Align (S)-citramalyl-CoA lyase (EC 4.1.3.25) (characterized)
to candidate BPHYT_RS32670 BPHYT_RS32670 aldolase
Query= BRENDA::Q9I562 (275 letters) >FitnessBrowser__BFirm:BPHYT_RS32670 Length = 270 Score = 184 bits (466), Expect = 2e-51 Identities = 113/278 (40%), Positives = 159/278 (57%), Gaps = 15/278 (5%) Query: 1 MNRQIVRSALFVPATRPERIPKALASGADRVIVDLEDAVEEGLKVEARANLRRFLVDTPE 60 M+ + RS LFVP RPER KA A+GAD VI+DLEDAV+ K ARA + + Sbjct: 1 MSAALPRSYLFVPGNRPERFEKAHAAGADAVILDLEDAVQPAEKPAARAAVLAAVSSEAS 60 Query: 61 ARVLVRINAAEHPGHADDLALCRDHAGVIGLLLPKVESAAQVR------HAAVASGKPVW 114 VRIN ++ P +D+A GV G++LPK E+ Q+ HAA++ + Sbjct: 61 RPAWVRINGSDTPWFNEDVAALSGQPGVAGIVLPKAETREQIEAVLATAHAALS----IL 116 Query: 115 PIVESARGLAALGEIAAAAGVERLSFGSLDLALDLDLNSGSNAAEQILGHARYALLLQTR 174 PI+E+ARG A+L + AA V+R+ FG+LD +DL G + + L R ++L +R Sbjct: 117 PIIETARGFASLAVLCAAPRVQRIVFGTLDFQIDL----GIDGDGEELYLFRSQIVLASR 172 Query: 175 LAGLAPPLDGVYPAIQNRAGLVEAVRFARDMGFGGLLCIHPSQVEPIHQTLMPSPAELEW 234 LAG+ P+DGV I + + R R GFGG LCIHP Q++ +H+ S A+ W Sbjct: 173 LAGIGAPVDGVSTTITDTDAIEADARLGRRFGFGGKLCIHPKQIDAVHRAYAWSDADKAW 232 Query: 235 ARRVAEAGASGAGVFV-VDGEMVDAPVLGRARRLLERA 271 A+RV A + G V VDG+MVD PV+ +ARR+L A Sbjct: 233 AQRVLAAVETSHGAAVAVDGKMVDMPVILKARRILAGA 270 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: 190 Number of extensions: 6 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: 275 Length of database: 270 Length adjustment: 25 Effective length of query: 250 Effective length of database: 245 Effective search space: 61250 Effective search space used: 61250 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