Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Putida:PP_1484 Length = 343 Score = 225 bits (574), Expect = 1e-63 Identities = 114/281 (40%), Positives = 180/281 (64%), Gaps = 12/281 (4%) Query: 1 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60 M ++ +++ FG+ V+ + +V I + GEF ++GPSG GK+T L +IAG ++P Sbjct: 1 MPLAVQFTQVSRTFGE----VKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQP 56 Query: 61 TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120 + G IRI G G+PP RD+ VFQ YAL+P ++V +NI + L+++ + K ER R + Sbjct: 57 SSGSIRIQGVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVKGVGKAERHSRAE 116 Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 E AM+ ++ R+P+QLSGGQRQRVA+ RAL +P++ L DEPL LD KLR +M+ E Sbjct: 117 EALAMVALAGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGE 176 Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 +K+L + GIT ++VTHDQ EA+++ R+AV G ++Q+ TP +Y +P+ T+VA F+G Sbjct: 177 LKKLQRQLGITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVG 236 Query: 241 SPTMNLLRGAV------TGGQFGIQGAALNLAPPPSSANEV 275 T N++RG + + F I+ + L P +++EV Sbjct: 237 --TSNVVRGELAMQINGSPAPFSIRPELIRLGDPVVTSHEV 275 Lambda K H 0.318 0.135 0.388 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: 302 Number of extensions: 13 Number of successful extensions: 1 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: 355 Length of database: 343 Length adjustment: 29 Effective length of query: 326 Effective length of database: 314 Effective search space: 102364 Effective search space used: 102364 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (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