Align [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase (EC 2.5.1.113); O-phosphoserine sulfhydrylase (EC 2.5.1.65) (characterized)
to candidate SMc00421 SMc00421 O-acetylserine sulfhydrylase A
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Smeli:SMc00421 Length = 322 Score = 200 bits (508), Expect = 4e-56 Identities = 119/314 (37%), Positives = 173/314 (55%), Gaps = 16/314 (5%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 + S+ + +G+TP+V L +L+ G L AKLE NP GS+KDR V MIE E Sbjct: 13 FSSITETIGDTPIVRLDKLAKE-----KGVKANLLAKLEFFNPIGSVKDRIGVAMIESLE 67 Query: 64 ADGLLRPG-ATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF 122 A G + PG T++EPTSGNTGI+LA A KGYRLI MPE SVERR++L L GA+++ Sbjct: 68 AQGKITPGRTTLVEPTSGNTGIALAFVAAAKGYRLILTMPETMSVERRKMLTLLGAELVL 127 Query: 123 SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVA 181 + G A+A A+EL T P ++ Q+ NPAN + H T E+ D + V+ Sbjct: 128 TEGAKGMKGAIAKAQELTETLPDAIIPQQFENPANPEIHRTTTAEEIWNDTEGAVDILVS 187 Query: 182 GLGTTGTLMGTGRFLREHVANVKIVAAEPRY-------GEGVYALRNMDEGFVPELYDPE 234 G+GT GT+ G G+ L+ +V+++A EP G + ++ + GF P + D Sbjct: 188 GIGTGGTITGAGQVLKARKPSVRVIAVEPEESPILSGGAPGPHKIQGIGAGFAPAILDTS 247 Query: 235 ILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVA 294 + +V A +A+ R + EG+ GIS GA L AA+ VG AG +I +++ Sbjct: 248 VYDEVVTVNAGEAIEAARLVARLEGVPVGISAGAALQAAIEVGQREENAGR--NIVVIIP 305 Query: 295 DAGWKYLSTGAYAG 308 +YLST + G Sbjct: 306 SFAERYLSTVLFEG 319 Lambda K H 0.317 0.134 0.398 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: 258 Number of extensions: 14 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: 323 Length of database: 322 Length adjustment: 28 Effective length of query: 295 Effective length of database: 294 Effective search space: 86730 Effective search space used: 86730 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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