Align citrate lyase β subunit (EC 4.1.3.34) (characterized)
to candidate BPHYT_RS32670 BPHYT_RS32670 aldolase
Query= metacyc::MONOMER-16999 (289 letters) >FitnessBrowser__BFirm:BPHYT_RS32670 Length = 270 Score = 132 bits (331), Expect = 1e-35 Identities = 94/279 (33%), Positives = 147/279 (52%), Gaps = 19/279 (6%) Query: 5 RSMLFIPGANAAMLSTSFVYGADAVMFDLEDAVSLREKDTARLLVYQALQHPLYQDIETV 64 RS LF+PG + GADAV+ DLEDAV EK AR V A+ + Sbjct: 7 RSYLFVPGNRPERFEKAHAAGADAVILDLEDAVQPAEKPAARAAVLAAVSSEASRP--AW 64 Query: 65 VRINPLNTPFGLADLEAVV-RAGVDMVRLPKTDSKEDIHELEAHVERIERECGREVGSTK 123 VRIN +TP+ D+ A+ + GV + LPK +++E I + A + Sbjct: 65 VRINGSDTPWFNEDVAALSGQPGVAGIVLPKAETREQIEAVLATAH----------AALS 114 Query: 124 LMAAIESALGVVNAVEIARASPRLAAIALAAFDYVMDMGTSRGDGTELFYARCAVLHAAR 183 ++ IE+A G + + A+PR+ I D+ +D+G GDG EL+ R ++ A+R Sbjct: 115 ILPIIETARGFASLAVLC-AAPRVQRIVFGTLDFQIDLGID-GDGEELYLFRSQIVLASR 172 Query: 184 VAGIAA-YDVVWSDINNEEGFLAEANLAKNLGFNGKSLVNPRQIELLHQVYAPTRKEVDH 242 +AGI A D V + I + + A+A L + GF GK ++P+QI+ +H+ YA + + Sbjct: 173 LAGIGAPVDGVSTTITDTDAIEADARLGRRFGFGGKLCIHPKQIDAVHRAYAWSDADKAW 232 Query: 243 ALEVIAAAEEAETRGLGVVSLNGKMIDGPIIDHARKVVA 281 A V+AA ET V+++GKM+D P+I AR+++A Sbjct: 233 AQRVLAA---VETSHGAAVAVDGKMVDMPVILKARRILA 268 Lambda K H 0.319 0.134 0.375 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: 11 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: 289 Length of database: 270 Length adjustment: 26 Effective length of query: 263 Effective length of database: 244 Effective search space: 64172 Effective search space used: 64172 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