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 GFF3630 HP15_3572 aminotransferase, classes I and II
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__Marino:GFF3630 Length = 401 Score = 316 bits (809), Expect = 8e-91 Identities = 161/391 (41%), Positives = 231/391 (59%), Gaps = 8/391 (2%) Query: 3 FDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYTT 62 FD R T SVK+D +FG + +P+WVADMDF APEA+T AL ER H I+GYT Sbjct: 5 FDDPVSRENTCSVKFDARQAVFGTEEVIPVWVADMDFAAPEAVTRALAERAAHPIYGYTL 64 Query: 63 PDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTPF 122 ++ W NRHGW++ E I +PGVV +++ A A+ PG+ V++QPPVY PF Sbjct: 65 FPDSLYQSMIDWFANRHGWEIQREWILMAPGVVPSINAACMAYAGPGEGVIIQPPVYPPF 124 Query: 123 YHMVEKNGRHILHNPLLEKD------GAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRS 176 + V +GR ++ NPL+ +D G Y +D + LE + P + +LC+PHNP GR Sbjct: 125 FSSVRHSGRVVIENPLVPEDPDTGDPGHYRMDLDHLEECAARPDARVLLLCSPHNPVGRV 184 Query: 177 WSREDLLKLGELCLEHGVTVVSDEIHSDLMLYGH-KHTPFASLSDDFADISVTCAAPSKT 235 WS E+L + ++ H + VVSDEIH DL+ +HT A+L+ D V APSK+ Sbjct: 185 WSEEELRAVLDIARRHQLVVVSDEIHCDLVFPDKPRHTMLANLAGP-DDALVMAVAPSKS 243 Query: 236 FNIAGLQASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYI 295 FN+ GL SA++IPD +R A + L N F++ EA Y GGPWLD+L+ Y+ Sbjct: 244 FNMPGLGLSALVIPDAERRKAMKAVFESMHLPQCNPFSIAGFEAGYRHGGPWLDDLMAYL 303 Query: 296 EKNMNEAEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTK 355 + N + + LP V++ P+ +YL+WLD GL DA L++ ++K V + PG Sbjct: 304 QANRDYVVEAVGQRLPGVRVSAPEGTYLMWLDCRELGLDDAGLKRFFVRKAGVGMNPGLS 363 Query: 356 YGPGGEGFMRLNAGCSLATLQDGLRRIKAAL 386 +G G GFMRLN GC + L++ + RI+AAL Sbjct: 364 FGDPGSGFMRLNIGCPRSVLEEVIGRIEAAL 394 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: 498 Number of extensions: 29 Number of successful extensions: 3 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: 401 Length adjustment: 31 Effective length of query: 356 Effective length of database: 370 Effective search space: 131720 Effective search space used: 131720 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