Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate GFF3700 PS417_18935 amino acid ABC transporter ATPase
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__WCS417:GFF3700 Length = 505 Score = 89.7 bits (221), Expect = 2e-22 Identities = 60/172 (34%), Positives = 94/172 (54%), Gaps = 10/172 (5%) Query: 203 RDWRWLYGAIAVVTVLMLLTQLSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITE 262 R + WL+ ++ ++ +L+ + L PQ L PG L+ F + LL LV A++ E Sbjct: 58 RGYIWLFRSLPLLVLLIFIYNL--PQAL-PGT---SAILADPFWSGLLALVICETAYVAE 111 Query: 263 IIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIA 322 I RGG+LS+P GQ EAA ALGL T W++V+PQALRV +PSL ++Y+ K +SL Sbjct: 112 IHRGGLLSIPKGQAEAARALGLKFFGTQWRVVIPQALRVALPSLANEYISIVKLTSLVSV 171 Query: 323 VGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRLQRW 374 + ++ Q +Q +E + Y+ I V + L +RL+R+ Sbjct: 172 ISLTEILMVGQRLYSQNFLVIETMAAVAFFYVFIVTV----FDFLLKRLERF 219 Score = 31.2 bits (69), Expect = 7e-05 Identities = 17/53 (32%), Positives = 31/53 (58%) Query: 90 LRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWY 142 +++ + +L+ +G L +A S + LL +RGY+ + R+ PLL+ LI Y Sbjct: 25 IKLSTLTWVLSIGLGFLLALAKQSRHGLLSVPARGYIWLFRSLPLLVLLIFIY 77 Lambda K H 0.326 0.140 0.445 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: 398 Number of extensions: 19 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 505 Length adjustment: 32 Effective length of query: 345 Effective length of database: 473 Effective search space: 163185 Effective search space used: 163185 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: 51 (24.3 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