Align Extracellular solute-binding protein, family 3 (characterized, see rationale)
to candidate 209037 DVU0107 glutamine ABC transporter, periplasmic glutamine-binding protein
Query= uniprot:E4PNW5 (250 letters) >MicrobesOnline__882:209037 Length = 249 Score = 115 bits (287), Expect = 1e-30 Identities = 76/238 (31%), Positives = 128/238 (53%), Gaps = 7/238 (2%) Query: 12 LALIAG-GAQAQERDLRIAFDVPYEPFEYKDENGELTGFEVELAEAMCEEMNANCEFVIQ 70 LAL+ G A A + L +A D ++PFE+K E+G+ TGF++EL +A+ + + + Sbjct: 11 LALVLGLAATASAKQLVVAHDTNFKPFEFKGEDGKYTGFDIELWQAIAKIAGVDYKLQPM 70 Query: 71 AWDGMIPGLLARKFDLIMSSMSITPERAERVLFSEPYYNTPGGWFGPESFNTDVTDMSAM 130 ++G+IPGL D+ ++ ++I PERA V FS+PYY++ G T + + + Sbjct: 71 DFNGIIPGLQTGNVDVGIAGITIKPERAAVVDFSDPYYDS-GLMILVRENETGIKAVEDL 129 Query: 131 EGKTVGVQRGTTMDTYVTENMGGIVTIKRYTTADDMVLDLEGQRLDVVFVDYPVGEQTVL 190 GK V V+ T+ ++ ++ G +K + D M +L D V D PV ++ + Sbjct: 130 AGKIVAVKTATSSVDFM-KSFGKAKELKLFPNNDSMFFELMAGGADAVIFDMPVVKEFAM 188 Query: 191 T--KEGFKEVGEAVKLGEGVGVAMRQRDTDLAEEVNAALRTLKEDGTYDTIMQKYFAY 246 T K K VG + G+ G+ + ++L +VN AL+ LK DG+YD + K+F Y Sbjct: 189 TAGKGKVKVVGPLYQ-GQSYGIGF-PKGSELVGKVNDALKQLKADGSYDKLFVKWFGY 244 Lambda K H 0.318 0.135 0.389 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: 155 Number of extensions: 6 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: 250 Length of database: 249 Length adjustment: 24 Effective length of query: 226 Effective length of database: 225 Effective search space: 50850 Effective search space used: 50850 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 46 (22.3 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