Align phosphotransacetylase (EC 2.3.1.8) (characterized)
to candidate RR42_RS33690 RR42_RS33690 phosphate acetyltransferase
Query= metacyc::PTACLOS-MONOMER (333 letters) >FitnessBrowser__Cup4G11:RR42_RS33690 Length = 346 Score = 303 bits (776), Expect = 4e-87 Identities = 157/330 (47%), Positives = 226/330 (68%) Query: 1 MDLIESIWECAKQDKKRIILAEGEEKRNLIAADKIIKEGLAELVLVGDENKIKEKASELN 60 M I I E A+ + +RI+L E E+ R L AA + EG+A +VLVGD +I++ A+ + Sbjct: 1 MKAINRIIERARAEPRRIVLCEAEDPRILQAAQRAAHEGIARIVLVGDAARIRQAAASED 60 Query: 61 LDISKAEIMDPETSLKTETYARDFYELRKHKGMTIEKSEKMVRDPLYFATMALKDGYVDG 120 +D++ +++DP TS T + AR + LR+ KGMT+E++ + V PL FA + ++ G+ DG Sbjct: 61 IDLAGMDVIDPATSALTPSLARKLFALREKKGMTLEEARREVLKPLCFANLMVRLGHADG 120 Query: 121 MVSGAVHTTGDLLRPGLQIIKTAPGVKIVSGFFVMIIPDCDYGEEGLLLFADCAVNPNPT 180 V+GAVHTT D++R +Q+I P K+VS FF+M++ + + +G L+F+DC + +P Sbjct: 121 SVAGAVHTTADVVRTAIQVIGIHPAFKLVSSFFLMMLCEPFHALKGGLIFSDCGLVVDPG 180 Query: 181 SDELADIAITTAETARKLCNVEPKVAMLSFSTMGSAKGEMVDKVKNAVEITKKFRPDLAI 240 + ELA+IA+ A++A+ L P+VAMLSFST GSA+ VDKV A + + RP LAI Sbjct: 181 AAELAEIAMAAADSAQNLLMDAPRVAMLSFSTSGSARHAAVDKVVQATRLVQAQRPALAI 240 Query: 241 DGELQLDAAIDSEVAALKAPSSNVAGNANVLVFPDLQTGNIGYKLVQRFAKAKAIGPICQ 300 DG++QLDAAI +E+A+ K S V G ANVLVFP L+ GNIGYKL +R AKAIGP+ Q Sbjct: 241 DGDVQLDAAIVAEIASKKIEHSKVEGRANVLVFPSLEAGNIGYKLAERVGGAKAIGPLLQ 300 Query: 301 GFAKPINDLSRGCSSEDIVNVVAITVVQAQ 330 G KP NDLSRGCS++D+ V+A+T VQAQ Sbjct: 301 GLQKPANDLSRGCSADDVFYVIAVTAVQAQ 330 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: 294 Number of extensions: 8 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: 346 Length adjustment: 28 Effective length of query: 305 Effective length of database: 318 Effective search space: 96990 Effective search space used: 96990 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 RR42_RS33690 RR42_RS33690 (phosphate acetyltransferase)
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.13775.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-111 358.3 0.4 2.3e-111 358.1 0.4 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS33690 RR42_RS33690 phosphate acetyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS33690 RR42_RS33690 phosphate acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.1 0.4 2.3e-111 2.3e-111 1 304 [] 18 326 .. 18 326 .. 0.98 Alignments for each domain: == domain 1 score: 358.1 bits; conditional E-value: 2.3e-111 TIGR00651 1 ivlPEgseervlkAaallaekkiaekvllvnkeeevknkakevnlklgkvvvedpdvskdiekyverly 69 ivl E++++r+l+Aa+ a+++ia+ vl+++ +++ + +a++ +++l+ + v+dp +s + +++ +l+ lcl|FitnessBrowser__Cup4G11:RR42_RS33690 18 IVLCEAEDPRILQAAQRAAHEGIARIVLVGDAARIRQ-AAASEDIDLAGMDVIDPATSALTPSLARKLF 85 89**********************9999999988888.7888899************************ PP TIGR00651 70 ekrkhkGvtekeareqlrDevslaallvelgeadglvsGavsttaktlrpalqiiktlegvklvssvfi 138 +r +kG+t++ear+++ ++ +a l+v+lg+adg v+Gav+tta+++r+a+q+i+ ++++klvss+f+ lcl|FitnessBrowser__Cup4G11:RR42_RS33690 86 ALREKKGMTLEEARREVLKPLCFANLMVRLGHADGSVAGAVHTTADVVRTAIQVIGIHPAFKLVSSFFL 154 ********************************************************************* PP TIGR00651 139 mekee......evlvfaDCavavdPnaeeLAeiAlqsaksakslgeeepkvallsystkgsgkgeevek 201 m + e + l+f+DC ++vdP a eLAeiA+ +a+sa++l + p+va+ls+st gs++ ++v+k lcl|FitnessBrowser__Cup4G11:RR42_RS33690 155 MMLCEpfhalkGGLIFSDCGLVVDPGAAELAEIAMAAADSAQNLLMDAPRVAMLSFSTSGSARHAAVDK 223 **99999999999******************************************************** PP TIGR00651 202 vkeAvkilkekepdllldGelqfDaAlvekvaekkapesevagkanvfvFPdLdaGnigYkivqRlada 270 v++A+++++ ++p l++dG++q+DaA+v+++a kk+ +s+v+g+anv+vFP+L+aGnigYk+++R+++a lcl|FitnessBrowser__Cup4G11:RR42_RS33690 224 VVQATRLVQAQRPALAIDGDVQLDAAIVAEIASKKIEHSKVEGRANVLVFPSLEAGNIGYKLAERVGGA 292 ********************************************************************* PP TIGR00651 271 eaiGPilqGlakPvnDLsRGasvedivnvviita 304 +aiGP+lqGl+kP nDLsRG+s++d+++v+++ta lcl|FitnessBrowser__Cup4G11:RR42_RS33690 293 KAIGPLLQGLQKPANDLSRGCSADDVFYVIAVTA 326 ********************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (346 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.23 // [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