GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PGA1_c12640 in Pseudomonas fluorescens GW456-L13

Align D-lactate transporter, ATP-binding component (characterized)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD

Query= reanno::Phaeo:GFF1248
         (251 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Urea ABC
           transporter, ATPase protein UrtD
          Length = 290

 Score =  155 bits (393), Expect = 7e-43
 Identities = 91/247 (36%), Positives = 144/247 (58%), Gaps = 7/247 (2%)

Query: 3   ILEVKNVGKRFGGLQALSDVNLSVRENTVHAIIGPNGAGKSTLLNCLVGKLIPDTGSVMF 62
           IL ++++   F G +AL+++NL +    +  IIGPNGAGK+TL++ + GK  P  G   F
Sbjct: 49  ILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 108

Query: 63  -DGKSVLGRAPYEINQMGISRVFQTPEIFGDLSVLENMMIPCFAKRDGAFEMNAISAVSG 121
            +   +   +  +I Q GI R FQ P +F  LSV EN+ +    K D +   +  + +SG
Sbjct: 109 GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA--QKTDKSVWASLRARLSG 166

Query: 122 QRDILEKAEHMLEEMNMADKRHMNAASMSRGDKRRLEIGMCLSQEPRLLLLDEPTAGMAR 181
           ++   ++   +L+ + +    +  A  +S G K+ LEIGM L Q+P+LLLLDEP AGM  
Sbjct: 167 EQK--DRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVAGMTD 224

Query: 182 ADTNNTIDLLKQIKSERDITIAIIEHDMHVVFSLADRITVLAQGTPLVEDDPQNIKGNPK 241
           A+T  T +L K +  +   ++ ++EHDM  V S+AD +TVL QG+ L E   + ++ N +
Sbjct: 225 AETEFTAELFKSLAGKH--SLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQDNER 282

Query: 242 VREAYLG 248
           V E YLG
Sbjct: 283 VIEVYLG 289


Lambda     K      H
   0.318    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: 203
Number of extensions: 8
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: 251
Length of database: 290
Length adjustment: 25
Effective length of query: 226
Effective length of database: 265
Effective search space:    59890
Effective search space used:    59890
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: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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