Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate Echvi_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases
Query= SwissProt::Q83A83 (387 letters) >lcl|FitnessBrowser__Cola:Echvi_2080 Echvi_2080 Cystathionine beta-lyases/cystathionine gamma-synthases Length = 381 Score = 419 bits (1077), Expect = e-122 Identities = 204/376 (54%), Positives = 269/376 (71%), Gaps = 3/376 (0%) Query: 13 TRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGVHQGYEYSRSQNPTRFAYERCVADLES 72 T+VIHAG PDP TGA+MTPI+ STY QKSPG H+G+EYSR+ NPTR A ++ +A LE+ Sbjct: 5 TKVIHAGVAPDPTTGAIMTPIFQTSTYVQKSPGQHKGFEYSRTHNPTRDALQKSIAALEN 64 Query: 73 GQHGFAFASGMAATATILELLQPGDHVVVMDDVYGGSYRLFENVRKRSAGLSFSFVDFTD 132 G+HG F+SGM A +++LL PGD V+ +D+YGG+YR+F V + G+ F FV D Sbjct: 65 GKHGLCFSSGMGAIDALIKLLSPGDEVISTNDLYGGTYRIFTKVFAK-YGIKFHFVSMDD 123 Query: 133 ENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIAVADNTFATPIIQRPLE 192 + + + KT+++W E+P+NP + I+D+ +A IA + +++ DNTFATP +Q PL+ Sbjct: 124 PASIEKYINDKTRLIWAETPTNPMMNIIDIKALAAIAGKHDLLLGVDNTFATPYLQNPLD 183 Query: 193 LGFDIVTHSATKYLNGHSDIIGGVAVVGDNKTLAEQLKYLQNAIGAIAAPFDSFMVLRGL 252 LG D+V HS TKYL GHSD++ G VV D++ LAE L ++QN+ GA P D F+VLRG+ Sbjct: 184 LGADLVMHSVTKYLAGHSDVVMGALVVNDDR-LAEDLAFIQNSCGATPGPQDCFLVLRGI 242 Query: 253 KTLAIRMERHCENAMQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVELK 312 KTL +RMERHC+N +A +L HPKV +VY+PG HP H IA KQMR FGGMIS + Sbjct: 243 KTLHLRMERHCQNGKTIAGYLRHHPKVDKVYWPGFEDHPNHDIAAKQMRDFGGMISFSIV 302 Query: 313 CDLNE-TKKVLERCQLFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSV 371 D E KKVLE F+LAESLGGVESL HPA MTHASIP+ ER+K+G+TD IRLSV Sbjct: 303 GDKQEDAKKVLENLHYFSLAESLGGVESLCGHPASMTHASIPKVEREKVGLTDSLIRLSV 362 Query: 372 GIEAITDLRHDLEAAL 387 G+E DL++DL AAL Sbjct: 363 GVEDAEDLKNDLAAAL 378 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: 453 Number of extensions: 11 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 357 Effective length of database: 351 Effective search space: 125307 Effective search space used: 125307 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.
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