Align citrate (pro-3S)-lyase (EC 4.1.3.6) (characterized)
to candidate Ga0059261_0896 Ga0059261_0896 Citrate lyase beta subunit
Query= BRENDA::Q8N0X4 (340 letters) >FitnessBrowser__Korea:Ga0059261_0896 Length = 272 Score = 113 bits (282), Expect = 6e-30 Identities = 90/287 (31%), Positives = 146/287 (50%), Gaps = 27/287 (9%) Query: 42 YIPRRAVLYVPGNDEKKIKKIPSLNVDCAVLDCEDGVAANKKNEARLRIVKTLEDIDLGP 101 YI R L++P ++ + I+K +L D +LD ED V A K+ AR ++ E G Sbjct: 6 YIAPRTALFLPASNPRAIEKARTLAADMIILDLEDAVKAGDKDAAR-EAAQSAEGF--GD 62 Query: 102 TEKCVRVNSVSSGLAEEDLETLLQSRVLPSSLMLPKVESPEEIQWFADKFSFHLKGRKLE 161 +RVN+ S EDLE + +S + +++PKVE E I + +FH E Sbjct: 63 RLFGIRVNAEDSAHWIEDLEAVRKSAA--THVIVPKVEKAETIV----RAAFHS-----E 111 Query: 162 QPMNLIPFVETAMGLLNFKAVCEETLKVGPQVGLFLDAVVFGGEDFRASIGATSSKETLD 221 +P+ + +ETA G+++ A+ T G+ + ++ G D AS+ + Sbjct: 112 RPV--LAMIETAAGVMHAGAIAGATGS-----GVEMAGLIAGTNDLAASLRLPPAAGRTQ 164 Query: 222 ILYARQKIVVIAKAFGLQAIDLVYIDFRDGAGLLRQSREGAAMGFTGKQVIHPNQIAVVQ 281 + + Q IV+ A+A + +D V+ DG GL ++ EG +GF GK +IHPNQI +V+ Sbjct: 165 MQLSLQLIVLAARAAEIWVLDGVFNRLDDGDGLAAEAAEGRLLGFDGKSLIHPNQIDIVR 224 Query: 282 EQFSPSPEKIKWAEELIAAFKEHQQLGKGAFTFQGSMIDMPLLKQAQ 328 F PSP ++ A LIAA G GA ++ MI+ ++QA+ Sbjct: 225 AAFDPSPAELDDARALIAA------AGGGAERYKDRMIEDMHVEQAK 265 Lambda K H 0.319 0.135 0.378 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: 146 Number of extensions: 5 Number of successful extensions: 2 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: 340 Length of database: 272 Length adjustment: 27 Effective length of query: 313 Effective length of database: 245 Effective search space: 76685 Effective search space used: 76685 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