Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3279 PS417_16785 ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__WCS417:GFF3279 Length = 349 Score = 124 bits (312), Expect = 3e-33 Identities = 104/345 (30%), Positives = 165/345 (47%), Gaps = 53/345 (15%) Query: 12 AVALLVLPLILQSFGNA-WVRIADLALLYVLLA-LGLNIVVGYAGLLDLGYVAFYAVGAY 69 A+A +V+PL +GN W+ + L + LA LGLN++ GY G +G F AVGA+ Sbjct: 28 ALAFIVVPL----WGNDYWLNAILIPFLVLSLAGLGLNLLTGYTGQTSVGAAGFMAVGAF 83 Query: 70 LFA--LMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAAL----LAAFFGAMLGAPTLKL 123 L+ P L +PVA L ++A G + G P+ ++ Sbjct: 84 ATYGFLLRLPELG---------------------LPVALLGGGIISALVGLLFGLPSSRI 122 Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI 183 +G YL + TL + FL L G I + K L +FG D+ Sbjct: 123 KGFYLMVTTLA----AQFFLEWLFVKFPWFYNYGSSGTISAPK---------LALFGHDL 169 Query: 184 NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGM 243 N+ Y L LV V++ L S++GR WMAIR+ + AA +GI K LAF + Sbjct: 170 NTPLGRYLLTLVTVLLLTWTAINLVRSQVGRNWMAIRDMDTAAAVVGIPVVRYKRLAFAV 229 Query: 244 GASFGGVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPE 302 + + G++GA++ A+ G S SF + S I+ ++++GG+G I G +GA +S LP Sbjct: 230 SSFYLGIAGALWAFAYLGTASASSFDINRSFQILFIIIIGGMGSIAGNFVGAAFISLLPI 289 Query: 303 VLRYVAGPLQAMTDGRLDSAILRQL---LIALAMIIIMLLRPRGL 344 L + QA+ G +D+ L+ L + + +I+ ++ P GL Sbjct: 290 FLSHAG---QALFGGSVDAGQLQNLQKIIFGVLIIVFLIKEPEGL 331 Lambda K H 0.328 0.144 0.430 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: 297 Number of extensions: 13 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: 358 Length of database: 349 Length adjustment: 29 Effective length of query: 329 Effective length of database: 320 Effective search space: 105280 Effective search space used: 105280 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 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