Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate GFF4108 PS417_21045 cysteine synthase
Query= BRENDA::Q2V0C9 (504 letters) >FitnessBrowser__WCS417:GFF4108 Length = 304 Score = 198 bits (503), Expect = 2e-55 Identities = 118/308 (38%), Positives = 179/308 (58%), Gaps = 13/308 (4%) Query: 39 ILTAIGQTPLIKLNNIPKSYGIKCEIYAKCEFLNPGGSVKDRIAYRMIQDAEDKGLL--K 96 IL IGQTP+++L + GI E+YAK E LNPGGS K RIA MI DAE +G+L Sbjct: 6 ILDVIGQTPIVRLAQFSEDLGI--EVYAKLESLNPGGSHKARIALGMILDAERRGVLIRD 63 Query: 97 PGCTIIEPTSGNTGIGLAMAAAVRGYKCIIVMPEKMSDEKISTLYALGAKIIRTPTEASW 156 G TIIEP+ GNTGIGL MA V GYK ++V+P+ S EK L GAK++ + + Sbjct: 64 SGQTIIEPSGGNTGIGLVMAGNVLGYKVVLVIPDNYSPEKQKLLRLYGAKVVLSDSRLGN 123 Query: 157 HSPEAHISVAQKLQKEIPNSIILDQYTNPGNPLAHYDQTAIEIWKQC-EGKIDYLVAGAG 215 +S H +LQ E P+ ++L+Q N NP H D TA EI + E + DY V G G Sbjct: 124 NS---HGEKCMELQLENPSYVMLNQQRNGANPQTHRDTTAPEILRAFGEKRADYFVCGIG 180 Query: 216 TGGTISGIGRKLKELSPNIKIIAVDPKGSILDPSSDSQNEVGFYEVEGIGYDFIPTVLDR 275 TGG I+GIG LK P ++++ V+P+ L +N+ + ++G+ IP++L+ Sbjct: 181 TGGHITGIGETLKTAWPELRVMGVEPEECDL-----LKNQHAPHHIQGLSIGLIPSILNL 235 Query: 276 NVIDKWIKTEDNESLNAARMLIRQEGLLCGGSSGAALIAALKIAKDIPEEKRMVIILPDG 335 +VID +K + ++ + ++R + + G SS A ++A ++A ++P E ++ ++ D Sbjct: 236 DVIDGMLKVSRQDCIDMMKRIMRTDAISLGLSSAANMVAIARLAPELPPETVVLTMVYDN 295 Query: 336 IRNYLTKF 343 +YL F Sbjct: 296 ADSYLPGF 303 Lambda K H 0.318 0.135 0.404 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: 373 Number of extensions: 21 Number of successful extensions: 6 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: 504 Length of database: 304 Length adjustment: 31 Effective length of query: 473 Effective length of database: 273 Effective search space: 129129 Effective search space used: 129129 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 (21.7 bits) S2: 50 (23.9 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