Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate 351941 BT2413 homoserine O-succinyltransferase (NCBI ptt file)
Query= SwissProt::Q72X44 (301 letters) >FitnessBrowser__Btheta:351941 Length = 305 Score = 379 bits (973), Expect = e-110 Identities = 174/299 (58%), Positives = 227/299 (75%) Query: 1 MPIIIDKDLPARKVLQEENIFVMTKERAETQDIRALKIAILNLMPTKQETEAQLLRLIGN 60 MP+ + LPA ++L+EENIFV+ RA QDIR L+I ILNLMP K TE L+RL+ N Sbjct: 1 MPLNLPDKLPAIELLKEENIFVIDTSRATQQDIRPLRIVILNLMPLKITTETDLVRLLSN 60 Query: 61 TPLQLDVHLLHMESHLSRNVAQEHLTSFYKTFRDIENEKFDGLIITGAPVETLSFEEVDY 120 TPLQ+++ + ++SH S+N EH+ +FY F + NEK+DG+IITGAPVE + FEEV Y Sbjct: 61 TPLQVEISFMKIKSHTSKNTPIEHMQTFYTDFEQMRNEKYDGMIITGAPVEQMDFEEVTY 120 Query: 121 WEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEVREQHVKLL 180 WEE+ I ++++T+VTSTL+ICW AQAGLYHHYGV KYPL +KMFG+FEH V E + Sbjct: 121 WEEITEIFDWARTHVTSTLYICWAAQAGLYHHYGVPKYPLDQKMFGIFEHRVLEPFHSIF 180 Query: 181 QGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYSC 240 +GFD+ F+ PHSRHTEVR DI +V ELTLL+ S++AGV++ + + GR+ F GHSEYS Sbjct: 181 RGFDDCFYVPHSRHTEVRREDILKVPELTLLSESKDAGVYMAMARGGREFFVTGHSEYSP 240 Query: 241 DTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQETPY 299 TL EY RD KGL I++P+NY+ D+P++ PLVRWR+H NLLFSNWLNY+VYQETPY Sbjct: 241 YTLDTEYRRDLGKGLPIEIPRNYYVDDDPDKGPLVRWRAHANLLFSNWLNYFVYQETPY 299 Lambda K H 0.319 0.136 0.403 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: 319 Number of extensions: 6 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: 301 Length of database: 305 Length adjustment: 27 Effective length of query: 274 Effective length of database: 278 Effective search space: 76172 Effective search space used: 76172 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 bits)
Align candidate 351941 BT2413 (homoserine O-succinyltransferase (NCBI ptt file))
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))
# 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.aa/TIGR01001.hmm # target sequence database: /tmp/gapView.13495.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01001 [M=301] Accession: TIGR01001 Description: metA: homoserine O-succinyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-142 458.4 0.2 7.4e-142 458.3 0.2 1.0 1 lcl|FitnessBrowser__Btheta:351941 BT2413 homoserine O-succinyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:351941 BT2413 homoserine O-succinyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.3 0.2 7.4e-142 7.4e-142 1 300 [. 1 301 [. 1 302 [. 1.00 Alignments for each domain: == domain 1 score: 458.3 bits; conditional E-value: 7.4e-142 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsrk 76 mp+++pd+lpa+ellkeenifv+ ++ra++qdirpl+++ilnlmp ki te+ l+rllsn+plqv+i +++i+s++ lcl|FitnessBrowser__Btheta:351941 1 MPLNLPDKLPAIELLKEENIFVIDTSRATQQDIRPLRIVILNLMPLKITTETDLVRLLSNTPLQVEISFMKIKSHT 76 9*************************************************************************** PP TIGR01001 77 skntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalkll 152 skntpieh+++fy+++e+++++k+dG+i+tGapve+++fe+v ywee++ei++w++++vtstlyicwaaqa+l+ lcl|FitnessBrowser__Btheta:351941 77 SKNTPIEHMQTFYTDFEQMRNEKYDGMIITGAPVEQMDFEEVTYWEEITEIFDWARTHVTSTLYICWAAQAGLYHH 152 **************************************************************************** PP TIGR01001 153 ygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaaskder 227 yg+pk+ l++k++G+++h+++ +++ ++rgfdd f++phsr++++ +e+i ++++l +l es++agvy+a+++ r lcl|FitnessBrowser__Btheta:351941 153 YGVPKYPLDQKMFGIFEHRVLePFHSIFRGFDDCFYVPHSRHTEVRREDILKVPELTLLSESKDAGVYMAMARGGR 228 ********************999***************************************************** PP TIGR01001 228 nifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpydl 300 + fvtGh ey +tl ey rd+g+gl ++ip nyy +ddp+k p + wr+hanllf+nwlny vyq+tpy++ lcl|FitnessBrowser__Btheta:351941 229 EFFVTGHSEYSPYTLDTEYRRDLGKGLPIEIPRNYYVDDDPDKGPLVRWRAHANLLFSNWLNYFVYQETPYNI 301 ***********************************************************************86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (305 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: 00:00:00.00 # Mc/sec: 9.27 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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