Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate Pf6N2E2_1831 Citrate lyase beta chain (EC 4.1.3.6)
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1831 Length = 299 Score = 131 bits (329), Expect = 2e-35 Identities = 94/296 (31%), Positives = 144/296 (48%), Gaps = 21/296 (7%) Query: 9 RALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGILER 68 R+LL++P +F +K+ AD DLEDSV P +K +AR A + G L+ Sbjct: 9 RSLLFVPAHIGKFTEKAHERNADACILDLEDSVAPGQKTQARDAASSAAQNISNRG-LDV 67 Query: 69 AVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHT---LSQLPLSQ 125 VRIN++DSG L DL ++ SP + +V+PKV SA +V+ H L +L + Sbjct: 68 LVRINTLDSG-GLLDLQAIV-SPAVCAVVLPKVASA-------EVVRHVALQLDRLETER 118 Query: 126 SASRPPISLLALVESAKSLTNLSQICAASPLLQGLIFAAEDFALDLSLTRTPALTEFLFA 185 +LA +E +L L +I ASP L G+ EDF++ + P L+ Sbjct: 119 GMDAGQTLILAQIEDVAALPLLDEIATASPRLMGMSLGPEDFSVSAGMEPVPET--LLWP 176 Query: 186 RSAIATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHPSQV 245 +A A R A + + + D S +Q G+ LG G CIHP QV Sbjct: 177 NQQVAFACRRAGI------LPFGFPGSIADFSDIPRFRQALVLGRQLGMIGAFCIHPEQV 230 Query: 246 STVQQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIVKK 301 + + ++F P EV+++V + A GRGA+ GKMID P+ +AR ++ + Sbjct: 231 AVLNEVFSPGDAEVEYSVALLAEYACAEAEGRGAFAFRGKMIDAPIVARARELLTR 286 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: 183 Number of extensions: 7 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: 299 Length adjustment: 27 Effective length of query: 295 Effective length of database: 272 Effective search space: 80240 Effective search space used: 80240 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