Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate Pf1N1B4_4890 Cystathionine gamma-lyase (EC 4.4.1.1)
Query= SwissProt::Q83A83 (387 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4890 Length = 393 Score = 512 bits (1318), Expect = e-150 Identities = 249/375 (66%), Positives = 298/375 (79%) Query: 13 TRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGVHQGYEYSRSQNPTRFAYERCVADLES 72 TRVIHAGQ PDP TGA+M PIY STY Q+SPGVH+G++Y RS NPTRFA ERCVADLE Sbjct: 15 TRVIHAGQTPDPSTGALMPPIYANSTYLQQSPGVHKGFDYGRSHNPTRFALERCVADLEG 74 Query: 73 GQHGFAFASGMAATATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAGLSFSFVDFTD 132 G FAFASG+AA A +LELL G H+V +D+YGG++RLF+ VR+RSAG FSFVD TD Sbjct: 75 GTRAFAFASGLAAIANVLELLDAGAHIVSGNDLYGGTFRLFDKVRRRSAGHRFSFVDLTD 134 Query: 133 ENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTFATPIIQRPLE 192 A+ T+M+WVE+PSNP L + DL +A I +++ II VADNTFA+P IQRPLE Sbjct: 135 LAAFEAALEDDTRMVWVETPSNPLLSLTDLDAVARICRQRGIICVADNTFASPWIQRPLE 194 Query: 193 LGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKYLQNAIGAIAAPFDSFMVLRGL 252 LGFDIV HS TKYLNGHSD+IGG+AVVG N LAE+L +LQNA+GAIA PFD+F+ LRG+ Sbjct: 195 LGFDIVLHSTTKYLNGHSDVIGGIAVVGQNAELAERLGFLQNAVGAIAGPFDAFLTLRGV 254 Query: 253 KTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVELK 312 KTLA+RMERHC NA++LAQWLE+ P+V RVYYPGLPSHPQH +A++QMR FGGMIS++L Sbjct: 255 KTLALRMERHCSNALELAQWLERQPQVARVYYPGLPSHPQHELARRQMRGFGGMISLDLN 314 Query: 313 CDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVG 372 DL K+ LE ++F LAESLGGVESLIEHPAIMTHASIP R +LGI D +RLSVG Sbjct: 315 SDLAGAKRFLESVRIFALAESLGGVESLIEHPAIMTHASIPVETRAQLGIGDALVRLSVG 374 Query: 373 IEAITDLRHDLEAAL 387 +E + DLR DL AL Sbjct: 375 VEDVEDLRADLAQAL 389 Lambda K H 0.319 0.134 0.385 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: 483 Number of extensions: 13 Number of successful extensions: 1 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: 393 Length adjustment: 31 Effective length of query: 356 Effective length of database: 362 Effective search space: 128872 Effective search space used: 128872 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.
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