Query T0537 ZP_02066290.1, Bacteroides ovatus, 381 residues
Match_columns 381
No_of_seqs 211 out of 469
Neff 7.2
Searched_HMMs 11830
Date Fri May 21 18:07:27 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0537.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0537.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05342 Peptidase_M26_N: M26 99.1 6.7E-11 5.6E-15 78.1 5.1 123 54-193 111-250 (250)
2 PF07581 Glug: The GLUG motif; 95.3 0.0061 5.1E-07 32.3 3.6 26 236-262 3-28 (28)
3 PF07581 Glug: The GLUG motif; 94.5 0.013 1.1E-06 30.4 3.6 26 266-293 3-28 (28)
4 PF09251 PhageP22-tail: Salmon 35.5 8.2 0.0007 14.2 2.7 10 123-132 311-320 (551)
5 PF10178 DUF2372: Uncharacteri 20.7 7.8 0.00066 14.4 -0.2 15 2-16 2-16 (90)
6 PF12421 DUF3672: Fibronectin 15.9 20 0.0017 12.0 3.9 44 150-206 6-51 (136)
7 PF01215 COX5B: Cytochrome c o 11.5 15 0.0012 12.8 -0.8 22 58-79 38-59 (99)
8 PF06527 TniQ: TniQ; InterPro 10.8 29 0.0024 11.1 0.9 28 8-35 144-172 (405)
9 PF00295 Glyco_hydro_28: Glyco 9.6 32 0.0027 10.9 8.2 68 126-193 207-277 (326)
10 PF02630 SCO1-SenC: SCO1/SenC; 6.9 19 0.0016 12.1 -1.6 18 7-27 52-69 (174)
No 1
>PF05342 Peptidase_M26_N: M26 IgA1-specific Metallo-endopeptidase N-terminal region; InterPro: IPR008006 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of metallopeptidases corresponds to MEROPS peptidase family M26 (clan MA(E)). The active site residues for members of this family and family M4 occur in the motif HEXXH. The type example is IgA1-specific metalloendopeptidase from Streptococcus sanguinis (Q59986 from SWISSPROT).
Probab=99.05 E-value=6.7e-11 Score=78.07 Aligned_cols=123 Identities=21% Similarity=0.308 Sum_probs=81.0
Q ss_pred CCEECCCCCCCCCCEE--ECC--------HHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCC--CCCEEEEEC
Q ss_conf 5400155788788868--748--------7999999876632784699960562346777630468888--877778840
Q T0537 54 GGLFEKGNGTDSKPYM--IMN--------ATQIRNMRSVLKSGMKVYFQLGADIDMAGIDDWQSLNGSG--DFPYEIDFD 121 (381)
Q Consensus 54 ~~lf~~G~GT~~~PY~--I~t--------~~~L~~l~~~~~~~~~~~f~L~~DIdlsg~~~W~pi~g~~--~~~F~GtFD 121 (381)
..|-..++.+-.+-|. |+- -+.+..|-.+.+++.+-.|+|.+|+|+.+++ -.| .+.. ...|+|++.
T Consensus 111 ~~LvQ~~~~~~~~~y~fYi~K~~~~~~~vy~sF~~Lv~am~~Np~Gtf~Lga~l~A~~V~-l~~-~~ksYv~g~FtG~L~ 188 (250)
T PF05342_consen 111 PNLVQRGDNKYSENYTFYIEKPKPSENNVYYSFKELVDAMNSNPSGTFKLGADLNAREVE-LPP-NQKSYVTGEFTGKLI 188 (250)
T ss_pred HHHEECCCCCEEEEEEEEEECCCCCCCCCEECHHHHHHHHHHCCCCCEEEECCCCCCCCC-CCC-CCCEEEECEEEEEEE
T ss_conf 674213688507114899303567767616169999999973999518960654534422-289-873077011789982
Q ss_pred ----CCCEEEEEEEECCCCCCEEEEEE-CCEEEEEEEEEEEEEECCCCCEEEEEEEECCEEEEEEECCEEEEEEEEE
Q ss_conf ----79838970274787753045887-1569995886107983133320456553011243332001799989741
Q T0537 122 ----GDSHVIKNFKCSAGDYPSFFGVL-CGDCRNVGFVNASVSSARQGIGIITGYLGLKDKGNGNKTGRIVNCYTTG 193 (381)
Q Consensus 122 ----GnGhtIsnL~i~~~~~~GLFG~i-~g~ikNl~i~n~~i~g~~~~~G~~~g~~~~~~~~~~~~~g~I~n~~~~g 193 (381)
|.+|+|.||..| ||..+ +++|+||.|+++.|+.... .+.++..+ .+..+|+|++++|
T Consensus 189 G~~dgk~yaIyNL~~P------LF~~l~~atI~nl~lknVnI~~~d~-ia~lA~~a--------kn~t~IenV~v~G 250 (250)
T PF05342_consen 189 GSNDGKHYAIYNLKKP------LFDNLNGATIKNLNLKNVNISMPDD-IASLANEA--------KNGTTIENVKVTG 250 (250)
T ss_pred CCCCCCEEEEECCCCH------HHHHCCCCEEEECCCCEEEEECCCC-HHHHHHHH--------CCCCEEEEEEECC
T ss_conf 3469943678636731------4442347688712021124306862-78998762--------2785788887439
No 2
>PF07581 Glug: The GLUG motif; InterPro: IPR011493 This domain is found in the IgA1-specific metalloendopeptidases, which attach to the cell wall peptidoglycan by an amide bond . IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens including Giardia spp. . This domain is also found in various other contexts, including with IPR008638 from INTERPRO. It is named GLUG after the mostly conserved G-L-any-G motif. The IgA1-specific metalloendopeptidases belong to MEROPS peptidase family M26, clan MA(E).
Probab=95.28 E-value=0.0061 Score=32.28 Aligned_cols=26 Identities=50% Similarity=0.957 Sum_probs=14.9
Q ss_pred CCCEEEEEEECCCCEEEEEEEEEEEEE
Q ss_conf 310022344125750899978776887
Q T0537 236 GKAGGIAGRKVGVGGFIENCYAYGAVS 262 (381)
Q Consensus 236 ~~vGGivG~~~~~~~~I~n~y~~G~V~ 262 (381)
.++|||+|.... .++|+|||++|+|+
T Consensus 3 ~~vGGLvG~n~~-~~~I~nc~atg~Vt 28 (28)
T PF07581_consen 3 SYVGGLVGYNDG-GGTISNCYATGTVT 28 (28)
T ss_pred CCEEEEEEECCC-CCEEEEEEEEEEEC
T ss_conf 218999987689-97799889985859
No 3
>PF07581 Glug: The GLUG motif; InterPro: IPR011493 This domain is found in the IgA1-specific metalloendopeptidases, which attach to the cell wall peptidoglycan by an amide bond . IgA1 protease selectively cleaves human IgA1 and is likely to be a pathogenicity factor in some pathogens including Giardia spp. . This domain is also found in various other contexts, including with IPR008638 from INTERPRO. It is named GLUG after the mostly conserved G-L-any-G motif. The IgA1-specific metalloendopeptidases belong to MEROPS peptidase family M26, clan MA(E).
Probab=94.52 E-value=0.013 Score=30.38 Aligned_cols=26 Identities=35% Similarity=0.382 Sum_probs=16.7
Q ss_pred CCCCEEEECCCCCCCCEEEEEEEEEEEE
Q ss_conf 5634589814687651589748887676
Q T0537 266 GGVGGILGQIDKSCDIAIKNSAAWSNLT 293 (381)
Q Consensus 266 ~~~GGivG~~~~~~~~~I~n~ya~g~v~ 293 (381)
.++|||+|+.... .+|+|||+.++|+
T Consensus 3 ~~vGGLvG~n~~~--~~I~nc~atg~Vt 28 (28)
T PF07581_consen 3 SYVGGLVGYNDGG--GTISNCYATGTVT 28 (28)
T ss_pred CCEEEEEEECCCC--CEEEEEEEEEEEC
T ss_conf 2189999876899--7799889985859
No 4
>PF09251 PhageP22-tail: Salmonella phage P22 tailspike; InterPro: IPR015331 Members of this entry contain a domain that adopts a structure consisting of a single-stranded right-handed beta-helix, which in turn is made of parallel beta-strands and short turns. They are required for recognition of the 0-antigenic repeating units of the cell surface, and for subsequent infection of the bacterial cell by the phage . ; PDB: 1tyw_A 1qrc_A 2vfq_A 1qa1_A 1qa3_A 2vfm_A 2vky_B 2vfo_A 1qq1_A 1tyu_A ....
Probab=35.48 E-value=8.2 Score=14.24 Aligned_cols=10 Identities=30% Similarity=0.604 Sum_probs=4.0
Q ss_pred CCEEEEEEEE
Q ss_conf 9838970274
Q T0537 123 DSHVIKNFKC 132 (381)
Q Consensus 123 nGhtIsnL~i 132 (381)
++|.|.||.+
T Consensus 311 ~nhlidn~lv 320 (551)
T PF09251_consen 311 NNHLIDNILV 320 (551)
T ss_dssp ---EEEEEEE
T ss_pred HHHHHHHHHE
T ss_conf 4454444410
No 5
>PF10178 DUF2372: Uncharacterised conserved protein (DUF2372); PDB: 2z5e_A.
Probab=20.74 E-value=7.8 Score=14.40 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=11.8
Q ss_pred CCCCCCHHHHHHHHH
Q ss_conf 610000255300122
Q T0537 2 NITQIGRFGMLLMMA 16 (381)
Q Consensus 2 ~~~~~~~~~~~~~~~ 16 (381)
-+|||||..+||--.
T Consensus 2 vvTQ~GK~gti~~v~ 16 (90)
T PF10178_consen 2 VVTQIGKMGTIVHVT 16 (90)
T ss_dssp EEEE------EEEEE
T ss_pred EEEECCCCCEEEEEC
T ss_conf 567504322689962
No 6
>PF12421 DUF3672: Fibronectin type III protein
Probab=15.94 E-value=20 Score=12.03 Aligned_cols=44 Identities=25% Similarity=0.309 Sum_probs=22.1
Q ss_pred EEEEEEEEEEECCCCCEEEEEEEECCEEEEEEECC--EEEEEEEEEEEEECCCCCEEEE
Q ss_conf 95886107983133320456553011243332001--7999897417875256423788
Q T0537 150 NVGFVNASVSSARQGIGIITGYLGLKDKGNGNKTG--RIVNCYTTGEVIGSGAAGGIAG 206 (381)
Q Consensus 150 Nl~i~n~~i~g~~~~~G~~~g~~~~~~~~~~~~~g--~I~n~~~~g~v~g~~~~gGi~G 206 (381)
+|..+|+.|+|.-... .+..++ .-++|.+.|+|....-.|-++.
T Consensus 6 ~lta~Na~isG~I~A~-------------sGtf~~v~ia~~c~i~Gtv~A~~ieGDIvk 51 (136)
T PF12421_consen 6 NLTANNADISGTINAN-------------SGTFNNVTIAENCTINGTVYAEQIEGDIVK 51 (136)
T ss_pred CEEEECCEEEEEEEEC-------------CCEECCEEECCCCEEEEEEEEEEEECCCCE
T ss_conf 3898600898699932-------------524806396255338469998656372210
No 7
>PF01215 COX5B: Cytochrome c oxidase subunit Vb This family consists of chains F and S ; InterPro: IPR002124 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. One of these subunits is known as Vb in mammals, V in Dictyostelium discoideum (Slime mold) and IV in yeast, binds a zinc atom. The sequence of subunit Vb is well conserved and includes three conserved cysteines that coordinate the zinc ion , . Two of these cysteines are clustered in the C-terminal section of the subunit.; GO: 0004129 cytochrome-c oxidase activity, 0006118 electron transport, 0005740 mitochondrial envelope; PDB: 2odx_A 2eil_F 2eij_F 1v55_S 2ein_F 2zxw_F 1occ_F 1ocr_F 2dys_F 2eim_S ....
Probab=11.45 E-value=15 Score=12.83 Aligned_cols=22 Identities=18% Similarity=0.206 Sum_probs=15.8
Q ss_pred CCCCCCCCCCEEECCHHHHHHH
Q ss_conf 1557887888687487999999
Q T0537 58 EKGNGTDSKPYMIMNATQIRNM 79 (381)
Q Consensus 58 ~~G~GT~~~PY~I~t~~~L~~l 79 (381)
.+-.||+++|.+|.+..+-+.+
T Consensus 38 ~~~~GT~e~P~lVpS~~~~RiV 59 (99)
T PF01215_consen 38 RGPFGTKEDPILVPSYFDERIV 59 (99)
T ss_dssp ------TSS-CEEEESSSCEEE
T ss_pred CCCCCCCCCCEEEECCCCCEEE
T ss_conf 4889985599782068897788
No 8
>PF06527 TniQ: TniQ; InterPro: IPR009492 This family consists of several bacterial TniQ proteins. TniQ along with TniA and B is involved in the transposition of the mercury-resistance transposon Tn5053 that carries the mer operon. It has been suggested that the tni genes are involved in the dissemination of integrons .
Probab=10.81 E-value=29 Score=11.14 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHCCCCCCCCC-CCCCCCC
Q ss_conf 255300122122057776877-5324656
Q T0537 8 RFGMLLMMASVAISCSDPNPL-DSYTRVP 35 (381)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~~~~-~~~~~~~ 35 (381)
-|++|+|-..+..+||+|--+ .+++.++
T Consensus 144 ~y~~l~WrLpl~t~Cp~H~c~Le~~~~~~ 172 (405)
T PF06527_consen 144 PYFRLYWRLPLMTSCPKHGCRLESYFGLP 172 (405)
T ss_pred HHHHHHHHHHHHHCCCCCCHHHHHHCCCC
T ss_conf 89999985157630664220154402788
No 9
>PF00295 Glyco_hydro_28: Glycosyl hydrolases family 28; InterPro: IPR000743 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families , , . This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site . Because the fold of proteins is better conserved than their sequences, some of the families can be grouped in 'clans'. Glycoside hydrolase family 28 GH28 from CAZY comprises enzymes with several known activities; polygalacturonase (3.2.1.15 from EC); exo-polygalacturonase (3.2.1.67 from EC); exo-polygalacturonase (3.2.1.82 from EC); rhamnogalacturonase (EC not defined). Polygalacturonase (PG) (pectinase) , catalyzes the random hydrolysis of 1,4-alpha-D-galactosiduronic linkages in pectate and other galacturonans. In fruit, polygalacturonase plays an important role in cell wall metabolism during ripening. In plant bacterial pathogens such as Erwinia carotovora or Ralstonia solanacearum (Pseudomonas solanacearum) and fungal pathogens such as Aspergillus niger, polygalacturonase is involved in maceration and soft-rotting of plant tissue. Exo-poly-alpha-D-galacturonosidase (3.2.1.82 from EC) (exoPG) hydrolyzes peptic acid from the non-reducing end, releasing digalacturonate. PG and exoPG share a few regions of sequence similarity, and belong to family 28 of the glycosyl hydrolases.; GO: 0004650 polygalacturonase activity, 0005975 carbohydrate metabolic process; PDB: 1bhe_A 2uvf_A 1czf_B 1nhc_C 1ia5_A 1ib4_B 2iq7_D 1kcd_A 1kcc_A 1k5c_A ....
Probab=9.61 E-value=32 Score=10.88 Aligned_cols=68 Identities=18% Similarity=0.112 Sum_probs=0.0
Q ss_pred EEEEEEECCCCCCEEEEEE---CCEEEEEEEEEEEEEECCCCCEEEEEEEECCEEEEEEECCEEEEEEEEE
Q ss_conf 8970274787753045887---1569995886107983133320456553011243332001799989741
Q T0537 126 VIKNFKCSAGDYPSFFGVL---CGDCRNVGFVNASVSSARQGIGIITGYLGLKDKGNGNKTGRIVNCYTTG 193 (381)
Q Consensus 126 tIsnL~i~~~~~~GLFG~i---~g~ikNl~i~n~~i~g~~~~~G~~~g~~~~~~~~~~~~~g~I~n~~~~g 193 (381)
+++|.++....+.=-|... +|.|+|++++|..+.......-+-..|..............|+|.....
T Consensus 207 ~v~n~~i~~t~~g~riKs~~g~~G~v~nI~f~ni~~~~v~~pi~i~~~y~~~~~~~~~~~~~~i~nI~~~n 277 (326)
T PF00295_consen 207 TVENCTIIGTDNGIRIKSWPGGGGTVENITFENITMENVSNPIIIDQNYCDGNPCGTPPSGVTISNITFEN 277 (326)
T ss_dssp EEEEEEEESCSECEEEEEETTTS-EEEEEEEEEEEEEEESESEEEEEEETT-SBTS-------EEEEEEEE
T ss_pred EEECCEEECCCEEEEEEEECCCCEEEEEEEEECEEECCCCEEEEEECCCCCCCCCCCCCCCCEEEEEEEEE
T ss_conf 99885682565699998871687779899996638857670499993135899988777787798799986
No 10
>PF02630 SCO1-SenC: SCO1/SenC; InterPro: IPR003782 This family is involved in biogenesis of respiratory and photosynthetic systems. In yeast the SCO1 protein is specifically required for a post-translational step in the accumulation of subunits 1 and 2 of cytochrome c oxidase (COXI and COX-II) . It is a mitochondrion-associated cytochrome c oxidase assembly factor. The purple nonsulphur photosynthetic eubacterium Rhodobacter capsulatus is a versatile organism that can obtain cellular energy by several means, including the capture of light energy for photosynthesis as well as the use of light-independent respiration, in which molecular oxygen serves as a terminal electron acceptor. The SENC protein is required for optimal cytochrome c oxidase activity in aerobically grown R. capsulatus cells and is involved in the induction of structural polypeptides of the light-harvesting and reaction centre complexes .; GO: 0006118 electron transport; PDB: 2b7k_B 2b7j_B 2ggt_B 2gt5_A 1wp0_B 2gqm_A 2hrf_A 2gvp_A 2gt6_A 2hrn_A ....
Probab=6.93 E-value=19 Score=12.13 Aligned_cols=18 Identities=28% Similarity=0.674 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHHHCCCCCCCC
Q ss_conf 025530012212205777687
Q T0537 7 GRFGMLLMMASVAISCSDPNP 27 (381)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~ 27 (381)
||+.++++.|| .|||+-|
T Consensus 52 Gk~~lv~F~yT---~CpdvCP 69 (174)
T PF02630_consen 52 GKWVLVFFGYT---SCPDVCP 69 (174)
T ss_dssp TSEEEEEEE-T---TSSSHHH
T ss_pred CCEEEEEEEEC---CCCCCCH
T ss_conf 98899999827---9887588
Done!