Align cystathionine β-synthase (O-acetyl-L-serine) monomer (EC 4.2.1.22; EC 2.5.1.134; EC 2.5.1.47) (characterized)
to candidate 202029 SO2903 cysteine synthase A (NCBI ptt file)
Query= metacyc::HP_RS00545-MONOMER (306 letters) >FitnessBrowser__MR1:202029 Length = 322 Score = 197 bits (502), Expect = 2e-55 Identities = 122/306 (39%), Positives = 177/306 (57%), Gaps = 17/306 (5%) Query: 11 IGRTPVFKFTNKDYPIPLNSAIYAKLEHLNPGGSVKDRLGQYLIGEGFKTGKITSKTTII 70 IG TP+ + + AK+E NP SVK R+G +I + K G +T +I Sbjct: 12 IGNTPLVRLNRVS-----QGKVLAKVESRNPSFSVKCRIGANMIWDAEKKGLLTKDHELI 66 Query: 71 EPTAGNTGIALALVAIKHHLKTIFVVPEKFSTEKQQIMRALGALVINTPTSEGISGAIKK 130 EPT+GNTGIALA VA K +P S E++++++ALGA ++ T ++G+ GAI K Sbjct: 67 EPTSGNTGIALAYVAAARGYKLTLTMPNTMSLERRKLLKALGANLVLTEGAKGMKGAIDK 126 Query: 131 SKELAESIPDSYLPL-QFENPDNPAAYYHTLAPEIVQELGTNLTSFVAGIGSGGTFAGTA 189 ++E+ +S P+ Y+ L QF NP NP + T PEI + + FVAG+G+GGT G + Sbjct: 127 AEEIRQSAPEKYILLQQFNNPANPEIHEKTTGPEIWNDTDGAVDVFVAGVGTGGTITGVS 186 Query: 190 RYLKERI-PAIRLIGVEPEGS-----ILNG--GEPGPHEIEGIGVEFIPPFFENLDIDGF 241 RYLK+ AI + VEP S L G +PGPH+I+GIG FIP + ID Sbjct: 187 RYLKKVAGKAITSVAVEPADSPVITQTLAGLPVQPGPHKIQGIGAGFIPGNLDIELIDRV 246 Query: 242 ETISDEEGFSYTRKLAKKNGLLVGSSSGAAFVAALKEAQRLPE--GSQVLTIFPDVADRY 299 ET++++E R+L ++ G+LVG SSGAA VAA + A LPE ++ + P A+RY Sbjct: 247 ETVTNDEAIEMARRLMQEEGILVGISSGAAVVAANRIA-ALPEFADKTIVVVLPSAAERY 305 Query: 300 LSKGIY 305 LS ++ Sbjct: 306 LSSVLF 311 Lambda K H 0.316 0.137 0.389 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: 254 Number of extensions: 10 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: 306 Length of database: 322 Length adjustment: 27 Effective length of query: 279 Effective length of database: 295 Effective search space: 82305 Effective search space used: 82305 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: 48 (23.1 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