Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_074201059.1 BUQ81_RS03740 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_900141795.1:WP_074201059.1 Length = 391 Score = 370 bits (950), Expect = e-107 Identities = 189/388 (48%), Positives = 255/388 (65%), Gaps = 2/388 (0%) Query: 15 WKPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVE 74 W T AI GG R+ GE SEA+F TS +A+D A AAARFSGD+ G YSR NPTV Sbjct: 3 WSEETFAIHGGYRRTPEGENSEAIFPTSSFAFDSAAQAAARFSGDEPGNIYSRFTNPTVR 62 Query: 75 MLEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKF 134 EQR+A +EG EAC TASGM+A+ + +L L +GDH++ ++ FG+ + L L K Sbjct: 63 TFEQRLAAMEGGEACVGTASGMSAILSLMLGMLESGDHIVSSQSIFGTTKVLFSKYLGKL 122 Query: 135 GIETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNA 194 GI+TT V D + AIRP T++ F ETP+NP DV D++ + IA + VVDN Sbjct: 123 GIDTTYVPLTDYDAWAAAIRPETRMLFLETPSNPMTDVADIQRLAEIAHAHDCLLVVDNC 182 Query: 195 FATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSP 254 F TPALQ+P+ GAD+V +SATK +DGQGR + GAV G E + + F R GP++SP Sbjct: 183 FCTPALQQPLKLGADLVIHSATKFLDGQGRCVGGAVVGPESLVEEHVRGFLRTCGPSMSP 242 Query: 255 FNAWVVLKGLETLDLRIQRQSENALKVARFLEGR--VPRVNFPGLPSHPQHNLAMSQMAA 312 FNAWV KGLETL +R+Q S NAL +A++L V +V +PGLPSHPQH LAM Q A Sbjct: 243 FNAWVFFKGLETLHVRMQAHSANALALAQWLSDHPAVEQVFYPGLPSHPQHELAMRQQKA 302 Query: 313 AGPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGV 372 G + S + GGR A ++D+L +I I+ N+GD+++L+THPA+TTHS V + RL G+ Sbjct: 303 GGGLVSFRIKGGRGDAWKVVDSLEMIHITANLGDTKTLITHPATTTHSRVEPEARLAAGI 362 Query: 373 GEGMLRLNVGLEDPEDLIADLDQALGSV 400 + +LR++VGLE ED+ ADL + L + Sbjct: 363 TDNLLRVSVGLESIEDIKADLGRGLDQI 390 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: 416 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: 391 Length adjustment: 31 Effective length of query: 371 Effective length of database: 360 Effective search space: 133560 Effective search space used: 133560 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