Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_015907626.1 CALKRO_RS07945 homoserine O-acetyltransferase
Query= SwissProt::D3P9D1 (377 letters) >NCBI__GCF_000166775.1:WP_015907626.1 Length = 381 Score = 399 bits (1024), Expect = e-116 Identities = 200/366 (54%), Positives = 252/366 (68%), Gaps = 5/366 (1%) Query: 12 KYVTF--KDDFYFESGRILSPITVAYETYGKLNEKKDNAILICHALTGSAHAAGYNSPDD 69 K+V F DF ESG+ PITVAYE YG++N++K+N ILI HALTG +H A + S DD Sbjct: 13 KFVRFAHNKDFVLESGKTFGPITVAYEVYGEINKEKNNIILITHALTGDSHVAKH-SEDD 71 Query: 70 QKPGWWDDMIGPGKAFDTDKYFIICSNFLGSCYGTTGPASIDPSTGKPYGLKFPVFTVKD 129 KPGWWD +GPGK DT+KYF+ICSN G C GTTGP+SIDP TGKPYG +FP+ T+KD Sbjct: 72 PKPGWWDKFVGPGKMIDTNKYFVICSNVFGGCQGTTGPSSIDPETGKPYGARFPIITIKD 131 Query: 130 MVKLQKKLIDYLGIEKLLCVAGGSMGGMQALEWAVTFPEKTYSIIPIATAGRITPMAIAF 189 MV +QKKL++ L I+ +LCV GGSMGGMQALEWAV++P+ +I IA+ ++ +IAF Sbjct: 132 MVNVQKKLLEALKIDHILCVVGGSMGGMQALEWAVSYPDFMDGVINIASPLKLNAQSIAF 191 Query: 190 NTIGRFAIMKDPNWMNGDYYGKTFPRDGLAIARMAGHITYMSDKSFHKKFGRRYA-TFGG 248 N + R AIM DPNW GDYY KT P GL+IARM G ITY SDK KKF RR Sbjct: 192 NEVMRRAIMADPNWHGGDYYDKTGPSQGLSIARMLGMITYQSDKLMDKKFNRRMKDPVES 251 Query: 249 IYDFFG-YFEVENYLRYNGYKFTERFDANSYLYIIKAMDIFDLSYGYGSYEEAIGRIEAD 307 ++ F FEVE+YL Y G K +RFDAN+YLY+ +AMD++DL YGS EEA+ RI+A Sbjct: 252 FFESFNTEFEVESYLHYQGMKLVQRFDANTYLYLTRAMDLYDLGRTYGSEEEALRRIKAK 311 Query: 308 SLFITFTSDFLFPSYQTEEIVNIMKNHGKNPEWVNIESDYGHDAFLLEFDTQTSCIKEFL 367 L I TSD LFP Q + + + G + + IESDYGHD+FL+E + + I EFL Sbjct: 312 FLLIAITSDILFPLSQMRYMRDKLLEAGVDLVYKEIESDYGHDSFLVEEEKYRNIISEFL 371 Query: 368 SKIYNK 373 +YNK Sbjct: 372 ELLYNK 377 Lambda K H 0.321 0.140 0.432 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: 555 Number of extensions: 26 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: 377 Length of database: 381 Length adjustment: 30 Effective length of query: 347 Effective length of database: 351 Effective search space: 121797 Effective search space used: 121797 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 (21.8 bits) S2: 50 (23.9 bits)
Align candidate WP_015907626.1 CALKRO_RS07945 (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.3882060.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-150 485.6 0.0 4.7e-150 485.4 0.0 1.0 1 NCBI__GCF_000166775.1:WP_015907626.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166775.1:WP_015907626.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 485.4 0.0 4.7e-150 4.7e-150 2 350 .. 20 371 .. 19 372 .. 0.97 Alignments for each domain: == domain 1 score: 485.4 bits; conditional E-value: 4.7e-150 TIGR01392 2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk.GWWdellGpgraldtsry 73 +++++lesG++ ++vay+ yG++n+e++N++l+ Haltg++hva++ +++ k GWWd+++Gpg+ +dt++y NCBI__GCF_000166775.1:WP_015907626.1 20 NKDFVLESGKTFGPITVAYEVYGEINKEKNNIILITHALTGDSHVAKHSEDDPKpGWWDKFVGPGKMIDTNKY 92 6899******************************************887777668****************** PP TIGR01392 74 fvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGGmqalewa 146 fv+c+Nv+G+c+G+tgP+si+petgkpyga+fP +ti+D+v++qk+ll++L ++++ +vvGgS+GGmqalewa NCBI__GCF_000166775.1:WP_015907626.1 93 FVICSNVFGGCQGTTGPSSIDPETGKPYGARFPIITIKDMVNVQKKLLEALKIDHILCVVGGSMGGMQALEWA 165 ************************************************************************* PP TIGR01392 147 lsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmlalltYrseesle 219 +syp++++ ++++a++++++aq iafnev+r+ai++Dp++++G+y++++ P++GL++ARml+++tY+s++ ++ NCBI__GCF_000166775.1:WP_015907626.1 166 VSYPDFMDGVINIASPLKLNAQSIAFNEVMRRAIMADPNWHGGDYYDKTGPSQGLSIARMLGMITYQSDKLMD 238 ************************************************************************* PP TIGR01392 220 erfgreakse.eslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlargrrdslkealkkika 291 ++f+r++k+ es s+++ef+vesyl+yqg k+v+rFdAn+Yl+lt+a+d +dl+r +s +eal++ika NCBI__GCF_000166775.1:WP_015907626.1 239 KKFNRRMKDPvESFFESFNTEFEVESYLHYQGMKLVQRFDANTYLYLTRAMDLYDLGRT-YGSEEEALRRIKA 310 *****9998714455567****************************************8.9************ PP TIGR01392 292 pvlvvgiesDllftleeqeelakalkaakle..yaeieseeGHDaFllekekveelirefl 350 ++l+++i+sD+lf+l++ + ++++l +a+++ y+eies++GHD+Fl+e+ek++++i+efl NCBI__GCF_000166775.1:WP_015907626.1 311 KFLLIAITSDILFPLSQMRYMRDKLLEAGVDlvYKEIESDYGHDSFLVEEEKYRNIISEFL 371 **************************9999999**************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (381 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: 00:00:00.00 # Mc/sec: 22.53 // [ok]
This GapMind analysis is from Jul 26 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