Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_092345077.1 BLU87_RS04325 cystathionine beta-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_900107645.1:WP_092345077.1 Length = 388 Score = 173 bits (439), Expect = 7e-48 Identities = 111/360 (30%), Positives = 183/360 (50%), Gaps = 12/360 (3%) Query: 38 LFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMA 97 +F S +D + + SG QG+TY + PT E+ + LEG RA SG++ Sbjct: 29 IFRGSTVLFDNFAELSLANSGKYQGITYGTDRMPTQRAFEEAVRELEGGALTRAFQSGIS 88 Query: 98 AMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNT 157 A+ L +GDH++ A+ L KF IETT + ++ ++ NT Sbjct: 89 AIINTFLAFTKSGDHILVCDNAYAPTVHYCTQILTKFNIETTFIPPAAGEEIQSYLKDNT 148 Query: 158 KVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATK 217 K+ F E+P + T ++ D+ A+ +A++RGI+TV+DN +ATP P G ++ SATK Sbjct: 149 KLIFLESPGSNTFELQDIPAITTLAKKRGIITVLDNTWATPLYLDPFALGINISIQSATK 208 Query: 218 MMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSEN 277 + G +L G V T+ TL ++R T + + + L+GL TL LR+++ ++ Sbjct: 209 YLTGHSDILMGTVT-TDHPHAATLQEYYRITETYTAEEDCYTALRGLRTLALRLRQHEQS 267 Query: 278 ALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIEL--DGGRTQAHGLLD 333 AL +A++LE ++ V P LPSHPQH + + + +F+ + + +D Sbjct: 268 ALAIAQWLESLPQIGNVIHPALPSHPQHQIWQRDFSGSSGLFAFTFKEEYPAEKLAAFID 327 Query: 334 ALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADL 393 +L L I + G RSL+T + + G+ ++RLN+GLEDP D+I DL Sbjct: 328 SLQLFGIGYSWGGFRSLIT-------AAKYNRTQTSRYAGKMVIRLNIGLEDPGDIIKDL 380 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: 310 Number of extensions: 20 Number of successful extensions: 5 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 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