Align malyl-CoA lyase (EC 4.1.3.24) (characterized)
to candidate N515DRAFT_3215 N515DRAFT_3215 citrate lyase subunit beta / citryl-CoA lyase
Query= BRENDA::Q3J5L6 (318 letters) >FitnessBrowser__Dyella79:N515DRAFT_3215 Length = 284 Score = 149 bits (376), Expect = 8e-41 Identities = 95/301 (31%), Positives = 145/301 (48%), Gaps = 23/301 (7%) Query: 15 RCQLFGPGSRPALFEKMAASAADVINLDLEDSVAPDDKAQARANIIE--AINGLDWGRKY 72 R +LF PG RP LF K A AD ++ DLEDSV P+ K AR I A K Sbjct: 2 RSKLFVPGGRPELFAKALAGEADALSFDLEDSVTPELKGAARTAIASFLATEAARQSPKL 61 Query: 73 LSVRINGLDTPFWYRDVVDLLEQAGDRLDQIMIPKVGCAADVYAVDALVTAIERAKGRTK 132 + VR N TP++ D+ ++ GD + I +PK+ A +V A ++ +E +G + Sbjct: 62 MIVRTNAPSTPYFADDIEAVV---GDGVTLINLPKIESAEEVRAAVDMIARVEATRGWQR 118 Query: 133 PLSFEVIIESAAGIAHVEEIAASSPRLQAMSLGAADFAASMGMQTTGIGGTQENYYMLHD 192 V IE+ +A IA + PR+ + LG AD G++ + Sbjct: 119 RTRLLVNIETPLALARAASIAGAHPRVAGLQLGLADMFEPYGIERRDLANV--------- 169 Query: 193 GQKHWSDPWHWAQAAIVAACRTHGILPVDGPFGDFSDDEGFRAQARRSATLGMVGKWAIH 252 H A+ A + +DG F D +D EG+R +A + LG +GK IH Sbjct: 170 ---------HSVLFAMRMAAAQADVFALDGAFADVADSEGYREEAALARRLGYLGKSCIH 220 Query: 253 PKQVALANEVFTPSETAVTEAREILAAMDAAKARGEGATVYKGRLVDIASIKQAEVIVRQ 312 P+QVALAN+ F S+ + AR I+ A +G GA + G++VD+ +K+A+ ++ Sbjct: 221 PRQVALANQAFAVSDAEIESARRIVEAAREPGNQGRGAFMVDGKMVDLPFLKRAQALLAA 280 Query: 313 A 313 A Sbjct: 281 A 281 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: 212 Number of extensions: 10 Number of successful extensions: 3 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: 284 Length adjustment: 27 Effective length of query: 291 Effective length of database: 257 Effective search space: 74787 Effective search space used: 74787 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