Align ABC transporter for D-Glucosamine, permease component 2 (characterized)
to candidate GFF773 PGA1_c07870 alpha-glucoside transport system permease protein AglF
Query= reanno::Smeli:SM_b21220 (293 letters) >FitnessBrowser__Phaeo:GFF773 Length = 335 Score = 132 bits (331), Expect = 1e-35 Identities = 88/273 (32%), Positives = 141/273 (51%), Gaps = 11/273 (4%) Query: 9 RAWLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRAL 68 R WL + P L+ + + +P+V+T+RLS T+ ++ G FVG ANY +ML + F AL Sbjct: 52 RPWLFLFPALLALGLYLAYPVVETLRLSVTE-RVPGGGSEFVGLANYQQMLAEAKFWEAL 110 Query: 69 VTTTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNP 128 + ++ AA G+LAA L ++ G A ++L+ +P A+ V A +W+L+Y+ Sbjct: 111 QNNFLWLLVVPAASTAFGLLAAQLTDRLAWGNIA-KSLIFMPMAISFVGAAVIWKLVYDA 169 Query: 129 ------EYGALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQA 182 + G LNA G D WL P L++ W +I AAL+ Sbjct: 170 RPEGTDQIGVLNALYIYFGG-DGPMQWLTIPFWNSFFLMMVLIWIQTGFAMVILSAALRG 228 Query: 183 VPRDITAASLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPAN 242 +P + A++VDGAGPF F + +P + ++V TI KVFDI++ MT G Sbjct: 229 IPEETVEAAIVDGAGPFQIFFKIKVPQIMDTIVVVWTTITIVVLKVFDIVFAMTNG--QW 286 Query: 243 STRTLSILVYQEAFSFQRAGSGASLALIVTLLV 275 T+ L+ +Y + F G G++ A+++ LLV Sbjct: 287 ETQVLANYMYDKLFRANDWGVGSASAMVIMLLV 319 Lambda K H 0.326 0.138 0.417 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: 253 Number of extensions: 15 Number of successful extensions: 4 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: 293 Length of database: 335 Length adjustment: 27 Effective length of query: 266 Effective length of database: 308 Effective search space: 81928 Effective search space used: 81928 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: 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