Query 537021.9.peg.254_1 Match_columns 38 No_of_seqs 1 out of 3 Neff 1.0 Searched_HMMs 39220 Date Wed May 25 16:14:11 2011 Command /home/congqian_1/programs/hhpred/hhsearch -i peg_254.hhm -d /home/congqian_1/database/cdd/Cdd.hhm No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 pfam05541 Spheroidin Entomopox 25.1 52 0.0013 16.8 2.1 19 8-31 141-159 (943) 2 COG3564 Uncharacterized protei 20.9 81 0.0021 15.8 2.4 25 6-34 89-113 (116) 3 PRK09441 cytoplasmic alpha-amy 20.7 32 0.00083 17.7 0.3 11 1-11 360-370 (482) 4 COG3660 Predicted nucleoside-d 17.2 47 0.0012 16.9 0.5 17 14-30 191-207 (329) 5 pfam08413 Metallophos_C Calcin 15.8 88 0.0022 15.7 1.6 16 19-36 1-16 (38) 6 TIGR02485 CobZ_N-term precorri 11.3 95 0.0024 15.5 0.7 11 27-37 260-270 (467) 7 PRK02259 aspartoacylase; Provi 10.3 52 0.0013 16.7 -0.9 25 10-34 236-260 (263) 8 pfam11305 DUF3107 Protein of u 10.1 2E+02 0.005 14.0 2.6 20 17-36 44-63 (74) 9 KOG0546 consensus 10.0 85 0.0022 15.7 0.1 21 6-26 92-112 (372) 10 TIGR01271 CFTR_protein cystic 10.0 97 0.0025 15.4 0.4 7 3-9 625-631 (1534) No 1 >pfam05541 Spheroidin Entomopoxvirus spheroidin protein. Entomopoxviruses (EPVs) are large (300-400 nm) oval-shaped viruses replicating in the cytoplasm of their insect host cells. At the end of their replicative cycle EPVs virions are occluded in a highly expressed protein called spheroidin. This protein forms large (5-20 mm long) oval-shaped occlusion bodies (OBs) called spherules. The infectious cycle of EPVs begins with the ingestion by the insect host of the spherules, their dissolution by the alkaline reducing conditions of the midgut fluid and the release of virions in the midgut lumen. The infective particles first replicate in midgut epithelial cells, then pass the gut barrier to colonize the internal tissues, mainly the fat body cells. Whilst spheroidin has been demonstrated to be non-essential for viral replication, it plays an essential role in the natural biological cycle of the virus in protecting virions from adverse environmental conditions (e.g. UV degradation) and thus Probab=25.13 E-value=52 Score=16.76 Aligned_cols=19 Identities=42% Similarity=0.534 Sum_probs=15.0 Q ss_pred EEEECCCCCCCCCEEEEEECCEEE Q ss_conf 076348873123346677335278 Q 537021.9.peg.2 8 GYFHNENGYEKKGIKFLISKSRIR 31 (38) Q Consensus 8 gyfhnengyekkgikflisksrir 31 (38) -|||+.||+ +|||+++.|- T Consensus 141 i~f~ddng~-----ygLit~~nI~ 159 (943) T pfam05541 141 IYFVDDNGV-----YGLITKENIV 159 (943) T ss_pred EEEECCCCC-----EEEEECCCEE T ss_conf 999927981-----7887511002 No 2 >COG3564 Uncharacterized protein conserved in bacteria [Function unknown] Probab=20.88 E-value=81 Score=15.83 Aligned_cols=25 Identities=48% Similarity=0.850 Sum_probs=18.4 Q ss_pred EEEEEECCCCCCCCCEEEEEECCEEEEEE Q ss_conf 70076348873123346677335278986 Q 537021.9.peg.2 6 YGGYFHNENGYEKKGIKFLISKSRIRCVQ 34 (38) Q Consensus 6 yggyfhnengyekkgikflisksrircvq 34 (38) -||-|.-+||-|| .| .+.||+-.|| T Consensus 89 RGGmFSLdng~E~---RF-LtRsrv~~~~ 113 (116) T COG3564 89 RGGMFSLDNGREK---RF-LTRSRVCSVQ 113 (116) T ss_pred CCCEEECCCCCCE---EE-EEEEEEEECC T ss_conf 8864572578513---56-6511266314 No 3 >PRK09441 cytoplasmic alpha-amylase; Reviewed Probab=20.75 E-value=32 Score=17.74 Aligned_cols=11 Identities=55% Similarity=1.509 Sum_probs=8.8 Q ss_pred CCEEEEEEEEE Q ss_conf 96057700763 Q 537021.9.peg.2 1 VPCYFYGGYFH 11 (38) Q Consensus 1 vpcyfyggyfh 11 (38) +||-|||-|+- T Consensus 360 ~PcvfYgDyyg 370 (482) T PRK09441 360 YPCVFYGDYYG 370 (482) T ss_pred EEEEEEHHHCC T ss_conf 42477213206 No 4 >COG3660 Predicted nucleoside-diphosphate-sugar epimerase [Cell envelope biogenesis, outer membrane] Probab=17.18 E-value=47 Score=16.94 Aligned_cols=17 Identities=47% Similarity=0.448 Sum_probs=14.3 Q ss_pred CCCCCCCEEEEEECCEE Q ss_conf 87312334667733527 Q 537021.9.peg.2 14 NGYEKKGIKFLISKSRI 30 (38) Q Consensus 14 ngyekkgikflisksri 30 (38) .+||+.|+.|+||-||- T Consensus 191 k~l~~~g~~~lisfSRR 207 (329) T COG3660 191 KILENQGGSFLISFSRR 207 (329) T ss_pred HHHHHCCCEEEEEEECC T ss_conf 99874785189996068 No 5 >pfam08413 Metallophos_C Calcineurin-like phosphoesterase C-terminal. This domain is found to the C-terminus of Calcineurin-like phosphoesterase domains (pfam00149) in cAMP phosphodiesterases and the homologous Icc proteins. Probab=15.78 E-value=88 Score=15.66 Aligned_cols=16 Identities=44% Similarity=0.933 Sum_probs=11.4 Q ss_pred CCEEEEEECCEEEEEEEC Q ss_conf 334667733527898632 Q 537021.9.peg.2 19 KGIKFLISKSRIRCVQFG 36 (38) Q Consensus 19 kgikflisksrircvqfg 36 (38) .||.++-+-| .|+||- T Consensus 1 ~gv~~l~tPS--TC~QF~ 16 (38) T pfam08413 1 NGVRLLATPS--TCVQFK 16 (38) T ss_pred CCCEEEECCC--CEEEEC T ss_conf 9977984897--536545 No 6 >TIGR02485 CobZ_N-term precorrin 3B synthase CobZ; InterPro: IPR012831 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase . There are at least two distinct cobalamin biosynthetic pathways in bacteria : Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CobZ, which is essential for cobalamin biosynthesis and is complemented by precorrin 3B synthase CobG (188.8.131.52 from EC). The enzyme has been shown to contain flavin, haem and Fe-S cluster cofactors, and is believed to require dioxygen as a substrate. In Rhodobacter capsulatus, CobZ is found as a N-terminal domain, whereas in other species it exists as a separate protein. The C-terminal portion is homologous to the 2-component signal transduction system protein CitB (IPR012830 from INTERPRO).. Probab=11.27 E-value=95 Score=15.48 Aligned_cols=11 Identities=36% Similarity=0.715 Sum_probs=8.6 Q ss_pred CCEEEEEEECC Q ss_conf 35278986326 Q 537021.9.peg.2 27 KSRIRCVQFGI 37 (38) Q Consensus 27 ksrircvqfgi 37 (38) -|||.|+|.|| T Consensus 260 vtRid~~~lG~ 270 (467) T TIGR02485 260 VTRIDSVSLGV 270 (467) T ss_pred EEEECEEECCE T ss_conf 74412121131 No 7 >PRK02259 aspartoacylase; Provisional Probab=10.32 E-value=52 Score=16.73 Aligned_cols=25 Identities=36% Similarity=0.579 Sum_probs=0.0 Q ss_pred EECCCCCCCCCEEEEEECCEEEEEE Q ss_conf 6348873123346677335278986 Q 537021.9.peg.2 10 FHNENGYEKKGIKFLISKSRIRCVQ 34 (38) Q Consensus 10 fhnengyekkgikflisksrircvq 34 (38) |-||-.|-.|+|-|..++.+.-.+. T Consensus 236 FINEAAYyEK~iA~~lt~K~~i~~~ 260 (263) T PRK02259 236 FINEAAYYEKGIAMSLTKKEVINVK 260 (263) T ss_pred EECHHHHHHHHHHHHHHEEEEEECC T ss_conf 6238886652256543200796069 No 8 >pfam11305 DUF3107 Protein of unknown function (DUF3107). Some members in this family of proteins are annotated as ATP-binding proteins however this cannot be confirmed. Currently no function is known. Probab=10.07 E-value=2e+02 Score=13.96 Aligned_cols=20 Identities=25% Similarity=0.591 Sum_probs=0.0 Q ss_pred CCCCEEEEEECCEEEEEEEC Q ss_conf 12334667733527898632 Q 537021.9.peg.2 17 EKKGIKFLISKSRIRCVQFG 36 (38) Q Consensus 17 ekkgikflisksrircvqfg 36 (38) .+||-++++.-++|--|++| T Consensus 44 D~kGr~vlVpa~~iaYVEiG 63 (74) T pfam11305 44 DDKGRRVLVPAAALAYVEIG 63 (74) T ss_pred ECCCCEEEEECCCEEEEEEC T ss_conf 38998999985528999976 No 9 >KOG0546 consensus Probab=9.95 E-value=85 Score=15.71 Aligned_cols=21 Identities=43% Similarity=0.551 Sum_probs=0.0 Q ss_pred EEEEEECCCCCCCCCEEEEEE Q ss_conf 700763488731233466773 Q 537021.9.peg.2 6 YGGYFHNENGYEKKGIKFLIS 26 (38) Q Consensus 6 yggyfhnengyekkgikflis 26 (38) ||++|..||=--|.--.||+| T Consensus 92 YG~~FdDEnF~lKHdrpflLS 112 (372) T KOG0546 92 YGEKFDDENFELKHDRPFLLS 112 (372) T ss_pred CCCCCCCCCCEECCCCCHHHH T ss_conf 056304653021468601101 No 10 >TIGR01271 CFTR_protein cystic fibrosis transmembrane conductor regulator (CFTR); InterPro: IPR005291 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). These proteins are integral membrane proteins and they are involved in the transport of chloride ions. Many of these proteins are the cystis fibrosis transmembrane conductor regulators (CFTR) in eukaryotes. The principal role of this protein is chloride ion conductance. The protein is predicted to consist of 12 transmembrane domains. Mutations or lesions in the genetic loci have been linked to the aetiology of asthma, bronchiectasis, chronic obstructive pulmonary disease etc. Disease-causing mutations have been studied by 36Cl efflux assays in vitro cell cultures and electrophysiology, all of which point to the impairment of chloride channel stability and not the biosynthetic processing per se.; GO: 0005254 chloride channel activity, 0006811 ion transport, 0016020 membrane. Probab=9.95 E-value=97 Score=15.44 Aligned_cols=7 Identities=71% Similarity=2.124 Sum_probs=0.0 Q ss_pred EEEEEEE Q ss_conf 0577007 Q 537021.9.peg.2 3 CYFYGGY 9 (38) Q Consensus 3 cyfyggy 9 (38) |||||.+ T Consensus 625 cYFYG~F 631 (1534) T TIGR01271 625 CYFYGTF 631 (1534) T ss_pred EEEECCH T ss_conf 1242474 Done!