Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate WP_043743637.1 AMB_RS06615 cysteine synthase A
Query= BRENDA::Q2V0C9 (504 letters) >NCBI__GCF_000009985.1:WP_043743637.1 Length = 334 Score = 223 bits (567), Expect = 1e-62 Identities = 134/332 (40%), Positives = 187/332 (56%), Gaps = 10/332 (3%) Query: 33 TKIMPDILTAIGQTPLIKLNNIPKSYGIKCEIYAKCEFLNPGGSVKDRIAYRMIQDAEDK 92 T I L +IG TPLI+L + G C I K EFLNPGGSVKDR A +IQDAE K Sbjct: 2 TDIRDGFLDSIGNTPLIRLKRASEETG--CNILGKAEFLNPGGSVKDRAALAIIQDAERK 59 Query: 93 GLLKPGCTIIEPTSGNTGIGLAMAAAVRGYKCIIVMPEKMSDEKISTLYALGAKIIRTPT 152 GLLKPG I+E T+GNTGIGLA+ A GY+ +IVMPE S EK L +GA + P Sbjct: 60 GLLKPGGVIVEGTAGNTGIGLALVANALGYRTVIVMPETQSQEKKDMLRLVGADLRLVPA 119 Query: 153 EASWHSPEAHI----SVAQKLQKEIPNSII-LDQYTNPGNPLAHYDQTAIEIWKQCEGKI 207 + +P ++ ++A +L K PN ++ +Q+ N N + H++ T EIW+Q +G + Sbjct: 120 -VPYANPGNYVRYSETLANELAKTEPNGVLWANQFDNTANRMGHFNTTGQEIWRQTDGTV 178 Query: 208 DYLVAGAGTGGTISGIGRKLKELSPNIKIIAVDPKGSIL--DPSSDSQNEVGFYEVEGIG 265 D GTGGT++G G LKE + +IK++ DP GS L + G EGIG Sbjct: 179 DAFTCAVGTGGTLAGTGMALKEHNKDIKVVLADPMGSALYHHYAHGELKAEGTSITEGIG 238 Query: 266 YDFIPTVLDRNVIDKWIKTEDNESLNAARMLIRQEGLLCGGSSGAALIAALKIAKDIPEE 325 I LD ID ++ D+E+L L+RQEGL+ GGSSG ++AA+K+A+ + Sbjct: 239 QGRITRNLDGAPIDDQVQVTDHEALPLIFDLVRQEGLVLGGSSGINVMAAIKVARILGPG 298 Query: 326 KRMVIILPDGIRNYLTKFVSEYWMETRGFLQP 357 +V +L D Y +K + ++ R P Sbjct: 299 HTVVTVLCDYGTRYQSKLFNPAFLRERNLPVP 330 Lambda K H 0.318 0.135 0.404 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: 368 Number of extensions: 18 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: 504 Length of database: 334 Length adjustment: 31 Effective length of query: 473 Effective length of database: 303 Effective search space: 143319 Effective search space used: 143319 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 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