Query 033256
Match_columns 123
No_of_seqs 94 out of 96
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 11:43:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033256.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033256hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00234 variable surface prot 32.2 2.5E+02 0.0054 25.2 7.5 19 6-24 228-246 (433)
2 PF15034 KRTAP7: KRTAP type 7 27.9 25 0.00055 25.5 0.5 12 10-21 48-59 (87)
3 PF10587 EF-1_beta_acid: Eukar 22.6 36 0.00077 20.2 0.4 7 17-23 1-7 (28)
4 cd05403 NT_KNTase_like Nucleot 21.6 31 0.00067 21.6 -0.0 9 15-23 21-29 (93)
5 COG1708 Predicted nucleotidylt 17.4 48 0.001 21.9 0.2 10 14-23 28-37 (128)
6 cd05397 NT_Pol-beta-like Nucle 16.7 52 0.0011 20.2 0.2 9 15-23 20-28 (49)
7 COG2316 Predicted hydrolase (H 14.6 52 0.0011 27.2 -0.2 19 89-107 11-29 (212)
8 PHA01732 proline-rich protein 12.7 4.4E+02 0.0096 19.5 4.2 8 17-24 3-10 (94)
9 PF01963 TraB: TraB family; I 12.4 73 0.0016 24.2 0.0 15 8-24 7-21 (259)
10 PF07845 DUF1636: Protein of u 12.1 1.4E+02 0.0031 22.0 1.5 22 97-121 52-73 (116)
No 1
>PTZ00234 variable surface protein Vir12; Provisional
Probab=32.23 E-value=2.5e+02 Score=25.15 Aligned_cols=19 Identities=32% Similarity=0.669 Sum_probs=13.4
Q ss_pred cCCCCccccccccCCCCCC
Q 033256 6 SSGGGQSSLGYLFGTGEAS 24 (123)
Q Consensus 6 SsGGGQSSLGYLFGsgE~p 24 (123)
+.|||-|-+|++||.....
T Consensus 228 ~~~~~~~~~~~~~g~~s~~ 246 (433)
T PTZ00234 228 SNGSQSSFLGWFWGSSSPK 246 (433)
T ss_pred cCCCCcccccccccccCCC
Confidence 4566677788889866554
No 2
>PF15034 KRTAP7: KRTAP type 7 family
Probab=27.91 E-value=25 Score=25.47 Aligned_cols=12 Identities=67% Similarity=1.068 Sum_probs=10.2
Q ss_pred CccccccccCCC
Q 033256 10 GQSSLGYLFGTG 21 (123)
Q Consensus 10 GQSSLGYLFGsg 21 (123)
|-|||||-||..
T Consensus 48 gy~slgy~fggs 59 (87)
T PF15034_consen 48 GYSSLGYSFGGS 59 (87)
T ss_pred cccccceeccCc
Confidence 689999999864
No 3
>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=22.63 E-value=36 Score=20.22 Aligned_cols=7 Identities=43% Similarity=1.042 Sum_probs=5.7
Q ss_pred ccCCCCC
Q 033256 17 LFGTGEA 23 (123)
Q Consensus 17 LFGsgE~ 23 (123)
||||++-
T Consensus 1 LFGSddE 7 (28)
T PF10587_consen 1 LFGSDDE 7 (28)
T ss_pred CCCCccc
Confidence 8999865
No 4
>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=21.58 E-value=31 Score=21.65 Aligned_cols=9 Identities=44% Similarity=0.704 Sum_probs=6.1
Q ss_pred ccccCCCCC
Q 033256 15 GYLFGTGEA 23 (123)
Q Consensus 15 GYLFGsgE~ 23 (123)
=|||||=..
T Consensus 21 i~LfGS~ar 29 (93)
T cd05403 21 VYLFGSYAR 29 (93)
T ss_pred EEEEeeeec
Confidence 489998433
No 5
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=17.40 E-value=48 Score=21.87 Aligned_cols=10 Identities=50% Similarity=0.727 Sum_probs=6.4
Q ss_pred cccccCCCCC
Q 033256 14 LGYLFGTGEA 23 (123)
Q Consensus 14 LGYLFGsgE~ 23 (123)
+=|||||=..
T Consensus 28 ~v~LfGS~ar 37 (128)
T COG1708 28 LIYLFGSYAR 37 (128)
T ss_pred EEEEEccCcc
Confidence 3488987543
No 6
>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=16.69 E-value=52 Score=20.18 Aligned_cols=9 Identities=11% Similarity=0.095 Sum_probs=6.1
Q ss_pred ccccCCCCC
Q 033256 15 GYLFGTGEA 23 (123)
Q Consensus 15 GYLFGsgE~ 23 (123)
=|||||=-.
T Consensus 20 v~lfGS~ar 28 (49)
T cd05397 20 IVVYGSLVR 28 (49)
T ss_pred EEEECCcCC
Confidence 488998543
No 7
>COG2316 Predicted hydrolase (HD superfamily) [General function prediction only]
Probab=14.56 E-value=52 Score=27.24 Aligned_cols=19 Identities=42% Similarity=0.527 Sum_probs=16.1
Q ss_pred CCccccccccCCCcceeeC
Q 033256 89 GQNCGNFLTDRPTTKVHAA 107 (123)
Q Consensus 89 gqN~GNfiTdrpstrv~a~ 107 (123)
.-|.|||+|-|.+|+|.+.
T Consensus 11 ~~~~~~~~~~~r~~~i~~~ 29 (212)
T COG2316 11 SLHSGLFLTTRRRTTIMAA 29 (212)
T ss_pred eecccceeeccccccHHHh
Confidence 4689999999999998653
No 8
>PHA01732 proline-rich protein
Probab=12.68 E-value=4.4e+02 Score=19.51 Aligned_cols=8 Identities=13% Similarity=0.405 Sum_probs=4.6
Q ss_pred ccCCCCCC
Q 033256 17 LFGTGEAS 24 (123)
Q Consensus 17 LFGsgE~p 24 (123)
+||.-..+
T Consensus 3 ~fgAP~~p 10 (94)
T PHA01732 3 IFRAPKPP 10 (94)
T ss_pred ccCCCCCC
Confidence 57755444
No 9
>PF01963 TraB: TraB family; InterPro: IPR002816 In prokaryotes, for example Enterococcus faecalis (Streptococcus faecalis), the conjugative transfer of certain plasmids is controlled by peptide pheromones []. Plasmid free recipient cells secret plasmid specific oligopeptides, termed sex pheromones. They induce bacterial clumping and specifically activate the conjugative transfer of the corresponding plasmid. Once recipient cells acquire the plasmid they start to produce a pheromone inhibitor to block the activity of the pheromone and to prevent plasmid containing cells from clumping; they also become donor cells able to transfer the plasmid to plasmid free recipient cells. Examples of such plasmid-pheromone systems are bacteriocin plasmid pPD1 [], haemolysin/bacteriocin plasmid, pAD1 [], tetracycline-resistance plasmid, pCF10 [], and the haemolysin/bacteriocin plasmid, pOB1 []. TraB in combination with another factor contributes to pheromone shutdown in cells that have acquired a plasmid. It exact function has not yet been determined [, ]. This entry also contains plant and mammalian proteins, suggesting that these Trab-related proteins may have a somewhat wider or different function in eukaryotes.
Probab=12.38 E-value=73 Score=24.16 Aligned_cols=15 Identities=40% Similarity=0.645 Sum_probs=10.2
Q ss_pred CCCccccccccCCCCCC
Q 033256 8 GGGQSSLGYLFGTGEAS 24 (123)
Q Consensus 8 GGGQSSLGYLFGsgE~p 24 (123)
++|.++ ||||+=-..
T Consensus 7 ~~g~~~--yL~GT~H~~ 21 (259)
T PF01963_consen 7 KNGKTV--YLLGTIHVS 21 (259)
T ss_pred cCCeEE--EEEeccCCC
Confidence 345555 999986664
No 10
>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=12.07 E-value=1.4e+02 Score=22.00 Aligned_cols=22 Identities=50% Similarity=0.739 Sum_probs=16.9
Q ss_pred ccCCCcceeeCCCCCcccceeccCC
Q 033256 97 TDRPTTKVHAAPGGGSSLDYLFGGN 121 (123)
Q Consensus 97 Tdrpstrv~a~PGG~Ssl~~lFg~~ 121 (123)
-|||-|=.++.||.- .||||+=
T Consensus 52 C~r~CtVA~~~~gK~---tYlfGdl 73 (116)
T PF07845_consen 52 CDRPCTVALQAPGKW---TYLFGDL 73 (116)
T ss_pred CCCceEEEEEcCCCc---EEEEecC
Confidence 378888888888764 4999973
Done!