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 GFF4108 PS417_21045 cysteine synthase
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__WCS417:GFF4108 Length = 304 Score = 155 bits (392), Expect = 1e-42 Identities = 94/275 (34%), Positives = 151/275 (54%), Gaps = 17/275 (6%) Query: 4 YDSLLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAE 63 ++S+L +G TP+V L + S D G + ++AKLE NP GS K R A+ MI AE Sbjct: 3 HNSILDVIGQTPIVRLAQFSE--DLG-----IEVYAKLESLNPGGSHKARIALGMILDAE 55 Query: 64 ADGLL--RPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQII 121 G+L G TI+EP+ GNTGI L MA + GY+++ V+P+N S E+++LL LYGA+++ Sbjct: 56 RRGVLIRDSGQTIIEPSGGNTGIGLVMAGNVLGYKVVLVIPDNYSPEKQKLLRLYGAKVV 115 Query: 122 FSAAEGGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLPE--ITHF 179 S + G+N+ EL NPS+VML Q N AN +H T PE+L E +F Sbjct: 116 LSDSRLGNNSHGEKCMELQLENPSYVMLNQQRNGANPQTHRDTTAPEILRAFGEKRADYF 175 Query: 180 VAGLGTTGTLMGTGRFLREHVANVKIVAAEP------RYGEGVYALRNMDEGFVPELYDP 233 V G+GT G + G G L+ ++++ EP + + ++ + G +P + + Sbjct: 176 VCGIGTGGHITGIGETLKTAWPELRVMGVEPEECDLLKNQHAPHHIQGLSIGLIPSILNL 235 Query: 234 EILTARYSVGAVDAVRRTRELVHTEGIFAGISTGA 268 +++ V D + + ++ T+ I G+S+ A Sbjct: 236 DVIDGMLKVSRQDCIDMMKRIMRTDAISLGLSSAA 270 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: 261 Number of extensions: 13 Number of successful extensions: 4 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: 304 Length adjustment: 27 Effective length of query: 296 Effective length of database: 277 Effective search space: 81992 Effective search space used: 81992 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