Query psy11008
Match_columns 96
No_of_seqs 96 out of 98
Neff 2.6
Searched_HMMs 46136
Date Fri Aug 16 15:49:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11008.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11008hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09756 DDRGK: DDRGK domain; 100.0 4.5E-38 9.7E-43 236.1 3.7 73 1-88 116-188 (188)
2 KOG3054|consensus 100.0 1.3E-36 2.9E-41 242.9 7.9 80 1-95 217-296 (299)
3 smart00418 HTH_ARSR helix_turn 97.4 0.00098 2.1E-08 37.4 5.8 50 2-51 14-63 (66)
4 PF09743 DUF2042: Uncharacteri 96.9 0.0063 1.4E-07 48.0 8.1 61 9-84 20-81 (272)
5 PRK14165 winged helix-turn-hel 96.8 0.0054 1.2E-07 47.2 6.5 54 2-55 25-78 (217)
6 smart00753 PAM PCI/PINT associ 96.7 0.004 8.7E-08 39.1 4.7 45 1-45 27-71 (88)
7 smart00088 PINT motif in prote 96.7 0.004 8.7E-08 39.1 4.7 45 1-45 27-71 (88)
8 PF01399 PCI: PCI domain; Int 96.2 0.014 3E-07 36.3 4.9 42 1-42 63-104 (105)
9 PRK11169 leucine-responsive tr 96.0 0.019 4.2E-07 40.7 5.4 55 2-56 32-100 (164)
10 PF13463 HTH_27: Winged helix 96.0 0.018 3.9E-07 34.2 4.4 43 2-44 22-67 (68)
11 TIGR02337 HpaR homoprotocatech 95.8 0.034 7.4E-07 36.8 5.5 54 2-55 46-102 (118)
12 cd07377 WHTH_GntR Winged helix 95.6 0.039 8.5E-07 31.8 4.5 38 2-42 29-66 (66)
13 smart00347 HTH_MARR helix_turn 95.5 0.088 1.9E-06 32.1 6.1 55 2-56 28-85 (101)
14 PLN03083 E3 UFM1-protein ligas 95.5 0.057 1.2E-06 49.1 7.3 61 8-84 22-85 (803)
15 smart00344 HTH_ASNC helix_turn 95.3 0.065 1.4E-06 34.6 5.3 55 2-56 21-87 (108)
16 COG1522 Lrp Transcriptional re 95.3 0.022 4.7E-07 38.5 3.2 55 2-56 26-93 (154)
17 smart00345 HTH_GNTR helix_turn 95.2 0.038 8.3E-07 31.3 3.6 28 2-29 24-51 (60)
18 PRK06266 transcription initiat 95.0 0.14 3.1E-06 38.0 7.2 55 2-56 40-100 (178)
19 cd00090 HTH_ARSR Arsenical Res 94.9 0.21 4.6E-06 28.2 6.2 42 2-43 24-65 (78)
20 PRK03573 transcriptional regul 94.5 0.18 3.8E-06 34.2 6.1 55 2-56 50-107 (144)
21 TIGR01889 Staph_reg_Sar staphy 94.0 0.22 4.8E-06 33.1 5.6 55 2-56 47-104 (109)
22 PRK11179 DNA-binding transcrip 93.9 0.08 1.7E-06 37.1 3.5 55 2-56 27-93 (153)
23 cd04761 HTH_MerR-SF Helix-Turn 93.9 0.15 3.3E-06 28.6 4.1 44 2-50 4-47 (49)
24 PF13545 HTH_Crp_2: Crp-like h 93.9 0.22 4.7E-06 30.2 5.0 44 2-48 32-75 (76)
25 PRK11512 DNA-binding transcrip 93.8 0.3 6.5E-06 33.4 6.1 53 2-54 58-113 (144)
26 TIGR01884 cas_HTH CRISPR locus 93.7 0.098 2.1E-06 38.1 3.8 42 2-44 161-202 (203)
27 TIGR02944 suf_reg_Xantho FeS a 93.2 0.11 2.4E-06 35.1 3.2 55 2-56 29-83 (130)
28 smart00419 HTH_CRP helix_turn_ 93.1 0.26 5.6E-06 27.2 4.0 28 2-29 12-39 (48)
29 PRK10870 transcriptional repre 93.0 0.46 1E-05 34.3 6.3 55 2-56 75-132 (176)
30 PF13551 HTH_29: Winged helix- 92.8 0.2 4.4E-06 31.6 3.8 54 2-56 16-73 (112)
31 TIGR01764 excise DNA binding d 92.8 0.61 1.3E-05 25.5 5.3 42 2-49 5-46 (49)
32 PRK09391 fixK transcriptional 92.5 0.44 9.6E-06 34.7 5.6 47 2-50 183-229 (230)
33 PF09743 DUF2042: Uncharacteri 92.4 0.65 1.4E-05 36.8 6.8 66 2-82 74-139 (272)
34 PF01978 TrmB: Sugar-specific 92.3 0.59 1.3E-05 28.4 5.2 43 2-44 26-68 (68)
35 smart00529 HTH_DTXR Helix-turn 92.1 0.67 1.4E-05 29.2 5.5 49 2-53 3-51 (96)
36 PRK03902 manganese transport t 92.0 0.84 1.8E-05 31.4 6.3 51 2-56 26-76 (142)
37 COG1339 Transcriptional regula 91.9 0.41 8.8E-06 38.1 5.2 53 2-54 23-75 (214)
38 PRK13918 CRP/FNR family transc 91.7 0.7 1.5E-05 32.0 5.7 46 2-51 153-199 (202)
39 PF13404 HTH_AsnC-type: AsnC-t 91.7 0.23 5E-06 29.3 2.8 22 2-23 21-42 (42)
40 cd00092 HTH_CRP helix_turn_hel 91.5 0.46 1E-05 27.8 4.0 35 2-38 29-63 (67)
41 TIGR00122 birA_repr_reg BirA b 91.4 0.51 1.1E-05 28.9 4.2 30 2-31 17-46 (69)
42 PRK04172 pheS phenylalanyl-tRN 91.1 0.88 1.9E-05 37.9 6.7 74 2-82 24-97 (489)
43 PF13412 HTH_24: Winged helix- 91.0 0.39 8.4E-06 27.5 3.2 27 2-28 21-47 (48)
44 PF13518 HTH_28: Helix-turn-he 90.9 0.26 5.7E-06 27.9 2.5 35 2-37 16-50 (52)
45 PF01726 LexA_DNA_bind: LexA D 90.8 0.36 7.8E-06 30.7 3.3 28 2-29 29-57 (65)
46 PF09012 FeoC: FeoC like trans 90.7 0.22 4.8E-06 31.0 2.1 33 1-33 17-49 (69)
47 smart00346 HTH_ICLR helix_turn 90.6 1.4 3E-05 27.3 5.7 53 2-56 24-76 (91)
48 TIGR03697 NtcA_cyano global ni 90.6 0.96 2.1E-05 30.8 5.4 44 2-49 147-191 (193)
49 COG1846 MarR Transcriptional r 90.5 1 2.2E-05 27.9 5.0 53 2-54 40-95 (126)
50 TIGR03338 phnR_burk phosphonat 90.4 1.1 2.5E-05 31.8 5.8 47 2-49 38-85 (212)
51 COG3140 Uncharacterized protei 90.3 0.55 1.2E-05 31.1 3.8 48 6-66 4-54 (60)
52 PRK10402 DNA-binding transcrip 90.0 1.3 2.7E-05 32.0 5.9 48 2-53 173-221 (226)
53 PF09012 FeoC: FeoC like trans 89.9 0.21 4.6E-06 31.1 1.6 22 63-84 4-25 (69)
54 cd04764 HTH_MlrA-like_sg1 Heli 89.6 2.1 4.6E-05 25.8 5.9 64 2-84 4-67 (67)
55 PRK10141 DNA-binding transcrip 89.6 1.8 4E-05 30.4 6.3 68 2-69 34-101 (117)
56 PF13730 HTH_36: Helix-turn-he 89.6 0.56 1.2E-05 27.2 3.2 27 2-28 29-55 (55)
57 PF12728 HTH_17: Helix-turn-he 89.4 1.8 3.9E-05 24.9 5.2 42 2-49 5-46 (51)
58 PRK13777 transcriptional regul 89.4 1.2 2.6E-05 33.3 5.6 54 2-55 63-119 (185)
59 PF12419 DUF3670: SNF2 Helicas 89.4 0.73 1.6E-05 32.6 4.2 50 19-82 89-138 (141)
60 PF08220 HTH_DeoR: DeoR-like h 89.0 0.5 1.1E-05 28.8 2.8 38 1-41 17-54 (57)
61 smart00422 HTH_MERR helix_turn 88.9 2.2 4.7E-05 25.3 5.5 51 2-56 4-54 (70)
62 PRK09392 ftrB transcriptional 88.8 0.9 2E-05 32.5 4.4 46 2-52 177-223 (236)
63 smart00420 HTH_DEOR helix_turn 88.5 0.82 1.8E-05 25.1 3.2 28 2-29 18-45 (53)
64 PRK10512 selenocysteinyl-tRNA- 88.3 2.4 5.2E-05 36.7 7.4 67 2-83 510-576 (614)
65 PF08279 HTH_11: HTH domain; 88.3 1.2 2.5E-05 25.9 3.9 34 2-37 19-52 (55)
66 PRK11414 colanic acid/biofilm 88.2 1.5 3.3E-05 31.6 5.3 48 2-50 38-86 (221)
67 PRK00215 LexA repressor; Valid 87.3 0.86 1.9E-05 32.8 3.5 42 2-44 27-69 (205)
68 TIGR00498 lexA SOS regulatory 87.2 1.1 2.3E-05 32.1 4.0 41 2-43 29-70 (199)
69 PF13411 MerR_1: MerR HTH fami 86.6 4.3 9.3E-05 24.1 5.8 50 2-56 4-53 (69)
70 PF12840 HTH_20: Helix-turn-he 86.6 1.8 3.9E-05 26.0 4.2 32 2-33 28-59 (61)
71 TIGR02698 CopY_TcrY copper tra 86.6 2 4.2E-05 30.1 4.9 77 4-82 28-110 (130)
72 PF00392 GntR: Bacterial regul 86.3 1.5 3.3E-05 26.4 3.8 36 2-38 28-63 (64)
73 TIGR02702 SufR_cyano iron-sulf 86.2 1.5 3.3E-05 31.9 4.4 43 2-44 19-66 (203)
74 PF12802 MarR_2: MarR family; 86.0 2.2 4.8E-05 24.7 4.3 33 2-34 25-57 (62)
75 TIGR02787 codY_Gpos GTP-sensin 85.6 1.3 2.8E-05 35.8 4.1 41 2-42 202-243 (251)
76 cd04762 HTH_MerR-trunc Helix-T 85.4 2.9 6.2E-05 22.4 4.3 44 1-49 3-46 (49)
77 TIGR02812 fadR_gamma fatty aci 85.3 1.8 3.9E-05 31.4 4.3 37 2-39 34-70 (235)
78 PRK09954 putative kinase; Prov 84.8 2.4 5.2E-05 32.7 5.1 38 2-39 21-60 (362)
79 TIGR02051 MerR Hg(II)-responsi 84.7 4.1 8.9E-05 28.0 5.7 48 2-54 3-50 (124)
80 PF01402 RHH_1: Ribbon-helix-h 84.3 2.2 4.9E-05 23.4 3.6 28 39-82 4-31 (39)
81 PRK11161 fumarate/nitrate redu 84.0 3.7 8.1E-05 29.2 5.4 45 2-50 188-233 (235)
82 PRK11050 manganese transport r 83.9 5.2 0.00011 28.3 6.1 51 2-56 55-105 (152)
83 PF00325 Crp: Bacterial regula 83.8 2 4.3E-05 24.7 3.2 27 2-28 6-32 (32)
84 TIGR00373 conserved hypothetic 83.7 4.3 9.4E-05 29.4 5.7 52 2-56 32-89 (158)
85 PF14493 HTH_40: Helix-turn-he 83.6 3.6 7.7E-05 26.7 4.8 66 1-87 16-81 (91)
86 PF01325 Fe_dep_repress: Iron 83.4 1.7 3.8E-05 27.0 3.1 28 2-29 26-53 (60)
87 smart00342 HTH_ARAC helix_turn 83.3 2.4 5.1E-05 24.6 3.5 22 1-22 4-25 (84)
88 PRK04984 fatty acid metabolism 82.7 2.5 5.3E-05 30.7 4.1 38 2-42 35-72 (239)
89 PRK10421 DNA-binding transcrip 82.4 2.3 5.1E-05 31.3 4.0 38 2-40 30-67 (253)
90 PRK11534 DNA-binding transcrip 82.2 3.6 7.8E-05 29.6 4.8 47 2-49 34-81 (224)
91 COG1654 BirA Biotin operon rep 82.1 1.8 3.9E-05 29.0 3.0 26 2-27 23-48 (79)
92 COG1349 GlpR Transcriptional r 82.0 1.6 3.4E-05 33.4 3.1 31 1-31 22-52 (253)
93 PRK00135 scpB segregation and 81.8 7.7 0.00017 29.3 6.6 81 2-82 24-113 (188)
94 PF14947 HTH_45: Winged helix- 81.8 5.9 0.00013 25.2 5.2 47 2-52 23-69 (77)
95 smart00351 PAX Paired Box doma 81.7 7.4 0.00016 26.9 6.1 62 2-82 37-102 (125)
96 PF08784 RPA_C: Replication pr 81.7 1.6 3.5E-05 28.5 2.7 33 2-34 69-101 (102)
97 PF13601 HTH_34: Winged helix 81.2 12 0.00026 24.2 7.0 55 2-56 18-76 (80)
98 cd04768 HTH_BmrR-like Helix-Tu 81.0 8.5 0.00018 25.3 5.9 47 2-52 4-50 (96)
99 cd00131 PAX Paired Box domain 80.9 8.1 0.00018 27.0 6.1 64 3-82 38-102 (128)
100 KOG2235|consensus 80.7 3.4 7.3E-05 38.0 5.1 61 9-84 23-84 (776)
101 PRK11523 DNA-binding transcrip 80.7 3 6.5E-05 30.8 4.0 36 3-39 37-72 (253)
102 PRK09464 pdhR transcriptional 80.3 3.3 7.1E-05 30.4 4.1 39 2-43 38-76 (254)
103 PRK09990 DNA-binding transcrip 80.2 3.5 7.6E-05 30.2 4.2 38 2-40 35-72 (251)
104 PRK10079 phosphonate metabolis 79.9 3.1 6.8E-05 30.5 3.9 37 2-39 39-75 (241)
105 PRK11886 bifunctional biotin-- 79.9 4.2 9.1E-05 31.5 4.8 27 2-28 22-48 (319)
106 smart00550 Zalpha Z-DNA-bindin 79.8 3.7 8E-05 25.7 3.7 29 2-30 26-54 (68)
107 PRK10434 srlR DNA-bindng trans 79.8 1.9 4.1E-05 32.8 2.8 28 2-29 23-50 (256)
108 PRK10225 DNA-binding transcrip 79.5 3.5 7.6E-05 30.4 4.1 37 2-39 37-73 (257)
109 cd01104 HTH_MlrA-CarA Helix-Tu 79.3 10 0.00023 22.4 5.4 51 2-56 4-54 (68)
110 cd04789 HTH_Cfa Helix-Turn-Hel 79.3 8.2 0.00018 25.7 5.5 49 2-56 5-53 (102)
111 cd04773 HTH_TioE_rpt2 Second H 79.2 9.8 0.00021 25.6 5.9 47 2-52 4-50 (108)
112 PRK15002 redox-sensitivie tran 79.2 9.5 0.00021 27.8 6.2 47 2-54 15-61 (154)
113 PRK05114 hypothetical protein; 79.1 1.4 3E-05 29.1 1.7 32 12-56 13-44 (59)
114 TIGR01958 nuoE_fam NADH-quinon 78.8 3 6.6E-05 29.6 3.4 60 2-74 3-69 (148)
115 PRK07571 bidirectional hydroge 78.1 3.3 7.2E-05 30.9 3.6 61 3-76 26-91 (169)
116 TIGR03337 phnR transcriptional 78.0 3.4 7.4E-05 29.6 3.5 37 2-39 29-65 (231)
117 PF04703 FaeA: FaeA-like prote 78.0 5.5 0.00012 25.5 4.2 37 2-38 19-55 (62)
118 PRK14584 hmsS hemin storage sy 77.4 4.5 9.9E-05 30.5 4.2 38 2-43 102-139 (153)
119 PF03701 UPF0181: Uncharacteri 77.2 1.7 3.8E-05 27.9 1.6 32 12-56 13-44 (51)
120 cd01106 HTH_TipAL-Mta Helix-Tu 77.1 14 0.00029 24.3 6.0 46 2-51 4-49 (103)
121 PF01047 MarR: MarR family; I 77.0 4.2 9E-05 23.6 3.1 32 2-33 21-52 (59)
122 PF12514 DUF3718: Protein of u 76.7 2 4.4E-05 27.8 1.9 32 48-83 37-68 (68)
123 PF13442 Cytochrome_CBB3: Cyto 76.6 2.2 4.8E-05 25.5 1.9 33 17-53 35-67 (67)
124 cd01105 HTH_GlnR-like Helix-Tu 76.4 11 0.00024 24.5 5.3 66 2-85 5-70 (88)
125 smart00531 TFIIE Transcription 76.3 18 0.00039 25.6 6.8 61 2-62 19-88 (147)
126 TIGR02844 spore_III_D sporulat 75.8 1.6 3.4E-05 29.3 1.2 29 51-84 2-30 (80)
127 PF00034 Cytochrom_C: Cytochro 75.8 2.5 5.3E-05 24.6 2.0 17 40-56 74-90 (91)
128 COG1802 GntR Transcriptional r 75.7 4 8.7E-05 29.7 3.4 49 2-51 43-92 (230)
129 PF04760 IF2_N: Translation in 75.5 4 8.6E-05 24.2 2.8 44 1-53 6-51 (54)
130 PF01022 HTH_5: Bacterial regu 75.1 5.3 0.00012 23.0 3.2 28 2-29 19-46 (47)
131 cd04770 HTH_HMRTR Helix-Turn-H 74.9 12 0.00026 25.1 5.4 46 2-51 4-49 (123)
132 TIGR02404 trehalos_R_Bsub treh 74.9 3.9 8.4E-05 29.7 3.2 37 2-39 28-64 (233)
133 PRK05988 formate dehydrogenase 74.5 4.3 9.2E-05 29.6 3.3 62 2-76 12-78 (156)
134 cd04782 HTH_BltR Helix-Turn-He 74.3 14 0.00031 24.3 5.5 46 2-51 4-49 (97)
135 PF06969 HemN_C: HemN C-termin 74.1 3.7 8E-05 24.6 2.5 39 2-44 24-63 (66)
136 cd04783 HTH_MerR1 Helix-Turn-H 73.9 16 0.00034 24.9 5.8 45 2-50 4-48 (126)
137 PF03551 PadR: Transcriptional 73.9 10 0.00022 23.4 4.5 43 8-50 27-74 (75)
138 PRK14585 pgaD putative PGA bio 73.9 4 8.6E-05 30.5 3.1 41 2-46 93-133 (137)
139 COG2188 PhnF Transcriptional r 73.7 7.8 0.00017 28.9 4.6 54 3-59 36-96 (236)
140 PF07789 DUF1627: Protein of u 73.6 6.1 0.00013 30.2 4.0 42 2-44 10-51 (155)
141 PRK11753 DNA-binding transcrip 73.5 7.3 0.00016 27.0 4.2 37 2-42 172-208 (211)
142 PRK03837 transcriptional regul 73.5 7.3 0.00016 28.1 4.3 30 2-31 41-70 (241)
143 cd00592 HTH_MerR-like Helix-Tu 73.3 16 0.00035 23.4 5.5 50 2-56 4-53 (100)
144 cd04775 HTH_Cfa-like Helix-Tur 73.1 20 0.00043 23.8 6.0 48 2-54 5-52 (102)
145 PF07160 DUF1395: Protein of u 72.9 1.1 2.5E-05 34.8 0.0 16 39-54 130-145 (243)
146 PF09862 DUF2089: Protein of u 72.8 3.5 7.7E-05 29.5 2.5 22 36-57 29-50 (113)
147 TIGR02277 PaaX_trns_reg phenyl 72.6 14 0.0003 29.0 6.0 49 3-51 25-73 (280)
148 PF13994 PgaD: PgaD-like prote 72.5 5.1 0.00011 28.3 3.2 34 2-39 104-137 (138)
149 COG1497 Predicted transcriptio 72.3 14 0.0003 30.3 6.0 49 2-54 29-78 (260)
150 PRK09764 DNA-binding transcrip 71.8 5.1 0.00011 29.5 3.2 37 2-39 33-69 (240)
151 COG1725 Predicted transcriptio 71.7 18 0.00039 26.2 5.9 40 2-44 39-78 (125)
152 TIGR02018 his_ut_repres histid 71.6 5.2 0.00011 29.1 3.2 37 2-39 29-65 (230)
153 cd04777 HTH_MerR-like_sg1 Heli 71.5 18 0.00038 23.9 5.5 47 2-55 4-50 (107)
154 TIGR02325 C_P_lyase_phnF phosp 71.5 9.8 0.00021 27.4 4.6 38 2-42 36-73 (238)
155 PLN03083 E3 UFM1-protein ligas 71.4 13 0.00027 34.5 6.2 67 2-83 78-144 (803)
156 KOG0686|consensus 71.4 6 0.00013 34.7 4.0 43 2-44 369-411 (466)
157 PF09339 HTH_IclR: IclR helix- 70.9 5.6 0.00012 23.3 2.7 28 2-29 22-49 (52)
158 KOG1497|consensus 70.8 7.2 0.00016 33.6 4.2 70 2-72 321-391 (399)
159 COG3355 Predicted transcriptio 70.8 20 0.00043 26.2 6.0 47 1-47 45-97 (126)
160 TIGR03433 padR_acidobact trans 70.7 21 0.00045 23.5 5.7 49 8-56 35-88 (100)
161 PF02002 TFIIE_alpha: TFIIE al 70.6 10 0.00022 25.0 4.1 50 2-51 31-86 (105)
162 PRK14999 histidine utilization 70.5 5.5 0.00012 29.2 3.1 53 2-57 40-99 (241)
163 PRK13509 transcriptional repre 70.4 5.6 0.00012 30.2 3.2 29 2-30 23-51 (251)
164 PF03297 Ribosomal_S25: S25 ri 70.4 13 0.00028 26.2 4.8 39 3-41 64-102 (105)
165 PRK13697 cytochrome c6; Provis 70.4 3.7 8E-05 26.7 2.0 16 41-56 90-105 (111)
166 CHL00088 apcB allophycocyanin 70.2 2 4.3E-05 31.8 0.7 22 33-56 13-34 (161)
167 PLN02853 Probable phenylalanyl 69.8 14 0.0003 32.3 5.8 73 2-81 22-94 (492)
168 TIGR00738 rrf2_super rrf2 fami 69.4 10 0.00022 25.1 4.0 53 2-54 29-81 (132)
169 cd04788 HTH_NolA-AlbR Helix-Tu 69.4 28 0.0006 22.8 6.0 46 2-51 4-49 (96)
170 TIGR00475 selB selenocysteine- 68.7 14 0.0003 31.7 5.6 58 2-82 492-549 (581)
171 KOG2587|consensus 68.5 23 0.00051 31.7 7.0 67 4-81 40-127 (551)
172 PRK11402 DNA-binding transcrip 68.4 12 0.00025 27.5 4.4 39 2-43 37-75 (241)
173 PF10007 DUF2250: Uncharacteri 68.4 7 0.00015 26.9 3.1 36 4-42 27-62 (92)
174 TIGR03453 partition_RepA plasm 67.9 17 0.00038 28.8 5.7 88 2-93 37-145 (387)
175 PF02186 TFIIE_beta: TFIIE bet 67.7 6.2 0.00013 25.4 2.6 31 45-91 6-36 (65)
176 PF03965 Penicillinase_R: Peni 67.1 34 0.00074 22.7 7.7 78 3-82 26-109 (115)
177 cd01107 HTH_BmrR Helix-Turn-He 66.9 22 0.00048 23.7 5.2 47 2-52 4-51 (108)
178 PRK12423 LexA repressor; Provi 66.5 7.8 0.00017 28.5 3.2 28 2-29 29-57 (202)
179 PF08220 HTH_DeoR: DeoR-like h 66.2 9 0.0002 23.2 3.0 21 64-84 5-25 (57)
180 PRK15481 transcriptional regul 66.1 11 0.00024 29.7 4.2 38 2-40 33-70 (431)
181 PF04967 HTH_10: HTH DNA bindi 65.7 7.2 0.00016 24.4 2.5 24 1-24 26-49 (53)
182 PF14502 HTH_41: Helix-turn-he 65.7 7.5 0.00016 24.5 2.6 28 2-29 10-37 (48)
183 PRK10906 DNA-binding transcrip 65.4 6.9 0.00015 29.9 2.8 29 2-30 23-51 (252)
184 TIGR00683 nanA N-acetylneurami 65.2 20 0.00044 27.7 5.4 49 8-56 16-66 (290)
185 cd04772 HTH_TioE_rpt1 First He 64.9 20 0.00044 23.8 4.7 50 2-56 4-53 (99)
186 PRK05638 threonine synthase; V 64.8 17 0.00036 29.7 5.1 51 2-52 388-441 (442)
187 PF02082 Rrf2: Transcriptional 64.6 15 0.00032 23.3 3.8 37 2-38 29-65 (83)
188 cd07970 OBF_DNA_ligase_LigC Th 64.6 14 0.0003 25.7 4.0 32 27-58 20-57 (122)
189 TIGR01610 phage_O_Nterm phage 64.2 10 0.00022 25.0 3.2 28 2-29 51-78 (95)
190 cd04790 HTH_Cfa-like_unk Helix 64.0 19 0.00042 26.2 4.9 49 2-55 5-53 (172)
191 PRK09416 lstR lineage-specific 63.7 24 0.00052 26.0 5.3 49 8-56 73-122 (135)
192 cd04765 HTH_MlrA-like_sg2 Heli 63.5 34 0.00073 22.9 5.6 47 2-53 4-51 (99)
193 cd04763 HTH_MlrA-like Helix-Tu 63.3 30 0.00066 20.8 5.1 45 2-51 4-49 (68)
194 PF01257 2Fe-2S_thioredx: Thio 63.3 6.4 0.00014 27.8 2.2 55 2-69 2-56 (145)
195 PF13499 EF-hand_7: EF-hand do 63.0 10 0.00022 22.0 2.7 43 40-82 16-65 (66)
196 PRK09334 30S ribosomal protein 62.2 19 0.00042 24.7 4.3 39 3-41 46-84 (86)
197 PF08221 HTH_9: RNA polymerase 62.1 7.3 0.00016 24.3 2.1 21 64-84 18-38 (62)
198 PRK10263 DNA translocase FtsK; 62.0 7.9 0.00017 37.6 3.2 43 39-81 1246-1315(1355)
199 PF04182 B-block_TFIIIC: B-blo 61.7 14 0.00031 23.4 3.4 31 2-32 22-52 (75)
200 PRK03341 arginine repressor; P 61.5 9.5 0.00021 28.5 2.9 39 2-45 33-78 (168)
201 PHA02943 hypothetical protein; 60.8 46 0.001 25.7 6.6 53 2-56 28-83 (165)
202 PRK09802 DNA-binding transcrip 60.5 9.3 0.0002 29.5 2.8 28 2-29 35-62 (269)
203 PF07848 PaaX: PaaX-like prote 60.5 22 0.00047 23.0 4.1 42 3-44 28-69 (70)
204 cd04619 CBS_pair_6 The CBS dom 60.3 35 0.00075 21.1 4.9 37 9-48 9-47 (114)
205 TIGR01337 apcB allophycocyanin 59.8 4.1 8.9E-05 30.3 0.7 22 33-56 12-33 (167)
206 PF08448 PAS_4: PAS fold; Int 59.0 17 0.00037 21.3 3.2 26 22-47 1-26 (110)
207 cd04774 HTH_YfmP Helix-Turn-He 59.0 50 0.0011 21.9 6.2 46 2-52 4-49 (96)
208 PF05158 RNA_pol_Rpc34: RNA po 58.8 18 0.00039 29.3 4.3 85 3-87 105-249 (327)
209 COG2186 FadR Transcriptional r 58.8 12 0.00026 28.3 3.1 39 2-43 38-76 (241)
210 PF04679 DNA_ligase_A_C: ATP d 58.2 19 0.00041 23.4 3.6 29 28-56 9-45 (97)
211 PHA03033 hypothetical protein; 58.2 7.7 0.00017 29.4 1.9 53 4-56 26-90 (142)
212 PRK00441 argR arginine repress 58.0 40 0.00086 24.5 5.6 39 2-45 22-66 (149)
213 COG3343 RpoE DNA-directed RNA 57.8 9 0.00019 29.7 2.3 40 2-47 38-77 (175)
214 PRK11014 transcriptional repre 57.8 30 0.00065 23.8 4.7 54 2-56 29-83 (141)
215 PRK07539 NADH dehydrogenase su 57.5 15 0.00032 26.3 3.2 61 2-75 11-76 (154)
216 PF11761 CbiG_mid: Cobalamin b 57.4 18 0.00039 22.4 3.3 34 1-34 4-39 (93)
217 PF01638 HxlR: HxlR-like helix 56.7 30 0.00065 22.2 4.3 33 2-34 22-55 (90)
218 PF13384 HTH_23: Homeodomain-l 56.6 9.5 0.0002 21.5 1.8 29 2-31 21-49 (50)
219 PRK15431 ferrous iron transpor 56.5 22 0.00048 24.2 3.8 31 2-32 20-50 (78)
220 cd07972 OBF_DNA_ligase_Arch_Li 56.3 22 0.00048 24.3 3.8 30 29-58 26-63 (122)
221 cd01111 HTH_MerD Helix-Turn-He 56.1 61 0.0013 21.9 5.9 46 2-51 4-49 (107)
222 CHL00089 apcF allophycocyanin 56.0 5.5 0.00012 29.9 0.9 22 33-56 13-34 (169)
223 PF12793 SgrR_N: Sugar transpo 55.8 14 0.0003 25.7 2.8 56 1-56 22-83 (115)
224 cd04780 HTH_MerR-like_sg5 Heli 55.7 58 0.0013 21.6 5.9 46 2-51 4-49 (95)
225 PRK05066 arginine repressor; P 55.5 16 0.00034 26.9 3.2 34 9-46 37-73 (156)
226 TIGR01529 argR_whole arginine 55.3 28 0.00061 25.0 4.4 33 11-46 33-65 (146)
227 CHL00173 cpeA phycoerythrin al 54.9 5.9 0.00013 29.7 0.9 23 33-57 13-35 (164)
228 COG1695 Predicted transcriptio 54.6 56 0.0012 22.0 5.6 48 9-56 41-93 (138)
229 COG0329 DapA Dihydrodipicolina 54.2 37 0.00081 26.7 5.3 46 10-56 22-69 (299)
230 TIGR02431 pcaR_pcaU beta-ketoa 54.0 18 0.0004 26.7 3.4 40 1-44 27-66 (248)
231 cd01279 HTH_HspR-like Helix-Tu 53.9 37 0.00081 22.4 4.5 84 2-90 5-92 (98)
232 PF01710 HTH_Tnp_IS630: Transp 53.8 41 0.0009 22.8 4.8 59 2-82 22-80 (119)
233 PRK13749 transcriptional regul 53.7 32 0.00068 24.4 4.4 49 2-55 7-55 (121)
234 PRK04424 fatty acid biosynthes 53.7 8.8 0.00019 28.2 1.6 27 2-28 25-51 (185)
235 PF13814 Replic_Relax: Replica 53.6 59 0.0013 22.5 5.7 49 2-50 13-71 (191)
236 TIGR01338 phycocy_alpha phycoc 53.6 5.9 0.00013 29.7 0.7 22 33-56 12-33 (161)
237 PRK10163 DNA-binding transcrip 53.6 59 0.0013 24.7 6.1 45 1-47 43-87 (271)
238 TIGR01714 phage_rep_org_N phag 53.0 33 0.00072 24.5 4.4 40 2-44 55-94 (119)
239 KOG2908|consensus 52.9 23 0.00049 30.5 4.1 55 2-56 298-360 (380)
240 PF00486 Trans_reg_C: Transcri 52.8 35 0.00077 20.1 3.9 32 36-82 1-33 (77)
241 PF15615 TerB-C: TerB-C domain 52.6 35 0.00076 24.2 4.5 45 2-47 97-141 (144)
242 PF00989 PAS: PAS fold; Inter 52.6 15 0.00033 21.6 2.3 20 25-44 10-29 (113)
243 KOG3558|consensus 52.6 11 0.00024 34.8 2.4 46 22-72 125-172 (768)
244 PRK10411 DNA-binding transcrip 52.5 30 0.00065 26.3 4.4 38 2-42 22-59 (240)
245 TIGR02719 repress_PhaQ poly-be 52.5 67 0.0014 23.4 6.0 48 9-56 54-106 (138)
246 cd04787 HTH_HMRTR_unk Helix-Tu 52.1 76 0.0016 21.9 6.1 45 2-50 4-48 (133)
247 PF05158 RNA_pol_Rpc34: RNA po 52.0 63 0.0014 26.2 6.3 55 2-57 30-97 (327)
248 PF09669 Phage_pRha: Phage reg 52.0 34 0.00073 22.4 4.0 52 3-54 6-71 (93)
249 PRK09836 DNA-binding transcrip 51.8 28 0.00061 23.6 3.7 59 10-83 103-179 (227)
250 PRK06074 NADH dehydrogenase su 51.5 49 0.0011 24.7 5.3 47 10-57 2-49 (189)
251 COG5301 Phage-related tail fib 51.5 9.3 0.0002 34.3 1.7 14 29-42 91-104 (587)
252 COG1777 Predicted transcriptio 51.4 22 0.00048 28.4 3.6 41 3-43 33-78 (217)
253 PRK13869 plasmid-partitioning 51.4 52 0.0011 26.9 5.8 88 2-94 52-163 (405)
254 PF01316 Arg_repressor: Argini 51.1 19 0.00042 23.5 2.8 30 12-45 37-67 (70)
255 smart00862 Trans_reg_C Transcr 51.1 36 0.00078 20.0 3.8 22 36-57 1-22 (78)
256 PRK10857 DNA-binding transcrip 51.0 27 0.00058 25.5 3.8 39 2-40 29-67 (164)
257 PF10882 bPH_5: Bacterial PH d 50.9 17 0.00036 23.3 2.4 20 37-56 80-99 (100)
258 COG1321 TroR Mn-dependent tran 50.8 20 0.00043 26.1 3.0 51 2-55 28-78 (154)
259 PRK13877 conjugal transfer rel 50.7 27 0.00058 24.8 3.6 28 38-69 14-41 (114)
260 CHL00183 petJ cytochrome c553; 50.5 14 0.0003 24.2 2.0 17 40-56 87-103 (108)
261 PF06163 DUF977: Bacterial pro 49.7 22 0.00047 26.3 3.1 17 66-82 19-35 (127)
262 CHL00170 cpcA phycocyanin alph 49.7 7.2 0.00016 29.4 0.6 22 33-56 13-34 (162)
263 PF04157 EAP30: EAP30/Vps36 fa 49.6 49 0.0011 24.7 5.1 64 10-84 133-201 (223)
264 COG3753 Uncharacterized protei 49.2 15 0.00033 27.8 2.3 22 1-22 93-114 (143)
265 PF13833 EF-hand_8: EF-hand do 49.0 27 0.00059 19.7 2.9 13 70-82 38-50 (54)
266 TIGR02010 IscR iron-sulfur clu 48.9 42 0.0009 23.0 4.3 41 2-42 29-69 (135)
267 PRK13239 alkylmercury lyase; P 48.8 20 0.00043 27.9 2.9 33 2-39 40-72 (206)
268 COG0640 ArsR Predicted transcr 48.7 51 0.0011 18.9 6.3 55 2-56 43-97 (110)
269 PRK13705 plasmid-partitioning 48.5 34 0.00074 27.8 4.3 89 2-94 43-149 (388)
270 cd00383 trans_reg_C Effector d 48.4 41 0.00089 20.5 3.8 37 32-83 15-52 (95)
271 CHL00172 cpeB phycoerythrin be 47.9 8.5 0.00018 29.5 0.8 22 33-56 13-34 (177)
272 cd01109 HTH_YyaN Helix-Turn-He 47.8 75 0.0016 21.1 5.3 45 2-50 4-48 (113)
273 smart00434 TOP4c DNA Topoisome 47.8 17 0.00037 30.6 2.6 28 8-35 242-269 (445)
274 PHA00738 putative HTH transcri 47.2 42 0.0009 24.1 4.2 40 2-43 30-69 (108)
275 PF13613 HTH_Tnp_4: Helix-turn 47.0 20 0.00044 21.2 2.2 22 2-23 23-44 (53)
276 smart00421 HTH_LUXR helix_turn 46.7 33 0.00072 18.4 2.9 22 2-23 22-43 (58)
277 PRK07785 NADH dehydrogenase su 46.4 66 0.0014 25.6 5.5 45 12-56 63-110 (235)
278 PF00502 Phycobilisome: Phycob 46.0 9.3 0.0002 27.5 0.7 22 33-56 8-29 (157)
279 PF05732 RepL: Firmicute plasm 45.9 41 0.00088 24.7 4.1 41 2-45 79-119 (165)
280 TIGR03879 near_KaiC_dom probab 45.6 14 0.0003 24.6 1.5 28 2-29 36-63 (73)
281 PRK13752 putative transcriptio 45.3 1E+02 0.0022 22.0 5.9 46 2-51 11-56 (144)
282 TIGR00674 dapA dihydrodipicoli 45.1 72 0.0016 24.3 5.5 48 8-56 14-63 (285)
283 PRK11569 transcriptional repre 44.7 91 0.002 23.7 5.9 43 1-45 46-88 (274)
284 PF11462 DUF3203: Protein of u 44.6 20 0.00044 24.6 2.2 20 31-50 40-59 (74)
285 PRK10681 DNA-binding transcrip 44.6 15 0.00033 27.8 1.7 28 2-29 25-52 (252)
286 cd04781 HTH_MerR-like_sg6 Heli 44.4 97 0.0021 20.9 5.7 47 2-54 4-50 (120)
287 PF03444 HrcA_DNA-bdg: Winged 44.3 33 0.00072 23.3 3.2 38 2-39 27-64 (78)
288 PF10545 MADF_DNA_bdg: Alcohol 44.2 25 0.00054 21.0 2.3 23 2-24 30-54 (85)
289 cd04784 HTH_CadR-PbrR Helix-Tu 44.0 1E+02 0.0022 20.9 5.7 46 2-51 4-49 (127)
290 PF13591 MerR_2: MerR HTH fami 43.9 76 0.0016 20.6 4.7 50 1-56 3-52 (84)
291 PF07900 DUF1670: Protein of u 43.8 27 0.00058 27.8 3.0 36 2-37 109-148 (220)
292 PF13426 PAS_9: PAS domain; PD 43.8 25 0.00054 20.3 2.2 15 31-45 6-20 (104)
293 PF13182 DUF4007: Protein of u 43.6 38 0.00083 26.7 3.8 39 5-44 234-274 (286)
294 PRK11173 two-component respons 43.4 55 0.0012 22.6 4.2 23 34-56 154-176 (237)
295 PF12833 HTH_18: Helix-turn-he 43.4 57 0.0012 19.7 3.9 19 4-22 1-19 (81)
296 TIGR03070 couple_hipB transcri 43.2 54 0.0012 18.0 3.5 14 40-53 41-54 (58)
297 PF01418 HTH_6: Helix-turn-hel 43.1 26 0.00057 22.0 2.4 32 41-84 14-45 (77)
298 cd04624 CBS_pair_11 The CBS do 42.6 64 0.0014 19.4 4.0 37 8-47 8-46 (112)
299 PRK09514 zntR zinc-responsive 42.6 1.2E+02 0.0026 21.3 6.2 46 2-51 5-50 (140)
300 COG3415 Transposase and inacti 42.6 84 0.0018 23.0 5.2 53 2-56 25-79 (138)
301 cd07153 Fur_like Ferric uptake 42.6 87 0.0019 20.2 4.9 33 9-41 32-64 (116)
302 PHA02519 plasmid partition pro 42.4 70 0.0015 26.2 5.3 89 2-94 43-149 (387)
303 PHA02105 hypothetical protein 42.2 8.6 0.00019 25.9 0.1 23 34-56 39-61 (68)
304 cd04785 HTH_CadR-PbrR-like Hel 42.2 1.1E+02 0.0024 20.9 5.5 46 2-51 4-49 (126)
305 CHL00090 apcD allophycocyanin 41.9 12 0.00025 27.8 0.7 22 33-56 12-33 (161)
306 PF13274 DUF4065: Protein of u 41.8 39 0.00084 21.2 3.0 35 36-85 66-100 (108)
307 cd06170 LuxR_C_like C-terminal 41.8 43 0.00094 18.2 2.9 23 2-24 19-41 (57)
308 CHL00171 cpcB phycocyanin beta 41.5 11 0.00024 28.4 0.5 22 33-56 13-34 (172)
309 PHA01751 hypothetical protein 41.4 13 0.00028 27.1 0.9 19 13-31 15-33 (110)
310 cd04613 CBS_pair_SpoIVFB_EriC_ 40.9 60 0.0013 19.3 3.7 21 28-48 26-47 (114)
311 PF09999 DUF2240: Uncharacteri 40.7 25 0.00053 26.1 2.2 31 1-33 91-121 (144)
312 PF09643 YopX: YopX protein; 40.6 20 0.00044 22.6 1.6 16 26-41 49-64 (121)
313 PRK13696 hypothetical protein; 40.4 51 0.0011 21.7 3.5 27 37-81 4-30 (62)
314 COG3413 Predicted DNA binding 40.1 28 0.00061 25.5 2.5 24 1-24 181-204 (215)
315 PF12674 Zn_ribbon_2: Putative 40.1 46 0.001 22.1 3.3 23 34-56 34-58 (81)
316 TIGR02047 CadR-PbrR Cd(II)/Pb( 39.7 94 0.002 21.4 4.9 46 2-51 4-49 (127)
317 PRK10434 srlR DNA-bindng trans 39.5 42 0.00092 25.5 3.4 22 63-84 9-30 (256)
318 TIGR03046 PS_II_psbV2 photosys 39.4 23 0.00051 26.5 2.0 17 40-56 127-143 (155)
319 PRK02363 DNA-directed RNA poly 39.2 21 0.00046 25.7 1.7 39 2-46 27-65 (129)
320 PRK15466 carboxysome structura 38.9 34 0.00074 26.3 2.8 28 2-29 128-155 (166)
321 PF14277 DUF4364: Domain of un 38.9 96 0.0021 22.9 5.1 53 17-69 38-91 (163)
322 TIGR02044 CueR Cu(I)-responsiv 38.6 1.3E+02 0.0027 20.5 5.7 45 2-50 4-48 (127)
323 COG1349 GlpR Transcriptional r 38.5 44 0.00095 25.6 3.4 21 64-84 10-30 (253)
324 COG1414 IclR Transcriptional r 38.1 1.4E+02 0.003 22.7 6.0 78 1-90 22-99 (246)
325 PLN03238 probable histone acet 37.8 62 0.0014 26.8 4.4 44 1-49 226-269 (290)
326 PF05164 ZapA: Cell division p 37.7 64 0.0014 20.0 3.5 30 43-79 20-49 (89)
327 PRK15090 DNA-binding transcrip 37.7 51 0.0011 24.6 3.6 54 1-56 31-84 (257)
328 PTZ00246 proteasome subunit al 37.6 1.6E+02 0.0034 22.2 6.2 48 9-56 182-244 (253)
329 PF06224 HTH_42: Winged helix 37.6 70 0.0015 24.3 4.3 45 2-46 185-230 (327)
330 cd04801 CBS_pair_M50_like This 37.5 95 0.0021 18.8 4.4 37 9-48 9-48 (114)
331 KOG1610|consensus 37.4 39 0.00084 28.3 3.2 54 18-74 97-160 (322)
332 cd07357 HN_L-whirlin_R2_like S 37.4 47 0.001 23.1 3.1 35 40-87 15-49 (81)
333 PF09824 ArsR: ArsR transcript 37.3 51 0.0011 25.3 3.6 42 32-85 89-133 (160)
334 cd04766 HTH_HspR Helix-Turn-He 37.3 99 0.0021 19.8 4.5 48 2-54 5-52 (91)
335 TIGR01044 rplV_bact ribosomal 37.3 25 0.00053 24.0 1.7 47 35-81 2-48 (103)
336 cd01108 HTH_CueR Helix-Turn-He 36.8 1.4E+02 0.003 20.4 6.0 45 2-50 4-48 (127)
337 PF12668 DUF3791: Protein of u 36.8 31 0.00067 21.2 2.0 21 1-21 8-28 (62)
338 COG3877 Uncharacterized protei 36.7 42 0.00092 24.9 2.9 22 36-57 37-58 (122)
339 PRK09834 DNA-binding transcrip 36.6 1.1E+02 0.0025 22.9 5.3 42 1-44 29-70 (263)
340 PF06165 Glyco_transf_36: Glyc 35.9 14 0.0003 25.0 0.3 13 33-45 1-13 (110)
341 PF01886 DUF61: Protein of unk 35.8 83 0.0018 22.7 4.3 39 17-56 21-59 (132)
342 PF14056 DUF4250: Domain of un 35.8 34 0.00073 21.8 2.0 21 1-21 23-43 (55)
343 PF13359 DDE_Tnp_4: DDE superf 35.7 26 0.00056 23.5 1.6 18 27-44 31-48 (158)
344 PF11888 DUF3408: Protein of u 35.6 77 0.0017 22.3 4.0 31 39-82 83-113 (136)
345 PF06353 DUF1062: Protein of u 35.5 36 0.00079 25.0 2.4 30 4-37 109-138 (142)
346 PRK09863 putative frv operon r 35.4 1.5E+02 0.0032 24.9 6.3 78 2-84 21-103 (584)
347 cd04767 HTH_HspR-like_MBC Heli 35.3 1.3E+02 0.0028 21.4 5.2 47 2-54 5-51 (120)
348 PHA02762 hypothetical protein; 35.3 26 0.00057 23.3 1.5 34 22-55 24-58 (62)
349 COG2345 Predicted transcriptio 35.2 47 0.001 26.1 3.2 30 2-31 29-58 (218)
350 PF14903 WG_beta_rep: WG conta 35.0 33 0.00071 17.8 1.6 21 30-52 2-22 (35)
351 PF00126 HTH_1: Bacterial regu 34.9 46 0.00099 19.8 2.5 41 3-44 18-58 (60)
352 PF14394 DUF4423: Domain of un 34.7 72 0.0016 23.4 3.9 37 2-40 43-81 (171)
353 PF01476 LysM: LysM domain; I 34.6 25 0.00055 19.1 1.2 15 2-16 10-24 (44)
354 PRK11517 transcriptional regul 34.5 70 0.0015 21.4 3.5 48 10-57 102-164 (223)
355 PF09681 Phage_rep_org_N: N-te 34.3 1.3E+02 0.0029 21.2 5.1 39 2-43 57-95 (121)
356 PF06970 RepA_N: Replication i 34.3 36 0.00079 22.3 2.1 21 30-50 41-62 (76)
357 cd04593 CBS_pair_EriC_assoc_ba 34.2 80 0.0017 19.2 3.5 36 10-48 10-47 (115)
358 CHL00086 apcA allophycocyanin 34.2 18 0.00038 26.9 0.6 22 33-56 12-33 (161)
359 PRK10681 DNA-binding transcrip 34.1 51 0.0011 25.0 3.1 22 63-84 11-32 (252)
360 cd04769 HTH_MerR2 Helix-Turn-H 33.9 1.5E+02 0.0032 19.9 5.7 45 2-51 4-48 (116)
361 PF10335 DUF294_C: Putative nu 33.8 34 0.00073 24.0 2.0 26 4-29 53-78 (145)
362 cd07893 OBF_DNA_ligase The Oli 33.8 71 0.0015 22.1 3.6 29 28-56 25-61 (129)
363 PF00249 Myb_DNA-binding: Myb- 33.7 65 0.0014 18.3 2.9 28 42-69 5-32 (48)
364 PHA00542 putative Cro-like pro 33.7 89 0.0019 20.1 3.8 40 2-56 35-74 (82)
365 PF02682 AHS1: Allophanate hyd 33.6 25 0.00054 26.5 1.4 20 1-20 102-121 (202)
366 PRK14126 cell division protein 33.4 67 0.0015 21.3 3.3 15 42-56 25-39 (85)
367 PRK11642 exoribonuclease R; Pr 33.3 44 0.00096 30.4 3.1 28 2-29 38-69 (813)
368 PF00763 THF_DHG_CYH: Tetrahyd 33.3 68 0.0015 21.9 3.4 23 10-32 70-92 (117)
369 TIGR02054 MerD mercuric resist 33.3 1.7E+02 0.0037 20.5 5.6 49 2-55 7-55 (120)
370 COG1273 Ku-homolog [Replicatio 33.3 24 0.00053 29.1 1.4 31 21-51 56-86 (278)
371 TIGR02681 phage_pRha phage reg 33.2 76 0.0016 22.0 3.6 44 3-46 18-74 (108)
372 TIGR02147 Fsuc_second hypothet 32.8 84 0.0018 25.0 4.3 36 2-39 141-178 (271)
373 TIGR01439 lp_hng_hel_AbrB loop 32.8 29 0.00062 18.9 1.2 17 68-84 3-20 (43)
374 COG5027 SAS2 Histone acetyltra 32.7 34 0.00073 29.6 2.1 35 1-41 334-368 (395)
375 TIGR01339 phycocy_beta phycocy 32.7 20 0.00043 27.2 0.7 22 33-56 11-32 (170)
376 COG4901 Ribosomal protein S25 32.6 89 0.0019 22.8 4.0 40 3-42 64-103 (107)
377 PF10557 Cullin_Nedd8: Cullin 32.6 55 0.0012 20.3 2.6 28 2-29 34-61 (68)
378 cd05805 MPG1_transferase GTP-m 32.5 61 0.0013 26.2 3.5 25 29-55 242-267 (441)
379 cd04779 HTH_MerR-like_sg4 Heli 32.4 1.8E+02 0.004 20.6 6.1 44 2-50 4-47 (134)
380 smart00437 TOP1Ac Bacterial DN 32.2 1.4E+02 0.0031 23.1 5.3 51 3-56 21-71 (259)
381 TIGR02899 spore_safA spore coa 32.0 32 0.0007 18.0 1.3 15 1-15 7-21 (44)
382 TIGR03872 cytochrome_MoxG cyto 31.6 38 0.00083 24.1 2.0 17 40-56 105-121 (133)
383 PF04405 ScdA_N: Domain of Unk 31.5 34 0.00074 21.4 1.5 23 1-23 34-56 (56)
384 cd01110 HTH_SoxR Helix-Turn-He 31.4 1.9E+02 0.0041 20.3 6.2 45 2-51 5-49 (139)
385 CHL00034 rpl22 ribosomal prote 31.3 28 0.0006 24.5 1.2 47 35-81 13-59 (117)
386 PRK13621 psbV cytochrome c-550 31.3 37 0.0008 26.1 2.0 53 2-56 97-154 (170)
387 KOG0697|consensus 31.1 18 0.0004 30.9 0.3 29 41-88 244-272 (379)
388 PF00165 HTH_AraC: Bacterial r 31.1 36 0.00078 18.8 1.5 17 1-18 11-27 (42)
389 PRK00565 rplV 50S ribosomal pr 31.0 31 0.00068 23.8 1.4 47 35-81 6-52 (112)
390 TIGR02905 spore_yutH spore coa 30.8 50 0.0011 25.5 2.6 60 4-70 4-68 (313)
391 cd00377 ICL_PEPM Members of th 30.7 1.4E+02 0.003 22.8 5.0 70 10-91 157-227 (243)
392 PRK10816 DNA-binding transcrip 30.6 92 0.002 21.0 3.6 47 11-57 104-166 (223)
393 PF08222 HTH_CodY: CodY helix- 30.5 73 0.0016 21.2 3.0 43 3-45 9-52 (61)
394 COG3800 Predicted transcriptio 30.3 37 0.0008 28.8 2.0 26 2-27 154-179 (332)
395 cd00569 HTH_Hin_like Helix-tur 30.2 42 0.0009 15.3 1.4 15 2-16 25-39 (42)
396 cd04640 CBS_pair_27 The CBS do 30.0 1.4E+02 0.0031 18.6 4.7 37 9-48 9-47 (126)
397 PRK13501 transcriptional activ 29.7 1.2E+02 0.0027 22.5 4.5 32 49-84 221-252 (290)
398 TIGR02647 DNA conserved hypoth 29.7 1.3E+02 0.0028 20.7 4.2 33 12-49 33-65 (77)
399 PRK03170 dihydrodipicolinate s 29.7 1.8E+02 0.0038 22.1 5.4 48 8-56 17-66 (292)
400 cd06562 GH20_HexA_HexB-like Be 29.6 64 0.0014 25.8 3.1 41 36-76 150-206 (348)
401 COG2378 Predicted transcriptio 29.6 1.8E+02 0.0039 23.1 5.6 53 2-56 26-91 (311)
402 PF02042 RWP-RK: RWP-RK domain 29.3 42 0.0009 21.1 1.6 19 1-19 7-25 (52)
403 PRK10766 DNA-binding transcrip 29.1 90 0.0019 21.0 3.4 23 34-56 153-175 (221)
404 PRK10529 DNA-binding transcrip 29.1 1.1E+02 0.0023 20.7 3.7 33 35-82 146-179 (225)
405 TIGR01950 SoxR redox-sensitive 28.8 2.2E+02 0.0047 20.3 5.7 44 2-50 5-48 (142)
406 smart00595 MADF subfamily of S 28.5 69 0.0015 19.8 2.6 22 2-23 31-52 (89)
407 KOG3559|consensus 28.5 48 0.001 29.8 2.5 48 22-69 85-144 (598)
408 TIGR03045 PS_II_C550 cytochrom 28.4 40 0.00087 25.2 1.7 17 40-56 131-147 (159)
409 PRK13182 racA polar chromosome 28.4 1.9E+02 0.0041 21.7 5.3 48 2-55 4-51 (175)
410 TIGR02043 ZntR Zn(II)-responsi 28.3 2E+02 0.0044 19.8 6.0 46 2-51 5-50 (131)
411 PLN00104 MYST -like histone ac 28.3 1.1E+02 0.0023 26.8 4.4 45 1-51 377-422 (450)
412 PF09286 Pro-kuma_activ: Pro-k 28.3 2E+02 0.0043 19.6 5.1 40 2-42 51-91 (143)
413 COG2739 Uncharacterized protei 28.3 57 0.0012 23.6 2.4 23 1-23 36-58 (105)
414 COG1675 TFA1 Transcription ini 28.1 1.2E+02 0.0025 23.2 4.2 62 2-63 36-103 (176)
415 cd00904 Ferritin Ferritin iron 28.1 37 0.0008 24.0 1.4 16 42-57 47-65 (160)
416 PRK01546 hypothetical protein; 28.1 46 0.001 22.8 1.8 22 10-31 1-22 (79)
417 TIGR00370 conserved hypothetic 27.9 38 0.00082 25.7 1.5 21 1-21 93-113 (202)
418 PRK15414 phosphomannomutase Cp 27.8 84 0.0018 25.8 3.6 26 29-56 251-277 (456)
419 PLN03239 histone acetyltransfe 27.6 59 0.0013 27.5 2.7 46 1-52 287-333 (351)
420 PF05402 PqqD: Coenzyme PQQ sy 27.6 96 0.0021 18.3 3.0 27 2-28 37-67 (68)
421 TIGR02276 beta_rpt_yvtn 40-res 27.5 42 0.00092 17.6 1.3 12 34-45 1-12 (42)
422 KOG1273|consensus 27.3 31 0.00066 29.9 1.0 14 29-42 158-171 (405)
423 PRK11083 DNA-binding response 27.1 1.2E+02 0.0026 20.2 3.6 21 36-56 150-170 (228)
424 PF03869 Arc: Arc-like DNA bin 26.8 61 0.0013 19.6 2.0 28 3-30 21-50 (50)
425 PF14242 DUF4342: Domain of un 26.8 75 0.0016 21.4 2.7 29 6-34 9-37 (84)
426 COG1188 Ribosome-associated he 26.7 42 0.00092 23.8 1.5 25 46-76 14-38 (100)
427 PRK04280 arginine repressor; P 26.6 77 0.0017 23.0 2.9 31 12-46 36-67 (148)
428 cd04589 CBS_pair_CAP-ED_DUF294 26.6 1.5E+02 0.0033 17.7 4.8 36 9-48 9-46 (111)
429 TIGR03249 KdgD 5-dehydro-4-deo 26.6 1.7E+02 0.0038 22.5 5.0 47 9-56 22-70 (296)
430 CHL00133 psbV photosystem II c 26.6 45 0.00098 25.1 1.7 17 40-56 132-148 (163)
431 cd06171 Sigma70_r4 Sigma70, re 26.5 1.1E+02 0.0023 15.9 2.9 20 2-21 30-49 (55)
432 TIGR02675 tape_meas_nterm tape 26.3 65 0.0014 20.7 2.2 24 2-29 48-71 (75)
433 TIGR01387 cztR_silR_copR heavy 26.3 1.3E+02 0.0029 19.8 3.8 23 34-56 141-163 (218)
434 TIGR01143 murF UDP-N-acetylmur 26.3 2.1E+02 0.0045 22.8 5.5 52 4-56 265-322 (417)
435 cd04612 CBS_pair_SpoIVFB_EriC_ 26.3 1.5E+02 0.0032 17.5 4.3 20 28-48 26-46 (111)
436 cd02259 Peptidase_C39_like Pep 26.2 33 0.00071 21.4 0.8 42 2-43 45-86 (122)
437 PF08974 DUF1877: Domain of un 26.2 1.1E+02 0.0023 22.0 3.5 23 39-61 88-110 (167)
438 PF05043 Mga: Mga helix-turn-h 26.1 67 0.0014 20.0 2.2 46 1-47 33-78 (87)
439 cd01282 HTH_MerR-like_sg3 Heli 25.9 2.1E+02 0.0045 19.1 5.8 50 2-56 4-53 (112)
440 PRK11426 hypothetical protein; 25.9 60 0.0013 23.9 2.2 22 1-22 75-96 (132)
441 smart00796 AHS1 Allophanate hy 25.8 44 0.00095 25.1 1.5 20 1-20 103-122 (201)
442 cd06808 PLPDE_III Type III Pyr 25.8 1.8E+02 0.0039 20.0 4.5 34 6-39 120-155 (211)
443 PF04545 Sigma70_r4: Sigma-70, 25.8 85 0.0018 17.8 2.4 20 2-21 24-43 (50)
444 PF11042 DUF2750: Protein of u 25.6 1.5E+02 0.0032 19.7 3.9 37 12-48 63-101 (104)
445 PTZ00488 Proteasome subunit be 25.5 1.8E+02 0.004 22.3 4.9 47 9-56 185-241 (247)
446 cd03174 DRE_TIM_metallolyase D 25.5 2.2E+02 0.0049 20.5 5.1 45 10-57 143-188 (265)
447 PF01475 FUR: Ferric uptake re 25.4 1.9E+02 0.0042 18.9 4.4 33 8-40 38-70 (120)
448 PRK12494 NADH dehydrogenase su 25.4 1.4E+02 0.0031 22.2 4.1 44 14-57 18-61 (172)
449 cd00001 PTS_IIB_man PTS_IIB, P 25.4 63 0.0014 23.3 2.2 19 37-55 116-134 (151)
450 PRK11543 gutQ D-arabinose 5-ph 25.3 2.1E+02 0.0046 21.6 5.1 37 9-48 215-253 (321)
451 PF09601 DUF2459: Protein of u 25.3 73 0.0016 23.7 2.6 21 36-56 93-113 (173)
452 cd04585 CBS_pair_ACT_assoc2 Th 25.2 1.3E+02 0.0029 17.9 3.4 20 28-48 26-46 (122)
453 TIGR03834 EAGR_box EAGR box. T 25.1 33 0.00071 19.6 0.6 11 29-39 18-28 (28)
454 PF08280 HTH_Mga: M protein tr 25.1 68 0.0015 19.3 2.0 24 1-24 22-45 (59)
455 TIGR01051 topA_bact DNA topois 25.1 2E+02 0.0043 25.1 5.5 54 3-56 261-319 (610)
456 cd07969 OBF_DNA_ligase_I The O 25.0 1.3E+02 0.0028 21.3 3.7 30 28-57 26-63 (144)
457 PRK10701 DNA-binding transcrip 24.9 1.3E+02 0.0027 20.8 3.6 34 35-83 156-190 (240)
458 PF03705 CheR_N: CheR methyltr 24.7 78 0.0017 18.2 2.2 15 42-56 1-15 (57)
459 cd04611 CBS_pair_PAS_GGDEF_DUF 24.6 1.3E+02 0.0029 17.7 3.3 10 72-81 101-110 (111)
460 cd04606 CBS_pair_Mg_transporte 24.6 1.1E+02 0.0025 18.4 3.0 19 28-46 27-46 (109)
461 PRK10227 DNA-binding transcrip 24.6 2.6E+02 0.0055 19.7 5.3 46 2-51 4-49 (135)
462 cd01210 EPS8 Epidermal growth 24.4 67 0.0015 23.6 2.2 63 11-73 22-96 (127)
463 PF00237 Ribosomal_L22: Riboso 24.4 35 0.00075 22.8 0.7 47 35-81 2-48 (105)
464 PRK07218 replication factor A; 24.3 64 0.0014 27.4 2.4 24 1-24 8-31 (423)
465 TIGR03691 20S_bact_alpha prote 24.2 1.4E+02 0.0031 22.6 4.0 41 9-49 172-227 (228)
466 COG2161 StbD Antitoxin of toxi 24.2 1.4E+02 0.0029 19.7 3.5 30 24-53 24-56 (86)
467 COG1733 Predicted transcriptio 24.0 1.1E+02 0.0024 21.4 3.1 32 3-34 41-73 (120)
468 cd00130 PAS PAS domain; PAS mo 23.9 87 0.0019 15.0 2.0 15 30-44 6-20 (103)
469 PF13467 RHH_4: Ribbon-helix-h 23.9 61 0.0013 21.2 1.7 20 1-20 26-45 (67)
470 cd04626 CBS_pair_13 The CBS do 23.7 1.7E+02 0.0038 17.5 5.0 35 11-48 11-47 (111)
471 PRK09802 DNA-binding transcrip 23.7 1.1E+02 0.0024 23.6 3.4 20 65-84 23-42 (269)
472 cd03015 PRX_Typ2cys Peroxiredo 23.7 96 0.0021 21.5 2.8 28 29-56 123-156 (173)
473 cd04615 CBS_pair_2 The CBS dom 23.6 1.7E+02 0.0038 17.4 5.1 37 10-48 10-47 (113)
474 PF12272 DUF3610: Protein of u 23.5 21 0.00046 27.3 -0.5 16 61-76 38-53 (157)
475 PF12791 RsgI_N: Anti-sigma fa 23.5 59 0.0013 19.2 1.5 21 23-43 2-22 (56)
476 PF13202 EF-hand_5: EF hand; P 23.4 68 0.0015 16.6 1.6 12 70-81 12-23 (25)
477 PF05595 DUF771: Domain of unk 23.4 1.7E+02 0.0036 19.4 3.8 32 38-84 3-34 (91)
478 cd04786 HTH_MerR-like_sg7 Heli 23.4 2.7E+02 0.0058 19.5 5.7 45 2-50 4-48 (131)
479 PTZ00326 phenylalanyl-tRNA syn 23.3 1.9E+02 0.004 25.4 5.0 45 2-47 25-69 (494)
480 PF10543 ORF6N: ORF6N domain; 23.3 2.2E+02 0.0047 18.6 4.3 45 2-52 16-60 (88)
481 TIGR00854 pts-sorbose PTS syst 23.2 79 0.0017 22.9 2.4 19 37-55 117-135 (151)
482 PF08281 Sigma70_r4_2: Sigma-7 23.2 98 0.0021 17.5 2.4 20 2-21 30-49 (54)
483 PRK14324 glmM phosphoglucosami 23.1 1.1E+02 0.0025 24.9 3.5 26 29-56 248-274 (446)
484 PRK10371 DNA-binding transcrip 23.1 1.5E+02 0.0033 22.7 4.0 31 49-83 236-266 (302)
485 cd00336 Ribosomal_L22 Ribosoma 23.0 51 0.0011 21.9 1.3 45 36-80 5-49 (105)
486 COG0079 HisC Histidinol-phosph 23.0 1.2E+02 0.0027 24.4 3.6 38 19-57 276-315 (356)
487 smart00717 SANT SANT SWI3, AD 22.9 1.3E+02 0.0027 15.6 3.0 42 41-85 4-45 (49)
488 PTZ00068 60S ribosomal protein 22.9 66 0.0014 25.2 2.1 21 1-21 137-157 (202)
489 PRK13856 two-component respons 22.9 1.9E+02 0.0041 20.1 4.2 34 34-82 149-183 (241)
490 PRK13622 psbV cytochrome c-550 22.8 58 0.0013 25.1 1.7 21 36-56 138-158 (180)
491 PF01408 GFO_IDH_MocA: Oxidore 22.8 1.4E+02 0.0031 18.7 3.3 51 4-57 42-113 (120)
492 PRK08006 replicative DNA helic 22.8 1.3E+02 0.0029 25.3 4.0 69 10-87 263-331 (471)
493 KOG1498|consensus 22.7 3E+02 0.0064 24.3 6.1 53 2-54 357-414 (439)
494 PF05979 DUF896: Bacterial pro 22.5 62 0.0013 21.3 1.6 19 13-31 1-19 (65)
495 COG3710 CadC DNA-binding winge 22.4 1.8E+02 0.0039 20.9 4.1 27 30-56 21-47 (148)
496 PRK09726 antitoxin HipB; Provi 22.3 1.8E+02 0.0038 18.6 3.7 54 12-85 10-63 (88)
497 PF11305 DUF3107: Protein of u 22.3 1.8E+02 0.0039 19.5 3.8 39 4-42 14-53 (74)
498 PRK10336 DNA-binding transcrip 22.2 1.7E+02 0.0037 19.4 3.7 34 35-83 144-178 (219)
499 TIGR01285 nifN nitrogenase mol 22.2 91 0.002 25.7 2.8 59 1-59 276-336 (432)
500 PHA02592 52 DNA topisomerase I 22.2 78 0.0017 27.0 2.5 26 8-33 237-262 (439)
No 1
>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=100.00 E-value=4.5e-38 Score=236.14 Aligned_cols=73 Identities=67% Similarity=1.022 Sum_probs=33.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV 80 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~ 80 (96)
|+|||++|||+|++||+||++|+++|+|||||||||||||||++||++||+||++| ||||++||+
T Consensus 116 ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~va~fi~~r---------------GRvsi~el~ 180 (188)
T PF09756_consen 116 LEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEAVAKFIKQR---------------GRVSISELA 180 (188)
T ss_dssp HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE----------------------------------------
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHHHHHHHHHc---------------CCccHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred Hhccccee
Q psy11008 81 ENSNQLVT 88 (96)
Q Consensus 81 ~~sN~lI~ 88 (96)
++||+||+
T Consensus 181 ~~~N~~i~ 188 (188)
T PF09756_consen 181 QESNRLIN 188 (188)
T ss_dssp --------
T ss_pred HHHHhhcC
Confidence 99999996
No 2
>KOG3054|consensus
Probab=100.00 E-value=1.3e-36 Score=242.93 Aligned_cols=80 Identities=61% Similarity=0.893 Sum_probs=77.3
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV 80 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~ 80 (96)
|||||++|||+||++|+|||+|+++|.|||||||||||||||++||.+||+||+|| |||||+||+
T Consensus 217 ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~AVAkfIkqr---------------GRVSIaelA 281 (299)
T KOG3054|consen 217 LEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELAAVAKFIKQR---------------GRVSIAELA 281 (299)
T ss_pred HHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHHHHHHHHHHc---------------CceeHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred HhcccceeccccccC
Q psy11008 81 ENSNQLVTLIPDQIA 95 (96)
Q Consensus 81 ~~sN~lI~L~p~~~~ 95 (96)
+.||+||+|.|...+
T Consensus 282 e~SN~lI~l~~es~s 296 (299)
T KOG3054|consen 282 EKSNQLIDLETESPS 296 (299)
T ss_pred HhhcchhccccCCCC
Confidence 999999999877653
No 3
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=97.37 E-value=0.00098 Score=37.38 Aligned_cols=50 Identities=12% Similarity=0.319 Sum_probs=44.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
+|||.+++++...+-..|+.|.+.|.+.-.-+.+.++.+++++.+..+..
T Consensus 14 ~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~ 63 (66)
T smart00418 14 CELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLE 63 (66)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHH
Confidence 68999999999999999999999999998888888899999986665544
No 4
>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=96.91 E-value=0.0063 Score=47.99 Aligned_cols=61 Identities=26% Similarity=0.430 Sum_probs=52.2
Q ss_pred CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH-HHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 9 RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS-VATFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~-Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
+|+--.||+=|+.|.+.+.|.=|....||- |||++++.. +..-+..+| |||++.||+..-|
T Consensus 20 rLSErnciEiv~kL~~~~~ldli~T~dGke-yiT~~~L~~EI~~el~~~g--------------GRv~~~dL~~~Ln 81 (272)
T PF09743_consen 20 RLSERNCIEIVNKLIEKKLLDLIHTTDGKE-YITPEQLEKEIKDELYVHG--------------GRVNLVDLAQALN 81 (272)
T ss_pred hcchhhHHHHHHHHHHcCCeeEEEECCCCE-EECHHHHHHHHHHHHHHcC--------------CceEHHHHHHhcC
Confidence 677788999999999999999888889985 899999865 555777887 9999999997644
No 5
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=96.76 E-value=0.0054 Score=47.21 Aligned_cols=54 Identities=19% Similarity=0.287 Sum_probs=48.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.|||..++++.+.+-.+++.|++.|-++-..|.|+.+|++|+.-...+.+-...
T Consensus 25 ~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d 78 (217)
T PRK14165 25 SEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYAD 78 (217)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHH
Confidence 589999999999999999999999999999999999999999988776544433
No 6
>smart00753 PAM PCI/PINT associated module.
Probab=96.73 E-value=0.004 Score=39.09 Aligned_cols=45 Identities=18% Similarity=0.336 Sum_probs=41.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE 45 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE 45 (96)
+++||..|+++.+++-.-|.++..+|.|.|-||...++++++...
T Consensus 27 ~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~ 71 (88)
T smart00753 27 LSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD 71 (88)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence 478999999999999999999999999999999999999998654
No 7
>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=96.73 E-value=0.004 Score=39.09 Aligned_cols=45 Identities=18% Similarity=0.336 Sum_probs=41.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE 45 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE 45 (96)
+++||..|+++.+++-.-|.++..+|.|.|-||...++++++...
T Consensus 27 ~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~~ 71 (88)
T smart00088 27 LSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEEVD 71 (88)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECCCc
Confidence 478999999999999999999999999999999999999998654
No 8
>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=96.22 E-value=0.014 Score=36.33 Aligned_cols=42 Identities=17% Similarity=0.371 Sum_probs=37.9
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
++++|..++++.+++-.-+.++..+|.|.|.||..=+.|+++
T Consensus 63 ~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 63 ISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred hHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 468999999999999999999999999999999887777765
No 9
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=96.03 E-value=0.019 Score=40.74 Aligned_cols=55 Identities=13% Similarity=0.373 Sum_probs=44.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeC--CCc----eEEE-----cHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDD--RGK----FIYI-----SQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDD--RGK----fIyI-----s~eEl~~Va~fI~~r 56 (96)
.+||...|++...|..||+.|++.|.|.| ++|. -|. |+-| .++.++.+++.+.+.
T Consensus 32 ~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~~~~~~~~~~~~~~l~~~ 100 (164)
T PRK11169 32 VELSKRVGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNRGAPDVFEQFNAAVQKL 100 (164)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEcCCChHHHHHHHHHHhcC
Confidence 58999999999999999999999999865 4553 243 5666 466788888888776
No 10
>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=95.98 E-value=0.018 Score=34.17 Aligned_cols=43 Identities=23% Similarity=0.294 Sum_probs=34.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDRGKfIyIs~e 44 (96)
.+||..++++.+.+..-|++|.+.|-|.=. -|.|.+++.+|++
T Consensus 22 ~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~ 67 (68)
T PF13463_consen 22 SDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPA 67 (68)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HH
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCC
Confidence 589999999999999999999999999544 4567789999986
No 11
>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=95.80 E-value=0.034 Score=36.80 Aligned_cols=54 Identities=19% Similarity=0.233 Sum_probs=45.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.+||..+++....+-..|+.|++.|-|+..-| .|-+++++|++-...+......
T Consensus 46 ~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~ 102 (118)
T TIGR02337 46 TQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQ 102 (118)
T ss_pred HHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHH
Confidence 48999999999999999999999999999884 5778999999877766655443
No 12
>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=95.55 E-value=0.039 Score=31.84 Aligned_cols=38 Identities=18% Similarity=0.368 Sum_probs=31.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
.|||.+|+++.+.+-.-++.|++.|-|+ -.+|+..+++
T Consensus 29 ~~la~~~~is~~~v~~~l~~L~~~G~i~---~~~~~~~~l~ 66 (66)
T cd07377 29 RELAEELGVSRTTVREALRELEAEGLVE---RRPGRGTFVA 66 (66)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE---ecCCCeEEeC
Confidence 5899999999999999999999999865 2456676664
No 13
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=95.47 E-value=0.088 Score=32.13 Aligned_cols=55 Identities=16% Similarity=0.322 Sum_probs=45.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.+||..++++...+-.-|+.|++.|.++=.-| .|.+++++|+.....+.......
T Consensus 28 ~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~~~~~~ 85 (101)
T smart00347 28 SELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEELLEAR 85 (101)
T ss_pred HHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHHHHHHH
Confidence 57999999999999999999999999975433 57789999999887776655544
No 14
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=95.45 E-value=0.057 Score=49.09 Aligned_cols=61 Identities=30% Similarity=0.497 Sum_probs=50.8
Q ss_pred hCCChHHHHHHHHHHHHcCCcc--EEeeCCCceEEEcHHHHH-HHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 8 FRMKTQSVIDRIVELQKTGALT--GVIDDRGKFIYISQEELN-SVATFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~lt--GViDDRGKfIyIs~eEl~-~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
.+|+--.||+=++.|.+.|.|- =|.--.|| =|||+++|. .+...|. +| |||++.||+..-|
T Consensus 22 ~rLSErNcIEiV~KLie~~~ld~dll~T~DGK-EYiT~~qL~~EI~~El~-~g--------------GRvnlvdLa~~Ln 85 (803)
T PLN03083 22 VRLSERNVVELVQKLQELGIIDFDLLHTVSGK-EYITQDQLRNEIEAEIK-KL--------------GRVSLVDLADTIG 85 (803)
T ss_pred hhcchhhHHHHHHHHHHhcccCcceEEecCCc-eeeCHHHHHHHHHHHHH-hC--------------CCeeHHHHhhhcC
Confidence 3678889999999999999773 66778999 999999996 4777784 45 9999999987655
No 15
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.29 E-value=0.065 Score=34.63 Aligned_cols=55 Identities=22% Similarity=0.469 Sum_probs=43.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeCC--Cc----e--EEEc-HHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDDR--GK----F--IYIS-QEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDDR--GK----f--IyIs-~eEl~~Va~fI~~r 56 (96)
.+||..+|++...+..||+.|++.|.+.| ++|.+ |. + |.++ ++..+.+++.+++.
T Consensus 21 ~~la~~l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~~~~~~v~~~l~~~ 87 (108)
T smart00344 21 AELAKKVGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESPDKLEEFLEKLEKL 87 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECChhHHHHHHHHHhCC
Confidence 58999999999999999999999998874 34422 22 2 4455 67888999888876
No 16
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.25 E-value=0.022 Score=38.48 Aligned_cols=55 Identities=25% Similarity=0.481 Sum_probs=41.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCC--C----ceEEEcHHH----HHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDR--G----KFIYISQEE----LNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDR--G----KfIyIs~eE----l~~Va~fI~~r 56 (96)
.+||...|++...|.+||+.|++.|-|.|. +|.+ | =|+-+..+. +..++..+.+-
T Consensus 26 ~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~~~~~~~~~~~~~~~~~ 93 (154)
T COG1522 26 AELAERVGLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLERSLEDLEEFAEALAKL 93 (154)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEecCChhHHHHHHHHHhCC
Confidence 589999999999999999999999988764 4531 3 466665554 66666666543
No 17
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=95.19 E-value=0.038 Score=31.33 Aligned_cols=28 Identities=21% Similarity=0.382 Sum_probs=25.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.+||..|+++...+-..++.|++.|.|.
T Consensus 24 ~~la~~~~vs~~tv~~~l~~L~~~g~i~ 51 (60)
T smart00345 24 RELAAQLGVSRTTVREALSRLEAEGLVQ 51 (60)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5799999999999999999999999876
No 18
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=95.05 E-value=0.14 Score=38.01 Aligned_cols=55 Identities=18% Similarity=0.186 Sum_probs=46.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc--EEee-CCCceEE---EcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT--GVID-DRGKFIY---ISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt--GViD-DRGKfIy---Is~eEl~~Va~fI~~r 56 (96)
||||...|+++.+|-.-+..|.++|-++ -+-| ++|.|.| ++.+++..+-.+-..+
T Consensus 40 eeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~ 100 (178)
T PRK06266 40 EEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKME 100 (178)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHH
Confidence 7999999999999999999999999998 5556 7899888 9998887766655444
No 19
>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=94.88 E-value=0.21 Score=28.24 Aligned_cols=42 Identities=14% Similarity=0.319 Sum_probs=37.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.|||..++++...+-..+..|.+.|-+...-+.+.++..+++
T Consensus 24 ~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~ 65 (78)
T cd00090 24 SELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD 65 (78)
T ss_pred HHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC
Confidence 589999999988888999999999999988887778888885
No 20
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=94.51 E-value=0.18 Score=34.25 Aligned_cols=55 Identities=15% Similarity=0.187 Sum_probs=47.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|||..++++.+.+-.-|..|++.|-|+=.-| -|.++|++|++-...++......
T Consensus 50 ~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~ 107 (144)
T PRK03573 50 IQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVI 107 (144)
T ss_pred HHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHH
Confidence 48999999999999999999999999998865 58999999999887777655444
No 21
>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=94.01 E-value=0.22 Score=33.07 Aligned_cols=55 Identities=22% Similarity=0.356 Sum_probs=46.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE---eeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV---IDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV---iDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.+||..+++....+-.-|..|++.|-|+=+ -|-|-.+|++|++-...++....+.
T Consensus 47 ~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~ 104 (109)
T TIGR01889 47 KEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEI 104 (109)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHHH
Confidence 479999999888888889999999999854 4568999999999988888776654
No 22
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.93 E-value=0.08 Score=37.12 Aligned_cols=55 Identities=22% Similarity=0.371 Sum_probs=43.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccE---EeeC--CCc----eEEEc---HHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTG---VIDD--RGK----FIYIS---QEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltG---ViDD--RGK----fIyIs---~eEl~~Va~fI~~r 56 (96)
.+||...|++.+.|-.||+.|+++|.|.| ++|. -|. |+.|+ ++.+..++..+.+.
T Consensus 27 ~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~~~~v~~~~lg~~~~a~v~v~v~~~~~~~~~~~~l~~~ 93 (153)
T PRK11179 27 AELAKQFGVSPGTIHVRVEKMKQAGIITGTRVDVNPKQLGYDVCCFIGIILKSAKDYPSALAKLESL 93 (153)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeeeEEEEECHHHcCCCEEEEEEEEEcccccHHHHHHHHhCC
Confidence 48999999999999999999999999974 4563 343 45543 45688888888876
No 23
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=93.92 E-value=0.15 Score=28.55 Aligned_cols=44 Identities=18% Similarity=0.276 Sum_probs=33.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.|+|..+|++.. .|...++.|.|...-++.|... .+++++..+.
T Consensus 4 ~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~-y~~~~v~~l~ 47 (49)
T cd04761 4 GELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRL-YSDADLERLR 47 (49)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEE-eCHHHHHHhh
Confidence 588999999765 4567789999997666656654 5999988753
No 24
>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=93.88 E-value=0.22 Score=30.17 Aligned_cols=44 Identities=25% Similarity=0.479 Sum_probs=33.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS 48 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~ 48 (96)
+|||...|++.+.+-.-+++|+++|.|. -.+|+++-..++.|++
T Consensus 32 ~~iA~~~g~sr~tv~r~l~~l~~~g~I~---~~~~~i~I~d~~~L~~ 75 (76)
T PF13545_consen 32 EEIADMLGVSRETVSRILKRLKDEGIIE---VKRGKIIILDPERLEE 75 (76)
T ss_dssp HHHHHHHTSCHHHHHHHHHHHHHTTSEE---EETTEEEESSHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE---EcCCEEEECCHHHHhc
Confidence 6899999999999888899999998765 2455555445665554
No 25
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.82 E-value=0.3 Score=33.42 Aligned_cols=53 Identities=9% Similarity=0.159 Sum_probs=45.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~ 54 (96)
.+||..++++...+-.-|..|++.|-|.=.-| -|.+.||+|++-...+.....
T Consensus 58 ~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~~ 113 (144)
T PRK11512 58 VELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQ 113 (144)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHHHH
Confidence 48999999999999999999999999987754 689999999998877666443
No 26
>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=93.72 E-value=0.098 Score=38.13 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=37.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
.|||..++++...+-..++.|++.|-+.-.-+ |++.+++|+.
T Consensus 161 ~eia~~l~is~stv~r~L~~Le~~GlI~r~~~-r~~~~~lT~~ 202 (203)
T TIGR01884 161 KNIAKKLGKSLSTISRHLRELEKKGLVEQKGR-KGKRYSLTKL 202 (203)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC-CccEEEeCCC
Confidence 58999999999999999999999999987654 9999999874
No 27
>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=93.20 E-value=0.11 Score=35.08 Aligned_cols=55 Identities=16% Similarity=0.196 Sum_probs=43.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|||..++++..-+-.+++.|.+.|-+.+.-...|.|-...+-+--.+.+++..-
T Consensus 29 ~eia~~l~is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~~~v~~~l 83 (130)
T TIGR02944 29 AEIAEQTGLNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITVADIVKAV 83 (130)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCHHHHHHHH
Confidence 5899999999999999999999999998876666777766655444455555554
No 28
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=93.05 E-value=0.26 Score=27.16 Aligned_cols=28 Identities=21% Similarity=0.496 Sum_probs=26.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||..++++.+.+-.-+..|++.|-+.
T Consensus 12 ~~la~~l~~s~~tv~~~l~~L~~~g~l~ 39 (48)
T smart00419 12 QEIAELLGLTRETVSRTLKRLEKEGLIS 39 (48)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5899999999999999999999999885
No 29
>PRK10870 transcriptional repressor MprA; Provisional
Probab=92.95 E-value=0.46 Score=34.35 Aligned_cols=55 Identities=11% Similarity=0.137 Sum_probs=47.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|||..++++.+.+-.-|..|++.|-+.=.-| -|.++|++|++-...+.......
T Consensus 75 ~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~~~ 132 (176)
T PRK10870 75 SELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQ 132 (176)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHH
Confidence 48999999999999899999999999997765 48899999999888887765544
No 30
>PF13551 HTH_29: Winged helix-turn helix
Probab=92.83 E-value=0.2 Score=31.61 Aligned_cols=54 Identities=15% Similarity=0.376 Sum_probs=44.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC--C-CceEE-EcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD--R-GKFIY-ISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD--R-GKfIy-Is~eEl~~Va~fI~~r 56 (96)
.++|..+|++.+-|-+-++...+.| +.|+.++ + |+.-- +|+++.+.|-+++.+.
T Consensus 16 ~~ia~~lg~s~~Tv~r~~~~~~~~G-~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~ 73 (112)
T PF13551_consen 16 AEIARRLGISRRTVYRWLKRYREGG-IEGLLPRKPRGGRPRKRLSEEQRAQLIELLREN 73 (112)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHccc-HHHHHhccccCCCCCCCCCHHHHHHHHHHHHHC
Confidence 5789999998888888888888777 8888884 3 55554 9999999999999987
No 31
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=92.79 E-value=0.61 Score=25.45 Aligned_cols=42 Identities=19% Similarity=0.354 Sum_probs=32.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV 49 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V 49 (96)
+|+|..+|++..- |..+.++|.|.++.. |+-..++.+|++..
T Consensus 5 ~e~a~~lgis~~t----i~~~~~~g~i~~~~~--g~~~~~~~~~l~~~ 46 (49)
T TIGR01764 5 EEAAEYLGVSKDT----VYRLIHEGELPAYRV--GRHYRIPREDVDEY 46 (49)
T ss_pred HHHHHHHCCCHHH----HHHHHHcCCCCeEEe--CCeEEEeHHHHHHH
Confidence 6889999997653 555678999999876 66778898887653
No 32
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=92.45 E-value=0.44 Score=34.65 Aligned_cols=47 Identities=15% Similarity=0.319 Sum_probs=33.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
+|||...|++.+.+-.-+++|+++|.|. ...+|++.-...+.|.+++
T Consensus 183 ~~IA~~lGisretlsR~L~~L~~~GlI~--~~~~~~i~I~D~~~L~~l~ 229 (230)
T PRK09391 183 RDIADYLGLTIETVSRALSQLQDRGLIG--LSGARQIELRNRQALRNLD 229 (230)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCcEE--ecCCceEEEcCHHHHHHhh
Confidence 6899999998888777799999997652 2223455555677777665
No 33
>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=92.35 E-value=0.65 Score=36.77 Aligned_cols=66 Identities=27% Similarity=0.418 Sum_probs=56.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
-|||...|+....|=.+++++.++.. ++.=-.|- .||.+=++.+|.-|+.+ +++.|.||++||+.
T Consensus 74 ~dL~~~LnVd~~~ie~~~~~i~~~~~--~~~l~~ge--lit~~Yld~l~~Eine~-----------Lqe~G~vsi~eLa~ 138 (272)
T PF09743_consen 74 VDLAQALNVDLDHIERRAQEIVKSDK--SLQLVQGE--LITDSYLDSLAEEINEK-----------LQESGQVSISELAK 138 (272)
T ss_pred HHHHHhcCcCHHHHHHHHHHHHhCCC--cEEEECCE--EccHHHHHHHHHHHHHH-----------HHHcCeEeHHHHHH
Confidence 48999999988888888999998887 55555675 78999999999999998 78889999999986
Q ss_pred h
Q psy11008 82 N 82 (96)
Q Consensus 82 ~ 82 (96)
.
T Consensus 139 ~ 139 (272)
T PF09743_consen 139 Q 139 (272)
T ss_pred h
Confidence 5
No 34
>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=92.27 E-value=0.59 Score=28.43 Aligned_cols=43 Identities=14% Similarity=0.226 Sum_probs=34.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
+|||...|++...|-+-++.|++.|-+.-.-...-.|-.+.+|
T Consensus 26 ~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~~pe 68 (68)
T PF01978_consen 26 EEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAVPPE 68 (68)
T ss_dssp HHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE-HH
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEeCCC
Confidence 6899999999999999999999999998776554444445443
No 35
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.13 E-value=0.67 Score=29.18 Aligned_cols=49 Identities=12% Similarity=0.216 Sum_probs=37.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFI 53 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI 53 (96)
.+||..++++...+-..++.|++.|-|.= .+++.+++|+.-..-+..+.
T Consensus 3 ~ela~~l~is~stvs~~l~~L~~~glI~r---~~~~~~~lT~~g~~~~~~~~ 51 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLKKLEKDGLVEY---EPYRGITLTEKGRRLARRLL 51 (96)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHCCCEEE---cCCCceEechhHHHHHHHHH
Confidence 58999999999999999999999854432 34478999997655544443
No 36
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=92.02 E-value=0.84 Score=31.43 Aligned_cols=51 Identities=16% Similarity=0.184 Sum_probs=40.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.+||..++++...|-.-|+.|++.|-|.= .+++.|++|+.-... |..+..+
T Consensus 26 ~ela~~l~vs~~svs~~l~~L~~~Gli~~---~~~~~i~LT~~G~~~-a~~~~~~ 76 (142)
T PRK03902 26 SDIAEALSVHPSSVTKMVQKLDKDEYLIY---EKYRGLVLTPKGKKI-GKRLVYR 76 (142)
T ss_pred HHHHHHhCCChhHHHHHHHHHHHCCCEEE---ecCceEEECHHHHHH-HHHHHHH
Confidence 58999999999999999999999987652 366789999997664 4445433
No 37
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=91.89 E-value=0.41 Score=38.09 Aligned_cols=53 Identities=23% Similarity=0.410 Sum_probs=47.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.+||.+.+.+.|.+-.+|++|++.|-|+=-+-.+|.+|-||+.-++-+-+-..
T Consensus 23 ~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~~~ 75 (214)
T COG1339 23 SELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKEYE 75 (214)
T ss_pred HHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999988776655443
No 38
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=91.75 E-value=0.7 Score=31.95 Aligned_cols=46 Identities=24% Similarity=0.263 Sum_probs=34.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~ 51 (96)
+|||...|++.+.|-.-+.+|+++|.|. -.++.|.| ..+.|.++|.
T Consensus 153 ~~iA~~lG~tretvsR~l~~l~~~g~I~----~~~~~i~I~d~~~L~~~~~ 199 (202)
T PRK13918 153 DELAAAVGSVRETVTKVIGELSREGYIR----SGYGKIQLLDLKGLEELAE 199 (202)
T ss_pred HHHHHHhCccHHHHHHHHHHHHHCCCEE----cCCCEEEEECHHHHHHHHh
Confidence 6899999998888777799999988764 34344555 5777776653
No 39
>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=91.65 E-value=0.23 Score=29.28 Aligned_cols=22 Identities=27% Similarity=0.385 Sum_probs=19.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQ 23 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~ 23 (96)
.+||...|++...|..||+.|+
T Consensus 21 ~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 21 AELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHHHhC
Confidence 5899999999999999999986
No 40
>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=91.49 E-value=0.46 Score=27.76 Aligned_cols=35 Identities=23% Similarity=0.527 Sum_probs=28.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF 38 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf 38 (96)
.|||..+|++...+-.-++.|++.|.|.-. .+|+|
T Consensus 29 ~ela~~~g~s~~tv~r~l~~L~~~g~i~~~--~~~~~ 63 (67)
T cd00092 29 QEIADYLGLTRETVSRTLKELEEEGLISRR--GRGKY 63 (67)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEec--CCCeE
Confidence 589999999999999999999999887632 24554
No 41
>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=91.39 E-value=0.51 Score=28.88 Aligned_cols=30 Identities=23% Similarity=0.216 Sum_probs=26.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV 31 (96)
.+||..|+++...+-.+|+.|++.|-..-.
T Consensus 17 ~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 17 EKLGEALGMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 589999999999999999999998875533
No 42
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=91.11 E-value=0.88 Score=37.86 Aligned_cols=74 Identities=20% Similarity=0.278 Sum_probs=53.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.+||..++++.+.|..-|..|++.|-++= -|.|=+++++|++-...+..-.... .-+.. ++.+|.+++.||..
T Consensus 24 ~eLA~~l~l~~~tVt~~i~~Le~kGlV~~-~~~~~~~i~LTeeG~~~~~~g~pE~-----rl~~~-l~~~~g~~~~el~~ 96 (489)
T PRK04172 24 EELAEKLGLPPEAVMRAAEWLEEKGLVKV-EERVEEVYVLTEEGKKYAEEGLPER-----RLLNA-LKDGGEVSLDELKE 96 (489)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHhCCCEEE-EeeeEEEEEECHHHHHHHHhcCHHH-----HHHHh-hHhcCCcCHHHHHH
Confidence 58999999999999999999999998874 4667799999998766555433322 22222 33345577777665
Q ss_pred h
Q psy11008 82 N 82 (96)
Q Consensus 82 ~ 82 (96)
.
T Consensus 97 ~ 97 (489)
T PRK04172 97 A 97 (489)
T ss_pred h
Confidence 3
No 43
>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=90.98 E-value=0.39 Score=27.49 Aligned_cols=27 Identities=19% Similarity=0.363 Sum_probs=24.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGAL 28 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~l 28 (96)
.|||..+|++..-+-.++++|++.|-|
T Consensus 21 ~ela~~~~is~~tv~~~l~~L~~~g~I 47 (48)
T PF13412_consen 21 KELAEKLGISRSTVNRYLKKLEEKGLI 47 (48)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCcCc
Confidence 589999999999999999999999976
No 44
>PF13518 HTH_28: Helix-turn-helix domain
Probab=90.94 E-value=0.26 Score=27.87 Aligned_cols=35 Identities=17% Similarity=0.381 Sum_probs=26.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK 37 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK 37 (96)
.++|.+||++...|-.=++..++.| +.|+.+.+|+
T Consensus 16 ~~~a~~~gis~~tv~~w~~~y~~~G-~~~l~~~~~r 50 (52)
T PF13518_consen 16 REIAREFGISRSTVYRWIKRYREGG-IEGLKPKKRR 50 (52)
T ss_pred HHHHHHHCCCHhHHHHHHHHHHhcC-HHHhccCCCC
Confidence 5799999997766666677777766 7899887663
No 45
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=90.84 E-value=0.36 Score=30.74 Aligned_cols=28 Identities=21% Similarity=0.438 Sum_probs=25.2
Q ss_pred hhhhhhhCCC-hHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMK-TQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lk-tq~vI~RI~eL~~~g~lt 29 (96)
.|||..||++ +..|-..++.|++.|.|.
T Consensus 29 rEIa~~~g~~S~~tv~~~L~~Le~kG~I~ 57 (65)
T PF01726_consen 29 REIAEALGLKSTSTVQRHLKALERKGYIR 57 (65)
T ss_dssp HHHHHHHTSSSHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHhCCCChHHHHHHHHHHHHCcCcc
Confidence 5899999998 888889999999999875
No 46
>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=90.65 E-value=0.22 Score=30.98 Aligned_cols=33 Identities=21% Similarity=0.291 Sum_probs=27.1
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVID 33 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViD 33 (96)
+.|||.+|+++.+.+-.-|..|+..|.|-=+-+
T Consensus 17 ~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 17 LAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 368999999999999999999999999875544
No 47
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=90.64 E-value=1.4 Score=27.30 Aligned_cols=53 Identities=13% Similarity=0.186 Sum_probs=39.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|||.+++++...+-..++.|++.|-|.- +..++...+++.=++--..++...
T Consensus 24 ~~ia~~l~i~~~tv~r~l~~L~~~g~l~~--~~~~~~y~l~~~~~~~~~~~~~~~ 76 (91)
T smart00346 24 AELAERLGLSKSTAHRLLNTLQELGYVEQ--DGQNGRYRLGPKVLELGQSYLSSL 76 (91)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCeee--cCCCCceeecHHHHHHHHHHHhcC
Confidence 58999999999999999999999999975 333445567776555555555433
No 48
>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=90.59 E-value=0.96 Score=30.83 Aligned_cols=44 Identities=14% Similarity=0.132 Sum_probs=32.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSV 49 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~V 49 (96)
+|||...|++.+.|-.-+++|+++|.|.- +++.|.| ..+.|...
T Consensus 147 ~~iA~~lG~tretvsR~l~~l~~~g~I~~----~~~~i~I~d~~~L~~~ 191 (193)
T TIGR03697 147 QAIAEAIGSTRVTITRLLGDLRKKKLISI----HKKKITVHDPIALGQR 191 (193)
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHCCCEEe----cCCEEEEeCHHHHHHh
Confidence 68999999977777666999999987643 3445666 46655543
No 49
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=90.49 E-value=1 Score=27.92 Aligned_cols=53 Identities=13% Similarity=0.308 Sum_probs=45.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee---CCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID---DRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD---DRGKfIyIs~eEl~~Va~fI~ 54 (96)
.+||...+++...+-.-|+.|++.|-+.=..| -|.+++.+|++--..++....
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 48999999999999999999999999988777 478899999987766665544
No 50
>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=90.37 E-value=1.1 Score=31.75 Aligned_cols=47 Identities=26% Similarity=0.399 Sum_probs=35.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE-EEcHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI-YISQEELNSV 49 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI-yIs~eEl~~V 49 (96)
.+||..||++..-|.+-|+.|+.+|-|. +.--+|-|| .++.+++..+
T Consensus 38 ~~La~~lgVSRtpVReAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~ei 85 (212)
T TIGR03338 38 SDIAARLGVSRGPVREAFRALEEAGLVR-NEKNRGVFVREISLAEADEI 85 (212)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHCCCEE-EecCCCeEEecCCHHHHHHH
Confidence 4799999999999999999999999876 233455554 3456665544
No 51
>COG3140 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.30 E-value=0.55 Score=31.10 Aligned_cols=48 Identities=29% Similarity=0.389 Sum_probs=34.4
Q ss_pred hhhCCC---hHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhh
Q psy11008 6 ALFRMK---TQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVAT 66 (96)
Q Consensus 6 a~F~lk---tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~ 66 (96)
..++|+ .|.+++||++|.++|.-+| |-+.-||+-|+++-..+-+.++.
T Consensus 4 ~lp~LtHeqQQ~AVE~Iq~lMaeGmSsG-------------EAIa~VA~elRe~hk~~~~~~~~ 54 (60)
T COG3140 4 GLPSLTHEQQQKAVERIQELMAEGMSSG-------------EAIALVAQELRENHKGENRIVAR 54 (60)
T ss_pred ccccccHHHHHHHHHHHHHHHHccccch-------------hHHHHHHHHHHHHhccccccccc
Confidence 344444 4789999999999998776 67888999998884333333333
No 52
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=90.04 E-value=1.3 Score=32.04 Aligned_cols=48 Identities=13% Similarity=0.220 Sum_probs=36.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVATFI 53 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~fI 53 (96)
+|||..+|++.+.+-.-+++|+++|.| .-.|+-|+| ..+.|.++|.-+
T Consensus 173 ~~lA~~lG~sretvsR~L~~L~~~G~I----~~~~~~i~I~d~~~L~~~~~~~ 221 (226)
T PRK10402 173 TQAAEYLGVSYRHLLYVLAQFIQDGYL----KKSKRGYLIKNRKQLSGLALEL 221 (226)
T ss_pred HHHHHHHCCcHHHHHHHHHHHHHCCCE----EeeCCEEEEeCHHHHHHHHHHh
Confidence 689999999888887779999999765 434555666 567777776654
No 53
>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=89.89 E-value=0.21 Score=31.05 Aligned_cols=22 Identities=27% Similarity=0.668 Sum_probs=15.1
Q ss_pred hhhhhhccccceeHHHHHHhcc
Q psy11008 63 SVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 63 ~~~~~~~~~GRVsi~eL~~~sN 84 (96)
.+.+||+++|++|+.||+..-|
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~ 25 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFG 25 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT
T ss_pred HHHHHHHHcCCcCHHHHHHHHC
Confidence 3445555559999999998765
No 54
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=89.61 E-value=2.1 Score=25.77 Aligned_cols=64 Identities=17% Similarity=0.232 Sum_probs=45.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.|+|..+|+++.- |.-.++.|.+... .+.|.+=+.|++++..+.....-+ +.| +|+.++.+
T Consensus 4 ~evA~~~gvs~~t----lR~~~~~g~l~~~-~~~~g~R~y~~~~l~~l~~i~~l~-------------~~g-~~l~~i~~ 64 (67)
T cd04764 4 KEVSEIIGVKPHT----LRYYEKEFNLYIP-RTENGRRYYTDEDIELLKKIKTLL-------------EKG-LSIKEIKE 64 (67)
T ss_pred HHHHHHHCcCHHH----HHHHHHhcCCCCC-CCCCCceeeCHHHHHHHHHHHHHH-------------HCC-CCHHHHHH
Confidence 5899999998763 4466777777743 566777788999999877655444 224 78888776
Q ss_pred hcc
Q psy11008 82 NSN 84 (96)
Q Consensus 82 ~sN 84 (96)
..|
T Consensus 65 ~l~ 67 (67)
T cd04764 65 ILN 67 (67)
T ss_pred HhC
Confidence 543
No 55
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=89.60 E-value=1.8 Score=30.44 Aligned_cols=68 Identities=16% Similarity=0.139 Sum_probs=47.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIK 69 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~ 69 (96)
-|||..|+++..-+=.-++.|.+.|-++.--+-|=.|.++.++-..-++.++++.-...+..+..+++
T Consensus 34 ~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~~~~~~~~~~w~~~~~~l~~~l~ 101 (117)
T PRK10141 34 CDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPAWAAKIIEQAWLCEQEDVQAIVR 101 (117)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47999999977777778999999999999888777777777654444555455443334444444443
No 56
>PF13730 HTH_36: Helix-turn-helix domain
Probab=89.60 E-value=0.56 Score=27.24 Aligned_cols=27 Identities=30% Similarity=0.406 Sum_probs=24.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGAL 28 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~l 28 (96)
+.||...|++...|..-|++|++.|-|
T Consensus 29 ~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 29 ETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 679999999999999999999999864
No 57
>PF12728 HTH_17: Helix-turn-helix domain
Probab=89.44 E-value=1.8 Score=24.88 Aligned_cols=42 Identities=14% Similarity=0.275 Sum_probs=34.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV 49 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V 49 (96)
+|+|..+|++.+. +..+...|.|..+- .|+-++++.+++++.
T Consensus 5 ~e~a~~l~is~~t----v~~~~~~g~i~~~~--~g~~~~~~~~~l~~~ 46 (51)
T PF12728_consen 5 KEAAELLGISRST----VYRWIRQGKIPPFK--IGRKWRIPKSDLDRW 46 (51)
T ss_pred HHHHHHHCcCHHH----HHHHHHcCCCCeEE--eCCEEEEeHHHHHHH
Confidence 6899999997765 45677899999995 788899999987753
No 58
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=89.41 E-value=1.2 Score=33.35 Aligned_cols=54 Identities=17% Similarity=0.243 Sum_probs=43.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.|||...+++...+..-|+.|++.|-|.=.. |-|-++|++|++-...+.+....
T Consensus 63 ~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~ 119 (185)
T PRK13777 63 SEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETMEE 119 (185)
T ss_pred HHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHH
Confidence 4799999998777888899999999998554 56999999999877766655443
No 59
>PF12419 DUF3670: SNF2 Helicase protein ; InterPro: IPR022138 This domain family is found in bacteria, archaea and eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00271 from PFAM, PF00176 from PFAM. Most of the proteins in this family are annotated as SNF2 helicases but there is little accompanying literature to confirm this.
Probab=89.36 E-value=0.73 Score=32.57 Aligned_cols=50 Identities=16% Similarity=0.379 Sum_probs=38.3
Q ss_pred HHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHh
Q psy11008 19 IVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVEN 82 (96)
Q Consensus 19 I~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~ 82 (96)
+++|.+.+ .|++==||+||++.++++.++.+|+++++ ..+++|..|+.+.
T Consensus 89 f~~L~~~~--~~LV~~rg~WV~ld~~~l~~~~~~~~~~~------------~~~~lt~~e~Lr~ 138 (141)
T PF12419_consen 89 FEQLVEQK--RPLVRFRGRWVELDPEELRRALAFLEKAP------------KGEKLTLAEALRA 138 (141)
T ss_pred HHHHHHcC--CCeEEECCEEEEECHHHHHHHHHHHHhcc------------ccCCCCHHHHHHH
Confidence 44555544 47888899999999999999999999983 1125888887654
No 60
>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=89.00 E-value=0.5 Score=28.75 Aligned_cols=38 Identities=18% Similarity=0.353 Sum_probs=29.2
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI 41 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI 41 (96)
++|||.+|+++..-+-.=++.|++.|.+. =-+|-..++
T Consensus 17 ~~ela~~~~VS~~TiRRDl~~L~~~g~i~---r~~GG~~~~ 54 (57)
T PF08220_consen 17 VKELAEEFGVSEMTIRRDLNKLEKQGLIK---RTHGGAVLN 54 (57)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEE---EEcCEEEeC
Confidence 36899999999888888899999999843 234544444
No 61
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=88.87 E-value=2.2 Score=25.33 Aligned_cols=51 Identities=18% Similarity=0.299 Sum_probs=37.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|+|..+|++.+.+ ...++.|.+.....+.|.+-+.|++++..+.....-|
T Consensus 4 ~eva~~~gvs~~tl----r~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~lr 54 (70)
T smart00422 4 GEVAKLAGVSVRTL----RYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKRLK 54 (70)
T ss_pred HHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHHHH
Confidence 57899999976544 4557799999874444445578999999887776665
No 62
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=88.85 E-value=0.9 Score=32.47 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=33.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE-cHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI-SQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI-s~eEl~~Va~f 52 (96)
+|||...|++.+.+-.-+++|+++| + .. .+| .|.| ..+.|...|.+
T Consensus 177 ~~iA~~lG~tretvsR~l~~L~~~g-l--~~-~~~-~i~I~d~~~L~~~~~~ 223 (236)
T PRK09392 177 RVLASYLGMTPENLSRAFAALASHG-V--HV-DGS-AVTITDPAGLARFAKP 223 (236)
T ss_pred HHHHHHhCCChhHHHHHHHHHHhCC-e--Ee-eCC-EEEEcCHHHHHHhhcc
Confidence 5899999997776555589999999 5 33 345 5666 56777766654
No 63
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=88.51 E-value=0.82 Score=25.11 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=25.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.+||..|+++...+-..|+.|++.|.|.
T Consensus 18 ~~l~~~l~~s~~tv~~~l~~L~~~g~i~ 45 (53)
T smart00420 18 EELAELLGVSEMTIRRDLNKLEEQGLLT 45 (53)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 5899999999999999999999998764
No 64
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=88.31 E-value=2.4 Score=36.70 Aligned_cols=67 Identities=15% Similarity=0.240 Sum_probs=55.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
+||+..+++....+.+-+..|.++|.+.-|-+ .+|++.+-++.+.+.+++. ++..|.++++++-+
T Consensus 510 ~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~----~~~~~~~~~~~~~~~~~~~-----------~~~~~~~~~~~~r~ 574 (614)
T PRK10512 510 RDLAKETGTDEQAMRLTLRQAAQQGIITAIVK----DRYYRNDRIVQFANMIREL-----------DQECGSTCAADFRD 574 (614)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC----CEEECHHHHHHHHHHHHHH-----------HhhCCcEeHHHHHH
Confidence 68899999999998999999999999998876 5899999888776666554 45569999988876
Q ss_pred hc
Q psy11008 82 NS 83 (96)
Q Consensus 82 ~s 83 (96)
..
T Consensus 575 ~~ 576 (614)
T PRK10512 575 RL 576 (614)
T ss_pred Hh
Confidence 54
No 65
>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=88.25 E-value=1.2 Score=25.89 Aligned_cols=34 Identities=26% Similarity=0.418 Sum_probs=26.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK 37 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK 37 (96)
++||..|+++..-+.+-|++|.+.| .-|.-.+|+
T Consensus 19 ~eLa~~l~vS~rTi~~~i~~L~~~~--~~I~~~~~~ 52 (55)
T PF08279_consen 19 KELAEELGVSRRTIRRDIKELREWG--IPIESKRGK 52 (55)
T ss_dssp HHHHHHCTS-HHHHHHHHHHHHHTT---EEEEETTT
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCC--CeEEeeCCC
Confidence 6899999999999999999999999 334445554
No 66
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=88.21 E-value=1.5 Score=31.60 Aligned_cols=48 Identities=21% Similarity=0.339 Sum_probs=35.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va 50 (96)
++||.+||++...|.+-|+.|+.+|-++ +.-.+|-|+- ++.+++..+.
T Consensus 38 ~~La~~lgVSRtpVREAL~~L~~eGLV~-~~~~~g~~v~~~~~~~~~ei~ 86 (221)
T PRK11414 38 KNLAEQLGMSITPVREALLRLVSVNALS-VAPAQAFTVPEVSKRQLDEIN 86 (221)
T ss_pred HHHHHHHCCCchhHHHHHHHHHHCCCEE-ecCCCceeecCCCHHHHHHHH
Confidence 4799999999999999999999999886 3344564442 4555554443
No 67
>PRK00215 LexA repressor; Validated
Probab=87.30 E-value=0.86 Score=32.80 Aligned_cols=42 Identities=12% Similarity=0.256 Sum_probs=34.7
Q ss_pred hhhhhhhCC-ChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRM-KTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~l-ktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
.|||..+|+ +...+-.+|+.|++.|.|...-++ ++-+.++++
T Consensus 27 ~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~-~r~~~l~~~ 69 (205)
T PRK00215 27 REIADALGLRSPSAVHEHLKALERKGFIRRDPGR-SRAIEVAAP 69 (205)
T ss_pred HHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC-cceEEeccc
Confidence 589999999 677777889999999999887655 677788554
No 68
>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=87.18 E-value=1.1 Score=32.14 Aligned_cols=41 Identities=12% Similarity=0.261 Sum_probs=32.7
Q ss_pred hhhhhhhCCC-hHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMK-TQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lk-tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.|||..+|++ ...|-.+|+.|++.|-|... +.+.+.+.+..
T Consensus 29 ~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~-~~~~~~~~~~~ 70 (199)
T TIGR00498 29 REIARAVGLRSPSAAEEHLKALERKGYIERD-PGKPRAIRILD 70 (199)
T ss_pred HHHHHHhCCCChHHHHHHHHHHHHCCCEecC-CCCCCeEEeCC
Confidence 4899999999 89999999999999998875 33333566653
No 69
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=86.64 E-value=4.3 Score=24.13 Aligned_cols=50 Identities=20% Similarity=0.365 Sum_probs=37.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|+|..+|++.. .|...++.|.|.-.-+++|. -|.|++.+..+.....-+
T Consensus 4 ~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~ 53 (69)
T PF13411_consen 4 KEVAKLLGVSPS----TLRYYEREGLLPPPRDENGY-RYYSEEDVERLREIKELR 53 (69)
T ss_dssp HHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSS-EEE-HHHHHHHHHHHHHH
T ss_pred HHHHHHHCcCHH----HHHHHHHhcCcccccccCce-eeccHHHHHHHHHHHHHH
Confidence 589999999764 46677889999888855555 788999999887665555
No 70
>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=86.63 E-value=1.8 Score=26.01 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=27.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID 33 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD 33 (96)
.+||..+|++.+.+-..++.|++.|-|+.+-+
T Consensus 28 ~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 28 SELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 58999999999999999999999999887644
No 71
>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=86.61 E-value=2 Score=30.08 Aligned_cols=77 Identities=25% Similarity=0.320 Sum_probs=46.5
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE---EcHHHHH-HHHHHHHhh--chhchhhhhhhhccccceeHH
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY---ISQEELN-SVATFIKQR--GREELNSVATFIKQKGRVSVS 77 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy---Is~eEl~-~Va~fI~~r--gr~~~~~~~~~~~~~GRVsi~ 77 (96)
|+..++++...+.--|..|.+.|.|.=.-+.| .|.| ||++|+. ..++.+-.+ |..--+-|+.|+.. ..+|-.
T Consensus 28 l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr-~~~Y~p~vs~ee~~~~~~~~~~~~~f~gs~~~ll~~l~~~-~~ls~e 105 (130)
T TIGR02698 28 LAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGR-KFIYTALVSEDEAVENAAQELFSRICSRKVGAVIADLIEE-SPLSQT 105 (130)
T ss_pred HhhccCCcHHHHHHHHHHHHHCCceeeecCCC-cEEEEecCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHhc-CCCCHH
Confidence 55556788788888899999999986544445 4555 7889883 333333222 11112335566653 567776
Q ss_pred HHHHh
Q psy11008 78 ELVEN 82 (96)
Q Consensus 78 eL~~~ 82 (96)
||.+.
T Consensus 106 ele~L 110 (130)
T TIGR02698 106 DIEKL 110 (130)
T ss_pred HHHHH
Confidence 66543
No 72
>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=86.25 E-value=1.5 Score=26.43 Aligned_cols=36 Identities=22% Similarity=0.431 Sum_probs=28.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF 38 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf 38 (96)
.+||..|+++...+.+-+..|+++|.+.- ..-+|-|
T Consensus 28 ~~la~~~~vsr~tvr~al~~L~~~g~i~~-~~~~G~~ 63 (64)
T PF00392_consen 28 RELAERYGVSRTTVREALRRLEAEGLIER-RPGRGTF 63 (64)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEE-ETTTEEE
T ss_pred HHHHHHhccCCcHHHHHHHHHHHCCcEEE-ECCceEE
Confidence 47999999999999999999999998863 3444444
No 73
>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=86.25 E-value=1.5 Score=31.92 Aligned_cols=43 Identities=19% Similarity=0.255 Sum_probs=33.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe--e--CCC-ceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI--D--DRG-KFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi--D--DRG-KfIyIs~e 44 (96)
.+||..++++...|-..++.|++.|-+.-.- + +|- +.+++|+.
T Consensus 19 ~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~ 66 (203)
T TIGR02702 19 AALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ 66 (203)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence 5899999999999999999999999997663 2 222 34577865
No 74
>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=86.02 E-value=2.2 Score=24.70 Aligned_cols=33 Identities=21% Similarity=0.284 Sum_probs=28.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD 34 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD 34 (96)
.|||..++++.+.+-.-|+.|++.|-+.=.-|.
T Consensus 25 ~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 25 SELAERLGISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 589999999999999999999999999877663
No 75
>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=85.62 E-value=1.3 Score=35.83 Aligned_cols=41 Identities=12% Similarity=0.333 Sum_probs=33.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe-eCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI-DDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi-DDRGKfIyIs 42 (96)
.+||..+|++...|.+|++.|++.|-|.+.= --+|-||-.-
T Consensus 202 ~eLAerlGVSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l 243 (251)
T TIGR02787 202 SKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVL 243 (251)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCC
Confidence 4799999999999999999999999888765 2257777443
No 76
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=85.43 E-value=2.9 Score=22.40 Aligned_cols=44 Identities=18% Similarity=0.317 Sum_probs=31.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV 49 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V 49 (96)
+.|+|..+|++...+- .+.++|.+...-.+ |+..+++.+|+..+
T Consensus 3 ~~e~a~~lgvs~~tl~----~~~~~g~~~~~~~~-~~~~~~~~~ei~~~ 46 (49)
T cd04762 3 TKEAAELLGVSPSTLR----RWVKEGKLKAIRTP-GGHRRFPEEDLERL 46 (49)
T ss_pred HHHHHHHHCcCHHHHH----HHHHcCCCCceeCC-CCceecCHHHHHHH
Confidence 3689999999766544 45567888876544 46667899988765
No 77
>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=85.33 E-value=1.8 Score=31.42 Aligned_cols=37 Identities=16% Similarity=0.323 Sum_probs=31.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||..||++..-|.+-++.|+.+|-|+ +.--+|-|+
T Consensus 34 ~~La~~lgVSRtpVREAL~~Le~eGlV~-~~~~~G~~V 70 (235)
T TIGR02812 34 RELSELIGVTRTTLREVLQRLARDGWLT-IQHGKPTKV 70 (235)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEE-EeCCCccEe
Confidence 3799999999999999999999999887 344566555
No 78
>PRK09954 putative kinase; Provisional
Probab=84.82 E-value=2.4 Score=32.72 Aligned_cols=38 Identities=18% Similarity=0.468 Sum_probs=29.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc--EEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT--GVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt--GViDDRGKfI 39 (96)
.+||..++++..-|-.||+.|++.|.+. |.+-+..+||
T Consensus 21 ~~la~~l~~s~~~v~~~i~~L~~~g~i~~~~~~l~~~~~v 60 (362)
T PRK09954 21 NEIADILQISRSRVAAHIMDLMRKGRIKGKGYILTEQEYC 60 (362)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCcCCcEEEEcCCccE
Confidence 5899999999999999999999999884 3333444444
No 79
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=84.67 E-value=4.1 Score=27.96 Aligned_cols=48 Identities=19% Similarity=0.304 Sum_probs=38.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.++|..+|+++.-+ .--++.|-|.-..++.|.|-|-|++.+..+. ||+
T Consensus 3 ~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~-~I~ 50 (124)
T TIGR02051 3 GELAKAAGVNVETI----RYYERKGLLPEPDRPEGGYRRYPEETVKRLR-FIK 50 (124)
T ss_pred HHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCEeECHHHHHHHH-HHH
Confidence 58999999977643 5668999998666777888888999998874 554
No 80
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=84.34 E-value=2.2 Score=23.41 Aligned_cols=28 Identities=29% Similarity=0.383 Sum_probs=24.4
Q ss_pred EEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHh
Q psy11008 39 IYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVEN 82 (96)
Q Consensus 39 IyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~ 82 (96)
|+++++.++.+-+..++. | .|.+++++.
T Consensus 4 i~l~~~~~~~l~~~a~~~---------------g-~s~s~~ir~ 31 (39)
T PF01402_consen 4 IRLPDELYERLDELAKEL---------------G-RSRSELIRE 31 (39)
T ss_dssp EEEEHHHHHHHHHHHHHH---------------T-SSHHHHHHH
T ss_pred EEeCHHHHHHHHHHHHHH---------------C-cCHHHHHHH
Confidence 789999999999999999 6 888888764
No 81
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=83.96 E-value=3.7 Score=29.19 Aligned_cols=45 Identities=24% Similarity=0.476 Sum_probs=33.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc-HHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS-QEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs-~eEl~~Va 50 (96)
++||...|++.+.+-.-+++|+++|.| .-.++.|.|. .+.|.++|
T Consensus 188 ~~iA~~lG~sr~tvsR~l~~l~~~g~I----~~~~~~i~i~d~~~L~~~~ 233 (235)
T PRK11161 188 GDIGNYLGLTVETISRLLGRFQKSGML----AVKGKYITIENNDALAQLA 233 (235)
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHCCCE----EecCCEEEEcCHHHHHHHh
Confidence 689999999777776668999998754 5555667774 66676665
No 82
>PRK11050 manganese transport regulator MntR; Provisional
Probab=83.85 E-value=5.2 Score=28.35 Aligned_cols=51 Identities=18% Similarity=0.255 Sum_probs=38.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|||..|+++...+-..++.|++.|.|. ..+++-+++|+.-.. ++..+.++
T Consensus 55 ~eLA~~l~is~stVsr~l~~Le~~GlI~---r~~~~~v~LT~~G~~-l~~~~~~~ 105 (152)
T PRK11050 55 VDIAARLGVSQPTVAKMLKRLARDGLVE---MRPYRGVFLTPEGEK-LAQESRER 105 (152)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE---EecCCceEECchHHH-HHHHHHHH
Confidence 5899999999999999999999997553 234567899986654 34444443
No 83
>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=83.76 E-value=2 Score=24.72 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=22.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGAL 28 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~l 28 (96)
+|||...|+..+-|-.-+..|+++|-|
T Consensus 6 ~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 6 QDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 699999999888887889999999864
No 84
>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=83.69 E-value=4.3 Score=29.43 Aligned_cols=52 Identities=21% Similarity=0.337 Sum_probs=38.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe---eCCCceEE---EcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI---DDRGKFIY---ISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi---DDRGKfIy---Is~eEl~~Va~fI~~r 56 (96)
||||...||+..+|-.-+..|.+.|-++-.- ++.|.+-| |..++ +-+.|+.+
T Consensus 32 EeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~---i~d~Ik~~ 89 (158)
T TIGR00373 32 EEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEK---ALDVLKRK 89 (158)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHH---HHHHHHHH
Confidence 7999999999999999999999999985433 35576654 55554 44445444
No 85
>PF14493 HTH_40: Helix-turn-helix domain
Probab=83.57 E-value=3.6 Score=26.68 Aligned_cols=66 Identities=18% Similarity=0.340 Sum_probs=51.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV 80 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~ 80 (96)
++++|..-+++..-+.+-+.++...|.-..+ ..| +++++++.+.+.+++- |..+++++-
T Consensus 16 i~eIA~~R~L~~sTI~~HL~~~~~~g~~~~~----~~~--l~~e~~~~I~~~~~~~---------------~~~~lk~i~ 74 (91)
T PF14493_consen 16 IEEIAKIRGLKESTIYGHLAELIESGEPLDI----EEL--LSEEEIKQIEDAIEKL---------------GSEKLKPIK 74 (91)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHhCCCCCH----HHh--CCHHHHHHHHHHHHHc---------------CcccHHHHH
Confidence 4799999999999999999999999883222 133 8999999999999888 555666666
Q ss_pred Hhcccce
Q psy11008 81 ENSNQLV 87 (96)
Q Consensus 81 ~~sN~lI 87 (96)
+.++.-+
T Consensus 75 e~l~~~~ 81 (91)
T PF14493_consen 75 EALPGDY 81 (91)
T ss_pred HHCCCCC
Confidence 6666433
No 86
>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=83.42 E-value=1.7 Score=26.96 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=24.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||..++++...|-+-++.|++.|-+.
T Consensus 26 ~~iA~~L~vs~~tvt~ml~~L~~~GlV~ 53 (60)
T PF01325_consen 26 KDIAERLGVSPPTVTEMLKRLAEKGLVE 53 (60)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHCCChHHHHHHHHHHHHCCCEE
Confidence 4899999999999999999999999764
No 87
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=83.26 E-value=2.4 Score=24.56 Aligned_cols=22 Identities=23% Similarity=0.277 Sum_probs=16.7
Q ss_pred ChhhhhhhCCChHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVEL 22 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL 22 (96)
+++||.++|++...+-..+.+.
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHH
Confidence 4789999999877666666654
No 88
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=82.66 E-value=2.5 Score=30.68 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=30.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
.+||.+||++..-|.+-+..|+.+|.|.- .+|+-.||+
T Consensus 35 ~eLae~~gVSRt~VReAL~~L~~eGlv~~---~~g~G~~V~ 72 (239)
T PRK04984 35 RELSELIGVTRTTLREVLQRLARDGWLTI---QHGKPTKVN 72 (239)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE---eCCCeeEeC
Confidence 37999999999999999999999998873 234444554
No 89
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=82.42 E-value=2.3 Score=31.34 Aligned_cols=38 Identities=24% Similarity=0.349 Sum_probs=31.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY 40 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy 40 (96)
.+||..||++-.-|.+-|+.|+.+|-+. +.--+|-||-
T Consensus 30 ~eLae~~gVSRtpVREAL~~Le~~GlV~-~~~~~G~~V~ 67 (253)
T PRK10421 30 RQLAMQLGVSRNSLREALAKLVSEGVLL-SRRGGGTFIR 67 (253)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEE-EeCCCeEEEe
Confidence 3899999999999999999999999887 3334565553
No 90
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=82.21 E-value=3.6 Score=29.63 Aligned_cols=47 Identities=17% Similarity=0.324 Sum_probs=35.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE-EEcHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI-YISQEELNSV 49 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI-yIs~eEl~~V 49 (96)
++||..||++..-|.+-++.|+.+|-+. +.--+|-|| .+|++++..+
T Consensus 34 ~eLae~lgVSRtpVREAL~~L~~eGlv~-~~~~~G~~V~~~~~~~~~ei 81 (224)
T PRK11534 34 SLLTSRYALGVGPLREALSQLVAERLVT-VVNQKGYRVASMSEQELLDI 81 (224)
T ss_pred HHHHHHHCCChHHHHHHHHHHHHCCCEE-EeCCCceEeCCCCHHHHHHH
Confidence 5899999999999999999999999886 344556443 2355554443
No 91
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=82.06 E-value=1.8 Score=29.03 Aligned_cols=26 Identities=27% Similarity=0.417 Sum_probs=24.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCC
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGA 27 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ 27 (96)
|+||+..|++...|-..|+.|.+.|-
T Consensus 23 e~La~~LgiSRtaVwK~Iq~Lr~~G~ 48 (79)
T COG1654 23 EKLAEELGISRTAVWKHIQQLREEGV 48 (79)
T ss_pred HHHHHHHCccHHHHHHHHHHHHHhCC
Confidence 68999999999999999999999985
No 92
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=82.03 E-value=1.6 Score=33.38 Aligned_cols=31 Identities=32% Similarity=0.518 Sum_probs=25.9
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGV 31 (96)
++|||..|+++.+-+..=|.+|++.|.|..+
T Consensus 22 v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 22 VEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 3799999999666555569999999999875
No 93
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=81.77 E-value=7.7 Score=29.27 Aligned_cols=81 Identities=20% Similarity=0.270 Sum_probs=56.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHc----CCccEEeeCCCceEEEcHHHHHH-HHHHHHhhchhchhhh----hhhhcccc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKT----GALTGVIDDRGKFIYISQEELNS-VATFIKQRGREELNSV----ATFIKQKG 72 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~----g~ltGViDDRGKfIyIs~eEl~~-Va~fI~~rgr~~~~~~----~~~~~~~G 72 (96)
++||.-+++...++.+-|.+|.++ ++=-=+.--.|+|-+.|..|+.. |.+|....-+..|..- -..|..++
T Consensus 24 ~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLEtLaiIay~q 103 (188)
T PRK00135 24 EQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALEVLAIIAYKQ 103 (188)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHHHHHHHHHcC
Confidence 689999999988888888888654 43333455678898888887764 4556554323345432 35677788
Q ss_pred ceeHHHHHHh
Q psy11008 73 RVSVSELVEN 82 (96)
Q Consensus 73 RVsi~eL~~~ 82 (96)
-||.+|+.+.
T Consensus 104 PiTr~eI~~i 113 (188)
T PRK00135 104 PITRIEIDEI 113 (188)
T ss_pred CcCHHHHHHH
Confidence 9999998875
No 94
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=81.77 E-value=5.9 Score=25.21 Aligned_cols=47 Identities=6% Similarity=0.152 Sum_probs=34.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f 52 (96)
.+|+..-+|+...+..-|..|++.|-+.+ +++..+||+.-.+.+-.+
T Consensus 23 t~i~~~~~L~~~~~~~yL~~L~~~gLI~~----~~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 23 TEIMYKANLNYSTLKKYLKELEEKGLIKK----KDGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp HHHHTTST--HHHHHHHHHHHHHTTSEEE----ETTEEEE-HHHHHHHHHH
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHCcCeeC----CCCEEEECccHHHHHHHH
Confidence 36788889999999999999999999844 555669999876655544
No 95
>smart00351 PAX Paired Box domain.
Probab=81.73 E-value=7.4 Score=26.86 Aligned_cols=62 Identities=13% Similarity=0.179 Sum_probs=45.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCC---C-ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDR---G-KFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVS 77 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDR---G-KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~ 77 (96)
.++|..||++..-|..=|+...++|.+ ..+ | +-=-+++++...+..+++++ ...+..
T Consensus 37 ~~iA~~~gvs~~tV~kwi~r~~~~G~~----~pk~~gg~rp~~~~~~~~~~I~~~~~~~---------------p~~t~~ 97 (125)
T smart00351 37 CDISRQLCVSHGCVSKILGRYYETGSI----RPGAIGGSKPKVATPKVVKKIADYKQEN---------------PGIFAW 97 (125)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHcCCc----CCcCCCCCCCCccCHHHHHHHHHHHHHC---------------CCCCHH
Confidence 478999999887777778888888763 342 3 44456777777777788888 788888
Q ss_pred HHHHh
Q psy11008 78 ELVEN 82 (96)
Q Consensus 78 eL~~~ 82 (96)
||++.
T Consensus 98 el~~~ 102 (125)
T smart00351 98 EIRDR 102 (125)
T ss_pred HHHHH
Confidence 87643
No 96
>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=81.73 E-value=1.6 Score=28.50 Aligned_cols=33 Identities=24% Similarity=0.378 Sum_probs=29.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD 34 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD 34 (96)
++||+.++|...+|.+-|++|..+|.|-=-|||
T Consensus 69 ~~I~~~l~~~~~~v~~al~~L~~eG~IYsTiDd 101 (102)
T PF08784_consen 69 DEIAQQLGMSENEVRKALDFLSNEGHIYSTIDD 101 (102)
T ss_dssp HHHHHHSTS-HHHHHHHHHHHHHTTSEEESSST
T ss_pred HHHHHHhCcCHHHHHHHHHHHHhCCeEecccCC
Confidence 689999999999999999999999998777776
No 97
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=81.24 E-value=12 Score=24.18 Aligned_cols=55 Identities=7% Similarity=0.225 Sum_probs=42.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc----eEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK----FIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK----fIyIs~eEl~~Va~fI~~r 56 (96)
.+|....|++...+-.-++.|++.|-+.---.-.|+ ++-||+.-.+++..|+..-
T Consensus 18 ~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~~L 76 (80)
T PF13601_consen 18 SELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVAAL 76 (80)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHHHH
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHHHH
Confidence 478899999999999999999999999865554444 7889999998888887643
No 98
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=80.99 E-value=8.5 Score=25.27 Aligned_cols=47 Identities=13% Similarity=0.184 Sum_probs=39.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f 52 (96)
.|+|..+|+++. .|.--++.|-|..+-.+.+.|=|-|++++..+..-
T Consensus 4 ~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~~I 50 (96)
T cd04768 4 GEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFI 50 (96)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHHHH
Confidence 589999999764 46778899999998877788999999999987643
No 99
>cd00131 PAX Paired Box domain
Probab=80.86 E-value=8.1 Score=26.99 Aligned_cols=64 Identities=14% Similarity=0.173 Sum_probs=44.6
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCC-ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRG-KFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRG-KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
++|..|+++..-|..=++...++|.+.-.-- .| +-=.++++....+-.+++++ +..|..||.+
T Consensus 38 ~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~-gg~rpr~~~~~~~~~i~~~v~~~---------------p~~Tl~El~~ 101 (128)
T cd00131 38 DISRQLRVSHGCVSKILNRYYETGSIRPGAI-GGSKPRVATPEVVKKIEIYKQEN---------------PGMFAWEIRD 101 (128)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHcCCcCCCCC-CCCCCCcCCHHHHHHHHHHHHHC---------------CCCCHHHHHH
Confidence 6899999988877777888999998652111 12 12245666667777788888 6777777766
Q ss_pred h
Q psy11008 82 N 82 (96)
Q Consensus 82 ~ 82 (96)
.
T Consensus 102 ~ 102 (128)
T cd00131 102 R 102 (128)
T ss_pred H
Confidence 5
No 100
>KOG2235|consensus
Probab=80.72 E-value=3.4 Score=37.97 Aligned_cols=61 Identities=23% Similarity=0.386 Sum_probs=50.2
Q ss_pred CCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHH-HHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 9 RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNS-VATFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~-Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
+|+--.||+-++.|++.-+|-=|..-.||= ||||+.++. +-.-+-.+| ||+|+-||+..-|
T Consensus 23 kLSerNcvEivqkLie~~~ldvvhT~dGke-YIT~~hLe~EI~dEl~v~G--------------gRaslvDla~tln 84 (776)
T KOG2235|consen 23 KLSERNCVEIVQKLIESHRLDVVHTRDGKE-YITPNHLETEIKDELIVAG--------------GRASLVDLAVTLN 84 (776)
T ss_pred HhhhccHHHHHHHHHHhhhcceEEecCCcc-ccCHHHHHHHHHHHHHHhC--------------CcchhHHHHHHhC
Confidence 355567899999999999999999999994 999999863 555566665 8999999998766
No 101
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=80.69 E-value=3 Score=30.76 Aligned_cols=36 Identities=19% Similarity=0.207 Sum_probs=31.0
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
+||..||++..-|.+-++.|+.+|-|+ +.--+|-||
T Consensus 37 eLae~~gVSRtpVREAL~~L~~eGlV~-~~~~~G~~V 72 (253)
T PRK11523 37 FIADEKNVSRTVVREAIIMLEVEGYVE-VRKGSGIHV 72 (253)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEE-EecCCeeEE
Confidence 799999999999999999999999887 333567666
No 102
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=80.35 E-value=3.3 Score=30.38 Aligned_cols=39 Identities=23% Similarity=0.364 Sum_probs=31.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.+||..||++...|.+-++.|+.+|-|+=. .|+-.||++
T Consensus 38 ~eLa~~lgVSRtpVREAL~~L~~eGlv~~~---~~~G~~V~~ 76 (254)
T PRK09464 38 RELAKQFDVSRPSLREAIQRLEAKGLLLRR---QGGGTFVQS 76 (254)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEEEe---cCceeEEec
Confidence 479999999999999999999999988733 344445543
No 103
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=80.17 E-value=3.5 Score=30.19 Aligned_cols=38 Identities=16% Similarity=0.355 Sum_probs=31.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY 40 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy 40 (96)
.+||..||++...|.+-++.|+.+|-|.-. --+|-||-
T Consensus 35 ~eLa~~~gVSRtpVREAL~~L~~eGlV~~~-~~~G~~V~ 72 (251)
T PRK09990 35 RRLCEKLGFSRSALREGLTVLRGRGIIETA-QGRGSFVA 72 (251)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCCeeEEe
Confidence 389999999999999999999999988733 34666654
No 104
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=79.91 E-value=3.1 Score=30.55 Aligned_cols=37 Identities=19% Similarity=0.318 Sum_probs=29.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||++||++..-|.+-|.+|.++|.|.- .--+|-|+
T Consensus 39 ~eLa~~~~VSR~TVR~Al~~L~~eGli~r-~~G~GtfV 75 (241)
T PRK10079 39 QQLAARYEVNRHTLRRAIDQLVEKGWVQR-RQGVGVLV 75 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE-ecCCEEEE
Confidence 37999999999999999999999999873 23344454
No 105
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=79.87 E-value=4.2 Score=31.45 Aligned_cols=27 Identities=19% Similarity=0.250 Sum_probs=25.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGAL 28 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~l 28 (96)
++||.+||++...|-.+|+.|++.|-.
T Consensus 22 ~~LA~~lgvsr~tV~~~l~~L~~~G~~ 48 (319)
T PRK11886 22 EQLGEELGISRAAIWKHIQTLEEWGLD 48 (319)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 579999999999999999999999983
No 106
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=79.80 E-value=3.7 Score=25.71 Aligned_cols=29 Identities=21% Similarity=0.251 Sum_probs=25.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTG 30 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltG 30 (96)
.|||..+|+.+..|-.-+..|++.|.+.-
T Consensus 26 ~eLa~~lgl~~~~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 26 LQLAKNLGLPKKEVNRVLYSLEKKGKVCK 54 (68)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEe
Confidence 48999999999977777899999999854
No 107
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=79.77 E-value=1.9 Score=32.83 Aligned_cols=28 Identities=25% Similarity=0.463 Sum_probs=25.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||..|+++..-+...|++|+++|.|.
T Consensus 23 ~eLa~~l~VS~~TIRRDL~~Le~~g~l~ 50 (256)
T PRK10434 23 EELAQYFDTTGTTIRKDLVILEHAGTVI 50 (256)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 6899999999888889999999999664
No 108
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=79.48 E-value=3.5 Score=30.40 Aligned_cols=37 Identities=16% Similarity=0.398 Sum_probs=30.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||.+||++..-|.+-++.|+.+|-+. +.--+|-||
T Consensus 37 ~eLa~~~gVSRtpVREAL~~L~~eGlV~-~~~~~G~~V 73 (257)
T PRK10225 37 REIAEMLDVTRTVVREALIMLEIKGLVE-VRRGAGIYV 73 (257)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEE-EecCCEEEE
Confidence 3799999999999999999999999887 233455555
No 109
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=79.29 E-value=10 Score=22.38 Aligned_cols=51 Identities=10% Similarity=0.044 Sum_probs=32.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|+|..+|++...+-.-.++ .|.+...- +.|.+-+.|++++..+......+
T Consensus 4 ~eva~~~gvs~~tlr~w~~~---~g~~~~~r-~~~~~r~yt~~~v~~l~~i~~l~ 54 (68)
T cd01104 4 GAVARLTGVSPDTLRAWERR---YGLPAPQR-TDGGHRLYSEADVARLRLIRRLT 54 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh---CCCCCCCc-CCCCCeecCHHHHHHHHHHHHHH
Confidence 58999999976655443322 24444333 34566778999998877665555
No 110
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=79.26 E-value=8.2 Score=25.68 Aligned_cols=49 Identities=18% Similarity=0.334 Sum_probs=36.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|+|..+|+++.- |.--++.|-|...-++ |.|-+-+++.+..+. +|+.-
T Consensus 5 ~eva~~~gvs~~t----lR~ye~~Gll~~~r~~-~g~R~Y~~~~l~~l~-~I~~l 53 (102)
T cd04789 5 SELAEKAGISRST----LLYYEKLGLITGTRNA-NGYRLYPDSDLQRLL-LIQQL 53 (102)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCcCC-CCCeeCCHHHHHHHH-HHHHH
Confidence 5789999997654 4578888999886555 667777999988766 55543
No 111
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=79.20 E-value=9.8 Score=25.57 Aligned_cols=47 Identities=13% Similarity=0.220 Sum_probs=37.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f 52 (96)
.++|..+|+++.- |.-.++.|-|...-++.+.|-|.|++++..+..-
T Consensus 4 ~eva~~~gvs~~t----lR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I 50 (108)
T cd04773 4 GELAHLLGVPPST----LRHWEKEGLLSPDREPETGYRVYDPSDVRDARLI 50 (108)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHH
Confidence 5789999997654 4556889999988888889999999999876543
No 112
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=79.16 E-value=9.5 Score=27.81 Aligned_cols=47 Identities=17% Similarity=0.242 Sum_probs=35.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.|+|..+|+++. -|.--++.|-|...-++.|...| +++.+..+ .||+
T Consensus 15 gevAk~~gvs~~----TlRyYE~~GLi~~~r~~~g~R~Y-~~~~i~~L-~~I~ 61 (154)
T PRK15002 15 GEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRY-KRDVLRYV-AIIK 61 (154)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEE-CHHHHHHH-HHHH
Confidence 578999999764 46788999999997666665444 88887776 5554
No 113
>PRK05114 hypothetical protein; Provisional
Probab=79.12 E-value=1.4 Score=29.09 Aligned_cols=32 Identities=31% Similarity=0.474 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 12 TQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 12 tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|.+++||++|.++|.=+| |-+.-||+-|+++
T Consensus 13 QQ~AVErIq~LMaqGmSsg-------------EAI~~VA~eiRe~ 44 (59)
T PRK05114 13 QQKAVERIQELMAQGMSSG-------------EAIALVAEELRAN 44 (59)
T ss_pred HHHHHHHHHHHHHccccHH-------------HHHHHHHHHHHHH
Confidence 4789999999999998766 6788899999887
No 114
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=78.76 E-value=3 Score=29.56 Aligned_cols=60 Identities=23% Similarity=0.399 Sum_probs=46.5
Q ss_pred hhhhhhhCC--ChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhh-----ccccce
Q psy11008 2 EDLAALFRM--KTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFI-----KQKGRV 74 (96)
Q Consensus 2 edLAa~F~l--ktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~-----~~~GRV 74 (96)
+++-+.|+- +...+|.-++++|+. -| |||++-++.||+.+.-. .-++..||||- +++|+.
T Consensus 3 ~~i~~~~~~~~~~~~li~~L~~vQ~~---------~G---~i~~~~~~~iA~~l~~~-~~~v~~v~tFY~~f~~~p~gk~ 69 (148)
T TIGR01958 3 EEIIAKYPDDQKRSAIMPALMIAQEQ---------KG---WVTPEAIAAVAEMLGIP-PVWVYEVATFYSMFDTEPVGRY 69 (148)
T ss_pred HHHHHHCCCCCChhHHHHHHHHHHHH---------hC---CCCHHHHHHHHHHhCcC-HHHHHHHHhHHhhcCcCCCCCE
Confidence 456677776 778888988888853 34 89999999999998865 66788899985 456653
No 115
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=78.06 E-value=3.3 Score=30.87 Aligned_cols=61 Identities=23% Similarity=0.288 Sum_probs=44.5
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhh-----ccccceeH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFI-----KQKGRVSV 76 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~-----~~~GRVsi 76 (96)
++-++|+-+...+|.-++++|+. -| ||+++-++.||+.+.-. .-++..|+||- +.+|+-.|
T Consensus 26 ~ii~~~~~~~~~li~~L~~iQ~~---------~G---yIp~e~~~~iA~~l~v~-~a~V~gVatFY~~f~~~P~Gk~~I 91 (169)
T PRK07571 26 ATMKRNQYRQDALIEVLHKAQEL---------FG---YLERDLLLYVARQLKLP-LSRVYGVATFYHLFSLKPSGEHTC 91 (169)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHH---------cC---CCCHHHHHHHHHHhCcC-HHHHHHHHHHccccCcCCCCCEEE
Confidence 44455666677777777777742 33 89999999999998866 67788999986 55676543
No 116
>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=77.99 E-value=3.4 Score=29.62 Aligned_cols=37 Identities=24% Similarity=0.458 Sum_probs=30.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||.+||++.--+.+++..|..+|.|.-+ .-+|-||
T Consensus 29 ~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~-~g~Gt~V 65 (231)
T TIGR03337 29 RDLGERFNTTRVTIREALQQLEAEGLIYRE-DRRGWFV 65 (231)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCeEEEe-CCCEEEE
Confidence 489999999999999999999999998753 2245554
No 117
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=77.98 E-value=5.5 Score=25.53 Aligned_cols=37 Identities=19% Similarity=0.222 Sum_probs=29.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF 38 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf 38 (96)
.|+|..+|++.-.+..=+..|+++|.+.=+=--||+=
T Consensus 19 ~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~ 55 (62)
T PF04703_consen 19 REIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKS 55 (62)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcc
Confidence 5899999999999999999999999986444456663
No 118
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=77.42 E-value=4.5 Score=30.45 Aligned_cols=38 Identities=26% Similarity=0.453 Sum_probs=34.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
+|+|..|++..+. +++|++.+.+|==.||.|+-|-|..
T Consensus 102 dElA~sF~l~~e~----i~qLr~~kiltVh~De~G~Ii~V~~ 139 (153)
T PRK14584 102 DELASSFALSPEL----IAQLKSGSCLTLYNDEHGHIIDVKE 139 (153)
T ss_pred HHHHHHcCCCHHH----HHHHHhCCeEEEEECCCCCEEEeec
Confidence 7999999998876 4899999999999999999998854
No 119
>PF03701 UPF0181: Uncharacterised protein family (UPF0181); InterPro: IPR005371 This family contains small proteins of about 50 amino acids of unknown function. The family includes YoaH P76260 from SWISSPROT.
Probab=77.15 E-value=1.7 Score=27.91 Aligned_cols=32 Identities=34% Similarity=0.512 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 12 TQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 12 tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|.+++||++|.++|.=+| |-+.-||+-|++.
T Consensus 13 QQ~AvE~Iq~LMaqGmSsg-------------EAI~~VA~~iRe~ 44 (51)
T PF03701_consen 13 QQQAVERIQELMAQGMSSG-------------EAIAIVAQEIREE 44 (51)
T ss_pred HHHHHHHHHHHHHhcccHH-------------HHHHHHHHHHHHH
Confidence 4789999999999998655 6677888888765
No 120
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=77.07 E-value=14 Score=24.31 Aligned_cols=46 Identities=13% Similarity=0.230 Sum_probs=34.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|+++.-+ ...++.|.+.-.-.+.|.|=|.|++++..+-.
T Consensus 4 ~eva~~~gvs~~tl----R~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~ 49 (103)
T cd01106 4 GEVAKLTGVSVRTL----HYYDEIGLLKPSRRTENGYRLYTEEDLERLQQ 49 (103)
T ss_pred HHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCceeeCHHHHHHHHH
Confidence 57999999976543 46678898865445556778899999987743
No 121
>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=77.01 E-value=4.2 Score=23.57 Aligned_cols=32 Identities=25% Similarity=0.331 Sum_probs=27.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID 33 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD 33 (96)
.+||..++++...+-.-++.|++.|-|.=-.|
T Consensus 21 ~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~ 52 (59)
T PF01047_consen 21 SELAEKLGISRSTVTRIIKRLEKKGLIERERD 52 (59)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHCCChhHHHHHHHHHHHCCCEEeccC
Confidence 48999999999999999999999999876655
No 122
>PF12514 DUF3718: Protein of unknown function (DUF3718); InterPro: IPR022193 This entry is represented by Bacteriophage Aaphi23, Orf19. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. There is a single completely conserved residue C that may be functionally important.
Probab=76.67 E-value=2 Score=27.80 Aligned_cols=32 Identities=31% Similarity=0.474 Sum_probs=24.6
Q ss_pred HHHHHHHhhchhchhhhhhhhccccceeHHHHHHhc
Q psy11008 48 SVATFIKQRGREELNSVATFIKQKGRVSVSELVENS 83 (96)
Q Consensus 48 ~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~s 83 (96)
++.+|-.+.| .+.++.|| -.|++|++||+.++
T Consensus 37 sl~~FA~~~~---A~kt~~~l-~~~~~~~~dla~~~ 68 (68)
T PF12514_consen 37 SLLRFAASYG---ANKTAEFL-AVKRVSIKDLAAAE 68 (68)
T ss_pred CHHHHHHHcC---HHHHHHHH-hcCCccHHHHhhcC
Confidence 4566766664 77788888 67999999998764
No 123
>PF13442 Cytochrome_CBB3: Cytochrome C oxidase, cbb3-type, subunit III ; PDB: 1KB0_A 2DGE_D 2CE1_A 2CE0_A 2V07_A 1W2L_A 2ZOO_A 2ZBO_G 1DVV_A 2EXV_A ....
Probab=76.58 E-value=2.2 Score=25.45 Aligned_cols=33 Identities=24% Similarity=0.532 Sum_probs=25.3
Q ss_pred HHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008 17 DRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFI 53 (96)
Q Consensus 17 ~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI 53 (96)
+.|......|. |.|-.-+. .+|++|+.+|+.||
T Consensus 35 ~~l~~~i~~g~--~~Mp~~~~--~ls~~e~~~l~~yi 67 (67)
T PF13442_consen 35 EELYNIIRNGR--GGMPPFGG--QLSDEEIEALAAYI 67 (67)
T ss_dssp HHHHHHHHHTB--TTBSCTTT--TSTHHHHHHHHHHH
T ss_pred HHHHHHHHhCc--CCCCCCCC--CCCHHHHHHHHHHC
Confidence 45555666665 56776666 89999999999997
No 124
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=76.44 E-value=11 Score=24.45 Aligned_cols=66 Identities=11% Similarity=0.171 Sum_probs=46.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.|+|..+|+++.. |.-.++.|.+.-.-++.|.+=|-|++++..+.....-+. .-+|+++..+
T Consensus 5 ~evA~~~gvs~~t----LR~ye~~Gll~p~r~~~~g~R~Ys~~dv~~l~~I~~Lr~--------------~G~sl~~i~~ 66 (88)
T cd01105 5 GEVSKLTGVSPRQ----LRYWEEKGLIKSIRSDGGGQRKYSLADVDRLLVIKELLD--------------EGFTLAAAVE 66 (88)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceecCHHHHHHHHHHHHHHH--------------CCCCHHHHHH
Confidence 5889999997654 556789999886555555777889999997766555441 3357766666
Q ss_pred hccc
Q psy11008 82 NSNQ 85 (96)
Q Consensus 82 ~sN~ 85 (96)
.-+.
T Consensus 67 ~l~~ 70 (88)
T cd01105 67 KLRR 70 (88)
T ss_pred HHHH
Confidence 5543
No 125
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.32 E-value=18 Score=25.61 Aligned_cols=61 Identities=25% Similarity=0.327 Sum_probs=43.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCC--ccEE--eeCCCc-----eEEEcHHHHHHHHHHHHhhchhchh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGA--LTGV--IDDRGK-----FIYISQEELNSVATFIKQRGREELN 62 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~--ltGV--iDDRGK-----fIyIs~eEl~~Va~fI~~rgr~~~~ 62 (96)
||||...||+..+|-.-+..|.+++. .... .|..++ |-||.-+.+..+..|=..+=++.|.
T Consensus 19 edLa~~l~i~~n~vRkiL~~L~ed~~~~~~~~~e~~~~~~~~~~~yw~i~y~~~~~vik~r~~~~~~~L~ 88 (147)
T smart00531 19 EDLAELLGIKQKQLRKILYLLYDEKLIKIDYKREKDPETKTWYRYYWYINYDTLLDVVKYKLDKMRKRLE 88 (147)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhhhcchhheeeeeCCCCceEEEEEEEecHHHHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999554 3322 454444 5568888887777775555444443
No 126
>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=75.84 E-value=1.6 Score=29.31 Aligned_cols=29 Identities=17% Similarity=0.391 Sum_probs=22.6
Q ss_pred HHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 51 TFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 51 ~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
.||.+| +.-+..++.+ |++++.++++.++
T Consensus 2 ~~~~~R----~~~I~e~l~~-~~~ti~dvA~~~g 30 (80)
T TIGR02844 2 DYIEER----VLEIGKYIVE-TKATVRETAKVFG 30 (80)
T ss_pred CcHHHH----HHHHHHHHHH-CCCCHHHHHHHhC
Confidence 366666 5667778888 9999999998775
No 127
>PF00034 Cytochrom_C: Cytochrome c; InterPro: IPR003088 Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler [] recognised four classes of cytC. Class I includes the low-spin soluble cytC of mitochondria and bacteria, with the haem-attachment site towards the N terminus, and the sixth ligand provided by a methionine residue about 40 residues further on towards the C terminus. On the basis of sequence similarity, class I cytC were further subdivided into five classes, IA to IE. Class IB includes the eukaryotic mitochondrial cytC and prokaryotic 'short' cyt c2 exemplified by Rhodopila globiformis cyt c2; class IA includes 'long' cyt c2, such as Rhodospirillum rubrum cyt c2 and Aquaspirillum itersonii cyt c-550, which have several extra loops by comparison with class IB cytC.; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding; PDB: 1YNR_B 2AI5_A 1AYG_A 3O5C_C 1YEA_A 3CXH_W 1YTC_A 1YEB_A 2YBB_Y 2B4Z_A ....
Probab=75.84 E-value=2.5 Score=24.55 Aligned_cols=17 Identities=24% Similarity=0.565 Sum_probs=15.0
Q ss_pred EEcHHHHHHHHHHHHhh
Q psy11008 40 YISQEELNSVATFIKQR 56 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~r 56 (96)
-+|++|+.+|+.||++.
T Consensus 74 ~ls~~e~~~l~ayl~sl 90 (91)
T PF00034_consen 74 ILSDEEIADLAAYLRSL 90 (91)
T ss_dssp TSSHHHHHHHHHHHHHT
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 48999999999999874
No 128
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=75.72 E-value=4 Score=29.67 Aligned_cols=49 Identities=22% Similarity=0.344 Sum_probs=40.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va~ 51 (96)
++||..||++..-|-+=+..|+++|-|.=. -.||-||- +|.+++..+-.
T Consensus 43 ~~La~~~gvSrtPVReAL~rL~~eGlv~~~-p~rG~~V~~~~~~~~~ei~~ 92 (230)
T COG1802 43 EELAEELGVSRTPVREALRRLEAEGLVEIE-PNRGAFVAPLSLAEAREIFE 92 (230)
T ss_pred HHHHHHhCCCCccHHHHHHHHHHCCCeEec-CCCCCeeCCCCHHHHHHHHH
Confidence 579999999999999999999999988754 78888874 67777766443
No 129
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=75.53 E-value=4 Score=24.21 Aligned_cols=44 Identities=18% Similarity=0.322 Sum_probs=27.9
Q ss_pred ChhhhhhhCCChHHHHHHH-HHHHHc-CCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRI-VELQKT-GALTGVIDDRGKFIYISQEELNSVATFI 53 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI-~eL~~~-g~ltGViDDRGKfIyIs~eEl~~Va~fI 53 (96)
+.|||.++|++..++|..+ +++=-. -..+- .|++++...|+...
T Consensus 6 V~elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~---------~ld~e~~~~i~~~~ 51 (54)
T PF04760_consen 6 VSELAKELGVPSKEIIKKLFKELGIMVKSINS---------SLDEEEAELIAEEF 51 (54)
T ss_dssp TTHHHHHHSSSHHHHHHHH-HHHTS---SSSS----------EETTGGGHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHHHhCCcCcCCCCC---------cCCHHHHHHHHHHh
Confidence 3689999999999999988 545221 11122 24556666666554
No 130
>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=75.13 E-value=5.3 Score=23.03 Aligned_cols=28 Identities=18% Similarity=0.375 Sum_probs=23.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||..++++...+-.-+..|++.|-++
T Consensus 19 ~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 19 SELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred hhHHHhccccchHHHHHHHHHHHCcCee
Confidence 5899999999888889999999999763
No 131
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=74.93 E-value=12 Score=25.07 Aligned_cols=46 Identities=13% Similarity=0.177 Sum_probs=36.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..||+++.- |.--++.|-|.-.--+.|.|=|-|++++..+..
T Consensus 4 ~eva~~~gvs~~t----LRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~~ 49 (123)
T cd04770 4 GELAKAAGVSPDT----IRYYERIGLLPPPQRSENGYRLYGEADLARLRF 49 (123)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCCCCCCCCccCCHHHHHHHHH
Confidence 4899999997764 457999999986555567899999999988754
No 132
>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=74.90 E-value=3.9 Score=29.73 Aligned_cols=37 Identities=14% Similarity=0.355 Sum_probs=29.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||++||++..-|.+-|++|+++|.|.=+ --+|-||
T Consensus 28 ~eLa~~~gVSR~TVR~Al~~L~~eGli~r~-~G~GTfV 64 (233)
T TIGR02404 28 HELMDQYGASRETVRKALNLLTEAGYIQKI-QGKGSIV 64 (233)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-CCceEEE
Confidence 479999999999999999999999987643 1345554
No 133
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=74.47 E-value=4.3 Score=29.63 Aligned_cols=62 Identities=19% Similarity=0.354 Sum_probs=46.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhh-----ccccceeH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFI-----KQKGRVSV 76 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~-----~~~GRVsi 76 (96)
+++-+.|+-+...+|.-+.+.|+. -| ||+++-++.||+.+.-. .-++.+||||- ++.|+-.|
T Consensus 12 ~~ii~~y~~~~~~li~~L~~vQ~~---------~G---~Ip~e~~~~iA~~l~v~-~~~V~~vatFY~~f~~~p~Gk~~I 78 (156)
T PRK05988 12 AAIIAEHKHLEGALLPILHAIQDE---------FG---YVPEDAVPVIAEALNLS-RAEVHGVITFYHDFRTHPPGRHVL 78 (156)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHH---------cC---CCCHHHHHHHHHHhCCC-HHHHHHHHHHhhccCCCCCCCEEE
Confidence 455667777777888888888853 33 89999999999998765 67788899984 45676543
No 134
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=74.25 E-value=14 Score=24.27 Aligned_cols=46 Identities=17% Similarity=0.323 Sum_probs=36.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|+++. -|.-.++.|-|.....+.|.|=|-|++++..+..
T Consensus 4 ~eva~~~gvs~~----tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~ 49 (97)
T cd04782 4 GEFAKLCGISKQ----TLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDI 49 (97)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHH
Confidence 589999999764 4566788999988766667788889999887654
No 135
>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=74.10 E-value=3.7 Score=24.55 Aligned_cols=39 Identities=18% Similarity=0.320 Sum_probs=26.9
Q ss_pred hhhhhhhCCChHHH-HHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSV-IDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~v-I~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
+++...||.+-.+. -+.|+.|++.|-+ .-.|..|++|++
T Consensus 24 ~~~~~~~g~~~~~~~~~~l~~l~~~Gll----~~~~~~l~lT~~ 63 (66)
T PF06969_consen 24 SEFEQRFGIDFAEEFQKELEELQEDGLL----EIDGGRLRLTEK 63 (66)
T ss_dssp HHHHHHTT--THHH-HHHHHHHHHTTSE----EE-SSEEEE-TT
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHCCCE----EEeCCEEEECcc
Confidence 57788999987666 5669999999655 556678888875
No 136
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=73.95 E-value=16 Score=24.90 Aligned_cols=45 Identities=18% Similarity=0.237 Sum_probs=35.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.|+|..+|+++.- |.-.++.|-|.-.-.+.|.|-|-+++++..+.
T Consensus 4 ~e~a~~~gvs~~t----lR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~ 48 (126)
T cd04783 4 GELAKAAGVNVET----IRYYQRRGLLPEPPRPEGGYRRYPEETVTRLR 48 (126)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH
Confidence 5899999997764 37789999998444456779999999998864
No 137
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=73.94 E-value=10 Score=23.43 Aligned_cols=43 Identities=12% Similarity=0.312 Sum_probs=36.1
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEeeC-----CCceEEEcHHHHHHHH
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVIDD-----RGKFIYISQEELNSVA 50 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViDD-----RGKfIyIs~eEl~~Va 50 (96)
+.++...+-..+..|++.|.|+....+ +-|+-.||+.-.+.+.
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 578888899999999999999999998 4677889988766553
No 138
>PRK14585 pgaD putative PGA biosynthesis protein; Provisional
Probab=73.93 E-value=4 Score=30.53 Aligned_cols=41 Identities=15% Similarity=0.254 Sum_probs=35.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEEL 46 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl 46 (96)
+|||+.|++.++ .+++|++.+.+|==.||.|.-+.+..|.+
T Consensus 93 ~eLA~Sf~is~e----l~~qL~~~~~lTvh~D~~G~i~~v~~~~~ 133 (137)
T PRK14585 93 QEYAESLAIPDE----LYQQLQKSHRMSVHFTSQGQIKMVVSEKA 133 (137)
T ss_pred HHHHHHcCCCHH----HHHHHhcCCeEEEEEcCCCCchhhhHHHH
Confidence 689999999876 47899999999999999999998877643
No 139
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=73.71 E-value=7.8 Score=28.93 Aligned_cols=54 Identities=28% Similarity=0.426 Sum_probs=41.3
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH-------HHHHHHHHHHhhchh
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE-------ELNSVATFIKQRGRE 59 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e-------El~~Va~fI~~rgr~ 59 (96)
+||.+||++.--|..-|.+|+++|-|. --+||=.||++. ++.++.+-+..+|.+
T Consensus 36 eLa~~f~VSR~TvRkAL~~L~~eGli~---r~~G~GtfV~~~~~~~~~~~~~~f~e~~~~~g~~ 96 (236)
T COG2188 36 ELAEQFGVSRMTVRKALDELVEEGLIV---RRQGKGTFVASPKEQSPLLELTSFSEELKSQGLE 96 (236)
T ss_pred HHHHHHCCcHHHHHHHHHHHHHCCcEE---EEecCeeEEcCccccccccccccHHHHHHhCCCC
Confidence 799999999999999999999999875 345555555543 566677777777543
No 140
>PF07789 DUF1627: Protein of unknown function (DUF1627); InterPro: IPR012432 This is a group of sequences found in hypothetical proteins predicted to be expressed in a number of bacterial species. The region in question is approximately 150 amino acid residues long.
Probab=73.62 E-value=6.1 Score=30.20 Aligned_cols=42 Identities=33% Similarity=0.470 Sum_probs=36.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
|+||..||..|--|-.-+.-+-..|+|-=|- -.|||=|-=+.
T Consensus 10 eELA~~FGvttRkvaStLa~~ta~Grl~Rv~-q~gkfRy~iPg 51 (155)
T PF07789_consen 10 EELAGKFGVTTRKVASTLAMVTATGRLIRVN-QNGKFRYCIPG 51 (155)
T ss_pred HHHHHHhCcchhhhHHHHHHHHhcceeEEec-CCCceEEeCCC
Confidence 7999999999999999999999999998764 57999996543
No 141
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=73.52 E-value=7.3 Score=26.96 Aligned_cols=37 Identities=16% Similarity=0.289 Sum_probs=26.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
++||...|++.+.+-.=+++|+++|.|. -.|+.|.|.
T Consensus 172 ~~lA~~lG~tr~tvsR~l~~l~~~gii~----~~~~~i~i~ 208 (211)
T PRK11753 172 QEIGRIVGCSREMVGRVLKMLEDQGLIS----AHGKTIVVY 208 (211)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEE----ecCCEEEEe
Confidence 6899999996665555588999998664 334445553
No 142
>PRK03837 transcriptional regulator NanR; Provisional
Probab=73.52 E-value=7.3 Score=28.08 Aligned_cols=30 Identities=20% Similarity=0.361 Sum_probs=27.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV 31 (96)
.+||..||++..-|.+-++.|+.+|-++-.
T Consensus 41 ~~Lae~~gVSRt~VREAL~~L~~eGlv~~~ 70 (241)
T PRK03837 41 RELMAFFGVGRPAVREALQALKRKGLVQIS 70 (241)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 489999999999999999999999998763
No 143
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=73.33 E-value=16 Score=23.38 Aligned_cols=50 Identities=18% Similarity=0.296 Sum_probs=35.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|+|..+|++.+- |...++.|.|....+..|. -+.|++++..+.....-+
T Consensus 4 ~eva~~~gi~~~t----lr~~~~~Gll~~~~~~~g~-r~y~~~dv~~l~~i~~l~ 53 (100)
T cd00592 4 GEVAKLLGVSVRT----LRYYEEKGLLPPERSENGY-RLYSEEDLERLRLIRRLR 53 (100)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCcCCCcCCCCC-cccCHHHHHHHHHHHHHH
Confidence 5789999996543 4456778999866555554 467999999776655554
No 144
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=73.09 E-value=20 Score=23.75 Aligned_cols=48 Identities=8% Similarity=0.268 Sum_probs=35.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.|+|..+|+++.-+ .-.++.|-|.= ..+.|.|=|.|++.+..+..-..
T Consensus 5 ~eva~~~gvs~~tL----R~ye~~Gll~~-~r~~~g~R~Y~~~dl~~l~~I~~ 52 (102)
T cd04775 5 GQMSRKFGVSRSTL----LYYESIGLIPS-ARSEANYRLYSEADLSRLEKIVF 52 (102)
T ss_pred HHHHHHHCcCHHHH----HHHHHCCCCCC-CCCCCCCeeeCHHHHHHHHHHHH
Confidence 58999999976544 77888898843 34556788889999987654433
No 145
>PF07160 DUF1395: Protein of unknown function (DUF1395); InterPro: IPR009829 This family consists of several hypothetical eukaryotic proteins of around 250 residues in length. The function of this family is unknown.; PDB: 4AJ5_G.
Probab=72.86 E-value=1.1 Score=34.79 Aligned_cols=16 Identities=25% Similarity=0.723 Sum_probs=0.0
Q ss_pred EEEcHHHHHHHHHHHH
Q psy11008 39 IYISQEELNSVATFIK 54 (96)
Q Consensus 39 IyIs~eEl~~Va~fI~ 54 (96)
=|||.+|+++|-+|++
T Consensus 130 ~~IT~eEF~sIPkYMr 145 (243)
T PF07160_consen 130 WFITVEEFDSIPKYMR 145 (243)
T ss_dssp ----------------
T ss_pred ccccHHHHhcchHHHH
Confidence 3899999999999985
No 146
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=72.85 E-value=3.5 Score=29.52 Aligned_cols=22 Identities=41% Similarity=0.593 Sum_probs=20.7
Q ss_pred CceEEEcHHHHHHHHHHHHhhc
Q psy11008 36 GKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~rg 57 (96)
++|-++|+|+++=|-.||+.||
T Consensus 29 ~~~~~L~~E~~~Fi~~Fi~~rG 50 (113)
T PF09862_consen 29 PWFARLSPEQLEFIKLFIKNRG 50 (113)
T ss_pred chhhcCCHHHHHHHHHHHHhcC
Confidence 6889999999999999999996
No 147
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=72.62 E-value=14 Score=29.01 Aligned_cols=49 Identities=16% Similarity=0.196 Sum_probs=42.2
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
++.+.||++...+---+..|+++|.|+..-..|-+|-++|++-...+..
T Consensus 25 ~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~ 73 (280)
T TIGR02277 25 EFLAGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAA 73 (280)
T ss_pred HHHHhcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHH
Confidence 5778999999999999999999999999877777999999987655444
No 148
>PF13994 PgaD: PgaD-like protein
Probab=72.49 E-value=5.1 Score=28.27 Aligned_cols=34 Identities=32% Similarity=0.541 Sum_probs=29.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
+|+|+.|+++.+ -+++|++...++==.||.|+-|
T Consensus 104 ~elA~~f~l~~~----~l~~lr~~k~~~V~~d~~G~I~ 137 (138)
T PF13994_consen 104 EELARSFGLSPE----QLQQLRQAKVLTVHHDDHGRII 137 (138)
T ss_pred HHHHHHcCCCHH----HHHHHHhCCeEEEEeCCCCCcC
Confidence 799999999865 4789999999999999999754
No 149
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=72.31 E-value=14 Score=30.28 Aligned_cols=49 Identities=22% Similarity=0.333 Sum_probs=38.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc-eEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK-FIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK-fIyIs~eEl~~Va~fI~ 54 (96)
.|+|.+.|++.|-|.+-|++|-++|- ++.+|+ +--||.+-.+.+-..+.
T Consensus 29 ~eIA~~lgiT~QaVsehiK~Lv~eG~----i~~~gR~~Y~iTkkG~e~l~~~~~ 78 (260)
T COG1497 29 KEIAKKLGITLQAVSEHIKELVKEGL----IEKEGRGEYEITKKGAEWLLEQLS 78 (260)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHhccc----eeecCCeeEEEehhHHHHHHHHHH
Confidence 48999999999999999999999864 566666 55588887665544443
No 150
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=71.80 E-value=5.1 Score=29.52 Aligned_cols=37 Identities=16% Similarity=0.317 Sum_probs=30.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||.+||++..-|.+-|++|+.+|.|.-+- -+|-||
T Consensus 33 ~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~-G~GtfV 69 (240)
T PRK09764 33 SALQTEFGVSRVTVRQALRQLVEQQILESIQ-GSGTYV 69 (240)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEec-CceeEE
Confidence 4799999999999999999999999987442 245555
No 151
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=71.69 E-value=18 Score=26.21 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=34.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
-+||.+.++..--|-.--++|+.+|-+. -.||+-.|||+.
T Consensus 39 RelA~~~~VNpnTv~raY~eLE~eG~i~---t~rg~G~fV~~~ 78 (125)
T COG1725 39 RELAKDLGVNPNTVQRAYQELEREGIVE---TKRGKGTFVTED 78 (125)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEE---EecCeeEEEcCC
Confidence 4799999998887778899999999865 579999999966
No 152
>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=71.59 E-value=5.2 Score=29.11 Aligned_cols=37 Identities=24% Similarity=0.388 Sum_probs=29.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
.+||..||++..-|.+-|..|+++|.|.-+ --+|-|+
T Consensus 29 ~eLa~~~~VSR~TVR~Al~~L~~eGli~r~-~G~GtfV 65 (230)
T TIGR02018 29 HELVAQYGCSRMTVNRALRELTDAGLLERR-QGVGTFV 65 (230)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe-cCCEEEE
Confidence 479999999999999999999999987543 2244454
No 153
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=71.52 E-value=18 Score=23.93 Aligned_cols=47 Identities=13% Similarity=0.276 Sum_probs=34.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.++|..+|+++. -|.--++.|-|.-. ++.|.+.| ++++++.+ .||+.
T Consensus 4 ge~a~~~gvs~~----tlRyYe~~GLl~p~-~~~g~r~Y-~~~~~~~l-~~I~~ 50 (107)
T cd04777 4 GKFAKKNNITID----TVRHYIDLGLLIPE-KKGGQYFF-DEKCQDDL-EFILE 50 (107)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCcCCc-cCCCcccc-CHHHHHHH-HHHHH
Confidence 578999999764 56788899998763 56787877 88888544 45543
No 154
>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=71.49 E-value=9.8 Score=27.37 Aligned_cols=38 Identities=24% Similarity=0.385 Sum_probs=31.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
.+||++||++..-|.+-|..|+++|.|.-. +||=.||+
T Consensus 36 ~eLa~~~~VSR~TvR~Al~~L~~eGli~r~---~G~GtfV~ 73 (238)
T TIGR02325 36 MQLAERFGVNRHTVRRAIAALVERGLLRAE---QGRGTFVA 73 (238)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe---cCCEEEEC
Confidence 489999999999999999999999988654 45544444
No 155
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=71.44 E-value=13 Score=34.46 Aligned_cols=67 Identities=22% Similarity=0.313 Sum_probs=54.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
-|||.-.|+....|-.+++.+.+.+ -|++=-.|- -||+.=++.||.-|+.+ +++.|.|||+||+.
T Consensus 78 vdLa~~LnVD~~hiEr~~~~iv~~d--~~~~l~~Ge--Lit~~Yld~iaeEIne~-----------LqE~G~isI~eLa~ 142 (803)
T PLN03083 78 VDLADTIGVDLYHVERQAQQVVSDD--PGLMLVQGE--IISQSYWDSIAEEINER-----------LQECSQIALAELAR 142 (803)
T ss_pred HHHhhhcCCCHHHHHHHHHHHhcCC--CceEEecCE--ecchHHHHHHHHHHHHH-----------HHHcCcChHHHHHH
Confidence 4788889998888878888887776 344444553 58899999999999988 88899999999987
Q ss_pred hc
Q psy11008 82 NS 83 (96)
Q Consensus 82 ~s 83 (96)
.=
T Consensus 143 ~~ 144 (803)
T PLN03083 143 QL 144 (803)
T ss_pred hc
Confidence 53
No 156
>KOG0686|consensus
Probab=71.41 E-value=6 Score=34.66 Aligned_cols=43 Identities=23% Similarity=0.448 Sum_probs=39.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
.-+|..|+++....=+++.+|..+|.|.|-||---|-+|+-++
T Consensus 369 ~~mA~af~~sv~~le~~l~~LI~~~~i~~rIDs~~ki~~~~~~ 411 (466)
T KOG0686|consen 369 SKMAEAFNTSVAILESELLELILEGKISGRIDSHNKILYARDA 411 (466)
T ss_pred HHHHHHhcccHHHHHHHHHHHHHccchheeeccccceeeeccc
Confidence 3478999999999999999999999999999999999999665
No 157
>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=70.87 E-value=5.6 Score=23.25 Aligned_cols=28 Identities=14% Similarity=0.251 Sum_probs=24.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||...|++...+-.-++.|++.|-+.
T Consensus 22 ~eia~~~gl~~stv~r~L~tL~~~g~v~ 49 (52)
T PF09339_consen 22 SEIARALGLPKSTVHRLLQTLVEEGYVE 49 (52)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcCee
Confidence 5899999999999999999999999763
No 158
>KOG1497|consensus
Probab=70.79 E-value=7.2 Score=33.58 Aligned_cols=70 Identities=21% Similarity=0.314 Sum_probs=51.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH-HHHHHHHHHHHhhchhchhhhhhhhcccc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ-EELNSVATFIKQRGREELNSVATFIKQKG 72 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~-eEl~~Va~fI~~rgr~~~~~~~~~~~~~G 72 (96)
++|+++|++++..+=.-.-++.-+|++.|-||----+|+.-+ |||..--+-|..- -+.+|++++-|.++|
T Consensus 321 ~~Lg~ll~i~~ekaekiaa~MI~qeRmng~IDQ~egiihFe~~e~l~~wdkqi~sl-~~qvNki~~~i~~~~ 391 (399)
T KOG1497|consen 321 EELGALLKIDAEKAEKIAAQMITQERMNGSIDQIEGIIHFEDREELPQWDKQIQSL-CNQVNKILDKISHYG 391 (399)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhHHHhccchHhhcceEeecchhhhhhhhHHHHHH-HHHHHHHHHHHHHhC
Confidence 689999999998887777889999999999997666666544 6664444444422 234567777777666
No 159
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=70.75 E-value=20 Score=26.16 Aligned_cols=47 Identities=21% Similarity=0.441 Sum_probs=34.0
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEee--CCCc--eEE--EcHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVID--DRGK--FIY--ISQEELN 47 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DRGK--fIy--Is~eEl~ 47 (96)
.+|||...+..-..|=.-+|.|...|.+.=.-+ +.|. ||| |..+|+.
T Consensus 45 vdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k 97 (126)
T COG3355 45 VDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIK 97 (126)
T ss_pred HHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHH
Confidence 379999999977777677999999998865544 5665 455 4455544
No 160
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=70.75 E-value=21 Score=23.52 Aligned_cols=49 Identities=14% Similarity=0.261 Sum_probs=37.6
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEe--eC---CCceEEEcHHHHHHHHHHHHhh
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVI--DD---RGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGVi--DD---RGKfIyIs~eEl~~Va~fI~~r 56 (96)
+.++...+-.-+..|++.|-|+... ++ |=|+..||+.--..++......
T Consensus 35 ~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~ 88 (100)
T TIGR03433 35 LQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESW 88 (100)
T ss_pred cccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 4677777778899999999999853 22 3489999999877777766554
No 161
>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=70.62 E-value=10 Score=24.96 Aligned_cols=50 Identities=28% Similarity=0.426 Sum_probs=29.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE--ee-CCCc---eEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV--ID-DRGK---FIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV--iD-DRGK---fIyIs~eEl~~Va~ 51 (96)
||||...+|+..++-.-+..|.++|-+.-. -| ++|. |-||..+.+..+-.
T Consensus 31 e~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~d~~~~~~~~yw~i~~~~~~~~ik 86 (105)
T PF02002_consen 31 EDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRKDDERGWTRYYWYIDYDQIIDVIK 86 (105)
T ss_dssp HHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE--------EEEEE-THHHH-----
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEEcCCCcEEEEEEEEcHHHHHHHHH
Confidence 689999999999999999999999998554 23 5565 45677766544433
No 162
>PRK14999 histidine utilization repressor; Provisional
Probab=70.51 E-value=5.5 Score=29.24 Aligned_cols=53 Identities=23% Similarity=0.325 Sum_probs=36.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH-------HHHHHHHHHHhhc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE-------ELNSVATFIKQRG 57 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e-------El~~Va~fI~~rg 57 (96)
.+||.+||++..-|.+-|..|+.+|.|.= -+||=.||.+. .+.+....+..+|
T Consensus 40 ~eLa~~~gVSR~TVR~Al~~L~~eGli~r---~~GkGTfV~~~~~~~~~~~~~~~~~~~~~~g 99 (241)
T PRK14999 40 AELVAQYGFSRMTINRALRELTDEGWLVR---LQGVGTFVAEPKGQSALFEVRSIAEEIAARR 99 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE---ecCcEEEECCCCccccHHHHHHHHHHHHHcC
Confidence 37999999999999999999999998743 34444444332 2344444455554
No 163
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=70.42 E-value=5.6 Score=30.23 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=26.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTG 30 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltG 30 (96)
.|||..|+++..-+...|++|++.|.+.-
T Consensus 23 ~ela~~l~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 23 EKVIERLGISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 68999999988888888999999999864
No 164
>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=70.41 E-value=13 Score=26.22 Aligned_cols=39 Identities=18% Similarity=0.268 Sum_probs=35.5
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI 41 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI 41 (96)
.||..|+++-.-+-.-|++|++.|.|-=|.-.++-.||.
T Consensus 64 ~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYt 102 (105)
T PF03297_consen 64 VLSERLKINGSLARKALRELESKGLIKPVSKHHRQRIYT 102 (105)
T ss_dssp HHHHHHCCSCHHHHHHHHHHHHCCSSEEEECCTTCEEEE
T ss_pred HHHHhHhhHHHHHHHHHHHHHHCCCEEEEeccCCeEEEe
Confidence 478889998888888899999999999999999999996
No 165
>PRK13697 cytochrome c6; Provisional
Probab=70.38 E-value=3.7 Score=26.68 Aligned_cols=16 Identities=19% Similarity=0.607 Sum_probs=15.2
Q ss_pred EcHHHHHHHHHHHHhh
Q psy11008 41 ISQEELNSVATFIKQR 56 (96)
Q Consensus 41 Is~eEl~~Va~fI~~r 56 (96)
+|++|+..++.||.+.
T Consensus 90 ls~~di~~l~~Yi~~~ 105 (111)
T PRK13697 90 LSPDQIEDVAAYVLEQ 105 (111)
T ss_pred CCHHHHHHHHHHHHHH
Confidence 7999999999999987
No 166
>CHL00088 apcB allophycocyanin beta subunit
Probab=70.20 E-value=2 Score=31.85 Aligned_cols=22 Identities=14% Similarity=0.540 Sum_probs=19.2
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|++|+| +|..||+.+..|+++-
T Consensus 13 D~~gRy--ls~~eL~~l~~~~~~~ 34 (161)
T CHL00088 13 DVQGKY--LDDNSVEKLRSYFQTG 34 (161)
T ss_pred HhcCCC--CCHHHHHHHHHHHHHH
Confidence 677885 7999999999999886
No 167
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=69.79 E-value=14 Score=32.25 Aligned_cols=73 Identities=19% Similarity=0.236 Sum_probs=46.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
++||...|++.++++.-+..|++.|.++ +-...=++..+|+|-...+.. |--|.. +..+++.+|.++++||..
T Consensus 22 ~~la~~~g~~~~~v~~~~~~L~~kg~v~-~~~~~~~~~~LT~eG~~~l~~-----G~PE~r-l~~~l~~~~~~~~~eL~~ 94 (492)
T PLN02853 22 GQFAASHGLDHNEVVGVIKSLHGFRYVD-AQDIKRETWVLTEEGKKYAAE-----GSPEVQ-LFAAVPAEGSISKDELQK 94 (492)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHhCCCEE-EEEEEEEEEEECHHHHHHHHc-----CCHHHH-HHHHHhhcCCccHHHHHH
Confidence 5799999999999999999999998554 334444566678775443321 211111 233444445556666553
No 168
>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=69.42 E-value=10 Score=25.12 Aligned_cols=53 Identities=13% Similarity=0.212 Sum_probs=38.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
++||..++++...+-+-++.|.+.|-|...-...|.|..-.+-|--.++.-++
T Consensus 29 ~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~itl~~I~~ 81 (132)
T TIGR00738 29 KEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEITVGDVVR 81 (132)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHCCHHHHHH
Confidence 68999999999999999999999999876555666666544334333444444
No 169
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=69.41 E-value=28 Score=22.82 Aligned_cols=46 Identities=11% Similarity=0.190 Sum_probs=35.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|+++. -|.--++.|-|.-...+.|.|=|.|++.+..+..
T Consensus 4 ~eva~~~gvs~~----tlR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~ 49 (96)
T cd04788 4 GELARRTGLSVR----TLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQ 49 (96)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHH
Confidence 589999999764 4567788999987666667777789999987654
No 170
>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=68.69 E-value=14 Score=31.68 Aligned_cols=58 Identities=12% Similarity=0.251 Sum_probs=46.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
+|++..++++...+.+.+..|..+|.++-+.+| +|.+ +.+.+++... |.+|++|+-+
T Consensus 492 ~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~~----~~~~----~~~~~~~~~~---------------~~~~~~~~r~ 548 (581)
T TIGR00475 492 REFAEEVNGDEKVMLKRVRKAGHRGGETLIVKD----RLLK----KYINELKEEG---------------GTFNVQQARD 548 (581)
T ss_pred HHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeCC----eEHH----HHHHHHHhcC---------------CcCcHHHHHH
Confidence 689999999988889999999999999999876 3555 6666666555 8999988765
Q ss_pred h
Q psy11008 82 N 82 (96)
Q Consensus 82 ~ 82 (96)
.
T Consensus 549 ~ 549 (581)
T TIGR00475 549 K 549 (581)
T ss_pred H
Confidence 4
No 171
>KOG2587|consensus
Probab=68.52 E-value=23 Score=31.69 Aligned_cols=67 Identities=22% Similarity=0.391 Sum_probs=50.9
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCccEEeeCCC---------------------ceEEEcHHHHHHHHHHHHhhchhchh
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALTGVIDDRG---------------------KFIYISQEELNSVATFIKQRGREELN 62 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~ltGViDDRG---------------------KfIyIs~eEl~~Va~fI~~rgr~~~~ 62 (96)
++..=||+...|-+-+..|...+.++=+.+.++ ||+||..++++.-|.-|-+.
T Consensus 40 ~~~~t~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~ei~hilry~r~~~i~~~~~~q~~~sIv~~------ 113 (551)
T KOG2587|consen 40 IAKDTGISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCSEILHILRYPRYIYITKTLYSQTAESIVEE------ 113 (551)
T ss_pred HHhhcCCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhhHHHHHHhcccceeeHHHHhhhHHHHHHHH------
Confidence 455667888888888999999999988888766 89999999997666554433
Q ss_pred hhhhhhccccceeHHHHHH
Q psy11008 63 SVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 63 ~~~~~~~~~GRVsi~eL~~ 81 (96)
+-..||.+++|..+
T Consensus 114 -----Lls~GrLTv~e~i~ 127 (551)
T KOG2587|consen 114 -----LLSNGRLTVSEVIK 127 (551)
T ss_pred -----HHhcCceeHHHHHH
Confidence 22338888888764
No 172
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=68.44 E-value=12 Score=27.48 Aligned_cols=39 Identities=18% Similarity=0.365 Sum_probs=31.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.+||+.||++.--|..-|.+|+++|.|.=. +||=-||++
T Consensus 37 ~eLa~~~~VSR~TvR~Al~~L~~eGli~r~---~G~GTfV~~ 75 (241)
T PRK11402 37 NELCTQYNVSRITIRKAISDLVADGVLIRW---QGKGTFVQS 75 (241)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEEe---cCceeEECC
Confidence 479999999999999999999999998743 555445544
No 173
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=68.38 E-value=7 Score=26.92 Aligned_cols=36 Identities=28% Similarity=0.366 Sum_probs=29.6
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
+|..++++-++|.+.+.+|++.|-|.=|- |+.|.=|
T Consensus 27 ia~~l~~~~~~v~~~l~~Le~~GLler~~---g~~iK~~ 62 (92)
T PF10007_consen 27 IARRLKIPLEEVREALEKLEEMGLLERVE---GKTIKRS 62 (92)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeEEec---Ccccchh
Confidence 68899999999999999999999887653 6655443
No 174
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=67.91 E-value=17 Score=28.82 Aligned_cols=88 Identities=20% Similarity=0.219 Sum_probs=61.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchh-----------chhhhhhhhcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGRE-----------ELNSVATFIKQ 70 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~-----------~~~~~~~~~~~ 70 (96)
.++|..+|+++. . |.-.+++|.+.++-.+.|.+-+.|++++..+...+..++++ +--.|.++.-+
T Consensus 37 ~eva~~~gv~~~-t---lr~~e~~~~~~~~~r~~~g~r~yt~~di~~l~~~~~~~~~~~~~~~~~r~~g~~~~vI~v~n~ 112 (387)
T TIGR03453 37 GEVAKLLGVSDS-Y---LRQLSLEGKGPEPETLSNGRRSYTLEQINELRRHLAQRGREARRYLPHRRGGEHLQVIAVTNF 112 (387)
T ss_pred HHHHHHHCcCHH-H---HHHHHHcCCCCCCCcCCCCceeeCHHHHHHHHHHHHhccccccccCCCcCCCCCceEEEEEcc
Confidence 478889998543 3 34489999988887777778889999999999888764222 12247788889
Q ss_pred ccceeHHH--------HHHhccc--ceeccccc
Q psy11008 71 KGRVSVSE--------LVENSNQ--LVTLIPDQ 93 (96)
Q Consensus 71 ~GRVsi~e--------L~~~sN~--lI~L~p~~ 93 (96)
||=|..+- |++.--+ ||+++|..
T Consensus 113 KGGvGKTT~a~nLA~~La~~G~rVLlID~DpQ~ 145 (387)
T TIGR03453 113 KGGSGKTTTAAHLAQYLALRGYRVLAIDLDPQA 145 (387)
T ss_pred CCCcCHHHHHHHHHHHHHhcCCCEEEEecCCCC
Confidence 99885543 3332222 78888754
No 175
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=67.73 E-value=6.2 Score=25.40 Aligned_cols=31 Identities=13% Similarity=0.362 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcccceeccc
Q psy11008 45 ELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVTLIP 91 (96)
Q Consensus 45 El~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~lI~L~p 91 (96)
.|..+.+||++|+ .-+|++|+.+.+| +++.+
T Consensus 6 ql~~~VeymK~r~--------------~Plt~~eI~d~l~--~d~~~ 36 (65)
T PF02186_consen 6 QLAKAVEYMKKRD--------------HPLTLEEILDYLS--LDIGK 36 (65)
T ss_dssp HHHHHHHHHHHH---------------S-B-HHHHHHHHT--SSS-H
T ss_pred HHHHHHHHHHhcC--------------CCcCHHHHHHHHc--CCCCH
Confidence 4667889999996 8889999999998 55543
No 176
>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=67.14 E-value=34 Score=22.74 Aligned_cols=78 Identities=22% Similarity=0.196 Sum_probs=46.0
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE---cHHHHHH--HHHHHHhhch-hchhhhhhhhccccceeH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI---SQEELNS--VATFIKQRGR-EELNSVATFIKQKGRVSV 76 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI---s~eEl~~--Va~fI~~rgr-~~~~~~~~~~~~~GRVsi 76 (96)
.|+...+.+...|.--+..|.+.|.|+=--+ ...|+|- |++|+.+ +-+|+..--. .--+-++.|++.. .+|-
T Consensus 26 ~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~-gr~~~Y~p~is~~e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~-~ls~ 103 (115)
T PF03965_consen 26 ALPEERSWAYSTVQTLLNRLVEKGFLTREKI-GRAYVYSPLISREEYLAQELRQFLDRLFDGSIPQLVAALVESE-ELSP 103 (115)
T ss_dssp HHCTTSS--HHHHHHHHHHHHHTTSEEEEEE-TTCEEEEESSSHHHHHHHHHHHHHHHHSTTHHHHHHHHHHHCT--S-H
T ss_pred HHHhccccchhHHHHHHHHHHhCCceeEeec-CCceEEEeCCcHHHHHHHHHHHHHHHHhCCCHHHHHHHHHhcC-CCCH
Confidence 3445556777778888999999999987655 4577774 6777543 3334443221 2233455666655 8888
Q ss_pred HHHHHh
Q psy11008 77 SELVEN 82 (96)
Q Consensus 77 ~eL~~~ 82 (96)
.|+.+.
T Consensus 104 ~el~~L 109 (115)
T PF03965_consen 104 EELEEL 109 (115)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 777653
No 177
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=66.89 E-value=22 Score=23.69 Aligned_cols=47 Identities=21% Similarity=0.306 Sum_probs=37.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeC-CCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDD-RGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDD-RGKfIyIs~eEl~~Va~f 52 (96)
.|+|..+|+++. -|.-.++.|.|...-.+ .+.|=+-+++++..+...
T Consensus 4 ~eva~~~gis~~----tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~~I 51 (108)
T cd01107 4 GEFAKLSNLSIK----ALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLNRI 51 (108)
T ss_pred HHHHHHHCcCHH----HHHHHHHcCCCCCCcCCCCCCccccCHHHHHHHHHH
Confidence 589999999765 46778889999887644 578888899999988533
No 178
>PRK12423 LexA repressor; Provisional
Probab=66.53 E-value=7.8 Score=28.45 Aligned_cols=28 Identities=14% Similarity=0.326 Sum_probs=23.8
Q ss_pred hhhhhhhCC-ChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRM-KTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~l-ktq~vI~RI~eL~~~g~lt 29 (96)
.|||.+||+ ++..+-+.++.|++.|.|+
T Consensus 29 ~eia~~~g~~s~~~v~~~l~~L~~~G~l~ 57 (202)
T PRK12423 29 AEIAQAFGFASRSVARKHVQALAEAGLIE 57 (202)
T ss_pred HHHHHHhCCCChHHHHHHHHHHHHCCCEE
Confidence 589999996 5666679999999999886
No 179
>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=66.19 E-value=9 Score=23.17 Aligned_cols=21 Identities=43% Similarity=0.681 Sum_probs=15.1
Q ss_pred hhhhhccccceeHHHHHHhcc
Q psy11008 64 VATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 64 ~~~~~~~~GRVsi~eL~~~sN 84 (96)
+..+++++|.+|++||++.-|
T Consensus 5 Il~~l~~~~~~s~~ela~~~~ 25 (57)
T PF08220_consen 5 ILELLKEKGKVSVKELAEEFG 25 (57)
T ss_pred HHHHHHHcCCEEHHHHHHHHC
Confidence 344555559999999998643
No 180
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=66.13 E-value=11 Score=29.66 Aligned_cols=38 Identities=18% Similarity=0.246 Sum_probs=32.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY 40 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy 40 (96)
.+||.+|+++...|.+-+.+|+++|-|.. .--+|-||.
T Consensus 33 r~la~~~~vsr~tv~~a~~~L~~~g~i~~-~~~~G~~v~ 70 (431)
T PRK15481 33 RELASELGVNRNTVAAAYKRLVTAGLAQS-QGRNGTVIR 70 (431)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE-eCCCceEEc
Confidence 37999999999999999999999998875 335677764
No 181
>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=65.72 E-value=7.2 Score=24.36 Aligned_cols=24 Identities=17% Similarity=0.382 Sum_probs=20.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQK 24 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~ 24 (96)
++|||.++|++.+-+-.+|..-++
T Consensus 26 l~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 26 LEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Confidence 479999999999999999876543
No 182
>PF14502 HTH_41: Helix-turn-helix domain
Probab=65.67 E-value=7.5 Score=24.48 Aligned_cols=28 Identities=14% Similarity=0.349 Sum_probs=25.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
+|+|.+|++..--+=+-|+.|++.|++.
T Consensus 10 ~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 10 SEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred HHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 6899999999998889999999999985
No 183
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=65.37 E-value=6.9 Score=29.90 Aligned_cols=29 Identities=17% Similarity=0.348 Sum_probs=24.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTG 30 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltG 30 (96)
+|||..|+++..-+..-+.+|+++|.|.-
T Consensus 23 ~ela~~l~vS~~TiRRdL~~Le~~g~l~r 51 (252)
T PRK10906 23 EELVEHFSVSPQTIRRDLNDLAEQNKILR 51 (252)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 68999999976655555999999999864
No 184
>TIGR00683 nanA N-acetylneuraminate lyase. N-acetylneuraminate lyase is also known as N-acetylneuraminic acid aldolase, sialic acid aldolase, or sialate lyase. It is an intracellular enzyme. The structure of this homotetrameric enzyme related to dihydrodipicolinate synthase is known. In Clostridium tertium, the enzyme appears to be in an operon with a secreted sialidase that releases sialic acid from host sialoglycoconjugates. In several E. coli strains, however, this enzyme is responsible for N-acetyl-D-neuraminic acid synthesis for capsule production by condensing N-acetyl-D-mannosamine and pyruvate.
Probab=65.25 E-value=20 Score=27.68 Aligned_cols=49 Identities=14% Similarity=0.142 Sum_probs=40.6
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEee--CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVID--DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
..+..+....-|+.|.+.|.+.|++= .-|-|-++|.||...+.+...+.
T Consensus 16 g~iD~~~~~~~i~~~i~~G~v~gi~~~GstGE~~~Lt~eEr~~~~~~~~~~ 66 (290)
T TIGR00683 16 GTINEKGLRQIIRHNIDKMKVDGLYVGGSTGENFMLSTEEKKEIFRIAKDE 66 (290)
T ss_pred CCcCHHHHHHHHHHHHhCCCcCEEEECCcccccccCCHHHHHHHHHHHHHH
Confidence 45667777788888999888999754 78999999999999998877665
No 185
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=64.87 E-value=20 Score=23.76 Aligned_cols=50 Identities=10% Similarity=0.185 Sum_probs=38.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.|+|..+|+++.- |.-.++.|.|..+-.+.+-|=+.|++++..+ .||+.-
T Consensus 4 ~e~A~~~gvs~~t----lR~Ye~~Gll~~~~r~~~g~R~Y~~~~v~~l-~~I~~l 53 (99)
T cd04772 4 VDLARAIGLSPQT----VRNYESLGLIPPAERTANGYRIYTDKHIAAL-RAYRAL 53 (99)
T ss_pred HHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCCeecCHHHHHHH-HHHHHH
Confidence 5899999998754 4567899999987666666888899999876 455543
No 186
>PRK05638 threonine synthase; Validated
Probab=64.77 E-value=17 Score=29.74 Aligned_cols=51 Identities=16% Similarity=0.261 Sum_probs=37.7
Q ss_pred hhhhhhhC--CChHHHHHHHHHHHHcCCccEEee-CCCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFR--MKTQSVIDRIVELQKTGALTGVID-DRGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~--lktq~vI~RI~eL~~~g~ltGViD-DRGKfIyIs~eEl~~Va~f 52 (96)
-||+..++ ++...+-..++.|++.|-++.... .|-+|-+||++-...+.+|
T Consensus 388 ~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 388 YEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLENL 441 (442)
T ss_pred HHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHhc
Confidence 37888998 888888899999999999987532 3445556888766655443
No 187
>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=64.60 E-value=15 Score=23.26 Aligned_cols=37 Identities=14% Similarity=0.296 Sum_probs=29.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF 38 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf 38 (96)
++||..++++..-+..=++.|.+.|-|...--..|-|
T Consensus 29 ~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy 65 (83)
T PF02082_consen 29 KEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGY 65 (83)
T ss_dssp HHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEE
T ss_pred HHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCce
Confidence 6899999999999999999999999877665444444
No 188
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Mycobacterium tuberculosis LigC and similar ba
Probab=64.58 E-value=14 Score=25.69 Aligned_cols=32 Identities=22% Similarity=0.396 Sum_probs=27.1
Q ss_pred CccEEeeCCCceEEE------cHHHHHHHHHHHHhhch
Q psy11008 27 ALTGVIDDRGKFIYI------SQEELNSVATFIKQRGR 58 (96)
Q Consensus 27 ~ltGViDDRGKfIyI------s~eEl~~Va~fI~~rgr 58 (96)
-|-|+.|+.|+++|| |++++.++.++++...+
T Consensus 20 LlLg~~~~~g~l~yvG~vtGf~~~~~~~L~~~l~~l~~ 57 (122)
T cd07970 20 LLLGLYDDGGRLRHVGRTSPLAAAERRELAELLEPARA 57 (122)
T ss_pred EEEEEECCCCCEEEEEEECCCCHHHHHHHHHHHHHhhc
Confidence 356889998999996 89999999999988743
No 189
>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=64.23 E-value=10 Score=25.00 Aligned_cols=28 Identities=21% Similarity=0.226 Sum_probs=23.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.+||...|++.+-|-.-|.+|++.|-|.
T Consensus 51 ~eLa~~~g~sr~tVsr~L~~Le~~GlI~ 78 (95)
T TIGR01610 51 TVIAELTGLSRTHVSDAIKSLARRRIIF 78 (95)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 4799999997776656699999999886
No 190
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=64.03 E-value=19 Score=26.21 Aligned_cols=49 Identities=14% Similarity=0.292 Sum_probs=38.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.++|..+|+++.- |.-.++.|-|.-...+.+.|=|-|++++..+ .+|+.
T Consensus 5 ~evA~~~gvs~~t----LRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL-~~I~~ 53 (172)
T cd04790 5 SQLARQFGLSRST----LLYYERIGLLSPSARSESNYRLYGERDLERL-EQICA 53 (172)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCccCCHHHHHHH-HHHHH
Confidence 5899999998754 5677889999876666778888899999888 44443
No 191
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=63.74 E-value=24 Score=26.02 Aligned_cols=49 Identities=14% Similarity=0.208 Sum_probs=40.4
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEeeCCC-ceEEEcHHHHHHHHHHHHhh
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVIDDRG-KFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViDDRG-KfIyIs~eEl~~Va~fI~~r 56 (96)
|.++...+---+..|+++|.|+.-.+.++ ||-.||+.-...+..|...-
T Consensus 73 ~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~~~ 122 (135)
T PRK09416 73 FEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEKNA 122 (135)
T ss_pred ccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHhCH
Confidence 45666777788999999999998776554 88889999999999998744
No 192
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=63.55 E-value=34 Score=22.87 Aligned_cols=47 Identities=9% Similarity=0.164 Sum_probs=32.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHc-CCccEEeeCCCceEEEcHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKT-GALTGVIDDRGKFIYISQEELNSVATFI 53 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~-g~ltGViDDRGKfIyIs~eEl~~Va~fI 53 (96)
.|+|..+|++..- |.-.++. |.+ ...-+.|.+=|.|++++..+....
T Consensus 4 ~EvA~~~gVs~~t----LR~ye~~~gli-~p~r~~~g~R~Yt~~di~~l~~I~ 51 (99)
T cd04765 4 GEVAEILGLPPHV----LRYWETEFPQL-KPVKRAGGRRYYRPKDVELLLLIK 51 (99)
T ss_pred HHHHHHHCcCHHH----HHHHHHHcCCC-CCcCCCCCCeeeCHHHHHHHHHHH
Confidence 5789999997643 4456666 444 444455668889999999876544
No 193
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=63.31 E-value=30 Score=20.77 Aligned_cols=45 Identities=16% Similarity=0.301 Sum_probs=31.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHc-CCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKT-GALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~-g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|++..- |...++. |-+...-++ |-+=+.|+++++.+..
T Consensus 4 ~e~A~~~gVs~~t----lr~ye~~~gl~~~~r~~-~g~R~yt~~di~~l~~ 49 (68)
T cd04763 4 GEVALLTGIKPHV----LRAWEREFGLLKPQRSD-GGHRLFNDADIDRILE 49 (68)
T ss_pred HHHHHHHCcCHHH----HHHHHHhcCCCCCCcCC-CCCcccCHHHHHHHHH
Confidence 5889999997654 4456766 655454444 5556789999987755
No 194
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=63.28 E-value=6.4 Score=27.84 Aligned_cols=55 Identities=27% Similarity=0.428 Sum_probs=41.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIK 69 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~ 69 (96)
+++-++|.-+...++..+.++|+. |=||+++-++.||+.+.-. .-++.+|+||-.
T Consensus 2 ~~i~~~~~~~~~~ll~~L~~~Q~~------------~g~i~~~~~~~iA~~l~i~-~~~v~~v~tFY~ 56 (145)
T PF01257_consen 2 EEIIARYPSKRSALLPILHEVQEE------------YGYIPEEALEEIAEALGIP-PAEVYGVATFYS 56 (145)
T ss_dssp HHHHHTS--GGGGHHHHHHHHHHH------------HSS--HHHHHHHHHHHTS--HHHHHHHHHHSS
T ss_pred hHHHHHCCCCHHHHHHHHHHHHHH------------cCCCCHHHHHHHHHHHCCC-HHHHHHHHHHHH
Confidence 567788888888899999999876 3399999999999998766 678889999853
No 195
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=62.98 E-value=10 Score=22.05 Aligned_cols=43 Identities=30% Similarity=0.442 Sum_probs=25.7
Q ss_pred EEcHHHHHHHHHHHHhhc-hhchhhhhhhh------ccccceeHHHHHHh
Q psy11008 40 YISQEELNSVATFIKQRG-REELNSVATFI------KQKGRVSVSELVEN 82 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~rg-r~~~~~~~~~~------~~~GRVsi~eL~~~ 82 (96)
|||.+|+..+..-+...- .++....+..+ ...|+||..|+...
T Consensus 16 ~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~D~d~dG~i~~~Ef~~~ 65 (66)
T PF13499_consen 16 YISKEELRRALKHLGRDMSDEESDEMIDQIFREFDTDGDGRISFDEFLNF 65 (66)
T ss_dssp EEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHHTTTSSSSEEHHHHHHH
T ss_pred CCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCCCCcCCCcHHHHhcc
Confidence 688888887766554221 22333333322 24799999998764
No 196
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=62.16 E-value=19 Score=24.74 Aligned_cols=39 Identities=28% Similarity=0.381 Sum_probs=34.3
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI 41 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI 41 (96)
-||..++++-.-+-.-|++|++.|.|.=|.-.+.--||.
T Consensus 46 ~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt 84 (86)
T PRK09334 46 TLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYV 84 (86)
T ss_pred HHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEec
Confidence 378888888888888899999999999998899999985
No 197
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=62.14 E-value=7.3 Score=24.31 Aligned_cols=21 Identities=24% Similarity=0.574 Sum_probs=14.9
Q ss_pred hhhhhccccceeHHHHHHhcc
Q psy11008 64 VATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 64 ~~~~~~~~GRVsi~eL~~~sN 84 (96)
|..++-++||.|+.+|++.++
T Consensus 18 V~~~Ll~~G~ltl~~i~~~t~ 38 (62)
T PF08221_consen 18 VGEVLLSRGRLTLREIVRRTG 38 (62)
T ss_dssp HHHHHHHC-SEEHHHHHHHHT
T ss_pred HHHHHHHcCCcCHHHHHHHhC
Confidence 344444459999999999887
No 198
>PRK10263 DNA translocase FtsK; Provisional
Probab=62.02 E-value=7.9 Score=37.64 Aligned_cols=43 Identities=23% Similarity=0.480 Sum_probs=32.1
Q ss_pred EEEcHHHHHHHHHHHHhhchhch---------------------------hhhhhhhccccceeHHHHHH
Q psy11008 39 IYISQEELNSVATFIKQRGREEL---------------------------NSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 39 IyIs~eEl~~Va~fI~~rgr~~~---------------------------~~~~~~~~~~GRVsi~eL~~ 81 (96)
-|||++|++.|+.|++.+|+-+. +.+..|+.++|++|+|-|-+
T Consensus 1246 afvsD~Ei~~vv~~~k~~~~p~y~~~~~~~~~~~~~~~~~~~~~~~D~l~~~a~~~v~~~~~~S~S~lQR 1315 (1355)
T PRK10263 1246 AFVRDQEVHAVVQDWKARGRPQYVDGITSDSESEGGAGGFDGAEELDPLFDQAVQFVTEKRKASISGVQR 1315 (1355)
T ss_pred ccCCHHHHHHHHHHHHhcCCCchhhhhcccccccccccCcCCCccccHHHHHHHHHHHhcCccCHHHHHH
Confidence 48999999999999998865332 33456777777777776654
No 199
>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=61.70 E-value=14 Score=23.41 Aligned_cols=31 Identities=26% Similarity=0.458 Sum_probs=27.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI 32 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi 32 (96)
-||+..||++...+--+++.|++.|-|+..-
T Consensus 22 ~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~ 52 (75)
T PF04182_consen 22 SDLSKLLGIDPRSIFYRLKKLEKKGLIVKQS 52 (75)
T ss_pred hHHHHHhCCCchHHHHHHHHHHHCCCEEEEE
Confidence 3799999999999999999999999988653
No 200
>PRK03341 arginine repressor; Provisional
Probab=61.46 E-value=9.5 Score=28.50 Aligned_cols=39 Identities=33% Similarity=0.558 Sum_probs=27.6
Q ss_pred hhhhhhh-----CCChHHHHHH-HHHHHHcCCccEEeeCCCce-EEEcHHH
Q psy11008 2 EDLAALF-----RMKTQSVIDR-IVELQKTGALTGVIDDRGKF-IYISQEE 45 (96)
Q Consensus 2 edLAa~F-----~lktq~vI~R-I~eL~~~g~ltGViDDRGKf-IyIs~eE 45 (96)
+||+..+ .+ ||..|.| |++|.... |-|..|+| .|.-++|
T Consensus 33 ~eL~~~L~~~Gi~v-TQaTiSRDl~eL~~~K----v~~~~G~~~~Y~lp~~ 78 (168)
T PRK03341 33 AELAALLADEGIEV-TQATLSRDLDELGAVK----LRGADGGLGVYVVPEE 78 (168)
T ss_pred HHHHHHHHHcCCcc-cHHHHHHHHHHhcCEe----eecCCCCEEEEEeccc
Confidence 4566665 53 7888888 66665432 78899999 9986554
No 201
>PHA02943 hypothetical protein; Provisional
Probab=60.78 E-value=46 Score=25.75 Aligned_cols=53 Identities=15% Similarity=0.211 Sum_probs=43.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce--EEEcHHHH-HHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF--IYISQEEL-NSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf--IyIs~eEl-~~Va~fI~~r 56 (96)
.++|..+|++-.++-.=|.-||++|.+.=|- +|++ -++.+++. +.|+.|++.-
T Consensus 28 seIAkaLGlS~~qa~~~LyvLErEG~VkrV~--~G~~tyw~l~~day~~~v~~~~Rel 83 (165)
T PHA02943 28 SRIANKLGVSHSMARNALYQLAKEGMVLKVE--IGRAAIWCLDEDAYTNLVFEIKREL 83 (165)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHcCceEEEe--ecceEEEEEChHHHHHHHHHHHHHH
Confidence 4799999999999999999999999999976 7865 45666554 5677777665
No 202
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=60.49 E-value=9.3 Score=29.46 Aligned_cols=28 Identities=29% Similarity=0.483 Sum_probs=24.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||.+|+++..-+..-|..|+++|.+.
T Consensus 35 ~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 35 NDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 6899999998877777799999999986
No 203
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=60.47 E-value=22 Score=23.01 Aligned_cols=42 Identities=19% Similarity=0.286 Sum_probs=33.5
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
++.+.||+..+.+---+-.|-++|.|...-+.|--|-.+|+.
T Consensus 28 ~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 28 RLLAAFGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp HHHCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred HHHHHcCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 578899999999999999999999999888777777667664
No 204
>cd04619 CBS_pair_6 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=60.26 E-value=35 Score=21.05 Aligned_cols=37 Identities=19% Similarity=0.299 Sum_probs=24.9
Q ss_pred CCChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHHH
Q psy11008 9 RMKTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
+++.+++.+++ .+.+ ..--|+|++|+|+ +||..++..
T Consensus 9 ~~~l~~a~~~~---~~~~~~~~~Vvd~~g~~~G~vt~~dl~~ 47 (114)
T cd04619 9 NATLQRAAKIL---GEPGIDLVVVCDPHGKLAGVLTKTDVVR 47 (114)
T ss_pred CCcHHHHHHHH---HhcCCCEEEEECCCCCEEEEEehHHHHH
Confidence 44556666655 2333 3557889999998 788888764
No 205
>TIGR01337 apcB allophycocyanin, beta subunit. The alpha and beta subunits of allophycocyanin form heterodimers, six of which associate into larger aggregates as part of the phycobilisome, a light-harvesting complex of phycobiliproteins and linker proteins. This model describes allophycocyanin beta subunit. Other, homologous phyobiliproteins include allophycocyanin alpha chain and the phycocyanin and phycoerythrin alpha and beta chains.
Probab=59.81 E-value=4.1 Score=30.33 Aligned_cols=22 Identities=14% Similarity=0.453 Sum_probs=19.0
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|++|+| .|..||+.+-.|+++-
T Consensus 12 D~~gRY--ls~~eL~~l~~~~~~~ 33 (167)
T TIGR01337 12 DLTGKY--LDDNAVTKLKGYFQTG 33 (167)
T ss_pred HhcCCC--CCHHHHHHHHHHHHHH
Confidence 677885 7999999999999865
No 206
>PF08448 PAS_4: PAS fold; InterPro: IPR013656 The PAS fold corresponds to the structural domain that has previously been defined as PAS and PAC motifs []. The PAS fold appears in archaea, eubacteria and eukarya. ; PDB: 3K3D_A 3K3C_B 3KX0_X 3FC7_B 3LUQ_D 3MXQ_A 3BWL_C 3FG8_A.
Probab=58.97 E-value=17 Score=21.34 Aligned_cols=26 Identities=27% Similarity=0.376 Sum_probs=18.9
Q ss_pred HHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008 22 LQKTGALTGVIDDRGKFIYISQEELN 47 (96)
Q Consensus 22 L~~~g~ltGViDDRGKfIyIs~eEl~ 47 (96)
|+......-|+|..|+|+|.++.-.+
T Consensus 1 l~~~p~~i~v~D~~~~i~~~N~~~~~ 26 (110)
T PF08448_consen 1 LDSSPDGIFVIDPDGRIVYANQAAAE 26 (110)
T ss_dssp HHHCSSEEEEEETTSBEEEE-HHHHH
T ss_pred CCCCCceeEEECCCCEEEEEHHHHHH
Confidence 34556667899999999999987433
No 207
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=58.95 E-value=50 Score=21.85 Aligned_cols=46 Identities=13% Similarity=0.335 Sum_probs=33.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f 52 (96)
.|+|..+|+++..+ ..-++.|.|.-+-+ .|.|=+.+++++..+..-
T Consensus 4 ~e~a~~~gvs~~tL----R~ye~~Gll~p~r~-~~g~R~Y~~~dv~~l~~I 49 (96)
T cd04774 4 DEVAKRLGLTKRTL----KYYEEIGLVSPERS-EGRYRLYSEEDLKRLERI 49 (96)
T ss_pred HHHHHHHCcCHHHH----HHHHHCCCCCCCcC-CCCCEEECHHHHHHHHHH
Confidence 58999999976543 44467798885554 466777799998877653
No 208
>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=58.84 E-value=18 Score=29.30 Aligned_cols=85 Identities=19% Similarity=0.366 Sum_probs=26.1
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEee--CCCceEEE----------------cHHHH---------HHHHHHHHh
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVID--DRGKFIYI----------------SQEEL---------NSVATFIKQ 55 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyI----------------s~eEl---------~~Va~fI~~ 55 (96)
||...-+|....+-.=++.|+..+.|--|-. .++|=+|+ ++.|+ ..+-.||++
T Consensus 105 ~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~ 184 (327)
T PF05158_consen 105 DIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQ 184 (327)
T ss_dssp HHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESSS-----------------------------------
T ss_pred HHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHh
Confidence 6778888877777777999999999888765 56776665 34444 346788888
Q ss_pred hch-----------------------------hchhhhhhhhcccc----ceeHHHHHHhcccce
Q psy11008 56 RGR-----------------------------EELNSVATFIKQKG----RVSVSELVENSNQLV 87 (96)
Q Consensus 56 rgr-----------------------------~~~~~~~~~~~~~G----RVsi~eL~~~sN~lI 87 (96)
+.. --+..|++||+..| .+|..|+.+.+|-||
T Consensus 185 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~T~~eI~~fI~~sgIs~v~Ls~eDI~~LL~tLV 249 (327)
T PF05158_consen 185 KSFPSSEQISQKTSSSSADPQALPYPAGYASYPTLEEIAEFINKSGISNVELSEEDIESLLDTLV 249 (327)
T ss_dssp -----------------------------------------------------------------
T ss_pred CcCccccccccccccccccccccccccccCCCCCHHHHHHHHHHcCCCceecCHHHHHHHHHHHh
Confidence 866 34567888998888 234455555555543
No 209
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=58.76 E-value=12 Score=28.28 Aligned_cols=39 Identities=18% Similarity=0.312 Sum_probs=31.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.|||..||++-..+.+-|+.|+..|.+.- -.|+=+|+.+
T Consensus 38 reLae~fgVSR~~vREAl~~L~a~Glve~---r~G~Gt~V~~ 76 (241)
T COG2186 38 RELAERFGVSRTVVREALKRLEAKGLVEI---RQGSGTFVRP 76 (241)
T ss_pred HHHHHHHCCCcHHHHHHHHHHHHCCCeee---cCCCceEecC
Confidence 37999999999999999999999876542 4566666654
No 210
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=58.21 E-value=19 Score=23.36 Aligned_cols=29 Identities=34% Similarity=0.636 Sum_probs=24.3
Q ss_pred ccEEeeCC-CceEEE-------cHHHHHHHHHHHHhh
Q psy11008 28 LTGVIDDR-GKFIYI-------SQEELNSVATFIKQR 56 (96)
Q Consensus 28 ltGViDDR-GKfIyI-------s~eEl~~Va~fI~~r 56 (96)
|-|+.|+. |+|+|| |++++..+-..++..
T Consensus 9 llg~~d~~~~~l~~vg~vgtG~~~~~~~~l~~~l~~~ 45 (97)
T PF04679_consen 9 LLGVYDPDSGRLVYVGKVGTGFSDEELRELRERLEPL 45 (97)
T ss_dssp EEEEEETTTTEEEEEEEE-SS--HHHHHHHHHHHGGG
T ss_pred EEEEEcCCCCcEEEEEEECCCCCHHHHHHHHHHhhCc
Confidence 56999987 999996 789999999888866
No 211
>PHA03033 hypothetical protein; Provisional
Probab=58.19 E-value=7.7 Score=29.37 Aligned_cols=53 Identities=23% Similarity=0.290 Sum_probs=40.0
Q ss_pred hhhhhCCChHHH-------HHHHHHHHHcCCccE---EeeCCCceEE--EcHHHHHHHHHHHHhh
Q psy11008 4 LAALFRMKTQSV-------IDRIVELQKTGALTG---VIDDRGKFIY--ISQEELNSVATFIKQR 56 (96)
Q Consensus 4 LAa~F~lktq~v-------I~RI~eL~~~g~ltG---ViDDRGKfIy--Is~eEl~~Va~fI~~r 56 (96)
+|+.+.|-.-.+ -..|.+|+++..-+| |+-+.++||| ||.+=++....-|+-+
T Consensus 26 IsAD~~MGaGIA~v~FKkkyg~V~eLk~Qkk~~GeVAvLk~d~RyIYYLITKdyie~~v~~~ni~ 90 (142)
T PHA03033 26 ISADFILCKDDCFIYIKKKYNSIKELKKQKKKKGEVAYIYKNNKYIIYIIIADYIEDIVDDINIL 90 (142)
T ss_pred ehhhhhcCCChhhhhHHHHhCCHHHHHhhccCCCeEEEEecCCEEEEEEEeHHHHHHHHHHHHHH
Confidence 355566555444 556999999999998 4569999998 7888888887777655
No 212
>PRK00441 argR arginine repressor; Provisional
Probab=57.97 E-value=40 Score=24.46 Aligned_cols=39 Identities=36% Similarity=0.606 Sum_probs=27.9
Q ss_pred hhhhhhh-----CCChHHHHHH-HHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008 2 EDLAALF-----RMKTQSVIDR-IVELQKTGALTGVIDDRGKFIYISQEE 45 (96)
Q Consensus 2 edLAa~F-----~lktq~vI~R-I~eL~~~g~ltGViDDRGKfIyIs~eE 45 (96)
+||+..+ +. ||..|.| |++|. +.=|-|..|+|.|.-+.|
T Consensus 22 ~eL~~~L~~~G~~v-SqaTisRDl~~L~----lvKv~~~~G~~~Y~l~~~ 66 (149)
T PRK00441 22 EELAEELKKMGFDV-TQATVSRDIKELK----LIKVLSNDGKYKYATISK 66 (149)
T ss_pred HHHHHHHHhcCCCc-CHHHHHHHHHHcC----cEEeECCCCCEEEEeCcc
Confidence 5777774 75 7788877 66663 445678999999985543
No 213
>COG3343 RpoE DNA-directed RNA polymerase, delta subunit [Transcription]
Probab=57.85 E-value=9 Score=29.74 Aligned_cols=40 Identities=15% Similarity=0.405 Sum_probs=32.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN 47 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~ 47 (96)
.++++++|++-+++-+||-.+=.. +.-.|+||++....+.
T Consensus 38 ~EI~~~~~~s~~ei~~~i~~FYTd------ln~DgrFi~LGdn~Wg 77 (175)
T COG3343 38 NEIQKLLGVSKEEIRSRIGQFYTD------LNIDGRFISLGDNKWG 77 (175)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHH------hccCCceeeccccccc
Confidence 468899999999999999877653 4467999999887654
No 214
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=57.84 E-value=30 Score=23.83 Aligned_cols=54 Identities=11% Similarity=0.288 Sum_probs=40.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE-EcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY-ISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy-Is~eEl~~Va~fI~~r 56 (96)
.+||..||++..-+.+=++.|.+.|-+.-+---.|-|.- -.+++ -.+.+-+.--
T Consensus 29 ~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~~~~~-itl~dI~~ai 83 (141)
T PRK11014 29 SEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGKPAST-IRIGDVVREL 83 (141)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecCCHHH-CCHHHHHHHH
Confidence 589999999999999999999999988877655566644 44444 3555555544
No 215
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=57.54 E-value=15 Score=26.31 Aligned_cols=61 Identities=23% Similarity=0.318 Sum_probs=45.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhh-----cccccee
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFI-----KQKGRVS 75 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~-----~~~GRVs 75 (96)
+++-++|+-+.+.++.-+.++|+. |=||+++-+..||+.+.-. .-++..|+||- +.+|+-.
T Consensus 11 ~~i~~~~~~~~~~ll~~L~~vQ~~------------~g~ip~~~~~~iA~~l~v~-~~~v~~v~tFY~~f~~~p~gk~~ 76 (154)
T PRK07539 11 EREIAKYPRPRSAVIPALKIVQEQ------------RGWVPDEAIEAVADYLGMP-AIDVEEVATFYSMIFRQPVGRHV 76 (154)
T ss_pred HHHHHHCCCCHHHHHHHHHHHHHH------------hCCCCHHHHHHHHHHhCcC-HHHHHHHHHHHhhhCcCCCCCEE
Confidence 345566776777788888888753 3489999999999998765 67888999985 4566643
No 216
>PF11761 CbiG_mid: Cobalamin biosynthesis central region; InterPro: IPR021745 Members of this family are involved in cobalamin synthesis. The gene encoded by P72862 from SWISSPROT has been designated cbiH but in fact represents a fusion between cbiH and cbiG. As other multi-functional proteins involved in cobalamin biosynthesis catalyse adjacent steps in the pathway, including CysG, CobL (CbiET), CobIJ and CobA-HemD, it is therefore possible that CbiG catalyses a reaction step adjacent to CbiH. In the anaerobic pathway such a step could be the formation of a gamma lactone, which is thought to help to mediate the anaerobic ring contraction process [].
Probab=57.43 E-value=18 Score=22.37 Aligned_cols=34 Identities=15% Similarity=0.248 Sum_probs=30.5
Q ss_pred ChhhhhhhCCCh--HHHHHHHHHHHHcCCccEEeeC
Q psy11008 1 MEDLAALFRMKT--QSVIDRIVELQKTGALTGVIDD 34 (96)
Q Consensus 1 ledLAa~F~lkt--q~vI~RI~eL~~~g~ltGViDD 34 (96)
++-+|+++|++. -+.+.+|....-+|.-.|+++|
T Consensus 4 vD~la~~~g~~i~~~~~~k~vsaalv~g~~V~~~~~ 39 (93)
T PF11761_consen 4 VDLLARELGWRIENREAVKRVSAALVNGEPVALYQD 39 (93)
T ss_pred cchhhhhCCCEEcCHHHHHHHHHHHHCCCEEEEEEe
Confidence 467899999987 4789999999999999999999
No 217
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=56.68 E-value=30 Score=22.20 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=27.4
Q ss_pred hhhhhhh-CCChHHHHHHHHHHHHcCCccEEeeC
Q psy11008 2 EDLAALF-RMKTQSVIDRIVELQKTGALTGVIDD 34 (96)
Q Consensus 2 edLAa~F-~lktq~vI~RI~eL~~~g~ltGViDD 34 (96)
.||.... ++++..+-+|+++|++.|-++=....
T Consensus 22 ~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~ 55 (90)
T PF01638_consen 22 SELQRRLPGISPKVLSQRLKELEEAGLVERRVYP 55 (90)
T ss_dssp HHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEES
T ss_pred HHHHHhcchhHHHHHHHHHHHHHHcchhhccccc
Confidence 4677777 89999999999999999999887664
No 218
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=56.57 E-value=9.5 Score=21.55 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=14.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV 31 (96)
.++|..||++.+.|-.=++...+.| +.|+
T Consensus 21 ~~ia~~lgvs~~Tv~~w~kr~~~~G-~~gL 49 (50)
T PF13384_consen 21 REIAKRLGVSRSTVYRWIKRYREEG-LEGL 49 (50)
T ss_dssp HHHHHHHTS-HHHHHHHHT-----------
T ss_pred HHHHHHHCcCHHHHHHHHHHccccc-cccc
Confidence 4789999997777666666666666 5554
No 219
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=56.52 E-value=22 Score=24.21 Aligned_cols=31 Identities=6% Similarity=0.158 Sum_probs=27.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI 32 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi 32 (96)
.+||.+|+++..-|-.=+..|+..|++.=|-
T Consensus 20 ~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 20 AQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 4899999998887778899999999998886
No 220
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of Pyrococcus furiosus DN
Probab=56.32 E-value=22 Score=24.27 Aligned_cols=30 Identities=20% Similarity=0.366 Sum_probs=25.1
Q ss_pred cEEeeCC-CceEEE-------cHHHHHHHHHHHHhhch
Q psy11008 29 TGVIDDR-GKFIYI-------SQEELNSVATFIKQRGR 58 (96)
Q Consensus 29 tGViDDR-GKfIyI-------s~eEl~~Va~fI~~rgr 58 (96)
-|+.|+. |+|+|+ |+++++.+.++++...+
T Consensus 26 lg~~d~~~g~l~~vg~vgtG~~~~~~~~l~~~l~~~~~ 63 (122)
T cd07972 26 LAVRDEETGELVPVGKVATGLTDEELEELTERLRELII 63 (122)
T ss_pred EEEEcCCCCeEEEEEEEccCCCHHHHHHHHHHhhhhhc
Confidence 5899987 899995 78999999999987643
No 221
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=56.13 E-value=61 Score=21.93 Aligned_cols=46 Identities=15% Similarity=0.137 Sum_probs=37.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|++++ -|.-.++.|-|..+-.+.|.|=|.|++++..+..
T Consensus 4 ge~A~~~gvs~~----tlR~ye~~GLl~p~~r~~~g~R~Y~~~~l~~l~~ 49 (107)
T cd01111 4 SQLALDAGVSVH----IVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRF 49 (107)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHH
Confidence 589999999865 4677889999988766778899999999988753
No 222
>CHL00089 apcF allophycocyanin beta 18 subunit
Probab=55.97 E-value=5.5 Score=29.93 Aligned_cols=22 Identities=14% Similarity=0.507 Sum_probs=19.4
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|+.|+| .|..||+.+..|+++-
T Consensus 13 D~~gRY--ls~~eL~~l~~~~~~~ 34 (169)
T CHL00089 13 DLTGKY--LDKNAITQLNSYFSSA 34 (169)
T ss_pred hccCCC--CCHHHHHHHHHHHHhH
Confidence 788885 6999999999999876
No 223
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=55.85 E-value=14 Score=25.73 Aligned_cols=56 Identities=23% Similarity=0.278 Sum_probs=39.2
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEee-CCCce----EEEcHHH-HHHHHHHHHhh
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVID-DRGKF----IYISQEE-LNSVATFIKQR 56 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViD-DRGKf----IyIs~eE-l~~Va~fI~~r 56 (96)
|+|||..|..++-.+-.-|+.|++.|-|+=.=- -|||- +.++++| +...|.-.-+.
T Consensus 22 l~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~~~~~~~~~~~l~~ 83 (115)
T PF12793_consen 22 LDELAELLFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPEELLEQQAEELLEQ 83 (115)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHHHHHHHHHHHHHHc
Confidence 579999999999999999999999998862221 36663 3345544 34455544444
No 224
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=55.74 E-value=58 Score=21.58 Aligned_cols=46 Identities=11% Similarity=0.008 Sum_probs=35.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|++++ -|...++.|-|.-.-.+.+.|-|-+++++..+-.
T Consensus 4 ~eva~~~gvs~~----tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~ 49 (95)
T cd04780 4 SELSKRSGVSVA----TIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRL 49 (95)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHH
Confidence 589999999765 5677888999998765555555669999988754
No 225
>PRK05066 arginine repressor; Provisional
Probab=55.47 E-value=16 Score=26.90 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=25.9
Q ss_pred CCC--hHHHHHH-HHHHHHcCCccEEeeCCCceEEEcHHHH
Q psy11008 9 RMK--TQSVIDR-IVELQKTGALTGVIDDRGKFIYISQEEL 46 (96)
Q Consensus 9 ~lk--tq~vI~R-I~eL~~~g~ltGViDDRGKfIyIs~eEl 46 (96)
|+. ||..|.| |++| |. .=|-+..|+|+|.-+.+.
T Consensus 37 Gi~~vTQATiSRDikeL---~l-vKv~~~~G~~~Y~l~~~~ 73 (156)
T PRK05066 37 GFDNINQSKVSRMLTKF---GA-VRTRNAKMEMVYCLPAEL 73 (156)
T ss_pred CCCeecHHHHHHHHHHc---CC-EEeeCCCCCEEEEeCCCC
Confidence 888 8999998 6666 33 338889999999866543
No 226
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=55.31 E-value=28 Score=24.98 Aligned_cols=33 Identities=30% Similarity=0.575 Sum_probs=25.8
Q ss_pred ChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHH
Q psy11008 11 KTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEEL 46 (96)
Q Consensus 11 ktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl 46 (96)
=||..|.| .|.+.|.+. +.+..|++.|--+.+.
T Consensus 33 vsqaTIsR--dL~elglvk-~~~~~g~~~Y~~~~~~ 65 (146)
T TIGR01529 33 VTQATVSR--DLRELGAVK-VRDEDGSYVYSLPADG 65 (146)
T ss_pred cCHHHHHH--HHHHcCCEE-EECCCCcEEEeecccc
Confidence 37999999 888888875 7779999999655433
No 227
>CHL00173 cpeA phycoerythrin alpha subunit; Provisional
Probab=54.93 E-value=5.9 Score=29.70 Aligned_cols=23 Identities=35% Similarity=0.520 Sum_probs=19.6
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhhc
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~rg 57 (96)
|+.|+| +|..||+++..|+++-.
T Consensus 13 D~~gRy--ls~~eL~~l~~~~~~a~ 35 (164)
T CHL00173 13 DAAGRF--PSSSDLESVQGNIQRAA 35 (164)
T ss_pred HhccCC--CCHHHHHHHHHHHHHHH
Confidence 678885 69999999999998763
No 228
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=54.56 E-value=56 Score=22.04 Aligned_cols=48 Identities=13% Similarity=0.288 Sum_probs=39.1
Q ss_pred CCChHHHHHHHHHHHHcCCccEEeeCCC-----ceEEEcHHHHHHHHHHHHhh
Q psy11008 9 RMKTQSVIDRIVELQKTGALTGVIDDRG-----KFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~ltGViDDRG-----KfIyIs~eEl~~Va~fI~~r 56 (96)
..+...+---+..|+++|-+++...+.+ |+--||+.-.+.++.+.++.
T Consensus 41 ~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~ 93 (138)
T COG1695 41 EPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEW 93 (138)
T ss_pred cCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 3566677778999999999999877553 89999999999999887554
No 229
>COG0329 DapA Dihydrodipicolinate synthase/N-acetylneuraminate lyase [Amino acid transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=54.22 E-value=37 Score=26.70 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=37.9
Q ss_pred CChHHHHHHHHHHHHcCCccEEee--CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVID--DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+..+....-++.|.+.| +.||+= .-|-|.+.|.||-..+.++..+-
T Consensus 22 vD~~a~~~lv~~li~~G-v~gi~~~GttGE~~~Ls~eEr~~v~~~~v~~ 69 (299)
T COG0329 22 VDEEALRRLVEFLIAAG-VDGLVVLGTTGESPTLTLEERKEVLEAVVEA 69 (299)
T ss_pred cCHHHHHHHHHHHHHcC-CCEEEECCCCccchhcCHHHHHHHHHHHHHH
Confidence 45555666677788888 888876 78999999999999999888776
No 230
>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=54.02 E-value=18 Score=26.69 Aligned_cols=40 Identities=18% Similarity=0.312 Sum_probs=31.9
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
+.|||...||+...+-.=++.|++.|-+.- | .|+| .+.+.
T Consensus 27 l~eia~~lglpksT~~RlL~tL~~~G~l~~--~-~~~Y-~lG~~ 66 (248)
T TIGR02431 27 LTDVAEATGLTRAAARRFLLTLVELGYVTS--D-GRLF-WLTPR 66 (248)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEEe--C-CCEE-EecHH
Confidence 368999999999999999999999999963 4 4664 44553
No 231
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=53.87 E-value=37 Score=22.42 Aligned_cols=84 Identities=14% Similarity=0.155 Sum_probs=49.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhc--hhchhhhhhhhccccceeH--H
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRG--REELNSVATFIKQKGRVSV--S 77 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rg--r~~~~~~~~~~~~~GRVsi--~ 77 (96)
.++|..+|+++.-+ ...++.|-+...- +.|.+=|.|++++..+..-..-+. --.+..+..++.....+.. .
T Consensus 5 ~eva~~~gVs~~tL----R~ye~~Gli~p~r-~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l~~~~~~l~~ 79 (98)
T cd01279 5 SVAAELLGIHPQTL----RVYDRLGLVSPAR-TNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLLQC 79 (98)
T ss_pred HHHHHHHCcCHHHH----HHHHHCCCCCCCc-CCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhHHHHHHH
Confidence 57899999976543 4457788887743 456677889999988876544331 1233444444444333321 4
Q ss_pred HHHHhcccceecc
Q psy11008 78 ELVENSNQLVTLI 90 (96)
Q Consensus 78 eL~~~sN~lI~L~ 90 (96)
++.+....++.|.
T Consensus 80 ~~~~~~~~~~~~~ 92 (98)
T cd01279 80 RSCEHATELIGCA 92 (98)
T ss_pred HHHHHHHHHHhcc
Confidence 4444444555443
No 232
>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=53.76 E-value=41 Score=22.82 Aligned_cols=59 Identities=20% Similarity=0.354 Sum_probs=39.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.++|..|+++...|..-++ -.+.|.+. --+||.- -| +.+.+..+|... ...++.||++
T Consensus 22 ~eaa~~F~VS~~Tv~~W~k-~~~~G~~~--~k~r~~~-Ki---d~~~L~~~v~~~---------------pd~tl~Ela~ 79 (119)
T PF01710_consen 22 REAAKRFGVSRNTVYRWLK-RKETGDLE--PKPRGRK-KI---DRDELKALVEEN---------------PDATLRELAE 79 (119)
T ss_pred HHHHHHhCcHHHHHHHHHH-hccccccc--ccccccc-cc---cHHHHHHHHHHC---------------CCcCHHHHHH
Confidence 4789999998877777666 56666552 2345532 23 245577888888 7778888776
Q ss_pred h
Q psy11008 82 N 82 (96)
Q Consensus 82 ~ 82 (96)
.
T Consensus 80 ~ 80 (119)
T PF01710_consen 80 R 80 (119)
T ss_pred H
Confidence 4
No 233
>PRK13749 transcriptional regulator MerD; Provisional
Probab=53.67 E-value=32 Score=24.40 Aligned_cols=49 Identities=16% Similarity=0.219 Sum_probs=40.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.|+|..+|++++ -|.-.++.|-|..+-.+.|.|=|-+++.+..+ .||+.
T Consensus 7 gelA~~~gvS~~----tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL-~~I~~ 55 (121)
T PRK13749 7 SRLALDAGVSVH----IVRDYLLRGLLRPVACTTGGYGLFDDAALQRL-CFVRA 55 (121)
T ss_pred HHHHHHHCCCHH----HHHHHHHCCCCCCCCcCCCCCccCCHHHHHHH-HHHHH
Confidence 489999999865 46788999999998777799999999999998 56654
No 234
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=53.65 E-value=8.8 Score=28.17 Aligned_cols=27 Identities=26% Similarity=0.223 Sum_probs=22.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGAL 28 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~l 28 (96)
+|||.+|+++.+-+..=+++|++.|.+
T Consensus 25 ~~La~~~~vS~~TiRRDl~~L~~~g~~ 51 (185)
T PRK04424 25 EELAEKFGVSIQTIRLDRMELGIPELR 51 (185)
T ss_pred HHHHHHHCcCHHHHHHHHHHHhcchHH
Confidence 689999999777666669999988866
No 235
>PF13814 Replic_Relax: Replication-relaxation
Probab=53.60 E-value=59 Score=22.53 Aligned_cols=49 Identities=14% Similarity=0.302 Sum_probs=37.7
Q ss_pred hhhhhhhCCChH---HHHHHHHHHHHcCCccEEeeC------CCceE-EEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQ---SVIDRIVELQKTGALTGVIDD------RGKFI-YISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq---~vI~RI~eL~~~g~ltGViDD------RGKfI-yIs~eEl~~Va 50 (96)
+.|+..|..+.. .+-.|++.|.+.|-|.-.-.. .+.+| |+|+.-.+.++
T Consensus 13 ~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~ 71 (191)
T PF13814_consen 13 DQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLA 71 (191)
T ss_pred HHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHH
Confidence 467888888887 789999999999988776653 34455 78888877775
No 236
>TIGR01338 phycocy_alpha phycocyanin, alpha subunit. This model excludes the closely related phycoerythrocyanin alpha subunit.
Probab=53.56 E-value=5.9 Score=29.69 Aligned_cols=22 Identities=32% Similarity=0.581 Sum_probs=19.0
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|++|+| +|..||+++..|+++-
T Consensus 12 D~qgRy--ls~~eL~~l~~~~~~g 33 (161)
T TIGR01338 12 DSQGRF--LSNGELQSIFGRFQRA 33 (161)
T ss_pred HhccCC--CCHHHHHHHHHHHHch
Confidence 778886 5899999999999876
No 237
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=53.55 E-value=59 Score=24.71 Aligned_cols=45 Identities=13% Similarity=0.138 Sum_probs=35.6
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN 47 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~ 47 (96)
+.|||...||....+-.=++.|++.|-| .-|++++.-++...=+.
T Consensus 43 l~eIa~~lglpkStv~RlL~tL~~~G~l--~~~~~~~~Y~lG~~l~~ 87 (271)
T PRK10163 43 VSDISLNLDLPLSTTFRLLKVLQAADFV--YQDSQLGWWHIGLGVFN 87 (271)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCE--EEcCCCCeEEecHHHHH
Confidence 3689999999999999999999999998 45766665566665443
No 238
>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=52.96 E-value=33 Score=24.54 Aligned_cols=40 Identities=20% Similarity=0.321 Sum_probs=33.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
|.||..|+-+...|.--|+-|++-|.|. ++|.| .|||++=
T Consensus 55 e~LA~~~~~~~~~V~~Al~~f~k~glIe--~~d~g-~i~i~~~ 94 (119)
T TIGR01714 55 EMLATMFNRNVGDIRITLQTLESLGLIE--KKNNG-DIFLENW 94 (119)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE--EecCC-cEEehhH
Confidence 6899999999999999999999999986 33545 6888763
No 239
>KOG2908|consensus
Probab=52.85 E-value=23 Score=30.47 Aligned_cols=55 Identities=15% Similarity=0.303 Sum_probs=43.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc--------HHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS--------QEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs--------~eEl~~Va~fI~~r 56 (96)
+++|..-.++..+|.=-+-.=..-|-|+|.||+-+.-+|+| .+++-..+.-+...
T Consensus 298 ~~Ia~~tkip~~eVE~LVMKAlslgLikG~Idqv~~~v~~swvqPRvl~~~qI~~Mk~rl~~W 360 (380)
T KOG2908|consen 298 KEIAEATKIPNKEVELLVMKALSLGLIKGSIDQVEGVVYMSWVQPRVLDRSQIVKMKDRLDEW 360 (380)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhccceeeeecccccEEEEecccccccCHHHHHhHHHHHHHH
Confidence 68999999999999888888888999999999999999986 34555555444433
No 240
>PF00486 Trans_reg_C: Transcriptional regulatory protein, C terminal; InterPro: IPR001867 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. This entry represents a domain that is almost always found associated with the response regulator receiver domain (see IPR001789 from INTERPRO). It may play a role in DNA binding [].; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2K4J_A 2JPB_A 1ODD_A 1OPC_A 1KGS_A 2PMU_E 2JZY_A 1GXP_B 1QQI_A 2Z33_A ....
Probab=52.84 E-value=35 Score=20.13 Aligned_cols=32 Identities=28% Similarity=0.535 Sum_probs=26.3
Q ss_pred CceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccc-eeHHHHHHh
Q psy11008 36 GKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGR-VSVSELVEN 82 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GR-Vsi~eL~~~ 82 (96)
|+=|-+|+.|..-++-++... |+ ||..+|.+.
T Consensus 1 G~~v~Lt~~e~~lL~~L~~~~---------------~~~vs~~~l~~~ 33 (77)
T PF00486_consen 1 GQPVKLTPKEFRLLELLLRNP---------------GRVVSREELIEA 33 (77)
T ss_dssp TEEEESSHHHHHHHHHHHHTT---------------TSEEEHHHHHHH
T ss_pred CcEEecCHHHHHHHHHHHhCC---------------CCCCCHHHhCCh
Confidence 556788999999999999998 66 488888764
No 241
>PF15615 TerB-C: TerB-C domain
Probab=52.63 E-value=35 Score=24.18 Aligned_cols=45 Identities=22% Similarity=0.138 Sum_probs=35.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN 47 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~ 47 (96)
+++|+..|+-..-+|+.|++..-+--=.=||+. |-.|+|.++=..
T Consensus 97 ~~~a~~~glm~~~~ie~INE~afd~~gd~vie~-~d~i~I~~dy~e 141 (144)
T PF15615_consen 97 EDIARDHGLMPDGAIESINEKAFDYFGDPVIEG-DDPIEINEDYRE 141 (144)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHhcCCeeEeC-CCCceEcHHHHH
Confidence 689999999999999999987655444457777 888888876444
No 242
>PF00989 PAS: PAS fold; InterPro: IPR013767 PAS domains are involved in many signalling proteins where they are used as a signal sensor domain []. PAS domains appear in archaea, bacteria and eukaryotes. Several PAS-domain proteins are known to detect their signal by way of an associated cofactor. Haeme, flavin, and a 4-hydroxycinnamyl chromophore are used in different proteins. The PAS domain was named after three proteins that it occurs in: Per- period circadian protein Arnt- Ah receptor nuclear translocator protein Sim- single-minded protein. PAS domains are often associated with PAC domains IPR001610 from INTERPRO. It appears that these domains are directly linked, and that together they form the conserved 3D PAS fold. The division between the PAS and PAC domains is caused by major differences in sequences in the region connecting these two motifs []. In human PAS kinase, this region has been shown to be very flexible, and adopts different conformations depending on the bound ligand []. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels [].; GO: 0006355 regulation of transcription, DNA-dependent; PDB: 2GJ3_A 4F3L_B 1XFN_A 1OTD_A 2PYR_A 1KOU_A 1XFQ_A 2ZOI_A 2ZOH_A 1OTA_A ....
Probab=52.59 E-value=15 Score=21.64 Aligned_cols=20 Identities=30% Similarity=0.526 Sum_probs=15.2
Q ss_pred cCCccEEeeCCCceEEEcHH
Q psy11008 25 TGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 25 ~g~ltGViDDRGKfIyIs~e 44 (96)
...-.=++|..|+++|+++.
T Consensus 10 ~~~~i~~~d~~g~I~~~N~a 29 (113)
T PF00989_consen 10 SPDGIFVIDEDGRILYVNQA 29 (113)
T ss_dssp SSSEEEEEETTSBEEEECHH
T ss_pred CCceEEEEeCcCeEEEECHH
Confidence 33444578999999999975
No 243
>KOG3558|consensus
Probab=52.58 E-value=11 Score=34.83 Aligned_cols=46 Identities=30% Similarity=0.517 Sum_probs=28.4
Q ss_pred HHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhch--hhhhhhhcccc
Q psy11008 22 LQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREEL--NSVATFIKQKG 72 (96)
Q Consensus 22 L~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~--~~~~~~~~~~G 72 (96)
|+.-+-..=|++..|+|||||+ .|+.|+--- .-|| .||-.||.+--
T Consensus 125 LqsLDGFVm~l~~dG~~lYiSE----tVS~yLGLS-QvELTG~SvFDfiHP~D 172 (768)
T KOG3558|consen 125 LQSLDGFVMALTQDGDFLYISE----TVSIYLGLS-QVELTGSSVFDFIHPCD 172 (768)
T ss_pred HhhccceEEEEccCCCEEEEec----hhHhhhCcc-ceeeecchhhhccCccC
Confidence 3333444558899999999997 477776322 1122 36667776643
No 244
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=52.48 E-value=30 Score=26.25 Aligned_cols=38 Identities=26% Similarity=0.461 Sum_probs=30.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
+|||..|+++..-+-.-+.+|++.|.|.= .+|..+|+.
T Consensus 22 ~eLa~~l~VS~~TiRRdL~~L~~~~~l~r---~~Gga~~~~ 59 (240)
T PRK10411 22 EALAEQLNVSKETIRRDLNELQTQGKILR---NHGRAKYIH 59 (240)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCeEEEec
Confidence 68999999988777777999999888753 467776664
No 245
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=52.46 E-value=67 Score=23.39 Aligned_cols=48 Identities=10% Similarity=0.191 Sum_probs=35.8
Q ss_pred CCChHHHHHHHHHHHHcCCccEEeeC--CC---ceEEEcHHHHHHHHHHHHhh
Q psy11008 9 RMKTQSVIDRIVELQKTGALTGVIDD--RG---KFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~ltGViDD--RG---KfIyIs~eEl~~Va~fI~~r 56 (96)
.++.-.+---+..|+++|-|..-.+. .| ||..||+.-...+..+.+.-
T Consensus 54 ~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w 106 (138)
T TIGR02719 54 SVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSF 106 (138)
T ss_pred CCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHH
Confidence 45566677789999999999875442 22 55559999988888887665
No 246
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=52.13 E-value=76 Score=21.86 Aligned_cols=45 Identities=16% Similarity=0.220 Sum_probs=35.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.|+|..+|+++. -|.--++.|-|.-.-++.|.|=|-+++.+..+.
T Consensus 4 gE~A~~~gvs~~----TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~ 48 (133)
T cd04787 4 KELANAAGVTPD----TVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLR 48 (133)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHH
Confidence 489999999765 346678999999877765778888999888763
No 247
>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=51.99 E-value=63 Score=26.24 Aligned_cols=55 Identities=33% Similarity=0.460 Sum_probs=36.7
Q ss_pred hhhhhh-hCCChHHHHHHHHHHHHcCCccEEeeCCCceEE--EcHHHHH----------HHHHHHHhhc
Q psy11008 2 EDLAAL-FRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY--ISQEELN----------SVATFIKQRG 57 (96)
Q Consensus 2 edLAa~-F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy--Is~eEl~----------~Va~fI~~rg 57 (96)
+||... .++..++...-|+.|.+.|.+.-+- ..|+.+| .+++|.. -|=+.|+.-|
T Consensus 30 ~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~ag 97 (327)
T PF05158_consen 30 EDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEEAG 97 (327)
T ss_dssp HHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE--SSS-----SSSCCHHHHHHHHHHHT
T ss_pred HHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHHhC
Confidence 567777 5889999999999999999999888 4454444 4333322 5566677664
No 248
>PF09669 Phage_pRha: Phage regulatory protein Rha (Phage_pRha); InterPro: IPR019104 This entry represents a family of proteins which are encoded in temperate phages and bacterial prophage regions. They include the product of the late operon rha gene from lambdoid phage phi-80. The presence of this gene interferes with the infection of bacterial strains lacking the integration host factor that regulates the rha gene. Rha is thought to function as a phage regulatory protein.
Probab=51.96 E-value=34 Score=22.37 Aligned_cols=52 Identities=17% Similarity=0.364 Sum_probs=38.3
Q ss_pred hhhhhhCCChHHHHHHHHHHHHc------CCcc-----EEeeCCCc---eEEEcHHHHHHHHHHHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKT------GALT-----GVIDDRGK---FIYISQEELNSVATFIK 54 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~------g~lt-----GViDDRGK---fIyIs~eEl~~Va~fI~ 54 (96)
++|..||-+..+|+.-|..+... |.+. ...|.+|+ +..++.+...-++....
T Consensus 6 ~IAe~~gk~H~~Vlr~I~~~~~~~~~~~~~~~~f~~~~~y~~~~gr~~~~y~Ltk~g~~lL~~~~~ 71 (93)
T PF09669_consen 6 EIAEMFGKRHKNVLRDIRKLIEKECSPEFGQLNFFIESKYKDGQGRSYPCYLLTKDGFTLLVMGYS 71 (93)
T ss_pred HHHHHHCccHHHHHHHHHHHHhhhcchhhhhccCcceeeeECCCCcEeEEEEEccChhheehhhhc
Confidence 79999999999999999999976 3332 23356665 56778777776666554
No 249
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=51.83 E-value=28 Score=23.65 Aligned_cols=59 Identities=20% Similarity=0.428 Sum_probs=40.0
Q ss_pred CChHHHHHHHHHHHHcCC--cc------E--Eee-------CCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhcccc
Q psy11008 10 MKTQSVIDRIVELQKTGA--LT------G--VID-------DRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKG 72 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~--lt------G--ViD-------DRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~G 72 (96)
...+++..||..+...+. .. | .+| .+|+-|.+|+.|++-+.-++... |
T Consensus 103 ~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Lt~~E~~ll~~l~~~~---------------g 167 (227)
T PRK09836 103 FAFAELLARVRTLLRRGAAVIIESQFQVADLMVDLVSRKVTRSGTRITLTSKEFTLLEFFLRHQ---------------G 167 (227)
T ss_pred CCHHHHHHHHHHHHhcccccCCCCcEEEcCEEEEcccCEEEECCEEEecCHHHHHHHHHHHhCC---------------C
Confidence 345777888887765432 00 1 112 35888999999999999998888 6
Q ss_pred ce-eHHHHHHhc
Q psy11008 73 RV-SVSELVENS 83 (96)
Q Consensus 73 RV-si~eL~~~s 83 (96)
+| |-.+|.+..
T Consensus 168 ~~~sr~~l~~~~ 179 (227)
T PRK09836 168 EVLPRSLIASQV 179 (227)
T ss_pred eeEcHHHHHHHH
Confidence 64 667666653
No 250
>PRK06074 NADH dehydrogenase subunit C; Provisional
Probab=51.53 E-value=49 Score=24.75 Aligned_cols=47 Identities=17% Similarity=0.236 Sum_probs=34.9
Q ss_pred CChHHHHHHHHHHHHcCCccEEe-eCCCceEEEcHHHHHHHHHHHHhhc
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVI-DDRGKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGVi-DDRGKfIyIs~eEl~~Va~fI~~rg 57 (96)
|+.++++++|++--. +.+..+. -.+=-+|.|+.+.+.+++.+++..|
T Consensus 2 ~~~~~~~~~l~~~f~-~~~~~~~~~~~~~~~~v~~~~l~~v~~~L~~~~ 49 (189)
T PRK06074 2 EKLEELVAKLLEKLP-DAIGKVTVAFGELTLKVPAEKILEVLTFLRDDP 49 (189)
T ss_pred CcHHHHHHHHHHHcc-ccEEEEEEeCCeEEEEEcHHHHHHHHHHHHhCc
Confidence 788999999987443 3444442 2344679999999999999999863
No 251
>COG5301 Phage-related tail fibre protein [General function prediction only]
Probab=51.51 E-value=9.3 Score=34.29 Aligned_cols=14 Identities=36% Similarity=0.729 Sum_probs=13.1
Q ss_pred cEEeeCCCceEEEc
Q psy11008 29 TGVIDDRGKFIYIS 42 (96)
Q Consensus 29 tGViDDRGKfIyIs 42 (96)
.|++|+.||||||+
T Consensus 91 vGlfDadG~liavg 104 (587)
T COG5301 91 VGLFDADGKLIAVG 104 (587)
T ss_pred eeeecCCCCEEEEc
Confidence 59999999999997
No 252
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=51.44 E-value=22 Score=28.39 Aligned_cols=41 Identities=22% Similarity=0.505 Sum_probs=35.1
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeC--CC---ceEEEcH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDD--RG---KFIYISQ 43 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDD--RG---KfIyIs~ 43 (96)
+++...|+..+.|++-++-|+..|-++--+|. || ||-+||.
T Consensus 33 EiS~~lgvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~ 78 (217)
T COG1777 33 EISRELGVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISR 78 (217)
T ss_pred HHHhhcCcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccC
Confidence 67888999999999999999999999997774 43 6887763
No 253
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=51.37 E-value=52 Score=26.86 Aligned_cols=88 Identities=18% Similarity=0.264 Sum_probs=59.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee-CCCceEEEcHHHHHHHHHHHHh--hchhc-----------hhhhhhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID-DRGKFIYISQEELNSVATFIKQ--RGREE-----------LNSVATF 67 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD-DRGKfIyIs~eEl~~Va~fI~~--rgr~~-----------~~~~~~~ 67 (96)
.++|...|+++. .|+.+..+|.+.+.-. +.|+- +.|.+|++.+.+++.. ++|.- --.|.++
T Consensus 52 ~e~A~~lgvs~~----tlr~~~~~g~~~~~~~~~~grR-~yt~~di~~lr~~l~~~~~~~~~~~~~~~r~~~~~~~vIav 126 (405)
T PRK13869 52 GEAARLMKISDS----TLRKMTLAGEGPQPELASNGRR-FYTLGQINEIRQMLAGSTRGRESIDFVPHRRGSEHLQVIAV 126 (405)
T ss_pred HHHHHHhCcCHH----HHHHHHHcCCCCCCccCCCCce-eecHHHHHHHHHHHHhhccccccccccCCCCCCCCceEEEE
Confidence 367888888643 4556667788877644 56665 5799999999999975 32221 2257788
Q ss_pred hccccceeHHH--------HHHhccc--ceecccccc
Q psy11008 68 IKQKGRVSVSE--------LVENSNQ--LVTLIPDQI 94 (96)
Q Consensus 68 ~~~~GRVsi~e--------L~~~sN~--lI~L~p~~~ 94 (96)
.-+||-|..+- |+...-+ ||+++|..+
T Consensus 127 ~n~KGGvGKTTta~nLA~~LA~~G~rVLlIDlDpQ~~ 163 (405)
T PRK13869 127 TNFKGGSGKTTTSAHLAQYLALQGYRVLAVDLDPQAS 163 (405)
T ss_pred EcCCCCCCHHHHHHHHHHHHHhcCCceEEEcCCCCCC
Confidence 89999985543 3333333 688888643
No 254
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=51.14 E-value=19 Score=23.45 Aligned_cols=30 Identities=50% Similarity=0.737 Sum_probs=20.3
Q ss_pred hHHHHHH-HHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008 12 TQSVIDR-IVELQKTGALTGVIDDRGKFIYISQEE 45 (96)
Q Consensus 12 tq~vI~R-I~eL~~~g~ltGViDDRGKfIyIs~eE 45 (96)
||..|.| |++| |. .=|-|..|+|+|.=++|
T Consensus 37 TQaTiSRDLkeL---~~-vKv~~~~g~~~Y~l~~~ 67 (70)
T PF01316_consen 37 TQATISRDLKEL---GA-VKVPDGNGKYRYVLPEE 67 (70)
T ss_dssp -HHHHHHHHHHH---T--EEEECTTSSEEEE-TTS
T ss_pred chhHHHHHHHHc---Cc-EEeeCCCCCEEEEecCc
Confidence 7888877 4444 43 34889999999987765
No 255
>smart00862 Trans_reg_C Transcriptional regulatory protein, C terminal. This domain is almost always found associated with the response regulator receiver domain. It may play a role in DNA binding.
Probab=51.13 E-value=36 Score=20.00 Aligned_cols=22 Identities=18% Similarity=0.446 Sum_probs=18.6
Q ss_pred CceEEEcHHHHHHHHHHHHhhc
Q psy11008 36 GKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~rg 57 (96)
|+-|.+|+.|+.-++-++..+|
T Consensus 1 ~~~v~Lt~~e~~lL~~L~~~~~ 22 (78)
T smart00862 1 GEPIKLTPKEFRLLELLLRNPG 22 (78)
T ss_pred CCeEecCHHHHHHHHHHHhCCC
Confidence 4668889999999999999884
No 256
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=50.96 E-value=27 Score=25.48 Aligned_cols=39 Identities=15% Similarity=0.273 Sum_probs=34.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY 40 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy 40 (96)
++||..++++..-+-+=++.|.+.|-+...-...|-|.-
T Consensus 29 ~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~L 67 (164)
T PRK10857 29 ADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLL 67 (164)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeec
Confidence 689999999999999999999999999987777787765
No 257
>PF10882 bPH_5: Bacterial PH domain; InterPro: IPR020482 This entry contains membrane proteins with no known function.
Probab=50.87 E-value=17 Score=23.30 Aligned_cols=20 Identities=30% Similarity=0.325 Sum_probs=18.2
Q ss_pred ceEEEcHHHHHHHHHHHHhh
Q psy11008 37 KFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 37 KfIyIs~eEl~~Va~fI~~r 56 (96)
+-++||+++.+.+.+.+++|
T Consensus 80 ~~y~isp~~~~~fi~~l~~r 99 (100)
T PF10882_consen 80 KTYVISPEDPEEFIEALKKR 99 (100)
T ss_pred ceEEEcCCCHHHHHHHHHhc
Confidence 66789999999999999988
No 258
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=50.80 E-value=20 Score=26.10 Aligned_cols=51 Identities=12% Similarity=0.281 Sum_probs=36.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.|||..++++...|-+-++.|++.|-+. .+ .-+.|-+|+..-...-..++.
T Consensus 28 ~diA~~L~Vsp~sVt~ml~rL~~~GlV~--~~-~y~gi~LT~~G~~~a~~~~r~ 78 (154)
T COG1321 28 KDIAERLKVSPPSVTEMLKRLERLGLVE--YE-PYGGVTLTEKGREKAKELLRK 78 (154)
T ss_pred HHHHHHhCCCcHHHHHHHHHHHHCCCeE--Ee-cCCCeEEChhhHHHHHHHHHH
Confidence 4899999999999999999999998764 22 334466776665444443333
No 259
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=50.67 E-value=27 Score=24.76 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=20.6
Q ss_pred eEEEcHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008 38 FIYISQEELNSVATFIKQRGREELNSVATFIK 69 (96)
Q Consensus 38 fIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~ 69 (96)
-+|+||+|...+-.=-++-| + |+++|+.
T Consensus 14 ~vrvt~eE~~~I~~kA~~AG---l-S~SeYLR 41 (114)
T PRK13877 14 RVPVLPDEKAEIEANAAAAG---L-SVARYLR 41 (114)
T ss_pred EEEeCHHHHHHHHHHHHHhC---C-CHHHHHH
Confidence 47889999998877777775 2 6666654
No 260
>CHL00183 petJ cytochrome c553; Provisional
Probab=50.54 E-value=14 Score=24.25 Aligned_cols=17 Identities=24% Similarity=0.563 Sum_probs=15.6
Q ss_pred EEcHHHHHHHHHHHHhh
Q psy11008 40 YISQEELNSVATFIKQR 56 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~r 56 (96)
.+|++|+..|+.||..+
T Consensus 87 ~Ls~~ei~~i~aYi~~~ 103 (108)
T CHL00183 87 RLSDEDIEDVANYVLSQ 103 (108)
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 48999999999999877
No 261
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=49.66 E-value=22 Score=26.34 Aligned_cols=17 Identities=24% Similarity=0.765 Sum_probs=12.3
Q ss_pred hhhccccceeHHHHHHh
Q psy11008 66 TFIKQKGRVSVSELVEN 82 (96)
Q Consensus 66 ~~~~~~GRVsi~eL~~~ 82 (96)
.|.++.||+|+.+++..
T Consensus 19 ElVRe~GRiTi~ql~~~ 35 (127)
T PF06163_consen 19 ELVREHGRITIKQLVAK 35 (127)
T ss_pred HHHHHcCCccHHHHHHH
Confidence 34555599999998764
No 262
>CHL00170 cpcA phycocyanin alpha subunit; Reviewed
Probab=49.66 E-value=7.2 Score=29.36 Aligned_cols=22 Identities=27% Similarity=0.548 Sum_probs=18.9
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|++|+| +|..||+++..|+++-
T Consensus 13 D~qgRy--ls~~eL~~l~~~~~~g 34 (162)
T CHL00170 13 DSQGRF--LSNGELQACNGRFQRA 34 (162)
T ss_pred HhccCC--CCHHHHHHHHHHHhcc
Confidence 678886 6899999999999865
No 263
>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=49.62 E-value=49 Score=24.69 Aligned_cols=64 Identities=20% Similarity=0.159 Sum_probs=42.6
Q ss_pred CChHHHHHHHHHHHHcCCccEEeeCC-CceEEEcH--HHHHHHHHHHHhhchhchhhhhhhh--ccccceeHHHHHHhcc
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVIDDR-GKFIYISQ--EELNSVATFIKQRGREELNSVATFI--KQKGRVSVSELVENSN 84 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGViDDR-GKfIyIs~--eEl~~Va~fI~~rgr~~~~~~~~~~--~~~GRVsi~eL~~~sN 84 (96)
++++|+..-++.|+..|.=--++.=. |+.+-.|. .|+..+..-|-+. + ...|.||..+|++.-|
T Consensus 133 ISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~~~~e~~~~~~~il~~-----------~~~~~~g~vt~~~l~~~~~ 201 (223)
T PF04157_consen 133 ISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSVPYSELSKDQSRILEL-----------AEEENGGGVTASELAEKLG 201 (223)
T ss_dssp --HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECST-CHH-HHHHHHHHH-----------H--TTTSEEEHHHHHHHHT
T ss_pred cCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeCCchhhhHHHHHHHHH-----------HHhhcCCCCCHHHHHHHhC
Confidence 57899999999999999767777633 65554444 4774444433332 3 3449999999998766
No 264
>COG3753 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.23 E-value=15 Score=27.83 Aligned_cols=22 Identities=18% Similarity=0.324 Sum_probs=19.6
Q ss_pred ChhhhhhhCCChHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVEL 22 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL 22 (96)
|.+||.++|+.++++++|+-+.
T Consensus 93 l~~la~~~Gld~~El~~~Ls~~ 114 (143)
T COG3753 93 LSQLAQKTGLDEQELLKQLSEQ 114 (143)
T ss_pred HHHHHHHhCCCHHHHHHHHHHH
Confidence 4789999999999999998765
No 265
>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=48.95 E-value=27 Score=19.70 Aligned_cols=13 Identities=23% Similarity=0.434 Sum_probs=10.6
Q ss_pred cccceeHHHHHHh
Q psy11008 70 QKGRVSVSELVEN 82 (96)
Q Consensus 70 ~~GRVsi~eL~~~ 82 (96)
.+|.||..|+...
T Consensus 38 ~~G~I~~~EF~~~ 50 (54)
T PF13833_consen 38 GDGYISFDEFISM 50 (54)
T ss_dssp SSSSEEHHHHHHH
T ss_pred CCCCCCHHHHHHH
Confidence 5799999998764
No 266
>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=48.94 E-value=42 Score=23.02 Aligned_cols=41 Identities=15% Similarity=0.188 Sum_probs=33.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
++||..++++..-+-+=++.|.+.|-+..+-...|-|----
T Consensus 29 ~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~ 69 (135)
T TIGR02010 29 ADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGR 69 (135)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccC
Confidence 68999999999999999999999999987666666665443
No 267
>PRK13239 alkylmercury lyase; Provisional
Probab=48.76 E-value=20 Score=27.92 Aligned_cols=33 Identities=24% Similarity=0.330 Sum_probs=26.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
++||+.+|.+.+.|-.++++|... ++|+.|+-|
T Consensus 40 ~~lA~~~~~~~~~v~~~L~~l~~~-----~~d~~g~iv 72 (206)
T PRK13239 40 TTLAAALGWPVEEVEAVLEAMPDT-----EYDEDGRII 72 (206)
T ss_pred HHHHHHhCCCHHHHHHHHHhCCCe-----EECCCCCEE
Confidence 689999999999999888887422 778887754
No 268
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=48.68 E-value=51 Score=18.89 Aligned_cols=55 Identities=13% Similarity=0.242 Sum_probs=42.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.+++..++++-..+-.-+..|.+.|-+.-..+.+..|..++.+.+.....++...
T Consensus 43 ~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 97 (110)
T COG0640 43 GELAEALGLSQSTVSHHLKVLREAGLVELRREGRLRLYRLADEKVAELLELLLEV 97 (110)
T ss_pred HHHHHHHCCChhHHHHHHHHHHHCCCeEEEecccEEEEecCcHHHHHHHHHHHHH
Confidence 4677788888888888899999999999988888877777777655555554443
No 269
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=48.49 E-value=34 Score=27.84 Aligned_cols=89 Identities=22% Similarity=0.252 Sum_probs=61.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEe-eCCCc---eEEEcHHHHHHHHHHHHhhchhchh---hhhhhhccccce
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVI-DDRGK---FIYISQEELNSVATFIKQRGREELN---SVATFIKQKGRV 74 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGVi-DDRGK---fIyIs~eEl~~Va~fI~~rgr~~~~---~~~~~~~~~GRV 74 (96)
.++|..+|++. +.|..++++|.+.+.- .+.|+ =+..|-+|+..+-++...+.|..-. .|-+|.-+||-|
T Consensus 43 ~e~A~~~gvs~----~tiR~ye~~gll~~~~~~~~gr~~~~~~ftL~ei~~lr~~~~~~~~r~~~~~~~vIai~n~KGGV 118 (388)
T PRK13705 43 GEAADLVGVSS----QAIRDAEKAGRLPHPDMEMRGRVEQRVGYTIEQINHMRDVFGTRLRRAEDVFPPVIGVAAHKGGV 118 (388)
T ss_pred HHHHHHHCcCH----HHHHHHHHcCCCCCCCcCCCCcchhhcCcCHHHHHHHHHhhcccccccCCCCCeEEEEECCCCCc
Confidence 46888888854 4567889999998853 35564 4578999999998887655544333 567888999999
Q ss_pred eHHH--------HHHhccc--ceec-ccccc
Q psy11008 75 SVSE--------LVENSNQ--LVTL-IPDQI 94 (96)
Q Consensus 75 si~e--------L~~~sN~--lI~L-~p~~~ 94 (96)
..+- |+...-+ ||++ +|..+
T Consensus 119 GKTT~a~nLA~~LA~~G~rVLlID~~DpQ~n 149 (388)
T PRK13705 119 YKTSVSVHLAQDLALKGLRVLLVEGNDPQGT 149 (388)
T ss_pred hHHHHHHHHHHHHHhcCCCeEEEcCCCCCCc
Confidence 6543 3333223 6774 77554
No 270
>cd00383 trans_reg_C Effector domain of response regulator. Bacteria and certain eukaryotes like protozoa and higher plants use two-component signal transduction systems to detect and respond to changes in the environment. The system consists of a sensor histidine kinase and a response regulator. The former autophosphorylates in a histidine residue on detecting an external stimulus. The phosphate is then transferred to an invariant aspartate residue in a highly conserved receiver domain of the response regulator. Phosphorylation activates a variable effector domain of the response regulator, which triggers the cellular response. The C-terminal effector domain contains DNA and RNA polymerase binding sites. Several dimers or monomers bind head to tail to small tandem repeats upstream of the genes. The RNA polymerase binding sites interact with the alpha or sigma subunite of RNA polymerase.
Probab=48.44 E-value=41 Score=20.50 Aligned_cols=37 Identities=22% Similarity=0.413 Sum_probs=28.9
Q ss_pred eeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccce-eHHHHHHhc
Q psy11008 32 IDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRV-SVSELVENS 83 (96)
Q Consensus 32 iDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRV-si~eL~~~s 83 (96)
+--.|+=|.+|+.|+.-++-++... |++ |..+|.+..
T Consensus 15 l~~~~~~v~Lt~~e~~lL~~L~~~~---------------~~~vs~~~l~~~l 52 (95)
T cd00383 15 VTRDGEPVELTPKEFELLELLARNP---------------GRVLSREQLLEAV 52 (95)
T ss_pred EEECCEEEEeCHHHHHHHHHHHhCC---------------CCcCCHHHHHHHh
Confidence 3346788999999999999999999 554 667776544
No 271
>CHL00172 cpeB phycoerythrin beta subunit; Provisional
Probab=47.92 E-value=8.5 Score=29.50 Aligned_cols=22 Identities=18% Similarity=0.558 Sum_probs=19.2
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|++|+| +|..||+++..|+++-
T Consensus 13 D~qgRY--Ls~~eL~~L~~~~~~g 34 (177)
T CHL00172 13 DAKAAY--VGGSDLQALKKFISEG 34 (177)
T ss_pred HhccCC--CCHHHHHHHHHHHHhh
Confidence 778885 6999999999999876
No 272
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=47.77 E-value=75 Score=21.11 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=33.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.++|..+|+++.- |.-.++.|-|...-.+.+-|=|-|++++..+.
T Consensus 4 ~e~a~~~gvs~~t----lr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~ 48 (113)
T cd01109 4 KEVAEKTGLSADT----LRYYEKEGLLPPVKRDENGIRDFTEEDLEWLE 48 (113)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCCCcCCCCCccCCHHHHHHHH
Confidence 5899999997654 55678889885544455667788999999875
No 273
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=47.76 E-value=17 Score=30.61 Aligned_cols=28 Identities=32% Similarity=0.655 Sum_probs=25.3
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEeeCC
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVIDDR 35 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViDDR 35 (96)
++..|++.++.|.+|.+.+.+.|++|.+
T Consensus 242 ~~~~~~~~~e~I~~lv~~~ki~~i~~~~ 269 (445)
T smart00434 242 YQVNKAKLIEKIAELVKDKKIEGIIDVR 269 (445)
T ss_pred CcccHHHHHHHHHHHHhcCCCCcceehh
Confidence 5788999999999999999999999854
No 274
>PHA00738 putative HTH transcription regulator
Probab=47.18 E-value=42 Score=24.14 Aligned_cols=40 Identities=13% Similarity=0.241 Sum_probs=31.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.|||..|+|+..-+-.-++-|.+.|-|+-- .+|+++|.+-
T Consensus 30 ~eLae~l~lSQptVS~HLKvLreAGLV~sr--K~Gr~vyY~L 69 (108)
T PHA00738 30 SLISHTLLLSYTTVLRHLKILNEQGYIELY--KEGRTLYAKI 69 (108)
T ss_pred HHHHHhhCCCHHHHHHHHHHHHHCCceEEE--EECCEEEEEE
Confidence 379999999877777889999999888754 4566666653
No 275
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=46.95 E-value=20 Score=21.23 Aligned_cols=22 Identities=27% Similarity=0.268 Sum_probs=15.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQ 23 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~ 23 (96)
++||..||++...|-+.+.+.+
T Consensus 23 ~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 23 QDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred hHHhhheeecHHHHHHHHHHHH
Confidence 6899999996655555555443
No 276
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.69 E-value=33 Score=18.43 Aligned_cols=22 Identities=9% Similarity=0.302 Sum_probs=18.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQ 23 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~ 23 (96)
.++|..++++...+-.++..+.
T Consensus 22 ~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 22 KEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred HHHHHHHCCCHHHHHHHHHHHH
Confidence 5789999998888888877753
No 277
>PRK07785 NADH dehydrogenase subunit C; Provisional
Probab=46.35 E-value=66 Score=25.63 Aligned_cols=45 Identities=29% Similarity=0.412 Sum_probs=33.9
Q ss_pred hHHHHHHHHHHHHc--CCccEEeeCCCc-eEEEcHHHHHHHHHHHHhh
Q psy11008 12 TQSVIDRIVELQKT--GALTGVIDDRGK-FIYISQEELNSVATFIKQR 56 (96)
Q Consensus 12 tq~vI~RI~eL~~~--g~ltGViDDRGK-fIyIs~eEl~~Va~fI~~r 56 (96)
-.++.|++.+..+. +.+..+.-++|. .++|..+.+.+|++|++..
T Consensus 63 ~d~~~~~l~~~~~~f~~ai~~~~~~~~~~~~~V~~e~l~~v~~~Lkd~ 110 (235)
T PRK07785 63 FDEVADRLEEALPEFADAIERVVVDRGELTLHVRREHLVEVAQTLRDD 110 (235)
T ss_pred HHHHHHHHHHHHHhhhhheeEEEEeCCeEEEEEcHHHHHHHHHHHHhC
Confidence 35678888877743 556666556655 5899999999999999974
No 278
>PF00502 Phycobilisome: Phycobilisome protein; InterPro: IPR012128 Cyanobacteria and red algae harvest light through water-soluble complexes, called phycobilisomes, which are attached to the outer face of the thylakoid membrane []. These complexes are capable of transferring the absorbed energy to the photosynthetic reaction centre with greater than 95% efficiency. Phycobilisomes contain various photosynthetic light harvesting proteins known as biliproteins, and linker proteins which help assemble the structure. The two main structural elements of the complex are a core located near the photosynthetic reaction centre, and rods attached to this core. Allophycocyanin is the major component of the core, while the rods contain phycocyanins, phycoerythrins and linker proteins. The rod biliproteins harvest photons, with the excitation energy being passed through the rods into the allophycocyanin in the core. Other core biliproteins subsequently pass this energy to chlorophyll within the thylakoid membrane. This entry represents the alpha and beta subunits found in biliproteins from cyanobacteria and red algae. Structural studies indicate that the basic structural unit of most biliproteins is a heterodimer composed of these alpha and beta subunits [, , , ]. The full protein is a ring-like trimer assembly of these heterodimers. Each subunit of the heterodimer has eight helices and binds chromophores through thioester bonds formed at particular cysteine residues. These chromophores, also known as bilins, are open-chain tetrapyrroles whose number and type vary with the particular biliprotein eg R-phyocerythrin binds five phycoerythrobilins per heterodimer, while allophycocyanin binds two phycocyanobilins per heterodimer.; GO: 0015979 photosynthesis, 0030089 phycobilisome; PDB: 2VML_I 2VJR_A 1KTP_B 3L0F_B 1JBO_B 3KVS_B 1PHN_B 3BRP_B 2C7K_B 2C7L_B ....
Probab=45.96 E-value=9.3 Score=27.48 Aligned_cols=22 Identities=27% Similarity=0.665 Sum_probs=18.3
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|..|+ |+|.+||+++..|++.-
T Consensus 8 D~egR--yls~~EL~~l~~~~~~~ 29 (157)
T PF00502_consen 8 DAEGR--YLSDGELQALKGYFQSA 29 (157)
T ss_dssp HHTTS--ECEHHHHHHHHHHHHTH
T ss_pred HhcCC--CCCHHHHHHHHHHHHhH
Confidence 66777 47999999999998765
No 279
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=45.92 E-value=41 Score=24.74 Aligned_cols=41 Identities=17% Similarity=0.303 Sum_probs=32.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE 45 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE 45 (96)
.+||..++++.+.+..-|++|++.|-|.=+ ..|- .+|.|+-
T Consensus 79 ~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~--~~G~-Y~iNP~~ 119 (165)
T PF05732_consen 79 KEIAEKLGISKPTVSRAIKELEEKNIIKKI--RNGA-YMINPNF 119 (165)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhCCcEEEc--cCCe-EEECcHH
Confidence 579999999999999999999999988643 3453 4566653
No 280
>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=45.63 E-value=14 Score=24.61 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=25.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|+|..+|++.+.|-.++..+...|.|.
T Consensus 36 kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 36 SEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred HHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 5899999999999999999999888764
No 281
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=45.35 E-value=1e+02 Score=22.03 Aligned_cols=46 Identities=15% Similarity=0.116 Sum_probs=37.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|+++ +-|.--++.|-|.-..++.|.|=|-|++.+..+..
T Consensus 11 gevAk~~Gvs~----~TLRyYE~~GLl~p~~r~~~gyR~Y~~~~l~rl~~ 56 (144)
T PRK13752 11 GVFAKAAGVNV----ETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRF 56 (144)
T ss_pred HHHHHHHCcCH----HHHHHHHHCCCCCCCccCCCCCeecCHHHHHHHHH
Confidence 47899999975 45778889999987777778899999999987753
No 282
>TIGR00674 dapA dihydrodipicolinate synthase. Dihydrodipicolinate synthase is a homotetrameric enzyme of lysine biosynthesis. E. coli has several paralogs closely related to dihydrodipicoline synthase (DapA), as well as the more distant N-acetylneuraminate lyase. In Pyrococcus horikoshii, the bidirectional best hit with E. coli is to an uncharacterized paralog of DapA, not DapA itself, and it is omitted from the seed. The putative members from the Chlamydias (pathogens with a parasitic metabolism) are easily the most divergent members of the multiple alignment.
Probab=45.11 E-value=72 Score=24.27 Aligned_cols=48 Identities=17% Similarity=0.138 Sum_probs=37.5
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEee--CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVID--DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
..+..+...+-|+.|.+.| +.|++= .-|-|.++|.+|...+.+...+.
T Consensus 14 g~iD~~~~~~~i~~l~~~G-v~Gi~~~GstGE~~~Ls~~Er~~~~~~~~~~ 63 (285)
T TIGR00674 14 GSVDFAALEKLIDFQIENG-TDAIVVVGTTGESPTLSHEEHKKVIEFVVDL 63 (285)
T ss_pred CCcCHHHHHHHHHHHHHcC-CCEEEECccCcccccCCHHHHHHHHHHHHHH
Confidence 3566666677777777755 788764 78999999999999998876665
No 283
>PRK11569 transcriptional repressor IclR; Provisional
Probab=44.66 E-value=91 Score=23.66 Aligned_cols=43 Identities=12% Similarity=0.101 Sum_probs=33.0
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEE 45 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eE 45 (96)
+.|||...||....+-.=++.|++.|-|. -|++++.-.+...=
T Consensus 46 lseia~~lglpksTv~RlL~tL~~~G~l~--~~~~~~~Y~lG~~l 88 (274)
T PRK11569 46 LTELAQQAGLPNSTTHRLLTTMQQQGFVR--QVGELGHWAIGAHA 88 (274)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEE--EcCCCCeEecCHHH
Confidence 35899999999999989999999999995 56544433455443
No 284
>PF11462 DUF3203: Protein of unknown function (DUF3203); InterPro: IPR021564 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria. ; PDB: 1YWY_A.
Probab=44.63 E-value=20 Score=24.56 Aligned_cols=20 Identities=30% Similarity=0.610 Sum_probs=12.3
Q ss_pred EeeCCCceEEEcHHHHHHHH
Q psy11008 31 VIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 31 ViDDRGKfIyIs~eEl~~Va 50 (96)
|+.=.|+=||||+.|.+++-
T Consensus 40 v~~l~g~Ri~ItEaEAdaLt 59 (74)
T PF11462_consen 40 VVELDGERIYITEAEADALT 59 (74)
T ss_dssp EEEETT--EE--HHHHHHHH
T ss_pred EEEEcCcEEecCHHHhhhee
Confidence 44557999999999998864
No 285
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=44.59 E-value=15 Score=27.80 Aligned_cols=28 Identities=18% Similarity=0.178 Sum_probs=21.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.|||..|+++..-+..=+.+|++.+...
T Consensus 25 ~eLa~~~~VS~~TIRRDL~~Le~~~~~~ 52 (252)
T PRK10681 25 KDAAALLGVSEMTIRRDLNAHSAPVVLL 52 (252)
T ss_pred HHHHHHhCCCHHHHHHHHHHhhcCeEEE
Confidence 6899999997555555599999776543
No 286
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=44.39 E-value=97 Score=20.89 Aligned_cols=47 Identities=13% Similarity=0.175 Sum_probs=37.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.|+|..+|+++. -|.--++.|-|..+-++ |.|=|-|++++..+. +|+
T Consensus 4 gevA~~~gvs~~----tlRyYe~~GLl~p~~~~-~gyR~Y~~~~l~~l~-~I~ 50 (120)
T cd04781 4 AEVARQSGLPAS----TLRYYEEKGLIASIGRR-GLRRQYDPQVLDRLA-LIA 50 (120)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCcCC-CCceecCHHHHHHHH-HHH
Confidence 589999999764 46678889999987764 689999999998875 553
No 287
>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=44.28 E-value=33 Score=23.29 Aligned_cols=38 Identities=13% Similarity=0.246 Sum_probs=31.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
..||..++++..-|.|-+..|++.|-|.++=-..|-||
T Consensus 27 k~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~Gri 64 (78)
T PF03444_consen 27 KTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRI 64 (78)
T ss_pred HHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCC
Confidence 36889999999999999999999999987766555554
No 288
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=44.21 E-value=25 Score=20.95 Aligned_cols=23 Identities=13% Similarity=0.245 Sum_probs=18.7
Q ss_pred hhhhhhhC--CChHHHHHHHHHHHH
Q psy11008 2 EDLAALFR--MKTQSVIDRIVELQK 24 (96)
Q Consensus 2 edLAa~F~--lktq~vI~RI~eL~~ 24 (96)
+++|..++ ++.++|..|++.|..
T Consensus 30 ~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 30 QEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHccchhHHHHHHHHHHHHH
Confidence 57888888 888888899888753
No 289
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.00 E-value=1e+02 Score=20.91 Aligned_cols=46 Identities=17% Similarity=0.197 Sum_probs=35.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|+++. -|.--++.|-|.-.-.+.+.|=|-|++.+..+..
T Consensus 4 gevA~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T cd04784 4 GELAKKTGCSVE----TIRYYEKEGLLPAPARSANNYRLYDEEHLERLLF 49 (127)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHH
Confidence 588999999764 4677899999986555556788889999986654
No 290
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=43.93 E-value=76 Score=20.56 Aligned_cols=50 Identities=14% Similarity=0.282 Sum_probs=39.7
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+++++..+|+..+- |.+|.+.|-+.-..++.+.| ++.+++..+....+-+
T Consensus 3 ~~e~~~~~~i~~~~----l~~lve~Gli~p~~~~~~~~--f~~~~l~rl~~~~rL~ 52 (84)
T PF13591_consen 3 LEEFCEACGIEPEF----LRELVEEGLIEPEGEEEEWY--FSEEDLARLRRIRRLH 52 (84)
T ss_pred HHHHHHHHCcCHHH----HHHHHHCCCeeecCCCCeee--ECHHHHHHHHHHHHHH
Confidence 36788888887654 56788899988877775554 8999999999988876
No 291
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=43.82 E-value=27 Score=27.85 Aligned_cols=36 Identities=39% Similarity=0.607 Sum_probs=31.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHc-CCc---cEEeeCCCc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKT-GAL---TGVIDDRGK 37 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~-g~l---tGViDDRGK 37 (96)
+|||..++.++.-+.+.|++++++ |.+ -|-+=|.|.
T Consensus 109 ~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG~i~DiGp 148 (220)
T PF07900_consen 109 EDLAMLLGISPRTISKDIKEYQKEHGVVVPTRGTIHDIGP 148 (220)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCceeccCCcccccCC
Confidence 699999999999999999999999 765 377778775
No 292
>PF13426 PAS_9: PAS domain; PDB: 3ULF_B 3UE6_E 2Z6D_B 2Z6C_B 3P7N_B 1LL8_A 3MJQ_A 3BWL_A 4EET_B 4EEP_A ....
Probab=43.77 E-value=25 Score=20.29 Aligned_cols=15 Identities=20% Similarity=0.676 Sum_probs=11.9
Q ss_pred EeeCCCceEEEcHHH
Q psy11008 31 VIDDRGKFIYISQEE 45 (96)
Q Consensus 31 ViDDRGKfIyIs~eE 45 (96)
++|.+|+++|+++.=
T Consensus 6 i~d~~g~i~~~N~~~ 20 (104)
T PF13426_consen 6 ILDPDGRILYVNPAF 20 (104)
T ss_dssp EEETTSBEEEE-HHH
T ss_pred EECCcCcEEehhHHH
Confidence 689999999999753
No 293
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=43.64 E-value=38 Score=26.67 Aligned_cols=39 Identities=23% Similarity=0.581 Sum_probs=33.4
Q ss_pred hhhhCCChHHHHHHHHHHHHc-CCccEEeeCCC-ceEEEcHH
Q psy11008 5 AALFRMKTQSVIDRIVELQKT-GALTGVIDDRG-KFIYISQE 44 (96)
Q Consensus 5 Aa~F~lktq~vI~RI~eL~~~-g~ltGViDDRG-KfIyIs~e 44 (96)
..-|+|+.+++++++..|++. |.|+ +.|.-| +-||+.++
T Consensus 234 GriF~L~~~~l~~~L~~l~~~~g~i~-~~~TaGl~qv~~~~~ 274 (286)
T PF13182_consen 234 GRIFKLDEESLAERLEQLEEIYGFIS-WSDTAGLDQVYLKDE 274 (286)
T ss_pred ceEeccCHHHHHHHHHHHHhhcCcEE-EEEcCCCeEEEeccc
Confidence 356999999999999999999 7776 788888 78888874
No 294
>PRK11173 two-component response regulator; Provisional
Probab=43.39 E-value=55 Score=22.61 Aligned_cols=23 Identities=13% Similarity=0.296 Sum_probs=21.0
Q ss_pred CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 34 DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 34 DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
-.|+-+..|+.|+.-+.-|+...
T Consensus 154 ~~~~~~~Lt~~E~~ll~~l~~~~ 176 (237)
T PRK11173 154 PDGEQYKLPRSEFRAMLHFCENP 176 (237)
T ss_pred cCCeEEeCCHHHHHHHHHHHhCC
Confidence 47899999999999999999888
No 295
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=43.35 E-value=57 Score=19.65 Aligned_cols=19 Identities=16% Similarity=0.059 Sum_probs=11.3
Q ss_pred hhhhhCCChHHHHHHHHHH
Q psy11008 4 LAALFRMKTQSVIDRIVEL 22 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL 22 (96)
||..+||+...+-..+++.
T Consensus 1 lA~~~~~s~~~l~~~f~~~ 19 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKE 19 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHH
T ss_pred ChHHhCcCHHHHHHHHHHH
Confidence 5667777666666665554
No 296
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=43.18 E-value=54 Score=18.03 Aligned_cols=14 Identities=7% Similarity=0.112 Sum_probs=8.8
Q ss_pred EEcHHHHHHHHHHH
Q psy11008 40 YISQEELNSVATFI 53 (96)
Q Consensus 40 yIs~eEl~~Va~fI 53 (96)
.++.+.+..+|+++
T Consensus 41 ~~~~~~~~~i~~~l 54 (58)
T TIGR03070 41 TVRLDKVLRVLDAL 54 (58)
T ss_pred CCCHHHHHHHHHHc
Confidence 35667777766654
No 297
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=43.12 E-value=26 Score=22.04 Aligned_cols=32 Identities=31% Similarity=0.483 Sum_probs=18.6
Q ss_pred EcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 41 ISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 41 Is~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
.|+.| ..+|+||...- ++ -...|+.||++.|+
T Consensus 14 ls~~e-~~Ia~yil~~~-~~----------~~~~si~elA~~~~ 45 (77)
T PF01418_consen 14 LSPTE-KKIADYILENP-DE----------IAFMSISELAEKAG 45 (77)
T ss_dssp S-HHH-HHHHHHHHH-H-HH----------HCT--HHHHHHHCT
T ss_pred CCHHH-HHHHHHHHhCH-HH----------HHHccHHHHHHHcC
Confidence 35565 66999998872 11 14568888888775
No 298
>cd04624 CBS_pair_11 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=42.64 E-value=64 Score=19.37 Aligned_cols=37 Identities=8% Similarity=0.136 Sum_probs=24.2
Q ss_pred hCCChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHH
Q psy11008 8 FRMKTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELN 47 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~ 47 (96)
.+.+.+++++++. +.+ ..--|+|+.|+|+ +|+..++.
T Consensus 8 ~~~~~~~~~~~~~---~~~~~~~~v~d~~~~~~G~v~~~~l~ 46 (112)
T cd04624 8 PDTSIREAAKLMA---EENVGSVVVVDPDERPIGIVTERDIV 46 (112)
T ss_pred CCCcHHHHHHHHH---HcCCCEEEEECCCCCEEEEeeHHHHH
Confidence 4455666666653 233 2345779889998 78888874
No 299
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=42.64 E-value=1.2e+02 Score=21.34 Aligned_cols=46 Identities=15% Similarity=0.309 Sum_probs=36.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|+++.- |.--++.|-|.-.-.+.+.|=|.+++++..+..
T Consensus 5 ~e~a~~~gvs~~t----lR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 50 (140)
T PRK09514 5 GELAKLAEVTPDT----LRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRF 50 (140)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHH
Confidence 5789999997653 567788999988766677788889999987753
No 300
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.61 E-value=84 Score=22.98 Aligned_cols=53 Identities=17% Similarity=0.276 Sum_probs=46.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee--CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID--DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD--DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.++|..||+.-..+.+=+....++|.+ ... -+|+==.+|+++++-+..+++++
T Consensus 25 re~Ak~~gvs~sTvy~wv~r~~e~G~~--l~~~~~~GrP~kl~~~q~~~l~e~~~~k 79 (138)
T COG3415 25 REAAKRFGVSISTVYRWVRRYRETGLD--LPPKPRKGRPRKLSEEQLEILLERLREK 79 (138)
T ss_pred HHHHHHhCccHHHHHHHHHHhcccccc--ccCccCCCCCcccCHHHHHHHHHHHhcc
Confidence 478999999999999999999999988 444 47888899999999999999988
No 301
>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=42.56 E-value=87 Score=20.19 Aligned_cols=33 Identities=18% Similarity=0.232 Sum_probs=27.6
Q ss_pred CCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008 9 RMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI 41 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI 41 (96)
++....|-.-++.|.+.|.|.=+-.+.|++-|-
T Consensus 32 ~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~ 64 (116)
T cd07153 32 SISLATVYRTLELLEEAGLVREIELGDGKARYE 64 (116)
T ss_pred CCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence 577777778899999999999988877877774
No 302
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=42.42 E-value=70 Score=26.18 Aligned_cols=89 Identities=19% Similarity=0.250 Sum_probs=59.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEee-CCCc---eEEEcHHHHHHHHHHHHhhc-hhc--hhhhhhhhccccce
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVID-DRGK---FIYISQEELNSVATFIKQRG-REE--LNSVATFIKQKGRV 74 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViD-DRGK---fIyIs~eEl~~Va~fI~~rg-r~~--~~~~~~~~~~~GRV 74 (96)
-++|..+|++++ .|..++.+|.+.+.-. .+|+ =++.|-+|+..+........ |.+ -..|-+|.-+||=|
T Consensus 43 ~eaA~l~gvs~~----~lr~~~~~g~~p~~~~~~~gr~~~R~~ytl~eI~~lr~~~~~~~~r~~~~~~~vIav~n~KGGV 118 (387)
T PHA02519 43 TEVADLIGVTPQ----AIRDAEKSGRLPPPDFETRGRVERRAGYTIDQISHMRDHFGNPNQRPDDKNPVVLAVMSHKGGV 118 (387)
T ss_pred HHHHHHhCcCHH----HHHHHHHcCCCCCCccCCCCcccccceEcHHHHHHHHHHhhccccCcCCCCceEEEEecCCCCC
Confidence 368889999643 4567789999887633 5564 34689999999988876432 222 23678899999998
Q ss_pred eHHH--------HHHhccc--ceec-ccccc
Q psy11008 75 SVSE--------LVENSNQ--LVTL-IPDQI 94 (96)
Q Consensus 75 si~e--------L~~~sN~--lI~L-~p~~~ 94 (96)
..+- |+..--+ +|++ +|..+
T Consensus 119 GKTTta~nLA~~LA~~G~rVLlIDl~DpQ~n 149 (387)
T PHA02519 119 YKTSSAVHTAQWLALQGHRVLLIEGNDPQGT 149 (387)
T ss_pred cHHHHHHHHHHHHHhCCCcEEEEeCCCCCCC
Confidence 5532 3333334 6785 77554
No 303
>PHA02105 hypothetical protein
Probab=42.24 E-value=8.6 Score=25.95 Aligned_cols=23 Identities=43% Similarity=0.769 Sum_probs=20.6
Q ss_pred CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 34 DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 34 DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
..=||+|+|-+|++++--||-.+
T Consensus 39 pqi~yvyls~~e~~si~p~ip~~ 61 (68)
T PHA02105 39 PQIKYVYLSYEEFNSIMPFIPRR 61 (68)
T ss_pred cceEEEEEeHHHhcccccccccc
Confidence 56799999999999999998777
No 304
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=42.16 E-value=1.1e+02 Score=20.87 Aligned_cols=46 Identities=13% Similarity=0.158 Sum_probs=36.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|+++. -|.--++.|-|.-...+.|.|=|.|++++..+..
T Consensus 4 ~e~a~~~gvs~~----tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~ 49 (126)
T cd04785 4 GELARRTGVNVE----TIRYYESIGLLPEPARTAGGYRLYGAAHVERLRF 49 (126)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHH
Confidence 578999999765 4567899999987666677888899999987653
No 305
>CHL00090 apcD allophycocyanin gamma subunit
Probab=41.89 E-value=12 Score=27.79 Aligned_cols=22 Identities=32% Similarity=0.543 Sum_probs=18.6
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|..|+ |.|..||+++..|++.-
T Consensus 12 D~~gR--yls~~EL~~l~~~~~~~ 33 (161)
T CHL00090 12 DDELR--YPTIGELESIQDYLKTG 33 (161)
T ss_pred hhccC--CCCHHHHHHHHHHHHhH
Confidence 56677 57999999999999876
No 306
>PF13274 DUF4065: Protein of unknown function (DUF4065)
Probab=41.84 E-value=39 Score=21.19 Aligned_cols=35 Identities=29% Similarity=0.247 Sum_probs=29.5
Q ss_pred CceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhccc
Q psy11008 36 GKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQ 85 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~ 85 (96)
-....+|++|.+.+-.-|++- |..|-.+|.+.|++
T Consensus 66 ~~~~~l~~~~~~~i~~V~~~~---------------~~~s~~~L~~~sH~ 100 (108)
T PF13274_consen 66 FDLEELSEEEKEIIDEVINKY---------------GDKSAWELSELSHK 100 (108)
T ss_pred cccccCCHHHHHHHHHHHHHH---------------cCCCHHHHHHHHcC
Confidence 456789999998888888888 89999999998873
No 307
>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=41.83 E-value=43 Score=18.21 Aligned_cols=23 Identities=9% Similarity=0.381 Sum_probs=18.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQK 24 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~ 24 (96)
.++|..++++...+-.++..+.+
T Consensus 19 ~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 19 KEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHH
Confidence 57899999998888888877543
No 308
>CHL00171 cpcB phycocyanin beta subunit; Reviewed
Probab=41.53 E-value=11 Score=28.38 Aligned_cols=22 Identities=27% Similarity=0.705 Sum_probs=18.8
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|.+|+| .|..||+++..|+++-
T Consensus 13 D~~gRy--ls~~EL~~l~~~~~~~ 34 (172)
T CHL00171 13 DARGEF--LSNTQLDALSKMVAEG 34 (172)
T ss_pred hhccCC--CCHHHHHHHHHHHHhH
Confidence 666775 7999999999999886
No 309
>PHA01751 hypothetical protein
Probab=41.43 E-value=13 Score=27.07 Aligned_cols=19 Identities=37% Similarity=0.693 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHcCCccEE
Q psy11008 13 QSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 13 q~vI~RI~eL~~~g~ltGV 31 (96)
--+||+|+|||..|.+-|.
T Consensus 15 Rl~vDKIrELE~~GQiYGl 33 (110)
T PHA01751 15 RIAIDKIRELEQRGQIYGL 33 (110)
T ss_pred eehHHHHHHHHHhhhhhhH
Confidence 3478999999999999884
No 310
>cd04613 CBS_pair_SpoIVFB_EriC_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase a
Probab=40.94 E-value=60 Score=19.32 Aligned_cols=21 Identities=24% Similarity=0.555 Sum_probs=16.8
Q ss_pred ccEEeeCCCceE-EEcHHHHHH
Q psy11008 28 LTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 28 ltGViDDRGKfI-yIs~eEl~~ 48 (96)
...|+|+.|+|+ +|+..++..
T Consensus 26 ~~~v~~~~~~~~G~v~~~~l~~ 47 (114)
T cd04613 26 NFPVVDDDGRLVGIVSLDDIRE 47 (114)
T ss_pred ceeEECCCCCEEEEEEHHHHHH
Confidence 456779999998 889888864
No 311
>PF09999 DUF2240: Uncharacterized protein conserved in archaea (DUF2240); InterPro: IPR018716 This family of various hypothetical archaeal proteins has no known function.
Probab=40.71 E-value=25 Score=26.06 Aligned_cols=31 Identities=35% Similarity=0.542 Sum_probs=24.0
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEee
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVID 33 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViD 33 (96)
|+-||+.-|+.-++++.+|++++++ +.|.+|
T Consensus 91 ld~ia~~~g~~~~evv~~in~~q~~--~~~~l~ 121 (144)
T PF09999_consen 91 LDYIAAKTGIEKQEVVAEINELQEE--LGGLLD 121 (144)
T ss_pred HHHHHHhcCCCHHHHHHHHHHHHHH--HhccCC
Confidence 3568889999999999999997653 444444
No 312
>PF09643 YopX: YopX protein; InterPro: IPR019096 YopX is a protein of plasmid origin found in bacteria. It is of approx. 135 residues and is largely helical, with three identical chains probably complexing into a twelve-chain structure. Yop proteins are a subset of pathogenicity factors known as (Yersinia) outer proteins - Yops - which act as chaperones for other proteins such as X. They are exported by the type III secretion system (TTSS) upon bacterial infection of host cells. The TTSS is encoded on a virulence plasmid and is necessary for the survival and replication of the bacterium within host lymphoid tissues []. ; PDB: 2QYZ_A 2P84_A 2OX7_D 2I2L_B.
Probab=40.61 E-value=20 Score=22.63 Aligned_cols=16 Identities=44% Similarity=0.534 Sum_probs=12.8
Q ss_pred CCccEEeeCCCceEEE
Q psy11008 26 GALTGVIDDRGKFIYI 41 (96)
Q Consensus 26 g~ltGViDDRGKfIyI 41 (96)
+.-||+-|-.||-||-
T Consensus 49 ~Q~TGlkDknGkeIyE 64 (121)
T PF09643_consen 49 MQYTGLKDKNGKEIYE 64 (121)
T ss_dssp EEEEEEE-TTSEEEET
T ss_pred ccccCcEecCCCEecc
Confidence 5569999999999994
No 313
>PRK13696 hypothetical protein; Provisional
Probab=40.43 E-value=51 Score=21.68 Aligned_cols=27 Identities=30% Similarity=0.404 Sum_probs=20.6
Q ss_pred ceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 37 KFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 37 KfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
|=|-||++.++.+. ..+ |..|.||++.
T Consensus 4 K~ItI~dd~Y~~L~---~kk---------------~~~SFSevi~ 30 (62)
T PRK13696 4 KTITISDDVYEKLL---EIK---------------GDKSFSEVIR 30 (62)
T ss_pred ceEEeCHHHHHHHH---HHh---------------CCCCHHHHHH
Confidence 67899999999988 556 5567776654
No 314
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.11 E-value=28 Score=25.53 Aligned_cols=24 Identities=13% Similarity=0.349 Sum_probs=19.9
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQK 24 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~ 24 (96)
+.|||.+||++.+.+-+.++.=|+
T Consensus 181 l~dLA~~lGISkst~~ehLRrAe~ 204 (215)
T COG3413 181 LKDLAKELGISKSTLSEHLRRAER 204 (215)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHH
Confidence 479999999999999888876543
No 315
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=40.10 E-value=46 Score=22.13 Aligned_cols=23 Identities=26% Similarity=0.455 Sum_probs=18.8
Q ss_pred CCCceEE-EcHHHHH-HHHHHHHhh
Q psy11008 34 DRGKFIY-ISQEELN-SVATFIKQR 56 (96)
Q Consensus 34 DRGKfIy-Is~eEl~-~Va~fI~~r 56 (96)
+.|.|.+ +|-|||- .++.|+.+.
T Consensus 34 ~~G~Ft~~~t~eemie~~~~~~~~~ 58 (81)
T PF12674_consen 34 QNGEFTQDITMEEMIEFCVPFMDEF 58 (81)
T ss_pred cCCceeecCCHHHHHHHHHHHHHHh
Confidence 4799999 8988874 567888888
No 316
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=39.74 E-value=94 Score=21.37 Aligned_cols=46 Identities=15% Similarity=0.146 Sum_probs=35.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|+++. -|.--++.|-|.....+.|.|=|.|++++..+..
T Consensus 4 ~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T TIGR02047 4 GELAQKTGVSVE----TIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAF 49 (127)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHH
Confidence 589999999765 4667788999987655566788889999887754
No 317
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=39.54 E-value=42 Score=25.54 Aligned_cols=22 Identities=23% Similarity=0.573 Sum_probs=15.3
Q ss_pred hhhhhhccccceeHHHHHHhcc
Q psy11008 63 SVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 63 ~~~~~~~~~GRVsi~eL~~~sN 84 (96)
.+..+++++|+|+++||++..+
T Consensus 9 ~Il~~L~~~~~v~v~eLa~~l~ 30 (256)
T PRK10434 9 AILEYLQKQGKTSVEELAQYFD 30 (256)
T ss_pred HHHHHHHHcCCEEHHHHHHHHC
Confidence 3444445559999999998653
No 318
>TIGR03046 PS_II_psbV2 photosystem II cytochrome PsbV2. Members of this protein family are PsbV2, a protein closely related cytochrome c-550 (PsbV), a protein important to the water-splitting and oxygen-evolving activity of photosystem II. Mutant studies in Thermosynechococcus elongatus showed PsbV2 can partially replace PsbV, from which it appears to have arisen first by duplication, then by intergenic recombination with a different gene.
Probab=39.42 E-value=23 Score=26.55 Aligned_cols=17 Identities=29% Similarity=0.655 Sum_probs=15.7
Q ss_pred EEcHHHHHHHHHHHHhh
Q psy11008 40 YISQEELNSVATFIKQR 56 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~r 56 (96)
.+|++|+.+||.||.+.
T Consensus 127 ~LsdeEL~aIAaYLl~q 143 (155)
T TIGR03046 127 WMDDEEVENLAAFILRA 143 (155)
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 49999999999999887
No 319
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=39.21 E-value=21 Score=25.73 Aligned_cols=39 Identities=13% Similarity=0.397 Sum_probs=29.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEEL 46 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl 46 (96)
.++++.+|++.+++.+||-+|-.. +.-.|+||++.+..+
T Consensus 27 ~ev~~~~~~s~e~~~~~iaq~Ytd------Ln~DGRFi~lG~n~W 65 (129)
T PRK02363 27 NEIQKYLGKSDEEIRERIAQFYTD------LNLDGRFISLGDNKW 65 (129)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHH------HhccCCeeEcCCCce
Confidence 467788899988988888887654 445689999887654
No 320
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=38.91 E-value=34 Score=26.34 Aligned_cols=28 Identities=21% Similarity=0.317 Sum_probs=25.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
-++|++|+.+-+...+-++.|-..|.|-
T Consensus 128 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 155 (166)
T PRK15466 128 GEVAAHFGWPLEKARNALEQLFSAGTLR 155 (166)
T ss_pred HHHHHHhCCcHHHHHHHHHHHHhccchh
Confidence 3789999999999999999999999874
No 321
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=38.89 E-value=96 Score=22.85 Aligned_cols=53 Identities=15% Similarity=0.218 Sum_probs=42.0
Q ss_pred HHHHHHHHcCCccEEe-eCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008 17 DRIVELQKTGALTGVI-DDRGKFIYISQEELNSVATFIKQRGREELNSVATFIK 69 (96)
Q Consensus 17 ~RI~eL~~~g~ltGVi-DDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~ 69 (96)
.-|.+|.+.|-|+--. .+...+..||++--+.+.-|.++-...-.+.+..|++
T Consensus 38 q~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~~Ip~~i~~~i~~~l~ 91 (163)
T PF14277_consen 38 QALSELVESGLITLETDSDNKTRYSITEKGKETLEFFENRIPESIREDIDEYLK 91 (163)
T ss_pred HHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 3477999999999775 4555788999999998888888877666677777776
No 322
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=38.56 E-value=1.3e+02 Score=20.53 Aligned_cols=45 Identities=16% Similarity=0.290 Sum_probs=36.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.|+|..+|+++. -|.--++.|-|.-.-.+.|.|=+-|++++..+.
T Consensus 4 ~e~a~~~gvs~~----tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~ 48 (127)
T TIGR02044 4 GQVAKLTGLSSK----MIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELR 48 (127)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH
Confidence 578999999764 456889999998766666668888999998876
No 323
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=38.51 E-value=44 Score=25.56 Aligned_cols=21 Identities=43% Similarity=0.621 Sum_probs=14.8
Q ss_pred hhhhhccccceeHHHHHHhcc
Q psy11008 64 VATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 64 ~~~~~~~~GRVsi~eL~~~sN 84 (96)
+..+++++|.|+++||++.-|
T Consensus 10 Il~~l~~~g~v~v~eLa~~~~ 30 (253)
T COG1349 10 ILELLKEKGKVSVEELAELFG 30 (253)
T ss_pred HHHHHHHcCcEEHHHHHHHhC
Confidence 334444449999999998654
No 324
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=38.10 E-value=1.4e+02 Score=22.67 Aligned_cols=78 Identities=18% Similarity=0.186 Sum_probs=53.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV 80 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~ 80 (96)
+.|||...|+....+-.-++.|++.|-+. -|+.++-.++++.=+.-=+.|..+.. +..-.+--+.+|+
T Consensus 22 l~ela~~~glpksT~~RlL~tL~~~G~v~--~d~~~g~Y~Lg~~~~~lg~~~l~~~~----------l~~~a~p~l~~L~ 89 (246)
T COG1414 22 LAELAERLGLPKSTVHRLLQTLVELGYVE--QDPEDGRYRLGPRLLELGAAALSSLD----------LVSLARPLLEELA 89 (246)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHCCCEE--EcCCCCcEeehHHHHHHHHHHHhcCC----------HHHHhHHHHHHHH
Confidence 35899999999999999999999999875 56644444788877766666666541 1111233346777
Q ss_pred Hhcccceecc
Q psy11008 81 ENSNQLVTLI 90 (96)
Q Consensus 81 ~~sN~lI~L~ 90 (96)
+..+..+.|.
T Consensus 90 ~~tgetv~L~ 99 (246)
T COG1414 90 EETGETVHLS 99 (246)
T ss_pred HHhCCcEEEE
Confidence 7777665554
No 325
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=37.85 E-value=62 Score=26.76 Aligned_cols=44 Identities=11% Similarity=0.194 Sum_probs=33.1
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV 49 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V 49 (96)
++|||..-+|+.+|||.-++ ..|.+ ..-..+-+|+++++.++..
T Consensus 226 i~~is~~T~i~~~Dii~tL~---~l~~l--~~~~g~~~i~~~~~~~~~~ 269 (290)
T PLN03238 226 IKDLSLATGIRGEDIVSTLQ---SLNLI--KYWKGQHVIHVDQRVLDEH 269 (290)
T ss_pred HHHHHHHhCCCHHHHHHHHH---HCCcE--EEECCcEEEEeCHHHHHHH
Confidence 47899999999999987655 45555 3456677888998876654
No 326
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=37.71 E-value=64 Score=19.97 Aligned_cols=30 Identities=23% Similarity=0.365 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHH
Q psy11008 43 QEELNSVATFIKQRGREELNSVATFIKQKGRVSVSEL 79 (96)
Q Consensus 43 ~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL 79 (96)
++.+.++|.+|+++ +..+-+..+..+...+
T Consensus 20 ee~l~~~a~~i~~~-------i~~~~~~~~~~~~~~~ 49 (89)
T PF05164_consen 20 EEYLRKAAELINEK-------INEIKKKYPKLSPERL 49 (89)
T ss_dssp HHHHHHHHHHHHHH-------HHHHCTTCCTSSHHHH
T ss_pred HHHHHHHHHHHHHH-------HHHHHHHcCCCCHHHH
Confidence 67899999999999 3444344344554443
No 327
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=37.71 E-value=51 Score=24.55 Aligned_cols=54 Identities=11% Similarity=0.186 Sum_probs=37.6
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+.|||.+.||+...+-.=++.|++.|-+.=- ++.|+| ++.+.=+.--..+..+.
T Consensus 31 l~eia~~lgl~kstv~Rll~tL~~~G~l~~~-~~~~~Y-~lG~~~~~lg~~~~~~~ 84 (257)
T PRK15090 31 ITELSQRVMMSKSTVYRFLQTMKTLGYVAQE-GESEKY-SLTLKLFELGAKALQNV 84 (257)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc-CCCCcE-EecHHHHHHHHHHHhhC
Confidence 3589999999999999999999999987431 244554 56665444434444433
No 328
>PTZ00246 proteasome subunit alpha; Provisional
Probab=37.63 E-value=1.6e+02 Score=22.19 Aligned_cols=48 Identities=8% Similarity=0.138 Sum_probs=32.6
Q ss_pred CCChHHHHHH----HHHHHHcCCc------cEEeeCCC-----ceEEEcHHHHHHHHHHHHhh
Q psy11008 9 RMKTQSVIDR----IVELQKTGAL------TGVIDDRG-----KFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 9 ~lktq~vI~R----I~eL~~~g~l------tGViDDRG-----KfIyIs~eEl~~Va~fI~~r 56 (96)
+|+.+++++- |..+...+.. .+|++..| .|..+|++|++.+-+-+.+.
T Consensus 182 ~ms~eeai~l~~~al~~~~~~d~~s~~~vev~ii~~~~~~~~~~~~~l~~~ei~~~l~~~~~~ 244 (253)
T PTZ00246 182 DLTLEQGLLLAAKVLTKSMDSTSPKADKIEVGILSHGETDGEPIQKMLSEKEIAELLKKVTQE 244 (253)
T ss_pred CCCHHHHHHHHHHHHHHHHhccCCCCCcEEEEEEecCCcCCCCCeEECCHHHHHHHHHHHhhh
Confidence 4677777765 3444444444 56898654 49999999999877766544
No 329
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=37.58 E-value=70 Score=24.27 Aligned_cols=45 Identities=24% Similarity=0.288 Sum_probs=39.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc-eEEEcHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK-FIYISQEEL 46 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK-fIyIs~eEl 46 (96)
.|+|.-+|++..++-.-+++|.+.|.|..|-.++|+ ..|+.++.+
T Consensus 185 ~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~~G~~~~~~~~~~~ 230 (327)
T PF06224_consen 185 ADFAWWSGLPKTQARRALAQLVEEGELVEVEVEGGKEPLYDLPEDL 230 (327)
T ss_pred HHHHHHhccCHHHHHHHHHhhccCCcEEEEEEcCcceeEEechhhh
Confidence 689999999999999999999999999999998777 488888755
No 330
>cd04801 CBS_pair_M50_like This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with the metalloprotease peptidase M50. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=37.55 E-value=95 Score=18.81 Aligned_cols=37 Identities=19% Similarity=0.407 Sum_probs=22.0
Q ss_pred CCChHHHHHHHHHHHHcCCcc--EEeeCCCceE-EEcHHHHHH
Q psy11008 9 RMKTQSVIDRIVELQKTGALT--GVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~lt--GViDDRGKfI-yIs~eEl~~ 48 (96)
+++..++++++. +.+... =|+|+.|+++ +++...+..
T Consensus 9 ~~~l~~~~~~~~---~~~~~~~~~V~d~~~~~~G~v~~~dl~~ 48 (114)
T cd04801 9 HLTLREFVREYV---LGSNQRRFVVVDNEGRYVGIISLADLRA 48 (114)
T ss_pred CCCHHHHHHHHh---ccCCceeEEEEcCCCcEEEEEEHHHHHH
Confidence 445555655442 222133 3569999998 678887654
No 331
>KOG1610|consensus
Probab=37.44 E-value=39 Score=28.31 Aligned_cols=54 Identities=20% Similarity=0.382 Sum_probs=40.3
Q ss_pred HHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhh---------hh-ccccce
Q psy11008 18 RIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVAT---------FI-KQKGRV 74 (96)
Q Consensus 18 RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~---------~~-~~~GRV 74 (96)
.+++-.+++-|.||+..-|-+....|.|+..+.+|.+.- +.|-+.+ ++ +++|||
T Consensus 97 ~V~~~l~~~gLwglVNNAGi~~~~g~~ewl~~~d~~~~l---~vNllG~irvT~~~lpLlr~arGRv 160 (322)
T KOG1610|consen 97 WVKKHLGEDGLWGLVNNAGISGFLGPDEWLTVEDYRKVL---NVNLLGTIRVTKAFLPLLRRARGRV 160 (322)
T ss_pred HHHHhcccccceeEEeccccccccCccccccHHHHHHHH---hhhhhhHHHHHHHHHHHHHhccCeE
Confidence 344444445599999999999999999999999999887 4554432 12 467887
No 332
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=37.40 E-value=47 Score=23.06 Aligned_cols=35 Identities=23% Similarity=0.429 Sum_probs=27.3
Q ss_pred EEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcccce
Q psy11008 40 YISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLV 87 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~lI 87 (96)
-.|+.|.++++-|+.+- +.|.+|+..|+..-=.|+
T Consensus 15 lL~e~E~~tm~yyl~eY-------------~~~~~tVealV~aL~elL 49 (81)
T cd07357 15 LLSENERATLSYYLDEY-------------RSGHISVDALVMALFELL 49 (81)
T ss_pred HcCHHHHHHHHHHHHHH-------------HcCCCCHHHHHHHHHHHh
Confidence 36888999999999886 458999999987654443
No 333
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=37.32 E-value=51 Score=25.29 Aligned_cols=42 Identities=31% Similarity=0.506 Sum_probs=28.9
Q ss_pred eeCCCceEEE---cHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhccc
Q psy11008 32 IDDRGKFIYI---SQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQ 85 (96)
Q Consensus 32 iDDRGKfIyI---s~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~ 85 (96)
++|=+.-||| +.||+..++.-|.+- ++. |++|+.+|++.-|.
T Consensus 89 ~~DLsdii~i~f~~deel~~~~e~i~~~-----------v~~-Gn~Sl~~lsr~l~~ 133 (160)
T PF09824_consen 89 MEDLSDIIYIAFMSDEELRDYVEKIEKE-----------VEA-GNTSLSDLSRKLGI 133 (160)
T ss_pred HHHHHHHHheeecCHHHHHHHHHHHHHH-----------HHc-CCCcHHHHHHHhCC
Confidence 3333444444 578888888777765 444 99999999987653
No 334
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.26 E-value=99 Score=19.80 Aligned_cols=48 Identities=17% Similarity=0.185 Sum_probs=35.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.++|..+|+++.- |...++.|-|.-.-+ .|.|-|.|++++..+..-..
T Consensus 5 ~e~A~~~gvs~~t----Lr~ye~~Gli~p~r~-~~g~R~y~~~dv~~l~~i~~ 52 (91)
T cd04766 5 SVAAELSGMHPQT----LRLYERLGLLSPSRT-DGGTRRYSERDIERLRRIQR 52 (91)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCcCCCcC-CCCCeeECHHHHHHHHHHHH
Confidence 5889999997654 456678899986544 45678899999988765443
No 335
>TIGR01044 rplV_bact ribosomal protein L22, bacterial type. This model decribes bacterial and chloroplast ribosomal protein L22.
Probab=37.25 E-value=25 Score=24.01 Aligned_cols=47 Identities=17% Similarity=0.340 Sum_probs=36.4
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.+|++.+|+.-+..||..|+-.--++--..-.|...|+---+..|..
T Consensus 2 ~~r~~r~SpkK~~~va~~IrG~~v~~A~~~L~f~pkk~a~~i~klL~ 48 (103)
T TIGR01044 2 KARFVRISPRKARLVADLIRGKSVSQALDILRFTPKKAAPLIKKVLA 48 (103)
T ss_pred cccccccCHHHHHHHHHHHcCCcHHHHHHHHhhCCHhHHHHHHHHHH
Confidence 47899999999999999999876555556667777777766655543
No 336
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=36.84 E-value=1.4e+02 Score=20.42 Aligned_cols=45 Identities=11% Similarity=0.175 Sum_probs=34.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.|+|..+|+++. -|.--++.|-|.-.-.+.|.|=|.|++++..+.
T Consensus 4 ~e~a~~~gvs~~----tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~ 48 (127)
T cd01108 4 GEAAKLTGLSAK----MIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELR 48 (127)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHHHHHH
Confidence 578999999764 456788899998554455667788999988764
No 337
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=36.76 E-value=31 Score=21.25 Aligned_cols=21 Identities=10% Similarity=0.254 Sum_probs=18.1
Q ss_pred ChhhhhhhCCChHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~e 21 (96)
+|.+|.++|++.+++.+++.+
T Consensus 8 Ie~~A~~~~~s~~ea~~~~~~ 28 (62)
T PF12668_consen 8 IEEFAKKLNISGEEAYNYFKR 28 (62)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 478899999999999998774
No 338
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.74 E-value=42 Score=24.87 Aligned_cols=22 Identities=36% Similarity=0.761 Sum_probs=20.4
Q ss_pred CceEEEcHHHHHHHHHHHHhhc
Q psy11008 36 GKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~rg 57 (96)
-+|=|++.++|+-|--|++-||
T Consensus 37 s~F~~Lt~d~LeFv~lf~r~RG 58 (122)
T COG3877 37 SKFEYLTSDQLEFVELFLRCRG 58 (122)
T ss_pred ccccccCHhHhHHHHHHHHHcc
Confidence 4789999999999999999996
No 339
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=36.61 E-value=1.1e+02 Score=22.92 Aligned_cols=42 Identities=19% Similarity=0.228 Sum_probs=32.2
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
+.|||..+|+....+-.=++.|++.|-+.=.- +.|+| .+++.
T Consensus 29 ~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~-~~~~Y-~Lg~~ 70 (263)
T PRK09834 29 VGLLAELTGLHRTTVRRLLETLQEEGYVRRSA-SDDSF-RLTLK 70 (263)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec-CCCcE-EEcHH
Confidence 36899999999999999999999999987432 23444 45544
No 340
>PF06165 Glyco_transf_36: Glycosyltransferase family 36; InterPro: IPR010383 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyltransferase family 36 includes cellobiose phosphorylase (2.4.1.20 from EC), cellodextrin phosphorylase (2.4.1.49 from EC), and chitobiose phosphorylase. Many members of this family contain two copies of the domain represented in this entry.; PDB: 3QDE_A 3RRS_B 1V7V_A 1V7W_A 1V7X_A 3ACT_B 2CQT_A 3QFY_B 3QFZ_A 2CQS_A ....
Probab=35.94 E-value=14 Score=24.99 Aligned_cols=13 Identities=54% Similarity=1.043 Sum_probs=10.5
Q ss_pred eCCCceEEEcHHH
Q psy11008 33 DDRGKFIYISQEE 45 (96)
Q Consensus 33 DDRGKfIyIs~eE 45 (96)
|..|.||||-+++
T Consensus 1 D~~G~~~YirD~~ 13 (110)
T PF06165_consen 1 DPPGEFIYIRDED 13 (110)
T ss_dssp TBSBSEEEEEETT
T ss_pred CCCeeEEEEEECC
Confidence 6789999998654
No 341
>PF01886 DUF61: Protein of unknown function DUF61; InterPro: IPR002746 The proteins in this entry are functionally uncharacterised.
Probab=35.84 E-value=83 Score=22.74 Aligned_cols=39 Identities=21% Similarity=0.291 Sum_probs=31.9
Q ss_pred HHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 17 DRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 17 ~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
..+.+|.+++..+=+.-| |.+-|+-.+|++.+++-+-.-
T Consensus 21 ktL~eLL~ee~P~i~lrd-G~~h~f~k~ELe~L~~~lp~~ 59 (132)
T PF01886_consen 21 KTLKELLEEEKPSIILRD-GSRHRFDKEELERLAEILPEY 59 (132)
T ss_pred hhHHHHHhCCCCeEEecC-CCEEEEcHHHHHHHHHhCCHH
Confidence 458899999998877745 999999999999998866543
No 342
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=35.77 E-value=34 Score=21.83 Aligned_cols=21 Identities=5% Similarity=0.381 Sum_probs=18.7
Q ss_pred ChhhhhhhCCChHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~e 21 (96)
|++|+..|++..+++++|+..
T Consensus 23 Ld~Lc~~~~id~~~l~~kL~~ 43 (55)
T PF14056_consen 23 LDELCYDYDIDKEELEEKLAS 43 (55)
T ss_pred HHHHHHHhCCCHHHHHHHHHH
Confidence 578999999999999998865
No 343
>PF13359 DDE_Tnp_4: DDE superfamily endonuclease
Probab=35.66 E-value=26 Score=23.49 Aligned_cols=18 Identities=33% Similarity=0.519 Sum_probs=15.2
Q ss_pred CccEEeeCCCceEEEcHH
Q psy11008 27 ALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 27 ~ltGViDDRGKfIyIs~e 44 (96)
.+..|+|.+|+|+|++-.
T Consensus 31 ~~q~v~d~~g~i~~v~~~ 48 (158)
T PF13359_consen 31 KVQIVCDPDGRIIYVSVG 48 (158)
T ss_pred eEEEEEeccceeEeeecc
Confidence 356899999999999874
No 344
>PF11888 DUF3408: Protein of unknown function (DUF3408); InterPro: IPR021823 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 128 to 160 amino acids in length.
Probab=35.55 E-value=77 Score=22.28 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=24.9
Q ss_pred EEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHh
Q psy11008 39 IYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVEN 82 (96)
Q Consensus 39 IyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~ 82 (96)
+|||.|=.+.++..+.--| .+.+|++-++.+
T Consensus 83 vyI~~e~h~~l~~Iv~~ig-------------~~~~si~~yidN 113 (136)
T PF11888_consen 83 VYISRETHERLSRIVRVIG-------------ERKMSISGYIDN 113 (136)
T ss_pred eEECHHHHHHHHHHHHHHC-------------CCCCcHHHHHHH
Confidence 9999999999999998885 245788776654
No 345
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=35.50 E-value=36 Score=24.97 Aligned_cols=30 Identities=23% Similarity=0.312 Sum_probs=23.0
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK 37 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK 37 (96)
||.++|++. .+++.|.++|.|.|.-+-.+|
T Consensus 109 La~~L~lSr----s~l~~l~~~G~I~~~~~~~~~ 138 (142)
T PF06353_consen 109 LARQLGLSR----SRLKRLIEQGLIRSDPDKSKK 138 (142)
T ss_pred HHHHhCcCH----HHHHHHHHCCCEEecCccchh
Confidence 677778775 467899999999998775443
No 346
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=35.45 E-value=1.5e+02 Score=24.95 Aligned_cols=78 Identities=13% Similarity=0.205 Sum_probs=41.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHH----cCCccEEeeC-CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQK----TGALTGVIDD-RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSV 76 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~----~g~ltGViDD-RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi 76 (96)
.+||..||+++.-+.+-|++|.. .|. +++-. .|-.+-+... +....+..+...|...-....+. ..-+++
T Consensus 21 ~~LA~~l~VS~RTIr~dI~~in~~l~~~~~--~~i~~~~Gy~l~~~~~--~~~~~~~~~~~~e~~~il~~Ll~-~~~~~~ 95 (584)
T PRK09863 21 GELAQQLGVSRRTIVRDIAYINFTLNGKAI--GSISGSAKYHLEILNR--RSLFQLLQKSDNEDRLLLLRLLL-NTFTPM 95 (584)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhcch--hheecCCceEEEeCCH--HHHHHHHhcCCHHHHHHHHHHHH-cCCccH
Confidence 58999999999999888887744 222 22332 4533333322 22223332221111111222333 567888
Q ss_pred HHHHHhcc
Q psy11008 77 SELVENSN 84 (96)
Q Consensus 77 ~eL~~~sN 84 (96)
.+|++.-+
T Consensus 96 ~~La~~l~ 103 (584)
T PRK09863 96 AQLASALN 103 (584)
T ss_pred HHHHHHhC
Confidence 88887643
No 347
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=35.34 E-value=1.3e+02 Score=21.38 Aligned_cols=47 Identities=15% Similarity=0.227 Sum_probs=35.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~ 54 (96)
.++|..+|++++. |...++.|.|... . +|.+-+-|++++..+..-..
T Consensus 5 ~eVA~~~GVs~~T----LR~wE~~GLl~p~-r-~~G~R~Ys~~dv~rL~~I~~ 51 (120)
T cd04767 5 GVVAELLNIHPET----LRIWERHGLIKPA-R-RNGQRLYSNNDLKRLRFIKK 51 (120)
T ss_pred HHHHHHHCcCHHH----HHHHHHCCCCCCc-C-CCCcEEECHHHHHHHHHHHH
Confidence 5899999998763 4477788999875 3 57888889999987754433
No 348
>PHA02762 hypothetical protein; Provisional
Probab=35.28 E-value=26 Score=23.27 Aligned_cols=34 Identities=32% Similarity=0.375 Sum_probs=23.5
Q ss_pred HHHcCCccEEeeCCCceEEEcHHHHH-HHHHHHHh
Q psy11008 22 LQKTGALTGVIDDRGKFIYISQEELN-SVATFIKQ 55 (96)
Q Consensus 22 L~~~g~ltGViDDRGKfIyIs~eEl~-~Va~fI~~ 55 (96)
.+-.--+|==+|+.|+.-|||-|-++ .++.||+.
T Consensus 24 ~eg~afvtigide~g~iayisiep~dkdl~~~i~r 58 (62)
T PHA02762 24 FEGEAFVTIGIDENDKISYISIEPLDKDLKEGIKR 58 (62)
T ss_pred ccccEEEEEeECCCCcEEEEEecccchHHHHhhhh
Confidence 33344456568999999999977554 46777764
No 349
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=35.22 E-value=47 Score=26.08 Aligned_cols=30 Identities=17% Similarity=0.266 Sum_probs=27.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEE
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGV 31 (96)
.|||...|+++.-|..-++.|+++|.+.=.
T Consensus 29 ~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 29 DELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 589999999999999999999999977655
No 350
>PF14903 WG_beta_rep: WG containing repeat
Probab=34.96 E-value=33 Score=17.78 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=15.0
Q ss_pred EEeeCCCceEEEcHHHHHHHHHH
Q psy11008 30 GVIDDRGKFIYISQEELNSVATF 52 (96)
Q Consensus 30 GViDDRGKfIyIs~eEl~~Va~f 52 (96)
|++|..||.|. +-+++.+..|
T Consensus 2 G~id~~G~~vi--~~~yd~i~~~ 22 (35)
T PF14903_consen 2 GYIDKNGKIVI--PPKYDEIYPF 22 (35)
T ss_pred EEEeCCCCEEE--EccccCcccc
Confidence 89999999863 4466665555
No 351
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=34.92 E-value=46 Score=19.77 Aligned_cols=41 Identities=12% Similarity=0.251 Sum_probs=26.7
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQE 44 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~e 44 (96)
.-|..++++...+-.+|++||+.=-.. +++-.|+-+..|++
T Consensus 18 ~AA~~l~is~~~vs~~i~~LE~~lg~~-Lf~r~~~~~~lT~~ 58 (60)
T PF00126_consen 18 AAAEELGISQSAVSRQIKQLEEELGVP-LFERSGRGLRLTEA 58 (60)
T ss_dssp HHHHHCTSSHHHHHHHHHHHHHHHTS--SEEECSSSEEE-HH
T ss_pred HHHHHhhccchHHHHHHHHHHHHhCCe-EEEECCCCeeEChh
Confidence 357889999999999999999753222 34444444555553
No 352
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=34.66 E-value=72 Score=23.38 Aligned_cols=37 Identities=27% Similarity=0.433 Sum_probs=31.7
Q ss_pred hhhhhhh--CCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008 2 EDLAALF--RMKTQSVIDRIVELQKTGALTGVIDDRGKFIY 40 (96)
Q Consensus 2 edLAa~F--~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy 40 (96)
+.||..+ ++++.++-+-|+-|++.|-|. .|..|+|.-
T Consensus 43 ~~iak~l~p~is~~ev~~sL~~L~~~gli~--k~~~g~y~~ 81 (171)
T PF14394_consen 43 EWIAKRLRPKISAEEVRDSLEFLEKLGLIK--KDGDGKYVQ 81 (171)
T ss_pred HHHHHHhcCCCCHHHHHHHHHHHHHCCCeE--ECCCCcEEE
Confidence 5789999 999999999999999999986 455588863
No 353
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=34.56 E-value=25 Score=19.06 Aligned_cols=15 Identities=7% Similarity=0.244 Sum_probs=10.8
Q ss_pred hhhhhhhCCChHHHH
Q psy11008 2 EDLAALFRMKTQSVI 16 (96)
Q Consensus 2 edLAa~F~lktq~vI 16 (96)
..||..|+++.+++.
T Consensus 10 ~~IA~~~~~~~~~l~ 24 (44)
T PF01476_consen 10 WSIAKRYGISVDELM 24 (44)
T ss_dssp HHHHHHTTS-HHHHH
T ss_pred HHHHhhhhhhHhHHH
Confidence 578999999766654
No 354
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=34.51 E-value=70 Score=21.39 Aligned_cols=48 Identities=10% Similarity=0.197 Sum_probs=32.9
Q ss_pred CChHHHHHHHHHHHHcCC-----cc-E---------EeeCCCceEEEcHHHHHHHHHHHHhhc
Q psy11008 10 MKTQSVIDRIVELQKTGA-----LT-G---------VIDDRGKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~-----lt-G---------ViDDRGKfIyIs~eEl~~Va~fI~~rg 57 (96)
+..+++..+|+.+..... +. | .....|+.+-+|+.|++-+.-+....|
T Consensus 102 ~~~~~l~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Lt~~E~~il~~l~~~~g 164 (223)
T PRK11517 102 FSFSELLARVRAQLRQHHALNSTLEISGLRMDSVSQSVSRDNISITLTRKEFQLLWLLASRAG 164 (223)
T ss_pred CCHHHHHHHHHHHHccccCcCCeEEECCEEEEcCCCEEEECCEEEeCCHHHHHHHHHHHhCCC
Confidence 345778888877654321 11 1 122358899999999999999888884
No 355
>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=34.31 E-value=1.3e+02 Score=21.20 Aligned_cols=39 Identities=31% Similarity=0.347 Sum_probs=32.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
|+||..|+-+...|---+.-|++-|.|.- ++. +.|||++
T Consensus 57 e~LA~~~~~~~~~V~~AL~~f~k~glIe~--~ed-~~i~i~~ 95 (121)
T PF09681_consen 57 EMLALEFDRPVDTVRLALAVFQKLGLIEI--DED-GVIYIPN 95 (121)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEEE--ecC-CeEEeec
Confidence 78999999999999999999999999976 444 4566665
No 356
>PF06970 RepA_N: Replication initiator protein A (RepA) N-terminus; InterPro: IPR010724 This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids []. Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=34.28 E-value=36 Score=22.27 Aligned_cols=21 Identities=43% Similarity=0.637 Sum_probs=17.4
Q ss_pred EEeeCCC-ceEEEcHHHHHHHH
Q psy11008 30 GVIDDRG-KFIYISQEELNSVA 50 (96)
Q Consensus 30 GViDDRG-KfIyIs~eEl~~Va 50 (96)
|-+|+.| =||+-|-||+...-
T Consensus 41 ~wiDe~G~vYi~~s~eel~~~L 62 (76)
T PF06970_consen 41 GWIDENGNVYIIFSIEELMELL 62 (76)
T ss_pred CcCCCCCCEEEEeeHHHHHHHH
Confidence 5799999 69999999987643
No 357
>cd04593 CBS_pair_EriC_assoc_bac_arch This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the EriC CIC-type chloride channels in bacteria and archaea. These ion channels are proteins with a seemingly simple task of allowing the passive flow of chloride ions across biological membranes. CIC-type chloride channels come from all kingdoms of life, have several gene families, and can be gated by voltage. The members of the CIC-type chloride channel are double-barreled: two proteins forming homodimers at a broad interface formed by four helices from each protein. The two pores are not found at this interface, but are completely contained within each subunit, as deduced from the mutational analyses, unlike many other channels, in which four or five identical or structurally related subunits jointly form one pore. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS d
Probab=34.24 E-value=80 Score=19.19 Aligned_cols=36 Identities=14% Similarity=0.236 Sum_probs=21.7
Q ss_pred CChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHHH
Q psy11008 10 MKTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
++..++++++ .+.+ ..--|+|+.|+|+ +++..++..
T Consensus 10 ~~~~~~~~~~---~~~~~~~~~V~d~~~~~~G~v~~~dl~~ 47 (115)
T cd04593 10 TPLREAAEQL---IESKHGSALVVDRDGGVVGIITLPDLLR 47 (115)
T ss_pred CCHHHHHHHH---HhCCCcEEEEEcCCCCEEEEEEHHHHHH
Confidence 3444555544 3333 2234779899999 678887754
No 358
>CHL00086 apcA allophycocyanin alpha subunit
Probab=34.23 E-value=18 Score=26.91 Aligned_cols=22 Identities=23% Similarity=0.578 Sum_probs=18.8
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|..|+| .|..||+++..|++.-
T Consensus 12 D~~gRy--ls~~eL~~l~~~~~~~ 33 (161)
T CHL00086 12 DAEARY--LSPGELDRIKSFVLSG 33 (161)
T ss_pred HhccCC--CCHHHHHHHHHHHHhh
Confidence 567775 7999999999999886
No 359
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=34.09 E-value=51 Score=24.99 Aligned_cols=22 Identities=5% Similarity=0.143 Sum_probs=15.2
Q ss_pred hhhhhhccccceeHHHHHHhcc
Q psy11008 63 SVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 63 ~~~~~~~~~GRVsi~eL~~~sN 84 (96)
.+..+++++|+|+++||++.-|
T Consensus 11 ~I~~~l~~~~~v~v~eLa~~~~ 32 (252)
T PRK10681 11 QLLQALKRSDKLHLKDAAALLG 32 (252)
T ss_pred HHHHHHHHcCCCcHHHHHHHhC
Confidence 3444445559999999998643
No 360
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.94 E-value=1.5e+02 Score=19.90 Aligned_cols=45 Identities=11% Similarity=0.140 Sum_probs=35.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|++.. -|.--++.|-|.-+-++. .|=|.+++++..+..
T Consensus 4 ge~a~~~gvs~~----tLryYe~~GLi~p~~~~~-~yR~Y~~~d~~~l~~ 48 (116)
T cd04769 4 GELAQQTGVTIK----AIRLYEEKGLLPSPKRSG-NYRVYDAQHVECLRF 48 (116)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCCCC-CceeeCHHHHHHHHH
Confidence 588999999764 467889999999877665 688889999888654
No 361
>PF10335 DUF294_C: Putative nucleotidyltransferase substrate binding domain; InterPro: IPR018821 This entry is found associated with presumed nucleotidyltransferase domains and seems to be distantly related to other helical substrate binding domains.
Probab=33.85 E-value=34 Score=23.97 Aligned_cols=26 Identities=27% Similarity=0.456 Sum_probs=22.5
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
+|-..|+....+.+||..|.+.|.++
T Consensus 53 lAL~~gi~~~~T~eRl~~L~~~g~l~ 78 (145)
T PF10335_consen 53 LALRHGISETSTLERLEALAEAGVLS 78 (145)
T ss_pred HHHHcCCCCCCHHHHHHHHHHcCCCC
Confidence 57778899999999999999988763
No 362
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit of ATP dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and V
Probab=33.78 E-value=71 Score=22.08 Aligned_cols=29 Identities=31% Similarity=0.494 Sum_probs=23.7
Q ss_pred ccEEeeCC-CceEEE-------cHHHHHHHHHHHHhh
Q psy11008 28 LTGVIDDR-GKFIYI-------SQEELNSVATFIKQR 56 (96)
Q Consensus 28 ltGViDDR-GKfIyI-------s~eEl~~Va~fI~~r 56 (96)
|-|+.|+. |+|.|+ |++++..+.++++..
T Consensus 25 Llg~~d~~~~~l~~vgkvgtGfs~~~~~~l~~~l~~~ 61 (129)
T cd07893 25 LCAVYDPERDEFQTICKVGSGFTDEELEELRELLKEL 61 (129)
T ss_pred EEEEEcCCCCEEEEEeEECCCCCHHHHHHHHHHhhcc
Confidence 45888864 899995 699999999988766
No 363
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=33.75 E-value=65 Score=18.31 Aligned_cols=28 Identities=18% Similarity=0.347 Sum_probs=23.2
Q ss_pred cHHHHHHHHHHHHhhchhchhhhhhhhc
Q psy11008 42 SQEELNSVATFIKQRGREELNSVATFIK 69 (96)
Q Consensus 42 s~eEl~~Va~fI~~rgr~~~~~~~~~~~ 69 (96)
|+||-..+.+.|++-|..--..+|..+.
T Consensus 5 t~eE~~~l~~~v~~~g~~~W~~Ia~~~~ 32 (48)
T PF00249_consen 5 TEEEDEKLLEAVKKYGKDNWKKIAKRMP 32 (48)
T ss_dssp -HHHHHHHHHHHHHSTTTHHHHHHHHHS
T ss_pred CHHHHHHHHHHHHHhCCcHHHHHHHHcC
Confidence 7899999999999998776777777776
No 364
>PHA00542 putative Cro-like protein
Probab=33.67 E-value=89 Score=20.07 Aligned_cols=40 Identities=18% Similarity=0.197 Sum_probs=27.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.+||...|+ ++..|.|+. +|+.-+.+.+.+.++|+++++-
T Consensus 35 ~elA~~lgI-s~~tIsr~e--------------~g~~~~p~~~~l~ki~~~~~~~ 74 (82)
T PHA00542 35 EQIADATDV-SQPTICRIY--------------SGRHKDPRYSVVEKLRHLVLNL 74 (82)
T ss_pred HHHHHHHCc-CHHHHHHHH--------------cCCCCCCCHHHHHHHHHHHHHh
Confidence 357777777 455555553 3554467889999999998876
No 365
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=33.61 E-value=25 Score=26.48 Aligned_cols=20 Identities=20% Similarity=0.232 Sum_probs=16.6
Q ss_pred ChhhhhhhCCChHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIV 20 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~ 20 (96)
|+++|++.||+.+++|++.-
T Consensus 102 L~~vA~~~gls~~evi~~H~ 121 (202)
T PF02682_consen 102 LEEVAEHNGLSVEEVIRLHS 121 (202)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHhCcCHHHHHHHHH
Confidence 57899999999999999864
No 366
>PRK14126 cell division protein ZapA; Provisional
Probab=33.43 E-value=67 Score=21.31 Aligned_cols=15 Identities=20% Similarity=0.426 Sum_probs=13.7
Q ss_pred cHHHHHHHHHHHHhh
Q psy11008 42 SQEELNSVATFIKQR 56 (96)
Q Consensus 42 s~eEl~~Va~fI~~r 56 (96)
+++.|..+|.|+..+
T Consensus 25 ~ee~l~~vA~~vd~k 39 (85)
T PRK14126 25 STSHIRMVAAIVDDK 39 (85)
T ss_pred cHHHHHHHHHHHHHH
Confidence 578899999999998
No 367
>PRK11642 exoribonuclease R; Provisional
Probab=33.34 E-value=44 Score=30.37 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=23.2
Q ss_pred hhhhhhhCCCh----HHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKT----QSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lkt----q~vI~RI~eL~~~g~lt 29 (96)
.+||..|+++. +.+..+|.+|++.|.|.
T Consensus 38 ~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~ 69 (813)
T PRK11642 38 EELAVELNIEGEEQLEALRRRLRAMERDGQLV 69 (813)
T ss_pred HHHHHHhCCCChHHHHHHHHHHHHHHHCCCEE
Confidence 68999999975 34778899999999874
No 368
>PF00763 THF_DHG_CYH: Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain; InterPro: IPR020630 Enzymes that participate in the transfer of one-carbon units require the coenzyme tetrahydrofolate (THF). Various reactions generate one-carbon derivatives of THF, which can be interconverted between different oxidation states by methylene-THF dehydrogenase (1.5.1.5 from EC), methenyl-THF cyclohydrolase (3.5.4.9 from EC) and formyl-THF synthetase (6.3.4.3 from EC) [, ]. The dehydrogenase and cyclohydrolase activities are expressed by a variety of multifunctional enzymes, including the tri-functional eukaryotic C1-tetrahydrofolate synthase []; a bifunctional eukaryotic mitochondrial protein; and the bifunctional Escherichia coli folD protein [, ]. Methylene-tetrahydrofolate dehydrogenase and methenyltetrahydrofolate cyclo-hydrolase share an overlapping active site [], and as such are usually located together in proteins, acting in tandem on the carbon-nitrogen bonds of substrates other than peptide bonds. This entry represents the N-terminal catalytic domain of these enzymes. ; GO: 0003824 catalytic activity, 0004488 methylenetetrahydrofolate dehydrogenase (NADP+) activity, 0009396 folic acid-containing compound biosynthetic process, 0055114 oxidation-reduction process; PDB: 2C2X_B 2C2Y_A 1EDZ_A 1EE9_A 4A26_B 3NGL_C 3NGX_A 1B0A_A 1DIA_A 1A4I_B ....
Probab=33.34 E-value=68 Score=21.88 Aligned_cols=23 Identities=13% Similarity=0.468 Sum_probs=19.2
Q ss_pred CChHHHHHHHHHHHHcCCccEEe
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVI 32 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGVi 32 (96)
.+++++++.|.+|-++..++|++
T Consensus 70 ~~~~el~~~i~~lN~D~~V~GIl 92 (117)
T PF00763_consen 70 ISEEELLELIEKLNEDPSVHGIL 92 (117)
T ss_dssp SSHHHHHHHHHHHHH-TT-SEEE
T ss_pred cCHHHHHHHHHHHhCCCCCCEEE
Confidence 46889999999999999999997
No 369
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=33.34 E-value=1.7e+02 Score=20.49 Aligned_cols=49 Identities=14% Similarity=0.192 Sum_probs=37.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.|+|..+|+++. -|.--++.|-|.-.-.+.|-|=+-+++++..+. ||+.
T Consensus 7 ~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~-~I~~ 55 (120)
T TIGR02054 7 SRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLR-FVRA 55 (120)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHH-HHHH
Confidence 589999999764 467788899998775555778889999998874 4443
No 370
>COG1273 Ku-homolog [Replication, recombination, and repair]
Probab=33.29 E-value=24 Score=29.12 Aligned_cols=31 Identities=26% Similarity=0.528 Sum_probs=25.1
Q ss_pred HHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 21 ELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 21 eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
+++.++-+-|.==+.|+||-|++||+.+|+.
T Consensus 56 ~Ve~~d~VKGYE~~~~~yViledeel~s~~~ 86 (278)
T COG1273 56 EVERDDIVKGYEYGKGDYVILEDEELESVPL 86 (278)
T ss_pred ccCccceeeeeEecCCcEEEecHHHHhhccc
Confidence 4555666777777899999999999999874
No 371
>TIGR02681 phage_pRha phage regulatory protein, rha family. Members of this protein family are found in temperate phage and bacterial prophage regions. Members include the product of the rha gene of the lambdoid phage phi-80, a late operon gene. The presence of this gene interferes with infection of bacterial strains that lack integration host factor (IHF), which regulates the rha gene. It is suggested that pRha is a phage regulatory protein.
Probab=33.16 E-value=76 Score=21.95 Aligned_cols=44 Identities=20% Similarity=0.333 Sum_probs=30.6
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcC---C-------ccEEeeCCCc---eEEEcHHHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTG---A-------LTGVIDDRGK---FIYISQEEL 46 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g---~-------ltGViDDRGK---fIyIs~eEl 46 (96)
++|..||-+..+|+..|+.|...- . .+-..|.+|+ +.++|.+..
T Consensus 18 ~IAe~fgK~H~~VlR~Ir~l~~~~~~~~f~~~~F~~~~y~~~~g~~~~~Y~ltkdgf 74 (108)
T TIGR02681 18 TMAQMFGKRHDNVIRDIKVLLIEANETEFGQLNFEETQYQDEQNKKQPMFNLTEDGF 74 (108)
T ss_pred HHHHHHCcchHHHHHHHHHHHhhhccccccccCceeeEEEcCCCcEEEEEEEcCCce
Confidence 789999999999999999996531 1 1233566665 455665543
No 372
>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=32.84 E-value=84 Score=24.95 Aligned_cols=36 Identities=19% Similarity=0.337 Sum_probs=30.8
Q ss_pred hhhhhhhC--CChHHHHHHHHHHHHcCCccEEeeCCCceE
Q psy11008 2 EDLAALFR--MKTQSVIDRIVELQKTGALTGVIDDRGKFI 39 (96)
Q Consensus 2 edLAa~F~--lktq~vI~RI~eL~~~g~ltGViDDRGKfI 39 (96)
+.||...+ ++..+|-+-|+-|++.|-|. -|..|+|.
T Consensus 141 ~~ia~~l~p~is~~ev~~sL~~L~~~glik--k~~~g~y~ 178 (271)
T TIGR02147 141 EELAKRCFPKISAEQVKESLDLLERLGLIK--KNEDGFYK 178 (271)
T ss_pred HHHHHHhCCCCCHHHHHHHHHHHHHCCCee--ECCCCcEE
Confidence 46899998 88999999999999999997 56778775
No 373
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=32.84 E-value=29 Score=18.91 Aligned_cols=17 Identities=24% Similarity=0.565 Sum_probs=12.9
Q ss_pred hccccceeH-HHHHHhcc
Q psy11008 68 IKQKGRVSV-SELVENSN 84 (96)
Q Consensus 68 ~~~~GRVsi-~eL~~~sN 84 (96)
+..|||+++ +++.+.-+
T Consensus 3 i~~kgri~iP~~~r~~l~ 20 (43)
T TIGR01439 3 VDKKGQIVIPKEIREKLG 20 (43)
T ss_pred ECcCCeEEecHHHHHHcC
Confidence 457899999 88877653
No 374
>COG5027 SAS2 Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=32.72 E-value=34 Score=29.60 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=27.4
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEE
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYI 41 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyI 41 (96)
++|||+.-||++.|||--++.|.--+. +.|+||+-
T Consensus 334 I~~Is~~TgM~~dDVI~tLe~L~il~~------~~~~yI~~ 368 (395)
T COG5027 334 INEISKETGMSTDDVIHTLEALNILRE------YKGQYIIS 368 (395)
T ss_pred HHHHHhhhCCchhhHHHHHHHhccchh------hCceEEEE
Confidence 479999999999999998888854443 36777763
No 375
>TIGR01339 phycocy_beta phycocyanin, beta subunit. This model excludes the closely related phycoerythrocyanin beta subunit.
Probab=32.70 E-value=20 Score=27.15 Aligned_cols=22 Identities=27% Similarity=0.696 Sum_probs=18.7
Q ss_pred eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 33 DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 33 DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
|..|+| +|..||+++..|+++-
T Consensus 11 D~~gRy--l~~~eL~~l~~~~~~~ 32 (170)
T TIGR01339 11 DARGEF--ISSSQIDALSKLVADG 32 (170)
T ss_pred HhccCC--CCHHHHHHHHHHHHhh
Confidence 667775 6999999999999884
No 376
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=32.63 E-value=89 Score=22.75 Aligned_cols=40 Identities=20% Similarity=0.253 Sum_probs=34.9
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs 42 (96)
.||..+|++-.-+-.-+..|+++|-+.=|--.|--=||+-
T Consensus 64 ~la~r~gI~~SvAr~vLR~LeeeGvv~lvsknrR~~IY~~ 103 (107)
T COG4901 64 VLASRYGINGSVARIVLRHLEEEGVVQLVSKNRRQAIYTR 103 (107)
T ss_pred HHHHHhccchHHHHHHHHHHHhCCceeeeccCccceeeec
Confidence 4889999999999999999999999988887888788863
No 377
>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=32.57 E-value=55 Score=20.34 Aligned_cols=28 Identities=21% Similarity=0.280 Sum_probs=20.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
+.|...|....+++-.+|+.|.+.|-|.
T Consensus 34 ~~l~~~f~~~~~~ik~~Ie~LIekeyi~ 61 (68)
T PF10557_consen 34 EELKKRFPPSVSDIKKRIESLIEKEYIE 61 (68)
T ss_dssp HHTTTTS---HHHHHHHHHHHHHTTSEE
T ss_pred HHhcCCcCCCHHHHHHHHHHHHHhhhhh
Confidence 4566689999999999999999988764
No 378
>cd05805 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity. The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily. This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional
Probab=32.54 E-value=61 Score=26.20 Aligned_cols=25 Identities=24% Similarity=0.476 Sum_probs=19.8
Q ss_pred cEEeeCCCceEEEcHHHHHH-HHHHHHh
Q psy11008 29 TGVIDDRGKFIYISQEELNS-VATFIKQ 55 (96)
Q Consensus 29 tGViDDRGKfIyIs~eEl~~-Va~fI~~ 55 (96)
-|++|++|+|+ +.+++-+ +|.|+-+
T Consensus 242 ~~vvd~~G~~~--~gd~l~~l~a~~ll~ 267 (441)
T cd05805 242 LILVDEAGRVI--SDDLLTALVSLLVLK 267 (441)
T ss_pred EEEECCCCCEE--ChhHHHHHHHHHHHH
Confidence 47899999987 9999877 5667654
No 379
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=32.40 E-value=1.8e+02 Score=20.59 Aligned_cols=44 Identities=23% Similarity=0.299 Sum_probs=32.5
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.++|..+|+++. -|.--++.|-|...-++ |.|-|.+++++..+.
T Consensus 4 ~e~a~~~gvs~~----TLR~Ye~~GLl~p~r~~-~g~R~Y~~~~l~~l~ 47 (134)
T cd04779 4 GQLAHLAGVSKR----TIDYYTNLGLLTPERSD-SNYRYYDETALDRLQ 47 (134)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCccCC-CCCeeECHHHHHHHH
Confidence 588999999765 34556788999955444 568888998887654
No 380
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=32.18 E-value=1.4e+02 Score=23.09 Aligned_cols=51 Identities=14% Similarity=0.221 Sum_probs=40.7
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+.+..||++.+.+.+-.|.|=+.|.||-=--|- =|++++....+..++...
T Consensus 21 ~a~~~~g~sa~~tl~iaQ~LYe~g~iTYPRTds---~~l~~~~~~~~~~~l~~~ 71 (259)
T smart00437 21 EASRKLGFSAKKTMQIAQKLYEKGLITYPRTDS---TRLSEEAVLEARNYISKH 71 (259)
T ss_pred HHHHhcCCCHHHHHHHHHHHHhCCeeEecCCCC---CcCCHHHHHHHHHHHHHh
Confidence 567899999999999999999976666543343 378999988888877765
No 381
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=32.03 E-value=32 Score=17.95 Aligned_cols=15 Identities=7% Similarity=0.193 Sum_probs=11.3
Q ss_pred ChhhhhhhCCChHHH
Q psy11008 1 MEDLAALFRMKTQSV 15 (96)
Q Consensus 1 ledLAa~F~lktq~v 15 (96)
|.++|..|+++.+++
T Consensus 7 l~~IA~~~~~~~~~l 21 (44)
T TIGR02899 7 LWKIAKKYGVDFDEL 21 (44)
T ss_pred HHHHHHHHCcCHHHH
Confidence 357999999986544
No 382
>TIGR03872 cytochrome_MoxG cytochrome c(L), periplasmic. This model describes a periplasmic c-type cytochrome that serves as the primary electron acceptor for the quinoprotein methanol dehydrogenase, a PQQ enzyme. The member from Paracoccus denitrificans is also characterized as an electron acceptor for methylamine dehydrogenase, a tryptophan tryptophylquinone enzyme. This protein is called cytochrome c(L) in methylotrophic bacteria such Methylobacterium extorquens, but c551i in Paracoccus denitrificans.
Probab=31.63 E-value=38 Score=24.10 Aligned_cols=17 Identities=12% Similarity=0.391 Sum_probs=15.8
Q ss_pred EEcHHHHHHHHHHHHhh
Q psy11008 40 YISQEELNSVATFIKQR 56 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~r 56 (96)
.+|++|+.+|+.||++.
T Consensus 105 ~LsdeeI~aLaaYI~sl 121 (133)
T TIGR03872 105 NLTLDEMLQIMAWIRHL 121 (133)
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 49999999999999987
No 383
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=31.47 E-value=34 Score=21.35 Aligned_cols=23 Identities=17% Similarity=0.338 Sum_probs=19.3
Q ss_pred ChhhhhhhCCChHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQ 23 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~ 23 (96)
|++.+.+-|+..+.++.++++||
T Consensus 34 L~eA~~~~~ld~~~vl~~L~~lq 56 (56)
T PF04405_consen 34 LEEACEEKGLDPEEVLEELNALQ 56 (56)
T ss_pred HHHHHHHcCCCHHHHHHHHHHcC
Confidence 46778888999999999998875
No 384
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=31.37 E-value=1.9e+02 Score=20.35 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=34.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|+++. -|.--++.|-|...-+. |.|=|.|++++..+..
T Consensus 5 ~EvA~~~Gvs~~----tLRyYE~~GLl~p~r~~-~g~R~Y~~~dl~~l~~ 49 (139)
T cd01110 5 GEVAKRSGVAVS----ALHFYEQKGLIASWRNA-GNQRRYPRDVLRRIAF 49 (139)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCcCC-CCCeEECHHHHHHHHH
Confidence 478999999764 45677888999886554 5577789988887653
No 385
>CHL00034 rpl22 ribosomal protein L22
Probab=31.32 E-value=28 Score=24.48 Aligned_cols=47 Identities=23% Similarity=0.289 Sum_probs=35.8
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.++++.+|+.-+..||..|+-.--++--..-.|+..|+-.-+..|..
T Consensus 13 ~~~~ir~SpkK~r~va~~IRG~~v~~A~~~L~~~pkk~a~~i~klL~ 59 (117)
T CHL00034 13 LAKYIRMSAHKARRVIDQIRGRSYEEALMILEFMPYRACYPILKLVY 59 (117)
T ss_pred EeCCcccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHHHHHHHHHHHH
Confidence 57899999999999999999886555555666777777665655543
No 386
>PRK13621 psbV cytochrome c-550; Provisional
Probab=31.30 E-value=37 Score=26.05 Aligned_cols=53 Identities=25% Similarity=0.370 Sum_probs=29.9
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCC-ccEEeeCCC----ceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGA-LTGVIDDRG----KFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~-ltGViDDRG----KfIyIs~eEl~~Va~fI~~r 56 (96)
++|+.. +.+.|.|..+.+-.++-+ .-|-..--| -+=.+|+||+.+||.||.+.
T Consensus 97 ~~L~~a--~p~rd~I~~LV~~iknPms~kg~~~~~~~~mps~~~LSdeEL~aIAaYLL~q 154 (170)
T PRK13621 97 KDLRGA--TPPRDNIAALVAYQRDPMSYDGSEESYGCRQVPEDWMTDEELQNLAAFILRA 154 (170)
T ss_pred HHHhcC--CCchHHHHHHHHHhhCCCCCCcccccccccCCccCCCCHHHHHHHHHHHHhh
Confidence 345444 666666666665554422 111000000 01249999999999999876
No 387
>KOG0697|consensus
Probab=31.15 E-value=18 Score=30.90 Aligned_cols=29 Identities=38% Similarity=0.594 Sum_probs=21.5
Q ss_pred EcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhccccee
Q psy11008 41 ISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLVT 88 (96)
Q Consensus 41 Is~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~lI~ 88 (96)
.|.|| ||.||+.| =+|+ ++|.+.||.+++
T Consensus 244 Mtnee---lcefv~sR---------------l~Vt-~dL~~vcn~VvD 272 (379)
T KOG0697|consen 244 MTNEE---LCEFVKSR---------------LEVT-SDLEEVCNDVVD 272 (379)
T ss_pred cccHH---HHHHHHhh---------------heec-ccHHHHHHHHHH
Confidence 45554 68999988 3443 799999999875
No 388
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=31.11 E-value=36 Score=18.82 Aligned_cols=17 Identities=29% Similarity=0.425 Sum_probs=11.4
Q ss_pred ChhhhhhhCCChHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDR 18 (96)
Q Consensus 1 ledLAa~F~lktq~vI~R 18 (96)
++|||.++|+ .+....|
T Consensus 11 l~~iA~~~g~-S~~~f~r 27 (42)
T PF00165_consen 11 LEDIAEQAGF-SPSYFSR 27 (42)
T ss_dssp HHHHHHHHTS--HHHHHH
T ss_pred HHHHHHHHCC-CHHHHHH
Confidence 4799999999 4444444
No 389
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=30.96 E-value=31 Score=23.75 Aligned_cols=47 Identities=19% Similarity=0.355 Sum_probs=36.9
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.++|+.+|+.-+..||..|+-+--++--..-.|...|+-.-+..+.+
T Consensus 6 ~~~~~~~SpkK~~~v~~~IrG~~v~~A~~~L~~~pkk~a~~i~k~L~ 52 (112)
T PRK00565 6 KARYVRVSPRKARLVADLIRGKKVEEALAILKFSPKKAARLVKKVLK 52 (112)
T ss_pred EeCccccCHHHHHHHHHHHcCCcHHHHHHHHHHCcHhHHHHHHHHHH
Confidence 47899999999999999999886566566667778887776666553
No 390
>TIGR02905 spore_yutH spore coat protein YutH. Members of this family are homologs of the Bacillus subtilis spore coat protein CotS. Members of this family, designated YutH, are found only in the family Bacillaceae from among the endospore-forming members of the Firmicutes branch of the Bacteria.
Probab=30.77 E-value=50 Score=25.48 Aligned_cols=60 Identities=15% Similarity=0.222 Sum_probs=39.8
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceE-----EEcHHHHHHHHHHHHhhchhchhhhhhhhcc
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFI-----YISQEELNSVATFIKQRGREELNSVATFIKQ 70 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfI-----yIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~ 70 (96)
+-.+|+|..+ ..+..|++-.|..|.|.|+ ..+++++.-+...+..-.+.-.+.|+++++.
T Consensus 4 vl~~Y~l~~~-------~~~~~g~~~~~~t~~g~y~Lk~~e~~~~~~l~f~~~~~~~L~~~G~~~v~~~i~t 68 (313)
T TIGR02905 4 LYDQFGLYCD-------ERFRVGRYEAFRANNQAYLIVPVDGLEEEELAELMAMSDYLQQAGDETVLELVKT 68 (313)
T ss_pred hHHhhCcCcc-------cceecCceeeEEeCCceEEEEEecCCCHHHHHHHHHHHHHHHHcCCCcccceeec
Confidence 3445666543 3445699999999999998 6777777766554444433346677777774
No 391
>cd00377 ICL_PEPM Members of the ICL/PEPM enzyme family catalyze either P-C or C-C bond formation/cleavage. Known members are phosphoenolpyruvate mutase (PEPM), phosphonopyruvate hydrolase (PPH), carboxyPEP mutase (CPEP mutase), oxaloacetate hydrolase (OAH), isocitrate lyase (ICL), and 2-methylisocitrate lyase (MICL). Isocitrate lyase (ICL) catalyzes the conversion of isocitrate to succinate and glyoxylate, the first committed step in the glyoxylate pathway. This carbon-conserving pathway is present in most prokaryotes, lower eukaryotes and plants, but has not been observed in vertebrates. PEP mutase (PEPM) turns phosphoenolpyruvate (PEP) into phosphonopyruvate (P-pyr), an important intermediate in the formation of organophosphonates, which function as antibiotics or play a role in pathogenesis or signaling. P-pyr can be hydrolyzed by phosphonopyruvate hydrolase (PPH) to from pyruvate and phosphate. Oxaloacetate acetylhydrolase (OAH) catalyzes the hydrolytic cleavage of oxaloacetate to
Probab=30.72 E-value=1.4e+02 Score=22.75 Aligned_cols=70 Identities=21% Similarity=0.241 Sum_probs=46.9
Q ss_pred CChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccc-eeHHHHHHhccccee
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGR-VSVSELVENSNQLVT 88 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GR-Vsi~eL~~~sN~lI~ 88 (96)
-..+++|+|.+...+.|. .+|+=.--+ +++++..+++-+.-. +.-+....+. +|.+||.+.-=+++.
T Consensus 157 ~~~~eai~Ra~ay~~AGA-D~v~v~~~~----~~~~~~~~~~~~~~P-------l~~~~~~~~~~~~~~~l~~lG~~~v~ 224 (243)
T cd00377 157 EGLDEAIERAKAYAEAGA-DGIFVEGLK----DPEEIRAFAEAPDVP-------LNVNMTPGGNLLTVAELAELGVRRVS 224 (243)
T ss_pred CCHHHHHHHHHHHHHcCC-CEEEeCCCC----CHHHHHHHHhcCCCC-------EEEEecCCCCCCCHHHHHHCCCeEEE
Confidence 368999999999999997 555544222 888888888764221 2222333343 899999887766665
Q ss_pred ccc
Q psy11008 89 LIP 91 (96)
Q Consensus 89 L~p 91 (96)
..+
T Consensus 225 ~~~ 227 (243)
T cd00377 225 YGL 227 (243)
T ss_pred ECh
Confidence 544
No 392
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=30.55 E-value=92 Score=21.04 Aligned_cols=47 Identities=19% Similarity=0.368 Sum_probs=32.1
Q ss_pred ChHHHHHHHHHHHHcCC------cc--E-EeeC-------CCceEEEcHHHHHHHHHHHHhhc
Q psy11008 11 KTQSVIDRIVELQKTGA------LT--G-VIDD-------RGKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 11 ktq~vI~RI~eL~~~g~------lt--G-ViDD-------RGKfIyIs~eEl~~Va~fI~~rg 57 (96)
...++..||+.+..... +. . .+|- .|+-+.+|+-|+.-+.-+++..|
T Consensus 104 ~~~eL~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~Lt~~E~~ll~~L~~~~~ 166 (223)
T PRK10816 104 HIEEVMARMQALMRRNSGLASQVISLPPFQVDLSRRELSINDEVIKLTAFEYTIMETLIRNNG 166 (223)
T ss_pred CHHHHHHHHHHHHhccccCCCCeEEECCEEEEcccCEEEECCEEEeCCHHHHHHHHHHHhCCC
Confidence 45677788877765421 10 0 2221 57789999999999999999884
No 393
>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=30.50 E-value=73 Score=21.21 Aligned_cols=43 Identities=12% Similarity=0.357 Sum_probs=28.0
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCccEE-eeCCCceEEEcHHH
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALTGV-IDDRGKFIYISQEE 45 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~ltGV-iDDRGKfIyIs~eE 45 (96)
.+|.+.|+....+++-++.|+..|-|.-- .--.|-||.+-.++
T Consensus 9 ~iAd~~GiTRSvIVNALRKleSaGvIesrSlGmKGT~ikvlN~~ 52 (61)
T PF08222_consen 9 KIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDY 52 (61)
T ss_dssp HHHHHHT--HHHHHHHHHHHHHTTSEEEEETTSS-EEEEE--TH
T ss_pred HHHHHhCccHHHHHHHHHHHHhcCceeecccCCCceeeeeecHH
Confidence 57999999999999999999998654311 11358899876544
No 394
>COG3800 Predicted transcriptional regulator [General function prediction only]
Probab=30.34 E-value=37 Score=28.77 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=24.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCC
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGA 27 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ 27 (96)
|=|++.||++-+.+.+|+-.||..|.
T Consensus 154 e~L~~rFgvS~Eq~ahRLsTLQR~g~ 179 (332)
T COG3800 154 ELLRSRFGVSFEQAAHRLSTLQRPGQ 179 (332)
T ss_pred HHHHHHhCccHHHHHHHHHHhcCCCC
Confidence 56899999999999999999999986
No 395
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=30.20 E-value=42 Score=15.34 Aligned_cols=15 Identities=7% Similarity=0.233 Sum_probs=10.2
Q ss_pred hhhhhhhCCChHHHH
Q psy11008 2 EDLAALFRMKTQSVI 16 (96)
Q Consensus 2 edLAa~F~lktq~vI 16 (96)
.++|.+||++.+.+.
T Consensus 25 ~~ia~~~~is~~tv~ 39 (42)
T cd00569 25 AEIARRLGVSRSTLY 39 (42)
T ss_pred HHHHHHHCCCHHHHH
Confidence 467888888665544
No 396
>cd04640 CBS_pair_27 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=30.01 E-value=1.4e+02 Score=18.63 Aligned_cols=37 Identities=24% Similarity=0.367 Sum_probs=23.5
Q ss_pred CCChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHHH
Q psy11008 9 RMKTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
+.+..++++++ .+.+ ...=|+|++|+|+ +++..++..
T Consensus 9 ~~~i~~a~~~~---~~~~~~~~~V~d~~~~~~Giv~~~dl~~ 47 (126)
T cd04640 9 DTSIDEALELM---IKHGVRLLLVVDSDDNFIGVITAVDLLG 47 (126)
T ss_pred CCcHHHHHHHH---HHcCCcEEEEEcCCCcEEEEEEHHHHhh
Confidence 34555666665 2333 3445668899987 688888765
No 397
>PRK13501 transcriptional activator RhaR; Provisional
Probab=29.72 E-value=1.2e+02 Score=22.47 Aligned_cols=32 Identities=9% Similarity=0.346 Sum_probs=16.9
Q ss_pred HHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 49 VATFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 49 Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
..+||+++ .++.....|. .+..||+|++..|.
T Consensus 221 ~~qyi~~~---Ri~~A~~LL~-~t~~sI~eIA~~~G 252 (290)
T PRK13501 221 ISHYLRQI---RLCHAKCLLR-GSEHRISDIAARCG 252 (290)
T ss_pred HHHHHHHH---HHHHHHHHHH-cCCCCHHHHHHHhC
Confidence 34566655 2333333333 35557888877663
No 398
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=29.67 E-value=1.3e+02 Score=20.71 Aligned_cols=33 Identities=18% Similarity=0.382 Sum_probs=25.7
Q ss_pred hHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHH
Q psy11008 12 TQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSV 49 (96)
Q Consensus 12 tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~V 49 (96)
.+++|.-.+.|=+.|-++ +..|| |.|++-++..
T Consensus 33 ~p~~i~a~~RLheKGLI~---~pdGg--yLT~~G~~~a 65 (77)
T TIGR02647 33 SPAAVAAAARLHEKGLTT---QPDGG--YLTSLGLEAA 65 (77)
T ss_pred CHHHHHHHHHHHHcCCcc---CCCCC--EecHHHHHHH
Confidence 357788888888888765 67888 9999988753
No 399
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=29.66 E-value=1.8e+02 Score=22.11 Aligned_cols=48 Identities=13% Similarity=0.161 Sum_probs=36.4
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEe--eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVI--DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGVi--DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
..+..+...+-|+.|.+.| +.|++ -.-|-|.++|.+|...+.+...+.
T Consensus 17 g~iD~~~l~~~i~~l~~~G-v~gi~~~Gs~GE~~~ls~~Er~~~~~~~~~~ 66 (292)
T PRK03170 17 GSVDFAALRKLVDYLIANG-TDGLVVVGTTGESPTLTHEEHEELIRAVVEA 66 (292)
T ss_pred CCcCHHHHHHHHHHHHHcC-CCEEEECCcCCccccCCHHHHHHHHHHHHHH
Confidence 3455556666677777755 78876 478999999999999998877765
No 400
>cd06562 GH20_HexA_HexB-like Beta-N-acetylhexosaminidases catalyze the removal of beta-1,4-linked N-acetyl-D-hexosamine residues from the non-reducing ends of N-acetyl-beta-D-hexosaminides including N-acetylglucosides and N-acetylgalactosides. The hexA and hexB genes encode the alpha- and beta-subunits of the two major beta-N-acetylhexosaminidase isoenzymes, N-acetyl-beta-D-hexosaminidase A (HexA) and beta-N-acetylhexosaminidase B (HexB). Both the alpha and the beta catalytic subunits have a TIM-barrel fold and belong to the glycosyl hydrolase family 20 (GH20). The HexA enzyme is a heterodimer containing one alpha and one beta subunit while the HexB enzyme is a homodimer containing two beta-subunits. Hexosaminidase mutations cause an inability to properly hydrolyze certain sphingolipids which accumulate in lysosomes within the brain, resulting in the lipid storage disorders Tay-Sachs and Sandhoff. Mutations in the alpha subunit cause in a deficiency in the HexA enzyme and result in
Probab=29.63 E-value=64 Score=25.76 Aligned_cols=41 Identities=12% Similarity=0.390 Sum_probs=30.7
Q ss_pred CceEEEcHHHH--------HHHHHHHHhhc--------hhchhhhhhhhccccceeH
Q psy11008 36 GKFIYISQEEL--------NSVATFIKQRG--------REELNSVATFIKQKGRVSV 76 (96)
Q Consensus 36 GKfIyIs~eEl--------~~Va~fI~~rg--------r~~~~~~~~~~~~~GRVsi 76 (96)
++||+|--+|. .++.+|+++.| ..-++.++.+++++|+-.+
T Consensus 150 ~~~iHiGgDE~~~~~w~~~p~~~~~m~~~g~~~~~~l~~~f~~~~~~~l~~~Gk~~i 206 (348)
T cd06562 150 DKYFHLGGDEVNFNCWNSNPEIQKFMKKNNGTDYSDLESYFIQRALDIVRSLGKTPI 206 (348)
T ss_pred CcceEeecCCCCCCcccCCHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHHcCCeEE
Confidence 89999999997 35788888877 2345667777888887544
No 401
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=29.56 E-value=1.8e+02 Score=23.09 Aligned_cols=53 Identities=21% Similarity=0.396 Sum_probs=40.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc-------------eEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK-------------FIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK-------------fIyIs~eEl~~Va~fI~~r 56 (96)
.+||.+|+++...+-.=|..|+..|.- +--++|+ -.-.|++|..+++.-++.-
T Consensus 26 ~~lA~~~~VS~RTi~RDi~~L~~~gvP--I~~e~G~~~gy~~~~~~~L~pl~ft~~E~~Al~~~l~~l 91 (311)
T COG2378 26 AELADEFEVSVRTIYRDIATLRAAGVP--IEGERGKGGGYRLRPGFKLPPLMFTEEEAEALLLALRAL 91 (311)
T ss_pred HHHHHhcCCCHHHHHHHHHHHHHCCCC--eEeecCCCccEEEccCCCCCcccCCHHHHHHHHHHHHHH
Confidence 579999999999888889999999988 2224552 2346899999887655543
No 402
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=29.31 E-value=42 Score=21.11 Aligned_cols=19 Identities=21% Similarity=0.525 Sum_probs=15.1
Q ss_pred ChhhhhhhCCChHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRI 19 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI 19 (96)
++||+..|.|+.+++-..+
T Consensus 7 ~~~L~~~fhlp~~eAA~~L 25 (52)
T PF02042_consen 7 LEDLSQYFHLPIKEAAKEL 25 (52)
T ss_pred HHHHHHHhCCCHHHHHHHh
Confidence 4788999999888887654
No 403
>PRK10766 DNA-binding transcriptional regulator TorR; Provisional
Probab=29.13 E-value=90 Score=20.98 Aligned_cols=23 Identities=17% Similarity=0.387 Sum_probs=20.0
Q ss_pred CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 34 DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 34 DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
-.|+-|..|+.|++=+..++...
T Consensus 153 ~~~~~v~Lt~~E~~ll~~l~~~~ 175 (221)
T PRK10766 153 RNGEPIKLTKAEYELLVAFVTNP 175 (221)
T ss_pred ECCEEecCCHHHHHHHHHHHHCC
Confidence 47889999999999888888877
No 404
>PRK10529 DNA-binding transcriptional activator KdpE; Provisional
Probab=29.06 E-value=1.1e+02 Score=20.67 Aligned_cols=33 Identities=15% Similarity=0.336 Sum_probs=26.2
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccce-eHHHHHHh
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRV-SVSELVEN 82 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRV-si~eL~~~ 82 (96)
.|+=+..|+.|++-+..++... |+| |..+|.+.
T Consensus 146 ~~~~~~Lt~~E~~ll~~L~~~~---------------~~~~s~~~l~~~ 179 (225)
T PRK10529 146 GEEEVHLTPIEFRLLAVLLNNA---------------GKVLTQRQLLNQ 179 (225)
T ss_pred CCEEEECCHHHHHHHHHHHhCC---------------CeeEcHHHHHHH
Confidence 6777899999999888888888 666 77776554
No 405
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=28.78 E-value=2.2e+02 Score=20.26 Aligned_cols=44 Identities=18% Similarity=0.215 Sum_probs=32.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.|+|..+|+++. -|.--++.|-|...-++ |.|=+.+++.+..+.
T Consensus 5 gevA~~~Gvs~~----tLRyYE~~GLl~~~r~~-~g~R~Y~~~di~~l~ 48 (142)
T TIGR01950 5 GELAKRSGVAVS----ALHFYESKGLITSIRNS-GNQRRYKRDVLRRVA 48 (142)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCccCC-CCCEEECHHHHHHHH
Confidence 589999999754 46778899999885544 446667788877654
No 406
>smart00595 MADF subfamily of SANT domain.
Probab=28.54 E-value=69 Score=19.83 Aligned_cols=22 Identities=18% Similarity=0.312 Sum_probs=18.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQ 23 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~ 23 (96)
++||..+|.+..+|..+++.|.
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR 52 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHH
Confidence 4688999999999999988874
No 407
>KOG3559|consensus
Probab=28.53 E-value=48 Score=29.75 Aligned_cols=48 Identities=35% Similarity=0.544 Sum_probs=36.8
Q ss_pred HHHcCCccEEeeCCCceEEEcHH----------HH--HHHHHHHHhhchhchhhhhhhhc
Q psy11008 22 LQKTGALTGVIDDRGKFIYISQE----------EL--NSVATFIKQRGREELNSVATFIK 69 (96)
Q Consensus 22 L~~~g~ltGViDDRGKfIyIs~e----------El--~~Va~fI~~rgr~~~~~~~~~~~ 69 (96)
|+--+-..=|+|.|||-.|||+. || |++-+||....-.|.|+|-++-.
T Consensus 85 LqtLDGF~fvva~dGkimYISETaSvhLGLSQVElTGNsi~eYIH~~D~demna~L~~h~ 144 (598)
T KOG3559|consen 85 LQTLDGFIFVVAPDGKIMYISETASVHLGLSQVELTGNSIYEYIHPQDHDEMNAVLTAHQ 144 (598)
T ss_pred HHhhcceEEEEeCCCCEEEEecceeeeecceeeEeecchhhhhhcccchHHHHHHHhhhh
Confidence 33344455588999999999874 43 68889999888889999887654
No 408
>TIGR03045 PS_II_C550 cytochrome c-550. Members of this protein family are cytochrome c-550, the PsbV extrinsic protein of photosystem II, from both Cyanobacteria and chloroplasts. A paralog to this protein, PsbV2, is found in some species in addition to PsbV itself.
Probab=28.42 E-value=40 Score=25.17 Aligned_cols=17 Identities=24% Similarity=0.364 Sum_probs=15.5
Q ss_pred EEcHHHHHHHHHHHHhh
Q psy11008 40 YISQEELNSVATFIKQR 56 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~r 56 (96)
.+|++|+.+||.||...
T Consensus 131 ~LsdeEL~avAaYIl~q 147 (159)
T TIGR03045 131 NLTDEDLRLIAGHILVQ 147 (159)
T ss_pred CCCHHHHHHHHHHHHHh
Confidence 59999999999999875
No 409
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=28.38 E-value=1.9e+02 Score=21.69 Aligned_cols=48 Identities=19% Similarity=0.349 Sum_probs=32.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~ 55 (96)
.++|..+|+++.-+ ..-++.|.|...-|+.|.++| +++++. .-.||+.
T Consensus 4 ~evA~~lGVS~~TL----Rrw~k~g~L~~~R~~~G~R~y-~~~dl~-~L~~I~~ 51 (175)
T PRK13182 4 PFVAKKLGVSPKTV----QRWVKQLNLPCEKNEYGHYIF-TEEDLQ-LLEYVKS 51 (175)
T ss_pred HHHHHHHCcCHHHH----HHHHHcCCCCCCcCCCCCEEE-CHHHHH-HHHHHHH
Confidence 57899999976544 334557888766666776655 888885 4455553
No 410
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=28.34 E-value=2e+02 Score=19.79 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=35.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.++|..+|+++. -|.--++.|-|.-...+.+.|=|.+++.+..+..
T Consensus 5 ~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 50 (131)
T TIGR02043 5 GELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRF 50 (131)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHH
Confidence 578999999765 3566778899987666667788889999887753
No 411
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=28.32 E-value=1.1e+02 Score=26.77 Aligned_cols=45 Identities=13% Similarity=0.339 Sum_probs=32.5
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce-EEEcHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF-IYISQEELNSVAT 51 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf-IyIs~eEl~~Va~ 51 (96)
++||+..-+|+.+|||.-++.| |.|. --+|.| |+++++-++...+
T Consensus 377 i~~is~~T~i~~~Dii~tL~~l---~~l~---~~kg~~~i~~~~~~i~~~~~ 422 (450)
T PLN00104 377 IKELSDMTAIKAEDIVSTLQSL---NLIQ---YRKGQHVICADPKVLEEHLK 422 (450)
T ss_pred HHHHHHHhCCCHHHHHHHHHHC---CCEE---ecCCcEEEEECHHHHHHHHH
Confidence 4789999999999998765554 5543 245666 8899887766544
No 412
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=28.32 E-value=2e+02 Score=19.61 Aligned_cols=40 Identities=25% Similarity=0.401 Sum_probs=24.4
Q ss_pred hhhhhhhCCChHHHHHHHHH-HHHcCCccEEeeCCCceEEEc
Q psy11008 2 EDLAALFRMKTQSVIDRIVE-LQKTGALTGVIDDRGKFIYIS 42 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~e-L~~~g~ltGViDDRGKfIyIs 42 (96)
+++++.|+-. ++.++.+.. |++.|.-..-++..|-+|.++
T Consensus 51 ~e~~~~~~p~-~~~v~~V~~wL~~~G~~~~~~~~~~~~i~~~ 91 (143)
T PF09286_consen 51 EEFAALFAPS-PEDVAAVKSWLKSHGLTVVEVSANGDWITVS 91 (143)
T ss_dssp HHHHHHHS---HHHHHHHHHHHHHCT-EEEEEETTTTEEEEE
T ss_pred HHHHHHHCCC-HHHHHHHHHHHHHcCCceeEEeCCCCEEEEE
Confidence 5778888864 555555555 666663333347888888775
No 413
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.25 E-value=57 Score=23.63 Aligned_cols=23 Identities=22% Similarity=0.453 Sum_probs=18.7
Q ss_pred ChhhhhhhCCChHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQ 23 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~ 23 (96)
|.++|.+|+++.|.|-|-|+.=+
T Consensus 36 l~EIAee~~VSRqAIyDnIKr~~ 58 (105)
T COG2739 36 LSEIAEEFNVSRQAIYDNIKRTE 58 (105)
T ss_pred HHHHHHHhCccHHHHHHHHHHHH
Confidence 46899999999998888776543
No 414
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=28.11 E-value=1.2e+02 Score=23.19 Aligned_cols=62 Identities=26% Similarity=0.297 Sum_probs=43.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc---EEeeCCCc---eEEEcHHHHHHHHHHHHhhchhchhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT---GVIDDRGK---FIYISQEELNSVATFIKQRGREELNS 63 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt---GViDDRGK---fIyIs~eEl~~Va~fI~~rgr~~~~~ 63 (96)
|+||..+|++..+|-.-|..|-..|.++ ..-.+.|- |.|++-++...+...-..+-.+.|..
T Consensus 36 eela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~~~~~~~y~w~~~~~~v~~~l~~~~~~~le~Lk~ 103 (176)
T COG1675 36 EELAELLGIKKNEVRRILYALYEDGLISYRKKRDEESGWEEYTWYINYEKVLEVLKGKKRKILEKLKR 103 (176)
T ss_pred HHHHHHhCccHHHHHHHHHHHHhCCceEEEeecccCCCcEEEEEEechHHHHHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999988776 22234454 45677777766665555443444433
No 415
>cd00904 Ferritin Ferritin iron storage proteins. Ferritins are the primary iron storage proteins of most living organisms and members of a broad superfamily of ferritin-like diiron-carboxylate proteins. The iron-free (apoferritin) ferritin molecule is a protein shell composed of 24 protein chains arranged in 432 symmetry. Iron storage involves the uptake of iron (II) at the protein shell, its oxidation by molecular oxygen at the dinuclear ferroxidase centers, and the movement of iron (III) into the cavity for deposition as ferrihydrite; the protein shell can hold up to 4500 iron atoms. In vertebrates, two types of chains (subunits) have been characterized, H or M (fast) and L (slow), which differ in rates of iron uptake and mineralization. Bacterial non-heme ferritins are composed only of H chains. Fe(II) oxidation in the H/M subunits take place initially at the ferroxidase center, a carboxylate-bridged diiron center, located within the subunit four-helix bundle. In a complementary rol
Probab=28.07 E-value=37 Score=24.00 Aligned_cols=16 Identities=31% Similarity=0.518 Sum_probs=10.7
Q ss_pred cHHHHH---HHHHHHHhhc
Q psy11008 42 SQEELN---SVATFIKQRG 57 (96)
Q Consensus 42 s~eEl~---~Va~fI~~rg 57 (96)
|+||++ .+.+||..||
T Consensus 47 s~eE~~HA~~l~~yi~~rg 65 (160)
T cd00904 47 AQEEREHAEKFYKYQNERG 65 (160)
T ss_pred HHHHHHHHHHHHHHHHHCC
Confidence 445544 7777888887
No 416
>PRK01546 hypothetical protein; Provisional
Probab=28.07 E-value=46 Score=22.77 Aligned_cols=22 Identities=27% Similarity=0.449 Sum_probs=17.2
Q ss_pred CChHHHHHHHHHHHHcCCccEE
Q psy11008 10 MKTQSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGV 31 (96)
|-++++|+||++|-+--.-.|+
T Consensus 1 M~~~~~i~RINeLakK~K~~gL 22 (79)
T PRK01546 1 MLSHELVERINFLAKKAKAEGL 22 (79)
T ss_pred CCcHHHHHHHHHHHHhhcccCC
Confidence 4578899999999887775553
No 417
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=27.89 E-value=38 Score=25.72 Aligned_cols=21 Identities=24% Similarity=0.420 Sum_probs=18.0
Q ss_pred ChhhhhhhCCChHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~e 21 (96)
|+++|.+-||+.+++|++.-.
T Consensus 93 L~~vA~~~gLs~eevi~~Hs~ 113 (202)
T TIGR00370 93 LEEVAKINQLSPEEVIDIHSN 113 (202)
T ss_pred HHHHHHHhCcCHHHHHHHHhC
Confidence 578999999999999987643
No 418
>PRK15414 phosphomannomutase CpsG; Provisional
Probab=27.79 E-value=84 Score=25.77 Aligned_cols=26 Identities=19% Similarity=0.337 Sum_probs=20.5
Q ss_pred cEEeeCCCceEEEcHHHHHH-HHHHHHhh
Q psy11008 29 TGVIDDRGKFIYISQEELNS-VATFIKQR 56 (96)
Q Consensus 29 tGViDDRGKfIyIs~eEl~~-Va~fI~~r 56 (96)
-|++|++|+| ++.+++-+ +|.|+.++
T Consensus 251 ~~~vde~G~~--l~~d~~~~l~a~~ll~~ 277 (456)
T PRK15414 251 CFLFDEKGQF--IEGYYIVGLLAEAFLEK 277 (456)
T ss_pred EEEECCCCCE--ecHHHHHHHHHHHHHHh
Confidence 4689999998 89999988 56677554
No 419
>PLN03239 histone acetyltransferase; Provisional
Probab=27.62 E-value=59 Score=27.55 Aligned_cols=46 Identities=17% Similarity=0.224 Sum_probs=33.7
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCce-EEEcHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKF-IYISQEELNSVATF 52 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKf-IyIs~eEl~~Va~f 52 (96)
++|||..-||+.+|||.-+ +..|.|. ..+|.+ |+++++-++..++-
T Consensus 287 i~dis~~Tgi~~~DIi~tL---~~l~~l~---~~~g~~~i~~~~~~l~~~~~~ 333 (351)
T PLN03239 287 IMDIAKKTSIMAEDIVFAL---NQLGILK---FINGIYFIAAEKGLLEELAEK 333 (351)
T ss_pred HHHHHHHhCCCHHHHHHHH---HHCCcEE---EECCeEEEEeCHHHHHHHHHH
Confidence 4789999999999998655 5556663 234554 88899988886553
No 420
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=27.59 E-value=96 Score=18.34 Aligned_cols=27 Identities=15% Similarity=0.400 Sum_probs=15.1
Q ss_pred hhhhhhhCCChHHHHHH----HHHHHHcCCc
Q psy11008 2 EDLAALFRMKTQSVIDR----IVELQKTGAL 28 (96)
Q Consensus 2 edLAa~F~lktq~vI~R----I~eL~~~g~l 28 (96)
+.|+.+|+...+++-+. |.+|.+.|-|
T Consensus 37 ~~l~~~y~~~~~~~~~dv~~fl~~L~~~glI 67 (68)
T PF05402_consen 37 DALAEEYDVDPEEAEEDVEEFLEQLREKGLI 67 (68)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHHHTT--
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHCcCc
Confidence 45788888877755444 5666666654
No 421
>TIGR02276 beta_rpt_yvtn 40-residue YVTN family beta-propeller repeat. This repeat of about 40 amino acids is found in up to 14 copies per protein. Archaea Methanosarcina mazei and Methanosarcina acetivorans each have over 10 genes that encode tandem copies of this repeat, which is also found in other species. PSIPRED predicts with high confidence that each 40-residue repeats contains four beta strands. This model overlaps somewhat with the NHL repeat (Pfam pfam01436) and also shows sequence similarity to the WD domain, G-beta repeat (Pfam pfam00400).
Probab=27.51 E-value=42 Score=17.60 Aligned_cols=12 Identities=17% Similarity=0.493 Sum_probs=8.9
Q ss_pred CCCceEEEcHHH
Q psy11008 34 DRGKFIYISQEE 45 (96)
Q Consensus 34 DRGKfIyIs~eE 45 (96)
+.||++|++...
T Consensus 1 pd~~~lyv~~~~ 12 (42)
T TIGR02276 1 PDGTKLYVTNSG 12 (42)
T ss_pred CCCCEEEEEeCC
Confidence 368899998654
No 422
>KOG1273|consensus
Probab=27.27 E-value=31 Score=29.89 Aligned_cols=14 Identities=50% Similarity=0.899 Sum_probs=11.5
Q ss_pred cEEeeCCCceEEEc
Q psy11008 29 TGVIDDRGKFIYIS 42 (96)
Q Consensus 29 tGViDDRGKfIyIs 42 (96)
.|++|.||||||.-
T Consensus 158 ~~~fdr~g~yIitG 171 (405)
T KOG1273|consen 158 HGVFDRRGKYIITG 171 (405)
T ss_pred cccccCCCCEEEEe
Confidence 46899999999853
No 423
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=27.12 E-value=1.2e+02 Score=20.19 Aligned_cols=21 Identities=14% Similarity=0.213 Sum_probs=16.5
Q ss_pred CceEEEcHHHHHHHHHHHHhh
Q psy11008 36 GKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~r 56 (96)
|+.+-+|+-|.+-+.-+.+..
T Consensus 150 ~~~~~Lt~~E~~il~~l~~~~ 170 (228)
T PRK11083 150 GTPLTLTRYEFLLLKTLLLSP 170 (228)
T ss_pred CEEeecCHHHHHHHHHHHhCC
Confidence 556778999988888777776
No 424
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=26.82 E-value=61 Score=19.63 Aligned_cols=28 Identities=21% Similarity=0.340 Sum_probs=17.6
Q ss_pred hhhhhhCCCh-HHHHHHHHH-HHHcCCccE
Q psy11008 3 DLAALFRMKT-QSVIDRIVE-LQKTGALTG 30 (96)
Q Consensus 3 dLAa~F~lkt-q~vI~RI~e-L~~~g~ltG 30 (96)
..|..-|-+. .+++.+|++ |.++|+|+|
T Consensus 21 ~~A~~~gRS~NsEIv~~L~~~l~~e~~i~~ 50 (50)
T PF03869_consen 21 ERAEENGRSMNSEIVQRLEEALKKEGRIQA 50 (50)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHHHHCTSSCT
T ss_pred HHHHHhCCChHHHHHHHHHHHHhccccCCC
Confidence 3444444443 456788776 889998874
No 425
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=26.78 E-value=75 Score=21.41 Aligned_cols=29 Identities=34% Similarity=0.556 Sum_probs=25.1
Q ss_pred hhhCCChHHHHHHHHHHHHcCCccEEeeC
Q psy11008 6 ALFRMKTQSVIDRIVELQKTGALTGVIDD 34 (96)
Q Consensus 6 a~F~lktq~vI~RI~eL~~~g~ltGViDD 34 (96)
.+|..+-++++++|++|.+.|..+=++=.
T Consensus 9 e~~~~~g~~~~~~iK~li~kGNv~Ri~Ik 37 (84)
T PF14242_consen 9 EEFQVKGEELVDKIKELIKKGNVTRIIIK 37 (84)
T ss_pred ceeeecHHHHHHHHHHHHHhcCeEEEEEE
Confidence 46778889999999999999999987753
No 426
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=26.67 E-value=42 Score=23.82 Aligned_cols=25 Identities=44% Similarity=0.501 Sum_probs=22.1
Q ss_pred HHHHHHHHHhhchhchhhhhhhhccccceeH
Q psy11008 46 LNSVATFIKQRGREELNSVATFIKQKGRVSV 76 (96)
Q Consensus 46 l~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi 76 (96)
+-.+|.|+|.| |+|+=.-..|||.+
T Consensus 14 wL~~aR~~KrR------slAk~~~~~GrV~v 38 (100)
T COG1188 14 WLWAARFIKRR------SLAKEMIEGGRVKV 38 (100)
T ss_pred HHHHHHHhhhH------HHHHHHHHCCeEEE
Confidence 45688999999 89999999999987
No 427
>PRK04280 arginine repressor; Provisional
Probab=26.64 E-value=77 Score=23.01 Aligned_cols=31 Identities=29% Similarity=0.383 Sum_probs=23.0
Q ss_pred hHHHHHH-HHHHHHcCCccEEeeCCCceEEEcHHHH
Q psy11008 12 TQSVIDR-IVELQKTGALTGVIDDRGKFIYISQEEL 46 (96)
Q Consensus 12 tq~vI~R-I~eL~~~g~ltGViDDRGKfIyIs~eEl 46 (96)
||..|.| |++| |.+ =|-|..|+|.|.-++|.
T Consensus 36 TQATiSRDikeL---~lv-Kv~~~~G~~~Y~lp~~~ 67 (148)
T PRK04280 36 TQATVSRDIKEL---HLV-KVPLPDGRYKYSLPADQ 67 (148)
T ss_pred ehHHHHHHHHHc---CCE-EeecCCCcEEEeecccc
Confidence 6888888 6665 333 37889999999877654
No 428
>cd04589 CBS_pair_CAP-ED_DUF294_assoc_bac This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the bacterial CAP_ED (cAMP receptor protein effector domain) family of transcription factors and the DUF294 domain. Members of CAP_ED, include CAP which binds cAMP, FNR (fumarate and nitrate reductase) which uses an iron-sulfur cluster to sense oxygen, and CooA a heme containing CO sensor. In all cases binding of the effector leads to conformational changes and the ability to activate transcription. DUF294 is a putative nucleotidyltransferase with a conserved DxD motif. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or
Probab=26.60 E-value=1.5e+02 Score=17.74 Aligned_cols=36 Identities=11% Similarity=0.120 Sum_probs=22.0
Q ss_pred CCChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHHH
Q psy11008 9 RMKTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
..+-.++++.+. +.+ ...-|.|+ |+|+ +++.+.+..
T Consensus 9 ~~~~~~~~~~~~---~~~~~~~~V~d~-~~~~G~v~~~~l~~ 46 (111)
T cd04589 9 STSIRDAARLMR---EHGADALLVRDG-DPRLGIVTRTDLLD 46 (111)
T ss_pred CCcHHHHHHHHH---HcCCCEEEEecC-CeEEEEEEHHHHHH
Confidence 445566666552 233 34456677 8988 788887654
No 429
>TIGR03249 KdgD 5-dehydro-4-deoxyglucarate dehydratase. 5-dehydro-4-deoxyglucarate dehydratase not only catalyzes the dehydration of the substrate (diol to ketone + water), but causes the decarboxylation of the intermediate product to yield 2-oxoglutarate semialdehyde (2,5-dioxopentanoate). The gene for the enzyme is usually observed in the vicinity of transporters and dehydratases handling D-galactarate and D-gluconate as well as aldehyde dehydrogenases which convert the product to alpha-ketoglutarate.
Probab=26.59 E-value=1.7e+02 Score=22.45 Aligned_cols=47 Identities=15% Similarity=0.212 Sum_probs=33.6
Q ss_pred CCChHHHHHHHHHHHHcCCccEEe--eCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 9 RMKTQSVIDRIVELQKTGALTGVI--DDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g~ltGVi--DDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.+..+....-++.|.+ .-+.|++ -.-|-|.++|.||...|.+...+.
T Consensus 22 ~iD~~~l~~li~~l~~-~Gv~gi~v~GstGE~~~Lt~eEr~~v~~~~~~~ 70 (296)
T TIGR03249 22 SFDEAAYRENIEWLLG-YGLEALFAAGGTGEFFSLTPAEYEQVVEIAVST 70 (296)
T ss_pred CcCHHHHHHHHHHHHh-cCCCEEEECCCCcCcccCCHHHHHHHHHHHHHH
Confidence 3444555555555555 5577865 489999999999999999866654
No 430
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=26.57 E-value=45 Score=25.14 Aligned_cols=17 Identities=24% Similarity=0.382 Sum_probs=15.3
Q ss_pred EEcHHHHHHHHHHHHhh
Q psy11008 40 YISQEELNSVATFIKQR 56 (96)
Q Consensus 40 yIs~eEl~~Va~fI~~r 56 (96)
.+|+||+.+||.||-.+
T Consensus 132 ~LsdeEL~aVAaYIl~q 148 (163)
T CHL00133 132 SLTDEDLYAIAGHILLQ 148 (163)
T ss_pred CCCHHHHHHHHHHHHhc
Confidence 59999999999999855
No 431
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=26.45 E-value=1.1e+02 Score=15.87 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=14.6
Q ss_pred hhhhhhhCCChHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~e 21 (96)
.++|..+|++...+-.++..
T Consensus 30 ~~ia~~~~~s~~~i~~~~~~ 49 (55)
T cd06171 30 EEIAEILGISRSTVRQRLHR 49 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 57899999977766555554
No 432
>TIGR02675 tape_meas_nterm tape measure domain. Proteins containing this domain are strictly bacterial, including bacteriophage and prophage regions of bacterial genomes. Most members are 800 to 1800 amino acids long, making them among the longest predicted proteins of their respective phage genomes, where they are encoded in tail protein regions. This roughly 80-residue domain described here usually begins between residue 100 and 250. Many members are known or predicted to act as phage tail tape measure proteins, a minor tail component that regulates tail length.
Probab=26.32 E-value=65 Score=20.68 Aligned_cols=24 Identities=21% Similarity=0.328 Sum_probs=19.0
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCcc
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALT 29 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~lt 29 (96)
.-||..+|+.+.+ +++|.++|.||
T Consensus 48 ~~lAk~~G~t~~~----l~~~~~~Gkit 71 (75)
T TIGR02675 48 QALAKAMGVTRGE----LRKMLSDGKLT 71 (75)
T ss_pred HHHHHHhCCCHHH----HHHHHHCCCCc
Confidence 4588899987664 57888999987
No 433
>TIGR01387 cztR_silR_copR heavy metal response regulator. Members of this family contain a response regulator receiver domain (Pfam:PF00072) and an associated transcriptional regulatory region (Pfam:PF00486). This group is separated phylogenetically from related proteins with similar architecture and contains a number of proteins associated with heavy metal resistance efflux systems for copper, silver, cadmium, and/or zinc. Most members encoded by genes adjacent to genes for encoding a member of the heavy metal sensor histidine kinase family (TIGRFAMs:TIGR01386), its partner in the two-component response regulator system.
Probab=26.32 E-value=1.3e+02 Score=19.78 Aligned_cols=23 Identities=9% Similarity=0.183 Sum_probs=19.5
Q ss_pred CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 34 DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 34 DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
..|+-+.+|+.|.+-+.-+.+..
T Consensus 141 ~~~~~~~Lt~~E~~il~~l~~~~ 163 (218)
T TIGR01387 141 RGNIRITLTRKEFQLLWLLMRRT 163 (218)
T ss_pred ECCEEEeCCHHHHHHHHHHHhCC
Confidence 36788899999999888888877
No 434
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase. This family consists of the strictly bacterial MurF gene of peptidoglycan biosynthesis. This enzyme is almost always UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D-alanyl-D-alanyl ligase, but in a few species, MurE adds lysine rather than diaminopimelate. This enzyme acts on the product from MurE activity, and so is also subfamily rather than equivalog. Staphylococcus aureus is an example of species in this MurF protein would differ.
Probab=26.29 E-value=2.1e+02 Score=22.79 Aligned_cols=52 Identities=12% Similarity=0.232 Sum_probs=40.4
Q ss_pred hhhhhCCChHHHHHHHHHHH-HcCCccEEeeCCCceEEE-----cHHHHHHHHHHHHhh
Q psy11008 4 LAALFRMKTQSVIDRIVELQ-KTGALTGVIDDRGKFIYI-----SQEELNSVATFIKQR 56 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~-~~g~ltGViDDRGKfIyI-----s~eEl~~Va~fI~~r 56 (96)
+|..+|++.+++.+.|..+. -.||+. +....|..|+. +|+.+.++-+.+++.
T Consensus 265 ~~~~lGi~~~~i~~~l~~~~~~~gR~e-~~~~~~~~vidDsya~np~s~~~al~~l~~~ 322 (417)
T TIGR01143 265 LALELGIPLEEIAEGLAELKLVKGRFE-IQTKNGLTLIDDTYNANPDSMRAALDALARF 322 (417)
T ss_pred HHHHcCCCHHHHHHHHHhCCCCCCcee-EEcCCCcEEEEcCCCCCHHHHHHHHHHHHhC
Confidence 35567999999999999998 589999 76555544544 489999999999864
No 435
>cd04612 CBS_pair_SpoIVFB_EriC_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with either the SpoIVFB domain (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) or the chloride channel protein EriC. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A ), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. EriC is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase an
Probab=26.28 E-value=1.5e+02 Score=17.54 Aligned_cols=20 Identities=20% Similarity=0.506 Sum_probs=14.8
Q ss_pred ccEEeeCCCceE-EEcHHHHHH
Q psy11008 28 LTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 28 ltGViDDRGKfI-yIs~eEl~~ 48 (96)
.-.|+|+ |+|+ +++..++..
T Consensus 26 ~~~v~~~-~~~~G~v~~~dl~~ 46 (111)
T cd04612 26 GYPVVDD-GRLVGIVTLADIRR 46 (111)
T ss_pred cceEeeC-CeEEEEEEHHHHHH
Confidence 3456688 9988 788888754
No 436
>cd02259 Peptidase_C39_like Peptidase family C39 mostly contains bacteriocin-processing endopeptidases from bacteria. The cysteine peptidases in family C39 cleave the "double-glycine" leader peptides from the precursors of various bacteriocins (mostly non-lantibiotic). The cleavage is mediated by the transporter as part of the secretion process. Bacteriocins are antibiotic proteins secreted by some species of bacteria that inhibit the growth of other bacterial species. The bacteriocin is synthesized as a precursor with an N-terminal leader peptide, and processing involves removal of the leader peptide by cleavage at a Gly-Gly bond, followed by translocation of the mature bacteriocin across the cytoplasmic membrane. Most endopeptidases of family C39 are N-terminal domains in larger proteins (ABC transporters) that serve both functions. The proposed protease active site is not conserved in all sub-families.
Probab=26.19 E-value=33 Score=21.44 Aligned_cols=42 Identities=17% Similarity=0.198 Sum_probs=28.4
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~ 43 (96)
.++|..+|++.+.+--....|.+.+.-.=+.+..|.|+-|..
T Consensus 45 ~~~a~~~gl~~~~~~~~~~~l~~~~~P~i~~~~~~~~~Vl~~ 86 (122)
T cd02259 45 VSLANKLGLTAQGVKLPLAALSRLQLPALLLWKQGHFVILYG 86 (122)
T ss_pred HHHHHHcCCeeeEEEcCHHHhccCCCCEEEEcCCCcEEEEEE
Confidence 467888888887654455667776665555577777766554
No 437
>PF08974 DUF1877: Domain of unknown function (DUF1877); InterPro: IPR015068 This entry represents a family of hypothetical proteins.; PDB: 1RYL_B.
Probab=26.15 E-value=1.1e+02 Score=22.03 Aligned_cols=23 Identities=26% Similarity=0.416 Sum_probs=17.6
Q ss_pred EEEcHHHHHHHHHHHHhhchhch
Q psy11008 39 IYISQEELNSVATFIKQRGREEL 61 (96)
Q Consensus 39 IyIs~eEl~~Va~fI~~rgr~~~ 61 (96)
-|+++++...+|+++.+...++|
T Consensus 88 ~~~~~~~V~~ia~aL~~~~~~~l 110 (167)
T PF08974_consen 88 RYLTPEQVKEIAEALAAIDFEEL 110 (167)
T ss_dssp EEE-HHHHHHHHHHHHHS-HHHH
T ss_pred EEecHHHHHHHHHHHHcCCHHHH
Confidence 59999999999999998844444
No 438
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 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 []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=26.10 E-value=67 Score=20.03 Aligned_cols=46 Identities=24% Similarity=0.194 Sum_probs=25.2
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN 47 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~ 47 (96)
++++|..+.++...+...|+.+.+.=.-.|+-= +.+-+.|+=+|.+
T Consensus 33 ~~~la~~~~iS~sti~~~i~~l~~~l~~~~l~i-~~~~~~l~G~E~~ 78 (87)
T PF05043_consen 33 IEDLAEELFISRSTIYRDIKKLNKYLKKYGLKI-SKKGYRLEGDESN 78 (87)
T ss_dssp HHHHHHHHT--HHHHHHHHHHHHHHHHCCT-EE--SSEEEEES-HHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHcCeEE-eCCCeEEEeCHHH
Confidence 478999999998888777666654322222211 5555666655544
No 439
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.93 E-value=2.1e+02 Score=19.14 Aligned_cols=50 Identities=12% Similarity=0.119 Sum_probs=36.3
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
.++|..+|+++. -|.--++.|-|.-.-+ .|.|=|-|++++..+..-..-|
T Consensus 4 ~eva~~~gvs~~----tlR~Ye~~GLl~p~r~-~~g~R~Y~~~~~~~l~~I~~lr 53 (112)
T cd01282 4 GELAARTGVSVR----SLRYYEEQGLLVPERS-ANGYRDYDEAAVDRVRQIRRLL 53 (112)
T ss_pred HHHHHHHCCCHH----HHHHHHHCCCCCCCcC-CCCCeecCHHHHHHHHHHHHHH
Confidence 589999999765 3566788899987544 5668888999888775443333
No 440
>PRK11426 hypothetical protein; Provisional
Probab=25.92 E-value=60 Score=23.93 Aligned_cols=22 Identities=18% Similarity=0.267 Sum_probs=18.9
Q ss_pred ChhhhhhhCCChHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVEL 22 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL 22 (96)
+++||.++|++++++.+++-+.
T Consensus 75 i~~lA~q~Gl~~~~~~~~LA~~ 96 (132)
T PRK11426 75 VSDLGQKLGVDTSTASSLLAEQ 96 (132)
T ss_pred HHHHHHHHCcCHHHHHHHHHHH
Confidence 4689999999999999998765
No 441
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=25.84 E-value=44 Score=25.13 Aligned_cols=20 Identities=20% Similarity=0.089 Sum_probs=17.4
Q ss_pred ChhhhhhhCCChHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIV 20 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~ 20 (96)
|+++|..-||+.+++|++.-
T Consensus 103 L~~vA~~~gLs~~evi~~Hs 122 (201)
T smart00796 103 LEFVARHNGLSVDEVIRLHS 122 (201)
T ss_pred HHHHHHHhCcCHHHHHHHHh
Confidence 57899999999999998764
No 442
>cd06808 PLPDE_III Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzymes. The fold type III PLP-dependent enzyme family is predominantly composed of two-domain proteins with similarity to bacterial alanine racemases (AR) including eukaryotic ornithine decarboxylases (ODC), prokaryotic diaminopimelate decarboxylases (DapDC), biosynthetic arginine decarboxylases (ADC), carboxynorspermidine decarboxylases (CANSDC), and similar proteins. AR-like proteins contain an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. They exist as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. These proteins play important roles in the biosynthesis of amino acids and polyamine. The family also includes the single-domain YBL036c-like proteins, which contain a single PLP-binding TIM-barrel domain without any N- or C-terminal extensions. Due to the lack of a second domain, these p
Probab=25.80 E-value=1.8e+02 Score=20.03 Aligned_cols=34 Identities=12% Similarity=0.151 Sum_probs=25.8
Q ss_pred hhhCCChHHHHHHHHHHHHcC--CccEEeeCCCceE
Q psy11008 6 ALFRMKTQSVIDRIVELQKTG--ALTGVIDDRGKFI 39 (96)
Q Consensus 6 a~F~lktq~vI~RI~eL~~~g--~ltGViDDRGKfI 39 (96)
..||+..+++.+-++.+.+.+ .+.|+.-.-|...
T Consensus 120 ~R~G~~~~e~~~~~~~i~~~~~l~l~Gl~~H~~~~~ 155 (211)
T cd06808 120 GKFGVRPEELKALLERAKELPHLRLVGLHTHFGSAD 155 (211)
T ss_pred CCCCCCHHHHHHHHHHHHhCCCCcEEEEEEecCCCC
Confidence 578998888777777777777 7888887666544
No 443
>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=25.78 E-value=85 Score=17.78 Aligned_cols=20 Identities=15% Similarity=0.238 Sum_probs=15.4
Q ss_pred hhhhhhhCCChHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~e 21 (96)
+|+|..+|++.+.|-.+...
T Consensus 24 ~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 24 EEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp HHHHHHHTSCHHHHHHHHHH
T ss_pred HHHHHHHCCcHHHHHHHHHH
Confidence 68999999987777666543
No 444
>PF11042 DUF2750: Protein of unknown function (DUF2750); InterPro: IPR021284 This family is conserved in Proteobacteria. The function is not known.
Probab=25.58 E-value=1.5e+02 Score=19.70 Aligned_cols=37 Identities=27% Similarity=0.397 Sum_probs=29.8
Q ss_pred hHHHHHH-HHHHHHcCCccEEe-eCCCceEEEcHHHHHH
Q psy11008 12 TQSVIDR-IVELQKTGALTGVI-DDRGKFIYISQEELNS 48 (96)
Q Consensus 12 tq~vI~R-I~eL~~~g~ltGVi-DDRGKfIyIs~eEl~~ 48 (96)
-.+-+++ +-.|.++|...||. +..+.-+-+++.||..
T Consensus 63 L~~Fle~wl~~L~~d~~~vgv~~~~~~~g~~v~p~el~~ 101 (104)
T PF11042_consen 63 LDEFLEEWLPGLQEDGVLVGVFPNPDLEGIEVEPEELAE 101 (104)
T ss_pred HHHHHHHHhHhHHHCCCEEEEecCCCCcEEEEcHHHHHH
Confidence 4455553 67899999999998 7788889999999854
No 445
>PTZ00488 Proteasome subunit beta type-5; Provisional
Probab=25.47 E-value=1.8e+02 Score=22.26 Aligned_cols=47 Identities=11% Similarity=0.037 Sum_probs=31.3
Q ss_pred CCChHHHHHHH----HHHHHcCCc------cEEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 9 RMKTQSVIDRI----VELQKTGAL------TGVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 9 ~lktq~vI~RI----~eL~~~g~l------tGViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+|+.+++++-+ .++...+.+ -+++|.+| |-.++++|++...+=+..+
T Consensus 185 dms~eEai~l~~kal~~~~~Rd~~sg~~~ei~iI~k~g-~~~l~~~ei~~~l~~~~~~ 241 (247)
T PTZ00488 185 DLNDEEAQDLGRRAIYHATFRDAYSGGAINLYHMQKDG-WKKISADDCFDLHQKYAAE 241 (247)
T ss_pred CCCHHHHHHHHHHHHHHHHHhccccCCCeEEEEEcCCc-cEECCHHHHHHHHHHHhhh
Confidence 46667766653 345553434 46888776 8999999988777655543
No 446
>cd03174 DRE_TIM_metallolyase DRE-TIM metallolyase superfamily. The DRE-TIM metallolyase superfamily includes 2-isopropylmalate synthase (IPMS), alpha-isopropylmalate synthase (LeuA), 3-hydroxy-3-methylglutaryl-CoA lyase, homocitrate synthase, citramalate synthase, 4-hydroxy-2-oxovalerate aldolase, re-citrate synthase, transcarboxylase 5S, pyruvate carboxylase, AksA, and FrbC. These members all share a conserved triose-phosphate isomerase (TIM) barrel domain consisting of a core beta(8)-alpha(8) motif with the eight parallel beta strands forming an enclosed barrel surrounded by eight alpha helices. The domain has a catalytic center containing a divalent cation-binding site formed by a cluster of invariant residues that cap the core of the barrel. In addition, the catalytic site includes three invariant residues - an aspartate (D), an arginine (R), and a glutamate (E) - which is the basis for the domain name "DRE-TIM".
Probab=25.46 E-value=2.2e+02 Score=20.51 Aligned_cols=45 Identities=18% Similarity=0.283 Sum_probs=31.4
Q ss_pred CChHHHHHHHHHHHHcCC-ccEEeeCCCceEEEcHHHHHHHHHHHHhhc
Q psy11008 10 MKTQSVIDRIVELQKTGA-LTGVIDDRGKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~-ltGViDDRGKfIyIs~eEl~~Va~fI~~rg 57 (96)
...+.+.+.++.+.+.|. .-.+.|.-| +.+|+++..+..+++++-
T Consensus 143 ~~~~~l~~~~~~~~~~g~~~i~l~Dt~G---~~~P~~v~~li~~l~~~~ 188 (265)
T cd03174 143 TDPEYVLEVAKALEEAGADEISLKDTVG---LATPEEVAELVKALREAL 188 (265)
T ss_pred CCHHHHHHHHHHHHHcCCCEEEechhcC---CcCHHHHHHHHHHHHHhC
Confidence 556667777777777765 445666666 478888888888887773
No 447
>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=25.45 E-value=1.9e+02 Score=18.92 Aligned_cols=33 Identities=18% Similarity=0.237 Sum_probs=24.6
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEeeCCCceEE
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVIDDRGKFIY 40 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIy 40 (96)
.+++...|-.-|..|++.|.|.-+-.+.|...|
T Consensus 38 ~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y 70 (120)
T PF01475_consen 38 PRISLATVYRTLDLLEEAGLIRKIEFGDGESRY 70 (120)
T ss_dssp TT--HHHHHHHHHHHHHTTSEEEEEETTSEEEE
T ss_pred CCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceE
Confidence 356666777889999999999998877665555
No 448
>PRK12494 NADH dehydrogenase subunit J; Provisional
Probab=25.45 E-value=1.4e+02 Score=22.16 Aligned_cols=44 Identities=18% Similarity=0.055 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhc
Q psy11008 14 SVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRG 57 (96)
Q Consensus 14 ~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rg 57 (96)
.|..+++++.=...+.++-=+.=.++.|+.+.+..++.+++..|
T Consensus 18 ~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~~~l~~v~~~L~~~g 61 (172)
T PRK12494 18 PVSQWLTENGFEHESLGPDHLGVEIIKVEPDFLLPIATALYAYG 61 (172)
T ss_pred hHHHHHHHcCCCccccccccCCCEEEEEcHHHHHHHHHHHHHCC
Confidence 46677777755566666543333579999999999999999886
No 449
>cd00001 PTS_IIB_man PTS_IIB, PTS system, Mannose/sorbose specific IIB subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIB PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. The active site histidine receives a phosphate group from the IIA subunit and transfers it to the substrate.
Probab=25.44 E-value=63 Score=23.28 Aligned_cols=19 Identities=11% Similarity=0.349 Sum_probs=15.1
Q ss_pred ceEEEcHHHHHHHHHHHHh
Q psy11008 37 KFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 37 KfIyIs~eEl~~Va~fI~~ 55 (96)
+.||+|++|++++-....+
T Consensus 116 ~~v~l~~~e~~~lk~l~~~ 134 (151)
T cd00001 116 KAVSLDEEDVAAFKELAQK 134 (151)
T ss_pred cceecCHHHHHHHHHHHHc
Confidence 5699999999998665543
No 450
>PRK11543 gutQ D-arabinose 5-phosphate isomerase; Provisional
Probab=25.31 E-value=2.1e+02 Score=21.62 Aligned_cols=37 Identities=16% Similarity=0.296 Sum_probs=24.1
Q ss_pred CCChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHHH
Q psy11008 9 RMKTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 9 ~lktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
+++..++++++ .+.+ ....|+|++|+++ +||..++..
T Consensus 215 ~~sv~~a~~~~---~~~~~~~~~Vvd~~g~~iG~vt~~dl~~ 253 (321)
T PRK11543 215 TASVMDAMLEL---SRTGLGLVAVCDAQQQVQGVFTDGDLRR 253 (321)
T ss_pred CCCHHHHHHHH---HHcCCCEEEEEcCCCcEEEEecHHHHHH
Confidence 34445555544 3333 4556889999999 578888764
No 451
>PF09601 DUF2459: Protein of unknown function (DUF2459); InterPro: IPR011727 This conserved hypothetical protein of unknown function is predominantly found in proteobacteria. Its function is unknown and its genome context is not well-conserved. It is found amid urease genes in at least one species.
Probab=25.31 E-value=73 Score=23.65 Aligned_cols=21 Identities=19% Similarity=0.352 Sum_probs=18.2
Q ss_pred CceEEEcHHHHHHHHHHHHhh
Q psy11008 36 GKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~r 56 (96)
=+=|.||++++.++..||++-
T Consensus 93 ~~~i~ls~~~y~~L~~~I~~s 113 (173)
T PF09601_consen 93 VRPIRLSEAQYRRLVAFIRAS 113 (173)
T ss_pred eEEEEcCHHHHHHHHHHHHHH
Confidence 345899999999999999875
No 452
>cd04585 CBS_pair_ACT_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms. They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The i
Probab=25.22 E-value=1.3e+02 Score=17.93 Aligned_cols=20 Identities=25% Similarity=0.522 Sum_probs=15.0
Q ss_pred ccEEeeCCCceE-EEcHHHHHH
Q psy11008 28 LTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 28 ltGViDDRGKfI-yIs~eEl~~ 48 (96)
..-|+|+ |+|+ +||..++..
T Consensus 26 ~~~V~d~-~~~~G~i~~~~l~~ 46 (122)
T cd04585 26 RLPVVDR-GKLVGIVTDRDLKL 46 (122)
T ss_pred eeeEecC-CeEEEEEeHHHHHH
Confidence 3456788 9998 688888765
No 453
>TIGR03834 EAGR_box EAGR box. The EAGR box (Enriched in Aromatic and Glycine Residues) is found in three different proteins of the Mycoplasma genitalium terminal organelle, which acts in both cytadherence and gliding motility. The presence of this domain in a genome predicts the Mycoplasma-type terminal organelle structure, gliding motility, and cytadherence. The EAGR box may occur from one to nine times in a protein.
Probab=25.09 E-value=33 Score=19.61 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=9.5
Q ss_pred cEEeeCCCceE
Q psy11008 29 TGVIDDRGKFI 39 (96)
Q Consensus 29 tGViDDRGKfI 39 (96)
+|.+|+.|+||
T Consensus 18 ~GyFDe~~~w~ 28 (28)
T TIGR03834 18 KGYFDEDGNWV 28 (28)
T ss_pred eeEeCccCCCC
Confidence 68999999985
No 454
>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=25.09 E-value=68 Score=19.32 Aligned_cols=24 Identities=21% Similarity=0.454 Sum_probs=20.0
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQK 24 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~ 24 (96)
+.+||..+|++...+.+-|.+|..
T Consensus 22 ~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 22 LKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 368999999999999999999874
No 455
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=25.05 E-value=2e+02 Score=25.06 Aligned_cols=54 Identities=13% Similarity=0.172 Sum_probs=39.6
Q ss_pred hhhhhhCCChHHHHHHHHHHHHcCCcc----EEee-CCCceEEEcHHHHHHHHHHHHhh
Q psy11008 3 DLAALFRMKTQSVIDRIVELQKTGALT----GVID-DRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 3 dLAa~F~lktq~vI~RI~eL~~~g~lt----GViD-DRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+.+..||++.+.+.+-.|.|=+.+.+. |.|- .|=-=-|+|++..+.+..++...
T Consensus 261 ~a~~~~g~S~~~tl~iaQ~LYe~~~~~~~~~g~iSYPRTds~~l~~~~~~~~~~~l~~~ 319 (610)
T TIGR01051 261 EASRKLGFSAKKTMMIAQRLYEGVSTGDGTIGLITYMRTDSTRLSNQAVNEARNLIDKN 319 (610)
T ss_pred HHHHhcCCCHHHHHHHHHHHHhcccccCCceeEEeecCcCccccCHHHHHHHHHHHHHh
Confidence 456789999999999999999973322 2332 22222389999999999888765
No 456
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consist
Probab=25.00 E-value=1.3e+02 Score=21.35 Aligned_cols=30 Identities=23% Similarity=0.259 Sum_probs=24.4
Q ss_pred ccEEeeCC-CceEEE-------cHHHHHHHHHHHHhhc
Q psy11008 28 LTGVIDDR-GKFIYI-------SQEELNSVATFIKQRG 57 (96)
Q Consensus 28 ltGViDDR-GKfIyI-------s~eEl~~Va~fI~~rg 57 (96)
|-|+-|+. |+|+|| |+++++.+.+.++...
T Consensus 26 llG~~~~~~~~l~~vgkvgtGft~~~~~~L~~~l~~~~ 63 (144)
T cd07969 26 LLACYDPETEEFQTVCKIGTGFSDEFLEELYESLKEHV 63 (144)
T ss_pred EEEEEeCCCCEEEEEeEEccCCCHHHHHHHHHHhhhhc
Confidence 34888876 799997 4999999999887764
No 457
>PRK10701 DNA-binding transcriptional regulator RstA; Provisional
Probab=24.87 E-value=1.3e+02 Score=20.77 Aligned_cols=34 Identities=18% Similarity=0.336 Sum_probs=26.1
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccce-eHHHHHHhc
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRV-SVSELVENS 83 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRV-si~eL~~~s 83 (96)
+|+=|.+|+.|+.-+..+++.. |+| |..+|.+.-
T Consensus 156 ~~~~i~Lt~~E~~lL~~l~~~~---------------~~v~sr~~l~~~v 190 (240)
T PRK10701 156 AGEEISLSTADFDLLWELATHA---------------GQIMDRDALLKNL 190 (240)
T ss_pred CCeEeecCHHHHHHHHHHHhCC---------------CccCcHHHHHHHh
Confidence 5777888899999888888888 666 767766543
No 458
>PF03705 CheR_N: CheR methyltransferase, all-alpha domain; InterPro: IPR022641 CheR proteins are part of the chemotaxis signaling mechanism which methylates the chemotaxis receptor at specific glutamate residues. This entry refers to the N-terminal domain of the CherR-type MCP methyltransferases, which are found in bacteria, archaea and green plants. This entry is found in association with PF01739 from PFAM. Methyl transfer from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms ranging from bacteria to plants and mammals. The reaction is catalysed by methyltransferases (Mtases) and modifies DNA, RNA, proteins and small molecules, such as catechol for regulatory purposes. The various aspects of the role of DNA methylation in prokaryotic restriction-modification systems and in a number of cellular processes in eukaryotes including gene regulation and differentiation is well documented. Three classes of DNA Mtases transfer the methyl group from AdoMet to the target base to form either N-6-methyladenine, or N-4-methylcytosine, or C-5- methylcytosine. In C-5-cytosine Mtases, ten conserved motifs are arranged in the same order []. Motif I (a glycine-rich or closely related consensus sequence; FAGxGG in M.HhaI []), shared by other AdoMet-Mtases [], is part of the cofactor binding site and motif IV (PCQ) is part of the catalytic site. In contrast, sequence comparison among N-6-adenine and N-4-cytosine Mtases indicated two of the conserved segments [], although more conserved segments may be present. One of them corresponds to motif I in C-5-cytosine Mtases, and the other is named (D/N/S)PP(Y/F). Crystal structures are known for a number of Mtases [, , , ]. The cofactor binding sites are almost identical and the essential catalytic amino acids coincide. The comparable protein folding and the existence of equivalent amino acids in similar secondary and tertiary positions indicate that many (if not all) AdoMet-Mtases have a common catalytic domain structure. This permits tertiary structure prediction of other DNA, RNA, protein, and small-molecule AdoMet-Mtases from their amino acid sequences []. Flagellated bacteria swim towards favourable chemicals and away from deleterious ones. Sensing of chemoeffector gradients involves chemotaxis receptors, transmembrane (TM) proteins that detect stimuli through their periplasmic domains and transduce the signals via their cytoplasmic domains []. Signalling outputs from these receptors are influenced both by the binding of the chemoeffector ligand to their periplasmic domains and by methylation of specific glutamate residues on their cytoplasmic domains. Methylation is catalysed by CheR, an S-adenosylmethionine-dependent methyltransferase [], which reversibly methylates specific glutamate residues within a coiled coil region, to form gamma-glutamyl methyl ester residues [, ]. The structure of the Salmonella typhimurium chemotaxis receptor methyltransferase CheR, bound to S-adenosylhomocysteine, has been determined to a resolution of 2.0 A []. The structure reveals CheR to be a two-domain protein, with a smaller N-terminal helical domain linked via a single polypeptide connection to a larger C-terminal alpha/beta domain. The C-terminal domain has the characteristics of a nucleotide-binding fold, with an insertion of a small anti-parallel beta-sheet subdomain. The S-adenosylhomocysteine-binding site is formed mainly by the large domain, with contributions from residues within the N-terminal domain and the linker region [].; PDB: 1AF7_A 1BC5_A.
Probab=24.68 E-value=78 Score=18.21 Aligned_cols=15 Identities=27% Similarity=0.421 Sum_probs=12.1
Q ss_pred cHHHHHHHHHHHHhh
Q psy11008 42 SQEELNSVATFIKQR 56 (96)
Q Consensus 42 s~eEl~~Va~fI~~r 56 (96)
|+++++.++++|.++
T Consensus 1 sd~~f~~~~~~i~~~ 15 (57)
T PF03705_consen 1 SDAEFERFRELIYRR 15 (57)
T ss_dssp -HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHH
Confidence 678889999998887
No 459
>cd04611 CBS_pair_PAS_GGDEF_DUF1_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in association with a PAS domain, a GGDEF (DiGuanylate-Cyclase (DGC) domain, and a DUF1 domain downstream. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction. The GGDEF domain has been suggested to be homologous to the adenylyl cyclase catalytic domain and is thought to be involved in regulating cell surface adhesiveness in bacteria. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CB
Probab=24.63 E-value=1.3e+02 Score=17.73 Aligned_cols=10 Identities=30% Similarity=0.620 Sum_probs=5.3
Q ss_pred cceeHHHHHH
Q psy11008 72 GRVSVSELVE 81 (96)
Q Consensus 72 GRVsi~eL~~ 81 (96)
|-|+.+++.+
T Consensus 101 Gvi~~~di~~ 110 (111)
T cd04611 101 GLLSQTDLLQ 110 (111)
T ss_pred EEEEhHHhhc
Confidence 4456666543
No 460
>cd04606 CBS_pair_Mg_transporter This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain in the magnesium transporter, MgtE. MgtE and its homologs are found in eubacteria, archaebacteria, and eukaryota. Members of this family transport Mg2+ or other divalent cations into the cell via two highly conserved aspartates. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=24.56 E-value=1.1e+02 Score=18.37 Aligned_cols=19 Identities=26% Similarity=0.538 Sum_probs=13.0
Q ss_pred ccEEeeCCCceEE-EcHHHH
Q psy11008 28 LTGVIDDRGKFIY-ISQEEL 46 (96)
Q Consensus 28 ltGViDDRGKfIy-Is~eEl 46 (96)
..-|+|+.|+|+- |+.+.+
T Consensus 27 ~~~vvd~~~~~~G~v~~~~l 46 (109)
T cd04606 27 YIYVVDEEGRLLGVVSLRDL 46 (109)
T ss_pred EEEEECCCCCEEEEEEHHHH
Confidence 4557788899874 665544
No 461
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=24.55 E-value=2.6e+02 Score=19.67 Aligned_cols=46 Identities=17% Similarity=0.283 Sum_probs=38.2
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVAT 51 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~ 51 (96)
.|+|..+|+++. -|.--++.|-|.-.-.+.+-|=|-|++.+..+..
T Consensus 4 ge~a~~~gvs~~----tlRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 49 (135)
T PRK10227 4 SDVAKITGLTSK----AIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTL 49 (135)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCcccCCHHHHHHHHH
Confidence 589999999765 4678899999987777778899999999988764
No 462
>cd01210 EPS8 Epidermal growth factor receptor kinase substrate (EPS8) Phosphotyrosine-binding (PTB) domain. Epidermal growth factor receptor kinase substrate (EPS8) Phosphotyrosine-binding (PTB) domain. EPS8 is a regulator of Rac signaling. It consists of a PTB and an SH3 domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=24.43 E-value=67 Score=23.57 Aligned_cols=63 Identities=21% Similarity=0.334 Sum_probs=41.9
Q ss_pred ChHHHHHHHHHHHHcCCccE---EeeCCCceEEEcH----HHHHHHHHHHHh-----hchhchhhhhhhhccccc
Q psy11008 11 KTQSVIDRIVELQKTGALTG---VIDDRGKFIYISQ----EELNSVATFIKQ-----RGREELNSVATFIKQKGR 73 (96)
Q Consensus 11 ktq~vI~RI~eL~~~g~ltG---ViDDRGKfIyIs~----eEl~~Va~fI~~-----rgr~~~~~~~~~~~~~GR 73 (96)
.++|++.++++|++.|++-+ +++=+++++-+-+ +|++++.-=.-+ .+.+-.||+-+|.-|.++
T Consensus 22 ~~~D~i~kL~~le~~G~iW~Q~m~lqv~~~~v~LlD~etk~elE~fpl~~I~~~~a~~~~~~ynslL~~vvq~~~ 96 (127)
T cd01210 22 YPEDAMRKLLQMDKQGRVWSQKMILRVRYQWVTLLDYETKEELESYPLSLIQEPTAFTSMELYNSILLFVVQEPG 96 (127)
T ss_pred CHHHHHHHHHHHHhcCCccccceEEEEcCCeEEEEcCCCcChhhcCCHhhccccceecCCCCcCceEEEEEeCCC
Confidence 36899999999999998865 5666777777644 555544211111 235677888777766553
No 463
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 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 [, ]. Ribosomal protein L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=24.38 E-value=35 Score=22.78 Aligned_cols=47 Identities=23% Similarity=0.304 Sum_probs=32.0
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHH
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVE 81 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~ 81 (96)
.++++-+|+.-+..+|.+|+-.--++--..-.|...|+--.+..+..
T Consensus 2 ~~~~i~~S~kk~~~v~~~Irg~~v~~A~~~L~~~~~k~a~~i~k~L~ 48 (105)
T PF00237_consen 2 KLRNIRISPKKLREVARLIRGMSVDEAIAQLKFVPKKAAKFILKLLK 48 (105)
T ss_dssp EEEEESS-HHHHHHHHHHHTTSBHHHHHHHHHHHSSHHHHHHHHHHH
T ss_pred ccccccCCHHHHHHHHHHHcCCCHHHHHHHHHhCcHHHHHHHHhhHH
Confidence 36889999999999999998774444444456666666555544443
No 464
>PRK07218 replication factor A; Provisional
Probab=24.34 E-value=64 Score=27.40 Aligned_cols=24 Identities=21% Similarity=0.314 Sum_probs=22.0
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQK 24 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~ 24 (96)
.||||.++|+..+++-+||+.|.+
T Consensus 8 ~~el~~~lgv~~~~i~~~l~~Lv~ 31 (423)
T PRK07218 8 AEELASDLGVDKEEVKEELENLVA 31 (423)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHh
Confidence 379999999999999999999985
No 465
>TIGR03691 20S_bact_alpha proteasome, alpha subunit, bacterial type. Members of this family are the alpha subunit of the 20S proteasome as found in Actinobacteria such as Mycobacterium, Rhodococcus, and Streptomyces. In most Actinobacteria (an exception is Propionibacterium acnes), the proteasome is accompanied by a system of tagging proteins for degradation with Pup.
Probab=24.25 E-value=1.4e+02 Score=22.60 Aligned_cols=41 Identities=22% Similarity=0.326 Sum_probs=27.4
Q ss_pred CCChHHHHHHHHH-HHH-----------cCCccEEeeC---CCceEEEcHHHHHHH
Q psy11008 9 RMKTQSVIDRIVE-LQK-----------TGALTGVIDD---RGKFIYISQEELNSV 49 (96)
Q Consensus 9 ~lktq~vI~RI~e-L~~-----------~g~ltGViDD---RGKfIyIs~eEl~~V 49 (96)
+|+.+++++-... |.+ .+-=.||+|. +..|-.+|++|++..
T Consensus 172 ~ms~eeai~la~~aL~~~~~~~r~~~~~~~iEv~ii~k~~~~~~f~~l~~~ei~~~ 227 (228)
T TIGR03691 172 GLSLADALGLAVQALRAGGNGEKRELDAASLEVAVLDRSRPRRAFRRITGEALERL 227 (228)
T ss_pred CCCHHHHHHHHHHHHHHHhccccccCCccceEEEEEeCCCCccceEECCHHHHHhh
Confidence 4788888876333 222 2225689994 456999999998753
No 466
>COG2161 StbD Antitoxin of toxin-antitoxin stability system [Cell division and chromosome partitioning]
Probab=24.23 E-value=1.4e+02 Score=19.72 Aligned_cols=30 Identities=13% Similarity=0.179 Sum_probs=19.1
Q ss_pred HcCCccEEeeCCC-ceEEEcHHHHH--HHHHHH
Q psy11008 24 KTGALTGVIDDRG-KFIYISQEELN--SVATFI 53 (96)
Q Consensus 24 ~~g~ltGViDDRG-KfIyIs~eEl~--~Va~fI 53 (96)
..+...=|.+..+ -+++||.+|++ +.-.-+
T Consensus 24 ~~~~pv~It~~~~~~avlis~~eye~~s~~et~ 56 (86)
T COG2161 24 SDHEPVAITNRNKPAAVLISASEYERLSLQETL 56 (86)
T ss_pred cCCCcEEEecCCCccEEEecHHHHHHHHHHHHH
Confidence 3445555555444 69999999999 544333
No 467
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=24.02 E-value=1.1e+02 Score=21.38 Aligned_cols=32 Identities=19% Similarity=0.328 Sum_probs=25.4
Q ss_pred hhhhhhC-CChHHHHHHHHHHHHcCCccEEeeC
Q psy11008 3 DLAALFR-MKTQSVIDRIVELQKTGALTGVIDD 34 (96)
Q Consensus 3 dLAa~F~-lktq~vI~RI~eL~~~g~ltGViDD 34 (96)
+|-...+ ++..-+-+|+++|++.|.+.=....
T Consensus 41 eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~ 73 (120)
T COG1733 41 ELRRSIGGISPKMLSRRLKELEEDGLVERVVYP 73 (120)
T ss_pred HHHHHccccCHHHHHHHHHHHHHCCCEEeeecC
Confidence 4555555 7778888999999999999877764
No 468
>cd00130 PAS PAS domain; PAS motifs appear in archaea, eubacteria and eukarya. Probably the most surprising identification of a PAS domain was that in EAG-like K+-channels. PAS domains have been found to bind ligands, and to act as sensors for light and oxygen in signal transduction.
Probab=23.93 E-value=87 Score=15.01 Aligned_cols=15 Identities=27% Similarity=0.510 Sum_probs=12.0
Q ss_pred EEeeCCCceEEEcHH
Q psy11008 30 GVIDDRGKFIYISQE 44 (96)
Q Consensus 30 GViDDRGKfIyIs~e 44 (96)
-++|..|+++|+++.
T Consensus 6 ~~~d~~~~~~~~n~~ 20 (103)
T cd00130 6 IVLDLDGRILYANPA 20 (103)
T ss_pred EEECCCCcEEEECHH
Confidence 367889999999864
No 469
>PF13467 RHH_4: Ribbon-helix-helix domain; PDB: 3KK4_C.
Probab=23.86 E-value=61 Score=21.18 Aligned_cols=20 Identities=25% Similarity=0.335 Sum_probs=16.0
Q ss_pred ChhhhhhhCCChHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIV 20 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~ 20 (96)
|+|+|+.=|+++...|.+|.
T Consensus 26 L~eiA~~~g~s~~~li~~id 45 (67)
T PF13467_consen 26 LEEIAAREGLSLNALIAEID 45 (67)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 58999999999999999983
No 470
>cd04626 CBS_pair_13 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=23.74 E-value=1.7e+02 Score=17.46 Aligned_cols=35 Identities=11% Similarity=0.135 Sum_probs=21.2
Q ss_pred ChHHHHHHHHHHHHcC-CccEEeeCCCceE-EEcHHHHHH
Q psy11008 11 KTQSVIDRIVELQKTG-ALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 11 ktq~vI~RI~eL~~~g-~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
+..++++++ .+.+ ...-|.|+.|+|+ +++...+..
T Consensus 11 ~~~~~~~~~---~~~~~~~~~v~d~~~~~~G~v~~~dl~~ 47 (111)
T cd04626 11 SIREALHEM---LKYNTNEIIVKDNEEKLKGVVTFTDILD 47 (111)
T ss_pred cHHHHHHHH---HHhCCCeEEEEcCCCCEEEEEehHHhHH
Confidence 344555544 2223 2335668889988 788877654
No 471
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=23.73 E-value=1.1e+02 Score=23.58 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=13.5
Q ss_pred hhhhccccceeHHHHHHhcc
Q psy11008 65 ATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 65 ~~~~~~~GRVsi~eL~~~sN 84 (96)
..+++++|+|++.||++.-+
T Consensus 23 l~~L~~~~~vtv~eLa~~l~ 42 (269)
T PRK09802 23 IQRLRQQGSVQVNDLSALYG 42 (269)
T ss_pred HHHHHHcCCEeHHHHHHHHC
Confidence 33344449999999998643
No 472
>cd03015 PRX_Typ2cys Peroxiredoxin (PRX) family, Typical 2-Cys PRX subfamily; PRXs are thiol-specific antioxidant (TSA) proteins, which confer a protective role in cells through its peroxidase activity by reducing hydrogen peroxide, peroxynitrite, and organic hydroperoxides. The functional unit of typical 2-cys PRX is a homodimer. A unique intermolecular redox-active disulfide center is utilized for its activity. Upon reaction with peroxides, its peroxidatic cysteine is oxidized into a sulfenic acid intermediate which is resolved by bonding with the resolving cysteine from the other subunit of the homodimer. This intermolecular disulfide bond is then reduced by thioredoxin, tryparedoxin or AhpF. Typical 2-cys PRXs, like 1-cys PRXs, form decamers which are stabilized by reduction of the active site cysteine. Typical 2-cys PRX interacts through beta strands at one edge of the monomer (B-type interface) to form the functional homodimer, and uses an A-type interface (similar to the dimeric
Probab=23.69 E-value=96 Score=21.49 Aligned_cols=28 Identities=18% Similarity=0.233 Sum_probs=18.2
Q ss_pred cEEeeCCCceEEEc----H--HHHHHHHHHHHhh
Q psy11008 29 TGVIDDRGKFIYIS----Q--EELNSVATFIKQR 56 (96)
Q Consensus 29 tGViDDRGKfIyIs----~--eEl~~Va~fI~~r 56 (96)
+=|||..|+..|.- + ..++.+-+.|+..
T Consensus 123 ~~lID~~G~I~~~~~~~~~~~~~~~~il~~l~~~ 156 (173)
T cd03015 123 TFIIDPEGIIRHITVNDLPVGRSVDETLRVLDAL 156 (173)
T ss_pred EEEECCCCeEEEEEecCCCCCCCHHHHHHHHHHh
Confidence 55899999877776 2 2345566666544
No 473
>cd04615 CBS_pair_2 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria. The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=23.63 E-value=1.7e+02 Score=17.44 Aligned_cols=37 Identities=14% Similarity=0.279 Sum_probs=23.3
Q ss_pred CChHHHHHHHHHHHHcCCccEEeeCCCceE-EEcHHHHHH
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVIDDRGKFI-YISQEELNS 48 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGViDDRGKfI-yIs~eEl~~ 48 (96)
.+..++++++.+ .....--|.|+.|+|+ +++..++..
T Consensus 10 ~~~~~~~~~~~~--~~~~~~~vvd~~~~~~G~v~~~dl~~ 47 (113)
T cd04615 10 TDIARAVAEMYT--SGSRALPVVDDKKRLVGIITRYDVLS 47 (113)
T ss_pred CcHHHHHHHHHH--cCCceEeEEcCCCCEEEEEEHHHHHH
Confidence 344555555432 2223445779899998 789888865
No 474
>PF12272 DUF3610: Protein of unknown function (DUF3610); InterPro: IPR022058 This domain family is found in eukaryotes, and is typically between 146 and 160 amino acids in length. There are two conserved sequence motifs: FNN and IDS.
Probab=23.47 E-value=21 Score=27.28 Aligned_cols=16 Identities=38% Similarity=0.646 Sum_probs=14.3
Q ss_pred hhhhhhhhccccceeH
Q psy11008 61 LNSVATFIKQKGRVSV 76 (96)
Q Consensus 61 ~~~~~~~~~~~GRVsi 76 (96)
=||+.||+--+||+|+
T Consensus 38 NNsLGTFVE~~Gqasi 53 (157)
T PF12272_consen 38 NNSLGTFVEYSGQASI 53 (157)
T ss_pred cCccceeEeecceEEE
Confidence 3889999999999987
No 475
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=23.45 E-value=59 Score=19.21 Aligned_cols=21 Identities=24% Similarity=0.347 Sum_probs=15.8
Q ss_pred HHcCCccEEeeCCCceEEEcH
Q psy11008 23 QKTGALTGVIDDRGKFIYISQ 43 (96)
Q Consensus 23 ~~~g~ltGViDDRGKfIyIs~ 43 (96)
+..+.-.=|+.+.|.|+.|--
T Consensus 2 ei~~~~aiVlT~dGeF~~ik~ 22 (56)
T PF12791_consen 2 EIKKKYAIVLTPDGEFIKIKR 22 (56)
T ss_pred cCcCCEEEEEcCCCcEEEEeC
Confidence 345566778999999998853
No 476
>PF13202 EF-hand_5: EF hand; PDB: 3DD4_A 2Q4U_A 2BE4_A 1UHJ_B 1UHI_A 1UHH_B 1EJ3_B 1UHK_A 2ZFD_A 1UHN_A ....
Probab=23.39 E-value=68 Score=16.61 Aligned_cols=12 Identities=25% Similarity=0.526 Sum_probs=9.6
Q ss_pred cccceeHHHHHH
Q psy11008 70 QKGRVSVSELVE 81 (96)
Q Consensus 70 ~~GRVsi~eL~~ 81 (96)
..|+||..|+.+
T Consensus 12 ~DG~is~~E~~~ 23 (25)
T PF13202_consen 12 GDGKISFEEFQR 23 (25)
T ss_dssp SSSEEEHHHHHH
T ss_pred CCCcCCHHHHHH
Confidence 469999999875
No 477
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=23.38 E-value=1.7e+02 Score=19.36 Aligned_cols=32 Identities=13% Similarity=0.121 Sum_probs=22.9
Q ss_pred eEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcc
Q psy11008 38 FIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSN 84 (96)
Q Consensus 38 fIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN 84 (96)
+|-|+.+|++.+..--... --.|++||.+.++
T Consensus 3 ~vii~k~ey~el~~~~~~~---------------~~W~~~dl~k~~~ 34 (91)
T PF05595_consen 3 KVIIDKEEYEELKKKDLEG---------------KWWDMKDLRKRTG 34 (91)
T ss_pred eEEeeHHHHHHHHHHhhcc---------------ceeeHHHHHHHHC
Confidence 5778999998886544433 2358999988876
No 478
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=23.37 E-value=2.7e+02 Score=19.48 Aligned_cols=45 Identities=20% Similarity=0.175 Sum_probs=36.1
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVA 50 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va 50 (96)
.++|..+|+++. -|.--++.|-|.-...+.|.|=|.+++.+..+-
T Consensus 4 ge~a~~~gvs~~----tLRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~ 48 (131)
T cd04786 4 GELAKRSGMAAS----RIRFYEAEGLLSSVERSANGYRDYPPETVWVLE 48 (131)
T ss_pred HHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH
Confidence 578999999754 567889999998776677888888999887653
No 479
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=23.30 E-value=1.9e+02 Score=25.40 Aligned_cols=45 Identities=18% Similarity=0.212 Sum_probs=34.7
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELN 47 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~ 47 (96)
++||..+|++.++++.-+..|++.|.++ +-...=+..-+|+|-..
T Consensus 25 ~~la~~~~~~~~~v~~~~~~L~~kg~v~-~~~~~~~~~~LT~eG~~ 69 (494)
T PTZ00326 25 LALAESLNIDHQKVVGAIKSLESANYIT-TEMKKSNTWTLTEEGED 69 (494)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHhCCCEE-EEEEEEEEEEECHHHHH
Confidence 5799999999999999999999998554 44444455667777543
No 480
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=23.29 E-value=2.2e+02 Score=18.60 Aligned_cols=45 Identities=20% Similarity=0.360 Sum_probs=31.6
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATF 52 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~f 52 (96)
+|||..+|..+..+-..++.=.+. +.+..-|+.++.+|+..+..-
T Consensus 16 ~~lA~~yg~~~~~i~~~~~rN~~r------F~eg~~~f~L~~~e~~~~~~~ 60 (88)
T PF10543_consen 16 EDLAELYGVETKTINRNFKRNKDR------FIEGKDYFQLTGEELKELKSQ 60 (88)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHh------CCCCCcEEEecchhhhhhhhh
Confidence 689999999877665555543322 344566888999999887543
No 481
>TIGR00854 pts-sorbose PTS system, mannose/fructose/sorbose family, IIB component. Bacterial PTS transporters transport and concomitantly phosphorylate their sugar substrates, and typically consist of multiple subunits or protein domains.The Man family is unique in several respects among PTS permease families.It is the only PTS family in which members possess a IID protein. It is the only PTS family in which the IIB constituent is phosphorylated on a histidyl rather than a cysteyl residue. Its permease members exhibit broad specificity for a range of sugars, rather than being specific for just one or a few sugars. The mannose permease of E. coli, for example, can transport and phosphorylate glucose, mannose, fructose, glucosamine, N-acetylglucosamine, and other sugars. Other members of this can transport sorbose, fructose and N-acetylglucosamine. This family is specific for the IIB components of this family of PTS transporters.
Probab=23.25 E-value=79 Score=22.86 Aligned_cols=19 Identities=5% Similarity=0.258 Sum_probs=15.2
Q ss_pred ceEEEcHHHHHHHHHHHHh
Q psy11008 37 KFIYISQEELNSVATFIKQ 55 (96)
Q Consensus 37 KfIyIs~eEl~~Va~fI~~ 55 (96)
+.||+|++|++++-....+
T Consensus 117 ~~v~l~~~e~~~l~~l~~~ 135 (151)
T TIGR00854 117 KKVSVDDQDITAFRFLKQR 135 (151)
T ss_pred cceeeCHHHHHHHHHHHHc
Confidence 5799999999998665543
No 482
>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=23.16 E-value=98 Score=17.53 Aligned_cols=20 Identities=15% Similarity=0.381 Sum_probs=15.5
Q ss_pred hhhhhhhCCChHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~e 21 (96)
.|+|..+|++...|-.++..
T Consensus 30 ~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 30 AEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp HHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 58999999988888777754
No 483
>PRK14324 glmM phosphoglucosamine mutase; Provisional
Probab=23.15 E-value=1.1e+02 Score=24.94 Aligned_cols=26 Identities=23% Similarity=0.590 Sum_probs=20.8
Q ss_pred cEEeeCCCceEEEcHHHHHH-HHHHHHhh
Q psy11008 29 TGVIDDRGKFIYISQEELNS-VATFIKQR 56 (96)
Q Consensus 29 tGViDDRGKfIyIs~eEl~~-Va~fI~~r 56 (96)
-+++|++|+ +|+++++-+ +|.|+.++
T Consensus 248 ~~vvd~~G~--~l~~d~~~~l~a~~ll~~ 274 (446)
T PRK14324 248 LVVVDEKGE--IVHGDKLLGVLAVYLKEK 274 (446)
T ss_pred EEEECCCCC--EeCHHHHHHHHHHHHHHh
Confidence 388999999 679999866 67787665
No 484
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=23.12 E-value=1.5e+02 Score=22.74 Aligned_cols=31 Identities=13% Similarity=0.313 Sum_probs=17.4
Q ss_pred HHHHHHhhchhchhhhhhhhccccceeHHHHHHhc
Q psy11008 49 VATFIKQRGREELNSVATFIKQKGRVSVSELVENS 83 (96)
Q Consensus 49 Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~s 83 (96)
+.+||++. .++.....+.. +..|++|++..|
T Consensus 236 ~~~~l~~~---Rl~~A~~lL~~-~~~si~eIA~~~ 266 (302)
T PRK10371 236 MKQYITAM---RINHVRALLSD-TDKSILDIALTA 266 (302)
T ss_pred HHHHHHHH---HHHHHHHHHhc-CCCCHHHHHHHc
Confidence 45566555 23333344433 567888888765
No 485
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=23.04 E-value=51 Score=21.91 Aligned_cols=45 Identities=22% Similarity=0.370 Sum_probs=33.7
Q ss_pred CceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHH
Q psy11008 36 GKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELV 80 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~ 80 (96)
.++|-+|+.-+..||..|+-+--++--..-.|...|+-.-+..+.
T Consensus 5 ~~~i~~S~kK~~~v~~~Irg~~v~~A~~~L~~~~kk~a~~i~k~l 49 (105)
T cd00336 5 GRYLRISPKKARLVARLIRGMSVDEALAQLEFVPKKAAKIILKLL 49 (105)
T ss_pred EccCccCHHHHHHHHHHHcCCcHHHHHHHHHhCCHHHHHHHHHHH
Confidence 578999999999999999988666655566677666665554443
No 486
>COG0079 HisC Histidinol-phosphate/aromatic aminotransferase and cobyric acid decarboxylase [Amino acid transport and metabolism]
Probab=22.97 E-value=1.2e+02 Score=24.42 Aligned_cols=38 Identities=21% Similarity=0.455 Sum_probs=31.1
Q ss_pred HHHHHHcCCccEEeeCCCceEEEcHHH--HHHHHHHHHhhc
Q psy11008 19 IVELQKTGALTGVIDDRGKFIYISQEE--LNSVATFIKQRG 57 (96)
Q Consensus 19 I~eL~~~g~ltGViDDRGKfIyIs~eE--l~~Va~fI~~rg 57 (96)
.++|.+.| +.||+...+.||.+.-.. ...+.+++.++|
T Consensus 276 ~~~l~~~~-~~~v~pS~aNFvlv~~~~~~~~~l~~~L~~~g 315 (356)
T COG0079 276 YAALKALG-LFGVFPSQANFVLVRVPDAEAAALAEALLKKG 315 (356)
T ss_pred HHHHHhCC-CCeecCCCCcEEEEECCCccHHHHHHHHHHCC
Confidence 56788889 999999999999998643 557888888874
No 487
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=22.94 E-value=1.3e+02 Score=15.58 Aligned_cols=42 Identities=21% Similarity=0.351 Sum_probs=28.4
Q ss_pred EcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhccc
Q psy11008 41 ISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQ 85 (96)
Q Consensus 41 Is~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~ 85 (96)
-|++|-..+...+.+-|....+.+|.++. +| |..++..-.+.
T Consensus 4 Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~--~r-t~~~~~~~~~~ 45 (49)
T smart00717 4 WTEEEDELLIELVKKYGKNNWEKIAKELP--GR-TAEQCRERWNN 45 (49)
T ss_pred CCHHHHHHHHHHHHHHCcCCHHHHHHHcC--CC-CHHHHHHHHHH
Confidence 37889999999999987666777777775 33 44455444433
No 488
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=22.90 E-value=66 Score=25.16 Aligned_cols=21 Identities=29% Similarity=0.404 Sum_probs=18.5
Q ss_pred ChhhhhhhCCChHHHHHHHHH
Q psy11008 1 MEDLAALFRMKTQSVIDRIVE 21 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~e 21 (96)
|.+||.++|-+-+++|+++++
T Consensus 137 lg~ls~~vGwky~~vv~~le~ 157 (202)
T PTZ00068 137 LGDLSAHVGWKYADVVAKLEE 157 (202)
T ss_pred HHHHHHHhCccHHHHHHHHHH
Confidence 468999999999999998854
No 489
>PRK13856 two-component response regulator VirG; Provisional
Probab=22.90 E-value=1.9e+02 Score=20.12 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=27.0
Q ss_pred CCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccce-eHHHHHHh
Q psy11008 34 DRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRV-SVSELVEN 82 (96)
Q Consensus 34 DRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRV-si~eL~~~ 82 (96)
.+|+-|-+|+.|++-+-.++... |+| |-.+|.+.
T Consensus 149 ~~~~~i~Lt~~E~~lL~~l~~~~---------------~~v~sr~~l~~~ 183 (241)
T PRK13856 149 EAGGEVKLTAGEFNLLVAFLEKP---------------RDVLSREQLLIA 183 (241)
T ss_pred CCCcEeecCHHHHHHHHHHHhCC---------------CCccCHHHHHHH
Confidence 46788899999999999999888 665 66766643
No 490
>PRK13622 psbV cytochrome c-550; Provisional
Probab=22.83 E-value=58 Score=25.09 Aligned_cols=21 Identities=19% Similarity=0.396 Sum_probs=17.5
Q ss_pred CceEEEcHHHHHHHHHHHHhh
Q psy11008 36 GKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 36 GKfIyIs~eEl~~Va~fI~~r 56 (96)
+++=-+|++|++.||.||...
T Consensus 138 p~~~~LsdeEI~~VA~yIl~q 158 (180)
T PRK13622 138 PRLRNLTDEDLKLIAGYILVQ 158 (180)
T ss_pred ccccCCCHHHHHHHHHHHHhC
Confidence 444469999999999999876
No 491
>PF01408 GFO_IDH_MocA: Oxidoreductase family, NAD-binding Rossmann fold; InterPro: IPR000683 This group of enzymes utilise NADP or NAD, and is known as the GFO/IDH/MOCA family in UniProtKB/Swiss-Prot. GFO is a glucose--fructose oxidoreductase, which converts D-glucose and D-fructose into D-gluconolactone and D-glucitol in the sorbitol-gluconate pathway. MOCA is a rhizopine catabolism protein which may catalyse the NADH-dependent dehydrogenase reaction involved in rhizopine catabolism. Other proteins belonging to this family include Gal80, a negative regulator for the expression of lactose and galactose metabolic genes; and several hypothetical proteins from yeast, Escherichia coli and Bacillus subtilis. The oxidoreductase, N-terminal domain is almost always associated with the oxidoreductase, C-terminal domain (see IPR004104 from INTERPRO).; GO: 0016491 oxidoreductase activity; PDB: 1LC0_A 1LC3_A 1GCU_A 3IP3_E 3CEA_C 3EVN_A 3NTQ_A 3NTR_B 3NT5_A 3MZ0_A ....
Probab=22.81 E-value=1.4e+02 Score=18.70 Aligned_cols=51 Identities=24% Similarity=0.393 Sum_probs=36.2
Q ss_pred hhhhhCCChHHHHHHHHHHHHcCCccEEee---------------CCCceEEE------cHHHHHHHHHHHHhhc
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTGALTGVID---------------DRGKFIYI------SQEELNSVATFIKQRG 57 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g~ltGViD---------------DRGKfIyI------s~eEl~~Va~fI~~rg 57 (96)
.+..|+.+ +..-+.+|.+...+..|+- ++||.|++ |.+|...+.+..++.|
T Consensus 42 ~~~~~~~~---~~~~~~~ll~~~~~D~V~I~tp~~~h~~~~~~~l~~g~~v~~EKP~~~~~~~~~~l~~~a~~~~ 113 (120)
T PF01408_consen 42 FAEKYGIP---VYTDLEELLADEDVDAVIIATPPSSHAEIAKKALEAGKHVLVEKPLALTLEEAEELVEAAKEKG 113 (120)
T ss_dssp HHHHTTSE---EESSHHHHHHHTTESEEEEESSGGGHHHHHHHHHHTTSEEEEESSSSSSHHHHHHHHHHHHHHT
T ss_pred HHHHhccc---chhHHHHHHHhhcCCEEEEecCCcchHHHHHHHHHcCCEEEEEcCCcCCHHHHHHHHHHHHHhC
Confidence 34555655 4444677777667777765 28888886 7888988888888883
No 492
>PRK08006 replicative DNA helicase; Provisional
Probab=22.80 E-value=1.3e+02 Score=25.34 Aligned_cols=69 Identities=12% Similarity=0.241 Sum_probs=45.9
Q ss_pred CChHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhcccce
Q psy11008 10 MKTQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQLV 87 (96)
Q Consensus 10 lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~lI 87 (96)
|+.+++++|+-.-+..=....+- .|+ ++++|+..+...+... ++..--||-..+.+++.++...|.++.
T Consensus 263 M~~~ql~~Rlla~~~~v~~~~i~--~~~---l~~~e~~~~~~a~~~~----~~~~~l~I~d~~~~t~~~i~~~~r~~~ 331 (471)
T PRK08006 263 MPGEQIMMRMLASLSRVDQTRIR--TGQ---LDDEDWARISGTMGIL----LEKRNMYIDDSSGLTPTEVRSRARRIF 331 (471)
T ss_pred CCHHHHHHHHHHHhcCCCHHHhh--cCC---CCHHHHHHHHHHHHHH----HhcCCEEEECCCCCCHHHHHHHHHHHH
Confidence 78889999987665443333332 343 7899998888766433 011224777888889988888886654
No 493
>KOG1498|consensus
Probab=22.72 E-value=3e+02 Score=24.33 Aligned_cols=53 Identities=25% Similarity=0.327 Sum_probs=40.8
Q ss_pred hhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCceEEEc-----HHHHHHHHHHHH
Q psy11008 2 EDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGKFIYIS-----QEELNSVATFIK 54 (96)
Q Consensus 2 edLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGKfIyIs-----~eEl~~Va~fI~ 54 (96)
..+|+..+++++++..-|-.|-.+|.++--||---.-|+.. .++++.-|.=+.
T Consensus 357 ~rl~eLLdl~~ee~E~~LS~lv~t~ti~aKidrpsgII~F~k~K~~~~~LneW~~nve 414 (439)
T KOG1498|consen 357 KRLAELLDLPVEEMEKFLSDLVVTGTIYAKIDRPSGIINFQKVKDSNEILNEWASNVE 414 (439)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHhccceEEEecCCCceEEEEecccHHHHHHHHHhhHH
Confidence 46899999999999999999999999999998666666653 344554444433
No 494
>PF05979 DUF896: Bacterial protein of unknown function (DUF896); InterPro: IPR009242 This family consists of several short, hypothetical bacterial proteins of unknown function. They may be involved in the bacterial SOS response [].; PDB: 2HEP_A 3BHP_C 2JVD_A.
Probab=22.45 E-value=62 Score=21.31 Aligned_cols=19 Identities=42% Similarity=0.552 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHcCCccEE
Q psy11008 13 QSVIDRIVELQKTGALTGV 31 (96)
Q Consensus 13 q~vI~RI~eL~~~g~ltGV 31 (96)
++.|+||++|-+--.-.|+
T Consensus 1 Ke~i~RINeLa~K~K~~gL 19 (65)
T PF05979_consen 1 KEKIDRINELAKKSKEEGL 19 (65)
T ss_dssp -HHHHHHHHHHHHHHTT--
T ss_pred CcHHHHHHHHHHHhccCCC
Confidence 4789999999876555553
No 495
>COG3710 CadC DNA-binding winged-HTH domains [Transcription]
Probab=22.44 E-value=1.8e+02 Score=20.91 Aligned_cols=27 Identities=7% Similarity=0.201 Sum_probs=22.8
Q ss_pred EEeeCCCceEEEcHHHHHHHHHHHHhh
Q psy11008 30 GVIDDRGKFIYISQEELNSVATFIKQR 56 (96)
Q Consensus 30 GViDDRGKfIyIs~eEl~~Va~fI~~r 56 (96)
+.+...|+=|.+++-++..+--.+...
T Consensus 21 ~~L~r~~~~v~l~~~~~~lL~~L~e~~ 47 (148)
T COG3710 21 RSLLRGDEVVKLGPRELKLLSLLLERA 47 (148)
T ss_pred ceEEECCeEEEecHHHHHHHHHHHhcc
Confidence 445567799999999999999888877
No 496
>PRK09726 antitoxin HipB; Provisional
Probab=22.30 E-value=1.8e+02 Score=18.56 Aligned_cols=54 Identities=7% Similarity=0.181 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHcCCccEEeeCCCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccceeHHHHHHhccc
Q psy11008 12 TQSVIDRIVELQKTGALTGVIDDRGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRVSVSELVENSNQ 85 (96)
Q Consensus 12 tq~vI~RI~eL~~~g~ltGViDDRGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRVsi~eL~~~sN~ 85 (96)
.+.+-+||+.+.+.-. +|++|+...+..-.+ .|..+.+.+..+++..|...|+.
T Consensus 10 ~~~l~~~lk~~R~~~g-------------ltq~elA~~~gvs~~-------tis~~e~g~~~ps~~~l~~ia~~ 63 (88)
T PRK09726 10 PTQLANAMKLVRQQNG-------------WTQSELAKKIGIKQA-------TISNFENNPDNTTLTTFFKILQS 63 (88)
T ss_pred HHHHHHHHHHHHHHcC-------------CCHHHHHHHHCcCHH-------HHHHHHCCCCCCCHHHHHHHHHH
Confidence 3455577777755432 577777665542222 24444444445677777766654
No 497
>PF11305 DUF3107: Protein of unknown function (DUF3107); InterPro: IPR021456 Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=22.26 E-value=1.8e+02 Score=19.54 Aligned_cols=39 Identities=13% Similarity=0.267 Sum_probs=29.7
Q ss_pred hhhhhCCChHHHHHHHHHHHHcC-CccEEeeCCCceEEEc
Q psy11008 4 LAALFRMKTQSVIDRIVELQKTG-ALTGVIDDRGKFIYIS 42 (96)
Q Consensus 4 LAa~F~lktq~vI~RI~eL~~~g-~ltGViDDRGKfIyIs 42 (96)
|.-+-..+.+++...|.+-.+.| .+--+-|++|+=+.|.
T Consensus 14 l~ies~~s~dev~~~v~~Al~~~~~~l~LtD~kGr~~lVp 53 (74)
T PF11305_consen 14 LVIESDQSADEVEAAVTDALADGSGVLTLTDEKGRRVLVP 53 (74)
T ss_pred EEEecCCCHHHHHHHHHHHHhCCCceEEEEeCCCCEEEEE
Confidence 44445667888999999988888 6666899999865553
No 498
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=22.23 E-value=1.7e+02 Score=19.38 Aligned_cols=34 Identities=18% Similarity=0.323 Sum_probs=24.5
Q ss_pred CCceEEEcHHHHHHHHHHHHhhchhchhhhhhhhccccce-eHHHHHHhc
Q psy11008 35 RGKFIYISQEELNSVATFIKQRGREELNSVATFIKQKGRV-SVSELVENS 83 (96)
Q Consensus 35 RGKfIyIs~eEl~~Va~fI~~rgr~~~~~~~~~~~~~GRV-si~eL~~~s 83 (96)
+|..+.+|+.|++=+.-+.+.. |++ |.+++++.-
T Consensus 144 ~~~~~~Lt~~E~~il~~l~~~~---------------~~~~s~~~i~~~l 178 (219)
T PRK10336 144 AGEPLTLKPKEFALLELLMRNA---------------GRVLPRKLIEEKL 178 (219)
T ss_pred CCEEEecCHHHHHHHHHHHhCC---------------CccCcHHHHHHHh
Confidence 4667789999998877777666 665 777776653
No 499
>TIGR01285 nifN nitrogenase molybdenum-iron cofactor biosynthesis protein NifN. This protein forms a complex with NifE, and appears as a NifEN in some species. NifEN is a required for producing the molybdenum-iron cofactor of molybdenum-requiring nitrogenases. NifN is closely related to the nitrogenase molybdenum-iron protein beta chain NifK. This model describes most examples of NifN but excludes some cases, such as the putative NifN of Chlorobium tepidum, for which a separate model may be created.
Probab=22.21 E-value=91 Score=25.72 Aligned_cols=59 Identities=19% Similarity=0.134 Sum_probs=35.5
Q ss_pred ChhhhhhhCCChHHHHHHHHHHHHcCCccEEeeCCCc--eEEEcHHHHHHHHHHHHhhchh
Q psy11008 1 MEDLAALFRMKTQSVIDRIVELQKTGALTGVIDDRGK--FIYISQEELNSVATFIKQRGRE 59 (96)
Q Consensus 1 ledLAa~F~lktq~vI~RI~eL~~~g~ltGViDDRGK--fIyIs~eEl~~Va~fI~~rgr~ 59 (96)
|.+||..||.+..+.++|-.....+....--..-.|| .||..+.-.-+++.|+..-|-+
T Consensus 276 l~~l~~~~g~~~~~~~~~~r~~~~~~l~~~~~~l~Gkrvai~~~~~~~~~l~~~l~elGm~ 336 (432)
T TIGR01285 276 LHVLMKISGRAVPERFERQRRQLQDAMLDTHFFLGGKKVAIAAEPDLLAAWATFFTSMGAQ 336 (432)
T ss_pred HHHHHHHHCCCccHHHHHHHHHHHHHHHHHHHhhCCCEEEEEcCHHHHHHHHHHHHHCCCE
Confidence 4678889998766665543322211000000011366 7788888889999999988743
No 500
>PHA02592 52 DNA topisomerase II medium subunit; Provisional
Probab=22.19 E-value=78 Score=27.03 Aligned_cols=26 Identities=12% Similarity=0.276 Sum_probs=24.2
Q ss_pred hCCChHHHHHHHHHHHHcCCccEEee
Q psy11008 8 FRMKTQSVIDRIVELQKTGALTGVID 33 (96)
Q Consensus 8 F~lktq~vI~RI~eL~~~g~ltGViD 33 (96)
+++.|++.++.|.+|.+.|.|+|+.|
T Consensus 237 ~~~~~~~~~~~i~~l~~~~~i~~i~d 262 (439)
T PHA02592 237 VKYDRETYVAVLDPLEEKGKIVSYDD 262 (439)
T ss_pred CcccHHHHHHHHHHHHhcCCcCCccc
Confidence 47889999999999999999999998
Done!