Align Putative cystathionine beta-lyase; CBL; EC 4.4.1.13; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; ORF5 (uncharacterized)
to candidate WP_029000337.1 H537_RS0126900 cystathionine beta-lyase
Query= curated2:Q52811 (396 letters) >NCBI__GCF_000430725.1:WP_029000337.1 Length = 394 Score = 235 bits (600), Expect = 1e-66 Identities = 149/379 (39%), Positives = 206/379 (54%), Gaps = 18/379 (4%) Query: 29 GFINPPV-VH-ASTVLFPNARAMETRT----QKYTYGTRGTPTTDALCEAIDALEGSAGT 82 GF +P V VH ASTV FPN A+ T + YTYG GTPTT L I +LEG Sbjct: 20 GFGSPVVAVHKASTVFFPNTAALRTHSWLDKSAYTYGLHGTPTTFTLEARIASLEGGKHA 79 Query: 83 ILVPSGLAAVTIPFLGFVAAGDHALVVDSVYGPTRHFCDTMLKRLGVEVEYYHPEIGAGI 142 +L PSGLAA+++ +G +A+GD L+ D+ YGP + F LK G+ + Y A + Sbjct: 80 LLAPSGLAAISLVDIGLLASGDEVLLPDNAYGPGKTFARHELKSWGIAHKVYDAMDPASL 139 Query: 143 ETLFRSNTKLVHTEAPGSNTFEMQDIPAISAVAHRHG--AVVMMDNTWATPVYFRPLDHG 200 L KLV EA GS T E D+ A+ AV+ +DNTW + F G Sbjct: 140 AELLTPQAKLVWLEAAGSVTMEFPDLRALIRTVRERAPQAVIALDNTWGAGIAFDAFALG 199 Query: 201 VDISIHASTKYPSGHSDILLGT-VSANAEHWERLKEANGVLGICGAPDDAYQILRGLRTM 259 VD+++HA TKYPSG D+L+G+ V+A+ + RL A+ LG +D +LR L ++ Sbjct: 200 VDLTVHALTKYPSGGGDVLMGSVVTADQALYRRLALAHSRLGFGVGLNDVEAVLRALPSL 259 Query: 260 GLRLERHYESALDIAKWLEGRDDVARVLHPALPSFPSHHLWKRDFKGASGIFSFVLAADG 319 LR + +A+W R + RVLHPALP P H W A+G+F+ L Sbjct: 260 PLRYAAQDAAGRQLARWCAQRSEFVRVLHPALPGAPGHEHWADTCSAAAGLFTVEL---D 316 Query: 320 PEKSRAKAHAFLDALRIFGLGYSWGGFESLAL---HAYLNDRTVAKAPTDGPVIRLQIGI 376 P + A+A A +DAL++F +G+SWGG SLA+ A L R V P G +IR +G+ Sbjct: 317 PRYTPAQADAVVDALKLFRIGWSWGGPVSLAVPYDAASLRSRPV---PYRGTLIRFSLGL 373 Query: 377 EDVADLKADIERGFAAASA 395 E V DL+AD+E+ A A Sbjct: 374 EAVEDLQADLEQALAVLHA 392 Lambda K H 0.320 0.137 0.417 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: 443 Number of extensions: 20 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: 396 Length of database: 394 Length adjustment: 31 Effective length of query: 365 Effective length of database: 363 Effective search space: 132495 Effective search space used: 132495 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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