GapMind for catabolism of small carbon sources

 

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

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate Ac3H11_2066 SN-glycerol-3-phosphate transport ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2066
          Length = 355

 Score =  267 bits (682), Expect = 4e-76
 Identities = 153/327 (46%), Positives = 209/327 (63%), Gaps = 20/327 (6%)

Query: 2   ADLKLTGVEKAYG----DVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITG 57
           + L + G+ K +G     V+VL  +++ +  GE ++ VGPSGCGKSTLL +IAGL++ T 
Sbjct: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62

Query: 58  GTLEIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAA 117
           G + I G  V  +PP  R IAMVFQSYALYP ++V +N+ FAL++ K  + E    ++  
Sbjct: 63  GEIRIGGKNVVGMPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKRIDEV 122

Query: 118 AEKLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIA 177
           A  LQ+   LDR P  LSGGQRQRVA+GR++ R P+++LFDEPLSNLDA LRV  R EI 
Sbjct: 123 AAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMRAEIK 182

Query: 178 QLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGS 237
           +L +A    T VYVTHDQVEAMTL +RI V+ GG + Q+G+P E+Y +P N +VA FIGS
Sbjct: 183 RLHQA-SGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATFIGS 241

Query: 238 PKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMV--EAAPGG 295
           P MNLL G +  TG Q  ++    G A++  P   S     V +GVRPE +V  E AP  
Sbjct: 242 PTMNLLRGAV--TGGQFGIQ----GAALNLAPPPSS--ANEVLLGVRPEHLVMQETAP-- 291

Query: 296 DYVFEGKVAITEALGEVTLLYFEAPSG 322
              + G+V++ E  G  T +  +  +G
Sbjct: 292 ---WRGRVSVVEPTGPDTYVMVDTAAG 315


Lambda     K      H
   0.316    0.135    0.379 

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: 359
Number of extensions: 15
Number of successful extensions: 3
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: 373
Length of database: 355
Length adjustment: 29
Effective length of query: 344
Effective length of database: 326
Effective search space:   112144
Effective search space used:   112144
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 (21.6 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