Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_027458847.1 K420_RS0115425 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000519045.1:WP_027458847.1 Length = 423 Score = 242 bits (617), Expect = 2e-68 Identities = 141/399 (35%), Positives = 224/399 (56%), Gaps = 15/399 (3%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ + ++ ++ + A++F K PG Y R NPT LE ++ ME G + + A+GM Sbjct: 24 PIYQTTSYAFDSTQHGADLFDLKVPGNIYTRIMNPTQDVLEKRVAAMEGGIAALAVASGM 83 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AAI A +Q + GD++V+S+ L+G T +L+ T+ G +V D D E I A Sbjct: 84 AAITAAIQTIAEAGDNIVTSSTLYGGTYNLFAHTLPQYGIEVRFADYRDPDAFEKLIDAK 143 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ VF E++ NP V D +++ E+ + G+ +VDNT+ SPYL RP GA +VV++LT Sbjct: 144 TKAVFCESVGNPLGNVTDFEKLAEIAHKHGVPVIVDNTVPSPYLCRPFEHGADIVVHALT 203 Query: 209 KSIGGHGNALGGALTDTGEFDWTRY---------PHIAEN---YKKNPAPQWGMAQIRAK 256 K +GGHGN+LGG + D+G+F W + P ++ + Y + P + + R Sbjct: 204 KYLGGHGNSLGGIIVDSGKFPWAEHKAKFKRLNEPDVSYHGVVYTEALGPAAYIGRARVV 263 Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316 LR+ G ++ P A I G ET+ALR +R C N+L +A+ L+ + + V Y GLE H Sbjct: 264 PLRNMGAAISPFNAFLILQGIETLALRMDRICTNSLKIARFLKDHPKCSWVNYAGLEDHK 323 Query: 317 QHAL-SKALFRSFGSLMSFELKDGID-CFDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFY 374 + L K + +++F +K G + + + L+L N+GD +TL A T Sbjct: 324 DYPLVQKYMGGRASGILNFGVKGGREGGGKFQDALKLVTRLVNIGDCKTLACHPASTTHR 383 Query: 375 EMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 ++ E A G++E +IR+SVG+E DDL+AD QAL+A Sbjct: 384 QLSPEELAKAGVSEDMIRLSVGIEHIDDLIADLDQALNA 422 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: 486 Number of extensions: 30 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: 423 Length adjustment: 32 Effective length of query: 381 Effective length of database: 391 Effective search space: 148971 Effective search space used: 148971 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