Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate Ga0059261_3671 Ga0059261_3671 Citrate lyase beta subunit
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Korea:Ga0059261_3671 Length = 278 Score = 129 bits (323), Expect = 1e-34 Identities = 94/301 (31%), Positives = 146/301 (48%), Gaps = 31/301 (10%) Query: 15 RCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIEAINGLDWGRKYLS 74 R LF PG RP EK AS AD + LDLEDSV P +K AR + + + R +S Sbjct: 4 RSMLFVPGDRPDRMEKALASGADALILDLEDSVTPANKGAARLAVAKFLAET---RSEVS 60 Query: 75 --VRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTK 132 VRIN LD+ D+ A D I++PK ADV ++DA++ I R Sbjct: 61 HWVRINPLDSGMTQDDLA-----AAHGADGIVLPKAENGADVASLDAMLGGIA---ARIL 112 Query: 133 PLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHD 192 P++ E+ A + + A SPRL ++ GA D A++G ++ + Sbjct: 113 PIA----TETPAAVFGLGSYAGCSPRLAGITWGAEDLPAAIGAVSS------------RE 156 Query: 193 GQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIH 252 ++ P+ +A + G+ ++ + DF + +G +A R+ G G AIH Sbjct: 157 KDGSYTSPYEIVRALTLFGAHAAGVRAIETVYPDFRNLDGLKAYCARAMRDGFTGMMAIH 216 Query: 253 PKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEVIVRQ 312 P Q+ + N FTPSE AV A+ ++AA A GA G+++D +KQAE ++++ Sbjct: 217 PAQIEIINAAFTPSEEAVAHAQRVVAAFSANPE--AGALQLDGKMIDAPHLKQAEALLKR 274 Query: 313 A 313 A Sbjct: 275 A 275 Lambda K H 0.319 0.132 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: 191 Number of extensions: 8 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: 318 Length of database: 278 Length adjustment: 26 Effective length of query: 292 Effective length of database: 252 Effective search space: 73584 Effective search space used: 73584 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