GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Sinorhizobium meliloti 1021

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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