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 351380 BT1852 cysteine synthase A (NCBI ptt file)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Btheta:351380 Length = 317 Score = 221 bits (563), Expect = 2e-62 Identities = 132/311 (42%), Positives = 183/311 (58%), Gaps = 15/311 (4%) Query: 5 DSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEA 64 + L +GNTPL+ L S G+ G + + AKLE NP GS+KDR A+ MIE AEA Sbjct: 7 NKLTDLVGNTPLMELSGYS-----GKYGLNQNIIAKLEAFNPAGSVKDRVALSMIEDAEA 61 Query: 65 DGLLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSA 124 G L+PGATI+EPTSGNTG+ LAM A +KGY LI MPE S+ERR LL+ GAQI+ + Sbjct: 62 RGALKPGATIIEPTSGNTGVGLAMVATIKGYHLILTMPETMSLERRNLLKALGAQIVLTD 121 Query: 125 AEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGL 183 GG ++A A+EL + P V+L Q+ NP+N H TG E+ D E+ FVAG+ Sbjct: 122 GLGGMAASIAKAQELRDSIPGSVILQQFENPSNAAVHERTTGEEIWRDTDGEVAVFVAGV 181 Query: 184 GTTGTLMGTGRFLREHVANVKIVAAEPRYG-------EGVYALRNMDEGFVPELYDPEIL 236 GT GT+ G R L++H +V IVA EP + ++ + F+P+LYD ++ Sbjct: 182 GTGGTICGVARALKKHNPDVHIVAVEPASSPILAGGQAASHRIQGIGANFIPKLYDASVV 241 Query: 237 TARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADA 296 V +A+R REL TEG+ AGIS+GA ++AA + ++ I ++ D Sbjct: 242 DEVIGVPDDEAIRAGRELAATEGLLAGISSGAAVYAARQLAQRPEFRNKK--IVALLPDT 299 Query: 297 GWKYLSTGAYA 307 G +YLST +A Sbjct: 300 GERYLSTELFA 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: 296 Number of extensions: 14 Number of successful extensions: 3 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: 317 Length adjustment: 28 Effective length of query: 295 Effective length of database: 289 Effective search space: 85255 Effective search space used: 85255 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