Align Glucose/galactose porter (characterized)
to candidate 353115 BT3589 glucose/galactose transporter (NCBI ptt file)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__Btheta:353115 Length = 438 Score = 221 bits (562), Expect = 4e-62 Identities = 131/432 (30%), Positives = 235/432 (54%), Gaps = 40/432 (9%) Query: 15 TSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQSMLIQFCFFGAYFIV 74 ++ +K Y +L L +FF++GF++ +N ILIP+ + +L + +S + F F+ AYF++ Sbjct: 7 SARKKTYYISLAILAGMFFIFGFVSWVNSILIPYFRISCELTHFESYFVAFAFYIAYFVM 66 Query: 75 SLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGALFVLASGVTILQVA 134 ++P+G L+K++ +K+GI+ G ++ A+G +F+PAA R + +FL LF + +G+ ILQ A Sbjct: 67 AIPSGILLKKVGFKKGIMYGFMLTALGAFIFVPAALARQFEIFLIGLFSIGTGLAILQTA 126 Query: 135 ANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLIL-----------------SA 177 ANPYVTI+G ++AA R+++ N + ++P+ A LIL A Sbjct: 127 ANPYVTIIGPIDSAARRISIMGICNKVAGIISPLIFAALILKANDSELFALIESGALDEA 186 Query: 178 ATDATVNAEADAVRFPYLLLA--LAFTVLAIIFAILKPPDVQEDEPALSDKKEG------ 229 +A +N V PY++L L T + I +++L P++ DE +D+++ Sbjct: 187 TKNAMLNELIQRVIIPYIILGIILLLTGIGIRYSVL--PEINTDEQNATDEQDNKHTDKK 244 Query: 230 SAWQYRHLVLGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVG 289 S + +L+LGA+ IF +VG +V ++N+ + G+ +A +Y G M+G Sbjct: 245 SILDFPYLILGALAIFFHVGTQVIAIDTIINYANS---MGMDLLEAKVFPSYTLGCTMIG 301 Query: 290 RFIGSAAM-RYIDDGKALAFNAFVAIILLF------ITVATTGHIAMWSVL---AIGLFN 339 +G + +YI AL + + L F + GH A S+ A+G N Sbjct: 302 YILGIILIPKYISQKNALIGCTLLGLALSFGVVWADFDMTLFGHQANASIFFLNALGFPN 361 Query: 340 SIMFPTIFSLALHGLGSHTSQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICY 399 ++++ I+ L++HGLG T GS +L + + G AI+PL+ G AD + + + + I C+ Sbjct: 362 ALIYAGIWPLSIHGLGKFTKTGSSLLIMGLCGNAILPLVYGHFADQYSLRIGYWVLIPCF 421 Query: 400 AYIAFYGLIGSK 411 Y+ F+ + G K Sbjct: 422 IYLVFFAIKGHK 433 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: 546 Number of extensions: 30 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: 412 Length of database: 438 Length adjustment: 32 Effective length of query: 380 Effective length of database: 406 Effective search space: 154280 Effective search space used: 154280 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