Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate CCNA_02321 CCNA_02321 O-succinylhomoserine sulfhydrylase
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__Caulo:CCNA_02321 Length = 394 Score = 270 bits (690), Expect = 5e-77 Identities = 153/384 (39%), Positives = 237/384 (61%), Gaps = 14/384 (3%) Query: 5 TLMIHGGITGDE-KTGAVSVPIYQVSTYKQPK------AGQHTGYEYSRTANPTRTALEA 57 T +I GGI + A ++ + Q TY + AG+ G+ YSR NPT E Sbjct: 12 TKLIRGGIARSQFMETAEALYLTQGFTYDSAEGADRRFAGEDPGFVYSRFNNPTVKMFED 71 Query: 58 LVTELESGEAGYAFSSGMAAITAVMM-LFNSGDHVVLTDDVYGGTYRVMTKVLNRLGIES 116 + LE E A ++GMA+I A +M L +GDHVV ++G ++++ L R G+E+ Sbjct: 72 RLALLEGAEVCRAQATGMASIHAALMGLVRAGDHVVAGRALFGSCRWIVSEWLPRFGVET 131 Query: 117 TFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDNTFNTP 176 TFVD + + E A+RPNTKA+ +ETP+NP+L+ITD+ ++++A G +IVDN F TP Sbjct: 132 TFVDATDPKAWEAAMRPNTKAVLVETPSNPVLEITDIRAVSELAHAVGAKVIVDNVFATP 191 Query: 177 YFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKELGEELHFVQNS---TGGVLGPQ 233 FQ+PL LGAD+V++SATK++ G V+GG ++T S+ + EE F ++S TG L P Sbjct: 192 IFQKPLELGADVVVYSATKHIDGQGRVLGGAILT-SEAINEE--FYRDSLRHTGPSLSPF 248 Query: 234 DSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHELAKTQGAGF 293 ++W++++G++TL LR+ +A +A+ + H VQT+ YP +HPGH +AK Q G Sbjct: 249 NAWVMLKGLETLDLRVRRQADSAFALANTIAEHKKVQTVLYPFRPDHPGHNVAKAQMTGG 308 Query: 294 GGMISFDIGSEERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRERRLELGITD 353 G +I+ D+GS E FL L++ I+ +LG +S+ + P TH S+P R LG+T+ Sbjct: 309 GTVIALDLGSREAAFKFLNALEIVDISNNLGDAKSMATHPPTTTHRSVPEAERPSLGVTE 368 Query: 354 GLIRISVGIEDAEDLLEDIGQALE 377 G +R+SVG+E EDL D+ +AL+ Sbjct: 369 GGVRLSVGLESVEDLKRDVIRALD 392 Lambda K H 0.316 0.134 0.375 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: 369 Number of extensions: 12 Number of successful extensions: 3 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: 379 Length of database: 394 Length adjustment: 30 Effective length of query: 349 Effective length of database: 364 Effective search space: 127036 Effective search space used: 127036 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