Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_086508787.1 BZY95_RS04510 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_002151265.1:WP_086508787.1 Length = 398 Score = 320 bits (821), Expect = 4e-92 Identities = 169/388 (43%), Positives = 238/388 (61%), Gaps = 3/388 (0%) Query: 15 WKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVE 74 W T AIR G R+ E E +F TS + Y A +AA +F G+++G YSR NPTV Sbjct: 11 WALETLAIRAGHQRTHEQEHGEPIFPTSSFVYGSAAEAARKFGGEERGNVYSRFTNPTVH 70 Query: 75 MLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKF 134 E+R+A LEG E C AT+SGMAA+ + +L L AGD ++ R+ FGS L D K Sbjct: 71 TFERRLAALEGGERCVATSSGMAAILSTVLALLQAGDEIVASRSLFGSTVSLFDKYFGKL 130 Query: 135 GIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNA 194 GI T V+ D + AI P+T++ F ETP+NP +VVD+ A+ IA + +DN Sbjct: 131 GITTRYVELSDLAAWEAAITPHTRLLFAETPSNPLSEVVDIAALAEIAHRHQALLAIDNC 190 Query: 195 FATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSP 254 F TPALQ+P+ GAD+V +SATK +DGQGR + GAV G ++ + + R GP LSP Sbjct: 191 FLTPALQQPLALGADLVIHSATKYLDGQGRAVGGAVVGRDKELEE-VFGVVRTCGPCLSP 249 Query: 255 FNAWVVLKGLETLDLRIQRQSENALKVARFLE--GRVPRVNFPGLPSHPQHNLAMSQMAA 312 FNAW+ KGLETL LR++ NA +A +L+ V RV++ GLP HPQH LA Q A Sbjct: 250 FNAWIFTKGLETLSLRMRAHCGNAQALAEWLQVHPAVARVHYSGLPDHPQHELAGRQQAG 309 Query: 313 AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV 372 G + E+ GGR A ++DA ++ I+ N+GD ++ +THPA+TTH ++ Q+ G+ Sbjct: 310 YGAVLGFEVKGGREAAWSVIDATRMLSITGNLGDVKTTITHPATTTHGRLSPAQKDAAGI 369 Query: 373 GEGMLRLNVGLEDPEDLIADLDQALGSV 400 EG++R+ VGLE ED+ DL + L ++ Sbjct: 370 SEGLIRVAVGLESIEDIRLDLARGLDAL 397 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: 404 Number of extensions: 21 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: 398 Length adjustment: 31 Effective length of query: 371 Effective length of database: 367 Effective search space: 136157 Effective search space used: 136157 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