Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_083931444.1 A3OQ_RS0101625 homoserine O-acetyltransferase
Query= SwissProt::Q9AAS1 (382 letters) >NCBI__GCF_000385335.1:WP_083931444.1 Length = 449 Score = 509 bits (1311), Expect = e-149 Identities = 243/366 (66%), Positives = 298/366 (81%), Gaps = 2/366 (0%) Query: 17 FPANEPLRLDSGGVIEGLEIAYQTYGQLNADKSNAVLICHALTGDQHVASPHPTTGKPGW 76 F A+ PL++D+G ++ L +AYQTYG LNA KSNA+L+CHALTGDQHVA+ HP TGKPGW Sbjct: 77 FGADRPLKMDAGVLLSPLTVAYQTYGTLNAQKSNAILVCHALTGDQHVANTHPVTGKPGW 136 Query: 77 WQRLVGPGKPLDPARHFIICSNVIGGCMGSTGPASINPATGKTYGLSFPVITIADMVRAQ 136 W+ +VGPG+P+D R+F+I SNV+GGCMG+TGP+S NPATG+ YGL PV+TI DMVRAQ Sbjct: 137 WEIMVGPGRPIDTDRYFVISSNVVGGCMGTTGPSSTNPATGRAYGLDLPVVTIKDMVRAQ 196 Query: 137 AMLVSALGVETLFAVVGGSMGGMQVQQWAVDYPERMFSAVVLASASRHSAQNIAFHEVGR 196 AMLV LG++TL VVGGSMGGMQV QWA YPER+F+A+ +A+A+RHS+QNIAFHEVGR Sbjct: 197 AMLVDHLGIDTLCCVVGGSMGGMQVLQWAASYPERVFAAMPIATAARHSSQNIAFHEVGR 256 Query: 197 QAIMADPDWRGGAYAEHGVRPEKGLAVARMAAHITYLSEPALQRKFGRELQ-RDGLSWGF 255 QAIMADPDW G Y + G +P KGLAVARMAAHITY+S+ ALQRKFGR+LQ R ++ F Sbjct: 257 QAIMADPDWCKGRYLDEGRQPTKGLAVARMAAHITYMSDEALQRKFGRKLQDRIAPTFSF 316 Query: 256 DADFQVESYLRHQGSSFVDRFDANSYLYITRAMDYFDIAASHGGVLAKAFTRARNVRFCV 315 DADFQ+E+YLR+QGSSFVDRFDANSYLY+TRA DYFD+A +GG LA AF + RFCV Sbjct: 317 DADFQIENYLRYQGSSFVDRFDANSYLYVTRACDYFDLAEDYGGSLALAF-KGSKTRFCV 375 Query: 316 LSFSSDWLYPTAENRHLVRALTAAGARAAFAEIESDKGHDAFLLDEPVMDAALEGFLASA 375 +SF+SDWLYPTA +R +V AL A GA +F +IE+++GHDAFLLD P A GFL +A Sbjct: 376 VSFNSDWLYPTAASRAIVHALNAGGASVSFVDIETERGHDAFLLDVPDFIATTRGFLEAA 435 Query: 376 ERDRGL 381 R RG+ Sbjct: 436 ARARGI 441 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: 535 Number of extensions: 18 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: 449 Length adjustment: 31 Effective length of query: 351 Effective length of database: 418 Effective search space: 146718 Effective search space used: 146718 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_083931444.1 A3OQ_RS0101625 (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.14913.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.1e-146 472.2 0.0 5.9e-146 472.0 0.0 1.0 1 lcl|NCBI__GCF_000385335.1:WP_083931444.1 A3OQ_RS0101625 homoserine O-acet Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000385335.1:WP_083931444.1 A3OQ_RS0101625 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 472.0 0.0 5.9e-146 5.9e-146 3 350 .. 81 432 .. 79 433 .. 0.98 Alignments for each domain: == domain 1 score: 472.0 bits; conditional E-value: 5.9e-146 TIGR01392 3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldt 70 ++l++++G ls ++vay+tyGtlna+++Na+lvcHaltg++hva+++ + k GWW+ ++Gpgr++dt lcl|NCBI__GCF_000385335.1:WP_083931444.1 81 RPLKMDAGVLLSPLTVAYQTYGTLNAQKSNAILVCHALTGDQHVANTHPVTGKpGWWEIMVGPGRPIDT 149 6899******************************************99987767*************** PP TIGR01392 71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139 +ryfv+++Nv+G+c G+tgP+s+np+tg+ yg ++P+vti+D+v+aq++l+d+Lg+++l +vvGgS+GG lcl|NCBI__GCF_000385335.1:WP_083931444.1 150 DRYFVISSNVVGGCMGTTGPSSTNPATGRAYGLDLPVVTIKDMVRAQAMLVDHLGIDTLCCVVGGSMGG 218 ********************************************************************* PP TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalARml 207 mq+l+wa+syperv +++++at+ar+s+q+iaf+ev rqai++Dp++ +G+y +e+ qP+kGLa+ARm lcl|NCBI__GCF_000385335.1:WP_083931444.1 219 MQVLQWAASYPERVFAAMPIATAARHSSQNIAFHEVGRQAIMADPDWCKGRYLDEGrQPTKGLAVARMA 287 ******************************************************999************ PP TIGR01392 208 alltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlar 276 a++tY s+e+l+++fgr+ +++ ++++s++++f++e ylryqg++fv+rFdAnsYl++t+a d++dla+ lcl|NCBI__GCF_000385335.1:WP_083931444.1 288 AHITYMSDEALQRKFGRKLQDRIAPTFSFDADFQIENYLRYQGSSFVDRFDANSYLYVTRACDYFDLAE 356 ********************************************************************* PP TIGR01392 277 grrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekve 343 ++ +sl+ a+k k++++vv+++sD+l++++ ++ +++al+a +++ ++ ie+e+GHDaFll+ + lcl|NCBI__GCF_000385335.1:WP_083931444.1 357 DYGGSLALAFKGSKTRFCVVSFNSDWLYPTAASRAIVHALNAGGASvsFVDIETERGHDAFLLDVPDFI 425 *****************************************9998888****************99988 PP TIGR01392 344 elirefl 350 ++ r fl lcl|NCBI__GCF_000385335.1:WP_083931444.1 426 ATTRGFL 432 8777776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (449 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 12.52 // [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