Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate SMc03793 SMc03793 citrate lyase subunit beta
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__Smeli:SMc03793 Length = 300 Score = 119 bits (297), Expect = 1e-31 Identities = 89/301 (29%), Positives = 141/301 (46%), Gaps = 24/301 (7%) Query: 7 LRRALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGIL 66 LRR++L +P +QR + K+ L AD V +DLEDSV+P +KA AR + R L P G Sbjct: 11 LRRSVLSVPADNQRALAKACELAADAVIFDLEDSVSPDRKAAARDALVRHLAGNRPQG-- 68 Query: 67 ERAVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHTLSQLPLSQS 126 E +R+N+ SG ADL L + I++PKV S +D+ D LS+ Sbjct: 69 ETVIRVNAAGSGFGEADLAAALAA-RPDAILLPKVESPADIQGALDW---------LSER 118 Query: 127 ASRPPISLLALVESAKSLTNLSQICAASPLLQG----LIFAAEDFALDLSLTRTPALTEF 182 + + L A++E+ + + N I G + D + + T Sbjct: 119 DAPDELRLWAMIETPRGVVNGPAIAETGRTSGGRLDCFVVGLNDLRKETGVPALSGRTYL 178 Query: 183 LFARSAIATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHP 242 + I AAR + L + ID V ++ +G + ECR G+++GF+GK IHP Sbjct: 179 VPWLMQILLAARGSGLDA-IDAVFNDFRDPEG-------FEAECRQGRDMGFDGKMLIHP 230 Query: 243 SQVSTVQQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIVKKA 302 +Q+ + F + V+ A + A +G+G L G+M++ E+A I KA Sbjct: 231 AQIDAANRHFAADEAAVEEARAIIEAFALPDNSGKGVINLHGRMVERLHLEQAMKIAAKA 290 Query: 303 D 303 D Sbjct: 291 D 291 Lambda K H 0.316 0.130 0.369 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: 217 Number of extensions: 9 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: 322 Length of database: 300 Length adjustment: 27 Effective length of query: 295 Effective length of database: 273 Effective search space: 80535 Effective search space used: 80535 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 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