Query psy15026
Match_columns 98
No_of_seqs 121 out of 140
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 18:30:20 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15026.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15026hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06701 MIB_HERC2: Mib_herc2; 99.5 1.8E-15 4E-20 99.4 2.2 28 67-94 1-28 (68)
2 KOG4582|consensus 96.4 0.00071 1.5E-08 53.7 -0.4 52 44-95 204-255 (278)
3 KOG4582|consensus 70.9 6.1 0.00013 31.5 3.7 33 62-94 59-94 (278)
4 COG4672 gp18 Phage-related pro 64.3 6.7 0.00015 31.6 2.7 31 6-39 65-95 (231)
5 KOG3360|consensus 59.8 8.3 0.00018 27.5 2.2 20 16-35 3-22 (98)
6 PF13304 AAA_21: AAA domain; P 36.6 12 0.00025 24.7 0.0 15 9-23 5-19 (303)
7 PF03811 Zn_Tnp_IS1: InsA N-te 35.9 30 0.00065 20.1 1.7 16 6-21 17-32 (36)
8 smart00712 PUR DNA/RNA-binding 34.8 32 0.00068 22.1 1.8 24 2-25 25-48 (63)
9 TIGR00739 yajC preprotein tran 33.3 47 0.001 22.2 2.5 20 54-73 28-47 (84)
10 PF00488 MutS_V: MutS domain V 30.6 12 0.00025 28.6 -0.8 16 7-22 47-62 (235)
11 PF05986 ADAM_spacer1: ADAM-TS 28.5 61 0.0013 22.2 2.5 19 2-24 27-45 (114)
12 PF06934 CTI: Fatty acid cis/t 27.8 11 0.00023 34.5 -1.7 18 17-34 422-439 (694)
13 PF13752 DUF4165: Domain of un 27.7 69 0.0015 23.6 2.8 18 17-34 71-88 (124)
14 smart00534 MUTSac ATPase domai 27.1 19 0.00041 25.8 -0.2 19 6-24 2-20 (185)
15 PF14652 DUF4457: Domain of un 26.9 38 0.00083 27.4 1.5 16 15-30 9-24 (329)
16 PRK05585 yajC preprotein trans 26.2 71 0.0015 22.3 2.5 18 56-73 45-62 (106)
17 PRK06531 yajC preprotein trans 26.1 69 0.0015 22.9 2.5 28 56-94 29-56 (113)
18 cd03280 ABC_MutS2 MutS2 homolo 24.6 27 0.00058 25.2 0.2 19 6-24 31-49 (200)
19 PRK05886 yajC preprotein trans 24.5 73 0.0016 22.7 2.4 18 56-73 31-48 (109)
20 cd03227 ABC_Class2 ABC-type Cl 23.7 25 0.00054 24.6 -0.1 20 6-25 24-43 (162)
21 COG1862 YajC Preprotein transl 23.4 85 0.0018 21.9 2.5 30 54-94 34-63 (97)
22 PF02699 YajC: Preprotein tran 23.2 48 0.001 21.8 1.2 19 54-72 27-45 (82)
23 cd03284 ABC_MutS1 MutS1 homolo 22.5 18 0.00038 27.0 -1.1 19 6-24 33-51 (216)
24 cd03243 ABC_MutS_homologs The 22.0 33 0.00071 24.7 0.2 20 5-24 31-50 (202)
25 KOG4660|consensus 21.4 34 0.00074 30.7 0.2 16 25-40 96-111 (549)
No 1
>PF06701 MIB_HERC2: Mib_herc2; InterPro: IPR010606 Mib is a RING ubiquitin ligase in the Notch pathway. Mib interacts with the intracellular domain of Delta to promote its ubiquitylation and internalisation. Cell transplantation studies suggest that mib function is essential in the signalling cell for efficient activation of Notch in neighbouring cells. This domain has been named 'mib/herc2 domain' in []and usually the protein also contains an E3 ligase domain (either Ring or Hect).; GO: 0004842 ubiquitin-protein ligase activity, 0046872 metal ion binding, 0016567 protein ubiquitination; PDB: 2DK3_A 3DKM_A.
Probab=99.55 E-value=1.8e-15 Score=99.42 Aligned_cols=28 Identities=57% Similarity=0.955 Sum_probs=20.5
Q ss_pred cceEeeCCCCcccCCCCCCCCCCeeeee
Q psy15026 67 GARVQRGLDWKWRDQDGIPPGEGNLKPI 94 (98)
Q Consensus 67 G~RVvRG~DWkW~dQDGg~g~~GtV~~~ 94 (98)
|+||||||||+|+||||+++++|||++|
T Consensus 1 G~rVvRGpDW~WgdQDGG~g~~GtV~~i 28 (68)
T PF06701_consen 1 GARVVRGPDWKWGDQDGGEGHVGTVVSI 28 (68)
T ss_dssp TSEEEE-TT--STTTTSSTT--EEE-S-
T ss_pred CCeeeeCcCCCccCcCCCCCcceEEEec
Confidence 7999999999999999999999999986
No 2
>KOG4582|consensus
Probab=96.38 E-value=0.00071 Score=53.67 Aligned_cols=52 Identities=19% Similarity=0.283 Sum_probs=43.0
Q ss_pred hhhhHHHHhhhhHHHHhhhhccccceEeeCCCCcccCCCCCCCCCCeeeeeE
Q psy15026 44 EAEASVRKARRLVRTQVMRHLIIGARVQRGLDWKWRDQDGIPPGEGNLKPII 95 (98)
Q Consensus 44 ~ae~~l~~~R~~~r~~~~~~i~~G~RVvRG~DWkW~dQDGg~g~~GtV~~~i 95 (98)
.+..+++..++.++......++++..++||++|+|+++++++++.|++.++-
T Consensus 204 ~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 255 (278)
T KOG4582|consen 204 FSGYVMLSSPPNPVNLNKRPIFVGHSKVRGNDWYWTSLGGGEGRIGRVNEIV 255 (278)
T ss_pred CCcceeccCCCCcccccccccccccccccccCCccccccCCCCCCccccccc
Confidence 3344556667777766678999999999999999999999999999998753
No 3
>KOG4582|consensus
Probab=70.93 E-value=6.1 Score=31.52 Aligned_cols=33 Identities=18% Similarity=0.068 Sum_probs=24.2
Q ss_pred hhccccceEeeCCCCcccCCC---CCCCCCCeeeee
Q psy15026 62 RHLIIGARVQRGLDWKWRDQD---GIPPGEGNLKPI 94 (98)
Q Consensus 62 ~~i~~G~RVvRG~DWkW~dQD---Gg~g~~GtV~~~ 94 (98)
-....+.+|+||.||+|-.+. +..++.+++...
T Consensus 59 ~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~~~~ 94 (278)
T KOG4582|consen 59 DEDGVGMRVVRGNDLFDVTNQRLADEIGHVNAVRSF 94 (278)
T ss_pred hccccceeEEecCCceEeecccCccccccccceeee
Confidence 456789999999999999994 444455555444
No 4
>COG4672 gp18 Phage-related protein [Function unknown]
Probab=64.26 E-value=6.7 Score=31.61 Aligned_cols=31 Identities=39% Similarity=0.716 Sum_probs=25.5
Q ss_pred EeecCCCCCCceeeEEeeceEEEeccchhhhhhh
Q psy15026 6 IQQNGKNASGQTHYLSLSGFEIYGTLTGVCEDLG 39 (98)
Q Consensus 6 i~q~g~nss~~~~yls~sgfe~yg~v~~~~Ed~~ 39 (98)
+.++||++|-+. -|++|- ++|.|++.|||+.
T Consensus 65 Fe~~GkG~sarP-~L~VsN--l~G~Vt~m~~~~~ 95 (231)
T COG4672 65 FEMNGKGSSARP-SLTVSN--LFGLVTGMAEDLQ 95 (231)
T ss_pred eeecCCCCCCCC-ceEEee--cchhHHHHHHHhh
Confidence 458999999995 788875 6999999999843
No 5
>KOG3360|consensus
Probab=59.76 E-value=8.3 Score=27.52 Aligned_cols=20 Identities=35% Similarity=0.855 Sum_probs=17.0
Q ss_pred ceeeEEeeceEEEeccchhh
Q psy15026 16 QTHYLSLSGFEIYGTLTGVC 35 (98)
Q Consensus 16 ~~~yls~sgfe~yg~v~~~~ 35 (98)
+.+-|-.-.|||||.|-++|
T Consensus 3 ~~~~i~s~dfEvfGRVQGv~ 22 (98)
T KOG3360|consen 3 QAESIKSCDFEVFGRVQGVC 22 (98)
T ss_pred ccceeEEEeEEEEeeeccch
Confidence 45567778999999999998
No 6
>PF13304 AAA_21: AAA domain; PDB: 3QKS_B 1US8_B 1F2U_B 1F2T_B 3QKT_A 1II8_B 3QKR_B 3QKU_A.
Probab=36.62 E-value=12 Score=24.71 Aligned_cols=15 Identities=33% Similarity=0.468 Sum_probs=0.0
Q ss_pred cCCCCCCceeeEEee
Q psy15026 9 NGKNASGQTHYLSLS 23 (98)
Q Consensus 9 ~g~nss~~~~yls~s 23 (98)
.|+|+||.|+.|..-
T Consensus 5 iG~N~sGKS~il~ai 19 (303)
T PF13304_consen 5 IGPNGSGKSNILEAI 19 (303)
T ss_dssp ---------------
T ss_pred ccccccccccccccc
Confidence 599999999887543
No 7
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=35.85 E-value=30 Score=20.12 Aligned_cols=16 Identities=38% Similarity=0.775 Sum_probs=13.7
Q ss_pred EeecCCCCCCceeeEE
Q psy15026 6 IQQNGKNASGQTHYLS 21 (98)
Q Consensus 6 i~q~g~nss~~~~yls 21 (98)
+..+|++++|+..|+-
T Consensus 17 v~k~G~~~~G~qryrC 32 (36)
T PF03811_consen 17 VKKNGKSPSGHQRYRC 32 (36)
T ss_pred ceeCCCCCCCCEeEec
Confidence 5689999999988974
No 8
>smart00712 PUR DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria.
Probab=34.82 E-value=32 Score=22.12 Aligned_cols=24 Identities=21% Similarity=0.275 Sum_probs=15.0
Q ss_pred eeEEEeecCCCCCCceeeEEeece
Q psy15026 2 RHVRIQQNGKNASGQTHYLSLSGF 25 (98)
Q Consensus 2 r~~ri~q~g~nss~~~~yls~sgf 25 (98)
+|+||...+++...++-+|..++|
T Consensus 25 ~fLrIsE~~~~~~r~~I~lp~~~~ 48 (63)
T smart00712 25 RFLRISEVKNNGGRSSITVPEQGA 48 (63)
T ss_pred cEEEEEEecCCCCceEEEEEHHHH
Confidence 567777777776555555555444
No 9
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=33.26 E-value=47 Score=22.16 Aligned_cols=20 Identities=20% Similarity=0.257 Sum_probs=15.1
Q ss_pred hhHHHHhhhhccccceEeeC
Q psy15026 54 RLVRTQVMRHLIIGARVQRG 73 (98)
Q Consensus 54 ~~~r~~~~~~i~~G~RVvRG 73 (98)
++.+.++...|.+|.+|+-.
T Consensus 28 ~k~~~~m~~~L~~Gd~VvT~ 47 (84)
T TIGR00739 28 RKAHKKLIESLKKGDKVLTI 47 (84)
T ss_pred HHHHHHHHHhCCCCCEEEEC
Confidence 33445677899999999864
No 10
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=30.59 E-value=12 Score=28.62 Aligned_cols=16 Identities=31% Similarity=0.520 Sum_probs=13.0
Q ss_pred eecCCCCCCceeeEEe
Q psy15026 7 QQNGKNASGQTHYLSL 22 (98)
Q Consensus 7 ~q~g~nss~~~~yls~ 22 (98)
.-+|+|++|+|.||.-
T Consensus 47 iiTGpN~sGKSt~lk~ 62 (235)
T PF00488_consen 47 IITGPNMSGKSTFLKQ 62 (235)
T ss_dssp EEESSTTSSHHHHHHH
T ss_pred EEeCCCccchhhHHHH
Confidence 4589999999988753
No 11
>PF05986 ADAM_spacer1: ADAM-TS Spacer 1; InterPro: IPR010294 This domain represents the Spacer-1 domain from the ADAM-TS family of metalloproteinases []. A cellular disintegrin and metalloproteinase (ADAM) is a family of genes with structural homology to the snake venom metalloproteinases and disintegrins []. There is variation amongst members of the family, however, all have a similar domain organisation comprising a preproregion, a reprolysin-type catalytic domain, a disintegrin-like domain, a thrombospondin type-1 (TS) module, a cysteine-rich domain, a spacer domain without cysteine residues, and a COOH-terminal TS module [, ]. They are involved in embryogenesis and have been implicated in some cancers and inflammatory diseases [].; GO: 0004222 metalloendopeptidase activity, 0031012 extracellular matrix
Probab=28.53 E-value=61 Score=22.16 Aligned_cols=19 Identities=32% Similarity=0.679 Sum_probs=15.0
Q ss_pred eeEEEeecCCCCCCceeeEEeec
Q psy15026 2 RHVRIQQNGKNASGQTHYLSLSG 24 (98)
Q Consensus 2 r~~ri~q~g~nss~~~~yls~sg 24 (98)
|+++|.|.++.. |||.|..
T Consensus 27 ~nI~I~e~~~s~----n~Lalk~ 45 (114)
T PF05986_consen 27 RNIRITERRPSS----NYLALKN 45 (114)
T ss_pred eEEEEEEeecCc----cEEEEEe
Confidence 689999997665 7998874
No 12
>PF06934 CTI: Fatty acid cis/trans isomerase (CTI); InterPro: IPR010706 This family consists of several fatty acid cis/trans isomerase proteins, which appear to be found exclusively in bacteria of the orders Vibrionales and Pseudomonadales. Cis/trans isomerase (CTI) catalyses the cis-trans isomerisation of esterified fatty acids in phospholipids, mainly cis-oleic acid (C(16:1,9)) and cis-vaccenic acid (C(18:1,11)), in response to solvents. The CTI protein has been shown to be involved in solvent resistance in Pseudomonas putida [].
Probab=27.76 E-value=11 Score=34.55 Aligned_cols=18 Identities=39% Similarity=0.927 Sum_probs=15.7
Q ss_pred eeeEEeeceEEEeccchh
Q psy15026 17 THYLSLSGFEIYGTLTGV 34 (98)
Q Consensus 17 ~~yls~sgfe~yg~v~~~ 34 (98)
.|||-+-||.|||.|-.=
T Consensus 422 ihYlLVAgFDVyGNvgHQ 439 (694)
T PF06934_consen 422 IHYLLVAGFDVYGNVGHQ 439 (694)
T ss_pred HHHHHhhcceeccChhHH
Confidence 599999999999998653
No 13
>PF13752 DUF4165: Domain of unknown function (DUF4165)
Probab=27.69 E-value=69 Score=23.60 Aligned_cols=18 Identities=28% Similarity=0.401 Sum_probs=14.2
Q ss_pred eeeEEeeceEEEeccchh
Q psy15026 17 THYLSLSGFEIYGTLTGV 34 (98)
Q Consensus 17 ~~yls~sgfe~yg~v~~~ 34 (98)
+.=++.+|.|.||+..-+
T Consensus 71 d~~~s~~G~efYGk~ltl 88 (124)
T PF13752_consen 71 DRRISSNGKEFYGKELTL 88 (124)
T ss_pred eeeEEeCCceeeeeEEEe
Confidence 445788999999987655
No 14
>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family.
Probab=27.14 E-value=19 Score=25.81 Aligned_cols=19 Identities=32% Similarity=0.601 Sum_probs=15.6
Q ss_pred EeecCCCCCCceeeEEeec
Q psy15026 6 IQQNGKNASGQTHYLSLSG 24 (98)
Q Consensus 6 i~q~g~nss~~~~yls~sg 24 (98)
+.-+|+|.+|+++||...|
T Consensus 2 ~~ltG~N~~GKst~l~~i~ 20 (185)
T smart00534 2 VIITGPNMGGKSTYLRQVG 20 (185)
T ss_pred EEEECCCCCcHHHHHHHHH
Confidence 3458999999999987766
No 15
>PF14652 DUF4457: Domain of unknown function (DUF4457)
Probab=26.90 E-value=38 Score=27.45 Aligned_cols=16 Identities=38% Similarity=0.929 Sum_probs=14.2
Q ss_pred CceeeEEeeceEEEec
Q psy15026 15 GQTHYLSLSGFEIYGT 30 (98)
Q Consensus 15 ~~~~yls~sgfe~yg~ 30 (98)
|..||+-|+|+|+++.
T Consensus 9 G~~~~iGLTgie~~d~ 24 (329)
T PF14652_consen 9 GDPHYIGLTGIEVLDK 24 (329)
T ss_pred CCCCeEecceEEEEcC
Confidence 6779999999999975
No 16
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=26.15 E-value=71 Score=22.28 Aligned_cols=18 Identities=17% Similarity=0.265 Sum_probs=14.1
Q ss_pred HHHHhhhhccccceEeeC
Q psy15026 56 VRTQVMRHLIIGARVQRG 73 (98)
Q Consensus 56 ~r~~~~~~i~~G~RVvRG 73 (98)
.+.++...|++|.+|+-.
T Consensus 45 ~~~~~~~~Lk~Gd~VvT~ 62 (106)
T PRK05585 45 EHKKMLSSLAKGDEVVTN 62 (106)
T ss_pred HHHHHHHhcCCCCEEEEC
Confidence 445667899999999853
No 17
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=26.05 E-value=69 Score=22.87 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=19.8
Q ss_pred HHHHhhhhccccceEeeCCCCcccCCCCCCCCCCeeeee
Q psy15026 56 VRTQVMRHLIIGARVQRGLDWKWRDQDGIPPGEGNLKPI 94 (98)
Q Consensus 56 ~r~~~~~~i~~G~RVvRG~DWkW~dQDGg~g~~GtV~~~ 94 (98)
-+..++.+|++|.+|+-. .|-.|+|+++
T Consensus 29 e~~em~~sLk~GD~VvT~-----------GGi~G~V~~I 56 (113)
T PRK06531 29 ERQNQLNAIQKGDEVVTI-----------GGLYGTVDEV 56 (113)
T ss_pred HHHHHHHhcCCCCEEEEC-----------CCcEEEEEEE
Confidence 445667899999999954 3456776543
No 18
>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a
Probab=24.56 E-value=27 Score=25.20 Aligned_cols=19 Identities=37% Similarity=0.466 Sum_probs=16.5
Q ss_pred EeecCCCCCCceeeEEeec
Q psy15026 6 IQQNGKNASGQTHYLSLSG 24 (98)
Q Consensus 6 i~q~g~nss~~~~yls~sg 24 (98)
+.-+|+|.+|+|.+|..-|
T Consensus 31 ~~ltG~Ng~GKStll~~i~ 49 (200)
T cd03280 31 LVITGPNAGGKTVTLKTLG 49 (200)
T ss_pred EEEECCCCCChHHHHHHHH
Confidence 6778999999999998755
No 19
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=24.50 E-value=73 Score=22.66 Aligned_cols=18 Identities=22% Similarity=0.274 Sum_probs=14.1
Q ss_pred HHHHhhhhccccceEeeC
Q psy15026 56 VRTQVMRHLIIGARVQRG 73 (98)
Q Consensus 56 ~r~~~~~~i~~G~RVvRG 73 (98)
-+.+++..|++|.+|+-.
T Consensus 31 ~~~~m~~~Lk~GD~VvT~ 48 (109)
T PRK05886 31 ATIDLHESLQPGDRVHTT 48 (109)
T ss_pred HHHHHHHhcCCCCEEEEC
Confidence 345667899999999864
No 20
>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.
Probab=23.70 E-value=25 Score=24.58 Aligned_cols=20 Identities=30% Similarity=0.456 Sum_probs=16.1
Q ss_pred EeecCCCCCCceeeEEeece
Q psy15026 6 IQQNGKNASGQTHYLSLSGF 25 (98)
Q Consensus 6 i~q~g~nss~~~~yls~sgf 25 (98)
+..+|+|.||++++|..-+|
T Consensus 24 ~~i~G~NgsGKS~~l~~i~~ 43 (162)
T cd03227 24 TIITGPNGSGKSTILDAIGL 43 (162)
T ss_pred EEEECCCCCCHHHHHHHHHH
Confidence 56789999999999876443
No 21
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=23.41 E-value=85 Score=21.90 Aligned_cols=30 Identities=13% Similarity=0.079 Sum_probs=21.7
Q ss_pred hhHHHHhhhhccccceEeeCCCCcccCCCCCCCCCCeeeee
Q psy15026 54 RLVRTQVMRHLIIGARVQRGLDWKWRDQDGIPPGEGNLKPI 94 (98)
Q Consensus 54 ~~~r~~~~~~i~~G~RVvRG~DWkW~dQDGg~g~~GtV~~~ 94 (98)
++-+..++.+|..|.+|+-. .|-.|+|+.+
T Consensus 34 ~K~~~~ml~sL~kGD~VvT~-----------gGi~G~V~~v 63 (97)
T COG1862 34 MKEHQELLNSLKKGDEVVTI-----------GGIVGTVTKV 63 (97)
T ss_pred HHHHHHHHHhccCCCEEEEc-----------CCeEEEEEEE
Confidence 44667778999999999964 3456777654
No 22
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=23.24 E-value=48 Score=21.82 Aligned_cols=19 Identities=16% Similarity=0.197 Sum_probs=5.2
Q ss_pred hhHHHHhhhhccccceEee
Q psy15026 54 RLVRTQVMRHLIIGARVQR 72 (98)
Q Consensus 54 ~~~r~~~~~~i~~G~RVvR 72 (98)
++.+.++...|.+|++|+-
T Consensus 27 ~k~~~~m~~~Lk~Gd~VvT 45 (82)
T PF02699_consen 27 QKEHQEMLASLKPGDEVVT 45 (82)
T ss_dssp HHHHTTGGG----------
T ss_pred HHHHHHHHHcCCCCCEEEE
Confidence 3345566789999999985
No 23
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes. The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=22.46 E-value=18 Score=27.03 Aligned_cols=19 Identities=26% Similarity=0.506 Sum_probs=16.3
Q ss_pred EeecCCCCCCceeeEEeec
Q psy15026 6 IQQNGKNASGQTHYLSLSG 24 (98)
Q Consensus 6 i~q~g~nss~~~~yls~sg 24 (98)
+...|+|.+|+|+||...|
T Consensus 33 ~~l~Gpn~sGKstllr~i~ 51 (216)
T cd03284 33 LLITGPNMAGKSTYLRQVA 51 (216)
T ss_pred EEEECCCCCChHHHHHHHH
Confidence 5678999999999998764
No 24
>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch. Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily. MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes. The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis. All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru
Probab=21.97 E-value=33 Score=24.72 Aligned_cols=20 Identities=30% Similarity=0.512 Sum_probs=16.9
Q ss_pred EEeecCCCCCCceeeEEeec
Q psy15026 5 RIQQNGKNASGQTHYLSLSG 24 (98)
Q Consensus 5 ri~q~g~nss~~~~yls~sg 24 (98)
++.-+|+|.+|+|.+|.+.+
T Consensus 31 ~~~l~G~Ng~GKStll~~i~ 50 (202)
T cd03243 31 LLLITGPNMGGKSTYLRSIG 50 (202)
T ss_pred EEEEECCCCCccHHHHHHHH
Confidence 56778999999999987665
No 25
>KOG4660|consensus
Probab=21.44 E-value=34 Score=30.70 Aligned_cols=16 Identities=25% Similarity=0.559 Sum_probs=12.9
Q ss_pred eEEEeccchhhhhhhh
Q psy15026 25 FEIYGTLTGVCEDLGR 40 (98)
Q Consensus 25 fe~yg~v~~~~Ed~~k 40 (98)
||.||+|.++.|.+.+
T Consensus 96 f~~yGeir~ir~t~~~ 111 (549)
T KOG4660|consen 96 FGAYGEIREIRETPNK 111 (549)
T ss_pred HHhhcchhhhhccccc
Confidence 8999999999775443
Done!