Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate WP_011383705.1 AMB_RS06585 cystathionine beta-lyase
Query= BRENDA::O05394 (379 letters) >NCBI__GCF_000009985.1:WP_011383705.1 Length = 390 Score = 205 bits (522), Expect = 2e-57 Identities = 135/391 (34%), Positives = 208/391 (53%), Gaps = 18/391 (4%) Query: 1 MKKKTLMIHGGITGDEKTGAVSVPIYQVSTYKQP------KAGQ--HTGYEYSRTANPTR 52 MKK T ++H G + GAV+ P+Y ST P K+G+ G Y R PT Sbjct: 1 MKKSTRILHAGRKPEAFHGAVNPPVYHASTILHPSVAAMEKSGKTPFEGVRYGRFGTPTT 60 Query: 53 TALEALVTELESGEAGYAFSSGMAAITAVMMLF-NSGDHVVLTDDVYGGTYRVMTKVLNR 111 ALE V ELE G A SSG+AAIT ++ F +GDH+++ D Y T + VL Sbjct: 61 FALEEAVAELEGGHRTVATSSGLAAITGALLAFLKAGDHLLMVDTTYFPTRKFCDSVLGG 120 Query: 112 LGIESTFVDTSSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDN 171 LGIE+T+ D + +RPNT+ ++ E+P + ++ D+ +A+ A G ++++DN Sbjct: 121 LGIETTYYDPLVGAGITALMRPNTRVVFTESPGSLTFEVQDIPAIAEAAHAGGAVVMMDN 180 Query: 172 TFNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTASKELGEELHFVQNSTGGVLG 231 T+ +FQ P T G DI + +ATKY+ GH+D + G + A+ EL ++ + G G Sbjct: 181 TWGVLHFQ-PFTKGIDISIQAATKYIVGHADAMLGTITAATPELWLQVKTSLAAFGASPG 239 Query: 232 PQDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTLYYPGSSNHPGHELAK---T 288 ++ +L +RG++TL +R+ ++A ++ +LE P V + YP ++ PGHEL K T Sbjct: 240 TEEMYLGLRGLRTLPVRLRQHAESALRLTRWLEARPEVDRVLYPPLASDPGHELWKRDFT 299 Query: 289 QGAGFGGMISFDIGSEERVDAFLGNLKLFTIAESLGAVESLISVPARMTHASIPRERRLE 348 G G G+I S+ VDA L F + S G ESL+ +P + SI R Sbjct: 300 GGCGLFGVI-LKPASKAAVDAMLDGYSHFKLGFSWGGFESLV-IPT--SGHSIIRTATPW 355 Query: 349 LGITDGLIRISVGIEDAEDLLEDIGQALENI 379 + L R G+EDA+DL ED+ + E + Sbjct: 356 TPVGPSL-RFHAGLEDADDLEEDLERGFERL 385 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: 430 Number of extensions: 21 Number of successful extensions: 6 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: 390 Length adjustment: 30 Effective length of query: 349 Effective length of database: 360 Effective search space: 125640 Effective search space used: 125640 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