Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_012505314.1 PAES_RS03660 homoserine O-acetyltransferase
Query= SwissProt::Q3M5Q6 (359 letters) >NCBI__GCF_000020625.1:WP_012505314.1 Length = 357 Score = 404 bits (1038), Expect = e-117 Identities = 202/352 (57%), Positives = 249/352 (70%), Gaps = 4/352 (1%) Query: 1 MNYQDFISEQTEYYHLPVPFELEGGGVLTGVQVAYRTWGKLNSAGDNGVLICHALTGSAD 60 MNY IS+ T ++ PF LE GGVL V VAYRTWG+LN N VL+CHALTGSAD Sbjct: 1 MNYIKPISKHTGFFVSRQPFTLESGGVLPEVTVAYRTWGRLNRDRSNAVLVCHALTGSAD 60 Query: 61 ADEWWEGLLGANKALDSDRDFIICSNILGSCYGTTGATSINPQTGIPYGASFPAITIRDM 120 ADEWW G+ G A D D DF+ICSN+LGSCYGTTG S+NPQ+G YG FPAITIRDM Sbjct: 61 ADEWWPGMFGKGCAFDPDHDFVICSNVLGSCYGTTGPLSVNPQSGRHYGPDFPAITIRDM 120 Query: 121 VRLQAALIQHLGIKSLQLVIGGSLGGMQVLEWALLYPEIVQAIAPIATSGRHSAWCIGLS 180 V LQ L+ LGI+ L+LV+G SLGGMQVLEW LYPE V A+ P+ SGRHSAWCI S Sbjct: 121 VHLQRLLLDELGIERLRLVVGASLGGMQVLEWGCLYPEKVHALMPMGISGRHSAWCIAQS 180 Query: 181 EAQRQAIYADPNWKGGNYTKEQPPSQGLAVARMMAMSAYRSWQSFTARFGR-QYDAVADQ 239 EAQR AI AD W G Y P GL ARMMAM YRS+++F RFGR + D++ Sbjct: 181 EAQRSAIMADREWNDGWYDPAHQPKGGLGAARMMAMCTYRSFENFQERFGRKRKDSLL-- 238 Query: 240 FAIASYLQHHGQKLVQRFDANTYITLTQAMDSHDVAQGRD-YKSVLQSIKQPALVVAIDS 298 F SYL + G+KLV+RFDANTYI LT+AMD HD+ +GR+ Y++ L +I+ P +++I S Sbjct: 239 FQAESYLHYQGEKLVRRFDANTYIALTRAMDMHDLGRGRESYEAALDAIRVPVAILSITS 298 Query: 299 DILYPPTEQQELADFIPDAQLGWLQSSYGHDAFLIDIATLSQLVINFRQSLS 350 DILYPP EQ+ELA IPD+ +G+L+ YGHDAFLI +S +V F++ ++ Sbjct: 299 DILYPPEEQEELAKLIPDSSIGYLREPYGHDAFLILTDEVSAMVRQFKERIA 350 Lambda K H 0.319 0.134 0.406 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: 402 Number of extensions: 19 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: 359 Length of database: 357 Length adjustment: 29 Effective length of query: 330 Effective length of database: 328 Effective search space: 108240 Effective search space used: 108240 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: 49 (23.5 bits)
Align candidate WP_012505314.1 PAES_RS03660 (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.19534.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-142 459.3 0.0 4.8e-142 459.1 0.0 1.0 1 lcl|NCBI__GCF_000020625.1:WP_012505314.1 PAES_RS03660 homoserine O-acetyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020625.1:WP_012505314.1 PAES_RS03660 homoserine O-acetyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 459.1 0.0 4.8e-142 4.8e-142 2 350 .. 17 346 .. 16 347 .. 0.98 Alignments for each domain: == domain 1 score: 459.1 bits; conditional E-value: 4.8e-142 TIGR01392 2 eeeltlesGevlsevevayktyGtlnaerdNavlvcHaltgsahvagkadeedkGWWdellGpgraldt 70 ++++tlesG+vl+ev+vay+t+G+ln++r+NavlvcHaltgsa+++ + WW ++G+g a+d+ lcl|NCBI__GCF_000020625.1:WP_012505314.1 17 RQPFTLESGGVLPEVTVAYRTWGRLNRDRSNAVLVCHALTGSADAD---E-----WWPGMFGKGCAFDP 77 689******************************************9...5.....************** PP TIGR01392 71 sryfvvclNvlGsckGstgPlsinpetgkpygaefPlvtirDlvkaqkalldsLgveklaavvGgSlGG 139 ++ fv+c+NvlGsc+G+tgPls+np++g++yg++fP++tirD+v+ q+ lld+Lg+e+l++vvG+SlGG lcl|NCBI__GCF_000020625.1:WP_012505314.1 78 DHDFVICSNVLGSCYGTTGPLSVNPQSGRHYGPDFPAITIRDMVHLQRLLLDELGIERLRLVVGASLGG 146 ********************************************************************* PP TIGR01392 140 mqalewalsypervkkivvlatsarasaqaiafnevqrqailsDpeyndGeyaeeeqPekGLalARmla 208 mq+lew + ype+v++++++ s r+sa++ia +e+qr ai++D e+ndG+y+ +qP+ GL++ARm+a lcl|NCBI__GCF_000020625.1:WP_012505314.1 147 MQVLEWGCLYPEKVHALMPMGISGRHSAWCIAQSEAQRSAIMADREWNDGWYDPAHQPKGGLGAARMMA 215 ********************************************************************* PP TIGR01392 209 lltYrseesleerfgreakseeslassleeefsvesylryqgkkfverFdAnsYllltkaldthdlarg 277 ++tYrs e+++erfgr++k++ f++esyl+yqg+k+v+rFdAn+Y++lt+a+d+hdl+rg lcl|NCBI__GCF_000020625.1:WP_012505314.1 216 MCTYRSFENFQERFGRKRKDS--------LLFQAESYLHYQGEKLVRRFDANTYIALTRAMDMHDLGRG 276 ***************988877........479************************************* PP TIGR01392 278 rrdslkealkkikapvlvvgiesDllftleeqeelakalkaakleyaeieseeGHDaFllekekveeli 346 r+s+++al++i++pv +++i+sD+l+++eeqeelak +++++ +++++GHDaFl+ +++v++++ lcl|NCBI__GCF_000020625.1:WP_012505314.1 277 -RESYEAALDAIRVPVAILSITSDILYPPEEQEELAKLIPDSSIG--YLREPYGHDAFLILTDEVSAMV 342 .8******************************************9..899******************* PP TIGR01392 347 refl 350 r+f lcl|NCBI__GCF_000020625.1:WP_012505314.1 343 RQFK 346 *996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (351 nodes) Target sequences: 1 (357 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.86 // [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