Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_012592297.1 MSIL_RS16900 PLP-dependent transferase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000021745.1:WP_012592297.1 Length = 392 Score = 197 bits (502), Expect = 3e-55 Identities = 129/384 (33%), Positives = 202/384 (52%), Gaps = 10/384 (2%) Query: 16 KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75 +PAT + G T S +F TS + +D D A ++G + + YSR NPTV Sbjct: 12 EPATGSA-GRTRAYALDAASPPIFQTSSFFFDNFDDMADVYAGRSRRLIYSRGDNPTVME 70 Query: 76 LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135 E+ +A L+GAEA RA +SGM A+ A ++ +SAGD ++ R + L + L KFG Sbjct: 71 FERVMAELDGAEAARAFSSGMGAIAATIIAFVSAGDRIVTVRNVYSDAYRLFELVLAKFG 130 Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195 + +D D A+ P K+ + ETP + T ++ D+ + A+AR +G+V+V+DN++ Sbjct: 131 VTVDYLDGADAGAIAAAL-PGAKLLYLETPTSLTFELQDIATLAALARAQGVVSVIDNSW 189 Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPF 255 ATP Q+P+ G D+V ++A+K + G +AG V G+ E + + G LSPF Sbjct: 190 ATPQFQKPIAHGVDLVIHAASKYLGGHSDTVAGVVSGSAEHVARINAGAYAYLGAKLSPF 249 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAA 313 AW++L+GL TL+LR+ R ++ L +A L+ V V P HP + ++ Sbjct: 250 EAWLLLRGLATLELRLPRHMQSGLLIAGRLKAHPNVSLVRHPAYSDHP----GKATLSGF 305 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 +FSIE+ G +AL L + + G SL+ PA + GV Sbjct: 306 SGLFSIEV-GENIDVRTFANALKLFRLGVSWGGPESLVV-PALAPLQLRTANCFARFGVS 363 Query: 374 EGMLRLNVGLEDPEDLIADLDQAL 397 ++RL+VGLED E L DL++AL Sbjct: 364 PRLIRLHVGLEDAEALWDDLERAL 387 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: 20 Number of successful extensions: 3 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 Jul 25 2024. The underlying query database was built on Jul 25 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