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_012631087.1 MNOD_RS45110 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q08432 (387 letters) >NCBI__GCF_000022085.1:WP_012631087.1 Length = 412 Score = 318 bits (816), Expect = 1e-91 Identities = 162/386 (41%), Positives = 231/386 (59%), Gaps = 7/386 (1%) Query: 3 FDKREERLGTQSVKWDKTGELFGVTDA----LPMWVADMDFRAPEAITEALKERLDHGIF 58 FD+ ER T S+KW + +L + LPMWVAD D+RAP + +AL++ + HG+F Sbjct: 21 FDEIIERRDTNSLKWTYSEKLLAPEEVAAGPLPMWVADTDWRAPAPVIDALQDAIKHGVF 80 Query: 59 GYTT-PDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPP 117 GY AV W R GW++ E +T + G++TAL AVQAF+ PGD +++QPP Sbjct: 81 GYPAGATNGYMKAVTDWQARRFGWEIAEEWVTQTAGIITALKTAVQAFSSPGDSILIQPP 140 Query: 118 VYTPFYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSW 177 VY+ F+ V NGR + PLL + Y D E + + LFIL NPHNP+G W Sbjct: 141 VYSHFHDDVLVNGRQLALAPLLRWENGYRFDESIFEAAIGE-GTKLFILSNPHNPTGNVW 199 Query: 178 SREDLLKLGELCLEHGVTVVSDEIHSDLMLYGHK-HTPFASLSDDFADISVTCAAPSKTF 236 S +L +GE+CL H V V+SDEIH DL++ K H PFAS+S++FA S+TC APSKTF Sbjct: 200 SEAELRVMGEICLRHNVLVLSDEIHQDLIINPEKRHIPFASISEEFAQNSITCTAPSKTF 259 Query: 237 NIAGLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIE 296 N+AGLQ + I IP+ R +F+ RN +N + A EAAYS+G PWL+E++ Y+ Sbjct: 260 NLAGLQCANIFIPNARIRNQFARQYNRNVYPRVNVLGMVATEAAYSEGEPWLEEMLIYLR 319 Query: 297 KNMNEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKY 356 N + + ++ L K+K++ D+ YL W+D GL L + ML K +V L+ G K+ Sbjct: 320 TNHDHFASSINNSLSKIKVLPADSLYLAWMDCRGLGLDAETLDKLMLTKARVWLDKGQKF 379 Query: 357 GPGGEGFMRLNAGCSLATLQDGLRRI 382 G G G+MR N GC +T+ + R+ Sbjct: 380 GAEGRGYMRANLGCPRSTVDVAINRL 405 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: 412 Number of extensions: 12 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: 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