Query psy5619
Match_columns 66
No_of_seqs 103 out of 293
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 22:18:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5619.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5619hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2046|consensus 99.8 5.8E-22 1.3E-26 138.5 3.7 63 2-64 127-190 (193)
2 PF00402 Calponin: Calponin fa 99.7 1.7E-18 3.7E-23 88.0 1.3 25 39-63 1-26 (26)
3 COG5199 SCP1 Calponin [Cytoske 98.6 4.9E-08 1.1E-12 67.6 2.9 61 2-62 114-177 (178)
4 PF14495 Cytochrom_C550: Cytoc 40.9 27 0.00058 23.7 2.3 29 2-35 86-114 (135)
5 PF11792 Baculo_LEF5_C: Baculo 40.7 6.8 0.00015 21.8 -0.5 20 22-41 14-33 (43)
6 PF03494 Beta-APP: Beta-amyloi 38.8 12 0.00027 20.3 0.3 11 40-50 18-28 (39)
7 PHA00650 hypothetical protein 25.2 38 0.00083 20.7 0.9 12 7-18 47-58 (82)
8 PF01244 Peptidase_M19: Membra 19.9 71 0.0015 23.4 1.6 24 20-43 207-233 (320)
9 COG2355 Zn-dependent dipeptida 15.9 1.2E+02 0.0025 22.9 2.0 28 18-45 194-224 (313)
10 PF04624 Dec-1: Dec-1 repeat; 14.0 62 0.0013 16.3 0.1 11 24-34 8-18 (27)
No 1
>KOG2046|consensus
Probab=99.85 E-value=5.8e-22 Score=138.50 Aligned_cols=63 Identities=46% Similarity=0.714 Sum_probs=57.6
Q ss_pred cccccCCCCCCCccCccCCccccccCcHHHHhcccCeeeecccccccccccCCC-CCccccccc
Q psy5619 2 DECYKHPEFRGPFLGPKPSEENKRFFTEDQLRAGEGMIGLQAGTNKLASQSGQN-FGATRKIIL 64 (66)
Q Consensus 2 ~~~~~~~~~~gp~~G~K~a~k~~R~fteeql~~g~~ii~LQ~GtNk~ASQ~Gmt-~G~~R~i~~ 64 (66)
|+|+++--+.+|.||||+|++++|+|++++|++|+++|+|||||||||||+||+ ||++|++++
T Consensus 127 ~~a~~~~~~~~~~~g~k~a~kq~r~f~~~~lk~g~~vi~LQmGtnk~asq~g~~~~G~~R~l~d 190 (193)
T KOG2046|consen 127 RKAQKKGLFSGPGIGPKLAEKQPREFTDEQLKAGQNVIGLQMGTNKGASQAGMTAYGTRRHLYD 190 (193)
T ss_pred HHHhhccccCCCCcCCchhhcCcccCCHHHHhcccceEEEeeeccchhhcccccccccccccCC
Confidence 456666446789999999999999999999999999999999999999999999 999998875
No 2
>PF00402 Calponin: Calponin family repeat; InterPro: IPR000557 Calponin [, ] is a thin filament-associated protein that is implicated in the regulation and modulation of smooth muscle contraction. It is capable of binding to actin, calmodulin, troponin C and tropomyosin. The interaction of calponin with actin inhibits the actomyosin MgATPase activity. Calponin is a basic protein of approximately 34 Kd. Multiple isoforms are found in smooth muscles. Calponin contains three repeats of a well conserved 26 amino acid domain. Such a domain is also found in vertebrate smooth muscle protein (SM22 or transgelin), and a number of other proteins whose physiological role is not yet established, including Drosophila synchronous flight muscle protein SM20, Caenorhabditis elegans unc-87 protein [], rat neuronal protein NP25 [], and an Onchocerca volvulus antigen [].
Probab=99.72 E-value=1.7e-18 Score=87.99 Aligned_cols=25 Identities=68% Similarity=0.890 Sum_probs=23.9
Q ss_pred eeecccccccccccCCC-CCcccccc
Q psy5619 39 IGLQAGTNKLASQSGQN-FGATRKII 63 (66)
Q Consensus 39 i~LQ~GtNk~ASQ~Gmt-~G~~R~i~ 63 (66)
|+|||||||||||+||| ||++|||+
T Consensus 1 i~LQ~GtNk~aSQ~Gmt~~G~~R~i~ 26 (26)
T PF00402_consen 1 IGLQMGTNKGASQSGMTAFGTPRHIY 26 (26)
T ss_pred CcccccccccccccCCccCCCCcccC
Confidence 79999999999999998 99999985
No 3
>COG5199 SCP1 Calponin [Cytoskeleton]
Probab=98.55 E-value=4.9e-08 Score=67.62 Aligned_cols=61 Identities=33% Similarity=0.550 Sum_probs=53.6
Q ss_pred cccccCCCCCCCccCccCCccccccC-cHHHHhcccCeeeecccccccccccCCC--CCccccc
Q psy5619 2 DECYKHPEFRGPFLGPKPSEENKRFF-TEDQLRAGEGMIGLQAGTNKLASQSGQN--FGATRKI 62 (66)
Q Consensus 2 ~~~~~~~~~~gp~~G~K~a~k~~R~f-teeql~~g~~ii~LQ~GtNk~ASQ~Gmt--~G~~R~i 62 (66)
|-|++.--|.+|.+||+.|+|.+|.| ..++|..+++.|.||||.-+.++|++=- ++.+|.+
T Consensus 114 Rya~K~~~~~~p~lGP~LatKkprvfS~q~~l~~~~g~~~lqyGy~d~~~q~tek~a~~~rrD~ 177 (178)
T COG5199 114 RYAQKERMFSGPFLGPHLATKKPRVFSSQEVLDRSKGAIHLQYGYSDLSEQSTEKGASNVRRDL 177 (178)
T ss_pred HHHHHhcCCCCCccCccccccCCcccccHHHHhhcccceEeeecccccchhcccccccceecCC
Confidence 44666646789999999999999999 8899999999999999999999999875 7777765
No 4
>PF14495 Cytochrom_C550: Cytochrome c-550 domain; PDB: 3ARC_V 1IZL 3A0H_V 3A0B_v 1E29_A 1F1C_B 1S5L_V 4FBY_i 3PRR_V 3PRQ_V ....
Probab=40.91 E-value=27 Score=23.65 Aligned_cols=29 Identities=31% Similarity=0.315 Sum_probs=19.3
Q ss_pred cccccCCCCCCCccCccCCccccccCcHHHHhcc
Q psy5619 2 DECYKHPEFRGPFLGPKPSEENKRFFTEDQLRAG 35 (66)
Q Consensus 2 ~~~~~~~~~~gp~~G~K~a~k~~R~fteeql~~g 35 (66)
+++..||.-.-++++|++ |+++||+|.+=
T Consensus 86 ~i~e~hp~~~s~di~p~m-----r~ltdddL~~i 114 (135)
T PF14495_consen 86 SISELHPSIKSADIFPKM-----RNLTDDDLYAI 114 (135)
T ss_dssp BGTTTS-STTCTTTSGGG-----TS--HHHHHHH
T ss_pred hHHHhCcCcccchhhHhh-----cCCCHHHHHHH
Confidence 356677777778888876 88999999753
No 5
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=40.68 E-value=6.8 Score=21.80 Aligned_cols=20 Identities=35% Similarity=0.516 Sum_probs=14.7
Q ss_pred cccccCcHHHHhcccCeeee
Q psy5619 22 ENKRFFTEDQLRAGEGMIGL 41 (66)
Q Consensus 22 k~~R~fteeql~~g~~ii~L 41 (66)
+++-..-|.|+|+|+..+++
T Consensus 14 ~H~f~~~E~Q~RAGDE~VSf 33 (43)
T PF11792_consen 14 KHKFVTIEKQLRAGDEAVSF 33 (43)
T ss_pred eeeeeehhhhhcccchHHHH
Confidence 34455678999999987763
No 6
>PF03494 Beta-APP: Beta-amyloid peptide (beta-APP); InterPro: IPR013803 Amyloid-beta precursor protein (APP, or A4) is associated with Alzheimer's disease (AD), because one of its breakdown products, amyloid-beta (A-beta), aggregates to form amyloid or senile plaques [, ]. Mutations in APP or in proteins that process APP have been linked with early-onset, familial AD. Individuals with Down's syndrome carry an extra copy of chromosome 21, which contains the APP gene, and almost invariably develop amyloid plaques and Alzheimer's symptoms. APP is important for the neurogenesis and neuronal regeneration, either through the intact protein, or through its many breakdown products []. APP consists of a large N-terminal extracellular region containing heparin-binding and copper-binding sites, a short hydrophobic transmembrane domain, and a short C-terminal intracellular domain. The N-terminal region is similar in structure to cysteine-rich growth factors and appears to function as a cell surface receptor, contributing to neurite growth, neuronal adhesion, axonogenesis and cell mobility []. APP acts as a kinesin I membrane receptor to mediate the axonal transport of beta-secretase and presenilin 1. The N-terminal domain can regulate neurite outgrowth through its binding to heparin and collagen I and IV, which are components of the extracellular matrix. APP is also coupled to apoptosis-inducing pathways, and is involved in copper homeostasis/oxidative stress through copper ion reduction, where copper-metallated APP induces neuronal death []. The C-terminal intracellular domain appears to be involved in transcription regulation through protein-protein interactions. APP can promote transcription activation through binding to APBB1/Tip60, and may bind to the adaptor protein FE65 to transactivate a wide variety of different promoters. APP can be processed by different sets of enzymes: In the non-amyloidogenic (non-plaque-forming) pathway, APP is cleaved by alpha-secretase to yield a soluble N-terminal sAPP-alpha (neuroprotective) and a membrane-bound CTF-alpha. CTF-alpha is broken-down by presenilin-containing gamma-secretase to yield soluble p3 and membrane-bound AICD (nuclear signalling). In the amyloidogenic pathway (plaque-forming), APP is broken down by beta-secretase to yield soluble sAPP-beta and membrane-bound CTF-beta. CTF-beta is broken down by gamma-secretase to yield soluble amyloid-beta and membrane-bound AICD. Amyloid-beta is required for neuronal function, but can aggregate to form amyloid plaques that seem to disrupt brain cells by clogging points of cell-cell contact. This entry represents the amyloid-beta peptide (A-beta), which originates as a breakdown product from the cleavage of amyloid-beta precursor protein (APP, or A4), an integral, glycosylated membrane brain protein. More information about these protein can be found at Protein of the Month: Amyloid-beta Precursor Protein [].; GO: 0005488 binding, 0016021 integral to membrane; PDB: 2LMQ_F 3JTI_B 2LMO_B 3MOQ_D 2LNQ_E 2LMP_G 2BEG_B 1AMC_A 3OW9_B 3U0T_F ....
Probab=38.81 E-value=12 Score=20.31 Aligned_cols=11 Identities=36% Similarity=0.305 Sum_probs=8.2
Q ss_pred eeccccccccc
Q psy5619 40 GLQAGTNKLAS 50 (66)
Q Consensus 40 ~LQ~GtNk~AS 50 (66)
.-.||+||+|-
T Consensus 18 aEDvgSNKGAI 28 (39)
T PF03494_consen 18 AEDVGSNKGAI 28 (39)
T ss_dssp CCCCSSSSSEE
T ss_pred hhHcCCCCceE
Confidence 33589999984
No 7
>PHA00650 hypothetical protein
Probab=25.16 E-value=38 Score=20.75 Aligned_cols=12 Identities=42% Similarity=1.041 Sum_probs=9.2
Q ss_pred CCCCCCCccCcc
Q psy5619 7 HPEFRGPFLGPK 18 (66)
Q Consensus 7 ~~~~~gp~~G~K 18 (66)
-|+|.||++.|-
T Consensus 47 tpdyegptldpv 58 (82)
T PHA00650 47 TPDYEGPTLDPV 58 (82)
T ss_pred CCCCcCCCcChH
Confidence 467889998874
No 8
>PF01244 Peptidase_M19: Membrane dipeptidase (Peptidase family M19); InterPro: IPR008257 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 peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ. Renal dipeptidase (rDP) (3.4.13.19 from EC), also known as microsomal dipeptidase, is a zinc-dependent metalloenzyme that hydrolyzes a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown [,] to be important for the catalytic activity of rDP. rDP seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae.; GO: 0008235 metalloexopeptidase activity, 0008239 dipeptidyl-peptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis; PDB: 3NEH_B 2RAG_D 3LU2_A 3B40_A 3LY0_A 3FDG_B 2I5G_B 3S2J_A 3S2N_A 3S2L_A ....
Probab=19.86 E-value=71 Score=23.44 Aligned_cols=24 Identities=33% Similarity=0.519 Sum_probs=15.8
Q ss_pred CccccccCcHHHHhc---ccCeeeecc
Q psy5619 20 SEENKRFFTEDQLRA---GEGMIGLQA 43 (66)
Q Consensus 20 a~k~~R~fteeql~~---g~~ii~LQ~ 43 (66)
--.++|+.++||+++ ..++||+-+
T Consensus 207 l~~h~RNltDe~iraia~~GGviGi~~ 233 (320)
T PF01244_consen 207 LCPHPRNLTDEQIRAIAERGGVIGINF 233 (320)
T ss_dssp TS--TTSB-HHHHHHHHHTT-EEEEES
T ss_pred hCCCCCCCCHHHHHHHHHCCcEEEEEc
Confidence 335899999999986 568888864
No 9
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=15.86 E-value=1.2e+02 Score=22.93 Aligned_cols=28 Identities=25% Similarity=0.445 Sum_probs=21.2
Q ss_pred cCCccccccCcHHHHhc---ccCeeeecccc
Q psy5619 18 KPSEENKRFFTEDQLRA---GEGMIGLQAGT 45 (66)
Q Consensus 18 K~a~k~~R~fteeql~~---g~~ii~LQ~Gt 45 (66)
+---.++|+.+++|+++ ..++||+-+-.
T Consensus 194 ~al~~h~RNl~D~qlkaI~~~gGvIgv~~~~ 224 (313)
T COG2355 194 RALVDHPRNLSDEQLKAIAETGGVIGVNFIP 224 (313)
T ss_pred hhccCCCCCCCHHHHHHHHhcCCEEEEEeeh
Confidence 33456899999999976 66888886544
No 10
>PF04624 Dec-1: Dec-1 repeat; InterPro: IPR006718 The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing []. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This repeat is usually found in 12 copies in the central region of the protein. Its function is unknown. Length polymorphisms of Dec-1 have been observed in wild-type strains, and are caused by changes in the numbers of the first five repeats [].; GO: 0005213 structural constituent of chorion, 0007304 chorion-containing eggshell formation, 0005576 extracellular region, 0042600 chorion
Probab=14.03 E-value=62 Score=16.34 Aligned_cols=11 Identities=27% Similarity=0.558 Sum_probs=8.8
Q ss_pred cccCcHHHHhc
Q psy5619 24 KRFFTEDQLRA 34 (66)
Q Consensus 24 ~R~fteeql~~ 34 (66)
.|.|+||+.+.
T Consensus 8 qRQwsEeqAk~ 18 (27)
T PF04624_consen 8 QRQWSEEQAKI 18 (27)
T ss_pred HHHhhHHHHHH
Confidence 38899999875
Done!