Align sodium:C4-dicarboxylate symporter (dctA) (characterized)
to candidate Pf6N2E2_2249 Proton/glutamate symport protein @ Sodium/glutamate symport protein
Query= reanno::pseudo5_N2C3_1:AO356_18980 (450 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2249 Length = 420 Score = 292 bits (748), Expect = 1e-83 Identities = 172/408 (42%), Positives = 258/408 (63%), Gaps = 17/408 (4%) Query: 17 VAIAIGILLG---HFYPQTGVALKPFG-------DGFIKLIKMVIAPIIFCTVVSGIGGM 66 + IA+G+L+G H + + + K D F+++IKM+IAP++F T+V GI M Sbjct: 1 MGIALGVLVGWACHHFAGSEQSAKEIASYFSMVTDIFLRMIKMIIAPLVFATLVGGIASM 60 Query: 67 QNMKSVGKTGGYALLYFEIVSTIALLIGLVVVNVVQPGAGMHIDVSTLDTSKIAGFISAG 126 N +SVG+ G A+ +F S ++LLIG+ +VN+ QPGAG+++DV+ T+ + ++ G Sbjct: 61 GNSRSVGRIGARAMAWFVTASVVSLLIGMGLVNLFQPGAGLNMDVAQHATAAVP--VNTG 118 Query: 127 KDQSIIAFILNVIPNTIVGAFANGDILQVLMFSVLFGFALHRLGAYGKP-VLDFIDRFAH 185 D S+ AFI +V P +I A AN +ILQ+++FS+ FGFAL + G + D I+ A Sbjct: 119 -DFSLKAFIGHVFPRSIAEAMANNEILQIVVFSLFFGFALAGVKRAGYTRITDCIEELAK 177 Query: 186 VMFIIINMIMKLAPLGAFGAMAFTIGAYGVGSLVQLGQLMICFYITCVVFVLVVLGAICR 245 VMF I + +M AP+G F A+A I G+G LV G+L+ FY+ ++ ++ GA Sbjct: 178 VMFKITDYVMAFAPIGVFAAIASAITTQGLGLLVDYGKLIAEFYLGILILWALLFGAGYL 237 Query: 246 AHGFSVIKLIRYIREELLIVLGTSSSESALPRMLIKMERLGAKKSVVGLVIPTGYSFNLD 305 G SV L + IRE +L+ T+SSESA P+ + +E+ GA K V V+P GYSFNLD Sbjct: 238 FLGRSVFHLGKLIREPILLAFSTASSESAYPKTIEALEKFGAPKRVSSFVLPLGYSFNLD 297 Query: 306 GTSIYLTMAAVFIAQATDTPMDLTHQITLLLVLLLSSKGAAGVTGSGFIVLAATLSAVGH 365 G+ +Y A +FIAQA + + T Q+ +LL L+++SKG AGV + +V+AATL + + Sbjct: 298 GSMMYQAFAILFIAQAYNIDLSFTQQLLILLTLMVTSKGMAGVARASVVVVAATL-PMFN 356 Query: 366 LPVAGLALILGIDRFMSEARALTNLVGNAVATIVVAKWV--KELDEDQ 411 LP AGL LI+GID+F+ AR TN+VGN++AT VVAK +E DED+ Sbjct: 357 LPEAGLLLIIGIDQFLDMARTATNVVGNSIATAVVAKSEPHEEADEDE 404 Lambda K H 0.326 0.142 0.402 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: 482 Number of extensions: 21 Number of successful extensions: 4 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: 450 Length of database: 420 Length adjustment: 32 Effective length of query: 418 Effective length of database: 388 Effective search space: 162184 Effective search space used: 162184 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