GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pseudomonas fluorescens FW300-N2C3

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate AO356_27685 AO356_27685 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27685
          Length = 367

 Score =  335 bits (859), Expect = 1e-96
 Identities = 182/362 (50%), Positives = 252/362 (69%), Gaps = 5/362 (1%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           MA+LK+  ++K +    ++  I+L++   E +VFVGPSGCGKSTLLR+IAGLE+++ GT+
Sbjct: 1   MANLKIKNLQKGFEGFSIIKGIDLEVNDREFVVFVGPSGCGKSTLLRLIAGLEEVSDGTI 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
           E+DG  + +V PA+R +AMVFQ+YALYPHM+VR+NMSFAL +A   +AE++  V  AA  
Sbjct: 61  ELDGRDITEVSPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVPKAEVEKKVNEAARI 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           L+LG  L+R PK LSGGQRQRVAIGR+IVR+PK++LFDEPLSNLDAALRV  RLE+A+L 
Sbjct: 121 LELGPMLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLH 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + + ++TM+YVTHDQVEAMTLA ++VVL GG I QVGSPLELY +P N FVA F+G+PKM
Sbjct: 181 KEL-QATMIYVTHDQVEAMTLADKVVVLNGGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSL-MGAAVNVGVRPEDMVEAAPGGDYVF 299
             L GK+    +Q    + D G  ++   S  +L +G AV +G+RPE +  A P GD   
Sbjct: 240 GFLKGKVTALDSQGCEVLLDAGTRINLPRSGANLSVGGAVTLGIRPEHLNLAQP-GDCTL 298

Query: 300 EGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF-KDGV 358
           +    ++E LG  T  +    SGE  T+ +++G      G+   L  +    H+F  +GV
Sbjct: 299 QVTADVSERLGSDTFCHVVTTSGEALTM-RVRGDLASRFGEQLNLHLDAEHCHLFDAEGV 357

Query: 359 SL 360
           ++
Sbjct: 358 AV 359


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: 418
Number of extensions: 20
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: 367
Length adjustment: 30
Effective length of query: 343
Effective length of database: 337
Effective search space:   115591
Effective search space used:   115591
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