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 Ga0059261_3452 Ga0059261_3452 Cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Korea:Ga0059261_3452 Length = 330 Score = 147 bits (371), Expect = 3e-40 Identities = 101/309 (32%), Positives = 153/309 (49%), Gaps = 26/309 (8%) Query: 11 LGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADGLLRP 70 +GNTPLV L+ P G D ++ K E NP S+KDR A+ +++ AEA GLL P Sbjct: 11 IGNTPLVRLK--GPSTAAGCD-----IYGKCEFANPGASVKDRAALFIVQDAEARGLLAP 63 Query: 71 GATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAEGGSN 130 G TI+E T+GNTGI LA+ KGY+ I VMPE S E+ L GA+++ A SN Sbjct: 64 GGTIVEGTAGNTGIGLALVGNAKGYKTIIVMPETQSREKMDTLRALGAELVLVPAAPYSN 123 Query: 131 TA--VATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGTTG 187 V T++ +A P+ + Q+ N AN +H GT E+ + I F GT G Sbjct: 124 PGHFVHTSRRIAEETPNAIWANQFDNIANRKAHIVGTAEEIWTQMEGRIDGFTCAAGTGG 183 Query: 188 TLMGTGRFLREHVANVKIVAAEPR-------------YGEGVYALRNMDEGFVPELYDPE 234 T+ G G L+E V I ++P EG + +G + + Sbjct: 184 TIAGVGLGLKEKDERVTIALSDPHGAALYEYYAHGELKAEGSSVAEGIGQGRITANLEGA 243 Query: 235 ILTARYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVA 294 + ++ + + + L+ EG+ G+S+G + A+ +G L G+R IA ++ Sbjct: 244 PIDTQFRISDEEGLEWVERLLAEEGLCLGLSSGINVAGAVRLGR-ELGPGKR--IATILC 300 Query: 295 DAGWKYLST 303 D G++YLST Sbjct: 301 DTGFRYLST 309 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: 304 Number of extensions: 13 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: 330 Length adjustment: 28 Effective length of query: 295 Effective length of database: 302 Effective search space: 89090 Effective search space used: 89090 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