Query 034289
Match_columns 99
No_of_seqs 30 out of 32
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 11:51:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034289.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034289hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12714 TILa: TILa domain 45.7 11 0.00024 23.3 0.9 18 73-90 36-53 (56)
2 PF10736 DUF2527: Protein of u 34.1 14 0.00031 22.7 0.1 7 1-7 1-7 (38)
3 PF07629 DUF1590: Protein of u 30.6 23 0.0005 21.0 0.6 10 75-84 5-14 (32)
4 PF03145 Sina: Seven in absent 20.7 36 0.00077 24.8 0.2 10 72-81 42-51 (198)
5 PRK13867 type IV secretion sys 19.0 50 0.0011 22.3 0.6 11 74-84 51-61 (65)
6 KOG2004 Mitochondrial ATP-depe 16.6 66 0.0014 30.7 1.0 15 4-18 465-486 (906)
7 KOG0124 Polypyrimidine tract-b 16.0 42 0.00092 29.9 -0.4 30 2-34 498-527 (544)
8 PF01308 Chlam_OMP: Chlamydia 14.0 80 0.0017 27.5 0.8 14 80-93 29-42 (389)
9 PRK09511 nirD nitrite reductas 13.6 1.1E+02 0.0024 20.6 1.2 21 76-96 45-72 (108)
10 PF13465 zf-H2C2_2: Zinc-finge 12.7 65 0.0014 16.8 -0.1 8 71-78 11-18 (26)
No 1
>PF12714 TILa: TILa domain
Probab=45.67 E-value=11 Score=23.29 Aligned_cols=18 Identities=22% Similarity=0.479 Sum_probs=16.1
Q ss_pred CCcCCCCCCCcccccccc
Q 034289 73 LPIQCPLPEPSILNVSLK 90 (99)
Q Consensus 73 ~PV~CP~PE~sIl~Dgl~ 90 (99)
+|.+|++-|-+.++||+.
T Consensus 36 ~~~~C~~~e~C~~~~G~~ 53 (56)
T PF12714_consen 36 QPSSCPPGEVCQIQNGVR 53 (56)
T ss_pred eCCCCCCCCEeEeCCCEE
Confidence 578999999999999975
No 2
>PF10736 DUF2527: Protein of unknown function (DUF2627) ; InterPro: IPR019672 This entry represents small proteins with unknown function and appear to be restricted to a family of Enterobacterial proteins. It has a highly conserved sequence. Some proteins are annotated as YobF and may be involved in stress responses in E. coli.
Probab=34.13 E-value=14 Score=22.70 Aligned_cols=7 Identities=71% Similarity=1.170 Sum_probs=5.9
Q ss_pred Ccceeee
Q 034289 1 MVGIFSR 7 (99)
Q Consensus 1 MVGiFsR 7 (99)
|-|||||
T Consensus 1 M~GIFSK 7 (38)
T PF10736_consen 1 MNGIFSK 7 (38)
T ss_pred CcccccH
Confidence 7899986
No 3
>PF07629 DUF1590: Protein of unknown function (DUF1590); InterPro: IPR011481 These hypothetical proteins in Rhodopirellula baltica have a conserved C-terminal region.
Probab=30.62 E-value=23 Score=21.02 Aligned_cols=10 Identities=50% Similarity=1.016 Sum_probs=8.0
Q ss_pred cCCCCCCCcc
Q 034289 75 IQCPLPEPSI 84 (99)
Q Consensus 75 V~CP~PE~sI 84 (99)
..||+||-|+
T Consensus 5 a~~pppeisl 14 (32)
T PF07629_consen 5 ADCPPPEISL 14 (32)
T ss_pred CCCCCCccee
Confidence 4699999775
No 4
>PF03145 Sina: Seven in absentia protein family; InterPro: IPR018121 The seven in absentia (sina) gene was first identified in Drosophila. The Drosophila Sina protein is essential for the determination of the R7 pathway in photoreceptor cell development: the loss of functional Sina results in the transformation of the R7 precursor cell to a non-neuronal cell type. The Sina protein contains an N-terminal RING finger domain C3HC4-type. Through this domain, Sina binds E2 ubiquitin-conjugating enzymes (UbcD1) Sina also interacts with Tramtrack (TTK88) via PHYL. Tramtrack is a transcriptional repressor that blocks photoreceptor determination, while PHYL down-regulates the activity of TTK88. In turn, the activity of PHYL requires the activation of the Sevenless receptor tyrosine kinase, a process essential for R7 determination. It is thought that Sina targets TTK88 for degradation, therefore promoting the R7 pathway. Murine and human homologues of Sina have also been identified. The human homologue Siah-1 [] also binds E2 enzymes (UbcH5) and through a series of physical interactions, targets beta-catenin for ubiquitin degradation. Siah-1 expression is enhanced by p53, itself promoted by DNA damage. Thus this pathway links DNA damage to beta-catenin degradation [, ]. Sina proteins, therefore, physically interact with a variety of proteins. The N-terminal RING finger domain that binds ubiquitin conjugating enzymes is a C3HC4-type, and does not form part of the alignment for this family. The remainder C-terminal part is involved in interactions with other proteins, and is included in this alignment. In addition to the Drosophila protein and mammalian homologues, whose similarity was noted previously, this family also includes putative homologues from Caenorhabditis elegans, Arabidopsis thaliana.; GO: 0006511 ubiquitin-dependent protein catabolic process, 0007275 multicellular organismal development, 0005634 nucleus; PDB: 2A25_A 1K2F_B 2AN6_C.
Probab=20.74 E-value=36 Score=24.78 Aligned_cols=10 Identities=40% Similarity=0.929 Sum_probs=7.0
Q ss_pred CCCcCCCCCC
Q 034289 72 DLPIQCPLPE 81 (99)
Q Consensus 72 D~PV~CP~PE 81 (99)
=+|+.||.|.
T Consensus 42 ~~p~~CP~~~ 51 (198)
T PF03145_consen 42 FRPCSCPFPG 51 (198)
T ss_dssp TSEEE-SSSS
T ss_pred CcCCcCCCCC
Confidence 3789999875
No 5
>PRK13867 type IV secretion system chaperone VirE1; Provisional
Probab=19.04 E-value=50 Score=22.28 Aligned_cols=11 Identities=45% Similarity=1.204 Sum_probs=8.3
Q ss_pred CcCCCCCCCcc
Q 034289 74 PIQCPLPEPSI 84 (99)
Q Consensus 74 PV~CP~PE~sI 84 (99)
-.+||+||-..
T Consensus 51 vl~cplpednl 61 (65)
T PRK13867 51 VLRCPLPEDNL 61 (65)
T ss_pred hhcCCCCcccc
Confidence 46999998653
No 6
>KOG2004 consensus Mitochondrial ATP-dependent protease PIM1/LON [Posttranslational modification, protein turnover, chaperones]
Probab=16.61 E-value=66 Score=30.66 Aligned_cols=15 Identities=73% Similarity=1.090 Sum_probs=12.2
Q ss_pred eeeeecccc-------cCcccc
Q 034289 4 IFSRFSVGR-------AGHRRT 18 (99)
Q Consensus 4 iFsRfs~gr-------~~hRrt 18 (99)
=|-|||+|. .|||||
T Consensus 465 kFfRfSvGG~tDvAeIkGHRRT 486 (906)
T KOG2004|consen 465 KFFRFSVGGMTDVAEIKGHRRT 486 (906)
T ss_pred ceEEEeccccccHHhhccccee
Confidence 388999995 489998
No 7
>KOG0124 consensus Polypyrimidine tract-binding protein PUF60 (RRM superfamily) [RNA processing and modification]
Probab=16.00 E-value=42 Score=29.90 Aligned_cols=30 Identities=37% Similarity=0.557 Sum_probs=23.3
Q ss_pred cceeeeecccccCccccccccccccccCCCCCc
Q 034289 2 VGIFSRFSVGRAGHRRTQSAIDEREVLPPNPAV 34 (99)
Q Consensus 2 VGiFsRfs~gr~~hRrtqs~~d~re~~~~~~~i 34 (99)
|-||-.||.+.-.| |.+.+||+| |--|-.+
T Consensus 498 VKIFVefS~~~e~~-rak~ALdGR--fFgGr~V 527 (544)
T KOG0124|consen 498 VKIFVEFSIASETH-RAKQALDGR--FFGGRKV 527 (544)
T ss_pred heeeeeechhhHHH-HHHHhhccc--eecCcee
Confidence 77999999999888 677899999 5444333
No 8
>PF01308 Chlam_OMP: Chlamydia major outer membrane protein; InterPro: IPR000604 The major outer membrane protein of Chlamydia contains four symmetrically spaced variable domains (VDs I to IV). This protein maintains the structural rigidity of the outer membrane and facilitates porin formation, permitting diffusion of solutes through the intracellular reticulate body membrane. It is believed to play a role in pathogenesis and possibly adhesion. Along with the lipopolysaccharide, the major out membrane protein (MOMP) makes up the surface of the elementary body cell. Disulphide bond interactions within and between MOMP molecules and other components form high molecular weight oligomers. The MOMP is the protein used to determine the different serotypes.; GO: 0005198 structural molecule activity, 0015288 porin activity, 0009279 cell outer membrane
Probab=13.99 E-value=80 Score=27.45 Aligned_cols=14 Identities=21% Similarity=0.121 Sum_probs=11.4
Q ss_pred CCCcccccccccce
Q 034289 80 PEPSILNVSLKNLV 93 (99)
Q Consensus 80 PE~sIl~Dgl~~~~ 93 (99)
-|||++.||++|.-
T Consensus 29 AePsl~IdGi~wEg 42 (389)
T PF01308_consen 29 AEPSLMIDGILWEG 42 (389)
T ss_pred CCcccccCCccccc
Confidence 46789999999964
No 9
>PRK09511 nirD nitrite reductase small subunit; Provisional
Probab=13.61 E-value=1.1e+02 Score=20.59 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=13.2
Q ss_pred CCCCCCCccccccccc-------ceeee
Q 034289 76 QCPLPEPSILNVSLKN-------LVCSF 96 (99)
Q Consensus 76 ~CP~PE~sIl~Dgl~~-------~~c~~ 96 (99)
.||=-.-+.|.+|++. +.|||
T Consensus 45 ~CpH~~~~~L~~G~~~~~~g~~~V~CP~ 72 (108)
T PRK09511 45 IDPFFQASVLSRGLIAEHQGELWVASPL 72 (108)
T ss_pred cCCCCCCcccCCceEccCCCeEEEECCC
Confidence 5666555566666652 77776
No 10
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=12.75 E-value=65 Score=16.82 Aligned_cols=8 Identities=38% Similarity=1.186 Sum_probs=0.0
Q ss_pred CCCCcCCC
Q 034289 71 NDLPIQCP 78 (99)
Q Consensus 71 ~D~PV~CP 78 (99)
.++|++||
T Consensus 11 ~~k~~~C~ 18 (26)
T PF13465_consen 11 GEKPYKCP 18 (26)
T ss_dssp SSSSEEES
T ss_pred CCCCCCCC
Done!