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_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_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_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 ( 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_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_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_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_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