Query T0564 SlR115, , 89 residues
Match_columns 89
No_of_seqs 91 out of 93
Neff 4.7
Searched_HMMs 11830
Date Tue Jun 1 15:08:37 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0564.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0564.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF10694 DUF2500: Protein of u 100.0 6.8E-31 5.7E-35 179.7 9.9 80 1-83 31-110 (110)
2 PF03539 Spuma_A9PTase: Spumav 37.5 6.7 0.00056 17.2 1.9 33 34-68 43-77 (163)
3 PF01071 GARS_A: Phosphoribosy 27.3 15 0.0012 15.4 2.3 35 38-72 92-126 (194)
4 PF07563 DUF1541: Protein of u 24.6 19 0.0016 14.9 2.7 22 31-52 25-46 (53)
5 PF09831 DUF2058: Uncharacteri 17.9 27 0.0023 14.1 4.1 41 39-79 92-132 (177)
6 PF11385 DUF3189: Protein of u 17.5 8.6 0.00073 16.7 -0.6 31 46-76 27-57 (148)
7 PF04597 Ribophorin_I: Ribopho 16.1 30 0.0025 13.8 5.4 71 7-79 52-130 (432)
8 PF07116 DUF1372: Protein of u 15.5 25 0.0021 14.3 1.4 28 36-68 70-97 (104)
9 PF03459 TOBE: TOBE domain; I 9.3 49 0.0042 12.7 3.6 40 37-77 20-61 (64)
10 PF11025 GP40: Glycoprotein GP 7.7 58 0.0049 12.3 3.9 23 36-59 111-133 (165)
No 1
>PF10694 DUF2500: Protein of unknown function (DUF2500)
Probab=99.97 E-value=6.8e-31 Score=179.66 Aligned_cols=80 Identities=43% Similarity=0.703 Sum_probs=75.6
Q ss_pred CCCCEEEEEEEECCCCEECCCCCCCCCCCCCCCCCEEEEEEEEECCCCCEEEEEECHHHCCCCCCCCEEEEEECCEEEEE
Q ss_conf 98721356898634212247743222564358765489988887489966899916578176387877899853137875
Q T0564 1 MAPLQQKQVVVSNKREKPVNDRRSRQQEVSPAGTSMRYEASFKPLNGGLEKTFRLQAQQYHALTVGDQGTLSYKGTRFVG 80 (89)
Q Consensus 1 ~aP~~sv~v~Vv~KR~~~~~~~rsrq~~~~~~~~~~~Y~vtF~p~~~G~~~ef~v~~~~Y~~l~~Gd~G~L~~QGtrfi~ 80 (89)
.||+++++|+|+|||+++++++|++++++ ++ ++++|||||| .++|+++||+|++++||+|++||+|+|+||||||++
T Consensus 31 ~aP~~~~~v~Vv~Kr~~~~~~~~~~~~~~-~~-~~~~YyitF~-~~~G~~~ef~V~~~~Y~~l~eGd~G~Lt~QGtrf~~ 107 (110)
T PF10694_consen 31 NAPRLSVPVTVVDKREEVSPNRRSRERDV-GA-ESTRYYITFE-FESGGRIEFRVSGHEYGQLAEGDKGTLTYQGTRFLG 107 (110)
T ss_pred CCCCEEEEEEEEEEEEEECCCCCCCCCCC-CC-CCEEEEEEEE-ECCCCEEEEEECHHHHCCCCCCCEEEEEECCCEEEE
T ss_conf 79837888999976678858986678745-77-4069999999-678977999989899577899988889983678855
Q ss_pred ECC
Q ss_conf 403
Q T0564 81 FVS 83 (89)
Q Consensus 81 Fe~ 83 (89)
|++
T Consensus 108 F~r 110 (110)
T PF10694_consen 108 FER 110 (110)
T ss_pred EEC
T ss_conf 339
No 2
>PF03539 Spuma_A9PTase: Spumavirus aspartic protease (A9); InterPro: IPR001641 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. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised . More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin and archaean preflagellin have been described , . Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localized between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This group of aspartic peptidases belong to MEROPS peptidase family A9 (spumapepsin family, clan AA). Foamy viruses are single-stranded enveloped retroviruses that have been noted to infect monkeys, cats and humans. In the human virus, the aspartic protease is encoded by the retroviral gag gene , and in monkeys by the pol gene . At present, the virus has not been proven to cause any particular disease. However, studies have shown Human foamy virus causes neurological disorders in infected mice . It is not clear whether the Foamy virus/spumavirus proteases share a common evolutionary origin with other aspartic proteases. ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis; PDB: 2jys_A.
Probab=37.52 E-value=6.7 Score=17.24 Aligned_cols=33 Identities=21% Similarity=0.285 Sum_probs=24.0
Q ss_pred CCEEEEEEEEECCCCCEEEEEE--CHHHCCCCCCCCE
Q ss_conf 6548998888748996689991--6578176387877
Q T0564 34 TSMRYEASFKPLNGGLEKTFRL--QAQQYHALTVGDQ 68 (89)
Q Consensus 34 ~~~~Y~vtF~p~~~G~~~ef~v--~~~~Y~~l~~Gd~ 68 (89)
...-||++|. +. |-+++-.| +.-+|-.|+++|.
T Consensus 43 ~q~vYYl~fK-i~-gRkv~aEVi~s~~dYill~P~Di 77 (163)
T PF03539_consen 43 EQDVYYLTFK-IQ-GRKVEAEVIASPLDYILLAPSDI 77 (163)
T ss_dssp EEEEEEEEEE-E----EEEEEEEEESSSSEEE-TTT-
T ss_pred CCCEEEEEEE-EC-CEEEEEEEECCCCCEEEECCCCC
T ss_conf 1536999999-85-64877789515330799757676
No 3
>PF01071 GARS_A: Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain; InterPro: IPR000115 Phosphoribosylglycinamide synthetase (6.3.4.13 from EC) (GARS) (phosphoribosylamine glycine ligase) catalyzes the second step in the de novo biosynthesis of purine: ATP + 5-phosphoribosylamine + glycine = ADP + P_i + 5'-phosphoribosylglycinamide In bacteria, GARS is a monofunctional enzyme (encoded by the purD gene). In yeast, GARS is part of a bifunctional enzyme (encoded by the ADE5/7 gene) in conjunction with phosphoribosylformylglycinamidine cyclo-ligase (AIRS) (IPR000728 from INTERPRO). In higher eukaryotes, GARS is part of a trifunctional enzyme in conjunction with AIRS (IPR000728 from INTERPRO) and with phosphoribosylglycinamide formyltransferase (GART) (), forming GARS-AIRS-GART.; GO: 0004637 phosphoribosylamine-glycine ligase activity, 0009113 purine base biosynthetic process; PDB: 2yw2_B 2yya_A 1gso_A 2ip4_B 2qk4_A 2ys6_A 2yrw_A 2ys7_A 2yrx_A 1vkz_B ....
Probab=27.34 E-value=15 Score=15.44 Aligned_cols=35 Identities=23% Similarity=0.078 Sum_probs=29.2
Q ss_pred EEEEEEECCCCCEEEEEECHHHCCCCCCCCEEEEE
Q ss_conf 99888874899668999165781763878778998
Q T0564 38 YEASFKPLNGGLEKTFRLQAQQYHALTVGDQGTLS 72 (89)
Q Consensus 38 Y~vtF~p~~~G~~~ef~v~~~~Y~~l~~Gd~G~L~ 72 (89)
.|+++.-+.+|..+......++|..+-+||+|--|
T Consensus 92 ~E~Sv~a~~dG~~~~~l~~~qd~Kr~~dgd~GpnT 126 (194)
T PF01071_consen 92 EEVSVFAFVDGKTIVPLPPAQDHKRAFDGDTGPNT 126 (194)
T ss_dssp -EEEEEEEE----EEEEEEBB---EEETTTE-EE-
T ss_pred CEEEEEEEECCCEEEECCCCCCCCCCCCCCCCCCC
T ss_conf 37899999879979974230236666689999877
No 4
>PF07563 DUF1541: Protein of unknown function (DUF1541); InterPro: IPR011438 This domain is found in several hypothetical bacterial proteins as a tandem repeat.
Probab=24.60 E-value=19 Score=14.86 Aligned_cols=22 Identities=27% Similarity=0.403 Sum_probs=17.9
Q ss_pred CCCCCEEEEEEEEECCCCCEEE
Q ss_conf 5876548998888748996689
Q T0564 31 PAGTSMRYEASFKPLNGGLEKT 52 (89)
Q Consensus 31 ~~~~~~~Y~vtF~p~~~G~~~e 52 (89)
.+...+-|-|.|.|.++|++++
T Consensus 25 ~a~~tTvY~V~ytpt~gg~~V~ 46 (53)
T PF07563_consen 25 GAYDTTVYMVDYTPTTGGEEVK 46 (53)
T ss_pred EEEEEEEEEEEEEECCCCCEEE
T ss_conf 3234379999868779994803
No 5
>PF09831 DUF2058: Uncharacterized protein conserved in bacteria (DUF2058)
Probab=17.91 E-value=27 Score=14.09 Aligned_cols=41 Identities=12% Similarity=0.174 Sum_probs=33.3
Q ss_pred EEEEEECCCCCEEEEEECHHHCCCCCCCCEEEEEECCEEEE
Q ss_conf 98888748996689991657817638787789985313787
Q T0564 39 EASFKPLNGGLEKTFRLQAQQYHALTVGDQGTLSYKGTRFV 79 (89)
Q Consensus 39 ~vtF~p~~~G~~~ef~v~~~~Y~~l~~Gd~G~L~~QGtrfi 79 (89)
+|.|....++....+-|+......|..|--|+..+.|.-+|
T Consensus 92 di~ynFtd~~kIK~iyV~~~~q~qL~~G~LaIv~l~~~y~l 132 (177)
T PF09831_consen 92 DIAYNFTDGNKIKKIYVTEKQQKQLSNGRLAIVRLEDGYEL 132 (177)
T ss_pred CEEEECCCCCEEEEEEECHHHHHHHHCCEEEEEEECCEEEE
T ss_conf 60576477999889987999999985587899998899899
No 6
>PF11385 DUF3189: Protein of unknown function (DUF3189)
Probab=17.46 E-value=8.6 Score=16.65 Aligned_cols=31 Identities=26% Similarity=0.290 Sum_probs=22.9
Q ss_pred CCCCEEEEEECHHHCCCCCCCCEEEEEECCE
Q ss_conf 8996689991657817638787789985313
Q T0564 46 NGGLEKTFRLQAQQYHALTVGDQGTLSYKGT 76 (89)
Q Consensus 46 ~~G~~~ef~v~~~~Y~~l~~Gd~G~L~~QGt 76 (89)
+..+..|-..+-..|..+..+|.|.|.|-|+
T Consensus 27 ~r~p~~eel~~lp~fd~~~~~~~G~l~y~G~ 57 (148)
T PF11385_consen 27 DRIPTKEELLKLPYFDKLSQEDIGKLIYMGK 57 (148)
T ss_pred CCCCCHHHHHCCHHHHCCCCCCCCEEEEEEE
T ss_conf 6688999984871542467677633899767
No 7
>PF04597 Ribophorin_I: Ribophorin I; InterPro: IPR007676 Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (2.4.1.119 from EC). OST catalyses the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are thought to be responsible for OST catalytic activity . Both yeast and mammalian proteins are glycosylated but the sites are not conserved. Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function . Most family members are predicted to have a transmembrane helix at the C terminus of this region.; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0006486 protein amino acid glycosylation, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=16.10 E-value=30 Score=13.84 Aligned_cols=71 Identities=23% Similarity=0.348 Sum_probs=45.3
Q ss_pred EEEEEECCCCEECCCCCCCCCCCCCCCCCEEEEEEEE-ECCCCCEEEEEECHHHCCC-------CCCCCEEEEEECCEEE
Q ss_conf 5689863421224774322256435876548998888-7489966899916578176-------3878778998531378
Q T0564 7 KQVVVSNKREKPVNDRRSRQQEVSPAGTSMRYEASFK-PLNGGLEKTFRLQAQQYHA-------LTVGDQGTLSYKGTRF 78 (89)
Q Consensus 7 v~v~Vv~KR~~~~~~~rsrq~~~~~~~~~~~Y~vtF~-p~~~G~~~ef~v~~~~Y~~-------l~~Gd~G~L~~QGtrf 78 (89)
+.|...++...... .....++........|.|+|. |+..|+...+.|....-+. +..+|+=.|.|+|+.|
T Consensus 52 ~~a~~~~~~~~~~~--~~~~~~~~~~~~~~~~~i~Lp~pl~p~~~~tl~v~y~~~~~l~P~P~~I~q~e~Q~v~y~~~~~ 129 (432)
T PF04597_consen 52 LSAKDKDKKEKGKF--SVEPEEVEEGSNNQYYEITLPKPLAPGEKVTLEVEYVLTHALEPLPAEISQGEKQLVLYTGNAY 129 (432)
T ss_pred EEEEECCCCCCCCC--CCCCCCCCCCCCCCEEEEECCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCCCCEEEEEECCCE
T ss_conf 99998887533433--3111003677776069999488889887389999999856542568242678824999971603
Q ss_pred E
Q ss_conf 7
Q T0564 79 V 79 (89)
Q Consensus 79 i 79 (89)
.
T Consensus 130 ~ 130 (432)
T PF04597_consen 130 P 130 (432)
T ss_pred E
T ss_conf 1
No 8
>PF07116 DUF1372: Protein of unknown function (DUF1372); InterPro: IPR010779 This family consists of several Streptococcus bacteriophage sequences and related proteins from Streptococcus species. Members of this family are typically around 100 residues in length and their function is unknown.
Probab=15.46 E-value=25 Score=14.26 Aligned_cols=28 Identities=25% Similarity=0.447 Sum_probs=22.9
Q ss_pred EEEEEEEEECCCCCEEEEEECHHHCCCCCCCCE
Q ss_conf 489988887489966899916578176387877
Q T0564 36 MRYEASFKPLNGGLEKTFRLQAQQYHALTVGDQ 68 (89)
Q Consensus 36 ~~Y~vtF~p~~~G~~~ef~v~~~~Y~~l~~Gd~ 68 (89)
-+|.|+-+ .-=+|-|+..+|+.+..||.
T Consensus 70 ~lYTvt~~-----~YGkFlVTkeqY~~ikVGDd 97 (104)
T PF07116_consen 70 GLYTVTAR-----AYGKFLVTKEQYESIKVGDD 97 (104)
T ss_pred CEEEEEEC-----CCEEEEEEHHHHCCEECCCC
T ss_conf 68999964-----66169975666101403785
No 9
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1h9s_A 1o7l_B 1b9n_A 1b9m_B 1h9r_B 1h9k_A 1h9m_B 1h9j_A 1gun_F 1gut_D ....
Probab=9.33 E-value=49 Score=12.68 Aligned_cols=40 Identities=25% Similarity=0.330 Sum_probs=32.7
Q ss_pred EEEEEEEECCCCCEEEEEECHHHCCC--CCCCCEEEEEECCEE
Q ss_conf 89988887489966899916578176--387877899853137
Q T0564 37 RYEASFKPLNGGLEKTFRLQAQQYHA--LTVGDQGTLSYKGTR 77 (89)
Q Consensus 37 ~Y~vtF~p~~~G~~~ef~v~~~~Y~~--l~~Gd~G~L~~QGtr 77 (89)
..+|++. +.+|..+.-.++...... |.+|++=.+.++-.+
T Consensus 20 ~~~v~l~-~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik~~~ 61 (64)
T PF03459_consen 20 ETEVTLD-LGGGETLTARITPESAERLGLKPGDEVFAQIKASS 61 (64)
T ss_dssp EEEEEEE-----EEEEEEEEHHHHHHCT-----EEEEEE-GGG
T ss_pred CEEEEEE-ECCCCEEEEEECHHHHHHCCCCCCCEEEEEEEHHH
T ss_conf 1999999-89999999998889997738999999999994565
No 10
>PF11025 GP40: Glycoprotein GP40 of Cryptosporidium
Probab=7.75 E-value=58 Score=12.31 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=16.5
Q ss_pred EEEEEEEEECCCCCEEEEEECHHH
Q ss_conf 489988887489966899916578
Q T0564 36 MRYEASFKPLNGGLEKTFRLQAQQ 59 (89)
Q Consensus 36 ~~Y~vtF~p~~~G~~~ef~v~~~~ 59 (89)
+-.-.-|- |++|.+||..|+..+
T Consensus 111 tvdlfaft-L~GGkRiEvaVp~~~ 133 (165)
T PF11025_consen 111 TVDLFAFT-LDGGKRIEVAVPSSE 133 (165)
T ss_pred EEEEEEEE-CCCCCEEEEEECCCH
T ss_conf 78899986-068817889806614
Done!