Query psy29
Match_columns 222
No_of_seqs 137 out of 182
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:26:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy29.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/29hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF03343 SART-1: SART-1 family 100.0 1.8E-37 3.9E-42 299.3 0.0 166 6-182 132-323 (613)
2 KOG2217|consensus 100.0 7E-32 1.5E-36 263.4 6.5 167 9-185 186-373 (705)
3 PF06375 BLVR: Bovine leukaemi 22.4 36 0.00078 29.1 0.5 13 132-144 63-76 (154)
4 PHA00726 hypothetical protein 11.5 98 0.0021 24.5 0.5 11 143-153 25-35 (89)
5 KOG2217|consensus 11.3 47 0.001 34.6 -1.6 22 47-68 228-249 (705)
6 cd02252 nylC_like nylC-like fa 9.9 1.9E+02 0.0041 26.8 1.9 23 13-35 3-26 (260)
7 COG3191 DmpA L-aminopeptidase/ 8.4 2.4E+02 0.0051 27.3 1.9 24 12-35 18-44 (348)
8 PF15333 TAF1D: TATA box-bindi 8.2 83 0.0018 28.5 -1.1 9 143-151 57-65 (217)
9 PF03303 WTF: WTF protein; In 7.5 3.1E+02 0.0068 25.3 2.2 14 94-107 27-40 (247)
10 PF03576 Peptidase_S58: Peptid 7.4 1.6E+02 0.0035 27.8 0.3 23 13-35 6-31 (326)
No 1
>PF03343 SART-1: SART-1 family; InterPro: IPR005011 This family of proteins appear to contain a leucine zipper [] and may therefore be a family of transcription factors.; PDB: 3PLV_C 3PLU_D.
Probab=100.00 E-value=1.8e-37 Score=299.26 Aligned_cols=166 Identities=47% Similarity=0.669 Sum_probs=0.0
Q ss_pred cccccccCCCCceeeecccccCCCCcEEEEeecccccccCCC-CeeeccccchHHHHHHHHHHhhhcCCCCCCCCCCCcc
Q psy29 6 VEHDIKDFTEGRNVEHDIKDFTEGRNVILTLKDQDILAEDAS-DTLVNVNMVDDERHKKNVLNRKQKVGGKFGYSALDED 84 (222)
Q Consensus 6 ~~yt~~d~L~GlkV~H~~~~f~eG~~vILTLKD~~ILde~e~-D~LeNv~L~e~ek~kknle~kkkk~~~~~~Y~~ydDe 84 (222)
..|++.+ |+||||+|++++|.+|++|||||||++||+++++ |+||||+|++++++++|+++|++++ .|++++
T Consensus 132 ~~y~~~d-L~glkV~H~~~~f~eg~~vILTLKD~~VLdd~~~~D~LeNv~l~e~ek~kknle~kkk~~----~~d~~e-- 204 (613)
T PF03343_consen 132 KEYTSKD-LAGLKVAHDLDEFEEGEEVILTLKDSSVLDDDDEGDVLENVNLAEDEKRKKNLELKKKKK----GYDPDE-- 204 (613)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred ccccccc-CCCCeeecchhhhccCCCeEEEeCCCCcCcCCCCCCEEechhhHHHHHHHHHHHHhccCc----cccccc--
Confidence 3577777 9999999999999999999999999999998854 9999999999999999999999999 566554
Q ss_pred ccccCCCccccccccCcccccccccccc---eEechh------------hhhhhcc------C--CCCCCcCCCCCCccc
Q psy29 85 EFDEDGNPRESQLLSKYDEEIEGTKKKS---FAIARW------------TLNLKVG------G--SSPSQLASDYLTEDE 141 (222)
Q Consensus 85 efDe~G~~k~k~iL~KYDEEieg~k~~~---F~Lg~~------------~lkk~l~------~--~~~~~~aSDY~t~eE 141 (222)
| +.+..++||+|||++|+|++... |+|+.. .++.++. . +....++|||||++|
T Consensus 205 -~---~~~~~k~iL~kYDeeie~~~~~~~~~f~L~~~g~~~~~~~~~~~~~~~k~~~~~~~l~~~~~~~~~~sDy~t~~E 280 (613)
T PF03343_consen 205 -D---GNGKKKSILSKYDEEIEGEKKKSDNSFTLDEGGSVDDEKEKKEQEIKEKLKLSSLSLDSLDSKEKIASDYYTEEE 280 (613)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred -c---cccCCCCccccCcccccCcccccccceEecCCCcchHHHHHHHhhHHHHHhhccccccccCCcccccccccCccc
Confidence 2 44457899999999999998777 999753 1222221 1 356789999999999
Q ss_pred c-cccCCCcccchhhhcccccccccCCC-CCCCCCCCcccccc
Q psy29 142 V-KFKKPKKKVRKIRKTKLRADDLLNMD-SGADQSSEMMKREV 182 (222)
Q Consensus 142 m-kFKKpKKKkkk~Rkk~~~~ddL~~~~-~~~~~~~D~GsR~~ 182 (222)
| +|||||||+++.+++....|++.+++ +.+.+++++|||..
T Consensus 281 m~kfKK~KkKk~kk~~r~~~~D~~~~~~~~~~~~~~~~~sr~~ 323 (613)
T PF03343_consen 281 MIKFKKPKKKKKKKKKRKKKADDLELEPEEAASGSSDSGSRKM 323 (613)
T ss_dssp -------------------------------------------
T ss_pred cccccccccccchhhhhhhhhhccccccccccccccccccccc
Confidence 8 99999999855444433445555544 67889999999976
No 2
>KOG2217|consensus
Probab=99.97 E-value=7e-32 Score=263.39 Aligned_cols=167 Identities=40% Similarity=0.589 Sum_probs=143.2
Q ss_pred ccccCCCCceeeecccccCCCCcEEEEeecccccccCCCCeeeccccchHHHHHHHHHHhhhcCCCCCCCCCCCcccccc
Q psy29 9 DIKDFTEGRNVEHDIKDFTEGRNVILTLKDQDILAEDASDTLVNVNMVDDERHKKNVLNRKQKVGGKFGYSALDEDEFDE 88 (222)
Q Consensus 9 t~~d~L~GlkV~H~~~~f~eG~~vILTLKD~~ILde~e~D~LeNv~L~e~ek~kknle~kkkk~~~~~~Y~~ydDeefDe 88 (222)
+...+|+||+|+|+++.|.+|.+|||||||++||+|+ | + |||++.++..+|++++++++ .|-+|-++-+|+
T Consensus 186 ~~~sdL~G~kV~Hg~e~f~eg~~~ILTLKD~~VLdd~--d--v-~n~~D~lenvk~ve~kkrne----~~~~~~~e~ydD 256 (705)
T KOG2217|consen 186 YGNSDLHGVKVSHGIEAFSEGKDVILTLKDQSVLDDG--D--V-VNLVDVLENVKNVELKKRNE----KYELYPDEMYDD 256 (705)
T ss_pred CCCcccccceeecchhhhccCCceEEEeccccccccc--c--c-hhhHHHHHHHHHHHHhccCc----hhcccccccchh
Confidence 4455699999999999999999999999999999998 4 4 99999999999999999998 566653344788
Q ss_pred CCCccccccccCcccccccccccceEechh------------hhhhhcc-------CCCCCCcCCCCCCcccc-cccCCC
Q psy29 89 DGNPRESQLLSKYDEEIEGTKKKSFAIARW------------TLNLKVG-------GSSPSQLASDYLTEDEV-KFKKPK 148 (222)
Q Consensus 89 ~G~~k~k~iL~KYDEEieg~k~~~F~Lg~~------------~lkk~l~-------~~~~~~~aSDY~t~eEm-kFKKpK 148 (222)
+|+++++++|++||++.+|+..++|+|... .++.++. ......++|+||+++|| +|||||
T Consensus 257 ~~n~k~~s~l~k~dee~E~e~~k~~~l~~~g~id~e~ekkl~e~r~ki~gk~~~~~e~~n~~las~~~S~eem~kFkk~K 336 (705)
T KOG2217|consen 257 LGNKKPRSELSKYDEELEGEGKKQFRLTTHGTIDGEREKKLEEIRNKIAGKTLTGLEDVNYRLASDYYSQEEMGKFKKPK 336 (705)
T ss_pred hccccchhhhccCChhhhcccCcceeeecccccchhhHHHHHHHHHHhccCCccchhhcCHHHhhhhcCHHHhhcccchh
Confidence 999999999999999999999999998864 2344443 34456889999999999 999999
Q ss_pred cccchhhhcccccccccCCC-CCCCCCCCcccccccCC
Q psy29 149 KKVRKIRKTKLRADDLLNMD-SGADQSSEMMKREVKSE 185 (222)
Q Consensus 149 KKkkk~Rkk~~~~ddL~~~~-~~~~~~~D~GsR~~~~~ 185 (222)
| +|++|++.+++.||.|++ +.+.+.+|||||.+.+.
T Consensus 337 k-~kklrkk~l~asdl~~~~~~~~~~~~Dlgsr~~gr~ 373 (705)
T KOG2217|consen 337 K-KKKLRKKNLRASDLRPLAIGDGMEISDLGSRDSGRR 373 (705)
T ss_pred H-Hhhhhcccccccccchhhcccccccccccccccchh
Confidence 9 689999989999999986 78999999999776443
No 3
>PF06375 BLVR: Bovine leukaemia virus receptor (BLVR); InterPro: IPR010474 Bovine leukemia virus (BLV) is one of the most common infectious cattle viruses, with between 30 and 40% of cows in the United States being infected. It is closely related to the human T-cell leukaemia virus type 1 (HTLV-1) and has highly conserved envelope glycoprotein functional domains []. BLV is an oncogenic C-type retrovirus, which results in the animals developing a malignant lymphoma. BLV, like the human and simian T cell leukaemia viruses, is a deltaretrovirus. 182 residues at the amino-terminal of the BLV envelope glycoprotein surface unit encompass the receptor-binding domain. The metabolic activity in B cells, T cells, and thymocytes is indicated by the expression of the BLV-binding receptor []. A candidate gene of the receptor (BLVR) is related, but unique, to a gene family of the delta subunit of the adaptor protein (AP) complex 3, AP-3 []. The AP-3 complex is not clathrin-associated but is associated with the Golgi region as well as more peripheral structures. It facilitates the budding of vesicles from the Golgi membrane and may be directly involved in trafficking to lysosomes. ; PDB: 4AFI_B.
Probab=22.38 E-value=36 Score=29.09 Aligned_cols=13 Identities=15% Similarity=0.097 Sum_probs=4.9
Q ss_pred cCCCCCCcccc-cc
Q psy29 132 LASDYLTEDEV-KF 144 (222)
Q Consensus 132 ~aSDY~t~eEm-kF 144 (222)
..||.|-..+- .+
T Consensus 63 ~~sdkYl~~~~~~~ 76 (154)
T PF06375_consen 63 KGSDKYLKQQQERR 76 (154)
T ss_dssp SS-SSEEESST---
T ss_pred chhHHHHHHHHhhh
Confidence 45565544444 65
No 4
>PHA00726 hypothetical protein
Probab=11.53 E-value=98 Score=24.48 Aligned_cols=11 Identities=55% Similarity=0.718 Sum_probs=8.3
Q ss_pred cccCCCcccch
Q psy29 143 KFKKPKKKVRK 153 (222)
Q Consensus 143 kFKKpKKKkkk 153 (222)
=|+|||-|+.+
T Consensus 25 LFRKpK~k~~~ 35 (89)
T PHA00726 25 LFRKPKPKKVK 35 (89)
T ss_pred HhcCCCCchhh
Confidence 48999987654
No 5
>KOG2217|consensus
Probab=11.27 E-value=47 Score=34.58 Aligned_cols=22 Identities=23% Similarity=0.188 Sum_probs=18.7
Q ss_pred CCeeeccccchHHHHHHHHHHh
Q psy29 47 SDTLVNVNMVDDERHKKNVLNR 68 (222)
Q Consensus 47 ~D~LeNv~L~e~ek~kknle~k 68 (222)
.|+|+||.+++..+.+...+..
T Consensus 228 ~D~lenvk~ve~kkrne~~~~~ 249 (705)
T KOG2217|consen 228 VDVLENVKNVELKKRNEKYELY 249 (705)
T ss_pred HHHHHHHHHHHHhccCchhccc
Confidence 5899999999998887777666
No 6
>cd02252 nylC_like nylC-like family; composed of proteins with similarity to Flavobacterium endo-type 6-aminohexanoate-oligomer hydrolase (EIII), the product of the nylon oligomer degradation gene, nylC. EIII is an amide hydrolase that catalyzes the degradation of highly-polymerized 6-aminohexanoate oligomers. Together with other nylon degradation enzymes, such as 6-aminohexanoate cyclic dimer hydrolase (EI) and 6-aminohexanoate dimer hydrolase (EII), EIII plays a role in the detoxification and biological removal of the synthetic by-products of nylon manufacture. EIII shows sequence similarity to L-aminopeptidase D-amidase/D-esterase (DmpA), an aminopeptidase that releases N-terminal D and L amino acids from peptide substrates. Like DmpA, EIII undergoes autocatalytic cleavage in front of a nucleophile to form a heterodimer. DmpA shows similarity in catalytic mechanism to N-terminal nucleophile (Ntn) hydrolases, which are enzymes that catalyze the cleavage of amide bonds through the nucl
Probab=9.93 E-value=1.9e+02 Score=26.77 Aligned_cols=23 Identities=30% Similarity=0.289 Sum_probs=16.8
Q ss_pred CCCCceeeeccc-ccCCCCcEEEE
Q psy29 13 FTEGRNVEHDIK-DFTEGRNVILT 35 (222)
Q Consensus 13 ~L~GlkV~H~~~-~f~eG~~vILT 35 (222)
|..||+|+|... +...|=++||-
T Consensus 3 DV~Gv~VGh~t~~~~~TGvTvIl~ 26 (260)
T cd02252 3 DVPGIRVGHATDEEGLTGVTVILC 26 (260)
T ss_pred CCCCcEEeceEcCCCCceeEEEEe
Confidence 489999999854 34456677775
No 7
>COG3191 DmpA L-aminopeptidase/D-esterase [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=8.37 E-value=2.4e+02 Score=27.32 Aligned_cols=24 Identities=29% Similarity=0.218 Sum_probs=19.2
Q ss_pred cCCCCceeeecccc---cCCCCcEEEE
Q psy29 12 DFTEGRNVEHDIKD---FTEGRNVILT 35 (222)
Q Consensus 12 d~L~GlkV~H~~~~---f~eG~~vILT 35 (222)
.|.+||+|+|-... +..|=++||.
T Consensus 18 TDV~Gi~VGh~T~~~~~~~TGVTvILp 44 (348)
T COG3191 18 TDVPGIKVGHVTLIRGDVRTGVTVILP 44 (348)
T ss_pred ecCCceEeeeEecccCCccCceEEEec
Confidence 45899999998854 6778888885
No 8
>PF15333 TAF1D: TATA box-binding protein-associated factor 1D
Probab=8.23 E-value=83 Score=28.48 Aligned_cols=9 Identities=56% Similarity=0.837 Sum_probs=4.9
Q ss_pred cccCCCccc
Q psy29 143 KFKKPKKKV 151 (222)
Q Consensus 143 kFKKpKKKk 151 (222)
.|||+|||+
T Consensus 57 ~fkkrkrKk 65 (217)
T PF15333_consen 57 RFKKRKRKK 65 (217)
T ss_pred HHHHHHHHH
Confidence 476665443
No 9
>PF03303 WTF: WTF protein; InterPro: IPR004982 This is a family of mainly hypothetical Schizosacchoromyces pombe proteins that are often encoded near long terminal repeats within the genome. Their function is unknown but they contain several predicted transmembrane regions and at least one protein is up-regulated during meiosis []. Upregulation is also observed in histone deacetylase mutants, indicating their transcription is normally inhibited by hypoacetylation [].
Probab=7.55 E-value=3.1e+02 Score=25.33 Aligned_cols=14 Identities=36% Similarity=0.503 Sum_probs=11.8
Q ss_pred ccccccCccccccc
Q psy29 94 ESQLLSKYDEEIEG 107 (222)
Q Consensus 94 ~k~iL~KYDEEieg 107 (222)
++|.|++|+-|.+|
T Consensus 27 EKG~lpeynSeees 40 (247)
T PF03303_consen 27 EKGPLPEYNSEEES 40 (247)
T ss_pred ccCCCCcccCCCCC
Confidence 67899999988666
No 10
>PF03576 Peptidase_S58: Peptidase family S58 ; InterPro: IPR005321 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) [, ]. This group of serine peptidases belong to MEROPS peptidase family S58 (DmpA aminopeptidase family, clan PB(S)). The protein fold of the peptidase unit for members of this family resembles that of archaean proteasome subunit B, the type example of clan PB. The type example is aminopeptidase DmpA from OOchrobactrum anthropi. This family also contains proteins that have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the family. L-aminopeptidase D-Ala-esterase/amidase (DmpA) from O. anthropi releases the N-terminal L and/or D-Ala residues from peptide substrates. This is the only known enzyme to liberate N-terminal amino acids with both D and L stereospecificity. DmpA active form is an alphabeta heterodimer, which results from a putative autocatalytic cleavage of an inactive precursor polypeptide. DmpA shows structural homology to N-terminal nucleophile (Ntn) hydrolase family members, and may work by a similar catalytic mechanism, however their secondary structure elements differ significantly [].; PDB: 2DRH_D 3N5I_D 3N33_A 3NFB_A 3N2W_C 3NDV_D 1B65_C 3AXG_O 3S3U_A.
Probab=7.39 E-value=1.6e+02 Score=27.80 Aligned_cols=23 Identities=30% Similarity=0.361 Sum_probs=17.7
Q ss_pred CCCCceeeecccc---cCCCCcEEEE
Q psy29 13 FTEGRNVEHDIKD---FTEGRNVILT 35 (222)
Q Consensus 13 ~L~GlkV~H~~~~---f~eG~~vILT 35 (222)
|..||+|+|-... ...|=++||.
T Consensus 6 DV~Gv~VGh~t~~~~~~~TGvTvIl~ 31 (326)
T PF03576_consen 6 DVPGVRVGHATDEDGEARTGVTVILP 31 (326)
T ss_dssp GSTT-EEEEEEEEETTEEEEEEEEET
T ss_pred cCCCcEEEeEECCCCCcCcceEEEEe
Confidence 4899999999885 5667788877
Done!