Align citrate lyase holo-[acyl-carrier protein] synthase (EC 2.7.7.61) (characterized)
to candidate BWI76_RS04430 BWI76_RS04430 citrate carrier protein
Query= BRENDA::Q8VS41 (454 letters) >FitnessBrowser__Koxy:BWI76_RS04430 Length = 446 Score = 197 bits (502), Expect = 4e-55 Identities = 127/418 (30%), Positives = 218/418 (52%), Gaps = 15/418 (3%) Query: 33 WKVGIVPLPLFLLAGGLIALDCLGGKLPSDIVVMVATLAFFGFACGEFGKRLPVLGK-LG 91 +K+ +PLPL+ A + L LP+DIV A + G GE GKRLP+ K +G Sbjct: 21 FKIFGMPLPLYAFALITLLLSHFYNALPTDIVGGFAIMFIIGAVFGEIGKRLPIFNKYIG 80 Query: 92 AAAICATFIPSALVHYGLLPDVVIESTTKFYKSTNILYLYICCIIVGSIMSMNRTTLIQG 151 A + + + V+ G+ IE+ T +N L L+I +I G+I+S+NR L++ Sbjct: 81 GAPVMIFLVAAYFVYAGIFTQKEIEAITNVMDKSNFLNLFIAVLITGAILSVNRKLLLKS 140 Query: 152 FLKIFFPMLCGEVVGMLVGIGVGTLLGMEPFQVFFFIVLPIMAGGVGEGAIPLSMGYAAL 211 L +L G + + GI +G G+ ++ VLPIM GG G GA+PLS Y ++ Sbjct: 141 LLGYIPTILMGILGASIFGILIGLCFGISVDRIMMLYVLPIMGGGNGAGAVPLSEIYHSV 200 Query: 212 MHMEQGVALGRVLPMVMLGSLTAIVISGCLNQLGKRFPHLTGEGQLMPNRSHETRSLSES 271 + + ++ + ++ AIV + L+ +GK+ L+GEG+L+ S + E Sbjct: 201 TGRSREEYYSTAIAILTIANIFAIVFAALLDIIGKKHTWLSGEGELVRKASFKV----ED 256 Query: 272 EGVSGKTDVGTLASGALLAVLLYMMGMLGHKLIGLPAPVG--------MLFLAVLLKLAN 323 + +G+ A G +LA +++ + K I LP+ G M+ + L + Sbjct: 257 DEKAGQITHRETAVGLVLATTCFLLAYVIAKKI-LPSIGGVSIHYFAWMVLIVAALNASG 315 Query: 324 VVSPRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQELVNAFTLTNLLVIVSTVSALVA 383 + SP ++ G++ + FF + + ++ VGV T QE+++A T N+++ V V Sbjct: 316 LCSPEIKAGAKRLSDFFSKQLLWVLMVGVGVCYTDLQEIIDAITFANVVIAAVIVVGAVV 375 Query: 384 TGFLVGKKIGMHPIDVAIVS-CCQSGQGGTGDVAILTAGNRMSLMPFAQIATRIGGAI 440 + G IG PI+ AI + C + +GG+GD+ +L+A NRM+L+ +AQI++R+GG I Sbjct: 376 GAAVGGWLIGFFPIESAITAGLCMANRGGSGDLEVLSACNRMNLISYAQISSRLGGGI 433 Lambda K H 0.326 0.142 0.428 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: 629 Number of extensions: 43 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 454 Length of database: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 51 (24.3 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