Align Homoserine O-acetyltransferase; HAT; Homoserine transacetylase; HTA; EC 2.3.1.31 (characterized)
to candidate WP_075386127.1 BK574_RS00460 homoserine O-succinyltransferase
Query= SwissProt::Q72X44 (301 letters) >NCBI__GCF_002019605.1:WP_075386127.1 Length = 304 Score = 430 bits (1105), Expect = e-125 Identities = 200/302 (66%), Positives = 251/302 (83%), Gaps = 1/302 (0%) Query: 1 MPIIIDKDLPARKVLQEENIFVMTKERAETQDIRALKIAILNLMPTKQETEAQLLRLIGN 60 MPI + LPA+++L +ENIFVM + RA QDIR LKI ILNLMP K+ TE QLLRL+GN Sbjct: 1 MPIRVPDHLPAKEILNKENIFVMDESRAYKQDIRPLKIVILNLMPIKEVTETQLLRLLGN 60 Query: 61 TPLQLDVHLLHMESHLSRNVAQEHLTSFYKTFRDIENEKFDGLIITGAPVETLSFEEVDY 120 TPLQ+DV +H ++H S+N ++EHL+SFYKTF DI+N+KFDG+IITGAP+E L FEEV+Y Sbjct: 61 TPLQVDVVFIHPDTHKSKNTSEEHLSSFYKTFDDIKNQKFDGMIITGAPIEKLVFEEVNY 120 Query: 121 WEELKRIMEYSKTNVTSTLHICWGAQAGLYHHYGVQKYPLKEKMFGVFEHEV-REQHVKL 179 WEELK+IME++ TNVTSTLHICWGAQAGLY+HYGV KYPL++K+FGVF H+V E +VKL Sbjct: 121 WEELKQIMEWTITNVTSTLHICWGAQAGLYYHYGVPKYPLEKKLFGVFAHQVNNESNVKL 180 Query: 180 LQGFDELFFAPHSRHTEVRESDIREVKELTLLANSEEAGVHLVIGQEGRQVFALGHSEYS 239 L+GFD++F APHSRHTEVR DI +V +L +L+ S EAG+++V + G+Q+F GHSEY Sbjct: 181 LRGFDDVFLAPHSRHTEVRREDIEKVPDLEILSESNEAGIYIVASKNGKQIFISGHSEYD 240 Query: 240 CDTLKQEYERDRDKGLNIDVPKNYFKHDNPNEKPLVRWRSHGNLLFSNWLNYYVYQETPY 299 C TL+ EYERD +KGLNID+P NYF +++ N KPL+RWR+H NLLFSNWLNYYVYQETPY Sbjct: 241 CTTLQDEYERDVNKGLNIDMPINYFPNNDANSKPLLRWRAHSNLLFSNWLNYYVYQETPY 300 Query: 300 VL 301 L Sbjct: 301 DL 302 Lambda K H 0.319 0.136 0.403 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: 345 Number of extensions: 9 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: 301 Length of database: 304 Length adjustment: 27 Effective length of query: 274 Effective length of database: 277 Effective search space: 75898 Effective search space used: 75898 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_075386127.1 BK574_RS00460 (homoserine O-succinyltransferase)
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))
# 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/TIGR01001.hmm # target sequence database: /tmp/gapView.23274.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01001 [M=301] Accession: TIGR01001 Description: metA: homoserine O-succinyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-144 467.2 2.6 1.6e-144 467.0 2.6 1.0 1 lcl|NCBI__GCF_002019605.1:WP_075386127.1 BK574_RS00460 homoserine O-succi Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002019605.1:WP_075386127.1 BK574_RS00460 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 467.0 2.6 1.6e-144 1.6e-144 1 300 [. 1 302 [. 1 303 [. 0.99 Alignments for each domain: == domain 1 score: 467.0 bits; conditional E-value: 1.6e-144 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 mpirvpd+lpa e+l++enifvm e+ra +qdirpl+++ilnlmp k te+qllrll+n+plqvd+ + lcl|NCBI__GCF_002019605.1:WP_075386127.1 1 MPIRVPDHLPAKEILNKENIFVMDESRAYKQDIRPLKIVILNLMPIKEVTETQLLRLLGNTPLQVDVVF 69 9******************************************************************** PP TIGR01001 70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138 ++ d++ksknt +ehl fyk+++++k++kfdG+i+tGap+e+l fe+v+yweelk+i+ew+ +nvtst lcl|NCBI__GCF_002019605.1:WP_075386127.1 70 IHPDTHKSKNTSEEHLSSFYKTFDDIKNQKFDGMIITGAPIEKLVFEEVNYWEELKQIMEWTITNVTST 138 ********************************************************************* PP TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv..kedlllrgfddkflaphsryadldeeliaelt 205 l+icw+aqa+l++ yg+pk+ le+kl+Gv+ h++ ++ llrgfdd flaphsr++++ +e+i++++ lcl|NCBI__GCF_002019605.1:WP_075386127.1 139 LHICWGAQAGLYYHYGVPKYPLEKKLFGVFAHQVNneSNVKLLRGFDDVFLAPHSRHTEVRREDIEKVP 207 **********************************96556679*************************** PP TIGR01001 206 dleilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpia 274 dleil es+eag+y++ask+ ++if+ Gh eyd tl++ey rdv++gl++d+p ny+p++d + +p + lcl|NCBI__GCF_002019605.1:WP_075386127.1 208 DLEILSESNEAGIYIVASKNGKQIFISGHSEYDCTTLQDEYERDVNKGLNIDMPINYFPNNDANSKPLL 276 ********************************************************************* PP TIGR01001 275 swrshanllfanwlnyavyqktpydl 300 wr+h+nllf+nwlny+vyq+tpydl lcl|NCBI__GCF_002019605.1:WP_075386127.1 277 RWRAHSNLLFSNWLNYYVYQETPYDL 302 *************************9 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (304 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: 9.82 // [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