Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate WP_027667634.1 RL_RS14045 ABC transporter permease
Query= uniprot:D8J112 (347 letters) >NCBI__GCF_000009265.1:WP_027667634.1 Length = 326 Score = 219 bits (559), Expect = 6e-62 Identities = 122/304 (40%), Positives = 186/304 (61%), Gaps = 9/304 (2%) Query: 43 LLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTMMTFCAV 102 LL + +F S ++ F+ V N ++IL V G++A+ T+VI+ GIDLSVG+ + + Sbjct: 30 LLALCVFLSLSTDTFLSVRNGLNILDQITVLGIMAVGMTFVILIGGIDLSVGSALALAMM 89 Query: 103 MAGVVLTNWGMPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMMLLKGLS-LV 161 + G G+PLP+GI A+ +SG I G+++ + +VP FIATL MM +G++ ++ Sbjct: 90 VMGWTANVAGLPLPVGIVFALVASGVSGLIVGLLVTQFRVPAFIATLAMMSAARGVANMI 149 Query: 162 ISGTRPIYFNDTEGFSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIILNKTVFGRYT 221 G + + F D F +A D G L + V ++ V + A + L+ GR Sbjct: 150 TDGQQIVGFPDW--FMMLAIDRHFGVLTAT------VFLMLAVVLAAWLFLHFRSEGRML 201 Query: 222 FALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALGQGYELDAIA 281 +A+G N E RL+G+ V + VY S + G+AG+++A+RL+S QP+ G GYELD IA Sbjct: 202 YAVGGNPEVARLAGINVPLVTIGVYVASSVLAGLAGIVLAARLDSVQPSSGLGYELDTIA 261 Query: 282 AVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVIIILAVYLDIL 341 AVVIGGTSLSGG G I GT+IG I+ VL NGL +++V+ Q V+ G++I+LAV + + Sbjct: 262 AVVIGGTSLSGGAGGIGGTLIGVLIIGVLRNGLNLLNVSPFLQQVIIGIVIVLAVGAETI 321 Query: 342 RRRR 345 RRRR Sbjct: 322 RRRR 325 Lambda K H 0.326 0.139 0.398 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: 262 Number of extensions: 14 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: 347 Length of database: 326 Length adjustment: 28 Effective length of query: 319 Effective length of database: 298 Effective search space: 95062 Effective search space used: 95062 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: 49 (23.5 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