Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate 200974 SO1812 methionine gamma-lyase (NCBI ptt file)
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__MR1:200974 Length = 397 Score = 345 bits (884), Expect = 2e-99 Identities = 181/396 (45%), Positives = 252/396 (63%), Gaps = 3/396 (0%) Query: 7 QDRSITQNWKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYS 66 QD+S ++ WK ATQAI G R +G L+ T+ + +D A RF+G++ G Y+ Sbjct: 2 QDKS-SKMWKAATQAIHAGHEREAFGSLVTPLYQTATFVFDSAQQGGERFAGNEPGYIYT 60 Query: 67 RLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWL 126 RL NPTV LE+++A+LE AEA ATASGM A++AALL L GDHL+ A +G L Sbjct: 61 RLGNPTVAELERKMAILERAEAAAATASGMGAVSAALLANLQIGDHLVASNAVYGCTFAL 120 Query: 127 TDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERG 186 Q +FGIE T+VD D + AI+PNTKV F ETP NP + V DL A+ AIA+ Sbjct: 121 MTNQFARFGIEVTLVDFSDVELIERAIKPNTKVIFCETPVNPHLQVFDLSAIAAIAKRHS 180 Query: 187 IVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHR 246 + ++VDN F TP LQ+P+ G DVV +SATK ++G G V+AG VCG+E ++ + Sbjct: 181 LTSIVDNTFMTPLLQQPIALGIDVVVHSATKYLNGHGDVIAGIVCGSEAQLHRVKYEILK 240 Query: 247 NTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHN 304 + G +SP +AW++L+GL+TLD+R+QR E+A +VA FLE V RV +PGL SH H Sbjct: 241 DIGAVMSPHDAWLILRGLKTLDVRLQRHCESAQRVAEFLEQHPAVTRVYYPGLKSHSGHR 300 Query: 305 LAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAE 364 QM AG + + EL TQA + L L I+ ++GD+ SL+ HPAS THS + Sbjct: 301 FIGQQMRRAGGVIAFELAADFTQAMAFVGNLKLFSIAVSLGDAESLIQHPASMTHSPYSP 360 Query: 365 DQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGSV 400 + R G+G+ +LR++VGLED +D+IADL QAL ++ Sbjct: 361 EARAAAGIGDNLLRISVGLEDCDDIIADLSQALAAL 396 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: 339 Number of extensions: 11 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: 397 Length adjustment: 31 Effective length of query: 371 Effective length of database: 366 Effective search space: 135786 Effective search space used: 135786 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