Query psy10312
Match_columns 73
No_of_seqs 19 out of 21
Neff 1.7
Searched_HMMs 46136
Date Fri Aug 16 23:17:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10312.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10312hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14737 DUF4470: Domain of un 68.6 1.6 3.4E-05 27.1 -0.0 13 45-57 1-13 (100)
2 PF03991 Prion_octapep: Copper 60.8 3.9 8.4E-05 17.5 0.4 7 54-60 2-8 (8)
3 PF08736 FA: FERM adjacent (FA 43.9 9.3 0.0002 22.3 0.4 8 1-8 6-13 (47)
4 PHA02673 ORF109 EEV glycoprote 34.7 14 0.00031 27.0 0.2 48 13-64 83-135 (161)
5 KOG0570|consensus 33.4 25 0.00053 27.1 1.3 29 29-62 25-53 (223)
6 PRK07772 single-stranded DNA-b 31.5 60 0.0013 23.3 3.0 23 39-64 161-183 (186)
7 PF10185 Mesd: Chaperone for w 25.9 34 0.00074 24.4 0.9 16 19-34 80-95 (158)
8 COG4750 LicC CTP:phosphocholin 23.3 38 0.00083 26.2 0.8 30 1-31 10-39 (231)
9 cd06588 PhnB_like Escherichia 22.9 53 0.0012 20.0 1.3 23 23-47 89-111 (128)
10 TIGR03074 PQQ_membr_DH membran 21.9 28 0.00061 29.6 -0.2 23 17-39 707-729 (764)
11 COG0491 GloB Zn-dependent hydr 21.6 46 0.00099 20.9 0.8 12 40-52 141-152 (252)
12 PF11946 DUF3463: Domain of un 20.4 54 0.0012 23.3 1.0 19 39-59 56-74 (138)
13 PRK12404 stage V sporulation p 20.4 41 0.0009 26.8 0.5 8 4-11 145-152 (334)
No 1
>PF14737 DUF4470: Domain of unknown function (DUF4470)
Probab=68.59 E-value=1.6 Score=27.15 Aligned_cols=13 Identities=54% Similarity=1.135 Sum_probs=10.1
Q ss_pred CCcCCCCCCCCCc
Q psy10312 45 PWGHTPATNIGGT 57 (73)
Q Consensus 45 PWGhtP~~N~GGT 57 (73)
||||+|+.++=-.
T Consensus 1 ~wG~tpA~dl~~~ 13 (100)
T PF14737_consen 1 PWGNTPATDLLNL 13 (100)
T ss_pred CcCCcccHHHHHh
Confidence 7999999876433
No 2
>PF03991 Prion_octapep: Copper binding octapeptide repeat; InterPro: IPR020949 Prion protein (PrP-c) [, , ] is a small glycoprotein found in high quantity in the brain of animals infected with certain degenerative neurological diseases, such as sheep scrapie and bovine spongiform encephalopathy (BSE), and the human dementias Creutzfeldt-Jacob disease (CJD) and Gerstmann-Straussler syndrome (GSS). PrP-c is encoded in the host genome and is expressed both in normal and infected cells. During infection, however, the PrP-c molecule become altered (conformationally rather than at the amino acid level) to an abnormal isoform, PrP-sc. In detergent-treated brain extracts from infected individuals, fibrils composed of polymers of PrP-sc, namely scrapie-associated fibrils or prion rods, can be evidenced by electron microscopy. The precise function of the normal PrP isoform in healthy individuals remains unknown. Several results, mainly obtained in transgenic animals, indicate that PrP-c might play a role in long-term potentiation, in sleep physiology, in oxidative burst compensation (PrP can fix four Cu2+ through its octarepeat domain), in interactions with the extracellular matrix (PrP-c can bind to the precursor of the laminin receptor, LRP), in apoptosis and in signal transduction (costimulation of PrP-c induces a modulation of Fyn kinase phosphorylation) []. The normal isoform, PrP-c, is anchored at the cell membrane, in rafts, through a glycosyl phosphatidyl inositol (GPI); its half-life at the cell surface is 5 h, after which the protein is internalised through a caveolae-dependent mechanism and degraded in the endolysosome compartment. Conversion between PrP-c and PrP-sc occurs likely during the internalisation process. This repeat is found at the amino terminus of mammalian prion proteins. It has been shown to bind to copper [].
Probab=60.77 E-value=3.9 Score=17.45 Aligned_cols=7 Identities=57% Similarity=1.541 Sum_probs=5.4
Q ss_pred CCCcccc
Q psy10312 54 IGGTWGE 60 (73)
Q Consensus 54 ~GGTWGe 60 (73)
+||+||.
T Consensus 2 hgG~Wgq 8 (8)
T PF03991_consen 2 HGGGWGQ 8 (8)
T ss_pred CCCcCCC
Confidence 6899983
No 3
>PF08736 FA: FERM adjacent (FA); InterPro: IPR014847 This region is found adjacent to Band 4.1 / FERM domains (IPR000299 from INTERPRO) in a subset of FERM containing protein. The region has been hypothesised to play a role in regulatory adaptation, based on similarity to other protein kinase substrates [].
Probab=43.94 E-value=9.3 Score=22.29 Aligned_cols=8 Identities=50% Similarity=1.310 Sum_probs=6.3
Q ss_pred CCccccce
Q psy10312 1 MGSRFRFP 8 (73)
Q Consensus 1 ~~~~~~~~ 8 (73)
+||+|||-
T Consensus 6 ~GSkFRYS 13 (47)
T PF08736_consen 6 LGSKFRYS 13 (47)
T ss_pred CcCcceec
Confidence 68899874
No 4
>PHA02673 ORF109 EEV glycoprotein; Provisional
Probab=34.70 E-value=14 Score=27.00 Aligned_cols=48 Identities=31% Similarity=0.626 Sum_probs=30.6
Q ss_pred CCceeccccchhhh-Hhhh---hcCCCCCCCCc-cCCCCcCCCCCCCCCccccCCCC
Q psy10312 13 GANCCFIFTGTELW-EANL---RNGGQPPPQVA-QKTPWGHTPATNIGGTWGEDDEG 64 (73)
Q Consensus 13 g~~~~~~nnGTelW-EaNL---RNGGQpp~q~~-~ktPWGhtP~~N~GGTWGeDDd~ 64 (73)
|-.|...+.. ..| |||. +.|+..|.+-. .|.|| =..-+=||||+|-.+
T Consensus 83 ~~~Cltl~~p-~tf~eAn~~C~~~g~~LPs~~l~~~~pW---L~dYL~gTWg~~g~~ 135 (161)
T PHA02673 83 GNKCLTLKYP-DTWTNANERCKELGQRLPSPSINKKYPW---LTDYLVGTWGNIKER 135 (161)
T ss_pred CCeeEEeCCC-CcHHHHHHHHHhcCCcCCCCcccccCcH---HHHHhhcccccCCCC
Confidence 4444444533 345 5665 35667776654 56799 577888999997655
No 5
>KOG0570|consensus
Probab=33.42 E-value=25 Score=27.13 Aligned_cols=29 Identities=31% Similarity=0.637 Sum_probs=18.9
Q ss_pred hhhcCCCCCCCCccCCCCcCCCCCCCCCccccCC
Q psy10312 29 NLRNGGQPPPQVAQKTPWGHTPATNIGGTWGEDD 62 (73)
Q Consensus 29 NLRNGGQpp~q~~~ktPWGhtP~~N~GGTWGeDD 62 (73)
|+-+|-+|||+++-+.-+ --.|++|-+||
T Consensus 25 ni~~~sAP~pP~p~~~tY-----~~FG~~~~~dd 53 (223)
T KOG0570|consen 25 NINKGSAPPPPPPILGTY-----KMFGEEYREDD 53 (223)
T ss_pred cccCCCCCcccCCCccch-----hhhccccchhc
Confidence 444577777766545444 36799999655
No 6
>PRK07772 single-stranded DNA-binding protein; Provisional
Probab=31.47 E-value=60 Score=23.31 Aligned_cols=23 Identities=26% Similarity=0.758 Sum_probs=13.6
Q ss_pred CCccCCCCcCCCCCCCCCccccCCCC
Q psy10312 39 QVAQKTPWGHTPATNIGGTWGEDDEG 64 (73)
Q Consensus 39 q~~~ktPWGhtP~~N~GGTWGeDDd~ 64 (73)
+.+..-||.-.| -.|-+|-+||.
T Consensus 161 ~~~~~~~w~~~~---~~~~~~~~~~~ 183 (186)
T PRK07772 161 SAPADDPWSSAP---ASGGFGGGDDE 183 (186)
T ss_pred CCCCCCccccCC---CCCCcCCCCCC
Confidence 346788998666 33445554443
No 7
>PF10185 Mesd: Chaperone for wingless signalling and trafficking of LDL receptor; InterPro: IPR019330 Mesoderm development candidate 2 (also known as LDLR chaperone MESD)represents a set of highly conserved proteins found from nematodes to humans. It is a chaperone that specifically assists with the folding of beta-propeller/EGF modules within the family of low-density lipoprotein receptors (LDLRs). It also acts as a modulator of the Wnt pathway, since some LDLRs are coreceptors for the canonical Wnt pathway and is essential for specification of embryonic polarity and mesoderm induction []. The final C-terminal residues, KEDL, are the endoplasmic reticulum retention sequence as it is an ER protein specifically required for the intracellular trafficking of members of the low-density lipoprotein family of receptors (LDLRs) []. The N- and C-terminal sequences are predicted to adopt a random coil conformation, with the exception of an isolated predicted helix within the N-terminal region, The central folded domain flanked by natively unstructured regions is the necessary structure for facilitating maturation of LRP6 (Low-Density Lipoprotein Receptor-Related Protein 6 Maturation) []. ; PDB: 2RQM_A 2I9S_A 3OFH_A 2KGL_A 2RQK_A 2KMI_A 3OFG_A 3OFE_B 3OFF_A.
Probab=25.93 E-value=34 Score=24.44 Aligned_cols=16 Identities=38% Similarity=0.574 Sum_probs=12.4
Q ss_pred cccchhhhHhhhhcCC
Q psy10312 19 IFTGTELWEANLRNGG 34 (73)
Q Consensus 19 ~nnGTelWEaNLRNGG 34 (73)
+..=|.+|.++|||+.
T Consensus 80 ~e~i~~~Wq~~L~N~h 95 (158)
T PF10185_consen 80 TEEITKLWQTSLRNNH 95 (158)
T ss_dssp HHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHhhCC
Confidence 3344679999999995
No 8
>COG4750 LicC CTP:phosphocholine cytidylyltransferase involved in choline phosphorylation for cell surface LPS epitopes [Cell envelope biogenesis, outer membrane]
Probab=23.28 E-value=38 Score=26.23 Aligned_cols=30 Identities=30% Similarity=0.471 Sum_probs=24.0
Q ss_pred CCccccceeeccCCceeccccchhhhHhhhh
Q psy10312 1 MGSRFRFPLEFLGANCCFIFTGTELWEANLR 31 (73)
Q Consensus 1 ~~~~~~~~~~~~g~~~~~~nnGTelWEaNLR 31 (73)
|||||+ ||.+--++.----+|+++=|-+++
T Consensus 10 ~gsR~~-plT~~tpK~LlkV~g~plIErqI~ 39 (231)
T COG4750 10 LGSRFV-PLTQSTPKSLLKVNGEPLIERQIE 39 (231)
T ss_pred cccccc-cccccCChHHHHhcCcccHHHHHH
Confidence 689997 887777777777789999888765
No 9
>cd06588 PhnB_like Escherichia coli PhnB and similar proteins; the E. coli phnB gene is found next to an operon involved in the cleavage of carbon-phosphorus bonds in unactivated alkylphosphonates. The Escherichia coli phnB gene is found next to an operon of fourteen genes (phnC-to-phnP) related to the cleavage of carbon-phosphorus (C-P) bonds in unactivated alkylphosphonates, supporting bacterial growth on alkylphosphonates as the sole phosphorus source. It was originally considered part of that operon. PhnB appears to play no direct catalytic role in the usage of alkylphosphonate. Although many of the proteins in this family have been annotated as 3-demethylubiquinone-9 3-methyltransferase enzymes by automatic annotation programs, the experimental evidence for this assignment is lacking. In Escherichia coli, the gene coding 3-demethylubiquinone-9 3-methyltransferase enzyme is ubiG, which belongs to the AdoMet-MTase protein family. PhnB-like proteins adopt a structural fold similar to
Probab=22.93 E-value=53 Score=19.99 Aligned_cols=23 Identities=43% Similarity=0.624 Sum_probs=15.6
Q ss_pred hhhhHhhhhcCCCCCCCCccCCCCc
Q psy10312 23 TELWEANLRNGGQPPPQVAQKTPWG 47 (73)
Q Consensus 23 TelWEaNLRNGGQpp~q~~~ktPWG 47 (73)
.++|+. |..||+. -++.+++|||
T Consensus 89 ~~~~~~-l~~~g~~-~~~~~~~~~g 111 (128)
T cd06588 89 DRLFEA-LSEGGTV-LMPLQKTFWS 111 (128)
T ss_pred HHHHHH-HhcCCeE-eccchhcCcc
Confidence 367775 9999843 3455677998
No 10
>TIGR03074 PQQ_membr_DH membrane-bound PQQ-dependent dehydrogenase, glucose/quinate/shikimate family. This protein family has a phylogenetic distribution very similar to that coenzyme PQQ biosynthesis enzymes, as shown by partial phylogenetic profiling. Members of this family have several predicted transmembrane helices in the N-terminal region, and include the quinoprotein glucose dehydrogenase (EC 1.1.5.2) of Escherichia coli and the quinate/shikimate dehydrogenase of Acinetobacter sp. ADP1 (EC 1.1.99.25). Sequences closely related except for the absense of the N-terminal hydrophobic region, scoring in the gray zone between the trusted and noise cutoffs, include PQQ-dependent glycerol (EC 1.1.99.22) and and other polyol (sugar alcohol) dehydrogenases.
Probab=21.90 E-value=28 Score=29.63 Aligned_cols=23 Identities=48% Similarity=0.806 Sum_probs=19.5
Q ss_pred eccccchhhhHhhhhcCCCCCCC
Q psy10312 17 CFIFTGTELWEANLRNGGQPPPQ 39 (73)
Q Consensus 17 ~~~nnGTelWEaNLRNGGQpp~q 39 (73)
....||.+||++.|-.+++..|.
T Consensus 707 ~D~~tGk~lW~~~l~~~~~a~P~ 729 (764)
T TIGR03074 707 YDLSTGKELWKARLPAGGQATPM 729 (764)
T ss_pred EECCCCceeeEeeCCCCcccCCE
Confidence 34678999999999999988874
No 11
>COG0491 GloB Zn-dependent hydrolases, including glyoxylases [General function prediction only]
Probab=21.63 E-value=46 Score=20.87 Aligned_cols=12 Identities=50% Similarity=0.839 Sum_probs=9.0
Q ss_pred CccCCCCcCCCCC
Q psy10312 40 VAQKTPWGHTPAT 52 (73)
Q Consensus 40 ~~~ktPWGhtP~~ 52 (73)
.+-.+| ||||..
T Consensus 141 ~~i~tp-GHT~g~ 152 (252)
T COG0491 141 EVLHTP-GHTPGH 152 (252)
T ss_pred EEEECC-CCCCCe
Confidence 356788 999964
No 12
>PF11946 DUF3463: Domain of unknown function (DUF3463); InterPro: IPR022563 This functionally uncharacterised domain is found in bacteria and archaea, which is about 140 amino acids in length and is found C-terminal to PF04055 from PFAM. It contains two conserved sequence motifs: CTPWG and PCYL. This domain is associated with hopanoid biosynthesis associated radical SAM proteins.
Probab=20.41 E-value=54 Score=23.26 Aligned_cols=19 Identities=42% Similarity=0.886 Sum_probs=15.6
Q ss_pred CCccCCCCcCCCCCCCCCccc
Q psy10312 39 QVAQKTPWGHTPATNIGGTWG 59 (73)
Q Consensus 39 q~~~ktPWGhtP~~N~GGTWG 59 (73)
+.-.-|||| +|+-|+=| |-
T Consensus 56 ~~~~CtPWg-~pt~n~~G-wq 74 (138)
T PF11946_consen 56 RDYECTPWG-NPTRNPFG-WQ 74 (138)
T ss_pred CCCcccCCC-CCccCccc-cc
Confidence 466889999 89999877 74
No 13
>PRK12404 stage V sporulation protein AD; Provisional
Probab=20.37 E-value=41 Score=26.78 Aligned_cols=8 Identities=50% Similarity=1.385 Sum_probs=7.0
Q ss_pred cccceeec
Q psy10312 4 RFRFPLEF 11 (73)
Q Consensus 4 ~~~~~~~~ 11 (73)
.||||+|.
T Consensus 145 qfR~P~ey 152 (334)
T PRK12404 145 QFRYPTEY 152 (334)
T ss_pred hccCcccc
Confidence 59999996
Done!