Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_086509774.1 BZY95_RS09910 aminotransferase class V-fold PLP-dependent enzyme
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_002151265.1:WP_086509774.1 Length = 424 Score = 246 bits (629), Expect = 7e-70 Identities = 143/418 (34%), Positives = 230/418 (55%), Gaps = 16/418 (3%) Query: 11 TTILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALE 70 T LH +H ++ PIH + +F ++ A+ A++F K G Y R NPT A LE Sbjct: 5 TIALHHGYAPDDQH-AVAVPIHQTTSFSFDSAQHAADLFDLKVEGNIYSRIMNPTCAVLE 63 Query: 71 DKITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAK 129 ++ +E G + + A+GMAAI +Q + GD++VS + L+G T +L+ T+ QG + Sbjct: 64 QRVAALEGGIAGLAVASGMAAITYAIQTIAEAGDNIVSISELYGGTYNLFAHTLPRQGIE 123 Query: 130 VSMVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTS 189 V D D+ +E+ I A T+ VF E++ NP V D+ R+ E+ G+ +VDNT+ + Sbjct: 124 VRFADKDDIDGIESLIDARTKAVFCESVGNPSGSVVDMARLAEVAHRHGVPVIVDNTVPT 183 Query: 190 PYLFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT----RYPHIAEN------ 239 P+L+RP GA +V++S TK IGGHG +GG + D+G F W R+P + E Sbjct: 184 PFLWRPIEHGADIVIHSATKYIGGHGTTVGGVIVDSGRFPWADHPQRFPLLNEPDVSYHG 243 Query: 240 --YKKNPAPQWGMAQIRAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNALALAQM 297 Y ++ +A+ R LR+ G +L +AA ++ G ET+ALR ER C NAL +A+ Sbjct: 244 VCYTRDIGEAAFIARARVVPLRNMGAALSAQAAWNLLQGLETLALRIERICDNALKVAEY 303 Query: 298 LQADERVAAVYYPGLESHPQHALSKALFRSFGS-LMSFELKDGIDC-FDYLNRLRLAIPT 355 L+A + V V Y GL H H L++ S ++SF ++ G + + + L + + Sbjct: 304 LEAHDAVTWVQYAGLPGHKDHQLAQRYMGGRASGILSFGIQGGREAGARFYDALGMILRL 363 Query: 356 SNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQALDA 413 N+GD +T A T ++ E A+ + ++R+S+G+E DD++AD QAL A Sbjct: 364 VNIGDAKTCSSIPASTTHRQLSDEELAAASVTPDMVRLSIGIEHVDDIIADLEQALAA 421 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: 456 Number of extensions: 17 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: 424 Length adjustment: 32 Effective length of query: 381 Effective length of database: 392 Effective search space: 149352 Effective search space used: 149352 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