Query 026455
Match_columns 238
No_of_seqs 73 out of 75
Neff 2.6
Searched_HMMs 46136
Date Fri Mar 29 08:15:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026455.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026455hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05678 VQ: VQ motif; InterP 99.0 2.9E-10 6.3E-15 74.0 3.6 29 117-145 1-29 (31)
2 PF00760 Cucumo_coat: Cucumovi 35.3 11 0.00023 34.2 -0.5 31 109-139 3-33 (209)
3 smart00653 eIF2B_5 domain pres 23.1 72 0.0016 25.8 2.4 24 24-47 27-50 (110)
4 cd04750 Commd2 COMM_Domain con 22.0 74 0.0016 26.9 2.3 21 121-141 138-158 (166)
5 TIGR00311 aIF-2beta translatio 19.4 93 0.002 26.0 2.4 24 24-47 45-68 (133)
6 PF01873 eIF-5_eIF-2B: Domain 18.4 1E+02 0.0022 25.4 2.4 23 24-46 40-62 (125)
7 PRK03988 translation initiatio 18.3 1E+02 0.0022 25.9 2.4 24 24-47 50-73 (138)
8 COG1601 GCD7 Translation initi 17.1 1.2E+02 0.0026 26.1 2.6 26 23-48 51-76 (151)
9 COG2089 SpsE Sialic acid synth 17.0 1.1E+02 0.0024 29.8 2.6 26 115-140 240-265 (347)
10 PF02809 UIM: Ubiquitin intera 15.8 1.3E+02 0.0028 17.5 1.7 13 33-45 5-17 (18)
No 1
>PF05678 VQ: VQ motif; InterPro: IPR008889 This short motif is found in a variety of plant proteins. These proteins vary greatly in length and are mostly composed of low complexity regions. They all conserve a short motif FXhVQChTG, where X is any amino acid and h is a hydrophobic amino acid. The function of this motif is uncertain, however one protein in this family has been found to bind the SigA sigma factor Q9LDH1 from SWISSPROT. It would seem plausible that this motif is needed for this activity and that this whole family might be involved in modulating plastid sigma factors.
Probab=99.01 E-value=2.9e-10 Score=74.03 Aligned_cols=29 Identities=38% Similarity=0.646 Sum_probs=26.5
Q ss_pred CCCCceEeecCchHHHHHHHHHhcCCCCC
Q 026455 117 KKTQTTFITADPANFRQMVQQVTGVRFGS 145 (238)
Q Consensus 117 rR~ptT~i~ad~anFRaMVQq~TG~p~~~ 145 (238)
++.+++||.+|++|||+||||+||.+..+
T Consensus 1 ~~~~p~vi~~d~~~Fr~lVQ~LTG~~~~~ 29 (31)
T PF05678_consen 1 YRSPPTVIHTDPSNFRALVQRLTGAPSAP 29 (31)
T ss_pred CCCCCEEEEeCHHHHHHHHHHhHCcCCCC
Confidence 46899999999999999999999999754
No 2
>PF00760 Cucumo_coat: Cucumovirus coat protein; InterPro: IPR023800 Cucumoviruses are tripartite RNA plant viruses believed to share a close evolutionary relationship with Brome mosaic virus (BMV). The cucumoviruses include: Cucumber mosaic virus [], Peanut stunt virus [] and Tomato aspermy virus []. The viral coat proteins show a high degree of sequence similarity []. The core structure of cucumber mosaic virus (CMV) and chlorotic mottle virus (CCMV), both members of the Bromoviridae family, are highly homologous. In CCMV, the structures of the A, B, and C subunits are nearly identical except in their N termini. In contrast, the structures of two loops in subunit A of CMV differ from those in B and C []. This entry represents the structural domain of subunit A of the cucumber mosaic virus and other cucumovirusus [].; GO: 0019028 viral capsid; PDB: 1LAJ_B 1F15_A.
Probab=35.25 E-value=11 Score=34.25 Aligned_cols=31 Identities=19% Similarity=0.379 Sum_probs=10.0
Q ss_pred ccccccccCCCCceEeecCchHHHHHHHHHh
Q 026455 109 TKRKARASKKTQTTFITADPANFRQMVQQVT 139 (238)
Q Consensus 109 ~kRR~RaSrR~ptT~i~ad~anFRaMVQq~T 139 (238)
++||+|..||.+..--.+-..++|++-||+-
T Consensus 3 gsrrpRRg~Rs~~~~~~~~~~~Lralt~Ql~ 33 (209)
T PF00760_consen 3 GSRRPRRGRRSNSNKSDAHDRELRALTQQLN 33 (209)
T ss_dssp --------------------TCHHHHHCCHH
T ss_pred CCcCCCCcccCCCcCcchhhhHHHHHHHHHH
Confidence 5788888888877777778899999999985
No 3
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=23.08 E-value=72 Score=25.78 Aligned_cols=24 Identities=17% Similarity=0.293 Sum_probs=21.9
Q ss_pred HHHHhhhcHHHHHHHHHhHhhcCC
Q 026455 24 LSEAYARDTETLTKALQKTFSNNN 47 (238)
Q Consensus 24 lseafarD~e~LtkALqkSlsn~~ 47 (238)
|.++..||-++|.|+|.++|....
T Consensus 27 I~~~L~R~p~hv~kyl~~ELgt~g 50 (110)
T smart00653 27 IAKALNRPPDHVLKFLLAELGTQG 50 (110)
T ss_pred HHHHHCCCHHHHHHHHHHHhCCce
Confidence 889999999999999999997654
No 4
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=22.04 E-value=74 Score=26.88 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=18.7
Q ss_pred ceEeecCchHHHHHHHHHhcC
Q 026455 121 TTFITADPANFRQMVQQVTGV 141 (238)
Q Consensus 121 tT~i~ad~anFRaMVQq~TG~ 141 (238)
..++.+|+++|+-|+|++-.+
T Consensus 138 ~~~l~td~~~l~~l~~eLe~A 158 (166)
T cd04750 138 THLLQTDPANLVHLTQTLEQA 158 (166)
T ss_pred ceEEEeCHHHHHHHHHHHHHH
Confidence 789999999999999998654
No 5
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=19.40 E-value=93 Score=25.97 Aligned_cols=24 Identities=29% Similarity=0.405 Sum_probs=22.0
Q ss_pred HHHHhhhcHHHHHHHHHhHhhcCC
Q 026455 24 LSEAYARDTETLTKALQKTFSNNN 47 (238)
Q Consensus 24 lseafarD~e~LtkALqkSlsn~~ 47 (238)
|.++..||-++|+|+|.++|-...
T Consensus 45 Ia~~L~R~~~~v~ky~~~ELgt~g 68 (133)
T TIGR00311 45 VAKALNRDEQHLLKYLLKELGTAG 68 (133)
T ss_pred HHHHHCCCHHHHHHHHHHHhCCCc
Confidence 899999999999999999997655
No 6
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=18.44 E-value=1e+02 Score=25.39 Aligned_cols=23 Identities=26% Similarity=0.410 Sum_probs=21.3
Q ss_pred HHHHhhhcHHHHHHHHHhHhhcC
Q 026455 24 LSEAYARDTETLTKALQKTFSNN 46 (238)
Q Consensus 24 lseafarD~e~LtkALqkSlsn~ 46 (238)
|.++..||-++|+|+|.++|...
T Consensus 40 I~~~L~R~p~~~~ky~~~ELgt~ 62 (125)
T PF01873_consen 40 ICKALNRDPEHVLKYFGKELGTQ 62 (125)
T ss_dssp HHHHHTSSHHHHHHHHHHHSSSE
T ss_pred HHHHHCCCHHHHHHHHHHHHCCc
Confidence 89999999999999999999664
No 7
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=18.30 E-value=1e+02 Score=25.91 Aligned_cols=24 Identities=21% Similarity=0.389 Sum_probs=22.0
Q ss_pred HHHHhhhcHHHHHHHHHhHhhcCC
Q 026455 24 LSEAYARDTETLTKALQKTFSNNN 47 (238)
Q Consensus 24 lseafarD~e~LtkALqkSlsn~~ 47 (238)
|.++..||.++|.|+|.++|-...
T Consensus 50 I~~~L~R~~~hv~ky~~~ELgt~g 73 (138)
T PRK03988 50 IADRLNRDPKHVAKFLLKELGTAG 73 (138)
T ss_pred HHHHHCCCHHHHHHHHHHHhCCce
Confidence 899999999999999999997655
No 8
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=17.14 E-value=1.2e+02 Score=26.06 Aligned_cols=26 Identities=35% Similarity=0.445 Sum_probs=23.6
Q ss_pred HHHHHhhhcHHHHHHHHHhHhhcCCC
Q 026455 23 WLSEAYARDTETLTKALQKTFSNNNN 48 (238)
Q Consensus 23 wlseafarD~e~LtkALqkSlsn~~~ 48 (238)
|++++.-||=+++.|.|+|.|-.+.+
T Consensus 51 dia~~l~rDp~h~~k~l~kel~t~g~ 76 (151)
T COG1601 51 DIAEALNRDPEHLVKFLKKELGTAGS 76 (151)
T ss_pred HHHHHhcCCHHHHHHHHHHHhccccc
Confidence 89999999999999999999976654
No 9
>COG2089 SpsE Sialic acid synthase [Cell envelope biogenesis, outer membrane]
Probab=16.98 E-value=1.1e+02 Score=29.83 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=21.6
Q ss_pred ccCCCCceEeecCchHHHHHHHHHhc
Q 026455 115 ASKKTQTTFITADPANFRQMVQQVTG 140 (238)
Q Consensus 115 aSrR~ptT~i~ad~anFRaMVQq~TG 140 (238)
.++.-|--.++.||..||.||++.--
T Consensus 240 k~~~GpD~~fSldP~efk~mv~~ir~ 265 (347)
T COG2089 240 KSREGPDHAFSLDPDEFKEMVDAIRQ 265 (347)
T ss_pred CCCCCCCcceecCHHHHHHHHHHHHH
Confidence 45568999999999999999987643
No 10
>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]. In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.
Probab=15.78 E-value=1.3e+02 Score=17.53 Aligned_cols=13 Identities=31% Similarity=0.554 Sum_probs=11.1
Q ss_pred HHHHHHHHhHhhc
Q 026455 33 ETLTKALQKTFSN 45 (238)
Q Consensus 33 e~LtkALqkSlsn 45 (238)
+.|++||+.|+..
T Consensus 5 ~~L~~Al~~S~~e 17 (18)
T PF02809_consen 5 EDLQRALEMSLEE 17 (18)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHhhhcc
Confidence 7899999999853
Done!