Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011881440.1 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000016205.1:WP_011881440.1 Length = 431 Score = 235 bits (599), Expect = 2e-66 Identities = 142/400 (35%), Positives = 216/400 (54%), Gaps = 21/400 (5%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ +V + ++D + A++F K G Y R NPT LE +I +E G + A+G Sbjct: 32 PIYQTVAYAFDDTQHGADLFDLKVQGNIYTRIMNPTTDVLEQRIAALEGGVGALALASGQ 91 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AA+ +Q + GD++VS++ L+G T +L+ T+ G D D + +A I A Sbjct: 92 AAVTYSIQTIAEAGDNIVSASSLYGGTYNLFAHTLPQYGITTRFADPRDPASFDALIDAR 151 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ +F E++ NP V D+ + ++ GI +VDNT+ SPYL RP GA +VV+SLT Sbjct: 152 TKAIFAESVGNPLGNVTDIAALADIAHRHGIPLIVDNTVPSPYLLRPFEHGADIVVHSLT 211 Query: 209 KSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNPAPQ-----------WGMA----QI 253 K +GGHG +LGGA+ D+G+F W ++ A+ +K+ P +G A + Sbjct: 212 KYLGGHGTSLGGAIVDSGKFPWAQH---ADRFKRLNEPDVSYHGVVYTEAFGAAAYIGRA 268 Query: 254 RAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLE 313 R LR+ G ++ P A I G ET+ALR ER NAL +AQ L E V V Y GL Sbjct: 269 RVVPLRNMGAAISPFNAFQILQGIETLALRIERISDNALKVAQHLARHENVEWVNYAGLP 328 Query: 314 SHPQHAL-SKALFRSFGSLMSFELKDGID-CFDYLNRLRLAIPTSNLGDTRTLVIPVAHT 371 HP H L ++ L +++F +K G D + + L+L N+GDT++L A T Sbjct: 329 DHPDHPLVARYLSGRAPGILTFGVKGGRDGGAKFQDALKLFTRLVNIGDTKSLATHPAST 388 Query: 372 IFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQAL 411 ++ A G+ E +R+S+G+E DDL+AD QAL Sbjct: 389 THRQLSPAELAKAGVKEETVRLSIGIEHIDDLLADLDQAL 428 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: 500 Number of extensions: 25 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: 431 Length adjustment: 32 Effective length of query: 381 Effective length of database: 399 Effective search space: 152019 Effective search space used: 152019 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