Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate HSERO_RS14995 HSERO_RS14995 cystathionine beta-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >FitnessBrowser__HerbieS:HSERO_RS14995 Length = 392 Score = 146 bits (369), Expect = 9e-40 Identities = 108/354 (30%), Positives = 169/354 (47%), Gaps = 14/354 (3%) Query: 51 DAAARFSGDQQ---GMTYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQL 107 D AA S D + G TY PT +LE R+A +EG + CR T SG+AA+ L Sbjct: 43 DVAAMRSRDWREKLGYTYGLHGTPTSFVLEARLAEIEGGKYCRVTPSGLAAIAMVNFAFL 102 Query: 108 SAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPAN 167 +GD ++ +G + L F I D + + IRP T++ + E P + Sbjct: 103 KSGDDVLLPDNVYGPSKDLGQWLERDFQITARFYDPMIGEGLAELIRPTTRLVWTEAPGS 162 Query: 168 PTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLA 227 +M+V D+ A+C A +G++ +DN ++ + + G D+V + TK G VL Sbjct: 163 VSMEVPDIPALCRAAHAKGVLVAIDNTWSAGIAFKAFEHGVDIVMQAVTKYQSGGSDVLM 222 Query: 228 GAVCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEG 287 GAV ++ +N L H G + + ++VL+ L ++ LR + A KVA +L+ Sbjct: 223 GAVIVRDQALNEKLELAHMRLGFGVGMDDVYMVLRSLSSMRLRFEAHDAAARKVAAWLKQ 282 Query: 288 R--VPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGG--RTQAHGLLDALGLIDISNN 343 R + V P P H + AG +FS+ D Q +D+L L I + Sbjct: 283 RPEIVAVLHPAFEDCPGHAHWKRDFSGAGGLFSVIFDPRYVEAQTDRFVDSLRLFKIGYS 342 Query: 344 IGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQAL 397 G + SL G+ +R M G+ ++R N+GLE PEDLIAD++QAL Sbjct: 343 WGGAHSLC---VPYRMKGM---RRAWMREGQ-LVRFNIGLESPEDLIADIEQAL 389 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: 342 Number of extensions: 13 Number of successful extensions: 2 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: 392 Length adjustment: 31 Effective length of query: 371 Effective length of database: 361 Effective search space: 133931 Effective search space used: 133931 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