Query 044024
Match_columns 296
No_of_seqs 27 out of 29
Neff 2.4
Searched_HMMs 46136
Date Fri Mar 29 10:44:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/044024.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/044024hhsearch_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 58.3 10 0.00022 27.0 2.4 25 226-251 9-33 (46)
2 PF00023 Ank: Ankyrin repeat H 44.2 19 0.00041 22.5 1.8 21 127-147 12-32 (33)
3 PF03765 CRAL_TRIO_N: CRAL/TRI 34.0 33 0.00071 23.9 1.9 24 225-248 30-54 (55)
4 smart00755 Grip golgin-97, Ran 25.0 65 0.0014 23.2 2.2 23 226-250 8-30 (46)
5 PF15611 EH_Signature: EH_Sign 20.1 96 0.0021 28.7 2.8 50 187-236 199-251 (389)
6 PF13490 zf-HC2: Putative zinc 14.6 1.4E+02 0.003 19.1 1.8 30 224-253 3-32 (36)
7 PF09507 CDC27: DNA polymerase 13.5 49 0.0011 30.8 -0.7 22 228-249 3-26 (430)
8 COG5567 Predicted small peripl 13.4 2.3E+02 0.0049 22.1 2.9 33 242-276 10-42 (58)
9 PF06870 RNA_pol_I_A49: A49-li 12.2 77 0.0017 30.0 0.2 21 235-256 329-349 (385)
10 PF01042 Ribonuc_L-PSP: Endori 11.0 2E+02 0.0044 22.7 2.2 42 109-152 25-70 (121)
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=58.26 E-value=10 Score=27.00 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=18.9
Q ss_pred hhHHHHHHhccCCcchhhHHhhhhhc
Q 044024 226 KSIVFRWLASKLDPSSANGVLRALSN 251 (296)
Q Consensus 226 K~VVlrwLa~KL~p~~An~~lR~LSn 251 (296)
||||++||..+= ++....+++.|+.
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 7788888888763
No 2
>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=44.22 E-value=19 Score=22.48 Aligned_cols=21 Identities=29% Similarity=0.374 Sum_probs=17.0
Q ss_pred hhHHHHHHHHHhcCccccccc
Q 044024 127 HCLSDFEKILETQGANRNLKT 147 (296)
Q Consensus 127 ~C~SDi~~iL~sqGAn~~l~~ 147 (296)
+--.|+.++|.++||+-++.+
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 336799999999999987653
No 3
>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=34.02 E-value=33 Score=23.92 Aligned_cols=24 Identities=29% Similarity=0.445 Sum_probs=20.0
Q ss_pred chhHHHHHH-hccCCcchhhHHhhh
Q 044024 225 CKSIVFRWL-ASKLDPSSANGVLRA 248 (296)
Q Consensus 225 CK~VVlrwL-a~KL~p~~An~~lR~ 248 (296)
-.++++||| |+|.+-+.|.+||+.
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 4
>smart00755 Grip golgin-97, RanBP2alpha,Imh1p and p230/golgin-245.
Probab=24.99 E-value=65 Score=23.24 Aligned_cols=23 Identities=17% Similarity=0.455 Sum_probs=17.6
Q ss_pred hhHHHHHHhccCCcchhhHHhhhhh
Q 044024 226 KSIVFRWLASKLDPSSANGVLRALS 250 (296)
Q Consensus 226 K~VVlrwLa~KL~p~~An~~lR~LS 250 (296)
|||+++||..|=.. ...+++.|+
T Consensus 8 KNVll~fl~~~e~~--r~~ll~vi~ 30 (46)
T smart00755 8 KNVLLQFLTLRESE--RETLLKVIS 30 (46)
T ss_pred HHHHHHHhccCcch--HHHHHHHHH
Confidence 89999999988653 566666654
No 5
>PF15611 EH_Signature: EH_Signature domain
Probab=20.05 E-value=96 Score=28.75 Aligned_cols=50 Identities=20% Similarity=0.270 Sum_probs=32.7
Q ss_pred chhHHh-HHHHHHHHHHHHHHHhccCCCCC--CCCCcccccchhHHHHHHhcc
Q 044024 187 PVKECC-QQVCQNAILDAARKIAMDGMVSM--PENSTRIDDCKSIVFRWLASK 236 (296)
Q Consensus 187 PvkECC-~~vCQ~AI~eAA~~Is~~~~~~~--~~~s~~v~DCK~VVlrwLa~K 236 (296)
+..+|= .+.++.+|+|.++.+.++..-.- ..=...-.+++++|.+||+++
T Consensus 199 ~~~~~~~~~~~~~~l~~~~l~~~GdPr~~~~~~~W~~v~e~a~~~v~~Wl~~~ 251 (389)
T PF15611_consen 199 RYIDRSPDEPVHEALRDLLLAIWGDPRLPSSQPNWSGVSEEARQMVRRWLSKE 251 (389)
T ss_pred HHHhcCccchhhHHHHHHHHHHhCCCCCCccccchhhcCHHHHHHHHHHHHHH
Confidence 333333 45788899999988777421111 112346679999999999876
No 6
>PF13490 zf-HC2: Putative zinc-finger; PDB: 2Z2S_F 2Q1Z_B 3HUG_T.
Probab=14.58 E-value=1.4e+02 Score=19.13 Aligned_cols=30 Identities=17% Similarity=0.460 Sum_probs=21.6
Q ss_pred cchhHHHHHHhccCCcchhhHHhhhhhcCc
Q 044024 224 DCKSIVFRWLASKLDPSSANGVLRALSNCK 253 (296)
Q Consensus 224 DCK~VVlrwLa~KL~p~~An~~lR~LSnCk 253 (296)
+.+..+..|+-+.|++.....+-.-|..|.
T Consensus 3 ~~~~~l~~y~dg~L~~~~~~~~~~HL~~C~ 32 (36)
T PF13490_consen 3 EVRELLSAYLDGELSPEERARLEAHLASCP 32 (36)
T ss_dssp --HHHHHHHHCT-S-HHHHHHHHHHHCT-H
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHHcCH
Confidence 446678899999999999999888888873
No 7
>PF09507 CDC27: DNA polymerase subunit Cdc27; InterPro: IPR019038 This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. ; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 1U76_B 3E0J_B.
Probab=13.50 E-value=49 Score=30.79 Aligned_cols=22 Identities=23% Similarity=0.634 Sum_probs=16.0
Q ss_pred HHHHHHhccCCc--chhhHHhhhh
Q 044024 228 IVFRWLASKLDP--SSANGVLRAL 249 (296)
Q Consensus 228 VVlrwLa~KL~p--~~An~~lR~L 249 (296)
|=|||||+.|+- ..|+.||...
T Consensus 3 VTYk~LSr~l~ihvn~AK~~L~ef 26 (430)
T PF09507_consen 3 VTYKWLSRELGIHVNQAKQMLYEF 26 (430)
T ss_dssp EEHHHHHHHHT--HHHHHHHHHHH
T ss_pred eeHHHHHHHhCCCHHHHHHHHHHH
Confidence 559999998865 5788887643
No 8
>COG5567 Predicted small periplasmic lipoprotein [Cell motility and secretion]
Probab=13.37 E-value=2.3e+02 Score=22.12 Aligned_cols=33 Identities=24% Similarity=0.274 Sum_probs=23.6
Q ss_pred hhHHhhhhhcCcCCcccccCCCCCCCCCccccccc
Q 044024 242 ANGVLRALSNCKVNKASKLPARPTAKPSQATAGFQ 276 (296)
Q Consensus 242 An~~lR~LSnCkVNkvCPL~F~d~~~~s~~~ag~q 276 (296)
|-.+|-.|.+|-.-+ ||.||+-.|.++--++-|
T Consensus 10 ala~l~sLA~CG~KG--PLy~Ppadk~a~~D~~~q 42 (58)
T COG5567 10 ALATLFSLAGCGLKG--PLYFPPADKNAPPDQQTQ 42 (58)
T ss_pred HHHHHHHHHhcccCC--CccCChhhccCCcccccc
Confidence 344555999998776 999999888666444433
No 9
>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=12.21 E-value=77 Score=30.00 Aligned_cols=21 Identities=43% Similarity=0.695 Sum_probs=15.8
Q ss_pred ccCCcchhhHHhhhhhcCcCCc
Q 044024 235 SKLDPSSANGVLRALSNCKVNK 256 (296)
Q Consensus 235 ~KL~p~~An~~lR~LSnCkVNk 256 (296)
=|+++....+.||.| ||+|.+
T Consensus 329 Lkl~~~~l~~~~r~L-GC~v~~ 349 (385)
T PF06870_consen 329 LKLSPKKLTQYFREL-GCKVKK 349 (385)
T ss_dssp HT--HHHHHHHHHHT-T-EEEE
T ss_pred hCCCHHHHHHHHHHh-CCEecc
Confidence 378899999999998 799988
No 10
>PF01042 Ribonuc_L-PSP: Endoribonuclease L-PSP; InterPro: IPR006175 This domain is found in endoribonuclease, that is active on single-stranded mRNA and inhibits protein synthesis by cleavage of mRNA []. Previously it was thought to inhibit protein synthesis initiation []. This endoribonuclease may also be involved in the regulation of purine biosynthesis []. ; PDB: 3GTZ_B 3V4D_E 1J7H_A 3R0P_D 2IG8_A 1QD9_B 3L7Q_E 3VCZ_A 3QUW_A 2EWC_K ....
Probab=11.04 E-value=2e+02 Score=22.73 Aligned_cols=42 Identities=24% Similarity=0.461 Sum_probs=0.0
Q ss_pred hhccCC--ccce-ecc-ccchhhhHHHHHHHHHhcCcccccccccccc
Q 044024 109 GQYSKY--SGML-SLN-TTNAQHCLSDFEKILETQGANRNLKTICSIH 152 (296)
Q Consensus 109 Gq~Sk~--s~~L-aLn-~t~A~~C~SDi~~iL~sqGAn~~l~~iCSv~ 152 (296)
||...+ +|.+ .-+ ...+..+|..|+.+|.+.|++ +.++.+++
T Consensus 25 Gq~~~d~~~~~~~~~~~~~Q~~~~l~ni~~~L~~~G~~--~~dvv~~~ 70 (121)
T PF01042_consen 25 GQVGIDPATGQVVPGDIEEQTRQALDNIERILAAAGAS--LDDVVKVT 70 (121)
T ss_dssp EEESBCTTTSSBSSSSHHHHHHHHHHHHHHHHHHTTS---GGGEEEEE
T ss_pred eeCCcCCCCCcCCCCCHHHHHHHHHHhhhhhhhcCCCc--ceeEeeee
Done!