Align Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized)
to candidate WP_054656487.1 CES79_RS12280 sugar porter family MFS transporter
Query= SwissProt::P11168 (524 letters) >NCBI__GCF_002217945.1:WP_054656487.1 Length = 455 Score = 177 bits (448), Expect = 1e-48 Identities = 131/407 (32%), Positives = 204/407 (50%), Gaps = 18/407 (4%) Query: 102 SSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSIS 161 S+ G + G L D LGR K +L++ ++ V +LL G + S LII R Sbjct: 54 SAVMFGAIFGGALAGQLSDRLGRRKMILISAVIFAVFSLLSGIAPNDGSIYLIIV-RIFL 112 Query: 162 GLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDL---W 218 GL G S LVP Y+ E+AP LRG L +Q IV+G+LIS I ++F+L W Sbjct: 113 GLAVGAASALVPPYMSELAPARLRGRLSGLNQTMIVSGMLISYI--MDFVLKGLPTGWGW 170 Query: 219 HILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLR-GYDDVTKDINEMR 277 ++L + V AI+ + PESPR+L +K +E AK+ L +R D++ ++ +++ Sbjct: 171 RVMLAFAAVPAIILFFGVLRLPESPRFL-VKHGDEEAAKRVLSYVRDSQDEIDGELKDIK 229 Query: 278 KEREEASSEQKVSIIQLFTNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTA---G 334 K + ++ K + YR ++ + + QQF G N IFYY I + A Sbjct: 230 KTASQETAASKSTHYSTLFTGKYRYLVIAGVGVAAFQQFQGANAIFYYIPLIVEKATGSA 289 Query: 335 ISKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFVCAIFMSVGLVLLNKFS 394 S + I G + ++ + + + + EK RR+L ++G S M + F+ ++NK Sbjct: 290 ASNALMWPIIQGVILVLGSLLYMAIAEKFKRRTLIMMGGSVM-ALSFFLP---AIINKMD 345 Query: 395 WMSYVSMIAIFL--FVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVAL 452 + MI +FL +V+F+ P+ W +V E F R A +A+ NW +F V L Sbjct: 346 PNANPMMIVVFLSIYVAFYSFTWAPLTWVIVGEMFPLAIRGKAAGLASSFNWIGSFAVGL 405 Query: 453 CFQYI-ADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAE 498 F + A VF +F + + LFT F VPETKGK+ EEI AE Sbjct: 406 LFPIMTAAMSQEAVFAIFGAICVLGVLFTHFFVPETKGKTLEEIEAE 452 Lambda K H 0.326 0.140 0.418 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: 582 Number of extensions: 39 Number of successful extensions: 7 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: 524 Length of database: 455 Length adjustment: 34 Effective length of query: 490 Effective length of database: 421 Effective search space: 206290 Effective search space used: 206290 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: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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