Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate AO353_24330 AO353_24330 cystathionine beta-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__pseudo3_N2E3:AO353_24330 Length = 389 Score = 182 bits (461), Expect = 2e-50 Identities = 114/347 (32%), Positives = 175/347 (50%), Gaps = 11/347 (3%) Query: 60 QQGMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAA 119 +Q TY R NP+ E L Q + LEGAE SG++A T A+L + AGDHL+ Sbjct: 47 RQKYTYGRWNNPSTEALTQALQQLEGAEGTVLCPSGLSACTTAILSVVGAGDHLLIADNV 106 Query: 120 FGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVC 179 + R + + GIE T D +D ++PNTK + E+P + T+++ D+ A+ Sbjct: 107 YSPIRAFCEQVGQRLGIEVTFYDPTIGAGIVDFLKPNTKAIYTESPGSLTLEIQDIPAIA 166 Query: 180 AIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINN 239 +A E I+ + DN + TP ++ G D+ +ATK + G + G V ++ + Sbjct: 167 KVAHEHDILVITDNTWGTPLYFPSLELGVDLSIMAATKYIVGHSDAVLGTVSASKR-AWD 225 Query: 240 TLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGL 297 +L FH N G SP + + L+G+ TLD+R++R +NA VA++LE R V V +P L Sbjct: 226 SLKRFHFNMGLFASPDDVTLALRGMRTLDVRLERHYKNATTVAKWLETREEVEAVYYPAL 285 Query: 298 PSHPQHNLAMSQMAAAGPIFS-IELDGGRTQAHGLLDALGLIDISNNIGDSRSL-MTHPA 355 SHPQH L A + S + + A LLD+L L I + G SL M Sbjct: 286 ESHPQHQLWKRDFKGASGLLSFVTKPSTQAAADALLDSLSLFSIGYSWGGFESLAMIADP 345 Query: 356 STTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGSVGL 402 S + + + ++RL++GLEDP DLI DL+Q + Sbjct: 346 KPVRSATSWE------IDGHLVRLHIGLEDPSDLIEDLEQGFAKFNM 386 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: 361 Number of extensions: 18 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: 389 Length adjustment: 31 Effective length of query: 371 Effective length of database: 358 Effective search space: 132818 Effective search space used: 132818 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