Align Cystathionine beta-lyase; CBL; Beta-cystathionase; Cysteine lyase; Cysteine-S-conjugate beta-lyase; EC 4.4.1.13 (characterized)
to candidate WP_011188941.1 DP_RS08645 O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase
Query= SwissProt::Q83A83 (387 letters) >NCBI__GCF_000025945.1:WP_011188941.1 Length = 423 Score = 230 bits (586), Expect = 6e-65 Identities = 142/421 (33%), Positives = 223/421 (52%), Gaps = 42/421 (9%) Query: 7 KKSHIDTRVIHAGQKPDPLTGAVMTPIYTASTYAQKSPGV--------HQGYEYSRSQNP 58 K HIDT + AG +P ++ PI ++T+ + G G+ YSR NP Sbjct: 2 KNWHIDTLAVQAGYEPKNGEPRIV-PIAQSTTFKYDTAGAIADLFDLKAAGHMYSRISNP 60 Query: 59 TRFAYERCVADLESGQHGFAFASGMAA-TATILELLQPGDHVVVMDDVYGGSYRLFENVR 117 T +E +A +E G A +SG AA T +++ + Q GDH + + +YGG++ LF++ Sbjct: 61 TVAVFEDKIAAMEGGVGALAVSSGQAASTISVINICQAGDHFIALATLYGGTFNLFKHSM 120 Query: 118 KRSAGLSFSFVD-FTDENKVREAVTAKTKMLWVESPSNPRLKIVDLAKIAEIAKEKNIIA 176 K+ G+ +FVD +++ A TK+++ ES SNP ++D K I E + Sbjct: 121 KKW-GIEVTFVDPAASPEEIKAAFKDNTKLIFGESLSNPGTDVLDFEKFVAIKNEMGVPL 179 Query: 177 VADNTFATPIIQRPLELGFDIVTHSATKYLNGHSDIIGGVAVVGDN--------KTLAE- 227 + DNTF TPI+ RP+ELG DIVTHS TKY++GH+ +GG+ + N L E Sbjct: 180 IVDNTFPTPILCRPIELGADIVTHSTTKYIDGHATSVGGIIIDSGNFDWTNGKFPGLTEP 239 Query: 228 --------------QLKYLQNA-------IGAIAAPFDSFMVLRGLKTLAIRMERHCENA 266 + Y+ A IG P ++F+ GL+TL +RMERH ENA Sbjct: 240 DDSYHGLSYTETFGKAAYIVKARVQWIRDIGCYQTPQNAFLSNLGLETLHLRMERHSENA 299 Query: 267 MQLAQWLEKHPKVKRVYYPGLPSHPQHSIAKKQMRYFGGMISVELKCDLNETKKVLERCQ 326 ++LA++L+ H KV+ V YP LP+ +++ KK + G+++ +K + +K++ Q Sbjct: 300 LRLAEFLDGHDKVEWVKYPMLPADSNYALCKKYLSAGSGVLTFGVKGSAQDAEKIMNSLQ 359 Query: 327 LFTLAESLGGVESLIEHPAIMTHASIPQAERQKLGITDGFIRLSVGIEAITDLRHDLEAA 386 L + + V + + HPA MTH + + +K GIT IR+SVGIE I D+ D + A Sbjct: 360 LAAIVVHVADVRTGVLHPASMTHRQLSSEDLEKAGITPQLIRVSVGIEKIDDIIADFKQA 419 Query: 387 L 387 L Sbjct: 420 L 420 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: 384 Number of extensions: 13 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 387 Length of database: 423 Length adjustment: 31 Effective length of query: 356 Effective length of database: 392 Effective search space: 139552 Effective search space used: 139552 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 Apr 10 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