Align Glucose/galactose transporter (characterized, see rationale)
to candidate 7025545 Shewana3_2696 major facilitator transporter (RefSeq)
Query= uniprot:A0KXM0 (423 letters) >FitnessBrowser__ANA3:7025545 Length = 452 Score = 198 bits (504), Expect = 2e-55 Identities = 143/447 (31%), Positives = 232/447 (51%), Gaps = 42/447 (9%) Query: 8 SSHTSSVSEAGNGNYRFALVSLTSLFFMWGFITCLNDILIPHLKAVFSLNYTQAMLIQFC 67 +S ++ + + G++ ++ + LFF++GF+T LN LIP LK LN +A L+ F Sbjct: 4 TSDSTQATASPQGSF-IPMLLIGILFFVFGFVTWLNGALIPFLKIACQLNEFEAYLVTFV 62 Query: 68 FFGAYFLVSIPAGQLVKRLGYQKGIVTGLVIASIGCGLFYPAASFATYGLFLGALFVLAS 127 F+ AYF++++P ++ RLGY+ G+ GL I + G GLF AA + FL ALFVL + Sbjct: 63 FYIAYFVMALPTSSILTRLGYKMGMTLGLGIMAAGAGLFIVAALVGHFATFLLALFVLGT 122 Query: 128 GITILQVAANPYVNALGSSETASSRLNLTQAFNALGTTVAPFFGSILILS----VAASVS 183 G+T+LQ AANPY+ +G E+A+ R++L N + P + IL+ + + Sbjct: 123 GLTLLQTAANPYIVCIGPRESAAMRISLMGIVNKGAGFIVPIIFTAWILTGMEPYSETAL 182 Query: 184 SELAQANAEAEVVKL------PYLLLAAALAVLA--IIFAKLDLPVIREHSQAAAEEVQT 235 + L++A + + +L PYL++ L L + F+ L P + E + +T Sbjct: 183 ASLSEAQRQLALTELANRLVHPYLMMMLVLLGLMAFVWFSPLPEPELGERVE------RT 236 Query: 236 HLGKTSALQSMHLVLGAVGIFVYVGAEVSIGSFLVNF---LGEAHIVGMPEEQAAHY--I 290 + LQ ++LGA+ +F YVGAEV G + F LG AH GM + + Sbjct: 237 QTDWKAILQYPQVILGALTLFCYVGAEVIAGDSIGLFSQGLGVAHF-GMMTSYTMGFMVL 295 Query: 291 AYYWGGAMVGRFIGSAVMQKIPAGTVLAFNAFMAALLVLVAMTTSGSVAMWAILGV---- 346 Y G ++ R+I Q G+ +A F +L+ + + + S + LGV Sbjct: 296 GYVLGILLIPRWIS---QQTALVGSAIAGLLFTLGVLLSDSQSQALSELLLGWLGVLPVP 352 Query: 347 ---------GLFNSIMFPTIFSLALRDLGPHTSQGSGILCLAIVGGAIVPLLQGVLADNL 397 GL N++++P ++ LAL LG T+ S +L + I GGAI+PLL G +A + Sbjct: 353 DPVLYLALLGLANALVWPAVWPLALEGLGRLTATASALLIMGIAGGAILPLLYGYIAHSQ 412 Query: 398 G-IQLAFILPVVCYGFILFYGAKGSKM 423 G Q+A+ L + CYG I +Y G K+ Sbjct: 413 GDSQMAYFLLLPCYGLIFYYAIWGHKL 439 Lambda K H 0.326 0.138 0.402 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: 508 Number of extensions: 34 Number of successful extensions: 4 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: 423 Length of database: 452 Length adjustment: 32 Effective length of query: 391 Effective length of database: 420 Effective search space: 164220 Effective search space used: 164220 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: 51 (24.3 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