Align Inositol transport system permease protein (characterized)
to candidate 3606962 Dshi_0389 Monosaccharide-transporting ATPase (RefSeq)
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Dino:3606962 Length = 357 Score = 164 bits (416), Expect = 2e-45 Identities = 106/319 (33%), Positives = 163/319 (51%), Gaps = 26/319 (8%) Query: 30 LIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSV 89 LI + +FG ++ + F + L L++ QV I+G++A + VI+T GIDLS G++ Sbjct: 49 LIVLVAAIAVFGLLLGSKFF--SPFALTLILQQVQIVGIVAAAQSLVILTAGIDLSVGAI 106 Query: 90 LALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPF 149 + +S+++ F LPV + VA GL G L G ING ++A +PPF Sbjct: 107 MVMSSVVMGQ-----------FTFRYGLPVEVAVACGLLCGTLLGFINGWLVAKVKLPPF 155 Query: 150 IATLGMMVSARGLARYYTEGQ-----------PVSMLSDSYTAIGHGAMP--VIIFLVVA 196 I TLGM Y+ + P+ + IG + VI +++ Sbjct: 156 IVTLGMWQIVLAANFLYSRNETIRSQDIRDQAPLLQFFGTTLEIGGARLTYGVIFMVLLV 215 Query: 197 VIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAA 256 ++ ALR+T +G++ YA+G + +AA SG+ V R LI VY ++GL+ AG R Sbjct: 216 IVLAYALRHTAWGRHVYAVGDDPEAAELSGVQVSRTLISVYMLSGLICAFAGWALIGRIG 275 Query: 257 TGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYIQD 316 + G +++I A VIGG SL GG G I G GALI+GV G +G DA Sbjct: 276 SVSPTSGQLANIESITAVVIGGISLFGGRGSILGAFFGALIVGVFTLGLRLLGADAQWTF 335 Query: 317 IIKGLIIVVAVVIDQYRNK 335 ++ GL+I+ AV +DQ+ K Sbjct: 336 LLIGLLIIAAVAVDQWIRK 354 Lambda K H 0.325 0.140 0.394 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: 269 Number of extensions: 15 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: 340 Length of database: 357 Length adjustment: 29 Effective length of query: 311 Effective length of database: 328 Effective search space: 102008 Effective search space used: 102008 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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