Query 042109
Match_columns 61
No_of_seqs 117 out of 646
Neff 4.2
Searched_HMMs 46136
Date Fri Mar 29 02:58:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042109.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042109hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0545 FkpA FKBP-type peptidy 99.1 8.8E-11 1.9E-15 82.6 4.8 50 12-61 77-126 (205)
2 PRK11570 peptidyl-prolyl cis-t 99.1 1.7E-10 3.7E-15 79.6 4.3 44 18-61 84-127 (206)
3 PRK10902 FKBP-type peptidyl-pr 98.9 9E-10 1.9E-14 78.9 4.4 44 18-61 128-171 (269)
4 KOG0552 FKBP-type peptidyl-pro 98.5 1.4E-07 3.1E-12 67.0 3.8 30 32-61 116-145 (226)
5 TIGR03516 ppisom_GldI peptidyl 98.1 8.9E-06 1.9E-10 55.1 4.9 42 19-61 53-96 (177)
6 PF01346 FKBP_N: Domain amino 97.5 2.8E-05 6.1E-10 48.3 0.8 26 17-42 99-124 (124)
7 KOG0544 FKBP-type peptidyl-pro 96.7 0.0017 3.8E-08 42.2 3.0 25 37-61 2-27 (108)
8 KOG0549 FKBP-type peptidyl-pro 63.6 11 0.00023 26.8 3.3 29 33-61 65-95 (188)
9 KOG0543 FKBP-type peptidyl-pro 62.8 8.3 0.00018 29.9 2.9 27 35-61 83-111 (397)
10 CHL00084 rpl19 ribosomal prote 35.1 26 0.00057 22.8 1.5 13 49-61 21-33 (117)
11 PF07076 DUF1344: Protein of u 31.7 51 0.0011 19.5 2.2 30 32-61 19-48 (61)
12 COG0335 RplS Ribosomal protein 31.0 35 0.00075 22.5 1.5 13 49-61 19-31 (115)
13 PF01245 Ribosomal_L19: Riboso 30.5 36 0.00079 21.8 1.6 13 49-61 17-29 (113)
14 PRK05338 rplS 50S ribosomal pr 28.9 40 0.00086 21.9 1.5 13 49-61 17-29 (116)
15 KOG0545 Aryl-hydrocarbon recep 27.7 29 0.00063 26.4 0.9 27 35-61 9-37 (329)
16 COG1581 Ssh10b Archaeal DNA-bi 26.2 92 0.002 19.8 2.8 23 37-59 58-81 (91)
17 TIGR01024 rplS_bact ribosomal 25.8 47 0.001 21.5 1.5 13 49-61 17-29 (113)
18 PF14444 S1-like: S1-like 21.5 1.4E+02 0.003 17.4 2.8 18 43-60 26-43 (58)
No 1
>COG0545 FkpA FKBP-type peptidyl-prolyl cis-trans isomerases 1 [Posttranslational modification, protein turnover, chaperones]
Probab=99.12 E-value=8.8e-11 Score=82.64 Aligned_cols=50 Identities=34% Similarity=0.527 Sum_probs=45.4
Q ss_pred hhhcccHHHHhhCCCCCCCcccCCCCCeEEEeEcccCCCcCCCCeEEEeC
Q 042109 12 EAVSTSRRALRASKIPESEFTTLPNGLKYYDVKVGGGPVAKKGSRVAVRL 61 (61)
Q Consensus 12 ~~~~~~~~a~~~~~~~~~~~v~~pSGLqy~dl~~G~G~~p~~G~tV~VhY 61 (61)
++...-..+|+++|.++.++.++||||||++++.|+|+.|++|++|.|||
T Consensus 77 ~~~~~~~~~f~~~~~k~~~v~~~~sgl~y~~~~~G~G~~~~~~~~V~vhY 126 (205)
T COG0545 77 AANAAEGKAFLEKNAKEKGVKTLPSGLQYKVLKAGDGAAPKKGDTVTVHY 126 (205)
T ss_pred HHhHHhHHHHHhhhcccCCceECCCCcEEEEEeccCCCCCCCCCEEEEEE
Confidence 33444566899999999999999999999999999999999999999999
No 2
>PRK11570 peptidyl-prolyl cis-trans isomerase; Provisional
Probab=99.06 E-value=1.7e-10 Score=79.56 Aligned_cols=44 Identities=16% Similarity=0.305 Sum_probs=42.2
Q ss_pred HHHHhhCCCCCCCcccCCCCCeEEEeEcccCCCcCCCCeEEEeC
Q 042109 18 RRALRASKIPESEFTTLPNGLKYYDVKVGGGPVAKKGSRVAVRL 61 (61)
Q Consensus 18 ~~a~~~~~~~~~~~v~~pSGLqy~dl~~G~G~~p~~G~tV~VhY 61 (61)
-.+|+++|.+++++.++||||+|++++.|+|+.|+++++|.|||
T Consensus 84 ~~~fl~~~~k~~gv~~t~sGl~y~vi~~G~G~~p~~~d~V~v~Y 127 (206)
T PRK11570 84 GVKFLEENAKKEGVNSTESGLQFRVLTQGEGAIPARTDRVRVHY 127 (206)
T ss_pred HHHHHHHhhhcCCcEECCCCcEEEEEeCCCCCCCCCCCEEEEEE
Confidence 35799999999999999999999999999999999999999998
No 3
>PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=98.95 E-value=9e-10 Score=78.91 Aligned_cols=44 Identities=27% Similarity=0.311 Sum_probs=42.2
Q ss_pred HHHHhhCCCCCCCcccCCCCCeEEEeEcccCCCcCCCCeEEEeC
Q 042109 18 RRALRASKIPESEFTTLPNGLKYYDVKVGGGPVAKKGSRVAVRL 61 (61)
Q Consensus 18 ~~a~~~~~~~~~~~v~~pSGLqy~dl~~G~G~~p~~G~tV~VhY 61 (61)
-.+|+.+|..+++++++||||+|++|++|+|+.|+.||+|.|||
T Consensus 128 ~~~fl~~~~k~~gv~~t~sGl~y~Vi~~G~G~~p~~gD~V~V~Y 171 (269)
T PRK10902 128 GKKYREKFAKEKGVKTTSTGLLYKVEKEGTGEAPKDSDTVVVNY 171 (269)
T ss_pred HHHHHHHhccCCCcEECCCccEEEEEeCCCCCCCCCCCEEEEEE
Confidence 35799999999999999999999999999999999999999998
No 4
>KOG0552 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=1.4e-07 Score=67.05 Aligned_cols=30 Identities=63% Similarity=1.091 Sum_probs=29.3
Q ss_pred ccCCCCCeEEEeEcccCCCcCCCCeEEEeC
Q 042109 32 TTLPNGLKYYDVKVGGGPVAKKGSRVAVRL 61 (61)
Q Consensus 32 v~~pSGLqy~dl~~G~G~~p~~G~tV~VhY 61 (61)
.++++||+|+||++|+|+.|.+|++|.+||
T Consensus 116 ~tl~~Gl~y~D~~vG~G~~a~~G~rV~v~Y 145 (226)
T KOG0552|consen 116 RTLPGGLRYEDLRVGSGPSAKKGKRVSVRY 145 (226)
T ss_pred eecCCCcEEEEEEecCCCCCCCCCEEEEEE
Confidence 689999999999999999999999999999
No 5
>TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype.
Probab=98.05 E-value=8.9e-06 Score=55.10 Aligned_cols=42 Identities=21% Similarity=0.380 Sum_probs=34.0
Q ss_pred HHHhhCCCCCCCcccCCCCCeEEEeEc--ccCCCcCCCCeEEEeC
Q 042109 19 RALRASKIPESEFTTLPNGLKYYDVKV--GGGPVAKKGSRVAVRL 61 (61)
Q Consensus 19 ~a~~~~~~~~~~~v~~pSGLqy~dl~~--G~G~~p~~G~tV~VhY 61 (61)
.+++++| +...+.+++|||+|+.+++ |+|..|+.||+|.+||
T Consensus 53 ~~~i~~~-~~~~~~~t~sGl~Y~v~~~~~g~g~~p~~gd~V~v~Y 96 (177)
T TIGR03516 53 KRIISAD-SIVKYETSQNGFWYYYNQKDTGEGTTPEFGDLVTFEY 96 (177)
T ss_pred HHHHHhC-CCCCceECCCccEEEEEEecCCCCCcCCCCCEEEEEE
Confidence 3455554 3356788999999999976 7788999999999998
No 6
>PF01346 FKBP_N: Domain amino terminal to FKBP-type peptidyl-prolyl isomerase; InterPro: IPR000774 Peptidyl-prolyl cis-trans isomerase (PPIase) catalyses the cis-trans isomerisation of proline imidic peptide bonds in oligopeptides [, ]. This alpha helical domain is found at the N terminus of proteins belonging to the FKBP-type peptidyl-prolyl cis-trans isomerase(IPR001179 from INTERPRO) family. Peptidyl-prolyl cis-trans isomerase has been shown to accelerate the refolding of several proteins in vitro [, , ]; the FKPB-type enzymes probably act in the folding of extracytoplasmic proteins.; GO: 0006457 protein folding; PDB: 1FD9_A 2VCD_A 3OE2_A 2UZ5_A 3B09_A 1Q6H_B 1Q6I_B 1Q6U_A.
Probab=97.54 E-value=2.8e-05 Score=48.34 Aligned_cols=26 Identities=23% Similarity=0.272 Sum_probs=21.6
Q ss_pred cHHHHhhCCCCCCCcccCCCCCeEEE
Q 042109 17 SRRALRASKIPESEFTTLPNGLKYYD 42 (61)
Q Consensus 17 ~~~a~~~~~~~~~~~v~~pSGLqy~d 42 (61)
.-.+|+.+|..+++++++||||||++
T Consensus 99 ~~~~fla~n~k~~GV~~t~SGLqY~V 124 (124)
T PF01346_consen 99 EGEAFLAENAKKEGVKTTESGLQYKV 124 (124)
T ss_dssp HHHHHHHHHHTSTTEEE-TTS-EEEE
T ss_pred HHHHHHHHHcCCCCCEECCCCCeeeC
Confidence 44689999999999999999999985
No 7
>KOG0544 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=96.72 E-value=0.0017 Score=42.23 Aligned_cols=25 Identities=32% Similarity=0.522 Sum_probs=23.5
Q ss_pred CCeEEEeEcccC-CCcCCCCeEEEeC
Q 042109 37 GLKYYDVKVGGG-PVAKKGSRVAVRL 61 (61)
Q Consensus 37 GLqy~dl~~G~G-~~p~~G~tV~VhY 61 (61)
|++.+.|..|+| .-|++||+|.|||
T Consensus 2 Gv~~~~i~~Gdg~tfpK~Gqtvt~hY 27 (108)
T KOG0544|consen 2 GVEKQVISPGDGRTFPKKGQTVTVHY 27 (108)
T ss_pred CceeEEeeCCCCcccCCCCCEEEEEE
Confidence 688999999999 7999999999999
No 8
>KOG0549 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=63.56 E-value=11 Score=26.75 Aligned_cols=29 Identities=24% Similarity=0.150 Sum_probs=21.9
Q ss_pred cCCCCCeEEEeEc--ccCCCcCCCCeEEEeC
Q 042109 33 TLPNGLKYYDVKV--GGGPVAKKGSRVAVRL 61 (61)
Q Consensus 33 ~~pSGLqy~dl~~--G~G~~p~~G~tV~VhY 61 (61)
...++||+..++. .-..++++||++.+||
T Consensus 65 ~~~~~l~I~v~~~p~~C~~kak~GD~l~~HY 95 (188)
T KOG0549|consen 65 NPDEELQIGVLKKPEECPEKAKKGDTLHVHY 95 (188)
T ss_pred CCCCceeEEEEECCccccccccCCCEEEEEE
Confidence 3456777777754 2467889999999999
No 9
>KOG0543 consensus FKBP-type peptidyl-prolyl cis-trans isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=62.81 E-value=8.3 Score=29.91 Aligned_cols=27 Identities=30% Similarity=0.433 Sum_probs=22.7
Q ss_pred CCCCeEEEeEcccC--CCcCCCCeEEEeC
Q 042109 35 PNGLKYYDVKVGGG--PVAKKGSRVAVRL 61 (61)
Q Consensus 35 pSGLqy~dl~~G~G--~~p~~G~tV~VhY 61 (61)
.-+|.-+.|+.|.| ..|-.|.+|.|||
T Consensus 83 Dg~iiKriir~G~gd~~~P~~g~~V~v~~ 111 (397)
T KOG0543|consen 83 DGGIIKRIIREGEGDYSRPNKGAVVKVHL 111 (397)
T ss_pred CCceEEeeeecCCCCCCCCCCCcEEEEEE
Confidence 45666677899999 7899999999997
No 10
>CHL00084 rpl19 ribosomal protein L19
Probab=35.14 E-value=26 Score=22.83 Aligned_cols=13 Identities=31% Similarity=0.519 Sum_probs=11.1
Q ss_pred CCcCCCCeEEEeC
Q 042109 49 PVAKKGSRVAVRL 61 (61)
Q Consensus 49 ~~p~~G~tV~VhY 61 (61)
+...+||+|.|||
T Consensus 21 p~f~~GDtV~V~~ 33 (117)
T CHL00084 21 PKIRVGDTVKVGV 33 (117)
T ss_pred CccCCCCEEEEEE
Confidence 5678999999986
No 11
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=31.71 E-value=51 Score=19.45 Aligned_cols=30 Identities=27% Similarity=0.112 Sum_probs=15.9
Q ss_pred ccCCCCCeEEEeEcccCCCcCCCCeEEEeC
Q 042109 32 TTLPNGLKYYDVKVGGGPVAKKGSRVAVRL 61 (61)
Q Consensus 32 v~~pSGLqy~dl~~G~G~~p~~G~tV~VhY 61 (61)
+++.+|=.|+--.+=+=+..++|..|.|+|
T Consensus 19 itLdDGksy~lp~ef~~~~L~~G~kV~V~y 48 (61)
T PF07076_consen 19 ITLDDGKSYKLPEEFDFDGLKPGMKVVVFY 48 (61)
T ss_pred EEecCCCEEECCCcccccccCCCCEEEEEE
Confidence 344444444332222234456777888877
No 12
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=31.01 E-value=35 Score=22.50 Aligned_cols=13 Identities=31% Similarity=0.562 Sum_probs=10.8
Q ss_pred CCcCCCCeEEEeC
Q 042109 49 PVAKKGSRVAVRL 61 (61)
Q Consensus 49 ~~p~~G~tV~VhY 61 (61)
|...+||||.||+
T Consensus 19 P~f~~GDtvrv~v 31 (115)
T COG0335 19 PSFRPGDTVRVHV 31 (115)
T ss_pred CCCCCCCEEEEEE
Confidence 6678899999985
No 13
>PF01245 Ribosomal_L19: Ribosomal protein L19; InterPro: IPR001857 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L19 is one of the proteins from the large ribosomal subunit [, ]. In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface [] and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae. L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3HUZ_T 3V2D_T 3I8I_R 2XG2_T 2V49_T 2XUX_T 3HUX_T 3I9C_R 3V25_T 3UZ2_R ....
Probab=30.54 E-value=36 Score=21.80 Aligned_cols=13 Identities=31% Similarity=0.445 Sum_probs=11.0
Q ss_pred CCcCCCCeEEEeC
Q 042109 49 PVAKKGSRVAVRL 61 (61)
Q Consensus 49 ~~p~~G~tV~VhY 61 (61)
+...+||+|.|+|
T Consensus 17 p~f~~GD~v~V~~ 29 (113)
T PF01245_consen 17 PEFRVGDTVRVTY 29 (113)
T ss_dssp SSSSSSSEEEEEE
T ss_pred CCcCCCCEEEEEE
Confidence 5678999999986
No 14
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=28.86 E-value=40 Score=21.94 Aligned_cols=13 Identities=31% Similarity=0.539 Sum_probs=11.0
Q ss_pred CCcCCCCeEEEeC
Q 042109 49 PVAKKGSRVAVRL 61 (61)
Q Consensus 49 ~~p~~G~tV~VhY 61 (61)
|...+||+|.|+|
T Consensus 17 p~f~~GD~V~V~~ 29 (116)
T PRK05338 17 PEFRPGDTVRVHV 29 (116)
T ss_pred CCcCCCCEEEEEE
Confidence 6678999999986
No 15
>KOG0545 consensus Aryl-hydrocarbon receptor-interacting protein [Posttranslational modification, protein turnover, chaperones]
Probab=27.73 E-value=29 Score=26.39 Aligned_cols=27 Identities=26% Similarity=0.400 Sum_probs=23.4
Q ss_pred CCCCeEEEeEcccCCCc--CCCCeEEEeC
Q 042109 35 PNGLKYYDVKVGGGPVA--KKGSRVAVRL 61 (61)
Q Consensus 35 pSGLqy~dl~~G~G~~p--~~G~tV~VhY 61 (61)
..|++-..|..|+|+-| ..|..|..||
T Consensus 9 ~~gv~Kril~~G~g~l~e~~dGTrv~FHf 37 (329)
T KOG0545|consen 9 VEGVKKRILHGGTGELPEFIDGTRVIFHF 37 (329)
T ss_pred chhhhHhhccCCCccCccccCCceEEEEE
Confidence 46888899999999755 6999999998
No 16
>COG1581 Ssh10b Archaeal DNA-binding protein [Transcription]
Probab=26.16 E-value=92 Score=19.83 Aligned_cols=23 Identities=22% Similarity=0.385 Sum_probs=15.9
Q ss_pred CCeEEEeEcccCC-CcCCCCeEEE
Q 042109 37 GLKYYDVKVGGGP-VAKKGSRVAV 59 (61)
Q Consensus 37 GLqy~dl~~G~G~-~p~~G~tV~V 59 (61)
++|+++|+.|+-. +-..|.+..|
T Consensus 58 ~v~ik~Iki~se~~~~~~gr~~~V 81 (91)
T COG1581 58 DVQIKDIKIGTEELEGEDGRTRNV 81 (91)
T ss_pred CceEEEEEecceeeecCCCceeeE
Confidence 8999999999843 3344555444
No 17
>TIGR01024 rplS_bact ribosomal protein L19, bacterial type. This model describes bacterial ribosomoal protein L19 and its chloroplast equivalent. Putative mitochondrial L19 are found in several species (but not Saccharomyces cerevisiae) and score between trusted and noise cutoffs.
Probab=25.85 E-value=47 Score=21.50 Aligned_cols=13 Identities=31% Similarity=0.485 Sum_probs=10.9
Q ss_pred CCcCCCCeEEEeC
Q 042109 49 PVAKKGSRVAVRL 61 (61)
Q Consensus 49 ~~p~~G~tV~VhY 61 (61)
|+..+||+|.|+|
T Consensus 17 p~f~~GD~v~V~~ 29 (113)
T TIGR01024 17 PDFRVGDTVRVHV 29 (113)
T ss_pred CccCCCCEEEEEE
Confidence 5678999999986
No 18
>PF14444 S1-like: S1-like
Probab=21.48 E-value=1.4e+02 Score=17.44 Aligned_cols=18 Identities=44% Similarity=0.523 Sum_probs=13.5
Q ss_pred eEcccCCCcCCCCeEEEe
Q 042109 43 VKVGGGPVAKKGSRVAVR 60 (61)
Q Consensus 43 l~~G~G~~p~~G~tV~Vh 60 (61)
...=.|..|+.||+|.|.
T Consensus 26 ~~vv~G~~P~vGdrV~v~ 43 (58)
T PF14444_consen 26 TDVVKGNVPKVGDRVLVE 43 (58)
T ss_pred cccEecCCCccCCEEEEE
Confidence 333458899999999874
Done!