Query 046463
Match_columns 102
No_of_seqs 97 out of 99
Neff 2.7
Searched_HMMs 46136
Date Fri Mar 29 12:24:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046463.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046463hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10587 EF-1_beta_acid: Eukar 22.5 38 0.00083 19.6 0.5 7 17-23 1-7 (28)
2 PF15034 KRTAP7: KRTAP type 7 22.3 38 0.00082 23.9 0.6 13 10-22 48-60 (87)
3 cd05403 NT_KNTase_like Nucleot 18.4 39 0.00085 20.4 -0.0 9 15-23 21-29 (93)
4 PF00263 Secretin: Bacterial t 17.3 56 0.0012 22.6 0.6 11 14-24 139-149 (165)
5 PTZ00234 variable surface prot 16.8 1.6E+02 0.0036 25.4 3.3 19 6-24 228-246 (433)
6 PF07845 DUF1636: Protein of u 15.2 1E+02 0.0023 22.0 1.5 21 76-99 52-72 (116)
7 COG1708 Predicted nucleotidylt 14.8 61 0.0013 20.6 0.2 10 14-23 28-37 (128)
8 COG2316 Predicted hydrolase (H 14.5 56 0.0012 26.4 -0.0 19 68-86 11-29 (212)
9 cd05397 NT_Pol-beta-like Nucle 13.6 71 0.0015 19.0 0.2 9 15-23 20-28 (49)
10 KOG4492 Chorismate synthase [A 10.9 1E+02 0.0022 26.6 0.5 9 6-14 118-126 (368)
No 1
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=22.49 E-value=38 Score=19.58 Aligned_cols=7 Identities=86% Similarity=1.379 Sum_probs=5.9
Q ss_pred ccCCCCC
Q 046463 17 LFGSDQE 23 (102)
Q Consensus 17 LFGsge~ 23 (102)
||||++.
T Consensus 1 LFGSddE 7 (28)
T PF10587_consen 1 LFGSDDE 7 (28)
T ss_pred CCCCccc
Confidence 8999876
No 2
>PF15034 KRTAP7: KRTAP type 7 family
Probab=22.27 E-value=38 Score=23.95 Aligned_cols=13 Identities=62% Similarity=1.032 Sum_probs=10.6
Q ss_pred CccccccccCCCC
Q 046463 10 GHSSLGYLFGSDQ 22 (102)
Q Consensus 10 GQSSLGYLFGsge 22 (102)
|.|||||-||.-.
T Consensus 48 gy~slgy~fggsn 60 (87)
T PF15034_consen 48 GYSSLGYSFGGSN 60 (87)
T ss_pred cccccceeccCcc
Confidence 6899999998643
No 3
>cd05403 NT_KNTase_like Nucleotidyltransferase (NT) domain of Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. S. aureus KNTase is a plasmid encoded enzyme which confers resistance to a wide range of aminoglycoside antibiotics which have a 4'- or 4''-hydroxyl group in the equatorial position, such as kanamycin A. This enzyme transfers a nucleoside monophosphate group from a nucleotide (ATP,GTP, or UTP) to the 4'-hydroxyl group of kanamycin A. This enzyme is a homodimer, having two NT active sites. The nucleotide and antibiotic binding sites of each active site include residues from each monomer. Included in this subgroup is Escherichia coli AadA5 which confers resistance to the antibiotic spectinomycin and is a putative aminoglycoside-3'-adenylyltransferase. It is part of the aadA5 cassette of a class 1 integron. This subgroup also includes Haemophilus influenzae HI0073 which forms a 2:2 heterotetramer with an unrelated protein HI0074. Structurally HI0074 is
Probab=18.36 E-value=39 Score=20.39 Aligned_cols=9 Identities=56% Similarity=0.803 Sum_probs=6.3
Q ss_pred ccccCCCCC
Q 046463 15 GYLFGSDQE 23 (102)
Q Consensus 15 GYLFGsge~ 23 (102)
=|||||--.
T Consensus 21 i~LfGS~ar 29 (93)
T cd05403 21 VYLFGSYAR 29 (93)
T ss_pred EEEEeeeec
Confidence 489998544
No 4
>PF00263 Secretin: Bacterial type II and III secretion system protein; InterPro: IPR004846 This family includes: protein D that is involved in the general (type II) secretion pathway (GSP) within Gram-negative bacteria, a signal sequence-dependent process responsible for protein export [, , ,, , , ] and protein G from the type III secretion system. A number of proteins are involved in the GSP; one of these is known as protein D (GSPD protein), the most probable location of which is the outer membrane []. This suggests that protein D constitutes the apparatus of the accessory mechanism, and is thus involved in transporting exoproteins from the periplasm, across the outer membrane, to the extracellular environment. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself [], type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Protein G aids in the structural assembly of the invasion complex []. ; GO: 0009306 protein secretion
Probab=17.31 E-value=56 Score=22.62 Aligned_cols=11 Identities=64% Similarity=1.226 Sum_probs=8.9
Q ss_pred cccccCCCCCC
Q 046463 14 LGYLFGSDQEP 24 (102)
Q Consensus 14 LGYLFGsge~~ 24 (102)
|||||++....
T Consensus 139 lg~Lf~~~~~~ 149 (165)
T PF00263_consen 139 LGYLFGSKSKS 149 (165)
T ss_pred hhhhcCCCccc
Confidence 79999987664
No 5
>PTZ00234 variable surface protein Vir12; Provisional
Probab=16.77 E-value=1.6e+02 Score=25.45 Aligned_cols=19 Identities=37% Similarity=0.649 Sum_probs=13.1
Q ss_pred cCCCCccccccccCCCCCC
Q 046463 6 SSGGGHSSLGYLFGSDQEP 24 (102)
Q Consensus 6 SsGGGQSSLGYLFGsge~~ 24 (102)
+.|||-|-+|++||.....
T Consensus 228 ~~~~~~~~~~~~~g~~s~~ 246 (433)
T PTZ00234 228 SNGSQSSFLGWFWGSSSPK 246 (433)
T ss_pred cCCCCcccccccccccCCC
Confidence 4566667788888865554
No 6
>PF07845 DUF1636: Protein of unknown function (DUF1636); InterPro: IPR012863 The sequences featured in this family are derived from a number of hypothetical prokaryotic proteins. The region in question is approximately 130 amino acids long.
Probab=15.19 E-value=1e+02 Score=22.00 Aligned_cols=21 Identities=57% Similarity=0.936 Sum_probs=16.7
Q ss_pred ccCCccceeeCCCCCcccceecCC
Q 046463 76 TDRPTTRVQSAPGGDSSLGYLFGD 99 (102)
Q Consensus 76 TdRpstrv~a~PGG~Ssl~~lfg~ 99 (102)
-+||-|=.++.||- +.||||+
T Consensus 52 C~r~CtVA~~~~gK---~tYlfGd 72 (116)
T PF07845_consen 52 CDRPCTVALQAPGK---WTYLFGD 72 (116)
T ss_pred CCCceEEEEEcCCC---cEEEEec
Confidence 37888888888875 5599997
No 7
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=14.77 E-value=61 Score=20.56 Aligned_cols=10 Identities=60% Similarity=0.816 Sum_probs=6.5
Q ss_pred cccccCCCCC
Q 046463 14 LGYLFGSDQE 23 (102)
Q Consensus 14 LGYLFGsge~ 23 (102)
.=|||||-..
T Consensus 28 ~v~LfGS~ar 37 (128)
T COG1708 28 LIYLFGSYAR 37 (128)
T ss_pred EEEEEccCcc
Confidence 3488887544
No 8
>COG2316 Predicted hydrolase (HD superfamily) [General function prediction only]
Probab=14.51 E-value=56 Score=26.35 Aligned_cols=19 Identities=37% Similarity=0.520 Sum_probs=16.3
Q ss_pred CCcccceeccCCccceeeC
Q 046463 68 GQNSGNFITDRPTTRVQSA 86 (102)
Q Consensus 68 gqN~GNfiTdRpstrv~a~ 86 (102)
.-|.|||+|-|.+|+|.+.
T Consensus 11 ~~~~~~~~~~~r~~~i~~~ 29 (212)
T COG2316 11 SLHSGLFLTTRRRTTIMAA 29 (212)
T ss_pred eecccceeeccccccHHHh
Confidence 4689999999999998764
No 9
>cd05397 NT_Pol-beta-like Nucleotidyltransferase (NT) domain of DNA polymerase beta and similar proteins. This superfamily includes the NT domains of DNA polymerase beta and other family X DNA polymerases, as well as the NT domains of Class I and Class II CCA-adding enzymes, RelA- and SpoT-like ppGpp synthetases and hydrolases, 2'5'-oligoadenylate (2-5A)synthetases, Escherichia coli adenylyltransferase (GlnE), Escherichia coli uridylyl transferase (GlnD), poly (A) polymerases, terminal uridylyl transferases, and Staphylococcus aureus kanamycin nucleotidyltransferase, and similar proteins. The Escherichia coli CCA-adding enzyme belongs to this superfamily but is not included as this enzyme lacks the N-terminal helix conserved in the remainder of the superfamily. In the majority of the Pol beta-like superfamily NTs, two carboxylates, Dx[D/E], together with a third more distal carboxylate coordinate two divalent metal cations that are essential for catalysis. These divalent metal ions are
Probab=13.59 E-value=71 Score=18.95 Aligned_cols=9 Identities=22% Similarity=0.187 Sum_probs=6.0
Q ss_pred ccccCCCCC
Q 046463 15 GYLFGSDQE 23 (102)
Q Consensus 15 GYLFGsge~ 23 (102)
=|||||--.
T Consensus 20 v~lfGS~ar 28 (49)
T cd05397 20 IVVYGSLVR 28 (49)
T ss_pred EEEECCcCC
Confidence 378888543
No 10
>KOG4492 consensus Chorismate synthase [Amino acid transport and metabolism]
Probab=10.87 E-value=1e+02 Score=26.59 Aligned_cols=9 Identities=78% Similarity=1.036 Sum_probs=6.3
Q ss_pred cCCCCcccc
Q 046463 6 SSGGGHSSL 14 (102)
Q Consensus 6 SsGGGQSSL 14 (102)
|||||+||-
T Consensus 118 SSGGGRsSA 126 (368)
T KOG4492|consen 118 SSGGGRSSA 126 (368)
T ss_pred ccCCCchhh
Confidence 677777764
Done!