Query T0573 NP_419019.1, CAULOBACTER CRESCENTUS, 311 residues Match_columns 311 No_of_seqs 130 out of 2009 Neff 8.1 Searched_HMMs 11830 Date Fri Jun 4 14:34:57 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0573.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0573.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF03171 2OG-FeII_Oxy: 2OG-Fe( 99.6 1.6E-16 1.4E-20 131.9 4.2 93 168-270 2-96 (96) 2 PF07350 DUF1479: Protein of u 73.1 2.4 0.0002 19.4 5.1 54 3-59 47-100 (415) 3 PF03668 ATP_bind_2: P-loop AT 45.1 7.1 0.0006 16.1 3.8 29 25-55 17-45 (284) 4 PF05559 DUF763: Protein of un 40.1 7.8 0.00066 15.8 2.6 16 23-38 72-89 (319) 5 PF08239 SH3_3: Bacterial SH3 24.6 15 0.0013 13.8 2.9 40 183-225 3-42 (52) 6 PF06874 FBPase_2: Firmicute f 22.8 16 0.0014 13.6 6.2 19 133-151 379-397 (640) 7 PF11243 DUF3045: Protein of u 22.3 17 0.0014 13.5 2.3 22 22-43 35-56 (89) 8 PF05410 Peptidase_C31: Porcin 20.4 13 0.0011 14.3 0.9 19 206-224 62-81 (105) 9 PF09508 Lact_bio_phlase: Lact 19.3 11 0.00096 14.7 0.4 17 226-242 500-516 (716) 10 PF02678 Pirin: Pirin; InterP 18.3 20 0.0017 13.0 1.4 46 174-219 25-83 (107) No 1 >PF03171 2OG-FeII_Oxy: 2OG-Fe(II) oxygenase superfamily Entry for Lysyl hydrolases This Prosite entry is a sub-family of the Pfam entry; InterPro: IPR005123 This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily . This family includes the C-terminal of prolyl 4-hydroxylase alpha subunit. The holoenzyme has the activity (1.14.11.2 from EC) catalysing the reaction:Procollagen L-proline + 2-oxoglutarate + O2 = procollagen trans-4-hydroxy-L-proline + succinate + CO2. The full enzyme consists of a alpha2 beta2 complex with the alpha subunit contributing most of the parts of the active site . The family also includes lysyl hydrolases, isopenicillin synthases and AlkB. ; PDB: 2brt_A 1gp5_A 1gp4_A 1gp6_A 1w28_A 1e5h_A 1unb_A 1e5i_A 1hjf_A 1dcs_A .... Probab=99.60 E-value=1.6e-16 Score=131.91 Aligned_cols=93 Identities=38% Similarity=0.627 Sum_probs=83.6 Q ss_pred HHHHHHHCCCCCCCHHCCCCCCCCCC--CEEEEEECCCCCCCEEEECCCCEEEEEECCCCEEEECHHHHHHCCCCEEECC Q ss_conf 01032203565763101775688886--4389984157786213523884588631797179871134533048865057 Q T0573 168 SVLRLLHYPPIPKDATGVRAGAHGDI--NTITLLLGAEEGGLEVLDRDGQWLPINPPPGCLVINIGDMLERLTNNVLPST 245 (311) Q Consensus 168 ~~lr~~~Yp~~~~~~~~~~~~~HtD~--g~lTll~qd~~~GLqv~~~~g~W~~V~p~~~~liVniGd~l~~~TnG~~ks~ 245 (311) ..+++++|+ +.+.++++|+|. +++|+++|++.+|||+...+ +|+.+++.|++++|+.|++|++||||.++++ T Consensus 2 ~~~~v~~Y~-----~~~~~~~~H~D~~~~~~T~l~~~~~~~l~~~~~~-~~~~~~~~~~~~~v~~g~~l~~~t~~~~~~~ 75 (96) T PF03171_consen 2 NHMRVNRYP-----DPGQGIGPHTDNSQRIITVLLQDSGGGLQFRPDD-EWVDVPPDPGSLVVNFGSALQIMTGGRYPSW 75 (96) T ss_dssp -EEEEEEEE-----CGCEEEEEEESSSESCEEEEEETSSEEEEEEECC-TEEECEE-TCEEEEEEECHHHHHTTTHCCCE T ss_pred CEEEEEECC-----CCCCEEECCCCCCCCEEEEEECCCCCCEEEECCC-CCCCCCCCCCCEEEECCEEEECCCCCCCCCC T ss_conf 689999879-----9998087689899980999976675660343047-3032054688122302213202479885964 Q ss_pred CCEEECCCCCCCCCCCEEEEEECCC Q ss_conf 2056327544357751488874268 Q T0573 246 VHRVVNPPPERRGVPRYSTPFFLHF 270 (311) Q Consensus 246 ~HRV~~p~~~~~~~~R~S~~~F~~p 270 (311) +|||+.+. ...|+|++||++| T Consensus 76 ~H~V~~~~----~~~R~sl~~~~~p 96 (96) T PF03171_consen 76 LHRVRPVT----RGERISLTFFLRP 96 (96) T ss_dssp EEEEEEES----CS-EEEEEEEEE- T ss_pred EEECCCCC----CCCEEEEEEEECC T ss_conf 64886489----9999999999696 No 2 >PF07350 DUF1479: Protein of unknown function (DUF1479); InterPro: IPR010856 This family consists of several hypothetical Enterobacterial proteins, of around 420 residues in length. Members of this family are often known as YbiU. The function of this family is unknown.; PDB: 2dbi_A 2dbn_A 2csg_A. Probab=73.13 E-value=2.4 Score=19.40 Aligned_cols=54 Identities=19% Similarity=0.250 Sum_probs=40.4 Q ss_pred CCCCCEEEHHHCCCCHHHHHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHHHHHHHC Q ss_conf 667880113114440799999999998738848997379898999999999999863 Q T0573 3 TSAIDPVSFSLYAKDFTRFAQELGASFERYGFAVLSDYDLDQARIDAAVDSAKAFFA 59 (311) Q Consensus 3 ~~~iP~IDls~~~~d~~~~~~~l~~A~~~~Gff~l~nHGI~~~li~~~~~~~~~fF~ 59 (311) ...||.||++...+. ++.++..+..++.||..|.|+ ||.+...+-....+++.+ T Consensus 47 ~~~IP~i~f~di~~~--~v~~~~~~~ir~rG~~VIRgV-vp~~~A~~w~~ei~~Y~~ 100 (415) T PF07350_consen 47 SDVIPEIDFSDIKNG--TVSEEQRAEIRRRGCAVIRGV-VPREQALAWKQEIVDYLS 100 (415) T ss_dssp --SS-EEEHHHHH-------HHHHHHHHH---EEEE-----HHHHHHHHHHHHHHHH T ss_pred CCCCCEEEHHHHHCC--CCCHHHHHHHHHCCEEEECCC-CCHHHHHHHHHHHHHHHH T ss_conf 998714448995468--989999999986287998376-999999999999999998 No 3 >PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This is a family of putative P-loop ATPases . Many of the proteins in this family are hypothetical and kinase activity has been proposed for some family members. This family contains an ATP-binding site and could be an ATPase. Probab=45.08 E-value=7.1 Score=16.06 Aligned_cols=29 Identities=10% Similarity=0.226 Sum_probs=24.6 Q ss_pred HHHHHHHCCEEEEECCCCCHHHHHHHHHHHH Q ss_conf 9999873884899737989899999999999 Q T0573 25 LGASFERYGFAVLSDYDLDQARIDAAVDSAK 55 (311) Q Consensus 25 l~~A~~~~Gff~l~nHGI~~~li~~~~~~~~ 55 (311) ..+|+++.|||+|-| +|..++..+.+... T Consensus 17 Al~~lED~GyycvDN--lP~~Ll~~l~~~~~ 45 (284) T PF03668_consen 17 ALRALEDLGYYCVDN--LPPSLLPQLIELLS 45 (284) T ss_pred HHHHHHCCCCEEECC--CCHHHHHHHHHHHH T ss_conf 999997079455648--88999999999986 No 4 >PF05559 DUF763: Protein of unknown function (DUF763); InterPro: IPR008482 This family consists of several uncharacterised bacterial and archaeal proteins of unknown function. Probab=40.09 E-value=7.8 Score=15.82 Aligned_cols=16 Identities=25% Similarity=0.335 Sum_probs=6.5 Q ss_pred HHHHHHH--HHCCEEEEE Q ss_conf 9999998--738848997 Q T0573 23 QELGASF--ERYGFAVLS 38 (311) Q Consensus 23 ~~l~~A~--~~~Gff~l~ 38 (311) -.|.+++ ++.|+..+= T Consensus 72 gaLKe~l~~~elGi~V~G 89 (319) T PF05559_consen 72 GALKEGLNSEELGIYVCG 89 (319) T ss_pred HHHHHHCCCCCCCEEEEC T ss_conf 999975374438669967 No 5 >PF08239 SH3_3: Bacterial SH3 domain; InterPro: IPR013247 A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins. Probab=24.60 E-value=15 Score=13.82 Aligned_cols=40 Identities=25% Similarity=0.392 Sum_probs=30.0 Q ss_pred HCCCCCCCCCCCEEEEEECCCCCCCEEEECCCCEEEEEECCCC Q ss_conf 0177568888643899841577862135238845886317971 Q T0573 183 TGVRAGAHGDINTITLLLGAEEGGLEVLDRDGQWLPINPPPGC 225 (311) Q Consensus 183 ~~~~~~~HtD~g~lTll~qd~~~GLqv~~~~g~W~~V~p~~~~ 225 (311) ..+|.+|-++...|+.|...+ -++|....+.|..|.. .|. T Consensus 3 lnvR~~p~~~s~ii~~l~~g~--~v~v~~~~~~W~~V~~-~g~ 42 (52) T PF08239_consen 3 LNVRSGPSTSSKIIGTLPKGT--RVTVLGESGGWYKVRY-NGK 42 (52) T ss_pred EEEECCCCCCCHHHEEECCCC--EEEEECCCCCEEEEEE-CCE T ss_conf 999489999984669993999--9999651296999998-999 No 6 >PF06874 FBPase_2: Firmicute fructose-1,6-bisphosphatase; InterPro: IPR009164 Fructose 1,6-bisphosphatase catalyses the hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate . This is an essential reaction in the process of gluconeogenesis, the process by which non-carbohydrate precursors are converted to glucose, and hence this enzyme is found almost universally. Enzyme activity can be regulated by a number of different mechanisms including AMP inhibition, cylic AMP-dependent phosphorylation and light-dependent-activation. This entry represents a group of fructose 1,6-bisphosphatases found within the Firmicutes (low GC Gram-positive bacteria) which do not show any significant sequence similarity to the enzymes from other organisms. The Bacillus subtilis enzyme is inhibited by AMP, though this can be overcome by phosphoenolpyruvate, and is dependent on Mn(2+) , . Mutants lacking this enzyme are apparently still able to grow on gluconeogenic growth substrates such as malate and glycerol. Probab=22.81 E-value=16 Score=13.59 Aligned_cols=19 Identities=0% Similarity=-0.062 Sum_probs=7.6 Q ss_pred HHHHHHHHHHHHHHHHHHH Q ss_conf 9999999999888999863 Q T0573 133 LYNSLDGMGGKVLEAIATY 151 (311) Q Consensus 133 y~~~~~~l~~~ll~~la~~ 151 (311) -+..+.+|...+-=+++.+ T Consensus 379 sF~~sekLqrH~~fL~~kG 397 (640) T PF06874_consen 379 SFQNSEKLQRHMRFLYSKG 397 (640) T ss_pred HHHCCHHHHHHHHHHHHCC T ss_conf 9863899999999999759 No 7 >PF11243 DUF3045: Protein of unknown function (DUF3045) Probab=22.26 E-value=17 Score=13.52 Aligned_cols=22 Identities=18% Similarity=0.338 Sum_probs=16.9 Q ss_pred HHHHHHHHHHCCEEEEECCCCC Q ss_conf 9999999873884899737989 Q T0573 22 AQELGASFERYGFAVLSDYDLD 43 (311) Q Consensus 22 ~~~l~~A~~~~Gff~l~nHGI~ 43 (311) -++|..-|-+.||.||..|-|. T Consensus 35 De~IFk~CVeqGFiYv~ey~~~ 56 (89) T PF11243_consen 35 DEDIFKQCVEQGFIYVSEYWMQ 56 (89) T ss_pred HHHHHHHHHHCCEEEEEHHHHC T ss_conf 1899999997053885541423 No 8 >PF05410 Peptidase_C31: Porcine arterivirus-type cysteine proteinase alpha; InterPro: IPR008741 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad . This group of cysteine peptidases corresponds to MEROPS peptidase family C31 (clan CA). Type example is porcine respiratory and reproductive syndrome arterivirus-type cysteine proteinase alpha (lactate-dehydrogenase-elevating virus), which is involved in viral polyprotein processing . Probab=20.39 E-value=13 Score=14.31 Aligned_cols=19 Identities=47% Similarity=1.095 Sum_probs=9.8 Q ss_pred CCEEEECCCCEEEEE-ECCC Q ss_conf 621352388458863-1797 Q T0573 206 GLEVLDRDGQWLPIN-PPPG 224 (311) Q Consensus 206 GLqv~~~~g~W~~V~-p~~~ 224 (311) -|||+.+.-+|.++. |+|| T Consensus 62 ~~qvyergcrwypitgpvpg 81 (105) T PF05410_consen 62 DLQVYERGCRWYPITGPVPG 81 (105) T ss_pred HHHHHHCCCCEEECCCCCCC T ss_conf 77776537733433478876 No 9 >PF09508 Lact_bio_phlase: Lacto-N-biose phosphorylase; PDB: 2zut_A 2zus_C 2zuu_C 2zuw_C 2zuv_A. Probab=19.35 E-value=11 Score=14.65 Aligned_cols=17 Identities=24% Similarity=0.389 Sum_probs=0.0 Q ss_pred EEEECHHHHHHCCCCEE Q ss_conf 79871134533048865 Q T0573 226 LVINIGDMLERLTNNVL 242 (311) Q Consensus 226 liVniGd~l~~~TnG~~ 242 (311) +|+|+||+-..||||.+ T Consensus 500 ViIN~G~a~TA~SGG~~ 516 (716) T PF09508_consen 500 VIINAGDAGTAFSGGEY 516 (716) T ss_dssp EEE----TTSST----G T ss_pred EEEECCCCCCCCCCCCC T ss_conf 89963665554567412 No 10 >PF02678 Pirin: Pirin; InterPro: IPR003829 This entry represents N-terminal domain of Pirin proteins from both eukaryotes and prokaryotes. The function of Pirin is unknown but the gene coding for this protein is known to be expressed in all tissues in the human body although it is expressed most strongly in the liver and heart. Pirin is known to be a nuclear protein, exclusively localised within the nucleoplasma and predominantly concentrated within dot-like subnuclear structures . Pirin is composed of two structurally similar domains arranged face to face. The N-terminal domain additionally features four beta-strands, and the C-terminal domain also includes four additional -strands and a short alpha-helix. Although the two domains are similar, the C-terminal domain of Pirin differs from the N-terminal domain as it does not contain a metal binding site and its sequence does not contain the conserved metal-coordinating residues . Pirin is confirmed to be a member of the cupin superfamily on the basis of primary sequence and structural similarity. The presence of a metal binding site in the N-terminal beta-barrel of Pirin, may be significant in its role in regulating NFI DNA replication and NF-kappaB transcription factor activity . Pirin structure has been found to closely resemble members of the cupin superfamily. Pirin contains the two characteristic sequences of the cupin superfamily, namely PG-(X)5-HXH-(X)4-E-(X)6-G and G-(X)5-PXG-(X)2-H-(X)3-N separated by a variable stretch of 15-50 amino acids. These motifs are best conserved in the N-terminal where the conserved histidine and glutamic acid residues correspond to the metal-coordinating residues. The C-terminal domain motifs lack the metal binding residues normally associated with the cupin fold . Pirin was identified to be a metal-binding protein , and was found that the metal-binding residues of Pirins are highly conserved across mammals, plants, fungi, and prokaryotic organisms. Pirin acts as a cofactor for the transcription factor NFI, the regulatory mechanism of which is generally believed to require the assistance of a metal ion . Structural data supports the hypothesis that the bound iron of Pirin may participate in this transcriptional regulation by enhancing and stabilizing the formation of the p50·Bcl-3·DNA complex . Metals have been implicated directly or indirectly in the NF-kappaB family of transcription factors that control expression of a number of early response genes associated with inflammatory responses, cell growth, cell cycle progression, and neoplastic transformation . However, most metal-dependent transcription factors are DNA-binding proteins that bind to specific sequences when the metal binds to the protein. Pirin, on the other hand, appears to function differently and bind to the transcription factor DNA complex . ; PDB: 1tq5_A 1j1l_A 2p17_A 2vec_A. Probab=18.25 E-value=20 Score=13.01 Aligned_cols=46 Identities=20% Similarity=0.419 Sum_probs=0.0 Q ss_pred HCCCCCCC------HHCCCCCCCCCCCEEEEE------ECCCCCCCEEEECCC-CEEEE Q ss_conf 03565763------101775688886438998------415778621352388-45886 Q T0573 174 HYPPIPKD------ATGVRAGAHGDINTITLL------LGAEEGGLEVLDRDG-QWLPI 219 (311) Q Consensus 174 ~Yp~~~~~------~~~~~~~~HtD~g~lTll------~qd~~~GLqv~~~~g-~W~~V 219 (311) ||.|.... ..+++.-||.++.++|++ +.|..+.-++....+ .|+.+ T Consensus 25 ~~~p~~~~~g~d~i~~gf~~HPHrg~eivTyvl~G~i~H~DS~G~~~~i~~G~vq~mtA 83 (107) T PF02678_consen 25 HFDPAHMHFGPDRIGAGFPPHPHRGFEIVTYVLEGEIEHRDSLGNHGVIRPGDVQWMTA 83 (107) T ss_dssp EEETCEE--TTEEE--EEEEEE-CSEEEEEEEEE--EEEEES---EEEE----EEEEE- T ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCEEEECCCCCCCEEECCCEEEEEEC T ss_conf 26854357763122677888888998899997178898613899956789980899858 Done!