Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate GFF1863 HP15_1820 methionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Marino:GFF1863 Length = 413 Score = 324 bits (831), Expect = 3e-93 Identities = 166/379 (43%), Positives = 243/379 (64%), Gaps = 3/379 (0%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T A+R G R+ E S+A+F TS + Y A AAARF G++ G YSR NPTV+ E Sbjct: 23 TLAVRAGQIRTGQLEHSDAIFPTSSFVYGSAAQAAARFGGEEPGNIYSRFTNPTVQAFEG 82 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 RIA +EG E ATASGM+A+ + + L +GDH+I R FG+ L + +FG+ET Sbjct: 83 RIAAMEGGERAVATASGMSAILSTCMALLKSGDHVICSRGVFGTTNVLFQKYMARFGVET 142 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 T V D +++ +IR T++ F ETP+NP +V D++ + +AR+ + VVDN F TP Sbjct: 143 TFVSLTDMEEWQASIRSETRMLFIETPSNPLCEVADMEILGQLARDNDALFVVDNCFCTP 202 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 LQRP++ GAD+V +SATK +DGQGR + G V G+E+ + + F R+ GPT+SPFNAW Sbjct: 203 VLQRPLEQGADIVIHSATKYLDGQGRCVGGVVVGSEKMMEE-VYGFLRSAGPTMSPFNAW 261 Query: 259 VVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 V KGLETL +R++ +NAL++A +LE + V RV + GL SHPQH LA Q G + Sbjct: 262 VFQKGLETLPIRMRAHCDNALELALWLEQQPAVERVFYAGLQSHPQHELAKKQQTGFGGV 321 Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376 S +L G R +A +D +I I+ N+GD ++ +THPA+TTH ++ + + G+ E + Sbjct: 322 LSFQLKGAREEAWRFIDGTRMISITANLGDVKTTITHPATTTHGRLSPEDKARAGITENL 381 Query: 377 LRLNVGLEDPEDLIADLDQ 395 +R++VG+E EDL DL++ Sbjct: 382 IRISVGIEAVEDLKTDLER 400 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: 415 Number of extensions: 12 Number of successful extensions: 3 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: 413 Length adjustment: 31 Effective length of query: 371 Effective length of database: 382 Effective search space: 141722 Effective search space used: 141722 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