Query T0629 long tail fibre protein gp37, bacteriophage T4, 216 residues
Match_columns 216
No_of_seqs 122 out of 393
Neff 9.6
Searched_HMMs 11830
Date Thu Jul 22 15:01:14 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0629.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0629.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF07484 Collar: Phage Tail Co 99.7 2.5E-18 2.1E-22 121.0 2.8 48 6-53 1-57 (57)
2 PF03235 DUF262: Protein of un 35.8 9.1 0.00077 15.6 2.4 38 1-38 41-80 (224)
3 PF02741 FTR_C: FTR, proximal 19.7 10 0.00087 15.2 0.3 40 5-51 46-85 (150)
4 PF02285 COX8: Cytochrome oxid 17.8 2.3 0.00019 19.0 -3.4 24 5-28 17-40 (44)
5 PF06836 DUF1240: Protein of u 10.2 38 0.0032 12.0 1.0 18 17-34 70-88 (95)
6 PF02343 TRA-1_regulated: TRA- 8.9 31 0.0026 12.5 0.2 12 29-40 6-17 (129)
7 PF00706 Toxin_4: Anenome neur 8.8 39 0.0033 11.9 0.7 12 14-25 23-34 (43)
8 PF00844 Gemini_coat: Geminivi 8.2 46 0.0039 11.6 1.2 23 32-54 132-159 (244)
9 PF09979 DUF2213: Uncharacteri 8.1 46 0.0039 11.5 0.9 15 17-31 7-21 (170)
10 PF08677 GP11: GP11 baseplate 7.8 40 0.0034 11.9 0.3 25 1-25 63-92 (218)
No 1
>PF07484 Collar: Phage Tail Collar Domain; InterPro: IPR011083 This region is occasionally found in conjunction with IPR005003 from INTERPRO. Most of the proteins appear to be phage tail proteins; however some appear to be involved in other processes. For instance the RhiB protein (Q03314 from SWISSPROT) from Rhizobium leguminosarum may be involved in plant-microbe interactions . A related protein, microcystin related protein (MrpB, Q9L3N1 from SWISSPROT) is involved in the pathogenicity of Microcystis aeruginosa. The finding of this family in a structural component of the phage tail fibre baseplate (P10930 from SWISSPROT) suggests that its function is structural rather than enzymatic. Structural studies show this region consists of a helix and a loop and three beta-strands. This alignment does not catch the third strand as it is separated from the rest of the structure by around 100 residues. This strand is conserved in homologues but the intervening sequence is not. Much of the function of P10930 from SWISSPROT appears to reside in this intervening region. In the tertiary structure of the phage baseplate this domain forms part of the collar and may bind SO_4. The long unconserved region maybe due to domain swapping in and out of a loop or due to rapid evolution.; PDB: 1ocy_A 1h6w_A.
Probab=99.69 E-value=2.5e-18 Score=121.00 Aligned_cols=48 Identities=33% Similarity=0.614 Sum_probs=45.8
Q ss_pred CCEEECCCCCCCCCEEEECCCEECHHHHHHHHHHCC---------CCCCCCCCCCCC
Q ss_conf 613507778788871863781226332057886607---------777775456510
Q T0629 6 GAPIPWPSDSVPAGFALMEGQTFDKSAYPKLAVAYP---------SGVIPDMRGQTI 53 (216)
Q Consensus 6 G~iv~f~~~~~P~Gwl~cdG~~~s~~~Yp~L~~~~g---------s~~lPdlrg~f~ 53 (216)
|+|++|+.+.+|+|||+||||++++++||+||++|| +|+||||||||+
T Consensus 1 G~I~~f~~~~~P~gwl~cdG~~~~~~~yp~Lf~~iGt~yGGdg~~tF~lPDlrG~~~ 57 (57)
T PF07484_consen 1 GSIVPFAGNFAPEGWLLCDGQTLSISQYPALFSLIGTTYGGDGSTTFNLPDLRGRFP 57 (57)
T ss_dssp --EEEESSSS-SSTEEE-------TTT-HHHHHH----------S------------
T ss_pred CCEEEECCCCCCCHHHHHCCCCCCHHHCHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 947993388896378871886768778999999867013787888677965046788
No 2
>PF03235 DUF262: Protein of unknown function DUF262; InterPro: IPR004919 This entry is found in prokaryotic proteins of unknown function.
Probab=35.75 E-value=9.1 Score=15.55 Aligned_cols=38 Identities=21% Similarity=0.431 Sum_probs=26.5
Q ss_pred CCCCCCCEEECC--CCCCCCCEEEECCCEECHHHHHHHHH
Q ss_conf 988876135077--78788871863781226332057886
Q T0629 1 SSYPIGAPIPWP--SDSVPAGFALMEGQTFDKSAYPKLAV 38 (216)
Q Consensus 1 ~~~PvG~iv~f~--~~~~P~Gwl~cdG~~~s~~~Yp~L~~ 38 (216)
..||+|+|+.|. ......-+...|||.=-.+.|--|.+
T Consensus 41 ~~y~iG~iv~~~~~~~~~~~~~~vIDGQQRLTTl~l~l~~ 80 (224)
T PF03235_consen 41 RGYFIGSIVLWEKEKNDSNNKYEVIDGQQRLTTLYLLLKA 80 (224)
T ss_pred CCCCCCEEEEECCCCCCCCCEEEEECCHHHHHHHHHHHHH
T ss_conf 6821071788614567898838984670899999999984
No 3
>PF02741 FTR_C: FTR, proximal lobe; InterPro: IPR002770 Formylmethanofuran:tetrahyromethanopterin formyltransferase (Ftr) is involved in C1 metabolism in methanogenic archaea, sulphate-reducing archaea and methylotrophic bacteria. It catalyses the following reversible reaction: N-formylmethanofuran + 5,6,7,8-tetrahydromethanopterin = methanofuran + 5-formyl-5,6,7,8-tetrahydromethanopterin Ftr from the thermophilic methanogen Methanopyrus kandleri (optimum growth temperature 98 degrees C) is a hyperthermophilic enzyme that is absolutely dependent on the presence of lyotropic salts for activity and thermostability. The crystal structure of Ftr, determined to a reveals a homotetramer composed essentially of two dimers. Each subunit is subdivided into two tightly associated lobes both consisting of a predominantly antiparallel beta sheet flanked by alpha helices forming an alpha/beta sandwich structure. The approximate location of the active site was detected in a region close to the dimer interface . Ftr from the mesophilic methanogen Methanosarcina barkeri and the sulphate-reducing archaeon Archaeoglobus fulgidus have a similar structure In the methylotrophic bacterium Methylobacterium extorquens, Ftr interacts with three other polypeptides to form an Ftr/cyclohydrolase complex which catalyses the hydrolysis of formyl-tetrahydromethanopterin to formate during growth on C1 substrates . ; GO: 0016740 transferase activity, 0006730 one-carbon compound metabolic process; PDB: 1ftr_C 2fhj_A 2fhk_D 1m5s_A 1m5h_H.
Probab=19.73 E-value=10 Score=15.22 Aligned_cols=40 Identities=25% Similarity=0.485 Sum_probs=23.9
Q ss_pred CCCEEECCCCCCCCCEEEECCCEECHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 76135077787888718637812263320578866077777754565
Q T0629 5 IGAPIPWPSDSVPAGFALMEGQTFDKSAYPKLAVAYPSGVIPDMRGQ 51 (216)
Q Consensus 5 vG~iv~f~~~~~P~Gwl~cdG~~~s~~~Yp~L~~~~gs~~lPdlrg~ 51 (216)
.|.|.|||+-.+..| +.+... |+.|.+.--.-.-|-||++
T Consensus 46 ~gvI~PFPGGivrSG------SKVGsk-Yk~l~ASTNdayCPTLr~~ 85 (150)
T PF02741_consen 46 PGVITPFPGGIVRSG------SKVGSK-YKFLGASTNDAYCPTLRGK 85 (150)
T ss_dssp ---B-------BSS-------EB------TT-S-BE-GGG-GGGGCC
T ss_pred CCEEECCCCCEECCC------CCCCCC-CCCCCCCCCCCCCCCHHCC
T ss_conf 995735899842457------746546-6878686676748442202
No 4
>PF02285 COX8: Cytochrome oxidase c subunit VIII; InterPro: IPR003205 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen . In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits.This family is composed of cytochrome c oxidase subunit VIII. ; GO: 0004129 cytochrome-c oxidase activity, 0006118 electron transport; PDB: 1ocr_Z 1occ_Z 2dyr_Z 1oco_M 2dys_Z 2ein_Z 2eik_Z 2eim_Z 2eij_M 1v55_M ....
Probab=17.84 E-value=2.3 Score=18.95 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=15.1
Q ss_pred CCCEEECCCCCCCCCEEEECCCEE
Q ss_conf 761350777878887186378122
Q T0629 5 IGAPIPWPSDSVPAGFALMEGQTF 28 (216)
Q Consensus 5 vG~iv~f~~~~~P~Gwl~cdG~~~ 28 (216)
||..+.|..=-.|+||.+|+=..|
T Consensus 17 igl~~~f~~~l~PagWVL~hL~~Y 40 (44)
T PF02285_consen 17 IGLTVFFATFLGPAGWVLSHLEDY 40 (44)
T ss_dssp ---HHHHHHHHTT---TTTTHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 889999999971189999999871
No 5
>PF06836 DUF1240: Protein of unknown function (DUF1240); InterPro: IPR010665 This family consists of a number of hypothetical putative membrane proteins which seem to be specific to Yersinia pestis. The function of this family is unknown.
Probab=10.20 E-value=38 Score=12.03 Aligned_cols=18 Identities=11% Similarity=0.469 Sum_probs=11.7
Q ss_pred CCCEEEECCCEE-CHHHHH
Q ss_conf 887186378122-633205
Q T0629 17 PAGFALMEGQTF-DKSAYP 34 (216)
Q Consensus 17 P~Gwl~cdG~~~-s~~~Yp 34 (216)
-+||+.|+...| +-++|-
T Consensus 70 s~gY~~C~k~SwmSPN~YV 88 (95)
T PF06836_consen 70 SEGYVVCDKISWMSPNTYV 88 (95)
T ss_pred CCCEEECCCCEEECCCCEE
T ss_conf 3890880531022741276
No 6
>PF02343 TRA-1_regulated: TRA-1 regulated protein R03H10.4; InterPro: IPR003326 This domain is found in a family of proteins from Caenorhabditis elegans. The domain has no known function, but has 4 conserved cysteine residues and is a maximum of 175 residues long.
Probab=8.95 E-value=31 Score=12.51 Aligned_cols=12 Identities=17% Similarity=0.426 Sum_probs=5.7
Q ss_pred CHHHHHHHHHHC
Q ss_conf 633205788660
Q T0629 29 DKSAYPKLAVAY 40 (216)
Q Consensus 29 s~~~Yp~L~~~~ 40 (216)
+..+.|+|...+
T Consensus 6 ~~~~Cpdl~~~~ 17 (129)
T PF02343_consen 6 STCECPDLSSYF 17 (129)
T ss_pred CCCCCCCHHHHH
T ss_conf 877895978950
No 7
>PF00706 Toxin_4: Anenome neurotoxin; InterPro: IPR000693 Sea anemones produce many different neurotoxins with related structure and function. Proteins belonging to this family include the neurotoxins, of which there are several, including calitoxin and anthopleurin. The neurotoxins bind specifically to the sodium channel, thereby delaying its inactivation during signal transduction, resulting in strong stimulation of mammalian cardiac muscle contraction. Calitoxin 1 has been found in neuromuscular prearations of crustaceans, where it increases transmitter release, causing firing of the axons. Three disulphide bonds are present in this protein , , .; GO: 0009966 regulation of signal transduction, 0005576 extracellular region; PDB: 1atx_A 2h9x_A 2sh1_A 1shi_A 1sh1_A 1apf_A 1ahl_A.
Probab=8.84 E-value=39 Score=11.94 Aligned_cols=12 Identities=17% Similarity=0.351 Sum_probs=8.6
Q ss_pred CCCCCCEEEECC
Q ss_conf 878887186378
Q T0629 14 DSVPAGFALMEG 25 (216)
Q Consensus 14 ~~~P~Gwl~cdG 25 (216)
..-|.||-+|.+
T Consensus 23 ~~CpsGWhkC~~ 34 (43)
T PF00706_consen 23 FGCPSGWHKCKS 34 (43)
T ss_dssp -------EECCC
T ss_pred CCCCCHHHHHHC
T ss_conf 578831555424
No 8
>PF00844 Gemini_coat: Geminivirus coat protein/nuclear export factor BR1 family; InterPro: IPR000263 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name . Most geminiviruses can be divided into 2 subgroups on the basis of host range and/or insect vector: i.e. those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. It has been shown that the 104 N-terminal amino acids of the Maize streak virus coat protein bind DNA non-specifically .; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=8.19 E-value=46 Score=11.56 Aligned_cols=23 Identities=17% Similarity=0.241 Sum_probs=9.6
Q ss_pred HHHHHHHHCCC-----CCCCCCCCCCCC
Q ss_conf 20578866077-----777754565100
Q T0629 32 AYPKLAVAYPS-----GVIPDMRGQTIK 54 (216)
Q Consensus 32 ~Yp~L~~~~gs-----~~lPdlrg~f~r 54 (216)
++.+||-++-. -..+||++||.+
T Consensus 132 ~f~elFg~~~~~~~t~~v~~~~~~RF~V 159 (244)
T PF00844_consen 132 TFDELFGMYINSPGTLTVKRDLKDRFYV 159 (244)
T ss_pred CHHHHCCCCCCCCCCEEECHHHCCCEEE
T ss_conf 7777347765676776986572875899
No 9
>PF09979 DUF2213: Uncharacterized protein conserved in bacteria (DUF2213)
Probab=8.09 E-value=46 Score=11.53 Aligned_cols=15 Identities=13% Similarity=0.479 Sum_probs=0.0
Q ss_pred CCCEEEECCCEECHH
Q ss_conf 887186378122633
Q T0629 17 PAGFALMEGQTFDKS 31 (216)
Q Consensus 17 P~Gwl~cdG~~~s~~ 31 (216)
+.|||.|....++|+
T Consensus 7 ~~G~L~v~~~piar~ 21 (170)
T PF09979_consen 7 ADGYLVVEAVPIART 21 (170)
T ss_pred CCEEEEEEEEEEEEE
T ss_conf 980699652477343
No 10
>PF08677 GP11: GP11 baseplate wedge protein; InterPro: IPR014791 The bacteriophage baseplate controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. The baseplate is a multi-subunit assembly at the distal end of the tail, which is composed of long and short tail fibres . The tail region is responsible for attachment to the host bacteria during infection: long tail fibres enable host receptor recognition, while irreversible attachment is via short tail fibres. Recognition and attachment induce a conformational transition of the baseplate from a hexagonal to a star-shaped structure. In viruses such as Bacteriophage T4, GP11 acts as a structural protein to connect the short tail fibres to the baseplate, while GP9 connects the baseplate with the long tail fibres. Both GP9 and GP11 are trimers. Each GP11 monomer consists of three domains, which are entwined together in the trimer: the N-terminal domains of the three monomers form a central, trimeric, parallel coiled coil surrounded by the entwined middle finger domains; the C-terminal domains appear to be responsible for trimerisation .; PDB: 1el6_C.
Probab=7.75 E-value=40 Score=11.88 Aligned_cols=25 Identities=24% Similarity=0.432 Sum_probs=0.0
Q ss_pred CCCCCCCEEECCCCCCCCC-----EEEECC
Q ss_conf 9888761350777878887-----186378
Q T0629 1 SSYPIGAPIPWPSDSVPAG-----FALMEG 25 (216)
Q Consensus 1 ~~~PvG~iv~f~~~~~P~G-----wl~cdG 25 (216)
+.+|||.|+.--..++|.| +|-++|
T Consensus 63 ~~~pVg~Vii~t~~~~P~g~~Q~e~ltFsG 92 (218)
T PF08677_consen 63 AMLPVGTVIISTENVSPEGVQQIETLTFSG 92 (218)
T ss_dssp H------EEEE-----------EEEEEEE-
T ss_pred HHCCCCCEEEECCCCCCCCCCCEEEEEEEE
T ss_conf 507513199844778976523136999876
Done!