Align ABC-type permease for basic amino acids and glutamine (characterized, see rationale)
to candidate PP_4749 PP_4749 Amino acid ABC transporter, permease protein
Query= uniprot:Q31RP0 (377 letters) >FitnessBrowser__Putida:PP_4749 Length = 219 Score = 83.6 bits (205), Expect = 5e-21 Identities = 68/193 (35%), Positives = 98/193 (50%), Gaps = 11/193 (5%) Query: 180 LVVILAIALVLFVSWLAQRQRSPRDWRWL-YGAIAVVTVLMLLTQLSWPQQLQPGQIRGG 238 L V+L + L L VS SP RWL Y ++ VV + L Q G Sbjct: 32 LGVVLGLLLALGVS-------SPS--RWLRYPSLVVVELGRGAPALILLQYFYFGLPSVN 82 Query: 239 LRLSLEFTALLLGLVAYTGAFITEIIRGGILSVPAGQWEAAAALGLTRSQTLWQIVVPQA 298 L L+ F A L + T A+ +EIIRGGI SV AGQ EAA +GL R L +++PQA Sbjct: 83 LTLT-SFWAAALAMAYCTAAYTSEIIRGGIESVAAGQTEAAEVIGLNRFDALRFVILPQA 141 Query: 299 LRVIVPSLNSQYVGFAKNSSLAIAVGYPDLYATAQTTLNQTGRPVEVFLILMLTYLAINA 358 LRV +PSL + + SSL + P++ + A + + T + V ++ L Y A+ A Sbjct: 142 LRVALPSLLGFSIMMFQASSLCFTIALPEIVSRASSIGSSTFEYMPVLILAGLMYAAVCA 201 Query: 359 VISAGMNGLQQRL 371 + G+ L++RL Sbjct: 202 PATLGVAALEKRL 214 Score = 32.0 bits (71), Expect = 2e-05 Identities = 21/59 (35%), Positives = 30/59 (50%) Query: 85 GLVNSLRVIAIGLILTTVIGTLAGVAAFSENWLLRQLSRGYVAVVRNTPLLLQLIVWYF 143 G V S++V A+ L L V+G L + S + LR S V + R P L+ L +YF Sbjct: 18 GFVLSMQVTAVSLGLGVVLGLLLALGVSSPSRWLRYPSLVVVELGRGAPALILLQYFYF 76 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: 235 Number of extensions: 10 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: 219 Length adjustment: 26 Effective length of query: 351 Effective length of database: 193 Effective search space: 67743 Effective search space used: 67743 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