Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate CCNA_03094 CCNA_03094 citrate lyase beta subunit
Query= BRENDA::Q037K5 (292 letters) >FitnessBrowser__Caulo:CCNA_03094 Length = 352 Score = 81.6 bits (200), Expect = 2e-20 Identities = 75/288 (26%), Positives = 128/288 (44%), Gaps = 35/288 (12%) Query: 28 DAIMFDLEDAVSLKEKDTARMLVYSALKTFDYSS--VETVVRVNALDAGGDQDIEAMVL- 84 D I+ +LEDA+ K A + + + D+ + V R+N L++ D A ++ Sbjct: 55 DVILANLEDAIPADAKGAALAGLVAMSREVDFKALGVGFWTRINCLNSPWHLDEIATIVE 114 Query: 85 ---GGINVVRLPKTETAQDIIDVDAVITAVEEKYGIQNGTTHMMAAIESAEGVLNAREIA 141 I+V+ +PK E DI +D ++ ++E K+G+ + A +E+AEGV+N IA Sbjct: 115 KAGDKIDVIMVPKVEGPWDIFYMDQLLASLEAKHGVTRPIL-LHAILETAEGVMNVEAIA 173 Query: 142 QASSRMIGIALGAEDYLTSQHTHRS----------------TDGAELSFARNYILH---- 181 AS RM GI+LG D S+ + DG+ + + H Sbjct: 174 AASPRMQGISLGPADLAASRAMKTTRVGGGHPGYRVIEDPHADGSARVSVQQDLWHYTFA 233 Query: 182 ----AAREAGIAAIDTVYTQVDNEEGLRHETALIKQLGFDGKSVINPRQIPVINGVFAPA 237 A GI + +D+ + +G G ++P QI + VF+P Sbjct: 234 KMVDACAAHGIKPFYGPFGAIDDPVACEQQFRNAFLMGCAGAWSLHPSQIEIAKRVFSPD 293 Query: 238 LAEVQKAREIVAGLKEAEAKGAGVVSVNGQMVDKPVVERAQYTIALAK 285 AEV A++I+ EA G GV ++G+M D ++A+ + A+ Sbjct: 294 PAEVAFAKKIL----EAMPDGTGVAMIDGKMQDDATWKQAKVMVDCAR 337 Lambda K H 0.316 0.132 0.355 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: 202 Number of extensions: 10 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 1 Length of query: 292 Length of database: 352 Length adjustment: 28 Effective length of query: 264 Effective length of database: 324 Effective search space: 85536 Effective search space used: 85536 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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