Query 018851
Match_columns 349
No_of_seqs 159 out of 1285
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 04:34:29 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018851.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018851hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2784 Phenylalanyl-tRNA synt 100.0 1E-107 3E-112 787.5 23.7 342 1-349 3-345 (483)
2 PLN02853 Probable phenylalanyl 100.0 1E-103 3E-108 795.6 36.1 349 1-349 3-354 (492)
3 PTZ00326 phenylalanyl-tRNA syn 100.0 2E-100 4E-105 774.7 35.3 347 2-349 7-369 (494)
4 PRK04172 pheS phenylalanyl-tRN 100.0 1.1E-84 2.4E-89 665.6 34.3 342 2-349 7-362 (489)
5 COG0016 PheS Phenylalanyl-tRNA 100.0 2.5E-47 5.5E-52 370.9 6.2 198 99-349 2-204 (335)
6 PF01409 tRNA-synt_2d: tRNA sy 100.0 6.2E-34 1.4E-38 268.8 8.7 114 200-349 1-114 (247)
7 PRK00488 pheS phenylalanyl-tRN 100.0 5.9E-33 1.3E-37 271.4 9.4 106 200-349 92-197 (339)
8 PLN02788 phenylalanine-tRNA sy 100.0 2.1E-32 4.6E-37 272.9 9.9 113 190-349 44-159 (402)
9 TIGR00468 pheS phenylalanyl-tR 99.9 5.9E-28 1.3E-32 233.3 7.1 132 175-349 31-162 (294)
10 TIGR00469 pheS_mito phenylalan 99.9 2.5E-27 5.5E-32 238.7 9.2 110 200-349 26-145 (460)
11 TIGR00470 sepS O-phosphoseryl- 99.6 6.4E-16 1.4E-20 156.1 7.0 146 199-349 30-219 (533)
12 COG2024 Phenylalanyl-tRNA synt 99.4 5.8E-14 1.3E-18 138.1 2.2 144 201-349 32-219 (536)
13 KOG2783 Phenylalanyl-tRNA synt 99.3 5E-12 1.1E-16 124.7 5.9 113 190-349 48-163 (436)
14 PRK06253 O-phosphoseryl-tRNA s 99.1 6.9E-11 1.5E-15 121.4 7.3 146 199-349 30-220 (529)
15 cd00496 PheRS_alpha_core Pheny 99.0 1.7E-09 3.6E-14 100.4 8.7 92 216-349 1-92 (218)
16 TIGR02367 PylS pyrrolysyl-tRNA 98.6 1.1E-07 2.3E-12 96.8 8.7 97 210-349 234-330 (453)
17 PRK09616 pheT phenylalanyl-tRN 98.6 3.5E-07 7.6E-12 95.9 11.0 160 139-348 289-449 (552)
18 PRK09537 pylS pyrolysyl-tRNA s 98.5 1.3E-07 2.8E-12 95.8 6.7 98 209-349 197-294 (417)
19 TIGR00442 hisS histidyl-tRNA s 97.8 3.6E-05 7.9E-10 77.0 7.2 100 209-349 8-109 (397)
20 PRK00037 hisS histidyl-tRNA sy 97.7 5.1E-05 1.1E-09 76.2 6.5 98 209-349 12-110 (412)
21 PF13601 HTH_34: Winged helix 97.6 0.00017 3.6E-09 57.3 6.7 65 3-68 2-71 (80)
22 PF14947 HTH_45: Winged helix- 97.6 0.00013 2.8E-09 57.3 6.0 61 3-68 8-68 (77)
23 TIGR02337 HpaR homoprotocatech 97.6 0.00022 4.7E-09 59.7 7.6 72 2-74 29-104 (118)
24 PF13463 HTH_27: Winged helix 97.6 0.00026 5.6E-09 53.0 6.7 60 2-62 4-68 (68)
25 PRK11512 DNA-binding transcrip 97.5 0.00066 1.4E-08 58.7 8.7 88 2-92 41-134 (144)
26 smart00347 HTH_MARR helix_turn 97.4 0.00056 1.2E-08 54.0 7.3 66 2-68 11-80 (101)
27 PRK03573 transcriptional regul 97.3 0.0012 2.7E-08 56.8 8.5 72 3-74 33-108 (144)
28 PF01978 TrmB: Sugar-specific 97.3 0.00047 1E-08 52.3 5.1 57 2-59 9-65 (68)
29 COG1846 MarR Transcriptional r 97.2 0.0017 3.7E-08 52.7 8.3 74 2-76 23-100 (126)
30 cd00768 class_II_aaRS-like_cor 97.1 0.001 2.2E-08 59.4 6.5 85 219-349 3-87 (211)
31 cd00773 HisRS-like_core Class 97.1 0.0018 3.9E-08 61.4 8.3 90 218-349 5-94 (261)
32 smart00550 Zalpha Z-DNA-bindin 97.0 0.0017 3.6E-08 49.9 5.4 59 2-60 7-66 (68)
33 PF03551 PadR: Transcriptional 97.0 0.0031 6.7E-08 48.8 6.9 42 27-68 28-75 (75)
34 PRK10870 transcriptional repre 97.0 0.0036 7.9E-08 56.4 8.3 72 3-74 57-133 (176)
35 TIGR01889 Staph_reg_Sar staphy 97.0 0.0029 6.4E-08 52.4 7.1 70 3-73 27-104 (109)
36 TIGR00471 pheT_arch phenylalan 96.9 0.0023 5E-08 67.4 7.0 95 211-348 357-451 (551)
37 PF13412 HTH_24: Winged helix- 96.8 0.0039 8.6E-08 44.0 5.6 45 2-47 4-48 (48)
38 TIGR03433 padR_acidobact trans 96.8 0.0042 9.1E-08 51.0 6.5 73 2-76 5-91 (100)
39 cd00090 HTH_ARSR Arsenical Res 96.8 0.0096 2.1E-07 43.8 8.0 63 2-67 8-71 (78)
40 PRK13777 transcriptional regul 96.8 0.0054 1.2E-07 56.2 7.8 73 3-76 47-123 (185)
41 PRK03902 manganese transport t 96.7 0.006 1.3E-07 52.8 7.4 60 6-68 13-72 (142)
42 PLN02265 probable phenylalanyl 96.6 0.0041 8.9E-08 66.2 6.8 96 211-347 392-487 (597)
43 PF07381 DUF1495: Winged helix 96.6 0.009 2E-07 48.7 6.9 65 3-67 11-88 (90)
44 TIGR02702 SufR_cyano iron-sulf 96.5 0.0085 1.8E-07 55.0 7.6 66 2-68 2-73 (203)
45 PRK12293 hisZ ATP phosphoribos 96.5 0.0095 2.1E-07 57.7 8.1 90 214-349 18-107 (281)
46 TIGR00443 hisZ_biosyn_reg ATP 96.5 0.008 1.7E-07 58.7 7.4 90 217-349 10-99 (314)
47 TIGR01884 cas_HTH CRISPR locus 96.5 0.0065 1.4E-07 55.8 6.3 59 3-62 145-203 (203)
48 PF10007 DUF2250: Uncharacteri 96.4 0.012 2.6E-07 48.2 7.1 67 1-68 7-91 (92)
49 PRK14165 winged helix-turn-hel 96.4 0.0084 1.8E-07 56.3 6.7 57 17-73 22-79 (217)
50 smart00418 HTH_ARSR helix_turn 96.4 0.017 3.7E-07 41.3 6.9 59 6-66 2-62 (66)
51 PF03501 S10_plectin: Plectin/ 96.3 0.007 1.5E-07 49.8 4.8 43 26-68 33-76 (95)
52 PTZ00034 40S ribosomal protein 96.3 0.0075 1.6E-07 51.7 5.1 50 26-75 36-88 (124)
53 PRK12420 histidyl-tRNA synthet 96.1 0.018 4E-07 58.5 8.2 93 214-349 17-111 (423)
54 COG1321 TroR Mn-dependent tran 96.1 0.014 3.1E-07 51.9 6.3 60 6-68 15-74 (154)
55 cd00670 Gly_His_Pro_Ser_Thr_tR 96.1 0.01 2.2E-07 54.6 5.5 95 218-349 5-100 (235)
56 PRK12292 hisZ ATP phosphoribos 96.1 0.015 3.3E-07 58.6 7.2 92 217-349 19-110 (391)
57 PRK12295 hisZ ATP phosphoribos 96.0 0.02 4.3E-07 57.7 7.7 88 218-349 7-94 (373)
58 PLN02530 histidine-tRNA ligase 96.0 0.019 4E-07 59.7 7.6 94 214-349 83-176 (487)
59 PF13393 tRNA-synt_His: Histid 96.0 0.017 3.6E-07 55.8 6.6 88 218-349 13-100 (311)
60 cd00769 PheRS_beta_core Phenyl 95.9 0.0096 2.1E-07 54.2 4.6 87 219-348 3-89 (198)
61 smart00529 HTH_DTXR Helix-turn 95.9 0.016 3.4E-07 46.3 4.9 50 20-71 3-52 (96)
62 PRK11050 manganese transport r 95.8 0.032 6.9E-07 49.2 7.2 70 5-77 41-110 (152)
63 COG4754 Uncharacterized conser 95.6 0.034 7.4E-07 49.1 6.3 67 6-76 17-85 (157)
64 CHL00201 syh histidine-tRNA sy 95.6 0.044 9.6E-07 56.0 8.1 95 215-349 18-114 (430)
65 PF01047 MarR: MarR family; I 95.6 0.024 5.3E-07 41.2 4.6 50 2-52 4-53 (59)
66 PF01638 HxlR: HxlR-like helix 95.5 0.05 1.1E-06 43.6 6.8 60 5-66 9-73 (90)
67 COG1497 Predicted transcriptio 95.5 0.048 1E-06 52.0 7.4 73 2-76 11-83 (260)
68 PF12802 MarR_2: MarR family; 95.5 0.04 8.6E-07 40.3 5.5 50 2-51 6-56 (62)
69 cd00771 ThrRS_core Threonyl-tR 95.5 0.044 9.5E-07 53.3 7.4 90 217-349 32-123 (298)
70 PRK09416 lstR lineage-specific 95.5 0.037 8.1E-07 48.4 6.1 65 2-69 44-118 (135)
71 COG1695 Predicted transcriptio 95.4 0.046 9.9E-07 46.9 6.5 67 2-70 10-90 (138)
72 PRK12421 ATP phosphoribosyltra 95.4 0.048 1E-06 55.2 7.7 95 213-349 19-113 (392)
73 COG2345 Predicted transcriptio 95.4 0.044 9.5E-07 51.5 6.8 64 2-66 12-81 (218)
74 PF03444 HrcA_DNA-bdg: Winged 95.4 0.029 6.2E-07 44.6 4.7 68 2-69 5-76 (78)
75 PF08220 HTH_DeoR: DeoR-like h 95.3 0.037 8E-07 40.9 4.9 46 3-49 2-47 (57)
76 TIGR02719 repress_PhaQ poly-be 95.3 0.079 1.7E-06 46.5 7.6 74 2-77 25-110 (138)
77 COG0124 HisS Histidyl-tRNA syn 95.1 0.032 7E-07 57.3 5.5 97 213-348 16-112 (429)
78 COG5045 Ribosomal protein S10E 95.0 0.046 1E-06 44.7 4.9 44 25-68 34-78 (105)
79 smart00346 HTH_ICLR helix_turn 94.9 0.1 2.2E-06 41.0 6.6 62 4-66 8-69 (91)
80 PRK05638 threonine synthase; V 94.9 0.064 1.4E-06 55.0 6.8 65 2-68 372-440 (442)
81 COG4742 Predicted transcriptio 94.8 0.078 1.7E-06 51.1 6.7 74 4-82 16-89 (260)
82 PHA02943 hypothetical protein; 94.7 0.15 3.2E-06 45.6 7.7 59 4-66 14-73 (165)
83 PF09339 HTH_IclR: IclR helix- 94.7 0.037 8E-07 39.9 3.3 45 4-48 6-50 (52)
84 PRK12294 hisZ ATP phosphoribos 94.7 0.088 1.9E-06 51.0 6.9 88 217-349 9-96 (272)
85 PF12840 HTH_20: Helix-turn-he 94.6 0.1 2.2E-06 38.7 5.7 48 3-51 12-59 (61)
86 CHL00192 syfB phenylalanyl-tRN 94.6 0.062 1.3E-06 58.5 6.2 88 211-347 393-480 (704)
87 PF08279 HTH_11: HTH domain; 94.5 0.12 2.6E-06 37.2 5.7 42 3-44 2-43 (55)
88 cd00779 ProRS_core_prok Prolyl 94.5 0.028 6.1E-07 53.4 3.0 92 217-349 33-125 (255)
89 PF08461 HTH_12: Ribonuclease 94.4 0.07 1.5E-06 40.8 4.5 60 5-66 2-66 (66)
90 cd00772 ProRS_core Prolyl-tRNA 94.4 0.11 2.4E-06 49.8 6.8 97 216-349 33-131 (264)
91 COG2512 Predicted membrane-ass 94.3 0.073 1.6E-06 51.3 5.4 60 2-61 196-256 (258)
92 COG0072 PheT Phenylalanyl-tRNA 94.3 0.071 1.5E-06 57.5 5.7 91 215-348 350-440 (650)
93 COG3355 Predicted transcriptio 94.2 0.12 2.6E-06 44.7 5.8 50 2-52 28-78 (126)
94 PRK09350 poxB regulator PoxA; 94.1 0.084 1.8E-06 51.7 5.5 36 219-256 9-44 (306)
95 PLN02972 Histidyl-tRNA synthet 94.1 0.14 3E-06 56.2 7.5 89 215-349 341-429 (763)
96 smart00420 HTH_DEOR helix_turn 94.1 0.21 4.5E-06 34.7 6.0 46 3-49 2-47 (53)
97 PF01726 LexA_DNA_bind: LexA D 94.0 0.11 2.3E-06 39.8 4.8 48 3-50 8-60 (65)
98 PF02295 z-alpha: Adenosine de 94.0 0.041 8.9E-07 42.3 2.4 59 2-61 5-65 (66)
99 PF09012 FeoC: FeoC like trans 93.9 0.15 3.2E-06 39.0 5.4 47 4-51 3-49 (69)
100 PRK09194 prolyl-tRNA synthetas 93.9 0.1 2.2E-06 55.2 6.0 91 217-349 49-141 (565)
101 PRK12305 thrS threonyl-tRNA sy 93.8 0.07 1.5E-06 56.3 4.6 94 215-349 206-300 (575)
102 COG3432 Predicted transcriptio 93.7 0.1 2.2E-06 43.0 4.4 63 4-68 21-84 (95)
103 PF04458 DUF505: Protein of un 93.7 0.11 2.4E-06 55.0 5.7 109 2-113 433-575 (591)
104 smart00344 HTH_ASNC helix_turn 93.7 0.15 3.2E-06 41.6 5.3 45 2-47 4-48 (108)
105 COG1733 Predicted transcriptio 93.6 0.28 6E-06 41.9 7.1 60 5-66 27-91 (120)
106 PF01022 HTH_5: Bacterial regu 93.5 0.13 2.8E-06 36.3 4.1 43 3-47 4-46 (47)
107 PF05158 RNA_pol_Rpc34: RNA po 93.4 0.3 6.4E-06 48.6 7.9 115 2-116 10-134 (327)
108 PRK00629 pheT phenylalanyl-tRN 93.3 0.16 3.4E-06 56.0 6.5 94 211-348 482-575 (791)
109 PRK00413 thrS threonyl-tRNA sy 93.3 0.11 2.4E-06 55.4 5.1 93 216-349 271-364 (638)
110 PF01325 Fe_dep_repress: Iron 93.2 0.21 4.6E-06 37.4 5.1 44 6-50 13-56 (60)
111 PRK06266 transcription initiat 93.2 0.31 6.8E-06 44.3 7.1 58 4-62 25-89 (178)
112 PRK11179 DNA-binding transcrip 93.1 0.18 3.9E-06 44.2 5.3 46 2-48 10-55 (153)
113 COG1339 Transcriptional regula 93.0 0.27 5.9E-06 45.6 6.3 64 5-68 4-72 (214)
114 PRK09834 DNA-binding transcrip 92.8 0.31 6.6E-06 46.4 6.8 62 5-67 15-76 (263)
115 TIGR02716 C20_methyl_CrtF C-20 92.7 0.19 4E-06 48.6 5.3 66 3-73 12-77 (306)
116 PRK11169 leucine-responsive tr 92.6 0.24 5.1E-06 44.0 5.4 45 2-47 15-59 (164)
117 TIGR01610 phage_O_Nterm phage 92.5 0.36 7.7E-06 39.3 5.9 48 3-50 27-81 (95)
118 PHA00738 putative HTH transcri 92.4 0.6 1.3E-05 39.4 7.2 66 3-77 14-80 (108)
119 PF04703 FaeA: FaeA-like prote 92.4 0.15 3.2E-06 38.8 3.2 55 4-58 3-60 (62)
120 TIGR00472 pheT_bact phenylalan 92.3 0.25 5.4E-06 54.5 6.3 95 212-348 486-581 (798)
121 PRK10141 DNA-binding transcrip 92.3 0.71 1.5E-05 39.4 7.7 60 4-64 19-79 (117)
122 COG1522 Lrp Transcriptional re 92.3 0.27 5.8E-06 42.3 5.2 50 2-52 9-58 (154)
123 cd00092 HTH_CRP helix_turn_hel 92.2 0.64 1.4E-05 34.1 6.5 42 17-60 26-67 (67)
124 TIGR02698 CopY_TcrY copper tra 92.2 1.3 2.9E-05 38.1 9.3 88 2-91 5-108 (130)
125 TIGR00418 thrS threonyl-tRNA s 92.2 0.21 4.5E-06 52.6 5.2 93 216-349 201-294 (563)
126 PRK00215 LexA repressor; Valid 92.1 0.3 6.6E-06 44.5 5.5 63 2-64 5-72 (205)
127 KOG3344 40s ribosomal protein 92.0 0.09 2E-06 46.0 1.9 44 26-69 35-79 (150)
128 TIGR00409 proS_fam_II prolyl-t 91.8 0.34 7.4E-06 51.6 6.3 89 217-349 49-141 (568)
129 PF10771 DUF2582: Protein of u 91.8 0.21 4.7E-06 38.4 3.5 43 74-116 12-56 (65)
130 PF09821 AAA_assoc_C: C-termin 91.6 0.34 7.3E-06 41.5 5.0 53 21-76 2-54 (120)
131 TIGR02277 PaaX_trns_reg phenyl 91.6 0.23 4.9E-06 48.2 4.4 56 20-77 24-80 (280)
132 PF13730 HTH_36: Helix-turn-he 91.3 0.51 1.1E-05 33.8 5.0 44 3-46 7-55 (55)
133 PF00587 tRNA-synt_2b: tRNA sy 91.3 0.11 2.4E-06 46.0 1.8 89 219-349 3-95 (173)
134 TIGR02787 codY_Gpos GTP-sensin 91.2 0.4 8.6E-06 45.9 5.4 47 4-50 186-232 (251)
135 PF02082 Rrf2: Transcriptional 91.0 0.26 5.6E-06 38.8 3.5 59 5-63 12-72 (83)
136 PF07848 PaaX: PaaX-like prote 90.8 0.36 7.9E-06 37.5 4.0 43 20-62 27-70 (70)
137 PRK12325 prolyl-tRNA synthetas 90.7 0.39 8.4E-06 49.4 5.3 94 215-349 47-141 (439)
138 PF09202 Rio2_N: Rio2, N-termi 90.7 1 2.2E-05 36.1 6.6 66 2-67 7-75 (82)
139 COG1378 Predicted transcriptio 90.7 0.51 1.1E-05 45.1 5.8 56 3-59 18-73 (247)
140 smart00345 HTH_GNTR helix_turn 90.5 0.63 1.4E-05 33.1 4.9 33 18-50 22-54 (60)
141 cd00770 SerRS_core Seryl-tRNA 90.5 0.23 5E-06 48.4 3.3 86 219-349 56-143 (297)
142 TIGR00498 lexA SOS regulatory 90.3 0.46 1E-05 43.1 4.8 59 2-60 7-70 (199)
143 PF13404 HTH_AsnC-type: AsnC-t 90.1 0.83 1.8E-05 31.9 4.9 39 2-41 4-42 (42)
144 PF14338 Mrr_N: Mrr N-terminal 90.0 1.2 2.6E-05 35.8 6.6 65 3-69 6-91 (92)
145 cd07377 WHTH_GntR Winged helix 89.8 0.9 2E-05 32.9 5.3 41 17-59 26-66 (66)
146 PRK10163 DNA-binding transcrip 89.7 0.75 1.6E-05 44.0 6.1 58 4-62 28-85 (271)
147 TIGR02431 pcaR_pcaU beta-ketoa 89.7 0.76 1.6E-05 43.2 5.9 55 5-62 13-67 (248)
148 smart00419 HTH_CRP helix_turn_ 89.5 0.94 2E-05 31.0 4.9 40 17-59 9-48 (48)
149 PF10771 DUF2582: Protein of u 89.2 0.89 1.9E-05 35.0 4.9 51 5-56 12-62 (65)
150 PRK11569 transcriptional repre 89.2 0.81 1.8E-05 43.8 5.8 56 5-61 32-87 (274)
151 PRK15090 DNA-binding transcrip 89.1 0.81 1.8E-05 43.2 5.7 57 4-62 17-73 (257)
152 PF03965 Penicillinase_R: Peni 89.0 2.2 4.8E-05 35.5 7.7 88 2-91 4-107 (115)
153 TIGR00738 rrf2_super rrf2 fami 88.7 0.73 1.6E-05 38.8 4.6 60 5-64 12-73 (132)
154 COG4189 Predicted transcriptio 88.7 0.77 1.7E-05 44.0 5.1 48 4-52 26-73 (308)
155 TIGR00373 conserved hypothetic 88.5 1.1 2.3E-05 40.0 5.8 46 4-50 17-62 (158)
156 cd00778 ProRS_core_arch_euk Pr 88.5 0.37 8E-06 46.0 2.9 98 216-349 33-131 (261)
157 TIGR00637 ModE_repress ModE mo 88.4 1.5 3.3E-05 36.0 6.2 60 4-66 7-71 (99)
158 COG1349 GlpR Transcriptional r 88.3 0.71 1.5E-05 44.0 4.7 45 3-48 7-51 (253)
159 PF00126 HTH_1: Bacterial regu 88.3 0.48 1E-05 35.0 2.8 56 4-63 4-60 (60)
160 PRK08661 prolyl-tRNA synthetas 88.0 0.61 1.3E-05 48.5 4.4 96 217-349 46-143 (477)
161 PF00325 Crp: Bacterial regula 88.0 0.69 1.5E-05 30.7 3.1 29 18-46 4-32 (32)
162 PF14277 DUF4364: Domain of un 87.7 2 4.3E-05 38.7 7.0 61 6-66 5-71 (163)
163 cd07153 Fur_like Ferric uptake 87.7 2.6 5.7E-05 34.6 7.3 57 3-59 3-66 (116)
164 PRK09954 putative kinase; Prov 87.7 1.1 2.4E-05 44.2 5.9 52 2-59 4-55 (362)
165 PF04182 B-block_TFIIIC: B-blo 87.6 1.7 3.7E-05 33.8 5.7 51 1-51 2-53 (75)
166 PRK06474 hypothetical protein; 87.6 1.9 4.2E-05 39.0 6.9 63 3-65 13-82 (178)
167 PF09639 YjcQ: YjcQ protein; 87.5 0.6 1.3E-05 37.6 3.2 75 3-81 1-82 (88)
168 TIGR00122 birA_repr_reg BirA b 87.1 2.2 4.7E-05 32.2 6.0 52 4-59 3-54 (69)
169 PF06969 HemN_C: HemN C-termin 87.1 0.99 2.1E-05 33.6 4.0 54 6-63 11-65 (66)
170 PRK10434 srlR DNA-bindng trans 87.1 0.98 2.1E-05 43.1 4.9 47 3-50 7-53 (256)
171 PF02002 TFIIE_alpha: TFIIE al 87.1 0.81 1.8E-05 37.5 3.8 48 4-52 16-63 (105)
172 COG2524 Predicted transcriptio 87.0 0.74 1.6E-05 44.6 4.0 73 2-74 7-83 (294)
173 PF05584 Sulfolobus_pRN: Sulfo 87.0 1.8 4E-05 34.0 5.5 45 3-49 7-51 (72)
174 PF13814 Replic_Relax: Replica 86.9 1.4 3.1E-05 39.1 5.7 61 7-68 1-72 (191)
175 PRK13509 transcriptional repre 86.9 1.3 2.7E-05 42.2 5.5 45 3-48 7-51 (251)
176 COG3373 Uncharacterized protei 86.4 2.8 6E-05 34.5 6.4 64 3-66 19-94 (108)
177 PRK10906 DNA-binding transcrip 86.4 1.2 2.5E-05 42.6 5.0 45 3-48 7-51 (252)
178 TIGR00414 serS seryl-tRNA synt 86.3 0.83 1.8E-05 46.8 4.2 86 218-349 176-264 (418)
179 cd00774 GlyRS-like_core Glycyl 86.2 1 2.2E-05 42.8 4.6 30 216-246 33-64 (254)
180 PRK12444 threonyl-tRNA synthet 86.2 1.1 2.3E-05 48.2 5.2 91 217-349 276-367 (639)
181 PF14502 HTH_41: Helix-turn-he 86.2 1.5 3.2E-05 31.9 4.2 38 14-51 4-41 (48)
182 PRK00135 scpB segregation and 86.0 16 0.00034 33.7 12.0 103 12-115 15-134 (188)
183 PRK03601 transcriptional regul 85.4 2 4.3E-05 40.4 6.0 61 4-68 6-67 (275)
184 PF08784 RPA_C: Replication pr 85.2 1.5 3.3E-05 35.7 4.5 47 2-48 48-97 (102)
185 COG1725 Predicted transcriptio 85.1 3.5 7.6E-05 35.7 6.8 50 13-64 32-81 (125)
186 COG1414 IclR Transcriptional r 84.7 2 4.3E-05 40.8 5.7 60 4-64 7-66 (246)
187 PRK11242 DNA-binding transcrip 84.7 2 4.3E-05 40.2 5.7 62 4-68 6-67 (296)
188 PRK14799 thrS threonyl-tRNA sy 84.2 1.8 3.8E-05 46.1 5.6 90 218-349 171-261 (545)
189 TIGR00408 proS_fam_I prolyl-tR 84.0 0.91 2E-05 47.2 3.3 96 218-349 41-137 (472)
190 COG4190 Predicted transcriptio 83.9 2.5 5.3E-05 37.1 5.3 46 4-50 67-112 (144)
191 TIGR02944 suf_reg_Xantho FeS a 83.9 1.6 3.4E-05 37.0 4.2 46 5-50 13-59 (130)
192 PF13545 HTH_Crp_2: Crp-like h 83.7 2.2 4.9E-05 32.2 4.6 35 17-51 29-63 (76)
193 COG4565 CitB Response regulato 83.6 2.4 5.1E-05 40.1 5.5 48 4-51 161-208 (224)
194 PRK05431 seryl-tRNA synthetase 83.5 1.6 3.5E-05 44.8 4.8 88 218-349 173-262 (425)
195 TIGR00635 ruvB Holliday juncti 83.5 1.3 2.9E-05 42.3 4.0 63 3-68 240-305 (305)
196 PRK04424 fatty acid biosynthes 83.4 1.4 3E-05 40.2 3.9 45 3-48 9-53 (185)
197 PRK11014 transcriptional repre 83.1 2.8 6.2E-05 36.1 5.5 47 14-60 23-69 (141)
198 PF00392 GntR: Bacterial regul 83.0 2.1 4.5E-05 31.9 4.1 35 18-52 26-60 (64)
199 PRK09802 DNA-binding transcrip 82.1 2.3 5.1E-05 40.8 5.1 44 3-47 19-62 (269)
200 PF11313 DUF3116: Protein of u 82.1 4.7 0.0001 32.7 6.0 41 27-67 38-79 (85)
201 PF09756 DDRGK: DDRGK domain; 81.9 1.5 3.3E-05 40.4 3.5 79 5-93 103-182 (188)
202 PHA02701 ORF020 dsRNA-binding 81.7 2.4 5.3E-05 38.9 4.7 61 2-62 5-65 (183)
203 PF01978 TrmB: Sugar-specific 81.6 0.88 1.9E-05 34.2 1.6 47 71-117 9-57 (68)
204 PRK10837 putative DNA-binding 80.9 3.5 7.5E-05 38.5 5.7 61 4-68 8-69 (290)
205 COG1959 Predicted transcriptio 80.8 3.1 6.8E-05 36.7 5.0 61 5-65 12-74 (150)
206 PRK10094 DNA-binding transcrip 80.7 4.3 9.3E-05 38.9 6.4 62 4-68 7-68 (308)
207 TIGR03339 phn_lysR aminoethylp 80.6 2.5 5.5E-05 38.9 4.6 60 5-68 3-63 (279)
208 TIGR02036 dsdC D-serine deamin 80.3 3.9 8.5E-05 38.9 6.0 60 5-68 14-74 (302)
209 PRK09791 putative DNA-binding 80.2 3.7 7.9E-05 38.9 5.7 61 5-69 11-72 (302)
210 PLN02678 seryl-tRNA synthetase 80.0 2.3 4.9E-05 44.2 4.4 91 218-349 177-267 (448)
211 PRK10341 DNA-binding transcrip 79.9 4.2 9E-05 38.9 6.0 60 5-68 13-73 (312)
212 PF13412 HTH_24: Winged helix- 79.9 2.8 6.1E-05 29.2 3.6 42 72-113 5-48 (48)
213 TIGR02424 TF_pcaQ pca operon t 79.8 3.4 7.4E-05 38.9 5.3 60 4-67 8-68 (300)
214 COG1568 Predicted methyltransf 79.7 4.1 9E-05 40.2 5.8 57 5-67 26-82 (354)
215 TIGR02010 IscR iron-sulfur clu 79.5 4.6 0.0001 34.6 5.6 57 5-61 12-70 (135)
216 PRK10411 DNA-binding transcrip 79.5 3.9 8.5E-05 38.6 5.6 45 3-48 6-50 (240)
217 PLN02908 threonyl-tRNA synthet 79.3 2.9 6.2E-05 45.6 5.1 92 216-349 322-414 (686)
218 PRK09986 DNA-binding transcrip 79.2 3.4 7.3E-05 38.7 5.0 62 4-68 12-73 (294)
219 PRK15421 DNA-binding transcrip 79.1 4.7 0.0001 38.9 6.1 60 5-68 8-68 (317)
220 TIGR03338 phnR_burk phosphonat 78.9 3.4 7.4E-05 37.4 4.8 39 17-55 35-73 (212)
221 PRK11062 nhaR transcriptional 78.9 4.8 0.0001 38.2 6.0 60 5-68 10-70 (296)
222 PRK12679 cbl transcriptional r 78.9 4.5 9.8E-05 38.8 5.9 63 4-68 6-69 (316)
223 PRK10079 phosphonate metabolis 78.6 4.7 0.0001 37.6 5.8 52 5-56 24-75 (241)
224 PTZ00417 lysine-tRNA ligase; P 78.3 4.3 9.4E-05 43.5 6.0 27 219-246 257-283 (585)
225 PRK14997 LysR family transcrip 78.2 5.3 0.00012 37.7 6.1 61 4-68 7-68 (301)
226 PRK00082 hrcA heat-inducible t 77.9 3 6.6E-05 41.6 4.5 64 3-68 8-78 (339)
227 PRK09906 DNA-binding transcrip 77.7 3.9 8.3E-05 38.5 5.0 61 5-68 7-67 (296)
228 PRK12682 transcriptional regul 77.3 4.9 0.00011 38.3 5.6 61 6-69 8-70 (309)
229 PRK10632 transcriptional regul 77.1 4.6 0.0001 38.6 5.4 63 4-69 7-69 (309)
230 PRK09863 putative frv operon r 77.1 11 0.00025 39.9 8.8 88 3-95 6-103 (584)
231 PRK13348 chromosome replicatio 77.0 4.4 9.5E-05 38.1 5.1 60 4-68 7-67 (294)
232 PRK06462 asparagine synthetase 76.7 6.6 0.00014 39.0 6.5 27 219-246 34-60 (335)
233 PRK11013 DNA-binding transcrip 76.7 4.9 0.00011 38.3 5.5 61 4-68 9-70 (309)
234 COG0583 LysR Transcriptional r 76.5 5.3 0.00012 36.7 5.5 60 5-68 7-67 (297)
235 PRK10082 cell density-dependen 76.3 5.1 0.00011 38.0 5.4 61 5-69 17-78 (303)
236 PRK05159 aspC aspartyl-tRNA sy 76.2 6.8 0.00015 40.3 6.6 24 219-243 140-163 (437)
237 TIGR03418 chol_sulf_TF putativ 76.1 3.3 7.2E-05 38.8 4.0 61 5-68 7-67 (291)
238 PRK11074 putative DNA-binding 75.9 5.7 0.00012 37.7 5.6 61 4-68 7-68 (300)
239 PRK10086 DNA-binding transcrip 75.8 5.2 0.00011 38.3 5.4 61 5-68 20-80 (311)
240 TIGR03298 argP transcriptional 75.7 4.4 9.5E-05 38.1 4.7 60 4-68 6-66 (292)
241 PF09382 RQC: RQC domain; Int 75.6 5.9 0.00013 32.0 4.9 43 27-69 53-97 (106)
242 PF04458 DUF505: Protein of un 75.5 3.9 8.6E-05 43.6 4.7 43 27-69 326-370 (591)
243 PRK11534 DNA-binding transcrip 75.5 5.4 0.00012 36.6 5.2 39 17-55 31-69 (224)
244 PRK11233 nitrogen assimilation 75.2 5.9 0.00013 37.7 5.5 63 5-71 7-70 (305)
245 PF05732 RepL: Firmicute plasm 75.1 5.3 0.00012 35.9 4.9 53 17-74 76-128 (165)
246 PF01475 FUR: Ferric uptake re 75.0 4.2 9.1E-05 33.8 3.9 57 4-60 11-74 (120)
247 COG0640 ArsR Predicted transcr 74.9 15 0.00033 27.7 6.9 58 4-62 28-86 (110)
248 PRK15092 DNA-binding transcrip 74.9 6.3 0.00014 38.0 5.7 62 4-69 16-78 (310)
249 PF01047 MarR: MarR family; I 74.6 2.7 5.8E-05 30.3 2.3 44 71-114 4-49 (59)
250 PRK11151 DNA-binding transcrip 74.1 5.2 0.00011 37.9 4.8 61 4-68 6-67 (305)
251 PRK10402 DNA-binding transcrip 74.0 9.9 0.00021 34.9 6.5 34 18-51 171-204 (226)
252 PRK12683 transcriptional regul 73.9 6.2 0.00013 37.8 5.3 61 5-68 7-69 (309)
253 TIGR03697 NtcA_cyano global ni 73.8 6.2 0.00013 34.6 4.9 36 17-52 144-179 (193)
254 CHL00180 rbcR LysR transcripti 73.5 6.9 0.00015 37.2 5.5 62 4-69 10-72 (305)
255 PRK09801 transcriptional activ 73.4 6.3 0.00014 37.9 5.3 63 5-71 12-75 (310)
256 PRK10681 DNA-binding transcrip 73.4 6.9 0.00015 37.1 5.5 41 3-44 9-49 (252)
257 cd00669 Asp_Lys_Asn_RS_core As 73.4 8.7 0.00019 37.0 6.2 27 219-246 5-31 (269)
258 PRK04984 fatty acid metabolism 73.1 6.7 0.00015 36.2 5.2 39 18-56 33-71 (239)
259 PF13463 HTH_27: Winged helix 73.0 5.6 0.00012 29.2 3.8 45 71-115 4-51 (68)
260 cd00776 AsxRS_core Asx tRNA sy 72.9 8.3 0.00018 38.0 6.1 26 219-245 28-53 (322)
261 PRK11402 DNA-binding transcrip 72.8 7.4 0.00016 36.2 5.4 43 14-56 31-73 (241)
262 PF09114 MotA_activ: Transcrip 72.6 15 0.00033 30.1 6.4 59 6-68 21-81 (96)
263 PRK11886 bifunctional biotin-- 72.6 9.5 0.0002 37.3 6.4 56 3-60 6-61 (319)
264 PRK03635 chromosome replicatio 72.5 6.9 0.00015 37.0 5.3 59 5-68 8-67 (294)
265 PRK10225 DNA-binding transcrip 72.5 8.4 0.00018 36.1 5.8 39 18-56 35-73 (257)
266 cd00777 AspRS_core Asp tRNA sy 72.4 11 0.00023 36.7 6.6 25 219-244 5-29 (280)
267 PRK12423 LexA repressor; Provi 72.0 11 0.00023 34.6 6.2 56 3-58 8-68 (202)
268 PRK11139 DNA-binding transcrip 71.9 7.8 0.00017 36.5 5.5 61 5-69 12-73 (297)
269 PRK15243 transcriptional regul 71.9 8.4 0.00018 37.4 5.8 61 4-68 9-70 (297)
270 PF09669 Phage_pRha: Phage reg 71.3 7.1 0.00015 31.4 4.3 54 17-70 2-70 (93)
271 PRK11920 rirA iron-responsive 71.1 9.4 0.0002 33.7 5.4 60 5-64 12-72 (153)
272 PRK03837 transcriptional regul 70.9 8.8 0.00019 35.4 5.5 39 18-56 39-77 (241)
273 TIGR02404 trehalos_R_Bsub treh 70.5 9.6 0.00021 35.2 5.6 44 13-56 21-64 (233)
274 PF10711 DUF2513: Hypothetical 70.5 8.4 0.00018 31.6 4.7 65 4-68 8-79 (102)
275 PRK11523 DNA-binding transcrip 70.0 8.4 0.00018 36.1 5.2 39 18-56 34-72 (253)
276 TIGR02018 his_ut_repres histid 70.0 10 0.00022 35.0 5.6 42 15-56 24-65 (230)
277 TIGR00462 genX lysyl-tRNA synt 69.6 13 0.00029 36.4 6.6 27 219-246 5-31 (304)
278 PRK11512 DNA-binding transcrip 69.5 20 0.00043 30.7 7.0 46 70-115 40-87 (144)
279 PRK05472 redox-sensing transcr 68.8 6.8 0.00015 36.0 4.2 43 3-45 18-61 (213)
280 PRK08898 coproporphyrinogen II 68.8 17 0.00038 36.7 7.5 58 6-67 329-386 (394)
281 PRK11414 colanic acid/biofilm 68.7 6.8 0.00015 35.9 4.2 36 17-52 35-70 (221)
282 PF03965 Penicillinase_R: Peni 68.6 15 0.00032 30.5 5.9 47 70-116 3-55 (115)
283 PRK05660 HemN family oxidoredu 68.5 15 0.00031 37.0 6.8 57 7-67 313-369 (378)
284 TIGR02325 C_P_lyase_phnF phosp 68.5 11 0.00023 34.7 5.5 42 15-56 31-72 (238)
285 PRK14999 histidine utilization 68.4 11 0.00023 35.2 5.5 42 15-56 35-76 (241)
286 COG1654 BirA Biotin operon rep 68.1 13 0.00027 29.7 5.0 46 13-59 16-61 (79)
287 PRK10421 DNA-binding transcrip 68.1 11 0.00025 35.2 5.6 39 18-56 28-66 (253)
288 PRK09391 fixK transcriptional 67.9 12 0.00027 34.4 5.8 33 18-50 181-213 (230)
289 COG1675 TFA1 Transcription ini 67.9 13 0.00027 34.1 5.6 47 4-51 21-67 (176)
290 TIGR01889 Staph_reg_Sar staphy 67.8 18 0.00039 29.6 6.1 46 70-115 25-76 (109)
291 TIGR02681 phage_pRha phage reg 67.7 5.8 0.00012 33.3 3.1 55 16-70 13-81 (108)
292 PRK09764 DNA-binding transcrip 67.6 11 0.00024 35.1 5.4 43 14-56 27-69 (240)
293 PRK09508 leuO leucine transcri 67.5 8.8 0.00019 36.7 4.8 60 5-68 28-88 (314)
294 PRK10676 DNA-binding transcrip 67.1 16 0.00035 35.1 6.5 60 4-66 22-86 (263)
295 TIGR02812 fadR_gamma fatty aci 67.0 9.7 0.00021 35.1 4.9 38 18-55 32-69 (235)
296 PRK12445 lysyl-tRNA synthetase 66.9 15 0.00033 38.7 6.8 25 219-244 188-212 (505)
297 PRK10736 hypothetical protein; 66.8 9.4 0.0002 38.9 5.0 48 3-52 310-357 (374)
298 PRK00476 aspS aspartyl-tRNA sy 66.6 14 0.00031 39.7 6.6 25 219-244 145-169 (588)
299 PRK05799 coproporphyrinogen II 66.6 21 0.00046 35.5 7.5 58 6-67 308-366 (374)
300 TIGR02698 CopY_TcrY copper tra 66.4 39 0.00084 29.0 8.1 44 72-115 6-55 (130)
301 PRK13918 CRP/FNR family transc 66.3 9.4 0.0002 33.8 4.5 35 17-51 150-184 (202)
302 PF08222 HTH_CodY: CodY helix- 66.0 24 0.00052 26.7 5.7 34 18-51 6-39 (61)
303 PRK08208 coproporphyrinogen II 65.8 18 0.0004 37.0 7.0 57 6-66 352-408 (430)
304 PRK10857 DNA-binding transcrip 65.7 11 0.00023 33.9 4.6 50 13-62 22-71 (164)
305 TIGR02647 DNA conserved hypoth 65.6 5.2 0.00011 31.8 2.3 34 31-68 34-67 (77)
306 PRK09990 DNA-binding transcrip 65.5 13 0.00028 34.7 5.4 39 18-56 33-71 (251)
307 PRK03932 asnC asparaginyl-tRNA 65.5 16 0.00034 37.9 6.5 27 219-246 137-163 (450)
308 PRK12680 transcriptional regul 65.4 10 0.00022 36.9 4.9 63 4-70 6-71 (327)
309 PRK13347 coproporphyrinogen II 65.4 20 0.00044 36.9 7.3 59 5-67 371-432 (453)
310 smart00531 TFIIE Transcription 65.4 8.9 0.00019 33.6 4.0 44 5-49 5-48 (147)
311 PF14090 HTH_39: Helix-turn-he 65.3 30 0.00066 26.3 6.5 46 3-51 3-48 (70)
312 PRK09464 pdhR transcriptional 65.3 13 0.00029 34.6 5.5 38 18-55 36-73 (254)
313 smart00550 Zalpha Z-DNA-bindin 65.2 12 0.00026 28.5 4.2 47 70-116 6-56 (68)
314 PF12802 MarR_2: MarR family; 65.0 6.9 0.00015 28.2 2.8 45 71-115 6-54 (62)
315 COG1510 Predicted transcriptio 64.4 6.8 0.00015 35.8 3.2 74 6-80 31-107 (177)
316 COG1542 Uncharacterized conser 64.3 4.9 0.00011 42.0 2.5 45 24-69 317-363 (593)
317 COG2188 PhnF Transcriptional r 64.0 24 0.00052 33.0 6.9 44 13-56 28-71 (236)
318 PF14394 DUF4423: Domain of un 63.7 14 0.0003 33.3 5.0 57 6-64 29-87 (171)
319 PRK10046 dpiA two-component re 63.3 22 0.00047 32.3 6.4 47 4-50 165-211 (225)
320 KOG3054 Uncharacterized conser 62.6 26 0.00055 33.9 6.7 77 7-93 206-283 (299)
321 COG2186 FadR Transcriptional r 62.4 11 0.00023 35.7 4.2 41 16-56 34-74 (241)
322 TIGR00458 aspS_arch aspartyl-t 62.4 19 0.0004 37.1 6.3 24 219-243 137-160 (428)
323 PRK12684 transcriptional regul 62.0 16 0.00034 35.1 5.4 61 5-67 7-68 (313)
324 PHA03103 double-strand RNA-bin 61.9 15 0.00033 33.8 5.0 53 3-56 15-67 (183)
325 COG2269 Truncated, possibly in 61.6 7.7 0.00017 38.3 3.1 31 219-251 20-50 (322)
326 PLN02603 asparaginyl-tRNA synt 61.5 15 0.00033 39.4 5.6 26 220-246 231-256 (565)
327 PF01710 HTH_Tnp_IS630: Transp 61.2 34 0.00073 28.7 6.7 96 2-116 7-102 (119)
328 PRK08599 coproporphyrinogen II 60.7 29 0.00063 34.6 7.3 58 6-67 309-367 (377)
329 COG0735 Fur Fe2+/Zn2+ uptake r 60.7 33 0.00071 30.0 6.7 59 4-62 24-89 (145)
330 PF07106 TBPIP: Tat binding pr 60.6 29 0.00063 30.8 6.5 63 2-64 2-67 (169)
331 PRK06582 coproporphyrinogen II 60.3 27 0.00059 35.4 7.0 57 6-67 324-382 (390)
332 PRK11482 putative DNA-binding 60.2 15 0.00032 35.5 4.9 61 5-69 35-96 (317)
333 PF06971 Put_DNA-bind_N: Putat 60.2 16 0.00034 26.7 3.8 34 4-37 15-49 (50)
334 PRK12681 cysB transcriptional 60.1 16 0.00035 35.3 5.2 60 5-67 7-68 (324)
335 PLN02502 lysyl-tRNA synthetase 59.8 21 0.00045 38.2 6.3 25 220-245 234-258 (553)
336 COG3682 Predicted transcriptio 59.2 21 0.00046 30.8 5.1 48 68-115 4-57 (123)
337 PF05491 RuvB_C: Holliday junc 59.1 37 0.00081 27.0 6.1 63 2-67 9-74 (76)
338 PRK10216 DNA-binding transcrip 58.9 17 0.00037 34.8 5.1 58 4-65 13-71 (319)
339 PRK11161 fumarate/nitrate redu 58.8 16 0.00034 33.3 4.7 36 17-52 185-220 (235)
340 COG4738 Predicted transcriptio 58.6 21 0.00045 30.6 4.8 43 72-114 29-73 (124)
341 PF08280 HTH_Mga: M protein tr 57.8 19 0.00042 26.5 4.1 39 3-42 7-45 (59)
342 PRK00080 ruvB Holliday junctio 57.6 8.3 0.00018 37.7 2.7 63 3-68 261-326 (328)
343 PF13182 DUF4007: Protein of u 57.6 17 0.00036 35.5 4.8 61 4-66 16-76 (286)
344 PRK09462 fur ferric uptake reg 57.3 26 0.00057 30.3 5.5 56 4-59 20-83 (148)
345 PRK11639 zinc uptake transcrip 55.3 23 0.0005 31.7 4.9 47 4-50 29-80 (169)
346 PF08221 HTH_9: RNA polymerase 55.3 29 0.00063 26.0 4.8 46 4-50 16-61 (62)
347 PRK09249 coproporphyrinogen II 55.3 36 0.00079 35.0 7.0 59 6-68 371-433 (453)
348 TIGR00457 asnS asparaginyl-tRN 55.3 22 0.00048 36.9 5.5 25 219-244 140-164 (453)
349 smart00420 HTH_DEOR helix_turn 55.1 20 0.00044 24.4 3.7 45 73-117 3-49 (53)
350 smart00347 HTH_MARR helix_turn 54.4 21 0.00045 27.5 4.0 45 71-115 11-57 (101)
351 PTZ00401 aspartyl-tRNA synthet 54.1 34 0.00073 36.6 6.7 23 220-243 218-240 (550)
352 PF13384 HTH_23: Homeodomain-l 53.9 19 0.00041 25.0 3.3 38 5-45 9-46 (50)
353 KOG1936 Histidyl-tRNA syntheta 52.7 14 0.00029 38.5 3.3 85 219-349 78-162 (518)
354 PRK09333 30S ribosomal protein 52.7 25 0.00053 31.5 4.6 60 5-68 57-130 (150)
355 TIGR00459 aspS_bact aspartyl-t 52.6 41 0.00089 36.2 7.1 24 220-244 143-166 (583)
356 PF01325 Fe_dep_repress: Iron 52.4 29 0.00062 25.8 4.3 52 58-115 2-55 (60)
357 COG3327 PaaX Phenylacetic acid 52.4 15 0.00033 35.7 3.4 89 20-114 32-136 (291)
358 PLN02903 aminoacyl-tRNA ligase 52.3 37 0.00079 37.1 6.7 24 219-243 207-231 (652)
359 TIGR02337 HpaR homoprotocatech 52.1 22 0.00047 29.3 4.0 47 69-115 27-75 (118)
360 COG0478 RIO-like serine/threon 52.0 34 0.00074 33.8 5.8 64 3-66 15-81 (304)
361 TIGR00538 hemN oxygen-independ 51.6 46 0.001 34.2 7.1 61 7-71 372-436 (455)
362 PF09681 Phage_rep_org_N: N-te 51.2 37 0.00081 29.0 5.3 44 16-61 53-96 (121)
363 COG2469 Uncharacterized conser 51.0 12 0.00027 36.5 2.6 63 2-68 217-279 (284)
364 PTZ00385 lysyl-tRNA synthetase 50.8 38 0.00082 37.1 6.5 24 219-243 237-260 (659)
365 COG1802 GntR Transcriptional r 50.7 17 0.00037 33.5 3.5 43 14-56 37-79 (230)
366 PRK15481 transcriptional regul 50.4 27 0.00059 35.1 5.2 43 14-56 27-69 (431)
367 KOG2165 Anaphase-promoting com 50.4 21 0.00045 39.1 4.4 64 3-67 604-669 (765)
368 PF04079 DUF387: Putative tran 50.2 61 0.0013 29.0 6.8 102 13-116 10-127 (159)
369 TIGR03337 phnR transcriptional 50.0 56 0.0012 29.8 6.8 42 15-56 24-65 (231)
370 TIGR00499 lysS_bact lysyl-tRNA 49.9 37 0.00081 35.7 6.2 26 219-245 176-201 (496)
371 PF13518 HTH_28: Helix-turn-he 49.8 41 0.00089 23.1 4.6 39 5-46 4-42 (52)
372 PRK09775 putative DNA-binding 49.5 42 0.00091 34.9 6.4 57 4-64 3-60 (442)
373 PRK12820 bifunctional aspartyl 49.5 35 0.00077 37.6 6.1 25 219-244 160-184 (706)
374 PRK04172 pheS phenylalanyl-tRN 48.6 44 0.00095 34.9 6.5 37 35-71 156-192 (489)
375 PF05158 RNA_pol_Rpc34: RNA po 48.2 37 0.00081 33.8 5.6 59 2-60 85-148 (327)
376 PLN02837 threonine-tRNA ligase 47.9 17 0.00037 39.2 3.4 25 218-243 250-274 (614)
377 TIGR00331 hrcA heat shock gene 47.7 30 0.00065 34.5 4.9 63 3-67 4-73 (337)
378 PRK13777 transcriptional regul 47.3 66 0.0014 29.4 6.7 46 70-115 45-92 (185)
379 COG1777 Predicted transcriptio 47.2 18 0.00039 34.1 3.0 43 4-48 18-60 (217)
380 COG3888 Predicted transcriptio 46.9 57 0.0012 32.0 6.4 51 3-53 6-57 (321)
381 PRK11716 DNA-binding transcrip 46.5 22 0.00048 32.3 3.5 42 26-68 1-43 (269)
382 PF13936 HTH_38: Helix-turn-he 45.9 36 0.00078 23.6 3.7 34 3-38 9-42 (44)
383 PLN02850 aspartate-tRNA ligase 45.7 53 0.0011 35.0 6.5 23 220-243 230-252 (530)
384 COG3705 HisZ ATP phosphoribosy 45.6 44 0.00095 34.3 5.7 88 218-349 20-107 (390)
385 PF00196 GerE: Bacterial regul 45.1 28 0.00061 25.1 3.2 39 2-43 7-45 (58)
386 PF12324 HTH_15: Helix-turn-he 44.8 47 0.001 26.5 4.6 38 4-42 27-64 (77)
387 PF06163 DUF977: Bacterial pro 44.3 55 0.0012 28.5 5.3 47 2-49 13-59 (127)
388 PF04492 Phage_rep_O: Bacterio 44.2 29 0.00063 28.7 3.5 34 17-50 55-88 (100)
389 COG3398 Uncharacterized protei 43.8 1.3E+02 0.0028 28.9 8.0 111 4-115 104-221 (240)
390 PF07927 YcfA: YcfA-like prote 43.8 14 0.0003 26.5 1.4 21 223-243 2-23 (56)
391 COG4465 CodY Pleiotropic trans 43.2 29 0.00064 33.0 3.7 46 6-51 194-239 (261)
392 PRK09334 30S ribosomal protein 42.8 71 0.0015 26.0 5.4 43 6-49 32-74 (86)
393 TIGR00281 segregation and cond 42.5 2.7E+02 0.006 25.5 13.1 104 12-116 12-132 (186)
394 PF03297 Ribosomal_S25: S25 ri 42.4 36 0.00077 28.6 3.8 43 6-49 50-92 (105)
395 cd04897 ACT_ACR_3 ACT domain-c 42.3 51 0.0011 25.9 4.4 54 221-290 14-67 (75)
396 PRK09057 coproporphyrinogen II 42.2 64 0.0014 32.4 6.3 57 6-67 316-372 (380)
397 COG5340 Predicted transcriptio 41.8 32 0.00069 33.0 3.7 75 4-79 17-92 (269)
398 KOG3233 RNA polymerase III, su 41.2 42 0.00092 33.0 4.6 91 3-93 13-109 (297)
399 PRK04158 transcriptional repre 41.1 18 0.00039 35.0 2.0 47 5-51 190-236 (256)
400 PRK03573 transcriptional regul 40.8 1.1E+02 0.0025 25.8 6.9 46 70-115 31-79 (144)
401 cd04895 ACT_ACR_1 ACT domain-c 40.6 65 0.0014 25.1 4.8 54 221-290 14-67 (72)
402 smart00344 HTH_ASNC helix_turn 40.5 37 0.00081 27.2 3.6 42 72-113 5-48 (108)
403 PRK04214 rbn ribonuclease BN/u 40.3 59 0.0013 33.1 5.8 42 6-47 297-341 (412)
404 COG3355 Predicted transcriptio 40.1 39 0.00085 29.3 3.8 43 72-114 29-74 (126)
405 TIGR01714 phage_rep_org_N phag 40.1 79 0.0017 27.1 5.6 43 16-60 51-93 (119)
406 PF11994 DUF3489: Protein of u 39.8 1.3E+02 0.0028 23.7 6.2 47 4-51 13-61 (72)
407 PF13542 HTH_Tnp_ISL3: Helix-t 39.5 80 0.0017 21.9 4.8 35 2-39 16-50 (52)
408 PRK08629 coproporphyrinogen II 38.9 1E+02 0.0023 31.7 7.4 58 5-67 349-407 (433)
409 TIGR02844 spore_III_D sporulat 38.2 64 0.0014 25.7 4.5 32 4-37 9-40 (80)
410 COG2996 Predicted RNA-bindinin 37.8 65 0.0014 31.6 5.3 62 55-118 212-282 (287)
411 PRK07379 coproporphyrinogen II 37.8 85 0.0018 31.8 6.4 49 17-68 336-387 (400)
412 COG5631 Predicted transcriptio 37.5 74 0.0016 29.1 5.2 92 2-93 84-181 (199)
413 TIGR00415 serS_MJ seryl-tRNA s 36.5 59 0.0013 34.6 5.1 108 228-349 237-348 (520)
414 COG0172 SerS Seryl-tRNA synthe 35.6 71 0.0015 33.2 5.5 85 220-349 179-265 (429)
415 PRK10870 transcriptional repre 35.4 1.7E+02 0.0036 26.2 7.3 45 71-115 56-104 (176)
416 PF02387 IncFII_repA: IncFII R 35.0 1.1E+02 0.0024 30.0 6.4 61 17-79 96-174 (281)
417 COG0173 AspS Aspartyl-tRNA syn 34.9 1.1E+02 0.0023 33.1 6.7 25 219-244 145-169 (585)
418 COG3398 Uncharacterized protei 34.6 99 0.0021 29.6 5.8 58 3-61 176-234 (240)
419 PF09012 FeoC: FeoC like trans 34.4 28 0.0006 26.3 1.8 41 74-114 4-46 (69)
420 COG2005 ModE N-terminal domain 33.8 98 0.0021 27.0 5.3 62 4-68 22-88 (130)
421 PLN02320 seryl-tRNA synthetase 33.7 56 0.0012 34.6 4.5 24 219-243 237-260 (502)
422 smart00422 HTH_MERR helix_turn 33.3 86 0.0019 22.9 4.3 65 18-94 2-67 (70)
423 COG2390 DeoR Transcriptional r 32.5 52 0.0011 32.8 3.9 35 17-51 27-61 (321)
424 COG4738 Predicted transcriptio 32.5 36 0.00079 29.2 2.3 55 6-61 32-93 (124)
425 COG1542 Uncharacterized conser 32.4 29 0.00063 36.5 2.1 43 20-64 446-488 (593)
426 COG0442 ProS Prolyl-tRNA synth 32.1 49 0.0011 35.0 3.8 91 217-348 49-140 (500)
427 PRK15431 ferrous iron transpor 32.0 1.3E+02 0.0028 24.1 5.2 43 6-49 7-49 (78)
428 smart00874 B5 tRNA synthetase 31.9 1.3E+02 0.0029 22.3 5.2 15 222-236 21-35 (71)
429 PF05584 Sulfolobus_pRN: Sulfo 30.9 70 0.0015 25.2 3.5 40 74-114 9-50 (72)
430 COG3046 Uncharacterized protei 30.9 61 0.0013 33.8 4.0 63 242-312 166-232 (505)
431 PRK11169 leucine-responsive tr 30.7 84 0.0018 27.7 4.5 43 71-113 15-59 (164)
432 PF04157 EAP30: EAP30/Vps36 fa 30.6 1.8E+02 0.004 27.0 7.0 83 28-114 133-222 (223)
433 TIGR02147 Fsuc_second hypothet 30.5 95 0.0021 30.2 5.2 45 17-63 138-184 (271)
434 PRK03991 threonyl-tRNA synthet 30.4 68 0.0015 34.8 4.5 25 218-243 230-254 (613)
435 PF01418 HTH_6: Helix-turn-hel 30.3 73 0.0016 24.5 3.6 43 3-45 18-63 (77)
436 PLN03238 probable histone acet 29.9 85 0.0019 31.0 4.7 54 4-61 211-264 (290)
437 KOG3233 RNA polymerase III, su 29.2 34 0.00073 33.6 1.8 47 2-48 85-132 (297)
438 PF13551 HTH_29: Winged helix- 28.7 1.1E+02 0.0025 24.1 4.6 41 5-47 3-43 (112)
439 COG1693 Repressor of nif and g 28.5 1.4E+02 0.0031 29.6 5.9 71 3-75 8-83 (325)
440 PF09397 Ftsk_gamma: Ftsk gamm 28.4 1.4E+02 0.0031 22.9 4.8 52 6-58 11-62 (65)
441 PF04967 HTH_10: HTH DNA bindi 28.2 1.4E+02 0.003 21.9 4.5 41 2-42 4-49 (53)
442 cd01104 HTH_MlrA-CarA Helix-Tu 28.0 1.3E+02 0.0028 21.9 4.5 65 18-93 2-66 (68)
443 COG4344 Uncharacterized protei 28.0 2.1E+02 0.0046 25.8 6.4 70 21-91 36-126 (175)
444 PF11625 DUF3253: Protein of u 27.7 2E+02 0.0044 23.2 5.7 52 2-53 8-66 (83)
445 cd06171 Sigma70_r4 Sigma70, re 27.7 1.4E+02 0.0031 19.5 4.4 37 3-41 15-51 (55)
446 PRK10512 selenocysteinyl-tRNA- 27.5 2.9E+02 0.0063 29.9 8.7 102 4-117 496-601 (614)
447 cd01105 HTH_GlnR-like Helix-Tu 27.2 1.2E+02 0.0025 24.1 4.3 66 17-94 2-68 (88)
448 PRK09392 ftrB transcriptional 27.1 1.3E+02 0.0029 27.3 5.3 43 19-64 176-218 (236)
449 COG2852 Very-short-patch-repai 26.9 56 0.0012 28.5 2.6 33 213-253 73-106 (129)
450 PF03484 B5: tRNA synthetase B 26.6 1E+02 0.0022 23.3 3.8 47 221-291 20-68 (70)
451 COG1437 CyaB Adenylate cyclase 26.5 54 0.0012 30.1 2.6 36 222-267 13-48 (178)
452 cd04900 ACT_UUR-like_1 ACT dom 26.4 69 0.0015 24.1 2.8 55 221-290 14-68 (73)
453 KOG2224 Uncharacterized conser 26.4 42 0.0009 35.1 2.0 61 192-255 491-570 (781)
454 COG1167 ARO8 Transcriptional r 26.3 74 0.0016 32.9 3.8 40 13-52 25-64 (459)
455 PRK15418 transcriptional regul 26.1 79 0.0017 31.2 3.9 36 17-52 30-65 (318)
456 TIGR01884 cas_HTH CRISPR locus 26.1 3.7E+02 0.008 24.3 8.0 90 27-116 97-191 (203)
457 COG2378 Predicted transcriptio 26.1 93 0.002 30.6 4.3 57 5-62 12-69 (311)
458 PRK00960 seryl-tRNA synthetase 26.0 69 0.0015 34.1 3.6 47 220-272 228-275 (517)
459 smart00421 HTH_LUXR helix_turn 26.0 1.4E+02 0.003 20.1 4.1 37 3-42 8-44 (58)
460 PF01710 HTH_Tnp_IS630: Transp 26.0 1.4E+02 0.003 24.9 4.8 35 6-41 62-96 (119)
461 PF13613 HTH_Tnp_4: Helix-turn 26.0 1E+02 0.0022 22.0 3.5 41 2-42 5-45 (53)
462 COG1522 Lrp Transcriptional re 25.4 92 0.002 26.4 3.7 43 72-114 10-54 (154)
463 TIGR03879 near_KaiC_dom probab 25.0 1.2E+02 0.0025 23.9 3.8 30 17-46 33-62 (73)
464 PRK00135 scpB segregation and 24.7 2.2E+02 0.0047 26.2 6.2 59 4-66 93-156 (188)
465 PHA02591 hypothetical protein; 24.6 1.7E+02 0.0038 23.5 4.7 32 6-39 51-82 (83)
466 PF04545 Sigma70_r4: Sigma-70, 24.5 2.2E+02 0.0047 19.7 4.9 34 3-38 9-42 (50)
467 TIGR01610 phage_O_Nterm phage 24.4 1.3E+02 0.0028 24.1 4.2 35 83-117 46-82 (95)
468 PRK03911 heat-inducible transc 24.2 1.3E+02 0.0028 29.3 4.7 63 3-66 5-73 (260)
469 PF07900 DUF1670: Protein of u 24.2 1.4E+02 0.003 28.4 4.8 45 4-48 90-138 (220)
470 PRK03902 manganese transport t 23.9 3.1E+02 0.0068 23.2 6.8 52 58-115 2-55 (142)
471 cd04927 ACT_ACR-like_2 Second 23.5 84 0.0018 24.1 2.8 54 221-290 13-66 (76)
472 PF02796 HTH_7: Helix-turn-hel 23.4 1.7E+02 0.0036 20.2 4.1 32 4-38 12-43 (45)
473 PRK15201 fimbriae regulatory p 23.0 1.2E+02 0.0027 28.2 4.1 39 2-43 137-175 (198)
474 PRK07726 DNA topoisomerase III 22.5 1.6E+02 0.0036 32.0 5.8 67 3-73 483-554 (658)
475 COG4901 Ribosomal protein S25 22.5 1.4E+02 0.0031 25.2 4.0 34 15-48 58-91 (107)
476 PF01090 Ribosomal_S19e: Ribos 22.5 87 0.0019 27.7 3.0 61 5-68 56-130 (139)
477 COG1386 scpB Chromosome segreg 22.3 6.1E+02 0.013 23.2 10.9 104 12-116 19-137 (184)
478 PRK06294 coproporphyrinogen II 21.9 2.3E+02 0.0049 28.4 6.3 32 33-67 332-363 (370)
479 COG1321 TroR Mn-dependent tran 21.9 3.6E+02 0.0077 23.9 6.8 54 57-116 3-58 (154)
480 PRK13239 alkylmercury lyase; P 21.4 1.8E+02 0.004 27.2 5.1 37 4-41 25-61 (206)
481 COG2344 AT-rich DNA-binding pr 21.3 1.5E+02 0.0033 27.8 4.4 38 4-41 19-57 (211)
482 PRK09058 coproporphyrinogen II 21.2 2E+02 0.0044 29.6 5.9 47 17-68 383-430 (449)
483 COG2512 Predicted membrane-ass 21.2 90 0.002 30.2 3.1 45 72-116 197-244 (258)
484 PF02954 HTH_8: Bacterial regu 21.2 2.3E+02 0.005 19.2 4.4 36 2-39 5-41 (42)
485 PRK10840 transcriptional regul 21.0 1.4E+02 0.0031 26.5 4.2 39 2-43 154-192 (216)
486 TIGR02277 PaaX_trns_reg phenyl 21.0 1E+02 0.0022 30.0 3.4 81 146-243 40-124 (280)
487 PF10826 DUF2551: Protein of u 21.0 3E+02 0.0064 22.3 5.4 59 3-62 13-79 (83)
488 cd04763 HTH_MlrA-like Helix-Tu 20.9 1.8E+02 0.004 21.3 4.2 65 18-94 2-67 (68)
489 PLN00104 MYST -like histone ac 20.9 1.5E+02 0.0033 31.1 4.8 54 4-61 362-415 (450)
490 smart00351 PAX Paired Box doma 20.7 2.6E+02 0.0057 23.6 5.5 79 4-94 24-103 (125)
491 COG2771 CsgD DNA-binding HTH d 20.7 1.9E+02 0.0041 20.3 4.1 39 2-43 8-46 (65)
492 PRK00441 argR arginine repress 20.6 2E+02 0.0042 25.4 4.9 69 3-80 6-80 (149)
493 PRK10141 DNA-binding transcrip 20.5 3.1E+02 0.0067 23.2 5.9 47 69-115 14-63 (117)
494 TIGR00475 selB selenocysteine- 20.4 3.3E+02 0.0072 29.2 7.5 75 4-97 478-553 (581)
495 PF05043 Mga: Mga helix-turn-h 20.3 1.4E+02 0.0031 23.0 3.6 39 3-42 18-56 (87)
496 COG2238 RPS19A Ribosomal prote 20.3 2E+02 0.0044 25.6 4.7 60 5-68 57-130 (147)
497 cd06170 LuxR_C_like C-terminal 20.2 2.1E+02 0.0045 19.3 4.1 36 3-41 5-40 (57)
498 cd06571 Bac_DnaA_C C-terminal 20.0 1.6E+02 0.0034 23.4 3.8 26 17-42 45-71 (90)
499 PF09929 DUF2161: Uncharacteri 20.0 2.3E+02 0.0049 24.5 4.9 54 6-65 64-117 (118)
No 1
>KOG2784 consensus Phenylalanyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-107 Score=787.49 Aligned_cols=342 Identities=53% Similarity=0.875 Sum_probs=329.8
Q ss_pred CHHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcC
Q 018851 1 MAEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVP 80 (349)
Q Consensus 1 ~~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~ 80 (349)
+++.+||..|...++ .++.+++...+.+|++++++++||++.|+|+++..+++.|.||+||++++++||||++|+++++
T Consensus 3 ~~~~~iL~~L~~~de-~~s~~l~a~~~~~h~~~v~al~SL~a~~~i~~~~~~~~~~~LT~EG~~i~~eGS~E~~v~~~i~ 81 (483)
T KOG2784|consen 3 ALAEKILEKLQESDE-VDSSDLAAPFNEDHQQVVGALKSLQAGGVIEVKDVETKTYELTAEGEEIAREGSHEALVFESIP 81 (483)
T ss_pred hHHHHHHHHHHhccC-CChhhhcCchhhhhHHHHHHHHHHhhcCceEEEeeeeEEEeeChhHHHHHhcCCcceeeeeccC
Confidence 367899999999888 7888999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCce-eeeccccchHHHHHHHHHHHcCCCCCHHHHHHHhhcCceeee
Q 018851 81 AEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGKQ-VSRKVQNVEDKVKDLLLQVQNGHALSKEEISSLKARKLIVPQ 159 (349)
Q Consensus 81 ~~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~~-i~~~~~~~~d~~~~~L~~i~~g~~~~~~~~~~LkkRkLi~~~ 159 (349)
+.| +.++||++.+ ..||+++|+|+|||+++++ +.++++++.|.+++.|+.|..|.. +.+++++|||||||.+.
T Consensus 82 ~~g-l~~~el~~k~----~giG~~~A~~nkWI~~d~~~~~r~v~~itD~v~~~l~~ik~g~~-~ake~~dlkKrKLi~~~ 155 (483)
T KOG2784|consen 82 EEG-LAIAELMKKL----VGIGQSKAFKNKWIRVDKSRVVRDVDSITDEVRNQLQQIKRGSA-DAKEVEDLKKRKLISEV 155 (483)
T ss_pred ccc-cCHHHHHhhh----hccchhhhhccceEEecCcccccchhhhhHHHHHHHHHHHcCcc-hHHHHHHHHhhhhhccc
Confidence 887 9999999875 2399999999999999999 778899999999999999998764 37899999999999999
Q ss_pred EEEEEEEecCCCCCcchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCC
Q 018851 160 TWKGYSVRKGPNYAPKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPT 239 (349)
Q Consensus 160 ~~~~~~i~kg~~~~~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~ 239 (349)
+++.|.++||++|+.++.+..||||+|||.||+|++..||+|||++.|.++.+|++|||++|++++|+||.+|||+||+|
T Consensus 156 ~~~~f~v~KGp~Fst~l~k~eTdLT~emi~~gsw~dl~FK~YNF~a~G~~p~~G~lHPLmKvR~eFRqiF~emGFsEMpt 235 (483)
T KOG2784|consen 156 KIKVFSVTKGPNFSTSLTKLETDLTSEMIASGSWKDLKFKPYNFNAEGVPPSSGHLHPLMKVREEFRQIFFEMGFSEMPT 235 (483)
T ss_pred eeEEEEEecCCcccchHHHHhhhccHHHhccCchhhccCcccCcccCCCCCCCCccchHHHHHHHHHHHHHHcccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCC
Q 018851 240 NNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHT 319 (349)
Q Consensus 240 ~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHT 319 (349)
|++|||+|||||||||||+|||||.||||||++|+.+..+|+||++|||++|+.|||||+||+|+|+.+||+++||||||
T Consensus 236 n~yVEssFWNFDALfqPQqHpARDahDTFfl~~Pa~s~~~p~dY~~rVk~vH~~G~ygs~GY~y~wk~eEaqKnvLRTHT 315 (483)
T KOG2784|consen 236 NNYVESSFWNFDALFQPQQHPARDAHDTFFLKDPATSTKFPEDYLERVKAVHEQGGYGSIGYRYNWKLEEAQKNVLRTHT 315 (483)
T ss_pred ccchhhccccchhhcCcccCCccccccceEecChhhcccCCHHHHHHHHHHHhcCCcCCcccCCCCCHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 320 TAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 320 Tavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
||||||+||+||+++|.|.||||||||||+
T Consensus 316 TavSArmLy~LAk~~f~p~K~FSIDrVFRN 345 (483)
T KOG2784|consen 316 TAVSARMLYRLAKKGFKPAKYFSIDRVFRN 345 (483)
T ss_pred HHhhHHHHHHHHhCCCCcccccchhhhhhc
Confidence 999999999999999999999999999995
No 2
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=100.00 E-value=1.2e-103 Score=795.58 Aligned_cols=349 Identities=79% Similarity=1.229 Sum_probs=328.4
Q ss_pred CHHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcC
Q 018851 1 MAEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVP 80 (349)
Q Consensus 1 ~~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~ 80 (349)
++|++||.+|.+.+...+++++|+.+|+++++|+++++||+++|+|++++.+.+.|+||+||++|+++||||+||+++|+
T Consensus 3 ~~e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG~~~l~~G~PE~rl~~~l~ 82 (492)
T PLN02853 3 MAEEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIKRETWVLTEEGKKYAAEGSPEVQLFAAVP 82 (492)
T ss_pred hHHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHHHh
Confidence 47899999999866446899999999999999999999999999999999999999999999999999999999999998
Q ss_pred cCCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCc-e-eeeccccchHHHHHHHHHHHcCCCCCHHHHHHHhhcC-cee
Q 018851 81 AEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGK-Q-VSRKVQNVEDKVKDLLLQVQNGHALSKEEISSLKARK-LIV 157 (349)
Q Consensus 81 ~~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~-~-i~~~~~~~~d~~~~~L~~i~~g~~~~~~~~~~LkkRk-Li~ 157 (349)
++|+++++||++.+++++++||+|+|+|+|||++++ + +.+..+.+.|.++.+|+.+.++..++++.+++||||| ||+
T Consensus 83 ~~~~~~~~eL~~~l~~~~~~i~~g~a~k~gwi~i~~~~~v~~~~~~~~d~~~~~L~~l~~~~~~~~~~l~~LkkRk~Li~ 162 (492)
T PLN02853 83 AEGSISKDELQKKLDPAVFDIGFKQAMKNKWLEMGGKPQVSRKVQHVEDEVKELLLAIQEGKEVDDKDIDALKKRRKLIT 162 (492)
T ss_pred hcCCccHHHHHHhhCchhHHHHHHHHHHCCcEEECCCCcEEeccCccchHHHHHHHHHhcCCCCCHHHHHHHHhhhcceE
Confidence 766689999998887678999999999999999994 5 6777777788899999999876556777899999998 999
Q ss_pred eeEEEEEEEecCCCCCcchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceec
Q 018851 158 PQTWKGYSVRKGPNYAPKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEM 237 (349)
Q Consensus 158 ~~~~~~~~i~kg~~~~~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~ 237 (349)
..+.+.|.|++|++++.+..+++|+||+|||.||+||++.||+|||+++|+.+++|+.|||++++++|++||.+|||+||
T Consensus 163 ~~~~~~~~v~~~~~~~~~~~~~~t~LT~eml~sg~Wk~~~fk~Yn~~a~g~~~~~G~~HPl~~~~~ei~~if~~mGF~e~ 242 (492)
T PLN02853 163 LETWKGYSIKKGPNYAPERKKAATDLTREMLQSGDWKDLEFKEYNFNALGAPPEGGHLHPLLKVRQQFRKIFLQMGFEEM 242 (492)
T ss_pred EEEEEEEEEEECCccccccccccccCCHHHhcCCCcccCCCCccccCCCCCCCCCCCCCHHHHHHHHHHHHHHhCCCEEe
Confidence 99999999999999988889999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCC
Q 018851 238 PTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRT 317 (349)
Q Consensus 238 ~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRT 317 (349)
++||+||++||||||||||||||||||||||||++|.....+|++|++||++|||+||+||+||+|+||.++|.++||||
T Consensus 243 ~~g~~ves~f~NFDaL~~PqdHPARd~qDTFyl~~~~~~~~~p~~~~erVk~~He~G~~gS~Gw~y~W~~~~a~~~vLRT 322 (492)
T PLN02853 243 PTNNFVESSFWNFDALFQPQQHPARDSHDTFFLKAPATTRQLPEDYVERVKTVHESGGYGSIGYGYDWKREEANKNLLRT 322 (492)
T ss_pred cCCCCeechhhhhhhhcCCCCCCCCCccceEEEcCccccccCcHHHHHHHHHHHhcCCCCccccccccccchhcccccCC
Confidence 77999999999999999999999999999999999887777899999999999999999999999999999999999999
Q ss_pred CCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 318 HTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 318 HTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
||||+|+|+|+++++.+++|.|+|||||||||
T Consensus 323 HTTa~s~r~L~~~~~~~~~p~k~fsigrVfR~ 354 (492)
T PLN02853 323 HTTAVSSRMLYKLAQKGFKPKRYFSIDRVFRN 354 (492)
T ss_pred CCCHHHHHHHHHhhccCCCCcEEEeccceecC
Confidence 99999999999887666789999999999997
No 3
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=100.00 E-value=2e-100 Score=774.72 Aligned_cols=347 Identities=53% Similarity=0.846 Sum_probs=320.0
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPA 81 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~ 81 (349)
+|++||.+|.+.....+++++|+.+|++|++|+++++||+++|+|++++.+.+.|+||+||++|+++||||+||+++|++
T Consensus 7 ~e~~iL~~l~~~~~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~~~~~~LT~eG~~~~~~G~PE~rl~~~l~~ 86 (494)
T PTZ00326 7 EENTILSKLESENEIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKKSNTWTLTEEGEDYLKNGSPEYRLWQKLKE 86 (494)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEEEEEEECHHHHHHHHcCCHHHHHHHHhhh
Confidence 68999999987333478999999999999999999999999999999999999999999999999999999999999987
Q ss_pred CCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCce---ee---eccccchHHHHHHHHHHHcC---CCCCHHHHHHHhh
Q 018851 82 EGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGKQ---VS---RKVQNVEDKVKDLLLQVQNG---HALSKEEISSLKA 152 (349)
Q Consensus 82 ~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~~---i~---~~~~~~~d~~~~~L~~i~~g---~~~~~~~~~~Lkk 152 (349)
+| .++.++.+.+++++++||+|+|+|+|||++++| +. ...+.+.|.++.+|+.+.++ ..++++++++|||
T Consensus 87 ~~-~~~~~l~~~~~~~~~~i~~g~~~k~~wi~i~~~~~~i~~~~~~~~~~~d~~~~~L~~i~~~~~~~~~~~~~~~~Lkk 165 (494)
T PTZ00326 87 GG-ISKADDAKKLGGKVADIGLGNAMKKKWIKLNKGDKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKELKK 165 (494)
T ss_pred cC-CCHHHHHhhhcchhHHHHHHHHHHCCcEEEcCCCceeecccccccccccHHHHHHHHHhccCccccCCHHHHHHHhc
Confidence 55 788888877666789999999999999999965 22 22455678899999999865 3567788999999
Q ss_pred cCceeeeEEEEEEEecCCCCCcchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhC
Q 018851 153 RKLIVPQTWKGYSVRKGPNYAPKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQM 232 (349)
Q Consensus 153 RkLi~~~~~~~~~i~kg~~~~~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~m 232 (349)
||||+..+.+.|.|++|++++.+..+++|+||+|||.||+||++.||+|||++||+.+++|++|||++++++|++||.+|
T Consensus 166 RkLi~~~~~~~~~i~~~~~~~~~~~~~~t~LT~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~i~~if~~m 245 (494)
T PTZ00326 166 RKLATLEKIKYFVVTKGPKFAKEIKKQITDLTQEMLLNGSWKNAEFKEYNFNALGKKIGGGNLHPLLKVRREFREILLEM 245 (494)
T ss_pred CCCeEEEEEEEEEEEECCccccccccccccCCHHHhhCCccccCCcccceecCCCCCCCCCCCChHHHHHHHHHHHHHhC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCC--CCCHHHHHHHHHHhhcCCCCCCCcccccchhhh
Q 018851 233 GFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTR--ELPEDYVERVKRVHESGGYGSRGYGYEWKREEA 310 (349)
Q Consensus 233 GF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~--~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a 310 (349)
||+||+++++|||+|||||||||||||||||+||||||++|.... ++|++|++||++|||.||+||+||+|+||.++|
T Consensus 246 GF~e~~~~~~ves~f~NFDaL~~PqdHPARd~~DTFyl~~~~~~~~~~~p~~~~~~Vk~~He~G~~gS~Gw~y~W~~e~a 325 (494)
T PTZ00326 246 GFEEMPTNRYVESSFWNFDALFQPQQHPARDAQDTFFLSKPETSKVNDLDDDYVERVKKVHEVGGYGSIGWRYDWKLEEA 325 (494)
T ss_pred CCEEecCCCCccccchhhhhhcCCCCCCCCCcCceEEEcCccccccccCcHHHHHHHHHHhccCCcCCcccccccccchh
Confidence 999998778999999999999999999999999999999887664 689999999999999999999999999999999
Q ss_pred hccccCCCCchhHHHHHHHhhc-----CCCCCceEEecCceecC
Q 018851 311 NKNLLRTHTTAVSSRMLKALAE-----KPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 311 ~~~vLRTHTTavs~r~L~~l~~-----~~~~p~k~fsi~rVfR~ 349 (349)
++++|||||||+|+|+|+++++ .+++|.|+||||||||+
T Consensus 326 ~~~vLRtHtTa~~aR~l~~~~~~~~~~~~~~P~k~fsigrVfR~ 369 (494)
T PTZ00326 326 RKNILRTHTTAVSARMLYKLAQEYKKTGPFKPKKYFSIDRVFRN 369 (494)
T ss_pred ccccccCCCCHHHHHHHHhhccccccccCCCCceEEecCCEecC
Confidence 9999999999999999998753 34579999999999997
No 4
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=100.00 E-value=1.1e-84 Score=665.62 Aligned_cols=342 Identities=38% Similarity=0.617 Sum_probs=314.3
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPA 81 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~ 81 (349)
.|..||..|...+. .++.++|+.+|+++++|++++++|+++|||+.+......+.||+||++|+++|+||+|+++++.+
T Consensus 7 ~e~~vL~~L~~~~~-~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g~pE~rl~~~l~~ 85 (489)
T PRK04172 7 NEKKVLKALKELKE-ATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEGLPERRLLNALKD 85 (489)
T ss_pred HHHHHHHHHHhCCC-CCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhcCHHHHHHHhhHh
Confidence 57899999987775 68899999999999999999999999999999988888999999999999999999999999986
Q ss_pred CCCCCHHHHHhh-cCchhhhhHHHHHhhCCcEeeCce-eeeccccchHHHHHHHHHHHcCCC-----CCHHHHHHHhhcC
Q 018851 82 EGSISKDELQKK-LDPAVFKIGCSQAGKNKWVEMGKQ-VSRKVQNVEDKVKDLLLQVQNGHA-----LSKEEISSLKARK 154 (349)
Q Consensus 82 ~g~~~~~el~~~-~~~~~~~ig~g~~~k~~wi~i~~~-i~~~~~~~~d~~~~~L~~i~~g~~-----~~~~~~~~LkkRk 154 (349)
.++++++||... ++.+++++|+++|+|+||+++++| +.+..+...|.++.+|+.+.+|.. .+.+.+++|+|||
T Consensus 86 ~~g~~~~el~~~aL~~~~~~i~~~~l~k~g~i~i~~G~~i~~~~~~~d~~~~~L~~l~~g~~~~~~~~~~~~l~~LkkRk 165 (489)
T PRK04172 86 GGEVSLDELKEALLDKKEVGIALGNLARKGWAKIEKGKVILKPDAYEDPEEKALKALAEGDKEELSEEDLKVLKELKKRK 165 (489)
T ss_pred cCCcCHHHHHHhhccchhHHHHHHHHHHCCCeecCCCceeecCcccCcHHHHHHHHHhccCccccccCCHHHHHHHHhcC
Confidence 556899999987 776789999999999999999888 666666668889999999987653 5778899999999
Q ss_pred ceeeeEEEEEEEe---cCCCCC---cchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHH
Q 018851 155 LIVPQTWKGYSVR---KGPNYA---PKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDI 228 (349)
Q Consensus 155 Li~~~~~~~~~i~---kg~~~~---~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~i 228 (349)
||+..+.+.+.|+ +|.+++ ++..+++|+||+|||.||+||++.||+||+++||+.+.+|..||+++++++||++
T Consensus 166 L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lt~e~l~~g~w~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 245 (489)
T PRK04172 166 LVEEKERTERSVELTDAGLELLKEGIELKEEITQLTPELLKSGEWKEKEFRPYNVKAPPPKIYPGKKHPYREFIDEVRDI 245 (489)
T ss_pred CeEEEEEEEEEEEEccchhhhhhcccccccccccCCHHHhcCCCccCCCCccceeCCCCCCCCCCCCChHHHHHHHHHHH
Confidence 9999999999864 677776 5677899999999999999999999999999999999999999999999999999
Q ss_pred HhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC-CCCCCcccccch
Q 018851 229 FLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG-YGSRGYGYEWKR 307 (349)
Q Consensus 229 f~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg-~gS~Gw~Y~W~~ 307 (349)
|.+|||+||. +|.||++|||||+|||||||||||+|||||++.|. ..++|++|+++|+++||+|| +||+||+|.|+.
T Consensus 246 f~~~Gf~e~~-~p~vE~~~~nfd~lf~p~~hpaR~~~dtf~~~~~~-~~~~~~~~~~~v~~~he~g~~~~~~~~~y~~~~ 323 (489)
T PRK04172 246 LVEMGFEEMK-GPLVETEFWNFDALFQPQDHPAREMQDTFYLKYPG-IGDLPEELVERVKEVHEHGGDTGSRGWGYKWDE 323 (489)
T ss_pred HHHCCCEEee-CCeeeecCcccccccCCCCCCCCCccceEEECCcc-cccCcHHHHHHHHHHHhccCCCCCccccCCcch
Confidence 9999999997 89999999999999999999999999999999887 44788999999999999997 788999999999
Q ss_pred hhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 308 EEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 308 ~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
++|++++|||||||+++|+|++. ...|.|+|+||||||+
T Consensus 324 ~~~~~~~LR~~~T~~~~r~l~~~---~~~p~rlFeiGrVFR~ 362 (489)
T PRK04172 324 DIAKRLVLRTHTTALSARYLASR---PEPPQKYFSIGRVFRP 362 (489)
T ss_pred hhhhccccccCChHHHHHHHHhc---CCCCeEEEEecceEcC
Confidence 99999999999999999999853 3469999999999985
No 5
>COG0016 PheS Phenylalanyl-tRNA synthetase alpha subunit [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.5e-47 Score=370.87 Aligned_cols=198 Identities=33% Similarity=0.468 Sum_probs=154.7
Q ss_pred hhhHHHHHhhCCcEeeCceeeeccccchHHHHHHHHHHHcCCCCCHHHHHHH-hhcC-ceeeeEEEEEEEecCCCCC---
Q 018851 99 FKIGCSQAGKNKWVEMGKQVSRKVQNVEDKVKDLLLQVQNGHALSKEEISSL-KARK-LIVPQTWKGYSVRKGPNYA--- 173 (349)
Q Consensus 99 ~~ig~g~~~k~~wi~i~~~i~~~~~~~~d~~~~~L~~i~~g~~~~~~~~~~L-kkRk-Li~~~~~~~~~i~kg~~~~--- 173 (349)
..++++++++++|..++ ...+. ...|+.+.....-....+.+| ++.| +...++++.+.+ .+.
T Consensus 2 ~~~~l~~l~~~~~~~i~--------~~~~~-~~~L~~~~~~~lgk~g~l~~~~k~l~~~~~~eer~~~g~----~in~~~ 68 (335)
T COG0016 2 VMIALGRLAKKGIAAIE--------LASDL-LKALEELKVKYLGKKGVLTDLLKKLGKLSPLEERKEVGA----LINELK 68 (335)
T ss_pred chHHHHHHHHHHHHHHH--------hhccH-HHHHHHHHHHhcCcccchHHHHHHhccCChhhhhhhhhh----hHHhhH
Confidence 35799999999998775 22232 345555542111122335544 4443 444344444332 111
Q ss_pred cchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhcc
Q 018851 174 PKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDAL 253 (349)
Q Consensus 174 ~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaL 253 (349)
....+.++++|++++.++.|+...|++||+++||+.+++|+.|||++++++|++||.+|||+++. ||+||++|||||||
T Consensus 69 ~~~~~~~~~~~~~l~~~~~~~~l~~e~~dv~lp~~~~~~G~~Hpl~~~~e~i~~iF~~mGF~~~~-gp~IE~d~~NFDaL 147 (335)
T COG0016 69 KEVEDAITELTPELEAAGLWERLAFEKIDVTLPGRRIYPGSLHPLTQTIEEIEDIFLGMGFTEVE-GPEIETDFYNFDAL 147 (335)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhccCCCcCCCCccCCCCCcChHHHHHHHHHHHHHHcCceecc-CCcccccccchhhh
Confidence 12567789999999999999999999999999999999999999999999999999999999997 89999999999999
Q ss_pred CCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcC
Q 018851 254 FQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK 333 (349)
Q Consensus 254 f~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~ 333 (349)
|+||||||||||||||+++. .+ ++|||||||+||+|+|++.
T Consensus 148 n~P~dHPARdmqDTFy~~~~---------------------------------~~---~~lLRTHTs~vq~R~l~~~--- 188 (335)
T COG0016 148 NIPQDHPARDMQDTFYLKDD---------------------------------RE---KLLLRTHTSPVQARTLAEN--- 188 (335)
T ss_pred cCCCCCCcccccceEEEcCC---------------------------------CC---ceeecccCcHhhHHHHHhC---
Confidence 99999999999999999851 01 6899999999999999853
Q ss_pred CCCCceEEecCceecC
Q 018851 334 PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 334 ~~~p~k~fsi~rVfR~ 349 (349)
..+|+|+||+|||||+
T Consensus 189 ~~~P~k~~~~grvyR~ 204 (335)
T COG0016 189 AKIPIKIFSPGRVYRN 204 (335)
T ss_pred CCCCceEecccceecC
Confidence 2249999999999996
No 6
>PF01409 tRNA-synt_2d: tRNA synthetases class II core domain (F); InterPro: IPR002319 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases [].; GO: 0000049 tRNA binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 3TUP_A 3HFV_A 3CMQ_A 3TEG_A 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B ....
Probab=100.00 E-value=6.2e-34 Score=268.84 Aligned_cols=114 Identities=39% Similarity=0.685 Sum_probs=100.6
Q ss_pred ccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCC
Q 018851 200 EYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTREL 279 (349)
Q Consensus 200 ~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~ 279 (349)
+||+++|++....|+.||+++++++|+++|.+|||+|+. +++||+++||||+||+|||||||+++||||+++|...
T Consensus 1 ~~d~~~p~~~~~~G~~hp~~~~~~~i~~~~~~~Gf~e~~-~~~v~s~~~nFD~Ln~p~dHpaR~~~Dtfyi~~p~~~--- 76 (247)
T PF01409_consen 1 KIDVTLPGKRFTPGRLHPITKFIREIRDIFVGMGFQEVE-GPEVESEFYNFDALNIPQDHPARDMQDTFYISNPYSA--- 76 (247)
T ss_dssp ---TTSGCTTCCCSBTSHHHHHHHHHHHHHHCTTSEEES-TTSEEEHHHHTGGGTSTTTSCGGCGTTSEBSCSSSBC---
T ss_pred CccccCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCeEee-CCeEEeeHHHHHhhCcCCCccccccccceeeeccccc---
Confidence 589999999999999999999999999999999999997 8999999999999999999999999999999987531
Q ss_pred CHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 280 PEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 280 p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.|||||||++++|+|+ +...+|.|+|+||+|||+
T Consensus 77 -----------------------------~~~~~vLRThts~~~~~~l~---~~~~~p~kif~iG~VyR~ 114 (247)
T PF01409_consen 77 -----------------------------EEDYSVLRTHTSPGQLRTLN---KHRPPPIKIFEIGKVYRR 114 (247)
T ss_dssp -----------------------------ECSSEEE-SSTHHHHHHHHT---TTSHSSEEEEEEEEEESS
T ss_pred -----------------------------cchhhhhhhhhhHHHHHHHH---HhcCCCeEEEecCceEec
Confidence 13479999999999999993 333479999999999997
No 7
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=99.98 E-value=5.9e-33 Score=271.45 Aligned_cols=106 Identities=34% Similarity=0.652 Sum_probs=99.5
Q ss_pred ccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCC
Q 018851 200 EYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTREL 279 (349)
Q Consensus 200 ~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~ 279 (349)
.||+++||++...|+.||+++++++|+++|.+|||+++. ||+||+++||||+||+|+|||||||||||||++
T Consensus 92 ~~d~t~p~~~~~~G~~HPl~~~~~~Ir~if~~mGF~ev~-gpeIes~~~NFdaLn~P~dHPaR~~~DTfyI~~------- 163 (339)
T PRK00488 92 TIDVTLPGRRIELGSLHPITQTIEEIEDIFVGMGFEVAE-GPEIETDYYNFEALNIPKDHPARDMQDTFYIDD------- 163 (339)
T ss_pred cccccCCCCCCCCCCCCHHHHHHHHHHHHHHhCCCEEEe-CCccccHHHHHHHhCCCCCCcccccCceEEEcC-------
Confidence 488999999899999999999999999999999999996 899999999999999999999999999999964
Q ss_pred CHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 280 PEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 280 p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
..|||||||++++|+|.+ ..+|.|+|++|+|||+
T Consensus 164 --------------------------------~~lLRThTSp~qir~L~~----~~~Pirif~~G~VyR~ 197 (339)
T PRK00488 164 --------------------------------GLLLRTHTSPVQIRTMEK----QKPPIRIIAPGRVYRN 197 (339)
T ss_pred --------------------------------CceeeccCcHHHHHHHHh----cCCCeEEEEeeeEEEc
Confidence 589999999999999974 2369999999999996
No 8
>PLN02788 phenylalanine-tRNA synthetase
Probab=99.97 E-value=2.1e-32 Score=272.93 Aligned_cols=113 Identities=21% Similarity=0.385 Sum_probs=103.0
Q ss_pred CCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhC---CceecCCCCceeeeehhhhccCCCCCCCCCCCCC
Q 018851 190 KGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQM---GFEEMPTNNFVESSFWNFDALFQPQQHPARDSHD 266 (349)
Q Consensus 190 sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~m---GF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~D 266 (349)
...|-|.+ ++++++.|+.++.|..|||++++++|+++|.+| ||+++++.++||++|||||+||+|||||||++||
T Consensus 44 ~~~~~n~~--~~i~~~~~~~l~~~~~HPl~~~~~~i~~~f~~~~~~gf~~~~~~~~iv~~~~NFD~L~~P~dHPaR~~~D 121 (402)
T PLN02788 44 DDPTNNVP--DHIFSKIGMQLHRRPDHPLGILKNAIYDYFDENYSNKFKKFDDLSPIVSTKQNFDDVLVPPDHVSRSYND 121 (402)
T ss_pred CCccCCCC--hhHhccCCccCCCCCCChHHHHHHHHHHHHhhcccCCcEEecCCCCccchhhhhhhhCCCCCCCccCccc
Confidence 44687775 999999999999999999999999999999998 9999973389999999999999999999999999
Q ss_pred eeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCce
Q 018851 267 TFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSC 346 (349)
Q Consensus 267 TFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rV 346 (349)
||||++ +.||||||||+|+|+|.+ .+ | ++|++|+|
T Consensus 122 Tfy~~~---------------------------------------~~lLRTHTSa~q~~~l~~---~~--~-~~~~~g~V 156 (402)
T PLN02788 122 TYYVDA---------------------------------------QTVLRCHTSAHQAELLRA---GH--T-HFLVTGDV 156 (402)
T ss_pred eEEecC---------------------------------------CccccCCCcHHHHHHHHh---CC--C-cEEEEeeE
Confidence 999975 589999999999999984 22 3 99999999
Q ss_pred ecC
Q 018851 347 FQK 349 (349)
Q Consensus 347 fR~ 349 (349)
|||
T Consensus 157 yRr 159 (402)
T PLN02788 157 YRR 159 (402)
T ss_pred eec
Confidence 997
No 9
>TIGR00468 pheS phenylalanyl-tRNA synthetase, alpha subunit. Most phenylalanyl-tRNA synthetases are heterodimeric, with 2 alpha (pheS) and 2 beta (pheT) subunits. This model describes the alpha subunit, which shows some similarity to class II aminoacyl-tRNA ligases. Mitochondrial phenylalanyl-tRNA synthetase is a single polypeptide chain, active as a monomer, and similar to this chain rather than to the beta chain, but excluded from this model. An interesting feature of the alignment of all sequences captured by this model is a deep split between non-spirochete bacterial examples and all other examples; supporting this split is a relative deletion of about 50 residues in the former set between two motifs well conserved throughout the alignment.
Probab=99.94 E-value=5.9e-28 Score=233.30 Aligned_cols=132 Identities=41% Similarity=0.719 Sum_probs=121.4
Q ss_pred chhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccC
Q 018851 175 KRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALF 254 (349)
Q Consensus 175 ~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf 254 (349)
+..+.++++|.++..++.|++..|++||+++|+.....|..||+.+++++||++|.+|||.|+. ++.+++++||||+|+
T Consensus 31 ~~~~~~~~~~~~~~~~~~~~~~~~~~~d~tlp~~~~~~g~~~p~~~~~~~ir~~l~~~Gf~Ev~-~~~~~s~~~~fd~l~ 109 (294)
T TIGR00468 31 ELEDELTKLKPELEKAGLWSKLKFETYDVTLPGTKIYPGSLHPLTRVIDEIRDIFLGLGFTEEK-GPEVETDFWNFDALN 109 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhccCcccCCCCCCCCCCcCHHHHHHHHHHHHHHHCCCEEee-CCceeccHHHHHHhC
Confidence 3467778999999999999999999999999997778899999999999999999999999997 789999999999999
Q ss_pred CCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCC
Q 018851 255 QPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKP 334 (349)
Q Consensus 255 ~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~ 334 (349)
+|++||||++|||||+.+ ..+|||||++++.++|+....
T Consensus 110 ~~~~hpar~~~d~~~l~d---------------------------------------~~vLRtsl~p~ll~~l~~N~~-- 148 (294)
T TIGR00468 110 IPQDHPARDMQDTFYIKD---------------------------------------RLLLRTHTTAVQLRTMEENEK-- 148 (294)
T ss_pred CCCCCcchhhccceeecC---------------------------------------CcceecccHHHHHHHHHhcCC--
Confidence 999999999999999974 579999999999999985322
Q ss_pred CCCceEEecCceecC
Q 018851 335 FAPKKVFLHRSCFQK 349 (349)
Q Consensus 335 ~~p~k~fsi~rVfR~ 349 (349)
+|+|+|.||||||+
T Consensus 149 -~pirlFEiGrVfr~ 162 (294)
T TIGR00468 149 -PPIRIFSPGRVFRN 162 (294)
T ss_pred -CCceEEEecceEEc
Confidence 69999999999985
No 10
>TIGR00469 pheS_mito phenylalanyl-tRNA synthetase, mitochondrial. Unlike all other known phenylalanyl-tRNA synthetases, the mitochondrial form demonstrated from yeast is monomeric. It is similar to but longer than the alpha subunit (PheS) of the alpha 2 beta 2 form found in Bacteria, Archaea, and eukaryotes, and shares the characteristic motifs of class II aminoacyl-tRNA ligases. This alignment models the experimental example from Saccharomyces cerevisiae (designated MSF1) and its orthologs from other eukaryotic species.
Probab=99.94 E-value=2.5e-27 Score=238.75 Aligned_cols=110 Identities=22% Similarity=0.310 Sum_probs=96.2
Q ss_pred ccccccCCCCCCCCCCChHHHHHHHHHHHHhhC--------CceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeec
Q 018851 200 EYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQM--------GFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLE 271 (349)
Q Consensus 200 ~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~m--------GF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~ 271 (349)
|-.++.-|+..+.|..|||+.++++|.++|.+| ||+...+-++||+.++|||+|++|+|||||+++||||++
T Consensus 26 ~~i~~~~~r~~~~~~~HPl~~~~~~I~~~F~~~~~~~~~~~gf~v~~~~~Pvvt~~~NFD~Ln~P~dHPaR~~~DT~Yi~ 105 (460)
T TIGR00469 26 DKIIKLTDANKHLKEDHPLGIIRDLIEKKFNGADNNQRGNPLFKIFDNFKPVVTTMENFDNLGFPADHPGRQKSDCYYIN 105 (460)
T ss_pred hHHHHhhccCccCCCCCcHHHHHHHHHHHHHhhhcccccCCCeEEeeCCCCccchhhhhhhcCCCCCCcccCcccceEec
Confidence 556677899999999999999999999999999 999886223399999999999999999999999999997
Q ss_pred CCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCce--EEecCceecC
Q 018851 272 EPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKK--VFLHRSCFQK 349 (349)
Q Consensus 272 ~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k--~fsi~rVfR~ 349 (349)
+ +.||||||||+|+|+|.+. ....+|.+ +++.|+||||
T Consensus 106 ~---------------------------------------~~lLRTHTSa~q~~~~~~~-~~~~~~~~~~~i~~G~VYRr 145 (460)
T TIGR00469 106 E---------------------------------------QHLLRAHTSAHELECFQGG-LDDSDNIKSGFLISADVYRR 145 (460)
T ss_pred C---------------------------------------CceeCCCCcHHHHHHHHhc-cccCCCcceeeEeecceeeC
Confidence 5 5899999999999999842 21125787 9999999998
No 11
>TIGR00470 sepS O-phosphoseryl-tRNA(Cys) synthetase. This family of archaeal proteins resembles known phenylalanyl-tRNA synthetase alpha chains. Recently, it was shown to act in a proposed pathway of tRNA(Cys) indirect aminoacylation, resulting in Cys biosynthesis from O-phosphoserine, in certain archaea. It charges tRNA(Cys) with O-phosphoserine. The pscS gene product converts the phosphoserine to Cys.
Probab=99.61 E-value=6.4e-16 Score=156.15 Aligned_cols=146 Identities=25% Similarity=0.414 Sum_probs=112.8
Q ss_pred cccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCC-eeeecC-CCC-
Q 018851 199 KEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHD-TFFLEE-PST- 275 (349)
Q Consensus 199 k~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~D-TFyl~~-p~~- 275 (349)
+..|-..|-..+..|+.||+.++|+++|+..++|||+||- ||.|..+-.-|-.. .+-|-..-| .|||.+ |..
T Consensus 30 ~~~~~~ypr~~~~~gk~hpv~~ti~~lreayl~~gf~e~~-np~iv~e~~v~kqf----g~ea~avldrcfyl~glprp~ 104 (533)
T TIGR00470 30 KHIDNKYPRLKFVYGKPHPLMETIERLREAYLRMGFSEMV-NPLIVDEMHIYKQF----GPEAMAVLDRCFYLAGLPRPD 104 (533)
T ss_pred CCccccCCcccccCCCCCcHHHHHHHHHHHHHhcChHhhc-CceeecHHHHHHhh----CHHHHHHHHHhhhhcCCCCCC
Confidence 4466777888899999999999999999999999999996 89998888777665 566778888 899987 332
Q ss_pred --------------CCCCCHHHHHHHHHH-hhc--CC-CC---------------CCCcc--------cccchhhhhccc
Q 018851 276 --------------TRELPEDYVERVKRV-HES--GG-YG---------------SRGYG--------YEWKREEANKNL 314 (349)
Q Consensus 276 --------------~~~~p~~~~erVk~v-He~--Gg-~g---------------S~Gw~--------Y~W~~~~a~~~v 314 (349)
+.++.++-.|+.+++ |.. |. .| +.+-. ++=-.++|.+++
T Consensus 105 vgis~~~~~~i~~~g~~~~~~~~e~lr~~lh~ykkg~idgddl~~eia~~l~~~d~~~~~ild~vfpefk~l~p~s~~~l 184 (533)
T TIGR00470 105 VGLGNEKIEIIENLGIDIDDEKKERLREVFHLYKKGAIDGDDLVFEIAKALNVSNEMGLKVLETVFPEFKDLKPESTTLT 184 (533)
T ss_pred cCcCHHHHHHHHHhCCCCChhHHHHHHHHHHHhhcCCCccchhHHHHHHhhCCchHHHHHHHHHhChhhhhcChHhhCcc
Confidence 235566667787777 642 21 11 01110 122246799999
Q ss_pred cCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 315 LRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 315 LRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
||||||++++++|..++++..+|.|+||+|||||+
T Consensus 185 LRTHTTpgqirtL~~L~~~~~~PiRIFsIGRVfRr 219 (533)
T TIGR00470 185 LRSHMTSGWFITLSSIIDKRKLPLKLFSIDRCFRR 219 (533)
T ss_pred cccCChhHHHHHHHHHhhcCCCCeEEEeeeeEEec
Confidence 99999999999999877666689999999999996
No 12
>COG2024 Phenylalanyl-tRNA synthetase alpha subunit (archaeal type) [Translation, ribosomal structure and biogenesis]
Probab=99.41 E-value=5.8e-14 Score=138.11 Aligned_cols=144 Identities=28% Similarity=0.461 Sum_probs=107.9
Q ss_pred cccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCC-eeeecC-CC--CC
Q 018851 201 YNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHD-TFFLEE-PS--TT 276 (349)
Q Consensus 201 yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~D-TFyl~~-p~--~~ 276 (349)
-|-..|...+..|+.||+...|+++|+.+++|||.||- ||.|..+-..+-.. ..-|-..-| -|||.+ |. .+
T Consensus 32 ~~~~YPRl~f~~Gk~Hpl~~TIq~lReAYLr~GF~Emv-NPlivde~evykQF----GpEA~AVLDRCFYLagLPrPdVG 106 (536)
T COG2024 32 LDERYPRLKFETGKPHPLYETIQRLREAYLRMGFSEMV-NPLIVDEEEVYKQF----GPEALAVLDRCFYLAGLPRPDVG 106 (536)
T ss_pred ccccCCccccccCCcCcHHHHHHHHHHHHHHhhHHHhc-CccccCHHHHHHHh----ChHHHHHHHHHHHhcCCCCCCcC
Confidence 45667888889999999999999999999999999996 89998887766544 333456667 799987 32 21
Q ss_pred -------------CCCCHHHHHHHHHH-hhc--CC-CC-------------C--CCcc-----c-ccc--hhhhhccccC
Q 018851 277 -------------RELPEDYVERVKRV-HES--GG-YG-------------S--RGYG-----Y-EWK--REEANKNLLR 316 (349)
Q Consensus 277 -------------~~~p~~~~erVk~v-He~--Gg-~g-------------S--~Gw~-----Y-~W~--~~~a~~~vLR 316 (349)
.+.|.+-+++++++ |.. |. .| + .|-+ + .++ -.++..+.||
T Consensus 107 lg~eki~~i~~i~~d~~de~~e~lrevlh~YKKG~idGDdLv~eIa~aL~v~d~~~~~vle~vFPEfk~Lkp~s~tlTLR 186 (536)
T COG2024 107 LGAEKIEQIEEIGIDEPDEKVERLREVLHAYKKGEIDGDDLVHEIAEALEVDDGTGLRVLEEVFPEFKDLKPESSTLTLR 186 (536)
T ss_pred ccHHHHHHHHHhcCCCchhhHHHHHHHHHHHhcCCCCcchhHHHHHHHhccCcchHHHHHHHhChHHhhcCCCCCceehh
Confidence 35566668999988 632 21 11 1 1111 0 111 2347789999
Q ss_pred CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 317 THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 317 THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
+|+|+.+.-+|+.+..+..+|.|+|||||||||
T Consensus 187 SHMTsGWFItLs~i~~r~~~PlklFSIDRCFRR 219 (536)
T COG2024 187 SHMTSGWFITLSEILKREDPPLKLFSIDRCFRR 219 (536)
T ss_pred hhcccceeeeHHHHHhccCCCceeeehhHHhhh
Confidence 999999999999888776789999999999997
No 13
>KOG2783 consensus Phenylalanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=99.26 E-value=5e-12 Score=124.67 Aligned_cols=113 Identities=21% Similarity=0.432 Sum_probs=93.5
Q ss_pred CCCcccccccccccccCCCCCCCCCCChHHHHHHHHHHHHhhCC---ceecCCCCceeeeehhhhccCCCCCCCCCCCCC
Q 018851 190 KGDWKELEFKEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMG---FEEMPTNNFVESSFWNFDALFQPQQHPARDSHD 266 (349)
Q Consensus 190 sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mG---F~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~D 266 (349)
...|-|..++ ....-|...+.--.|||..+++.|.+.|..-+ |+..+.-++|++...|||.|++|.|||+|...|
T Consensus 48 ~d~~~Nv~~~--i~~~~gr~lh~~~~hplg~lr~~i~~~f~~~~~~~fs~~~~~spvvt~~qnfdsl~~p~dh~sr~ksd 125 (436)
T KOG2783|consen 48 TDAWSNVTPS--ILSLLGRNLHQKESHPLGILRQRIEDYFYKTYRNLFSIFENESPVVTTYQNFDSLLFPADHVSRSKSD 125 (436)
T ss_pred CcccccCChh--hhhhcccchhhhccCchhHHHHHHHHHHHHhhcccchhccCCCceeehhhhcccccCcccccccCcCC
Confidence 3456666643 34556788888889999999999999887754 676666678999999999999999999999999
Q ss_pred eeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCce
Q 018851 267 TFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSC 346 (349)
Q Consensus 267 TFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rV 346 (349)
|||++. ..+||+||+|+++..+++. --.+-..+.|
T Consensus 126 tyy~n~---------------------------------------~~~lr~htsahq~e~~~~~------~~~flv~~DV 160 (436)
T KOG2783|consen 126 TYYVNH---------------------------------------THCLRAHTSAHQHELFQKG------LDGFLVTGDV 160 (436)
T ss_pred ceeecc---------------------------------------eeeehhcchhhHHHHHHhc------ccccceeeee
Confidence 999986 6899999999999999753 3456677889
Q ss_pred ecC
Q 018851 347 FQK 349 (349)
Q Consensus 347 fR~ 349 (349)
|||
T Consensus 161 yrr 163 (436)
T KOG2783|consen 161 YRR 163 (436)
T ss_pred eee
Confidence 987
No 14
>PRK06253 O-phosphoseryl-tRNA synthetase; Reviewed
Probab=99.14 E-value=6.9e-11 Score=121.43 Aligned_cols=146 Identities=27% Similarity=0.401 Sum_probs=112.6
Q ss_pred cccccccCCCCCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCC-eeeecC-CCC-
Q 018851 199 KEYNFNAKGQPAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHD-TFFLEE-PST- 275 (349)
Q Consensus 199 k~yn~~~~~~~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~D-TFyl~~-p~~- 275 (349)
+..|-..|...+..|+.||+.++|+++|+..++|||+||- ||.|..+..-+-.. .|-|-..-| .|||.+ |..
T Consensus 30 ~~~~~~yp~~~~~~~~~hp~~~ti~~lr~ayl~~gf~e~~-np~iv~~~~~~~qf----g~ea~avldr~fyl~glprp~ 104 (529)
T PRK06253 30 PGLNERYPRLKPSYGKPHPVYDTIERLREAYLRMGFEEMI-NPVIVDEQDIYKQF----GPEAMAVLDRCFYLAGLPRPN 104 (529)
T ss_pred CCccccCCcccccCCCCCcHHHHHHHHHHHHHhcChHhhc-CceeecHHHHHHhh----CHHHHHHHHHhhhhcCCCCCC
Confidence 4466777888899999999999999999999999999996 89999988887776 677888889 899987 332
Q ss_pred ---------------CCCCCHHHHHHHHHH-hhc--CC-CC---------------CCCcc--------cccchhhhhcc
Q 018851 276 ---------------TRELPEDYVERVKRV-HES--GG-YG---------------SRGYG--------YEWKREEANKN 313 (349)
Q Consensus 276 ---------------~~~~p~~~~erVk~v-He~--Gg-~g---------------S~Gw~--------Y~W~~~~a~~~ 313 (349)
+.++.++-.|.++++ |.. |. .| +.+-. ++=-.++|...
T Consensus 105 vg~~~~~~~~i~~~~~~~~~~~~~e~l~~~lh~ykkg~~~gddl~~e~~~~l~~~~~~~~~~l~~vfpe~k~l~p~~~~s 184 (529)
T PRK06253 105 VGISDEKIEQIEEILGRDLSEEKIESLREVLHSYKKGEIDGDDLVLEISKALEVSDEMVLKILDEVFPEFKELKPESSRL 184 (529)
T ss_pred CCcCHHHHHHHHHHhCCCCChhHHHHHHHHHHHhhcCCCccchhHHHHHHhcCCChHHHHHHHHHhChHhhhcCCccccC
Confidence 135566667777777 642 21 11 01110 12224568899
Q ss_pred ccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 314 LLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 314 vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
+||||+++.....++.+..+...|.++|.+|||||+
T Consensus 185 vLRtSLlPGLL~tLs~Nl~Rg~~piRLFEIGRVFr~ 220 (529)
T PRK06253 185 TLRSHMTSGWFITLSSLLEKRPLPIKLFSIDRCFRR 220 (529)
T ss_pred ccccchHHHHHHHHHHHHhCCCCCEEEEEEeeEEec
Confidence 999999999999998776566689999999999974
No 15
>cd00496 PheRS_alpha_core Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.
Probab=98.98 E-value=1.7e-09 Score=100.37 Aligned_cols=92 Identities=48% Similarity=0.844 Sum_probs=80.6
Q ss_pred ChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
||+.++.+.||++|..+||.|+.+.+ ..+...+||.+..+.+||+|.+.++++|.+|-
T Consensus 1 ~~~~~~~~~ir~~L~~~Gf~Ev~tys-~~~~~~~~~~~~~~~~~~~~~~~~~v~l~NP~--------------------- 58 (218)
T cd00496 1 HPLNKVIEEIEDIFVSMGFTEVEGPE-VETDFYNFDALNIPQDHPARDMQDTFYINDPA--------------------- 58 (218)
T ss_pred ChHHHHHHHHHHHHHHCCCEEEeCCc-ccccchhhhhcCCCCCCcccccCceEEECCCc---------------------
Confidence 89999999999999999999998644 44655789999899999999999999999873
Q ss_pred CCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
..+|||++++.-.+.++.. ..|.|+|.||+|||+
T Consensus 59 ----------------~~~LR~sLlp~LL~~l~~N----~~~~~lFEiG~Vf~~ 92 (218)
T cd00496 59 ----------------RLLLRTHTSAVQARALAKL----KPPIRIFSIGRVYRN 92 (218)
T ss_pred ----------------eEEEeccCcHHHHHHHHhc----CCCeeEEEEcCeEEC
Confidence 3699999999999998754 468999999999974
No 16
>TIGR02367 PylS pyrrolysyl-tRNA synthetase. PylS is the archaeal enzyme responsible for charging the pyrrolysine tRNA, PylT, by ligating a free molecule of pyrrolysine. Pyrrolysine is encoded at an in-frame UAG (amber) at least in several corrinoid-dependent methyltransferases of the archaeal genera Methanosarcina and Methanococcoides, such as trimethylamine methyltransferase.
Probab=98.62 E-value=1.1e-07 Score=96.78 Aligned_cols=97 Identities=18% Similarity=0.236 Sum_probs=75.3
Q ss_pred CCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHH
Q 018851 210 AEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKR 289 (349)
Q Consensus 210 ~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~ 289 (349)
...|..||+..+.+.||++|..+||+|+. .|.+++. -.||.+..+++++ -.++.|.+.+
T Consensus 234 ~TiG~~~~~~~Led~IRevfvg~GFqEV~-TPtLt~e-E~~E~m~~~~g~e--I~n~Iyk~ee----------------- 292 (453)
T TIGR02367 234 YAEDREDYLGKLERDITKFFVDRGFLEIK-SPILIPA-EYIERMGIDNDTE--LSKQIFRVDK----------------- 292 (453)
T ss_pred cccCcccHHHHHHHHHHHHHHHCCCEEEE-CCeecch-HHHHhhcCccCCc--ccccceEecC-----------------
Confidence 47899999999999999999999999997 4777633 4478887776543 2345665532
Q ss_pred HhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 290 VHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 290 vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
..+||+..|+.-+|++......-..|.|+|+||+|||.
T Consensus 293 ----------------------~lvLRPdLTPsLaR~La~N~~~l~~PqKIFEIGkVFR~ 330 (453)
T TIGR02367 293 ----------------------NFCLRPMLAPNLYNYLRKLDRALPDPIKIFEIGPCYRK 330 (453)
T ss_pred ----------------------ceEecccCHHHHHHHHHHhhhhccCCeeEEEEcCeEec
Confidence 47999999999999886532222469999999999984
No 17
>PRK09616 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=98.56 E-value=3.5e-07 Score=95.95 Aligned_cols=160 Identities=19% Similarity=0.206 Sum_probs=104.5
Q ss_pred CCCCCH-HHHHHHhhcCceeeeEEEEEEEecCCCCCcchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCCh
Q 018851 139 GHALSK-EEISSLKARKLIVPQTWKGYSVRKGPNYAPKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHP 217 (349)
Q Consensus 139 g~~~~~-~~~~~LkkRkLi~~~~~~~~~i~kg~~~~~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HP 217 (349)
|..++. +..+.|++-|+-.......+.|+. +.+-..+. ...||-.|.+.---|.+-. -..|. ....|..||
T Consensus 289 G~~i~~~~i~~iL~~Lgf~~~~~~~~~~v~v-P~~R~DI~-~~~DliEEiaR~yGyd~i~-----~~~p~-~~~~~~~~~ 360 (552)
T PRK09616 289 GIDLSAEEIIELLERMRYDAEIGDDKVKVTV-PPYRVDIL-HEVDVIEDVAIAYGYNNLE-----PELPK-VFTIGRLHP 360 (552)
T ss_pred CCCCCHHHHHHHHHHcCCCcEecCCeEEEEe-CCCccccc-ccchHHHHHHHHhCcccCC-----ccCCC-CccCCCCCh
Confidence 334554 445677777774432222344421 11211211 1235555544422222211 12232 344588999
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
..++.+.+|++|.++||.|+-+.++ .+..+||+.++++.+|+ +.-|.+|-..
T Consensus 361 ~~~~~~~ir~~L~~~Gf~Ev~tys~-~s~~~~~~~~~~~~~~~------~i~l~NPls~--------------------- 412 (552)
T PRK09616 361 IEKLERAIRDLMVGLGFQEVMNFTL-TSEEVLFEKMNLEPEED------YVEVLNPISE--------------------- 412 (552)
T ss_pred HHHHHHHHHHHHHhCCcceeccceE-echHHHHHHhCCCCCCC------eEEEcCCCcc---------------------
Confidence 9999999999999999999986544 47788999998888873 5777776322
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
...+|||+.++...+.+.... +...|.++|.+|+||+
T Consensus 413 -------------e~svLRtsLlpgLL~~~~~N~-~~~~~~~lFEiG~Vf~ 449 (552)
T PRK09616 413 -------------DYTVVRTSLLPSLLEFLSNNK-HREYPQKIFEIGDVVL 449 (552)
T ss_pred -------------chheEeccchHHHHHHHHhcc-CCCCCeeEEEeeEEEe
Confidence 158999999999999998765 4457899999999996
No 18
>PRK09537 pylS pyrolysyl-tRNA synthetase; Reviewed
Probab=98.54 E-value=1.3e-07 Score=95.84 Aligned_cols=98 Identities=17% Similarity=0.231 Sum_probs=76.2
Q ss_pred CCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHH
Q 018851 209 PAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVK 288 (349)
Q Consensus 209 ~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk 288 (349)
....|..||+..+.+.||++|..+||+|+.| |.+++. ..|+.+..+.+++.++ +.|++++
T Consensus 197 ~~~~g~~~~~s~Le~aIR~~f~~~GF~EV~T-PtLt~e-e~~e~~g~~~g~~i~~--~my~ide---------------- 256 (417)
T PRK09537 197 MYEEDREDYLGKLERDITKFFVDRGFLEIKS-PILIPA-EYIERMGIDNDTELSK--QIFRVDK---------------- 256 (417)
T ss_pred hhccCCCCHHHHHHHHHHHHHHHCCCEEEEC-CeeecH-HHHHHhCCCCcccchh--hheeeCC----------------
Confidence 4567999999999999999999999999974 777644 3489988776655442 4466532
Q ss_pred HHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 289 RVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 289 ~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
..+||+..|+.-++++..+......|.|+|.||+|||.
T Consensus 257 -----------------------el~LRpsLtPsLlr~la~n~k~~~~P~RIFEIG~VFR~ 294 (417)
T PRK09537 257 -----------------------NFCLRPMLAPGLYNYLRKLDRILPDPIKIFEIGPCYRK 294 (417)
T ss_pred -----------------------ceEehhhhHHHHHHHHHhhhhcccCCeeEEEEeceEec
Confidence 47999999999888876543323369999999999985
No 19
>TIGR00442 hisS histidyl-tRNA synthetase. This model finds a histidyl-tRNA synthetase in every completed genome. Apparent second copies from Bacillus subtilis, Synechocystis sp., and Aquifex aeolicus are slightly shorter, more closely related to each other than to other hisS proteins, and actually serve as regulatory subunits for an enzyme of histidine biosynthesis. They were excluded from the seed alignment and score much lower than do single copy histidyl-tRNA synthetases of other genomes not included in the seed alignment. These putative second copies of HisS score below the trusted cutoff. The regulatory protein kinase GCN2 of Saccharomyces cerevisiae (YDR283c), and related proteins from other species designated eIF-2 alpha kinase, have a domain closely related to histidyl-tRNA synthetase that may serve to detect and respond to uncharged tRNA(his), an indicator of amino acid starvation; these regulatory proteins are not orthologous and so score below the noise cutoff.
Probab=97.84 E-value=3.6e-05 Score=77.03 Aligned_cols=100 Identities=14% Similarity=0.194 Sum_probs=68.3
Q ss_pred CCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCC--CCCeeeecCCCCCCCCCHHHHHH
Q 018851 209 PAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARD--SHDTFFLEEPSTTRELPEDYVER 286 (349)
Q Consensus 209 ~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd--~~DTFyl~~p~~~~~~p~~~~er 286 (349)
...+...+...++++.++++|..+||+++. .|.+|. +|.+.. ...+.-+ ...+|-+.+
T Consensus 8 d~~p~~~~~~~~i~~~i~~~f~~~Gy~~i~-~P~le~----~~~~~~-~~g~~~~~~~~~~~~~~d-------------- 67 (397)
T TIGR00442 8 DFLPEEMIKWQYIEETIREVFELYGFKEIR-TPIFEY----TELFAR-KVGEETDIVEKEMYTFKD-------------- 67 (397)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHcCCeEec-Ccccch----HHHhhh-ccCccccccccceEEEEC--------------
Confidence 345566788999999999999999999997 477755 233321 1111000 123454433
Q ss_pred HHHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 287 VKRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 287 Vk~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
...+..+||+++|+..+|++.+..+....|.|+|++++|||.
T Consensus 68 ---------------------~~g~~l~LRpD~T~~iaR~~~~~~~~~~~p~r~~y~g~vfR~ 109 (397)
T TIGR00442 68 ---------------------KGGRSLTLRPEGTAPVARAVIENKLLLPKPFKLYYIGPMFRY 109 (397)
T ss_pred ---------------------CCCCEEeecCCCcHHHHHHHHhcccccCCCeEEEEEcCeecC
Confidence 223478999999999999987543222358999999999994
No 20
>PRK00037 hisS histidyl-tRNA synthetase; Reviewed
Probab=97.74 E-value=5.1e-05 Score=76.24 Aligned_cols=98 Identities=15% Similarity=0.200 Sum_probs=68.1
Q ss_pred CCCCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCC-CCCCeeeecCCCCCCCCCHHHHHHH
Q 018851 209 PAEGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPAR-DSHDTFFLEEPSTTRELPEDYVERV 287 (349)
Q Consensus 209 ~~~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPAR-d~~DTFyl~~p~~~~~~p~~~~erV 287 (349)
...+...|.+..+++.++++|...||+++.+ |.+|. +|.+..-..|... ...++|-+.+
T Consensus 12 d~~p~~~~~~~~i~~~i~~~~~~~Gy~ei~t-P~le~----~~~~~~~~g~~~~~~~~~~~~~~d--------------- 71 (412)
T PRK00037 12 DILPEESAKWQYVEDTIREVFERYGFSEIRT-PIFEY----TELFKRKVGEETDIVEKEMYTFQD--------------- 71 (412)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHcCCeEeec-cccch----HHHhccccCcccccccceeEEEEc---------------
Confidence 4456677899999999999999999999974 66644 3433221122210 0123443333
Q ss_pred HHHhhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 288 KRVHESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 288 k~vHe~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
...+..+||+++|+..+|++.... . .|.|+|++|+|||.
T Consensus 72 --------------------~~g~~l~LRpd~T~~~ar~~~~~~--~-~p~r~~~~g~vfR~ 110 (412)
T PRK00037 72 --------------------KGGRSLTLRPEGTAPVVRAVIEHK--L-QPFKLYYIGPMFRY 110 (412)
T ss_pred --------------------CCCCEEEecCCCcHHHHHHHHhCC--C-CCeEEEEEcCcccc
Confidence 233578999999999999987432 2 69999999999994
No 21
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=97.64 E-value=0.00017 Score=57.27 Aligned_cols=65 Identities=23% Similarity=0.345 Sum_probs=52.8
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee-----eEEEEeChhHHHHhhc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK-----RETWVLTGEGKKYAAE 68 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~-----~~~~~LTeEG~~~l~~ 68 (349)
...||..|...+. .+..+|.+.+|++.+.+...++.|+..|||+++... .+.|.||++|++.+++
T Consensus 2 Rl~Il~~L~~~~~-~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~ 71 (80)
T PF13601_consen 2 RLAILALLYANEE-ATFSELKEELGLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFER 71 (80)
T ss_dssp HHHHHHHHHHHSE-EEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHH
T ss_pred HHHHHHHHhhcCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHH
Confidence 4578999988676 577899999999999999999999999999997653 5579999999998753
No 22
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=97.63 E-value=0.00013 Score=57.30 Aligned_cols=61 Identities=21% Similarity=0.260 Sum_probs=47.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
-..||..+...+ ....+++..+|+++..+...+.+|+++|+| ......|.||+.|+++++.
T Consensus 8 i~~IL~~l~~~~--~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI---~~~~~~Y~lTekG~~~l~~ 68 (77)
T PF14947_consen 8 IFDILKILSKGG--AKKTEIMYKANLNYSTLKKYLKELEEKGLI---KKKDGKYRLTEKGKEFLEE 68 (77)
T ss_dssp HHHHHHHH-TT---B-HHHHHTTST--HHHHHHHHHHHHHTTSE---EEETTEEEE-HHHHHHHHH
T ss_pred HHHHHHHHHcCC--CCHHHHHHHhCcCHHHHHHHHHHHHHCcCe---eCCCCEEEECccHHHHHHH
Confidence 457899997333 466789999999999999999999999999 3367799999999999864
No 23
>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=97.63 E-value=0.00022 Score=59.65 Aligned_cols=72 Identities=17% Similarity=0.185 Sum_probs=60.2
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee----eeEEEEeChhHHHHhhcCChHHH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI----KRETWVLTGEGKKYAAEGSPEVQ 74 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~----~~~~~~LTeEG~~~l~~G~PE~r 74 (349)
.+..||..|...+. .+..++|..+|++...+.+.+..|+.+|+|..... -...+.||++|+++++.-.|..+
T Consensus 29 ~q~~iL~~l~~~~~-~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~~~~~~~ 104 (118)
T TIGR02337 29 QQWRILRILAEQGS-MEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYASLSPQIE 104 (118)
T ss_pred HHHHHHHHHHHcCC-cCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHHhhHHHH
Confidence 35679999987776 56789999999999999999999999999998642 34589999999999987666443
No 24
>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=97.57 E-value=0.00026 Score=52.98 Aligned_cols=60 Identities=18% Similarity=0.277 Sum_probs=46.3
Q ss_pred HHHHHHHHHh-hCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee----eEEEEeChhH
Q 018851 2 AEEAILGYLE-KNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK----RETWVLTGEG 62 (349)
Q Consensus 2 ~e~~iL~~L~-~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~----~~~~~LTeEG 62 (349)
.|..||..|. ..+. .+..+++..++++...+.+.++.|..+|+|+-.... ...|.||++|
T Consensus 4 ~q~~vL~~l~~~~~~-~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 4 PQWQVLRALAHSDGP-MTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHHHHT--TS--BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHHHHccCCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 3678899998 4444 567899999999999999999999999999665543 3589999998
No 25
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.46 E-value=0.00066 Score=58.74 Aligned_cols=88 Identities=13% Similarity=0.110 Sum_probs=66.8
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee----eeEEEEeChhHHHHhhcCChHH--HH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI----KRETWVLTGEGKKYAAEGSPEV--QL 75 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~----~~~~~~LTeEG~~~l~~G~PE~--rl 75 (349)
.+..||..|...+. .+..+||..++++...|.+.++.|+.+|+|.-+.. -...+.||++|++.++...++. .+
T Consensus 41 ~q~~vL~~l~~~~~-~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~~~~ 119 (144)
T PRK11512 41 AQFKVLCSIRCAAC-ITPVELKKVLSVDLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICEQCHQLVGQDL 119 (144)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHHHHHHHHHHHH
Confidence 36778988876655 56789999999999999999999999999987543 4457899999999998876653 34
Q ss_pred HHhcCcCCCCCHHHHHh
Q 018851 76 FLAVPAEGSISKDELQK 92 (349)
Q Consensus 76 ~~~l~~~g~~~~~el~~ 92 (349)
...+-+ + ++-+|+..
T Consensus 120 ~~~l~~-~-ls~ee~~~ 134 (144)
T PRK11512 120 HQELTK-N-LTADEVAT 134 (144)
T ss_pred HHHHHc-c-CCHHHHHH
Confidence 444432 2 56555543
No 26
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=97.43 E-value=0.00056 Score=54.02 Aligned_cols=66 Identities=20% Similarity=0.201 Sum_probs=56.6
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee----eeEEEEeChhHHHHhhc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI----KRETWVLTGEGKKYAAE 68 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~----~~~~~~LTeEG~~~l~~ 68 (349)
.+..||..|...+. .+..++|..+++++..|.+.++.|+++|+|..... ....+.||+.|.+++..
T Consensus 11 ~~~~il~~l~~~~~-~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 11 TQFLVLRILYEEGP-LSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHHHHHHHcCC-cCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 46789999987765 67789999999999999999999999999987644 44689999999998865
No 27
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=97.30 E-value=0.0012 Score=56.77 Aligned_cols=72 Identities=14% Similarity=0.138 Sum_probs=58.2
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee----eeEEEEeChhHHHHhhcCChHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI----KRETWVLTGEGKKYAAEGSPEVQ 74 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~----~~~~~~LTeEG~~~l~~G~PE~r 74 (349)
+..||..|...+...+..+||+.++++.+.|.+.+..|+.+|+|.-... -...+.||++|+++++...+-..
T Consensus 33 q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~~~~~~~~ 108 (144)
T PRK03573 33 HWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEVEAVIN 108 (144)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHHHHHHHHH
Confidence 5568888876543246689999999999999999999999999988643 34588999999999987666443
No 28
>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=97.29 E-value=0.00047 Score=52.30 Aligned_cols=57 Identities=19% Similarity=0.250 Sum_probs=49.6
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
.|.+|+..|...+. .+..++|+.+|++.+.|.+++++|+.+|+|.........|...
T Consensus 9 ~E~~vy~~Ll~~~~-~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a~ 65 (68)
T PF01978_consen 9 NEAKVYLALLKNGP-ATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRAV 65 (68)
T ss_dssp HHHHHHHHHHHHCH-EEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEEE
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEEe
Confidence 47889988876665 6789999999999999999999999999999988777777654
No 29
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=97.25 E-value=0.0017 Score=52.74 Aligned_cols=74 Identities=20% Similarity=0.199 Sum_probs=60.6
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee----eEEEEeChhHHHHhhcCChHHHHH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK----RETWVLTGEGKKYAAEGSPEVQLF 76 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~----~~~~~LTeEG~~~l~~G~PE~rl~ 76 (349)
.|..+|..|...+.+.. .++|+.++++.+.|.+.++.|+.+|+|...... ...+.||++|++.++.-.+....+
T Consensus 23 ~q~~~L~~l~~~~~~~~-~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~~~~~~ 100 (126)
T COG1846 23 PQYQVLLALYEAGGITV-KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLPAAQEL 100 (126)
T ss_pred HHHHHHHHHHHhCCCcH-HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhccHHHHH
Confidence 46778888888776321 699999999999999999999999999886653 448899999999998888844433
No 30
>cd00768 class_II_aaRS-like_core Class II tRNA amino-acyl synthetase-like catalytic core domain. Class II amino acyl-tRNA synthetases (aaRS) share a common fold and generally attach an amino acid to the 3' OH of ribose of the appropriate tRNA. PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. These enzymes are usually homodimers. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. The substrate specificity of this reaction is further determined by additional domains. Intererestingly, this domain is also found is asparagine synthase A (AsnA), in the accessory subunit of mitochondrial polymerase gamma and in the bacterial ATP phosphoribosyltransferase regulatory subunit HisZ.
Probab=97.15 E-value=0.001 Score=59.36 Aligned_cols=85 Identities=18% Similarity=0.256 Sum_probs=56.9
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCC
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGS 298 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS 298 (349)
..+.+.++++|.++||.|+.+ |.+++. ..++.+-. .| .....++ |..
T Consensus 3 ~~~~~~~r~~l~~~Gf~Ev~t-~~l~~~-~~~~~~~~---~~----~~~~~~~-~~~----------------------- 49 (211)
T cd00768 3 SKIEQKLRRFMAELGFQEVET-PIVERE-PLLEKAGH---EP----KDLLPVG-AEN----------------------- 49 (211)
T ss_pred HHHHHHHHHHHHHcCCEEeEc-ceecHH-HHHHHcCc---cH----hheeeee-cCC-----------------------
Confidence 568899999999999999974 555454 11222211 11 1223332 211
Q ss_pred CCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 299 RGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 299 ~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
....+||++.|..-.+++.... ...|.|+|.+|+|||.
T Consensus 50 -----------~~~~~LR~s~~~~l~~~~~~n~--~~~~~~lfeig~vfr~ 87 (211)
T cd00768 50 -----------EEDLYLRPTLEPGLVRLFVSHI--RKLPLRLAEIGPAFRN 87 (211)
T ss_pred -----------CCEEEECCCCcHHHHHHHHhhc--ccCCEEEEEEcceeec
Confidence 1257999999999999887543 3469999999999984
No 31
>cd00773 HisRS-like_core Class II Histidinyl-tRNA synthetase (HisRS)-like catalytic core domain. HisRS is a homodimer. It is responsible for the attachment of histidine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ. HisZ along with HisG catalyze the first reaction in histidine biosynthesis. HisZ is found only in a subset of bacteria and differs from HisRS in lacking a C-terminal anti-codon binding domain.
Probab=97.13 E-value=0.0018 Score=61.40 Aligned_cols=90 Identities=18% Similarity=0.278 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+++.++++|..-||+++.+ |.+| +.|.+..=..+.. ..++|-+.++.
T Consensus 5 ~~~l~~~l~~~f~~~Gy~~v~t-P~le----~~~~~~~~~~~~~--~~~~~~~~d~~----------------------- 54 (261)
T cd00773 5 RRYIEDTLREVFERYGYEEIDT-PVFE----YTELFLRKSGDEV--SKEMYRFKDKG----------------------- 54 (261)
T ss_pred HHHHHHHHHHHHHHcCCEEeec-ccee----eHHHhcccccccc--cceEEEEECCC-----------------------
Confidence 4678899999999999999974 5554 3444422112222 24577776532
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+..+||+..|..-+|++......-..|.|+|++++|||.
T Consensus 55 ------------g~~l~LRpd~T~~iaR~~a~~~~~~~~p~k~~y~g~vfR~ 94 (261)
T cd00773 55 ------------GRDLALRPDLTAPVARAVAENLLSLPLPLKLYYIGPVFRY 94 (261)
T ss_pred ------------CCEEEeCCCCcHHHHHHHHhcCccCCCCeEEEEEcCEEec
Confidence 1268999999999999887532211369999999999994
No 32
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=96.98 E-value=0.0017 Score=49.87 Aligned_cols=59 Identities=29% Similarity=0.340 Sum_probs=50.1
Q ss_pred HHHHHHHHHhhCCC-CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeCh
Q 018851 2 AEEAILGYLEKNEQ-ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60 (349)
Q Consensus 2 ~e~~iL~~L~~~~~-~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTe 60 (349)
.+.+||..|...+. ..+..+||+.+|++...|.+.+..|+..|+|.........|.++.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 57899999998765 257889999999999999999999999999987665446888764
No 33
>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=96.97 E-value=0.0031 Score=48.77 Aligned_cols=42 Identities=17% Similarity=0.229 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHhccCCcEEEEeee------eEEEEeChhHHHHhhc
Q 018851 27 GFDHNDVVNVIKSLHGFRYIDAQDIK------RETWVLTGEGKKYAAE 68 (349)
Q Consensus 27 g~~~~~v~~~~~~L~~kgli~~~~~~------~~~~~LTeEG~~~l~~ 68 (349)
.+++..|-.++..|+.+|+|+..... .+.|.||+.|++++++
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~E 75 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELRE 75 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHHH
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhcC
Confidence 57899999999999999999987665 7799999999998864
No 34
>PRK10870 transcriptional repressor MprA; Provisional
Probab=96.96 E-value=0.0036 Score=56.44 Aligned_cols=72 Identities=15% Similarity=0.185 Sum_probs=58.2
Q ss_pred HHHHHHHHhhC-CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee----eEEEEeChhHHHHhhcCChHHH
Q 018851 3 EEAILGYLEKN-EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK----RETWVLTGEGKKYAAEGSPEVQ 74 (349)
Q Consensus 3 e~~iL~~L~~~-~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~----~~~~~LTeEG~~~l~~G~PE~r 74 (349)
+..||..|... +...+..+||+.++++...+.+.+..|+.+|+|.-.... ...+.||++|++++++-.|...
T Consensus 57 q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~i~~~~~ 133 (176)
T PRK10870 57 LFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLREVLPPQH 133 (176)
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHH
Confidence 56788888643 222455799999999999999999999999999886553 3588999999999988777544
No 35
>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=96.96 E-value=0.0029 Score=52.44 Aligned_cols=70 Identities=19% Similarity=0.202 Sum_probs=56.3
Q ss_pred HHHHHHHHh----hCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee----eEEEEeChhHHHHhhcCChHH
Q 018851 3 EEAILGYLE----KNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK----RETWVLTGEGKKYAAEGSPEV 73 (349)
Q Consensus 3 e~~iL~~L~----~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~----~~~~~LTeEG~~~l~~G~PE~ 73 (349)
|..||..|. ..+. .+..++|..++++...|.+.+..|+.+|+|.-.... ...+.||++|++.++.-.+|.
T Consensus 27 q~~vL~~l~~~~~~~~~-~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~~~~~~~~~~ 104 (109)
T TIGR01889 27 ELLILYYLGKLENNEGK-LTLKEIIKEILIKQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRSKIESLISEI 104 (109)
T ss_pred HHHHHHHHHhhhccCCc-CcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHHHHHHHHHHH
Confidence 567888777 3344 577899999999999999999999999999864433 447899999999887766554
No 36
>TIGR00471 pheT_arch phenylalanyl-tRNA synthetase, beta subunit. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from eukaryotic cytosol, the Archaea, and spirochetes.
Probab=96.86 E-value=0.0023 Score=67.45 Aligned_cols=95 Identities=22% Similarity=0.295 Sum_probs=73.0
Q ss_pred CCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 211 EGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 211 ~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
..|..+|..++.+.+|+.|..+||.|+-+.+++ +.-.+|+.+..|.+ +..-|.+|-. +|
T Consensus 357 ~~~~~~~~~~~~~~ir~~L~~~Gf~E~itysf~-s~~~~~~~~~~~~~-------~~v~l~NPis-----~e-------- 415 (551)
T TIGR00471 357 TIGRLKPLNKVSDIIREIMVGLGFQEVIPLTLT-SEEVNFKRMRIEDN-------NDVKVANPKT-----LE-------- 415 (551)
T ss_pred ccCCcChHHHHHHHHHHHHHhCCceeeccceEc-cHHHHHHHhccCCC-------CcEEeCCCCc-----hh--------
Confidence 457899999999999999999999999876555 44466777755432 2355666632 22
Q ss_pred hhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 291 HESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 291 He~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
..+|||...+.-.+.++... +...|.++|-||+||.
T Consensus 416 ---------------------~s~lR~SLlp~LL~~~~~N~-~~~~~~~lFEiG~Vf~ 451 (551)
T TIGR00471 416 ---------------------YTIVRTSLLPGLLETLSENK-HHELPQKIFEIGDVVV 451 (551)
T ss_pred ---------------------hhHhHhhhHHHHHHHHHhcc-cCCCCeeEEEEEEEEE
Confidence 58999999999999988765 5557899999999993
No 37
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=96.78 E-value=0.0039 Score=43.99 Aligned_cols=45 Identities=24% Similarity=0.391 Sum_probs=39.6
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
.+.+||..|.+++. .+..++|+.+|++...|.+.++.|+.+|+|+
T Consensus 4 ~~~~Il~~l~~~~~-~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 4 TQRKILNYLRENPR-ITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHHCTT-S-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 46889999999887 6788999999999999999999999999985
No 38
>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=96.78 E-value=0.0042 Score=50.97 Aligned_cols=73 Identities=16% Similarity=0.140 Sum_probs=55.8
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHH--------hCCCHHHHHHHHHHhccCCcEEEEe------eeeEEEEeChhHHHHhh
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAE--------RGFDHNDVVNVIKSLHGFRYIDAQD------IKRETWVLTGEGKKYAA 67 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~--------~g~~~~~v~~~~~~L~~kgli~~~~------~~~~~~~LTeEG~~~l~ 67 (349)
++..||..|...+ ..-+++.+. ..+++.+|..++..|+.+|+|+... .....|.||+.|+++++
T Consensus 5 l~~~iL~~L~~~~--~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~ 82 (100)
T TIGR03433 5 LDLLILKTLSLGP--LHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLA 82 (100)
T ss_pred HHHHHHHHHhcCC--CCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHH
Confidence 5778999997543 355666654 3688999999999999999999842 12478999999999998
Q ss_pred cCChHHHHH
Q 018851 68 EGSPEVQLF 76 (349)
Q Consensus 68 ~G~PE~rl~ 76 (349)
+-.++.+-+
T Consensus 83 ~~~~~~~~~ 91 (100)
T TIGR03433 83 AETESWARL 91 (100)
T ss_pred HHHHHHHHH
Confidence 766655543
No 39
>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=96.77 E-value=0.0096 Score=43.83 Aligned_cols=63 Identities=19% Similarity=0.248 Sum_probs=51.9
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee-eEEEEeChhHHHHhh
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK-RETWVLTGEGKKYAA 67 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~-~~~~~LTeEG~~~l~ 67 (349)
.+..||..+...+ .+..++++.+|++...+.+++..|.++|+|...... ...|.+|+ |++++.
T Consensus 8 ~~~~il~~l~~~~--~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~ 71 (78)
T cd00090 8 TRLRILRLLLEGP--LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLA 71 (78)
T ss_pred HHHHHHHHHHHCC--cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHH
Confidence 3567888887665 578899999999999999999999999999876543 56899998 777653
No 40
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=96.76 E-value=0.0054 Score=56.19 Aligned_cols=73 Identities=18% Similarity=0.083 Sum_probs=60.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe----eeeEEEEeChhHHHHhhcCChHHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD----IKRETWVLTGEGKKYAAEGSPEVQLF 76 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~----~~~~~~~LTeEG~~~l~~G~PE~rl~ 76 (349)
|..||..|...+. .+..+||+.++++.+.+.+.+..|+.+|+|.-.. +-...+.||++|++.+++-.+...-+
T Consensus 47 q~~iL~~L~~~~~-itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~~l~~~~~~~ 123 (185)
T PRK13777 47 EHHILWIAYHLKG-ASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLLETMEEYDPE 123 (185)
T ss_pred HHHHHHHHHhCCC-cCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHHHHHHHHHH
Confidence 5678999987776 5678999999999999999999999999998753 34558899999999988766544433
No 41
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=96.71 E-value=0.006 Score=52.79 Aligned_cols=60 Identities=20% Similarity=0.257 Sum_probs=48.4
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
|+..+...+. ....++|..+++++.+|.+.++.|+.+|+|..+. ...+.||+.|+..+..
T Consensus 13 I~~l~~~~~~-~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~--~~~i~LT~~G~~~a~~ 72 (142)
T PRK03902 13 IYLLIEEKGY-ARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK--YRGLVLTPKGKKIGKR 72 (142)
T ss_pred HHHHHhcCCC-cCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec--CceEEECHHHHHHHHH
Confidence 4444544554 5778999999999999999999999999998543 3579999999997755
No 42
>PLN02265 probable phenylalanyl-tRNA synthetase beta chain
Probab=96.61 E-value=0.0041 Score=66.24 Aligned_cols=96 Identities=22% Similarity=0.257 Sum_probs=71.9
Q ss_pred CCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 211 EGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 211 ~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
..|..||+.++.+.+|+.|..+||.|+-+-..+ +.--||+.|+.|.+. .+..-|.+|-.. |
T Consensus 392 ~~g~~~~~~~~~~~iR~~l~~~Gf~Ev~t~sl~-s~~~~~~~~~~~~~~-----~~~v~I~NP~s~-----e-------- 452 (597)
T PLN02265 392 TVGKQQPLNQFSDLLRAEVAMAGFTEVLTWILC-SHKENFAMLNREDDG-----NSAVIIGNPRSA-----D-------- 452 (597)
T ss_pred cCCCCCHHHHHHHHHHHHHHHCCceeeeceeeC-ChHHHHHhhcCCccC-----CceEEECCCcch-----h--------
Confidence 458899999999999999999999999754333 444668887655321 123556676432 2
Q ss_pred hhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCcee
Q 018851 291 HESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCF 347 (349)
Q Consensus 291 He~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVf 347 (349)
..+|||.--..-..+++.....+. |.|+|-+|+||
T Consensus 453 ---------------------~~vlRtSLlPgLL~~l~~N~~~~~-p~klFEiG~V~ 487 (597)
T PLN02265 453 ---------------------FEVVRTSLLPGLLKTLGHNKDAPK-PIKLFEVSDVV 487 (597)
T ss_pred ---------------------HHHHHHhhHHHHHHHHHHhhcCCC-CeeEEEeEeEE
Confidence 479999988888888876654565 99999999999
No 43
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=96.56 E-value=0.009 Score=48.75 Aligned_cols=65 Identities=23% Similarity=0.347 Sum_probs=52.8
Q ss_pred HHHHHHHHhhC-CCCCChHHHHHHhCCCHHHHHHHHH----------HhccCCcEE--EEeeeeEEEEeChhHHHHhh
Q 018851 3 EEAILGYLEKN-EQISDSGNFAAERGFDHNDVVNVIK----------SLHGFRYID--AQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 3 e~~iL~~L~~~-~~~~~~~~la~~~g~~~~~v~~~~~----------~L~~kgli~--~~~~~~~~~~LTeEG~~~l~ 67 (349)
-.+||..|.+. +......++|...|.+++.|.+|+. ||-.-|||. .+..-.+.|.|||+|+.+++
T Consensus 11 R~~vl~~L~~~yp~~~~~~eIar~v~~~~snV~GaL~G~g~rY~~e~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~ 88 (90)
T PF07381_consen 11 RKKVLEYLCSIYPEPAYPSEIARSVGSDYSNVLGALRGDGKRYNKEDSLVGLGLVEEEEEKGGFKYYRLTEKGKRIAE 88 (90)
T ss_pred HHHHHHHHHHcCCCcCCHHHHHHHHCCCHHHHHHHHhcCCCCcCcchhHHHcCCeeEeeecCCeeEEEeChhhhhHHh
Confidence 46799999876 5556678999999999999999985 899999992 33334559999999999874
No 44
>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=96.54 E-value=0.0085 Score=54.98 Aligned_cols=66 Identities=21% Similarity=0.292 Sum_probs=56.0
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe------eeeEEEEeChhHHHHhhc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD------IKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~------~~~~~~~LTeEG~~~l~~ 68 (349)
...+||..|...+. .+..+||+.+|++...|.+.+..|+.+|+|.... +....|.||+.|+..+.+
T Consensus 2 tr~~IL~~L~~~~~-~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~~~~ 73 (203)
T TIGR02702 2 TKEDILSYLLKQGQ-ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQFPQ 73 (203)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhhccc
Confidence 45789999987776 6788999999999999999999999999998662 244578999999987754
No 45
>PRK12293 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=96.51 E-value=0.0095 Score=57.73 Aligned_cols=90 Identities=18% Similarity=0.231 Sum_probs=63.0
Q ss_pred CCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhc
Q 018851 214 HLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHES 293 (349)
Q Consensus 214 ~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~ 293 (349)
...-...+.+.++++|..-||+++.| |-+| .+|.+- +. ....+|-+.++.
T Consensus 18 e~~~~~~i~~~l~~vf~~~Gy~~I~t-P~lE----~~e~~~----~~--~~~~~y~~~D~~------------------- 67 (281)
T PRK12293 18 SAKLKREIENVASEILYENGFEEIVT-PFFS----YHQHQS----IA--DEKELIRFSDEK------------------- 67 (281)
T ss_pred HHHHHHHHHHHHHHHHHHcCCeEeec-ccee----ehhhhc----cc--chhceEEEECCC-------------------
Confidence 34456788899999999999999985 7775 224331 11 124566665531
Q ss_pred CCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 294 GGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 294 Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+--||++.+.......|.|+|++|.|||.
T Consensus 68 ----------------g~~l~LRpD~T~~iaR~~a~~~~~~~~p~r~~Y~g~vfR~ 107 (281)
T PRK12293 68 ----------------NHQISLRADSTLDVVRIVTKRLGRSTEHKKWFYIQPVFRY 107 (281)
T ss_pred ----------------CCEEEECCcCCHHHHHHHHHhcccCCCceeEEEeccEEec
Confidence 1368999999999999886432222358999999999993
No 46
>TIGR00443 hisZ_biosyn_reg ATP phosphoribosyltransferase, regulatory subunit. Apparant second copies of histidyl-tRNA synthetase, found in Bacillus subtilis, Synechocystis sp., Aquifex aeolicus, and others, are in fact a regulatory subunit of ATP phosphoribosyltransferase, and usually encoded by a gene adjacent to that encoding the catalytic subunit.
Probab=96.48 E-value=0.008 Score=58.71 Aligned_cols=90 Identities=21% Similarity=0.264 Sum_probs=63.4
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-...+++.++++|..-||+++.+ |.+|. +|.+ ..-.|+.+ .++|-+.++.
T Consensus 10 ~~~~i~~~l~~~~~~~Gy~~i~t-P~le~----~~~~-~~~~~~~~--~~~~~~~d~~---------------------- 59 (314)
T TIGR00443 10 RKEEIERQLQDVFRSWGYQEIIT-PTLEY----LDTL-SAGGGILN--EDLFKLFDSL---------------------- 59 (314)
T ss_pred HHHHHHHHHHHHHHHcCCeeccC-cchhh----HHHh-cccCCcch--hceEEEECCC----------------------
Confidence 46788999999999999999974 66544 3333 33344322 3577675532
Q ss_pred CCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+--+|+.....+....|.|+|++|+|||.
T Consensus 60 -------------g~~l~LRpD~T~~iaR~~~~~~~~~~~p~r~~y~g~VfR~ 99 (314)
T TIGR00443 60 -------------GRVLGLRPDMTTPIARAVSTRLRDRPLPLRLCYAGNVFRT 99 (314)
T ss_pred -------------CCEEeecCcCcHHHHHHHHHhcccCCCCeEEEEeceEeec
Confidence 1258999999999999876432222369999999999994
No 47
>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=96.46 E-value=0.0065 Score=55.76 Aligned_cols=59 Identities=19% Similarity=0.254 Sum_probs=52.1
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG 62 (349)
+..||..|...+. .+..++|+.+|++...+.+.+..|+.+|+|.........|.||+.|
T Consensus 145 ~~~IL~~l~~~g~-~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 145 ELKVLEVLKAEGE-KSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHcCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 5689999987665 5788999999999999999999999999999887556789999987
No 48
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=96.44 E-value=0.012 Score=48.16 Aligned_cols=67 Identities=19% Similarity=0.206 Sum_probs=54.7
Q ss_pred CHHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee------------------eEEEEeChhH
Q 018851 1 MAEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK------------------RETWVLTGEG 62 (349)
Q Consensus 1 ~~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~------------------~~~~~LTeEG 62 (349)
+++.+||..|..-+. ..+-.+|..++++.+.|..++..|+..|||+--.-. .+.|.||.+|
T Consensus 7 ~l~~~IL~hl~~~~~-Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~k~K~~~e~~~hHtYY~LTr~G 85 (92)
T PF10007_consen 7 PLDLKILQHLKKAGP-DYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGKTIKRSEAKFKPKKEVHKHHTYYRLTREG 85 (92)
T ss_pred hhHHHHHHHHHHHCC-CcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCcccchhhhhcccchhhhcCCceeeecHhH
Confidence 356789999988775 556779999999999999999999999999653322 3579999999
Q ss_pred HHHhhc
Q 018851 63 KKYAAE 68 (349)
Q Consensus 63 ~~~l~~ 68 (349)
+.+++.
T Consensus 86 ~~llR~ 91 (92)
T PF10007_consen 86 ELLLRE 91 (92)
T ss_pred HHHHhc
Confidence 988753
No 49
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=96.40 E-value=0.0084 Score=56.30 Aligned_cols=57 Identities=18% Similarity=0.256 Sum_probs=48.2
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhcCChHH
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAEGSPEV 73 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~G~PE~ 73 (349)
.+..+||+.++++.+.+.+.++.|+.+|+|+-+.. ....+.||+.|++.+++-..++
T Consensus 22 IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~ 79 (217)
T PRK14165 22 ISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADY 79 (217)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999976543 4468999999999996655554
No 50
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.37 E-value=0.017 Score=41.35 Aligned_cols=59 Identities=20% Similarity=0.219 Sum_probs=48.3
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe-eeeEEEEeCh-hHHHHh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD-IKRETWVLTG-EGKKYA 66 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~-~~~~~~~LTe-EG~~~l 66 (349)
||..|. .+. .+..++++.+|++...+.+++..|.++|+|.... .....|.+|+ .|.+.+
T Consensus 2 il~~l~-~~~-~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~ 62 (66)
T smart00418 2 ILKLLA-EGE-LCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLL 62 (66)
T ss_pred HHHHhh-cCC-ccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHH
Confidence 566776 444 5788999999999999999999999999999766 4456889999 776654
No 51
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=96.29 E-value=0.007 Score=49.79 Aligned_cols=43 Identities=28% Similarity=0.443 Sum_probs=37.6
Q ss_pred hCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhc
Q 018851 26 RGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAE 68 (349)
Q Consensus 26 ~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~ 68 (349)
++++-=.|+.++.||.|+|+|+..-. ..-.|.||+||.+||++
T Consensus 33 l~vpNL~V~k~mqSL~SrgyVke~faWrh~Yw~LT~eGIeyLR~ 76 (95)
T PF03501_consen 33 LNVPNLHVIKAMQSLKSRGYVKEQFAWRHYYWYLTNEGIEYLRE 76 (95)
T ss_dssp TSSBHHHHHHHHHHHHHCTSEEEEECTTEEEEEE-HHHHHHHHH
T ss_pred cCCCcHHHHHHHhcccchhhhcCeecceEEEEEEcchhHHHHHH
Confidence 47788889999999999999988777 67799999999999986
No 52
>PTZ00034 40S ribosomal protein S10; Provisional
Probab=96.28 E-value=0.0075 Score=51.73 Aligned_cols=50 Identities=20% Similarity=0.225 Sum_probs=41.3
Q ss_pred hCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhc--CChHHHH
Q 018851 26 RGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAE--GSPEVQL 75 (349)
Q Consensus 26 ~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~--G~PE~rl 75 (349)
++++--.|+.++.||.|+|+|+..-. ..-.|.||+||.+||++ ++|+..+
T Consensus 36 l~vpNL~Vik~mqSL~Srg~Vke~f~WrhyYw~LT~eGieyLR~yL~LP~eiv 88 (124)
T PTZ00034 36 LNVPNLHVMMLMRSLKSRGLVKEQFAWQHYYYYLTDEGIEYLRTYLHLPPDVF 88 (124)
T ss_pred cCCccHHHHHHHHccccCCceEEEEeeEEEEEEEchHHHHHHHHHhCCCcccC
Confidence 35666789999999999999988777 67799999999999987 3555543
No 53
>PRK12420 histidyl-tRNA synthetase; Provisional
Probab=96.15 E-value=0.018 Score=58.47 Aligned_cols=93 Identities=14% Similarity=0.168 Sum_probs=64.9
Q ss_pred CCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCC--CCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHh
Q 018851 214 HLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQ--PQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVH 291 (349)
Q Consensus 214 ~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~--PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vH 291 (349)
..+-...+.+.++++|..-||.++.+ |.+ .-+|.+.. ...... ...+|-+.++.
T Consensus 17 ~~~~~~~i~~~l~~~f~~~Gy~~i~t-P~l----E~~~~~~~~~~~~~~~--~~~~~~~~D~~----------------- 72 (423)
T PRK12420 17 EQVLRNKIKRALEDVFERYGCKPLET-PTL----NMYELMSSKYGGGDEI--LKEIYTLTDQG----------------- 72 (423)
T ss_pred HHHHHHHHHHHHHHHHHHcCCEeccc-ccc----chHHHHhcccCCCccc--ccceEEEecCC-----------------
Confidence 34456788899999999999999974 444 44555532 112211 24577776642
Q ss_pred hcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 292 ESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 292 e~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.++||.=.|+--||++.... ....|.|.|++|+|||.
T Consensus 73 ------------------g~~l~LRpD~T~~iaR~va~~~-~~~~p~r~~y~g~vfR~ 111 (423)
T PRK12420 73 ------------------KRDLALRYDLTIPFAKVVAMNP-NIRLPFKRYEIGKVFRD 111 (423)
T ss_pred ------------------CceecccccccHHHHHHHHhCc-CCCCCeeEEEEcceECC
Confidence 1358999999999999987532 22258999999999994
No 54
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=96.12 E-value=0.014 Score=51.91 Aligned_cols=60 Identities=20% Similarity=0.273 Sum_probs=48.8
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
|......++. ..+.++|+.+++++.+|...++.|+++|||+.+.. .-+.||+.|++.+..
T Consensus 15 Iy~l~~~~~~-~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y--~gi~LT~~G~~~a~~ 74 (154)
T COG1321 15 IYELLEEKGF-ARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPY--GGVTLTEKGREKAKE 74 (154)
T ss_pred HHHHHhccCc-ccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecC--CCeEEChhhHHHHHH
Confidence 4444444444 67789999999999999999999999999988764 468999999987744
No 55
>cd00670 Gly_His_Pro_Ser_Thr_tRS_core Gly_His_Pro_Ser_Thr_tRNA synthetase class II core domain. This domain is the core catalytic domain of tRNA synthetases of the subgroup containing glycyl, histidyl, prolyl, seryl and threonyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. These enzymes belong to class II aminoacyl-tRNA synthetases (aaRS) based upon their structure and the presence of three characteristic sequence motifs in the core domain. This domain is also found at the C-terminus of eukaryotic GCN2 protein kinase and at the N-terminus of the ATP phosphoribosyltransferase accessory subunit, HisZ and the accessory subunit of mitochondrial polymerase gamma (Pol gamma b) . Most class II tRNA synthetases are dimers, with this subgroup consisting of mostly homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=96.09 E-value=0.01 Score=54.58 Aligned_cols=95 Identities=13% Similarity=0.164 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+.+.+++.|...||.++.+ |.++ +.|.+ ....|-..-..+.|.+.++..
T Consensus 5 ~~~l~~~~~~~~~~~G~~ei~~-P~l~----~~~~~-~~~~~~~~~~~~~~~~~~~~~---------------------- 56 (235)
T cd00670 5 WRALERFLDDRMAEYGYQEILF-PFLA----PTVLF-FKGGHLDGYRKEMYTFEDKGR---------------------- 56 (235)
T ss_pred HHHHHHHHHHHHHHcCCEEEEC-CeEc----CHHHH-hhcCCcccchhhcCeeccCcc----------------------
Confidence 4678889999999999999974 5553 33333 223466555566777765310
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcC-CCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK-PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~-~~~p~k~fsi~rVfR~ 349 (349)
| ......+||.=+|..-++++...... ...|.|++.+++|||.
T Consensus 57 -------~--~~~~~~~LrP~~~~~i~~~~~~~~~~~~~lP~r~~~~g~~fR~ 100 (235)
T cd00670 57 -------E--LRDTDLVLRPAACEPIYQIFSGEILSYRALPLRLDQIGPCFRH 100 (235)
T ss_pred -------c--ccCCeEEEecCCCHHHHHHHhccCccchhcCeeeeeecccccC
Confidence 1 11235899988888888877643211 2469999999999995
No 56
>PRK12292 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=96.09 E-value=0.015 Score=58.61 Aligned_cols=92 Identities=23% Similarity=0.298 Sum_probs=63.7
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-...+.+.++++|...||.++.+ |.+| .+|.+..-..+..+ ..+|-+.++..
T Consensus 19 ~~~~i~~~l~~~f~~~Gy~~i~t-P~lE----~~e~~~~~~g~~~~--~~~~~f~d~~~--------------------- 70 (391)
T PRK12292 19 KIEEIRRRLLDLFRRWGYEEVIT-PTLE----YLDTLLAGGGAILD--LRTFKLVDQLS--------------------- 70 (391)
T ss_pred HHHHHHHHHHHHHHHcCCceeeC-cchh----hHHHHhccCCccch--hhhEEEeecCC---------------------
Confidence 45678899999999999999974 6664 34444322234333 34666654311
Q ss_pred CCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+--||++.+.......|.|+|++|.|||.
T Consensus 71 -------------g~~l~LRpD~T~~iaR~~a~~~~~~~~p~r~~y~g~vfR~ 110 (391)
T PRK12292 71 -------------GRTLGLRPDMTAQIARIAATRLANRPGPLRLCYAGNVFRA 110 (391)
T ss_pred -------------CCEEEECCCCcHHHHHHHHHhccCCCCCeEEEeeceeeec
Confidence 1268999999999999887543233469999999999994
No 57
>PRK12295 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=96.04 E-value=0.02 Score=57.71 Aligned_cols=88 Identities=14% Similarity=0.129 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
+..+.+.++++|...||.++.+ |.+|. +|.+..-...-.+ ..+|.+.++.
T Consensus 7 ~~~i~~~i~~~f~~~Gy~~I~t-P~lE~----~e~~~~~~g~~~~--~~~~~f~D~~----------------------- 56 (373)
T PRK12295 7 SAAAAEALLASFEAAGAVRVDP-PILQP----AEPFLDLSGEDIR--RRIFVTSDEN----------------------- 56 (373)
T ss_pred HHHHHHHHHHHHHHcCCEEeeC-Ccccc----HHHhhhccCchhh--cceEEEECCC-----------------------
Confidence 5678899999999999999974 55543 3443221111111 3467666532
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+--||+.... ....|.|+|++++|||.
T Consensus 57 ------------G~~l~LRpD~T~piaR~~~~~--~~~~p~R~~Y~g~VfR~ 94 (373)
T PRK12295 57 ------------GEELCLRPDFTIPVCRRHIAT--AGGEPARYAYLGEVFRQ 94 (373)
T ss_pred ------------CCEEeeCCCCcHHHHHHHHHc--CCCCCeEEEEEccEEEC
Confidence 125899999999999975432 23368999999999994
No 58
>PLN02530 histidine-tRNA ligase
Probab=96.02 E-value=0.019 Score=59.74 Aligned_cols=94 Identities=16% Similarity=0.223 Sum_probs=63.2
Q ss_pred CCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhc
Q 018851 214 HLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHES 293 (349)
Q Consensus 214 ~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~ 293 (349)
...-...+.+.++++|...||+++.| |.+|. +|.+ .-...+. ...++|-+.++.
T Consensus 83 ~~~~~~~i~~~~~~~~~~~Gy~~I~t-P~lE~----~el~-~~~~g~~-~~~~~y~f~D~~------------------- 136 (487)
T PLN02530 83 DMRLRNWLFDHFREVSRLFGFEEVDA-PVLES----EELY-IRKAGEE-ITDQLYNFEDKG------------------- 136 (487)
T ss_pred HHHHHHHHHHHHHHHHHHcCCEeccc-cccch----HHHh-ccccCcc-cccceEEEECCC-------------------
Confidence 34456788899999999999999985 66654 3333 2221221 123355444321
Q ss_pred CCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 294 GGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 294 Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+--||+..+.......|.|+|++|.|||.
T Consensus 137 ----------------g~~l~LRpD~T~~iaR~~~~~~~~~~~P~r~~y~g~vfR~ 176 (487)
T PLN02530 137 ----------------GRRVALRPELTPSLARLVLQKGKSLSLPLKWFAIGQCWRY 176 (487)
T ss_pred ----------------CCEEecCCCCcHHHHHHHHhcccccCCCeEEEEEcCEEcC
Confidence 2368999999999999987532222369999999999993
No 59
>PF13393 tRNA-synt_His: Histidyl-tRNA synthetase; PDB: 3HRI_E 3HRK_A 3LC0_A 1Z7N_A 1Z7M_D 3NET_A 1H4V_B 3OD1_A 4E51_B 3RAC_A ....
Probab=95.97 E-value=0.017 Score=55.84 Aligned_cols=88 Identities=19% Similarity=0.244 Sum_probs=60.0
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+.+.++++|..-||.++.+ |.+|.. -.|-.- ...+ ..++|.+.++. +
T Consensus 13 ~~~i~~~l~~~f~~~Gy~~i~~-P~le~~-~~~~~~----~~~~--~~~~~~~~D~~-G--------------------- 62 (311)
T PF13393_consen 13 RERIESKLREVFERHGYEEIET-PLLEYY-ELFLDK----SGED--SDNMYRFLDRS-G--------------------- 62 (311)
T ss_dssp HHHHHHHHHHHHHHTT-EE-B---SEEEH-HHHHCH----SSTT--GGCSEEEECTT-S---------------------
T ss_pred HHHHHHHHHHHHHHcCCEEEEC-CeEeec-HHhhhc----cccc--hhhhEEEEecC-C---------------------
Confidence 4578899999999999999985 777644 222221 1221 23778887642 1
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
+.+.||.=.|.--+|++....+ ...|.|+|++|+|||.
T Consensus 63 -------------~~l~LR~D~T~~iaR~~a~~~~-~~~~~r~~y~g~vfR~ 100 (311)
T PF13393_consen 63 -------------RVLALRPDLTVPIARYVARNLN-LPRPKRYYYIGPVFRY 100 (311)
T ss_dssp -------------SEEEE-SSSHHHHHHHHHHCCG-SSSSEEEEEEEEEEEE
T ss_pred -------------cEeccCCCCcHHHHHHHHHhcC-cCCCceEEEEcceeec
Confidence 2689999999999999986432 4579999999999994
No 60
>cd00769 PheRS_beta_core Phenylalanyl-tRNA synthetase (PheRS) beta chain core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer. While the alpha chain contains a catalytic core domain, the beta chain has a non-catalytic core domain.
Probab=95.94 E-value=0.0096 Score=54.23 Aligned_cols=87 Identities=18% Similarity=0.276 Sum_probs=61.4
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCC
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGS 298 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS 298 (349)
..+.+.+|++|..+||.|+-+-+.+... .+ +.+ ..+. .+..=|.+|-. +|
T Consensus 3 ~~~~~~ir~~L~~~G~~E~~tys~~~~~-~~-~~~----~~~~---~~~i~l~NPis-----~e---------------- 52 (198)
T cd00769 3 QKLERKLRRLLAGLGFQEVITYSLTSPE-EA-ELF----DGGL---DEAVELSNPLS-----EE---------------- 52 (198)
T ss_pred hHHHHHHHHHHHHCCCceeecccCCCHH-HH-Hhc----cCCC---CCeEEEcCCCc-----hh----------------
Confidence 4678899999999999999876665332 22 222 1111 13455666532 22
Q ss_pred CCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 299 RGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 299 ~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
..+|||...+.-.+.+.........|+++|-||+||.
T Consensus 53 -------------~~~lR~sLlp~LL~~~~~N~~~~~~~~~lFEiG~vf~ 89 (198)
T cd00769 53 -------------YSVLRTSLLPGLLDALARNLNRKNKPLRLFEIGRVFL 89 (198)
T ss_pred -------------HHHHHHHHHHHHHHHHHHHhcCCCCCEeEEEeEeEEe
Confidence 5799999999999988876555668999999999995
No 61
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=95.86 E-value=0.016 Score=46.30 Aligned_cols=50 Identities=16% Similarity=0.179 Sum_probs=42.7
Q ss_pred HHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCCh
Q 018851 20 GNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSP 71 (349)
Q Consensus 20 ~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~P 71 (349)
-++|+.+|++...|.+++..|+++|+|..... ..+.||+.|+..+..=.+
T Consensus 3 ~ela~~l~is~stvs~~l~~L~~~glI~r~~~--~~~~lT~~g~~~~~~~~~ 52 (96)
T smart00529 3 SEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY--RGITLTEKGRRLARRLLR 52 (96)
T ss_pred HHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC--CceEechhHHHHHHHHHH
Confidence 47899999999999999999999999998764 379999999998744333
No 62
>PRK11050 manganese transport regulator MntR; Provisional
Probab=95.82 E-value=0.032 Score=49.19 Aligned_cols=70 Identities=21% Similarity=0.246 Sum_probs=55.2
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHH
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFL 77 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~ 77 (349)
.|+.++...+. ....++|+.++++...|.+.+..|+++|+|.... ...+.||+.|+..+....+-.+.+.
T Consensus 41 ~I~~~l~~~~~-~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~--~~~v~LT~~G~~l~~~~~~~~~~le 110 (152)
T PRK11050 41 LIADLIAEVGE-ARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRP--YRGVFLTPEGEKLAQESRERHQIVE 110 (152)
T ss_pred HHHHHHHhcCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec--CCceEECchHHHHHHHHHHHHHHHH
Confidence 34556655554 5678999999999999999999999999997643 3468999999998877766555554
No 63
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=95.58 E-value=0.034 Score=49.11 Aligned_cols=67 Identities=22% Similarity=0.316 Sum_probs=57.3
Q ss_pred HHHHHhh--CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHH
Q 018851 6 ILGYLEK--NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLF 76 (349)
Q Consensus 6 iL~~L~~--~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~ 76 (349)
+|..+.+ ++. .|..-++++.+++.++++.++.-++.-|+|+.+.- -+.||++|++|++.+.+|++.+
T Consensus 17 LL~~l~n~fnGr-aDl~~L~~e~~vdidDL~piv~ta~~Lglv~~e~G---DiilT~~Gk~~v~~~~~erK~l 85 (157)
T COG4754 17 LLYVLNNIFNGR-ADLPYLEKEMEVDIDDLMPIVETASLLGLVTAESG---DIILTDEGKEYVESPIRERKEL 85 (157)
T ss_pred HHHHHHHHhCCc-ccchhHHHHhCCChhhHHHHHHHHHhcCceeccCC---CEEEehhhHHHHhCChHHHHHH
Confidence 4555554 444 78888999999999999999999999999998765 4689999999999999999865
No 64
>CHL00201 syh histidine-tRNA synthetase; Provisional
Probab=95.56 E-value=0.044 Score=56.00 Aligned_cols=95 Identities=11% Similarity=0.062 Sum_probs=63.7
Q ss_pred CChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCC-CCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhc
Q 018851 215 LHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQP-QQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHES 293 (349)
Q Consensus 215 ~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~P-qdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~ 293 (349)
..-...+.+.++++|...||.++.| |.+ ...|.+..- -+|-.-...++|-+.++.
T Consensus 18 ~~~~~~i~~~i~~~~~~~Gy~~I~T-P~~----E~~e~~~~~~G~~~~~~~~~my~~~d~~------------------- 73 (430)
T CHL00201 18 INYWQFIHDKALTLLSLANYSEIRT-PIF----ENSSLYDRGIGETTDIVNKEMYRFTDRS------------------- 73 (430)
T ss_pred HHHHHHHHHHHHHHHHHcCCeeecC-ccc----chHHHHhcccCCcccccccceEEEEcCC-------------------
Confidence 3457788899999999999999985 555 444544321 123211124566665421
Q ss_pred CCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhc-CCCCCceEEecCceecC
Q 018851 294 GGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAE-KPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 294 Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~-~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+.-||+...... ....|.|+|++|.|||.
T Consensus 74 ----------------g~~l~LRpd~T~~iaR~~~~~~~~~~~~p~R~~y~g~vfR~ 114 (430)
T CHL00201 74 ----------------NRDITLRPEGTAGIVRAFIENKMDYHSNLQRLWYSGPMFRY 114 (430)
T ss_pred ----------------CCEEEeCCCCcHHHHHHHHHccccccCCCeEEEEEcceecC
Confidence 12589999999999998643222 23468999999999994
No 65
>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=95.55 E-value=0.024 Score=41.25 Aligned_cols=50 Identities=22% Similarity=0.253 Sum_probs=43.0
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.|..+|..|...+. .+..++|+.+++++..+.+.++.|+.+|+|.-+...
T Consensus 4 ~q~~iL~~l~~~~~-~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 4 SQFRILRILYENGG-ITQSELAEKLGISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHHHHHSS-EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEeccCC
Confidence 36788999988877 567899999999999999999999999999887654
No 66
>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=95.55 E-value=0.05 Score=43.60 Aligned_cols=60 Identities=18% Similarity=0.204 Sum_probs=46.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHh-CCCHHHHHHHHHHhccCCcEEEEee----eeEEEEeChhHHHHh
Q 018851 5 AILGYLEKNEQISDSGNFAAER-GFDHNDVVNVIKSLHGFRYIDAQDI----KRETWVLTGEGKKYA 66 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~-g~~~~~v~~~~~~L~~kgli~~~~~----~~~~~~LTeEG~~~l 66 (349)
.||..|.. +. ....++.+.+ |++...+...++.|++.|+|.-... ....|.||+.|++.+
T Consensus 9 ~IL~~l~~-g~-~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 9 LILRALFQ-GP-MRFSELQRRLPGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHHTT-SS-EEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHHh-CC-CcHHHHHHhcchhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 57777776 33 4567888888 9999999999999999999977644 245899999999865
No 67
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=95.51 E-value=0.048 Score=51.97 Aligned_cols=73 Identities=19% Similarity=0.256 Sum_probs=61.5
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLF 76 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~ 76 (349)
...+||..|.....-....++|.++|+..|.|.-.++.|-..|+|+.+. .-.|++|.+|.+-+.+-+-|.|-|
T Consensus 11 t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~g--R~~Y~iTkkG~e~l~~~~~dlr~f 83 (260)
T COG1497 11 TRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEG--RGEYEITKKGAEWLLEQLSDLRRF 83 (260)
T ss_pred hHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecC--CeeEEEehhHHHHHHHHHHHHHHH
Confidence 3567888887653336778999999999999999999999999999843 458999999999998888888876
No 68
>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=95.48 E-value=0.04 Score=40.31 Aligned_cols=50 Identities=14% Similarity=0.193 Sum_probs=41.1
Q ss_pred HHHHHHHHHhhCCCC-CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 2 AEEAILGYLEKNEQI-SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~-~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
.+..||..|...+.- .+..+||+.++++++.|.+.++.|+++|||..+..
T Consensus 6 ~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 6 SQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 467899999877652 35789999999999999999999999999987654
No 69
>cd00771 ThrRS_core Threonyl-tRNA synthetase (ThrRS) class II core catalytic domain. ThrRS is a homodimer. It is responsible for the attachment of threonine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=95.48 E-value=0.044 Score=53.30 Aligned_cols=90 Identities=12% Similarity=0.125 Sum_probs=60.4
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-...+.+.+++.|..-||+++.+ |.+ -+.|.+.. ..|-..-..+.|.+....
T Consensus 32 l~~~l~~~~~~~~~~~Gy~ev~t-P~l----~~~~l~~~-sg~~~~~~~~my~~~~~~---------------------- 83 (298)
T cd00771 32 IRNELEDFLRELQRKRGYQEVET-PII----YNKELWET-SGHWDHYRENMFPFEEED---------------------- 83 (298)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEC-Cee----cCHHHHhh-CCCccccccCceEeccCC----------------------
Confidence 35778888899999999999975 555 34454444 466555455678874310
Q ss_pred CCCCcccccchhhhhccccCCCCchhHHHHHHHhh--cCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALA--EKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~--~~~~~p~k~fsi~rVfR~ 349 (349)
+.++||+ |++..+..++... +...-|.|++.++.|||.
T Consensus 84 --------------~~l~LRP-~~~~~~~~~~~~~~~s~~~LPlr~~~~g~vfR~ 123 (298)
T cd00771 84 --------------EEYGLKP-MNCPGHCLIFKSKPRSYRDLPLRLAEFGTVHRY 123 (298)
T ss_pred --------------ceEEEcc-cCCHHHHHHHHhhccchhhCCeEEEEecCcccC
Confidence 2689999 6666654343221 112469999999999995
No 70
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=95.47 E-value=0.037 Score=48.37 Aligned_cols=65 Identities=17% Similarity=0.158 Sum_probs=48.9
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHH--------hCCCHHHHHHHHHHhccCCcEEEEe--eeeEEEEeChhHHHHhhcC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAE--------RGFDHNDVVNVIKSLHGFRYIDAQD--IKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~--------~g~~~~~v~~~~~~L~~kgli~~~~--~~~~~~~LTeEG~~~l~~G 69 (349)
+...||..|... . .-+++.+. +.+++.+|..++..|+.+|+|+... .....|.||+.|+++++.=
T Consensus 44 ~~l~IL~lL~~~-~--yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~ 118 (135)
T PRK09416 44 ILLAILQLLMNE-K--TGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKA 118 (135)
T ss_pred HHHHHHHHHhCC-C--CHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHH
Confidence 456788888654 2 44555543 2357899999999999999998854 3467999999999988653
No 71
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=95.41 E-value=0.046 Score=46.87 Aligned_cols=67 Identities=25% Similarity=0.248 Sum_probs=51.3
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHH----h-C---CCHHHHHHHHHHhccCCcEEEEeee------eEEEEeChhHHHHhh
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAE----R-G---FDHNDVVNVIKSLHGFRYIDAQDIK------RETWVLTGEGKKYAA 67 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~----~-g---~~~~~v~~~~~~L~~kgli~~~~~~------~~~~~LTeEG~~~l~ 67 (349)
++..||..|.... ..-+++.+. . | .++..|...+..|+..|+|+..... ...|.||+.|++.+.
T Consensus 10 l~~~iL~~L~~~~--~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~ 87 (138)
T COG1695 10 LELLILSLLSEKP--SHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELA 87 (138)
T ss_pred HHHHHHHHHhcCC--chHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHH
Confidence 5677888887653 345565543 2 2 7899999999999999999986442 579999999999997
Q ss_pred cCC
Q 018851 68 EGS 70 (349)
Q Consensus 68 ~G~ 70 (349)
+-.
T Consensus 88 ~~~ 90 (138)
T COG1695 88 ELR 90 (138)
T ss_pred HHH
Confidence 644
No 72
>PRK12421 ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=95.41 E-value=0.048 Score=55.22 Aligned_cols=95 Identities=16% Similarity=0.250 Sum_probs=62.7
Q ss_pred CCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhh
Q 018851 213 GHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHE 292 (349)
Q Consensus 213 g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe 292 (349)
........+.+.++++|...||.++.| |.+| .+|.+-.-.....+ ..+|-+.++..+
T Consensus 19 ~e~~~~~~i~~~l~~~f~~~Gy~~I~t-P~~E----~~e~~~~~~g~~~~--~~~y~f~D~~~g---------------- 75 (392)
T PRK12421 19 EEAQKIERLRRRLLDLFASRGYQLVMP-PLIE----YLESLLTGAGQDLK--LQTFKLIDQLSG---------------- 75 (392)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCEEeeC-cchh----hHHHHhccCCccch--hceEEEEcCCCC----------------
Confidence 334557788999999999999999975 5553 33433111111111 236666653111
Q ss_pred cCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 293 SGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 293 ~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
+.+.||.=.|+--||+....... ..|.|+|++|.|||.
T Consensus 76 ------------------~~l~LRpD~T~~iaR~~a~~~~~-~~p~R~~Y~g~VfR~ 113 (392)
T PRK12421 76 ------------------RLMGVRADITPQVARIDAHLLNR-EGVARLCYAGSVLHT 113 (392)
T ss_pred ------------------cEEEECCcCCHHHHHHHHhhcCC-CCceEEEEeeeEEEc
Confidence 24779999999999987654222 359999999999983
No 73
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=95.39 E-value=0.044 Score=51.54 Aligned_cols=64 Identities=20% Similarity=0.296 Sum_probs=55.2
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee------eEEEEeChhHHHHh
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK------RETWVLTGEGKKYA 66 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~------~~~~~LTeEG~~~l 66 (349)
...+||..|...+. .+..++|+.+|++...|.+=+..|+++|+|.++... ...|.||+.|.+..
T Consensus 12 tr~~il~lL~~~g~-~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~~f 81 (218)
T COG2345 12 TRERILELLKKSGP-VSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGREQF 81 (218)
T ss_pred HHHHHHHHHhccCC-ccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchhhc
Confidence 35678888887776 688999999999999999999999999999998543 46899999999844
No 74
>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=95.38 E-value=0.029 Score=44.65 Aligned_cols=68 Identities=16% Similarity=0.151 Sum_probs=57.5
Q ss_pred HHHHHHHHHhh----CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 2 AEEAILGYLEK----NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 2 ~e~~iL~~L~~----~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
.++.||.+|-+ .+.+..+.++|+.+++++..|...+..|++.|||+-.....--+..|+.|-+++...
T Consensus 5 rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~~ 76 (78)
T PF03444_consen 5 RQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNRQ 76 (78)
T ss_pred HHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHccc
Confidence 36778877753 566678899999999999999999999999999987777777899999998887643
No 75
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=95.31 E-value=0.037 Score=40.93 Aligned_cols=46 Identities=17% Similarity=0.238 Sum_probs=41.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
...||..|...+. .+..++|+.+|++...|.+.+..|+..|+|.-.
T Consensus 2 ~~~Il~~l~~~~~-~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 2 QQQILELLKEKGK-VSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHHcCC-EEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 4679999998887 678999999999999999999999999997643
No 76
>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=95.27 E-value=0.079 Score=46.48 Aligned_cols=74 Identities=15% Similarity=0.171 Sum_probs=53.3
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHH------hCCCHHHHHHHHHHhccCCcEEEEee------eeEEEEeChhHHHHhhcC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAE------RGFDHNDVVNVIKSLHGFRYIDAQDI------KRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~------~g~~~~~v~~~~~~L~~kgli~~~~~------~~~~~~LTeEG~~~l~~G 69 (349)
++.-||..|...+ ..-+++.+. ..+++.+|..+++.|+..|+|..... ....|.||+.|++++..-
T Consensus 25 l~~~IL~~L~~~p--~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~ 102 (138)
T TIGR02719 25 LVPFLLLCLKDWN--LHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMC 102 (138)
T ss_pred HHHHHHHHHccCC--CCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHH
Confidence 4556888886543 234454432 25788899999999999999987432 247899999999999876
Q ss_pred ChHHHHHH
Q 018851 70 SPEVQLFL 77 (349)
Q Consensus 70 ~PE~rl~~ 77 (349)
..+.+.+.
T Consensus 103 ~~~w~~~~ 110 (138)
T TIGR02719 103 ANSFEHYQ 110 (138)
T ss_pred HHHHHHHH
Confidence 66655543
No 77
>COG0124 HisS Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=95.12 E-value=0.032 Score=57.32 Aligned_cols=97 Identities=21% Similarity=0.270 Sum_probs=63.8
Q ss_pred CCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhh
Q 018851 213 GHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHE 292 (349)
Q Consensus 213 g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe 292 (349)
.-......+.+.++++|...||.++.| |.+|. .+.+ +|..-| .++.+.
T Consensus 16 ~d~~~~~~i~~~~~~v~~~yGf~eI~T-PifE~----telf-------~r~~Ge--------~td~v~------------ 63 (429)
T COG0124 16 EDMALREYIESTIRKVFESYGFSEIRT-PIFEY----TELF-------ARKSGE--------ETDVVE------------ 63 (429)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCEeccC-ccccc----hhHh-------hhccCC--------cccccc------------
Confidence 344566789999999999999999986 65543 3332 121111 000000
Q ss_pred cCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 293 SGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 293 ~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
.=-|.|.-+-.+.+-||.-.||--+|++.........|.|+|++|.|||
T Consensus 64 -------kemY~F~Dkggr~laLRpe~Tapv~R~~~en~~~~~~p~k~yy~g~vfR 112 (429)
T COG0124 64 -------KEMYTFKDKGGRSLALRPELTAPVARAVAENKLDLPKPLKLYYFGPVFR 112 (429)
T ss_pred -------cceEEEEeCCCCEEEecccCcHHHHHHHHhccccccCCeeEEEecceec
Confidence 0113333344557999999999999998754333337999999999999
No 78
>COG5045 Ribosomal protein S10E [Translation, ribosomal structure and biogenesis]
Probab=94.99 E-value=0.046 Score=44.69 Aligned_cols=44 Identities=25% Similarity=0.477 Sum_probs=37.6
Q ss_pred HhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhc
Q 018851 25 ERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAE 68 (349)
Q Consensus 25 ~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~ 68 (349)
+++++--.|..++.+|-|+|+|+..-. ....|.||+||.+||++
T Consensus 34 el~ipNL~vika~qsl~S~GYvkt~~~W~~~YytLT~eGveyLRE 78 (105)
T COG5045 34 ELEIPNLHVIKAMQSLISYGYVKTIHVWRHSYYTLTPEGVEYLRE 78 (105)
T ss_pred ccCCCchHHHHHHHHHhhcceeEEEeeeeeeEEEecHHHHHHHHH
Confidence 357777789999999999999987655 66788999999999976
No 79
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=94.92 E-value=0.1 Score=41.02 Aligned_cols=62 Identities=13% Similarity=0.221 Sum_probs=49.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYA 66 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l 66 (349)
..||..|...+...+..++|+.+|++...|.+.+..|++.|+|.... ....|.|+.....+.
T Consensus 8 ~~Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~-~~~~y~l~~~~~~~~ 69 (91)
T smart00346 8 LAVLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG-QNGRYRLGPKVLELG 69 (91)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC-CCCceeecHHHHHHH
Confidence 46888888763347789999999999999999999999999998753 245788888765544
No 80
>PRK05638 threonine synthase; Validated
Probab=94.86 E-value=0.064 Score=54.99 Aligned_cols=65 Identities=22% Similarity=0.257 Sum_probs=53.5
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhC--CCHHHHHHHHHHhccCCcEEEE--eeeeEEEEeChhHHHHhhc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERG--FDHNDVVNVIKSLHGFRYIDAQ--DIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g--~~~~~v~~~~~~L~~kgli~~~--~~~~~~~~LTeEG~~~l~~ 68 (349)
....||..|.... ....++++.++ ++...|...++.|+..|||+.. +.....|.||+.|++++.+
T Consensus 372 ~r~~IL~~L~~~~--~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~Lt~~g~~~l~~ 440 (442)
T PRK05638 372 TKLEILKILSERE--MYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYKLTEKGRRLLEN 440 (442)
T ss_pred hHHHHHHHHhhCC--ccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEEECcHHHHHHHh
Confidence 3567999998654 46789999998 8899999999999999999874 2345589999999998753
No 81
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=94.77 E-value=0.078 Score=51.10 Aligned_cols=74 Identities=14% Similarity=0.190 Sum_probs=64.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPAE 82 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~ 82 (349)
++||.+|.+.. -+.+++-..++++..+|+..++.|...|||.-+ ...|.||+.|+-++++-.|=...++.+.++
T Consensus 16 k~lLllL~egP--kti~EI~~~l~vs~~ai~pqiKkL~~~~LV~~~---~~~Y~LS~~G~iiv~km~~ll~tl~v~e~n 89 (260)
T COG4742 16 KDLLLLLKEGP--KTIEEIKNELNVSSSAILPQIKKLKDKGLVVQE---GDRYSLSSLGKIIVEKMEPLLDTLEVFEEN 89 (260)
T ss_pred HHHHHHHHhCC--CCHHHHHHHhCCCcHHHHHHHHHHhhCCCEEec---CCEEEecchHHHHHHHHHHHHHHHHHHHhh
Confidence 56899998754 478999999999999999999999999999766 679999999999999998888888888643
No 82
>PHA02943 hypothetical protein; Provisional
Probab=94.71 E-value=0.15 Score=45.56 Aligned_cols=59 Identities=19% Similarity=0.276 Sum_probs=48.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYA 66 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l 66 (349)
.+||..| +.|. .++.++|+.+|+++.++...++-|+..|.|..-++ ....|.|.+ .+|+
T Consensus 14 ~eILE~L-k~G~-~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~~--day~ 73 (165)
T PHA02943 14 IKTLRLL-ADGC-KTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLDE--DAYT 73 (165)
T ss_pred HHHHHHH-hcCC-ccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEECh--HHHH
Confidence 4688888 4443 67889999999999999999999999999965444 677999999 4444
No 83
>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=94.70 E-value=0.037 Score=39.87 Aligned_cols=45 Identities=18% Similarity=0.217 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
..||.+|...+...+..++|+.+|++...+.+.+..|++.|+|.-
T Consensus 6 l~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 6 LRILEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 358888887776557889999999999999999999999999974
No 84
>PRK12294 hisZ ATP phosphoribosyltransferase regulatory subunit; Provisional
Probab=94.67 E-value=0.088 Score=50.98 Aligned_cols=88 Identities=14% Similarity=0.015 Sum_probs=57.7
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
.+.++.+.++++|..-||+++.+ |.+ .-+|.+-...... + +++|+.=.+..
T Consensus 9 ~~~~ie~~l~~~f~~~GY~~I~t-P~~----E~~d~~~~~~~~~--~-~~~~~~~~~~~--------------------- 59 (272)
T PRK12294 9 ALKESETAFLKYFNKADYELVDF-SVI----EKLDWKQLNHEDL--Q-QMGERSFWQHE--------------------- 59 (272)
T ss_pred HHHHHHHHHHHHHHHcCCeEeeC-Ccc----hhHHhhhccccch--h-hhheeeeecCC---------------------
Confidence 46789999999999999999975 544 3444431111111 1 33344322111
Q ss_pred CCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+-++||.=.|.--||+.... ...|.|++++|.|||.
T Consensus 60 -------------Gr~laLRpD~T~~iAR~~a~~---~~~~~Rl~Y~g~VfR~ 96 (272)
T PRK12294 60 -------------HQIYALRNDFTDQLLRYYSMY---PTAATKVAYAGLIIRN 96 (272)
T ss_pred -------------CCEEEEcCCCCHHHHHHHHhc---CCCCceEEEeccEecc
Confidence 236899999999999987532 1235699999999994
No 85
>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=94.62 E-value=0.1 Score=38.68 Aligned_cols=48 Identities=23% Similarity=0.257 Sum_probs=40.5
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
-.+||..|...+. .+..++|+.+|++.+.+..-++.|+..|+|+++..
T Consensus 12 R~~Il~~L~~~~~-~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 12 RLRILRLLASNGP-MTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHHHCST-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHhcCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 3578999955555 67889999999999999999999999999998764
No 86
>CHL00192 syfB phenylalanyl-tRNA synthetase beta chain; Provisional
Probab=94.59 E-value=0.062 Score=58.47 Aligned_cols=88 Identities=16% Similarity=0.201 Sum_probs=68.2
Q ss_pred CCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 211 EGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 211 ~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
..|..+|..++.+.+|+.|..+||.|+-+-+++..++ + . .+..-|.+|-. +|
T Consensus 393 ~~~~~~~~~~~~~~ir~~L~~~Gf~Evitysf~s~~~------~-~--------~~~i~l~NPiS-----~e-------- 444 (704)
T CHL00192 393 FIGRLDIDYNTRDKIRSYLRNLGLTELIHYSLVKQES------F-S--------KNEIKLKNPLI-----KD-------- 444 (704)
T ss_pred cCCCCCHHHHHHHHHHHHHHhCCCceEecccccChhh------c-C--------CCcEEEeCCCc-----hH--------
Confidence 4578899999999999999999999998777765543 1 1 02455666532 22
Q ss_pred hhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCcee
Q 018851 291 HESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCF 347 (349)
Q Consensus 291 He~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVf 347 (349)
..+|||...+.-.+.+.....++..+.++|-+|+||
T Consensus 445 ---------------------~s~lR~SLlpgLL~~~~~N~~r~~~~~rlFEiG~Vf 480 (704)
T CHL00192 445 ---------------------YSTLRSSLLPGLIEAVQENLKQGNSTLEGFEIGHVF 480 (704)
T ss_pred ---------------------HHHHHHHHHHHHHHHHHHHHhcCCCCEeEEEeeeeE
Confidence 589999999888888877655566899999999999
No 87
>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=94.52 E-value=0.12 Score=37.21 Aligned_cols=42 Identities=21% Similarity=0.307 Sum_probs=35.5
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCC
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFR 44 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg 44 (349)
+.+||..|...+...+..+||+.+|++...|.+.++.|++.|
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 568899995544447899999999999999999999999998
No 88
>cd00779 ProRS_core_prok Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from prokaryotes and from the mitochondria of eukaryotes.
Probab=94.51 E-value=0.028 Score=53.45 Aligned_cols=92 Identities=12% Similarity=0.210 Sum_probs=55.7
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-...+++.+++.|...||+++.+ |.++. .|.+ .-..|=..-..+.|.+.+..
T Consensus 33 l~~~i~~~~~~~~~~~G~~ei~~-P~l~~----~~~~-~~sg~~~~~~~emy~~~d~~---------------------- 84 (255)
T cd00779 33 VLKKIENIIREEMNKIGAQEILM-PILQP----AELW-KESGRWDAYGPELLRLKDRH---------------------- 84 (255)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEC-CccCC----HHHH-HhcCCccccCcccEEEecCC----------------------
Confidence 36788889999999999999975 66533 2222 11244333334577775421
Q ss_pred CCCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.|| |+++++++-+-....+...-|.|++.++.|||.
T Consensus 85 -------------~~~l~LrPt~e~~~t~~~~~~i~s~~~LPlr~~~~~~~FR~ 125 (255)
T cd00779 85 -------------GKEFLLGPTHEEVITDLVANEIKSYKQLPLNLYQIQTKFRD 125 (255)
T ss_pred -------------CCeEEEecCCcHHHHHHHHhccccHhhCCHHHHhCcceecC
Confidence 1257888 555444422211111222359999999999995
No 89
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=94.43 E-value=0.07 Score=40.84 Aligned_cols=60 Identities=17% Similarity=0.204 Sum_probs=46.9
Q ss_pred HHHHHHhhCCCCCChHHHHHHh---CCCH--HHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHh
Q 018851 5 AILGYLEKNEQISDSGNFAAER---GFDH--NDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYA 66 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~---g~~~--~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l 66 (349)
.||..|.+.+.+.....+++.+ |.+. ++|-+-++.|+..|++.- .-..-..||+.|.+.|
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~--~g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRK--VGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccc--cCCcccccCHHHHhhC
Confidence 4899999888878888888765 5554 889999999999997763 3333568999998754
No 90
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=94.41 E-value=0.11 Score=49.82 Aligned_cols=97 Identities=15% Similarity=0.136 Sum_probs=57.1
Q ss_pred ChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
.-+.++.+.+++.|...||+++.+ |.++. -+.+.-=-+||.-...+.|.+.+....
T Consensus 33 ~i~~~I~~~i~~~~~~~G~~ev~~-P~l~~----~~~~~~~g~~~~~~~~e~~~~~~~~~~------------------- 88 (264)
T cd00772 33 AILDKIENVLDKMFKEHGAQNALF-PFFIL----ASFLEKEAEHDEGFSKELAVFKDAGDE------------------- 88 (264)
T ss_pred HHHHHHHHHHHHHHHHcCCeEEEC-Ceecc----HHHHhhcCCcccccCccceEEEeCCCC-------------------
Confidence 347788888888999999999974 55543 232221124443232456777542100
Q ss_pred CCCCCcccccchhhhhccccC-CCCchhHHHHHHHh-hcCCCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLR-THTTAVSSRMLKAL-AEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l-~~~~~~p~k~fsi~rVfR~ 349 (349)
+..+.+.|| |||+++. ++.... .+...-|.|++.++.|||.
T Consensus 89 ------------~~~~~l~LrPt~e~~~~-~~~~~~i~s~~~LPlrl~~~~~~fR~ 131 (264)
T cd00772 89 ------------ELEEDFALRPTLEENIG-EIAAKFIKSWKDLPQHLNQIGNKFRD 131 (264)
T ss_pred ------------ccCceEEECCCCCHHHH-HHHHhhhhhhhccCeeEEEEeCeEeC
Confidence 001257899 6666554 333321 1112359999999999995
No 91
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=94.35 E-value=0.073 Score=51.26 Aligned_cols=60 Identities=15% Similarity=0.234 Sum_probs=51.6
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeE-EEEeChh
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRE-TWVLTGE 61 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~-~~~LTeE 61 (349)
.|+.||+++..++....-.+|.+++|++...|.+.+..||.+|||+.++.-.+ .++|.++
T Consensus 196 ~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~~~ 256 (258)
T COG2512 196 DEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELRDK 256 (258)
T ss_pred HHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEEecc
Confidence 58899999999887667789999999999999999999999999999888554 6666554
No 92
>COG0072 PheT Phenylalanyl-tRNA synthetase beta subunit [Translation, ribosomal structure and biogenesis]
Probab=94.26 E-value=0.071 Score=57.54 Aligned_cols=91 Identities=20% Similarity=0.238 Sum_probs=69.6
Q ss_pred CChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcC
Q 018851 215 LHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESG 294 (349)
Q Consensus 215 ~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~G 294 (349)
.+++.++...+|+++..+||+|+-|...+ +..++++..+.+.+ .--|.+|-..
T Consensus 350 ~~~~~~~~r~vr~~l~~~G~~Evitysl~-s~e~~~~~~~~~~~--------~~~l~NPiS~------------------ 402 (650)
T COG0072 350 LTPLQKFRRKVRRALVGLGFQEVITYSLT-SPEEAKLFGLENDE--------ALELANPISE------------------ 402 (650)
T ss_pred CChHHHHHHHHHHHHHhCCcceEeeeccC-CHHHHHHhccCCCc--------ceEecCCcch------------------
Confidence 89999999999999999999999865444 77888888876655 5666666422
Q ss_pred CCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 295 GYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 295 g~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
...+|||=.=+.-...+........+-.++|-+|.||-
T Consensus 403 ----------------e~s~mR~sLlp~LL~~~~~N~~r~~~~~~iFEiG~v~~ 440 (650)
T COG0072 403 ----------------EYSVLRTSLLPGLLEALSYNKNRKNPDVRIFEIGDVFV 440 (650)
T ss_pred ----------------hHHHHHHHHHHHHHHHHHHhhccCCCCeeEEEeeeeEe
Confidence 25789987667667777655444444499999999995
No 93
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.15 E-value=0.12 Score=44.70 Aligned_cols=50 Identities=10% Similarity=0.118 Sum_probs=41.6
Q ss_pred HHHHHHHHHh-hCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 2 AEEAILGYLE-KNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 2 ~e~~iL~~L~-~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.+..++.+|- .++. .+.++||+.++.+.+.|.++++.|...|+|.-++..
T Consensus 28 ~Dv~v~~~LL~~~~~-~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 28 LDVEVYKALLEENGP-LTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHHHHHHHHhhcCC-cCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeec
Confidence 3556777776 4554 789999999999999999999999999999876654
No 94
>PRK09350 poxB regulator PoxA; Provisional
Probab=94.14 E-value=0.084 Score=51.74 Aligned_cols=36 Identities=22% Similarity=0.284 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCC
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQP 256 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~P 256 (349)
.+++..||++|.+.||.|+.| |.+ +.++++|+...|
T Consensus 9 ~~i~~~ir~~f~~~gf~EV~T-P~l-~~~~~~~~~~~~ 44 (306)
T PRK09350 9 AKIIAEIRRFFADRGVLEVET-PIL-SQATVTDIHLVP 44 (306)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-CeE-ecccCCCccCCc
Confidence 578899999999999999975 666 567888875433
No 95
>PLN02972 Histidyl-tRNA synthetase
Probab=94.11 E-value=0.14 Score=56.20 Aligned_cols=89 Identities=16% Similarity=0.141 Sum_probs=60.9
Q ss_pred CChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcC
Q 018851 215 LHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESG 294 (349)
Q Consensus 215 ~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~G 294 (349)
..-...+.+.++++|...||.++.| |.+| .+|.|.- ..-+ +...+|-+.++.
T Consensus 341 ~~~re~I~~~L~~vFk~hGy~eI~T-PvfE----~~Ell~~-k~Ge--d~k~mY~f~D~g-------------------- 392 (763)
T PLN02972 341 MAIREKAFSIITSVFKRHGATALDT-PVFE----LRETLMG-KYGE--DSKLIYDLADQG-------------------- 392 (763)
T ss_pred HHHHHHHHHHHHHHHHHcCCEEccC-Cccc----chHHhhc-ccCc--chhheEEEECCC--------------------
Confidence 3446678889999999999999975 6665 2343321 1111 113466665531
Q ss_pred CCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 295 GYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 295 g~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.+.||.=.|+--||++... ...|.|.|++|+|||+
T Consensus 393 ---------------Gr~LaLRPDlTvPiAR~vA~n---~~~p~KrYyiG~VFR~ 429 (763)
T PLN02972 393 ---------------GELCSLRYDLTVPFARYVAMN---GITSFKRYQIAKVYRR 429 (763)
T ss_pred ---------------CCEEEeCCCChHHHHHHHHhC---CCCcceEEEeccEEec
Confidence 136899999999999988642 2348899999999995
No 96
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=94.07 E-value=0.21 Score=34.67 Aligned_cols=46 Identities=13% Similarity=0.173 Sum_probs=40.4
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
+..||..|...+. .+..++++.++++...+.+.+..|+.+|+|...
T Consensus 2 ~~~il~~l~~~~~-~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~ 47 (53)
T smart00420 2 QQQILELLAQQGK-VSVEELAELLGVSEMTIRRDLNKLEEQGLLTRV 47 (53)
T ss_pred HHHHHHHHHHcCC-cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 5678888887665 688999999999999999999999999998754
No 97
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=94.05 E-value=0.11 Score=39.76 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=38.0
Q ss_pred HHHHHHHHhh----CCCCCChHHHHHHhCCC-HHHHHHHHHHhccCCcEEEEe
Q 018851 3 EEAILGYLEK----NEQISDSGNFAAERGFD-HNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 3 e~~iL~~L~~----~~~~~~~~~la~~~g~~-~~~v~~~~~~L~~kgli~~~~ 50 (349)
|.+||..+.+ .+..-+..|+|+.+|+. +..|...++.|+.||+|+-..
T Consensus 8 Q~~vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 8 QKEVLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 6778877754 55555778999999996 999999999999999998654
No 98
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=94.00 E-value=0.041 Score=42.26 Aligned_cols=59 Identities=24% Similarity=0.306 Sum_probs=45.5
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCC--CHHHHHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGF--DHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~--~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
+|.+||.+|.+.+. ...-.+|...|+ +..+|.+.+..|+.+|.|..+...--.|.||++
T Consensus 5 ~ee~Il~~L~~~g~-~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~PP~W~l~~~ 65 (66)
T PF02295_consen 5 LEEKILDFLKELGG-STATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGTPPKWSLTEK 65 (66)
T ss_dssp HHHHHHHHHHHHTS-SEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSSSTEEEE-HC
T ss_pred HHHHHHHHHHhcCC-ccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCCCCceEeccC
Confidence 68899999998773 455556665555 479999999999999999877766668888864
No 99
>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=93.94 E-value=0.15 Score=38.96 Aligned_cols=47 Identities=23% Similarity=0.348 Sum_probs=38.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
.+|+..|...+. .+..+||..++++++.|...+.-|..+|+|.-...
T Consensus 3 ~~i~~~l~~~~~-~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRERGR-VSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHHS-S-EEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHHcCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecC
Confidence 467888888886 78899999999999999999999999999975543
No 100
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=93.89 E-value=0.1 Score=55.23 Aligned_cols=91 Identities=12% Similarity=0.207 Sum_probs=54.6
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-+..+.+.+++.|...||+++.+ |.++.. +.+ .--.|=.--..+.|.+.+..
T Consensus 49 ~~~~i~~~i~~~~~~~G~~ei~~-P~l~~~----~l~-~~sg~~~~~~~emf~~~d~~---------------------- 100 (565)
T PRK09194 49 VLRKIENIVREEMNKIGAQEVLM-PALQPA----ELW-QESGRWEEYGPELLRLKDRH---------------------- 100 (565)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEC-cccCcH----HHH-hhcCCccccchhceEEecCC----------------------
Confidence 36788889999999999999975 665422 111 11233222222466665421
Q ss_pred CCCCcccccchhhhhccccC-CCCchhHHHHHHHhh-cCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALA-EKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~-~~~~~p~k~fsi~rVfR~ 349 (349)
.+...|| ||+..+. .+..... +-..-|.|+|.++.|||.
T Consensus 101 -------------~~~l~LrPt~e~~~~-~~~~~~~~s~~~LP~r~yqi~~~fR~ 141 (565)
T PRK09194 101 -------------GRDFVLGPTHEEVIT-DLVRNEIKSYKQLPLNLYQIQTKFRD 141 (565)
T ss_pred -------------CCEEEECCCChHHHH-HHHHhhhhhcccCCeEEEEeeCCccC
Confidence 1368999 5654333 3332221 112359999999999994
No 101
>PRK12305 thrS threonyl-tRNA synthetase; Reviewed
Probab=93.82 E-value=0.07 Score=56.29 Aligned_cols=94 Identities=13% Similarity=0.067 Sum_probs=57.9
Q ss_pred CChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcC
Q 018851 215 LHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESG 294 (349)
Q Consensus 215 ~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~G 294 (349)
..-.+.+.+.+++.|...||+++.| |.++. .|.+-. ..|=.--..+.|-+.+..
T Consensus 206 ~~~~~~l~~~~~~~~~~~Gy~ev~t-P~le~----~~l~~~-sg~~~~~~~~my~~~d~~-------------------- 259 (575)
T PRK12305 206 AIIRREIEDYLRKEHLKRGYEFVYT-PHIGK----SDLWKT-SGHLDNYKENMFPPMEID-------------------- 259 (575)
T ss_pred HHHHHHHHHHHHHHHHHcCCEEEEC-CccCC----HHHHhh-cCCcccchhhcccccccC--------------------
Confidence 3457889999999999999999975 55543 333322 344222223455553210
Q ss_pred CCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhc-CCCCCceEEecCceecC
Q 018851 295 GYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAE-KPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 295 g~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~-~~~~p~k~fsi~rVfR~ 349 (349)
.+...||.-||+.-+|+...... ....|.|++.+|+|||.
T Consensus 260 ---------------~~~~~LRP~~~~~~~~~~~~~~~s~~~lP~r~~~~g~~fR~ 300 (575)
T PRK12305 260 ---------------EEEYYLKPMNCPGHILIYKSRLRSYRDLPLRLAEFGTVYRY 300 (575)
T ss_pred ---------------CceEEEecCCCHHHHHHHhcccCChhhCCHhhEEecccccC
Confidence 13689999444444566543211 12359999999999994
No 102
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=93.72 E-value=0.1 Score=43.04 Aligned_cols=63 Identities=19% Similarity=0.183 Sum_probs=46.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee-eEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK-RETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~-~~~~~LTeEG~~~l~~ 68 (349)
..||++..+.+. ..--+.-..++++.-....++.|.++|+|...... ...|.||+.|++.+++
T Consensus 21 ~dIL~~~~~~~~--~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~ 84 (95)
T COG3432 21 FDILKAISEGGI--GITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEK 84 (95)
T ss_pred HHHHHHhcCCCC--CceeeeeecCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHH
Confidence 456776433332 23346666799999999999999999977665554 5599999999998654
No 103
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=93.71 E-value=0.11 Score=54.98 Aligned_cols=109 Identities=19% Similarity=0.314 Sum_probs=76.5
Q ss_pred HHHHHHHHHhhCCCCCChHHHHH----HhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHH--hhcCChH---
Q 018851 2 AEEAILGYLEKNEQISDSGNFAA----ERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKY--AAEGSPE--- 72 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~----~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~--l~~G~PE--- 72 (349)
.|..||..+-..+. ...+++.+ ..|.+...+..|+.+|+++|+|++=. ...+.||+-|+.+ +-.|-|+
T Consensus 433 ~E~~vl~kiP~~~~-i~~~~~~e~~~d~~~~ee~~i~~AL~kLEArGfI~~Lp--~g~iilTeaG~~ik~Alsg~p~~e~ 509 (591)
T PF04458_consen 433 YEMEVLHKIPDKGY-IHREELVEFIKDHVGKEEEEIIEALEKLEARGFIEILP--NGMIILTEAGELIKRALSGVPEQEI 509 (591)
T ss_pred HHHHHHHhCCcccc-ccHHHHHHHhhcccccchHHHHHHHHHHHhcchHHHcC--CCcEEEehhhHHHHHHHhcCCcccc
Confidence 35677777766664 23445444 46778889999999999999987644 5678999999864 5578888
Q ss_pred -----------HHHHHhcCcCCCC------------CHHHHHhh--cCchhhhhHHHHHhhCCcEe
Q 018851 73 -----------VQLFLAVPAEGSI------------SKDELQKK--LDPAVFKIGCSQAGKNKWVE 113 (349)
Q Consensus 73 -----------~rl~~~l~~~g~~------------~~~el~~~--~~~~~~~ig~g~~~k~~wi~ 113 (349)
+||+++|.+.|.. .++++.+. +++++++-++..|+..|.|.
T Consensus 510 ~g~~~PVtP~~~rVL~Ai~~~g~lyvKe~KvRi~pk~~ke~~K~sgL~~e~f~kaL~~aR~~~~iG 575 (591)
T PF04458_consen 510 LGFGFPVTPTIYRVLKAIREVGTLYVKEKKVRILPKNIKEAIKLSGLTPEEFKKALEVAREAGFIG 575 (591)
T ss_pred cccCCCCCHHHHHHHHHHHHhhhhhhhhhhhhcCccchHHHHHhcCCCHHHHHHHHHHHHHhcccc
Confidence 8888888654422 33445443 45666777777777777764
No 104
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.65 E-value=0.15 Score=41.61 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=41.2
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
++.+||..|..++. .+..++|+.+|+++..+.+.+..|+++|+|.
T Consensus 4 ~D~~il~~L~~~~~-~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 4 IDRKILEELQKDAR-ISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHhCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 57889999998776 6778999999999999999999999999998
No 105
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=93.63 E-value=0.28 Score=41.91 Aligned_cols=60 Identities=17% Similarity=0.155 Sum_probs=48.2
Q ss_pred HHHHHHhhCCCCCChHHHHHHhC-CCHHHHHHHHHHhccCCcEEEEeee----eEEEEeChhHHHHh
Q 018851 5 AILGYLEKNEQISDSGNFAAERG-FDHNDVVNVIKSLHGFRYIDAQDIK----RETWVLTGEGKKYA 66 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g-~~~~~v~~~~~~L~~kgli~~~~~~----~~~~~LTeEG~~~l 66 (349)
.||..|.. +. .-..+|...++ +++..+.+-++.|+..|+|.-+.-. ...|.||+.|+...
T Consensus 27 lIl~~L~~-g~-~RF~eL~r~i~~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~ 91 (120)
T COG1733 27 LILRDLFD-GP-KRFNELRRSIGGISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLL 91 (120)
T ss_pred HHHHHHhc-CC-CcHHHHHHHccccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHH
Confidence 46666765 32 34568887776 9999999999999999999876664 77999999999854
No 106
>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=93.52 E-value=0.13 Score=36.34 Aligned_cols=43 Identities=21% Similarity=0.299 Sum_probs=37.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
-.+||.+|.++. .+..++++.+|++...|..-++.|+..|+|+
T Consensus 4 R~~Il~~L~~~~--~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 4 RLRILKLLSEGP--LTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp HHHHHHHHTTSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHhCC--CchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 357999998743 5788999999999999999999999999996
No 107
>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=93.42 E-value=0.3 Score=48.61 Aligned_cols=115 Identities=15% Similarity=0.157 Sum_probs=77.1
Q ss_pred HHHHHHHHHhhC--CCCCChHHHHHH-hCCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeC--hhHHHHhhcCChHHHH
Q 018851 2 AEEAILGYLEKN--EQISDSGNFAAE-RGFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLT--GEGKKYAAEGSPEVQL 75 (349)
Q Consensus 2 ~e~~iL~~L~~~--~~~~~~~~la~~-~g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LT--eEG~~~l~~G~PE~rl 75 (349)
++.+||..+... +...+.++|.+. .+++.+.++.++..|.+.|++.+-.... ..|.+- ++...+..--.-|..|
T Consensus 10 ~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e~lv 89 (327)
T PF05158_consen 10 LEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEERLV 89 (327)
T ss_dssp HHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE--SSS-----SSSCCHHHH
T ss_pred HHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHH
Confidence 678999999876 555667788777 6899999999999999999999877533 367665 4444433333347778
Q ss_pred HHhcCc--CCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeCc
Q 018851 76 FLAVPA--EGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 76 ~~~l~~--~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
|.+|.+ +.++-..+|+... ......-.+..+-.++.|+--+
T Consensus 90 y~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vk 134 (327)
T PF05158_consen 90 YQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVK 134 (327)
T ss_dssp HHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE-
T ss_pred HHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEec
Confidence 888864 3347789998774 3445666788888888887643
No 108
>PRK00629 pheT phenylalanyl-tRNA synthetase subunit beta; Reviewed
Probab=93.34 E-value=0.16 Score=56.00 Aligned_cols=94 Identities=16% Similarity=0.176 Sum_probs=68.0
Q ss_pred CCCCCChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 211 EGGHLHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 211 ~~g~~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
..|..++...+.+.+|+.|..+||.|+-+-.++.. ..+. .++ |.+ +..-|.+|-. +|
T Consensus 482 ~~~~~~~~~~~~~~ir~~L~~~Gf~Ev~tysf~~~-~~~~-~~~-~~~-------~~i~l~NPis-----~e-------- 538 (791)
T PRK00629 482 TMGGLTEAQRLLRRLRRALAALGYQEVITYSFVSP-EDAK-LFG-LNP-------EPLLLLNPIS-----EE-------- 538 (791)
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCcEEeccccCCH-HHHH-hcC-CCC-------CeEEEeCCCc-----hH--------
Confidence 44688999999999999999999999987655533 2222 232 221 2344666532 22
Q ss_pred hhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 291 HESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 291 He~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
..+|||.-...-.+.+.....+...+.++|-+|+||.
T Consensus 539 ---------------------~~~lR~SLlp~LL~~~~~N~~~~~~~i~lFEiG~Vf~ 575 (791)
T PRK00629 539 ---------------------LSVMRTSLLPGLLEAVAYNLNRGNKDVALFEIGRVFL 575 (791)
T ss_pred ---------------------HHHHHHhhHHHHHHHHHHHHhCCCCCEeEEeeeeeeC
Confidence 5899999888888888766545567999999999994
No 109
>PRK00413 thrS threonyl-tRNA synthetase; Reviewed
Probab=93.30 E-value=0.11 Score=55.38 Aligned_cols=93 Identities=10% Similarity=0.085 Sum_probs=57.1
Q ss_pred ChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
.-...+.+.+++.|...||+++.| |.+| +.|.+-. ..|=.--..+.|.+.+.
T Consensus 271 ~~~~~i~~~~~~~~~~~Gy~ei~t-P~le----~~~l~~~-~g~~~~~~~~my~~~d~---------------------- 322 (638)
T PRK00413 271 TIRRELERYIRRKLRKAGYQEVKT-PQIL----DRELWET-SGHWDHYRENMFPTTES---------------------- 322 (638)
T ss_pred HHHHHHHHHHHHHHHHCCCEEEEC-CeeC----CHHHHHh-cCChhhhhhccceeecC----------------------
Confidence 346788889999999999999975 5553 3343322 12210001234444321
Q ss_pred CCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcC-CCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK-PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~-~~~p~k~fsi~rVfR~ 349 (349)
..+...||.-||+.-+|+..+.... ...|.|+|.+|.|||.
T Consensus 323 -------------~~~~~~LRP~~~~~~~r~~~~~~~s~~~lP~r~~~~g~~fR~ 364 (638)
T PRK00413 323 -------------DGEEYALKPMNCPGHVQIYKQGLRSYRDLPLRLAEFGTVHRY 364 (638)
T ss_pred -------------CCcEEEEecCCcHHHHHHHhCcCCChhhCCceeeeccCeecC
Confidence 1237999995556557776532211 1359999999999994
No 110
>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=93.22 E-value=0.21 Score=37.41 Aligned_cols=44 Identities=16% Similarity=0.182 Sum_probs=35.5
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
|..+-. .+....+.++|+.+|+++.+|...++.|+.+|||+.+.
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 444444 44447788999999999999999999999999999875
No 111
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=93.21 E-value=0.31 Score=44.35 Aligned_cols=58 Identities=24% Similarity=0.244 Sum_probs=47.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-------EEEEeChhH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-------ETWVLTGEG 62 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-------~~~~LTeEG 62 (349)
..||.+|..++. .+.++||..+|++..+|.+.+..|...|||....... ..|.||.+-
T Consensus 25 ~~Vl~~L~~~g~-~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~ 89 (178)
T PRK06266 25 FEVLKALIKKGE-VTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEK 89 (178)
T ss_pred hHHHHHHHHcCC-cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHH
Confidence 468898988776 6789999999999999999999999999999755333 356777654
No 112
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=93.15 E-value=0.18 Score=44.23 Aligned_cols=46 Identities=15% Similarity=0.215 Sum_probs=41.9
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
+..+||.+|..++. .+..++|+.+|++..+|.+-++.|++.|+|..
T Consensus 10 ~D~~Il~~Lq~d~R-~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 10 LDRGILEALMENAR-TPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHcCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 56789999998887 67789999999999999999999999999974
No 113
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=92.97 E-value=0.27 Score=45.65 Aligned_cols=64 Identities=17% Similarity=0.175 Sum_probs=52.0
Q ss_pred HHHHHHhhCCC----CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe-eeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQ----ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD-IKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~----~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~-~~~~~~~LTeEG~~~l~~ 68 (349)
++|+.|+..+. -.++.++|+.+|.+.+...+.+++|+..|+|+-+. ..-....+||.|.+.|.+
T Consensus 4 ~~lk~l~~~~a~~~~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~ 72 (214)
T COG1339 4 RLLKKLALRGAVRGVKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYK 72 (214)
T ss_pred HHHHHHHHhhhhcCccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHH
Confidence 56777765332 24578999999999999999999999999998766 455688999999999855
No 114
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=92.79 E-value=0.31 Score=46.39 Aligned_cols=62 Identities=16% Similarity=0.258 Sum_probs=51.2
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
.||..|...+...+..++|+.+|++...+.+.+..|++.|+|.-... ...|.||....++..
T Consensus 15 ~iL~~l~~~~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~-~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 15 MVLRALNRLDGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSAS-DDSFRLTLKVRQLSE 76 (263)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC-CCcEEEcHHHHHHHH
Confidence 57888876654467889999999999999999999999999986543 347999998877554
No 115
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=92.72 E-value=0.19 Score=48.63 Aligned_cols=66 Identities=18% Similarity=0.249 Sum_probs=55.1
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEV 73 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~ 73 (349)
+..|...|.+. ..+.++||+.+|+++..+.+.+..|.+-|+++.. ...|.+|+.+..++..++|.+
T Consensus 12 ~Lglfd~L~~g--p~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~---~~~y~~t~~~~~~l~~~~~~~ 77 (306)
T TIGR02716 12 ELDLFSHMAEG--PKDLATLAADTGSVPPRLEMLLETLRQMRVINLE---DGKWSLTEFADYMFSPTPKEP 77 (306)
T ss_pred HcCcHHHHhcC--CCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEec---CCcEecchhHHhhccCCccch
Confidence 44566677543 3688999999999999999999999999999864 368999999999998888753
No 116
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=92.60 E-value=0.24 Score=44.01 Aligned_cols=45 Identities=16% Similarity=0.310 Sum_probs=41.3
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
+..+||.+|..++. .+..++|+.+|++...|.+-++.|++.|+|.
T Consensus 15 ~D~~IL~~Lq~d~R-~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 15 IDRNILNELQKDGR-ISNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHhccCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 56889999998887 6678999999999999999999999999997
No 117
>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=92.54 E-value=0.36 Score=39.27 Aligned_cols=48 Identities=25% Similarity=0.210 Sum_probs=37.4
Q ss_pred HHHHHHHHhh-------CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 3 EEAILGYLEK-------NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 3 e~~iL~~L~~-------~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
+.++|..|.. .....+..+||+.+|++.+.|.+++..|+.+|+|..+.
T Consensus 27 ~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 27 EFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeec
Confidence 3456666652 22235678999999999999999999999999998654
No 118
>PHA00738 putative HTH transcription regulator
Probab=92.42 E-value=0.6 Score=39.38 Aligned_cols=66 Identities=18% Similarity=0.154 Sum_probs=52.9
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeChhHHHHhhcCChHHHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLTGEGKKYAAEGSPEVQLFL 77 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LTeEG~~~l~~G~PE~rl~~ 77 (349)
-.+||..|...+. ...-++++.++++...|.+=++-|+..|||..+..-. ..|.|.++ .|++++++
T Consensus 14 Rr~IL~lL~~~e~-~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~--------~~~~~l~~ 80 (108)
T PHA00738 14 RRKILELIAENYI-LSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIREN--------SKEIQILN 80 (108)
T ss_pred HHHHHHHHHHcCC-ccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCC--------ccHHHHHh
Confidence 3579999987654 4677899999999999999999999999999988844 47787765 55566553
No 119
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=92.37 E-value=0.15 Score=38.81 Aligned_cols=55 Identities=18% Similarity=0.302 Sum_probs=41.6
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee---eeEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI---KRETWVL 58 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~---~~~~~~L 58 (349)
.+||..|.....+.++.++|+.+|+++.++...+..|+..|.|..... ....|.|
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~l 60 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWRL 60 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEEE
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceeeee
Confidence 358899988333478899999999999999999999999999976442 3345655
No 120
>TIGR00472 pheT_bact phenylalanyl-tRNA synthetase, beta subunit, non-spirochete bacterial. Every known example of the phenylalanyl-tRNA synthetase, except the monomeric form of mitochondrial, is an alpha 2 beta 2 heterotetramer. The beta subunits break into two subfamilies that are considerably different in sequence, length, and pattern of gaps. This model represents the subfamily that includes the beta subunit from Bacteria other than spirochetes, as well as a chloroplast-encoded form from Porphyra purpurea. The chloroplast-derived sequence is considerably shorter at the amino end, however.
Probab=92.35 E-value=0.25 Score=54.51 Aligned_cols=95 Identities=16% Similarity=0.215 Sum_probs=64.9
Q ss_pred CCCCChHHHHH-HHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 212 GGHLHPLLKVR-KQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 212 ~g~~HPl~~~~-~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
.+..++..+.. ..+|+.|..+||.|+-+-+++..+. ++.+..|.+. +..-|.+|-. +|
T Consensus 486 ~~~~~~~~~~~~~~~r~~L~~~Gf~Ev~tysl~s~~~--~~~~~~~~~~------~~i~l~NPis-----~e-------- 544 (798)
T TIGR00472 486 KLNKNNENYLLLRKLRTLLVGLGLNEVITYSLVSSEK--AEKFNFPKLE------NLVEIKNPLS-----NE-------- 544 (798)
T ss_pred CCCCCCHHHHHHHHHHHHHHHCCCcEEeccccCCHHH--HHhhcCCCCC------ceEEEeCCCc-----hH--------
Confidence 44566666655 7999999999999998766653322 2223223211 1355766632 22
Q ss_pred hhcCCCCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 291 HESGGYGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 291 He~Gg~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
..+|||...+.-.+.++........|.++|-+|+||.
T Consensus 545 ---------------------~s~lR~SLlpgLL~~~~~N~~~~~~~~~lFEiG~V~~ 581 (798)
T TIGR00472 545 ---------------------RSVLRTSLLPSLLEVLAYNQNRKNKDVKIFEIGKVFA 581 (798)
T ss_pred ---------------------HHHHHHhhHHHHHHHHHHHHhCCCCCEeEEeeecccC
Confidence 5899999988888888766545568999999999994
No 121
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=92.33 E-value=0.71 Score=39.35 Aligned_cols=60 Identities=7% Similarity=0.001 Sum_probs=49.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeChhHHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLTGEGKK 64 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LTeEG~~ 64 (349)
.+||..|...++ .+.-++++.+|++...|..-++-|+..|+|+.+..-. ..|.|.+...+
T Consensus 19 l~IL~~L~~~~~-~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~Y~l~~~~~~ 79 (117)
T PRK10141 19 LGIVLLLRESGE-LCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVHYRLSPHIPA 79 (117)
T ss_pred HHHHHHHHHcCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEEEEECchHHH
Confidence 468888876554 5677999999999999999999999999999888744 48899776433
No 122
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=92.32 E-value=0.27 Score=42.34 Aligned_cols=50 Identities=20% Similarity=0.274 Sum_probs=43.7
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
+..+||..|+.+.. .+..++|+.+|++..++..-++.|+..|+|.-....
T Consensus 9 ~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~~~ 58 (154)
T COG1522 9 IDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYTAV 58 (154)
T ss_pred HHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEEEE
Confidence 56789999998887 667899999999999999999999999999765443
No 123
>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=92.21 E-value=0.64 Score=34.12 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=35.8
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeCh
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTe 60 (349)
.+..++|+.+|++...|.+.+..|+.+|+|.... ...|.||+
T Consensus 26 ~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~--~~~~~l~~ 67 (67)
T cd00092 26 LTRQEIADYLGLTRETVSRTLKELEEEGLISRRG--RGKYRVNP 67 (67)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC--CCeEEeCC
Confidence 5678999999999999999999999999998865 34676663
No 124
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=92.19 E-value=1.3 Score=38.06 Aligned_cols=88 Identities=7% Similarity=0.163 Sum_probs=56.1
Q ss_pred HHHHHHHHHhhCCCCCChHH----HHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEE--eChhHH------HH---
Q 018851 2 AEEAILGYLEKNEQISDSGN----FAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWV--LTGEGK------KY--- 65 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~----la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~--LTeEG~------~~--- 65 (349)
.|..|+..|=..+. .+..+ +++..++++..|...+..|..||+|..... ....|. .|++-- +.
T Consensus 5 ~E~~VM~vlW~~~~-~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p~vs~ee~~~~~~~~~~~~ 83 (130)
T TIGR02698 5 AEWEVMRVVWTLGE-TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTEKEGRKFIYTALVSEDEAVENAAQELFSR 83 (130)
T ss_pred HHHHHHHHHHcCCC-CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeeecCCCcEEEEecCCHHHHHHHHHHHHHHH
Confidence 58889999976665 46666 444458999999999999999999987643 233555 343321 11
Q ss_pred hhcCChHHHHHHhcCcCCCCCHHHHH
Q 018851 66 AAEGSPEVQLFLAVPAEGSISKDELQ 91 (349)
Q Consensus 66 l~~G~PE~rl~~~l~~~g~~~~~el~ 91 (349)
+=+|++..-|..++.+. .++.+|+.
T Consensus 84 ~f~gs~~~ll~~l~~~~-~ls~eele 108 (130)
T TIGR02698 84 ICSRKVGAVIADLIEES-PLSQTDIE 108 (130)
T ss_pred HHCCCHHHHHHHHHhcC-CCCHHHHH
Confidence 12356665555555432 35555544
No 125
>TIGR00418 thrS threonyl-tRNA synthetase. This model represents the threonyl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. Note that B. subtilis has closely related isozymes thrS and thrZ. The N-terminal regions are quite dissimilar between archaeal and eubacterial forms, while some eukaryotic forms are missing sequence there altogether..
Probab=92.19 E-value=0.21 Score=52.62 Aligned_cols=93 Identities=11% Similarity=0.075 Sum_probs=59.9
Q ss_pred ChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
.-...+.+.++++|...||+++.+ |.++.. .||.-..|=..-..+.|-+.+.
T Consensus 201 ~~~~~i~~~~~~~~~~~G~~ev~t-P~l~~~-----~l~~~sg~~~~~~~emy~~~d~---------------------- 252 (563)
T TIGR00418 201 TIRNLLEDFVRQKQIKYGYMEVET-PIMYDL-----ELWEISGHWDNYKERMFPFTEL---------------------- 252 (563)
T ss_pred HHHHHHHHHHHHHHHHcCCEEEEC-CccCCH-----HHHHhcCCcccchhhcceeccC----------------------
Confidence 346888999999999999999985 666522 2222223332222234444321
Q ss_pred CCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcC-CCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK-PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~-~~~p~k~fsi~rVfR~ 349 (349)
..+..+||+=+|+.-+|+....... ...|.|+|.+++|||.
T Consensus 253 -------------~~~~~~LrP~~~~~i~~~~~~~~~s~~~lP~rl~~~g~~fR~ 294 (563)
T TIGR00418 253 -------------DNREFMLKPMNCPGHFLIFKSSLRSYRDLPLRIAELGYSHRY 294 (563)
T ss_pred -------------CCceEEEecCCCHHHHHHHhCcCCChHHCCceeeEeccccCC
Confidence 1146899988888778876542111 2359999999999995
No 126
>PRK00215 LexA repressor; Validated
Probab=92.05 E-value=0.3 Score=44.51 Aligned_cols=63 Identities=13% Similarity=0.201 Sum_probs=51.6
Q ss_pred HHHHHHHHHhh----CCCCCChHHHHHHhCC-CHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 2 AEEAILGYLEK----NEQISDSGNFAAERGF-DHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 2 ~e~~iL~~L~~----~~~~~~~~~la~~~g~-~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
-|..||..|.. .+...+..+||..+|+ +..++.+.+..|+.+|+|+-.......+.|+++|..
T Consensus 5 ~q~~il~~i~~~~~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~~~~~ 72 (205)
T PRK00215 5 RQQEILDFIRDHIEETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRAIEVAAPAQL 72 (205)
T ss_pred HHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCcceEEecccccc
Confidence 36778888863 3433567899999999 999999999999999999888777778888877654
No 127
>KOG3344 consensus 40s ribosomal protein s10 [Translation, ribosomal structure and biogenesis]
Probab=92.02 E-value=0.09 Score=46.00 Aligned_cols=44 Identities=27% Similarity=0.385 Sum_probs=37.0
Q ss_pred hCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhcC
Q 018851 26 RGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 26 ~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~G 69 (349)
+.++--.|+.++.||.|+|+|+..-. ..-.|.||.||.+||.+-
T Consensus 35 l~vpNL~vikaMQSl~SrgYvkeqfaWrH~Yw~LTneGi~yLR~Y 79 (150)
T KOG3344|consen 35 LEVPNLHVIKAMQSLKSRGYVKEQFAWRHFYWYLTNEGIEYLREY 79 (150)
T ss_pred cCCccHHHHHHHHHHhhhhhHHhhhhhheeeeeechhHHHHHHHH
Confidence 34666789999999999999987666 566899999999999763
No 128
>TIGR00409 proS_fam_II prolyl-tRNA synthetase, family II. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent groups. This group includes enzymes from Escherichia coli, Bacillus subtilis, Aquifex aeolicus, the spirochete Treponema pallidum, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae. The other group includes the Pro-specific domain of a human multifunctional tRNA ligase and the prolyl-tRNA synthetases from the Archaea, the Mycoplasmas, and the spirochete Borrelia burgdorferi.
Probab=91.82 E-value=0.34 Score=51.57 Aligned_cols=89 Identities=16% Similarity=0.206 Sum_probs=54.3
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-+.++.+.+++.|...||+++.+ |.+++. .||.--.|-.---...|.+.+..
T Consensus 49 v~~~I~~~i~~~~~~~G~~ei~~-P~l~~~-----el~~~sg~~~~~~~emf~~~dr~---------------------- 100 (568)
T TIGR00409 49 VLKKVENIVREEMNKDGAIEVLL-PALQPA-----ELWQESGRWDTYGPELLRLKDRK---------------------- 100 (568)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEC-CccchH-----HHHhhcCCCCccchhcEEEecCC----------------------
Confidence 47788889999999999999975 666541 12221222221123466665421
Q ss_pred CCCCcccccchhhhhccccC-CCCchhH---HHHHHHhhcCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLR-THTTAVS---SRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLR-THTTavs---~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+.++|| ||-..++ ++.+.. ...-|.+++.++.|||.
T Consensus 101 -------------~~~l~LrPT~Ee~~t~~~~~~i~s---yr~LPlrlyqi~~~fR~ 141 (568)
T TIGR00409 101 -------------GREFVLGPTHEEVITDLARNEIKS---YKQLPLNLYQIQTKFRD 141 (568)
T ss_pred -------------CCEEEEcCCCcHHHHHHHHHHHhh---ccccCeEEEEeeCEeeC
Confidence 1258999 5544444 333322 22359999999999994
No 129
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=91.80 E-value=0.21 Score=38.35 Aligned_cols=43 Identities=16% Similarity=0.251 Sum_probs=35.7
Q ss_pred HHHHhcCcCCCCCHHHHHhh--cCchhhhhHHHHHhhCCcEeeCc
Q 018851 74 QLFLAVPAEGSISKDELQKK--LDPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 74 rl~~~l~~~g~~~~~el~~~--~~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
.|+++|.+.+++++.+|.+. +...+...|+||+.|.+-|.++.
T Consensus 12 ~Vw~~L~~~~~~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~ 56 (65)
T PF10771_consen 12 KVWQLLNENGEWSVSELKKATGLSDKEVYLAIGWLARENKIEFEE 56 (65)
T ss_dssp HHHHHHCCSSSEEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEE
T ss_pred HHHHHHhhCCCcCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEe
Confidence 57899988788999999987 44567778999999999998754
No 130
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=91.62 E-value=0.34 Score=41.47 Aligned_cols=53 Identities=15% Similarity=0.307 Sum_probs=47.0
Q ss_pred HHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHH
Q 018851 21 NFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLF 76 (349)
Q Consensus 21 ~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~ 76 (349)
.||..++++.+++..++.-++--|+|++.. -.+.||+.|+++++.+..|++-+
T Consensus 2 ~La~~l~~eiDdL~p~~eAaelLgf~~~~~---Gdi~LT~~G~~f~~a~~~~rK~i 54 (120)
T PF09821_consen 2 QLADELHLEIDDLLPIVEAAELLGFAEVEE---GDIRLTPLGRRFAEADIDERKEI 54 (120)
T ss_pred chHHHhCCcHHHHHHHHHHHHHcCCeeecC---CcEEeccchHHHHHCChHHHHHH
Confidence 478889999999999999999999999975 47899999999999888887644
No 131
>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=91.57 E-value=0.23 Score=48.25 Aligned_cols=56 Identities=18% Similarity=0.306 Sum_probs=46.9
Q ss_pred HHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhcCChHHHHHH
Q 018851 20 GNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAEGSPEVQLFL 77 (349)
Q Consensus 20 ~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~G~PE~rl~~ 77 (349)
..+.+.+|++...|..++..|+.+|+|+.+.. ....|.||+.|++.++.+ ..|+|.
T Consensus 24 i~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~--~~rIy~ 80 (280)
T TIGR02277 24 IEFLAGLGINERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAA--AQRIYD 80 (280)
T ss_pred HHHHHhcCCCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHH--hhhhcC
Confidence 44567789999999999999999999988754 346999999999999874 456664
No 132
>PF13730 HTH_36: Helix-turn-helix domain
Probab=91.35 E-value=0.51 Score=33.84 Aligned_cols=44 Identities=23% Similarity=0.265 Sum_probs=33.1
Q ss_pred HHHHHHHHhh----CCCCC-ChHHHHHHhCCCHHHHHHHHHHhccCCcE
Q 018851 3 EEAILGYLEK----NEQIS-DSGNFAAERGFDHNDVVNVIKSLHGFRYI 46 (349)
Q Consensus 3 e~~iL~~L~~----~~~~~-~~~~la~~~g~~~~~v~~~~~~L~~kgli 46 (349)
++.|+..|.. .+.+. +.+.+|+.+|++...|.++++.|+.+|+|
T Consensus 7 ~~~v~~~l~~~~~~~~~~~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 7 AKLVYLYLASYANKNGGCFPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHhcCCCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 4555555543 22222 45889999999999999999999999986
No 133
>PF00587 tRNA-synt_2b: tRNA synthetase class II core domain (G, H, P, S and T) This Prosite entry contains all class II enzymes. seryl tRNA synthetase structure; InterPro: IPR002314 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain includes the glycine, histidine, proline, threonine and serine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 3UH0_A 3UGT_C 3UGQ_A 1B76_B 1GGM_B 1ATI_A 1ADY_C 1ADJ_C 2I4O_A 2I4M_B ....
Probab=91.31 E-value=0.11 Score=45.97 Aligned_cols=89 Identities=19% Similarity=0.355 Sum_probs=54.2
Q ss_pred HHHHHHHHHHHh-hCCceecCCCCcee-eeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 219 LKVRKQLKDIFL-QMGFEEMPTNNFVE-SSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 219 ~~~~~~ir~if~-~mGF~e~~~~~~Ve-s~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
+.+++.+++.+. ..||++|.+ |.+. ++.|.- -.|-..-..+.|.+.+..
T Consensus 3 ~~l~~~~~~~~~~~~G~~ev~~-P~l~~~~~~~~------sg~~~~~~~~~~~~~~~~---------------------- 53 (173)
T PF00587_consen 3 NALERFIREEFVLKFGFQEVDT-PILIPSEVWEK------SGHWDNFSDEMFKVKDRG---------------------- 53 (173)
T ss_dssp HHHHHHHHHHHHHHTTEEEEB---SEEEHHHHHH------HSHHHHHGGGSEEEEETT----------------------
T ss_pred HHHHHHHHHHhHHhcCCEEEEC-CeEEehHHhhh------ccccccccCCeeeeeecc----------------------
Confidence 467889999999 999999985 4443 333322 122111122355555421
Q ss_pred CCCCcccccchhhhhccccCCCCchhHHHHHHHhhcC--CCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK--PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~--~~~p~k~fsi~rVfR~ 349 (349)
.+..+||+=++...+.++...... ..-|.+++.+++|||+
T Consensus 54 -------------~~~~~L~pt~~~~~~~~~~~~~~~~~~~LP~~~~~~g~~fR~ 95 (173)
T PF00587_consen 54 -------------DEEYCLRPTSEPGIYSLFKNEIRSSYRDLPLKLYQIGTCFRN 95 (173)
T ss_dssp -------------TEEEEE-SSSHHHHHHHHHHHEEBHGGGSSEEEEEEEEEEBS
T ss_pred -------------cccEEeccccccceeeeecceeeeccccCCeEEeeccccccc
Confidence 125799976666666666544222 2369999999999996
No 134
>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=91.17 E-value=0.4 Score=45.89 Aligned_cols=47 Identities=23% Similarity=0.365 Sum_probs=41.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
++||..|..++...+..++|+.+|++...+..+++.|++.|+|....
T Consensus 186 ~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 186 EHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 56899998753346778999999999999999999999999999988
No 135
>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=91.05 E-value=0.26 Score=38.77 Aligned_cols=59 Identities=17% Similarity=0.232 Sum_probs=45.7
Q ss_pred HHHHHHhhCCC--CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHH
Q 018851 5 AILGYLEKNEQ--ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGK 63 (349)
Q Consensus 5 ~iL~~L~~~~~--~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~ 63 (349)
++|..|...+. ..++.++|+.+++++..+...+..|+..|+|+...-..--|.|+..-+
T Consensus 12 ~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 12 RILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPE 72 (83)
T ss_dssp HHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CC
T ss_pred HHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHH
Confidence 46666664332 367899999999999999999999999999998877777888876543
No 136
>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=90.78 E-value=0.36 Score=37.47 Aligned_cols=43 Identities=19% Similarity=0.249 Sum_probs=34.5
Q ss_pred HHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee-eEEEEeChhH
Q 018851 20 GNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK-RETWVLTGEG 62 (349)
Q Consensus 20 ~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~-~~~~~LTeEG 62 (349)
-++.+.+|++.+.+..++..|.++|+++.+..- ...|.|||.|
T Consensus 27 i~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~g 70 (70)
T PF07848_consen 27 IRLLAAFGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTERG 70 (70)
T ss_dssp HHHHCCTT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HHH
T ss_pred HHHHHHcCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCCC
Confidence 345667899999999999999999999998875 5699999987
No 137
>PRK12325 prolyl-tRNA synthetase; Provisional
Probab=90.74 E-value=0.39 Score=49.39 Aligned_cols=94 Identities=12% Similarity=0.144 Sum_probs=55.7
Q ss_pred CChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcC
Q 018851 215 LHPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESG 294 (349)
Q Consensus 215 ~HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~G 294 (349)
..-+..+.+.+++.|...||+++.+ |.+++ .| ||.-..|=.-=..+.|.+.+..
T Consensus 47 ~~i~~~i~~~i~~~~~~~G~~ev~~-P~l~~----~~-l~~~sg~~~~~~~emf~~~d~~-------------------- 100 (439)
T PRK12325 47 LKVLKKIENIVREEQNRAGAIEILM-PTIQP----AD-LWRESGRYDAYGKEMLRIKDRH-------------------- 100 (439)
T ss_pred HHHHHHHHHHHHHHHHHcCCEEEEC-Ccccc----HH-HHhhcCCccccchhheEEecCC--------------------
Confidence 4457888999999999999999975 66543 22 2222233222223456665321
Q ss_pred CCCCCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 295 GYGSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 295 g~gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+..+|| ||+.++..-+-....+-..-|.|++.++.|||.
T Consensus 101 ---------------~~~~~L~Pt~e~~~~~~~~~~~~syrdLPlrl~q~~~~fR~ 141 (439)
T PRK12325 101 ---------------DREMLYGPTNEEMITDIFRSYVKSYKDLPLNLYHIQWKFRD 141 (439)
T ss_pred ---------------CCEEEEcCCCcHHHHHHHHHHhhhchhhchHheEecCEecC
Confidence 1257899 555444422211111212369999999999994
No 138
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=90.72 E-value=1 Score=36.08 Aligned_cols=66 Identities=18% Similarity=0.224 Sum_probs=50.5
Q ss_pred HHHHHHHHHhh---CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 2 AEEAILGYLEK---NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 2 ~e~~iL~~L~~---~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
.+.+||.+++. +-+....+.+++..|++++.+...+..|-..++|.-....-.-|.||-.|-+++.
T Consensus 7 ~d~rvL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~LA 75 (82)
T PF09202_consen 7 EDFRVLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYLA 75 (82)
T ss_dssp HHHHHHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHHH
T ss_pred HHHHHHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHHH
Confidence 36789999875 2334556788899999999999999999999999997667778999999999874
No 139
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=90.72 E-value=0.51 Score=45.09 Aligned_cols=56 Identities=13% Similarity=0.162 Sum_probs=47.6
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
|.++..+|-..+. .+..++|+..|++...|-..+++|+.||+|.+..-....|+.-
T Consensus 18 Ea~vY~aLl~~g~-~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av 73 (247)
T COG1378 18 EAKVYLALLCLGE-ATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAV 73 (247)
T ss_pred HHHHHHHHHHhCC-ccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeC
Confidence 5667777777776 6788999999999999999999999999999987777777654
No 140
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=90.54 E-value=0.63 Score=33.06 Aligned_cols=33 Identities=15% Similarity=0.249 Sum_probs=30.2
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
+..++|+.+|++...|.+++..|+..|+|....
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 678899999999999999999999999997654
No 141
>cd00770 SerRS_core Seryl-tRNA synthetase (SerRS) class II core catalytic domain. SerRS is responsible for the attachment of serine to the 3' OH group of ribose of the appropriate tRNA. This domain It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. SerRS synthetase is a homodimer.
Probab=90.53 E-value=0.23 Score=48.37 Aligned_cols=86 Identities=15% Similarity=0.178 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee-eeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE-SSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve-s~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
+.+.+-+++.+.+.||+++.+ |.+. .+.| .. -.|=..--.+.|.+++
T Consensus 56 ~~l~~~~~~~~~~~G~~ev~~-P~l~~~~l~--~~----sg~~~~~~~~~f~v~~------------------------- 103 (297)
T cd00770 56 RALINFALDFLTKRGFTPVIP-PFLVRKEVM--EG----TGQLPKFDEQLYKVEG------------------------- 103 (297)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-cccccHHHH--hh----cCcCccChhcccEecC-------------------------
Confidence 458888899999999999974 5442 2222 11 1221111224555542
Q ss_pred CCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
...+|| ||+.++..-+-...-+...-|.|++.+++|||.
T Consensus 104 -------------~~~~L~pt~e~~~~~l~~~~~~s~~~LPlr~~~~~~~fR~ 143 (297)
T cd00770 104 -------------EDLYLIATAEVPLAALHRDEILEEEELPLKYAGYSPCFRK 143 (297)
T ss_pred -------------CCEEEeecCCHHHHHHHhcccCCHhhCCchheecChhHhC
Confidence 146777 676665433221111112369999999999994
No 142
>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=90.26 E-value=0.46 Score=43.12 Aligned_cols=59 Identities=14% Similarity=0.174 Sum_probs=47.8
Q ss_pred HHHHHHHHHhhC----CCCCChHHHHHHhCCC-HHHHHHHHHHhccCCcEEEEeeeeEEEEeCh
Q 018851 2 AEEAILGYLEKN----EQISDSGNFAAERGFD-HNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60 (349)
Q Consensus 2 ~e~~iL~~L~~~----~~~~~~~~la~~~g~~-~~~v~~~~~~L~~kgli~~~~~~~~~~~LTe 60 (349)
.|.+||..|... +...+..++|+.+|++ ...|.+.+..|+.+|+|.-+......+.+++
T Consensus 7 ~q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~~~ 70 (199)
T TIGR00498 7 RQQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGKPRAIRILD 70 (199)
T ss_pred HHHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCCCCeEEeCC
Confidence 478899999742 3334567999999998 9999999999999999998776655666765
No 143
>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=90.06 E-value=0.83 Score=31.88 Aligned_cols=39 Identities=23% Similarity=0.385 Sum_probs=31.5
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLH 41 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~ 41 (349)
+..+||..|..++. .+..++|+.+|++..+|..-+..|+
T Consensus 4 ~D~~Il~~Lq~d~r-~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 4 LDRKILRLLQEDGR-RSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHHH-TT-S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCC-ccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 45789999998876 6788999999999999999888875
No 144
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=90.00 E-value=1.2 Score=35.76 Aligned_cols=65 Identities=23% Similarity=0.264 Sum_probs=42.1
Q ss_pred HHHHHHHHhhCCCCCChHH----HHHHhCCCHHH-----------------HHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 3 EEAILGYLEKNEQISDSGN----FAAERGFDHND-----------------VVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~----la~~~g~~~~~-----------------v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
..-||++|.+.+...+..+ +++..+++.++ |.=++..|...|+|+- ...-.|.||++
T Consensus 6 ~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~--~~rG~~~iT~~ 83 (92)
T PF14338_consen 6 MPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIER--PKRGIWRITEK 83 (92)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccC--CCCCceEECHh
Confidence 3457888887333244333 44445554433 3335677889999943 33559999999
Q ss_pred HHHHhhcC
Q 018851 62 GKKYAAEG 69 (349)
Q Consensus 62 G~~~l~~G 69 (349)
|++++.++
T Consensus 84 G~~~l~~~ 91 (92)
T PF14338_consen 84 GRKALAEH 91 (92)
T ss_pred HHHHHhhC
Confidence 99998763
No 145
>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=89.82 E-value=0.9 Score=32.89 Aligned_cols=41 Identities=12% Similarity=0.217 Sum_probs=32.9
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
.+..++|..+|++...|..+++.|+..|+|+... ...|.||
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~--~~~~~l~ 66 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERRP--GRGTFVA 66 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC--CCeEEeC
Confidence 4467899999999999999999999999987653 2344443
No 146
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.71 E-value=0.75 Score=44.01 Aligned_cols=58 Identities=19% Similarity=0.256 Sum_probs=47.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG 62 (349)
..||..|...+...+..++|+.+|++.+.+.+.+..|.+.|||.-.. ....|.|+..-
T Consensus 28 l~IL~~~~~~~~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~-~~~~Y~lG~~l 85 (271)
T PRK10163 28 IAILQYLEKSGGSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDS-QLGWWHIGLGV 85 (271)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC-CCCeEEecHHH
Confidence 35888887765546788999999999999999999999999996653 34578887654
No 147
>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=89.66 E-value=0.76 Score=43.16 Aligned_cols=55 Identities=13% Similarity=0.181 Sum_probs=45.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhH
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG 62 (349)
.||..|...+...+..++|+.+|++.+.+.+.+..|++.|+|.-+ ...|.|+..=
T Consensus 13 ~IL~~l~~~~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~---~~~Y~lG~~~ 67 (248)
T TIGR02431 13 AVIEAFGAERPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD---GRLFWLTPRV 67 (248)
T ss_pred HHHHHHhcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC---CCEEEecHHH
Confidence 588888765555788999999999999999999999999999743 3579887653
No 148
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=89.53 E-value=0.94 Score=30.96 Aligned_cols=40 Identities=18% Similarity=0.175 Sum_probs=33.0
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
.+..++|+.+|++...+.+.+..|++.|+|.... ..|.+|
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~---~~~~i~ 48 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISREG---GRIVIL 48 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC---CEEEEC
Confidence 3567899999999999999999999999997653 345554
No 149
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=89.19 E-value=0.89 Score=34.97 Aligned_cols=51 Identities=16% Similarity=0.209 Sum_probs=42.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
.|..+|.+.+. .+..++++.+|++..++..|+.||.-.|=|.+++.....|
T Consensus 12 ~Vw~~L~~~~~-~s~~el~k~~~l~~~~~~~AiGWLarE~KI~~~~~~~~~~ 62 (65)
T PF10771_consen 12 KVWQLLNENGE-WSVSELKKATGLSDKEVYLAIGWLARENKIEFEEKNGELY 62 (65)
T ss_dssp HHHHHHCCSSS-EEHHHHHHHCT-SCHHHHHHHHHHHCTTSEEEEEETTEEE
T ss_pred HHHHHHhhCCC-cCHHHHHHHhCcCHHHHHHHHHHHhccCceeEEeeCCEEE
Confidence 47788888676 6788999999999999999999999999999987765533
No 150
>PRK11569 transcriptional repressor IclR; Provisional
Probab=89.16 E-value=0.81 Score=43.81 Aligned_cols=56 Identities=7% Similarity=0.296 Sum_probs=46.4
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
.||..|...+...+..++|+.+|++.+.+.+.+..|...||+.-.. ....|.|+..
T Consensus 32 ~IL~~l~~~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~-~~~~Y~lG~~ 87 (274)
T PRK11569 32 KLLEWIAESNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG-ELGHWAIGAH 87 (274)
T ss_pred HHHHHHHhCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC-CCCeEecCHH
Confidence 5888888765557889999999999999999999999999997433 3557888765
No 151
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=89.14 E-value=0.81 Score=43.25 Aligned_cols=57 Identities=14% Similarity=0.193 Sum_probs=46.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG 62 (349)
..||..|...+. .+..++|+.+|++.+.+.+.+..|...|+|.-. .....|.|+..-
T Consensus 17 l~IL~~l~~~~~-l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~-~~~~~Y~lG~~~ 73 (257)
T PRK15090 17 FGILQALGEERE-IGITELSQRVMMSKSTVYRFLQTMKTLGYVAQE-GESEKYSLTLKL 73 (257)
T ss_pred HHHHHHhhcCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc-CCCCcEEecHHH
Confidence 358888876654 678899999999999999999999999999765 334578888553
No 152
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=89.00 E-value=2.2 Score=35.49 Aligned_cols=88 Identities=18% Similarity=0.226 Sum_probs=56.8
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHh----CCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeChhHHHHhh---------
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAER----GFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLTGEGKKYAA--------- 67 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~----g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LTeEG~~~l~--------- 67 (349)
.|..|++.|=+.+. .++.++.+.+ ++..+.|.-.+..|..||+|+.+..-. ..|..+=.=++|+.
T Consensus 4 ~E~~IM~~lW~~~~-~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~gr~~~Y~p~is~~e~~~~~~~~~l~~ 82 (115)
T PF03965_consen 4 LELEIMEILWESGE-ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKIGRAYVYSPLISREEYLAQELRQFLDR 82 (115)
T ss_dssp HHHHHHHHHHHHSS-EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCC-CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeecCCceEEEeCCcHHHHHHHHHHHHHHH
Confidence 68899999988777 5666666554 566999999999999999999987533 34553322223332
Q ss_pred --cCChHHHHHHhcCcCCCCCHHHHH
Q 018851 68 --EGSPEVQLFLAVPAEGSISKDELQ 91 (349)
Q Consensus 68 --~G~PE~rl~~~l~~~g~~~~~el~ 91 (349)
+|++..-+..++... .++.+|+.
T Consensus 83 ~~~gs~~~l~~~l~~~~-~ls~~el~ 107 (115)
T PF03965_consen 83 LFDGSIPQLVAALVESE-ELSPEELE 107 (115)
T ss_dssp HSTTHHHHHHHHHHHCT--S-HHHHH
T ss_pred HhCCCHHHHHHHHHhcC-CCCHHHHH
Confidence 566666655555533 35555544
No 153
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=88.72 E-value=0.73 Score=38.82 Aligned_cols=60 Identities=13% Similarity=0.145 Sum_probs=44.7
Q ss_pred HHHHHHhhC--CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 5 AILGYLEKN--EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 5 ~iL~~L~~~--~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
.+|..|... +...+..++|+.+|++...|.+.+..|...|+|........-|.|+...++
T Consensus 12 ~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~ 73 (132)
T TIGR00738 12 RALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEE 73 (132)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHH
Confidence 345555433 335788999999999999999999999999999765434446677666554
No 154
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=88.68 E-value=0.77 Score=43.96 Aligned_cols=48 Identities=23% Similarity=0.297 Sum_probs=42.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.+||+.|...+. .+..++|+.+|++.+.+...++.|+..|||.++...
T Consensus 26 v~Il~lL~~k~p-lNvneiAe~lgLpqst~s~~ik~Le~aGlirT~t~k 73 (308)
T COG4189 26 VAILQLLHRKGP-LNVNEIAEALGLPQSTMSANIKVLEKAGLIRTETVK 73 (308)
T ss_pred HHHHHHHHHhCC-CCHHHHHHHhCCchhhhhhhHHHHHhcCceeeeeec
Confidence 468888887775 688999999999999999999999999999987653
No 155
>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=88.51 E-value=1.1 Score=40.00 Aligned_cols=46 Identities=17% Similarity=0.141 Sum_probs=39.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
..||.+|-.++. .+.++||..+|++..+|.+.+..|..+|||...+
T Consensus 17 v~Vl~aL~~~~~-~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 17 GLVLFSLGIKGE-FTDEEISLELGIKLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred HHHHHHHhccCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeee
Confidence 467888876665 6789999999999999999999999999997654
No 156
>cd00778 ProRS_core_arch_euk Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain. This subfamily contains the core domain of ProRS from archaea, the cytoplasm of eukaryotes and some bacteria.
Probab=88.47 E-value=0.37 Score=46.00 Aligned_cols=98 Identities=16% Similarity=0.111 Sum_probs=58.2
Q ss_pred ChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
.-...+++.+++.+...||+++.+ |.++.. |.+..--.|-..-..+.|.+.+....
T Consensus 33 ~l~~~l~~~~~~~~~~~G~~ev~~-P~l~~~----~~~~~~sg~~~~f~~~~f~~~~~~~~------------------- 88 (261)
T cd00778 33 AIWENIQKILDKEIKETGHENVYF-PLLIPE----SELEKEKEHIEGFAPEVAWVTHGGLE------------------- 88 (261)
T ss_pred HHHHHHHHHHHHHHHHcCCEEEEC-CccccH----HHhhhhhcchhhcCcceEEEEecCCc-------------------
Confidence 346778888899999999999975 666442 22211123332223357777542100
Q ss_pred CCCCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.......|| ||.++++.-+-....+...-|.|++.+++|||.
T Consensus 89 ------------~~~~~~~L~Pt~e~~~~~~~~~~i~s~r~LPlr~~~~~~~fR~ 131 (261)
T cd00778 89 ------------ELEEPLALRPTSETAIYPMFSKWIRSYRDLPLKINQWVNVFRW 131 (261)
T ss_pred ------------ccCCcEEEcCCCCHHHHHHHHhhccchhhcCHHHHhhhhhccC
Confidence 001257888 766666644333222223369999999999995
No 157
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=88.41 E-value=1.5 Score=36.00 Aligned_cols=60 Identities=15% Similarity=0.159 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeee----eEEEEeChhHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIK----RETWVLTGEGKKYA 66 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~----~~~~~LTeEG~~~l 66 (349)
.++|.++...+. ...-|+.+|+++..|.+.++.||.. |.-=++... ..-+.||+.|+.++
T Consensus 7 l~~~~av~~~gS---is~AA~~L~iS~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 7 VALLKAIARMGS---ISQAAKDAGISYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred HHHHHHHHHhCC---HHHHHHHHCCCHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 456677766664 4567888999999999999999995 554444432 35899999999977
No 158
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=88.28 E-value=0.71 Score=44.03 Aligned_cols=45 Identities=13% Similarity=0.148 Sum_probs=41.2
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
..+||+.|..++. .+.++||+.+|++...|.+.+..|+.+|++.-
T Consensus 7 ~~~Il~~l~~~g~-v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R 51 (253)
T COG1349 7 HQKILELLKEKGK-VSVEELAELFGVSEMTIRRDLNELEEQGLLLR 51 (253)
T ss_pred HHHHHHHHHHcCc-EEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEE
Confidence 4679999999887 67899999999999999999999999999865
No 159
>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=88.26 E-value=0.48 Score=34.99 Aligned_cols=56 Identities=18% Similarity=0.074 Sum_probs=39.6
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGK 63 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~ 63 (349)
.+++.++...+ +...-|+.+|+++..|.+.++.||.. |.-=++. ....+.||++|+
T Consensus 4 l~~f~~v~~~g---s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r-~~~~~~lT~~G~ 60 (60)
T PF00126_consen 4 LRYFLAVAETG---SISAAAEELGISQSAVSRQIKQLEEELGVPLFER-SGRGLRLTEAGE 60 (60)
T ss_dssp HHHHHHHHHHS---SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEE-CSSSEEE-HHHH
T ss_pred HHHHHHHHHhC---CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEE-CCCCeeEChhhC
Confidence 35666666665 35577889999999999999999995 4332222 233599999996
No 160
>PRK08661 prolyl-tRNA synthetase; Provisional
Probab=88.02 E-value=0.61 Score=48.53 Aligned_cols=96 Identities=15% Similarity=0.100 Sum_probs=57.0
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceee-eehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVES-SFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves-~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
-...+.+.+++.|...||+++.+ |.+++ +.|.-. ..|-.-=..+.|.+.+...
T Consensus 46 i~~~i~~~~~~~~~~~G~~ev~~-P~l~~~~~~~~~-----~~h~~~f~~e~~~v~~~~~-------------------- 99 (477)
T PRK08661 46 IWENIQKILDKLFKETGHENVYF-PLLIPESLLEKE-----KEHVEGFAPEVAWVTHGGG-------------------- 99 (477)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEC-CccCCHHHHhhh-----cCchhhcccccEEEEccCC--------------------
Confidence 35678888899999999999975 55432 333221 2333222235777764110
Q ss_pred CCCCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+......|| ||.++++.-+-....+...-|.|++.++.|||.
T Consensus 100 -----------~~~~e~l~LrPtsE~~i~~~~~~~i~SyrdLPlrl~q~~~vfR~ 143 (477)
T PRK08661 100 -----------EKLEEKLALRPTSETIIYPMYKKWIQSYRDLPLLYNQWVNVVRW 143 (477)
T ss_pred -----------CccCceEEEecCCcHHHHHHHHhhhcchhhcCHHHhcccceeeC
Confidence 0112368899 665555543322222323469999999999994
No 161
>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=88.00 E-value=0.69 Score=30.72 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=25.3
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYI 46 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli 46 (349)
+-.++|..+|+..+.|.+.++.|+.+|+|
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 45789999999999999999999999987
No 162
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=87.74 E-value=2 Score=38.66 Aligned_cols=61 Identities=15% Similarity=0.095 Sum_probs=44.9
Q ss_pred HHHHHhhCCCCCChHHHHHH----hCCCHHHHHHHHHHhccCCcEEEE--eeeeEEEEeChhHHHHh
Q 018851 6 ILGYLEKNEQISDSGNFAAE----RGFDHNDVVNVIKSLHGFRYIDAQ--DIKRETWVLTGEGKKYA 66 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~----~g~~~~~v~~~~~~L~~kgli~~~--~~~~~~~~LTeEG~~~l 66 (349)
||=.|..-+.+.+..++..- --++.=.+..++..|.+.|+|..+ ......|.+|++|++.|
T Consensus 5 ILYiL~~v~~pltn~qit~~iL~~~~~nYF~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl 71 (163)
T PF14277_consen 5 ILYILKKVKFPLTNSQITEFILENEYTNYFTLQQALSELVESGLITLETDSDNKTRYSITEKGKETL 71 (163)
T ss_pred HhHHHHhCCCCCCHHHHHHHHHhcCcccHHHHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHH
Confidence 44445554544555555432 246888999999999999999986 45667999999999876
No 163
>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=87.72 E-value=2.6 Score=34.57 Aligned_cols=57 Identities=12% Similarity=0.142 Sum_probs=44.9
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHh-----CCCHHHHHHHHHHhccCCcEEEEeee--eEEEEeC
Q 018851 3 EEAILGYLEKNEQISDSGNFAAER-----GFDHNDVVNVIKSLHGFRYIDAQDIK--RETWVLT 59 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~-----g~~~~~v~~~~~~L~~kgli~~~~~~--~~~~~LT 59 (349)
-..||..|...+...+.+++.+.+ +++..+|.+.++.|++.|+|..-... ...|.++
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 357899998766667888887766 68999999999999999999765432 3567665
No 164
>PRK09954 putative kinase; Provisional
Probab=87.66 E-value=1.1 Score=44.16 Aligned_cols=52 Identities=23% Similarity=0.248 Sum_probs=44.3
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
.+++||..|.+++. .+..++|+.+|++...|...++.|+++|+|. ...|.|.
T Consensus 4 ~~~~il~~l~~~~~-~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~-----~~~~~l~ 55 (362)
T PRK09954 4 REKEILAILRRNPL-IQQNEIADILQISRSRVAAHIMDLMRKGRIK-----GKGYILT 55 (362)
T ss_pred HHHHHHHHHHHCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC-----CcEEEEc
Confidence 57889999998876 6778999999999999999999999999983 3345554
No 165
>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=87.61 E-value=1.7 Score=33.77 Aligned_cols=51 Identities=14% Similarity=0.169 Sum_probs=42.0
Q ss_pred CHHHHHHHHHhhCC-CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 1 MAEEAILGYLEKNE-QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 1 ~~e~~iL~~L~~~~-~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
++++.+|+.+.... ......+++..+|+|+..+...++.|+.+|||.-...
T Consensus 2 ~~~~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 2 DIQYCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred chHHHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 46889999998533 1234568999999999999999999999999987665
No 166
>PRK06474 hypothetical protein; Provisional
Probab=87.56 E-value=1.9 Score=39.01 Aligned_cols=63 Identities=8% Similarity=0.057 Sum_probs=50.8
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHh-CCCHHHHHHHHHHhccCCcEEEEee------eeEEEEeChhHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAER-GFDHNDVVNVIKSLHGFRYIDAQDI------KRETWVLTGEGKKY 65 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~-g~~~~~v~~~~~~L~~kgli~~~~~------~~~~~~LTeEG~~~ 65 (349)
-.+||..|...+...+..+++..+ +++...|.+.++.|+..|+|..... ....|.+++++-..
T Consensus 13 R~~Il~~L~~~~~~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~~~~~ 82 (178)
T PRK06474 13 RMKICQVLMRNKEGLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEEDAKI 82 (178)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccceeee
Confidence 357899998765436788999988 7999999999999999999987543 34689999988653
No 167
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=87.51 E-value=0.6 Score=37.62 Aligned_cols=75 Identities=17% Similarity=0.163 Sum_probs=41.7
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE-------EEeeeeEEEEeChhHHHHhhcCChHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID-------AQDIKRETWVLTGEGKKYAAEGSPEVQL 75 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~-------~~~~~~~~~~LTeEG~~~l~~G~PE~rl 75 (349)
.++||+.|...-+-.... ..++.......++..|...|||+ .-........+|.+|.+||++.|==.++
T Consensus 1 ~YkIL~~l~~~~~~~~~~----~~~~~~~~~~~il~~L~d~GyI~G~~~~~~~~~~~~~~~~IT~~Gi~YL~ENS~mkKa 76 (88)
T PF09639_consen 1 IYKILKYLYKCMKNGKEP----DPDITDSYWSDILRMLQDEGYIKGVSVVRYSPYVALSDPRITLKGIEYLEENSMMKKA 76 (88)
T ss_dssp HHHHHHHHHHH-S---HH----HHTS-HHHHHHHHHHHHHHTSEE--EESSSSEE--SS--EE-HHHHHHHHHHT-S---
T ss_pred CchHHHHHHHHHcCCCCC----CcchhHHHHHHHHHHHHHCCCccceEEEeccceeecCCceEcHHHHHHHHHHHHHHHH
Confidence 368898887532201111 23555688999999999999996 2223345678999999999998877777
Q ss_pred HHhcCc
Q 018851 76 FLAVPA 81 (349)
Q Consensus 76 ~~~l~~ 81 (349)
++.+++
T Consensus 77 ~k~lKe 82 (88)
T PF09639_consen 77 YKFLKE 82 (88)
T ss_dssp ------
T ss_pred HHHHHH
Confidence 777763
No 168
>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=87.15 E-value=2.2 Score=32.16 Aligned_cols=52 Identities=15% Similarity=0.171 Sum_probs=41.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
.+||..|.+.. .+..++|+.+|++...|.+.+..|++.|+..... ..-|.|.
T Consensus 3 ~~il~~L~~~~--~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~--~~g~~l~ 54 (69)
T TIGR00122 3 LRLLALLADNP--FSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV--GKGYRLP 54 (69)
T ss_pred HHHHHHHHcCC--cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec--CCceEec
Confidence 57888887554 4588999999999999999999999999976654 4455553
No 169
>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=87.12 E-value=0.99 Score=33.58 Aligned_cols=54 Identities=22% Similarity=0.273 Sum_probs=38.1
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHH-HHHHHHhccCCcEEEEeeeeEEEEeChhHH
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDV-VNVIKSLHGFRYIDAQDIKRETWVLTGEGK 63 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v-~~~~~~L~~kgli~~~~~~~~~~~LTeEG~ 63 (349)
|+..|.-... .+..++.+.+|.+..+. ...+..|.+.|+|+.+. ..+.||++|.
T Consensus 11 i~~~LR~~~G-i~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~---~~l~lT~~G~ 65 (66)
T PF06969_consen 11 IMLGLRCNEG-IDLSEFEQRFGIDFAEEFQKELEELQEDGLLEIDG---GRLRLTEKGR 65 (66)
T ss_dssp HHHHHHHHSE-EEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-S---SEEEE-TTTG
T ss_pred HHHHHHhHCC-cCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEeC---CEEEECcccC
Confidence 3444444444 57889999999987665 67799999999997654 6899999984
No 170
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=87.11 E-value=0.98 Score=43.06 Aligned_cols=47 Identities=17% Similarity=0.128 Sum_probs=41.4
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
..+||..|..++. .+..+||+.+|++...|.+.+..|+..|+|.-..
T Consensus 7 ~~~Il~~L~~~~~-v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 7 QAAILEYLQKQGK-TSVEELAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHcCC-EEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 4679999998887 6789999999999999999999999999886543
No 171
>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=87.06 E-value=0.81 Score=37.52 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=35.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
..||.+|...+. .+.+++|+.+|++..+|...+..|...|+|.+....
T Consensus 16 ~~Il~~L~~~~~-l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~~~~ 63 (105)
T PF02002_consen 16 VRILDALLRKGE-LTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYRRRK 63 (105)
T ss_dssp HHHHHHHHHH---B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEEEE-
T ss_pred HHHHHHHHHcCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEEEEE
Confidence 468888886676 567899999999999999999999999999887543
No 172
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=86.99 E-value=0.74 Score=44.59 Aligned_cols=73 Identities=14% Similarity=0.126 Sum_probs=63.2
Q ss_pred HHHHHHHHHhh----CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHH
Q 018851 2 AEEAILGYLEK----NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQ 74 (349)
Q Consensus 2 ~e~~iL~~L~~----~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~r 74 (349)
+|+.||.+|-+ ++.....+++|+.++.++..|...+.||.+-|||+-..-.+--|..|-..-+.+..-.||.-
T Consensus 7 ~QkeIL~aLi~LY~~~~r~IKgeeIA~~l~rnpGTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~iqt~~~~ 83 (294)
T COG2524 7 SQKEILQALINLYRRKKRPIKGEEIAEVLNRNPGTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALSIQTLETE 83 (294)
T ss_pred HHHHHHHHHHHHHHhcCCCcchHHHHHHHccCcchHHHHHHHHHhcCccccccCCCCCccccHHHHHHhccCCCCcc
Confidence 68899998854 34346789999999999999999999999999999999999999999999888888777544
No 173
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=86.96 E-value=1.8 Score=33.96 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=39.8
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
-.+||..|+.. ..+.++|.+.+|++.+.+.-.+..|..+|+|.-.
T Consensus 7 ~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 7 TQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 46788888766 5789999999999999999999999999999775
No 174
>PF13814 Replic_Relax: Replication-relaxation
Probab=86.90 E-value=1.4 Score=39.14 Aligned_cols=61 Identities=16% Similarity=0.146 Sum_probs=49.1
Q ss_pred HHHHhhCCCCCChHHHHHHhCCCHH---HHHHHHHHhccCCcEEEEee--------eeEEEEeChhHHHHhhc
Q 018851 7 LGYLEKNEQISDSGNFAAERGFDHN---DVVNVIKSLHGFRYIDAQDI--------KRETWVLTGEGKKYAAE 68 (349)
Q Consensus 7 L~~L~~~~~~~~~~~la~~~g~~~~---~v~~~~~~L~~kgli~~~~~--------~~~~~~LTeEG~~~l~~ 68 (349)
|..|..... .++++++..++.+.. .+.+.+..|...|+|..... ....|.||+.|.+++..
T Consensus 1 L~~L~~~r~-lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l~~ 72 (191)
T PF13814_consen 1 LRLLARHRF-LTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLLAD 72 (191)
T ss_pred ChhHHHhcC-cCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHHHh
Confidence 345555554 788899998887776 79999999999999988765 44689999999999964
No 175
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=86.89 E-value=1.3 Score=42.20 Aligned_cols=45 Identities=11% Similarity=0.073 Sum_probs=40.6
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
..+||..|..++. .+..++|+.+|++...|.+.++.|++.|+|.-
T Consensus 7 ~~~Il~~l~~~~~-~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r 51 (251)
T PRK13509 7 HQILLELLAQLGF-VTVEKVIERLGISPATARRDINKLDESGKLKK 51 (251)
T ss_pred HHHHHHHHHHcCC-cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 4679999998887 67899999999999999999999999999954
No 176
>COG3373 Uncharacterized protein conserved in archaea [Function unknown]
Probab=86.41 E-value=2.8 Score=34.50 Aligned_cols=64 Identities=23% Similarity=0.227 Sum_probs=47.5
Q ss_pred HHHHHHHHhhC-CCCCChHHHHHHhCCCHHHHHHHHH----------HhccCCcEEEEee-eeEEEEeChhHHHHh
Q 018851 3 EEAILGYLEKN-EQISDSGNFAAERGFDHNDVVNVIK----------SLHGFRYIDAQDI-KRETWVLTGEGKKYA 66 (349)
Q Consensus 3 e~~iL~~L~~~-~~~~~~~~la~~~g~~~~~v~~~~~----------~L~~kgli~~~~~-~~~~~~LTeEG~~~l 66 (349)
-.+||-.|-+- .-..-..|++...+-|++.|.+.++ ||-..|||+++++ -.+.|.|||.|+.+.
T Consensus 19 RrkiL~yLy~iYP~~~YLSEIsR~V~SDPSNV~GcL~Glg~RYnGe~SLi~LGLVe~~~~nGfKyykltdygkk~v 94 (108)
T COG3373 19 RRKILFYLYSIYPYRSYLSEISRAVKSDPSNVKGCLEGLGVRYNGEESLIGLGLVEVEQKNGFKYYKLTEYGKKMV 94 (108)
T ss_pred HHHHHHHHHHHccchhHHHHHHHHHcCCchHHHHHHHhcCCcccCchhhhhcceeEeeecCCEEEEehhHHHHHHH
Confidence 45677776542 1112346788888999999999986 6677899988776 566899999999865
No 177
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=86.41 E-value=1.2 Score=42.56 Aligned_cols=45 Identities=9% Similarity=0.115 Sum_probs=40.5
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
..+||..|...+. .+..+||+.++++...|.+.+..|++.|++.-
T Consensus 7 ~~~Il~~l~~~~~-~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r 51 (252)
T PRK10906 7 HDAIIELVKQQGY-VSTEELVEHFSVSPQTIRRDLNDLAEQNKILR 51 (252)
T ss_pred HHHHHHHHHHcCC-EeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 4679999988886 67899999999999999999999999999854
No 178
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=86.28 E-value=0.83 Score=46.81 Aligned_cols=86 Identities=19% Similarity=0.287 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+++.+.+.+...||+++.+ |.+... + ++.--.|...--.+.|.|.+.
T Consensus 176 ~~aL~~~~~~~~~~~G~~~v~~-P~lv~~----~-~~~~~G~~~~f~~~~y~i~~~------------------------ 225 (418)
T TIGR00414 176 ERALINFMLDLLEKNGYQEIYP-PYLVNE----E-SLDGTGQLPKFEEDIFKLEDT------------------------ 225 (418)
T ss_pred HHHHHHHHHHHHHHcCCEEEeC-CccccH----H-HHhhcCccccccccceEecCC------------------------
Confidence 4566777788888899999974 554322 2 112223333333467777531
Q ss_pred CCCcccccchhhhhccccC-CCCchhHHHHHHHhh--cCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLR-THTTAVSSRMLKALA--EKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~--~~~~~p~k~fsi~rVfR~ 349 (349)
...|| ||.+++.. |+... +...-|.|++.+++|||+
T Consensus 226 --------------~~~L~pTsE~~~~~--~~~~~i~s~~~LPlr~~~~s~~FR~ 264 (418)
T TIGR00414 226 --------------DLYLIPTAEVPLTN--LHRNEILEEEELPIKYTAHSPCFRS 264 (418)
T ss_pred --------------CEEEEeCCcHHHHH--HHhCcCCChHhCCeeEEEEcccccC
Confidence 35677 56555543 33211 112359999999999995
No 179
>cd00774 GlyRS-like_core Glycyl-tRNA synthetase (GlyRS)-like class II core catalytic domain. GlyRS functions as a homodimer in eukaryotes, archaea and some bacteria and as a heterotetramer in the remainder of prokaryotes. It is responsible for the attachment of glycine to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP binding and hydrolysis. This alignment contains only sequences from the GlyRS form which homodimerizes. The heterotetramer glyQ is in a different family of class II aaRS. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. This domain is also found at the N-terminus of the accessory subunit of mitochondrial polymerase gamma (Pol gamma b). Pol gamma b stimulates processive DNA synthesis and is functional as a homodimer, which can associate with the catalytic subunit Pol gamma alpha to form a heterotrimer. Despite significant both structural and sequence similarity with Gly
Probab=86.23 E-value=1 Score=42.77 Aligned_cols=30 Identities=7% Similarity=0.158 Sum_probs=25.0
Q ss_pred ChHHHHHHHHHHHHhhCC--ceecCCCCceeee
Q 018851 216 HPLLKVRKQLKDIFLQMG--FEEMPTNNFVESS 246 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mG--F~e~~~~~~Ves~ 246 (349)
.-.+.+.+.+++.|...| |.++.+ |.|++.
T Consensus 33 ~l~~~i~~~~~~~~~~~g~~~~~i~t-P~i~~~ 64 (254)
T cd00774 33 ELKNNIKSAWRKSFVLEEEDMLEIDS-PIITPE 64 (254)
T ss_pred HHHHHHHHHHHHHHHhcCCCeEEEec-cccCCH
Confidence 346788999999999996 999974 888777
No 180
>PRK12444 threonyl-tRNA synthetase; Reviewed
Probab=86.17 E-value=1.1 Score=48.20 Aligned_cols=91 Identities=13% Similarity=0.172 Sum_probs=55.1
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-...+.+.+++.+.+.||+++.+ |.++.. +. |.--.|=.-=..+.|+++.
T Consensus 276 ~~~~i~~~~~~~~~~~G~~~v~t-P~l~~~----~l-~~~sG~~~~~~~emy~~d~------------------------ 325 (639)
T PRK12444 276 IRNELEAFLREIQKEYNYQEVRT-PFMMNQ----EL-WERSGHWDHYKDNMYFSEV------------------------ 325 (639)
T ss_pred HHHHHHHHHHHHHHHcCCEEEEC-CccCCH----HH-HhhcCChhhhhhhcCeecC------------------------
Confidence 35678889999999999999985 555432 22 2222332111123343321
Q ss_pred CCCCcccccchhhhhccccCCCCchhHHHHHHHhhcC-CCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK-PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~-~~~p~k~fsi~rVfR~ 349 (349)
..+...||.=.|+.-+++....... ...|.|+|.++.|||.
T Consensus 326 ------------~~~~~~LrP~~~~~~~~~~~~~~~sy~~LP~r~~~~g~~fR~ 367 (639)
T PRK12444 326 ------------DNKSFALKPMNCPGHMLMFKNKLHSYRELPIRMCEFGQVHRH 367 (639)
T ss_pred ------------CCcEEEEccCCCHHHHHHHhCcccChhhCCceeEEeccccCC
Confidence 0125679976676667766422111 2359999999999995
No 181
>PF14502 HTH_41: Helix-turn-helix domain
Probab=86.16 E-value=1.5 Score=31.88 Aligned_cols=38 Identities=16% Similarity=0.261 Sum_probs=33.9
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 14 EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 14 ~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
+.+...++++++++++...|..|++.|++.|-|..+.+
T Consensus 4 dRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~r 41 (48)
T PF14502_consen 4 DRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLESR 41 (48)
T ss_pred cccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeec
Confidence 34566789999999999999999999999999998865
No 182
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=86.03 E-value=16 Score=33.70 Aligned_cols=103 Identities=8% Similarity=-0.005 Sum_probs=73.1
Q ss_pred hCCCC-CChHHHHHHhCCCHHHHHHHHHHhcc------CCcEEEEeeeeEEEEeChhHHHHhhcCCh----------HHH
Q 018851 12 KNEQI-SDSGNFAAERGFDHNDVVNVIKSLHG------FRYIDAQDIKRETWVLTGEGKKYAAEGSP----------EVQ 74 (349)
Q Consensus 12 ~~~~~-~~~~~la~~~g~~~~~v~~~~~~L~~------kgli~~~~~~~~~~~LTeEG~~~l~~G~P----------E~r 74 (349)
..+.+ .+..+||+.++++.++|..++..|.. .|+.-++....-.+.+-++=..++..=.+ .-.
T Consensus 15 ~sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~~~~~~~~LS~aaLE 94 (188)
T PRK00135 15 VSGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLVKTPIKQSLSQAALE 94 (188)
T ss_pred HcCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHhcccccCCCCHHHHH
Confidence 34443 78999999999999999999999944 36655555555567777776666653221 334
Q ss_pred HHHhcCcCCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeC
Q 018851 75 LFLAVPAEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 75 l~~~l~~~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~ 115 (349)
++..|.-.++++..+|.+..|.+. .=.+..++..|||...
T Consensus 95 tLaiIay~qPiTr~eI~~irGv~~-~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 95 VLAIIAYKQPITRIEIDEIRGVNS-DGALQTLLAKGLIKEV 134 (188)
T ss_pred HHHHHHHcCCcCHHHHHHHHCCCH-HHHHHHHHHCCCeEEc
Confidence 455555567899999998877554 4458999999999863
No 183
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=85.37 E-value=2 Score=40.40 Aligned_cols=61 Identities=15% Similarity=0.095 Sum_probs=46.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++..+.+.+. .-.-|+.+++++.+|.+.++.||+. |. ..=.+....+.||++|+.+++.
T Consensus 6 l~~f~~v~~~gs---~s~AA~~L~isqpavS~~I~~LE~~lG~-~LF~R~~r~~~lT~~G~~l~~~ 67 (275)
T PRK03601 6 LKTFLEVSRTRH---FGRAAESLYLTQSAVSFRIRQLENQLGV-NLFTRHRNNIRLTAAGERLLPY 67 (275)
T ss_pred HHHHHHHHHcCC---HHHHHHHhCCChHHHHHHHHHHHHHhCC-ceEEECCCceEECHhHHHHHHH
Confidence 455666666663 4567889999999999999999995 54 4444456789999999997754
No 184
>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=85.15 E-value=1.5 Score=35.67 Aligned_cols=47 Identities=17% Similarity=0.303 Sum_probs=37.8
Q ss_pred HHHHHHHHHhh---CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 2 AEEAILGYLEK---NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 2 ~e~~iL~~L~~---~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
+..+||.+|+. .+.-...+++++.++++..+|..++..|.+.|+|=.
T Consensus 48 ~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 48 LQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp HHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEec
Confidence 46789999987 222356789999999999999999999999999843
No 185
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=85.11 E-value=3.5 Score=35.68 Aligned_cols=50 Identities=16% Similarity=0.258 Sum_probs=41.6
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
.+.+-|.-++|..+|+++..|.+|-..|+..|+|.+....-.+ .|+.|.+
T Consensus 32 GdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~f--V~~~~~~ 81 (125)
T COG1725 32 GDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTF--VTEDAKE 81 (125)
T ss_pred CCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCeeEE--EcCCchh
Confidence 5567788999999999999999999999999999988876544 4555554
No 186
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=84.74 E-value=2 Score=40.78 Aligned_cols=60 Identities=17% Similarity=0.205 Sum_probs=48.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
..||.+|...+...+..++|+.+|++.+++.+.+..|+..|||.-... ...|.|+..=-+
T Consensus 7 l~iL~~l~~~~~~l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~-~g~Y~Lg~~~~~ 66 (246)
T COG1414 7 LAILDLLAEGPGGLSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPE-DGRYRLGPRLLE 66 (246)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCC-CCcEeehHHHHH
Confidence 368899987554345789999999999999999999999999987765 347888765443
No 187
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=84.73 E-value=2 Score=40.25 Aligned_cols=62 Identities=15% Similarity=0.038 Sum_probs=46.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++.+.+. ...-|+.+++++.+|.+.++.||+.==+..-.+....+.||++|+..+..
T Consensus 6 L~~f~~v~~~gs---~s~AA~~L~isqsavS~~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~ 67 (296)
T PRK11242 6 IRYFLAVAEHGN---FTRAAEALHVSQPTLSQQIRQLEESLGVQLFDRSGRTVRLTDAGEVYLRY 67 (296)
T ss_pred HHHHHHHHHhCC---HHHHHHHcCCCchHHHHHHHHHHHHhCCeeEeEcCCceeechhHHHHHHH
Confidence 356666766664 44678899999999999999999952233344457789999999987754
No 188
>PRK14799 thrS threonyl-tRNA synthetase; Provisional
Probab=84.23 E-value=1.8 Score=46.06 Aligned_cols=90 Identities=12% Similarity=0.076 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+.+.+++.+.+.||+++.| |.|+. .+-+-. ..|=..-..+.|.++.
T Consensus 171 ~~~L~~~~r~~~~~~Gy~eV~T-P~i~~----~eL~k~-SGh~~~y~~~mf~~~~------------------------- 219 (545)
T PRK14799 171 RNELIAFMREINDSMGYQEVYT-SHVFK----TDIWKI-SGHYTLYRDKLIVFNM------------------------- 219 (545)
T ss_pred HHHHHHHHHHHHHHcCCeEEEC-Cccch----HHHHhh-ccccccchhhcceeec-------------------------
Confidence 5678888999999999999985 66532 222222 3443222222333321
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcC-CCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK-PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~-~~~p~k~fsi~rVfR~ 349 (349)
+.+...||.=.|+.-+++....... ..-|.|++.++.|||.
T Consensus 220 -----------~~e~~~LrPm~cp~~~~~~~~~~~SyrdLPlR~~e~g~vfR~ 261 (545)
T PRK14799 220 -----------EGDEYGVKPMNCPAHILIYKSKPRTYRDLPIRFSEFGHVYRW 261 (545)
T ss_pred -----------cCceEEeccCCCHHHHHHHhccccChhhCCHhhEEecceecC
Confidence 0136889987777777776532211 2469999999999995
No 189
>TIGR00408 proS_fam_I prolyl-tRNA synthetase, family I. Prolyl-tRNA synthetase is a class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes tRNA synthetases for Gly, His, Ser, and Pro. The prolyl-tRNA synthetases are divided into two widely divergent families. This family includes the archaeal enzyme, the Pro-specific domain of a human multifunctional tRNA ligase, and the enzyme from the spirochete Borrelia burgdorferi. The other family includes enzymes from Escherichia coli, Bacillus subtilis, Synechocystis PCC6803, and one of the two prolyL-tRNA synthetases of Saccharomyces cerevisiae.
Probab=84.03 E-value=0.91 Score=47.21 Aligned_cols=96 Identities=18% Similarity=0.184 Sum_probs=56.7
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+.+.+++.|.+.||+++.+ |.+++ -+.+..=-.|-.-=..+.|.+.+...
T Consensus 41 ~~~I~~~i~~~~~~~G~~ev~~-P~l~~----~~~~~~~~~h~~~f~~e~f~v~~~g~---------------------- 93 (472)
T TIGR00408 41 WKNIQKILRNILDEIGHEEVYF-PMLIP----ESELAKEKDHIKGFEPEVYWITHGGL---------------------- 93 (472)
T ss_pred HHHHHHHHHHHHHHcCCEEEEC-CccCC----HHHHHhhcchhhhcchhcEEEecCCC----------------------
Confidence 6778888899999999999974 66543 22222112333222235788865210
Q ss_pred CCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.+..+.+.|| ||++++..-+-....+...-|.|++.+++|||.
T Consensus 94 ---------~~~~e~l~LrPt~e~~i~~~~~~~i~S~rdLPlr~~q~~~vfR~ 137 (472)
T TIGR00408 94 ---------SKLDEPLALRPTSETAMYPMFKKWVKSYTDLPLKINQWVNVFRY 137 (472)
T ss_pred ---------CccCCcEEEeCCCcHHHHHHHhccccChhhcCHHHhheeeeecC
Confidence 0112368999 566555432222112223469999999999994
No 190
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=83.91 E-value=2.5 Score=37.10 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=40.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
.++|+.+...+. .+..|+|+..|-+...|.+.+..|+.-|+|..+.
T Consensus 67 leLl~~Ia~~~P-~Si~ElAe~vgRdv~nvhr~Ls~l~~~GlI~fe~ 112 (144)
T COG4190 67 LELLELIAQEEP-ASINELAELVGRDVKNVHRTLSTLADLGLIFFEE 112 (144)
T ss_pred HHHHHHHHhcCc-ccHHHHHHHhCcchHHHHHHHHHHHhcCeEEEec
Confidence 457777777665 7889999999999999999999999999999987
No 191
>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=83.89 E-value=1.6 Score=36.96 Aligned_cols=46 Identities=20% Similarity=0.298 Sum_probs=37.9
Q ss_pred HHHHHHhhC-CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 5 AILGYLEKN-EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 5 ~iL~~L~~~-~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
.+|..|... +...+..++|+.+|++...|.+.+..|+..|+|....
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEecC
Confidence 466677643 3446889999999999999999999999999997643
No 192
>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=83.69 E-value=2.2 Score=32.17 Aligned_cols=35 Identities=17% Similarity=0.192 Sum_probs=31.5
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
.+.+++|..+|++.+.|.+.++.|+..|+|.++..
T Consensus 29 lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 29 LTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp SSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 35689999999999999999999999999997654
No 193
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=83.61 E-value=2.4 Score=40.08 Aligned_cols=48 Identities=13% Similarity=0.111 Sum_probs=41.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
.+|...++..+...+++++|+.+|+++.++.+++.+|++.|.+..+..
T Consensus 161 ~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~i~ 208 (224)
T COG4565 161 QKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAEIH 208 (224)
T ss_pred HHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEEee
Confidence 567777875556688999999999999999999999999999988753
No 194
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=83.52 E-value=1.6 Score=44.84 Aligned_cols=88 Identities=13% Similarity=0.197 Sum_probs=51.6
Q ss_pred HHHHHHHHHHHHh-hCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 218 LLKVRKQLKDIFL-QMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 218 l~~~~~~ir~if~-~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
...+++.+.+.+. ..||+++.+ |.+.. -+.+ .--.|=.+...+.|.|.+.
T Consensus 173 ~~aL~~~~~~~~~~~~G~~ev~~-P~lv~----~~~~-~~~G~~~~f~~~ly~i~~~----------------------- 223 (425)
T PRK05431 173 ERALIQFMLDLHTEEHGYTEVIP-PYLVN----EESM-YGTGQLPKFEEDLYKIEDD----------------------- 223 (425)
T ss_pred HHHHHHHHHHHHHHhcCCEEEec-ccccc----HHHH-hhcCccccchhhceEecCC-----------------------
Confidence 3455556677777 899999974 54432 2222 2235555556667777531
Q ss_pred CCCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 297 GSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
...|+ ||..++.+-+-...-+...-|.|++.+++|||+
T Consensus 224 ---------------~~~L~pTsE~~l~~l~~~~~~s~~dLPlr~~~~s~~fR~ 262 (425)
T PRK05431 224 ---------------DLYLIPTAEVPLTNLHRDEILDEEELPLKYTAYSPCFRS 262 (425)
T ss_pred ---------------CEEEEeCCcHHHHHHHhcccCCHHhCCeeEEEEcCEecC
Confidence 34666 666666422221111112359999999999995
No 195
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=83.50 E-value=1.3 Score=42.28 Aligned_cols=63 Identities=14% Similarity=0.118 Sum_probs=48.9
Q ss_pred HHHHHHHHhh--CCCCCChHHHHHHhCCCHHHHHHHHH-HhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 3 EEAILGYLEK--NEQISDSGNFAAERGFDHNDVVNVIK-SLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 3 e~~iL~~L~~--~~~~~~~~~la~~~g~~~~~v~~~~~-~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+...|.++.. .+...+..++|..+|.++..+...+. .|-.+|+|. ....-...|++|.+|+++
T Consensus 240 ~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~---~~~~g~~~~~~~~~~~~~ 305 (305)
T TIGR00635 240 DRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ---RTPRGRIATELAYEHLGL 305 (305)
T ss_pred HHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc---cCCchhhhhHHHHHHhCC
Confidence 3446665533 23236789999999999999999999 699999994 445567889999999864
No 196
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=83.44 E-value=1.4 Score=40.16 Aligned_cols=45 Identities=13% Similarity=0.053 Sum_probs=40.5
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
+.+||..|..++. .+..+||+.+|++...|.+.+..|+..|++.-
T Consensus 9 ~~~Il~~l~~~~~-~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r 53 (185)
T PRK04424 9 QKALQELIEENPF-ITDEELAEKFGVSIQTIRLDRMELGIPELRER 53 (185)
T ss_pred HHHHHHHHHHCCC-EEHHHHHHHHCcCHHHHHHHHHHHhcchHHHH
Confidence 4679999998887 67899999999999999999999999999854
No 197
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=83.11 E-value=2.8 Score=36.12 Aligned_cols=47 Identities=19% Similarity=0.241 Sum_probs=41.0
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeCh
Q 018851 14 EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60 (349)
Q Consensus 14 ~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTe 60 (349)
+...+..++|+.+|++..-|..++..|+..|+|+......--|.|+.
T Consensus 23 g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 23 GRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred CCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 34567789999999999999999999999999999988877777764
No 198
>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=83.01 E-value=2.1 Score=31.85 Aligned_cols=35 Identities=14% Similarity=0.237 Sum_probs=30.1
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
+..++|+.+|++...|..++..|++.|+|......
T Consensus 26 s~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 26 SERELAERYGVSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred CHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence 67889999999999999999999999999887643
No 199
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=82.13 E-value=2.3 Score=40.85 Aligned_cols=44 Identities=16% Similarity=0.137 Sum_probs=40.1
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
..+|+..|...+. .+..+||+.+|++...|.+.+..|++.|++.
T Consensus 19 ~~~Il~~L~~~~~-vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~ 62 (269)
T PRK09802 19 REQIIQRLRQQGS-VQVNDLSALYGVSTVTIRNDLAFLEKQGIAV 62 (269)
T ss_pred HHHHHHHHHHcCC-EeHHHHHHHHCCCHHHHHHHHHHHHhCCCeE
Confidence 4578999988887 7789999999999999999999999999997
No 200
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=82.06 E-value=4.7 Score=32.66 Aligned_cols=41 Identities=24% Similarity=0.367 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhh
Q 018851 27 GFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAA 67 (349)
Q Consensus 27 g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~ 67 (349)
.....++.-++.|||..|+|.-... ..++|.+|+.|...+.
T Consensus 38 ~~TKNelL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~ 79 (85)
T PF11313_consen 38 DFTKNELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLA 79 (85)
T ss_pred cccHHHHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHH
Confidence 3456789999999999999965443 5568999999998664
No 201
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=81.88 E-value=1.5 Score=40.42 Aligned_cols=79 Identities=19% Similarity=0.296 Sum_probs=34.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe-eeeEEEEeChhHHHHhhcCChHHHHHHhcCcCC
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD-IKRETWVLTGEGKKYAAEGSPEVQLFLAVPAEG 83 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~-~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~g 83 (349)
..+.++.... +...++||..+|+..++++.-|..|++.|.|+--. ..-.++-+|++--.. |..+|...|
T Consensus 103 ~Fi~yIK~~K-vv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~eE~~~---------va~fi~~rG 172 (188)
T PF09756_consen 103 EFINYIKEHK-VVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISEEEMEA---------VAKFIKQRG 172 (188)
T ss_dssp HHHHHHHH-S-EE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--------------------------
T ss_pred HHHHHHHHcc-eeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecHHHHHH---------HHHHHHHcC
Confidence 3455665555 47889999999999999999999999998875422 233566777776543 457888888
Q ss_pred CCCHHHHHhh
Q 018851 84 SISKDELQKK 93 (349)
Q Consensus 84 ~~~~~el~~~ 93 (349)
.+|+.+|...
T Consensus 173 Rvsi~el~~~ 182 (188)
T PF09756_consen 173 RVSISELAQE 182 (188)
T ss_dssp ----------
T ss_pred CccHHHHHHH
Confidence 8999998763
No 202
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=81.67 E-value=2.4 Score=38.91 Aligned_cols=61 Identities=16% Similarity=0.189 Sum_probs=51.4
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG 62 (349)
-+.+||..|...+.-...-++|.++|++...|.+.+..|+..|.|......--.|.++-+-
T Consensus 5 ~~~~i~~~l~~~~~~~~a~~i~k~l~i~k~~vNr~LY~L~~~~~v~~~~~~pP~W~~~~~~ 65 (183)
T PHA02701 5 CASLILTLLSSSGDKLPAKRIAKELGISKHEANRCLYRLLESDAVSCEDGCPPLWSVECEP 65 (183)
T ss_pred HHHHHHHHHHhcCCCCcHHHHHHHhCccHHHHHHHHHHHhhcCcEecCCCCCCccccccCC
Confidence 3678999999887326678999999999999999999999999998887766677776554
No 203
>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=81.61 E-value=0.88 Score=34.19 Aligned_cols=47 Identities=17% Similarity=0.273 Sum_probs=38.7
Q ss_pred hHHHHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeCce
Q 018851 71 PEVQLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMGKQ 117 (349)
Q Consensus 71 PE~rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~~~ 117 (349)
-|.++|.+|-..|+.+..||.+.+| .+...-.+..+.++|||...++
T Consensus 9 ~E~~vy~~Ll~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 9 NEAKVYLALLKNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHHHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 4889998886667799999998865 5566678999999999988766
No 204
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=80.86 E-value=3.5 Score=38.49 Aligned_cols=61 Identities=11% Similarity=0.100 Sum_probs=46.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++.+.+. .-.-|+.+++.+.+|.+.++.||+. |.-=. .+....+.||+.|+.++..
T Consensus 8 L~~f~~v~e~~s---~t~AA~~L~isqpavS~~I~~LE~~lg~~Lf-~R~~r~~~lT~~G~~l~~~ 69 (290)
T PRK10837 8 LEVFAEVLKSGS---TTQASVMLALSQSAVSAALTDLEGQLGVQLF-DRVGKRLVVNEHGRLLYPR 69 (290)
T ss_pred HHHHHHHHHcCC---HHHHHHHhCCCccHHHHHHHHHHHHhCCccE-eecCCeEEECHhHHHHHHH
Confidence 345566666653 4567889999999999999999996 54444 4455679999999998764
No 205
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=80.83 E-value=3.1 Score=36.67 Aligned_cols=61 Identities=15% Similarity=0.140 Sum_probs=49.9
Q ss_pred HHHHHHhhCCC--CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHH
Q 018851 5 AILGYLEKNEQ--ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKY 65 (349)
Q Consensus 5 ~iL~~L~~~~~--~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~ 65 (349)
.+|-.|+.... +.++.++|+..|+++.-+.+.+..|...|||+...-..-=|.|.-...++
T Consensus 12 ~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~~~I 74 (150)
T COG1959 12 RALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPPEEI 74 (150)
T ss_pred HHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCChHHC
Confidence 45666665333 67789999999999999999999999999999998888788887666553
No 206
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=80.66 E-value=4.3 Score=38.91 Aligned_cols=62 Identities=11% Similarity=-0.031 Sum_probs=46.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++..+...+ +....|+.+++++.+|.+.++.||+.==+..=.+....+.||++|+.+++.
T Consensus 7 L~~f~~v~e~g---s~s~AA~~L~iSQpavS~~I~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~ 68 (308)
T PRK10094 7 LRTFIAVAETG---SFSKAAERLCKTTATISYRIKLLEENTGVALFFRTTRSVTLTAAGEHLLSQ 68 (308)
T ss_pred HHHHHHHHHhC---CHHHHHHHhcCCHHHHHHHHHHHHHHhCCEEEeeCCCceeECHhHHHHHHH
Confidence 34555665555 345778999999999999999999963234444556689999999998754
No 207
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=80.59 E-value=2.5 Score=38.94 Aligned_cols=60 Identities=12% Similarity=0.107 Sum_probs=45.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+.+.++.+.+. ....|+.+++++.+|.+.++.||+. |. ..-.+....+.||++|+..++.
T Consensus 3 ~~f~~v~~~gs---~~~AA~~L~isqsavS~~i~~LE~~lg~-~Lf~R~~~~~~lT~~G~~l~~~ 63 (279)
T TIGR03339 3 KAFHAVARCGS---FTRAAERLGLSQPTVTDQVRKLEERYGV-ELFHRNGRRLELTDAGHRLLPI 63 (279)
T ss_pred hhhHHHHhcCC---HHHHHHHhcCCchHHHHHHHHHHHHhCC-ccEEEcCCeEEEChhHHHHHHH
Confidence 45566666653 4467889999999999999999996 43 3333466789999999987744
No 208
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=80.33 E-value=3.9 Score=38.94 Aligned_cols=60 Identities=15% Similarity=0.036 Sum_probs=45.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++...+. ...-|+.+++++.+|.+.++.||+. |.- .-.+....+.||++|+.++..
T Consensus 14 ~~F~~va~~gs---~s~AA~~L~isQpavS~~I~~LE~~lg~~-Lf~R~~r~~~lT~~G~~l~~~ 74 (302)
T TIGR02036 14 HTFEVAARHQS---FSLAAEELSLTPSAISHRINQLEEELGIQ-LFVRSHRKVELTHEGKRIYWA 74 (302)
T ss_pred HHHHHHHHhCC---HHHHHHHHCCCHHHHHHHHHHHHHHhCCc-eEEECCCceeECHhHHHHHHH
Confidence 44455555553 4467888999999999999999996 543 345567799999999998754
No 209
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=80.24 E-value=3.7 Score=38.88 Aligned_cols=61 Identities=8% Similarity=0.020 Sum_probs=47.2
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
+++.++.+.+. .-.-|+.+++++.+|.+.++.||+. |.-=.++ ....+.||++|+.++...
T Consensus 11 ~~f~~v~~~gs---~s~AA~~L~isQ~avS~~i~~LE~~lG~~LF~R-~~r~~~lT~~G~~l~~~a 72 (302)
T PRK09791 11 RAFVEVARQGS---IRGASRMLNMSQPALTKSIQELEEGLAAQLFFR-RSKGVTLTDAGESFYQHA 72 (302)
T ss_pred HHHHHHHHcCC---HHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEE-cCCCceECccHHHHHHHH
Confidence 45566665653 4567889999999999999999996 6655554 556799999999987543
No 210
>PLN02678 seryl-tRNA synthetase
Probab=80.04 E-value=2.3 Score=44.22 Aligned_cols=91 Identities=12% Similarity=0.136 Sum_probs=55.9
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
-+.+++.+.+.+..-||+++.+ |.+.. ..++.--.|+..-..|.|.+.....
T Consensus 177 ~~AL~~y~ld~~~~~Gy~~V~~-P~lv~-----~~~~~~sG~~~~f~e~my~i~~~~~---------------------- 228 (448)
T PLN02678 177 NQALINFGLAFLRKRGYTPLQT-PFFMR-----KDVMAKCAQLAQFDEELYKVTGEGD---------------------- 228 (448)
T ss_pred HHHHHHHHHHHHHHcCCEEEEC-ccccc-----HHHHhhcCCcccchhcCceecCCCC----------------------
Confidence 4567777888888889999974 66643 2333444566666668888853100
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
...++.|.-.+...-+.-..-+...-|.||+.+++|||+
T Consensus 229 -------------~~yLi~TaE~~l~~~h~~~~~s~~eLPlr~~~~s~cfR~ 267 (448)
T PLN02678 229 -------------DKYLIATSEQPLCAYHRGDWIDPKELPIRYAGYSTCFRK 267 (448)
T ss_pred -------------ceeeecccccccChHHhcccCCHHhCCceeEEecccccc
Confidence 146777753333333321111112359999999999996
No 211
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=79.95 E-value=4.2 Score=38.89 Aligned_cols=60 Identities=17% Similarity=0.200 Sum_probs=46.1
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++.+.+ +....|+.+++++.+|.+.++.||.. |.-=. .+....+.||++|+.+++.
T Consensus 13 ~~F~av~e~g---s~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF-~R~~r~~~lT~~G~~l~~~ 73 (312)
T PRK10341 13 VVFQEVIRSG---SIGSAAKELGLTQPAVSKIINDIEDYFGVELI-VRKNTGVTLTPAGQVLLSR 73 (312)
T ss_pred HHHHHHHHcC---CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEE-EEcCCCceEChhHHHHHHH
Confidence 4455565555 35577889999999999999999996 54444 4455689999999998864
No 212
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=79.86 E-value=2.8 Score=29.21 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=31.8
Q ss_pred HHHHHHhcCcCCCCCHHHHHhhcCch--hhhhHHHHHhhCCcEe
Q 018851 72 EVQLFLAVPAEGSISKDELQKKLDPA--VFKIGCSQAGKNKWVE 113 (349)
Q Consensus 72 E~rl~~~l~~~g~~~~~el~~~~~~~--~~~ig~g~~~k~~wi~ 113 (349)
+.+|+.+|.++++++..+|.+.+|-+ ...--+..+.+.|+|+
T Consensus 5 ~~~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 57889999887789999999986533 4455678888888874
No 213
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=79.83 E-value=3.4 Score=38.88 Aligned_cols=60 Identities=12% Similarity=0.034 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
.+++.++.+.+. .-..|+.+++++.+|.+.++.||+. |.-=.+ +....+.||+.|+.+++
T Consensus 8 l~~f~~v~~~gS---~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~-R~~~~~~lT~~G~~l~~ 68 (300)
T TIGR02424 8 LQCFVEVARQGS---VKRAAEALHITQPAVSKTLRELEEILGTPLFE-RDRRGIRLTRYGELFLR 68 (300)
T ss_pred HHHHHHHHHhCC---HHHHHHHhCCChHHHHHHHHHHHHHhCCeEEE-EcCCCccccHhHHHHHH
Confidence 345666666653 4567889999999999999999996 544444 45667899999999874
No 214
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=79.74 E-value=4.1 Score=40.16 Aligned_cols=57 Identities=14% Similarity=0.126 Sum_probs=47.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
.||.++-..+ |.-.++....++.-.+.+.+..|+..|+|++++.. ..||+.|++.++
T Consensus 26 ~vl~ail~~~---d~wkIvd~s~~plp~v~~i~~~l~~egiv~~~~g~---v~~TekG~E~~e 82 (354)
T COG1568 26 NVLSAILATN---DFWKIVDYSDLPLPLVASILEILEDEGIVKIEEGG---VELTEKGEELAE 82 (354)
T ss_pred HHHHHHHcCc---chHhhhhhccCCchHHHHHHHHHHhcCcEEEecCc---EeehhhhHHHHH
Confidence 4666665554 56677777888999999999999999999998876 889999999886
No 215
>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=79.54 E-value=4.6 Score=34.59 Aligned_cols=57 Identities=7% Similarity=0.029 Sum_probs=42.9
Q ss_pred HHHHHHhh--CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 5 AILGYLEK--NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 5 ~iL~~L~~--~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
++|..|+. .+...++.++|+.++++..-+...+..|...|+|....-..--|.|+..
T Consensus 12 ~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~ 70 (135)
T TIGR02010 12 TAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRP 70 (135)
T ss_pred HHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCC
Confidence 45666653 2335788999999999999999999999999999875444435555543
No 216
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=79.46 E-value=3.9 Score=38.64 Aligned_cols=45 Identities=13% Similarity=0.149 Sum_probs=40.3
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
+.+||..|...+. .+..++|+.+|++...|.+.++.|+..|+|..
T Consensus 6 ~~~Il~~l~~~~~-~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r 50 (240)
T PRK10411 6 QQAIVDLLLNHTS-LTTEALAEQLNVSKETIRRDLNELQTQGKILR 50 (240)
T ss_pred HHHHHHHHHHcCC-CcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE
Confidence 5679999988776 77899999999999999999999999998865
No 217
>PLN02908 threonyl-tRNA synthetase
Probab=79.28 E-value=2.9 Score=45.56 Aligned_cols=92 Identities=15% Similarity=0.181 Sum_probs=58.1
Q ss_pred ChHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC
Q 018851 216 HPLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG 295 (349)
Q Consensus 216 HPl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg 295 (349)
+-.+.+++.+++.+...||+++.| |.+ .|.+.+-. -.|=..-..+.|-++.
T Consensus 322 ~i~~~l~~~~~~~~~~~G~~ev~t-P~l----~~~~l~~~-sGh~~~~~~~mf~~~~----------------------- 372 (686)
T PLN02908 322 RIYNKLMDFIREQYWERGYDEVIT-PNI----YNMDLWET-SGHAAHYKENMFVFEI----------------------- 372 (686)
T ss_pred HHHHHHHHHHHHHHHHcCCEEEEC-Ccc----ccHHHHhh-cCCccccchhccEEec-----------------------
Confidence 346788899999999999999975 554 33333322 4555444444555421
Q ss_pred CCCCCcccccchhhhhccccCCCCchhHHHHHHHhhcC-CCCCceEEecCceecC
Q 018851 296 YGSRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEK-PFAPKKVFLHRSCFQK 349 (349)
Q Consensus 296 ~gS~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~-~~~p~k~fsi~rVfR~ 349 (349)
+.+...||.=++..-+++....... ..-|.|++.+++|||.
T Consensus 373 -------------~~~~~~Lrp~~~~~~~~~~~~~~~s~r~LPlr~~~~g~~fR~ 414 (686)
T PLN02908 373 -------------EKQEFGLKPMNCPGHCLMFAHRVRSYRELPLRLADFGVLHRN 414 (686)
T ss_pred -------------CCeeEEEcCCCcHHHHHHHhccccChhhCCHhHEEeeccccC
Confidence 0125789966665556655432111 2369999999999995
No 218
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=79.24 E-value=3.4 Score=38.65 Aligned_cols=62 Identities=19% Similarity=0.037 Sum_probs=46.0
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++...+. ...-|+.+++++.+|.+.++.||+.==+..-.+....+.||+.|+.+++.
T Consensus 12 l~~f~~v~~~gs---~t~AA~~L~itq~avS~~i~~LE~~lg~~Lf~R~~r~~~lT~~G~~l~~~ 73 (294)
T PRK09986 12 LRYFLAVAEELH---FGRAAARLNISQPPLSIHIKELEDQLGTPLFIRHSRSVVLTHAGKILMEE 73 (294)
T ss_pred HHHHHHHHHhcC---HHHHHHHhCCCCCHHHHHHHHHHHHhCCeeEeeCCCceeECHhHHHHHHH
Confidence 345556665653 44678889999999999999999962233444456789999999988743
No 219
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=79.05 E-value=4.7 Score=38.94 Aligned_cols=60 Identities=13% Similarity=0.020 Sum_probs=45.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++.+.+ +...-|+++++++.+|.+.++.||+. |.-=.+. ....+.||++|+..++.
T Consensus 8 ~~f~av~~~g---s~s~AA~~L~iSqpaVS~~Ik~LE~~lg~~LF~R-~~r~v~lT~~G~~l~~~ 68 (317)
T PRK15421 8 KTLQALRNCG---SLAAAAATLHQTQSALSHQFSDLEQRLGFRLFVR-KSQPLRFTPQGEILLQL 68 (317)
T ss_pred HHHHHHHHcC---CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEEEEe-cCCCceECHhHHHHHHH
Confidence 4555555555 34567889999999999999999996 5544444 45678999999998744
No 220
>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=78.88 E-value=3.4 Score=37.44 Aligned_cols=39 Identities=13% Similarity=0.185 Sum_probs=34.0
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEE
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRET 55 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~ 55 (349)
.+..+||+.+|++...|..|+..|++.|+|++....-..
T Consensus 35 L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~G~~ 73 (212)
T TIGR03338 35 LNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNRGVF 73 (212)
T ss_pred ecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCCCeE
Confidence 456789999999999999999999999999987765443
No 221
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=78.86 E-value=4.8 Score=38.17 Aligned_cols=60 Identities=13% Similarity=-0.110 Sum_probs=44.9
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++..+.+.+. .-.-|+.+|+++.+|.+.++.||+. |.-= -.+....+.||++|+.+++.
T Consensus 10 ~~F~~v~e~gs---~s~AA~~L~isqpavS~~I~~LE~~lg~~L-f~R~~r~~~lT~~G~~l~~~ 70 (296)
T PRK11062 10 YYFWMVCKEGS---VVGAAEALFLTPQTITGQIKALEERLQGKL-FKRKGRGLEPTELGELVFRY 70 (296)
T ss_pred HHHHHHHhcCC---HHHHHHHhCCChHHHHHHHHHHHHHcCccc-eeecCCceeECHhHHHHHHH
Confidence 44555555553 4467889999999999999999996 5433 34456789999999987744
No 222
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=78.86 E-value=4.5 Score=38.84 Aligned_cols=63 Identities=13% Similarity=-0.020 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++..+...+. +.-.-|+.+++++.+|.+.++.||.. |.-=.+......+.||+.|+.++..
T Consensus 6 l~~f~~v~~~~~--s~s~AA~~L~iSQ~avSr~I~~LE~~lg~~LF~R~~~~~~~lT~~G~~l~~~ 69 (316)
T PRK12679 6 LKIIREAARQDY--NLTEVANMLFTSQSGVSRHIRELEDELGIEIFIRRGKRLLGMTEPGKALLVI 69 (316)
T ss_pred HHHHHHHHHcCC--CHHHHHHHhcCCchHHHHHHHHHHHHhCCEEEEECCCcccccCHhHHHHHHH
Confidence 345555555542 34567889999999999999999995 6555555444447899999987644
No 223
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=78.60 E-value=4.7 Score=37.59 Aligned_cols=52 Identities=8% Similarity=0.045 Sum_probs=40.8
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+|...+..++.+-+-.+||+.+|++...|.+|+..|...|+|......-+++
T Consensus 24 ~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~GtfV 75 (241)
T PRK10079 24 ELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQGVGVLV 75 (241)
T ss_pred HHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 3433344455566667899999999999999999999999999877766554
No 224
>PTZ00417 lysine-tRNA ligase; Provisional
Probab=78.30 E-value=4.3 Score=43.54 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESS 246 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~ 246 (349)
.+++..||++|.+.||.|+.| |.+.+.
T Consensus 257 S~Ii~aiR~Ff~~rGFlEVeT-PiL~~~ 283 (585)
T PTZ00417 257 TKIINYLRNFLNDRGFIEVET-PTMNLV 283 (585)
T ss_pred HHHHHHHHHHHHHCCeEEEeC-Ceeecc
Confidence 467889999999999999986 666443
No 225
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=78.18 E-value=5.3 Score=37.65 Aligned_cols=61 Identities=10% Similarity=-0.037 Sum_probs=46.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++.+.+. ...-|+.+++++.+|.+.++.||+. |.-=.+ +....++||+.|+.++..
T Consensus 7 L~~f~~va~~gs---~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~-R~~r~~~lT~~G~~l~~~ 68 (301)
T PRK14997 7 FAWFVHVVEEGG---FAAAGRALDEPKSKLSRRIAQLEERLGVRLIQ-RTTRQFNVTEVGQTFYEH 68 (301)
T ss_pred HHHHHHHHHcCC---HHHHHHHhCCCHHHHHHHHHHHHHHhCCEeee-eccCcceEcHhHHHHHHH
Confidence 355666666653 4567889999999999999999996 554444 456689999999987744
No 226
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=77.94 E-value=3 Score=41.58 Aligned_cols=64 Identities=17% Similarity=0.316 Sum_probs=50.7
Q ss_pred HHHHHH-----HHhhCCCCCChHHHHHH--hCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 3 EEAILG-----YLEKNEQISDSGNFAAE--RGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 3 e~~iL~-----~L~~~~~~~~~~~la~~--~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++||. .+...+ +..+.++|+. +++++..|.+.+..|++.|++. .....--...|+.|-+|--+
T Consensus 8 ~~~Il~~IV~~yi~~~~-pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~-~~h~sagrIPT~kGYR~YVd 78 (339)
T PRK00082 8 QREILRAIVEDYIATGE-PVGSKTLSKRYGLGVSSATIRNDMADLEELGLLE-KPHTSSGRIPTDKGYRYFVD 78 (339)
T ss_pred HHHHHHHHHHHHHhcCC-CcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcC-CCcCCCCCCcCHHHHHHHHH
Confidence 466787 455444 4788899966 9999999999999999999998 45555577999999886533
No 227
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=77.74 E-value=3.9 Score=38.45 Aligned_cols=61 Identities=11% Similarity=0.060 Sum_probs=46.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++.+.+. ....|+.+++++.+|.+.++.||..==+..=.+....+.||++|+..++.
T Consensus 7 ~~f~~v~~~gs---~s~AA~~L~isQ~avSr~i~~LE~~lg~~Lf~R~~~~~~lT~~G~~l~~~ 67 (296)
T PRK09906 7 RYFVAVAEELN---FTKAAEKLHTAQPSLSQQIKDLENCVGVPLLVRDKRKVALTAAGEVFLQD 67 (296)
T ss_pred HHHHHHHhhCC---HHHHHHHhCCCCcHHHHHHHHHHHHhCCeeeeeCCCcceEcHhHHHHHHH
Confidence 45566666653 45678899999999999999999963334445567789999999998753
No 228
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=77.29 E-value=4.9 Score=38.30 Aligned_cols=61 Identities=13% Similarity=-0.065 Sum_probs=43.4
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEE-EeChhHHHHhhcC
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETW-VLTGEGKKYAAEG 69 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~-~LTeEG~~~l~~G 69 (349)
.+.++...+. +....|+.+++++.+|.+.++.||+. |.-=.+. ....+ .||+.|+.+++..
T Consensus 8 ~F~~v~~~~~--s~s~AA~~L~isq~avSr~I~~LE~~lg~~LF~R-~~~~~~~lT~~G~~l~~~~ 70 (309)
T PRK12682 8 FVREAVRRNL--NLTEAAKALHTSQPGVSKAIIELEEELGIEIFIR-HGKRLKGLTEPGKAVLDVI 70 (309)
T ss_pred HHHHHHHccC--CHHHHHHHhcCccHHHHHHHHHHHHHhCCeeEEE-CCCCcCccCHhHHHHHHHH
Confidence 3334444442 35577889999999999999999995 5544444 44454 8999999987553
No 229
>PRK10632 transcriptional regulator; Provisional
Probab=77.15 E-value=4.6 Score=38.58 Aligned_cols=63 Identities=10% Similarity=0.060 Sum_probs=46.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
.+++.++.+.+. .-.-|+.+++++.+|.+.++.||..==+..=.+....+.||++|+.+++..
T Consensus 7 L~~F~~v~e~gS---~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R~~r~i~lT~~G~~l~~~a 69 (309)
T PRK10632 7 MSVFAKVVEFGS---FTAAARQLQMSVSSISQTVSKLEDELQVKLLNRSTRSIGLTEAGRIYYQGC 69 (309)
T ss_pred HHHHHHHHhcCC---HHHHHHHhCCCHHHHHHHHHHHHHHhCCeeecccCCCceechhHHHHHHHH
Confidence 345566666653 446788999999999999999999622334445566799999999987543
No 230
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=77.10 E-value=11 Score=39.86 Aligned_cols=88 Identities=17% Similarity=0.201 Sum_probs=57.7
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHh----ccCCcEEEEeeeeEEEEeC----hhHHHHhhcCChHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSL----HGFRYIDAQDIKRETWVLT----GEGKKYAAEGSPEVQ 74 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L----~~kgli~~~~~~~~~~~LT----eEG~~~l~~G~PE~r 74 (349)
+.+||..|.. +. .+..+||+.+|++...|.+.++.| +..|+..+.... -|.|. +....++..-.||++
T Consensus 6 ~~~iL~~L~~-~~-~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~~~--Gy~l~~~~~~~~~~~~~~~~~e~~ 81 (584)
T PRK09863 6 ELKIVDLLEQ-QD-RSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISGSA--KYHLEILNRRSLFQLLQKSDNEDR 81 (584)
T ss_pred HHHHHHHHHc-CC-CCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheecCC--ceEEEeCCHHHHHHHHhcCCHHHH
Confidence 5778888853 43 678999999999999999999966 445664343322 45553 223334444466666
Q ss_pred H-H-HhcCcCCCCCHHHHHhhcC
Q 018851 75 L-F-LAVPAEGSISKDELQKKLD 95 (349)
Q Consensus 75 l-~-~~l~~~g~~~~~el~~~~~ 95 (349)
. + ..|. ..++++.+|...+.
T Consensus 82 ~il~~Ll~-~~~~~~~~La~~l~ 103 (584)
T PRK09863 82 LLLLRLLL-NTFTPMAQLASALN 103 (584)
T ss_pred HHHHHHHH-cCCccHHHHHHHhC
Confidence 2 2 2344 45689999988753
No 231
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=76.99 E-value=4.4 Score=38.11 Aligned_cols=60 Identities=15% Similarity=-0.022 Sum_probs=45.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++...+. .-.-|+.+++++.+|.+.++.||+. |.-=.+.. . .+.||++|+.+++.
T Consensus 7 L~~f~~v~~~gs---~t~AA~~L~iSQ~avS~~i~~LE~~lg~~Lf~R~-r-~i~lT~~G~~l~~~ 67 (294)
T PRK13348 7 LEALAAVVETGS---FERAARRLHVTPSAVSQRIKALEESLGQPLLVRG-R-PCRPTPAGQRLLRH 67 (294)
T ss_pred HHHHHHHHHcCC---HHHHHHHhCCCchHHHHHHHHHHHHhCceeeecC-C-CCccChhHHHHHHH
Confidence 345556655653 4467889999999999999999995 66656553 4 69999999887643
No 232
>PRK06462 asparagine synthetase A; Reviewed
Probab=76.71 E-value=6.6 Score=39.02 Aligned_cols=27 Identities=15% Similarity=0.261 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESS 246 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~ 246 (349)
.+++..+|++|.+.||.|+.| |.+..+
T Consensus 34 s~i~~~iR~ff~~~~f~EV~T-P~l~~~ 60 (335)
T PRK06462 34 SSILRYTREFLDGRGFVEVLP-PIISPS 60 (335)
T ss_pred HHHHHHHHHHHHHCCCEEEeC-CeEecC
Confidence 467888999999999999975 666443
No 233
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=76.69 E-value=4.9 Score=38.32 Aligned_cols=61 Identities=11% Similarity=-0.057 Sum_probs=46.5
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++.+.+ +...-|+.+++++.+|.+.++.||+. |.-=.+ +....+.||++|+.+++.
T Consensus 9 L~~f~av~~~g---S~s~AAe~L~isqsavS~~Ik~LE~~lg~~Lf~-R~~~~v~LT~~G~~l~~~ 70 (309)
T PRK11013 9 IEIFHAVMTAG---SLTEAARLLHTSQPTVSRELARFEKVIGLKLFE-RVRGRLHPTVQGLRLFEE 70 (309)
T ss_pred HHHHHHHHHhC---cHHHHHHHHCCCcHHHHHHHHHHHHHhCceeee-ecCCCcccCHHHHHHHHH
Confidence 45666666665 34567889999999999999999996 544444 445578999999998764
No 234
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=76.48 E-value=5.3 Score=36.70 Aligned_cols=60 Identities=17% Similarity=0.099 Sum_probs=43.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++...+ +.-.-|+.+++++.+|.+.++.||.. |.-=...... .+.||++|+.++..
T Consensus 7 ~~F~~v~~~~---s~t~AA~~L~isqsavS~~I~~LE~~lg~~Lf~R~~~-~~~lT~~G~~l~~~ 67 (297)
T COG0583 7 RAFVAVAEEG---SFTRAAERLGLSQSAVSRQIKRLEEELGVPLFERTTR-RVRLTEAGERLLER 67 (297)
T ss_pred HHHHHHHHcC---cHHHHHHHhCCCChHHHHHHHHHHHHhCchheeecCC-ceeeCHhHHHHHHH
Confidence 3445555544 34567889999999999999999995 5444444333 39999999998754
No 235
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=76.32 E-value=5.1 Score=38.04 Aligned_cols=61 Identities=16% Similarity=0.066 Sum_probs=46.0
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
+++.++.+.+. ...-|+.+++++.+|.+.++.||+. |.-=.+ +....+.||++|+.+++..
T Consensus 17 ~~F~av~e~gS---~t~AA~~L~iSQpavS~~I~~LE~~lG~~Lf~-R~~r~~~lT~~G~~l~~~a 78 (303)
T PRK10082 17 YDFLTLEKCRN---FSQAAVSRNVSQPAFSRRIRALEQAIGVELFN-RQVTPLQLSEQGKIFHSQI 78 (303)
T ss_pred HHHHHHHhcCC---HHHHHHHhCCChHHHHHHHHHHHHHcCCEEEE-ecCCCCccCHHHHHHHHHH
Confidence 44555555553 4567889999999999999999995 654444 4455789999999988653
No 236
>PRK05159 aspC aspartyl-tRNA synthetase; Provisional
Probab=76.18 E-value=6.8 Score=40.33 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhhCCceecCCCCce
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
..++..||++|.+.||.|+.| |.+
T Consensus 140 s~i~~~iR~ff~~~gf~EV~T-P~L 163 (437)
T PRK05159 140 SEVLRAFREFLYENGFTEIFT-PKI 163 (437)
T ss_pred HHHHHHHHHHHHHCCCEEEeC-Ccc
Confidence 356788999999999999975 555
No 237
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=76.06 E-value=3.3 Score=38.77 Aligned_cols=61 Identities=15% Similarity=0.055 Sum_probs=45.7
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++.+.+ +...-|+.+++++.+|.+.++.||+.==+..=.+....+.||+.|+..++.
T Consensus 7 ~~f~~v~~~g---s~s~AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~~~lT~~G~~l~~~ 67 (291)
T TIGR03418 7 RVFESAARLA---SFTAAARELGSTQPAVSQQVKRLEEELGTPLFERGHRGIELTEDGQRLFEA 67 (291)
T ss_pred HHHHHHHHhC---CHHHHHHHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCceeEcHhHHHHHHH
Confidence 4555565555 345778899999999999999999963233334556789999999987654
No 238
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=75.92 E-value=5.7 Score=37.66 Aligned_cols=61 Identities=13% Similarity=0.112 Sum_probs=46.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++.+.+. ...-|+.+++++.+|.+.++.||.. |. ..-.+....+.||++|+.+++.
T Consensus 7 L~~f~~v~e~~s---~s~AA~~L~isQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~~~ 68 (300)
T PRK11074 7 LEVVDAVARTGS---FSAAAQELHRVPSAVSYTVRQLEEWLAV-PLFERRHRDVELTPAGEWFVKE 68 (300)
T ss_pred HHHHHHHHHhCC---HHHHHHHhCCCHHHHHHHHHHHHHHhCC-eeEEeCCCCceECccHHHHHHH
Confidence 456666666653 4467888999999999999999995 43 3344456689999999998743
No 239
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=75.79 E-value=5.2 Score=38.25 Aligned_cols=61 Identities=18% Similarity=0.047 Sum_probs=46.4
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++...+. .-.-|+.+|+++.+|.+.++.||+.==+..-.+....+.||+.|+.++..
T Consensus 20 ~~f~~va~~gs---~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R~~r~~~LT~~G~~l~~~ 80 (311)
T PRK10086 20 HTFEVAARHQS---FALAADELSLTPSAVSHRINQLEEELGIKLFVRSHRKVELTEEGKRVFWA 80 (311)
T ss_pred HHHHHHHHcCC---HHHHHHHHCCCHHHHHHHHHHHHHHhCCeeEEEcCCCcccCHhHHHHHHH
Confidence 44555555553 44678889999999999999999963345555667799999999998754
No 240
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=75.73 E-value=4.4 Score=38.07 Aligned_cols=60 Identities=17% Similarity=0.035 Sum_probs=45.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++...+. .-.-|+.+++++.+|.+.++.||.. |.-=.+. . ..++||++|+.++..
T Consensus 6 l~~f~~v~~~~s---~t~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R-~-r~~~lT~~G~~l~~~ 66 (292)
T TIGR03298 6 LAALAAVVEEGS---FERAAAALSVTPSAVSQRIKALEERLGQPLLVR-T-QPCRATEAGQRLLRH 66 (292)
T ss_pred HHHHHHHHHcCC---HHHHHHHhCCCHHHHHHHHHHHHHHhCchheec-C-CCCcCCHhHHHHHHH
Confidence 345556655553 4467888999999999999999995 5544454 3 489999999998754
No 241
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=75.63 E-value=5.9 Score=32.03 Aligned_cols=43 Identities=19% Similarity=0.181 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHhccCCcEEEEee--eeEEEEeChhHHHHhhcC
Q 018851 27 GFDHNDVVNVIKSLHGFRYIDAQDI--KRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 27 g~~~~~v~~~~~~L~~kgli~~~~~--~~~~~~LTeEG~~~l~~G 69 (349)
+++...+.+.+..|...|++.+... ....+.||+.|++++.+.
T Consensus 53 ~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~l~g~ 97 (106)
T PF09382_consen 53 DMSKDDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKELLNGK 97 (106)
T ss_dssp TS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHHHCTT
T ss_pred cCCHHHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHHHCCC
Confidence 5788899999999999999987777 777999999999999654
No 242
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=75.51 E-value=3.9 Score=43.61 Aligned_cols=43 Identities=23% Similarity=0.346 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHhccCCcEEEEee-e-eEEEEeChhHHHHhhcC
Q 018851 27 GFDHNDVVNVIKSLHGFRYIDAQDI-K-RETWVLTGEGKKYAAEG 69 (349)
Q Consensus 27 g~~~~~v~~~~~~L~~kgli~~~~~-~-~~~~~LTeEG~~~l~~G 69 (349)
.-+.+.+-.++.+|+|.+||+.+.. . +..|.||+.|+++++.-
T Consensus 326 ~~~~d~l~~~Ly~LEsf~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 326 RKNFDDLRESLYSLESFGLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred hcchhHHHHHHHHHHhhhhHHhhhhccCceeEEechhHHHHHHhh
Confidence 4566779999999999999988764 3 56999999999998743
No 243
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=75.47 E-value=5.4 Score=36.56 Aligned_cols=39 Identities=8% Similarity=0.043 Sum_probs=34.0
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEE
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRET 55 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~ 55 (349)
.+..+||+.+|++...|..|+..|++.|||++....-..
T Consensus 31 L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~ 69 (224)
T PRK11534 31 LRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYR 69 (224)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceE
Confidence 456899999999999999999999999999987665443
No 244
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=75.24 E-value=5.9 Score=37.73 Aligned_cols=63 Identities=10% Similarity=-0.033 Sum_probs=47.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcCCh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEGSP 71 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G~P 71 (349)
+++.++...+ +.-.-|+.+|+++.+|.+.++.||+. |.-=.++ ....+.||++|+.++....+
T Consensus 7 ~~F~~v~~~~---S~s~AA~~L~isQ~avS~~I~~LE~~lg~~LF~R-~~r~v~lT~~G~~l~~~a~~ 70 (305)
T PRK11233 7 KYFVKIVDIG---SLTQAAEVLHIAQPALSQQVATLEGELNQQLLIR-TKRGVTPTEAGKILYTHARA 70 (305)
T ss_pred HHHHHHHHcC---CHHHHHHHhCCCchHHHHHHHHHHHHhCCceEEe-CCCCceECHhHHHHHHHHHH
Confidence 3455555555 34567889999999999999999996 5544444 45689999999998866554
No 245
>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=75.10 E-value=5.3 Score=35.90 Aligned_cols=53 Identities=15% Similarity=0.285 Sum_probs=41.1
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHH
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQ 74 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~r 74 (349)
.+..++|+.+|++...|.++++.|+.+++|... ..-.|.+.+. ++=+|+.-.+
T Consensus 76 ~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~--~~G~Y~iNP~---~~~kG~~~~~ 128 (165)
T PF05732_consen 76 ATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI--RNGAYMINPN---FFFKGDRDKR 128 (165)
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc--cCCeEEECcH---HheeCcHHHH
Confidence 345779999999999999999999999999654 3457888885 3446666443
No 246
>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=74.96 E-value=4.2 Score=33.80 Aligned_cols=57 Identities=14% Similarity=0.137 Sum_probs=42.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHh-----CCCHHHHHHHHHHhccCCcEEEEee--eeEEEEeCh
Q 018851 4 EAILGYLEKNEQISDSGNFAAER-----GFDHNDVVNVIKSLHGFRYIDAQDI--KRETWVLTG 60 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~-----g~~~~~v~~~~~~L~~kgli~~~~~--~~~~~~LTe 60 (349)
..||..|.+.+...+.+++...+ .++..+|.+++..|++.|+|..-.. ....|.+..
T Consensus 11 ~~Il~~l~~~~~~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 11 LAILELLKESPEHLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHSSSEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred HHHHHHHHcCCCCCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 56899998866667888876543 6888999999999999999976544 345777776
No 247
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=74.91 E-value=15 Score=27.68 Aligned_cols=58 Identities=21% Similarity=0.301 Sum_probs=44.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeChhH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLTGEG 62 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LTeEG 62 (349)
.+||..|..... .+..+++..+++++..+..-+..|+..|+|....... ..|.|.++.
T Consensus 28 ~~il~~l~~~~~-~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~~~~~~~~~l~~~~ 86 (110)
T COG0640 28 LEILSLLAEGGE-LTVGELAEALGLSQSTVSHHLKVLREAGLVELRREGRLRLYRLADEK 86 (110)
T ss_pred HHHHHHHHhcCC-ccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEEecccEEEEecCcHH
Confidence 457777776433 4577899999999999999999999999999865533 466666665
No 248
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=74.89 E-value=6.3 Score=38.05 Aligned_cols=62 Identities=11% Similarity=-0.046 Sum_probs=46.0
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
.+++.++.+.+. .-.-|+.+++++.+|.+.++.||+. |.-= -.+....+.||+.|+.++...
T Consensus 16 L~~F~~v~e~gs---~s~AA~~L~iSQpavS~~I~~LE~~lG~~L-F~R~~~~~~LT~~G~~l~~~a 78 (310)
T PRK15092 16 LRTFVAVADLNT---FAAAAAAVCRTQSAVSQQMQRLEQLVGKEL-FARHGRNKLLTEHGIQLLGYA 78 (310)
T ss_pred HHHHHHHHHcCC---HHHHHHHhCCChHHHHHHHHHHHHHhCcce-EEECCCCceECHhHHHHHHHH
Confidence 345556665553 4467889999999999999999996 5443 344555779999999987553
No 249
>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=74.56 E-value=2.7 Score=30.30 Aligned_cols=44 Identities=18% Similarity=0.265 Sum_probs=36.4
Q ss_pred hHHHHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEee
Q 018851 71 PEVQLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEM 114 (349)
Q Consensus 71 PE~rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i 114 (349)
+|+.++..|...+++++.+|.+.++ ++...-.+..+.++|||..
T Consensus 4 ~q~~iL~~l~~~~~~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r 49 (59)
T PF01047_consen 4 SQFRILRILYENGGITQSELAEKLGISRSTVTRIIKRLEKKGLIER 49 (59)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHCCChhHHHHHHHHHHHCCCEEe
Confidence 6888999998777799999998854 5566778899999999975
No 250
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=74.11 E-value=5.2 Score=37.90 Aligned_cols=61 Identities=11% Similarity=0.046 Sum_probs=46.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++.+.+ +...-|+.+++++.+|.+.++.||.. |.- .-.+....+.||+.|+.+++.
T Consensus 6 L~~f~~v~~~g---S~s~AA~~L~itQpavS~~i~~LE~~lg~~-LF~R~~r~~~lT~~G~~l~~~ 67 (305)
T PRK11151 6 LEYLVALAEHR---HFRRAADSCHVSQPTLSGQIRKLEDELGVM-LLERTSRKVLFTQAGLLLVDQ 67 (305)
T ss_pred HHHHHHHHHhC---CHHHHHHHhCCCchHHHHHHHHHHHHhCch-heeeCCCceeECccHHHHHHH
Confidence 45566666665 35567889999999999999999995 543 334467799999999998754
No 251
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=74.03 E-value=9.9 Score=34.86 Aligned_cols=34 Identities=12% Similarity=0.113 Sum_probs=31.2
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
+-+++|+.+|+..+.|.+.++.|+..|+|.....
T Consensus 171 t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~ 204 (226)
T PRK10402 171 KHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKR 204 (226)
T ss_pred hHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCC
Confidence 4588999999999999999999999999998764
No 252
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=73.88 E-value=6.2 Score=37.84 Aligned_cols=61 Identities=16% Similarity=0.031 Sum_probs=44.3
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEE-EeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETW-VLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~-~LTeEG~~~l~~ 68 (349)
+++.++.+.+. +...-|+.+++++.+|.+.++.||+. |.-=... ....+ .||+.|+.+++.
T Consensus 7 ~~F~~v~~~~~--S~s~AA~~L~isQpavS~~I~~LE~~lg~~Lf~R-~~r~~~~lT~~G~~l~~~ 69 (309)
T PRK12683 7 RIIREAVRQNF--NLTEVANALYTSQSGVSKQIKDLEDELGVEIFIR-RGKRLTGLTEPGKELLQI 69 (309)
T ss_pred HHHHHHHHccC--CHHHHHHHhcCCcHHHHHHHHHHHHHhCCeeEee-CCCCcCCcCHHHHHHHHH
Confidence 44444444442 35567888999999999999999996 6555554 44555 899999998754
No 253
>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=73.85 E-value=6.2 Score=34.63 Aligned_cols=36 Identities=14% Similarity=0.158 Sum_probs=32.3
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.+-+++|..+|+..+.|.++++.|+..|+|+.....
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~~ 179 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHKKK 179 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCE
Confidence 456899999999999999999999999999987643
No 254
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=73.45 E-value=6.9 Score=37.16 Aligned_cols=62 Identities=18% Similarity=0.044 Sum_probs=47.6
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
.+++.++.+.+. ....|+.+++++.+|.+.++.||.. |.-=.+. ....+.||+.|+..++..
T Consensus 10 L~~f~~v~e~gs---~s~AA~~L~isqpavS~~i~~LE~~lg~~Lf~R-~~r~~~lT~~G~~l~~~a 72 (305)
T CHL00180 10 LRILKAIATEGS---FKKAAESLYISQPAVSLQIKNLEKQLNIPLFDR-SKNKASLTEAGELLLRYG 72 (305)
T ss_pred HHHHHHHHHcCC---HHHHHHHhcCCChHHHHHHHHHHHHhCCEEEEe-cCCCceECHhHHHHHHHH
Confidence 345566666664 4467889999999999999999996 6555554 456899999999987554
No 255
>PRK09801 transcriptional activator TtdR; Provisional
Probab=73.45 E-value=6.3 Score=37.89 Aligned_cols=63 Identities=16% Similarity=0.031 Sum_probs=47.7
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcCCh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEGSP 71 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G~P 71 (349)
+++.++.+.+. .-.-|+.+++++.+|.+.++.||+. |.-=.+ +....+.||++|+.++.....
T Consensus 12 ~~F~~v~~~gs---~t~AA~~L~iSQpavS~~I~~LE~~LG~~Lf~-R~~r~~~lT~~G~~l~~~a~~ 75 (310)
T PRK09801 12 QVLVEIVHSGS---FSAAAATLGQTPAFVTKRIQILENTLATTLLN-RSARGVALTESGQRCYEHALE 75 (310)
T ss_pred HHHHHHHHcCC---HHHHHHHhCcCHHHHHHHHHHHHHHhCCEeee-ecCCCCcccHhHHHHHHHHHH
Confidence 45555655553 4467889999999999999999996 654444 456699999999998865543
No 256
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=73.45 E-value=6.9 Score=37.14 Aligned_cols=41 Identities=12% Similarity=0.075 Sum_probs=36.6
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCC
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFR 44 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg 44 (349)
+.+|+..|..++. .+..+||+.+|++...|.+.+..|+..+
T Consensus 9 ~~~I~~~l~~~~~-v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 9 IGQLLQALKRSDK-LHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHcCC-CcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 4679999998887 6789999999999999999999999654
No 257
>cd00669 Asp_Lys_Asn_RS_core Asp_Lys_Asn_tRNA synthetase class II core domain. This domain is the core catalytic domain of class II aminoacyl-tRNA synthetases of the subgroup containing aspartyl, lysyl, and asparaginyl tRNA synthetases. It is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. Nearly all class II tRNA synthetases are dimers and enzymes in this subgroup are homodimers. These enzymes attach a specific amino acid to the 3' OH group of ribose of the appropriate tRNA.
Probab=73.37 E-value=8.7 Score=37.05 Aligned_cols=27 Identities=26% Similarity=0.412 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESS 246 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~ 246 (349)
.++++.+|++|.+.||.|+.| |.+++.
T Consensus 5 s~i~~~ir~~f~~~gf~ev~t-P~l~~~ 31 (269)
T cd00669 5 SKIIKAIRDFMDDRGFLEVET-PMLQKI 31 (269)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-CEEecc
Confidence 578999999999999999975 777543
No 258
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=73.12 E-value=6.7 Score=36.24 Aligned_cols=39 Identities=13% Similarity=0.129 Sum_probs=34.3
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+..+||+.+|++...|..|+..|++.|+|......-..+
T Consensus 33 sE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g~G~~V 71 (239)
T PRK04984 33 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTKV 71 (239)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEe
Confidence 556899999999999999999999999999987765444
No 259
>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=72.97 E-value=5.6 Score=29.19 Aligned_cols=45 Identities=18% Similarity=0.328 Sum_probs=35.2
Q ss_pred hHHHHHHhcC-cCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeC
Q 018851 71 PEVQLFLAVP-AEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 71 PE~rl~~~l~-~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~ 115 (349)
+|..++..|. ..+++++.+|.+.++ +....-.+..+.++|||...
T Consensus 4 ~q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 4 PQWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 6888999998 667799999998864 44667788999999999653
No 260
>cd00776 AsxRS_core Asx tRNA synthetase (AspRS/AsnRS) class II core domain. Assignment to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs in the core domain. This family includes AsnRS as well as a subgroup of AspRS. AsnRS and AspRS are homodimers, which attach either asparagine or aspartate to the 3'OH group of ribose of the appropriate tRNA. While archaea lack asnRS, they possess a non-discriminating aspRS, which can mischarge Asp-tRNA with Asn. Subsequently, a tRNA-dependent aspartate amidotransferase converts the bound aspartate to asparagine. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.
Probab=72.94 E-value=8.3 Score=38.05 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVES 245 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves 245 (349)
..++..+|++|.+.||.|+.| |.++.
T Consensus 28 s~i~~~ir~~f~~~gf~eV~T-P~l~~ 53 (322)
T cd00776 28 SEVLRAFREFLRENGFTEVHT-PKITS 53 (322)
T ss_pred HHHHHHHHHHHHHCCCEEeeC-Cceec
Confidence 467788899999999999975 77765
No 261
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=72.80 E-value=7.4 Score=36.19 Aligned_cols=43 Identities=12% Similarity=0.033 Sum_probs=36.9
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 14 EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 14 ~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+.+-+-.+||+.+|++...|.+|+..|+..|+|.-....-+++
T Consensus 31 ~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~GTfV 73 (241)
T PRK11402 31 QQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQGKGTFV 73 (241)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCceeEE
Confidence 4455667899999999999999999999999999887766555
No 262
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=72.63 E-value=15 Score=30.13 Aligned_cols=59 Identities=19% Similarity=0.171 Sum_probs=42.7
Q ss_pred HHHHHhhCCCCCChHHHHHHh--CCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 6 ILGYLEKNEQISDSGNFAAER--GFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~--g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
||-.+.+++- .++.++++.+ .+....|.+-+.-|-.+|||+-+- .-|.+|++|..++.+
T Consensus 21 ilI~v~Kk~F-it~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEKSG---DGlv~T~~g~~Ii~~ 81 (96)
T PF09114_consen 21 ILIQVAKKNF-ITASEVREALATEMNKASVNSNIGVLIKKGLIEKSG---DGLVITEEGMDIIIQ 81 (96)
T ss_dssp HHHHHHHSTT-B-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEEET---TEEEE-HHHHHHHHH
T ss_pred HHHHHHHHcc-CCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccccC---CceEEechHHHHHHH
Confidence 5666666665 5677888865 677888999999999999997543 349999999997743
No 263
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=72.61 E-value=9.5 Score=37.28 Aligned_cols=56 Identities=13% Similarity=0.145 Sum_probs=42.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeCh
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTe 60 (349)
..+||..|..... .+..+||+.+|++...|.+.++.|++.|++-...... -|.|..
T Consensus 6 ~~~il~~L~~~~~-~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~-Gy~L~~ 61 (319)
T PRK11886 6 MLQLLSLLADGDF-HSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGK-GYRLAE 61 (319)
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCC-eEEecC
Confidence 4578888876543 6778999999999999999999999999944333222 455533
No 264
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=72.51 E-value=6.9 Score=36.97 Aligned_cols=59 Identities=14% Similarity=0.073 Sum_probs=44.9
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++.+.+ +...-|+.+|+++.+|.+.++.||+. |.-=.++ . ..++||+.|+..++.
T Consensus 8 ~~f~~v~e~g---s~s~AA~~L~isq~avS~~I~~LE~~lg~~LF~R-~-~~~~lT~~G~~l~~~ 67 (294)
T PRK03635 8 EALAAVVREG---SFERAAQKLHITQSAVSQRIKALEERVGQVLLVR-T-QPCRPTEAGQRLLRH 67 (294)
T ss_pred HHHHHHHHcC---CHHHHHHHhCCChHHHHHHHHHHHHHhCceeeec-C-CCCccCHHHHHHHHH
Confidence 3445555555 34567889999999999999999995 6665555 3 489999999987744
No 265
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=72.49 E-value=8.4 Score=36.13 Aligned_cols=39 Identities=8% Similarity=-0.097 Sum_probs=33.8
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+..+||+.+|++...|..|+..|++.|||++....-..+
T Consensus 35 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 73 (257)
T PRK10225 35 PEREIAEMLDVTRTVVREALIMLEIKGLVEVRRGAGIYV 73 (257)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 456899999999999999999999999999887754433
No 266
>cd00777 AspRS_core Asp tRNA synthetase (aspRS) class II core domain. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs. AspRS is a homodimer, which attaches a specific amino acid to the 3' OH group of ribose of the appropriate tRNA. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. AspRS in this family differ from those found in the AsxRS family by a GAD insert in the core domain.
Probab=72.38 E-value=11 Score=36.66 Aligned_cols=25 Identities=24% Similarity=0.449 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
.+++..||++|.+.||.|+.| |.+.
T Consensus 5 s~i~~~iR~f~~~~gfiEV~T-P~L~ 29 (280)
T cd00777 5 SRVIKAIRNFLDEQGFVEIET-PILT 29 (280)
T ss_pred HHHHHHHHHHHHHCCCEEEeC-Ceee
Confidence 468899999999999999975 6663
No 267
>PRK12423 LexA repressor; Provisional
Probab=71.98 E-value=11 Score=34.60 Aligned_cols=56 Identities=18% Similarity=0.220 Sum_probs=42.8
Q ss_pred HHHHHHHHhh----CCCCCChHHHHHHhCC-CHHHHHHHHHHhccCCcEEEEeeeeEEEEe
Q 018851 3 EEAILGYLEK----NEQISDSGNFAAERGF-DHNDVVNVIKSLHGFRYIDAQDIKRETWVL 58 (349)
Q Consensus 3 e~~iL~~L~~----~~~~~~~~~la~~~g~-~~~~v~~~~~~L~~kgli~~~~~~~~~~~L 58 (349)
+.+||..|.+ .+-.-+..++|+.+|+ +.+.|...+..|+.+|+|...........+
T Consensus 8 q~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~~~~~~~~~v 68 (202)
T PRK12423 8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVVPNQARGIRL 68 (202)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEecCCCcceeee
Confidence 5677777765 3333467899999995 899999999999999999998775443333
No 268
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=71.94 E-value=7.8 Score=36.51 Aligned_cols=61 Identities=20% Similarity=0.165 Sum_probs=46.1
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
+++.++...+ +...-|+.+++++.+|.+.++.||.. |.-=. .+....+.||++|+.++...
T Consensus 12 ~~f~~v~~~g---s~s~AA~~L~isq~avS~~i~~LE~~lg~~Lf-~R~~r~l~lT~~G~~l~~~~ 73 (297)
T PRK11139 12 RAFEAAARHL---SFTRAAEELFVTQAAVSHQIKALEDFLGLKLF-RRRNRSLLLTEEGQRYFLDI 73 (297)
T ss_pred HHHHHHHHhC---CHHHHHHHhCCChHHHHHHHHHHHHHhCchhe-EecCCceeECHhHHHHHHHH
Confidence 4555555555 34567889999999999999999996 54433 45567899999999987554
No 269
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=71.90 E-value=8.4 Score=37.42 Aligned_cols=61 Identities=13% Similarity=-0.068 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+.+.++...+. .-.-|+.++++..+|...++.||.. |.- .-.+....+.||++|+.+++.
T Consensus 9 L~~F~aVae~gS---fs~AA~~L~isQpavS~~Ik~LE~eLG~~-LF~R~~r~~~LT~aG~~ll~~ 70 (297)
T PRK15243 9 LKIFITLMETGS---FSIATSVLYITRTPLSRVISDLERELKQR-LFIRKNGTLIPTEFAQTIYRK 70 (297)
T ss_pred HHHHHHHHHcCC---HHHHHHHHCcCHHHHHHHHHHHHHHhCCc-cEEeCCCCeeECHHHHHHHHH
Confidence 344555555553 4467889999999999999999995 543 444566789999999998854
No 270
>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=71.26 E-value=7.1 Score=31.44 Aligned_cols=54 Identities=20% Similarity=0.233 Sum_probs=40.7
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccC------CcE----EEEe-----eeeEEEEeChhHHHHhhcCC
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGF------RYI----DAQD-----IKRETWVLTGEGKKYAAEGS 70 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~k------gli----~~~~-----~~~~~~~LTeEG~~~l~~G~ 70 (349)
.+|.++|+.+|..|..|++.|..+..+ |.. .... +....|.||+.|-..|-.|.
T Consensus 2 ~tS~~IAe~~gk~H~~Vlr~I~~~~~~~~~~~~~~~~f~~~~~y~~~~gr~~~~y~Ltk~g~~lL~~~~ 70 (93)
T PF09669_consen 2 TTSREIAEMFGKRHKNVLRDIRKLIEKECSPEFGQLNFFIESKYKDGQGRSYPCYLLTKDGFTLLVMGY 70 (93)
T ss_pred CCHHHHHHHHCccHHHHHHHHHHHHhhhcchhhhhccCcceeeeECCCCcEeEEEEEccChhheehhhh
Confidence 467899999999999999999999965 222 2221 13458899999988776664
No 271
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=71.10 E-value=9.4 Score=33.66 Aligned_cols=60 Identities=12% Similarity=0.122 Sum_probs=47.5
Q ss_pred HHHHHHhh-CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 5 AILGYLEK-NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 5 ~iL~~L~~-~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
++|-.|+. .+...++.++|+..++++.-+...+..|...|+|....-..-=|.|+..-++
T Consensus 12 r~L~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p~e 72 (153)
T PRK11920 12 RMLMYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPAAD 72 (153)
T ss_pred HHHHHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCHHH
Confidence 35555653 2334678999999999999999999999999999998887777777665443
No 272
>PRK03837 transcriptional regulator NanR; Provisional
Probab=70.86 E-value=8.8 Score=35.37 Aligned_cols=39 Identities=13% Similarity=0.112 Sum_probs=34.0
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+..+||+.+|++...|..|+..|++.|+|++....-..+
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~G~~V 77 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQALKRKGLVQISHGERARV 77 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCceeE
Confidence 567899999999999999999999999999987665433
No 273
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=70.53 E-value=9.6 Score=35.17 Aligned_cols=44 Identities=14% Similarity=0.164 Sum_probs=37.5
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
.+.+-+-.+||+.+|++...|.+|+..|++.|+|.-....-+++
T Consensus 21 G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G~GTfV 64 (233)
T TIGR02404 21 GDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQGKGSIV 64 (233)
T ss_pred CCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCceEEE
Confidence 33455667899999999999999999999999999888776655
No 274
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=70.52 E-value=8.4 Score=31.65 Aligned_cols=65 Identities=17% Similarity=0.153 Sum_probs=47.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-------EEEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-------ETWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-------~~~~LTeEG~~~l~~ 68 (349)
..||-.+++.....+.-....-.+.+.+.|.-.+..|...|+|....... ....||-+|-++|.+
T Consensus 8 R~iLl~iE~~~~~~~~~~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~ 79 (102)
T PF10711_consen 8 RDILLEIEENPDPPNPIEEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDA 79 (102)
T ss_pred HHHHHHHHcCCCcCcccchhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHH
Confidence 56888887765422221222336889999999999999999999876655 345899999987743
No 275
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=70.02 E-value=8.4 Score=36.09 Aligned_cols=39 Identities=15% Similarity=0.072 Sum_probs=34.0
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+-.+||+.+|++...|..|+..|++.|+|++....-..+
T Consensus 34 sE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 72 (253)
T PRK11523 34 AERFIADEKNVSRTVVREAIIMLEVEGYVEVRKGSGIHV 72 (253)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCeeEE
Confidence 346899999999999999999999999999988765444
No 276
>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=69.99 E-value=10 Score=35.01 Aligned_cols=42 Identities=12% Similarity=0.147 Sum_probs=36.4
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 15 QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 15 ~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
.+-+-.+||+.+|++...|.+|+..|+..|+|......-+++
T Consensus 24 ~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G~GtfV 65 (230)
T TIGR02018 24 RIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQGVGTFV 65 (230)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 344567899999999999999999999999999888776655
No 277
>TIGR00462 genX lysyl-tRNA synthetase-like protein GenX. Many Gram-negative bacteria have a protein closely homologous to the C-terminal region of lysyl-tRNA synthetase (LysS). Multiple sequence alignment of these proteins with the homologous regions of collected LysS proteins shows that these proteins form a distinct set rather than just similar truncations of LysS. The protein is termed GenX after its designation in E. coli. Interestingly, genX often is located near a homolog of lysine-2,3-aminomutase. Its function is unknown.
Probab=69.56 E-value=13 Score=36.37 Aligned_cols=27 Identities=15% Similarity=0.349 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESS 246 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~ 246 (349)
..++..||++|.+.||.|+.| |.++++
T Consensus 5 s~i~~~ir~~f~~~gF~EV~T-P~l~~~ 31 (304)
T TIGR00462 5 ARLLAAIRAFFAERGVLEVET-PLLSPA 31 (304)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-CeEecC
Confidence 578899999999999999985 777654
No 278
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=69.52 E-value=20 Score=30.69 Aligned_cols=46 Identities=20% Similarity=0.257 Sum_probs=37.3
Q ss_pred ChHHHHHHhcCcCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 70 SPEVQLFLAVPAEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 70 ~PE~rl~~~l~~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
.+++.++..|...+++++.+|...+ +++...-.+..+-++|||...
T Consensus 40 ~~q~~vL~~l~~~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 40 AAQFKVLCSIRCAACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 3688888888666679999999885 566777788999999999764
No 279
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=68.84 E-value=6.8 Score=36.04 Aligned_cols=43 Identities=16% Similarity=0.145 Sum_probs=36.8
Q ss_pred HHHHHHHHhhCC-CCCChHHHHHHhCCCHHHHHHHHHHhccCCc
Q 018851 3 EEAILGYLEKNE-QISDSGNFAAERGFDHNDVVNVIKSLHGFRY 45 (349)
Q Consensus 3 e~~iL~~L~~~~-~~~~~~~la~~~g~~~~~v~~~~~~L~~kgl 45 (349)
..+||+.|...+ ...++.+||+.+|+++..|.+.+.+|+..|.
T Consensus 18 ~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 18 YYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence 467999999887 2367899999999999999999999988774
No 280
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=68.80 E-value=17 Score=36.67 Aligned_cols=58 Identities=10% Similarity=0.148 Sum_probs=44.6
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
++..|..... .+...+....|.+...+...+..|++.|++..+ ...+.||++|.-.+.
T Consensus 329 ~~l~LR~~~G-ld~~~f~~~~g~~~~~~~~~l~~l~~~gll~~~---~~~~~LT~~G~~~~d 386 (394)
T PRK08898 329 MLNALRLTDG-VPAHLFQERTGLPLAAIEPQLAAAEQRGLLERD---HTRIRPTPLGQRFLN 386 (394)
T ss_pred HHHHHHHhCC-cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE---CCEEEEChhHhHHHH
Confidence 4444554444 577788888899888888899999999999864 358999999987653
No 281
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=68.68 E-value=6.8 Score=35.88 Aligned_cols=36 Identities=14% Similarity=0.143 Sum_probs=32.1
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.+..+||+.+|++...|..|+..|++.|||++....
T Consensus 35 L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~ 70 (221)
T PRK11414 35 LITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQ 70 (221)
T ss_pred cCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCC
Confidence 456789999999999999999999999999986554
No 282
>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=68.56 E-value=15 Score=30.45 Aligned_cols=47 Identities=11% Similarity=0.142 Sum_probs=36.4
Q ss_pred ChHHHHHHhcCcCCCCCHHHHHhhcCch------hhhhHHHHHhhCCcEeeCc
Q 018851 70 SPEVQLFLAVPAEGSISKDELQKKLDPA------VFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 70 ~PE~rl~~~l~~~g~~~~~el~~~~~~~------~~~ig~g~~~k~~wi~i~~ 116 (349)
-.|..|+++|=+.|+++..|+.+.+... ...--+..+.++|+|....
T Consensus 3 ~~E~~IM~~lW~~~~~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~ 55 (115)
T PF03965_consen 3 DLELEIMEILWESGEATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK 55 (115)
T ss_dssp HHHHHHHHHHHHHSSEEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee
Confidence 3588999999766678999998776432 4556679999999998864
No 283
>PRK05660 HemN family oxidoreductase; Provisional
Probab=68.54 E-value=15 Score=37.03 Aligned_cols=57 Identities=16% Similarity=0.324 Sum_probs=43.9
Q ss_pred HHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 7 LGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 7 L~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
+..|..... .+...+.+..|.+..+....+..|++.|++..+ ...+.||++|.-++.
T Consensus 313 ~~~Lr~~~G-~~~~~~~~~~g~~~~~~~~~l~~l~~~gl~~~~---~~~~~lt~~G~~~~d 369 (378)
T PRK05660 313 MNRFRLLEA-APRADFEAYTGLPESVIRPQLDEALAQGYLTET---ADHWQITEHGKLFLN 369 (378)
T ss_pred HHhchhccC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe---CCEEEECcchhHHHH
Confidence 334444333 577788888999988888899999999998864 458999999987653
No 284
>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=68.47 E-value=11 Score=34.71 Aligned_cols=42 Identities=14% Similarity=0.115 Sum_probs=36.3
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 15 QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 15 ~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
.+-+-.+||+.+|++...|.+|+..|+..|+|......-+++
T Consensus 31 ~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G~GtfV 72 (238)
T TIGR02325 31 YLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQGRGTFV 72 (238)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCEEEE
Confidence 444567899999999999999999999999999888766655
No 285
>PRK14999 histidine utilization repressor; Provisional
Probab=68.38 E-value=11 Score=35.16 Aligned_cols=42 Identities=12% Similarity=0.172 Sum_probs=36.1
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 15 QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 15 ~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
.+-+-.+||+.+|++...|.+|+..|+..|+|......-+++
T Consensus 35 ~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~GkGTfV 76 (241)
T PRK14999 35 RIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQGVGTFV 76 (241)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCcEEEE
Confidence 344667899999999999999999999999998887766554
No 286
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=68.13 E-value=13 Score=29.71 Aligned_cols=46 Identities=17% Similarity=0.292 Sum_probs=35.6
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeC
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLT 59 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LT 59 (349)
++...+-++||+++|++..+|-..++.|+..|+ .++.....-|.|.
T Consensus 16 ~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~-~I~s~~~kGY~L~ 61 (79)
T COG1654 16 TGNFVSGEKLAEELGISRTAVWKHIQQLREEGV-DIESVRGKGYLLP 61 (79)
T ss_pred CCCcccHHHHHHHHCccHHHHHHHHHHHHHhCC-ceEecCCCceecc
Confidence 333356789999999999999999999999985 5555555555554
No 287
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=68.06 E-value=11 Score=35.21 Aligned_cols=39 Identities=10% Similarity=0.045 Sum_probs=33.7
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+..+||+.+|++...|..|+..|++.|+|++....-..+
T Consensus 28 sE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~~~G~~V 66 (253)
T PRK10421 28 AERQLAMQLGVSRNSLREALAKLVSEGVLLSRRGGGTFI 66 (253)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeCCCeEEE
Confidence 456899999999999999999999999999987654433
No 288
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=67.92 E-value=12 Score=34.43 Aligned_cols=33 Identities=15% Similarity=0.176 Sum_probs=29.9
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
+-.++|+.+|+..+.|.++++.|+..|+|+...
T Consensus 181 t~~~IA~~lGisretlsR~L~~L~~~GlI~~~~ 213 (230)
T PRK09391 181 SRRDIADYLGLTIETVSRALSQLQDRGLIGLSG 213 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecC
Confidence 447999999999999999999999999998754
No 289
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=67.87 E-value=13 Score=34.12 Aligned_cols=47 Identities=15% Similarity=0.152 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
..|+++|-..+. .+.+++|..+|+....|.+++..|-..|+|.....
T Consensus 21 ~~v~~~l~~kge-~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~ 67 (176)
T COG1675 21 VLVVDALLEKGE-LTDEELAELLGIKKNEVRRILYALYEDGLISYRKK 67 (176)
T ss_pred hHHHHHHHhcCC-cChHHHHHHhCccHHHHHHHHHHHHhCCceEEEee
Confidence 356777777665 56789999999999999999999999999996544
No 290
>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=67.76 E-value=18 Score=29.65 Aligned_cols=46 Identities=13% Similarity=0.220 Sum_probs=37.2
Q ss_pred ChHHHHHHhcC----cCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 70 SPEVQLFLAVP----AEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 70 ~PE~rl~~~l~----~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
.+|..++..|. .+|++++.+|...+ +++...-.+..+-++|||...
T Consensus 25 ~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~ 76 (109)
T TIGR01889 25 LEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKE 76 (109)
T ss_pred HHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEecc
Confidence 56888888886 45679999999874 566777889999999999763
No 291
>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=67.74 E-value=5.8 Score=33.31 Aligned_cols=55 Identities=29% Similarity=0.326 Sum_probs=40.0
Q ss_pred CCChHHHHHHhCCCHHHHHHHHHHhccC---------CcEEEE-----eeeeEEEEeChhHHHHhhcCC
Q 018851 16 ISDSGNFAAERGFDHNDVVNVIKSLHGF---------RYIDAQ-----DIKRETWVLTGEGKKYAAEGS 70 (349)
Q Consensus 16 ~~~~~~la~~~g~~~~~v~~~~~~L~~k---------gli~~~-----~~~~~~~~LTeEG~~~l~~G~ 70 (349)
..+|.++|+.+|-.|.+|++.++.|... ++...+ .+....|.||.+|-..|-.|.
T Consensus 13 ~ttS~~IAe~fgK~H~~VlR~Ir~l~~~~~~~~f~~~~F~~~~y~~~~g~~~~~Y~ltkdgf~lLvmg~ 81 (108)
T TIGR02681 13 VTDSLTMAQMFGKRHDNVIRDIKVLLIEANETEFGQLNFEETQYQDEQNKKQPMFNLTEDGFTIVAMGY 81 (108)
T ss_pred EEeHHHHHHHHCcchHHHHHHHHHHHhhhccccccccCceeeEEEcCCCcEEEEEEEcCCceEEEEecC
Confidence 4678999999999999999999999532 122211 122357888988887777775
No 292
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=67.61 E-value=11 Score=35.09 Aligned_cols=43 Identities=9% Similarity=0.136 Sum_probs=36.4
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 14 EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 14 ~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
..+-+-.+||+.+|++...|.+|+..|+..|+|.-....-+++
T Consensus 27 ~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G~GtfV 69 (240)
T PRK09764 27 DALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQGSGTYV 69 (240)
T ss_pred CcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCceeEE
Confidence 3444567899999999999999999999999999887766554
No 293
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=67.46 E-value=8.8 Score=36.68 Aligned_cols=60 Identities=10% Similarity=0.066 Sum_probs=44.9
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++.++.+.+. .-..|+.+++++.+|.+.++.||.. |. ..-.+....+.||+.|+.++..
T Consensus 28 ~~f~avae~gs---~s~AA~~L~isQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l~~~ 88 (314)
T PRK09508 28 TVFDAVMQEQN---ITRAAHNLGMSQPAVSNAVARLKVMFND-ELFVRYGRGIQPTARARQLFGP 88 (314)
T ss_pred HHHHHHHhcCC---HHHHHHHhCCCHHHHHHHHHHHHHhhCC-CcEEEcCCCCcCcHHHHHHHHH
Confidence 44555555553 4467888999999999999999996 43 3344456679999999998754
No 294
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=67.06 E-value=16 Score=35.10 Aligned_cols=60 Identities=15% Similarity=0.113 Sum_probs=46.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEee----eeEEEEeChhHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDI----KRETWVLTGEGKKYA 66 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~----~~~~~~LTeEG~~~l 66 (349)
.++|.++...+. .-.-|+.+|+++.++...++.|+.. |.--++.. ......||++|+..+
T Consensus 22 l~~l~~v~~~gS---~s~AA~~l~~s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~~lT~~G~~l~ 86 (263)
T PRK10676 22 ISLLKQIALTGS---ISQGAKLAGISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVLTRYGERLI 86 (263)
T ss_pred HHHHHHHHHHCC---HHHHHHHhCCCHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCcEECHHHHHHH
Confidence 456777777764 4467888999999999999999994 66555444 144699999999988
No 295
>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=66.98 E-value=9.7 Score=35.14 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=33.5
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRET 55 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~ 55 (349)
+..+||+.+|++...|..|+..|++.|+|++....-..
T Consensus 32 sE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~~G~~ 69 (235)
T TIGR02812 32 AERELSELIGVTRTTLREVLQRLARDGWLTIQHGKPTK 69 (235)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCCCccE
Confidence 56789999999999999999999999999998765433
No 296
>PRK12445 lysyl-tRNA synthetase; Reviewed
Probab=66.86 E-value=15 Score=38.67 Aligned_cols=25 Identities=20% Similarity=0.442 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
.+++..||++|.+.||.|+.| |.+.
T Consensus 188 s~i~~~iR~f~~~~gFiEVeT-PiL~ 212 (505)
T PRK12445 188 SKILAAIRQFMVARGFMEVET-PMMQ 212 (505)
T ss_pred HHHHHHHHHHHHHCCCEEeeC-CeeE
Confidence 356788999999999999985 6663
No 297
>PRK10736 hypothetical protein; Provisional
Probab=66.82 E-value=9.4 Score=38.85 Aligned_cols=48 Identities=17% Similarity=0.113 Sum_probs=39.6
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
+..||..|... ..+.++|+..+|++..++...+..||-+|+|....-.
T Consensus 310 ~~~v~~~l~~~--~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~g~ 357 (374)
T PRK10736 310 FPELLANVGDE--VTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPGG 357 (374)
T ss_pred HHHHHHhcCCC--CCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcCCc
Confidence 45777777533 2578999999999999999999999999999876543
No 298
>PRK00476 aspS aspartyl-tRNA synthetase; Validated
Probab=66.58 E-value=14 Score=39.66 Aligned_cols=25 Identities=24% Similarity=0.405 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
.+++..+|++|.+.||.|+.| |.+.
T Consensus 145 s~i~~~iR~ff~~~gFiEV~T-P~L~ 169 (588)
T PRK00476 145 SKVTSAIRNFLDDNGFLEIET-PILT 169 (588)
T ss_pred HHHHHHHHHHHHHCCCEEEEC-Ceee
Confidence 467788999999999999985 6553
No 299
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=66.56 E-value=21 Score=35.50 Aligned_cols=58 Identities=14% Similarity=0.086 Sum_probs=42.8
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHH-HHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHND-VVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~-v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
++..|..... .+...+++..|.+..+ +...+..|+++|++..+ ...+.||++|..++.
T Consensus 308 ~~~~lr~~~g-~~~~~~~~~~~~~~~~~~~~~l~~l~~~gl~~~~---~~~~~lT~~G~~~~~ 366 (374)
T PRK05799 308 MFMGLRKIKG-ICIEDFKKRFGKNIYEVYGEVINKYIKLGLLIEK---EGRIYLSERGIEVSN 366 (374)
T ss_pred HHHHHHhhCC-cCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEE---CCEEEEChhHHHHHH
Confidence 4445554444 5777888888887664 66678899999999864 347999999988664
No 300
>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=66.38 E-value=39 Score=28.96 Aligned_cols=44 Identities=11% Similarity=0.083 Sum_probs=32.3
Q ss_pred HHHHHHhcCcCCCCCHHHHHhhcC------chhhhhHHHHHhhCCcEeeC
Q 018851 72 EVQLFLAVPAEGSISKDELQKKLD------PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 72 E~rl~~~l~~~g~~~~~el~~~~~------~~~~~ig~g~~~k~~wi~i~ 115 (349)
|..|++.|-..|+++..||.+.++ .....--|..+.++|+|...
T Consensus 6 E~~VM~vlW~~~~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 6 EWEVMRVVWTLGETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence 788888886667789988766542 23344467889999999865
No 301
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=66.30 E-value=9.4 Score=33.84 Aligned_cols=35 Identities=26% Similarity=0.211 Sum_probs=30.9
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
.+-+++|..+|+..+.|.+.++.|+..|+|.....
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~~ 184 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIRSGYG 184 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcCCC
Confidence 34688999999999999999999999999986543
No 302
>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=65.96 E-value=24 Score=26.74 Aligned_cols=34 Identities=18% Similarity=0.355 Sum_probs=27.7
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
....+|...|+-.+-|+.|+..|++.|+|+....
T Consensus 6 vas~iAd~~GiTRSvIVNALRKleSaGvIesrSl 39 (61)
T PF08222_consen 6 VASKIADRVGITRSVIVNALRKLESAGVIESRSL 39 (61)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEET
T ss_pred hHHHHHHHhCccHHHHHHHHHHHHhcCceeeccc
Confidence 3457899999999999999999999999997654
No 303
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=65.75 E-value=18 Score=36.98 Aligned_cols=57 Identities=18% Similarity=0.175 Sum_probs=43.6
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYA 66 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l 66 (349)
++..|..... .+...+++..|.+..+....+..|+++|+|..+ ...+.||++|.-..
T Consensus 352 ~~~~Lr~~~g-l~~~~~~~~~g~~~~~~~~~l~~l~~~gll~~~---~~~l~lT~~G~~~~ 408 (430)
T PRK08208 352 IIKSLLQAQG-LDLADYRQRFGSDPLRDFPELELLIDRGWLEQN---GGRLRLTEEGLALS 408 (430)
T ss_pred HHHHHHHhCC-cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE---CCEEEECcchhhHH
Confidence 3344444444 577788888999887777889999999999875 45899999998754
No 304
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=65.66 E-value=11 Score=33.89 Aligned_cols=50 Identities=6% Similarity=0.089 Sum_probs=39.8
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhH
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEG 62 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG 62 (349)
.+...+++++|+.+|++..-+...+..|...|||....-..--|.|.-.-
T Consensus 22 ~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~p 71 (164)
T PRK10857 22 EAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKDA 71 (164)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCCH
Confidence 33457889999999999999999999999999999755555455554433
No 305
>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=65.58 E-value=5.2 Score=31.78 Aligned_cols=34 Identities=24% Similarity=0.130 Sum_probs=28.5
Q ss_pred HHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 31 NDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 31 ~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+++.++..|-+||||+-..-. .||++|.+.++.
T Consensus 34 p~~i~a~~RLheKGLI~~pdGg----yLT~~G~~~aEh 67 (77)
T TIGR02647 34 PAAVAAAARLHEKGLTTQPDGG----YLTSLGLEAAEH 67 (77)
T ss_pred HHHHHHHHHHHHcCCccCCCCC----EecHHHHHHHHH
Confidence 4688999999999999865544 899999998754
No 306
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=65.53 E-value=13 Score=34.68 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=34.1
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+..+||+.+|++...|.-|+..|++.|+|++....-..+
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~G~~V 71 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVLRGRGIIETAQGRGSFV 71 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCeeEE
Confidence 556899999999999999999999999999988754443
No 307
>PRK03932 asnC asparaginyl-tRNA synthetase; Validated
Probab=65.51 E-value=16 Score=37.88 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESS 246 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~ 246 (349)
..++..||++|.+.||.|+.| |.+.++
T Consensus 137 s~i~~~iR~f~~~~gf~EV~T-P~L~~~ 163 (450)
T PRK03932 137 NTLAQAIHEFFNENGFVWVDT-PIITAS 163 (450)
T ss_pred HHHHHHHHHHHHHCCCEEecC-Cceecc
Confidence 457788999999999999985 666543
No 308
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=65.44 E-value=10 Score=36.90 Aligned_cols=63 Identities=13% Similarity=0.025 Sum_probs=46.1
Q ss_pred HHHHHHHhhC-CCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEE-EeChhHHHHhhcCC
Q 018851 4 EAILGYLEKN-EQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETW-VLTGEGKKYAAEGS 70 (349)
Q Consensus 4 ~~iL~~L~~~-~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~-~LTeEG~~~l~~G~ 70 (349)
.+++.++.+. + +.-.-|+.+++++.+|.+.++.||+. |.-=.+. ....+ .||+.|+.+++...
T Consensus 6 L~~F~~vae~~g---S~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R-~~r~v~~LT~~G~~l~~~a~ 71 (327)
T PRK12680 6 LRYLVAIADAEL---NITLAAARVHATQPGLSKQLKQLEDELGFLLFVR-KGRSLESVTPAGVEVIERAR 71 (327)
T ss_pred HHHHHHHHHccC---CHHHHHHHhcCCchHHHHHHHHHHHHhCCeEEEE-CCCcCCccCccHHHHHHHHH
Confidence 3556666654 4 34567889999999999999999996 5544444 44567 49999998876543
No 309
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=65.40 E-value=20 Score=36.88 Aligned_cols=59 Identities=22% Similarity=0.172 Sum_probs=43.4
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHH---HHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHND---VVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~---v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
.|+..|..... .+...+.+.+|++... ....+..|++.|+|..+ ...+.||+.|.-++.
T Consensus 371 ~~~~~L~~~~~-ld~~~~~~~~g~~~~~~~~~~~~l~~l~~~gl~~~~---~~~~~lT~~G~~~~~ 432 (453)
T PRK13347 371 AIIETLMCNFP-VDLAAIAARHGFFARYFLDELARLEPLAADGLVTID---GGGIRVTPEGRPLIR 432 (453)
T ss_pred HHHHHHHhhCC-cCHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEE---CCEEEECcchhHHHH
Confidence 34455554444 5777888888988654 35778899999999875 347999999988664
No 310
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=65.40 E-value=8.9 Score=33.57 Aligned_cols=44 Identities=16% Similarity=0.212 Sum_probs=35.8
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
.||.+|-..+. .+-++||+.+|++...|.+.+..|...+++.+.
T Consensus 5 ~v~d~L~~~~~-~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~~ 48 (147)
T smart00531 5 LVLDALMRNGC-VTEEDLAELLGIKQKQLRKILYLLYDEKLIKID 48 (147)
T ss_pred eehHHHHhcCC-cCHHHHHHHhCCCHHHHHHHHHHHHhhhcchhh
Confidence 46777766665 567899999999999999999999997665443
No 311
>PF14090 HTH_39: Helix-turn-helix domain
Probab=65.32 E-value=30 Score=26.34 Aligned_cols=46 Identities=17% Similarity=0.115 Sum_probs=32.8
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
..+||.+|...+. .++.+....+|+-+ ...-+..|..+|+--....
T Consensus 3 ~~rIL~~L~~~~~-it~~ea~~~~gi~~--~~aRI~eLR~~G~~I~t~~ 48 (70)
T PF14090_consen 3 CKRILAALRRGGS-ITTLEARRELGIMR--LAARISELRKKGYPIVTEW 48 (70)
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHcCCCC--HHHHHHHHHHcCCeeeEEE
Confidence 4689999988887 45556556677544 5567888999998655444
No 312
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=65.30 E-value=13 Score=34.65 Aligned_cols=38 Identities=8% Similarity=0.013 Sum_probs=33.5
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEE
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRET 55 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~ 55 (349)
+-.+||+.+|++...|..|+..|++.|||++....-..
T Consensus 36 sE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~ 73 (254)
T PRK09464 36 PERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTF 73 (254)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCceeE
Confidence 56789999999999999999999999999998765433
No 313
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=65.20 E-value=12 Score=28.45 Aligned_cols=47 Identities=17% Similarity=0.027 Sum_probs=37.2
Q ss_pred ChHHHHHHhcCcCCC--CCHHHHHhhcC--chhhhhHHHHHhhCCcEeeCc
Q 018851 70 SPEVQLFLAVPAEGS--ISKDELQKKLD--PAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 70 ~PE~rl~~~l~~~g~--~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~~ 116 (349)
..|.+|+.+|...|+ ++..||.+.+| +....-.|..+.+.|+|..++
T Consensus 6 ~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 6 SLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred HHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 458899999987666 99999999865 445666778889999997754
No 314
>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=64.96 E-value=6.9 Score=28.19 Aligned_cols=45 Identities=16% Similarity=0.265 Sum_probs=35.6
Q ss_pred hHHHHHHhcCcCCC--CCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 71 PEVQLFLAVPAEGS--ISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 71 PE~rl~~~l~~~g~--~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
++++++.+|...++ +++.+|.+.+ .++..+-.+..+.++|||...
T Consensus 6 ~q~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 6 SQFRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 57888888876555 8999999885 456777788999999999764
No 315
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=64.43 E-value=6.8 Score=35.77 Aligned_cols=74 Identities=15% Similarity=0.096 Sum_probs=50.9
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee--eE-EEEeChhHHHHhhcCChHHHHHHhcC
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK--RE-TWVLTGEGKKYAAEGSPEVQLFLAVP 80 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~--~~-~~~LTeEG~~~l~~G~PE~rl~~~l~ 80 (349)
|+..|--.+.+.+.+++++.+|++.+.|..+++.|+.-|+|.-.... .. .|.-++.=-+... -+++.+.-+.+.
T Consensus 31 iYgilyls~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~~G~Rk~~F~a~~df~~~f~-t~f~ek~~ReId 107 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFEKGDRKDYFEAEKDFSQIFR-TLFEEKWKREID 107 (177)
T ss_pred HhhhheecCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhccCcchhhhcccchHHHHHH-HHHHHHHHHHhh
Confidence 44444444555788999999999999999999999999999654443 33 4444444444443 366666666664
No 316
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=64.32 E-value=4.9 Score=41.98 Aligned_cols=45 Identities=29% Similarity=0.337 Sum_probs=35.0
Q ss_pred HHhCCCHHHHHHHHHHhccCCcEEEEeeeeE--EEEeChhHHHHhhcC
Q 018851 24 AERGFDHNDVVNVIKSLHGFRYIDAQDIKRE--TWVLTGEGKKYAAEG 69 (349)
Q Consensus 24 ~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~--~~~LTeEG~~~l~~G 69 (349)
...+++.- +--++.+|++.|+|+.+..... .|+||+.|+++++.+
T Consensus 317 ~e~k~~Dl-vt~aL~~LEs~glik~ev~k~g~l~yvlTe~Gekvle~l 363 (593)
T COG1542 317 WETKIDDL-VTAALYTLESFGLIKREVVKNGDLTYVLTEFGEKVLEDL 363 (593)
T ss_pred HHhcccch-HHHHHHhhhhccchhhhhhhcCceEEEehhhhHHHHhcc
Confidence 34555433 7889999999999987665443 899999999988765
No 317
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=63.97 E-value=24 Score=33.01 Aligned_cols=44 Identities=14% Similarity=0.114 Sum_probs=36.2
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+..+-+-.+||+.+|++.-.|.+|+..|++.|+|.-....-+++
T Consensus 28 G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~GtfV 71 (236)
T COG2188 28 GDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKGTFV 71 (236)
T ss_pred CCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecCeeEE
Confidence 34455567899999999999999999999999998877655433
No 318
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=63.66 E-value=14 Score=33.35 Aligned_cols=57 Identities=16% Similarity=0.111 Sum_probs=43.6
Q ss_pred HHHHHhhCCCCCChHHHHHHh--CCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 6 ILGYLEKNEQISDSGNFAAER--GFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~--g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
|+.++.-.+.-.+...+|+.+ +++.++|..++.-|..-|+|+-... ..|..|+..-.
T Consensus 29 ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~--g~y~~t~~~l~ 87 (171)
T PF14394_consen 29 IRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD--GKYVQTDKSLT 87 (171)
T ss_pred HHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC--CcEEEecceee
Confidence 334343333323889999999 9999999999999999999987665 57888876643
No 319
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=63.26 E-value=22 Score=32.34 Aligned_cols=47 Identities=9% Similarity=0.003 Sum_probs=38.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
..||..+.......+..++|+.+|+++.+|...+..|++-|++..+.
T Consensus 165 r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~ 211 (225)
T PRK10046 165 NAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEI 211 (225)
T ss_pred HHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEe
Confidence 46788776542224688999999999999999999999999998765
No 320
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=62.60 E-value=26 Score=33.94 Aligned_cols=77 Identities=21% Similarity=0.265 Sum_probs=56.4
Q ss_pred HHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhcCChHHHHHHhcCcCCCC
Q 018851 7 LGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAEGSPEVQLFLAVPAEGSI 85 (349)
Q Consensus 7 L~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~g~~ 85 (349)
+.+++++. +...++||..+|+..++.+.-+..|.+.|+++--.. --+++..|+|--. -|.++|+..|.+
T Consensus 206 v~YIk~nK-vV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS~eEl~---------AVAkfIkqrGRV 275 (299)
T KOG3054|consen 206 VEYIKKNK-VVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYISMEELA---------AVAKFIKQRGRV 275 (299)
T ss_pred HHHHHhcC-eeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEecHHHHH---------HHHHHHHHcCce
Confidence 34555444 578999999999999999999999999999864322 2234455555433 245789888999
Q ss_pred CHHHHHhh
Q 018851 86 SKDELQKK 93 (349)
Q Consensus 86 ~~~el~~~ 93 (349)
||.+|...
T Consensus 276 SIaelAe~ 283 (299)
T KOG3054|consen 276 SIAELAEK 283 (299)
T ss_pred eHHHHHHh
Confidence 99999864
No 321
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=62.44 E-value=11 Score=35.68 Aligned_cols=41 Identities=12% Similarity=0.138 Sum_probs=35.2
Q ss_pred CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 16 ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 16 ~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
+-+--+||+.+|++...|.-+++.|+++|+|++....-.++
T Consensus 34 LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V 74 (241)
T COG2186 34 LPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTFV 74 (241)
T ss_pred CCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCceEe
Confidence 33457899999999999999999999999999988766544
No 322
>TIGR00458 aspS_arch aspartyl-tRNA synthetase, archaeal type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_arch, represents aspartyl-tRNA synthetases from the eukaryotic cytosol and from the Archaea. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn).
Probab=62.40 E-value=19 Score=37.11 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhhCCceecCCCCce
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
..++..||++|.+.||.|+.| |.+
T Consensus 137 s~i~~~iR~ff~~~gf~EV~T-P~L 160 (428)
T TIGR00458 137 SGVLESVREFLAEEGFIEVHT-PKL 160 (428)
T ss_pred HHHHHHHHHHHHHCCCEEEeC-Cce
Confidence 356778899999999999985 555
No 323
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=62.00 E-value=16 Score=35.07 Aligned_cols=61 Identities=13% Similarity=-0.049 Sum_probs=43.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
+++..+...+. +...-|+.+++++.+|.+.++.||+. |.==........+.||+.|+.+++
T Consensus 7 ~~f~~v~~~g~--S~s~AA~~L~isQpavS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~ 68 (313)
T PRK12684 7 RFVREAVRQNF--NLTEAAKALYTSQPGVSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILA 68 (313)
T ss_pred HHHHHHHHcCC--CHHHHHHHhcCCChHHHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHH
Confidence 45555555551 34467888999999999999999995 544444433333589999998875
No 324
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=61.95 E-value=15 Score=33.76 Aligned_cols=53 Identities=11% Similarity=0.134 Sum_probs=43.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
-.+++..|..++. ...-++|.++|++..+|.+.+..|+..|.|.......-.|
T Consensus 15 v~~~~~~l~~~~~-~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~pp~w 67 (183)
T PHA03103 15 VKKEVKNLGLGEG-ITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSNPPKW 67 (183)
T ss_pred HHHHHHHhccCCC-ccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCCCCCc
Confidence 4567788876665 6678999999999999999999999999997765544444
No 325
>COG2269 Truncated, possibly inactive, lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=61.56 E-value=7.7 Score=38.26 Aligned_cols=31 Identities=19% Similarity=0.157 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeeeehhhh
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFD 251 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFD 251 (349)
..++..||++|.+-||.|++| |-. +.+=|-|
T Consensus 20 a~i~~~iR~FF~erg~lEVeT-p~L-s~a~vtd 50 (322)
T COG2269 20 AAIIAAIRRFFAERGVLEVET-PAL-SVAPVTD 50 (322)
T ss_pred HHHHHHHHHHHHHcCceEecc-hHh-hcCCCCc
Confidence 578999999999999999986 433 4444333
No 326
>PLN02603 asparaginyl-tRNA synthetase
Probab=61.47 E-value=15 Score=39.36 Aligned_cols=26 Identities=15% Similarity=0.277 Sum_probs=20.7
Q ss_pred HHHHHHHHHHhhCCceecCCCCceeee
Q 018851 220 KVRKQLKDIFLQMGFEEMPTNNFVESS 246 (349)
Q Consensus 220 ~~~~~ir~if~~mGF~e~~~~~~Ves~ 246 (349)
+++..+|++|.+.||.|+.| |.+.++
T Consensus 231 ~i~~air~ff~~~gF~eV~T-PiLt~s 256 (565)
T PLN02603 231 ALAYATHKFFQENGFVWVSS-PIITAS 256 (565)
T ss_pred HHHHHHHHHHHHCCCEEEEC-Ceeccc
Confidence 45677889999999999975 777554
No 327
>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=61.23 E-value=34 Score=28.71 Aligned_cols=96 Identities=19% Similarity=0.159 Sum_probs=62.2
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPA 81 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~ 81 (349)
+-++||.+..... +..+.|..++++...|.+.++ -...|-+........ . .+...|-..+.+
T Consensus 7 lR~rVl~~~~~g~---s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~---------K-----id~~~L~~~v~~ 68 (119)
T PF01710_consen 7 LRQRVLAYIEKGK---SIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRK---------K-----IDRDELKALVEE 68 (119)
T ss_pred HHHHHHHHHHccc---hHHHHHHHhCcHHHHHHHHHH-hcccccccccccccc---------c-----ccHHHHHHHHHH
Confidence 5678898887643 567899999999999998877 444554433332211 1 123446666766
Q ss_pred CCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCc
Q 018851 82 EGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 82 ~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
....++.|+.+.+|-+...|. -.+.+.|+....+
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~-~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIW-RALKRLGITRKKK 102 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHH-HHHHHcCchhccC
Confidence 666899999988864433322 4567778876544
No 328
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=60.74 E-value=29 Score=34.59 Aligned_cols=58 Identities=19% Similarity=0.235 Sum_probs=42.9
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHH-HHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHND-VVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~-v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
|+..|..... .+...+.+..|.+..+ +...+..|++.|++... ...+.||++|.-.+.
T Consensus 309 ~~~~Lr~~~g-l~~~~~~~~~~~~~~~~~~~~~~~l~~~gl~~~~---~~~~~lt~~G~~~~~ 367 (377)
T PRK08599 309 MFLGLRKKSG-VSKARFEEKFGQSFEDVFGETIQELQEQGLLEED---DDHVRLTKKGKFLGN 367 (377)
T ss_pred HHHhHHhhCC-cCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEE---CCEEEECccHhHHHH
Confidence 4444544433 5677888888988776 56688899999999864 457999999987653
No 329
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=60.66 E-value=33 Score=29.99 Aligned_cols=59 Identities=15% Similarity=0.203 Sum_probs=44.1
Q ss_pred HHHHHHHhhCCCCCChHHHHH-----HhCCCHHHHHHHHHHhccCCcEEEEeee--eEEEEeChhH
Q 018851 4 EAILGYLEKNEQISDSGNFAA-----ERGFDHNDVVNVIKSLHGFRYIDAQDIK--RETWVLTGEG 62 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~-----~~g~~~~~v~~~~~~L~~kgli~~~~~~--~~~~~LTeEG 62 (349)
.+||++|...+...+.+++=. ..+++..+|.++++.|+..|+|..-... ...|.+..++
T Consensus 24 ~~vl~~L~~~~~~~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~~~~~y~~~~~~ 89 (145)
T COG0735 24 LAVLELLLEADGHLSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEGGKTRYELNSEP 89 (145)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCCCEEEEecCCCC
Confidence 568999987655467766532 2468899999999999999999876553 4567776665
No 330
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=60.62 E-value=29 Score=30.80 Aligned_cols=63 Identities=17% Similarity=0.243 Sum_probs=51.3
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHh--CCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAER--GFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKK 64 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~--g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~ 64 (349)
-|..||.+|...+.+.+..++...+ ++....|..++..|.+.|.|..... ....|......-.
T Consensus 2 Ae~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~~~~ 67 (169)
T PF07106_consen 2 AEDAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQDELE 67 (169)
T ss_pred hHHHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCccccC
Confidence 4778999999999889988887766 5788999999999999999988766 4457777666543
No 331
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=60.29 E-value=27 Score=35.37 Aligned_cols=57 Identities=14% Similarity=0.193 Sum_probs=42.6
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHH--HHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDV--VNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v--~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
|+..|..... .+...+.+..|.+.... ...+..|+..|++.. . ..+.||++|..++.
T Consensus 324 i~l~LR~~~G-l~~~~~~~~~g~~~~~~~~~~~l~~l~~~gll~~---~-~~l~lT~~G~~~~d 382 (390)
T PRK06582 324 LMMGLRLSKG-INISTLEQKLNTKLENILDMNNLKHYQALDLIRL---D-ENIYLTDKGLMLHS 382 (390)
T ss_pred HHHHHHhhCC-CCHHHHHHHHCcCHHHhhhHHHHHHHHHCCCEEE---C-CEEEECcchhHHHH
Confidence 4444544444 57778888899887764 478899999999886 2 56999999987653
No 332
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=60.20 E-value=15 Score=35.46 Aligned_cols=61 Identities=11% Similarity=-0.095 Sum_probs=45.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcC
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEG 69 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G 69 (349)
+++.++.+.+. .-.-|+.+++++.+|.+.++.||.. |.-=.+ +....+.||++|+.+++..
T Consensus 35 ~~f~av~e~gs---~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~-R~~r~v~lT~~G~~l~~~~ 96 (317)
T PRK11482 35 TIFEAVYVHKG---IVNAAKILNLTPSAISQSIQKLRVIFPDPLFI-RKGQGVTPTAYATHLHEYI 96 (317)
T ss_pred HHHHHHHHcCC---HHHHHHHhCCChHHHHHHHHHHHHHhCCcceE-ecCCCccCCHHHHHHHHHH
Confidence 44555555553 4467889999999999999999994 654444 4456899999999877653
No 333
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=60.18 E-value=16 Score=26.66 Aligned_cols=34 Identities=18% Similarity=0.130 Sum_probs=25.0
Q ss_pred HHHHHHHhhCCC-CCChHHHHHHhCCCHHHHHHHH
Q 018851 4 EAILGYLEKNEQ-ISDSGNFAAERGFDHNDVVNVI 37 (349)
Q Consensus 4 ~~iL~~L~~~~~-~~~~~~la~~~g~~~~~v~~~~ 37 (349)
.++|+.|...|. ..++.+||+.+|+++.+|...+
T Consensus 15 ~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 15 LRYLEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 457888877553 5678999999999999998765
No 334
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=60.12 E-value=16 Score=35.35 Aligned_cols=60 Identities=7% Similarity=-0.033 Sum_probs=42.9
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEE-EeChhHHHHhh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETW-VLTGEGKKYAA 67 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~-~LTeEG~~~l~ 67 (349)
+.+.++...+. +...-|+.+++++.+|.+.++.||+. |.==.+. ....+ .||+.|+.++.
T Consensus 7 ~~f~avae~g~--S~s~AA~~L~iSQpavS~~I~~LE~~lG~~LF~R-~~r~~~~LT~~G~~l~~ 68 (324)
T PRK12681 7 RYIVEVVNHNL--NVSATAEGLYTSQPGISKQVRMLEDELGIQIFAR-SGKHLTQVTPAGEEIIR 68 (324)
T ss_pred HHHHHHHHccC--CHHHHHHHhcCCcHHHHHHHHHHHHHhCCEeEEE-CCCCCCccCHHHHHHHH
Confidence 44555555531 34467888999999999999999996 5444444 34455 79999999873
No 335
>PLN02502 lysyl-tRNA synthetase
Probab=59.80 E-value=21 Score=38.20 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhhCCceecCCCCceee
Q 018851 220 KVRKQLKDIFLQMGFEEMPTNNFVES 245 (349)
Q Consensus 220 ~~~~~ir~if~~mGF~e~~~~~~Ves 245 (349)
.++..||++|.+.||.|+.| |.+.+
T Consensus 234 ~i~~~iR~fl~~~gF~EVeT-PiL~~ 258 (553)
T PLN02502 234 KIISYIRRFLDDRGFLEVET-PMLNM 258 (553)
T ss_pred HHHHHHHHHHHHCCCEEEEC-Ceeec
Confidence 45688999999999999985 66643
No 336
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=59.25 E-value=21 Score=30.83 Aligned_cols=48 Identities=13% Similarity=0.069 Sum_probs=37.1
Q ss_pred cCChHHHHHHhcCcCCCCCHHHHHhhcC------chhhhhHHHHHhhCCcEeeC
Q 018851 68 EGSPEVQLFLAVPAEGSISKDELQKKLD------PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 68 ~G~PE~rl~~~l~~~g~~~~~el~~~~~------~~~~~ig~g~~~k~~wi~i~ 115 (349)
-|.-|..|+++|=..|+.+.+|+...+. ....+.=|+.+.|+||+.-.
T Consensus 4 Is~aE~eVM~ilW~~~~~t~~eI~~~l~~~~ews~sTV~TLl~RL~KKg~l~~~ 57 (123)
T COG3682 4 ISAAEWEVMEILWSRGPATVREIIEELPADREWSYSTVKTLLNRLVKKGLLTRK 57 (123)
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHHhhcccccHHHHHHHHHHHHhccchhhh
Confidence 4567999999997777888888776543 33667788999999999653
No 337
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=59.14 E-value=37 Score=26.96 Aligned_cols=63 Identities=21% Similarity=0.191 Sum_probs=47.0
Q ss_pred HHHHHHHHHhh--CCCCCChHHHHHHhCCCHHHHHHHHHH-hccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 2 AEEAILGYLEK--NEQISDSGNFAAERGFDHNDVVNVIKS-LHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 2 ~e~~iL~~L~~--~~~~~~~~~la~~~g~~~~~v~~~~~~-L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
+..++|+.|.. ++.+...+.+|..+|.+.+.|...++- |-..|+|.-+.+-. .+|+.|.+|+.
T Consensus 9 ~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR---~~T~~a~~~l~ 74 (76)
T PF05491_consen 9 LDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGR---VATPKAYEHLG 74 (76)
T ss_dssp HHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEE---EE-HHHHHHTT
T ss_pred HHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHH---HhHHHHHHHhC
Confidence 45688999977 355688999999999999999877764 66689998766544 78999999875
No 338
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=58.92 E-value=17 Score=34.76 Aligned_cols=58 Identities=10% Similarity=-0.088 Sum_probs=43.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKY 65 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~ 65 (349)
.+++.++.+.+. .-.-|+.+++++.+|.+.++.||.. |. ..-.+....+.||+.|+..
T Consensus 13 L~~f~av~e~gs---~t~AA~~L~iSQpavS~~I~~LE~~lg~-~LF~R~~r~~~lT~~G~~l 71 (319)
T PRK10216 13 LLCLQLLMQERS---VTKAAKRMNVTPSAVSKSLAKLRAWFDD-PLFVNTPLGLSPTPLMVSM 71 (319)
T ss_pred HHHHHHHHHhCC---HHHHHHHhCCCHHHHHHHHHHHHHHhCC-ceEEecCCCcccCHHHHHH
Confidence 345566666653 4467889999999999999999995 54 3344456679999999864
No 339
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=58.83 E-value=16 Score=33.34 Aligned_cols=36 Identities=6% Similarity=0.139 Sum_probs=32.1
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.+-.++|+.+|+..+.|.+.++.|+.+|+|......
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~~~~ 220 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKY 220 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecCCE
Confidence 345789999999999999999999999999988753
No 340
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=58.63 E-value=21 Score=30.64 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=28.2
Q ss_pred HHHHHHhcCcCCCCCHHHHHhh--cCchhhhhHHHHHhhCCcEee
Q 018851 72 EVQLFLAVPAEGSISKDELQKK--LDPAVFKIGCSQAGKNKWVEM 114 (349)
Q Consensus 72 E~rl~~~l~~~g~~~~~el~~~--~~~~~~~ig~g~~~k~~wi~i 114 (349)
..-.+-+|...++++-.++... +-.++.+||+.+++.+|||..
T Consensus 29 vA~tlv~L~~~~E~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~ 73 (124)
T COG4738 29 VATTLVCLAKGDEASSREIERVSGLRQPEVSIAMRYLRENGWVDE 73 (124)
T ss_pred HHHHHHHHhcCcchhhhhhHHhhcCCCchhHHHHHHHHHccccch
Confidence 5555556654444443333322 445689999999999999965
No 341
>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=57.78 E-value=19 Score=26.47 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=32.4
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhcc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHG 42 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~ 42 (349)
+.+||..|-+.+. .+..++|+.+|++...|...+..|..
T Consensus 7 q~~Ll~~L~~~~~-~~~~ela~~l~~S~rti~~~i~~L~~ 45 (59)
T PF08280_consen 7 QLKLLELLLKNKW-ITLKELAKKLNISERTIKNDINELNE 45 (59)
T ss_dssp HHHHHHHHHHHTS-BBHHHHHHHCTS-HHHHHHHHHHHHT
T ss_pred HHHHHHHHHcCCC-CcHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 5678888877555 67899999999999999999999884
No 342
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=57.63 E-value=8.3 Score=37.70 Aligned_cols=63 Identities=14% Similarity=0.090 Sum_probs=49.5
Q ss_pred HHHHHHHHhhC--CCCCChHHHHHHhCCCHHHHHHHHH-HhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 3 EEAILGYLEKN--EQISDSGNFAAERGFDHNDVVNVIK-SLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 3 e~~iL~~L~~~--~~~~~~~~la~~~g~~~~~v~~~~~-~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+...|.++... +...+.+.+|..+|.+.+.+...+. .|-..|+|. ....--.+|+.|.+|++.
T Consensus 261 ~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~---~~~~gr~~~~~~~~~~~~ 326 (328)
T PRK00080 261 DRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQ---RTPRGRVATPKAYEHLGL 326 (328)
T ss_pred HHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcc---cCCchHHHHHHHHHHhCC
Confidence 45666645432 3347789999999999999999999 999999994 445566889999999864
No 343
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=57.58 E-value=17 Score=35.46 Aligned_cols=61 Identities=16% Similarity=0.171 Sum_probs=49.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYA 66 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l 66 (349)
++.+..+.+++.+.+.++....+|+-...|.+.-.||.+-|+|+....... .||+.|+.++
T Consensus 16 ~K~~~~v~~~~~~F~~~~a~~~lGvGkNMV~siryWl~a~gli~~~~~~~~--~~T~lG~~i~ 76 (286)
T PF13182_consen 16 KKGYDAVENDPDVFSDEDAIVRLGVGKNMVKSIRYWLRAFGLIEEDNKGKR--KLTPLGELIF 76 (286)
T ss_pred HHHHHHHhcCcccccchhHHHHcCCCHhHHHHHHHHHHHcCCcccCCCCCc--ccCHHHHHHH
Confidence 345666666665566677777899999999999999999999988776554 9999999988
No 344
>PRK09462 fur ferric uptake regulator; Provisional
Probab=57.26 E-value=26 Score=30.31 Aligned_cols=56 Identities=13% Similarity=0.191 Sum_probs=41.3
Q ss_pred HHHHHHHhhC-CCCCChHHHHHHh-----CCCHHHHHHHHHHhccCCcEEEEee--eeEEEEeC
Q 018851 4 EAILGYLEKN-EQISDSGNFAAER-----GFDHNDVVNVIKSLHGFRYIDAQDI--KRETWVLT 59 (349)
Q Consensus 4 ~~iL~~L~~~-~~~~~~~~la~~~-----g~~~~~v~~~~~~L~~kgli~~~~~--~~~~~~LT 59 (349)
..||+.|... +...+.+++-+.+ +++..+|.+.+..|+..|+|.--.. ....|.++
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~ 83 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFELT 83 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence 5689999864 3457888875543 5789999999999999999965432 34567665
No 345
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=55.32 E-value=23 Score=31.70 Aligned_cols=47 Identities=6% Similarity=0.014 Sum_probs=37.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHh-----CCCHHHHHHHHHHhccCCcEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAER-----GFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~-----g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
..||.+|...+...+.++|...+ +++..+|.+.+..|+..|+|..-.
T Consensus 29 ~~IL~~l~~~~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~ 80 (169)
T PRK11639 29 LEVLRLMSLQPGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVE 80 (169)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEe
Confidence 46889998766667888876543 578999999999999999996543
No 346
>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=55.31 E-value=29 Score=25.98 Aligned_cols=46 Identities=9% Similarity=0.078 Sum_probs=36.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
.+|...|...+. .+..++.+.++++..+|..++-.|-..|+|....
T Consensus 16 ~~V~~~Ll~~G~-ltl~~i~~~t~l~~~~Vk~~L~~LiQh~~v~y~~ 61 (62)
T PF08221_consen 16 AKVGEVLLSRGR-LTLREIVRRTGLSPKQVKKALVVLIQHNLVQYFE 61 (62)
T ss_dssp HHHHHHHHHC-S-EEHHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHcCC-cCHHHHHHHhCCCHHHHHHHHHHHHHcCCeeeec
Confidence 467777877776 5678999999999999999999999999998754
No 347
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=55.26 E-value=36 Score=35.02 Aligned_cols=59 Identities=15% Similarity=0.210 Sum_probs=42.7
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHH----HHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVV----NVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~----~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
++..|..... .+...+....|.+..+.. ..+..|+.+|++..+. ..+.||++|..++..
T Consensus 371 ~~~~Lr~~~g-l~~~~~~~~fg~~~~~~~~~~~~~l~~l~~~gll~~~~---~~~~lT~~G~~~~d~ 433 (453)
T PRK09249 371 VIEQLMCNFE-LDFAAIEAAFGIDFAEYFAEELERLAPLEADGLVELDE---NGITVTPKGRLLVRN 433 (453)
T ss_pred HHHHHhhcCC-cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCEEEEC---CEEEECccchHHHHH
Confidence 4455555544 577788888898866544 3467999999998653 579999999987643
No 348
>TIGR00457 asnS asparaginyl-tRNA synthetase. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, asnS, represents asparaginyl-tRNA synthetases from the three domains of life. Some species lack this enzyme and charge tRNA(asn) by misacylation with Asp, followed by transamidation of Asp to Asn.
Probab=55.25 E-value=22 Score=36.89 Aligned_cols=25 Identities=12% Similarity=0.267 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
..++..+|++|.+.||.|+.| |.+.
T Consensus 140 s~i~~~~r~~~~~~gf~eV~T-P~l~ 164 (453)
T TIGR00457 140 NALSQAIHRYFQENGFTWVSP-PILT 164 (453)
T ss_pred HHHHHHHHHHHHHCCCEEecC-CeEe
Confidence 356788899999999999975 6664
No 349
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=55.12 E-value=20 Score=24.35 Aligned_cols=45 Identities=13% Similarity=0.185 Sum_probs=32.6
Q ss_pred HHHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeCce
Q 018851 73 VQLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMGKQ 117 (349)
Q Consensus 73 ~rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~~~ 117 (349)
..++..|..++++++.+|.+.++ .....-.+..+.++|||....+
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 45667776656689999998854 4455667888899999876543
No 350
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=54.44 E-value=21 Score=27.55 Aligned_cols=45 Identities=20% Similarity=0.245 Sum_probs=36.7
Q ss_pred hHHHHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeC
Q 018851 71 PEVQLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 71 PE~rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~ 115 (349)
.|.+++..|...++++..+|...++ .+...-.+..+.+.|||...
T Consensus 11 ~~~~il~~l~~~~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 11 TQFLVLRILYEEGPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 4788888887666789999987764 56777899999999999764
No 351
>PTZ00401 aspartyl-tRNA synthetase; Provisional
Probab=54.15 E-value=34 Score=36.60 Aligned_cols=23 Identities=13% Similarity=0.351 Sum_probs=19.6
Q ss_pred HHHHHHHHHHhhCCceecCCCCce
Q 018851 220 KVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 220 ~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
.++..||++|.+.||.|+.| |.+
T Consensus 218 ~i~~~~R~fl~~~gFiEV~T-P~L 240 (550)
T PTZ00401 218 RVCQYFRQFLIDSDFCEIHS-PKI 240 (550)
T ss_pred HHHHHHHHHHHHCCCEEEeC-Ccc
Confidence 67788999999999999986 554
No 352
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=53.86 E-value=19 Score=24.99 Aligned_cols=38 Identities=18% Similarity=0.155 Sum_probs=22.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRY 45 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgl 45 (349)
.++..+.. + .+..++|+.+|++.+.|.+.++.....|+
T Consensus 9 ~ii~l~~~-G--~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 9 QIIRLLRE-G--WSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp -HHHHHHH-T----HHHHHHHHTS-HHHHHHHHT-------
T ss_pred HHHHHHHC-C--CCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 35566655 3 46789999999999999999998887775
No 353
>KOG1936 consensus Histidyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=52.75 E-value=14 Score=38.55 Aligned_cols=85 Identities=21% Similarity=0.273 Sum_probs=59.5
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCC
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGS 298 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS 298 (349)
..+.+.|+++|...|.+.++| | | | ++.++|-=+. |-.|
T Consensus 78 e~if~~i~~vFkrhGa~~iDT-P-V---F---------------ElkeiL~gKY----------------------GEds 115 (518)
T KOG1936|consen 78 EKIFSTIKEVFKRHGAETIDT-P-V---F---------------ELKEILTGKY----------------------GEDS 115 (518)
T ss_pred HHHHHHHHHHHHHcCCeeccc-c-c---h---------------hHHHHHhhhc----------------------cccc
Confidence 357788999999999999975 3 3 1 2222221111 1112
Q ss_pred CCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 299 RGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 299 ~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
.--|+..-.-.+..-||---|.--||+|.. +....+|-|-|++||||
T Consensus 116 -kLiYdlkDQGGEl~SLRYDLTVPfARylAm---Nki~sikRy~iAkVyRR 162 (518)
T KOG1936|consen 116 -KLIYDLKDQGGELCSLRYDLTVPFARYLAM---NKITSIKRYHIAKVYRR 162 (518)
T ss_pred -ceeEehhhcCCcEEEeecccccHHHHHHHH---cccccceeeeEEEEEec
Confidence 444666666667889999999999999974 34578999999999997
No 354
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=52.71 E-value=25 Score=31.46 Aligned_cols=60 Identities=12% Similarity=0.177 Sum_probs=45.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCC-------CHH-------HHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGF-------DHN-------DVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~-------~~~-------~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.||..+-..+. .....|++.+|. +.. -+..++..||..|||+... .--.||+.|++.|.+
T Consensus 57 sIlR~vY~~gp-vGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~---~GR~lT~~G~~~LD~ 130 (150)
T PRK09333 57 SILRKVYIDGP-VGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK---KGRVITPKGRSLLDN 130 (150)
T ss_pred HHHHHHHHcCC-ccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC---CCCEeCHHHHHHHHH
Confidence 57777766664 567888888886 332 3888999999999999765 445699999987754
No 355
>TIGR00459 aspS_bact aspartyl-tRNA synthetase, bacterial type. In a multiple sequence alignment of representative asparaginyl-tRNA synthetases (asnS), archaeal/eukaryotic type aspartyl-tRNA synthetases (aspS_arch), and bacterial type aspartyl-tRNA synthetases (aspS_bact), there is a striking similarity between asnS and aspS_arch in gap pattern and in sequence, and a striking divergence of aspS_bact. Consequently, a separate model was built for each of the three groups. This model, aspS_bact, represents aspartyl-tRNA synthetases from the Bacteria and from mitochondria. In some species, this enzyme aminoacylates tRNA for both Asp and Asn; Asp-tRNA(asn) is subsequently transamidated to Asn-tRNA(asn). This model generates very low scores for the archaeal type of aspS and for asnS; scores between the trusted and noise cutoffs represent fragmentary sequences.
Probab=52.57 E-value=41 Score=36.25 Aligned_cols=24 Identities=33% Similarity=0.530 Sum_probs=20.0
Q ss_pred HHHHHHHHHHhhCCceecCCCCcee
Q 018851 220 KVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 220 ~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
+++..||++|.+.||.|+.| |.+.
T Consensus 143 ~i~~~iR~ff~~~gFiEVeT-P~L~ 166 (583)
T TIGR00459 143 KVTKAVRNFLDQQGFLEIET-PMLT 166 (583)
T ss_pred HHHHHHHHHHHHCCCEEEEC-Ceec
Confidence 57788999999999999985 6653
No 356
>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=52.42 E-value=29 Score=25.84 Aligned_cols=52 Identities=15% Similarity=0.296 Sum_probs=40.0
Q ss_pred eChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeC
Q 018851 58 LTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 58 LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~ 115 (349)
||+--++||+- ||.+-.+++.++..+|.+.++ ++...-.+..+.+.|+|..+
T Consensus 2 Lt~~~e~YL~~------Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 2 LTESEEDYLKA------IYELSEEGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp CSCHHHHHHHH------HHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCcHHHHHHHH------HHHHHcCCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 67778888843 565555566789999998864 66777889999999999764
No 357
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=52.40 E-value=15 Score=35.66 Aligned_cols=89 Identities=13% Similarity=0.250 Sum_probs=61.3
Q ss_pred HHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeE-EEEeChhHHHHhhcCChHHHHHHhcCc---------------CC
Q 018851 20 GNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRE-TWVLTGEGKKYAAEGSPEVQLFLAVPA---------------EG 83 (349)
Q Consensus 20 ~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~-~~~LTeEG~~~l~~G~PE~rl~~~l~~---------------~g 83 (349)
..+-+.+|++...|.-++..|...|.+..+.+-.. +|.|||.|..-...+ ++++|..-.. .+
T Consensus 32 I~il~~fG~sE~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkgl~r~~~a--~~riy~~~r~aWdgkW~lli~~~~e~d 109 (291)
T COG3327 32 IQILAEFGISETTVRAALSRMVKAGWLVGEREGRKSFYRLSDKGLARQRRA--ARRIYPRTRPAWDGKWHLLIYTIPETD 109 (291)
T ss_pred HHHHHHcCccHHHHHHHHHHHHhccchheeecccccceeecHHHHHHHHHH--hhhhcCCCCcccCCceEEEEEecCccc
Confidence 34456789999999999999999999988886444 699999999877664 5666654431 11
Q ss_pred CCCHHHHHhhcCchhhhhHHHHHhhCCcEee
Q 018851 84 SISKDELQKKLDPAVFKIGCSQAGKNKWVEM 114 (349)
Q Consensus 84 ~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i 114 (349)
....++|++.+ .--|+|.+..-=||+-
T Consensus 110 r~~r~~lR~~l----~w~GFG~LA~s~w~sP 136 (291)
T COG3327 110 RRTRAALRKEL----HWLGFGELAESVWISP 136 (291)
T ss_pred HHHHHHHHHhh----hhcchhhhccccccCC
Confidence 11224444432 3457777777777754
No 358
>PLN02903 aminoacyl-tRNA ligase
Probab=52.31 E-value=37 Score=37.13 Aligned_cols=24 Identities=25% Similarity=0.401 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHhh-CCceecCCCCce
Q 018851 219 LKVRKQLKDIFLQ-MGFEEMPTNNFV 243 (349)
Q Consensus 219 ~~~~~~ir~if~~-mGF~e~~~~~~V 243 (349)
.+++..||++|.+ .||.|+.| |.+
T Consensus 207 s~i~~~iR~fl~~~~gFiEVeT-PiL 231 (652)
T PLN02903 207 HRVVKLIRRYLEDVHGFVEIET-PIL 231 (652)
T ss_pred HHHHHHHHHHHHhcCCeEEEEC-Cee
Confidence 4577889999997 99999985 665
No 359
>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=52.12 E-value=22 Score=29.32 Aligned_cols=47 Identities=9% Similarity=0.051 Sum_probs=38.0
Q ss_pred CChHHHHHHhcCcCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 69 GSPEVQLFLAVPAEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 69 G~PE~rl~~~l~~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
..++++++..|...+++++.+|.+.+ .++...-.+..+-++|||...
T Consensus 27 t~~q~~iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~ 75 (118)
T TIGR02337 27 TEQQWRILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRL 75 (118)
T ss_pred CHHHHHHHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEec
Confidence 35688899999777779999999885 455677788999999999874
No 360
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=52.01 E-value=34 Score=33.85 Aligned_cols=64 Identities=16% Similarity=0.202 Sum_probs=54.1
Q ss_pred HHHHHHHHhhC---CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHh
Q 018851 3 EEAILGYLEKN---EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYA 66 (349)
Q Consensus 3 e~~iL~~L~~~---~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l 66 (349)
..+||.++... -+....+.+.+..+++.+++...++.|-..++|.-......-|.||..|-++|
T Consensus 15 D~rlLraiE~~mR~~e~VP~~~i~~~ar~~~~~~~~~L~~L~~l~lv~r~~~~y~Gy~lT~~GyD~L 81 (304)
T COG0478 15 DFRLLRAIEGGMRSHEWVPLELIKKRARMDEEELLYRLKRLDKLKLVSRRTISYEGYQLTFSGYDAL 81 (304)
T ss_pred HHHHHHHHHhcccccccccHHHHHHHcCCCHHHHHHHHHHHHhcCceeccCCcceeEEEEecchhHH
Confidence 46788888642 23455788889999999999999999999999998777888999999999988
No 361
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=51.56 E-value=46 Score=34.22 Aligned_cols=61 Identities=16% Similarity=0.152 Sum_probs=41.9
Q ss_pred HHHHhhCCCCCChHHHHHHhCCCHHHHHH----HHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCCh
Q 018851 7 LGYLEKNEQISDSGNFAAERGFDHNDVVN----VIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSP 71 (349)
Q Consensus 7 L~~L~~~~~~~~~~~la~~~g~~~~~v~~----~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~P 71 (349)
+..|..... .+...+....|.+..+... .++.|+.+|++..+ ...+.||++|.-.+.+=.+
T Consensus 372 ~~~l~~~~g-l~~~~~~~~~g~~~~~~~~~~~~~l~~l~~~gll~~~---~~~~~lT~~G~~~~~~i~~ 436 (455)
T TIGR00538 372 IKSLMCNFK-LDYSKIEEKFDLDFADYFAKELELLKPLEEDGLLDVD---EKGIEVTPKGRLLIRNIAM 436 (455)
T ss_pred HHHHHhcCC-cCHHHHHHHHCCCHHHHHHHHHHHHHHHHhCCCEEEE---CCEEEECcCChHHHHHHHH
Confidence 333443444 4677788888888665333 46788899999864 4589999999987754333
No 362
>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=51.21 E-value=37 Score=29.05 Aligned_cols=44 Identities=9% Similarity=0.011 Sum_probs=36.5
Q ss_pred CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 16 ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 16 ~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
+.+.++||..++.+.+.|..|+.-|+..|||.+.. ...+.++.-
T Consensus 53 py~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~e--d~~i~i~~~ 96 (121)
T PF09681_consen 53 PYTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDE--DGVIYIPNW 96 (121)
T ss_pred CCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec--CCeEEeecH
Confidence 46789999999999999999999999999999854 345555553
No 363
>COG2469 Uncharacterized conserved protein [Function unknown]
Probab=50.95 E-value=12 Score=36.48 Aligned_cols=63 Identities=21% Similarity=0.227 Sum_probs=48.2
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.|.+||-++-+.+. +-+++.-+|++...+......|-.+||..+-... ....||++|+.++.+
T Consensus 217 ~E~qiLvalYSg~~---~~sl~~~lGv~~~el~~l~drlI~~gl~~iV~iR-k~ielt~~Gr~~vse 279 (284)
T COG2469 217 IEKQILVALYSGGD---SASLELFLGVDTDELEILYDRLIDKGLLKIVKIR-KEIELTPRGRAIVSE 279 (284)
T ss_pred hhheeeeeEecCCC---chhhhhHhCCcHHHHHHHHHHHHHhchhheEeee-hheecchhHHHHHHH
Confidence 46667776665543 4466677999999999999999999988765443 378999999987743
No 364
>PTZ00385 lysyl-tRNA synthetase; Provisional
Probab=50.78 E-value=38 Score=37.07 Aligned_cols=24 Identities=25% Similarity=0.355 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhhCCceecCCCCce
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
.+++..||++|.+.||.|+.| |.+
T Consensus 237 s~I~~aiR~ff~~~gFlEVeT-PiL 260 (659)
T PTZ00385 237 HVMLQALRDYFNERNFVEVET-PVL 260 (659)
T ss_pred HHHHHHHHHHHHHCCCEEeeC-CEe
Confidence 467888999999999999986 665
No 365
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=50.72 E-value=17 Score=33.50 Aligned_cols=43 Identities=12% Similarity=0.145 Sum_probs=36.7
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 14 EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 14 ~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
|...+..+||+.+|++..-|..|+..|++.|+|.+....-..+
T Consensus 37 G~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~rG~~V 79 (230)
T COG1802 37 GERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNRGAFV 79 (230)
T ss_pred CCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCCCCee
Confidence 4446778999999999999999999999999999987655444
No 366
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=50.38 E-value=27 Score=35.13 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=35.5
Q ss_pred CCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 14 EQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 14 ~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
..+-+..+||+.+|++...|..|...|++.|+|......-..+
T Consensus 27 ~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~~~G~~v 69 (431)
T PRK15481 27 DSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQGRNGTVI 69 (431)
T ss_pred CcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCCceEE
Confidence 3444667899999999999999999999999998876654444
No 367
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=50.36 E-value=21 Score=39.09 Aligned_cols=64 Identities=8% Similarity=0.099 Sum_probs=50.2
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee--eeEEEEeChhHHHHhh
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI--KRETWVLTGEGKKYAA 67 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~--~~~~~~LTeEG~~~l~ 67 (349)
+..||....+.+. .+.+++|+.+|++...+.+-+.++..+|++.-+.. ....+.++|.+...-+
T Consensus 604 qA~iI~~Fqek~t-wt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~iEse~d~~q 669 (765)
T KOG2165|consen 604 QAAIINLFQEKNT-WTLEELSESLGIPVPALRRRLSFWIQKGVLREEPIISDTGTLTVIESEMDFDQ 669 (765)
T ss_pred HHHHHHHhcCccc-ccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCCCCCceeeeccccccccc
Confidence 4456666666666 78899999999999999999999999999987763 3446777776655444
No 368
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=50.22 E-value=61 Score=29.00 Aligned_cols=102 Identities=10% Similarity=-0.001 Sum_probs=64.8
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhcc------CCcEEEEeeeeEEEEeChhHHHHhhcCChH---HHH-------H
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHG------FRYIDAQDIKRETWVLTGEGKKYAAEGSPE---VQL-------F 76 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~------kgli~~~~~~~~~~~LTeEG~~~l~~G~PE---~rl-------~ 76 (349)
.+...+.++||+.++ +.++|..++..|.. .|+--++....-.+.+-++=..+++.=.+. .+| +
T Consensus 10 s~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~~~~~LS~aalEtL 88 (159)
T PF04079_consen 10 SGEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKPKPPKLSQAALETL 88 (159)
T ss_dssp -SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTCCCHHHHHHHHHHH
T ss_pred cCCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccCccCCCCHHHHHHH
Confidence 444478999999999 99999999988864 456555555566677777766666543333 222 2
Q ss_pred HhcCcCCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCc
Q 018851 77 LAVPAEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 77 ~~l~~~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
..+.=..|++..|+.+.-|-+ ..=.+..++.+|||+..+
T Consensus 89 AiIAY~QPiTr~eIe~IRGv~-s~~~i~~L~e~glI~~~g 127 (159)
T PF04079_consen 89 AIIAYKQPITRAEIEEIRGVN-SDSVIKTLLERGLIEEVG 127 (159)
T ss_dssp HHHHHH-SEEHHHHHHHHTS---HCHHHHHHHTTSEEEEE
T ss_pred HHHHhcCCcCHHHHHHHcCCC-hHHHHHHHHHCCCEEecC
Confidence 222223578888888765644 455789999999998865
No 369
>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=49.99 E-value=56 Score=29.81 Aligned_cols=42 Identities=7% Similarity=0.056 Sum_probs=35.4
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEE
Q 018851 15 QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETW 56 (349)
Q Consensus 15 ~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~ 56 (349)
.+-+..+||+.+|++...|.+|+..|...|+|......-..+
T Consensus 24 ~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g~Gt~V 65 (231)
T TIGR03337 24 KLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDRRGWFV 65 (231)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCCCEEEE
Confidence 344567899999999999999999999999999877665444
No 370
>TIGR00499 lysS_bact lysyl-tRNA synthetase, eukaryotic and non-spirochete bacterial. This model represents the lysyl-tRNA synthetases that are class II amino-acyl tRNA synthetases. It includes all eukaryotic and most bacterial examples of the enzyme, but not archaeal or spirochete forms.
Probab=49.95 E-value=37 Score=35.73 Aligned_cols=26 Identities=23% Similarity=0.379 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhhCCceecCCCCceee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVES 245 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ves 245 (349)
.+++..||++|.+.||.|+.| |.+.+
T Consensus 176 s~i~~~iR~fl~~~gF~EVeT-P~L~~ 201 (496)
T TIGR00499 176 SKIIKAIRRFLDDRGFIEVET-PMLQV 201 (496)
T ss_pred HHHHHHHHHHHHHCcCEEEeC-Ceeec
Confidence 356788999999999999986 66643
No 371
>PF13518 HTH_28: Helix-turn-helix domain
Probab=49.79 E-value=41 Score=23.13 Aligned_cols=39 Identities=18% Similarity=0.115 Sum_probs=30.4
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcE
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYI 46 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli 46 (349)
+|+..+. .+. +..++|..+|++..+|.+.++..+..|+-
T Consensus 4 ~iv~~~~-~g~--s~~~~a~~~gis~~tv~~w~~~y~~~G~~ 42 (52)
T PF13518_consen 4 QIVELYL-EGE--SVREIAREFGISRSTVYRWIKRYREGGIE 42 (52)
T ss_pred HHHHHHH-cCC--CHHHHHHHHCCCHhHHHHHHHHHHhcCHH
Confidence 3455554 343 67899999999999999999999887753
No 372
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=49.51 E-value=42 Score=34.87 Aligned_cols=57 Identities=11% Similarity=0.106 Sum_probs=44.6
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhHHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKK 64 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~ 64 (349)
..|+..|.. ++ .+..+|++.+|++...|++.+.-| .|+|..... ....|.|++..+-
T Consensus 3 ~~~~~~L~~-g~-~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~~gr~~~Y~l~~~~~g 60 (442)
T PRK09775 3 SLLTTLLLQ-GP-LSAAELAARLGVSQATLSRLLAAL--GDQVVRFGKARATRYALLRPLRG 60 (442)
T ss_pred hHHHHHHhc-CC-CCHHHHHHHhCCCHHHHHHHHHHh--hcceeEeccCceEEEEecccccC
Confidence 346666764 44 578899999999999999999999 788766555 6668899887654
No 373
>PRK12820 bifunctional aspartyl-tRNA synthetase/aspartyl/glutamyl-tRNA amidotransferase subunit C; Provisional
Probab=49.47 E-value=35 Score=37.58 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
.+++..||++|.+.||.|+.| |.+.
T Consensus 160 s~i~~~iR~fl~~~gFiEVeT-PiL~ 184 (706)
T PRK12820 160 HRIIKCARDFLDSRGFLEIET-PILT 184 (706)
T ss_pred HHHHHHHHHHHHHCCCEEEeC-Cccc
Confidence 356788999999999999986 6653
No 374
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=48.61 E-value=44 Score=34.94 Aligned_cols=37 Identities=22% Similarity=0.339 Sum_probs=32.6
Q ss_pred HHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCCh
Q 018851 35 NVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSP 71 (349)
Q Consensus 35 ~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~P 71 (349)
..++.|..++||+.++.....+.+|+.|.+++++|+-
T Consensus 156 ~~l~~LkkRkL~~~~~~~~~~~~~~~~~~~~~~~~~~ 192 (489)
T PRK04172 156 KVLKELKKRKLVEEKERTERSVELTDAGLELLKEGIE 192 (489)
T ss_pred HHHHHHHhcCCeEEEEEEEEEEEEccchhhhhhcccc
Confidence 3678899999999999999999999999999988733
No 375
>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=48.17 E-value=37 Score=33.82 Aligned_cols=59 Identities=14% Similarity=0.262 Sum_probs=40.2
Q ss_pred HHHHHHHHHhhCC-CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee----eeEEEEeCh
Q 018851 2 AEEAILGYLEKNE-QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI----KRETWVLTG 60 (349)
Q Consensus 2 ~e~~iL~~L~~~~-~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~----~~~~~~LTe 60 (349)
.|..|+.++.+.+ ...-+-+|...+|+....|.++++.|++|+||+.-.. ..+.|-|.+
T Consensus 85 ~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~~ 148 (327)
T PF05158_consen 85 EERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLYD 148 (327)
T ss_dssp CHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEESS
T ss_pred HHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEcc
Confidence 3667788776522 2245678999999999999999999999999987443 344666654
No 376
>PLN02837 threonine-tRNA ligase
Probab=47.91 E-value=17 Score=39.18 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCce
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
...+++.+++.....||+++.+ |.+
T Consensus 250 ~~~L~~~~~~~~~~~G~~~v~t-P~l 274 (614)
T PLN02837 250 RHIIEDSWKKMHFEHGYDLLYT-PHV 274 (614)
T ss_pred HHHHHHHHHHHHHHCCCEEEEC-Ccc
Confidence 4556667777777889999975 554
No 377
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=47.67 E-value=30 Score=34.52 Aligned_cols=63 Identities=17% Similarity=0.333 Sum_probs=47.1
Q ss_pred HHHHHH-----HHhhCCCCCChHHHHHH--hCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 3 EEAILG-----YLEKNEQISDSGNFAAE--RGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 3 e~~iL~-----~L~~~~~~~~~~~la~~--~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
+..||. .+...+ +..+.++++. +|++...|.+.+..|++.|++.- ....--...|+.|-++-.
T Consensus 4 ~~~il~aIV~~~l~~~~-pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~-~h~sagript~kGYR~yv 73 (337)
T TIGR00331 4 QRKILKAIVEEYIKTGQ-PVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEK-PHTSSGRIPTDKGYRYYV 73 (337)
T ss_pred HHHHHHHHHHHHHhcCC-CcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccC-CCCCCCcCcChhHHHHHH
Confidence 456775 454444 4788999999 99999999999999999999965 333335567887776643
No 378
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=47.31 E-value=66 Score=29.44 Aligned_cols=46 Identities=9% Similarity=-0.058 Sum_probs=35.6
Q ss_pred ChHHHHHHhcCcCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 70 SPEVQLFLAVPAEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 70 ~PE~rl~~~l~~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
.+++.++..|...+++++.+|.+.+ +++...-.+..+-++|||...
T Consensus 45 ~~q~~iL~~L~~~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 45 INEHHILWIAYHLKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred HHHHHHHHHHHhCCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence 4678888888766679999999874 444555567899999999863
No 379
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=47.23 E-value=18 Score=34.10 Aligned_cols=43 Identities=16% Similarity=0.288 Sum_probs=36.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
.+||..|.... +. ..+++..+|+++.+|..-+.-|+..|+|+.
T Consensus 18 R~Il~lLt~~p-~y-vsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 18 RRILQLLTRRP-CY-VSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHHHhcCc-hH-HHHHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 46888887665 34 458889999999999999999999999987
No 380
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=46.94 E-value=57 Score=32.05 Aligned_cols=51 Identities=12% Similarity=0.200 Sum_probs=40.8
Q ss_pred HHHHHHHHhhCCC-CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee
Q 018851 3 EEAILGYLEKNEQ-ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR 53 (349)
Q Consensus 3 e~~iL~~L~~~~~-~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~ 53 (349)
-.+|+..|+..++ ..+-.++.+..|++.+.|.-++..||..|+|.-.+..-
T Consensus 6 reklir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsG 57 (321)
T COG3888 6 REKLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSG 57 (321)
T ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeecC
Confidence 3567778876543 35667888899999999999999999999998776643
No 381
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=46.53 E-value=22 Score=32.33 Aligned_cols=42 Identities=12% Similarity=-0.032 Sum_probs=33.2
Q ss_pred hCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 26 RGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 26 ~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
+++++.+|.+.++.||.. |.-=. .+....++||+.|+.++..
T Consensus 1 L~isQpavS~~I~~LE~~lg~~Lf-~R~~r~~~lT~~G~~l~~~ 43 (269)
T PRK11716 1 MHVSPSTLSRQIQRLEEELGQPLF-VRDNRSVTLTEAGEELRPF 43 (269)
T ss_pred CCcChHHHHHHHHHHHHHhCCeeE-EecCCceeECHhHHHHHHH
Confidence 478899999999999996 54444 4466789999999987744
No 382
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=45.85 E-value=36 Score=23.60 Aligned_cols=34 Identities=18% Similarity=0.144 Sum_probs=21.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIK 38 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~ 38 (349)
|...+..|-+.+ .+..++|..+|.+++.|.+.++
T Consensus 9 eR~~I~~l~~~G--~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 9 ERNQIEALLEQG--MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---HHHHHHCS-----HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHcC--CCHHHHHHHHCcCcHHHHHHHh
Confidence 334555665565 4788999999999999998875
No 383
>PLN02850 aspartate-tRNA ligase
Probab=45.65 E-value=53 Score=34.96 Aligned_cols=23 Identities=26% Similarity=0.463 Sum_probs=19.3
Q ss_pred HHHHHHHHHHhhCCceecCCCCce
Q 018851 220 KVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 220 ~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
.++..||++|.+.||.|+.| |.+
T Consensus 230 ~i~~~~R~fl~~~gF~EV~T-P~L 252 (530)
T PLN02850 230 QVCNLFREFLLSKGFVEIHT-PKL 252 (530)
T ss_pred HHHHHHHHHHHHCCcEEEeC-Ccc
Confidence 56788899999999999975 555
No 384
>COG3705 HisZ ATP phosphoribosyltransferase involved in histidine biosynthesis [Amino acid transport and metabolism]
Probab=45.55 E-value=44 Score=34.31 Aligned_cols=88 Identities=24% Similarity=0.321 Sum_probs=58.8
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCC
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYG 297 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~g 297 (349)
...+.+.+++.|..-||+.+.+ |.+|. .|.|.-=-.|-.| +-+|=+.++
T Consensus 20 ~~~i~~~l~~~f~~~Gy~~v~t-P~lE~----~d~~l~~~g~~l~--~~~f~l~d~------------------------ 68 (390)
T COG3705 20 KEEIRDQLLALFRAWGYERVET-PTLEP----ADPLLDGAGEDLR--RRLFKLEDE------------------------ 68 (390)
T ss_pred HHHHHHHHHHHHHHhCCccccc-cccch----hhhhhhccchhhh--hhheEEecC------------------------
Confidence 3467788888999999998874 55542 2332111122111 225655542
Q ss_pred CCCcccccchhhhhccccCCCCchhHHHHHHHhhcCCCCCceEEecCceecC
Q 018851 298 SRGYGYEWKREEANKNLLRTHTTAVSSRMLKALAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 298 S~Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~l~~~~~~p~k~fsi~rVfR~ 349 (349)
..+.+.||.-.|.--+|.-...... .|.|+-+-|+|||+
T Consensus 69 -----------~g~~l~LRpD~T~pVaR~~~~~~~~--~P~Rl~Y~G~Vfr~ 107 (390)
T COG3705 69 -----------TGGRLGLRPDFTIPVARIHATLLAG--TPLRLSYAGKVFRA 107 (390)
T ss_pred -----------CCCeEEecccccHHHHHHHHHhcCC--CCceeeecchhhhc
Confidence 1247999999999999987654333 69999999999995
No 385
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=45.06 E-value=28 Score=25.08 Aligned_cols=39 Identities=18% Similarity=0.201 Sum_probs=31.0
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF 43 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k 43 (349)
.|..||..+.... +..++|..+|+++..|...+..+..|
T Consensus 7 ~E~~vl~~l~~G~---~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 7 RELEVLRLLAQGM---SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp HHHHHHHHHHTTS----HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcC---CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 4788999887553 68899999999999998888777554
No 386
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=44.81 E-value=47 Score=26.47 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=27.3
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhcc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHG 42 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~ 42 (349)
..+|..|+. +.+.+.++||..+|.+.++|..++..+-+
T Consensus 27 r~LLr~LA~-G~PVt~~~LA~a~g~~~e~v~~~L~~~p~ 64 (77)
T PF12324_consen 27 RPLLRLLAK-GQPVTVEQLAAALGWPVEEVRAALAAMPD 64 (77)
T ss_dssp HHHHHHHTT-TS-B-HHHHHHHHT--HHHHHHHHHH-TT
T ss_pred HHHHHHHHc-CCCcCHHHHHHHHCCCHHHHHHHHHhCCC
Confidence 457888876 44588999999999999999999887754
No 387
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=44.31 E-value=55 Score=28.50 Aligned_cols=47 Identities=13% Similarity=0.166 Sum_probs=40.9
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
+..+|+..+..++. .+..+++..+|++...+-..+..|.+.|-|-..
T Consensus 13 Lk~rIvElVRe~GR-iTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~~ 59 (127)
T PF06163_consen 13 LKARIVELVREHGR-ITIKQLVAKTGASRNTVKRYLRELVARGDLYRH 59 (127)
T ss_pred HHHHHHHHHHHcCC-ccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEeC
Confidence 44678999998887 678899999999999999999999999987654
No 388
>PF04492 Phage_rep_O: Bacteriophage replication protein O ; InterPro: IPR006497 This entry is represented by the N-terminal domain of Bacteriophage lambda, GpO. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; GO: 0006260 DNA replication
Probab=44.19 E-value=29 Score=28.74 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=29.8
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEe
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQD 50 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~ 50 (349)
.+...+|+.+|++++.|..+++.|...|+|..+.
T Consensus 55 Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~~~g 88 (100)
T PF04492_consen 55 ISNSQIAEMTGLSRDHVSKALNELIRRGVIIRDG 88 (100)
T ss_pred eeHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCC
Confidence 3456899999999999999999999999996655
No 389
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=43.83 E-value=1.3e+02 Score=28.87 Aligned_cols=111 Identities=9% Similarity=0.098 Sum_probs=76.1
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee-eEEEE---eChhHHH-HhhcCChHHHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK-RETWV---LTGEGKK-YAAEGSPEVQLFLA 78 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~-~~~~~---LTeEG~~-~l~~G~PE~rl~~~ 78 (349)
..|++.+...+. .+.-|+++.++++.+++..-++-|++.++|+..... ...|. -|-.+.+ +.-+|---.+++..
T Consensus 104 ~~Iy~~i~~nPG-~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~yfpa~~t~~~~e~~~Lkn~~~k~I~~e 182 (240)
T COG3398 104 DGIYNYIKPNPG-FSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGGALRYFPADMTYGEAEVLSLKNETSKAIIYE 182 (240)
T ss_pred HHHHHHhccCCC-ccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceEEccCCCCcccchHHHhhchhHHHHHHH
Confidence 346677766665 677899999999999999999999999999876553 23443 3444543 33344445666767
Q ss_pred cCcCCCCCHHHHHhhcCchhh--hhHHHHHhhCCcEeeC
Q 018851 79 VPAEGSISKDELQKKLDPAVF--KIGCSQAGKNKWVEMG 115 (349)
Q Consensus 79 l~~~g~~~~~el~~~~~~~~~--~ig~g~~~k~~wi~i~ 115 (349)
|++++..+.-+|...++-+.+ .-.+.++...|+|.-+
T Consensus 183 iq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~ 221 (240)
T COG3398 183 IQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIPED 221 (240)
T ss_pred HhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCccc
Confidence 765543567788777654433 3455777888888766
No 390
>PF07927 YcfA: YcfA-like protein; InterPro: IPR012933 This entry represents UPF0395, which contains viral, archaeal and bacterial proteins. It includes YncN of Escherichia coli K12. Most of these proteins are hypothetical proteins of unknown function. ; GO: 0016788 hydrolase activity, acting on ester bonds; PDB: 1WHZ_A.
Probab=43.78 E-value=14 Score=26.47 Aligned_cols=21 Identities=24% Similarity=0.482 Sum_probs=14.7
Q ss_pred HHHHHHHhhCCceecCC-CCce
Q 018851 223 KQLKDIFLQMGFEEMPT-NNFV 243 (349)
Q Consensus 223 ~~ir~if~~mGF~e~~~-~~~V 243 (349)
.++..+|..+||++... |+.+
T Consensus 2 ~el~k~L~~~G~~~~r~~GSH~ 23 (56)
T PF07927_consen 2 RELIKLLEKAGFEEVRQKGSHH 23 (56)
T ss_dssp HHHHHHHHHTT-EEEEEETTEE
T ss_pred hHHHHHHHHCCCEEecCCCCEE
Confidence 57889999999997642 4544
No 391
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=43.22 E-value=29 Score=33.02 Aligned_cols=46 Identities=22% Similarity=0.373 Sum_probs=36.1
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
|+.-|..++...-..-+|...|+-.+-|+.|+..|++.|+|+....
T Consensus 194 I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSRSL 239 (261)
T COG4465 194 IFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSL 239 (261)
T ss_pred HHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeeccc
Confidence 4555554444444567899999999999999999999999988654
No 392
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=42.79 E-value=71 Score=25.95 Aligned_cols=43 Identities=16% Similarity=0.168 Sum_probs=33.9
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
|++-+.. -.+.++..+|+.+++.-+-.-.++..|+++|+|..-
T Consensus 32 l~kEV~~-~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 74 (86)
T PRK09334 32 VAKEVKK-EKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLY 74 (86)
T ss_pred HHHHhcc-CcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEE
Confidence 3444433 335678899999999999999999999999999643
No 393
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=42.49 E-value=2.7e+02 Score=25.54 Aligned_cols=104 Identities=7% Similarity=-0.044 Sum_probs=68.1
Q ss_pred hCCCC-CChHHHHHHhCCCH-HHHHHHHHHhcc------CCcEEEEeeeeEEEEeChhHHHHhhcCChH---------HH
Q 018851 12 KNEQI-SDSGNFAAERGFDH-NDVVNVIKSLHG------FRYIDAQDIKRETWVLTGEGKKYAAEGSPE---------VQ 74 (349)
Q Consensus 12 ~~~~~-~~~~~la~~~g~~~-~~v~~~~~~L~~------kgli~~~~~~~~~~~LTeEG~~~l~~G~PE---------~r 74 (349)
..+.+ .+..++|+.++++. +.+..++..|.. .|+.-++....-.+.+-++=..|+..=.+. -.
T Consensus 12 ~sg~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~~~i~~~~~~~~~~LS~aaLE 91 (186)
T TIGR00281 12 VSGEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFADYIHRFLPAKLKNLNSASLE 91 (186)
T ss_pred HcCCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccccccCCHHHHH
Confidence 34444 78899999999984 456566666633 355555555555677777777777652221 22
Q ss_pred HHHhcCcCCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCc
Q 018851 75 LFLAVPAEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 75 l~~~l~~~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
.+..|.=+.|++..|+.+.-|-+ ..=.+..++.+|||+..|
T Consensus 92 tLAIIAY~QPITr~eIe~IRGv~-s~~~l~~L~ergLI~~~G 132 (186)
T TIGR00281 92 VLAIIAYKQPITRARINEIRGVK-SYQIVDDLVEKGLVVELG 132 (186)
T ss_pred HHHHHHHcCCcCHHHHHHHcCCC-HHHHHHHHHHCCCeEecC
Confidence 23333324579999988765644 345789999999998863
No 394
>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=42.39 E-value=36 Score=28.62 Aligned_cols=43 Identities=9% Similarity=0.109 Sum_probs=34.4
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
|++-+..- .+.++..+|+.+++.-+-...++..|+++|+|..-
T Consensus 50 l~kEV~~~-K~ITp~~lserlkI~~SlAr~~Lr~L~~kG~Ik~V 92 (105)
T PF03297_consen 50 LLKEVPKM-KLITPSVLSERLKINGSLARKALRELESKGLIKPV 92 (105)
T ss_dssp HHHHCTTS-SCECHHHHHHHHCCSCHHHHHHHHHHHHCCSSEEE
T ss_pred HHHHhccC-cEeeHHHHHHhHhhHHHHHHHHHHHHHHCCCEEEE
Confidence 34444333 35778999999999999999999999999999653
No 395
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=42.32 E-value=51 Score=25.89 Aligned_cols=54 Identities=11% Similarity=0.190 Sum_probs=35.1
Q ss_pred HHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 221 VRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 221 ~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
++..|-.+|..||+.... -.|.+.= =...|+|||.+....+..+++-.+++++.
T Consensus 14 LL~~i~~~l~~~~l~I~~--A~I~T~g--------------era~D~FyV~d~~g~kl~~~~~~~~l~~~ 67 (75)
T cd04897 14 LLFDVVCTLTDMDYVVFH--ATIDTDG--------------DDAHQEYYIRHKDGRTLSTEGERQRVIKC 67 (75)
T ss_pred HHHHHHHHHHhCCeEEEE--EEEeecC--------------ceEEEEEEEEcCCCCccCCHHHHHHHHHH
Confidence 456788899999999753 3453321 14689999987544444456666666554
No 396
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=42.25 E-value=64 Score=32.41 Aligned_cols=57 Identities=19% Similarity=0.118 Sum_probs=39.3
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
++..|..... .+...+.+..|.+.. ...+..|.+.|++..+. ...+.||++|...+.
T Consensus 316 ~~~~Lr~~~g-id~~~~~~~~g~~~~--~~~l~~l~~~gl~~~~~--~~~~~lT~~G~~~~d 372 (380)
T PRK09057 316 LLMGLRLREG-IDLARYAALSGRPLD--PERLADLIEEGLIERDG--GSRLRATPAGRLVLD 372 (380)
T ss_pred HHHHHHHhCC-CCHHHHHHHHCCCch--HHHHHHHHHCCCEEEcC--CCEEEECcchhHHHH
Confidence 3344444443 567778777887754 25788999999988542 237999999987654
No 397
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=41.81 E-value=32 Score=33.00 Aligned_cols=75 Identities=15% Similarity=0.098 Sum_probs=48.1
Q ss_pred HHHHHHHhh-CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhc
Q 018851 4 EAILGYLEK-NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAV 79 (349)
Q Consensus 4 ~~iL~~L~~-~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l 79 (349)
-+.|..|.. ...+.+.++.|+.+|++++.+.-++.+|+.||++.--.+-.-.+-.-+-|++ ..--.+|+-+.+.+
T Consensus 17 ~e~l~~laae~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~rG~YlI~~lpage~-~~~t~he~~~~S~~ 92 (269)
T COG5340 17 SELLSHLAAEGHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERILRGRYLIIPLPAGEE-AVYTTHEYLIASHV 92 (269)
T ss_pred HHHHHHHHHHhCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhcCccEEEeecCCCcc-cceeehhHHHHHHH
Confidence 345555553 3457888999999999999999999999999998654444433333333332 11224444444444
No 398
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=41.21 E-value=42 Score=32.95 Aligned_cols=91 Identities=12% Similarity=0.146 Sum_probs=53.1
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHh-CCCHHHHHHHHHHhccCCcEEEEeee-eEEEEeChhHH-HHhhcCChHHHH-HHh
Q 018851 3 EEAILGYLEKNEQISDSGNFAAER-GFDHNDVVNVIKSLHGFRYIDAQDIK-RETWVLTGEGK-KYAAEGSPEVQL-FLA 78 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~-g~~~~~v~~~~~~L~~kgli~~~~~~-~~~~~LTeEG~-~~l~~G~PE~rl-~~~ 78 (349)
+..++..+..-....+-++|.++. +++..+++.++..|-++|.++.-+.. .-.|..-+.-. .-...-.||+++ |.+
T Consensus 13 ~~~~~~~~~~~p~git~q~L~~~~p~~~~~~~~salN~lLs~~~l~llr~~~~l~yr~~d~~~a~~~~~~e~eEk~vy~l 92 (297)
T KOG3233|consen 13 ENILIQIVKQIPEGITQQELQSEMPQISATDRASALNILLSRGLLDLLRQNTGLVYRAKDPKSASKGKGMENEEKLVYSL 92 (297)
T ss_pred HHHHHHHHHhccccccHHHHHHHcCCCcHHHHHHHHHHHHhcCcchhhccCCcceEeccCchhhcccccCChHHHHHHHH
Confidence 344455554444445567777665 57889999999999999999886554 33443322222 111122455554 456
Q ss_pred cCcCC--CCCHHHHHhh
Q 018851 79 VPAEG--SISKDELQKK 93 (349)
Q Consensus 79 l~~~g--~~~~~el~~~ 93 (349)
+.+.| ++-+.+|+..
T Consensus 93 Ie~sg~~GIW~k~ik~k 109 (297)
T KOG3233|consen 93 IEESGNEGIWSKEIKRK 109 (297)
T ss_pred HHHcCCCceeeehhhhc
Confidence 65432 3666777644
No 399
>PRK04158 transcriptional repressor CodY; Validated
Probab=41.05 E-value=18 Score=35.04 Aligned_cols=47 Identities=21% Similarity=0.360 Sum_probs=37.6
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
-|+..|...+.+.-...+|...|+-.+-|+.|+..|||.|+|+...-
T Consensus 190 hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIESrSl 236 (256)
T PRK04158 190 HIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRSL 236 (256)
T ss_pred HHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceeeccC
Confidence 35666655555455567899999999999999999999999998665
No 400
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=40.75 E-value=1.1e+02 Score=25.76 Aligned_cols=46 Identities=9% Similarity=0.009 Sum_probs=34.7
Q ss_pred ChHHHHHHhcCcC-CCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 70 SPEVQLFLAVPAE-GSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 70 ~PE~rl~~~l~~~-g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
.++..++..|... +++++.+|.+.+ .++...-.+..+-++|||...
T Consensus 31 ~~q~~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 31 QTHWVTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 3467778777643 358899999885 456677788999999999764
No 401
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=40.62 E-value=65 Score=25.06 Aligned_cols=54 Identities=6% Similarity=0.148 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 221 VRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 221 ~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
++.+|-++|.++|...-. -.|.+. .-...|+||+.++...+..+++-.+.+++.
T Consensus 14 LL~~i~~~l~~~gl~I~~--AkIsT~--------------Gerv~DvFyV~d~~g~kl~d~~~~~~l~~~ 67 (72)
T cd04895 14 ILLEAVQVLTDLDLCITK--AYISSD--------------GGWFMDVFHVTDQLGNKLTDDSLIAYIEKS 67 (72)
T ss_pred HHHHHHHHHHHCCcEEEE--EEEeec--------------CCeEEEEEEEECCCCCCCCCHHHHHHHHHH
Confidence 456788899999998642 345332 225689999987643333355666666553
No 402
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=40.50 E-value=37 Score=27.23 Aligned_cols=42 Identities=14% Similarity=0.207 Sum_probs=33.5
Q ss_pred HHHHHHhcCcCCCCCHHHHHhhcCch--hhhhHHHHHhhCCcEe
Q 018851 72 EVQLFLAVPAEGSISKDELQKKLDPA--VFKIGCSQAGKNKWVE 113 (349)
Q Consensus 72 E~rl~~~l~~~g~~~~~el~~~~~~~--~~~ig~g~~~k~~wi~ 113 (349)
+.+|+.+|..+++++..+|.+.+|-+ ...=-+..+.++|||+
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 67889999887789999999887644 4444678889999987
No 403
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=40.31 E-value=59 Score=33.14 Aligned_cols=42 Identities=14% Similarity=0.252 Sum_probs=35.1
Q ss_pred HHHHHh---hCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 6 ILGYLE---KNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 6 iL~~L~---~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
||..+. ..++..+.+++++.++++.+.+.+.+..|+..|+|.
T Consensus 297 iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~ 341 (412)
T PRK04214 297 LLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLR 341 (412)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeE
Confidence 555552 345557889999999999999999999999999997
No 404
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=40.13 E-value=39 Score=29.34 Aligned_cols=43 Identities=21% Similarity=0.274 Sum_probs=34.3
Q ss_pred HHHHHHhcC-cCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEee
Q 018851 72 EVQLFLAVP-AEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEM 114 (349)
Q Consensus 72 E~rl~~~l~-~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i 114 (349)
+..+|..|- .+|+.+.++|.+.+ +.+.+.-++.+++..|.|..
T Consensus 29 Dv~v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~R 74 (126)
T COG3355 29 DVEVYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVER 74 (126)
T ss_pred HHHHHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeee
Confidence 456666665 57889999999886 46677789999999999855
No 405
>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=40.13 E-value=79 Score=27.11 Aligned_cols=43 Identities=12% Similarity=0.134 Sum_probs=35.5
Q ss_pred CCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeCh
Q 018851 16 ISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTG 60 (349)
Q Consensus 16 ~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTe 60 (349)
+.+.+.||..++-+.+.|.-|+.-|+..|||.+... ..+.++.
T Consensus 51 py~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d~--g~i~i~~ 93 (119)
T TIGR01714 51 PYNAEMLATMFNRNVGDIRITLQTLESLGLIEKKNN--GDIFLEN 93 (119)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC--CcEEehh
Confidence 456788999999999999999999999999998742 3455554
No 406
>PF11994 DUF3489: Protein of unknown function (DUF3489); InterPro: IPR021880 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 84 to 211 amino acids in length. This protein has a single completely conserved residue W that may be functionally important.
Probab=39.76 E-value=1.3e+02 Score=23.71 Aligned_cols=47 Identities=11% Similarity=0.246 Sum_probs=36.6
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHh--ccCCcEEEEee
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSL--HGFRYIDAQDI 51 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L--~~kgli~~~~~ 51 (349)
..|+..|...+. .+.+++++.+|.-+..|.+++.-| ...|+.-+.+.
T Consensus 13 a~li~mL~rp~G-ATi~ei~~atGWq~HTvRgalsg~~kKklGl~i~s~k 61 (72)
T PF11994_consen 13 AQLIAMLRRPEG-ATIAEICEATGWQPHTVRGALSGLLKKKLGLTITSEK 61 (72)
T ss_pred HHHHHHHcCCCC-CCHHHHHHhhCCchhhHHHHHHHHHHHhcCcEEEeee
Confidence 457777765554 788999999999999999999999 55677655444
No 407
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=39.47 E-value=80 Score=21.90 Aligned_cols=35 Identities=23% Similarity=0.293 Sum_probs=27.9
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKS 39 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~ 39 (349)
++..|+..|... .+..++|..+|++.+.|.+.+..
T Consensus 16 ~~~~i~~~~~~~---~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 16 LEQYILKLLRES---RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred HHHHHHHHHhhc---CCHHHHHHHHCCCHHHHHHHHHh
Confidence 467788888655 25678999999999999998764
No 408
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=38.87 E-value=1e+02 Score=31.69 Aligned_cols=58 Identities=14% Similarity=0.084 Sum_probs=42.9
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHH-HHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHND-VVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~-v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
.++..|.. .. .|...+.+..|.+... +...+..|++.|++..+ ...+.||+.|.-++.
T Consensus 349 ~~~~~L~~-~g-ld~~~f~~~~g~~~~~~~~~~l~~l~~~Gll~~~---~~~l~lT~~G~~~~d 407 (433)
T PRK08629 349 RFLLGMFS-GR-LSIKYFRETFGVNLDKALFKEMLLLKLIGAIKND---PGDLIVTDFGKYLGV 407 (433)
T ss_pred HHHHHHHh-CC-cCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEEE---CCEEEECcchhHHHH
Confidence 34444543 33 5777888889998776 55688899999999864 457999999987653
No 409
>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=38.24 E-value=64 Score=25.71 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=28.0
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVI 37 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~ 37 (349)
..|+..|.. +. .+..++|+.+|++...|.+++
T Consensus 9 ~~I~e~l~~-~~-~ti~dvA~~~gvS~~TVsr~L 40 (80)
T TIGR02844 9 LEIGKYIVE-TK-ATVRETAKVFGVSKSTVHKDV 40 (80)
T ss_pred HHHHHHHHH-CC-CCHHHHHHHhCCCHHHHHHHh
Confidence 568899988 76 678999999999999999976
No 410
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=37.85 E-value=65 Score=31.63 Aligned_cols=62 Identities=11% Similarity=0.112 Sum_probs=40.2
Q ss_pred EEEeChhHHHHhhcCChHHHHHHhcCc-CCC------CCHHHHHhhcC--chhhhhHHHHHhhCCcEeeCcee
Q 018851 55 TWVLTGEGKKYAAEGSPEVQLFLAVPA-EGS------ISKDELQKKLD--PAVFKIGCSQAGKNKWVEMGKQV 118 (349)
Q Consensus 55 ~~~LTeEG~~~l~~G~PE~rl~~~l~~-~g~------~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~~~i 118 (349)
-.+|-+-+.+.+.+ .- ..|+..|.. +|. .+.+++++.|| +..++-|||-+||+|.|.+++..
T Consensus 212 nLSl~p~~~E~l~~-da-q~Il~yL~~~gG~mpf~DKSsPEdIk~~FgiSKg~FKrAiGgL~K~g~I~q~g~~ 282 (287)
T COG2996 212 NLSLRPRAHEMLDE-DA-QMILTYLESNGGFMPFNDKSSPEDIKATFGISKGQFKRAIGGLMKAGKIKQDGDG 282 (287)
T ss_pred ecccccccHHhhhh-hH-HHHHHHHHHcCCccccCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCeEEEcCce
Confidence 34444555555533 33 345666653 332 34678888864 55888999999999999996543
No 411
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=37.81 E-value=85 Score=31.84 Aligned_cols=49 Identities=10% Similarity=0.247 Sum_probs=37.7
Q ss_pred CChHHHHHHhCCCH-HHHHHHHHHhccCCcEEEEeeeeEE-EEeCh-hHHHHhhc
Q 018851 17 SDSGNFAAERGFDH-NDVVNVIKSLHGFRYIDAQDIKRET-WVLTG-EGKKYAAE 68 (349)
Q Consensus 17 ~~~~~la~~~g~~~-~~v~~~~~~L~~kgli~~~~~~~~~-~~LTe-EG~~~l~~ 68 (349)
.+...+.+.+|.+. +.+...+..|+.+|++..+. .. +.||+ .|..++..
T Consensus 336 l~~~~~~~~~g~~~~~~~~~~l~~l~~~gll~~~~---~~~~~lT~~~G~~~~~~ 387 (400)
T PRK07379 336 VSLSALTERFGKEIVEQILQCLQPYFQQGWVELEG---DRRLRLTDPEGFLFSNT 387 (400)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEEeC---CeEEEECchHHhHHHHH
Confidence 56777888888876 44667899999999988653 35 99995 89887654
No 412
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=37.46 E-value=74 Score=29.11 Aligned_cols=92 Identities=17% Similarity=0.182 Sum_probs=59.5
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHH-HHHHHHHHhccCCcEEEEee-eeEEEEeChhHHHHhhcC--ChHHHHHH
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHN-DVVNVIKSLHGFRYIDAQDI-KRETWVLTGEGKKYAAEG--SPEVQLFL 77 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~-~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG~~~l~~G--~PE~rl~~ 77 (349)
+|..||-.+.-.+..-+..+++..++++.. .+.=+++.|+.-|||+.... ....|+.|.-|.+.-..- --|.-|+.
T Consensus 84 ~e~l~lH~irhrdR~K~laDic~~ln~eDth~itYslrKL~k~gLit~t~~gkevTy~vTa~G~~acarYa~IRe~lLid 163 (199)
T COG5631 84 PENLLLHIIRHRDRPKSLADICQMLNREDTHNITYSLRKLLKGGLITRTGSGKEVTYEVTALGHRACARYADIREVLLID 163 (199)
T ss_pred hHHHHHHHHhhcCchhhHHHHHHHhccccchhHHHHHHHHHhccceecCCCCceEEEEEecchHHHHHHHHHHHHHHHHh
Confidence 466777777766655566778877787544 46678899999999988666 445899999998754331 12444445
Q ss_pred hcCcCCCC--CHHHHHhh
Q 018851 78 AVPAEGSI--SKDELQKK 93 (349)
Q Consensus 78 ~l~~~g~~--~~~el~~~ 93 (349)
.+...++. .+.||...
T Consensus 164 ~vt~~~e~~~~l~elArl 181 (199)
T COG5631 164 AVTRIPEMADKLEELARL 181 (199)
T ss_pred cccCCchhhhHHHHHHHH
Confidence 55432221 34555544
No 413
>TIGR00415 serS_MJ seryl-tRNA synthetase, Methanococcus jannaschii family. The seryl-tRNA synthetases from a few of the Archaea, represented by this model, are very different from the set of mutually more closely related seryl-tRNA synthetases from Eubacteria, Eukaryotes, and other Archaea. Although distantly homologous, the present set differs enough not to be recognized by the pfam model tRNA-synt_2b that recognizes the remainder of seryl-tRNA synthetases among oither class II amino-acyl tRNA synthetases.
Probab=36.54 E-value=59 Score=34.60 Aligned_cols=108 Identities=11% Similarity=0.010 Sum_probs=51.1
Q ss_pred HHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCCCcccccc-
Q 018851 228 IFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSRGYGYEWK- 306 (349)
Q Consensus 228 if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~Gw~Y~W~- 306 (349)
.+...||+++. .|.+.+. +.|.-= +|-..-.++.||+..+.. ++++.+.+..-+.. ++.+=-. .-.
T Consensus 237 ~~~k~Gy~ev~-fP~LIp~----e~l~k~-ghl~gF~~e~y~Vt~~~~----d~d~~~~f~~~~~~--~~eipi~-~L~~ 303 (520)
T TIGR00415 237 IVKKIGFQECL-FPKLIPL----DIMNKM-RYLEGLPEGMYYCCAPKR----DPELFEEFKNELII--KKEIPID-KLKN 303 (520)
T ss_pred HHHhcCCeEEe-CCcEecH----HHHccc-CCCCCCchhheEEecCCC----Ccchhhcccccccc--ccccccc-cccc
Confidence 44557999997 4655433 233222 555556678888854321 11222222211110 0000000 000
Q ss_pred hhhhhccccCCCCchhHHHHHHHhhcC--CCCCceEEe-cCceecC
Q 018851 307 REEANKNLLRTHTTAVSSRMLKALAEK--PFAPKKVFL-HRSCFQK 349 (349)
Q Consensus 307 ~~~a~~~vLRTHTTavs~r~L~~l~~~--~~~p~k~fs-i~rVfR~ 349 (349)
.-+....+|| .|+|+..-.|+.-.-. ..-|++++. .+.|||+
T Consensus 304 ~le~~~~vL~-PTSE~ply~~~a~~Ils~~dLPlk~~~~s~~CFR~ 348 (520)
T TIGR00415 304 GIKDPGYVIA-PAQCEPFYQFFEGEVIDAEDKPIKFFDRSGWTYRW 348 (520)
T ss_pred cccCCceEEe-CccHHHHHHHHhccccChhhCCeeEEEEecCeEeC
Confidence 0011246677 4666665555532211 235999999 6799995
No 414
>COG0172 SerS Seryl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=35.62 E-value=71 Score=33.22 Aligned_cols=85 Identities=20% Similarity=0.276 Sum_probs=50.6
Q ss_pred HHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCCCCC
Q 018851 220 KVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGYGSR 299 (349)
Q Consensus 220 ~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~gS~ 299 (349)
-+++-+-+.....||+++. -|++....=-|-.=+.|. --.|.|++.++.
T Consensus 179 AL~~f~ld~~~~~Gf~e~~-~P~lv~~e~m~gtgqlpk-----f~e~~y~v~~~~------------------------- 227 (429)
T COG0172 179 ALIQFMLDLHTKHGFTEVL-PPYLVNLESMFGTGQLPK-----FEEDLYKVEDPD------------------------- 227 (429)
T ss_pred HHHHHHHHHHHHcCceEee-CceeecHHHhhccCCCCC-----CcccceEecCCC-------------------------
Confidence 3455555666678999997 477755544444444444 457899997631
Q ss_pred CcccccchhhhhccccCCCCchhHHHHHHH--hhcCCCCCceEEecCceecC
Q 018851 300 GYGYEWKREEANKNLLRTHTTAVSSRMLKA--LAEKPFAPKKVFLHRSCFQK 349 (349)
Q Consensus 300 Gw~Y~W~~~~a~~~vLRTHTTavs~r~L~~--l~~~~~~p~k~fsi~rVfR~ 349 (349)
-.|.= |.+++.-.|+. .-....-|+||+..-.|||+
T Consensus 228 ------------~~Lip--TaEvpl~~l~~~Eil~~~~LP~k~~~~S~cFR~ 265 (429)
T COG0172 228 ------------LYLIP--TAEVPLTNLHRDEILDEEDLPIKYTAYSPCFRS 265 (429)
T ss_pred ------------EEEEe--cchhhhHHhhcccccccccCCeeeEEEChhhhc
Confidence 12332 33444333331 11123469999999999996
No 415
>PRK10870 transcriptional repressor MprA; Provisional
Probab=35.43 E-value=1.7e+02 Score=26.21 Aligned_cols=45 Identities=18% Similarity=0.203 Sum_probs=33.6
Q ss_pred hHHHHHHhcCc--CCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeC
Q 018851 71 PEVQLFLAVPA--EGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 71 PE~rl~~~l~~--~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~ 115 (349)
+.+.++..|.. ++++++.+|.+.++ ++...-.+..+-++|||...
T Consensus 56 ~q~~iL~~L~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 56 TLFMALITLESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 46777877753 34688899998854 44555577999999999873
No 416
>PF02387 IncFII_repA: IncFII RepA protein family; InterPro: IPR003446 These proteins are plasmid encoded and essential for plasmid replication, they are also involved in copy control functions [].; GO: 0006276 plasmid maintenance
Probab=35.02 E-value=1.1e+02 Score=30.04 Aligned_cols=61 Identities=18% Similarity=0.088 Sum_probs=44.8
Q ss_pred CChHHHHHHhCCCH---------HHHHHHHHH-hccCCcEEEEeeee--------EEEEeChhHHHHhhcCChHHHHHHh
Q 018851 17 SDSGNFAAERGFDH---------NDVVNVIKS-LHGFRYIDAQDIKR--------ETWVLTGEGKKYAAEGSPEVQLFLA 78 (349)
Q Consensus 17 ~~~~~la~~~g~~~---------~~v~~~~~~-L~~kgli~~~~~~~--------~~~~LTeEG~~~l~~G~PE~rl~~~ 78 (349)
.+.+.||.++|+++ .-+.+++.. |+.-|+|+.+..-+ ..+.||+.+=..+ |-++.++...
T Consensus 96 ~sie~LA~ecGLst~s~~Gn~sitRasR~i~e~le~~Gli~~~~~~D~~~~~~~Pk~I~lT~~ff~l~--gi~~~kl~~~ 173 (281)
T PF02387_consen 96 ASIEQLADECGLSTKSAAGNKSITRASRLISEFLEPLGLITCEKEWDPYNGNYIPKHIWLTPLFFMLL--GISEDKLRRE 173 (281)
T ss_pred ecHHHHHHHhCCcccCCCCCeeHHHHHHHHHHHHHhcCCeeeeeeechhhccccCeEEEECHHHHHHh--CCCHHHHHHH
Confidence 45688999887654 457788855 88899998866522 3789999997765 7777776655
Q ss_pred c
Q 018851 79 V 79 (349)
Q Consensus 79 l 79 (349)
.
T Consensus 174 ~ 174 (281)
T PF02387_consen 174 Q 174 (281)
T ss_pred H
Confidence 4
No 417
>COG0173 AspS Aspartyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=34.86 E-value=1.1e+02 Score=33.06 Aligned_cols=25 Identities=28% Similarity=0.462 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhhCCceecCCCCcee
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFVE 244 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~Ve 244 (349)
.++...||+.|-.+||.|+.| |...
T Consensus 145 ~kv~~~iR~~ld~~gF~EiET-PiLt 169 (585)
T COG0173 145 SKVTKAIRNFLDDQGFLEIET-PILT 169 (585)
T ss_pred HHHHHHHHHHHhhcCCeEeec-Cccc
Confidence 367788999999999999986 6653
No 418
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.56 E-value=99 Score=29.59 Aligned_cols=58 Identities=16% Similarity=0.147 Sum_probs=45.9
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChh
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGE 61 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeE 61 (349)
.+.|+..+.+.+- ...-.+|.++|++...|.=.++.|+.-|+|..++. ....|..|+-
T Consensus 176 ~k~I~~eiq~~~~-~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~~~Gr~iiy~in~s 234 (240)
T COG3398 176 SKAIIYEIQENKC-NTNLLIAYELNLSVATVAYHLKKLEELGIIPEDREGRSIIYSINPS 234 (240)
T ss_pred HHHHHHHHhcCCc-chHHHHHHHcCccHHHHHHHHHHHHHcCCCcccccCceEEEEeCHH
Confidence 4677777775553 56678999999999999999999999999987655 4446676663
No 419
>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=34.39 E-value=28 Score=26.29 Aligned_cols=41 Identities=15% Similarity=0.230 Sum_probs=31.5
Q ss_pred HHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEee
Q 018851 74 QLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEM 114 (349)
Q Consensus 74 rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i 114 (349)
.|.++|..+|.+++++|...|+ ++....-|..+.++|.|+.
T Consensus 4 ~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~ 46 (69)
T PF09012_consen 4 EIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRK 46 (69)
T ss_dssp HHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEE
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEE
Confidence 4566777778899999998864 5577778889999998865
No 420
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=33.80 E-value=98 Score=27.03 Aligned_cols=62 Identities=19% Similarity=0.218 Sum_probs=45.2
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhc---cCCcEEEEeeeeE--EEEeChhHHHHhhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLH---GFRYIDAQDIKRE--TWVLTGEGKKYAAE 68 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~---~kgli~~~~~~~~--~~~LTeEG~~~l~~ 68 (349)
.++|+++...+. ...-|+..|++.-.+-.+++.|+ .+-+|....--+. --+||+.|+++++.
T Consensus 22 ~~LL~~I~etGS---Is~AAk~~GiSYk~AW~~i~~~n~~~~~plVe~~rGGk~gGga~LT~~g~~ll~~ 88 (130)
T COG2005 22 IELLKAIAETGS---ISAAAKAAGISYKSAWDYIKALNRLLGEPLVERRRGGKGGGGAVLTDFGERLLEE 88 (130)
T ss_pred HHHHHHHHHhCC---HHHHHHHcCCCHHHHHHHHHHHHHHhCCCeeeeccCCCCCCcchhHHHHHHHHHH
Confidence 468888888875 44667889999998655555554 4567777665443 57899999998854
No 421
>PLN02320 seryl-tRNA synthetase
Probab=33.74 E-value=56 Score=34.64 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHhhCCceecCCCCce
Q 018851 219 LKVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 219 ~~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
+.+++.+++....-||+++.+ |.+
T Consensus 237 ~ALi~f~ld~~~~~Gy~eV~t-P~l 260 (502)
T PLN02320 237 MALVNWTLSEVMKKGFTPLTT-PEI 260 (502)
T ss_pred HHHHHHHHHHHHHcCCEEEEC-Ccc
Confidence 688889999998899999975 554
No 422
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.25 E-value=86 Score=22.87 Aligned_cols=65 Identities=12% Similarity=0.160 Sum_probs=41.7
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE-eeeeEEEEeChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhhc
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ-DIKRETWVLTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKL 94 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~-~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~~ 94 (349)
+..++|+.+|++++.|.... ..|++... .........|++--. ..+.+..|.+.| ++++++...+
T Consensus 2 s~~eva~~~gvs~~tlr~~~----~~gli~~~~~~~~g~r~y~~~dl~-------~l~~i~~lr~~g-~~~~~i~~~l 67 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE----RIGLLPPPIRTEGGYRLYSDEDLE-------RLRFIKRLKELG-FSLEEIKELL 67 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH----HCCCCCCCccCCCCCEecCHHHHH-------HHHHHHHHHHcC-CCHHHHHHHH
Confidence 45688999999999887554 58888754 333334445554433 344555665544 8888887654
No 423
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=32.55 E-value=52 Score=32.79 Aligned_cols=35 Identities=9% Similarity=0.058 Sum_probs=32.5
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI 51 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~ 51 (349)
.+-.++|+.+|++...|.+.+......|+|++...
T Consensus 27 ltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~ 61 (321)
T COG2390 27 LTQSEIAERLGISRATVSRLLAKAREEGIVKISIN 61 (321)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence 46689999999999999999999999999999877
No 424
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=32.52 E-value=36 Score=29.21 Aligned_cols=55 Identities=20% Similarity=0.314 Sum_probs=41.6
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-------EEEEeChh
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-------ETWVLTGE 61 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-------~~~~LTeE 61 (349)
.|..|++.++ .++-++.-..|+.+-+|.=|+.+|...|.|+..+..+ ..|.||--
T Consensus 32 tlv~L~~~~E-~sS~~IE~~sgLRQPEVSiAMr~Lre~gWV~~R~eKKkGKGRPik~Y~Lt~~ 93 (124)
T COG4738 32 TLVCLAKGDE-ASSREIERVSGLRQPEVSIAMRYLRENGWVDEREEKKKGKGRPIKLYRLTVP 93 (124)
T ss_pred HHHHHhcCcc-hhhhhhHHhhcCCCchhHHHHHHHHHccccchHHhcccCCCCCceEEEecCc
Confidence 4556666676 5566777789999999999999999999998865443 35666643
No 425
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=32.39 E-value=29 Score=36.49 Aligned_cols=43 Identities=16% Similarity=0.281 Sum_probs=35.9
Q ss_pred HHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 20 GNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 20 ~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
+++-...|.+..+|.-++.+|+|||+|++- ...-+.||+-|+.
T Consensus 446 edi~~~~g~~eeev~~sl~kleskgfveeL--~n~gv~LTeaGe~ 488 (593)
T COG1542 446 EDIQGHVGGDEEEVIKSLGKLESKGFVEEL--PNKGVKLTEAGEL 488 (593)
T ss_pred HHHHhhcCccHHHHHHHHHHHhhcchHHHh--ccCcEEeehhhHH
Confidence 455567789999999999999999998654 4667899999975
No 426
>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=32.14 E-value=49 Score=35.02 Aligned_cols=91 Identities=15% Similarity=0.161 Sum_probs=55.9
Q ss_pred hHHHHHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCCC
Q 018851 217 PLLKVRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGGY 296 (349)
Q Consensus 217 Pl~~~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg~ 296 (349)
-+.++.+-||+.|.+.|.+|+- -|-+.+ ..|.+=.+|=.-=--..|.|++- |
T Consensus 49 v~~kI~~iir~em~~~G~~Evl-~P~L~p-----~eLwkEs~r~~~f~~El~~v~dr-----------------g----- 100 (500)
T COG0442 49 VLEKIENIIREEMDKIGAQEVL-FPTLIP-----AELWKESGRWEGFGPELFRVKDR-----------------G----- 100 (500)
T ss_pred HHHHHHHHHHHHHHhcCceEEe-chhcCH-----HHHHHHhChhhhcchhhEEEEcc-----------------C-----
Confidence 4778888889999999999885 344422 12222222221111134555431 1
Q ss_pred CCCCcccccchhhhhccccC-CCCchhHHHHHHHhhcCCCCCceEEecCceec
Q 018851 297 GSRGYGYEWKREEANKNLLR-THTTAVSSRMLKALAEKPFAPKKVFLHRSCFQ 348 (349)
Q Consensus 297 gS~Gw~Y~W~~~~a~~~vLR-THTTavs~r~L~~l~~~~~~p~k~fsi~rVfR 348 (349)
.+.++|| ||=|+++.-+=....+...-|.+++-|..|||
T Consensus 101 -------------~~~l~L~PTsEe~it~~~~~~i~SYkdLPl~lYQi~~kfR 140 (500)
T COG0442 101 -------------DRPLALRPTSEEVITDMFRKWIRSYKDLPLKLYQIQSKFR 140 (500)
T ss_pred -------------CceeeeCCCcHHHHHHHHHHHhhhhhhCCcceeeeeeEEe
Confidence 3479999 89888876543222233446999999999999
No 427
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=31.97 E-value=1.3e+02 Score=24.09 Aligned_cols=43 Identities=5% Similarity=0.047 Sum_probs=36.2
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEE
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQ 49 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~ 49 (349)
|=.+|+.++. .+..+||..++.+...|-.-+.-|.++|-|.-.
T Consensus 7 lRd~l~~~gr-~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv 49 (78)
T PRK15431 7 VRDLLALRGR-MEAAQISQTLNTPQPMINAMLQQLESMGKAVRI 49 (78)
T ss_pred HHHHHHHcCc-ccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEee
Confidence 3356777776 788899999999999999999999999988643
No 428
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=31.95 E-value=1.3e+02 Score=22.29 Aligned_cols=15 Identities=27% Similarity=0.722 Sum_probs=13.1
Q ss_pred HHHHHHHHhhCCcee
Q 018851 222 RKQLKDIFLQMGFEE 236 (349)
Q Consensus 222 ~~~ir~if~~mGF~e 236 (349)
.+++.++|..|||+.
T Consensus 21 ~~ei~~~L~~lg~~~ 35 (71)
T smart00874 21 AEEIEEILKRLGFEV 35 (71)
T ss_pred HHHHHHHHHHCCCeE
Confidence 468999999999985
No 429
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=30.94 E-value=70 Score=25.19 Aligned_cols=40 Identities=15% Similarity=0.283 Sum_probs=30.7
Q ss_pred HHHHhcCcCCCCCHHHHHhh--cCchhhhhHHHHHhhCCcEee
Q 018851 74 QLFLAVPAEGSISKDELQKK--LDPAVFKIGCSQAGKNKWVEM 114 (349)
Q Consensus 74 rl~~~l~~~g~~~~~el~~~--~~~~~~~ig~g~~~k~~wi~i 114 (349)
+++..+..+ .++++||.+. +..+...+-+.++.+.|+|.-
T Consensus 9 ~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~R 50 (72)
T PF05584_consen 9 KILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIER 50 (72)
T ss_pred HHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeee
Confidence 445555544 5899999887 456788899999999998854
No 430
>COG3046 Uncharacterized protein related to deoxyribodipyrimidine photolyase [General function prediction only]
Probab=30.88 E-value=61 Score=33.78 Aligned_cols=63 Identities=29% Similarity=0.436 Sum_probs=41.7
Q ss_pred ceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHHhhcCC---CCC-CCcccccchhhhhc
Q 018851 242 FVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRVHESGG---YGS-RGYGYEWKREEANK 312 (349)
Q Consensus 242 ~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~vHe~Gg---~gS-~Gw~Y~W~~~~a~~ 312 (349)
-=+-.-||||+=|.-.-.|.- ..|.....+|.+++..|++-=|.+. +|+ .|++|+=...+|.+
T Consensus 166 qP~GGrWnFDaeNR~~~~pdL--------~~P~pl~fppd~~vq~v~e~Ve~~f~~~~G~~e~F~wpvtr~~A~~ 232 (505)
T COG3046 166 QPEGGRWNFDAENRKKLPPDL--------LPPKPLKFPPDEIVQEVKERVERLFPDNFGQVEGFGWPVTRTQALR 232 (505)
T ss_pred CCCCCcCCcCcccccCCCCcC--------CCCCCCCCCCcchhHHHHHHHHhhCCCCCCccccCCCCCCHHHHHH
Confidence 444678999998875554532 2366555667788888888877763 666 46666655555544
No 431
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.72 E-value=84 Score=27.66 Aligned_cols=43 Identities=14% Similarity=0.255 Sum_probs=34.9
Q ss_pred hHHHHHHhcCcCCCCCHHHHHhhcCchhhhh--HHHHHhhCCcEe
Q 018851 71 PEVQLFLAVPAEGSISKDELQKKLDPAVFKI--GCSQAGKNKWVE 113 (349)
Q Consensus 71 PE~rl~~~l~~~g~~~~~el~~~~~~~~~~i--g~g~~~k~~wi~ 113 (349)
-..+|+++|..++.++..+|.+.+|-+...+ =+..+.+.|.|+
T Consensus 15 ~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 15 IDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeE
Confidence 3789999999988899999999987554444 358889999986
No 432
>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=30.60 E-value=1.8e+02 Score=26.95 Aligned_cols=83 Identities=11% Similarity=0.086 Sum_probs=53.5
Q ss_pred CCHHHHHHHHHHhccCCc-EEEEeee-eE-EEEeChhHHHHhhcCChHHHHHHhc--CcCCCCCHHHHHhhcC--chhhh
Q 018851 28 FDHNDVVNVIKSLHGFRY-IDAQDIK-RE-TWVLTGEGKKYAAEGSPEVQLFLAV--PAEGSISKDELQKKLD--PAVFK 100 (349)
Q Consensus 28 ~~~~~v~~~~~~L~~kgl-i~~~~~~-~~-~~~LTeEG~~~l~~G~PE~rl~~~l--~~~g~~~~~el~~~~~--~~~~~ 100 (349)
+++++|.+|++.|+..|. +.+.... .. .+...+.... ..=-.+++..+ ...|.++..+|...++ ...+.
T Consensus 133 ISp~Di~~A~~~l~~lg~g~~l~~~~sg~~vv~s~~~~e~----~~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~ 208 (223)
T PF04157_consen 133 ISPEDILRACKLLEVLGLGFRLRKFGSGVKVVQSVPYSEL----SKDQSRILELAEEENGGGVTASELAEKLGWSVERAK 208 (223)
T ss_dssp --HHHHHHHHHHHCCCTSSEEEEEETTTEEEEECST-CHH-----HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHH
T ss_pred cCHHHHHHHHHHHHHcCCCeEEEEeCCCcEEEEeCCchhh----hHHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHH
Confidence 699999999999999875 5555443 33 3344332321 01124778888 5566789999998754 44666
Q ss_pred hHHHHHhhCCcEee
Q 018851 101 IGCSQAGKNKWVEM 114 (349)
Q Consensus 101 ig~g~~~k~~wi~i 114 (349)
-.|-.|.+.|++=+
T Consensus 209 ~~L~~~~~~G~l~~ 222 (223)
T PF04157_consen 209 EALEELEREGLLWR 222 (223)
T ss_dssp HHHHHHHHTTSEEE
T ss_pred HHHHHHHhCCCEee
Confidence 77788888887644
No 433
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=30.52 E-value=95 Score=30.19 Aligned_cols=45 Identities=13% Similarity=0.150 Sum_probs=37.4
Q ss_pred CChHHHHHHhC--CCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHH
Q 018851 17 SDSGNFAAERG--FDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGK 63 (349)
Q Consensus 17 ~~~~~la~~~g--~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~ 63 (349)
.+.+++|+.++ ++..+|..++.-|..-|+|+-.. ...|..|+..-
T Consensus 138 ~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~--~g~y~~t~~~l 184 (271)
T TIGR02147 138 DDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE--DGFYKQTDKAV 184 (271)
T ss_pred CCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC--CCcEEeeccee
Confidence 37888999998 89999999999999999998543 45788887643
No 434
>PRK03991 threonyl-tRNA synthetase; Validated
Probab=30.44 E-value=68 Score=34.77 Aligned_cols=25 Identities=8% Similarity=0.147 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHhhCCceecCCCCce
Q 018851 218 LLKVRKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 218 l~~~~~~ir~if~~mGF~e~~~~~~V 243 (349)
...+.+.+++.+.+.||+++.+ |.+
T Consensus 230 ~~~L~~~~~~~~~~~G~~~V~t-P~~ 254 (613)
T PRK03991 230 RDLLEDYVYNLVVELGAMPVET-PIM 254 (613)
T ss_pred HHHHHHHHHHHHHHCCCEEEEC-Cee
Confidence 5667788889999999999974 554
No 435
>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=30.26 E-value=73 Score=24.51 Aligned_cols=43 Identities=21% Similarity=0.302 Sum_probs=29.7
Q ss_pred HHHHHHHHhhCC---CCCChHHHHHHhCCCHHHHHHHHHHhccCCc
Q 018851 3 EEAILGYLEKNE---QISDSGNFAAERGFDHNDVVNVIKSLHGFRY 45 (349)
Q Consensus 3 e~~iL~~L~~~~---~~~~~~~la~~~g~~~~~v~~~~~~L~~kgl 45 (349)
|++|...+-++. .-.+..++|+.+|+++..|++-++.|==.|+
T Consensus 18 e~~Ia~yil~~~~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf 63 (77)
T PF01418_consen 18 EKKIADYILENPDEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGF 63 (77)
T ss_dssp HHHHHHHHHH-HHHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCH
T ss_pred HHHHHHHHHhCHHHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCH
Confidence 556666655422 1246789999999999999999999876665
No 436
>PLN03238 probable histone acetyltransferase MYST; Provisional
Probab=29.93 E-value=85 Score=30.98 Aligned_cols=54 Identities=15% Similarity=0.181 Sum_probs=37.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
..||..|.+.....+.++++..+|+..++|+.++..| |+++.... ...+.++.+
T Consensus 211 ~~il~~L~~~~~~isi~~is~~T~i~~~Dii~tL~~l---~~l~~~~g-~~~i~~~~~ 264 (290)
T PLN03238 211 RVLLEQLRDVKGDVSIKDLSLATGIRGEDIVSTLQSL---NLIKYWKG-QHVIHVDQR 264 (290)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC---CcEEEECC-cEEEEeCHH
Confidence 3578888765545788999999999999998887654 66655333 334555544
No 437
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=29.20 E-value=34 Score=33.60 Aligned_cols=47 Identities=17% Similarity=0.226 Sum_probs=35.7
Q ss_pred HHHHHHHHHhhCC-CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 2 AEEAILGYLEKNE-QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 2 ~e~~iL~~L~~~~-~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
-|+.++..++..+ +..-+-++-.+.++++..|.+.+++|++|.||+.
T Consensus 85 eEk~vy~lIe~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKs 132 (297)
T KOG3233|consen 85 EEKLVYSLIEESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKS 132 (297)
T ss_pred HHHHHHHHHHHcCCCceeeehhhhccCCCHHHHHHHHHHHHHHHHHHH
Confidence 4667777776533 2233457777889999999999999999999964
No 438
>PF13551 HTH_29: Winged helix-turn helix
Probab=28.71 E-value=1.1e+02 Score=24.08 Aligned_cols=41 Identities=20% Similarity=0.124 Sum_probs=31.8
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEE
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYID 47 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~ 47 (349)
.+|.++.... .+..++|..+|++...|.+.++..++.|+-.
T Consensus 3 ~~l~l~~~g~--~~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~ 43 (112)
T PF13551_consen 3 QILLLLAEGV--STIAEIARRLGISRRTVYRWLKRYREGGIEG 43 (112)
T ss_pred HHHHHHHcCC--CcHHHHHHHHCcCHHHHHHHHHHHHcccHHH
Confidence 4555554332 2478999999999999999999999998433
No 439
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=28.51 E-value=1.4e+02 Score=29.63 Aligned_cols=71 Identities=18% Similarity=0.092 Sum_probs=53.2
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHh---C--CCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAER---G--FDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQL 75 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~---g--~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl 75 (349)
+-.||+.|++.+.+..+-.+|.++ | +..-+|.=-++.|+.+|++.-.. ----++||-|.+-++.++-=+|+
T Consensus 8 ~ieIl~il~esd~plgak~Ia~el~kRGy~igeRavRYhlk~lderglt~kvg--yagr~iTe~Gl~el~~~~~~~R~ 83 (325)
T COG1693 8 LIEILRILAESDEPLGAKIIALELRKRGYNIGERAVRYHLKKLDERGLTRKVG--YAGREITEKGLKELKRALISERL 83 (325)
T ss_pred HHHHHHHHHhcCCccchHHHHHHHHhcccchhHHHHHHHHHHHhhccchhhcc--ccceeehHhhHHHHhhhhhHHHH
Confidence 456899999888767777777654 4 44556777899999999985433 22447999999999888776664
No 440
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=28.41 E-value=1.4e+02 Score=22.85 Aligned_cols=52 Identities=10% Similarity=0.117 Sum_probs=34.3
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEe
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVL 58 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~L 58 (349)
++..+...+. .++..|-..+++.+....+.+..|+..|+|.-......+-+|
T Consensus 11 a~~~V~~~~~-~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~~~R~Vl 62 (65)
T PF09397_consen 11 AVEFVIEEGK-ASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGSKPREVL 62 (65)
T ss_dssp HHHHHHHCTC-ECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TTSEEEB-
T ss_pred HHHHHHHcCC-ccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCCCCeec
Confidence 3444445555 567778888999999999999999999999876554443333
No 441
>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=28.17 E-value=1.4e+02 Score=21.92 Aligned_cols=41 Identities=15% Similarity=0.126 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhCC-----CCCChHHHHHHhCCCHHHHHHHHHHhcc
Q 018851 2 AEEAILGYLEKNE-----QISDSGNFAAERGFDHNDVVNVIKSLHG 42 (349)
Q Consensus 2 ~e~~iL~~L~~~~-----~~~~~~~la~~~g~~~~~v~~~~~~L~~ 42 (349)
-|.++|..--..| .-.+..+||+.+|++.+.+..-+..-+.
T Consensus 4 ~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 4 RQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3566665544432 2256789999999999998777665443
No 442
>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=28.04 E-value=1.3e+02 Score=21.86 Aligned_cols=65 Identities=11% Similarity=0.149 Sum_probs=38.3
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhh
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKK 93 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~ 93 (349)
+..++|+.+|++++.+....+. .|++...........-|++= .-+.+.+..+...| ++++++.+.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~---~g~~~~~r~~~~~r~yt~~~-------v~~l~~i~~l~~~g-~~l~~i~~~ 66 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR---YGLPAPQRTDGGHRLYSEAD-------VARLRLIRRLTSEG-VRISQAAAL 66 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh---CCCCCCCcCCCCCeecCHHH-------HHHHHHHHHHHHCC-CCHHHHHHH
Confidence 4568999999999999876542 35554322222222223321 23445566666555 999998764
No 443
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.95 E-value=2.1e+02 Score=25.83 Aligned_cols=70 Identities=19% Similarity=0.208 Sum_probs=50.2
Q ss_pred HHHHHhCCCHHHHHHHHHHhccCCcEEEEee------------------eeEEEEeChhHHHHhhcCChHH--HHH-Hhc
Q 018851 21 NFAAERGFDHNDVVNVIKSLHGFRYIDAQDI------------------KRETWVLTGEGKKYAAEGSPEV--QLF-LAV 79 (349)
Q Consensus 21 ~la~~~g~~~~~v~~~~~~L~~kgli~~~~~------------------~~~~~~LTeEG~~~l~~G~PE~--rl~-~~l 79 (349)
.++.-+.++.-.|..+++-|..-|||+.-.. -.+.|.||-||+..+++=.||- .+| ..+
T Consensus 36 ~i~r~tkiPl~~i~e~l~dL~elGLier~tgttiKrteAKfKksaEVHKHHTYYrl~rege~~lr~i~~~~l~~~y~~~l 115 (175)
T COG4344 36 NITRYTKIPLPRIREYLKDLKELGLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNREGEAVLREITPEWLGKLYVRLL 115 (175)
T ss_pred HHHHHccCChHHHHHHHHHHHHcCCeeeccCchhhhhHHHHHHhHHHHhchhhheechhHHHHHHhcCHHHHHHHHHHHc
Confidence 3445578899999999999999999976332 1357999999999999988864 223 444
Q ss_pred CcCCCCCHHHHH
Q 018851 80 PAEGSISKDELQ 91 (349)
Q Consensus 80 ~~~g~~~~~el~ 91 (349)
+ ++-..+..++
T Consensus 116 ~-n~~l~l~ilr 126 (175)
T COG4344 116 K-NGWLVLLILR 126 (175)
T ss_pred C-cchHHHHHHH
Confidence 4 3335555544
No 444
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=27.73 E-value=2e+02 Score=23.21 Aligned_cols=52 Identities=21% Similarity=0.149 Sum_probs=38.3
Q ss_pred HHHHHHHHHhhCCC--CCChHHHHHHhCCC-----HHHHHHHHHHhccCCcEEEEeeee
Q 018851 2 AEEAILGYLEKNEQ--ISDSGNFAAERGFD-----HNDVVNVIKSLHGFRYIDAQDIKR 53 (349)
Q Consensus 2 ~e~~iL~~L~~~~~--~~~~~~la~~~g~~-----~~~v~~~~~~L~~kgli~~~~~~~ 53 (349)
+|..||.+|...+. -..+.|+|..++-+ ...|..++..|...|-|.+.++-+
T Consensus 8 l~~~Il~ll~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~~G~i~I~qkG~ 66 (83)
T PF11625_consen 8 LEAAILALLAARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLARAGRIEITQKGK 66 (83)
T ss_dssp HHHHHHHHHHHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHHTTSEEEEETTE
T ss_pred HHHHHHHHHHhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHHHCCcEEEEECCE
Confidence 67889999987653 23457889887654 367889999999999999887644
No 445
>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=27.66 E-value=1.4e+02 Score=19.50 Aligned_cols=37 Identities=11% Similarity=0.032 Sum_probs=26.1
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLH 41 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~ 41 (349)
+..++..+...+ .+..++|+.+|++...|.+.+....
T Consensus 15 ~~~~~~~~~~~~--~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 15 EREVILLRFGEG--LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred HHHHHHHHHhcC--CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345555544344 4678999999999999988776543
No 446
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=27.53 E-value=2.9e+02 Score=29.93 Aligned_cols=102 Identities=9% Similarity=0.005 Sum_probs=64.2
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcE-EEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYI-DAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPAE 82 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli-~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~ 82 (349)
.+|+..+.. .+....+++..+|++...+..++..|...|.+ .+. . .+.++.+--.-+ -..+...+..+
T Consensus 496 ~~l~~~~~~--~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~---~-~~~~~~~~~~~~-----~~~~~~~~~~~ 564 (614)
T PRK10512 496 QKAEPLFGD--EPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIV---K-DRYYRNDRIVQF-----ANMIRELDQEC 564 (614)
T ss_pred HHHHHHHhc--CCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec---C-CEEECHHHHHHH-----HHHHHHHHhhC
Confidence 445555542 23567889999999999999999999998854 333 3 334444433322 13455666666
Q ss_pred CCCCHHHHHhhcCchhhhhHH---HHHhhCCcEeeCce
Q 018851 83 GSISKDELQKKLDPAVFKIGC---SQAGKNKWVEMGKQ 117 (349)
Q Consensus 83 g~~~~~el~~~~~~~~~~ig~---g~~~k~~wi~i~~~ 117 (349)
|.+++.+++..+|-+ =+.++ -.+=+.|+.+..++
T Consensus 565 ~~~~~~~~r~~~g~s-RK~~i~lLE~~D~~~~T~r~g~ 601 (614)
T PRK10512 565 GSTCAADFRDRLGVG-RKLAIQILEYFDRIGFTRRRGN 601 (614)
T ss_pred CcEeHHHHHHHhCcc-HHHHHHHHHHhccCCCEEEECC
Confidence 779999999887644 23333 34445566555444
No 447
>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=27.22 E-value=1.2e+02 Score=24.06 Aligned_cols=66 Identities=11% Similarity=0.051 Sum_probs=43.0
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhhc
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKL 94 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~~ 94 (349)
.+..++|+.+|+++..+... +.+|++....... -.-.-|++=-. ..+.+..|...| ++++++.+.+
T Consensus 2 ~ti~evA~~~gvs~~tLR~y----e~~Gll~p~r~~~~g~R~Ys~~dv~-------~l~~I~~Lr~~G-~sl~~i~~~l 68 (88)
T cd01105 2 IGIGEVSKLTGVSPRQLRYW----EEKGLIKSIRSDGGGQRKYSLADVD-------RLLVIKELLDEG-FTLAAAVEKL 68 (88)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCceecCHHHHH-------HHHHHHHHHHCC-CCHHHHHHHH
Confidence 45678999999999887544 7789987644433 22233333322 345566666655 9999988765
No 448
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=27.07 E-value=1.3e+02 Score=27.28 Aligned_cols=43 Identities=9% Similarity=0.112 Sum_probs=31.5
Q ss_pred hHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHH
Q 018851 19 SGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKK 64 (349)
Q Consensus 19 ~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~ 64 (349)
-.++|..+|+..+.|.++++.|+.+|+ .... .....+-.+|.+
T Consensus 176 ~~~iA~~lG~tretvsR~l~~L~~~gl-~~~~--~~i~I~d~~~L~ 218 (236)
T PRK09392 176 KRVLASYLGMTPENLSRAFAALASHGV-HVDG--SAVTITDPAGLA 218 (236)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHhCCe-EeeC--CEEEEcCHHHHH
Confidence 368999999999999999999999996 4432 233334445543
No 449
>COG2852 Very-short-patch-repair endonuclease [Replication, recombination, and repair]
Probab=26.88 E-value=56 Score=28.47 Aligned_cols=33 Identities=33% Similarity=0.573 Sum_probs=26.4
Q ss_pred CCCChHHHHHHHHHHHHh-hCCceecCCCCceeeeehhhhcc
Q 018851 213 GHLHPLLKVRKQLKDIFL-QMGFEEMPTNNFVESSFWNFDAL 253 (349)
Q Consensus 213 g~~HPl~~~~~~ir~if~-~mGF~e~~~~~~Ves~fwNFDaL 253 (349)
|.-|+...--+--|+.|+ +.||+.+. |||=+.+
T Consensus 73 G~qH~~~~~~Da~Rd~~L~~~G~~VLR--------f~N~ev~ 106 (129)
T COG2852 73 GGQHEEREEYDAERDAFLESQGFTVLR--------FWNDEVL 106 (129)
T ss_pred CccchhhhhhhHHHHHHHHhCCceEEE--------eccHHHH
Confidence 778999999999998554 56999885 8987665
No 450
>PF03484 B5: tRNA synthetase B5 domain; InterPro: IPR005147 Domain B5 is found in phenylalanine-tRNA synthetase beta subunits. This domain has been shown to bind DNA through a winged helix-turn-helix motif []. Phenylalanine-tRNA synthetase may influence common cellular processes via DNA binding, in addition to its aminoacylation function.; GO: 0000287 magnesium ion binding, 0003723 RNA binding, 0005524 ATP binding, 0006432 phenylalanyl-tRNA aminoacylation; PDB: 2AKW_B 1B70_B 1B7Y_B 2ALY_B 2IY5_B 2AMC_B 3PCO_D 2CXI_C 1JJC_B 1EIY_B ....
Probab=26.64 E-value=1e+02 Score=23.28 Aligned_cols=47 Identities=23% Similarity=0.376 Sum_probs=29.5
Q ss_pred HHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCC--CCHHHHHHHHHHh
Q 018851 221 VRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRE--LPEDYVERVKRVH 291 (349)
Q Consensus 221 ~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~--~p~~~~erVk~vH 291 (349)
-.+++.++|..|||+.-.. -.|++-+.-|..-.| -+.|++|.|..+|
T Consensus 20 ~~~~i~~~L~~lg~~~~~~------------------------~~~~~~v~vP~~R~Di~~~~DliEEiaR~y 68 (70)
T PF03484_consen 20 SPEEIIKILKRLGFKVEKI------------------------DGDTLEVTVPSYRFDIEHEEDLIEEIARIY 68 (70)
T ss_dssp -HHHHHHHHHHTT-EEEE-------------------------CTTEEEEEEETTSTT-SSHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHCCCEEEEC------------------------CCCEEEEEcCCCcCCcCcccHHHHHHHHHh
Confidence 4578999999999996531 233444444433333 3578999998886
No 451
>COG1437 CyaB Adenylate cyclase, class 2 (thermophilic) [Nucleotide transport and metabolism]
Probab=26.47 E-value=54 Score=30.11 Aligned_cols=36 Identities=22% Similarity=0.447 Sum_probs=27.4
Q ss_pred HHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCe
Q 018851 222 RKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDT 267 (349)
Q Consensus 222 ~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DT 267 (349)
.+.++..+.+.||..+.. ..=+..|+ +||.||+.||
T Consensus 13 ~e~i~~~l~~~~~~~~~~-e~q~DiYf---------~~p~rdf~~t 48 (178)
T COG1437 13 LEEIRERLASLGAKFIKE-EEQEDIYF---------DHPCRDFADT 48 (178)
T ss_pred HHHHHHHHHhccccccce-eeeeeeee---------ecCCcchhcC
Confidence 478899999999998753 34445566 8999988876
No 452
>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=26.45 E-value=69 Score=24.07 Aligned_cols=55 Identities=13% Similarity=0.215 Sum_probs=34.9
Q ss_pred HHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 221 VRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 221 ~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
+...+-.+|..+|..... -.|.+. +.--.-|+||+.++......+++..+++++.
T Consensus 14 Ll~~i~~~l~~~~l~I~~--A~i~T~-------------~~~~v~D~F~v~~~~~~~~~~~~~~~~l~~~ 68 (73)
T cd04900 14 LFARIAGALDQLGLNILD--ARIFTT-------------RDGYALDTFVVLDPDGEPIGERERLARIREA 68 (73)
T ss_pred HHHHHHHHHHHCCCCeEE--eEEEEe-------------CCCeEEEEEEEECCCCCCCChHHHHHHHHHH
Confidence 456778899999999874 344222 1123679999987654433356666666553
No 453
>KOG2224 consensus Uncharacterized conserved protein, contains TBC domain [Signal transduction mechanisms; General function prediction only]
Probab=26.40 E-value=42 Score=35.10 Aligned_cols=61 Identities=28% Similarity=0.491 Sum_probs=35.7
Q ss_pred Ccccccccc-ccc--ccCCCCCCCCCCChHHHHHHHHHHHHh----hCCce------------ecCCCCceeeeehhhhc
Q 018851 192 DWKELEFKE-YNF--NAKGQPAEGGHLHPLLKVRKQLKDIFL----QMGFE------------EMPTNNFVESSFWNFDA 252 (349)
Q Consensus 192 ~Wk~~~fk~-yn~--~~~~~~~~~g~~HPl~~~~~~ir~if~----~mGF~------------e~~~~~~Ves~fwNFDa 252 (349)
=||++.|-- -|| +--..+..+|--+|=++.+..|-=-|. .|||. |+. ++- ..||||-.
T Consensus 491 fwknvq~tvdkdvvrtdrnn~ff~gddnpn~e~mk~illn~avyn~~m~ysqgmsdllapvlcevq--nes-etfwcfvg 567 (781)
T KOG2224|consen 491 FWKNVQFTVDKDVVRTDRNNPFFCGDDNPNTESMKNILLNFAVYNPAMGYSQGMSDLLAPVLCEVQ--NES-ETFWCFVG 567 (781)
T ss_pred HHhheEEEEecceeeccCCCCcccCCCCCcHHHHHHHHHhheeecccccccccchhhcchhhhhhc--ccc-chhhhhhh
Confidence 499998731 222 223345678999998877654432221 36776 232 222 35888888
Q ss_pred cCC
Q 018851 253 LFQ 255 (349)
Q Consensus 253 Lf~ 255 (349)
|.|
T Consensus 568 lmq 570 (781)
T KOG2224|consen 568 LMQ 570 (781)
T ss_pred hhc
Confidence 876
No 454
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=26.28 E-value=74 Score=32.86 Aligned_cols=40 Identities=15% Similarity=0.300 Sum_probs=35.0
Q ss_pred CCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 13 NEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 13 ~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
...+-+.-++|..+|++.+.|.++...|++.|+|......
T Consensus 25 g~rLPs~R~la~~l~vs~~Tv~~ay~~L~~~G~i~~~~gs 64 (459)
T COG1167 25 GDRLPSIRQLAQDLGVSRSTVSRAYEELEARGYIESRPGS 64 (459)
T ss_pred CCcCCcHHHHHHHhCCcHHHHHHHHHHHHhCcceeeccCC
Confidence 3445667899999999999999999999999999988764
No 455
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=26.11 E-value=79 Score=31.21 Aligned_cols=36 Identities=11% Similarity=0.050 Sum_probs=32.7
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeee
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIK 52 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~ 52 (349)
.+-.++|+++|++...|.+.++.-...|+|+++-..
T Consensus 30 ~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~ 65 (318)
T PRK15418 30 LTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINS 65 (318)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeC
Confidence 356799999999999999999999999999998754
No 456
>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=26.08 E-value=3.7e+02 Score=24.35 Aligned_cols=90 Identities=16% Similarity=0.051 Sum_probs=54.3
Q ss_pred CCCHHHHHHHHHHhccCC-cEEEEeeeeEEEEeChhHHHHhhcCC--hHHHHHHhcCcCCCCCHHHHHhhcC--chhhhh
Q 018851 27 GFDHNDVVNVIKSLHGFR-YIDAQDIKRETWVLTGEGKKYAAEGS--PEVQLFLAVPAEGSISKDELQKKLD--PAVFKI 101 (349)
Q Consensus 27 g~~~~~v~~~~~~L~~kg-li~~~~~~~~~~~LTeEG~~~l~~G~--PE~rl~~~l~~~g~~~~~el~~~~~--~~~~~i 101 (349)
|+..-.+...+..+..+. ...+.........+..+-..+...++ ++.+++..|...|++++.++.+.++ ++...-
T Consensus 97 G~R~l~~~~~~a~~~~~~~~~~v~~~~e~~~~~~~~~~~~~~~~ls~~~~~IL~~l~~~g~~s~~eia~~l~is~stv~r 176 (203)
T TIGR01884 97 GMRILILILLLLAILVKTRVFRVYYESEELIDFILLDLVPLLAGLSREELKVLEVLKAEGEKSVKNIAKKLGKSLSTISR 176 (203)
T ss_pred CchHHHHHHHHHHHhcccceEEEEEEeccccchhhhhhhhhhcCCCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHH
Confidence 555555544444444433 33343332223344444444444443 3668888887656789999998865 344555
Q ss_pred HHHHHhhCCcEeeCc
Q 018851 102 GCSQAGKNKWVEMGK 116 (349)
Q Consensus 102 g~g~~~k~~wi~i~~ 116 (349)
-+..+.++|||...+
T Consensus 177 ~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 177 HLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHHCCCEEEEc
Confidence 678889999998765
No 457
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=26.06 E-value=93 Score=30.63 Aligned_cols=57 Identities=16% Similarity=0.085 Sum_probs=44.0
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-eeEEEEeChhH
Q 018851 5 AILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-KRETWVLTGEG 62 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-~~~~~~LTeEG 62 (349)
.|+..|...+. .+..++|+.+|++..+|.+.+..|++-|+=-.-+. ....|.+-+-+
T Consensus 12 ~ii~~L~~~~~-vta~~lA~~~~VS~RTi~RDi~~L~~~gvPI~~e~G~~~gy~~~~~~ 69 (311)
T COG2378 12 QIIQILRAKET-VTAAELADEFEVSVRTIYRDIATLRAAGVPIEGERGKGGGYRLRPGF 69 (311)
T ss_pred HHHHHHHhCcc-chHHHHHHhcCCCHHHHHHHHHHHHHCCCCeEeecCCCccEEEccCC
Confidence 46777777777 78899999999999999999999999998633333 34456665555
No 458
>PRK00960 seryl-tRNA synthetase; Provisional
Probab=25.99 E-value=69 Score=34.07 Aligned_cols=47 Identities=9% Similarity=0.188 Sum_probs=27.0
Q ss_pred HHHHHHHHH-HhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecC
Q 018851 220 KVRKQLKDI-FLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEE 272 (349)
Q Consensus 220 ~~~~~ir~i-f~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~ 272 (349)
.+.+.+++. +...||++|.+ |.+.. -+.+..= .|=..-.++.|++..
T Consensus 228 aL~~~i~d~~~~k~Gyeev~~-P~Li~----~ell~ks-Ghl~~F~e~my~V~~ 275 (517)
T PRK00960 228 AFEKLVIEEVLKPLGFDECLF-PKLIP----LEVMYKM-RYLEGLPEGMYYVCP 275 (517)
T ss_pred HHHHHHHHhhHhhcCCeEEEC-CcccC----HHHHhhc-CCccCChhhceEeec
Confidence 333444443 44569999974 55532 2333222 666666778888864
No 459
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=25.97 E-value=1.4e+02 Score=20.11 Aligned_cols=37 Identities=16% Similarity=0.256 Sum_probs=27.2
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhcc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHG 42 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~ 42 (349)
|..|+..+. .+ .+..++|+.+|++...|...+..+..
T Consensus 8 e~~i~~~~~-~g--~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 8 EREVLRLLA-EG--LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred HHHHHHHHH-cC--CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 556666553 44 36789999999999998888776543
No 460
>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=25.96 E-value=1.4e+02 Score=24.95 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=26.3
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhc
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLH 41 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~ 41 (349)
+...+.+... ....|+|+.+|++++.|..+++.|-
T Consensus 62 L~~~v~~~pd-~tl~Ela~~l~Vs~~ti~~~Lkrlg 96 (119)
T PF01710_consen 62 LKALVEENPD-ATLRELAERLGVSPSTIWRALKRLG 96 (119)
T ss_pred HHHHHHHCCC-cCHHHHHHHcCCCHHHHHHHHHHcC
Confidence 3444455544 5678999999999999999988764
No 461
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=25.96 E-value=1e+02 Score=22.02 Aligned_cols=41 Identities=15% Similarity=0.062 Sum_probs=27.9
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhcc
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHG 42 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~ 42 (349)
.+.+++-.|..-..-.+-+.+|...|++.+.+.+.+.++..
T Consensus 5 ~~d~lll~L~~LR~~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 5 LEDQLLLTLMYLRLNLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred HHHHHHHHHHHHHcCCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 45555554443222135678999999999999999887653
No 462
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=25.43 E-value=92 Score=26.41 Aligned_cols=43 Identities=9% Similarity=0.174 Sum_probs=32.9
Q ss_pred HHHHHHhcCcCCCCCHHHHHhhcCchhhhh--HHHHHhhCCcEee
Q 018851 72 EVQLFLAVPAEGSISKDELQKKLDPAVFKI--GCSQAGKNKWVEM 114 (349)
Q Consensus 72 E~rl~~~l~~~g~~~~~el~~~~~~~~~~i--g~g~~~k~~wi~i 114 (349)
+.++++.|..++.+++.+|.+.+|-+...+ =+..+.+.|.|+.
T Consensus 10 D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 10 DRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceee
Confidence 678999999888899999999877554333 3467788887754
No 463
>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=24.96 E-value=1.2e+02 Score=23.93 Aligned_cols=30 Identities=20% Similarity=0.143 Sum_probs=26.3
Q ss_pred CChHHHHHHhCCCHHHHHHHHHHhccCCcE
Q 018851 17 SDSGNFAAERGFDHNDVVNVIKSLHGFRYI 46 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~v~~~~~~L~~kgli 46 (349)
.+..++|+.+|++.+.|...+..+...|.+
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcCcccchH
Confidence 477899999999999999999998887643
No 464
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=24.65 E-value=2.2e+02 Score=26.18 Aligned_cols=59 Identities=14% Similarity=0.101 Sum_probs=42.7
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEee-----eeEEEEeChhHHHHh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDI-----KRETWVLTGEGKKYA 66 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~-----~~~~~~LTeEG~~~l 66 (349)
.++|..++-+.. .+..++++..|++. .+.++.|..+|||...-+ ....|.+|+.=..++
T Consensus 93 LEtLaiIay~qP-iTr~eI~~irGv~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~tT~~F~~~f 156 (188)
T PRK00135 93 LEVLAIIAYKQP-ITRIEIDEIRGVNS---DGALQTLLAKGLIKEVGRKEVPGRPILYGTTDEFLDYF 156 (188)
T ss_pred HHHHHHHHHcCC-cCHHHHHHHHCCCH---HHHHHHHHHCCCeEEcCcCCCCCCCeeeehhHHHHHHc
Confidence 457777776665 67789999999997 577899999999976321 245677787655544
No 465
>PHA02591 hypothetical protein; Provisional
Probab=24.64 E-value=1.7e+02 Score=23.52 Aligned_cols=32 Identities=16% Similarity=0.136 Sum_probs=24.9
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHH
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKS 39 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~ 39 (349)
+-..|.+.| .+.+++|..+|++...|...+.+
T Consensus 51 vA~eL~eqG--lSqeqIA~~LGVsqetVrKYL~~ 82 (83)
T PHA02591 51 VTHELARKG--FTVEKIASLLGVSVRKVRRYLES 82 (83)
T ss_pred HHHHHHHcC--CCHHHHHHHhCCCHHHHHHHHhc
Confidence 344555566 47889999999999999988765
No 466
>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=24.50 E-value=2.2e+02 Score=19.66 Aligned_cols=34 Identities=15% Similarity=0.185 Sum_probs=24.6
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIK 38 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~ 38 (349)
|..||...--.+ .+..++|..+|++.+.|.+...
T Consensus 9 er~vi~~~y~~~--~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 9 EREVIRLRYFEG--LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp HHHHHHHHHTST---SHHHHHHHHTSCHHHHHHHHH
T ss_pred HHHHHHHHhcCC--CCHHHHHHHHCCcHHHHHHHHH
Confidence 566776665444 4688999999999998866543
No 467
>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=24.38 E-value=1.3e+02 Score=24.14 Aligned_cols=35 Identities=0% Similarity=-0.053 Sum_probs=27.9
Q ss_pred CCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeCce
Q 018851 83 GSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMGKQ 117 (349)
Q Consensus 83 g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~~~ 117 (349)
.+++..||.+.+| +...+=++..+.+.|||...+|
T Consensus 46 ~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~ 82 (95)
T TIGR01610 46 DRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM 82 (95)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC
Confidence 4578889988754 4566778999999999998874
No 468
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=24.22 E-value=1.3e+02 Score=29.30 Aligned_cols=63 Identities=11% Similarity=0.053 Sum_probs=46.6
Q ss_pred HHHHHHHHh----hCCCCCChHHHHHHh--CCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHh
Q 018851 3 EEAILGYLE----KNEQISDSGNFAAER--GFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYA 66 (349)
Q Consensus 3 e~~iL~~L~----~~~~~~~~~~la~~~--g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l 66 (349)
+..||+++- ..+.+..+..|++.. ++++.+|...+..|+..|++.-. ....=-..|+.|-+|-
T Consensus 5 ~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~qp-HtSsGRIPT~~gyr~Y 73 (260)
T PRK03911 5 KDLLLDSIIQTYLQDNEPIGSNELKSLMNLKISAATIRNYFKKLSDEGLLTQL-HISGGRIPTIKAMKNY 73 (260)
T ss_pred HHHHHHHHHHHHhccCCccCHHHHHHHcCCCCCcHHHHHHHHHHHHCcCccCC-cCCCCcCCCHHHHHHH
Confidence 455666554 356667888999875 57889999999999999998643 3333457899998754
No 469
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=24.15 E-value=1.4e+02 Score=28.40 Aligned_cols=45 Identities=11% Similarity=0.105 Sum_probs=36.1
Q ss_pred HHHHHHHh---hCCCCCChHHHHHHhCCCHHHHHHHHHHhccC-CcEEE
Q 018851 4 EAILGYLE---KNEQISDSGNFAAERGFDHNDVVNVIKSLHGF-RYIDA 48 (349)
Q Consensus 4 ~~iL~~L~---~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~ 48 (349)
.+|+..+. +++.+.+..++|-.+|++...|...++.++.+ |++-=
T Consensus 90 ~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvP 138 (220)
T PF07900_consen 90 HRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVP 138 (220)
T ss_pred HHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceec
Confidence 34555554 36777888999999999999999999999998 76643
No 470
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=23.93 E-value=3.1e+02 Score=23.24 Aligned_cols=52 Identities=15% Similarity=0.296 Sum_probs=36.8
Q ss_pred eChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeC
Q 018851 58 LTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 58 LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~ 115 (349)
||+--++|++ .|+..+..+|..++++|...+ .++...-.+..+.++|||...
T Consensus 2 ~t~~~edyL~------~I~~l~~~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 2 PTPSMEDYIE------QIYLLIEEKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred CChhHHHHHH------HHHHHHhcCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 3444455652 356666666778999999875 455677788999999999753
No 471
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=23.45 E-value=84 Score=24.12 Aligned_cols=54 Identities=11% Similarity=0.189 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhCCceecCCCCceeeeehhhhccCCCCCCCCCCCCCeeeecCCCCCCCCCHHHHHHHHHH
Q 018851 221 VRKQLKDIFLQMGFEEMPTNNFVESSFWNFDALFQPQQHPARDSHDTFFLEEPSTTRELPEDYVERVKRV 290 (349)
Q Consensus 221 ~~~~ir~if~~mGF~e~~~~~~Ves~fwNFDaLf~PqdHPARd~~DTFyl~~p~~~~~~p~~~~erVk~v 290 (349)
+...+-.+|.+.|..... -.|-+. +.--.-||||+.++... ..+++..+++++.
T Consensus 13 Lfa~i~~~l~~~~l~I~~--A~I~Tt-------------~~~~v~D~F~V~d~~~~-~~~~~~~~~l~~~ 66 (76)
T cd04927 13 LLHDVTEVLYELELTIER--VKVSTT-------------PDGRVLDLFFITDAREL-LHTKKRREETYDY 66 (76)
T ss_pred HHHHHHHHHHHCCCeEEE--EEEEEC-------------CCCEEEEEEEEeCCCCC-CCCHHHHHHHHHH
Confidence 455778889999999874 245322 11135799999876433 3455666666554
No 472
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=23.35 E-value=1.7e+02 Score=20.16 Aligned_cols=32 Identities=16% Similarity=0.198 Sum_probs=22.0
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHH
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIK 38 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~ 38 (349)
..|++.+. .+ .+..++|+.+|++...|.+.+.
T Consensus 12 ~~i~~l~~-~G--~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 12 EEIKELYA-EG--MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH-TT----HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHH-CC--CCHHHHHHHHCcCHHHHHHHHh
Confidence 34566554 44 4678999999999999988764
No 473
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=23.01 E-value=1.2e+02 Score=28.17 Aligned_cols=39 Identities=13% Similarity=0.114 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF 43 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k 43 (349)
-|.+||..+..+- +..++|+.+++++..|...+..+-.|
T Consensus 137 RErEVLrLLAqGk---TnKEIAe~L~IS~rTVkth~srImkK 175 (198)
T PRK15201 137 TERHLLKLIASGY---HLSETAALLSLSEEQTKSLRRSIMRK 175 (198)
T ss_pred HHHHHHHHHHCCC---CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4889999987543 57899999999999988777766554
No 474
>PRK07726 DNA topoisomerase III; Provisional
Probab=22.54 E-value=1.6e+02 Score=32.03 Aligned_cols=67 Identities=18% Similarity=0.305 Sum_probs=47.4
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHh----CC-CHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhcCChHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAER----GF-DHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAEGSPEV 73 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~----g~-~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~G~PE~ 73 (349)
|..+|+++.+-+.-.+.+++.+.+ |+ -+..-.+.+..|..+|||... ...+..|+.|+... +.+|+.
T Consensus 483 e~tLi~~Me~~~k~v~d~~~~~~l~e~~GIGTpATra~iIe~L~~R~Yi~~~---~k~l~pT~~G~~li-~~l~~~ 554 (658)
T PRK07726 483 EGTLLSAMENIARFVQDKELKKTLKETDGLGTEATRAGIIEKLFKRGYLEKK---GKYIHATDKGKQLI-DALPEE 554 (658)
T ss_pred HHHHHHHHHhhhhhccCHHHHHhhcccCCCCccccHHHHHHHHHhCCCEEec---CCEEEECHHHHHHH-HHHHHH
Confidence 566788887654434445665554 66 455578899999999999754 34699999999865 567664
No 475
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=22.52 E-value=1.4e+02 Score=25.18 Aligned_cols=34 Identities=12% Similarity=0.127 Sum_probs=30.4
Q ss_pred CCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEE
Q 018851 15 QISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDA 48 (349)
Q Consensus 15 ~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~ 48 (349)
.+.+.+.||+..|++-+-...++.-|+..|+|..
T Consensus 58 r~VTpy~la~r~gI~~SvAr~vLR~LeeeGvv~l 91 (107)
T COG4901 58 RVVTPYVLASRYGINGSVARIVLRHLEEEGVVQL 91 (107)
T ss_pred eeecHHHHHHHhccchHHHHHHHHHHHhCCceee
Confidence 4577899999999999999999999999998864
No 476
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 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 [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=22.46 E-value=87 Score=27.66 Aligned_cols=61 Identities=15% Similarity=0.160 Sum_probs=39.4
Q ss_pred HHHHHHhhCCCCCChHHHHHHhCC--------------CHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERGF--------------DHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g~--------------~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.||..|--.+. .....|....|- +-.-+..++..||+-|+|+..+ ..-=.||++|+..|.+
T Consensus 56 SilRklY~~g~-~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~--~~GR~lT~~G~~~lD~ 130 (139)
T PF01090_consen 56 SILRKLYIRGP-VGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP--KGGRRLTPKGQRDLDR 130 (139)
T ss_dssp HHHHHHHHCTS-B-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEET--TTEEEE-HHHHHHHHH
T ss_pred HHHHHHHHhcC-cchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecC--CCCCEECHHHHHHHHH
Confidence 45666655554 456666655441 2234778899999999999886 3334899999987743
No 477
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=22.35 E-value=6.1e+02 Score=23.24 Aligned_cols=104 Identities=9% Similarity=0.041 Sum_probs=65.8
Q ss_pred hCCCCCChHHHHHHhCC-CHHHHHHHHHHhcc----CCcEEEEeeeeEEEEeChhHHHHhhc----CCh------HHHHH
Q 018851 12 KNEQISDSGNFAAERGF-DHNDVVNVIKSLHG----FRYIDAQDIKRETWVLTGEGKKYAAE----GSP------EVQLF 76 (349)
Q Consensus 12 ~~~~~~~~~~la~~~g~-~~~~v~~~~~~L~~----kgli~~~~~~~~~~~LTeEG~~~l~~----G~P------E~rl~ 76 (349)
..+.+.+..+|++.+|+ +..++..++..|.. .|+.-++....-.+..=++=..|+.. ..+ +-.++
T Consensus 19 a~~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t~~~~~~~~~~l~~~~~~~~LSraalEtL 98 (184)
T COG1386 19 AGGEPLSLKELAEILGIVSADAIIDALAELKEEYEDRGLELVEVAEGWRLQTKQEYAEYLEKLQEQRPKRELSRAALETL 98 (184)
T ss_pred hcCCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEehHHHHHHHHHHhcccccccccHHHHHHH
Confidence 34545889999999998 77878887777755 45544443333334333443344322 221 23334
Q ss_pred HhcCcCCCCCHHHHHhhcCchhhhhHHHHHhhCCcEeeCc
Q 018851 77 LAVPAEGSISKDELQKKLDPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 77 ~~l~~~g~~~~~el~~~~~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
..|.=+.|++..++.+.-|..... .+..+...|||+..+
T Consensus 99 AiIAY~QPiTR~eI~~iRGv~~~~-~i~~L~e~glI~~~g 137 (184)
T COG1386 99 AIIAYKQPVTRSEIEEIRGVAVSQ-VISTLLERGLIREVG 137 (184)
T ss_pred HHHHHcCCccHHHHHHHhCccHHH-HHHHHHHCCCeEecC
Confidence 444324578888888876755555 899999999998865
No 478
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=21.95 E-value=2.3e+02 Score=28.40 Aligned_cols=32 Identities=9% Similarity=0.110 Sum_probs=25.4
Q ss_pred HHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhh
Q 018851 33 VVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAA 67 (349)
Q Consensus 33 v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~ 67 (349)
+...+..|++.|++..+ ...+.||++|.-++.
T Consensus 332 ~~~~l~~~~~~gll~~~---~~~i~lT~~G~~~~~ 363 (370)
T PRK06294 332 TSELIMHPIIQELFTKN---DQALSLNKKGRLFHD 363 (370)
T ss_pred HHHHHHHHHHCCCEEEE---CCEEEECcchhhHHH
Confidence 34678899999999864 457999999987664
No 479
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=21.87 E-value=3.6e+02 Score=23.88 Aligned_cols=54 Identities=13% Similarity=0.246 Sum_probs=40.5
Q ss_pred EeChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhhc--CchhhhhHHHHHhhCCcEeeCc
Q 018851 57 VLTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKL--DPAVFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 57 ~LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~~--~~~~~~ig~g~~~k~~wi~i~~ 116 (349)
.+|+.-++||+ .++.+....|.+...+|.+.+ .++...-.+..+.+.|+|...+
T Consensus 3 ~~s~~~edYL~------~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 3 MLSETEEDYLE------TIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred ccchHHHHHHH------HHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 36777778884 466666666778889999875 4556666899999999998843
No 480
>PRK13239 alkylmercury lyase; Provisional
Probab=21.44 E-value=1.8e+02 Score=27.24 Aligned_cols=37 Identities=19% Similarity=0.291 Sum_probs=31.1
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhc
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLH 41 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~ 41 (349)
..||+.|. +|.+.+..+||+.+|.+.++|..++..|.
T Consensus 25 ~~llr~la-~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 25 VPLLRLLA-KGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred HHHHHHHH-cCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 46888887 55557889999999999999999988875
No 481
>COG2344 AT-rich DNA-binding protein [General function prediction only]
Probab=21.25 E-value=1.5e+02 Score=27.83 Aligned_cols=38 Identities=13% Similarity=0.144 Sum_probs=30.0
Q ss_pred HHHHHHHhhCC-CCCChHHHHHHhCCCHHHHHHHHHHhc
Q 018851 4 EAILGYLEKNE-QISDSGNFAAERGFDHNDVVNVIKSLH 41 (349)
Q Consensus 4 ~~iL~~L~~~~-~~~~~~~la~~~g~~~~~v~~~~~~L~ 41 (349)
+++|+.|.+.+ ...+|.++|+.+|+++..|.+.+.-+=
T Consensus 19 yR~le~l~a~~v~rvsS~els~~~~vdsatIRrDfSYFG 57 (211)
T COG2344 19 YRVLERLHASGVERVSSKELSEALGVDSATIRRDFSYFG 57 (211)
T ss_pred HHHHHHHHHcCCceecHHHHHHHhCCCHHHHhhhhHHHH
Confidence 57888787654 357889999999999999988776543
No 482
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=21.23 E-value=2e+02 Score=29.59 Aligned_cols=47 Identities=19% Similarity=0.281 Sum_probs=35.0
Q ss_pred CChHHHHHHhCCCHHH-HHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 17 SDSGNFAAERGFDHND-VVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 17 ~~~~~la~~~g~~~~~-v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.+...+. .|.+... +...+..|++.|++..+ ...+.||++|.-++.+
T Consensus 383 l~~~~~~--~g~~~~~~~~~~l~~~~~~Gll~~~---~~~l~lT~~G~~~~~~ 430 (449)
T PRK09058 383 LDLSELA--LGTPHADHLAPLLAQWQQAGLVELS---SDCLRLTLAGRFWAVN 430 (449)
T ss_pred ccHHHhh--cCCcHHHHHHHHHHHHHHCCCEEEE---CCEEEECCCcccHHHH
Confidence 4555555 6776554 55688899999999864 4579999999887654
No 483
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=21.21 E-value=90 Score=30.16 Aligned_cols=45 Identities=20% Similarity=0.251 Sum_probs=34.5
Q ss_pred HHHHHHhcCcCC-CCCHHHHHhhcCch--hhhhHHHHHhhCCcEeeCc
Q 018851 72 EVQLFLAVPAEG-SISKDELQKKLDPA--VFKIGCSQAGKNKWVEMGK 116 (349)
Q Consensus 72 E~rl~~~l~~~g-~~~~~el~~~~~~~--~~~ig~g~~~k~~wi~i~~ 116 (349)
|.-++++|.+.| .+.++||.+.+|-+ ...=.+..+-|+|+|++.+
T Consensus 197 e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K 244 (258)
T COG2512 197 EKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEK 244 (258)
T ss_pred HHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEE
Confidence 566778887655 48999999997644 4556789999999997743
No 484
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=21.21 E-value=2.3e+02 Score=19.18 Aligned_cols=36 Identities=17% Similarity=0.212 Sum_probs=24.5
Q ss_pred HHHHHH-HHHhhCCCCCChHHHHHHhCCCHHHHHHHHHH
Q 018851 2 AEEAIL-GYLEKNEQISDSGNFAAERGFDHNDVVNVIKS 39 (349)
Q Consensus 2 ~e~~iL-~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~ 39 (349)
+|+.+| .+|...+. +....|..+|++...+.+-++.
T Consensus 5 ~E~~~i~~aL~~~~g--n~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 5 FEKQLIRQALERCGG--NVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHHTTT---HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhCC--CHHHHHHHHCCCHHHHHHHHHh
Confidence 455544 66666654 6778899999999999876653
No 485
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=21.03 E-value=1.4e+02 Score=26.52 Aligned_cols=39 Identities=13% Similarity=-0.007 Sum_probs=30.8
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF 43 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k 43 (349)
-|.+||..+... .+..++|+.++++...|-..+..+-.|
T Consensus 154 rE~evl~~~~~G---~s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 154 KESEVLRLFAEG---FLVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred HHHHHHHHHHCC---CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 478899998744 367899999999999887777666554
No 486
>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=20.98 E-value=1e+02 Score=29.98 Aligned_cols=81 Identities=20% Similarity=0.290 Sum_probs=46.6
Q ss_pred HHHHHhhcCceeeeEE---EEEEEe-cCCCCCcchhhhhcccccccccCCCcccccccccccccCCCCCCCCCCChHHHH
Q 018851 146 EISSLKARKLIVPQTW---KGYSVR-KGPNYAPKRKKAATDLTRENLQKGDWKELEFKEYNFNAKGQPAEGGHLHPLLKV 221 (349)
Q Consensus 146 ~~~~LkkRkLi~~~~~---~~~~i~-kg~~~~~~~~~~~~~lt~e~l~sg~Wk~~~fk~yn~~~~~~~~~~g~~HPl~~~ 221 (349)
.+.-|+|+|+|+.... ++|.|+ +|.+...+...-|-. +...==+|.|.=+. ++.|+ +..
T Consensus 40 al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy~-~~~~~WdG~W~lv~-----~~~pe-----------~~~ 102 (280)
T TIGR02277 40 AVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIYD-PPAPAWDGKWRLLL-----LSGPE-----------ESL 102 (280)
T ss_pred HHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhcC-CCCCCCCCceEEEE-----eCCCc-----------hhh
Confidence 4677889999988654 788885 455432221111111 11111245555443 22222 127
Q ss_pred HHHHHHHHhhCCceecCCCCce
Q 018851 222 RKQLKDIFLQMGFEEMPTNNFV 243 (349)
Q Consensus 222 ~~~ir~if~~mGF~e~~~~~~V 243 (349)
++.+|+-|..+||-.+..|=+|
T Consensus 103 R~~lR~~L~~~Gfg~l~~glwi 124 (280)
T TIGR02277 103 RDELRKELVWSGFGLLAPSLWV 124 (280)
T ss_pred HHHHHHHHHhCCCCccCCCeEE
Confidence 8889999999999987655444
No 487
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=20.96 E-value=3e+02 Score=22.33 Aligned_cols=59 Identities=10% Similarity=0.146 Sum_probs=44.5
Q ss_pred HHHHHHHHhhCCCCCChHH----HHHHhCCCHHHHHHHHHHhccC-CcEEE---EeeeeEEEEeChhH
Q 018851 3 EEAILGYLEKNEQISDSGN----FAAERGFDHNDVVNVIKSLHGF-RYIDA---QDIKRETWVLTGEG 62 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~----la~~~g~~~~~v~~~~~~L~~k-gli~~---~~~~~~~~~LTeEG 62 (349)
-..+|+.+-+.+. .++++ |++.+.++...|.+-+.-..++ |++.+ .......|.|-|+=
T Consensus 13 Rr~vL~~fl~~~~-~T~~di~e~L~~~f~vs~~~VasMVG~i~SrlGIL~~~k~~~g~~~~Y~LKe~Y 79 (83)
T PF10826_consen 13 RRAVLKLFLKGKK-FTTDDIYERLKEKFDVSYRGVASMVGLIHSRLGILSIHKDSYGDHNVYSLKEKY 79 (83)
T ss_pred HHHHHHHHHhCCC-eeHHHHHHHHHHHcCchHHHHHHHHHHHHHhhhheeecccccCCccEEEecHHh
Confidence 3568888776665 44443 6677889999999999999997 99999 44567789998763
No 488
>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=20.89 E-value=1.8e+02 Score=21.33 Aligned_cols=65 Identities=11% Similarity=0.072 Sum_probs=38.1
Q ss_pred ChHHHHHHhCCCHHHHHHHHHHhccC-CcEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCcCCCCCHHHHHhhc
Q 018851 18 DSGNFAAERGFDHNDVVNVIKSLHGF-RYIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPAEGSISKDELQKKL 94 (349)
Q Consensus 18 ~~~~la~~~g~~~~~v~~~~~~L~~k-gli~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~g~~~~~el~~~~ 94 (349)
++.++|+.+|++...+... +.+ |++.......-.-.-|++=-.. .+.+..+.+.| ++++++++.+
T Consensus 2 ~i~e~A~~~gVs~~tlr~y----e~~~gl~~~~r~~~g~R~yt~~di~~-------l~~i~~l~~~g-~~l~~i~~~l 67 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAW----EREFGLLKPQRSDGGHRLFNDADIDR-------ILEIKRWIDNG-VQVSKVKKLL 67 (68)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHhcCCCCCCcCCCCCcccCHHHHHH-------HHHHHHHHHcC-CCHHHHHHHh
Confidence 4568999999999988644 333 7775543333232334332222 23344555555 8999887643
No 489
>PLN00104 MYST -like histone acetyltransferase; Provisional
Probab=20.87 E-value=1.5e+02 Score=31.08 Aligned_cols=54 Identities=15% Similarity=0.231 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChh
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGE 61 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeE 61 (349)
..||..|.......+..++++.+|+..++|+.++..| |++..-. ....+.+|++
T Consensus 362 ~~i~~~L~~~~~~~si~~is~~T~i~~~Dii~tL~~l---~~l~~~k-g~~~i~~~~~ 415 (450)
T PLN00104 362 RVLLEILKKHKGNISIKELSDMTAIKAEDIVSTLQSL---NLIQYRK-GQHVICADPK 415 (450)
T ss_pred HHHHHHHHhcCCCccHHHHHHHhCCCHHHHHHHHHHC---CCEEecC-CcEEEEECHH
Confidence 4578888776545788999999999999998887665 5665432 2335566653
No 490
>smart00351 PAX Paired Box domain.
Probab=20.73 E-value=2.6e+02 Score=23.58 Aligned_cols=79 Identities=14% Similarity=0.068 Sum_probs=48.8
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeee-EEEEeChhHHHHhhcCChHHHHHHhcCcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKR-ETWVLTGEGKKYAAEGSPEVQLFLAVPAE 82 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~-~~~~LTeEG~~~l~~G~PE~rl~~~l~~~ 82 (349)
.+|+.+.. .+ .+..++|..+|++...|...++.-.+.|.+.-...-. ..-.+|++- +..|..++.++
T Consensus 24 ~riv~~~~-~G--~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~---------~~~I~~~~~~~ 91 (125)
T smart00351 24 QRIVELAQ-NG--VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKV---------VKKIADYKQEN 91 (125)
T ss_pred HHHHHHHH-cC--CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHH---------HHHHHHHHHHC
Confidence 34555544 44 3678999999999999999999999888744322111 111222221 22234455555
Q ss_pred CCCCHHHHHhhc
Q 018851 83 GSISKDELQKKL 94 (349)
Q Consensus 83 g~~~~~el~~~~ 94 (349)
..+++.||...+
T Consensus 92 p~~t~~el~~~L 103 (125)
T smart00351 92 PGIFAWEIRDRL 103 (125)
T ss_pred CCCCHHHHHHHH
Confidence 668888887654
No 491
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=20.65 E-value=1.9e+02 Score=20.34 Aligned_cols=39 Identities=15% Similarity=0.221 Sum_probs=30.6
Q ss_pred HHHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccC
Q 018851 2 AEEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGF 43 (349)
Q Consensus 2 ~e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~k 43 (349)
-|..++..+... .+..++|..++++...|...+..+..|
T Consensus 8 rE~~v~~l~~~G---~s~~eia~~l~is~~tV~~h~~~i~~K 46 (65)
T COG2771 8 REREILRLVAQG---KSNKEIARILGISEETVKTHLRNIYRK 46 (65)
T ss_pred HHHHHHHHHHCC---CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 367777777644 367899999999999998888877654
No 492
>PRK00441 argR arginine repressor; Provisional
Probab=20.64 E-value=2e+02 Score=25.43 Aligned_cols=69 Identities=16% Similarity=0.161 Sum_probs=47.8
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHh-----CCCHHHHHHHHHHhccCCcEEEEe-eeeEEEEeChhHHHHhhcCChHHHHH
Q 018851 3 EEAILGYLEKNEQISDSGNFAAER-----GFDHNDVVNVIKSLHGFRYIDAQD-IKRETWVLTGEGKKYAAEGSPEVQLF 76 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~-----g~~~~~v~~~~~~L~~kgli~~~~-~~~~~~~LTeEG~~~l~~G~PE~rl~ 76 (349)
+..|+..|...+. .+.++|++.+ +++...|.+.++.|. +|++.. .-...|.|..+... .++.++-
T Consensus 6 ~~~I~~ll~~~~~-~~q~eL~~~L~~~G~~vSqaTisRDl~~L~---lvKv~~~~G~~~Y~l~~~~~~-----~~~~~l~ 76 (149)
T PRK00441 6 HAKILEIINSKEI-ETQEELAEELKKMGFDVTQATVSRDIKELK---LIKVLSNDGKYKYATISKTES-----NLSDRLV 76 (149)
T ss_pred HHHHHHHHHHcCC-CcHHHHHHHHHhcCCCcCHHHHHHHHHHcC---cEEeECCCCCEEEEeCccccc-----chHHHHH
Confidence 4678888887765 7788999886 888899999888774 677743 34458888665421 2334555
Q ss_pred HhcC
Q 018851 77 LAVP 80 (349)
Q Consensus 77 ~~l~ 80 (349)
..+.
T Consensus 77 ~~~~ 80 (149)
T PRK00441 77 NIFS 80 (149)
T ss_pred HHHH
Confidence 5553
No 493
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=20.47 E-value=3.1e+02 Score=23.24 Aligned_cols=47 Identities=11% Similarity=0.062 Sum_probs=33.8
Q ss_pred CChHH-HHHHhcCcCCCCCHHHHHhhcC--chhhhhHHHHHhhCCcEeeC
Q 018851 69 GSPEV-QLFLAVPAEGSISKDELQKKLD--PAVFKIGCSQAGKNKWVEMG 115 (349)
Q Consensus 69 G~PE~-rl~~~l~~~g~~~~~el~~~~~--~~~~~ig~g~~~k~~wi~i~ 115 (349)
|.|=+ +++..|...|+.++.||.+.++ ++..+-=++.+.+.|+|...
T Consensus 14 adptRl~IL~~L~~~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~ 63 (117)
T PRK10141 14 SDETRLGIVLLLRESGELCVCDLCTALDQSQPKISRHLALLRESGLLLDR 63 (117)
T ss_pred CCHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 44533 6777776556689999988754 44556667899999999764
No 494
>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=20.44 E-value=3.3e+02 Score=29.21 Aligned_cols=75 Identities=12% Similarity=0.039 Sum_probs=53.2
Q ss_pred HHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCC-cEEEEeeeeEEEEeChhHHHHhhcCChHHHHHHhcCcC
Q 018851 4 EAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFR-YIDAQDIKRETWVLTGEGKKYAAEGSPEVQLFLAVPAE 82 (349)
Q Consensus 4 ~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg-li~~~~~~~~~~~LTeEG~~~l~~G~PE~rl~~~l~~~ 82 (349)
.+|+..+... +....++++.+|++...+...+..|...| ++.+.. ..|.+ ..+.+.+.++
T Consensus 478 ~~i~~~~~~~--~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~---~~~~~--------------~~~~~~~~~~ 538 (581)
T TIGR00475 478 QKIKGTFGTK--GAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVK---DRLLK--------------KYINELKEEG 538 (581)
T ss_pred HHHHHHHhcC--CCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeC---CeEHH--------------HHHHHHHhcC
Confidence 4566666522 35678899999999999999999999977 444443 23333 5566677767
Q ss_pred CCCCHHHHHhhcCch
Q 018851 83 GSISKDELQKKLDPA 97 (349)
Q Consensus 83 g~~~~~el~~~~~~~ 97 (349)
+++++.+++..+|-+
T Consensus 539 ~~~~~~~~r~~~g~s 553 (581)
T TIGR00475 539 GTFNVQQARDKLGLG 553 (581)
T ss_pred CcCcHHHHHHHHCcc
Confidence 789999999887643
No 495
>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=20.31 E-value=1.4e+02 Score=22.99 Aligned_cols=39 Identities=23% Similarity=0.215 Sum_probs=28.0
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhcc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHG 42 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~ 42 (349)
...++..|-..+. .+.+++|+.+.++.+.+.+.++.|..
T Consensus 18 ~~~ll~~ll~~~~-~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 18 NYQLLKLLLNNEY-VSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp HHHHHHHHHH-SE-EEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567777765555 68899999999999998888876654
No 496
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=20.28 E-value=2e+02 Score=25.60 Aligned_cols=60 Identities=15% Similarity=0.185 Sum_probs=41.5
Q ss_pred HHHHHHhhCCCCCChHHHHHHhC------C--------CHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHHhhc
Q 018851 5 AILGYLEKNEQISDSGNFAAERG------F--------DHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKYAAE 68 (349)
Q Consensus 5 ~iL~~L~~~~~~~~~~~la~~~g------~--------~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~l~~ 68 (349)
.||..+.-++. ...+.|.+..| . +.+-+..++..|++.|+|.-.. .--+||++|+..|.+
T Consensus 57 SilRkiyi~gp-vGi~rL~t~YGg~k~rG~rP~~~~~gsgsI~RkilqqLE~~G~V~k~~---~GR~ltp~GrsllD~ 130 (147)
T COG2238 57 SILRKIYIDGP-VGIERLRTAYGGRKNRGSRPEKFRKGSGSIIRKVLQQLEKAGLVEKTP---KGRVLTPKGRSLLDR 130 (147)
T ss_pred HHHHHHHhcCc-hhHHHHHHHHCccccCCCCchhhhcCCchHHHHHHHHHHHCCceeecC---CCceeCccchhHHHH
Confidence 46666665654 45566665443 2 2244667889999999998766 345799999988765
No 497
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=20.20 E-value=2.1e+02 Score=19.32 Aligned_cols=36 Identities=17% Similarity=0.285 Sum_probs=26.8
Q ss_pred HHHHHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhc
Q 018851 3 EEAILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLH 41 (349)
Q Consensus 3 e~~iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~ 41 (349)
|..++..+. .+ .+..++|+.+|++...|...+..+.
T Consensus 5 e~~i~~~~~-~~--~s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 5 EREVLRLLA-EG--KTNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred HHHHHHHHH-cC--CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 556666554 33 4778999999999999888877653
No 498
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=20.01 E-value=1.6e+02 Score=23.38 Aligned_cols=26 Identities=15% Similarity=0.298 Sum_probs=23.1
Q ss_pred CChHHHHHHhC-CCHHHHHHHHHHhcc
Q 018851 17 SDSGNFAAERG-FDHNDVVNVIKSLHG 42 (349)
Q Consensus 17 ~~~~~la~~~g-~~~~~v~~~~~~L~~ 42 (349)
.+..+++..+| .+|+.|+.+++.++.
T Consensus 45 ~s~~~Ig~~fg~r~hStV~~a~~ri~~ 71 (90)
T cd06571 45 LSLPEIGRAFGGRDHSTVLHAVRKIEE 71 (90)
T ss_pred CCHHHHHHHhCCCCHhHHHHHHHHHHH
Confidence 57789999999 999999999998875
No 499
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.00 E-value=2.3e+02 Score=24.46 Aligned_cols=54 Identities=17% Similarity=0.218 Sum_probs=38.0
Q ss_pred HHHHHhhCCCCCChHHHHHHhCCCHHHHHHHHHHhccCCcEEEEeeeeEEEEeChhHHHH
Q 018851 6 ILGYLEKNEQISDSGNFAAERGFDHNDVVNVIKSLHGFRYIDAQDIKRETWVLTGEGKKY 65 (349)
Q Consensus 6 iL~~L~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kgli~~~~~~~~~~~LTeEG~~~ 65 (349)
+-.+|...+. ....++++..|++. +-.-|...-|==.+..+.-.|.||+.|+..
T Consensus 64 ~A~~L~~~Gp-~~~~~l~~~~~~~~-----A~~IL~~N~YGWFeRv~rGvY~LT~~G~~a 117 (118)
T PF09929_consen 64 CAAALAEHGP-SRPADLRKATGVPK-----ATSILRDNHYGWFERVERGVYALTPAGRAA 117 (118)
T ss_pred HHHHHHHcCC-CCHHHHHHhcCCCh-----HHHHHHhCcccceeeeccceEecCcchhhc
Confidence 4456666665 66778888777663 334455655666788888899999999864
Done!