Align Probable cystathionine beta-synthase Rv1077; Beta-thionase; Serine sulfhydrase; EC 4.2.1.22 (characterized)
to candidate WP_086510266.1 BZY95_RS12545 cysteine synthase CysM
Query= SwissProt::P9WP51 (464 letters) >NCBI__GCF_002151265.1:WP_086510266.1 Length = 298 Score = 208 bits (529), Expect = 2e-58 Identities = 119/298 (39%), Positives = 175/298 (58%), Gaps = 14/298 (4%) Query: 7 ISELIGGTPLVRLNSVVPDGAGTVAAKVEYLNPGGSSKDRIAVKMIEAAEASGQLKPGGT 66 I +++G TPLVRL + T+ AK+E NP GS KDR A+ M+E AEA G + PG T Sbjct: 6 IEDVVGHTPLVRLKRITAGRNNTLLAKLEGNNPAGSVKDRPALSMLEQAEARGDITPGDT 65 Query: 67 IVEPTSGNTGVGLALVAQRRGYKCVFVCPDKVSEDKRNVLIAYGAEVVVCPTAVPPHDPA 126 ++E TSGNTG+ LA+ A +GY+ V + PD S +++ + AYGA ++ T Sbjct: 66 LIEATSGNTGIALAMAAAIKGYRMVLIMPDSASSERKQAMAAYGARLI---TVSKEGGME 122 Query: 127 SYYSVSDRLVRDIDGAWKP-DQYANPEGPASHYVTTGPEIWADTEGKVTHFVAGIGTGGT 185 +++ +V +G KP +Q+ANP+ P +HY TGPE+W T G +THFV+ +GT GT Sbjct: 123 EARDLAEAMVSRGEG--KPLNQFANPDNPLAHYRGTGPELWEQTGGTITHFVSSMGTTGT 180 Query: 186 ITGAGRYLKEVSGGRVRIVGADPEGSVYSGGAGRPYLVEGVGEDFWPAAYDPSVPDEIIA 245 I G RYLKE V+IVG PE G R +++ P+ +D + D ++ Sbjct: 181 IMGVSRYLKE-RNPEVQIVGLQPEDGASIAGIRR------WPKEYLPSIFDATRVDRVLD 233 Query: 246 VSDSDSFDMTRRLAREEAMLVGGSCGMAVVAALKVAEEAGPDALIVVLLPDGGRGYMS 303 + ++ + RRLAREE +L G S G A+ AL+VAEE +A+IV ++ D G Y+S Sbjct: 234 IGQHEAEEHMRRLAREEGILAGVSSGGALAGALRVAEEV-ENAVIVFIVCDRGDRYLS 290 Lambda K H 0.316 0.135 0.398 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: 400 Number of extensions: 25 Number of successful extensions: 3 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: 464 Length of database: 298 Length adjustment: 30 Effective length of query: 434 Effective length of database: 268 Effective search space: 116312 Effective search space used: 116312 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 (21.6 bits) S2: 49 (23.5 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