Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_092056754.1 BQ4888_RS09545 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_900111775.1:WP_092056754.1 Length = 425 Score = 231 bits (589), Expect = 3e-65 Identities = 136/394 (34%), Positives = 212/394 (53%), Gaps = 14/394 (3%) Query: 34 SVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDKITKMEDGKSTICFATGMAAIG 93 S TF Y+ A +A++F P Y R GNPT A E KI ME G + ++G AA Sbjct: 31 STTFKYDSAEHVAKLFDLDLPDPFYTRLGNPTTDAFEGKIALMEGGVGALATSSGQAATA 90 Query: 94 AIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVSMVDA-TDVKNVEAAITANTRL 151 + + R G H+V++ L+G T SL+ T+ G +VS V+ + + ++ T+ Sbjct: 91 LSIMNICRAGQHIVTAGTLYGGTYSLFANTLPKLGIEVSFVNPDSSAEEIKKHFRPETKA 150 Query: 152 VFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPYLFRPKTVGAGLVVNSLTKSI 211 +F ETI NP V D ++ + R G+ ++DNT +PYL RP GA +V++S TK I Sbjct: 151 LFAETIGNPGLNVLDFEKFSAVARATGVPLLIDNTFPTPYLCRPLDHGADIVIHSATKYI 210 Query: 212 GGHGNALGGALTDTGEFDWT--RYPHIAE--------NYKKNPAPQWGMAQIRAKALRDF 261 GH ++LGG + D G+FDWT ++P + E Y + P + + RA+ +RD Sbjct: 211 DGHASSLGGVIVDGGKFDWTSGKFPELTEPDSSYHGLRYVEKFGPSAYIVKARAQYMRDL 270 Query: 262 GGSLGPEAAHHIAVGAETIALRQERECKNALALAQMLQADERVAAVYYPGLESHPQHALS 321 G + P + G T+ LR ER NALALA LQ +V+ V YPGLESHP + L+ Sbjct: 271 GVTPSPFNSFLFHQGLTTLPLRMERHSANALALAHFLQGHPKVSWVNYPGLESHPSYPLA 330 Query: 322 KALF-RSFGSLMSFELKDGIDC-FDYLNRLRLAIPTSNLGDTRTLVIPVAHTIFYEMGAE 379 + + +++F +K + ++ R+ ++GD R+ V+ A T ++ Sbjct: 331 QRYMPKGASGVLTFGIKGAREAGIRFMEATRIIALVVHVGDARSCVLHPASTTHRQLSEA 390 Query: 380 RRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 ++ + G+ LIR+SVG+E DDL+AD QAL+A Sbjct: 391 QQIASGVTPDLIRLSVGIEHIDDLIADVEQALNA 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: 428 Number of extensions: 19 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: 425 Length adjustment: 32 Effective length of query: 381 Effective length of database: 393 Effective search space: 149733 Effective search space used: 149733 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