GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livG in Pseudomonas fluorescens FW300-N1B4

Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate Pf1N1B4_1346 Urea ABC transporter, ATPase protein UrtD

Query= uniprot:A0A159ZWS6
         (255 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1346 Urea ABC transporter,
           ATPase protein UrtD
          Length = 289

 Score =  153 bits (386), Expect = 4e-42
 Identities = 95/251 (37%), Positives = 151/251 (60%), Gaps = 12/251 (4%)

Query: 5   ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64
           IL +E++S+ F G  A+N + L +   ++  +IGPNGAGKTT+ + +TG  +P+ G    
Sbjct: 48  ILTLEDISVSFDGFKALNDLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAWF 107

Query: 65  DGEPIQ--GLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPA 122
            GE +    +    IA+ G+ R FQ   +F+ ++  ENL +AQ    + + +A L     
Sbjct: 108 -GETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELAQKT--DKSVWASL----R 160

Query: 123 FRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182
            R S  +    +E  L+ + LT   NRPAG L++GQ++ LEI   +M  P++L+LDEP A
Sbjct: 161 ARLSGEQKDRISEV-LETIRLTASVNRPAGMLSHGQKQFLEIGMLLMQDPQLLLLDEPVA 219

Query: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242
           G+   ETE    L   L  +H  +++++EHDM  V SI+DH+ V++QG+ LA+G+ EQ++
Sbjct: 220 GMTDAETEFTAELFKSLAGKH--SLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQ 277

Query: 243 DNPEVIKAYLG 253
           DN  VI+ YLG
Sbjct: 278 DNERVIEVYLG 288


Lambda     K      H
   0.321    0.138    0.398 

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: 184
Number of extensions: 12
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: 289
Length adjustment: 25
Effective length of query: 230
Effective length of database: 264
Effective search space:    60720
Effective search space used:    60720
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, 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