Align Inositol transport system permease protein (characterized)
to candidate N515DRAFT_2415 N515DRAFT_2415 simple sugar transport system permease protein
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Dyella79:N515DRAFT_2415 Length = 337 Score = 137 bits (345), Expect = 4e-37 Identities = 107/359 (29%), Positives = 184/359 (51%), Gaps = 43/359 (11%) Query: 1 MNAITDNKPATVPTKSRRR----------LPTELSIFLVLIGIGLVFELFGWIVRDQSFL 50 MNA+ PA + RR L L +F+ + G G V L+ + Q FL Sbjct: 1 MNAVA---PAATSAAAGRRPWWRRRAQVPLLVTLVLFVAMAGAGGV--LYHGFLTPQVFL 55 Query: 51 MNSQRLVLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAV 110 +++ + + ++A+G+T VI+ GIDLS G+V+A S ++ A L Q R Sbjct: 56 N-------LLIDNAFLCIVAVGMTFVILAGGIDLSVGAVVAFSTVLLAELVQ-----RHG 103 Query: 111 FPSLTDLPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTEG- 169 +P L + + + V G G G+ G +I + PF+ TL M ARG+A + Sbjct: 104 WPPLAAIALVLAVGTGFGAGM------GVLIQRFRLQPFVVTLAGMFLARGVATLISVDS 157 Query: 170 ----QP-VSMLSDSYTAIGHGAM---PVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQA 221 QP ++ +++ +G G+M ++ L V + + +G+ YAIGG+ + Sbjct: 158 IDIDQPWLASVANLRLPLGGGSMLSVGALVALAVVAAGALLAGASSFGRTVYAIGGSESS 217 Query: 222 ARTSGINVKRHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSL 281 AR G+ V ++ VY+++G A LAGVV + +G + + ELDAIAA VIGGT L Sbjct: 218 ARLMGLPVDATVVRVYALSGFCAALAGVVYTLYMLSGYSQHALGLELDAIAAVVIGGTVL 277 Query: 282 AGGVGRITGTVIGALILGVMASGFTFVG-VDAYIQDIIKGLIIVVAVVIDQYRNKRKLK 339 AGG G + GT++G L+LG++ + F G + ++ I+ G +++ ++ + ++++K Sbjct: 278 AGGSGYVLGTLLGVLVLGLIQTLIVFDGELSSWWTRIVIGALLLAFCLLQRLFRRKEIK 336 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: 277 Number of extensions: 19 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: 337 Length adjustment: 28 Effective length of query: 312 Effective length of database: 309 Effective search space: 96408 Effective search space used: 96408 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 Apr 09 2024. 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