Query T0589 3NET, Nostoc sp. PCC 7120, 465 residues
Match_columns 465
No_of_seqs 146 out of 4687
Neff 11.0
Searched_HMMs 11830
Date Mon Jul 5 09:45:45 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0589.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0589.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00587 tRNA-synt_2b: tRNA sy 99.9 9.5E-26 8E-30 188.4 14.3 163 28-203 1-169 (173)
2 PF03129 HGTP_anticodon: Antic 99.8 3E-18 2.5E-22 138.0 11.0 91 373-463 1-94 (94)
3 PF00152 tRNA-synt_2: tRNA syn 98.6 4E-07 3.4E-11 63.0 12.9 112 25-163 21-133 (323)
4 PF01409 tRNA-synt_2d: tRNA sy 98.1 1.6E-05 1.4E-09 52.1 10.4 119 23-153 13-135 (247)
5 PF03740 PdxJ: Pyridoxal phosp 45.3 5.5 0.00046 14.9 6.6 12 390-401 116-127 (239)
6 PF03853 YjeF_N: YjeF-related 29.0 9.8 0.00083 13.2 4.4 95 368-462 26-133 (173)
7 PF04430 DUF498: Protein of un 25.4 11 0.00095 12.8 1.4 50 371-421 53-102 (110)
8 PF01981 PTH2: Peptidyl-tRNA h 24.1 12 0.001 12.6 1.9 33 409-441 62-96 (116)
9 PF01520 Amidase_3: N-acetylmu 20.2 14 0.0012 12.1 6.4 18 27-44 24-41 (175)
10 PF08141 SspH: Small acid-solu 20.1 14 0.0012 12.1 2.6 35 421-457 22-57 (58)
No 1
>PF00587 tRNA-synt_2b: tRNA synthetase class II core domain (G, H, P, S and T) This Prosite entry contains all class II enzymes. seryl tRNA synthetase structure; InterPro: IPR002314 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . This domain includes the glycine, histidine, proline, threonine and serine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1sry_B 1ses_B 3err_A 1ser_A 1set_B 1wle_A 2i4o_A 2i4m_B 2i4l_C 2i4n_C ....
Probab=99.93 E-value=9.5e-26 Score=188.43 Aligned_cols=163 Identities=33% Similarity=0.462 Sum_probs=146.5
Q ss_pred HHHHHHHHHHHHHH-HCCCCEECCCCCCCHHHHHHCCCCCHHHHHHHHHCCHHHHHHHCCCCCCCCCCEEEECCCCHHHH
Q ss_conf 99999999999999-73992500654332677631156310234343320201112213554478885578547760999
Q T0589 28 LELYLLDTIRRVYE-SYGFTPIETPAVERLEVLQAKGNQGDNIIYGLEPILPPNRQAEKDKSGDTGSEARALKFDQTVPL 106 (465)
Q Consensus 28 ~~~~i~~~~~~~~~-~~G~~ei~~P~i~~~~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~~~~d~~g~~~~Lrpd~t~~~ 106 (465)
++++|++.|+++|. ++||++|.||+|++.++|+++|| .....++||++.|++|+.++||||+|+++
T Consensus 1 l~~~l~~~~~~~~~~~~G~~~v~tP~l~~~~~~~~~g~-------------~~~~~~~~~~~~d~~~~~~~Lrp~~t~~~ 67 (173)
T PF00587_consen 1 LRRALENFLRDVFVLKYGFQEVETPILEPYEVLEKSGH-------------WEKFPEEMYKFKDRGGEDLVLRPDSTPPI 67 (173)
T ss_dssp HHHHHHHHHHHHHHHHCT-EEEB--SEEEHHHHHHSCC-------------TTTTGGGSEEEETTTCSEEEE-SSSHHHH
T ss_pred CHHHHHHHHHHHHHHHCCCEEEECCEEEEHHHHHHCCC-------------CCCCCCEEEEECCCCCCEEEECCCCCCCH
T ss_conf 98999999999857866989999391988788745699-------------64244205897159975078644676300
Q ss_pred HHHHHHHHHH-C-CCCCCEEEECCCCCCC-C--CCCCCCCEEEEEEEEEEECCCHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf 9999998751-5-7745157752400266-7--77775300000000135257521789999999999999973998259
Q T0589 107 AAYIARHLND-L-TFPFARYQMDVVFRGE-R--AKDGRFRQFRQCDIDVVGREKLSLLYDAQMPAIITEIFEAVNIGDFV 181 (465)
Q Consensus 107 ~r~~~~~~~~-~-~~~~~~~~~g~~fR~~-~--~~~~r~ref~q~~~~~f~~~~~~~~~~~e~i~~~~e~~~~lgl~~~~ 181 (465)
+++++....+ + ..|+|+||+|++||+| . .|++|.|||+|.++++|+.++++...+++++.++.++++.||+.+++
T Consensus 68 ~~~~~~~~~~~~~~lP~r~~~~g~~fR~E~~~~~gl~R~rEF~q~~~~~~~~~~~~~~~~~e~~~~~~~~~~~lgl~~~~ 147 (173)
T PF00587_consen 68 ARLYANNLRSNYKDLPIRLYYIGKVFRYEAGPQRGLGRVREFTQAEIEIFGSPEQSEEADAELLELAIEFLKALGLEDFR 147 (173)
T ss_dssp HHHHHHHEEBTGGGSSEEEEEEEEEEBSSSSTBBTTTS-SEEEEEEEEEEESSHHHHHHHHHHHHHHHHHHHHTT-GSEE
T ss_pred HHHHHHHHHCCCCCCCEEEEECCCEECCCCCCCCCCCCEEEEEECCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEE
T ss_conf 34443200023446865787236215577776555673278998260999577521999999999999999985998679
Q ss_pred EEECCHHHHHHHHHHHCCCHHH
Q ss_conf 9972768899999872451037
Q T0589 182 IRINNRKVLTGFFQSLNISETQ 203 (465)
Q Consensus 182 ~~~~~~~~~~~~~~~~~~~~~~ 203 (465)
+.+++.+.+.+....++..+.|
T Consensus 148 i~~~~~~~~~~~~~~~~d~E~~ 169 (173)
T PF00587_consen 148 IRLNHRGELGAYAKYCGDIEAW 169 (173)
T ss_dssp EEEEETTTHHHHHHEEEEEEEE
T ss_pred EEECCCCCCCCCHHHCCCHHHH
T ss_conf 9995776567865643138996
No 2
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases it is probably the anticodon binding domain .; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006412 translation; PDB: 1nyq_B 1nyr_B 1h4q_B 1hc7_B 1h4t_C 1h4s_A 1nj5_A 1nj1_A 1nj2_A 1nj6_A ....
Probab=99.76 E-value=3e-18 Score=137.96 Aligned_cols=91 Identities=36% Similarity=0.553 Sum_probs=88.2
Q ss_pred EEEEEECCH---HHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHCCCCEEEEECHHHHHCCEEEEEECCCCCEE
Q ss_conf 289984687---89999999999998769859997289897789999996589799998602343882899985888658
Q T0589 373 QVVVVNMQD---ELMPTYLKVSQQLRQAGLNVITNFEKRQLGKQFQAADKQGIRFCVIIGADEAAAQKSSLKDLQSGEQV 449 (465)
Q Consensus 373 ~V~v~~~~~---~~~~~a~~i~~~Lr~~gi~v~~d~~~~sig~k~~~ad~~G~p~~i~ig~~~~~~~~vtir~r~t~~q~ 449 (465)
||+|+|+++ +..++|.+|++.||++||+|++|+++.++|+++++|+..|+||+|+||++++++|+|+||+|++++|.
T Consensus 1 qv~Vi~v~~~~~~~~~~a~~l~~~L~~~gi~v~~d~~~~~l~kk~~~a~~~g~p~~iiiG~~e~~~~~v~vr~~~~~~~~ 80 (94)
T PF03129_consen 1 QVVVIPVGDNDEELLEYAEKLAQKLRSAGIRVELDDRNKSLGKKIKYADKIGIPYVIIIGEKELENGTVTVRNRDTGEQE 80 (94)
T ss_dssp SEEEEESSSSHHHHHHHHHHHHHHHHTT-SEEEEESSSS-SHHHHHHHHHTTESEEEEE-HHHHHTTEEEEEESTTTBEE
T ss_pred CEEEEEECCCHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHCCCCEEEEECCHHHHCCEEEEEECCCCCEE
T ss_conf 99999968983999999999999998789989998899987799999998399899999984786898999999999589
Q ss_pred EECHHHHHHHHHHH
Q ss_conf 71489999999996
Q T0589 450 EVALADLAEEIKRR 463 (465)
Q Consensus 450 ~v~~~el~~~l~~~ 463 (465)
.|+++|++++|+++
T Consensus 81 ~v~~~el~~~l~~~ 94 (94)
T PF03129_consen 81 TVSIEELIEYLKEL 94 (94)
T ss_dssp EEETTCHHHHHHHH
T ss_pred EEEHHHHHHHHHHC
T ss_conf 98999999999739
No 3
>PF00152 tRNA-synt_2: tRNA synthetases class II (D, K and N) ; InterPro: IPR004364 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . This entry includes the asparagine, aspartic acid and lysine tRNA synthetases.; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 1eqr_C 1il2_A 1c0a_A 1efw_B 1g51_B 1l0w_B 1asy_B 1eov_A 1asz_A 1n9w_B ....
Probab=98.65 E-value=4e-07 Score=62.96 Aligned_cols=112 Identities=19% Similarity=0.229 Sum_probs=76.5
Q ss_pred HHHHHHHHHHHHHHHHHHCCCCEECCCCCCCHHHHHHCCCCCHHHHHHHHHCCHHHHHHHCCCCCCCCCCEEEECCCCHH
Q ss_conf 79999999999999999739925006543326776311563102343433202011122135544788855785477609
Q T0589 25 EKRLELYLLDTIRRVYESYGFTPIETPAVERLEVLQAKGNQGDNIIYGLEPILPPNRQAEKDKSGDTGSEARALKFDQTV 104 (465)
Q Consensus 25 g~~~~~~i~~~~~~~~~~~G~~ei~~P~i~~~~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~~~~d~~g~~~~Lrpd~t~ 104 (465)
-.+++..|...+|+.|...||.||+||+|.+... ++ +.+.|....-.++...|+.-...
T Consensus 21 ~~~~Rs~i~~~iR~ff~~~gf~EV~TP~L~~~~~----~~-----------------~~~~f~v~~~~~~~~yL~~Spql 79 (323)
T PF00152_consen 21 IFRIRSRIIQAIREFFDERGFIEVETPILSPSAS----EG-----------------GAEPFKVPEYFGEPAYLRQSPQL 79 (323)
T ss_dssp HHHHHHHHHHHHHHHHHHTT-EE----SEESSS------------------------TSBCEEEEEETTEEEEE-SSSHH
T ss_pred HHHHHHHHHHHHHHHHHHCCEEEEECCEEECCCC----CC-----------------CCCCCEEECCCCCCEECCCCHHH
T ss_conf 9999999999999999869918984997765677----66-----------------55430365255534321678678
Q ss_pred HHHHHHHHHHHHCCCCCCEEEECCCCCCCCC-CCCCCCEEEEEEEEEEECCCHHHHHHHH
Q ss_conf 9999999987515774515775240026677-7775300000000135257521789999
Q T0589 105 PLAAYIARHLNDLTFPFARYQMDVVFRGERA-KDGRFRQFRQCDIDVVGREKLSLLYDAQ 163 (465)
Q Consensus 105 ~~~r~~~~~~~~~~~~~~~~~~g~~fR~~~~-~~~r~ref~q~~~~~f~~~~~~~~~~~e 163 (465)
..-++++ ....++|||+++||+|.. +..+.-||||.++|.-+.+...+....|
T Consensus 80 ~lk~ll~------~g~~rVfei~~~FR~E~~~~~rHl~EFtmlE~e~~~~d~~~~m~~~e 133 (323)
T PF00152_consen 80 YLKRLLA------AGFERVFEIGPVFRAEESNTSRHLPEFTMLEWEMAFADYEDLMDLTE 133 (323)
T ss_dssp HHHHHHH------TT-SEEEEEEEEE-BSSSCBTTBSSEEEEEEEEEETSSHHHHHHHHH
T ss_pred HHHHHHH------CCCCCEEEEECCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHH
T ss_conf 8898865------06654278622311456542106788875104025898999999999
No 4
>PF01409 tRNA-synt_2d: tRNA synthetases class II core domain (F); InterPro: IPR002319 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Phenylalanyl-tRNA synthetase (6.1.1.20 from EC) is an alpha2/beta2 tetramer composed of 2 subunits that belongs to class IIc. In eubacteria, a small subunit (pheS gene) can be designated as beta (E. coli) or alpha subunit (nomenclature adopted in InterPro). Reciprocally the large subunit (pheT gene) can be designated as alpha (E. coli) or beta (see IPR004531 from INTERPRO and IPR004532 from INTERPRO). In all other kingdoms the two subunits have equivalent length in eukaryota, and can be identified by specific signatures. The enzyme from Thermus thermophilus has an alpha 2 beta 2 type quaternary structure and is one of the most complicated members of the synthetase family. Identification of phenylalanyl-tRNA synthetase as a member of class II aaRSs was based only on sequence alignment of the small alpha-subunit with other synthetases .; GO: 0000166 nucleotide binding, 0004826 phenylalanine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006432 phenylalanyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3cmq_A 2du6_B 2du4_A 2du3_B 2du5_B 2du7_D 2odr_D 2iy5_B 2aly_B 2amc_B ....
Probab=98.10 E-value=1.6e-05 Score=52.11 Aligned_cols=119 Identities=15% Similarity=0.229 Sum_probs=83.2
Q ss_pred CHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCH-HHHHHCCCCCHHHHHHHHHCCHHHHHHHCCCCCCC-C--CCEEEE
Q ss_conf 2679999999999999999739925006543326-77631156310234343320201112213554478-8--855785
Q T0589 23 PSEKRLELYLLDTIRRVYESYGFTPIETPAVERL-EVLQAKGNQGDNIIYGLEPILPPNRQAEKDKSGDT-G--SEARAL 98 (465)
Q Consensus 23 P~g~~~~~~i~~~~~~~~~~~G~~ei~~P~i~~~-~~~~~sg~~~~~~~~~~~~~~~~~~~~~~~~~~d~-~--g~~~~L 98 (465)
+-+.--...+++.++++|...|+++++.|.++.. ..|.+-. ...-|........|.+..+ + .....|
T Consensus 13 ~G~~Hpi~~~~~~i~~if~~~Gf~~~~~~~ves~~~NFD~Ln---------~P~dHpaR~~~Dtfyi~~p~~~~~~~~~L 83 (247)
T PF01409_consen 13 IGKLHPITQVIDEIREIFVGLGFQEVDGPEVESEFYNFDALN---------IPQDHPARDMQDTFYIANPLSAEEDYTVL 83 (247)
T ss_dssp CTTTSHHHHHHHHHHHHHHTCT-EEE---TEEEHHHHTGGGT---------STTTSGGGGGSSSEBCETT--BBCCSEEE
T ss_pred CCCCCHHHHHHHHHHHHHHHCCCEEEECCEEEEHHHHHHHHC---------CCCCCCHHCCCCCEEEECCCCCCCCCCEE
T ss_conf 899898999999999999877975864864342187787457---------99876300025523550223456643021
Q ss_pred CCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCCCEEEEEEEEEEEC
Q ss_conf 4776099999999987515774515775240026677777530000000013525
Q T0589 99 KFDQTVPLAAYIARHLNDLTFPFARYQMDVVFRGERAKDGRFRQFRQCDIDVVGR 153 (465)
Q Consensus 99 rpd~t~~~~r~~~~~~~~~~~~~~~~~~g~~fR~~~~~~~r~ref~q~~~~~f~~ 153 (465)
|.-.|+..++.. ....+.|.|++++|+|||++.....+..+|.|.+.-..+.
T Consensus 84 RThts~~~~r~L---~~~~~~p~kif~~G~VyR~D~~D~tH~~~FhQ~eg~~v~~ 135 (247)
T PF01409_consen 84 RTHTSPVQIRTL---NKHRPPPIKIFEIGRVYRRDEIDATHLPEFHQVEGLVVDK 135 (247)
T ss_dssp -SSSTHHHHHHH---CCHSHSSEEEEEEEEEESSSC-BSSBESEEEEEEEEEEST
T ss_pred EHHHHHHHHHHH---HHHCCCCEEEEEEEEEEECCCCCCCCCCCCCEEEEEEEEC
T ss_conf 111077699999---8708998489985059826785434486431388999925
No 5
>PF03740 PdxJ: Pyridoxal phosphate biosynthesis protein PdxJ; InterPro: IPR004569 Pyridoxal phosphate is the active form of vitamin B6 (pyridoxine or pyridoxal). PLP is a versatile catalyst, acting as a coenzyme in a multitude of reactions, including decarboxylation, deamination and transamination , , . PLP-dependent enzymes are primarily involved in the biosynthesis of amino acids and amino acid-derived metabolites, but they are also found in the biosynthetic pathways of amino sugars and in the synthesis or catabolism of neurotransmitters; pyridoxal phosphate can also inhibit DNA polymerases and several steroid receptors . Inadequate levels of pyridoxal phosphate in the brain can cause neurological dysfunction, particularly epilepsy . PLP enzymes exist in their resting state as a Schiff base, the aldehyde group of PLP forming a linkage with the epsilon-amino group of an active site lysine residue on the enzyme. The alpha-amino group of the substrate displaces the lysine epsilon-amino group, in the process forming a new aldimine with the substrate. This aldimine is the common central intermediate for all PLP-catalyzed reactions, enzymatic and non-enzymatic . In Escherichia coli, the pdx genes involved in vitamin B6 have been characterised , , . This entry represents PdxJ, which catalyses the condensation of 1-amino-3-oxo-4-(phosphohydroxy)propan-2-one and 1-deoxy-D-xylulose-5-phosphate to form pyridoxine-5'-phosphate. The product of the PdxJ reaction is then oxidized by PdxH to pyridoxal 5'-phosphate.; GO: 0008615 pyridoxine biosynthetic process, 0005737 cytoplasm; PDB: 3gk0_D 1m5w_B 1ixp_C 1ho4_C 1ho1_A 1ixq_D 1ixo_B 1ixn_B 3f4n_B.
Probab=45.32 E-value=5.5 Score=14.94 Aligned_cols=12 Identities=33% Similarity=0.761 Sum_probs=4.1
Q ss_pred HHHHHHHCCCEE
Q ss_conf 999998769859
Q T0589 390 VSQQLRQAGLNV 401 (465)
Q Consensus 390 i~~~Lr~~gi~v 401 (465)
+..+|+++||+|
T Consensus 116 ~i~~l~~~gIrV 127 (239)
T PF03740_consen 116 IIKRLKDAGIRV 127 (239)
T ss_dssp HHHHHHH---EE
T ss_pred HHHHHHHCCCEE
T ss_conf 999999879979
No 6
>PF03853 YjeF_N: YjeF-related protein N-terminus; InterPro: IPR004443 The C-terminal region of yjeF from Escherichia coli shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Saccharomyces cerevisiae YKL151C and Bacillus subtilis yxkO match the yjeF C-terminal domain but lack this region. The proteins in this group are of unknown function.; PDB: 3d3k_B 3d3j_A 2dg2_F 2o8n_A 1jzt_A 2ax3_A.
Probab=29.00 E-value=9.8 Score=13.23 Aligned_cols=95 Identities=20% Similarity=0.233 Sum_probs=48.1
Q ss_pred CCCCCEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEE-C---CCC--CHHHHHHHHHHCCCCEEEEECHHHHH----CCE
Q ss_conf 5687028998468789999999999998769859997-2---898--97789999996589799998602343----882
Q T0589 368 PPTPAQVVVVNMQDELMPTYLKVSQQLRQAGLNVITN-F---EKR--QLGKQFQAADKQGIRFCVIIGADEAA----AQK 437 (465)
Q Consensus 368 ~~~p~~V~v~~~~~~~~~~a~~i~~~Lr~~gi~v~~d-~---~~~--sig~k~~~ad~~G~p~~i~ig~~~~~----~~~ 437 (465)
.+.+..|+|+.-..+.=..+.-+++.|++.|++|.+- . +.. .....++.+...|.+........+.. ...
T Consensus 26 ~~~~~~v~vl~G~GNNGGDglv~AR~L~~~G~~V~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d 105 (173)
T PF03853_consen 26 DPKPPRVLVLCGPGNNGGDGLVAARHLAQRGYKVTVFLLGPPEKLSEDARQNLNILEKAGGPIVELEPDEDLSELLEPAD 105 (173)
T ss_dssp TTTT-EEEEEE----------HHHHHHHHTTSEEEEEEE-CCSTTSHHHHHHHHHHCCTT--EESSGGGSGGGHHGSCES
T ss_pred CCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCEECCCCCCCCCCCCCCCC
T ss_conf 46799799998999876999999999998799339998578777989999999999977998032455210123466667
Q ss_pred EEEEEC-CCCCE--EEECHHHHHHHHHH
Q ss_conf 899985-88865--87148999999999
Q T0589 438 SSLKDL-QSGEQ--VEVALADLAEEIKR 462 (465)
Q Consensus 438 vtir~r-~t~~q--~~v~~~el~~~l~~ 462 (465)
+-|=-+ .+|-. .+-+..++++++++
T Consensus 106 liIDalfG~Gl~~~l~~~~~~~i~~iN~ 133 (173)
T PF03853_consen 106 LIIDALFGTGLSRPLRGPYAELIEWINA 133 (173)
T ss_dssp EEEE----T-GGCCGSTTHHHHHHHHHH
T ss_pred EEEECCCCCCCCCCCCHHHHHHHHHHHC
T ss_conf 8998888878887776899999999972
No 7
>PF04430 DUF498: Protein of unknown function (DUF498/DUF598); InterPro: IPR007523 This is a family of uncharacterised proteins possibly involved in DNA repair. The crystal structure of this protein revealed a 3-layer beta+alpha/beta/alpha topology .; PDB: 3cpk_A 2k2e_A 2q4q_B 2ab1_A 1ihn_A 2cyj_A 2fvt_A 2fi9_A 2gm2_A.
Probab=25.43 E-value=11 Score=12.81 Aligned_cols=50 Identities=10% Similarity=0.148 Sum_probs=33.9
Q ss_pred CCEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHCC
Q ss_conf 702899846878999999999999876985999728989778999999658
Q T0589 371 PAQVVVVNMQDELMPTYLKVSQQLRQAGLNVITNFEKRQLGKQFQAADKQG 421 (465)
Q Consensus 371 p~~V~v~~~~~~~~~~a~~i~~~Lr~~gi~v~~d~~~~sig~k~~~ad~~G 421 (465)
+.+++++-.+....--..++.+.|+++||.+++.+.+ ..-+.|+---..|
T Consensus 53 ~peiliiGTG~~~~~~~~~~~~~l~~~gi~vE~m~T~-~A~rTyNiL~~Eg 102 (110)
T PF04430_consen 53 DPEILIIGTGQRQRFLPPELREYLRKKGIGVEVMDTP-AACRTYNILLSEG 102 (110)
T ss_dssp S-SEEEE------SEE-HHHHHHHHTTT-EEEE--HH-HHHHHHHHHHHTT
T ss_pred CCCEEEECCCCCCCCCCHHHHHHHHHCCCEEEEECHH-HHHHHHHHHHHCC
T ss_conf 9878999069988889999999999869979997869-9999999988376
No 8
>PF01981 PTH2: Peptidyl-tRNA hydrolase PTH2; InterPro: IPR002833 Peptidyl-tRNA hydrolases are enzymes that release tRNAs from peptidyl-tRNA during translation.; PDB: 1q7s_A 1rzw_A 3erj_B 2d3k_B 1wn2_A 1rlk_A 2zv3_A 1xty_D.
Probab=24.08 E-value=12 Score=12.65 Aligned_cols=33 Identities=18% Similarity=0.195 Sum_probs=21.3
Q ss_pred CHHHHHHHHHHCCCCEEEEECH--HHHHCCEEEEE
Q ss_conf 9778999999658979999860--23438828999
Q T0589 409 QLGKQFQAADKQGIRFCVIIGA--DEAAAQKSSLK 441 (465)
Q Consensus 409 sig~k~~~ad~~G~p~~i~ig~--~~~~~~~vtir 441 (465)
.+-.-.+.+...|+|+.++.|. .+++.|+.|+-
T Consensus 62 ~l~~l~~~a~~~gl~~~~i~DaG~Tqi~~gs~Tvl 96 (116)
T PF01981_consen 62 ELLELAKKAKDAGLPHYVIRDAGRTQIPPGSVTVL 96 (116)
T ss_dssp HHHHHHHHHHHTT---EEEEE---TSSEE-EEEEE
T ss_pred HHHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEEE
T ss_conf 99999999998599779999099740499983899
No 9
>PF01520 Amidase_3: N-acetylmuramoyl-L-alanine amidase; InterPro: IPR002508 The cell wall envelope of Gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. The cell wall also functions as a surface organelle that allows Gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. All of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. Two basic mechanisms, cell wall sorting and targeting, have been identified. Cell well sorting is the covalent attachment of surface proteins to the peptidoglycan via a C-terminal sorting signal that contains a consensus LPXTG sequence. More than 100 proteins that possess cell wall-sorting signals, including the M proteins of Streptococcus pyogenes, protein A of Staphylococcus aureus, and several internalins of Listeria monocytogenes, have been identified. Cell wall targeting involves the noncovalent attachment of proteins to the cell surface via specialised binding domains. Several of these wall-binding domains appear to interact with secondary wall polymers that are associated with the peptidoglycan, for example teichoic acids and polysaccharides. Proteins that are targeted to the cell surface include muralytic enzymes such as autolysins, lysostaphin, and phage lytic enzymes. Other examples for targeted proteins are the surface S-layer proteins of bacilli and clostridia, as well as virulence factors required for the pathogenesis of L. monocytogenes (internalin B) and Streptococcus pneumoniae (PspA) infections . Autolysin 3.5.1.28 from EC hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain bacterial cell wall glycopeptides.; GO: 0008745 N-acetylmuramoyl-L-alanine amidase activity, 0009253 peptidoglycan catabolic process; PDB: 1jwq_A 3czx_C 1xov_A.
Probab=20.22 E-value=14 Score=12.14 Aligned_cols=18 Identities=17% Similarity=0.385 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHHCC
Q ss_conf 999999999999999739
Q T0589 27 RLELYLLDTIRRVYESYG 44 (465)
Q Consensus 27 ~~~~~i~~~~~~~~~~~G 44 (465)
.+-..|-..+.+.+++.|
T Consensus 24 ~~~l~ia~~l~~~L~~~G 41 (175)
T PF01520_consen 24 DVNLDIAKRLKKYLEKAG 41 (175)
T ss_dssp HHHHHHHHHHHHHHHHCT
T ss_pred HHHHHHHHHHHHHHHHCC
T ss_conf 999999999999998789
No 10
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties .; GO: 0030436 sporulation (sensu Bacteria), 0042601 endospore-forming forespore
Probab=20.05 E-value=14 Score=12.12 Aligned_cols=35 Identities=20% Similarity=0.370 Sum_probs=25.2
Q ss_pred CCCEEEEECHHHHHCCEEEEEEC-CCCCEEEECHHHHH
Q ss_conf 89799998602343882899985-88865871489999
Q T0589 421 GIRFCVIIGADEAAAQKSSLKDL-QSGEQVEVALADLA 457 (465)
Q Consensus 421 G~p~~i~ig~~~~~~~~vtir~r-~t~~q~~v~~~el~ 457 (465)
|.|..| ..=+..+++-+|..+ ..+++..|++.+|.
T Consensus 22 G~pV~I--e~vde~~~tA~V~~~~~p~~~~~Vpv~~L~ 57 (58)
T PF08141_consen 22 GVPVWI--EHVDEQNETARVHPLGNPEEEQEVPVNDLE 57 (58)
T ss_pred CEEEEE--EEECCCCCEEEEEECCCCCCEEEEEHHHCC
T ss_conf 979999--987588984899977899948997789836
Done!