Align Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized)
to candidate Echvi_2805 Echvi_2805 MFS transporter, sugar porter (SP) family
Query= SwissProt::P11168 (524 letters) >FitnessBrowser__Cola:Echvi_2805 Length = 448 Score = 187 bits (474), Expect = 9e-52 Identities = 145/507 (28%), Positives = 239/507 (47%), Gaps = 76/507 (14%) Query: 10 LVFTVITAVLGSFQFGYDIGVINAPQQVIISHYRHVLGVPLDDRKAINNYVINSTDELPT 69 ++F I A LG F FG+D VI+ ++ I ++ L D Sbjct: 7 VIFLSIVAALGGFLFGFDTAVISGAERFIQEKWQ------LSD----------------- 43 Query: 70 ISYSMNPKPTPWAEEETVAAAQLITMLWSLSVSSFAVGGMTASFFGGWLGDTLGRIKAML 129 W VA A T++ +L FGG D GR ++L Sbjct: 44 -----------WTHGMAVAIALYGTVIGAL--------------FGGIPADKYGRKTSLL 78 Query: 130 VANILSLVGALLMGFSKLGPSHILIIAGRSISGLYCGLISGLVPMYIGEIAPTALRGALG 189 +L + AL S L P + R I GL G S + PMYI EIAP RG L Sbjct: 79 WIGVLYFISAL---GSALAPDVYSFMFFRFIGGLGVGASSVVAPMYISEIAPAKNRGVLV 135 Query: 190 TFHQLAIVTGILISQIIGLEFILGNYDL---WHILLGLSGVRAILQSLLLFFCPESPRYL 246 +Q IV GIL++ +++ DL W ++G+ + A++ +LL P+SPR+L Sbjct: 136 ALYQFNIVFGILMAYFSN--YLIEMADLNESWRWMMGMEAIPALIYTLLSIRVPKSPRWL 193 Query: 247 YIKLDEEVKAKQSLKRL--RGYDD-VTKDINEMRKEREEASSEQKVSIIQLFTNSSYRQP 303 ++ +A Q L++ G D+ + I E +E+ KV LF +S + Sbjct: 194 IAHHNKVEEATQILRKTDPEGVDEAIHLAIEERNREKI------KVGFAVLFKHSHLKTT 247 Query: 304 ILVALMLHVAQQFSGINGIFYYSTSIFQTAGISKP--VYATIGVGAVNMVFTAVSVFLVE 361 +L A+M+ + Q SGIN I Y++ +F+ AGI + + +TIG+G VNM+ T + ++L++ Sbjct: 248 LL-AIMIALFNQLSGINAIIYFAPRVFEMAGIDQKSALLSTIGIGVVNMIATMIGLYLID 306 Query: 362 KAGRRSLFLIGMSGMFVCAIFMSVGLV--LLNKFSWMSYVSMIAIFLFVSFFEIGPGPIP 419 + GR+ L +IG G + + M+ ++N Y+ + +F+F++ +G G + Sbjct: 307 RIGRKKLMVIGSIGYIISLLLMAYSFSGGVINS----GYLPLF-VFVFIASHAVGQGSVI 361 Query: 420 WFMVAEFFSQGPRPAALAIAAFSNWTCNFIVALCFQYIADFCGPYVFFLFAGVLLAF-TL 478 W ++E F R +I F++W ++A F + A+ GP F F V++ L Sbjct: 362 WVFISEVFPNETRAFGQSIGCFTHWILAAVIANVFPFFANSFGPASIFGFFAVMMGLQLL 421 Query: 479 FTFFKVPETKGKSFEEIAAEFQKKSGS 505 + K+PETKG+S EEI + + K G+ Sbjct: 422 WVLTKMPETKGRSLEEIQQDLKIKQGT 448 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: 565 Number of extensions: 30 Number of successful extensions: 8 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: 448 Length adjustment: 34 Effective length of query: 490 Effective length of database: 414 Effective search space: 202860 Effective search space used: 202860 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 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