Align Homoserine O-acetyltransferase; HAT; EC 2.3.1.31; Homoserine transacetylase; HTA (uncharacterized)
to candidate WP_011767693.1 AZO_RS19920 homoserine O-acetyltransferase
Query= curated2:Q1QQD3 (399 letters) >NCBI__GCF_000061505.1:WP_011767693.1 Length = 375 Score = 374 bits (960), Expect = e-108 Identities = 186/353 (52%), Positives = 238/353 (67%), Gaps = 2/353 (0%) Query: 33 DQPLPLDCGIDLAPFQIAYQTYGELNAGKSNAILVCHALTGDQHVANVHPVTGKP-GWWV 91 D+PLPL G LA + + Y+TYG+LNA +SNA+LVCHAL+G HVA V+ + GWW Sbjct: 18 DEPLPLRSGGTLAGYDLVYETYGQLNAARSNAVLVCHALSGSHHVAGVYADDPRNVGWWD 77 Query: 92 TLVGPGKPLDTDKYFVICSNVIGGCMGSTGPASTNPATGTVWGLDFPVITIPDMVRAQAM 151 LVGPGKPLDT K+FVI N +GGC GSTGP S NPATG WG DFP +T+ D V AQA Sbjct: 78 NLVGPGKPLDTRKFFVIGVNNLGGCYGSTGPGSVNPATGRPWGADFPFVTVEDWVDAQAR 137 Query: 152 LIDRLGIDTLFSVVGGSMGGMQVLQWCVAYPQRVFSALPIACSTRHSAQNIAFHELGRQA 211 L DRLGI ++VGGS+GGMQ L W + YP+RV A IA + + +AQNIAF+E+ RQA Sbjct: 138 LADRLGIQRFAAIVGGSLGGMQALSWTLQYPERVGHAAVIASAPKLTAQNIAFNEVARQA 197 Query: 212 VMADPDWRDGRYVEQGTYPHRGLGVARMAAHITYLSDAALHRKFGRRMQDRDLPTFSFDA 271 ++ DPD+ G Y E G P RGL +ARM HITYLSD ++ KFGR ++ +S+D Sbjct: 198 ILTDPDFHGGHYYEHGVVPARGLKLARMVGHITYLSDDSMGEKFGRSLR-HGKAVYSYDV 256 Query: 272 DFQVESYLRHQGSSFVERFDANSYLYLTRAMDYFDIAADHNGVLAAAFRDTRTRFCVVSF 331 +F++ESYLR+QG F FDAN+YL T+ +DYFD A +H G L AA F VVSF Sbjct: 257 EFEIESYLRYQGDKFAGYFDANTYLLTTKTLDYFDPAFEHGGNLNAALARASADFLVVSF 316 Query: 332 TSDWLFPTSESRATVHALNAGGARVSFAEIETDRGHDAFLLDLPEFFDIAHAF 384 T+DW F + SR V+AL VS+AEI+ GHD+FLLD P++ + A+ Sbjct: 317 TTDWRFSPARSREIVYALLHNRRNVSYAEIDCPAGHDSFLLDDPQYHALLSAW 369 Lambda K H 0.323 0.136 0.427 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: 464 Number of extensions: 14 Number of successful extensions: 3 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: 399 Length of database: 375 Length adjustment: 30 Effective length of query: 369 Effective length of database: 345 Effective search space: 127305 Effective search space used: 127305 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (22.0 bits) S2: 50 (23.9 bits)
Align candidate WP_011767693.1 AZO_RS19920 (homoserine O-acetyltransferase)
to HMM TIGR01392 (metX: homoserine O-acetyltransferase (EC 2.3.1.31))
# 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/TIGR01392.hmm # target sequence database: /tmp/gapView.28551.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01392 [M=351] Accession: TIGR01392 Description: homoserO_Ac_trn: homoserine O-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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-142 460.9 0.0 1.6e-142 460.7 0.0 1.0 1 lcl|NCBI__GCF_000061505.1:WP_011767693.1 AZO_RS19920 homoserine O-acetylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000061505.1:WP_011767693.1 AZO_RS19920 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 460.7 0.0 1.6e-142 1.6e-142 2 348 .. 18 368 .. 17 371 .. 0.97 Alignments for each domain: == domain 1 score: 460.7 bits; conditional E-value: 1.6e-142 TIGR01392 2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgral 68 +e+l l sG++l ++++y+tyG+lna+r+NavlvcHal+gs+hvag + ++ + GWWd+l+Gpg++l lcl|NCBI__GCF_000061505.1:WP_011767693.1 18 DEPLPLRSGGTLAGYDLVYETYGQLNAARSNAVLVCHALSGSHHVAGVYADDPRnvGWWDNLVGPGKPL 86 57899*******************************************99887789************* PP TIGR01392 69 dtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSl 137 dt+++fv+++N+lG+c+GstgP s+np+tg+p+ga+fP+vt++D+v aq++l+d+Lg++++aa+vGgSl lcl|NCBI__GCF_000061505.1:WP_011767693.1 87 DTRKFFVIGVNNLGGCYGSTGPGSVNPATGRPWGADFPFVTVEDWVDAQARLADRLGIQRFAAIVGGSL 155 ********************************************************************* PP TIGR01392 138 GGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalAR 205 GGmqal w+l+yperv +++v+a++++++aq+iafnev+rqail+Dp++++G+y+e++ P++GL+lAR lcl|NCBI__GCF_000061505.1:WP_011767693.1 156 GGMQALSWTLQYPERVGHAAVIASAPKLTAQNIAFNEVARQAILTDPDFHGGHYYEHGvVPARGLKLAR 224 **********************************************************9********** PP TIGR01392 206 mlalltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdl 274 m++++tY+s++s+ e+fgr+ ++ ++ +s++ ef++esylryqg+kf+ FdAn+Yll tk ld++d lcl|NCBI__GCF_000061505.1:WP_011767693.1 225 MVGHITYLSDDSMGEKFGRSLRHGKA-VYSYDVEFEIESYLRYQGDKFAGYFDANTYLLTTKTLDYFDP 292 *********************99955.6669************************************** PP TIGR01392 275 argrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekek 341 a ++ ++l++al++++a++lvv++++D++f++++++e++ al +++ + yaei+ ++GHD+Fll++ + lcl|NCBI__GCF_000061505.1:WP_011767693.1 293 AFEHGGNLNAALARASADFLVVSFTTDWRFSPARSREIVYALLHNRRNvsYAEIDCPAGHDSFLLDDPQ 361 ***************************************99988877778******************* PP TIGR01392 342 veelire 348 +++l+++ lcl|NCBI__GCF_000061505.1:WP_011767693.1 362 YHALLSA 368 *999876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (375 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: 9.32 // [ok]
This GapMind analysis is from Apr 10 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