Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate GFF1560 PGA1_c15810 pyridoxal phosphate-dependent enzyme, cysteine / methionine metabolism
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Phaeo:GFF1560 Length = 385 Score = 229 bits (583), Expect = 1e-64 Identities = 128/359 (35%), Positives = 196/359 (54%), Gaps = 3/359 (0%) Query: 44 YAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAAL 103 YA + ++ G G TYSR +P +++ +R+ +EG T SGMAA++A L Sbjct: 24 YASETPDALDDQYEGRVHGYTYSREGHPNADVVAKRLDAMEGMPGGVVTGSGMAAVSAVL 83 Query: 104 LCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFE 163 L L GDH+IGG +G L LP+ GIETT+ + D AIRP T + E Sbjct: 84 LGLLKTGDHVIGGNQLYGRSMRLMAEDLPRLGIETTLANPGDVAAVKAAIRPETTMILVE 143 Query: 164 TPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQG 223 +NPT+ V D+ + + ++R I+ VVDN F TP +P D GAD+V +S TK++ G Sbjct: 144 AVSNPTLAVADIDGLAQLCKDRDILLVVDNTFTTPRGFQPFDHGADIVIHSITKLLAGHS 203 Query: 224 RVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVAR 283 V+ G V + IN L + TG T SPF+ W+ +G+ + +LR +R A+ +A Sbjct: 204 DVMLGYVVAKDPEINTRLSVYVVTTGMTPSPFDCWLAERGMLSFELRFERAQATAVTLAD 263 Query: 284 FLEG--RVPRVNFPGLPSHPQHNLAMSQMAAAG-PIFSIELDGGRTQAHGLLDALGLIDI 340 L G V RV +P HP H AM+ + G + S EL+GGR A+ ++ Sbjct: 264 HLAGLPGVKRVIYPTRKDHPDHERAMALLDGKGCNMVSFELEGGRAAANAFTRGADGLNF 323 Query: 341 SNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGS 399 + +GD + ++HPAS++H ++ + R +G+ EG R++VGLEDPE L A +A+ + Sbjct: 324 APTLGDVGTTLSHPASSSHRALSTEDRAKLGLSEGFFRISVGLEDPETLCAVFTEAVAA 382 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: 377 Number of extensions: 14 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: 402 Length of database: 385 Length adjustment: 31 Effective length of query: 371 Effective length of database: 354 Effective search space: 131334 Effective search space used: 131334 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 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