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_2941 Various polyols ABC transporter, ATP-binding component

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2941
          Length = 350

 Score =  333 bits (855), Expect = 3e-96
 Identities = 193/355 (54%), Positives = 238/355 (67%), Gaps = 18/355 (5%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA L+L G+EK +G+ + +  I+L IQQGE IVFVGPSGCGKSTLLR+IAGLE I GG+L
Sbjct: 1   MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            +DG  + D P ++R +AMVFQSYALYPHM+V ENMSFALK+AK  +  ID  V+ AA  
Sbjct: 61  MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L L QYL R PK LSGGQRQRVAIGR+IVR PKV+LFDEPLSNLDAALR  TR+EIA+L 
Sbjct: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
             +  +T +YVTHDQVEAMTLA R+VVL  G I QVG+PLELY+KP N+FVAQFIG+P+M
Sbjct: 181 RDL-GATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300
           N++P   +    Q        G AV          GA   +G+RPE++     G   V  
Sbjct: 240 NVVPVDKLPQPVQQQAPAAPAGAAV----------GA---IGLRPENITVRTTGATPV-G 285

Query: 301 GKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLK-GQVTRLTAEPAKVHVF 354
           G+V + EALG  TL+Y   P G        Q    DL+ G    L  + ++ H F
Sbjct: 286 GQVDLIEALGAETLIYVTTPGGAQ--FVSRQNDRTDLRVGDAVSLDIDASQAHWF 338


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: 442
Number of extensions: 23
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: 350
Length adjustment: 29
Effective length of query: 344
Effective length of database: 321
Effective search space:   110424
Effective search space used:   110424
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.

Links

Downloads

Related tools

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