Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_050461123.1 AKL27_RS02665 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_001189915.1:WP_050461123.1 Length = 423 Score = 236 bits (603), Expect = 7e-67 Identities = 139/399 (34%), Positives = 216/399 (54%), Gaps = 15/399 (3%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ +V++ ++D + A++F K G Y R NPT LE ++ ++E G + + A+G Sbjct: 24 PIYQTVSYAFDDTQHGADLFDLKVAGNIYTRIMNPTQDVLEKRVAELEGGIAALALASGQ 83 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AAI +Q + GD++VS++ L+G T +L+ T+ G + D D ++ I Sbjct: 84 AAITYAIQTIAEAGDNIVSASTLYGGTYNLFAHTLPQFGIETRFADYRDPESFGKLIDDK 143 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ VFVE+I NP + D+++I E+ G+ +VDNT+ SPYL RP GA +VV+SLT Sbjct: 144 TKAVFVESIGNPLGNITDIEKIAEIAHRHGVPLIVDNTVPSPYLLRPIDFGADIVVHSLT 203 Query: 209 KSIGGHGNALGGALTDTGEFDWTRYPHIAENYKKNPAPQWG------------MAQIRAK 256 K +GGHGN+LGGA+ D+G+F W + + + G + + R Sbjct: 204 KYLGGHGNSLGGAIVDSGKFPWAEHKQKFKRLNEPDVSYHGVVYTEALGAAAYIGRARVV 263 Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316 LR+ G ++ P A I G ET+ALR ER N +AQ LQ +V V Y GL HP Sbjct: 264 PLRNTGAAISPFNAFLILQGIETLALRMERITSNTAHIAQFLQQHAKVQWVNYAGLPDHP 323 Query: 317 QHALS-KALFRSFGSLMSFELKDGI-DCFDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFY 374 HAL+ K L +++F +K G+ + + L+L N+GD ++L A T Sbjct: 324 DHALAQKYLGGRPSGILTFGVKGGLAGGTRFQDALKLFTRLVNIGDAKSLACHPASTTHR 383 Query: 375 EMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 ++ E G+ E +R+S+G+E DDL+AD QAL A Sbjct: 384 QLNPEELVKAGVTEDTVRLSIGIEHIDDLLADLEQALAA 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: 488 Number of extensions: 26 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