Align Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized)
to candidate WP_058857557.1 AS188_RS02770 sugar porter family MFS transporter
Query= SwissProt::P11168 (524 letters) >NCBI__GCF_001482365.1:WP_058857557.1 Length = 471 Score = 183 bits (465), Expect = 1e-50 Identities = 140/419 (33%), Positives = 210/419 (50%), Gaps = 31/419 (7%) Query: 100 SVSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRS 159 +V+S +G +FFGG + D LGR+ M +A +L LV A+ G + S +I R Sbjct: 61 AVASALLGAAAGAFFGGRIADRLGRVPVMKIAAVLFLVSAIGCGVVE---SFEWLIFWRV 117 Query: 160 ISGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGL----------E 209 + G+ G+ S + P YI EIAP ++RG LG+ Q+ IV GI IS + E Sbjct: 118 VGGVGVGVASIIAPAYIAEIAPASVRGRLGSLQQMGIVLGIFISLAVDAWLAALAGGSGE 177 Query: 210 FILGNYDLWHILLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYDDV 269 + + W + V A+ + F PESPRYL + + +A+ L L+G Sbjct: 178 PLWWGLEAWRWMFMAEAVPALAYLIGAFTIPESPRYLVAEGRAD-EARAVLTDLQGEASA 236 Query: 270 TKDINEMRKEREEASSEQKVSIIQLFTNSSYRQPIL-VALMLHVAQQFSGINGIFYYSTS 328 T+ + R ++ +E+K + L + +PI+ V + L QQF GIN IFYYS Sbjct: 237 TERV---RLIQQTLRTERKPRMSDLKGRMAGLKPIVWVGIGLAALQQFVGINVIFYYSNV 293 Query: 329 IFQTAGISKPVYATIGV--GAVNMVFTAVSVFLVEKAGRRSLFLIGMSGMFV-----CAI 381 ++Q+ G ++ TI V N+V T V++ LVE+ GRR L LIG GM + I Sbjct: 294 LWQSVGFTEADSFTITVITSVTNVVVTVVAIALVERVGRRRLLLIGSGGMTLMLGTLAVI 353 Query: 382 FMSVGLV----LLNKFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALA 437 F + LV +L + V+++A LFV FF + GP+ W ++ E F R AALA Sbjct: 354 FATAPLVDGAPVLGPTA--GPVALVAANLFVVFFGVSWGPMMWVLLGEMFPNQIRGAALA 411 Query: 438 IAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIA 496 +A F W N++V + F +A + L+A L LFT V ET G E++A Sbjct: 412 VAGFVQWIANWVVTVTFPALAAASLGLAYGLYAFFALVSLLFTIRMVRETTGIELEDMA 470 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: 614 Number of extensions: 42 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: 2 Length of query: 524 Length of database: 471 Length adjustment: 34 Effective length of query: 490 Effective length of database: 437 Effective search space: 214130 Effective search space used: 214130 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