Query psy6159
Match_columns 101
No_of_seqs 115 out of 121
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 19:08:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6159.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6159hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3922|consensus 99.7 2.5E-18 5.4E-23 141.1 2.9 75 1-80 246-323 (361)
2 PF03567 Sulfotransfer_2: Sulf 92.0 0.18 3.9E-06 35.9 3.1 37 4-40 167-203 (253)
3 PF06990 Gal-3-0_sulfotr: Gala 63.0 8.9 0.00019 32.2 3.3 59 2-70 234-292 (402)
4 KOG2878|consensus 26.1 38 0.00083 27.8 1.3 19 17-35 10-28 (282)
5 KOG3043|consensus 24.6 29 0.00062 28.2 0.4 61 25-98 70-136 (242)
6 PF10985 DUF2805: Protein of u 23.7 44 0.00095 22.6 1.1 19 61-79 26-44 (73)
7 COG4769 Predicted membrane pro 22.7 16 0.00035 28.5 -1.3 31 5-35 7-37 (181)
8 PF07932 DAP_C: D-aminopeptida 22.2 38 0.00083 24.1 0.6 13 84-96 80-92 (97)
9 TIGR03643 conserved hypothetic 22.1 54 0.0012 22.2 1.3 19 61-79 27-45 (72)
10 PHA00002 A DNA replication ini 21.6 71 0.0015 28.2 2.2 61 7-70 31-91 (515)
11 KOG2181|consensus 20.3 42 0.00092 28.9 0.6 17 25-41 105-126 (415)
No 1
>KOG3922|consensus
Probab=99.71 E-value=2.5e-18 Score=141.14 Aligned_cols=75 Identities=23% Similarity=0.391 Sum_probs=58.8
Q ss_pred CcccceeeEEeeehhhhHHHHHHHHhhchhhhhHHHHHhcc-cccccccccccccCCCCCCCHHHHHHHHhC--CCcccc
Q psy6159 1 MAVEKHYAVVGLLEDLNVTLTVMENYIPRFFAHASQIYNEG-RLDRWIGERQPFREQTLSVEDKIRQERESN--PRPSAY 77 (101)
Q Consensus 1 ~NVe~~Y~vVGilEeln~tL~VLE~~lPrfFkGA~~~Y~~~-~~~~~~~tkn~~Kp~~~~~Seev~~~lr~n--~t~E~~ 77 (101)
.||+++|++|||+|||+++|.+||+++||||+||+++|.+. +.++.+ +++++|| ||+++.++++++ +++|..
T Consensus 246 ~nv~e~y~LVGvtEel~d~l~LLE~~lPrfFkGv~~iY~~~~~~~hlr-~t~~k~p----Ps~etvk~i~r~~~~~mE~e 320 (361)
T KOG3922|consen 246 FNVEEEYLLVGVTEELEDFLSLLERYLPRFFKGVREIYATSAKKSHLR-VTNKKKP----PSSETVKDIQRRMIYKMENE 320 (361)
T ss_pred HHHhhhheeeeeHHHHHHHHHHHHHHhHHHHHHHHHHHhhhhhhhcee-eecccCC----CCHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999999999999999999999999964 444333 3345565 777777777665 566655
Q ss_pred ccc
Q psy6159 78 KAD 80 (101)
Q Consensus 78 ~~~ 80 (101)
-||
T Consensus 321 fY~ 323 (361)
T KOG3922|consen 321 FYD 323 (361)
T ss_pred HHH
Confidence 554
No 2
>PF03567 Sulfotransfer_2: Sulfotransferase family; InterPro: IPR005331 This entry consists of a number of carbohydrate sulphotransferases that transfer sulphate to carbohydrate groups in glycoproteins and glycolipids. These include: Carbohydrate sulphotransferases 8 and 9, which transfer sulphate to position 4 of non-reducing N-acetylgalactosamine (GalNAc) residues in both N-glycans and O-glycans []. They function in the biosynthesis of glycoprotein hormones lutropin and thyrotropin, by mediating sulphation of their carbohydrate structures. Carbohydrate sulphotransferase 10, which transfers sulphate to position 3 of the terminal glucuronic acid in both protein- and lipid-linked oligosaccharides []. It directs the biosynthesis of the HNK-1 carbohydrate structure, a sulphated glucuronyl-lactosaminyl residue carried by many neural recognition molecules, which is involved in cell interactions during ontogenetic development and in synaptic plasticity in the adult. Carbohydrate sulphotransferases 11 - 13, which catalyze the transfer of sulphate to position 4 of the GalNAc residue of chondroitin []. Chondroitin sulphate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Some, thought not all, of these enzymes also transfer sulphate to dermatan. Carbohydrate sulphotransferase D4ST1, which transfers sulphate to position 4 of the GalNAc residue of dermatan sulphate []. Heparan sulphate 2-O-sulphotransferase (HS2ST). Heparan sulphate (HS) is a co-receptor for a number of growth factors, morphogens, and adhesion proteins. HS biosynthetic modifications may determine the strength and outcome of HS-ligand interactions. Mice that lack HS2ST undergo developmental failure only after midgestation,the most dramatic effect being the complete failure of kidney development []. Heparan-sulphate 6-O-sulphotransferase (HS6ST), which catalyses the transfer of sulphate from adenosine 3'-phosphate, 5'-phosphosulphate to the 6th position of the N -sulphoglucosamine residue in heparan sulphate []. Chondroitin 6-sulphotransferase catalyses the transfer of sulphate to position 6 of the N-acetylgalactosamine residue of chondroitin []. ; GO: 0008146 sulfotransferase activity, 0016021 integral to membrane; PDB: 3F5F_A.
Probab=91.99 E-value=0.18 Score=35.87 Aligned_cols=37 Identities=24% Similarity=0.468 Sum_probs=31.3
Q ss_pred cceeeEEeeehhhhHHHHHHHHhhchhhhhHHHHHhc
Q psy6159 4 EKHYAVVGLLEDLNVTLTVMENYIPRFFAHASQIYNE 40 (101)
Q Consensus 4 e~~Y~vVGilEeln~tL~VLE~~lPrfFkGA~~~Y~~ 40 (101)
..+|-+||.+|++++.+..|...+..++.+....+..
T Consensus 167 ~~~~d~Vg~~E~~~~~~~~l~~~~~~~~~~~~~~~~~ 203 (253)
T PF03567_consen 167 LRDYDFVGRLENFDEDLRRLLRLLGLFFENGPPFFNL 203 (253)
T ss_dssp HHTEEEEEEGGGHHHHHHHHHHH-HHHHTTHHHHHHT
T ss_pred ccccceeeecccHHHHHHHHHHhhhhhhhcCccchhc
Confidence 4579999999999999999999999988888877443
No 3
>PF06990 Gal-3-0_sulfotr: Galactose-3-O-sulfotransferase ; InterPro: IPR009729 This family consists of several mammalian galactose-3-O-sulphotransferase proteins. Gal-3-O-sulphotransferase is thought to play a critical role in 3'-sulphation of N-acetyllactosamine in both O- and N-glycans [].; GO: 0001733 galactosylceramide sulfotransferase activity, 0009058 biosynthetic process, 0005794 Golgi apparatus, 0016021 integral to membrane
Probab=62.98 E-value=8.9 Score=32.22 Aligned_cols=59 Identities=10% Similarity=0.189 Sum_probs=37.8
Q ss_pred cccceeeEEeeehhhhHHHHHHHHhhchhhhhHHHHHhcccccccccccccccCCCCCCCHHHHHHHHh
Q psy6159 2 AVEKHYAVVGLLEDLNVTLTVMENYIPRFFAHASQIYNEGRLDRWIGERQPFREQTLSVEDKIRQERES 70 (101)
Q Consensus 2 NVe~~Y~vVGilEeln~tL~VLE~~lPrfFkGA~~~Y~~~~~~~~~~tkn~~Kp~~~~~Seev~~~lr~ 70 (101)
.++++|-+|.|+|-++++|-+|=+.+===..++. |.. .|..+...+. .+|++.++.+++
T Consensus 234 ~le~~F~LVLI~EyfDESLVLLk~~LCW~l~DIl--y~~-----~N~r~~~~~~---~ls~~~~~~ir~ 292 (402)
T PF06990_consen 234 ELERRFDLVLIAEYFDESLVLLKRLLCWDLEDIL--YFK-----LNARSASSVS---RLSPELREKIRK 292 (402)
T ss_pred HhcccCcEEEEeHhHHHHHHHHHHHhCCCHHHhh--hhh-----hcCccccccC---CCCHHHHHHHHH
Confidence 4678999999999999999999887741111111 211 1111222234 689999988765
No 4
>KOG2878|consensus
Probab=26.06 E-value=38 Score=27.85 Aligned_cols=19 Identities=26% Similarity=0.630 Sum_probs=15.5
Q ss_pred hHHHHHHHHhhchhhhhHH
Q psy6159 17 NVTLTVMENYIPRFFAHAS 35 (101)
Q Consensus 17 n~tL~VLE~~lPrfFkGA~ 35 (101)
.-+++.|++|+|.||+.-.
T Consensus 10 d~~~~fl~kyiP~~f~~G~ 28 (282)
T KOG2878|consen 10 DQKARFLHKYIPVFFKDGD 28 (282)
T ss_pred HHHHHHHHhhCcccccCCC
Confidence 4568999999999997654
No 5
>KOG3043|consensus
Probab=24.55 E-value=29 Score=28.20 Aligned_cols=61 Identities=20% Similarity=0.409 Sum_probs=33.1
Q ss_pred HhhchhhhhHHHHHhccccc----ccccccccccCCCCCCCHHHHHHHHhCCCccccccccCccceee-e-eeeehhhcc
Q psy6159 25 NYIPRFFAHASQIYNEGRLD----RWIGERQPFREQTLSVEDKIRQERESNPRPSAYKADAQPTKLTI-G-CRLANFILT 98 (101)
Q Consensus 25 ~~lPrfFkGA~~~Y~~~~~~----~~~~tkn~~Kp~~~~~Seev~~~lr~n~t~E~~~~~~~~~~~~~-~-~~~~~~~~~ 98 (101)
.++|.||+| +-|..+.+. .+.+..+.-+ .-+++..++ |.||..+|+.|+-+ | |-=|-+..+
T Consensus 70 v~vPD~~~G--dp~~~~~~~~~~~~w~~~~~~~~-----~~~~i~~v~------k~lk~~g~~kkIGv~GfCwGak~vv~ 136 (242)
T KOG3043|consen 70 VLVPDFFRG--DPWSPSLQKSERPEWMKGHSPPK-----IWKDITAVV------KWLKNHGDSKKIGVVGFCWGAKVVVT 136 (242)
T ss_pred EEcchhhcC--CCCCCCCChhhhHHHHhcCCccc-----chhHHHHHH------HHHHHcCCcceeeEEEEeecceEEEE
Confidence 479999999 444333111 2222222222 345555555 67888999988754 1 444444333
No 6
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=23.66 E-value=44 Score=22.64 Aligned_cols=19 Identities=21% Similarity=0.401 Sum_probs=16.7
Q ss_pred CHHHHHHHHhCCCcccccc
Q psy6159 61 EDKIRQERESNPRPSAYKA 79 (101)
Q Consensus 61 Seev~~~lr~n~t~E~~~~ 79 (101)
..+++++||++|+..++|.
T Consensus 26 E~eVi~lMR~~Lk~~sfk~ 44 (73)
T PF10985_consen 26 EKEVIKLMRKELKPSSFKL 44 (73)
T ss_pred HHHHHHHHHhhcChhHHHH
Confidence 5789999999999998874
No 7
>COG4769 Predicted membrane protein [Function unknown]
Probab=22.74 E-value=16 Score=28.49 Aligned_cols=31 Identities=35% Similarity=0.573 Sum_probs=23.6
Q ss_pred ceeeEEeeehhhhHHHHHHHHhhchhhhhHH
Q psy6159 5 KHYAVVGLLEDLNVTLTVMENYIPRFFAHAS 35 (101)
Q Consensus 5 ~~Y~vVGilEeln~tL~VLE~~lPrfFkGA~ 35 (101)
+++..|-++--+..++.++|+.||..|-=+.
T Consensus 7 rr~vylslL~a~~~~lsllE~~iP~PfpF~r 37 (181)
T COG4769 7 RREVYLSLLTALAVVLSLLENIIPKPFPFAR 37 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCCCcch
Confidence 4455566777888999999999998776443
No 8
>PF07932 DAP_C: D-aminopeptidase, domain C; InterPro: IPR012857 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. D-aminopeptidase (Q9ZBA9 from SWISSPROT) is a dimeric enzyme with each monomer being composed of three domains. Domain C is organised to form a beta barrel made up of eight antiparallel beta strands. It is connected to domain B by a short linker sequence, and interacts extensively with the domain A, the catalytic domain. The gamma loop of domain C forms part of the wall of the catalytic pocket; domain C is in fact thought to confer substrate and inhibitor specificity to the enzyme. This domain is found in peptidases that belong to MEROPS peptidase family S12 (D-Ala-D-Ala carboxypeptidase B family, clan ME).; GO: 0004177 aminopeptidase activity; PDB: 1EI5_A.
Probab=22.20 E-value=38 Score=24.12 Aligned_cols=13 Identities=62% Similarity=0.861 Sum_probs=10.1
Q ss_pred cceeeeeeeehhh
Q psy6159 84 TKLTIGCRLANFI 96 (101)
Q Consensus 84 ~~~~~~~~~~~~~ 96 (101)
+.+||||-||.=|
T Consensus 80 ~gvtiGCWLAR~i 92 (97)
T PF07932_consen 80 TGVTIGCWLARKI 92 (97)
T ss_dssp EEEEEEETTEEEE
T ss_pred EEEEEEEEEecce
Confidence 5689999998643
No 9
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=22.08 E-value=54 Score=22.17 Aligned_cols=19 Identities=26% Similarity=0.454 Sum_probs=16.6
Q ss_pred CHHHHHHHHhCCCcccccc
Q psy6159 61 EDKIRQERESNPRPSAYKA 79 (101)
Q Consensus 61 Seev~~~lr~n~t~E~~~~ 79 (101)
..+++++||++|+..++|.
T Consensus 27 E~eVi~lMR~~lk~~Sfk~ 45 (72)
T TIGR03643 27 EKEVIKLMRQNLKPSSFKL 45 (72)
T ss_pred HHHHHHHHHhhcChhHHHH
Confidence 5789999999999999874
No 10
>PHA00002 A DNA replication initiation protein gpA
Probab=21.61 E-value=71 Score=28.15 Aligned_cols=61 Identities=11% Similarity=0.231 Sum_probs=42.3
Q ss_pred eeEEeeehhhhHHHHHHHHhhchhhhhHHHHHhcccccccccccccccCCCCCCCHHHHHHHHh
Q psy6159 7 YAVVGLLEDLNVTLTVMENYIPRFFAHASQIYNEGRLDRWIGERQPFREQTLSVEDKIRQERES 70 (101)
Q Consensus 7 Y~vVGilEeln~tL~VLE~~lPrfFkGA~~~Y~~~~~~~~~~tkn~~Kp~~~~~Seev~~~lr~ 70 (101)
....++|.+.++-+++||-++-++-+|... .++.-.+ +.---..+|-.+.+|+|+.+..+.
T Consensus 31 sp~lr~~kq~~~r~klleeil~~~~~gi~~--dngd~~~-~gh~p~~~p~El~L~DEi~edYr~ 91 (515)
T PHA00002 31 SPNLRIWKQVDNRIKLLEEILYHYTNGIRR--DNGDFWM-NGHLPQRAPEELHLDDEIGEDYRS 91 (515)
T ss_pred CCchhHHHHhccHHHHHHHHHHHHhccccc--cCCccee-cCCCccCCchhhccchHHHHHHHH
Confidence 455789999999999999999999988864 3332221 111123456666889998887653
No 11
>KOG2181|consensus
Probab=20.31 E-value=42 Score=28.87 Aligned_cols=17 Identities=35% Similarity=0.637 Sum_probs=13.4
Q ss_pred Hhhchhhh-----hHHHHHhcc
Q psy6159 25 NYIPRFFA-----HASQIYNEG 41 (101)
Q Consensus 25 ~~lPrfFk-----GA~~~Y~~~ 41 (101)
.+|||||+ |++++|+.-
T Consensus 105 tlIPrfFrsIfegG~~eLyyvL 126 (415)
T KOG2181|consen 105 TLIPRFFRSIFEGGMRELYYVL 126 (415)
T ss_pred chhHHHHHHHHhcchhhhhhhh
Confidence 47999998 678888754
Done!