Query psy8399
Match_columns 167
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 46136
Date Fri Aug 16 17:38:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8399.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8399hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PHA02151 hypothetical protein 10.7 1.7E+02 0.0037 24.8 1.7 16 132-147 197-212 (217)
2 TIGR00164 PS_decarb_rel phosph 6.1 1.6E+02 0.0035 22.5 -0.3 7 8-14 2-8 (189)
3 KOG3311|consensus 6.1 2.1E+02 0.0046 23.0 0.3 16 143-158 31-46 (152)
4 PF05508 Ran-binding: RanGTP-b 5.2 2.8E+02 0.006 24.3 0.5 12 139-150 195-206 (302)
5 PF00549 Ligase_CoA: CoA-ligas 4.7 3.2E+02 0.0069 20.9 0.5 11 49-59 50-60 (153)
6 PHA02705 hypothetical protein; 4.6 3.3E+02 0.0071 19.8 0.5 15 105-119 25-39 (72)
7 PF05299 Peptidase_M61: M61 gl 4.4 2.7E+02 0.0059 20.8 -0.0 15 72-86 9-23 (122)
8 PF03153 TFIIA: Transcription 3.6 6.2E+02 0.013 20.6 1.4 8 155-162 334-341 (375)
9 TIGR03511 GldH_lipo gliding mo 3.6 1.2E+03 0.026 17.9 2.9 23 130-152 45-67 (156)
10 PF11777 DUF3316: Protein of u 3.5 5.9E+02 0.013 17.9 1.1 10 40-49 105-114 (114)
No 1
>PHA02151 hypothetical protein
Probab=10.65 E-value=1.7e+02 Score=24.82 Aligned_cols=16 Identities=56% Similarity=1.003 Sum_probs=14.0
Q ss_pred EEEEecCceeEEEEee
Q psy8399 132 SMYINRNHSMYTLFYG 147 (167)
Q Consensus 132 smyinrnhsmytlfyg 147 (167)
..||||+|.-|.-||.
T Consensus 197 gayinr~h~~~v~fy~ 212 (217)
T PHA02151 197 GAYINRNHDRYVHFYK 212 (217)
T ss_pred ceeecccCceEEEEeh
Confidence 4699999999999984
No 2
>TIGR00164 PS_decarb_rel phosphatidylserine decarboxylase precursor-related protein. It is unclear whether this protein is a form of phosphatidylserine decarboxylase or is a related enzyme. It is found in Neisseria gonorrhoeae, Mycobacterium tuberculosis, and several archaeal species, all of which lack known phosphatidylserine decarboxylase.
Probab=6.13 E-value=1.6e+02 Score=22.48 Aligned_cols=7 Identities=71% Similarity=1.630 Sum_probs=4.6
Q ss_pred cceeeec
Q psy8399 8 SMYHAWY 14 (167)
Q Consensus 8 smyhawy 14 (167)
||||+|.
T Consensus 2 ~~~~~~~ 8 (189)
T TIGR00164 2 SMYHGWI 8 (189)
T ss_pred ccchhHH
Confidence 5677764
No 3
>KOG3311|consensus
Probab=6.12 E-value=2.1e+02 Score=23.04 Aligned_cols=16 Identities=31% Similarity=0.580 Sum_probs=14.1
Q ss_pred EEEeeeecCceeEEee
Q psy8399 143 TLFYGIRNRNVNVLCL 158 (167)
Q Consensus 143 tlfygirnrnvnvlcl 158 (167)
|.||||.-+..++.|-
T Consensus 31 ~~i~Gig~~~A~~ic~ 46 (152)
T KOG3311|consen 31 TSIKGIGRRYAEIVCK 46 (152)
T ss_pred EEEeeechhhhhhhhh
Confidence 6699999999999993
No 4
>PF05508 Ran-binding: RanGTP-binding protein; InterPro: IPR008812 The small Ras-like GTPase Ran plays an essential role in the transport of macromolecules in and out of the nucleus and has been implicated in spindle and nuclear envelope formation during mitosis in higher eukaryotes. The Saccharomyces cerevisiae ORF YGL164c encoding a novel RanGTP-binding protein, termed Yrb30p was identified. The protein competes with S. cerevisiae RanBP1 (Yrb1p) for binding to the GTP-bound form of S. cerevisiae Ran (Gsp1p) and is, like Yrb1p, able to form trimeric complexes with RanGTP and some of the karyopherins [].
Probab=5.21 E-value=2.8e+02 Score=24.28 Aligned_cols=12 Identities=50% Similarity=0.933 Sum_probs=9.5
Q ss_pred ceeEEEEeeeec
Q psy8399 139 HSMYTLFYGIRN 150 (167)
Q Consensus 139 hsmytlfygirn 150 (167)
-++|++|||--.
T Consensus 195 lslY~lF~~~sr 206 (302)
T PF05508_consen 195 LSLYMLFYGHSR 206 (302)
T ss_pred EEeeheeccccc
Confidence 378999999753
No 5
>PF00549 Ligase_CoA: CoA-ligase; InterPro: IPR005811 This entry represents a domain found in both the alpha and beta chains of succinyl-CoA synthase (6.2.1.4 from EC (GDP-forming) and 6.2.1.5 from EC (ADP-forming)) [, ]. This domain can also be found in ATP citrate synthase (2.3.3.8 from EC) and malate-CoA ligase (6.2.1.9 from EC). Some members of the domain utilise ATP others use GTP.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 3DMY_B 3MWE_B 3PFF_A 3MWD_B 2YV1_A 1EUC_A 2FP4_A 1EUD_A 2FPI_A 2FPG_A ....
Probab=4.67 E-value=3.2e+02 Score=20.92 Aligned_cols=11 Identities=45% Similarity=0.751 Sum_probs=5.6
Q ss_pred CccccccccCC
Q psy8399 49 NRIHPMYDNTR 59 (167)
Q Consensus 49 nrihpmydntr 59 (167)
.|-|||.|-+.
T Consensus 50 GrphPmid~~~ 60 (153)
T PF00549_consen 50 GRPHPMIDPST 60 (153)
T ss_dssp TS--TTT-SSH
T ss_pred cCcCCCcCHHH
Confidence 57789988654
No 6
>PHA02705 hypothetical protein; Provisional
Probab=4.60 E-value=3.3e+02 Score=19.79 Aligned_cols=15 Identities=53% Similarity=0.780 Sum_probs=11.6
Q ss_pred ccccccccccccccc
Q psy8399 105 NHSMYNTRNINRNHS 119 (167)
Q Consensus 105 nhsmyntrninrnhs 119 (167)
|-.|-|.+|||.||+
T Consensus 25 nvemennkninknhp 39 (72)
T PHA02705 25 NVEMENNKNINKNHP 39 (72)
T ss_pred hhhhhccccccccCc
Confidence 345778889999986
No 7
>PF05299 Peptidase_M61: M61 glycyl aminopeptidase; InterPro: IPR007963 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 M61 (glycyl aminopeptidase family, clan MA(E)).The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. The type example is glycyl aminopeptidase from Sphingomonas capsulata.
Probab=4.44 E-value=2.7e+02 Score=20.79 Aligned_cols=15 Identities=33% Similarity=0.882 Sum_probs=11.8
Q ss_pred CccceeecccCCCcc
Q psy8399 72 NHSMYHAWNDNRNHS 86 (167)
Q Consensus 72 nhsmyhawndnrnhs 86 (167)
.|..+|+||-.|-++
T Consensus 9 sHEffH~WnvkrirP 23 (122)
T PF05299_consen 9 SHEFFHSWNVKRIRP 23 (122)
T ss_pred hhhccccccceEecc
Confidence 488899999877665
No 8
>PF03153 TFIIA: Transcription factor IIA, alpha/beta subunit; InterPro: IPR004855 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the precursor that yields both the alpha and beta subunits of TFIIA. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II []. ; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_B 1YTF_B 1RM1_C 1NH2_B.
Probab=3.64 E-value=6.2e+02 Score=20.64 Aligned_cols=8 Identities=38% Similarity=1.265 Sum_probs=4.8
Q ss_pred EEeeeeee
Q psy8399 155 VLCLFNRI 162 (167)
Q Consensus 155 vlclfnri 162 (167)
|||+|.+|
T Consensus 334 ~~c~~~kv 341 (375)
T PF03153_consen 334 VLCQYDKV 341 (375)
T ss_dssp EEEEEEEE
T ss_pred EEEEeecc
Confidence 56666654
No 9
>TIGR03511 GldH_lipo gliding motility-associated lipoprotein GldH. Members of this protein family are predicted lipoproteins, exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). Members include GldH, a protein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Not all Bacteroidetes with members of this protein family may have gliding motility.
Probab=3.64 E-value=1.2e+03 Score=17.94 Aligned_cols=23 Identities=35% Similarity=0.544 Sum_probs=15.8
Q ss_pred eeEEEEecCceeEEEEeeeecCc
Q psy8399 130 HYSMYINRNHSMYTLFYGIRNRN 152 (167)
Q Consensus 130 hysmyinrnhsmytlfygirnrn 152 (167)
-|..-+.-...-|.||.+||+.+
T Consensus 45 ~F~~~~~d~~~~y~l~l~lR~n~ 67 (156)
T TIGR03511 45 DFEIPITDYTASYRLFLLIRNDN 67 (156)
T ss_pred EEEEeecCCCCcEEEEEEEEcCC
Confidence 34445555566788999999864
No 10
>PF11777 DUF3316: Protein of unknown function (DUF3316); InterPro: IPR016879 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=3.52 E-value=5.9e+02 Score=17.92 Aligned_cols=10 Identities=70% Similarity=1.149 Sum_probs=6.7
Q ss_pred eeeeeccCCC
Q psy8399 40 HYMYNTRNNN 49 (167)
Q Consensus 40 hymyntrnnn 49 (167)
+|-|++|+.|
T Consensus 105 ~y~Yn~RnsN 114 (114)
T PF11777_consen 105 DYQYNTRNSN 114 (114)
T ss_pred EEeeecCCCC
Confidence 4557888765
Done!