Align D-mannose and D-mannitol transporter (characterized)
to candidate 18380 b4356 predicted transporter (NCBI)
Query= reanno::pseudo5_N2C3_1:AO356_28540 (430 letters) >FitnessBrowser__Keio:18380 Length = 453 Score = 214 bits (546), Expect = 3e-60 Identities = 125/399 (31%), Positives = 200/399 (50%), Gaps = 14/399 (3%) Query: 10 IIMLFLAGVINYLDRSALSVAAPFIQKDYGLSTGEMGMIFSSFFVGYAAFNFIGGWAADR 69 +++LF A VINYLDRS+LSVA I+++ GLS E+G + S F + Y G DR Sbjct: 44 MLLLFFAAVINYLDRSSLSVANLTIREELGLSATEIGALLSVFSLAYGIAQLPCGPLLDR 103 Query: 70 YGAKTTLLLAMVLWSLFSGLTVLTVGFASLVLIRILFGMGEGPLSVTTSKMVNNWYTPKR 129 G + L L M WSLF ++ + F VL+RI G+GE P++ K++N+W+ K Sbjct: 104 KGPRLMLGLGMFFWSLFQAMSGMVHNFTQFVLVRIGMGIGEAPMNPCGVKVINDWFNIKE 163 Query: 130 RARAIGASMSGTPLGGAISGPVVGFIAVTYGWKISFIIIMLIGLVWAAVWFKFVKERPEG 189 R R +G + + +G A+S P++ + + GW+ FI I ++G+ A W+ + R Sbjct: 164 RGRPMGFFNAASTIGVAVSPPILAAMMLVMGWRGMFITIGVLGIFLAIGWYMLYRNREHV 223 Query: 190 EGAEDILRAEGQGELAAQPV----FPLRF-----YLKQPTVLFTSLAFFSYNYTLFFFLT 240 E L A Q L A V PL F + T+ L F NYT + +L Sbjct: 224 E-----LTAVEQAYLNAGSVNARRDPLSFAEWRSLFRNRTMWGMMLGFSGINYTAWLYLA 278 Query: 241 WFPSYLTMAHGLNVKDMSIATVIPWVLGFLGLALGGFISDFVFKKTGRMMFSRKVVLVTC 300 W P YL A+ L++K + IP++ G G+ + G+++D++ K + SRK+ ++ Sbjct: 279 WLPGYLQTAYNLDLKSTGLMAAIPFLFGAAGMLVNGYVTDWLVKGGMAPIKSRKICIIAG 338 Query: 301 LLACAVCIACAGMVTTLYPAVILVALAVFFLYLTGAIYWAIIQDTVPAARVGGVSGFMHF 360 + A TT AV+L+ +A+F ++ G W +I V + V +F Sbjct: 339 MFCSAAFTLIVPQATTSMTAVLLIGMALFCIHFAGTSCWGLIHVAVASRMTASVGSIQNF 398 Query: 361 LANTSGIVGPTLTGFLVQFTGSFTSAFLLAGLLTVIGAV 399 + P +TGF+V T SF A ++ G +T GA+ Sbjct: 399 ASFICASFAPIITGFIVDTTHSFRLALIICGCVTAAGAL 437 Lambda K H 0.329 0.142 0.439 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: 497 Number of extensions: 29 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: 430 Length of database: 453 Length adjustment: 32 Effective length of query: 398 Effective length of database: 421 Effective search space: 167558 Effective search space used: 167558 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 (21.8 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