Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate GFF2614 Psest_2665 Citrate lyase beta subunit
Query= BRENDA::Q9I562 (275 letters) >FitnessBrowser__psRCH2:GFF2614 Length = 275 Score = 374 bits (961), Expect = e-109 Identities = 198/273 (72%), Positives = 221/273 (80%), Gaps = 1/273 (0%) Query: 1 MNRQIVRSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTPE 60 MN I+RSALFVPATRPERIPKALASGAD VIVDLEDAV E LK EAR NL FL P+ Sbjct: 1 MNSSIIRSALFVPATRPERIPKALASGADAVIVDLEDAVAENLKAEARGNLDAFLAANPD 60 Query: 61 ARVLVRINAAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAAVASGKPVWPIVESA 120 AR+LVRINA H A DLALC HAGV+G+LLPKVESA QV AA + GKPVWPIVESA Sbjct: 61 ARLLVRINAPTHAEQAADLALCARHAGVVGVLLPKVESAVQVALAA-SCGKPVWPIVESA 119 Query: 121 RGLAALGEIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTRLAGLAP 180 RGLA L EIA A GVERLSFG+LDL LDL L +G+ AE++L ARYALLLQ+RLAGLA Sbjct: 120 RGLANLAEIAHAQGVERLSFGALDLGLDLGLANGTAGAERMLDQARYALLLQSRLAGLAA 179 Query: 181 PLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWARRVAE 240 PLD V+P I+N GL A ARDMGFGGLLCIHPSQV +H+TLMPS AEL+WA+R+ Sbjct: 180 PLDSVFPDIKNLDGLTRAAADARDMGFGGLLCIHPSQVAVVHETLMPSAAELDWAQRILA 239 Query: 241 AGASGAGVFVVDGEMVDAPVLGRARRLLERAGE 273 AGASG GVFVVDG+MVDAPV+GRARRLL+RAG+ Sbjct: 240 AGASGDGVFVVDGQMVDAPVIGRARRLLQRAGQ 272 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: 270 Number of extensions: 10 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: 275 Length of database: 275 Length adjustment: 25 Effective length of query: 250 Effective length of database: 250 Effective search space: 62500 Effective search space used: 62500 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: 47 (22.7 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