Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate Echvi_2283 Echvi_2283 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__Cola:Echvi_2283 Length = 391 Score = 322 bits (824), Expect = 2e-92 Identities = 163/381 (42%), Positives = 247/381 (64%), Gaps = 3/381 (0%) Query: 19 TQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQ 78 T+A+R +++S E S +++TS + +D A +A F+ + G YSR NP L + Sbjct: 8 TEAVRIASSKSNQREHSAPIYMTSSFTFDSAEEARQMFAEEIPGNIYSRYANPNSSDLIE 67 Query: 79 RIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIET 138 ++ +EG E ATASGMAAM ++ L GDH++ R+ FGS L PK+GI + Sbjct: 68 KVCAVEGTEDGIATASGMAAMFGSMASLLEQGDHILASRSLFGSTHQLLTRVFPKWGITS 127 Query: 139 TVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATP 198 T D D + + ++PNTK+ F ETP+NP ++V+DL+ + A+ ++ VVDN FATP Sbjct: 128 TYGDISDIENWDKLVKPNTKMLFIETPSNPGLEVIDLEWIGKFAKAHNLILVVDNCFATP 187 Query: 199 ALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAW 258 LQ+P +GAD+VA+SATK +DGQGRVL G + G +E I F R+TGP++SPFNAW Sbjct: 188 YLQQPAKWGADIVAHSATKYIDGQGRVLGGLILGKQELIKEVQF-FTRHTGPSISPFNAW 246 Query: 259 VVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAAGPI 316 ++ + +ETL +R++R NAL VA + + + V +P L SHPQH+LA QM G I Sbjct: 247 ILSRSMETLAIRMERHCANALAVASYFQDNKELEFVKYPFLKSHPQHDLAKKQMKHGGGI 306 Query: 317 FSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGM 376 ++ L GG +A +D L +I ++ N+GD+RS++THPASTTHS + E++R +G+ G+ Sbjct: 307 VTLTLKGGIERAQRFIDELQMITVTANLGDTRSIITHPASTTHSKLTEEERQRVGILPGL 366 Query: 377 LRLNVGLEDPEDLIADLDQAL 397 +RL+ GLE +D+IAD+++AL Sbjct: 367 IRLSAGLEHHDDIIADIERAL 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: 383 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: 391 Length adjustment: 31 Effective length of query: 371 Effective length of database: 360 Effective search space: 133560 Effective search space used: 133560 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