Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate GFF851 Psest_0865 ABC-type maltose transport systems, permease component
Query= uniprot:A3DHA2 (303 letters) >FitnessBrowser__psRCH2:GFF851 Length = 296 Score = 79.0 bits (193), Expect = 1e-19 Identities = 75/297 (25%), Positives = 133/297 (44%), Gaps = 24/297 (8%) Query: 20 KLKRFGVYVILIVITVVLLFPILFTIANSFMSDKEVLDTYQKKIEEVEEGESTEFLGFKL 79 + + + + L+ +LFP+L I+ SF + + +E + + Sbjct: 10 RYRLWATHAALLAFVAAILFPLLMVISISFREGNFATGSLFPENPTLEHWSLALGIPYTH 69 Query: 80 IPDMVSMKQYYTVLFRKPTFLLMFLNSAIMTIPIVIIQVIVGVFAAYAFAKLRFPLRDKL 139 V+ + +L+ + + F++S I+ +++ +AYAFA++RF + + Sbjct: 70 ADGSVTQPPFPVLLWLWNSVKIAFVSS--------ILILLLSTTSAYAFARMRFGGKAPI 121 Query: 140 FFVFIVVMLMPLQVTLVPNYILLRKLDMIGSFLSVILPG-------GFSAFGVVLLRQYM 192 ++ + P ++LV Y L +L S+L V G G A + ++ Y Sbjct: 122 LKSMLIFQMFPPVLSLVAIYALFDQLGQHVSWLGVNSHGAVIVASLGGMALHIWTIKGYF 181 Query: 193 RGIPDECCEAAMIDGAGYLKTFTKIILPQCKSIIASLAILAFIDNWNMVEQPL--IFLSD 250 I EAA++DGA + F I+LP I+A + ILAFI ++ E P+ + L D Sbjct: 182 ESIDASLEEAAIVDGATTWQAFFHILLPMSVPILAVVFILAFIT--SVTEYPIASVLLMD 239 Query: 251 SAKYPLSV----YLAYINEGDLGLAFASGVLYMIPTVLIYLYGEKYFVEGIQLTGIK 303 K LSV YL Y G A+ VL +P ++LY +K+ V G+ G+K Sbjct: 240 VDKLTLSVGAQQYL-YPQNYLWGDFAAAAVLSGLPITAVFLYCQKWIVGGLTAGGVK 295 Lambda K H 0.331 0.147 0.425 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: 163 Number of extensions: 7 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: 303 Length of database: 296 Length adjustment: 27 Effective length of query: 276 Effective length of database: 269 Effective search space: 74244 Effective search space used: 74244 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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