Align Cystathionine beta-lyase PatB; CBL; Beta-cystathionase PatB; Cysteine lyase PatB; Cysteine-S-conjugate beta-lyase PatB; EC 4.4.1.13 (characterized)
to candidate WP_050782025.1 aspartate aminotransferase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000016205.1:WP_050782025.1 Length = 412 Score = 315 bits (807), Expect = 1e-90 Identities = 161/391 (41%), Positives = 235/391 (60%), Gaps = 7/391 (1%) Query: 3 FDKREERLGTQSVKWDKTGELFGV----TDALPMWVADMDFRAPEAITEALKERLDHGIF 58 FD +R + S+KW +L D LPMWVADMDFRAP+ + +AL E +++G+F Sbjct: 21 FDDVIDRRNSNSLKWAFGEKLLSAEECAADPLPMWVADMDFRAPQPVIDALHEAVEYGVF 80 Query: 59 GYTT-PDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPP 117 GY+ + +AV GW R GW V + + S G++TAL A+QAF+ PGD V++QPP Sbjct: 81 GYSCGATGRYVEAVTGWQARRFGWDVPKDWVLQSSGIITALKTAIQAFSAPGDTVLIQPP 140 Query: 118 VYTPFYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSW 177 VY F+ V NGRH+++ PL AY + + E + + LFIL NPHNP+G W Sbjct: 141 VYAHFHDDVLLNGRHLVYAPLERAGTAYRFNEKTFEAAIRSDT-KLFILSNPHNPTGNVW 199 Query: 178 SREDLLKLGELCLEHGVTVVSDEIHSDLMLYG-HKHTPFASLSDDFADISVTCAAPSKTF 236 S ++LL +GE+C HGV VVSDEIH DL++ KH PF SL D FAD SVTC APSKTF Sbjct: 200 SEDELLAMGEICARHGVLVVSDEIHQDLIVNPLKKHIPFGSLGDRFADNSVTCTAPSKTF 259 Query: 237 NIAGLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIE 296 N+ GLQ++ + + +R +R + RN +N + A EAAYS+G WL+EL+ Y+ Sbjct: 260 NLPGLQSANLFVANRQRREELRRQFDRNMYQSVNTLGMVAAEAAYSQGESWLEELLMYLR 319 Query: 297 KNMNEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKY 356 +N + + K++++ D+ YL W+D G+ L + ML + ++ + G K+ Sbjct: 320 ENHAHFRDAVHSITSKIEILPADSLYLAWIDCRGLGMDADVLNRFMLTEARLWFDKGQKF 379 Query: 357 GPGGEGFMRLNAGCSLATLQDGLRRIKAALS 387 G G G+MR N GC +T+ + +RR+ AL+ Sbjct: 380 GIEGHGYMRANLGCPRSTIDEAIRRLTNALT 410 Lambda K H 0.318 0.135 0.408 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: 451 Number of extensions: 25 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: 387 Length of database: 412 Length adjustment: 31 Effective length of query: 356 Effective length of database: 381 Effective search space: 135636 Effective search space used: 135636 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 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