Align cystathionine beta-synthase (EC 4.2.1.22) (characterized)
to candidate CCNA_01493 CCNA_01493 cysteine synthase
Query= BRENDA::P35520 (551 letters) >FitnessBrowser__Caulo:CCNA_01493 Length = 332 Score = 218 bits (554), Expect = 4e-61 Identities = 129/325 (39%), Positives = 186/325 (57%), Gaps = 9/325 (2%) Query: 77 LPDILKKIGDTPMVRINKIGKKFGLKCELLAKCEFFNAGGSVKDRISLRMIEDAERDGTL 136 LP +L IG+TP++R+ + + G CE+L K EF N G SVKDR +L +I DAE G L Sbjct: 4 LPSVLDAIGNTPLIRLARASEATG--CEILGKAEFMNPGQSVKDRAALAIIRDAEAKGLL 61 Query: 137 KPGDTIIEPTSGNTGIGLALAAAVRGYRCIIVMPEKMSSEKVDVLRALGAEIVRTPTNAR 196 +PG I+E T+GNTGIGLA+ A+ GY+ IV+P S EK D +R LGAE+V Sbjct: 62 RPGGRIVEGTAGNTGIGLAMVASALGYKTTIVIPRTQSQEKKDAIRLLGAELVEVDA-VP 120 Query: 197 FDSPESHVGVAWRLKNEI----PNSHI-LDQYRNASNPLAHYDTTADEILQQCDGKLDML 251 + +P+++V + RL E+ P+ I +Q+ N +N AHY TT EI Q GK+D Sbjct: 121 YSNPDNYVRYSGRLAEELARTEPHGVIWANQFDNTANRDAHYHTTGPEIFDQTSGKVDGF 180 Query: 252 VASVGTGGTITGIARKLKEKCPGCRIIGVDPEGSIL-AEPEELNQTEQTTYEVEGIGYDF 310 + +VG+GGT+ G+A L+E+ PG RI DP G+ L A ++ + + EGIG Sbjct: 181 ICAVGSGGTLAGVAAALRERKPGVRIGLADPYGAALYAWYKDGELKSEGSSISEGIGQGR 240 Query: 311 IPTVLDRTVVDKWFKSNDEEAFTFARMLIAQEGLLCGGSAGSTVAVAVKAAQELQEGQRC 370 I L+ +D F+ +D+E L+ EGL GGSAG VA A+K A + G Sbjct: 241 ITANLEGLAIDDPFRVSDQEMLEVLYDLVQHEGLCLGGSAGINVAGAIKLATAMGPGHTI 300 Query: 371 VVILPDSVRNYMTKFLSDRWMLQKG 395 V +L D Y +K + ++ +KG Sbjct: 301 VTVLCDHGSRYQSKLFNPVFLKEKG 325 Lambda K H 0.317 0.135 0.402 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: 499 Number of extensions: 26 Number of successful extensions: 5 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: 551 Length of database: 332 Length adjustment: 32 Effective length of query: 519 Effective length of database: 300 Effective search space: 155700 Effective search space used: 155700 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: 51 (24.3 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