Query psy8052
Match_columns 67
No_of_seqs 38 out of 40
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 17:10:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8052.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8052hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2346|consensus 99.6 3.1E-16 6.7E-21 126.0 6.2 61 5-67 443-503 (636)
2 PF01402 RHH_1: Ribbon-helix-h 80.7 2.4 5.2E-05 21.9 2.6 25 13-37 10-34 (39)
3 TIGR03687 pupylate_cterm ubiqu 72.4 3.8 8.2E-05 22.5 2.0 22 5-26 12-33 (33)
4 PHA01623 hypothetical protein 59.9 8.9 0.00019 22.3 2.0 23 15-37 26-48 (56)
5 PHA01748 hypothetical protein 57.9 12 0.00027 21.9 2.4 23 15-37 15-37 (60)
6 PF12651 RHH_3: Ribbon-helix-h 56.4 13 0.00028 20.5 2.2 23 15-37 15-37 (44)
7 KOG2888|consensus 55.3 11 0.00023 30.5 2.4 38 26-63 198-235 (453)
8 PRK11675 LexA regulated protei 45.7 19 0.0004 23.4 2.0 26 13-38 61-86 (90)
9 PF08681 DUF1778: Protein of u 45.5 26 0.00057 21.2 2.6 25 12-36 9-33 (80)
10 PF08221 HTH_9: RNA polymerase 42.3 47 0.001 19.2 3.2 46 5-58 7-52 (62)
11 PF05639 Pup: Pup-like protein 37.7 8.8 0.00019 24.0 -0.4 21 6-26 49-69 (69)
12 PF02637 GatB_Yqey: GatB domai 37.5 77 0.0017 20.6 4.0 47 10-61 59-105 (148)
13 PRK13858 type IV secretion sys 35.9 90 0.0019 21.9 4.3 47 15-63 37-84 (147)
14 PF09274 ParG: ParG; InterPro 32.3 50 0.0011 20.8 2.4 30 15-46 47-76 (76)
15 PF03685 UPF0147: Uncharacteri 31.8 30 0.00065 22.3 1.3 20 44-63 22-41 (85)
16 COG1698 Uncharacterized protei 30.3 46 0.00099 22.0 2.0 20 44-63 29-48 (93)
17 PF11757 RSS_P20: Suppressor o 29.3 98 0.0021 21.6 3.6 35 15-63 86-120 (137)
18 PF03487 IL13: Interleukin-13; 28.6 72 0.0016 18.4 2.4 23 43-65 18-40 (43)
19 PF04336 DUF479: Protein of un 28.0 99 0.0021 19.4 3.3 51 9-60 20-71 (106)
20 PHA00617 ribbon-helix-helix do 27.6 64 0.0014 20.4 2.3 24 14-37 51-74 (80)
21 PRK04330 hypothetical protein; 24.7 71 0.0015 20.7 2.1 19 44-62 25-43 (88)
22 PF01291 LIF_OSM: LIF / OSM fa 23.7 83 0.0018 22.2 2.5 23 5-28 9-31 (162)
23 PF07377 DUF1493: Protein of u 23.1 54 0.0012 20.8 1.4 14 29-42 96-109 (111)
24 PF07304 SRA1: Steroid recepto 22.5 1.4E+02 0.0031 20.2 3.4 39 18-65 104-142 (157)
25 PF11738 DUF3298: Protein of u 22.3 80 0.0017 17.5 1.9 19 5-23 1-19 (78)
26 PF10723 RepB-RCR_reg: Replica 21.7 1.5E+02 0.0033 18.4 3.2 27 12-38 51-77 (84)
27 PRK13877 conjugal transfer rel 20.5 1.6E+02 0.0034 19.4 3.2 23 15-37 23-45 (114)
No 1
>KOG2346|consensus
Probab=99.64 E-value=3.1e-16 Score=126.03 Aligned_cols=61 Identities=33% Similarity=0.522 Sum_probs=57.0
Q ss_pred HHHHhhchHHHHHHHHHHHHhHHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHHhhhhcC
Q psy8052 5 LSLLFGSSPDFLGVVVLEIERSIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEELTLVDNQ 67 (67)
Q Consensus 5 ~~~~~~~aaq~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel~aiD~~ 67 (67)
+---|+ |++|+.||++.+|+.+|+||||+++++||+...|||+||++|+|+|||+++||.|
T Consensus 443 lc~~~r--a~kLl~hY~~~~gl~vs~~LrK~~~t~~w~~~~epr~vra~v~r~vee~~~~d~e 503 (636)
T KOG2346|consen 443 LCRVFR--AEKLLQHYIDTRGLKVSVLLRKRFKTPNWVKHKEPREVRAYVDRFVEELEEVDKE 503 (636)
T ss_pred HHHHHH--HHHHHHHHHhhcchhHHHHHHHHhcCCccccccccchHHHHHHHHHHHHHHHhHH
Confidence 344566 9999999999999999999999999999999999999999999999999999974
No 2
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=80.71 E-value=2.4 Score=21.86 Aligned_cols=25 Identities=8% Similarity=-0.124 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 13 PDFLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 13 aq~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
-.+.++.+++..|...|++||..++
T Consensus 10 ~~~~l~~~a~~~g~s~s~~ir~ai~ 34 (39)
T PF01402_consen 10 LYERLDELAKELGRSRSELIREAIR 34 (39)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHH
Confidence 4567899999999999999999854
No 3
>TIGR03687 pupylate_cterm ubiquitin-like protein Pup. Members of this protein family are Pup, a small protein whose ligation to target proteins steers them toward degradation. This protein family occurs in a number of bacteria, especially Actinobacteria such as Mycobacterium tuberculosis, that possess an archeal-type proteasome. All members of this protein family known during model construction end with the C-terminal motif [FY][VI]QKGG[QE]. Ligation is thought to occur between the C-terminal COOH of Pup and an epsilon-amino group of a Lys on the target protein. The N-terminal half of this protein is poorly conserved and not represented in the seed alignment.
Probab=72.37 E-value=3.8 Score=22.54 Aligned_cols=22 Identities=5% Similarity=-0.037 Sum_probs=18.7
Q ss_pred HHHHhhchHHHHHHHHHHHHhH
Q psy8052 5 LSLLFGSSPDFLGVVVLEIERS 26 (67)
Q Consensus 5 ~~~~~~~aaq~Ll~~yv~~qG~ 26 (67)
+.++.+.-|+.+++.||++.|.
T Consensus 12 Id~vLe~NAe~FV~~fVQKGGe 33 (33)
T TIGR03687 12 IDGVLESNAEEFVRGFVQKGGE 33 (33)
T ss_pred HHHHHHHhHHHHHHHHHHccCC
Confidence 4567889999999999999873
No 4
>PHA01623 hypothetical protein
Probab=59.90 E-value=8.9 Score=22.33 Aligned_cols=23 Identities=9% Similarity=0.024 Sum_probs=20.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
.-|+-|....|...|+.||.+|.
T Consensus 26 ~~Ld~y~~~~g~~rSe~IreAI~ 48 (56)
T PHA01623 26 TRLKVYCAKNNLQLTQAIEEAIK 48 (56)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 45788999999999999999865
No 5
>PHA01748 hypothetical protein
Probab=57.93 E-value=12 Score=21.86 Aligned_cols=23 Identities=22% Similarity=-0.034 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
.-++.|++..|..-|+.||++++
T Consensus 15 ~eld~~a~~~g~~RSE~Ir~Ai~ 37 (60)
T PHA01748 15 ELLDRYAIKHGLNRSEAIRKAIE 37 (60)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH
Confidence 46789999999999999999865
No 6
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=56.39 E-value=13 Score=20.50 Aligned_cols=23 Identities=22% Similarity=0.030 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
.-|+.+.+..|...|..|+++|+
T Consensus 15 ~~L~~ls~~t~i~~S~Ll~eAle 37 (44)
T PF12651_consen 15 EKLKELSEETGIPKSKLLREALE 37 (44)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHH
Confidence 35788999999999999999976
No 7
>KOG2888|consensus
Probab=55.32 E-value=11 Score=30.51 Aligned_cols=38 Identities=32% Similarity=0.430 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHHhh
Q psy8052 26 SIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEELTL 63 (67)
Q Consensus 26 ~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel~a 63 (67)
..++||+|.-+.-=||..+.=||-|=||+|.+.+.|..
T Consensus 198 mTiGqmvr~~l~kLdwf~TLFPRIPVPvqkqId~~ie~ 235 (453)
T KOG2888|consen 198 MTIGQMVRTFLTKLDWFSTLFPRIPVPVQKQIDEKIEE 235 (453)
T ss_pred eeHHHHHHHHHhhhhHHhccCCCCCchHHHHHHHHHHh
Confidence 35789999999999999999999999999999988754
No 8
>PRK11675 LexA regulated protein; Provisional
Probab=45.69 E-value=19 Score=23.39 Aligned_cols=26 Identities=8% Similarity=-0.158 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHhh
Q psy8052 13 PDFLGVVVLEIERSIISQMLRKSVEA 38 (67)
Q Consensus 13 aq~Ll~~yv~~qG~~lsqmlrkSVe~ 38 (67)
.-.-|+.|.+.+|..-|+.|++.+..
T Consensus 61 l~ekL~eyAe~~nitRSElIr~~I~k 86 (90)
T PRK11675 61 LVDALNELAEARNISRSELIEEILMK 86 (90)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34568999999999999999999763
No 9
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=45.51 E-value=26 Score=21.17 Aligned_cols=25 Identities=8% Similarity=-0.005 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHHhHHHHHHHHHHH
Q psy8052 12 SPDFLGVVVLEIERSIISQMLRKSV 36 (67)
Q Consensus 12 aaq~Ll~~yv~~qG~~lsqmlrkSV 36 (67)
....+++......|..+|+++++++
T Consensus 9 e~k~li~~AA~~~G~sls~Fi~~aa 33 (80)
T PF08681_consen 9 EEKELIERAAALSGVSLSDFILSAA 33 (80)
T ss_dssp HHHHHHHHHHHHTTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3467899999999999999998874
No 10
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=42.31 E-value=47 Score=19.24 Aligned_cols=46 Identities=24% Similarity=0.504 Sum_probs=31.0
Q ss_pred HHHHhhchHHHHHHHHHHHHhHHHHHHHHHHHhhccccccCCCchHHHHHHHHH
Q psy8052 5 LSLLFGSSPDFLGVVVLEIERSIISQMLRKSVEAKDWLHGIEPRNVRAVMKRII 58 (67)
Q Consensus 5 ~~~~~~~aaq~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvv 58 (67)
+.+.|+..+.+....-+....+.+.+..+++ ..-|+.||..+--++
T Consensus 7 i~~~fG~~~~~V~~~Ll~~G~ltl~~i~~~t--------~l~~~~Vk~~L~~Li 52 (62)
T PF08221_consen 7 IEEHFGEIVAKVGEVLLSRGRLTLREIVRRT--------GLSPKQVKKALVVLI 52 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHC-SEEHHHHHHHH--------T--HHHHHHHHHHHH
T ss_pred HHHHcChHHHHHHHHHHHcCCcCHHHHHHHh--------CCCHHHHHHHHHHHH
Confidence 5678999999998888777777788877665 144566666554443
No 11
>PF05639 Pup: Pup-like protein; InterPro: IPR008515 This family consists of several short bacterial proteins formely known as (DUF797). It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD) []. Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages []. The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup []). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier. ; PDB: 3M91_D 3M9D_I.
Probab=37.74 E-value=8.8 Score=23.95 Aligned_cols=21 Identities=0% Similarity=-0.021 Sum_probs=4.6
Q ss_pred HHHhhchHHHHHHHHHHHHhH
Q psy8052 6 SLLFGSSPDFLGVVVLEIERS 26 (67)
Q Consensus 6 ~~~~~~aaq~Ll~~yv~~qG~ 26 (67)
..+.+.-|+.+|+.||++.|.
T Consensus 49 D~vLE~NAeeFVr~fVQKGGq 69 (69)
T PF05639_consen 49 DSVLETNAEEFVRSFVQKGGQ 69 (69)
T ss_dssp TTTSSSC--------------
T ss_pred HHHHHHHHHHHHHHHHhccCC
Confidence 345678899999999999884
No 12
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=37.45 E-value=77 Score=20.61 Aligned_cols=47 Identities=17% Similarity=0.152 Sum_probs=31.4
Q ss_pred hchHHHHHHHHHHHHhHHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHH
Q psy8052 10 GSSPDFLGVVVLEIERSIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEEL 61 (67)
Q Consensus 10 ~~aaq~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel 61 (67)
+.+|..++..++.- |....+.+ +..+|..-..+...+++|+.++++-
T Consensus 59 ~~~ak~ll~~~~~~-~~~~~~ii----~~~~l~~i~d~~el~~~v~~vi~~n 105 (148)
T PF02637_consen 59 KKSAKELLRELLEN-GKSPEEII----EENGLWQISDEEELEALVEEVIAEN 105 (148)
T ss_dssp HHHHHHHHHHHHHH-TS-HHHHH----HHTT---B--CCHHHHHHHHHHHC-
T ss_pred HHHHHHHHHHHHHc-CCCHHHHH----HHcCCCcCCCHHHHHHHHHHHHHHC
Confidence 56789999999976 66665554 5568888888889999999988753
No 13
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=35.90 E-value=90 Score=21.86 Aligned_cols=47 Identities=15% Similarity=0.016 Sum_probs=31.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhhccccccCC-CchHHHHHHHHHHHHhh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVEAKDWLHGIE-PRNVRAVMKRIIEELTL 63 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~E-PR~VRav~krvveel~a 63 (67)
..+..-++.-|.+.|+.||+.+...- ...+ +|--+.-|..++-++..
T Consensus 37 ~~L~~rA~~aGlS~SEfIRqAi~~~~--g~V~v~r~T~e~~~~lir~l~g 84 (147)
T PRK13858 37 ESFSAQARLLGLSDSMAIRVAVRRIG--GFLEIDAETREKMEAILQSIGT 84 (147)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhcC--CeEeecccCHHHHHHHHHHHHH
Confidence 46778889999999999999986422 2234 55555555555555544
No 14
>PF09274 ParG: ParG; InterPro: IPR015354 This entry represents plasmid partition proteins; it adopts a ribbon-helix-helix fold, with a core of four alpha-helices. The proteins are an essential component of the DNA partition complex of the multi drug resistance plasmid TP228 []. ; PDB: 1P94_B.
Probab=32.29 E-value=50 Score=20.83 Aligned_cols=30 Identities=20% Similarity=0.245 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhhccccccCC
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVEAKDWLHGIE 46 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~E 46 (67)
.-+..+...+|..+++.++--| ..||+..|
T Consensus 47 ~r~K~~ca~~G~sisdvv~eLi--d~wL~ene 76 (76)
T PF09274_consen 47 RRFKAACAKQGTSISDVVRELI--DKWLKENE 76 (76)
T ss_dssp HHHHHHHHHHT--HHHHHHHHH--HHHHCC--
T ss_pred HHHHHHHHHcCCcHHHHHHHHH--HHHHhccC
Confidence 4567888999999999999997 46887654
No 15
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=31.78 E-value=30 Score=22.28 Aligned_cols=20 Identities=30% Similarity=0.318 Sum_probs=15.6
Q ss_pred cCCCchHHHHHHHHHHHHhh
Q psy8052 44 GIEPRNVRAVMKRIIEELTL 63 (67)
Q Consensus 44 ~~EPR~VRav~krvveel~a 63 (67)
..-||++|.++....+.|..
T Consensus 22 ~sVPRNIRr~a~ea~~~L~~ 41 (85)
T PF03685_consen 22 TSVPRNIRRAAEEAKEILNN 41 (85)
T ss_dssp TTS-HHHHHHHHHHHHHCT-
T ss_pred CCCChHHHHHHHHHHHHHhC
Confidence 67899999999998887753
No 16
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=30.31 E-value=46 Score=21.96 Aligned_cols=20 Identities=30% Similarity=0.383 Sum_probs=16.8
Q ss_pred cCCCchHHHHHHHHHHHHhh
Q psy8052 44 GIEPRNVRAVMKRIIEELTL 63 (67)
Q Consensus 44 ~~EPR~VRav~krvveel~a 63 (67)
+.=||++|.+.....|.|..
T Consensus 29 ttVPRNIRraA~~a~e~L~~ 48 (93)
T COG1698 29 TTVPRNIRRAAEEAKEALNN 48 (93)
T ss_pred ccccHHHHHHHHHHHHHHhC
Confidence 67899999999988887754
No 17
>PF11757 RSS_P20: Suppressor of RNA silencing P21-like; InterPro: IPR021742 This is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins.
Probab=29.32 E-value=98 Score=21.61 Aligned_cols=35 Identities=14% Similarity=0.272 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHHhh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEELTL 63 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel~a 63 (67)
.+++-|.+..+..+++.++.+ +|++++.|+++|..
T Consensus 86 Ff~~ky~~lt~v~~~e~~~~~--------------~k~~~~~VL~~lS~ 120 (137)
T PF11757_consen 86 FFVKKYSELTHVPFSEAMEMK--------------MKPLSKAVLRDLSR 120 (137)
T ss_pred HHHHHHHhcCCCCHHHHHHHH--------------HHHHHHHHHHHHHH
Confidence 456677777778888777655 78888999988853
No 18
>PF03487 IL13: Interleukin-13; InterPro: IPR020470 Interleukin-13 (IL-13) is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses []. It inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.; PDB: 3G6D_A 3L5W_J 3BPO_A 1GA3_A 1IK0_A 3L5X_A 3L5Y_A 1IJZ_A 3LB6_B.
Probab=28.63 E-value=72 Score=18.36 Aligned_cols=23 Identities=26% Similarity=0.362 Sum_probs=14.6
Q ss_pred ccCCCchHHHHHHHHHHHHhhhh
Q psy8052 43 HGIEPRNVRAVMKRIIEELTLVD 65 (67)
Q Consensus 43 ~~~EPR~VRav~krvveel~aiD 65 (67)
.+.-|-.+..+.|.++||+..|-
T Consensus 18 asPgPvp~~~alkELIeELvNIT 40 (43)
T PF03487_consen 18 ASPGPVPSSTALKELIEELVNIT 40 (43)
T ss_dssp -----S-HHHHHHHHHHHHHHHH
T ss_pred CCCCCCCchHHHHHHHHHHHhhc
Confidence 34556667789999999998874
No 19
>PF04336 DUF479: Protein of unknown function, DUF479; InterPro: IPR007431 This entry contains the Escherichia coli gene yajB, now renamed acpH, which encodes an ACP hydrolase. AcpH converts holo-ACP to apo-ACP by hydrolytic cleavage of the phosphopantetheine prosthetic group from ACP []. A mutant E. coli strain having a total deletion of the acpH grows normally, showing that phosphodiesterase activity is not essential for growth, although it is required for turnover of the ACP prosthetic group in vivo. AcpH is found only in Gram-negative organisms suggesting that it plays a role in some aspect of lipid metabolism that is unique to these organisms. The most obvious of which is biosynthesis of lipid A. Because AcpH is a hydrolase, it could possibly be an editing enzyme that intercepts acyl-ACPs that would give an inappropriate lipid A structure if used as acyl donors []. ; GO: 0008770 [acyl-carrier-protein] phosphodiesterase activity, 0006633 fatty acid biosynthetic process
Probab=28.03 E-value=99 Score=19.37 Aligned_cols=51 Identities=16% Similarity=0.137 Sum_probs=32.3
Q ss_pred hhchHHHHHHHHHHHHhHHHHHHHHHHHhhccccc-cCCCchHHHHHHHHHHH
Q psy8052 9 FGSSPDFLGVVVLEIERSIISQMLRKSVEAKDWLH-GIEPRNVRAVMKRIIEE 60 (67)
Q Consensus 9 ~~~aaq~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~-~~EPR~VRav~krvvee 60 (67)
|.+.+-..|..+-..---++.+|+ ..+...|||. +.+.-++..++.++..-
T Consensus 20 f~~~~Y~~L~~~~~~lP~~~~~~~-~~m~~~dWL~~Y~~~egi~~al~~m~~R 71 (106)
T PF04336_consen 20 FAQRFYQQLEANQPILPPRFQRML-PYMIEHDWLSSYRTLEGIERALQRMSRR 71 (106)
T ss_pred HHHHHHHHHHhccccCCHHHHHHH-HHHHHhCHHHHcCCHHHHHHHHHHHHhc
Confidence 444444445544444445555554 5666789998 88888888888777543
No 20
>PHA00617 ribbon-helix-helix domain containing protein
Probab=27.57 E-value=64 Score=20.37 Aligned_cols=24 Identities=17% Similarity=0.084 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 14 DFLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 14 q~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
.+-|+.+++..|+.-|..||+.++
T Consensus 51 ~erLD~LA~~~GrsRSelIreAI~ 74 (80)
T PHA00617 51 NAKLEQVAIKMKKSKSEIIREALE 74 (80)
T ss_pred HHHHHHHHHHhCcCHHHHHHHHHH
Confidence 356899999999999999998865
No 21
>PRK04330 hypothetical protein; Provisional
Probab=24.72 E-value=71 Score=20.70 Aligned_cols=19 Identities=32% Similarity=0.336 Sum_probs=16.4
Q ss_pred cCCCchHHHHHHHHHHHHh
Q psy8052 44 GIEPRNVRAVMKRIIEELT 62 (67)
Q Consensus 44 ~~EPR~VRav~krvveel~ 62 (67)
+.-||++|.+.....+.|.
T Consensus 25 ~sVPRNIRraa~ea~~~L~ 43 (88)
T PRK04330 25 TSVPRNIRRAATEAKEILL 43 (88)
T ss_pred CCCChHHHHHHHHHHHHHh
Confidence 6789999999998888775
No 22
>PF01291 LIF_OSM: LIF / OSM family; InterPro: IPR001581 On the basis of functional and structural similarities, the small cytokines leukemia inhibitory factor (LIF) and oncostatin (OSM) can be classified into a single family [, ]. It has been said [] that LIF and OSM can be included in the IL-6 family of cytokines (IPR003573 from INTERPRO), but while all these cytokines seem to be structurally related, the sequence similarity is not high enough to allow the use of a single consensus pattern.; GO: 0005125 cytokine activity, 0006955 immune response, 0005576 extracellular region; PDB: 1LKI_A 1A7M_A 1EVS_A 1PVH_B 2Q7N_D 1EMR_A.
Probab=23.66 E-value=83 Score=22.19 Aligned_cols=23 Identities=13% Similarity=0.056 Sum_probs=19.0
Q ss_pred HHHHhhchHHHHHHHHHHHHhHHH
Q psy8052 5 LSLLFGSSPDFLGVVVLEIERSII 28 (67)
Q Consensus 5 ~~~~~~~aaq~Ll~~yv~~qG~~l 28 (67)
..++-++.| .|+.-|++.||.--
T Consensus 9 q~~~l~~ta-~Ll~~Y~~~QG~~~ 31 (162)
T PF01291_consen 9 QARLLNSTA-DLLIPYIRSQGEPF 31 (162)
T ss_dssp HHHHHHHHH-HHHHHHHHHHTTTS
T ss_pred HHHHHcCHH-HHHHHHHHHcCCCC
Confidence 446677788 99999999999875
No 23
>PF07377 DUF1493: Protein of unknown function (DUF1493); InterPro: IPR010862 This family consists of several bacterial proteins of around 115 residues in length. Members of this family are largely found in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.
Probab=23.12 E-value=54 Score=20.77 Aligned_cols=14 Identities=43% Similarity=0.662 Sum_probs=12.2
Q ss_pred HHHHHHHHhhcccc
Q psy8052 29 SQMLRKSVEAKDWL 42 (67)
Q Consensus 29 sqmlrkSVe~rDWl 42 (67)
=.||..|+.++-||
T Consensus 96 v~ML~esakaGrWl 109 (111)
T PF07377_consen 96 VGMLIESAKAGRWL 109 (111)
T ss_pred HHHHHHHHHcCCcc
Confidence 46999999999997
No 24
>PF07304 SRA1: Steroid receptor RNA activator (SRA1); InterPro: IPR009917 This entry consists of several hypothetical mammalian steroid receptor RNA activator proteins. The SRA-RNAs encode stable proteins that are widely expressed and upregulated in breast cancer cell lines. SRA-RNA is a steroid receptor co-activator which acts as a functional RNA. This domain is also found at the C terminus of Sec31, a component of the coat protein complex II (COPII, which promotes the formation of transport vesicles from the endoplasmic reticulum (ER). COPII has two main functions, the physical deformation of the endoplasmic reticulum membrane into vesicles and the selection of cargo molecules. ; PDB: 2YRU_A.
Probab=22.46 E-value=1.4e+02 Score=20.25 Aligned_cols=39 Identities=15% Similarity=0.153 Sum_probs=29.6
Q ss_pred HHHHHHHhHHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHHhhhh
Q psy8052 18 VVVLEIERSIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEELTLVD 65 (67)
Q Consensus 18 ~~yv~~qG~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel~aiD 65 (67)
+.|-.....+++-|.-..=||..||. .+||++....+..
T Consensus 104 ~d~~~A~~Ih~~L~t~h~~E~~~Wmv---------GVKRLI~~~r~~~ 142 (157)
T PF07304_consen 104 RDYDAADEIHVDLMTDHVDECGNWMV---------GVKRLIAMARNLP 142 (157)
T ss_dssp T-HHHHHHHHHHHHHSSHHHHTTTHH---------HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHhccHHHhhhHHH---------HHHHHHHHHHhcC
Confidence 45777888888888888889999985 4788887776654
No 25
>PF11738 DUF3298: Protein of unknown function (DUF3298); InterPro: IPR021729 This family of bacterial protein C-terminal regions is highly conserved but the function is not known. Several members are annotated as being endo-1,4-beta-xylanase-like, but this could not be confirmed. ; PDB: 2HHI_A 3S5T_A 3CYG_B.
Probab=22.35 E-value=80 Score=17.50 Aligned_cols=19 Identities=16% Similarity=-0.127 Sum_probs=10.3
Q ss_pred HHHHhhchHHHHHHHHHHH
Q psy8052 5 LSLLFGSSPDFLGVVVLEI 23 (67)
Q Consensus 5 ~~~~~~~aaq~Ll~~yv~~ 23 (67)
|.|+|.......+...++.
T Consensus 1 L~Dlf~~~~~~~l~~~i~~ 19 (78)
T PF11738_consen 1 LKDLFKDDYLEKLNDLIQK 19 (78)
T ss_dssp HHHCC-SCGHHHHHHHHHH
T ss_pred CccccCccHHHHHHHHHHH
Confidence 5677777555555544443
No 26
>PF10723 RepB-RCR_reg: Replication regulatory protein RepB; InterPro: IPR019661 This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication []. ; PDB: 2KEL_B.
Probab=21.70 E-value=1.5e+02 Score=18.44 Aligned_cols=27 Identities=4% Similarity=-0.055 Sum_probs=18.9
Q ss_pred hHHHHHHHHHHHHhHHHHHHHHHHHhh
Q psy8052 12 SPDFLGVVVLEIERSIISQMLRKSVEA 38 (67)
Q Consensus 12 aaq~Ll~~yv~~qG~~lsqmlrkSVe~ 38 (67)
.+-..|..+...+|+.-++||.+-|+.
T Consensus 51 ~~K~~L~~lc~~~GlTQae~IE~LI~~ 77 (84)
T PF10723_consen 51 ELKERLEELCKEQGLTQAEMIERLIKS 77 (84)
T ss_dssp HHHHHHHHHHHHS---HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 345667889999999999999887753
No 27
>PRK13877 conjugal transfer relaxosome component TraJ; Provisional
Probab=20.55 E-value=1.6e+02 Score=19.43 Aligned_cols=23 Identities=9% Similarity=-0.119 Sum_probs=16.1
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
.++..=++.-|+++|+.||+..-
T Consensus 23 ~~I~~kA~~AGlS~SeYLR~~aL 45 (114)
T PRK13877 23 AEIEANAAAAGLSVARYLRDVGQ 45 (114)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHc
Confidence 45666677778888888887643
Done!