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 Echvi_4660 Echvi_4660 cystathionine beta-synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Cola:Echvi_4660 Length = 456 Score = 159 bits (401), Expect = 2e-43 Identities = 104/317 (32%), Positives = 164/317 (51%), Gaps = 28/317 (8%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 Y+S++ +G+TPLV L RL+ G ++ K+E NP S+KDR A++MI+ AE Sbjct: 3 YNSIIDTIGDTPLVKLNRLNK-------GIKGTIYVKVEYFNPGNSVKDRMAIKMIDDAE 55 Query: 64 ADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIF- 122 G+L+PG TI+E TSGNTG+ LA+ +GY+ I M + S E+ +L+ GA+++ Sbjct: 56 KAGILKPGGTIIEGTSGNTGMGLALVGIARGYKCIFTMADKQSKEKIDVLKAMGAEVVVC 115 Query: 123 --SAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHF 179 + + + + AK+L P+ QY N +N +HY TGPE+ D +ITHF Sbjct: 116 PTNVSPDDPRSYYSVAKKLNKDIPNSFYPNQYDNLSNWKAHYETTGPEIWKDTEGKITHF 175 Query: 180 VAGLGTTGTLMGTGRFLREHVANVKIVAAE------PRYGEG---------VYALRNMDE 224 AG+GT GT+ GT ++L+E ++ V + +Y E Y + E Sbjct: 176 AAGVGTGGTMSGTAKYLKEQNPSIVSVGIDTYGSVFKKYKETGEFDENEIYPYLTEGIGE 235 Query: 225 GFVPELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAG 284 +P D ++ V D+ TR L EG+F G S G+ +H AL L Sbjct: 236 DILPANVDFSMIDHFVKVTDKDSAVMTRRLSREEGLFVGWSCGSAVHGALEYARQHLT-- 293 Query: 285 ERADIALVVADAGWKYL 301 E+ + +++ D G +YL Sbjct: 294 EQDTMVIILPDHGTRYL 310 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: 337 Number of extensions: 26 Number of successful extensions: 6 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: 456 Length adjustment: 30 Effective length of query: 293 Effective length of database: 426 Effective search space: 124818 Effective search space used: 124818 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: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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