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 8501944 DvMF_2658 cysteine synthase (RefSeq)
Query= BRENDA::P9WP53 (323 letters) >FitnessBrowser__Miya:8501944 Length = 310 Score = 191 bits (485), Expect = 2e-53 Identities = 119/305 (39%), Positives = 168/305 (55%), Gaps = 17/305 (5%) Query: 7 LLQALGNTPLVGLQRLSPRWDDGRDGPHVRLWAKLEDRNPTGSIKDRPAVRMIEQAEADG 66 + + +G TPLV L R+S +G + AKLE NP S+KDR A+ MI+ A G Sbjct: 7 MTELVGRTPLVRLNRVS-------EGCAAEVVAKLEFNNPCASVKDRIALAMIDGAMERG 59 Query: 67 LLRPGATILEPTSGNTGISLAMAARLKGYRLICVMPENTSVERRQLLELYGAQIIFSAAE 126 L PG ++EPTSGNTG+ LA A ++G L+ MPE+ S ER+ LL +GA+++ + A Sbjct: 60 ELAPGGLLVEPTSGNTGVGLAFVAAVRGLTLVLTMPESMSNERKALLRGFGARLVLTPAS 119 Query: 127 GGSNTAVATAKELAATNPSWVMLYQYGNPANTDSHYCGTGPELLADLP-EITHFVAGLGT 185 G A+ A+ + A P VML Q+ NP N H T E+ AD ++ FVAG+GT Sbjct: 120 KGMRGAIEEAERIVAETPGAVMLGQFVNPDNPLVHRKTTAEEIWADTDGKVDAFVAGVGT 179 Query: 186 TGTLMGTGRFLREHVANVKIVAAEPRY-------GEGVYALRNMDEGFVPELYDPEILTA 238 GT+ GTGR LRE ++K+ A EP G + ++ + GFVP + D ++ Sbjct: 180 GGTVTGTGRRLRELNPDIKVFAVEPDESPVLSGGAPGPHPIQGIGAGFVPPVLDTKVYDE 239 Query: 239 RYSVGAVDAVRRTRELVHTEGIFAGISTGAVLHAALGVGAGALAAGERADIALVVADAGW 298 V DA+ R L+ EGI G+S+GA AA+ V AG+R + VV D G Sbjct: 240 IIRVPGKDALVTARRLLREEGILCGVSSGANAFAAMAVARRPEMAGKR--VVFVVCDTGE 297 Query: 299 KYLST 303 +YLST Sbjct: 298 RYLST 302 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: 285 Number of extensions: 19 Number of successful extensions: 5 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