Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_004514406.1 GMET_RS04100 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000012925.1:WP_004514406.1 Length = 427 Score = 227 bits (578), Expect = 6e-64 Identities = 136/394 (34%), Positives = 211/394 (53%), Gaps = 14/394 (3%) Query: 34 SVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGMAAIG 93 S TF Y++A + ++F ++PG+ Y R GNPT A E K+ ME G + + G AA Sbjct: 31 STTFKYDNADHVTKLFDLEEPGFFYTRLGNPTTDAFEQKLAMMEGGVGALATSAGQAATT 90 Query: 94 AIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDA-TDVKNVEAAITANTRL 151 + + + G H V+++ L+G T +L+ T+ G +VS VD + AA NT+ Sbjct: 91 LSIFNICQAGQHFVTASTLYGGTYNLFACTLPKMGIEVSFVDPEAPADEILAAFRPNTKA 150 Query: 152 VFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSI 211 +F ETI NP V D + + +E+G+ ++D+T +PYL RP GA +VV+S TK I Sbjct: 151 LFAETIGNPGLNVLDFAKFSAIAQEKGVPLIIDSTFATPYLCRPFEHGANVVVHSATKYI 210 Query: 212 GGHGNALGGALTDTGEFDW--TRYPHIAE--------NYKKNPAPQWGMAQIRAKALRDF 261 G ++GG + D G FDW R+P + E Y K + + R + +RD Sbjct: 211 DGLATSVGGVIVDGGNFDWGNGRFPELTEPDSSYHGLQYVKTFGNLAYIIKARVQLMRDI 270 Query: 262 GGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHPQH-AL 320 G + P + G +T+ LR +R NALALAQ L++ V+ V YPGL SH H Sbjct: 271 GTTPSPFNSFLFTNGLQTLPLRMQRHSDNALALAQFLESHPSVSWVKYPGLSSHASHDRA 330 Query: 321 SKALFRSFGSLMSFELKDGIDC-FDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAE 379 K L + +++F +K G + ++ RL ++GD R+ V+ A T ++ AE Sbjct: 331 QKYLPQGCSGVLTFGIKGGTEAGKKFMEACRLVALVVHVGDARSCVLHPASTTHRQLTAE 390 Query: 380 RRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 ++ + G+ LIR+SVG+E DD++AD QAL A Sbjct: 391 QQTASGVTPDLIRLSVGIEHIDDIIADVDQALAA 424 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: 409 Number of extensions: 18 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: 427 Length adjustment: 32 Effective length of query: 381 Effective length of database: 395 Effective search space: 150495 Effective search space used: 150495 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