Query psy12298
Match_columns 68
No_of_seqs 99 out of 101
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 15:22:25 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12298.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12298hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2301|consensus 98.0 1E-06 2.2E-11 78.1 -0.4 42 24-66 39-80 (1592)
2 PF06512 Na_trans_assoc: Sodiu 87.6 0.18 3.8E-06 35.2 0.1 16 50-66 218-233 (239)
3 PF03531 SSrecog: Structure-sp 46.9 4.8 0.0001 29.7 -0.7 15 39-53 189-203 (222)
4 PF10217 DUF2039: Uncharacteri 43.5 6.6 0.00014 25.9 -0.3 14 52-67 34-47 (92)
5 KOG2452|consensus 30.3 17 0.00038 31.5 0.1 32 31-64 546-577 (881)
6 PRK05500 bifunctional orotidin 27.9 45 0.00098 27.0 2.0 24 37-60 13-52 (477)
7 PF01785 Closter_coat: Closter 24.6 43 0.00094 23.2 1.2 13 45-57 94-106 (188)
8 PF06744 DUF1215: Protein of u 24.5 55 0.0012 21.0 1.6 18 50-67 43-60 (125)
9 PF02407 Viral_Rep: Putative v 23.7 39 0.00085 21.3 0.8 10 42-51 4-13 (86)
10 PF10765 DUF2591: Protein of u 23.0 56 0.0012 20.4 1.4 15 44-58 92-106 (109)
11 PF13789 DUF4181: Domain of un 20.9 38 0.00083 21.6 0.3 9 54-62 74-82 (110)
No 1
>KOG2301|consensus
Probab=98.01 E-value=1e-06 Score=78.13 Aligned_cols=42 Identities=19% Similarity=0.137 Sum_probs=36.1
Q ss_pred CCCCCCCCCCCCCCCceeEEeeccChHHHHhhHhhhccCCCCC
Q psy12298 24 RPIRRAGKPPPDRPQRALFCLTLKNPLRKMCIDVVEWKYPLSS 66 (68)
Q Consensus 24 k~~~~~g~~~~~rp~RSLFcltl~NPiRk~ci~IVEWkyPFey 66 (68)
.....+++.....++|+|||||.+||+||.||+|+||+ ||++
T Consensus 39 ~~~~k~~~~~~~~~~~~l~~~s~~n~~R~~~i~i~~~~-~f~~ 80 (1592)
T KOG2301|consen 39 GVLAKGKAIFRFSAISALLSLSPFNPIRSSAIKILVHP-WFSL 80 (1592)
T ss_pred cccccccccCCCCcchhhhhcCcccchhhheeeeeccc-cHHH
Confidence 33444567777899999999999999999999999999 7986
No 2
>PF06512 Na_trans_assoc: Sodium ion transport-associated; InterPro: IPR010526 Members of this entry contain a region found exclusively in eukaryotic sodium channels or their subunits, many of which are voltage-gated. Members very often also contain between one and four copies of IPR005821 from INTERPRO and, less often, one copy of IPR000048 from INTERPRO.; GO: 0005248 voltage-gated sodium channel activity, 0006814 sodium ion transport, 0001518 voltage-gated sodium channel complex
Probab=87.59 E-value=0.18 Score=35.16 Aligned_cols=16 Identities=44% Similarity=0.877 Sum_probs=14.7
Q ss_pred HHHHhhHhhhccCCCCC
Q psy12298 50 LRKMCIDVVEWKYPLSS 66 (68)
Q Consensus 50 iRk~ci~IVEWkyPFey 66 (68)
||+.|-+|||-+| ||.
T Consensus 218 ~R~~c~~iVeh~~-FEt 233 (239)
T PF06512_consen 218 LRKTCYRIVEHKW-FET 233 (239)
T ss_pred HHhhheeeecccc-hhh
Confidence 8999999999998 983
No 3
>PF03531 SSrecog: Structure-specific recognition protein (SSRP1); InterPro: IPR000969 Human structure-specific recognition protein, SSRP1, [] binds specifically to DNA modified with the anti-cancer drug cisplatin. An 81kDa protein is predicted, containing several highly-charged domains and a stretch of 75 residues that share 47% identity with a portion of the high mobility group (HMG) protein HMG1. This HMG box probably constitutes the structure recognition element for cisplatin-modified DNA, the probable recognition motif being the local duplex unwinding and bending that occurs on formation of intra-strand cross-links []. SSRP1 is the human homologue of a recently identified mouse protein that binds to recombination signal sequences []. These sequences have been postulated to form stem-loop structures, further implicating local bends and unwinding in DNA as a recognition target for HMG-box proteins. A Drosophila melanogaster cDNA encoding an HMG-box-containing protein has also been isolated [, ]. This protein shares 50% sequence identity with human SSRP1. In vitro binding studies using Drosophila SSRP showed that the protein binds to single-stranded DNA and RNA, with highest affinity for nucleotides G and U. Comparison of the predicted amino acid sequences among SSRP family members reveals 48% identity, with structural conservation in the C terminus of the HMG box, as well as domains of highly charged residues. The most highly conserved regions lie in the poorly understood N terminus, suggesting that this portion of the protein is critical for its function []. This entry contains Pob3 Q04636 from SWISSPROT, which is a subunit of the heterodimeric yeast FACT complex (Spt16p (IPR013953 from INTERPRO)-Pob3p) []. The FACT complex facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilising and then reassembling nucleosome structure [, ].; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 3F5R_A 2GCL_B 2GCJ_D.
Probab=46.94 E-value=4.8 Score=29.71 Aligned_cols=15 Identities=27% Similarity=0.682 Sum_probs=13.4
Q ss_pred ceeEEeeccChHHHH
Q psy12298 39 RALFCLTLKNPLRKM 53 (68)
Q Consensus 39 RSLFcltl~NPiRk~ 53 (68)
-.+|+++|+.|||+.
T Consensus 189 ~~~~Vi~LdpPiRQG 203 (222)
T PF03531_consen 189 HVFFVISLDPPIRQG 203 (222)
T ss_dssp EEEEEEEEEEEEEET
T ss_pred ccccccccccccccc
Confidence 569999999999975
No 4
>PF10217 DUF2039: Uncharacterized conserved protein (DUF2039); InterPro: IPR019351 This entry is a region of approximately 100 residues containing three pairs of cysteine residues. The region is conserved from plants to humans but its function is unknown.
Probab=43.50 E-value=6.6 Score=25.90 Aligned_cols=14 Identities=36% Similarity=0.952 Sum_probs=10.9
Q ss_pred HHhhHhhhccCCCCCC
Q psy12298 52 KMCIDVVEWKYPLSSK 67 (68)
Q Consensus 52 k~ci~IVEWkyPFey~ 67 (68)
.-|..||||+ +.|+
T Consensus 34 ~rC~~~IeWK--~kY~ 47 (92)
T PF10217_consen 34 QRCKDIIEWK--VKYG 47 (92)
T ss_pred HhHHHHHHHH--HHhc
Confidence 4699999998 5554
No 5
>KOG2452|consensus
Probab=30.33 E-value=17 Score=31.54 Aligned_cols=32 Identities=41% Similarity=0.812 Sum_probs=25.4
Q ss_pred CCCCCCCCceeEEeeccChHHHHhhHhhhccCCC
Q psy12298 31 KPPPDRPQRALFCLTLKNPLRKMCIDVVEWKYPL 64 (68)
Q Consensus 31 ~~~~~rp~RSLFcltl~NPiRk~ci~IVEWkyPF 64 (68)
...+.||+|-| ||+++.||- .|--|+-|-||.
T Consensus 546 pi~~arpn~nl-~lt~~epig-v~g~i~pwnypl 577 (881)
T KOG2452|consen 546 PINQARPNRNL-TLTRKEPVG-VCGIIIPWNYPL 577 (881)
T ss_pred ccccCCCCCcc-eeeecCcce-eEEEeccCCchH
Confidence 34556889886 899999995 566788999985
No 6
>PRK05500 bifunctional orotidine 5'-phosphate decarboxylase/orotate phosphoribosyltransferase protein; Validated
Probab=27.90 E-value=45 Score=27.01 Aligned_cols=24 Identities=17% Similarity=0.170 Sum_probs=19.2
Q ss_pred CCceeEEeeccC----------------hHHHHhhHhhhc
Q psy12298 37 PQRALFCLTLKN----------------PLRKMCIDVVEW 60 (68)
Q Consensus 37 p~RSLFcltl~N----------------PiRk~ci~IVEW 60 (68)
..+|+.|++||= +|+.+|..|||-
T Consensus 13 ~~~s~LcvGLDP~~~~lp~~~~~~~~~~~~~~f~~~ii~a 52 (477)
T PRK05500 13 QNQSLLVVGLDPNPEMMPGRYSSQSLIQQLWTWLKFIIEE 52 (477)
T ss_pred HhCCCEEEEECCChhhChhhcCCcchHHHHHHHHHHHHHH
Confidence 357888887764 899999999984
No 7
>PF01785 Closter_coat: Closterovirus coat protein; InterPro: IPR002679 This family consist of coat proteins from closterovirus, which belong to the Closteroviridae, which have a positive strand ssRNA genome with no DNA stage during replication. The viral coat protein encapsulates and protects the viral genome. Both the large cp1 and smaller cp2 coat protein originate from the same primary transcript []. Members of the Closterovirus include Beet yellows virus (BYV) (Sugar beet yellows virus) and Grapevine leafroll-associated virus 7.; GO: 0044423 virion part
Probab=24.63 E-value=43 Score=23.19 Aligned_cols=13 Identities=31% Similarity=0.483 Sum_probs=10.7
Q ss_pred eccChHHHHhhHh
Q psy12298 45 TLKNPLRKMCIDV 57 (68)
Q Consensus 45 tl~NPiRk~ci~I 57 (68)
...||+|++|...
T Consensus 94 ~~~N~lR~f~R~~ 106 (188)
T PF01785_consen 94 GYPNPLRQFMRSF 106 (188)
T ss_pred CCCcHHHHHHHHh
Confidence 4679999999864
No 8
>PF06744 DUF1215: Protein of unknown function (DUF1215); InterPro: IPR010623 This domain represents a conserved region situated towards the C-terminal end of several hypothetical bacterial proteins of unknown function. A few members resemble the ImcF protein, which has been proposed [] to be involved in Vibrio cholerae cell surface reorganisation that results in increased adherence to epithelial cells line and increased conjugation frequency.
Probab=24.50 E-value=55 Score=21.00 Aligned_cols=18 Identities=17% Similarity=0.587 Sum_probs=14.1
Q ss_pred HHHHhhHhhhccCCCCCC
Q psy12298 50 LRKMCIDVVEWKYPLSSK 67 (68)
Q Consensus 50 iRk~ci~IVEWkyPFey~ 67 (68)
+=..|...++=+|||+-.
T Consensus 43 V~~~~~~~i~gRYPF~~~ 60 (125)
T PF06744_consen 43 VYPFCRQAIAGRYPFDPD 60 (125)
T ss_pred HHHHHHHHhcCCCCCCCC
Confidence 345789999999999843
No 9
>PF02407 Viral_Rep: Putative viral replication protein; InterPro: IPR003365 Proteins in this entry are essential for the replication of viral ssDNA. The closed circular ssDNA genome is first converted to a superhelical dsDNA. Rep and/or Rep' binds a specific hairpin at the genome origin of replication introducing an endonucleolytic nick within the conserved sequence 5'-AGTATTAC-3'. This initiates rolling circle replication (RCR). Following cleavage, the protein binds covalently to the 5'-phosphate of DNA as a tyrosyl ester. The cleavage gives rise to a free 3'-OH that serves as a primer for the cellular DNA polymerase. The polymerase synthesizes the (+) strand DNA by rolling circle mechanism. After one round of replication, a Rep-catalyzed nucleotidyl transfer reaction releases a circular single-stranded virus genome, thereby terminating the replication.; GO: 0016779 nucleotidyltransferase activity, 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters, 0042624 ATPase activity, uncoupled, 0006260 DNA replication, 0018142 protein-DNA covalent cross-linking; PDB: 2HW0_A 2HWT_A.
Probab=23.66 E-value=39 Score=21.28 Aligned_cols=10 Identities=50% Similarity=1.162 Sum_probs=7.2
Q ss_pred EEeeccChHH
Q psy12298 42 FCLTLKNPLR 51 (68)
Q Consensus 42 Fcltl~NPiR 51 (68)
+|||+.||--
T Consensus 4 WcFTlNn~~~ 13 (86)
T PF02407_consen 4 WCFTLNNPTE 13 (86)
T ss_dssp EEEEEES--H
T ss_pred EEEEEeCCCc
Confidence 7999999965
No 10
>PF10765 DUF2591: Protein of unknown function (DUF2591); InterPro: IPR019701 This entry is represented by Bacteriophage P22, NinX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=23.05 E-value=56 Score=20.42 Aligned_cols=15 Identities=27% Similarity=0.180 Sum_probs=12.2
Q ss_pred eeccChHHHHhhHhh
Q psy12298 44 LTLKNPLRKMCIDVV 58 (68)
Q Consensus 44 ltl~NPiRk~ci~IV 58 (68)
..=+||||-++|-+|
T Consensus 92 ~~~~~pLrAAM~~fl 106 (109)
T PF10765_consen 92 QYGENPLRAAMRVFL 106 (109)
T ss_pred ecCCCHHHHHHHHHh
Confidence 346799999999876
No 11
>PF13789 DUF4181: Domain of unknown function (DUF4181)
Probab=20.92 E-value=38 Score=21.65 Aligned_cols=9 Identities=44% Similarity=0.999 Sum_probs=6.9
Q ss_pred hhHhhhccC
Q psy12298 54 CIDVVEWKY 62 (68)
Q Consensus 54 ci~IVEWky 62 (68)
+..++||||
T Consensus 74 ~ra~mEWKy 82 (110)
T PF13789_consen 74 FRAFMEWKY 82 (110)
T ss_pred HHHHHHHHh
Confidence 456889996
Done!