Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011446307.1 SARO_RS13530 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000013325.1:WP_011446307.1 Length = 402 Score = 615 bits (1585), Expect = 0.0 Identities = 305/402 (75%), Positives = 340/402 (84%) Query: 1 MKRRTGQDRSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQ 60 MKR TGQDRSIT+ W+PATQAIRGGT RSE GETSEALFLTSG+ YD A AARF+G+ Sbjct: 1 MKRTTGQDRSITRKWRPATQAIRGGTWRSEMGETSEALFLTSGFTYDDAATVAARFAGEA 60 Query: 61 QGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAF 120 +GMTYSRLQNPTV+MLE+RIALLEGAEACR A+GMAAMT ALLCQLSAGDH++ +AAF Sbjct: 61 EGMTYSRLQNPTVQMLEERIALLEGAEACRTQATGMAAMTTALLCQLSAGDHIVAAKAAF 120 Query: 121 GSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCA 180 GSCRWL D LP+FG++ T +DA D + AIRPNTKVFFFE+PANPTMD+VDL+ VC Sbjct: 121 GSCRWLVDNLLPRFGVQGTTIDASDNAAWEAAIRPNTKVFFFESPANPTMDIVDLEFVCG 180 Query: 181 IARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNT 240 +A++ GI TVVDNAFAT ALQRPMDFGADVVAYSATKMMDGQGRV+AGAVCG+ ++INN Sbjct: 181 LAKKHGITTVVDNAFATAALQRPMDFGADVVAYSATKMMDGQGRVMAGAVCGSADWINNV 240 Query: 241 LLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGRVPRVNFPGLPSH 300 LLPF RNTGP ++ FNAWVVLKGLETLDLRI RQSENALKVA F+E RVPR+ +PGLPSH Sbjct: 241 LLPFQRNTGPNIAAFNAWVVLKGLETLDLRIHRQSENALKVASFVEKRVPRLLYPGLPSH 300 Query: 301 PQHNLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHS 360 PQH LA QM A G IFS +LDGGR QAH LLDAL LIDISNNIGDSRSLM HPASTTH Sbjct: 301 PQHALAQKQMKAGGTIFSFDLDGGRAQAHALLDALQLIDISNNIGDSRSLMCHPASTTHH 360 Query: 361 GVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGSVGL 402 GV + R MGVGEGMLRLNVGLED +DLI DLDQAL GL Sbjct: 361 GVGPETRADMGVGEGMLRLNVGLEDADDLIEDLDQALRKAGL 402 Lambda K H 0.319 0.134 0.396 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: 552 Number of extensions: 14 Number of successful extensions: 1 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: 402 Length of database: 402 Length adjustment: 31 Effective length of query: 371 Effective length of database: 371 Effective search space: 137641 Effective search space used: 137641 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)
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