Align ABC transporter for N-Acetyl-D-glucosamine, permease protein 2 (characterized)
to candidate 3607127 Dshi_0549 binding-protein-dependent transport systems inner membrane component (RefSeq)
Query= reanno::Smeli:SMc02871 (279 letters) >FitnessBrowser__Dino:3607127 Length = 272 Score = 129 bits (323), Expect = 9e-35 Identities = 83/265 (31%), Positives = 136/265 (51%), Gaps = 5/265 (1%) Query: 16 AALIAYTLIALFPVFLTIVNSFKSRNAIFREPLAVPTPETFSLIGYETVLKQGDFIGYFQ 75 A L+ + +FP + + S K++ P T S Y L + + Sbjct: 12 ALLVLIITVCVFPFYWMVTTSLKTQIVALEAPPVWIFEPTLS--NYREALFEDGVLRTLI 69 Query: 76 NSIIVTVVSIALVLLFGAMAAFALSEYRFRGNTLMGLYLALGIMI-PIRLGTVAILQGMV 134 NS+I+ + + L L+ G AAFAL+ + FRG + + MI PI L L Sbjct: 70 NSLIIAISTTFLALVLGVPAAFALARFEFRGKKDLWFWFITNRMISPIVLALPFFLIAR- 128 Query: 135 ATGLVNTLTALILVYTAQGLPLAVFILSEFMRTVSDDLKNAGRIDGLSEYAIFLRLVLPL 194 GL++ LIL+Y LP+ ++I+++ R + DL A R++G S++ I ++ LPL Sbjct: 129 NLGLLDKHITLILIYLTFNLPIVIWIVTDQFRGIPYDLDEAARLEGASQFTIMRKICLPL 188 Query: 195 IRPAMATVAVFTMIPIWNDLWFPLILAPAEATKTVTLGSQIFIGQFVTNWNAVLSALSLA 254 P +A A+F+ I WN+L F LIL +EA KT + F+ + + +++ +L Sbjct: 189 AMPGVAVSAIFSFIFSWNELMFGLILTRSEA-KTAPAMAVSFMEGYNLPYGKIMATSTLI 247 Query: 255 IFPVLVLYVIFSRQLIRGITAGAVK 279 + PVL+ +I S+QL+RG+T GAVK Sbjct: 248 VIPVLIFALIASKQLVRGLTMGAVK 272 Lambda K H 0.330 0.142 0.409 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: 231 Number of extensions: 15 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: 279 Length of database: 272 Length adjustment: 25 Effective length of query: 254 Effective length of database: 247 Effective search space: 62738 Effective search space used: 62738 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: 47 (22.7 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