Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF1915 PGA1_c19470 ABC transporter, ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Phaeo:GFF1915 Length = 363 Score = 340 bits (872), Expect = 3e-98 Identities = 181/359 (50%), Positives = 234/359 (65%), Gaps = 10/359 (2%) Query: 1 MASSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEP 60 M S + ++ RFG +VEVL+ +++ + GEFL+L+G SGCGKSTLLN IAGL E Sbjct: 9 MTSHVSARDLSVRFG----AVEVLKSLNLDIQKGEFLVLLGASGCGKSTLLNTIAGLQEA 64 Query: 61 TEGEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRID 120 TEG+I I +NV P+DR +AMVFQSYALYP ++V N+ F L M K+PK E K +D Sbjct: 65 TEGQIWINDENVTWREPKDRGLAMVFQSYALYPKMTVRGNLAFGLRMNKVPKAEADKLVD 124 Query: 121 EVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAE 180 E A +LQ+ LLDRRP +LSGGQRQRVA+GRAL R+ +FLFDEPLSNLDAKLR E+R E Sbjct: 125 EAARVLQLEELLDRRPGELSGGQRQRVAIGRALVRKVDVFLFDEPLSNLDAKLRAELRVE 184 Query: 181 IKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIG 240 +KRLHQ G T +YVTHDQVEA+TL RIAVMK GVVQQL +P+EIY RPAN YVA F+G Sbjct: 185 LKRLHQELGATMIYVTHDQVEALTLADRIAVMKDGVVQQLDSPEEIYRRPANRYVAQFVG 244 Query: 241 SPTMNLLRGAVTGG------QFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRG 294 P+MN + G VT F + NLA P+ EV +G+RPEH+ + Sbjct: 245 LPSMNFVNGVVTESGAIQTEDFELALDQCNLASTPAPGTEVEIGIRPEHVHPANAGGFML 304 Query: 295 RVSVVEPTGPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERL 353 V +VE G + + S+ +R D T ++ G+ V + L P F A++ R+ Sbjct: 305 DVGMVELLGSERLIWGKVGNTSIVMRDDPDTTIRSGDQVRINLKPGAFSVFSAKTGLRI 363 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: 355 Number of extensions: 12 Number of successful extensions: 2 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: 363 Length adjustment: 29 Effective length of query: 326 Effective length of database: 334 Effective search space: 108884 Effective search space used: 108884 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