GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Acidovorax sp. GW101-3H11

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Ac3H11_1002 ABC transporter ATP-binding protein

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1002
          Length = 356

 Score =  231 bits (588), Expect = 3e-65
 Identities = 126/344 (36%), Positives = 205/344 (59%), Gaps = 14/344 (4%)

Query: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62
           ++++I  + KR+  G  +V+    +++ +A G +  L+GPSGCGKST L +IAG +  T 
Sbjct: 11  AAIEIVALTKRYASGKPAVDA---INLRIASGSYCCLLGPSGCGKSTTLRMIAGHESVTS 67

Query: 63  GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122
           G+I +  +N+  +P   R  AM+FQS+AL+P LS  DN+ F+L+M+ +PK ERQ +  ++
Sbjct: 68  GDILLENRNITDLPAAARGTAMMFQSFALFPHLSALDNVAFSLKMKGVPKAERQAKARDL 127

Query: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182
              + + HL +R+P++LSGGQ+QRVA+ RAL  QP++ L DEPLS LD  LR++MRAE++
Sbjct: 128 LERVALGHLAERKPAELSGGQQQRVALARALITQPRVLLLDEPLSALDPFLRIQMRAELR 187

Query: 183 RLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGSP 242
           R  +  G+T ++VTH Q EAM L   + VM  GV++Q+G+P E+YNRPA+ +VA F+G  
Sbjct: 188 RWQKELGLTFIHVTHSQEEAMALADTMVVMNHGVIEQVGSPHEVYNRPASEFVARFMGGH 247

Query: 243 TMNLLRGAVTGGQFGIQGAALNLAPPPSSANEVLLGVRPEHLVMQETAPWRGRVSVVEPT 302
            +         G+ G++   L +AP   ++ E+  G +   L +     ++G   ++   
Sbjct: 248 NVI----DTPEGKVGVRTDHLQIAP---ASAELPWGAQ-RMLAVVTDVEYQGTYVLLGLQ 299

Query: 303 GPDTYVMVDTAAGSVTLRTDAQTRVQP---GEHVGLALAPAHAH 343
                +  +  A    + ++A    QP   G+ V L   P  AH
Sbjct: 300 KQGVALSANATAAYSVMVSEAAFAAQPYRVGQGVQLHWTPDQAH 343


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: 289
Number of extensions: 12
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: 356
Length adjustment: 29
Effective length of query: 326
Effective length of database: 327
Effective search space:   106602
Effective search space used:   106602
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