Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate AO356_13410 AO356_13410 homoserine O-acetyltransferase
Query= SwissProt::D7E9E0 (489 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_13410 Length = 379 Score = 377 bits (967), Expect = e-109 Identities = 192/368 (52%), Positives = 256/368 (69%), Gaps = 6/368 (1%) Query: 5 SIGNVETKYYQIPEELVLESGKKISDVTLAYETYGTLNWDKSNAILVCHALTGDAHAAGW 64 S+G V + E L L G+ + L YETYGTLN SNA+L+CHAL+G HAAG+ Sbjct: 9 SVGLVTPQTAHFSEPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGY 68 Query: 65 HE-GDRKPGWWDIIIGPGKALDTRKYFIICSNVIGGCKGSTGPSSINPDTGESYGLDFPV 123 H DRKPGWWD IGPGK +DT K+F++ N +GGC GSTGPSS+NPDTG+ +G DFPV Sbjct: 69 HSIDDRKPGWWDSCIGPGKPIDTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPV 128 Query: 124 VTIKDMVNAQKKLIDYLGISKLLAVIGGSMGGLQVLQWSVSYPDMVKKAIPIATAGYSTP 183 +T++D V++Q +L D LGI + AVIGGS+GG+Q LQW+++YPD V+ + IA+A + Sbjct: 129 LTVEDWVHSQARLADRLGIGQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSA 188 Query: 184 QQIAFNEVGRIAIVSDPNWNSGNYYGEKE-PTHGLALARMIGHITYLSDDSMHQKFGRRL 242 Q IAFNEV R AI++DP ++ G++ P GL LARM+GHITYLSDDSM +KFGR L Sbjct: 189 QNIAFNEVARQAILTDPEFHGGSFQEHGVIPKRGLMLARMVGHITYLSDDSMGEKFGRGL 248 Query: 243 Q-DKNEYEFDFSREFEVESYLHYQGLTFTERFDANSYLYLTKAIDYFDLTEN--NSLAEG 299 + +K Y+F S EF+VESYL YQG F+ RFDAN+YL +TKA+DYFD N ++LA+ Sbjct: 249 KSEKLNYDF-HSVEFQVESYLRYQGEEFSGRFDANTYLLMTKALDYFDPAANFDDNLAKT 307 Query: 300 LKNVEAKFLVISFTSDWLYPPYQLREIVMALSANNADVTYREIESNYGHDSFLLESGQLN 359 N AKF V+SFT+DW + P + RE+V AL A DV Y EI++ GHD+FL+ + Sbjct: 308 FANATAKFCVMSFTTDWRFSPARSRELVDALMAARKDVCYLEIDAPQGHDAFLIPIPRYL 367 Query: 360 YVLNNFLS 367 N+++ Sbjct: 368 QAFGNYMN 375 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: 500 Number of extensions: 21 Number of successful extensions: 4 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: 379 Length adjustment: 32 Effective length of query: 457 Effective length of database: 347 Effective search space: 158579 Effective search space used: 158579 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 AO356_13410 AO356_13410 (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.32625.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.4e-142 458.9 0.0 6.2e-142 458.8 0.0 1.0 1 lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 AO356_13410 homoserine O-acetylt Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 AO356_13410 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 458.8 0.0 6.2e-142 6.2e-142 3 345 .. 22 369 .. 20 375 .. 0.97 Alignments for each domain: == domain 1 score: 458.8 bits; conditional E-value: 6.2e-142 TIGR01392 3 eeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedk..GWWdellG 63 e+l l +G l+ +++ y+tyGtlna +Navl+cHal+g++h+ag+++ +d+ GWWd+ +G lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 22 EPLALACGRSLPAYDLIYETYGTLNATASNAVLICHALSGHHHAAGYHSIDDRkpGWWDSCIG 84 789*******************************************998777678******** PP TIGR01392 64 pgraldtsryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgv 126 pg+++dts++fvv+lN+lG+c+GstgP+s+np+tgkp+ga+fP++t++D+v+ q++l+d+Lg+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 85 PGKPIDTSKFFVVSLNNLGGCNGSTGPSSLNPDTGKPFGADFPVLTVEDWVHSQARLADRLGI 147 *************************************************************** PP TIGR01392 127 eklaavvGgSlGGmqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndG 189 ++aav+GgSlGGmqal+w+++yp+rv++++++a+++++saq+iafnev+rqail+Dpe+++G lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 148 GQWAAVIGGSLGGMQALQWTITYPDRVRHCLAIASAPKLSAQNIAFNEVARQAILTDPEFHGG 210 *************************************************************** PP TIGR01392 190 eyaeee.qPekGLalARmlalltYrseesleerfgreakseeslassleeefsvesylryqgk 251 +++e++ P++GL lARm++++tY+s++s+ e+fgr kse+ ++ ef+vesylryqg+ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 211 SFQEHGvIPKRGLMLARMVGHITYLSDDSMGEKFGRGLKSEKLNYDFHSVEFQVESYLRYQGE 273 ******9********************************9977777779************** PP TIGR01392 252 kfverFdAnsYllltkaldthdlargrrdslkealkkikapvlvvgiesDllftleeqeelak 314 +f rFdAn+Yll+tkald++d a++ +d+l++++++++a+++v+++++D++f++++++el++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 274 EFSGRFDANTYLLMTKALDYFDPAANFDDNLAKTFANATAKFCVMSFTTDWRFSPARSRELVD 336 *************************************************************** PP TIGR01392 315 alkaakle..yaeieseeGHDaFllekekveel 345 al aa+++ y ei+ ++GHDaFl+ ++ ++ lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_13410 337 ALMAARKDvcYLEIDAPQGHDAFLIPIPRYLQA 369 ****999999**************988776665 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (379 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: 12.03 // [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