GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG' in Pseudomonas putida KT2440

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate PP_2263 PP_2263 Sugar ABC transporter, permease protein

Query= uniprot:A8LLL4
         (385 letters)



>FitnessBrowser__Putida:PP_2263
          Length = 266

 Score =  110 bits (274), Expect = 6e-29
 Identities = 71/233 (30%), Positives = 120/233 (51%), Gaps = 9/233 (3%)

Query: 153 PPEFTFANYENMLLDPNNSEGMARAFFNTLTVTIPATIIPILVAAFAAYALAWMEFPGRA 212
           P  FT  NY  +  D +   G    + N+L      T+I +LVA  AAYA +   F G  
Sbjct: 42  PQAFTLDNYRVIFTDASWYSG----YINSLYYVCLNTLISLLVALPAAYAFSRYRFLGDR 97

Query: 213 LLIALIVGLLVVPLQLALIPLLTLHNAIGIGKGYLGTWLAHTGFGMPLAIYLLRNYMVGL 272
            L   ++   + P  + L+P   L+++IG+   ++   LAH  F +PLA+++L  +M G+
Sbjct: 98  HLFFWLLTNRMAPPAVFLLPFFQLYSSIGLFDTHIAVALAHCLFNVPLAVWILEGFMSGV 157

Query: 273 PRDIIENAKVDGATDFQIFTKIVLPLSFPALASFAIFQFLWTWNDLLVAKVFL-IDATGQ 331
           PR+I E A +DG +  + F KI +PL    +   A F F+++W +LL+A+    ++A   
Sbjct: 158 PREIDETAYIDGYSFPRFFVKIFIPLIGSGIGVTAFFCFMFSWVELLLARTLTSVNAKPI 217

Query: 332 TTVMTNQIVELLGTRGGNWEILATAAFVSIAVPLLVFFSMQRFLVRGLLAGSV 384
             VMT  +       G +W +LA A  ++I   +LV + ++  + +G   G V
Sbjct: 218 AAVMTRTV----SASGIDWGVLAAAGVLTILPGMLVIWFVRNHVAKGFALGRV 266


Lambda     K      H
   0.323    0.138    0.419 

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: 263
Number of extensions: 17
Number of successful extensions: 1
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: 385
Length of database: 266
Length adjustment: 28
Effective length of query: 357
Effective length of database: 238
Effective search space:    84966
Effective search space used:    84966
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 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