Query 016268
Match_columns 392
No_of_seqs 26 out of 28
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 05:19:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016268.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016268hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01465 GRIP: GRIP domain; I 48.0 19 0.00041 26.6 2.6 25 266-291 9-33 (46)
2 KOG1996 mRNA splicing factor [ 45.6 22 0.00047 36.6 3.4 65 27-92 38-113 (378)
3 PF09588 YqaJ: YqaJ-like viral 45.0 14 0.0003 30.8 1.7 18 326-343 135-152 (152)
4 PF00023 Ank: Ankyrin repeat H 33.2 38 0.00082 22.0 2.0 21 159-179 12-32 (33)
5 PF03765 CRAL_TRIO_N: CRAL/TRI 28.6 65 0.0014 23.3 2.8 24 265-288 30-54 (55)
6 PF14967 FAM70: FAM70 protein 27.3 99 0.0021 31.8 4.7 24 60-83 304-327 (327)
7 PRK13855 type IV secretion sys 22.3 2E+02 0.0043 30.1 5.8 18 13-30 37-54 (376)
8 PF06870 RNA_pol_I_A49: A49-li 22.2 43 0.00094 32.9 1.1 32 275-307 329-380 (385)
9 smart00755 Grip golgin-97, Ran 19.0 1.1E+02 0.0024 23.0 2.4 23 266-290 8-30 (46)
10 PF06755 DUF1219: Protein of u 17.9 46 0.00099 29.7 0.3 17 362-378 67-83 (114)
No 1
>PF01465 GRIP: GRIP domain; InterPro: IPR000237 The GRIP (golgin-97, RanBP2alpha,Imh1p and p230/golgin-245) domain [, , ] is found in many large coiled-coil proteins. It has been shown to be sufficient for targeting to the Golgi []. The GRIP domain contains a completely conserved tyrosine residue.; GO: 0005515 protein binding, 0000042 protein targeting to Golgi; PDB: 1R4A_H 1UPT_B.
Probab=47.95 E-value=19 Score=26.61 Aligned_cols=25 Identities=16% Similarity=0.347 Sum_probs=18.9
Q ss_pred hhhHHHHhhcCCCHHHHHHHHHhhhc
Q 016268 266 KGVAYSYLSSKLSAEAANSAFRILSA 291 (392)
Q Consensus 266 K~VVl~wLa~KL~~~~An~~~R~LS~ 291 (392)
||||++||..+= ++....+++.|+.
T Consensus 9 KNvl~~fl~~~~-~~~~~~llpvi~t 33 (46)
T PF01465_consen 9 KNVLLQFLESRE-PSEREQLLPVIAT 33 (46)
T ss_dssp HHHHHHHHTTSS----HHHHHHHHHH
T ss_pred HHHHHHHhcCCc-hhhHHHHHHHHHH
Confidence 899999999985 7788888888764
No 2
>KOG1996 consensus mRNA splicing factor [RNA processing and modification]
Probab=45.59 E-value=22 Score=36.59 Aligned_cols=65 Identities=25% Similarity=0.297 Sum_probs=45.0
Q ss_pred hhhhHhhhhcccCCCCccCccccCCCCCCC-----CCCCcccCCCCCCCCCCCCCCC------CCCCCCCCCCCCCC
Q 016268 27 SFQDVVALHNVLGPSHVSSTSELANPPTTG-----LFEPIEISPAVIPPYPYAGEPL------PPMYPTFPTTYEPN 92 (392)
Q Consensus 27 ~~q~v~~~~~~~~~~~~~~~~~l~~pp~~g-----l~~pieiSPs~~P~~~~P~~a~------sPm~P~f~n~~~P~ 92 (392)
..|.-.+++++..|.-+-+.. +-++|++. +|+||+-.|..-|-++.|.-+. --.+|-|||.|+-.
T Consensus 38 al~qq~~~r~l~kp~pvi~~~-~k~~~~s~~~qs~~~pp~~aap~~dpi~~g~~a~~~~~~v~~EYdPm~PNdye~v 113 (378)
T KOG1996|consen 38 ALQQQAARRKLVKPPPVIDLS-TKNRTISTAVQSVSFPPIRAAPVSDPISFGPKAATDEEHVKCEYDPMFPNDYEKV 113 (378)
T ss_pred ccChHHHhccccCCCCceecc-cCCCCCCccccccccCcccccCccCcccccccccccccchhhhcCCCCcchHHHH
Confidence 346677888888888877665 44444443 8999999999999888885531 12356666887643
No 3
>PF09588 YqaJ: YqaJ-like viral recombinase domain; InterPro: IPR019080 This protein is found in many different bacterial species but is of viral origin. The protein forms an oligomer and functions as a processive alkaline exonuclease that digests linear double-stranded DNA in a Mg(2+)-dependent reaction, It has a preference for 5'-phosphorylated DNA ends. It thus forms part of the two-component SynExo viral recombinase functional unit []. ; PDB: 3SZ5_A 3SZ4_A 3SYY_A 3K93_A 1AVQ_A 3SM4_C 3SLP_A.
Probab=44.99 E-value=14 Score=30.83 Aligned_cols=18 Identities=39% Similarity=0.464 Sum_probs=15.7
Q ss_pred hHHHHHHhhhHhhhhhhh
Q 016268 326 LNAYIAGVQKQMLITNKQ 343 (392)
Q Consensus 326 l~sYvs~lQkQ~lITNlQ 343 (392)
-+.|...+|-||+||++|
T Consensus 135 p~~Y~~QvQ~qm~vtg~e 152 (152)
T PF09588_consen 135 PHYYYAQVQHQMAVTGAE 152 (152)
T ss_dssp HHHHHHHHHHHHHHHT-S
T ss_pred CHHHHHHHHHHHHHHCcC
Confidence 689999999999999975
No 4
>PF00023 Ank: Ankyrin repeat Hereditary spherocytosis; InterPro: IPR002110 The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers []. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators, cytoskeletal, ion transporters and signal transducers. The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it. The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures [, , , ]. Each repeat folds into a helix-loop-helix structure with a beta-hairpin/loop region projecting out from the helices at a 90o angle. The repeats stack together to form an L-shaped structure [, ].; GO: 0005515 protein binding; PDB: 1D9S_A 1NFI_F 1IKN_D 1WDY_A 1OT8_C 1QYM_A 1TR4_A 1UOH_A 1N11_A 1K1A_A ....
Probab=33.15 E-value=38 Score=21.96 Aligned_cols=21 Identities=24% Similarity=0.362 Sum_probs=17.0
Q ss_pred hhHHHHHHHHhhcCCcCCcCc
Q 016268 159 DCFSDILSILASRGANHTIPT 179 (392)
Q Consensus 159 ~CfSDi~~iL~s~GAn~~l~~ 179 (392)
+--.|+.++|.++||+-++.+
T Consensus 12 ~~~~~~v~~Ll~~ga~~~~~d 32 (33)
T PF00023_consen 12 RGHPDIVKLLLKHGADINARD 32 (33)
T ss_dssp TTCHHHHHHHHHTTSCTTCBC
T ss_pred HHHHHHHHHHHHCcCCCCCCC
Confidence 346799999999999987653
No 5
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=28.59 E-value=65 Score=23.34 Aligned_cols=24 Identities=17% Similarity=0.234 Sum_probs=20.2
Q ss_pred chhhHHHHh-hcCCCHHHHHHHHHh
Q 016268 265 CKGVAYSYL-SSKLSAEAANSAFRI 288 (392)
Q Consensus 265 CK~VVl~wL-a~KL~~~~An~~~R~ 288 (392)
-.++++||| |+|.+-+.|.+||+.
T Consensus 30 ~d~~llRFLRARkf~v~~A~~mL~~ 54 (55)
T PF03765_consen 30 DDNFLLRFLRARKFDVEKAFKMLKK 54 (55)
T ss_dssp SHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred CHHHHHHHHHHccCCHHHHHHHHHh
Confidence 449999999 799999999999974
No 6
>PF14967 FAM70: FAM70 protein
Probab=27.32 E-value=99 Score=31.80 Aligned_cols=24 Identities=42% Similarity=0.759 Sum_probs=17.7
Q ss_pred CcccCCCCCCCCCCCCCCCCCCCC
Q 016268 60 PIEISPAVIPPYPYAGEPLPPMYP 83 (392)
Q Consensus 60 pieiSPs~~P~~~~P~~a~sPm~P 83 (392)
|....|--.|.+|.|+|-|||-.|
T Consensus 304 p~~aPp~y~P~yf~PgEKPPPYaP 327 (327)
T PF14967_consen 304 PPNAPPRYAPPYFPPGEKPPPYAP 327 (327)
T ss_pred CCCCCCCCCCCCCCCCCCCcCCCC
Confidence 555566667888889999888655
No 7
>PRK13855 type IV secretion system protein VirB10; Provisional
Probab=22.31 E-value=2e+02 Score=30.15 Aligned_cols=18 Identities=22% Similarity=0.329 Sum_probs=13.7
Q ss_pred hhhHHHHHHHHHhhhhhh
Q 016268 13 SMCHAFLLFIAWLFSFQD 30 (392)
Q Consensus 13 ~~~~~~~lf~iwl~~~q~ 30 (392)
..+-.|.+|+||+.+-|.
T Consensus 37 ~~~~~~~~~~~w~~~~~~ 54 (376)
T PRK13855 37 GLVLALSLSLIWLGGRSK 54 (376)
T ss_pred HHHHHHHHHHHHhccCCC
Confidence 345678999999987654
No 8
>PF06870 RNA_pol_I_A49: A49-like RNA polymerase I associated factor ; InterPro: IPR009668 Saccharomyces cerevisiae A49 is a specific subunit associated with RNA polymerase I (Pol I) in eukaryotes. Pol I maintains transcription activities in A49 deletion mutants. However, such mutants are deficient in transcription activity at low temperatures. Deletion analysis of the fusion yeast homologue indicates that only the C-terminal two thirds are required for function. Transcript analysis has demonstrated that A49 is maximising transcription of ribosomal DNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 3NFG_A 3NFH_B.
Probab=22.19 E-value=43 Score=32.92 Aligned_cols=32 Identities=44% Similarity=0.687 Sum_probs=16.3
Q ss_pred cCCCHHHHHHHHHhhhcCcCCc--------------------cccccCCCchH
Q 016268 275 SKLSAEAANSAFRILSACKVNK--------------------VCPLDFKQPSE 307 (392)
Q Consensus 275 ~KL~~~~An~~~R~LS~CkVNk--------------------vCPL~F~d~s~ 307 (392)
-|+++....+.||.| ||+|.+ .=||.||.++.
T Consensus 329 Lkl~~~~l~~~~r~L-GC~v~~~~~~~~~~~~~~~~~~~a~L~~PL~fP~~~~ 380 (385)
T PF06870_consen 329 LKLSPKKLTQYFREL-GCKVKKATEALGLSKSEAKTHKIATLKLPLKFPKPRR 380 (385)
T ss_dssp HT--HHHHHHHHHHT-T-EEEE--HHHT--GGGGGGSEEEE------------
T ss_pred hCCCHHHHHHHHHHh-CCEecccccccccccccccceeEEEEeCCCCCCCccc
Confidence 489999999999999 799988 35889988764
No 9
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=18.95 E-value=1.1e+02 Score=22.99 Aligned_cols=23 Identities=22% Similarity=0.436 Sum_probs=17.4
Q ss_pred hhhHHHHhhcCCCHHHHHHHHHhhh
Q 016268 266 KGVAYSYLSSKLSAEAANSAFRILS 290 (392)
Q Consensus 266 K~VVl~wLa~KL~~~~An~~~R~LS 290 (392)
|||++.||..|=.. ....++.|+
T Consensus 8 KNVll~fl~~~e~~--r~~ll~vi~ 30 (46)
T smart00755 8 KNVLLQFLTLRESE--RETLLKVIS 30 (46)
T ss_pred HHHHHHHhccCcch--HHHHHHHHH
Confidence 89999999998754 556666554
No 10
>PF06755 DUF1219: Protein of unknown function (DUF1219); InterPro: IPR009610 This family consists of several hypothetical proteins which seem to be specific to the enterobacteria Escherichia coli and Shigella flexneri. Family members are often known as YeeV proteins and are around 125 residues in length. The function of this family is unknown.
Probab=17.91 E-value=46 Score=29.74 Aligned_cols=17 Identities=41% Similarity=0.599 Sum_probs=15.6
Q ss_pred cccccccccccccceec
Q 016268 362 TNIYELCDVDLKDFSIQ 378 (392)
Q Consensus 362 ~nIY~LC~I~LKDFSLQ 378 (392)
-+.|+|.+||=++||.|
T Consensus 67 VeKY~LvRiD~~gFs~~ 83 (114)
T PF06755_consen 67 VEKYELVRIDRNGFSWQ 83 (114)
T ss_pred HHHHhhhhcCCcccCcc
Confidence 46799999999999998
Done!