Align citrate lyase holo-[acyl-carrier protein] synthase (EC 2.7.7.61) (characterized)
to candidate PfGW456L13_3595 Citrate-sodium symport
Query= BRENDA::Q8VS41 (454 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3595 Length = 448 Score = 312 bits (800), Expect = 1e-89 Identities = 160/423 (37%), Positives = 253/423 (59%), Gaps = 13/423 (3%) Query: 33 WKVGIVPLPLFLLAGGLIALDCLGGKLPSDIVVMVATLAFFGFACGEFGKRLPVLGKLGA 92 +++G++PLP+FL ++ L G LP +++ +A + G G+ G RLP+L ++G Sbjct: 29 YEIGVIPLPIFLGIAVIVYLSAHLGFLPKNMIGGLAVIMTMGVFFGQMGSRLPILKEIGG 88 Query: 93 AAICATFIPSALVHYGLLPDVVIESTTKFYKSTNILYLYICCIIVGSIMSMNRTTLIQGF 152 AI +PS LV YG I++T K N LY I ++VGSI+ M+R L+QG Sbjct: 89 GAILCLMLPSILVFYGFFGPATIDATKMLMKEANFLYFVIASLVVGSILGMSRFILVQGM 148 Query: 153 LKIFFPMLCGEVVGMLVGIGVGTLLGMEPFQVFFFIVLPIMAGGVGEGAIPLSMGYAALM 212 L++F P+L G + + G+ VG L+G FFFI++PI+ GG+GEG +PLS+ Y+A++ Sbjct: 149 LRMFIPLLVGTLAAVASGLIVGKLVGYSFHHTFFFIIVPIIGGGIGEGILPLSLAYSAIL 208 Query: 213 HMEQGVALGRVLPMVMLGSLTAIVISGCLNQLGKRFPHLTGEGQLMPNRSHETRSLSESE 272 + + ++ P ++G++ AI+ +G L +L + P + GEG L+ R+ E++ Sbjct: 209 GGTPDIYVAQLAPAAVVGNIVAIICAGYLARLALKRPTINGEGSLI-------RAKDEND 261 Query: 273 GVSGKTDVGT------LASGALLAVLLYMMGMLGHKLIGLPAPVGMLFLAVLLKLANVVS 326 K D GT + +G L+ +++G L K++G+P PV M+ AVL K V+ Sbjct: 262 QFLVKEDTGTIVDFRVMGAGVLVICAFFVLGGLLEKVVGIPGPVMMILAAVLFKYLRVLP 321 Query: 327 PRLQEGSQMVYKFFRTAVTYPILFAVGVAITPWQELVNAFTLTNLLVIVSTVSALVATGF 386 +L++G+ YK +A +P++ +G+ P +V F++ +LV VS V ++ GF Sbjct: 322 EKLEKGANSFYKLVSSAFIWPVMIGLGMLYVPLDSVVKVFSVGYVLVCVSVVVSMTVAGF 381 Query: 387 LVGKKIGMHPIDVAIVSCCQSGQGGTGDVAILTAGNRMSLMPFAQIATRIGGAINVSLGL 446 +G + M+PI+ AIV+CC SG GGTGDVAIL+A NRMSLMPFAQI+TRIGGA V L Sbjct: 382 FIGNLMKMYPIESAIVTCCHSGLGGTGDVAILSASNRMSLMPFAQISTRIGGASTVILAT 441 Query: 447 LFL 449 + L Sbjct: 442 ILL 444 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: 762 Number of extensions: 63 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: 454 Length of database: 448 Length adjustment: 33 Effective length of query: 421 Effective length of database: 415 Effective search space: 174715 Effective search space used: 174715 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