Query T0563 NP_718175.1, Shewanella oneidensis MR-1, 279 residues Match_columns 279 No_of_seqs 137 out of 2114 Neff 8.4 Searched_HMMs 11830 Date Wed May 26 17:52:09 2010 Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0563.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0563.hhr No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM 1 PF03171 2OG-FeII_Oxy: 2OG-Fe( 99.7 1.5E-17 1.2E-21 132.7 8.7 93 149-253 2-96 (96) 2 PF07350 DUF1479: Protein of u 71.8 2 0.00017 19.6 4.0 49 3-52 50-101 (415) 3 PF03668 ATP_bind_2: P-loop AT 60.1 3.9 0.00033 17.6 3.7 46 199-244 210-255 (284) 4 PF06560 GPI: Glucose-6-phosph 32.5 8.6 0.00073 15.4 1.8 20 197-216 117-136 (182) 5 PF02678 Pirin: Pirin; InterP 31.6 11 0.00095 14.6 5.2 20 165-184 39-58 (107) 6 PF11243 DUF3045: Protein of u 19.4 19 0.0016 13.1 2.3 21 15-35 36-56 (89) 7 PF10055 DUF2292: Uncharacteri 16.3 22 0.0019 12.6 1.8 19 174-193 13-31 (38) 8 PF10547 P22_AR_N: P22_AR N-te 15.6 23 0.0019 12.5 3.5 70 192-261 15-85 (120) 9 PF06742 DUF1214: Protein of u 15.3 23 0.002 12.5 2.1 30 174-207 45-74 (87) 10 PF09508 Lact_bio_phlase: Lact 15.1 7.4 0.00063 15.8 -1.4 17 209-225 500-516 (716) 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=99.71 E-value=1.5e-17 Score=132.70 Aligned_cols=93 Identities=39% Similarity=0.651 Sum_probs=83.4 Q ss_pred CEEEEECCCCCCCCCCCCCEEEEEEECC--EEEEEEEECCCCCEEEEECCCCEEEEECCCCCEEEEHHHHHHHHHCCEEC Q ss_conf 0455502665566645452345331176--07899852687740688238816874238982487166899998589020 Q T0563 149 TLLRILHYPPMTGDEEMGAIRAAAHEDI--NLITVLPTANEPGLQVKAKDGSWLDVPSDFGNIIINIGDMLQEASDGYFP 226 (279) Q Consensus 149 ~~lRl~~Yp~~~~~~~~~~~~~~~HtD~--g~lTlL~qd~~~GLqv~~~~g~W~~V~p~~~~lvVn~Gd~l~~~TnG~~~ 226 (279) ..+++++|+ ..+.++++|+|. +++|+++|+..+|||+...+ +|+.+++.|++++|+.|++|++||||.++ T Consensus 2 ~~~~v~~Y~-------~~~~~~~~H~D~~~~~~T~l~~~~~~~l~~~~~~-~~~~~~~~~~~~~v~~g~~l~~~t~~~~~ 73 (96) T PF03171_consen 2 NHMRVNRYP-------DPGQGIGPHTDNSQRIITVLLQDSGGGLQFRPDD-EWVDVPPDPGSLVVNFGSALQIMTGGRYP 73 (96) T ss_dssp -EEEEEEEE-------CGCEEEEEEESSSESCEEEEEETSSEEEEEEECC-TEEECEE-TCEEEEEEECHHHHHTTTHCC T ss_pred CEEEEEECC-------CCCCEEECCCCCCCCEEEEEECCCCCCEEEECCC-CCCCCCCCCCCEEEECCEEEECCCCCCCC T ss_conf 689999879-------9998087689899980999976675660343047-30320546881223022132024798859 Q ss_pred CCCCEEECCCCCCCCCCCEEEEEEECC Q ss_conf 662236436666667762578985248 Q T0563 227 STSHRVINPEGTDKTKSRISLPLFLHP 253 (279) Q Consensus 227 s~~HRVv~p~~~~~~~~R~S~~~F~~P 253 (279) ++.|||+.+. ...|+|++||++| T Consensus 74 ~~~H~V~~~~----~~~R~sl~~~~~p 96 (96) T PF03171_consen 74 SWLHRVRPVT----RGERISLTFFLRP 96 (96) T ss_dssp CEEEEEEEES----CS-EEEEEEEEE- T ss_pred CCEEECCCCC----CCCEEEEEEEECC T ss_conf 6464886489----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=71.82 E-value=2 Score=19.58 Aligned_cols=49 Identities=14% Similarity=0.273 Sum_probs=39.5 Q ss_pred CCCCCCCCHH---HHHHHHHHHHHCCEEEEECCCCCHHHHHHHHHHHHHHHCC Q ss_conf 7710477789---9999999987388389973698989999999999986157 Q T0563 3 LETIDYRAAD---SAKRFVESLRETGFGVLSNHPIDKELVERIYTEWQAFFNS 52 (279) Q Consensus 3 ip~iDl~~~~---~~~~l~~A~~~~GFF~l~NHGI~~~~i~~~~~~~~~fF~l 52 (279) ||.||+++.. ..+...+..++-|+..|.|+ ||.+...+.......|.+. T Consensus 50 IP~i~f~di~~~~v~~~~~~~ir~rG~~VIRgV-vp~~~A~~w~~ei~~Y~~~ 101 (415) T PF07350_consen 50 IPEIDFSDIKNGTVSEEQRAEIRRRGCAVIRGV-VPREQALAWKQEIVDYLSA 101 (415) T ss_dssp S-EEEHHHHH-----HHHHHHHHH---EEEE-----HHHHHHHHHHHHHHHHH T ss_pred CCEEEHHHHHCCCCCHHHHHHHHHCCEEEECCC-CCHHHHHHHHHHHHHHHHH T ss_conf 714448995468989999999986287998376-9999999999999999985 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=60.13 E-value=3.9 Score=17.64 Aligned_cols=46 Identities=13% Similarity=0.087 Sum_probs=30.1 Q ss_pred EEEEECCCCCEEEEHHHHHHHHHCCEECCCCCEEECCCCCCCCCCC Q ss_conf 6874238982487166899998589020662236436666667762 Q T0563 199 WLDVPSDFGNIIINIGDMLQEASDGYFPSTSHRVINPEGTDKTKSR 244 (279) Q Consensus 199 W~~V~p~~~~lvVn~Gd~l~~~TnG~~~s~~HRVv~p~~~~~~~~R 244 (279) |+.-.|....++-.+-++++.|=..+.+...+.+...=+..+.+.| T Consensus 210 yv~~~~~~~~f~~~~~~~l~~~lp~y~~egk~~ltIaIGCTGGqHR 255 (284) T PF03668_consen 210 YVLSFPEAQEFLDKIEDLLDFLLPRYEKEGKSYLTIAIGCTGGQHR 255 (284) T ss_pred HHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCH T ss_conf 9976925999999999999999998997598479999726999701 No 4 >PF06560 GPI: Glucose-6-phosphate isomerase (GPI); InterPro: IPR010551 This family consists of several bacterial and archaeal glucose-6-phosphate isomerase (GPI) proteins (5.3.1.9 from EC), which are involved in glycolysis and in gluconeogenesis and catalyse the conversion of D-glucose 6-phosphate to D-fructose 6-phosphate. The deduced amino acid sequence of the first archaeal PGI isolated from Pyrococcus furiosus revealed that it is not related to its eukaryotic and many of its bacterial counterparts. In contrast, this archaeal PGI shares similarity with the cupin superfamily that consists of a variety of proteins that are generally involved in sugar metabolism in both prokaryotes and eukaryotes .; GO: 0004347 glucose-6-phosphate isomerase activity, 0006094 gluconeogenesis, 0006096 glycolysis, 0005737 cytoplasm; PDB: 1j3q_A 1j3p_B 1j3r_B 1qxj_B 2gc1_B 1x8e_A 2gc2_B 1qy4_A 1qxr_A 2gc0_B .... Probab=32.48 E-value=8.6 Score=15.35 Aligned_cols=20 Identities=30% Similarity=0.584 Sum_probs=8.8 Q ss_pred CCEEEEECCCCCEEEEHHHH Q ss_conf 81687423898248716689 Q T0563 197 GSWLDVPSDFGNIIINIGDM 216 (279) Q Consensus 197 g~W~~V~p~~~~lvVn~Gd~ 216 (279) |.-+.|||--++.+||+||. T Consensus 117 G~~v~IPp~~~H~tiN~g~~ 136 (182) T PF06560_consen 117 GDVVYIPPGYAHRTINTGDE 136 (182) T ss_dssp --EEEE-TT-EEE-B----- T ss_pred CCEEEECCCCEEEEECCCCC T ss_conf 96899699924998718998 No 5 >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=31.61 E-value=11 Score=14.58 Aligned_cols=20 Identities=10% Similarity=0.210 Sum_probs=16.8 Q ss_pred CCCEEEEEEECCEEEEEEEE Q ss_conf 45234533117607899852 Q T0563 165 MGAIRAAAHEDINLITVLPT 184 (279) Q Consensus 165 ~~~~~~~~HtD~g~lTlL~q 184 (279) ..+++.-+|.++.++|++++ T Consensus 39 ~~gf~~HPHrg~eivTyvl~ 58 (107) T PF02678_consen 39 GAGFPPHPHRGFEIVTYVLE 58 (107) T ss_dssp --EEEEEE-CSEEEEEEEEE T ss_pred CCCCCCCCCCCEEEEEEECC T ss_conf 67788888899889999717 No 6 >PF11243 DUF3045: Protein of unknown function (DUF3045) Probab=19.37 E-value=19 Score=13.10 Aligned_cols=21 Identities=19% Similarity=0.202 Sum_probs=15.4 Q ss_pred HHHHHHHHHCCEEEEECCCCC Q ss_conf 999999873883899736989 Q T0563 15 KRFVESLRETGFGVLSNHPID 35 (279) Q Consensus 15 ~~l~~A~~~~GFF~l~NHGI~ 35 (279) +++-..|-+.||.||..|-|. T Consensus 36 e~IFk~CVeqGFiYv~ey~~~ 56 (89) T PF11243_consen 36 EDIFKQCVEQGFIYVSEYWMQ 56 (89) T ss_pred HHHHHHHHHCCEEEEEHHHHC T ss_conf 899999997053885541423 No 7 >PF10055 DUF2292: Uncharacterized small protein (DUF2292) Probab=16.31 E-value=22 Score=12.63 Aligned_cols=19 Identities=11% Similarity=0.109 Sum_probs=12.9 Q ss_pred ECCEEEEEEEECCCCCEEEE Q ss_conf 17607899852687740688 Q T0563 174 EDINLITVLPTANEPGLQVK 193 (279) Q Consensus 174 tD~g~lTlL~qd~~~GLqv~ 193 (279) -++|++|+..||+. =.|+. T Consensus 13 l~yGsvti~vqdg~-VvQIe 31 (38) T PF10055_consen 13 LRYGSVTITVQDGR-VVQIE 31 (38) T ss_pred CCCCEEEEEEECCE-EEEEE T ss_conf 85035999999899-99998 No 8 >PF10547 P22_AR_N: P22_AR N-terminal domain Probab=15.62 E-value=23 Score=12.52 Aligned_cols=70 Identities=14% Similarity=0.190 Sum_probs=43.2 Q ss_pred EEECCC-CEEEEECCCCCEEEEHHHHHHHHHCCEECCCCCEEECCCCCCCCCCCEEEEEEECCCCCCEECC Q ss_conf 882388-1687423898248716689999858902066223643666666776257898524899876747 Q T0563 192 VKAKDG-SWLDVPSDFGNIIINIGDMLQEASDGYFPSTSHRVINPEGTDKTKSRISLPLFLHPHPSVVLSE 261 (279) Q Consensus 192 v~~~~g-~W~~V~p~~~~lvVn~Gd~l~~~TnG~~~s~~HRVv~p~~~~~~~~R~S~~~F~~P~~d~vi~~ 261 (279) +...+| -|+.+.|+-+++=+.-.-+.+.+-+.++.++..+....+.....++.+.++.-.-|..=+.|.| T Consensus 15 ~~~~~g~~yvamkpI~e~lGL~w~~Q~~KL~~~~~~~~~~~~~~v~~dGk~~~mlcl~l~~l~~WL~~I~p 85 (120) T PF10547_consen 15 VVEHNGEPYVAMKPICEALGLDWASQFKKLKKDKFLSTGVEITIVPSDGKQREMLCLPLRKLPGWLASINP 85 (120) T ss_pred EEEECCEEEEECHHHHHHCCCCHHHHHHHHHCCCCCCCEEEEEEECCCCCCEEEEEEEHHHHHHHHHHCCH T ss_conf 99679908986179898729986999999734612035179997657887116999768888999865895 No 9 >PF06742 DUF1214: Protein of unknown function (DUF1214); InterPro: IPR010621 This entry represents the C-terminal region of several hypothetical proteins of unknown function. Proteins in this entry are mostly bacterial, but a few are also found in eukaryotes and archaea.; PDB: 2p3y_A. Probab=15.32 E-value=23 Score=12.47 Aligned_cols=30 Identities=20% Similarity=0.449 Sum_probs=19.4 Q ss_pred ECCEEEEEEEECCCCCEEEEECCCCEEEEECCCC Q ss_conf 1760789985268774068823881687423898 Q T0563 174 EDINLITVLPTANEPGLQVKAKDGSWLDVPSDFG 207 (279) Q Consensus 174 tD~g~lTlL~qd~~~GLqv~~~~g~W~~V~p~~~ 207 (279) .+-|.+||.++...+ ....+.|++++...+ T Consensus 45 n~DGs~tI~~~~~~p----~~~~~NWLpt~~~~~ 74 (87) T PF06742_consen 45 NADGSVTIYFSPEPP----AGPEGNWLPTPGGGN 74 (87) T ss_dssp -----EEEEE------------TTSB-------- T ss_pred CCCCCEEEEECCCCC----CCCCCCCEECCCCCC T ss_conf 999849999817899----988675284799998 No 10 >PF09508 Lact_bio_phlase: Lacto-N-biose phosphorylase; PDB: 2zut_A 2zus_C 2zuu_C 2zuw_C 2zuv_A. Probab=15.06 E-value=7.4 Score=15.76 Aligned_cols=17 Identities=41% Similarity=0.575 Sum_probs=0.0 Q ss_pred EEEEHHHHHHHHHCCEE Q ss_conf 48716689999858902 Q T0563 209 IIINIGDMLQEASDGYF 225 (279) Q Consensus 209 lvVn~Gd~l~~~TnG~~ 225 (279) +|||+||+-..||+|.+ 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 Done!