Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate AZOBR_RS26360 AZOBR_RS26360 Citrate lyase
Query= BRENDA::Q9I562 (275 letters) >FitnessBrowser__azobra:AZOBR_RS26360 Length = 305 Score = 116 bits (290), Expect = 7e-31 Identities = 97/288 (33%), Positives = 141/288 (48%), Gaps = 28/288 (9%) Query: 7 RSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTPEARV--- 63 RS LFVPA+RP+R KALA+GAD V VDLEDAV K +ARA RF+ D Sbjct: 7 RSVLFVPASRPDRFDKALAAGADAVCVDLEDAVAPAHKQDARAAAMRFVADGSNGGSGGG 66 Query: 64 ------------LVRINAAEH-PGHADDLALCRDHAGVIGLLLPKVESAAQV---RHAAV 107 ++RIN G D LAL +++PK++S +V Sbjct: 67 GGGGGGGGGPDRVIRINTLRSVAGMRDALALIEARPSGGTVVVPKIDSPEEVCWLDQLLT 126 Query: 108 ASGKPVWPI--VESARGLAALGEIAAAA-GVERLSFGSLDLALDLDLNSGSNAAEQILGH 164 +G + + +E+ RG+ I AA+ V + FG LDLA +L G A+ L + Sbjct: 127 EAGLDLRLVAQIETLRGVDQAAAITAASRRVSAVMFGGLDLAAEL----GVPASWDGLLY 182 Query: 165 ARYALLLQTRLAGLAPPLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQT 224 R ++ AG+ P +D + A+++ G + A +GF + IHP QV I+ Sbjct: 183 GRSRVVHAAARAGI-PAIDMPFVAVRDADGCRAEAQRALALGFTAKMAIHPGQVPTINDA 241 Query: 225 LMPSPAELEWARRVAEAGASGA-GVFVVDGEMVDAPVLGRARRLLERA 271 P+P E+ A R+ A + GV VDG+MV+ P++ RR L RA Sbjct: 242 YTPTPDEVADAERIVTAWKNAPDGVIQVDGKMVERPIVLAMRRTLARA 289 Lambda K H 0.320 0.137 0.394 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: 208 Number of extensions: 13 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: 275 Length of database: 305 Length adjustment: 26 Effective length of query: 249 Effective length of database: 279 Effective search space: 69471 Effective search space used: 69471 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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