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 AO356_28790 AO356_28790 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28790 Length = 347 Score = 108 bits (269), Expect = 2e-28 Identities = 93/309 (30%), Positives = 135/309 (43%), Gaps = 30/309 (9%) Query: 11 LGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRP 70 +GNTP++G+ H RL K+E NP GSIKDR A M+ A G L+P Sbjct: 10 IGNTPMLGIDI---------PDTHARLLLKIEKNNPGGSIKDRMARNMVLAALKSGRLKP 60 Query: 71 GATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSN 130 G ++E +SGNTGI LAMAA G I V+ + + ++ +++ GA + F A + Sbjct: 61 GGVVVESSSGNTGIGLAMAAVEFGLHFIAVVDHHAAQDKIAVMKALGADVRFVAGHYRED 120 Query: 131 TAVAT-----AKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLG 184 A ELA P V + Q N AN Y E +A + ++ +V +G Sbjct: 121 EVAVVERQRMAAELAQQIPGAVFMNQSDNAANAGG-YSDFVRETIAQVEGKVGAYVGCVG 179 Query: 185 TTGTLMGTGRFLREHVANVKIVAAEPR----YGEGVYALRNMDEG-----FVPELYDPEI 235 T G++ G R L+ H + VA EP +G Y G V + D Sbjct: 180 TGGSMTGIARGLKLHNPDTVTVAVEPAGSIVFGHPGYPYYQSGTGTPAGDTVGLVLDYSC 239 Query: 236 LTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALG-VGAGALAAGERADIALVVA 294 + V A R + G+ G STG + AL + G L ++ + +A Sbjct: 240 IDLGVQVTDSQAFETARYIARNLGLLVGGSTGGAIFKALEFIHKGVLT----GNVVVPIA 295 Query: 295 DAGWKYLST 303 D G KYL T Sbjct: 296 DGGEKYLHT 304 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: 263 Number of extensions: 11 Number of successful extensions: 1 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: 347 Length adjustment: 28 Effective length of query: 295 Effective length of database: 319 Effective search space: 94105 Effective search space used: 94105 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: 49 (23.5 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