Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate BPHYT_RS21700 BPHYT_RS21700 phosphotransacetylase
Query= metacyc::PTACLOS-MONOMER (333 letters) >FitnessBrowser__BFirm:BPHYT_RS21700 Length = 344 Score = 316 bits (810), Expect = 5e-91 Identities = 166/333 (49%), Positives = 230/333 (69%) Query: 1 MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60 M I I E A++ RI+L+E E+ R L AA + +EG+A ++LVGD +I+E A+ + Sbjct: 1 MKAINRIIEQARRSPMRIVLSEAEDPRVLQAAQRATREGIARILLVGDATRIREAAAGFD 60 Query: 61 LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDG 120 +D+S E++DP TS +YA + + LR KGMT+E++ K + +PL FA + ++ G+ DG Sbjct: 61 VDLSGMELVDPATSALASSYADELFALRSKKGMTLEQARKEILNPLCFANLMVRLGHADG 120 Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180 VSGAV+TT D++R +QII AP K+VS FF+M++ + + +G L+F+DCA+ P Sbjct: 121 SVSGAVNTTADVVRTAIQIIGIAPSFKLVSSFFLMMLCEPFHTLKGGLIFSDCALVVEPD 180 Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240 + +LA+IA+ A++AR L EP+VAMLSFST GSA VDKV NA I ++ RP LAI Sbjct: 181 AAQLAEIAMAAADSARSLLMDEPRVAMLSFSTSGSAHHAAVDKVVNATHIVQERRPHLAI 240 Query: 241 DGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQ 300 DG++QLDAAI SE+A K S V G+ANVLVFP L+ GNIGYKL +R AKAIGP+ Q Sbjct: 241 DGDVQLDAAIVSEIALRKVKHSQVEGHANVLVFPSLEAGNIGYKLAERIGGAKAIGPLLQ 300 Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQAQRGI 333 G KP NDLSRGCS++DI V A+T VQAQ + Sbjct: 301 GLRKPANDLSRGCSADDIYYVTAVTAVQAQAAL 333 Lambda K H 0.316 0.134 0.374 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 287 Number of extensions: 12 Number of successful extensions: 1 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 333 Length of database: 344 Length adjustment: 28 Effective length of query: 305 Effective length of database: 316 Effective search space: 96380 Effective search space used: 96380 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate BPHYT_RS21700 BPHYT_RS21700 (phosphotransacetylase)
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00651.hmm # target sequence database: /tmp/gapView.681.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00651 [M=304] Accession: TIGR00651 Description: pta: phosphate acetyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.5e-118 379.2 0.2 9.8e-118 379.0 0.2 1.0 1 lcl|FitnessBrowser__BFirm:BPHYT_RS21700 BPHYT_RS21700 phosphotransacetyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__BFirm:BPHYT_RS21700 BPHYT_RS21700 phosphotransacetylase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 379.0 0.2 9.8e-118 9.8e-118 1 304 [] 18 326 .. 18 326 .. 0.98 Alignments for each domain: == domain 1 score: 379.0 bits; conditional E-value: 9.8e-118 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverlye 70 ivl E++++rvl+Aa+ ++++ia+ l+++ ++ + +a++++ +l+ ++++dp +s +y+++l+ lcl|FitnessBrowser__BFirm:BPHYT_RS21700 18 IVLSEAEDPRVLQAAQRATREGIARILLVGDATRIRE-AAAGFDVDLSGMELVDPATSALASSYADELFA 86 8**********************98777776666666.9******************************* PP TIGR00651 71 krkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfime 140 +r +kG+t+++ar+++ +++ +a l+v+lg+adg vsGav+tta+++r+a+qii+ ++++klvss+f+m lcl|FitnessBrowser__BFirm:BPHYT_RS21700 87 LRSKKGMTLEQARKEILNPLCFANLMVRLGHADGSVSGAVNTTADVVRTAIQIIGIAPSFKLVSSFFLMM 156 ********************************************************************** PP TIGR00651 141 kee......evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevekvke 204 + e + l+f+DCa++v+P+a +LAeiA+ +a+sa+sl +ep+va+ls+st gs++ ++v+kv++ lcl|FitnessBrowser__BFirm:BPHYT_RS21700 157 LCEpfhtlkGGLIFSDCALVVEPDAAQLAEIAMAAADSARSLLMDEPRVAMLSFSTSGSAHHAAVDKVVN 226 99999999999*********************************************************** PP TIGR00651 205 AvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRladaeaiG 274 A++i++e++p l++dG++q+DaA+v+++a +k+++s+v+g+anv+vFP+L+aGnigYk+++R+++a+aiG lcl|FitnessBrowser__BFirm:BPHYT_RS21700 227 ATHIVQERRPHLAIDGDVQLDAAIVSEIALRKVKHSQVEGHANVLVFPSLEAGNIGYKLAERIGGAKAIG 296 ********************************************************************** PP TIGR00651 275 PilqGlakPvnDLsRGasvedivnvviita 304 P+lqGl+kP nDLsRG+s++di++v+++ta lcl|FitnessBrowser__BFirm:BPHYT_RS21700 297 PLLQGLRKPANDLSRGCSADDIYYVTAVTA 326 ****************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (344 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.47 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory