Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_011307957.1 MBAR_RS16035 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000195895.1:WP_011307957.1 Length = 394 Score = 288 bits (736), Expect = 3e-82 Identities = 156/371 (42%), Positives = 225/371 (60%), Gaps = 5/371 (1%) Query: 31 WGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRL--QNPTVEMLEQRIALLEGAEA 88 +G + +F TS + ++ A AARF+G++ G Y+R+ PT +L ++ A LEG EA Sbjct: 22 FGAHTTPIFQTSTFIFENARQGAARFAGEESGYVYARIPPNTPTHAVLAEKFAALEGGEA 81 Query: 89 CRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFGIETTVVDARDPQQ 148 + ASGMAA+TA L L GDHLI +G L LP GIE + VD + Sbjct: 82 GQTFASGMAAVTAIALTALKQGDHLISTDVVYGCTYSLFSQVLPGLGIEVSFVDTSKTEN 141 Query: 149 FIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAFATPALQRPMDFGA 208 A +P TK+ F E+PANPT++V D+ + IARE + VVDN FATP QRP++ GA Sbjct: 142 VKRAFKPETKMVFLESPANPTLNVCDIPEIARIARENEALCVVDNTFATPYFQRPLELGA 201 Query: 209 DVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPFNAWVVLKGLETLD 268 D+ S TK + G +L G V G +FI+ + TG + P AW+ ++GL+TL Sbjct: 202 DLSLSSCTKYIGGHADLLGGIVAGNNDFIDR-MSEVVGYTGGIMGPHEAWLCIRGLKTLH 260 Query: 269 LRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAAAGPIFSIELDGGRT 326 +R++R +ENA+KVA FLE R V V +PGLP HPQ+ LA QM+ + S E+ GG Sbjct: 261 IRMERHAENAMKVAEFLESRPEVEWVRYPGLPGHPQYELARKQMSGFSGMLSFEVKGGIE 320 Query: 327 QAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVGEGMLRLNVGLEDP 386 L+D + L ++ ++G + +L+ HPAS TH+ V + R +G+ +G++RL+VG+EDP Sbjct: 321 AGRKLMDNVKLCSLAVSLGATDTLIQHPASMTHACVPHEVRKSVGITDGLVRLSVGIEDP 380 Query: 387 EDLIADLDQAL 397 ED+IADL QAL Sbjct: 381 EDIIADLKQAL 391 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: 393 Number of extensions: 17 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: 394 Length adjustment: 31 Effective length of query: 371 Effective length of database: 363 Effective search space: 134673 Effective search space used: 134673 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