Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate GFF2301 PS417_11735 methionine gamma-lyase
Query= SwissProt::Q83A83 (387 letters) >FitnessBrowser__WCS417:GFF2301 Length = 411 Score = 310 bits (793), Expect = 6e-89 Identities = 172/397 (43%), Positives = 251/397 (63%), Gaps = 17/397 (4%) Query: 5 NNKKSHI--DTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSP--------GVHQGYEYSR 54 NNK + TR IH G P GA++ PIY ++T+A + G G+ Y+R Sbjct: 2 NNKHNAFGFSTRAIHHGYDPKDHHGALVPPIYLSATFAFPTAEYGAACFAGEASGHFYTR 61 Query: 55 SQNPTRFAYERCVADLESGQHGFAFASGMAA-TATILELLQPGDHVVVMDDVYGGSYRLF 113 NPT E +A LE+G AF+SGM A AT LL+PGD V+V +YG ++ L Sbjct: 62 ISNPTLALLESRMATLENGDAAVAFSSGMGAIAATFWTLLRPGDEVIVSQTLYGCTFALL 121 Query: 114 ENVRKRSAGLSFSFVDFTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEK- 172 + G+ VD TD ++ A+T T+M++ E+P+NP L++VD+A +A +A ++ Sbjct: 122 HH-GIGEFGIKVRHVDLTDLTALQAALTPATRMIYCETPANPNLRLVDIAAVAALAHQQP 180 Query: 173 NIIAVADNTFATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKY- 231 N+ V DNT+ TP +QRPLELG D+V HSATKYL+GH DI G+AV N+ LA++++ Sbjct: 181 NVTLVVDNTYCTPYLQRPLELGADVVVHSATKYLSGHGDITAGIAV--SNQALAQRIRLQ 238 Query: 232 -LQNAIGAIAAPFDSFMVLRGLKTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSH 290 L++ GA+ +P D+ +++RGLKTLA+RM+RHC NA +A+ L+ HP V+ V YPGL S Sbjct: 239 GLKDLTGAVMSPQDASLLMRGLKTLALRMDRHCSNAQAVAEALQAHPAVQSVTYPGLRSF 298 Query: 291 PQHSIAKKQMRYFGGMISVELKCDLNETKKVLERCQLFTLAESLGGVESLIEHPAIMTHA 350 PQ+ +A +QM+ GGMI+ ELK + ++ + +LFT A SLG ESL +HPA MTH+ Sbjct: 299 PQYELATQQMKMPGGMIAFELKGGIETGRRFMNALKLFTRAVSLGDAESLAQHPASMTHS 358 Query: 351 SIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAAL 387 + ER GI++G +RLSVG+E + DL D++ AL Sbjct: 359 TYTPQERAAHGISEGLVRLSVGLEDVADLLADVQQAL 395 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: 417 Number of extensions: 21 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 387 Length of database: 411 Length adjustment: 31 Effective length of query: 356 Effective length of database: 380 Effective search space: 135280 Effective search space used: 135280 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