Query psy5620
Match_columns 72
No_of_seqs 104 out of 310
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:20:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5620.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5620hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2046|consensus 99.9 1.6E-26 3.6E-31 159.8 5.0 71 1-71 120-191 (193)
2 PF00402 Calponin: Calponin fa 99.7 5.5E-19 1.2E-23 87.9 1.4 25 45-69 1-26 (26)
3 COG5199 SCP1 Calponin [Cytoske 99.3 3.2E-12 6.9E-17 86.8 4.6 68 1-68 107-177 (178)
4 PF03494 Beta-APP: Beta-amyloi 40.6 11 0.00024 20.0 0.3 10 47-56 19-28 (39)
5 PF11792 Baculo_LEF5_C: Baculo 26.9 15 0.00033 20.0 -0.6 18 29-46 15-32 (43)
6 PF01244 Peptidase_M19: Membra 20.3 71 0.0015 23.4 1.7 27 23-49 204-233 (320)
7 PF08846 DUF1816: Domain of un 18.1 34 0.00073 20.2 -0.3 32 16-47 24-55 (68)
8 PF04624 Dec-1: Dec-1 repeat; 16.0 52 0.0011 16.2 0.1 11 30-40 8-18 (27)
9 COG2355 Zn-dependent dipeptida 15.9 1.2E+02 0.0026 22.8 2.0 29 23-51 193-224 (313)
10 KOG0918|consensus 14.7 60 0.0013 25.7 0.2 24 47-70 78-101 (476)
No 1
>KOG2046|consensus
Probab=99.93 E-value=1.6e-26 Score=159.75 Aligned_cols=71 Identities=46% Similarity=0.718 Sum_probs=67.6
Q ss_pred ChhhhHhHHHhhCCCCCCCccCccCCccccCcccHHHHhcccCeeeeccccccccccCCCC-CCCccccccC
Q psy5620 1 MTIFALGRTCYKHPEFRGPFLGPKPSEENKRFFTEDQLRAGEGMIGLQAGTNKLASQSGQN-FGATRKIILG 71 (72)
Q Consensus 1 ~tL~aLg~~a~~~~~~~gp~~g~K~a~kn~R~fteeqlk~g~~~i~lq~Gtnk~asQ~gm~-~g~~r~~~~~ 71 (72)
.||+||+++|+++..+.+|.||||+|++++|+|+++++++|+++|+|||||||||||+||+ ||++||+++-
T Consensus 120 vtL~aLa~~a~~~~~~~~~~~g~k~a~kq~r~f~~~~lk~g~~vi~LQmGtnk~asq~g~~~~G~~R~l~dp 191 (193)
T KOG2046|consen 120 VTLLALARKAQKKGLFSGPGIGPKLAEKQPREFTDEQLKAGQNVIGLQMGTNKGASQAGMTAYGTRRHLYDP 191 (193)
T ss_pred HHHHHHHHHHhhccccCCCCcCCchhhcCcccCCHHHHhcccceEEEeeeccchhhcccccccccccccCCC
Confidence 3899999999999877899999999999999999999999999999999999999999999 9999988764
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=99.74 E-value=5.5e-19 Score=87.90 Aligned_cols=25 Identities=68% Similarity=0.890 Sum_probs=23.9
Q ss_pred eeeccccccccccCCCC-CCCccccc
Q psy5620 45 IGLQAGTNKLASQSGQN-FGATRKII 69 (72)
Q Consensus 45 i~lq~Gtnk~asQ~gm~-~g~~r~~~ 69 (72)
|+|||||||||||+||+ ||++|||+
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=99.30 E-value=3.2e-12 Score=86.84 Aligned_cols=68 Identities=32% Similarity=0.597 Sum_probs=62.9
Q ss_pred ChhhhHhHHHhhCCCCCCCccCccCCccccCcc-cHHHHhcccCeeeeccccccccccCCCC--CCCcccc
Q psy5620 1 MTIFALGRTCYKHPEFRGPFLGPKPSEENKRFF-TEDQLRAGEGMIGLQAGTNKLASQSGQN--FGATRKI 68 (72)
Q Consensus 1 ~tL~aLg~~a~~~~~~~gp~~g~K~a~kn~R~f-teeqlk~g~~~i~lq~Gtnk~asQ~gm~--~g~~r~~ 68 (72)
.||++|+|.|++.-.+.+|.|||+.|+|.+|.| ..+++..+++.+.||||+-+.++|++=. ++.+|++
T Consensus 107 ~~l~slSRya~K~~~~~~p~lGP~LatKkprvfS~q~~l~~~~g~~~lqyGy~d~~~q~tek~a~~~rrD~ 177 (178)
T COG5199 107 ICLYSLSRYAQKERMFSGPFLGPHLATKKPRVFSSQEVLDRSKGAIHLQYGYSDLSEQSTEKGASNVRRDL 177 (178)
T ss_pred HHHHHHHHHHHHhcCCCCCccCccccccCCcccccHHHHhhcccceEeeecccccchhcccccccceecCC
Confidence 489999999999767899999999999999999 8999999999999999999999999864 8888875
No 4
>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=40.59 E-value=11 Score=19.99 Aligned_cols=10 Identities=40% Similarity=0.318 Sum_probs=7.7
Q ss_pred eccccccccc
Q psy5620 47 LQAGTNKLAS 56 (72)
Q Consensus 47 lq~Gtnk~as 56 (72)
-.||+||+|-
T Consensus 19 EDvgSNKGAI 28 (39)
T PF03494_consen 19 EDVGSNKGAI 28 (39)
T ss_dssp CCCSSSSSEE
T ss_pred hHcCCCCceE
Confidence 3589999974
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=26.93 E-value=15 Score=19.98 Aligned_cols=18 Identities=39% Similarity=0.514 Sum_probs=13.8
Q ss_pred ccCcccHHHHhcccCeee
Q psy5620 29 NKRFFTEDQLRAGEGMIG 46 (72)
Q Consensus 29 n~R~fteeqlk~g~~~i~ 46 (72)
++-..-|.|+|+|+..++
T Consensus 15 H~f~~~E~Q~RAGDE~VS 32 (43)
T PF11792_consen 15 HKFVTIEKQLRAGDEAVS 32 (43)
T ss_pred eeeeehhhhhcccchHHH
Confidence 445567899999998775
No 6
>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=20.31 E-value=71 Score=23.41 Aligned_cols=27 Identities=30% Similarity=0.502 Sum_probs=17.3
Q ss_pred ccCCccccCcccHHHHhc---ccCeeeecc
Q psy5620 23 PKPSEENKRFFTEDQLRA---GEGMIGLQA 49 (72)
Q Consensus 23 ~K~a~kn~R~fteeqlk~---g~~~i~lq~ 49 (72)
++---.++|+.++|++++ ..++||+-+
T Consensus 204 ~ral~~h~RNltDe~iraia~~GGviGi~~ 233 (320)
T PF01244_consen 204 ARALCPHPRNLTDEQIRAIAERGGVIGINF 233 (320)
T ss_dssp BTTTS--TTSB-HHHHHHHHHTT-EEEEES
T ss_pred hHhhCCCCCCCCHHHHHHHHHCCcEEEEEc
Confidence 344445899999999987 568888864
No 7
>PF08846 DUF1816: Domain of unknown function (DUF1816); InterPro: IPR014945 Q4C9H3 from SWISSPROT is associated with the IPR008213 from INTERPRO domain suggesting this protein could have a role in phycobilisomes.
Probab=18.14 E-value=34 Score=20.22 Aligned_cols=32 Identities=25% Similarity=0.335 Sum_probs=27.7
Q ss_pred CCCCccCccCCccccCcccHHHHhcccCeeee
Q psy5620 16 FRGPFLGPKPSEENKRFFTEDQLRAGEGMIGL 47 (72)
Q Consensus 16 ~~gp~~g~K~a~kn~R~fteeqlk~g~~~i~l 47 (72)
|-||.+..++|+.+.-.|-|+--.+|...|..
T Consensus 24 yFGPF~s~~eA~~~~~gyieDL~~Ega~~I~~ 55 (68)
T PF08846_consen 24 YFGPFDSREEAEAALPGYIEDLESEGAQGISV 55 (68)
T ss_pred EeCCcCCHHHHHHHhccHHHHHHhhCcceEEE
Confidence 66999999999999999999988888777653
No 8
>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=16.05 E-value=52 Score=16.22 Aligned_cols=11 Identities=27% Similarity=0.558 Sum_probs=8.7
Q ss_pred cCcccHHHHhc
Q psy5620 30 KRFFTEDQLRA 40 (72)
Q Consensus 30 ~R~fteeqlk~ 40 (72)
.|.|+||+.+.
T Consensus 8 qRQwsEeqAk~ 18 (27)
T PF04624_consen 8 QRQWSEEQAKI 18 (27)
T ss_pred HHHhhHHHHHH
Confidence 38899999775
No 9
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=15.91 E-value=1.2e+02 Score=22.76 Aligned_cols=29 Identities=24% Similarity=0.433 Sum_probs=21.9
Q ss_pred ccCCccccCcccHHHHhc---ccCeeeecccc
Q psy5620 23 PKPSEENKRFFTEDQLRA---GEGMIGLQAGT 51 (72)
Q Consensus 23 ~K~a~kn~R~fteeqlk~---g~~~i~lq~Gt 51 (72)
++---.++|+.+++|+++ ..++|++-+-.
T Consensus 193 ~~al~~h~RNl~D~qlkaI~~~gGvIgv~~~~ 224 (313)
T COG2355 193 ARALVDHPRNLSDEQLKAIAETGGVIGVNFIP 224 (313)
T ss_pred chhccCCCCCCCHHHHHHHHhcCCEEEEEeeh
Confidence 444456899999999987 66888886543
No 10
>KOG0918|consensus
Probab=14.73 E-value=60 Score=25.70 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=20.9
Q ss_pred eccccccccccCCCCCCCcccccc
Q psy5620 47 LQAGTNKLASQSGQNFGATRKIIL 70 (72)
Q Consensus 47 lq~Gtnk~asQ~gm~~g~~r~~~~ 70 (72)
-|+|.|.|+|=-|++++.+|++..
T Consensus 78 hhsgwn~~ssc~~~~~~~R~~LVl 101 (476)
T KOG0918|consen 78 HHSGWNSCSSCHGDSSFKRRYLVL 101 (476)
T ss_pred cccchhhhhhhccCcchhhhheee
Confidence 478999999999999999988753
Done!