Align O-succinylhomoserine sulfhydrylase (EC 2.5.1.48) (characterized)
to candidate WP_013011779.1 DACET_RS12695 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= reanno::HerbieS:HSERO_RS16440 (413 letters) >NCBI__GCF_000025725.1:WP_013011779.1 Length = 428 Score = 248 bits (633), Expect = 2e-70 Identities = 150/423 (35%), Positives = 239/423 (56%), Gaps = 27/423 (6%) Query: 13 ILHSDRQKGIEHGSLHKPIHTSVTFGYEDARQLAEVFQGKQPGYRYGRQGNPTVAALEDK 72 +LH + G E GS PI+ + ++ ++ + A +F K+ G Y R NPT LE + Sbjct: 8 LLHGGYEPG-ETGSRAVPIYQTTSYVFKSSEHAANLFGLKEFGNIYSRIMNPTNDVLEKR 66 Query: 73 ITKMEDGKSTICFATGMAAIGAIVQGLLREGDHVVSSAFLFGNTNSLWM-TVGAQGAKVS 131 + +E G + ++G AAI V + G ++V+S+ ++G T +L+ T+G G +V Sbjct: 67 LADLEGGTGALSLSSGQAAITFSVLNITAAGQNIVASSSIYGGTYNLFKYTLGRLGIEVR 126 Query: 132 MVDATDVKNVEAAITANTRLVFVETIANPRTQVADLKRIGELCRERGILYVVDNTMTSPY 191 VD TD ++ A NTR + E+I NP ++AD++ I +L E GI +VDNT+T PY Sbjct: 127 FVDGTDPESFIKAADENTRAFYTESIGNPAGRLADIRGISDLAHEAGIPLIVDNTIT-PY 185 Query: 192 LFRPKTVGAGLVVNSLTKSIGGHGNALGGALTDTGEFDWT--RYPHIAE----------- 238 +F+P GA +VV SLTK I G+G ++GGA+ + G+F+W RYP I E Sbjct: 186 IFKPFDHGADIVVYSLTKFISGNGTSIGGAVIEKGDFNWANGRYPEITEPDPSYHGLSYW 245 Query: 239 ----NYKKNPAPQWGMAQI---RAKALRDFGGSLGPEAAHHIAVGAETIALRQERECKNA 291 N+ K A G + I R + LRD G L P +A+ I +G ET+ LR ++ C+N+ Sbjct: 246 DAFGNHDK--AVLRGASYILKARVQLLRDLGSCLSPYSANQILLGLETLPLRIKKHCENS 303 Query: 292 LALAQMLQADERVAAVYYPGLESHPQH-ALSKALFRSFGSLMSFELKDGIDC-FDYLNRL 349 L +A+ L +V+ V Y GL HP H S+ L +G+++ F +K G++ ++ + Sbjct: 304 LTVAEFLAKHPKVSWVNYAGLSDHPDHKKASEILKHGYGAIIGFGIKGGLESGKKFIESV 363 Query: 350 RLAIPTSNLGDTRTLVIPVAHTIFYEMGAERRASMGIAESLIRVSVGLEDTDDLVADFRQ 409 ++ +N+GD R+LVI A T ++ E R S G+ + +R+SVG+ED DL+AD Q Sbjct: 364 KVFSHLANVGDARSLVIHPASTTHQQLTTEERISAGVTDDYVRLSVGIEDVSDLIADLEQ 423 Query: 410 ALD 412 AL+ Sbjct: 424 ALE 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: 439 Number of extensions: 17 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: 428 Length adjustment: 32 Effective length of query: 381 Effective length of database: 396 Effective search space: 150876 Effective search space used: 150876 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