Query psy3368
Match_columns 169
No_of_seqs 186 out of 1120
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 23:16:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3368.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3368hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00135 COesterase: Carboxyle 100.0 2.3E-29 5E-34 220.9 4.9 107 21-146 17-123 (535)
2 KOG4389|consensus 99.9 3.7E-27 8.1E-32 204.8 10.4 125 1-140 1-129 (601)
3 COG2272 PnbA Carboxylesterase 99.9 2.8E-26 6.2E-31 200.0 8.1 87 27-140 2-88 (491)
4 cd00312 Esterase_lipase Estera 99.9 2.1E-25 4.5E-30 196.1 9.1 89 29-142 1-89 (493)
5 KOG1516|consensus 99.9 6E-23 1.3E-27 182.8 9.3 98 25-145 13-110 (545)
6 PF07172 GRP: Glycine rich pro 62.7 8.8 0.00019 27.0 2.8 12 1-12 1-12 (95)
7 KOG1762|consensus 53.5 7.4 0.00016 28.3 1.2 29 138-166 75-103 (114)
8 PRK11548 outer membrane biogen 44.3 9 0.0002 27.5 0.4 21 51-71 53-73 (113)
9 cd05832 Ribosomal_L12p Ribosom 43.0 15 0.00032 26.5 1.4 10 152-161 83-92 (106)
10 PF06316 Ail_Lom: Enterobacter 37.3 40 0.00086 27.0 3.1 30 3-32 4-33 (199)
11 PHA03292 envelope glycoprotein 34.2 67 0.0015 28.3 4.2 32 66-97 52-87 (413)
12 COG4549 Uncharacterized protei 31.1 96 0.0021 24.2 4.2 22 54-81 55-76 (178)
13 PF11214 Med2: Mediator comple 30.5 49 0.0011 23.8 2.4 10 159-168 96-105 (105)
14 KOG0607|consensus 27.2 40 0.00087 29.5 1.7 60 59-131 240-299 (463)
15 COG4808 Uncharacterized protei 25.1 77 0.0017 24.0 2.7 18 1-18 1-18 (152)
16 PF00428 Ribosomal_60s: 60s Ac 24.4 25 0.00053 24.0 -0.0 9 152-160 67-75 (88)
17 PF02950 Conotoxin: Conotoxin; 23.8 26 0.00057 22.7 0.0 15 1-15 1-15 (75)
18 PRK12450 foldase protein PrsA; 22.7 1.1E+02 0.0024 25.7 3.6 12 27-38 30-41 (309)
19 KOG0100|consensus 22.6 1.3E+02 0.0029 27.2 4.1 45 1-45 1-46 (663)
20 PF10880 DUF2673: Protein of u 22.6 1E+02 0.0022 19.7 2.5 8 26-33 26-33 (65)
21 PRK09495 glnH glutamine ABC tr 22.0 83 0.0018 24.6 2.6 15 28-42 37-51 (247)
22 PF03839 Sec62: Translocation 21.0 37 0.0008 27.6 0.3 23 126-148 182-204 (224)
23 PRK11029 FtsH protease regulat 20.3 1.2E+02 0.0027 26.0 3.4 12 29-40 29-40 (334)
No 1
>PF00135 COesterase: Carboxylesterase family The prints entry is specific to acetylcholinesterase; InterPro: IPR002018 Higher eukaryotes have many distinct esterases. Among the different types are those which act on carboxylic esters (3.1.1 from EC). Carboxyl-esterases have been classified into three categories (A, B and C) on the basis of differential patterns of inhibition by organophosphates. The sequence of a number of type-B carboxylesterases indicates [, , ] that the majority are evolutionary related. As is the case for lipases and serine proteases, the catalytic apparatus of esterases involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.; PDB: 3B3Q_A 1CLE_B 1GQS_A 2VJD_A 1HBJ_A 2C5G_A 1U65_A 2WG1_A 1FSS_A 3M3D_A ....
Probab=99.95 E-value=2.3e-29 Score=220.90 Aligned_cols=107 Identities=38% Similarity=0.735 Sum_probs=70.2
Q ss_pred hccCCCCceEEccceEEEeEEecccCCCCccceeeecccccCCCCCCCCCCCCCCCCCCCCCceeccccCCCCCCCCCCC
Q psy3368 21 MSSKEYTNIIELKQGRLRGVVRSPVHNGNLNNIHMYLGIPYAAPPVGQLRFMAPQSPQPWPGLMIADSFSPVCPQKLPNL 100 (169)
Q Consensus 21 ~~~~~~~p~V~t~~G~i~G~~~~~~~~~~~~~v~~F~GIPYA~~PvG~~RF~~P~p~~~w~g~~dAt~~gp~CpQ~~~~~ 100 (169)
.....+.++|+|.+|+|+|+..... ...+|++|+|||||+||+|++||++|+++.+|.+++|||++|+.|||.....
T Consensus 17 ~~~~~~~~~v~~~~g~i~G~~~~~~---~~~~v~~f~gIpYA~pP~g~~Rf~~p~~~~~~~~~~~a~~~~~~C~Q~~~~~ 93 (535)
T PF00135_consen 17 SQAQASSPVVTTSYGKIRGIRVNTD---DGKGVYSFLGIPYAQPPVGELRFRPPQPPPPWSGVRDATKYGPACPQPPPPG 93 (535)
T ss_dssp -ECCSTCCEEEETTEEEEEEEEEES---TCCEEEEEEEEESSE---GGGTTS--EB--S-SSEEETBS---BESCECTTS
T ss_pred hcccCCCCEEEECCeEEEeEEEecC---CCcceEEEeCcccCCCCCCCcccccccccccchhhhhhhhcccccccccccc
Confidence 3344456899999999999776543 1147999999999999999999999999999999999999999999986543
Q ss_pred CCchhhhhhchhhhhhhhhhCCCCCCCCCCceEEEEEccCCCCchh
Q psy3368 101 DDDDFSKKMSKGRLQYYQALMPYLKNQSEDCLYLNIYTPLQEEEEE 146 (169)
Q Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~sEDCL~LNI~tP~~~~~~~ 146 (169)
... .......+||||||||||+|.....++
T Consensus 94 ~~~----------------~~~~~~~~sEDCL~LnI~~P~~~~~~~ 123 (535)
T PF00135_consen 94 PSP----------------GFNPPVGQSEDCLYLNIYTPSNASSNS 123 (535)
T ss_dssp SHH----------------HCSHSSHBES---EEEEEEETSSSSTT
T ss_pred ccc----------------ccccccCCCchHHHHhhhhcccccccc
Confidence 100 000012369999999999999887664
No 2
>KOG4389|consensus
Probab=99.94 E-value=3.7e-27 Score=204.76 Aligned_cols=125 Identities=34% Similarity=0.569 Sum_probs=92.4
Q ss_pred CcchhHHHHHHHHHHHHHHhhc----cCCCCceEEccceEEEeEEecccCCCCccceeeecccccCCCCCCCCCCCCCCC
Q psy3368 1 MASCGALFTGLLLLLLLQVTMS----SKEYTNIIELKQGRLRGVVRSPVHNGNLNNIHMYLGIPYAAPPVGQLRFMAPQS 76 (169)
Q Consensus 1 M~~~~~l~~~l~~l~~~~~~~~----~~~~~p~V~t~~G~i~G~~~~~~~~~~~~~v~~F~GIPYA~~PvG~~RF~~P~p 76 (169)
|+...+++++++++.++.+... ...+..+|+|..|+|||+..... +..|..|+|||||+||+|++||+.|+|
T Consensus 1 m~~~~~~~~l~~~~t~llv~~~~~~~~~~~~~vv~t~~G~vRG~~~t~~----g~~V~aFlGIPfAePPvg~~RFkkP~p 76 (601)
T KOG4389|consen 1 MHPKSLLFPLFLLLTLLLVDSVHAEGPEDDDLVVQTKLGTVRGTELTFP----GKPVSAFLGIPFAEPPVGDLRFKKPEP 76 (601)
T ss_pred CCcchHHHHHHHHHHHHHhhhhcccCCcccceEEeccCCcccceEEecC----CceEEEEecCccCCCCCccccCCCCCc
Confidence 5554455544444333333222 22456899999999999987543 478999999999999999999999999
Q ss_pred CCCCCCceeccccCCCCCCCCCCCCCchhhhhhchhhhhhhhhhCCCCCCCCCCceEEEEEccC
Q psy3368 77 PQPWPGLMIADSFSPVCPQKLPNLDDDDFSKKMSKGRLQYYQALMPYLKNQSEDCLYLNIYTPL 140 (169)
Q Consensus 77 ~~~w~g~~dAt~~gp~CpQ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sEDCL~LNI~tP~ 140 (169)
..+|.|++|||++.+.|.|........ +. ...++......||||||||||+|.
T Consensus 77 ~~pW~g~ldAtt~a~~C~Q~~D~yfp~-----F~------GsEMWNpNt~lSEDCLYlNVW~P~ 129 (601)
T KOG4389|consen 77 KQPWSGVLDATTLANTCYQTRDTYFPG-----FW------GSEMWNPNTELSEDCLYLNVWAPA 129 (601)
T ss_pred CCCccceecccccchhhhccccccCCC-----CC------cccccCCCCCcChhceEEEEeccC
Confidence 999999999999999999976443221 11 111233456789999999999995
No 3
>COG2272 PnbA Carboxylesterase type B [Lipid metabolism]
Probab=99.93 E-value=2.8e-26 Score=200.03 Aligned_cols=87 Identities=46% Similarity=0.928 Sum_probs=76.5
Q ss_pred CceEEccceEEEeEEecccCCCCccceeeecccccCCCCCCCCCCCCCCCCCCCCCceeccccCCCCCCCCCCCCCchhh
Q psy3368 27 TNIIELKQGRLRGVVRSPVHNGNLNNIHMYLGIPYAAPPVGQLRFMAPQSPQPWPGLMIADSFSPVCPQKLPNLDDDDFS 106 (169)
Q Consensus 27 ~p~V~t~~G~i~G~~~~~~~~~~~~~v~~F~GIPYA~~PvG~~RF~~P~p~~~w~g~~dAt~~gp~CpQ~~~~~~~~~~~ 106 (169)
.++++|.+|++.|+.. ++|+.|+|||||.||+|++||++|+|+++|.+++||+++||.|||.......
T Consensus 2 ~~~~~t~~G~~~g~~~--------~~v~~w~GIpYA~pPvG~~Rfr~p~~~~~w~~~rda~~~gp~~~Q~~~~~~~---- 69 (491)
T COG2272 2 APVAETTTGKVEGITV--------NGVHSWLGIPYAAPPVGELRFRRPVPPEPWSGVRDATQFGPACPQPFNRMGS---- 69 (491)
T ss_pred Cceeecccceeecccc--------cceeEEeecccCCCCCCcccccCCCCCcCCCcccchhccCCCCCCccccccc----
Confidence 4789999999999976 6899999999999999999999999999999999999999999998531111
Q ss_pred hhhchhhhhhhhhhCCCCCCCCCCceEEEEEccC
Q psy3368 107 KKMSKGRLQYYQALMPYLKNQSEDCLYLNIYTPL 140 (169)
Q Consensus 107 ~~~~~~~~~~~~~~~~~~~~~sEDCL~LNI~tP~ 140 (169)
......||||||||||+|.
T Consensus 70 ---------------~~~~~~sEDCL~LNIwaP~ 88 (491)
T COG2272 70 ---------------GEDFTGSEDCLYLNIWAPE 88 (491)
T ss_pred ---------------cccCCccccceeEEeeccC
Confidence 1135689999999999999
No 4
>cd00312 Esterase_lipase Esterases and lipases (includes fungal lipases, cholinesterases, etc.) These enzymes act on carboxylic esters (EC: 3.1.1.-). The catalytic apparatus involves three residues (catalytic triad): a serine, a glutamate or aspartate and a histidine.These catalytic residues are responsible for the nucleophilic attack on the carbonyl carbon atom of the ester bond. In contrast with other alpha/beta hydrolase fold family members, p-nitrobenzyl esterase and acetylcholine esterase have a Glu instead of Asp at the active site carboxylate.
Probab=99.92 E-value=2.1e-25 Score=196.13 Aligned_cols=89 Identities=42% Similarity=0.739 Sum_probs=74.6
Q ss_pred eEEccceEEEeEEecccCCCCccceeeecccccCCCCCCCCCCCCCCCCCCCCCceeccccCCCCCCCCCCCCCchhhhh
Q psy3368 29 IIELKQGRLRGVVRSPVHNGNLNNIHMYLGIPYAAPPVGQLRFMAPQSPQPWPGLMIADSFSPVCPQKLPNLDDDDFSKK 108 (169)
Q Consensus 29 ~V~t~~G~i~G~~~~~~~~~~~~~v~~F~GIPYA~~PvG~~RF~~P~p~~~w~g~~dAt~~gp~CpQ~~~~~~~~~~~~~ 108 (169)
+|+|.+|+|+|... .+|+.|+|||||+||+|++||++|+|+.+|++++||+++|+.|||........
T Consensus 1 ~v~t~~G~v~G~~~--------~~~~~F~GIPYA~pP~g~~Rf~~p~~~~~w~~~~~a~~~g~~c~Q~~~~~~~~----- 67 (493)
T cd00312 1 LVVTPNGKVRGVDE--------GGVYSFLGIPYAEPPVGDLRFKEPQPYEPWSDVLDATSYPPSCMQWDQLGGGL----- 67 (493)
T ss_pred CEEeCCceEEeEEe--------CCEEEEeccccCCCCCccccCCCCCCCCCCcCceeccccCCCCccCCcccccc-----
Confidence 58899999999875 47999999999999999999999999999999999999999999975332110
Q ss_pred hchhhhhhhhhhCCCCCCCCCCceEEEEEccCCC
Q psy3368 109 MSKGRLQYYQALMPYLKNQSEDCLYLNIYTPLQE 142 (169)
Q Consensus 109 ~~~~~~~~~~~~~~~~~~~sEDCL~LNI~tP~~~ 142 (169)
......+|||||+||||+|...
T Consensus 68 ------------~~~~~~~sEdcl~l~i~~p~~~ 89 (493)
T cd00312 68 ------------WNAKLPGSEDCLYLNVYTPKNT 89 (493)
T ss_pred ------------ccCCCCCCCcCCeEEEEeCCCC
Confidence 0012357999999999999864
No 5
>KOG1516|consensus
Probab=99.88 E-value=6e-23 Score=182.82 Aligned_cols=98 Identities=41% Similarity=0.782 Sum_probs=83.0
Q ss_pred CCCceEEccceEEEeEEecccCCCCccceeeecccccCCCCCCCCCCCCCCCCCCCCCceeccccCCCCCCCCCCCCCch
Q psy3368 25 EYTNIIELKQGRLRGVVRSPVHNGNLNNIHMYLGIPYAAPPVGQLRFMAPQSPQPWPGLMIADSFSPVCPQKLPNLDDDD 104 (169)
Q Consensus 25 ~~~p~V~t~~G~i~G~~~~~~~~~~~~~v~~F~GIPYA~~PvG~~RF~~P~p~~~w~g~~dAt~~gp~CpQ~~~~~~~~~ 104 (169)
...++|.|.+|.++|...... .. ..++.|+|||||+||+|++||++|+|+.+|++++||+++++.|+|.......
T Consensus 13 ~~~~~~~t~~G~i~G~~~~~~--~~-~~~~~F~gIpya~PP~G~lRF~~P~p~~~W~gv~~at~~~~~C~q~~~~~~~-- 87 (545)
T KOG1516|consen 13 PSPPVVGTPYGKIRGKTVSST--YD-VDVDRFLGIPYAKPPVGELRFRKPQPPEPWTGVLDATKYGPACPQNDELTGQ-- 87 (545)
T ss_pred cCCceEecccceEeeeEeecc--CC-ceeEEEcccccCCCCCccccCCCCCCCCCCccccccccCCCCCCCccccccc--
Confidence 457899999999999987653 22 6799999999999999999999999999999999999999999997643321
Q ss_pred hhhhhchhhhhhhhhhCCCCCCCCCCceEEEEEccCCCCch
Q psy3368 105 FSKKMSKGRLQYYQALMPYLKNQSEDCLYLNIYTPLQEEEE 145 (169)
Q Consensus 105 ~~~~~~~~~~~~~~~~~~~~~~~sEDCL~LNI~tP~~~~~~ 145 (169)
....++|||||||||+|.....+
T Consensus 88 ------------------~~~~~sEDCLylNV~tp~~~~~~ 110 (545)
T KOG1516|consen 88 ------------------NRVFGSEDCLYLNVYTPQGCSES 110 (545)
T ss_pred ------------------cCCCCcCCCceEEEeccCCCccC
Confidence 02468999999999999876543
No 6
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=62.67 E-value=8.8 Score=26.96 Aligned_cols=12 Identities=58% Similarity=0.656 Sum_probs=6.8
Q ss_pred CcchhHHHHHHH
Q psy3368 1 MASCGALFTGLL 12 (169)
Q Consensus 1 M~~~~~l~~~l~ 12 (169)
|.|-.+|++.|+
T Consensus 1 MaSK~~llL~l~ 12 (95)
T PF07172_consen 1 MASKAFLLLGLL 12 (95)
T ss_pred CchhHHHHHHHH
Confidence 776555555444
No 7
>KOG1762|consensus
Probab=53.54 E-value=7.4 Score=28.32 Aligned_cols=29 Identities=38% Similarity=0.396 Sum_probs=15.7
Q ss_pred ccCCCCchhhhhhHHHHHHHHHHhhhhhh
Q psy3368 138 TPLQEEEEEKKEEREEKKKEEKKKEEGEE 166 (169)
Q Consensus 138 tP~~~~~~~k~~~~~~~~~~~~~~~~~~~ 166 (169)
+|......+-..-.+++||+|.|+||.||
T Consensus 75 ~~~~~aa~~~~aA~~~Ekk~eak~Eesee 103 (114)
T KOG1762|consen 75 AAAGGAAAAGGAAAAEEKKEEAKKEESEE 103 (114)
T ss_pred ccccccccccccccchHHHHHhhhhhhcc
Confidence 44444444444455566666666666554
No 8
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=44.25 E-value=9 Score=27.49 Aligned_cols=21 Identities=24% Similarity=0.510 Sum_probs=13.5
Q ss_pred cceeeecccccCCCCCCCCCC
Q psy3368 51 NNIHMYLGIPYAAPPVGQLRF 71 (169)
Q Consensus 51 ~~v~~F~GIPYA~~PvG~~RF 71 (169)
..|..-+|-|=...+.|..||
T Consensus 53 ~qV~~lLGtP~~~~~f~~~~W 73 (113)
T PRK11548 53 QQVAYTLGTPMMQDPFGTNTW 73 (113)
T ss_pred HHHHHHcCCCccccCCCCceE
Confidence 567788888866665444433
No 9
>cd05832 Ribosomal_L12p Ribosomal protein L12p. This subfamily includes archaeal L12p, the protein that is functionally equivalent to L7/L12 in bacteria and the P1 and P2 proteins in eukaryotes. L12p is homologous to P1 and P2 but is not homologous to bacterial L7/L12. It is located in the L12 stalk, with proteins L10, L11, and 23S rRNA. L12p is the only protein in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain six copies of L12p (three homodimers), while eukaryotes have four copies (two heterodimers), and bacteria may have four or six copies (two or three homodimers), depending on the species. The organization of proteins within the stalk has been characterized primarily in bacteria, where L7/L12 forms either two or three homodimers and each homodimer binds to the extended C-terminal helix of L10. L7/L12 is attached to the ribosome through L10 and is the only ribosomal protein that does not directly intera
Probab=43.00 E-value=15 Score=26.46 Aligned_cols=10 Identities=80% Similarity=0.986 Sum_probs=4.0
Q ss_pred HHHHHHHHHh
Q psy3368 152 EEKKKEEKKK 161 (169)
Q Consensus 152 ~~~~~~~~~~ 161 (169)
+|+|+||+|+
T Consensus 83 ~e~~~e~~~~ 92 (106)
T cd05832 83 EEKKKEEEKE 92 (106)
T ss_pred hhhhhhhhcc
Confidence 3444444333
No 10
>PF06316 Ail_Lom: Enterobacterial Ail/Lom protein; InterPro: IPR000758 Virulence-related outer membrane proteins are expressed in Gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion. Members of this group include: PagC, required by Salmonella typhimurium for survival in macrophages and for virulence in mice [] Rck outer membrane protein of the S. typhimurium virulence plasmid [] Ail, a product of the Yersinia enterocolitica chromosome capable of mediating bacterial adherence to and invasion of epithelial cell lines [] OmpX from Escherichia coli that promotes adhesion to and entry into mammalian cells. It also has a role in the resistance against attack by the human complement system [] a Bacteriophage lambda outer membrane protein, Lom [] The crystal structure of OmpX from E. coli reveals that OmpX consists of an eight-stranded antiparallel all-next-neighbour beta barrel []. The structure shows two girdles of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the membrane interior. The core of the barrel consists of an extended hydrogen-bonding network of highly conserved residues. OmpX thus resembles an inverse micelle. The OmpX structure shows that the membrane-spanning part of the protein is much better conserved than the extracellular loops. Moreover, these loops form a protruding beta sheet, the edge of which presumably binds to external proteins. It is suggested that this type of binding promotes cell adhesion and invasion and helps defend against the complement system. Although OmpX has the same beta-sheet topology as the structurally related outer membrane protein A (OmpA) IPR000498 from INTERPRO, their barrels differ with respect to the shear numbers and internal hydrogen-bonding networks.; GO: 0009279 cell outer membrane
Probab=37.32 E-value=40 Score=26.97 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=15.2
Q ss_pred chhHHHHHHHHHHHHHHhhccCCCCceEEc
Q psy3368 3 SCGALFTGLLLLLLLQVTMSSKEYTNIIEL 32 (169)
Q Consensus 3 ~~~~l~~~l~~l~~~~~~~~~~~~~p~V~t 32 (169)
+|..|+.++++++++...+.++.+..++.+
T Consensus 4 ~~~~ils~~~~l~~~~~pA~a~~~~~tlS~ 33 (199)
T PF06316_consen 4 LCAAILSAAVLLAVSGLPASAAAHQSTLSV 33 (199)
T ss_pred HHHHHHHHHHHHHHhcchhhhhcccceecc
Confidence 577776655555555444444333333333
No 11
>PHA03292 envelope glycoprotein I; Provisional
Probab=34.24 E-value=67 Score=28.30 Aligned_cols=32 Identities=22% Similarity=0.345 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCC--CCCCCceeccccCCC--CCCCC
Q psy3368 66 VGQLRFMAPQSP--QPWPGLMIADSFSPV--CPQKL 97 (169)
Q Consensus 66 vG~~RF~~P~p~--~~w~g~~dAt~~gp~--CpQ~~ 97 (169)
.|.+.|...|.+ ..|+|++.-..|... |++..
T Consensus 52 ~G~LlFLGdQ~p~~t~YsGTVELLhyn~s~~Cy~Vl 87 (413)
T PHA03292 52 VGHLIFLDGQRLPTTNYNGTIELIHYNYSSDCYVVI 87 (413)
T ss_pred eeEEEecCCCCCCCcccCceEEEEEeCCCCCcccee
Confidence 466778877764 568887666555544 88754
No 12
>COG4549 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.06 E-value=96 Score=24.19 Aligned_cols=22 Identities=23% Similarity=0.539 Sum_probs=15.2
Q ss_pred eeecccccCCCCCCCCCCCCCCCCCCCC
Q psy3368 54 HMYLGIPYAAPPVGQLRFMAPQSPQPWP 81 (169)
Q Consensus 54 ~~F~GIPYA~~PvG~~RF~~P~p~~~w~ 81 (169)
.+-.-||=+- -|..|+|.+.|.
T Consensus 55 kV~vklPeGv------i~~kp~PkpGW~ 76 (178)
T COG4549 55 KVRVKLPEGV------IFAKPQPKPGWT 76 (178)
T ss_pred EEEEeCCCce------eeecccCCCCcE
Confidence 3345555554 488999999996
No 13
>PF11214 Med2: Mediator complex subunit 2; InterPro: IPR021017 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression [, ].
Probab=30.55 E-value=49 Score=23.76 Aligned_cols=10 Identities=60% Similarity=0.873 Sum_probs=4.2
Q ss_pred HHhhhhhhhc
Q psy3368 159 KKKEEGEEKK 168 (169)
Q Consensus 159 ~~~~~~~~~~ 168 (169)
+++.|.|++|
T Consensus 96 ~~rkE~e~~k 105 (105)
T PF11214_consen 96 RKRKEEEEKK 105 (105)
T ss_pred HHHHHhhhcC
Confidence 3333444443
No 14
>KOG0607|consensus
Probab=27.16 E-value=40 Score=29.52 Aligned_cols=60 Identities=22% Similarity=0.371 Sum_probs=41.5
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCceeccccCCCCCCCCCCCCCchhhhhhchhhhhhhhhhCCCCCCCCCCc
Q psy3368 59 IPYAAPPVGQLRFMAPQSPQPWPGLMIADSFSPVCPQKLPNLDDDDFSKKMSKGRLQYYQALMPYLKNQSEDC 131 (169)
Q Consensus 59 IPYA~~PvG~~RF~~P~p~~~w~g~~dAt~~gp~CpQ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sEDC 131 (169)
-|=-..|+|..-|++|..+..+.+ +|+.|-..|=-- -++...++.+..+.|+...-.|||
T Consensus 240 tP~L~tPvGSAEfMAPEVVd~fv~--qA~~YDKrCDlw-----------SLGvIlYImLsGYpPFvG~Cg~dC 299 (463)
T KOG0607|consen 240 TPELLTPVGSAEFMAPEVVDVFVD--QATFYDKRCDLW-----------SLGVILYIMLSGYPPFVGHCGADC 299 (463)
T ss_pred CccccCcccchhhcchhHHhhhcc--ccccccccccHH-----------HHHHHHHHHHhCCCCccCccCCcC
Confidence 344456899999999999887766 788888888321 133334555666666666667888
No 15
>COG4808 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.08 E-value=77 Score=23.98 Aligned_cols=18 Identities=28% Similarity=0.427 Sum_probs=9.9
Q ss_pred CcchhHHHHHHHHHHHHH
Q psy3368 1 MASCGALFTGLLLLLLLQ 18 (169)
Q Consensus 1 M~~~~~l~~~l~~l~~~~ 18 (169)
|+..+.++++++.++++.
T Consensus 1 Mk~l~kl~~~~~alil~~ 18 (152)
T COG4808 1 MKALNKLFSLVVALVLVF 18 (152)
T ss_pred ChhHHHHHHHHHHHHHHH
Confidence 776666665544444333
No 16
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 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 [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=24.44 E-value=25 Score=24.01 Aligned_cols=9 Identities=67% Similarity=0.903 Sum_probs=3.1
Q ss_pred HHHHHHHHH
Q psy3368 152 EEKKKEEKK 160 (169)
Q Consensus 152 ~~~~~~~~~ 160 (169)
+++|+||++
T Consensus 67 ~e~kkEeee 75 (88)
T PF00428_consen 67 EEEKKEEEE 75 (88)
T ss_dssp STTHHHHT-
T ss_pred hhccccccc
Confidence 333344333
No 17
>PF02950 Conotoxin: Conotoxin; InterPro: IPR004214 Cone snail toxins, conotoxins, are small neurotoxic peptides with disulphide connectivity that target ion-channels or G-protein coupled receptors. Based on the number and pattern of disulphide bonds and biological activities, conotoxins can be classified into several families []. Omega, delta and kappa families of conotoxins have a knottin or inhibitor cysteine knot scaffold. The knottin scaffold is a very special disulphide-through-disulphide knot, in which the III-VI disulphide bond crosses the macrocycle formed by two other disulphide bonds (I-IV and II-V) and the interconnecting backbone segments, where I-VI indicates the six cysteine residues starting from the N terminus. The disulphide bonding network, as well as specific amino acids in inter-cysteine loops, provide the specificity of conotoxins []. The cysteine arrangements are the same for omega, delta and kappa families, even though omega conotoxins are calcium channel blockers, whereas delta conotoxins delay the inactivation of sodium channels, and kappa conotoxins are potassium channel blockers []. Mu conotoxins have two types of cysteine arrangements, but the knottin scaffold is not observed. Mu conotoxins target the voltage-gated sodium channels [], and are useful probes for investigating voltage-dependent sodium channels of excitable tissues []. Alpha conotoxins have two types of cysteine arrangements [], and are competitive nicotinic acetylcholine receptor antagonists. ; GO: 0008200 ion channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 2EFZ_A 1FYG_A 1RMK_A 1DG0_A 1DFY_A 1DFZ_A 2JQC_A 2YYF_A 2JQB_A 1F3K_A ....
Probab=23.84 E-value=26 Score=22.72 Aligned_cols=15 Identities=33% Similarity=0.388 Sum_probs=0.0
Q ss_pred CcchhHHHHHHHHHH
Q psy3368 1 MASCGALFTGLLLLL 15 (169)
Q Consensus 1 M~~~~~l~~~l~~l~ 15 (169)
||+..+|+++++++.
T Consensus 1 mKLt~vliVavLllt 15 (75)
T PF02950_consen 1 MKLTCVLIVAVLLLT 15 (75)
T ss_dssp ---------------
T ss_pred CCcchHHHHHHHHHH
Confidence 676666665555444
No 18
>PRK12450 foldase protein PrsA; Reviewed
Probab=22.73 E-value=1.1e+02 Score=25.73 Aligned_cols=12 Identities=17% Similarity=0.470 Sum_probs=7.3
Q ss_pred CceEEccceEEE
Q psy3368 27 TNIIELKQGRLR 38 (169)
Q Consensus 27 ~p~V~t~~G~i~ 38 (169)
.+++.+..+.|.
T Consensus 30 ~~VAtvng~~IT 41 (309)
T PRK12450 30 TKLVSMKGDTIT 41 (309)
T ss_pred ceEEEECCeeec
Confidence 356666666664
No 19
>KOG0100|consensus
Probab=22.62 E-value=1.3e+02 Score=27.17 Aligned_cols=45 Identities=18% Similarity=0.027 Sum_probs=21.0
Q ss_pred CcchhHHHHHHHHHHHHHHhhccC-CCCceEEccceEEEeEEeccc
Q psy3368 1 MASCGALFTGLLLLLLLQVTMSSK-EYTNIIELKQGRLRGVVRSPV 45 (169)
Q Consensus 1 M~~~~~l~~~l~~l~~~~~~~~~~-~~~p~V~t~~G~i~G~~~~~~ 45 (169)
|+.+.++.+++++++++..+..+. ...---...+|++.|+...++
T Consensus 1 mk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gtvigIdLGTT 46 (663)
T KOG0100|consen 1 MKLSFLLAMLLFLAVLFFGCSEAASTEKEDEAEKLGTVIGIDLGTT 46 (663)
T ss_pred CchHHHHHHHHHHHHHHhhhhhhhhhccccchhccceEEEEecCCc
Confidence 776666655444443333221110 001111235788888876433
No 20
>PF10880 DUF2673: Protein of unknown function (DUF2673); InterPro: IPR024247 This family of proteins with unknown function appears to be restricted to Rickettsiae spp.
Probab=22.60 E-value=1e+02 Score=19.68 Aligned_cols=8 Identities=0% Similarity=-0.122 Sum_probs=3.8
Q ss_pred CCceEEcc
Q psy3368 26 YTNIIELK 33 (169)
Q Consensus 26 ~~p~V~t~ 33 (169)
++..|.|.
T Consensus 26 ~pasvttt 33 (65)
T PF10880_consen 26 DPASVTTT 33 (65)
T ss_pred CCcceeHH
Confidence 34455554
No 21
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=22.02 E-value=83 Score=24.64 Aligned_cols=15 Identities=7% Similarity=-0.128 Sum_probs=8.2
Q ss_pred ceEEccceEEEeEEe
Q psy3368 28 NIIELKQGRLRGVVR 42 (169)
Q Consensus 28 p~V~t~~G~i~G~~~ 42 (169)
|-.-...|.+.|+..
T Consensus 37 P~~~~~~g~~~G~~v 51 (247)
T PRK09495 37 PFEFKQGDKYVGFDI 51 (247)
T ss_pred CeeecCCCceEEEeH
Confidence 443344566777654
No 22
>PF03839 Sec62: Translocation protein Sec62; InterPro: IPR004728 Members of the NSCC2 family have been sequenced from various yeast, fungal and animals species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins have been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.; GO: 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane
Probab=20.97 E-value=37 Score=27.61 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=16.9
Q ss_pred CCCCCceEEEEEccCCCCchhhh
Q psy3368 126 NQSEDCLYLNIYTPLQEEEEEKK 148 (169)
Q Consensus 126 ~~sEDCL~LNI~tP~~~~~~~k~ 148 (169)
+-.|||=.+..|.|--......+
T Consensus 182 NLfeD~Gf~eSF~Ply~~~~~~~ 204 (224)
T PF03839_consen 182 NLFEDVGFFESFKPLYSWEYKGD 204 (224)
T ss_pred ccccccchhhheeecccccccCc
Confidence 45699999999999765554433
No 23
>PRK11029 FtsH protease regulator HflC; Provisional
Probab=20.32 E-value=1.2e+02 Score=25.97 Aligned_cols=12 Identities=25% Similarity=0.188 Sum_probs=6.7
Q ss_pred eEEccceEEEeE
Q psy3368 29 IIELKQGRLRGV 40 (169)
Q Consensus 29 ~V~t~~G~i~G~ 40 (169)
-|-+..|.+.+.
T Consensus 29 gVV~rFGk~~~~ 40 (334)
T PRK11029 29 GIVLRFGKVLRD 40 (334)
T ss_pred EEEEECCceecc
Confidence 344456777654
Done!