Query 041836
Match_columns 574
No_of_seqs 9 out of 11
Neff 1.4
Searched_HMMs 46136
Date Fri Mar 29 11:09:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041836.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041836hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01433 Peptidase_M1: Peptida 5.4 2.7E+02 0.0059 26.4 0.6 13 62-74 138-150 (390)
2 PF13041 PPR_2: PPR repeat fam 4.3 1.1E+03 0.024 16.3 3.0 27 307-333 20-46 (50)
3 PF05419 GUN4: GUN4-like ; In 3.9 1.9E+02 0.0041 26.0 -1.4 10 59-68 37-46 (132)
4 KOG1046 Puromycin-sensitive am 3.8 4E+02 0.0087 30.1 0.7 18 61-78 166-183 (882)
5 PF08776 VASP_tetra: VASP tetr 3.6 7.1E+02 0.015 19.5 1.6 19 537-555 11-29 (40)
6 PRK00907 hypothetical protein; 3.2 4.9E+02 0.011 22.4 0.4 12 62-74 13-24 (92)
7 TIGR00756 PPR pentatricopeptid 3.0 1.1E+03 0.023 14.0 1.7 17 307-323 17-33 (35)
8 PRK14082 hypothetical protein; 3.0 3.4E+02 0.0073 23.0 -0.7 16 56-71 45-60 (65)
9 COG2238 RPS19A Ribosomal prote 3.0 8.3E+02 0.018 23.4 1.7 31 532-564 91-121 (147)
10 PF08529 NusA_N: NusA N-termin 2.8 6.9E+02 0.015 21.5 0.9 37 536-572 18-54 (122)
No 1
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 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 M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=5.36 E-value=2.7e+02 Score=26.35 Aligned_cols=13 Identities=38% Similarity=0.677 Sum_probs=8.0
Q ss_pred CCCCCCCCccccc
Q 041836 62 NFPCTDVPAEVNN 74 (574)
Q Consensus 62 nfpctdvpaevnn 74 (574)
-|||.|-|..-..
T Consensus 138 ~fPc~D~p~~ka~ 150 (390)
T PF01433_consen 138 WFPCFDEPSFKAT 150 (390)
T ss_dssp TSSB--STTSEEE
T ss_pred eeeeeccCCccce
Confidence 4999999976543
No 2
>PF13041 PPR_2: PPR repeat family
Probab=4.26 E-value=1.1e+03 Score=16.29 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=21.1
Q ss_pred chhhHHHHhhhhCCCCCchhhHHHHHH
Q 041836 307 SKAMAIVDEMKAKPQEPSKVIVEEFAE 333 (574)
Q Consensus 307 skamaivdemkakpqepskviveefae 333 (574)
..|..++++|+...-.|..+...-+..
T Consensus 20 ~~a~~l~~~M~~~g~~P~~~Ty~~li~ 46 (50)
T PF13041_consen 20 EEALKLFKEMKKRGIKPDSYTYNILIN 46 (50)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHH
Confidence 578999999999998888776554443
No 3
>PF05419 GUN4: GUN4-like ; InterPro: IPR008629 In Arabidopsis, GUN4 is required for the functioning of the plastid mediated repression of nuclear transcription that is involved in controlling the levels of magnesium- protoporphyrin IX. GUN4 binds the product and substrate of Mg-chelatase, an enzyme that produces Mg-Proto, and activates Mg-chelatase. GUN4 is thought to participate in plastid-to-nucleus signalling by regulating magnesium-protoporphyrin IX synthesis or trafficking.; PDB: 1Y6I_A 1Z3X_A 1Z3Y_A.
Probab=3.88 E-value=1.9e+02 Score=26.04 Aligned_cols=10 Identities=50% Similarity=1.345 Sum_probs=5.3
Q ss_pred ccCCCCCCCC
Q 041836 59 KVDNFPCTDV 68 (574)
Q Consensus 59 kvdnfpctdv 68 (574)
.+.+|||.|+
T Consensus 37 ~i~~~pc~dL 46 (132)
T PF05419_consen 37 DIKNFPCEDL 46 (132)
T ss_dssp HHCTS-HHHH
T ss_pred HHHhCCHHHH
Confidence 4566666654
No 4
>KOG1046 consensus Puromycin-sensitive aminopeptidase and related aminopeptidases [Amino acid transport and metabolism; Posttranslational modification, protein turnover, chaperones]
Probab=3.84 E-value=4e+02 Score=30.08 Aligned_cols=18 Identities=39% Similarity=0.565 Sum_probs=12.7
Q ss_pred CCCCCCCCCcccccCccc
Q 041836 61 DNFPCTDVPAEVNNVDNT 78 (574)
Q Consensus 61 dnfpctdvpaevnnvdnt 78 (574)
--|||.|-|+---...-+
T Consensus 166 ~~FPCfDeP~~KAtF~It 183 (882)
T KOG1046|consen 166 RAFPCFDEPAFKATFTIT 183 (882)
T ss_pred hcCCCCCcccccCceEEE
Confidence 469999999875544433
No 5
>PF08776 VASP_tetra: VASP tetramerisation domain; InterPro: IPR014885 Vasodilator-stimulated phosphoprotein (VASP) is an actin cytoskeletal regulatory protein. This region corresponds to the tetramerisation domain which forms a right handed alpha helical coiled coil structure []. ; PDB: 1USE_A 1USD_A.
Probab=3.63 E-value=7.1e+02 Score=19.52 Aligned_cols=19 Identities=37% Similarity=0.653 Sum_probs=15.0
Q ss_pred hhHHHHHHHHhhhhhhhcc
Q 041836 537 NLLSKVKQSLGKVKKAIVG 555 (574)
Q Consensus 537 NiisKVKQSLVKaKKAI~G 555 (574)
-||.-|+.-|.|+|.-||.
T Consensus 11 EIL~EvrkEl~K~K~EIIe 29 (40)
T PF08776_consen 11 EILEEVRKELQKVKEEIIE 29 (40)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4778888888888888774
No 6
>PRK00907 hypothetical protein; Provisional
Probab=3.20 E-value=4.9e+02 Score=22.44 Aligned_cols=12 Identities=17% Similarity=0.285 Sum_probs=8.9
Q ss_pred CCCCCCCCccccc
Q 041836 62 NFPCTDVPAEVNN 74 (574)
Q Consensus 62 nfpctdvpaevnn 74 (574)
.||| |.|--|-.
T Consensus 13 EFPc-~fpiKVmG 24 (92)
T PRK00907 13 QFPG-TFELSAMG 24 (92)
T ss_pred ecCC-CCeEEEEE
Confidence 5999 78877743
No 7
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=2.97 E-value=1.1e+03 Score=14.02 Aligned_cols=17 Identities=29% Similarity=0.515 Sum_probs=11.9
Q ss_pred chhhHHHHhhhhCCCCC
Q 041836 307 SKAMAIVDEMKAKPQEP 323 (574)
Q Consensus 307 skamaivdemkakpqep 323 (574)
.+|+.++++|+..--.|
T Consensus 17 ~~a~~~~~~M~~~g~~p 33 (35)
T TIGR00756 17 EEALELFKEMLERGIEP 33 (35)
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 36788888887765444
No 8
>PRK14082 hypothetical protein; Provisional
Probab=2.96 E-value=3.4e+02 Score=23.02 Aligned_cols=16 Identities=38% Similarity=0.652 Sum_probs=13.5
Q ss_pred eecccCCCCCCCCCcc
Q 041836 56 EVEKVDNFPCTDVPAE 71 (574)
Q Consensus 56 evekvdnfpctdvpae 71 (574)
-++|++++-|..+|.-
T Consensus 45 i~eK~~~~~~~e~PGF 60 (65)
T PRK14082 45 IIEKADMLLCQEVPGF 60 (65)
T ss_pred HHHHHHHhhcccCCcH
Confidence 4789999999999963
No 9
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=2.95 E-value=8.3e+02 Score=23.39 Aligned_cols=31 Identities=39% Similarity=0.640 Sum_probs=22.3
Q ss_pred CcccchhHHHHHHHHhhhhhhhccCCCCCcccc
Q 041836 532 QKSSGNLLSKVKQSLGKVKKAIVGKSPSSKTLQ 564 (574)
Q Consensus 532 QK~SNNiisKVKQSLVKaKKAI~GKSPssKtls 564 (574)
-+-|.+|+.+|-|.|-+| -++-|+|--..|+
T Consensus 91 ~~gsgsI~RkilqqLE~~--G~V~k~~~GR~lt 121 (147)
T COG2238 91 RKGSGSIIRKVLQQLEKA--GLVEKTPKGRVLT 121 (147)
T ss_pred hcCCchHHHHHHHHHHHC--CceeecCCCceeC
Confidence 378999999999999886 3555666433443
No 10
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=2.76 E-value=6.9e+02 Score=21.48 Aligned_cols=37 Identities=16% Similarity=0.204 Sum_probs=24.8
Q ss_pred chhHHHHHHHHhhhhhhhccCCCCCccccccccCCCC
Q 041836 536 GNLLSKVKQSLGKVKKAIVGKSPSSKTLQSEAKGDEN 572 (574)
Q Consensus 536 NNiisKVKQSLVKaKKAI~GKSPssKtlssdaKGDiK 572 (574)
.-|+..++++|.+|=+--.|......-.-..-+|+++
T Consensus 18 e~v~~ale~al~~a~kK~~~~~~~~~v~id~~~g~i~ 54 (122)
T PF08529_consen 18 EVVIEALEEALIKAYKKKYGPEANIRVEIDEDTGEIK 54 (122)
T ss_dssp HHHHHHHHHHHHHHHHCCTTSSSSEEEEEETTTTEEE
T ss_pred HHHHHHHHHHHHHHHHHhhCCCCCEEEEEECCCCeEE
Confidence 3578999999999988888755444333344455544
Done!