Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_081442714.1 ALVIN_RS05095 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000025485.1:WP_081442714.1 Length = 431 Score = 345 bits (885), Expect = 1e-99 Identities = 182/386 (47%), Positives = 249/386 (64%), Gaps = 6/386 (1%) Query: 18 ATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLE 77 AT+AIR G R+ E SE +F TS + + A +AAARF+G+Q G YSR NPTV E Sbjct: 38 ATRAIRVGHRRTGESEHSEPIFATSSFVFASAAEAAARFAGEQAGNIYSRFTNPTVRAFE 97 Query: 78 QRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIE 137 +R+A LEG E+C ATASGMAA+ + L L GD ++ R+ FGS L D L +FGI Sbjct: 98 ERLAALEGGESCVATASGMAAILSVCLGLLKTGDRILAARSLFGSTTMLFDKYLARFGIR 157 Query: 138 TTVVDARDPQQFIDAIRPN----TKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDN 193 T V D + A+ + T++ F ETP+NP ++VDL+ + A+A G + VVDN Sbjct: 158 TDYVPLSDLSAWETALERDGERRTRLLFCETPSNPLTEMVDLRQLAALAHRHGALLVVDN 217 Query: 194 AFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLS 253 F TPALQRP+ GAD+V +SATK +DGQGR + GAV G + + + R GPTLS Sbjct: 218 CFCTPALQRPLALGADIVVHSATKYLDGQGRCVGGAVVGDRKRVGEEVYGVLRTAGPTLS 277 Query: 254 PFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMA 311 PFNAW+ LKGLETL+LR+ QS A ++A +L+ + V RV++PGL +HPQH+L SQ Sbjct: 278 PFNAWIFLKGLETLELRMLAQSRAAAELAEWLQRQPAVERVHYPGLANHPQHHLVGSQQR 337 Query: 312 AAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMG 371 G I + + GGR A ++DA L+ I+ N+GD ++ +THPA+TTH + +QR G Sbjct: 338 TGGAIVAFAVRGGREAAWRVIDATRLLSITANLGDVKTTITHPATTTHGRLTPEQRAETG 397 Query: 372 VGEGMLRLNVGLEDPEDLIADLDQAL 397 +GEG++RL VGLEDP D+ ADL+ L Sbjct: 398 IGEGLIRLAVGLEDPADIRADLEYGL 423 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: 493 Number of extensions: 20 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: 431 Length adjustment: 31 Effective length of query: 371 Effective length of database: 400 Effective search space: 148400 Effective search space used: 148400 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 10 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