Query 537021.9.peg.598_1
Match_columns 38
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Wed May 25 00:07:50 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_598.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2005 consensus 35.5 19 0.00048 18.8 1.3 17 18-34 91-107 (878)
2 TIGR00630 uvra excinuclease AB 18.2 62 0.0016 16.3 1.3 22 13-36 480-501 (956)
3 pfam05112 Baculo_p47 Baculovir 16.6 70 0.0018 16.0 1.3 14 25-38 190-203 (313)
4 TIGR02171 Fb_sc_TIGR02171 Fibr 14.0 17 0.00044 19.0 -2.4 17 15-31 752-768 (982)
5 KOG3252 consensus 13.2 41 0.0011 17.1 -0.6 16 6-21 18-33 (217)
6 KOG0558 consensus 11.2 40 0.001 17.2 -1.2 18 14-31 258-275 (474)
7 TIGR01393 lepA GTP-binding pro 8.9 84 0.0022 15.6 -0.3 12 26-37 517-528 (598)
8 pfam06421 LepA_C GTP-binding p 8.3 1.3E+02 0.0034 14.7 0.5 13 25-37 27-39 (108)
9 TIGR01478 STEVOR variant surfa 7.5 1.6E+02 0.004 14.3 0.6 18 16-33 53-73 (315)
10 TIGR00403 ndhI NADH-plastoquin 6.8 1.4E+02 0.0036 14.6 0.1 15 11-25 118-132 (187)
No 1
>KOG2005 consensus
Probab=35.54 E-value=19 Score=18.78 Aligned_cols=17 Identities=53% Similarity=0.970 Sum_probs=14.0
Q ss_pred CCCCCHHHHHHHHHHHH
Q ss_conf 20142177999998655
Q 537021.9.peg.5 18 NYVIPHYGVLKEIISRH 34 (38)
Q Consensus 18 nyviphygvlkeiisrh 34 (38)
.|.-||||+||+|-.+-
T Consensus 91 KfLrphy~~L~~i~~~~ 107 (878)
T KOG2005 91 KFLRPHYGVLKEIYESM 107 (878)
T ss_pred HHHCCCHHHHHHHHHHC
T ss_conf 55235423799999851
No 2
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602 ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs. ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain . The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , . The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , . Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1). During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=18.20 E-value=62 Score=16.28 Aligned_cols=22 Identities=41% Similarity=0.508 Sum_probs=13.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf 211002014217799999865530
Q 537021.9.peg.5 13 LSMTENYVIPHYGVLKEIISRHKF 36 (38)
Q Consensus 13 lsmtenyviphygvlkeiisrhkf 36 (38)
|.+.+..+. --|||||++|-+|
T Consensus 480 L~~~~~~IA--~~iLKEI~~RL~F 501 (956)
T TIGR00630 480 LTEEEKKIA--EEILKEIKERLKF 501 (956)
T ss_pred CCHHHHHHH--HHHHHHHHHHHHH
T ss_conf 666789999--9999999988888
No 3
>pfam05112 Baculo_p47 Baculovirus P47 protein. This family consists of several Baculovirus P47 proteins which is one of the primary components of Baculovirus encoded RNA polymerase, which initiates transcription from late and very late promoters.
Probab=16.56 E-value=70 Score=16.04 Aligned_cols=14 Identities=43% Similarity=0.648 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHCCC
Q ss_conf 79999986553059
Q 537021.9.peg.5 25 GVLKEIISRHKFSK 38 (38)
Q Consensus 25 gvlkeiisrhkfsk 38 (38)
--+-+||.|||||+
T Consensus 190 tSisdIiKRhk~~~ 203 (313)
T pfam05112 190 TSISDVIKRHKSSK 203 (313)
T ss_pred CHHHHHHHHHCCCC
T ss_conf 25999998740564
No 4
>TIGR02171 Fb_sc_TIGR02171 Fibrobacter succinogenes paralogous family TIGR02171.
Probab=14.02 E-value=17 Score=18.98 Aligned_cols=17 Identities=41% Similarity=0.806 Sum_probs=13.5
Q ss_pred CCCCCCCCHHHHHHHHH
Q ss_conf 10020142177999998
Q 537021.9.peg.5 15 MTENYVIPHYGVLKEII 31 (38)
Q Consensus 15 mtenyviphygvlkeii 31 (38)
+-+||.|||+--||-||
T Consensus 752 l~~nY~~pH~kkLKy~V 768 (982)
T TIGR02171 752 LLENYALPHLKKLKYVV 768 (982)
T ss_pred HHHHHHHHHHCCCCEEE
T ss_conf 99875432212474899
No 5
>KOG3252 consensus
Probab=13.23 E-value=41 Score=17.13 Aligned_cols=16 Identities=56% Similarity=0.754 Sum_probs=13.2
Q ss_pred CCCCCCCCCCCCCCCC
Q ss_conf 1388100211002014
Q 537021.9.peg.5 6 AHDNPENLSMTENYVI 21 (38)
Q Consensus 6 ahdnpenlsmtenyvi 21 (38)
-.-|||||.--|+||-
T Consensus 18 nryNPE~latLe~yVq 33 (217)
T KOG3252 18 NRYNPENLATLENYVQ 33 (217)
T ss_pred CCCCHHHHHHHHHHHH
T ss_conf 6578567778999999
No 6
>KOG0558 consensus
Probab=11.20 E-value=40 Score=17.19 Aligned_cols=18 Identities=50% Similarity=0.837 Sum_probs=15.1
Q ss_pred CCCCCCCCCHHHHHHHHH
Q ss_conf 110020142177999998
Q 537021.9.peg.5 14 SMTENYVIPHYGVLKEII 31 (38)
Q Consensus 14 smtenyviphygvlkeii 31 (38)
+|||..-|||+|...||-
T Consensus 258 tMt~alkiPHF~y~dEIn 275 (474)
T KOG0558 258 TMTEALKIPHFGYVDEIN 275 (474)
T ss_pred HHHHHHCCCCCCCCCCCC
T ss_conf 988874588544244247
No 7
>TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297 LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding.
Probab=8.93 E-value=84 Score=15.64 Aligned_cols=12 Identities=50% Similarity=0.858 Sum_probs=8.8
Q ss_pred HHHHHHHHHHCC
Q ss_conf 999998655305
Q 537021.9.peg.5 26 VLKEIISRHKFS 37 (38)
Q Consensus 26 vlkeiisrhkfs 37 (38)
-|||+|.|+.|.
T Consensus 517 KLKE~IPRQqF~ 528 (598)
T TIGR01393 517 KLKELIPRQQFE 528 (598)
T ss_pred HHHHCCCCCCCC
T ss_conf 866228634666
No 8
>pfam06421 LepA_C GTP-binding protein LepA C-terminus. This family consists of the C-terminal region of several pro- and eukaryotic GTP-binding LepA proteins.
Probab=8.34 E-value=1.3e+02 Score=14.70 Aligned_cols=13 Identities=46% Similarity=0.772 Sum_probs=9.7
Q ss_pred HHHHHHHHHHHCC
Q ss_conf 7999998655305
Q 537021.9.peg.5 25 GVLKEIISRHKFS 37 (38)
Q Consensus 25 gvlkeiisrhkfs 37 (38)
--|||+|.|+-|.
T Consensus 27 ~kLKe~IPrq~f~ 39 (108)
T pfam06421 27 EKLKELIPRQQFE 39 (108)
T ss_pred HHHHHHCCHHHHH
T ss_conf 9999868797847
No 9
>TIGR01478 STEVOR variant surface antigen, stevor family; InterPro: IPR006374 Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see . This entry represents the stevor (short for "subtelomeric variable open reading frame") family of predicted variant surface antigens. This is the third largest variant surface antigen family in P. falciparum, with 33 genes identified in the genome of this parasite . The function of these proteins is not known, but they are expressed during several stages of the parasite life-cycle and may play a variety of roles in parasite survival and infection ..
Probab=7.54 E-value=1.6e+02 Score=14.32 Aligned_cols=18 Identities=44% Similarity=0.624 Sum_probs=11.9
Q ss_pred CCCCCCCHH---HHHHHHHHH
Q ss_conf 002014217---799999865
Q 537021.9.peg.5 16 TENYVIPHY---GVLKEIISR 33 (38)
Q Consensus 16 tenyviphy---gvlkeiisr 33 (38)
+|+--=||| .-|||||..
T Consensus 53 iq~P~NPHYhNDPELKeIIDK 73 (315)
T TIGR01478 53 IQRPKNPHYHNDPELKEIIDK 73 (315)
T ss_pred HCCCCCCCCCCCHHHHHHHHH
T ss_conf 357632298987346668624
No 10
>TIGR00403 ndhI NADH-plastoquinone oxidoreductase, I subunit; InterPro: IPR004497 NADH-plastoquinone oxidoreductase subunit I (1.6.5.3 from EC) catalyses the conversion of plastoquinone and NADH to plastoquinol and NAD(+). The enzyme binds two 4FE-4S clusters at iron-sulphur centres which are similar to those of the bacterial-type 4FE-4S ferredoxins.; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006118 electron transport.
Probab=6.78 E-value=1.4e+02 Score=14.57 Aligned_cols=15 Identities=47% Similarity=0.740 Sum_probs=11.7
Q ss_pred CCCCCCCCCCCCHHH
Q ss_conf 002110020142177
Q 537021.9.peg.5 11 ENLSMTENYVIPHYG 25 (38)
Q Consensus 11 enlsmtenyviphyg 25 (38)
.-|||||.|-+..|.
T Consensus 118 nClsmteeyel~~y~ 132 (187)
T TIGR00403 118 NCLSMTEEYELSTYD 132 (187)
T ss_pred CCCCCCHHHHHHHCC
T ss_conf 300000001110000
Done!