Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate WP_049991587.1 LT39_RS16410 sugar ABC transporter permease
Query= reanno::Smeli:SMc03062 (336 letters) >NCBI__GCF_000784335.1:WP_049991587.1 Length = 319 Score = 111 bits (278), Expect = 2e-29 Identities = 84/287 (29%), Positives = 141/287 (49%), Gaps = 25/287 (8%) Query: 45 RNLRIANSIRPWLFLAPALLALTLYLVYPVVQSVWLSLHGRGG------QNFVGLSNYSW 98 R SI WL P L + L++ + +V +SL G G NF L Y Sbjct: 36 RRSDFVESIPFWL---PPTLLVLLFVYGAIGWNVVISLTGWSGLGQPEYTNF-SLEMYRQ 91 Query: 99 MINDGEFRQSIFNNFLWLLVVPALSTFFGLIIAALTDR-IWWGNIAKTLIFMPMAISFVG 157 + D FR ++ N L+ +S GL +A L DR I + N +T+ +PMA+SFV Sbjct: 92 LPADQNFRAALRNTVALLVGFTGVSLLVGLGLALLVDRKIRFENTFRTIYLLPMALSFVV 151 Query: 158 AAVIWKFIYDYRAAGSEQIGLLNAIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAM 217 A+ W ++Y GL+NA++ W+ P ++ L+W +G+ M Sbjct: 152 TAIFWSWMYASN-------GLINAVLPI----SPDWLGNPRLKLAAVIFALVWQFSGYCM 200 Query: 218 VILSAALRGIPEETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVL 277 ++ A LR IP++ EAA IDGA+ ++++++++PQ+ + + + LK FD + Sbjct: 201 IVYLAGLRSIPDDHYEAARIDGASTLKLYWRVIIPQLRSSTVGATVVLMVFALKAFDFIY 260 Query: 278 AM--TNGQWQSQVLANLMFDWMFRGGGDFGRGAAIAVVIMILVVPIM 322 M TN +LA +M+ F ++ GAA+AVV+ +L + I+ Sbjct: 261 VMFGTNPGRSVDILAVMMYREAF-SAAEWAYGAAVAVVLFLLALTII 306 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: 308 Number of extensions: 11 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: 336 Length of database: 319 Length adjustment: 28 Effective length of query: 308 Effective length of database: 291 Effective search space: 89628 Effective search space used: 89628 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 24 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