Query 041772
Match_columns 188
No_of_seqs 111 out of 192
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 10:29:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041772.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041772hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05603 DUF775: Protein of un 100.0 1.1E-69 2.4E-74 452.4 18.0 175 1-183 1-202 (202)
2 KOG4067 Uncharacterized conser 100.0 6.6E-63 1.4E-67 402.0 15.5 179 1-187 1-194 (195)
3 PF04711 ApoA-II: Apolipoprote 70.8 2.1 4.5E-05 30.7 0.9 23 130-152 47-69 (76)
4 PF15187 Augurin: Oesophageal 49.2 9.8 0.00021 29.1 1.3 23 164-186 49-77 (114)
5 PF09195 Endonuc-BglII: Restri 40.1 13 0.00028 30.1 0.8 40 139-178 98-149 (164)
6 PF03475 3-alpha: 3-alpha doma 34.2 29 0.00064 22.0 1.6 14 165-178 31-44 (47)
7 PF08987 DUF1892: Protein of u 30.9 45 0.00097 25.8 2.4 17 162-178 51-67 (115)
8 KOG1966 Sodium/hydrogen exchan 30.2 37 0.0008 33.5 2.2 64 111-176 436-502 (670)
9 PF04254 DUF432: Protein of un 29.4 1.1E+02 0.0024 23.6 4.4 44 39-82 8-60 (123)
10 PRK06330 transcript cleavage f 25.4 47 0.001 33.2 2.1 27 158-184 239-265 (718)
11 KOG4439 RNA polymerase II tran 25.0 59 0.0013 32.9 2.6 45 133-179 365-409 (901)
12 PF07888 CALCOCO1: Calcium bin 24.9 1.3E+02 0.0027 29.3 4.8 40 45-93 7-50 (546)
13 PF09175 DUF1944: Domain of un 24.8 2.4E+02 0.0053 23.1 5.8 85 55-153 16-125 (165)
14 KOG1110 Putative steroid membr 23.1 50 0.0011 27.6 1.5 19 160-178 131-149 (183)
15 PF01846 FF: FF domain; Inter 21.7 57 0.0012 20.5 1.3 16 169-184 21-36 (51)
16 PRK14720 transcript cleavage f 21.6 62 0.0013 33.3 2.1 54 132-185 368-433 (906)
17 PF14969 DUF4508: Domain of un 20.6 63 0.0014 24.4 1.5 47 140-186 36-93 (98)
18 PF11514 DUF3219: Protein of u 20.5 55 0.0012 24.7 1.1 44 25-83 31-74 (99)
No 1
>PF05603 DUF775: Protein of unknown function (DUF775); InterPro: IPR008493 This family consists of several eukaryotic proteins of unknown function.
Probab=100.00 E-value=1.1e-69 Score=452.37 Aligned_cols=175 Identities=34% Similarity=0.706 Sum_probs=153.0
Q ss_pred CeEEEcCCCCcCcccCcceeeCCceEEEEccCCccCCCCCcceEEEEecCCCCCCCCceEEEEEEcC--CCCceEeeeec
Q 041772 1 MFGVVFPNRSFPMDISTFSQIDTFHWILDMNSFVGEAYDQVRDMCIFLLNNFTLPPDKALAVYIQSP--GSPFLYCGAVT 78 (188)
Q Consensus 1 MFG~iv~Grp~~~~~t~f~qv~~~~~~~~l~~~~~~~~~~v~hivVFLl~~~~~p~g~~a~VY~~~P--~~~w~~LG~is 78 (188)
|||||+|||| ++|+++|+|+|||++++ +++++||||||||||++||||||||+|||+|| +++|||||+|+
T Consensus 1 MFGviv~Grp---v~t~~~~v~~t~f~~~l-----~~~~~v~hivVFLl~~~p~P~g~aa~VY~~~P~~~~~w~~LG~Is 72 (202)
T PF05603_consen 1 MFGVIVPGRP---VQTDFQQVDETKFVFDL-----PNADSVNHIVVFLLPNVPFPPGYAAAVYFQWPAGGPEWQLLGAIS 72 (202)
T ss_pred CeEEEeCCCc---ccccceEcCCCEEEEEC-----CCCCCCCEEEEEECCCCCCCcceeEEEEEEcCCCCCCeEEecccc
Confidence 9999999995 57999999999999999 78999999999999999999999999999999 77999999999
Q ss_pred CCCCceEEECCCCCCCCCCc-ccCCCCCCceeEEEEeeccccccccccccc----------------------hhHHHHH
Q 041772 79 VARPSAVLSLPWPEPGGGMQ-LTAPDSTPLSAKIGVSVEDLTSLPSLDVTA----------------------EKRIERL 135 (188)
Q Consensus 79 n~KPSaIFk~~~~~~~~~~~-~~~~~~~~~~~~IGISiEpl~~i~~~~~~~----------------------~~~~~~~ 135 (188)
|+||||||||+|++...... .........+|+|||||||+++++++.+.. ..++++|
T Consensus 73 n~KPSAIFki~~~~~~~~~~~~~~~~~~~~~a~IGISiEp~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 152 (202)
T PF05603_consen 73 NEKPSAIFKISWPEDDMLDSGSPSSNNSSGTAQIGISIEPLAQIAQQLAALKAQQSSQSSSAMSSSSSSSAQSPDSTKEF 152 (202)
T ss_pred CCCCceEEEcCCcccccccccCcccCCCCceEEEEEeeCcHHHHHHHHHhhhccccccccccccccccccccccccHHHH
Confidence 99999999999953321111 001125568999999999999998753221 1378999
Q ss_pred HHHHHHHHhhhhcccccCC--CCeeEEehHHHHHHHHHHHHHHhcCcccc
Q 041772 136 AMKVGENLFNFMQSFCGVD--GSKLIVPMDILDRWFKKFQEKAKRDPEYL 183 (188)
Q Consensus 136 A~ki~~nlfNyl~SF~~~~--~~~~~VP~~~~~~W~~kF~~Kl~~dP~Fl 183 (188)
|+||++||||||+||++++ +++++||+++||+||+|||+||++||+||
T Consensus 153 A~ki~~NlfNyl~SF~~~~~~~~~~~VP~~~~~~W~~kFe~Kl~~dP~Fl 202 (202)
T PF05603_consen 153 AQKIAENLFNYLSSFSGSQPQGGEEVVPLSVFDKWWEKFERKLRNDPNFL 202 (202)
T ss_pred HHHHHHHHHHHHHhccCCCCCCCceEEeHHHHHHHHHHHHHHHhcCCCCC
Confidence 9999999999999999985 57899999999999999999999999998
No 2
>KOG4067 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=6.6e-63 Score=401.98 Aligned_cols=179 Identities=33% Similarity=0.594 Sum_probs=157.8
Q ss_pred CeEEEcCCCCcCcccCcceeeCCceEEEEccCCccCCCCCcceEEEEecCCCCCCCCceEEEEEEcCCC-CceEeeeecC
Q 041772 1 MFGVVFPNRSFPMDISTFSQIDTFHWILDMNSFVGEAYDQVRDMCIFLLNNFTLPPDKALAVYIQSPGS-PFLYCGAVTV 79 (188)
Q Consensus 1 MFG~iv~Grp~~~~~t~f~qv~~~~~~~~l~~~~~~~~~~v~hivVFLl~~~~~p~g~~a~VY~~~P~~-~w~~LG~isn 79 (188)
|||||++|| ++|++++|||++||++++ +++++||||||||||+.|||+|+||+|||+||++ +|+|||+|+|
T Consensus 1 mFG~IvsGR---~~q~~~~qv~~~~~v~~l-----~~~esinhvvvFLl~n~pfP~g~~asVYf~~P~~~~f~~lG~vtn 72 (195)
T KOG4067|consen 1 MFGVIVSGR---LPQSEVVQVDDTQFVFDL-----PDYESINHVVVFLLGNSPFPVGMGASVYFQWPGQPEFQLLGFVTN 72 (195)
T ss_pred CeeEEecCC---CCccceeeecCcEEEEee-----CChhHhcEEEEEEeCCcCCCCCceeEEEEeCCCCCceEEEeeecC
Confidence 999999999 668999999999999999 7999999999999999999999999999999998 9999999999
Q ss_pred CCCceEEECCCCCCCCCCccc----CCCCCCceeEEEEeeccccccccccc---cchhHHHHHHHHHHHHHhhhhccccc
Q 041772 80 ARPSAVLSLPWPEPGGGMQLT----APDSTPLSAKIGVSVEDLTSLPSLDV---TAEKRIERLAMKVGENLFNFMQSFCG 152 (188)
Q Consensus 80 ~KPSaIFk~~~~~~~~~~~~~----~~~~~~~~~~IGISiEpl~~i~~~~~---~~~~~~~~~A~ki~~nlfNyl~SF~~ 152 (188)
+||||||||.|+++.++..+. +.......++||||+||++...+.+. +.....+.+|+||.+|+||||+||++
T Consensus 73 eKPSAIfkv~~~~~~dgs~~~~~fg~~n~~s~ia~iGVSvEp~~~~a~~~~N~vs~~~~~~~~aqki~~nf~Nf~qsfa~ 152 (195)
T KOG4067|consen 73 EKPSAIFKVQQPKSGDGSGHADPFGDTNISSNIAQIGVSVEPLETSAQSTPNAVSLSRPNKSFAQKILTNFFNFMQSFAV 152 (195)
T ss_pred CCCceeEEEecccccchhhccCccccccccchhheeeeeeccchhhhhcCCCceeecCchHHHHHHHHHHHHHHHHHHhh
Confidence 999999999999988765321 11111234999999999997655443 23456789999999999999999999
Q ss_pred CC-------CCeeEEehHHHHHHHHHHHHHHhcCcccccccC
Q 041772 153 VD-------GSKLIVPMDILDRWFKKFQEKAKRDPEYLKGFA 187 (188)
Q Consensus 153 ~~-------~~~~~VP~~~~~~W~~kF~~Kl~~dP~Fl~~~~ 187 (188)
.. +.+++||++++|+||+||++|+++||+|||..+
T Consensus 153 ~~~q~~~n~~s~~~VP~~v~~~W~~kFq~rl~~npnFlk~~~ 194 (195)
T KOG4067|consen 153 SIAQIPPNLPSETFVPIRVFDDWYDKFQNRLANNPNFLKSVT 194 (195)
T ss_pred hhhccCCCCcccccccHHHHHHHHHHHHHHHhcCCchHhhhc
Confidence 74 568999999999999999999999999999864
No 3
>PF04711 ApoA-II: Apolipoprotein A-II (ApoA-II); InterPro: IPR006801 Apolipoprotein A-II (ApoA-II) is the second major apolipoprotein of high density lipoprotein in human plasma. Mature ApoA-II is present as a dimer of two 77-amino acid chains joined by a disulphide bridge []. ApoA-II regulates many steps in HDL metabolism, and its role in coronary heart disease is unclear []. In bovine serum, the ApoA-II homologue is present in almost free form. Bovine ApoA-II shows antimicrobial activity against Escherichia coli and yeasts in phosphate buffered saline (PBS) [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0042157 lipoprotein metabolic process, 0005576 extracellular region; PDB: 1L6L_W 2OU1_E.
Probab=70.81 E-value=2.1 Score=30.72 Aligned_cols=23 Identities=35% Similarity=0.681 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHHHhhhhccccc
Q 041772 130 KRIERLAMKVGENLFNFMQSFCG 152 (188)
Q Consensus 130 ~~~~~~A~ki~~nlfNyl~SF~~ 152 (188)
....-+++|.+.+|+||++||..
T Consensus 47 eQltPlvkKagtdl~nflS~~v~ 69 (76)
T PF04711_consen 47 EQLTPLVKKAGTDLMNFLSSFVE 69 (76)
T ss_dssp HHHHHHHHGGHHTHHHHHHHHHH
T ss_pred HHHhHHHHHHhHHHHHHHHHhhc
Confidence 34566999999999999999964
No 4
>PF15187 Augurin: Oesophageal cancer-related gene 4
Probab=49.23 E-value=9.8 Score=29.12 Aligned_cols=23 Identities=22% Similarity=0.562 Sum_probs=20.1
Q ss_pred HHHHHHHHH------HHHHhcCccccccc
Q 041772 164 ILDRWFKKF------QEKAKRDPEYLKGF 186 (188)
Q Consensus 164 ~~~~W~~kF------~~Kl~~dP~Fl~~~ 186 (188)
-+++||+.| |.|++.|-++|...
T Consensus 49 dVQQW~qQFlYmGFDEak~E~DlsYWm~~ 77 (114)
T PF15187_consen 49 DVQQWYQQFLYMGFDEAKFEDDLSYWMNR 77 (114)
T ss_pred HHHHHHHHHHHhcchHHHhhhhHHHHHhc
Confidence 479999999 79999999999754
No 5
>PF09195 Endonuc-BglII: Restriction endonuclease BglII; InterPro: IPR015278 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents BglII restriction endonucleases, which recognise AGATCT and cleaves after A-1 [, ]. BglII adopts a structure consisting of an alpha/beta core containing a six-stranded beta-sheet surrounded by five alpha-helices, two of which are involved in homodimerisation of the endonuclease.; PDB: 1DFM_B 1D2I_B 1ES8_A 2P0J_B 1VRR_A 1SDO_A.
Probab=40.06 E-value=13 Score=30.10 Aligned_cols=40 Identities=18% Similarity=0.346 Sum_probs=31.4
Q ss_pred HHHHHhhhhcccccCC--CCeeEEehHHHHH----------HHHHHHHHHhc
Q 041772 139 VGENLFNFMQSFCGVD--GSKLIVPMDILDR----------WFKKFQEKAKR 178 (188)
Q Consensus 139 i~~nlfNyl~SF~~~~--~~~~~VP~~~~~~----------W~~kF~~Kl~~ 178 (188)
+..||++|...|.... -+-.++|++.|++ ||+|...||++
T Consensus 98 ~~~DL~~~~~~~~~~~IdvGIiIt~~~~l~~~~~~~~s~~~~~ek~~~~l~~ 149 (164)
T PF09195_consen 98 FYRDLLKFQLFYESGAIDVGIIITPTKSLQKRSDKMGSGTTYYEKLVYRLRR 149 (164)
T ss_dssp HHHHHHCHHHHHHTTS-SEEEEEEE-CCCHT---TSSTTB--HHHHHHHHCC
T ss_pred HHHHHHHHHHHhhcCCceEEEEEecCHHHHhhcccCCcceeeHHHHHHHHHc
Confidence 5589999888887654 3578999999999 99999999965
No 6
>PF03475 3-alpha: 3-alpha domain; InterPro: IPR005163 This small triple helical domain has been predicted to assume a topology similar to helix-turn-helix domains. These domains are found at the C terminus of proteins related to the YiiM protein (P32157 from SWISSPROT) from Escherichia coli.; PDB: 1O67_C 1O65_C.
Probab=34.17 E-value=29 Score=21.96 Aligned_cols=14 Identities=21% Similarity=0.736 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHhc
Q 041772 165 LDRWFKKFQEKAKR 178 (188)
Q Consensus 165 ~~~W~~kF~~Kl~~ 178 (188)
=..|.++|++|+++
T Consensus 31 a~~Wr~~~~kRL~~ 44 (47)
T PF03475_consen 31 AESWRKSFEKRLEK 44 (47)
T ss_dssp -HHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHc
Confidence 36899999999975
No 7
>PF08987 DUF1892: Protein of unknown function (DUF1892); InterPro: IPR015080 Proteins in this entry, which are synthesised by Saccharomycetes, adopt a structure consisting of a four-stranded beta-sheet, with strand order beta2-beta1-beta4-beta3, and two alpha-helices, with an overall topology of beta-beta-alpha-beta-beta-alpha. They have no known function []. ; PDB: 1N6Z_A.
Probab=30.89 E-value=45 Score=25.84 Aligned_cols=17 Identities=41% Similarity=0.819 Sum_probs=14.6
Q ss_pred hHHHHHHHHHHHHHHhc
Q 041772 162 MDILDRWFKKFQEKAKR 178 (188)
Q Consensus 162 ~~~~~~W~~kF~~Kl~~ 178 (188)
++.++.|++||-.++.-
T Consensus 51 ~d~lN~wFDkFDEeIci 67 (115)
T PF08987_consen 51 FDELNEWFDKFDEEICI 67 (115)
T ss_dssp HHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHhhcceeec
Confidence 56899999999998865
No 8
>KOG1966 consensus Sodium/hydrogen exchanger protein [Inorganic ion transport and metabolism]
Probab=30.18 E-value=37 Score=33.47 Aligned_cols=64 Identities=14% Similarity=0.234 Sum_probs=48.5
Q ss_pred EEEeecccccccc---ccccchhHHHHHHHHHHHHHhhhhcccccCCCCeeEEehHHHHHHHHHHHHHH
Q 041772 111 IGVSVEDLTSLPS---LDVTAEKRIERLAMKVGENLFNFMQSFCGVDGSKLIVPMDILDRWFKKFQEKA 176 (188)
Q Consensus 111 IGISiEpl~~i~~---~~~~~~~~~~~~A~ki~~nlfNyl~SF~~~~~~~~~VP~~~~~~W~~kF~~Kl 176 (188)
-||.|.|+.+.-+ .+...+.-.+++.+|..+++.-+++-.++..|. +-+.+.+++|-+|+.+|+
T Consensus 436 QGiTIkplvk~L~Vk~~~~~~~~m~e~i~~~~~dhlm~gIEDi~G~~gh--~~~rdk~~~fn~kylrp~ 502 (670)
T KOG1966|consen 436 QGITIKPLVKFLKVKRKNKRDPTMNEEIYNRLLDHLMAGIEDIAGQKGH--YYWRDKFERFNNKYLRPL 502 (670)
T ss_pred cccchHHHHHHHccccccccCchhhHHHHHHHHHHHHHHHHHHhccccc--chhhhhHHHHHhhhchHH
Confidence 4889999988554 233344456889999999999999888876553 577888888888887776
No 9
>PF04254 DUF432: Protein of unknown function (DUF432); InterPro: IPR007366 This is an archaeal protein of unknown function.
Probab=29.36 E-value=1.1e+02 Score=23.63 Aligned_cols=44 Identities=16% Similarity=0.362 Sum_probs=33.1
Q ss_pred CCcceEEEEecCCCCCCCCceEEEEEEcCCC---------CceEeeeecCCCC
Q 041772 39 DQVRDMCIFLLNNFTLPPDKALAVYIQSPGS---------PFLYCGAVTVARP 82 (188)
Q Consensus 39 ~~v~hivVFLl~~~~~p~g~~a~VY~~~P~~---------~w~~LG~isn~KP 82 (188)
.-.+++.|-|-..+.+|||-...+|+..|=+ +.+.|..++-.|+
T Consensus 8 ~~t~~l~i~f~~pi~v~P~~~~~iyv~~PveI~V~~~~~~~~~~iD~~~~~~~ 60 (123)
T PF04254_consen 8 YITNYLLIRFEEPIVVPPGSSVTIYVSFPVEIGVFVGSGDNYRLIDVFPLGRP 60 (123)
T ss_pred ccceEEEEEcCCCEEECCCCcEEEEEEccEEEEEEEccCCcceEEEEeccCce
Confidence 4467788888788888999999999999942 4566666555544
No 10
>PRK06330 transcript cleavage factor/unknown domain fusion protein; Validated
Probab=25.38 E-value=47 Score=33.21 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=24.8
Q ss_pred eEEehHHHHHHHHHHHHHHhcCccccc
Q 041772 158 LIVPMDILDRWFKKFQEKAKRDPEYLK 184 (188)
Q Consensus 158 ~~VP~~~~~~W~~kF~~Kl~~dP~Fl~ 184 (188)
.|+|-+-..+||++=..+++.||.|--
T Consensus 239 ~vi~~~~W~kWW~~aKk~lKkd~~i~~ 265 (718)
T PRK06330 239 LVIPEADWSRWWQSAKAKIKKDTRIET 265 (718)
T ss_pred hhCCHHHHHHHHHHHHHHHhhCCcccC
Confidence 589999999999999999999999854
No 11
>KOG4439 consensus RNA polymerase II transcription termination factor TTF2/lodestar, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=25.01 E-value=59 Score=32.86 Aligned_cols=45 Identities=11% Similarity=0.194 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHhhhhcccccCCCCeeEEehHHHHHHHHHHHHHHhcC
Q 041772 133 ERLAMKVGENLFNFMQSFCGVDGSKLIVPMDILDRWFKKFQEKAKRD 179 (188)
Q Consensus 133 ~~~A~ki~~nlfNyl~SF~~~~~~~~~VP~~~~~~W~~kF~~Kl~~d 179 (188)
.-+++|..+.+=+= .|......-.++|++++.+|+.-+++|+..|
T Consensus 365 lil~qK~~~~~~~~--~~~~a~~TLII~PaSli~qW~~Ev~~rl~~n 409 (901)
T KOG4439|consen 365 LILHQKAARKAREK--KGESASKTLIICPASLIHQWEAEVARRLEQN 409 (901)
T ss_pred HHHHHHHHHHhhcc--cccccCCeEEeCcHHHHHHHHHHHHHHHhhc
Confidence 34677777766441 1211112236899999999999999999886
No 12
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=24.87 E-value=1.3e+02 Score=29.31 Aligned_cols=40 Identities=15% Similarity=0.219 Sum_probs=27.7
Q ss_pred EEEecCCCCCCCCceEEEEEEcCC----CCceEeeeecCCCCceEEECCCCCC
Q 041772 45 CIFLLNNFTLPPDKALAVYIQSPG----SPFLYCGAVTVARPSAVLSLPWPEP 93 (188)
Q Consensus 45 vVFLl~~~~~p~g~~a~VY~~~P~----~~w~~LG~isn~KPSaIFk~~~~~~ 93 (188)
|||.-=.-..+||....+||.+.. ..|-.+| ||||+|.+.
T Consensus 7 ViF~nV~~~Y~P~~~v~C~Ytlt~~~~ps~~DWIG---------iFKVGw~s~ 50 (546)
T PF07888_consen 7 VIFNNVAKSYIPGTDVECHYTLTPGFHPSSKDWIG---------IFKVGWSST 50 (546)
T ss_pred EEEeccccccCCCCCeEEEEecCCCCCCCCCCeeE---------EeecCCCch
Confidence 566533334488888999999743 3666666 999998654
No 13
>PF09175 DUF1944: Domain of unknown function (DUF1944); InterPro: IPR015258 Vitellinogen precursors provide the major egg yolk proteins that are a source of nutrients during early development of oviparous vertebrates and invertebrates. Vitellinogen precursors are multi-domain apolipoproteins that are cleaved into distinct yolk proteins. Different vitellinogen precursors exist, which are composed of variable combinations of yolk protein components; however, the cleavage sites are conserved [, ]. In vertebrates, a complete vitellinogen is composed of an N-terminal signal peptide for export, followed by four regions that can be cleaved into yolk proteins: lipovitellin-1, phosvitin, lipovitellin-2, and a von Willebrand factor type D domain (YGP40). Vitellinogens are post-translationally glycosylated and phosphorylated in the endoplasmic reticulum and Golgi complex of hepatocytes, before being secreted into the circulatory system to be taken up by oocytes. In the ovary, vitellinogens bind to specific Vtgr receptors on oocyte membranes to become internalised by endocytosis, where they are cleaved into yolk proteins by cathepsin D. YGP40 is released into the yolk plasma before or during compartmentation of lipovitellin-phosvitin complex into the yolk granule. The different yolk proteins have distinct roles. Phosvitins are important in sequestering calcium, iron and other cations for the developing embryo. Phosvitins are one of the most phosphorylated (10%) proteins in nature, the high concentration of phosphate groups providing efficient metal-binding sites in clusters [, ]. Lipovitellins are involved in lipid and metal storage, and contain a heterogeneous mixture of about 16% (w/w) noncovalently bound lipid, most being phospholipid. Lipovitellin-1 contains two chains, LV1N and LV1C [, ]. This entry represents the beta-sheet shell domain found in vitellinogen, which generally corresponds to the lipovitellin-2 peptide product. This domain consists of several large open beta-sheets []. It is often found C-terminal to IPR001747 from INTERPRO and IPR015255 from INTERPRO. ; GO: 0005319 lipid transporter activity, 0006869 lipid transport; PDB: 1LSH_B.
Probab=24.84 E-value=2.4e+02 Score=23.07 Aligned_cols=85 Identities=21% Similarity=0.322 Sum_probs=43.9
Q ss_pred CCCceEEEEEEcCC-------------CCceEee---eecCCCCceEEECCCCCCCCCCcccCCCCCCceeEEEEeecc-
Q 041772 55 PPDKALAVYIQSPG-------------SPFLYCG---AVTVARPSAVLSLPWPEPGGGMQLTAPDSTPLSAKIGVSVED- 117 (188)
Q Consensus 55 p~g~~a~VY~~~P~-------------~~w~~LG---~isn~KPSaIFk~~~~~~~~~~~~~~~~~~~~~~~IGISiEp- 117 (188)
+.||-+++|+-.+. ++|+++. .++..| +.=+++|-.. +..-.+-|..|-
T Consensus 16 ~~GYQ~a~Y~d~~~~rvQlivs~l~e~~nWk~CaD~~~ls~hK--~~A~l~WG~e------------Cq~Y~~~~~aeTG 81 (165)
T PF09175_consen 16 PQGYQLAAYYDKPTSRVQLIVSNLAENSNWKICADAVLLSKHK--AKAKLAWGAE------------CQQYKVSITAETG 81 (165)
T ss_dssp --EEEEEEEEE-TTTSEEEEEEES-TT---EEEEEEE--SSSE--EEEEEEESSS------------S-SEEEEEEEEEE
T ss_pred ceeeEEEEEEcCCCceEEEEEEecCcCCCeEEEehhhcccccc--eEEEEecchh------------hhheeeeeeehhh
Confidence 67888999988763 4899997 456666 5666767322 222222222221
Q ss_pred ------ccccccccccchhHHHHHHHHHHHHH--hhhhcccccC
Q 041772 118 ------LTSLPSLDVTAEKRIERLAMKVGENL--FNFMQSFCGV 153 (188)
Q Consensus 118 ------l~~i~~~~~~~~~~~~~~A~ki~~nl--fNyl~SF~~~ 153 (188)
...+.-.=..-+...+++++++-+.. .-||.+|...
T Consensus 82 ~~g~~PA~r~kv~W~~lP~~~k~~~k~~~~yIpg~a~~~Gf~~~ 125 (165)
T PF09175_consen 82 LLGSKPAARLKVEWPRLPSSMKRYAKRVYEYIPGAAYLLGFSQK 125 (165)
T ss_dssp ESSSSEEEEEEEEE----HHHHHHHHHHHHTHHHHHHTTT-EEE
T ss_pred cccCCcceEEEeecccCcHHHHHHHHHHHHhccchHHHcCcchh
Confidence 11111100123567788999999988 8899999864
No 14
>KOG1110 consensus Putative steroid membrane receptor Hpr6.6/25-Dx [General function prediction only]
Probab=23.08 E-value=50 Score=27.60 Aligned_cols=19 Identities=26% Similarity=0.517 Sum_probs=16.2
Q ss_pred EehHHHHHHHHHHHHHHhc
Q 041772 160 VPMDILDRWFKKFQEKAKR 178 (188)
Q Consensus 160 VP~~~~~~W~~kF~~Kl~~ 178 (188)
.=++++++|-.+|+.|+..
T Consensus 131 ~e~eal~eWE~~fk~KY~~ 149 (183)
T KOG1110|consen 131 EELEALNEWETKFKAKYPV 149 (183)
T ss_pred HHHHHHHHHHHHHhhcCce
Confidence 4578999999999999853
No 15
>PF01846 FF: FF domain; InterPro: IPR002713 The FF domain may be involved in protein-protein interaction []. It often occurs as multiple copies and often accompanies WW domains IPR001202 from INTERPRO. PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [].; PDB: 3HFH_B 2KIS_A 2DOD_A 2JUC_A 2LKS_A 1UZC_A 2KZG_A 2L9V_A 2DOF_A 2KFD_A ....
Probab=21.67 E-value=57 Score=20.51 Aligned_cols=16 Identities=25% Similarity=0.623 Sum_probs=13.6
Q ss_pred HHHHHHHHhcCccccc
Q 041772 169 FKKFQEKAKRDPEYLK 184 (188)
Q Consensus 169 ~~kF~~Kl~~dP~Fl~ 184 (188)
|+.+.+++..||.|+.
T Consensus 21 W~~~~~~l~~dpry~~ 36 (51)
T PF01846_consen 21 WEEVKPKLSKDPRYKA 36 (51)
T ss_dssp HHHHHHHHTTSCHHHH
T ss_pred HHHHHHHHccCHHHHH
Confidence 5689999999999864
No 16
>PRK14720 transcript cleavage factor/unknown domain fusion protein; Provisional
Probab=21.62 E-value=62 Score=33.27 Aligned_cols=54 Identities=17% Similarity=0.309 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHH----hhhhcccccC-C-----C--CeeEEehHHHHHHHHHHHHHHhcCcccccc
Q 041772 132 IERLAMKVGENL----FNFMQSFCGV-D-----G--SKLIVPMDILDRWFKKFQEKAKRDPEYLKG 185 (188)
Q Consensus 132 ~~~~A~ki~~nl----fNyl~SF~~~-~-----~--~~~~VP~~~~~~W~~kF~~Kl~~dP~Fl~~ 185 (188)
..++.+++.+|. ---|.||... + . -..|+|-+-..+||++=..+++.||+|--.
T Consensus 368 ~~~l~~~~~~dp~~~ik~~lks~~~~~t~~~ik~eL~~~vi~~~~W~kWw~~aKk~lkkd~~~~~~ 433 (906)
T PRK14720 368 KEELVDKFKKDIPWALKTIIKSYDNRMDLKDIKSELVPSLLTQSEWSKWSTKAKQILKKNPNFGMD 433 (906)
T ss_pred HHHHHHHHHhCHHHHHHHHHHhcCCccCHHHHHHHHHHhhCCHHHHHHHHHHHHHHHhhCCcccCC
Confidence 344555555553 4456788652 1 0 136899999999999999999999998654
No 17
>PF14969 DUF4508: Domain of unknown function (DUF4508)
Probab=20.61 E-value=63 Score=24.39 Aligned_cols=47 Identities=23% Similarity=0.572 Sum_probs=29.3
Q ss_pred HHHHhhhhcccccCC--CCeeEEehHHHHHHHH--------HHHHHHhc-Cccccccc
Q 041772 140 GENLFNFMQSFCGVD--GSKLIVPMDILDRWFK--------KFQEKAKR-DPEYLKGF 186 (188)
Q Consensus 140 ~~nlfNyl~SF~~~~--~~~~~VP~~~~~~W~~--------kF~~Kl~~-dP~Fl~~~ 186 (188)
+.-|.+=|++-+..+ ++--=.=++.+++|+. +|.+||+. ||+|-.+.
T Consensus 36 v~~Ll~~l~~l~v~dkppsiFqCqlkLf~qWf~~W~~~ern~fl~~Lee~D~~f~~k~ 93 (98)
T PF14969_consen 36 VNGLLDSLENLSVQDKPPSIFQCQLKLFRQWFPKWSEEERNKFLEQLEEIDPDFVAKF 93 (98)
T ss_pred HHHHHHHHHhCcCCCCCCcHHHHhHHHHHHHHhhccHHHHHHHHHHHHHhChHHHHHH
Confidence 445556566555533 1211145678889974 58888887 99987653
No 18
>PF11514 DUF3219: Protein of unknown function (DUF3219); InterPro: IPR021596 This family of proteins with unknown function appears to be restricted to Bacillaceae. Some members in this family of proteins are annotated as YkvR however this cannot be confirmed. ; PDB: 2JN9_A.
Probab=20.46 E-value=55 Score=24.65 Aligned_cols=44 Identities=14% Similarity=0.270 Sum_probs=30.0
Q ss_pred eEEEEccCCccCCCCCcceEEEEecCCCCCCCCceEEEEEEcCCCCceEeeeecCCCCc
Q 041772 25 HWILDMNSFVGEAYDQVRDMCIFLLNNFTLPPDKALAVYIQSPGSPFLYCGAVTVARPS 83 (188)
Q Consensus 25 ~~~~~l~~~~~~~~~~v~hivVFLl~~~~~p~g~~a~VY~~~P~~~w~~LG~isn~KPS 83 (188)
.|.|.+ ..+..++|++-| |-....++.|..+-.|.|.|.|.--|
T Consensus 31 sf~fkV------tSe~YHDIatLL---------Ye~tFdV~vPe~~l~FrgtI~~YsTS 74 (99)
T PF11514_consen 31 SFDFKV------TSEEYHDIATLL---------YEKTFDVEVPERDLEFRGTITNYSTS 74 (99)
T ss_dssp EEEEEE-------TTTHHHHTT-B---------S-S-EEEEETTTTEEEEEB--S-SS-
T ss_pred EEEEEe------ccchhhHHHHhh---------hhceeeeecCcccceeeeehhhheeh
Confidence 466666 567889999888 55667889999999999999998765
Done!