Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_015819756.1 TERTU_RS11015 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000023025.1:WP_015819756.1 Length = 402 Score = 333 bits (854), Expect = 5e-96 Identities = 173/382 (45%), Positives = 247/382 (64%), Gaps = 4/382 (1%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T A+R G R GE SE ++ TS + + AG AAARF GD G YSR NPTV E Sbjct: 19 TLAVRAGQVRGPEGEHSEPIYTTSSFVFASAGQAAARFRGDDPGNVYSRYTNPTVRTFED 78 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 RIA LEG EA ATASGMAA+ + + LSAGDH++ R+ FG+ L L KFG++ Sbjct: 79 RIAALEGGEAGVATASGMAAILSTCMALLSAGDHVVCSRSVFGTTTVLFTKYLQKFGVQV 138 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 +V D + +++PNT++ F ETP+NP DV D++ + +A G + VVDN F TP Sbjct: 139 DLVGLTDLAAWEQSLKPNTRLLFLETPSNPICDVADVRKLADLAHSNGCLLVVDNCFCTP 198 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 ALQ+P+ GAD+V +SATK +DGQGR + GAV G + + + F R GPT+SPFNAW Sbjct: 199 ALQKPLALGADIVVHSATKFLDGQGRCMGGAVVGRADQMAE-VTAFLRTCGPTMSPFNAW 257 Query: 259 VVLKGLETLDLRIQRQSENALKVARFLE--GRVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 V +KGLETL LR++ S +AL +A++L+ +V +VN+ GLP HP H+LA+ Q +A G + Sbjct: 258 VFVKGLETLRLRMEAHSASALALAQWLDEHPKVGKVNYAGLPEHPGHSLAVQQQSAFGGV 317 Query: 317 FSIE-LDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEG 375 S E L R A ++DA ++ ++ N+GD+++ + HPA+TTH +++++R G+ EG Sbjct: 318 LSFEVLPNTREAAWTVVDAARIMSLTANLGDAKTTIVHPATTTHGRLSDEERSAAGISEG 377 Query: 376 MLRLNVGLEDPEDLIADLDQAL 397 ++R+ VGLE DL DLD+ L Sbjct: 378 LIRVAVGLESINDLKKDLDRGL 399 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: 429 Number of extensions: 19 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: 402 Length adjustment: 31 Effective length of query: 371 Effective length of database: 371 Effective search space: 137641 Effective search space used: 137641 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