Align (S)-citramalyl-CoA lyase (EC 4.1.3.25); (R)-citramalyl-CoA lyase (EC 4.1.3.46) (characterized)
to candidate AZOBR_RS17450 AZOBR_RS17450 putative SIMILAR TO BETA SUBuniT OF CITRATE LYASE protein
Query= BRENDA::A0A172MLA1 (322 letters) >FitnessBrowser__azobra:AZOBR_RS17450 Length = 287 Score = 139 bits (351), Expect = 6e-38 Identities = 103/293 (35%), Positives = 155/293 (52%), Gaps = 16/293 (5%) Query: 9 RALLYIPGSSQRFIDKSRTLTADCVAYDLEDSVTPHKKAEARSLVRRALDQPAPAGILER 68 ++ L++P + + ++K+ AD + DLED+V P K EAR + +D+ G+ Sbjct: 6 QSYLFVPADNAKLLEKAHQRGADALILDLEDAVLPAGKPEARRGLPEPIDRLHGLGV-PV 64 Query: 69 AVRINSVDSGLALADLTEVLQSPNLSTIVIPKVNSASDLTFVTDVITHTLSQLPLSQSAS 128 VRINS A+ADL E P ++ +V+PK A L ++ +I ++ L+ A Sbjct: 65 LVRINSGWRD-AVADL-EAAVRPGVAALVVPKAEDAGALRVLSAMIAEWEAERGLTPGA- 121 Query: 129 RPPISLLALVESAKSLTNLSQICAASPLLQGLIFAAEDFALDLSLTRTPALTEFLFARSA 188 I L+AL+ES L LS I AA P + L +EDFAL L + T AL + A Sbjct: 122 ---IGLVALIESPLGLERLSGI-AAVPRVAALALGSEDFALTLGVEPTEALLALPCRQIA 177 Query: 189 IATAARAANLPSTIDLVCTTYKSDKGDGSPPVVLQQECRDGKNLGFNGKQCIHPSQVSTV 248 +A AAR + I L + + D +V Q + +G G CIHP+Q+ V Sbjct: 178 LAAAARGL---AAIGLPGSLAEFRDLDAYRAMVAQ-----ARAVGMTGALCIHPAQLPVV 229 Query: 249 QQIFGPELEEVQWAVRVTIADDKASKAGRGAWTLDGKMIDIPVAEKARAIVKK 301 + +F P +V WA RV A D+A AGRGA +DG+M+D PVAE+A+AI+ + Sbjct: 230 RDVFSPSAADVAWAGRVVAAWDEAQAAGRGAVQVDGRMVDRPVAERAKAILAR 282 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: 195 Number of extensions: 8 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: 287 Length adjustment: 27 Effective length of query: 295 Effective length of database: 260 Effective search space: 76700 Effective search space used: 76700 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