Query 031351
Match_columns 161
No_of_seqs 113 out of 1051
Neff 7.2
Searched_HMMs 46136
Date Fri Mar 29 12:52:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031351.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031351hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07107 WI12: Wound-induced p 99.8 2E-18 4.3E-23 122.2 6.6 92 68-161 12-109 (109)
2 COG3631 Ketosteroid isomerase- 99.7 8.9E-17 1.9E-21 118.8 12.7 115 12-128 1-133 (133)
3 PF07858 LEH: Limonene-1,2-epo 99.7 1.1E-16 2.4E-21 117.0 12.6 108 16-125 2-123 (125)
4 TIGR02096 conserved hypothetic 99.7 1.9E-15 4.1E-20 108.7 12.8 106 19-126 2-129 (129)
5 PRK08241 RNA polymerase factor 99.6 4.6E-14 1E-18 117.9 14.3 112 13-129 212-335 (339)
6 TIGR02960 SigX5 RNA polymerase 99.5 4.5E-13 9.7E-18 111.0 14.1 108 15-126 204-323 (324)
7 PF07366 SnoaL: SnoaL-like pol 99.5 3.2E-13 6.8E-18 97.4 11.5 104 20-125 2-126 (126)
8 cd00781 ketosteroid_isomerase 99.5 3.2E-13 6.9E-18 96.5 9.1 106 14-121 2-120 (122)
9 PF12680 SnoaL_2: SnoaL-like d 99.4 2E-12 4.4E-17 87.7 11.0 90 21-112 1-102 (102)
10 COG4308 LimA Limonene-1,2-epox 99.4 4.1E-12 8.9E-17 91.1 8.9 110 15-126 6-127 (130)
11 PRK09636 RNA polymerase sigma 99.2 5.1E-10 1.1E-14 92.1 13.2 107 13-122 169-287 (293)
12 TIGR02957 SigX4 RNA polymerase 98.9 2.1E-08 4.6E-13 82.1 12.4 105 13-122 162-278 (281)
13 COG4922 Uncharacterized protei 98.8 4.9E-08 1.1E-12 69.8 7.9 100 15-116 5-113 (129)
14 COG5485 Predicted ester cyclas 98.8 8.9E-08 1.9E-12 69.2 9.1 105 19-126 10-131 (131)
15 PRK09635 sigI RNA polymerase s 98.7 2.6E-07 5.7E-12 76.3 10.6 103 15-122 174-281 (290)
16 COG4538 Uncharacterized conser 98.4 6.4E-06 1.4E-10 57.4 11.1 97 16-114 4-109 (112)
17 PF14534 DUF4440: Domain of un 98.2 2.9E-05 6.3E-10 52.8 9.9 73 18-90 2-77 (107)
18 PF03284 PHZA_PHZB: Phenazine 98.0 5.3E-05 1.1E-09 56.5 8.6 113 15-132 18-155 (162)
19 TIGR02246 conserved hypothetic 98.0 4.8E-05 1E-09 53.9 8.0 74 15-88 4-85 (128)
20 PF13474 SnoaL_3: SnoaL-like d 97.7 0.0004 8.6E-09 48.4 9.0 71 18-88 2-79 (121)
21 cd00531 NTF2_like Nuclear tran 97.4 0.011 2.5E-07 40.1 12.7 48 18-65 2-56 (124)
22 COG4319 Ketosteroid isomerase 97.3 0.0018 3.8E-08 48.1 7.7 72 17-88 12-90 (137)
23 PF12893 Lumazine_bd_2: Putati 97.2 0.0063 1.4E-07 43.1 9.5 93 16-108 5-107 (116)
24 PF07080 DUF1348: Protein of u 96.3 0.083 1.8E-06 39.1 9.8 106 13-119 8-124 (143)
25 PF13577 SnoaL_4: SnoaL-like d 95.2 0.14 3.1E-06 35.7 7.5 50 15-64 7-61 (127)
26 PF08332 CaMKII_AD: Calcium/ca 94.4 1.5 3.2E-05 32.2 12.1 34 16-49 4-37 (128)
27 PF12870 Lumazine_bd: Lumazine 93.9 0.076 1.7E-06 36.3 3.4 31 15-45 7-37 (111)
28 cd00667 ring_hydroxylating_dio 90.1 0.43 9.4E-06 35.4 3.8 35 16-50 5-39 (160)
29 PF02136 NTF2: Nuclear transpo 89.4 5.3 0.00012 27.6 10.6 85 18-103 3-103 (118)
30 PF10184 DUF2358: Uncharacteri 88.0 6.8 0.00015 27.6 8.6 78 30-111 16-112 (113)
31 PF11533 DUF3225: Protein of u 85.9 4.5 9.8E-05 29.6 6.7 66 17-82 12-82 (125)
32 TIGR03231 anthran_1_2_B anthra 84.3 1.6 3.4E-05 32.9 3.9 31 20-50 4-34 (155)
33 PRK10069 3-phenylpropionate di 83.7 1.5 3.2E-05 33.7 3.6 32 18-49 23-54 (183)
34 PF05223 MecA_N: NTF2-like N-t 82.7 1.6 3.4E-05 31.0 3.2 107 16-128 2-117 (118)
35 TIGR03232 benzo_1_2_benB benzo 80.9 1.6 3.5E-05 32.9 2.8 23 28-50 12-34 (155)
36 PF00866 Ring_hydroxyl_B: Ring 72.6 3.2 6.9E-05 30.7 2.4 24 27-50 5-28 (145)
37 PF11453 DUF2950: Protein of u 68.9 21 0.00046 29.5 6.5 79 16-102 6-87 (271)
38 cd00780 NTF2 Nuclear transport 64.8 45 0.00097 23.2 11.7 85 17-103 6-102 (119)
39 PF04280 Tim44: Tim44-like dom 64.0 36 0.00077 24.5 6.5 28 17-44 24-51 (147)
40 COG4460 Uncharacterized protei 57.4 43 0.00094 24.2 5.6 57 21-77 16-75 (130)
41 COG5517 Small subunit of pheny 54.6 9.4 0.0002 29.1 1.9 24 27-50 20-43 (164)
42 PLN02382 probable sucrose-phos 53.4 96 0.0021 26.9 8.3 71 17-87 284-371 (413)
43 PF11006 DUF2845: Protein of u 47.3 45 0.00097 22.4 4.3 30 83-114 54-85 (87)
44 COG4875 Uncharacterized protei 47.0 1.2E+02 0.0025 22.5 8.6 30 18-47 40-69 (156)
45 COG0268 RpsT Ribosomal protein 29.7 74 0.0016 21.8 3.1 26 17-42 28-53 (88)
46 PF14326 DUF4384: Domain of un 27.9 1.7E+02 0.0037 19.0 4.7 35 78-114 3-37 (83)
47 TIGR00984 3a0801s03tim44 mitoc 26.0 44 0.00095 29.0 1.8 24 21-44 255-278 (378)
48 PF02607 B12-binding_2: B12 bi 25.6 54 0.0012 20.9 1.8 26 19-44 3-28 (79)
49 PF06594 HCBP_related: Haemoly 25.4 1.4E+02 0.0031 17.0 4.1 31 78-110 7-38 (43)
50 PF01649 Ribosomal_S20p: Ribos 21.5 1.3E+02 0.0029 20.2 3.1 25 17-41 27-51 (84)
51 PF02512 UK: Virulence determi 20.9 72 0.0016 21.6 1.6 30 3-32 34-63 (96)
52 PF13616 Rotamase_3: PPIC-type 20.0 1.7E+02 0.0036 20.4 3.5 33 12-44 31-64 (117)
No 1
>PF07107 WI12: Wound-induced protein WI12; InterPro: IPR009798 This entry consists of several plant wound-induced protein sequences related to WI12 from Mesembryanthemum crystallinum (Common ice plant) (Q9XES3 from SWISSPROT). Wounding, methyl jasmonate, and pathogen infection is known to induce local WI12 expression. WI12 expression is also thought to be developmentally controlled in the placenta and developing seeds. WI12 preferentially accumulates in the cell wall and it has been suggested that it plays a role in the reinforcement of cell wall composition after wounding and during plant development [].
Probab=99.75 E-value=2e-18 Score=122.23 Aligned_cols=92 Identities=51% Similarity=0.844 Sum_probs=80.9
Q ss_pred ceeEEEeeEEEEeCCEEEEEeec-CCCceEEEEEEEEecCCeEEEEEEeeChHHHHHHcCCCc--cc---ccccCcccee
Q 031351 68 ATFKFEPRSVEVVGDCVIAEGWE-GAPAYWVHVWTVNVKDGLITQFREYFNTWLTVKDLRPPR--WE---IRVRHERNTL 141 (161)
Q Consensus 68 ~~~~~~~~~vi~~Gd~Vvv~G~~-~~~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg~~~--~~---~~~~~~~~~~ 141 (161)
..|+|.|.++.+-|+.|++||.. ..+.||||+|++ .||+|+++||||||.....-+++.. ++ .-.++....|
T Consensus 12 ~sF~F~P~sV~afG~~ViaEG~~~~~~~yWVHaWTV--~dGiITqlREYFNT~ltVt~l~~~~~~~~~~~~~~~~~~~~v 89 (109)
T PF07107_consen 12 SSFRFVPRSVDAFGSTVIAEGCDETRSVYWVHAWTV--KDGIITQLREYFNTSLTVTRLGPGASGSSSSDSAPSSHCPCV 89 (109)
T ss_pred CcEEEeccEEEEECCEEEEecccCcCcEEEEEEEEe--cCCEEEeeeeeeeeEEEEEeccccCCcccccccccCCCCCce
Confidence 57999999999999999999944 456999999999 9999999999999998888888543 43 2445777899
Q ss_pred eeeccccccCCCCCceeeeC
Q 031351 142 WQSQPRDLARRSLPSLLLTI 161 (161)
Q Consensus 142 ~~~~~~~~~~~~~~~~~~~~ 161 (161)
|||+..+.+++|+|||.|+|
T Consensus 90 WqS~~~d~~~~SlPGLVLAI 109 (109)
T PF07107_consen 90 WQSRLPDRAGKSLPGLVLAI 109 (109)
T ss_pred ecccccccccCCcCCEEEeC
Confidence 99999999999999999987
No 2
>COG3631 Ketosteroid isomerase-related protein [General function prediction only]
Probab=99.73 E-value=8.9e-17 Score=118.80 Aligned_cols=115 Identities=24% Similarity=0.331 Sum_probs=89.5
Q ss_pred CccccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCc--c------HHHHHHHHhccccc-ceeEEEeeEEEEeCC
Q 031351 12 MAEQNQEAIVKALYKALANDEMENVAKYLASDLEYWFHGPP--T------CQHMVRLLTGESSK-ATFKFEPRSVEVVGD 82 (161)
Q Consensus 12 Ms~~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~--~------~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd 82 (161)
|+.++|+++|+++|+|+.+||.+.+.+|+++|++|..||.+ . .+....++...... ...++++..++.+||
T Consensus 1 m~~~~~~~~v~~~f~a~~~GD~~~~~~l~a~D~v~~~p~~~~~~~~~~~g~~~~~~~~~~~~r~~~~~~~~~~~~~~~gD 80 (133)
T COG3631 1 MTEMDNTDLVRRYFAALSRGDLDGLLALLAEDVVWEVPGTPPLSGTFRGGVAIRRDVFALLPRLIEDGRFTVETVYVSGD 80 (133)
T ss_pred CCcchhhhHHHHHHHHHhcCCHHHHHhhccCceEEEeeCCCCCccccccchhhhhHHhhhChhhcccccccceEEEEcCC
Confidence 45678999999999999999999999999999999998722 1 12233444433333 366888999999999
Q ss_pred EEEEEeecC------CC---ceEEEEEEEEecCCeEEEEEEeeChHHHHHHcCCC
Q 031351 83 CVIAEGWEG------AP---AYWVHVWTVNVKDGLITQFREYFNTWLTVKDLRPP 128 (161)
Q Consensus 83 ~Vvv~G~~~------~~---~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg~~ 128 (161)
.+++.+..+ ++ ..+++++++ +||||+++++|+|+..+.+++|++
T Consensus 81 ~~~~v~~~~~~~~~~G~~~~~~~~~v~~v--rdGrI~~~~~y~D~~~~~~a~~~~ 133 (133)
T COG3631 81 PVGAVFRTRGRVSRTGKPYENRYAFVIRV--RDGRITRYREYVDTLALAEALGGS 133 (133)
T ss_pred ceEEEEEecCcccccCceeecceEEEEEE--eCCEEEEEEEEechHhHHHHhcCC
Confidence 877443222 11 444999999 999999999999999999999864
No 3
>PF07858 LEH: Limonene-1,2-epoxide hydrolase catalytic domain; InterPro: IPR013100 Epoxide hydrolases catalyse the hydrolysis of epoxides to corresponding diols, which is important in detoxification, synthesis of signal molecules, or metabolism. Limonene-1,2- epoxide hydrolase (LEH) differs from many other epoxide hydrolases in its structure and its novel one-step catalytic mechanism. Its main fold consists of a six-stranded mixed beta-sheet, with three N-terminal alpha helices packed to one side to create a pocket that extends into the protein core. A fourth helix lies in such a way that it acts as a rim to this pocket. Although mainly lined by hydrophobic residues, this pocket features a cluster of polar groups that lie at its deepest point and constitute the enzymes active site []. ; PDB: 2BNG_C 1NWW_A 1NU3_B.
Probab=99.72 E-value=1.1e-16 Score=116.96 Aligned_cols=108 Identities=27% Similarity=0.433 Sum_probs=86.8
Q ss_pred cHHHHHHHHHHHHhCCCHHH-HHhhccCCeEEEecC-Cc--cHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEeec
Q 031351 16 NQEAIVKALYKALANDEMEN-VAKYLASDLEYWFHG-PP--TCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGWE 90 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~-l~~lla~Dvv~~~~G-p~--~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~~ 90 (161)
++.++|++|++||..+|+++ +..++++|++|++.| |+ +.+++.+++..+... ..+.++++++.++|+.|..|-..
T Consensus 2 ~~~~vV~~F~~a~~~~D~~~a~~~~~~~d~vy~Nvplp~i~G~~~~~~~l~~~~~~~~~~e~~i~~iaadg~~VltER~D 81 (125)
T PF07858_consen 2 TPEEVVRAFLAALEDRDVDAALASLFDDDAVYHNVPLPPIRGRDAIRAFLRGFLDSLSGFEFDIHRIAADGDVVLTERTD 81 (125)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHCEECC-EEEETTTEEEESHHHHHHHHHCCHCCCEEEEEEEEEEEEETTEEEEEEEE
T ss_pred ChHHHHHHHHHHHHcCCHHHHHHHhcCCCcEEEeCCCCCcccHHHHHHHHHHHhcccceeEEEEEEEeecCCEEEEEeEe
Confidence 58899999999999999765 567999999999998 44 467888888877433 67899999999999999988322
Q ss_pred ------CC---CceEEEEEEEEecCCeEEEEEEeeChHHHHHHc
Q 031351 91 ------GA---PAYWVHVWTVNVKDGLITQFREYFNTWLTVKDL 125 (161)
Q Consensus 91 ------~~---~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~al 125 (161)
+. ..+.|.+|++ +||||+.||+|||...+.+++
T Consensus 82 ~l~~~dG~~~~~~~V~GvfEv--~dGkI~~WRDYFD~~~~~~a~ 123 (125)
T PF07858_consen 82 VLRFADGPLRIQFPVCGVFEV--RDGKITLWRDYFDLADFLKAT 123 (125)
T ss_dssp EEEETTTTEEEEEEEEEEEEE--ETTEEEEEEEE--HHHHHHHH
T ss_pred eeeeecCCeEEEEEEEEEEEE--ECCEEEEEeccCCHHHHHHHh
Confidence 21 3777999999 999999999999999998875
No 4
>TIGR02096 conserved hypothetical protein, steroid delta-isomerase-related. This family of proteins about 135 amino acids in length largely restricted to the Proteobacteria. This family and a delta5-3-ketosteroid isomerase from Pseudomonas testosteroni appear homologous, especially toward their respective N-termini. Members, therefore, probably are enzymes.
Probab=99.67 E-value=1.9e-15 Score=108.75 Aligned_cols=106 Identities=19% Similarity=0.191 Sum_probs=85.6
Q ss_pred HHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCc---c-HHHHHHHHhccccc-ceeEEEeeEEEEeCC-EEEEE----e
Q 031351 19 AIVKALYKALANDEMENVAKYLASDLEYWFHGPP---T-CQHMVRLLTGESSK-ATFKFEPRSVEVVGD-CVIAE----G 88 (161)
Q Consensus 19 ~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~---~-~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd-~Vvv~----G 88 (161)
+++++||+|++++|++.+.++++||++|+.+++. . .+++.+++..++.. +++++++.+++..++ .++++ |
T Consensus 2 ~iv~~~~~a~~~~d~~~~~~~~~~d~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~v~~~~~~~g 81 (129)
T TIGR02096 2 ELAQHWIEAFNRGDMDAVLALLAEDVLYDDNQGGRVLGGKAQLARFLAPYRTAFPDLLVDVVVCRNDEGVRVAAEWTVHG 81 (129)
T ss_pred HHHHHHHHHHHCCCHHHHHHhcCCCeEEEcCCCCcEeccHHHHHHHHHHHHHhCchhhceeEEEEecCCcEEEEEEEEee
Confidence 6899999999999999999999999999987532 2 56666666655544 577888888887665 88776 3
Q ss_pred ecC---------C---CceEEEEEEEEecCCeEEEEEEeeChHHHHHHcC
Q 031351 89 WEG---------A---PAYWVHVWTVNVKDGLITQFREYFNTWLTVKDLR 126 (161)
Q Consensus 89 ~~~---------~---~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg 126 (161)
++. + ....+++|+| +||||++++.|+|+..+.+|+|
T Consensus 82 ~~~g~~~g~~~~g~~~~~~~~~~~~~--~~gkI~~~~~y~D~~~~~~qlg 129 (129)
T TIGR02096 82 TYRTAFLGLPASGKTYSIRGVTFFVF--DDGKIKRETTYYNLATFLRQLG 129 (129)
T ss_pred eeccccCCCCCCCCEEEeeeeEEEEE--eCCEEEEEEEEecHHHHHHhhC
Confidence 321 1 1567999999 9999999999999999999987
No 5
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=99.58 E-value=4.6e-14 Score=117.88 Aligned_cols=112 Identities=13% Similarity=0.254 Sum_probs=86.2
Q ss_pred ccccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCc----cHHHHHHHHhccccc---ceeEEEeeEEEEeCCEEE
Q 031351 13 AEQNQEAIVKALYKALANDEMENVAKYLASDLEYWFHGPP----TCQHMVRLLTGESSK---ATFKFEPRSVEVVGDCVI 85 (161)
Q Consensus 13 s~~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~----~~~~v~~~l~~~~~~---~~~~~~~~~vi~~Gd~Vv 85 (161)
..+.++++|++||+||++||++++.+||+||++|+.|+.+ +.+++..++...... ..+++ ...+++|+.|+
T Consensus 212 ~~~~~~~~v~~~~~A~~~gD~~~l~~lla~Dv~~~~p~~~~~~~G~~~v~~~~~~~~~~~~~~~~~~--~~~~~~g~~v~ 289 (339)
T PRK08241 212 DDPEERALLARYVAAFEAYDVDALVALLTEDATWSMPPFPLWYRGRDAIAAFLAGQCPGAGCGGSRL--VPTRANGQPAF 289 (339)
T ss_pred CChHHHHHHHHHHHHHhcCCHHHHHHHhcCCEEEEcCCCCCcccCHHHHHHHHHhhccccCCCceEE--EEeecCCCeEE
Confidence 3467999999999999999999999999999999988522 357788888775322 23344 44478899888
Q ss_pred EEeecC--C---CceEEEEEEEEecCCeEEEEEEeeChHHHHHHcCCCc
Q 031351 86 AEGWEG--A---PAYWVHVWTVNVKDGLITQFREYFNTWLTVKDLRPPR 129 (161)
Q Consensus 86 v~G~~~--~---~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg~~~ 129 (161)
+.+... + ...+|++|+| +||||+++++|+|+. .+.++|.+.
T Consensus 290 ~~~~~~~~g~~~~~~~v~v~~v--~dGkI~~~~~y~d~~-~~~~~~~~~ 335 (339)
T PRK08241 290 AQYMRDPDGGGHRPWALHVLEL--RGGRIAHVTSFLDTT-LFPRFGLPA 335 (339)
T ss_pred EEEEEcCCCCeeecceEEEEEE--eCCEEEEEEEEcChh-hhhhcCCCC
Confidence 874331 1 2566999999 999999999999994 667777553
No 6
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=99.51 E-value=4.5e-13 Score=111.01 Aligned_cols=108 Identities=13% Similarity=0.175 Sum_probs=85.5
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC---Cc-cHHHHHHHHhccc--cc-ceeEEEeeEEEEeCCEEEEE
Q 031351 15 QNQEAIVKALYKALANDEMENVAKYLASDLEYWFHG---PP-TCQHMVRLLTGES--SK-ATFKFEPRSVEVVGDCVIAE 87 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G---p~-~~~~v~~~l~~~~--~~-~~~~~~~~~vi~~Gd~Vvv~ 87 (161)
+.+.++|++||+|+++||++++.+||+||++|+.|+ |. +.+.+..++.... .. .++++.+ ...+|+.+++.
T Consensus 204 ~~~~~~v~~~~~a~~~gD~~~l~~Lla~Dv~~~~p~~~~~~~G~~~v~~~~~~~~~~~~~~~~~~~~--~~~~g~~~~v~ 281 (324)
T TIGR02960 204 PEEQDLLERYIAAFESYDLDALTALLHEDAIWEMPPYTLWYQGRPAIVGFIHTVCPGEGAAGMRLLP--TIANGQPAAAM 281 (324)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHHhcCCeEEEcCCCCcceeCHHHHHHHHHHhcccccCCceeEEE--eeecCCceEEE
Confidence 568899999999999999999999999999999873 22 3567777777762 22 3455544 45888887776
Q ss_pred eecCC-----CceEEEEEEEEecCCeEEEEEEeeChHHHHHHcC
Q 031351 88 GWEGA-----PAYWVHVWTVNVKDGLITQFREYFNTWLTVKDLR 126 (161)
Q Consensus 88 G~~~~-----~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg 126 (161)
..... ...+|++|+| +||||++++.|+|++.+++++|
T Consensus 282 ~~~~~~~~~~~~~~v~~~~~--~dGkI~~~~~~~~~~~~~~~~~ 323 (324)
T TIGR02960 282 YMRRPDAERHTAFQLHVLEI--RGGRITHVTAFLDGPSLFAAFG 323 (324)
T ss_pred EEEcCCCCeeeeeEEEEEEE--cCCcEEEEEEEcCCHHHHhhcC
Confidence 43221 2677999999 9999999999999999999987
No 7
>PF07366 SnoaL: SnoaL-like polyketide cyclase; InterPro: IPR009959 This domain is found in SnoaL [] a polyketide cyclase involved in nogalamycin biosynthesis. This domain was formerly known as DUF1486. It adopts a distorted alpha-beta barrel fold []. Structural data together with site-directed mutagenesis experiments have shown that SnoaL has a different mechanism to that of the classical aldolase for catalysing intramolecular aldol condensation [].; PDB: 2GEY_C 3F9S_A 2GEX_A 3EHC_B 2F99_D 2F98_D 1SJW_A 3K0Z_B.
Probab=99.51 E-value=3.2e-13 Score=97.35 Aligned_cols=104 Identities=20% Similarity=0.355 Sum_probs=82.1
Q ss_pred HHHHHH-HHHhCCCHHHHHhhccCCeEEEecCCc---cHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEE----eec
Q 031351 20 IVKALY-KALANDEMENVAKYLASDLEYWFHGPP---TCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAE----GWE 90 (161)
Q Consensus 20 lV~~f~-~A~~~gD~e~l~~lla~Dvv~~~~Gp~---~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~----G~~ 90 (161)
+|.++| ++|+++|++.+.++++||++++.+++. +.+++..++...... +++++++.+++++||.|+++ |++
T Consensus 2 ~v~~~~~~~~n~~d~~~~~~~~~~d~~~~~~~~~~~~G~~~~~~~~~~~~~afPD~~~~i~~~~~~gd~v~~~~~~~Gth 81 (126)
T PF07366_consen 2 IVRRFYEEVWNRGDLDALDELVAPDVVFHDPGPGPPVGREGFKEFLKELRAAFPDLRFEIEDVVAEGDRVAVRWTFTGTH 81 (126)
T ss_dssp HHHHHHHHHHHTT-GCHHHGTEEEEEEEEGCTTTEEEHHHHHHHHHHHHHHHSTTTEEEEEEEEEETTEEEEEEEEEEEE
T ss_pred HHHHHHHHHHhCCCHHHHHHhcCCCEEEEecCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEEECCEEEEEEEEEEee
Confidence 455555 567999999999999999999977532 356666666555444 68899999999999999887 555
Q ss_pred CC------------CceEEEEEEEEecCCeEEEEEEeeChHHHHHHc
Q 031351 91 GA------------PAYWVHVWTVNVKDGLITQFREYFNTWLTVKDL 125 (161)
Q Consensus 91 ~~------------~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~al 125 (161)
.+ ....+.+|+| +||||++.+.|+|...+++||
T Consensus 82 ~g~~~g~~ptgk~v~~~~~~~~~~--~~gkI~e~~~~~D~~~~~~QL 126 (126)
T PF07366_consen 82 TGEFMGIPPTGKPVEFRGMSIFRF--EDGKIVEEWVYFDELSLLRQL 126 (126)
T ss_dssp SSEBTTBE-TTEEEEEEEEEEEEE--ETTEEEEEEEEECHHHHHHHT
T ss_pred cCCcCCcCCCCCEEEEEEEEEEEE--ECCEEEEEEEEECHHHHHhhC
Confidence 22 1555899999 999999999999999999886
No 8
>cd00781 ketosteroid_isomerase ketosteroid isomerase: Many biological reactions proceed by enzymatic cleavage of a C-H bond adjacent to carbonyl or a carboxyl group, leading to an enol or a enolate intermediate that is subsequently re-protonated at the same or an adjacent carbon. Ketosteroid isomerases are important members of this class of enzymes which are the most proficient of all enzymes known and have served as a paradigm for enzymatic enolizations since its discovery in 1954. This CD includes members of this class that calalyze the isomerization of various beta,gamma-unsaturated isomers at nearly a diffusion-controlled rate. These enzymes are widely distributed in bacteria.
Probab=99.47 E-value=3.2e-13 Score=96.46 Aligned_cols=106 Identities=15% Similarity=0.114 Sum_probs=79.3
Q ss_pred cccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC-Cc---cHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEe
Q 031351 14 EQNQEAIVKALYKALANDEMENVAKYLASDLEYWFHG-PP---TCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEG 88 (161)
Q Consensus 14 ~~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G-p~---~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G 88 (161)
.+++++++++|++|++++|.+.+.+||+||++|+.|. +. +.+++.+++...... ..+++........|+.+++..
T Consensus 2 ~~~~~~~v~~~~~a~~~~D~~~~~~l~aed~~~~~p~~~~~~~G~~~i~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ 81 (122)
T cd00781 2 PQEMKAAVQRYVEAVNAGDPEGIVALFADDATVEDPVGSPPRSGRAAIAAFYAQSLGGAKRLELTGPVRASHGGEAAFAF 81 (122)
T ss_pred cHHHHHHHHHHHHHHHCCCHHHHHHHcCCCeEEeCCCCCCCccCHHHHHHHHHHHhccCceEEecCceeeecCCEEEEEE
Confidence 3578999999999999999999999999999998763 22 356777777665442 345555555566778766552
Q ss_pred ----ecCC-C--ceEEEEEEEEec-CCeEEEEEEeeChHHH
Q 031351 89 ----WEGA-P--AYWVHVWTVNVK-DGLITQFREYFNTWLT 121 (161)
Q Consensus 89 ----~~~~-~--~~~v~vf~v~~~-DGkI~~~~ey~D~~~l 121 (161)
...+ + ..++++|+| + ||||+++++|||...+
T Consensus 82 ~~~~~~~g~~~~~~~~~v~~~--~~dGkI~~~~~y~d~~~~ 120 (122)
T cd00781 82 RVEFEWEGQPCVVRVIDVMRF--DADGRIVSMRAYWGPVNL 120 (122)
T ss_pred EEEEEeCCceEEEEEEEEEEE--CCCccChHHHHhcCcccc
Confidence 2222 2 556899999 7 7999999999998754
No 9
>PF12680 SnoaL_2: SnoaL-like domain; PDB: 3F40_A 3RGA_A 3G8Z_A 3DMC_A 3FH1_A 1TUH_A 3F14_A 3ER7_A 1Z1S_A 3F7X_A ....
Probab=99.44 E-value=2e-12 Score=87.72 Aligned_cols=90 Identities=18% Similarity=0.248 Sum_probs=74.0
Q ss_pred HHHHHHHHhCCCHHHHHhhccCCeEEEecCCc--cHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEeecC------
Q 031351 21 VKALYKALANDEMENVAKYLASDLEYWFHGPP--TCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGWEG------ 91 (161)
Q Consensus 21 V~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~--~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~~~------ 91 (161)
|++||+|++++|.+.+.++++||++|+.|+++ +.+++..++...... .+.++++..+..+|+.|++.+...
T Consensus 1 V~~~~~a~~~~d~~~i~~~~~~d~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~gd~v~~~~~~~~~~~~~ 80 (102)
T PF12680_consen 1 VRRFFEAWNAGDLDAIAALFAPDAVFHDPGGTLRGREAIREFFEEFFESFPDIRFEIHDIFADGDRVVVEWTVTGTTPPT 80 (102)
T ss_dssp HHHHHHHHHTTHHHHHHHTEEEEEEEEETTSEEESHHHHHHHHHHHHHHEEEEEEEEEEEEEETTEEEEEEEEEEEETTT
T ss_pred CHHHHHHHHcCCHHHHHHHcCCCEEEEeCCCcccCHHHHHHHHHHHHhcCCceEEEEEEEEEcCCEEEEEEEEEEEEcCC
Confidence 78999999999999999999999999988533 467777777665543 678999999999999998885441
Q ss_pred CC---ceEEEEEEEEecCCeEEEE
Q 031351 92 AP---AYWVHVWTVNVKDGLITQF 112 (161)
Q Consensus 92 ~~---~~~v~vf~v~~~DGkI~~~ 112 (161)
++ ...+.+|++ +||||++.
T Consensus 81 g~~~~~~~~~~~~~--~dgkI~~~ 102 (102)
T PF12680_consen 81 GQPISFRGCSVFRF--EDGKIVEH 102 (102)
T ss_dssp SCEEEEEEEEEEEE--ETTEEEEE
T ss_pred CCEEEEEEEEEEEE--ECCEEEEC
Confidence 11 667999999 99999984
No 10
>COG4308 LimA Limonene-1,2-epoxide hydrolase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=99.37 E-value=4.1e-12 Score=91.11 Aligned_cols=110 Identities=22% Similarity=0.294 Sum_probs=86.6
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHH-hhccCCeEEEecCCc---cHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEee
Q 031351 15 QNQEAIVKALYKALANDEMENVA-KYLASDLEYWFHGPP---TCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGW 89 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~-~lla~Dvv~~~~Gp~---~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~ 89 (161)
.+++++|++|++|+..-|.++.. .++.+|-+|.++|-+ +.++.+.++...+.. ..+.+.++.+.++|..|..+-.
T Consensus 6 ~~pi~~V~aF~aA~~~~d~~~avr~~~~~d~v~~n~gis~i~G~~~~ia~l~~~~~~~~~~ef~I~riAadg~~VltER~ 85 (130)
T COG4308 6 PEPIRTVEAFLAALQEDDGDAAVRRLGTPDTVYNNVGISTIHGPAETIALLRPRMAGILGFEFKILRIAADGGAVLTERL 85 (130)
T ss_pred CCcHHHHHHHHHHHHhcCccHHHHHhcCCCeeeccCCcccccchhhhhhhhccccCCcceeEEEEEEEecccceehhhhh
Confidence 47999999999999888887655 577799999888843 246666777753332 6789999999999999987732
Q ss_pred cC-------CCceEEEEEEEEecCCeEEEEEEeeChHHHHHHcC
Q 031351 90 EG-------APAYWVHVWTVNVKDGLITQFREYFNTWLTVKDLR 126 (161)
Q Consensus 90 ~~-------~~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg 126 (161)
.. .....|.+|++ +||||+.||+|||-..++++.-
T Consensus 86 D~~~~g~~~~~~~V~GvfEV--~~~rI~~WRDYFDv~~l~k~~~ 127 (130)
T COG4308 86 DARIDGPLWVQFWVCGVFEV--EDGRIVLWRDYFDVNDLFKQTP 127 (130)
T ss_pred hhhccCCcEEEEEEEEEEEE--eCCEEEeehhhhhHHHHHhhcc
Confidence 21 13777999999 9999999999999998887753
No 11
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=99.19 E-value=5.1e-10 Score=92.06 Aligned_cols=107 Identities=19% Similarity=0.205 Sum_probs=79.0
Q ss_pred ccccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC----Cc------cHHHHHHHHhccccc--ceeEEEeeEEEEe
Q 031351 13 AEQNQEAIVKALYKALANDEMENVAKYLASDLEYWFHG----PP------TCQHMVRLLTGESSK--ATFKFEPRSVEVV 80 (161)
Q Consensus 13 s~~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G----p~------~~~~v~~~l~~~~~~--~~~~~~~~~vi~~ 80 (161)
..+.+.++|++|++|+++||++++.+||+||++|+.+| |+ +.+.+..++...... .........+..+
T Consensus 169 ~~~~~~~~v~~f~~A~~~gD~~~l~~Lla~Dv~~~~dggg~~~~~~~~~~G~~~v~~~l~~~~~~~~~~~~~~~~~~~vn 248 (293)
T PRK09636 169 SDEEGAELVEAFFAALASGDLDALVALLAPDVVLHADGGGKVPTALRPIYGADKVARFFLGLARRYGPGGSTLVRLALVN 248 (293)
T ss_pred CchHHHHHHHHHHHHHHhCCHHHHHHHHhhCeEEEecCCCccCCCCccccCHHHHHHHHHHHhhhccCCCceEEEEEEEC
Confidence 34568899999999999999999999999999999875 22 235677777665432 1112233345677
Q ss_pred CCEEEEEeecCCCceEEEEEEEEecCCeEEEEEEeeChHHHH
Q 031351 81 GDCVIAEGWEGAPAYWVHVWTVNVKDGLITQFREYFNTWLTV 122 (161)
Q Consensus 81 Gd~Vvv~G~~~~~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~ 122 (161)
|+..++.... +....+..|++ +||||++++.+.||.++.
T Consensus 249 G~~a~~~~~~-~~~~~~~~~~~--~~g~I~~i~~~~~p~kl~ 287 (293)
T PRK09636 249 GLPGFVTAEA-DGEPQTTALEV--EDGKIVAIYDVRNPDKLT 287 (293)
T ss_pred CceeEEEEeC-CceEEEEEEEE--ECCEEEEEEEEcCHHHhc
Confidence 7766665433 33455889999 999999999999999874
No 12
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=98.92 E-value=2.1e-08 Score=82.14 Aligned_cols=105 Identities=13% Similarity=0.229 Sum_probs=75.0
Q ss_pred ccccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC----Cc------cHHHHHHHHhccccc--ceeEEEeeEEEEe
Q 031351 13 AEQNQEAIVKALYKALANDEMENVAKYLASDLEYWFHG----PP------TCQHMVRLLTGESSK--ATFKFEPRSVEVV 80 (161)
Q Consensus 13 s~~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G----p~------~~~~v~~~l~~~~~~--~~~~~~~~~vi~~ 80 (161)
..+++.+++++|.+|+.+||++++.+||+||++++.+| |+ +.+.+..++...... ..+++.+. ..+
T Consensus 162 ~~~~~~~~~~~f~~a~~~gD~~~l~~lL~~dv~~~~dggg~~~~~~~p~~G~~~v~~~~~~~~~~~~~~~~~~~~--~vn 239 (281)
T TIGR02957 162 SREESRQLLERFVEAAQTGDLDGLLELLAEDVVLYGDGGGKVRAALRPIYGADRVARFFFGLVRRLGPGGRVDPV--DVN 239 (281)
T ss_pred ChHHHHHHHHHHHHHHHhCCHHHHHHHHhhceEEEecCCCcCCCCCcccccHHHHHHHHHHHhcccCCCceEEEE--EEC
Confidence 34567899999999999999999999999999999874 22 235667776554432 23344444 345
Q ss_pred CCEEEEEeecCCCceEEEEEEEEecCCeEEEEEEeeChHHHH
Q 031351 81 GDCVIAEGWEGAPAYWVHVWTVNVKDGLITQFREYFNTWLTV 122 (161)
Q Consensus 81 Gd~Vvv~G~~~~~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~ 122 (161)
|...++.-. .+....+..|++ .||+|++++.+.||.++.
T Consensus 240 G~p~~~~~~-~~~~~~~~~~~~--~~g~I~~i~~~~nP~kl~ 278 (281)
T TIGR02957 240 GQPAVLVRI-DGKLAYVVTFAI--EGGGIQNIYIVRNPEKLA 278 (281)
T ss_pred CCceEEEEe-CCcEEEEEEEEE--ECCEEEEEEEEcCHHHhc
Confidence 554433322 233445788899 999999999999999863
No 13
>COG4922 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.76 E-value=4.9e-08 Score=69.79 Aligned_cols=100 Identities=17% Similarity=0.216 Sum_probs=80.0
Q ss_pred ccHHHHHHHHHHH-HhCCCHHHHHhhccCCeEEEecC-CccHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEeecC
Q 031351 15 QNQEAIVKALYKA-LANDEMENVAKYLASDLEYWFHG-PPTCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGWEG 91 (161)
Q Consensus 15 ~~~~~lV~~f~~A-~~~gD~e~l~~lla~Dvv~~~~G-p~~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~~~ 91 (161)
..|+++|-.||.. |++|.++...+++.|-+.-++|+ |.+.+++.+||.+.+.. +.....+...+++||.|.+.-+.+
T Consensus 5 ~~N~~~v~~~y~~~~~~g~veka~a~~vd~YiQHnp~vpdGk~~fv~fFt~ffk~~P~~~~kiVr~iadGdLV~vh~hqt 84 (129)
T COG4922 5 HANKQVVIQFYRTLFEAGEVEKADAYLVDRYIQHNPMVPDGKDGFVRFFTEFFKEKPRISTKIVRVIADGDLVTVHYHQT 84 (129)
T ss_pred hhhHHHHHHHHHHHHHCCCHHHhhhhhhhHHHhcCCCCCCchHHHHHHHHHHHHhCccccceeeEEeccCCEEEEEEeee
Confidence 3588999999985 79999999999999878877777 56788888988887765 566778889999999998874332
Q ss_pred C------CceEEEEEEEEecCCeEEEEEEee
Q 031351 92 A------PAYWVHVWTVNVKDGLITQFREYF 116 (161)
Q Consensus 92 ~------~~~~v~vf~v~~~DGkI~~~~ey~ 116 (161)
. ..-++++|++ .||||++-++-.
T Consensus 85 ~~~pg~~~~v~~DtfR~--ddgkivEHWDvi 113 (129)
T COG4922 85 VSEPGSYTTVTFDTFRI--DDGKIVEHWDVI 113 (129)
T ss_pred eCCCCcceeEEEEEEEe--eCCceeeccchh
Confidence 1 2455799999 999999877643
No 14
>COG5485 Predicted ester cyclase [General function prediction only]
Probab=98.75 E-value=8.9e-08 Score=69.22 Aligned_cols=105 Identities=12% Similarity=0.135 Sum_probs=79.4
Q ss_pred HHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCccHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEeecC------
Q 031351 19 AIVKALYKALANDEMENVAKYLASDLEYWFHGPPTCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGWEG------ 91 (161)
Q Consensus 19 ~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~~~------ 91 (161)
+..++|++..+..+++.+....... +.+...+.+..+..+.+...+++ +++.++++.++++|+.|++.+...
T Consensus 10 ~~y~Ay~d~ln~q~~~~l~~fv~~~-v~~ng~~~glsgyr~ml~~df~aiPdl~f~ie~lvae~~~vaarl~Fdctp~G~ 88 (131)
T COG5485 10 DRYRAYLDCLNRQAWDELGSFVDGN-VMHNGRLQGLSGYREMLVRDFSAIPDLSFEIERLVAEGDRVAARLTFDCTPSGE 88 (131)
T ss_pred HHHHHHHHhhhhhhhhhcccCCcCe-eeeCCceechHHHHHHHHhhHhhCCCcceEEEEEeecCCceEEEEEEccCcCce
Confidence 6788888888888888875554444 33333355566666666666665 789999999999999999885442
Q ss_pred -------C-CceE--EEEEEEEecCCeEEEEEEeeChHHHHHHcC
Q 031351 92 -------A-PAYW--VHVWTVNVKDGLITQFREYFNTWLTVKDLR 126 (161)
Q Consensus 92 -------~-~~~~--v~vf~v~~~DGkI~~~~ey~D~~~l~~alg 126 (161)
+ ...| .++++| .||||++.|.-+|..++.+|++
T Consensus 89 i~Gip~nGkrV~Fse~vfy~f--~~~KI~~vwsv~Dk~ai~rQL~ 131 (131)
T COG5485 89 IMGIPPNGKRVRFSENVFYEF--ENGKIVEVWSVIDKMAIERQLG 131 (131)
T ss_pred EeccCCCCcEEEeehhhhhhh--cCCeEEeeehhccHHHHHHhhC
Confidence 1 1333 489999 9999999999999999999986
No 15
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=98.66 E-value=2.6e-07 Score=76.33 Aligned_cols=103 Identities=11% Similarity=0.094 Sum_probs=71.6
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCc-----cHHHHHHHHhcccccceeEEEeeEEEEeCCEEEEEee
Q 031351 15 QNQEAIVKALYKALANDEMENVAKYLASDLEYWFHGPP-----TCQHMVRLLTGESSKATFKFEPRSVEVVGDCVIAEGW 89 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~-----~~~~v~~~l~~~~~~~~~~~~~~~vi~~Gd~Vvv~G~ 89 (161)
.+..+++++|.+|+.+||++++.+||+||+..-.+.+. +.+.+.+++........+++.+.. .+|...++.-.
T Consensus 174 ~~~~~~~~~f~~a~~~gd~~~l~~ll~~d~~~~~~~~~~~~~~G~~~v~~~~~~~~~~~~~~~~~~~--~ng~p~~~~~~ 251 (290)
T PRK09635 174 AQHRVVTRAFIEACSNGDLDTLLEVLDPGVAGEIDARKGVVVVGADRVGPTILRHWSHPATVLVAQP--VCGQPAVLAFV 251 (290)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHhhhhhcCCCcCCCCccccCHHHHHHHHHHhhccCceEEEEee--eCCCceEEEEe
Confidence 45789999999999999999999999999964222111 245677777655432344554443 44544333211
Q ss_pred cCCCceEEEEEEEEecCCeEEEEEEeeChHHHH
Q 031351 90 EGAPAYWVHVWTVNVKDGLITQFREYFNTWLTV 122 (161)
Q Consensus 90 ~~~~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~ 122 (161)
.+....+.+|++ .||||+.++.+.||.++.
T Consensus 252 -~~~~~~~~~~~~--~~~~I~~i~~~~np~kl~ 281 (290)
T PRK09635 252 -NRALAGVLALSI--EAGKITKIHVLVQPSTLD 281 (290)
T ss_pred -CCceEEEEEEEE--ECCEEEEEEEEcCHHHhh
Confidence 223455889999 999999999999999763
No 16
>COG4538 Uncharacterized conserved protein [Function unknown]
Probab=98.44 E-value=6.4e-06 Score=57.41 Aligned_cols=97 Identities=16% Similarity=0.158 Sum_probs=65.9
Q ss_pred cHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEe-cC---CccHHHHHHHHhcccccceeEEEeeEEEEeCCEEEEE----
Q 031351 16 NQEAIVKALYKALANDEMENVAKYLASDLEYWF-HG---PPTCQHMVRLLTGESSKATFKFEPRSVEVVGDCVIAE---- 87 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~-~G---p~~~~~v~~~l~~~~~~~~~~~~~~~vi~~Gd~Vvv~---- 87 (161)
+...+|++=++|.++||+++....|++|+++.- ++ ....+++..+....|..+....+...-+.-|+.|+=+
T Consensus 4 e~ed~vq~Ql~AYNa~Dvdaf~a~f~DD~vv~~f~a~~~~gg~aaira~y~e~FaEp~~~~~ll~Rv~vGs~ViDHEhvt 83 (112)
T COG4538 4 EPEDVVQRQLAAYNAGDVDAFAAEFDDDAVVTTFDALDGDGGTAAIRAAYGEQFAEPAPEISLLDRVSVGSYVIDHEHVT 83 (112)
T ss_pred chhHHHHHHHHhhccccHHHHHhhcccceEEEecccccccCcHHHHHHHHHHHhcCCCccceeeeeEEeccEEecceeec
Confidence 467889999999999999999999999998763 33 2234555544444333233344444445556655422
Q ss_pred -eecCCCceEEEEEEEEecCCeEEEEEE
Q 031351 88 -GWEGAPAYWVHVWTVNVKDGLITQFRE 114 (161)
Q Consensus 88 -G~~~~~~~~v~vf~v~~~DGkI~~~~e 114 (161)
|.-++......+|+| .+|||.+.+-
T Consensus 84 r~~g~ge~dvaciYtv--~~g~Iar~wf 109 (112)
T COG4538 84 RGTGGGERDVACIYTV--VEGLIARLWF 109 (112)
T ss_pred cCCCCCceeEEEEEEE--eCCeeeeeee
Confidence 333344666899999 9999999874
No 17
>PF14534 DUF4440: Domain of unknown function (DUF4440); PDB: 3HX8_A 3SOY_A 3ROB_B 3GZR_A 3B7C_A 3CU3_A 3FSD_A 2R4I_C 1TP6_A.
Probab=98.19 E-value=2.9e-05 Score=52.81 Aligned_cols=73 Identities=19% Similarity=0.303 Sum_probs=54.9
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCC-c-cHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEeec
Q 031351 18 EAIVKALYKALANDEMENVAKYLASDLEYWFHGP-P-TCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGWE 90 (161)
Q Consensus 18 ~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp-~-~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~~ 90 (161)
.++.++|++|++++|.+++.++++||+++..++. . +.+++...+...+.. ..++++...+...||.+++.|..
T Consensus 2 ~a~~~~~~~A~~~~D~~~~~~~~~~d~~~~~~~g~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~gd~a~~~~~~ 77 (107)
T PF14534_consen 2 RALEEQYEDAFNAGDIDALASLYADDFVFVGPGGTILGKEAILAAFKSGFARFSSIKFEDVEVRVLGDTAVVRGRW 77 (107)
T ss_dssp HHHHHHHHHHHHTTHHHHHHTTEEEEEEEEETTSEEEEHHHHHHHHHHHCEEEEEEEEEEEEEEEETTEEEEEEEE
T ss_pred HHHHHHHHHHHHhCCHHHHHhhhCCCEEEECCCCCEeCHHHHHHHHhhccCCCceEEEEEEEEEEECCEEEEEEEE
Confidence 4788999999999999999999999999987752 2 456666555542222 56677777777789988777543
No 18
>PF03284 PHZA_PHZB: Phenazine biosynthesis protein A/B; InterPro: IPR004964 The phenazine biosynthesis proteins A and B are involved in the biosynthesis of this antibiotic. Phenazine is a nitrogen-containing heterocyclic molecule with important implications in virulence, competition and biological control.; GO: 0017000 antibiotic biosynthetic process; PDB: 3EX9_A 3JUP_B 3DZL_A 3JUN_A 3JUO_A 3CNM_A 3JUM_B 3JUQ_A 3B4O_A 3B4P_B ....
Probab=98.00 E-value=5.3e-05 Score=56.50 Aligned_cols=113 Identities=15% Similarity=0.165 Sum_probs=66.0
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEe---c-C-Cc---cHHHH---HHHHhcccccceeEEEeeEEEEe--C
Q 031351 15 QNQEAIVKALYKALANDEMENVAKYLASDLEYWF---H-G-PP---TCQHM---VRLLTGESSKATFKFEPRSVEVV--G 81 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~---~-G-p~---~~~~v---~~~l~~~~~~~~~~~~~~~vi~~--G 81 (161)
+.|++.|..|-.. ...|-=.--.||++|-.--. . | |. +.+.+ ..+...-+ +++.+--..++.. +
T Consensus 18 ~~NR~~Ve~Ym~t-~g~~RL~Rh~LF~eDG~~glwtTdtG~Piv~~G~~~L~~havwslkcF--PDWeW~nv~ifeT~DP 94 (162)
T PF03284_consen 18 RINRATVEQYMNT-KGQDRLRRHELFTEDGCGGLWTTDTGEPIVIRGRDRLAEHAVWSLKCF--PDWEWYNVRIFETQDP 94 (162)
T ss_dssp HHHHHHHHHHHC---GGGGGGGGGGEEEEEEEEESS-TTSS-EEEESHHHHHHHHHHHHHHS--TT-EEEEEEEEEBSST
T ss_pred HhhHHHHHHHHHc-CchhhhhhheeeccCCccccccCCCCceEEEEhHHHHHHHHHHHHHHC--CCcEEEEEEeecccCC
Confidence 4577888887652 22222223479999964432 2 3 22 23333 33444444 4777776677664 5
Q ss_pred CEEEEE----eecC--C------CceEEEEEEEEecCCeEEEEEEeeChHHHHHHcCCCcccc
Q 031351 82 DCVIAE----GWEG--A------PAYWVHVWTVNVKDGLITQFREYFNTWLTVKDLRPPRWEI 132 (161)
Q Consensus 82 d~Vvv~----G~~~--~------~~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg~~~~~~ 132 (161)
+.+.|+ |... + .-.++|.|++ +||||++.++|+|+..-++|+|=+.-+|
T Consensus 95 ~~fwVEcdG~G~i~fpGypeg~y~NHfiHsFel--~nGkI~~~REFmNp~qq~RaLgi~vP~I 155 (162)
T PF03284_consen 95 NHFWVECDGRGKILFPGYPEGYYENHFIHSFEL--ENGKIKRNREFMNPFQQLRALGIPVPEI 155 (162)
T ss_dssp TEEEEEEEEEEEE--TTS--EEEEEEEEEEEEE--ETTEEEEEEEEE-HHHHHHHTT------
T ss_pred CEEEEEecCccceecCCCCcccceeeeEEEEEe--eCCEEEeehhhcCHHHHHHHcCCCCCcc
Confidence 677777 2220 1 1444999999 9999999999999999999999666444
No 19
>TIGR02246 conserved hypothetical protein. This family consists of uncharacterized proteins found in a number of genera and species, including Streptomyces, Xanthomonas, Oceanobacillus iheyensis, Caulobacter crescentus CB15, and Xylella fastidiosa. The function is unknown.
Probab=97.98 E-value=4.8e-05 Score=53.87 Aligned_cols=74 Identities=16% Similarity=0.168 Sum_probs=51.2
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEE-ecCCc--cHHHHHHHHhccccc----ceeEEEeeEEEEeC-CEEEE
Q 031351 15 QNQEAIVKALYKALANDEMENVAKYLASDLEYW-FHGPP--TCQHMVRLLTGESSK----ATFKFEPRSVEVVG-DCVIA 86 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~-~~Gp~--~~~~v~~~l~~~~~~----~~~~~~~~~vi~~G-d~Vvv 86 (161)
++.++++.+|++|++++|.+.+.+++++|++|. .+|.. +.+++.+++...... ..+++++..+...| +.+++
T Consensus 4 ~~i~~l~~~~~~a~~~~D~~~~~~~~~~Da~~~~~~g~~~~G~~~i~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~A~~ 83 (128)
T TIGR02246 4 RAIRALVATWEAAWAAGDAEGFADLFTPDGVFVTVPGQVWKGREAIAAAHEAFLAGPYKGTRVTIDVIEVRFLGPDLAIV 83 (128)
T ss_pred HHHHHHHHHHHHHHHcCCHHHHHHhhCCCceEECCCCCeecCHHHHHHHHHHHhcccCCCcEEEeeeEEEEecCCCEEEE
Confidence 456799999999999999999999999999997 44532 356666666543322 12566655555555 45555
Q ss_pred Ee
Q 031351 87 EG 88 (161)
Q Consensus 87 ~G 88 (161)
.+
T Consensus 84 ~~ 85 (128)
T TIGR02246 84 HA 85 (128)
T ss_pred EE
Confidence 43
No 20
>PF13474 SnoaL_3: SnoaL-like domain; PDB: 2GXF_A 3KSP_A 3KE7_A 3BB9_E 3CNX_A 3F7S_A 3GWR_B.
Probab=97.72 E-value=0.0004 Score=48.42 Aligned_cols=71 Identities=17% Similarity=0.364 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCc----cHHHHHHHHhccccc-ceeEEE--eeEEEEeCCEEEEEe
Q 031351 18 EAIVKALYKALANDEMENVAKYLASDLEYWFHGPP----TCQHMVRLLTGESSK-ATFKFE--PRSVEVVGDCVIAEG 88 (161)
Q Consensus 18 ~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~----~~~~v~~~l~~~~~~-~~~~~~--~~~vi~~Gd~Vvv~G 88 (161)
.+++++|++|++++|++.+.++++||+++..+++. +.+++..++...+.. ..+.++ ...+...++.+++.+
T Consensus 2 ~~~~~~~~~a~~~~D~~~~~~~~~~d~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~a~~~~ 79 (121)
T PF13474_consen 2 EALLEEWIEAFERGDIDALLSLFSDDFVFFGTGPGEIWRGREAIRAYFERDFESFRPISIEFEDVQVSVSGDVAVVTG 79 (121)
T ss_dssp HHHHHHHHHHHHCT-HHHHHHHEEEEEEEEETTSSSEEESHHHHHHHHHHHHHTHSEEEEEEEEEEEEEETTEEEEEE
T ss_pred HHHHHHHHHHHHhCCHHHHHHhhCCCEEEEcCCCCceECCHHHHHHHHHHHhhhCceEEEEEEEEEEEECCCEEEEEE
Confidence 46899999999999999999999999999876653 356666666543332 334443 445556788777664
No 21
>cd00531 NTF2_like Nuclear transport factor 2 (NTF2-like) superfamily. This family includes members of the NTF2 family, Delta-5-3-ketosteroid isomerases, Scytalone Dehydratases, and the beta subunit of Ring hydroxylating dioxygenases. This family is a classic example of divergent evolution wherein the proteins have many common structural details but diverge greatly in their function. For example, nuclear transport factor 2 (NTF2) mediates the nuclear import of RanGDP and binds to both RanGDP and FxFG repeat-containing nucleoporins while Ketosteroid isomerases catalyze the isomerization of delta-5-3-ketosteroid to delta-4-3-ketosteroid, by intramolecular transfer of the C4-beta proton to the C6-beta position. While the function of the beta sub-unit of the Ring hydroxylating dioxygenases is not known, Scytalone Dehydratases catalyzes two reactions in the biosynthetic pathway that produces fungal melanin. Members of the NTF2-like superfamily are widely distributed among bacteria, archaea
Probab=97.40 E-value=0.011 Score=40.11 Aligned_cols=48 Identities=15% Similarity=0.036 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCC----c---cHHHHHHHHhccc
Q 031351 18 EAIVKALYKALANDEMENVAKYLASDLEYWFHGP----P---TCQHMVRLLTGES 65 (161)
Q Consensus 18 ~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp----~---~~~~v~~~l~~~~ 65 (161)
.+++.+|+.+++++|.+.+..+++||+++..+++ . +.+++..++....
T Consensus 2 ~~l~~~y~~~ld~~~~~~l~~~~~~d~~~~~~~~~~~~~~~~g~~~i~~~~~~~~ 56 (124)
T cd00531 2 EQFLYRYARLLDAGDREWLALLYADDAYFEPPGGDGLIYPDDGREAIEDRVRRLP 56 (124)
T ss_pred HHHHHHHHHHhCCchHHHHHhhCcCcEEEEEccCCEEEEcCChHHHHHHHHHhcC
Confidence 4789999999999999999999999999987763 2 2457777776654
No 22
>COG4319 Ketosteroid isomerase homolog [Function unknown]
Probab=97.27 E-value=0.0018 Score=48.05 Aligned_cols=72 Identities=17% Similarity=0.219 Sum_probs=49.4
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhccCCeEEEec-CCc--cHHHHHHHHhccccc--ceeEEE--eeEEEEeCCEEEEEe
Q 031351 17 QEAIVKALYKALANDEMENVAKYLASDLEYWFH-GPP--TCQHMVRLLTGESSK--ATFKFE--PRSVEVVGDCVIAEG 88 (161)
Q Consensus 17 ~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~-Gp~--~~~~v~~~l~~~~~~--~~~~~~--~~~vi~~Gd~Vvv~G 88 (161)
-++++..+-+|++++|+++++++++||+++-.+ |+. +.+++.+.|...+.. .+.+++ -..+.+.||.+.+.+
T Consensus 12 I~a~i~dw~~Av~a~D~~av~~~YtdDav~f~~~~~~~~Gk~~i~k~~~~~~~~~~~~~~f~~~el~v~~~GD~a~~~~ 90 (137)
T COG4319 12 IRAAIADWAAAVRAKDADAVADFYTDDAVVFPPPGLQRKGKAAIRKAFEGIFAMGIGPLKFTLEELQVHESGDVAFVTA 90 (137)
T ss_pred HHHHHHHHHHHHhcccHHHHHHhcCCceEEecCCCCcccCHHHHHHHHHHHHHhccCCCcceeeeeeeeccCCEEEEEE
Confidence 457778888899999999999999999998655 433 244444444443332 333444 455558999887764
No 23
>PF12893 Lumazine_bd_2: Putative lumazine-binding; PDB: 3BLZ_C 3DUK_F 3FKA_C.
Probab=97.17 E-value=0.0063 Score=43.13 Aligned_cols=93 Identities=17% Similarity=0.145 Sum_probs=61.2
Q ss_pred cHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC--Cc---cHHHHHHHHhccc---cc-ceeEEEeeEEEEeCCEEEE
Q 031351 16 NQEAIVKALYKALANDEMENVAKYLASDLEYWFHG--PP---TCQHMVRLLTGES---SK-ATFKFEPRSVEVVGDCVIA 86 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G--p~---~~~~v~~~l~~~~---~~-~~~~~~~~~vi~~Gd~Vvv 86 (161)
+-+++|..|++++..||.+.+.++|+||+...... +. ..+++...+.... .. ......+..+-.+|+...|
T Consensus 5 ~I~~~v~~Y~dg~~~gD~~~l~~~f~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~i~~i~i~g~~A~a 84 (116)
T PF12893_consen 5 AIEATVQDYFDGLYNGDSEKLRSAFHPDARLQGVRKGKLRTMPIEEFIARVKSRVSPKPPGQERKESILSIDIDGDVASA 84 (116)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHGGGEEEEEEEEEEETTEEEEEETHHHHHHHHHC---H-SSTT-EEEEEEEEEETTEEEE
T ss_pred HHHHHHHHHHHHHHhcCHHHHHHhhCCCcEEEEEcCCceEEeCHHHHHHHHHhhccccCCCCCceeEEEEEEEECCEEEE
Confidence 35689999999999999999999999999776553 22 2466666665431 11 4556777777778887665
Q ss_pred EeecC-CCceEEEEEEEEecCCe
Q 031351 87 EGWEG-APAYWVHVWTVNVKDGL 108 (161)
Q Consensus 87 ~G~~~-~~~~~v~vf~v~~~DGk 108 (161)
.-... .+..+++.|.+-+.||+
T Consensus 85 ~v~~~~~~~~~~d~~~L~K~dg~ 107 (116)
T PF12893_consen 85 KVEYEFPGFWFVDYFTLVKTDGG 107 (116)
T ss_dssp EEEEEEETEEEEEEEEEEEETTE
T ss_pred EEEEEECCCceEEEEEEEEECCE
Confidence 53221 13455777777545664
No 24
>PF07080 DUF1348: Protein of unknown function (DUF1348); InterPro: IPR009783 This family consists of several highly conserved hypothetical proteins of around 150 residues in length. The function of this family is unknown.; PDB: 2IMJ_B.
Probab=96.27 E-value=0.083 Score=39.12 Aligned_cols=106 Identities=15% Similarity=0.161 Sum_probs=75.4
Q ss_pred ccccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC--CccHHHHHHHHhccccc-ceeEEEeeEEEEeCCEEEEEee
Q 031351 13 AEQNQEAIVKALYKALANDEMENVAKYLASDLEYWFHG--PPTCQHMVRLLTGESSK-ATFKFEPRSVEVVGDCVIAEGW 89 (161)
Q Consensus 13 s~~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G--p~~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd~Vvv~G~ 89 (161)
+.+...+-|+..=+|+++.|.+.+.--+++|.+|++-. ..+.+++..||..-... .+++..-+-..-.|++++|.-.
T Consensus 8 t~etA~~KVr~AEdaWNsrdP~~ValaYT~Ds~WRNR~eF~~GR~~I~~FLtrKW~rE~~YrLiKELwaf~~nRIAVRF~ 87 (143)
T PF07080_consen 8 TRETAIQKVRAAEDAWNSRDPEKVALAYTPDSVWRNRDEFLTGREEIVAFLTRKWERELDYRLIKELWAFTDNRIAVRFA 87 (143)
T ss_dssp -HHHHHHHHHHHHHHHTTT-HHHHHTTEEEEEEEEETTEEE-SHHHHHHHHHHHHHHSEEEEEEEEEEEEETTEEEEEEE
T ss_pred CHHHHHHHHHHHHhccccCChhHheeccCCCCcccCcccccCcHHHHHHHHHHHHHHhhhhhhHHhhhhccCCeEEEEEe
Confidence 45667888999999999999999999999999999776 34677888888765543 4556655656667899998743
Q ss_pred cC-----CC---ceEEEEEEEEecCCeEEEEEEeeChH
Q 031351 90 EG-----AP---AYWVHVWTVNVKDGLITQFREYFNTW 119 (161)
Q Consensus 90 ~~-----~~---~~~v~vf~v~~~DGkI~~~~ey~D~~ 119 (161)
+. ++ .|.---|+|+ .+|++.+-..-.+..
T Consensus 88 YE~~d~~gqW~RsyGnEnWeFd-~~GlM~~R~aSiND~ 124 (143)
T PF07080_consen 88 YEWHDDSGQWFRSYGNENWEFD-EDGLMRRRHASINDV 124 (143)
T ss_dssp EEEE-TTS-EEEEEEEEEEEE--TTS-EEEEEEEEEEE
T ss_pred EEEEcCCCCEEecccccccccC-CCccHHHhhcccCCc
Confidence 31 12 6667789997 789988766555443
No 25
>PF13577 SnoaL_4: SnoaL-like domain; PDB: 3S5C_B 3EJV_A 2RFR_A 3B8L_F 2CHC_A 3A76_A 3EF8_B.
Probab=95.19 E-value=0.14 Score=35.66 Aligned_cols=50 Identities=16% Similarity=0.209 Sum_probs=39.1
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCC--c---cHHHHHHHHhcc
Q 031351 15 QNQEAIVKALYKALANDEMENVAKYLASDLEYWFHGP--P---TCQHMVRLLTGE 64 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp--~---~~~~v~~~l~~~ 64 (161)
.+-++++.+|..++..+|++.+.++|++|+++..++. . +.+++..++...
T Consensus 7 ~~I~~l~~~~~~~~D~~~~~~~~~lft~d~~~~~~~~~~~~~~G~~~i~~~~~~~ 61 (127)
T PF13577_consen 7 AAIRDLIARYARALDTGDWEEWADLFTEDAVFDFPGFGFGRYRGRDAIRAFLRAR 61 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-HHHHHTTEEEEEEEEETTTCEEEEESHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCCHHHHHhccCCcEEEEEeCccccccCCHHHHHHHHHHh
Confidence 4567899999999999999999999999999998863 2 356666655544
No 26
>PF08332 CaMKII_AD: Calcium/calmodulin dependent protein kinase II Association; InterPro: IPR013543 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This domain is found at the C terminus of the Calcium/calmodulin dependent protein kinases II (CaMKII). These proteins also have a Ser/Thr protein kinase domain (IPR000719 from INTERPRO) at their N terminus []. The function of the CaMKII association domain is the assembly of the single proteins into large (8 to 14 subunits) multimers [] and is a prominent kinase in the central nervous system that may function in long-term potentiation and neurotransmitter release. ; GO: 0004683 calmodulin-dependent protein kinase activity, 0005516 calmodulin binding, 0006468 protein phosphorylation; PDB: 2W2C_F 3H51_B 3SOA_A 2UX0_A 1HKX_M 2F86_B.
Probab=94.37 E-value=1.5 Score=32.20 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=27.8
Q ss_pred cHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEec
Q 031351 16 NQEAIVKALYKALANDEMENVAKYLASDLEYWFH 49 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~ 49 (161)
+-.++.+++.+|+.+||.+++.++++||+..-.|
T Consensus 4 eI~~l~~~w~~ai~tgD~~~~~~ly~~d~av~~P 37 (128)
T PF08332_consen 4 EIAALFDRWNDAIQTGDPETYAKLYAPDVAVFEP 37 (128)
T ss_dssp HHHHHHHHHHHHHHHT-HHHHHHHEEEEEEEEEG
T ss_pred HHHHHHHHHHHHHHcCCHHHHhhhcCCCeeEecc
Confidence 4567889999999999999999999999554445
No 27
>PF12870 Lumazine_bd: Lumazine-binding domain; InterPro: IPR024267 This entry represents a lumazine-binding domain found in a family of putative lipoproteins from bacteria. Lumazine is a fluorescent accessory protein having 6,7-dimethyl-8-(1'-D-ribityl) lumazine (DMRL) as its authentic chromophore; it modulates the emission of bacterial luciferase to shorter wavelengths with increasing luminous strength.; PDB: 3K7C_C.
Probab=93.85 E-value=0.076 Score=36.25 Aligned_cols=31 Identities=29% Similarity=0.535 Sum_probs=23.9
Q ss_pred ccHHHHHHHHHHHHhCCCHHHHHhhccCCeE
Q 031351 15 QNQEAIVKALYKALANDEMENVAKYLASDLE 45 (161)
Q Consensus 15 ~~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv 45 (161)
.++.++++.||.|+..||++.+.++++++..
T Consensus 7 ~~P~~~v~~f~~al~~gd~~~a~~~~~~~~~ 37 (111)
T PF12870_consen 7 STPEEVVKNFFDALKNGDYEKAYAYLSPESR 37 (111)
T ss_dssp --HHHHHHHHHHHHCTT-HHHHHHTB--TT-
T ss_pred CCHHHHHHHHHHHHHcCCHHHHHHhhCcccc
Confidence 4678999999999999999999999998864
No 28
>cd00667 ring_hydroxylating_dioxygenases_beta Ring hydroxylating dioxygenase beta subunit. This subunit has a similar structure to NTF-2, Ketosteroid isomerase and scytalone dehydratase.The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the substrate by nonheme iron-containing dioxygenases. These enzymes consist of two or three soluble proteins that interact to form an electron-transport chain that transfers electrons from reduced nucleotides (NADH) via flavin and [2Fe-2S] redox centers to a terminal dioxygenase. Aromatic-ring-hydroxylating dioxygenases oxidize aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilize a mononuclear non-heme iron center to catalyze the addition of dioxygen to their respective substrates. The active site of these enzymes however is in the alpha sub-unit. No functional role has been attributed to the beta sub-unit except for a structural role.
Probab=90.15 E-value=0.43 Score=35.39 Aligned_cols=35 Identities=17% Similarity=0.321 Sum_probs=30.0
Q ss_pred cHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC
Q 031351 16 NQEAIVKALYKALANDEMENVAKYLASDLEYWFHG 50 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G 50 (161)
+-.+++-+|-.+++.+|++.+.++|++|++++.++
T Consensus 5 ~I~~ll~~ya~~LD~~~~~~w~~lft~D~~y~~~~ 39 (160)
T cd00667 5 EVEQFLYREARLLDDRRWDEWLALFAEDCHYWVPA 39 (160)
T ss_pred HHHHHHHHHHHHhcccCHHHHHHhhccccEEEcce
Confidence 34567788888899999999999999999998763
No 29
>PF02136 NTF2: Nuclear transport factor 2 (NTF2) domain; InterPro: IPR002075 Nuclear transport factor 2 (NTF2) is a homodimer which stimulates efficient nuclear import of a cargo protein. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins. NTF2 folds into a cone with a deep hydrophobic cavity, the opening of which is surrounded by several negatively charged residues. RanGDP binds to NTF2 by inserting a conserved phenylalanine residue into the hydrophobic pocket of NTF2 and making electrostatic interactions with the conserved negatively charged residues that surround the cavity []. This entry represent the main structural domain of NTF2 and related domains which are found in other nuclear import proteins.; GO: 0006810 transport, 0005622 intracellular; PDB: 3UJM_B 1JKG_B 1JN5_B 1M98_A 3MG1_A 3MG2_A 3MG3_B 2Z76_A 2Z7A_D 2Z77_A ....
Probab=89.45 E-value=5.3 Score=27.55 Aligned_cols=85 Identities=12% Similarity=0.236 Sum_probs=53.6
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhccCCeEEEec-CC-c--cHHHHHHHHhcccccceeEEEeeEEEEe-----CCE--EEE
Q 031351 18 EAIVKALYKALANDEMENVAKYLASDLEYWFH-GP-P--TCQHMVRLLTGESSKATFKFEPRSVEVV-----GDC--VIA 86 (161)
Q Consensus 18 ~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~-Gp-~--~~~~v~~~l~~~~~~~~~~~~~~~vi~~-----Gd~--Vvv 86 (161)
...|+.||.+++++|.+.+.+++++|...... |. . +.+++.+++..+.... .++.+..+-.+ .+. +.|
T Consensus 3 ~~Fv~~Yy~~~d~~~~~~L~~~Y~~~~s~~~~~~~~~~~G~~~I~~~~~~l~~~~-~~~~i~~~d~qp~~~~~~~i~i~v 81 (118)
T PF02136_consen 3 NSFVQQYYQLFDSGDREGLHKLYHDDASFLTWNGNRPVVGREAIQEFFQSLPATG-VQHRITSVDCQPSPSSDGSILITV 81 (118)
T ss_dssp HHHHHHHHHHHHHTHGGGGGGGEEEEEEEEEETTECEEESHHHHHHHHHHHTTSS-EEEEEEEEEEEEEEECCSEEEEEE
T ss_pred HHHHHHHHHHHccCCHHHHHHHHcCCCeeecCCCchhhhhHHHHHHHHhcCCCcc-cEEEecccccccccccCCcEEEEE
Confidence 46789999999999999999999877765544 55 3 4677777777664422 23444333332 333 345
Q ss_pred EeecCC--C---ceEEEEEEEE
Q 031351 87 EGWEGA--P---AYWVHVWTVN 103 (161)
Q Consensus 87 ~G~~~~--~---~~~v~vf~v~ 103 (161)
.|.... . ..|.+.|-+.
T Consensus 82 ~G~~~~~~~~~~~~F~q~FvL~ 103 (118)
T PF02136_consen 82 TGQFKEDDNPNPRRFSQTFVLV 103 (118)
T ss_dssp EEEEEETTSEEEEEEEEEEEEE
T ss_pred EeEEEecCCCcccEEEEEEEEE
Confidence 565431 1 3556677663
No 30
>PF10184 DUF2358: Uncharacterized conserved protein (DUF2358); InterPro: IPR018790 This entry represents a family of conserved proteins. The function is unknown.
Probab=88.02 E-value=6.8 Score=27.64 Aligned_cols=78 Identities=21% Similarity=0.202 Sum_probs=47.8
Q ss_pred CCCHHHHHhhccCCeEEEecC--Ccc---HHHH---HHHHhcccccceeEEEeeEEEEeCC-EEEEE----eecC---CC
Q 031351 30 NDEMENVAKYLASDLEYWFHG--PPT---CQHM---VRLLTGESSKATFKFEPRSVEVVGD-CVIAE----GWEG---AP 93 (161)
Q Consensus 30 ~gD~e~l~~lla~Dvv~~~~G--p~~---~~~v---~~~l~~~~~~~~~~~~~~~vi~~Gd-~Vvv~----G~~~---~~ 93 (161)
.|+.+ .+++++||++..|= -.+ +..+ .+++...+- .+..+++.++...++ .|.+. |... .+
T Consensus 16 ~~~~~--~~iY~~dv~F~Dp~~~f~g~~~Y~~~~~~l~~l~~~~~-~~~~~~v~~i~~~~~~~I~~rW~~~g~~~l~w~p 92 (113)
T PF10184_consen 16 TGDLD--YSIYDEDVVFIDPIVSFKGLDRYKRNLWALRFLGRLFF-SDPSLEVLSIEQDGEDTIRARWRLRGVPRLPWRP 92 (113)
T ss_pred cCCCC--hhhcCCCeEEECCCCceecHHHHHHHHHHHHHHHhhcc-CCcEEEEEEEEECCCCEEEEEEEEEEEeCCCcCC
Confidence 44443 45899999998662 122 3333 455555221 356888888888776 66555 3221 11
Q ss_pred ---ceEEEEEEEEecCCeEEE
Q 031351 94 ---AYWVHVWTVNVKDGLITQ 111 (161)
Q Consensus 94 ---~~~v~vf~v~~~DGkI~~ 111 (161)
......|+++ .||||.+
T Consensus 93 ~~~~~G~S~~~ln-~~g~I~~ 112 (113)
T PF10184_consen 93 RISFDGTSTYTLN-SDGLIYR 112 (113)
T ss_pred cEEEEEEEEEEEC-CCCcEEe
Confidence 3446899997 7899975
No 31
>PF11533 DUF3225: Protein of unknown function (DUF3225); InterPro: IPR024507 This family of proteins has no known function.; PDB: 2OWP_A 2RCD_B.
Probab=85.91 E-value=4.5 Score=29.58 Aligned_cols=66 Identities=11% Similarity=0.153 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhccCCe-EEEec-CC--ccHHHHHHHHhccccc-ceeEEEeeEEEEeCC
Q 031351 17 QEAIVKALYKALANDEMENVAKYLASDL-EYWFH-GP--PTCQHMVRLLTGESSK-ATFKFEPRSVEVVGD 82 (161)
Q Consensus 17 ~~~lV~~f~~A~~~gD~e~l~~lla~Dv-v~~~~-Gp--~~~~~v~~~l~~~~~~-~~~~~~~~~vi~~Gd 82 (161)
-.+...+|.+|+.++|++.+.+||.+|- +...- +. .+++++..|-..-.+. ..-+.....+..-|+
T Consensus 12 v~aaf~~YE~AL~~nDv~~Ld~lFw~~p~TvRyg~~E~LyG~~aI~aFR~~R~~~~~~R~l~~~~itt~G~ 82 (125)
T PF11533_consen 12 VTAAFDRYERALMANDVDALDALFWDDPRTVRYGAGENLYGHDAIRAFRAARPGGGPARTLERTVITTFGR 82 (125)
T ss_dssp HHHHHHHHHHHHHCT-HHHHHHCB--STT-EEEETTEEEESHHHHHHHHHHS--TTTT-EEEEEEEEEETT
T ss_pred HHHHHHHHHHHHhhCCHHHHHHHhccCCceEEECCCccccCHHHHHHHHhcCCCCCCCcEEEEEEEEEecC
Confidence 3567889999999999999999999773 22222 11 1466666655443222 334555566666664
No 32
>TIGR03231 anthran_1_2_B anthranilate 1,2-dioxygenase, small subunit. Anthranilate (2-aminobenzoate) is an intermediate of tryptophan (Trp) biosynthesis and degradation. Members of this family are the small subunit of anthranilate 1,2-dioxygenase, which acts in Trp degradation by converting anthranilate to catechol. Closely related paralogs typically are the benzoate 1,2-dioxygenase small subunit, among the larger set of ring-hydroxylating dioxygenases.
Probab=84.30 E-value=1.6 Score=32.88 Aligned_cols=31 Identities=6% Similarity=0.101 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCHHHHHhhccCCeEEEecC
Q 031351 20 IVKALYKALANDEMENVAKYLASDLEYWFHG 50 (161)
Q Consensus 20 lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G 50 (161)
++-.+-..+.+++++.+.++|++|+.++.|.
T Consensus 4 ~l~~ea~llD~~~~~~W~~lf~~d~~Y~vP~ 34 (155)
T TIGR03231 4 FLYRKAELCDAQDWDAYLDLFDEDSEFHLPQ 34 (155)
T ss_pred HHHHHHHHhcccCHHHHHHHhCcCceEEeec
Confidence 4445556689999999999999999999864
No 33
>PRK10069 3-phenylpropionate dioxygenase subunit beta; Provisional
Probab=83.65 E-value=1.5 Score=33.71 Aligned_cols=32 Identities=16% Similarity=0.171 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhccCCeEEEec
Q 031351 18 EAIVKALYKALANDEMENVAKYLASDLEYWFH 49 (161)
Q Consensus 18 ~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~ 49 (161)
.+++-++-..++.+|++.+.+||++|+.++.|
T Consensus 23 ~~~l~~eA~lLD~~d~~~Wl~lft~D~~Y~~P 54 (183)
T PRK10069 23 SQFLYREARLLDEWRYDDWLALLAEDIHYTMP 54 (183)
T ss_pred HHHHHHHHHHhchhhHHHHHHhhccccEEEcc
Confidence 35556666678999999999999999988864
No 34
>PF05223 MecA_N: NTF2-like N-terminal transpeptidase domain; InterPro: IPR007887 The multiple antibiotic resistance of methicillin-resistant strains of Staphylococcus aureus (MRSA) has become a major clinical problem worldwide. Methicillin resistance in MRSA strains is due to the acquisition of the mecA gene via horizontal transfer from an unidentified species which encodes penicillin-binding protein 2a (PBP2a). The structure of the N-terminal domain from MecA is known [] Q53707 from SWISSPROT and is found to be similar to that found in NTF2 IPR002075 from INTERPRO. The length of the PBP2A N-terminal domain (which positions the transpeptidase active site more than 100A from the expected C terminus of the transmembrane anchor) suggests a possible structural role and potentially gives the transpeptidase domain substantial reach from the cell membrane. This domain seems unlikely to have an enzymatic function.; GO: 0046677 response to antibiotic; PDB: 1MWS_B 1MWT_B 1MWR_A 1MWU_A 1VQQ_A.
Probab=82.71 E-value=1.6 Score=31.01 Aligned_cols=107 Identities=12% Similarity=0.115 Sum_probs=48.4
Q ss_pred cHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCCccH-HHHHHHHhcccccceeEEEeeEEEEe-CCEEEEEeec---
Q 031351 16 NQEAIVKALYKALANDEMENVAKYLASDLEYWFHGPPTC-QHMVRLLTGESSKATFKFEPRSVEVV-GDCVIAEGWE--- 90 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~~~-~~v~~~l~~~~~~~~~~~~~~~vi~~-Gd~Vvv~G~~--- 90 (161)
+..+.+++|++||++||++++.++++.+.... .+.... +.+...+.++.. ..++++....... ++...+--..
T Consensus 2 ~p~~~~~~f~~aw~~~dy~~m~~~~~~~~k~~-~s~~~~~~~~~~i~~~l~~-~~l~v~~~~~~~~~~~~~~~~~~~~~~ 79 (118)
T PF05223_consen 2 SPEETAEAFLEAWEKGDYAAMYELTSDPSKSQ-YSKEDFVERYQNIYEGLGA-ENLKVEAEKVKKDEDDTATVPYTVTMD 79 (118)
T ss_dssp ---HHHHHHHHHHHTT-HHHHHHTB-HHHHHH-HHHHHHHTHHHHHHHHHT---EEEEEEEEEEECCTTEEEEEEEEEEE
T ss_pred CHHHHHHHHHHHHHcCCHHHHHHhhchhhhcc-ccHHHHHHHHHHHHhhCCc-cceEEEeccceecCCCceEEEEEEEEE
Confidence 46788999999999999999999888763100 000011 111222232222 3455544444333 3443332111
Q ss_pred --CCC--ceEEEEEEEEecCCeEEEEEEeeChHHHHHHcCCC
Q 031351 91 --GAP--AYWVHVWTVNVKDGLITQFREYFNTWLTVKDLRPP 128 (161)
Q Consensus 91 --~~~--~~~v~vf~v~~~DGkI~~~~ey~D~~~l~~alg~~ 128 (161)
.++ .+ ...+++...++. |+.-|+|..+++.|++.
T Consensus 80 t~~g~~~~~-~~~~~l~~~~~~---W~V~W~ps~I~P~L~~g 117 (118)
T PF05223_consen 80 TPAGGIWTY-NYTLTLVKEDDD---WKVDWDPSLIFPGLKDG 117 (118)
T ss_dssp ETTEEE-EE-EEEEEEEEETTC---EEE---GGGTSTT--TT
T ss_pred eCCCCceee-EEEEEEEecCCc---EEEEeCccCCCCCCCCC
Confidence 111 22 334444212343 77889999888888754
No 35
>TIGR03232 benzo_1_2_benB benzoate 1,2-dioxygenase, small subunit. Benzoate 1,2-dioxygenase (EC 1.14.12.10) belongs to the larger family of aromatic ring-hydroxylating dioxygenases. Members of this family should all act on benzoate, but several have additional known activities on various benozate analogs. Some members actually may be named more suitably according to such alternate an activity, such as 2-chlorobenzoate 1,2-dioxygenase (1.14.12.13).
Probab=80.91 E-value=1.6 Score=32.86 Aligned_cols=23 Identities=13% Similarity=0.517 Sum_probs=21.4
Q ss_pred HhCCCHHHHHhhccCCeEEEecC
Q 031351 28 LANDEMENVAKYLASDLEYWFHG 50 (161)
Q Consensus 28 ~~~gD~e~l~~lla~Dvv~~~~G 50 (161)
+.+++++.+.+||++|+.+++|.
T Consensus 12 LD~~~~~eWl~L~~eD~~Y~vP~ 34 (155)
T TIGR03232 12 LDDEQWDDWLECYRADASFWMPA 34 (155)
T ss_pred hhhhhHHHHHHhcccCeEEEEEe
Confidence 78999999999999999999875
No 36
>PF00866 Ring_hydroxyl_B: Ring hydroxylating beta subunit; InterPro: IPR000391 The degradation of aromatic compounds by aerobic bacteria frequently begins with the dihydroxylation of the substrate by nonhaem iron-containing dioxygenases. These enzymes consist of two or three soluble proteins that interact to form an electron-transport chain that transfers electrons from reduced nucleotides (NADH) via flavin and [2Fe-2S] redox centres to a terminal dioxygenase []. Aromatic-ring-hydroxylating dioxygenases oxidise aromatic hydrocarbons and related compounds to cis-arene diols. These enzymes utilise a mononuclear non-haem iron centre to catalyse the addition of dioxygen to their respective substrates. Naphthalene 1,2-dioxygenase (NDO) from Pseudomonas sp. NCIB9816-4 has a domain structure and iron coordination of the Rieske domain is very similar to that of the cytochrome bc1 domain. The active-site iron centre of one of the alpha subunits is directly connected by hydrogen bonds through a single amino acid, Asp205, to the Rieske [2Fe-2S] centre in a neighbouring alpha subunit. This may be the main route for electron transfer [].; GO: 0003824 catalytic activity, 0006725 cellular aromatic compound metabolic process, 0055114 oxidation-reduction process; PDB: 1ULJ_B 1ULI_D 1WQL_B 2GBX_D 2GBW_B 2XSH_D 2XR8_X 2XRX_V 2YFL_B 2YFJ_J ....
Probab=72.61 E-value=3.2 Score=30.66 Aligned_cols=24 Identities=17% Similarity=0.426 Sum_probs=20.8
Q ss_pred HHhCCCHHHHHhhccCCeEEEecC
Q 031351 27 ALANDEMENVAKYLASDLEYWFHG 50 (161)
Q Consensus 27 A~~~gD~e~l~~lla~Dvv~~~~G 50 (161)
.+..++++.+++||++|+.+++|.
T Consensus 5 lLD~~~~~eWl~l~~~D~~Y~vp~ 28 (145)
T PF00866_consen 5 LLDERRYDEWLALFTEDCHYWVPA 28 (145)
T ss_dssp HHHTT-HHHHHHTEEEEEEEEEEE
T ss_pred HhhhhHHHHHHHHhccCeEEEEEe
Confidence 478999999999999999999873
No 37
>PF11453 DUF2950: Protein of unknown function (DUF2950); InterPro: IPR021556 This is a bacterial family of uncharacterised proteins.
Probab=68.89 E-value=21 Score=29.45 Aligned_cols=79 Identities=22% Similarity=0.229 Sum_probs=51.4
Q ss_pred cHHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecCC-ccHHHHHHHHhcccccceeEEEeeEEEEe-CCEE-EEEeecCC
Q 031351 16 NQEAIVKALYKALANDEMENVAKYLASDLEYWFHGP-PTCQHMVRLLTGESSKATFKFEPRSVEVV-GDCV-IAEGWEGA 92 (161)
Q Consensus 16 ~~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp-~~~~~v~~~l~~~~~~~~~~~~~~~vi~~-Gd~V-vv~G~~~~ 92 (161)
+..+.+.+|-+|+.++|.++|.++|-+|..-..++. ...+.+.+|+..... -+.+..+ +++. ...|...+
T Consensus 6 tPe~Aa~Al~~Av~~~d~~aL~~vLG~~~~~~vp~~~~d~~~~~~Fl~~w~~-------~h~i~~~g~~~a~L~VG~~~W 78 (271)
T PF11453_consen 6 TPEAAADALVDAVATNDEDALAKVLGPDWRDLVPSGGADREDRYRFLRAWAE-------KHRIVQDGDDRAHLAVGDDGW 78 (271)
T ss_pred CHHHHHHHHHHHHhcCCHHHHHHHhCccHHhccCCCCccHHHHHHHHHHHHh-------hceeeecCCCceEEEecCCCC
Confidence 467889999999999999999999999986655643 344555566654321 1234444 3433 34477777
Q ss_pred CceEEEEEEE
Q 031351 93 PAYWVHVWTV 102 (161)
Q Consensus 93 ~~~~v~vf~v 102 (161)
+.+ +=+.+-
T Consensus 79 ~lP-iPlvk~ 87 (271)
T PF11453_consen 79 PLP-IPLVKT 87 (271)
T ss_pred ccc-eeeEEc
Confidence 655 334444
No 38
>cd00780 NTF2 Nuclear transport factor 2 (NTF2) domain plays an important role in the trafficking of macromolecules, ions and small molecules between the cytoplasm and nucleus. This bi-directional transport of macromolecules across the nuclear envelope requires many soluble factors that includes GDP-binding protein Ran (RanGDP). RanGDP is required for both import and export of proteins and poly(A) RNA. RanGDP also has been implicated in cell cycle control, specifically in mitotic spindle assembly. In interphase cells, RanGDP is predominately nuclear and thought to be GTP bound, but it is also present in the cytoplasm, probably in the GDP-bound state. NTF2 mediates the nuclear import of RanGDP. NTF2 binds to both RanGDP and FxFG repeat-containing nucleoporins.
Probab=64.79 E-value=45 Score=23.20 Aligned_cols=85 Identities=15% Similarity=0.216 Sum_probs=55.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhccCCeEEEecC-Cc--cHHHHHHHHhcccccceeEEEeeEEEEe----CC-EEEEEe
Q 031351 17 QEAIVKALYKALANDEMENVAKYLASDLEYWFHG-PP--TCQHMVRLLTGESSKATFKFEPRSVEVV----GD-CVIAEG 88 (161)
Q Consensus 17 ~~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~~~G-p~--~~~~v~~~l~~~~~~~~~~~~~~~vi~~----Gd-~Vvv~G 88 (161)
..+-|+.||..++ .+.+.+..+++++..+...| .. +.+++..++..+.. ...++++..+-.+ +. .|.|.|
T Consensus 6 ~~~Fv~~YY~~l~-~~~~~L~~fY~~~s~~~~~~~~~~~g~~~I~~~l~~lp~-~~~~~~i~~~d~q~~~~~~ili~V~G 83 (119)
T cd00780 6 AKAFVQQYYSIFD-NNREGLHRLYGDTSMLSREGMKQVTGRDAIVEKLSSLPF-QKTKHKITTVDSQPTPSGGVIVMVTG 83 (119)
T ss_pred HHHHHHHHHHHHh-cCHHHHHhhcCCCcEEEECCceEecCHHHHHHHHHhCCC-cceEEEEEEEeeeEcCCCCEEEEEEE
Confidence 3467899999999 78999999999999988888 32 45677777776642 1224444333221 22 445667
Q ss_pred ecC----CCceEEEEEEEE
Q 031351 89 WEG----APAYWVHVWTVN 103 (161)
Q Consensus 89 ~~~----~~~~~v~vf~v~ 103 (161)
... ....|.+.|-+.
T Consensus 84 ~~~~~~~~~~~F~q~F~L~ 102 (119)
T cd00780 84 SLKLDEQPPRKFSQTFVLA 102 (119)
T ss_pred EEEECCCCceeEeEEEEEE
Confidence 542 125556667663
No 39
>PF04280 Tim44: Tim44-like domain; InterPro: IPR007379 Tim44 is an essential component of the machinery that mediates the translocation of nuclear-encoded proteins across the mitochondrial inner membrane []. Tim44 is thought to bind phospholipids of the mitochondrial inner membrane both by electrostatic interactions and by penetrating the polar head group region [].; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005744 mitochondrial inner membrane presequence translocase complex; PDB: 2CW9_A 2FXT_A 3QK9_A.
Probab=63.99 E-value=36 Score=24.49 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhccCCe
Q 031351 17 QEAIVKALYKALANDEMENVAKYLASDL 44 (161)
Q Consensus 17 ~~~lV~~f~~A~~~gD~e~l~~lla~Dv 44 (161)
.+++...+..||.+||.+.+..++++++
T Consensus 24 ak~~f~~i~~A~~~~D~~~l~~~~t~~~ 51 (147)
T PF04280_consen 24 AKEAFLPIQEAWAKGDLEALRPLLTEEL 51 (147)
T ss_dssp HHHTHHHHHHHHHHT-HHHHHHHB-HHH
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHhCHHH
Confidence 4566677888999999999999999885
No 40
>COG4460 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.40 E-value=43 Score=24.20 Aligned_cols=57 Identities=7% Similarity=0.060 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCHHHHHhhccCCeEEEecCCc--cHHHHHHHHhccccc-ceeEEEeeEE
Q 031351 21 VKALYKALANDEMENVAKYLASDLEYWFHGPP--TCQHMVRLLTGESSK-ATFKFEPRSV 77 (161)
Q Consensus 21 V~~f~~A~~~gD~e~l~~lla~Dvv~~~~Gp~--~~~~v~~~l~~~~~~-~~~~~~~~~v 77 (161)
+..++.+-..+-.+.+..-|++|++..-|+.. ++.++..++...... +.+.+.++++
T Consensus 16 i~dWl~~~~adtldal~arfaedftMitP~GviLD~~Alg~~frs~racrpGl~I~ie~i 75 (130)
T COG4460 16 IVDWLVAARADTLDALRARFAEDFTMITPSGVILDRDALGDHFRSSRACRPGLAISIEDI 75 (130)
T ss_pred HHHHHHhcccccHHHHHHHHhcCceEecCCceEeccHHHHHHHHhccCCCCCeEEEEecc
Confidence 34444444566788888889999998877543 456777777765544 6676666554
No 41
>COG5517 Small subunit of phenylpropionate dioxygenase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=54.65 E-value=9.4 Score=29.07 Aligned_cols=24 Identities=17% Similarity=0.400 Sum_probs=21.6
Q ss_pred HHhCCCHHHHHhhccCCeEEEecC
Q 031351 27 ALANDEMENVAKYLASDLEYWFHG 50 (161)
Q Consensus 27 A~~~gD~e~l~~lla~Dvv~~~~G 50 (161)
++..+|++++.++|.+++.+++++
T Consensus 20 llDd~dwd~Wla~f~e~~~y~m~~ 43 (164)
T COG5517 20 LLDDRDWDAWLAQFDEQAEYWMPP 43 (164)
T ss_pred HhccccHHHHHHHHHhhheEeCCc
Confidence 378999999999999999999764
No 42
>PLN02382 probable sucrose-phosphatase
Probab=53.38 E-value=96 Score=26.93 Aligned_cols=71 Identities=11% Similarity=0.084 Sum_probs=44.0
Q ss_pred HHHHH--HHHHHHHhCCC-------HHHHHhhccCCeEEEecCCc--cHHHHHHHHhccccc-ce--eEEEeeEEE--E-
Q 031351 17 QEAIV--KALYKALANDE-------MENVAKYLASDLEYWFHGPP--TCQHMVRLLTGESSK-AT--FKFEPRSVE--V- 79 (161)
Q Consensus 17 ~~~lV--~~f~~A~~~gD-------~e~l~~lla~Dvv~~~~Gp~--~~~~v~~~l~~~~~~-~~--~~~~~~~vi--~- 79 (161)
..++| ..+|+.|-+|+ ++.+++.|+|+++...|... .+.+....|+..... ++ +++.+.++. .
T Consensus 284 ~~evv~~~~~~e~W~~~~~~~~~~~~~~l~~~~~p~~~~v~p~G~~~~~~~~~~~~~~~~G~~~g~~~~i~vd~~~~~~~ 363 (413)
T PLN02382 284 AHEVVKFYLFYEKWRRGEVENSDEVFQRLKSSCAPNGVFVHPSGVEKSLHDSIDELRSCYGDKKGKKFRVWVDRVLSTQL 363 (413)
T ss_pred HHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCeeEECCCcccCCHHHHHHHHHHhhCCCCCCEEEEEEeeEEEEEE
Confidence 34454 45677787876 67899999999998766422 355555655554433 34 777765553 2
Q ss_pred eCCEEEEE
Q 031351 80 VGDCVIAE 87 (161)
Q Consensus 80 ~Gd~Vvv~ 87 (161)
.++..+|.
T Consensus 364 ~~~~~~v~ 371 (413)
T PLN02382 364 GPDTWLVK 371 (413)
T ss_pred cCCeEEEE
Confidence 24555443
No 43
>PF11006 DUF2845: Protein of unknown function (DUF2845); InterPro: IPR021268 This bacterial family of proteins has no known function.
Probab=47.32 E-value=45 Score=22.36 Aligned_cols=30 Identities=20% Similarity=0.443 Sum_probs=21.6
Q ss_pred EEEEEeecC--CCceEEEEEEEEecCCeEEEEEE
Q 031351 83 CVIAEGWEG--APAYWVHVWTVNVKDGLITQFRE 114 (161)
Q Consensus 83 ~Vvv~G~~~--~~~~~v~vf~v~~~DGkI~~~~e 114 (161)
.+.++-..| ++..+..+++| +|||+++++.
T Consensus 54 ~~~vE~W~Yn~Gp~~~~~~l~f--~~Gkl~~I~~ 85 (87)
T PF11006_consen 54 EVPVEEWTYNFGPNGFMQILTF--ENGKLVRIES 85 (87)
T ss_pred ceeeeEEEEeCCCCCcEEEEEE--ECCEEEEEEe
Confidence 344554445 35666889999 9999999863
No 44
>COG4875 Uncharacterized protein conserved in bacteria with a cystatin-like fold [Function unknown]
Probab=47.00 E-value=1.2e+02 Score=22.49 Aligned_cols=30 Identities=23% Similarity=0.224 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhccCCeEEE
Q 031351 18 EAIVKALYKALANDEMENVAKYLASDLEYW 47 (161)
Q Consensus 18 ~~lV~~f~~A~~~gD~e~l~~lla~Dvv~~ 47 (161)
.++..++=+++..||.+.+.+.++||++.-
T Consensus 40 AaLFdrWN~~L~TGdP~kV~anyApDaVLL 69 (156)
T COG4875 40 AALFDRWNAALTTGDPNKVAANYAPDAVLL 69 (156)
T ss_pred HHHHHHHHhhhhcCChHHHHhhcCCceEee
Confidence 355566666777999999999999999863
No 45
>COG0268 RpsT Ribosomal protein S20 [Translation, ribosomal structure and biogenesis]
Probab=29.70 E-value=74 Score=21.83 Aligned_cols=26 Identities=15% Similarity=0.178 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhccC
Q 031351 17 QEAIVKALYKALANDEMENVAKYLAS 42 (161)
Q Consensus 17 ~~~lV~~f~~A~~~gD~e~l~~lla~ 42 (161)
-+..|+.|..++..||.+...++|..
T Consensus 28 ~rT~iKk~~~ai~~gd~~~A~~~l~~ 53 (88)
T COG0268 28 LRTAIKKVEAAIEAGDKEAAKAALKE 53 (88)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 45689999999999999998888764
No 46
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=27.86 E-value=1.7e+02 Score=19.04 Aligned_cols=35 Identities=20% Similarity=0.242 Sum_probs=23.7
Q ss_pred EEeCCEEEEEeecCCCceEEEEEEEEecCCeEEEEEE
Q 031351 78 EVVGDCVIAEGWEGAPAYWVHVWTVNVKDGLITQFRE 114 (161)
Q Consensus 78 i~~Gd~Vvv~G~~~~~~~~v~vf~v~~~DGkI~~~~e 114 (161)
...||.+.+.-+.....| +.+|.++ .+|+++.+.-
T Consensus 3 ~~~Ge~v~~~~~~~~~~Y-l~l~~~~-~~G~v~~L~P 37 (83)
T PF14326_consen 3 YRVGERVRFRVTSNRDGY-LYLFYID-ADGKVTLLFP 37 (83)
T ss_pred ccCCCEEEEEEEeCCCeE-EEEEEEC-CCCCEEEEec
Confidence 346777666544444455 7788886 7899988864
No 47
>TIGR00984 3a0801s03tim44 mitochondrial import inner membrane, translocase subunit. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tim proteins.
Probab=26.00 E-value=44 Score=28.98 Aligned_cols=24 Identities=13% Similarity=0.278 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCHHHHHhhccCCe
Q 031351 21 VKALYKALANDEMENVAKYLASDL 44 (161)
Q Consensus 21 V~~f~~A~~~gD~e~l~~lla~Dv 44 (161)
+...+.||..||.+.|..||++++
T Consensus 255 ~p~ILeAf~kGD~e~LK~~lse~v 278 (378)
T TIGR00984 255 VPEILEAYVKGDLEVLKSWCSEAP 278 (378)
T ss_pred HHHHHHHHHcCCHHHHHHhhCHHH
Confidence 577789999999999999999984
No 48
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=25.64 E-value=54 Score=20.89 Aligned_cols=26 Identities=23% Similarity=0.371 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhCCCHHHHHhhccCCe
Q 031351 19 AIVKALYKALANDEMENVAKYLASDL 44 (161)
Q Consensus 19 ~lV~~f~~A~~~gD~e~l~~lla~Dv 44 (161)
++.+++++|+.+||.+.+.+++..=+
T Consensus 3 ~~~~~l~~al~~~d~~~~~~~~~~~l 28 (79)
T PF02607_consen 3 ELIERLLDALLAGDEEEAEALLEEAL 28 (79)
T ss_dssp HHHHHHHHHHHTT-CCHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 57899999999999988887776543
No 49
>PF06594 HCBP_related: Haemolysin-type calcium binding protein related domain; InterPro: IPR010566 This family consists of a number of bacteria specific domains, which are found in haemolysin-type calcium binding proteins. This family is found in conjunction with IPR001343 from INTERPRO and is often found in multiple copies.
Probab=25.40 E-value=1.4e+02 Score=17.00 Aligned_cols=31 Identities=19% Similarity=0.425 Sum_probs=22.9
Q ss_pred EEeCCEEEEEeecCCC-ceEEEEEEEEecCCeEE
Q 031351 78 EVVGDCVIAEGWEGAP-AYWVHVWTVNVKDGLIT 110 (161)
Q Consensus 78 i~~Gd~Vvv~G~~~~~-~~~v~vf~v~~~DGkI~ 110 (161)
...+|.+.+.+..... .+.+.-|+| .||.+-
T Consensus 7 ~~s~d~iti~~~f~~~~~~~Ie~i~F--aDGt~w 38 (43)
T PF06594_consen 7 KGSGDSITIKNWFSSDGSYRIEQIEF--ADGTVW 38 (43)
T ss_pred cCCCcEEEEeeeECccCCCcEeEEEE--cCCCEe
Confidence 3446888888766554 566889999 999764
No 50
>PF01649 Ribosomal_S20p: Ribosomal protein S20; InterPro: IPR002583 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 [, ]. This family consists of bacterial (and chloroplast) examples of the ribosomal small subunit protein S20. Bacterial ribosomal protein S20 forms part of the 30S ribosomal subunit, and interacts with 16S rRNA.; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1I94_T 1FJG_T 4DH9_T 3KNJ_T 3TVG_W 3UYF_W 3V28_T 3KIS_t 3HUY_T 1HNX_T ....
Probab=21.46 E-value=1.3e+02 Score=20.19 Aligned_cols=25 Identities=16% Similarity=0.283 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhcc
Q 031351 17 QEAIVKALYKALANDEMENVAKYLA 41 (161)
Q Consensus 17 ~~~lV~~f~~A~~~gD~e~l~~lla 41 (161)
-+..++.|..|+..||-+.+.++|.
T Consensus 27 ~rT~iKk~~~ai~~~~~~~a~~~l~ 51 (84)
T PF01649_consen 27 VRTAIKKFREAIEAGDKEEAKELLR 51 (84)
T ss_dssp HHHHHHHHHHHHHTT-HHHHHHHHH
T ss_pred HHHHHHHHHHHHHccChHHHHHHHH
Confidence 4568899999999999997777664
No 51
>PF02512 UK: Virulence determinant
Probab=20.94 E-value=72 Score=21.61 Aligned_cols=30 Identities=20% Similarity=0.306 Sum_probs=22.3
Q ss_pred CCcCCccCCCccccHHHHHHHHHHHHhCCC
Q 031351 3 GTTNNVETSMAEQNQEAIVKALYKALANDE 32 (161)
Q Consensus 3 ~~~~~~e~~Ms~~~~~~lV~~f~~A~~~gD 32 (161)
|..|+-|++..++..-+-+.+||..+++|+
T Consensus 34 ~~N~i~EKsa~~mtssewiaeywkgi~rgn 63 (96)
T PF02512_consen 34 GANNIPEKSAREMTSSEWIAEYWKGIKRGN 63 (96)
T ss_pred cccccchhHHhhhhhHHHHHHHHHhcccCC
Confidence 345666777666667788899999998874
No 52
>PF13616 Rotamase_3: PPIC-type PPIASE domain; PDB: 3RFW_A 3UI5_A 3UI4_A 1FJD_A 1EQ3_A 1ZK6_A.
Probab=20.02 E-value=1.7e+02 Score=20.37 Aligned_cols=33 Identities=15% Similarity=0.284 Sum_probs=24.0
Q ss_pred CccccHHHHHHHHHHHHhCC-CHHHHHhhccCCe
Q 031351 12 MAEQNQEAIVKALYKALAND-EMENVAKYLASDL 44 (161)
Q Consensus 12 Ms~~~~~~lV~~f~~A~~~g-D~e~l~~lla~Dv 44 (161)
.+..+.++.+...+.++.+| |++.+..-+++|-
T Consensus 31 ~~~~~ak~~a~~i~~~l~~G~dF~~lA~~yS~D~ 64 (117)
T PF13616_consen 31 RSKEEAKKKADSILKQLKSGADFAELAKKYSQDP 64 (117)
T ss_dssp ------HHHHHHHHHHHHCTCCHHHHHHHHTSSC
T ss_pred chhHHHHHHHHHHHHHHHCCCCHHHHHHHhCCCC
Confidence 44456789999999999776 9999999999774
Done!