Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_004511679.1 GMET_RS13945 homoserine O-acetyltransferase
Query= SwissProt::B3E278 (367 letters) >NCBI__GCF_000012925.1:WP_004511679.1 Length = 369 Score = 637 bits (1643), Expect = 0.0 Identities = 299/365 (81%), Positives = 330/365 (90%) Query: 1 MSIGVVHEQTITFEAGIRLESGRILAPITLVYELYGTMNADCSNVIMVEHAWTGDAHLAG 60 MS+G+V EQ++TF+ +RLESGRIL PITL YE YG +NAD SN I+V HAWTG+AHLAG Sbjct: 1 MSVGIVQEQSVTFDTELRLESGRILGPITLAYETYGELNADRSNAILVAHAWTGNAHLAG 60 Query: 61 KRREDDPKPGWWDAIVGPGRLLDTDRYCVLCSNVIGSCYGSTGPASINPRTGKRYNLSFP 120 K E+D KPGWWDAIVGPGRLLDTDR V+CSNVIGSCYGSTGPASINP+TGKRYNL+FP Sbjct: 61 KNSEEDTKPGWWDAIVGPGRLLDTDRCFVICSNVIGSCYGSTGPASINPKTGKRYNLTFP 120 Query: 121 VITVRDMVRAQELLLDHLGIRRLLCVMGGSMGGMQALEWATQYPERVASVVALATTPRPS 180 VITVRDMVRAQ LLLDHLGI RLL V+GGSMGGMQALEWATQ+P+R+ S +ALATT RPS Sbjct: 121 VITVRDMVRAQALLLDHLGIDRLLTVLGGSMGGMQALEWATQFPDRIRSAIALATTSRPS 180 Query: 181 PQAISLNAVARWAIYNDPTWKKGEYKHNPKDGLALARGIGHITFLSDESMWQKFERRFSA 240 PQAISLNAVARWAI+NDPTWKKGEY+ NPKDGLALARGIGHITFLSDESMWQKF RRF+A Sbjct: 181 PQAISLNAVARWAIFNDPTWKKGEYRKNPKDGLALARGIGHITFLSDESMWQKFGRRFNA 240 Query: 241 KDGLFDFFGQFEVERYLNYNGYNFVDRFDANCFLYLAKALDLYDVAWGYESMTDAFSRIT 300 +DGLFDFFGQFEVERYL+YNGYNFVDRFD N FLYLAKALDLYD AWGYES+ +AFSR+ Sbjct: 241 RDGLFDFFGQFEVERYLSYNGYNFVDRFDTNSFLYLAKALDLYDTAWGYESLEEAFSRVK 300 Query: 301 APIQFFAFSSDWLYPPYQTEEMVTCLQGLGKEVEYHLIQSAYGHDAFLLEHETFTPMVRS 360 APIQFFAF+SDWLYPPYQTEEM T L+ LGK VEYHLI+SAYGHDAFLLEHETF PMVR Sbjct: 301 APIQFFAFTSDWLYPPYQTEEMATILRSLGKPVEYHLIESAYGHDAFLLEHETFAPMVRE 360 Query: 361 LLERV 365 L++V Sbjct: 361 FLDKV 365 Lambda K H 0.323 0.138 0.439 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: 550 Number of extensions: 11 Number of successful extensions: 2 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: 367 Length of database: 369 Length adjustment: 30 Effective length of query: 337 Effective length of database: 339 Effective search space: 114243 Effective search space used: 114243 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: 49 (23.5 bits)
Align candidate WP_004511679.1 GMET_RS13945 (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.34367.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.3e-135 435.1 0.0 1.1e-134 434.9 0.0 1.0 1 NCBI__GCF_000012925.1:WP_004511679.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000012925.1:WP_004511679.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 434.9 0.0 1.1e-134 1.1e-134 3 350 .. 15 362 .. 13 363 .. 0.98 Alignments for each domain: == domain 1 score: 434.9 bits; conditional E-value: 1.1e-134 TIGR01392 3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellGpgraldtsry 73 +el lesG +l +++ay+tyG+lna+r+Na+lv Ha tg+ah+agk++eed+ GWWd ++Gpgr ldt+r NCBI__GCF_000012925.1:WP_004511679.1 15 TELRLESGRILGPITLAYETYGELNADRSNAILVAHAWTGNAHLAGKNSEEDTkpGWWDAIVGPGRLLDTDRC 87 789*******************************************999887779****************** PP TIGR01392 74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewa 146 fv+c+Nv+Gsc+GstgP+sinp+tgk+y fP++t+rD+v+aq+ lld+Lg+++l +v+GgS+GGmqalewa NCBI__GCF_000012925.1:WP_004511679.1 88 FVICSNVIGSCYGSTGPASINPKTGKRYNLTFPVITVRDMVRAQALLLDHLGIDRLLTVLGGSMGGMQALEWA 160 ************************************************************************* PP TIGR01392 147 lsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesle 219 ++ p+r++++++lat+ r s+qai++n+v+r ai +Dp +++Gey++ +P+ GLalAR ++++t++s+es+ NCBI__GCF_000012925.1:WP_004511679.1 161 TQFPDRIRSAIALATTSRPSPQAISLNAVARWAIFNDPTWKKGEYRK--NPKDGLALARGIGHITFLSDESMW 231 **********************************************9..9*********************** PP TIGR01392 220 erfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkikap 292 ++fgr+ ++++ + + +f+ve yl+y+g +fv+rFd ns+l+l+kald +d a g +sl+ea++++kap NCBI__GCF_000012925.1:WP_004511679.1 232 QKFGRRFNARDG-LFDFFGQFEVERYLSYNGYNFVDRFDTNSFLYLAKALDLYDTAWG-YESLEEAFSRVKAP 302 *****9999965.677999***************************************.8************* PP TIGR01392 293 vlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350 + + +++sD+l+++ ++ee+a+ l++ ++ y+ ies++GHDaFlle+e+++ ++refl NCBI__GCF_000012925.1:WP_004511679.1 303 IQFFAFTSDWLYPPYQTEEMATILRSLGKPveYHLIESAYGHDAFLLEHETFAPMVREFL 362 **************************999888**************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (369 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 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 18.69 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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