Query 029524
Match_columns 192
No_of_seqs 131 out of 625
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 14:17:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029524.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029524hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00538 Linker_histone: linke 99.9 1.9E-24 4E-29 156.4 8.8 71 50-120 1-77 (77)
2 cd00073 H15 linker histone 1 a 99.9 7.7E-24 1.7E-28 157.2 8.9 70 49-119 2-76 (88)
3 smart00526 H15 Domain in histo 99.9 2.5E-23 5.5E-28 146.1 8.6 65 49-114 2-66 (66)
4 KOG4012 Histone H1 [Chromatin 99.8 4E-20 8.8E-25 160.9 8.5 80 43-122 36-120 (243)
5 PF10264 Stork_head: Winged he 96.1 0.032 6.8E-07 41.9 7.0 67 52-119 10-77 (80)
6 PF14338 Mrr_N: Mrr N-terminal 95.8 0.035 7.5E-07 41.0 6.1 72 53-124 1-86 (92)
7 PF00250 Fork_head: Fork head 94.8 0.048 1E-06 41.5 4.4 58 52-113 4-63 (96)
8 cd00059 FH Forkhead (FH), also 94.2 0.083 1.8E-06 39.0 4.2 34 52-86 4-37 (78)
9 smart00339 FH FORKHEAD. FORKHE 92.4 0.23 4.9E-06 37.4 4.2 33 53-86 5-37 (89)
10 PF08672 APC2: Anaphase promot 86.8 0.84 1.8E-05 32.2 3.2 26 93-118 35-60 (60)
11 PF08784 RPA_C: Replication pr 84.8 1.8 3.9E-05 32.2 4.4 54 50-112 44-98 (102)
12 PF05066 HARE-HTH: HB1, ASXL, 84.5 3.8 8.3E-05 28.7 5.7 63 53-119 2-70 (72)
13 PF14947 HTH_45: Winged helix- 80.7 1.6 3.4E-05 31.4 2.6 60 55-124 5-64 (77)
14 PF05732 RepL: Firmicute plasm 77.6 10 0.00022 31.4 6.8 71 52-122 36-119 (165)
15 PF05402 PqqD: Coenzyme PQQ sy 74.7 8.8 0.00019 26.1 4.8 47 62-110 22-68 (68)
16 cd00092 HTH_CRP helix_turn_hel 71.2 7.7 0.00017 25.7 3.8 42 70-120 25-67 (67)
17 smart00550 Zalpha Z-DNA-bindin 71.2 32 0.00069 24.1 7.1 61 50-120 3-66 (68)
18 smart00346 HTH_ICLR helix_turn 66.3 33 0.00072 24.0 6.5 45 69-122 19-65 (91)
19 cd01392 HTH_LacI Helix-turn-he 63.8 7.8 0.00017 24.8 2.6 37 64-102 2-38 (52)
20 PF02295 z-alpha: Adenosine de 63.1 25 0.00055 25.0 5.3 51 54-114 5-55 (66)
21 PRK14900 valS valyl-tRNA synth 62.1 4.5 9.7E-05 42.2 1.7 20 91-110 936-956 (1052)
22 KOG3563 Forkhead/HNF-3-related 61.0 17 0.00037 34.7 5.1 62 47-112 169-234 (454)
23 smart00347 HTH_MARR helix_turn 60.4 31 0.00067 23.9 5.4 57 54-122 11-74 (101)
24 PF13463 HTH_27: Winged helix 60.1 12 0.00026 24.9 3.0 46 57-113 7-52 (68)
25 cd07153 Fur_like Ferric uptake 59.5 58 0.0013 24.0 7.0 59 55-119 3-66 (116)
26 PF01475 FUR: Ferric uptake re 57.9 52 0.0011 24.7 6.6 60 55-120 10-74 (120)
27 PF06969 HemN_C: HemN C-termin 57.6 22 0.00048 24.0 4.1 53 62-122 12-64 (66)
28 PF08220 HTH_DeoR: DeoR-like h 57.5 31 0.00067 23.3 4.8 27 94-120 29-55 (57)
29 smart00354 HTH_LACI helix_turn 56.7 11 0.00025 26.2 2.5 39 62-102 3-41 (70)
30 PF07037 DUF1323: Putative tra 56.6 5.7 0.00012 32.1 1.1 24 63-86 4-27 (122)
31 TIGR02404 trehalos_R_Bsub treh 54.7 18 0.00039 30.2 3.9 27 93-119 38-66 (233)
32 PF02082 Rrf2: Transcriptional 53.2 43 0.00094 23.9 5.2 45 71-124 26-73 (83)
33 TIGR02325 C_P_lyase_phnF phosp 52.5 21 0.00044 29.6 3.9 47 68-120 27-75 (238)
34 PF08671 SinI: Anti-repressor 50.6 31 0.00068 21.4 3.5 25 54-83 5-29 (30)
35 PRK10079 phosphonate metabolis 49.9 23 0.00051 29.7 3.9 28 93-120 49-78 (241)
36 PF02796 HTH_7: Helix-turn-hel 49.7 4.8 0.0001 26.1 -0.3 22 62-83 24-45 (45)
37 PF00356 LacI: Bacterial regul 49.4 15 0.00033 24.4 2.1 39 62-102 2-40 (46)
38 PRK14999 histidine utilization 49.1 24 0.00052 29.7 3.8 62 52-119 12-78 (241)
39 PF01726 LexA_DNA_bind: LexA D 48.8 66 0.0014 22.7 5.4 22 94-115 41-62 (65)
40 TIGR02431 pcaR_pcaU beta-ketoa 48.3 61 0.0013 27.4 6.1 47 67-122 21-67 (248)
41 TIGR00738 rrf2_super rrf2 fami 48.1 56 0.0012 24.7 5.4 59 58-125 13-74 (132)
42 PF03551 PadR: Transcriptional 47.6 31 0.00068 24.0 3.6 53 70-123 9-70 (75)
43 COG2188 PhnF Transcriptional r 47.2 25 0.00055 29.9 3.7 28 93-120 45-74 (236)
44 smart00420 HTH_DEOR helix_turn 46.7 67 0.0015 19.7 5.1 39 68-115 12-50 (53)
45 PRK11402 DNA-binding transcrip 45.8 30 0.00064 29.1 3.9 28 93-120 47-76 (241)
46 PRK09764 DNA-binding transcrip 45.7 30 0.00065 29.1 3.9 27 93-119 43-71 (240)
47 PF01325 Fe_dep_repress: Iron 45.3 46 0.00099 23.0 4.1 48 56-112 7-55 (60)
48 COG1414 IclR Transcriptional r 44.9 61 0.0013 28.0 5.7 55 57-122 8-64 (246)
49 PF09106 SelB-wing_2: Elongati 44.5 19 0.00042 24.4 2.1 45 66-117 13-58 (59)
50 smart00419 HTH_CRP helix_turn_ 44.3 37 0.00081 20.8 3.3 26 93-118 22-47 (48)
51 PF08461 HTH_12: Ribonuclease 43.8 82 0.0018 22.1 5.3 59 56-121 1-61 (66)
52 COG1737 RpiR Transcriptional r 43.3 41 0.00089 29.4 4.5 49 54-103 31-79 (281)
53 TIGR02018 his_ut_repres histid 43.1 83 0.0018 26.1 6.1 57 57-119 9-67 (230)
54 PF13309 HTH_22: HTH domain 43.1 7.8 0.00017 27.2 -0.1 23 58-80 41-63 (64)
55 COG4742 Predicted transcriptio 42.3 21 0.00046 32.0 2.5 30 94-123 41-70 (260)
56 PF12029 DUF3516: Domain of un 41.9 90 0.0019 30.4 6.8 59 56-120 62-129 (461)
57 PF07106 TBPIP: Tat binding pr 41.8 1E+02 0.0022 24.8 6.3 41 74-114 4-54 (169)
58 PF01418 HTH_6: Helix-turn-hel 40.8 21 0.00046 25.4 1.9 45 55-100 30-74 (77)
59 PF12990 DUF3874: Domain of un 38.8 68 0.0015 23.5 4.3 53 51-103 3-58 (73)
60 PF01381 HTH_3: Helix-turn-hel 38.2 24 0.00051 22.7 1.7 23 63-85 13-35 (55)
61 PF13412 HTH_24: Winged helix- 37.9 51 0.0011 20.9 3.2 38 64-110 11-48 (48)
62 PRK09834 DNA-binding transcrip 37.8 1.3E+02 0.0029 25.7 6.7 54 58-122 16-71 (263)
63 TIGR02607 antidote_HigA addict 37.0 68 0.0015 21.9 4.0 23 63-85 22-44 (78)
64 PRK11050 manganese transport r 36.8 2E+02 0.0043 23.0 7.2 60 53-124 37-97 (152)
65 cd00591 HU_IHF Integration hos 36.4 72 0.0016 22.5 4.1 46 64-122 8-55 (87)
66 PF09012 FeoC: FeoC like trans 35.8 29 0.00064 24.0 2.0 40 74-113 3-48 (69)
67 PRK11569 transcriptional repre 35.5 1.3E+02 0.0029 26.0 6.4 47 67-122 40-88 (274)
68 PRK03902 manganese transport t 34.9 87 0.0019 24.4 4.7 58 58-124 9-68 (142)
69 PF07022 Phage_CI_repr: Bacter 34.5 69 0.0015 22.1 3.7 47 56-107 4-56 (66)
70 PF01047 MarR: MarR family; I 34.4 29 0.00062 22.7 1.6 39 65-112 12-50 (59)
71 PF06322 Phage_NinH: Phage Nin 33.9 28 0.00061 25.3 1.6 33 53-85 7-42 (64)
72 TIGR01201 HU_rel DNA-binding p 33.6 72 0.0016 25.6 4.1 27 96-122 58-86 (145)
73 PRK02363 DNA-directed RNA poly 33.3 1.9E+02 0.0041 23.3 6.5 67 55-122 3-71 (129)
74 PRK09462 fur ferric uptake reg 32.3 2.5E+02 0.0054 22.0 7.2 63 52-119 16-83 (148)
75 COG2522 Predicted transcriptio 32.0 45 0.00098 26.7 2.7 41 68-108 31-78 (119)
76 PF09382 RQC: RQC domain; Int 32.0 58 0.0013 23.8 3.1 61 54-114 5-77 (106)
77 PF07848 PaaX: PaaX-like prote 31.9 57 0.0012 23.4 3.0 45 71-121 21-69 (70)
78 PRK15431 ferrous iron transpor 31.8 1E+02 0.0022 23.1 4.4 43 71-113 2-50 (78)
79 PHA03103 double-strand RNA-bin 31.7 1.4E+02 0.0029 25.7 5.7 53 53-114 10-62 (183)
80 PF06044 DRP: Dam-replacing fa 31.6 68 0.0015 29.0 4.0 63 54-118 188-253 (254)
81 PF10557 Cullin_Nedd8: Cullin 31.6 1.8E+02 0.0039 20.2 5.6 56 57-113 8-64 (68)
82 PF13730 HTH_36: Helix-turn-he 31.5 1.4E+02 0.0031 19.1 5.8 48 53-109 5-55 (55)
83 PF08766 DEK_C: DEK C terminal 31.2 1.5E+02 0.0033 19.7 4.8 36 67-103 17-52 (54)
84 PF00392 GntR: Bacterial regul 31.1 1.7E+02 0.0036 19.7 6.2 54 55-114 6-59 (64)
85 smart00345 HTH_GNTR helix_turn 31.0 1.4E+02 0.003 18.7 5.7 22 93-114 34-55 (60)
86 COG0735 Fur Fe2+/Zn2+ uptake r 30.3 2.8E+02 0.006 22.1 7.0 54 54-113 22-75 (145)
87 TIGR02702 SufR_cyano iron-sulf 29.1 1.5E+02 0.0032 24.6 5.4 58 55-124 3-69 (203)
88 PF08279 HTH_11: HTH domain; 29.0 29 0.00062 22.5 0.9 15 93-107 29-43 (55)
89 TIGR02944 suf_reg_Xantho FeS a 28.3 1.7E+02 0.0037 22.3 5.3 60 54-123 10-72 (130)
90 PF01527 HTH_Tnp_1: Transposas 28.2 37 0.00079 23.2 1.4 22 62-83 26-47 (76)
91 PRK09249 coproporphyrinogen II 28.0 1.8E+02 0.0039 27.2 6.3 62 57-123 367-428 (453)
92 PF01402 RHH_1: Ribbon-helix-h 27.9 27 0.00059 21.3 0.6 27 58-84 10-36 (39)
93 smart00530 HTH_XRE Helix-turn- 27.8 61 0.0013 18.8 2.2 23 63-85 14-36 (56)
94 TIGR03433 padR_acidobact trans 27.7 2.1E+02 0.0046 21.1 5.6 66 55-124 5-79 (100)
95 PRK11639 zinc uptake transcrip 26.5 2.9E+02 0.0062 22.5 6.6 60 53-118 26-87 (169)
96 PF03234 CDC37_N: Cdc37 N term 26.1 2.5E+02 0.0055 23.8 6.3 40 46-85 101-141 (177)
97 TIGR01610 phage_O_Nterm phage 25.9 97 0.0021 22.9 3.4 30 93-122 61-92 (95)
98 PF12363 DUF3647: Phage protei 25.8 2.3E+02 0.0051 21.8 5.7 51 55-109 54-104 (113)
99 PF08280 HTH_Mga: M protein tr 25.6 36 0.00077 23.1 0.9 23 62-84 22-44 (59)
100 TIGR02698 CopY_TcrY copper tra 25.4 2.9E+02 0.0062 21.7 6.2 49 67-120 15-65 (130)
101 smart00411 BHL bacterial (prok 25.4 1.8E+02 0.0038 20.6 4.6 46 64-122 9-56 (90)
102 PRK10753 transcriptional regul 25.1 1.4E+02 0.0031 21.9 4.2 44 64-120 9-54 (90)
103 TIGR02844 spore_III_D sporulat 25.1 65 0.0014 23.9 2.3 39 62-101 22-60 (80)
104 smart00544 MA3 Domain in DAP-5 24.7 2.5E+02 0.0054 20.6 5.5 57 52-109 50-112 (113)
105 PRK03573 transcriptional regul 24.5 2.1E+02 0.0047 21.8 5.3 32 93-124 60-98 (144)
106 TIGR02337 HpaR homoprotocatech 24.3 1E+02 0.0022 22.9 3.3 31 94-124 57-94 (118)
107 PRK10710 DNA-binding transcrip 24.3 2.7E+02 0.0058 21.8 5.9 62 58-120 168-234 (240)
108 PF09312 SurA_N: SurA N-termin 24.1 87 0.0019 23.9 2.9 44 55-100 69-112 (118)
109 COG1654 BirA Biotin operon rep 23.7 1.2E+02 0.0025 22.6 3.4 30 53-82 3-42 (79)
110 KOG2165 Anaphase-promoting com 23.6 73 0.0016 32.8 3.0 27 93-119 738-764 (765)
111 PF12674 Zn_ribbon_2: Putative 23.4 1.3E+02 0.0028 22.3 3.6 35 51-85 41-75 (81)
112 PRK10163 DNA-binding transcrip 23.1 3.1E+02 0.0067 23.7 6.5 54 58-122 30-85 (271)
113 PF14420 Clr5: Clr5 domain 22.8 2.4E+02 0.0052 19.0 4.6 29 58-86 8-36 (54)
114 PRK11534 DNA-binding transcrip 22.8 2.9E+02 0.0062 22.7 6.0 60 54-120 12-72 (224)
115 PRK11557 putative DNA-binding 22.7 1E+02 0.0022 26.3 3.4 46 54-100 25-70 (278)
116 PF01978 TrmB: Sugar-specific 22.4 1E+02 0.0022 20.8 2.8 40 67-115 19-58 (68)
117 PRK11302 DNA-binding transcrip 22.2 1.2E+02 0.0025 25.8 3.6 45 55-100 30-74 (284)
118 PF00216 Bac_DNA_binding: Bact 21.9 1.2E+02 0.0025 21.5 3.1 28 95-122 27-56 (90)
119 COG1497 Predicted transcriptio 21.8 1.9E+02 0.0041 26.3 5.0 60 64-123 3-70 (260)
120 PRK15482 transcriptional regul 21.8 1.2E+02 0.0026 26.2 3.6 47 54-101 29-75 (285)
121 cd04761 HTH_MerR-SF Helix-Turn 21.8 42 0.00092 20.8 0.7 23 62-84 3-25 (49)
122 COG5643 Protein containing a m 21.5 92 0.002 31.7 3.2 36 51-86 510-545 (685)
123 cd04762 HTH_MerR-trunc Helix-T 21.5 43 0.00093 20.2 0.7 22 63-84 4-25 (49)
124 COG3355 Predicted transcriptio 21.5 1.1E+02 0.0023 24.8 3.1 21 93-113 56-76 (126)
125 PF12802 MarR_2: MarR family; 21.3 1.6E+02 0.0035 19.0 3.5 35 70-113 21-55 (62)
126 TIGR00538 hemN oxygen-independ 21.2 3.1E+02 0.0068 25.6 6.5 66 53-123 362-428 (455)
127 PF03882 KicB: KicB killing fa 21.1 1.5E+02 0.0033 28.7 4.5 67 55-122 28-107 (440)
128 KOG0183 20S proteasome, regula 20.9 1.1E+02 0.0024 27.5 3.3 37 69-105 162-198 (249)
129 PF14277 DUF4364: Domain of un 20.9 3.4E+02 0.0074 22.4 6.1 61 57-124 4-69 (163)
130 COG3432 Predicted transcriptio 20.8 66 0.0014 24.9 1.7 60 55-124 17-80 (95)
131 TIGR03337 phnR transcriptional 20.6 3.2E+02 0.0069 22.4 5.9 57 57-119 9-67 (231)
132 COG1849 Uncharacterized protei 20.5 1.4E+02 0.003 23.1 3.3 31 53-83 12-48 (90)
133 PF13338 DUF4095: Domain of un 20.5 1E+02 0.0023 22.4 2.7 26 97-122 4-30 (124)
134 KOG2933 Uncharacterized conser 20.5 59 0.0013 30.4 1.6 59 54-112 127-188 (334)
135 PF05225 HTH_psq: helix-turn-h 20.1 1.4E+02 0.0031 19.4 3.0 22 55-77 2-23 (45)
No 1
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=99.91 E-value=1.9e-24 Score=156.42 Aligned_cols=71 Identities=46% Similarity=0.709 Sum_probs=66.1
Q ss_pred CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCch-hHHHHHHHHHHHHHhcCceEecC-----CceecCc
Q 029524 50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPA-NFRKILAVQLKHFAAKGNLIKIR-----ASYKLSE 120 (192)
Q Consensus 50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~-nf~~lLk~aLKk~Ve~G~LVqvK-----GSFKLs~ 120 (192)
+||+|.+||.|||.+|+||+|||+++|.+||+++|+++++. +|+.+|+.+|+++|++|.|+|++ |||+|+.
T Consensus 1 shP~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G~sgsfkl~k 77 (77)
T PF00538_consen 1 SHPPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGKGASGSFKLSK 77 (77)
T ss_dssp -SSCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCSTTSSEEEESS
T ss_pred CCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeecccCCccceecCC
Confidence 69999999999999999999999999999999999865554 89999999999999999999999 8999973
No 2
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=99.90 E-value=7.7e-24 Score=157.23 Aligned_cols=70 Identities=51% Similarity=0.784 Sum_probs=66.7
Q ss_pred CCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-----CceecC
Q 029524 49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-----ASYKLS 119 (192)
Q Consensus 49 ~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-----GSFKLs 119 (192)
++||+|.+||.|||.+|+||+|||+++|.+||+++|+. +..+|+.+|+.+|+++|++|.|+|++ |+|+|+
T Consensus 2 ~~hP~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~-~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~ 76 (88)
T cd00073 2 PSHPPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKV-DDENFNKLLKLALKKGVAKGKLVQVKGTGASGSFKLS 76 (88)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCc-chHHHHHHHHHHHHHHHHCCCeEeecCCCCccceEeC
Confidence 58999999999999999999999999999999999995 34889999999999999999999999 899997
No 3
>smart00526 H15 Domain in histone families 1 and 5.
Probab=99.89 E-value=2.5e-23 Score=146.14 Aligned_cols=65 Identities=51% Similarity=0.861 Sum_probs=62.2
Q ss_pred CCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC
Q 029524 49 PSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA 114 (192)
Q Consensus 49 ~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG 114 (192)
.+||+|.+||.|||.+|+||+|||+++|.+||+++|++ ++.+|+.+|+.+|+++|++|.|+|++|
T Consensus 2 ~~hP~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~-~~~~~~~~l~~~Lk~~v~~G~l~q~kg 66 (66)
T smart00526 2 PSHPPYSEMITEAISALKERKGSSLQAIKKYIEANYKV-LPNNFRSLLKLALKKLVASGKLVQVKG 66 (66)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCC-ChHHHHHHHHHHHHHHHhcCceeecCC
Confidence 58999999999999999999999999999999999985 678999999999999999999999987
No 4
>KOG4012 consensus Histone H1 [Chromatin structure and dynamics]
Probab=99.81 E-value=4e-20 Score=160.91 Aligned_cols=80 Identities=39% Similarity=0.571 Sum_probs=71.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-----cee
Q 029524 43 PKQSKTPSHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-----SYK 117 (192)
Q Consensus 43 ~~~~k~~sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-----SFK 117 (192)
+.......||+|.+||.|||..|+||+|+|+.+|.+||.+||..++-.+|+.+|+++|++||.+|.|+|++| ||+
T Consensus 36 ~~~k~~a~~P~~~~mi~eAi~a~keR~GsS~aAikK~i~~~Y~g~~v~k~n~~lk~alK~~v~~g~l~QtkG~GAsGsFk 115 (243)
T KOG4012|consen 36 PKVKKKAAHPPYSEMITEAISALKERKGSSLAAIKKYIAANYPGDDVEKNNSRLKLALKKGVSKGVLVQTKGTGASGSFK 115 (243)
T ss_pred cccccccCCCcHHHHHHHHHHHhhhcccchHHHHHHHHhhcCccchhhhhhHHHHHHHHhhhccCceeeeccCCcccccc
Confidence 344567899999999999999999999999999999999999654457899999999999999999999984 999
Q ss_pred cCccc
Q 029524 118 LSEAA 122 (192)
Q Consensus 118 Ls~~~ 122 (192)
|....
T Consensus 116 ~~KK~ 120 (243)
T KOG4012|consen 116 LAKKA 120 (243)
T ss_pred ccccc
Confidence 87655
No 5
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=96.08 E-value=0.032 Score=41.94 Aligned_cols=67 Identities=7% Similarity=0.129 Sum_probs=56.3
Q ss_pred CCHHHHHHHHHHHcCC-CCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecC
Q 029524 52 PPYFQMITEALMALQD-KSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLS 119 (192)
Q Consensus 52 P~Y~eMI~EAI~aLke-R~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs 119 (192)
-+..|.|..+|.+|+. ...++..+|..||...|+. +..--...|..+|-.|+..|+|-.+.+-|.|.
T Consensus 10 iPL~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~-i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfiv 77 (80)
T PF10264_consen 10 IPLPEVLCWVISDLNAAGQPATQETLREHLRKHYPG-IAIPSQEVLYNTLGTLIKERKIYHTGEGYFIV 77 (80)
T ss_pred eeHHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCC-CCCCCHHHHHHHHHHHHHcCceeeCCCceEee
Confidence 3688999999999995 7779999999999999995 43223568999999999999999988666554
No 6
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=95.78 E-value=0.035 Score=41.04 Aligned_cols=72 Identities=18% Similarity=0.294 Sum_probs=60.3
Q ss_pred CHHHHHHHHHHHcCC-CCCCcHHHHHHHHHHhCCCC-------Cc-----hhHHHHHHHHHHHHHhcCceEecC-Cceec
Q 029524 53 PYFQMITEALMALQD-KSGSSPYAIAKYMEEKHKDE-------LP-----ANFRKILAVQLKHFAAKGNLIKIR-ASYKL 118 (192)
Q Consensus 53 ~Y~eMI~EAI~aLke-R~GSS~~AIkKYIe~~Y~~~-------lp-----~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKL 118 (192)
+|.+|+.-.|..|.| ....++..|..+|.++++.. ++ ..|...+.=++..|...|.|..++ |.|+|
T Consensus 1 ~~~~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~sg~~~~~~~~ri~Wa~~~L~~aGli~~~~rG~~~i 80 (92)
T PF14338_consen 1 TYDELMPPILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPSGQGYSRFKNRIRWARSYLKKAGLIERPKRGIWRI 80 (92)
T ss_pred CHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHcccCCcchhHHHhHHHHHHHHHHCCCccCCCCCceEE
Confidence 588999999999999 77799999999999988632 11 147888999999999999999965 89999
Q ss_pred Cccccc
Q 029524 119 SEAAAG 124 (192)
Q Consensus 119 s~~~Kk 124 (192)
.+.+.+
T Consensus 81 T~~G~~ 86 (92)
T PF14338_consen 81 TEKGRK 86 (92)
T ss_pred CHhHHH
Confidence 988764
No 7
>PF00250 Fork_head: Fork head domain; InterPro: IPR001766 The fork head protein of Drosophila melanogaster, a transcription factor that promotes terminal rather than segmental development, contains neither homeodomains nor zinc-fingers characteristic of other transcription factors []. Instead, it contains a distinct type of DNA-binding region, containing around 100 amino acids, which has since been identified in a number of transcription factors (including D. melanogaster FD1-5, mammalian HNF-3, human HTLF, Saccharomyces cerevisiae HCM1, etc.). This is referred to as the fork head domain but is also known as a 'winged helix' [, , ]. The fork head domain binds B-DNA as a monomer [], but shows no similarity to previously identified DNA-binding motifs. Although the domain is found in several different transcription factors, a common function is their involvement in early developmental decisions of cell fates during embryogenesis [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2UZK_A 2K86_A 1JXS_A 2C6Y_A 2A3S_A 2D2W_A 2KIU_A 1VTN_C 2A07_J 2AS5_F ....
Probab=94.83 E-value=0.048 Score=41.47 Aligned_cols=58 Identities=14% Similarity=0.261 Sum_probs=42.5
Q ss_pred CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEecC
Q 029524 52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqvK 113 (192)
-+|..||..||.. ...++.+..-|..||+.+|+. ..+..+..-|++.|. .+.-|+++.
T Consensus 4 ~sY~~LI~~Ai~~-sp~~~Ltl~eIy~~i~~~~pyyr~~~~~WknSIRHnLS---~~~~F~kv~ 63 (96)
T PF00250_consen 4 YSYATLIAMAILS-SPDKRLTLSEIYEWIEENFPYYRDASKGWKNSIRHNLS---LNKCFVKVP 63 (96)
T ss_dssp S-HHHHHHHHHHT-STTSEBEHHHHHHHHHHHCGHHHCTHCHHHHHHHHHHH---HSTTEEEES
T ss_pred CcHHHHHHHHHHh-CCCCCccHHHHHHHHHHhhccccccchhhhhHHhhhcc---ccceeeecC
Confidence 4699999999998 445569999999999999973 123456666777663 346777764
No 8
>cd00059 FH Forkhead (FH), also known as a "winged helix". FH is named for the Drosophila fork head protein, a transcription factor which promotes terminal rather than segmental development. This family of transcription factor domains, which bind to B-DNA as monomers, are also found in the Hepatocyte nuclear factor (HNF) proteins, which provide tissue-specific gene regulation. The structure contains 2 flexible loops or "wings" in the C-terminal region, hence the term winged helix.
Probab=94.18 E-value=0.083 Score=38.97 Aligned_cols=34 Identities=15% Similarity=0.176 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC
Q 029524 52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD 86 (192)
Q Consensus 52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~ 86 (192)
-+|..||..||.+.. ..+.+..-|-.||+++|+.
T Consensus 4 ~sY~~LI~~Ai~~sp-~~~lTL~eIy~~I~~~~py 37 (78)
T cd00059 4 YSYSALIAMAIQSSP-EKRLTLSEIYKWISDNFPY 37 (78)
T ss_pred CCHHHHHHHHHHhCC-CCCeeHHHHHHHHHHhCCc
Confidence 479999999999965 5569999999999999974
No 9
>smart00339 FH FORKHEAD. FORKHEAD, also known as a "winged helix"
Probab=92.40 E-value=0.23 Score=37.35 Aligned_cols=33 Identities=18% Similarity=0.312 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC
Q 029524 53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD 86 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~ 86 (192)
+|..||..||.+. ...+.+..-|-.||+++|+.
T Consensus 5 sY~~lI~~ai~~s-p~~~ltl~~Iy~~I~~~~py 37 (89)
T smart00339 5 SYIALIAMAILSS-PDKRLTLSEIYKWIEDNFPY 37 (89)
T ss_pred CHHHHHHHHHHhC-CCCCeeHHHHHHHHHHhCch
Confidence 5999999999995 45579999999999999974
No 10
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=86.82 E-value=0.84 Score=32.18 Aligned_cols=26 Identities=31% Similarity=0.319 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHhcCceEecCCceec
Q 029524 93 RKILAVQLKHFAAKGNLIKIRASYKL 118 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKGSFKL 118 (192)
...|...|.++|+.|+|+.+.|+|||
T Consensus 35 ~~eL~~fL~~lv~e~~L~~~~G~YkL 60 (60)
T PF08672_consen 35 LEELQEFLDRLVEEGKLECSGGSYKL 60 (60)
T ss_dssp HHHHHHHHHHHHHTTSEE--TTEEEE
T ss_pred HHHHHHHHHHHHHCCcEEecCCEEeC
Confidence 56799999999999999999999997
No 11
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=84.84 E-value=1.8 Score=32.16 Aligned_cols=54 Identities=11% Similarity=0.177 Sum_probs=40.8
Q ss_pred CCCCHHHHHHHHHHH-cCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec
Q 029524 50 SHPPYFQMITEALMA-LQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI 112 (192)
Q Consensus 50 sHP~Y~eMI~EAI~a-LkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv 112 (192)
..-+..++|++.|.. .....|+++..|...+ .+. ..-|+.+|..|+..|.|--+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~-------~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMS-------ENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS--------HHHHHHHHHHHHHTTSEEES
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcC-------HHHHHHHHHHHHhCCeEecc
Confidence 356678999999999 7778999999999888 443 33699999999999998643
No 12
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=84.46 E-value=3.8 Score=28.68 Aligned_cols=63 Identities=13% Similarity=0.119 Sum_probs=37.2
Q ss_pred CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCC-chh----HHHHHHHHHHHHHhcCceEec-CCceecC
Q 029524 53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDEL-PAN----FRKILAVQLKHFAAKGNLIKI-RASYKLS 119 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~l-p~n----f~~lLk~aLKk~Ve~G~LVqv-KGSFKLs 119 (192)
+|.+++.+.|.+.+ ...+..-|...|.+...... ... ....|...++ -.+|.|+++ .|.|-|.
T Consensus 2 t~~eaa~~vL~~~~--~pm~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~--~~d~~F~~vg~~~~~L~ 70 (72)
T PF05066_consen 2 TFKEAAYEVLEEAG--RPMTFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK--NEDSRFVKVGPGRWGLR 70 (72)
T ss_dssp -HHHHHHHHHHHH---S-EEHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH---T-SS-EESSSSEEE-G
T ss_pred CHHHHHHHHHHhcC--CCcCHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc--cCCCCEEEeCCCcEEee
Confidence 45666666666665 67999999999998875421 122 2334445555 488999999 5888764
No 13
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=80.67 E-value=1.6 Score=31.38 Aligned_cols=60 Identities=28% Similarity=0.377 Sum_probs=40.2
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCccccc
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAAG 124 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~Kk 124 (192)
.++|.+=+..|. .+|.+..-|. |..+|+ -..+...|..|++.|-|....+.|.|.+.+.+
T Consensus 5 ~~Ii~~IL~~l~-~~~~~~t~i~------~~~~L~---~~~~~~yL~~L~~~gLI~~~~~~Y~lTekG~~ 64 (77)
T PF14947_consen 5 LEIIFDILKILS-KGGAKKTEIM------YKANLN---YSTLKKYLKELEEKGLIKKKDGKYRLTEKGKE 64 (77)
T ss_dssp THHHHHHHHHH--TT-B-HHHHH------TTST-----HHHHHHHHHHHHHTTSEEEETTEEEE-HHHHH
T ss_pred HHHHHHHHHHHH-cCCCCHHHHH------HHhCcC---HHHHHHHHHHHHHCcCeeCCCCEEEECccHHH
Confidence 466777777776 6667766555 222232 34688999999999999888899999988764
No 14
>PF05732 RepL: Firmicute plasmid replication protein (RepL); InterPro: IPR008813 This entry consists of proteins thought to be involved in plasmid replication. ; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=77.58 E-value=10 Score=31.38 Aligned_cols=71 Identities=17% Similarity=0.419 Sum_probs=50.1
Q ss_pred CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCC---------CchhH---HHHHHHHHHHHHhcCceEecC-Cceec
Q 029524 52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDE---------LPANF---RKILAVQLKHFAAKGNLIKIR-ASYKL 118 (192)
Q Consensus 52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~---------lp~nf---~~lLk~aLKk~Ve~G~LVqvK-GSFKL 118 (192)
+.|..|-.+-|..+-|-.|.....|..||.++...+ +...+ ..-|.+.|+.|.+.|.|.+++ |.|.|
T Consensus 36 ~~Fvkl~~~ni~~~l~l~g~k~~~Vl~~il~~~d~~N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~i 115 (165)
T PF05732_consen 36 PNFVKLYLENIIKVLDLIGNKAFRVLMYILENMDKDNAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMI 115 (165)
T ss_pred CChhhhHHHHHHHHhhhhchhHHHHHHHHHHhcCCCCeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEE
Confidence 345444444444444445777899999999987531 11111 455899999999999999988 89999
Q ss_pred Cccc
Q 029524 119 SEAA 122 (192)
Q Consensus 119 s~~~ 122 (192)
++..
T Consensus 116 NP~~ 119 (165)
T PF05732_consen 116 NPNF 119 (165)
T ss_pred CcHH
Confidence 9985
No 15
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=74.65 E-value=8.8 Score=26.06 Aligned_cols=47 Identities=17% Similarity=0.157 Sum_probs=32.1
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceE
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLI 110 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LV 110 (192)
|-.+.+ ++.|...|..+|.+.|.+ .+.....-+..-|..|.+.|.|+
T Consensus 22 Iw~~~~-g~~t~~ei~~~l~~~y~~-~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 22 IWELLD-GPRTVEEIVDALAEEYDV-DPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHH---SSS-HHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHTT---
T ss_pred HHHHcc-CCCCHHHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHCcCcC
Confidence 333443 469999999999999974 45557888999999999998764
No 16
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=71.21 E-value=7.7 Score=25.66 Aligned_cols=42 Identities=19% Similarity=0.346 Sum_probs=30.4
Q ss_pred CCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-CceecCc
Q 029524 70 GSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-ASYKLSE 120 (192)
Q Consensus 70 GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKLs~ 120 (192)
..|...|..++.- . ...+.+.|..+.+.|.|.... |.|.|.+
T Consensus 25 ~~s~~ela~~~g~------s---~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 25 PLTRQEIADYLGL------T---RETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CcCHHHHHHHHCC------C---HHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 3566555555432 1 456899999999999999887 8888753
No 17
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=71.16 E-value=32 Score=24.09 Aligned_cols=61 Identities=26% Similarity=0.330 Sum_probs=43.2
Q ss_pred CCCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---CceecCc
Q 029524 50 SHPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---ASYKLSE 120 (192)
Q Consensus 50 sHP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---GSFKLs~ 120 (192)
++..+.+-|++.|....+. |.+...|.+.+ + ++ ..-++++|.+|.+.|.|++.. +.|.|..
T Consensus 3 ~~~~~~~~IL~~L~~~g~~-~~ta~eLa~~l----g--l~---~~~v~r~L~~L~~~G~V~~~~~~~~~W~i~~ 66 (68)
T smart00550 3 TQDSLEEKILEFLENSGDE-TSTALQLAKNL----G--LP---KKEVNRVLYSLEKKGKVCKQGGTPPLWKLTD 66 (68)
T ss_pred CchHHHHHHHHHHHHCCCC-CcCHHHHHHHH----C--CC---HHHHHHHHHHHHHCCCEEecCCCCCceEeec
Confidence 3455677788877765433 58877777655 3 33 346999999999999999853 5777764
No 18
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=66.32 E-value=33 Score=24.03 Aligned_cols=45 Identities=16% Similarity=0.225 Sum_probs=35.0
Q ss_pred CCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec--CCceecCccc
Q 029524 69 SGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI--RASYKLSEAA 122 (192)
Q Consensus 69 ~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv--KGSFKLs~~~ 122 (192)
.+.|...|...+ + ++ ...+.+.|..+++.|.|++. .|.|.|....
T Consensus 19 ~~~t~~~ia~~l----~--i~---~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~ 65 (91)
T smart00346 19 GGLTLAELAERL----G--LS---KSTAHRLLNTLQELGYVEQDGQNGRYRLGPKV 65 (91)
T ss_pred CCcCHHHHHHHh----C--CC---HHHHHHHHHHHHHCCCeeecCCCCceeecHHH
Confidence 579999998888 2 33 45688999999999999986 4678887643
No 19
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=63.79 E-value=7.8 Score=24.77 Aligned_cols=37 Identities=11% Similarity=0.235 Sum_probs=25.3
Q ss_pred HcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHH
Q 029524 64 ALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKH 102 (192)
Q Consensus 64 aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk 102 (192)
+|.++-|.|+.+|..|+..++. +.......|...+..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~~--vs~~~~~~i~~~~~~ 38 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKPR--VSEETRERVLAAAEE 38 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCCC--CCHHHHHHHHHHHHH
Confidence 3556789999999999988764 344555555554444
No 20
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=63.14 E-value=25 Score=24.96 Aligned_cols=51 Identities=25% Similarity=0.232 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA 114 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG 114 (192)
..+.|++.|..+. |++..+|.+.+.=+-+ ++-|++.|-+|-..|.|.+..|
T Consensus 5 ~ee~Il~~L~~~g---~~~a~~ia~~~~L~~~-------kk~VN~~LY~L~k~g~v~k~~~ 55 (66)
T PF02295_consen 5 LEEKILDFLKELG---GSTATAIAKALGLSVP-------KKEVNRVLYRLEKQGKVCKEGG 55 (66)
T ss_dssp HHHHHHHHHHHHT---SSEEEHHHHHHHHTS--------HHHHHHHHHHHHHTTSEEEECS
T ss_pred HHHHHHHHHHhcC---CccHHHHHHHhCcchh-------HHHHHHHHHHHHHCCCEeeCCC
Confidence 4677888888877 5666666665544322 5679999999999999998766
No 21
>PRK14900 valS valyl-tRNA synthetase; Provisional
Probab=62.11 E-value=4.5 Score=42.23 Aligned_cols=20 Identities=5% Similarity=-0.037 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHHHHhc-CceE
Q 029524 91 NFRKILAVQLKHFAAK-GNLI 110 (192)
Q Consensus 91 nf~~lLk~aLKk~Ve~-G~LV 110 (192)
.+..-|-.+|+++++. |.+-
T Consensus 936 ~~~~~~~~~~~~~~~~~~~~~ 956 (1052)
T PRK14900 936 AQENTVVESAEKAVAAVSEAA 956 (1052)
T ss_pred hhhhhHHHHHHHHHHhcccch
Confidence 4556677777777766 4443
No 22
>KOG3563 consensus Forkhead/HNF-3-related transcription factor [Transcription]
Probab=60.97 E-value=17 Score=34.75 Aligned_cols=62 Identities=18% Similarity=0.292 Sum_probs=43.2
Q ss_pred CCCCCCC--HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC--CCchhHHHHHHHHHHHHHhcCceEec
Q 029524 47 KTPSHPP--YFQMITEALMALQDKSGSSPYAIAKYMEEKHKD--ELPANFRKILAVQLKHFAAKGNLIKI 112 (192)
Q Consensus 47 k~~sHP~--Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~--~lp~nf~~lLk~aLKk~Ve~G~LVqv 112 (192)
-+-..|+ |..+|.-||..-..|- .++.-|-.||.+=|+. ..+.+|..-|++.| -=+.-||+|
T Consensus 169 Y~haKPPYSYISLITMAIQ~~pskm-LTLSEIYqwIMDLFPyYrqNQQRWQNSIRHSL---SFNDCFVKV 234 (454)
T KOG3563|consen 169 YTHAKPPYSYISLITMAIQQAPSKM-LTLSEIYQWIMDLFPYYRQNQQRWQNSIRHSL---SFNDCFVKV 234 (454)
T ss_pred ccCCCCChhHHHHHHHHHHhCCccc-eeHHHHHHHHHHhhhHhhhhHHHHHhhhhhhc---cccceeeec
Confidence 3334454 6789999999876665 7899999999999874 23445555566554 346667776
No 23
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=60.39 E-value=31 Score=23.89 Aligned_cols=57 Identities=16% Similarity=0.142 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-------ceecCccc
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-------SYKLSEAA 122 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-------SFKLs~~~ 122 (192)
...+|+..|... .+.+...|..++.= . ...|...|++|++.|.|....+ .|.|.+.+
T Consensus 11 ~~~~il~~l~~~---~~~~~~~la~~~~~------s---~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g 74 (101)
T smart00347 11 TQFLVLRILYEE---GPLSVSELAKRLGV------S---PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEG 74 (101)
T ss_pred HHHHHHHHHHHc---CCcCHHHHHHHHCC------C---chhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhH
Confidence 445566666653 36888888777622 1 3358899999999999997653 45555544
No 24
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=60.07 E-value=12 Score=24.95 Aligned_cols=46 Identities=17% Similarity=0.223 Sum_probs=28.3
Q ss_pred HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC
Q 029524 57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK 113 (192)
.|+..|. .+..+.+...|..++.-. ...+...|++|++.|.|.+..
T Consensus 7 ~vL~~l~--~~~~~~t~~~l~~~~~~~---------~~~vs~~i~~L~~~glv~~~~ 52 (68)
T PF13463_consen 7 QVLRALA--HSDGPMTQSDLAERLGIS---------KSTVSRIIKKLEEKGLVEKER 52 (68)
T ss_dssp HHHHHHT----TS-BEHHHHHHHTT-----------HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHH--ccCCCcCHHHHHHHHCcC---------HHHHHHHHHHHHHCCCEEecC
Confidence 4444444 355567766666554321 345889999999999998754
No 25
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=59.48 E-value=58 Score=24.05 Aligned_cols=59 Identities=17% Similarity=0.198 Sum_probs=44.8
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---C--ceecC
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---A--SYKLS 119 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---G--SFKLs 119 (192)
..+|++.|... ..-.|...|...+.+.++. +. ..-+-+.|+.|++.|.|.++. | .|.+.
T Consensus 3 R~~Il~~l~~~--~~~~sa~ei~~~l~~~~~~-i~---~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~~~ 66 (116)
T cd07153 3 RLAILEVLLES--DGHLTAEEIYERLRKKGPS-IS---LATVYRTLELLEEAGLVREIELGDGKARYELN 66 (116)
T ss_pred HHHHHHHHHhC--CCCCCHHHHHHHHHhcCCC-CC---HHHHHHHHHHHHhCCCEEEEEeCCCceEEEeC
Confidence 46788888775 3558999999999988752 22 456889999999999999864 2 46654
No 26
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=57.86 E-value=52 Score=24.70 Aligned_cols=60 Identities=20% Similarity=0.182 Sum_probs=46.0
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---C--ceecCc
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---A--SYKLSE 120 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---G--SFKLs~ 120 (192)
..+|++.|....+ -.|...|...|...++. +. ..-+-+.|..|++.|.|.++. | .|.+..
T Consensus 10 R~~Il~~l~~~~~--~~ta~ei~~~l~~~~~~-is---~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 10 RLAILELLKESPE--HLTAEEIYDKLRKKGPR-IS---LATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHSS--SEEHHHHHHHHHHTTTT------HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred HHHHHHHHHcCCC--CCCHHHHHHHhhhccCC-cC---HHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 4678888888777 69999999999987653 22 456889999999999999865 2 555543
No 27
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=57.58 E-value=22 Score=23.95 Aligned_cols=53 Identities=15% Similarity=0.240 Sum_probs=35.1
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCccc
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAA 122 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~ 122 (192)
|..|-=..|.+...+. ..|+. +|...+...|..+++.|-|+...|+++|.+.+
T Consensus 12 ~~~LR~~~Gi~~~~~~----~~~g~----~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G 64 (66)
T PF06969_consen 12 MLGLRCNEGIDLSEFE----QRFGI----DFAEEFQKELEELQEDGLLEIDGGRLRLTEKG 64 (66)
T ss_dssp HHHHHHHSEEEHHHHH----HHTT------THHH-HHHHHHHHHTTSEEE-SSEEEE-TTT
T ss_pred HHHHHhHCCcCHHHHH----HHHCc----CHHHHHHHHHHHHHHCCCEEEeCCEEEECccc
Confidence 3444446677776554 44542 35556788899999999999999999998754
No 28
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=57.52 E-value=31 Score=23.32 Aligned_cols=27 Identities=11% Similarity=0.239 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhcCceEecCCceecCc
Q 029524 94 KILAVQLKHFAAKGNLIKIRASYKLSE 120 (192)
Q Consensus 94 ~lLk~aLKk~Ve~G~LVqvKGSFKLs~ 120 (192)
.-+++-|..|.+.|.|.++-|.+.+..
T Consensus 29 ~TiRRDl~~L~~~g~i~r~~GG~~~~~ 55 (57)
T PF08220_consen 29 MTIRRDLNKLEKQGLIKRTHGGAVLND 55 (57)
T ss_pred HHHHHHHHHHHHCCCEEEEcCEEEeCC
Confidence 458889999999999999999877754
No 29
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=56.68 E-value=11 Score=26.24 Aligned_cols=39 Identities=8% Similarity=0.236 Sum_probs=25.9
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHH
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKH 102 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk 102 (192)
|.+|.++.|.|+.+|..++..+.. +.+.....|...++.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~~--v~~~t~~~i~~~~~~ 41 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNGR--VSEETREKVLAAMEE 41 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCCC--CCHHHHHHHHHHHHH
Confidence 445666779999999999977655 344445455544443
No 30
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=56.57 E-value=5.7 Score=32.14 Aligned_cols=24 Identities=17% Similarity=0.270 Sum_probs=20.7
Q ss_pred HHcCCCCCCcHHHHHHHHHHhCCC
Q 029524 63 MALQDKSGSSPYAIAKYMEEKHKD 86 (192)
Q Consensus 63 ~aLkeR~GSS~~AIkKYIe~~Y~~ 86 (192)
.+|.+-.|.|+|+|.+||.+..+.
T Consensus 4 eELA~~tG~srQTINrWvRkegW~ 27 (122)
T PF07037_consen 4 EELAELTGYSRQTINRWVRKEGWK 27 (122)
T ss_pred HHHHHHhCccHHHHHHHHHhcCce
Confidence 467788999999999999998763
No 31
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=54.75 E-value=18 Score=30.16 Aligned_cols=27 Identities=26% Similarity=0.368 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHhcCceEecCC--ceecC
Q 029524 93 RKILAVQLKHFAAKGNLIKIRA--SYKLS 119 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKG--SFKLs 119 (192)
+.-|+++|..|+..|.|++..| +|-..
T Consensus 38 R~TVR~Al~~L~~eGli~r~~G~GTfV~~ 66 (233)
T TIGR02404 38 RETVRKALNLLTEAGYIQKIQGKGSIVLN 66 (233)
T ss_pred HHHHHHHHHHHHHCCCEEEeCCceEEEec
Confidence 5679999999999999999874 88643
No 32
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=53.18 E-value=43 Score=23.86 Aligned_cols=45 Identities=20% Similarity=0.289 Sum_probs=32.3
Q ss_pred CcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---CceecCccccc
Q 029524 71 SSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---ASYKLSEAAAG 124 (192)
Q Consensus 71 SS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---GSFKLs~~~Kk 124 (192)
.|...|...+ + ++ ..+|..-|..|+..|.|...+ |-|.|+.+..+
T Consensus 26 ~s~~eiA~~~----~--i~---~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~~ 73 (83)
T PF02082_consen 26 VSSKEIAERL----G--IS---PSYLRKILQKLKKAGLIESSRGRGGGYRLARPPEE 73 (83)
T ss_dssp BEHHHHHHHH----T--S----HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CCG
T ss_pred CCHHHHHHHH----C--cC---HHHHHHHHHHHhhCCeeEecCCCCCceeecCCHHH
Confidence 7777776643 3 33 346899999999999998876 48999876544
No 33
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=52.51 E-value=21 Score=29.61 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=31.5
Q ss_pred CCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC--ceecCc
Q 029524 68 KSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA--SYKLSE 120 (192)
Q Consensus 68 R~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG--SFKLs~ 120 (192)
.-|.-..+-.. |.+.|++. +.-|+++|..|+..|.|++..| +|-...
T Consensus 27 ~~G~~LPsE~e-La~~~~VS-----R~TvR~Al~~L~~eGli~r~~G~GtfV~~~ 75 (238)
T TIGR02325 27 RAGDYLPAEMQ-LAERFGVN-----RHTVRRAIAALVERGLLRAEQGRGTFVAAR 75 (238)
T ss_pred CCCCcCcCHHH-HHHHHCCC-----HHHHHHHHHHHHHCCCEEEecCCEEEECCC
Confidence 44554444332 34455532 5679999999999999999875 777543
No 34
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=50.58 E-value=31 Score=21.43 Aligned_cols=25 Identities=28% Similarity=0.430 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHh
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEK 83 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~ 83 (192)
+.++|.||+.. |.|..-|+.|+..+
T Consensus 5 W~~Li~eA~~~-----Gls~eeir~FL~~~ 29 (30)
T PF08671_consen 5 WVELIKEAKES-----GLSKEEIREFLEFN 29 (30)
T ss_dssp HHHHHHHHHHT-----T--HHHHHHHHHHH
T ss_pred HHHHHHHHHHc-----CCCHHHHHHHHHhC
Confidence 56788999874 99999999999754
No 35
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=49.87 E-value=23 Score=29.75 Aligned_cols=28 Identities=18% Similarity=0.254 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhcCceEecCC--ceecCc
Q 029524 93 RKILAVQLKHFAAKGNLIKIRA--SYKLSE 120 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKG--SFKLs~ 120 (192)
+.-++++|..|+..|.|++..| +|-...
T Consensus 49 R~TVR~Al~~L~~eGli~r~~G~GtfV~~~ 78 (241)
T PRK10079 49 RHTLRRAIDQLVEKGWVQRRQGVGVLVLMR 78 (241)
T ss_pred HHHHHHHHHHHHHCCCEEEecCCEEEEecC
Confidence 5679999999999999999874 786543
No 36
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=49.72 E-value=4.8 Score=26.06 Aligned_cols=22 Identities=14% Similarity=0.404 Sum_probs=15.7
Q ss_pred HHHcCCCCCCcHHHHHHHHHHh
Q 029524 62 LMALQDKSGSSPYAIAKYMEEK 83 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~ 83 (192)
|.++.+..|+|+.+|.+|+.+|
T Consensus 24 i~~IA~~~gvsr~TvyR~l~~~ 45 (45)
T PF02796_consen 24 IAEIAKQFGVSRSTVYRYLNKN 45 (45)
T ss_dssp HHHHHHHTTS-HHHHHHHHCC-
T ss_pred HHHHHHHHCcCHHHHHHHHhcC
Confidence 4566678899999999988653
No 37
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=49.42 E-value=15 Score=24.40 Aligned_cols=39 Identities=8% Similarity=0.221 Sum_probs=28.8
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHH
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKH 102 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk 102 (192)
|.++-+..|+|..++.++|-.... +.+..+..|...+..
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~~~--vs~~tr~rI~~~a~~ 40 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGPPR--VSEETRERILEAAEE 40 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTCSS--STHHHHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhCCCC--CCHHHHHHHHHHHHH
Confidence 456667789999999999988754 556666666666554
No 38
>PRK14999 histidine utilization repressor; Provisional
Probab=49.08 E-value=24 Score=29.69 Aligned_cols=62 Identities=11% Similarity=0.139 Sum_probs=36.8
Q ss_pred CCHHHH---HHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--CceecC
Q 029524 52 PPYFQM---ITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKLS 119 (192)
Q Consensus 52 P~Y~eM---I~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKLs 119 (192)
|.|.++ |.+.|.+-.=.-|.-..+- .-|.+.|++. +.-|+++|..|+..|.|++.. |+|-..
T Consensus 12 ply~qi~~~i~~~I~~g~~~~G~~LPsE-~eLa~~~gVS-----R~TVR~Al~~L~~eGli~r~~GkGTfV~~ 78 (241)
T PRK14999 12 PFYETVKQDICKKIAGGVWQPHDRIPSE-AELVAQYGFS-----RMTINRALRELTDEGWLVRLQGVGTFVAE 78 (241)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCH-HHHHHHHCCC-----HHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence 555542 4444443221344433222 2344556532 667999999999999999876 588644
No 39
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=48.81 E-value=66 Score=22.66 Aligned_cols=22 Identities=18% Similarity=0.237 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHhcCceEecCCc
Q 029524 94 KILAVQLKHFAAKGNLIKIRAS 115 (192)
Q Consensus 94 ~lLk~aLKk~Ve~G~LVqvKGS 115 (192)
..+..+|+.|.+.|.|.+..|.
T Consensus 41 ~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 41 STVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp HHHHHHHHHHHHTTSEEEGCCS
T ss_pred HHHHHHHHHHHHCcCccCCCCC
Confidence 4588999999999999988764
No 40
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=48.26 E-value=61 Score=27.43 Aligned_cols=47 Identities=13% Similarity=0.078 Sum_probs=36.1
Q ss_pred CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCccc
Q 029524 67 DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAA 122 (192)
Q Consensus 67 eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~ 122 (192)
++.|.|..-|..-+. ++ +.-+.+.|..|++.|-|.+..|+|.|+...
T Consensus 21 ~~~~~~l~eia~~lg------lp---ksT~~RlL~tL~~~G~l~~~~~~Y~lG~~~ 67 (248)
T TIGR02431 21 ERPRLTLTDVAEATG------LT---RAAARRFLLTLVELGYVTSDGRLFWLTPRV 67 (248)
T ss_pred CCCCCCHHHHHHHHC------cC---HHHHHHHHHHHHHCCCEEeCCCEEEecHHH
Confidence 366788887776552 44 445778889999999999988899998764
No 41
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=48.14 E-value=56 Score=24.69 Aligned_cols=59 Identities=20% Similarity=0.224 Sum_probs=39.0
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---CceecCcccccc
Q 029524 58 ITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---ASYKLSEAAAGK 125 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---GSFKLs~~~Kk~ 125 (192)
|..-|....++...|...|...+. ++ ...|...|..|+..|.|+... |.|.|......-
T Consensus 13 ~l~~la~~~~~~~~s~~eia~~~~------i~---~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~i 74 (132)
T TIGR00738 13 ALLDLALNPDEGPVSVKEIAERQG------IS---RSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEEI 74 (132)
T ss_pred HHHHHHhCCCCCcCcHHHHHHHHC------cC---HHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHHC
Confidence 333343333455678777766543 33 346899999999999998764 478887766543
No 42
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=47.61 E-value=31 Score=23.99 Aligned_cols=53 Identities=19% Similarity=0.222 Sum_probs=37.9
Q ss_pred CCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-----C----ceecCcccc
Q 029524 70 GSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-----A----SYKLSEAAA 123 (192)
Q Consensus 70 GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-----G----SFKLs~~~K 123 (192)
-.+-..|.+.|.+.+......+ ...|-..|++|.+.|.|...- | -|.|.+.+.
T Consensus 9 ~~~Gyei~~~l~~~~~~~~~i~-~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~ 70 (75)
T PF03551_consen 9 PMHGYEIKQELEERTGGFWKIS-PGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGR 70 (75)
T ss_dssp -EEHHHHHHHHHHCSTTTEETT-HHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHH
T ss_pred CCcHHHHHHHHHHHhCCCcccC-hhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHH
Confidence 3577899999999875312222 557999999999999998643 1 577776654
No 43
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=47.22 E-value=25 Score=29.88 Aligned_cols=28 Identities=14% Similarity=0.328 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhcCceEecC--CceecCc
Q 029524 93 RKILAVQLKHFAAKGNLIKIR--ASYKLSE 120 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~ 120 (192)
+--|+++|.-|++.|.|++.. |+|-...
T Consensus 45 R~TvRkAL~~L~~eGli~r~~G~GtfV~~~ 74 (236)
T COG2188 45 RMTVRKALDELVEEGLIVRRQGKGTFVASP 74 (236)
T ss_pred HHHHHHHHHHHHHCCcEEEEecCeeEEcCc
Confidence 456999999999999999987 4888776
No 44
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=46.73 E-value=67 Score=19.68 Aligned_cols=39 Identities=13% Similarity=0.262 Sum_probs=28.5
Q ss_pred CCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCc
Q 029524 68 KSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRAS 115 (192)
Q Consensus 68 R~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGS 115 (192)
..+.|...|..++ + ++ ..-+...|+.+...|.|....|-
T Consensus 12 ~~~~s~~~l~~~l----~--~s---~~tv~~~l~~L~~~g~i~~~~~~ 50 (53)
T smart00420 12 QGKVSVEELAELL----G--VS---EMTIRRDLNKLEEQGLLTRVHGG 50 (53)
T ss_pred cCCcCHHHHHHHH----C--CC---HHHHHHHHHHHHHCCCEEEeecC
Confidence 4568888887776 2 22 44578889999999999886653
No 45
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=45.77 E-value=30 Score=29.05 Aligned_cols=28 Identities=21% Similarity=0.395 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhcCceEecC--CceecCc
Q 029524 93 RKILAVQLKHFAAKGNLIKIR--ASYKLSE 120 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~ 120 (192)
+.-|+++|..|++.|.|++.. |+|-...
T Consensus 47 R~TvR~Al~~L~~eGli~r~~G~GTfV~~~ 76 (241)
T PRK11402 47 RITIRKAISDLVADGVLIRWQGKGTFVQSQ 76 (241)
T ss_pred HHHHHHHHHHHHHCCCEEEecCceeEECCC
Confidence 566999999999999999987 4776543
No 46
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=45.74 E-value=30 Score=29.14 Aligned_cols=27 Identities=19% Similarity=0.282 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhcCceEecCC--ceecC
Q 029524 93 RKILAVQLKHFAAKGNLIKIRA--SYKLS 119 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKG--SFKLs 119 (192)
+.-|+++|..|+..|.|++..| +|-..
T Consensus 43 R~TvR~Al~~L~~eGli~r~~G~GtfV~~ 71 (240)
T PRK09764 43 RVTVRQALRQLVEQQILESIQGSGTYVKE 71 (240)
T ss_pred HHHHHHHHHHHHHCCCEEEecCceeEEcc
Confidence 5679999999999999998874 77644
No 47
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=45.30 E-value=46 Score=22.96 Aligned_cols=48 Identities=19% Similarity=0.146 Sum_probs=34.0
Q ss_pred HHHHHHHHHcC-CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec
Q 029524 56 QMITEALMALQ-DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI 112 (192)
Q Consensus 56 eMI~EAI~aLk-eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv 112 (192)
++-+++|-.|. ++..++...|+.++.=. ..-+...|++|.+.|.|+..
T Consensus 7 e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs---------~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 7 EDYLKAIYELSEEGGPVRTKDIAERLGVS---------PPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHHHHHHHCTSSBBHHHHHHHHTS----------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHHcCCCCccHHHHHHHHCCC---------hHHHHHHHHHHHHCCCEEec
Confidence 44455555554 56778999998887432 33588899999999998864
No 48
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=44.93 E-value=61 Score=27.96 Aligned_cols=55 Identities=20% Similarity=0.280 Sum_probs=40.4
Q ss_pred HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--CceecCccc
Q 029524 57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
+|+++|.. ...|.+...|.+-+ ++| +.-+.+.|..|++.|-|.|.. |+|.|....
T Consensus 8 ~iL~~l~~--~~~~l~l~ela~~~------glp---ksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~~~ 64 (246)
T COG1414 8 AILDLLAE--GPGGLSLAELAERL------GLP---KSTVHRLLQTLVELGYVEQDPEDGRYRLGPRL 64 (246)
T ss_pred HHHHHHHh--CCCCCCHHHHHHHh------CcC---HHHHHHHHHHHHHCCCEEEcCCCCcEeehHHH
Confidence 46667766 55667888877643 244 445778899999999999987 689998653
No 49
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=44.49 E-value=19 Score=24.38 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=29.9
Q ss_pred CCCCCCcHHHHHHHHHH-hCCCCCchhHHHHHHHHHHHHHhcCceEecCCcee
Q 029524 66 QDKSGSSPYAIAKYMEE-KHKDELPANFRKILAVQLKHFAAKGNLIKIRASYK 117 (192)
Q Consensus 66 keR~GSS~~AIkKYIe~-~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFK 117 (192)
-.+.|.++..+..-+.. ++ +. ..+..-|..++++|.|++..+...
T Consensus 13 Plr~G~~keeLrsrl~~~~l----~~---k~~~~ll~~l~~~g~l~~~g~~v~ 58 (59)
T PF09106_consen 13 PLRPGMPKEELRSRLFKPRL----PP---KLFNALLEALVAEGRLKVEGDWVR 58 (59)
T ss_dssp TTSS-EEHHHHHHHCST-TS-----H---CCHHHHHHHHHHTTSEEEESSEEE
T ss_pred cCccCcCHHHHHHHHhhccC----CH---HHHHHHHHHHHHCCCeeeECCEee
Confidence 46899999988854433 33 32 345667788999999998776544
No 50
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=44.29 E-value=37 Score=20.79 Aligned_cols=26 Identities=15% Similarity=0.272 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHhcCceEecCCceec
Q 029524 93 RKILAVQLKHFAAKGNLIKIRASYKL 118 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKGSFKL 118 (192)
...+.+.|+.+.+.|.|....|.|.|
T Consensus 22 ~~tv~~~l~~L~~~g~l~~~~~~~~i 47 (48)
T smart00419 22 RETVSRTLKRLEKEGLISREGGRIVI 47 (48)
T ss_pred HHHHHHHHHHHHHCCCEEEeCCEEEE
Confidence 34588899999999999987787765
No 51
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=43.85 E-value=82 Score=22.14 Aligned_cols=59 Identities=15% Similarity=0.239 Sum_probs=39.4
Q ss_pred HHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC--ceecCcc
Q 029524 56 QMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA--SYKLSEA 121 (192)
Q Consensus 56 eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG--SFKLs~~ 121 (192)
++|++.|...+++ .++..|...+..+ +.++. ...|+..|+-|=..| |+...| -+.|...
T Consensus 1 ~~IL~~L~~~~~P--~g~~~l~~~L~~~-g~~~s---e~avRrrLr~me~~G-lt~~~g~~G~~iT~~ 61 (66)
T PF08461_consen 1 EFILRILAESDKP--LGRKQLAEELKLR-GEELS---EEAVRRRLRAMERDG-LTRKVGRQGRIITEK 61 (66)
T ss_pred CHHHHHHHHcCCC--CCHHHHHHHHHhc-Chhhh---HHHHHHHHHHHHHCC-CccccCCcccccCHH
Confidence 3677777776655 7788899998887 32232 456889999999999 444322 3346544
No 52
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=43.34 E-value=41 Score=29.42 Aligned_cols=49 Identities=16% Similarity=0.282 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHH
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHF 103 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~ 103 (192)
+.+++...|.+|-++-|+|..+|-+|...=...+. ..|+..|...|...
T Consensus 31 ~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf-~efk~~l~~~l~~~ 79 (281)
T COG1737 31 PDEVALLSIAELAERAGVSPATVVRFARKLGFEGF-SEFKLALAQELAEG 79 (281)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCH-HHHHHHHHHHHhhc
Confidence 56788899999999999999999999987654333 56777777777654
No 53
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=43.12 E-value=83 Score=26.15 Aligned_cols=57 Identities=12% Similarity=0.086 Sum_probs=34.8
Q ss_pred HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC--ceecC
Q 029524 57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA--SYKLS 119 (192)
Q Consensus 57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG--SFKLs 119 (192)
.|.+.|.+-.=.-|.-..+... |.+.|++. +.-++++|..|+..|.|++..| +|-..
T Consensus 9 ~l~~~I~~g~~~~g~~LPsE~e-La~~~~VS-----R~TVR~Al~~L~~eGli~r~~G~GtfV~~ 67 (230)
T TIGR02018 9 DILERIRSGEWPPGHRIPSEHE-LVAQYGCS-----RMTVNRALRELTDAGLLERRQGVGTFVAE 67 (230)
T ss_pred HHHHHHHhCCCCCCCcCcCHHH-HHHHHCCC-----HHHHHHHHHHHHHCCCEEEecCCEEEEcc
Confidence 3444444422244543333332 33445532 5679999999999999999874 77644
No 54
>PF13309 HTH_22: HTH domain
Probab=43.06 E-value=7.8 Score=27.19 Aligned_cols=23 Identities=22% Similarity=0.381 Sum_probs=19.7
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHH
Q 029524 58 ITEALMALQDKSGSSPYAIAKYM 80 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYI 80 (192)
|..|+..+.+.-|+|+++|-+||
T Consensus 41 lKgav~~vA~~L~iS~~TVY~YL 63 (64)
T PF13309_consen 41 LKGAVEYVAEKLGISRATVYRYL 63 (64)
T ss_pred cCcHHHHHHHHHCCCHHHHHHHc
Confidence 56677778888899999999997
No 55
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=42.27 E-value=21 Score=32.04 Aligned_cols=30 Identities=23% Similarity=0.356 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhcCceEecCCceecCcccc
Q 029524 94 KILAVQLKHFAAKGNLIKIRASYKLSEAAA 123 (192)
Q Consensus 94 ~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~K 123 (192)
..|..+|+++.+.|.|+|..+.|+|+.-++
T Consensus 41 ~ai~pqiKkL~~~~LV~~~~~~Y~LS~~G~ 70 (260)
T COG4742 41 SAILPQIKKLKDKGLVVQEGDRYSLSSLGK 70 (260)
T ss_pred HHHHHHHHHHhhCCCEEecCCEEEecchHH
Confidence 358889999999999999999999997664
No 56
>PF12029 DUF3516: Domain of unknown function (DUF3516); InterPro: IPR021904 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 460 to 473 amino acids in length. This domain is found associated with PF00270 from PFAM, PF00271 from PFAM.
Probab=41.92 E-value=90 Score=30.44 Aligned_cols=59 Identities=17% Similarity=0.387 Sum_probs=43.2
Q ss_pred HHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHH---HHHHHhcCceEecC-----C-ceecCc
Q 029524 56 QMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQ---LKHFAAKGNLIKIR-----A-SYKLSE 120 (192)
Q Consensus 56 eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~a---LKk~Ve~G~LVqvK-----G-SFKLs~ 120 (192)
.||++-| .|.|-...++...|.+||.. ....+++++++ .+.|+..|.|+++. | .|+|..
T Consensus 62 aMlLnvl----~r~gd~~~~~~~Ll~~nhe~--~~~~~~~~~ra~~i~r~L~~agvve~~~~~~~~G~~~~ltv 129 (461)
T PF12029_consen 62 AMLLNVL----ARPGDAFAAMRHLLRDNHEP--RARQRRLIRRAIEIYRSLLDAGVVERLPEPDEGGRRYRLTV 129 (461)
T ss_pred HHHHHHH----cCCCcHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHHHHhCCCEEEeccCCCCCceEEEec
Confidence 4666555 78999999999999999973 34445555555 47899999999854 2 565554
No 57
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=41.78 E-value=1e+02 Score=24.84 Aligned_cols=41 Identities=20% Similarity=0.425 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCC----CCchhH-----HHHHHHHHHHHHhcCceEe-cCC
Q 029524 74 YAIAKYMEEKHKD----ELPANF-----RKILAVQLKHFAAKGNLIK-IRA 114 (192)
Q Consensus 74 ~AIkKYIe~~Y~~----~lp~nf-----~~lLk~aLKk~Ve~G~LVq-vKG 114 (192)
.+|..||...|.. ++-.|+ +..+-.+|..||++|.|+. +=|
T Consensus 4 ~~Il~y~~~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~G 54 (169)
T PF07106_consen 4 DAILEYMKEQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYG 54 (169)
T ss_pred HHHHHHHHHcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeec
Confidence 4567777766632 122332 4668999999999999984 336
No 58
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=40.79 E-value=21 Score=25.37 Aligned_cols=45 Identities=22% Similarity=0.359 Sum_probs=28.6
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHH
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQL 100 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aL 100 (192)
.++....|.+|-+..|+|..+|-+|+..=...+. ..|+..|...|
T Consensus 30 ~~~~~~si~elA~~~~vS~sti~Rf~kkLG~~gf-~efk~~l~~~~ 74 (77)
T PF01418_consen 30 DEIAFMSISELAEKAGVSPSTIVRFCKKLGFSGF-KEFKIALAQEL 74 (77)
T ss_dssp HHHCT--HHHHHHHCTS-HHHHHHHHHHCTTTCH-HHHHHHHHCHH
T ss_pred HHHHHccHHHHHHHcCCCHHHHHHHHHHhCCCCH-HHHHHHHHHHH
Confidence 4455566888889999999999999987543222 34555555444
No 59
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=38.85 E-value=68 Score=23.53 Aligned_cols=53 Identities=17% Similarity=0.238 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHcCC-CCC--CcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHH
Q 029524 51 HPPYFQMITEALMALQD-KSG--SSPYAIAKYMEEKHKDELPANFRKILAVQLKHF 103 (192)
Q Consensus 51 HP~Y~eMI~EAI~aLke-R~G--SS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~ 103 (192)
+|+..+++..+...-.| ..| .|...|..+|..+++..|..+.-..+.+.|.++
T Consensus 3 ~~p~EqlF~~~FR~a~~~Ee~e~lsa~~If~~L~k~~~~~l~~~~~~~FGriL~~~ 58 (73)
T PF12990_consen 3 RPPEEQLFHCCFRPAEEGEEGEWLSAAEIFERLQKKSPAALRGSNPNHFGRILQKL 58 (73)
T ss_pred CCHHHHHHHHHccCCCCCccceeecHHHHHHHHHHhCccccccCCHHHHHHHHHHc
Confidence 57788888888765433 444 789999999999999766555455666666654
No 60
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=38.24 E-value=24 Score=22.65 Aligned_cols=23 Identities=26% Similarity=0.303 Sum_probs=18.0
Q ss_pred HHcCCCCCCcHHHHHHHHHHhCC
Q 029524 63 MALQDKSGSSPYAIAKYMEEKHK 85 (192)
Q Consensus 63 ~aLkeR~GSS~~AIkKYIe~~Y~ 85 (192)
.+|.+..|.|+++|.+|+..+..
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~~ 35 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKRN 35 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSST
T ss_pred HHHHHHhCCCcchhHHHhcCCCC
Confidence 45667889999999999998654
No 61
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=37.94 E-value=51 Score=20.86 Aligned_cols=38 Identities=18% Similarity=0.281 Sum_probs=24.5
Q ss_pred HcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceE
Q 029524 64 ALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLI 110 (192)
Q Consensus 64 aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LV 110 (192)
.|.+..|.|+.-|+..+. ++ ...++.+|+.+++.|.|.
T Consensus 11 ~l~~~~~~t~~ela~~~~------is---~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 11 YLRENPRITQKELAEKLG------IS---RSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHCTTS-HHHHHHHHT------S----HHHHHHHHHHHHHTTSEE
T ss_pred HHHHcCCCCHHHHHHHhC------CC---HHHHHHHHHHHHHCcCcC
Confidence 334455577777666553 11 446899999999999873
No 62
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=37.85 E-value=1.3e+02 Score=25.74 Aligned_cols=54 Identities=19% Similarity=0.246 Sum_probs=38.6
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec--CCceecCccc
Q 029524 58 ITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI--RASYKLSEAA 122 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv--KGSFKLs~~~ 122 (192)
|+++|.. ...|.|...|...+ + ++ +.-+.+.|..|++.|-|.+. .|.|.|+...
T Consensus 16 iL~~l~~--~~~~ls~~eia~~l----g--l~---kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~ 71 (263)
T PRK09834 16 VLRALNR--LDGGATVGLLAELT----G--LH---RTTVRRLLETLQEEGYVRRSASDDSFRLTLKV 71 (263)
T ss_pred HHHHHHh--cCCCCCHHHHHHHH----C--cC---HHHHHHHHHHHHHCCCEEEecCCCcEEEcHHH
Confidence 3444432 34458888888777 2 33 45688899999999999986 4789998654
No 63
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=36.96 E-value=68 Score=21.91 Aligned_cols=23 Identities=17% Similarity=0.261 Sum_probs=18.4
Q ss_pred HHcCCCCCCcHHHHHHHHHHhCC
Q 029524 63 MALQDKSGSSPYAIAKYMEEKHK 85 (192)
Q Consensus 63 ~aLkeR~GSS~~AIkKYIe~~Y~ 85 (192)
..|.+..|.|+++|.+|+..+..
T Consensus 22 ~~lA~~~gis~~tis~~~~g~~~ 44 (78)
T TIGR02607 22 RALAKALGVSRSTLSRIVNGRRG 44 (78)
T ss_pred HHHHHHhCCCHHHHHHHHcCCCC
Confidence 45567899999999999887654
No 64
>PRK11050 manganese transport regulator MntR; Provisional
Probab=36.85 E-value=2e+02 Score=22.98 Aligned_cols=60 Identities=17% Similarity=0.207 Sum_probs=38.3
Q ss_pred CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-CceecCccccc
Q 029524 53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-ASYKLSEAAAG 124 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKLs~~~Kk 124 (192)
.|.++|...|.. ..|.+...|...+ + +. ...|+..|+++.+.|.|.+.. +.+.|...+..
T Consensus 37 ~~l~~I~~~l~~---~~~~t~~eLA~~l----~--is---~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~ 97 (152)
T PRK11050 37 DYVELIADLIAE---VGEARQVDIAARL----G--VS---QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEK 97 (152)
T ss_pred HHHHHHHHHHHh---cCCCCHHHHHHHH----C--CC---HHHHHHHHHHHHHCCCEEEecCCceEECchHHH
Confidence 355566665543 3467776666655 2 12 446899999999999887643 45666665543
No 65
>cd00591 HU_IHF Integration host factor (IHF) and HU are small heterodimeric members of the DNABII protein family that bind and bend DNA, functioning as architectural factors in many cellular processes including transcription, site-specific recombination, and higher-order nucleoprotein complex assembly. The dimer subunits associate to form a compact globular core from which two beta ribbon arms (one from each subunit) protrude. The beta arms track and bind the DNA minor groove. Despite sequence and structural similarity, IHF and HU can be distinguished by their different DNA substrate preferences.
Probab=36.40 E-value=72 Score=22.48 Aligned_cols=46 Identities=20% Similarity=0.333 Sum_probs=27.9
Q ss_pred HcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--CceecCccc
Q 029524 64 ALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 64 aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
.|.++.|.|+..+...|.. |...|...+.+|.-|... |+|.+....
T Consensus 8 ~ia~~~~~~~~~v~~vl~~-------------~~~~i~~~L~~g~~V~l~~~G~F~~~~~~ 55 (87)
T cd00591 8 AIAEKTGLSKKDAEAAVDA-------------FLDVITEALAKGEKVELPGFGTFEVRERA 55 (87)
T ss_pred HHHHHhCcCHHHHHHHHHH-------------HHHHHHHHHhCCCeEEEeCCEEEEEEEEC
Confidence 3444555555555555433 445566666788777777 588887654
No 66
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=35.75 E-value=29 Score=24.05 Aligned_cols=40 Identities=23% Similarity=0.433 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCCc---hhH---HHHHHHHHHHHHhcCceEecC
Q 029524 74 YAIAKYMEEKHKDELP---ANF---RKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 74 ~AIkKYIe~~Y~~~lp---~nf---~~lLk~aLKk~Ve~G~LVqvK 113 (192)
..|..||.++....+. ..| ...|..-|..++..|.|.++.
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~ 48 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVD 48 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEec
Confidence 4566666666543111 111 356888999999999999865
No 67
>PRK11569 transcriptional repressor IclR; Provisional
Probab=35.54 E-value=1.3e+02 Score=25.98 Aligned_cols=47 Identities=13% Similarity=0.208 Sum_probs=35.2
Q ss_pred CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--CceecCccc
Q 029524 67 DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 67 eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
...+.+...|..-+. ++ +.-+.+.|..|++.|-|.+.. |.|.|+...
T Consensus 40 ~~~~~~lseia~~lg------lp---ksTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~l 88 (274)
T PRK11569 40 SNGSVALTELAQQAG------LP---NSTTHRLLTTMQQQGFVRQVGELGHWAIGAHA 88 (274)
T ss_pred CCCCcCHHHHHHHHC------cC---HHHHHHHHHHHHHCCCEEEcCCCCeEecCHHH
Confidence 356688888877652 33 445778899999999999864 789987654
No 68
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=34.93 E-value=87 Score=24.38 Aligned_cols=58 Identities=12% Similarity=0.106 Sum_probs=37.5
Q ss_pred HHHHHHHcCCC-CCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-CceecCccccc
Q 029524 58 ITEALMALQDK-SGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-ASYKLSEAAAG 124 (192)
Q Consensus 58 I~EAI~aLkeR-~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKLs~~~Kk 124 (192)
.+++|-.|-+. ++.+...|..++.-. ..-+...|++|...|.|.+.. +.|.|.+.+..
T Consensus 9 yL~~I~~l~~~~~~~~~~ela~~l~vs---------~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~ 68 (142)
T PRK03902 9 YIEQIYLLIEEKGYARVSDIAEALSVH---------PSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKK 68 (142)
T ss_pred HHHHHHHHHhcCCCcCHHHHHHHhCCC---------hhHHHHHHHHHHHCCCEEEecCceEEECHHHHH
Confidence 55555555443 445555555554221 335888999999999998654 67888877754
No 69
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=34.51 E-value=69 Score=22.13 Aligned_cols=47 Identities=17% Similarity=0.309 Sum_probs=28.1
Q ss_pred HHHHHHH-----HHcCCCCCCcHHHHH-HHHHHhCCCCCchhHHHHHHHHHHHHHhcC
Q 029524 56 QMITEAL-----MALQDKSGSSPYAIA-KYMEEKHKDELPANFRKILAVQLKHFAAKG 107 (192)
Q Consensus 56 eMI~EAI-----~aLkeR~GSS~~AIk-KYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G 107 (192)
+-|.+++ .+|.+.-|+|.++|. .|+..+- +| +..++..++..+|.=.
T Consensus 4 ~rl~~~~g~~~~~~lA~~lgis~st~s~~~~~r~~---~P--~~~l~~ia~~~gvsl~ 56 (66)
T PF07022_consen 4 ERLKEALGVKSDKELAERLGISKSTLSNNWKKRGS---IP--AEWLIKIALETGVSLD 56 (66)
T ss_dssp HHHHHHHT-SSCHHHHCCTT--HHHHH-HHHHSSS-------HHHHHHHHHHH---HH
T ss_pred HHHHHHhCCCCHHHHHHHhCcCHHHhhHHHHhCCC---CC--HHHHHHHHHHHCcCHH
Confidence 3455554 567889999999999 7887543 45 5667777777776543
No 70
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=34.36 E-value=29 Score=22.66 Aligned_cols=39 Identities=18% Similarity=0.274 Sum_probs=28.6
Q ss_pred cCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec
Q 029524 65 LQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI 112 (192)
Q Consensus 65 LkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv 112 (192)
|.+..|.+...|..++.-. ...+...|++|+..|.|++.
T Consensus 12 l~~~~~~~~~~la~~~~~~---------~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 12 LYENGGITQSELAEKLGIS---------RSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHSSEEHHHHHHHHTS----------HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHcCCCCHHHHHHHHCCC---------hhHHHHHHHHHHHCCCEEec
Confidence 3445568888877776432 44589999999999999874
No 71
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=33.86 E-value=28 Score=25.34 Aligned_cols=33 Identities=15% Similarity=0.302 Sum_probs=25.8
Q ss_pred CHHHHHHHH---HHHcCCCCCCcHHHHHHHHHHhCC
Q 029524 53 PYFQMITEA---LMALQDKSGSSPYAIAKYMEEKHK 85 (192)
Q Consensus 53 ~Y~eMI~EA---I~aLkeR~GSS~~AIkKYIe~~Y~ 85 (192)
+..+|+.++ .+++.-+-|+++.+|.+|+.+...
T Consensus 7 TIPelLi~~~GnqtEvaR~l~c~R~TVrKY~~D~~a 42 (64)
T PF06322_consen 7 TIPELLIETYGNQTEVARRLGCNRATVRKYSRDKDA 42 (64)
T ss_pred ehhHHHHHHhCcHHHHHHHhcccHHHHHHHhccccc
Confidence 345777776 455666899999999999998764
No 72
>TIGR01201 HU_rel DNA-binding protein, histone-like, putative. This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe.
Probab=33.61 E-value=72 Score=25.64 Aligned_cols=27 Identities=30% Similarity=0.518 Sum_probs=21.6
Q ss_pred HHHHHHHHHhcCceEecC--CceecCccc
Q 029524 96 LAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 96 Lk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
|...|...+..|.-|+.. |+|.+.-..
T Consensus 58 l~~~i~~~L~~G~~V~L~gfGtF~~~~~s 86 (145)
T TIGR01201 58 LAYVLRRELANGKTVRLGEIGTFRLSATA 86 (145)
T ss_pred HHHHHHHHHhCCCeEEeCCCEEEEEEecc
Confidence 566777788999999988 599988764
No 73
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=33.33 E-value=1.9e+02 Score=23.28 Aligned_cols=67 Identities=16% Similarity=0.220 Sum_probs=50.8
Q ss_pred HHHHHHHHHHcCC-CCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-CceecCccc
Q 029524 55 FQMITEALMALQD-KSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-ASYKLSEAA 122 (192)
Q Consensus 55 ~eMI~EAI~aLke-R~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKLs~~~ 122 (192)
..||--|..-|++ +.-.+...|.+.|....+. -.......|.+--.-+.-.|+|+.+. |.+-|...+
T Consensus 3 ~S~idvAy~iL~~~~~~m~f~dL~~ev~~~~~~-s~e~~~~~iaq~YtdLn~DGRFi~lG~n~WgLr~w~ 71 (129)
T PRK02363 3 LSLIEVAYEILKEKKEPMSFYDLVNEIQKYLGK-SDEEIRERIAQFYTDLNLDGRFISLGDNKWGLRSWY 71 (129)
T ss_pred ccHHHHHHHHHHHcCCcccHHHHHHHHHHHhCC-CHHHHHHHHHHHHHHHhccCCeeEcCCCceeccccc
Confidence 3567777777765 4779999999999999874 23456777888788899999999987 566666554
No 74
>PRK09462 fur ferric uptake regulator; Provisional
Probab=32.28 E-value=2.5e+02 Score=22.05 Aligned_cols=63 Identities=16% Similarity=0.145 Sum_probs=45.7
Q ss_pred CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---C--ceecC
Q 029524 52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---A--SYKLS 119 (192)
Q Consensus 52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---G--SFKLs 119 (192)
-+-..+|++.|... ...-.|..-|..++...++. +. ..-|-+.|..|++.|.|..+. | .|.+.
T Consensus 16 T~qR~~Il~~l~~~-~~~h~sa~eI~~~l~~~~~~-i~---~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~~~ 83 (148)
T PRK09462 16 TLPRLKILEVLQEP-DNHHVSAEDLYKRLIDMGEE-IG---LATVYRVLNQFDDAGIVTRHNFEGGKSVFELT 83 (148)
T ss_pred CHHHHHHHHHHHhC-CCCCCCHHHHHHHHHhhCCC-CC---HHHHHHHHHHHHHCCCEEEEEcCCCcEEEEeC
Confidence 34567788888764 23358999999999888763 22 346889999999999998764 3 56654
No 75
>COG2522 Predicted transcriptional regulator [General function prediction only]
Probab=32.02 E-value=45 Score=26.70 Aligned_cols=41 Identities=20% Similarity=0.291 Sum_probs=28.5
Q ss_pred CCCCcHHHHHHHHHHhCC-C------CCchhHHHHHHHHHHHHHhcCc
Q 029524 68 KSGSSPYAIAKYMEEKHK-D------ELPANFRKILAVQLKHFAAKGN 108 (192)
Q Consensus 68 R~GSS~~AIkKYIe~~Y~-~------~lp~nf~~lLk~aLKk~Ve~G~ 108 (192)
=-|.|+.|..+||..+-+ . +...+++.++...++.+++.-.
T Consensus 31 LLGltqaAVS~Yls~krg~~~~~~~~e~~e~i~~l~~~~~~~~v~~~~ 78 (119)
T COG2522 31 LLGLTQAAVSQYLSGKRGSARLEDIGETDEEIRSLVAELIKNLVEGFE 78 (119)
T ss_pred HhCCCHHHHHHHHccCCchHHHHHHHHHHHHHHHHHHHHHHHhhhhhH
Confidence 357889999999999887 2 1224566777777777776553
No 76
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=31.99 E-value=58 Score=23.78 Aligned_cols=61 Identities=10% Similarity=0.117 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHcCCCCCC----------cHHHHHHHHHHhCCC-CCchhH-HHHHHHHHHHHHhcCceEecCC
Q 029524 54 YFQMITEALMALQDKSGS----------SPYAIAKYMEEKHKD-ELPANF-RKILAVQLKHFAAKGNLIKIRA 114 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GS----------S~~AIkKYIe~~Y~~-~lp~nf-~~lLk~aLKk~Ve~G~LVqvKG 114 (192)
+..+|+++|..++++-|. ...-|..|--++.+. +...++ ...+..-|..|+..|.|....+
T Consensus 5 ~a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~ 77 (106)
T PF09382_consen 5 EAKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNG 77 (106)
T ss_dssp HHHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEEC
T ss_pred HHHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCC
Confidence 456899999999886432 222233331111110 122232 5678999999999999977665
No 77
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=31.86 E-value=57 Score=23.44 Aligned_cols=45 Identities=16% Similarity=0.251 Sum_probs=29.5
Q ss_pred CcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-C---ceecCcc
Q 029524 71 SSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-A---SYKLSEA 121 (192)
Q Consensus 71 SS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-G---SFKLs~~ 121 (192)
.+...|-..++ .++ +. ...++.+|-+++.+|.|+..+ | .|.|++.
T Consensus 21 i~~~~Li~ll~-~~G--v~---e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 21 IWVASLIRLLA-AFG--VS---ESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp EEHHHHHHHHC-CTT-------HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred eeHHHHHHHHH-HcC--CC---hHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 35555554443 333 33 346899999999999999987 3 6888753
No 78
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=31.80 E-value=1e+02 Score=23.10 Aligned_cols=43 Identities=12% Similarity=0.312 Sum_probs=31.7
Q ss_pred CcHHHHHHHHHHhCCCCC---chhH---HHHHHHHHHHHHhcCceEecC
Q 029524 71 SSPYAIAKYMEEKHKDEL---PANF---RKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 71 SS~~AIkKYIe~~Y~~~l---p~nf---~~lLk~aLKk~Ve~G~LVqvK 113 (192)
.|...|+.||..+...++ ...| ..+|.--|.+++..|+|+++-
T Consensus 2 ~~L~qlRd~l~~~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 2 ASLIQVRDLLALRGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred ccHHHHHHHHHHcCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 467888999988876432 1223 346788899999999999884
No 79
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=31.75 E-value=1.4e+02 Score=25.69 Aligned_cols=53 Identities=11% Similarity=0.247 Sum_probs=44.2
Q ss_pred CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC
Q 029524 53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA 114 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG 114 (192)
...++|.+.|..|....|++-.-|.+-|. +. ++-++++|=+|..+|.|-.+.|
T Consensus 10 ~~~~lv~~~~~~l~~~~~~~a~~i~~~l~------~~---k~~vNr~LY~l~~~~~v~~~~~ 62 (183)
T PHA03103 10 DIYELVKKEVKNLGLGEGITAIEISRKLN------IE---KSEVNKQLYKLQREGMVYMSDS 62 (183)
T ss_pred HHHHHHHHHHHHhccCCCccHHHHHHHhC------CC---HHHHHHHHHHHHhcCceecCCC
Confidence 35689999999999999999999988663 22 3459999999999999988776
No 80
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=31.64 E-value=68 Score=28.97 Aligned_cols=63 Identities=14% Similarity=0.234 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHcCCC--CCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-Cceec
Q 029524 54 YFQMITEALMALQDK--SGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-ASYKL 118 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR--~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-GSFKL 118 (192)
|.--|..+|..|..+ +=...++...++...|+.. .+.+.-|+++|.-|-..|.|..+. |.|+.
T Consensus 188 Wlldi~~cid~i~~~~FtL~diY~Fe~~L~~~~P~N--~~Ik~KIRQqLQ~LRD~g~IeFl~rG~Yrk 253 (254)
T PF06044_consen 188 WLLDIMKCIDKIPKNEFTLDDIYAFEDELQIKYPNN--NHIKAKIRQQLQILRDKGIIEFLGRGRYRK 253 (254)
T ss_dssp HHHHHHHHHHHS-SSEEEHHHHHTTHHHHHHHSTT---S-HHHHHHHHHHHHHHTTSEEE-STTEEEE
T ss_pred hHHHHHHHHHhcCccceeHHHHHHHHHHHHHhCCCC--CChhHHHHHHHHHHhhCCceEEecCCcccc
Confidence 555678888877633 2233444455677788731 345778999999999999999976 88874
No 81
>PF10557 Cullin_Nedd8: Cullin protein neddylation domain; InterPro: IPR019559 This is the neddylation site of cullin proteins, which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognises and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae (Baker's yeast), and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenesis in metazoans. The only identified Nedd8 substrates are cullins. Neddylation results in covalent conjugation of a Nedd8 moiety onto a conserved cullin lysine residue []. ; GO: 0031625 ubiquitin protein ligase binding, 0006511 ubiquitin-dependent protein catabolic process, 0031461 cullin-RING ubiquitin ligase complex; PDB: 3RTR_G 3TDU_D 1LDJ_A 3TDZ_D 1LDK_B 1U6G_A 3O6B_J 3O2P_E 4A0K_A 2HYE_C ....
Probab=31.56 E-value=1.8e+02 Score=20.21 Aligned_cols=56 Identities=13% Similarity=0.176 Sum_probs=38.2
Q ss_pred HHHHHHH-HcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC
Q 029524 57 MITEALM-ALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 57 MI~EAI~-aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK 113 (192)
.|..||. -|+.++-.+...|...+.+.-...++.. ...|+..|..|+++|-|.+..
T Consensus 8 ~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~-~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 8 QIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPS-VSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS----HHHHHHHHHHHHHTTSEEEES
T ss_pred hhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCC-HHHHHHHHHHHHHhhhhhcCC
Confidence 3444443 3566666888888888877664222222 567999999999999998754
No 82
>PF13730 HTH_36: Helix-turn-helix domain
Probab=31.47 E-value=1.4e+02 Score=19.10 Aligned_cols=48 Identities=23% Similarity=0.383 Sum_probs=31.4
Q ss_pred CHHHHHHHHHHHcCCCCCC---cHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCce
Q 029524 53 PYFQMITEALMALQDKSGS---SPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~GS---S~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~L 109 (192)
+..-+|.-.|..+.+..|- |...|.+.+ + +. ++-+.++|+.|++.|-|
T Consensus 5 ~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~----g--~s---~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 5 PTAKLVYLYLASYANKNGGCFPSQETLAKDL----G--VS---RRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHHHHHHhcCCCCCCCcCHHHHHHHH----C--cC---HHHHHHHHHHHHHCcCC
Confidence 3455677777777654444 555555554 3 22 56789999999998865
No 83
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=31.18 E-value=1.5e+02 Score=19.73 Aligned_cols=36 Identities=17% Similarity=0.293 Sum_probs=23.0
Q ss_pred CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHH
Q 029524 67 DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHF 103 (192)
Q Consensus 67 eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~ 103 (192)
|-.-.|...|.+-+++.|+.+|. .++.+|+..+...
T Consensus 17 dl~~vT~k~vr~~Le~~~~~dL~-~~K~~I~~~I~~~ 52 (54)
T PF08766_consen 17 DLDTVTKKQVREQLEERFGVDLS-SRKKFIKELIDEF 52 (54)
T ss_dssp -GGG--HHHHHHHHHHH-SS--S-HHHHHHHHHHHHH
T ss_pred CHhHhhHHHHHHHHHHHHCCCcH-HHHHHHHHHHHHH
Confidence 55558999999999999987664 5677777766544
No 84
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=31.07 E-value=1.7e+02 Score=19.66 Aligned_cols=54 Identities=13% Similarity=0.217 Sum_probs=35.9
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA 114 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG 114 (192)
.+.|.+.|.+-.=+.|.....+.. |.+.|++ . +.-++.+|..|.+.|.|....|
T Consensus 6 ~~~l~~~I~~g~~~~g~~lps~~~-la~~~~v--s---r~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 6 YDQLRQAILSGRLPPGDRLPSERE-LAERYGV--S---RTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHHTTSS-TTSBE--HHH-HHHHHTS------HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHcCCCCCCCEeCCHHH-HHHHhcc--C---CcHHHHHHHHHHHCCcEEEECC
Confidence 456777777766677776655554 4455553 2 5579999999999999987654
No 85
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=31.03 E-value=1.4e+02 Score=18.72 Aligned_cols=22 Identities=18% Similarity=0.259 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHhcCceEecCC
Q 029524 93 RKILAVQLKHFAAKGNLIKIRA 114 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKG 114 (192)
...+..+|+.|.+.|.|....|
T Consensus 34 ~~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 34 RTTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHHHHHHHHHHCCCEEEecC
Confidence 4569999999999999987654
No 86
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=30.27 E-value=2.8e+02 Score=22.14 Aligned_cols=54 Identities=13% Similarity=0.130 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK 113 (192)
-...|++.|....++ .|...|-..+.+.++. +. -.-+-+.|+-+++.|.|....
T Consensus 22 qR~~vl~~L~~~~~~--~sAeei~~~l~~~~p~-is---laTVYr~L~~l~e~Glv~~~~ 75 (145)
T COG0735 22 QRLAVLELLLEADGH--LSAEELYEELREEGPG-IS---LATVYRTLKLLEEAGLVHRLE 75 (145)
T ss_pred HHHHHHHHHHhcCCC--CCHHHHHHHHHHhCCC-CC---HhHHHHHHHHHHHCCCEEEEE
Confidence 345677777776666 8888888888888773 32 345888999999999998754
No 87
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=29.13 E-value=1.5e+02 Score=24.59 Aligned_cols=58 Identities=17% Similarity=0.233 Sum_probs=40.2
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec-----CC----ceecCccccc
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI-----RA----SYKLSEAAAG 124 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv-----KG----SFKLs~~~Kk 124 (192)
.+.|+..|.. ..+.|...|..++ + +. ...++.+|+.|+..|.|... .| .|.|.+.+..
T Consensus 3 r~~IL~~L~~---~~~~t~~eLA~~l----g--is---~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~ 69 (203)
T TIGR02702 3 KEDILSYLLK---QGQATAAALAEAL----A--IS---PQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGRE 69 (203)
T ss_pred HHHHHHHHHH---cCCCCHHHHHHHH----C--cC---HHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhh
Confidence 3455555544 4558888888887 2 22 34699999999999999875 23 4788877643
No 88
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=29.02 E-value=29 Score=22.53 Aligned_cols=15 Identities=20% Similarity=0.419 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHhcC
Q 029524 93 RKILAVQLKHFAAKG 107 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G 107 (192)
.+.|.+.|+.+-+.|
T Consensus 29 ~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 29 RRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHCC
Confidence 344556666666666
No 89
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=28.27 E-value=1.7e+02 Score=22.26 Aligned_cols=60 Identities=23% Similarity=0.309 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC---CceecCcccc
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR---ASYKLSEAAA 123 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK---GSFKLs~~~K 123 (192)
|.-.|+..|.. ......|...|...+. ++ ...+.+.|..|.+.|.|.... |-|.|.....
T Consensus 10 yal~~l~~la~-~~~~~~s~~eia~~l~------is---~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~ 72 (130)
T TIGR02944 10 YATLVLTTLAQ-NDSQPYSAAEIAEQTG------LN---APTVSKILKQLSLAGIVTSKRGVEGGYTLARAPR 72 (130)
T ss_pred HHHHHHHHHHh-CCCCCccHHHHHHHHC------cC---HHHHHHHHHHHHHCCcEEecCCCCCChhhcCCcc
Confidence 44555555544 2234577777765543 33 346899999999999998754 5888876543
No 90
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=28.23 E-value=37 Score=23.17 Aligned_cols=22 Identities=14% Similarity=0.288 Sum_probs=17.8
Q ss_pred HHHcCCCCCCcHHHHHHHHHHh
Q 029524 62 LMALQDKSGSSPYAIAKYMEEK 83 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~ 83 (192)
|.++....|+|..+|.+|+...
T Consensus 26 v~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 26 VSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHH
T ss_pred eEeeecccccccccccHHHHHH
Confidence 5667778899999999999887
No 91
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=28.01 E-value=1.8e+02 Score=27.19 Aligned_cols=62 Identities=15% Similarity=0.099 Sum_probs=40.8
Q ss_pred HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCcccc
Q 029524 57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAA 123 (192)
Q Consensus 57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~K 123 (192)
|....|..|....|.+...+ ...|+..+...|...+. .|..+.+.|.|....+.++|...+.
T Consensus 367 ~~~~~~~~Lr~~~gl~~~~~----~~~fg~~~~~~~~~~~~-~l~~l~~~gll~~~~~~~~lT~~G~ 428 (453)
T PRK09249 367 LRRDVIEQLMCNFELDFAAI----EAAFGIDFAEYFAEELE-RLAPLEADGLVELDENGITVTPKGR 428 (453)
T ss_pred HHHHHHHHHhhcCCcCHHHH----HHHHCCCHHHHHHHHHH-HHHHHHHCCCEEEECCEEEECccch
Confidence 34455577888888886444 44455333233443333 5889999999998778898887654
No 92
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=27.90 E-value=27 Score=21.30 Aligned_cols=27 Identities=19% Similarity=0.151 Sum_probs=19.6
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHhC
Q 029524 58 ITEALMALQDKSGSSPYAIAKYMEEKH 84 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYIe~~Y 84 (192)
+.+.|..+.++.|.|+..+-.++...|
T Consensus 10 ~~~~l~~~a~~~g~s~s~~ir~ai~~~ 36 (39)
T PF01402_consen 10 LYERLDELAKELGRSRSELIREAIREY 36 (39)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHHHH
Confidence 456777777888888877777666654
No 93
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=27.83 E-value=61 Score=18.79 Aligned_cols=23 Identities=26% Similarity=0.323 Sum_probs=17.9
Q ss_pred HHcCCCCCCcHHHHHHHHHHhCC
Q 029524 63 MALQDKSGSSPYAIAKYMEEKHK 85 (192)
Q Consensus 63 ~aLkeR~GSS~~AIkKYIe~~Y~ 85 (192)
..|.+..|.|...|.+|...++.
T Consensus 14 ~~la~~~~i~~~~i~~~~~~~~~ 36 (56)
T smart00530 14 EELAEKLGVSRSTLSRIENGKRK 36 (56)
T ss_pred HHHHHHhCCCHHHHHHHHCCCCC
Confidence 34556778999999999887764
No 94
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=27.69 E-value=2.1e+02 Score=21.11 Aligned_cols=66 Identities=17% Similarity=0.251 Sum_probs=43.9
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec---C--C----ceecCccccc
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI---R--A----SYKLSEAAAG 124 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv---K--G----SFKLs~~~Kk 124 (192)
.+|++=++.. ...++-+.|.+.|...+...+..+ ...|-..|++|..+|-|... . | .|.|.+.++.
T Consensus 5 l~~~iL~~L~---~~~~~GYei~~~l~~~~~~~~~i~-~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~ 79 (100)
T TIGR03433 5 LDLLILKTLS---LGPLHGYGIAQRIQQISEDVLQVE-EGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRK 79 (100)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHHHHHcCCccccC-CCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHH
Confidence 3444444444 235788999999998764222222 24588999999999988862 1 2 5888877764
No 95
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=26.50 E-value=2.9e+02 Score=22.55 Aligned_cols=60 Identities=17% Similarity=0.217 Sum_probs=41.8
Q ss_pred CHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--Cceec
Q 029524 53 PYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKL 118 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKL 118 (192)
+-..+|++.|.... .-.|...|..++.+.++. +. ..-|-+.|..|++.|.|..+. ++|.+
T Consensus 26 ~qR~~IL~~l~~~~--~hlSa~eI~~~L~~~~~~-is---~aTVYRtL~~L~e~Glv~~~~~~~~~~~ 87 (169)
T PRK11639 26 PQRLEVLRLMSLQP--GAISAYDLLDLLREAEPQ-AK---PPTVYRALDFLLEQGFVHKVESTNSYVL 87 (169)
T ss_pred HHHHHHHHHHHhcC--CCCCHHHHHHHHHhhCCC-CC---cchHHHHHHHHHHCCCEEEEecCCcEEE
Confidence 34556777776642 347778888888777652 22 345889999999999999875 46654
No 96
>PF03234 CDC37_N: Cdc37 N terminal kinase binding; InterPro: IPR013855 In Saccharomyces cerevisiae (Baker's yeast), cell division control protein Cdc37 is required for the productive formation of Cdc28-cyclin complexes. Cdc37 may be a kinase targeting subunit of Hsp90 [].
Probab=26.09 E-value=2.5e+02 Score=23.77 Aligned_cols=40 Identities=25% Similarity=0.365 Sum_probs=31.1
Q ss_pred CCCCCCCCHHHHHHHHHHHcCC-CCCCcHHHHHHHHHHhCC
Q 029524 46 SKTPSHPPYFQMITEALMALQD-KSGSSPYAIAKYMEEKHK 85 (192)
Q Consensus 46 ~k~~sHP~Y~eMI~EAI~aLke-R~GSS~~AIkKYIe~~Y~ 85 (192)
.....+|+|.+||..-+..+++ ..+.+..++..+|.....
T Consensus 101 ~~~~~~p~y~~Mi~~L~~qvk~~~de~~~~~~~~~l~~H~~ 141 (177)
T PF03234_consen 101 NKDPEQPTYDEMIEDLLDQVKKEPDEKSGKAELEELQEHRA 141 (177)
T ss_pred cCCCCCCCHHHHHHHHHHHHhcccCcccHHHHHHHHHHHHH
Confidence 4567899999999999988875 445568888888877654
No 97
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=25.87 E-value=97 Score=22.92 Aligned_cols=30 Identities=10% Similarity=0.143 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHhcCceEecC--CceecCccc
Q 029524 93 RKILAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
+..+++.|..|...|.|++.. |.|=++.+.
T Consensus 61 r~tVsr~L~~Le~~GlI~r~~~~~~~~~n~~~ 92 (95)
T TIGR01610 61 RTHVSDAIKSLARRRIIFRQGMMGIVGVNTPL 92 (95)
T ss_pred HHHHHHHHHHHHHCCCeeeecCCceeecCCCc
Confidence 456999999999999999887 788777554
No 98
>PF12363 DUF3647: Phage protein ; InterPro: IPR024410 Proteins in this entry are frequently annotated as phage proteins, however there is little accompanying literature to back this up or to describe the nature of these phage proteins.
Probab=25.85 E-value=2.3e+02 Score=21.81 Aligned_cols=51 Identities=18% Similarity=0.261 Sum_probs=32.5
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCce
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNL 109 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~L 109 (192)
.++|.-|...++++ -|+..|-.||++-+.. ...+..++...|.-+..+|-+
T Consensus 54 ~d~i~~a~~~~~~~--~s~~eIe~~ie~~~e~--~~~~~~l~~~vl~el~~s~~~ 104 (113)
T PF12363_consen 54 ADIIYAATAHEKKR--PSREEIEDYIEDIIED--EDDIEELFDEVLKELKKSNFF 104 (113)
T ss_pred HHHHHHHhcccCCC--CCHHHHHHHHHHHHhc--chhHHHHHHHHHHHHHhChhH
Confidence 34444444444455 4999999999984432 233667777777777766644
No 99
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=25.56 E-value=36 Score=23.12 Aligned_cols=23 Identities=26% Similarity=0.216 Sum_probs=18.0
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhC
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKH 84 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y 84 (192)
|.+|.+.-|+|.-+|.+||..=.
T Consensus 22 ~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 22 LKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHHHHH
Confidence 45677889999999999998643
No 100
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=25.40 E-value=2.9e+02 Score=21.66 Aligned_cols=49 Identities=14% Similarity=0.252 Sum_probs=34.1
Q ss_pred CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-C-ceecCc
Q 029524 67 DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-A-SYKLSE 120 (192)
Q Consensus 67 eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-G-SFKLs~ 120 (192)
+..+.|..-|..++.+.++ + + ..-+..-|++|+++|.|...+ | +|...+
T Consensus 15 ~~~~~t~~eI~~~l~~~~~--~--~-~tTv~T~L~rL~~KG~v~~~k~gr~~~Y~p 65 (130)
T TIGR02698 15 TLGETTSRDIIRILAEKKD--W--S-DSTIKTLLGRLVDKGCLTTEKEGRKFIYTA 65 (130)
T ss_pred cCCCCCHHHHHHHHhhccC--C--c-HHHHHHHHHHHHHCCceeeecCCCcEEEEe
Confidence 4456788888888877654 1 2 456888999999999998654 3 454443
No 101
>smart00411 BHL bacterial (prokaryotic) histone like domain.
Probab=25.38 E-value=1.8e+02 Score=20.61 Aligned_cols=46 Identities=17% Similarity=0.331 Sum_probs=25.4
Q ss_pred HcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--CceecCccc
Q 029524 64 ALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 64 aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
.|.++.|.|+..+...|.. |...|...+.+|.-|... |+|.+....
T Consensus 9 ~ia~~~~~~~~~v~~vl~~-------------l~~~i~~~L~~g~~V~i~g~G~F~~~~~~ 56 (90)
T smart00411 9 AIAEKAGLSKKDAKAAVDA-------------FLEIITEALKKGEKVELRGFGTFEVRERK 56 (90)
T ss_pred HHHHHhCCCHHHHHHHHHH-------------HHHHHHHHHhCCCeEEEeCcEEEEEEeec
Confidence 3344555555555544443 333444555556666666 588877543
No 102
>PRK10753 transcriptional regulator HU subunit alpha; Provisional
Probab=25.14 E-value=1.4e+02 Score=21.91 Aligned_cols=44 Identities=14% Similarity=0.267 Sum_probs=24.5
Q ss_pred HcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC--CceecCc
Q 029524 64 ALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR--ASYKLSE 120 (192)
Q Consensus 64 aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK--GSFKLs~ 120 (192)
.|.++.|.|...+...|.. |-..|...+.+|.-|+.. |+|.+..
T Consensus 9 ~ia~~~~~s~~~~~~~v~~-------------~~~~i~~~L~~g~~V~i~gfG~F~v~~ 54 (90)
T PRK10753 9 VIADKAELSKTQAKAALES-------------TLAAITESLKEGDAVQLVGFGTFKVNH 54 (90)
T ss_pred HHHHHhCCCHHHHHHHHHH-------------HHHHHHHHHHcCCeEEEcCCEEEEEee
Confidence 3445566777666655543 222334444556555555 6998853
No 103
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=25.07 E-value=65 Score=23.94 Aligned_cols=39 Identities=15% Similarity=0.152 Sum_probs=26.6
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHH
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLK 101 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLK 101 (192)
|..+.+..|+|..+|..++..+++ .+.+..+..+...+.
T Consensus 22 i~dvA~~~gvS~~TVsr~L~~~~~-~Vs~~Tr~rV~~aa~ 60 (80)
T TIGR02844 22 VRETAKVFGVSKSTVHKDVTERLP-EINPELAEEVKEVLD 60 (80)
T ss_pred HHHHHHHhCCCHHHHHHHhcCCCC-CCCHHHHHHHHHHHc
Confidence 445667899999999999977643 244555555555544
No 104
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=24.72 E-value=2.5e+02 Score=20.55 Aligned_cols=57 Identities=21% Similarity=0.143 Sum_probs=41.6
Q ss_pred CCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCc------hhHHHHHHHHHHHHHhcCce
Q 029524 52 PPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELP------ANFRKILAVQLKHFAAKGNL 109 (192)
Q Consensus 52 P~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp------~nf~~lLk~aLKk~Ve~G~L 109 (192)
..|.+++..-+..|.+.+-.|...|..=++.-+.. ++ ++....|..-+-++|..|.|
T Consensus 50 ~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~~-l~dl~~D~P~a~~~la~~~a~~v~~~~l 112 (113)
T smart00544 50 RTYREMYSVLLSRLCQANVISTKQFEKGFWRLLED-IEDLELDIPNAWRNLAEFVARLISDGIL 112 (113)
T ss_pred ccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhh-ChhhhcccccHHHHHHHHHHHHHHcCCC
Confidence 56888888888888888888888888777777653 11 24456677778888887765
No 105
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=24.45 E-value=2.1e+02 Score=21.85 Aligned_cols=32 Identities=25% Similarity=0.310 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHhcCceEecCC-------ceecCccccc
Q 029524 93 RKILAVQLKHFAAKGNLIKIRA-------SYKLSEAAAG 124 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKG-------SFKLs~~~Kk 124 (192)
...+...|.+|+..|-|.+... .+.|.+.+..
T Consensus 60 ~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~ 98 (144)
T PRK03573 60 QPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEP 98 (144)
T ss_pred hhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHH
Confidence 3458999999999999998753 5556655544
No 106
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=24.32 E-value=1e+02 Score=22.95 Aligned_cols=31 Identities=16% Similarity=0.232 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhcCceEecCC-------ceecCccccc
Q 029524 94 KILAVQLKHFAAKGNLIKIRA-------SYKLSEAAAG 124 (192)
Q Consensus 94 ~lLk~aLKk~Ve~G~LVqvKG-------SFKLs~~~Kk 124 (192)
..+...|++|...|-|++... .|.|.+.+..
T Consensus 57 ~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~ 94 (118)
T TIGR02337 57 PSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQA 94 (118)
T ss_pred hhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHH
Confidence 358999999999999998652 5666666543
No 107
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=24.31 E-value=2.7e+02 Score=21.83 Aligned_cols=62 Identities=5% Similarity=0.034 Sum_probs=37.6
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhc---Cc-eEecCC-ceecCc
Q 029524 58 ITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAK---GN-LIKIRA-SYKLSE 120 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~---G~-LVqvKG-SFKLs~ 120 (192)
|...|.. +...|.|+..|...+...+....+...+.++.+-.+++-.. +. |..+.| -|+|..
T Consensus 168 il~~l~~-~~~~~~s~~~i~~~~~~~~~~~~~~tv~~~i~~lr~kl~~~~~~~~~i~~~~~~Gy~~~~ 234 (240)
T PRK10710 168 LLKTLSH-EPGKVFSREQLLNHLYDDYRVVTDRTIDSHIKNLRRKLESLDAEQSFIRAVYGVGYRWEA 234 (240)
T ss_pred HHHHHHh-CCCceEcHHHHHHHhcCcCcCCCccCHHHHHHHHHHHhhcCCCCCCcEEEeCCCceEECc
Confidence 4443333 66778999999999998775323334556666655555422 23 444555 677753
No 108
>PF09312 SurA_N: SurA N-terminal domain; InterPro: IPR015391 The correct folding of outer membrane proteins in Gram negative bacteria is facilitated by the survival protein SurA []. This entry represents the domain found at the N terminus of the chaperone SurA. It is a helical domain of unknown function. The C terminus of the SurA protein folds back and forms part of this domain also but is not included in the current alignment. ; PDB: 3RGC_B 2PV3_B 1M5Y_A.
Probab=24.06 E-value=87 Score=23.88 Aligned_cols=44 Identities=14% Similarity=0.191 Sum_probs=29.2
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHH
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQL 100 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aL 100 (192)
.+-|-++|..+..++|.|...+..+++.. +. ....|+..|+..|
T Consensus 69 d~evd~~i~~ia~~n~ls~~ql~~~L~~~-G~-s~~~~r~~ir~~i 112 (118)
T PF09312_consen 69 DEEVDEAIANIAKQNNLSVEQLRQQLEQQ-GI-SYEEYREQIRKQI 112 (118)
T ss_dssp HHHHHHHHHHHHHHTT--HHHHHHHCHHC-T---HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHc-CC-CHHHHHHHHHHHH
Confidence 44566778888889999999999999874 32 2355766666655
No 109
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=23.73 E-value=1.2e+02 Score=22.58 Aligned_cols=30 Identities=27% Similarity=0.234 Sum_probs=17.5
Q ss_pred CHHHHHHHHHHHcCC----------CCCCcHHHHHHHHHH
Q 029524 53 PYFQMITEALMALQD----------KSGSSPYAIAKYMEE 82 (192)
Q Consensus 53 ~Y~eMI~EAI~aLke----------R~GSS~~AIkKYIe~ 82 (192)
.+.+|+..-+..+.+ .-|.||.||-++|+.
T Consensus 3 ~~~~~~~~ll~~~~~~~~SGe~La~~LgiSRtaVwK~Iq~ 42 (79)
T COG1654 3 DTSQMLLLLLLLLTGNFVSGEKLAEELGISRTAVWKHIQQ 42 (79)
T ss_pred chHHHHHHHHHHcCCCcccHHHHHHHHCccHHHHHHHHHH
Confidence 345566555544433 456777777777664
No 110
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=23.63 E-value=73 Score=32.81 Aligned_cols=27 Identities=30% Similarity=0.299 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhcCceEecCCceecC
Q 029524 93 RKILAVQLKHFAAKGNLIKIRASYKLS 119 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvKGSFKLs 119 (192)
-..|...|.++|..|+|+...|+|+|.
T Consensus 738 lqeL~~fLq~kV~e~kL~f~~G~Y~l~ 764 (765)
T KOG2165|consen 738 LQELQGFLQRKVREGKLEFIAGSYRLK 764 (765)
T ss_pred HHHHHHHHHHHhhccceEEecceeeec
Confidence 356899999999999999999999985
No 111
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=23.36 E-value=1.3e+02 Score=22.31 Aligned_cols=35 Identities=17% Similarity=0.137 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCC
Q 029524 51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHK 85 (192)
Q Consensus 51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~ 85 (192)
.-++.+||.-.|.-|.+.+|.+..-+..++...++
T Consensus 41 ~~t~eemie~~~~~~~~~~~~~~~~a~~~~~~~lp 75 (81)
T PF12674_consen 41 DITMEEMIEFCVPFMDEFNGMTPEEARKMMPRYLP 75 (81)
T ss_pred cCCHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHcc
Confidence 35899999999999999999999999999988877
No 112
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=23.09 E-value=3.1e+02 Score=23.71 Aligned_cols=54 Identities=19% Similarity=0.118 Sum_probs=37.3
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec--CCceecCccc
Q 029524 58 ITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI--RASYKLSEAA 122 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv--KGSFKLs~~~ 122 (192)
|+++|.. .+.|.+..-|..-+. ++ +.-+.+-|..|++.|-|.+. .|.|.|+...
T Consensus 30 IL~~~~~--~~~~~tl~eIa~~lg------lp---kStv~RlL~tL~~~G~l~~~~~~~~Y~lG~~l 85 (271)
T PRK10163 30 ILQYLEK--SGGSSSVSDISLNLD------LP---LSTTFRLLKVLQAADFVYQDSQLGWWHIGLGV 85 (271)
T ss_pred HHHHHHh--CCCCcCHHHHHHHHC------cC---HHHHHHHHHHHHHCCCEEEcCCCCeEEecHHH
Confidence 4444432 345688877776542 44 44577889999999999995 4789887654
No 113
>PF14420 Clr5: Clr5 domain
Probab=22.84 E-value=2.4e+02 Score=18.97 Aligned_cols=29 Identities=17% Similarity=0.134 Sum_probs=23.8
Q ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHhCCC
Q 029524 58 ITEALMALQDKSGSSPYAIAKYMEEKHKD 86 (192)
Q Consensus 58 I~EAI~aLkeR~GSS~~AIkKYIe~~Y~~ 86 (192)
..+-|..|-=-.|-|...|..||+.+|+.
T Consensus 8 ~K~~I~~LY~~e~~tl~~v~~~M~~~~~F 36 (54)
T PF14420_consen 8 HKEEIERLYIDENKTLEEVMEIMKEEHGF 36 (54)
T ss_pred HHHHHHHHHHhCCCcHHHHHHHHHHHhCC
Confidence 45667777766789999999999999985
No 114
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=22.83 E-value=2.9e+02 Score=22.69 Aligned_cols=60 Identities=7% Similarity=0.095 Sum_probs=41.7
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC-ceecCc
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA-SYKLSE 120 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG-SFKLs~ 120 (192)
..+.|.+.|....=+-|.-... .-|.+.|++. +.-|+.+|..|...|.|+...| -|.+..
T Consensus 12 vy~~i~~~I~~g~l~pG~~L~e--~eLae~lgVS-----RtpVREAL~~L~~eGlv~~~~~~G~~V~~ 72 (224)
T PRK11534 12 GYRWLKNDIIRGNFQPDEKLRM--SLLTSRYALG-----VGPLREALSQLVAERLVTVVNQKGYRVAS 72 (224)
T ss_pred HHHHHHHHHHhCCCCCCCcCCH--HHHHHHHCCC-----hHHHHHHHHHHHHCCCEEEeCCCceEeCC
Confidence 3455677777755566765543 4688888853 5679999999999999987654 344443
No 115
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=22.69 E-value=1e+02 Score=26.30 Aligned_cols=46 Identities=13% Similarity=0.130 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHH
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQL 100 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aL 100 (192)
+.+++...|.+|-++.|+|..+|-+|...=...+. ..|+..|...|
T Consensus 25 ~~~v~~~si~elA~~~~vS~aTv~Rf~kklG~~Gf-~efk~~l~~~~ 70 (278)
T PRK11557 25 PDTARHLSSQQLANEAGVSQSSVVKFAQKLGYKGF-PALKLALSEAL 70 (278)
T ss_pred HHHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCH-HHHHHHHHHHh
Confidence 35777888999999999999999999977544332 44555555544
No 116
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=22.39 E-value=1e+02 Score=20.84 Aligned_cols=40 Identities=18% Similarity=0.232 Sum_probs=28.9
Q ss_pred CCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCc
Q 029524 67 DKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRAS 115 (192)
Q Consensus 67 eR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGS 115 (192)
+..+++...|...+. ++ +..+...|++|++.|.+.+..|.
T Consensus 19 ~~~~~t~~eIa~~l~------i~---~~~v~~~L~~L~~~GlV~~~~~~ 58 (68)
T PF01978_consen 19 KNGPATAEEIAEELG------IS---RSTVYRALKSLEEKGLVEREEGR 58 (68)
T ss_dssp HHCHEEHHHHHHHHT------SS---HHHHHHHHHHHHHTTSEEEEEEC
T ss_pred HcCCCCHHHHHHHHC------cC---HHHHHHHHHHHHHCCCEEEEcCc
Confidence 445566666665442 22 55699999999999999998763
No 117
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=22.18 E-value=1.2e+02 Score=25.85 Aligned_cols=45 Identities=16% Similarity=0.256 Sum_probs=33.5
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHH
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQL 100 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aL 100 (192)
.+.....|.+|-+..|+|..+|-+|...=...+. ..|+..|...|
T Consensus 30 ~~v~~~si~~lA~~~~vS~aTv~Rf~kklG~~gf-~e~k~~l~~~~ 74 (284)
T PRK11302 30 QTAIHSSIATLAKMANVSEPTVNRFCRSLDTKGF-PDFKLHLAQSL 74 (284)
T ss_pred HHHHhcCHHHHHHHhCCCHHHHHHHHHHcCCCCH-HHHHHHHHHHh
Confidence 4566678999999999999999999988655333 34555555544
No 118
>PF00216 Bac_DNA_binding: Bacterial DNA-binding protein; InterPro: IPR000119 Bacteria synthesise a set of small, usually basic proteins of about 90 residues that bind DNA and are known as histone-like proteins [, ]. Examples include the HU protein in Escherichia coli is a dimer of closely related alpha and beta chains and in other bacteria can be a dimer of identical chains. HU-type proteins have been found in a variety of eubacteria, cyanobacteria and archaebacteria, and are also encoded in the chloroplast genome of some algae []. The integration host factor (IHF), a dimer of closely related chains which seem to function in genetic recombination as well as in translational and transcriptional control [] is found in enterobacteria and viral proteins include the African Swine fever virus protein A104R (or LMW5-AR) []. The exact function of these proteins is not yet clear but they are capable of wrapping DNA and stabilising it from denaturation under extreme environmental conditions. The structure is known for one of these proteins []. The protein exists as a dimer and two "beta-arms" function as the non-specific binding site for bacterial DNA. ; GO: 0003677 DNA binding; PDB: 3C4I_B 2O97_A 1MUL_A 1P78_A 1P51_C 1P71_B 2HT0_A 1OWG_A 2IIF_A 1OUZ_A ....
Probab=21.88 E-value=1.2e+02 Score=21.47 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=18.4
Q ss_pred HHHHHHHHHHhcCceEecC--CceecCccc
Q 029524 95 ILAVQLKHFAAKGNLIKIR--ASYKLSEAA 122 (192)
Q Consensus 95 lLk~aLKk~Ve~G~LVqvK--GSFKLs~~~ 122 (192)
.|...|...+.+|.-|... |+|.+....
T Consensus 27 ~~~~~i~~~L~~g~~V~l~g~G~F~~~~~~ 56 (90)
T PF00216_consen 27 ALFDVIKEALKEGESVKLPGFGTFSVKERK 56 (90)
T ss_dssp HHHHHHHHHHHTT-EEEETTTEEEEEEEET
T ss_pred HHHHHHHHHHhcCCeEEeeceeEEEEeccc
Confidence 3555666667888888877 588876543
No 119
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=21.81 E-value=1.9e+02 Score=26.26 Aligned_cols=60 Identities=13% Similarity=0.239 Sum_probs=43.2
Q ss_pred HcCCCCCCcHHHHHHHHHHhCCCCCchhH-------HHHHHHHHHHHHhcCceEecC-CceecCcccc
Q 029524 64 ALQDKSGSSPYAIAKYMEEKHKDELPANF-------RKILAVQLKHFAAKGNLIKIR-ASYKLSEAAA 123 (192)
Q Consensus 64 aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf-------~~lLk~aLKk~Ve~G~LVqvK-GSFKLs~~~K 123 (192)
.|..+++..+.-|--+|.-+++..-+... -.-+..+|+.||..|.+..-. |.|.|...+-
T Consensus 3 ~L~~kk~~t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG~ 70 (260)
T COG1497 3 VLMSKKNLTRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGRGEYEITKKGA 70 (260)
T ss_pred chhccccchHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCCeeEEEehhHH
Confidence 46677778888888888888764323221 234889999999999999844 3799987663
No 120
>PRK15482 transcriptional regulator MurR; Provisional
Probab=21.76 E-value=1.2e+02 Score=26.17 Aligned_cols=47 Identities=13% Similarity=0.172 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHH
Q 029524 54 YFQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLK 101 (192)
Q Consensus 54 Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLK 101 (192)
+.+++...|.+|-++.|+|..+|-+|...=...+. ..|+..|...|.
T Consensus 29 ~~~v~~~si~elA~~~~vS~aTv~Rf~kkLGf~Gf-~efk~~l~~~~~ 75 (285)
T PRK15482 29 VSELKSVSSRKMAKQLGISQSSIVKFAQKLGAQGF-TELRMALIGEYS 75 (285)
T ss_pred HHHHHhcCHHHHHHHhCCCHHHHHHHHHHhCCCCH-HHHHHHHHHHHh
Confidence 45677788999999999999999999987654333 456666665554
No 121
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.76 E-value=42 Score=20.83 Aligned_cols=23 Identities=22% Similarity=0.258 Sum_probs=18.2
Q ss_pred HHHcCCCCCCcHHHHHHHHHHhC
Q 029524 62 LMALQDKSGSSPYAIAKYMEEKH 84 (192)
Q Consensus 62 I~aLkeR~GSS~~AIkKYIe~~Y 84 (192)
|.++.+..|+|..+|..|+....
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 44566678999999999987765
No 122
>COG5643 Protein containing a metal-binding domain shared with formylmethanofuran dehydrogenase subunit E [General function prediction only]
Probab=21.52 E-value=92 Score=31.69 Aligned_cols=36 Identities=31% Similarity=0.207 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCC
Q 029524 51 HPPYFQMITEALMALQDKSGSSPYAIAKYMEEKHKD 86 (192)
Q Consensus 51 HP~Y~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~ 86 (192)
.|+|..|..-.+..---+.-+|-.-|.+||++||+.
T Consensus 510 d~pyd~L~~~lfHnH~CpGvssGy~iakyi~enyPl 545 (685)
T COG5643 510 DPPYDLLGCFLFHNHFCPGVSSGYLIAKYIFENYPL 545 (685)
T ss_pred CCcHHHhHhHHhhcccCCCCCcchhhHHhHhhcCCc
Confidence 567887777777665567789999999999999984
No 123
>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=21.48 E-value=43 Score=20.15 Aligned_cols=22 Identities=18% Similarity=0.376 Sum_probs=17.1
Q ss_pred HHcCCCCCCcHHHHHHHHHHhC
Q 029524 63 MALQDKSGSSPYAIAKYMEEKH 84 (192)
Q Consensus 63 ~aLkeR~GSS~~AIkKYIe~~Y 84 (192)
.++.+.-|+|..+|.+|+....
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcCC
Confidence 4455667899999999998754
No 124
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=21.47 E-value=1.1e+02 Score=24.83 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHhcCceEecC
Q 029524 93 RKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 93 ~~lLk~aLKk~Ve~G~LVqvK 113 (192)
++.+.++|++|++.|.+.+.+
T Consensus 56 rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 56 RSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHHHHHHHHHHHHcCCeeeee
Confidence 677999999999999999876
No 125
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=21.34 E-value=1.6e+02 Score=19.00 Aligned_cols=35 Identities=14% Similarity=0.243 Sum_probs=25.2
Q ss_pred CCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC
Q 029524 70 GSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR 113 (192)
Q Consensus 70 GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK 113 (192)
+.+...|..++. ++ ...+...|++|++.|-|.+..
T Consensus 21 ~~t~~~la~~l~------~~---~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 21 ELTQSELAERLG------IS---KSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp GEEHHHHHHHHT------S----HHHHHHHHHHHHHTTSEEEEE
T ss_pred CcCHHHHHHHHC------cC---HHHHHHHHHHHHHCCCEEEeC
Confidence 366666666552 22 456999999999999999864
No 126
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=21.24 E-value=3.1e+02 Score=25.59 Aligned_cols=66 Identities=17% Similarity=0.074 Sum_probs=40.4
Q ss_pred CHHHHHH-HHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCCceecCcccc
Q 029524 53 PYFQMIT-EALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRASYKLSEAAA 123 (192)
Q Consensus 53 ~Y~eMI~-EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKGSFKLs~~~K 123 (192)
+-.+++. ..|..|....|.+...+..+ |+..+...|...| ..|+.+++.|.|....+.++|...+.
T Consensus 362 s~~~~~~~~~~~~l~~~~gl~~~~~~~~----~g~~~~~~~~~~~-~~l~~l~~~gll~~~~~~~~lT~~G~ 428 (455)
T TIGR00538 362 SQDDCIRREVIKSLMCNFKLDYSKIEEK----FDLDFADYFAKEL-ELLKPLEEDGLLDVDEKGIEVTPKGR 428 (455)
T ss_pred CHHHHHHHHHHHHHHhcCCcCHHHHHHH----HCCCHHHHHHHHH-HHHHHHHhCCCEEEECCEEEECcCCh
Confidence 3344443 55666777788886554443 4432222333222 45788899999988777888887653
No 127
>PF03882 KicB: KicB killing factor; InterPro: IPR005582 This family contains MukF, which are proteins involved in chromosome condensation, segregation and cell cycle progression. MukE (IPR007385 from INTERPRO) along with MukF interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli []. The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC []. ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; GO: 0005509 calcium ion binding, 0006260 DNA replication, 0007059 chromosome segregation, 0005737 cytoplasm; PDB: 1T98_B 3RPU_X 3EUH_B 3EUK_J 3EUJ_B.
Probab=21.13 E-value=1.5e+02 Score=28.67 Aligned_cols=67 Identities=10% Similarity=0.142 Sum_probs=48.7
Q ss_pred HHHHHHHHHHcCCCC--C----CcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecC-------CceecCcc
Q 029524 55 FQMITEALMALQDKS--G----SSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIR-------ASYKLSEA 121 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~--G----SS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvK-------GSFKLs~~ 121 (192)
.--.+-||..|++.. | .....|..|+...|.. .+.+...+.+++|+.+|+.+.|.+.. |-|+|.+=
T Consensus 28 rlaFL~aia~~~~er~~~e~~E~~L~D~Fr~Vs~~f~q-~~et~~~RANNAIndlv~QrlLsRf~se~~eg~~iYRLT~L 106 (440)
T PF03882_consen 28 RLAFLLAIAVLNNERFDGELSEGELHDAFRYVSKGFEQ-SAETSTVRANNAINDLVRQRLLSRFTSEFTEGASIYRLTPL 106 (440)
T ss_dssp HHHHHHHHHHHHHT--SSSEEHHHHHHHHHHHHHHTT---STTHHHHHHHHHHHHHHTTSEEEEE-SSSTTSEEEEE-HH
T ss_pred HHHHHHHHHHHcccccccccchhHHHHHHHHHHHhhcc-CcchHHHHHHHHHHHHHHHHHHHHhccccccccceeeechh
Confidence 334566777776432 2 4567899999999984 56778889999999999999999865 37888764
Q ss_pred c
Q 029524 122 A 122 (192)
Q Consensus 122 ~ 122 (192)
+
T Consensus 107 ~ 107 (440)
T PF03882_consen 107 G 107 (440)
T ss_dssp H
T ss_pred h
Confidence 3
No 128
>KOG0183 consensus 20S proteasome, regulatory subunit alpha type PSMA7/PRE6 [Posttranslational modification, protein turnover, chaperones]
Probab=20.92 E-value=1.1e+02 Score=27.46 Aligned_cols=37 Identities=16% Similarity=0.312 Sum_probs=25.8
Q ss_pred CCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHh
Q 029524 69 SGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAA 105 (192)
Q Consensus 69 ~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve 105 (192)
.|=+-+.+..|++.||...-..+-...|+.+++.|++
T Consensus 162 iGr~sk~VrEflEK~y~e~~~~~~~~~ikL~ir~Lle 198 (249)
T KOG0183|consen 162 IGRSSKTVREFLEKNYKEEAIATEGETIKLAIRALLE 198 (249)
T ss_pred cccccHHHHHHHHHhcccccccccccHHHHHHHHHHH
Confidence 4778899999999999854223334556666666653
No 129
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=20.87 E-value=3.4e+02 Score=22.39 Aligned_cols=61 Identities=16% Similarity=0.203 Sum_probs=44.5
Q ss_pred HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec-----CCceecCccccc
Q 029524 57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI-----RASYKLSEAAAG 124 (192)
Q Consensus 57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv-----KGSFKLs~~~Kk 124 (192)
||+==|..++. ..|...|..||.++-.. | =-.|.++|.-|+++|-|... .+.|.|...+++
T Consensus 4 lILYiL~~v~~--pltn~qit~~iL~~~~~----n-YF~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~ 69 (163)
T PF14277_consen 4 LILYILKKVKF--PLTNSQITEFILENEYT----N-YFTLQQALSELVESGLITLETDSDNKTRYSITEKGKE 69 (163)
T ss_pred hHhHHHHhCCC--CCCHHHHHHHHHhcCcc----c-HHHHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHH
Confidence 33333444443 48999999999997542 3 12499999999999999963 259999999875
No 130
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=20.77 E-value=66 Score=24.88 Aligned_cols=60 Identities=25% Similarity=0.294 Sum_probs=35.8
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC----ceecCccccc
Q 029524 55 FQMITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA----SYKLSEAAAG 124 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG----SFKLs~~~Kk 124 (192)
.+||.+-|.. ...+|+-..-|. |.+.+ | -......|.-|+++|.++...| -|.|.+.+.+
T Consensus 17 ~eIi~dIL~~-~~~~~~~~Tri~------y~aNl--n-y~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~ 80 (95)
T COG3432 17 LEIIFDILKA-ISEGGIGITRII------YGANL--N-YKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKR 80 (95)
T ss_pred HHHHHHHHHH-hcCCCCCceeee------eecCc--C-HHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHH
Confidence 6777777775 333333222221 33222 2 2357889999999995555444 4999887654
No 131
>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=20.65 E-value=3.2e+02 Score=22.37 Aligned_cols=57 Identities=12% Similarity=0.138 Sum_probs=35.6
Q ss_pred HHHHHHHHcCCCCCCcHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcCceEecCC--ceecC
Q 029524 57 MITEALMALQDKSGSSPYAIAKYMEEKHKDELPANFRKILAVQLKHFAAKGNLIKIRA--SYKLS 119 (192)
Q Consensus 57 MI~EAI~aLkeR~GSS~~AIkKYIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqvKG--SFKLs 119 (192)
.|.+.|.+-.=.-|+-..+ -.-|.+.|++ . +..++++|..++..|.|+...| +|-..
T Consensus 9 ~l~~~I~~g~~~~g~~lPs-E~eLa~~~~V--s---r~Tvr~Al~~L~~eGli~~~~g~Gt~V~~ 67 (231)
T TIGR03337 9 HLSYQIRAGALLPGDKLPS-ERDLGERFNT--T---RVTIREALQQLEAEGLIYREDRRGWFVSP 67 (231)
T ss_pred HHHHHHHcCCCCCCCcCcC-HHHHHHHHCC--C---HHHHHHHHHHHHHCCeEEEeCCCEEEECC
Confidence 3444444422234443323 3445566663 2 6679999999999999999874 77543
No 132
>COG1849 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.55 E-value=1.4e+02 Score=23.11 Aligned_cols=31 Identities=26% Similarity=0.508 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHcCCCCC--C----cHHHHHHHHHHh
Q 029524 53 PYFQMITEALMALQDKSG--S----SPYAIAKYMEEK 83 (192)
Q Consensus 53 ~Y~eMI~EAI~aLkeR~G--S----S~~AIkKYIe~~ 83 (192)
.|.+++.+||..++-+.| | ....|..|+++-
T Consensus 12 kYi~~leeaL~~~k~~~~~~s~ae~~~~ma~~Y~~Da 48 (90)
T COG1849 12 KYIELLEEALKEIKSRPGDRSAAEDFVDMAESYFEDA 48 (90)
T ss_pred HHHHHHHHHHHHhccCCCcchHHHHHHHHHHHHHHHH
Confidence 499999999999998777 3 556666666653
No 133
>PF13338 DUF4095: Domain of unknown function (DUF4095)
Probab=20.52 E-value=1e+02 Score=22.38 Aligned_cols=26 Identities=27% Similarity=0.530 Sum_probs=20.5
Q ss_pred HHHHHHHHhcCceEecC-CceecCccc
Q 029524 97 AVQLKHFAAKGNLIKIR-ASYKLSEAA 122 (192)
Q Consensus 97 k~aLKk~Ve~G~LVqvK-GSFKLs~~~ 122 (192)
...|.+++++|.|+++. |-|-+....
T Consensus 4 r~~l~~~~~~G~l~rl~rGvY~~~~~~ 30 (124)
T PF13338_consen 4 RRALRRLVRRGELIRLRRGVYASPEYP 30 (124)
T ss_pred HHHHHHHHHCCCEEEeeCCEEEcCCCC
Confidence 36789999999999986 788765443
No 134
>KOG2933 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.49 E-value=59 Score=30.43 Aligned_cols=59 Identities=10% Similarity=0.198 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHcCC-CCCCcHHHHHH--HHHHhCCCCCchhHHHHHHHHHHHHHhcCceEec
Q 029524 54 YFQMITEALMALQD-KSGSSPYAIAK--YMEEKHKDELPANFRKILAVQLKHFAAKGNLIKI 112 (192)
Q Consensus 54 Y~eMI~EAI~aLke-R~GSS~~AIkK--YIe~~Y~~~lp~nf~~lLk~aLKk~Ve~G~LVqv 112 (192)
+.+.|..-+.+|+. |+|+|+.||.. -|-+.|+..+....+.+|..-|.++.....||..
T Consensus 127 L~~vii~vvkslKNlRS~VsraA~~t~~difs~ln~~i~~~ld~lv~~Ll~ka~~dnrFvre 188 (334)
T KOG2933|consen 127 LHEVIIAVVKSLKNLRSAVSRAACMTLADIFSSLNNSIDQELDDLVTQLLHKASQDNRFVRE 188 (334)
T ss_pred HHHHHHHHHHHhcChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccchHHHH
Confidence 33444555566776 99999999864 4666666545556677788888888887777753
No 135
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=20.12 E-value=1.4e+02 Score=19.41 Aligned_cols=22 Identities=18% Similarity=0.101 Sum_probs=14.1
Q ss_pred HHHHHHHHHHcCCCCCCcHHHHH
Q 029524 55 FQMITEALMALQDKSGSSPYAIA 77 (192)
Q Consensus 55 ~eMI~EAI~aLkeR~GSS~~AIk 77 (192)
.+-|.+||.++.... .|.....
T Consensus 2 ee~l~~Ai~~v~~g~-~S~r~AA 23 (45)
T PF05225_consen 2 EEDLQKAIEAVKNGK-MSIRKAA 23 (45)
T ss_dssp HHHHHHHHHHHHTTS-S-HHHHH
T ss_pred HHHHHHHHHHHHhCC-CCHHHHH
Confidence 466889999988543 6655443
Done!