GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00895 in Pseudomonas fluorescens GW456-L13

Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD

Query= uniprot:D8J1T6
         (255 letters)



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

 Score =  137 bits (346), Expect = 2e-37
 Identities = 90/250 (36%), Positives = 141/250 (56%), Gaps = 9/250 (3%)

Query: 4   TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG-TF 62
           T+L + D+S  F G +ALN + + I  G++  +IGPNGAGKTT  +VITG  +P  G  +
Sbjct: 48  TILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAW 107

Query: 63  ELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122
             +    +  +  ++A+AGI R FQ   +F  ++V EN+ +    +T ++V+ A  R + 
Sbjct: 108 FGETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA--QKTDKSVW-ASLRARL 164

Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182
           + E+    +++  ++LD + +     R A  LS+G ++ LEI   L  DPQLL LDEP A
Sbjct: 165 SGEQ----KDRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVA 220

Query: 183 GMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242
           GM   E     EL  K  A   +++++EHD+  +  + + +TVL  G  +AEG    VQ 
Sbjct: 221 GMTDAETEFTAELF-KSLAGKHSLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQD 279

Query: 243 NPAVIEAYLG 252
           N  VIE YLG
Sbjct: 280 NERVIEVYLG 289


Lambda     K      H
   0.320    0.138    0.394 

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: 173
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: 255
Length of database: 290
Length adjustment: 25
Effective length of query: 230
Effective length of database: 265
Effective search space:    60950
Effective search space used:    60950
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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