Query 031021
Match_columns 167
No_of_seqs 102 out of 182
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 08:03:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031021.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031021hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3252 Uncharacterized conser 100.0 5.5E-53 1.2E-57 329.0 10.5 157 1-166 60-216 (217)
2 PF10075 PCI_Csn8: COP9 signal 100.0 2.4E-34 5.1E-39 218.3 9.5 131 2-141 3-137 (143)
3 KOG4414 COP9 signalosome, subu 99.5 1.8E-14 3.9E-19 110.0 5.4 130 19-162 52-188 (197)
4 PF03399 SAC3_GANP: SAC3/GANP/ 99.2 5.4E-11 1.2E-15 94.0 7.6 103 2-104 98-204 (204)
5 PF01399 PCI: PCI domain; Int 97.8 0.00058 1.3E-08 47.6 10.4 79 41-119 2-87 (105)
6 KOG3151 26S proteasome regulat 97.3 0.0012 2.7E-08 54.3 7.4 112 10-125 107-222 (260)
7 smart00088 PINT motif in prote 96.7 0.0079 1.7E-07 41.2 6.7 65 71-138 3-69 (88)
8 smart00753 PAM PCI/PINT associ 96.7 0.0079 1.7E-07 41.2 6.7 65 71-138 3-69 (88)
9 KOG1861 Leucine permease trans 96.5 0.039 8.5E-07 49.6 10.9 105 19-127 403-510 (540)
10 KOG2758 Translation initiation 93.1 0.29 6.2E-06 42.6 6.3 59 65-123 322-380 (432)
11 cd07377 WHTH_GntR Winged helix 90.5 0.77 1.7E-05 28.8 4.7 48 76-124 8-56 (66)
12 KOG2581 26S proteasome regulat 90.3 0.9 2E-05 40.6 6.4 80 37-116 316-402 (493)
13 KOG0687 26S proteasome regulat 86.4 12 0.00026 32.7 10.6 76 40-115 257-340 (393)
14 PF13412 HTH_24: Winged helix- 84.6 4.9 0.00011 24.0 5.6 46 76-123 2-47 (48)
15 COG5071 RPN5 26S proteasome re 84.1 4.1 8.8E-05 35.4 6.6 57 81-138 342-398 (439)
16 PF08279 HTH_11: HTH domain; 83.4 5.8 0.00013 24.3 5.7 46 81-127 4-49 (55)
17 smart00345 HTH_GNTR helix_turn 83.2 2.9 6.2E-05 25.5 4.2 33 92-125 19-52 (60)
18 COG5187 RPN7 26S proteasome re 82.8 5.4 0.00012 34.5 6.9 78 36-113 267-356 (412)
19 COG1654 BirA Biotin operon rep 81.8 6.3 0.00014 27.1 5.7 54 85-141 12-65 (79)
20 TIGR01610 phage_O_Nterm phage 81.1 12 0.00027 26.0 7.3 62 76-140 25-92 (95)
21 KOG1464 COP9 signalosome, subu 80.2 9 0.0002 33.0 7.3 79 35-113 300-385 (440)
22 PF13730 HTH_36: Helix-turn-he 80.2 2.9 6.3E-05 25.7 3.4 28 94-122 27-54 (55)
23 PF13545 HTH_Crp_2: Crp-like h 79.7 3.2 7E-05 27.0 3.7 33 92-125 28-60 (76)
24 KOG1463 26S proteasome regulat 79.1 14 0.00029 32.6 8.1 116 22-140 255-393 (411)
25 PF10255 Paf67: RNA polymerase 79.0 22 0.00047 31.7 9.6 103 21-125 221-358 (404)
26 PF07037 DUF1323: Putative tra 78.7 2.4 5.2E-05 31.5 3.0 29 94-126 2-30 (122)
27 PF10537 WAC_Acf1_DNA_bd: ATP- 77.7 1.8 3.8E-05 31.2 2.0 60 37-98 18-84 (102)
28 PF13463 HTH_27: Winged helix 77.7 6 0.00013 25.0 4.5 45 79-124 5-49 (68)
29 PF01022 HTH_5: Bacterial regu 76.6 6.7 0.00015 23.6 4.2 45 76-123 1-45 (47)
30 PF04801 Sin_N: Sin-like prote 76.3 2.7 5.9E-05 37.1 3.2 101 17-125 282-388 (421)
31 KOG0686 COP9 signalosome, subu 76.1 10 0.00022 34.0 6.6 110 4-120 270-393 (466)
32 smart00550 Zalpha Z-DNA-bindin 74.2 14 0.0003 24.2 5.5 49 76-125 5-54 (68)
33 KOG1498 26S proteasome regulat 73.5 12 0.00026 33.3 6.4 87 37-124 288-384 (439)
34 PF00325 Crp: Bacterial regula 73.0 7.2 0.00016 22.2 3.3 28 93-121 3-30 (32)
35 PF01466 Skp1: Skp1 family, di 72.7 9.3 0.0002 25.7 4.5 50 71-124 28-77 (78)
36 TIGR01889 Staph_reg_Sar staphy 71.1 17 0.00036 25.7 5.8 70 53-124 2-74 (109)
37 smart00419 HTH_CRP helix_turn_ 70.0 8.8 0.00019 22.3 3.6 33 92-125 8-40 (48)
38 PF12840 HTH_20: Helix-turn-he 70.0 14 0.00031 23.3 4.7 50 73-124 6-55 (61)
39 smart00420 HTH_DEOR helix_turn 68.0 22 0.00047 20.8 5.2 35 90-125 12-46 (53)
40 PF01978 TrmB: Sugar-specific 67.6 22 0.00048 22.7 5.4 51 73-126 5-55 (68)
41 COG5484 Uncharacterized conser 67.5 5.1 0.00011 33.6 2.7 30 92-125 19-48 (279)
42 PRK13918 CRP/FNR family transc 66.8 28 0.00061 26.6 6.7 33 92-125 149-181 (202)
43 KOG1076 Translation initiation 66.8 11 0.00024 35.9 5.0 80 40-120 655-746 (843)
44 PRK11161 fumarate/nitrate redu 65.7 22 0.00047 28.0 6.0 33 92-125 184-216 (235)
45 cd00092 HTH_CRP helix_turn_hel 62.3 29 0.00064 21.5 5.1 34 91-125 24-57 (67)
46 PF05687 DUF822: Plant protein 61.7 7.3 0.00016 29.9 2.4 26 107-135 45-70 (150)
47 PF08220 HTH_DeoR: DeoR-like h 59.9 31 0.00067 21.6 4.8 43 80-124 3-45 (57)
48 PF06627 DUF1153: Protein of u 59.9 18 0.00039 25.5 3.9 38 78-115 35-72 (90)
49 PF09339 HTH_IclR: IclR helix- 59.7 16 0.00036 22.2 3.4 44 81-125 7-50 (52)
50 PF12802 MarR_2: MarR family; 59.1 33 0.00071 21.1 4.9 45 80-125 8-53 (62)
51 PF03484 B5: tRNA synthetase B 57.8 23 0.0005 23.2 4.1 45 92-140 5-51 (70)
52 PRK09391 fixK transcriptional 57.7 22 0.00048 28.3 4.8 32 92-124 179-210 (230)
53 PF12643 MazG-like: MazG-like 56.5 40 0.00087 24.0 5.4 38 75-118 34-71 (98)
54 TIGR00122 birA_repr_reg BirA b 55.4 53 0.0011 21.0 6.0 43 82-127 5-47 (69)
55 PF12123 Amidase02_C: N-acetyl 55.3 10 0.00022 23.4 1.8 22 103-125 23-44 (45)
56 smart00418 HTH_ARSR helix_turn 54.8 37 0.00079 20.2 4.5 35 90-125 8-42 (66)
57 PF01325 Fe_dep_repress: Iron 54.8 43 0.00092 21.4 4.9 37 89-126 19-55 (60)
58 PRK10402 DNA-binding transcrip 54.5 58 0.0013 25.7 6.7 48 77-125 150-201 (226)
59 PF13384 HTH_23: Homeodomain-l 54.4 21 0.00046 21.2 3.3 36 78-116 6-41 (50)
60 PF13977 TetR_C_6: Bacterial t 54.4 19 0.00041 24.6 3.5 49 54-102 26-79 (115)
61 smart00344 HTH_ASNC helix_turn 53.8 45 0.00097 23.0 5.3 44 79-124 5-48 (108)
62 PF08784 RPA_C: Replication pr 52.4 36 0.00079 23.6 4.7 47 77-124 47-96 (102)
63 PRK10681 DNA-binding transcrip 51.8 39 0.00085 27.6 5.4 43 78-122 8-50 (252)
64 PF04703 FaeA: FaeA-like prote 51.8 59 0.0013 21.2 5.2 45 80-125 3-47 (62)
65 TIGR02702 SufR_cyano iron-sulf 51.1 40 0.00087 26.5 5.2 46 78-125 2-47 (203)
66 smart00874 B5 tRNA synthetase 51.1 52 0.0011 21.1 5.0 45 92-140 5-52 (71)
67 PF06056 Terminase_5: Putative 51.0 24 0.00051 22.6 3.2 31 91-125 12-42 (58)
68 COG2522 Predicted transcriptio 51.0 43 0.00093 24.8 4.9 39 73-113 5-43 (119)
69 PF02082 Rrf2: Transcriptional 49.7 76 0.0016 21.1 6.3 47 93-141 26-72 (83)
70 PF10410 DnaB_bind: DnaB-helic 49.6 13 0.00027 23.1 1.7 53 57-109 5-59 (59)
71 PF06971 Put_DNA-bind_N: Putat 49.4 31 0.00068 21.5 3.4 32 82-113 18-49 (50)
72 PRK11014 transcriptional repre 49.3 44 0.00096 24.7 4.9 46 91-138 24-69 (141)
73 PF09012 FeoC: FeoC like trans 49.2 20 0.00044 23.2 2.7 35 89-124 11-45 (69)
74 PRK11753 DNA-binding transcrip 48.3 42 0.00091 25.7 4.9 29 92-121 168-196 (211)
75 PRK10411 DNA-binding transcrip 48.2 1E+02 0.0022 25.1 7.2 45 79-125 6-50 (240)
76 PRK10906 DNA-binding transcrip 47.2 86 0.0019 25.7 6.7 47 77-125 5-51 (252)
77 TIGR02010 IscR iron-sulfur clu 47.0 55 0.0012 24.0 5.1 33 92-125 25-57 (135)
78 PF01047 MarR: MarR family; I 46.9 65 0.0014 19.6 4.9 36 89-125 14-49 (59)
79 TIGR03697 NtcA_cyano global ni 46.1 55 0.0012 24.6 5.2 33 92-125 143-175 (193)
80 PF12728 HTH_17: Helix-turn-he 45.8 24 0.00053 21.1 2.5 21 93-113 2-22 (51)
81 TIGR00738 rrf2_super rrf2 fami 45.0 65 0.0014 23.1 5.2 33 92-125 25-57 (132)
82 PF13601 HTH_34: Winged helix 45.0 61 0.0013 21.8 4.7 45 78-124 1-45 (80)
83 PF08471 Ribonuc_red_2_N: Clas 44.4 16 0.00034 26.0 1.7 39 49-87 8-61 (93)
84 COG3415 Transposase and inacti 44.1 63 0.0014 24.5 5.0 45 78-123 7-51 (138)
85 TIGR01764 excise DNA binding d 44.1 28 0.00061 20.0 2.6 21 93-113 2-22 (49)
86 cd00090 HTH_ARSR Arsenical Res 43.9 72 0.0016 19.4 4.7 45 78-125 8-52 (78)
87 PF15297 CKAP2_C: Cytoskeleton 43.6 17 0.00036 31.9 2.0 67 21-87 105-186 (353)
88 PF00392 GntR: Bacterial regul 43.5 79 0.0017 19.9 4.9 36 91-127 22-58 (64)
89 PF14555 UBA_4: UBA-like domai 43.3 25 0.00054 20.8 2.2 26 96-125 5-30 (43)
90 PRK10434 srlR DNA-bindng trans 43.1 54 0.0012 26.9 5.0 45 79-125 7-51 (256)
91 PF10671 TcpQ: Toxin co-regula 43.0 18 0.00039 24.6 1.8 21 105-125 8-28 (84)
92 cd06170 LuxR_C_like C-terminal 42.3 71 0.0015 18.7 4.5 32 90-121 13-44 (57)
93 PF06708 DUF1195: Protein of u 40.6 31 0.00068 26.4 2.9 79 5-83 41-140 (157)
94 PF13518 HTH_28: Helix-turn-he 39.6 80 0.0017 18.5 4.6 30 91-121 11-40 (52)
95 cd04762 HTH_MerR-trunc Helix-T 39.3 38 0.00082 19.2 2.6 20 94-113 2-21 (49)
96 PF03374 ANT: Phage antirepres 38.9 53 0.0011 23.0 3.8 33 89-125 21-53 (111)
97 smart00421 HTH_LUXR helix_turn 38.5 81 0.0018 18.3 4.6 32 90-121 16-47 (58)
98 PF04967 HTH_10: HTH DNA bindi 37.9 62 0.0013 20.4 3.5 25 91-115 22-46 (53)
99 PRK11511 DNA-binding transcrip 36.6 1.2E+02 0.0026 21.9 5.5 39 78-116 11-49 (127)
100 KOG2072 Translation initiation 36.5 1.4E+02 0.003 29.4 7.0 74 63-137 418-492 (988)
101 COG1522 Lrp Transcriptional re 36.1 1.1E+02 0.0025 22.2 5.4 45 75-121 6-50 (154)
102 PF08280 HTH_Mga: M protein tr 36.0 1.1E+02 0.0024 19.1 4.6 35 81-116 9-43 (59)
103 PF05584 Sulfolobus_pRN: Sulfo 35.8 1.4E+02 0.003 20.2 5.3 43 78-123 6-48 (72)
104 smart00347 HTH_MARR helix_turn 35.8 1.3E+02 0.0028 19.7 5.4 45 79-125 12-56 (101)
105 COG2074 2-phosphoglycerate kin 35.6 33 0.00071 29.2 2.5 45 37-82 126-172 (299)
106 COG2186 FadR Transcriptional r 35.3 1.1E+02 0.0025 24.7 5.7 45 95-142 37-81 (241)
107 PF05295 Luciferase_N: Lucifer 34.9 12 0.00025 25.8 -0.2 25 51-75 32-60 (82)
108 PRK03573 transcriptional regul 34.6 1E+02 0.0022 22.4 4.9 44 81-125 35-78 (144)
109 smart00346 HTH_ICLR helix_turn 34.5 1.1E+02 0.0024 20.1 4.7 43 82-125 10-52 (91)
110 PF04492 Phage_rep_O: Bacterio 34.5 1.2E+02 0.0026 21.5 5.0 50 73-123 29-84 (100)
111 PF04539 Sigma70_r3: Sigma-70 34.2 1.2E+02 0.0025 19.7 4.7 37 78-114 6-42 (78)
112 cd04761 HTH_MerR-SF Helix-Turn 34.2 47 0.001 19.3 2.5 20 94-113 2-21 (49)
113 COG1349 GlpR Transcriptional r 33.3 89 0.0019 25.6 4.8 45 79-125 7-51 (253)
114 PRK10225 DNA-binding transcrip 33.0 1.5E+02 0.0032 23.8 6.0 66 73-141 13-79 (257)
115 TIGR03338 phnR_burk phosphonat 32.9 1.2E+02 0.0026 23.4 5.3 62 75-139 17-78 (212)
116 PF11198 DUF2857: Protein of u 32.6 1.2E+02 0.0026 23.7 5.2 23 6-28 3-25 (180)
117 COG1577 ERG12 Mevalonate kinas 32.4 1.4E+02 0.0031 25.5 6.0 41 98-139 238-281 (307)
118 PRK10857 DNA-binding transcrip 32.3 1.5E+02 0.0032 22.8 5.6 47 92-140 25-71 (164)
119 PF08461 HTH_12: Ribonuclease 31.7 1.3E+02 0.0028 19.5 4.5 44 81-125 2-50 (66)
120 KOG1497 COP9 signalosome, subu 31.5 3.1E+02 0.0067 24.2 7.8 73 43-116 266-341 (399)
121 PRK11534 DNA-binding transcrip 31.4 1.2E+02 0.0027 23.7 5.2 46 91-139 29-74 (224)
122 PRK03902 manganese transport t 31.2 1.7E+02 0.0036 21.4 5.6 43 80-124 11-53 (142)
123 PF10668 Phage_terminase: Phag 31.1 1.4E+02 0.0031 19.3 4.4 41 81-125 11-51 (60)
124 PRK13509 transcriptional repre 30.4 1.3E+02 0.0027 24.6 5.2 45 77-123 5-49 (251)
125 TIGR02944 suf_reg_Xantho FeS a 30.4 1.9E+02 0.004 20.8 5.6 34 91-125 24-57 (130)
126 COG2944 Predicted transcriptio 30.4 51 0.0011 23.8 2.5 22 91-112 56-77 (104)
127 PRK10141 DNA-binding transcrip 30.2 1.1E+02 0.0023 22.4 4.3 55 69-125 8-62 (117)
128 TIGR02337 HpaR homoprotocatech 29.6 1.6E+02 0.0035 20.6 5.1 44 80-125 31-74 (118)
129 cd05295 MDH_like Malate dehydr 29.6 60 0.0013 29.4 3.3 31 95-125 10-52 (452)
130 COG3413 Predicted DNA binding 28.8 1.2E+02 0.0026 24.0 4.7 71 44-116 127-202 (215)
131 PF00165 HTH_AraC: Bacterial r 28.8 97 0.0021 17.7 3.2 31 91-124 7-37 (42)
132 PRK09392 ftrB transcriptional 28.7 1.3E+02 0.0028 23.5 4.9 29 93-122 174-202 (236)
133 PRK04214 rbn ribonuclease BN/u 28.7 3.2E+02 0.0069 24.0 7.7 53 72-127 289-344 (412)
134 smart00311 PWI PWI, domain in 28.6 86 0.0019 20.7 3.3 24 96-119 15-38 (74)
135 PF04147 Nop14: Nop14-like fam 28.4 77 0.0017 30.8 4.1 37 7-55 542-580 (840)
136 PF03793 PASTA: PASTA domain; 28.2 1.3E+02 0.0029 18.5 4.0 21 100-124 5-25 (63)
137 PRK14137 recX recombination re 27.8 1.8E+02 0.0038 23.2 5.4 51 72-125 36-89 (195)
138 KOG3364 Membrane protein invol 27.4 1E+02 0.0023 23.7 3.8 79 44-122 26-123 (149)
139 PF13591 MerR_2: MerR HTH fami 27.0 79 0.0017 21.4 2.9 28 93-125 1-28 (84)
140 PRK09954 putative kinase; Prov 26.9 1.5E+02 0.0032 25.2 5.2 45 78-124 4-48 (362)
141 PF07927 YcfA: YcfA-like prote 26.8 91 0.002 18.9 3.0 16 108-127 3-18 (56)
142 COG5340 Predicted transcriptio 26.5 1.3E+02 0.0027 25.2 4.4 53 73-126 11-63 (269)
143 PRK03837 transcriptional regul 26.5 1.7E+02 0.0037 23.0 5.3 47 91-140 35-82 (241)
144 PF12793 SgrR_N: Sugar transpo 26.4 99 0.0022 22.4 3.5 35 89-124 16-50 (115)
145 PF00196 GerE: Bacterial regul 26.2 1.4E+02 0.0031 18.2 3.8 32 90-121 16-47 (58)
146 PF07900 DUF1670: Protein of u 26.2 2.5E+02 0.0053 23.1 6.0 52 73-124 83-137 (220)
147 PRK04424 fatty acid biosynthes 25.5 1.4E+02 0.003 23.3 4.5 42 78-121 8-49 (185)
148 COG4199 Uncharacterized protei 24.9 64 0.0014 26.0 2.4 110 41-163 63-177 (201)
149 PRK11920 rirA iron-responsive 24.5 2.3E+02 0.005 21.3 5.4 47 92-140 24-70 (153)
150 PHA00738 putative HTH transcri 24.3 2.3E+02 0.0049 20.7 5.0 64 76-143 11-74 (108)
151 KOG2908 26S proteasome regulat 24.3 5E+02 0.011 23.0 9.3 90 43-136 238-337 (380)
152 smart00422 HTH_MERR helix_turn 24.2 1E+02 0.0022 19.3 2.9 20 94-113 2-21 (70)
153 PHA02699 hypothetical protein; 23.8 1E+02 0.0022 27.4 3.6 63 52-127 397-460 (466)
154 PF01710 HTH_Tnp_IS630: Transp 23.8 1.9E+02 0.0041 20.8 4.6 35 89-127 68-102 (119)
155 PRK09990 DNA-binding transcrip 23.5 2.5E+02 0.0054 22.4 5.7 64 75-141 13-77 (251)
156 PF14821 Thr_synth_N: Threonin 23.3 71 0.0015 21.5 2.1 34 81-114 41-76 (79)
157 PRK11512 DNA-binding transcrip 23.3 2.2E+02 0.0048 20.7 5.0 44 80-125 43-86 (144)
158 KOG2745 Mitochondrial carrier 23.1 1.2E+02 0.0026 26.0 3.8 42 53-103 129-170 (321)
159 PF10771 DUF2582: Protein of u 23.0 67 0.0014 21.2 1.8 36 82-125 13-48 (65)
160 PRK11402 DNA-binding transcrip 22.7 2.2E+02 0.0049 22.6 5.3 44 93-139 34-77 (241)
161 PRK09464 pdhR transcriptional 22.7 2.3E+02 0.0049 22.6 5.4 58 75-138 16-77 (254)
162 PF12046 DUF3529: Protein of u 22.6 1.3E+02 0.0028 23.8 3.7 30 107-136 43-72 (173)
163 cd03527 RuBisCO_small Ribulose 22.4 83 0.0018 22.5 2.4 24 101-125 8-32 (99)
164 COG2188 PhnF Transcriptional r 22.0 1.9E+02 0.004 23.3 4.7 42 94-138 33-74 (236)
165 PF08727 P3A: Poliovirus 3A pr 21.9 52 0.0011 21.3 1.1 23 99-125 21-44 (57)
166 COG0549 ArcC Carbamate kinase 21.8 1.3E+02 0.0028 25.9 3.7 25 114-138 141-165 (312)
167 PF11338 DUF3140: Protein of u 21.6 48 0.001 23.5 1.0 28 98-125 2-30 (92)
168 PF08621 RPAP1_N: RPAP1-like, 21.6 1.5E+02 0.0033 18.3 3.2 30 91-120 2-31 (49)
169 PF02002 TFIIE_alpha: TFIIE al 21.5 1.8E+02 0.0039 20.2 4.0 40 80-121 16-55 (105)
170 PRK14165 winged helix-turn-hel 21.3 2.5E+02 0.0055 22.8 5.3 35 90-125 19-53 (217)
171 PF08281 Sigma70_r4_2: Sigma-7 21.3 1.3E+02 0.0028 17.9 2.9 28 89-116 23-50 (54)
172 PF09494 Slx4: Slx4 endonuclea 21.2 94 0.002 20.0 2.3 18 88-105 20-37 (64)
173 PRK09802 DNA-binding transcrip 21.2 2.3E+02 0.0049 23.4 5.1 46 79-126 19-64 (269)
174 TIGR01884 cas_HTH CRISPR locus 21.0 2.7E+02 0.0058 21.7 5.3 44 80-125 146-189 (203)
175 COG1321 TroR Mn-dependent tran 20.8 3.7E+02 0.008 20.4 5.9 38 89-127 21-58 (154)
176 PRK10219 DNA-binding transcrip 20.6 2.9E+02 0.0063 18.9 5.6 35 87-124 16-50 (107)
177 KOG4567 GTPase-activating prot 20.1 1.1E+02 0.0023 26.9 2.9 48 4-53 316-363 (370)
178 PRK15431 ferrous iron transpor 20.1 1.8E+02 0.004 19.9 3.6 32 89-121 13-44 (78)
179 PF01726 LexA_DNA_bind: LexA D 20.1 2.6E+02 0.0056 18.0 6.0 47 78-125 11-58 (65)
No 1
>KOG3252 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=5.5e-53 Score=329.03 Aligned_cols=157 Identities=40% Similarity=0.696 Sum_probs=143.7
Q ss_pred CCHHHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhhcccchHHHHHH
Q 031021 1 MSTQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQS 80 (167)
Q Consensus 1 ~~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed~IR~ 80 (167)
||.+++++|||||||++|||||+||+||||+++|.++++++|+.||++||+|+|+.||++.+.++++++.|+||||+||+
T Consensus 60 ~nt~itaqILlKaL~~lP~tDF~l~kcli~~~~~~ee~~r~ii~L~~~LEt~~Fq~FW~~~~~N~~mle~itGFedsvr~ 139 (217)
T KOG3252|consen 60 FNTTITAQILLKALTNLPHTDFTLAKCLIDERVQMEEPFRSIIDLGDYLETCRFQQFWQEADENRDMLEGITGFEDSVRK 139 (217)
T ss_pred hhhHHHHHHHHHHHhcCCCcchhHHHHhcCHHHhcccchhHHHhHHHHHhhchHHHHhhhhccchHHhcCCCcHHHHHHH
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCccccccccccccCCcccc
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHIT 160 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i~E~i~f~~~~ 160 (167)
|+|||||.|||+|+++.|+++|| ...+++++.|++++||..+.. | .+++|.++++ .++|||.|||+||+|+
T Consensus 140 yachvv~iTyQkI~k~lLaellG---~~sDs~le~~~~~~GW~a~e~---G-~ifv~~qE~~--iKtkNi~EkI~fd~Va 210 (217)
T KOG3252|consen 140 YACHVVGITYQKIDKWLLAELLG---GLSDSQLEVWMTKYGWIADES---G-QIFVASQEEE--IKTKNIVEKIDFDHVA 210 (217)
T ss_pred HHHHheechHhhchHHHHHHhhC---cccHHHHHHHHHHccceecCC---c-eEEEeccccc--cccCCccccCCcchHH
Confidence 99999999999999999999997 444566777779999999843 4 6777777763 3459999999999999
Q ss_pred cccccC
Q 031021 161 RIFPIL 166 (167)
Q Consensus 161 ~i~~~~ 166 (167)
++||.+
T Consensus 211 ~ima~~ 216 (217)
T KOG3252|consen 211 SIMASL 216 (217)
T ss_pred HHHHhc
Confidence 999975
No 2
>PF10075 PCI_Csn8: COP9 signalosome, subunit CSN8; InterPro: IPR019280 The photomorphogenic 9 (COP9) signalosome or CSN complex is composed of eight subunits: Cops1/GPS1, Cops2, Cops3, Cops4, Cops5, Cop6, Cops7 (Cops7A or Cops7B) and Cops8. In the complex, Cops8, which is the smallest subunit, probably interacts directly with Cops3, Cops4 and Cops7 (Cops7A or Cops7B). This signalosome is homologous to the lid subcomplex of the 26S proteasome and regulates the ubiquitin-proteasome pathway. It functions as a structural scaffold for subunit-subunit interactions within the complex and is a key regulator of photomorphogenic development [].; PDB: 1RZ4_A.
Probab=100.00 E-value=2.4e-34 Score=218.32 Aligned_cols=131 Identities=33% Similarity=0.570 Sum_probs=107.7
Q ss_pred CHHHHHHHHHHHHHcCCccchhhhhcCCCccccC-chhHHHHHHHHHHHHcCChHHHHHHHhhc---cchhhcccchHHH
Q 031021 2 STQIVARILIKALMAMPAPDFSLCLFLIPERVQM-EDQFKTLIVLSHYLETGRFRHFWDEAAKH---RNIVEAVPGFEQA 77 (167)
Q Consensus 2 ~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~-~~~i~~i~~L~~lLe~c~F~~FW~~l~~~---~~~~~~i~gFed~ 77 (167)
++++++.+|+|+|++.|.+||.+|.++||++.+. +++|+.++.|+++||+|+|++||+.++++ +++.+.|+||+|+
T Consensus 3 ~~~~~~~~Ll~~L~~~~~~df~~~~~rip~~~~~~~~~i~~i~~l~~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~ 82 (143)
T PF10075_consen 3 NPEIYALILLKYLMQNDLSDFRLLWKRIPEELKQSDPEIKAIWSLGQALWEGDYSKFWQALRSNPWSPDYKPFVPGFEDT 82 (143)
T ss_dssp -HHHHHHHHHHHHHTTTSTHHHHHHHTS-HHHHTS-TTHHHHHHHHHHHHTT-HHHHHHHS-TT----HHHHTSTTHHHH
T ss_pred chhHHHHHHHHHHHcCCchHHHHHHHcCCHHHHhhhHHHHHHHHHHHHHHCCCHHHHHHHHHhccchHHHHHHHHHHHHH
Confidence 6899999999999999999999999999999987 59999999999999999999999999887 8999999999999
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF 141 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~ 141 (167)
||++|+++|+.||++|+.+.+++|||++++++.+++ +++||+++++ .++++.|++
T Consensus 83 iR~~i~~~i~~aY~sIs~~~la~~Lg~~~~el~~~~----~~~gW~~d~~-----~~~~~~~~~ 137 (143)
T PF10075_consen 83 IRERIAHLISKAYSSISLSDLAEMLGLSEEELEKFI----KSRGWTVDGD-----GVLFPPNPE 137 (143)
T ss_dssp HHHHHHHHHHHH-SEE-HHHHHHHTTS-HHHHHHHH----HHHT-EE----------EE---HH
T ss_pred HHHHHHHHHHHHHhHcCHHHHHHHhCCCHHHHHHHH----HHcCCEECCC-----ccEEecCCc
Confidence 999999999999999999999999999988888888 7779999843 455655555
No 3
>KOG4414 consensus COP9 signalosome, subunit CSN8 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=99.51 E-value=1.8e-14 Score=109.96 Aligned_cols=130 Identities=17% Similarity=0.248 Sum_probs=102.1
Q ss_pred ccchhhhhcC---CCcccc-CchhHHHHHHHHHHHHcCChHHHHHHHhhc---cchhhcccchHHHHHHHHHHHHHHhcc
Q 031021 19 APDFSLCLFL---IPERVQ-MEDQFKTLIVLSHYLETGRFRHFWDEAAKH---RNIVEAVPGFEQAIQSFAIHVLSLTYQ 91 (167)
Q Consensus 19 ~~DF~lc~~L---l~~~~~-~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~---~~~~~~i~gFed~IR~~i~~vV~~tyq 91 (167)
+.|..-..+| ||+... ..+|+..+|.+|+.+|+.+|+..|++++.. ++..+.|..|.|.-|++.+.++.++|+
T Consensus 52 ~dD~dnARfLWKRIP~AIKe~k~El~aaWgiGQkiWq~Df~GiYeaI~~~dWSeeak~imaAf~D~~~kR~FaLl~qAYs 131 (197)
T KOG4414|consen 52 HDDCDNARFLWKRIPPAIKEAKPELGAAWGIGQKIWQHDFAGIYEAINAHDWSEEAKDIMAAFRDATRKRAFALLLQAYS 131 (197)
T ss_pred hccchhHHHHHHhCCHHHhhcCchhhhhhhhhHHHHhcccchHHHHHhhhcchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444443 566555 378999999999999999999999999876 778889999999999999999999999
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCccccccccccccCCcccccc
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRI 162 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i~E~i~f~~~~~i 162 (167)
+|-.+.++.+|||+.++.-+.+ -++||+.|.. ++.+.+|+.+-. =.-+++|+++.++
T Consensus 132 sI~~~D~A~FlGl~~ddAtk~i----lEnGWqaDaa---sqMasl~kk~V~-------~a~~Vd~nK~~~L 188 (197)
T KOG4414|consen 132 SIIADDFAAFLGLPEDDATKGI----LENGWQADAA---SQMASLKKKAVA-------GALDVDFNKFIPL 188 (197)
T ss_pred HHHHHHHHHHhCCCHHHHHHHH----HHcccchhhH---HHHhhccchhcc-------cccccchhhceec
Confidence 9999999999999999888888 7889999855 234446543321 2235666665443
No 4
>PF03399 SAC3_GANP: SAC3/GANP/Nin1/mts3/eIF-3 p25 family; InterPro: IPR005062 This large family includes diverse proteins involved in large complexes [, , ]. The alignment contains one highly conserved negatively charged residue and one highly conserved positively charged residue that are probably important for the function of these proteins. The family includes the yeast nuclear export factor Sac3 [], and mammalian GANP/MCM3-associated proteins, which facilitate the nuclear localisation of MCM3, a protein that associates with chromatin in the G1 phase of the cell-cycle. The 26S protease (or 26S proteasome) is responsible for degrading ubiquitin conjugates. It consists of 19S regulatory complexes associated with the ends of 20S proteasomes. The 19S regulatory complex is composed of about 20 different polypeptides and confers ATP-dependence and substrate specificity to the 26S enzyme. The conserved region occurs at the C-terminal of the Nin1-like regulatory subunit [, , ]. This family includes several eukaryotic translation initiation factor 3 subunit 11 (eIF-3 p25) proteins. Eukaryotic initiation factor 3 (eIF3) is a multisubunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits [].; PDB: 3T5V_D.
Probab=99.19 E-value=5.4e-11 Score=93.99 Aligned_cols=103 Identities=22% Similarity=0.346 Sum_probs=83.8
Q ss_pred CHHHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHH--hhccchhhcccc-hHHHH
Q 031021 2 STQIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEA--AKHRNIVEAVPG-FEQAI 78 (167)
Q Consensus 2 ~~~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l--~~~~~~~~~i~g-Fed~I 78 (167)
..++++..||..|++-+.+||..++..+|+....++.|+....+...+.+++|..||..+ ++.+.+...+.. |.+.|
T Consensus 98 ~~ef~~y~lL~~l~~~~~~~~~~~l~~l~~~~~~~~~i~~al~l~~a~~~gny~~ff~l~~~~~~~~l~~~l~~~~~~~i 177 (204)
T PF03399_consen 98 EAEFIAYYLLYLLCQNNIPDFHMELELLPSEILSSPYIQFALELCRALMEGNYVRFFRLYRSKSAPYLFACLMERFFNRI 177 (204)
T ss_dssp HHHHHHHHHHHTT-T---THHHHHHTTS-HHHHTSHHHHHHHHHHHHH--TTHHHHHHHHT-TTS-HHHHHHHGGGHHHH
T ss_pred HHHHHHHHHHHHHHcccchHHHHHHHHCchhhhcCHHHHHHHHHHHHHHcCCHHHHHHHHhccCCChHHHHHHHHHHHHH
Confidence 357889999999999999999999999998888899999999999999999999999999 544545444444 99999
Q ss_pred HHHHHHHHHHhccc-ccHHHHHHHhcC
Q 031021 79 QSFAIHVLSLTYQK-IPRTVLAEAINL 104 (167)
Q Consensus 79 R~~i~~vV~~tyqs-I~~~~L~~~Lgl 104 (167)
|..+++.++.||++ |+.+.|+++||+
T Consensus 178 R~~al~~i~~ay~~~i~l~~l~~~L~F 204 (204)
T PF03399_consen 178 RLRALQSISKAYRSSIPLSFLAELLGF 204 (204)
T ss_dssp HHHHHHHHHHHS-T-EEHHHHHHHTT-
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHcCC
Confidence 99999999999999 999999999974
No 5
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=97.76 E-value=0.00058 Score=47.63 Aligned_cols=79 Identities=22% Similarity=0.281 Sum_probs=65.2
Q ss_pred HHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHH
Q 031021 41 TLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 41 ~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~ 113 (167)
.+..|-+.+.+++|..|-+.++.. +.+...+..+...+|...+..++..|++|+.+.+++.|+++.++++.++
T Consensus 2 ~~~~l~~~~~~~~~~~~~~~l~~~~~~~~~~~~l~~~~~~l~~~i~~~~l~~l~~~y~~i~~~~ia~~l~~~~~~vE~~l 81 (105)
T PF01399_consen 2 PYSELLRAFRSGDLQEFEEFLEKHSESLFKDPFLAEYVEQLKEKIRRRNLRQLSKPYSSISISEIAKALQLSEEEVESIL 81 (105)
T ss_dssp HHHHHHHHHHCT-HHHHHHHHHHTCHHHHHCTTHHHHHHHHHHHHHHHHHHHHHHC-SEEEHHHHHHHHTCCHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHhccchHHHHHHH
Confidence 356788889999999998887765 3444567778899999999999999999999999999999999999999
Q ss_pred HHHhhh
Q 031021 114 EHQKAN 119 (167)
Q Consensus 114 ~~~~~~ 119 (167)
.+.+..
T Consensus 82 ~~~I~~ 87 (105)
T PF01399_consen 82 IDLISN 87 (105)
T ss_dssp HHHHHT
T ss_pred HHHHHC
Confidence 777543
No 6
>KOG3151 consensus 26S proteasome regulatory complex, subunit RPN12/PSMD8 [Posttranslational modification, protein turnover, chaperones]
Probab=97.26 E-value=0.0012 Score=54.26 Aligned_cols=112 Identities=15% Similarity=0.232 Sum_probs=89.1
Q ss_pred HHHHHHcCCccchhhhhcCCCccccCc-hhHHHHHHHHHHHHcCChHHHHHHHhhcc--chhhcccchHHHHHHHHHHHH
Q 031021 10 LIKALMAMPAPDFSLCLFLIPERVQME-DQFKTLIVLSHYLETGRFRHFWDEAAKHR--NIVEAVPGFEQAIQSFAIHVL 86 (167)
Q Consensus 10 LlKaL~~~P~~DF~lc~~Ll~~~~~~~-~~i~~i~~L~~lLe~c~F~~FW~~l~~~~--~~~~~i~gFed~IR~~i~~vV 86 (167)
|+--|.+=--+||-.-+-+||.+.+.+ +=|...+.|.+-+=...|...|++.++.+ .+.-=|.=+.+.||..|+..+
T Consensus 107 LL~LLsqNRiaeFHteLe~lp~~~l~~~~~I~~~v~LEq~~MEGaYnKv~~a~~s~p~~~y~~FmdIl~~tiRdEIA~c~ 186 (260)
T KOG3151|consen 107 LLYLLSQNRIAEFHTELELLPKKILQHNPYISHPVSLEQSLMEGAYNKVLSAKQSIPSEEYTYFMDILLDTIRDEIAGCI 186 (260)
T ss_pred HHHHHHhccHHHHHHHHHhccHHHhhccchhhhHHHHHHHHHhhHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444589999999999987654 78899999999999999999999988763 222223334678999999999
Q ss_pred HHhcccccHHHHHHHhcCCc-hHHHHHHHHHhhhcCceee
Q 031021 87 SLTYQKIPRTVLAEAINLKG-LSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 87 ~~tyqsI~~~~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~ 125 (167)
-.+|..|+.+.-+++|+++. .++.++. .+.+|.++
T Consensus 187 EKsYd~l~~s~a~~~L~f~~~~e~~~~~----~~r~W~l~ 222 (260)
T KOG3151|consen 187 EKSYDKLSASDATQMLLFNNDKELKKFA----TERQWPLD 222 (260)
T ss_pred HHHHhhcCHHHHHHHHhcCChHHHHHHH----HhcCCccc
Confidence 99999999999999999865 4566665 77789987
No 7
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=96.72 E-value=0.0079 Score=41.18 Aligned_cols=65 Identities=15% Similarity=0.199 Sum_probs=52.3
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhc--CceeeccCCCceEEEeCC
Q 031021 71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC--GWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~--GW~~~~~~~~~~~vv~p~ 138 (167)
+..+...+|.....-++.+|++|+.+.|++.++++.++++.++.+.+.+. ..++|.. .+++.+-.
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~---~~~v~~~~ 69 (88)
T smart00088 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV---NGIVEFEE 69 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc---CCEEEECC
Confidence 45678899999999999999999999999999999999999998876542 3666643 24566643
No 8
>smart00753 PAM PCI/PINT associated module.
Probab=96.72 E-value=0.0079 Score=41.18 Aligned_cols=65 Identities=15% Similarity=0.199 Sum_probs=52.3
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhc--CceeeccCCCceEEEeCC
Q 031021 71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC--GWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~--GW~~~~~~~~~~~vv~p~ 138 (167)
+..+...+|.....-++.+|++|+.+.|++.++++.++++.++.+.+.+. ..++|.. .+++.+-.
T Consensus 3 ~~~l~~~~~~~~l~~l~~~y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~---~~~v~~~~ 69 (88)
T smart00753 3 VERLQRKIRLTNLLQLSEPYSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQV---NGIVEFEE 69 (88)
T ss_pred HHHHHHHHHHHHHHHHhHHhceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCc---CCEEEECC
Confidence 45678899999999999999999999999999999999999998876542 3666643 24566643
No 9
>KOG1861 consensus Leucine permease transcriptional regulator [Transcription]
Probab=96.48 E-value=0.039 Score=49.59 Aligned_cols=105 Identities=13% Similarity=0.193 Sum_probs=86.0
Q ss_pred ccchhhhhcCCCccccCchhHHHHHHHHHHHHcCChHHHHHHHhhccchhh-cccchHHHHHHHHHHHHHHhcc-cccHH
Q 031021 19 APDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVE-AVPGFEQAIQSFAIHVLSLTYQ-KIPRT 96 (167)
Q Consensus 19 ~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~-~i~gFed~IR~~i~~vV~~tyq-sI~~~ 96 (167)
.+|.+..+.=|.+...+++-|...+.+....-..+|..|+..+..-+.+-. .|.-|.|.-|+.++.++..+|+ +|+.+
T Consensus 403 ~~di~sll~~lt~E~ked~~V~hAL~vR~A~~~GNY~kFFrLY~~AP~M~~yLmdlF~erER~~Al~ii~KsyrP~i~~~ 482 (540)
T KOG1861|consen 403 YPDILSLLRDLTEEDKEDEAVAHALEVRSAVTLGNYHKFFRLYLTAPNMSGYLMDLFLERERKKALTIICKSYRPTITVD 482 (540)
T ss_pred chHHHHHHHhccHhhccCHHHHHHHHHHHHHHhccHHHHHHHHhhcccchhHHHHHHHHHHHHHHHHHHHHHcCCCccHH
Confidence 357777777777778889999999999999999999999999876443333 3556999999999999999999 99999
Q ss_pred HHHHHhcCCc-hHHHHHHHHHhhhcCceeecc
Q 031021 97 VLAEAINLKG-LSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 97 ~L~~~Lgl~~-~~l~~~~~~~~~~~GW~~~~~ 127 (167)
.+++-|.+.+ +....|+ +.++|+.+..
T Consensus 483 fi~~~laf~~~e~c~~~l----~~~~~~~~~~ 510 (540)
T KOG1861|consen 483 FIASELAFDSMEDCVNFL----NEQNLTYDSL 510 (540)
T ss_pred HHhhhhhhchHHHHHHHH----hccCcccccc
Confidence 9999998866 3344444 8889998754
No 10
>KOG2758 consensus Translation initiation factor 3, subunit e (eIF-3e) [Translation, ribosomal structure and biogenesis]
Probab=93.13 E-value=0.29 Score=42.57 Aligned_cols=59 Identities=12% Similarity=0.124 Sum_probs=50.7
Q ss_pred cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 65 RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 65 ~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
.-+++-...|.+.-|.+|+..-..-.|.|+.+.||.-|||++++.+.|+-..++...=.
T Consensus 322 fFLva~l~~F~E~ARl~ifEtfCRIHqcIti~mLA~kLnm~~eeaErwivnlIr~~rl~ 380 (432)
T KOG2758|consen 322 FFLVALLDEFLENARLLIFETFCRIHQCITIDMLADKLNMDPEEAERWIVNLIRTARLD 380 (432)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHheeHHHHHHHhcCCHHHHHHHHHHHHHHhhhh
Confidence 44456677899999999999999999999999999999999999999998777655433
No 11
>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=90.46 E-value=0.77 Score=28.79 Aligned_cols=48 Identities=13% Similarity=0.166 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHhccccc-HHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 76 QAIQSFAIHVLSLTYQKIP-RTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 76 d~IR~~i~~vV~~tyqsI~-~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
+.+++.+....-..-+.++ ...|++.+|++...+.+.+..+ .+.||-.
T Consensus 8 ~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L-~~~G~i~ 56 (66)
T cd07377 8 DQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALREL-EAEGLVE 56 (66)
T ss_pred HHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEE
Confidence 3444444433222333455 8999999999999999998777 7899943
No 12
>KOG2581 consensus 26S proteasome regulatory complex, subunit RPN3/PSMD3 [Posttranslational modification, protein turnover, chaperones]
Probab=90.28 E-value=0.9 Score=40.56 Aligned_cols=80 Identities=13% Similarity=0.277 Sum_probs=61.2
Q ss_pred hhHHHHHHHHHHHHcCChHHHHHHHhhc------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchH-H
Q 031021 37 DQFKTLIVLSHYLETGRFRHFWDEAAKH------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLS-L 109 (167)
Q Consensus 37 ~~i~~i~~L~~lLe~c~F~~FW~~l~~~------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~-l 109 (167)
..+..-+.|.+.....+-..|=+.+.+. .+....+..+.-.|=+--.+-||.+|++||....|.-||++.++ .
T Consensus 316 ksL~~Yf~Lt~AVr~gdlkkF~~~leq~k~~f~~D~ty~LivRLR~NVIkTgIR~ISlsYSRISl~DIA~kL~l~Seed~ 395 (493)
T KOG2581|consen 316 KSLRPYFKLTQAVRLGDLKKFNETLEQFKDKFQADGTYTLIVRLRHNVIKTGIRKISLSYSRISLQDIAKKLGLNSEEDA 395 (493)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhhCCcchHHHHHHHHHHHHhhhheeeeeeeccHHHHHHHhcCCCchhH
Confidence 3677778999999999999999888776 23333455566666677788999999999999999999997766 4
Q ss_pred HHHHHHH
Q 031021 110 DKFLEHQ 116 (167)
Q Consensus 110 ~~~~~~~ 116 (167)
+-.|.+.
T Consensus 396 EyiVakA 402 (493)
T KOG2581|consen 396 EYIVAKA 402 (493)
T ss_pred HHHHHHH
Confidence 4444433
No 13
>KOG0687 consensus 26S proteasome regulatory complex, subunit RPN7/PSMD6 [Posttranslational modification, protein turnover, chaperones]
Probab=86.37 E-value=12 Score=32.72 Aligned_cols=76 Identities=13% Similarity=0.173 Sum_probs=53.0
Q ss_pred HHHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccc-hHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHH
Q 031021 40 KTLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPG-FEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDK 111 (167)
Q Consensus 40 ~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~g-Fed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~ 111 (167)
+.+.++..-|-.|+|..|+..+... .-++..... |-.-+|.++-.=+=-+|++.+.+.+|+-.|+|-+=+++
T Consensus 257 ~~~~q~l~SLY~C~Y~~Ff~~L~~~~~~~lk~D~~l~~h~~yyvREMR~rvY~QlLESYrsl~l~~MA~aFgVSVefiDr 336 (393)
T KOG0687|consen 257 PSVSQLLNSLYECDYSDFFNDLAAVEAKQLKDDRYLGPHYRYYVREMRRRVYAQLLESYRSLTLESMAKAFGVSVEFIDR 336 (393)
T ss_pred chHHHHHHHHHhccHHHHHHHHHHHHHHhhccchhcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCchHHHHHh
Confidence 3445677788899999999987432 122221222 34457777777777899999999999999998765555
Q ss_pred HHHH
Q 031021 112 FLEH 115 (167)
Q Consensus 112 ~~~~ 115 (167)
.+.+
T Consensus 337 eL~r 340 (393)
T KOG0687|consen 337 ELGR 340 (393)
T ss_pred HHHH
Confidence 4433
No 14
>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=84.65 E-value=4.9 Score=24.04 Aligned_cols=46 Identities=20% Similarity=0.332 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 76 QAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 76 d~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
+..+..|+..+.. -..++...+|+.+|++...+...+++. .+.||-
T Consensus 2 ~~~~~~Il~~l~~-~~~~t~~ela~~~~is~~tv~~~l~~L-~~~g~I 47 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRITQKELAEKLGISRSTVNRYLKKL-EEKGLI 47 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS-HHHHHHHHTS-HHHHHHHHHHH-HHTTSE
T ss_pred CHHHHHHHHHHHH-cCCCCHHHHHHHhCCCHHHHHHHHHHH-HHCcCc
Confidence 4567777877777 455999999999999999998888776 666763
No 15
>COG5071 RPN5 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]
Probab=84.05 E-value=4.1 Score=35.42 Aligned_cols=57 Identities=18% Similarity=0.289 Sum_probs=42.8
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCC
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~ 138 (167)
.=+++|+.-|++|+..+|+.+|++++++.++++... ..+|-....-+-..+++-+-+
T Consensus 342 HN~RvI~~yYSrI~~~rl~~lld~~~s~te~~ISdl-VN~G~~yaKiNrpa~Ii~FEK 398 (439)
T COG5071 342 HNIRVIANYYSRIHCSRLGVLLDMSPSETEQFISDL-VNKGHFYAKINRPAQIISFEK 398 (439)
T ss_pred hhHhHHHHHhhhhhHHHHHHHHcCCHHHHHHHHHHH-HhcCcEEEEecCccceEEeec
Confidence 346899999999999999999999999999999776 567766532222124555533
No 16
>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=83.42 E-value=5.8 Score=24.32 Aligned_cols=46 Identities=15% Similarity=0.211 Sum_probs=33.6
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
.|...+-.+=..++...||+.||+|...+...++.. ++.|..+...
T Consensus 4 ~il~~L~~~~~~it~~eLa~~l~vS~rTi~~~i~~L-~~~~~~I~~~ 49 (55)
T PF08279_consen 4 QILKLLLESKEPITAKELAEELGVSRRTIRRDIKEL-REWGIPIESK 49 (55)
T ss_dssp HHHHHHHHTTTSBEHHHHHHHCTS-HHHHHHHHHHH-HHTT-EEEEE
T ss_pred HHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHH-HHCCCeEEee
Confidence 455666444445999999999999999999998877 7778666543
No 17
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=83.18 E-value=2.9 Score=25.52 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=27.8
Q ss_pred cc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.+ +...|++.+|++...+.+.++.+ .+.||-..
T Consensus 19 ~l~s~~~la~~~~vs~~tv~~~l~~L-~~~g~i~~ 52 (60)
T smart00345 19 KLPSERELAAQLGVSRTTVREALSRL-EAEGLVQR 52 (60)
T ss_pred cCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence 46 79999999999999999998777 67899643
No 18
>COG5187 RPN7 26S proteasome regulatory complex component, contains PCI domain [Posttranslational modification, protein turnover, chaperones]
Probab=82.84 E-value=5.4 Score=34.53 Aligned_cols=78 Identities=13% Similarity=0.154 Sum_probs=57.0
Q ss_pred chhHHHHHHHHHHHHcCChHHHHHHHhhc-------cchh-hcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCch
Q 031021 36 EDQFKTLIVLSHYLETGRFRHFWDEAAKH-------RNIV-EAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGL 107 (167)
Q Consensus 36 ~~~i~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~-~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~ 107 (167)
.+.+..|..|..-|-.|+|..|+..+... .-++ .-+.=|-..+|+++-.-+=-+|+..+.+.+|+-.|+|-+
T Consensus 267 ~e~l~sl~~l~~SLy~cdY~~~F~~ll~~~~n~L~~d~fl~rh~d~fvREMRrrvYaQlLESYr~lsl~sMA~tFgVSV~ 346 (412)
T COG5187 267 SEKLGSLVQLATSLYECDYGGDFMNLLYLFCNSLQDDVFLGRHVDLFVREMRRRVYAQLLESYRLLSLESMAQTFGVSVE 346 (412)
T ss_pred hhhhhhHHHHHHHHHHhccchhhHHHHHHHHhhccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHhCccHH
Confidence 45678888999999999999888765332 1112 222335556888887778889999999999999999875
Q ss_pred H----HHHHH
Q 031021 108 S----LDKFL 113 (167)
Q Consensus 108 ~----l~~~~ 113 (167)
= |.+|+
T Consensus 347 yvdrDLg~FI 356 (412)
T COG5187 347 YVDRDLGEFI 356 (412)
T ss_pred HHhhhHHhhC
Confidence 3 44554
No 19
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=81.78 E-value=6.3 Score=27.06 Aligned_cols=54 Identities=20% Similarity=0.189 Sum_probs=42.0
Q ss_pred HHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021 85 VLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF 141 (167)
Q Consensus 85 vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~ 141 (167)
+.-.++.-+|=+.|++.||+|...+-+.++.+ ++.|-.++...++|. .+|+.++
T Consensus 12 l~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~L-r~~G~~I~s~~~kGY--~L~~~~~ 65 (79)
T COG1654 12 LLLLTGNFVSGEKLAEELGISRTAVWKHIQQL-REEGVDIESVRGKGY--LLPQLPD 65 (79)
T ss_pred HHHcCCCcccHHHHHHHHCccHHHHHHHHHHH-HHhCCceEecCCCce--eccCccc
Confidence 34457778999999999999999999999887 899999987655454 4444443
No 20
>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=81.13 E-value=12 Score=26.00 Aligned_cols=62 Identities=15% Similarity=0.149 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHHHh------cccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCC
Q 031021 76 QAIQSFAIHVLSLT------YQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE 140 (167)
Q Consensus 76 d~IR~~i~~vV~~t------yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~ 140 (167)
-.+.+.+..+...+ .-.++...|++++|++.+.+-+.+.++ .+.||-.-.. + .+.|.+++|.
T Consensus 25 ~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g~sr~tVsr~L~~L-e~~GlI~r~~-~-~~~~~~n~~~ 92 (95)
T TIGR01610 25 GREFRVLLAIIRLTYGWNKKQDRVTATVIAELTGLSRTHVSDAIKSL-ARRRIIFRQG-M-MGIVGVNTPL 92 (95)
T ss_pred HHHHHHHHHHHHHHhCccccCCccCHHHHHHHHCcCHHHHHHHHHHH-HHCCCeeeec-C-CceeecCCCc
Confidence 34445555555433 567889999999999999888888777 7899997432 2 2578886654
No 21
>KOG1464 consensus COP9 signalosome, subunit CSN2 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=80.24 E-value=9 Score=33.03 Aligned_cols=79 Identities=13% Similarity=0.172 Sum_probs=67.1
Q ss_pred CchhHHHHHHHHHHHHcCChHHHHHHHhhc-------cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCch
Q 031021 35 MEDQFKTLIVLSHYLETGRFRHFWDEAAKH-------RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGL 107 (167)
Q Consensus 35 ~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~-------~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~ 107 (167)
.+|+|.....|-+.-+..+-.+|=+-++++ +-+.+.+..+...||.-++--+-.-|.+|..+-++.-|+++..
T Consensus 300 NdPEIlAMTnlv~aYQ~NdI~eFE~Il~~~~~~IM~DpFIReh~EdLl~niRTQVLlkLIkPYt~i~Ipfis~~Lnv~~~ 379 (440)
T KOG1464|consen 300 NDPEILAMTNLVAAYQNNDIIEFERILKSNRSNIMDDPFIREHIEDLLRNIRTQVLLKLIKPYTNIGIPFISKELNVPEA 379 (440)
T ss_pred CCHHHHHHHHHHHHHhcccHHHHHHHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHhccccccCchhhHhhcCCCHH
Confidence 589999999999999999999999888776 3444556677778888888778889999999999999999998
Q ss_pred HHHHHH
Q 031021 108 SLDKFL 113 (167)
Q Consensus 108 ~l~~~~ 113 (167)
++...+
T Consensus 380 dV~~LL 385 (440)
T KOG1464|consen 380 DVESLL 385 (440)
T ss_pred HHHHHH
Confidence 877765
No 22
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.19 E-value=2.9 Score=25.72 Aligned_cols=28 Identities=11% Similarity=0.268 Sum_probs=25.2
Q ss_pred cHHHHHHHhcCCchHHHHHHHHHhhhcCc
Q 031021 94 PRTVLAEAINLKGLSLDKFLEHQKANCGW 122 (167)
Q Consensus 94 ~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW 122 (167)
|.+.|++.+|++...+.+.++++ ++.||
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L-~~~G~ 54 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKEL-EEKGL 54 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH-HHCcC
Confidence 78999999999999999999887 77888
No 23
>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=79.66 E-value=3.2 Score=27.02 Aligned_cols=33 Identities=12% Similarity=0.253 Sum_probs=28.9
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++.+.+|+++|++...+.+.+.++ ++.||-.-
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l-~~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRL-KDEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHH-HHTTSEEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence 4689999999999999999988777 88999864
No 24
>KOG1463 consensus 26S proteasome regulatory complex, subunit RPN6/PSMD11 [Posttranslational modification, protein turnover, chaperones]
Probab=79.11 E-value=14 Score=32.62 Aligned_cols=116 Identities=16% Similarity=0.212 Sum_probs=77.4
Q ss_pred hhhhhcCCCccc-------------cCchhHHHHHHHHHHHHcCChHHHHHHHhhc------cchh-hcccchHHH-HHH
Q 031021 22 FSLCLFLIPERV-------------QMEDQFKTLIVLSHYLETGRFRHFWDEAAKH------RNIV-EAVPGFEQA-IQS 80 (167)
Q Consensus 22 F~lc~~Ll~~~~-------------~~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~------~~~~-~~i~gFed~-IR~ 80 (167)
+.||+-|+...- +..+.|..+-.+++.-.++....|=.++.+. ..++ .-...+.|. .-+
T Consensus 255 MlLcKIMln~~ddv~~lls~K~~l~y~g~~i~AmkavAeA~~nRSLkdF~~AL~~yk~eL~~D~ivr~Hl~~Lyd~lLEk 334 (411)
T KOG1463|consen 255 MLLCKIMLNLPDDVAALLSAKLALKYAGRDIDAMKAVAEAFGNRSLKDFEKALADYKKELAEDPIVRSHLQSLYDNLLEK 334 (411)
T ss_pred HHHHHHHhcCHHHHHHHHhhHHHHhccCcchHHHHHHHHHhcCCcHHHHHHHHHHhHHHHhcChHHHHHHHHHHHHHHHH
Confidence 457777776542 2457788888999999999999998877653 2222 223344553 446
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhc--CceeeccCCCceEEEeCCCC
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC--GWILEGDQSTSQLIVLPPNE 140 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~--GW~~~~~~~~~~~vv~p~n~ 140 (167)
-+|++|- -|+++..+..++.+|++-+.+++-+.+-+-.. -=+.| +|+|-+++++..+
T Consensus 335 nl~riIE-PyS~Vei~hIA~~IGl~~~~VEkKLsqMILDKkf~G~LD--Qg~g~Liv~~e~~ 393 (411)
T KOG1463|consen 335 NLCRIIE-PYSRVEISHIAEVIGLDVPQVEKKLSQMILDKKFYGTLD--QGEGCLIVFEEPP 393 (411)
T ss_pred hHHHHcC-chhhhhHHHHHHHHCCCcHHHHHHHHHHHHHHHhhcccc--cCCCeEEEeCCCC
Confidence 6777774 69999999999999999888777664433222 12333 3556778886443
No 25
>PF10255 Paf67: RNA polymerase I-associated factor PAF67; InterPro: IPR019382 RNA polymerase I is a multi-subunit enzyme and its transcription competence is dependent on the presence of PAF67 [].
Probab=79.03 E-value=22 Score=31.69 Aligned_cols=103 Identities=17% Similarity=0.287 Sum_probs=63.8
Q ss_pred chhhhhcCCCccccCchhHHHHH--HHHH---HHHcCChHHHHHHHhhc-cchhhcc---------------------cc
Q 031021 21 DFSLCLFLIPERVQMEDQFKTLI--VLSH---YLETGRFRHFWDEAAKH-RNIVEAV---------------------PG 73 (167)
Q Consensus 21 DF~lc~~Ll~~~~~~~~~i~~i~--~L~~---lLe~c~F~~FW~~l~~~-~~~~~~i---------------------~g 73 (167)
.+..|.+|-|.+. ++.|...+ .-++ .|+..+-..||+..... |.+++.+ .-
T Consensus 221 LlAic~~l~p~~l--de~i~~~lkeky~ek~~kmq~gd~~~f~elF~~acPKFIsp~~pp~~~~~~~~~~~e~~~~Ql~~ 298 (404)
T PF10255_consen 221 LLAICLSLCPQRL--DESISSQLKEKYGEKMEKMQRGDEEAFEELFSFACPKFISPVSPPDYDGPSQNKNKEPYRRQLKL 298 (404)
T ss_pred HHHHHHHhCCCCC--CHHHHHHHHHHHHHHHHHHHccCHHHHHHHHHhhCCCccCCCCCCCcccccchhhhhHHHHHHHH
Confidence 4577888888773 55554433 1222 47777889999876543 3333322 12
Q ss_pred hHHHHHH----HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHH---HHhhhc-Cceee
Q 031021 74 FEQAIQS----FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLE---HQKANC-GWILE 125 (167)
Q Consensus 74 Fed~IR~----~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~---~~~~~~-GW~~~ 125 (167)
|.+.|+. -..+..-.=|++|+.+.||.+|+++++++...+- +..+.. -|+..
T Consensus 299 Fl~eV~~q~~l~~lRSyLKLYtti~l~KLA~fl~vd~~~lr~~Ll~~K~k~~ql~~w~~g 358 (404)
T PF10255_consen 299 FLDEVKQQQKLPTLRSYLKLYTTIPLEKLASFLDVDEEELRSQLLCFKHKSRQLVRWSGG 358 (404)
T ss_pred HHHHHHHhhhhhHHHHHHHhhcCCCHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhccCC
Confidence 3333332 2234444569999999999999999988877753 233334 58754
No 26
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=78.68 E-value=2.4 Score=31.51 Aligned_cols=29 Identities=21% Similarity=0.398 Sum_probs=22.1
Q ss_pred cHHHHHHHhcCCchHHHHHHHHHhhhcCceeec
Q 031021 94 PRTVLAEAINLKGLSLDKFLEHQKANCGWILEG 126 (167)
Q Consensus 94 ~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~ 126 (167)
..+.||+++|++...+.+|+ ++.||+-+.
T Consensus 2 T~eELA~~tG~srQTINrWv----RkegW~T~p 30 (122)
T PF07037_consen 2 TPEELAELTGYSRQTINRWV----RKEGWKTEP 30 (122)
T ss_pred CHHHHHHHhCccHHHHHHHH----HhcCceecc
Confidence 45789999999875555555 999999763
No 27
>PF10537 WAC_Acf1_DNA_bd: ATP-utilising chromatin assembly and remodelling N-terminal; InterPro: IPR013136 ACF (for ATP-utilising chromatin assembly and remodeling factor) is a chromatin-remodeling complex that catalyzes the ATP-dependent assembly of periodic nucleosome arrays. This reaction utilises the energy of ATP hydrolysis by ISWI, the smaller of the two subunits of ACF. Acf1, the large subunit of ACF, is essential for the full activity of the complex. The WAC (WSTF/Acf1/cbp146) domain is an ~110-residue module present at the N-termini of Acf1-related proteins in a variety of organisms. It is found in association with other domains such as the bromodomain, the PHD-type zinc finger, DDT or WAKS. The DNA-binding region of Acf1 includes the WAC domain, which is necessary for the efficient binding of ACF complex to DNA. It seems probable that the WAC domain will be involved in DNA binding in other related factors [, ]. Some proteins known to contain a WAC domain are the Drosophila melanogaster (Fruit fly) ATP-dependent chromatin assembly factor large subunit Acf1, human WSTF (Williams syndrome transcription factor), mouse cbp146, yeast imitation switch two complex protein 1 (ITC1 or YGL133w), and yeast protein YPL216w.
Probab=77.68 E-value=1.8 Score=31.23 Aligned_cols=60 Identities=8% Similarity=0.241 Sum_probs=48.5
Q ss_pred hhHHHHHHHHHHHHcCChHH-----HHHHHhhccchhhcccc-hHHHHHHHHHHHHHHhccccc-HHHH
Q 031021 37 DQFKTLIVLSHYLETGRFRH-----FWDEAAKHRNIVEAVPG-FEQAIQSFAIHVLSLTYQKIP-RTVL 98 (167)
Q Consensus 37 ~~i~~i~~L~~lLe~c~F~~-----FW~~l~~~~~~~~~i~g-Fed~IR~~i~~vV~~tyqsI~-~~~L 98 (167)
+=+.++....+..|+|...+ |.+++++...-...+.. |=+..|.-|++.|. |+.++ .+.|
T Consensus 18 ~Y~~R~~~y~~~vwtC~~TGk~~LTy~eAl~SE~~a~~~l~~~fP~~l~~piL~~v~--~s~~~rld~L 84 (102)
T PF10537_consen 18 EYLKRMILYNQRVWTCEITGKSNLTYFEALESEKEARKKLEERFPEELREPILRLVQ--FSTRSRLDDL 84 (102)
T ss_pred HHHHHHHHHhCCeeEEecCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH--ccccccHHHH
Confidence 45688888999999999986 88899888666667777 98999999999998 66665 4444
No 28
>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=77.65 E-value=6 Score=25.02 Aligned_cols=45 Identities=13% Similarity=0.228 Sum_probs=33.4
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
+-.|++.|......++...|++.+|++...+-..+++. .+.||-.
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L-~~~glv~ 49 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKL-EEKGLVE 49 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHH-HHTTSEE
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEE
Confidence 34567777778899999999999999998888888776 6789995
No 29
>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=76.61 E-value=6.7 Score=23.58 Aligned_cols=45 Identities=18% Similarity=0.268 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 76 QAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 76 d~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
|..|..|+..+.. ...+...+++-+|++...+-..+... .+.|+.
T Consensus 1 d~~R~~Il~~L~~--~~~~~~el~~~l~~s~~~vs~hL~~L-~~~glV 45 (47)
T PF01022_consen 1 DPTRLRILKLLSE--GPLTVSELAEELGLSQSTVSHHLKKL-REAGLV 45 (47)
T ss_dssp SHHHHHHHHHHTT--SSEEHHHHHHHHTS-HHHHHHHHHHH-HHTTSE
T ss_pred CHHHHHHHHHHHh--CCCchhhHHHhccccchHHHHHHHHH-HHCcCe
Confidence 3578889888888 78889999999999998888888665 667764
No 30
>PF04801 Sin_N: Sin-like protein conserved region; InterPro: IPR006886 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. RNA polymerase III (Pol III) is a complex consisting of 17 subunits, which synthesizes small RNAs, such as 5S rRNA and tRNAs. Pol III is essential for efficient transcription from both the type 2 VAI and type 3 U6 RNA polymerase III promoters and plays a key role in sensing and limiting infection by intracellular bacteria and DNA viruses. Subunit c5 is a specific peripheric component of RNA polymerase III complex. ; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=76.33 E-value=2.7 Score=37.09 Aligned_cols=101 Identities=15% Similarity=0.223 Sum_probs=68.1
Q ss_pred CCccchhhhhcCCCcccc-CchhHHHHHHHHHHHHcCChHHHHHHHhhccchhh-cccchHHHHHHHHHHHHHHhccccc
Q 031021 17 MPAPDFSLCLFLIPERVQ-MEDQFKTLIVLSHYLETGRFRHFWDEAAKHRNIVE-AVPGFEQAIQSFAIHVLSLTYQKIP 94 (167)
Q Consensus 17 ~P~~DF~lc~~Ll~~~~~-~~~~i~~i~~L~~lLe~c~F~~FW~~l~~~~~~~~-~i~gFed~IR~~i~~vV~~tyqsI~ 94 (167)
.+---|.--+.++|++.. .++-|..|-..|-++..+ |.. ++ .-+.+ .-++.....|.+|+-....+ ..|+
T Consensus 282 ~~v~~Fs~L~~ll~~~~~~~~~lL~~L~~~AvLV~G~-----WV~-kS-~ll~~~~~~e~~~~aRD~iL~~F~~~-~~v~ 353 (421)
T PF04801_consen 282 ARVISFSELRKLLPSNSDTDEELLRALQQVAVLVQGN-----WVV-KS-ELLYPDVPAEQLCRARDYILLLFTKS-RYVK 353 (421)
T ss_pred CCcccHHHHHHHhccccchHHHHHHHHHhheEEEeee-----EEE-eh-hhccCCCcchhhhhhHHHHHHHhcCC-Ccee
Confidence 344556666667776664 344555554555544443 211 12 11222 23558889999999999998 7799
Q ss_pred HHHHHHHhcCCchHHHHHHHHHhhhc----Cceee
Q 031021 95 RTVLAEAINLKGLSLDKFLEHQKANC----GWILE 125 (167)
Q Consensus 95 ~~~L~~~Lgl~~~~l~~~~~~~~~~~----GW~~~ 125 (167)
+..|....+++.+++.++++..+... ||++-
T Consensus 354 r~~l~~~~~l~~~~~~eiL~~~a~~~~~~~~W~lk 388 (421)
T PF04801_consen 354 RKELMSATKLPPEDVKEILKEIAVLRPSNRGWKLK 388 (421)
T ss_pred HHHhhhhcCCCHHHHHHHHHHHhhccCCCCceEEc
Confidence 99999999999999989888777655 78874
No 31
>KOG0686 consensus COP9 signalosome, subunit CSN1 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=76.10 E-value=10 Score=34.03 Aligned_cols=110 Identities=18% Similarity=0.121 Sum_probs=75.0
Q ss_pred HHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCCh-------HHHHHHHhhc-------cchhh
Q 031021 4 QIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGRF-------RHFWDEAAKH-------RNIVE 69 (167)
Q Consensus 4 ~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~F-------~~FW~~l~~~-------~~~~~ 69 (167)
|++.-..+.||.-|-..|.-+ .+-.++..+....|.-.|+.|-| ..--+.+++. .-+.+
T Consensus 270 dv~iYggLcALAtfdr~~Lk~-------~vi~n~~Fk~flel~Pqlr~il~~fy~sky~~cl~~L~~~k~~llLD~yLap 342 (466)
T KOG0686|consen 270 DVAIYGGLCALATFDRQDLKL-------NVIKNESFKLFLELEPQLREILFKFYSSKYASCLELLREIKPRLLLDMYLAP 342 (466)
T ss_pred hhHHHHhhHhhccCCHHHHHH-------HHHcchhhhhHHhcChHHHHHHHHHhhhhHHHHHHHHHHhccceeechhcch
Confidence 455566666666655555211 11134555666666666665544 3333334333 33445
Q ss_pred cccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhc
Q 031021 70 AVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANC 120 (167)
Q Consensus 70 ~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~ 120 (167)
-+..+.+.||++.+-=.-+-|.+++-..+|+-.|.+...+++.+.+++...
T Consensus 343 hVd~Ly~~IR~r~llqy~~py~s~~m~~mA~af~~sv~~le~~l~~LI~~~ 393 (466)
T KOG0686|consen 343 HVDNLYSLIRNRALLQYLSPYSSADMSKMAEAFNTSVAILESELLELILEG 393 (466)
T ss_pred hHHHHHHHHHHhhHHHhcCccccchHHHHHHHhcccHHHHHHHHHHHHHcc
Confidence 678899999999999999999999999999999999999999888876543
No 32
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=74.22 E-value=14 Score=24.18 Aligned_cols=49 Identities=12% Similarity=0.149 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHhcc-cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 76 QAIQSFAIHVLSLTYQ-KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 76 d~IR~~i~~vV~~tyq-sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+..++.|+..+...=. .++...|+..||++...+.+.+... .+.|+...
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L-~~~G~V~~ 54 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSL-EKKGKVCK 54 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEe
Confidence 5678889999987633 3999999999999999999998776 77788754
No 33
>KOG1498 consensus 26S proteasome regulatory complex, subunit RPN5/PSMD12 [Posttranslational modification, protein turnover, chaperones]
Probab=73.53 E-value=12 Score=33.35 Aligned_cols=87 Identities=22% Similarity=0.305 Sum_probs=56.0
Q ss_pred hhHHHHHHHHHHHHcCChHHHHHHHhhc---cchh---h----cccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCc
Q 031021 37 DQFKTLIVLSHYLETGRFRHFWDEAAKH---RNIV---E----AVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKG 106 (167)
Q Consensus 37 ~~i~~i~~L~~lLe~c~F~~FW~~l~~~---~~~~---~----~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~ 106 (167)
|.-..+..|=---|--+|+.+|+.+... .++. . ....+...|=+.=.++|+.=|++|+..+++++||++.
T Consensus 288 p~~k~lLklfv~~EL~rw~s~~~~yg~~l~~~~~~~~~~~gek~~~dL~~RIiEHNiRiiA~yYSrIt~~rl~eLLdl~~ 367 (439)
T KOG1498|consen 288 PDYKELLKLFVTMELIRWVSLVESYGDELRTNDFFDGGEEGEKRWSDLKLRIIEHNIRIIAKYYSRITLKRLAELLDLPV 367 (439)
T ss_pred ccHHHHHHHHHhcceeeehhHhhhhHHHHhhcccccccchhhhHHHHHHHHHHHHHHHHHHHHHhhccHHHHHHHhCCCH
Confidence 3444555555555556777777754321 1111 1 1222333444445689999999999999999999999
Q ss_pred hHHHHHHHHHhhhcCcee
Q 031021 107 LSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 107 ~~l~~~~~~~~~~~GW~~ 124 (167)
++.++++... ...|=..
T Consensus 368 ee~E~~LS~l-v~t~ti~ 384 (439)
T KOG1498|consen 368 EEMEKFLSDL-VVTGTIY 384 (439)
T ss_pred HHHHHHHHHH-HhccceE
Confidence 9999999776 4455443
No 34
>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=73.04 E-value=7.2 Score=22.21 Aligned_cols=28 Identities=18% Similarity=0.356 Sum_probs=19.0
Q ss_pred ccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 93 IPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
++.+.+|++||++.+.+-..+.++ ++.|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l-~~~g 30 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKL-ERQG 30 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH-HHTT
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHH-HHcC
Confidence 678899999999988777766555 4444
No 35
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=72.74 E-value=9.3 Score=25.68 Aligned_cols=50 Identities=6% Similarity=0.115 Sum_probs=28.6
Q ss_pred ccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 71 VPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 71 i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
|+++.+ ..|+.|+..-+.-+.+.+..++|++.+.-.+.-++.-+++-|..
T Consensus 28 I~~L~~----~~~~~iA~~i~gks~eeir~~fgi~~d~t~eee~~i~~e~~w~~ 77 (78)
T PF01466_consen 28 IKGLLD----LCCKYIANMIKGKSPEEIRKYFGIENDLTPEEEEEIRKENEWAF 77 (78)
T ss_dssp -HHHHH----HHHHHHHHHHTTS-HHHHHHHHT---TSSHHHHHHHHHHCCCTB
T ss_pred chHHHH----HHHHHHHHHhcCCCHHHHHHHcCCCCCCCHHHHHHHHHHcchhc
Confidence 455544 55666666666789999999999866432232234446678864
No 36
>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=71.11 E-value=17 Score=25.73 Aligned_cols=70 Identities=10% Similarity=0.110 Sum_probs=47.2
Q ss_pred ChHHHHHHHhhccchhhcccchHHHHHHHHHHHHH--Hhc-ccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 53 RFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLS--LTY-QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 53 ~F~~FW~~l~~~~~~~~~i~gFed~IR~~i~~vV~--~ty-qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
+|-.||..++.-.+.+..--|+ ..-.-.++..+. ... ..++...|++.++++...+-..+... .+.||-.
T Consensus 2 ~~~~~~~~~~~~~~~l~~~~~l-s~~q~~vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~L-e~kg~I~ 74 (109)
T TIGR01889 2 DLLSLYLYIKSLKRYLKKEFNL-SLEELLILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKL-SKKGYLS 74 (109)
T ss_pred cHHHHHHHHHHHHHHHHHHcCC-CHHHHHHHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHH-HHCCCEe
Confidence 4667777766543333322233 123344666776 333 45999999999999999888888776 7899987
No 37
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=70.05 E-value=8.8 Score=22.34 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=27.8
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++...+++.+|++...+.+.+... .+.||-..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L-~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRL-EKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence 4678899999999998888888776 78899864
No 38
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=70.02 E-value=14 Score=23.26 Aligned_cols=50 Identities=14% Similarity=0.220 Sum_probs=40.8
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 73 GFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 73 gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
.+.+..|..|+..+ ......+...|++-||++...+-..++.. .+.|+-.
T Consensus 6 aL~~p~R~~Il~~L-~~~~~~t~~ela~~l~~~~~t~s~hL~~L-~~aGli~ 55 (61)
T PF12840_consen 6 ALSDPTRLRILRLL-ASNGPMTVSELAEELGISQSTVSYHLKKL-EEAGLIE 55 (61)
T ss_dssp HHTSHHHHHHHHHH-HHCSTBEHHHHHHHHTS-HHHHHHHHHHH-HHTTSEE
T ss_pred HhCCHHHHHHHHHH-hcCCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCeE
Confidence 34567899999999 77889999999999999998888888666 6778764
No 39
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=68.03 E-value=22 Score=20.77 Aligned_cols=35 Identities=17% Similarity=0.271 Sum_probs=29.3
Q ss_pred cccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 90 YQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 90 yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
...++...+++.+|++...+...+..+ .+.||-..
T Consensus 12 ~~~~s~~~l~~~l~~s~~tv~~~l~~L-~~~g~i~~ 46 (53)
T smart00420 12 QGKVSVEELAELLGVSEMTIRRDLNKL-EEQGLLTR 46 (53)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence 356899999999999999988888776 67799654
No 40
>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=67.61 E-value=22 Score=22.73 Aligned_cols=51 Identities=12% Similarity=0.178 Sum_probs=40.5
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeec
Q 031021 73 GFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEG 126 (167)
Q Consensus 73 gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~ 126 (167)
||.+.=.+....++ .....+...+++-+|++...+...++.+ .+.||....
T Consensus 5 gLs~~E~~vy~~Ll--~~~~~t~~eIa~~l~i~~~~v~~~L~~L-~~~GlV~~~ 55 (68)
T PF01978_consen 5 GLSENEAKVYLALL--KNGPATAEEIAEELGISRSTVYRALKSL-EEKGLVERE 55 (68)
T ss_dssp CHHHHHHHHHHHHH--HHCHEEHHHHHHHHTSSHHHHHHHHHHH-HHTTSEEEE
T ss_pred CcCHHHHHHHHHHH--HcCCCCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEEE
Confidence 56555555555555 7888999999999999999999999887 789998753
No 41
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=67.53 E-value=5.1 Score=33.61 Aligned_cols=30 Identities=13% Similarity=0.283 Sum_probs=25.5
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.+....+++.||+++..+.+|- ...||+.+
T Consensus 19 gmk~~dIAeklGvspntiksWK----rr~gWs~~ 48 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWK----RRDGWSAT 48 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHH----HhcCCCch
Confidence 3778889999999999988887 88899743
No 42
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=66.83 E-value=28 Score=26.57 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=28.7
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++.+.+|++||++.+.+-..+.++ ++.|+-.-
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l-~~~g~I~~ 181 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGEL-SREGYIRS 181 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHH-HHCCCEEc
Confidence 5789999999999999888888777 78899864
No 43
>KOG1076 consensus Translation initiation factor 3, subunit c (eIF-3c) [Translation, ribosomal structure and biogenesis]
Probab=66.77 E-value=11 Score=35.94 Aligned_cols=80 Identities=11% Similarity=0.297 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHcCChHHHHHHHhhc----------cchhhcccch--HHHHHHHHHHHHHHhcccccHHHHHHHhcCCch
Q 031021 40 KTLIVLSHYLETGRFRHFWDEAAKH----------RNIVEAVPGF--EQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGL 107 (167)
Q Consensus 40 ~~i~~L~~lLe~c~F~~FW~~l~~~----------~~~~~~i~gF--ed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~ 107 (167)
..+...+..|...+|..-.+.+..+ ..+...+..+ +++.|.|.+.- +..|.|+|...||.+.+|+..
T Consensus 655 ehVvaAsKAm~~Gnw~~c~~fi~nn~KvW~Lfpn~d~V~~Ml~~rIqEEsLRTYLftY-ss~Y~SvSl~~LA~mFdLp~~ 733 (843)
T KOG1076|consen 655 EHVVAASKAMQKGNWQKCFEFIVNNIKVWDLFPNADTVLDMLTERIQEESLRTYLFTY-SSVYDSVSLAKLADMFDLPEP 733 (843)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHhhhhHHHhcccHHHHHHHHHHHHHHHHHHHHHHHh-hhhhhhccHHHHHHHhCCCch
Confidence 4566788899999987755543332 3333333332 55666666544 555999999999999999998
Q ss_pred HHHHHHHHHhhhc
Q 031021 108 SLDKFLEHQKANC 120 (167)
Q Consensus 108 ~l~~~~~~~~~~~ 120 (167)
.+-..+.+.+.+.
T Consensus 734 ~VhsIiSkmiine 746 (843)
T KOG1076|consen 734 KVHSIISKMIINE 746 (843)
T ss_pred hHHHHHHHHHHHH
Confidence 8877776655443
No 44
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=65.72 E-value=22 Score=28.02 Aligned_cols=33 Identities=12% Similarity=0.237 Sum_probs=28.3
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++...+|++||++...+-..++++ ++.||-.-
T Consensus 184 ~lt~~~iA~~lG~sr~tvsR~l~~l-~~~g~I~~ 216 (235)
T PRK11161 184 TMTRGDIGNYLGLTVETISRLLGRF-QKSGMLAV 216 (235)
T ss_pred cccHHHHHHHhCCcHHHHHHHHHHH-HHCCCEEe
Confidence 4788999999999999988888766 88999764
No 45
>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=62.25 E-value=29 Score=21.52 Aligned_cols=34 Identities=18% Similarity=0.267 Sum_probs=29.0
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
..++...+++.+|++...+.+.+..+ .+.||-..
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L-~~~g~i~~ 57 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKEL-EEEGLISR 57 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEe
Confidence 35899999999999999988888777 67899864
No 46
>PF05687 DUF822: Plant protein of unknown function (DUF822); InterPro: IPR008540 This group of proteins contains members of the BZR1/LAT61 family of plant transcriptional repressors involved in controlling the response to Brassinosteroids (BRs). BRs are plant hormones that play essential roles in growth and development. BZR1 binds directly to DNA repressing the synthesis of genes involved in BR synthesis. Phosphorylation of BZR1 by BIN1 targets BZR1 to the 20S proteosome, while dephosphorylation leads to nuclear accumulation of BZR1 [].
Probab=61.71 E-value=7.3 Score=29.91 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=18.8
Q ss_pred hHHHHHHHHHhhhcCceeeccCCCceEEE
Q 031021 107 LSLDKFLEHQKANCGWILEGDQSTSQLIV 135 (167)
Q Consensus 107 ~~l~~~~~~~~~~~GW~~~~~~~~~~~vv 135 (167)
.+..+.++.+|.+.||+++.| |.++.
T Consensus 45 aD~NeVLkALc~eAGw~Ve~D---GTtyr 70 (150)
T PF05687_consen 45 ADNNEVLKALCREAGWTVEPD---GTTYR 70 (150)
T ss_pred CCHHHHHHHHHHhCCEEEccC---CCeec
Confidence 346667777789999999965 45554
No 47
>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=59.95 E-value=31 Score=21.62 Aligned_cols=43 Identities=19% Similarity=0.238 Sum_probs=34.3
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
..|...+.. -..++...|++.||+|...+..-+... .+.|.-.
T Consensus 3 ~~Il~~l~~-~~~~s~~ela~~~~VS~~TiRRDl~~L-~~~g~i~ 45 (57)
T PF08220_consen 3 QQILELLKE-KGKVSVKELAEEFGVSEMTIRRDLNKL-EKQGLIK 45 (57)
T ss_pred HHHHHHHHH-cCCEEHHHHHHHHCcCHHHHHHHHHHH-HHCCCEE
Confidence 456666644 589999999999999999998888776 6778744
No 48
>PF06627 DUF1153: Protein of unknown function (DUF1153); InterPro: IPR009534 This family consists of several short, hypothetical bacterial proteins of unknown function.; PDB: 2OA4_A 2JRT_A.
Probab=59.90 E-value=18 Score=25.49 Aligned_cols=38 Identities=11% Similarity=0.002 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHH
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEH 115 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~ 115 (167)
+|+...-|-+..|--|+.+.-++--||+.++++.|.+.
T Consensus 35 a~RKAaVV~aV~~Glis~~EA~~rY~Ls~eEf~~W~~a 72 (90)
T PF06627_consen 35 ARRKAAVVRAVRGGLISVEEACRRYGLSEEEFESWQRA 72 (90)
T ss_dssp HHHHHHHHHHHHCTTS-HHHHHHCTTSSHHHHHHHHHH
T ss_pred hhHHHHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 67888889999999999999999999999999998744
No 49
>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=59.71 E-value=16 Score=22.23 Aligned_cols=44 Identities=14% Similarity=0.235 Sum_probs=35.5
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.|+..++.+=..++...+++-+|++...+-..++.. .+.||-..
T Consensus 7 ~iL~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL-~~~g~v~~ 50 (52)
T PF09339_consen 7 RILEALAESGGPLTLSEIARALGLPKSTVHRLLQTL-VEEGYVER 50 (52)
T ss_dssp HHHHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHH-HHTTSEEE
T ss_pred HHHHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHH-HHCcCeec
Confidence 466777777788899999999999999888888776 67899764
No 50
>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=59.08 E-value=33 Score=21.09 Aligned_cols=45 Identities=11% Similarity=0.193 Sum_probs=33.5
Q ss_pred HHHHHHHHHhccc-ccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 80 SFAIHVLSLTYQK-IPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 80 ~~i~~vV~~tyqs-I~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
-.++..|...=.. ++...|++.+|++...+-..++.. .+.||...
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L-~~~Glv~r 53 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRL-EKKGLVER 53 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHH-HHTTSEEE
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEE
Confidence 3455555554443 899999999999998888888776 78899864
No 51
>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=57.80 E-value=23 Score=23.16 Aligned_cols=45 Identities=11% Similarity=0.212 Sum_probs=29.0
Q ss_pred cccHHHHHHHhcC--CchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCC
Q 031021 92 KIPRTVLAEAINL--KGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE 140 (167)
Q Consensus 92 sI~~~~L~~~Lgl--~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~ 140 (167)
.++.+.+.++||+ +.+++.+.+ ++.|-+++..+++.-.|.+|.-.
T Consensus 5 ~~~~~~i~~~lG~~i~~~~i~~~L----~~lg~~~~~~~~~~~~v~vP~~R 51 (70)
T PF03484_consen 5 TLSLDKINKLLGIDISPEEIIKIL----KRLGFKVEKIDGDTLEVTVPSYR 51 (70)
T ss_dssp EEEHHHHHHHHTS---HHHHHHHH----HHTT-EEEE-CTTEEEEEEETTS
T ss_pred EecHHHHHHHhCCCCCHHHHHHHH----HHCCCEEEECCCCEEEEEcCCCc
Confidence 3577889999996 445555555 88899998633545567777544
No 52
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=57.66 E-value=22 Score=28.27 Aligned_cols=32 Identities=19% Similarity=0.240 Sum_probs=27.4
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
.++...||++||++.+.+-..++++ ++.|+-.
T Consensus 179 ~lt~~~IA~~lGisretlsR~L~~L-~~~GlI~ 210 (230)
T PRK09391 179 PMSRRDIADYLGLTIETVSRALSQL-QDRGLIG 210 (230)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHH-HHCCcEE
Confidence 4678999999999999888888776 8889885
No 53
>PF12643 MazG-like: MazG-like family
Probab=56.50 E-value=40 Score=23.98 Aligned_cols=38 Identities=21% Similarity=0.369 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhh
Q 031021 75 EQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKA 118 (167)
Q Consensus 75 ed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~ 118 (167)
.+.|+..++.++..+| .||.=||++..++++.+.+.++
T Consensus 34 ~e~i~deLAdvii~~y------lLa~rLGid~~~lD~~i~~KL~ 71 (98)
T PF12643_consen 34 QEAIKDELADVIIYCY------LLADRLGIDFRELDEIIKEKLK 71 (98)
T ss_pred HHHHHHHHHHHHHHHH------HHHHHhCCCHHHHHHHHHHHHH
Confidence 4789999999999998 6999999998888888877654
No 54
>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=55.45 E-value=53 Score=21.01 Aligned_cols=43 Identities=14% Similarity=0.152 Sum_probs=33.4
Q ss_pred HHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 82 AIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 82 i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
+...++..+ ++...|++.+|++...+.+.+... .+.|+-+...
T Consensus 5 il~~L~~~~--~~~~eLa~~l~vS~~tv~~~l~~L-~~~g~~i~~~ 47 (69)
T TIGR00122 5 LLALLADNP--FSGEKLGEALGMSRTAVNKHIQTL-REWGVDVLTV 47 (69)
T ss_pred HHHHHHcCC--cCHHHHHHHHCCCHHHHHHHHHHH-HHCCCeEEec
Confidence 445566665 458899999999999988888776 7889977644
No 55
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=55.34 E-value=10 Score=23.37 Aligned_cols=22 Identities=36% Similarity=0.554 Sum_probs=14.0
Q ss_pred cCCchHHHHHHHHHhhhcCceee
Q 031021 103 NLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 103 gl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
++|+++|+++ +.|+.+.||--+
T Consensus 23 ~~s~~~L~k~-~~wld~rgWwYe 44 (45)
T PF12123_consen 23 PLSDAELDKF-TAWLDERGWWYE 44 (45)
T ss_dssp ---HHHHHHH-HHHHHHTT--EE
T ss_pred CCCHHHHHHH-HHHHHhcCcEEe
Confidence 4677888886 889999999653
No 56
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=54.80 E-value=37 Score=20.25 Aligned_cols=35 Identities=17% Similarity=0.210 Sum_probs=29.5
Q ss_pred cccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 90 YQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 90 yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
-..++...+++.||++...+.+.++.. .+.||-..
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L-~~~g~i~~ 42 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKL-REAGLVES 42 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHH-HHCCCeee
Confidence 567788899999999999999988776 67899874
No 57
>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=54.78 E-value=43 Score=21.38 Aligned_cols=37 Identities=14% Similarity=0.150 Sum_probs=30.5
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeec
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEG 126 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~ 126 (167)
.-..++...+|+.||+++..+-+.++++ .+.|+-.-.
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L-~~~GlV~~~ 55 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRL-AEKGLVEYE 55 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHH-HHTTSEEEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHH-HHCCCEEec
Confidence 5688999999999999999988888777 778887643
No 58
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=54.54 E-value=58 Score=25.67 Aligned_cols=48 Identities=17% Similarity=0.121 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhcc----cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 77 AIQSFAIHVLSLTYQ----KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 77 ~IR~~i~~vV~~tyq----sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+++.++++.+-...+ ..+...+|++||++.+.+-..+.++ ++.|+-.-
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L-~~~G~I~~ 201 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQF-IQDGYLKK 201 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHH-HHCCCEEe
Confidence 355666665543211 2578999999999999988888777 88999754
No 59
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=54.43 E-value=21 Score=21.21 Aligned_cols=36 Identities=8% Similarity=0.138 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHH
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQ 116 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~ 116 (167)
.|..+...+.. -.+...+|+.||++...+..|++.+
T Consensus 6 ~R~~ii~l~~~---G~s~~~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 6 RRAQIIRLLRE---GWSIREIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp ----HHHHHHH---T--HHHHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHHHHHC---CCCHHHHHHHHCcCHHHHHHHHHHc
Confidence 34445555444 7788899999999998888888544
No 60
>PF13977 TetR_C_6: Bacterial transcriptional repressor; PDB: 2NX4_C 3CRJ_C 3E7Q_B 2NP5_A 3QBM_B 2G3B_B 2GFN_A.
Probab=54.40 E-value=19 Score=24.59 Aligned_cols=49 Identities=16% Similarity=0.231 Sum_probs=39.8
Q ss_pred hHHHHHHHhhccchhhcccchHHHHHHHHHHHHHHhcc-----cccHHHHHHHh
Q 031021 54 FRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQ-----KIPRTVLAEAI 102 (167)
Q Consensus 54 F~~FW~~l~~~~~~~~~i~gFed~IR~~i~~vV~~tyq-----sI~~~~L~~~L 102 (167)
|.+||.....++++...+..+.+..|..+..++..... ..+...++.+|
T Consensus 26 ~~~~~~~a~~~p~l~~~~~~~~~~~~~~l~~~l~~~~~g~~~~~~~~~~~A~~l 79 (115)
T PF13977_consen 26 WLEFWAEARRDPELRALLREAYARWRSRLAELLRRAVAGGIRADVDPERLARML 79 (115)
T ss_dssp HHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHHHHHHHTSSSTTSTHHHHHHHH
T ss_pred HHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCHHHHHHHH
Confidence 67888888888999999999999999999999887666 66777777766
No 61
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=53.81 E-value=45 Score=23.05 Aligned_cols=44 Identities=16% Similarity=0.166 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
-+.|.+.+..- .+++...|++.+|++...+.+.+..+ .+.||-.
T Consensus 5 D~~il~~L~~~-~~~~~~~la~~l~~s~~tv~~~l~~L-~~~g~i~ 48 (108)
T smart00344 5 DRKILEELQKD-ARISLAELAKKVGLSPSTVHNRVKRL-EEEGVIK 48 (108)
T ss_pred HHHHHHHHHHh-CCCCHHHHHHHHCcCHHHHHHHHHHH-HHCCCee
Confidence 34566666553 57999999999999999999988877 6788865
No 62
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=52.43 E-value=36 Score=23.61 Aligned_cols=47 Identities=15% Similarity=0.245 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHH---hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 77 AIQSFAIHVLSL---TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 77 ~IR~~i~~vV~~---tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
.+++.|..++.. +=.=++++.+++-|+++.+++++.|+.+ ...|...
T Consensus 47 ~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L-~~eG~IY 96 (102)
T PF08784_consen 47 PLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFL-SNEGHIY 96 (102)
T ss_dssp HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHH-HHTTSEE
T ss_pred HHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHH-HhCCeEe
Confidence 477788888877 3334999999999999999999999887 5566544
No 63
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=51.82 E-value=39 Score=27.63 Aligned_cols=43 Identities=9% Similarity=0.030 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCc
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGW 122 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW 122 (167)
=|..|.+.+.. +.+++...|++.||+|+.-++.-++.. ...|.
T Consensus 8 R~~~I~~~l~~-~~~v~v~eLa~~~~VS~~TIRRDL~~L-e~~~~ 50 (252)
T PRK10681 8 RIGQLLQALKR-SDKLHLKDAAALLGVSEMTIRRDLNAH-SAPVV 50 (252)
T ss_pred HHHHHHHHHHH-cCCCcHHHHHHHhCCCHHHHHHHHHHh-hcCeE
Confidence 45677777765 889999999999999998888888765 45564
No 64
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=51.79 E-value=59 Score=21.16 Aligned_cols=45 Identities=13% Similarity=0.137 Sum_probs=35.0
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+.|...+.....-.+...+|+.+|++.-+...+++.+ .+.|....
T Consensus 3 e~Il~~i~~~~~p~~T~eiA~~~gls~~~aR~yL~~L-e~eG~V~~ 47 (62)
T PF04703_consen 3 EKILEYIKEQNGPLKTREIADALGLSIYQARYYLEKL-EKEGKVER 47 (62)
T ss_dssp HCHHHHHHHHTS-EEHHHHHHHHTS-HHHHHHHHHHH-HHCTSEEE
T ss_pred HHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHHH-HHCCCEEE
Confidence 4566677777888999999999999999999999777 66776653
No 65
>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=51.11 E-value=40 Score=26.51 Aligned_cols=46 Identities=17% Similarity=0.154 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.|+.|+..+.. ...++...|++.||++...+.+.++.+ .+.||...
T Consensus 2 tr~~IL~~L~~-~~~~t~~eLA~~lgis~~tV~~~L~~L-e~~GlV~r 47 (203)
T TIGR02702 2 TKEDILSYLLK-QGQATAAALAEALAISPQAVRRHLKDL-ETEGLIEY 47 (203)
T ss_pred HHHHHHHHHHH-cCCCCHHHHHHHHCcCHHHHHHHHHHH-HHCCCeEE
Confidence 47788888865 467999999999999999999998777 67899864
No 66
>smart00874 B5 tRNA synthetase B5 domain. This domain is found in phenylalanine-tRNA synthetase beta subunits.
Probab=51.09 E-value=52 Score=21.10 Aligned_cols=45 Identities=13% Similarity=0.302 Sum_probs=27.9
Q ss_pred cccHHHHHHHhcCC--chHHHHHHHHHhhhcCceeeccC-CCceEEEeCCCC
Q 031021 92 KIPRTVLAEAINLK--GLSLDKFLEHQKANCGWILEGDQ-STSQLIVLPPNE 140 (167)
Q Consensus 92 sI~~~~L~~~Lgl~--~~~l~~~~~~~~~~~GW~~~~~~-~~~~~vv~p~n~ 140 (167)
+++.+.+.++||++ .++..+.+ ++.|..++..+ +++-.|.+|...
T Consensus 5 ~~~~~~i~~llG~~i~~~ei~~~L----~~lg~~~~~~~~~~~~~v~~P~~R 52 (71)
T smart00874 5 TLRRERINRLLGLDLSAEEIEEIL----KRLGFEVEVSGDDDTLEVTVPSYR 52 (71)
T ss_pred EecHHHHHHHHCCCCCHHHHHHHH----HHCCCeEEecCCCCeEEEECCCCc
Confidence 46778899999964 44444444 88899986432 122346666543
No 67
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=51.02 E-value=24 Score=22.62 Aligned_cols=31 Identities=13% Similarity=0.125 Sum_probs=24.3
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+--+....|+.||++...+..|. .+.||...
T Consensus 12 ~G~~~~eIA~~Lg~~~~TV~~W~----~r~~W~~~ 42 (58)
T PF06056_consen 12 QGWSIKEIAEELGVPRSTVYSWK----DRYKWDEL 42 (58)
T ss_pred cCCCHHHHHHHHCCChHHHHHHH----HhhCcccc
Confidence 55677888999999976666665 88899864
No 68
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=51.00 E-value=43 Score=24.80 Aligned_cols=39 Identities=15% Similarity=0.235 Sum_probs=33.3
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHH
Q 031021 73 GFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 73 gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~ 113 (167)
-|.-+||..+++.+..- ..+....|.+||++..++-+++
T Consensus 5 ~vlPaiRa~lA~~L~ee--G~Sq~~iA~LLGltqaAVS~Yl 43 (119)
T COG2522 5 EVLPAIRALLAKELIEE--GLSQYRIAKLLGLTQAAVSQYL 43 (119)
T ss_pred HHHHHHHHHHHHHHHHc--CCcHHHHHHHhCCCHHHHHHHH
Confidence 35567999999887765 8899999999999999988888
No 69
>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=49.68 E-value=76 Score=21.14 Aligned_cols=47 Identities=17% Similarity=0.169 Sum_probs=34.1
Q ss_pred ccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021 93 IPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF 141 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~ 141 (167)
++...+++-+|++...+.+.++.+ ++.|--.. ..|.++-+....+++
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L-~~~Gli~s-~~G~~GGy~L~~~~~ 72 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKL-KKAGLIES-SRGRGGGYRLARPPE 72 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHH-HHTTSEEE-ETSTTSEEEESS-CC
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHH-hhCCeeEe-cCCCCCceeecCCHH
Confidence 899999999999999999998877 78897543 224334567765554
No 70
>PF10410 DnaB_bind: DnaB-helicase binding domain of primase; InterPro: IPR019475 This entry represents the C-terminal region three-helical domain of DNA primase []. Primases synthesise short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. Primases are recruited to single-stranded DNA by helicases - this domain binds DnaB-helicase []. It is associated with the Toprim domain IPR006171 from INTERPRO, which is the central catalytic core. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=49.56 E-value=13 Score=23.07 Aligned_cols=53 Identities=11% Similarity=0.103 Sum_probs=33.7
Q ss_pred HHHHHhhccch--hhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHH
Q 031021 57 FWDEAAKHRNI--VEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSL 109 (167)
Q Consensus 57 FW~~l~~~~~~--~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l 109 (167)
+|+.+....++ .+.-..|...+...|..+=+..++......|++.+|++.++|
T Consensus 5 ~~~~l~~~~dl~~~egk~~~~~~~~~~i~~i~~~i~r~~y~~~la~~~~i~~~~L 59 (59)
T PF10410_consen 5 LIERLSKGYDLDTPEGKAEAVREAAPLIAQIPDPIERELYIRELAERLGISEDAL 59 (59)
T ss_dssp HHHHHGGGS-TTSHHHHHHHHHHHHHHHTT--SHHHHHHHHHHHHHHCT-SSTT-
T ss_pred HHHHHHhcCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHhCcCcccC
Confidence 34455444222 223445677777888888888899999999999999987653
No 71
>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=49.37 E-value=31 Score=21.52 Aligned_cols=32 Identities=19% Similarity=0.190 Sum_probs=22.3
Q ss_pred HHHHHHHhcccccHHHHHHHhcCCchHHHHHH
Q 031021 82 AIHVLSLTYQKIPRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 82 i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~ 113 (167)
.-++-......|+-..|++++|+++.++.+-+
T Consensus 18 L~~l~~~G~~~vSS~~La~~~gi~~~qVRKDl 49 (50)
T PF06971_consen 18 LEQLKEEGVERVSSQELAEALGITPAQVRKDL 49 (50)
T ss_dssp HHHHHHTT-SEE-HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHcCCeeECHHHHHHHHCCCHHHhcccC
Confidence 33445556789999999999999998887644
No 72
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=49.26 E-value=44 Score=24.68 Aligned_cols=46 Identities=11% Similarity=0.137 Sum_probs=34.0
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCC
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~ 138 (167)
+.++...+++-+|+|..-+.+.+..+ ++.|+-.... |.|+-+....
T Consensus 24 ~~~s~~~ia~~~~is~~~vrk~l~~L-~~~Glv~s~~-G~~GG~~l~~ 69 (141)
T PRK11014 24 RMTSISEVTEVYGVSRNHMVKIINQL-SRAGYVTAVR-GKNGGIRLGK 69 (141)
T ss_pred CccCHHHHHHHHCcCHHHHHHHHHHH-HhCCEEEEec-CCCCCeeecC
Confidence 35789999999999999999988776 8899987544 3323344443
No 73
>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=49.19 E-value=20 Score=23.22 Aligned_cols=35 Identities=17% Similarity=0.284 Sum_probs=27.3
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
....++...|+.-||++++.++..++.| .+.|--.
T Consensus 11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l-~~kG~I~ 45 (69)
T PF09012_consen 11 ERGRVSLAELAREFGISPEAVEAMLEQL-IRKGYIR 45 (69)
T ss_dssp HS-SEEHHHHHHHTT--HHHHHHHHHHH-HCCTSCE
T ss_pred HcCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCcEE
Confidence 4678999999999999999999999888 5667654
No 74
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=48.30 E-value=42 Score=25.71 Aligned_cols=29 Identities=17% Similarity=0.269 Sum_probs=24.7
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
.++...||++||++...+-..++++ ++.|
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l-~~~g 196 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKML-EDQG 196 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH-HHCC
Confidence 6888999999999999888888766 5666
No 75
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=48.23 E-value=1e+02 Score=25.11 Aligned_cols=45 Identities=22% Similarity=0.282 Sum_probs=35.5
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
++.|...+. ....++...|+++||+|...++..+.+. ++.|.-..
T Consensus 6 ~~~Il~~l~-~~~~~~~~eLa~~l~VS~~TiRRdL~~L-~~~~~l~r 50 (240)
T PRK10411 6 QQAIVDLLL-NHTSLTTEALAEQLNVSKETIRRDLNEL-QTQGKILR 50 (240)
T ss_pred HHHHHHHHH-HcCCCcHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEE
Confidence 345666666 5789999999999999999899988776 55677654
No 76
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=47.23 E-value=86 Score=25.70 Aligned_cols=47 Identities=15% Similarity=0.130 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 77 AIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 77 ~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.-|+.|...+ .....++...|++.||+|...+...+... .+.|--.-
T Consensus 5 ~R~~~Il~~l-~~~~~~~~~ela~~l~vS~~TiRRdL~~L-e~~g~l~r 51 (252)
T PRK10906 5 QRHDAIIELV-KQQGYVSTEELVEHFSVSPQTIRRDLNDL-AEQNKILR 51 (252)
T ss_pred HHHHHHHHHH-HHcCCEeHHHHHHHhCCCHHHHHHHHHHH-HHCCCEEE
Confidence 3567778888 67899999999999999999998888776 67887653
No 77
>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=47.02 E-value=55 Score=24.00 Aligned_cols=33 Identities=9% Similarity=0.174 Sum_probs=29.4
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++...+++-++++..-+++.+..+ ++.||...
T Consensus 25 ~~s~~~ia~~~~ip~~~l~kil~~L-~~~glv~s 57 (135)
T TIGR02010 25 PVTLADISERQGISLSYLEQLFAKL-RKAGLVKS 57 (135)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHH-HHCCceEE
Confidence 4899999999999999999998776 88999875
No 78
>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=46.91 E-value=65 Score=19.59 Aligned_cols=36 Identities=17% Similarity=0.277 Sum_probs=29.5
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.+..++...|++.++++...+-..+... .+.||-.-
T Consensus 14 ~~~~~~~~~la~~~~~~~~~~t~~i~~L-~~~g~I~r 49 (59)
T PF01047_consen 14 ENGGITQSELAEKLGISRSTVTRIIKRL-EKKGLIER 49 (59)
T ss_dssp HHSSEEHHHHHHHHTS-HHHHHHHHHHH-HHTTSEEE
T ss_pred HcCCCCHHHHHHHHCCChhHHHHHHHHH-HHCCCEEe
Confidence 5677999999999999998888888766 78899863
No 79
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=46.12 E-value=55 Score=24.58 Aligned_cols=33 Identities=18% Similarity=0.272 Sum_probs=28.4
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++.+.+|++||++.+.+-..++++ ++.|+-.-
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l-~~~g~I~~ 175 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDL-RKKKLISI 175 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHH-HHCCCEEe
Confidence 5789999999999999988888777 88898754
No 80
>PF12728 HTH_17: Helix-turn-helix domain
Probab=45.83 E-value=24 Score=21.14 Aligned_cols=21 Identities=10% Similarity=0.245 Sum_probs=17.7
Q ss_pred ccHHHHHHHhcCCchHHHHHH
Q 031021 93 IPRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~ 113 (167)
++.+..+++||++...+.+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~ 22 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWI 22 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHH
Confidence 467889999999998887776
No 81
>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=45.00 E-value=65 Score=23.07 Aligned_cols=33 Identities=18% Similarity=0.241 Sum_probs=29.0
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++...|++.+|++...+.+.+... .+.||-..
T Consensus 25 ~~s~~eia~~~~i~~~~v~~il~~L-~~~gli~~ 57 (132)
T TIGR00738 25 PVSVKEIAERQGISRSYLEKILRTL-RRAGLVES 57 (132)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHH-HHCCcEEe
Confidence 6899999999999999999988776 78999764
No 82
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=44.96 E-value=61 Score=21.82 Aligned_cols=45 Identities=18% Similarity=0.273 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
||-.|+..+.. -..++-..|.+.||+++..+-+.++.. .+.|.-.
T Consensus 1 vRl~Il~~L~~-~~~~~f~~L~~~l~lt~g~Ls~hL~~L-e~~GyV~ 45 (80)
T PF13601_consen 1 VRLAILALLYA-NEEATFSELKEELGLTDGNLSKHLKKL-EEAGYVE 45 (80)
T ss_dssp HHHHHHHHHHH-HSEEEHHHHHHHTT--HHHHHHHHHHH-HHTTSEE
T ss_pred CHHHHHHHHhh-cCCCCHHHHHHHhCcCHHHHHHHHHHH-HHCCCEE
Confidence 56667777666 567889999999999999999988776 6778754
No 83
>PF08471 Ribonuc_red_2_N: Class II vitamin B12-dependent ribonucleotide reductase; InterPro: IPR013678 This domain is found to the N terminus of the ribonucleotide reductase barrel domain (IPR000788 from INTERPRO). It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine) []. ; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0050897 cobalt ion binding, 0055114 oxidation-reduction process
Probab=44.35 E-value=16 Score=25.98 Aligned_cols=39 Identities=15% Similarity=0.238 Sum_probs=26.6
Q ss_pred HHcCChHHHHHHHhhc-----cchhhcccch----------HHHHHHHHHHHHH
Q 031021 49 LETGRFRHFWDEAAKH-----RNIVEAVPGF----------EQAIQSFAIHVLS 87 (167)
Q Consensus 49 Le~c~F~~FW~~l~~~-----~~~~~~i~gF----------ed~IR~~i~~vV~ 87 (167)
+....||++|+.+..+ --....+|.- |.++|..+=++++
T Consensus 8 ~~~vEvP~~WSq~AtdI~AqKYFRk~Gvp~~~~~~~~~~g~E~S~rQv~~Rla~ 61 (93)
T PF08471_consen 8 QKDVEVPEFWSQVATDILAQKYFRKAGVPARDPDEEARFGGETSVRQVFDRLAG 61 (93)
T ss_pred ecCcccCchHHHHHHHHHHHHHhhhcCCCcccccccccccccchHHHHHHHHHH
Confidence 3567899999987654 1113456666 8888888777765
No 84
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.11 E-value=63 Score=24.48 Aligned_cols=45 Identities=7% Similarity=-0.038 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
...+...++...|+-+|....|..+|++-.....|+..+ ++.|+-
T Consensus 7 ~~~R~~~~~~~~~~G~S~re~Ak~~gvs~sTvy~wv~r~-~e~G~~ 51 (138)
T COG3415 7 NDLRERVVDAVVGEGLSCREAAKRFGVSISTVYRWVRRY-RETGLD 51 (138)
T ss_pred HHHHHHHHHHHHHcCccHHHHHHHhCccHHHHHHHHHHh-cccccc
Confidence 444556677888999999999999999998888888766 666776
No 85
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=44.10 E-value=28 Score=19.99 Aligned_cols=21 Identities=10% Similarity=0.153 Sum_probs=17.8
Q ss_pred ccHHHHHHHhcCCchHHHHHH
Q 031021 93 IPRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~ 113 (167)
++....+++||++...+.+++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHH
Confidence 467889999999998888877
No 86
>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=43.87 E-value=72 Score=19.42 Aligned_cols=45 Identities=16% Similarity=0.226 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.+..|...+... . ++...+++.+|++...+...++.. .+.||-..
T Consensus 8 ~~~~il~~l~~~-~-~~~~ei~~~~~i~~~~i~~~l~~L-~~~g~i~~ 52 (78)
T cd00090 8 TRLRILRLLLEG-P-LTVSELAERLGLSQSTVSRHLKKL-EEAGLVES 52 (78)
T ss_pred HHHHHHHHHHHC-C-cCHHHHHHHHCcCHhHHHHHHHHH-HHCCCeEE
Confidence 344555554432 2 899999999999999888888775 77898864
No 87
>PF15297 CKAP2_C: Cytoskeleton-associated protein 2 C-terminus
Probab=43.57 E-value=17 Score=31.87 Aligned_cols=67 Identities=25% Similarity=0.425 Sum_probs=41.5
Q ss_pred chhhhhcCCCccccCchhHHHHHHHHHHH-HcCChHHHHHHHhhc----cchhhcccchHHHH----------HHHHHHH
Q 031021 21 DFSLCLFLIPERVQMEDQFKTLIVLSHYL-ETGRFRHFWDEAAKH----RNIVEAVPGFEQAI----------QSFAIHV 85 (167)
Q Consensus 21 DF~lc~~Ll~~~~~~~~~i~~i~~L~~lL-e~c~F~~FW~~l~~~----~~~~~~i~gFed~I----------R~~i~~v 85 (167)
=|.=|+-||.+--..++-+..|-.|-... ..-+|+.||-.+..- ..+-..|+-||++| |..|+..
T Consensus 105 tlsECl~Li~eGcp~eei~~~L~~li~~IP~A~K~aKYWIC~Arl~~~~~~~e~vi~iyEeAi~agAqPieElR~~l~di 184 (353)
T PF15297_consen 105 TLSECLNLIEEGCPKEEILATLSDLIKNIPDAKKLAKYWICLARLEPRTGPIEDVIAIYEEAILAGAQPIEELRHVLVDI 184 (353)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHhcCchHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHHHcCCChHHHHHHHHHHH
Confidence 36779999988776444444444444333 667899999876443 34434566677655 4555555
Q ss_pred HH
Q 031021 86 LS 87 (167)
Q Consensus 86 V~ 87 (167)
+.
T Consensus 185 L~ 186 (353)
T PF15297_consen 185 LK 186 (353)
T ss_pred HH
Confidence 55
No 88
>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=43.47 E-value=79 Score=19.85 Aligned_cols=36 Identities=17% Similarity=0.202 Sum_probs=28.2
Q ss_pred ccc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 91 QKI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 91 qsI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
+.+ +...|++.+|+|...+.+.+..+ .+.||-.-..
T Consensus 22 ~~lps~~~la~~~~vsr~tvr~al~~L-~~~g~i~~~~ 58 (64)
T PF00392_consen 22 DRLPSERELAERYGVSRTTVREALRRL-EAEGLIERRP 58 (64)
T ss_dssp SBE--HHHHHHHHTS-HHHHHHHHHHH-HHTTSEEEET
T ss_pred CEeCCHHHHHHHhccCCcHHHHHHHHH-HHCCcEEEEC
Confidence 478 99999999999999999888776 7889986533
No 89
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=43.32 E-value=25 Score=20.79 Aligned_cols=26 Identities=15% Similarity=0.194 Sum_probs=16.5
Q ss_pred HHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 96 TVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 96 ~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
..+.+..|.+++...+++ +.++|-++
T Consensus 5 ~~F~~iTg~~~~~A~~~L----~~~~wdle 30 (43)
T PF14555_consen 5 AQFMSITGADEDVAIQYL----EANNWDLE 30 (43)
T ss_dssp HHHHHHH-SSHHHHHHHH----HHTTT-HH
T ss_pred HHHHHHHCcCHHHHHHHH----HHcCCCHH
Confidence 455666777666666666 77899876
No 90
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=43.06 E-value=54 Score=26.88 Aligned_cols=45 Identities=20% Similarity=0.198 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
|+.|...+.. ..+++...|++.||+|...++.-++.+ .+.|--..
T Consensus 7 ~~~Il~~L~~-~~~v~v~eLa~~l~VS~~TIRRDL~~L-e~~g~l~r 51 (256)
T PRK10434 7 QAAILEYLQK-QGKTSVEELAQYFDTTGTTIRKDLVIL-EHAGTVIR 51 (256)
T ss_pred HHHHHHHHHH-cCCEEHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEE
Confidence 5566666665 788999999999999999999998876 67786654
No 91
>PF10671 TcpQ: Toxin co-regulated pilus biosynthesis protein Q; InterPro: IPR018927 The toxin-coregulated pilus (TCP) of Vibrio cholerae and the soluble TcpF protein that is secreted via the TCP biogenesis apparatus are essential for intestinal colonisation in the disease of cholera. TCP fibres are homopolymers of TcpA pilin, encoded by the first gene in the tcp biogenesis operon. TcpQ is part of an outer membrane complex of the TCP biogenesis apparatus, comprised of TcpC and TcpQ. TcpQ is required for proper localisation of TcpC to the outer membrane [, ]. This entry represents a C-terminal domain found in TcpQ and other pilus biosynthesis proteins.; PDB: 3OV5_A 2L4W_A.
Probab=43.00 E-value=18 Score=24.57 Aligned_cols=21 Identities=38% Similarity=0.624 Sum_probs=15.6
Q ss_pred CchHHHHHHHHHhhhcCceee
Q 031021 105 KGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 105 ~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.|..|.+.+++|+++.||++-
T Consensus 8 ~g~tL~~~L~~Wa~~aGw~l~ 28 (84)
T PF10671_consen 8 KGETLREALERWAKQAGWTLV 28 (84)
T ss_dssp TT-BHHHHHHHHHHCTT-EEE
T ss_pred CCCcHHHHHHHHHHHCCCEEE
Confidence 456788888899899999984
No 92
>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=42.34 E-value=71 Score=18.69 Aligned_cols=32 Identities=9% Similarity=0.175 Sum_probs=25.6
Q ss_pred cccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 90 YQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 90 yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
+...+...+++.+|++...+...+.+..++.|
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~~~~~~~~l~ 44 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTHLRNIMRKLG 44 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHhC
Confidence 46789999999999999988888876655444
No 93
>PF06708 DUF1195: Protein of unknown function (DUF1195); InterPro: IPR010608 This family consists of several plant specific hypothetical proteins of around 160 residues in length. The function of this family is unknown.
Probab=40.62 E-value=31 Score=26.39 Aligned_cols=79 Identities=20% Similarity=0.201 Sum_probs=50.1
Q ss_pred HHHHHHHHHHHcCC---------ccchhhhhcCCCccccC----------chhHHHHHHHHHHHHcCChHHHHHHHhh--
Q 031021 5 IVARILIKALMAMP---------APDFSLCLFLIPERVQM----------EDQFKTLIVLSHYLETGRFRHFWDEAAK-- 63 (167)
Q Consensus 5 iv~~ILlKaL~~~P---------~~DF~lc~~Ll~~~~~~----------~~~i~~i~~L~~lLe~c~F~~FW~~l~~-- 63 (167)
+.+-|||.|+-.+= ..|++.--.=++...++ +.-+++.|.++..=..-+.|.||++.=+
T Consensus 41 aLaAIlLLAfWSM~tgsvtLrwS~g~l~~~~~dl~~~~~dDlDvLEmEeREKvVr~MWDvYt~s~~vrLPrFWqEAFeAA 120 (157)
T PF06708_consen 41 ALAAILLLAFWSMFTGSVTLRWSAGNLNSVSDDLDFPIHDDLDVLEMEEREKVVRHMWDVYTRSRRVRLPRFWQEAFEAA 120 (157)
T ss_pred HHHHHHHHHHHHHhheeeEEEeccCcccccccccCCcccccccHHHHHHHHHHHHHHHHHhcCCCCccCchHHHHHHHHH
Confidence 45667777775432 23333333333333331 3478999999988889999999997522
Q ss_pred ccchhhcccchHHHHHHHHH
Q 031021 64 HRNIVEAVPGFEQAIQSFAI 83 (167)
Q Consensus 64 ~~~~~~~i~gFed~IR~~i~ 83 (167)
-+++...+++..|.-=..|+
T Consensus 121 Ye~L~sD~~~VrdaAisEIA 140 (157)
T PF06708_consen 121 YEELASDVPQVRDAAISEIA 140 (157)
T ss_pred HHHHhccCcchhHHHHHHHH
Confidence 26788888888775444443
No 94
>PF13518 HTH_28: Helix-turn-helix domain
Probab=39.58 E-value=80 Score=18.51 Aligned_cols=30 Identities=7% Similarity=0.175 Sum_probs=24.0
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
+.-+...+|.-+|++...+..|+... ...|
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~~y-~~~G 40 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIKRY-REGG 40 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHHHH-HhcC
Confidence 34488999999999999999998666 4455
No 95
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=39.28 E-value=38 Score=19.24 Aligned_cols=20 Identities=15% Similarity=0.275 Sum_probs=16.9
Q ss_pred cHHHHHHHhcCCchHHHHHH
Q 031021 94 PRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 94 ~~~~L~~~Lgl~~~~l~~~~ 113 (167)
+...++++||++...+..|+
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56788999999998888876
No 96
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=38.93 E-value=53 Score=23.02 Aligned_cols=33 Identities=15% Similarity=0.232 Sum_probs=28.5
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+=..++...+|..||+....+-+|+ .+.||-..
T Consensus 21 ~~~~~ti~~~AK~L~i~~~~l~~~L----r~~g~l~~ 53 (111)
T PF03374_consen 21 SDGLYTIREAAKLLGIGRNKLFQWL----REKGWLYR 53 (111)
T ss_pred CCCCccHHHHHHHhCCCHHHHHHHH----HhCCceEE
Confidence 3378899999999999999988888 77899987
No 97
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=38.49 E-value=81 Score=18.27 Aligned_cols=32 Identities=13% Similarity=0.235 Sum_probs=26.4
Q ss_pred cccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 90 YQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 90 yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
++..+...+++.||++...+...+....++.|
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~~~~~~~kl~ 47 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTHLSNIMRKLG 47 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHC
Confidence 46679999999999999999988877666555
No 98
>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=37.86 E-value=62 Score=20.39 Aligned_cols=25 Identities=20% Similarity=0.360 Sum_probs=20.4
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHH
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEH 115 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~ 115 (167)
+.++...||+-||++...+...+..
T Consensus 22 R~~tl~elA~~lgis~st~~~~LRr 46 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLRR 46 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHHH
Confidence 4688899999999999887776643
No 99
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=36.65 E-value=1.2e+02 Score=21.90 Aligned_cols=39 Identities=10% Similarity=0.109 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHH
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQ 116 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~ 116 (167)
|++.+..+-..-.+.++.+.||+.+|++...+...+++.
T Consensus 11 i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 11 IHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 444444444444477999999999999998887777544
No 100
>KOG2072 consensus Translation initiation factor 3, subunit a (eIF-3a) [Translation, ribosomal structure and biogenesis]
Probab=36.54 E-value=1.4e+02 Score=29.40 Aligned_cols=74 Identities=14% Similarity=0.200 Sum_probs=55.4
Q ss_pred hccchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhc-CCchHHHHHHHHHhhhcCceeeccCCCceEEEeC
Q 031021 63 KHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAIN-LKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLP 137 (167)
Q Consensus 63 ~~~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lg-l~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p 137 (167)
+.++..+.|+.+.+-+=.+++.-||.-|++|+.+.|..+-- ++.-++++.+-+.++.+--++--|+-. ..|.+.
T Consensus 418 ~~~~~~QYI~sLq~v~~~RllqQvSqiY~sIs~~~l~~La~F~~~~~lEk~~v~a~k~~~v~iriDH~~-~~v~Fg 492 (988)
T KOG2072|consen 418 ESPDKSQYIPSLQDVIILRLLQQVSQIYESISFERLYKLAPFFSAFELEKLLVEAAKHNDVSIRIDHES-NSVSFG 492 (988)
T ss_pred cCCCccccchhHHHHHHHHHHHHHHHHHHHHhHHHHHHHHhhcCHHHHHHHHHHHHhccceeEEecccc-ceeeec
Confidence 34777889999999999999999999999999999888775 467789998877655555555433222 345553
No 101
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=36.09 E-value=1.1e+02 Score=22.23 Aligned_cols=45 Identities=18% Similarity=0.205 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 75 EQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 75 ed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
.|.+-+.|++.+..--+ ++...||+.+|+|...+..-++++ .+.|
T Consensus 6 lD~~D~~IL~~L~~d~r-~~~~eia~~lglS~~~v~~Ri~~L-~~~G 50 (154)
T COG1522 6 LDDIDRRILRLLQEDAR-ISNAELAERVGLSPSTVLRRIKRL-EEEG 50 (154)
T ss_pred ccHHHHHHHHHHHHhCC-CCHHHHHHHHCCCHHHHHHHHHHH-HHCC
Confidence 35677788888888777 999999999999999888888777 5666
No 102
>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=36.04 E-value=1.1e+02 Score=19.15 Aligned_cols=35 Identities=14% Similarity=0.138 Sum_probs=28.2
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHH
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQ 116 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~ 116 (167)
.++..+-. -..++...|++.||+|.-.+...+++.
T Consensus 9 ~Ll~~L~~-~~~~~~~ela~~l~~S~rti~~~i~~L 43 (59)
T PF08280_consen 9 KLLELLLK-NKWITLKELAKKLNISERTIKNDINEL 43 (59)
T ss_dssp HHHHHHHH-HTSBBHHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHHHHHc-CCCCcHHHHHHHHCCCHHHHHHHHHHH
Confidence 45566666 788999999999999999999998665
No 103
>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=35.83 E-value=1.4e+02 Score=20.19 Aligned_cols=43 Identities=21% Similarity=0.176 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
+...|.-+++.. +++.+.|.+..|++.+.+--.++.. .+.|+.
T Consensus 6 ~~~~IL~~ls~~--c~TLeeL~ekTgi~k~~LlV~LsrL-~k~GiI 48 (72)
T PF05584_consen 6 VTQKILIILSKR--CCTLEELEEKTGISKNTLLVYLSRL-AKRGII 48 (72)
T ss_pred HHHHHHHHHHhc--cCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCe
Confidence 455666666666 9999999999999999988888777 556644
No 104
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.75 E-value=1.3e+02 Score=19.73 Aligned_cols=45 Identities=16% Similarity=0.228 Sum_probs=34.9
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+-.|+.++.. ...++...+++.++++...+-..+.+. .+.||-..
T Consensus 12 ~~~il~~l~~-~~~~~~~~la~~~~~s~~~i~~~l~~L-~~~g~v~~ 56 (101)
T smart00347 12 QFLVLRILYE-EGPLSVSELAKRLGVSPSTVTRVLDRL-EKKGLIRR 56 (101)
T ss_pred HHHHHHHHHH-cCCcCHHHHHHHHCCCchhHHHHHHHH-HHCCCeEe
Confidence 4456666664 346889999999999998888888777 67899863
No 105
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=35.64 E-value=33 Score=29.18 Aligned_cols=45 Identities=18% Similarity=0.380 Sum_probs=34.1
Q ss_pred hhHHHHHH--HHHHHHcCChHHHHHHHhhccchhhcccchHHHHHHHH
Q 031021 37 DQFKTLIV--LSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQSFA 82 (167)
Q Consensus 37 ~~i~~i~~--L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed~IR~~i 82 (167)
+-+++++. +.-.|.+.-|.+ |++++...+--+.++||+|..+...
T Consensus 126 EvlR~ii~~~l~PtLh~Ssy~A-wkalr~~~~~~piiaGF~dqa~~V~ 172 (299)
T COG2074 126 EVLRKIISPELLPTLHTSSYDA-WKALRDPTDENPIIAGFEDQASAVM 172 (299)
T ss_pred HHHHHhCCHHhcchhhHhHHHH-HHHhcCCCCCcchhhhHHHHhHHHH
Confidence 34455554 777888888876 9999887777779999999877543
No 106
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=35.27 E-value=1.1e+02 Score=24.73 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=35.7
Q ss_pred HHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCC
Q 031021 95 RTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFN 142 (167)
Q Consensus 95 ~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N 142 (167)
...|++.||+|-..+.+.+..+ ...||-.-.. | ++++|.+..+.|
T Consensus 37 EreLae~fgVSR~~vREAl~~L-~a~Glve~r~-G-~Gt~V~~~~~~~ 81 (241)
T COG2186 37 ERELAERFGVSRTVVREALKRL-EAKGLVEIRQ-G-SGTFVRPRSEWN 81 (241)
T ss_pred HHHHHHHHCCCcHHHHHHHHHH-HHCCCeeecC-C-CceEecCCccCc
Confidence 7789999999999999999777 7899997644 4 367888755443
No 107
>PF05295 Luciferase_N: Luciferase/LBP N-terminal domain; InterPro: IPR007959 Proteins in this entry belong to a family of dinoflagellate luciferase and luciferin binding proteins. Luciferase is involved in catalysing the light emitting reaction in bioluminescence and luciferin binding protein (LBP) is known to bind to luciferin (the substrate for luciferase) to stop it reacting with the enzyme and therefore switching off the bioluminescence function. The expression of these two proteins is controlled by a circadian clock at the translational level, with synthesis and degradation occurring on a daily basis []. This entry consists of a presumed N-terminal domain that is conserved between dinoflagellate luciferase and luciferin binding proteins. This domain is not, however, the catalytic part of the protein. It has been suggested that this region may mediate an interaction between LBP and Luciferase or their association with the vacuolar membrane []. More information about these proteins can be found at Protein of the Month: Luciferase [].
Probab=34.87 E-value=12 Score=25.77 Aligned_cols=25 Identities=24% Similarity=0.662 Sum_probs=18.3
Q ss_pred cCChHHHHHHHhhc----cchhhcccchH
Q 031021 51 TGRFRHFWDEAAKH----RNIVEAVPGFE 75 (167)
Q Consensus 51 ~c~F~~FW~~l~~~----~~~~~~i~gFe 75 (167)
-.+|+.||..-+.. .|++..++.|.
T Consensus 32 vsDFAn~WTs~eyE~GvqdDIi~kv~~f~ 60 (82)
T PF05295_consen 32 VSDFANYWTSAEYEKGVQDDIISKVAAFQ 60 (82)
T ss_pred HHHHHhhhhHHHHHhhhHHHHHHHhhccc
Confidence 37899999976544 56777777775
No 108
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=34.58 E-value=1e+02 Score=22.44 Aligned_cols=44 Identities=23% Similarity=0.262 Sum_probs=34.0
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.++..|...-..++...|++.+|++...+-..+... .+.||-.-
T Consensus 35 ~vL~~l~~~~~~~t~~eLa~~l~~~~~tvt~~v~~L-e~~GlV~r 78 (144)
T PRK03573 35 VTLHNIHQLPPEQSQIQLAKAIGIEQPSLVRTLDQL-EEKGLISR 78 (144)
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCChhhHHHHHHHH-HHCCCEee
Confidence 456666543345788999999999998888888776 78999873
No 109
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=34.52 E-value=1.1e+02 Score=20.13 Aligned_cols=43 Identities=16% Similarity=0.264 Sum_probs=34.0
Q ss_pred HHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 82 AIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 82 i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
|+..++..=..++...+++.+|++...+...+... .+.||-..
T Consensus 10 Il~~l~~~~~~~t~~~ia~~l~i~~~tv~r~l~~L-~~~g~l~~ 52 (91)
T smart00346 10 VLRALAEEPGGLTLAELAERLGLSKSTAHRLLNTL-QELGYVEQ 52 (91)
T ss_pred HHHHHHhCCCCcCHHHHHHHhCCCHHHHHHHHHHH-HHCCCeee
Confidence 45555543257999999999999999988888776 67899875
No 110
>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=34.50 E-value=1.2e+02 Score=21.52 Aligned_cols=50 Identities=20% Similarity=0.262 Sum_probs=36.2
Q ss_pred chHHHHHHHHHHHHHHhc------ccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 73 GFEQAIQSFAIHVLSLTY------QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 73 gFed~IR~~i~~vV~~ty------qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
+|-..-.+.+..++..|| ..|+.+.++++.|++...+.+.+++++ +.|=-
T Consensus 29 dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~tg~~~~~V~~al~~Li-~~~vI 84 (100)
T PF04492_consen 29 DLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMTGLSRDHVSKALNELI-RRGVI 84 (100)
T ss_pred cccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHHCcCHHHHHHHHHHHH-HCCCE
Confidence 333344466677777776 489999999999999988888877764 34433
No 111
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=34.23 E-value=1.2e+02 Score=19.65 Aligned_cols=37 Identities=11% Similarity=0.083 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHH
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLE 114 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~ 114 (167)
|++.+-++-...=+.-+...+|+.||++.+++.+.+.
T Consensus 6 i~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 6 IERARRELEQELGREPTDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHH
Confidence 4444444444444778899999999999999888774
No 112
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.22 E-value=47 Score=19.29 Aligned_cols=20 Identities=15% Similarity=0.077 Sum_probs=16.7
Q ss_pred cHHHHHHHhcCCchHHHHHH
Q 031021 94 PRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 94 ~~~~L~~~Lgl~~~~l~~~~ 113 (167)
+...+|+++|++...+..|.
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 46788999999998888775
No 113
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=33.29 E-value=89 Score=25.62 Aligned_cols=45 Identities=18% Similarity=0.259 Sum_probs=36.2
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
|+.|+..+.. -.+++.+.|++.||+|+.-.+.-+.++ .+.|=-.-
T Consensus 7 ~~~Il~~l~~-~g~v~v~eLa~~~~VS~~TIRRDL~~L-e~~g~l~R 51 (253)
T COG1349 7 HQKILELLKE-KGKVSVEELAELFGVSEMTIRRDLNEL-EEQGLLLR 51 (253)
T ss_pred HHHHHHHHHH-cCcEEHHHHHHHhCCCHHHHHHhHHHH-HHCCcEEE
Confidence 4567777776 789999999999999999888887766 66776543
No 114
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=32.97 E-value=1.5e+02 Score=23.82 Aligned_cols=66 Identities=14% Similarity=0.132 Sum_probs=44.6
Q ss_pred chHHHHHHHHHHHHHHhcccc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021 73 GFEQAIQSFAIHVLSLTYQKI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF 141 (167)
Q Consensus 73 gFed~IR~~i~~vV~~tyqsI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~ 141 (167)
...+.||..|+.=-=..=+.+ +...|++.+|+|-.-+.+.+..+ ...|.-.-.. |. |++|.+...+
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L-~~eGlV~~~~-~~-G~~V~~~~~~ 79 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIML-EIKGLVEVRR-GA-GIYVLDSSGS 79 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHH-HHCCCEEEec-CC-EEEEeCCCcc
Confidence 345556666654322233567 58899999999999999998777 7889986433 33 5666655443
No 115
>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=32.90 E-value=1.2e+02 Score=23.44 Aligned_cols=62 Identities=8% Similarity=0.070 Sum_probs=43.0
Q ss_pred HHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCC
Q 031021 75 EQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPN 139 (167)
Q Consensus 75 ed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n 139 (167)
.+.||+.|..--=..=+.|+...|++.||+|...+.+.+..+ ...|+-.-.. ++ |.+|.+.+
T Consensus 17 ~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVReAL~~L-~~eGlv~~~~-~~-G~~V~~~~ 78 (212)
T TIGR03338 17 QDEIERAILSGELPPGAKLNESDIAARLGVSRGPVREAFRAL-EEAGLVRNEK-NR-GVFVREIS 78 (212)
T ss_pred HHHHHHHHHcCCCCCCCEecHHHHHHHhCCChHHHHHHHHHH-HHCCCEEEec-CC-CeEEecCC
Confidence 345555555432233357889999999999999999998777 7889986533 33 46666543
No 116
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=32.65 E-value=1.2e+02 Score=23.70 Aligned_cols=23 Identities=22% Similarity=0.314 Sum_probs=19.0
Q ss_pred HHHHHHHHHHcCCccchhhhhcC
Q 031021 6 VARILIKALMAMPAPDFSLCLFL 28 (167)
Q Consensus 6 v~~ILlKaL~~~P~~DF~lc~~L 28 (167)
...+|-.+++.+-+.|+-.|..|
T Consensus 3 n~avL~~~l~~l~~G~~~~c~~l 25 (180)
T PF11198_consen 3 NQAVLTQALHDLKEGNIRRCEAL 25 (180)
T ss_pred HHHHHHHHHHHHHcccHHHHHHc
Confidence 34578888899999999999887
No 117
>COG1577 ERG12 Mevalonate kinase [Lipid metabolism]
Probab=32.44 E-value=1.4e+02 Score=25.52 Aligned_cols=41 Identities=27% Similarity=0.409 Sum_probs=27.3
Q ss_pred HHHHhcCCchHHHHHHHHHhhhcCce---eeccCCCceEEEeCCC
Q 031021 98 LAEAINLKGLSLDKFLEHQKANCGWI---LEGDQSTSQLIVLPPN 139 (167)
Q Consensus 98 L~~~Lgl~~~~l~~~~~~~~~~~GW~---~~~~~~~~~~vv~p~n 139 (167)
|..-||++.+++++.++.. +++||. ..+++++|-++.+.++
T Consensus 238 LL~~LgVs~~~L~~lv~~a-~~~Ga~gaKlTGAGgGGc~IaL~~~ 281 (307)
T COG1577 238 LLKALGVSTPELDELVEAA-RSLGALGAKLTGAGGGGCIIALAKN 281 (307)
T ss_pred HHHhcCcCcHHHHHHHHHH-HhcCccccccccCCCCceEEEEecc
Confidence 3344688999999988665 889987 3455444455556554
No 118
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=32.32 E-value=1.5e+02 Score=22.82 Aligned_cols=47 Identities=11% Similarity=0.140 Sum_probs=35.1
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCC
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE 140 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~ 140 (167)
.++.+.+++.+|++..-+.+.++.+ ++.|+....- |.++-+...+.+
T Consensus 25 ~vs~~eIA~~~~ip~~~l~kIl~~L-~~aGLv~s~r-G~~GGy~Lar~p 71 (164)
T PRK10857 25 PVPLADISERQGISLSYLEQLFSRL-RKNGLVSSVR-GPGGGYLLGKDA 71 (164)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEeCC-CCCCCeeccCCH
Confidence 4899999999999999999998777 8899998632 222335554444
No 119
>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=31.71 E-value=1.3e+02 Score=19.50 Aligned_cols=44 Identities=25% Similarity=0.388 Sum_probs=32.6
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHH-----HHHHHHHhhhcCceee
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSL-----DKFLEHQKANCGWILE 125 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l-----~~~~~~~~~~~GW~~~ 125 (167)
+|+.++..+=.-++...|++.|.+.+.++ ...+ .++.+.|++..
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g~~~se~avRrrL-r~me~~Glt~~ 50 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRGEELSEEAVRRRL-RAMERDGLTRK 50 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcChhhhHHHHHHHH-HHHHHCCCccc
Confidence 68888888888899999999997766544 3333 34577888864
No 120
>KOG1497 consensus COP9 signalosome, subunit CSN4 [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=31.54 E-value=3.1e+02 Score=24.23 Aligned_cols=73 Identities=14% Similarity=0.183 Sum_probs=48.1
Q ss_pred HHHHHHHHcCChHHHHHHHhhccchhhcccchHH---HHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHH
Q 031021 43 IVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQ---AIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQ 116 (167)
Q Consensus 43 ~~L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed---~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~ 116 (167)
++|-..+..-+-.+|=..+..+ -....+.|-.. .+-+-=.-.+|.=|..|+-+.|+.+|+++.++.++.+.+-
T Consensus 266 myl~riI~k~el~ef~~~L~pH-Qka~~~dgssil~ra~~EhNlls~Skly~nisf~~Lg~ll~i~~ekaekiaa~M 341 (399)
T KOG1497|consen 266 MYLERIIRKEELQEFEAFLQPH-QKAHTMDGSSILDRAVIEHNLLSASKLYNNISFEELGALLKIDAEKAEKIAAQM 341 (399)
T ss_pred HHHHHHhcchhHHHHHHHhcch-hhhcccCcchhhhhHHHHHhHHHHHHHHHhccHHHHHHHhCCCHHHHHHHHHHH
Confidence 4677777777777766665443 11122333322 3333344567888999999999999999999888876443
No 121
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=31.39 E-value=1.2e+02 Score=23.68 Aligned_cols=46 Identities=13% Similarity=0.042 Sum_probs=35.2
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCC
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPN 139 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n 139 (167)
+.++...|++.||+|-.-+.+.+..+ ...|+-.-.. +. |.+|.+.+
T Consensus 29 ~~L~e~eLae~lgVSRtpVREAL~~L-~~eGlv~~~~-~~-G~~V~~~~ 74 (224)
T PRK11534 29 EKLRMSLLTSRYALGVGPLREALSQL-VAERLVTVVN-QK-GYRVASMS 74 (224)
T ss_pred CcCCHHHHHHHHCCChHHHHHHHHHH-HHCCCEEEeC-CC-ceEeCCCC
Confidence 68899999999999999999998776 7889886433 33 45666543
No 122
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=31.18 E-value=1.7e+02 Score=21.44 Aligned_cols=43 Identities=12% Similarity=0.132 Sum_probs=31.8
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
+.|..+. ..-..++...|++.||++...+-..+... .+.||-.
T Consensus 11 ~~I~~l~-~~~~~~~~~ela~~l~vs~~svs~~l~~L-~~~Gli~ 53 (142)
T PRK03902 11 EQIYLLI-EEKGYARVSDIAEALSVHPSSVTKMVQKL-DKDEYLI 53 (142)
T ss_pred HHHHHHH-hcCCCcCHHHHHHHhCCChhHHHHHHHHH-HHCCCEE
Confidence 3344433 23456678899999999999998988776 6779976
No 123
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=31.07 E-value=1.4e+02 Score=19.35 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=28.8
Q ss_pred HHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.+..+--.+=..|..-.+|+.||+++..+..|= +...|...
T Consensus 11 kA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr~WK----~~dkW~~~ 51 (60)
T PF10668_consen 11 KAFEIYKESNGKIKLKDIAEKLGVSESTIRKWK----SRDKWDEK 51 (60)
T ss_pred HHHHHHHHhCCCccHHHHHHHHCCCHHHHHHHh----hhcchhhH
Confidence 333333334457899999999999987777664 55678864
No 124
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=30.43 E-value=1.3e+02 Score=24.64 Aligned_cols=45 Identities=7% Similarity=0.140 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCce
Q 031021 77 AIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWI 123 (167)
Q Consensus 77 ~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~ 123 (167)
.-|+.|...+. ....++...|++.||+|...+...+..+ .+.|=-
T Consensus 5 ~R~~~Il~~l~-~~~~~~~~ela~~l~vS~~TirRdL~~L-e~~g~i 49 (251)
T PRK13509 5 QRHQILLELLA-QLGFVTVEKVIERLGISPATARRDINKL-DESGKL 49 (251)
T ss_pred HHHHHHHHHHH-HcCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCCE
Confidence 34566777776 5899999999999999999888888776 555644
No 125
>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=30.42 E-value=1.9e+02 Score=20.78 Aligned_cols=34 Identities=21% Similarity=0.291 Sum_probs=29.7
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
..++...+++.+|++...+.+.++.+ .+.||-..
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L-~~~Gli~~ 57 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQL-SLAGIVTS 57 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHH-HHCCcEEe
Confidence 35899999999999999999998777 78999864
No 126
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=30.41 E-value=51 Score=23.85 Aligned_cols=22 Identities=14% Similarity=0.268 Sum_probs=18.5
Q ss_pred ccccHHHHHHHhcCCchHHHHH
Q 031021 91 QKIPRTVLAEAINLKGLSLDKF 112 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~ 112 (167)
..++.+.+|.+||++..-+++|
T Consensus 56 ~~lSQ~vFA~~L~vs~~Tv~~W 77 (104)
T COG2944 56 LGLSQPVFARYLGVSVSTVRKW 77 (104)
T ss_pred hCCCHHHHHHHHCCCHHHHHHH
Confidence 3689999999999998777665
No 127
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=30.17 E-value=1.1e+02 Score=22.38 Aligned_cols=55 Identities=11% Similarity=0.128 Sum_probs=43.6
Q ss_pred hcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 69 EAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 69 ~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.....+-|..|..|+..+... ...+...|++-||++...+-+.+... ++.|+...
T Consensus 8 ~~fkaLadptRl~IL~~L~~~-~~~~v~ela~~l~lsqstvS~HL~~L-~~AGLV~~ 62 (117)
T PRK10141 8 QLFKILSDETRLGIVLLLRES-GELCVCDLCTALDQSQPKISRHLALL-RESGLLLD 62 (117)
T ss_pred HHHHHhCCHHHHHHHHHHHHc-CCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCceEE
Confidence 444556788999999998642 46788899999999998888887665 88898864
No 128
>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=29.65 E-value=1.6e+02 Score=20.62 Aligned_cols=44 Identities=18% Similarity=0.135 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
-.|+..+. ....++...|++.+|++...+-..+... .+.||-.-
T Consensus 31 ~~iL~~l~-~~~~~t~~ela~~~~~~~~tvs~~l~~L-e~~GlI~r 74 (118)
T TIGR02337 31 WRILRILA-EQGSMEFTQLANQACILRPSLTGILARL-ERDGLVTR 74 (118)
T ss_pred HHHHHHHH-HcCCcCHHHHHHHhCCCchhHHHHHHHH-HHCCCEEe
Confidence 34666665 3678999999999999998888888776 78899874
No 129
>cd05295 MDH_like Malate dehydrogenase-like. These MDH-like proteins are related to other groups in the MDH family but do not have conserved substrate and cofactor binding residues. MDH is one of the key enzymes in the citric acid cycle, facilitating both the conversion of malate to oxaloacetate and replenishing levels of oxalacetate by reductive carboxylation of pyruvate. Members of this subgroup are uncharacterized MDH-like proteins from animals. They are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others.
Probab=29.62 E-value=60 Score=29.39 Aligned_cols=31 Identities=23% Similarity=0.415 Sum_probs=24.7
Q ss_pred HHHHHHHh--cC----------CchHHHHHHHHHhhhcCceee
Q 031021 95 RTVLAEAI--NL----------KGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 95 ~~~L~~~L--gl----------~~~~l~~~~~~~~~~~GW~~~ 125 (167)
.+.||.+| || .+++-++|++..|+++||+-.
T Consensus 10 ~ellad~l~~~l~~f~~~ki~~~p~~w~~wl~~~c~~~~w~~~ 52 (452)
T cd05295 10 AELLADYLQKNLPDFRVHKIVKHPDEWEDWLQDLCKKNGWSHK 52 (452)
T ss_pred HHHHHHHHHhhCCCceEEEccCChHHHHHHHHHHHHhcCCccC
Confidence 35678887 34 457889999999999999974
No 130
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=28.83 E-value=1.2e+02 Score=24.02 Aligned_cols=71 Identities=14% Similarity=0.143 Sum_probs=51.6
Q ss_pred HHHHHHHcCChHHHHHHHhhc-cchhhcccchHHHHHHHHHHHHHHhc----ccccHHHHHHHhcCCchHHHHHHHHH
Q 031021 44 VLSHYLETGRFRHFWDEAAKH-RNIVEAVPGFEQAIQSFAIHVLSLTY----QKIPRTVLAEAINLKGLSLDKFLEHQ 116 (167)
Q Consensus 44 ~L~~lLe~c~F~~FW~~l~~~-~~~~~~i~gFed~IR~~i~~vV~~ty----qsI~~~~L~~~Lgl~~~~l~~~~~~~ 116 (167)
.+....+...+...+...... .... -.++-|.-|+.+-.....-| ++++...||+.||++...+.+.+.+.
T Consensus 127 ~l~~~~~~~~~~~~~~~~~~~~~~~~--~~~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrA 202 (215)
T COG3413 127 ELRDLLEILNFEDKEEVIESAFVEIG--KNDLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRA 202 (215)
T ss_pred HHHHHHHHhcccceeeeccccccccc--cccCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 666777777777766433222 2211 13688999999988888888 67888999999999998877777554
No 131
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=28.79 E-value=97 Score=17.69 Aligned_cols=31 Identities=16% Similarity=0.251 Sum_probs=19.4
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
+.++++.+|+.+|+|..-+....++. .|.+.
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk~~---~g~tp 37 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFKKE---TGMTP 37 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHHHH---TSS-H
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHH---HCcCH
Confidence 56889999999999877776666332 36653
No 132
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=28.68 E-value=1.3e+02 Score=23.54 Aligned_cols=29 Identities=21% Similarity=0.257 Sum_probs=23.7
Q ss_pred ccHHHHHHHhcCCchHHHHHHHHHhhhcCc
Q 031021 93 IPRTVLAEAINLKGLSLDKFLEHQKANCGW 122 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW 122 (167)
++...+|++||++...+-..+.++ ++.|=
T Consensus 174 ~t~~~iA~~lG~tretvsR~l~~L-~~~gl 202 (236)
T PRK09392 174 YEKRVLASYLGMTPENLSRAFAAL-ASHGV 202 (236)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHH-HhCCe
Confidence 446789999999999888888776 77783
No 133
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=28.66 E-value=3.2e+02 Score=24.03 Aligned_cols=53 Identities=13% Similarity=0.137 Sum_probs=38.3
Q ss_pred cchHHHHHHHHHHHHHHhcc---cccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 72 PGFEQAIQSFAIHVLSLTYQ---KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 72 ~gFed~IR~~i~~vV~~tyq---sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
..|.+.++ +...+..++. ..+.+.|++.++++.+.+++.++.. .+.||-...+
T Consensus 289 ~~~~~al~--iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L-~~agLI~~~~ 344 (412)
T PRK04214 289 GRFYDLLR--LLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCEL-ARIGLLRRGE 344 (412)
T ss_pred hhHHHHHH--HHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHH-HhCCCeEecC
Confidence 34545443 5555554443 6789999999999999998888776 8899998643
No 134
>smart00311 PWI PWI, domain in splicing factors.
Probab=28.64 E-value=86 Score=20.72 Aligned_cols=24 Identities=17% Similarity=0.191 Sum_probs=17.6
Q ss_pred HHHHHHhcCCchHHHHHHHHHhhh
Q 031021 96 TVLAEAINLKGLSLDKFLEHQKAN 119 (167)
Q Consensus 96 ~~L~~~Lgl~~~~l~~~~~~~~~~ 119 (167)
+.+-++||.+++.+-.++-+.+++
T Consensus 15 ~kv~e~LG~~d~~vvd~i~~~l~~ 38 (74)
T smart00311 15 KKVIEFLGFEEDTLVEFILSQIRQ 38 (74)
T ss_pred HHHHHHHCCChHHHHHHHHHHHHh
Confidence 345678898888888888666554
No 135
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=28.44 E-value=77 Score=30.84 Aligned_cols=37 Identities=30% Similarity=0.537 Sum_probs=24.8
Q ss_pred HHHHHHHHHc-CCccchhhhhcCCCccccCchh-HHHHHHHHHHHHcCChH
Q 031021 7 ARILIKALMA-MPAPDFSLCLFLIPERVQMEDQ-FKTLIVLSHYLETGRFR 55 (167)
Q Consensus 7 ~~ILlKaL~~-~P~~DF~lc~~Ll~~~~~~~~~-i~~i~~L~~lLe~c~F~ 55 (167)
..||++.+.. ||.+||- |+- -+.++.++++|.+|++.
T Consensus 542 ~Lvllklv~~lFPTSD~~------------HpVVTPalllm~~~L~q~~v~ 580 (840)
T PF04147_consen 542 DLVLLKLVGTLFPTSDFR------------HPVVTPALLLMSEYLSQCRVR 580 (840)
T ss_pred HHHHHHHHHHhcCccccc------------CcchhHHHHHHHHHHhcCCCC
Confidence 3455565555 6777743 332 26678999999999876
No 136
>PF03793 PASTA: PASTA domain; InterPro: IPR005543 The PASTA domain is found at the C-termini of several Penicillin-binding proteins (PBP) and bacterial serine/threonine kinases. It binds the beta-lactam stem, which implicates it in sensing D-alanyl-D-alanine - the PBP transpeptidase substrate. In PknB of Mycobacterium tuberculosis (P71584 from SWISSPROT), all of the extracellular portion is predicted to be made up of four PASTA domains, which strongly suggests that it is a signal-binding sensor domain. The domain has also been found in proteins involved in cell wall biosynthesis, where it is implicated in localizing the biosynthesis complex to unlinked peptidoglycan. PASTA is a small globular fold consisting of 3 beta-sheets and an alpha-helix, with a loop region of variable length between the first and second beta-strands. The name PASTA is derived from PBP and Serine/Threonine kinase Associated domain [].; GO: 0008658 penicillin binding; PDB: 2ZC3_C 1QME_A 1RP5_B 2Z2M_C 2Z2L_F 2ZC4_C 1QMF_A 3M9G_A 3PY9_A 1K25_B ....
Probab=28.19 E-value=1.3e+02 Score=18.49 Aligned_cols=21 Identities=10% Similarity=0.189 Sum_probs=13.7
Q ss_pred HHhcCCchHHHHHHHHHhhhcCcee
Q 031021 100 EAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 100 ~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
.+.|++-++..+.+ ++.||++
T Consensus 5 d~~g~~~~~a~~~l----~~~g~~~ 25 (63)
T PF03793_consen 5 DLVGMTYDEAKSIL----EAAGLTV 25 (63)
T ss_dssp TTTTSBHHHHHHHH----HHTT-EE
T ss_pred CcCCCcHHHHHHHH----HHCCCEE
Confidence 35677777766666 7789954
No 137
>PRK14137 recX recombination regulator RecX; Provisional
Probab=27.75 E-value=1.8e+02 Score=23.18 Aligned_cols=51 Identities=14% Similarity=0.222 Sum_probs=39.3
Q ss_pred cchHHHHHHHHHHHHHHhcccccHHHHHHHh---cCCchHHHHHHHHHhhhcCceee
Q 031021 72 PGFEQAIQSFAIHVLSLTYQKIPRTVLAEAI---NLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 72 ~gFed~IR~~i~~vV~~tyqsI~~~~L~~~L---gl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
..+.+.++.++++.++ |+--+...|.+.| |.+++.+++.|+.. +++||--|
T Consensus 36 ~e~~~~~~~~Al~~Ls--~R~rS~~ELr~KL~~kg~~~e~Ie~vI~rL-~e~gyLDD 89 (195)
T PRK14137 36 DEAREALLAYAFRALA--ARAMTAAELRAKLERRSEDEALVTEVLERV-QELGYQDD 89 (195)
T ss_pred HHHHHHHHHHHHHHHh--cchhhHHHHHHHHHhcCCCHHHHHHHHHHH-HHcCCCCH
Confidence 4577788888888764 5666777888888 67888888888666 88999865
No 138
>KOG3364 consensus Membrane protein involved in organellar division [Cell wall/membrane/envelope biogenesis]
Probab=27.36 E-value=1e+02 Score=23.66 Aligned_cols=79 Identities=11% Similarity=0.184 Sum_probs=51.7
Q ss_pred HHHHHHHcCChHHHHHHHhhc--cchhhcccchHHHHH-------HHHHHHHHHhcccc-----cHHHHHHHhcCCch--
Q 031021 44 VLSHYLETGRFRHFWDEAAKH--RNIVEAVPGFEQAIQ-------SFAIHVLSLTYQKI-----PRTVLAEAINLKGL-- 107 (167)
Q Consensus 44 ~L~~lLe~c~F~~FW~~l~~~--~~~~~~i~gFed~IR-------~~i~~vV~~tyqsI-----~~~~L~~~Lgl~~~-- 107 (167)
.-++.=-+|+|.--|..+++. .|+...|.-|++..+ +.-++-++.++-++ ++..+-.+|...++
T Consensus 26 a~~~~s~~s~f~lAwaLV~S~~~~dv~~GI~iLe~l~~~~~~~~rRe~lyYLAvg~yRlkeY~~s~~yvd~ll~~e~~n~ 105 (149)
T KOG3364|consen 26 ARSDVSKQSQFNLAWALVRSRDTEDVQEGIVILEDLLKSAHPERRRECLYYLAVGHYRLKEYSKSLRYVDALLETEPNNR 105 (149)
T ss_pred HhccchHHHHHHHHHHHHcccchHHHHHhHHHHHHHhhhcCcccchhhhhhhHHHHHHHhhHHHHHHHHHHHHhhCCCcH
Confidence 344666789999999999876 888888888998884 33344444444443 34455555655432
Q ss_pred ---HHHHHHHHHhhhcCc
Q 031021 108 ---SLDKFLEHQKANCGW 122 (167)
Q Consensus 108 ---~l~~~~~~~~~~~GW 122 (167)
+|++.++..+.+-|-
T Consensus 106 Qa~~Lk~~ied~itkegl 123 (149)
T KOG3364|consen 106 QALELKETIEDKITKEGL 123 (149)
T ss_pred HHHHHHHHHHHHHhhcce
Confidence 467777766665553
No 139
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=26.97 E-value=79 Score=21.44 Aligned_cols=28 Identities=21% Similarity=0.216 Sum_probs=22.4
Q ss_pred ccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 93 IPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
|+.+.+++..|++.+.+..++ ++||-.-
T Consensus 1 is~~e~~~~~~i~~~~l~~lv-----e~Gli~p 28 (84)
T PF13591_consen 1 ISLEEFCEACGIEPEFLRELV-----EEGLIEP 28 (84)
T ss_pred CCHHHHHHHHCcCHHHHHHHH-----HCCCeee
Confidence 678899999999986666665 6899874
No 140
>PRK09954 putative kinase; Provisional
Probab=26.86 E-value=1.5e+02 Score=25.19 Aligned_cols=45 Identities=11% Similarity=0.121 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
.+..|+..+.. -.+|+...|++.||++...+.+.++++ ++.|+..
T Consensus 4 ~~~~il~~l~~-~~~~s~~~la~~l~~s~~~v~~~i~~L-~~~g~i~ 48 (362)
T PRK09954 4 REKEILAILRR-NPLIQQNEIADILQISRSRVAAHIMDL-MRKGRIK 48 (362)
T ss_pred HHHHHHHHHHH-CCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCcC
Confidence 44556666653 358999999999999999999998777 6778863
No 141
>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=26.76 E-value=91 Score=18.93 Aligned_cols=16 Identities=25% Similarity=0.285 Sum_probs=10.0
Q ss_pred HHHHHHHHHhhhcCceeecc
Q 031021 108 SLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 108 ~l~~~~~~~~~~~GW~~~~~ 127 (167)
++.+.+ ++.||.....
T Consensus 3 el~k~L----~~~G~~~~r~ 18 (56)
T PF07927_consen 3 ELIKLL----EKAGFEEVRQ 18 (56)
T ss_dssp HHHHHH----HHTT-EEEEE
T ss_pred HHHHHH----HHCCCEEecC
Confidence 445555 8889998744
No 142
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=26.55 E-value=1.3e+02 Score=25.15 Aligned_cols=53 Identities=15% Similarity=0.212 Sum_probs=41.8
Q ss_pred chHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeec
Q 031021 73 GFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEG 126 (167)
Q Consensus 73 gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~ 126 (167)
|..-..-+...+++..-.+-|+....++.+|++++.+...+..+ .+.||-.--
T Consensus 11 ~~~m~~~e~l~~laae~hkiiTirdvae~~ev~~n~lr~lasrL-ekkG~LeRi 63 (269)
T COG5340 11 GLSMRESELLSHLAAEGHKIITIRDVAETLEVAPNTLRELASRL-EKKGWLERI 63 (269)
T ss_pred hhhHHHHHHHHHHHHHhCceEEeHHhhhhccCCHHHHHHHHhhh-hhcchhhhh
Confidence 34444445667788888888999999999999999999988776 788998643
No 143
>PRK03837 transcriptional regulator NanR; Provisional
Probab=26.47 E-value=1.7e+02 Score=23.02 Aligned_cols=47 Identities=11% Similarity=0.131 Sum_probs=35.7
Q ss_pred ccc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCC
Q 031021 91 QKI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE 140 (167)
Q Consensus 91 qsI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~ 140 (167)
+.+ +...|++.+|+|-..+.+.+..+ +..|+-.-.. |. +.+|.+.+.
T Consensus 35 ~~Lp~E~~Lae~~gVSRt~VREAL~~L-~~eGlv~~~~-~~-G~~V~~~~~ 82 (241)
T PRK03837 35 DQLPSERELMAFFGVGRPAVREALQAL-KRKGLVQISH-GE-RARVSRPSA 82 (241)
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHH-HHCCCEEEec-CC-ceeEecCCc
Confidence 468 79999999999999999998776 7899986533 44 456665443
No 144
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=26.38 E-value=99 Score=22.43 Aligned_cols=35 Identities=20% Similarity=0.260 Sum_probs=27.7
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
.-.+++.+.||+.|.-|.--....++++ .+.||-.
T Consensus 16 ~~~~vtl~elA~~l~cS~Rn~r~lLkkm-~~~gWi~ 50 (115)
T PF12793_consen 16 QPVEVTLDELAELLFCSRRNARTLLKKM-QEEGWIT 50 (115)
T ss_pred CCcceeHHHHHHHhCCCHHHHHHHHHHH-HHCCCee
Confidence 3457899999999999987767777665 7889875
No 145
>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=26.24 E-value=1.4e+02 Score=18.23 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=23.3
Q ss_pred cccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 90 YQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 90 yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
.+--+....|+.||++...+........++.|
T Consensus 16 ~~G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 16 AQGMSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp HTTS-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred HhcCCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 34445677788889988888888877777665
No 146
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=26.21 E-value=2.5e+02 Score=23.08 Aligned_cols=52 Identities=12% Similarity=0.258 Sum_probs=43.0
Q ss_pred chHHHHHHHHHHHHHHhccc---ccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 73 GFEQAIQSFAIHVLSLTYQK---IPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 73 gFed~IR~~i~~vV~~tyqs---I~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
|+.+--.++|+++..-||+. .+...|+-+||.|...+.+.++++.++.|=.+
T Consensus 83 ~~~elr~~rIvRl~~EAy~QgglLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vv 137 (220)
T PF07900_consen 83 GLSELRKHRIVRLTNEAYDQGGLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVV 137 (220)
T ss_pred CHHHHHHHHHHHHHHHHHHcCCcccHHHHHHHHCCCHHHHHHHHHHHHHHcCcee
Confidence 66777788999999999975 78899999999999999998887766655444
No 147
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=25.53 E-value=1.4e+02 Score=23.27 Aligned_cols=42 Identities=12% Similarity=-0.101 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
=|..|...+.. ...++...|++.||+|..-+..-+..+ .+.|
T Consensus 8 R~~~Il~~l~~-~~~~~~~~La~~~~vS~~TiRRDl~~L-~~~g 49 (185)
T PRK04424 8 RQKALQELIEE-NPFITDEELAEKFGVSIQTIRLDRMEL-GIPE 49 (185)
T ss_pred HHHHHHHHHHH-CCCEEHHHHHHHHCcCHHHHHHHHHHH-hcch
Confidence 34556666655 899999999999999998777776555 3344
No 148
>COG4199 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.95 E-value=64 Score=26.01 Aligned_cols=110 Identities=14% Similarity=0.224 Sum_probs=63.7
Q ss_pred HHHHHHHHHHcCChHHHHHHHhhc-cchhhcccchHHHHHHHHHHHHHHhcccc----cHHHHHHHhcCCchHHHHHHHH
Q 031021 41 TLIVLSHYLETGRFRHFWDEAAKH-RNIVEAVPGFEQAIQSFAIHVLSLTYQKI----PRTVLAEAINLKGLSLDKFLEH 115 (167)
Q Consensus 41 ~i~~L~~lLe~c~F~~FW~~l~~~-~~~~~~i~gFed~IR~~i~~vV~~tyqsI----~~~~L~~~Lgl~~~~l~~~~~~ 115 (167)
.+-.|.++++.-+|...|-....+ ..+++.+|. .|..++.-.-+. .|+.- ....|+.+||.+.+.+...++-
T Consensus 63 ~~~~l~~~~~e~~f~rIYf~~~~~e~~yltg~pt-Rd~Fa~lYk~i~--kf~eFdi~k~~~~La~~l~~~~e~l~fM~KV 139 (201)
T COG4199 63 SLEQLSNLFQEKDFSRIYFKFDISEDYYLTGIPT-RDHFAKLYKFIY--KFPEFDIRKKGKRLAQYLGWNKETLVFMIKV 139 (201)
T ss_pred cHHHHHHHHhccCcceEEEEeccCCCeeecCCCc-HHHHHHHHHHHH--hcCCccHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 345788889999998866544333 444554443 333444333222 23322 2468999999998777665533
Q ss_pred HhhhcCceeeccCCCceEEEeCCCCCCccccccccccccCCccccccc
Q 031021 116 QKANCGWILEGDQSTSQLIVLPPNEFNHPELKKNVADSIPLEHITRIF 163 (167)
Q Consensus 116 ~~~~~GW~~~~~~~~~~~vv~p~n~~N~~~~~~~i~E~i~f~~~~~i~ 163 (167)
. -+.|..--.+ |++.+++.+ + |++|.|...+-+....|
T Consensus 140 F-~eL~FVtidd----Glitvn~~a----~-KR~ideS~iYQ~kqe~v 177 (201)
T COG4199 140 F-FELGFVTIDD----GLITVNQQA----E-KREIDESQIYQQKQELV 177 (201)
T ss_pred H-HHcceeEeeC----CeEEeccCc----c-ccCCcHHHHHHHHHHHH
Confidence 3 5678764322 578884333 2 47888766554444333
No 149
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=24.51 E-value=2.3e+02 Score=21.33 Aligned_cols=47 Identities=17% Similarity=0.067 Sum_probs=34.3
Q ss_pred cccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCC
Q 031021 92 KIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNE 140 (167)
Q Consensus 92 sI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~ 140 (167)
.++...+|+-.|++..-+.+.+..+ ++.|+-...- |.+|-+.+.+.+
T Consensus 24 ~~s~~eIA~~~~is~~~L~kIl~~L-~~aGlv~S~r-G~~GGy~La~~p 70 (153)
T PRK11920 24 LSRIPEIARAYGVSELFLFKILQPL-VEAGLVETVR-GRNGGVRLGRPA 70 (153)
T ss_pred cCcHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEeec-CCCCCeeecCCH
Confidence 4789999999999999999988776 8899987533 222335554443
No 150
>PHA00738 putative HTH transcription regulator
Probab=24.26 E-value=2.3e+02 Score=20.67 Aligned_cols=64 Identities=8% Similarity=0.106 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCCCc
Q 031021 76 QAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEFNH 143 (167)
Q Consensus 76 d~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~N~ 143 (167)
|..|+.|+..++. ........|++.++++-+.+-+.++.+ ++.|=-...-. |.-+..--++++.
T Consensus 11 dptRr~IL~lL~~-~e~~~V~eLae~l~lSQptVS~HLKvL-reAGLV~srK~--Gr~vyY~Ln~~~~ 74 (108)
T PHA00738 11 KILRRKILELIAE-NYILSASLISHTLLLSYTTVLRHLKIL-NEQGYIELYKE--GRTLYAKIRENSK 74 (108)
T ss_pred CHHHHHHHHHHHH-cCCccHHHHHHhhCCCHHHHHHHHHHH-HHCCceEEEEE--CCEEEEEECCCcc
Confidence 6799999999965 335788899999999998888887655 77886654221 3445555555544
No 151
>KOG2908 consensus 26S proteasome regulatory complex, subunit RPN9/PSMD13 [Posttranslational modification, protein turnover, chaperones]
Probab=24.26 E-value=5e+02 Score=22.98 Aligned_cols=90 Identities=9% Similarity=0.124 Sum_probs=59.6
Q ss_pred HHHHHHHHcCChHHHHHHHhhccchhhcccchHHHHHH--HHHHHHHHhccc------ccHHHHHHHhcCCchHHHHHHH
Q 031021 43 IVLSHYLETGRFRHFWDEAAKHRNIVEAVPGFEQAIQS--FAIHVLSLTYQK------IPRTVLAEAINLKGLSLDKFLE 114 (167)
Q Consensus 43 ~~L~~lLe~c~F~~FW~~l~~~~~~~~~i~gFed~IR~--~i~~vV~~tyqs------I~~~~L~~~Lgl~~~~l~~~~~ 114 (167)
..+=..+-..+++.|-+..+.-.. .+..+.-++.+|+ ++.-++-++|++ +|-+..|+.+-++-++++-.+.
T Consensus 238 ~dll~Afn~Gdl~~f~~l~~~~~~-~p~L~~~e~~L~qKI~LmaLiEi~F~rpa~~R~lsf~~Ia~~tkip~~eVE~LVM 316 (380)
T KOG2908|consen 238 KDLLIAFNSGDLKRFESLKGVWGK-QPDLASNEDFLLQKIRLLALIEITFSRPANERTLSFKEIAEATKIPNKEVELLVM 316 (380)
T ss_pred HHHHHHhccCCHHHHHHHHHHhcc-CchHHHHHHHHHHHHHHHHHHHHHhcCcchhccccHHHHHHHhCCCHHHHHHHHH
Confidence 355556778899998887655422 2233333555554 456788999988 8999999999999999888885
Q ss_pred HHhhh--cCceeeccCCCceEEEe
Q 031021 115 HQKAN--CGWILEGDQSTSQLIVL 136 (167)
Q Consensus 115 ~~~~~--~GW~~~~~~~~~~~vv~ 136 (167)
+.... -.|.+|.. +++|.+
T Consensus 317 KAlslgLikG~Idqv---~~~v~~ 337 (380)
T KOG2908|consen 317 KALSLGLIKGSIDQV---EGVVYM 337 (380)
T ss_pred HHHhccceeeeeccc---ccEEEE
Confidence 54332 22556643 245544
No 152
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.15 E-value=1e+02 Score=19.27 Aligned_cols=20 Identities=10% Similarity=0.008 Sum_probs=16.8
Q ss_pred cHHHHHHHhcCCchHHHHHH
Q 031021 94 PRTVLAEAINLKGLSLDKFL 113 (167)
Q Consensus 94 ~~~~L~~~Lgl~~~~l~~~~ 113 (167)
+...+++++|++...+..|.
T Consensus 2 s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 46788999999998888875
No 153
>PHA02699 hypothetical protein; Provisional
Probab=23.79 E-value=1e+02 Score=27.45 Aligned_cols=63 Identities=24% Similarity=0.549 Sum_probs=47.8
Q ss_pred CChHHHHHHHhhc-cchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 52 GRFRHFWDEAAKH-RNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 52 c~F~~FW~~l~~~-~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
.+|.+.|..+.+- .++-+..|+= |.|-+||.+.+..+-.-|++..|.+-| .++ .-.|....+.
T Consensus 397 ~~~~elwd~i~~~asdlds~lp~c-e~ierfi~~~~c~s~a~~~r~~lvqrl--------~~l----ag~g~rltgs 460 (466)
T PHA02699 397 ARFSELWDDILEKAADLDSTLPRC-ECIEKFIHHMVCNSEAGIERNELVQRL--------TMI----AGAGYRLTGS 460 (466)
T ss_pred HHHHHHHHHHHHHHhhhhhcCCcc-hHHHHHHHHHHhcchhhhhHHHHHHHH--------HHH----hcCceEeecC
Confidence 4799999987554 6777778887 889999999988887788888888777 333 3447777643
No 154
>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=23.75 E-value=1.9e+02 Score=20.75 Aligned_cols=35 Identities=14% Similarity=0.089 Sum_probs=29.3
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
.+..++...+++-||++...+-.++ ++.||+....
T Consensus 68 ~~pd~tl~Ela~~l~Vs~~ti~~~L----krlg~t~KK~ 102 (119)
T PF01710_consen 68 ENPDATLRELAERLGVSPSTIWRAL----KRLGITRKKK 102 (119)
T ss_pred HCCCcCHHHHHHHcCCCHHHHHHHH----HHcCchhccC
Confidence 3888999999999999887777777 8889998743
No 155
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=23.48 E-value=2.5e+02 Score=22.38 Aligned_cols=64 Identities=16% Similarity=0.120 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHHhcccc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCCCC
Q 031021 75 EQAIQSFAIHVLSLTYQKI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPNEF 141 (167)
Q Consensus 75 ed~IR~~i~~vV~~tyqsI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n~~ 141 (167)
.+.||+.|..=-=..=+.+ +...|++.||+|-..+.+.+..+ ...|+-.-.. +. |++|.+.+..
T Consensus 13 ~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L-~~eGlV~~~~-~~-G~~V~~~~~~ 77 (251)
T PRK09990 13 AERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVL-RGRGIIETAQ-GR-GSFVARLNRV 77 (251)
T ss_pred HHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEEeC-CC-eeEEecCCcc
Confidence 3445555543222223678 78999999999999999998776 7889986543 33 5677765544
No 156
>PF14821 Thr_synth_N: Threonine synthase N terminus; PDB: 3V7N_A 1VB3_A 1KL7_A.
Probab=23.35 E-value=71 Score=21.51 Aligned_cols=34 Identities=15% Similarity=0.292 Sum_probs=26.4
Q ss_pred HHHHHHHHhcccccHHHHHHHh--cCCchHHHHHHH
Q 031021 81 FAIHVLSLTYQKIPRTVLAEAI--NLKGLSLDKFLE 114 (167)
Q Consensus 81 ~i~~vV~~tyqsI~~~~L~~~L--gl~~~~l~~~~~ 114 (167)
++-...+.+|+.+....|+.++ ++++++|.+.|+
T Consensus 41 ~l~~l~~~sy~elA~~il~~f~~~di~~~~L~~ii~ 76 (79)
T PF14821_consen 41 ELEELKNLSYAELAFEILSPFLGDDIPEEELKEIIE 76 (79)
T ss_dssp HHHHHTTS-HHHHHHHHHHHHCCCCS-HHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHHHHHccCCCHHHHHHHHH
Confidence 4667788899999999999999 467778887774
No 157
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=23.25 E-value=2.2e+02 Score=20.74 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=34.7
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
-.|+..+. .-..++...|++.+|++...+-..++.. .+.||-.-
T Consensus 43 ~~vL~~l~-~~~~~t~~eLa~~l~i~~~tvsr~l~~L-e~~GlI~R 86 (144)
T PRK11512 43 FKVLCSIR-CAACITPVELKKVLSVDLGALTRMLDRL-VCKGWVER 86 (144)
T ss_pred HHHHHHHH-HcCCCCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEe
Confidence 34555554 3567999999999999998888888776 78999873
No 158
>KOG2745 consensus Mitochondrial carrier protein [General function prediction only]
Probab=23.09 E-value=1.2e+02 Score=25.99 Aligned_cols=42 Identities=12% Similarity=0.181 Sum_probs=35.7
Q ss_pred ChHHHHHHHhhccchhhcccchHHHHHHHHHHHHHHhcccccHHHHHHHhc
Q 031021 53 RFRHFWDEAAKHRNIVEAVPGFEQAIQSFAIHVLSLTYQKIPRTVLAEAIN 103 (167)
Q Consensus 53 ~F~~FW~~l~~~~~~~~~i~gFed~IR~~i~~vV~~tyqsI~~~~L~~~Lg 103 (167)
+...||..+++ +|.|++++.++.+++.-|.=|+.-.++++.|
T Consensus 129 ~~~sF~~vik~---------t~rd~v~~~~~v~~ahPFhVi~~R~maQfVG 170 (321)
T KOG2745|consen 129 DAESFKKVIKR---------TFRDSVIRVVAVVAAHPFHVISLRQMAQFVG 170 (321)
T ss_pred HHHHHHHHHHH---------hHHHHHHHHHHHhhcCceeeeeHHHHHHHHc
Confidence 44557766654 5889999999999999999999999999998
No 159
>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=23.02 E-value=67 Score=21.17 Aligned_cols=36 Identities=17% Similarity=0.260 Sum_probs=26.0
Q ss_pred HHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 82 AIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 82 i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
|-+.++. -...+...|++.+|+++.++...+ ||=.-
T Consensus 13 Vw~~L~~-~~~~s~~el~k~~~l~~~~~~~Ai-------GWLar 48 (65)
T PF10771_consen 13 VWQLLNE-NGEWSVSELKKATGLSDKEVYLAI-------GWLAR 48 (65)
T ss_dssp HHHHHCC-SSSEEHHHHHHHCT-SCHHHHHHH-------HHHHC
T ss_pred HHHHHhh-CCCcCHHHHHHHhCcCHHHHHHHH-------HHHhc
Confidence 3444444 457889999999999998877766 88764
No 160
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=22.75 E-value=2.2e+02 Score=22.57 Aligned_cols=44 Identities=11% Similarity=0.151 Sum_probs=34.5
Q ss_pred ccHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCCC
Q 031021 93 IPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPPN 139 (167)
Q Consensus 93 I~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~n 139 (167)
=+...|++.+|+|-.-+.+.+..+ .+.|+-.... |. |+||.+..
T Consensus 34 PsE~eLa~~~~VSR~TvR~Al~~L-~~eGli~r~~-G~-GTfV~~~~ 77 (241)
T PRK11402 34 PTENELCTQYNVSRITIRKAISDL-VADGVLIRWQ-GK-GTFVQSQK 77 (241)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHH-HHCCCEEEec-Cc-eeEECCCc
Confidence 357789999999999999999887 7889988643 54 57776544
No 161
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=22.66 E-value=2.3e+02 Score=22.64 Aligned_cols=58 Identities=21% Similarity=0.307 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHhc---ccc-cHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCC
Q 031021 75 EQAIQSFAIHVLSLTY---QKI-PRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 75 ed~IR~~i~~vV~~ty---qsI-~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~ 138 (167)
.+.+|..|. ...| ..+ +...|++.||+|-..+.+.+..+ ...|+-.-.. + +|.+|.+.
T Consensus 16 ~~~l~~~I~---~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L-~~eGlv~~~~-~-~G~~V~~~ 77 (254)
T PRK09464 16 EQQLEFLIL---EGTLRPGEKLPPERELAKQFDVSRPSLREAIQRL-EAKGLLLRRQ-G-GGTFVQSS 77 (254)
T ss_pred HHHHHHHHH---cCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHH-HHCCCEEEec-C-ceeEEecC
Confidence 344555444 3445 578 78999999999999999998776 7889986543 3 35666653
No 162
>PF12046 DUF3529: Protein of unknown function (DUF3529); InterPro: IPR021919 This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 176 to 190 amino acids in length.
Probab=22.56 E-value=1.3e+02 Score=23.77 Aligned_cols=30 Identities=7% Similarity=0.063 Sum_probs=18.6
Q ss_pred hHHHHHHHHHhhhcCceeeccCCCceEEEe
Q 031021 107 LSLDKFLEHQKANCGWILEGDQSTSQLIVL 136 (167)
Q Consensus 107 ~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~ 136 (167)
+++...+.++.+++||.+.+.+..+.++.+
T Consensus 43 ~~~~~~l~~yf~~r~y~v~~~d~~~~~itF 72 (173)
T PF12046_consen 43 DEVLEQLKAYFEQRNYRVAEGDAEGEVITF 72 (173)
T ss_pred HHHHHHHHHHHHhcCceecccCccccEEEE
Confidence 344444555559999999754334556665
No 163
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=22.44 E-value=83 Score=22.51 Aligned_cols=24 Identities=17% Similarity=0.263 Sum_probs=19.1
Q ss_pred Hh-cCCchHHHHHHHHHhhhcCceee
Q 031021 101 AI-NLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 101 ~L-gl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
|| .|+++++.+.++.. -++||+..
T Consensus 8 ylp~lt~~~i~~QI~yl-l~qG~~~~ 32 (99)
T cd03527 8 YLPPLTDEQIAKQIDYI-ISNGWAPC 32 (99)
T ss_pred cCCCCCHHHHHHHHHHH-HhCCCEEE
Confidence 44 68889999888766 67999984
No 164
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=21.97 E-value=1.9e+02 Score=23.27 Aligned_cols=42 Identities=21% Similarity=0.338 Sum_probs=34.0
Q ss_pred cHHHHHHHhcCCchHHHHHHHHHhhhcCceeeccCCCceEEEeCC
Q 031021 94 PRTVLAEAINLKGLSLDKFLEHQKANCGWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 94 ~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~~~~~~~vv~p~ 138 (167)
+...|++.+|+|..-+.+.+..+ .+.|+-.-.. |. |+||.++
T Consensus 33 sE~eLa~~f~VSR~TvRkAL~~L-~~eGli~r~~-G~-GtfV~~~ 74 (236)
T COG2188 33 SERELAEQFGVSRMTVRKALDEL-VEEGLIVRRQ-GK-GTFVASP 74 (236)
T ss_pred CHHHHHHHHCCcHHHHHHHHHHH-HHCCcEEEEe-cC-eeEEcCc
Confidence 57789999999999999999877 7889987643 54 5788876
No 165
>PF08727 P3A: Poliovirus 3A protein like; InterPro: IPR014838 The 3A protein is found in positive-strand RNA viruses. It is a critical component of the poliovirus replication complex, and is also an inhibitor of host cell ER to Golgi transport. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0017111 nucleoside-triphosphatase activity; PDB: 1NG7_A.
Probab=21.88 E-value=52 Score=21.28 Aligned_cols=23 Identities=17% Similarity=0.573 Sum_probs=12.6
Q ss_pred HHHhc-CCchHHHHHHHHHhhhcCceee
Q 031021 99 AEAIN-LKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 99 ~~~Lg-l~~~~l~~~~~~~~~~~GW~~~ 125 (167)
+.+|- +.++++.++| +++||.+.
T Consensus 21 ~DLL~SV~~~eV~~YC----~~~GWIip 44 (57)
T PF08727_consen 21 ADLLRSVDSPEVREYC----EEQGWIIP 44 (57)
T ss_dssp HHHHHHH--HHHHHHH----HHHT--TT
T ss_pred HHHHHhcCCHHHHHHH----HHCCcccc
Confidence 34442 3457788888 77799985
No 166
>COG0549 ArcC Carbamate kinase [Amino acid transport and metabolism]
Probab=21.76 E-value=1.3e+02 Score=25.91 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=17.8
Q ss_pred HHHhhhcCceeeccCCCceEEEeCC
Q 031021 114 EHQKANCGWILEGDQSTSQLIVLPP 138 (167)
Q Consensus 114 ~~~~~~~GW~~~~~~~~~~~vv~p~ 138 (167)
++..+.+||++..|.++|..-|+|.
T Consensus 141 ~~l~~~~gw~~keD~~rG~RRVVpS 165 (312)
T COG0549 141 EELAKEYGWVFKEDAGRGYRRVVPS 165 (312)
T ss_pred HHHHhhcCcEEEecCCCCeeEecCC
Confidence 4444778999987767667767754
No 167
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=21.65 E-value=48 Score=23.51 Aligned_cols=28 Identities=18% Similarity=0.368 Sum_probs=20.3
Q ss_pred HHHHhcCCchHHHHHHH-HHhhhcCceee
Q 031021 98 LAEAINLKGLSLDKFLE-HQKANCGWILE 125 (167)
Q Consensus 98 L~~~Lgl~~~~l~~~~~-~~~~~~GW~~~ 125 (167)
+-+..||++.+|++|+. ....+.||+.+
T Consensus 2 F~~~VNMt~~EL~~WL~t~~S~~~g~~~~ 30 (92)
T PF11338_consen 2 FHEVVNMTPAELEDWLRTDESKSVGEKKD 30 (92)
T ss_pred hhhhhCCCHHHHHHHHcCccccccccCCC
Confidence 34567999999999986 33345688875
No 168
>PF08621 RPAP1_N: RPAP1-like, N-terminal; InterPro: IPR013930 Inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis in Saccharomyces cerevisiae (Baker's yeast) results in changes in global gene expression that are similar to those caused by the loss of the RNAPII subunit Rpb11 []. This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.
Probab=21.64 E-value=1.5e+02 Score=18.30 Aligned_cols=30 Identities=13% Similarity=0.050 Sum_probs=22.8
Q ss_pred ccccHHHHHHHhcCCchHHHHHHHHHhhhc
Q 031021 91 QKIPRTVLAEAINLKGLSLDKFLEHQKANC 120 (167)
Q Consensus 91 qsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~ 120 (167)
+.|..++++.+=+||+++..+.-++++...
T Consensus 2 ~~I~~EN~~rL~~MS~eEI~~er~eL~~~L 31 (49)
T PF08621_consen 2 QRIHEENEARLASMSPEEIEEEREELLESL 31 (49)
T ss_pred chHhHHHHHHHHhCCHHHHHHHHHHHHHhC
Confidence 678888888888999888777666665544
No 169
>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=21.55 E-value=1.8e+02 Score=20.16 Aligned_cols=40 Identities=20% Similarity=0.151 Sum_probs=26.5
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
..|++++.. ...++.+.|+..+|++..++.+.+..+ ...|
T Consensus 16 ~~Il~~L~~-~~~l~de~la~~~~l~~~~vRkiL~~L-~~~~ 55 (105)
T PF02002_consen 16 VRILDALLR-KGELTDEDLAKKLGLKPKEVRKILYKL-YEDG 55 (105)
T ss_dssp HHHHHHHHH-H--B-HHHHHHTT-S-HHHHHHHHHHH-HHHS
T ss_pred HHHHHHHHH-cCCcCHHHHHHHhCCCHHHHHHHHHHH-HHCC
Confidence 345666653 578999999999999999999998766 3444
No 170
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=21.28 E-value=2.5e+02 Score=22.76 Aligned_cols=35 Identities=17% Similarity=0.254 Sum_probs=29.9
Q ss_pred cccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 90 YQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 90 yqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
...|+...|++.||++...+...+.+. .+.||-.-
T Consensus 19 ~~~IS~~eLA~~L~iS~~Tvsr~Lk~L-Ee~GlI~R 53 (217)
T PRK14165 19 TVKISSSEFANHTGTSSKTAARILKQL-EDEGYITR 53 (217)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEE
Confidence 346899999999999999888888777 88999864
No 171
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=21.27 E-value=1.3e+02 Score=17.92 Aligned_cols=28 Identities=14% Similarity=0.286 Sum_probs=19.1
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHH
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQ 116 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~ 116 (167)
-++..+....|+.+|++...+...+...
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4667778888999999998888887544
No 172
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=21.21 E-value=94 Score=19.98 Aligned_cols=18 Identities=22% Similarity=0.248 Sum_probs=15.2
Q ss_pred HhcccccHHHHHHHhcCC
Q 031021 88 LTYQKIPRTVLAEAINLK 105 (167)
Q Consensus 88 ~tyqsI~~~~L~~~Lgl~ 105 (167)
.+|+-|..+.|.++|+.+
T Consensus 20 L~YePI~L~el~~~L~~~ 37 (64)
T PF09494_consen 20 LMYEPINLEELHAWLKAS 37 (64)
T ss_pred HcCCCccHHHHHHHHHHc
Confidence 479999999999999643
No 173
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=21.18 E-value=2.3e+02 Score=23.45 Aligned_cols=46 Identities=11% Similarity=0.100 Sum_probs=35.8
Q ss_pred HHHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeec
Q 031021 79 QSFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEG 126 (167)
Q Consensus 79 R~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~ 126 (167)
|..|...+.. ...++...|++.||+|..-++.-+..+ .+.|+-...
T Consensus 19 ~~~Il~~L~~-~~~vtv~eLa~~l~VS~~TIRRDL~~L-e~~G~l~r~ 64 (269)
T PRK09802 19 REQIIQRLRQ-QGSVQVNDLSALYGVSTVTIRNDLAFL-EKQGIAVRA 64 (269)
T ss_pred HHHHHHHHHH-cCCEeHHHHHHHHCCCHHHHHHHHHHH-HhCCCeEEE
Confidence 4455555554 556999999999999999888888776 778988753
No 174
>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=20.95 E-value=2.7e+02 Score=21.74 Aligned_cols=44 Identities=11% Similarity=0.101 Sum_probs=34.7
Q ss_pred HHHHHHHHHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceee
Q 031021 80 SFAIHVLSLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 80 ~~i~~vV~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~ 125 (167)
..|+..+.. ...++...+++.+|++...+...+... .+.||-..
T Consensus 146 ~~IL~~l~~-~g~~s~~eia~~l~is~stv~r~L~~L-e~~GlI~r 189 (203)
T TIGR01884 146 LKVLEVLKA-EGEKSVKNIAKKLGKSLSTISRHLREL-EKKGLVEQ 189 (203)
T ss_pred HHHHHHHHH-cCCcCHHHHHHHHCcCHHHHHHHHHHH-HHCCCEEE
Confidence 355555643 467999999999999998888888776 77899875
No 175
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=20.82 E-value=3.7e+02 Score=20.43 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=32.0
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcCceeecc
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWILEGD 127 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~~~~ 127 (167)
.-..+....+|+.||+++..+-+.++++ .+.||..-..
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL-~~~GlV~~~~ 58 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRL-ERLGLVEYEP 58 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHH-HHCCCeEEec
Confidence 6667889999999999999988888777 7899987533
No 176
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=20.65 E-value=2.9e+02 Score=18.85 Aligned_cols=35 Identities=14% Similarity=0.083 Sum_probs=25.5
Q ss_pred HHhcccccHHHHHHHhcCCchHHHHHHHHHhhhcCcee
Q 031021 87 SLTYQKIPRTVLAEAINLKGLSLDKFLEHQKANCGWIL 124 (167)
Q Consensus 87 ~~tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~GW~~ 124 (167)
..-...++.+.||+.+|+|...+...+++. .|.+.
T Consensus 16 ~~~~~~~~~~~lA~~~~~S~~~l~r~f~~~---~g~s~ 50 (107)
T PRK10219 16 EHIDQPLNIDVVAKKSGYSKWYLQRMFRTV---THQTL 50 (107)
T ss_pred HhcCCCCCHHHHHHHHCCCHHHHHHHHHHH---HCcCH
Confidence 334456899999999999988877777433 37664
No 177
>KOG4567 consensus GTPase-activating protein [General function prediction only]
Probab=20.11 E-value=1.1e+02 Score=26.87 Aligned_cols=48 Identities=15% Similarity=0.256 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHcCCccchhhhhcCCCccccCchhHHHHHHHHHHHHcCC
Q 031021 4 QIVARILIKALMAMPAPDFSLCLFLIPERVQMEDQFKTLIVLSHYLETGR 53 (167)
Q Consensus 4 ~iv~~ILlKaL~~~P~~DF~lc~~Ll~~~~~~~~~i~~i~~L~~lLe~c~ 53 (167)
.+.|.+|+-+=-++=..||..|+-||-... .-.+.+++++++.|...+
T Consensus 316 ~iCcsmlil~Re~il~~DF~~nmkLLQ~yp--~tdi~~~l~~A~~Lr~~k 363 (370)
T KOG4567|consen 316 YICCSMLILVRERILEGDFTVNMKLLQNYP--TTDISKMLAVADSLRDKK 363 (370)
T ss_pred HHHHHHHHHHHHHHHhcchHHHHHHHhcCC--CCCHHHHHHHHHHHHhcc
Confidence 567788887777788899999999974333 235788889999887543
No 178
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=20.07 E-value=1.8e+02 Score=19.88 Aligned_cols=32 Identities=9% Similarity=0.258 Sum_probs=27.6
Q ss_pred hcccccHHHHHHHhcCCchHHHHHHHHHhhhcC
Q 031021 89 TYQKIPRTVLAEAINLKGLSLDKFLEHQKANCG 121 (167)
Q Consensus 89 tyqsI~~~~L~~~Lgl~~~~l~~~~~~~~~~~G 121 (167)
-+.+.+...|+.-|+.+.+.++..++.|. ..|
T Consensus 13 ~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~-~kG 44 (78)
T PRK15431 13 LRGRMEAAQISQTLNTPQPMINAMLQQLE-SMG 44 (78)
T ss_pred HcCcccHHHHHHHHCcCHHHHHHHHHHHH-HCC
Confidence 47899999999999999999999998874 445
No 179
>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=20.05 E-value=2.6e+02 Score=18.05 Aligned_cols=47 Identities=19% Similarity=0.222 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHhcccccHHHHHHHhcCC-chHHHHHHHHHhhhcCceee
Q 031021 78 IQSFAIHVLSLTYQKIPRTVLAEAINLK-GLSLDKFLEHQKANCGWILE 125 (167)
Q Consensus 78 IR~~i~~vV~~tyqsI~~~~L~~~Lgl~-~~~l~~~~~~~~~~~GW~~~ 125 (167)
|=.||..-+...=..=+...+++.+|++ ...+...++.+ ++.||-.-
T Consensus 11 vL~~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~L-e~kG~I~r 58 (65)
T PF01726_consen 11 VLEFIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKAL-ERKGYIRR 58 (65)
T ss_dssp HHHHHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHH-HHTTSEEE
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHH-HHCcCccC
Confidence 4445555555555556788899999997 57788888766 78898764
Done!