Align cystathionine β-synthase (EC 4.2.1.22) (characterized)
to candidate AZOBR_RS08705 AZOBR_RS08705 cysteine synthase
Query= metacyc::MONOMER-22007 (524 letters) >FitnessBrowser__azobra:AZOBR_RS08705 Length = 334 Score = 218 bits (556), Expect = 2e-61 Identities = 132/341 (38%), Positives = 190/341 (55%), Gaps = 19/341 (5%) Query: 81 NILPNILNKVGNTPLVRINKIGKYFGLKCELLAKCEYFNAGGSVKDRISLRMVEDAERAG 140 +I + +GNTPL+R+ K G CE+L K E+ N GGSVKDR +L +V DAER G Sbjct: 2 DIRTGFIGSIGNTPLIRLEGPSKATG--CEILGKAEFLNPGGSVKDRAALAIVRDAERRG 59 Query: 141 ILKPGDTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTT 200 +L+PG TI+E T+GNTGIGLAL GYR +IVMPE S EK D+LR +GA++ P Sbjct: 60 LLRPGGTIVEGTAGNTGIGLALVGNALGYRTVIVMPETQSQEKKDMLRLIGADLRLVPAV 119 Query: 201 ARFDSPESHVGVAWRLKNEI----PNAHI-LDQYRNASNPLTHYDTTAEEILQQCEGKID 255 + +P+++V + RL E+ PN + +Q+ N +N H TT EI Q EG+ID Sbjct: 120 P-YSNPDNYVRYSGRLAEELAKTEPNGAVWANQFDNVANREGHRLTTGPEIWTQTEGRID 178 Query: 256 MLVATAGTGGTITGISRKLKEKCPGCKIIGVDPEGSILAQ---PDELNKTDKTMYEVEGI 312 G+GGT+ G+ LKE+ P +I+ DP G+ L L ++ EGI Sbjct: 179 AFTCAVGSGGTLAGVGLALKERNPDVRIVLADPMGASLYHHYAHGTLKAEGSSI--TEGI 236 Query: 313 GYDFVPTVLDRSLVDQWYKSNDEESFALARMLIREEGLLCGGSSGSAMSVAVKAAKELKE 372 G + L+ + VDQ + DEE+ + LI+ +GL+ GGSSG ++ A++ AKE+ Sbjct: 237 GQGRITANLEGAPVDQALQITDEEALPVIFDLIKSQGLVLGGSSGINIAAAIRIAKEMGP 296 Query: 373 GQRCVVIFPDSIRNYMSKFLSDKWMIQKGFMTEEDLVKKPW 413 G V I D + Y SK + F+ E++L W Sbjct: 297 GHTIVTILCDGGQRYQSK------LFNPAFLREKNLPVPDW 331 Lambda K H 0.316 0.134 0.399 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: 408 Number of extensions: 23 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: 524 Length of database: 334 Length adjustment: 32 Effective length of query: 492 Effective length of database: 302 Effective search space: 148584 Effective search space used: 148584 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: 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