Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate GFF2915 PS417_14915 host specificity protein
Query= BRENDA::Q9I562 (275 letters) >FitnessBrowser__WCS417:GFF2915 Length = 271 Score = 310 bits (795), Expect = 2e-89 Identities = 167/268 (62%), Positives = 198/268 (73%), Gaps = 1/268 (0%) Query: 1 MNRQIVRSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTPE 60 M + +VRSALFVP +RPER KALASGAD VIVD EDAVEE LK +AR NL FL P Sbjct: 1 MPKLLVRSALFVPGSRPERFSKALASGADAVIVDFEDAVEEPLKRQARDNLGAFLTANPA 60 Query: 61 ARVLVRINAAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVRHAAVASGKPVWPIVESA 120 A+V VRINA EH H +D+A C+ H V G+LLPKVESA+QV A A+GK +WPI+ESA Sbjct: 61 AQVWVRINAPEHAEHFEDVAFCKAHPTVAGVLLPKVESASQVAVVA-ATGKVIWPIIESA 119 Query: 121 RGLAALGEIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTRLAGLAP 180 RGL A+ EIA A VERLSFG LDLALDL+L+S S AA+ L AR AL++ +R AGL Sbjct: 120 RGLLAVAEIAHAPQVERLSFGGLDLALDLNLSSNSPAAQFALDQARLALIVHSRAAGLVA 179 Query: 181 PLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEWARRVAE 240 PLDGV+PAI + GL ++R A +MGF G LCIHP QV IHQ L PS +L WARRV + Sbjct: 180 PLDGVHPAIDDPEGLRRSIRHAYEMGFAGALCIHPKQVAVIHQALAPSAEDLAWARRVVD 239 Query: 241 AGASGAGVFVVDGEMVDAPVLGRARRLL 268 AGA GAG + +DG+MVDAPVL RA+RLL Sbjct: 240 AGAHGAGAYQIDGQMVDAPVLLRAQRLL 267 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: 261 Number of extensions: 13 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: 271 Length adjustment: 25 Effective length of query: 250 Effective length of database: 246 Effective search space: 61500 Effective search space used: 61500 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