Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate 200276 SO1095 O-acetylhomoserine (thiol)-lyase, putative (NCBI ptt file)
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >FitnessBrowser__MR1:200276 Length = 430 Score = 239 bits (609), Expect = 1e-67 Identities = 142/403 (35%), Positives = 224/403 (55%), Gaps = 20/403 (4%) Query: 30 PIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGM 89 PI+ + ++ ++D + A++F K G Y R NPT + LE ++ +E G + A+GM Sbjct: 24 PIYQTTSYTFDDTQHGADLFDLKVAGNIYTRIMNPTTSVLEQRLAAIEGGIGALAVASGM 83 Query: 90 AAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDATDVKNVEAAITAN 148 AAI +Q L + GD++VS++ L+G T +L+ T+ QG +V M D + +EA I A Sbjct: 84 AAITYAIQALTQVGDNIVSTSQLYGGTYNLFAHTLPRQGVEVRMAAFDDFEELEALIDAK 143 Query: 149 TRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLT 208 T+ +F E+I NP + DLKR+ E+ + G+ +VDNT+ +P L RP GA +V++SLT Sbjct: 144 TKALFCESIGNPAGNIVDLKRLAEIAHKHGVPLIVDNTVATPVLCRPFEHGADIVIHSLT 203 Query: 209 KSIGGHGNALGGALTDTGEFDWT----RYPHIAEN--------YKKNPAPQWGMAQIRAK 256 K IGGHG +GG + D+G+FDW R+ + + Y + P + + R Sbjct: 204 KYIGGHGTTIGGIIIDSGKFDWVANKERFSLLNQADPSYHGVVYTEAFGPAAFIGRCRVV 263 Query: 257 ALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHP 316 LR+ G +L P +A + G ET++LR ER C NALALA+ L V+ V Y L S P Sbjct: 264 PLRNTGAALSPHSAFLLLQGLETLSLRMERHCANALALAEYLILHPSVSWVNYGALPSSP 323 Query: 317 -QHALSKALFRSFGSLMSFELKDG------IDCFDYLNRLRLAIPTSNLGDTRTLVIPVA 369 + K ++SF +K I +++ L++ + N+GD ++L A Sbjct: 324 FRENCEKITGGKASGIISFGIKAATPEEGKIAGGKFIDALKMVLRLVNIGDAKSLACHPA 383 Query: 370 HTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALD 412 T ++ A A G++E LIR+SVG+E DD++AD QAL+ Sbjct: 384 STTHRQLDANELARAGVSEDLIRISVGIEHIDDIIADVSQALE 426 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: 483 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: 430 Length adjustment: 32 Effective length of query: 381 Effective length of database: 398 Effective search space: 151638 Effective search space used: 151638 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 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