Query gi|254781188|ref|YP_003065601.1| hypothetical protein CLIBASIA_05475 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 185
No_of_seqs 92 out of 94
Neff 3.5
Searched_HMMs 39220
Date Mon May 30 06:43:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781188.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00569 HTH_Hin_like Helix-tur 96.5 0.0042 1.1E-07 41.9 4.2 37 21-58 6-42 (42)
2 pfam01527 Transposase_8 Transp 96.0 0.012 3E-07 38.9 4.6 42 19-61 5-47 (75)
3 PRK13413 mpi multiple promoter 96.0 0.0097 2.5E-07 39.5 4.0 55 9-64 143-199 (200)
4 pfam02796 HTH_7 Helix-turn-hel 95.9 0.0099 2.5E-07 39.4 4.0 45 12-61 1-45 (45)
5 pfam01710 Transposase_14 Trans 95.7 0.0088 2.2E-07 39.8 2.8 75 20-95 2-78 (120)
6 pfam04218 CENP-B_N CENP-B N-te 94.6 0.078 2E-06 33.4 5.0 46 21-67 7-52 (53)
7 COG3415 Transposase and inacti 93.4 0.097 2.5E-06 32.8 3.6 42 21-63 5-47 (138)
8 pfam05225 HTH_psq helix-turn-h 91.2 0.33 8.4E-06 29.3 4.1 39 23-62 2-41 (45)
9 pfam07141 Phage_term_sma Putat 91.0 0.81 2.1E-05 26.6 6.0 133 9-146 4-156 (174)
10 COG2963 Transposase and inacti 89.1 0.74 1.9E-05 26.9 4.4 45 18-62 5-50 (116)
11 pfam03811 Ins_element1 Inserti 87.8 0.67 1.7E-05 27.2 3.5 40 21-61 48-87 (88)
12 pfam08822 DUF1804 Protein of u 83.4 2.9 7.3E-05 23.0 5.0 54 22-76 4-58 (165)
13 COG1710 Uncharacterized protei 79.1 3.4 8.8E-05 22.4 4.2 43 18-61 91-133 (139)
14 PRK09409 insertion element IS2 76.4 0.93 2.4E-05 26.2 0.6 38 27-65 2-39 (301)
15 pfam12017 Transposase_37 Trans 74.6 7.9 0.0002 20.0 5.0 65 10-74 61-130 (236)
16 pfam09339 HTH_IclR IclR helix- 72.7 5.8 0.00015 20.9 3.9 37 24-61 3-42 (52)
17 PRK11640 putative transcriptio 71.0 9.6 0.00024 19.5 6.8 61 24-85 8-69 (191)
18 smart00421 HTH_LUXR helix_turn 70.6 4.6 0.00012 21.6 3.0 34 26-60 8-41 (58)
19 PRK09413 insertion sequence 2 70.4 7.1 0.00018 20.3 4.0 39 21-60 14-52 (121)
20 smart00346 HTH_ICLR helix_turn 69.0 7.8 0.0002 20.1 3.9 36 24-60 5-43 (91)
21 COG2320 GrpB Uncharacterized c 68.2 8.2 0.00021 19.9 3.9 38 53-90 134-171 (185)
22 pfam00196 GerE Bacterial regul 66.6 6.6 0.00017 20.6 3.1 35 25-60 7-41 (58)
23 PRK06474 hypothetical protein; 66.2 9.4 0.00024 19.5 3.9 33 27-60 14-51 (180)
24 pfam07508 Recombinase Recombin 65.5 8.2 0.00021 19.9 3.5 38 23-60 4-51 (101)
25 cd06170 LuxR_C_like C-terminal 64.8 7.3 0.00018 20.3 3.1 34 26-60 5-38 (57)
26 TIGR03613 RutR pyrimidine util 64.1 13 0.00033 18.6 8.7 87 24-123 15-102 (202)
27 pfam08148 DSHCT DSHCT (NUC185) 63.6 13 0.00034 18.5 4.3 53 22-76 100-152 (179)
28 pfam12298 Bot1p Eukaryotic mit 63.0 14 0.00035 18.4 6.0 55 21-76 17-82 (171)
29 PRK09834 DNA-binding transcrip 62.9 11 0.00029 18.9 3.8 38 22-60 9-49 (264)
30 PRK10163 DNA-binding transcrip 61.9 13 0.00034 18.5 4.0 38 22-60 23-63 (271)
31 pfam01726 LexA_DNA_bind LexA D 61.6 14 0.00036 18.4 4.1 39 22-60 8-49 (65)
32 PRK11569 transcriptional repre 61.3 14 0.00036 18.3 4.1 41 22-63 26-78 (274)
33 pfam00440 TetR_N Bacterial reg 60.3 11 0.00028 19.0 3.3 39 26-65 5-44 (47)
34 COG3311 AlpA Predicted transcr 60.0 6.6 0.00017 20.6 2.1 23 38-61 15-37 (70)
35 PRK11202 DNA-binding transcrip 59.1 11 0.00028 19.1 3.2 42 24-66 15-61 (203)
36 pfam00195 Chal_sti_synt_N Chal 58.9 8 0.0002 20.0 2.4 66 20-85 30-104 (228)
37 COG2452 Predicted site-specifi 58.3 8.1 0.00021 19.9 2.4 24 37-61 2-25 (193)
38 PRK11886 biotin--protein ligas 58.2 16 0.00042 17.9 4.0 39 22-61 2-42 (319)
39 pfam05930 Phage_AlpA Prophage 57.7 7.6 0.00019 20.1 2.1 23 38-61 5-27 (51)
40 COG2826 Tra8 Transposase and i 55.7 18 0.00046 17.6 4.7 35 27-62 14-48 (318)
41 pfam06056 Terminase_5 Putative 55.6 6.6 0.00017 20.5 1.6 30 32-62 9-38 (58)
42 PRK00215 LexA repressor; Valid 54.8 19 0.00048 17.5 4.1 42 22-63 6-50 (204)
43 KOG2690 consensus 54.3 19 0.00048 17.5 6.0 35 23-57 177-213 (331)
44 TIGR03001 Sig-70_gmx1 RNA poly 53.9 18 0.00045 17.7 3.5 42 33-75 179-221 (249)
45 pfam00392 GntR Bacterial regul 52.9 20 0.00051 17.3 4.3 37 23-60 3-47 (64)
46 COG1414 IclR Transcriptional r 51.7 21 0.00053 17.2 4.0 36 24-60 4-42 (246)
47 PRK09958 DNA-binding transcrip 51.3 18 0.00047 17.6 3.2 27 102-128 143-169 (204)
48 PRK10840 transcriptional regul 49.5 21 0.00053 17.2 3.3 28 102-129 150-177 (216)
49 pfam04546 Sigma70_ner Sigma-70 49.1 23 0.00058 16.9 4.5 14 20-33 122-135 (210)
50 PRK10360 DNA-binding transcrip 49.1 21 0.00055 17.1 3.3 30 28-58 144-173 (196)
51 pfam06530 Phage_antitermQ Phag 49.0 23 0.00058 16.9 5.6 56 21-77 63-118 (126)
52 pfam00891 Methyltransf_2 O-met 47.1 25 0.00063 16.7 7.1 56 24-85 39-94 (239)
53 PRK09483 response regulator; P 47.0 24 0.00061 16.8 3.3 29 101-129 147-175 (216)
54 COG2005 ModE N-terminal domain 45.8 21 0.00053 17.2 2.8 66 27-112 22-87 (130)
55 pfam04229 UPF0157 Uncharacteri 45.6 20 0.00051 17.4 2.7 31 51-81 117-147 (167)
56 COG3677 Transposase and inacti 45.6 22 0.00055 17.1 2.9 40 22-62 75-114 (129)
57 cd07377 WHTH_GntR Winged helix 44.9 26 0.00068 16.5 4.2 37 23-60 4-48 (66)
58 cd04762 HTH_MerR-trunc Helix-T 44.1 17 0.00043 17.8 2.2 23 38-61 2-24 (49)
59 smart00345 HTH_GNTR helix_turn 44.1 27 0.00069 16.4 3.2 34 25-59 1-42 (60)
60 PRK10403 transcriptional regul 43.5 28 0.00071 16.4 3.2 27 103-129 154-180 (215)
61 cd00090 HTH_ARSR Arsenical Res 43.3 27 0.0007 16.4 3.1 37 23-60 6-43 (78)
62 TIGR01764 excise DNA binding d 42.9 17 0.00044 17.8 2.0 25 37-62 2-26 (49)
63 PRK10651 transcriptional regul 41.5 30 0.00076 16.2 3.3 30 101-130 154-183 (216)
64 TIGR02233 Myxo_sigma_rel Myxoc 41.4 27 0.00068 16.5 2.8 32 32-64 36-67 (106)
65 PRK12423 LexA repressor; Provi 39.5 32 0.00081 16.0 4.1 42 22-63 8-52 (202)
66 PRK09975 DNA-binding transcrip 39.4 32 0.00082 16.0 6.1 44 26-70 20-65 (213)
67 PRK10676 DNA-binding transcrip 38.7 33 0.00084 15.9 5.6 33 27-60 22-54 (262)
68 PRK09978 DNA-binding transcrip 38.3 33 0.00085 15.8 5.8 110 22-138 144-254 (274)
69 PRK09935 transcriptional regul 37.6 34 0.00087 15.8 3.4 25 103-127 150-174 (210)
70 TIGR03020 EpsA transcriptional 37.5 34 0.00087 15.8 3.4 79 50-128 134-216 (247)
71 TIGR02329 propionate_PrpR prop 35.3 16 0.00041 18.0 0.9 13 137-149 559-571 (658)
72 TIGR01932 hflC HflC protein; I 35.0 37 0.00095 15.5 5.4 63 18-81 228-294 (345)
73 PRK11475 DNA-binding transcrip 34.1 39 0.00098 15.4 3.2 25 103-127 135-159 (205)
74 PRK05634 nucleosidase; Provisi 33.5 6.8 0.00017 20.4 -1.2 50 34-85 135-186 (188)
75 pfam03333 PapB Adhesin biosynt 33.5 39 0.001 15.4 5.4 47 22-69 39-85 (91)
76 TIGR02564 cas_Csy1 CRISPR-asso 32.7 41 0.001 15.3 4.0 44 27-74 74-120 (413)
77 PRK10100 DNA-binding transcrip 32.3 41 0.0011 15.2 3.3 15 44-58 58-72 (216)
78 COG2197 CitB Response regulato 31.8 42 0.0011 15.2 3.2 33 26-59 153-185 (211)
79 KOG4398 consensus 31.5 42 0.0011 15.1 5.9 44 97-146 36-79 (359)
80 PRK09390 fixJ response regulat 30.9 43 0.0011 15.1 3.2 83 45-127 54-166 (202)
81 pfam03374 ANT Phage antirepres 30.9 43 0.0011 15.1 2.6 38 24-63 13-50 (112)
82 TIGR00089 TIGR00089 RNA modifi 30.8 41 0.001 15.3 2.4 106 15-128 284-396 (455)
83 PRK01381 Trp operon repressor; 30.3 27 0.00068 16.5 1.4 28 28-56 46-74 (99)
84 PRK09940 transcriptional regul 30.3 44 0.0011 15.0 5.1 95 20-129 134-229 (253)
85 pfam05009 EBV-NA3 Epstein-Barr 30.2 45 0.0011 15.0 3.5 42 22-63 105-150 (254)
86 cd06171 Sigma70_r4 Sigma70, re 29.7 45 0.0012 14.9 4.0 39 21-60 11-49 (55)
87 pfam03746 LamB_YcsF LamB/YcsF 29.6 46 0.0012 14.9 6.9 57 12-74 71-133 (242)
88 pfam00356 LacI Bacterial regul 29.5 46 0.0012 14.9 2.8 26 38-64 1-26 (46)
89 pfam11626 Rap1_C Rap1 - C term 29.2 38 0.00097 15.4 2.0 36 18-63 5-40 (68)
90 KOG2829 consensus 28.5 45 0.0011 15.0 2.2 43 15-58 59-101 (326)
91 COG1309 AcrR Transcriptional r 27.9 49 0.0012 14.7 4.9 47 23-70 15-65 (201)
92 PRK03333 coaE dephospho-CoA ki 27.7 49 0.0013 14.7 2.6 30 54-83 336-365 (394)
93 pfam00126 HTH_1 Bacterial regu 27.2 50 0.0013 14.7 2.8 34 28-62 5-38 (60)
94 PRK11523 DNA-binding transcrip 26.9 51 0.0013 14.6 3.8 38 21-59 9-54 (258)
95 PRK05406 LamB/YcsF family prot 26.7 51 0.0013 14.6 6.7 57 12-74 73-135 (246)
96 pfam08765 Mor Mor transcriptio 26.2 52 0.0013 14.5 3.3 34 25-60 61-94 (107)
97 TIGR03337 phnR transcriptional 26.1 53 0.0013 14.5 4.0 37 23-60 4-48 (231)
98 pfam09862 DUF2089 Protein of u 25.8 53 0.0014 14.5 4.0 39 21-60 34-72 (113)
99 pfam08281 Sigma70_r4_2 Sigma-7 25.7 53 0.0014 14.5 3.7 38 22-60 12-49 (54)
100 PHA00542 putative Cro-like pro 25.4 45 0.0011 15.0 1.8 47 20-66 15-63 (82)
101 pfam00165 HTH_AraC Bacterial r 25.2 52 0.0013 14.6 2.1 32 30-61 2-33 (43)
102 COG3645 Uncharacterized phage- 25.2 49 0.0012 14.7 2.0 27 35-62 45-72 (135)
103 COG2771 CsgD DNA-binding HTH d 24.9 55 0.0014 14.4 3.2 35 26-61 9-43 (65)
104 pfam12116 SpoIIID Stage III sp 24.8 55 0.0014 14.4 5.9 40 20-60 2-42 (82)
105 pfam07618 DUF1580 Protein of u 24.7 44 0.0011 15.0 1.7 22 40-61 4-25 (56)
106 TIGR01588 citE citrate lyase, 24.5 19 0.00048 17.5 -0.3 59 38-96 177-242 (288)
107 pfam07374 DUF1492 Protein of u 24.3 52 0.0013 14.6 2.0 25 35-60 70-94 (100)
108 TIGR03338 phnR_burk phosphonat 23.8 58 0.0015 14.2 3.9 38 21-59 12-56 (212)
109 KOG1488 consensus 23.8 58 0.0015 14.2 4.7 74 78-151 281-367 (503)
110 COG1922 WecG Teichoic acid bio 23.4 59 0.0015 14.2 3.2 130 1-157 1-141 (253)
111 COG1102 Cmk Cytidylate kinase 23.0 60 0.0015 14.1 4.4 60 12-73 7-67 (179)
112 pfam01418 HTH_6 Helix-turn-hel 23.0 60 0.0015 14.1 3.0 50 22-72 18-74 (106)
113 PRK09526 lacI lac repressor; R 22.9 60 0.0015 14.1 2.7 24 38-62 7-30 (342)
114 TIGR00637 ModE_repress ModE mo 22.8 60 0.0015 14.1 3.1 38 25-63 5-42 (101)
115 PRK10079 putative transcriptio 22.6 61 0.0016 14.1 3.6 36 23-60 15-58 (241)
116 COG5211 SSU72 RNA polymerase I 22.5 61 0.0016 14.1 3.0 57 19-83 110-167 (197)
117 COG3636 Predicted transcriptio 22.3 62 0.0016 14.1 3.7 48 23-71 36-85 (100)
118 KOG1986 consensus 21.7 63 0.0016 14.0 3.0 83 51-155 644-741 (745)
119 KOG0749 consensus 21.4 63 0.0016 14.0 1.9 56 27-83 211-266 (298)
120 PRK10014 DNA-binding transcrip 21.1 65 0.0017 13.9 2.7 21 39-60 9-29 (342)
121 COG5114 Histone acetyltransfer 21.1 65 0.0017 13.9 4.5 87 39-136 74-163 (432)
122 pfam02954 HTH_8 Bacterial regu 20.9 66 0.0017 13.9 3.5 32 29-61 10-42 (42)
123 pfam08279 HTH_11 HTH domain. T 20.6 67 0.0017 13.8 3.0 33 27-60 3-38 (55)
124 TIGR01884 cas_HTH CRISPR locus 20.6 67 0.0017 13.8 3.8 38 24-62 169-209 (231)
125 PRK04330 hypothetical protein; 20.2 68 0.0017 13.8 2.3 11 39-49 18-28 (88)
126 pfam01381 HTH_3 Helix-turn-hel 20.2 68 0.0017 13.8 3.9 39 32-71 5-45 (55)
127 pfam03685 UPF0147 Uncharacteri 20.1 68 0.0017 13.8 2.3 10 40-49 16-25 (85)
128 TIGR01422 phosphonatase phosph 20.1 53 0.0014 14.5 1.3 67 38-111 50-117 (199)
129 smart00530 HTH_XRE Helix-turn- 20.1 68 0.0017 13.8 3.9 29 32-61 6-34 (56)
130 TIGR00034 aroFGH phospho-2-deh 20.1 68 0.0017 13.8 1.9 17 22-38 278-294 (348)
131 KOG4565 consensus 20.0 48 0.0012 14.8 1.1 49 9-58 109-159 (206)
No 1
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=96.45 E-value=0.0042 Score=41.90 Aligned_cols=37 Identities=27% Similarity=0.591 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 58999999999985892389996158898888999998
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWI 58 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL 58 (185)
+|++-++++-..+++|+|..+||+..|+ |.+|+|+++
T Consensus 6 lt~~q~~~ar~l~~~G~~~~~iA~~~GV-sr~Tiyr~l 42 (42)
T cd00569 6 LTPEQIEEARRLLAAGESVAEIARRLGV-SRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHC
T ss_conf 9999999999999978989999999797-999998659
No 2
>pfam01527 Transposase_8 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family consists of various E. coli insertion elements and other bacterial transposases some of which are members of the IS3 family.
Probab=96.00 E-value=0.012 Score=38.90 Aligned_cols=42 Identities=29% Similarity=0.488 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHH-HCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 445899999999998-5892389996158898888999998339
Q gi|254781188|r 19 IYYSPELFAGILDQV-ANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 19 i~Ys~Eiad~Ic~rI-A~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
..||+|+-..|+... ..|.|+..||+..|+ +.+|||+|++..
T Consensus 5 rrys~efK~~~V~~~~~~g~sv~~var~~gi-~~~~l~~W~k~~ 47 (75)
T pfam01527 5 RRYSEEFKARAVKESLEPGASVSELAREHGV-SPATLYKWRKKY 47 (75)
T ss_pred CCCCHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHHH
T ss_conf 8899999999999998099849999999895-999999999998
No 3
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=95.96 E-value=0.0097 Score=39.47 Aligned_cols=55 Identities=18% Similarity=0.205 Sum_probs=41.2
Q ss_pred HHHCCCCCC--CCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHH
Q ss_conf 540246567--64458999999999985892389996158898888999998339899
Q gi|254781188|r 9 KKAVRAKKG--CIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKL 64 (185)
Q Consensus 9 ~Ka~R~Kk~--~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEf 64 (185)
++.||+|.+ ..+....-...|...+..|.|.++|++..|+ |.+|||+|++..+|+
T Consensus 143 ~~~GRpk~~~~~~~~~~~~~~~i~~~~~~g~s~~~iak~~gv-srsTvyR~lK~~~e~ 199 (200)
T PRK13413 143 AKLGRPKGDRPEKYKLHGKEEVITKELKKGTTKSEIAKKLKV-SRTTLARFLKTMYEI 199 (200)
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHHHHCC
T ss_conf 656888889864112479999999999888999999999892-999999999744107
No 4
>pfam02796 HTH_7 Helix-turn-helix domain of resolvase.
Probab=95.94 E-value=0.0099 Score=39.43 Aligned_cols=45 Identities=20% Similarity=0.398 Sum_probs=39.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 24656764458999999999985892389996158898888999998339
Q gi|254781188|r 12 VRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 12 ~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
||..+ ++++-++.|..++.+|.|+.+||+..|+ |.+|||+.+.+.
T Consensus 1 GRp~k----l~~~~~~~v~~L~~~G~~i~~IA~~~~v-srsTvYRyl~~~ 45 (45)
T pfam02796 1 GRPPK----LNEEDINEVITLLEEGISIKQIAKIFGI-SRSTVYRYLAAS 45 (45)
T ss_pred CCCCC----CCHHHHHHHHHHHHCCCCHHHHHHHHCC-HHHHHHHHCCCC
T ss_conf 98510----3899999999999879949999999860-088887644589
No 5
>pfam01710 Transposase_14 Transposase. Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis PCC 6803 three of which are characterized as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily.
Probab=95.67 E-value=0.0088 Score=39.76 Aligned_cols=75 Identities=21% Similarity=0.373 Sum_probs=50.4
Q ss_pred CCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHH--HHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 45899999999998589238999615889888899999833989--99999999997379999998620023005640
Q gi|254781188|r 20 YYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLK--LQEAYTEALQCRLDLLAEELLEEPAPTAEELA 95 (185)
Q Consensus 20 ~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeE--freqYa~Are~qaD~laEEILE~~a~~~ee~~ 95 (185)
.||-++-..|++-+-.|.|.+++++..++ |.+|+++|++..+. ..-+-....-.-.|.|.+.+-+.|+-+-.|.|
T Consensus 2 aYS~DlR~rVl~~ve~G~S~~eaA~~F~I-s~~Tv~rWlkr~~~~~~~~~~r~~~Kid~~~L~~~V~~~pD~tl~E~A 78 (120)
T pfam01710 2 AYSLDLRKKVIDYIESGGSITEASKVFQI-GRATIYRWLKREKLGALKVEPRGRHKIDRDALKNDVKDNPDAYLKERA 78 (120)
T ss_pred CCCHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHCHHCCCCCCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf 87689999999999869999999999370-299999998550014778888898877899999999988672099999
No 6
>pfam04218 CENP-B_N CENP-B N-terminal DNA-binding domain. Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure.
Probab=94.59 E-value=0.078 Score=33.45 Aligned_cols=46 Identities=17% Similarity=0.271 Sum_probs=39.8
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHH
Q ss_conf 58999999999985892389996158898888999998339899999
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEA 67 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreq 67 (185)
+|-+-=-.|+.++-+|+|-.+++++.|+| -+|++.|++..+.+-++
T Consensus 7 LTl~eKi~iI~~~e~G~s~~~lar~~gi~-~STl~~I~Knkekil~~ 52 (53)
T pfam04218 7 LTLREKIEVIQRSEEGESKASLARRFNVP-RSTLRDILKNKEKLLKE 52 (53)
T ss_pred ECHHHHHHHHHHHHCCCCHHHHHHHHCCC-HHHHHHHHHHHHHHHHH
T ss_conf 16999999999998589688999996987-97999999809999861
No 7
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.35 E-value=0.097 Score=32.80 Aligned_cols=42 Identities=26% Similarity=0.594 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHH-HCCHHHHHHHHCCCCCCHHHHHHHHHCCHH
Q ss_conf 5899999999998-589238999615889888899999833989
Q gi|254781188|r 21 YSPELFAGILDQV-ANGKALGHVLRKVGMPKYSTFYRWIKKDLK 63 (185)
Q Consensus 21 Ys~Eiad~Ic~rI-A~GeSLr~ICkd~gMPs~sTV~rWL~kdeE 63 (185)
|+.++-..++..+ ..|.|.++|.+..|+ |.+|+++|++...+
T Consensus 5 ~s~~~R~~~~~~~~~~G~S~re~Ak~~gv-s~sTvy~wv~r~~e 47 (138)
T COG3415 5 FSNDLRERVVDAVVGEGLSCREAAKRFGV-SISTVYRWVRRYRE 47 (138)
T ss_pred HHHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHHHCC
T ss_conf 47899999999999768549999999692-29999999987333
No 8
>pfam05225 HTH_psq helix-turn-helix, Psq domain. This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster. In pipsqueak this domain binds to GAGA sequence.
Probab=91.21 E-value=0.33 Score=29.26 Aligned_cols=39 Identities=36% Similarity=0.550 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHCC-HHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 99999999998589-23899961588988889999983398
Q gi|254781188|r 23 PELFAGILDQVANG-KALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 23 ~Eiad~Ic~rIA~G-eSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
+|-++.=++.|-+| .|+++.++..|+| ++|+|+.++-..
T Consensus 2 ee~l~~Al~av~~g~~S~~kAa~~ygIP-~sTL~~r~~g~~ 41 (45)
T pfam05225 2 EEDLAEALEAVRNGKMSLRKAARKYGIP-RSTLWRRLRGKY 41 (45)
T ss_pred HHHHHHHHHHHHCCCCCHHHHHHHHCCC-HHHHHHHHCCCC
T ss_conf 7899999999991996799999997898-589999975634
No 9
>pfam07141 Phage_term_sma Putative bacteriophage terminase small subunit. This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.
Probab=91.04 E-value=0.81 Score=26.64 Aligned_cols=133 Identities=24% Similarity=0.362 Sum_probs=82.9
Q ss_pred HHHCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHH--------HHH
Q ss_conf 540246567644589999999999858923899961588988889999983398999999999997379--------999
Q gi|254781188|r 9 KKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLD--------LLA 80 (185)
Q Consensus 9 ~Ka~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD--------~la 80 (185)
.|-||++-.+--|..-++.+|.+.|..|-.-|.|-...+- |-.||..|-.++- ..|..|+-..-- .++
T Consensus 4 qkggrptilpkmyeeplfsqiidkiesgcndreiytslhc-saktfrkwrddni---kaydeakgiargnllelaesala 79 (174)
T pfam07141 4 QKGGRPTILPKMYEEPLFSQIIDKIESGCNDREIYTSLHC-SAKTFRKWRDDNI---KAYDEAKGIARGNLLELAESALA 79 (174)
T ss_pred CCCCCCCCCHHHHCCHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHCCH---HHHHHHCCCCCCCHHHHHHHHHH
T ss_conf 6689874456653123799999999748851454554201-4788887631324---56566403000029999999875
Q ss_pred HHHH----HHCCCCHHHHHCCHHHHHHHHHHHHHH---HHHHHH-HHHHHHHH----HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9986----200230056403603789979999889---999987-64665343----420344331346788999999
Q gi|254781188|r 81 EELL----EEPAPTAEELANPVFYSKMRDRKQRMG---TFLLEK-LSNQKYGP----RVSVESKHTIDLRPAIERLRE 146 (185)
Q Consensus 81 EEIL----E~~a~~~ee~~~~~~~~~lr~~~~~~~---~w~l~k-~~p~~yg~----rvs~e~~h~~~~~~~~~~~~~ 146 (185)
..+. -+--.+-+...| |.+.+++....--. ....+| -+|+.|.+ |..||-+..|||+.-|+.+..
T Consensus 80 skltvrtlketetiydadgn-vekvkvkekeldkdslvammvakagnpelynptewrrlqqeessahdlkakieeldd 156 (174)
T pfam07141 80 SKLTVRTLKETETIYDADGN-VEKVKVKEKELDKDSLVAMMVAKAGNPELYNPTEWRRLQQEESSAHDLKAKIEELDD 156 (174)
T ss_pred HHHHHHHHCCCCEEECCCCC-EEEEEECHHHCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 33213301132125637898-655651054315365899999853895546838998988754104568887776532
No 10
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.07 E-value=0.74 Score=26.90 Aligned_cols=45 Identities=22% Similarity=0.386 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 64458999999999985-8923899961588988889999983398
Q gi|254781188|r 18 CIYYSPELFAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 18 ~i~Ys~Eiad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
+..||+|+=.+|..... .|.|+.+||+..|+-+-+++|+|+....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~~W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLYKWRIQLQ 50 (116)
T ss_pred CCCCCHHHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 3648999999999999817835999999948775378999999998
No 11
>pfam03811 Ins_element1 Insertion element protein.
Probab=87.81 E-value=0.67 Score=27.18 Aligned_cols=40 Identities=23% Similarity=0.257 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 58999999999985892389996158898888999998339
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
|.|++-++|.+.-.+|.++|++.+-.++ +..||.+||++.
T Consensus 48 ~~p~vkeqiv~m~~nG~GiRdtaRvl~I-s~nTVlrtLK~s 87 (88)
T pfam03811 48 RQPGTKEQIVDMAMNGAGCRYTARTLKI-GINTVIRTLKNS 87 (88)
T ss_pred CCCCHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHCC
T ss_conf 5814789999997679854044787375-689999987535
No 12
>pfam08822 DUF1804 Protein of unknown function (DUF1804). This family of bacterial protein is uncharacterized.
Probab=83.42 E-value=2.9 Score=22.95 Aligned_cols=54 Identities=19% Similarity=0.227 Sum_probs=40.5
Q ss_pred CHHHHHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 8999999999985-892389996158898888999998339899999999999737
Q gi|254781188|r 22 SPELFAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRL 76 (185)
Q Consensus 22 s~Eiad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qa 76 (185)
.+|.-+.+=.... ++.||...+...|+| ++|..+|=.+..+..+....||..+.
T Consensus 4 ~~e~r~~vR~~Yv~~~~~Le~aA~~~gV~-~~TArrWK~~Ak~~GDDWDkaRaA~~ 58 (165)
T pfam08822 4 PKETRDAVRRLYVFDRLTLEVAAAKAGVS-YSTARRWKREAKAKGDDWDKARAAYT 58 (165)
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHCCCC-HHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 68999999999996678799999880998-88899999988875883899999999
No 13
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=79.14 E-value=3.4 Score=22.44 Aligned_cols=43 Identities=26% Similarity=0.389 Sum_probs=36.9
Q ss_pred CCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 64458999999999985892389996158898888999998339
Q gi|254781188|r 18 CIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 18 ~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
..+|+.....-|-+-+-+|+.-|.|+++.|.| -.|||-.+.+-
T Consensus 91 prkyd~~t~~~i~emlr~gk~preIsk~lGIp-irTvyY~l~k~ 133 (139)
T COG1710 91 PRKYDRNTLLRIREMLRNGKTPREISKDLGIP-IRTVYYLLKKL 133 (139)
T ss_pred CCCCCHHHHHHHHHHHHCCCCHHHHHHHHCCC-HHHHHHHHHHH
T ss_conf 75434548999999998499877888860986-22069999987
No 14
>PRK09409 insertion element IS2 transposase InsD; Reviewed
Probab=76.42 E-value=0.93 Score=26.25 Aligned_cols=38 Identities=11% Similarity=0.080 Sum_probs=32.3
Q ss_pred HHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHH
Q ss_conf 999999858923899961588988889999983398999
Q gi|254781188|r 27 AGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQ 65 (185)
Q Consensus 27 d~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfr 65 (185)
|--+..++.|-++..+|+--|+ |.+++|.|++..++-.
T Consensus 2 ~~a~~l~a~g~~v~~~cr~LgV-SRS~~y~~~~r~~~~~ 39 (301)
T PRK09409 2 DSARALIARGWGVSLVSRCLRV-SRAQLHVILRRTDDWM 39 (301)
T ss_pred CHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHCCCCCCCC
T ss_conf 2588999689749999999786-6877444302675444
No 15
>pfam12017 Transposase_37 Transposase protein. Protein in this family are transposases found in insects. This region is about 230 amino acids in length and is found associated with pfam05485.
Probab=74.62 E-value=7.9 Score=20.03 Aligned_cols=65 Identities=17% Similarity=0.360 Sum_probs=44.4
Q ss_pred HHCCCCCCCCCCCH-HHHHHHHHHHHCCHHHHHHHH-CCCCCCHHHHHHHHHC---CHHHHHHHHHHHHH
Q ss_conf 40246567644589-999999999858923899961-5889888899999833---98999999999997
Q gi|254781188|r 10 KAVRAKKGCIYYSP-ELFAGILDQVANGKALGHVLR-KVGMPKYSTFYRWIKK---DLKLQEAYTEALQC 74 (185)
Q Consensus 10 Ka~R~Kk~~i~Ys~-Eiad~Ic~rIA~GeSLr~ICk-d~gMPs~sTV~rWL~k---deEfreqYa~Are~ 74 (185)
++++.+...+.||+ ++..+||-+-+.-..-+-+.+ ..-.||.+|+++|+.+ +|+|-+.--..++.
T Consensus 61 ~~l~~~~Kr~~wt~ed~~~Al~L~~~sPraY~yL~~k~fpLPs~rTL~r~l~~v~~~pG~l~~vl~~l~~ 130 (236)
T pfam12017 61 KILKSGGKRSTFNSDDMSAAICLHTAGPRAYNHLYKKGFPLPSRATLYRWLSDVEIKTGTLDVVIDLMEN 130 (236)
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHC
T ss_conf 9985688757258999999888875191999999980899998799999986277788743899999851
No 16
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=72.65 E-value=5.8 Score=20.92 Aligned_cols=37 Identities=30% Similarity=0.454 Sum_probs=29.0
Q ss_pred HHHHHHHHHHH---CCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 99999999985---892389996158898888999998339
Q gi|254781188|r 24 ELFAGILDQVA---NGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 24 Eiad~Ic~rIA---~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
+-+-.|++.++ .+.+++.||+.-||| .+|+||-++.=
T Consensus 3 ~r~l~iL~~~~~~~~~~~l~eia~~~gl~-kstv~RlL~tL 42 (52)
T pfam09339 3 DRALAILEALAEAPGGLSLTEIARRTGLP-KSTAHRLLQTL 42 (52)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHHH
T ss_conf 99999999986289998999999998919-99999999999
No 17
>PRK11640 putative transcriptional regulator; Provisional
Probab=70.96 E-value=9.6 Score=19.46 Aligned_cols=61 Identities=18% Similarity=0.170 Sum_probs=48.6
Q ss_pred HHHHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999985-892389996158898888999998339899999999999737999999862
Q gi|254781188|r 24 ELFAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLE 85 (185)
Q Consensus 24 Eiad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE 85 (185)
+.+...|.+=+ ..-++-.|+..-|+ +..|+|++....+++=..|.+-+..+.+....+.+.
T Consensus 8 ~~A~~LFy~~Gi~atGid~I~~eAgV-aK~TLY~hF~SKd~LI~a~L~~~~~~~~~w~~~~~~ 69 (191)
T PRK11640 8 GEALKLLEQQGIANTTLEMVAERVDY-PLDELQRFWPDKEALLYDALRYLSQQIDVWRRQLLL 69 (191)
T ss_pred HHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 99999999749420479999999599-899999877988999999999976799999999876
No 18
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=70.60 E-value=4.6 Score=21.58 Aligned_cols=34 Identities=15% Similarity=0.227 Sum_probs=30.4
Q ss_pred HHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 99999998589238999615889888899999833
Q gi|254781188|r 26 FAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 26 ad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
--+|+..++.|.|.+.|+..-|+ +.+||...+..
T Consensus 8 E~~il~~l~~G~s~~eIA~~L~i-s~~TV~~~~~~ 41 (58)
T smart00421 8 EREVLRLLAEGLTNKEIAERLGI-SEKTVKTHLSN 41 (58)
T ss_pred HHHHHHHHHHCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 99999999817999999989897-89899999999
No 19
>PRK09413 insertion sequence 2 OrfA protein; Reviewed
Probab=70.40 E-value=7.1 Score=20.32 Aligned_cols=39 Identities=23% Similarity=0.371 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 5899999999998589238999615889888899999833
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.++|-+.-+-+-+.-|.|...||+..|+ +.+.+|+|-+-
T Consensus 14 s~~EK~~IV~es~ePG~sVs~VARrHGi-~~~qlf~WRr~ 52 (121)
T PRK09413 14 TTQEKIAIVQQSFEPGMTVSLVARQHGV-AASQLFLWRKQ 52 (121)
T ss_pred CHHHHHHHHHHHHCCCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 8899999999995699849999999499-89999999999
No 20
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=69.05 E-value=7.8 Score=20.06 Aligned_cols=36 Identities=25% Similarity=0.356 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHC---CHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 999999999858---9238999615889888899999833
Q gi|254781188|r 24 ELFAGILDQVAN---GKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 24 Eiad~Ic~rIA~---GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
+-+-.|++.|+. +.++..|++.-||| .+|+|+-++.
T Consensus 5 ~ral~IL~~l~~~~~~~sl~eia~~~~l~-ksT~~RlL~t 43 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGLS-KSTAHRLLNT 43 (91)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 99999999997289998999999998909-9999999999
No 21
>COG2320 GrpB Uncharacterized conserved protein [Function unknown]
Probab=68.17 E-value=8.2 Score=19.91 Aligned_cols=38 Identities=24% Similarity=0.412 Sum_probs=32.5
Q ss_pred HHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999833989999999999973799999986200230
Q gi|254781188|r 53 TFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPT 90 (185)
Q Consensus 53 TV~rWL~kdeEfreqYa~Are~qaD~laEEILE~~a~~ 90 (185)
-|..||+.+|+.++.|++-+..-+.-..+|++.+-+-.
T Consensus 134 ~FrD~Lra~P~~~~~Y~~lKr~laa~~~~e~~~Y~~~K 171 (185)
T COG2320 134 LFRDWLRANPEIREAYAELKRELAAQEDDEILRYTAAK 171 (185)
T ss_pred HHHHHHHHCHHHHHHHHHHHHHHHHHCHHHHHHHHHHH
T ss_conf 99999985978899999999999985648898887600
No 22
>pfam00196 GerE Bacterial regulatory proteins, luxR family.
Probab=66.59 E-value=6.6 Score=20.56 Aligned_cols=35 Identities=17% Similarity=0.125 Sum_probs=30.7
Q ss_pred HHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 999999998589238999615889888899999833
Q gi|254781188|r 25 LFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 25 iad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
---+|+..++.|.+-+.|+..-|+ +.+||...+..
T Consensus 7 RE~~il~~l~~G~s~~eIA~~L~i-s~~TV~~h~~~ 41 (58)
T pfam00196 7 REREVLRLLAAGKSNKEIADILGI-SEKTVKVHRSN 41 (58)
T ss_pred HHHHHHHHHHHCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 999999999807999999999788-89999999999
No 23
>PRK06474 hypothetical protein; Provisional
Probab=66.22 E-value=9.4 Score=19.52 Aligned_cols=33 Identities=18% Similarity=0.272 Sum_probs=26.3
Q ss_pred HHHHHHHHCC----HHHHHHHH-CCCCCCHHHHHHHHHC
Q ss_conf 9999998589----23899961-5889888899999833
Q gi|254781188|r 27 AGILDQVANG----KALGHVLR-KVGMPKYSTFYRWIKK 60 (185)
Q Consensus 27 d~Ic~rIA~G----eSLr~ICk-d~gMPs~sTV~rWL~k 60 (185)
=.||..|..+ .+...+++ -+++| .+|+||.++.
T Consensus 14 mrI~q~l~~~~~~~lT~~eL~e~L~DVP-qATLYRHv~~ 51 (180)
T PRK06474 14 MKICQALMRNKEEGLSPLEMVKVIKDVP-QATLYRQIQT 51 (180)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHCCCCC-HHHHHHHHHH
T ss_conf 9999999658878868999997656998-7999999999
No 24
>pfam07508 Recombinase Recombinase. This domain is usually found associated with pfam00239 in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=65.47 E-value=8.2 Score=19.91 Aligned_cols=38 Identities=29% Similarity=0.448 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHCCHHHHHHHH---CCCCCC-------HHHHHHHHHC
Q ss_conf 9999999999858923899961---588988-------8899999833
Q gi|254781188|r 23 PELFAGILDQVANGKALGHVLR---KVGMPK-------YSTFYRWIKK 60 (185)
Q Consensus 23 ~Eiad~Ic~rIA~GeSLr~ICk---d~gMPs-------~sTV~rWL~k 60 (185)
-++...||+..++|.|+..||+ +.|+|+ .+|+.+.|.+
T Consensus 4 A~iVr~if~~~~~g~s~~~Ia~~Ln~~g~~~~~~~~w~~~~I~~iL~N 51 (101)
T pfam07508 4 AEVVRLIFELYLEGKSLREIARYLNERGIPTPRGKKWTKSTVRRILTN 51 (101)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHCC
T ss_conf 699999999998389999999999874996778982464435566208
No 25
>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=64.79 E-value=7.3 Score=20.27 Aligned_cols=34 Identities=18% Similarity=0.251 Sum_probs=30.2
Q ss_pred HHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 99999998589238999615889888899999833
Q gi|254781188|r 26 FAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 26 ad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
--+|+..++.|.|-+.|+..-|+ |.+||...+..
T Consensus 5 E~~il~~~~~G~s~~eIA~~L~i-s~~TV~~~~~~ 38 (57)
T cd06170 5 EREVLRLLAEGKTNKEIADILGI-SEKTVKTHLRN 38 (57)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 99999999807999999999897-89999999999
No 26
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=64.09 E-value=13 Score=18.56 Aligned_cols=87 Identities=16% Similarity=0.175 Sum_probs=54.2
Q ss_pred HHHHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHH
Q ss_conf 99999999985-89238999615889888899999833989999999999973799999986200230056403603789
Q gi|254781188|r 24 ELFAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSK 102 (185)
Q Consensus 24 Eiad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE~~a~~~ee~~~~~~~~~ 102 (185)
+.+...|.+-+ .|-|+..|++.-|++ .+++|.+....+++ |....+...+.+.+++.. .. +..+|..+.+
T Consensus 15 ~aa~~~f~~~G~~g~~~~~Ia~~ag~~-k~~i~yyF~~Ke~l---~~avl~~~~~~~~~~~~~----~~-~~~~P~~al~ 85 (202)
T TIGR03613 15 SAALDTFSRFGFHGTSLEQIAELAGVS-KTNLLYYFPSKDAL---YLAVLRQILDIWLSPLKA----FT-EDFAPLAAIK 85 (202)
T ss_pred HHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHCCCHHHH---HHHHHHHHHHHHHHHHHH----CC-CCCCHHHHHH
T ss_conf 999999998495648899999985998-88999985899999---999999999999978876----26-5799799999
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 979999889999987646653
Q gi|254781188|r 103 MRDRKQRMGTFLLEKLSNQKY 123 (185)
Q Consensus 103 lr~~~~~~~~w~l~k~~p~~y 123 (185)
--++. +|....-+|...
T Consensus 86 ~~I~~----~~~~~~~~P~~~ 102 (202)
T TIGR03613 86 AYIRA----KLEMSRDHPQAS 102 (202)
T ss_pred HHHHH----HHHHHHHCHHHH
T ss_conf 99999----999999782999
No 27
>pfam08148 DSHCT DSHCT (NUC185) domain. This C terminal domain is found in DOB1/SK12/helY-like DEAD box helicases.
Probab=63.63 E-value=13 Score=18.50 Aligned_cols=53 Identities=13% Similarity=0.088 Sum_probs=38.4
Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 8999999999985892389996158898888999998339899999999999737
Q gi|254781188|r 22 SPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRL 76 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qa 76 (185)
+..++.- ...=|+|.|+.+||+..+++ -..|-||+.+=.++-.|-..|.+...
T Consensus 100 ~~~l~~~-v~~Wa~G~~~~~i~~~t~i~-eGdfVR~i~rl~dll~ql~~aa~~~g 152 (179)
T pfam08148 100 DFGLMEV-VYEWARGASFAEICEMTDLD-EGDIVRLIRRLDELLRQIRNAARIIG 152 (179)
T ss_pred CHHHHHH-HHHHHCCCCHHHHHHHCCCC-CCHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf 7269999-99997699899999737988-63999999999999999999988539
No 28
>pfam12298 Bot1p Eukaryotic mitochondrial regulator protein. This family of proteins is found in eukaryotes. Proteins in this family are typically between 168 and 381 amino acids in length. Bot1p localizes to the mitochondria in live cells and cofractionates with purified mitochondrial ribosomes. Bot1p has a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery. Observations also indicate that in fission yeast, alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms.
Probab=63.04 E-value=14 Score=18.43 Aligned_cols=55 Identities=29% Similarity=0.424 Sum_probs=40.4
Q ss_pred CCHHHHHHHHHHH-HCCHHHHHHHHCCCCCCHHHH----------HHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 5899999999998-589238999615889888899----------9998339899999999999737
Q gi|254781188|r 21 YSPELFAGILDQV-ANGKALGHVLRKVGMPKYSTF----------YRWIKKDLKLQEAYTEALQCRL 76 (185)
Q Consensus 21 Ys~Eiad~Ic~rI-A~GeSLr~ICkd~gMPs~sTV----------~rWL~kdeEfreqYa~Are~qa 76 (185)
-++++-+.|++.+ .+|.|++.|+...|+ +..-| -+|.++...+..-|++|...-.
T Consensus 17 lse~lr~~I~~~v~~~g~s~~~vS~kygi-~~~RVeAivrL~eiEk~w~~~~kpl~~~ya~~~~~Ml 82 (171)
T pfam12298 17 ISEELREKIYEDVTVDGLSVQEVSVKYGL-KIPRVEAIVKLKEIEKEWKNKGKPLLKPYSRAMEKML 82 (171)
T ss_pred CCHHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf 89999999999998658889999999688-8899999999999999999705856789999999975
No 29
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=62.88 E-value=11 Score=18.93 Aligned_cols=38 Identities=16% Similarity=0.211 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHH---CCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 8999999999985---89238999615889888899999833
Q gi|254781188|r 22 SPELFAGILDQVA---NGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 22 s~Eiad~Ic~rIA---~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
+-+-+-.|++.|+ .|.++..|++.-||| .+|+++-|+.
T Consensus 9 sl~Ral~ILe~l~~~~~~lslsela~~lglp-ksTv~RlL~t 49 (264)
T PRK09834 9 GLSRGLMVLRALNRLDGGATVGLLAELTGLH-RTTVRRLLET 49 (264)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 9999999999874179997999999997909-9999999999
No 30
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=61.87 E-value=13 Score=18.47 Aligned_cols=38 Identities=21% Similarity=0.318 Sum_probs=32.7
Q ss_pred CHHHHHHHHHHHH---CCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 8999999999985---89238999615889888899999833
Q gi|254781188|r 22 SPELFAGILDQVA---NGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 22 s~Eiad~Ic~rIA---~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
+=+-+-.|++.|+ .|.+|..|++.-||| .+|+|+-|+.
T Consensus 23 sl~Ral~IL~~la~~~~~ltl~eia~~lglp-ksT~~RlL~t 63 (271)
T PRK10163 23 ALERGIAILQYLEKSGGSSSVSDISLNLDLP-LSTTFRLLKV 63 (271)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 9999999999997479997999999997919-9999999999
No 31
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=61.62 E-value=14 Score=18.37 Aligned_cols=39 Identities=10% Similarity=0.131 Sum_probs=32.6
Q ss_pred CHHHHHHHHHHHHC---CHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 89999999999858---9238999615889888899999833
Q gi|254781188|r 22 SPELFAGILDQVAN---GKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 22 s~Eiad~Ic~rIA~---GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
-.++.+-|.+.+.. .=|++.||+.-|+-|.+||...|..
T Consensus 8 Q~~il~~I~~~~~~~G~~Pt~rEI~~~~g~~S~s~v~~~l~~ 49 (65)
T pfam01726 8 QREVLDFIKASIEETGYPPSRREIAQALGLRSPNAAEEHLKA 49 (65)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCHHHHHHHHHH
T ss_conf 999999999999982889879999999389980999999999
No 32
>PRK11569 transcriptional repressor IclR; Provisional
Probab=61.34 E-value=14 Score=18.30 Aligned_cols=41 Identities=24% Similarity=0.297 Sum_probs=33.5
Q ss_pred CHHHHHHHHHHHH---CCHHHHHHHHCCCCCCHHHHHH---------HHHCCHH
Q ss_conf 8999999999985---8923899961588988889999---------9833989
Q gi|254781188|r 22 SPELFAGILDQVA---NGKALGHVLRKVGMPKYSTFYR---------WIKKDLK 63 (185)
Q Consensus 22 s~Eiad~Ic~rIA---~GeSLr~ICkd~gMPs~sTV~r---------WL~kdeE 63 (185)
+=+-+-.|++.|+ .|.+|..|++.-|+| .+|+|+ |+..|++
T Consensus 26 sl~Ral~IL~~la~~~~~lsl~eia~~lglp-ksT~~RlL~tL~~~G~v~~~~~ 78 (274)
T PRK11569 26 SLTRGLKLLEWIAESNGSVALTELAQQAGLP-NSTTHRLLTTMQQQGFVRQVGE 78 (274)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEECCC
T ss_conf 9999999999996389998999999987919-9999999999997698778699
No 33
>pfam00440 TetR_N Bacterial regulatory proteins, tetR family.
Probab=60.30 E-value=11 Score=19.05 Aligned_cols=39 Identities=10% Similarity=0.291 Sum_probs=30.4
Q ss_pred HHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHH
Q ss_conf 999999985-8923899961588988889999983398999
Q gi|254781188|r 26 FAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQ 65 (185)
Q Consensus 26 ad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfr 65 (185)
+.+++.+-+ +|-|++.|++.-|| +..|||.+..+.+++-
T Consensus 5 A~~l~~~~G~~~~s~~~Ia~~agv-s~~~iy~~F~~K~~L~ 44 (47)
T pfam00440 5 ALELFAEKGYDATTVREIAKEAGV-SKGALYRHFPSKEELL 44 (47)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCC-CHHHHHHHCCCHHHHH
T ss_conf 999999869150779999999796-9889998876999999
No 34
>COG3311 AlpA Predicted transcriptional regulator [Transcription]
Probab=59.96 E-value=6.6 Score=20.56 Aligned_cols=23 Identities=39% Similarity=0.534 Sum_probs=20.7
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 389996158898888999998339
Q gi|254781188|r 38 ALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 38 SLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
.++.++...|| |.+|||+++++.
T Consensus 15 rl~ev~~~~Gl-SrstiYr~i~~~ 37 (70)
T COG3311 15 RLPEVAQLTGL-SRSTIYRLIKDG 37 (70)
T ss_pred HHHHHHHHHCC-CHHHHHHHHCCC
T ss_conf 08999999776-689999998047
No 35
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=59.10 E-value=11 Score=19.06 Aligned_cols=42 Identities=26% Similarity=0.404 Sum_probs=32.4
Q ss_pred HHHHHHHHHHH-----CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHH
Q ss_conf 99999999985-----89238999615889888899999833989999
Q gi|254781188|r 24 ELFAGILDQVA-----NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQE 66 (185)
Q Consensus 24 Eiad~Ic~rIA-----~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfre 66 (185)
.+.+.-+..+. ++-||+.|++.-|+ +..|||+...+-+++--
T Consensus 15 ~lldAAl~~l~~~~gf~~lslreiar~aGv-~~~afYrHF~d~e~L~~ 61 (203)
T PRK11202 15 ALIDAAFSQLSAERSFSSLSLREVAREAGI-APTSFYRHFKDMDELGL 61 (203)
T ss_pred HHHHHHHHHHHCCCCCCCCCHHHHHHHHCC-CCCHHHHHCCCHHHHHH
T ss_conf 999999999860489330679999998489-97518887598899999
No 36
>pfam00195 Chal_sti_synt_N Chalcone and stilbene synthases, N-terminal domain. The C-terminal domain of Chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in this N-terminal domain.
Probab=58.92 E-value=8 Score=19.99 Aligned_cols=66 Identities=14% Similarity=0.192 Sum_probs=44.6
Q ss_pred CCCHHHHHHHHHHHHCC-------HHHHHHHHCCCCCCHHHHH--HHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 45899999999998589-------2389996158898888999--998339899999999999737999999862
Q gi|254781188|r 20 YYSPELFAGILDQVANG-------KALGHVLRKVGMPKYSTFY--RWIKKDLKLQEAYTEALQCRLDLLAEELLE 85 (185)
Q Consensus 20 ~Ys~Eiad~Ic~rIA~G-------eSLr~ICkd~gMPs~sTV~--rWL~kdeEfreqYa~Are~qaD~laEEILE 85 (185)
.|+++-+.+++.++.++ +.|+.||..-|+-.+-++. .|+.++|+|...-.--...|.+.|.++..+
T Consensus 30 ~~~Q~~~~d~~~~~~~~~~~~~~k~~l~ri~~~sgI~~R~~vl~~e~~~~~P~~~~~~~ps~~~R~~~~~~~a~~ 104 (228)
T pfam00195 30 CVDQSTYPDYYFRVTKSEHLTDLKEKFQRICEKSTIKKRYMVLTEEILKENPELCTEMAPSLDARQDIAVVEVPK 104 (228)
T ss_pred EECHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCEEEEECHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 524899999999973443242678999989984698831586176876149551025699989999999999999
No 37
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=58.32 E-value=8.1 Score=19.94 Aligned_cols=24 Identities=29% Similarity=0.621 Sum_probs=20.7
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 2389996158898888999998339
Q gi|254781188|r 37 KALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 37 eSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
+.+...|+.-|+ |+.|+++|+++-
T Consensus 2 m~~~e~~~~lgi-s~~Tl~rw~r~G 25 (193)
T COG2452 2 LRPKEACQLLGI-SYSTLLRWIREG 25 (193)
T ss_pred CCHHHHHHHHCC-CHHHHHHHHHCC
T ss_conf 888999998394-799999998768
No 38
>PRK11886 biotin--protein ligase; Provisional
Probab=58.24 E-value=16 Score=17.89 Aligned_cols=39 Identities=15% Similarity=0.320 Sum_probs=31.6
Q ss_pred CHHHHHHHHHHHHCCH--HHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 8999999999985892--389996158898888999998339
Q gi|254781188|r 22 SPELFAGILDQVANGK--ALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 22 s~Eiad~Ic~rIA~Ge--SLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
+-+-+-+|++.|++|+ |-..++..-|+ |+..||+.|+.=
T Consensus 2 ~~~~~~~lL~~L~~g~~~SGe~la~~Lgv-SR~aVwK~i~~L 42 (319)
T PRK11886 2 TYEKMLQLLSLLADGDFHSGEQLAEELGI-SRAAIWKHIQTL 42 (319)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHHHCC-CHHHHHHHHHHH
T ss_conf 17899999999737992969999998798-899999999999
No 39
>pfam05930 Phage_AlpA Prophage CP4-57 regulatory protein (AlpA). This family consists of several short bacterial and phage proteins which are related to the E. coli protein AlpA. AlpA suppress two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light. Several of the sequences in this family are thought to be DNA-binding proteins.
Probab=57.68 E-value=7.6 Score=20.14 Aligned_cols=23 Identities=39% Similarity=0.518 Sum_probs=20.1
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 389996158898888999998339
Q gi|254781188|r 38 ALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 38 SLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
.++.+|...|+ |.+|+|+|+++.
T Consensus 5 r~~eV~~~~gl-srstiyr~i~~G 27 (51)
T pfam05930 5 RLKEVEQLTGL-SRSTIYRLIKDG 27 (51)
T ss_pred CHHHHHHHHCC-CHHHHHHHHHCC
T ss_conf 79999999898-999999999879
No 40
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=55.69 E-value=18 Score=17.61 Aligned_cols=35 Identities=14% Similarity=0.155 Sum_probs=22.7
Q ss_pred HHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 999999858923899961588988889999983398
Q gi|254781188|r 27 AGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 27 d~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
-.|-.....|.|.++|.+..|- +.+|+.+=|+.+.
T Consensus 14 ~~I~~l~~~~~S~reIA~~LgR-h~sTIsRElkRn~ 48 (318)
T COG2826 14 YEIERLLKAKMSIREIAKQLNR-HHSTISRELKRNR 48 (318)
T ss_pred HHHHHHHHCCCCHHHHHHHHCC-CCCHHHHHHHCCC
T ss_conf 9999999859989999998576-8620427986687
No 41
>pfam06056 Terminase_5 Putative ATPase subunit of terminase (gpP-like). 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.
Probab=55.62 E-value=6.6 Score=20.54 Aligned_cols=30 Identities=20% Similarity=0.421 Sum_probs=25.5
Q ss_pred HHHCCHHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 9858923899961588988889999983398
Q gi|254781188|r 32 QVANGKALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 32 rIA~GeSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
..=.|-+...|+..-|+| .+|||.|-.++.
T Consensus 9 LY~qg~~~~eIA~~Lg~~-~~tVysWk~r~~ 38 (58)
T pfam06056 9 LYWQGYRPAEIAQELGLK-ARTVYSWKDRDK 38 (58)
T ss_pred HHHCCCCHHHHHHHHCCC-CCHHHHHHHHCC
T ss_conf 999689899999997899-314565865248
No 42
>PRK00215 LexA repressor; Validated
Probab=54.79 E-value=19 Score=17.52 Aligned_cols=42 Identities=14% Similarity=0.172 Sum_probs=34.0
Q ss_pred CHHHHHHHHHHHHC---CHHHHHHHHCCCCCCHHHHHHHHHCCHH
Q ss_conf 89999999999858---9238999615889888899999833989
Q gi|254781188|r 22 SPELFAGILDQVAN---GKALGHVLRKVGMPKYSTFYRWIKKDLK 63 (185)
Q Consensus 22 s~Eiad~Ic~rIA~---GeSLr~ICkd~gMPs~sTV~rWL~kdeE 63 (185)
-.++.+-|.+.+.. .=|++.||..-|+.|.+||+++|..=++
T Consensus 6 Q~~il~fI~~~~~~~g~~Ps~rEI~~~~g~~S~~tV~~~l~~Le~ 50 (204)
T PRK00215 6 QQEILDFIKDRIEETGYPPSRREIADALGLRSPSAVHEHLKALER 50 (204)
T ss_pred HHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 999999999999974889989999998099981899999999987
No 43
>KOG2690 consensus
Probab=54.34 E-value=19 Score=17.47 Aligned_cols=35 Identities=11% Similarity=0.127 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHC--CCCCCHHHHHHH
Q ss_conf 99999999998589238999615--889888899999
Q gi|254781188|r 23 PELFAGILDQVANGKALGHVLRK--VGMPKYSTFYRW 57 (185)
Q Consensus 23 ~Eiad~Ic~rIA~GeSLr~ICkd--~gMPs~sTV~rW 57 (185)
++-..+||..|.+..+||++-.+ |++-++.|||+.
T Consensus 177 DeK~eEI~~LL~gnpdir~ly~~lVP~~VshetFW~R 213 (331)
T KOG2690 177 DEKTEEISELLEGNPDIRKLYEDLVPSEVSHETFWHR 213 (331)
T ss_pred CCCHHHHHHHHHCCCCHHHHHHHHCCCCCCHHHHHHH
T ss_conf 3104799999843811999999738552558999999
No 44
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1; InterPro: IPR011745 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 recognized by the major sigma factors , . This entry describes sigma-70 factors in Myxococcus xanthus DK 1622 and in other members of the Mycococcales. Each of the six members in M. xanthusis is encoded near a gene for a predicted serine/threonine kinase. Members of this family show sequence similarity to members of Pfam family IPR007630 from INTERPRO (region 4 of sigma-70 like sigma-factors), a helix-turn-helix family in which trusted and noise cutoffs deliberately are set artificially high and which therefore has many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=53.86 E-value=18 Score=17.69 Aligned_cols=42 Identities=21% Similarity=0.304 Sum_probs=29.7
Q ss_pred HHCCHHHHHHHHCCCCCCHHHHHHHHHCC-HHHHHHHHHHHHHH
Q ss_conf 85892389996158898888999998339-89999999999973
Q gi|254781188|r 33 VANGKALGHVLRKVGMPKYSTFYRWIKKD-LKLQEAYTEALQCR 75 (185)
Q Consensus 33 IA~GeSLr~ICkd~gMPs~sTV~rWL~kd-eEfreqYa~Are~q 75 (185)
.-+|-|+-.|...+++ ++|||-|||..- +-.-+.-.++++.|
T Consensus 179 fv~~Ls~~r~g~my~~-~~STvsR~~~~ARe~lle~Tr~~La~R 221 (249)
T TIGR03001 179 FVEGLSMDRLGAMYQV-HRSTVSRWVAQARERLLERTRRRLAER 221 (249)
T ss_pred HHCCCCHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 8203329999877457-750789999999999999999999997
No 45
>pfam00392 GntR Bacterial regulatory proteins, gntR family. This family of regulatory proteins consists of the N-terminal HTH region of GntR-like bacterial transcription factors. At the C-terminus there is usually an effector-binding/oligomerisation domain. The GntR-like proteins include the following sub-families: MocR, YtrR, FadR, AraR, HutC and PlmA, DevA, DasR. Many of these proteins have been shown experimentally to be autoregulatory, enabling the prediction of operator sites and the discovery of cis/trans relationships. The DasR regulator has been shown to be a global regulator of primary metabolism and development in Streptomyces coelicolor.
Probab=52.88 E-value=20 Score=17.32 Aligned_cols=37 Identities=11% Similarity=0.349 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHCCH--------HHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 999999999985892--------38999615889888899999833
Q gi|254781188|r 23 PELFAGILDQVANGK--------ALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 23 ~Eiad~Ic~rIA~Ge--------SLr~ICkd~gMPs~sTV~rWL~k 60 (185)
+++++.|.++|.+|+ |.+.+|+..|+ |..|+.+-++.
T Consensus 3 ~qi~~~i~~~I~~g~~~~G~~LPs~~~La~~~~v-Sr~tvr~Al~~ 47 (64)
T pfam00392 3 EQVYARLREDILSGRLRPGDKLPSERELAAEFGV-SRTTVREALRR 47 (64)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 9999999999984999992998479999999796-99999999999
No 46
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=51.70 E-value=21 Score=17.20 Aligned_cols=36 Identities=31% Similarity=0.453 Sum_probs=28.4
Q ss_pred HHHHHHHHHHH-CCH--HHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 99999999985-892--38999615889888899999833
Q gi|254781188|r 24 ELFAGILDQVA-NGK--ALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 24 Eiad~Ic~rIA-~Ge--SLr~ICkd~gMPs~sTV~rWL~k 60 (185)
+.+-.|++.|+ .+. ++..|++.-|+| .+|+|+-|..
T Consensus 4 ~ral~iL~~l~~~~~~l~l~ela~~~glp-ksT~~RlL~t 42 (246)
T COG1414 4 ERALAILDLLAEGPGGLSLAELAERLGLP-KSTVHRLLQT 42 (246)
T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 99999999997188888799999987919-8899999999
No 47
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=51.27 E-value=18 Score=17.58 Aligned_cols=27 Identities=7% Similarity=0.241 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 997999988999998764665343420
Q gi|254781188|r 102 KMRDRKQRMGTFLLEKLSNQKYGPRVS 128 (185)
Q Consensus 102 ~lr~~~~~~~~w~l~k~~p~~yg~rvs 128 (185)
.|..+.+.+++.++.-+.++--+++..
T Consensus 143 ~Lt~RE~eVL~ll~~G~snkeIA~~L~ 169 (204)
T PRK09958 143 SLSKQEISVMRYILDGKDNNDIAEKMF 169 (204)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf 689999999999986999999998978
No 48
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=49.51 E-value=21 Score=17.23 Aligned_cols=28 Identities=4% Similarity=0.155 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9979999889999987646653434203
Q gi|254781188|r 102 KMRDRKQRMGTFLLEKLSNQKYGPRVSV 129 (185)
Q Consensus 102 ~lr~~~~~~~~w~l~k~~p~~yg~rvs~ 129 (185)
.|..|.+.+++++++-+.++--+++...
T Consensus 150 ~LT~RE~eVL~lla~G~snkeIA~~L~i 177 (216)
T PRK10840 150 RLSPKESEVLRLFAEGFLVTEIAKKLNR 177 (216)
T ss_pred CCCHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 9998999999999869999999989698
No 49
>pfam04546 Sigma70_ner Sigma-70, non-essential region. The domain is found in the primary vegetative sigma factor. The function of this domain is unclear and can be removed without loss of function.
Probab=49.08 E-value=23 Score=16.93 Aligned_cols=14 Identities=21% Similarity=0.522 Sum_probs=5.1
Q ss_pred CCCHHHHHHHHHHH
Q ss_conf 45899999999998
Q gi|254781188|r 20 YYSPELFAGILDQV 33 (185)
Q Consensus 20 ~Ys~Eiad~Ic~rI 33 (185)
+|++.+++.+|+.+
T Consensus 122 Kl~pk~~d~L~~~l 135 (210)
T pfam04546 122 RLVPKQFDRLVDNL 135 (210)
T ss_pred CCCHHHHHHHHHHH
T ss_conf 17689999999999
No 50
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=49.06 E-value=21 Score=17.12 Aligned_cols=30 Identities=17% Similarity=0.276 Sum_probs=13.8
Q ss_pred HHHHHHHCCHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 9999985892389996158898888999998
Q gi|254781188|r 28 GILDQVANGKALGHVLRKVGMPKYSTFYRWI 58 (185)
Q Consensus 28 ~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL 58 (185)
+|+..|+.|.|-++|...-++ |..||-..+
T Consensus 144 eVL~lia~G~snkeIA~~L~I-S~~TVk~h~ 173 (196)
T PRK10360 144 QVAEKLAQGMAVKEIAAELGL-SPKTVHVHR 173 (196)
T ss_pred HHHHHHHCCCCHHHHHHHHCC-CHHHHHHHH
T ss_conf 999999879999999999699-999999999
No 51
>pfam06530 Phage_antitermQ Phage antitermination protein Q. This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream.
Probab=49.04 E-value=23 Score=16.93 Aligned_cols=56 Identities=20% Similarity=0.328 Sum_probs=45.8
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf 589999999999858923899961588988889999983398999999999997379
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLD 77 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD 77 (185)
+.++..+-|+..-.-|.|.++|.+..+. +-..+.+.++.-+.|-+-.--....+-|
T Consensus 63 ~~~~~~~ll~~yYv~g~S~r~IA~~~~~-s~~~irk~lq~Aegfi~g~L~~l~~~lE 118 (126)
T pfam06530 63 IDPKLFGLLLSYYVHGSSKRAIARRYGC-SVTRIRKRLCKAEGFIDGCLSLLTVRLE 118 (126)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf 3989999999999748669999999688-8119999999846388775998315788
No 52
>pfam00891 Methyltransf_2 O-methyltransferase. This family includes a range of O-methyltransferases. These enzymes utilize S-adenosyl methionine.
Probab=47.10 E-value=25 Score=16.73 Aligned_cols=56 Identities=27% Similarity=0.542 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999985892389996158898888999998339899999999999737999999862
Q gi|254781188|r 24 ELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLE 85 (185)
Q Consensus 24 Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE 85 (185)
..|..+.+-|-.|++- -....|+| +|.|+.++|++...+.+|........+..+++
T Consensus 39 ~~w~~L~~avrtG~~~--f~~~~G~~----~~~~~~~~p~~~~~F~~aM~~~s~~~~~~~~~ 94 (239)
T pfam00891 39 ESWAHLKDAVREGGPP--FERAFGMP----FFEYLGADPEFNRVFNRAMAAHSRLVMKKILE 94 (239)
T ss_pred HHHHHHHHHHHCCCCH--HHHHCCCC----HHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999899999609974--66523998----89987519999999999998888888999998
No 53
>PRK09483 response regulator; Provisional
Probab=46.97 E-value=24 Score=16.79 Aligned_cols=29 Identities=3% Similarity=0.193 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89979999889999987646653434203
Q gi|254781188|r 101 SKMRDRKQRMGTFLLEKLSNQKYGPRVSV 129 (185)
Q Consensus 101 ~~lr~~~~~~~~w~l~k~~p~~yg~rvs~ 129 (185)
..|..|.+-+++|++.-+.++--+++...
T Consensus 147 ~~LT~RE~eVl~ll~~G~snkeIA~~L~i 175 (216)
T PRK09483 147 ASLSERELQIMLMITKGQKVNEISEQLNL 175 (216)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 56899999999999879999999999698
No 54
>COG2005 ModE N-terminal domain of molybdenum-binding protein [General function prediction only]
Probab=45.76 E-value=21 Score=17.22 Aligned_cols=66 Identities=18% Similarity=0.259 Sum_probs=47.3
Q ss_pred HHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHHHHH
Q ss_conf 99999985892389996158898888999998339899999999999737999999862002300564036037899799
Q gi|254781188|r 27 AGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDR 106 (185)
Q Consensus 27 d~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE~~a~~~ee~~~~~~~~~lr~~ 106 (185)
-+++..|+.--||...++.-|| ||...|..|+. .++++.+|+-.+..+.-.-..+.|...
T Consensus 22 ~~LL~~I~etGSIs~AAk~~Gi-SYk~AW~~i~~-------------------~n~~~~~plVe~~rGGk~gGga~LT~~ 81 (130)
T COG2005 22 IELLKAIAETGSISAAAKAAGI-SYKSAWDYIKA-------------------LNRLLGEPLVERRRGGKGGGGAVLTDF 81 (130)
T ss_pred HHHHHHHHHHCCHHHHHHHCCC-CHHHHHHHHHH-------------------HHHHHCCCEEEECCCCCCCCCCHHHHH
T ss_conf 9999999996889999998499-77999999999-------------------999838870663357788885113799
Q ss_pred HHHHHH
Q ss_conf 998899
Q gi|254781188|r 107 KQRMGT 112 (185)
Q Consensus 107 ~~~~~~ 112 (185)
.+++.+
T Consensus 82 g~~ll~ 87 (130)
T COG2005 82 GERLLE 87 (130)
T ss_pred HHHHHH
T ss_conf 999999
No 55
>pfam04229 UPF0157 Uncharacterized protein family (UPF0157). Also known as GrpB.
Probab=45.58 E-value=20 Score=17.35 Aligned_cols=31 Identities=10% Similarity=0.094 Sum_probs=23.9
Q ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8899999833989999999999973799999
Q gi|254781188|r 51 YSTFYRWIKKDLKLQEAYTEALQCRLDLLAE 81 (185)
Q Consensus 51 ~sTV~rWL~kdeEfreqYa~Are~qaD~laE 81 (185)
+-.|..||+.|++.+++|.+-+..-+..+..
T Consensus 117 ~l~FRD~Lr~~p~~~~~Y~~lK~~la~~~~~ 147 (167)
T pfam04229 117 HLAFRDYLRAHPEAAEEYEALKRELAAKYPG 147 (167)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 9999999981999999999999999987799
No 56
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.56 E-value=22 Score=17.09 Aligned_cols=40 Identities=18% Similarity=0.238 Sum_probs=35.2
Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 89999999999858923899961588988889999983398
Q gi|254781188|r 22 SPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
.++.-..+...+..|.+++++-+-.|+ ++.|+++|+.+--
T Consensus 75 ~~~~~~~~~~~~~~~~~i~~~a~~l~i-~~~~v~r~~~r~~ 114 (129)
T COG3677 75 LYKIKLQAVTLYMLGLGIRDIARTLGI-SINTVNRWSKRFG 114 (129)
T ss_pred CHHHHHHHHHHHHCCCCCCCHHHHHCC-CHHHHHHHHHHCC
T ss_conf 277999999998649996669999554-6999999999603
No 57
>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=44.88 E-value=26 Score=16.51 Aligned_cols=37 Identities=8% Similarity=0.249 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHCC-----H---HHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 99999999998589-----2---38999615889888899999833
Q gi|254781188|r 23 PELFAGILDQVANG-----K---ALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 23 ~Eiad~Ic~rIA~G-----e---SLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.++.+.|.++|.+| . |.+.+|+..|+ |..|+.+-+..
T Consensus 4 ~qi~~~i~~~I~~g~~~~G~~LPs~~~La~~~~v-Sr~tvr~Al~~ 48 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGV-SRTTVREALRE 48 (66)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 9999999999985999991999279999999798-88999999999
No 58
>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=44.10 E-value=17 Score=17.80 Aligned_cols=23 Identities=26% Similarity=0.497 Sum_probs=19.8
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 389996158898888999998339
Q gi|254781188|r 38 ALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 38 SLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
+..++|+..|+ |..|+.+|..+-
T Consensus 2 t~~e~A~~lgV-s~~TlrrW~~~G 24 (49)
T cd04762 2 TTKEAAELLGV-SPSTLRRWVKEG 24 (49)
T ss_pred CHHHHHHHHCC-CHHHHHHHHHCC
T ss_conf 88999999798-999999999879
No 59
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=44.05 E-value=27 Score=16.44 Aligned_cols=34 Identities=9% Similarity=0.238 Sum_probs=24.6
Q ss_pred HHHHHHHHHHCCH--------HHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 9999999985892--------3899961588988889999983
Q gi|254781188|r 25 LFAGILDQVANGK--------ALGHVLRKVGMPKYSTFYRWIK 59 (185)
Q Consensus 25 iad~Ic~rIA~Ge--------SLr~ICkd~gMPs~sTV~rWL~ 59 (185)
+++.|.+.|.+|. |.+.+|...++ |..|+.+-++
T Consensus 1 Ia~~i~~~I~~g~~~~G~~LPs~~~la~~~~v-Sr~tvr~A~~ 42 (60)
T smart00345 1 VAERLREDIVSGELRPGDKLPSERELAAQLGV-SRTTVREALS 42 (60)
T ss_pred CHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHH
T ss_conf 98999999983999983988109999999894-9999999999
No 60
>PRK10403 transcriptional regulator NarP; Provisional
Probab=43.54 E-value=28 Score=16.38 Aligned_cols=27 Identities=19% Similarity=0.282 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 979999889999987646653434203
Q gi|254781188|r 103 MRDRKQRMGTFLLEKLSNQKYGPRVSV 129 (185)
Q Consensus 103 lr~~~~~~~~w~l~k~~p~~yg~rvs~ 129 (185)
|..+.+.+++.+..-+.++--+.+...
T Consensus 154 LT~RE~eVL~lla~G~snkeIA~~L~i 180 (215)
T PRK10403 154 LTERELDVLHELAQGLSNKQIASVLNI 180 (215)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHHCC
T ss_conf 899999999999869999999999798
No 61
>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=43.32 E-value=27 Score=16.41 Aligned_cols=37 Identities=24% Similarity=0.335 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHCC-HHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 99999999998589-238999615889888899999833
Q gi|254781188|r 23 PELFAGILDQVANG-KALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 23 ~Eiad~Ic~rIA~G-eSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
...--.|+..|..| .+...|++..|+| .+|+.+.|+.
T Consensus 6 ~~~r~~Il~~L~~~~~~~~eia~~l~is-~~~vs~hL~~ 43 (78)
T cd00090 6 DPTRLRILRLLLEGPLTVSELAERLGLS-QSTVSRHLKK 43 (78)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 9999999999984890699998777848-7899999999
No 62
>TIGR01764 excise DNA binding domain, excisionase family; InterPro: IPR010093 An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This entry 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 entry 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 (IPR000551 from INTERPRO).; GO: 0003677 DNA binding.
Probab=42.87 E-value=17 Score=17.78 Aligned_cols=25 Identities=24% Similarity=0.344 Sum_probs=20.8
Q ss_pred HHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 23899961588988889999983398
Q gi|254781188|r 37 KALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 37 eSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
.|...+|+--|++ .+||++||++..
T Consensus 2 lTv~EaA~yLgv~-~~t~~~l~~~g~ 26 (49)
T TIGR01764 2 LTVEEAAEYLGVS-KSTVYRLIEEGE 26 (49)
T ss_pred CCHHHHHHHCCCC-HHHHHHHHHCCC
T ss_conf 8778899771999-057899997189
No 63
>PRK10651 transcriptional regulator NarL; Provisional
Probab=41.48 E-value=30 Score=16.17 Aligned_cols=30 Identities=17% Similarity=0.366 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 899799998899999876466534342034
Q gi|254781188|r 101 SKMRDRKQRMGTFLLEKLSNQKYGPRVSVE 130 (185)
Q Consensus 101 ~~lr~~~~~~~~w~l~k~~p~~yg~rvs~e 130 (185)
..|..+.+.+++++..-+.++--+.+...-
T Consensus 154 ~~LT~RE~eVL~ll~~G~snkeIA~~L~iS 183 (216)
T PRK10651 154 NQLTPRERDILKLIAQGLSNKMIARRLDIT 183 (216)
T ss_pred CCCCHHHHHHHHHHHCCCCHHHHHHHHCCC
T ss_conf 348989999999998599999999996978
No 64
>TIGR02233 Myxo_sigma_rel Myxococcus probable DNA-binding regulatory protein.
Probab=41.40 E-value=27 Score=16.47 Aligned_cols=32 Identities=25% Similarity=0.372 Sum_probs=27.1
Q ss_pred HHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHH
Q ss_conf 985892389996158898888999998339899
Q gi|254781188|r 32 QVANGKALGHVLRKVGMPKYSTFYRWIKKDLKL 64 (185)
Q Consensus 32 rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEf 64 (185)
..-+|-||-.|..-+|.| .|||-+|+..-.+.
T Consensus 36 H~~~gLsldR~~~lY~~h-rStvaR~v~~are~ 67 (106)
T TIGR02233 36 HHVEGLSLDRLGTLYGVH-RSTVARWVAGAREL 67 (106)
T ss_pred HHHCCCCHHHHHHHHCCC-CHHHHHHHHHHHHH
T ss_conf 762365589999884788-61699999999999
No 65
>PRK12423 LexA repressor; Provisional
Probab=39.47 E-value=32 Score=15.97 Aligned_cols=42 Identities=17% Similarity=0.290 Sum_probs=33.6
Q ss_pred CHHHHHHHHHHHHC-C--HHHHHHHHCCCCCCHHHHHHHHHCCHH
Q ss_conf 89999999999858-9--238999615889888899999833989
Q gi|254781188|r 22 SPELFAGILDQVAN-G--KALGHVLRKVGMPKYSTFYRWIKKDLK 63 (185)
Q Consensus 22 s~Eiad~Ic~rIA~-G--eSLr~ICkd~gMPs~sTV~rWL~kdeE 63 (185)
..++.+-|.+.+.. | =|++.||+..|+-|.+|++.+|+.=++
T Consensus 8 Q~~iL~fI~~~~~~~G~~Pt~rEI~~~~g~~S~~~v~~hl~~L~~ 52 (202)
T PRK12423 8 RAAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAE 52 (202)
T ss_pred HHHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf 999999999999962989889999998299986789999999998
No 66
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=39.40 E-value=32 Score=15.96 Aligned_cols=44 Identities=9% Similarity=0.163 Sum_probs=32.2
Q ss_pred HHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHH-HHHHH
Q ss_conf 999999985-8923899961588988889999983398999-99999
Q gi|254781188|r 26 FAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQ-EAYTE 70 (185)
Q Consensus 26 ad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfr-eqYa~ 70 (185)
+..+|..=+ .+-|+..||+.-|+ +..|||....+.+++- +-+.+
T Consensus 20 A~~lFae~G~~~tTl~~IA~~AGV-t~GaiY~HF~nKe~L~~a~~~~ 65 (213)
T PRK09975 20 AIAQFALRGVANTTLNDIADAANV-TRGAIYWHFENKTQLFNEMWLQ 65 (213)
T ss_pred HHHHHHHHCCCCCCHHHHHHHHCC-CHHHHHHHCCCHHHHHHHHHHH
T ss_conf 999999859455889999999689-8489998779999999999996
No 67
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=38.69 E-value=33 Score=15.89 Aligned_cols=33 Identities=18% Similarity=0.387 Sum_probs=28.6
Q ss_pred HHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 9999998589238999615889888899999833
Q gi|254781188|r 27 AGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 27 d~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
-++++.|+.--|+.+.|+.-|| ||.+-|.-+..
T Consensus 22 i~LL~~I~~~gSIs~Aak~~g~-SYk~AW~~i~~ 54 (262)
T PRK10676 22 ISLLKQIALSGSISQGAKDAGI-SYKSAWDAINE 54 (262)
T ss_pred HHHHHHHHHHCCHHHHHHHCCC-CHHHHHHHHHH
T ss_conf 9999999874999999998199-69999999999
No 68
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=38.30 E-value=33 Score=15.85 Aligned_cols=110 Identities=12% Similarity=0.040 Sum_probs=75.5
Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHH
Q ss_conf 8999999999985892389996158898888999998339-899999999999737999999862002300564036037
Q gi|254781188|r 22 SPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD-LKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFY 100 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd-eEfreqYa~Are~qaD~laEEILE~~a~~~ee~~~~~~~ 100 (185)
.+++..-|-.-|+.-=||..|.+.-.| |.+++.+.+++. -.|.+-..+.|-..|. ++|-..--+-.|.|..+++
T Consensus 144 r~~v~~iI~sNi~~~wsL~dIA~~L~M-SpS~LkKkLKeEGtSFS~yLte~RMqkAk----qLL~~t~~sI~EIA~~cGY 218 (274)
T PRK09978 144 RTRVCTVINNNIAHEWTLARIASELLM-SPSLLKKKLREEETSYSQLLTECRMQRAL----QLIVIHGFSIKRVAVSCGY 218 (274)
T ss_pred HHHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHHHHCCCCHHHHHHHHHHHHHH----HHHHCCCCCHHHHHHHHCC
T ss_conf 999999987400036139999988727-99999999998499999999999999999----9975589889999998389
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 89979999889999987646653434203443313467
Q gi|254781188|r 101 SKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLR 138 (185)
Q Consensus 101 ~~lr~~~~~~~~w~l~k~~p~~yg~rvs~e~~h~~~~~ 138 (185)
...+---+. -=-.-.+.|..|-+|+.|-....+.-+
T Consensus 219 ~stSYFIkv--FKK~~G~TP~EYRkr~~~~~~~~~~~~ 254 (274)
T PRK09978 219 HSVSYFIYV--FRNYYGMTPTEYQERSAQGLPNRDSAA 254 (274)
T ss_pred CCCCHHHHH--HHHHHCCCHHHHHHHHHCCCCCCCHHH
T ss_conf 986489999--998709893999999973788741366
No 69
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=37.57 E-value=34 Score=15.77 Aligned_cols=25 Identities=20% Similarity=0.388 Sum_probs=12.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9799998899999876466534342
Q gi|254781188|r 103 MRDRKQRMGTFLLEKLSNQKYGPRV 127 (185)
Q Consensus 103 lr~~~~~~~~w~l~k~~p~~yg~rv 127 (185)
|..|.+.++++++.-+.++--+++.
T Consensus 150 Lt~RE~eVL~ll~~G~snkeIA~~L 174 (210)
T PRK09935 150 LSNREVTVLRYLANGLSNKEIAEQL 174 (210)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9989999999998699999999894
No 70
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=37.50 E-value=34 Score=15.76 Aligned_cols=79 Identities=10% Similarity=0.111 Sum_probs=36.1
Q ss_pred CHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH----HCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 888999998339899999999999737999999862002300564----0360378997999988999998764665343
Q gi|254781188|r 50 KYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEEL----ANPVFYSKMRDRKQRMGTFLLEKLSNQKYGP 125 (185)
Q Consensus 50 s~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE~~a~~~ee~----~~~~~~~~lr~~~~~~~~w~l~k~~p~~yg~ 125 (185)
+..|+|........+..+.+-+.+.=.-++-.-+.-.......+. ...+...-|..|.+-+++|+..-+.++--|.
T Consensus 134 ~~~cl~~f~~~~~~~~~~~~~~LelL~P~Lh~AL~rv~~l~~q~~~~~~~~~~~~glLT~RE~EVL~~va~G~sn~eIA~ 213 (247)
T TIGR03020 134 RHDCLYSFSRSSVPLDARHAYFLELLLPYLDSALRRVLFLPNQHRTRPLGERHSAGLITAREAEILAWVRDGKTNEEIAA 213 (247)
T ss_pred CCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHH
T ss_conf 85559999715889987799999976889999999863164335455555677678999899999999987999999999
Q ss_pred HHH
Q ss_conf 420
Q gi|254781188|r 126 RVS 128 (185)
Q Consensus 126 rvs 128 (185)
...
T Consensus 214 ~L~ 216 (247)
T TIGR03020 214 ILG 216 (247)
T ss_pred HHC
T ss_conf 949
No 71
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR; InterPro: IPR012704 At least five distinct pathways exist for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR which is, in most cases, divergently transcribed from the operon that encodes the genes involved in the methylcitric acid cycle of propionate catabolism. This protein is required for the expression of the proteins involved in this pathway . 2-methylcitric acid, an intermediate in this pathway, has been proposed to be a co-activator of PrpR .; GO: 0000156 two-component response regulator activity, 0003677 DNA binding, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0019629 propionate catabolic process 2-methylcitrate cycle, 0005737 cytoplasm.
Probab=35.29 E-value=16 Score=17.95 Aligned_cols=13 Identities=38% Similarity=0.424 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 6788999999864
Q gi|254781188|r 137 LRPAIERLREHYK 149 (185)
Q Consensus 137 ~~~~~~~~~~~~~ 149 (185)
||-+|||+-=|++
T Consensus 559 Lrnl~ERl~~~l~ 571 (658)
T TIGR02329 559 LRNLVERLALYLS 571 (658)
T ss_pred HHHHHHHHHHHHH
T ss_conf 8779999988864
No 72
>TIGR01932 hflC HflC protein; InterPro: IPR010200 HflK and HflC are paralogs encoded by tandem genes in proteobacteria, spirochetes, and some other bacterial lineages. The HflKC complex is anchored in the membrane and exposed to the periplasm. The complex is not active as a protease, but rather binds to and appears to modulate the ATP-dependent protease FtsH. ; GO: 0005515 protein binding, 0008233 peptidase activity, 0016021 integral to membrane.
Probab=35.00 E-value=37 Score=15.51 Aligned_cols=63 Identities=22% Similarity=0.084 Sum_probs=48.9
Q ss_pred CCCCCHHHHHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCCHH---HHHHHHHHHHHHHHHHHH
Q ss_conf 64458999999999985-89238999615889888899999833989---999999999973799999
Q gi|254781188|r 18 CIYYSPELFAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKDLK---LQEAYTEALQCRLDLLAE 81 (185)
Q Consensus 18 ~i~Ys~Eiad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kdeE---freqYa~Are~qaD~laE 81 (185)
-|.|++|+.+.||+|+- +-+++-.-=+--|- ...+.|+--.+.|. +++.+..|+..+++.=|+
T Consensus 228 kI~~~~e~~esi~nRm~~ER~~iA~~~RS~G~-~~aee~~~~~~~Ev~~iLseA~~~A~~ikgEgDA~ 294 (345)
T TIGR01932 228 KINLSDELSESIYNRMRSEREQIARKHRSQGE-EKAEELRGKADYEVLKILSEAKRTARIIKGEGDAE 294 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 31378889999999899999999998443666-88999985252778878899887353431257699
No 73
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=34.12 E-value=39 Score=15.41 Aligned_cols=25 Identities=8% Similarity=0.183 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 9799998899999876466534342
Q gi|254781188|r 103 MRDRKQRMGTFLLEKLSNQKYGPRV 127 (185)
Q Consensus 103 lr~~~~~~~~w~l~k~~p~~yg~rv 127 (185)
|.-+.+-+++++..-+..+--+++.
T Consensus 135 Lt~rE~eVl~l~a~G~s~~eIA~~L 159 (205)
T PRK11475 135 LSPTEREILRFMSRGYSMPQIAEQL 159 (205)
T ss_pred CCHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 9858999999997699999999997
No 74
>PRK05634 nucleosidase; Provisional
Probab=33.53 E-value=6.8 Score=20.45 Aligned_cols=50 Identities=20% Similarity=0.351 Sum_probs=40.9
Q ss_pred HCCHHHHHHHHCCCCCCHHHHHHHHHC--CHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 589238999615889888899999833--9899999999999737999999862
Q gi|254781188|r 34 ANGKALGHVLRKVGMPKYSTFYRWIKK--DLKLQEAYTEALQCRLDLLAEELLE 85 (185)
Q Consensus 34 A~GeSLr~ICkd~gMPs~sTV~rWL~k--deEfreqYa~Are~qaD~laEEILE 85 (185)
++|-++-++|...|+| +. .+||+-+ |++-...|.+-....+..+++-++|
T Consensus 135 ME~~AiA~vc~~~~vP-f~-~~K~ISD~Ade~A~~dw~e~v~~ga~~~~e~v~e 186 (188)
T PRK05634 135 MEGAAVVGVAKHFGIP-VT-LLKQVSDSADESAAGSWFDAVDAGARELGEAVAE 186 (188)
T ss_pred EHHHHHHHHHHHCCCC-EE-EEEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 0588999999982998-89-9999701788754008999999999999999984
No 75
>pfam03333 PapB Adhesin biosynthesis transcription regulatory protein. This family includes PapB, DaaA, FanA, FanB, and AfaA.
Probab=33.51 E-value=39 Score=15.35 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=37.0
Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHH
Q ss_conf 899999999998589238999615889888899999833989999999
Q gi|254781188|r 22 SPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYT 69 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa 69 (185)
++.+..+.=+.+-+|.+-+.+|...|| +.+-|..-|++=........
T Consensus 39 S~kvI~AL~dylV~G~srkevCe~~~V-n~gyfS~~L~~L~~i~~~V~ 85 (91)
T pfam03333 39 SEKVINALRDYLVDGYSRKEVCERHNV-NNGYFSISLGRLQRISQIVA 85 (91)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHH
T ss_conf 389999999998768649999987297-79999999999999999999
No 76
>TIGR02564 cas_Csy1 CRISPR-associated protein, Csy1 family; InterPro: IPR013397 CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a widespread family of prokaryotic direct repeats with spacers of unique sequence between consecutive repeats. This entry, typified by YPO2465 of Yersinia pestis, is a CRISPR-associated (Cas) entry strictly associated with the Ypest subtype of CRISPR/Cas locus. It is designated Csy1, for CRISPR/Cas Subtype Ypest protein 1..
Probab=32.73 E-value=41 Score=15.27 Aligned_cols=44 Identities=20% Similarity=0.285 Sum_probs=36.1
Q ss_pred HHHHHHHHCCHH---HHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf 999999858923---899961588988889999983398999999999997
Q gi|254781188|r 27 AGILDQVANGKA---LGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQC 74 (185)
Q Consensus 27 d~Ic~rIA~GeS---Lr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~ 74 (185)
-.+|+.+.+|.| |+++...-|-- |.+-+.+|+|+.++|..+=+.
T Consensus 74 ~kll~~e~~g~s~~~L~~~L~~gD~~----~l~~fadD~El~~~w~~~F~~ 120 (413)
T TIGR02564 74 VKLLQLEHDGGSELKLRALLRAGDPR----VLKAFADDPELSEQWKTKFQA 120 (413)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHH----HHHHHCCCHHHHHHHHHHHHH
T ss_conf 99875540589746999997618988----999715898899999998888
No 77
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=32.33 E-value=41 Score=15.22 Aligned_cols=15 Identities=7% Similarity=0.029 Sum_probs=8.5
Q ss_pred HCCCCCCHHHHHHHH
Q ss_conf 158898888999998
Q gi|254781188|r 44 RKVGMPKYSTFYRWI 58 (185)
Q Consensus 44 kd~gMPs~sTV~rWL 58 (185)
-|..||..+.+-.|-
T Consensus 58 mDi~mp~~~gi~~~~ 72 (216)
T PRK10100 58 LDMMEADKKLIHYWQ 72 (216)
T ss_pred EECCCCCCHHHHHHH
T ss_conf 848878830899999
No 78
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=31.81 E-value=42 Score=15.17 Aligned_cols=33 Identities=12% Similarity=0.154 Sum_probs=18.4
Q ss_pred HHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 9999999858923899961588988889999983
Q gi|254781188|r 26 FAGILDQVANGKALGHVLRKVGMPKYSTFYRWIK 59 (185)
Q Consensus 26 ad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~ 59 (185)
--+|+..|+.|.|-+.|...-++ |-.||-..+.
T Consensus 153 E~eVl~lla~G~snkeIA~~L~i-S~~TVk~h~~ 185 (211)
T COG2197 153 ELEVLRLLAEGLSNKEIAEELNL-SEKTVKTHVS 185 (211)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHH
T ss_conf 99999999879988999999787-8989999999
No 79
>KOG4398 consensus
Probab=31.51 E-value=42 Score=15.14 Aligned_cols=44 Identities=34% Similarity=0.462 Sum_probs=28.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 60378997999988999998764665343420344331346788999999
Q gi|254781188|r 97 PVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVSVESKHTIDLRPAIERLRE 146 (185)
Q Consensus 97 ~~~~~~lr~~~~~~~~w~l~k~~p~~yg~rvs~e~~h~~~~~~~~~~~~~ 146 (185)
.--+++++.++-|. .--++++.|||+.|. +-|||+|--.||+-.
T Consensus 36 qkl~sr~~~~~ekk---e~i~r~n~k~~d~v~---~~~~~~~~~~erl~~ 79 (359)
T KOG4398 36 QKLYSRAQRHQEKK---EKIQRHNRKLGDLVE---KKTIDLRSHYERLAN 79 (359)
T ss_pred HHHHHHHHHHHHHH---HHHHHHHHHCCHHHH---HHHHHHHHHHHHHHH
T ss_conf 99999999988879---999986532004888---888899999999999
No 80
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=30.93 E-value=43 Score=15.07 Aligned_cols=83 Identities=18% Similarity=0.144 Sum_probs=37.5
Q ss_pred CCCCCCHH--HHHHHHHC-CHH----------HHHHHHHHHHHHHHHHHH------HHHHHCC----------CCHHHHH
Q ss_conf 58898888--99999833-989----------999999999973799999------9862002----------3005640
Q gi|254781188|r 45 KVGMPKYS--TFYRWIKK-DLK----------LQEAYTEALQCRLDLLAE------ELLEEPA----------PTAEELA 95 (185)
Q Consensus 45 d~gMPs~s--TV~rWL~k-deE----------freqYa~Are~qaD~laE------EILE~~a----------~~~ee~~ 95 (185)
|-.||..+ .+.+++++ .+. -.+...+|.+.+|+-|.. ++++..- +......
T Consensus 54 Di~mP~~~G~e~l~~l~~~~p~~~vivlT~~~~~~~~~~al~~GA~gyl~K~~~~~~L~~aI~~~l~~~~~~~~~~~~~~ 133 (202)
T PRK09390 54 DVRMPGIDGIELLRRLKARGSPLPVIVMTGHGDVPLAVEAMKLGAIDFIEKPFEDERLIGAIERALAQAPAAAKSEAVAA 133 (202)
T ss_pred CCCCCCCCCHHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHHCCCHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHH
T ss_conf 79999989607999987228998679997457488889999829464455999999999999999971523242146678
Q ss_pred -CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf -36037899799998899999876466534342
Q gi|254781188|r 96 -NPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRV 127 (185)
Q Consensus 96 -~~~~~~~lr~~~~~~~~w~l~k~~p~~yg~rv 127 (185)
..-.-..|..|.+.++.++..-+.++-.+...
T Consensus 134 ~~~~~~~~LT~RE~eVL~ll~~G~snkeIA~~L 166 (202)
T PRK09390 134 DIRARIASLSERERQVMDGLVAGLSNKVIARDL 166 (202)
T ss_pred HHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf 887400669989999999998389689999997
No 81
>pfam03374 ANT Phage antirepressor protein KilAC domain. This domain was called the KilAC domain by Iyer and colleagues.
Probab=30.93 E-value=43 Score=15.07 Aligned_cols=38 Identities=13% Similarity=0.377 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHH
Q ss_conf 9999999998589238999615889888899999833989
Q gi|254781188|r 24 ELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLK 63 (185)
Q Consensus 24 Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeE 63 (185)
+.+|.|.+. .+..+++.+++..||+ ...|++||++.-=
T Consensus 13 ~~~D~~~~~-~~~~~i~~~AK~l~i~-~~~L~~~L~~~~~ 50 (112)
T pfam03374 13 EYADAIAAS-DGLVLVGQIAKLLGIG-ENRLFKWLRENGI 50 (112)
T ss_pred HHHHHHHCC-CCCEEHHHHHHHHCCC-HHHHHHHHHHCCE
T ss_conf 999999757-9958799999992999-9999999998892
No 82
>TIGR00089 TIGR00089 RNA modification enzyme, MiaB family; InterPro: IPR005839 This entry represents a family defined on the basis of sequence similarity. Most of these proteins are not yet characterised, but those that are include CDK5 regulatory subunit-associated protein 1, which specifically inhibits CDK5 activation by CDK5R1 . MiaB, a tRNA modification enzyme . The size of proteins in this entry ranges from 47 to 61 kDa and they contain six conserved cysteines, three of which are clustered. .
Probab=30.85 E-value=41 Score=15.26 Aligned_cols=106 Identities=15% Similarity=0.190 Sum_probs=79.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHCCHHHHHHHHC--CCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH-----HC
Q ss_conf 5676445899999999998589238999615--8898888999998339899999999999737999999862-----00
Q gi|254781188|r 15 KKGCIYYSPELFAGILDQVANGKALGHVLRK--VGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLE-----EP 87 (185)
Q Consensus 15 Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd--~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE-----~~ 87 (185)
|.|+..||-|-...|.++|-.=-+--.|.-| .|.|.= .+++|.+.+.-=.+.+.|.+.-=+.. ..
T Consensus 284 K~M~R~Y~~e~~~~~~~k~r~~~P~~~i~TDiIVGFPGE--------TeEdF~~Tl~l~~ev~F~~~~~F~YSpR~gTpA 355 (455)
T TIGR00089 284 KRMNRKYTREEYLEIVEKLRAKVPDAAITTDIIVGFPGE--------TEEDFEETLDLVEEVKFDKLHSFIYSPRPGTPA 355 (455)
T ss_pred HCCCCCCCHHHHHHHHHHHHHHCCCCEEECCEEECCCCC--------CHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC
T ss_conf 703789888999999999998478817750268828999--------889999999998523844343120578888746
Q ss_pred CCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 23005640360378997999988999998764665343420
Q gi|254781188|r 88 APTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPRVS 128 (185)
Q Consensus 88 a~~~ee~~~~~~~~~lr~~~~~~~~w~l~k~~p~~yg~rvs 128 (185)
|...++.-..|-+.||+++....-+|..+++..+..|..+.
T Consensus 356 a~~~d~vP~~vk~~R~~~L~~l~~~i~~~~n~~~~~G~~~~ 396 (455)
T TIGR00089 356 ADMKDQVPEEVKKERLERLIALQKEISLEKNKRKYVGKTLE 396 (455)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEE
T ss_conf 35678889889999999999999999999998750498789
No 83
>PRK01381 Trp operon repressor; Provisional
Probab=30.33 E-value=27 Score=16.50 Aligned_cols=28 Identities=18% Similarity=0.431 Sum_probs=15.5
Q ss_pred HHHHHHHCCH-HHHHHHHCCCCCCHHHHHH
Q ss_conf 9999985892-3899961588988889999
Q gi|254781188|r 28 GILDQVANGK-ALGHVLRKVGMPKYSTFYR 56 (185)
Q Consensus 28 ~Ic~rIA~Ge-SLr~ICkd~gMPs~sTV~r 56 (185)
.||..+..|+ |=|.|.++.|+ +-.|+-|
T Consensus 46 ~I~~~Ll~ge~sQReIa~~lgv-siAtITR 74 (99)
T PRK01381 46 RIVEELLRGELSQREIKQELGV-GIATITR 74 (99)
T ss_pred HHHHHHHHCCCCHHHHHHHHCC-CCEECCC
T ss_conf 9999999487649999998497-4020000
No 84
>PRK09940 transcriptional regulator YdeO; Provisional
Probab=30.31 E-value=44 Score=15.00 Aligned_cols=95 Identities=11% Similarity=0.025 Sum_probs=66.1
Q ss_pred CCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCH
Q ss_conf 458999999999985892389996158898888999998339-8999999999997379999998620023005640360
Q gi|254781188|r 20 YYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD-LKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPV 98 (185)
Q Consensus 20 ~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd-eEfreqYa~Are~qaD~laEEILE~~a~~~ee~~~~~ 98 (185)
..+-.+-.-|...|+.-=+|+.||....| |-+|+.++|++. -.|.+-+.++|-..|..|. .-..| -.+.|.-+
T Consensus 134 s~s~Kv~~II~sDis~~W~L~dIA~~L~m-SEStLkRkLk~EgtsFs~ILld~RM~~A~~LL----~~~~~-I~~IA~~c 207 (253)
T PRK09940 134 SVSGKVRNIVNMKLAHPWKLKDICDCLYI-SESLLKKKLKQEQTTFSQILLDARMQHAKNLI----RVEGS-VNKIAEQC 207 (253)
T ss_pred HHHHHHHHHHHCCCCCCCCHHHHHHHHCC-CHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH----HCCCC-HHHHHHHH
T ss_conf 35698999996483004609999988745-89999999998699599999999999999998----61898-99999983
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 3789979999889999987646653434203
Q gi|254781188|r 99 FYSKMRDRKQRMGTFLLEKLSNQKYGPRVSV 129 (185)
Q Consensus 99 ~~~~lr~~~~~~~~w~l~k~~p~~yg~rvs~ 129 (185)
+++-.+---. .-.+.||-.-+|
T Consensus 208 GYsS~SYFi~---------~FK~~fGiTP~q 229 (253)
T PRK09940 208 GYASTSYFIY---------AFRKHFGNSPKR 229 (253)
T ss_pred CCCCCHHHHH---------HHHHHHCCCCHH
T ss_conf 8898239999---------999881979189
No 85
>pfam05009 EBV-NA3 Epstein-Barr virus nuclear antigen 3 (EBNA-3). This family contains EBNA-3A, -3B, and -3C which are latent infection nuclear proteins important for Epstein-Barr virus (EBV)-induced B-cell immortalisation and the immune response to EBV infection.
Probab=30.23 E-value=45 Score=14.99 Aligned_cols=42 Identities=26% Similarity=0.536 Sum_probs=31.9
Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHCCCCCC----HHHHHHHHHCCHH
Q ss_conf 89999999999858923899961588988----8899999833989
Q gi|254781188|r 22 SPELFAGILDQVANGKALGHVLRKVGMPK----YSTFYRWIKKDLK 63 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeSLr~ICkd~gMPs----~sTV~rWL~kdeE 63 (185)
+.....-||+.++.|.||..|=-...-|. +.-|..||.+-+.
T Consensus 105 ~~~rY~~fFDl~~~~~sL~~IW~~~l~~dqrv~FveFlG~l~k~d~ 150 (254)
T pfam05009 105 SQRRYRVFFDLVESGRSLYHIWENVLTPEQRVDFVEFLGWLQKTDN 150 (254)
T ss_pred CCCCHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHHHHHHHHHCCCC
T ss_conf 1655111144786336389998625780232009998788754774
No 86
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=29.74 E-value=45 Score=14.94 Aligned_cols=39 Identities=15% Similarity=0.189 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 5899999999998589238999615889888899999833
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.++.--.-|.-+.-+|.|...|+..-|+| .+||..++..
T Consensus 11 L~~~~r~vl~l~y~~~~s~~EIa~~lgis-~~tVk~~l~r 49 (55)
T cd06171 11 LPEREREVILLRFGEGLSYEEIAEILGIS-RSTVRQRLHR 49 (55)
T ss_pred CCHHHHHHHHHHHHCCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 99999898999998099999999998959-9999999999
No 87
>pfam03746 LamB_YcsF LamB/YcsF family. This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilisation of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The exact molecular function of the proteins in this family is unknown.
Probab=29.56 E-value=46 Score=14.92 Aligned_cols=57 Identities=32% Similarity=0.398 Sum_probs=44.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCC------CCHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf 2465676445899999999998589238999615889------88889999983398999999999997
Q gi|254781188|r 12 VRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGM------PKYSTFYRWIKKDLKLQEAYTEALQC 74 (185)
Q Consensus 12 ~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gM------Ps~sTV~rWL~kdeEfreqYa~Are~ 74 (185)
|| +++++ -.+|+.+.|..+|+ .|..||+..|+ | ..-+|..+.+|+++.+.+.+|...
T Consensus 71 GR-r~~~~-s~~el~~~i~~Qi~---al~~~a~~~g~~l~hVKP-HGALYn~~~~d~~la~~i~~ai~~ 133 (242)
T pfam03746 71 GR-RAMAL-SAEELYALVLYQIG---ALQAFARAQGLRLQHVKP-HGALYNMAAKDRALARAVAEAVYD 133 (242)
T ss_pred CC-CCCCC-CHHHHHHHHHHHHH---HHHHHHHHCCCCCCCCCH-HHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 99-98889-98999999999999---999999982996311353-199999996599999999999998
No 88
>pfam00356 LacI Bacterial regulatory proteins, lacI family.
Probab=29.51 E-value=46 Score=14.91 Aligned_cols=26 Identities=19% Similarity=0.298 Sum_probs=22.2
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCCHHH
Q ss_conf 389996158898888999998339899
Q gi|254781188|r 38 ALGHVLRKVGMPKYSTFYRWIKKDLKL 64 (185)
Q Consensus 38 SLr~ICkd~gMPs~sTV~rWL~kdeEf 64 (185)
+|+.|.+.-|+ |.+||-+-|+..+..
T Consensus 1 Ti~DIA~~agV-S~~TVSr~ln~~~~v 26 (46)
T pfam00356 1 TIKDVARLAGV-SKATVSRVLNNPERV 26 (46)
T ss_pred CHHHHHHHHCC-CHHHHHHHHCCCCCC
T ss_conf 99999999897-999999998797989
No 89
>pfam11626 Rap1_C Rap1 - C terminal domain. This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C terminal domain.
Probab=29.15 E-value=38 Score=15.45 Aligned_cols=36 Identities=28% Similarity=0.644 Sum_probs=26.4
Q ss_pred CCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHH
Q ss_conf 6445899999999998589238999615889888899999833989
Q gi|254781188|r 18 CIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLK 63 (185)
Q Consensus 18 ~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeE 63 (185)
++.|.+.+|+.+++.+..|..+ -.+||. -|-.+|.+
T Consensus 5 ~t~~~p~lA~~vl~~L~~g~GI-----P~n~pG-----IWT~eDDe 40 (68)
T pfam11626 5 CTSYDPSQADKVLEDLRDGKGI-----PDNVPG-----IWTKEDDE 40 (68)
T ss_pred CCCCCHHHHHHHHHHHHCCCCC-----CCCCCC-----CCCCCCHH
T ss_conf 2137887999999999807999-----999998-----67523389
No 90
>KOG2829 consensus
Probab=28.45 E-value=45 Score=15.00 Aligned_cols=43 Identities=16% Similarity=0.271 Sum_probs=33.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHH
Q ss_conf 56764458999999999985892389996158898888999998
Q gi|254781188|r 15 KKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWI 58 (185)
Q Consensus 15 Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL 58 (185)
+||.++|+ |+|+.+..+.+.-.....||.+..-+...++.|.+
T Consensus 59 ~Kg~TtYn-eVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRV 101 (326)
T KOG2829 59 RKGTTTYN-EVADELVAEFAGANNYSHICPNEQEYDQKNIRRRV 101 (326)
T ss_pred HCCCCCHH-HHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf 51776288-99999999985026634458210134247788999
No 91
>COG1309 AcrR Transcriptional regulator [Transcription]
Probab=27.88 E-value=49 Score=14.73 Aligned_cols=47 Identities=19% Similarity=0.299 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHH----CCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHH
Q ss_conf 999999999985----892389996158898888999998339899999999
Q gi|254781188|r 23 PELFAGILDQVA----NGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTE 70 (185)
Q Consensus 23 ~Eiad~Ic~rIA----~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~ 70 (185)
.++.+.-+..+. +|-|++.|++.-|+ +.+|||++..+.+++-....+
T Consensus 15 ~~ii~aa~~l~~~~G~~~~t~~~Ia~~agv-s~~~~Y~~f~~K~~l~~~~~~ 65 (201)
T COG1309 15 ERILDAALRLFAEKGYAATTVDEIAKAAGV-SKGTLYRHFPSKEDLLLALLE 65 (201)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHCC-CHHHHHHHCCCHHHHHHHHHH
T ss_conf 999999999998659322899999988794-978999887899999999999
No 92
>PRK03333 coaE dephospho-CoA kinase/unknown domain fusion protein; Provisional
Probab=27.68 E-value=49 Score=14.71 Aligned_cols=30 Identities=20% Similarity=0.341 Sum_probs=19.9
Q ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999983398999999999997379999998
Q gi|254781188|r 54 FYRWIKKDLKLQEAYTEALQCRLDLLAEEL 83 (185)
Q Consensus 54 V~rWL~kdeEfreqYa~Are~qaD~laEEI 83 (185)
|..||+.+++.++.|..-+..-+..+..++
T Consensus 336 FRDyLRahp~~r~~Y~~lKr~lA~~~~~d~ 365 (394)
T PRK03333 336 FRDWLRADPGAREEYLAVKRRAAARADGAL 365 (394)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHHHHCCCCH
T ss_conf 999986399999999999999997589767
No 93
>pfam00126 HTH_1 Bacterial regulatory helix-turn-helix protein, lysR family.
Probab=27.19 E-value=50 Score=14.65 Aligned_cols=34 Identities=18% Similarity=0.226 Sum_probs=28.6
Q ss_pred HHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 99999858923899961588988889999983398
Q gi|254781188|r 28 GILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 28 ~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
.+|..|+.-.|++..++.-+| +.+++.++|++=+
T Consensus 5 ~~f~~v~~~gs~~~AA~~l~i-sqs~vs~~i~~LE 38 (60)
T pfam00126 5 RVFVAVAEEGSFTAAAERLGL-SQPAVSRQIKRLE 38 (60)
T ss_pred HHHHHHHHCCCHHHHHHHHCC-CHHHHHHHHHHHH
T ss_conf 999999980999999999798-9889999999999
No 94
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=26.85 E-value=51 Score=14.61 Aligned_cols=38 Identities=13% Similarity=0.141 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHHCCH--------HHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 58999999999985892--------3899961588988889999983
Q gi|254781188|r 21 YSPELFAGILDQVANGK--------ALGHVLRKVGMPKYSTFYRWIK 59 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~Ge--------SLr~ICkd~gMPs~sTV~rWL~ 59 (185)
.+++++++|.+.|.+|. |=+.++...|+ |.++|..-|.
T Consensus 9 L~eqV~~~L~~~I~~G~l~pGdrLPsEreLAe~fGV-SRt~VREAL~ 54 (258)
T PRK11523 9 LYQQLAADLKERIEQGVYLVGDKLPAERFIADEKNV-SRTVVREAII 54 (258)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHH
T ss_conf 999999999999985999997909669999999798-8799999999
No 95
>PRK05406 LamB/YcsF family protein; Provisional
Probab=26.69 E-value=51 Score=14.59 Aligned_cols=57 Identities=32% Similarity=0.424 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCC------CCHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf 2465676445899999999998589238999615889------88889999983398999999999997
Q gi|254781188|r 12 VRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGM------PKYSTFYRWIKKDLKLQEAYTEALQC 74 (185)
Q Consensus 12 ~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gM------Ps~sTV~rWL~kdeEfreqYa~Are~ 74 (185)
|| ++..+ -.+|+.+.|..+|+ .|..||+..|+ | ..-+|..+.+|+++.+.+.+|-..
T Consensus 73 GR-r~~~~-s~~el~~~i~~Qi~---~l~~~a~~~g~~l~hvKp-HGALYn~~~~d~~~a~~i~~~i~~ 135 (246)
T PRK05406 73 GR-RNMDL-SPEELYALVLYQIG---ALQAIARAAGGRVRHVKP-HGALYNMAAKDPELADAIAEAVAA 135 (246)
T ss_pred CC-CCCCC-CHHHHHHHHHHHHH---HHHHHHHHCCCCCCEECC-CHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf 98-88989-99999999999999---999999984996313240-189999884599999999999998
No 96
>pfam08765 Mor Mor transcription activator family. Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N terminal region of Mor is the dimerization region, and the C terminal contains a helix-turn-helix motif which binds DNA.
Probab=26.18 E-value=52 Score=14.53 Aligned_cols=34 Identities=26% Similarity=0.379 Sum_probs=21.3
Q ss_pred HHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 999999998589238999615889888899999833
Q gi|254781188|r 25 LFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 25 iad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.-.+|+..+ +|.....+.+.+|| |-.++|+-|++
T Consensus 61 Rd~~I~~eF-nG~N~~eLArkY~l-s~~~i~~ii~~ 94 (107)
T pfam08765 61 RDLEIYNEF-NGNNHAELARKYGV-SEQWIYKIIKR 94 (107)
T ss_pred HHHHHHHHH-CCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 999999980-79879999999698-89999999999
No 97
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=26.05 E-value=53 Score=14.52 Aligned_cols=37 Identities=8% Similarity=0.016 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHCCH--------HHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 999999999985892--------38999615889888899999833
Q gi|254781188|r 23 PELFAGILDQVANGK--------ALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 23 ~Eiad~Ic~rIA~Ge--------SLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.++++.|.++|.+|+ |-+.+|+..|+ |..||.+-|..
T Consensus 4 ~qI~~~L~~~I~~G~~~~G~~LPsE~eLa~~~~V-SR~TvR~Al~~ 48 (231)
T TIGR03337 4 LYIKDHLSYQIRAGALLPGDKLPSERDLGERFNT-TRVTIREALQQ 48 (231)
T ss_pred HHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 8999999999981999995978589999999797-99999999999
No 98
>pfam09862 DUF2089 Protein of unknown function(DUF2089). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=25.76 E-value=53 Score=14.48 Aligned_cols=39 Identities=15% Similarity=0.257 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 5899999999998589238999615889888899999833
Q gi|254781188|r 21 YSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.++|-.+-|-.-|-..-||+.+-+..|+ ||.||...|.+
T Consensus 34 L~~E~l~Fi~~fi~~~Gnlke~~~~lgi-SYpTvR~rLd~ 72 (113)
T pfam09862 34 LTPEQLEFVELFIKCRGNIKEVEKELGI-SYPTVRNRLDE 72 (113)
T ss_pred CCHHHHHHHHHHHHHCCCHHHHHHHHCC-CCHHHHHHHHH
T ss_conf 8999999999999916889999999788-81889999999
No 99
>pfam08281 Sigma70_r4_2 Sigma-70, region 4. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.
Probab=25.70 E-value=53 Score=14.47 Aligned_cols=38 Identities=13% Similarity=0.190 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 899999999998589238999615889888899999833
Q gi|254781188|r 22 SPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.+.--.-|.-+.-+|.|...|+..-|+| .+||..++..
T Consensus 12 p~~~r~~~~l~~~~~~s~~eIA~~lg~s-~~tVk~~l~R 49 (54)
T pfam08281 12 PPRQREVFLLRYLEGLSYAEIAELLGIS-EGTVKSRLSR 49 (54)
T ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHCCC-HHHHHHHHHH
T ss_conf 9999989687998785999999998949-9999999999
No 100
>PHA00542 putative Cro-like protein
Probab=25.40 E-value=45 Score=14.97 Aligned_cols=47 Identities=13% Similarity=0.145 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHCCHHHHHHHHCCCC--CCHHHHHHHHHCCHHHHH
Q ss_conf 45899999999998589238999615889--888899999833989999
Q gi|254781188|r 20 YYSPELFAGILDQVANGKALGHVLRKVGM--PKYSTFYRWIKKDLKLQE 66 (185)
Q Consensus 20 ~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gM--Ps~sTV~rWL~kdeEfre 66 (185)
-|++.-.+-+|..|+.|-+-..|....|+ |+.+-++.=-++||-+.-
T Consensus 15 ~y~k~P~E~V~aLi~~G~tQ~qI~~~tgv~QpsisRilsGk~kDpR~s~ 63 (82)
T PHA00542 15 AYTQRPDELVCALIRAGWSQEQIADATDVSQPTICRIYSGRHKDPRYSV 63 (82)
T ss_pred HHHCCHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHCCCCCCCCCHH
T ss_conf 6532989999999982256999998608770368999808878972069
No 101
>pfam00165 HTH_AraC Bacterial regulatory helix-turn-helix proteins, AraC family. In the absence of arabinose, the N-terminal arm of AraC binds to the DNA binding domain (pfam00165) and helps to hold the two DNA binding domains in a relative orientation that favours DNA looping. In the presence of arabinose, the arms bind over the arabinose on the dimerization domain, thus freeing the DNA-binding domains. The freed DNA-binding domains are then able to assume a conformation suitable for binding to the adjacent DNA sites that are utilized when AraC activates transcription, and hence AraC ceases looping the DNA when arabinose is added.
Probab=25.20 E-value=52 Score=14.57 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=26.4
Q ss_pred HHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 99985892389996158898888999998339
Q gi|254781188|r 30 LDQVANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 30 c~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
.+.+....++..|+...|+.+.+.|.+..++.
T Consensus 2 ~~~~~~~~~i~~IA~~~g~~s~~~f~r~fk~~ 33 (43)
T pfam00165 2 EENLSTNWTIADIAEELGFSSQSYFSRLFKKY 33 (43)
T ss_pred HHHHCCCCCHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf 02520899799999996899768999999998
No 102
>COG3645 Uncharacterized phage-encoded protein [Function unknown]
Probab=25.16 E-value=49 Score=14.73 Aligned_cols=27 Identities=7% Similarity=0.420 Sum_probs=17.7
Q ss_pred CC-HHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 89-23899961588988889999983398
Q gi|254781188|r 35 NG-KALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 35 ~G-eSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
+| .+++.+|+..++- ..-|+.||.++.
T Consensus 45 ~gli~~re~AK~lkig-e~~l~~~L~e~~ 72 (135)
T COG3645 45 SGLILFRELAKLLKIG-ENRLFAWLRENK 72 (135)
T ss_pred CCCEEHHHHHHHHCCC-HHHHHHHHHHCC
T ss_conf 6625199999997637-789999999878
No 103
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=24.92 E-value=55 Score=14.38 Aligned_cols=35 Identities=26% Similarity=0.283 Sum_probs=29.9
Q ss_pred HHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 999999985892389996158898888999998339
Q gi|254781188|r 26 FAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 26 ad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
-.+++..++.|.|...|...-++ +..||+..+...
T Consensus 9 E~~~~~l~~~G~s~~eia~~l~i-s~~tV~~h~~~i 43 (65)
T COG2771 9 EREILRLVAQGKSNKEIARILGI-SEETVKTHLRNI 43 (65)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCC-CHHHHHHHHHHH
T ss_conf 99999999869989999999877-999999999999
No 104
>pfam12116 SpoIIID Stage III sporulation protein D. This stage III sporulation protein is a small DNA-binding family that is essential for gene expression of the mother-cell compartment during sporulation. The domain is found in bacteria and viruses, and is about 40 amino acids in length. It has a conserved RGG sequence motif.
Probab=24.84 E-value=55 Score=14.37 Aligned_cols=40 Identities=18% Similarity=0.197 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 458999999999985-89238999615889888899999833
Q gi|254781188|r 20 YYSPELFAGILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 20 ~Ys~Eiad~Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.|-++-+-+|+..|. ..-..|+..+-.|+ |.|||+.=+.+
T Consensus 2 ~yIeeR~~~i~~YIi~~~aTVR~tAk~FGv-SKSTVHkDvTe 42 (82)
T pfam12116 2 DYIEERVLEIANYIIENKATVRQAAKVFGV-SKSTVHKDVTE 42 (82)
T ss_pred CHHHHHHHHHHHHHHHCCHHHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 289999999999999626289999999696-09889887999
No 105
>pfam07618 DUF1580 Protein of unknown function (DUF1580). A family of short hypothetical proteins found in Rhodopirellula baltica.
Probab=24.70 E-value=44 Score=15.03 Aligned_cols=22 Identities=32% Similarity=0.454 Sum_probs=16.4
Q ss_pred HHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 9996158898888999998339
Q gi|254781188|r 40 GHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 40 r~ICkd~gMPs~sTV~rWL~kd 61 (185)
..|--..|-|+.+|+++|-.+.
T Consensus 4 ~a~~l~~grp~~stv~RW~~~~ 25 (56)
T pfam07618 4 DAIELETGRPAPSTVLRWSLKP 25 (56)
T ss_pred HHHHHHCCCCCCHHHHHHHCCC
T ss_conf 5788860996833777763077
No 106
>TIGR01588 citE citrate lyase, beta subunit; InterPro: IPR006475 This group of sequences represent the beta subunit of the holoenzyme citrate lyase (4.1.3.6 from EC) composed of alpha (2.8.3.10 from EC), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The beta subunit catalyzes the reaction (3S)-citryl-CoA = acetyl-CoA + oxaloacetate. The group contains an experimentally characterised member from Leuconostoc mesenteroides . The group contains sequences from a wide range of Gram-positive bacteria. For Gram-negative bacteria, it appears that only the sequences from gamma proteobacteria are present.; GO: 0008816 citryl-CoA lyase activity, 0006084 acetyl-CoA metabolic process, 0005737 cytoplasm, 0009346 citrate lyase complex.
Probab=24.48 E-value=19 Score=17.52 Aligned_cols=59 Identities=24% Similarity=0.258 Sum_probs=46.7
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH------HHHH-HCCCCHHHHHC
Q ss_conf 38999615889888899999833989999999999973799999------9862-00230056403
Q gi|254781188|r 38 ALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAE------ELLE-EPAPTAEELAN 96 (185)
Q Consensus 38 SLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laE------EILE-~~a~~~ee~~~ 96 (185)
.+-.-.+.-|.-+|.|||+=+++.+.|...-.-+++.+.|--.= ||+- .=+||.+|.-+
T Consensus 177 ~i~lAAR~AgI~AFDtVysdvNneeGF~~E~~Lik~LGFDGKSLinPrQi~llh~vY~PT~KEi~~ 242 (288)
T TIGR01588 177 AILLAARAAGIAAFDTVYSDVNNEEGFLKEAQLIKQLGFDGKSLINPRQIELLHKVYAPTEKEIDK 242 (288)
T ss_pred HHHHHHHHCCCEEEEEEEECCCCHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCHHHHHH
T ss_conf 999998652614544554047662357999999986389873125626788765314885778889
No 107
>pfam07374 DUF1492 Protein of unknown function (DUF1492). This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown. It appears to be distantly related to pfam08281.
Probab=24.30 E-value=52 Score=14.56 Aligned_cols=25 Identities=20% Similarity=0.343 Sum_probs=16.1
Q ss_pred CCHHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 89238999615889888899999833
Q gi|254781188|r 35 NGKALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 35 ~GeSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
++.+.=.||..-++ |.+|||++++.
T Consensus 70 d~~~~~~v~e~l~~-Sr~Tyyr~~r~ 94 (100)
T pfam07374 70 DKMTVWQVCDKLNC-SRTTYYRKLRV 94 (100)
T ss_pred CCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 34749999999766-66789999999
No 108
>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=23.84 E-value=58 Score=14.25 Aligned_cols=38 Identities=8% Similarity=0.156 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHCCH-------HHHHHHHCCCCCCHHHHHHHHH
Q ss_conf 58999999999985892-------3899961588988889999983
Q gi|254781188|r 21 YSPELFAGILDQVANGK-------ALGHVLRKVGMPKYSTFYRWIK 59 (185)
Q Consensus 21 Ys~Eiad~Ic~rIA~Ge-------SLr~ICkd~gMPs~sTV~rWL~ 59 (185)
.++.+++.|.+.|.+|+ +-+.+|...|| |.++|..-|.
T Consensus 12 L~~~v~~~lr~~I~~g~l~pG~~L~E~~La~~~gV-SRtpvREAL~ 56 (212)
T TIGR03338 12 LTTLVQDEIERAILSGELPPGAKLNESDIAARLGV-SRGPVREAFR 56 (212)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHH
T ss_conf 99999999999998399999098189999998896-9499999999
No 109
>KOG1488 consensus
Probab=23.80 E-value=58 Score=14.24 Aligned_cols=74 Identities=20% Similarity=0.215 Sum_probs=35.1
Q ss_pred HHHHHHHH-HCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH---------HHHHHHHHHH---HHHHHHHHHHHHHH
Q ss_conf 99999862-00230056403603789979999889999987646---------6534342034---43313467889999
Q gi|254781188|r 78 LLAEELLE-EPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSN---------QKYGPRVSVE---SKHTIDLRPAIERL 144 (185)
Q Consensus 78 ~laEEILE-~~a~~~ee~~~~~~~~~lr~~~~~~~~w~l~k~~p---------~~yg~rvs~e---~~h~~~~~~~~~~~ 144 (185)
-|.+|+.. ...-..||-.|||---=.--..-...+|++.-... -+||-||-|- --++-+.+|+|+-+
T Consensus 281 ~li~ELd~~v~~~~~DQngnHViQK~ie~~p~~~~~fiv~~f~~~~~~~~ls~~~YGCRVIQr~lE~c~~~~~~~i~~ei 360 (503)
T KOG1488 281 QLIDELDGHLLKCVKDQNGNHVIQKCIETLPPDAWQFIVDFFSGDDNLLELSTHKYGCRVIQRILEHCSEDQKQPLMEEI 360 (503)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHCCCHHHHHHHHHHH
T ss_conf 99999986789998613563015766630683898999998458996467623676347899876137767676789999
Q ss_pred HHHHHHC
Q ss_conf 9986410
Q gi|254781188|r 145 REHYKHL 151 (185)
Q Consensus 145 ~~~~~~~ 151 (185)
..|.+.|
T Consensus 361 ~~~~~~L 367 (503)
T KOG1488 361 IRNCDQL 367 (503)
T ss_pred HHHHHHH
T ss_conf 9999999
No 110
>COG1922 WecG Teichoic acid biosynthesis proteins [Cell envelope biogenesis, outer membrane]
Probab=23.41 E-value=59 Score=14.19 Aligned_cols=130 Identities=23% Similarity=0.228 Sum_probs=71.0
Q ss_pred CCCCCHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 98742455540246567644589999999999858923899961588988889999983398999999999997379999
Q gi|254781188|r 1 MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLA 80 (185)
Q Consensus 1 ~s~~~k~~~Ka~R~Kk~~i~Ys~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~la 80 (185)
|+++.+..+..+..-+....-..+.++.|+.++..|+.-.-+. + +-. +---..+|++|++.|.+|--.-+|.+-
T Consensus 1 m~~~~~~~~~~ilg~~v~~~~~~~~~~~i~~~~~~~~~~~vv~----~-N~e-~~~~a~~d~e~~~~i~~A~li~pDG~g 74 (253)
T COG1922 1 MSSMTRRPRINILGLPVDNVTWDEAVALILGRIEQGKPTTVVT----L-NAE-KVLLARKDPEFREILNQADLILPDGIG 74 (253)
T ss_pred CCCCCCCCEEEEECCEEECCCHHHHHHHHHHHHHCCCCCEEEE----C-CHH-HHHHHCCCHHHHHHHHHCCEECCCCHH
T ss_conf 9977766327871624531777999999998874377528998----4-799-999862389999998615788268653
Q ss_pred ----H-HHHHHCCCCHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf ----9-98620023005640360378997999988999998764665------343420344331346788999999864
Q gi|254781188|r 81 ----E-ELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQK------YGPRVSVESKHTIDLRPAIERLREHYK 149 (185)
Q Consensus 81 ----E-EILE~~a~~~ee~~~~~~~~~lr~~~~~~~~w~l~k~~p~~------yg~rvs~e~~h~~~~~~~~~~~~~~~~ 149 (185)
- ..+-+|.|+. +...++- +.|-++..++ ||-.=-+ +.-+-.+++.++.
T Consensus 75 vV~~ar~~~g~~~~~r------v~G~Dl~--------~~Ll~~a~~~~~~vfllGgkp~V-------~~~a~~~l~~~~p 133 (253)
T COG1922 75 VVRAARRLLGQPLPER------VAGTDLV--------EALLKRAAEEGKRVFLLGGKPGV-------AEQAAAKLRAKYP 133 (253)
T ss_pred HHHHHHHHHCCCCCCC------CCHHHHH--------HHHHHHHCCCCCEEEEECCCHHH-------HHHHHHHHHHHCC
T ss_conf 9999999817667654------7848999--------99999717568649996487789-------9999999998789
Q ss_pred HCCCHHHH
Q ss_conf 10411344
Q gi|254781188|r 150 HLKPIDSE 157 (185)
Q Consensus 150 ~~k~~~~~ 157 (185)
+++-+...
T Consensus 134 ~l~ivg~h 141 (253)
T COG1922 134 GLKIVGSH 141 (253)
T ss_pred CCEEEEEC
T ss_conf 95699951
No 111
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=23.02 E-value=60 Score=14.14 Aligned_cols=60 Identities=22% Similarity=0.303 Sum_probs=44.4
Q ss_pred CCCCCCCCCCCHHHHHHH-HHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf 246567644589999999-99985892389996158898888999998339899999999999
Q gi|254781188|r 12 VRAKKGCIYYSPELFAGI-LDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQ 73 (185)
Q Consensus 12 ~R~Kk~~i~Ys~Eiad~I-c~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are 73 (185)
|++-.|.++.+.++++.. +..+..|.-.|.+.+.-||+ ..-|.+.-.+||++-. +-..+|
T Consensus 7 G~pGsG~TTva~~lAe~~gl~~vsaG~iFR~~A~e~gms-l~ef~~~AE~~p~iD~-~iD~rq 67 (179)
T COG1102 7 GLPGSGKTTVARELAEHLGLKLVSAGTIFREMARERGMS-LEEFSRYAEEDPEIDK-EIDRRQ 67 (179)
T ss_pred CCCCCCCHHHHHHHHHHHCCCEEECCHHHHHHHHHCCCC-HHHHHHHHHCCCHHHH-HHHHHH
T ss_conf 799997027999999982971562127999999983999-9999998751921669-988999
No 112
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=22.96 E-value=60 Score=14.14 Aligned_cols=50 Identities=18% Similarity=0.208 Sum_probs=35.9
Q ss_pred CHHHHHHHHHHH--HCCHHHHHHHHCCCCCCHHHHHHHHHC-----CHHHHHHHHHHH
Q ss_conf 899999999998--589238999615889888899999833-----989999999999
Q gi|254781188|r 22 SPELFAGILDQV--ANGKALGHVLRKVGMPKYSTFYRWIKK-----DLKLQEAYTEAL 72 (185)
Q Consensus 22 s~Eiad~Ic~rI--A~GeSLr~ICkd~gMPs~sTV~rWL~k-----deEfreqYa~Ar 72 (185)
-..+++-|++.. ....|++.++..-|+ |-+||.|..++ ..+|+-.-++-.
T Consensus 18 e~~ia~yil~~~~~~~~~si~~lA~~~~v-S~atv~Rf~kklG~~Gf~efk~~La~~~ 74 (106)
T pfam01418 18 EKKIADYILASPDNAIHLSIAELAKAAGV-SEASVVRFCRKLGFSGFSDLKVALAGEL 74 (106)
T ss_pred HHHHHHHHHHCHHHHHHCCHHHHHHHHCC-CHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf 99999999929999988339999989699-8999999999958998999999999986
No 113
>PRK09526 lacI lac repressor; Reviewed
Probab=22.94 E-value=60 Score=14.13 Aligned_cols=24 Identities=29% Similarity=0.386 Sum_probs=12.8
Q ss_pred HHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 3899961588988889999983398
Q gi|254781188|r 38 ALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 38 SLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
+|+.|.+.-|+ |.+||-+-|+..+
T Consensus 7 TikDIA~~agV-S~sTVSrvLn~~~ 30 (342)
T PRK09526 7 TLYDVARYAGV-SYQTVSRVLNQAS 30 (342)
T ss_pred CHHHHHHHHCC-CHHHHHHHHCCCC
T ss_conf 69999999896-9999999978979
No 114
>TIGR00637 ModE_repress ModE molybdate transport repressor domain; InterPro: IPR003725 Molybdenum-dependent repression of transcription of the Escherichia coli modABCD operon, which encodes the high-affinity molybdate transporter, is mediated by the ModE protein. When molybdate or tungstate bind to ModE there is little change in its alpha-helical content, but a major change in the environment of tryptophan and tyrosine residues occurs . This is the N-terminal domain of molybdenum-binding proteins ModE, ModA, MopA and MopB. These proteins are involved in molybdenum transport. ModE acts both as a repressor and activator of the mod and moa operons, respectively, depending on the properties of the binding site .; GO: 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport.
Probab=22.79 E-value=60 Score=14.11 Aligned_cols=38 Identities=16% Similarity=0.337 Sum_probs=32.1
Q ss_pred HHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHH
Q ss_conf 999999998589238999615889888899999833989
Q gi|254781188|r 25 LFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLK 63 (185)
Q Consensus 25 iad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeE 63 (185)
-.-.++..|..--|+....++.|++ |.+.|..+..-.+
T Consensus 5 ~~~~ll~~i~~~G~i~~~~~~~g~~-y~~~w~~~~~~~~ 42 (101)
T TIGR00637 5 RRVALLKAIAREGSISAAAKDAGLS-YKSAWDYIKAMNN 42 (101)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHCCC-HHHHHHHHHHHHH
T ss_conf 7789999987612044555640561-6789899988887
No 115
>PRK10079 putative transcriptional regulator; Provisional
Probab=22.60 E-value=61 Score=14.09 Aligned_cols=36 Identities=17% Similarity=0.201 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHCCH--------HHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 999999999985892--------38999615889888899999833
Q gi|254781188|r 23 PELFAGILDQVANGK--------ALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 23 ~Eiad~Ic~rIA~Ge--------SLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.++++.|.++| .|+ |=+.+|...|+ |..||.+-|..
T Consensus 15 ~qI~~~L~~~I-~g~~~~G~~LPsE~eLa~~y~V-SR~TVR~Al~~ 58 (241)
T PRK10079 15 QEIAAKLEQEL-RQHYRCGDYLPAEQQLAARFEV-NRHTLRRAIDQ 58 (241)
T ss_pred HHHHHHHHHHH-CCCCCCCCCCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 99999999997-0778898919699999999798-89999999999
No 116
>COG5211 SSU72 RNA polymerase II-interacting protein involved in transcription start site selection [Transcription]
Probab=22.50 E-value=61 Score=14.08 Aligned_cols=57 Identities=25% Similarity=0.247 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHH-HHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 4458999999999-9858923899961588988889999983398999999999997379999998
Q gi|254781188|r 19 IYYSPELFAGILD-QVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEEL 83 (185)
Q Consensus 19 i~Ys~Eiad~Ic~-rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEI 83 (185)
++-.+..++.||+ ..+.|.||.++.-...+- |+++++-+..=++|--.-+|.|++++
T Consensus 110 iTCEERcfdaicEdly~rg~~ln~~v~~iNvD--------IkD~~e~A~~G~kaILelvd~L~~~~ 167 (197)
T COG5211 110 ITCEERCFDAICEDLYARGPSLNQCVFMINVD--------IKDTPEDAIAGAKAILELVDVLAKEE 167 (197)
T ss_pred EEEHHHHHHHHHHHHHHCCCCCCCCEEEEEEE--------CCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 87268888999999985085546507999851--------46783654330899999999998899
No 117
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=22.32 E-value=62 Score=14.05 Aligned_cols=48 Identities=23% Similarity=0.412 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHC--CHHHHHHHHHH
Q ss_conf 99999999998589238999615889888899999833--98999999999
Q gi|254781188|r 23 PELFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKK--DLKLQEAYTEA 71 (185)
Q Consensus 23 ~Eiad~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~k--deEfreqYa~A 71 (185)
+++...-+--++.-..+.+|.++-|| +..++|+-|.. +|.|.---+-.
T Consensus 36 ~a~i~~alg~var~~GMsqvA~~aGl-sRe~LYkaLS~~GNPtf~Til~V~ 85 (100)
T COG3636 36 PALIAAALGVVARSRGMSQVARKAGL-SREGLYKALSPGGNPTFDTILAVL 85 (100)
T ss_pred HHHHHHHHHHHHHHCCHHHHHHHHCC-CHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 99999999999986578999999496-699999984789997589999999
No 118
>KOG1986 consensus
Probab=21.71 E-value=63 Score=13.97 Aligned_cols=83 Identities=28% Similarity=0.331 Sum_probs=40.2
Q ss_pred HHHHHHHHHC----CHHHH--HHHHHHHHHHHHHHHHHHHH--HCCC---CHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 8899999833----98999--99999999737999999862--0023---005640360378997999988999998764
Q gi|254781188|r 51 YSTFYRWIKK----DLKLQ--EAYTEALQCRLDLLAEELLE--EPAP---TAEELANPVFYSKMRDRKQRMGTFLLEKLS 119 (185)
Q Consensus 51 ~sTV~rWL~k----deEfr--eqYa~Are~qaD~laEEILE--~~a~---~~ee~~~~~~~~~lr~~~~~~~~w~l~k~~ 119 (185)
-+|+..|.+. +|+-+ .+--+|.+. .|+||+. -|.| .||+..- -+| |+|+|.+
T Consensus 644 G~tIaqWR~~gy~~~pe~~~f~~LL~ap~~----dA~el~~~RFP~PR~v~~~q~GS---------QAR----FLlskln 706 (745)
T KOG1986 644 GSTIAQWRKAGYHEQPEYENFKELLEAPRE----DAQELLLERFPMPRYVVTDQGGS---------QAR----FLLSKLN 706 (745)
T ss_pred CCHHHHHHHCCCCCCHHHHHHHHHHHHHHH----HHHHHHHHHCCCCEEEEECCCCC---------HHH----HHHHHCC
T ss_conf 726999874443348356789999971788----89999985089872898338860---------777----6666528
Q ss_pred HHH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf 665----343420344331346788999999864104113
Q gi|254781188|r 120 NQK----YGPRVSVESKHTIDLRPAIERLREHYKHLKPID 155 (185)
Q Consensus 120 p~~----yg~rvs~e~~h~~~~~~~~~~~~~~~~~~k~~~ 155 (185)
|-- .-+.-..+.--|-|+- +++-..|||+++
T Consensus 707 PS~t~~~~~~~~~s~~I~TDDvS-----lq~fm~hLkkla 741 (745)
T KOG1986 707 PSETHNNLTAHGGSSIILTDDVS-----LQVFMEHLKKLA 741 (745)
T ss_pred CCHHCCCHHHCCCCCEEEECCCC-----HHHHHHHHHHHC
T ss_conf 40420432223677704554431-----999999988526
No 119
>KOG0749 consensus
Probab=21.37 E-value=63 Score=14.01 Aligned_cols=56 Identities=18% Similarity=0.204 Sum_probs=40.6
Q ss_pred HHHHHHHHCCHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 999999858923899961588988889999983398999999999997379999998
Q gi|254781188|r 27 AGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEEL 83 (185)
Q Consensus 27 d~Ic~rIA~GeSLr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEI 83 (185)
..++...+-|++.+.++--...| +.||.|.+.-..+-.-+|..+..|.-..+.+|=
T Consensus 211 ~~f~~sf~iaq~vT~~ag~~sYP-~DTVRRRmm~~~~~~~~Y~~TldC~rkI~~~EG 266 (298)
T KOG0749 211 GNFAASFAIAQVVTTGAGLLSYP-LDTVRRRMMQSKGADLKYTGTLDCWRKIYKEEG 266 (298)
T ss_pred CHHHHHHHHHHHHHHHCCEECCC-CHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf 14999999998998700000155-057889986336766332758999999998745
No 120
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=21.13 E-value=65 Score=13.89 Aligned_cols=21 Identities=19% Similarity=0.139 Sum_probs=8.1
Q ss_pred HHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 8999615889888899999833
Q gi|254781188|r 39 LGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 39 Lr~ICkd~gMPs~sTV~rWL~k 60 (185)
|+.|.+.-|+ |.+||-+-|+.
T Consensus 9 i~dIA~~aGV-S~aTVSrvLn~ 29 (342)
T PRK10014 9 IHDVALAAGV-SVSTVSLVLSG 29 (342)
T ss_pred HHHHHHHHCC-CHHHHHHHHCC
T ss_conf 9999999896-99999999779
No 121
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=21.06 E-value=65 Score=13.88 Aligned_cols=87 Identities=21% Similarity=0.250 Sum_probs=52.8
Q ss_pred HHHHHHCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH---HCCCCHHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf 89996158898888999998339899999999999737999999862---002300564036037899799998899999
Q gi|254781188|r 39 LGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLE---EPAPTAEELANPVFYSKMRDRKQRMGTFLL 115 (185)
Q Consensus 39 Lr~ICkd~gMPs~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE---~~a~~~ee~~~~~~~~~lr~~~~~~~~w~l 115 (185)
|-.-|..-|+.+|..+-.++-. +|++.--+.|.--.+| +|+|.-++----|+-.=+-.++-++++|.+
T Consensus 74 li~~~~TlGlGNW~dIadyiGs---------r~kee~k~HylK~y~es~~ypl~~i~~~~~v~q~~f~~qrr~rie~f~~ 144 (432)
T COG5114 74 LIECLDTLGLGNWEDIADYIGS---------RAKEEIKSHYLKMYDESKYYPLPDITQNIHVPQDEFLEQRRHRIETFEL 144 (432)
T ss_pred HHHHHHHCCCCCHHHHHHHHHH---------HHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 9988875187758899998744---------2317899999999863046446531247877568899988765440368
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q ss_conf 876466534342034433134
Q gi|254781188|r 116 EKLSNQKYGPRVSVESKHTID 136 (185)
Q Consensus 116 ~k~~p~~yg~rvs~e~~h~~~ 136 (185)
-...|+| +.+|.-+-|+|.
T Consensus 145 ppi~prk--P~aS~P~cheiq 163 (432)
T COG5114 145 PPINPRK--PKASNPYCHEIQ 163 (432)
T ss_pred CCCCCCC--CCCCCCCHHHHH
T ss_conf 9888888--877897413330
No 122
>pfam02954 HTH_8 Bacterial regulatory protein, Fis family.
Probab=20.90 E-value=66 Score=13.86 Aligned_cols=32 Identities=28% Similarity=0.392 Sum_probs=24.4
Q ss_pred HHHHHH-CCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 999985-892389996158898888999998339
Q gi|254781188|r 29 ILDQVA-NGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 29 Ic~rIA-~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
|..-+. .|-.....++.-|| +.+|+|+-|++.
T Consensus 10 I~~aL~~~~gn~~~aA~~LGi-sr~tL~~kmkky 42 (42)
T pfam02954 10 IEAALERTGGNKSKAARLLGI-SRRTLYRKLKKY 42 (42)
T ss_pred HHHHHHHHCCCHHHHHHHHCC-CHHHHHHHHHHC
T ss_conf 999999949979999999796-999999999739
No 123
>pfam08279 HTH_11 HTH domain. This family includes helix-turn-helix domains in a wide variety of proteins.
Probab=20.64 E-value=67 Score=13.83 Aligned_cols=33 Identities=24% Similarity=0.217 Sum_probs=24.7
Q ss_pred HHHHHHHH--CC-HHHHHHHHCCCCCCHHHHHHHHHC
Q ss_conf 99999985--89-238999615889888899999833
Q gi|254781188|r 27 AGILDQVA--NG-KALGHVLRKVGMPKYSTFYRWIKK 60 (185)
Q Consensus 27 d~Ic~rIA--~G-eSLr~ICkd~gMPs~sTV~rWL~k 60 (185)
.+|+..|. .| -|...++...++ |.+|||+.|+.
T Consensus 3 ~~il~~L~~~~~~vt~~~La~~l~V-Sr~TV~rdi~~ 38 (55)
T pfam08279 3 LQILELLLQAREPISGQELAEKLGV-SRRTIRRDIKA 38 (55)
T ss_pred HHHHHHHHHCCCCCCHHHHHHHHCC-CHHHHHHHHHH
T ss_conf 9999999976999189999999698-89999999999
No 124
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein; InterPro: IPR010163 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=20.63 E-value=67 Score=13.83 Aligned_cols=38 Identities=21% Similarity=0.302 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHC--C-HHHHHHHHCCCCCCHHHHHHHHHCCH
Q ss_conf 999999999858--9-23899961588988889999983398
Q gi|254781188|r 24 ELFAGILDQVAN--G-KALGHVLRKVGMPKYSTFYRWIKKDL 62 (185)
Q Consensus 24 Eiad~Ic~rIA~--G-eSLr~ICkd~gMPs~sTV~rWL~kde 62 (185)
.-+-+|++.+.+ | .+.+.|.+.-|. |.+|+++.|..=+
T Consensus 169 ~~~~~vL~~L~~~~Ge~~v~~iA~~lg~-s~~T~~~~~~~Le 209 (231)
T TIGR01884 169 REELKVLEALKAEKGEKSVKNIAKKLGK-SLSTISRHLAELE 209 (231)
T ss_pred HHHHHHHHHHHCCCCEECHHHHHHHHCC-CHHHHHHHHHHHH
T ss_conf 9999999998507880528779988578-8879999999887
No 125
>PRK04330 hypothetical protein; Provisional
Probab=20.23 E-value=68 Score=13.77 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=5.8
Q ss_pred HHHHHHCCCCC
Q ss_conf 89996158898
Q gi|254781188|r 39 LGHVLRKVGMP 49 (185)
Q Consensus 39 Lr~ICkd~gMP 49 (185)
|..|..|..+|
T Consensus 18 L~~I~~D~sVP 28 (88)
T PRK04330 18 LERIINDTTVP 28 (88)
T ss_pred HHHHHCCCCCC
T ss_conf 99985389887
No 126
>pfam01381 HTH_3 Helix-turn-helix. This large family of DNA binding helix-turn helix proteins includes Cro and CI.
Probab=20.18 E-value=68 Score=13.76 Aligned_cols=39 Identities=18% Similarity=0.128 Sum_probs=27.6
Q ss_pred HHHCCHHHHHHHHCCCCCCHHHHHHHHHCC--HHHHHHHHHH
Q ss_conf 985892389996158898888999998339--8999999999
Q gi|254781188|r 32 QVANGKALGHVLRKVGMPKYSTFYRWIKKD--LKLQEAYTEA 71 (185)
Q Consensus 32 rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd--eEfreqYa~A 71 (185)
|...|.|...+.+.-|+ +.+|+.+|-+.. |.+..-+.-|
T Consensus 5 R~~~g~tq~~lA~~~gi-s~~~is~~E~g~~~p~~~~l~~ia 45 (55)
T pfam01381 5 REELGLSQEELAEKLGV-SRSTISKIENGKREPSLETLKKLA 45 (55)
T ss_pred HHHCCCCHHHHHHHHCC-CHHHHHHHHCCCCCCCHHHHHHHH
T ss_conf 97829989999999896-999999998799999999999999
No 127
>pfam03685 UPF0147 Uncharacterized protein family (UPF0147). This family of small proteins have no known function.
Probab=20.09 E-value=68 Score=13.75 Aligned_cols=10 Identities=10% Similarity=0.517 Sum_probs=4.7
Q ss_pred HHHHHCCCCC
Q ss_conf 9996158898
Q gi|254781188|r 40 GHVLRKVGMP 49 (185)
Q Consensus 40 r~ICkd~gMP 49 (185)
..|..|..+|
T Consensus 16 ~~I~~D~sVP 25 (85)
T pfam03685 16 DRIINDTTVP 25 (85)
T ss_pred HHHHCCCCCC
T ss_conf 9984389887
No 128
>TIGR01422 phosphonatase phosphonoacetaldehyde hydrolase; InterPro: IPR006323 These sequences represent an enzyme that catalyzes the cleavage of the carbon phosphorous bond of a phosphonate. The mechanism depends on the substrate having a carbonyl one carbon away from the cleavage position. This enzyme is a member of the Haloacid Dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases, and contains a modified version of the conserved catalytic motifs of that superfamily: the first motif is usually DxDx(T/V), here it is DxAxT, and in the third motif the normal conserved lysine is instead an arginine. Additionally, the enzyme contains a unique conserved catalytic lysine (B. cereus pos. 53) which is involved in the binding and activation of the substrate through the formation of a Schiff base . The substrate of this enzyme is the product of 2-aminoethylphosphonate (AEP) transaminase, phosphonoacetaldehyde. This degradation pathway for AEP may be related to its toxic properties which are utilised by microorganisms as a chemical warfare agent..
Probab=20.09 E-value=53 Score=14.47 Aligned_cols=67 Identities=16% Similarity=0.384 Sum_probs=49.0
Q ss_pred HHHHHHHCCCC-CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHHHHHHHHHHHH
Q ss_conf 38999615889-888899999833989999999999973799999986200230056403603789979999889
Q gi|254781188|r 38 ALGHVLRKVGM-PKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQRMG 111 (185)
Q Consensus 38 SLr~ICkd~gM-Ps~sTV~rWL~kdeEfreqYa~Are~qaD~laEEILE~~a~~~ee~~~~~~~~~lr~~~~~~~ 111 (185)
-+|.+|+-|-+ -.|..+|+-+..+.+..+-|++=...|...+++... |-|-..|.= +.||.+-.|||
T Consensus 50 Hiral~~~P~iA~rw~~vFgrlp~~~Di~aiYe~F~pl~ia~~a~haa--pIp~~levi-----a~lR~rGiKIG 117 (199)
T TIGR01422 50 HIRALTELPRIAERWRRVFGRLPTEADIQAIYEEFMPLQIAKVAEHAA--PIPAVLEVI-----AELRERGIKIG 117 (199)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCC--CCHHHHHHH-----HHHHHCCCEEE
T ss_conf 999986302899999997089997745899998616899998655405--553689999-----99973884442
No 129
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=20.09 E-value=68 Score=13.75 Aligned_cols=29 Identities=21% Similarity=0.245 Sum_probs=25.0
Q ss_pred HHHCCHHHHHHHHCCCCCCHHHHHHHHHCC
Q ss_conf 985892389996158898888999998339
Q gi|254781188|r 32 QVANGKALGHVLRKVGMPKYSTFYRWIKKD 61 (185)
Q Consensus 32 rIA~GeSLr~ICkd~gMPs~sTV~rWL~kd 61 (185)
|...|.|...+.+.-|+ +.+++.+|.+..
T Consensus 6 R~~~glsq~~lA~~~gi-s~~~is~~E~g~ 34 (56)
T smart00530 6 REEKGLTQEELAEKLGV-SRSTLSRIENGK 34 (56)
T ss_pred HHHCCCCHHHHHHHHCC-CHHHHHHHHCCC
T ss_conf 97729999999999895-999999999799
No 130
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219 Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids. DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme . The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site . The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=20.08 E-value=68 Score=13.75 Aligned_cols=17 Identities=29% Similarity=0.642 Sum_probs=13.5
Q ss_pred CHHHHHHHHHHHHCCHH
Q ss_conf 89999999999858923
Q gi|254781188|r 22 SPELFAGILDQVANGKA 38 (185)
Q Consensus 22 s~Eiad~Ic~rIA~GeS 38 (185)
-+++++.||++|++|+.
T Consensus 278 Q~~V~~~v~~QI~~G~~ 294 (348)
T TIGR00034 278 QPDVAEDVCEQIANGSK 294 (348)
T ss_pred HHHHHHHHHHHHHCCCC
T ss_conf 17899999999735351
No 131
>KOG4565 consensus
Probab=20.02 E-value=48 Score=14.77 Aligned_cols=49 Identities=27% Similarity=0.399 Sum_probs=30.6
Q ss_pred HHHCCCCCC-CCCCCHHHHHHHHHHHHCCH-HHHHHHHCCCCCCHHHHHHHH
Q ss_conf 540246567-64458999999999985892-389996158898888999998
Q gi|254781188|r 9 KKAVRAKKG-CIYYSPELFAGILDQVANGK-ALGHVLRKVGMPKYSTFYRWI 58 (185)
Q Consensus 9 ~Ka~R~Kk~-~i~Ys~Eiad~Ic~rIA~Ge-SLr~ICkd~gMPs~sTV~rWL 58 (185)
+|--|.|+| -..|..|+.++-..-++.|+ |..+.---.|+| .+|+---+
T Consensus 109 sKqpRkKRGrYRqYd~eileEAi~~VmsGkMsVskAqsiyGvP-HSTLEYKV 159 (206)
T KOG4565 109 SKQPRKKRGRYRQYDKEILEEAIRSVMSGKMSVSKAQSIYGVP-HSTLEYKV 159 (206)
T ss_pred CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEECCCCEECCC-CCHHHHHH
T ss_conf 3475522440655208999999999861744451136320466-50110012
Done!