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 350926 BT1398 putative aminotransferase B (NCBI ptt file)
Query= SwissProt::Q08432 (387 letters) >FitnessBrowser__Btheta:350926 Length = 385 Score = 349 bits (895), Expect = e-101 Identities = 168/385 (43%), Positives = 243/385 (63%), Gaps = 4/385 (1%) Query: 2 NFDKREERLGTQSVKWDKTGELFGVTDALPMWVADMDFRAPEAITEALKERLDHGIFGYT 61 NFD+ R GT S KWD G+ D LPMWVADMDFR ++ EALK R++HGIFGY Sbjct: 4 NFDEIVPRRGTNSYKWDSAGD----ADVLPMWVADMDFRTAPSVVEALKRRVEHGIFGYV 59 Query: 62 TPDQKTKDAVCGWMQNRHGWKVNPESITFSPGVVTALSMAVQAFTEPGDQVVVQPPVYTP 121 +A+ W RHGW++ E I ++ GVV ALS ++A T PGD+V+VQ PVY Sbjct: 60 RVPDAYYEAITRWFAGRHGWQIEKEWIIYTTGVVPALSAVIKALTTPGDKVIVQTPVYNC 119 Query: 122 FYHMVEKNGRHILHNPLLEKDGAYAIDFEDLETKLSDPSVTLFILCNPHNPSGRSWSRED 181 F+ + NG ++ NPL+ +G Y IDF DLE K +DPSV + +LCNPHNP+GR W++++ Sbjct: 120 FFSSIRNNGCEVVANPLIYMNGTYQIDFIDLERKAADPSVKVLLLCNPHNPAGRVWTKQE 179 Query: 182 LLKLGELCLEHGVTVVSDEIHSDLMLYGHKHTPFASLSDDFADISVTCAAPSKTFNIAGL 241 L +LGE+CL + + VV+DEIH +L+ GH + PFAS+S++F SVTC +PSK FN+AGL Sbjct: 180 LTRLGEICLRNNIWVVADEIHCELVFPGHTYIPFASVSEEFLMHSVTCTSPSKAFNLAGL 239 Query: 242 QASAIIIPDRLKRAKFSASLQRNGLGGLNAFAVTAIEAAYSKGGPWLDELITYIEKNMNE 301 Q + I+ D R + ++ N + +N F V A+ AAY+ G WL+EL Y+ N + Sbjct: 240 QIANIVSADTDIRMQIDKAININEVCDVNPFGVEALIAAYNDGEEWLEELNQYLFANYHY 299 Query: 302 AEAFLSTELPKVKMMKPDASYLIWLDFSAYGLSDAELQQRMLKKGKVILEPGTKYGPGGE 361 A+ LP+ ++ + +YL+W+D SA S ++ + +L+K K+ + G YG GE Sbjct: 300 LRAYFDEYLPEFPVLPLEGTYLVWVDCSALKQSSEDIVKTLLEKEKLWVNEGNLYGEAGE 359 Query: 362 GFMRLNAGCSLATLQDGLRRIKAAL 386 F+R+N C L +GL R++ AL Sbjct: 360 RFIRINIACPRQRLIEGLNRLRRAL 384 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: 448 Number of extensions: 17 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: 385 Length adjustment: 30 Effective length of query: 357 Effective length of database: 355 Effective search space: 126735 Effective search space used: 126735 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