Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate WP_011386303.1 AMB_RS19980 CoA ester lyase
Query= BRENDA::Q037K5 (292 letters) >NCBI__GCF_000009985.1:WP_011386303.1 Length = 292 Score = 172 bits (437), Expect = 6e-48 Identities = 104/284 (36%), Positives = 160/284 (56%), Gaps = 12/284 (4%) Query: 5 RRTMMFVPGANPGMLRDAPIYGADAIMFDLEDAVSLKEKDTARMLVYSALKTFDYSSVET 64 RR+++++PG+NP L A AD ++ DLEDAV+ KD AR V A+K Y + E Sbjct: 8 RRSVLYMPGSNPRTLEKARTLPADGLILDLEDAVAPDAKDVARSQVVDAVKAGGYGAREL 67 Query: 65 VVRVNALDAG-GDQDIEAMVLGGINVVRLPKTETAQDIIDVDAVITAVEEKYGIQNGTTH 123 ++RVN+L G D+ A G + V +PK E+A + V+A++ A NG Sbjct: 68 LIRVNSLATPWGQADVAAAASSGTHAVLIPKVESADTVRQVEAIMVA--------NGAPA 119 Query: 124 MMAA---IESAEGVLNAREIAQASSRMIGIALGAEDYLTSQHTHRSTDGAELSFARNYIL 180 MA +E+ G+L A EIA +S RM G +G D H + D + + L Sbjct: 120 DMAIWCMMETPRGMLKAEEIAGSSPRMGGFVMGTSDLAKDLHCAHTRDRLPMITSLGLCL 179 Query: 181 HAAREAGIAAIDTVYTQVDNEEGLRHETALIKQLGFDGKSVINPRQIPVINGVFAPALAE 240 AAR G+AA+D VY ++++EG + +LGFDGK++I+P+ I N VFAPA E Sbjct: 180 LAARAYGLAALDGVYLDLNDDEGFAYSCQQGLELGFDGKTLIHPKTIETANRVFAPAEKE 239 Query: 241 VQKAREIVAGLKEAEAKGAGVVSVNGQMVDKPVVERAQYTIALA 284 ++ +++I+A EA A G GVV V+G++++ VE A+ +AL+ Sbjct: 240 IEWSKKIIAAHAEASAAGKGVVVVDGKLIENLHVENARRIVALS 283 Lambda K H 0.316 0.132 0.355 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: 195 Number of extensions: 8 Number of successful extensions: 2 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: 292 Length of database: 292 Length adjustment: 26 Effective length of query: 266 Effective length of database: 266 Effective search space: 70756 Effective search space used: 70756 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: 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