GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_1694 in Pseudomonas simiae WCS417

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate GFF3279 PS417_16785 ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>FitnessBrowser__WCS417:GFF3279
          Length = 349

 Score =  124 bits (312), Expect = 3e-33
 Identities = 104/345 (30%), Positives = 165/345 (47%), Gaps = 53/345 (15%)

Query: 12  AVALLVLPLILQSFGNA-WVRIADLALLYVLLA-LGLNIVVGYAGLLDLGYVAFYAVGAY 69
           A+A +V+PL    +GN  W+    +  L + LA LGLN++ GY G   +G   F AVGA+
Sbjct: 28  ALAFIVVPL----WGNDYWLNAILIPFLVLSLAGLGLNLLTGYTGQTSVGAAGFMAVGAF 83

Query: 70  LFA--LMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAAL----LAAFFGAMLGAPTLKL 123
                L+  P L                      +PVA L    ++A  G + G P+ ++
Sbjct: 84  ATYGFLLRLPELG---------------------LPVALLGGGIISALVGLLFGLPSSRI 122

Query: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDI 183
           +G YL + TL      + FL  L             G I + K         L +FG D+
Sbjct: 123 KGFYLMVTTLA----AQFFLEWLFVKFPWFYNYGSSGTISAPK---------LALFGHDL 169

Query: 184 NSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGM 243
           N+    Y L LV V++       L  S++GR WMAIR+ + AA  +GI     K LAF +
Sbjct: 170 NTPLGRYLLTLVTVLLLTWTAINLVRSQVGRNWMAIRDMDTAAAVVGIPVVRYKRLAFAV 229

Query: 244 GASFGGVSGAMFG-AFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPE 302
            + + G++GA++  A+ G  S  SF +  S  I+ ++++GG+G I G  +GA  +S LP 
Sbjct: 230 SSFYLGIAGALWAFAYLGTASASSFDINRSFQILFIIIIGGMGSIAGNFVGAAFISLLPI 289

Query: 303 VLRYVAGPLQAMTDGRLDSAILRQL---LIALAMIIIMLLRPRGL 344
            L +     QA+  G +D+  L+ L   +  + +I+ ++  P GL
Sbjct: 290 FLSHAG---QALFGGSVDAGQLQNLQKIIFGVLIIVFLIKEPEGL 331


Lambda     K      H
   0.328    0.144    0.430 

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: 297
Number of extensions: 13
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: 358
Length of database: 349
Length adjustment: 29
Effective length of query: 329
Effective length of database: 320
Effective search space:   105280
Effective search space used:   105280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 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