Align O-acetylhomoserine sulfhydrylase (EC:2.5.1.49) (characterized)
to candidate WP_036261931.1 DL86_RS12460 O-succinylhomoserine sulfhydrylase
Query= reanno::Korea:Ga0059261_3194 (402 letters) >NCBI__GCF_000746085.1:WP_036261931.1 Length = 408 Score = 404 bits (1037), Expect = e-117 Identities = 198/387 (51%), Positives = 268/387 (69%), Gaps = 2/387 (0%) Query: 16 KPATQAIRGGTARSEWGETSEALFLTSGYAYDCAGDAAARFSGDQQGMTYSRLQNPTVEM 75 +PATQ + GGT RS++GETSEA+FLT G+ Y+ A ARF GD+ G YSR NPTV M Sbjct: 14 RPATQLVHGGTQRSQFGETSEAIFLTQGFVYESMERAEARFKGDEPGYVYSRYSNPTVVM 73 Query: 76 LEQRIALLEGAEACRATASGMAAMTAALLCQLSAGDHLIGGRAAFGSCRWLTDTQLPKFG 135 E+R+AL EGAEA RATASGMAA+TA+L+ + AGDH++ RA FG+C ++ + LP+FG Sbjct: 74 FEERMALFEGAEAARATASGMAAVTASLMSLVKAGDHVVAARALFGACLYVVEDLLPRFG 133 Query: 136 IETTVVDARDPQQFIDAIRPNTKVFFFETPANPTMDVVDLKAVCAIARERGIVTVVDNAF 195 + +T+VD D Q+ A+RP TKV F E+P NP ++V D+ A+ AIA + G + VVDN F Sbjct: 134 VSSTLVDGADLSQWRAAMRPETKVLFLESPTNPCLEVYDIAAIAAIAHDNGSLLVVDNVF 193 Query: 196 ATPALQRPMDFGADVVAYSATKMMDGQGRVLAGAVCGTEEFINNTLLPFHRNTGPTLSPF 255 ATP LQ+P+ GAD V YSATK +DG GR L G + ++E I+ + F R TGP LSPF Sbjct: 194 ATPILQKPLALGADCVVYSATKHIDGHGRCLGGVILASQELIDTHIHAFLRQTGPVLSPF 253 Query: 256 NAWVVLKGLETLDLRIQRQSENALKVARFLEG--RVPRVNFPGLPSHPQHNLAMSQMAAA 313 NAWV+LK LETL LR+++Q ++A ++A FL G + V +PG HPQ +L QM Sbjct: 254 NAWVLLKSLETLPLRVRQQMQSAERIADFLSGCQHIRLVRYPGRSDHPQADLVKRQMRGG 313 Query: 314 GPIFSIELDGGRTQAHGLLDALGLIDISNNIGDSRSLMTHPASTTHSGVAEDQRLLMGVG 373 G + S E GG+ A + L +I ISNN+GD++SL+THPA+TTH + + R +GV Sbjct: 314 GTLVSFEFAGGKAAAFAFANQLSIIKISNNLGDAKSLITHPATTTHQRLTPEARAALGVN 373 Query: 374 EGMLRLNVGLEDPEDLIADLDQALGSV 400 +G+LRL+VGLED +DLI DL AL ++ Sbjct: 374 DGLLRLSVGLEDADDLIDDLGAALAAL 400 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: 409 Number of extensions: 8 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: 408 Length adjustment: 31 Effective length of query: 371 Effective length of database: 377 Effective search space: 139867 Effective search space used: 139867 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