GapMind for catabolism of small carbon sources

 

Aligments for a candidate for Ac3H11_1694 in Pseudomonas putida KT2440

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate PP_1139 PP_1139 branched chain amino acid transporter - permease subunit

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__Putida:PP_1139 PP_1139 branched chain amino
           acid transporter - permease subunit
          Length = 418

 Score =  266 bits (681), Expect = 6e-76
 Identities = 156/346 (45%), Positives = 214/346 (61%), Gaps = 45/346 (13%)

Query: 13  VALLVLPLILQSFGNAW-VRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLF 71
           + L+V+ L+   FG+   V IA L L+YVLL LGLNIVVG AGLLDLGYV FYAVGAY +
Sbjct: 96  IGLIVVALVWPFFGSRGAVDIATLILIYVLLGLGLNIVVGLAGLLDLGYVGFYAVGAYSY 155

Query: 72  ALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIV 131
           A+++                + L  S W+ +P+A L+AA FG +LG P L+LRGDYLAIV
Sbjct: 156 AMLS----------------HYLGWSFWVCLPIAGLMAATFGFLLGFPVLRLRGDYLAIV 199

Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRL--------EVFGFDI 183
           TLGFGEIIR+FL NL    + T GP G+  I   + FGL   +R         E FG   
Sbjct: 200 TLGFGEIIRLFLRNL---TDWTGGPNGISNIPKPEFFGLTFERRAAEGMQTFHEFFGLQY 256

Query: 184 NSVTLYYYLFLV---LVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLA 240
           NS+    +L+LV   L ++++ +  RL    IGRAW A+REDEIA +A+G+N   +KL A
Sbjct: 257 NSINKVIFLYLVALLLALLALFVINRLLRMPIGRAWEALREDEIACRALGLNPTVIKLSA 316

Query: 241 FGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300
           F +GA F G +G+ F A QG V+PESF+ +ES +I+A+VVLGG+G   GVIL A+++  L
Sbjct: 317 FTLGACFAGFAGSFFAARQGLVTPESFTFIESAIILAIVVLGGMGSQLGVILAAIVMILL 376

Query: 301 PEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWP 346
           PE++R              + +  R L+    M+++M+ RP+GL P
Sbjct: 377 PELMR--------------EFSEYRMLMFGALMVLMMIWRPQGLLP 408


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: 394
Number of extensions: 18
Number of successful extensions: 4
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: 418
Length adjustment: 30
Effective length of query: 328
Effective length of database: 388
Effective search space:   127264
Effective search space used:   127264
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: 50 (23.9 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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