Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate CA265_RS13080 CA265_RS13080 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Pedo557:CA265_RS13080 Length = 388 Score = 325 bits (832), Expect = 2e-93 Identities = 169/381 (44%), Positives = 246/381 (64%), Gaps = 3/381 (0%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T AIR T RS E S ++LTS Y ++ A + A F+ +++G YSR NP + Sbjct: 8 TIAIRTQTERSLHKEHSSPIYLTSSYKFEDAEEMRALFANEKEGNVYSRYSNPNTSEFIE 67 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 ++ LLEGAE ATA+GMAA+ L GDHL+ R+ FGS L +G+ Sbjct: 68 KMCLLEGAEDGFATATGMAAIFTTFGAFLKNGDHLVSSRSVFGSTHQLLTNVFSNWGVTF 127 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 D PQ + I+PNTK+ F ETP+NP +D++DL+ + +A++ ++ VVDN FATP Sbjct: 128 DYADLDKPQDWEALIKPNTKMIFVETPSNPGIDIIDLEFLGDLAKKHNVLLVVDNCFATP 187 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 LQ+P+ FGA + +SATK +DGQGRVL G + GT+E I + ++ F R++GP LSPFNAW Sbjct: 188 YLQQPIKFGAHISIHSATKYIDGQGRVLGGVILGTKELIAD-VIGFARHSGPALSPFNAW 246 Query: 259 VVLKGLETLDLRIQRQSENALKVARFLE--GRVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 ++ K LETL +R+ R ENALKVA +LE ++ V +P LPSHPQ+++A QM G I Sbjct: 247 ILSKSLETLAIRMDRHCENALKVAEYLEKHPKIKLVKYPFLPSHPQYDIAKKQMKQGGGI 306 Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376 +I ++GG A +D L + IS N+ D+RS+ THPA++THS + E+QR +G+ +G Sbjct: 307 VTIVVEGGIDAARKFMDGLQMFSISANLADTRSIATHPATSTHSKLTEEQRNEVGIEQGS 366 Query: 377 LRLNVGLEDPEDLIADLDQAL 397 +RL++GLE D++AD++QAL Sbjct: 367 IRLSIGLEHINDILADIEQAL 387 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: 381 Number of extensions: 19 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: 388 Length adjustment: 31 Effective length of query: 371 Effective length of database: 357 Effective search space: 132447 Effective search space used: 132447 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