Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011779371.1 MVAN_RS10745 cystathionine gamma-lyase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000015305.1:WP_011779371.1 Length = 369 Score = 177 bits (448), Expect = 6e-49 Identities = 126/352 (35%), Positives = 174/352 (49%), Gaps = 20/352 (5%) Query: 52 AAARFSGDQQGM--TYSRLQNPTVEMLEQRIALLEGAEACRATASGMAAMTAALLCQLSA 109 AA + D+ G +Y R NPT LE +A LEGA SGMAA+T+ L Sbjct: 33 AAYHLAPDEDGSLDSYGRSSNPTWRQLESALARLEGAATALVFGSGMAALTSVLRVVAEP 92 Query: 110 GDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQFIDAIRPNTKVFFFETPANPT 169 G L+ + R L G+ TVV+AR + DA R + V ETP+NP Sbjct: 93 GHTLVVPADGYYQVRAYAKEYLAPRGV--TVVEARCAEM-CDAAR-DADVVLAETPSNPG 148 Query: 170 MDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGADVVAYSATKMMDGQGRVLAGA 229 +DVVDL + R + + VVDN ATP Q+P+ GAD+V SATK + G VLAG Sbjct: 149 LDVVDLHRLAMTCRAQRTLLVVDNTTATPFGQQPLSLGADLVVASATKALAGHHDVLAGY 208 Query: 230 VCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLDLRIQRQSENALKVARFLEGR- 288 V G++ + + + GP L F AW+VL+ L + LR +RQ +NA +A L Sbjct: 209 VAGSQPELMERVQRERLHAGPILGAFEAWLVLRSLGSAGLRFERQCQNAAALALMLRSHP 268 Query: 289 -VPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDS 347 V V +PGLP P H +A QM G I + EL G H L+ L+ S + G Sbjct: 269 AVHTVRYPGLPEDPSHAVASMQMRRFGGIVAAEL-GDAQAVHDLVRRSALLIASTSFGG- 326 Query: 348 RSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDPEDLIADLDQALGS 399 H+ V R V +G R+++G+ED +DL+ D+ QALG+ Sbjct: 327 ----------IHTSVDRRARWGDHVSDGFARISLGIEDTDDLVDDVRQALGA 368 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: 349 Number of extensions: 19 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: 369 Length adjustment: 30 Effective length of query: 372 Effective length of database: 339 Effective search space: 126108 Effective search space used: 126108 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