Query 023938
Match_columns 275
No_of_seqs 48 out of 50
Neff 2.8
Searched_HMMs 46136
Date Fri Mar 29 07:44:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06678 DUF1179: Protein of u 36.1 30 0.00066 29.0 2.4 13 1-13 1-13 (103)
2 PF02257 RFX_DNA_binding: RFX 27.7 32 0.00069 27.5 1.1 11 148-158 72-82 (85)
3 PF12273 RCR: Chitin synthesis 20.2 95 0.0021 25.4 2.6 10 46-55 62-71 (130)
4 KOG2164 Predicted E3 ubiquitin 16.4 96 0.0021 32.3 2.1 47 44-95 165-220 (513)
5 PF08097 Toxin_26: Conotoxin T 16.0 58 0.0013 17.7 0.3 6 83-88 1-6 (11)
6 cd08066 MPN_AMSH_like Mov34/MP 14.7 92 0.002 27.2 1.3 22 235-256 128-149 (173)
7 cd03035 ArsC_Yffb Arsenate Red 13.9 1.4E+02 0.003 23.8 2.0 17 196-212 6-22 (105)
8 PF04135 Nop10p: Nucleolar RNA 13.6 82 0.0018 23.5 0.6 14 244-257 24-37 (53)
9 PRK13130 H/ACA RNA-protein com 13.4 1E+02 0.0023 23.1 1.1 15 244-258 24-38 (56)
10 PF13240 zinc_ribbon_2: zinc-r 13.0 85 0.0018 19.4 0.5 10 147-156 12-22 (23)
No 1
>PF06678 DUF1179: Protein of unknown function (DUF1179); InterPro: IPR009564 This family consists of several hypothetical Caenorhabditis elegans proteins of around 106 residues in length. The function of the family is unknown.
Probab=36.13 E-value=30 Score=29.04 Aligned_cols=13 Identities=38% Similarity=0.603 Sum_probs=10.5
Q ss_pred CCChhhHHHHHHH
Q 023938 1 MPPFTFIFTLVIL 13 (275)
Q Consensus 1 ~~~~~~~~~~~~~ 13 (275)
|-.|+|||-.+++
T Consensus 1 m~~f~~i~~~i~l 13 (103)
T PF06678_consen 1 MFSFWFILKSIFL 13 (103)
T ss_pred CcchHHHHHHHHH
Confidence 6789999877766
No 2
>PF02257 RFX_DNA_binding: RFX DNA-binding domain; InterPro: IPR003150 RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DP7_P 2KW3_A.
Probab=27.65 E-value=32 Score=27.51 Aligned_cols=11 Identities=45% Similarity=1.035 Sum_probs=8.4
Q ss_pred ceeeeeceeec
Q 023938 148 AILCFCGIRLH 158 (275)
Q Consensus 148 ~vfCyCGIRL~ 158 (275)
.=|||+|||+.
T Consensus 72 SkYhY~Gir~k 82 (85)
T PF02257_consen 72 SKYHYCGIRLK 82 (85)
T ss_dssp -EEEEEEEEE-
T ss_pred cceEEEeEEec
Confidence 55999999997
No 3
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=20.22 E-value=95 Score=25.40 Aligned_cols=10 Identities=20% Similarity=0.531 Sum_probs=5.0
Q ss_pred CccCCccccc
Q 023938 46 TVPAFPAQTQ 55 (275)
Q Consensus 46 TIPAfPeQs~ 55 (275)
-+|.+.++..
T Consensus 62 ~~P~y~~~~~ 71 (130)
T PF12273_consen 62 YVPPYTETAN 71 (130)
T ss_pred CCCCCCCCCC
Confidence 4555555444
No 4
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=16.37 E-value=96 Score=32.31 Aligned_cols=47 Identities=21% Similarity=0.372 Sum_probs=39.2
Q ss_pred CCCccCCccccc---------cccCCCCCCccchhhhHhhhcCCCCCCCCcHHHHHHHHHH
Q 023938 44 TNTVPAFPAQTQ---------AATCRLDLSAELFGGVNEACGRDLDRSRCCPVLAAWLFAA 95 (275)
Q Consensus 44 ~~TIPAfPeQs~---------aa~CPLdlS~~lF~gV~sAC~~~~~R~RCCPvLAAWLyaA 95 (275)
-++.|-+|++|+ ...||.=|.++.++..-. || +-.|||-|=.|+-.+
T Consensus 165 qn~dpD~p~~~e~i~qv~~~t~~~CPICL~~~~~p~~t~-CG----HiFC~~CiLqy~~~s 220 (513)
T KOG2164|consen 165 QNTDPDAPVDWEDIFQVYGSTDMQCPICLEPPSVPVRTN-CG----HIFCGPCILQYWNYS 220 (513)
T ss_pred hccCCccccchHHhhhhhcCcCCcCCcccCCCCcccccc-cC----ceeeHHHHHHHHhhh
Confidence 578999999999 679999999999988777 99 889999876554433
No 5
>PF08097 Toxin_26: Conotoxin T-superfamily; InterPro: IPR012631 This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species [].; GO: 0005576 extracellular region
Probab=15.98 E-value=58 Score=17.68 Aligned_cols=6 Identities=67% Similarity=1.863 Sum_probs=4.4
Q ss_pred CCcHHH
Q 023938 83 RCCPVL 88 (275)
Q Consensus 83 RCCPvL 88 (275)
.|||++
T Consensus 1 fccpvi 6 (11)
T PF08097_consen 1 FCCPVI 6 (11)
T ss_pred CCcchh
Confidence 488876
No 6
>cd08066 MPN_AMSH_like Mov34/MPN/PAD-1 family. AMSH (associated molecule with the Src homology 3 domain (SH3) of STAM (signal-transducing adapter molecule, also known as STAMBP)) and AMSH-like proteins (AMSH-LP) are members of JAMM/MPN+ deubiquitinases (DUBs), with Zn2+-dependent ubiquitin isopeptidase activity. AMSH specifically cleaves Lys 63 and not Lys48-linked polyubiquitin (poly-Ub) chains, thus facilitating the recycling and subsequent trafficking of receptors to the cell surface. AMSH and AMSH-LP are anchored on the early endosomal membrane via interaction with the clathrin coat. AMSH shares a common SH3-binding site with another endosomal DUB, UBPY (ubiquitin-specific protease Y; also known as USP8), the latter being a cysteine protease that does not discriminate between Lys48 and Lys63-linked ubiquitin. AMSH is involved in the degradation of EGF receptor (EGFR) and possibly other ubiquitinated endocytosed proteins. AMSH also interacts with CHMP1, CHMP2, and CHMP3 proteins, al
Probab=14.69 E-value=92 Score=27.19 Aligned_cols=22 Identities=27% Similarity=0.471 Sum_probs=18.6
Q ss_pred CCCCCCCCCCcccCCCCCcccc
Q 023938 235 PADGADVAPGAQQNGVHPHRFS 256 (275)
Q Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~ 256 (275)
+.+|.+..-..++.|.|||+--
T Consensus 128 ~~~g~~~~~~~~~~~~h~~~~~ 149 (173)
T cd08066 128 DPPGLDEILNCKKTGFHPHPKD 149 (173)
T ss_pred cCCcceecccCCcCccCCCCCC
Confidence 4689999888899999999844
No 7
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=13.86 E-value=1.4e+02 Score=23.76 Aligned_cols=17 Identities=18% Similarity=0.296 Sum_probs=14.9
Q ss_pred CCChhHHHHHHHHHhhc
Q 023938 196 YSGCTKCLGALQMVAKR 212 (275)
Q Consensus 196 l~GCSKCL~AL~~l~~~ 212 (275)
..+|++|-.|+..|+.+
T Consensus 6 ~~~C~~crka~~~L~~~ 22 (105)
T cd03035 6 IKNCDTVKKARKWLEAR 22 (105)
T ss_pred CCCCHHHHHHHHHHHHc
Confidence 46899999999999874
No 8
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=13.61 E-value=82 Score=23.46 Aligned_cols=14 Identities=43% Similarity=0.812 Sum_probs=9.8
Q ss_pred CcccCCCCCccccc
Q 023938 244 GAQQNGVHPHRFSR 257 (275)
Q Consensus 244 ~~~~~~~~~~~~~~ 257 (275)
|.+--..||.|||-
T Consensus 24 G~~T~~ahPaRFSP 37 (53)
T PF04135_consen 24 GGPTESAHPARFSP 37 (53)
T ss_dssp SSBSEESSSSSS-T
T ss_pred CCCCcCCcCCCCCC
Confidence 55566789999984
No 9
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=13.41 E-value=1e+02 Score=23.08 Aligned_cols=15 Identities=40% Similarity=0.702 Sum_probs=12.2
Q ss_pred CcccCCCCCcccccc
Q 023938 244 GAQQNGVHPHRFSRV 258 (275)
Q Consensus 244 ~~~~~~~~~~~~~~~ 258 (275)
|..-...||.|||-.
T Consensus 24 G~~t~~~~P~rfSp~ 38 (56)
T PRK13130 24 GGKTKNPHPPRFSPE 38 (56)
T ss_pred CCCCCCCCCCCCCCC
Confidence 677788999999853
No 10
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=12.98 E-value=85 Score=19.40 Aligned_cols=10 Identities=50% Similarity=1.066 Sum_probs=5.1
Q ss_pred cceee-eecee
Q 023938 147 DAILC-FCGIR 156 (275)
Q Consensus 147 D~vfC-yCGIR 156 (275)
|+.|| +||.+
T Consensus 12 ~~~fC~~CG~~ 22 (23)
T PF13240_consen 12 DAKFCPNCGTP 22 (23)
T ss_pred cCcchhhhCCc
Confidence 34555 55544
Done!