Query psy2257
Match_columns 75
No_of_seqs 159 out of 1042
Neff 7.7
Searched_HMMs 46136
Date Fri Aug 16 20:07:44 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2257.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2257hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3624|consensus 100.0 3.4E-30 7.5E-35 189.1 6.5 72 4-75 616-687 (687)
2 PF01431 Peptidase_M13: Peptid 100.0 1.1E-30 2.4E-35 168.3 3.4 72 3-74 135-206 (206)
3 COG3590 PepO Predicted metallo 99.9 2.1E-24 4.7E-29 155.5 6.5 75 1-75 578-654 (654)
4 PF01463 LRRCT: Leucine rich r 39.5 8.2 0.00018 16.6 -0.3 20 38-61 6-25 (25)
5 PF15021 DUF4521: Protein of u 32.1 41 0.00088 22.3 2.0 25 45-69 94-118 (206)
6 PF07576 BRAP2: BRCA1-associat 29.9 58 0.0013 19.3 2.3 36 38-74 51-89 (110)
7 PF10872 DUF2740: Protein of u 28.6 34 0.00074 17.0 0.9 14 31-44 20-33 (48)
8 smart00153 VHP Villin headpiec 23.8 57 0.0012 15.5 1.2 14 50-63 3-16 (36)
9 PF08880 QLQ: QLQ; InterPro: 23.0 50 0.0011 15.8 0.9 9 3-11 1-9 (37)
10 PF02707 MOSP_N: Major Outer S 22.6 33 0.00072 22.7 0.3 13 10-22 50-62 (204)
11 PF09080 K-cyclin_vir_C: K cyc 21.5 35 0.00076 19.9 0.2 12 3-14 15-26 (106)
12 COG2169 Ada Adenosine deaminas 21.1 87 0.0019 20.5 2.0 47 12-63 126-172 (187)
13 PF08099 Toxin_27: Scorpion ca 20.9 51 0.0011 15.3 0.7 7 67-73 27-33 (33)
No 1
>KOG3624|consensus
Probab=99.96 E-value=3.4e-30 Score=189.05 Aligned_cols=72 Identities=46% Similarity=0.784 Sum_probs=69.2
Q ss_pred CCChhhHHHHHHHHHhcccCChHHHHHHHHhCCCCCccccccccccChHhHHHhcCCCCCCCCCCCCceeeC
Q psy2257 4 SPTGAYAVTSKFTIYRCSLYRPESLKIRILTDTHSPGEFRVLGPLSNLKEFASDFQCPVGSRMNPPHKCEVW 75 (75)
Q Consensus 4 ~~t~~QlFF~~~Aq~~C~~~~~~~~~~~~~~d~h~p~~~RVn~~L~n~~~F~~aF~C~~gs~Mnp~~~C~iw 75 (75)
++|++||||++|||.||+..+++.....+.+|+|+|+++||||+|+|+|+|++||+||.||+|||.+||.||
T Consensus 616 ~~t~~QLFFl~~Aq~~C~~~~~~~~~~~~~~~~H~~~~~RVng~lsN~~eFa~aF~C~~gS~MnP~~kC~v~ 687 (687)
T KOG3624|consen 616 DLTPEQLFFLSYAQFFCSSEDPKKLPESLLTDPHSPESFRVNGVLSNSPEFAEAFNCPIGSPMNPEKKCKVW 687 (687)
T ss_pred CCChhHHHHHHHHHHHhccCChhhhhHHhhcCCCCCcceeEeeeccCcHHHHHhcCCCCCCCCCccccCcCC
Confidence 489999999999999999998888888888999999999999999999999999999999999999999999
No 2
>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification. ; InterPro: IPR018497 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. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M13 (neprilysin family, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.
Probab=99.96 E-value=1.1e-30 Score=168.32 Aligned_cols=72 Identities=44% Similarity=0.719 Sum_probs=56.4
Q ss_pred CCCChhhHHHHHHHHHhcccCChHHHHHHHHhCCCCCccccccccccChHhHHHhcCCCCCCCCCCCCceee
Q psy2257 3 SSPTGAYAVTSKFTIYRCSLYRPESLKIRILTDTHSPGEFRVLGPLSNLKEFASDFQCPVGSRMNPPHKCEV 74 (75)
Q Consensus 3 ~~~t~~QlFF~~~Aq~~C~~~~~~~~~~~~~~d~h~p~~~RVn~~L~n~~~F~~aF~C~~gs~Mnp~~~C~i 74 (75)
.++|.+||||++|||.||++.++......+..+.|+|+++|||++|+|+|+|++||+||.||+|||.+||++
T Consensus 135 ~~~t~~QlFF~~~a~~~C~~~~~~~~~~~~~~~~h~p~~~RvN~~L~n~~~Fa~aF~C~~gs~Mnp~~kC~~ 206 (206)
T PF01431_consen 135 EGLTPDQLFFISFAQSFCEKMSPESVYRQLQTDPHSPARFRVNGPLSNMPEFAEAFNCPSGSPMNPKKKCRC 206 (206)
T ss_dssp TTB-HHHHHHHHHHHHT-EEE-HHHHHHHHHH-SS--HHHHHHHHHHT-HHHHHHHT--TTSTTS-SSGG--
T ss_pred ccchhHHHHHHHHHHHHhcCcchhhhhhhhhcCCCCchHHHHHHHHhcCHHHHHHcCCCCCCCCCCCCCCcC
Confidence 368999999999999999998887777778889999999999999999999999999999999999999985
No 3
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=99.90 E-value=2.1e-24 Score=155.45 Aligned_cols=75 Identities=32% Similarity=0.560 Sum_probs=72.4
Q ss_pred CCCCCChhhHHHHHHHHHhcccCChHHHHHHHHhCCCCCccccccccccChHhHHHhcCCCCCCCC--CCCCceeeC
Q psy2257 1 MTSSPTGAYAVTSKFTIYRCSLYRPESLKIRILTDTHSPGEFRVLGPLSNLKEFASDFQCPVGSRM--NPPHKCEVW 75 (75)
Q Consensus 1 ~~~~~t~~QlFF~~~Aq~~C~~~~~~~~~~~~~~d~h~p~~~RVn~~L~n~~~F~~aF~C~~gs~M--np~~~C~iw 75 (75)
|+.+||.+|+||++|||+|..+.+++...+++..|+|+|+++|||+++.|+++|++||+|++|++| .|++|..||
T Consensus 578 v~dg~tg~qrfF~~wAqiWR~K~r~e~~~~~l~~DpHsP~~fR~Ng~~~N~~~FyeaFdVke~D~myr~pe~Rv~IW 654 (654)
T COG3590 578 VIDGFTGLQRFFLNWAQIWRMKARPEEQQMRLSVDPHSPAEFRVNGPVRNMDEFYEAFDVKEGDAMYRAPEERVVIW 654 (654)
T ss_pred cccccchHHHHHHHHHHHHhhccCHHHHHHHHccCCCCCceeeccCCCCChHHHHHHcCCCCCcccccChhhccccC
Confidence 467899999999999999999999999999999999999999999999999999999999999999 599999999
No 4
>PF01463 LRRCT: Leucine rich repeat C-terminal domain; InterPro: IPR000483 Leucine-rich repeats (LRR, see IPR001611 from INTERPRO) consist of 2-45 motifs of 20-30 amino acids in length that generally folds into an arc or horseshoe shape []. LRRs occur in proteins ranging from viruses to eukaryotes, and appear to provide a structural framework for the formation of protein-protein interactions []. Proteins containing LRRs include tyrosine kinase receptors, cell-adhesion molecules, virulence factors, and extracellular matrix-binding glycoproteins, and are involved in a variety of biological processes, including signal transduction, cell adhesion, DNA repair, recombination, transcription, RNA processing, disease resistance, apoptosis, and the immune response. LRRs are often flanked by cysteine-rich domains: an N-terminal LRR domain (IPR000372 from INTERPRO) and a C-terminal LRR domain. This entry represents the C-terminal LRR domain. ; PDB: 3RFE_B 3REZ_D 2WFH_A 2V70_B 2V9S_C 2V9T_B 1W8A_A.
Probab=39.53 E-value=8.2 Score=16.64 Aligned_cols=20 Identities=55% Similarity=0.951 Sum_probs=8.9
Q ss_pred CCccccccccccChHhHHHhcCCC
Q psy2257 38 SPGEFRVLGPLSNLKEFASDFQCP 61 (75)
Q Consensus 38 ~p~~~RVn~~L~n~~~F~~aF~C~ 61 (75)
+|..+|- +|...+. +.|.|+
T Consensus 6 ~P~~lrg--~l~~~~~--~~f~C~ 25 (25)
T PF01463_consen 6 SPPELRG--PLLDLPP--SDFKCS 25 (25)
T ss_dssp ESGGGTT--BGGGSSG--GG----
T ss_pred CChHHcC--cHhhCCc--ccCcCC
Confidence 4555554 5555555 566663
No 5
>PF15021 DUF4521: Protein of unknown function (DUF4521)
Probab=32.12 E-value=41 Score=22.26 Aligned_cols=25 Identities=24% Similarity=0.270 Sum_probs=19.7
Q ss_pred cccccChHhHHHhcCCCCCCCCCCC
Q psy2257 45 LGPLSNLKEFASDFQCPVGSRMNPP 69 (75)
Q Consensus 45 n~~L~n~~~F~~aF~C~~gs~Mnp~ 69 (75)
+|--.-...|+++|+.|.-..+||-
T Consensus 94 dglRkSLD~FYe~f~~pqP~s~dpl 118 (206)
T PF15021_consen 94 DGLRKSLDRFYEMFGHPQPASGDPL 118 (206)
T ss_pred chHHHHHHHHHHHhCCCCCCCCCcc
Confidence 3445567889999999998888873
No 6
>PF07576 BRAP2: BRCA1-associated protein 2; InterPro: IPR011422 These proteins include BRCA1-associated protein 2 (BRAP2), which binds nuclear localisation signals (NLSs) in vitro and in yeast two-hybrid screening []. These proteins share a region of sequence similarity at their N terminus. They also have IPR001607 from INTERPRO at the C terminus.
Probab=29.90 E-value=58 Score=19.29 Aligned_cols=36 Identities=25% Similarity=0.508 Sum_probs=24.9
Q ss_pred CCccccccccccC---hHhHHHhcCCCCCCCCCCCCceee
Q psy2257 38 SPGEFRVLGPLSN---LKEFASDFQCPVGSRMNPPHKCEV 74 (75)
Q Consensus 38 ~p~~~RVn~~L~n---~~~F~~aF~C~~gs~Mnp~~~C~i 74 (75)
.|.++=|..-..+ -.+|++.||=++=+.|-|+. |.|
T Consensus 51 ~pnrymVLikF~~~~~Ad~Fy~~fNGk~FnslEpE~-Chv 89 (110)
T PF07576_consen 51 TPNRYMVLIKFRDQESADEFYEEFNGKPFNSLEPET-CHV 89 (110)
T ss_pred CCceEEEEEEECCHHHHHHHHHHhCCCccCCCCCce-eEE
Confidence 4566666543333 57999999977777787755 875
No 7
>PF10872 DUF2740: Protein of unknown function (DUF2740); InterPro: IPR022626 This entry is represented by Bacteriophage P22, Orf48. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family of proteins with unknown function has a highly conserved sequence. They are found in Enterobacteria and Enterobacteria phages.
Probab=28.58 E-value=34 Score=17.05 Aligned_cols=14 Identities=43% Similarity=0.873 Sum_probs=7.6
Q ss_pred HHHhCCCCCccccc
Q psy2257 31 RILTDTHSPGEFRV 44 (75)
Q Consensus 31 ~~~~d~h~p~~~RV 44 (75)
+....-..|+++|.
T Consensus 20 rflssfkqpgrfra 33 (48)
T PF10872_consen 20 RFLSSFKQPGRFRA 33 (48)
T ss_pred HHHHHhcCcchHHH
Confidence 33344456777764
No 8
>smart00153 VHP Villin headpiece domain.
Probab=23.75 E-value=57 Score=15.50 Aligned_cols=14 Identities=14% Similarity=0.180 Sum_probs=11.0
Q ss_pred ChHhHHHhcCCCCC
Q psy2257 50 NLKEFASDFQCPVG 63 (75)
Q Consensus 50 n~~~F~~aF~C~~g 63 (75)
+..+|.++|+|...
T Consensus 3 sdeeF~~vfgmsr~ 16 (36)
T smart00153 3 SDEDFEEVFGMTRE 16 (36)
T ss_pred CHHHHHHHHCCCHH
Confidence 35789999998654
No 9
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.02 E-value=50 Score=15.80 Aligned_cols=9 Identities=33% Similarity=-0.082 Sum_probs=6.1
Q ss_pred CCCChhhHH
Q psy2257 3 SSPTGAYAV 11 (75)
Q Consensus 3 ~~~t~~QlF 11 (75)
|.||++|+-
T Consensus 1 s~FT~~Ql~ 9 (37)
T PF08880_consen 1 SPFTPAQLQ 9 (37)
T ss_pred CCCCHHHHH
Confidence 567777764
No 10
>PF02707 MOSP_N: Major Outer Sheath Protein N-terminal region; InterPro: IPR003857 This is a family of spirochete major outer sheath protein N-terminal regions. These proteins are present on the bacterial cell surface. In Treponema denticola the major outer sheath protein (Msp) binds immobilized laminin and fibronectin supporting the hypothesis that Msp mediates the extracellular matrix binding activity of T. denticola [].
Probab=22.56 E-value=33 Score=22.74 Aligned_cols=13 Identities=15% Similarity=0.171 Sum_probs=10.4
Q ss_pred HHHHHHHHHhccc
Q psy2257 10 AVTSKFTIYRCSL 22 (75)
Q Consensus 10 lFF~~~Aq~~C~~ 22 (75)
.|+.+|||.|=--
T Consensus 50 ~f~~NfAqlW~P~ 62 (204)
T PF02707_consen 50 DFKSNFAQLWKPF 62 (204)
T ss_pred Cchhhhhhhcccc
Confidence 5889999999643
No 11
>PF09080 K-cyclin_vir_C: K cyclin, C terminal; InterPro: IPR015164 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This domain adopts a secondary structure consisting of a five alpha-helix cyclin fold. Interaction with cyclin dependent kinases (CDKs) at a PSTAIRE sequence motif within the catalytic cleft of CDK results in the regulation of CDK activity []. ; PDB: 1G3N_C.
Probab=21.52 E-value=35 Score=19.92 Aligned_cols=12 Identities=17% Similarity=-0.128 Sum_probs=8.6
Q ss_pred CCCChhhHHHHH
Q psy2257 3 SSPTGAYAVTSK 14 (75)
Q Consensus 3 ~~~t~~QlFF~~ 14 (75)
++++.+||||+-
T Consensus 15 ~~~~~e~L~~~H 26 (106)
T PF09080_consen 15 SGFTKEQLFAWH 26 (106)
T ss_dssp HS-SSTTHHHHH
T ss_pred HcccHHHHHHHH
Confidence 578899999854
No 12
>COG2169 Ada Adenosine deaminase [Nucleotide transport and metabolism]
Probab=21.10 E-value=87 Score=20.51 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=30.9
Q ss_pred HHHHHHHhcccCChHHHHHHHHhCCCCCccccccccccChHhHHHhcCCCCC
Q psy2257 12 TSKFTIYRCSLYRPESLKIRILTDTHSPGEFRVLGPLSNLKEFASDFQCPVG 63 (75)
Q Consensus 12 F~~~Aq~~C~~~~~~~~~~~~~~d~h~p~~~RVn~~L~n~~~F~~aF~C~~g 63 (75)
|+.||+.+.- ...+.+|.... +....-......+.+.|.++|.=-.|
T Consensus 126 p~~ya~a~R~----~~a~~~L~~g~-sv~~a~~daGf~s~s~F~~af~~~~G 172 (187)
T COG2169 126 PKEYARARRM----GRARKQLRMGA-SVTDAQIDAGFESSSRFYDAFSKILG 172 (187)
T ss_pred HHHHHHHHHH----HHHHHHHhCCC-chhHHHHHhCCCChHHHHHHHHHHcC
Confidence 4667777543 34444554444 66666677888999999999874444
No 13
>PF08099 Toxin_27: Scorpion calcine family; InterPro: IPR012632 Toxins of the scorpion calcine family bind directly to ryanodine receptors (RyRs), intracellular channel targets of the endoplasmic reticulum, and induce long lasting channel openings in a mode of smaller conductance. They have the ability to translocate into cells by crossing the plasma membrane [, , ]. Toxins of scorpion calcine family are highly basic 33-amino acid peptides that present three disulphide bridges (C1-C4, C2-C5, and C3-C6) and fold along a knottin or inhibitor cystine knot motif (http://knottin.cbs.cnrs.fr) [, , ]. Their three dimensional structure consists of a compact disulphide-bonded core from which emerge loops and the N terminus. The main element of regular secondary structure is a double-stranded antiparallel beta-sheet. A third peripheral extended strand is almost perpendicular to the double-stranded antiparallel beta-sheet [, ]. Scorpion calcine mimic the activating segment of the dihydropyridine receptor II-III loop, which interacts with a region of the ryanodine receptor [, , ]. This family includes: Imperatoxin-A (IpTx A) from Pandinus imperator (Emperor scorpion). Opicalcin-1 and -2 from Opistophthalmus carinatus (African yellow leg scorpion). Maurocalcin (MCa) from Scorpio maurus palmatus (Chactoid scorpion). ; GO: 0019855 calcium channel inhibitor activity, 0009405 pathogenesis, 0005576 extracellular region; PDB: 1IE6_A.
Probab=20.90 E-value=51 Score=15.30 Aligned_cols=7 Identities=43% Similarity=1.241 Sum_probs=4.8
Q ss_pred CCCCcee
Q psy2257 67 NPPHKCE 73 (75)
Q Consensus 67 np~~~C~ 73 (75)
||+++|+
T Consensus 27 n~ekrcr 33 (33)
T PF08099_consen 27 NPEKRCR 33 (33)
T ss_dssp SSSSBB-
T ss_pred ChhhccC
Confidence 7888884
Done!