Align cystathionine beta-synthase (O-acetyl-L-serine) (EC 2.5.1.134) (characterized)
to candidate SMc01666 SMc01666 methionine gamma-lyase
Query= BRENDA::O05394 (379 letters) >FitnessBrowser__Smeli:SMc01666 Length = 427 Score = 236 bits (602), Expect = 9e-67 Identities = 147/410 (35%), Positives = 217/410 (52%), Gaps = 35/410 (8%) Query: 4 KTLMIHGGITGDEKTGAVSVPIYQVSTY------------------KQPKAGQHTGYEYS 45 +TLM++ G + GAV PI+ ST+ ++P AG G YS Sbjct: 19 ETLMLNYGYDPELSEGAVKPPIFLTSTFVFHSAEEGRDFFDFVSGRREPPAGVGAGLVYS 78 Query: 46 RTANPTRTALEALVTELESGEAGYAFSSGMAAITAVMMLF-NSGDHVVLTDDVYGGTYRV 104 R +P +E + E EAG FSSGM+AI ++ F GD ++ + +YGGT + Sbjct: 79 RFNHPNSEIVEDRLAIFERAEAGALFSSGMSAIATTLLAFVRPGDSILHSQPLYGGTETL 138 Query: 105 MTKVLNRLGIEST-FVDTSSREEVEKAI-----RPNTKAIYIETPTNPLLKITDLTLMAD 158 + K LG+ + F D + V A + I IETP NP + D+ L+ Sbjct: 139 LAKTFLNLGVSAVGFADGTDEAAVNAAAEEAMSKGRVSVILIETPANPTNSLVDVALVRR 198 Query: 159 IAKKAGV------LLIVDNTFNTPYFQQPLTLGADIVLHSATKYLGGHSDVVGGLVVTAS 212 IA++ G ++ DNT P FQ P+ GAD+ L+S TKY+GGHSD++ G V+ S Sbjct: 199 IAERIGERQAHRPIVACDNTLLGPVFQHPIEHGADLSLYSLTKYVGGHSDLIAGAVL-GS 257 Query: 213 KELGEELHFVQNSTGGVLGPQDSWLLMRGIKTLGLRMEAIDQNARKIASFLENHPAVQTL 272 K L ++ ++ S G L P W++ R ++TL +RME + NAR +A FL +HP V+ + Sbjct: 258 KALIRQVKALRGSIGTQLDPHSCWMIGRSLETLSVRMEKANDNARIVAEFLRDHPKVERI 317 Query: 273 YYPG--SSNHPGHELAKTQGAGFGGMISFDI-GSEERVDAFLGNLKLFTIAESLGAVESL 329 +Y ++ P + TQ G G SFDI G +E FL L++F +A SLG ESL Sbjct: 318 HYLPFHDADTPVGRVFATQCTGAGSTFSFDIAGGQEAAFRFLNALQIFKLAVSLGGTESL 377 Query: 330 ISVPARMTHASIPRERRLELGITDGLIRISVGIEDAEDLLEDIGQALENI 379 S PA MTH+ +P E R +G+ + IR+S+GIE +DL+ D+ AL I Sbjct: 378 ASHPAAMTHSGVPIEVRARIGVLESTIRLSIGIEHPDDLVADVANALTMI 427 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: 424 Number of extensions: 22 Number of successful extensions: 7 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: 427 Length adjustment: 31 Effective length of query: 348 Effective length of database: 396 Effective search space: 137808 Effective search space used: 137808 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