Align The glucose uptake porter, GluP (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family
Query= TCDB::Q0SE66 (483 letters) >FitnessBrowser__Korea:Ga0059261_1777 Length = 458 Score = 279 bits (713), Expect = 2e-79 Identities = 171/472 (36%), Positives = 258/472 (54%), Gaps = 25/472 (5%) Query: 10 AESPGDTAEGTSVPVRIAVVAALGGLLFGYDSAVINGAVSAIEGKFQVDSALLGFAIASA 69 A +P + A T + A AALGGLLFG+D+AVI+GA A++ +F + A+LGF +ASA Sbjct: 9 AGAPDEEARATVAIILSAAGAALGGLLFGFDTAVISGATQALQLQFGLTDAMLGFTVASA 68 Query: 70 LLGAAAGAMLAGRIADRYGRLVTMRAAAVMFLLSAIGTGFAANVEMLVTFRIVGGIGVGL 129 L+G G+++AG ADR+GR M A+ +++S++GTG A ++ + FR +GG+ +G Sbjct: 69 LIGTVLGSLIAGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGA 128 Query: 130 ASVIAPAYIAEISPARVRGRLGSLQQLAIVTGIFVSLLVDYALAAIAGGSQEELWFGLEA 189 ASV+ P YIAE+SPAR RGRL ++ QL IV GI ++ L +Y IAG Q ++ A Sbjct: 129 ASVVTPIYIAEVSPARFRGRLVAMNQLNIVLGILIAFLSNY---IIAGLVQYDV-----A 180 Query: 190 WRWMFLAMCVPALAYGLLSLTIPESPRYLIAQGRLGEARGILAVLLGEKGLDLKIESIRS 249 WRWMF + VP+ + L++L +PESPR+L G+ AR ++ L D + E R Sbjct: 181 WRWMFGIVAVPSTIFLLVTLLLPESPRWLAIHGQADRARDVMQRL---GFADPRAELARI 237 Query: 250 TLARETQPSIRDLKGSAFGLMPIVWIGIGLSVFQQFVGINVIFYYSSVLWQAVGFDEGSS 309 LA + + + V I +++F Q GIN + YY+ +++ G S+ Sbjct: 238 ELAEAREEAAGKPRLFQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSA 297 Query: 310 LQITVITSVVNIATTLIAIAYIDRVGRRPLLIIGSAGMAVTLATMAFIFGTASTTVVDGV 369 L ++ N+ T+ A+ IDR GRRPLL +GS A TL + + +A DG Sbjct: 298 LLQSIAVGGTNLVFTVAALFLIDRFGRRPLLFVGSVICAATLLLVGWQLESAKP---DG- 353 Query: 370 TTPQLTGLQGPIALVAANLFVVAFGMSWGPVVWVLLGEAFPNRIRAAALSLAAGAQWAAN 429 T L GL G F+ AF MS G V+WV + E FP+ +R +L + W Sbjct: 354 -TLILFGLLG---------FIAAFAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMA 403 Query: 430 WLITVTFPSMKDFSLGISYGFYAVCAVLSLVFVLRWVKETKGVELEAMHSDS 481 IT FP G + F+ +L L++ +++ ET G+ LE M+ S Sbjct: 404 AAITWAFPVFAASVGGWVFAFFGAMMLLQLLWTWKFMPETNGIALEDMNLGS 455 Lambda K H 0.324 0.138 0.405 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: 598 Number of extensions: 29 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: 483 Length of database: 458 Length adjustment: 33 Effective length of query: 450 Effective length of database: 425 Effective search space: 191250 Effective search space used: 191250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 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