Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate CCNA_03774 CCNA_03774 citrate lyase beta chain/citryl-CoA lyase subunit
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__Caulo:CCNA_03774 Length = 295 Score = 124 bits (311), Expect = 3e-33 Identities = 91/305 (29%), Positives = 144/305 (47%), Gaps = 23/305 (7%) Query: 2 ASRNTLRRALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPA 61 A N RR+ LY+P S+ + ++K+RTL AD + DLED+V P K AR A+ + Sbjct: 4 AQANRPRRSALYMPASNAKAVEKARTLDADVIILDLEDAVAPEMKPAAREAAVAAV-KAG 62 Query: 62 PAGILERAVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHTLSQL 121 G E +R+N +D+ DL ++ +++PKVN A+D+ + Sbjct: 63 GFGPREVVIRVNGLDTPWGADDLAAAAEA-GPDAVLVPKVNDAADVRLYDQHL------- 114 Query: 122 PLSQSASRPPISLLALVESAKSLTNLSQICAA--SPLLQGLIFAAEDFALDLSLTRTPAL 179 SA+ L ++E+AK+ +L +I A S L + DFA ++ +TP Sbjct: 115 ----SAAPTSTRLWTMIETAKAAFHLWEIAEAAHSTRLSAWVMGVNDFAKEMRARQTPDR 170 Query: 180 TEFLFARSAIATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQC 239 FL + AARA L ++ +D D + L+ C G + GF+GK Sbjct: 171 APFLPLLTLSVAAARAHGL-----MILDGVHNDIEDLA---ALEAVCVQGVDFGFDGKTL 222 Query: 240 IHPSQVSTVQQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIV 299 IHP + ++F P E+V W+ V A + AG+GA +DGKM + +A +V Sbjct: 223 IHPKHLEICNRVFSPSPEDVAWSHAVIAAFNAPENAGKGALRVDGKMAERLHLAQAERLV 282 Query: 300 KKADA 304 A A Sbjct: 283 AVAQA 287 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: 178 Number of extensions: 10 Number of successful extensions: 4 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: 295 Length adjustment: 27 Effective length of query: 295 Effective length of database: 268 Effective search space: 79060 Effective search space used: 79060 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