Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate Ac3H11_549 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_549 Length = 458 Score = 258 bits (659), Expect = 3e-73 Identities = 153/406 (37%), Positives = 227/406 (55%), Gaps = 25/406 (6%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ +V + ++ A+ A++F K PG Y R NPT LE ++ +E G + + A+GM Sbjct: 55 PIYQTVAYAFDSAQHGADLFDLKVPGNIYTRIMNPTTDVLEKRVAALEGGIAALAVASGM 114 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AAI +Q + GD++VS++ L+G T +L+ T+ QG D D + I A Sbjct: 115 AAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQQGITTRFADPRDPASFAQHIDAR 174 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ +F+E+I NP V D+ I ++ + G+ +VDNT+ SPYL RP GA +VV+SLT Sbjct: 175 TKAIFIESIGNPLGNVTDIAAIAKVAHDHGVPLIVDNTVPSPYLLRPIEHGADIVVHSLT 234 Query: 209 KSIGGHGNALGGALTDTGEFDW----TRYPHIAEN--------YKKNPAPQWGMAQIRAK 256 K +GGHGN++GGA+ D+G+F W R+P + E Y + P + + R Sbjct: 235 KYLGGHGNSVGGAIVDSGKFPWAEHKARFPRLNEPDVSYHGVVYTEALGPAAFIGRARVV 294 Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316 LR+ G +L P++A I G ET+ALR +R C N LALA+ LQ+ +V V Y GL HP Sbjct: 295 PLRNTGAALSPQSAFLILQGIETLALRMDRICDNTLALAKYLQSHPKVEWVRYAGLPDHP 354 Query: 317 QHALSKALFRSFGSLMSFELKDGIDCFD---------YLNRLRLAIPTSNLGDTRTLVIP 367 HAL + R G S L G+ D +L+ L+L N+GD ++L Sbjct: 355 DHALVQ---RQSGGKASGILSFGLKSTDADPRAAGARFLDALQLFTRLVNIGDAKSLATH 411 Query: 368 VAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 A T ++ E A G++ES++R+SVG+E DDL AD QALDA Sbjct: 412 PASTTHRQLNPEELAKAGVSESMVRLSVGIEHIDDLRADLVQALDA 457 Lambda K H 0.319 0.134 0.391 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: 517 Number of extensions: 28 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: 413 Length of database: 458 Length adjustment: 32 Effective length of query: 381 Effective length of database: 426 Effective search space: 162306 Effective search space used: 162306 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: 51 (24.3 bits)
This GapMind analysis is from Apr 09 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