Query 537021.9.peg.1128_1
Match_columns 41
No_of_seqs 1 out of 3
Neff 1.0
Searched_HMMs 39220
Date Wed May 25 07:05:51 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i peg_1128.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0667 consensus 24.9 17 0.00045 18.7 -0.4 17 22-38 255-271 (586)
2 KOG0452 consensus 22.5 22 0.00056 18.3 -0.2 31 5-35 398-429 (892)
3 TIGR02211 LolD_lipo_ex lipopro 17.8 41 0.0011 17.0 0.3 10 23-39 88-97 (221)
4 TIGR02415 23BDH acetoin reduct 8.0 83 0.0021 15.6 -0.6 16 7-22 123-139 (258)
5 KOG2841 consensus 7.8 75 0.0019 15.9 -0.9 14 11-24 214-227 (254)
6 pfam05244 Brucella_OMP2 Brucel 7.3 76 0.0019 15.8 -1.1 19 10-28 69-87 (240)
7 TIGR01124 ilvA_2Cterm threonin 6.6 1.1E+02 0.0028 15.1 -0.6 19 12-30 446-464 (508)
8 pfam05059 Orbi_VP4 Orbivirus V 6.4 83 0.0021 15.6 -1.3 17 17-33 53-69 (642)
9 pfam02641 DUF190 Uncharacteriz 5.8 1.7E+02 0.0044 14.2 0.1 22 8-29 42-63 (101)
10 COG1534 Predicted RNA-binding 5.0 1.7E+02 0.0043 14.2 -0.4 15 19-33 69-83 (97)
No 1
>KOG0667 consensus
Probab=24.89 E-value=17 Score=18.74 Aligned_cols=17 Identities=47% Similarity=0.680 Sum_probs=14.1
Q ss_pred EEEEECCHHHHHHHHHH
Q ss_conf 23343164366353554
Q 537021.9.peg.1 22 SIFQFRGHTFIVHHLLL 38 (41)
Q Consensus 22 sifqfrghtfivhhlll 38 (41)
.-|+||+|++||-.||-
T Consensus 255 d~F~fr~HlciVfELL~ 271 (586)
T KOG0667 255 DYFYFRNHLCIVFELLS 271 (586)
T ss_pred EECCCCCCEEEEEHHHH
T ss_conf 40110562255303446
No 2
>KOG0452 consensus
Probab=22.53 E-value=22 Score=18.30 Aligned_cols=31 Identities=35% Similarity=0.585 Sum_probs=20.7
Q ss_pred EEEEECCCCCCCEEEEE-EEEEECCHHHHHHH
Q ss_conf 20010145710013431-23343164366353
Q 537021.9.peg.1 5 GAVGFKGFNSSQRIINA-SIFQFRGHTFIVHH 35 (41)
Q Consensus 5 gavgfkgfnssqriina-sifqfrghtfivhh 35 (41)
..||||||.-...--++ --|||.|.++-.+|
T Consensus 398 ~~vgFKgFai~~e~q~~~v~f~~~g~~~~l~H 429 (892)
T KOG0452 398 SKVGFKGFAIAPEAQSKSVEFQYDGTTAKLKH 429 (892)
T ss_pred CCCCCCCCCCCHHHHHCEEEEEECCEEEEECC
T ss_conf 76663322248567503389998896667416
No 3
>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924 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). This entry represents LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane.
Probab=17.77 E-value=41 Score=17.04 Aligned_cols=10 Identities=70% Similarity=1.288 Sum_probs=7.2
Q ss_pred EEEECCHHHHHHHHHHC
Q ss_conf 33431643663535541
Q 537021.9.peg.1 23 IFQFRGHTFIVHHLLLN 39 (41)
Q Consensus 23 ifqfrghtfivhhllln 39 (41)
|||| ||||..
T Consensus 88 iYQF-------HHLL~d 97 (221)
T TIGR02211 88 IYQF-------HHLLPD 97 (221)
T ss_pred EEEH-------HHCCCC
T ss_conf 4432-------020300
No 4
>TIGR02415 23BDH acetoin reductases; InterPro: IPR014007 One member of this family, as characterised in Klebsiella terrigena , is able to interconvert acetoin + NADH with meso-2,3-butanediol + NAD(+). It is also capable of irreversible reduction of diacetyl with NADH to acetoin. There has been a reuctance to classify the enzyme as either 1.1.1.4 from EC, which is (R,R)-butanediol dehydrogenase, or 1.1.1.5 from EC, which is acetoin dehydrogenase without a specified stereochemistry . Another member of this family, from Corynebacterium glutamicum (Brevibacterium flavum), is called L-2,3-butanediol dehydrogenase . This enzyme is a homotetramer in the family of short chain dehydrogenases (IPR002198 from INTERPRO). .
Probab=7.95 E-value=83 Score=15.64 Aligned_cols=16 Identities=38% Similarity=0.441 Sum_probs=12.7
Q ss_pred EEECCCCCC-CEEEEEE
Q ss_conf 010145710-0134312
Q 537021.9.peg.1 7 VGFKGFNSS-QRIINAS 22 (41)
Q Consensus 7 vgfkgfnss-qriinas 22 (41)
--||-+++. -|||||.
T Consensus 123 ~~Fkk~~~~tGkIINAa 139 (258)
T TIGR02415 123 RQFKKQGHGTGKIINAA 139 (258)
T ss_pred HHHHHCCCCCCCHHHHH
T ss_conf 87787168987115776
No 5
>KOG2841 consensus
Probab=7.84 E-value=75 Score=15.85 Aligned_cols=14 Identities=50% Similarity=0.318 Sum_probs=11.0
Q ss_pred CCCCCCEEEEEEEE
Q ss_conf 45710013431233
Q 537021.9.peg.1 11 GFNSSQRIINASIF 24 (41)
Q Consensus 11 gfnssqriinasif 24 (41)
-|.|-|+|+|||+-
T Consensus 214 ~FgsLq~~~~AS~~ 227 (254)
T KOG2841 214 KFGSLQQISNASEG 227 (254)
T ss_pred HCCCHHHHHHCCHH
T ss_conf 55359998741776
No 6
>pfam05244 Brucella_OMP2 Brucella outer membrane protein 2. This family consists of several outer membrane proteins (2a and 2b) from brucella bacteria. Brucellae are Gram-negative, facultative intracellular bacteria that can infect many species of animals and man.
Probab=7.32 E-value=76 Score=15.82 Aligned_cols=19 Identities=47% Similarity=0.471 Sum_probs=14.9
Q ss_pred CCCCCCCEEEEEEEEEECC
Q ss_conf 1457100134312334316
Q 537021.9.peg.1 10 KGFNSSQRIINASIFQFRG 28 (41)
Q Consensus 10 kgfnssqriinasifqfrg 28 (41)
-|-|.|.|.-.|||||-..
T Consensus 69 ignntsdrtpaasifqaan 87 (240)
T pfam05244 69 IGNNTSDRTPAASIFQAAN 87 (240)
T ss_pred CCCCCCCCCHHHHHHHHHC
T ss_conf 1478777880578998614
No 7
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787 Serine and threonine dehydratases , are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue. This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=6.65 E-value=1.1e+02 Score=15.11 Aligned_cols=19 Identities=32% Similarity=0.534 Sum_probs=13.8
Q ss_pred CCCCCEEEEEEEEEECCHH
Q ss_conf 5710013431233431643
Q 537021.9.peg.1 12 FNSSQRIINASIFQFRGHT 30 (41)
Q Consensus 12 fnssqriinasifqfrght 30 (41)
.|.-|---|-|.|++|-|-
T Consensus 446 L~~lq~~WNISLFHYR~HG 464 (508)
T TIGR01124 446 LTTLQGEWNISLFHYRNHG 464 (508)
T ss_pred HHHCCCCCCCCHHHHHCCC
T ss_conf 8530665474155441123
No 8
>pfam05059 Orbi_VP4 Orbivirus VP4 core protein. Orbiviruses are double stranded RNA retroviruses of which the bluetongue virus is a member. The core of bluetongue virus (BTV) is a multienzyme complex composed of two major proteins (VP7 and VP3) and three minor proteins (VP1, VP4 and VP6) in addition to the viral genome. VP4 has been shown to perform all RNA capping activities and has both methyltransferase type 1 and type 2 activities associated with it.
Probab=6.39 E-value=83 Score=15.63 Aligned_cols=17 Identities=41% Similarity=0.618 Sum_probs=12.1
Q ss_pred EEEEEEEEEECCHHHHH
Q ss_conf 13431233431643663
Q 537021.9.peg.1 17 RIINASIFQFRGHTFIV 33 (41)
Q Consensus 17 riinasifqfrghtfiv 33 (41)
.|-+-||-|.|||.||.
T Consensus 53 ~i~kWsiRQLRghgFiF 69 (642)
T pfam05059 53 PLQKWTIRQLRGHGFIF 69 (642)
T ss_pred CHHHHHHHHHCCCCEEE
T ss_conf 55454078762671699
No 9
>pfam02641 DUF190 Uncharacterized ACR, COG1993.
Probab=5.83 E-value=1.7e+02 Score=14.20 Aligned_cols=22 Identities=18% Similarity=0.555 Sum_probs=17.7
Q ss_pred EECCCCCCCEEEEEEEEEECCH
Q ss_conf 1014571001343123343164
Q 537021.9.peg.1 8 GFKGFNSSQRIINASIFQFRGH 29 (41)
Q Consensus 8 gfkgfnssqriinasifqfrgh 29 (41)
|..||..+.++-.+++|.+..+
T Consensus 42 Gi~GfG~~~~ih~~~~~~ls~d 63 (101)
T pfam02641 42 GIAGYGKHKEVHSDKLFQLSRR 63 (101)
T ss_pred EEEECCCCCCCCCCCHHHHCCC
T ss_conf 0260278986316444442699
No 10
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=5.02 E-value=1.7e+02 Score=14.24 Aligned_cols=15 Identities=27% Similarity=0.496 Sum_probs=0.0
Q ss_pred EEEEEEEECCHHHHH
Q ss_conf 431233431643663
Q 537021.9.peg.1 19 INASIFQFRGHTFIV 33 (41)
Q Consensus 19 inasifqfrghtfiv 33 (41)
.+|...|.+|+++|.
T Consensus 69 ~~a~lVqviG~~~vl 83 (97)
T COG1534 69 TGAELVQVIGKTLVL 83 (97)
T ss_pred HCCEEEEEEEEEEEE
T ss_conf 599876566039999
Done!