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 Dsui_3208 Dsui_3208 cysteine synthase A
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__PS:Dsui_3208 Length = 310 Score = 176 bits (445), Expect = 9e-49 Identities = 112/306 (36%), Positives = 162/306 (52%), Gaps = 17/306 (5%) Query: 9 QALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLL 68 Q +G TPLV L R++ G + KLE NP S+KDR AV MI+ A+A G + Sbjct: 9 QLVGKTPLVQLNRVAA-------GIEGTVALKLEYFNPAHSVKDRIAVAMIDAAQAAGKI 61 Query: 69 RPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGG 128 +P +LEPTSGNTGI LAM +G + VMPE S ER+ LL+ YGA++I + G Sbjct: 62 KPDTIVLEPTSGNTGIGLAMVCAARGIKAAFVMPETMSRERKLLLKAYGAELILTPGPEG 121 Query: 129 SNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGTTG 187 A+ A+ELA ++ + + Q+ NPAN + H T E+ AD ++ FVAG+GT G Sbjct: 122 MGGAIKKAQELAESDSRYFIPQQFENPANPEVHRNTTAEEIWADTDGQVDIFVAGVGTGG 181 Query: 188 TLMGTGRFLREHVANVKIVAAEPRY-------GEGVYALRNMDEGFVPELYDPEILTARY 240 T+ G G L+ V++ A EP +G + ++ + GFVP + + ++ Sbjct: 182 TVTGVGEVLKARKPGVQVFAVEPDASPVLSGGAKGPHPIQGIGAGFVPAVLNTQVYDGVV 241 Query: 241 SVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGWKY 300 V DA R L EG+ GIS+GA + AAL + G+ +V+ G +Y Sbjct: 242 RVKNDDAFATARRLATEEGLLVGISSGAAVWAALEIARKPENKGKLT--VVVIPSFGERY 299 Query: 301 LSTGAY 306 LST Y Sbjct: 300 LSTALY 305 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: 272 Number of extensions: 12 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: 310 Length adjustment: 27 Effective length of query: 296 Effective length of database: 283 Effective search space: 83768 Effective search space used: 83768 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