Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate 351451 BT1923 O-acetylhomoserine (thiol)-lyase (NCBI ptt file)
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__Btheta:351451 Length = 426 Score = 224 bits (570), Expect = 5e-63 Identities = 149/420 (35%), Positives = 222/420 (52%), Gaps = 46/420 (10%) Query: 2 KKKTLMIHGGITGDEKTGAVSVPIYQVSTYKQPKAGQ--------HTGYEYSRTANPTRT 53 K +TL + G T + V +PIYQ +T+K + Q +GY Y+R NPT Sbjct: 6 KPETLCVQAGWTPKKGEPRV-LPIYQSTTFKYDTSEQMARLFDLEDSGYFYTRLQNPTND 64 Query: 54 ALEALVTELESGEAGYAFSSGMAA-ITAVMMLFNSGDHVVLTDDVYGGTYRVMTKVLNRL 112 A+ A + LE G A SSG AA A+ + +GDH V + +YGGT+ + + +L Sbjct: 65 AVAAKIAALEGGVAAMLTSSGQAANFYAIFNICQAGDHFVCSSAIYGGTFNLFGVTMKKL 124 Query: 113 GIESTFVDT-SSREEVEKAIRPNTKAIYIETPTNPLLKITDLTLMADIAKKAGVLLIVDN 171 GI+ TFV+ +S EE+ A +PNTKA++ ET +NP L++ D+ A IA GV LIVDN Sbjct: 125 GIDVTFVNPDASEEEISAAFQPNTKALFGETISNPSLEVLDIEKFARIAHSHGVPLIVDN 184 Query: 172 TFNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVV---------------------- 209 TF TP +P GADI++HS TKY+ GH+ VGG +V Sbjct: 185 TFPTPINCRPFEWGADIIVHSTTKYMDGHATSVGGCIVDSGNFDWDAHADKFPGLCTPDE 244 Query: 210 -----TASKELGEELHFVQNST------GGVLGPQDSWLLMRGIKTLGLRMEAIDQNARK 258 T +K G+ + + + G + PQ+S+LL G++TL LRM +NA+K Sbjct: 245 SYHGLTYTKAFGKGAYITKATAQLMRDLGSIQSPQNSFLLNLGLETLHLRMPQHCRNAQK 304 Query: 259 IASFLENHPAVQTLYYPGSSNHPGHELA-KTQGAGFGGMISFDI-GSEERVDAFLGNLKL 316 +A +L + V + Y G ++ + LA K G G+ISF + G + F+ +L+ Sbjct: 305 VAEYLSKNEKVAWVNYCGLPDNKYYALAQKYMPNGSCGVISFGLKGGRDVSIKFMDSLEF 364 Query: 317 FTIAESLGAVESLISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQAL 376 I + S + PA TH + E+ +E G+ LIR+SVGIE+A+D++ DI QAL Sbjct: 365 IAIVTHVADARSCVLHPASHTHRQLSDEQLMEAGVRPDLIRLSVGIENADDIIADIEQAL 424 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: 390 Number of extensions: 23 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 379 Length of database: 426 Length adjustment: 31 Effective length of query: 348 Effective length of database: 395 Effective search space: 137460 Effective search space used: 137460 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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