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_050462121.1 AKL27_RS06485 cystathionine beta-lyase
Query= curated2:Q52811 (396 letters) >NCBI__GCF_001189915.1:WP_050462121.1 Length = 390 Score = 267 bits (683), Expect = 3e-76 Identities = 154/383 (40%), Positives = 217/383 (56%), Gaps = 11/383 (2%) Query: 15 TRLTHIGNDPFDYHGFINPPVVHASTVLFPNARAMETRTQK----YTYGTRGTPTTDALC 70 T L H P + + HASTVLFP AM R K YTYG GTPTT L Sbjct: 9 TSLVHSDYTPPAGFSALPSSIHHASTVLFPTIAAMRARNWKEKSGYTYGLHGTPTTFTLE 68 Query: 71 EAIDALEGSAGTILVPSGLAAVTIPFLGFVAAGDHALVVDSVYGPTRHFCDTMLKRLGVE 130 + +EG L PSGLAA+++ + GD L+ ++VYGP++ + G+ Sbjct: 69 ARLAEIEGGRHCRLTPSGLAAISLVNFALLKTGDDVLLPENVYGPSKELSGWLQSDFGIT 128 Query: 131 VEYYHPEIGAGIETLFRSNTKLVHTEAPGSNTFEMQDIPAISAVAHRHGAVVMMDNTWAT 190 +Y P IGAGI L + +T+L+ TEAPGS + E+ D+PAI AH G V +DNTW+ Sbjct: 129 ARFYDPLIGAGIADLIQPDTRLIWTEAPGSVSMEVADLPAICKAAHAAGVTVALDNTWSA 188 Query: 191 PVYFRPLDHGVDISIHASTKYPSGHSDILLGTVSANAEHW-ERLKEANGVLGICGAPDDA 249 + R D G+DI + A TKY SG SDIL+G V + +L+ A+ LG+ DD Sbjct: 189 GLALRAFDLGIDIVMQALTKYQSGGSDILMGAVITRDDALNHKLELAHMRLGMGVGMDDV 248 Query: 250 YQILRGLRTMGLRLERHYESALDIAKWLEGRDDVARVLHPALPSFPSHHLWKRDFKGASG 309 Y +LR L +M LR + H +A +A WL R ++ +VLHPA P P H +W+RDF GA G Sbjct: 249 YLVLRSLPSMRLRFDAHDAAARKVAAWLTTRKEIGKVLHPAFPDCPGHAIWQRDFTGAGG 308 Query: 310 IFSFVLAADGPEKSRAKAHAFLDALRIFGLGYSWGGFESLALHAYLNDRTVAKAPTD-GP 368 +FS + DG + A+ F+++L +F +G+SWGG SL + + +T+ A +D G Sbjct: 309 LFSVIF--DG-RYTEAQIDRFVESLALFKIGFSWGGAHSLCVPYRM--QTMRSAWSDPGH 363 Query: 369 VIRLQIGIEDVADLKADIERGFA 391 ++R IG+ED DL ADIE+ A Sbjct: 364 LVRFNIGLEDPDDLIADIEQALA 386 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: 468 Number of extensions: 24 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: 396 Length of database: 390 Length adjustment: 31 Effective length of query: 365 Effective length of database: 359 Effective search space: 131035 Effective search space used: 131035 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