Query psy2256
Match_columns 103
No_of_seqs 104 out of 1203
Neff 8.2
Searched_HMMs 46136
Date Fri Aug 16 20:06:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2256hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3624|consensus 99.9 2.6E-24 5.7E-29 168.6 4.4 74 29-103 612-687 (687)
2 PF01431 Peptidase_M13: Peptid 99.9 2.3E-24 5E-29 147.5 -1.8 75 28-102 130-206 (206)
3 COG3590 PepO Predicted metallo 99.8 1.2E-19 2.7E-24 137.8 2.8 72 32-103 579-654 (654)
4 COG3590 PepO Predicted metallo 99.0 3.7E-10 8E-15 86.7 3.7 55 1-58 597-651 (654)
5 KOG3624|consensus 98.5 8.2E-08 1.8E-12 76.0 3.9 51 1-55 632-682 (687)
6 PF01431 Peptidase_M13: Peptid 98.4 4E-08 8.6E-13 67.2 -0.8 45 1-45 152-196 (206)
7 PF15021 DUF4521: Protein of u 26.2 54 0.0012 22.7 1.9 25 73-97 94-118 (206)
8 smart00153 VHP Villin headpiec 18.5 80 0.0017 15.6 1.1 13 79-91 4-16 (36)
9 PF15182 OTOS: Otospiralin 15.8 32 0.00069 19.5 -0.8 21 23-43 34-54 (69)
10 PF07576 BRAP2: BRCA1-associat 15.1 1.6E+02 0.0034 18.3 2.1 22 80-102 68-89 (110)
No 1
>KOG3624|consensus
Probab=99.89 E-value=2.6e-24 Score=168.63 Aligned_cols=74 Identities=46% Similarity=0.814 Sum_probs=70.1
Q ss_pred CCCcHHHH--HhcCCCchhhhcccCChHHhhhhhccCCCCCCcceeeecccCchhHHHhcCCCCCCCCCCCCceecC
Q psy2256 29 LSNLKEFA--RDFQCPEEFHMCALVRPERLKFLILTDTHSPSEFRVLGPLSNLKEFARDFQCPVGSRMNPPHKCEVW 103 (103)
Q Consensus 29 l~~~~~f~--q~Ff~~~a~~~C~~~~~~~~~~~~~~d~h~p~~~Rvn~~l~n~~~F~~aF~C~~g~~m~p~~~C~iw 103 (103)
|+.++ |+ |+||++|||.||+..+++.....+.+++|+|+++||||+|+|+++|++||+|+.||+|||.+||.||
T Consensus 612 lp~l~-~t~~QLFFl~~Aq~~C~~~~~~~~~~~~~~~~H~~~~~RVng~lsN~~eFa~aF~C~~gS~MnP~~kC~v~ 687 (687)
T KOG3624|consen 612 LPGLD-LTPEQLFFLSYAQFFCSSEDPKKLPESLLTDPHSPESFRVNGVLSNSPEFAEAFNCPIGSPMNPEKKCKVW 687 (687)
T ss_pred CCCCC-CChhHHHHHHHHHHHhccCChhhhhHHhhcCCCCCcceeEeeeccCcHHHHHhcCCCCCCCCCccccCcCC
Confidence 77776 65 9999999999999999888888889999999999999999999999999999999999999999999
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=99.87 E-value=2.3e-24 Score=147.46 Aligned_cols=75 Identities=43% Similarity=0.736 Sum_probs=56.6
Q ss_pred cCCCcHHHH--HhcCCCchhhhcccCChHHhhhhhccCCCCCCcceeeecccCchhHHHhcCCCCCCCCCCCCceec
Q psy2256 28 PLSNLKEFA--RDFQCPEEFHMCALVRPERLKFLILTDTHSPSEFRVLGPLSNLKEFARDFQCPVGSRMNPPHKCEV 102 (103)
Q Consensus 28 ~l~~~~~f~--q~Ff~~~a~~~C~~~~~~~~~~~~~~d~h~p~~~Rvn~~l~n~~~F~~aF~C~~g~~m~p~~~C~i 102 (103)
.|++++.++ |+||++||+.||+..++......+..++|+|.++|||++|+|+++|++||+|+.||+|||.+||.+
T Consensus 130 ~l~~~~~~t~~QlFF~~~a~~~C~~~~~~~~~~~~~~~~h~p~~~RvN~~L~n~~~Fa~aF~C~~gs~Mnp~~kC~~ 206 (206)
T PF01431_consen 130 RLPGLEGLTPDQLFFISFAQSFCEKMSPESVYRQLQTDPHSPARFRVNGPLSNMPEFAEAFNCPSGSPMNPKKKCRC 206 (206)
T ss_dssp B-TTCTTB-HHHHHHHHHHHHT-EEE-HHHHHHHHHH-SS--HHHHHHHHHHT-HHHHHHHT--TTSTTS-SSGG--
T ss_pred cccccccchhHHHHHHHHHHHHhcCcchhhhhhhhhcCCCCchHHHHHHHHhcCHHHHHHcCCCCCCCCCCCCCCcC
Confidence 455566665 999999999999998888777778889999999999999999999999999999999999999975
No 3
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=99.77 E-value=1.2e-19 Score=137.80 Aligned_cols=72 Identities=32% Similarity=0.579 Sum_probs=68.6
Q ss_pred cHHHH--HhcCCCchhhhcccCChHHhhhhhccCCCCCCcceeeecccCchhHHHhcCCCCCCCC--CCCCceecC
Q psy2256 32 LKEFA--RDFQCPEEFHMCALVRPERLKFLILTDTHSPSEFRVLGPLSNLKEFARDFQCPVGSRM--NPPHKCEVW 103 (103)
Q Consensus 32 ~~~f~--q~Ff~~~a~~~C~~~~~~~~~~~~~~d~h~p~~~Rvn~~l~n~~~F~~aF~C~~g~~m--~p~~~C~iw 103 (103)
+++|+ |+||++||++|..+.+++....++..|+|+|+++|||+++.|+++|++||.|++|++| .|++|..||
T Consensus 579 ~dg~tg~qrfF~~wAqiWR~K~r~e~~~~~l~~DpHsP~~fR~Ng~~~N~~~FyeaFdVke~D~myr~pe~Rv~IW 654 (654)
T COG3590 579 IDGFTGLQRFFLNWAQIWRMKARPEEQQMRLSVDPHSPAEFRVNGPVRNMDEFYEAFDVKEGDAMYRAPEERVVIW 654 (654)
T ss_pred ccccchHHHHHHHHHHHHhhccCHHHHHHHHccCCCCCceeeccCCCCChHHHHHHcCCCCCcccccChhhccccC
Confidence 45676 9999999999999999999999999999999999999999999999999999999999 499999999
No 4
>COG3590 PepO Predicted metalloendopeptidase [Posttranslational modification, protein turnover, chaperones]
Probab=98.98 E-value=3.7e-10 Score=86.75 Aligned_cols=55 Identities=36% Similarity=0.576 Sum_probs=49.5
Q ss_pred CCCCcHHHHHHHHhhCCCCCCCceeeccCCCcHHHHHhcCCCchhhhcccCChHHhhh
Q psy2256 1 CTLVRPERLKFLILTDTHSPSEFRVLGPLSNLKEFARDFQCPEEFHMCALVRPERLKF 58 (103)
Q Consensus 1 c~~~~~~~~~~~~~~d~h~p~~~R~~~~l~~~~~f~q~Ff~~~a~~~C~~~~~~~~~~ 58 (103)
+++.++|+++.++.+|+|||+++|+||++.|+++|+++|-|..++ .+++.++.+.
T Consensus 597 R~K~r~e~~~~~l~~DpHsP~~fR~Ng~~~N~~~FyeaFdVke~D---~myr~pe~Rv 651 (654)
T COG3590 597 RMKARPEEQQMRLSVDPHSPAEFRVNGPVRNMDEFYEAFDVKEGD---AMYRAPEERV 651 (654)
T ss_pred hhccCHHHHHHHHccCCCCCceeeccCCCCChHHHHHHcCCCCCc---ccccChhhcc
Confidence 368899999999999999999999999999999999999999998 7777665543
No 5
>KOG3624|consensus
Probab=98.53 E-value=8.2e-08 Score=76.03 Aligned_cols=51 Identities=47% Similarity=0.804 Sum_probs=46.1
Q ss_pred CCCCcHHHHHHHHhhCCCCCCCceeeccCCCcHHHHHhcCCCchhhhcccCChHH
Q psy2256 1 CTLVRPERLKFLILTDTHSPSEFRVLGPLSNLKEFARDFQCPEEFHMCALVRPER 55 (103)
Q Consensus 1 c~~~~~~~~~~~~~~d~h~p~~~R~~~~l~~~~~f~q~Ff~~~a~~~C~~~~~~~ 55 (103)
|+..+++.....+.+|+|+|..+||||+|+|+++|+++|.|+-+ +.++|..
T Consensus 632 C~~~~~~~~~~~~~~~~H~~~~~RVng~lsN~~eFa~aF~C~~g----S~MnP~~ 682 (687)
T KOG3624|consen 632 CSSEDPKKLPESLLTDPHSPESFRVNGVLSNSPEFAEAFNCPIG----SPMNPEK 682 (687)
T ss_pred hccCChhhhhHHhhcCCCCCcceeEeeeccCcHHHHHhcCCCCC----CCCCccc
Confidence 88889999999999999999999999999999999999999999 5555543
No 6
>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=98.39 E-value=4e-08 Score=67.16 Aligned_cols=45 Identities=49% Similarity=0.869 Sum_probs=34.1
Q ss_pred CCCCcHHHHHHHHhhCCCCCCCceeeccCCCcHHHHHhcCCCchh
Q psy2256 1 CTLVRPERLKFLILTDTHSPSEFRVLGPLSNLKEFARDFQCPEEF 45 (103)
Q Consensus 1 c~~~~~~~~~~~~~~d~h~p~~~R~~~~l~~~~~f~q~Ff~~~a~ 45 (103)
|++.+++....++.+|+|+|..+|||++|+|+++|+++|.|+-+.
T Consensus 152 C~~~~~~~~~~~~~~~~h~p~~~RvN~~L~n~~~Fa~aF~C~~gs 196 (206)
T PF01431_consen 152 CEKMSPESVYRQLQTDPHSPARFRVNGPLSNMPEFAEAFNCPSGS 196 (206)
T ss_dssp -EEE-HHHHHHHHHH-SS--HHHHHHHHHHT-HHHHHHHT--TTS
T ss_pred hcCcchhhhhhhhhcCCCCchHHHHHHHHhcCHHHHHHcCCCCCC
Confidence 677788888889999999999999999999999999999999994
No 7
>PF15021 DUF4521: Protein of unknown function (DUF4521)
Probab=26.24 E-value=54 Score=22.66 Aligned_cols=25 Identities=24% Similarity=0.272 Sum_probs=19.7
Q ss_pred eecccCchhHHHhcCCCCCCCCCCC
Q psy2256 73 LGPLSNLKEFARDFQCPVGSRMNPP 97 (103)
Q Consensus 73 n~~l~n~~~F~~aF~C~~g~~m~p~ 97 (103)
+|.-+-++.|+++|+.++...++|-
T Consensus 94 dglRkSLD~FYe~f~~pqP~s~dpl 118 (206)
T PF15021_consen 94 DGLRKSLDRFYEMFGHPQPASGDPL 118 (206)
T ss_pred chHHHHHHHHHHHhCCCCCCCCCcc
Confidence 3445567889999999999888863
No 8
>smart00153 VHP Villin headpiece domain.
Probab=18.52 E-value=80 Score=15.61 Aligned_cols=13 Identities=15% Similarity=0.176 Sum_probs=10.5
Q ss_pred chhHHHhcCCCCC
Q psy2256 79 LKEFARDFQCPVG 91 (103)
Q Consensus 79 ~~~F~~aF~C~~g 91 (103)
..+|.++|+|...
T Consensus 4 deeF~~vfgmsr~ 16 (36)
T smart00153 4 DEDFEEVFGMTRE 16 (36)
T ss_pred HHHHHHHHCCCHH
Confidence 5789999998654
No 9
>PF15182 OTOS: Otospiralin
Probab=15.84 E-value=32 Score=19.52 Aligned_cols=21 Identities=33% Similarity=0.621 Sum_probs=16.1
Q ss_pred ceeeccCCCcHHHHHhcCCCc
Q psy2256 23 FRVLGPLSNLKEFARDFQCPE 43 (103)
Q Consensus 23 ~R~~~~l~~~~~f~q~Ff~~~ 43 (103)
+|..|+...+++.++.||--+
T Consensus 34 FrtlGAY~~indmARtfFAh~ 54 (69)
T PF15182_consen 34 FRTLGAYNQINDMARTFFAHF 54 (69)
T ss_pred HHHhccHHHHHHHHHHHHhhC
Confidence 456688888888888888654
No 10
>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=15.09 E-value=1.6e+02 Score=18.29 Aligned_cols=22 Identities=27% Similarity=0.555 Sum_probs=0.0
Q ss_pred hhHHHhcCCCCCCCCCCCCceec
Q psy2256 80 KEFARDFQCPVGSRMNPPHKCEV 102 (103)
Q Consensus 80 ~~F~~aF~C~~g~~m~p~~~C~i 102 (103)
.+|.+.||=++=+.|-|+. |.|
T Consensus 68 d~Fy~~fNGk~FnslEpE~-Chv 89 (110)
T PF07576_consen 68 DEFYEEFNGKPFNSLEPET-CHV 89 (110)
T ss_pred HHHHHHhCCCccCCCCCce-eEE
Done!