Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_015817511.1 TERTU_RS00980 homoserine O-acetyltransferase
Query= SwissProt::D7E9E0 (489 letters) >NCBI__GCF_000023025.1:WP_015817511.1 Length = 383 Score = 353 bits (906), Expect = e-102 Identities = 181/376 (48%), Positives = 251/376 (66%), Gaps = 8/376 (2%) Query: 5 SIGNVETKYYQIPEELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAGW 64 S+G V + Q E L L G+ + L ETYGTLN ++NA+L+CHAL+G HAAG+ Sbjct: 9 SVGLVTPQLMQFDEPLALACGRTLDSYQLMVETYGTLNASRTNALLICHALSGHHHAAGY 68 Query: 65 HEGD-RKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123 H D RKPGWWD IGPGK LDT K+FI+ N IGGC GSTGP + NP TG+ +G DFP Sbjct: 69 HSMDERKPGWWDAYIGPGKPLDTNKFFIVSLNNIGGCHGSTGPVTPNPSTGQPWGGDFPT 128 Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183 + ++D V++Q +L D LGI K AV+GGS+GG+Q ++WS+ YPD V + IA+A + Sbjct: 129 LRVRDWVHSQARLADALGIQKWAAVVGGSLGGMQAMRWSLEYPDRVGHCVVIASAMKLSA 188 Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYYGEKE-PTHGLALARMIGHITYLSDDSMHQKFGRRL 242 Q IAFN R AI++DP+++ GN+ P GL+ AR+I H+TYLSDD M QKFGR L Sbjct: 189 QNIAFNHAAREAILTDPDFHDGNFLSHSTVPKRGLSTARVIAHLTYLSDDGMGQKFGREL 248 Query: 243 QDKN-EYEFDFSREFEVESYLHYQGLTFTERFDANSYLYLTKAIDYFDLTE--NNSLAEG 299 + + E + EF++ESYL YQ +F++ FDAN+Y+ +T+A+DYFDL + E Sbjct: 249 RSGSFEQGTEEPVEFQIESYLRYQADSFSKVFDANTYVLMTRALDYFDLAREYGDDPVEA 308 Query: 300 LKNVEAKFLVISFTSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQLN 359 K + K++VISFTSDW + P + REIV AL + DV Y E+ES++GHD+FL+ + Q Sbjct: 309 FKQAQCKYMVISFTSDWRFSPERSREIVNALIRADRDVVYGELESDFGHDAFLIPN-QPR 367 Query: 360 Y--VLNNFLSHTYVSD 373 Y +L +++S V+D Sbjct: 368 YWDLLTSYMSQIEVAD 383 Lambda K H 0.316 0.134 0.392 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: 551 Number of extensions: 30 Number of successful extensions: 5 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: 489 Length of database: 383 Length adjustment: 32 Effective length of query: 457 Effective length of database: 351 Effective search space: 160407 Effective search space used: 160407 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: 51 (24.3 bits)
Align candidate WP_015817511.1 TERTU_RS00980 (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.24861.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.7e-138 446.3 0.0 4.3e-138 446.1 0.0 1.0 1 lcl|NCBI__GCF_000023025.1:WP_015817511.1 TERTU_RS00980 homoserine O-acety Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023025.1:WP_015817511.1 TERTU_RS00980 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 446.1 0.0 4.3e-138 4.3e-138 2 339 .. 21 364 .. 20 377 .. 0.96 Alignments for each domain: == domain 1 score: 446.1 bits; conditional E-value: 4.3e-138 TIGR01392 2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgral 68 +e+l l +G +l++++++++tyGtlna+r Na+l+cHal+g++h+ag+++ +++ GWWd ++Gpg++l lcl|NCBI__GCF_000023025.1:WP_015817511.1 21 DEPLALACGRTLDSYQLMVETYGTLNASRTNALLICHALSGHHHAAGYHSMDERkpGWWDAYIGPGKPL 89 5799*******************************************998777778************* PP TIGR01392 69 dtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSl 137 dt+++f+v+lN++G+c+GstgP++ np+tg+p+g +fP++ +rD+v+ q++l+d+Lg++k+aavvGgSl lcl|NCBI__GCF_000023025.1:WP_015817511.1 90 DTNKFFIVSLNNIGGCHGSTGPVTPNPSTGQPWGGDFPTLRVRDWVHSQARLADALGIQKWAAVVGGSL 158 ********************************************************************* PP TIGR01392 138 GGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeee.qPekGLalAR 205 GGmqa+ w+l+yp+rv ++vv+a+++++saq+iafn+++r+ail+Dp+++dG++ +++ P++GL++AR lcl|NCBI__GCF_000023025.1:WP_015817511.1 159 GGMQAMRWSLEYPDRVGHCVVIASAMKLSAQNIAFNHAAREAILTDPDFHDGNFLSHStVPKRGLSTAR 227 *******************************************************9999********** PP TIGR01392 206 mlalltYrseesleerfgreakseeslassl.eeefsvesylryqgkkfverFdAnsYllltkaldthd 273 +a+ltY+s++ + ++fgre +s + + + ef++esylryq+++f + FdAn+Y+l+t+ald++d lcl|NCBI__GCF_000023025.1:WP_015817511.1 228 VIAHLTYLSDDGMGQKFGRELRSGSFEQGTEePVEFQIESYLRYQADSFSKVFDANTYVLMTRALDYFD 296 **********************9975554434789********************************** PP TIGR01392 274 largrrdslkealkkikapvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllek 339 lar++ d+ ea+k+++++++v++++sD++f++e+++e+++al +a+ + y e+es+ GHDaFl+ + lcl|NCBI__GCF_000023025.1:WP_015817511.1 297 LAREYGDDPVEAFKQAQCKYMVISFTSDWRFSPERSREIVNALIRADRDvvYGELESDFGHDAFLIPN 364 *******************************************99999889**************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (383 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: 7.39 // [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