Query 042237
Match_columns 115
No_of_seqs 23 out of 25
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 04:15:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042237.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042237hhsearch_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, 96.4 0.0059 1.3E-07 39.4 3.9 38 28-65 2-40 (72)
2 PF06163 DUF977: Bacterial pro 92.6 0.14 3E-06 38.9 3.2 27 22-48 6-32 (127)
3 PF11784 DUF3320: Protein of u 86.1 2 4.4E-05 27.0 4.3 39 24-62 8-47 (52)
4 PF03981 Ubiq_cyt_C_chap: Ubiq 85.2 2.7 5.9E-05 29.4 5.1 53 19-78 27-79 (141)
5 PF06224 HTH_42: Winged helix 85.0 2.4 5.2E-05 33.2 5.2 59 19-79 76-137 (327)
6 PF08100 Dimerisation: Dimeris 81.2 1.2 2.5E-05 28.4 1.8 21 32-52 10-32 (51)
7 PF12932 Sec16: Vesicle coat t 80.3 2.1 4.6E-05 30.2 3.0 14 63-76 67-80 (118)
8 PRK06474 hypothetical protein; 77.3 3.3 7.3E-05 31.3 3.5 39 31-71 14-53 (178)
9 cd07153 Fur_like Ferric uptake 75.4 4.4 9.5E-05 27.2 3.3 50 31-82 4-54 (116)
10 PF03965 Penicillinase_R: Peni 74.5 5.6 0.00012 27.4 3.8 60 32-98 7-66 (115)
11 COG0235 AraD Ribulose-5-phosph 72.5 3.6 7.7E-05 31.8 2.6 30 25-54 147-176 (219)
12 PF09582 AnfO_nitrog: Iron onl 71.2 1.2 2.6E-05 35.1 -0.2 30 55-87 145-176 (202)
13 PF01475 FUR: Ferric uptake re 69.1 8.3 0.00018 26.3 3.6 51 31-83 11-62 (120)
14 COG2345 Predicted transcriptio 66.5 5.5 0.00012 32.2 2.6 37 31-70 14-50 (218)
15 PF13412 HTH_24: Winged helix- 64.5 9.2 0.0002 22.3 2.7 36 29-67 4-39 (48)
16 PF12840 HTH_20: Helix-turn-he 61.9 11 0.00023 23.3 2.8 39 30-71 12-50 (61)
17 PRK09462 fur ferric uptake reg 59.9 14 0.0003 26.6 3.4 50 31-82 20-71 (148)
18 PRK08660 L-fuculose phosphate 59.6 4.7 0.0001 29.9 1.0 34 22-55 125-162 (181)
19 TIGR01086 fucA L-fuculose phos 59.4 8.6 0.00019 29.4 2.4 32 23-54 133-168 (214)
20 PF07237 DUF1428: Protein of u 59.0 3.2 7E-05 30.3 0.1 26 26-51 18-43 (103)
21 PRK05874 L-fuculose-phosphate 59.0 5.1 0.00011 31.1 1.2 42 14-55 130-175 (217)
22 PRK08193 araD L-ribulose-5-pho 58.4 5.9 0.00013 30.8 1.4 31 24-54 143-184 (231)
23 smart00550 Zalpha Z-DNA-bindin 58.1 13 0.00029 23.9 2.8 42 29-77 7-50 (68)
24 TIGR02698 CopY_TcrY copper tra 57.9 37 0.0008 24.4 5.4 59 32-97 8-66 (130)
25 PF01022 HTH_5: Bacterial regu 57.6 11 0.00024 22.4 2.2 36 32-71 6-41 (47)
26 PF08220 HTH_DeoR: DeoR-like h 57.1 9.8 0.00021 23.7 2.0 34 31-67 3-36 (57)
27 TIGR02940 anfO_nitrog Fe-only 55.4 3.6 7.9E-05 33.3 -0.2 30 55-87 154-185 (214)
28 cd07977 TFIIE_beta_winged_heli 54.8 25 0.00055 23.7 3.9 40 32-79 13-54 (75)
29 PF02295 z-alpha: Adenosine de 54.4 36 0.00078 22.3 4.5 59 26-92 2-60 (66)
30 smart00347 HTH_MARR helix_turn 53.8 40 0.00086 20.9 4.5 45 31-82 13-57 (101)
31 PRK08333 L-fuculose phosphate 53.4 8.2 0.00018 28.7 1.4 31 24-54 133-167 (184)
32 smart00420 HTH_DEOR helix_turn 52.3 28 0.0006 19.4 3.3 17 32-48 4-20 (53)
33 cd00736 bacteriophage_lambda_l 50.6 29 0.00062 26.7 4.0 56 46-103 71-130 (151)
34 cd00167 SANT 'SWI3, ADA2, N-Co 49.2 41 0.00089 18.0 3.7 35 31-73 8-42 (45)
35 PF07508 Recombinase: Recombin 48.9 71 0.0015 20.6 5.3 32 24-58 2-33 (102)
36 PRK06833 L-fuculose phosphate 48.7 8.6 0.00019 29.4 0.9 29 26-54 139-171 (214)
37 PF02581 TMP-TENI: Thiamine mo 48.6 21 0.00046 26.2 3.0 39 22-60 37-76 (180)
38 PF10557 Cullin_Nedd8: Cullin 48.3 52 0.0011 21.1 4.4 57 26-82 6-63 (68)
39 PRK06357 hypothetical protein; 48.3 12 0.00027 29.0 1.8 39 16-54 135-183 (216)
40 COG3355 Predicted transcriptio 46.0 16 0.00035 27.4 2.0 55 31-95 31-89 (126)
41 PF08461 HTH_12: Ribonuclease 45.6 48 0.001 21.5 4.0 45 32-79 2-48 (66)
42 PRK10141 DNA-binding transcrip 45.3 28 0.0006 25.3 3.1 37 31-70 19-55 (117)
43 PRK06557 L-ribulose-5-phosphat 44.7 8.9 0.00019 29.3 0.5 32 23-54 142-179 (221)
44 PF08221 HTH_9: RNA polymerase 44.1 25 0.00055 22.5 2.5 23 28-50 13-35 (62)
45 PF09107 SelB-wing_3: Elongati 44.0 18 0.00039 22.8 1.7 36 33-75 1-36 (50)
46 PRK07490 hypothetical protein; 43.7 8.4 0.00018 30.3 0.2 30 24-53 147-180 (245)
47 PF13331 DUF4093: Domain of un 43.1 26 0.00055 24.4 2.5 58 27-93 10-69 (87)
48 PF14769 CLAMP: Flagellar C1a 42.8 1.1E+02 0.0023 21.0 6.7 55 20-75 11-78 (101)
49 PRK09220 methylthioribulose-1- 42.7 12 0.00026 28.6 0.9 31 24-54 146-183 (204)
50 PF01250 Ribosomal_S6: Ribosom 40.3 43 0.00093 22.1 3.2 24 18-41 10-33 (92)
51 TIGR02757 conserved hypothetic 39.2 1.2E+02 0.0027 24.6 6.2 54 22-75 79-155 (229)
52 TIGR03328 salvage_mtnB methylt 39.2 7.1 0.00015 29.4 -0.8 20 36-55 157-176 (193)
53 KOG1613 Exosomal 3'-5' exoribo 38.5 36 0.00078 29.2 3.2 29 16-44 106-134 (298)
54 PHA00738 putative HTH transcri 38.3 38 0.00083 25.1 2.9 38 29-69 13-50 (108)
55 PF15645 Tox-PLDMTX: Dermonecr 38.2 34 0.00074 25.8 2.7 23 20-42 1-23 (135)
56 PF08158 NUC130_3NT: NUC130/3N 38.1 37 0.00081 21.8 2.5 20 23-42 10-29 (52)
57 PF14214 Helitron_like_N: Heli 37.6 39 0.00084 24.8 2.9 30 72-103 88-117 (184)
58 PRK06486 hypothetical protein; 37.4 13 0.00027 29.8 0.3 53 23-75 162-236 (262)
59 PRK03634 rhamnulose-1-phosphat 36.6 20 0.00043 29.0 1.3 33 22-54 190-226 (274)
60 PF10771 DUF2582: Protein of u 35.6 39 0.00084 22.6 2.4 42 26-74 6-47 (65)
61 PRK02363 DNA-directed RNA poly 34.6 64 0.0014 24.0 3.6 29 28-56 4-33 (129)
62 PF07798 DUF1640: Protein of u 34.2 43 0.00094 25.1 2.7 21 20-40 15-35 (177)
63 TIGR01568 A_thal_3678 uncharac 34.0 40 0.00087 22.9 2.3 42 28-72 13-56 (66)
64 PF07208 DUF1414: Protein of u 34.0 39 0.00084 21.7 2.1 23 17-39 20-42 (44)
65 PRK08087 L-fuculose phosphate 34.0 24 0.00052 27.0 1.4 31 24-54 135-169 (215)
66 PF00352 TBP: Transcription fa 33.8 52 0.0011 21.8 2.8 20 22-41 67-86 (86)
67 PF10330 Stb3: Putative Sin3 b 33.3 90 0.002 22.7 4.1 44 31-74 9-54 (92)
68 TIGR00760 araD L-ribulose-5-ph 33.2 19 0.00041 28.1 0.7 25 24-48 144-179 (231)
69 TIGR02702 SufR_cyano iron-sulf 32.2 58 0.0013 24.5 3.1 45 31-82 4-48 (203)
70 COG4901 Ribosomal protein S25 32.0 85 0.0018 23.5 3.9 68 22-96 35-103 (107)
71 CHL00123 rps6 ribosomal protei 31.5 68 0.0015 22.2 3.2 35 17-51 14-49 (97)
72 cd08304 DD_superfamily The Dea 30.6 1.1E+02 0.0024 19.9 3.9 38 21-58 24-63 (69)
73 PRK08130 putative aldolase; Va 29.9 20 0.00043 27.3 0.3 31 24-54 140-174 (213)
74 PRK06754 mtnB methylthioribulo 29.9 18 0.0004 27.6 0.1 33 23-55 148-185 (208)
75 smart00717 SANT SANT SWI3, AD 29.6 98 0.0021 16.6 3.7 35 32-74 11-45 (49)
76 PF07904 Eaf7: Chromatin modif 29.6 48 0.0011 23.0 2.2 30 32-61 26-63 (91)
77 PRK06512 thiamine-phosphate py 29.5 78 0.0017 24.7 3.6 40 21-60 51-91 (221)
78 PRK13247 dihydrobiliverdin:fer 29.1 60 0.0013 26.5 2.9 31 75-105 48-78 (238)
79 PHA02517 putative transposase 29.0 2.3E+02 0.005 21.6 6.0 49 25-78 27-76 (277)
80 PF01047 MarR: MarR family; I 29.0 81 0.0017 18.6 2.8 38 33-77 8-45 (59)
81 PF06999 Suc_Fer-like: Sucrase 28.8 18 0.0004 27.4 -0.0 10 81-90 173-182 (230)
82 PRK12347 sgbE L-ribulose-5-pho 28.5 25 0.00054 27.6 0.6 28 24-51 144-182 (231)
83 KOG4382 Uncharacterized conser 28.1 22 0.00047 30.2 0.3 22 38-59 135-157 (276)
84 COG1522 Lrp Transcriptional re 27.9 92 0.002 21.5 3.4 27 26-52 6-32 (154)
85 PRK13246 dihydrobiliverdin:fer 27.5 65 0.0014 26.4 2.9 31 75-105 48-78 (236)
86 PF10826 DUF2551: Protein of u 27.4 96 0.0021 22.2 3.4 45 28-76 11-56 (83)
87 cd03156 uroplakin_I_like_LEL T 27.1 1.1E+02 0.0025 19.7 3.5 33 27-59 11-49 (114)
88 PF09012 FeoC: FeoC like trans 27.1 55 0.0012 20.7 2.0 43 31-80 3-45 (69)
89 PF04675 DNA_ligase_A_N: DNA l 27.0 2.4E+02 0.0052 20.2 5.5 47 28-74 89-143 (177)
90 PF13565 HTH_32: Homeodomain-l 27.0 44 0.00096 20.8 1.5 19 44-62 1-19 (77)
91 PRK13250 phycoerythrobilin:fer 26.7 68 0.0015 26.4 2.9 30 75-104 57-86 (248)
92 cd00398 Aldolase_II Class II A 26.6 16 0.00035 27.5 -0.6 19 36-54 153-171 (209)
93 KOG3280 Mitochondrial/chloropl 26.5 1.7E+02 0.0037 23.5 5.0 63 18-82 16-89 (171)
94 PF10798 YmgB: Biofilm develop 26.5 69 0.0015 21.1 2.4 24 24-47 2-25 (61)
95 PF00102 Y_phosphatase: Protei 26.4 2.4E+02 0.0053 20.1 6.1 48 28-75 188-235 (235)
96 PRK12348 sgaE L-ribulose-5-pho 26.2 28 0.0006 27.1 0.5 27 24-50 142-177 (228)
97 PF12063 DUF3543: Domain of un 26.2 82 0.0018 25.3 3.2 43 40-83 85-135 (238)
98 PRK00441 argR arginine repress 25.9 96 0.0021 23.2 3.4 59 31-98 7-65 (149)
99 PF04358 DsrC: DsrC like prote 25.7 11 0.00024 27.2 -1.6 58 41-101 15-92 (109)
100 PF04806 EspF: EspF protein re 25.6 56 0.0012 21.3 1.8 13 29-41 35-47 (47)
101 PRK13249 phycoerythrobilin:fer 25.5 73 0.0016 26.4 2.9 61 40-104 35-100 (257)
102 PF09535 Gmx_para_CXXCG: Prote 25.4 28 0.00062 29.0 0.5 23 40-62 104-135 (237)
103 cd08329 CARD_BIRC2_BIRC3 Caspa 24.7 1.3E+02 0.0028 20.9 3.6 65 30-99 25-91 (94)
104 smart00346 HTH_ICLR helix_turn 24.5 1E+02 0.0023 19.3 2.9 45 29-80 6-51 (91)
105 PF14338 Mrr_N: Mrr N-terminal 23.9 1.9E+02 0.004 19.2 4.2 31 28-58 4-36 (92)
106 cd08768 Cdc6_C Winged-helix do 23.6 1.5E+02 0.0033 18.7 3.6 21 41-61 42-62 (87)
107 PRK06755 hypothetical protein; 23.3 49 0.0011 25.9 1.4 18 37-54 166-183 (209)
108 cd03154 TM4SF3_like_LEL Tetras 23.2 1.7E+02 0.0036 18.9 3.7 36 27-62 13-51 (100)
109 PF14090 HTH_39: Helix-turn-he 23.1 92 0.002 20.0 2.5 21 30-50 3-23 (70)
110 PF08279 HTH_11: HTH domain; 22.9 86 0.0019 18.4 2.2 39 32-73 4-43 (55)
111 TIGR00334 5S_RNA_mat_M5 ribonu 22.9 91 0.002 24.6 2.8 64 21-93 91-156 (174)
112 PRK13145 araD L-ribulose-5-pho 22.3 36 0.00078 26.7 0.5 29 24-52 144-183 (234)
113 TIGR00693 thiE thiamine-phosph 22.0 1.1E+02 0.0024 22.1 3.0 38 23-60 39-77 (196)
114 smart00441 FF Contains two con 21.8 1.1E+02 0.0025 18.0 2.6 26 30-55 4-29 (55)
115 PRK08570 rpl19e 50S ribosomal 21.6 2.6E+02 0.0057 21.8 5.1 46 26-71 98-143 (150)
116 PF09597 IGR: IGR protein moti 21.1 1.1E+02 0.0024 20.1 2.6 32 38-74 13-52 (57)
117 PRK06661 hypothetical protein; 20.9 30 0.00065 27.1 -0.2 30 23-52 137-170 (231)
118 PF11855 DUF3375: Protein of u 20.6 1.1E+02 0.0024 26.7 3.1 32 27-58 402-434 (478)
119 PRK02816 phycocyanobilin:ferre 20.4 69 0.0015 26.1 1.8 29 76-104 66-94 (243)
120 PF00596 Aldolase_II: Class II 20.2 28 0.00062 25.2 -0.4 31 24-54 136-171 (184)
121 KOG1575 Voltage-gated shaker-l 20.2 1.7E+02 0.0036 25.2 4.1 23 24-47 254-276 (336)
122 PF12777 MT: Microtubule-bindi 20.1 1.3E+02 0.0028 24.7 3.3 37 19-55 112-148 (344)
123 PRK11639 zinc uptake transcrip 20.1 1.5E+02 0.0033 22.0 3.5 49 32-82 30-79 (169)
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=96.38 E-value=0.0059 Score=39.36 Aligned_cols=38 Identities=32% Similarity=0.722 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHHhC-CcchHhHHHHHHHhccCCCCchhH
Q 042237 28 TITRVIFDIVKEHG-PLTVAETWERVQQAGVSGLTGKSH 65 (115)
Q Consensus 28 titr~l~dIvkeHG-PLTV~~tW~h~ke~g~~gL~SK~H 65 (115)
|+..+.+.||+++| |+|+.|.|+.+++.|+-.-.+|+=
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 57788999999998 999999999999998776555643
No 2
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=92.59 E-value=0.14 Score=38.86 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=24.7
Q ss_pred ChhHHHHHHHHHHHHHHHhCCcchHhH
Q 042237 22 PPEQTQTITRVIFDIVKEHGPLTVAET 48 (115)
Q Consensus 22 p~eqa~titr~l~dIvkeHGPLTV~~t 48 (115)
-+||.+.|...|.+++++||.+|+.+-
T Consensus 6 T~eer~eLk~rIvElVRe~GRiTi~ql 32 (127)
T PF06163_consen 6 TPEEREELKARIVELVREHGRITIKQL 32 (127)
T ss_pred CHHHHHHHHHHHHHHHHHcCCccHHHH
Confidence 369999999999999999999999873
No 3
>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=86.08 E-value=2 Score=27.05 Aligned_cols=39 Identities=31% Similarity=0.452 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHHHHhCCcchHhHHHHHHHh-ccCCCCc
Q 042237 24 EQTQTITRVIFDIVKEHGPLTVAETWERVQQA-GVSGLTG 62 (115)
Q Consensus 24 eqa~titr~l~dIvkeHGPLTV~~tW~h~ke~-g~~gL~S 62 (115)
+-+..+++.|.+||..-|||..+..=.++.++ |++-+.+
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 34567999999999999999999999999888 8876554
No 4
>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=85.16 E-value=2.7 Score=29.42 Aligned_cols=53 Identities=25% Similarity=0.333 Sum_probs=45.6
Q ss_pred CCCChhHHHHHHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhH
Q 042237 19 LKAPPEQTQTITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQK 78 (115)
Q Consensus 19 ~k~p~eqa~titr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~ 78 (115)
++.-++++..+.+.|+|.+ ..+.++++.|.|++.+.....||-|-..+.+|-.
T Consensus 27 Lk~~~~~~~~~~q~l~~~~-------~~d~~~~l~~~gv~d~~~~k~~k~l~~~~~g~~~ 79 (141)
T PF03981_consen 27 LKAEGKEGKELEQALFDKF-------FEDMDERLREMGVGDLSVGKRMKKLQEQFYGRLL 79 (141)
T ss_pred HccccccHHHHHHHHHHHH-------HHHHHHHHHHhcCcchhhhHHHHHHHHHHHHHHH
Confidence 4445578899999999987 5789999999999999999999999888888743
No 5
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=85.00 E-value=2.4 Score=33.23 Aligned_cols=59 Identities=32% Similarity=0.503 Sum_probs=46.8
Q ss_pred CCCChhHHHHHHHHHHHHHHHhCCcchHhHHHHHHHh---ccCCCCchhHHHHHHHHHHhhhHH
Q 042237 19 LKAPPEQTQTITRVIFDIVKEHGPLTVAETWERVQQA---GVSGLTGKSHMKIVLRWMRERQKL 79 (115)
Q Consensus 19 ~k~p~eqa~titr~l~dIvkeHGPLTV~~tW~h~ke~---g~~gL~SK~HMKi~LrWMreRq~l 79 (115)
.....++...++..|.+.|+++||+|-++.-+++.+. +.++.. ...+.+|..|..+-.|
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 4566778888999999999999999999999999888 343332 3677888888877544
No 6
>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=81.24 E-value=1.2 Score=28.43 Aligned_cols=21 Identities=38% Similarity=0.602 Sum_probs=16.1
Q ss_pred HHHHHHHHhC--CcchHhHHHHH
Q 042237 32 VIFDIVKEHG--PLTVAETWERV 52 (115)
Q Consensus 32 ~l~dIvkeHG--PLTV~~tW~h~ 52 (115)
-|+||+..|| |+|.+|.=.++
T Consensus 10 gI~dii~~~g~~~ls~~eia~~l 32 (51)
T PF08100_consen 10 GIPDIIHNAGGGPLSLSEIAARL 32 (51)
T ss_dssp THHHHHHHHTTS-BEHHHHHHTS
T ss_pred CcHHHHHHcCCCCCCHHHHHHHc
Confidence 4899999998 99999874443
No 7
>PF12932 Sec16: Vesicle coat trafficking protein Sec16 mid-region; InterPro: IPR024340 The yeast protein Sec16 plays a key role in the formation of coat protein II vesicles, which mediate protein transport from the endoplasmic reticulum (ER) to the Golgi apparatus []. Mammals have two isoforms of this protein - Sec16A and Sec16B. Sec16A appears to be the primary orthologue as it has the highest sequence similarity to the yeast sequence. Sec16B is involved in export of the peroxisomal membrane biogenesis factor peroxin 16 []. This entry represents the central conserved domain (CCD) of Sec16, found in all isoforms of this protein. The CCD is necessary for targeting of the protein to the ER [].; PDB: 3MZK_C.
Probab=80.33 E-value=2.1 Score=30.23 Aligned_cols=14 Identities=36% Similarity=0.854 Sum_probs=10.7
Q ss_pred hhHHHHHHHHHHhh
Q 042237 63 KSHMKIVLRWMRER 76 (115)
Q Consensus 63 K~HMKi~LrWMreR 76 (115)
|+|-|-+++|+.+|
T Consensus 67 ktkKkdV~kwl~~~ 80 (118)
T PF12932_consen 67 KTKKKDVIKWLEEK 80 (118)
T ss_dssp T--HHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH
Confidence 89999999999765
No 8
>PRK06474 hypothetical protein; Provisional
Probab=77.26 E-value=3.3 Score=31.30 Aligned_cols=39 Identities=18% Similarity=0.171 Sum_probs=30.6
Q ss_pred HHHHHHHHHhCC-cchHhHHHHHHHhccCCCCchhHHHHHHH
Q 042237 31 RVIFDIVKEHGP-LTVAETWERVQQAGVSGLTGKSHMKIVLR 71 (115)
Q Consensus 31 r~l~dIvkeHGP-LTV~~tW~h~ke~g~~gL~SK~HMKi~Lr 71 (115)
..|+++|.++|+ +|+.+..+++. +++.=+.-+|+++|.+
T Consensus 14 ~~Il~~L~~~~~~~ta~el~~~l~--~is~aTvYrhL~~L~e 53 (178)
T PRK06474 14 MKICQVLMRNKEGLTPLELVKILK--DVPQATLYRHLQTMVD 53 (178)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHhc--CCCHHHHHHHHHHHHH
Confidence 568888988875 99999999875 4555677789888754
No 9
>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=75.42 E-value=4.4 Score=27.21 Aligned_cols=50 Identities=28% Similarity=0.417 Sum_probs=36.8
Q ss_pred HHHHHHHHH-hCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 31 RVIFDIVKE-HGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 31 r~l~dIvke-HGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
+.|+++|.+ .+|+|+.+.++.+++.|.+ =|..=--..|+.|-+...|+.+
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 467888877 5799999999999987532 2334455677888888877764
No 10
>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=74.47 E-value=5.6 Score=27.41 Aligned_cols=60 Identities=22% Similarity=0.359 Sum_probs=44.5
Q ss_pred HHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCcceeeeecc
Q 042237 32 VIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQFLYTTWF 98 (115)
Q Consensus 32 ~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FLyttw~ 98 (115)
.|.+||=++||+|+.+..+.+.+. .++ +++=-+-+|+=|-++..|.. ... .+.|.|++--
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~l~~~--~~~-~~sTv~t~L~rL~~Kg~l~~--~~~--gr~~~Y~p~i 66 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEALPEE--RSW-AYSTVQTLLNRLVEKGFLTR--EKI--GRAYVYSPLI 66 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHCTT--SS---HHHHHHHHHHHHHTTSEEE--EEE--TTCEEEEESS
T ss_pred HHHHHHHhCCCCCHHHHHHHHHhc--ccc-chhHHHHHHHHHHhCCceeE--eec--CCceEEEeCC
Confidence 578999999999999999999887 555 55666777777888777654 233 4588887643
No 11
>COG0235 AraD Ribulose-5-phosphate 4-epimerase and related epimerases and aldolases [Carbohydrate transport and metabolism]
Probab=72.55 E-value=3.6 Score=31.81 Aligned_cols=30 Identities=10% Similarity=0.380 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHhCCcchHhHHHHHHH
Q 042237 25 QTQTITRVIFDIVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 25 qa~titr~l~dIvkeHGPLTV~~tW~h~ke 54 (115)
++..+.+...-++++||+++++.+++.|..
T Consensus 147 ~~~~~~~~~~~ll~~HG~~~~G~~l~eA~~ 176 (219)
T COG0235 147 EAADLAEAVLKLLRNHGVVAWGKTLAEAVH 176 (219)
T ss_pred HHHHHHHHHHHHHHcCCcEEECCCHHHHHH
Confidence 334455555667999999999998887754
No 12
>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=71.22 E-value=1.2 Score=35.08 Aligned_cols=30 Identities=37% Similarity=0.793 Sum_probs=26.0
Q ss_pred hccCCCCchhHHHHHHHHHHhh--hHHHHhhhccC
Q 042237 55 AGVSGLTGKSHMKIVLRWMRER--QKLRLICNHVG 87 (115)
Q Consensus 55 ~g~~gL~SK~HMKi~LrWMreR--q~lkl~C~hvG 87 (115)
.+..||||| ++++-.+++. +.|.++|+|+=
T Consensus 145 ~~~~~ltSK---qvL~PFL~~~~F~~LeViC~HvP 176 (202)
T PF09582_consen 145 AKNPGLTSK---QVLIPFLRNGPFRRLEVICDHVP 176 (202)
T ss_pred hhCCCCcHH---HHHHHHhcCCCceEEEEEeCCCC
Confidence 378899998 6899999988 78999999984
No 13
>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=69.06 E-value=8.3 Score=26.33 Aligned_cols=51 Identities=22% Similarity=0.342 Sum_probs=39.2
Q ss_pred HHHHHHHHHh-CCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhh
Q 042237 31 RVIFDIVKEH-GPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLIC 83 (115)
Q Consensus 31 r~l~dIvkeH-GPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C 83 (115)
++|+++|.++ +|+|+.+.|+.+++.|.+ -|..=--.-|+.+.+..+|+.+.
T Consensus 11 ~~Il~~l~~~~~~~ta~ei~~~l~~~~~~--is~~TVYR~L~~L~e~Gli~~~~ 62 (120)
T PF01475_consen 11 LAILELLKESPEHLTAEEIYDKLRKKGPR--ISLATVYRTLDLLEEAGLIRKIE 62 (120)
T ss_dssp HHHHHHHHHHSSSEEHHHHHHHHHHTTTT----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHcCCCCCCHHHHHHHhhhccCC--cCHHHHHHHHHHHHHCCeEEEEE
Confidence 4688999987 599999999999986543 14445567889999998887763
No 14
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=66.47 E-value=5.5 Score=32.16 Aligned_cols=37 Identities=22% Similarity=0.498 Sum_probs=31.4
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHH
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVL 70 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~L 70 (115)
+.|.-.+++|||+|+++. +++.||+.-.=++||.-+-
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 567788999999999975 7778999999999998764
No 15
>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=64.49 E-value=9.2 Score=22.34 Aligned_cols=36 Identities=25% Similarity=0.343 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHH
Q 042237 29 ITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMK 67 (115)
Q Consensus 29 itr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMK 67 (115)
.-+.|++.|.++|.+|+.+. ++..|++.=+-.+|++
T Consensus 4 ~~~~Il~~l~~~~~~t~~el---a~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKEL---AEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHH---HHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHH---HHHhCCCHHHHHHHHH
Confidence 34678999999999999875 5555666433333433
No 16
>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=61.95 E-value=11 Score=23.27 Aligned_cols=39 Identities=31% Similarity=0.411 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHH
Q 042237 30 TRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLR 71 (115)
Q Consensus 30 tr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~Lr 71 (115)
-..|++.|..+||+|+++.=+. .|++-=+=..|++.|.+
T Consensus 12 R~~Il~~L~~~~~~t~~ela~~---l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 12 RLRILRLLASNGPMTVSELAEE---LGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HHHHHHHHHHCSTBEHHHHHHH---HTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCCCCCHHHHHHH---HCCCHHHHHHHHHHHHH
Confidence 3578888899999999986443 35554445578877653
No 17
>PRK09462 fur ferric uptake regulator; Provisional
Probab=59.89 E-value=14 Score=26.56 Aligned_cols=50 Identities=14% Similarity=0.237 Sum_probs=36.4
Q ss_pred HHHHHHHHHh--CCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 31 RVIFDIVKEH--GPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 31 r~l~dIvkeH--GPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
++|+++|.++ +|+|+.+..+.+++.+-+ -|..=-=..|+.+.+-.+|+.+
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 4678888874 699999999999998643 1233345667888887777654
No 18
>PRK08660 L-fuculose phosphate aldolase; Provisional
Probab=59.55 E-value=4.7 Score=29.86 Aligned_cols=34 Identities=21% Similarity=0.427 Sum_probs=26.6
Q ss_pred ChhHHHHHHHHHHH----HHHHhCCcchHhHHHHHHHh
Q 042237 22 PPEQTQTITRVIFD----IVKEHGPLTVAETWERVQQA 55 (115)
Q Consensus 22 p~eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke~ 55 (115)
..|-|+.+++++-| |++.||.++++.+.+.+...
T Consensus 125 ~~~la~~v~~~l~~~~~vll~nHG~~~~G~~i~~A~~~ 162 (181)
T PRK08660 125 SGELAENVARALSEHKGVVVRGHGTFAIGKTLEEAYIY 162 (181)
T ss_pred CHHHHHHHHHHHhhCCEEEEcCCCceEeCCCHHHHHHH
Confidence 34667777777765 78999999999998887653
No 19
>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=59.38 E-value=8.6 Score=29.39 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=25.1
Q ss_pred hhHHHHHHHHHHH----HHHHhCCcchHhHHHHHHH
Q 042237 23 PEQTQTITRVIFD----IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 23 ~eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke 54 (115)
.|.++.+...+-| +|+.||.++++.++..+..
T Consensus 133 ~~la~~v~~~~~~~~~vLL~nHG~~~~G~~l~eA~~ 168 (214)
T TIGR01086 133 TKLASEVVAGILKSKAILLLHHGLIIACENLLKALW 168 (214)
T ss_pred HHHHHHHHHHhhhCCEEehhcCCCEEecCCHHHHHH
Confidence 4666777777665 7899999999999888754
No 20
>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=58.98 E-value=3.2 Score=30.26 Aligned_cols=26 Identities=31% Similarity=0.616 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHhCCcchHhHHHH
Q 042237 26 TQTITRVIFDIVKEHGPLTVAETWER 51 (115)
Q Consensus 26 a~titr~l~dIvkeHGPLTV~~tW~h 51 (115)
=...++.--.|++|||.|.|-+||.-
T Consensus 18 Y~~~A~~a~~vf~e~GAl~~vE~wgd 43 (103)
T PF07237_consen 18 YRAMAEKAAEVFKEHGALRVVECWGD 43 (103)
T ss_dssp HHHHHHHHHHHHHHTT-SEEEEEEEE
T ss_pred HHHHHHHHHHHHHHhCCEEEEEeecC
Confidence 34567778899999999999999964
No 21
>PRK05874 L-fuculose-phosphate aldolase; Validated
Probab=58.97 E-value=5.1 Score=31.11 Aligned_cols=42 Identities=17% Similarity=0.287 Sum_probs=31.3
Q ss_pred CCcccCCCChhHHHHHHHHHHH----HHHHhCCcchHhHHHHHHHh
Q 042237 14 MKPIELKAPPEQTQTITRVIFD----IVKEHGPLTVAETWERVQQA 55 (115)
Q Consensus 14 mrpi~~k~p~eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke~ 55 (115)
+.|..+..-.|.++.|++.+-| ||+.||.++++.+++.+...
T Consensus 130 ~~~y~~~gs~ela~~v~~~l~~~~~vlL~nHGv~~~G~~l~~A~~~ 175 (217)
T PRK05874 130 CTEYAASGTPEVGRNAVRALEGRAAALIANHGLVAVGPRPDQVLRV 175 (217)
T ss_pred eecCCCCCcHHHHHHHHHHhCcCCEEEEcCCCCeEecCCHHHHHHH
Confidence 3344444446788888888866 78999999999988887654
No 22
>PRK08193 araD L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=58.39 E-value=5.9 Score=30.85 Aligned_cols=31 Identities=26% Similarity=0.392 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHH-----------HHHHhCCcchHhHHHHHHH
Q 042237 24 EQTQTITRVIFD-----------IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 24 eqa~titr~l~d-----------IvkeHGPLTV~~tW~h~ke 54 (115)
|.+..|+..+-+ |++.||.++++.+++.+..
T Consensus 143 ~~~~~ia~~l~~~~~~~~~~~avLl~nHG~v~~G~~l~eA~~ 184 (231)
T PRK08193 143 ETGKVIVETFEKRGIDPAAVPGVLVHSHGPFTWGKDAEDAVH 184 (231)
T ss_pred hHHHHHHHHHhhccCCcccCCEEEEcCCCceEecCCHHHHHH
Confidence 677888888864 6889999999999988764
No 23
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=58.09 E-value=13 Score=23.90 Aligned_cols=42 Identities=19% Similarity=0.331 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCC--cchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhh
Q 042237 29 ITRVIFDIVKEHGP--LTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQ 77 (115)
Q Consensus 29 itr~l~dIvkeHGP--LTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq 77 (115)
.-+.|++.|+++|+ +|.++-+..+ ||+++. ....|.=|.++.
T Consensus 7 ~~~~IL~~L~~~g~~~~ta~eLa~~l------gl~~~~-v~r~L~~L~~~G 50 (68)
T smart00550 7 LEEKILEFLENSGDETSTALQLAKNL------GLPKKE-VNRVLYSLEKKG 50 (68)
T ss_pred HHHHHHHHHHHCCCCCcCHHHHHHHH------CCCHHH-HHHHHHHHHHCC
Confidence 34789999999999 9999987665 455543 334444444443
No 24
>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=57.86 E-value=37 Score=24.43 Aligned_cols=59 Identities=17% Similarity=0.259 Sum_probs=41.2
Q ss_pred HHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCcceeeeec
Q 042237 32 VIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQFLYTTW 97 (115)
Q Consensus 32 ~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FLyttw 97 (115)
.|.++|-+.||+|+.+.-+++.+. .|++ ++=+.-+|+=|-++..|... -..+.|+|++-
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~--~~~~-~tTv~T~L~rL~~KG~v~~~----k~gr~~~Y~p~ 66 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEK--KDWS-DSTIKTLLGRLVDKGCLTTE----KEGRKFIYTAL 66 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhc--cCCc-HHHHHHHHHHHHHCCceeee----cCCCcEEEEec
Confidence 477888889999999999998764 3333 45566677777777766543 22357888853
No 25
>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=57.64 E-value=11 Score=22.37 Aligned_cols=36 Identities=36% Similarity=0.477 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHH
Q 042237 32 VIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLR 71 (115)
Q Consensus 32 ~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~Lr 71 (115)
.|...|.+ ||.++++.-+.+. ++-=+=.+|++.|..
T Consensus 6 ~Il~~L~~-~~~~~~el~~~l~---~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 6 RILKLLSE-GPLTVSELAEELG---LSQSTVSHHLKKLRE 41 (47)
T ss_dssp HHHHHHTT-SSEEHHHHHHHHT---S-HHHHHHHHHHHHH
T ss_pred HHHHHHHh-CCCchhhHHHhcc---ccchHHHHHHHHHHH
Confidence 35556666 9999998876653 332222378777653
No 26
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=57.08 E-value=9.8 Score=23.74 Aligned_cols=34 Identities=29% Similarity=0.542 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHH
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMK 67 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMK 67 (115)
+.|.++|+++|.+||.+. +++-|+|.-|-.+...
T Consensus 3 ~~Il~~l~~~~~~s~~el---a~~~~VS~~TiRRDl~ 36 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKEL---AEEFGVSEMTIRRDLN 36 (57)
T ss_pred HHHHHHHHHcCCEEHHHH---HHHHCcCHHHHHHHHH
Confidence 468899999999999976 4445777555444443
No 27
>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=55.44 E-value=3.6 Score=33.27 Aligned_cols=30 Identities=23% Similarity=0.675 Sum_probs=25.5
Q ss_pred hccCCCCchhHHHHHHHHHHhh--hHHHHhhhccC
Q 042237 55 AGVSGLTGKSHMKIVLRWMRER--QKLRLICNHVG 87 (115)
Q Consensus 55 ~g~~gL~SK~HMKi~LrWMreR--q~lkl~C~hvG 87 (115)
.+..+|||| ++++-.+++. +.|-++|+|+=
T Consensus 154 ~~np~ltSK---qvL~PfL~~~~F~~LeIiC~HiP 185 (214)
T TIGR02940 154 QDDPDLNSK---KILIPYLKGKPFNQLDILCDHIP 185 (214)
T ss_pred hhCCCCCHH---HHHHHHHcCCCceeEEEEeCCCC
Confidence 388899999 5888888887 78999999984
No 28
>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=54.78 E-value=25 Score=23.66 Aligned_cols=40 Identities=20% Similarity=0.421 Sum_probs=28.8
Q ss_pred HHHHHHHHhC--CcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHH
Q 042237 32 VIFDIVKEHG--PLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKL 79 (115)
Q Consensus 32 ~l~dIvkeHG--PLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~l 79 (115)
-+.+-+|+++ |||+.|.=+++....++ ..++.|+++=-.+
T Consensus 13 ~aV~ymK~r~~~Plt~~EIl~~ls~~d~~--------~~~~~~L~~~~~~ 54 (75)
T cd07977 13 KIVDYMKKRHQHPLTLDEILDYLSLLDIG--------PKLKEWLKSEALV 54 (75)
T ss_pred HHHHHHHhcCCCCccHHHHHHHHhccCcc--------HHHHHHHHhhhhc
Confidence 3456778876 99999999999874443 5567898854443
No 29
>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=54.43 E-value=36 Score=22.34 Aligned_cols=59 Identities=25% Similarity=0.369 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCcce
Q 042237 26 TQTITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQF 92 (115)
Q Consensus 26 a~titr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~F 92 (115)
.+.+-+.|+++|+++|+.|.. ..++..|++ ..|..--..|- ..++=-.+|.+.|.++.+
T Consensus 2 ~~~~ee~Il~~L~~~g~~~a~---~ia~~~~L~--~~kk~VN~~LY---~L~k~g~v~k~~~~PP~W 60 (66)
T PF02295_consen 2 MQDLEEKILDFLKELGGSTAT---AIAKALGLS--VPKKEVNRVLY---RLEKQGKVCKEGGTPPKW 60 (66)
T ss_dssp HHHHHHHHHHHHHHHTSSEEE---HHHHHHHHT--S-HHHHHHHHH---HHHHTTSEEEECSSSTEE
T ss_pred chhHHHHHHHHHHhcCCccHH---HHHHHhCcc--hhHHHHHHHHH---HHHHCCCEeeCCCCCCce
Confidence 456788999999999987765 456676666 23444444444 334444557777777643
No 30
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=53.77 E-value=40 Score=20.92 Aligned_cols=45 Identities=31% Similarity=0.519 Sum_probs=32.2
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
-.|+.+|.++|++|+++- +++.+++ +.=....|+-|.++..|...
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 467888999999998855 4445554 34455678888888887655
No 31
>PRK08333 L-fuculose phosphate aldolase; Provisional
Probab=53.43 E-value=8.2 Score=28.66 Aligned_cols=31 Identities=19% Similarity=0.363 Sum_probs=23.6
Q ss_pred hHHHHHHHHHHH----HHHHhCCcchHhHHHHHHH
Q 042237 24 EQTQTITRVIFD----IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 24 eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke 54 (115)
|-|..+++.+-+ |++.||.++++.+++.+..
T Consensus 133 ~la~~~~~~l~~~~~vll~nHGv~~~G~~~~eA~~ 167 (184)
T PRK08333 133 ELAEQVAEAMKEYDAVIMERHGIVTVGRSLREAFY 167 (184)
T ss_pred HHHHHHHHHhccCCEEEEcCCCCEEEcCCHHHHHH
Confidence 456666665544 6789999999999988865
No 32
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=52.29 E-value=28 Score=19.42 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=14.0
Q ss_pred HHHHHHHHhCCcchHhH
Q 042237 32 VIFDIVKEHGPLTVAET 48 (115)
Q Consensus 32 ~l~dIvkeHGPLTV~~t 48 (115)
.|++.+.++|++|+.+-
T Consensus 4 ~il~~l~~~~~~s~~~l 20 (53)
T smart00420 4 QILELLAQQGKVSVEEL 20 (53)
T ss_pred HHHHHHHHcCCcCHHHH
Confidence 57888899999999854
No 33
>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=50.56 E-value=29 Score=26.74 Aligned_cols=56 Identities=23% Similarity=0.431 Sum_probs=42.7
Q ss_pred HhHHHHHHHh-ccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCcceee---eeccCCCCC
Q 042237 46 AETWERVQQA-GVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQFLY---TTWFTKPNN 103 (115)
Q Consensus 46 ~~tW~h~ke~-g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FLy---ttw~~~P~~ 103 (115)
..||.+++.. |+.+.+-..+=++.+.|+++|.-|..+=. |.-.+|+- -.|..=|++
T Consensus 71 ~~Tw~~~~~~~gl~~F~P~~QD~~A~~Li~~~gal~~i~~--G~~~~a~~~La~~WASLPg~ 130 (151)
T cd00736 71 SRTWDAYAKQYGLYDFSPESQDLVAYQLIRERGALPDILA--GRIEQAIAKLSNIWASLPGA 130 (151)
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHcCcHHHHHc--CCHHHHHHHHHhhccCCCCc
Confidence 4689887654 99999999999999999999987776665 66655543 467766643
No 34
>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=49.23 E-value=41 Score=17.96 Aligned_cols=35 Identities=26% Similarity=0.686 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHH
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWM 73 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWM 73 (115)
..|.+.+++||. ..|..+.+. +..++-..+..+|.
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 569998875 33367777777775
No 35
>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=48.91 E-value=71 Score=20.58 Aligned_cols=32 Identities=16% Similarity=0.392 Sum_probs=21.3
Q ss_pred hHHHHHHHHHHHHHHHhCCcchHhHHHHHHHhccC
Q 042237 24 EQTQTITRVIFDIVKEHGPLTVAETWERVQQAGVS 58 (115)
Q Consensus 24 eqa~titr~l~dIvkeHGPLTV~~tW~h~ke~g~~ 58 (115)
||| .+-+.||+.+- +-.++..+-+.+.+.|+.
T Consensus 2 eea-~vVr~if~~~~--~g~s~~~I~~~ln~~gi~ 33 (102)
T PF07508_consen 2 EEA-EVVREIFELYL--EGYSLRQIARELNEKGIP 33 (102)
T ss_pred hHH-HHHHHHHHHHH--cCCCHHHHHHHHHhcCCc
Confidence 444 45566777765 556777777777788873
No 36
>PRK06833 L-fuculose phosphate aldolase; Provisional
Probab=48.75 E-value=8.6 Score=29.38 Aligned_cols=29 Identities=17% Similarity=0.267 Sum_probs=21.4
Q ss_pred HHHHHHHHHH----HHHHhCCcchHhHHHHHHH
Q 042237 26 TQTITRVIFD----IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 26 a~titr~l~d----IvkeHGPLTV~~tW~h~ke 54 (115)
++.+++++-| +++.||.++++++++.+..
T Consensus 139 a~~v~~~l~~~~~vll~nHGv~~~G~~~~eA~~ 171 (214)
T PRK06833 139 AENAFEAMEDRRAVLLANHGLLAGANNLKNAFN 171 (214)
T ss_pred HHHHHHHhCcCCEEEECCCCCEEEeCCHHHHHH
Confidence 4455555533 6789999999999988765
No 37
>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=48.64 E-value=21 Score=26.16 Aligned_cols=39 Identities=18% Similarity=0.429 Sum_probs=32.0
Q ss_pred ChhHHHHHHHHHHHHHHHhC-CcchHhHHHHHHHhccCCC
Q 042237 22 PPEQTQTITRVIFDIVKEHG-PLTVAETWERVQQAGVSGL 60 (115)
Q Consensus 22 p~eqa~titr~l~dIvkeHG-PLTV~~tW~h~ke~g~~gL 60 (115)
..++-+...+.|.++.++++ ++-|.+-|+-+.+.|..|+
T Consensus 37 ~~~~~~~~a~~l~~~~~~~~~~liin~~~~la~~~~~dGv 76 (180)
T PF02581_consen 37 SDEELLELARRLAELCQKYGVPLIINDRVDLALELGADGV 76 (180)
T ss_dssp -HHHHHHHHHHHHHHHHHTTGCEEEES-HHHHHHCT-SEE
T ss_pred CccHHHHHHHHHHHHhhcceEEEEecCCHHHHHhcCCCEE
Confidence 55788889999999998875 9999999999999998876
No 38
>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=48.34 E-value=52 Score=21.12 Aligned_cols=57 Identities=18% Similarity=0.113 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHHhCCcchHhHHHHHHHh-ccCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 26 TQTITRVIFDIVKEHGPLTVAETWERVQQA-GVSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 26 a~titr~l~dIvkeHGPLTV~~tW~h~ke~-g~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
...|--+|..|+|.+.-++.++-.+.|.+. .-...-+-...|.-+.++-+|.-|+..
T Consensus 6 ~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd 63 (68)
T PF10557_consen 6 KYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERD 63 (68)
T ss_dssp HHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEE
T ss_pred hhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcC
Confidence 345677899999999999999999999987 436667889999999999998776543
No 39
>PRK06357 hypothetical protein; Provisional
Probab=48.30 E-value=12 Score=28.97 Aligned_cols=39 Identities=13% Similarity=0.411 Sum_probs=25.1
Q ss_pred cccCCCChhHHHHHHHHHHH----------HHHHhCCcchHhHHHHHHH
Q 042237 16 PIELKAPPEQTQTITRVIFD----------IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 16 pi~~k~p~eqa~titr~l~d----------IvkeHGPLTV~~tW~h~ke 54 (115)
|+.+..-.|-++.++..+-+ +++.||.++++.+++.+..
T Consensus 135 p~~~~gs~ela~~v~~~l~~~~~~~~~~~vLl~nHGvv~~G~~l~eA~~ 183 (216)
T PRK06357 135 PFAPATSPELAEIVRKHLIELGDKAVPSAFLLNSHGIVITDTSLHKAYD 183 (216)
T ss_pred cccCCCcHHHHHHHHHHHhhcCcccCCCEEEECCCCCeEecCCHHHHHH
Confidence 44433334555555555543 5788999999998887654
No 40
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=46.03 E-value=16 Score=27.43 Aligned_cols=55 Identities=31% Similarity=0.428 Sum_probs=32.5
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHH----hhhHHHHhhhccCCCcceeee
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMR----ERQKLRLICNHVGPHKQFLYT 95 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMr----eRq~lkl~C~hvG~~k~FLyt 95 (115)
..++.+|+++||+||.+.=+ ..+.+ --+=-|.+.+=|. +|.+.-+ -|+-..|+|.
T Consensus 31 ~v~~~LL~~~~~~tvdelae---~lnr~---rStv~rsl~~L~~~GlV~Rek~~~----~~Ggy~yiY~ 89 (126)
T COG3355 31 EVYKALLEENGPLTVDELAE---ILNRS---RSTVYRSLQNLLEAGLVEREKVNL----KGGGYYYLYK 89 (126)
T ss_pred HHHHHHHhhcCCcCHHHHHH---HHCcc---HHHHHHHHHHHHHcCCeeeeeecc----CCCceeEEEe
Confidence 56778888999999987533 33332 2233444444432 2332222 6788889984
No 41
>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=45.64 E-value=48 Score=21.52 Aligned_cols=45 Identities=22% Similarity=0.251 Sum_probs=31.5
Q ss_pred HHHHHHHHh-CCcchHhHHHHHHHhccCCCC-chhHHHHHHHHHHhhhHH
Q 042237 32 VIFDIVKEH-GPLTVAETWERVQQAGVSGLT-GKSHMKIVLRWMRERQKL 79 (115)
Q Consensus 32 ~l~dIvkeH-GPLTV~~tW~h~ke~g~~gL~-SK~HMKi~LrWMreRq~l 79 (115)
.|.++|+++ +|++=..-=+.++.. |.. |..-.+..|++|-+.-.+
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~---g~~~se~avRrrLr~me~~Glt 48 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLR---GEELSEEAVRRRLRAMERDGLT 48 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhc---ChhhhHHHHHHHHHHHHHCCCc
Confidence 367888887 678766555555554 443 577889999999887733
No 42
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=45.30 E-value=28 Score=25.27 Aligned_cols=37 Identities=19% Similarity=0.205 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHH
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVL 70 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~L 70 (115)
+.|++.|.++|+++|.+. +++.|++-=+=-.|+|+|-
T Consensus 19 l~IL~~L~~~~~~~v~el---a~~l~lsqstvS~HL~~L~ 55 (117)
T PRK10141 19 LGIVLLLRESGELCVCDL---CTALDQSQPKISRHLALLR 55 (117)
T ss_pred HHHHHHHHHcCCcCHHHH---HHHHCcCHHHHHHHHHHHH
Confidence 478888999999999865 3444554444447888764
No 43
>PRK06557 L-ribulose-5-phosphate 4-epimerase; Validated
Probab=44.68 E-value=8.9 Score=29.28 Aligned_cols=32 Identities=16% Similarity=0.268 Sum_probs=25.7
Q ss_pred hhHHHHHHHHH------HHHHHHhCCcchHhHHHHHHH
Q 042237 23 PEQTQTITRVI------FDIVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 23 ~eqa~titr~l------~dIvkeHGPLTV~~tW~h~ke 54 (115)
.|.++.|.+.| .=+++.||.++++.+.+.+..
T Consensus 142 ~ela~~i~~~l~~~~~~~vll~nHG~~~~G~~~~eA~~ 179 (221)
T PRK06557 142 EAIGKGIVETLKGGRSPAVLMQNHGVFTIGKDAEDAVK 179 (221)
T ss_pred HHHHHHHHHHhCcCCCCEEEECCCCceEEcCCHHHHHH
Confidence 46777888877 347899999999999888765
No 44
>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=44.15 E-value=25 Score=22.51 Aligned_cols=23 Identities=22% Similarity=0.291 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhCCcchHhHHH
Q 042237 28 TITRVIFDIVKEHGPLTVAETWE 50 (115)
Q Consensus 28 titr~l~dIvkeHGPLTV~~tW~ 50 (115)
.+...+++.|-.+|++|+.+.=.
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 57788999999999999988643
No 45
>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=43.96 E-value=18 Score=22.85 Aligned_cols=36 Identities=25% Similarity=0.467 Sum_probs=21.8
Q ss_pred HHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHh
Q 042237 33 IFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRE 75 (115)
Q Consensus 33 l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMre 75 (115)
|-+++++||++||++-=+.. |+| ....--+|.+|-.
T Consensus 1 i~~~~~~~~~itv~~~rd~l---g~s----RK~ai~lLE~lD~ 36 (50)
T PF09107_consen 1 IRELLQKNGEITVAEFRDLL---GLS----RKYAIPLLEYLDR 36 (50)
T ss_dssp HHHHHHTTSSBEHHHHHHHH---TS-----HHHHHHHHHHHHH
T ss_pred ChHHHhcCCcCcHHHHHHHH---Ccc----HHHHHHHHHHHhc
Confidence 34688899999999854433 433 3344445555543
No 46
>PRK07490 hypothetical protein; Provisional
Probab=43.70 E-value=8.4 Score=30.31 Aligned_cols=30 Identities=20% Similarity=0.359 Sum_probs=23.3
Q ss_pred hHHHHHHHHHHH----HHHHhCCcchHhHHHHHH
Q 042237 24 EQTQTITRVIFD----IVKEHGPLTVAETWERVQ 53 (115)
Q Consensus 24 eqa~titr~l~d----IvkeHGPLTV~~tW~h~k 53 (115)
|.++.++++|-| |++.||.++++.+++.+-
T Consensus 147 ela~~v~~~l~~~~avlL~nHG~v~~G~~~~eA~ 180 (245)
T PRK07490 147 EEGERLAGLLGDKRRLLMGNHGVLVTGDTVAEAF 180 (245)
T ss_pred HHHHHHHHHhCcCCEEEECCCCcEEecCCHHHHH
Confidence 666777776644 688999999999888765
No 47
>PF13331 DUF4093: Domain of unknown function (DUF4093)
Probab=43.10 E-value=26 Score=24.38 Aligned_cols=58 Identities=22% Similarity=0.272 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhCCcch-HhHHHHHHHhccCCC-CchhHHHHHHHHHHhhhHHHHhhhccCCCccee
Q 042237 27 QTITRVIFDIVKEHGPLTV-AETWERVQQAGVSGL-TGKSHMKIVLRWMRERQKLRLICNHVGPHKQFL 93 (115)
Q Consensus 27 ~titr~l~dIvkeHGPLTV-~~tW~h~ke~g~~gL-~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FL 93 (115)
++|-++|-.+...-..-.. .=||..+-+.|+.|= +||. |..+..+...---+|+||||
T Consensus 10 e~I~~AL~~~~~~~~~~~~~~it~~dL~~~GL~g~~~s~~---------rR~~l~~~L~iGy~N~Kqll 69 (87)
T PF13331_consen 10 EAIREALENARTEDEEPKESEITWEDLIELGLIGGPDSKE---------RREKLGEYLGIGYGNAKQLL 69 (87)
T ss_pred HHHHHHHHHhCccccCCccCcCCHHHHHHCCCCCCccHHH---------HHHHHHHHHCCCCCCHHHHH
Confidence 4566666666554333222 258999999999887 7773 22334445555677888887
No 48
>PF14769 CLAMP: Flagellar C1a complex subunit C1a-32
Probab=42.78 E-value=1.1e+02 Score=20.95 Aligned_cols=55 Identities=13% Similarity=0.317 Sum_probs=42.6
Q ss_pred CCChhHHHHHHHHHHHHHH---HhCCcchHhHHHHHHHh--ccC--------CCCchhHHHHHHHHHHh
Q 042237 20 KAPPEQTQTITRVIFDIVK---EHGPLTVAETWERVQQA--GVS--------GLTGKSHMKIVLRWMRE 75 (115)
Q Consensus 20 k~p~eqa~titr~l~dIvk---eHGPLTV~~tW~h~ke~--g~~--------gL~SK~HMKi~LrWMre 75 (115)
.-+.+|+.++-..+.+++. + +=.++.++++..++. +++ ++=|-.++|.+..+|-.
T Consensus 11 ~fs~~q~s~~~~i~~~ll~~~i~-~~~~~~~~~~~fk~~l~~~sv~rpp~~~~iFs~~~~~~i~~y~~~ 78 (101)
T PF14769_consen 11 GFSWEQTSAFLSILKELLEKNIE-KGMSLEDSFKYFKELLLRHSVQRPPFSIGIFSVDQVKAIIDYFHN 78 (101)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH-ccCCHHHHHHHHHHHHHHhccCCCCcccCcCCHHHHHHHHHHHHH
Confidence 4577888776666666666 6 889999999999998 444 44688899999988864
No 49
>PRK09220 methylthioribulose-1-phosphate dehydratase; Provisional
Probab=42.71 E-value=12 Score=28.57 Aligned_cols=31 Identities=6% Similarity=0.186 Sum_probs=22.4
Q ss_pred hHHHHHHHHHHH-------HHHHhCCcchHhHHHHHHH
Q 042237 24 EQTQTITRVIFD-------IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 24 eqa~titr~l~d-------IvkeHGPLTV~~tW~h~ke 54 (115)
|=|+.+...+-| +|+.||.++++.++..+.+
T Consensus 146 eLa~~v~~~l~~~~~~~avlL~nHGvi~~G~~~~eA~~ 183 (204)
T PRK09220 146 RLAARVAPYLDAQPLRYGYLIRGHGLYCWGRDMAEARR 183 (204)
T ss_pred HHHHHHHHHHHhCCCCcEEEECCCceEEEcCCHHHHHH
Confidence 445555555554 3778999999999887765
No 50
>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=40.26 E-value=43 Score=22.10 Aligned_cols=24 Identities=13% Similarity=0.304 Sum_probs=20.7
Q ss_pred cCCCChhHHHHHHHHHHHHHHHhC
Q 042237 18 ELKAPPEQTQTITRVIFDIVKEHG 41 (115)
Q Consensus 18 ~~k~p~eqa~titr~l~dIvkeHG 41 (115)
++..+.++..++.+.+.++|.++|
T Consensus 10 ~~~~~~~~~~~~~~~~~~~i~~~g 33 (92)
T PF01250_consen 10 RPDLSEEEIKKLIERVKKIIEKNG 33 (92)
T ss_dssp -TTSCHHHHHHHHHHHHHHHHHTT
T ss_pred CCCCCHHHHHHHHHHHHHHHHHCC
Confidence 567888999999999999999986
No 51
>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=39.23 E-value=1.2e+02 Score=24.63 Aligned_cols=54 Identities=20% Similarity=0.463 Sum_probs=32.8
Q ss_pred ChhHHHHHHHHHHHHHHHhCC-----------cchHhHHHHHHHh--ccCC----C---Cch---hHHHHHHHHHHh
Q 042237 22 PPEQTQTITRVIFDIVKEHGP-----------LTVAETWERVQQA--GVSG----L---TGK---SHMKIVLRWMRE 75 (115)
Q Consensus 22 p~eqa~titr~l~dIvkeHGP-----------LTV~~tW~h~ke~--g~~g----L---~SK---~HMKi~LrWMre 75 (115)
-.++...+-.+|-.|.++||- -++.+..++.++. ++.+ + .++ -=.-+.||||=.
T Consensus 79 ~~~D~~~~~~~l~~~~~~~~sle~~f~~~~~~~~~~~~i~~f~~~~~~~~~~~~~~~~~~~~Sa~KR~nMFLRWMVR 155 (229)
T TIGR02757 79 NEKDIQAIFKTLYRIYESHGSLEELFYAAYYKGPPIERLSSFRKHIIKLNSYNNTIADPSGGSPLKRLNMFLRWMIR 155 (229)
T ss_pred CHHHHHHHHHHHHHHHHhcCCHHHHHHhccccccHHHHHHHHHHHHHhccccccccCCCCCCchHHHHHHHHHhhcc
Confidence 467888888999999888764 2445555555442 2222 1 111 224489999954
No 52
>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=39.17 E-value=7.1 Score=29.36 Aligned_cols=20 Identities=20% Similarity=0.625 Sum_probs=17.0
Q ss_pred HHHHhCCcchHhHHHHHHHh
Q 042237 36 IVKEHGPLTVAETWERVQQA 55 (115)
Q Consensus 36 IvkeHGPLTV~~tW~h~ke~ 55 (115)
|++.||.++++.+|+.+.+.
T Consensus 157 ll~nHGv~~~G~~~~~A~~~ 176 (193)
T TIGR03328 157 LIRGHGLYAWGRDWEEAKRH 176 (193)
T ss_pred EEcCCcceEEcCCHHHHHHH
Confidence 46789999999999998764
No 53
>KOG1613 consensus Exosomal 3'-5' exoribonuclease complex, subunit Rrp43 [Translation, ribosomal structure and biogenesis]
Probab=38.55 E-value=36 Score=29.22 Aligned_cols=29 Identities=14% Similarity=0.294 Sum_probs=24.0
Q ss_pred cccCCCChhHHHHHHHHHHHHHHHhCCcc
Q 042237 16 PIELKAPPEQTQTITRVIFDIVKEHGPLT 44 (115)
Q Consensus 16 pi~~k~p~eqa~titr~l~dIvkeHGPLT 44 (115)
.+++--|.|+|+.|||.|.|.+..-+.|-
T Consensus 106 r~RpG~p~dea~viSq~LhdtIl~S~ii~ 134 (298)
T KOG1613|consen 106 RFRPGPPTDEAQVISQKLHDTILHSRIIP 134 (298)
T ss_pred CCCCCCCchHHHHHHHHHHHHHHhcCCcc
Confidence 45667789999999999999998777654
No 54
>PHA00738 putative HTH transcription regulator
Probab=38.26 E-value=38 Score=25.05 Aligned_cols=38 Identities=24% Similarity=0.230 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHH
Q 042237 29 ITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIV 69 (115)
Q Consensus 29 itr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~ 69 (115)
.=+.|++.|.++++++|++.=+. .+++-=+=-.|+|+|
T Consensus 13 tRr~IL~lL~~~e~~~V~eLae~---l~lSQptVS~HLKvL 50 (108)
T PHA00738 13 LRRKILELIAENYILSASLISHT---LLLSYTTVLRHLKIL 50 (108)
T ss_pred HHHHHHHHHHHcCCccHHHHHHh---hCCCHHHHHHHHHHH
Confidence 34678999999999999887333 245444444899886
No 55
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=38.19 E-value=34 Score=25.76 Aligned_cols=23 Identities=26% Similarity=0.510 Sum_probs=21.2
Q ss_pred CCChhHHHHHHHHHHHHHHHhCC
Q 042237 20 KAPPEQTQTITRVIFDIVKEHGP 42 (115)
Q Consensus 20 k~p~eqa~titr~l~dIvkeHGP 42 (115)
+.|.|+-.+.++.+++++|+||-
T Consensus 1 ~~P~~~C~~a~~~v~~~lk~~g~ 23 (135)
T PF15645_consen 1 NNPAEQCESAMKEVADFLKDKGY 23 (135)
T ss_pred CChhHHHHHHHHHHHHHHHhCCC
Confidence 36899999999999999999996
No 56
>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=38.07 E-value=37 Score=21.77 Aligned_cols=20 Identities=20% Similarity=0.610 Sum_probs=18.2
Q ss_pred hhHHHHHHHHHHHHHHHhCC
Q 042237 23 PEQTQTITRVIFDIVKEHGP 42 (115)
Q Consensus 23 ~eqa~titr~l~dIvkeHGP 42 (115)
|+++..+.+.|.|++++|.-
T Consensus 10 p~~~~~Fp~~L~~lL~~~~~ 29 (52)
T PF08158_consen 10 PKETKDFPQELIDLLRNHHT 29 (52)
T ss_pred HHHHHHHHHHHHHHHHhccc
Confidence 67999999999999999975
No 57
>PF14214 Helitron_like_N: Helitron helicase-like domain at N-terminus
Probab=37.63 E-value=39 Score=24.80 Aligned_cols=30 Identities=27% Similarity=0.553 Sum_probs=26.6
Q ss_pred HHHhhhHHHHhhhccCCCcceeeeeccCCCCC
Q 042237 72 WMRERQKLRLICNHVGPHKQFLYTTWFTKPNN 103 (115)
Q Consensus 72 WMreRq~lkl~C~hvG~~k~FLyttw~~~P~~ 103 (115)
|-..|+.|.-+|.+-|.+--|+ |...+|.-
T Consensus 88 ~~~~~~dl~a~~~~~G~P~~Fi--T~s~~~~w 117 (184)
T PF14214_consen 88 WQQRRQDLMAMVRQFGKPTLFI--TFSCNPQW 117 (184)
T ss_pred HHHHHHHHHHHHhccCCCcEEE--EEcCcccc
Confidence 7789999999999999999998 88888753
No 58
>PRK06486 hypothetical protein; Provisional
Probab=37.43 E-value=13 Score=29.84 Aligned_cols=53 Identities=23% Similarity=0.275 Sum_probs=35.3
Q ss_pred hhHHHHHHHHHHH----HHHHhCCcchHhHHHHHHH-----------------hccC-CCCchhHHHHHHHHHHh
Q 042237 23 PEQTQTITRVIFD----IVKEHGPLTVAETWERVQQ-----------------AGVS-GLTGKSHMKIVLRWMRE 75 (115)
Q Consensus 23 ~eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke-----------------~g~~-gL~SK~HMKi~LrWMre 75 (115)
.|.+..++..+-| ||+.||.++++.+++.|.. .|.. -+-+..-.+-+..+|.+
T Consensus 162 ~ela~~va~al~~~~avLL~nHG~v~~G~~l~eA~~~~~~lE~~a~i~~~a~~~G~~~~~~~~~~~~~~~~~~~~ 236 (262)
T PRK06486 162 AAEGDRIARAMGDADIVFLKNHGVMVCGPRIAEAWDDLYYLERACEVQVLAMSTGRPLVPVDPAIAAAVARQMRE 236 (262)
T ss_pred hhHHHHHHHHhCcCCEEEECCCCCeEecCCHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCHHHHHHHHHHHhc
Confidence 4667777777643 6899999999988876532 2321 24455666677777753
No 59
>PRK03634 rhamnulose-1-phosphate aldolase; Provisional
Probab=36.60 E-value=20 Score=28.99 Aligned_cols=33 Identities=15% Similarity=0.157 Sum_probs=24.6
Q ss_pred ChhHHHHHHHHHHH----HHHHhCCcchHhHHHHHHH
Q 042237 22 PPEQTQTITRVIFD----IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 22 p~eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke 54 (115)
-.|-|+.++.++-| |++.||.++++++++.|-.
T Consensus 190 s~eLa~~v~~~l~~~~avLL~nHGvv~~G~~l~eA~~ 226 (274)
T PRK03634 190 TDEIGQATAEKMQKHDLVLWPKHGVFGSGPTLDEAFG 226 (274)
T ss_pred CHHHHHHHHHHhccCCEEEEcCCCCeEecCCHHHHHH
Confidence 34666667766633 5899999999999888754
No 60
>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=35.60 E-value=39 Score=22.60 Aligned_cols=42 Identities=17% Similarity=0.456 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHH
Q 042237 26 TQTITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMR 74 (115)
Q Consensus 26 a~titr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMr 74 (115)
.-.-+..|+++|.++|++|+++- .++.|++ ..-.-.-+=|+-
T Consensus 6 IG~nAG~Vw~~L~~~~~~s~~el---~k~~~l~----~~~~~~AiGWLa 47 (65)
T PF10771_consen 6 IGENAGKVWQLLNENGEWSVSEL---KKATGLS----DKEVYLAIGWLA 47 (65)
T ss_dssp HHHHHHHHHHHHCCSSSEEHHHH---HHHCT-S----CHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhCCCcCHHHH---HHHhCcC----HHHHHHHHHHHh
Confidence 34557889999999999999874 2444442 334444556653
No 61
>PRK02363 DNA-directed RNA polymerase subunit delta; Reviewed
Probab=34.61 E-value=64 Score=24.01 Aligned_cols=29 Identities=21% Similarity=0.432 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHh-CCcchHhHHHHHHHhc
Q 042237 28 TITRVIFDIVKEH-GPLTVAETWERVQQAG 56 (115)
Q Consensus 28 titr~l~dIvkeH-GPLTV~~tW~h~ke~g 56 (115)
|..-..|.||+++ -|++..+-|+.|++..
T Consensus 4 S~idvAy~iL~~~~~~m~f~dL~~ev~~~~ 33 (129)
T PRK02363 4 SLIEVAYEILKEKKEPMSFYDLVNEIQKYL 33 (129)
T ss_pred cHHHHHHHHHHHcCCcccHHHHHHHHHHHh
Confidence 4556778999998 7999999999999873
No 62
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=34.16 E-value=43 Score=25.09 Aligned_cols=21 Identities=14% Similarity=0.352 Sum_probs=18.8
Q ss_pred CCChhHHHHHHHHHHHHHHHh
Q 042237 20 KAPPEQTQTITRVIFDIVKEH 40 (115)
Q Consensus 20 k~p~eqa~titr~l~dIvkeH 40 (115)
-.|++||++|+.++.+++.+.
T Consensus 15 Gft~~QAe~i~~~l~~~l~~~ 35 (177)
T PF07798_consen 15 GFTEEQAEAIMKALREVLNDS 35 (177)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999875
No 63
>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=34.05 E-value=40 Score=22.95 Aligned_cols=42 Identities=14% Similarity=0.374 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHhCCcchHhHHHHHHHh--ccCCCCchhHHHHHHHH
Q 042237 28 TITRVIFDIVKEHGPLTVAETWERVQQA--GVSGLTGKSHMKIVLRW 72 (115)
Q Consensus 28 titr~l~dIvkeHGPLTV~~tW~h~ke~--g~~gL~SK~HMKi~LrW 72 (115)
-+-++..+.|.+|| +...|+-+.|. =-=.||+|.|=+.+++=
T Consensus 13 DFr~SM~EMI~~~~---i~~~w~~LeeLL~cYL~LN~~~~H~~Iv~A 56 (66)
T TIGR01568 13 DFRRSMEEMIEERE---LEADWKELEELLACYLDLNPKKSHRFIVRA 56 (66)
T ss_pred HHHHHHHHHHHHcC---CCCCHHHHHHHHHHHHHhCCchhhhHHHHH
Confidence 35678889999998 45669999997 34468999999988763
No 64
>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=33.99 E-value=39 Score=21.66 Aligned_cols=23 Identities=26% Similarity=0.449 Sum_probs=17.9
Q ss_pred ccCCCChhHHHHHHHHHHHHHHH
Q 042237 17 IELKAPPEQTQTITRVIFDIVKE 39 (115)
Q Consensus 17 i~~k~p~eqa~titr~l~dIvke 39 (115)
|+-.+|++|.+.|++...|.|+.
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 45579999999999998887763
No 65
>PRK08087 L-fuculose phosphate aldolase; Provisional
Probab=33.97 E-value=24 Score=27.04 Aligned_cols=31 Identities=13% Similarity=0.307 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHH----HHHHhCCcchHhHHHHHHH
Q 042237 24 EQTQTITRVIFD----IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 24 eqa~titr~l~d----IvkeHGPLTV~~tW~h~ke 54 (115)
|-+..+.+.|-| +++.||.++++++.+.+-.
T Consensus 135 ~la~~~~~~l~~~~~vLl~nHGv~~~G~~~~~A~~ 169 (215)
T PRK08087 135 ELSEHVALALKNRKATLLQHHGLIACEVNLEKALW 169 (215)
T ss_pred HHHHHHHHHhCcCCEEEecCCCCEEEcCCHHHHHH
Confidence 445566665533 6889999999999887765
No 66
>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=33.83 E-value=52 Score=21.84 Aligned_cols=20 Identities=20% Similarity=0.388 Sum_probs=18.0
Q ss_pred ChhHHHHHHHHHHHHHHHhC
Q 042237 22 PPEQTQTITRVIFDIVKEHG 41 (115)
Q Consensus 22 p~eqa~titr~l~dIvkeHG 41 (115)
-.|++..+.+.+++||++.|
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 46899999999999999986
No 67
>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=33.27 E-value=90 Score=22.74 Aligned_cols=44 Identities=18% Similarity=0.376 Sum_probs=36.4
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHh--ccCCCCchhHHHHHHHHHH
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQA--GVSGLTGKSHMKIVLRWMR 74 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~--g~~gL~SK~HMKi~LrWMr 74 (115)
..|-+||-+||||-|--.=.++-+. |.++|.+--.-+.+..=|.
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 4678899999999999999998877 9999988777776665554
No 68
>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=33.23 E-value=19 Score=28.13 Aligned_cols=25 Identities=24% Similarity=0.466 Sum_probs=20.7
Q ss_pred hHHHHHHHHHHH-----------HHHHhCCcchHhH
Q 042237 24 EQTQTITRVIFD-----------IVKEHGPLTVAET 48 (115)
Q Consensus 24 eqa~titr~l~d-----------IvkeHGPLTV~~t 48 (115)
|++..+++++-+ |++.||.++++.+
T Consensus 144 ~~~~~la~~l~~~~~~~~~~~avlL~nHGvv~~G~~ 179 (231)
T TIGR00760 144 ETGKVIVETFEKRGIDPAQIPGVLVHSHGPFAWGKD 179 (231)
T ss_pred hHHHHHHHHHhhccCCcccCCEEEEcCCCceEecCC
Confidence 678899998866 5899999998765
No 69
>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=32.19 E-value=58 Score=24.46 Aligned_cols=45 Identities=13% Similarity=0.162 Sum_probs=30.0
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
+.|+..|.++||+|+.+- +++.|++ +.-+...|+=|.+...+...
T Consensus 4 ~~IL~~L~~~~~~t~~eL---A~~lgis----~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQGQATAAAL---AEALAIS----PQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHcCCCCHHHH---HHHHCcC----HHHHHHHHHHHHHCCCeEEe
Confidence 678899999999999865 4445665 44455555555556555543
No 70
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=32.03 E-value=85 Score=23.50 Aligned_cols=68 Identities=26% Similarity=0.418 Sum_probs=53.5
Q ss_pred ChhHHHHHHHHHHH-HHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCcceeeee
Q 042237 22 PPEQTQTITRVIFD-IVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQFLYTT 96 (115)
Q Consensus 22 p~eqa~titr~l~d-IvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FLytt 96 (115)
-.+.|+++++.++| |.+|=+--.|---..-+.-.||+| .=-+++||=+.++-.|+++.. |+++=+|+.
T Consensus 35 ~~~~av~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~----SvAr~vLR~LeeeGvv~lvsk---nrR~~IY~~ 103 (107)
T COG4901 35 EARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGING----SVARIVLRHLEEEGVVQLVSK---NRRQAIYTR 103 (107)
T ss_pred hhhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccch----HHHHHHHHHHHhCCceeeecc---Cccceeeec
Confidence 35678888888886 667777666666667788888886 456889999999999999875 788888875
No 71
>CHL00123 rps6 ribosomal protein S6; Validated
Probab=31.45 E-value=68 Score=22.19 Aligned_cols=35 Identities=6% Similarity=0.074 Sum_probs=27.8
Q ss_pred ccCCCChhHHHHHHHHHHHHHHHhC-CcchHhHHHH
Q 042237 17 IELKAPPEQTQTITRVIFDIVKEHG-PLTVAETWER 51 (115)
Q Consensus 17 i~~k~p~eqa~titr~l~dIvkeHG-PLTV~~tW~h 51 (115)
++|..+-||.+++...+-++|+++| -++-.+.|+.
T Consensus 14 l~p~l~e~~~~~~~~~~~~~i~~~gg~i~~~~~wG~ 49 (97)
T CHL00123 14 LKPDLNEEELLKWIENYKKLLRKRGAKNISVQNRGK 49 (97)
T ss_pred ECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEeecC
Confidence 5678889999999999999999988 3444455653
No 72
>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=30.58 E-value=1.1e+02 Score=19.89 Aligned_cols=38 Identities=18% Similarity=0.389 Sum_probs=30.9
Q ss_pred CChhHHHHH--HHHHHHHHHHhCCcchHhHHHHHHHhccC
Q 042237 21 APPEQTQTI--TRVIFDIVKEHGPLTVAETWERVQQAGVS 58 (115)
Q Consensus 21 ~p~eqa~ti--tr~l~dIvkeHGPLTV~~tW~h~ke~g~~ 58 (115)
.|.++.+.| ++.+++++.-+||=+++-+-+-+++.|..
T Consensus 24 ~~~~~~e~i~~a~~ll~~l~~~~~~a~~~~~~vL~~~~~~ 63 (69)
T cd08304 24 IPPDQVEQISAANELLNILESQYNHTLQLLFALFEDLGLH 63 (69)
T ss_pred CCHHHHHHhhHHHHHHHHHHHhCcchHHHHHHHHHHcCCH
Confidence 345555555 48899999999999999999999888876
No 73
>PRK08130 putative aldolase; Validated
Probab=29.90 E-value=20 Score=27.32 Aligned_cols=31 Identities=13% Similarity=0.297 Sum_probs=21.5
Q ss_pred hHHHHHHHHHH----HHHHHhCCcchHhHHHHHHH
Q 042237 24 EQTQTITRVIF----DIVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 24 eqa~titr~l~----dIvkeHGPLTV~~tW~h~ke 54 (115)
|-|..+.+.+- =+++.||.++++++++.+..
T Consensus 140 ~la~~~~~~l~~~~~vll~nHGvi~~G~s~~~A~~ 174 (213)
T PRK08130 140 AIAEALAGLAARYRAVLLANHGPVVWGSSLEAAVN 174 (213)
T ss_pred HHHHHHHHHhccCCEEEEcCCCCeeeCCCHHHHHH
Confidence 44555555442 26789999999998887765
No 74
>PRK06754 mtnB methylthioribulose-1-phosphate dehydratase; Reviewed
Probab=29.89 E-value=18 Score=27.63 Aligned_cols=33 Identities=15% Similarity=0.286 Sum_probs=22.5
Q ss_pred hhHHHHHHHHHH-H----HHHHhCCcchHhHHHHHHHh
Q 042237 23 PEQTQTITRVIF-D----IVKEHGPLTVAETWERVQQA 55 (115)
Q Consensus 23 ~eqa~titr~l~-d----IvkeHGPLTV~~tW~h~ke~ 55 (115)
+|=|+.+.++|- | +++.||.++++.++..|...
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 344455554443 3 36789999999999887653
No 75
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=29.57 E-value=98 Score=16.56 Aligned_cols=35 Identities=26% Similarity=0.702 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHH
Q 042237 32 VIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMR 74 (115)
Q Consensus 32 ~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMr 74 (115)
.|.+.+++||. ..|+.+.+. +.+++-.-+..+|..
T Consensus 11 ~l~~~~~~~g~----~~w~~Ia~~----~~~rt~~~~~~~~~~ 45 (49)
T smart00717 11 LLIELVKKYGK----NNWEKIAKE----LPGRTAEQCRERWNN 45 (49)
T ss_pred HHHHHHHHHCc----CCHHHHHHH----cCCCCHHHHHHHHHH
Confidence 56777889997 669998874 346676667666653
No 76
>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=29.55 E-value=48 Score=23.01 Aligned_cols=30 Identities=13% Similarity=0.454 Sum_probs=21.7
Q ss_pred HHHHHHHHh-------CCcchHhHHHHHHHh-ccCCCC
Q 042237 32 VIFDIVKEH-------GPLTVAETWERVQQA-GVSGLT 61 (115)
Q Consensus 32 ~l~dIvkeH-------GPLTV~~tW~h~ke~-g~~gL~ 61 (115)
.|.+.+.++ -.+|+.+.|+++.+. ++..|.
T Consensus 26 ~I~~~l~~~~~~~~~~~~~t~~~IW~kL~~~YdL~~ld 63 (91)
T PF07904_consen 26 CIVERLNNPGFDPKLNKHFTIDDIWKKLRTLYDLEALD 63 (91)
T ss_pred HHHHHHhccccCCccCCcCCHHHHHHHHHHhcCHHHhc
Confidence 345555555 789999999999987 555443
No 77
>PRK06512 thiamine-phosphate pyrophosphorylase; Provisional
Probab=29.54 E-value=78 Score=24.71 Aligned_cols=40 Identities=15% Similarity=0.193 Sum_probs=34.9
Q ss_pred CChhHHHHHHHHHHHHHHHhC-CcchHhHHHHHHHhccCCC
Q 042237 21 APPEQTQTITRVIFDIVKEHG-PLTVAETWERVQQAGVSGL 60 (115)
Q Consensus 21 ~p~eqa~titr~l~dIvkeHG-PLTV~~tW~h~ke~g~~gL 60 (115)
.+.++...+.+.|.++.+++| ||-|.+-|+-+.+.|..|+
T Consensus 51 l~~~~~~~~a~~l~~l~~~~gv~liINd~~dlA~~~~adGV 91 (221)
T PRK06512 51 LDEATFQKQAEKLVPVIQEAGAAALIAGDSRIAGRVKADGL 91 (221)
T ss_pred CCHHHHHHHHHHHHHHHHHhCCEEEEeCHHHHHHHhCCCEE
Confidence 456777888999999999987 9999999999999988775
No 78
>PRK13247 dihydrobiliverdin:ferredoxin oxidoreductase; Provisional
Probab=29.07 E-value=60 Score=26.46 Aligned_cols=31 Identities=16% Similarity=0.063 Sum_probs=27.1
Q ss_pred hhhHHHHhhhccCCCcceeeeeccCCCCCcc
Q 042237 75 ERQKLRLICNHVGPHKQFLYTTWFTKPNNLN 105 (115)
Q Consensus 75 eRq~lkl~C~hvG~~k~FLyttw~~~P~~~~ 105 (115)
+=+++|+.|...|++=|-|++.+|-+|....
T Consensus 48 ~fRk~r~~~~~~G~~lqVLn~V~fP~~~yDL 78 (238)
T PRK13247 48 GFRRWRVTRLDAGDSLQVLNSVAYPDYNYDL 78 (238)
T ss_pred hHHHHHHHHhhcCCCcEEEEEEecCCCCCCC
Confidence 3478999999999999999999999996543
No 79
>PHA02517 putative transposase OrfB; Reviewed
Probab=29.01 E-value=2.3e+02 Score=21.62 Aligned_cols=49 Identities=18% Similarity=0.306 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHHhCC-cchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhH
Q 042237 25 QTQTITRVIFDIVKEHGP-LTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQK 78 (115)
Q Consensus 25 qa~titr~l~dIvkeHGP-LTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~ 78 (115)
+-..+...|.+|..++.| ......+..+++.|+. ---+-+.|+|++...
T Consensus 27 ~~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~g~~-----vs~~tV~Rim~~~gl 76 (277)
T PHA02517 27 HDDWLKSEILRVYDENHQVYGVRKVWRQLNREGIR-----VARCTVGRLMKELGL 76 (277)
T ss_pred hhHHHHHHHHHHHHHhCCCCCHHHHHHHHHhcCcc-----cCHHHHHHHHHHcCC
Confidence 445577778888888654 5888889999887764 234457788887543
No 80
>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=29.01 E-value=81 Score=18.60 Aligned_cols=38 Identities=24% Similarity=0.473 Sum_probs=24.3
Q ss_pred HHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhh
Q 042237 33 IFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQ 77 (115)
Q Consensus 33 l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq 77 (115)
+..+|.++|++|+++--+ ..|+ |+.-+-.+++.|-++.
T Consensus 8 iL~~l~~~~~~~~~~la~---~~~~----~~~~~t~~i~~L~~~g 45 (59)
T PF01047_consen 8 ILRILYENGGITQSELAE---KLGI----SRSTVTRIIKRLEKKG 45 (59)
T ss_dssp HHHHHHHHSSEEHHHHHH---HHTS-----HHHHHHHHHHHHHTT
T ss_pred HHHHHHHcCCCCHHHHHH---HHCC----ChhHHHHHHHHHHHCC
Confidence 566788999999996543 3344 3555666666665543
No 81
>PF06999 Suc_Fer-like: Sucrase/ferredoxin-like; InterPro: IPR009737 This family contains a number of bacterial and eukaryotic proteins approximately 400 residues long that resemble ferredoxin and appear to have sucrolytic activity [].
Probab=28.81 E-value=18 Score=27.35 Aligned_cols=10 Identities=40% Similarity=0.657 Sum_probs=8.9
Q ss_pred HhhhccCCCc
Q 042237 81 LICNHVGPHK 90 (115)
Q Consensus 81 l~C~hvG~~k 90 (115)
-.|.|+|+||
T Consensus 173 ~~iSHiGGHk 182 (230)
T PF06999_consen 173 WEISHIGGHK 182 (230)
T ss_pred EEecccccce
Confidence 5799999998
No 82
>PRK12347 sgbE L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=28.47 E-value=25 Score=27.59 Aligned_cols=28 Identities=18% Similarity=0.375 Sum_probs=20.9
Q ss_pred hHHHHHHHHHHH-----------HHHHhCCcchHhHHHH
Q 042237 24 EQTQTITRVIFD-----------IVKEHGPLTVAETWER 51 (115)
Q Consensus 24 eqa~titr~l~d-----------IvkeHGPLTV~~tW~h 51 (115)
|.+..+++.+-+ |++.||.++++.+=..
T Consensus 144 e~~~~va~~l~~~~~~~~~~~avLL~NHG~v~~G~~l~e 182 (231)
T PRK12347 144 QTGEVIIETFEERGISPAQIPAVLVHSHGPFAWGKNAAD 182 (231)
T ss_pred hhHHHHHHHHhhccccccCCCEEEEcCCCceEecCCHHH
Confidence 677788888753 6899999998765443
No 83
>KOG4382 consensus Uncharacterized conserved protein, contains DTW domain [Function unknown]
Probab=28.09 E-value=22 Score=30.23 Aligned_cols=22 Identities=32% Similarity=0.545 Sum_probs=17.9
Q ss_pred HHhCCcchHhHHHHHHHh-ccCC
Q 042237 38 KEHGPLTVAETWERVQQA-GVSG 59 (115)
Q Consensus 38 keHGPLTV~~tW~h~ke~-g~~g 59 (115)
-.||-|-|++||+++|++ .+|-
T Consensus 135 ~p~~ll~id~Tw~~ak~l~~~S~ 157 (276)
T KOG4382|consen 135 VPHGLLEIDETWNLAKHLSEISY 157 (276)
T ss_pred CCceeEEEccchHHHHHHHhhcH
Confidence 357888899999999997 6653
No 84
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.89 E-value=92 Score=21.49 Aligned_cols=27 Identities=33% Similarity=0.453 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHhCCcchHhHHHHH
Q 042237 26 TQTITRVIFDIVKEHGPLTVAETWERV 52 (115)
Q Consensus 26 a~titr~l~dIvkeHGPLTV~~tW~h~ 52 (115)
--.+-+.|.++|.+.|++|.++.|+.+
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~l 32 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERV 32 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 345678899999999999999887765
No 85
>PRK13246 dihydrobiliverdin:ferredoxin oxidoreductase; Provisional
Probab=27.54 E-value=65 Score=26.42 Aligned_cols=31 Identities=19% Similarity=0.104 Sum_probs=27.1
Q ss_pred hhhHHHHhhhccCCCcceeeeeccCCCCCcc
Q 042237 75 ERQKLRLICNHVGPHKQFLYTTWFTKPNNLN 105 (115)
Q Consensus 75 eRq~lkl~C~hvG~~k~FLyttw~~~P~~~~ 105 (115)
+=+++|+.|..+|++=|-|++.+|-+|....
T Consensus 48 ~fRk~r~~~~~~G~~lqVLn~V~fP~p~yDL 78 (236)
T PRK13246 48 EYRKWRITRLDGGKKLQVFNTVAYPNFKSEL 78 (236)
T ss_pred hHHHHHHHHhhcCCCcEEEEEEecCCCCCCC
Confidence 3478999999999999999999999997543
No 86
>PF10826 DUF2551: Protein of unknown function (DUF2551) ; InterPro: IPR020501 This entry contains proteins with no known function.
Probab=27.37 E-value=96 Score=22.15 Aligned_cols=45 Identities=18% Similarity=0.345 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhCCcchHhHHHHHHHh-ccCCCCchhHHHHHHHHHHhh
Q 042237 28 TITRVIFDIVKEHGPLTVAETWERVQQA-GVSGLTGKSHMKIVLRWMRER 76 (115)
Q Consensus 28 titr~l~dIvkeHGPLTV~~tW~h~ke~-g~~gL~SK~HMKi~LrWMreR 76 (115)
-|-|.+..++=+-|.+|+++.-+++++. .++ -+---.|+--|--|
T Consensus 11 GiRr~vL~~fl~~~~~T~~di~e~L~~~f~vs----~~~VasMVG~i~Sr 56 (83)
T PF10826_consen 11 GIRRAVLKLFLKGKKFTTDDIYERLKEKFDVS----YRGVASMVGLIHSR 56 (83)
T ss_pred cHHHHHHHHHHhCCCeeHHHHHHHHHHHcCch----HHHHHHHHHHHHHh
Confidence 3678999999999999999999999987 333 22233455555444
No 87
>cd03156 uroplakin_I_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), uroplakin_I_like family. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". Uroplakin Ia and Ib are components of the 16nm protein particles, which are packed hexagonally to form 2D crystals of asymmetric unit membranes, and cover the apical surface of mammalian urothelium, contributing to the urinay bladder's permeability barrier function. Uroplakins Ia and Ib are ma
Probab=27.12 E-value=1.1e+02 Score=19.70 Aligned_cols=33 Identities=21% Similarity=0.431 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHhCC--cchHhHHHHHHHh----ccCC
Q 042237 27 QTITRVIFDIVKEHGP--LTVAETWERVQQA----GVSG 59 (115)
Q Consensus 27 ~titr~l~dIvkeHGP--LTV~~tW~h~ke~----g~~g 59 (115)
..|...|.+.++..+. -.+...||.+|+- |..|
T Consensus 11 ~~~~~~l~~~~~~~~~~~~~~~~~~d~iQ~~l~CCG~~~ 49 (114)
T cd03156 11 DSFKNLLKNNYGNYNSTGDAITSTWNRVMIELKCCGVNG 49 (114)
T ss_pred HHHHHHHHHHHHhccccchHHHHHHHHHHhcccCcCCCC
Confidence 3455666676766442 4688999999986 5554
No 88
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=27.08 E-value=55 Score=20.72 Aligned_cols=43 Identities=23% Similarity=0.416 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHH
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLR 80 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lk 80 (115)
..|.++|+++|.+|+++- +++.+++ ..=+..||.=|..+-.|+
T Consensus 3 ~~i~~~l~~~~~~S~~eL---a~~~~~s----~~~ve~mL~~l~~kG~I~ 45 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAEL---AREFGIS----PEAVEAMLEQLIRKGYIR 45 (69)
T ss_dssp HHHHHHHHHS-SEEHHHH---HHHTT------HHHHHHHHHHHHCCTSCE
T ss_pred HHHHHHHHHcCCcCHHHH---HHHHCcC----HHHHHHHHHHHHHCCcEE
Confidence 368899999999999986 3444433 344455554444443333
No 89
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=27.02 E-value=2.4e+02 Score=20.21 Aligned_cols=47 Identities=19% Similarity=0.309 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhC-------CcchHhHHHHHHHh-ccCCCCchhHHHHHHHHHH
Q 042237 28 TITRVIFDIVKEHG-------PLTVAETWERVQQA-GVSGLTGKSHMKIVLRWMR 74 (115)
Q Consensus 28 titr~l~dIvkeHG-------PLTV~~tW~h~ke~-g~~gL~SK~HMKi~LrWMr 74 (115)
.++.++.+++.+.. ||||++.-+.+.+. ..+|-.|..--.-+|..+-
T Consensus 89 D~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll 143 (177)
T PF04675_consen 89 DLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELL 143 (177)
T ss_dssp -HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHH
Confidence 35667777776655 99999999988887 5666556555555555443
No 90
>PF13565 HTH_32: Homeodomain-like domain
Probab=26.98 E-value=44 Score=20.75 Aligned_cols=19 Identities=32% Similarity=0.480 Sum_probs=16.0
Q ss_pred chHhHHHHHHHhccCCCCc
Q 042237 44 TVAETWERVQQAGVSGLTG 62 (115)
Q Consensus 44 TV~~tW~h~ke~g~~gL~S 62 (115)
||.....+..+-|+.||.+
T Consensus 1 Tv~rw~~ry~~~G~~gL~~ 19 (77)
T PF13565_consen 1 TVYRWLKRYREEGLEGLKD 19 (77)
T ss_pred CHHHHHHHHHhhCchhhhc
Confidence 6778888888899999985
No 91
>PRK13250 phycoerythrobilin:ferredoxin oxidoreductase; Provisional
Probab=26.65 E-value=68 Score=26.40 Aligned_cols=30 Identities=20% Similarity=0.127 Sum_probs=26.5
Q ss_pred hhhHHHHhhhccCCCcceeeeeccCCCCCc
Q 042237 75 ERQKLRLICNHVGPHKQFLYTTWFTKPNNL 104 (115)
Q Consensus 75 eRq~lkl~C~hvG~~k~FLyttw~~~P~~~ 104 (115)
+=+++|+.|..+|++=|-|++.+|-+|..+
T Consensus 57 ~fRk~r~~~~~~G~~lqVLn~V~fP~p~yD 86 (248)
T PRK13250 57 KLRQIRAAHVQGGSALQVLNFVIFPHLNYD 86 (248)
T ss_pred HHHHHHHHHHhcCCCcEEEEEEecCCcCCC
Confidence 347899999999999999999999999654
No 92
>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=26.64 E-value=16 Score=27.46 Aligned_cols=19 Identities=16% Similarity=0.389 Sum_probs=17.0
Q ss_pred HHHHhCCcchHhHHHHHHH
Q 042237 36 IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 36 IvkeHGPLTV~~tW~h~ke 54 (115)
|++.||.++++.+++.+..
T Consensus 153 ll~nHG~~~~G~~~~~A~~ 171 (209)
T cd00398 153 LLRNHGLFAWGPTLDEAFH 171 (209)
T ss_pred EEcCCCCeEecCCHHHHHH
Confidence 6899999999999998865
No 93
>KOG3280 consensus Mitochondrial/chloroplast ribosomal protein L17 [Translation, ribosomal structure and biogenesis]
Probab=26.55 E-value=1.7e+02 Score=23.48 Aligned_cols=63 Identities=22% Similarity=0.491 Sum_probs=49.0
Q ss_pred cCCCChhHHHHHHHHHHHHHHHhCCcchHhHHHHHHHh-c----------cCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 18 ELKAPPEQTQTITRVIFDIVKEHGPLTVAETWERVQQA-G----------VSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 18 ~~k~p~eqa~titr~l~dIvkeHGPLTV~~tW~h~ke~-g----------~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
++--|+++..+.-|.|.--+=.|+ .|.-||++++|| + =.|=.|.+-|.++.=|..|.+.|..+
T Consensus 16 Klgr~~~~R~~lLR~lvt~LvkHE--rIe~t~ara~Ear~~aEklIt~~~k~g~~~~~~~~~a~~~l~ekdli~Kl 89 (171)
T KOG3280|consen 16 KLGRPPAHRLALLRNLVTQLVKHE--RIETTWARAKEARRYAEKLITLGKKAGSLHERTARMADGWLREKDLLHKL 89 (171)
T ss_pred hcCCCcHHHHHHHHHHHHHHHHhh--hhhhHHHHHHHHHHHHHHHHHHHHhcCcHhHHHHHHHhcccccchHHHHH
Confidence 355678888888777766666677 567899999997 3 34667888899999999999987654
No 94
>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=26.52 E-value=69 Score=21.10 Aligned_cols=24 Identities=4% Similarity=0.295 Sum_probs=17.8
Q ss_pred hHHHHHHHHHHHHHHHhCCcchHh
Q 042237 24 EQTQTITRVIFDIVKEHGPLTVAE 47 (115)
Q Consensus 24 eqa~titr~l~dIvkeHGPLTV~~ 47 (115)
+|.+.+...+-+|+..+|++|=-+
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 578899999999999999998544
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=26.40 E-value=2.4e+02 Score=20.09 Aligned_cols=48 Identities=13% Similarity=0.241 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHh
Q 042237 28 TITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRE 75 (115)
Q Consensus 28 titr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMre 75 (115)
.+...+++-+++++.+.|.++...+.+.--..+.|..+...+.+.+-|
T Consensus 188 ~~~~~~~~~~~~~~~~~v~~~~~~lR~~R~~~i~~~~qy~f~~~~~~e 235 (235)
T PF00102_consen 188 CAIDILIEQLKKEGEVDVFEIVKKLRQQRPGAIQSPEQYRFCYMAVLE 235 (235)
T ss_dssp HHHHHHHHHHHHHSEECHHHHHHHHHTTSTTSSSSHHHHHHHHHHHHH
T ss_pred ccchhhccccccccchhhHHHHHHHHhhCCCccCCHHHHHHHHHHHhC
Confidence 345667777888888999999999988877788888887777665543
No 96
>PRK12348 sgaE L-ribulose-5-phosphate 4-epimerase; Reviewed
Probab=26.21 E-value=28 Score=27.14 Aligned_cols=27 Identities=19% Similarity=0.368 Sum_probs=19.5
Q ss_pred hHHHHHHHHHHH---------HHHHhCCcchHhHHH
Q 042237 24 EQTQTITRVIFD---------IVKEHGPLTVAETWE 50 (115)
Q Consensus 24 eqa~titr~l~d---------IvkeHGPLTV~~tW~ 50 (115)
+.+..++++|-+ |++.||.++++.+=.
T Consensus 142 ~~~~~la~~l~~~~~~~~~avlL~nHG~v~~G~~l~ 177 (228)
T PRK12348 142 NTGKVIIETLGNAEPLHTPGIVVYQHGPFAWGKDAH 177 (228)
T ss_pred hHHHHHHHHHhhcCcccCcEEEEcCCCeEEecCCHH
Confidence 356667777765 578999999876533
No 97
>PF12063 DUF3543: Domain of unknown function (DUF3543); InterPro: IPR022708 This domain belonging to serine/threonine-protein kinases is functionally uncharacterised. This domain is found in eukaryotes. It is typically between 217 to 291 amino acids in length and is found associated with PF00069 from PFAM. This domain has a single completely conserved residue A that may be functionally important. ; GO: 0004674 protein serine/threonine kinase activity
Probab=26.17 E-value=82 Score=25.27 Aligned_cols=43 Identities=28% Similarity=0.476 Sum_probs=27.1
Q ss_pred hCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhh--------hHHHHhh
Q 042237 40 HGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRER--------QKLRLIC 83 (115)
Q Consensus 40 HGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreR--------q~lkl~C 83 (115)
.|.-..++-|.+ +..+-+.+..-.-++.+++|||+| +.||+-+
T Consensus 85 ~am~~a~~~w~~-~~~~~~~~~~S~~vn~vVqwlr~rfneclekae~lr~~l 135 (238)
T PF12063_consen 85 KAMDIASAWWYS-KNRGSGSLNPSSRVNQVVQWLRERFNECLEKAEFLRLRL 135 (238)
T ss_pred HHHHHHHHHHHH-hcccccccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455554 332344566567899999999999 5566665
No 98
>PRK00441 argR arginine repressor; Provisional
Probab=25.92 E-value=96 Score=23.18 Aligned_cols=59 Identities=19% Similarity=0.254 Sum_probs=39.3
Q ss_pred HHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCcceeeeecc
Q 042237 31 RVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQFLYTTWF 98 (115)
Q Consensus 31 r~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FLyttw~ 98 (115)
+.|.++|++||..|+.+-=+.+++.|++ -|. + =+=|.+++-..+|. ..+ ..+|-|+.-.
T Consensus 7 ~~I~~ll~~~~~~~q~eL~~~L~~~G~~--vSq--a-TisRDl~~L~lvKv---~~~-~G~~~Y~l~~ 65 (149)
T PRK00441 7 AKILEIINSKEIETQEELAEELKKMGFD--VTQ--A-TVSRDIKELKLIKV---LSN-DGKYKYATIS 65 (149)
T ss_pred HHHHHHHHHcCCCcHHHHHHHHHhcCCC--cCH--H-HHHHHHHHcCcEEe---ECC-CCCEEEEeCc
Confidence 4678999999999999999999999887 222 2 23355555544443 222 2357787643
No 99
>PF04358 DsrC: DsrC like protein; InterPro: IPR007453 DsrC (P45573 from SWISSPROT) has been observed to co-purify with Desulphovibrio vulgaris dissimilatory sulphite reductase []. However, DsrC appears to be only loosely associated to the sulphite reductase, which suggests that it may not be an integral part of the dissimilatory sulphite reductase. Many proteins in this entry are found in organisms such as Escherichia coli and Haemophilus influenzae which do not contain dissimilatory sulphite reductases but can synthesise assimilatory sirohaem sulphite and nitrite reductases. It is speculated that DsrC may be involved in the assembly, folding or stabilisation of sirohaem proteins []. The strictly conserved cysteine in the C terminus suggests that DsrC may have a catalytic function in the metabolism of sulphur compounds []. Also included in this entry is TusE, a partner to TusBCD in a sulphur relay system for 2-thiouridine biosynthesis, a tRNA base modification process. Many proteins in this entry are annotated as the third (gamma) subunit of dissimilatory sulphite reductase ; PDB: 2V4J_F 2A5W_C 1SAU_A 1JI8_A 1YX3_A.
Probab=25.75 E-value=11 Score=27.21 Aligned_cols=58 Identities=26% Similarity=0.661 Sum_probs=33.3
Q ss_pred CCcchHhHHHH------HHHhccCCCCchhHHHHHHHHHHhh-------hHHHHhhhccCCC-------cceeeeeccCC
Q 042237 41 GPLTVAETWER------VQQAGVSGLTGKSHMKIVLRWMRER-------QKLRLICNHVGPH-------KQFLYTTWFTK 100 (115)
Q Consensus 41 GPLTV~~tW~h------~ke~g~~gL~SK~HMKi~LrWMreR-------q~lkl~C~hvG~~-------k~FLyttw~~~ 100 (115)
|=|.=.+-|+. |++-||. || -.|.+++ +.+|+- -.+|.+|...|-. .++||..|+..
T Consensus 15 GfL~~~~dW~eevA~~lA~~egI~-Lt-d~HW~vI-~flR~~y~~~~~~P~~R~l~K~~~~~~g~~~~~~k~L~~LFP~g 91 (109)
T PF04358_consen 15 GFLVDPEDWNEEVAEALAKEEGIE-LT-DEHWEVI-RFLRDYYQEYGVSPAIRMLIKALGEDLGEDKGNSKYLYQLFPGG 91 (109)
T ss_dssp SEESSGGG--HHHHHHHHHCTT-S----HHHHHHH-HHHHHHHHHHSS---HHHHHHHHHHHCSTT---HHHHHHHSTTH
T ss_pred cCcCChHhCCHHHHHHHHHHcCCC-CC-HHHHHHH-HHHHHHHHHHCCCCcHHHHHHHHhhhcCCCchhHHHHHHHcCCC
Confidence 33444455653 4555777 55 4788764 667653 2556666665555 89999999976
Q ss_pred C
Q 042237 101 P 101 (115)
Q Consensus 101 P 101 (115)
|
T Consensus 92 P 92 (109)
T PF04358_consen 92 P 92 (109)
T ss_dssp H
T ss_pred H
Confidence 6
No 100
>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=25.63 E-value=56 Score=21.34 Aligned_cols=13 Identities=31% Similarity=0.585 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHhC
Q 042237 29 ITRVIFDIVKEHG 41 (115)
Q Consensus 29 itr~l~dIvkeHG 41 (115)
|+|+|.|-|.|||
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 101
>PRK13249 phycoerythrobilin:ferredoxin oxidoreductase; Provisional
Probab=25.54 E-value=73 Score=26.40 Aligned_cols=61 Identities=13% Similarity=0.132 Sum_probs=39.5
Q ss_pred hCCcchHhHHHHHHHhccCC----CCchhHHHHHHHH-HHhhhHHHHhhhccCCCcceeeeeccCCCCCc
Q 042237 40 HGPLTVAETWERVQQAGVSG----LTGKSHMKIVLRW-MRERQKLRLICNHVGPHKQFLYTTWFTKPNNL 104 (115)
Q Consensus 40 HGPLTV~~tW~h~ke~g~~g----L~SK~HMKi~LrW-MreRq~lkl~C~hvG~~k~FLyttw~~~P~~~ 104 (115)
=-|+-|++--..+ |....| +...+.+ ..| ..+=+++|+.|...|+.=|-|++.+|-+|...
T Consensus 35 l~p~~ip~~l~~~-e~~~~~~~~~~~i~~~~---~~~~~~~fRk~r~~~~~~G~~lqVLn~V~fP~p~yD 100 (257)
T PRK13249 35 PEPYPVAEDFLQR-ESQTGSKSKPVKVTTAT---WACKTEKIRQVRAACVEAGEAASVLNFVINPSNRFD 100 (257)
T ss_pred CcccCCChhhhhh-hcccccccCcceEEEee---eccCChHHHHHHHHHhhcCCCcEEEEEEecCCcCCC
Confidence 3466677665544 222222 3333322 223 23457899999999999999999999998654
No 102
>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=25.35 E-value=28 Score=28.95 Aligned_cols=23 Identities=61% Similarity=1.175 Sum_probs=18.8
Q ss_pred hCCcchHhHH---------HHHHHhccCCCCc
Q 042237 40 HGPLTVAETW---------ERVQQAGVSGLTG 62 (115)
Q Consensus 40 HGPLTV~~tW---------~h~ke~g~~gL~S 62 (115)
-|||+.-+.| +++|++||.||.-
T Consensus 104 FG~l~~q~~w~l~vR~eAle~L~~~GvrGL~g 135 (237)
T PF09535_consen 104 FGPLTLQDPWTLLVRREALERLQAAGVRGLQG 135 (237)
T ss_pred ecceeecCCeeEeeeHHHHHHHHHhhhccccc
Confidence 4777777766 7999999999975
No 103
>cd08329 CARD_BIRC2_BIRC3 Caspase activation and recruitment domain found in Baculoviral IAP repeat-containing proteins, BIRC2 (c-IAP1) and BIRC3 (c-IAP2). Caspase activation and recruitment domain (CARD) similar to those found in Baculoviral IAP repeat (BIR)-containing protein 2 (BIRC2) or cellular Inhibitor of Apoptosis Protein 1 (c-IAP1), and BIRC3 (or c-IAP2). IAPs are anti-apoptotic proteins that contain at least one BIR domain. Most IAPs also contain a C-terminal RING domain. In addition, both BIRC2 and BIRC3 contain a CARD. BIRC2 and BIRC3, through their binding with TRAF (TNF receptor-associated factor) 2, are recruited to TNFR-1/2 signaling complexes, where they regulate caspase-8 activity. They also play important roles in pro-survival NF-kB signaling pathways. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interac
Probab=24.67 E-value=1.3e+02 Score=20.87 Aligned_cols=65 Identities=14% Similarity=0.160 Sum_probs=48.2
Q ss_pred HHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHH--hhhHHHHhhhccCCCcceeeeeccC
Q 042237 30 TRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMR--ERQKLRLICNHVGPHKQFLYTTWFT 99 (115)
Q Consensus 30 tr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMr--eRq~lkl~C~hvG~~k~FLyttw~~ 99 (115)
..-|+|.+-+.|=||..++ +.++. .-++...++.+|.=.. |.+--..+|++.....++||...++
T Consensus 25 v~~ilD~Ll~~~Vlt~ee~-e~I~~----~~t~~~qAr~Lld~l~~KG~~A~~~F~~~L~e~~~~L~~~L~~ 91 (94)
T cd08329 25 VLPILDSLLSANVITEQEY-DVIKQ----KTQTPLQARELIDTVLVKGNAAAEVFRNCLKKNDPVLYRDLFV 91 (94)
T ss_pred hHHHHHHHHHcCCCCHHHH-HHHHc----CCChHHHHHHHHHHHHhhhHHHHHHHHHHHHhcCHhHHHHHHh
Confidence 3447888999999998877 66665 3344567777666554 5588889999998889999877665
No 104
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=24.50 E-value=1e+02 Score=19.35 Aligned_cols=45 Identities=29% Similarity=0.318 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHh-CCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHH
Q 042237 29 ITRVIFDIVKEH-GPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLR 80 (115)
Q Consensus 29 itr~l~dIvkeH-GPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lk 80 (115)
-+-.|++.|.++ ||+|+++-=+ +.|++ +.=...+|+=|.+...|.
T Consensus 6 r~~~Il~~l~~~~~~~t~~~ia~---~l~i~----~~tv~r~l~~L~~~g~l~ 51 (91)
T smart00346 6 RGLAVLRALAEEPGGLTLAELAE---RLGLS----KSTAHRLLNTLQELGYVE 51 (91)
T ss_pred HHHHHHHHHHhCCCCcCHHHHHH---HhCCC----HHHHHHHHHHHHHCCCee
Confidence 345678888888 8999998644 34553 444455555555555554
No 105
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=23.88 E-value=1.9e+02 Score=19.20 Aligned_cols=31 Identities=29% Similarity=0.526 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHH-hCCcchHhHHHHHHHh-ccC
Q 042237 28 TITRVIFDIVKE-HGPLTVAETWERVQQA-GVS 58 (115)
Q Consensus 28 titr~l~dIvke-HGPLTV~~tW~h~ke~-g~~ 58 (115)
.+-.-|+.+|++ .|++|.++.=+.|.+. +++
T Consensus 4 ~~~~piL~~L~~~g~~~~~~ei~~~v~~~~~ls 36 (92)
T PF14338_consen 4 ELMPPILEALKDLGGSASRKEIYERVAERFGLS 36 (92)
T ss_pred HHHHHHHHHHHHcCCCcCHHHHHHHHHHHhCCC
Confidence 445678899999 8899999999999876 544
No 106
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=23.59 E-value=1.5e+02 Score=18.71 Aligned_cols=21 Identities=24% Similarity=0.313 Sum_probs=13.5
Q ss_pred CCcchHhHHHHHHHhccCCCC
Q 042237 41 GPLTVAETWERVQQAGVSGLT 61 (115)
Q Consensus 41 GPLTV~~tW~h~ke~g~~gL~ 61 (115)
.|+|-...++.+.+.+-.||=
T Consensus 42 ~~l~~~~~~~~l~~L~~~gli 62 (87)
T cd08768 42 DPLTQRRISDLLSELEMLGLL 62 (87)
T ss_pred CCCcHHHHHHHHHHHHHcCCe
Confidence 467777777777666655553
No 107
>PRK06755 hypothetical protein; Validated
Probab=23.25 E-value=49 Score=25.88 Aligned_cols=18 Identities=22% Similarity=0.250 Sum_probs=16.0
Q ss_pred HHHhCCcchHhHHHHHHH
Q 042237 37 VKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 37 vkeHGPLTV~~tW~h~ke 54 (115)
|+.||.++++.+|+.|..
T Consensus 166 l~~HGv~~~G~~l~eA~~ 183 (209)
T PRK06755 166 VHNYGMIVWGKTPEEAKK 183 (209)
T ss_pred EcCCCeEEEcCCHHHHHH
Confidence 678999999999998875
No 108
>cd03154 TM4SF3_like_LEL Tetraspanin, extracellular domain or large extracellular loop (LEL), TM4SF3_like subfamily. Tetraspanins are trans-membrane proteins with 4 trans-membrane segments. Both the N- and C-termini lie on the intracellular side of the membrane. This alignment model spans the extracellular domain between the 3rd and 4th trans-membrane segment. Tetraspanins are involved in diverse processes and their various functions may relate to their ability to act as molecular facilitators. Tetraspanins associate laterally with one another and cluster dynamically with numerous parnter domains in membrane microdomains, forming a network of multimolecular complexes, the "tetraspanin web". This subfamily contaions transmembrane 4 superfamily 3 (TM4SF3) or D6.1a and related proteins. D6.1a associates with alpha6beta4 integrin and supports cell motility, it has been ascribed a role in tumor progression and metastasis.
Probab=23.16 E-value=1.7e+02 Score=18.88 Aligned_cols=36 Identities=17% Similarity=0.271 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHhCC--cchHhHHHHHHHh-ccCCCCc
Q 042237 27 QTITRVIFDIVKEHGP--LTVAETWERVQQA-GVSGLTG 62 (115)
Q Consensus 27 ~titr~l~dIvkeHGP--LTV~~tW~h~ke~-g~~gL~S 62 (115)
..|.+.+.+.+++.+. -.+.++|+.+|+. +==|++|
T Consensus 13 ~~i~~~~~~~i~~y~~~~~~~~~~~d~lQ~~l~CCG~~~ 51 (100)
T cd03154 13 NELKEKNTKLLSLLGQNAKSVKKSLEKFQKELKCCGLVN 51 (100)
T ss_pred HHHHHHHHHHHHHcCCChHHHHHHHHHHHHcCCCCCCCC
Confidence 3456667777877653 2467899999996 3334444
No 109
>PF14090 HTH_39: Helix-turn-helix domain
Probab=23.10 E-value=92 Score=20.04 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=16.6
Q ss_pred HHHHHHHHHHhCCcchHhHHH
Q 042237 30 TRVIFDIVKEHGPLTVAETWE 50 (115)
Q Consensus 30 tr~l~dIvkeHGPLTV~~tW~ 50 (115)
.+.|.+.|+.+|+||--|.+.
T Consensus 3 ~~rIL~~L~~~~~it~~ea~~ 23 (70)
T PF14090_consen 3 CKRILAALRRGGSITTLEARR 23 (70)
T ss_pred HHHHHHHHHcCCCcCHHHHHH
Confidence 357899999999998666553
No 110
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=22.92 E-value=86 Score=18.41 Aligned_cols=39 Identities=26% Similarity=0.442 Sum_probs=25.4
Q ss_pred HHHHHH-HHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHH
Q 042237 32 VIFDIV-KEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWM 73 (115)
Q Consensus 32 ~l~dIv-keHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWM 73 (115)
.|..+| +.++|+|+.+- +++.|+|-=+=.++++.+-.|.
T Consensus 4 ~il~~L~~~~~~it~~eL---a~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 4 QILKLLLESKEPITAKEL---AEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHTTTSBEHHHH---HHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCCCcCHHHH---HHHhCCCHHHHHHHHHHHHHCC
Confidence 456666 77788999864 5556777666666766665554
No 111
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=22.86 E-value=91 Score=24.60 Aligned_cols=64 Identities=19% Similarity=0.218 Sum_probs=40.3
Q ss_pred CChhHH--HHHHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHhhhccCCCccee
Q 042237 21 APPEQT--QTITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLICNHVGPHKQFL 93 (115)
Q Consensus 21 ~p~eqa--~titr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~C~hvG~~k~FL 93 (115)
+=.|+| ++|-++|-.+..+-..-.=+=||+-+-+.|+.|=+||.--.. .-+..+---+|+||||
T Consensus 91 iGVE~As~e~I~~AL~~~~~~~~~~~~~it~~dl~~~gL~g~~sk~rR~~---------lg~~L~IGy~N~Kqll 156 (174)
T TIGR00334 91 IGVEEASVEAIIAALENVHEETKAQQSDISWEDLLELGLIGPASKCKRLR---------LCNLLKLGYFNHKQLF 156 (174)
T ss_pred cccCCCCHHHHHHHHHHhcccccCcccccCHHHHHHCCCCCccHHHHHHH---------HHHHhCCCCCcHHHHH
Confidence 344555 567777777765433222235799999999975588843222 2345555667888876
No 112
>PRK13145 araD L-ribulose-5-phosphate 4-epimerase; Provisional
Probab=22.31 E-value=36 Score=26.73 Aligned_cols=29 Identities=28% Similarity=0.424 Sum_probs=21.9
Q ss_pred hHHHHHHHHHHH-----------HHHHhCCcchHhHHHHH
Q 042237 24 EQTQTITRVIFD-----------IVKEHGPLTVAETWERV 52 (115)
Q Consensus 24 eqa~titr~l~d-----------IvkeHGPLTV~~tW~h~ 52 (115)
|.+..+++.+-+ |++.||.++++.+=+.|
T Consensus 144 ~~~~~va~~l~~~~~~~~~~~avLL~nHG~v~~G~~l~eA 183 (234)
T PRK13145 144 ETGSVIIEEFEKRGLDPMAVPGIVVRNHGPFTWGKNPEQA 183 (234)
T ss_pred hhHHHHHHHHhhhccccccCCEEEEcCCCeeEecCCHHHH
Confidence 566778888766 68899999998764444
No 113
>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=22.00 E-value=1.1e+02 Score=22.08 Aligned_cols=38 Identities=11% Similarity=0.279 Sum_probs=31.0
Q ss_pred hhHHHHHHHHHHHHHHHh-CCcchHhHHHHHHHhccCCC
Q 042237 23 PEQTQTITRVIFDIVKEH-GPLTVAETWERVQQAGVSGL 60 (115)
Q Consensus 23 ~eqa~titr~l~dIvkeH-GPLTV~~tW~h~ke~g~~gL 60 (115)
..+-..+.+.|.++.+.+ .|+-|.+-++-+.+.|..|+
T Consensus 39 ~~~~~~~~~~l~~~~~~~~~~l~i~~~~~la~~~g~~Gv 77 (196)
T TIGR00693 39 TRERLALAEKLQELCRRYGVPFIVNDRVDLALALGADGV 77 (196)
T ss_pred HHHHHHHHHHHHHHHHHhCCeEEEECHHHHHHHcCCCEE
Confidence 344567788888888775 79999999999999998875
No 114
>smart00441 FF Contains two conserved F residues. A novel motif that often accompanies WW domains. Often contains two conserved Phe (F) residues.
Probab=21.83 E-value=1.1e+02 Score=18.01 Aligned_cols=26 Identities=23% Similarity=0.500 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhCCcchHhHHHHHHHh
Q 042237 30 TRVIFDIVKEHGPLTVAETWERVQQA 55 (115)
Q Consensus 30 tr~l~dIvkeHGPLTV~~tW~h~ke~ 55 (115)
......+|++++-+|-..+|..++..
T Consensus 4 ~~~F~~LL~e~~~~~~~~~W~~~~~~ 29 (55)
T smart00441 4 KEAFKELLKEHEVITPDTTWSEARKK 29 (55)
T ss_pred HHHHHHHHHhCCCCCCCCcHHHHHHH
Confidence 45577889999999999999999864
No 115
>PRK08570 rpl19e 50S ribosomal protein L19e; Reviewed
Probab=21.57 E-value=2.6e+02 Score=21.79 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHhCCcchHhHHHHHHHhccCCCCchhHHHHHHH
Q 042237 26 TQTITRVIFDIVKEHGPLTVAETWERVQQAGVSGLTGKSHMKIVLR 71 (115)
Q Consensus 26 a~titr~l~dIvkeHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~Lr 71 (115)
..-.-|.++.-++|+|-|+=..-+.--..+..+-..|+.||+.-+.
T Consensus 98 riR~lRr~Lk~lR~~~kId~~~Yr~lY~kaKGn~Fkn~~~L~~~i~ 143 (150)
T PRK08570 98 RIRALRRYLRELRDEGKIDRKTYRKLYRKAKGGEFRSVSHLKTYIE 143 (150)
T ss_pred HHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccCCHHHHHHHHH
Confidence 3456688899999999999999999999998889999999976553
No 116
>PF09597 IGR: IGR protein motif; InterPro: IPR019083 This entry is found in fungal and plant proteins and contains a conserved IGR motif. Its function is unknown.
Probab=21.10 E-value=1.1e+02 Score=20.07 Aligned_cols=32 Identities=25% Similarity=0.707 Sum_probs=20.7
Q ss_pred HHhCCcchHhHHHH--------HHHhccCCCCchhHHHHHHHHHH
Q 042237 38 KEHGPLTVAETWER--------VQQAGVSGLTGKSHMKIVLRWMR 74 (115)
Q Consensus 38 keHGPLTV~~tW~h--------~ke~g~~gL~SK~HMKi~LrWMr 74 (115)
.+|-+ .+.+-|+. +|++|| .-++-|.+|+|+-
T Consensus 13 ~~~~~-kf~~~w~~lf~~~s~~LK~~GI----p~r~RryiL~~~e 52 (57)
T PF09597_consen 13 EEHAE-KFESDWEKLFTTSSKQLKELGI----PVRQRRYILRWRE 52 (57)
T ss_pred HHHHH-HHHHHHHHHHhcCHHHHHHCCC----CHHHHHHHHHHHH
Confidence 34444 34555664 577766 4678899999974
No 117
>PRK06661 hypothetical protein; Provisional
Probab=20.90 E-value=30 Score=27.06 Aligned_cols=30 Identities=17% Similarity=0.390 Sum_probs=22.0
Q ss_pred hhHHHHHHHHHHH----HHHHhCCcchHhHHHHH
Q 042237 23 PEQTQTITRVIFD----IVKEHGPLTVAETWERV 52 (115)
Q Consensus 23 ~eqa~titr~l~d----IvkeHGPLTV~~tW~h~ 52 (115)
.|++..+++++-+ +++.||.++++.+=+.|
T Consensus 137 ~~~~~~~a~~l~~~~avll~nHG~v~~G~sl~eA 170 (231)
T PRK06661 137 DKQSSRLVNDLKQNYVMLLRNHGAITCGKTIHEA 170 (231)
T ss_pred hhHHHHHHHHhCCCCEEEECCCCCeEecCCHHHH
Confidence 3557777777744 68999999998765544
No 118
>PF11855 DUF3375: Protein of unknown function (DUF3375); InterPro: IPR021804 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
Probab=20.63 E-value=1.1e+02 Score=26.66 Aligned_cols=32 Identities=22% Similarity=0.413 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHhCCcchHhHHHHHH-HhccC
Q 042237 27 QTITRVIFDIVKEHGPLTVAETWERVQ-QAGVS 58 (115)
Q Consensus 27 ~titr~l~dIvkeHGPLTV~~tW~h~k-e~g~~ 58 (115)
..+.+.|-+.+.++||+|+++.+++.= +.|+.
T Consensus 402 ~~L~~~v~~~l~~~~~~tLaevl~~~P~~~gLa 434 (478)
T PF11855_consen 402 AELRENVRAALAERGQVTLAEVLEHLPAEQGLA 434 (478)
T ss_pred HHHHHHHHHHHhhCCCCcHHHHHHhCCcccChH
Confidence 346677888899999999999999987 44554
No 119
>PRK02816 phycocyanobilin:ferredoxin oxidoreductase; Validated
Probab=20.37 E-value=69 Score=26.14 Aligned_cols=29 Identities=24% Similarity=0.260 Sum_probs=26.1
Q ss_pred hhHHHHhhhccCCCcceeeeeccCCCCCc
Q 042237 76 RQKLRLICNHVGPHKQFLYTTWFTKPNNL 104 (115)
Q Consensus 76 Rq~lkl~C~hvG~~k~FLyttw~~~P~~~ 104 (115)
=+++++.|...|++=|-|++.+|-+|..+
T Consensus 66 fRk~hle~~~~G~~lqVLn~V~fP~~~yD 94 (243)
T PRK02816 66 FRKLHLELARLGNGLDILHCVMFPDPRYD 94 (243)
T ss_pred hhhhheeeeccCCCceEEEEEecCCCCCC
Confidence 37899999999999999999999999654
No 120
>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=20.24 E-value=28 Score=25.19 Aligned_cols=31 Identities=19% Similarity=0.354 Sum_probs=23.4
Q ss_pred hHHHHHHHHHH-H----HHHHhCCcchHhHHHHHHH
Q 042237 24 EQTQTITRVIF-D----IVKEHGPLTVAETWERVQQ 54 (115)
Q Consensus 24 eqa~titr~l~-d----IvkeHGPLTV~~tW~h~ke 54 (115)
|-+..|+++|- + |++.||.++++++.+.+..
T Consensus 136 ~l~~~i~~~l~~~~~~vll~nHG~~~~G~s~~~A~~ 171 (184)
T PF00596_consen 136 ELAEAIAEALGEDRKAVLLRNHGVVVWGKSLEEAFY 171 (184)
T ss_dssp HHHHHHHHHHTCTSSEEEETTTEEEEEESSHHHHHH
T ss_pred hhhhhhhhhhcCCceEEeecCCceEEEeCCHHHHHH
Confidence 34566777776 3 6788999999998887765
No 121
>KOG1575 consensus Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion]
Probab=20.16 E-value=1.7e+02 Score=25.22 Aligned_cols=23 Identities=26% Similarity=0.508 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHHHHhCCcchHh
Q 042237 24 EQTQTITRVIFDIVKEHGPLTVAE 47 (115)
Q Consensus 24 eqa~titr~l~dIvkeHGPLTV~~ 47 (115)
+..+.+.++|-+|-++|| .|+++
T Consensus 254 ~~~~~~~~~~~~iA~k~g-~T~~q 276 (336)
T KOG1575|consen 254 DKQKPILEALSKIAEKHG-CTVPQ 276 (336)
T ss_pred hhHHHHHHHHHHHHHHcC-CCHHH
Confidence 668899999999999999 77766
No 122
>PF12777 MT: Microtubule-binding stalk of dynein motor; InterPro: IPR024743 The 380 kDa motor unit of dynein belongs to the AAA class of chaperone-like ATPases. The core of the 380 kDa motor unit contains a concatenated chain of six AAA modules (D1-6), of which four correspond to the ATP binding sites with P-loop signatures, and two are modules in which the P loop has been lost in evolution. This domain occurs between D4 and D5 and includes the two predicted alpha-helical coiled coil segments that form the stalk supporting the ATP-sensitive microtubule binding component [].; PDB: 3VKH_A 3VKG_A 3ERR_A 4AKI_A 4AI6_B 4AKH_A 4AKG_A 3QMZ_A 2RR7_A.
Probab=20.14 E-value=1.3e+02 Score=24.75 Aligned_cols=37 Identities=19% Similarity=0.471 Sum_probs=25.7
Q ss_pred CCCChhHHHHHHHHHHHHHHHhCCcchHhHHHHHHHh
Q 042237 19 LKAPPEQTQTITRVIFDIVKEHGPLTVAETWERVQQA 55 (115)
Q Consensus 19 ~k~p~eqa~titr~l~dIvkeHGPLTV~~tW~h~ke~ 55 (115)
+..||+-+..+..+|+-++.+.|-+.-..+|+.+|..
T Consensus 112 ~~~PP~~V~~V~~aV~iLl~~~~~~~k~~~W~~ak~~ 148 (344)
T PF12777_consen 112 YANPPEAVKLVMEAVCILLGPKGKLPKDTSWESAKKL 148 (344)
T ss_dssp SSS--HHHHHHHHHHHHHTT-S-SEE---HHHHHHCH
T ss_pred hCCCcHHHHHHHHHHhhHHhccccccccccHHHHHHH
Confidence 5689999999999999999887766667899999864
No 123
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=20.10 E-value=1.5e+02 Score=22.03 Aligned_cols=49 Identities=8% Similarity=0.217 Sum_probs=33.4
Q ss_pred HHHHHHH-HhCCcchHhHHHHHHHhccCCCCchhHHHHHHHHHHhhhHHHHh
Q 042237 32 VIFDIVK-EHGPLTVAETWERVQQAGVSGLTGKSHMKIVLRWMRERQKLRLI 82 (115)
Q Consensus 32 ~l~dIvk-eHGPLTV~~tW~h~ke~g~~gL~SK~HMKi~LrWMreRq~lkl~ 82 (115)
+|+++|. ..+++|..+..+++++.|-+ -|..=-=..|++|-+-.+|+.+
T Consensus 30 ~IL~~l~~~~~hlSa~eI~~~L~~~~~~--is~aTVYRtL~~L~e~Glv~~~ 79 (169)
T PRK11639 30 EVLRLMSLQPGAISAYDLLDLLREAEPQ--AKPPTVYRALDFLLEQGFVHKV 79 (169)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHhhCCC--CCcchHHHHHHHHHHCCCEEEE
Confidence 4555554 35799999999999998743 2233345678888887777543
Done!