Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate AO353_21715 AO353_21715 amino acid ABC transporter permease
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21715 Length = 220 Score = 85.1 bits (209), Expect = 2e-21 Identities = 51/157 (32%), Positives = 88/157 (56%), Gaps = 9/157 (5%) Query: 215 VTVLMLLTQLSWPQQLQPGQIRGGLRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAG 274 + VL+LL + P G+RL + + ++ L Y GA++TE+ RGG+LS+P G Sbjct: 69 ILVLILLIYFALPSL--------GIRLD-KLPSFIITLSLYAGAYLTEVFRGGLLSIPKG 119 Query: 275 QWEAAAALGLTRSQTLWQIVVPQALRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQT 334 EA A+GL Q + VP LR ++P+L++ ++ K++SLA A+ P+L A+ Sbjct: 120 LREAGLAIGLGEWQVKAYVTVPVMLRNVLPALSNNFISLFKDTSLAAAIAVPELTYYARK 179 Query: 335 TLNQTGRPVEVFLILMLTYLAINAVISAGMNGLQQRL 371 ++ R +E +L+ Y+A +I+ + L+QRL Sbjct: 180 INVESYRVIETWLVTTALYVAACYLIAMLLRYLEQRL 216 Score = 47.0 bits (110), Expect = 5e-10 Identities = 30/77 (38%), Positives = 44/77 (57%), Gaps = 4/77 (5%) Query: 69 AIAYRTADSYARALVVGLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAV 128 A +R D+ L +GL +L IAIG VIG L A S++ LR L+ YV V Sbjct: 8 AAVWRDFDTLLAGLGLGLELALVSIAIGC----VIGLLMAFALLSKHRALRVLASVYVTV 63 Query: 129 VRNTPLLLQLIVWYFPI 145 +RNTP+L+ +++ YF + Sbjct: 64 IRNTPILVLILLIYFAL 80 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: 245 Number of extensions: 16 Number of successful extensions: 3 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: 220 Length adjustment: 26 Effective length of query: 351 Effective length of database: 194 Effective search space: 68094 Effective search space used: 68094 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: 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