Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate SM_b20235 SM_b20235 sugar ABC transporter ATP-binding protein
Query= uniprot:A0A165KQ08 (355 letters) >FitnessBrowser__Smeli:SM_b20235 Length = 363 Score = 357 bits (916), Expect = e-103 Identities = 181/353 (51%), Positives = 250/353 (70%), Gaps = 5/353 (1%) Query: 3 SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62 +S++I + KRFG ++EV+ V +A GEF+ LVGPSGCGKSTLL +IAGL+E ++ Sbjct: 2 ASVEIRNVVKRFG----ALEVVHGVSAEIADGEFVALVGPSGCGKSTLLRMIAGLEEISD 57 Query: 63 GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122 G + IGG V + P+DR+I+MVFQ+YALYP ++VA+N+ FAL + ++PK E+++++ E Sbjct: 58 GAVVIGGDIVNEVAPKDRNISMVFQNYALYPHMTVAENMAFALRLARLPKDEQKRKVGEA 117 Query: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182 A ML + LLDR P QLSGGQRQRVAMGRA+ R+P++FLFDEPLSNLDAKLRV+MRAEIK Sbjct: 118 ATMLGLGGLLDRYPGQLSGGQRQRVAMGRAIVRRPEVFLFDEPLSNLDAKLRVQMRAEIK 177 Query: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242 LHQ TS+YVTHDQ+EAMT+ RI VM+ G V+Q+GTP EI++ P N +VA+FIGSP Sbjct: 178 GLHQRLRTTSIYVTHDQIEAMTMADRIVVMRDGNVEQIGTPLEIFDYPRNLFVASFIGSP 237 Query: 243 TMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVEPT 302 +MN + G V GG F G + AP + + G+RP L + T P +V +VEPT Sbjct: 238 SMNFIEGEVVGGTFRAPGGIIIPAPDLAHKGPTVAGIRPNKLQIGATGP-SAKVLIVEPT 296 Query: 303 GPDTYVMVDTAAGSVTLRTDAQTRVQPGEHVGLALAPAHAHWFDAQSEERLVA 355 G +T+++V+ + + +T + PG+ +GLA A A H+FD Q+ RL A Sbjct: 297 GDETHLLVELGGAQLAMLLRERTSLAPGDEIGLAFASADVHFFDGQTTLRLGA 349 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: 403 Number of extensions: 13 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