GapMind for catabolism of small carbon sources

 

Alignments for a candidate for argT in Shewanella sp. ANA-3

Align Amino acid (Lysine/arginine/ornithine/histidine/octopine) ABC transporter periplasmic binding protein, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 7023653 Shewana3_0882 extracellular solute-binding protein (RefSeq)

Query= TCDB::Q9HU31
         (250 letters)



>FitnessBrowser__ANA3:7023653
          Length = 244

 Score = 92.8 bits (229), Expect = 6e-24
 Identities = 73/238 (30%), Positives = 113/238 (47%), Gaps = 15/238 (6%)

Query: 9   LAAAATLAFALDASAADKLRIGTEGAYPPFN--GIDASGQAVGFDLDIGKALCAKMKTEC 66
           LA  ATL  A    + D L +GT  A+PPF   G  +  +  GFD+++ K +        
Sbjct: 10  LALTATLLLAGCGKSNDILVVGTNAAFPPFEYVGGQSGDEIKGFDIELAKRIAKDAGKTL 69

Query: 67  EVVTSDWDGIIPALNAKKFDFIVASMSITDERKQAVDFTDPYYTNKLQFVAPKSVDFKTD 126
           +V    +D +I ALN+ K DFI + M+IT ER+ +V+F++PYY      +  K  D    
Sbjct: 70  KVENMKFDSLIVALNSGKIDFIASGMTITPERQASVNFSEPYYEATQVLLVNKDNDTIHT 129

Query: 127 KDSLKGKVIGAQRATIAGTWLEDNMADVVT--IKLYDTQENAYLDLSSGRLDGVLADKFV 184
            D +K K    Q  + A     D M+   T  +  ++T   A ++L +G++D VL D   
Sbjct: 130 LDDIKDKHFAVQLGSTA-----DMMSKKYTQNVTAFNTGFEAIMELKNGKVDLVLFDSEP 184

Query: 185 QYDWL-KSDAGKEFEFKGEPVFDNDKIGIAVRKGDP-LREKLNAALKEIVADGTYKKI 240
             ++L K+   K  +    P F     G AV K  P L   +N  LK +   G Y+ +
Sbjct: 185 AANYLAKNPDLKLIKLDFPPEF----YGFAVSKQQPELLNSINNTLKNLKESGQYQTL 238


Lambda     K      H
   0.317    0.135    0.392 

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: 150
Number of extensions: 6
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: 250
Length of database: 244
Length adjustment: 24
Effective length of query: 226
Effective length of database: 220
Effective search space:    49720
Effective search space used:    49720
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 (21.7 bits)
S2: 46 (22.3 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