Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_011386326.1 AMB_RS20100 homoserine O-acetyltransferase
Query= SwissProt::Q9AAS1 (382 letters) >NCBI__GCF_000009985.1:WP_011386326.1 Length = 393 Score = 521 bits (1341), Expect = e-152 Identities = 253/363 (69%), Positives = 293/363 (80%), Gaps = 2/363 (0%) Query: 20 NEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGWWQR 79 + P+RLD G + +++AYQTYG+LNADKSNA+LICHALTGD +VA PHP T KPGWW Sbjct: 24 DRPIRLDCGVELGPIQVAYQTYGRLNADKSNAILICHALTGDHYVADPHPITAKPGWWHE 83 Query: 80 LVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQAML 139 LVGPG+ D R+F+ICSNV+GGCMG+TGP NPATG+ +GL FPVITI DMV+ QA L Sbjct: 84 LVGPGRVFDTDRYFLICSNVLGGCMGTTGPVDENPATGQAWGLDFPVITIGDMVKVQARL 143 Query: 140 VSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGRQAI 199 V LG++ LF VVGGSMGGMQV +WA YPER+FSA+ +ASA+RHSAQNIAFHEVGRQAI Sbjct: 144 VDHLGIDQLFCVVGGSMGGMQVLKWAQVYPERVFSAIPIASAARHSAQNIAFHEVGRQAI 203 Query: 200 MADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGFDAD 258 MADPDW G Y + G RP +GLAVARMAAHITYLSEPAL +KFGR LQ RD +++GFDAD Sbjct: 204 MADPDWCEGNYLQEGKRPHRGLAVARMAAHITYLSEPALHQKFGRNLQNRDTVTYGFDAD 263 Query: 259 FQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCVLSF 318 FQVESYLRHQG++FVDRFDANSYLYITRAMDYFD+AA GGVLA AF R RFCV+SF Sbjct: 264 FQVESYLRHQGNTFVDRFDANSYLYITRAMDYFDLAAESGGVLANAF-RGTRTRFCVVSF 322 Query: 319 SSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASAERD 378 +SDWL+PT E+R +V AL A A +F EI+SDKGHDAFLLDEP A L GFL A Sbjct: 323 TSDWLFPTPESRAVVHALNAVAANVSFVEIKSDKGHDAFLLDEPEFHATLTGFLEGAATH 382 Query: 379 RGL 381 RGL Sbjct: 383 RGL 385 Lambda K H 0.321 0.135 0.417 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: 564 Number of extensions: 24 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: 382 Length of database: 393 Length adjustment: 30 Effective length of query: 352 Effective length of database: 363 Effective search space: 127776 Effective search space used: 127776 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 (21.9 bits) S2: 50 (23.9 bits)
Align candidate WP_011386326.1 AMB_RS20100 (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.3947.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-149 482.4 0.0 4.4e-149 482.3 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011386326.1 AMB_RS20100 homoserine O-acetylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011386326.1 AMB_RS20100 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 482.3 0.0 4.4e-149 4.4e-149 3 350 .. 25 376 .. 23 377 .. 0.98 Alignments for each domain: == domain 1 score: 482.3 bits; conditional E-value: 4.4e-149 TIGR01392 3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 +++ l++G +l ++vay+tyG+lna+++Na+l+cHaltg++ va+ + ++k GWW+el+Gpgr +dt lcl|NCBI__GCF_000009985.1:WP_011386326.1 25 RPIRLDCGVELGPIQVAYQTYGRLNADKSNAILICHALTGDHYVADPHPITAKpGWWHELVGPGRVFDT 93 6789******************************************99988778*************** PP TIGR01392 71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139 +ryf++c+NvlG+c G+tgP++ np+tg+ +g +fP++ti D+vk+q++l+d+Lg+++l++vvGgS+GG lcl|NCBI__GCF_000009985.1:WP_011386326.1 94 DRYFLICSNVLGGCMGTTGPVDENPATGQAWGLDFPVITIGDMVKVQARLVDHLGIDQLFCVVGGSMGG 162 ********************************************************************* PP TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207 mq+l+wa yperv +++++a++ar+saq+iaf+ev rqai++Dp++ +G+y +e+ +P++GLa+ARm lcl|NCBI__GCF_000009985.1:WP_011386326.1 163 MQVLKWAQVYPERVFSAIPIASAARHSAQNIAFHEVGRQAIMADPDWCEGNYLQEGkRPHRGLAVARMA 231 ******************************************************999************ PP TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276 a++tY+se +l+++fgr+ ++++++++ ++++f+vesylr+qg++fv+rFdAnsYl++t+a+d++dla+ lcl|NCBI__GCF_000009985.1:WP_011386326.1 232 AHITYLSEPALHQKFGRNLQNRDTVTYGFDADFQVESYLRHQGNTFVDRFDANSYLYITRAMDYFDLAA 300 ********************************************************************* PP TIGR01392 277 grrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekve 343 + + l++a++ ++++++vv+++sD+lf++ e++ +++al+a++++ ++ei+s++GHDaFll++ +++ lcl|NCBI__GCF_000009985.1:WP_011386326.1 301 ESGGVLANAFRGTRTRFCVVSFTSDWLFPTPESRAVVHALNAVAANvsFVEIKSDKGHDAFLLDEPEFH 369 *999*************************************9998888********************* PP TIGR01392 344 elirefl 350 ++++ fl lcl|NCBI__GCF_000009985.1:WP_011386326.1 370 ATLTGFL 376 9999987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (393 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: 9.86 // [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