Query 034005
Match_columns 106
No_of_seqs 94 out of 96
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 08:44:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034005.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034005hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00234 variable surface prot 44.0 44 0.00096 29.1 4.6 20 6-25 228-247 (433)
2 PF15034 KRTAP7: KRTAP type 7 25.8 29 0.00064 24.6 0.6 12 10-21 48-59 (87)
3 PF10587 EF-1_beta_acid: Eukar 21.8 39 0.00084 19.6 0.4 7 17-23 1-7 (28)
4 cd05403 NT_KNTase_like Nucleot 19.6 36 0.00078 20.8 -0.0 9 15-23 21-29 (93)
5 COG2316 Predicted hydrolase (H 17.9 40 0.00086 27.3 -0.1 19 72-90 11-29 (212)
6 PF00263 Secretin: Bacterial t 17.8 54 0.0012 22.9 0.6 11 14-24 139-149 (165)
7 PHA01732 proline-rich protein 16.3 2.6E+02 0.0056 20.2 3.7 9 17-25 3-11 (94)
8 COG1708 Predicted nucleotidylt 15.8 55 0.0012 21.0 0.2 10 14-23 28-37 (128)
9 cd05397 NT_Pol-beta-like Nucle 14.8 63 0.0014 19.3 0.2 9 15-23 20-28 (49)
10 PF07845 DUF1636: Protein of u 12.4 1.4E+02 0.003 21.5 1.5 22 80-104 52-73 (116)
No 1
>PTZ00234 variable surface protein Vir12; Provisional
Probab=44.01 E-value=44 Score=29.06 Aligned_cols=20 Identities=25% Similarity=0.506 Sum_probs=13.8
Q ss_pred cCCCCccccccccCCCCCCC
Q 034005 6 SSGGGQSSLGYLFSDGEAPK 25 (106)
Q Consensus 6 SsGGGQSSLGYLFGsge~p~ 25 (106)
+.|||-|-+|++||......
T Consensus 228 ~~~~~~~~~~~~~g~~s~~~ 247 (433)
T PTZ00234 228 SNGSQSSFLGWFWGSSSPKT 247 (433)
T ss_pred cCCCCcccccccccccCCCc
Confidence 45666677888998666553
No 2
>PF15034 KRTAP7: KRTAP type 7 family
Probab=25.76 E-value=29 Score=24.60 Aligned_cols=12 Identities=58% Similarity=0.930 Sum_probs=10.3
Q ss_pred CccccccccCCC
Q 034005 10 GQSSLGYLFSDG 21 (106)
Q Consensus 10 GQSSLGYLFGsg 21 (106)
|.|||||-||..
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=21.75 E-value=39 Score=19.63 Aligned_cols=7 Identities=29% Similarity=0.700 Sum_probs=5.8
Q ss_pred ccCCCCC
Q 034005 17 LFSDGEA 23 (106)
Q Consensus 17 LFGsge~ 23 (106)
||||++.
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=19.62 E-value=36 Score=20.76 Aligned_cols=9 Identities=33% Similarity=0.438 Sum_probs=6.3
Q ss_pred ccccCCCCC
Q 034005 15 GYLFSDGEA 23 (106)
Q Consensus 15 GYLFGsge~ 23 (106)
=|||||=..
T Consensus 21 i~LfGS~ar 29 (93)
T cd05403 21 VYLFGSYAR 29 (93)
T ss_pred EEEEeeeec
Confidence 489998544
No 5
>COG2316 Predicted hydrolase (HD superfamily) [General function prediction only]
Probab=17.94 E-value=40 Score=27.30 Aligned_cols=19 Identities=37% Similarity=0.531 Sum_probs=16.2
Q ss_pred CCcccceeccCCCcceeeC
Q 034005 72 GQNTGNFITDRPSTKVHAA 90 (106)
Q Consensus 72 gQN~GNfiTdrpstrv~a~ 90 (106)
.-|.|||+|-|.+|+|.+.
T Consensus 11 ~~~~~~~~~~~r~~~i~~~ 29 (212)
T COG2316 11 SLHSGLFLTTRRRTTIMAA 29 (212)
T ss_pred eecccceeeccccccHHHh
Confidence 4689999999999998753
No 6
>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=17.80 E-value=54 Score=22.93 Aligned_cols=11 Identities=45% Similarity=0.890 Sum_probs=8.9
Q ss_pred cccccCCCCCC
Q 034005 14 LGYLFSDGEAP 24 (106)
Q Consensus 14 LGYLFGsge~p 24 (106)
|||||++....
T Consensus 139 lg~Lf~~~~~~ 149 (165)
T PF00263_consen 139 LGYLFGSKSKS 149 (165)
T ss_pred hhhhcCCCccc
Confidence 79999987664
No 7
>PHA01732 proline-rich protein
Probab=16.26 E-value=2.6e+02 Score=20.25 Aligned_cols=9 Identities=22% Similarity=0.667 Sum_probs=5.1
Q ss_pred ccCCCCCCC
Q 034005 17 LFSDGEAPK 25 (106)
Q Consensus 17 LFGsge~p~ 25 (106)
+||.-..+.
T Consensus 3 ~fgAP~~p~ 11 (94)
T PHA01732 3 IFRAPKPPE 11 (94)
T ss_pred ccCCCCCCC
Confidence 577555543
No 8
>COG1708 Predicted nucleotidyltransferases [General function prediction only]
Probab=15.82 E-value=55 Score=20.96 Aligned_cols=10 Identities=40% Similarity=0.487 Sum_probs=6.6
Q ss_pred cccccCCCCC
Q 034005 14 LGYLFSDGEA 23 (106)
Q Consensus 14 LGYLFGsge~ 23 (106)
+=|||||-..
T Consensus 28 ~v~LfGS~ar 37 (128)
T COG1708 28 LIYLFGSYAR 37 (128)
T ss_pred EEEEEccCcc
Confidence 3489997544
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=14.78 E-value=63 Score=19.32 Aligned_cols=9 Identities=0% Similarity=-0.171 Sum_probs=6.2
Q ss_pred ccccCCCCC
Q 034005 15 GYLFSDGEA 23 (106)
Q Consensus 15 GYLFGsge~ 23 (106)
=|||||--.
T Consensus 20 v~lfGS~ar 28 (49)
T cd05397 20 IVVYGSLVR 28 (49)
T ss_pred EEEECCcCC
Confidence 488998543
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=12.42 E-value=1.4e+02 Score=21.48 Aligned_cols=22 Identities=50% Similarity=0.711 Sum_probs=16.9
Q ss_pred ccCCCcceeeCCCCCcccceeccCC
Q 034005 80 TDRPSTKVHAAPGGGSSLGYLFGGG 104 (106)
Q Consensus 80 Tdrpstrv~a~PGG~Ssl~~lFg~~ 104 (106)
-+||-|=.++.||-- .||||+=
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!