Align Solute carrier family 2, facilitated glucose transporter member 2; Glucose transporter type 2, liver; GLUT-2 (characterized)
to candidate 17022 b2943 D-galactose transporter (NCBI)
Query= SwissProt::P11168 (524 letters) >FitnessBrowser__Keio:17022 Length = 464 Score = 179 bits (455), Expect = 2e-49 Identities = 127/411 (30%), Positives = 213/411 (51%), Gaps = 25/411 (6%) Query: 101 VSSFAVGGMTASFFGGWLGDTLGRIKAMLVANILSLVGALLMGFSKLGPSHILIIAGRSI 160 VSS G + GWL LGR K++++ IL + G+L FS P+ ++I R + Sbjct: 58 VSSMMFGAAVGAVGSGWLSFKLGRKKSLMIGAILFVAGSL---FSAAAPNVEVLILSRVL 114 Query: 161 SGLYCGLISGLVPMYIGEIAPTALRGALGTFHQLAIVTGILISQIIGLEFILGNYDLWHI 220 GL G+ S P+Y+ EIAP +RG++ + +QL I GIL + + F W Sbjct: 115 LGLAVGVASYTAPLYLSEIAPEKIRGSMISMYQLMITIGILGAYLSDTAF--SYTGAWRW 172 Query: 221 LLGLSGVRAILQSLLLFFCPESPRYLYIKLDEEVKAKQSLKRLRGYD-DVTKDINEMRKE 279 +LG+ + AIL + +FF P+SPR+ K V A++ L RLR + ++++E+R+ Sbjct: 173 MLGVIIIPAILLLIGVFFLPDSPRWFAAK-RRFVDAERVLLRLRDTSAEAKRELDEIRE- 230 Query: 280 REEASSEQKVSIIQLF-TNSSYRQPILVALMLHVAQQFSGINGIFYYSTSIFQTAG---I 335 S + K S LF NS++R+ + + ++L V QQF+G+N I YY+ IF+ AG Sbjct: 231 ----SLQVKQSGWALFKENSNFRRAVFLGVLLQVMQQFTGMNVIMYYAPKIFELAGYTNT 286 Query: 336 SKPVYATIGVGAVNMVFTAVSVFLVEKAGRRSL----FLIGMSGMFVCAIFMSVGLVLLN 391 ++ ++ T+ VG N++ T +++ LV++ GR+ FL+ +GM V M +G+ Sbjct: 287 TEQMWGTVIVGLTNVLATFIAIGLVDRWGRKPTLTLGFLVMAAGMGVLGTMMHIGI---- 342 Query: 392 KFSWMSYVSMIAIFLFVSFFEIGPGPIPWFMVAEFFSQGPRPAALAIAAFSNWTCNFIVA 451 Y ++ + +F+ F + GP+ W + +E R + + +NW N IV Sbjct: 343 HSPSAQYFAIAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITCSTATNWIANMIVG 402 Query: 452 LCFQYIADFCG-PYVFFLFAGVLLAFTLFTFFKVPETKGKSFEEIAAEFQK 501 F + + G F+++A + + F L T + VPETK S E I K Sbjct: 403 ATFLTMLNTLGNANTFWVYAALNVLFILLTLWLVPETKHVSLEHIERNLMK 453 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: 618 Number of extensions: 45 Number of successful extensions: 6 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: 464 Length adjustment: 34 Effective length of query: 490 Effective length of database: 430 Effective search space: 210700 Effective search space used: 210700 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