Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate SMc01497 SMc01497 sorbitol/mannitol transport inner membrane transmembrane protein
Query= reanno::Smeli:SMc03062 (336 letters) >FitnessBrowser__Smeli:SMc01497 Length = 290 Score = 97.4 bits (241), Expect = 4e-25 Identities = 85/275 (30%), Positives = 136/275 (49%), Gaps = 23/275 (8%) Query: 57 LFLAPALLALTLYLVYPVVQSVWLSLHGR-----GGQNFVGLSNYSWMINDGEFRQSIFN 111 L +AP++L L +++ P+ +++ SL G + F GL+NY++ + D F Q+IFN Sbjct: 12 LMIAPSVLLLLAWMIVPLAMTIYFSLLRYNLLMPGMEEFAGLTNYTYFLTDPAFFQAIFN 71 Query: 112 NFLWLLVVPALSTFFGLIIAALTDRIWWGN-IAKTLIFMPMAISFVGAAVIWKFIYDYRA 170 +L V ++ G+ +A L D+ +G I + L+ P I AA++WK ++ Sbjct: 72 TLAIVLGVLFITVVGGIGLALLLDQPMFGQGIVRILVIAPFLIMPTVAALVWKNMFM--- 128 Query: 171 AGSEQIGLLNAIVVALGGEPQAWITLPFWNNFFLMVILI--WIQTGFAMVILSAALRGIP 228 + GL + LG +P ++ N L +ILI W FA +IL AL+ + Sbjct: 129 --NPVNGLFAWLAKLLGLQPFDFLA----NAPLLSIILIVAWQWLPFATLILLTALQSLD 182 Query: 229 EETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVLAMTNG--QWQS 286 EE EAA +DGA F +++P + I +V TI +L VF +L TNG QS Sbjct: 183 EEQKEAAQMDGAGAVSRFIYLVLPHLSRAITMVILIQTIFLLSVFAEILVTTNGGPGTQS 242 Query: 287 QVLANLMFD---WMFRGGGDFGRGAAIAVVIMILV 318 L L++ F GG G IAV++ +V Sbjct: 243 TNLTFLVYAQALLQFDVGG-ASAGGIIAVILANIV 276 Lambda K H 0.330 0.142 0.466 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: 274 Number of extensions: 15 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: 336 Length of database: 290 Length adjustment: 27 Effective length of query: 309 Effective length of database: 263 Effective search space: 81267 Effective search space used: 81267 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: 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