Query 022697
Match_columns 293
No_of_seqs 49 out of 51
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 05:29:44 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022697.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022697hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF11571 Med27: Mediator compl 100.0 7.6E-30 1.7E-34 198.9 6.3 86 179-288 4-90 (90)
2 KOG3043 Predicted hydrolase re 70.8 4.6 0.0001 38.3 3.4 83 141-224 134-241 (242)
3 PF14053 DUF4248: Domain of un 62.3 7.7 0.00017 29.9 2.6 32 198-229 10-41 (69)
4 KOG1701 Focal adhesion adaptor 51.2 5.4 0.00012 40.8 0.2 12 229-240 335-346 (468)
5 PF10367 Vps39_2: Vacuolar sor 50.8 4.2 9.2E-05 30.8 -0.4 13 228-240 78-90 (109)
6 PF03297 Ribosomal_S25: S25 ri 34.2 28 0.0006 29.1 1.8 18 74-91 45-62 (105)
7 PRK09334 30S ribosomal protein 31.1 33 0.00072 27.9 1.8 18 74-91 27-44 (86)
8 PF06046 Sec6: Exocyst complex 29.3 18 0.00039 35.7 0.0 47 181-227 130-181 (566)
9 KOG2272 Focal adhesion protein 22.8 22 0.00047 34.8 -0.7 34 207-240 49-85 (332)
10 PF10892 DUF2688: Protein of u 21.9 28 0.00061 27.0 -0.2 15 226-240 8-22 (60)
11 PF13959 DUF4217: Domain of un 21.4 97 0.0021 23.1 2.6 24 209-234 17-40 (65)
12 COG0394 Wzb Protein-tyrosine-p 20.2 2.5E+02 0.0054 23.8 5.2 92 103-202 41-136 (139)
No 1
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=99.96 E-value=7.6e-30 Score=198.91 Aligned_cols=86 Identities=48% Similarity=0.790 Sum_probs=77.8
Q ss_pred ccCCcCcchhhHHhhHHhHHHHhhccc-CCCchhHHHHHHHHHHHhhhhchHhhhHHHHhhhccccccCCCCCccccCCC
Q 022697 179 IHARGSSVYHVFRHITEHAGTALQFFL-GIRTETSLYFLLHWICSYQTLFSKVCSKCGRLLAMDKRLALLLPPVSRPYRH 257 (293)
Q Consensus 179 l~~ws~Sry~VFRKITEHA~~AL~~F~-s~~PetaLrsFLtWL~SYr~LFs~PCkkCgklL~~Ds~~~~~LPPtwRDfR~ 257 (293)
+++|++|+|+|||++|+||++||+||. ++.|+.+|++||+||+||++||++||++|||+| ++.++|||+||+++.
T Consensus 4 ~~~~~~S~~~v~~~~t~~a~~al~~~~~~~~~~~~l~~ll~~l~sY~~lfs~pC~~C~klL----~~~~~LPP~~r~~~~ 79 (90)
T PF11571_consen 4 VDPWSPSRYKVFRKITEHANTALLHFINSRPPEWDLRSLLDWLSSYRNLFSTPCKKCGKLL----SSKAFLPPVRRPKDF 79 (90)
T ss_pred cccccchhhhhhhhhhHHHHHHHHHhhhcCCCccHHHHHHHHHHHHhhhccchhhHHHhHh----hhcccCCCeeecccC
Confidence 589999999999999999999988776 799999999999999999999999999999999 233599999998777
Q ss_pred CCcccccchhhccccccCCCccccccccccC
Q 022697 258 FFPTVTSSAQLISSTNEQSSDVVNAYHIGCF 288 (293)
Q Consensus 258 ~~~~~~~s~~~~~~~~~~~~d~~~AYH~gC~ 288 (293)
.+ .+|||++|+
T Consensus 80 ~~--------------------~~ayH~~C~ 90 (90)
T PF11571_consen 80 RS--------------------WEAYHEGCR 90 (90)
T ss_pred CC--------------------CcccCcccC
Confidence 63 499999995
No 2
>KOG3043 consensus Predicted hydrolase related to dienelactone hydrolase [General function prediction only]
Probab=70.80 E-value=4.6 Score=38.28 Aligned_cols=83 Identities=19% Similarity=0.264 Sum_probs=51.6
Q ss_pred Eeeeechh-hhhhheeeCCC--CCCCCce----eeEecCCCCCc----cc---------cCCcCcchhhHHhhHHhHHHH
Q 022697 141 VIELLFPS-IFRAIVSLHPV--GTIEPDA----VAFFSPDEGGN----YI---------HARGSSVYHVFRHITEHAGTA 200 (293)
Q Consensus 141 viel~~p~-vFkaiIsl~~a--gS~dpD~----VafFsp~E~g~----yl---------~~ws~Sry~VFRKITEHA~~A 200 (293)
||++..-. -|+|+||+||. .|-||.. |.|..-.+|-. -+ ++=..|+.++|-.++ |+..|
T Consensus 134 vv~~~~~~~~f~a~v~~hps~~d~~D~~~vk~Pilfl~ae~D~~~p~~~v~~~ee~lk~~~~~~~~v~~f~g~~-HGf~~ 212 (242)
T KOG3043|consen 134 VVTLSAKDPEFDAGVSFHPSFVDSADIANVKAPILFLFAELDEDVPPKDVKAWEEKLKENPAVGSQVKTFSGVG-HGFVA 212 (242)
T ss_pred EEEeeccchhheeeeEecCCcCChhHHhcCCCCEEEEeecccccCCHHHHHHHHHHHhcCcccceeEEEcCCcc-chhhh
Confidence 56666655 89999999998 7677655 44444433321 11 333337778887775 45444
Q ss_pred hhcccC-----CCchhHHHHHHHHHHHhh
Q 022697 201 LQFFLG-----IRTETSLYFLLHWICSYQ 224 (293)
Q Consensus 201 L~~F~s-----~~PetaLrsFLtWL~SYr 224 (293)
-.+=.+ ..-|.+...|+.||+.|-
T Consensus 213 ~r~~~~~Ped~~~~eea~~~~~~Wf~~y~ 241 (242)
T KOG3043|consen 213 RRANISSPEDKKAAEEAYQRFISWFKHYL 241 (242)
T ss_pred hccCCCChhHHHHHHHHHHHHHHHHHHhh
Confidence 332111 222479999999999984
No 3
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=62.33 E-value=7.7 Score=29.92 Aligned_cols=32 Identities=19% Similarity=0.346 Sum_probs=26.8
Q ss_pred HHHhhcccCCCchhHHHHHHHHHHHhhhhchH
Q 022697 198 GTALQFFLGIRTETSLYFLLHWICSYQTLFSK 229 (293)
Q Consensus 198 ~~AL~~F~s~~PetaLrsFLtWL~SYr~LFs~ 229 (293)
.-|+.||-...|..|++.|..||.-...|-.+
T Consensus 10 ELA~lYfP~~~~~sA~r~L~rwI~~~~~L~~~ 41 (69)
T PF14053_consen 10 ELAQLYFPDLTPSSAVRKLRRWIRRNPELLEE 41 (69)
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHCHHHHHH
Confidence 34688998889999999999999988777544
No 4
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=51.18 E-value=5.4 Score=40.78 Aligned_cols=12 Identities=33% Similarity=0.844 Sum_probs=9.6
Q ss_pred HhhhHHHHhhhc
Q 022697 229 KVCSKCGRLLAM 240 (293)
Q Consensus 229 ~PCkkCgklL~~ 240 (293)
++|..||+.+.+
T Consensus 335 ekC~~Cg~~I~d 346 (468)
T KOG1701|consen 335 EKCNKCGEPIMD 346 (468)
T ss_pred HHHhhhhhHHHH
Confidence 689999988764
No 5
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=50.82 E-value=4.2 Score=30.77 Aligned_cols=13 Identities=46% Similarity=0.856 Sum_probs=11.1
Q ss_pred hHhhhHHHHhhhc
Q 022697 228 SKVCSKCGRLLAM 240 (293)
Q Consensus 228 s~PCkkCgklL~~ 240 (293)
.+.|..|||-|.+
T Consensus 78 ~~~C~vC~k~l~~ 90 (109)
T PF10367_consen 78 STKCSVCGKPLGN 90 (109)
T ss_pred CCCccCcCCcCCC
Confidence 3789999999985
No 6
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 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 [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=34.18 E-value=28 Score=29.08 Aligned_cols=18 Identities=39% Similarity=0.582 Sum_probs=15.6
Q ss_pred HHHHHHhhhCCCceeeee
Q 022697 74 DVLMRLEKEVPNLKIFTY 91 (293)
Q Consensus 74 ~vl~~le~~~pn~ki~ty 91 (293)
+.+..|++|||++|+.|-
T Consensus 45 ~~~~kl~kEV~~~K~ITp 62 (105)
T PF03297_consen 45 ETYDKLLKEVPKMKLITP 62 (105)
T ss_dssp HHHHHHHHHCTTSSCECH
T ss_pred HHHHHHHHHhccCcEeeH
Confidence 567889999999999884
No 7
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=31.09 E-value=33 Score=27.90 Aligned_cols=18 Identities=44% Similarity=0.517 Sum_probs=15.5
Q ss_pred HHHHHHhhhCCCceeeee
Q 022697 74 DVLMRLEKEVPNLKIFTY 91 (293)
Q Consensus 74 ~vl~~le~~~pn~ki~ty 91 (293)
+.+.+|.||||++|+.|-
T Consensus 27 ~t~dkl~kEV~~~K~ITp 44 (86)
T PRK09334 27 ELLKRVAKEVKKEKIVTP 44 (86)
T ss_pred HHHHHHHHHhccCcEEcH
Confidence 467889999999999884
No 8
>PF06046 Sec6: Exocyst complex component Sec6; InterPro: IPR010326 Sec6 is a component of the multiprotein exocyst complex. Sec6 interacts with Sec8, Sec10 and Exo70.These exocyst proteins localise to regions of active exocytosis-at the growing ends of interphase cells and in the medial region of cells undergoing cytokinesis-in an F-actin-dependent and exocytosis- independent manner [].; PDB: 2FJI_2.
Probab=29.31 E-value=18 Score=35.66 Aligned_cols=47 Identities=21% Similarity=0.318 Sum_probs=0.0
Q ss_pred CCcCcchhhHHhhHHhHHHHhhcccC-----CCchhHHHHHHHHHHHhhhhc
Q 022697 181 ARGSSVYHVFRHITEHAGTALQFFLG-----IRTETSLYFLLHWICSYQTLF 227 (293)
Q Consensus 181 ~ws~Sry~VFRKITEHA~~AL~~F~s-----~~PetaLrsFLtWL~SYr~LF 227 (293)
+=-|..|+||+..+..-+.+|+-+.. ..+...+..++.|++.|.++-
T Consensus 130 ~cfPp~~~I~~~y~~~YH~~l~~~l~~l~~~~l~~~~ll~ll~W~~~Y~~~m 181 (566)
T PF06046_consen 130 PCFPPEYDIFNTYVSMYHNALSDHLQELISPDLEANDLLSLLSWVNTYPSIM 181 (566)
T ss_dssp ----------------------------------------------------
T ss_pred ccCCCCChHHHHHHHHHHHHHHHHHHHHccCCCCHHHHhhheechhhChHhh
Confidence 33456788999999988888875443 445579999999999999843
No 9
>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]
Probab=22.77 E-value=22 Score=34.83 Aligned_cols=34 Identities=21% Similarity=0.438 Sum_probs=24.1
Q ss_pred CCchhHHHHHHHH---HHHhhhhchHhhhHHHHhhhc
Q 022697 207 IRTETSLYFLLHW---ICSYQTLFSKVCSKCGRLLAM 240 (293)
Q Consensus 207 ~~PetaLrsFLtW---L~SYr~LFs~PCkkCgklL~~ 240 (293)
..|+...+.|=.- =|.|+.||.--|-+||.++.-
T Consensus 49 pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiG 85 (332)
T KOG2272|consen 49 PFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIG 85 (332)
T ss_pred cCCCceeEEecCcccccccchhhhchhhcccccchhh
Confidence 3455555444322 367899999999999998874
No 10
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=21.89 E-value=28 Score=27.03 Aligned_cols=15 Identities=20% Similarity=0.793 Sum_probs=12.4
Q ss_pred hchHhhhHHHHhhhc
Q 022697 226 LFSKVCSKCGRLLAM 240 (293)
Q Consensus 226 LFs~PCkkCgklL~~ 240 (293)
+-+.+|++||+-|.+
T Consensus 8 IV~t~CrRCGk~i~t 22 (60)
T PF10892_consen 8 IVETPCRRCGKSIRT 22 (60)
T ss_pred eeeehhhhhCccHHH
Confidence 557899999998865
No 11
>PF13959 DUF4217: Domain of unknown function (DUF4217)
Probab=21.40 E-value=97 Score=23.06 Aligned_cols=24 Identities=13% Similarity=0.192 Sum_probs=19.2
Q ss_pred chhHHHHHHHHHHHhhhhchHhhhHH
Q 022697 209 TETSLYFLLHWICSYQTLFSKVCSKC 234 (293)
Q Consensus 209 PetaLrsFLtWL~SYr~LFs~PCkkC 234 (293)
-+.|-+-|.+|+++|.+. .+|+.+
T Consensus 17 ~~lA~~Af~SyvraY~~~--~~~k~i 40 (65)
T PF13959_consen 17 KELAQKAFVSYVRAYASH--KELKDI 40 (65)
T ss_pred HHHHHHHHHHHHHHHHHH--hhhhhh
Confidence 347899999999999987 666654
No 12
>COG0394 Wzb Protein-tyrosine-phosphatase [Signal transduction mechanisms]
Probab=20.24 E-value=2.5e+02 Score=23.79 Aligned_cols=92 Identities=21% Similarity=0.188 Sum_probs=57.0
Q ss_pred CCCC-CCCCccchhcccccccCCCCCCCCcccccccceeEeeeechhhhhhheeeCCCCCCCCceeeEecCCCCCccccC
Q 022697 103 LPSS-ANESPLELLKEHNFHSSSKLRPGLQNTVAADKVSVIELLFPSIFRAIVSLHPVGTIEPDAVAFFSPDEGGNYIHA 181 (293)
Q Consensus 103 l~~~-~~~~~~~~sk~~~~~~~~k~r~~~~~~~~~d~vaviel~~p~vFkaiIsl~~agS~dpD~VafFsp~E~g~yl~~ 181 (293)
.++. .+..-++..+|+++..+. .|+-..+....++.=+|=-+.++-.+-+..+.|.+. .+-..++|...+|
T Consensus 41 ~~g~~~~~~a~~vl~e~Gid~~~-~~~k~i~~~~~~~~DlIitmd~~~~~~~~~~~p~~~-------~~~~~~~~~v~DP 112 (139)
T COG0394 41 HPGEPPDPRAVEVLAEHGIDISG-HRSKQLTEEDFDEFDLIITMDESNAADLCPLAPGNT-------LLLEYEHWEVPDP 112 (139)
T ss_pred CCCCCCCHHHHHHHHHcCCCcCC-ccCccCchhhhhhCCEEEEeChHHHhhHhhcCcccc-------ccccccCCCCCCC
Confidence 3444 777888899999999886 444444443333444444444555555555555543 2223344888899
Q ss_pred CcCc---chhhHHhhHHhHHHHhh
Q 022697 182 RGSS---VYHVFRHITEHAGTALQ 202 (293)
Q Consensus 182 ws~S---ry~VFRKITEHA~~AL~ 202 (293)
|..| .-++||.|.+.+..-+.
T Consensus 113 ~~~~~e~~~~~~~~i~~~~~~l~~ 136 (139)
T COG0394 113 YYGSGEEFEEVYRLIEDAIKALLK 136 (139)
T ss_pred CCCchHHHHHHHHHHHHHHHHHHH
Confidence 9887 46788888887665443
Done!