Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate CCNA_03271 CCNA_03271 methionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Caulo:CCNA_03271 Length = 401 Score = 296 bits (759), Expect = 5e-85 Identities = 168/384 (43%), Positives = 233/384 (60%), Gaps = 4/384 (1%) Query: 18 ATQAIRGG-TARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEML 76 +T+AI G E G + L LTS +A++ A F+G ++G YSR+ NPT ++L Sbjct: 9 STRAIHAGYDPADEHGALTPPLHLTSTFAFESAEAGGEMFAGTREGHFYSRISNPTTDLL 68 Query: 77 EQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGI 136 E+R+A LEGAEA ATASGM A+TA L L AGD +I + +G L +FG+ Sbjct: 69 ERRLASLEGAEAAVATASGMGAITATLWSFLRAGDEVITDQTLYGCTFAFLRDGLTRFGV 128 Query: 137 ETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFA 196 VD P+ AI T++ +FETPANP M +VD+ A+ IA G VVDN +A Sbjct: 129 TVKQVDMTRPETLAAAISDQTRIVYFETPANPNMRLVDIAAITRIAHAAGAKVVVDNTYA 188 Query: 197 TPALQRPMDFGADVVAYSATKMMDGQGRVLAG-AVCGTEEFINNTLLPFHRNTGPTLSPF 255 TP L RP+ GAD+V +SATK + G G ++ G A G E+ L TG +SPF Sbjct: 189 TPCLTRPLALGADIVVHSATKYLGGHGDLVGGIAAGGIEDMARVRLCGVKDMTGAVMSPF 248 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAA 313 A++VL+GL+TL LR+ R S++A VAR+LE V +V +PGL S PQ +LA QMAA Sbjct: 249 TAFLVLRGLKTLSLRMARHSQSAQAVARWLEDHPAVEQVFYPGLQSFPQRDLAARQMAAG 308 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 G + + EL GG +++ L LI + ++GD+ +L+ HPAS THS ++R G+G Sbjct: 309 GGMMAFELKGGHAAGVAMMNRLALIRRAVSLGDAETLIQHPASMTHSPYTPEERAAAGIG 368 Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397 EGM+RL+VGLED D++ADL AL Sbjct: 369 EGMVRLSVGLEDVADILADLAMAL 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: 377 Number of extensions: 16 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: 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 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