GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglK' in Pantoea rwandensis LMG 26275

Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_084934899.1 HA51_RS12950 ABC transporter ATP-binding protein

Query= uniprot:A8LLL2
         (373 letters)



>NCBI__GCF_002095475.1:WP_084934899.1
          Length = 367

 Score =  234 bits (596), Expect = 4e-66
 Identities = 135/354 (38%), Positives = 205/354 (57%), Gaps = 11/354 (3%)

Query: 1   MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60
           M+ L L  + KA+G+   L++I+ D  +G  +  +GPSGCGKSTLLR IAGLE    G +
Sbjct: 1   MSHLSLHHITKAWGEKIALNDISFDAAEGSFVALLGPSGCGKSTLLRTIAGLETADSGEI 60

Query: 61  EIDGTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEK 120
               + +  +PP+QR ++MVFQSYAL+PH+ VREN+ F LK   + +      ++  ++ 
Sbjct: 61  HFKHSDITHLPPSQRKLSMVFQSYALFPHLNVRENLLFGLKARGEDKQTFTTRLDDVSKL 120

Query: 121 LQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLK 180
           ++L + LDRLP  LSGGQ+QRVA+GR+++ +  + L DEPLSNLDA LR + R EI  L+
Sbjct: 121 MELDKLLDRLPSQLSGGQQQRVALGRAVIANNNLCLMDEPLSNLDAKLRQSMRREIRALQ 180

Query: 181 EAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKM 240
           + +   TM+YVTHDQ EAM++A  I++L  G I Q G+P +LY  P   F AQFIG+P M
Sbjct: 181 KKL-ALTMLYVTHDQTEAMSMADSIILLNDGHIEQHGTPNDLYNNPATIFAAQFIGAPPM 239

Query: 241 NLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFE 300
           N+LP    G     +   T         P  +     A+++G+R ED ++     +    
Sbjct: 240 NILPLHAKGEQHYLSHLQT---------PVVERCDEVALSLGLRAED-IQLISADNAALT 289

Query: 301 GKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354
            +V   E +G  TLL  +     +    K+ G+ +  +G +  L    A+ ++F
Sbjct: 290 ARVISYEYMGSDTLLACQLAGLSELVTVKVPGMQRYDEGSLVGLQWSAARQYLF 343


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: 286
Number of extensions: 16
Number of successful extensions: 2
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 24 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