Align aerobic C4-dicarboxylate transport protein (characterized)
to candidate N515DRAFT_0013 N515DRAFT_0013 aerobic C4-dicarboxylate transport protein
Query= CharProtDB::CH_014038 (428 letters) >FitnessBrowser__Dyella79:N515DRAFT_0013 Length = 433 Score = 514 bits (1324), Expect = e-150 Identities = 258/423 (60%), Positives = 334/423 (78%), Gaps = 1/423 (0%) Query: 4 SLFKSLYFQVLTAIAIGILLGHFYPEIGEQMKPLGDGFVKLIKMIIAPVIFCTVVTGIAG 63 + F+ YF VL AI G L+GH+ PE G +KPLGDGF+ L+KM+I P+IF TVV GIAG Sbjct: 3 AFFRHFYFWVLAAIVAGGLIGHYAPETGVALKPLGDGFIALVKMLIGPIIFLTVVLGIAG 62 Query: 64 MESMKAVGRTGAVALLYFEIVSTIALIIGLIIVNVVQPGAGMNVDPATLDAKAVAVYADQ 123 + +K VGR GA A+LYFE+VS+ AL+IGL++VN ++PGAG N PA+LDA AVA YA+ Sbjct: 63 VSDVKKVGRVGAKAILYFEVVSSFALVIGLVVVNTLKPGAGFNATPASLDATAVAKYANA 122 Query: 124 AKDQGIVAFIMDVIPASVIGAFAS-GNILQVLLFAVLFGFALHRLGSKGQLIFNVIESFS 182 A +QG V F++ +IP + AF+ G++LQVLL A+LFGFA+ LG + + + +E+ S Sbjct: 123 AHEQGTVPFLLHLIPKTFSDAFSGDGDLLQVLLLALLFGFAMIHLGERARPVMTFLEALS 182 Query: 183 QVIFGIINMIMRLAPIGAFGAMAFTIGKYGVGTLVQLGQLIICFYITCILFVVLVLGSIA 242 +V F I+ MIMRLAP+GA GAMAFTIGKYGV +L L +L+ FY+ CILFVV+VLG+IA Sbjct: 183 KVFFRIMGMIMRLAPLGAMGAMAFTIGKYGVHSLGPLLKLMGSFYLACILFVVVVLGAIA 242 Query: 243 KATGFSIFKFIRYIREELLIVLGTSSSESALPRMLDKMEKLGCRKSVVGLVIPTGYSFNL 302 +ATGFSIFKF+RYIREELL+VLGTSSSESAL ++ K+E+LGC KSVVGLV+P+GYSFNL Sbjct: 243 RATGFSIFKFLRYIREELLLVLGTSSSESALVPLMQKLERLGCSKSVVGLVVPSGYSFNL 302 Query: 303 DGTSIYLTMAAVFIAQATNSQMDIVHQITLLIVLLLSSKGAAGVTGSGFIVLAATLSAVG 362 DGT+IYLTMAA+F+AQA ++ + ++TLL V +L+SKGA+GVTG+GFI LAATL+ V Sbjct: 303 DGTNIYLTMAAIFVAQALGVELTLSQELTLLAVAMLTSKGASGVTGAGFITLAATLAVVP 362 Query: 363 HLPVAGLALILGIDRFMSEARALTNLVGNGVATIVVAKWVKELDHKKLDDVLNNRAPDGK 422 +PVAGL+LILGIDRFMSEARA+TN++GNGVAT+VV+ W KELDH L L+ R+P Sbjct: 363 SVPVAGLSLILGIDRFMSEARAITNIIGNGVATVVVSHWEKELDHASLQAALDGRSPSPA 422 Query: 423 THE 425 E Sbjct: 423 ADE 425 Lambda K H 0.327 0.142 0.401 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: 605 Number of extensions: 26 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: 428 Length of database: 433 Length adjustment: 32 Effective length of query: 396 Effective length of database: 401 Effective search space: 158796 Effective search space used: 158796 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