Align Glucose transporter, OEOE_0819. Does not transport fructose (characterized)
to candidate GFF971 PS417_04925 MFS transporter
Query= TCDB::Q04FN1 (395 letters) >FitnessBrowser__WCS417:GFF971 Length = 421 Score = 127 bits (319), Expect = 6e-34 Identities = 105/362 (29%), Positives = 170/362 (46%), Gaps = 25/362 (6%) Query: 14 IFLIAGNLRLTIIVIPPISSYIMQSFDLDQTKIGLLTSIPLICFGLLSVLAPLVIRKLGS 73 + L+A NLR + + P+ S + S L + GLLT++P++C GL + LAP++ R+ G+ Sbjct: 42 LVLVALNLRPALSSLSPLLSEVSSSLGLSAARAGLLTTLPVLCLGLFAPLAPILARRFGA 101 Query: 74 YRTMITALGILIIANFFRVLSAPW----LFVGSFFTGAAITILNILTPTVIVERAPKHAN 129 R + LGIL++ VL + + LFVGS GA+I I+ +L P ++ K A Sbjct: 102 ERVV---LGILLMLAGGIVLRSAFGEVGLFVGSLIAGASIGIIGVLLPGIVKRDFAKQAG 158 Query: 130 VLNGLYTATLNLWAAGIGYLVAPLAKQIG--WQAVVQLTSILPIITLAGWFLIKNKTSNN 187 + G+YT L L AA PL+ G W + + ++ W Sbjct: 159 TMTGVYTMALCLGAALAAGASVPLSDYFGHRWSIGLGFWMLPALLAALCWL--------P 210 Query: 188 DLEKNTVSNQQNIKLIEIINHPKIWLLAIFMGLQSFIYYGLIAWLPSILNHLKLSLLATG 247 + +++ ++ ++ P W + ++MGLQS + Y + W+PSIL + L AT Sbjct: 211 QIGHKHGAHRVAYRVKGLLRDPLAWQVTLYMGLQSSLAYIVFGWVPSIL--IDRGLSATD 268 Query: 248 SLFALFQFIGIPISYIIPRISAGKNAFKWVLGGLFVGYVSGLSLLNLKS---PTLPVITI 304 + AL G I ++ ++A A + L + V L+L L L + Sbjct: 269 AGLAL---SGSIIVQLLSALTAPWLATRGKDQRLAIVVVMLLTLGGLMGCLYAPLDGLWG 325 Query: 305 AIIALGLTTAAIFSLALGLITTLSDSAREISVIGGVVQSLGYLLACISPTLLGKLNSSFG 364 I LGL FSLAL LI S A + + G+ Q +GY LA + P +G ++ G Sbjct: 326 WAILLGLGQGGTFSLALTLIVLRSRDAHVAANLSGMAQGIGYTLASLGPLAVGLIHDWTG 385 Query: 365 NW 366 W Sbjct: 386 GW 387 Lambda K H 0.327 0.143 0.429 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: 533 Number of extensions: 42 Number of successful extensions: 5 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: 395 Length of database: 421 Length adjustment: 31 Effective length of query: 364 Effective length of database: 390 Effective search space: 141960 Effective search space used: 141960 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: 50 (23.9 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