Query 537021.9.peg.21_1 Match_columns 44 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Sun May 22 08:16:47 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_21.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PTZ00013 plasmepsin 4 (PM4); P 39.1 28 0.00072 17.0 2.6 23 4-26 91-113 (450) 2 PTZ00147 histoaspartic proteas 37.3 31 0.00078 16.8 2.6 23 4-26 92-114 (453) 3 PHA01750 hypothetical protein 30.6 33 0.00084 16.7 1.9 21 1-21 31-51 (75) 4 pfam06239 ECSIT Evolutionarily 29.2 54 0.0014 15.6 3.1 26 4-29 121-149 (229) 5 COG4670 Acyl CoA:acetate/3-ket 23.4 29 0.00074 16.9 0.5 14 3-16 482-495 (527) 6 pfam09274 ParG ParG. Members o 11.6 1.3E+02 0.0033 13.8 1.5 16 6-21 60-75 (76) 7 pfam09188 DUF1951 Domain of un 10.2 1.6E+02 0.0042 13.3 2.0 22 13-34 1-22 (137) 8 pfam01763 Herpes_UL6 Herpesvir 9.6 1.4E+02 0.0037 13.5 1.2 15 4-18 271-285 (551) 9 pfam07599 DUF1563 Protein of u 9.2 1.4E+02 0.0036 13.6 0.9 10 34-43 25-34 (46) 10 TIGR02982 heterocyst_DevA ABC 8.6 1.1E+02 0.0029 14.1 0.3 15 3-18 205-219 (220) No 1 >PTZ00013 plasmepsin 4 (PM4); Provisional Probab=39.06 E-value=28 Score=16.99 Aligned_cols=23 Identities=43% Similarity=0.686 Sum_probs=19.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68999997644434556589999 Q 537021.9.peg.2 4 DVAKDILNHMEDNYLKESYIYFF 26 (44) Q Consensus 4 dvakdilnhmednylkesyiyff 26 (44) .+-|.|.||--.||.|||+-.|- T Consensus 91 ~~~~~~~~~~~~~~~~~~~~~~~ 113 (450) T PTZ00013 91 KVLKSILKKKLKNYIKESFKFFK 113 (450) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999998768899999999876 No 2 >PTZ00147 histoaspartic protease (plasmepsin I or II); Provisional Probab=37.31 E-value=31 Score=16.81 Aligned_cols=23 Identities=39% Similarity=0.574 Sum_probs=19.2 Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH Q ss_conf 68999997644434556589999 Q 537021.9.peg.2 4 DVAKDILNHMEDNYLKESYIYFF 26 (44) Q Consensus 4 dvakdilnhmednylkesyiyff 26 (44) .+-|.|.+|--.||.|||+-.|- T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~ 114 (453) T PTZ00147 92 RIMKTIKEHKLKNYIKESVKFFN 114 (453) T ss_pred HHHHHHHHHHHHHHHHHHHHHHH T ss_conf 99999988667899999999876 No 3 >PHA01750 hypothetical protein Probab=30.59 E-value=33 Score=16.67 Aligned_cols=21 Identities=33% Similarity=0.365 Sum_probs=18.2 Q ss_pred CHHHHHHHHHHHHHHHHHHHH Q ss_conf 944689999976444345565 Q 537021.9.peg.2 1 MFYDVAKDILNHMEDNYLKES 21 (44) Q Consensus 1 mfydvakdilnhmednylkes 21 (44) ||-|..|||.|.--||..+|- T Consensus 31 ~~~davk~iv~~eldnl~~ei 51 (75) T PHA01750 31 ALKDAVKEIVNSELDNLKTEI 51 (75) T ss_pred HHHHHHHHHHHHHHHHHHHHH T ss_conf 999999999999898899999 No 4 >pfam06239 ECSIT Evolutionarily conserved signalling intermediate in Toll pathway. Activation of NF-kappaB as a consequence of signaling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signaling pathways between TRAF-6 and MEKK-1. Probab=29.19 E-value=54 Score=15.59 Aligned_cols=26 Identities=27% Similarity=0.480 Sum_probs=17.3 Q ss_pred HHHHHHHHHHHHHHHHH---HHHHHHHHH Q ss_conf 68999997644434556---589999998 Q 537021.9.peg.2 4 DVAKDILNHMEDNYLKE---SYIYFFDIF 29 (44) Q Consensus 4 dvakdilnhmednylke---syiyffdif 29 (44) ++|-|+|+.||+|-..- ..--..+|| T Consensus 121 ~cai~vLeqME~~gV~Pd~E~~~ll~~iF 149 (229) T pfam06239 121 QCAIDVLEQMENHGVMPDKETEFLLVNIF 149 (229) T ss_pred HHHHHHHHHHHHCCCCCCHHHHHHHHHHH T ss_conf 99999999999838889589999999996 No 5 >COG4670 Acyl CoA:acetate/3-ketoacid CoA transferase [Lipid metabolism] Probab=23.40 E-value=29 Score=16.93 Aligned_cols=14 Identities=50% Similarity=0.691 Sum_probs=10.8 Q ss_pred HHHHHHHHHHHHHH Q ss_conf 46899999764443 Q 537021.9.peg.2 3 YDVAKDILNHMEDN 16 (44) Q Consensus 3 ydvakdilnhmedn 16 (44) -|..||||++||-. T Consensus 482 vDlekDIL~qmef~ 495 (527) T COG4670 482 VDLEKDILDQMEFE 495 (527) T ss_pred CCHHHHHHHCCCCC T ss_conf 77417678506787 No 6 >pfam09274 ParG ParG. Members of this family of plasmid partition proteins adopt a ribbon-helix-helix fold, with a core of four alpha-helices. They are an essential component of the DNA partition complex of the multidrug resistance plasmid TP228. Probab=11.57 E-value=1.3e+02 Score=13.78 Aligned_cols=16 Identities=44% Similarity=0.835 Sum_probs=12.6 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 9999976444345565 Q 537021.9.peg.2 6 AKDILNHMEDNYLKES 21 (44) Q Consensus 6 akdilnhmednylkes 21 (44) -+|.+|..-||+|+|. T Consensus 60 itdVi~~LvD~WL~eN 75 (76) T pfam09274 60 ITDVINQLVDNWLKEN 75 (76) T ss_pred HHHHHHHHHHHHHHCC T ss_conf 9999999999988626 No 7 >pfam09188 DUF1951 Domain of unknown function (DUF1951). Members of this family of Mycoplasma hypothetical proteins adopt a helical structure, with a buried central helix. Their function has not, as yet, been determined. Probab=10.23 E-value=1.6e+02 Score=13.26 Aligned_cols=22 Identities=41% Similarity=0.532 Sum_probs=9.4 Q ss_pred HHHHHHHHHHHHHHHHHHHHHH Q ss_conf 4443455658999999888952 Q 537021.9.peg.2 13 MEDNYLKESYIYFFDIFLIYHD 34 (44) Q Consensus 13 mednylkesyiyffdifliyhd 34 (44) ||.|-+||..|-||.-----|. T Consensus 1 me~nnikeelis~f~kacsshk 22 (137) T pfam09188 1 MEPNNIKEELISFFEKACSSHK 22 (137) T ss_pred CCCCHHHHHHHHHHHHHHHHHH T ss_conf 9975078999999999875146 No 8 >pfam01763 Herpes_UL6 Herpesvirus UL6 like. This family consists of various proteins from the herpesviridae that are similar to herpes simplex virus type I UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome. Probab=9.61 E-value=1.4e+02 Score=13.53 Aligned_cols=15 Identities=27% Similarity=0.295 Sum_probs=8.2 Q ss_pred HHHHHHHHHHHHHHH Q ss_conf 689999976444345 Q 537021.9.peg.2 4 DVAKDILNHMEDNYL 18 (44) Q Consensus 4 dvakdilnhmednyl 18 (44) +++|+|++|||++-- T Consensus 271 ~~~k~ive~le~~~~ 285 (551) T pfam01763 271 DGYKRIVEKLEKESK 285 (551) T ss_pred CCHHHHHHHHHHHCC T ss_conf 438999999865224 No 9 >pfam07599 DUF1563 Protein of unknown function (DUF1563). A small family of short hypothetical proteins in Leptospira interrogans. Probab=9.19 E-value=1.4e+02 Score=13.61 Aligned_cols=10 Identities=60% Similarity=0.949 Sum_probs=7.7 Q ss_pred HHHHHHHHHC Q ss_conf 2778875540 Q 537021.9.peg.2 34 DEYFLHEIFL 43 (44) Q Consensus 34 deyflheifl 43 (44) -||||..+|| T Consensus 25 ve~flkq~fl 34 (46) T pfam07599 25 VECFLKQIFL 34 (46) T ss_pred HHHHHHHHHH T ss_conf 9999999999 No 10 >TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family; InterPro: IPR014324 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 the ATP-binding subunit DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts , . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation.. Probab=8.55 E-value=1.1e+02 Score=14.06 Aligned_cols=15 Identities=53% Similarity=0.725 Sum_probs=9.0 Q ss_pred HHHHHHHHHHHHHHHH Q ss_conf 4689999976444345 Q 537021.9.peg.2 3 YDVAKDILNHMEDNYL 18 (44) Q Consensus 3 ydvakdilnhmednyl 18 (44) .|||.-|+ +|||..| T Consensus 205 lDvADRI~-~MEdG~L 219 (220) T TIGR02982 205 LDVADRIV-QMEDGKL 219 (220) T ss_pred HHHHHHHH-HCCCCCC T ss_conf 00654442-1168635 Done!