Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate 3609760 Dshi_3143 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= uniprot:D8IPH8 (292 letters) >FitnessBrowser__Dino:3609760 Length = 290 Score = 137 bits (344), Expect = 4e-37 Identities = 82/273 (30%), Positives = 154/273 (56%), Gaps = 10/273 (3%) Query: 8 SLPYLFLGPSLLVMLVLGLVPTVAAINLALKNRVLRYPDS--DYV-WLRNLERLMSDRRF 64 +L Y + P+++V+ + P + A ++ L P S Y+ W + F Sbjct: 5 TLKYFLVLPAVVVVFATAIWPLIEAARMSFTVGRLNRPGSLEQYIGWENYAWAFFEEPAF 64 Query: 65 LNAIEVSAVWEVVTVLGAVIVGIAIAVYLFENVHGKWRQAMCVLLITPVLLPRVSAAFIW 124 N++ V+A++ VVTV ++ + +A+ L G+ R + LLI P + + Sbjct: 65 WNSVYVTALYTVVTVGLTTLLALGLALLLAPG--GRLRVSAQTLLILPFAMSPALIGVSF 122 Query: 125 KFMYSPLTGILGWLLGLV--GIHDTAFLSDPALALYAVALVDIWQWGLFFAVIVLKLLET 182 +FM++P G+ G++ + D ++L+DP LA V + D+W W F ++++ L + Sbjct: 123 RFMFNPEFGLFDAFFGVMIPPLADVSWLADPTLAFAVVVMADVWGWIPFLTLVLIGGLAS 182 Query: 183 LPPEPLEAARLDYARTWQVYAYIALPMLKGPLISLVFI-KMVESLRSFDLIYVMTKGGPG 241 +P + +EAA++D A +W+V+ + LP L GP++++V I K + SL++FD ++++T GGPG Sbjct: 183 VPRDTIEAAQVDGASSWRVFRDVTLPQL-GPVLAVVIILKSIFSLKTFDQVFMLTNGGPG 241 Query: 242 VATETLDMYAYAQGIGLSGKVSYASTMAVLMMI 274 AT+TL Y Y G+ G++ Y++++A LM+I Sbjct: 242 TATQTLSHYIYFNGMKY-GQIGYSASVAWLMVI 273 Lambda K H 0.328 0.141 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: 267 Number of extensions: 11 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: 292 Length of database: 290 Length adjustment: 26 Effective length of query: 266 Effective length of database: 264 Effective search space: 70224 Effective search space used: 70224 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: 48 (23.1 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