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 353664 BT4138 putative aminotransferase (NCBI ptt file)
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__Btheta:353664 Length = 389 Score = 338 bits (868), Expect = 1e-97 Identities = 161/386 (41%), Positives = 246/386 (63%), Gaps = 2/386 (0%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 NFD+ R GT SVKWD +G D +PMWVADMDFR + +ALK+RLDH + GYT Sbjct: 4 NFDEIINRNGTDSVKWDAVERRWGRNDLIPMWVADMDFRTAPFVIDALKKRLDHEVLGYT 63 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 ++ +++ W++ RHGW++ + +TF+PG+V L+ A+ FTE GD+V+V PPVY P Sbjct: 64 FACKEWAESIINWLKERHGWEIREDMLTFTPGIVRGLAFAIHCFTEKGDKVMVMPPVYHP 123 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 F+ + +KN R ++++PL+ KDG Y IDF+ + L IL NPHNP GR W++E+ Sbjct: 124 FFLVTQKNEREVVYSPLVLKDGQYHIDFDRFRKDVQ--GCKLLILSNPHNPGGRVWTKEE 181 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGL 241 L ++ ++C E+G V+SDEIH+DL L +KH FA +S+ S+ +PSK FN+ GL Sbjct: 182 LSQIADICYENGTLVISDEIHADLTLPPYKHPTFALISEKARMNSLVFMSPSKAFNMPGL 241 Query: 242 QASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMNE 301 +S II + R +F ++ + + FA ++ AAYS G WLD+++ YI+ N++ Sbjct: 242 ASSYAIIENDELRHQFQVYMEASEFSEGHLFAYLSVAAAYSHGTEWLDQVVAYIKGNIDF 301 Query: 302 AEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGGE 361 E++L +P ++M++P ASYLI+LD GL+ EL + ++ + L GT +G GE Sbjct: 302 TESYLKERIPAIRMIRPQASYLIFLDCRELGLNQEELNRLFVEDAHLALNEGTTFGKEGE 361 Query: 362 GFMRLNAGCSLATLQDGLRRIKAALS 387 GFMRLN C ATL+ LR+++ A++ Sbjct: 362 GFMRLNVACPRATLEKALRQLEQAVN 387 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: 445 Number of extensions: 16 Number of successful extensions: 2 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: 389 Length adjustment: 30 Effective length of query: 357 Effective length of database: 359 Effective search space: 128163 Effective search space used: 128163 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