Align Glucose/galactose porter (characterized)
to candidate 6937233 Sama_1403 glucose/galactose transporter (RefSeq)
Query= TCDB::P0C105 (412 letters) >FitnessBrowser__SB2B:6937233 Length = 415 Score = 545 bits (1403), Expect = e-159 Identities = 272/412 (66%), Positives = 333/412 (80%), Gaps = 6/412 (1%) Query: 1 MATSIPTNNPLHTETSSQKNYGFALTSLTLLFFMWGFITCLNDILIPHLKNVFQLNYTQS 60 MAT +P N H + +NY FAL SLT LFFMWGFITCLNDILIPHLK VF LNY Q+ Sbjct: 1 MAT-VPIANANHAGAAGAENYRFALGSLTTLFFMWGFITCLNDILIPHLKAVFSLNYAQA 59 Query: 61 MLIQFCFFGAYFIVSLPAGQLVKRISYKRGIVVGLIVAAIGCALFIPAASYRVYALFLGA 120 MLIQFCFFGAYF+VS+PAG LVKR+ Y++GIVVGL+ AA+GC LF PAA Y +FLGA Sbjct: 60 MLIQFCFFGAYFLVSVPAGVLVKRLGYQKGIVVGLLTAALGCGLFYPAAVSATYGVFLGA 119 Query: 121 LFVLASGVTILQVAANPYVTILGKPETAASRLTLTQAFNSLGTTVAPVFGAVLILSAATD 180 LFVLASG+T+LQVAANPYVT LG +TA+SRLTLTQAFNSLGTT+AP FG+VLILS A Sbjct: 120 LFVLASGITVLQVAANPYVTALGPVQTASSRLTLTQAFNSLGTTIAPAFGSVLILSVAVG 179 Query: 181 ATVNAEADAVRFPYLLLALAFTVLAIIFAILKPPDV--QEDEPALSDKKEGSAWQYRHLV 238 A+ AEADAV+ PYLLL VLA++FA+LK P + QEDE A + + SA +RHLV Sbjct: 180 ASAEAEADAVKLPYLLLCGMLIVLAVVFALLKLPHIHDQEDEVAATGQ---SALAHRHLV 236 Query: 239 LGAIGIFVYVGAEVSVGSFLVNFLSDPTVAGLSETDAAHHVAYFWGGAMVGRFIGSAAMR 298 LGAIGIFVYVG EV++GSFLVNFL + VAG++E DAAH++A++WGGAMVGRFIG+A M+ Sbjct: 237 LGAIGIFVYVGGEVAIGSFLVNFLGESHVAGMAEADAAHYIAFYWGGAMVGRFIGAAVMQ 296 Query: 299 YIDDGKALAFNAFVAIILLFITVATTGHIAMWSVLAIGLFNSIMFPTIFSLALHGLGSHT 358 +D GK L FNA +A +L+ + + ++G +AMW++LA+GLFNSIMFPTIFSLAL LG T Sbjct: 297 KVDAGKVLGFNATMAALLVLVAMNSSGALAMWAILAVGLFNSIMFPTIFSLALKNLGPAT 356 Query: 359 SQGSGILCLAIVGGAIVPLIQGALADAIGIHLAFLMPIICYAYIAFYGLIGS 410 +QGSGILCLAIVGGA+VPL+QG LAD++G+ +F++P++CY YI FYGL GS Sbjct: 357 AQGSGILCLAIVGGALVPLLQGLLADSVGLSASFILPVLCYGYILFYGLKGS 408 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: 688 Number of extensions: 27 Number of successful extensions: 2 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: 415 Length adjustment: 31 Effective length of query: 381 Effective length of database: 384 Effective search space: 146304 Effective search space used: 146304 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