Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_046009022.1 OLEAN_RS09365 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000967895.1:WP_046009022.1 Length = 405 Score = 355 bits (912), Expect = e-102 Identities = 180/385 (46%), Positives = 259/385 (67%), Gaps = 3/385 (0%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T A+R G RS GE SEA++LTS Y ++ A +AAARFSGD++G YSR NPTV E+ Sbjct: 22 TLAVRAGHVRSANGEHSEAIYLTSSYVFNSAAEAAARFSGDEEGNVYSRYTNPTVRTFEE 81 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 R+A LEG E C ATASGMAA+ + ++ L AGD ++ R FGS L + + KF I+ Sbjct: 82 RLAALEGGEDCAATASGMAAIYSVVIAHLKAGDSIVVSRNVFGSTNVLFEKFVRKFNIDV 141 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 VD D + + +AI T++ F E+P+NP ++ DL+A+ +A + + VVDN F TP Sbjct: 142 RYVDLLDLKAWAEAIDSTTRMLFLESPSNPMSEIADLQALADLAHKHDALLVVDNCFCTP 201 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 ALQ+P+ FGAD++ +SATK +DGQGR L GAV G+++ I ++ R+ GPTLSPFNAW Sbjct: 202 ALQQPLKFGADLIIHSATKYIDGQGRCLGGAVVGSKQLI-EPVIGVLRSAGPTLSPFNAW 260 Query: 259 VVLKGLETLDLRIQRQSENALKVARFL--EGRVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 V LKGLETL LR++ SENA+ +AR+L + ++ +VN+ GL HP H LA Q +A G + Sbjct: 261 VFLKGLETLSLRMKAHSENAMVLARWLQQQSQITKVNYSGLEDHPGHELAKKQQSAFGGV 320 Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376 S E+ GG+ A L+D +I I+ N+GD+++ +THPASTTHS ++ + R G+G+G+ Sbjct: 321 LSFEVKGGQQAAWQLIDGTRMISITANLGDTKTTVTHPASTTHSRLSPEDRARAGIGDGL 380 Query: 377 LRLNVGLEDPEDLIADLDQALGSVG 401 +R+ VGLE ED+ D+ L ++G Sbjct: 381 VRIAVGLESIEDIQKDIALGLAAIG 405 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: 410 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: 405 Length adjustment: 31 Effective length of query: 371 Effective length of database: 374 Effective search space: 138754 Effective search space used: 138754 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