Query 031883
Match_columns 151
No_of_seqs 24 out of 26
Neff 2.2
Searched_HMMs 46136
Date Fri Mar 29 06:41:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031883.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031883hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05066 HARE-HTH: HB1, ASXL, 95.8 0.013 2.9E-07 39.0 3.5 38 42-79 2-40 (72)
2 PF06163 DUF977: Bacterial pro 91.0 0.24 5.1E-06 39.0 3.1 27 36-62 6-32 (127)
3 PF03981 Ubiq_cyt_C_chap: Ubiq 83.9 4.4 9.6E-05 29.4 5.9 51 34-91 28-78 (141)
4 PF03965 Penicillinase_R: Peni 83.0 4.8 0.0001 28.7 5.7 61 46-113 7-67 (115)
5 PF06224 HTH_42: Winged helix 82.4 6.4 0.00014 31.9 6.9 59 33-93 76-137 (327)
6 PF11784 DUF3320: Protein of u 78.1 5 0.00011 26.3 4.1 39 38-76 8-47 (52)
7 COG0235 AraD Ribulose-5-phosph 75.8 3.4 7.3E-05 33.1 3.3 31 39-69 147-177 (219)
8 PF08100 Dimerisation: Dimeris 75.0 2 4.4E-05 28.4 1.6 22 46-67 10-33 (51)
9 PF01475 FUR: Ferric uptake re 70.6 23 0.00049 25.1 6.2 52 45-98 11-63 (120)
10 PRK06474 hypothetical protein; 69.8 5.5 0.00012 31.2 3.2 46 45-96 14-60 (178)
11 cd07153 Fur_like Ferric uptake 68.1 22 0.00049 24.6 5.7 50 45-96 4-54 (116)
12 TIGR02698 CopY_TcrY copper tra 65.1 28 0.0006 26.0 6.0 60 46-112 8-67 (130)
13 COG2345 Predicted transcriptio 61.1 6.8 0.00015 32.8 2.3 37 45-84 14-50 (218)
14 TIGR01086 fucA L-fuculose phos 60.6 9.8 0.00021 30.1 3.0 32 37-68 133-168 (214)
15 PRK08333 L-fuculose phosphate 60.5 6.3 0.00014 30.3 1.9 44 26-69 121-168 (184)
16 PRK08660 L-fuculose phosphate 59.9 5.5 0.00012 30.6 1.5 34 36-69 125-162 (181)
17 PRK05874 L-fuculose-phosphate 59.9 5.6 0.00012 32.1 1.6 44 26-69 128-175 (217)
18 PRK08193 araD L-ribulose-5-pho 59.4 6.2 0.00013 31.8 1.8 32 38-69 143-185 (231)
19 PRK06833 L-fuculose phosphate 54.5 7 0.00015 30.9 1.3 30 40-69 139-172 (214)
20 PF13412 HTH_24: Winged helix- 54.1 14 0.00031 22.4 2.4 27 44-73 5-31 (48)
21 PF05397 Med15_fungi: Mediator 54.1 35 0.00075 25.7 4.9 76 10-85 4-79 (115)
22 PF12840 HTH_20: Helix-turn-he 53.8 15 0.00031 23.5 2.5 39 44-85 12-50 (61)
23 PRK06512 thiamine-phosphate py 53.7 44 0.00094 27.1 5.7 67 33-99 49-119 (221)
24 PF07237 DUF1428: Protein of u 53.7 10 0.00022 28.8 1.9 25 41-65 19-43 (103)
25 PF02581 TMP-TENI: Thiamine mo 52.8 19 0.00041 27.4 3.3 65 35-99 36-104 (180)
26 PF01022 HTH_5: Bacterial regu 51.4 14 0.0003 22.8 2.0 36 46-85 6-41 (47)
27 PRK06557 L-ribulose-5-phosphat 50.0 7.6 0.00016 30.7 0.8 34 36-69 141-180 (221)
28 smart00550 Zalpha Z-DNA-bindin 49.5 18 0.00039 24.2 2.5 44 43-93 7-52 (68)
29 PF08220 HTH_DeoR: DeoR-like h 49.4 14 0.00029 24.0 1.8 42 45-93 3-44 (57)
30 PRK09462 fur ferric uptake reg 47.8 23 0.0005 26.3 3.1 50 45-96 20-71 (148)
31 PRK06357 hypothetical protein; 47.2 15 0.00033 29.6 2.2 40 30-69 135-184 (216)
32 PF09582 AnfO_nitrog: Iron onl 46.5 22 0.00047 29.2 3.0 29 70-101 146-176 (202)
33 smart00347 HTH_MARR helix_turn 46.4 77 0.0017 20.3 5.6 45 45-96 13-57 (101)
34 smart00420 HTH_DEOR helix_turn 45.2 36 0.00077 19.7 3.1 17 46-62 4-20 (53)
35 cd07977 TFIIE_beta_winged_heli 44.1 51 0.0011 23.1 4.2 52 47-110 14-70 (75)
36 PRK07490 hypothetical protein; 43.8 9.9 0.00021 31.0 0.6 31 38-68 147-181 (245)
37 PF01250 Ribosomal_S6: Ribosom 41.8 39 0.00084 23.2 3.3 34 31-64 9-43 (92)
38 PRK03634 rhamnulose-1-phosphat 41.8 17 0.00037 30.4 1.7 40 30-69 184-227 (274)
39 PF10557 Cullin_Nedd8: Cullin 40.7 1.1E+02 0.0024 20.4 6.0 59 40-98 6-65 (68)
40 PF14769 CLAMP: Flagellar C1a 39.9 1.4E+02 0.0029 21.3 6.3 55 33-88 10-77 (101)
41 PRK08087 L-fuculose phosphate 38.4 22 0.00048 28.2 1.8 33 37-69 134-170 (215)
42 PF08221 HTH_9: RNA polymerase 38.2 31 0.00068 23.0 2.3 23 42-64 13-35 (62)
43 COG4901 Ribosomal protein S25 37.7 1.1E+02 0.0023 23.9 5.4 67 37-110 36-103 (107)
44 TIGR03328 salvage_mtnB methylt 37.6 9 0.0002 29.9 -0.5 20 50-69 157-176 (193)
45 PRK06486 hypothetical protein; 37.0 15 0.00032 30.6 0.7 31 37-67 162-196 (262)
46 PF07208 DUF1414: Protein of u 36.4 26 0.00056 23.4 1.6 23 31-53 20-42 (44)
47 PRK10141 DNA-binding transcrip 35.7 40 0.00088 25.4 2.8 38 45-85 19-56 (117)
48 PF07508 Recombinase: Recombin 35.6 1.2E+02 0.0027 20.2 4.9 33 37-72 1-33 (102)
49 PF07798 DUF1640: Protein of u 35.3 42 0.00091 26.1 2.9 21 34-54 15-35 (177)
50 PF08461 HTH_12: Ribonuclease 35.1 86 0.0019 21.2 4.1 46 46-94 2-49 (66)
51 KOG1613 Exosomal 3'-5' exoribo 34.8 44 0.00096 29.8 3.3 30 29-58 105-134 (298)
52 PF09107 SelB-wing_3: Elongati 34.7 27 0.00059 22.9 1.5 41 47-95 1-42 (50)
53 PF08158 NUC130_3NT: NUC130/3N 34.6 45 0.00098 22.3 2.6 20 37-56 10-29 (52)
54 COG3355 Predicted transcriptio 34.4 28 0.0006 27.2 1.8 58 45-109 31-89 (126)
55 TIGR00760 araD L-ribulose-5-ph 34.2 21 0.00045 28.9 1.1 26 37-62 143-179 (231)
56 PRK08130 putative aldolase; Va 33.9 19 0.00041 28.4 0.8 32 38-69 140-175 (213)
57 PF10771 DUF2582: Protein of u 32.9 41 0.0009 23.4 2.3 50 40-96 6-55 (65)
58 CHL00123 rps6 ribosomal protei 32.5 63 0.0014 23.2 3.2 34 31-64 14-48 (97)
59 PRK09220 methylthioribulose-1- 31.7 30 0.00064 27.4 1.6 33 37-69 145-184 (204)
60 PRK06754 mtnB methylthioribulo 31.7 23 0.00051 28.0 1.0 33 37-69 148-185 (208)
61 PF00352 TBP: Transcription fa 31.5 60 0.0013 22.4 2.9 20 36-55 67-86 (86)
62 PF10330 Stb3: Putative Sin3 b 31.2 85 0.0018 23.8 3.8 44 45-88 9-54 (92)
63 cd00167 SANT 'SWI3, ADA2, N-Co 29.9 1E+02 0.0023 16.9 3.9 35 45-87 8-42 (45)
64 PRK12347 sgbE L-ribulose-5-pho 29.7 26 0.00057 28.5 1.0 29 38-66 144-183 (231)
65 PHA00738 putative HTH transcri 29.3 56 0.0012 25.2 2.6 44 44-94 14-57 (108)
66 cd08304 DD_superfamily The Dea 28.1 1.1E+02 0.0024 20.6 3.7 39 34-72 23-63 (69)
67 PF15645 Tox-PLDMTX: Dermonecr 28.1 56 0.0012 25.6 2.5 22 35-56 2-23 (135)
68 KOG1201 Hydroxysteroid 17-beta 27.7 1.2E+02 0.0026 27.0 4.7 54 4-59 45-117 (300)
69 TIGR02940 anfO_nitrog Fe-only 27.4 65 0.0014 27.2 2.9 29 70-101 155-185 (214)
70 PRK12348 sgaE L-ribulose-5-pho 27.3 30 0.00065 28.0 0.9 28 38-65 142-178 (228)
71 PF03279 Lip_A_acyltrans: Bact 27.1 2.1E+02 0.0045 23.0 5.7 92 10-122 132-223 (295)
72 cd00736 bacteriophage_lambda_l 27.0 37 0.0008 27.2 1.4 57 60-118 71-131 (151)
73 PRK04220 2-phosphoglycerate ki 26.5 2.3E+02 0.005 24.7 6.2 69 33-104 29-105 (301)
74 cd00398 Aldolase_II Class II A 26.5 19 0.00041 28.1 -0.3 20 50-69 153-172 (209)
75 TIGR01568 A_thal_3678 uncharac 26.0 72 0.0016 22.6 2.5 41 42-85 13-55 (66)
76 TIGR02702 SufR_cyano iron-sulf 25.8 76 0.0017 24.7 2.9 46 45-97 4-49 (203)
77 TIGR02757 conserved hypothetic 25.6 2.2E+02 0.0048 24.1 5.8 22 35-56 78-99 (229)
78 PF08863 YolD: YolD-like prote 25.4 1.4E+02 0.003 19.9 3.8 46 12-64 6-51 (92)
79 COG1564 THI80 Thiamine pyropho 25.2 53 0.0012 27.4 2.1 48 1-57 46-93 (212)
80 PRK00135 scpB segregation and 24.3 1.4E+02 0.0031 24.1 4.3 53 47-109 95-147 (188)
81 PF04806 EspF: EspF protein re 23.9 61 0.0013 22.1 1.8 13 43-55 35-47 (47)
82 PF02295 z-alpha: Adenosine de 23.7 91 0.002 21.3 2.7 49 40-93 2-50 (66)
83 PRK02363 DNA-directed RNA poly 23.7 1.1E+02 0.0023 23.8 3.3 66 42-113 4-72 (129)
84 TIGR00693 thiE thiamine-phosph 23.6 1.1E+02 0.0024 23.0 3.3 64 36-99 38-105 (196)
85 PF00596 Aldolase_II: Class II 23.6 24 0.00052 26.5 -0.2 33 37-69 135-172 (184)
86 PRK07044 aldolase II superfami 23.3 36 0.00078 27.8 0.7 33 37-69 151-187 (252)
87 PF01047 MarR: MarR family; I 23.2 97 0.0021 19.0 2.5 44 46-96 7-50 (59)
88 PF09535 Gmx_para_CXXCG: Prote 23.1 38 0.00083 29.3 0.8 24 54-77 104-136 (237)
89 PF01978 TrmB: Sugar-specific 23.1 2.1E+02 0.0046 18.2 4.8 45 46-97 12-56 (68)
90 KOG4382 Uncharacterized conser 23.0 33 0.00072 30.3 0.5 45 30-74 110-158 (276)
91 COG2715 SpmA Uncharacterized m 23.0 21 0.00045 30.4 -0.7 38 2-41 51-88 (206)
92 PRK13145 araD L-ribulose-5-pho 22.9 41 0.00088 27.4 0.9 30 38-67 144-184 (234)
93 PF04909 Amidohydro_2: Amidohy 22.3 1.3E+02 0.0029 22.4 3.5 15 89-103 161-175 (273)
94 PRK06755 hypothetical protein; 22.2 57 0.0012 26.5 1.7 20 50-69 165-184 (209)
95 PF00102 Y_phosphatase: Protei 22.1 3.1E+02 0.0067 20.3 5.4 49 40-88 186-234 (235)
96 PF04928 PAP_central: Poly(A) 21.9 1.5E+02 0.0034 24.9 4.2 56 28-89 7-62 (254)
97 TIGR00183 prok_nadp_idh isocit 21.6 1.4E+02 0.003 27.1 4.1 36 8-60 357-392 (416)
98 PF12385 Peptidase_C70: Papain 21.5 37 0.00081 28.1 0.5 25 35-60 90-114 (166)
99 PRK06661 hypothetical protein; 21.2 34 0.00073 27.8 0.1 31 37-67 137-171 (231)
100 PF10798 YmgB: Biofilm develop 21.1 1E+02 0.0022 21.2 2.5 24 38-61 2-25 (61)
101 TIGR02624 rhamnu_1P_ald rhamnu 21.1 68 0.0015 27.0 1.9 32 37-68 189-224 (270)
102 smart00346 HTH_ICLR helix_turn 21.0 1.2E+02 0.0026 19.8 2.8 46 43-95 6-52 (91)
103 PF07904 Eaf7: Chromatin modif 20.6 75 0.0016 22.9 1.8 21 55-75 42-63 (91)
104 TIGR00281 segregation and cond 20.4 2.1E+02 0.0045 23.3 4.5 53 48-110 93-145 (186)
105 COG1522 Lrp Transcriptional re 20.4 1.1E+02 0.0024 21.9 2.7 54 40-100 6-59 (154)
106 PF02186 TFIIE_beta: TFIIE bet 20.2 3E+02 0.0065 18.9 4.8 45 53-110 17-61 (65)
107 PF03283 PAE: Pectinacetyleste 20.2 45 0.00098 29.2 0.7 40 54-96 322-361 (361)
108 PRK08734 lipid A biosynthesis 20.1 1.8E+02 0.0039 24.1 4.2 46 76-121 169-214 (305)
No 1
>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=95.78 E-value=0.013 Score=39.04 Aligned_cols=38 Identities=24% Similarity=0.613 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHHhC-CcchhhhhHHHHHhccCCCCchhH
Q 031883 42 SIAQSLYGIIKQHG-PLTVSNTWIHAKDAGISGLNGKTH 79 (151)
Q Consensus 42 tItr~l~dIlkeHG-PLTVsntW~hake~gi~gL~SK~H 79 (151)
|+..+.+.||+++| |+|+.+.|+.+++.|+-.-.+|+=
T Consensus 2 t~~eaa~~vL~~~~~pm~~~eI~~~i~~~~~~~~~~k~p 40 (72)
T PF05066_consen 2 TFKEAAYEVLEEAGRPMTFKEIWEEIQERGLYKKSGKTP 40 (72)
T ss_dssp -HHHHHHHHHHHH-S-EEHHHHHHHHHHHHTS---GGGG
T ss_pred CHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCCCcccCCH
Confidence 56788999999998 999999999999998876656653
No 2
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=90.99 E-value=0.24 Score=39.03 Aligned_cols=27 Identities=11% Similarity=0.412 Sum_probs=24.6
Q ss_pred ChHHHHHHHHHHHHHHHHhCCcchhhh
Q 031883 36 PTQQAYSIAQSLYGIIKQHGPLTVSNT 62 (151)
Q Consensus 36 P~Eqa~tItr~l~dIlkeHGPLTVsnt 62 (151)
-+||...|...|.+++++||.+|+.+-
T Consensus 6 T~eer~eLk~rIvElVRe~GRiTi~ql 32 (127)
T PF06163_consen 6 TPEEREELKARIVELVREHGRITIKQL 32 (127)
T ss_pred CHHHHHHHHHHHHHHHHHcCCccHHHH
Confidence 379999999999999999999999863
No 3
>PF03981 Ubiq_cyt_C_chap: Ubiquinol-cytochrome C chaperone ; InterPro: IPR021150 Saccharomyces cerevisiae ubiquinol-cytochrome C chaperone is required for assembly of coenzyme QF-2-cytochrome C reductase. It appears to be found in a number of different organisms including Homo sapiens, Caenorhabditis elegans and Rhizobium meliloti. This entry also contains bacterial proteins belonging to the UPF0174 family.
Probab=83.93 E-value=4.4 Score=29.38 Aligned_cols=51 Identities=18% Similarity=0.275 Sum_probs=43.2
Q ss_pred CCChHHHHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccc
Q 031883 34 KVPTQQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRK 91 (151)
Q Consensus 34 kvP~Eqa~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq 91 (151)
+.-++++..|.|.|+|.+ ..+.++++.|.|++.+.....||-|-..+.++-
T Consensus 28 k~~~~~~~~~~q~l~~~~-------~~d~~~~l~~~gv~d~~~~k~~k~l~~~~~g~~ 78 (141)
T PF03981_consen 28 KAEGKEGKELEQALFDKF-------FEDMDERLREMGVGDLSVGKRMKKLQEQFYGRL 78 (141)
T ss_pred ccccccHHHHHHHHHHHH-------HHHHHHHHHHhcCcchhhhHHHHHHHHHHHHHH
Confidence 333378899999999987 568999999999999999999999888877764
No 4
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=83.01 E-value=4.8 Score=28.75 Aligned_cols=61 Identities=13% Similarity=0.201 Sum_probs=47.5
Q ss_pred HHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceeeecCCC
Q 031883 46 SLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHSTLPE 113 (151)
Q Consensus 46 ~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLytt~~~ 113 (151)
.|.+||=++||+|+.+..+++.+. .++ +++=.+-+|+=|-++..|... .. .+.|+|++-.+
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~l~~~--~~~-~~sTv~t~L~rL~~Kg~l~~~--~~--gr~~~Y~p~is 67 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEALPEE--RSW-AYSTVQTLLNRLVEKGFLTRE--KI--GRAYVYSPLIS 67 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHCTT--SS---HHHHHHHHHHHHHTTSEEEE--EE--TTCEEEEESSS
T ss_pred HHHHHHHhCCCCCHHHHHHHHHhc--ccc-chhHHHHHHHHHHhCCceeEe--ec--CCceEEEeCCc
Confidence 578999999999999999999887 555 566777888889999988764 22 46899986543
No 5
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=82.41 E-value=6.4 Score=31.93 Aligned_cols=59 Identities=20% Similarity=0.346 Sum_probs=47.4
Q ss_pred CCCChHHHHHHHHHHHHHHHHhCCcchhhhhHHHHHh---ccCCCCchhHHHHHHHHhhcccee
Q 031883 33 PKVPTQQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDA---GISGLNGKTHMKIMLKWMRGRKML 93 (151)
Q Consensus 33 pkvP~Eqa~tItr~l~dIlkeHGPLTVsntW~hake~---gi~gL~SK~HMKimLkWMreRq~l 93 (151)
.....++...++..|.+.|+++||+|-++.-+++.+. +..+.. ...+.+|..|..+-.|
T Consensus 76 ~~~~~~~~~~~~~~v~~~L~~~gplt~~eL~~~l~~~~~~~~~~~~--~~~~~~l~~l~~~G~l 137 (327)
T PF06224_consen 76 LGLTPEELERLAEAVLDALRADGPLTRAELREALAEAGWWGWGGPS--SPWKHLLEYLWYRGLL 137 (327)
T ss_pred cccccchHHHHHHHHHHHHHhcCCCCHHHHHHHhhhccccCCCCCC--chHHHHHHHHHhCCeE
Confidence 4567778888999999999999999999999999888 444333 3677888888877654
No 6
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=78.13 E-value=5 Score=26.26 Aligned_cols=39 Identities=18% Similarity=0.255 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHhCCcchhhhhHHHHHh-ccCCCCc
Q 031883 38 QQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDA-GISGLNG 76 (151)
Q Consensus 38 Eqa~tItr~l~dIlkeHGPLTVsntW~hake~-gi~gL~S 76 (151)
+-+..+++.|.+||..-|||..+..=.++.++ |++-+.+
T Consensus 8 ~~~~~L~~~i~~Iv~~EgPI~~~~L~~Ri~~a~G~~R~G~ 47 (52)
T PF11784_consen 8 EYRPQLARMIRQIVEVEGPIHEDELARRIARAWGLSRAGS 47 (52)
T ss_pred hHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHcCcccchH
Confidence 34567999999999999999999999988888 8875554
No 7
>COG0235 AraD Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases [Carbohydrate transport and metabolism]
Probab=75.83 E-value=3.4 Score=33.11 Aligned_cols=31 Identities=19% Similarity=0.358 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHHHHhCCcchhhhhHHHHHh
Q 031883 39 QAYSIAQSLYGIIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 39 qa~tItr~l~dIlkeHGPLTVsntW~hake~ 69 (151)
++..+.+.+.-+|+.||+++++.+++.|...
T Consensus 147 ~~~~~~~~~~~ll~~HG~~~~G~~l~eA~~~ 177 (219)
T COG0235 147 EAADLAEAVLKLLRNHGVVAWGKTLAEAVHL 177 (219)
T ss_pred HHHHHHHHHHHHHHcCCcEEECCCHHHHHHH
Confidence 3344555566679999999999998877643
No 8
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=75.05 E-value=2 Score=28.41 Aligned_cols=22 Identities=27% Similarity=0.412 Sum_probs=16.7
Q ss_pred HHHHHHHHhC--CcchhhhhHHHH
Q 031883 46 SLYGIIKQHG--PLTVSNTWIHAK 67 (151)
Q Consensus 46 ~l~dIlkeHG--PLTVsntW~hak 67 (151)
-|+|||..|| |+|.++.=.++.
T Consensus 10 gI~dii~~~g~~~ls~~eia~~l~ 33 (51)
T PF08100_consen 10 GIPDIIHNAGGGPLSLSEIAARLP 33 (51)
T ss_dssp THHHHHHHHTTS-BEHHHHHHTST
T ss_pred CcHHHHHHcCCCCCCHHHHHHHcC
Confidence 4899999998 999998755444
No 9
>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=70.65 E-value=23 Score=25.07 Aligned_cols=52 Identities=10% Similarity=0.138 Sum_probs=40.4
Q ss_pred HHHHHHHHHh-CCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEee
Q 031883 45 QSLYGIIKQH-GPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCN 98 (151)
Q Consensus 45 r~l~dIlkeH-GPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~Cn 98 (151)
++|+++|.++ +|+|+.+.|+.+++.|.+ -|..=--.-|+.+.+..+|.-+..
T Consensus 11 ~~Il~~l~~~~~~~ta~ei~~~l~~~~~~--is~~TVYR~L~~L~e~Gli~~~~~ 63 (120)
T PF01475_consen 11 LAILELLKESPEHLTAEEIYDKLRKKGPR--ISLATVYRTLDLLEEAGLIRKIEF 63 (120)
T ss_dssp HHHHHHHHHHSSSEEHHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHhhhccCC--cCHHHHHHHHHHHHHCCeEEEEEc
Confidence 4688999887 599999999999976543 144556678999999999987654
No 10
>PRK06474 hypothetical protein; Provisional
Probab=69.78 E-value=5.5 Score=31.25 Aligned_cols=46 Identities=13% Similarity=0.165 Sum_probs=33.9
Q ss_pred HHHHHHHHHhCC-cchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 45 QSLYGIIKQHGP-LTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 45 r~l~dIlkeHGP-LTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
..|+++|.++|+ +|+.+..+++. +++.-+.-+|+++|.+ -.+|+.+
T Consensus 14 ~~Il~~L~~~~~~~ta~el~~~l~--~is~aTvYrhL~~L~e----~GLI~~~ 60 (178)
T PRK06474 14 MKICQVLMRNKEGLTPLELVKILK--DVPQATLYRHLQTMVD----SGILHVV 60 (178)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhc--CCCHHHHHHHHHHHHH----CCCEEEe
Confidence 568888988875 99999998875 4555566789888754 4555544
No 11
>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=68.10 E-value=22 Score=24.61 Aligned_cols=50 Identities=12% Similarity=0.221 Sum_probs=37.5
Q ss_pred HHHHHHHHH-hCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 45 QSLYGIIKQ-HGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 45 r~l~dIlke-HGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
+.|+++|.+ ++|+|+.+.++.+++.|.+ -|..=--..|+.|.+.-+|+-+
T Consensus 4 ~~Il~~l~~~~~~~sa~ei~~~l~~~~~~--i~~~TVYR~L~~L~~~Gli~~~ 54 (116)
T cd07153 4 LAILEVLLESDGHLTAEEIYERLRKKGPS--ISLATVYRTLELLEEAGLVREI 54 (116)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHhcCCC--CCHHHHHHHHHHHHhCCCEEEE
Confidence 457888877 5799999999999987532 2344455678888888888765
No 12
>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=65.06 E-value=28 Score=26.03 Aligned_cols=60 Identities=15% Similarity=0.212 Sum_probs=43.9
Q ss_pred HHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceeeecCC
Q 031883 46 SLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHSTLP 112 (151)
Q Consensus 46 ~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLytt~~ 112 (151)
.|.++|-++||+|+.+.-+++.+. .|++ ++=+.-+|+=|-++..|...-+ | +.|+|++--
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~--~~~~-~tTv~T~L~rL~~KG~v~~~k~--g--r~~~Y~p~v 67 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEK--KDWS-DSTIKTLLGRLVDKGCLTTEKE--G--RKFIYTALV 67 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhc--cCCc-HHHHHHHHHHHHHCCceeeecC--C--CcEEEEecC
Confidence 377888899999999999988764 3443 5566777777888888866532 3 578998543
No 13
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=61.05 E-value=6.8 Score=32.82 Aligned_cols=37 Identities=22% Similarity=0.495 Sum_probs=31.7
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHH
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIML 84 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimL 84 (151)
+.|.-+|++|||+|+++- +++.||+.-.=++||.-+-
T Consensus 14 ~~il~lL~~~g~~sa~el---A~~Lgis~~avR~HL~~Le 50 (218)
T COG2345 14 ERILELLKKSGPVSADEL---AEELGISPMAVRRHLDDLE 50 (218)
T ss_pred HHHHHHHhccCCccHHHH---HHHhCCCHHHHHHHHHHHH
Confidence 567888999999999974 7788999999999998764
No 14
>TIGR01086 fucA L-fuculose phosphate aldolase. Members of this family are L-fuculose phosphate aldolase from various Proteobacteria, encoded in fucose utilization operons. Homologs in other bacteria given similar annotation may share extensive sequence similarity but are not experimenally characterized and are not found in apparent fucose utilization operons; we consider their annotation as L-fuculose phosphate aldolase to be tenuous. This model has been narrowed in scope from the previous version.
Probab=60.61 E-value=9.8 Score=30.12 Aligned_cols=32 Identities=16% Similarity=0.260 Sum_probs=25.5
Q ss_pred hHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHH
Q 031883 37 TQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKD 68 (151)
Q Consensus 37 ~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake 68 (151)
.|.++.+...+-| +|+.||+++++.++..|..
T Consensus 133 ~~la~~v~~~~~~~~~vLL~nHG~~~~G~~l~eA~~ 168 (214)
T TIGR01086 133 TKLASEVVAGILKSKAILLLHHGLIIACENLLKALW 168 (214)
T ss_pred HHHHHHHHHHhhhCCEEehhcCCCEEecCCHHHHHH
Confidence 4667777777765 7899999999999888754
No 15
>PRK08333 L-fuculose phosphate aldolase; Provisional
Probab=60.46 E-value=6.3 Score=30.35 Aligned_cols=44 Identities=20% Similarity=0.294 Sum_probs=29.0
Q ss_pred ccccccCCCCChHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 26 VNVRKINPKVPTQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 26 v~~r~I~pkvP~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
+.+-|..+.--.|-|..+++.|-+ ||+.||.++++.+++.|.+.
T Consensus 121 v~v~~~~~~g~~~la~~~~~~l~~~~~vll~nHGv~~~G~~~~eA~~~ 168 (184)
T PRK08333 121 IPILPFRPAGSVELAEQVAEAMKEYDAVIMERHGIVTVGRSLREAFYK 168 (184)
T ss_pred EeeecCCCCCcHHHHHHHHHHhccCCEEEEcCCCCEEEcCCHHHHHHH
Confidence 333343332234556666666644 68899999999999888653
No 16
>PRK08660 L-fuculose phosphate aldolase; Provisional
Probab=59.89 E-value=5.5 Score=30.61 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=27.4
Q ss_pred ChHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 36 PTQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 36 P~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
..|-|+.++++|-| ||+.||.++++.+.+.|...
T Consensus 125 ~~~la~~v~~~l~~~~~vll~nHG~~~~G~~i~~A~~~ 162 (181)
T PRK08660 125 SGELAENVARALSEHKGVVVRGHGTFAIGKTLEEAYIY 162 (181)
T ss_pred CHHHHHHHHHHHhhCCEEEEcCCCceEeCCCHHHHHHH
Confidence 45667888887766 78999999999999887654
No 17
>PRK05874 L-fuculose-phosphate aldolase; Validated
Probab=59.86 E-value=5.6 Score=32.07 Aligned_cols=44 Identities=16% Similarity=0.178 Sum_probs=32.8
Q ss_pred ccccccCCCCChHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 26 VNVRKINPKVPTQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 26 v~~r~I~pkvP~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
+.+-+..+.--.|.++.|++.|-| ||+.||.++++.+++.|...
T Consensus 128 v~~~~y~~~gs~ela~~v~~~l~~~~~vlL~nHGv~~~G~~l~~A~~~ 175 (217)
T PRK05874 128 VRCTEYAASGTPEVGRNAVRALEGRAAALIANHGLVAVGPRPDQVLRV 175 (217)
T ss_pred eeeecCCCCCcHHHHHHHHHHhCcCCEEEEcCCCCeEecCCHHHHHHH
Confidence 334444444446888888888866 78999999999999887665
No 18
>PRK08193 araD L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=59.43 E-value=6.2 Score=31.84 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHH-----------HHHHhCCcchhhhhHHHHHh
Q 031883 38 QQAYSIAQSLYG-----------IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 38 Eqa~tItr~l~d-----------IlkeHGPLTVsntW~hake~ 69 (151)
|.+..|+..|-+ ||+.||.++++.++..|...
T Consensus 143 ~~~~~ia~~l~~~~~~~~~~~avLl~nHG~v~~G~~l~eA~~~ 185 (231)
T PRK08193 143 ETGKVIVETFEKRGIDPAAVPGVLVHSHGPFTWGKDAEDAVHN 185 (231)
T ss_pred hHHHHHHHHHhhccCCcccCCEEEEcCCCceEecCCHHHHHHH
Confidence 678888888864 68999999999999887643
No 19
>PRK06833 L-fuculose phosphate aldolase; Provisional
Probab=54.50 E-value=7 Score=30.94 Aligned_cols=30 Identities=20% Similarity=0.249 Sum_probs=22.1
Q ss_pred HHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 40 AYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 40 a~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
++.|++.|-+ ||+.||.++++++++.|...
T Consensus 139 a~~v~~~l~~~~~vll~nHGv~~~G~~~~eA~~~ 172 (214)
T PRK06833 139 AENAFEAMEDRRAVLLANHGLLAGANNLKNAFNI 172 (214)
T ss_pred HHHHHHHhCcCCEEEECCCCCEEEeCCHHHHHHH
Confidence 4555555533 67899999999999987654
No 20
>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=54.10 E-value=14 Score=22.36 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhCCcchhhhhHHHHHhccCC
Q 031883 44 AQSLYGIIKQHGPLTVSNTWIHAKDAGISG 73 (151)
Q Consensus 44 tr~l~dIlkeHGPLTVsntW~hake~gi~g 73 (151)
-+.|++.|.++|.+|+.+. ++..|++.
T Consensus 5 ~~~Il~~l~~~~~~t~~el---a~~~~is~ 31 (48)
T PF13412_consen 5 QRKILNYLRENPRITQKEL---AEKLGISR 31 (48)
T ss_dssp HHHHHHHHHHCTTS-HHHH---HHHHTS-H
T ss_pred HHHHHHHHHHcCCCCHHHH---HHHhCCCH
Confidence 4678999999999999864 55567663
No 21
>PF05397 Med15_fungi: Mediator complex subunit 15; InterPro: IPR008626 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family represents subunit 15 of the Mediator complex in fungi. It contains Saccharomyces cerevisiae GAL11 (Med15) protein. Gal11 (Med15) and Sin4 (Med16) proteins are S. cerevisiae global transcription factors that regulate transcription of a variety of genes, both positively and negatively. Gal11, in a major part, functions in the activation of transcription, whereas Sin4 has an opposite role [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=54.07 E-value=35 Score=25.65 Aligned_cols=76 Identities=17% Similarity=0.235 Sum_probs=52.1
Q ss_pred HHHHHHHHhhhhhhccccccccCCCCChHHHHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHH
Q 031883 10 SMETLVRYYSSSRKAAVNVRKINPKVPTQQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLK 85 (151)
Q Consensus 10 ~~~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLk 85 (151)
.++.+.+-++.-.+..++..||.--..+||-.+|++.|-++.---|=+.==-.|-..=--.-.+++.=-.||+|++
T Consensus 4 ~~~~ik~l~~e~~~~~~~l~~v~~~ls~eeK~~i~~~l~~~~~m~~~vd~li~~f~~lt~ne~~~k~LlqMr~~~~ 79 (115)
T PF05397_consen 4 LPERIKQLYEEVSRNPVRLSPVTNSLSPEEKAAIRQQLQEIQDMLARVDSLIPWFYKLTKNEENTKRLLQMRIMLK 79 (115)
T ss_pred hHHHHHHHHHHHHhcCCCCCcccccCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHH
Confidence 3678889999888999999999999999999999999877654333222222333332234445555566776664
No 22
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=53.75 E-value=15 Score=23.54 Aligned_cols=39 Identities=26% Similarity=0.361 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHH
Q 031883 44 AQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLK 85 (151)
Q Consensus 44 tr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLk 85 (151)
-..|++.|..+||+|+++.=+ +.|++-=+=..|++.|.+
T Consensus 12 R~~Il~~L~~~~~~t~~ela~---~l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 12 RLRILRLLASNGPMTVSELAE---ELGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HHHHHHHHHHCSTBEHHHHHH---HHTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCHHHHHH---HHCCCHHHHHHHHHHHHH
Confidence 357888889999999998644 335554445578887754
No 23
>PRK06512 thiamine-phosphate pyrophosphorylase; Provisional
Probab=53.74 E-value=44 Score=27.12 Aligned_cols=67 Identities=12% Similarity=0.086 Sum_probs=49.6
Q ss_pred CCCChHHHHHHHHHHHHHHHHhC-CcchhhhhHHHHHhccCCC--Cch-hHHHHHHHHhhccceeeEEeec
Q 031883 33 PKVPTQQAYSIAQSLYGIIKQHG-PLTVSNTWIHAKDAGISGL--NGK-THMKIMLKWMRGRKMLKLFCNG 99 (151)
Q Consensus 33 pkvP~Eqa~tItr~l~dIlkeHG-PLTVsntW~hake~gi~gL--~SK-~HMKimLkWMreRq~lKL~Cnh 99 (151)
...+.++...+.+.|.++.+++| ||-|.+-|+-+.+.|..|+ ... -.....-+-+....+|=++|.|
T Consensus 49 K~l~~~~~~~~a~~l~~l~~~~gv~liINd~~dlA~~~~adGVHLg~~d~~~~~~r~~~~~~~iiG~s~~~ 119 (221)
T PRK06512 49 YGLDEATFQKQAEKLVPVIQEAGAAALIAGDSRIAGRVKADGLHIEGNLAALAEAIEKHAPKMIVGFGNLR 119 (221)
T ss_pred CCCCHHHHHHHHHHHHHHHHHhCCEEEEeCHHHHHHHhCCCEEEECccccCHHHHHHhcCCCCEEEecCCC
Confidence 34678888999999999999987 9999999999999998875 221 1233333344456678888766
No 24
>PF07237 DUF1428: Protein of unknown function (DUF1428); InterPro: IPR009874 This family consists of several hypothetical bacterial and one archaeal sequence of around 120 residues in length. The function of this family is unknown.; PDB: 2OKQ_A.
Probab=53.65 E-value=10 Score=28.82 Aligned_cols=25 Identities=28% Similarity=0.539 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHhCCcchhhhhHH
Q 031883 41 YSIAQSLYGIIKQHGPLTVSNTWIH 65 (151)
Q Consensus 41 ~tItr~l~dIlkeHGPLTVsntW~h 65 (151)
...++.--.|.+|||.|.|-+||.-
T Consensus 19 ~~~A~~a~~vf~e~GAl~~vE~wgd 43 (103)
T PF07237_consen 19 RAMAEKAAEVFKEHGALRVVECWGD 43 (103)
T ss_dssp HHHHHHHHHHHHHTT-SEEEEEEEE
T ss_pred HHHHHHHHHHHHHhCCEEEEEeecC
Confidence 4567778899999999999999975
No 25
>PF02581 TMP-TENI: Thiamine monophosphate synthase/TENI; InterPro: IPR003733 Thiamine monophosphate synthase (TMP) (2.5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway []. TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group [].; GO: 0004789 thiamine-phosphate diphosphorylase activity, 0009228 thiamine biosynthetic process; PDB: 3NL5_A 3NL2_A 3NM1_A 3NM3_C 3NL6_B 3NL3_A 3CEU_A 3O63_B 3QH2_C 1YAD_D ....
Probab=52.85 E-value=19 Score=27.41 Aligned_cols=65 Identities=18% Similarity=0.377 Sum_probs=42.9
Q ss_pred CChHHHHHHHHHHHHHHHHhC-CcchhhhhHHHHHhccCCCC-chhHH--HHHHHHhhccceeeEEeec
Q 031883 35 VPTQQAYSIAQSLYGIIKQHG-PLTVSNTWIHAKDAGISGLN-GKTHM--KIMLKWMRGRKMLKLFCNG 99 (151)
Q Consensus 35 vP~Eqa~tItr~l~dIlkeHG-PLTVsntW~hake~gi~gL~-SK~HM--KimLkWMreRq~lKL~Cnh 99 (151)
.+.++-+.+.+.|.++.++++ +|-|.+-|+-+.+.|..|+- +...+ .-.-+-+....++=.+|..
T Consensus 36 ~~~~~~~~~a~~l~~~~~~~~~~liin~~~~la~~~~~dGvHl~~~~~~~~~~r~~~~~~~~ig~S~h~ 104 (180)
T PF02581_consen 36 LSDEELLELARRLAELCQKYGVPLIINDRVDLALELGADGVHLGQSDLPPAEARKLLGPDKIIGASCHS 104 (180)
T ss_dssp S-HHHHHHHHHHHHHHHHHTTGCEEEES-HHHHHHCT-SEEEEBTTSSSHHHHHHHHTTTSEEEEEESS
T ss_pred CCccHHHHHHHHHHHHhhcceEEEEecCCHHHHHhcCCCEEEecccccchHHhhhhcccceEEEeecCc
Confidence 467888899999999998875 99999999999999988762 11111 1111223345677777753
No 26
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=51.41 E-value=14 Score=22.79 Aligned_cols=36 Identities=28% Similarity=0.417 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHH
Q 031883 46 SLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLK 85 (151)
Q Consensus 46 ~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLk 85 (151)
.|...|.+ ||++|.+..+++ |++-=+=.+|++.|..
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l---~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEEL---GLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHH---TS-HHHHHHHHHHHHH
T ss_pred HHHHHHHh-CCCchhhHHHhc---cccchHHHHHHHHHHH
Confidence 35566666 999999887665 3332223378877654
No 27
>PRK06557 L-ribulose-5-phosphate 4-epimerase; Validated
Probab=49.98 E-value=7.6 Score=30.73 Aligned_cols=34 Identities=21% Similarity=0.262 Sum_probs=27.0
Q ss_pred ChHHHHHHHHHH------HHHHHHhCCcchhhhhHHHHHh
Q 031883 36 PTQQAYSIAQSL------YGIIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 36 P~Eqa~tItr~l------~dIlkeHGPLTVsntW~hake~ 69 (151)
-.|.+..|++.| .=+|+.||.++++.+.+.|...
T Consensus 141 ~~ela~~i~~~l~~~~~~~vll~nHG~~~~G~~~~eA~~~ 180 (221)
T PRK06557 141 DEAIGKGIVETLKGGRSPAVLMQNHGVFTIGKDAEDAVKA 180 (221)
T ss_pred cHHHHHHHHHHhCcCCCCEEEECCCCceEEcCCHHHHHHH
Confidence 346788888887 3478999999999999887654
No 28
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=49.48 E-value=18 Score=24.16 Aligned_cols=44 Identities=11% Similarity=0.204 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhCC--cchhhhhHHHHHhccCCCCchhHHHHHHHHhhcccee
Q 031883 43 IAQSLYGIIKQHGP--LTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKML 93 (151)
Q Consensus 43 Itr~l~dIlkeHGP--LTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~l 93 (151)
.-+.|++.|+++|+ +|.++-+..+ |++ ++ -....|.=|.+.-.|
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l---gl~---~~-~v~r~L~~L~~~G~V 52 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL---GLP---KK-EVNRVLYSLEKKGKV 52 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH---CCC---HH-HHHHHHHHHHHCCCE
Confidence 34789999999999 9999887544 444 43 344444445555544
No 29
>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=49.43 E-value=14 Score=23.98 Aligned_cols=42 Identities=17% Similarity=0.425 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhcccee
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKML 93 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~l 93 (151)
+.|.++|+++|.+||.+- ++.-|+|.-+-.+.. .-+.+...|
T Consensus 3 ~~Il~~l~~~~~~s~~el---a~~~~VS~~TiRRDl----~~L~~~g~i 44 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKEL---AEEFGVSEMTIRRDL----NKLEKQGLI 44 (57)
T ss_pred HHHHHHHHHcCCEEHHHH---HHHHCcCHHHHHHHH----HHHHHCCCE
Confidence 468899999999999976 444577655544444 444455543
No 30
>PRK09462 fur ferric uptake regulator; Provisional
Probab=47.77 E-value=23 Score=26.33 Aligned_cols=50 Identities=8% Similarity=0.152 Sum_probs=36.9
Q ss_pred HHHHHHHHHh--CCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 45 QSLYGIIKQH--GPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 45 r~l~dIlkeH--GPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
++|+++|.++ +|+|+.+..+.+++.+-+ -|..=-=..|+.+.+-.+|+-+
T Consensus 20 ~~Il~~l~~~~~~h~sa~eI~~~l~~~~~~--i~~aTVYR~L~~L~e~Gli~~~ 71 (148)
T PRK09462 20 LKILEVLQEPDNHHVSAEDLYKRLIDMGEE--IGLATVYRVLNQFDDAGIVTRH 71 (148)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHHHhhCCC--CCHHHHHHHHHHHHHCCCEEEE
Confidence 4578888764 699999999999998743 2233445678888888888655
No 31
>PRK06357 hypothetical protein; Provisional
Probab=47.25 E-value=15 Score=29.58 Aligned_cols=40 Identities=18% Similarity=0.287 Sum_probs=26.1
Q ss_pred ccCCCCChHHHHHHHHHHHH----------HHHHhCCcchhhhhHHHHHh
Q 031883 30 KINPKVPTQQAYSIAQSLYG----------IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 30 ~I~pkvP~Eqa~tItr~l~d----------IlkeHGPLTVsntW~hake~ 69 (151)
|+.+..-.|-|+.++..+-+ ||+.||.++++.+++.|...
T Consensus 135 p~~~~gs~ela~~v~~~l~~~~~~~~~~~vLl~nHGvv~~G~~l~eA~~~ 184 (216)
T PRK06357 135 PFAPATSPELAEIVRKHLIELGDKAVPSAFLLNSHGIVITDTSLHKAYDI 184 (216)
T ss_pred cccCCCcHHHHHHHHHHHhhcCcccCCCEEEECCCCCeEecCCHHHHHHH
Confidence 44443334555555555543 57889999999998877543
No 32
>PF09582 AnfO_nitrog: Iron only nitrogenase protein AnfO (AnfO_nitrog); InterPro: IPR014287 Proteins in this entry include Anf1 from Rhodobacter capsulatus (Rhodopseudomonas capsulata) and AnfO from Azotobacter vinelandii. They are found exclusively in species which contain the iron-only nitrogenase, and are encoded immediately downstream of the structural genes for the nitrogenase enzyme in these species.
Probab=46.45 E-value=22 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.626 Sum_probs=24.0
Q ss_pred ccCCCCchhHHHHHHHHhhccce--eeEEeeccC
Q 031883 70 GISGLNGKTHMKIMLKWMRGRKM--LKLFCNGVG 101 (151)
Q Consensus 70 gi~gL~SK~HMKimLkWMreRq~--lKL~CnhvG 101 (151)
...||||| ++++-.+++... |.++|+|+=
T Consensus 146 ~~~~ltSK---qvL~PFL~~~~F~~LeViC~HvP 176 (202)
T PF09582_consen 146 KNPGLTSK---QVLIPFLRNGPFRRLEVICDHVP 176 (202)
T ss_pred hCCCCcHH---HHHHHHhcCCCceEEEEEeCCCC
Confidence 78899998 689999998754 566799984
No 33
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=46.41 E-value=77 Score=20.30 Aligned_cols=45 Identities=24% Similarity=0.445 Sum_probs=32.5
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
-.|+.+|.++|++|+++- ++..+++ +.-..-.|+-|.++..|...
T Consensus 13 ~~il~~l~~~~~~~~~~l---a~~~~~s----~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEEGPLSVSEL---AKRLGVS----PSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHcCCcCHHHH---HHHHCCC----chhHHHHHHHHHHCCCeEec
Confidence 457888999999988754 4445554 44455778888889888765
No 34
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=45.20 E-value=36 Score=19.68 Aligned_cols=17 Identities=18% Similarity=0.468 Sum_probs=13.9
Q ss_pred HHHHHHHHhCCcchhhh
Q 031883 46 SLYGIIKQHGPLTVSNT 62 (151)
Q Consensus 46 ~l~dIlkeHGPLTVsnt 62 (151)
.|+++|.++|++|+.+-
T Consensus 4 ~il~~l~~~~~~s~~~l 20 (53)
T smart00420 4 QILELLAQQGKVSVEEL 20 (53)
T ss_pred HHHHHHHHcCCcCHHHH
Confidence 57888889999998854
No 35
>cd07977 TFIIE_beta_winged_helix TFIIE_beta_winged_helix domain, located at the central core region of TFIIE beta, with double-stranded DNA binding activity. Transcription Factor IIE (TFIIE) beta winged-helix (or forkhead) domain is located at the central core region of TFIIE beta. The winged-helix is a form of helix-turn-helix (HTH) domain which typically binds DNA with the 3rd helix. The winged-helix domain is distinguished by the presence of a C-terminal beta-strand hairpin unit (the wing) that packs against the cleft of the tri-helical core. Although most winged-helix domains are multi-member families, TFIIE beta winged-helix domain is typically found as a single orthologous group. TFIIE is one of the six eukaryotic general transcription factors (TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are required for transcription initiation of protein-coding genes. TFIIE is a heterotetramer consisting of two copies each of alpha and beta subunits. TFIIE beta contains several functional
Probab=44.14 E-value=51 Score=23.09 Aligned_cols=52 Identities=15% Similarity=0.285 Sum_probs=35.0
Q ss_pred HHHHHHHhC--CcchhhhhHHHHHhccCCCCchhHHHHHHHHhhcccee---eEEeeccCCCcceeeec
Q 031883 47 LYGIIKQHG--PLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKML---KLFCNGVGSNKKFLHST 110 (151)
Q Consensus 47 l~dIlkeHG--PLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~l---KL~CnhvG~~KqFLytt 110 (151)
+.+.+|+++ |||+.|.=+++....++ ..++.|+++--.+ +..- ..-+|.|.+
T Consensus 14 aV~ymK~r~~~Plt~~EIl~~ls~~d~~--------~~~~~~L~~~~~~~n~~~~~----~~~tf~fkP 70 (75)
T cd07977 14 IVDYMKKRHQHPLTLDEILDYLSLLDIG--------PKLKEWLKSEALVNNPKIDP----KDGTFSFKP 70 (75)
T ss_pred HHHHHHhcCCCCccHHHHHHHHhccCcc--------HHHHHHHHhhhhccCceecc----CCCEEEecc
Confidence 456777776 99999999998874444 5567899854444 4332 134777764
No 36
>PRK07490 hypothetical protein; Provisional
Probab=43.81 E-value=9.9 Score=31.03 Aligned_cols=31 Identities=26% Similarity=0.311 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHH----HHHHhCCcchhhhhHHHHH
Q 031883 38 QQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKD 68 (151)
Q Consensus 38 Eqa~tItr~l~d----IlkeHGPLTVsntW~hake 68 (151)
|.++.++++|-| ||+.||.++++.+++.|-.
T Consensus 147 ela~~v~~~l~~~~avlL~nHG~v~~G~~~~eA~~ 181 (245)
T PRK07490 147 EEGERLAGLLGDKRRLLMGNHGVLVTGDTVAEAFD 181 (245)
T ss_pred HHHHHHHHHhCcCCEEEECCCCcEEecCCHHHHHH
Confidence 667777776644 6889999999999887753
No 37
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=41.85 E-value=39 Score=23.18 Aligned_cols=34 Identities=15% Similarity=0.427 Sum_probs=25.5
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHhC-CcchhhhhH
Q 031883 31 INPKVPTQQAYSIAQSLYGIIKQHG-PLTVSNTWI 64 (151)
Q Consensus 31 I~pkvP~Eqa~tItr~l~dIlkeHG-PLTVsntW~ 64 (151)
+.|..+.++..++...+.++|.++| -+.--+.|+
T Consensus 9 l~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G 43 (92)
T PF01250_consen 9 LRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWG 43 (92)
T ss_dssp E-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEE
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEe
Confidence 4578899999999999999999985 444444443
No 38
>PRK03634 rhamnulose-1-phosphate aldolase; Provisional
Probab=41.79 E-value=17 Score=30.44 Aligned_cols=40 Identities=13% Similarity=0.016 Sum_probs=27.9
Q ss_pred ccCCCCChHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 30 KINPKVPTQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 30 ~I~pkvP~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
|..+.--.|.|+.++..|-| ||+.||.++++.+++.|-..
T Consensus 184 py~~pgs~eLa~~v~~~l~~~~avLL~nHGvv~~G~~l~eA~~~ 227 (274)
T PRK03634 184 PWMVPGTDEIGQATAEKMQKHDLVLWPKHGVFGSGPTLDEAFGL 227 (274)
T ss_pred cCCCCCCHHHHHHHHHHhccCCEEEEcCCCCeEecCCHHHHHHH
Confidence 33333345677777776643 58999999999999887643
No 39
>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=40.68 E-value=1.1e+02 Score=20.39 Aligned_cols=59 Identities=12% Similarity=0.089 Sum_probs=48.3
Q ss_pred HHHHHHHHHHHHHHhCCcchhhhhHHHHHh-ccCCCCchhHHHHHHHHhhccceeeEEee
Q 031883 40 AYSIAQSLYGIIKQHGPLTVSNTWIHAKDA-GISGLNGKTHMKIMLKWMRGRKMLKLFCN 98 (151)
Q Consensus 40 a~tItr~l~dIlkeHGPLTVsntW~hake~-gi~gL~SK~HMKimLkWMreRq~lKL~Cn 98 (151)
...|--+|..|+|.+.-++.++-.+.+.+. .-...-+-.+.|--+.++-+|.-|+...+
T Consensus 6 ~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~ 65 (68)
T PF10557_consen 6 KYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDED 65 (68)
T ss_dssp HHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEESS
T ss_pred hhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCCC
Confidence 355677899999999999999999999988 44667888999999999999999887654
No 40
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=39.89 E-value=1.4e+02 Score=21.27 Aligned_cols=55 Identities=11% Similarity=0.232 Sum_probs=42.0
Q ss_pred CCCChHHHHHHHHHHHHHHH---HhCCcchhhhhHHHHHh--ccC--------CCCchhHHHHHHHHhh
Q 031883 33 PKVPTQQAYSIAQSLYGIIK---QHGPLTVSNTWIHAKDA--GIS--------GLNGKTHMKIMLKWMR 88 (151)
Q Consensus 33 pkvP~Eqa~tItr~l~dIlk---eHGPLTVsntW~hake~--gi~--------gL~SK~HMKimLkWMr 88 (151)
-..|++|+.++-..+.+++. + .=.++.+++...++. +++ ++=|-.++|.+..+|-
T Consensus 10 ~~fs~~q~s~~~~i~~~ll~~~i~-~~~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~~y~~ 77 (101)
T PF14769_consen 10 QGFSWEQTSAFLSILKELLEKNIE-KGMSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAIIDYFH 77 (101)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHH-ccCCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHHHHHH
Confidence 35678888776666666666 6 888999999999998 444 4468889999988874
No 41
>PRK08087 L-fuculose phosphate aldolase; Provisional
Probab=38.37 E-value=22 Score=28.24 Aligned_cols=33 Identities=15% Similarity=0.174 Sum_probs=24.3
Q ss_pred hHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 37 TQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 37 ~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
.|-|..+.+.|-+ +|+.||.++++++++.|-..
T Consensus 134 ~~la~~~~~~l~~~~~vLl~nHGv~~~G~~~~~A~~~ 170 (215)
T PRK08087 134 RELSEHVALALKNRKATLLQHHGLIACEVNLEKALWL 170 (215)
T ss_pred HHHHHHHHHHhCcCCEEEecCCCCEEEcCCHHHHHHH
Confidence 4556666666643 78899999999999877653
No 42
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=38.18 E-value=31 Score=22.97 Aligned_cols=23 Identities=17% Similarity=0.218 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhCCcchhhhhH
Q 031883 42 SIAQSLYGIIKQHGPLTVSNTWI 64 (151)
Q Consensus 42 tItr~l~dIlkeHGPLTVsntW~ 64 (151)
.+...+++.|-.||++|+.+.=.
T Consensus 13 ~~~~~V~~~Ll~~G~ltl~~i~~ 35 (62)
T PF08221_consen 13 EIVAKVGEVLLSRGRLTLREIVR 35 (62)
T ss_dssp HHHHHHHHHHHHC-SEEHHHHHH
T ss_pred hHHHHHHHHHHHcCCcCHHHHHH
Confidence 57788999999999999987643
No 43
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=37.71 E-value=1.1e+02 Score=23.91 Aligned_cols=67 Identities=18% Similarity=0.351 Sum_probs=52.8
Q ss_pred hHHHHHHHHHHHH-HHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceeeec
Q 031883 37 TQQAYSIAQSLYG-IIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHST 110 (151)
Q Consensus 37 ~Eqa~tItr~l~d-IlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLytt 110 (151)
.+.|+++++.++| |++|-+--.|---..-+.-.||+| -=-+++||=+.++-.|+|+.. ++++=+|+.
T Consensus 36 ~~~av~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~----SvAr~vLR~LeeeGvv~lvsk---nrR~~IY~~ 103 (107)
T COG4901 36 ARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGING----SVARIVLRHLEEEGVVQLVSK---NRRQAIYTR 103 (107)
T ss_pred hhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccch----HHHHHHHHHHHhCCceeeecc---Cccceeeec
Confidence 4667888888886 667777666666667778888886 345789999999999999975 788889974
No 44
>TIGR03328 salvage_mtnB methylthioribulose-1-phosphate dehydratase. Members of this family are the methylthioribulose-1-phosphate dehydratase of the methionine salvage pathway. This pathway allows methylthioadenosine, left over from polyamine biosynthesis, to be recycled to methionine.
Probab=37.64 E-value=9 Score=29.86 Aligned_cols=20 Identities=30% Similarity=0.566 Sum_probs=17.2
Q ss_pred HHHHhCCcchhhhhHHHHHh
Q 031883 50 IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 50 IlkeHGPLTVsntW~hake~ 69 (151)
||+.||.++++.+|+.|.+.
T Consensus 157 ll~nHGv~~~G~~~~~A~~~ 176 (193)
T TIGR03328 157 LIRGHGLYAWGRDWEEAKRH 176 (193)
T ss_pred EEcCCcceEEcCCHHHHHHH
Confidence 46789999999999998764
No 45
>PRK06486 hypothetical protein; Provisional
Probab=37.04 E-value=15 Score=30.55 Aligned_cols=31 Identities=19% Similarity=0.268 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHH----HHHHhCCcchhhhhHHHH
Q 031883 37 TQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAK 67 (151)
Q Consensus 37 ~Eqa~tItr~l~d----IlkeHGPLTVsntW~hak 67 (151)
.|.+..++..|-+ ||+.||.++++.+++.|.
T Consensus 162 ~ela~~va~al~~~~avLL~nHG~v~~G~~l~eA~ 196 (262)
T PRK06486 162 AAEGDRIARAMGDADIVFLKNHGVMVCGPRIAEAW 196 (262)
T ss_pred hhHHHHHHHHhCcCCEEEECCCCCeEecCCHHHHH
Confidence 5677777777744 689999999999887664
No 46
>PF07208 DUF1414: Protein of unknown function (DUF1414); InterPro: IPR009857 This family consists of several hypothetical bacterial proteins of around 70 residues in length. Members of this family are often referred to as YejL. The function of this family is unknown.; PDB: 2JPQ_A 2JUZ_B 2JUW_B 2QTI_A 2OTA_A 2JR2_A 2JRX_A.
Probab=36.45 E-value=26 Score=23.41 Aligned_cols=23 Identities=30% Similarity=0.459 Sum_probs=17.9
Q ss_pred cCCCCChHHHHHHHHHHHHHHHH
Q 031883 31 INPKVPTQQAYSIAQSLYGIIKQ 53 (151)
Q Consensus 31 I~pkvP~Eqa~tItr~l~dIlke 53 (151)
||-.||++|.+.|++...|.|+.
T Consensus 20 ln~~V~~~qR~~iAe~Fa~AL~~ 42 (44)
T PF07208_consen 20 LNTSVPPAQRQAIAEKFAQALKS 42 (44)
T ss_dssp HHHCS-HHHHHHHHHHHHHHHHH
T ss_pred HhhcCCHHHHHHHHHHHHHHHHh
Confidence 34578999999999998888764
No 47
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=35.73 E-value=40 Score=25.37 Aligned_cols=38 Identities=13% Similarity=0.224 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHH
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLK 85 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLk 85 (151)
+.|++.|.++||++|.+. ++..|++-=+=-.|+++|-+
T Consensus 19 l~IL~~L~~~~~~~v~el---a~~l~lsqstvS~HL~~L~~ 56 (117)
T PRK10141 19 LGIVLLLRESGELCVCDL---CTALDQSQPKISRHLALLRE 56 (117)
T ss_pred HHHHHHHHHcCCcCHHHH---HHHHCcCHHHHHHHHHHHHH
Confidence 478889999999999865 34445554444589988753
No 48
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=35.62 E-value=1.2e+02 Score=20.15 Aligned_cols=33 Identities=9% Similarity=0.266 Sum_probs=20.8
Q ss_pred hHHHHHHHHHHHHHHHHhCCcchhhhhHHHHHhccC
Q 031883 37 TQQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGIS 72 (151)
Q Consensus 37 ~Eqa~tItr~l~dIlkeHGPLTVsntW~hake~gi~ 72 (151)
|||| .|-+.||+.+- +-.++...-..+.+.|+.
T Consensus 1 peea-~vVr~if~~~~--~g~s~~~I~~~ln~~gi~ 33 (102)
T PF07508_consen 1 PEEA-EVVREIFELYL--EGYSLRQIARELNEKGIP 33 (102)
T ss_pred ChHH-HHHHHHHHHHH--cCCCHHHHHHHHHhcCCc
Confidence 3444 45566777655 556666677777778873
No 49
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=35.29 E-value=42 Score=26.09 Aligned_cols=21 Identities=19% Similarity=0.302 Sum_probs=19.1
Q ss_pred CCChHHHHHHHHHHHHHHHHh
Q 031883 34 KVPTQQAYSIAQSLYGIIKQH 54 (151)
Q Consensus 34 kvP~Eqa~tItr~l~dIlkeH 54 (151)
-.|++||++|+.++.+++.+.
T Consensus 15 Gft~~QAe~i~~~l~~~l~~~ 35 (177)
T PF07798_consen 15 GFTEEQAEAIMKALREVLNDS 35 (177)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999875
No 50
>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=35.12 E-value=86 Score=21.16 Aligned_cols=46 Identities=15% Similarity=0.151 Sum_probs=31.5
Q ss_pred HHHHHHHHh-CCcchhhhhHHHHHhccCCCC-chhHHHHHHHHhhccceee
Q 031883 46 SLYGIIKQH-GPLTVSNTWIHAKDAGISGLN-GKTHMKIMLKWMRGRKMLK 94 (151)
Q Consensus 46 ~l~dIlkeH-GPLTVsntW~hake~gi~gL~-SK~HMKimLkWMreRq~lK 94 (151)
.|+++|+++ +|++=..-=+.++.. |.+ |..-.+..|++|-+.-.++
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~---g~~~se~avRrrLr~me~~Glt~ 49 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLR---GEELSEEAVRRRLRAMERDGLTR 49 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhc---ChhhhHHHHHHHHHHHHHCCCcc
Confidence 367888888 677655554444444 444 5788899999998887444
No 51
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=34.81 E-value=44 Score=29.84 Aligned_cols=30 Identities=27% Similarity=0.360 Sum_probs=25.3
Q ss_pred cccCCCCChHHHHHHHHHHHHHHHHhCCcc
Q 031883 29 RKINPKVPTQQAYSIAQSLYGIIKQHGPLT 58 (151)
Q Consensus 29 r~I~pkvP~Eqa~tItr~l~dIlkeHGPLT 58 (151)
-+++|--|-|+|+.|||.|.|.|..-+.|.
T Consensus 105 ~r~RpG~p~dea~viSq~LhdtIl~S~ii~ 134 (298)
T KOG1613|consen 105 SRFRPGPPTDEAQVISQKLHDTILHSRIIP 134 (298)
T ss_pred cCCCCCCCchHHHHHHHHHHHHHHhcCCcc
Confidence 456778899999999999999998777664
No 52
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 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 3". 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: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=34.72 E-value=27 Score=22.94 Aligned_cols=41 Identities=17% Similarity=0.425 Sum_probs=26.9
Q ss_pred HHHHHHHhCCcchhhhhHHHHHh-ccCCCCchhHHHHHHHHhhccceeeE
Q 031883 47 LYGIIKQHGPLTVSNTWIHAKDA-GISGLNGKTHMKIMLKWMRGRKMLKL 95 (151)
Q Consensus 47 l~dIlkeHGPLTVsntW~hake~-gi~gL~SK~HMKimLkWMreRq~lKL 95 (151)
|-+++++||++||++- +|+ |+| ....--+|.+|-.....+.
T Consensus 1 i~~~~~~~~~itv~~~----rd~lg~s----RK~ai~lLE~lD~~g~T~R 42 (50)
T PF09107_consen 1 IRELLQKNGEITVAEF----RDLLGLS----RKYAIPLLEYLDREGITRR 42 (50)
T ss_dssp HHHHHHTTSSBEHHHH----HHHHTS-----HHHHHHHHHHHHHTTSEEE
T ss_pred ChHHHhcCCcCcHHHH----HHHHCcc----HHHHHHHHHHHhccCCEEE
Confidence 3478889999999974 444 543 4455567777766555543
No 53
>PF08158 NUC130_3NT: NUC130/3NT domain; InterPro: IPR012977 This N-terminal domain is found in a novel nucleolar protein family defined by NUC130/133 [].
Probab=34.61 E-value=45 Score=22.28 Aligned_cols=20 Identities=15% Similarity=0.394 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHHHHHhCC
Q 031883 37 TQQAYSIAQSLYGIIKQHGP 56 (151)
Q Consensus 37 ~Eqa~tItr~l~dIlkeHGP 56 (151)
|+++..+.+.|.|+|++|.-
T Consensus 10 p~~~~~Fp~~L~~lL~~~~~ 29 (52)
T PF08158_consen 10 PKETKDFPQELIDLLRNHHT 29 (52)
T ss_pred HHHHHHHHHHHHHHHHhccc
Confidence 67999999999999999974
No 54
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=34.44 E-value=28 Score=27.19 Aligned_cols=58 Identities=19% Similarity=0.239 Sum_probs=33.2
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE-eeccCCCcceeee
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF-CNGVGSNKKFLHS 109 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~-CnhvG~~KqFLyt 109 (151)
..++.+|+++||+||.+- ++..+++ --|=-|.+.+=| +.-++... =+-.|+--.|+|.
T Consensus 31 ~v~~~LL~~~~~~tvdel---ae~lnr~---rStv~rsl~~L~-~~GlV~Rek~~~~~Ggy~yiY~ 89 (126)
T COG3355 31 EVYKALLEENGPLTVDEL---AEILNRS---RSTVYRSLQNLL-EAGLVEREKVNLKGGGYYYLYK 89 (126)
T ss_pred HHHHHHHhhcCCcCHHHH---HHHHCcc---HHHHHHHHHHHH-HcCCeeeeeeccCCCceeEEEe
Confidence 467778889999999875 3333443 223334444433 33333222 2226777889996
No 55
>TIGR00760 araD L-ribulose-5-phosphate 4-epimerase. The homolog to this family from Mycobacterium smegmatis is flanked by putative araB and araA genes, consistent with it also being araD.
Probab=34.19 E-value=21 Score=28.94 Aligned_cols=26 Identities=15% Similarity=0.404 Sum_probs=21.4
Q ss_pred hHHHHHHHHHHHH-----------HHHHhCCcchhhh
Q 031883 37 TQQAYSIAQSLYG-----------IIKQHGPLTVSNT 62 (151)
Q Consensus 37 ~Eqa~tItr~l~d-----------IlkeHGPLTVsnt 62 (151)
+|++..+++.+-+ ||+.||.++++.+
T Consensus 143 ~~~~~~la~~l~~~~~~~~~~~avlL~nHGvv~~G~~ 179 (231)
T TIGR00760 143 LETGKVIVETFEKRGIDPAQIPGVLVHSHGPFAWGKD 179 (231)
T ss_pred HhHHHHHHHHHhhccCCcccCCEEEEcCCCceEecCC
Confidence 3778999999865 5899999998875
No 56
>PRK08130 putative aldolase; Validated
Probab=33.90 E-value=19 Score=28.45 Aligned_cols=32 Identities=22% Similarity=0.244 Sum_probs=22.9
Q ss_pred HHHHHHHHHHH----HHHHHhCCcchhhhhHHHHHh
Q 031883 38 QQAYSIAQSLY----GIIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 38 Eqa~tItr~l~----dIlkeHGPLTVsntW~hake~ 69 (151)
|-|..+++.+- =+|+.||.++++.++..|...
T Consensus 140 ~la~~~~~~l~~~~~vll~nHGvi~~G~s~~~A~~~ 175 (213)
T PRK08130 140 AIAEALAGLAARYRAVLLANHGPVVWGSSLEAAVNA 175 (213)
T ss_pred HHHHHHHHHhccCCEEEEcCCCCeeeCCCHHHHHHH
Confidence 44555555552 267899999999998877654
No 57
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=32.91 E-value=41 Score=23.39 Aligned_cols=50 Identities=14% Similarity=0.367 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 40 AYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 40 a~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
.-.-+..|+++|.++|++|+++- .++.|+ |..-.-+-+=|+-.=.++.+.
T Consensus 6 IG~nAG~Vw~~L~~~~~~s~~el---~k~~~l----~~~~~~~AiGWLarE~KI~~~ 55 (65)
T PF10771_consen 6 IGENAGKVWQLLNENGEWSVSEL---KKATGL----SDKEVYLAIGWLARENKIEFE 55 (65)
T ss_dssp HHHHHHHHHHHHCCSSSEEHHHH---HHHCT-----SCHHHHHHHHHHHCTTSEEEE
T ss_pred HHHHHHHHHHHHhhCCCcCHHHH---HHHhCc----CHHHHHHHHHHHhccCceeEE
Confidence 34568899999999999999874 244455 334555667787655555544
No 58
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=32.50 E-value=63 Score=23.23 Aligned_cols=34 Identities=6% Similarity=0.174 Sum_probs=27.8
Q ss_pred cCCCCChHHHHHHHHHHHHHHHHhC-CcchhhhhH
Q 031883 31 INPKVPTQQAYSIAQSLYGIIKQHG-PLTVSNTWI 64 (151)
Q Consensus 31 I~pkvP~Eqa~tItr~l~dIlkeHG-PLTVsntW~ 64 (151)
++|..+.+|..++...+-++|.++| -++-.+.|+
T Consensus 14 l~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG 48 (97)
T CHL00123 14 LKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRG 48 (97)
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeec
Confidence 6788999999999999999999988 344445565
No 59
>PRK09220 methylthioribulose-1-phosphate dehydratase; Provisional
Probab=31.67 E-value=30 Score=27.39 Aligned_cols=33 Identities=21% Similarity=0.250 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHHH-------HHHHhCCcchhhhhHHHHHh
Q 031883 37 TQQAYSIAQSLYG-------IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 37 ~Eqa~tItr~l~d-------IlkeHGPLTVsntW~hake~ 69 (151)
.|=|+.+...|-+ +|+.||.++++.++..|.+.
T Consensus 145 ~eLa~~v~~~l~~~~~~~avlL~nHGvi~~G~~~~eA~~~ 184 (204)
T PRK09220 145 ARLAARVAPYLDAQPLRYGYLIRGHGLYCWGRDMAEARRH 184 (204)
T ss_pred HHHHHHHHHHHHhCCCCcEEEECCCceEEEcCCHHHHHHH
Confidence 3455556655554 37889999999998877654
No 60
>PRK06754 mtnB methylthioribulose-1-phosphate dehydratase; Reviewed
Probab=31.65 E-value=23 Score=28.04 Aligned_cols=33 Identities=21% Similarity=0.248 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHH-H----HHHHhCCcchhhhhHHHHHh
Q 031883 37 TQQAYSIAQSLY-G----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 37 ~Eqa~tItr~l~-d----IlkeHGPLTVsntW~hake~ 69 (151)
+|=|+.+.++|- | +|+.||.++++.++..|...
T Consensus 148 ~eLa~~v~~~l~~~~~avLl~nHG~v~~G~~l~~A~~~ 185 (208)
T PRK06754 148 PTLAEEFAKHIQGDSGAVLIRNHGITVWGRDAFEAKKH 185 (208)
T ss_pred HHHHHHHHHHhccCCcEEEECCCceEEEeCCHHHHHHH
Confidence 455555555554 3 36789999999999888654
No 61
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=31.45 E-value=60 Score=22.40 Aligned_cols=20 Identities=15% Similarity=0.335 Sum_probs=18.2
Q ss_pred ChHHHHHHHHHHHHHHHHhC
Q 031883 36 PTQQAYSIAQSLYGIIKQHG 55 (151)
Q Consensus 36 P~Eqa~tItr~l~dIlkeHG 55 (151)
-.|++..+.+.+++||++.|
T Consensus 67 s~~~~~~a~~~i~~~L~~~~ 86 (86)
T PF00352_consen 67 SEEEAKKAIEKILPILQKLG 86 (86)
T ss_dssp SHHHHHHHHHHHHHHHHHTT
T ss_pred CHHHHHHHHHHHHHHHHHcC
Confidence 47999999999999999986
No 62
>PF10330 Stb3: Putative Sin3 binding protein; InterPro: IPR018818 This entry represents Sin3 binding proteins conserved in fungi. Sin3p does not bind DNA directly even though the yeast SIN3 gene functions as a transcriptional repressor. Sin3p is part of a large multiprotein complex []. Stb3 appears to bind directly to ribosomal RNA Processing Elements (RRPE) although there are no obvious domains which would accord with this, implying that Stb3 may be a novel RNA-binding protein [].
Probab=31.21 E-value=85 Score=23.83 Aligned_cols=44 Identities=20% Similarity=0.339 Sum_probs=38.2
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHh--ccCCCCchhHHHHHHHHhh
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDA--GISGLNGKTHMKIMLKWMR 88 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~--gi~gL~SK~HMKimLkWMr 88 (151)
..|-+||-+||||-|--.=.|+-.. |.++|.+--.-+++..=|.
T Consensus 9 ~~Lp~iLl~~GPLaIRhI~~~Lt~~vPgF~~ls~sKqRRLi~~ALE 54 (92)
T PF10330_consen 9 YHLPEILLNHGPLAIRHITGYLTTSVPGFSDLSPSKQRRLIMAALE 54 (92)
T ss_pred hhhHHHHHhcCcHHHHHHHHHHhccCCCcccCCHHHHHHHHHHHHh
Confidence 4678899999999999999998776 9999998888888877776
No 63
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=29.85 E-value=1e+02 Score=16.93 Aligned_cols=35 Identities=26% Similarity=0.504 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHh
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWM 87 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWM 87 (151)
..|.+.+++||. ..|..+.+. +..++-..+..+|.
T Consensus 8 ~~l~~~~~~~g~----~~w~~Ia~~----~~~rs~~~~~~~~~ 42 (45)
T cd00167 8 ELLLEAVKKYGK----NNWEKIAKE----LPGRTPKQCRERWR 42 (45)
T ss_pred HHHHHHHHHHCc----CCHHHHHhH----cCCCCHHHHHHHHH
Confidence 457778889997 669887776 12266677777775
No 64
>PRK12347 sgbE L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=29.70 E-value=26 Score=28.49 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHH-----------HHHHhCCcchhhhhHHH
Q 031883 38 QQAYSIAQSLYG-----------IIKQHGPLTVSNTWIHA 66 (151)
Q Consensus 38 Eqa~tItr~l~d-----------IlkeHGPLTVsntW~ha 66 (151)
|.+..|++.+-+ ||+.||.++++.+=..|
T Consensus 144 e~~~~va~~l~~~~~~~~~~~avLL~NHG~v~~G~~l~eA 183 (231)
T PRK12347 144 QTGEVIIETFEERGISPAQIPAVLVHSHGPFAWGKNAADA 183 (231)
T ss_pred hhHHHHHHHHhhccccccCCCEEEEcCCCceEecCCHHHH
Confidence 677788888753 68999999998764443
No 65
>PHA00738 putative HTH transcription regulator
Probab=29.26 E-value=56 Score=25.17 Aligned_cols=44 Identities=16% Similarity=0.120 Sum_probs=29.9
Q ss_pred HHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceee
Q 031883 44 AQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLK 94 (151)
Q Consensus 44 tr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lK 94 (151)
=+.|++.|.++++++|++.=+. .+++-=+=-+|+|+| ++-.+|.
T Consensus 14 Rr~IL~lL~~~e~~~V~eLae~---l~lSQptVS~HLKvL----reAGLV~ 57 (108)
T PHA00738 14 RRKILELIAENYILSASLISHT---LLLSYTTVLRHLKIL----NEQGYIE 57 (108)
T ss_pred HHHHHHHHHHcCCccHHHHHHh---hCCCHHHHHHHHHHH----HHCCceE
Confidence 4678899999999999876333 255444444899886 4555553
No 66
>cd08304 DD_superfamily The Death Domain Superfamily of protein-protein interaction domains. The Death Domain (DD) superfamily includes the DD, Pyrin, CARD (Caspase activation and recruitment domain) and DED (Death Effector Domain) families. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes. They are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways including those that impact innate immunity, inflammation, differentiation, and cancer.
Probab=28.15 E-value=1.1e+02 Score=20.62 Aligned_cols=39 Identities=23% Similarity=0.358 Sum_probs=31.5
Q ss_pred CCChHHHHHH--HHHHHHHHHHhCCcchhhhhHHHHHhccC
Q 031883 34 KVPTQQAYSI--AQSLYGIIKQHGPLTVSNTWIHAKDAGIS 72 (151)
Q Consensus 34 kvP~Eqa~tI--tr~l~dIlkeHGPLTVsntW~hake~gi~ 72 (151)
..|.++.+.| ++.+++++.-+||=+++-+-+-+++.|..
T Consensus 23 ~~~~~~~e~i~~a~~ll~~l~~~~~~a~~~~~~vL~~~~~~ 63 (69)
T cd08304 23 RIPPDQVEQISAANELLNILESQYNHTLQLLFALFEDLGLH 63 (69)
T ss_pred cCCHHHHHHhhHHHHHHHHHHHhCcchHHHHHHHHHHcCCH
Confidence 3455556555 58899999999999999999988888876
No 67
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=28.14 E-value=56 Score=25.59 Aligned_cols=22 Identities=23% Similarity=0.339 Sum_probs=20.5
Q ss_pred CChHHHHHHHHHHHHHHHHhCC
Q 031883 35 VPTQQAYSIAQSLYGIIKQHGP 56 (151)
Q Consensus 35 vP~Eqa~tItr~l~dIlkeHGP 56 (151)
-|.|+-.+.+..+++++|+||-
T Consensus 2 ~P~~~C~~a~~~v~~~lk~~g~ 23 (135)
T PF15645_consen 2 NPAEQCESAMKEVADFLKDKGY 23 (135)
T ss_pred ChhHHHHHHHHHHHHHHHhCCC
Confidence 4889999999999999999996
No 68
>KOG1201 consensus Hydroxysteroid 17-beta dehydrogenase 11 [Secondary metabolites biosynthesis, transport and catabolism]
Probab=27.71 E-value=1.2e+02 Score=26.98 Aligned_cols=54 Identities=17% Similarity=0.171 Sum_probs=35.8
Q ss_pred cchhhhHHHHHHHHhhhhhhccccccccCCCCChHHHHHHH-------------------HHHHHHHHHhCCcch
Q 031883 4 GNVKVLSMETLVRYYSSSRKAAVNVRKINPKVPTQQAYSIA-------------------QSLYGIIKQHGPLTV 59 (151)
Q Consensus 4 g~~~~~~~~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~tIt-------------------r~l~dIlkeHGPLTV 59 (151)
||-+++.+++.. .|+ .|...+-+--||..--.|.+..|. +..-+|-+|||+++|
T Consensus 45 Ggg~GlGr~ial-efa-~rg~~~vl~Din~~~~~etv~~~~~~g~~~~y~cdis~~eei~~~a~~Vk~e~G~V~I 117 (300)
T KOG1201|consen 45 GGGSGLGRLIAL-EFA-KRGAKLVLWDINKQGNEETVKEIRKIGEAKAYTCDISDREEIYRLAKKVKKEVGDVDI 117 (300)
T ss_pred CCCchHHHHHHH-HHH-HhCCeEEEEeccccchHHHHHHHHhcCceeEEEecCCCHHHHHHHHHHHHHhcCCceE
Confidence 555566565554 455 144445577778777777666665 567788899999987
No 69
>TIGR02940 anfO_nitrog Fe-only nitrogenase accessory protein AnfO. Members of this protein family, called Anf1 in Rhodobacter capsulatus and AnfO in Azotobacter vinelandii, are found only in species with the Fe-only nitrogenase and are encoded immediately downstream of the structural genes in the above named species.
Probab=27.41 E-value=65 Score=27.21 Aligned_cols=29 Identities=28% Similarity=0.699 Sum_probs=23.5
Q ss_pred ccCCCCchhHHHHHHHHhhccc--eeeEEeeccC
Q 031883 70 GISGLNGKTHMKIMLKWMRGRK--MLKLFCNGVG 101 (151)
Q Consensus 70 gi~gL~SK~HMKimLkWMreRq--~lKL~CnhvG 101 (151)
+..+|||| ++++-.+++.- .|-++|+|+=
T Consensus 155 ~np~ltSK---qvL~PfL~~~~F~~LeIiC~HiP 185 (214)
T TIGR02940 155 DDPDLNSK---KILIPYLKGKPFNQLDILCDHIP 185 (214)
T ss_pred hCCCCCHH---HHHHHHHcCCCceeEEEEeCCCC
Confidence 88999999 58888888775 5666799984
No 70
>PRK12348 sgaE L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=27.30 E-value=30 Score=27.96 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHH---------HHHHhCCcchhhhhHH
Q 031883 38 QQAYSIAQSLYG---------IIKQHGPLTVSNTWIH 65 (151)
Q Consensus 38 Eqa~tItr~l~d---------IlkeHGPLTVsntW~h 65 (151)
+.+..+++.|-+ ||+.||.++++.+=..
T Consensus 142 ~~~~~la~~l~~~~~~~~~avlL~nHG~v~~G~~l~e 178 (228)
T PRK12348 142 NTGKVIIETLGNAEPLHTPGIVVYQHGPFAWGKDAHD 178 (228)
T ss_pred hHHHHHHHHHhhcCcccCcEEEEcCCCeEEecCCHHH
Confidence 456677777765 5789999999876443
No 71
>PF03279 Lip_A_acyltrans: Bacterial lipid A biosynthesis acyltransferase; InterPro: IPR004960 Bacterial lipopolysachharides (LPS) are glycolipids that make up the outer monolayer of the outer membranes of most Gram-negative bacteria. Though LPS moleculesare variable, they all show the same general features: an outer polysaccharide which is attached to the lipid component, termed lipid A []. The polysaccharide component consists of a variable repeat-structure polysaccharide known as the O-antigen, and a highly conserved short core oligosaccharide which connects the O-antigen to lipid A. Lipid A is a glucosamine-based phospholipid that makes up the membrane anchor region of LPS []. The structure of lipid A is relatively invariant between species, presumably reflecting its fundamental role in membrane integrity. Recognition of lipid A by the innate immune system can lead to a response even at picomolar levels. In some genera, such as Neisseria and Haemophilus, lipooligosaccharides (LOS) are the predominant glycolipids []. These are analogous to LPS except that they lack O-antigens, with the LOS oligosaccharide structures limited to 10 saccharide units. The bacterial lipid A biosynthesis protein, or lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA acyltransferase 2.3.1 from EC, transfers myristate or laurate, activated on ACP, to the lipid IVA moiety of (KDO)2-(lauroyl)-lipid IVA during lipopolysaccharide core biosynthesis.; GO: 0016746 transferase activity, transferring acyl groups, 0009244 lipopolysaccharide core region biosynthetic process, 0016021 integral to membrane
Probab=27.14 E-value=2.1e+02 Score=22.96 Aligned_cols=92 Identities=11% Similarity=0.114 Sum_probs=58.6
Q ss_pred HHHHHHHHhhhhhhccccccccCCCCChHHHHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhc
Q 031883 10 SMETLVRYYSSSRKAAVNVRKINPKVPTQQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRG 89 (151)
Q Consensus 10 ~~~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMre 89 (151)
.||.+.++++ +. -. ++..=.++.+...+.+.+.++-...| +++-+ ...-++-+++.+++
T Consensus 132 nwE~~~~~l~--~~-~~---~~~~i~~~~~n~~~~~~~~~~R~~~g-~~~i~--------------~~~~~~~~~~~Lk~ 190 (295)
T PF03279_consen 132 NWELAGRALA--RR-GP---PVAVIYRPQKNPYIDRLLNKLRERFG-IELIP--------------KGEGIRELIRALKE 190 (295)
T ss_pred hHHHHHHHHH--hh-CC---ceEEEecCCccHhHHHHHHHHHHhcC-CeEec--------------chhhHHHHHHHhcc
Confidence 3777777776 21 11 33333333445556666666544444 22211 11118899999999
Q ss_pred cceeeEEeeccCCCcceeeecCCCCCCCCCCCC
Q 031883 90 RKMLKLFCNGVGSNKKFLHSTLPEEPQTDQLEI 122 (151)
Q Consensus 90 Rq~lKL~CnhvG~~KqFLytt~~~~P~~~~~~~ 122 (151)
-.+|=+.+++..+.+.-++.++|-.|-+.+..+
T Consensus 191 g~~v~~l~Dq~~~~~~~~~v~FfG~~a~~~~g~ 223 (295)
T PF03279_consen 191 GGIVGLLGDQDPGKKDGVFVPFFGRPASTPTGP 223 (295)
T ss_pred CCEEEEEECCCCCCCCceEEeECCeecccccHH
Confidence 999999999987777678999998887766543
No 72
>cd00736 bacteriophage_lambda_lysozyme The lysozyme from bacteriophage lambda hydrolyses the beta-1,4-glycosidic bond between N-acetylmuramic acid (MurNAc) and N-acetylglucosamine (GlcNAc), as do other lysozymes. But unlike other lysozymes, bacteriophage lambda does not produce a reducing end upon cleavage of the peptidoglycan but rather uses the 6-OH of the same MurNAc residue to produce a 1,6-anhydromuramic acid terminal residue and is therefore a lytic transglycosylase. An identical 1,6-anhydro bond is formed in bacterial peptidoglycans by the action of the lytic transglycosylases of E. coli. However, they differ structurally.
Probab=27.02 E-value=37 Score=27.18 Aligned_cols=57 Identities=16% Similarity=0.246 Sum_probs=44.9
Q ss_pred hhhhHHHHHh-ccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceee---ecCCCCCCCC
Q 031883 60 SNTWIHAKDA-GISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLH---STLPEEPQTD 118 (151)
Q Consensus 60 sntW~hake~-gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLy---tt~~~~P~~~ 118 (151)
..||.+++.. |+.+..-..+=++-+.|+++|.-|..+=. |.-.+|+. .+|..=|++.
T Consensus 71 ~~Tw~~~~~~~gl~~F~P~~QD~~A~~Li~~~gal~~i~~--G~~~~a~~~La~~WASLPg~g 131 (151)
T cd00736 71 SRTWDAYAKQYGLYDFSPESQDLVAYQLIRERGALPDILA--GRIEQAIAKLSNIWASLPGAG 131 (151)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHcCcHHHHHc--CCHHHHHHHHHhhccCCCCcC
Confidence 4689887654 99999999999999999999997755544 66666654 6898888665
No 73
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=26.49 E-value=2.3e+02 Score=24.73 Aligned_cols=69 Identities=14% Similarity=0.278 Sum_probs=50.5
Q ss_pred CCCChHHHHHHHHHHHHHHHHhCCcchhh------hhHHHHHhccCCCCchhHHHHHHHHhhccc--eeeEEeeccCCCc
Q 031883 33 PKVPTQQAYSIAQSLYGIIKQHGPLTVSN------TWIHAKDAGISGLNGKTHMKIMLKWMRGRK--MLKLFCNGVGSNK 104 (151)
Q Consensus 33 pkvP~Eqa~tItr~l~dIlkeHGPLTVsn------tW~hake~gi~gL~SK~HMKimLkWMreRq--~lKL~CnhvG~~K 104 (151)
-.++|..|+.||+.|..-|++-|=..|+. +-+.+++++...+. ++ =.+++..++.+ ++=++|--.|+-|
T Consensus 29 ~g~~~~~A~~iA~~i~~~L~~~g~~~i~~~el~~~V~~~L~~~~~~~~~-~~--y~~~~~i~~~~~p~iIlI~G~sgsGK 105 (301)
T PRK04220 29 AGMKPSIAYEIASEIEEELKKEGIKEITKEELRRRVYYKLIEKDYEEVA-EK--YLLWRRIRKSKEPIIILIGGASGVGT 105 (301)
T ss_pred cCCChhHHHHHHHHHHHHHHHcCCEEeeHHHHHHHHHHHHHHhCcHhHH-HH--HHHHHHHhcCCCCEEEEEECCCCCCH
Confidence 36889999999999999999999888764 66778888877774 33 35567788844 5555554444444
No 74
>cd00398 Aldolase_II Class II Aldolase and Adducin head (N-terminal) domain. Aldolases are ubiquitous enzymes catalyzing central steps of carbohydrate metabolism. Based on enzymatic mechanisms, this superfamily has been divided into two distinct classes (Class I and II). Class II enzymes are further divided into two sub-classes A and B. This family includes class II A aldolases and adducins which has not been ascribed any enzymatic function. Members of this class are primarily bacterial and eukaryotic in origin and include L-fuculose-1-phosphate, L-rhamnulose-1-phosphate aldolases and L-ribulose-5-phosphate 4-epimerases. They all share the ability to promote carbon-carbon bond cleavage and stabilize enolate intermediates using divalent cations.
Probab=26.47 E-value=19 Score=28.10 Aligned_cols=20 Identities=20% Similarity=0.260 Sum_probs=17.5
Q ss_pred HHHHhCCcchhhhhHHHHHh
Q 031883 50 IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 50 IlkeHGPLTVsntW~hake~ 69 (151)
||+.||.++++.+++.|...
T Consensus 153 ll~nHG~~~~G~~~~~A~~~ 172 (209)
T cd00398 153 LLRNHGLFAWGPTLDEAFHL 172 (209)
T ss_pred EEcCCCCeEecCCHHHHHHH
Confidence 68999999999999988654
No 75
>TIGR01568 A_thal_3678 uncharacterized plant-specific domain TIGR01568. This model describes an uncharacterized domain of about 70 residues found exclusively in plants, generally toward the C-terminus of proteins of 200 to 350 amino acids in length. At least 14 such proteins are found in Arabidopsis thaliana. Other regions of these proteins tend to consist largely of low-complexity sequence.
Probab=25.96 E-value=72 Score=22.62 Aligned_cols=41 Identities=15% Similarity=0.349 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhCCcchhhhhHHHHHh--ccCCCCchhHHHHHHH
Q 031883 42 SIAQSLYGIIKQHGPLTVSNTWIHAKDA--GISGLNGKTHMKIMLK 85 (151)
Q Consensus 42 tItr~l~dIlkeHGPLTVsntW~hake~--gi~gL~SK~HMKimLk 85 (151)
.+-++..+.|.+|| +...|+-+.|. =-=.||+|.|=+++++
T Consensus 13 DFr~SM~EMI~~~~---i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~ 55 (66)
T TIGR01568 13 DFRRSMEEMIEERE---LEADWKELEELLACYLDLNPKKSHRFIVR 55 (66)
T ss_pred HHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHHhCCchhhhHHHH
Confidence 36678889999998 55679999997 3445899999988876
No 76
>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=25.78 E-value=76 Score=24.71 Aligned_cols=46 Identities=15% Similarity=0.221 Sum_probs=32.3
Q ss_pred HHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEe
Q 031883 45 QSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFC 97 (151)
Q Consensus 45 r~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~C 97 (151)
+.|+..|.++||+|+.+- ++..|++ ..-+...|+=|.+...|....
T Consensus 4 ~~IL~~L~~~~~~t~~eL---A~~lgis----~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 4 EDILSYLLKQGQATAAAL---AEALAIS----PQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHHHcCCCCHHHH---HHHHCcC----HHHHHHHHHHHHHCCCeEEee
Confidence 678899999999999864 4455665 455556666666677776553
No 77
>TIGR02757 conserved hypothetical protein TIGR02757. Members of this uncharacterized protein family are found sporadically, so far only among spirochetes, epsilon and delta proteobacteria, and Bacteroides. The function is unknown and its gene neighborhoods show little conservation.
Probab=25.63 E-value=2.2e+02 Score=24.10 Aligned_cols=22 Identities=27% Similarity=0.481 Sum_probs=17.9
Q ss_pred CChHHHHHHHHHHHHHHHHhCC
Q 031883 35 VPTQQAYSIAQSLYGIIKQHGP 56 (151)
Q Consensus 35 vP~Eqa~tItr~l~dIlkeHGP 56 (151)
.-.++.+.+-.+|..|.++||-
T Consensus 78 ~~~~D~~~~~~~l~~~~~~~~s 99 (229)
T TIGR02757 78 QNEKDIQAIFKTLYRIYESHGS 99 (229)
T ss_pred CCHHHHHHHHHHHHHHHHhcCC
Confidence 3467888999999999988774
No 78
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=25.40 E-value=1.4e+02 Score=19.89 Aligned_cols=46 Identities=22% Similarity=0.353 Sum_probs=33.4
Q ss_pred HHHHHHhhhhhhccccccccCCCCChHHHHHHHHHHHHHHHHhCCcchhhhhH
Q 031883 12 ETLVRYYSSSRKAAVNVRKINPKVPTQQAYSIAQSLYGIIKQHGPLTVSNTWI 64 (151)
Q Consensus 12 ~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~tItr~l~dIlkeHGPLTVsntW~ 64 (151)
+.|.++.. .+.++. .|-...+|.+.|.+.|.+.+.++-|+||. .|+
T Consensus 6 e~L~~~~~--e~~k~~----kp~Lde~~leei~~~l~~a~~~~~~v~it-y~~ 51 (92)
T PF08863_consen 6 EALRELIK--EQNKVE----KPELDEQQLEEINEKLSEAYQENQPVTIT-YYE 51 (92)
T ss_pred HHHHHHHH--HhcccC----CCCCcHHHHHHHHHHHHHHhcCCCEEEEE-EEE
Confidence 45555555 333333 34567899999999999999999999983 554
No 79
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=25.22 E-value=53 Score=27.39 Aligned_cols=48 Identities=17% Similarity=0.288 Sum_probs=36.0
Q ss_pred CCccchhhhHHHHHHHHhhhhhhccccccccCCCCChHHHHHHHHHHHHHHHHhCCc
Q 031883 1 MWLGNVKVLSMETLVRYYSSSRKAAVNVRKINPKVPTQQAYSIAQSLYGIIKQHGPL 57 (151)
Q Consensus 1 ~~~g~~~~~~~~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~tItr~l~dIlkeHGPL 57 (151)
+|+|-+-++ -+-+..||. .+. .+-+.|+|+..|=+..-++.+.||||-
T Consensus 46 ~~vGDfDSv-~~e~~~~~~-------~~~-~~~~f~~eKd~TD~elAl~~a~e~g~d 93 (212)
T COG1564 46 LAVGDFDSV-SEELLAYYK-------EKT-VTIKFPAEKDSTDLELALDEALERGAD 93 (212)
T ss_pred EEEeccccc-CHHHHHHHh-------hcC-cceecChhhccchHHHHHHHHHHcCCC
Confidence 477877777 445556666 122 226779999999999999999999993
No 80
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=24.26 E-value=1.4e+02 Score=24.11 Aligned_cols=53 Identities=19% Similarity=0.303 Sum_probs=32.8
Q ss_pred HHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceeee
Q 031883 47 LYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHS 109 (151)
Q Consensus 47 l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLyt 109 (151)
++.||.-|+|+|-++. +.+.|++|-.|.+-|+ +|..++-.=......+-++|.
T Consensus 95 tLaiIay~qPiTr~eI------~~irGv~~~~ii~~L~----~~gLI~e~gr~~~~Grp~ly~ 147 (188)
T PRK00135 95 VLAIIAYKQPITRIEI------DEIRGVNSDGALQTLL----AKGLIKEVGRKEVPGRPILYG 147 (188)
T ss_pred HHHHHHHcCCcCHHHH------HHHHCCCHHHHHHHHH----HCCCeEEcCcCCCCCCCeeee
Confidence 4678899999998764 4677888866655544 566665421111122666663
No 81
>PF04806 EspF: EspF protein repeat; InterPro: IPR006891 Enteropathogenic Escherichia coli O127:H6 attaches to the intestinal muscosa through actin pedestals that are created after it has injected the Type III secretion protein EspF (E. coli secreted protein F-like protein from prophage U) into the cells. EspF recruits the actin machinery by activating the WASP (Wiscott-Aldrich syndrome protein) family of actin nucleating factors []. Subsequent cell-death (apoptosis) is caused by EspF being targeted to the mitochondria as a consequence of its mitochondrial targeting sequence. Import into mitochondria leads to a loss of membrane potential, leakage of cytochrome c and activation of the apoptotic caspase cascade. Mutation of leucine to glutamic at position 16 of EspF (L16E) resulted in the failure of EspF import into mitochondria; mitochondrial membrane potential was not affected and cell death abolished. This suggests that the targeting of EspF to mitochondria is essential for bacterial pathogenesis and apoptosis [, ].; PDB: 2KXC_B 2K42_B.
Probab=23.89 E-value=61 Score=22.10 Aligned_cols=13 Identities=38% Similarity=0.629 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHhC
Q 031883 43 IAQSLYGIIKQHG 55 (151)
Q Consensus 43 Itr~l~dIlkeHG 55 (151)
|+|+|.|-|.|||
T Consensus 35 vaq~l~~hla~hg 47 (47)
T PF04806_consen 35 VAQRLKDHLAEHG 47 (47)
T ss_dssp HHHHHHHHHHTTT
T ss_pred HHHHHHHHHHhcC
Confidence 7899999999998
No 82
>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=23.73 E-value=91 Score=21.26 Aligned_cols=49 Identities=18% Similarity=0.252 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhcccee
Q 031883 40 AYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKML 93 (151)
Q Consensus 40 a~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~l 93 (151)
.+.+-+.|+++|+++||.|.. ..++..|++ ..|..--..|-=|.....|
T Consensus 2 ~~~~ee~Il~~L~~~g~~~a~---~ia~~~~L~--~~kk~VN~~LY~L~k~g~v 50 (66)
T PF02295_consen 2 MQDLEEKILDFLKELGGSTAT---AIAKALGLS--VPKKEVNRVLYRLEKQGKV 50 (66)
T ss_dssp HHHHHHHHHHHHHHHTSSEEE---HHHHHHHHT--S-HHHHHHHHHHHHHTTSE
T ss_pred chhHHHHHHHHHHhcCCccHH---HHHHHhCcc--hhHHHHHHHHHHHHHCCCE
Confidence 456788999999999987764 567777776 2455555555555555554
No 83
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=23.70 E-value=1.1e+02 Score=23.75 Aligned_cols=66 Identities=12% Similarity=0.149 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHh-CCcchhhhhHHHHHhccCCCCchhH-HHHHHHHhhcccee-eEEeeccCCCcceeeecCCC
Q 031883 42 SIAQSLYGIIKQH-GPLTVSNTWIHAKDAGISGLNGKTH-MKIMLKWMRGRKML-KLFCNGVGSNKKFLHSTLPE 113 (151)
Q Consensus 42 tItr~l~dIlkeH-GPLTVsntW~hake~gi~gL~SK~H-MKimLkWMreRq~l-KL~CnhvG~~KqFLytt~~~ 113 (151)
|..-..|.||+++ -|++..+-|+.+++... . |+.- ...+-+-.+.-.+= |++|. |..+ +--+.|..
T Consensus 4 S~idvAy~iL~~~~~~m~f~dL~~ev~~~~~--~-s~e~~~~~iaq~YtdLn~DGRFi~l--G~n~-WgLr~w~p 72 (129)
T PRK02363 4 SLIEVAYEILKEKKEPMSFYDLVNEIQKYLG--K-SDEEIRERIAQFYTDLNLDGRFISL--GDNK-WGLRSWYP 72 (129)
T ss_pred cHHHHHHHHHHHcCCcccHHHHHHHHHHHhC--C-CHHHHHHHHHHHHHHHhccCCeeEc--CCCc-eecccccC
Confidence 4456678899998 79999999999998833 1 3322 34444443332221 56666 4443 33344543
No 84
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase. This model includes ThiE from Bacillus subtilis but excludes its paralog, the regulatory protein TenI, and neighbors of TenI.
Probab=23.63 E-value=1.1e+02 Score=22.97 Aligned_cols=64 Identities=14% Similarity=0.163 Sum_probs=42.3
Q ss_pred ChHHHHHHHHHHHHHHHHh-CCcchhhhhHHHHHhccCCCC--chhHHHHHHHHhh-ccceeeEEeec
Q 031883 36 PTQQAYSIAQSLYGIIKQH-GPLTVSNTWIHAKDAGISGLN--GKTHMKIMLKWMR-GRKMLKLFCNG 99 (151)
Q Consensus 36 P~Eqa~tItr~l~dIlkeH-GPLTVsntW~hake~gi~gL~--SK~HMKimLkWMr-eRq~lKL~Cnh 99 (151)
+..+-..+.+.|.++.+.+ .|+-|.+-++-+.+.|..|+- .+.-....++.+. ...+|-.+|..
T Consensus 38 ~~~~~~~~~~~l~~~~~~~~~~l~i~~~~~la~~~g~~GvHl~~~~~~~~~~r~~~~~~~~ig~s~h~ 105 (196)
T TIGR00693 38 NTRERLALAEKLQELCRRYGVPFIVNDRVDLALALGADGVHLGQDDLPASEARALLGPDKIIGVSTHN 105 (196)
T ss_pred CHHHHHHHHHHHHHHHHHhCCeEEEECHHHHHHHcCCCEEecCcccCCHHHHHHhcCCCCEEEEeCCC
Confidence 4455677888899998775 799999999999999988753 2221123334333 33556666643
No 85
>PF00596 Aldolase_II: Class II Aldolase and Adducin N-terminal domain; InterPro: IPR001303 This entry represents the alpha/beta/alpha domain found in class II aldolases and adducin, usually at the N terminus. These proteins form part of a family that includes: rhamnulose-1-phosphate aldolase (4.1.2.19 from EC), L-fuculose phosphate aldolase (4.1.2.17 from EC) [, ] that is involved in the third step in fucose metabolism, L-ribulose- 5-phosphate 4-epimerase (5.1.3.4 from EC) involved in the third step of L-arabinose catabolism, a probable sugar isomerase SgbE, hypothetical proteins and the metazoan adducins which have not been ascribed any enzymatic function but which play a role in cell membrane cytoskeleton organisation. Adducins are members of the Ig superfamily and encode cell surface sialoglycoproteins expressed by cytokine-activated endothelium. This type I membrane protein mediates leukocyte-endothelial cell adhesion and signal transduction, and may play a role in the development of artherosclerosis and rheumatoid arthritis. Adducin is a cell-membrane skeletal protein that was first purified from human erythrocytes and subsequently isolated from bovine brain membranes. Isoforms of this protein have been detected in lung, kidney, testes and liver. Erythrocyte adducin is a 200kDa heterodimer protein, composed of alpha and beta subunits, present at about 30,000 copies per cell. It binds with high affinity to Ca(2+)/calmodulin and is a substrate for protein kinases A and C. Both alpha-adducin and beta-adducin show alternative splicing. Thus, there may be several different heterodimeric or homodimeric forms of adducin, each with a different functional specificity. It is thought to play a role in assembly of the spectrin-actin lattice that underlies the plasma membrane []. Missense mutations in both the alpha- and beta-adducin genes that alter amino acids that are normally phosphorylated have been associated with the regulation of blood pressure in the Milan hypertensive strain (MHS) of rats. Gamma adducin was isolated from human foetal brain []. It shows a high degree of similarity to the alpha and beta adducins.; GO: 0046872 metal ion binding; PDB: 2V9N_B 1GT7_B 2V9O_E 2V9M_B 2V9F_A 2UYV_A 1OJR_A 2V9G_C 2V29_B 2V9I_A ....
Probab=23.59 E-value=24 Score=26.50 Aligned_cols=33 Identities=21% Similarity=0.249 Sum_probs=25.1
Q ss_pred hHHHHHHHHHHH-H----HHHHhCCcchhhhhHHHHHh
Q 031883 37 TQQAYSIAQSLY-G----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 37 ~Eqa~tItr~l~-d----IlkeHGPLTVsntW~hake~ 69 (151)
.|-+..|+++|- + |++.||.++++++.+.|...
T Consensus 135 ~~l~~~i~~~l~~~~~~vll~nHG~~~~G~s~~~A~~~ 172 (184)
T PF00596_consen 135 EELAEAIAEALGEDRKAVLLRNHGVVVWGKSLEEAFYR 172 (184)
T ss_dssp HHHHHHHHHHHTCTSSEEEETTTEEEEEESSHHHHHHH
T ss_pred hhhhhhhhhhhcCCceEEeecCCceEEEeCCHHHHHHH
Confidence 344577777777 3 67899999999998877543
No 86
>PRK07044 aldolase II superfamily protein; Provisional
Probab=23.30 E-value=36 Score=27.84 Aligned_cols=33 Identities=24% Similarity=0.259 Sum_probs=23.9
Q ss_pred hHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHHh
Q 031883 37 TQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 37 ~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake~ 69 (151)
.|++..++..|-+ ||+.||.++++.+...|...
T Consensus 151 ~e~~~~va~~l~~~~avLL~nHGvi~~G~~l~eA~~~ 187 (252)
T PRK07044 151 LDEGERLVADLGDKPAMLLRNHGLLTVGRTVAEAFLL 187 (252)
T ss_pred HHHHHHHHHHhccCCEEEECCCCceEecCCHHHHHHH
Confidence 4556666666533 68899999999988876543
No 87
>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=23.18 E-value=97 Score=18.97 Aligned_cols=44 Identities=16% Similarity=0.321 Sum_probs=30.4
Q ss_pred HHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 46 SLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 46 ~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
.+..+|.+|||+|+++-- +..++ ++.-+-.+++.|-++..|...
T Consensus 7 ~iL~~l~~~~~~~~~~la---~~~~~----~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 7 RILRILYENGGITQSELA---EKLGI----SRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp HHHHHHHHHSSEEHHHHH---HHHTS-----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHcCCCCHHHHH---HHHCC----ChhHHHHHHHHHHHCCCEEec
Confidence 356778899999999543 34455 466777788888777776443
No 88
>PF09535 Gmx_para_CXXCG: Protein of unknown function (Gmx_para_CXXCG); InterPro: IPR011750 This entry consists of at least 10 paralogous proteins from Myxococcus xanthus that lack detectable sequence similarity to any other protein family. An imperfectly conserved CXXCG motif, a probable binding site, appears twice in the multiple sequence alignment.
Probab=23.15 E-value=38 Score=29.34 Aligned_cols=24 Identities=42% Similarity=0.888 Sum_probs=19.6
Q ss_pred hCCcchhhhh---------HHHHHhccCCCCch
Q 031883 54 HGPLTVSNTW---------IHAKDAGISGLNGK 77 (151)
Q Consensus 54 HGPLTVsntW---------~hake~gi~gL~SK 77 (151)
-|||+.-+.| +++|++||.||.-=
T Consensus 104 FG~l~~q~~w~l~vR~eAle~L~~~GvrGL~g~ 136 (237)
T PF09535_consen 104 FGPLTLQDPWTLLVRREALERLQAAGVRGLQGC 136 (237)
T ss_pred ecceeecCCeeEeeeHHHHHHHHHhhhcccccC
Confidence 4778887777 78999999999753
No 89
>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=23.09 E-value=2.1e+02 Score=18.25 Aligned_cols=45 Identities=22% Similarity=0.348 Sum_probs=35.7
Q ss_pred HHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEe
Q 031883 46 SLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFC 97 (151)
Q Consensus 46 ~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~C 97 (151)
.+|..|-++||.|+.+. +++.|++ ++.--..|+.|.++-.+...=
T Consensus 12 ~vy~~Ll~~~~~t~~eI---a~~l~i~----~~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 12 KVYLALLKNGPATAEEI---AEELGIS----RSTVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHCHEEHHHH---HHHHTSS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCHHHH---HHHHCcC----HHHHHHHHHHHHHCCCEEEEc
Confidence 45666669999999984 6666876 778888999999999887764
No 90
>KOG4382 consensus Uncharacterized conserved protein, contains DTW domain [Function unknown]
Probab=23.00 E-value=33 Score=30.29 Aligned_cols=45 Identities=22% Similarity=0.237 Sum_probs=27.1
Q ss_pred ccCCCCChHHHHHHHHHHH---HHHHHhCCcchhhhhHHHHHh-ccCCC
Q 031883 30 KINPKVPTQQAYSIAQSLY---GIIKQHGPLTVSNTWIHAKDA-GISGL 74 (151)
Q Consensus 30 ~I~pkvP~Eqa~tItr~l~---dIlkeHGPLTVsntW~hake~-gi~gL 74 (151)
|-.+-||.++.-..-..=. -.+-.||-|-|++||+++|+. .+|--
T Consensus 110 ps~dsv~l~e~~~~~~l~~~~~~~~~p~~ll~id~Tw~~ak~l~~~S~~ 158 (276)
T KOG4382|consen 110 PSDDSVKLGESGNVENLESEKNVVLVPHGLLEIDETWNLAKHLSEISYR 158 (276)
T ss_pred CCCCceeeccccccccccccccccCCCceeEEEccchHHHHHHHhhcHH
Confidence 5555566665432211100 123457888899999999998 66643
No 91
>COG2715 SpmA Uncharacterized membrane protein, required for spore maturation in B.subtilis. [General function prediction only]
Probab=23.00 E-value=21 Score=30.44 Aligned_cols=38 Identities=26% Similarity=0.495 Sum_probs=32.7
Q ss_pred CccchhhhHHHHHHHHhhhhhhccccccccCCCCChHHHH
Q 031883 2 WLGNVKVLSMETLVRYYSSSRKAAVNVRKINPKVPTQQAY 41 (151)
Q Consensus 2 ~~g~~~~~~~~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~ 41 (151)
|||-+...-.+-|+.-|| |=-.+-+|+.=|.|||++..
T Consensus 51 WlG~MrIaE~aGLvd~la--rl~rP~~~~LFpdVpp~hpa 88 (206)
T COG2715 51 WLGLMRIAEKAGLVDLLA--RLLRPLLRRLFPDVPPGHPA 88 (206)
T ss_pred HHHHHHHHHHhcHHHHHH--HHHHHHHHHhCCCCCcCCch
Confidence 888777777778999999 88888889999999999864
No 92
>PRK13145 araD L-ribulose-5-phosphate 4-epimerase; Provisional
Probab=22.90 E-value=41 Score=27.44 Aligned_cols=30 Identities=20% Similarity=0.337 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHH-----------HHHHhCCcchhhhhHHHH
Q 031883 38 QQAYSIAQSLYG-----------IIKQHGPLTVSNTWIHAK 67 (151)
Q Consensus 38 Eqa~tItr~l~d-----------IlkeHGPLTVsntW~hak 67 (151)
|.+..|++.+-+ ||+.||.++++.+=..|-
T Consensus 144 ~~~~~va~~l~~~~~~~~~~~avLL~nHG~v~~G~~l~eA~ 184 (234)
T PRK13145 144 ETGSVIIEEFEKRGLDPMAVPGIVVRNHGPFTWGKNPEQAV 184 (234)
T ss_pred hhHHHHHHHHhhhccccccCCEEEEcCCCeeEecCCHHHHH
Confidence 567778888766 689999999987654443
No 93
>PF04909 Amidohydro_2: Amidohydrolase; InterPro: IPR006992 These proteins are related to the metal-dependent hydrolase superfamily []. The family includes 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase which converts alpha-amino-beta-carboxymuconate-epsilon- semialdehyde (ACMS) to alpha-aminomuconate semialdehyde (AMS). ACMS can be converted non-enzymatically to quinolate, a potent endogenous excitoxin of neuronal cells which is implicated in the pathogenesis of various neurodegenerative disorders. In the presence of AMCSD, ACMS is converted to AMS, a benign catabolite. 2-amino-3-(3-oxoprop-2-enyl)-but-2-enedioate = 2-aminomuconate semialdehyde + CO2. ; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 2QPX_A 4D8L_A 3K4W_I 3IRS_B 4DZI_B 3S4T_G 2GWG_B 3IJ6_A 2DVX_C 2DVT_C ....
Probab=22.27 E-value=1.3e+02 Score=22.41 Aligned_cols=15 Identities=13% Similarity=0.166 Sum_probs=12.4
Q ss_pred ccceeeEEeeccCCC
Q 031883 89 GRKMLKLFCNGVGSN 103 (151)
Q Consensus 89 eRq~lKL~CnhvG~~ 103 (151)
.=-.||+++.|.|.+
T Consensus 161 ~~P~l~ii~~H~G~~ 175 (273)
T PF04909_consen 161 RFPDLRIILAHLGGP 175 (273)
T ss_dssp HSTTSEEEESGGGTT
T ss_pred HhcCCeEEEecCccc
Confidence 334699999999998
No 94
>PRK06755 hypothetical protein; Validated
Probab=22.16 E-value=57 Score=26.47 Aligned_cols=20 Identities=20% Similarity=0.140 Sum_probs=16.9
Q ss_pred HHHHhCCcchhhhhHHHHHh
Q 031883 50 IIKQHGPLTVSNTWIHAKDA 69 (151)
Q Consensus 50 IlkeHGPLTVsntW~hake~ 69 (151)
+|+.||.++++.+|+.|...
T Consensus 165 Ll~~HGv~~~G~~l~eA~~~ 184 (209)
T PRK06755 165 LVHNYGMIVWGKTPEEAKKW 184 (209)
T ss_pred EEcCCCeEEEcCCHHHHHHH
Confidence 36789999999999988754
No 95
>PF00102 Y_phosphatase: Protein-tyrosine phosphatase; InterPro: IPR000242 Protein tyrosine (pTyr) phosphorylation is a common post-translational modification which can create novel recognition motifs for protein interactions and cellular localisation, affect protein stability, and regulate enzyme activity. Consequently, maintaining an appropriate level of protein tyrosine phosphorylation is essential for many cellular functions. Tyrosine-specific protein phosphatases (PTPase; 3.1.3.48 from EC) catalyse the removal of a phosphate group attached to a tyrosine residue, using a cysteinyl-phosphate enzyme intermediate. These enzymes are key regulatory components in signal transduction pathways (such as the MAP kinase pathway) and cell cycle control, and are important in the control of cell growth, proliferation, differentiation and transformation [, ]. The PTP superfamily can be divided into four subfamilies []: (1) pTyr-specific phosphatases (2) dual specificity phosphatases (dTyr and dSer/dThr) (3) Cdc25 phosphatases (dTyr and/or dThr) (4) LMW (low molecular weight) phosphatases Based on their cellular localisation, PTPases are also classified as: Receptor-like, which are transmembrane receptors that contain PTPase domains [] Non-receptor (intracellular) PTPases [] All PTPases carry the highly conserved active site motif C(X)5R (PTP signature motif), employ a common catalytic mechanism, and share a similar core structure made of a central parallel beta-sheet with flanking alpha-helices containing a beta-loop-alpha-loop that encompasses the PTP signature motif []. Functional diversity between PTPases is endowed by regulatory domains and subunits. This entry repesents several receptor and non-receptor protein-tyrosine phosphatases. Structurally, all known receptor PTPases, are made up of a variable length extracellular domain, followed by a transmembrane region and a C-terminal catalytic cytoplasmic domain. Some of the receptor PTPases contain fibronectin type III (FN-III) repeats, immunoglobulin-like domains, MAM domains or carbonic anhydrase-like domains in their extracellular region. The cytoplasmic region generally contains two copies of the PTPase domain. The first seems to have enzymatic activity, while the second is inactive. The inactive domains of tandem phosphatases can be divided into two classes. Those which bind phosphorylated tyrosine residues may recruit multi-phosphorylated substrates for the adjacent active domains and are more conserved, while the other class have accumulated several variable amino acid substitutions and have a complete loss of tyrosine binding capability. The second class shows a release of evolutionary constraint for the sites around the catalytic centre, which emphasises a difference in function from the first group. There is a region of higher conservation common to both classes, suggesting a new regulatory centre []. PTPase domains consist of about 300 amino acids. There are two conserved cysteines, the second one has been shown to be absolutely required for activity. Furthermore, a number of conserved residues in its immediate vicinity have also been shown to be important.; GO: 0004725 protein tyrosine phosphatase activity, 0006470 protein dephosphorylation; PDB: 3O4T_A 3O4S_A 3O4U_A 2A3K_A 2QDP_A 2QDC_A 2QDM_A 2HVL_A 1ZC0_A 3D44_A ....
Probab=22.14 E-value=3.1e+02 Score=20.28 Aligned_cols=49 Identities=8% Similarity=0.120 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhh
Q 031883 40 AYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMR 88 (151)
Q Consensus 40 a~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMr 88 (151)
+..+...+++-+++++.+.|.++...+.+.=-..+.|..+...+...+-
T Consensus 186 ~f~~~~~~~~~~~~~~~~~v~~~~~~lR~~R~~~i~~~~qy~f~~~~~~ 234 (235)
T PF00102_consen 186 TFCAIDILIEQLKKEGEVDVFEIVKKLRQQRPGAIQSPEQYRFCYMAVL 234 (235)
T ss_dssp HHHHHHHHHHHHHHHSEECHHHHHHHHHTTSTTSSSSHHHHHHHHHHHH
T ss_pred ccccchhhccccccccchhhHHHHHHHHhhCCCccCCHHHHHHHHHHHh
Confidence 4445667788888899999999999999887778888888877766554
No 96
>PF04928 PAP_central: Poly(A) polymerase central domain; InterPro: IPR007012 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase which specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analog at 2.5 A resolutio has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The central domain of Poly(A) polymerase shares structural similarity with the allosteric activity domain of ribonucleotide reductase R1, which comprises a four-helix bundle and a three-stranded mixed beta-sheet. Even though the two enzymes bind ATP, the ATP-recognition motifs are different.; GO: 0004652 polynucleotide adenylyltransferase activity, 0006351 transcription, DNA-dependent; PDB: 1Q79_A 1Q78_A 1F5A_A 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A.
Probab=21.85 E-value=1.5e+02 Score=24.93 Aligned_cols=56 Identities=16% Similarity=0.299 Sum_probs=33.1
Q ss_pred ccccCCCCChHHHHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhc
Q 031883 28 VRKINPKVPTQQAYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRG 89 (151)
Q Consensus 28 ~r~I~pkvP~Eqa~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMre 89 (151)
-.||...-|.++-..-+..|.+.|+++|++--.+.=.+-+++ ++ .=-+|+.+|.++
T Consensus 7 t~PIS~~~Pt~~Dl~~s~~L~~~l~~~~~~es~ee~~~R~~v-l~-----~L~~iv~~wv~~ 62 (254)
T PF04928_consen 7 TKPISLAPPTEKDLKRSASLEEFLKDYGLFESEEEEQKREEV-LR-----KLQQIVKEWVKQ 62 (254)
T ss_dssp T--S------HHHHHHHHHHHHHHHHCT-S--HHHHHHHHHH-HH-----HHHHHHHHHHHH
T ss_pred CCCccCCCCChhhHHhHHHHHHHHHHcCCCCChHHHhHHHHH-HH-----HHHHHHHHHHHh
Confidence 368999999999999999999999999999777644443333 22 223578889877
No 97
>TIGR00183 prok_nadp_idh isocitrate dehydrogenase, NADP-dependent, prokaryotic type. Prokaryotic NADP-dependent isocitrate dehydrogenases resemble their NAD-dependent counterparts and 3-isopropylmalate dehydrogenase (an NAD-dependent enzyme) more closely than they resemble eukaryotic NADP-dependent isocitrate dehydrogenases.
Probab=21.65 E-value=1.4e+02 Score=27.12 Aligned_cols=36 Identities=19% Similarity=0.164 Sum_probs=29.8
Q ss_pred hhHHHHHHHHhhhhhhccccccccCCCCChHHHHHHHHHHHHHHHHhCCcchh
Q 031883 8 VLSMETLVRYYSSSRKAAVNVRKINPKVPTQQAYSIAQSLYGIIKQHGPLTVS 60 (151)
Q Consensus 8 ~~~~~~~~R~fs~~rk~av~~r~I~pkvP~Eqa~tItr~l~dIlkeHGPLTVs 60 (151)
.+|+++++|||. . .+.|+.|-+++.++|++ |..|.+
T Consensus 357 IlS~amML~~lg--~--------------~~~A~~Ie~AV~~~l~~-G~~T~D 392 (416)
T TIGR00183 357 ILSGEMMLEHMG--W--------------KEAADLIKKAMEKAIAS-KIVTYD 392 (416)
T ss_pred HHHHHHHHHHcC--C--------------HHHHHHHHHHHHHHHHc-CCcccc
Confidence 357889999998 2 68899999999999986 777753
No 98
>PF12385 Peptidase_C70: Papain-like cysteine protease AvrRpt2; InterPro: IPR022118 This is a family of cysteine proteases, found in actinobacteria, protobacteria and firmicutes. Papain-like cysteine proteases play a crucial role in plant-pathogen/pest interactions. On entering the host they act on non-self substrates, thereby manipulating the host to evade proteolysis []. AvrRpt2 from Pseudomonas syringae pv tomato DC3000 triggers resistance to P. syringae-2-dependent defence responses, including hypersensitive cell death, by cleaving the Arabidopsis RIN4 protein which is monitored by the cognate resistance protein RPS2 [].
Probab=21.55 E-value=37 Score=28.05 Aligned_cols=25 Identities=28% Similarity=0.636 Sum_probs=17.7
Q ss_pred CChHHHHHHHHHHHHHHHHhCCcchh
Q 031883 35 VPTQQAYSIAQSLYGIIKQHGPLTVS 60 (151)
Q Consensus 35 vP~Eqa~tItr~l~dIlkeHGPLTVs 60 (151)
+|+.+-.+| +.+-+.|++||||=|+
T Consensus 90 ~P~~~~~t~-e~~~~LL~~yGPLwv~ 114 (166)
T PF12385_consen 90 EPANASYTA-EGLANLLREYGPLWVA 114 (166)
T ss_pred CCcccccCH-HHHHHHHHHcCCeEEE
Confidence 344344443 5678899999999888
No 99
>PRK06661 hypothetical protein; Provisional
Probab=21.17 E-value=34 Score=27.79 Aligned_cols=31 Identities=23% Similarity=0.394 Sum_probs=23.1
Q ss_pred hHHHHHHHHHHHH----HHHHhCCcchhhhhHHHH
Q 031883 37 TQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAK 67 (151)
Q Consensus 37 ~Eqa~tItr~l~d----IlkeHGPLTVsntW~hak 67 (151)
.+++..+++++-+ +|+.||.++++.+=+.|-
T Consensus 137 ~~~~~~~a~~l~~~~avll~nHG~v~~G~sl~eA~ 171 (231)
T PRK06661 137 DKQSSRLVNDLKQNYVMLLRNHGAITCGKTIHEAM 171 (231)
T ss_pred hhHHHHHHHHhCCCCEEEECCCCCeEecCCHHHHH
Confidence 3557777877744 689999999998766553
No 100
>PF10798 YmgB: Biofilm development protein YmgB/AriR; InterPro: IPR024753 YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid, which indicates that YmgB has an important function in acid-resistance []. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole) [].; GO: 0042710 biofilm formation, 0071229 cellular response to acid; PDB: 2OXL_B.
Probab=21.12 E-value=1e+02 Score=21.17 Aligned_cols=24 Identities=4% Similarity=0.144 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHhCCcchhh
Q 031883 38 QQAYSIAQSLYGIIKQHGPLTVSN 61 (151)
Q Consensus 38 Eqa~tItr~l~dIlkeHGPLTVsn 61 (151)
+|.+.+...+-+|+..++|+|=-+
T Consensus 2 ~E~~vL~~iv~ell~~g~~vsnKa 25 (61)
T PF10798_consen 2 SESEVLGAIVRELLASGGHVSNKA 25 (61)
T ss_dssp HHHHHHHHHHHHHHHTT---SHHH
T ss_pred cHHHHHHHHHHHHHHcCCCCCHHH
Confidence 578899999999999999988433
No 101
>TIGR02624 rhamnu_1P_ald rhamnulose-1-phosphate aldolase. Members of this family are the enzyme RhaD, rhamnulose-1-phosphate aldolase.
Probab=21.08 E-value=68 Score=27.02 Aligned_cols=32 Identities=9% Similarity=0.102 Sum_probs=22.4
Q ss_pred hHHHHHHHHHHHH----HHHHhCCcchhhhhHHHHH
Q 031883 37 TQQAYSIAQSLYG----IIKQHGPLTVSNTWIHAKD 68 (151)
Q Consensus 37 ~Eqa~tItr~l~d----IlkeHGPLTVsntW~hake 68 (151)
.|=|+.++..+-+ +|+.||.++++.+.+.|-.
T Consensus 189 ~eLA~~v~~~l~~~~avLL~nHGvva~G~~l~eA~~ 224 (270)
T TIGR02624 189 NEIGEATAEKMKEHRLVLWPHHGIFGAGPSLDETFG 224 (270)
T ss_pred HHHHHHHHHHhccCCEEEEcCCCCeEecCCHHHHHH
Confidence 3555555555543 6789999999988877654
No 102
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=21.03 E-value=1.2e+02 Score=19.81 Aligned_cols=46 Identities=13% Similarity=0.215 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHh-CCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeE
Q 031883 43 IAQSLYGIIKQH-GPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKL 95 (151)
Q Consensus 43 Itr~l~dIlkeH-GPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL 95 (151)
-+-.|++.|.++ ||+|+++-= ++.|+ |+.=...+|+=|.+...|..
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia---~~l~i----~~~tv~r~l~~L~~~g~l~~ 52 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELA---ERLGL----SKSTAHRLLNTLQELGYVEQ 52 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHH---HHhCC----CHHHHHHHHHHHHHCCCeee
Confidence 345678888888 899999764 34455 35555666666677777754
No 103
>PF07904 Eaf7: Chromatin modification-related protein EAF7; InterPro: IPR012423 The Saccharomyces cerevisiae (Baker's yeast) member of this family P53911 from SWISSPROT is part of NuA4, the only essential histone acetyltransferase complex in S. cerevisiae involved in global histone acetylation []. ; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus, 0043189 H4/H2A histone acetyltransferase complex
Probab=20.63 E-value=75 Score=22.94 Aligned_cols=21 Identities=14% Similarity=0.482 Sum_probs=16.7
Q ss_pred CCcchhhhhHHHHHh-ccCCCC
Q 031883 55 GPLTVSNTWIHAKDA-GISGLN 75 (151)
Q Consensus 55 GPLTVsntW~hake~-gi~gL~ 75 (151)
-.+|+.+.|+++... ++..|.
T Consensus 42 ~~~t~~~IW~kL~~~YdL~~ld 63 (91)
T PF07904_consen 42 KHFTIDDIWKKLRTLYDLEALD 63 (91)
T ss_pred CcCCHHHHHHHHHHhcCHHHhc
Confidence 689999999999887 655543
No 104
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=20.45 E-value=2.1e+02 Score=23.27 Aligned_cols=53 Identities=15% Similarity=0.245 Sum_probs=36.0
Q ss_pred HHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceeeec
Q 031883 48 YGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHST 110 (151)
Q Consensus 48 ~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLytt 110 (151)
.-||.=|.|+|-++. ..|+|.+|-.|++-|+ +|..++..=--..+.+-+||.|
T Consensus 93 LAIIAY~QPITr~eI------e~IRGv~s~~~l~~L~----ergLI~~~Gr~~~~Grp~ly~T 145 (186)
T TIGR00281 93 LAIIAYKQPITRARI------NEIRGVKSYQIVDDLV----EKGLVVELGRKDTPGRSFIYET 145 (186)
T ss_pred HHHHHHcCCcCHHHH------HHHcCCCHHHHHHHHH----HCCCeEecCcCCCCCCCeeehh
Confidence 457889999997653 4789999999888776 5666665422223345666654
No 105
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.39 E-value=1.1e+02 Score=21.87 Aligned_cols=54 Identities=9% Similarity=0.210 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHHHhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeecc
Q 031883 40 AYSIAQSLYGIIKQHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGV 100 (151)
Q Consensus 40 a~tItr~l~dIlkeHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~Cnhv 100 (151)
--.+-+.|+++|.+.|+++..+-|+.+ |+| ..+=.+++-+ |.++-+++-+...+
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~l---glS---~~~v~~Ri~~-L~~~GiI~~~~~~v 59 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERV---GLS---PSTVLRRIKR-LEEEGVIKGYTAVL 59 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHH---CCC---HHHHHHHHHH-HHHCCceeeEEEEE
Confidence 345678899999999999999887654 444 3333333333 45566665554433
No 106
>PF02186 TFIIE_beta: TFIIE beta subunit core domain; InterPro: IPR003166 Initiation of eukaryotic mRNA transcription requires melting of promoter DNA with the help of the general transcription factors TFIIE and TFIIH. In higher eukaryotes, the general transcription factor TFIIE consists of two subunits: the large alpha subunit (IPR002853 from INTERPRO) and the small beta (IPR003166 from INTERPRO). TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The approximately 120-residue central core domain of TFIIE beta plays a role in double-stranded DNA binding of TFIIE []. The TFIIE beta central core DNA-binding domain consists of three helices with a beta hairpin at the C terminus, resembling the winged helix proteins. It shows a novel double-stranded DNA-binding activity where the DNA-binding surface locates on the opposite side to the previously reported winged helix motif by forming a positively charged furrow []. This entry represents the beta subunit of the transcription factor TFIIE.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1D8K_A 1D8J_A.
Probab=20.21 E-value=3e+02 Score=18.87 Aligned_cols=45 Identities=20% Similarity=0.352 Sum_probs=24.9
Q ss_pred HhCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEEeeccCCCcceeeec
Q 031883 53 QHGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHST 110 (151)
Q Consensus 53 eHGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLytt 110 (151)
...|||+++.=++.. ..++ ..++.|++.-- |+..+.+| .+|.|.+
T Consensus 17 r~~Plt~~eI~d~l~-~d~~--------~~~~~~Lk~np--KI~~d~~~--~~f~fkp 61 (65)
T PF02186_consen 17 RDHPLTLEEILDYLS-LDIG--------KKLKQWLKNNP--KIEYDPDG--NTFSFKP 61 (65)
T ss_dssp H-S-B-HHHHHHHHT-SSS---------HHHHHHHHH-T--TEEEE-TT---CEEE--
T ss_pred cCCCcCHHHHHHHHc-CCCC--------HHHHHHHHcCC--CEEEecCC--CEEEecc
Confidence 367999999988887 5543 35778988444 44555334 5777764
No 107
>PF03283 PAE: Pectinacetylesterase
Probab=20.19 E-value=45 Score=29.15 Aligned_cols=40 Identities=28% Similarity=0.402 Sum_probs=30.5
Q ss_pred hCCcchhhhhHHHHHhccCCCCchhHHHHHHHHhhccceeeEE
Q 031883 54 HGPLTVSNTWIHAKDAGISGLNGKTHMKIMLKWMRGRKMLKLF 96 (151)
Q Consensus 54 HGPLTVsntW~hake~gi~gL~SK~HMKimLkWMreRq~lKL~ 96 (151)
|.=++.+++|..-. .--++.|+.-+.+-.|..+|+.+|.|
T Consensus 322 Hcq~~~~~~W~~~~---~p~v~g~tia~Av~dW~~~r~~~~~~ 361 (361)
T PF03283_consen 322 HCQSESSDTWNSPD---SPRVNGKTIAEAVGDWYFSRSEVKKI 361 (361)
T ss_pred hcccccCCcccCCC---cccCCCEEHHHHHHHHHhcccccccC
Confidence 56666677777544 33466789999999999999988764
No 108
>PRK08734 lipid A biosynthesis lauroyl acyltransferase; Provisional
Probab=20.11 E-value=1.8e+02 Score=24.12 Aligned_cols=46 Identities=4% Similarity=-0.003 Sum_probs=36.5
Q ss_pred chhHHHHHHHHhhccceeeEEeeccCCCcceeeecCCCCCCCCCCC
Q 031883 76 GKTHMKIMLKWMRGRKMLKLFCNGVGSNKKFLHSTLPEEPQTDQLE 121 (151)
Q Consensus 76 SK~HMKimLkWMreRq~lKL~CnhvG~~KqFLytt~~~~P~~~~~~ 121 (151)
....++.|++.+++-..|=+.+++.-+.+.-.+.++|-.|-..+..
T Consensus 169 ~~~~~r~li~~Lk~g~~v~~l~Dq~~~~~~gv~v~FfG~~a~t~~g 214 (305)
T PRK08734 169 EGPAVRQLFKVLKDGGAVGILPDQQPKMGDGVFAPFFGIPALTMTL 214 (305)
T ss_pred CchhHHHHHHHHhcCCeEEEeCCCCCCCCCCeEeccCCCccchhhH
Confidence 3456999999999999999999998544557888999887655543
Done!