Align Glucose/galactose porter (characterized)
to candidate 7025545 Shewana3_2696 major facilitator transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__ANA3:7025545 Length = 452 Score = 194 bits (493), Expect = 4e-54 Identities = 138/435 (31%), Positives = 222/435 (51%), Gaps = 45/435 (10%) Query: 15 TSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIV 74 T+S + + + +LFF++GF+T LN LIP LK QLN ++ L+ F F+ AYF++ Sbjct: 11 TASPQGSFIPMLLIGILFFVFGFVTWLNGALIPFLKIACQLNEFEAYLVTFVFYIAYFVM 70 Query: 75 SLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVA 134 +LP ++ R+ YK G+ +GL + A G LFI AA +A FL ALFVL +G+T+LQ A Sbjct: 71 ALPTSSILTRLGYKMGMTLGLGIMAAGAGLFIVAALVGHFATFLLALFVLGTGLTLLQTA 130 Query: 135 ANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILS---------------AAT 179 ANPY+ +G E+AA R++L N + P+ IL+ A Sbjct: 131 ANPYIVCIGPRESAAMRISLMGIVNKGAGFIVPIIFTAWILTGMEPYSETALASLSEAQR 190 Query: 180 DATVNAEADAVRFPYLLLALAFTVLA--IIFAILKPPDVQED-EPALSDKKEGSAWQYRH 236 + A+ + PYL++ L L + F+ L P++ E E +D K + QY Sbjct: 191 QLALTELANRLVHPYLMMMLVLLGLMAFVWFSPLPEPELGERVERTQTDWK--AILQYPQ 248 Query: 237 LVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAA 296 ++LGA+ +F YVGAEV G + F GL +Y G ++G +G Sbjct: 249 VILGALTLFCYVGAEVIAGDSIGLFSQ-----GLGVAHFGMMTSYTMGFMVLGYVLGILL 303 Query: 297 M-RYIDDGKALAFNAFVAIIL-LFITVATTGHIAMWSVL-----------------AIGL 337 + R+I AL +A ++ L + ++ + A+ +L +GL Sbjct: 304 IPRWISQQTALVGSAIAGLLFTLGVLLSDSQSQALSELLLGWLGVLPVPDPVLYLALLGL 363 Query: 338 FNSIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIG-IHLAFLMPI 396 N++++P ++ LAL GLG T+ S +L + I GGAI+PL+ G +A + G +A+ + + Sbjct: 364 ANALVWPAVWPLALEGLGRLTATASALLIMGIAGGAILPLLYGYIAHSQGDSQMAYFLLL 423 Query: 397 ICYAYIAFYGLIGSK 411 CY I +Y + G K Sbjct: 424 PCYGLIFYYAIWGHK 438 Lambda K H 0.328 0.141 0.420 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: 554 Number of extensions: 41 Number of successful extensions: 3 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: 412 Length of database: 452 Length adjustment: 32 Effective length of query: 380 Effective length of database: 420 Effective search space: 159600 Effective search space used: 159600 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