Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_011952121.1 SWIT_RS06485 O-acetylhomoserine aminocarboxypropyltransferase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000016765.1:WP_011952121.1 Length = 431 Score = 245 bits (626), Expect = 2e-69 Identities = 153/430 (35%), Positives = 225/430 (52%), Gaps = 21/430 (4%) Query: 3 DKKTYGFTTTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQG 62 DK Y T LH+ + G++ PI+ + ++ + DA A +F ++ G Y R G Sbjct: 2 DKPAYRPETLALHAGWRADPTTGAVAPPIYQTTSYQFHDAGHAARLFALEELGNIYTRIG 61 Query: 63 NPTVAALEDKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM- 121 NPT A LED+I +E G + + A+G AA +Q L R GD++V+ L+G T +L+ Sbjct: 62 NPTTAILEDRIAALEGGAAALAVASGQAASAYAIQNLARAGDNIVAGTHLYGGTWNLFAN 121 Query: 122 TVGAQGAKVSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILY 181 T+ QG +V VD D + AA TR +VET+ NP+ V + + R GI Sbjct: 122 TLRDQGIEVRFVDPADPQGFVAASDDRTRAWYVETLPNPKLVVCPIAELAAAGRPIGIPL 181 Query: 182 VVDNTMTSPYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWTRYPHIAENYK 241 +VDNT +P + RP GA +VV S TK IGGHG ++GG + D G FDW +P N Sbjct: 182 IVDNT-AAPLIARPLDHGAAIVVYSTTKYIGGHGTSIGGVIVDGGNFDWEAFPDRQPNL- 239 Query: 242 KNPAPQ-----WGMA-----------QIRAKALRDFGGSLGPEAAHHIAVGAETIALRQE 285 P P W A + R LRD G +L P A I G ET+ LR Sbjct: 240 NTPDPSYHGAVWAQAAKPLGPIAYILRARTILLRDLGAALSPFNAFQILQGLETLPLRMP 299 Query: 286 RECKNALALAQMLQADERVAAVYYPGLESHPQHA-LSKALFRSFGSLMSFELKDGIDC-F 343 R C+NALA+ + L V V +P +++ + A + L G L+ FEL G++ Sbjct: 300 RHCENALAVVRFLSGRADVTRVIHPSVQTGEERARADRVLTGGQGGLLGFELAGGVEAGR 359 Query: 344 DYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDL 403 +++ LRL +N+GD R+L I A T ++ AE +A+ G++ +R+S+GLE DD+ Sbjct: 360 RFIDALRLFYHVANIGDARSLAIHPASTTHSQLSAEEQAAAGVSPGYVRLSIGLEHIDDI 419 Query: 404 VADFRQALDA 413 +AD QAL A Sbjct: 420 LADLDQALRA 429 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: 427 Number of extensions: 20 Number of successful extensions: 5 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