Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_090218894.1 CV091_RS11625 methionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_002796795.1:WP_090218894.1 Length = 401 Score = 293 bits (749), Expect = 8e-84 Identities = 162/384 (42%), Positives = 237/384 (61%), Gaps = 4/384 (1%) Query: 18 ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76 +T+AI G A G + ++LTS + ++ A A F+G+QQG YSR+ NPT++ L Sbjct: 9 STRAIHHGYDAGQHQGSLNPPVYLTSTFTFETAEAGGAMFAGEQQGHFYSRISNPTLDQL 68 Query: 77 EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136 E+RIA LEGAEA ATASGM A+T+ + AGD +I + +G L KF + Sbjct: 69 EERIANLEGAEAGLATASGMGAITSVFWTLVKAGDEVIIDKTLYGCTFAFLSHGLTKFDV 128 Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196 + T VD DP+ DAI T+V +FETPANP +VD+ A+ IA +G VVDN +A Sbjct: 129 KVTPVDLTDPENLTDAITDRTRVVYFETPANPNNRLVDIAAISRIAHAKGAKVVVDNTYA 188 Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGT-EEFINNTLLPFHRNTGPTLSPF 255 TP L RP++ GAD+V +SATK + G G ++AG + G+ E+ L+ TG +SPF Sbjct: 189 TPVLTRPLEHGADIVLHSATKYLGGHGDLVAGLIAGSAEDMTQVRLVGLKDMTGSVMSPF 248 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAA 313 A ++L+GL+TL+LR++R +A+++A+ LE V V++PGL S PQ +LA QM+ Sbjct: 249 TAMLLLRGLKTLELRVERHCRSAMQIAQMLEDHPSVASVHYPGLDSFPQADLARRQMSDF 308 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 G + E+ GG+ +++ L LI + ++GD+ SL+ HPAS THS +R G+ Sbjct: 309 GGMIPFEVVGGKDGGIAMMNRLKLIQRAVSLGDAESLIQHPASMTHSTYTPQERAEHGIA 368 Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397 EG++RL+VGLE +DLI DL AL Sbjct: 369 EGLVRLSVGLETADDLIDDLMAAL 392 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: 399 Number of extensions: 13 Number of successful extensions: 4 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: 401 Length adjustment: 31 Effective length of query: 371 Effective length of database: 370 Effective search space: 137270 Effective search space used: 137270 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 Jul 26 2024. The underlying query database was built on Jul 25 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