
>PF13267 DUF4058: Protein of unknown function (DUF4058)
Probab=20.12 E-value=69 Score=29.45 Aligned_cols=29 Identities=28% Similarity=0.497 Sum_probs=25.4
Q ss_pred CCCCCCCCCcccccccccccchhhhHHHHHHHhhh
Q 025599 75 GVDPLASNKGFWAELLGIGDFYYELGVQIVEICLA 109 (250)
Q Consensus 75 GVDPL~s~k~~ws~~lG~gdfy~eLavqIvevC~~ 109 (250)
|.||.--...||+ ||+..|.+.|.+....
T Consensus 7 GMdPYLE~P~lWp------dVH~rLI~aiad~L~P 35 (254)
T PF13267_consen 7 GMDPYLEHPDLWP------DVHNRLIVAIADSLQP 35 (254)
T ss_pred CCCccccCcchHH------HHHHHHHHHHHHHhhh
Confidence 8999988889998 9999999988887765
No 440
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=20.01 E-value=4.4e+02 Score=26.95 Aligned_cols=86 Identities=23% Similarity=0.169 Sum_probs=52.3
Q ss_pred CCCHHHHHH---HHhhccccCCCeEEEEEC-CEEEEEecCCccch--hHHHHHHHHHh---CCCccHHH-----------
Q 025599 137 AVSEDDCLR---AISKLKVLGNGYEVISVG-KKKLVRSVPTELNK--DHNQILELAQA---QGFVTVDE----------- 196 (250)
Q Consensus 137 ~IS~~DI~r---Aik~L~~LG~g~~vi~ig-~~~~v~svp~El~~--D~~~vLela~~---~g~vt~~~----------- 196 (250)
.+|+.+... -.+.|+.|| |.+-.+| +..+|+++|.-+.. ....+.++++. .+..+...
T Consensus 488 ~Ls~~e~~~l~~~~~~L~~lG--f~~e~fg~~si~I~~vP~~l~~~~~~~~l~ell~~l~~~~~~~~~~~~~~las~ACr 565 (617)
T PRK00095 488 ELSEDEADRLEEHKELLARLG--LELEPFGPNSFAVREVPALLGQQELEELIRDLLDELAEEGDSDTLKERELLATMACH 565 (617)
T ss_pred eeCHHHHHHHHHHHHHHHhCC--cEEEEcCCCEEEEEecChhhcccCHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHH
Confidence 566666543 344556655 7777787 77899999973322 13335555542 22222222
Q ss_pred --HHHhcCCChHHHHHHHHHHHHcCCceee
Q 025599 197 --VERRLSWTSGRAIDALDILLEEGLAMVD 224 (250)
Q Consensus 197 --L~~~l~W~~~Ra~~~L~~l~~~Gl~WvD 224 (250)
++.+-.|+...++..|++|.+...-|-.
T Consensus 566 ~AIk~g~~Ls~~E~~~Ll~~L~~~~~P~~C 595 (617)
T PRK00095 566 GAIRAGRRLTLEEMNALLRQLEATENPGTC 595 (617)
T ss_pred HhhhccCCCCHHHHHHHHHHHHhcccccCC
Confidence 2233458999999999999887766544
Done!