GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pseudomonas fluorescens GW456-L13

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate PfGW456L13_1799 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)

Query= uniprot:A8LLL2
         (373 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1799
          Length = 351

 Score =  244 bits (622), Expect = 3e-69
 Identities = 140/313 (44%), Positives = 194/313 (61%), Gaps = 11/313 (3%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           M+ L L  VEK YG    + ++NL + +G+L+ F+GPSGCGK+TLLRMIAGLE ++GG +
Sbjct: 1   MSGLILENVEKHYGSACAVKDVNLHLPEGKLVCFLGPSGCGKTTLLRMIAGLETLSGGEI 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
            +DG  +   P   R   MVFQS AL+PHMTV EN+++ LK+   S+A+  A V    E 
Sbjct: 61  RLDGEDIGHTPAHLRNFGMVFQSLALFPHMTVGENIAYPLKLRGVSKADQQARVVELLEL 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           +QL   ++R    LSGGQRQRVAI R+I   PK+ L DEPLS LDA LR + ++EI QL+
Sbjct: 121 IQLQAMINRPVAKLSGGQRQRVAIARAIANHPKILLLDEPLSALDAKLRESMQVEIRQLQ 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +   T + VTHDQ EAMT+A  +VVL    + QVG+P+E+Y  P NEFVA FIGS   
Sbjct: 181 QRL-NITTIMVTHDQREAMTMADIVVVLGEHKVQQVGTPIEIYRHPANEFVADFIGSG-- 237

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAP---GGDY 297
           N+ P  ++G G  +      GG A+        ++G  V + +RPED+  +AP    G+ 
Sbjct: 238 NIFPATVLGNGKVS----LPGGDALQVPICSSIVVGEKVKMLIRPEDLQLSAPQATAGNR 293

Query: 298 VFEGKVAITEALG 310
           +  GKV     +G
Sbjct: 294 LL-GKVTFVRDIG 305


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: 364
Number of extensions: 17
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: 351
Length adjustment: 29
Effective length of query: 344
Effective length of database: 322
Effective search space:   110768
Effective search space used:   110768
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