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 GFF3511 HP15_3453 cysteine synthase A
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Marino:GFF3511 Length = 323 Score = 184 bits (467), Expect = 3e-51 Identities = 119/327 (36%), Positives = 183/327 (55%), Gaps = 27/327 (8%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 Y+ ++GNTPLV L R++ DG +WAK+E RNP S+K R MI AE Sbjct: 5 YEDNSLSIGNTPLVRLNRVN-------DG--ATIWAKIEGRNPAYSVKCRIGSAMIWDAE 55 Query: 64 ADGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFS 123 G L+ G TI+EPTSGNTGI+LA A +GY+LI MP + S+ERR++L+ GA+++ + Sbjct: 56 KRGTLKAGMTIVEPTSGNTGIALAYVAAARGYKLILTMPASMSLERRKVLKALGAELVLT 115 Query: 124 AAEGGSNTAVATAKELAATNP-SWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVA 181 G A+A A+E+ +++P ++ + Q+ NPAN H TGPE+ D EI FVA Sbjct: 116 EPAKGMPGAIAKAEEIFSSDPDNYFLPQQFQNPANPRIHEDTTGPEIWEDTDGEIDIFVA 175 Query: 182 GLGTTGTLMGTGRFLR----EHVANVKI------VAAEPRYGEGV----YALRNMDEGFV 227 G+GT GTL G R+++ + +A + + V + GE + + ++ + GFV Sbjct: 176 GVGTGGTLTGVSRYIKGTKGKQIATIAVEPTDSPVITQMMNGEDIKPAPHKIQGIGAGFV 235 Query: 228 PELYDPEILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERA 287 P+ D E++ +V +A+ L+ EGI GIS GA + AA+ + G+ Sbjct: 236 PKNLDLEMVDQVETVSNEEAMDMAHRLMQEEGILCGISCGAAVAAAVRISKQPEYQGK-- 293 Query: 288 DIALVVADAGWKYLSTGAYAGSLDDAE 314 +I +V+ D +YLST +AG + E Sbjct: 294 NIVVVLPDTAERYLSTALFAGQFGEQE 320 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: 300 Number of extensions: 19 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: 323 Length of database: 323 Length adjustment: 28 Effective length of query: 295 Effective length of database: 295 Effective search space: 87025 Effective search space used: 87025 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 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